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Alignment last updated: 02/11/2014 16:59:56

Join Legend

  • Red circle Serious alignment problem, requires review. (details...)
    • Zero, or more than one, overlaps
    • Half dove-tail >50 bp
    • Alignment identity <98%
    • Alignment length <50 bp
    • >2 gaps, each gap >25 bp, not marked as an SSR
    • >0 gaps, each gap >50 bp, not marked as an SSR
    • >0 gaps, each gap >500 bp, not marked as an SSR
    • >0 gaps, each gap >500 bp, marked as an SSR
  • Yellow circle Minor alignment problem. (details...)
    • Exactly one overlap
    • Half dove-tail >0 bp and <=50bp
    • Alignment identity <99.6%
    • Alignment length <2000 bp
    • >0 gaps, each gap >25 bp, not marked as an SSR
    • >0 gaps, each gap >50 bp, not marked as an SSR
    • >0 gaps, each gap >500 bp, not marked as an SSR
    • >0 gaps, each gap >500 bp, marked as an SSR
  • Green circle Excellent alignment, meets all defined criteria. (details...)
    • Exactly one RuleInfo
    • Half dove-tail <=0 bp
    • Alignment identity >=99.6%
    • Alignment length >=2000 bp
    • <=0 gaps, each gap >25 bp, not marked as an SSR
    • <=0 gaps, each gap >50 bp, not marked as an SSR
    • <=0 gaps, each gap >500 bp, not marked as an SSR
    • <=0 gaps, each gap >500 bp, marked as an SSR
  • Black circle Certificate submitted, not yet approved.
  • Purple circle Certificate submitted and approved.
  • Gray circle Valid, contained clone
  • White circle Join not evaluated due to one accession not being finished.

Alignment for AC219177.2 and AC190531.4

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AC219177.2 Zea mays chromosome 1 clone Z_AI-725F11, *** SEQUENCING IN PROGRESS ***, 3 unordered pieces [htgs_limited_order]

Length: 34,465 bp

AC190531.4 Zea mays chromosome 1 clone ZMMBBb-605C24, *** SEQUENCING IN PROGRESS ***, 8 unordered pieces [htgs_limited_order]

Length: 147,679 bp

Alignment Summary

Join evaluation: red (half-dovetail of >50bp)

Alignment count: 1

Go to Endhit Table

  • Alignment 1
  • Align ID: 120596
  • Total Length: 4410
  • Aligned Length: 4410
  • Percent Identity: 100
  • Number of Gaps: 0
  • Number of Mismatches: 0
  • First Tail: 2828bp
  • Source: CtgOverlap Seq-Align
Overlap Image
down arrow

Alignment 1 of 1

 AC219177.2 : + : 27228..31637
 AC190531.4 : + : 1..4410
 Mismatches = 0, Gaps = 0, Length = 4410
 Percent identity = 100%
 Score = 8145 bits (4410), Expect = 0
  0 BAC and 1 Fosmid bridging clones.
  0 BAC and 0 Fosmid concordant clones.
  0 BAC and 1 Fosmid discordant clones.

AC219177.2 >27228   aagcttatgaaggttcttcatcccaacatgtgctagacgacgatgccacatccaacctat 27287  
AC190531.4 >1       ............................................................ 60     

AC219177.2 >27288   attagtcttagcgattaagcatgcatctagattggcgttctctttcaaaaaatcaactaa 27347  
AC190531.4 >61      ............................................................ 120    

AC219177.2 >27348   gtagagcttgccgtctaatacacccttaaaagctaatgaaccatcactccttctaaagac 27407  
AC190531.4 >121     ............................................................ 180    

AC219177.2 >27408   agatacatctacatttgtgaataaacaattataacccatgttacataattgactcataga 27467  
AC190531.4 >181     ............................................................ 240    

AC219177.2 >27468   taacaaattatacccaagcgattcaactaaaaatacattagatatagaatgctcgaaggt 27527  
AC190531.4 >241     ............................................................ 300    

AC219177.2 >27528   gatggctatctttcccaatcctttgacctttccttggttcccatctccaaagatgatcga 27587  
AC190531.4 >301     ............................................................ 360    

AC219177.2 >27588   atcctgggaatccttgtttttgacataggaggtgaacattttcttctccctcgtcatgtg 27647  
AC190531.4 >361     ............................................................ 420    

AC219177.2 >27648   gtccgtgcatccgctgtcgataatccagcttgagcccccggatgcataaacctgcaagga 27707  
AC190531.4 >421     ............................................................ 480    

AC219177.2 >27708   atttaagcttgggttttaggtacccaactcttgttgggtcctacaaggttagtcacaata 27767  
AC190531.4 >481     ............................................................ 540    

AC219177.2 >27768   acttttggaacccaaatacaagtcttgtttcccttgcatttggatcccagcttcctagca 27827  
AC190531.4 >541     ............................................................ 600    

AC219177.2 >27828   actacttttgcattcttacatgaaagtacaaaagaagtattgcaagcatgataaacagta 27887  
AC190531.4 >601     ............................................................ 660    

AC219177.2 >27888   gaaggtccattgcacattctcctaggagcatgagacacaacatgatttctcctaggccta 27947  
AC190531.4 >661     ............................................................ 720    

AC219177.2 >27948   ctgagagcacctagagggggggggtgaataggtgatcctgtaaaacttgaaaacttaagc 28007  
AC190531.4 >721     ............................................................ 780    

AC219177.2 >28008   cacaaaaacttggttaagcgttagcacagtaaatgccaagtggctagagatgagtctcaa 28067  
AC190531.4 >781     ............................................................ 840    

AC219177.2 >28068   caaaacacaataaccacaagaaatcaatcacagagatggcacggtggttatcccgtggtt 28127  
AC190531.4 >841     ............................................................ 900    

AC219177.2 >28128   cggccaagaccaacgcttgcctactccacgttgtggcgtcccaacggacaagggttgcaa 28187  
AC190531.4 >901     ............................................................ 960    

AC219177.2 >28188   tcaacccctctcaagcggtccaaagacccacttgaataccacagtgttttgcttgctttt 28247  
AC190531.4 >961     ............................................................ 1020   

AC219177.2 >28248   cttaatcccgtttgcgaggaatctccacaacttgaagcctctcgcccttacacttgaagt 28307  
AC190531.4 >1021    ............................................................ 1080   

AC219177.2 >28308   tcacaaagaagcacggagcaagggagggattagcaatacactcaagacaagaaatcacag 28367  
AC190531.4 >1081    ............................................................ 1140   

AC219177.2 >28368   caacaccacgcacacaagtcgcaacgagagctcacaacacaactcaatgagttcaccact 28427  
AC190531.4 >1141    ............................................................ 1200   

AC219177.2 >28428   caactagagctctaattgctatcgcaaagaatcaaaggcgcggaatcgatgtcttggtgc 28487  
AC190531.4 >1201    ............................................................ 1260   

AC219177.2 >28488   ttaggaatgttgtaggaatgcttagtgttctcctccatgcgcctaggggtcccttttata 28547  
AC190531.4 >1261    ............................................................ 1320   

AC219177.2 >28548   gccacaaggcagctaggagccgttgagagcaatctaggaaggctgatcttgccttctgtc 28607  
AC190531.4 >1321    ............................................................ 1380   

AC219177.2 >28608   gagtggcgcaccggacagtccggtgcacaccggacactgtccggtgcccgatttccttcc 28667  
AC190531.4 >1381    ............................................................ 1440   

AC219177.2 >28668   ttaaatagcgaaaccgaccgttgcagatttgggagccgttgacgcaccggacatgtccgg 28727  
AC190531.4 >1441    ............................................................ 1500   

AC219177.2 >28728   tgcacaccggacagtccggtgcccccttctagccgttggcttggccacgtgtcccgcgca 28787  
AC190531.4 >1501    ............................................................ 1560   

AC219177.2 >28788   gattgcacggccgaccgttggcccggccgaccgttggctcaccggacagtccggtgcaca 28847  
AC190531.4 >1561    ............................................................ 1620   

AC219177.2 >28848   ccggacagtccggtgaattatagccgtacgtcgccggtgaattctcgagagcggccagtt 28907  
AC190531.4 >1621    ............................................................ 1680   

AC219177.2 >28908   cgctcgagccagcctggcgcaccggacattgtccggtgcaccaccggacattgtccggtg 28967  
AC190531.4 >1681    ............................................................ 1740   

AC219177.2 >28968   cacccagactgagcagagtcttggctgctcgagccaagacatttccagttggtcttttcc 29027  
AC190531.4 >1741    ............................................................ 1800   

AC219177.2 >29028   tgtttccagcacttagacacaatacattagtctctaaaacaatgtactaagtctgagaaa 29087  
AC190531.4 >1801    ............................................................ 1860   

AC219177.2 >29088   catacctttatccttgatttgtactttgtccaccattttacacttaggcacttgtgttgg 29147  
AC190531.4 >1861    ............................................................ 1920   

AC219177.2 >29148   acactaaatcaccaaaatacttagaaatggcccaagggcacatttccctttcaatctccc 29207  
AC190531.4 >1921    ............................................................ 1980   

AC219177.2 >29208   cctttttggtgatttatgccaacacaacataaagcaagtagaacaagtaaaaaatcaatt 29267  
AC190531.4 >1981    ............................................................ 2040   

AC219177.2 >29268   caaataagaactcaaattgttttgattcaaatttgacatatatggatcactctttgccac 29327  
AC190531.4 >2041    ............................................................ 2100   

AC219177.2 >29328   cacttggtttgtttttgcaaatcaaactcaaatttctatctctaagtcaaccacacatgt 29387  
AC190531.4 >2101    ............................................................ 2160   

AC219177.2 >29388   taagatataaagagagtcattccaagagaaattgattcaagatttcaaaaactccccttt 29447  
AC190531.4 >2161    ............................................................ 2220   

AC219177.2 >29448   ttcccataatcaacacttctccccacaagaagccaacttttgacaagaagccaacttttg 29507  
AC190531.4 >2221    ............................................................ 2280   

AC219177.2 >29508   acaagaagccaacttttgacaagagagacaacaaaagagttttgtcaaaccaaaaagctc 29567  
AC190531.4 >2281    ............................................................ 2340   

AC219177.2 >29568   tattctactattttcaaaatctctcaagtggtagctgatccatttatcgctttggccttt 29627  
AC190531.4 >2341    ............................................................ 2400   

AC219177.2 >29628   attttctcccctttggcatcaagcaccaaaacgggatcaatcttggccccagaacctcat 29687  
AC190531.4 >2401    ............................................................ 2460   

AC219177.2 >29688   tgcctcaccaaaatcttcaataagaatacaaaggcaataagagtacatgagatgaacttg 29747  
AC190531.4 >2461    ............................................................ 2520   

AC219177.2 >29748   gaatacgttaccctctcatcggagtgcagtggaagtctttcatggtccaagtccaccttt 29807  
AC190531.4 >2521    ............................................................ 2580   

AC219177.2 >29808   tccctttcaatccttctttgagactaaagcatcaacctcaagcacatggttagtctcaaa 29867  
AC190531.4 >2581    ............................................................ 2640   

AC219177.2 >29868   gggtcaagttgtaacacatctccccctaaatatgtgcatcactttgcaaaaaggacttgt 29927  
AC190531.4 >2641    ............................................................ 2700   

AC219177.2 >29928   gaggtccggggagtgtttgtacaacttgagcaccataagtaagcaacgaaatgcataagg 29987  
AC190531.4 >2701    ............................................................ 2760   

AC219177.2 >29988   aacatgatcaaaggcataaatacatgtatgctataaatcaatccaggttccgcgaatcta 30047  
AC190531.4 >2761    ............................................................ 2820   

AC219177.2 >30048   agacatttagctcactacgcaacctgcaaatggtcttctcatctagaggcttggtaaaga 30107  
AC190531.4 >2821    ............................................................ 2880   

AC219177.2 >30108   tatcggctagctggttctcggtgctaacatgaaacacttcgatatctcccttttgctggt 30167  
AC190531.4 >2881    ............................................................ 2940   

AC219177.2 >30168   ggtctctcaaaaagtgatgccggatgtcaatgtgcttagtgcggctgtgctcaacaggat 30227  
AC190531.4 >2941    ............................................................ 3000   

AC219177.2 >30228   tttccgctattcggatagcactctcattgtcacataggagtgggactttgctcagattgt 30287  
AC190531.4 >3001    ............................................................ 3060   

AC219177.2 >30288   agccaaagtcccagagggtttgcctcatccaaagtagttgcgcgcaacactgtcctgcgg 30347  
AC190531.4 >3061    ............................................................ 3120   

AC219177.2 >30348   caacgtactcggcctcagcggtggatagggcaacggaagtttgtttcttagagttccacg 30407  
AC190531.4 >3121    ............................................................ 3180   

AC219177.2 >30408   acaccagggaccttcctaagaattggcacgtccccgatgtactcttcctatcgaccttac 30467  
AC190531.4 >3181    ............................................................ 3240   

AC219177.2 >30468   atccagcatagtcggagtctgaatatccaatcaagtcaaagttagactcctttggatacc 30527  
AC190531.4 >3241    ............................................................ 3300   

AC219177.2 >30528   agatcccaaagcaaggcgtagcgactaaatatctaagaattcgcttcacagccactaagt 30587  
AC190531.4 >3301    ............................................................ 3360   

AC219177.2 >30588   gacactccttaggatcggattgaaatctagcacacatgcatacgctgagcataatatccg 30647  
AC190531.4 >3361    ............................................................ 3420   

AC219177.2 >30648   gtctactagcacataaataaagcaaagaacctatcatggaccggtatgctttttgatcaa 30707  
AC190531.4 >3421    ............................................................ 3480   

AC219177.2 >30708   cggacttaccacctttgttgaggtcggtgtgtccgtcggttcccatcggcgtctttgcgg 30767  
AC190531.4 >3481    ............................................................ 3540   

AC219177.2 >30768   gcttggcttccttcatcccaaaccgctttagcaagtcttgcgtatacttcgtttgggata 30827  
AC190531.4 >3541    ............................................................ 3600   

AC219177.2 >30828   tgaaggtgctgtccttgagttgcttcacttggaacccaaggaagtagttcaactcgccca 30887  
AC190531.4 >3601    ............................................................ 3660   

AC219177.2 >30888   tcattgacatctcgaatttctgcgtcattaccctgctaaactcttcacaagacttttgat 30947  
AC190531.4 >3661    ............................................................ 3720   

AC219177.2 >30948   tagtagaaccaaatattatgtcatcgacataaatttggcacacaaaaagatcaccatcgc 31007  
AC190531.4 >3721    ............................................................ 3780   

AC219177.2 >31008   aagtcttagtaaaaagagttggatcggctttcccgactttgaaggcattagcaattaaaa 31067  
AC190531.4 >3781    ............................................................ 3840   

AC219177.2 >31068   agtctctaaggcattcataccatgctcttggggcttgcttaagtccatagagcgccttag 31127  
AC190531.4 >3841    ............................................................ 3900   

AC219177.2 >31128   agagcttacacacgtggtcggggtaccgttcatcctcgaagccagggggttgctccacgt 31187  
AC190531.4 >3901    ............................................................ 3960   

AC219177.2 >31188   acacctcctccttgatcggcccgttgaggaaagcgctcttcacatccatttggtacaacc 31247  
AC190531.4 >3961    ............................................................ 4020   

AC219177.2 >31248   tgaaagaatggtgagcggcatatgctagcaaaatacgaattgattctagcctagccacag 31307  
AC190531.4 >4021    ............................................................ 4080   

AC219177.2 >31308   gagcgaatgtctcctcaaagtccaaacctgcgacttgggcataaccttttgccacaagtc 31367  
AC190531.4 >4081    ............................................................ 4140   

AC219177.2 >31368   gagccttgttccttgtcaccactccgtgctcgtcctgtttgttgcggaacacccacttgg 31427  
AC190531.4 >4141    ............................................................ 4200   

AC219177.2 >31428   ttcccacaacgttttgcttgggacgaggcaccagtgtccaaacttcattgcgcttgaagt 31487  
AC190531.4 >4201    ............................................................ 4260   

AC219177.2 >31488   tgttgagttcttcctgcatggccaacacccagtccggatctagcaaggcctcttctaccc 31547  
AC190531.4 >4261    ............................................................ 4320   

AC219177.2 >31548   tgaaaggctcaatagaagagacaaaagagtaatgctcacaaaaattaactaatctcgagc 31607  
AC190531.4 >4321    ............................................................ 4380   

AC219177.2 >31608   gagtagttactcccttgctaatatcaccca 31637  
AC190531.4 >4381    .............................. 4410

Events
IdTypeDateWhodidComment
295494InitNoAlign01/15/2014 17:23:48cgi_chen
find_overlapId: find_overlap_app.cpp 404199 2013-06-20 22:08:27Z rafanovi $ built Aug  1 2013. Toolkit wrapper  using /home/boukn/code/toolkit/c++/GCC442-ReleaseMT64/lib
Info: Blast Including ID: 545480145
Info: Running Blast Filter: 0
Warning: CBlastAligner found no hits this run.
Info: Blast Including ID: 545480145
Info: Running Blast Filter: 0
Warning: CBlastAligner found no hits this run.
Info: Blast Including ID: 545480145
Info: Running Blast Filter: 0
Warning: CBlastAligner found no hits this run.
Info:  NG returned 0 alignments

tpf_solo for TPF_updated_1_v2
300076ReRunFndOvlp02/11/2014 16:59:56cgi_chen
find_overlapId: find_overlap_app.cpp 404199 2013-06-20 22:08:27Z rafanovi $ built Feb  4 2014. Toolkit wrapper  using /home/boukn/code/toolkit/c++/GCC442-ReleaseMT64/lib
Info: Blast Including ID: 545480145
Info: Running Blast Filter: 
Warning: CBlastAligner found no hits this run.
Info: Blast Including ID: 545480145
Info: Running Blast Filter: 
Info: CBlastAligner found 14 hits.
Info: Determined ID: gi|545480145 needs Merging.
Info: Merged into 18 alignments.
Info: Blast Including ID: 545480145
Info: Running Blast Filter: 
Info: CBlastAligner found 19 hits.
Info: Determined ID: gi|545480145 needs Merging.
Info: Merged into 35 alignments.
Info: Best Rank: 11 in  for 545480145 of 1
Info:  NG returned 1 alignments


down arrow BAC Ends
CloneRF
Accession%idPosition (strand) Accession%idPosition (strand)
CH201-147A16AC190531.4100%pos 146349 (R+)  
AC190531.4100%pos 146416 (R+)  
CH201-148B12 AC190531.499.3%pos 14290 (F-)
CH201-153I21AC190531.499.86%pos 14332 (R+)  
CH201-154J2 AC190531.4100%pos 15163 (F+)
 AC190531.4100%pos 15165 (F+)
CH201-179H19AC190531.498.36%pos 115338 (R+)  
CH201-209F2 AC190531.499.74%pos 146417 (F+)
CH201-209O20AC219177.299.6%pos 721 (R-)  
CH201-221I18 AC190531.499.7%pos 95693 (F-)
CH201-223P10 AC190531.499.84%pos 100528 (F-)
CH201-259A17 AC190531.499.27%pos 43061 (F-)
 AC190531.499.37%pos 43668 (F-)
CH201-315I4AC190531.4100%pos 100013 (R+)  
CH201-32I21AC190531.4100%pos 70484 (R+)  
AC190531.4100%pos 70608 (R+)  
AC190531.4100%pos 70710 (R+)  
CH201-361C7 AC219177.2100%pos 2027 (F-)
CH201-438B16 AC190531.499.2%pos 126295 (F-)
CH201-572K9 AC190531.4100%pos 17231 (F+)
 AC190531.499.17%pos 17231 (F+)
CH201-574G3AC219177.2100%pos 1177 (R+)  
CH201-64C23AC190531.4100%pos 15048 (R+)  
ZMMBBb-108C13 AC190531.499.4%pos 50358 (F+)
 AC190531.498.76%pos 50170 (F+)
ZMMBBb-123I19 AC190531.499.74%pos 127766 (F+)
ZMMBBb-164L23 AC190531.497.81%pos 91147 (F-)
ZMMBBb-167P9AC190531.497.71%pos 103691 (R+)  
ZMMBBb-171N2AC190531.499.34%pos 53922 (R-)  
ZMMBBb-215J7 AC190531.497.55%pos 20363 (F-)
ZMMBBb-248C8AC190531.499.43%pos 12669 (R-)  
ZMMBBb-26O6 AC190531.497.99%pos 38163 (F+)
ZMMBBb-298I20AC190531.498.31%pos 28351 (R+)  
ZMMBBb-486C8 AC190531.498.4%pos 33863 (F-)
ZMMBBb-506A2AC190531.497.89%pos 6900 (R+)  
ZMMBBb-555F15AC190531.498.35%pos 12297 (R-)  
ZMMBBb-567E14 AC190531.498.63%pos 54811 (F+)
ZMMBBb-570M16 AC190531.497.29%pos 104729 (F-)
ZMMBBb-598N6 AC190531.499.65%pos 127383 (F-)
ZMMBBb-605C24AC190531.498.15%pos 146691 (R-)  
AC190531.499.71%pos 146989 (R-)  
ZMMBBb-607P17 AC219177.297.24%pos 19831 (F-)
ZMMBBb-643P9AC190531.498.04%pos 11533 (R-)  
down arrow Fosmid Ends
CloneRF
Accession%idPosition (strand) Accession%idPosition (strand)
Z_AI-1048C2AC190531.4100%pos 48366 (R+)  
Z_AI-1064B3AC190531.499.85%pos 14093 (R-) AC190531.4100%pos 97083 (F+)
Z_AI-1173J18AC219177.2100%pos 4306 (R+)  
Z_AI-1185O10AC190531.499.71%pos 53689 (R-) AC190531.4100%pos 22632 (F+)
Z_AI-1242A16 AC190531.499.86%pos 36324 (F-)
Z_AI-1257O13AC190531.4100%pos 38142 (R+)  
Z_AI-1348F19 AC190531.4100%pos 15288 (F+)
Z_AI-1437K3AC190531.499.7%pos 20446 (R+)  
Z_AI-1450H9 AC190531.4100%pos 121105 (F-)
Z_AI-1467B5AC190531.4100%pos 84140 (R-) AC219177.2100%pos 1249 (F+)
Z_AI-256M1AC190531.499.32%pos 96823 (R+)  
Z_AI-326B18AC190531.499.33%pos 101539 (R-)  
Z_AI-387G8 AC190531.499.03%pos 87363 (F-)
Z_AI-389H21 AC190531.499.68%pos 105381 (F-)
Z_AI-396M9 AC190531.4100%pos 95511 (F-)
Z_AI-418O3AC190531.497.14%pos 95195 (R+)  
Z_AI-469G12 AC190531.499.6%pos 93089 (F-)
Z_AI-531F22AC190531.4100%pos 123777 (R+) AC190531.499.7%pos 39508 (F-)
Z_AI-601M11 AC190531.499.77%pos 146381 (F+)
Z_AI-643P20 AC190531.4100%pos 108097 (F-)
Z_AI-702O11 AC190531.4100%pos 88424 (F-)
Z_AI-725F11 AC219177.2100%pos 2 (F+)
Z_AI-747O5 AC190531.4100%pos 105498 (F-)
Z_AI-763P6AC190531.4100%pos 8434 (R+)  
Z_AI-780F22 AC190531.4100%pos 19758 (F-)
Z_AI-787H16AC190531.4100%pos 87392 (R+) AC190531.4100%pos 118401 (F-)
Z_AI-902E4 AC190531.499.81%pos 127292 (F+)
Z_AI-907F15 AC190531.499.86%pos 44888 (F-)
Z_AI-927A9AC190531.4100%pos 95092 (R+) AC190531.4100%pos 122314 (F-)

down arrow Repeats
acc start stop repeat id strand name family class