Alignment last updated: 07/09/2010 12:44:32

Join Legend

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
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
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
Certificate submitted, not yet approved.
Certificate submitted and approved.
Valid, contained clone
Join not evaluated due to one accession not being finished.

Alignment for CU138535.6 and CU861655.2

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CU138535.6 Zebrafish DNA sequence from clone CH1073-36F4 in linkage group 20, complete sequence [htgs_phase3]

Length: 14,873 bp

CU861655.2 Zebrafish DNA sequence from clone CH73-319F15 in linkage group 20, complete sequence [htgs_phase3]

Length: 10,356 bp

Alignment Summary

Join evaluation: yellow (half-dovetail of >0bp and <=50bp)

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 86986
Total Length: 2000
Aligned Length: 2000
Percent Identity: 100
Number of Gaps: 0
Number of Mismatches: 0
First Tail: 3bp
Source: CtgOverlap Seq-Align
Valid Switchpoint: true (A)

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time	Id	Alignment	Releases
A	14870	2001	+	+	chenhc	Taxid 7955 chrom 20 Primary assembly	2010-07-09 12:44:32.780	85130	86986	GRCz10

Alignment 1 of 1

 CU138535.6 : + : 12871..14870
 CU861655.2 : + : 1..2000
 Mismatches = 0, Gaps = 0, Length = 2000
 Percent identity = 100%
 Score = 3965 bits (2000), Expect = 0
  0 BAC and 0 Fosmid bridging clones.
  0 BAC and 0 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

CU138535.6 >12871  aacagcagaaggaaattgcttgggtaggagaagctgcgtcaatcttttcttcatttaata 12930 
CU861655.2 >1      ............................................................ 60    

CU138535.6 >12931  aatgacttgcgcctcagaagacaatgctgacacacactgaacgcgtggtggcatttgaag 12990 
CU861655.2 >61     ............................................................ 120   

CU138535.6 >12991  gagtgagacgcggagtgacacttggaggcacagacgctcttaacaattctggaggtcatt 13050 
CU861655.2 >121    ............................................................ 180   

CU138535.6 >13051  aataatataataacactgatactgaaacggttaaggcgtttcagatggtttacagtgtgc 13110 
CU861655.2 >181    ............................................................ 240   

CU138535.6 >13111  tcagcctgctggttaatccattcacacacattattatcatcacatgatctcattcattca 13170 
CU861655.2 >241    ............................................................ 300   

CU138535.6 >13171  ttcattttcttgtcggcttagtccctttattaatctggggtcgccacagcggattgaacc 13230 
CU861655.2 >301    ............................................................ 360   

CU138535.6 >13231  gccaacttatcccgcaagtttttatgcagcggatgcccttacagccgcaacccatctctg 13290 
CU861655.2 >361    ............................................................ 420   

CU138535.6 >13291  ggaaacattcacacacacacactcatacactacggacaatttagcctacccaattcacct 13350 
CU861655.2 >421    ............................................................ 480   

CU138535.6 >13351  gtaccgcatgtttttggactgtaggagcacccggaggaaacgcagaacgcagggagaaca 13410 
CU861655.2 >481    ............................................................ 540   

CU138535.6 >13411  tgcaaactccacaaaaaatgccaacttagccgaggttcgaaccagcgacattcttgctgt 13470 
CU861655.2 >541    ............................................................ 600   

CU138535.6 >13471  gaggcgaacgtgctacccactgcgccgccccatcacatgatctcttataacaaaaatcac 13530 
CU861655.2 >601    ............................................................ 660   

CU138535.6 >13531  atgacccttttaatgagcatactggaatttctttgctaatagtgttttcgtcatagtgta 13590 
CU861655.2 >661    ............................................................ 720   

CU138535.6 >13591  cgtgcatcttttcctatcaaataaaaatattattattaatgcaaattttctaaatttatg 13650 
CU861655.2 >721    ............................................................ 780   

CU138535.6 >13651  cgcatcttggagtttcgtcaactgcatatccaatataggatatgcatatccaaacaatag 13710 
CU861655.2 >781    ............................................................ 840   

CU138535.6 >13711  gtagatggaaaatagctagtgacacttgccataagcatggtgtgctgctaggaggagcgg 13770 
CU861655.2 >841    ............................................................ 900   

CU138535.6 >13771  gtaactactaacttcccacaggcatactataagggggcccaaccccaaaaacaacccctc 13830 
CU861655.2 >901    ............................................................ 960   

CU138535.6 >13831  accccctactcgacactgcttttgacttccccccaaccccctcccagctatactcttcaa 13890 
CU861655.2 >961    ............................................................ 1020  

CU138535.6 >13891  ctcaaatgttaaatgcaaccacaggagcagagaagacgccctaactgacctgcacacttg 13950 
CU861655.2 >1021   ............................................................ 1080  

CU138535.6 >13951  gttctggtgatgagcgcgggcccgggctgtccggtgcccccctctccgggacgagtcagc 14010 
CU861655.2 >1081   ............................................................ 1140  

CU138535.6 >14011  agcacgcggatctcatattcggtgtcggggtccaggtgccagagcttgtagttgggcgag 14070 
CU861655.2 >1141   ............................................................ 1200  

CU138535.6 >14071  ttgacggcgtgggtttctgtccagctgccggacgtcatgcggtactccacctccttcagg 14130 
CU861655.2 >1201   ............................................................ 1260  

CU138535.6 >14131  atgatgggcccgtccccgaatatggagttagcattgagctggatcagcaggtatgtgggc 14190 
CU861655.2 >1261   ............................................................ 1320  

CU138535.6 >14191  ccgacgcccagcagctgaggtggagcgatgggtctcggcggctctgcaggaggacatgag 14250 
CU861655.2 >1321   ............................................................ 1380  

CU138535.6 >14251  agttatagaaagctgatctcagtttcagctgatagaaagctaggaaaacggtcagaattt 14310 
CU861655.2 >1381   ............................................................ 1440  

CU138535.6 >14311  actctggatataaggtttttatgaaaggaatcttacggaaaataacatgcaaaacatacc 14370 
CU861655.2 >1441   ............................................................ 1500  

CU138535.6 >14371  gttcctctattttatttattatatcatttgttctatgctgtaaatttttgtcaatgcctc 14430 
CU861655.2 >1501   ............................................................ 1560  

CU138535.6 >14431  aacattgttgatattgtgctttgtgtactgttatgtgtattcttgtattcccaacaaacg 14490 
CU861655.2 >1561   ............................................................ 1620  

CU138535.6 >14491  cacaaacgtacgaacgaacgcacacacatgcacaaatgaatgcacacacaaacaaatgca 14550 
CU861655.2 >1621   ............................................................ 1680  

CU138535.6 >14551  cgcatacatgcacaaacgaacgaatgaacatacgcaaacacaaacgcatgcaaaaacaaa 14610 
CU861655.2 >1681   ............................................................ 1740  

CU138535.6 >14611  agaacgaaagcacaaaccaaggaacacacacgtggaaacacgaacgcatgaacaaacaaa 14670 
CU861655.2 >1741   ............................................................ 1800  

CU138535.6 >14671  ggaacgaacgcaaaactgcatgaaggaacgaaggaacaaacgaacacacacatgcgcaaa 14730 
CU861655.2 >1801   ............................................................ 1860  

CU138535.6 >14731  tgaatgcacatacaaacaaatgcacacatgcatgcacaaatgaatgagtgaatgcaccaa 14790 
CU861655.2 >1861   ............................................................ 1920  

CU138535.6 >14791  tgtatgaacgaacaaacaaatgcacggacgaatgcataaacgcacacatgcacaaataaa 14850 
CU861655.2 >1921   ............................................................ 1980  

CU138535.6 >14851  cgcacgcacaaatgcatgca 14870 
CU861655.2 >1981   .................... 2000

Events

Type

Date

Whodid

Comment

206720

InitHasAlign

04/08/2010 05:47:08

boukn

find_overlap 1.33 built Aug  5 2009. Toolkit wrapper  using /netopt/ncbi_tools64/c++.by-date/20090802/GCC401-Release64/lib
Running blast for 133920062 and 213032436
Filtering on 0.97%, slop 1000bp, min length 50bp and strands Unknown, Unknown
Found 1 acceptable dovetail alignment(s) by blast  -W 28 -r 1 -q -3 -G 5 -E 2 -e 1e-05 -Z 200 -F F

tpf_solo for chr20

218442

CreateSwitchPt

07/09/2010 12:44:32

chenhc

tpf_m_Builder 1.43 Toolkit wrapper version: built Jun  7 2010 using /netopt/ncbi_tools64/c++.by-date/20100606/GCC401-Release64/lib

BAC Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
CH211-191O11	CU138535.6	99.47%	pos 4174 (R-)
CH211-201A2				CU138535.6	99.7%	pos 4545 (F+)
CH211-205B14				CU138535.6	100%	pos 1320 (F-)
CH211-281I24				CU138535.6	97.91%	pos 1209 (F-)
CH211-288F3				CU138535.6	99.88%	pos 4562 (F+)
CH211-64P3				CU138535.6	99.83%	pos 4545 (F+)
				CU138535.6	99.7%	pos 4545 (F+)
				CU138535.6	99.82%	pos 4556 (F+)
CH73-25P9	CU138535.6	100%	pos 4136 (R-)
CH73-319F15				CU138535.6	100%	pos 2111 (F+)
DKEY-126H10				CU861655.2	100%	pos 8427 (F+)
DKEY-187J6	CU138535.6	100%	pos 10732 (R-)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
CH1073-155I8	CU861655.2	100%	pos 3268 (R+)
CH1073-155I9	CU861655.2	100%	pos 3268 (R+)
CH1073-242G23	CU861655.2	100%	pos 8502 (R+)
CH1073-36D10	CU861655.2	99.42%	pos 1259 (R-)	CU138535.6	100%	pos 14128 (F-)
CH1073-36D10	CU138535.6	99.42%	pos 14129 (R-)	CU861655.2	100%	pos 1258 (F-)
CH1073-36F4	CU861655.2	100%	pos 1129 (R-)	CU138535.6	100%	pos 14279 (F-)
CH1073-36F4	CU138535.6	100%	pos 13999 (R-)	CU861655.2	100%	pos 1409 (F-)
CH1073-399M14				CU861655.2	100%	pos 8627 (F+)
ZFOS-1701B10	CU861655.2	100%	pos 6239 (R-)
ZFOS-217E7	CU861655.2	100%	pos 6546 (R-)
ZFOS-867G4	CU138535.6	99.82%	pos 1683 (R+)

Repeats

acc	start	stop	repeat id	strand	name	family	class
CU138535.6	8812	8840	7421163	+	(CA)n		Simple_repeat
CU138535.6	9009	9047	7421164	+	(GA)n		Simple_repeat
CU138535.6	9640	9669	7421165	+	(CA)n		Simple_repeat
CU138535.6	10039	10100	7421166	-	ANGEL	hAT	DNA
CU138535.6	10102	10273	7421167	+	(TTA)n
CU138535.6	10275	10373	7421168	-	DNA-1-7_DR	PIF-Harbinger	DNA
CU138535.6	10298	10437	7421169	+	(TTA)n
CU138535.6	10442	10507	7421170	+	(TAA)n		Simple_repeat
CU138535.6	10508	10638	7421171	+	(TTA)n
CU138535.6	10649	10839	7421172	+	TE-X-4_DR		Unknown
CU138535.6	10786	10878	7421173	-	DNA8-9_DR	hAT	DNA
CU138535.6	11280	11304	7421174	+	(TTCA)n
CU138535.6	11305	11655	7421175	-	HE2_DR	V	SINE
CU138535.6	11656	11870	7421176	-	DIRS-9_DR	Ngaro	LTR
CU138535.6	11871	12468	7421177	-	DIRS-1-LTR_DR	DIRS	LTR
CU138535.6	12744	13161	7421178	-	DNAX-1_DR		DNA
CU138535.6	13163	13498	7421179	-	HE2_DR	V	SINE
CU138535.6	13501	13731	7421180	-	DNAX-1_DR		DNA
CU138535.6	14488	14602	7421181	+	(CACG)n		Simple_repeat
CU138535.6	14612	14864	7421182	+	(CGAA)n		Simple_repeat
CU138535.6	8581	8811	7421162	+	TE-U_1_DR		Satellite?
CU138535.6	8328	8430	7421161	+	Harbinger-N12_DR	PIF-Harbinger	DNA
CU138535.6	8129	8308	7421160	+	hAT-N40_DR	hAT-Ac	DNA
CU138535.6	7859	8129	7421159	+	DNA-8-9_DR	hAT-Ac?	DNA
CU138535.6	7677	7993	7421157	+	TE-X-5_DR		Satellite
CU138535.6	7600	7666	7421158	+	(TAAA)n		Simple_repeat
CU138535.6	7387	7576	7421157	+	TE-X-5_DR		Satellite
CU138535.6	6603	7386	7421156	+	DNA-8-9_DR	hAT-Ac?	DNA
CU138535.6	6484	6562	7421155	+	hAT-N40_DR	hAT-Ac	DNA
CU138535.6	6360	6484	7421154	-	TDR3	hAT-Charlie	DNA
CU138535.6	5669	5718	7421153	+	AT_rich		Low_complexity
CU138535.6	4921	5597	7421152	-	HarbingerN4_DR	PIF-Harbinger	DNA
CU138535.6	4100	4222	7421151	+	(CA)n		Simple_repeat
CU138535.6	3505	3760	7421150	-	hAT-N21_DR	hAT-Charlie	DNA
CU138535.6	3448	3731	7421149	-	TDR18	TcMar	DNA
CU138535.6	3405	3451	7421148	+	DNA9NNN1_DR		DNA
CU138535.6	3092	3173	7421147	+	(CATA)n		Simple_repeat
CU138535.6	9013	9047	12147702	N	DUST
CU138535.6	9248	9260	12147703	N	DUST
CU138535.6	9640	9669	12147704	N	DUST
CU138535.6	10102	10649	12147705	N	DUST
CU138535.6	10846	10873	12147706	N	DUST
CU138535.6	11107	11114	12147707	N	DUST
CU138535.6	11829	11839	12147708	N	DUST
CU138535.6	12317	12323	12147709	N	DUST
CU138535.6	13129	13176	12147710	N	DUST
CU138535.6	13300	13312	12147711	N	DUST
CU138535.6	13808	13875	12147712	N	DUST
CU138535.6	14482	14649	12147713	N	DUST
CU138535.6	14651	14792	12147714	N	DUST
CU138535.6	2728	3037	7421146	-	HE2_DR	V	SINE
CU138535.6	2308	2435	7421145	+	DNA9NNN1_DR		DNA
CU138535.6	1449	1556	7421144	+	TDR2	TcMar-Tc1	DNA
CU138535.6	1391	1445	7421143	+	TDR2	TcMar-Tc1	DNA
CU138535.6	400	756	7421142	+	HE2_DR	V	SINE
CU138535.6	94	368	7421141	-	DNA-TTAA-2_DR	PiggyBac?	DNA
CU138535.6	13	78	7421140	-	DNA-TTAA-2_DR	PiggyBac?	DNA
CU138535.6	265	271	12147685	N	DUST
CU138535.6	338	344	12147686	N	DUST
CU138535.6	738	744	12147687	N	DUST
CU138535.6	1905	1918	12147688	N	DUST
CU138535.6	3092	3175	12147689	N	DUST
CU138535.6	4100	4222	12147690	N	DUST
CU138535.6	4943	4949	12147691	N	DUST
CU138535.6	5651	5728	12147692	N	DUST
CU138535.6	7260	7279	12147693	N	DUST
CU138535.6	7592	7666	12147694	N	DUST
CU138535.6	7675	7681	12147695	N	DUST
CU138535.6	7693	7700	12147696	N	DUST
CU138535.6	7828	7915	12147697	N	DUST
CU138535.6	8194	8205	12147698	N	DUST
CU138535.6	8511	8523	12147699	N	DUST
CU138535.6	8530	8536	12147700	N	DUST
CU138535.6	8818	8840	12147701	N	DUST
CU861655.2	6545	6569	7431818	+	(CA)n		Simple_repeat
CU861655.2	6669	6717	7431819	+	(CAGA)n		Simple_repeat
CU861655.2	6724	6932	7431820	+	Gypsy-23-LTR_DR	Gypsy	LTR
CU861655.2	6936	7006	7431821	+	(CA)n		Simple_repeat
CU861655.2	7381	7422	7431822	+	(CA)n		Simple_repeat
CU861655.2	7878	7987	7431823	+	HATN10_DR	hAT	DNA
CU861655.2	7988	8298	7431824	+	EnSpm-N7_DR	CMC-EnSpm	DNA
CU861655.2	8299	8468	7431825	+	HATN10_DR	hAT	DNA
CU861655.2	8469	8635	7431826	+	DNA-1-3B_DR		DNA
CU861655.2	8641	9251	7431827	+	hAT-N19_DR	hAT-Charlie	DNA
CU861655.2	9249	9794	7431828	+	DNA-1-3B_DR		DNA
CU861655.2	9803	9984	7431829	+	EnSpm-6N1_DR	CMC-EnSpm	DNA
CU861655.2	9985	10356	7431830	+	PROTOP1_DR	P	DNA
CU861655.2	6184	6440	7431817	-	DNA-2-2_DR		DNA
CU861655.2	5956	6183	7431816	-	TDR23		DNA
CU861655.2	5643	5713	7431815	+	(CA)n		Simple_repeat
CU861655.2	4825	5160	7431814	-	HE1_DR1	V	SINE
CU861655.2	4601	4767	7431813	+	TC1DR3	TcMar-Tc1	DNA
CU861655.2	4505	4606	7431811	+	(CA)n		Simple_repeat
CU861655.2	4329	4504	7431812	+	ERV1-N3-I_DR-int
CU861655.2	4274	4328	7431811	+	(CA)n		Simple_repeat
CU861655.2	4153	4182	7431810	+	(TG)n
CU861655.2	3843	3869	7431809	+	(TG)n
CU861655.2	3404	3732	7431808	-	LTR-11_DR		LTR
CU861655.2	3367	3390	7431805	-	DIRS-4N2_DR	Ngaro	LTR
CU861655.2	4153	4182	12657780	N	DUST
CU861655.2	4274	4585	12657781	N	DUST
CU861655.2	5643	5713	12657782	N	DUST
CU861655.2	6545	6569	12657783	N	DUST
CU861655.2	6657	6722	12657784	N	DUST
CU861655.2	6810	6816	12657785	N	DUST
CU861655.2	6928	7006	12657786	N	DUST
CU861655.2	7293	7308	12657787	N	DUST
CU861655.2	7381	7422	12657788	N	DUST
CU861655.2	8352	8358	12657789	N	DUST
CU861655.2	9855	9923	12657790	N	DUST
CU861655.2	10187	10205	12657791	N	DUST
CU861655.2	3360	3408	7431807	-	LTR-11_DR		LTR
CU861655.2	3227	3366	7431806	-	HE1_DR1	V	SINE
CU861655.2	3207	3226	7431805	-	DIRS-4N2_DR	Ngaro	LTR
CU861655.2	2811	3091	7431803	+	HarbingerN3_DR	PIF-Harbinger	DNA
CU861655.2	2778	2810	7431804	+	(TA)n		Simple_repeat
CU861655.2	2541	2777	7431803	+	HarbingerN3_DR	PIF-Harbinger	DNA
CU861655.2	2197	2538	7431802	+	(CGAA)n		Simple_repeat
CU861655.2	2016	2194	7431801	+	(CACG)n		Simple_repeat
CU861655.2	1615	2074	7431800	+	(CGAA)n		Simple_repeat
CU861655.2	631	861	7431799	-	DNAX-1_DR		DNA
CU861655.2	293	628	7431798	-	HE2_DR	V	SINE
CU861655.2	1	291	7431797	-	DNAX-1_DR		DNA
CU861655.2	259	306	12657768	N	DUST
CU861655.2	430	442	12657769	N	DUST
CU861655.2	938	1005	12657770	N	DUST
CU861655.2	1612	1779	12657771	N	DUST
CU861655.2	1781	1922	12657772	N	DUST
CU861655.2	1954	2022	12657773	N	DUST
CU861655.2	2054	2276	12657774	N	DUST
CU861655.2	2333	2409	12657775	N	DUST
CU861655.2	2443	2506	12657776	N	DUST
CU861655.2	2778	2810	12657777	N	DUST
CU861655.2	3122	3133	12657778	N	DUST
CU861655.2	3843	3869	12657779	N	DUST

Join Legend

Curator Links

Alignment for CU138535.6 and CU861655.2

Alignment Summary

Alignment 1 of 1