Alignment last updated: 11/20/2008 16:56:51

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 <99.1%
- 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 >=99.1%
- 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 AL596025.22 and AL596187.15

Download Genome Workbench

Swap Rows Rotate Orientations

AL596025.22 Mouse DNA sequence from clone RP23-215H18 on chromosome 11 Contains a novel gene and the 3' end of a gene that is a possible ortholog of human dynein axonemal heavy polypeptide 9 (DNAH9, complete sequence [htgs_phase3]

Length: 190,066 bp

AL596187.15 Mouse DNA sequence from clone RP23-287H9 on chromosome 11, complete sequence [htgs_phase3]

Length: 202,358 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 1880
Total Length: 2000
Aligned Length: 2000
Percent Identity: 100
Number of Gaps: 0
Number of Mismatches: 0
Source: CtgOverlap Seq-Align
Valid Switchpoint: true (A)

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time	Id	Alignment	Releases
A	190066	200358	+	-	chenhc	Taxid 10090 chrom 11 Primary assembly	2008-11-20 16:56:51.300	63739	1880	GRCm39, GRCm38, MGSCv37

Alignment 1 of 1

 AL596025.22 : + : 188067..190066
 AL596187.15 : - : 202358..200359
 Mismatches = 0, Gaps = 0, Length = 2000
 Percent identity = 100%
 Score = 3965 bits (2000), Expect = 0
  2 BAC and 3 Fosmid bridging clones.
  2 BAC and 3 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

AL596025.22 >188067  gaattccagggtagccagggcaaccctgtctcaaaaaagtcagatgacgatgatgatgat 188126 
AL596187.15 <202358  ............................................................ 202299 

AL596025.22 >188127  gaaggaagggagaaagaaagaaacagagagaaggagagcaagagtagaatagagagagaa 188186 
AL596187.15 <202298  ............................................................ 202239 

AL596025.22 >188187  agaaatagagagagacacaggggcccaattcatgaatatctaggtattggactgaataaa 188246 
AL596187.15 <202238  ............................................................ 202179 

AL596025.22 >188247  cgcatttcacaaaattgtgattgatacagcattcactagaggaatagcaaataaaatgta 188306 
AL596187.15 <202178  ............................................................ 202119 

AL596025.22 >188307  tatcttgaaagaaggaaaaaataaaacagcagaaatacacaataattccacagaattcaa 188366 
AL596187.15 <202118  ............................................................ 202059 

AL596025.22 >188367  gaagggagggaaaggaaacaatggaggaaacatataaaagtaacataggacgcctcaccc 188426 
AL596187.15 <202058  ............................................................ 201999 

AL596025.22 >188427  tcaaatgcatgactgggtatgacagcatgagcaaatggacagtattctgaaaaggcacaa 188486 
AL596187.15 <201998  ............................................................ 201939 

AL596025.22 >188487  ctgccaagcgtgttttctaaaagtcgaatgtatagacagcacttacatttattcccaagc 188546 
AL596187.15 <201938  ............................................................ 201879 

AL596025.22 >188547  ataagagtataggaaatctgagcatgaaacaaaaagaagcggttcctaacgatgggttct 188606 
AL596187.15 <201878  ............................................................ 201819 

AL596025.22 >188607  ccacccatggtccagccaatcttggataacaaatattcagaaaggactacgtctgcatca 188666 
AL596187.15 <201818  ............................................................ 201759 

AL596025.22 >188667  catgtatacaattcatctctaaataacaaacaatcacaactacctaagtaacaactagat 188726 
AL596187.15 <201758  ............................................................ 201699 

AL596025.22 >188727  tgtgttaggtattttgggtaacctaaagattatctgaagggggtgatgtgtgcgagttac 188786 
AL596187.15 <201698  ............................................................ 201639 

AL596025.22 >188787  atcaagttccaaaggaatgggcagaggttagaagatttgtgtattatgcttgaggctttg 188846 
AL596187.15 <201638  ............................................................ 201579 

AL596025.22 >188847  gctcaatatccagaattggataaaagataaaaaaaaaaacaataaaattcctctgatatt 188906 
AL596187.15 <201578  ............................................................ 201519 

AL596025.22 >188907  tcatataaaggacctgagcctctctagattttcatatagatgagggatcatggtccagtg 188966 
AL596187.15 <201518  ............................................................ 201459 

AL596025.22 >188967  tcttctggacaccaatggacaagtaaaactgaagactaaaggaatatgggttagtcgtgc 189026 
AL596187.15 <201458  ............................................................ 201399 

AL596025.22 >189027  tatcaccagacaaagttaactttaaagcaagggctatttttggaggtaaagaagtacatt 189086 
AL596187.15 <201398  ............................................................ 201339 

AL596025.22 >189087  taacatatgagcaacagttcaagaaggtgggcaggttgtaagtatactcacatatatgtg 189146 
AL596187.15 <201338  ............................................................ 201279 

AL596025.22 >189147  agaaaatagagttgtttaaatttctattttttgtcaacataactttattagtataaaaaa 189206 
AL596187.15 <201278  ............................................................ 201219 

AL596025.22 >189207  atgaataggaagaaaaggagaagcagatatgttcatatgtccataccacttgggagattt 189266 
AL596187.15 <201218  ............................................................ 201159 

AL596025.22 >189267  tcacaaatctttctcaaaggcttatagaacatacagattttttttaaaaaaatcagtacc 189326 
AL596187.15 <201158  ............................................................ 201099 

AL596025.22 >189327  agtaaaatgtattaaacttaagttacatgatttaaaaatgtgtactaattgatgtattga 189386 
AL596187.15 <201098  ............................................................ 201039 

AL596025.22 >189387  ttaaactatacctgatgtctgagaacacatttctcaaaactgcatgttaatggtattgtt 189446 
AL596187.15 <201038  ............................................................ 200979 

AL596025.22 >189447  cgaacaatggcaaatctcaatagatttcacttgaatgaaatcacatggaatttgctgaaa 189506 
AL596187.15 <200978  ............................................................ 200919 

AL596025.22 >189507  ttaagtagttatcaattaaaaaaaaccccaaaacttctaaatgtttgagaacgaatgcta 189566 
AL596187.15 <200918  ............................................................ 200859 

AL596025.22 >189567  cactgaagattttaagctataaaccatgcaaccggggaaagcctgaatgttgcaaatgaa 189626 
AL596187.15 <200858  ............................................................ 200799 

AL596025.22 >189627  gtcggaggaaaatgtataaccataaagtgaacactatagaagacttgggaggacagttac 189686 
AL596187.15 <200798  ............................................................ 200739 

AL596025.22 >189687  tgaggtaagaaaccctgtcaatatatgagaaaataaactaaaggaatcccatgtccaagt 189746 
AL596187.15 <200738  ............................................................ 200679 

AL596025.22 >189747  taaataggaaagcaacaaataaaagagtaaatattagcaatatatatttgaaaaaaaaca 189806 
AL596187.15 <200678  ............................................................ 200619 

AL596025.22 >189807  agcatcaaacccaaacagtcaataaagttgaatgttggattctttcaattttcattaaaa 189866 
AL596187.15 <200618  ............................................................ 200559 

AL596025.22 >189867  aacaaaaacaaggactggcaatggataactcctttgcagaagtaacacagagaaaaatga 189926 
AL596187.15 <200558  ............................................................ 200499 

AL596025.22 >189927  atgccacaggtaactgtggctgtggtcatgaagcctactgtataggcaggctgtcactac 189986 
AL596187.15 <200498  ............................................................ 200439 

AL596025.22 >189987  ccagacgaaggcttttttggggggaggggggtggcgaagacagtttctcggagagccaga 190046 
AL596187.15 <200438  ............................................................ 200379 

AL596025.22 >190047  attctgcctgcagaaagcct 190066 
AL596187.15 <200378  .................... 200359

Events

Id	Type	Date	Whodid	Comment
3617	ImportOldDb	09/02/2005 12:44:00	f_old_db
3618	ReSetShortOvlp	09/04/2008 10:31:48	dbo
174496	CreateSwitchPt	11/20/2008 16:56:51	chenhc	tpf_builder 1.6 Toolkit wrapper version: built Nov 19 2008 using /netopt/ncbi_tools64/c++.by-date/20081119/GCC401-Release64/lib

BAC Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
C3H-102E10	AL596025.22	100%	pos 42232 (R-)
C3H-155B19				AL596187.15	100%	pos 86136 (F-)
C3H-166P17				AL596187.15	100%	pos 56306 (F-)
C3H-21N23	AL596187.15	99.15%	pos 49640 (R-)
C3H-22E24	AL596187.15	99.68%	pos 49541 (R-)
C3H-22F23	AL596187.15	99.59%	pos 49601 (R-)
C3H-239H6				AL596025.22	99.47%	pos 53809 (F-)
C3H-24F21	AL596025.22	100%	pos 52992 (R-)
C3H-59P19				AL596187.15	99.48%	pos 81498 (F-)
C3H-91I21	AL596187.15	99.61%	pos 65407 (R-)
CH29-490H12	AL596025.22	99.63%	pos 8294 (R-)
CH29-528L17	AL596025.22	99.88%	pos 158025 (R-)	AL596025.22	99.74%	pos 15903 (F+)
CH29-618B4	AL596187.15	99.73%	pos 122271 (R+)
CH29-622M23				AL596025.22	99.34%	pos 13912 (F+)
RP23-26O12	AL596187.15	99.86%	pos 65359 (R-)
RP23-27F18				AL596025.22	99.86%	pos 32941 (F-)
RP23-55M7				AL596025.22	99.16%	pos 144187 (F+)
RP24-132H19	AL596025.22	99.15%	pos 19300 (R+)
RP24-146B22	AL596187.15	99.63%	pos 57630 (R-)
RP24-156B15	AL596025.22	99.64%	pos 170437 (R-)
RP24-164M23	AL596187.15	99.74%	pos 86648 (R+)	AL596025.22	99.84%	pos 164102 (F+)
RP24-166I16	AL596187.15	100%	pos 195371 (R-)	AL596187.15	99.23%	pos 14644 (F+)
RP24-168G17	AL596187.15	99.8%	pos 40977 (R+)	AL596187.15	99.08%	pos 199480 (F-)
RP24-289G17				AL596187.15	99.54%	pos 108616 (F-)
RP24-316L2	AL596187.15	99.78%	pos 107844 (R+)	AL596025.22	99.38%	pos 100922 (F+)
RP24-362E9				AL596187.15	100%	pos 7411 (F-)
RP24-367G12	AL596187.15	99.52%	pos 124914 (R-)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-101K1	AL596187.15	99.72%	pos 72528 (R+)	AL596187.15	99.79%	pos 109542 (F-)
WI1-1036L12				AL596025.22	100%	pos 36398 (F-)
WI1-1076D19				AL596025.22	99.43%	pos 684 (F+)
WI1-1098G20	AL596025.22	99.61%	pos 111300 (R-)	AL596025.22	99.59%	pos 72458 (F+)
WI1-114L16	AL596025.22	100%	pos 26976 (R+)	AL596025.22	100%	pos 68450 (F-)
WI1-1194K22	AL596187.15	100%	pos 49364 (R+)	AL596187.15	100%	pos 89953 (F-)
WI1-1216K24	AL596187.15	99.84%	pos 102206 (R+)	AL596187.15	100%	pos 143121 (F-)
WI1-1224M9	AL596187.15	99.68%	pos 149116 (R+)	AL596187.15	100%	pos 187049 (F-)
WI1-1261M1	AL596187.15	100%	pos 29664 (R-)
WI1-1284F21	AL596187.15	100%	pos 13297 (R-)
WI1-1284G9	AL596187.15	100%	pos 82276 (R-)	AL596187.15	99.83%	pos 40927 (F+)
WI1-1284H23	AL596187.15	100%	pos 82276 (R-)	AL596187.15	100%	pos 40929 (F+)
WI1-1295N13	AL596025.22	99.8%	pos 11015 (R-)
WI1-1314J19	AL596025.22	99.57%	pos 171431 (R-)	AL596025.22	99.57%	pos 134670 (F+)
WI1-1327C18	AL596187.15	100%	pos 118634 (R-)	AL596187.15	99.84%	pos 74696 (F+)
WI1-1367J3				AL596187.15	99.69%	pos 164070 (F+)
WI1-140E18	AL596025.22	100%	pos 132761 (R+)	AL596025.22	99.86%	pos 170338 (F-)
WI1-1418P13				AL596025.22	100%	pos 36084 (F-)
WI1-146P7	AL596187.15	100%	pos 77988 (R-)
WI1-1500E13	AL596025.22	100%	pos 56263 (R+)	AL596025.22	100%	pos 97573 (F-)
WI1-1586C17				AL596025.22	99.4%	pos 184966 (F-)
WI1-1594O13	AL596025.22	99.6%	pos 12768 (R+)	AL596025.22	100%	pos 51425 (F-)
WI1-15C5	AL596187.15	100%	pos 38589 (R+)	AL596187.15	100%	pos 75490 (F-)
WI1-161I14	AL596187.15	100%	pos 2415 (R+)
WI1-1671K12				AL596025.22	100%	pos 14020 (F-)
WI1-1700G8	AL596187.15	100%	pos 25327 (R+)	AL596187.15	100%	pos 63772 (F-)
WI1-1718P4	AL596187.15	100%	pos 61587 (R-)	AL596187.15	100%	pos 20962 (F+)
WI1-1759C19	AL596187.15	99.84%	pos 119677 (R-)
WI1-1839E4	AL596187.15	99.63%	pos 106088 (R+)	AL596187.15	100%	pos 144785 (F-)
WI1-184A21	AL596025.22	100%	pos 63774 (R-)	AL596025.22	100%	pos 22547 (F+)
WI1-1864N12	AL596187.15	100%	pos 18026 (R+)	AL596187.15	99.34%	pos 63877 (F-)
WI1-1896E13	AL596187.15	99.85%	pos 80998 (R+)	AL596187.15	100%	pos 118623 (F-)
WI1-1905G1	AL596025.22	99.82%	pos 150484 (R-)
WI1-1942B1	AL596187.15	100%	pos 172867 (R-)	AL596187.15	100%	pos 136310 (F+)
WI1-1961P20	AL596187.15	100%	pos 171442 (R+)
WI1-1977C22	AL596025.22	100%	pos 166323 (R-)	AL596025.22	99.83%	pos 120481 (F+)
WI1-2032E2	AL596187.15	100%	pos 67453 (R-)	AL596187.15	100%	pos 29750 (F+)
WI1-2079K2	AL596025.22	100%	pos 17987 (R+)	AL596025.22	100%	pos 62026 (F-)
WI1-2131N5	AL596187.15	99.81%	pos 85457 (R+)	AL596187.15	100%	pos 127270 (F-)
WI1-225A13				AL596187.15	100%	pos 38045 (F+)
WI1-225O14	AL596187.15	99.51%	pos 7715 (R-)
WI1-2266E3	AL596187.15	100%	pos 194539 (R+)	AL596025.22	100%	pos 156670 (F+)
WI1-2330L17	AL596187.15	100%	pos 73931 (R-)	AL596187.15	100%	pos 36987 (F+)
WI1-2366B5				AL596025.22	99.68%	pos 120042 (F-)
WI1-2374G6	AL596187.15	99.84%	pos 81544 (R+)	AL596187.15	100%	pos 123560 (F-)
WI1-2374N13	AL596187.15	100%	pos 81544 (R+)	AL596187.15	100%	pos 123560 (F-)
WI1-2386O17	AL596187.15	100%	pos 197735 (R-)	AL596187.15	99.1%	pos 155128 (F+)
WI1-2423N8	AL596187.15	100%	pos 137994 (R-)	AL596187.15	100%	pos 100350 (F+)
WI1-2472I17	AL596025.22	100%	pos 10853 (R+)	AL596025.22	100%	pos 49681 (F-)
WI1-2477P13	AL596187.15	100%	pos 125091 (R+)	AL596187.15	99.74%	pos 163696 (F-)
WI1-2585J4	AL596025.22	99.82%	pos 51719 (R-)	AL596025.22	99.74%	pos 11950 (F+)
WI1-2601O8				AL596025.22	99.81%	pos 94619 (F+)
WI1-2665L23				AL596187.15	99.66%	pos 161556 (F-)
WI1-2669I21	AL596025.22	99.24%	pos 108989 (R-)	AL596025.22	99.53%	pos 71674 (F+)
WI1-2691M17	AL596187.15	100%	pos 108644 (R-)	AL596187.15	100%	pos 70822 (F+)
WI1-2759H22	AL596187.15	99.41%	pos 38052 (R-)	AL596187.15	100%	pos 1188 (F+)
WI1-2767A5	AL596025.22	100%	pos 68524 (R-)
WI1-2781A9	AL596187.15	99.53%	pos 131473 (R+)	AL596187.15	100%	pos 169703 (F-)
WI1-2794H15	AL596187.15	100%	pos 172352 (R+)	AL596025.22	99.59%	pos 182256 (F+)
WI1-2823J23				AL596187.15	100%	pos 192966 (F+)
WI1-2829M17	AL596187.15	100%	pos 22609 (R+)	AL596187.15	100%	pos 61755 (F-)
WI1-363O5	AL596187.15	99.25%	pos 22734 (R+)	AL596187.15	99.69%	pos 62012 (F-)
WI1-38A8	AL596025.22	100%	pos 73380 (R-)	AL596025.22	99.69%	pos 35300 (F+)
WI1-393D20	AL596187.15	99.81%	pos 129222 (R+)	AL596187.15	99.68%	pos 170232 (F-)
WI1-427I15	AL596025.22	100%	pos 180620 (R+)
WI1-577H24	AL596187.15	100%	pos 79672 (R-)	AL596187.15	100%	pos 39105 (F+)
WI1-60P1				AL596187.15	100%	pos 47729 (F-)
WI1-625H6	AL596187.15	100%	pos 64689 (R+)	AL596187.15	100%	pos 104538 (F-)
WI1-710H12				AL596025.22	99.29%	pos 15747 (F-)
WI1-726L18	AL596187.15	100%	pos 38590 (R+)
WI1-766G6	AL596187.15	100%	pos 63945 (R+)
WI1-857H24	AL596025.22	100%	pos 167275 (R+)	AL596187.15	100%	pos 181164 (F+)
WI1-896L3	AL596187.15	99.47%	pos 67673 (R+)	AL596187.15	100%	pos 112272 (F-)
WI1-975H1	AL596025.22	99.81%	pos 100217 (R+)
WI1-986C13	AL596187.15	100%	pos 75766 (R-)	AL596187.15	99.46%	pos 35317 (F+)
WI1-986G21	AL596187.15	100%	pos 75763 (R-)	AL596187.15	100%	pos 35309 (F+)

Repeats

Too repeats, not showing repeat table.

Join Legend

Curator Links

Alignment for AL596025.22 and AL596187.15

Alignment Summary

Alignment 1 of 1