Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1952
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14107
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Found at i:937 original size:474 final size:472
Alignment explanation
Indices: 1--6301 Score: 6640
Period size: 475 Copynumber: 13.3 Consensus size: 472
* * * * * * * * *
1 TGGAAAAAAAAGCTTATCTTGTGAAACCAAAGCATCAACGTCATGTATCCCAATTAATGGAATAT
1 TGGAAAGAAAAGCTTCTCTTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATGT
* * *
66 G-TTTTGGTTCCCAATCTCGAAAA-AATTAGAGACTGTTACAAGAATCAATGCTTGTCTTATTTA
66 GTTTTTGGTT-CCAATCTTGAAAAGAA-TAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTT
* * * * *
129 AAGGTCAAACTTTGATTTTAAAGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAAAAAATCAT
129 AAGGACAAACTTTGATTTTAAGGAAAATAAGGCAAAG-AAAGATTTTCATGCAAAAGAAAACCAT
* * * * * * *
194 CAATATCATTTCTCTTATTAAGGAGAATGTGTTTATAATGCCTAATCACAAAATGAATTAAGATC
193 CAATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGATC
* ** * * * *
259 ATT-GCTAGAATCCACATTTGTCTTTTTTGAGGCATGAACTTTGGCTTTACAAAAATTGGTGGGA
258 CTTAG-TAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGA
* * * * *
323 AGAAAGCTGTTCCTACGAAACCAAAGTA-CTAATATTGTATATCCTTATGAGAAGACTATGTTTA
322 AGAAAGC-GTTTCTTCGAAACCAAAGCATC-AATATCGTGTATCCTTATGAGAAGACTATGTTTA
* * * * * * * * *
387 TGGTGCAC-AATCCTTAAAAGATTAGGGATTTGTATGAGTACTCAAGTTGGTCCTATTTAACAGA
385 TGGTGC-CTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGT-CTTTTTAAGAGA
**
451 TGAACTTTGATTCTATCAATAACGG
448 CAAACTTTGATTCTATCAATAACGG
* * * * * *
476 TGGAAAGAAAAACTTCTCTCGAGACCCCAAAACATCAACGTCGTGTATCCTAATGAAGGGAATGT
1 TGGAAAGAAAAGCTTCTCTTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATGT
* * * * *
541 GTTTTCGGTTCCAGTCTTGAAAAGAATGGAGACTGTTATGAGAATCAATGCTTGCCTTATTTTAA
66 GTTTTTGGTTCCAATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTTAA
* *
606 GGAAAAACTTTGATTTTAAGGAAAATGAGGCAAAGAAAGATTTTCATGCAAAAGAAAACCATCAA
131 GGACAAACTTTGATTTTAAGGAAAATAAGGCAAAGAAAGATTTTCATGCAAAAGAAAACCATCAA
* * * *
671 TATCATTTATCCTAATGAGGAGAATATGTTTACAGTGCCTAATCACAAAATGAACGAAAATACTT
196 TATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGATCCTT
* *
736 AGTAGAATCCATGTTTATCTCTTTTGAGGCACGAACTTAGACTTTACAAATATTGGTGGGAAGAA
261 AGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGAAGAA
* * *
801 AGCGTTTCTTCTGAAACCAAAGCATCAATATTGTGCATCCTTATGAGAAGACTAGGTTTATGGTG
326 AGCGTTTCTTC-GAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTTATGGTG
* * *
866 CCTAATCCTGAAAAGATTGGGGATTAGTATGAGTATTCATGATTGTCTTGTTTAAGAGACAAACC
390 CCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTT-TTTAAGAGACAAACT
*
931 TTGATTCTATCAATAACGA
454 TTGATTCTATCAATAACGG
* ** * ***
950 TGGAAAGAAAAGCTTCTCTT-ACGACACCAATGCGCCAATGTCATGTATCTTAATGAAAAAAATG
1 TGGAAAGAAAAGCTTCTCTTGA-GACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATG
* * * *
1014 TGTTTTCGGTTCCTAATCTCGAAAGGAATAGAGACTGTTACGAGAATCAATGCTTGCCTTGA-TT
65 TGTTTTTGGTTCC-AATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTT-ATTT
* * * * * *
1078 AAAGGACAAACTTTGATTTTATGGAAAATGAGGTAAAGAAAGATTTCCATGCAAAAGAAAATCAT
128 TAAGGACAAACTTTGATTTTAAGGAAAATAAGGCAAAGAAAGATTTTCATGCAAAAGAAAACCAT
* * * * * *
1143 CAATATCATTTATCTTAATGAGGAGAATATGTTGATAGTGCCTAAGCAAAAAATGAATGGAGATA
193 CAATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGATC
* * * *
1208 CTTAGTAGAATCCATGTTTATCTCTTTTGACGCAGGAACTTAGACTTTACAAATATTGGTGGGAA
258 CTTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGAA
* * * * *
1273 GAAAACGTTTCTTCTAAAACCAAAGCATCAATATCGTGCATCCTTATGAGAAAACTAGGTTTATG
323 GAAAGCGTTTCTTC-GAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTTATG
* * * *
1338 GTGCCTAAT-CTCGAAAAGATTGGGGATTAGTATGAGTATTCATGATTGTCTTGTTTGAGAGATA
387 GTGCCTAATCCT-GAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTT-TTTAAGAGACA
*
1402 AACTTTGATTCTATCAATAACGA
450 AACTTTGATTCTATCAATAACGG
** * * * * *
1425 TGGAAACTAAAGCTTCTCTT-ACAACACGAAATCATTAATGTCATGTATCCTAATGAAGGGATTG
1 TGGAAAGAAAAGCTTCTCTTGA-GACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATG
* * *
1489 TGTTTTTGGTTTCCAATCTTG-AAATAATAGAGACTGTTACAAGAATCAATTCTTGTCTTA-TTT
65 TGTTTTTGG-TTCCAATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTT
* * * * * *
1552 ATGTGTCAAACATTGATTTTAAGGAAAATAAGGCCAAGAAAAGATTTTCTGTGCCAAA-AAAACC
129 AAG-GACAAACTTTGATTTTAAGGAAAATAAGGCAAAG-AAAGATTTTC-ATGCAAAAGAAAACC
* * * * *
1616 ATCAATATCATTTATCCGAATGAGGAGAATGTGTTTATAGCGCTTAATCACAAAATGAAAGAAGA
191 ATCAATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGA
* ** * **
1681 TCCTTACTAGAATCCATGTTTGTCTAATTTGAGGCACAAACTTAGACTTTTTAAAAATTGGTGGG
256 TCCTTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGG
* * ** * * *
1746 AA-AAATGCCTTTCTTGCTAAATGAAAGCATTAATATCGTGTATCATTATGAGAAGACTAGGTTT
321 AAGAAA-GCGTTTCTT-CGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTT
* * * *
1810 ATGGTGCCTAATCTTGAAAAGAGTAGGGATTAGTATGAGTATTCATGTTTGTCTTATTAAAGAGA
384 ATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTT-TTTAAGAGA
*
1875 CAAACTTTGATTCTATCAATAATGG
448 CAAACTTTGATTCTATCAATAACGG
* * * * * *
1900 TGGAAAAAAAAGCTTCTCTTGCGAAACCAAAGCATCAATGTCATGTATCCCAATTAATGGAATGT
1 TGGAAAGAAAAGCTTCTCTTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATGT
* * * *
1965 GTTTTTGGTTCCAATCTCGACAAA-ATTAGAGACTGTTACAAGAATCAATGCTTGTCTTA-TTAA
66 GTTTTTGGTTCCAATCTTGA-AAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTTA
* * * * *
2028 AGGTCAAAACTTTGATTTTAAAGAAAATAGGGCAAAGAAAATATTTTCATGC--AA-AAAATCAT
130 AGGAC-AAACTTTGATTTTAAGGAAAATAAGGCAAAG-AAAGATTTTCATGCAAAAGAAAACCAT
* * * * *
2090 CAATATCA-TTCTCTTATTGAGGAGAATATGTTTATAGTGCCAAATCACAAAATGAATTAAGATC
193 CAATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGATC
* * ** * * * * *
2154 ATT-GCTAGAACCCACATTTGTCTTTTTTGAGGCACAAACTTTGGCTTTACAAATATTGGTGGGA
258 CTTAG-TAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGA
* * * * *
2218 AGAAAGCTGTTCCTACGAAACCAAAGTACCAATATCGTATATCCTTATGAGAAGACTATGTTTAT
322 AGAAAGC-GTTTCTTCGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTTAT
* * * * * * *
2283 GGTGCAC-AATCCTTAAAAGATTAGGGATTTGTATGAGTATTTAGGTTTGTCTTATTTAAGAGAT
386 GGTGC-CTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTT-TTTAAGAGAC
* **
2347 GAACTTTGATTCTATCAATAATTG
449 AAACTTTGATTCTATCAATAACGG
* * * * * *
2371 TGGAAAGAAAAACTTCTCTTGCGACCCCAAAACATCAATGTCTTGTATCCTAATGAAGGGACTGT
1 TGGAAAGAAAAGCTTCTCTTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATGT
* * * *
2436 GTTTTTGGTTCCTAATCTTGAAAAGAAAAGAGACTGTTACGAGAATCAATGCCTGCCTTATTTAA
66 GTTTTTGGTTCC-AATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTTA
* * *
2501 AGGAAAAACTTTGATTTTAAGGAAAATGAGGCAAAAGAAAGATTTTTCATGCAAAAGAAAACTAT
130 AGGACAAACTTTGATTTTAAGGAAAATAAGGC-AAAGAAAGA-TTTTCATGCAAAAGAAAACCAT
** * * *
2566 CAATATCATTTATCCTAACAAGGAGAATATGTTTACAGTGCCTAATCACAAAATGAATGAAAATA
193 CAATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGATC
* * * *
2631 CTTAGTAGAATCCATGTTTATCTCTTTTGAGGCATGAACTTAGAC-TTGCAAATATTGGTGGGAA
258 CTTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGAA
* * * *
2695 G-AAGCATTTCTTCTG-AACCAAAGCATCAATATCATGCATCCTTA-GAGAAGACTAAGTTTATG
323 GAAAGCGTTTCTTC-GAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTTATG
* *
2757 GTGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGATTGTCTGTTTAAGAGACAAA
387 GTGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTTTTAAGAGACAAA
*
2822 CTTTGATTCTAATCAATAACGA
452 CTTTGATTCT-ATCAATAACGG
* * ** * *
2844 TAGAAAGAAAAGCTTCTCTT-ACGACACCAATGCGCCAATGTCATGTATCTTAATGAAAGGAATG
1 TGGAAAGAAAAGCTTCTCTTGA-GACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATG
* * * *
2908 TGTTTTTGGTTCCCAATCTTGAAAGGAATGGAGACTGTTACGAGAATCAATGCTTGCCTT-GTTT
65 TGTTTTTGGTT-CCAATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTT
* * * * * *
2972 AAGGACAAACTTTGATTTTATGGAAAATGAGGTAAAGAGAGATTTCCATGCAAAAGAAAATCATC
129 AAGGACAAACTTTGATTTTAAGGAAAATAAGGCAAAGAAAGATTTTCATGCAAAAGAAAACCATC
* * *
3037 AATATCATTCATCCTAATGAGGAGAATATGTTGATAGTGCCTAATCACAAAATGAATGAAGATAC
194 AATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGATCC
* * **
3102 TTAGTAGAATCTATGTTTGTCTCTTTTGAGGCAGGAACTTAGACTTTACAAATGTTGGTGGGAAG
259 TTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGAAG
** * * * * *
3167 AAAGTATTTCTTCCAAAACCAAAGCATCAATATCGTGCATCCTTATGAGAAAACTAGGTTTATTG
324 AAAGCGTTTCTT-CGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTTATGG
* * *
3232 TGCCTAATCCCGAAAATAATGGGGATTAGTATGAGTATTCATGATTGTCTTGTTTAAGAGACAAA
388 TGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTT-TTTAAGAGACAAA
*
3297 CTTTGATTCTATCAATAACGA
452 CTTTGATTCTATCAATAACGG
* * ** * *
3318 TGGAAACAAAAGCTTTCTCCT-AGCAACATGAAATCATTAATGTCATGTAATCCTAATGAAGGGA
1 TGGAAAGAAAAGC-TTCTCTTGAG--ACACCAAAGCATCAATGTCATGT-ATCCTAATGAAGGGA
* * * *
3382 TTGTGTTTTTGGTTTCCAATCTTG-AAATAATAGAGACTGTTACAAGAATCAATTCTTGTCTTA-
62 ATGTGTTTTTGG-TTCCAATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTAT
* * * * * *
3445 TTTATGTGTCAAACGTTGATTTTAAGGAAAATATGGC-AAGAAAGATTTTCATGCAAAAAAAAAA
126 TTTAAG-GACAAACTTTGATTTTAAGGAAAATAAGGCAAAGAAAGATTTTCATGCAAAAGAAAAC
* * * * * * *
3509 CATCAATATAATTT-TCTCTTATAAAGGAGAATGTGTTTATAGTGCCTAATCGCAAAAGGAATTA
190 CATCAATATCATTTATC-CTAAT-GAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGA
* * * * *
3573 AGATCATT-GCTAGAATCCACGTTTGTCTTTTTTGAGGCACG-ACTTAGATTTTACAAATATTGG
253 AGATCCTTAG-TAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGG
* * * * * *
3636 TGGGAAAGAAAGC-TGTTCTTTGCAAAATCAAAGTATCAATATCGTATATCCTTATGAGCATACT
317 TGGG-AAGAAAGCGT-TTC-TT-CGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACT
* * * * * *
3700 -TTTGTTATGGCGCATAATCCTTAAATGAATTGGGATTAGTATGAG---T-A-----------TT
378 ATGT-TTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTTTT
* * *
3749 ------C--AC----ATTCTACCAATAATGA
442 AAGAGACAAACTTTGATTCTATCAATAACGG
* * * *
3768 TGGAAAGAAAAGCTTCTCCT-ATGACACCAAACCATCAATGTCATGGATCCTAATGAAGAGAATG
1 TGGAAAGAAAAGCTTCTCTTGA-GACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATG
* * * * * * *
3832 CGTTTTTGGTTCGCAATCTTG-AAAGCAATGGAGACTATTCCGAGAATCATTGCTTTTGTT-TTT
65 TGTTTTTGGTTC-CAATCTTGAAAAG-AATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTT
*
3895 TCAAGGACAAACTTTGATTTTAAGGAAAATAAGGCAAAGAAA-ATATTTCCACGCAAAAGAAAAC
128 T-AAGGACAAACTTTGATTTTAAGGAAAATAAGGCAAAGAAAGAT-TTT-CATGCAAAAGAAAAC
* * * * *
3959 CATAAATATCATTTATCCTAATAAGGAGAATTTGTTTATAATGCCAAATCACAAAATGAATGAAG
190 CATCAATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAG
* * * * * *
4024 ATCCTTACTAGAATCCATTTTTATCTCATTTGAGGCACGAACTTAGACTTTTCAAAAATTGGCGG
255 ATCCTTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGG
* * * * * * *
4089 GAAAAAAACGTTTCTTGCGAAACGAAAGCATCAATATCCTGTATCCTTATTAAAAGACTATGTCT
320 GAAGAAAGCGTTTCTT-CGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTT
** * * * * *
4154 ATGCAGCCTAATCCTGAAAAAAATGGGGACTAGTATAAGTATTCATTTTTGTCTTTTTTAGAGAC
384 ATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTTTTAAGAGAC
*
4219 AAACTTTGATTCTACCAATAACGG
449 AAACTTTGATTCTATCAATAACGG
* * *
4243 TGGAAACAAAAGCTTCTCTT-ACGACACCAATGCATCAATGTCATGTATCGTAATGAAGGGAATG
1 TGGAAAGAAAAGCTTCTCTTGA-GACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATG
* *
4307 TGTTTTTGGTTCCTAATCTTGAAAAGATTACAGACTGTTACGAGAATCAATGCTTGTCTTA-TTT
65 TGTTTTTGGTTCC-AATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTT
* * * *
4371 AAGGGTCATACTTTGATTTTAAGGAAAATAAGGGTAAAGAAAAGATTTTCAGTGC-CAAGAAAAC
129 AA-GGACAAACTTTGATTTTAAGGAAAATAA-GGCAAAG-AAAGATTTTCA-TGCAAAAGAAAAC
* * * * * * * *
4435 CATCAATAACATTTATCCTAATTAAAGAGAATTTATTTATAATG-CTGAATCCCAAAACGAATGA
190 CATCAATATCATTTATCCTAA-TGAGGAGAATATGTTTATAGTGCCT-AATCACAAAATGAATGA
* * * * * * *
4499 AGATCCTTACTAGAATCCATATTTATCTCATTTGAGACACGAACTTAGACTTTTCAAAAATTGGA
253 AGATCCTTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGT
* * * *** * **
4564 GGGAAAAAAGCATTTCTTGCGAAACCAAAGCATTAATATCACCTATCCTTATTAGAAGACTACAT
318 GGGAAGAAAGCGTTTCTT-CGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGT
* * * *
4629 TTATGGTTCCTATTCCTCAAAAGAATGGGGATTAGTATGAGAATTCATGTTTGTCTTTTTAAGAG
382 TTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTTTTAAGAG
* **
4694 AC-AACCTTGATTCTATCAATAACCA
447 ACAAACTTTGATTCTATCAATAACGG
* * **
4719 TGGAAAGAAAAGCTTCTCTTGCGACACCAAACCATCAATGTCATGTATCCTAATGAATAGAATGT
1 TGGAAAGAAAAGCTTCTCTTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATGT
* * * * * * * *
4784 GTTCTCGGTTCCCAATCTTGAAAGGAATAGAGACTGCTGCGAGAATCAATACTTGCCTTATTTCA
66 GTTTTTGGTT-CCAATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTTA
*
4849 AGGACAAACTTTGATTTTAAGCAAAATAAGGCAAAGAAAAGATTTTCATGCAAAAGAAAACCATC
130 AGGACAAACTTTGATTTTAAGGAAAATAAGGCAAAG-AAAGATTTTCATGCAAAAGAAAACCATC
*
4914 AATATCATTTATCCTAATAAGGAGAAGT-TGTTTATAGTGCCTAATCACAAAATGAATGAAGATC
194 AATATCATTTATCCTAATGAGGAGAA-TATGTTTATAGTGCCTAATCACAAAATGAATGAAGATC
* * * * *
4978 CTTACTAGAATCCATGTTTGTCTCATTTGAGGCACGAACTTACACTTTTCAAAAATTGGTGAGAA
258 CTTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGAA
* * **
5043 AAAAACGTTTCTTGCGAAACCAAAGCATCAATATTC-TGTATCCTTATTG-GAAGACTATGTCCA
323 GAAAGCGTTTCTT-CGAAACCAAAGCATCAATA-TCGTGTATCCTTA-TGAGAAGACTATGTTTA
*
5106 TGCG-GCCTAATCCTGAAAAGAATGGGGATTAGTATAAGTATTCATGTTTGTCTTTTTAAGAGAC
385 TG-GTGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTTTTAAGAGAC
* *
5170 AAGCTTTGATTCTACCAATAACGG
449 AAACTTTGATTCTATCAATAACGG
* * * *
5194 TGGAAAGAAAAGCTTTTCTTGCGACACCAACGCATCAATGTCTTGTATCCTAATGAAGGGAATGT
1 TGGAAAGAAAAGCTTCTCTTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATGT
* * * *
5259 GTTTTTGGTTCCTAATCTTGAAAAGATTAGAGACTGCTACGAGAATTAATGCTTGTCTTATTTAA
66 GTTTTTGGTTCC-AATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTTA
* * * * *
5324 AGGTCAAACTTTAATTTTAAGGAAAATAAGGCAAGGAAAAGATTTCCATGCCAAAGAAAACCATC
130 AGGACAAACTTTGATTTTAAGGAAAATAAGGCAAAG-AAAGATTTTCATGCAAAAGAAAACCATC
* * * * * *
5389 AATAACGTTTATCCTAATGAAGAGAATATGTTTATAGTGCCTAACCACGAAATGAATAAAGATCC
194 AATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGATCC
* * * ** * ** *
5454 TTACTAGATTCCATGTTTGTTTCACTTGAGGCACGAACTTAGACTTTTC-AAAATTAATGGGAAC
259 TTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGAAG
* * * * *
5518 AAAGCGTTTATTGCAAAACCAAAGCATCAATATTGTGTATCCTTATAAGAAGACTTTGTTTATGG
324 AAAGCGTTTCTT-CGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTTATGG
*** * * *
5583 TAATTAATCCTGAAACA-AATGGGGATTAGTATGAGTATTCGTGCTTATCTTTTTTAAGAGACAA
388 TGCCTAATCCTGAAA-AGAATGGGGATTAGTATGAGTATTCATGTTTGTC-TTTTTAAGAGACAA
5647 GA-TTTGATTCTATCAATAACGG
451 -ACTTTGATTCTATCAATAACGG
* * * *
5669 TGGAAAGAAAAGCTTCTCTTTCA-ACACCAGAGAATCAATGTCATGTATCCTAATAAAGGGAATG
1 TGGAAAGAAAAGCTTCTC-TTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATG
* * * * * * ** *
5733 TG-TTTTGGTTCCCAATCCTGAAAGGAATGGAGACTGTTATGAGAATTAATGTTTACCTTATTTA
65 TGTTTTTGGTT-CCAATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTT
* * *
5797 AAGGACAAACATTGATTTTAAGGAAAATAAGGCAAAGATAACATTTCCATGC-AAAGAAAAACCA
129 AAGGACAAACTTTGATTTTAAGGAAAATAAGGCAAAGA-AAGATTTTCATGCAAAAG-AAAACCA
* * * *
5861 -CTAATATCTTTTATCCTAATGAGGGGAATTTGTTTATAGTGCCTAATCACAAAATGAATGAGGA
192 TC-AATATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGA
* * * *
5925 TCCTTACTAGAATCCATGTTTGTCTCATTTGAGGCACAAACTTAAACTTTTA-AAAAATTGGTGG
256 TCCTTAGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGAC-TTTACAAAAATTGGTGG
* * * * * * *
5989 GAAGAAAGCCTTTCTTACAAAACCAAAGCATCAATATTGTCTATCCTTATTAGAGGACTACGTTT
320 GAAGAAAGCGTTTCTT-CGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTT
* * *
6054 ATGGTGTCTAATCCTGAAAAGAATGCGGATTAGTATGAGTATTCATGTTTCTCTTAATTT-AGAG
384 ATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTT--TTTAAGAG
** * *
6118 TTAAGCTTTGATTCTATCAATAATGG
447 ACAAACTTTGATTCTATCAATAACGG
* * * * * * * *
6144 TGG-ACGAAAAAG-TTGTTGTTGCGACACTAAAGCATCGATGTGATGTATCCAAATGAAGGGAAT
1 TGGAAAG-AAAAGCTT-CTCTTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAAT
* * * * * *
6207 ATGTTTTTGGTTCCCAATCTTGTAAAGATTAGAGATTGTTATGAGAATCAATGCTAGTCTTA-TT
64 GTGTTTTTGGTT-CCAATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTT
* * **
6271 TAAGGGTCAAACCTCAATTTTAAGGAAAATA
128 TAA-GGACAAACTTTGATTTTAAGGAAAATA
6302 GGTGTCGTAA
Statistics
Matches: 4930, Mismatches: 751, Indels: 289
0.83 0.13 0.05
Matches are distributed among these distances:
446 3 0.00
447 35 0.01
448 142 0.03
449 98 0.02
450 78 0.02
451 3 0.00
452 1 0.00
454 2 0.00
456 1 0.00
462 2 0.00
463 2 0.00
469 1 0.00
470 120 0.02
471 315 0.06
472 154 0.03
473 244 0.05
474 1033 0.21
475 1744 0.35
476 440 0.09
477 436 0.09
478 76 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (472 bp):
TGGAAAGAAAAGCTTCTCTTGAGACACCAAAGCATCAATGTCATGTATCCTAATGAAGGGAATGT
GTTTTTGGTTCCAATCTTGAAAAGAATAGAGACTGTTACGAGAATCAATGCTTGTCTTATTTTAA
GGACAAACTTTGATTTTAAGGAAAATAAGGCAAAGAAAGATTTTCATGCAAAAGAAAACCATCAA
TATCATTTATCCTAATGAGGAGAATATGTTTATAGTGCCTAATCACAAAATGAATGAAGATCCTT
AGTAGAATCCATGTTTGTCTCTTTTGAGGCACGAACTTAGACTTTACAAAAATTGGTGGGAAGAA
AGCGTTTCTTCGAAACCAAAGCATCAATATCGTGTATCCTTATGAGAAGACTATGTTTATGGTGC
CTAATCCTGAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTTTTAAGAGACAAACTTT
GATTCTATCAATAACGG
Found at i:9426 original size:52 final size:51
Alignment explanation
Indices: 9361--9510 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
9351 CGAAATATGA
9361 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * * *
9413 AAATTTGCTTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
9465 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACAT
9511 GTATCGATAC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:9515 original size:12 final size:12
Alignment explanation
Indices: 9498--9522 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9488 CAAAGATCAG
9498 TGTATCGATACA
1 TGTATCGATACA
9510 TGTATCGATACA
1 TGTATCGATACA
9522 T
1 T
9523 TTAAGTGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:9599 original size:33 final size:33
Alignment explanation
Indices: 9562--9628 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
9552 AGTAGCTTAA
9562 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
9595 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
9628 A
1 A
9629 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:9602 original size:13 final size:13
Alignment explanation
Indices: 9584--9608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9574 CAAAAAAATA
9584 TGTATCGATACAT
1 TGTATCGATACAT
9597 TGTATCGATACA
1 TGTATCGATACA
9609 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10518 original size:49 final size:49
Alignment explanation
Indices: 10393--10679 Score: 370
Period size: 49 Copynumber: 5.9 Consensus size: 49
10383 AAGATGAGAA
* * *
10393 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
10443 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
10495 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG--
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * * *
10542 --A--TGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAGAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
10587 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
10636 GAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
10680 GAAGGGTTGC
Statistics
Matches: 213, Mismatches: 15, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
43 37 0.17
45 1 0.00
47 1 0.00
49 129 0.61
52 40 0.19
53 5 0.02
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
Found at i:10608 original size:92 final size:92
Alignment explanation
Indices: 10446--10679 Score: 306
Period size: 92 Copynumber: 2.5 Consensus size: 92
10436 TAAAGATGGA
* * *
10446 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGATGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
10511 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTACATTGGACTT
* * * * *
10538 AAAGATGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAGAGATGAAGGTGCCAATGTGC
1 AAAGATGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
10603 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTACATTGGACTT
* * *
10630 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 -AA-A-G-A--TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTA
10680 GAAGGGTTGC
Statistics
Matches: 122, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
92 83 0.68
93 2 0.02
94 1 0.01
95 1 0.01
96 1 0.01
98 34 0.28
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (92 bp):
AAAGATGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTACATTGGACTT
Found at i:10659 original size:141 final size:143
Alignment explanation
Indices: 10397--10679 Score: 462
Period size: 141 Copynumber: 2.0 Consensus size: 143
10387 TGAGAAAAAG
* *
10397 GATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGC
1 GATGCCAATGTGCTGAGTCAAGGCCAGCTACATTGAACTTAAAGATGG-AAAGGTGCCAATATGC
*
10462 TGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
65 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
10527 ATATTGGACTTAAA
130 ATATTGGACTTAAA
* * * *
10541 GATGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAGAGAT-G-AAGGTGCCAATGTGCT
1 GATGCCAATGTGCTGAGTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCT
*
10604 GATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
66 GATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
*
10669 TATTGGGCTTA
131 TATTGGACTTA
10680 GAAGGGTTGC
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
141 88 0.68
143 1 0.01
144 41 0.32
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (143 bp):
GATGCCAATGTGCTGAGTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCT
GATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
TATTGGACTTAAA
Found at i:10762 original size:32 final size:32
Alignment explanation
Indices: 10672--10934 Score: 410
Period size: 32 Copynumber: 8.2 Consensus size: 32
10662 CCAGCTATAT
10672 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
10702 TGGGCTTTAGAGAGGG-TGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
10733 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
10765 TGGGCTTT-GAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
10797 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
10829 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTG
* * *
10862 TGGGCTTCGAAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTT-TAGAGAGGGTTGCCACCGACTTGTG
10895 TGGGCTTTA-AGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
10927 TGGGCTTT
1 TGGGCTTT
10935 GGGAAGGGAG
Statistics
Matches: 218, Mismatches: 7, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
30 5 0.02
31 40 0.18
32 112 0.51
33 60 0.28
34 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:11002 original size:70 final size:67
Alignment explanation
Indices: 10945--11396 Score: 412
Period size: 70 Copynumber: 6.9 Consensus size: 67
10935 GGGAAGGGAG
* *
10945 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTG-GGGCTTTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT--A
11008 AAGAA
63 AAGAA
11013 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT--
11078 AAAGAA
62 AAAGAA
* * *
11084 AAA-GTGCCACGAAGTGGTGGGCTTTGAAAA-GAAAAAG-GTTGCCACGGAATTGTGGGCTTT--
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTAA
11144 --AA
64 AGAA
* * * * *
11146 AATGGTGCCACGGAGTTGTGGAC-TTAAAAAG-AAAA-AGTGCCATGGAGTGGT-GGCTTTGAGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A-A
11207 AGAA
64 AGAA
** *
11211 AAAGGTTGCCACATAATTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAA
1 AAAGG-TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
11275 CG--
65 -GAA
* * *
11277 ---GGTGCCATGGAGTTGTGGGC-TTAAAAGG-AAAAGAGTGCCACGTAGTTGTGGGCTTTGAA-
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAG
11336 AA
66 AA
* ** * * * *
11338 GAAGGTGCCACGGAGTTGTGGATTTTGAAA-GAAAAAG-GTGCCACAGAGTCGTGGACTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
11397 GATGCCACTG
Statistics
Matches: 323, Mismatches: 34, Indels: 58
0.78 0.08 0.14
Matches are distributed among these distances:
59 6 0.02
60 35 0.11
61 21 0.07
62 21 0.07
63 18 0.06
64 36 0.11
65 16 0.05
66 14 0.04
67 10 0.03
68 54 0.17
69 18 0.06
70 56 0.17
71 18 0.06
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.22
Consensus pattern (67 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAG
AA
Found at i:11229 original size:94 final size:96
Alignment explanation
Indices: 11054--11241 Score: 308
Period size: 94 Copynumber: 2.0 Consensus size: 96
11044 GGGAAAAAGA
*
11054 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGAAGTGGTGGGCTTTGAAAAGAAAA
1 GTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGTGCCACGAAGTGGTGGGCTTTGAAAAGAAAA
*
11119 AGGTTGCCACGGAATTGTGGGCTTTAAAATG
66 AGGTTGCCACAGAATTGTGGGCTTTAAAATG
* * *
11150 GTGCCACGGAGTTGTGGAC-TTAAAAAGAAAAAGTGCCATGGAGTGGT-GGCTTTGAGAAGAAAA
1 GTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGTGCCACGAAGTGGTGGGCTTTGAAAAGAAAA
*
11213 AGGTTGCCACATAATTGTGGGCTTTAAAA
66 AGGTTGCCACAGAATTGTGGGCTTTAAAA
11242 GGAAAAAGAG
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
94 42 0.49
95 26 0.30
96 18 0.21
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.23
Consensus pattern (96 bp):
GTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGTGCCACGAAGTGGTGGGCTTTGAAAAGAAAA
AGGTTGCCACAGAATTGTGGGCTTTAAAATG
Found at i:11398 original size:33 final size:33
Alignment explanation
Indices: 10945--11396 Score: 395
Period size: 33 Copynumber: 13.8 Consensus size: 33
10935 GGGAAGGGAG
* *
10945 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA--GAA
10979 AAAGAGTGCCACGGAGTTG-GGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGAA
11013 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA--GAA
11049 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGAA
* *
11084 AAA-GTGCCACGAAGTGGTGGGCTTTGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGAA
*
11117 AAAGGTTGCCACGGAATTGTGGGCTTT-----AA
1 AAAGG-TGCCACGGAGTTGTGGGCTTTAAAAGAA
* * *
11146 AATGGTGCCACGGAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAA
* * *
11179 AAA-GTGCCATGGAGTGGT-GGCTTTGAGAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGAA
** *
11211 AAAGGTTGCCACATAATTGTGGGCTTTAAAAGGAA
1 AAAGG-TGCCACGGAGTTGTGGGCTTTAAAA-GAA
*
11246 AAAGAGTGCCACGGAGTTGTGGGC-TTAAACG--
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGAA
* *
11277 ---GGTGCCATGGAGTTGTGGGC-TTAAAAGGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAA
*
11306 AAAGAGTGCCACGTAGTTGTGGGCTTTGAAAAG--
1 AAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGAA
** *
11339 -AAGGTGCCACGGAGTTGTGGATTTTGAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAA
* * *
11371 AAAGGTGCCACAGAGTCGTGGACTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTT
11397 GATGCCACTG
Statistics
Matches: 346, Mismatches: 41, Indels: 63
0.77 0.09 0.14
Matches are distributed among these distances:
27 24 0.07
28 19 0.05
29 6 0.02
30 4 0.01
31 23 0.07
32 26 0.08
33 89 0.26
34 45 0.13
35 72 0.21
36 12 0.03
37 26 0.08
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.22
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAA
Found at i:11524 original size:30 final size:31
Alignment explanation
Indices: 11398--11570 Score: 158
Period size: 31 Copynumber: 5.7 Consensus size: 31
11388 GTGGACTTTG
* *
11398 ATGCCACTGAGTCGTGGAC-TT-A-AAAAGG
1 ATGCCACTGAGTCGTGGACTTTGAGAAGAGA
* * * * * *
11426 ATGCCACTGAATTGTGGACTTTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTTGAGAAGAGA
* * * * *
11457 ATGTCACTGAGTCGTGGGCTTGGAGAAAAGG
1 ATGCCACTGAGTCGTGGACTTTGAGAAGAGA
* *
11488 ATGCCACTAAGTCATGGACTTTGAGATA-A-A
1 ATGCCACTGAGTCGTGGACTTTGAGA-AGAGA
11518 ATGCCACTGAGTCGTGGACTTTGAGAAGAGA
1 ATGCCACTGAGTCGTGGACTTTGAGAAGAGA
*
11549 TTGCCACTGAGTCGTGGACTTT
1 ATGCCACTGAGTCGTGGACTTT
11571 AAAAAGGTAT
Statistics
Matches: 114, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
28 17 0.15
29 3 0.03
30 26 0.23
31 67 0.59
32 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (31 bp):
ATGCCACTGAGTCGTGGACTTTGAGAAGAGA
Found at i:11544 original size:61 final size:62
Alignment explanation
Indices: 11398--11570 Score: 205
Period size: 61 Copynumber: 2.9 Consensus size: 62
11388 GTGGACTTTG
* *
11398 ATGCCACTGAGTCGTGGAC-TT-A-AAAAGGATGCCACTGAA-TTGTGGACTTTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTTGAGAAAAGGATGCCACT-AAGTCGTGGACTTTGAGGACAAA
* * * * *
11457 ATGTCACTGAGTCGTGGGCTTGGAGAAAAGGATGCCACTAAGTCATGGACTTTGA-GATAAA
1 ATGCCACTGAGTCGTGGACTTTGAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGGACAAA
* *
11518 ATGCCACTGAGTCGTGGACTTTGAGAAGA-GATTGCCACTGAGTCGTGGACTTT
1 ATGCCACTGAGTCGTGGACTTTGAGAAAAGGA-TGCCACTAAGTCGTGGACTTT
11571 AAAAAGGTAT
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 17 0.18
60 3 0.03
61 52 0.54
62 24 0.25
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (62 bp):
ATGCCACTGAGTCGTGGACTTTGAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGGACAAA
Found at i:12526 original size:12 final size:12
Alignment explanation
Indices: 12517--12541 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12507 GGTTTTTTCT
12517 TTTTTTTTTTTG
1 TTTTTTTTTTTG
12529 TTTTTTTTTTTG
1 TTTTTTTTTTTG
12541 T
1 T
12542 GAAGATTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:12527 original size:13 final size:13
Alignment explanation
Indices: 12509--12539 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12499 TGAAAAGGGG
12509 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
*
12522 TTTTTTGTTTTTT
1 TTTTTTCTTTTTT
12535 TTTTT
1 TTTTT
12540 GTGAAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.94
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:12824 original size:12 final size:12
Alignment explanation
Indices: 12806--12854 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
12796 CCTTTGTACT
12806 CTTTTTTTTTTA
1 CTTTTTTTTTTA
*
12818 GTTTTTTTCTTT-
1 CTTTTTTT-TTTA
*
12830 CTTTTTTTTTGA
1 CTTTTTTTTTTA
*
12842 CTTTTTCTTTTA
1 CTTTTTTTTTTA
12854 C
1 C
12855 ATTTGTTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 2 0.07
12 25 0.83
13 3 0.10
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (12 bp):
CTTTTTTTTTTA
Done.