Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014906.1 Corchorus olitorius cultivar O-4 contig14939, whole genome shotgun sequence
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: 90842
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:997 original size:325 final size:320
Alignment explanation
Indices: 1--2714 Score: 3756
Period size: 320 Copynumber: 8.4 Consensus size: 320
* *
1 TTTGGTTCGATGAATATAGGTATTTCAAGGAGTCTTCACGCCAAAACTCATGCAAAACTGAGGCA
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* ** *
66 GAGCCCCGGAACTCGTTTTGGGCCCAAAAACCGTGA-----CGTACACGATTTCGGCTAAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
* ** * *
126 GACCCGAATATTTTTTTCTTTATTTTCTGCCACAATACTAAGAAAAAATATATAATTTAACGCCT
131 GACCC-AAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCCC
191 AAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTGCATTTTTTTTTCCGAATTTATTTC
195 AAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCA---TTTTTTCCGAATTTATTTC
255 TAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
257 TAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
* *
319 TTTGGTTCGATGAATATAGACATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGCA
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* * * * *
384 GAGCCCCGAAAATCGTTTTTGGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
* ** *
449 GACCTGAAAATTTTTTTCTTTATTTTCTGCCACAATACTCAG-AAAAATATATAATTTAACGCCT
131 GACC-CAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCCC
*
513 AAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTGCATCTTTTTCCGAAGTTATTTCTA
195 AAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCAT-TTTTTCCGAATTTATTTCTA
*
577 ATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTTGCTGGAA
259 ATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
* *
639 TTTGGTTCGATGAATATAGACATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCC
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* * * *
704 GGGCCACGGAACTCGTTTTTTGCTCAAAAACTGTGATGGTTAGTACACGATTACGGCTAAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
* ** *
769 GACCCTAAATTTTTTTTTTCTGTAATTTTCAACCACAATACTCAATAAAAAATATATAATTTAAC
131 GACCC-AAA--ATTTTTTTCTG-AATTTTCTGCCACAATACTC-AGAAAAAATATATAATTTAAC
834 GCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTGCATTTTTTCCGAATTTATTT
191 GCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTT
*
898 CTAATTAAATCGAAACAAGATTCAGATGCTCATTAAAAAAAATCGTTAAATCGAATTTGGCTGGA
256 CTAATTAAATCGAAACAAGATTCAGATGCTCGTT-AAAAAAATCGTTAAATCGAATTTGGCTGGA
963 A
320 A
* * *
964 TTTGGCTCGATGAATATAGGTATTTCAAGGAGTCTTCACGACAAAAATCATGCAAAACTGAGGCA
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
***
1029 GGGCCATAGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTTAAGTACACGATTTCGGCTAAAAA
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGG-TT-AGTACACGATTTCGGCTAAAAA
** * *
1094 CTGACCCGAAAATTTTTTTCTTTATTTTCTGCCACAATACTCATAAAAAATATATAATTTAATGC
129 CTGACCC-AAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGC
** * *
1159 CCAAACCATTGACAGACTTTTCACACTTCTAATATCA-TTTTGCATTTTTTCCGAATTTATTTCT
193 CCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTTCT
*
1223 AATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCAAATTTGGCTGGAA
258 AATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
1286 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGACCAAAAATCATGACAAAACTGAGG
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACG-CCAAAAATCATG-CAAAACTGAGG
* *
1351 CACGGACCCCGGAACTTCG-TTTTTGCCCAAGAACCGTGATGGTTAGTACACGATTTCGGCTTAA
64 CA-GGGCCCCGGAAC-TCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGC-TAA
** * * *
1415 AAACTGACCCGAATTTTTTTTTCTGAATTTTCTGCCACAATACCCATAAAAAATATATAACTTAA
126 AAACTGACCC-AAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAA
* * * * *
1480 CACCCACAATATTGACGGGCTTTTCACGCTTCTAATATAATTTTTGCATTTTTTCCGAATTTATT
190 CGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATT
*
1545 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGTTGGA
255 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGA
1610 A
320 A
*
1611 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGCA
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* * * * *** ** *
1676 GGGCCCTGGAACTCGTTTTTTGCCTAAAACGAGCATCGAACCAAATTCCAACCAAATTCGATTTC
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAA--ACCGT-G-A--TGGTT---AGTACA--CGATTTC
* * *
1741 GGCTAAAAACTGACCTGAAAATTTTTTTCTGAATTTTCTTCCACAATACTTTTAGAAAAAATATA
120 GGCTAAAAACTGACC-CAAAATTTTTTTCTGAATTTTCTGCCACAATAC--TCAGAAAAAATATA
* *
1806 TAATTTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTTTTTTC
182 TAA-TTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCA-TTTTTTC
* * *
1871 CGAATTTATTTCTAATTAAATCGAAACAATATTCAGAGGCTCGTAAAAAAAATCGTTAAATCGAA
245 CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAA
*
1936 TTTGGCTGGTA
310 TTTGGCTGGAA
** * * * *
1947 TTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTATGCCAAAAATGATGCAAAACTGAGGCA
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
** * * *
2012 GGGCCCCAAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACCATTTCGGC-AAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
* * * *
2076 GATTCAAAAATTTTTTTCTGAATTTTCTGCCACAATGCTCAGAAAAAATATATAATTTAACGCCA
131 GA-CCCAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCCC
* *
2141 AAAAGTTTGACGGGCTTTTCACGCTTCTAATATCATTTTTTGCA-TTTTTCCGAATTTATTTCTA
195 AAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTTGCATTTTTTCCGAATTTATTTCTA
* *
2205 ATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAGAATCATTAAATCGAATTTGGCTGGAA
259 ATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
* * *
2267 TTTGATTCGAAGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGCA
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* *
2332 GGGCCCCGGAACTCGTTTTTTGCCTAAAAACCGTGATTGTTAGTACACGATTTCGGCTAAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
*
2397 GATCCGAAAATTTTTCTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCC
131 GA-CCCAAAATTTTT-TTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCC
** * *
2462 CAAAAGATTGACGGGCTTTTCATGCTTCTAATATTATTTTTGCATTTTTT-CGAATTCATTTCTA
194 CAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTTCTA
* * * *
2526 ATTAAATTGAAACAATATTCAGAGGCTCG-TAAAAAAATCGTTAAATCGAATTTGGCTGGGA
259 ATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
*** * * * * *
2587 TTTGGTTCGATGAATATTTTCATTTTAAGGTGTCTTTACACCAAAAATGATGCAAAACT---G-A
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* * * * * *
2648 GGGCCCCGAAACGCATTTTTTGCCCAAAAACCGTGATGGTTATTACACAATTTCGGCAAAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
2713 GA
131 GA
2715 TATAGGATGT
Statistics
Matches: 2157, Mismatches: 195, Indels: 90
0.88 0.08 0.04
Matches are distributed among these distances:
316 60 0.03
317 1 0.00
318 93 0.04
319 1 0.00
320 468 0.22
321 112 0.05
322 271 0.13
323 230 0.11
324 229 0.11
325 367 0.17
326 6 0.00
327 34 0.02
328 2 0.00
330 2 0.00
331 3 0.00
332 42 0.02
333 11 0.01
334 17 0.01
335 48 0.02
336 160 0.07
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (320 bp):
TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
GACCCAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCCCA
AAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
Found at i:1226 original size:647 final size:643
Alignment explanation
Indices: 1--2714 Score: 3834
Period size: 647 Copynumber: 4.2 Consensus size: 643
* *
1 TTTGGTTCGATGAATATAGGTATTTCAAGGAGTCTTCACGCCAAAACTCATGCAAAACTGAGGCA
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* ** *
66 GAGCCCCGGAACTCGTTTTGGGCCCAAAAACCGTGA-----CGTACACGATTTCGGCTAAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
* **
126 GACCCGAATATTTTTTTCTTTATTTTCTGCCACAATACT-AAGAAAAAATATATAATTTAACGCC
131 GACCCAAATATTTTTTTCTGAATTTTCTGCCACAATACTCAAGAAAAAATATATAATTTAACGCC
*
190 TAAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTGCATTTTTTTTTCCGAATTTATTT
196 CAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCA---TTTTTTCCGAATTTATTT
254 CTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
258 CTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
*
319 TTTGGTTCGATGAATATAGACATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGCA
323 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGCA
* * * * *
384 GAGCCCCGAAAATCGTTTTTGGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACT
388 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
* ** *
449 GACCTGAAAATTTTTTTCTTTATTTTCTGCCACAATACTCAG-AAAAATATATAATTTAACGCCT
453 GACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCCC
*
513 AAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTGCATCTTTTTCCGAAGTTATTTCTA
518 AAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCAT-TTTTTCCGAATTTATTTCTA
* *
577 ATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTTGCTGGAA
582 ATTAAATCGAAACAAGATTCAGAGGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
* *
639 TTTGGTTCGATGAATATAGACATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCC
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* * * *
704 GGGCCACGGAACTCGTTTTTTGCTCAAAAACTGTGATGGTTAGTACACGATTACGGCTAAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
* ** *
769 GACCCTAAATTTTTTTTTTCTGTAATTTTCAACCACAATACTCAATAAAAAATATATAATTTAAC
131 GACCC-AAA-TATTTTTTTCTG-AATTTTCTGCCACAATACTCAAGAAAAAATATATAATTTAAC
834 GCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTGCATTTTTTCCGAATTTATTT
193 GCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTT
*
898 CTAATTAAATCGAAACAAGATTCAGATGCTCATTAAAAAAAATCGTTAAATCGAATTTGGCTGGA
258 CTAATTAAATCGAAACAAGATTCAGATGCTCGTT-AAAAAAATCGTTAAATCGAATTTGGCTGGA
* * * *
963 ATTTGGCTCGATGAATATAGGTATTTCAAGGAGTCTTCACGACAAAAATCATGCAAAACTGAGGC
322 ATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGC
***
1028 AGGGCCATAGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTTAAGTACACGATTTCGGCTAAAA
387 AGGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGG-TT-AGTACACGATTTCGGCTAAAA
** * *
1093 ACTGACCCGAAAATTTTTTTCTTTATTTTCTGCCACAATACTCATAAAAAATATATAATTTAATG
450 ACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACG
** * *
1158 CCCAAACCATTGACAGACTTTTCACACTTCTAATATCA-TTTTGCATTTTTTCCGAATTTATTTC
515 CCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTTC
* *
1222 TAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCAAATTTGGCTGGAA
580 TAATTAAATCGAAACAAGATTCAGAGGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
1286 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGACCAAAAATCATGACAAAACTGAGG
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACG-CCAAAAATCATG-CAAAACTGAGG
* *
1351 CACGGACCCCGGAACTTCG-TTTTTGCCCAAGAACCGTGATGGTTAGTACACGATTTCGGCTTAA
64 CA-GGGCCCCGGAAC-TCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGC-TAA
* * * * *
1415 AAACTGACCCGAATTTTTTTTTCTGAATTTTCTGCCACAATAC-CCATAAAAAATATATAACTTA
126 AAACTGACCCAAATATTTTTTTCTGAATTTTCTGCCACAATACTCAAGAAAAAATATATAATTTA
* * * * *
1479 ACACCCACAATATTGACGGGCTTTTCACGCTTCTAATATAATTTTTGCATTTTTTCCGAATTTAT
191 ACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTAT
*
1544 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGTTGG
256 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGG
1609 AATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGG
321 AATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGG
* * * * *** ** *
1674 CAGGGCCCTGGAACTCGTTTTTTGCCTAAAACGAGCATCGAACCAAATTCCAACCAAATTCGATT
386 CAGGGCCCCGGAACTCGTTTTTTGCCCAAAA--ACCGT-G-A--TGGTT---AGTACA--CGATT
* * *
1739 TCGGCTAAAAACTGACCTGAAAATTTTTTTCTGAATTTTCTTCCACAATACTTTTAGAAAAAATA
440 TCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATAC--TCAGAAAAAATA
* *
1804 TATAATTTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTTTTT
503 TATAA-TTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCA-TTTTT
* *
1869 TCCGAATTTATTTCTAATTAAATCGAAACAATATTCAGAGGCTCGTAAAAAAAATCGTTAAATCG
566 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTTAAAAAAATCGTTAAATCG
*
1934 AATTTGGCTGGTA
631 AATTTGGCTGGAA
** * * * *
1947 TTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTATGCCAAAAATGATGCAAAACTGAGGCA
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
** * * *
2012 GGGCCCCAAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACCATTTCGGC-AAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
** * *
2076 GATTCAAAAATTTTTTTCTGAATTTTCTGCCACAATGCTC-AGAAAAAATATATAATTTAACGCC
131 GACCCAAATATTTTTTTCTGAATTTTCTGCCACAATACTCAAGAAAAAATATATAATTTAACGCC
* * *
2140 AAAAAGTTTGACGGGCTTTTCACGCTTCTAATATCATTTTTTGCA-TTTTTCCGAATTTATTTCT
196 CAAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTTGCATTTTTTCCGAATTTATTTCT
* *
2204 AATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAGAATCATTAAATCGAATTTGGCTGGAATT
260 AATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAATT
* *
2269 TGATTCGAAGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGCAGG
325 TGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGCAGG
* *
2334 GCCCCGGAACTCGTTTTTTGCCTAAAAACCGTGATTGTTAGTACACGATTTCGGCTAAAAACTGA
390 GCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGA
*
2399 TCCGAAAATTTTTCTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCCCA
455 CCCGAAAATTTTT-TTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCCCA
** * *
2464 AAAGATTGACGGGCTTTTCATGCTTCTAATATTATTTTTGCATTTTTT-CGAATTCATTTCTAAT
519 AAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTTCTAAT
* * *
2528 TAAATTGAAACAATATTCAGAGGCTCG-TAAAAAAATCGTTAAATCGAATTTGGCTGGGA
584 TAAATCGAAACAAGATTCAGAGGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
*** * * * * *
2587 TTTGGTTCGATGAATATTTTCATTTTAAGGTGTCTTTACACCAAAAATGATGCAAAACT---G-A
1 TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
* * * * * *
2648 GGGCCCCGAAACGCATTTTTTGCCCAAAAACCGTGATGGTTATTACACAATTTCGGCAAAAAACT
66 GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
2713 GA
131 GA
2715 TATAGGATGT
Statistics
Matches: 1882, Mismatches: 155, Indels: 79
0.89 0.07 0.04
Matches are distributed among these distances:
636 55 0.03
637 10 0.01
638 91 0.05
640 85 0.05
641 41 0.02
642 6 0.00
643 79 0.04
644 69 0.04
645 163 0.09
646 40 0.02
647 423 0.22
648 145 0.08
649 27 0.01
650 52 0.03
651 17 0.01
652 3 0.00
653 1 0.00
654 7 0.00
656 313 0.17
657 11 0.01
658 62 0.03
659 51 0.03
660 18 0.01
661 113 0.06
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (643 bp):
TTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAGGCA
GGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
GACCCAAATATTTTTTTCTGAATTTTCTGCCACAATACTCAAGAAAAAATATATAATTTAACGCC
CAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTTCTA
ATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAATTT
GGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAAGGCAGGG
CCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGAC
CCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTTAACGCCCAAA
AGATTGACGGGCTTTTCACACTTCTAATATCATTTTTGCATTTTTTCCGAATTTATTTCTAATTA
AATCGAAACAAGATTCAGAGGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGAA
Found at i:2848 original size:2 final size:2
Alignment explanation
Indices: 2841--2867 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2831 AATATAATTA
2841 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2868 AAATTAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31323 original size:30 final size:30
Alignment explanation
Indices: 31267--31324 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
31257 TGGTGATAAA
*
31267 AGGGTTAGATTGGGAAGAAAATTGTAACTT
1 AGGGTTAGATTGGGAAGAAAAGTGTAACTT
*
31297 AGGGTTAGATTGGGAAGAAAGGTGTAAC
1 AGGGTTAGATTGGGAAGAAAAGTGTAAC
31325 ATGGAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.34, T:0.26
Consensus pattern (30 bp):
AGGGTTAGATTGGGAAGAAAAGTGTAACTT
Found at i:32807 original size:7 final size:7
Alignment explanation
Indices: 32795--32821 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
32785 ATAGAAAGGG
32795 TTGCAAC
1 TTGCAAC
32802 TTGCAAC
1 TTGCAAC
32809 TTGCAAC
1 TTGCAAC
32816 TTGCAA
1 TTGCAA
32822 TCTTCATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (7 bp):
TTGCAAC
Found at i:46616 original size:5 final size:5
Alignment explanation
Indices: 46608--46641 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
46598 TTTTTTTCAA
*
46608 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
46642 TCACTTACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:49232 original size:5 final size:5
Alignment explanation
Indices: 49202--49231 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
49192 CTGTCTTTTC
49202 TGTTT TGTTT TGTTT TGTTT TGTTT T-TTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT T
49232 TCTTCAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TGTTT
Found at i:49232 original size:15 final size:15
Alignment explanation
Indices: 49197--49232 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
49187 TCTGCCTGTC
*
49197 TTTTCTGTTTTGTTT
1 TTTTTTGTTTTGTTT
*
49212 TGTTTTGTTTTGTTT
1 TTTTTTGTTTTGTTT
49227 TTTTTT
1 TTTTTT
49233 CTTCAATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (15 bp):
TTTTTTGTTTTGTTT
Found at i:57015 original size:18 final size:18
Alignment explanation
Indices: 56992--57028 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56982 TTACAATACT
56992 TCAGAACCAGAATTAGAA
1 TCAGAACCAGAATTAGAA
* *
57010 TCAGAATCAGAATTGGAA
1 TCAGAACCAGAATTAGAA
57028 T
1 T
57029 ATTCCCTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.22
Consensus pattern (18 bp):
TCAGAACCAGAATTAGAA
Found at i:64352 original size:18 final size:18
Alignment explanation
Indices: 64319--64354 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
64309 GGAAGCAGAG
**
64319 TCATCATCACGGCCACCA
1 TCATCATCACCACCACCA
64337 TCATCATCACCACCACCA
1 TCATCATCACCACCACCA
64355 CCACCATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.47, G:0.06, T:0.17
Consensus pattern (18 bp):
TCATCATCACCACCACCA
Found at i:69686 original size:27 final size:25
Alignment explanation
Indices: 69627--69701 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 25
69617 CAAGTCAAAT
* *
69627 TTCTCTTCCTCCTCTCCTTCTTCTC
1 TTCTCTTCCTCTTCTCCTTCTTATC
69652 TCTCCTCTTCCTCTTCTTCCTTCTTATC
1 T-T-CTCTTCCTCTTC-TCCTTCTTATC
*
69680 ATTCTCTTTCTCTT-TCTCTTCT
1 -TTCTCTTCCTCTTCTC-CTTCT
69702 CTCCTTTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
25 3 0.07
26 6 0.14
27 21 0.50
28 11 0.26
29 1 0.02
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (25 bp):
TTCTCTTCCTCTTCTCCTTCTTATC
Found at i:69714 original size:21 final size:22
Alignment explanation
Indices: 69626--69714 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 22
69616 CCAAGTCAAA
*
69626 TTTCTCTTC-CTCCTCTCCTTC
1 TTTCTCTTCTCTCCTCTTCTTC
*
69647 TTCTCTCTCCTCTTCCTCTTCTTC
1 TT-TCTCTTCTC-TCCTCTTCTTC
*
69671 CTTCT-TATCAT-T-CTCTT-TCTC
1 TTTCTCT-TC-TCTCCTCTTCT-TC
69692 TTTCTCTTCTCTCCT-TTCTTC
1 TTTCTCTTCTCTCCTCTTCTTC
69713 TT
1 TT
69715 CAGTCTCTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
20 2 0.04
21 22 0.42
22 12 0.23
23 5 0.09
24 12 0.23
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTCTCTTCTCTCCTCTTCTTC
Found at i:90014 original size:332 final size:330
Alignment explanation
Indices: 88942--90257 Score: 1029
Period size: 332 Copynumber: 4.0 Consensus size: 330
88932 TTAATTGGTA
** * * * * * *
88942 TACTAACCATCACGGTTTTTGGCTAAAATCACGTTTCAGGG-CCCCGGCTCAATTTTGTATGGTT
1 TACTAACCATCAAAGTTTTTTGCTAAAAACGCGTTTC-GGGACCCCAGCTCAATTTTGCATGATT
*** * * * * *
89006 TTTGGCGTTGACACTCCTTGAAATATCTATATTCATCTAA-CAAAATCTTAGCCACATTGCATTT
65 TTTGGCACCGAGACTCCTAGAAATATCTATATTCATCTAATC-AAATCTCAACCACATTGCATTG
** * * * * * *
89070 AAGGATTTCTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAACTTAATTCAGAAAAAT
129 AAGGATTTGATTTTACAAGCATCTGAATATTGTTTCGATTTAATTAAAAATCAATTCAGAAAAAT
* * * * * * * **
89135 ATGAAAAACGATATTAAAAGCTTGAAAA-TCCCTTCAATCTTTTTGGCGTTGAATTATATATTTT
194 ATAAAAAACGATATTAAAAGCGTGAAAAGT-CCTCCAATATTTTTGGAGGTAAATTATATA-CAT
* * * * * * * *
89199 TTTATGAG-TATTATGGCTAAAAGTTGAGGAAATTAC-TTTCGGTTCAATTTTTACCAAATTTAA
257 TTTATGAGATTTTAT-AC-AAAAATTGAGGAAA-AACATTTCGGGTCAATTTTTTCAAAATTTTA
*
89262 GCCGAAATCGTG
319 GCCAAAATCGTG
* * * ** * * * ** * * *
89274 TAATAATCTTCACGGTTTTTAGCTAAAAACGTGTTCCGGG-TTCCGGTTCAATTTTGAATGATTT
1 TACTAACCATCAAAGTTTTTTGCTAAAAACGCGTTTCGGGACCCCAGCTCAATTTTGCATGATTT
* * * *
89338 TTGGCACCGAGACTCTTTGAAATATCTATATTCAT-T--T--AA-C-CAATC-C-TAGCCATT--
66 TTGGCACCGAGACTCCTAGAAATATCTATATTCATCTAATCAAATCTCAACCACATTG-CATTGA
* * * *
89392 --G---T--TTTTACAAACATCTGAATCA-TGTTTTGTTTTAATTAGAAA-CTAATTC-GTAAAA
130 AGGATTTGATTTTACAAGCATCTGAAT-ATTGTTTCGATTTAATTAAAAATC-AATTCAG-AAAA
* * * ** * * *
89447 AAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTTAATCTTTTTTGG-TGTGAATTATATA
192 ATATA--AAAAACGATATTAAAAGCGTGAAAAGTCCTCCAAT-ATTTTTGGAGGTAAATTATATA
** * * * *** * *
89511 TTTTTTATGAG-TATTATGGCTAAAAAATGAGGAAAATTTTTTCTGAT-AATTTTTTTTTTGCAA
254 CATTTTATGAGATTTTAT-AC-AAAAATTGAGGAAAAACATTTCGGGTCAA----TTTTTT-CAA
**
89574 AATTTTAGCTGAAATCGTG
312 AATTTTAGCCAAAATCGTG
** * * * * * * *
89593 TACTAACCATCATGGTTTTTTGCTAAAAATGTGTTTCGGGGCCTCAGTTCAGTTTTGCATTATTT
1 TACTAACCATCAAAGTTTTTTGCTAAAAACGCGTTTCGGGACCCCAGCTCAATTTTGCATGATTT
** * * * *
89658 TTGGCGTCGAGACTCCTAGAAATATCTTTATTCATCTAATCAGATCTCAACCATATTGCATTTAA
66 TTGGCACCGAGACTCCTAGAAATATCTATATTCATCTAATCAAATCTCAACCACATTGCATTGAA
* * * *
89723 GGATTTGATTTTACAAGCATCTGAATATTGTTTCGCTTTAATTAGAAATTAATTTAGAAAAATAT
131 GGATTTGATTTTACAAGCATCTGAATATTGTTTCGATTTAATTAAAAATCAATTCAGAAAAATAT
* *
89788 AAAAAATGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTT-GACGTTAAATTATATACATTTT
196 AAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGA-GGTAAATTATATACATTTT
* * * **
89852 ATGAGAATTTTATCCAAAAATTGTGGGAAAATTTTTCGGGTCAATTTTTTCAAAATTTTAGCCAA
260 ATGAG-ATTTTATACAAAAATTGAGGAAAAACATTTCGGGTCAATTTTTTCAAAATTTTAGCCAA
89917 AATCGTG
324 AATCGTG
* * *
89924 TACTAACCATCACAATTTTTTTGCTAAAAACGCGTTTCGGGACCCCGGCTCAATTTTGCATGGTT
1 TACTAACCATCA-AAGTTTTTTGCTAAAAACGCGTTTCGGGACCCCAGCTCAATTTTGCATGATT
* * *
89989 TTTGGCACCGATACTCCTTGAAATATCTATATTCATCTAATTAAATCTCAACCACATTGCATTGA
65 TTTGGCACCGAGACTCCTAGAAATATCTATATTCATCTAATCAAATCTCAACCACATTGCATTGA
* * * *
90054 AGGATTTGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATCAATTCAGAAAAATT
130 AGGATTTGATTTTACAAGCATCTGAATATTGTTTCGATTTAATTAAAAATCAATTCAGAAAAATA
** * * ** *
90119 TGTAAAACGATATTAAAAGTGTGAAAAGTCCTCCAATCTTTTTGGAGGTGGATTATATATATTTT
195 TAAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGAGGTAAATTATATACATTTT
* * * *
90184 ATGAGTTTTTATACAAAAATTGAGGAAAAACATTTCTGGTCAATTTTTGCAAAATATTAGCCAAA
260 ATGAGATTTTATACAAAAATTGAGGAAAAACATTTCGGGTCAATTTTTTCAAAATTTTAGCCAAA
90249 ATCGTG
325 ATCGTG
90255 TAC
1 TAC
90258 GTTGGTCGAA
Statistics
Matches: 793, Mismatches: 147, Indels: 89
0.77 0.14 0.09
Matches are distributed among these distances:
313 1 0.00
314 46 0.06
315 39 0.05
316 42 0.05
317 7 0.01
318 5 0.01
319 53 0.07
320 47 0.06
321 1 0.00
322 2 0.00
323 6 0.01
324 2 0.00
325 2 0.00
326 3 0.00
327 4 0.01
328 4 0.01
329 2 0.00
330 1 0.00
331 144 0.18
332 247 0.31
333 3 0.00
334 5 0.01
335 70 0.09
336 4 0.01
337 52 0.07
338 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (330 bp):
TACTAACCATCAAAGTTTTTTGCTAAAAACGCGTTTCGGGACCCCAGCTCAATTTTGCATGATTT
TTGGCACCGAGACTCCTAGAAATATCTATATTCATCTAATCAAATCTCAACCACATTGCATTGAA
GGATTTGATTTTACAAGCATCTGAATATTGTTTCGATTTAATTAAAAATCAATTCAGAAAAATAT
AAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGAGGTAAATTATATACATTTTA
TGAGATTTTATACAAAAATTGAGGAAAAACATTTCGGGTCAATTTTTTCAAAATTTTAGCCAAAA
TCGTG
Done.