Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020297.1 Corchorus olitorius cultivar O-4 contig20330, 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: 50636
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1232 original size:4 final size:4
Alignment explanation
Indices: 1223--1248 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1213 AGAAAAGGGG
1223 GAAA GAAA GAAA GAAA GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA
1249 GAAACTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:5474 original size:606 final size:605
Alignment explanation
Indices: 4270--5486 Score: 2179
Period size: 608 Copynumber: 2.0 Consensus size: 605
4260 GTAGAAGTGA
*
4270 TATAGATGCTCGTTATGATTATCTCCCATTTTTAATTCTTCTATTTGTTTCTAGCTAGTAAGGAG
1 TATAGATGCTCGTTATGATTATATCCCATTTTTAATTCTTCTATTTGTTTCTAGCTAGTAAGGAG
4335 AGAAAGAGGCAGCTAAGAGAGAAGAGGAGAGGGAGAATGAATATGAATGAATTAATGTGGAGGAA
66 AGAAAGAGGCAGCTAAGAGAGAAGAGGAGAGGGAGAATGAATATGAATGAATTAATGTGGAGGAA
* *
4400 CTGTTTCTATTCATATTTATAGAAGGAAATCTTTTTGGTATATTATACTAGGTAACTAAATGAAA
131 CTGTTTCTATTCATATTTATAGAACGAAATCTCTTTGGTATATTATACTAGGTAACTAAATGAAA
* *
4465 AGGATTTTGATTTGAATTTAGAAATTTGAAAATTTGGAAGGTAATGTTTTTTGGTATATTACATA
196 AGGATTTTGATTTGAATTTAGAAATTTGAAAATTCGGAAGGTAATGTTTTTTGGTATATTACAGA
* * *
4530 AGGTAACTTGTTTGTACCCAAACAAGAAAAAAGCCAATTTGGTATGCAAAAGTAGCCAAAAAAAG
261 AGGTAACTAGTTTGTACCCAAACAAGAAAAAAGCCAATTTGGCACGCAAAAGTAGCCAAAAAAAG
*
4595 TCTATGCAAAATTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCCAAAATTAGTGCCGCT
326 TCTATGCAAAATTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCCAAAATTAGTGCCACT
*
4660 AAATGACTCATAGATTAGTCACGCAATTTTGAAACGCATAGGCATCAAAATGGTTTGCATGTAAT
391 AAATGACTCATAGATTAGTCACGCAATTTTGAAACGCAAAGGCATCAAAATGGTTTGCATGTAAT
4725 GGTGTGCAATTGATAATCCAAATTTCGTGGCAAACTTAGTTACAAAGAGGGAGTTGAGAGAGAAG
456 GGTGTGCAATTGATAATCCAAATTTCGTGGCAAACTTAGTTACAAAGAGGGAGTTGAGAGAGAAG
*
4790 AGGAGAGGGAAAATGAATATGAATTAATTAATGTGGAGGAATTGTTTCTATTCATATTTATAGAA
521 AGGAGAGGGAAAATGAATATGAATTAATTAATATGGAGGAATTGTTTCTATTCATATTTATAGAA
*
4855 GGAAATTTTTTTTTGGTATAT
586 AGAAA-TTTTTTTTGGTATAT
*
4876 TATAGATGCTCGTTATGGTTATATCCCATTTTTAATTCTTCTATTTGTTTCTAGCTAGTAAGGAG
1 TATAGATGCTCGTTATGATTATATCCCATTTTTAATTCTTCTATTTGTTTCTAGCTAGTAAGGAG
*
4941 AGCAAGAGGCAGCTAAGAGAGAAGAGGAGAGGGAGAATGAATATGAATGAATTAATGTGGAGGAA
66 AGAAAGAGGCAGCTAAGAGAGAAGAGGAGAGGGAGAATGAATATGAATGAATTAATGTGGAGGAA
*
5006 CCT-TTTCTATTCATATTTATAGAACGAAATCTCTTTGGTATATTATTCTAGGTAACTAAATGAA
131 -CTGTTTCTATTCATATTTATAGAACGAAATCTCTTTGGTATATTATACTAGGTAACTAAATGAA
*
5070 AAGGATTTTGATTTGAATTTAGAAATTTGGAAATTCGGAAGGTAAT-TTTTTTGGTATATTACAG
195 AAGGATTTTGATTTGAATTTAGAAATTTGAAAATTCGGAAGGTAATGTTTTTTGGTATATTACAG
*
5134 AAGGTAACTAGTTTGTACCCCCAAACAAGAAAAAATCCAATTTGGCACGCAAAAGTAGCCAAAAA
260 AAGGTAACTAGTTTGTA--CCCAAACAAGAAAAAAGCCAATTTGGCACGCAAAAGTAGCC-AAAA
*
5199 AAAGTCTATGCCAAATTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCCAAAATTAGTGC
322 AAAGTCTATGCAAAATTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCCAAAATTAGTGC
* *
5264 CACTAAATGACTCATATATTAGTCACGCAATTTTGAAACGCAAAGGTATCAAAATGGTTTGCATG
387 CACTAAATGACTCATAGATTAGTCACGCAATTTTGAAACGCAAAGGCATCAAAATGGTTTGCATG
5329 TAATGGTGTGCAATTGATAATCCAAATTTCGTGGCAAACTTAGTTACAAAGAGGGAGTTGAGAGA
452 TAATGGTGTGCAATTGATAATCCAAATTTCGTGGCAAACTTAGTTACAAAGAGGGAGTTGAGAGA
5394 GAAGAGGAGAGGGAAAATGAATATGAATTAATTAATATGGAGGAATTGTTTCTATTCATATTTAT
517 GAAGAGGAGAGGGAAAATGAATATGAATTAATTAATATGGAGGAATTGTTTCTATTCATATTTAT
5459 A-AAAGATAATTTTTTTTGGTATAT
582 AGAAAGA-AATTTTTTTTGGTATAT
5483 TATA
1 TATA
5487 AAACGTAAAT
Statistics
Matches: 586, Mismatches: 20, Indels: 9
0.95 0.03 0.01
Matches are distributed among these distances:
605 33 0.06
606 229 0.39
607 63 0.11
608 261 0.45
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (605 bp):
TATAGATGCTCGTTATGATTATATCCCATTTTTAATTCTTCTATTTGTTTCTAGCTAGTAAGGAG
AGAAAGAGGCAGCTAAGAGAGAAGAGGAGAGGGAGAATGAATATGAATGAATTAATGTGGAGGAA
CTGTTTCTATTCATATTTATAGAACGAAATCTCTTTGGTATATTATACTAGGTAACTAAATGAAA
AGGATTTTGATTTGAATTTAGAAATTTGAAAATTCGGAAGGTAATGTTTTTTGGTATATTACAGA
AGGTAACTAGTTTGTACCCAAACAAGAAAAAAGCCAATTTGGCACGCAAAAGTAGCCAAAAAAAG
TCTATGCAAAATTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCCAAAATTAGTGCCACT
AAATGACTCATAGATTAGTCACGCAATTTTGAAACGCAAAGGCATCAAAATGGTTTGCATGTAAT
GGTGTGCAATTGATAATCCAAATTTCGTGGCAAACTTAGTTACAAAGAGGGAGTTGAGAGAGAAG
AGGAGAGGGAAAATGAATATGAATTAATTAATATGGAGGAATTGTTTCTATTCATATTTATAGAA
AGAAATTTTTTTTGGTATAT
Found at i:9039 original size:238 final size:238
Alignment explanation
Indices: 8621--9092 Score: 845
Period size: 238 Copynumber: 2.0 Consensus size: 238
8611 GAATTTTAGA
*
8621 ACAAAAATCACAAAATCAGAAATCTTGCAATGTGTTTTTGCGATGTGGAGGAAGAACTTGATGAA
1 ACAAAAATCACAAAATCAGAAATCTTCCAATGTGTTTTTGCGATGTGGAGGAAGAACTTGATGAA
* * * *
8686 TGATGGATAGATGAATAGATTTAACCAATTAAAGATGAAAAGCTAAGCCCTGATACCAATTTATA
66 TGATGGATAGATGAATAGATTTAACCAATTAAAGATAAAAACCTAAGCCCGGATACCAATTGATA
*
8751 ACAATCTAGTTGTTATTGGTTCAAATCCACCATCAAGAGCTGCCAATGATCAACTTGAATCACCA
131 ACAATCTAGTTGTTATTGGTTCAAATCCACCATCAAGACCTGCCAATGATCAACTTGAATCACCA
8816 AACTTCTAGTTCTTGTTAAATCTCGATAATCTTCAACAAAATC
196 AACTTCTAGTTCTTGTTAAATCTCGATAATCTTCAACAAAATC
*
8859 ACAAAAATCACAAAATCAGAAATCTTCCTATGTGTTTTTGCGATGTGGAGGAAGAACTTGATGAA
1 ACAAAAATCACAAAATCAGAAATCTTCCAATGTGTTTTTGCGATGTGGAGGAAGAACTTGATGAA
* * * *
8924 TGATGGATAGATGGATAGATTTAACCGATTGAAGATAAAAACCTAAGCTCGGATACCAATTGATA
66 TGATGGATAGATGAATAGATTTAACCAATTAAAGATAAAAACCTAAGCCCGGATACCAATTGATA
8989 ACAATCTAGTTGTTATTGGTTCAAATCCACCATCAAGACCTGCCAATGATCAACTTGAATCACCA
131 ACAATCTAGTTGTTATTGGTTCAAATCCACCATCAAGACCTGCCAATGATCAACTTGAATCACCA
9054 AACTTCTAGTTCTTGTTAAATCTCGATAATCTTCAACAA
196 AACTTCTAGTTCTTGTTAAATCTCGATAATCTTCAACAA
9093 TGGATCTAAT
Statistics
Matches: 223, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
238 223 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (238 bp):
ACAAAAATCACAAAATCAGAAATCTTCCAATGTGTTTTTGCGATGTGGAGGAAGAACTTGATGAA
TGATGGATAGATGAATAGATTTAACCAATTAAAGATAAAAACCTAAGCCCGGATACCAATTGATA
ACAATCTAGTTGTTATTGGTTCAAATCCACCATCAAGACCTGCCAATGATCAACTTGAATCACCA
AACTTCTAGTTCTTGTTAAATCTCGATAATCTTCAACAAAATC
Found at i:10454 original size:42 final size:43
Alignment explanation
Indices: 10402--10493 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 43
10392 TGCATTATCT
* *
10402 ATATTTTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTA
1 ATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTA
10444 ATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTA
1 ATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTA
10489 ATATT
1 ATATT
10494 AATTGCTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 7 0.16
45 38 0.84
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (43 bp):
ATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTA
Found at i:11517 original size:3 final size:3
Alignment explanation
Indices: 11509--11623 Score: 212
Period size: 3 Copynumber: 38.3 Consensus size: 3
11499 TTTTTTCTAC
*
11509 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11557 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
11605 TAA TAA TAA TAA GAA TAA T
1 TAA TAA TAA TAA TAA TAA T
11624 GAAAAGTCGT
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:13797 original size:610 final size:596
Alignment explanation
Indices: 12594--13884 Score: 1898
Period size: 610 Copynumber: 2.1 Consensus size: 596
12584 AATCAACTTG
*
12594 TGAATTAATTAATATGGAGGAATTGTTTCTATTCATATTTATAGAAGGTAATTTTTTTTGGTATA
1 TGAATTAATTAATGTGGAGGAATTGTTTCTATTCATATTTATAGAAGGTAATTTTTTTTGGTATA
*
12659 TTATAGATGCTCGTTATGATTATCTCCCATTTTTAATTTTACTATTTGTTTCTAGCTAGTAAGGA
66 TTATAGATGCTCATTATGATTATCTCCCATTTTTAATTTTACTATTTGTTTCTAGC-A-T-----
12724 GAGAAAGAGGCAGCTAAGAGAGAAGAGGAGAGGGAGAATGAATATATGAATGAATTAATGTGGAG
124 -----A-AGGCAGCTAAGAGAGAAGAGGAGAGGGAGAATGAATATATGAATGAATTAATGTGGAG
* * *
12789 GAAAAGTTTCTACTCATATTTTTAGAAGGAAATCTTTTTGGTATATTATAGTAGGTAACTAAATG
183 GAAAAGTTTCTACTCATATTTATACAAGGAAATCTTTTTGGTATATTATAGTAGGTAACTAAAGG
*
12854 AAAAGGATTTTGATTTGAATTTAGAAATTTGGAAATTTGGAAGGTAATTTTTTTGGTATATTAGA
248 AAAAGGATTTTGATTTGAATTTAGAAATTTGGAAATTTGGAAGGTAATTTTTTTGGTATATTACA
*
12919 GAAGGTAACTAGTTTGTACCCTCAAACAAGAAAAAAGCCAATTTAGCACGCAAAAATAGCCAAAA
313 GAAGGTAACTAGTTTGTACCCCCAAACAAGAAAAAAGCCAATTTAGCACGCAAAAATAGCCAAAA
12984 AAAAGTCTATGCCAAATTTGGCAGTGAAAATGACACGGAAACGAAAAGTCGTGCCAAAATTAGTG
378 AAAAGTCTATGCCAAATTTGGCAGTGAAAATGACACGGAAACGAAAAGTCGTGCCAAAATTAGTG
* * * *
13049 CCGCTAAATGATTCATAGATAAGTCACGCAATTTTGAAACGCAAAGGTATGAAAATGGTTTGCAT
443 CCGCTAAATGACTAATAGATAAGTCACGCAATTTTGAAACACAAAGGTATGAAAATGGTTTGCAG
13114 GTAATGGTGTGCAATTGATAATCCAAATTTCGTGCCAAACTTAGTTACAAAGAGGGAGCTGAGAG
508 GTAATGGTGTGCAATTGATAATCCAAATTTCGTGCCAAACTTAGTTACAAAGAGGGAGCTGAGAG
13179 AAAAGGGGAGAGGGAATATGAATATGAATA
573 AAAAGGGGAGAGGG---A--AA-ATGAATA
*
13209 TGAATTAATTAATGTGGAGGAATTGTTTCTATTCATATTTATAGAAGGTAATTTTTGTTGGTATA
1 TGAATTAATTAATGTGGAGGAATTGTTTCTATTCATATTTATAGAAGGTAATTTTTTTTGGTATA
*
13274 TTATAGATGCTCATTATGATTATCTCTCATTTTTAATTCTT-CTATTTGTTTCTAGC-T-A-GCA
66 TTATAGATGCTCATTATGATTATCTCCCATTTTTAATT-TTACTATTTGTTTCTAGCATAAGGCA
**
13335 GCTAAGAGAGAAGAGGAGAGGGAGAATG-A-ATATGAATGAATTAATGTGGAGGAATTGTTTCTA
130 GCTAAGAGAGAAGAGGAGAGGGAGAATGAATATATGAATGAATTAATGTGGAGGAAAAGTTTCTA
* ****
13398 TTCATATTTATACAAGGAAATCTTTTTGGTATATTATAGTAGGTAACTAAAGGATTTTGA-TTTG
195 CTCATATTTATACAAGGAAATCTTTTTGGTATATTATAGTAGGTAACTAAAGGAAAAGGATTTTG
*
13462 AATTTAGAAATTT-GCAAATTTGGAAATTTGGAAGGTGATTTTTTTGGTATATTACAGAAGGTAA
260 -ATTT-G-AATTTAG-AAATTTGGAAATTTGGAAGGTAATTTTTTTGGTATATTACAGAAGGTAA
* * **
13526 CTTGTTTGTACCCCCAAACAAGAAAAAAGCCAATTTGGCGTGCAAAAATAGCC-AAAAAAAGTCT
321 CTAGTTTGTACCCCCAAACAAGAAAAAAGCCAATTTAGCACGCAAAAATAGCCAAAAAAAAGTCT
*
13590 ATGCCAAATTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCAAAAATTAGTGCCAAAATT
386 ATGCCAAATTTGGCAGTGAAAATGACACGGAAACGAAAA---GT-C--------GTGCCAAAATT
* *
13655 AGTGCCGCTAAATGACTAATAGATTAGTCACGCACTTTTGAAACACAAAGGTATGAAAATGGTTT
439 AGTGCCGCTAAATGACTAATAGATAAGTCACGCAATTTTGAAACACAAAGGTATGAAAATGGTTT
*
13720 GCAGGTAATGGTGTGCAATTGATAATCCAAATTTCGTGCCAAACTTAGTTATAAAGAGGGAGCTG
504 GCAGGTAATGGTGTGCAATTGATAATCCAAATTTCGTGCCAAACTTAGTTACAAAGAGGGAGCTG
*
13785 AGAGAGAAGGGGAGAGGGAAAATGAATA
569 AGAGAAAAGGGGAGAGGGAAAATGAATA
* *
13813 TGAATTAATTAATGTGGAGGAATTGTTTCTATTCTTATTTACAGAAGGTAATTTTTTTTGGTATA
1 TGAATTAATTAATGTGGAGGAATTGTTTCTATTCATATTTATAGAAGGTAATTTTTTTTGGTATA
*
13878 TTGTAGA
66 TTATAGA
13885 ACGTAAATAA
Statistics
Matches: 625, Mismatches: 34, Indels: 45
0.89 0.05 0.06
Matches are distributed among these distances:
596 4 0.01
597 88 0.14
598 52 0.08
599 131 0.21
600 1 0.00
601 2 0.00
602 1 0.00
604 75 0.12
605 2 0.00
607 1 0.00
610 151 0.24
612 1 0.00
615 114 0.18
616 2 0.00
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (596 bp):
TGAATTAATTAATGTGGAGGAATTGTTTCTATTCATATTTATAGAAGGTAATTTTTTTTGGTATA
TTATAGATGCTCATTATGATTATCTCCCATTTTTAATTTTACTATTTGTTTCTAGCATAAGGCAG
CTAAGAGAGAAGAGGAGAGGGAGAATGAATATATGAATGAATTAATGTGGAGGAAAAGTTTCTAC
TCATATTTATACAAGGAAATCTTTTTGGTATATTATAGTAGGTAACTAAAGGAAAAGGATTTTGA
TTTGAATTTAGAAATTTGGAAATTTGGAAGGTAATTTTTTTGGTATATTACAGAAGGTAACTAGT
TTGTACCCCCAAACAAGAAAAAAGCCAATTTAGCACGCAAAAATAGCCAAAAAAAAGTCTATGCC
AAATTTGGCAGTGAAAATGACACGGAAACGAAAAGTCGTGCCAAAATTAGTGCCGCTAAATGACT
AATAGATAAGTCACGCAATTTTGAAACACAAAGGTATGAAAATGGTTTGCAGGTAATGGTGTGCA
ATTGATAATCCAAATTTCGTGCCAAACTTAGTTACAAAGAGGGAGCTGAGAGAAAAGGGGAGAGG
GAAAATGAATA
Found at i:14171 original size:441 final size:441
Alignment explanation
Indices: 13334--14201 Score: 991
Period size: 441 Copynumber: 2.0 Consensus size: 441
13324 TCTAGCTAGC
*
13334 AGCTAAGAGAGAAGAGGAGAGGGAGAATGAATATGAATGAATTAATGTGGAGGAATTGTTTCTAT
1 AGCTAAGAGAGAAGAGGAGAGGGAAAATGAATATGAATGAATTAATGTGGAGGAATTGTTTCTAT
* * * * ***
13399 TCATATTTATACAAGGAAATCTTTTTGGTATATTATAGTAGGTAACTAAAGGATTTTGATTTGAA
66 TCATATTTACACAAGGAAATCTTTTTGGTATATTATAGAACGTAAATAAA-GA--TTGAAAAGAA
* * * *
13464 TTTAGAAATTTGCAAATTTGGAAATTTGGAAGGTGATTTTTTTGGTATATTACAGAAGGTAACTT
128 TTTAGAAATTTG-AAACTTAGAAATTTGGAAGGTAATTTTTTTGGTATATTACAGAAGGTAACTA
* * * *
13529 GTTTGTACCCCCAAACAAGAAAAAAGCCAATTTGGCGTGCAAAAATAGCCAAAAAAAGTCTATGC
192 GTCTGTACCCCCAAACAAGAAAAAAGCCAATTTGGCATGCAAAAATAGCAAAAAAAAGTATATGC
* * **
13594 CAAATTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCAAAAATTAGTGCCAAAATTAGTG
257 CAAATTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCAAAAATCAGTGCCAAAACTAAAG
* * * * **
13659 CCGCTAAATGACTAATAGATTAGTCACGCACTTTTGAAACACAAAGGTATGAAAATGGTTTGCAG
322 -CGCTAAATGACTAATAGATTAGTCACACAATGTCGAAACACAAAGGTACCAAAATGGTTTGCAG
* *
13724 GTAATGGTGTGCAATTGATAATC-CAAATTTCGTGCCAAACTTAGTTATAAAGAGGG
386 GTAATGGCGTGCAATTGATAATCAAAAATTT-GTGCCAAACTTAGTTATAAAGAGGG
* * *
13780 AGCTGAGAGAGAAGGGGAGAGGGAAAATGAATATGAATTAATTAATGTGGAGGAATTGTTTCTAT
1 AGCTAAGAGAGAAGAGGAGAGGGAAAATGAATATGAATGAATTAATGTGGAGGAATTGTTTCTAT
* * * * * *
13845 TCTTATTTACAGAAGGTAATTTTTTTTGGTATATTGTAGAACGTAAAT-AA-A-TGAAAAGGATT
66 TCATATTTACACAAGG-AAATCTTTTTGGTATATTATAGAACGTAAATAAAGATTGAAAAGAATT
* * * * *
13907 T-G-GATTTG-AACTTAGAACTTTTGAAGTTAATTTTTTTGGTATATTATAGAAGGTAACTAGTC
130 TAGAAATTTGAAACTTAGAAATTTGGAAGGTAATTTTTTTGGTATATTACAGAAGGTAACTAGTC
* * * ** * *
13969 TGTAGCCCCACTACTAGAAAATGGCCAATTTGGCATGCACAAAATAGGTAAAAAAAAGTAATGTG
195 TGTACCCCCA-AACAAGAAAAAAGCCAATTTGGCATGCA-AAAATA-GCAAAAAAAAGT-ATATG
* * * * *
14034 TCAAATTTGGCACG-GAAAAT-AGCACGGAAATGAAAATTGGTGCCAAAATCGGTGCCAAAAACC
256 CCAAATTTGGCA-GTGAAAATGA-CACGGAAATGAAAAGTCGTGCAAAAATCAGTGCC-AAAA-C
* * * * *
14097 TAAAG-GGTAAATGACTCATAGATTAGTCACACAATGTCGGAACGCAAAGGTACCAAATTGGTTT
317 TAAAGCGCTAAATGACTAATAGATTAGTCACACAATGTCGAAACACAAAGGTACCAAAATGGTTT
*
14161 GCATGTAATGGCGTGCAATTGATAATCAAAAATTTGTGCCA
382 GCAGGTAATGGCGTGCAATTGATAATCAAAAATTTGTGCCA
14202 TTTTCGGTTA
Statistics
Matches: 352, Mismatches: 60, Indels: 25
0.81 0.14 0.06
Matches are distributed among these distances:
437 54 0.15
438 23 0.07
439 11 0.03
440 12 0.03
441 136 0.39
442 11 0.03
443 3 0.01
444 1 0.00
446 76 0.22
447 25 0.07
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (441 bp):
AGCTAAGAGAGAAGAGGAGAGGGAAAATGAATATGAATGAATTAATGTGGAGGAATTGTTTCTAT
TCATATTTACACAAGGAAATCTTTTTGGTATATTATAGAACGTAAATAAAGATTGAAAAGAATTT
AGAAATTTGAAACTTAGAAATTTGGAAGGTAATTTTTTTGGTATATTACAGAAGGTAACTAGTCT
GTACCCCCAAACAAGAAAAAAGCCAATTTGGCATGCAAAAATAGCAAAAAAAAGTATATGCCAAA
TTTGGCAGTGAAAATGACACGGAAATGAAAAGTCGTGCAAAAATCAGTGCCAAAACTAAAGCGCT
AAATGACTAATAGATTAGTCACACAATGTCGAAACACAAAGGTACCAAAATGGTTTGCAGGTAAT
GGCGTGCAATTGATAATCAAAAATTTGTGCCAAACTTAGTTATAAAGAGGG
Found at i:14728 original size:18 final size:18
Alignment explanation
Indices: 14697--14746 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
14687 ACCCAAAGTT
*
14697 AAAA-AAAAAAAAAAAAG
1 AAAAGAAAAACAAAAAAG
**
14714 AAAAGAAAAACAAAATCG
1 AAAAGAAAAACAAAAAAG
14732 AAAAGAAAAACAAAA
1 AAAAGAAAAACAAAA
14747 TGCTCCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.84, C:0.06, G:0.08, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAACAAAAAAG
Found at i:14747 original size:18 final size:18
Alignment explanation
Indices: 14713--14747 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
14703 AAAAAAAAAA
14713 GAAAAGAAAAACAAAATC
1 GAAAAGAAAAACAAAATC
14731 GAAAAGAAAAACAAAAT
1 GAAAAGAAAAACAAAAT
14748 GCTCCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.74, C:0.09, G:0.11, T:0.06
Consensus pattern (18 bp):
GAAAAGAAAAACAAAATC
Found at i:21617 original size:304 final size:296
Alignment explanation
Indices: 21015--21618 Score: 1037
Period size: 304 Copynumber: 2.0 Consensus size: 296
21005 TTAATCTAAC
21015 TTCAATACTCAAGACTTAATATGAACTAGATATTGAATTCTTACTCTTAAATACCATTTCTTCAA
1 TTCAATACTCAAGACTTAATATGAACTAGATATTGAATTCTTACTCTTAAATACCATTTCTTCAA
* *
21080 TAATCAGTAAGGAAGCTCTTCTCTCATGAGGAAGAATTTTAAAAAAATAAGGTTCTTTCTTAGTA
66 TAATCAGTAAGGAAGCTCTTCTCTCAGGAGGAAGAATTTAAAAAAAATAAGGTTCTTTCTTAGTA
*
21145 CGTAAGTTATGCTTATACATCAACCTTATACTAGCCAGTTCAATTTATTCTTACCTTTCATAACT
131 CGTAAGTTATGCTTATACATCAACCTTATACTAGCCAGTTCAATTTATTCTTACCTTTCAAAACT
*
21210 CACAATAATCTCAATTTCCATATTGTTTCTTAATTAGATATTCTCCACCTACAATTTCTTTACAC
196 CACAATAATCTCAATTTCCATATTGTTGCTTAATTAGATATTCTCCACCTACAATTTCTTTACAC
21275 TTCTAGTAAAAAAAAATCCTTCATTGTTCAACTTAG
261 TTCTAGTAAAAAAAAATCCTTCATTGTTCAACTTAG
*
21311 TTCAATACTCGAGACTTAATATGAACTAGATATTGAATTCTTACTCTTAAATACCATTTCTTCAA
1 TTCAATACTCAAGACTTAATATGAACTAGATATTGAATTCTTACTCTTAAATACCATTTCTTCAA
*
21376 TAATCAGTAAGGAAGCTCTTCTCATGAGGAGGAAGAATTTAAAAAAAATAAGGTTCTTTCTTAGT
66 TAATCAGTAAGGAAGCTCTTCTC-TCAGGAGGAAGAATTTAAAAAAAATAAGGTTCTTTCTTAGT
* *
21441 ACGTAAGTTATGCTTATTCATCAACCTTGTACTAGCCAGTTCAATTTATTCTTACCTCTCATAAC
130 ACGTAAGTTATGCTTATACATCAACCTTATACTAGCCAGTTCAATTTATTCTTACCT-T--T--C
*
21506 TAAAATCTCACAATAATCTCAATTTTCATATTGTTGCTTAATTAGATATTCTCCACCTACAATTT
190 -AAAA-CTCACAATAATCTCAATTTCCATATTGTTGCTTAATTAGATATTCTCCACCTACAATTT
* *
21571 CTTTACACTTCTAGTAAAAAACAATTCTTCATTGTTCAACTTAG
253 CTTTACACTTCTAGTAAAAAAAAATCCTTCATTGTTCAACTTAG
21615 TTCA
1 TTCA
21619 TCCCGTAACT
Statistics
Matches: 289, Mismatches: 11, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
296 87 0.30
297 93 0.32
298 1 0.00
300 1 0.00
302 1 0.00
303 3 0.01
304 103 0.36
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (296 bp):
TTCAATACTCAAGACTTAATATGAACTAGATATTGAATTCTTACTCTTAAATACCATTTCTTCAA
TAATCAGTAAGGAAGCTCTTCTCTCAGGAGGAAGAATTTAAAAAAAATAAGGTTCTTTCTTAGTA
CGTAAGTTATGCTTATACATCAACCTTATACTAGCCAGTTCAATTTATTCTTACCTTTCAAAACT
CACAATAATCTCAATTTCCATATTGTTGCTTAATTAGATATTCTCCACCTACAATTTCTTTACAC
TTCTAGTAAAAAAAAATCCTTCATTGTTCAACTTAG
Found at i:27708 original size:10 final size:10
Alignment explanation
Indices: 27689--27717 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
27679 CTTATTTTCC
27689 TATTTATTTT
1 TATTTATTTT
27699 TA-TTATTTT
1 TATTTATTTT
27708 TATTTATTTT
1 TATTTATTTT
27718 CCCTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TATTTATTTT
Found at i:27713 original size:19 final size:20
Alignment explanation
Indices: 27675--27717 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
27665 TATTTCCAAA
*
27675 TTTTCTTATTTTCCTATTTAT
1 TTTTATTATTTT-CTATTTAT
27696 TTTTATTATTTT-TATTTAT
1 TTTTATTATTTTCTATTTAT
27715 TTT
1 TTT
27718 CCCTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTATTTTCTATTTAT
Found at i:27740 original size:6 final size:6
Alignment explanation
Indices: 27721--27796 Score: 77
Period size: 6 Copynumber: 12.7 Consensus size: 6
27711 TTATTTTCCC
* *
27721 TTTTCT TTTCCT TTTTCT TTTTCT TTTTCT TTTCCT TTTT-T TTTT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
*
27767 ATTTCTT TCTTTCT TCTTTCT TTTT-T TTTT
1 TTTTC-T T-TTTCT T-TTTCT TTTTCT TTTT
27797 GACTTGGGCC
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
5 14 0.23
6 33 0.54
7 10 0.16
8 4 0.07
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:27765 original size:12 final size:12
Alignment explanation
Indices: 27714--27764 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
27704 TTTTTATTTA
*
27714 TTTTCCCTTTTC
1 TTTTCCTTTTTC
27726 TTTTCCTTTTTC
1 TTTTCCTTTTTC
*
27738 TTTTTCTTTTTC
1 TTTTCCTTTTTC
27750 TTTTCCTTTTT-
1 TTTTCCTTTTTC
27761 TTTT
1 TTTT
27765 TTATTTCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
11 4 0.11
12 32 0.89
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCCTTTTTC
Found at i:27766 original size:24 final size:25
Alignment explanation
Indices: 27721--27794 Score: 87
Period size: 24 Copynumber: 2.9 Consensus size: 25
27711 TTATTTTCCC
*
27721 TTTTCTTTTCCTTTTTCTTTTT-CT
1 TTTTCTTTTCCTTTTTTTTTTTACT
*
27745 TTTTCTTTTCCTTTTTTTTTTTATT
1 TTTTCTTTTCCTTTTTTTTTTTACT
*
27770 TCTTTCTTTCTTCTTTCTTTTTTTT
1 T-TTTCTTT-TCCTTT-TTTTTTTT
27795 TTGACTTGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
24 21 0.49
25 2 0.05
26 7 0.16
27 5 0.12
28 8 0.19
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTCTTTTCCTTTTTTTTTTTACT
Found at i:27854 original size:18 final size:18
Alignment explanation
Indices: 27831--27866 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27821 GCCCGCGTGT
27831 GGCCCGCGCGGCCTGCCA
1 GGCCCGCGCGGCCTGCCA
*
27849 GGCCCGCGTGGCCTGCCA
1 GGCCCGCGCGGCCTGCCA
27867 CACGGGTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.47, G:0.39, T:0.08
Consensus pattern (18 bp):
GGCCCGCGCGGCCTGCCA
Found at i:33683 original size:21 final size:21
Alignment explanation
Indices: 33634--33684 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
33624 TATTTCCAAA
* *
33634 TTTTTCTTTAATTTTCTTATT
1 TTTTTATTTAATTTTATTATT
** *
33655 TTCCTATTTATTTTTATTATT
1 TTTTTATTTAATTTTATTATT
33676 TTTTTATTT
1 TTTTTATTT
33685 TCCCTTTTCT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTATTTAATTTTATTATT
Found at i:33692 original size:12 final size:12
Alignment explanation
Indices: 33677--33721 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
33667 TTTATTATTT
*
33677 TTTTATTTTCCC
1 TTTTCTTTTCCC
*
33689 TTTTCTTTTCCT
1 TTTTCTTTTCCC
* *
33701 TTTTCTTTTTCT
1 TTTTCTTTTCCC
33713 TTTTCTTTT
1 TTTTCTTTT
33722 TCTTTCTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTCCC
Found at i:33702 original size:6 final size:6
Alignment explanation
Indices: 33689--33750 Score: 76
Period size: 6 Copynumber: 10.7 Consensus size: 6
33679 TTATTTTCCC
*
33689 TTTTCT TTTCCT TTTTCT TTTTCT TTTTCT TTTTC- -TTTCT TTCTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT-TTCT
*
33736 TTCTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTT
33751 TTTGACTTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
4 4 0.08
5 5 0.10
6 34 0.69
7 6 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:33703 original size:18 final size:18
Alignment explanation
Indices: 33682--33721 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33672 TATTTTTTTA
33682 TTTTCCCTTTTCTTTTCC
1 TTTTCCCTTTTCTTTTCC
* * *
33700 TTTTTCTTTTTCTTTTTC
1 TTTTCCCTTTTCTTTTCC
33718 TTTT
1 TTTT
33722 TCTTTCTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCCCTTTTCTTTTCC
Found at i:33720 original size:29 final size:28
Alignment explanation
Indices: 33688--33753 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
33678 TTTATTTTCC
*
33688 CTTTTCTTTTCCTTT-TTCTTTTTCTTTTT
1 CTTTT-TTTT-CTTTCTTCTTTCTCTTTTT
33717 CTTTTTCTTTCTTTCTTCTTTCTCTTTTT
1 CTTTTT-TTTCTTTCTTCTTTCTCTTTTT
33746 -TTTTTTTT
1 CTTTTTTTT
33754 GACTTGGGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 3 0.09
28 10 0.29
29 21 0.62
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (28 bp):
CTTTTTTTTCTTTCTTCTTTCTCTTTTT
Found at i:33735 original size:23 final size:22
Alignment explanation
Indices: 33702--33753 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
33692 TCTTTTCCTT
*
33702 TTTCTTTTTCTTTTTCTTTTTC
1 TTTCTTTTTCTTTCTCTTTTTC
33724 TTTCTTTCTTCTTTCTCTTTTT-
1 TTTCTTT-TTCTTTCTCTTTTTC
33746 TTT-TTTTT
1 TTTCTTTTT
33754 GACTTGGGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 3 0.11
22 10 0.36
23 13 0.46
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTTTTTC
Found at i:41993 original size:22 final size:22
Alignment explanation
Indices: 41965--42008 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41955 GGTTCTCAGG
* *
41965 CTACCCGGCCCCTGGCACCCCC
1 CTACCCGACCCCGGGCACCCCC
*
41987 CTACCCGACCCCGGGTACCCCC
1 CTACCCGACCCCGGGCACCCCC
42009 AGAAACTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.61, G:0.18, T:0.09
Consensus pattern (22 bp):
CTACCCGACCCCGGGCACCCCC
Found at i:46547 original size:5 final size:5
Alignment explanation
Indices: 46537--46568 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
46527 CCTATTTCCC
46537 TTCTT TTCTT TTCTT TTCTT TTCTT TCTCTT T
1 TTCTT TTCTT TTCTT TTCTT TTCTT T-TCTT T
46569 ACCTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:46720 original size:25 final size:25
Alignment explanation
Indices: 46655--46723 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
46645 TTCTCTCTTC
*
46655 GCGGCGCTGCTACC-CCCCTCCATCG
1 GCGGCGCTGCT-CCTCCTCTCCATCG
* *
46680 GCGGCGCTCCTACTCCTCTCCATCG
1 GCGGCGCTGCTCCTCCTCTCCATCG
*
46705 GCGGCGTTGCTCCTCCTCT
1 GCGGCGCTGCTCCTCCTCT
46724 TTCTCTGACC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.06, C:0.48, G:0.23, T:0.23
Consensus pattern (25 bp):
GCGGCGCTGCTCCTCCTCTCCATCG
Found at i:46778 original size:9 final size:9
Alignment explanation
Indices: 46740--46803 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
46730 GACCCGCAAC
*
46740 TCTCTCTCT
1 TCTCTTTCT
46749 CTCTCTTTC-
1 -TCTCTTTCT
46758 TCTCTTTCCT
1 TCTCTTT-CT
46768 T-TCTTTTCT
1 TCTC-TTTCT
* *
46777 TTTCTCTCT
1 TCTCTTTCT
46786 CTCTCTTTCT
1 -TCTCTTTCT
46796 TCTCTTTC
1 TCTCTTTC
46804 CCTTCCCCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.16
9 18 0.40
10 20 0.44
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (9 bp):
TCTCTTTCT
Done.