Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017453.1 Corchorus olitorius cultivar O-4 contig17486, 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: 27559
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:1582 original size:27 final size:27
Alignment explanation
Indices: 1547--1619 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1537 AGGGTCACCT
* *
1547 AGGGTCATTTTAGTCATTTGCACT-TCC
1 AGGGGCATTTTGGTCATTTGCA-TATCC
* *
1574 CGGGGCATTTTGGTCATTTGCATATTC
1 AGGGGCATTTTGGTCATTTGCATATCC
1601 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
1620 TAAGATCACA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCATATCC
Found at i:5567 original size:15 final size:16
Alignment explanation
Indices: 5547--5581 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5537 TTTAAAAATC
5547 ACAATTAAA-AAGAAA
1 ACAATTAAACAAGAAA
*
5562 ACAATTAAACTAGAAA
1 ACAATTAAACAAGAAA
5578 ACAA
1 ACAA
5582 AGCAAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (16 bp):
ACAATTAAACAAGAAA
Found at i:9761 original size:40 final size:40
Alignment explanation
Indices: 9716--9794 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
9706 GTTCAACATG
9716 GTCCCTGATTCAAGATTTGT-TTACTATTTGATGCAATTTA
1 GTCCCTGATTCAAGATTT-TATTACTATTTGATGCAATTTA
* * *
9756 GTCCCTGATTTAGGATTTTAGTTACTATTTGATTCAATT
1 GTCCCTGATTCAAGATTTTA-TTACTATTTGATGCAATT
9795 GGTTCCCTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 1 0.03
40 16 0.47
41 17 0.50
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (40 bp):
GTCCCTGATTCAAGATTTTATTACTATTTGATGCAATTTA
Found at i:15712 original size:19 final size:19
Alignment explanation
Indices: 15688--15726 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
15678 ATCTGACATA
15688 CACATTCATAGCATTCATC
1 CACATTCATAGCATTCATC
*
15707 CACATTTATAGCATTCATC
1 CACATTCATAGCATTCATC
15726 C
1 C
15727 TAGAGGCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (19 bp):
CACATTCATAGCATTCATC
Found at i:16190 original size:32 final size:32
Alignment explanation
Indices: 16154--16218 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
16144 GCAACAAGTT
16154 AAGTCATGAAGTCAGTAGCACATAATCACCAA
1 AAGTCATGAAGTCAGTAGCACATAATCACCAA
16186 AAGTCATGAAGTCAGTAGCACATAATCACCAA
1 AAGTCATGAAGTCAGTAGCACATAATCACCAA
16218 A
1 A
16219 TACAGCAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18
Consensus pattern (32 bp):
AAGTCATGAAGTCAGTAGCACATAATCACCAA
Found at i:18403 original size:15 final size:15
Alignment explanation
Indices: 18383--18415 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18373 AGTAAAGAGT
18383 AAATAGCAATCAGTA
1 AAATAGCAATCAGTA
*
18398 AAATAGTAATCAGTA
1 AAATAGCAATCAGTA
18413 AAA
1 AAA
18416 GAGTAAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (15 bp):
AAATAGCAATCAGTA
Found at i:18420 original size:15 final size:15
Alignment explanation
Indices: 18390--18552 Score: 122
Period size: 15 Copynumber: 11.1 Consensus size: 15
18380 AGTAAATAGC
*
18390 AATCAGTAAAATAGT
1 AATCAGTAAAAGAGT
18405 AATCAGTAAAAGAGT
1 AATCAGTAAAAGAGT
* **
18420 AA--AGTGTAATCAGT
1 AATCAGT-AAAAGAGT
**
18434 AAAAGAGT-AAAGAGT
1 -AATCAGTAAAAGAGT
*
18449 AATCAGGAAAAGAGT
1 AATCAGTAAAAGAGT
**
18464 AAT-AGT-AATCAGT
1 AATCAGTAAAAGAGT
**
18477 AAAGAGT-AAAGAGT
1 AATCAGTAAAAGAGT
*
18491 AATCAGTAAAAGTGT
1 AATCAGTAAAAGAGT
**
18506 AAAGAGTAAAAGAGT
1 AATCAGTAAAAGAGT
*
18521 AATCAGTAAAATAGT
1 AATCAGTAAAAGAGT
*
18536 AATCGGTAAAAGAGT
1 AATCAGTAAAAGAGT
18551 AA
1 AA
18553 AGAGCAATCA
Statistics
Matches: 115, Mismatches: 26, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
13 10 0.09
14 24 0.21
15 78 0.68
17 3 0.03
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (15 bp):
AATCAGTAAAAGAGT
Found at i:18423 original size:7 final size:7
Alignment explanation
Indices: 18413--18658 Score: 85
Period size: 7 Copynumber: 34.3 Consensus size: 7
18403 GTAATCAGTA
18413 AAAGAGT
1 AAAGAGT
*
18420 AAAGTGT
1 AAAGAGT
**
18427 AATCAGT
1 AAAGAGT
18434 AAAAGAGT
1 -AAAGAGT
18442 AAAGAGT
1 AAAGAGT
*
18449 AATCAG-GA
1 AA--AGAGT
18457 AAAGAGT
1 AAAGAGT
*
18464 -AATAGT
1 AAAGAGT
**
18470 AATCAGT
1 AAAGAGT
18477 AAAGAGT
1 AAAGAGT
18484 AAAGAGT
1 AAAGAGT
**
18491 AATCAGT
1 AAAGAGT
*
18498 AAAAGTGT
1 -AAAGAGT
18506 AAAGAGT
1 AAAGAGT
18513 AAAAGAGT
1 -AAAGAGT
**
18521 AATCAGT
1 AAAGAGT
*
18528 AAAATAGT
1 -AAAGAGT
*
18536 AATCG-GT
1 AA-AGAGT
18543 AAAAGAGT
1 -AAAGAGT
*
18551 AAAGAGC
1 AAAGAGT
*
18558 AATCAGA-A
1 AA--AGAGT
18566 AAAGAGT
1 AAAGAGT
*
18573 -AATAGT
1 AAAGAGT
**
18579 AATCTA-T
1 AA-AGAGT
18586 AAAGAGT
1 AAAGAGT
*
18593 AAATAGT
1 AAAGAGT
**
18600 AATCAGT
1 AAAGAGT
18607 AAAAGAGT
1 -AAAGAGT
18615 AAAGAGT
1 AAAGAGT
18622 AAAAGAGT
1 -AAAGAGT
18630 AATA-A-T
1 AA-AGAGT
***
18636 AGTCAGT
1 AAAGAGT
18643 AAAGAGT
1 AAAGAGT
18650 AAAGAGT
1 AAAGAGT
18657 AA
1 AA
18659 TCAAGGAAGA
Statistics
Matches: 174, Mismatches: 43, Indels: 44
0.67 0.16 0.17
Matches are distributed among these distances:
6 19 0.11
7 105 0.60
8 45 0.26
9 5 0.03
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (7 bp):
AAAGAGT
Found at i:18430 original size:22 final size:22
Alignment explanation
Indices: 18394--18623 Score: 190
Period size: 22 Copynumber: 10.5 Consensus size: 22
18384 AATAGCAATC
*
18394 AGTAAAATAGTAATCAGTAAAAG
1 AGTAAAGT-GTAATCAGTAAAAG
18417 AGTAAAGTGTAATCAGTAAAAG
1 AGTAAAGTGTAATCAGTAAAAG
* *
18439 AGTAAAGAGTAATCAGGAAAAG
1 AGTAAAGTGTAATCAGTAAAAG
18461 AGT-AA-TAGTAATCAGT-AAAG
1 AGTAAAGT-GTAATCAGTAAAAG
*
18481 AGTAAAGAGTAATCAGTAAAAG
1 AGTAAAGTGTAATCAGTAAAAG
* * ** **
18503 TGTAAAGAGTAAAAGAGT-AATC
1 AGTAAAGTGT-AATCAGTAAAAG
* *
18525 AGTAAAATAGTAATCGGTAAAAG
1 AGTAAAGT-GTAATCAGTAAAAG
* * *
18548 AGTAAAGAGCAATCAGAAAAAG
1 AGTAAAGTGTAATCAGTAAAAG
18570 AGT-AA-TAGTAATC--TATAAAG
1 AGTAAAGT-GTAATCAGTA-AAAG
18590 AGTAAA-TAGTAATCAGTAAAAG
1 AGTAAAGT-GTAATCAGTAAAAG
*
18612 AGTAAAGAGTAA
1 AGTAAAGTGTAA
18624 AAGAGTAATA
Statistics
Matches: 166, Mismatches: 28, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.01
20 14 0.08
21 38 0.23
22 89 0.54
23 24 0.14
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.20
Consensus pattern (22 bp):
AGTAAAGTGTAATCAGTAAAAG
Found at i:18613 original size:57 final size:57
Alignment explanation
Indices: 18551--18661 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
18541 GTAAAAGAGT
* * *
18551 AAAGAGCAATCAGAAAAAGAGTAATAGTAATCTA-TAAAGAGTAAATAGTAATCAGTA
1 AAAGAGCAAACAGAAAAAGAGTAATAATAATC-AGTAAAGAGTAAAGAGTAATCAGTA
* * * *
18608 AAAGAGTAAAGAGTAAAAGAGTAATAATAGTCAGTAAAGAGTAAAGAGTAATCA
1 AAAGAGCAAACAGAAAAAGAGTAATAATAATCAGTAAAGAGTAAAGAGTAATCA
18662 AGGAAGAGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
56 1 0.02
57 45 0.98
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (57 bp):
AAAGAGCAAACAGAAAAAGAGTAATAATAATCAGTAAAGAGTAAAGAGTAATCAGTA
Found at i:18622 original size:15 final size:15
Alignment explanation
Indices: 18585--18631 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
18575 TAGTAATCTA
*
18585 TAAAGAGT-AAATAG
1 TAAAGAGTAAAAGAG
**
18599 TAATCAGTAAAAGAG
1 TAAAGAGTAAAAGAG
18614 TAAAGAGTAAAAGAG
1 TAAAGAGTAAAAGAG
18629 TAA
1 TAA
18632 TAATAGTCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.57, C:0.02, G:0.21, T:0.19
Consensus pattern (15 bp):
TAAAGAGTAAAAGAG
Found at i:18644 original size:21 final size:21
Alignment explanation
Indices: 18619--18693 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
18609 AAGAGTAAAG
*
18619 AGTAAAAGAGTAATAATAGTC
1 AGTAAAAGAGTAATAATAATC
18640 AGT-AAAGAGTAA-AGAGTAATC
1 AGTAAAAGAGTAATA-A-TAATC
* *
18661 A--AGGAAGAGTAATAATAATT
1 AGTA-AAAGAGTAATAATAATC
18681 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
18694 ACTGTAAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
19 1 0.02
20 15 0.35
21 25 0.58
22 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTAAAAGAGTAATAATAATC
Found at i:18652 original size:35 final size:37
Alignment explanation
Indices: 18506--18694 Score: 127
Period size: 42 Copynumber: 4.9 Consensus size: 37
18496 GTAAAAGTGT
* *
18506 AAAGAGTAAA-AGAGTAATCAGTAAAATAGTAATCG-GTA
1 AAAGAGTAAATA-A-TAATCAGTAAAAGAGTAA-AGAGTA
* ** * *
18544 AAAGAGTAAAGAGCAATCAGAAAAAGAGTAATAGTAATCTA
1 AAAGAGTAAATAATAATCAGTAAAAGAGTAA-AG--A-GTA
*
18585 TAAAGAGTAAATAGTAATCAGTAAAAGAGTAAAGAGTA
1 -AAAGAGTAAATAATAATCAGTAAAAGAGTAAAGAGTA
*
18623 AAAGAGT-AATAATAGTCAGT-AAAGAGTAAAGAGTA
1 AAAGAGTAAATAATAATCAGTAAAAGAGTAAAGAGTA
*
18658 ATCAAGGAAG-AGTAATAATAATTAGTAAAAGAGTAAA
1 A--AA-G-AGTA--AATAATAATCAGTAAAAGAGTAAA
18695 CTGTAAACAG
Statistics
Matches: 123, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
35 16 0.13
36 11 0.09
37 26 0.21
38 13 0.11
39 4 0.03
41 15 0.12
42 38 0.31
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (37 bp):
AAAGAGTAAATAATAATCAGTAAAAGAGTAAAGAGTA
Found at i:18721 original size:77 final size:78
Alignment explanation
Indices: 18587--18735 Score: 169
Period size: 77 Copynumber: 1.9 Consensus size: 78
18577 GTAATCTATA
* * * * *
18587 AAGAGTAAATAGTAATCAGTAAAAGAGTAAAGAGTAAAAGAGTAATAATAGTCAGTAAAGAGTAA
1 AAGAGTAAATAATAATCAGTAAAAGAGTAAACAGTAAAACAGTAATAATAATCAGTAAACAGTAA
18652 AGAGTAATCAAGG
66 AGAGTAATCAAGG
* * * *
18665 AAGAGT-AATAATAATTAGTAAAAGAGTAAACTGT-AAACAGTAAAGTGATAAT-AGTAATCAGT
1 AAGAGTAAATAATAATCAGTAAAAGAGTAAACAGTAAAACAGT-AA-TAATAATCAGTAAACAGT
*
18727 AACGAGTAA
64 AAAGAGTAA
18736 ATGGCAATCA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
76 6 0.10
77 42 0.71
78 11 0.19
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (78 bp):
AAGAGTAAATAATAATCAGTAAAAGAGTAAACAGTAAAACAGTAATAATAATCAGTAAACAGTAA
AGAGTAATCAAGG
Found at i:18848 original size:25 final size:25
Alignment explanation
Indices: 18815--18869 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
18805 TAAAAAGAGA
18815 AAAAATGGTATTCAATAATTAAAGT
1 AAAAATGGTATTCAATAATTAAAGT
*
18840 AAAAATGGTATTCAGTAATTAAAGT
1 AAAAATGGTATTCAATAATTAAAGT
18865 AAAAA
1 AAAAA
18870 AGGCAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.29
Consensus pattern (25 bp):
AAAAATGGTATTCAATAATTAAAGT
Found at i:18946 original size:26 final size:27
Alignment explanation
Indices: 18900--18962 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
18890 TAAAAAAAAG
18900 AAAGAGTAAGAAAATGGTAAT-AAGTAA
1 AAAGAGTAAGAAAATGGTAATCAA-TAA
*
18927 AAAGAGTAA-AGAATGGTAATCAATAA
1 AAAGAGTAAGAAAATGGTAATCAATAA
18953 AAAGAGTAAG
1 AAAGAGTAAG
18963 GGTAATCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 22 0.67
27 11 0.33
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.17
Consensus pattern (27 bp):
AAAGAGTAAGAAAATGGTAATCAATAA
Found at i:18967 original size:22 final size:24
Alignment explanation
Indices: 18915--18974 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
18905 GTAAGAAAAT
18915 GGTAAT-AAGTAAAAAGAGTAAAGAA
1 GGTAATCAA-TAAAAAGAGTAAAG-A
18940 TGGTAATCAATAAAAAGAGT-AAG-
1 -GGTAATCAATAAAAAGAGTAAAGA
18963 GGTAATCAATAA
1 GGTAATCAATAA
18975 TTTAATTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 12 0.36
25 3 0.09
26 16 0.48
27 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.22, T:0.20
Consensus pattern (24 bp):
GGTAATCAATAAAAAGAGTAAAGA
Found at i:23018 original size:303 final size:303
Alignment explanation
Indices: 22452--23058 Score: 919
Period size: 303 Copynumber: 2.0 Consensus size: 303
22442 CTTGTTTTAA
* * * * *
22452 CAAGTGGAGTCGTTTCAGCTGCAGAAAACCCAGACTTGATTATTAAGCAAAATAATTGCAAGACA
1 CAAGCGGAGTCATTTCACCTGCAGAAAACCCAGACTTGATTATTAAGCAAAACAATTGCAAAACA
** * * * * *
22517 AAAATGGGTCTGGCCTGTTCCAAGGAAGTTTTCACAAGTATATTCTATACCGGATCTGTCACTAA
66 AAAATGGAACTGCCCTGTGCCAAGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTAA
* * *
22582 GAAGTGTTGCGGTGAACTCATGGTATTGGGTAAAGTTTGTCACGATGCATTTGTTAAGAAGACTC
131 GAAGTGTTGCAGTGAACTCAAGGTATTGGATAAAGTTTGTCACGATGCATTTGTTAAGAAGACTC
* * * * *
22647 ATGAAGATCCTTTATATAAAGACTTAACCGAGTCAACAATTGCGAAGAAGAGTACAACAACATGG
196 ATGAAGACCCTATATATAAAAACTTAACCGAGTCAACAATTGCAAAGAAGAGTACAAAAACATGG
*
22712 AAC-ACATGTGTCTCAGTCATCGACATTTCACCATCTTCTTCTG
261 AACAAC-TGTGCCTCAGTCATCGACATTTCACCATCTTCTTCTG
* * * *
22755 CAAGCGGAGTCATTTCACCTGCAGAAAACCCAGACTTGATTATTGAGGAAAACAATTTCAAAACG
1 CAAGCGGAGTCATTTCACCTGCAGAAAACCCAGACTTGATTATTAAGCAAAACAATTGCAAAACA
*
22820 AAAATGGAACTGCCCTGTGCCAGGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTAA
66 AAAATGGAACTGCCCTGTGCCAAGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTAA
22885 GAAGTGTTGCAGTGAACTCAAGGTATTGGATAAAGTTTGTCACGATGCATTTGTTAAGAAGACTC
131 GAAGTGTTGCAGTGAACTCAAGGTATTGGATAAAGTTTGTCACGATGCATTTGTTAAGAAGACTC
* ** * *
22950 TTGAAGACCCTATATATAAAAACTTAAGTGAGTCAACAATTGCAAAGAATAGTACAAAAACGTGG
196 ATGAAGACCCTATATATAAAAACTTAACCGAGTCAACAATTGCAAAGAAGAGTACAAAAACATGG
23015 AACAACTGTGCCTCAGTCATCGACATTTCACCATCTTCTTCTG
261 AACAACTGTGCCTCAGTCATCGACATTTCACCATCTTCTTCTG
23058 C
1 C
23059 TTGAGAAGCA
Statistics
Matches: 272, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
303 270 0.99
304 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (303 bp):
CAAGCGGAGTCATTTCACCTGCAGAAAACCCAGACTTGATTATTAAGCAAAACAATTGCAAAACA
AAAATGGAACTGCCCTGTGCCAAGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTAA
GAAGTGTTGCAGTGAACTCAAGGTATTGGATAAAGTTTGTCACGATGCATTTGTTAAGAAGACTC
ATGAAGACCCTATATATAAAAACTTAACCGAGTCAACAATTGCAAAGAAGAGTACAAAAACATGG
AACAACTGTGCCTCAGTCATCGACATTTCACCATCTTCTTCTG
Found at i:24638 original size:18 final size:19
Alignment explanation
Indices: 24615--24651 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
24605 CACCCTAGCC
24615 CTAGAACTAGAAGA-AAAA
1 CTAGAACTAGAAGAGAAAA
*
24633 CTAGAACTGGAAGAGAAAA
1 CTAGAACTAGAAGAGAAAA
24652 AGAAGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.57, C:0.11, G:0.22, T:0.11
Consensus pattern (19 bp):
CTAGAACTAGAAGAGAAAA
Found at i:25285 original size:19 final size:18
Alignment explanation
Indices: 25252--25287 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25242 TCGAGATAAT
25252 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
25270 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
25288 GAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:26161 original size:18 final size:18
Alignment explanation
Indices: 26126--26160 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26116 CTGCTCTATC
*
26126 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
26144 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
26161 TTTTAATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Done.