Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008167.1 Corchorus capsularis cultivar CVL-1 contig08188, 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: 46915
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:66 original size:2 final size:2
Alignment explanation
Indices: 5--49 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 CTAG
5 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
47 TC T
1 TC T
50 TTCTTCACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:685 original size:2 final size:2
Alignment explanation
Indices: 678--710 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
668 AGATCAGTAC
*
678 TA TA TA TA TA TG TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
711 GTATTAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:695 original size:12 final size:12
Alignment explanation
Indices: 678--714 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
668 AGATCAGTAC
678 TATATATATATG
1 TATATATATATG
*
690 TATATATATATA
1 TATATATATATG
702 TAT-TATATA-G
1 TATATATATATG
712 TAT
1 TAT
715 TAATGTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 3 0.13
11 6 0.26
12 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:2558 original size:13 final size:13
Alignment explanation
Indices: 2540--2571 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2530 CCTACTCTAT
*
2540 CACATGGTCAGTC
1 CACATGGCCAGTC
2553 CACATGGCCAGTC
1 CACATGGCCAGTC
2566 CACATG
1 CACATG
2572 TCATTCGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (13 bp):
CACATGGCCAGTC
Found at i:6217 original size:33 final size:33
Alignment explanation
Indices: 6175--6316 Score: 239
Period size: 33 Copynumber: 4.3 Consensus size: 33
6165 TTCTTTTCAC
* **
6175 CCAAAACAGAATTATTTTCAATATTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
6208 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
6241 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* *
6274 CCAAAACAAAATTATTTGCAATGCTATGATCAG
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
6307 CCAAAACAGA
1 CCAAAACAGA
6317 TTTGTTTTCA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 103 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:6344 original size:66 final size:66
Alignment explanation
Indices: 6175--6347 Score: 204
Period size: 66 Copynumber: 2.6 Consensus size: 66
6165 TTCTTTTCAC
* ** * *
6175 CCAAAACAGAATTATTTTCAATATTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAAAATTATTTGCAATGCTATGATCA
6240 A
66 A
* * *
6241 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAAAATTATTTGCAATGCTATGATCA
*
6306 G
66 A
* * * * *
6307 CCAAAACAGATTTGTTTTC-ATCACAATTAGCATCCAAAACA
1 CCAAAACAGAATTATTTGCAAT-ACAATGAGCAACCAAAACA
6348 GATTTAGTAT
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 2 0.02
66 91 0.98
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (66 bp):
CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAAAATTATTTGCAATGCTATGATCA
A
Found at i:6381 original size:33 final size:32
Alignment explanation
Indices: 6343--6446 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 32
6333 TTAGCATCCA
** *
6343 AAACAGATTTAGTATCATCACAAACAACACTT
1 AAACAGATTTAGTATCATTGCAAACAACACTC
*
6375 AGAACAGATTTAGTGTCATTGCAAACAACACTC
1 A-AACAGATTTAGTATCATTGCAAACAACACTC
* * *
6408 AAATTAGGTTTAGTATCATTGCAAACAACATCTA
1 AAA-CAGATTTAGTATCATTGCAAACAACA-CTC
6442 AAACA
1 AAACA
6447 CTCTCTTCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
32 3 0.05
33 52 0.87
34 5 0.08
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (32 bp):
AAACAGATTTAGTATCATTGCAAACAACACTC
Found at i:7925 original size:5 final size:5
Alignment explanation
Indices: 7915--7947 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
7905 GTCGAAATTT
7915 TTTTA TTTTA TTTTA TTTTA TTTT- TTTATA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTT
7948 GTGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:16282 original size:31 final size:28
Alignment explanation
Indices: 16226--16293 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 28
16216 GACACCTTGG
*
16226 AATAAAAATTGAGATTTCAAGTAACTTGTA
1 AATAAAAATTGAGATTTCAAATAAC-T-TA
*
16256 AATAAAAGATTGAAGCTTT-AAATAACTTA
1 AATAAAA-ATTG-AGATTTCAAATAACTTA
16285 AATAAAAAT
1 AATAAAAAT
16294 GTCATCTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.06
29 9 0.26
30 8 0.24
31 10 0.29
32 5 0.15
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (28 bp):
AATAAAAATTGAGATTTCAAATAACTTA
Found at i:16347 original size:49 final size:49
Alignment explanation
Indices: 16287--16475 Score: 279
Period size: 49 Copynumber: 3.8 Consensus size: 49
16277 ATAACTTAAA
16287 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAG
1 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAG
* * *
16336 TAAAAATGTCATCTTTGGGTAAAATATTGAATTCTTAGCAATTAGTAAG
1 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAG
* *
16385 TAAAAATGTCATATTTGGGTAAAAGATTGAAACTTTTAGTAATTAGTAAG
1 TAAAAATGTCATCTTTGGGTAAAAGATTG-AATTTTTAGTAATTAGTAAG
* * * * *
16435 TAAAGATGTCACCTTTGAGCAAAAGATTGATTTTTTAGTAA
1 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAA
16476 ATAGAGATGT
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
49 83 0.67
50 41 0.33
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.37
Consensus pattern (49 bp):
TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAG
Found at i:16445 original size:50 final size:50
Alignment explanation
Indices: 16258--16464 Score: 255
Period size: 49 Copynumber: 4.2 Consensus size: 50
16248 AACTTGTAAA
* * *
16258 TAAAAGATTGAAGCTTTAAATAACTTA--AA-TAAAAATGTCATCTTTGGG
1 TAAAAGATTGAAACTTTTAGTAA-TTAGTAAGTAAAAATGTCATCTTTGGG
*
16306 TAAAAGATTG-AATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
1 TAAAAGATTGAAACTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
* * *
16355 TAAAATATTG-AA-TTCTTAGCAATTAGTAAGTAAAAATGTCATATTTGGG
1 TAAAAGATTGAAACTT-TTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
* * *
16404 TAAAAGATTGAAACTTTTAGTAATTAGTAAGTAAAGATGTCACCTTTGAG
1 TAAAAGATTGAAACTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
*
16454 CAAAAGATTGA
1 TAAAAGATTGA
16465 TTTTTTAGTA
Statistics
Matches: 139, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
46 3 0.02
47 8 0.06
48 14 0.10
49 71 0.51
50 41 0.29
51 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (50 bp):
TAAAAGATTGAAACTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
Found at i:16464 original size:99 final size:98
Alignment explanation
Indices: 16287--16464 Score: 284
Period size: 99 Copynumber: 1.8 Consensus size: 98
16277 ATAACTTAAA
* * *
16287 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTT
1 TAAAAATGTCATATTTGGGTAAAAGATTGAACTTTTAGTAATTAGTAAGTAAAAATGTCACCTTT
* * *
16352 GGGTAAAATATTGAATTCTTAGCAATTAGTAAG
66 GAGCAAAAGATTGAATTCTTAGCAATTAGTAAG
*
16385 TAAAAATGTCATATTTGGGTAAAAGATTGAAACTTTTAGTAATTAGTAAGTAAAGATGTCACCTT
1 TAAAAATGTCATATTTGGGTAAAAGATTG-AACTTTTAGTAATTAGTAAGTAAAAATGTCACCTT
16450 TGAGCAAAAGATTGA
65 TGAGCAAAAGATTGA
16465 TTTTTTAGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
98 28 0.39
99 44 0.61
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (98 bp):
TAAAAATGTCATATTTGGGTAAAAGATTGAACTTTTAGTAATTAGTAAGTAAAAATGTCACCTTT
GAGCAAAAGATTGAATTCTTAGCAATTAGTAAG
Found at i:16474 original size:42 final size:42
Alignment explanation
Indices: 16427--16506 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
16417 CTTTTAGTAA
* * *
16427 TTAGTAAGTAAAGATGTCACCTTTGAGCAAAAGATTGATTTT
1 TTAGTAAATAAAGATGTAACCTTTGAACAAAAGATTGATTTT
* *
16469 TTAGTAAATAGAGATGTAACCTTTGAATAAAAGATTGA
1 TTAGTAAATAAAGATGTAACCTTTGAACAAAAGATTGA
16507 AGTTTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (42 bp):
TTAGTAAATAAAGATGTAACCTTTGAACAAAAGATTGATTTT
Found at i:17475 original size:43 final size:43
Alignment explanation
Indices: 17416--17631 Score: 344
Period size: 43 Copynumber: 5.0 Consensus size: 43
17406 GTTAAATCAG
*
17416 TTGGTAATA-AACTTAATTCGGTGTAATTAAGTAAGTTGGTAAT
1 TTGGTAA-ACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
*
17459 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTTGTAAT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
17502 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
* *
17545 TTGGTAAACAACTTAATTCGGTGTAATTAAGCAAATTAGTAAT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
* * * *
17588 TTGGTAAACAACTTATTTCAGTGTAATTAAGAAAATTCGTAAT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
17631 T
1 T
17632 AAGCTAAGTA
Statistics
Matches: 163, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
42 1 0.01
43 162 0.99
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (43 bp):
TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
Found at i:17541 original size:35 final size:35
Alignment explanation
Indices: 17497--17762 Score: 130
Period size: 35 Copynumber: 7.2 Consensus size: 35
17487 AAGTAAATTT
* *
17497 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAA
1 GTAAATTGGTAATCAACTTAATTCGGTGTAATTAA
17532 GTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAA
1 GTAAATTGGTAA-----T---CAACTTAATTCGGTGTAATTAA
* * *
17575 GCAAATTAGTAATTTGGTAAACAACTTATTTCAGTGTAATTAA
1 G-----TA--AA-TTGGTAATCAACTTAATTCGGTGTAATTAA
* * * *
17618 GAAAATTCGTAATTAAGCTAAGTAATT-TG-GTAA-T--
1 GTAAATTGGTAATCAA-CT---TAATTCGGTGTAATTAA
*
17652 -TAAATTAGGTAATTAACTTAATTCGGTGTAATTAA
1 GTAAATT-GGTAATCAACTTAATTCGGTGTAATTAA
** *
17687 GTAAATCAGTAGTCAACTTAATTCGGTGTAATTAA
1 GTAAATTGGTAATCAACTTAATTCGGTGTAATTAA
** *** *
17722 GTAAATCAGTAATTGGCTTAATTTGGTGTAATTAA
1 GTAAATTGGTAATCAACTTAATTCGGTGTAATTAA
17757 GTAAAT
1 GTAAAT
17763 AAATGGCTTA
Statistics
Matches: 181, Mismatches: 23, Indels: 54
0.70 0.09 0.21
Matches are distributed among these distances:
30 5 0.03
31 1 0.01
32 4 0.02
33 8 0.04
34 8 0.04
35 80 0.44
36 10 0.06
37 4 0.02
38 2 0.01
39 4 0.02
43 44 0.24
48 2 0.01
50 2 0.01
51 7 0.04
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (35 bp):
GTAAATTGGTAATCAACTTAATTCGGTGTAATTAA
Found at i:17684 original size:19 final size:19
Alignment explanation
Indices: 17660--17721 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
17650 ATTAAATTAG
17660 GTAATTAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
* * *
17679 GTAATTAA-GTAAATC--A
1 GTAATTAACTTAATTCGGT
* *
17695 GTAGTCAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
17714 GTAATTAA
1 GTAATTAA
17722 GTAAATCAGT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
16 6 0.20
17 5 0.17
18 5 0.17
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GTAATTAACTTAATTCGGT
Found at i:17773 original size:31 final size:34
Alignment explanation
Indices: 17668--17774 Score: 130
Period size: 35 Copynumber: 3.2 Consensus size: 34
17658 AGGTAATTAA
* ***
17668 CTTAATTCGGTGTAATTAAGTAAATCAGTAGTCAA
1 CTTAATTCGGTGTAATTAAGTAAATCAG-AATTGG
17703 CTTAATTCGGTGTAATTAAGTAAATCAGTAATTGG
1 CTTAATTCGGTGTAATTAAGTAAATCAG-AATTGG
*
17738 CTTAATTTGGTGTAATTAAGTAAAT-A-AA-TGG
1 CTTAATTCGGTGTAATTAAGTAAATCAGAATTGG
17769 CTTAAT
1 CTTAAT
17775 CTAGGAATCC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
31 9 0.13
32 2 0.03
34 1 0.01
35 55 0.82
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.37
Consensus pattern (34 bp):
CTTAATTCGGTGTAATTAAGTAAATCAGAATTGG
Found at i:20768 original size:33 final size:33
Alignment explanation
Indices: 20731--20826 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
20721 ATTAGCATCC
* *
20731 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACAATT
* * *
20764 AAAACAGATTTAGTGTCATTGCAAAGAACAATT
1 AAAACAGATTTAGTATCATCGCAAACAACAATT
** *
20797 AAATTAGGTTTAGTATCATCGCAAACAACA
1 AAAACAGATTTAGTATCATCGCAAACAACA
20827 TCTAAACATC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACAATT
Found at i:27729 original size:35 final size:35
Alignment explanation
Indices: 27683--27750 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
27673 GTTTGGTAAA
27683 TCAGATGACTCAGTGCAGCATCTTCAAAATTGGCT
1 TCAGATGACTCAGTGCAGCATCTTCAAAATTGGCT
* *
27718 TCAGATGACTCAGTGTAGCATTTTCAAAATTGG
1 TCAGATGACTCAGTGCAGCATCTTCAAAATTGG
27751 ATTCGGTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (35 bp):
TCAGATGACTCAGTGCAGCATCTTCAAAATTGGCT
Found at i:27909 original size:87 final size:86
Alignment explanation
Indices: 27744--27932 Score: 195
Period size: 87 Copynumber: 2.1 Consensus size: 86
27734 AGCATTTTCA
* * **
27744 AAATTGGATTCGGTGAGCTCGGTGCAACACATTTCAAAATGGTTCAGGAAGATTCGGTGAATCGG
1 AAATTGGATTCGGTGAGCTCGGTGCAACACATTACAAAA-GGTTCAGGAAGATTCAGTGAATCAA
*
27809 GTTAACACGGTGC-ATTTCTTCC
65 GTTAACACAGTGCAATTTCTT-C
*
27831 AAATTGGATTCGGTGAGCTCGGTGCAGCACATGTACAAACA-GTTCAGGATA-ATTCAGTGAATC
1 AAATTGGATTCGGTGAGCTCGGTGCAACACAT-TACAAA-AGGTTCAGGA-AGATTCAGTGAATC
* ***
27894 AAGTTGATGTAGTGCAGTATTTCTTC
63 AAGTTAACACAGTGCA--ATTTCTTC
27920 AAGATTGGATTCG
1 AA-ATTGGATTCG
27933 TGCGGTCCCT
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
87 58 0.68
88 6 0.07
89 4 0.05
90 17 0.20
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (86 bp):
AAATTGGATTCGGTGAGCTCGGTGCAACACATTACAAAAGGTTCAGGAAGATTCAGTGAATCAAG
TTAACACAGTGCAATTTCTTC
Found at i:32661 original size:31 final size:29
Alignment explanation
Indices: 32625--32692 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
32615 GACACCTTGG
*
32625 AATAAAAAATTG-AGATTTCAAGTAACTTGTA
1 AATAAAAAATTGAAGATTT-AAATAAC-T-TA
* *
32656 AATAAAAGATTGAAGCTTTAAATAACTTA
1 AATAAAAAATTGAAGATTTAAATAACTTA
32685 AATAAAAA
1 AATAAAAA
32693 TGTCATCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 9 0.28
30 1 0.03
31 17 0.53
32 5 0.16
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (29 bp):
AATAAAAAATTGAAGATTTAAATAACTTA
Found at i:32711 original size:48 final size:48
Alignment explanation
Indices: 32658--32880 Score: 254
Period size: 49 Copynumber: 4.6 Consensus size: 48
32648 AACTTGTAAA
* *
32658 TAAAAGATTGAAGCTTTAAATAACTTA-AA-TAAAAATGTCATCTTTGGG
1 TAAAAGATTGAA-CTTTTAGTAA-TTAGAAGTAAAAATGTCATCTTTGGG
*
32706 TAAAAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
1 TAAAAGATTGAACTTTTAGTAATTAG-AAGTAAAAATGTCATCTTTGGG
32755 TAAAAGATTGAA-TTCTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
1 TAAAAGATTGAACTT-TTAGTAATTAG-AAGTAAAAATGTCATCTTTGGG
* * * *
32804 TAAAAGATGGAAACTTTTAGTAATTAGTAAGTAAAGATGTCACCTTTGAG
1 TAAAAGATTG-AACTTTTAGTAATTAG-AAGTAAAAATGTCATCTTTGGG
* * ** *
32854 CAAAATATTGATTTTTTAGTAAATAGA
1 TAAAAGATTGAACTTTTAGTAATTAGA
32881 GATGTAACAT
Statistics
Matches: 156, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
46 3 0.02
47 7 0.04
48 17 0.11
49 87 0.56
50 40 0.26
51 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (48 bp):
TAAAAGATTGAACTTTTAGTAATTAGAAGTAAAAATGTCATCTTTGGG
Found at i:32747 original size:49 final size:49
Alignment explanation
Indices: 32687--32875 Score: 288
Period size: 49 Copynumber: 3.8 Consensus size: 49
32677 ATAACTTAAA
32687 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAG
1 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAG
*
32736 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTCTTAGTAATTAGTAAG
1 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAG
* *
32785 TAAAAATGTCATCTTTGGGTAAAAGATGGAAACTTTTAGTAATTAGTAAG
1 TAAAAATGTCATCTTTGGGTAAAAGATTG-AATTTTTAGTAATTAGTAAG
* * * * * *
32835 TAAAGATGTCACCTTTGAGCAAAATATTGATTTTTTAGTAA
1 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAA
32876 ATAGAGATGT
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
49 86 0.68
50 41 0.32
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (49 bp):
TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAG
Found at i:32845 original size:99 final size:98
Alignment explanation
Indices: 32687--32875 Score: 288
Period size: 99 Copynumber: 1.9 Consensus size: 98
32677 ATAACTTAAA
* * *
32687 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTT
1 TAAAAATGTCATCTTTGGGTAAAAGATGGAACTTTTAGTAATTAGTAAGTAAAAATGTCACCTTT
* *
32752 GGGTAAAAGATTGAATTCTTAGTAATTAGTAAG
66 GAGCAAAAGATTGAATTCTTAGTAATTAGTAAG
*
32785 TAAAAATGTCATCTTTGGGTAAAAGATGGAAACTTTTAGTAATTAGTAAGTAAAGATGTCACCTT
1 TAAAAATGTCATCTTTGGGTAAAAGATGG-AACTTTTAGTAATTAGTAAGTAAAAATGTCACCTT
* * *
32850 TGAGCAAAATATTGATTTTTTAGTAA
65 TGAGCAAAAGATTGAATTCTTAGTAA
32876 ATAGAGATGT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
98 28 0.35
99 53 0.65
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (98 bp):
TAAAAATGTCATCTTTGGGTAAAAGATGGAACTTTTAGTAATTAGTAAGTAAAAATGTCACCTTT
GAGCAAAAGATTGAATTCTTAGTAATTAGTAAG
Found at i:32906 original size:42 final size:42
Alignment explanation
Indices: 32827--32906 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
32817 CTTTTAGTAA
* * * * *
32827 TTAGTAAGTAAAGATGTCACCTTTGAGCAAAATATTGATTTT
1 TTAGTAAATAAAGATGTAACATTTGAACAAAAGATTGATTTT
* *
32869 TTAGTAAATAGAGATGTAACATTTGAATAAAAGATTGA
1 TTAGTAAATAAAGATGTAACATTTGAACAAAAGATTGA
32907 AGTTTTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (42 bp):
TTAGTAAATAAAGATGTAACATTTGAACAAAAGATTGATTTT
Found at i:33871 original size:43 final size:43
Alignment explanation
Indices: 33816--33898 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
33806 ATTAAATCAG
*
33816 TTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
33859 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGT
33899 GATTAAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (43 bp):
TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAAT
Found at i:33994 original size:18 final size:18
Alignment explanation
Indices: 33971--34009 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
33961 GTAAATAACT
33971 TAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAG
33989 TAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAG
34007 TAA
1 TAA
34010 GTTGGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (18 bp):
TAATTCGGTGTAATTAAG
Found at i:34000 original size:61 final size:61
Alignment explanation
Indices: 33928--34052 Score: 223
Period size: 61 Copynumber: 2.0 Consensus size: 61
33918 GTAAACAACT
*
33928 TAATTCGGTGTAATTAAATAAATTGGTAATTTGGTAAATAACTTAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAATAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
* *
33989 TAATTCGGTGTAATTAAGTAAGTTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAATAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
34050 TAA
1 TAA
34053 ATTGGTAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (61 bp):
TAATTCGGTGTAATTAAATAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
Found at i:34037 original size:43 final size:43
Alignment explanation
Indices: 33989--34095 Score: 196
Period size: 43 Copynumber: 2.5 Consensus size: 43
33979 TGTAATTAAG
*
33989 TAATTCGGTGTAATTAAGTAAGTTGGTAATTTGGTAAACAACT
1 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACT
34032 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACT
1 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACT
*
34075 TAATTCGCTGTAATTAAGTAA
1 TAATTCGGTGTAATTAAGTAA
34096 TTCGGTGTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.37
Consensus pattern (43 bp):
TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACT
Found at i:34059 original size:104 final size:102
Alignment explanation
Indices: 33816--34270 Score: 596
Period size: 104 Copynumber: 4.4 Consensus size: 102
33806 ATTAAATCAG
*
33816 TTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGT
*
33881 GTAATTAAGTAAATTGGTG--ATT-A--AATTAAGTAAT
66 GTAATTAAGT-AATTGGTGTAATTAAGTAATT-GGTAAT
* *
33915 TTGGTAAACAACTTAATTCGGTGTAATTAAATAAATTGGTAATTTGGTAAATAACTTAATTCGGT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGT
33980 GTAATTAAGTAATTCGGTGTAATTAAGTAAGTTGGTAAT
66 GTAATTAAGTAATT-GGTGTAATTAAGTAA-TTGGTAAT
*
34019 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGCT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGT
34084 GTAATTAAGTAATTCGGTGTAATTAAGTAAATTGGTAAT
66 GTAATTAAGTAATT-GGTGTAATTAAGT-AATTGGTAAT
* * * **
34123 TTGGTAAACAGCTTAATTCGGTGTAATTAAGCAAATTAGTAATTTGGTAAACAACTTAATTTTGT
1 TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGT
* * *
34188 GTAATTAAGAAAATTGGTAATTAAGCTAAGTAATTTGGTAATT
66 GTAATTAAG-TAATTGGT--GTAA-TTAAGTAA-TTGGTAA-T
**
34231 AAATTAGGTAATTAACTTAATTCGGTGTAATTAAGTAAAT
1 ---TT-GGTAAACAACTTAATTCGGTGTAATTAAGTAAAT
34271 CAGTAGTCAA
Statistics
Matches: 318, Mismatches: 20, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
98 4 0.01
99 76 0.24
101 3 0.01
102 1 0.00
104 176 0.55
105 8 0.03
106 5 0.02
107 12 0.04
108 1 0.00
111 2 0.01
112 30 0.09
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (102 bp):
TTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGT
GTAATTAAGTAATTGGTGTAATTAAGTAATTGGTAAT
Found at i:34097 original size:61 final size:61
Alignment explanation
Indices: 34032--34153 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
34022 GTAAACAACT
34032 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGCTGTAATTAAG
1 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGCTGTAATTAAG
* *
34093 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAGCTTAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGCTGTAATTAAG
34154 CAAATTAGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (61 bp):
TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGCTGTAATTAAG
Found at i:34098 original size:18 final size:18
Alignment explanation
Indices: 34075--34113 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
34065 GTAAACAACT
34075 TAATTCGCTGTAATTAAG
1 TAATTCGCTGTAATTAAG
*
34093 TAATTCGGTGTAATTAAG
1 TAATTCGCTGTAATTAAG
34111 TAA
1 TAA
34114 ATTGGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (18 bp):
TAATTCGCTGTAATTAAG
Found at i:34146 original size:43 final size:43
Alignment explanation
Indices: 34093--34209 Score: 180
Period size: 43 Copynumber: 2.7 Consensus size: 43
34083 TGTAATTAAG
* *
34093 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAGCT
1 TAATTCGGTGTAATTAAGAAAATTGGTAATTTGGTAAACAACT
* *
34136 TAATTCGGTGTAATTAAGCAAATTAGTAATTTGGTAAACAACT
1 TAATTCGGTGTAATTAAGAAAATTGGTAATTTGGTAAACAACT
**
34179 TAATTTTGTGTAATTAAGAAAATTGGTAATT
1 TAATTCGGTGTAATTAAGAAAATTGGTAATT
34210 AAGCTAAGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (43 bp):
TAATTCGGTGTAATTAAGAAAATTGGTAATTTGGTAAACAACT
Found at i:34217 original size:21 final size:21
Alignment explanation
Indices: 34193--34232 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34183 TTTGTGTAAT
34193 TAAGAAAATTGGTAATTAAGC
1 TAAGAAAATTGGTAATTAAGC
* *
34214 TAAGTAATTTGGTAATTAA
1 TAAGAAAATTGGTAATTAA
34233 ATTAGGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (21 bp):
TAAGAAAATTGGTAATTAAGC
Found at i:34241 original size:21 final size:21
Alignment explanation
Indices: 34201--34243 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34191 ATTAAGAAAA
*
34201 TTGGTAATTAAGCTAAGTAAT
1 TTGGTAATTAAACTAAGTAAT
* *
34222 TTGGTAATTAAATTAGGTAAT
1 TTGGTAATTAAACTAAGTAAT
34243 T
1 T
34244 AACTTAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (21 bp):
TTGGTAATTAAACTAAGTAAT
Found at i:34262 original size:19 final size:19
Alignment explanation
Indices: 34238--34299 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
34228 ATTAAATTAG
34238 GTAATTAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
* * *
34257 GTAATTAA-GTAAATC--A
1 GTAATTAACTTAATTCGGT
* *
34273 GTAGTCAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
34292 GTAATTAA
1 GTAATTAA
34300 GTAAATCAGT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
16 6 0.20
17 5 0.17
18 5 0.17
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GTAATTAACTTAATTCGGT
Found at i:34304 original size:35 final size:35
Alignment explanation
Indices: 34238--34340 Score: 152
Period size: 35 Copynumber: 2.9 Consensus size: 35
34228 ATTAAATTAG
*
34238 GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
*
34273 GTAGTCAACTTAATTCGGTGTAATTAAGTAAATCA
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
*** *
34308 GTAATTGGCTTAATTTGGTGTAATTAAGTAAAT
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAAT
34341 AAATGGCATA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 61 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (35 bp):
GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
Found at i:36097 original size:18 final size:19
Alignment explanation
Indices: 36074--36111 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
36064 GTGCATGGGC
*
36074 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
36092 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
36111 T
1 T
36112 AACGATGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:36887 original size:21 final size:20
Alignment explanation
Indices: 36857--36904 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
36847 CAAGCACTGG
* *
36857 AGCACCTGGGTGATCAGACAA
1 AGCACATGGGTCATCAGA-AA
*
36878 AGCACATGGGTCTTCAGAAA
1 AGCACATGGGTCATCAGAAA
36898 AGC-CATG
1 AGCACATG
36905 TGGGCGCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 5 0.21
21 15 0.62
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (20 bp):
AGCACATGGGTCATCAGAAA
Found at i:40464 original size:30 final size:30
Alignment explanation
Indices: 40430--40487 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
40420 CATCTTCAAG
40430 TCCATGATAAGTCCATGG-CGCATCATTCCC
1 TCCATGATAAG-CCATGGCCGCATCATTCCC
*
40460 TCCATGATAAGCCTTGGCCGCATCATTC
1 TCCATGATAAGCCATGGCCGCATCATTC
40488 TGTTCCCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (30 bp):
TCCATGATAAGCCATGGCCGCATCATTCCC
Found at i:42302 original size:30 final size:30
Alignment explanation
Indices: 42266--42323 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
42256 CATCTTCAAG
42266 TCCATGATAAGTCCTT-GGCGCATCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
42296 TCCATGATAAGCCTTGGGCGCATCATTC
1 TCCATGATAAGCCTTGGGCGCATCATTC
42324 TGTTCCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:43542 original size:28 final size:28
Alignment explanation
Indices: 43490--43559 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
43480 GTCTAAGGGT
43490 ATTTTGGTCA-TTTTTGCACCCAGGGGC
1 ATTTTGGTCATTTTTTGCACCCAGGGGC
**
43517 ATTTTGGTCATTTTTTGCACTTAGGGGC
1 ATTTTGGTCATTTTTTGCACCCAGGGGC
*
43545 ATTTTAGTCATTTTT
1 ATTTTGGTCATTTTT
43560 AGGTTCACCT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 10 0.26
28 29 0.74
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (28 bp):
ATTTTGGTCATTTTTTGCACCCAGGGGC
Found at i:46120 original size:50 final size:50
Alignment explanation
Indices: 45945--46284 Score: 304
Period size: 50 Copynumber: 6.9 Consensus size: 50
45935 GGGTTTATCA
* * *
45945 TTTGAATAAAAGATTGAATTTTT-GAGT-TTTTG-AAA-AAAAATGTCTC
1 TTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATATCTC
** * * * * **
45991 TTTGGGTAAAAGATTGAATTTTTATAGTGATTAGTAAATAAAATTTTAAGC
1 TTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATAT-CTC
* *
46042 TTTGAATAAAAGATTGAATTTTTA-AGTAATTGGTAAATAAAAATATCTT
1 TTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATATCTC
* * * *
46091 TTTGAGTAAAAGGTTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAAC-C
1 TTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAA-A-ATATCTC
* *
46142 TTTGAATAAAAGATTGAATTTTTA-AGTAAGTGGTAAATAAAAAT-TGCATC
1 TTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATAT-C-TC
** * * ** *
46192 TTTGGGTAAAAGATTGAATCTTTAGAGTGATTAGTAAATAAAGCTTTAAC-C
1 TTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAA--AATATCTC
*
46243 TTTGAATGAAAGATTGAATTTTTAG-GTAATTAGTAAATAAAA
1 TTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAA
46285 TGTCACCTTT
Statistics
Matches: 234, Mismatches: 45, Indels: 28
0.76 0.15 0.09
Matches are distributed among these distances:
46 21 0.09
47 3 0.01
48 5 0.02
49 26 0.11
50 92 0.39
51 82 0.35
52 3 0.01
53 2 0.01
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (50 bp):
TTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATATCTC
Found at i:46244 original size:101 final size:100
Alignment explanation
Indices: 45945--46284 Score: 467
Period size: 100 Copynumber: 3.4 Consensus size: 100
45935 GGGTTTATCA
* * *
45945 TTTGAATAAAAGATTGAATTTTTGAGT-TTTTG-AAA-AAAAA-TGTCTCTTTGGGTAAAAGATT
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATTG-CTCTTTGGGTAAAAGATT
* *
46006 GAATTTTTATAGTGATTAGTAAATAAA-ATTTTAAGC
65 GAATTTTTAGAGTGATTAGTAAATAAAGA-TTTAACC
* * *
46042 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATAT-CTTTTTGAGTAAAAGGTT
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAAT-TGCTCTTTGGGTAAAAGATT
*
46106 GAATTTTTAGAGTAATTAGTAAATAAAGATTTAACC
65 GAATTTTTAGAGTGATTAGTAAATAAAGATTTAACC
*
46142 TTTGAATAAAAGATTGAATTTTTAAGTAAGTGGTAAATAAAAATTGCATCTTTGGGTAAAAGATT
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATTGC-TCTTTGGGTAAAAGATT
* *
46207 GAATCTTTAGAGTGATTAGTAAATAAAGCTTTAACC
65 GAATTTTTAGAGTGATTAGTAAATAAAGATTTAACC
* * *
46243 TTTGAATGAAAGATTGAATTTTTAGGTAATTAGTAAATAAAA
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAA
46285 TGTCACCTTT
Statistics
Matches: 215, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
97 26 0.12
98 3 0.01
99 4 0.02
100 95 0.44
101 86 0.40
102 1 0.00
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (100 bp):
TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATTGCTCTTTGGGTAAAAGATTG
AATTTTTAGAGTGATTAGTAAATAAAGATTTAACC
Done.