Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013616.1 Corchorus capsularis cultivar CVL-1 contig13637, 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: 73960
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:6535 original size:21 final size:21
Alignment explanation
Indices: 6511--6551 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
6501 ACTGGCGGGC
6511 TTTACTTGCTGAGGAAGGCGT
1 TTTACTTGCTGAGGAAGGCGT
6532 TTTACTTGCTGAGGAAGGCG
1 TTTACTTGCTGAGGAAGGCG
6552 AACTCTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.32
Consensus pattern (21 bp):
TTTACTTGCTGAGGAAGGCGT
Found at i:6721 original size:17 final size:17
Alignment explanation
Indices: 6699--6737 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
6689 CTCATGGTAC
6699 CTAGGTAGTAGGAGGTG
1 CTAGGTAGTAGGAGGTG
*
6716 CTAGGTAGTATGAGGTG
1 CTAGGTAGTAGGAGGTG
*
6733 ATAGG
1 CTAGG
6738 CTGCATCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.44, T:0.26
Consensus pattern (17 bp):
CTAGGTAGTAGGAGGTG
Found at i:7376 original size:156 final size:154
Alignment explanation
Indices: 7069--7432 Score: 384
Period size: 156 Copynumber: 2.3 Consensus size: 154
7059 GAGCTTCTCA
* * *
7069 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTTTAAGTCTGAATGAGCTGAAA
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTG-AA
** * *
7134 TTTTGCCAAGGAGCTTAGATTATCCACAAAAGACTATGGAAAAATTTCTAAGTAAAACCGAGCTC
65 TTTTGCCAAGGAGCTTAGATTATCCACAAAAGACTATGGAAAAATACCTAAGTAAAACCAAACT-
* * *
7199 CCCTTGATGGTGAACTAGGTTTCTCT
129 CCCTTGATAGAGAACTAGGTTTCACT
* *
7225 CC-CTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-
1 CCTC-AAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGCTGA
*
7287 ATTTT-CCACCAGTAGACTTAGATTA-CCACCATAAAG-CTATTGGAAAAA-ACCTAAGTAAAAC
64 ATTTTGCCA--AGGAG-CTTAGATTATCCA-CA-AAAGACTA-TGGAAAAATACCTAAGTAAAAC
* * * *
7348 CAAACT-CTTTAGCATAGAGAAGTTGGTTTGACT
123 CAAACTCCCTT-G-ATAGAGAACTAGGTTTCACT
* * *
7381 CCTCAAACTGTCCTTAATTGAAAAACTAGCATAAGTTTTTCATGCTAAGTCT
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
7433 GTTTGAGATG
Statistics
Matches: 174, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
153 3 0.02
154 8 0.05
155 12 0.07
156 138 0.79
157 13 0.07
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (154 bp):
CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAAT
TTTGCCAAGGAGCTTAGATTATCCACAAAAGACTATGGAAAAATACCTAAGTAAAACCAAACTCC
CTTGATAGAGAACTAGGTTTCACT
Found at i:11346 original size:2 final size:2
Alignment explanation
Indices: 11341--11366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11331 GTTAACGTTC
11341 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11367 GCAACTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17747 original size:2 final size:2
Alignment explanation
Indices: 17740--17772 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17730 TAACTGATCA
17740 AT AT AT 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 AT AT AT A
17773 ATTTAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17818 original size:12 final size:12
Alignment explanation
Indices: 17801--17825 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17791 CTATATACAT
17801 GTTCGAGTTTGA
1 GTTCGAGTTTGA
17813 GTTCGAGTTTGA
1 GTTCGAGTTTGA
17825 G
1 G
17826 ATAAAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTCGAGTTTGA
Found at i:18511 original size:6 final size:6
Alignment explanation
Indices: 18497--18536 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
18487 TCCTCAACAA
* *
18497 ATATAT ATATCT ATATCT ATGTCT ATATCT ATATCT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
18537 ATTATATAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (6 bp):
ATATCT
Found at i:18816 original size:29 final size:30
Alignment explanation
Indices: 18751--18836 Score: 120
Period size: 32 Copynumber: 2.8 Consensus size: 30
18741 TCAAGGAACA
*
18751 TTAAAATTCCATTAGTTAAAATTATTAACAAG
1 TTAAAATTCCAATAGTTAAAATTATT-A-AAG
18783 TTAAAATTCCAATAGTTAAAATTATT-AAG
1 TTAAAATTCCAATAGTTAAAATTATTAAAG
18812 TTAAAATTCCAATAGTGATAAAATT
1 TTAAAATTCCAATAGT--TAAAATT
18837 CCAAATTACC
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
29 19 0.37
31 7 0.14
32 25 0.49
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (30 bp):
TTAAAATTCCAATAGTTAAAATTATTAAAG
Found at i:21569 original size:23 final size:23
Alignment explanation
Indices: 21520--21569 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
21510 CTTATAACTT
* ** *
21520 AAATACCTATGATATGTAAGGTT
1 AAATACCTATGATATCTAAAATC
*
21543 AAATACCTATGATGTCTAAAATC
1 AAATACCTATGATATCTAAAATC
21566 AAAT
1 AAAT
21570 TAAAAGAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (23 bp):
AAATACCTATGATATCTAAAATC
Found at i:29109 original size:61 final size:62
Alignment explanation
Indices: 28969--29120 Score: 227
Period size: 61 Copynumber: 2.5 Consensus size: 62
28959 GACGGCAGAG
* *
28969 ACTTATTTGAGTATTTTCGCAAA-TGTTGGACCCTGATTTAAGCATTTTTTTTTTCTTTGAGC
1 ACTTATTTGAGTATTTTCGCAAACT-TTGGACCCTAATTTAAGCATTTTTTTTTTCTTTGAAC
29031 ACTTATTTGAGTATTTTCGCAAACTTTGGACCCTAATTTAAGCA-TTTTTTTTTCTTTGAAC
1 ACTTATTTGAGTATTTTCGCAAACTTTGGACCCTAATTTAAGCATTTTTTTTTTCTTTGAAC
* * * *
29092 CCTTATTTAAGCATTTTCGCAAACGTTGG
1 ACTTATTTGAGTATTTTCGCAAACTTTGG
29121 GAACAAAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
61 41 0.49
62 41 0.49
63 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.46
Consensus pattern (62 bp):
ACTTATTTGAGTATTTTCGCAAACTTTGGACCCTAATTTAAGCATTTTTTTTTTCTTTGAAC
Found at i:30492 original size:22 final size:21
Alignment explanation
Indices: 30448--30493 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
30438 GAATTTCGAG
* **
30448 AACCTTTTTATAAATTTTTTT
1 AACCTTCTTATAAATTTGGTT
30469 AACCTTCTTATGAAATTTGGTT
1 AACCTTCTTAT-AAATTTGGTT
30491 AAC
1 AAC
30494 TTCCCTAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (21 bp):
AACCTTCTTATAAATTTGGTT
Found at i:30601 original size:45 final size:45
Alignment explanation
Indices: 30521--30606 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
30511 AAGACCTCAA
* * * *
30521 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATGACCAACAC
1 TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
* *
30566 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCA-ATGAAATATTGATAACCA
30607 TGTTATGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 3 0.09
45 31 0.91
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
Found at i:30670 original size:22 final size:22
Alignment explanation
Indices: 30645--30927 Score: 135
Period size: 22 Copynumber: 13.1 Consensus size: 22
30635 GAATTGTTAG
*
30645 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
30667 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* *
30689 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
30711 TAAATCTTC-CTATAAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
** * *
30734 TAACTTTC-TTATGAAATCTTG-
1 TAA-TCACACTATGAAATTTTGA
*
30755 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
**
30772 TAACCTC-CA-TATGATTTTTTGA
1 TAA--TCACACTATGAAATTTTGA
* * * *
30794 TAATCTCATTATAAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
30816 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
30838 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
30860 TAA-CCCTCTTGTGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
30882 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
30904 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
30926 TA
1 TA
30928 TCCTCCCTGA
Statistics
Matches: 200, Mismatches: 41, Indels: 40
0.71 0.15 0.14
Matches are distributed among these distances:
16 7 0.04
17 2 0.01
18 1 0.00
19 2 0.01
20 2 0.01
21 10 0.05
22 149 0.75
23 25 0.12
24 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:30832 original size:82 final size:83
Alignment explanation
Indices: 30680--30838 Score: 189
Period size: 82 Copynumber: 1.9 Consensus size: 83
30670 TCACACTATG
* * * *
30680 AAATTGTGATAATCTCCCTATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAACTTTCTTA
1 AAATTGTGATAACCTCCATATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAACTTCCCTA
30745 TGAAATCTTGATAACTAC
66 TGAAATCTTGATAACTAC
* ** * *
30763 AAATTTTGATAACCTCCATATGATTTTTTGAT-AATC-TCATTATAAAATTTTGTTAA-TCTCCC
1 AAATTGTGATAACCTCCATATGAAATTTTGATAAATCTTC-CTATAAAATTTTGATAACT-TCCC
*
30825 TATGAAATTTTGAT
64 TATGAAATCTTGAT
30839 CTACATACTA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
81 3 0.05
82 34 0.53
83 27 0.42
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (83 bp):
AAATTGTGATAACCTCCATATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAACTTCCCTA
TGAAATCTTGATAACTAC
Found at i:30942 original size:19 final size:19
Alignment explanation
Indices: 30918--30961 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
30908 CTTCATATGA
*
30918 AATTTTGATATCCTCCCTG
1 AATTTTAATATCCTCCCTG
*
30937 AATTTTAATATCCTCCTTG
1 AATTTTAATATCCTCCCTG
30956 AATTTT
1 AATTTT
30962 TTTTTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (19 bp):
AATTTTAATATCCTCCCTG
Found at i:31302 original size:44 final size:44
Alignment explanation
Indices: 31183--31373 Score: 174
Period size: 44 Copynumber: 4.4 Consensus size: 44
31173 GAAATACCAC
* * * *
31183 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAACCACATTATGAAATTTTGATAACCTCAT
* * * * * *
31227 TATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACC-CCT
1 TATGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCAT
* *
31270 CTATGAAATTCTGATAACCACATTATGTAATTTTGATAACCTCAT
1 -TATGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCAT
* * * * *
31315 TTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCT-TT
1 TATGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCAT
31358 CTAT-AAATTTTGATAA
1 -TATGAAATTTTGATAA
31374 TCCGATTTCT
Statistics
Matches: 118, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
43 20 0.17
44 96 0.81
45 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCAT
Found at i:31340 original size:66 final size:65
Alignment explanation
Indices: 31210--31352 Score: 171
Period size: 66 Copynumber: 2.2 Consensus size: 65
31200 CACATTTTGA
* * * * ** *
31210 AAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATG
1 AAATTTGATAACCACATTATGAAATTTTGATAACCTCTTTATAAAATTTTGATAACAACACTATG
* *
31275 AAATTCTGATAACCACATTATGTAATTTTGATAACCTCATTT-TGAAATTTTGATAACAACACTA
1 AAATT-TGATAACCACATTATGAAATTTTGATAACCTC-TTTATAAAATTTTGATAACAACACTA
31339 TG
64 TG
31341 AAATTTTGATAA
1 AAA-TTTGATAA
31353 TCTTTCTATA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
65 5 0.08
66 56 0.85
67 5 0.08
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.41
Consensus pattern (65 bp):
AAATTTGATAACCACATTATGAAATTTTGATAACCTCTTTATAAAATTTTGATAACAACACTATG
Found at i:31342 original size:22 final size:22
Alignment explanation
Indices: 31180--31512 Score: 140
Period size: 22 Copynumber: 15.0 Consensus size: 22
31170 CCAGAAATAC
*
31180 CACTATGAAATTTTTG-TAATCA
1 CACTATGAAA-TTTTGATAACCA
* * * *
31202 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** *
31224 CTTTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** * * * *
31246 CTTTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAACCA
* *
31268 CTCTATGAAATTCTGATAACCA
1 CACTATGAAATTTTGATAACCA
* * *
31290 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * *
31312 CATTTTGAAATTTTGATAACAA
1 CACTATGAAATTTTGATAACCA
* *
31334 CACTATGAAATTTTGATAATCT
1 CACTATGAAATTTTGATAACCA
**
31356 TTCTAT-AAATTTTGATAATCCGA
1 CACTATGAAATTTTGATAA-CC-A
** * *
31379 TTTCTATGAAATTTCGATAATCA
1 -CACTATGAAATTTTGATAACCA
* *
31402 CTCTATGAGA-TTTGATAA-CA
1 CACTATGAAATTTTGATAACCA
** * * **
31422 TTCTATCAAATTTTGGTATTC-
1 CACTATGAAATTTTGATAACCA
* *
31443 C-CTATGAAATTGAGACTTTTATAACCTT
1 CACTATGAAA-T-----TTTGATAACC-A
*
31471 CA-TACGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
*
31492 CACTATAAAATTTTGATAACC
1 CACTATGAAATTTTGATAACC
31513 TCCCCATTAA
Statistics
Matches: 237, Mismatches: 57, Indels: 34
0.72 0.17 0.10
Matches are distributed among these distances:
20 16 0.07
21 32 0.14
22 156 0.66
23 1 0.00
24 7 0.03
25 11 0.05
26 6 0.03
27 1 0.00
28 7 0.03
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:31434 original size:20 final size:22
Alignment explanation
Indices: 31336--31434 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 22
31326 GATAACAACA
* *
31336 CTATGAAATTTTGATAATCTTT
1 CTATGAAATTTCGATAATCATT
*
31358 CTAT-AAATTTTGATAATCCGATTT
1 CTATGAAATTTCGATAAT-C-A-TT
*
31382 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTCGATAATCATT
*
31404 CTATGAGATTT-GATAA-CATT
1 CTATGAAATTTCGATAATCATT
*
31424 CTATCAAATTT
1 CTATGAAATTT
31435 TGGTATTCCC
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
20 12 0.18
21 18 0.27
22 16 0.24
23 1 0.02
24 7 0.11
25 12 0.18
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTCGATAATCATT
Found at i:31555 original size:22 final size:23
Alignment explanation
Indices: 31530--31590 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
31520 TAAATATTTA
31530 ATGAAATTTTGT-TAACCACACT
1 ATGAAATTTTGTATAACCACACT
* * *
31552 ATGAAATTCTTATATAACCTCGCT
1 ATGAAATT-TTGTATAACCACACT
*
31576 ATGACATTTTG-ATAA
1 ATGAAATTTTGTATAA
31591 TCTCTTTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 12 0.38
23 5 0.16
24 15 0.47
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
ATGAAATTTTGTATAACCACACT
Found at i:31658 original size:22 final size:22
Alignment explanation
Indices: 31626--31765 Score: 113
Period size: 22 Copynumber: 6.3 Consensus size: 22
31616 TTATGATAAT
*
31626 TAACCATCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTAA
* * * *
31648 TAACCAACCTAAGAGATTTAAA
1 TAACCATCCTATGAAATTTTAA
* **
31670 TAATCTGATCCTATGAAATTTTGG
1 TAA-C-CATCCTATGAAATTTTAA
* *
31694 TAACCA-CACTATGGAATTTTGA
1 TAACCATC-CTATGAAATTTTAA
*
31716 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTAA
* *
31738 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTAA
31760 TAACCA
1 TAACCA
31766 CTTACAGACA
Statistics
Matches: 92, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
21 3 0.03
22 70 0.76
23 5 0.05
24 14 0.15
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTAA
Found at i:32554 original size:31 final size:31
Alignment explanation
Indices: 32516--32581 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
32506 TGGTAATTTA
* *
32516 GAAATATGTTTTCAAGAA-AAGGGTACAATTG
1 GAAATATGTTTT-AAAAATAAGGGTACAATCG
32547 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
32578 GAAA
1 GAAA
32582 ACATAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:32760 original size:62 final size:61
Alignment explanation
Indices: 32679--32833 Score: 211
Period size: 62 Copynumber: 2.5 Consensus size: 61
32669 TAAATATTCA
* * * *
32679 TATGAAATTATGATAACCTTCCCATTAAATTATGATAATTACACTATTTTTGGTGACGTACT
1 TATG-AATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGCTGACGTACT
* * *
32741 TATGATATTTTGATAACCTTCCTATGAAATTATGATAATTACATTATTTTTTCTGACGTCCT
1 TATGA-ATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGCTGACGTACT
*
32803 TATGAAGTTTTGATAACATTCCTATGAAATT
1 TATGAA-TTTTGATAACCTTCCTATGAAATT
32834 TCAATAACGA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
61 2 0.02
62 81 0.98
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (61 bp):
TATGAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGCTGACGTACT
Found at i:33127 original size:22 final size:22
Alignment explanation
Indices: 32891--33127 Score: 105
Period size: 22 Copynumber: 10.7 Consensus size: 22
32881 TTAAACTTCT
* * * *
32891 TATGAAATTTTGTTAATCTCTC
1 TATGAAATTTTGATAACCACAC
* * *
32913 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCACAC
32935 TATGAAATTTTGATAACTTC-CA-
1 TATGAAATTTTGATAAC--CACAC
*
32957 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-ACAC
* *
32980 TAT-AAGATGTTGATAACCTC-C
1 TATGAA-ATTTTGATAACCACAC
* **
33001 ATAT-AATATATTGATAACCACGT
1 -TATGAA-ATTTTGATAACCACAC
* *
33024 TATGAAAATTTT-AAAACCTC-C
1 TATG-AAATTTTGATAACCACAC
* * *
33045 ATATG-AATTGTCAGTAATCACAC
1 -TATGAAATTTTGA-TAACCACAC
* *
33068 TCTGAAATTTTGATAAGCACAC
1 TATGAAATTTTGATAACCACAC
* * *
33090 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCACAC
*
33112 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
33128 ACCTTCCTAT
Statistics
Matches: 164, Mismatches: 34, Indels: 34
0.71 0.15 0.15
Matches are distributed among these distances:
20 6 0.04
21 3 0.02
22 125 0.76
23 27 0.16
24 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:33147 original size:14 final size:14
Alignment explanation
Indices: 33124--33156 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
33114 TGAAATTTTA
*
33124 ATAAACCTTCCTAT
1 ATAAATCTTCCTAT
33138 ATAAATCTTCCTAT
1 ATAAATCTTCCTAT
33152 A-AAAT
1 ATAAAT
33157 TTTAATAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAATCTTCCTAT
Found at i:33178 original size:22 final size:21
Alignment explanation
Indices: 33146--33354 Score: 151
Period size: 22 Copynumber: 9.8 Consensus size: 21
33136 ATATAAATCT
* *
33146 TCCTATAAAATTTTAATAACC
1 TCCTATGAAATTTTGATAACC
*
33167 TCCTTATGAAATCTTGATAA--
1 TCC-TATGAAATTTTGATAACC
*
33187 --CTA-CAAATTTTGATAACC
1 TCCTATGAAATTTTGATAACC
**
33205 TCCCTATGATTTTTTGATAACC
1 T-CCTATGAAATTTTGATAACC
* * *
33227 TCATTATGAAATTTTGTTAATC
1 TC-CTATGAAATTTTGATAACC
* *
33249 TCCCTATGAAATTTTGATCTACA
1 T-CCTATGAAATTTTGAT-AACC
*
33272 TACTATGAAATTTTGATAACCC
1 TCCTATGAAATTTTGATAA-CC
* *
33294 TCTTATGAAATTTTGA-AAAC
1 TCCTATGAAATTTTGATAACC
*
33314 TAAACTATGAAATTTTGATAACC
1 T--CCTATGAAATTTTGATAACC
*
33337 TTCATATGAAATTTTGAT
1 -TCCTATGAAATTTTGAT
33355 TACTCCATAA
Statistics
Matches: 144, Mismatches: 29, Indels: 29
0.71 0.14 0.14
Matches are distributed among these distances:
16 11 0.08
17 2 0.01
18 1 0.01
20 2 0.01
21 10 0.07
22 111 0.77
23 6 0.04
24 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAACC
Found at i:33322 original size:66 final size:66
Alignment explanation
Indices: 33191--33354 Score: 172
Period size: 66 Copynumber: 2.5 Consensus size: 66
33181 TGATAACTAC
* * * ** * * **
33191 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTAT
1 AAATTTTGATAACATACATATGAAATTTTGATAACCTCATTATGAAATTTTGTAAAACTAACTAT
33256 G
66 G
*
33257 AAATTTTGATCTACATAC-TATGAAATTTTGATAACCCTC-TTATGAAATTTTG-AAAACTAAAC
1 AAATTTTGAT-AACATACATATGAAATTTTGATAA-CCTCATTATGAAATTTTGTAAAACT-AAC
33319 TATG
63 TATG
* *
33323 AAATTTTGATAACCTTCATATGAAATTTTGAT
1 AAATTTTGATAACATACATATGAAATTTTGAT
33355 TACTCCATAA
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
65 8 0.10
66 66 0.80
67 8 0.10
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (66 bp):
AAATTTTGATAACATACATATGAAATTTTGATAACCTCATTATGAAATTTTGTAAAACTAACTAT
G
Found at i:33485 original size:22 final size:22
Alignment explanation
Indices: 33460--33580 Score: 127
Period size: 22 Copynumber: 5.5 Consensus size: 22
33450 AATCACATTT
* *
33460 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
33482 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
33504 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
33526 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
33548 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
33570 TGAAATTTTGA
1 TGAAATTTTGA
33581 AATTGGACCA
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
22 79 0.99
23 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:33486 original size:44 final size:44
Alignment explanation
Indices: 33436--33580 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 44
33426 GAAGTACCAC
* *
33436 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
* * * * * *
33480 TATGAAATTTTGATAACCTC-TCTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACAT-TATGAAAA-TTTGATAACCTCTT
* * *
33524 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-TT
33569 T-TGAAATTTTGA
1 TATGAAATTTTGA
33581 AATTGGACCA
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
43 5 0.06
44 70 0.89
45 4 0.05
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
Found at i:33891 original size:30 final size:31
Alignment explanation
Indices: 33856--33914 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
33846 TGACAATTTA
* *
33856 GAAATATGTTTTAAAAA-AATGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
33886 GAAATATATTTTAAAAATAAGGGTACAAT
1 GAAATATATTTTAAAAATAAGGGTACAAT
33915 CGAAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.32
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATTG
Found at i:33979 original size:16 final size:15
Alignment explanation
Indices: 33952--33981 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
33942 GTACTTTTAT
33952 ATATAGTATAGATAA
1 ATATAGTATAGATAA
33967 ATATAGATATAGATA
1 ATATAG-TATAGATA
33982 GTAAGATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (15 bp):
ATATAGTATAGATAA
Found at i:35533 original size:2 final size:2
Alignment explanation
Indices: 35526--35564 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35516 ATATGCATGC
35526 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
35565 AATTTGACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41485 original size:21 final size:22
Alignment explanation
Indices: 41450--41491 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
41440 GTCGTTTTTT
41450 GGGTTGGGTCAGGTTCGGTTTC
1 GGGTTGGGTCAGGTTCGGTTTC
*
41472 GGGTTGGG-CAGGTTGGGTTT
1 GGGTTGGGTCAGGTTCGGTTT
41492 GTTAACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.05, C:0.10, G:0.50, T:0.36
Consensus pattern (22 bp):
GGGTTGGGTCAGGTTCGGTTTC
Found at i:42241 original size:34 final size:30
Alignment explanation
Indices: 42098--42280 Score: 133
Period size: 27 Copynumber: 6.4 Consensus size: 30
42088 TACTCCCTTT
*
42098 TTACCATTTTC-TAC-CTTCTTCTTTTACTAA
1 TTACCATTTTCTTACTC-TCTT-TTTTACTGA
42128 TTACC--TTTCTTA--CTC-TTTTTACTGA
1 TTACCATTTTCTTACTCTCTTTTTTACTGA
* *
42153 TTACCATTTTCCTA--C-CTTTTTTACCGA
1 TTACCATTTTCTTACTCTCTTTTTTACTGA
* * * *
42180 ATACCATTTT-TTA--CTCTTATCTGCTGA
1 TTACCATTTTCTTACTCTCTTTTTTACTGA
*
42207 TTACCATTTTCTTACTCTTTTTTTTTTCTACTGA
1 TTACCATTTTCTTACTC---TCTTTTT-TACTGA
*
42241 TTACCATTCT-TTACTCTCTTTTTTACTGA
1 TTACCATTTTCTTACTCTCTTTTTTACTGA
42270 TTACCATTTTC
1 TTACCATTTTC
42281 ACTTTACTGA
Statistics
Matches: 123, Mismatches: 17, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
25 13 0.11
26 5 0.04
27 44 0.36
28 8 0.07
29 17 0.14
30 12 0.10
33 10 0.08
34 14 0.11
ACGTcount: A:0.18, C:0.25, G:0.03, T:0.54
Consensus pattern (30 bp):
TTACCATTTTCTTACTCTCTTTTTTACTGA
Found at i:42286 original size:21 final size:21
Alignment explanation
Indices: 42262--42308 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
42252 TACTCTCTTT
*
42262 TTTACTGATTACCATTTTCAC
1 TTTACTGATTACCATTTACAC
* *
42283 TTTACTGATTACTATTTACTC
1 TTTACTGATTACCATTTACAC
42304 TTTAC
1 TTTAC
42309 CATTTTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTACTGATTACCATTTACAC
Found at i:42308 original size:14 final size:14
Alignment explanation
Indices: 42291--42640 Score: 82
Period size: 14 Copynumber: 25.1 Consensus size: 14
42281 ACTTTACTGA
42291 TTACTATTTACTCT
1 TTACTATTTACTCT
* *
42305 TTACCATTTTACTTT
1 TTACTA-TTTACTCT
42320 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
* *
42334 TCA-T-TTTACTTT
1 TTACTATTTACTCT
42346 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
* * *
42360 TCA-T-TTTTCTTT
1 TTACTATTTACTCT
*
42372 TTA-TCATCTTACTCC
1 TTACT-AT-TTACTCT
*
42387 TTACGGA-TTACTCT
1 TTAC-TATTTACTCT
*
42401 TTACTTTTTAC-CATT
1 TTACTATTTACTC--T
* *
42416 TTACTTTTTACT-G
1 TTACTATTTACTCT
* * *
42429 ATACTCTTTAACATTT
1 TTACTATTT-AC-TCT
**
42445 TTACT-TTTACTGA
1 TTACTATTTACTCT
*
42458 TTACTCTTTACT-T
1 TTACTATTTACTCT
* **
42471 TTCACCATTTACTGA
1 TT-ACTATTTACTCT
42486 TTA-TCA-TTACTCT
1 TTACT-ATTTACTCT
* **
42499 TTACTAATTACTGA
1 TTACTATTTACTCT
*
42513 TTACTAATTACTCT
1 TTACTATTTACTCT
* * **
42527 TTGCTCTTTACTGA
1 TTACTATTTACTCT
*
42541 TTACTCTTTACTCT
1 TTACTATTTACTCT
* *
42555 TTGCTCTTTACTCT
1 TTACTATTTACTCT
* **
42569 TTACCATTTACTGA
1 TTACTATTTACTCT
* *
42583 TTACCA-TTACTCC
1 TTACTATTTACTCT
* **
42596 TTACTGTTTACTGA
1 TTACTATTTACTCT
* * * *
42610 TTACCAATCACTTT
1 TTACTATTTACTCT
42624 TTACTATTTTACTCT
1 TTACTA-TTTACTCT
42639 TT
1 TT
42641 TTAACTGAAC
Statistics
Matches: 242, Mismatches: 67, Indels: 53
0.67 0.19 0.15
Matches are distributed among these distances:
12 16 0.07
13 37 0.15
14 140 0.58
15 43 0.18
16 6 0.02
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (14 bp):
TTACTATTTACTCT
Found at i:42385 original size:27 final size:26
Alignment explanation
Indices: 42260--42374 Score: 124
Period size: 26 Copynumber: 4.2 Consensus size: 26
42250 TTTACTCTCT
* *
42260 TTTTTACTGATTACCATTTTCACTTTAC
1 TTTTTACTGATTA-C-TCTTCATTTTAC
**
42288 TGATTACT-ATTTACTCTTTACCATTTTAC
1 TTTTTACTGA-TTACTC-TT--CATTTTAC
42317 TTTTTACTGATTACTCTTCATTTTAC
1 TTTTTACTGATTACTCTTCATTTTAC
*
42343 TTTTTACTGATTACTCTTCATTTTTC
1 TTTTTACTGATTACTCTTCATTTTAC
42369 TTTTTA
1 TTTTTA
42375 TCATCTTACT
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
26 40 0.53
27 4 0.05
28 11 0.15
29 19 0.25
30 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.03, T:0.57
Consensus pattern (26 bp):
TTTTTACTGATTACTCTTCATTTTAC
Found at i:42462 original size:35 final size:35
Alignment explanation
Indices: 42270--42462 Score: 116
Period size: 36 Copynumber: 5.6 Consensus size: 35
42260 TTTTTACTGA
* *
42270 TTACCATTTTCACT--TTACTGATTACTATTTACTCT
1 TTACCATTTT-ACTGATTACTGA-TACTCTTTACTTT
** *
42305 TTACCATTTTACTTTTTACTGATTACTC-TT-CATT
1 TTACCATTTTACTGATTACTGA-TACTCTTTACTTT
* * * *
42339 TTA-CTTTTTACTGATTACT-CTTCAT-TTTTCTTT
1 TTACCATTTTACTGATTACTGATAC-TCTTTACTTT
* * ** *
42372 TTATCATCTTACTCCTTACGGATTACTCTTTACTTT
1 TTACCATTTTACTGATTACTGA-TACTCTTTACTTT
**
42408 TTACCATTTTACTTTTTACTGATACTCTTTAACATTT
1 TTACCATTTTACTGATTACTGATACTCTTT-AC-TTT
42445 TTA-C-TTTTACTGATTACT
1 TTACCATTTTACTGATTACT
42463 CTTTACTTTT
Statistics
Matches: 123, Mismatches: 24, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
31 2 0.02
32 3 0.02
33 19 0.15
34 19 0.15
35 33 0.27
36 41 0.33
37 6 0.05
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.55
Consensus pattern (35 bp):
TTACCATTTTACTGATTACTGATACTCTTTACTTT
Found at i:42552 original size:28 final size:28
Alignment explanation
Indices: 42415--42566 Score: 152
Period size: 28 Copynumber: 5.5 Consensus size: 28
42405 TTTTTACCAT
* *
42415 TTTACTTTTTACTGA-TACTCTTTAACATT
1 TTTACTCTTTACTGATTACTCTTT-AC-TC
42444 TTTACT-TTTACTGATTACTCTTTACT-
1 TTTACTCTTTACTGATTACTCTTTACTC
*
42470 TTTCAC-CATTTACTGATTA-TCATTACTC
1 TTT-ACTC-TTTACTGATTACTCTTTACTC
** **
42498 TTTACTAATTACTGATTACTAATTACTC
1 TTTACTCTTTACTGATTACTCTTTACTC
*
42526 TTTGCTCTTTACTGATTACTCTTTACTC
1 TTTACTCTTTACTGATTACTCTTTACTC
*
42554 TTTGCTCTTTACT
1 TTTACTCTTTACT
42567 CTTTACCATT
Statistics
Matches: 107, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.03
27 22 0.21
28 68 0.64
29 14 0.13
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.53
Consensus pattern (28 bp):
TTTACTCTTTACTGATTACTCTTTACTC
Found at i:42599 original size:27 final size:27
Alignment explanation
Indices: 42562--42615 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
42552 TCTTTGCTCT
*
42562 TTACTCTTTACCATTTACTGATTACCA
1 TTACTCCTTACCATTTACTGATTACCA
**
42589 TTACTCCTTACTGTTTACTGATTACCA
1 TTACTCCTTACCATTTACTGATTACCA
42616 ATCACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (27 bp):
TTACTCCTTACCATTTACTGATTACCA
Found at i:42608 original size:7 final size:7
Alignment explanation
Indices: 42394--42607 Score: 84
Period size: 7 Copynumber: 30.7 Consensus size: 7
42384 TCCTTACGGA
42394 TTACTCT
1 TTACTCT
*
42401 TTACTTT
1 TTACTCT
42408 TTAC-CATT
1 TTACTC--T
*
42416 TTACTTT
1 TTACTCT
*
42423 TTACT-G
1 TTACTCT
*
42429 ATACTCT
1 TTACTCT
*
42436 TTAACATTT
1 TT-AC-TCT
42445 TTACT-T
1 TTACTCT
**
42451 TTACTGA
1 TTACTCT
42458 TTACTCT
1 TTACTCT
42465 TTACT-T
1 TTACTCT
42471 TTCAC-CAT
1 TT-ACTC-T
**
42479 TTACTGA
1 TTACTCT
*
42486 TTA-TCA
1 TTACTCT
42492 TTACTCT
1 TTACTCT
**
42499 TTACTAA
1 TTACTCT
**
42506 TTACTGA
1 TTACTCT
**
42513 TTACTAA
1 TTACTCT
42520 TTACTCT
1 TTACTCT
*
42527 TTGCTCT
1 TTACTCT
**
42534 TTACTGA
1 TTACTCT
42541 TTACTCT
1 TTACTCT
42548 TTACTCT
1 TTACTCT
*
42555 TTGCTCT
1 TTACTCT
42562 TTACTCT
1 TTACTCT
42569 TTAC-CAT
1 TTACTC-T
**
42576 TTACTGA
1 TTACTCT
*
42583 TTAC-CA
1 TTACTCT
*
42589 TTACTCC
1 TTACTCT
*
42596 TTACTGT
1 TTACTCT
42603 TTACT
1 TTACT
42608 GATTACCAAT
Statistics
Matches: 157, Mismatches: 35, Indels: 30
0.71 0.16 0.14
Matches are distributed among these distances:
6 24 0.15
7 117 0.75
8 12 0.08
9 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.52
Consensus pattern (7 bp):
TTACTCT
Found at i:49589 original size:150 final size:150
Alignment explanation
Indices: 49318--49605 Score: 567
Period size: 150 Copynumber: 1.9 Consensus size: 150
49308 AAAATAGTAC
49318 TAATAGGTATCACTTAGTTAATTTCAATCACTAATGTAAGTTTGTGTTTACCTTTTGCTTCCATT
1 TAATAGGTATCACTTAGTTAATTTCAATCACTAATGTAAGTTTGTGTTTACCTTTTGCTTCCATT
*
49383 ATTAATAAGTTCGATTAGGAATCAATACTAATGAAATAATAATAGCAGTAACTAATTGACCAAAA
66 ATTAATAAGTTAGATTAGGAATCAATACTAATGAAATAATAATAGCAGTAACTAATTGACCAAAA
49448 AGTGATTGTGTACCTATTAG
131 AGTGATTGTGTACCTATTAG
49468 TAATAGGTATCACTTAGTTAATTTCAATCACTAATGTAAGTTTGTGTTTACCTTTTGCTTCCATT
1 TAATAGGTATCACTTAGTTAATTTCAATCACTAATGTAAGTTTGTGTTTACCTTTTGCTTCCATT
49533 ATTAATAAGTTAGATTAGGAATCAATACTAATGAAATAATAATAGCAGTAACTAATTGACCAAAA
66 ATTAATAAGTTAGATTAGGAATCAATACTAATGAAATAATAATAGCAGTAACTAATTGACCAAAA
49598 AGTGATTG
131 AGTGATTG
49606 CTAACATATA
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 137 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (150 bp):
TAATAGGTATCACTTAGTTAATTTCAATCACTAATGTAAGTTTGTGTTTACCTTTTGCTTCCATT
ATTAATAAGTTAGATTAGGAATCAATACTAATGAAATAATAATAGCAGTAACTAATTGACCAAAA
AGTGATTGTGTACCTATTAG
Found at i:53524 original size:18 final size:18
Alignment explanation
Indices: 53491--53526 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53481 ATGCCTACGT
*
53491 CCTCGGATAATGCTACTA
1 CCTCGGATAATACTACTA
*
53509 CCTCGGATAGTACTACTA
1 CCTCGGATAATACTACTA
53527 AATCATATTT
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:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
CCTCGGATAATACTACTA
Found at i:55070 original size:12 final size:12
Alignment explanation
Indices: 55053--55077 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55043 TTGAAAAACC
55053 ATTCATTGTATT
1 ATTCATTGTATT
55065 ATTCATTGTATT
1 ATTCATTGTATT
55077 A
1 A
55078 CAAAATGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTCATTGTATT
Found at i:60285 original size:56 final size:54
Alignment explanation
Indices: 60207--60334 Score: 167
Period size: 52 Copynumber: 2.4 Consensus size: 54
60197 TTAATAGTTC
* *
60207 ATATAAATCATAAAAAACAAATAAATAAATATAATAAATTGCATATTAATTCGTA
1 ATATAAATCATAAAAAA-AAATAAATAAATATAATAAATCGCATAATAATTCGTA
*
60262 ATCATAAATCAT---AAAAAATAAATAAATATAATAAATCGCATAATAATTTGTA
1 AT-ATAAATCATAAAAAAAAATAAATAAATATAATAAATCGCATAATAATTCGTA
*
60314 ATAT-AA-CATAAAAAAATATAA
1 ATATAAATCATAAAAAAAAATAA
60335 TCTTCATCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
49 3 0.05
50 2 0.03
51 2 0.03
52 44 0.68
53 3 0.05
55 2 0.03
56 9 0.14
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (54 bp):
ATATAAATCATAAAAAAAAATAAATAAATATAATAAATCGCATAATAATTCGTA
Found at i:63792 original size:16 final size:16
Alignment explanation
Indices: 63771--63836 Score: 132
Period size: 16 Copynumber: 4.1 Consensus size: 16
63761 AATGATCTGT
63771 AATGACCCGAACCCGA
1 AATGACCCGAACCCGA
63787 AATGACCCGAACCCGA
1 AATGACCCGAACCCGA
63803 AATGACCCGAACCCGA
1 AATGACCCGAACCCGA
63819 AATGACCCGAACCCGA
1 AATGACCCGAACCCGA
63835 AA
1 AA
63837 AACCGAGGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.39, C:0.36, G:0.18, T:0.06
Consensus pattern (16 bp):
AATGACCCGAACCCGA
Found at i:63925 original size:15 final size:17
Alignment explanation
Indices: 63890--63927 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
63880 AACCGAAAGC
63890 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
63906 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
63921 GACCCGA
1 GACCCGA
63928 CATTTGAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:65093 original size:42 final size:40
Alignment explanation
Indices: 64999--65134 Score: 129
Period size: 42 Copynumber: 3.3 Consensus size: 40
64989 ATTTGTACAT
* *
64999 ATGC-TCATACATGCATTAGT-CAGTCACTTGTATATATG--
1 ATGCATCAT-CATGCATTA-TCCATTCATTTGTATATATGTC
*
65037 ATGCATTCATCATGCATTGTCCATCTC-TTTGTATATATGTTC
1 ATGCA-TCATCATGCATTATCCAT-TCATTTGTATATATG-TC
*
65079 ATGCATCGATCATGCATTATCCATTCATTAGTATATATGCTC
1 ATGCATC-ATCATGCATTATCCATTCATTTGTATATATG-TC
65121 ATGCATCCATCATG
1 ATGCAT-CATCATG
65135 TCATCACTTG
Statistics
Matches: 82, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
38 5 0.06
39 21 0.26
40 6 0.07
41 4 0.05
42 45 0.55
43 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (40 bp):
ATGCATCATCATGCATTATCCATTCATTTGTATATATGTC
Found at i:66925 original size:16 final size:15
Alignment explanation
Indices: 66904--66966 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 15
66894 CATTCAACTC
66904 AAAGAAAAGAAAAAAG
1 AAAGAAAA-AAAAAAG
*
66920 AAAGAAAAAAAAAGGG
1 AAAGAAAAAAAAA-AG
* *
66936 AGAGAGAAAGAAAAAG
1 AAAGA-AAAAAAAAAG
66952 AAAGGAAAAAAAAAA
1 AAA-GAAAAAAAAAA
66967 CTCAGCCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.13
16 24 0.63
17 9 0.24
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:68373 original size:70 final size:70
Alignment explanation
Indices: 68286--68814 Score: 647
Period size: 70 Copynumber: 7.7 Consensus size: 70
68276 ATTTTCAAGA
* *
68286 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCATAAGTCAAACTCGTTTCCATACGAG
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
68351 AT-AGT
66 -TCAGT
* * *
68356 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCATAAGTCAAACTCGTTGCCATACGAG
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
68421 AT-AGT
66 -TCAGT
* * * *
68426 TCAAGTTTTGGTTCCATCCAAACATGCAGGGGCTTTTCCACAAGTCAAACTCGTTTCCATATGAG
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
68491 TCAGT
66 TCAGT
*
68496 TCAAGGC-TTGGTTCCATCCAAGC-TGC-AGCGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
1 TCAA-GCTTTGGTTCCATCCAAACATGCAAG-GGCTTTTCCACAAGCCAAACTCGTTTCCATACG
68558 AGTCAGT
64 AGTCAGT
* *
68565 TCAAACTTTGGTTCCATCCAAGTAC-T-CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
1 TCAAGCTTTGGTTCCATCCAA--ACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
68628 AGTCAGT
64 AGTCAGT
* * * *
68635 TCAAGCCTTGGTTCCATCCAAGCA-GCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAG
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
*
68699 TCAAT
66 TCAGT
* * * * * *
68704 TTAGGCTTT-GTTCCATCCAAGCA-GTAAGGGCTTTTCCACTAGCCAAACTCGTTTCCATATGAG
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
*
68767 TTAGT
66 TCAGT
* * * *
68772 T-TAGCCTTGGTTCCATCC--A-A-GCAGGGGCTTTTCCATAAGCCAA
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAA
68815 GTTAATTTCC
Statistics
Matches: 412, Mismatches: 37, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
65 20 0.05
67 4 0.01
68 65 0.16
69 108 0.26
70 211 0.51
71 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (70 bp):
TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
TCAGT
Found at i:68595 original size:139 final size:139
Alignment explanation
Indices: 68286--68814 Score: 691
Period size: 139 Copynumber: 3.8 Consensus size: 139
68276 ATTTTCAAGA
* *
68286 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCATAAGTCAAACTCGTTTCCATACGAG
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
* * * * * *
68351 AT-AGTTCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCATAAGTCAAACTCGTTGCCA
66 -TCAGTTCAAGCCTTGGTTCCATCCAAGC-TGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCA
68415 TACGAGAT-AGT
129 TACGAG-TCAGT
* * * *
68426 TCAAGTTTTGGTTCCATCCAAACATGCAGGGGCTTTTCCACAAGTCAAACTCGTTTCCATATGAG
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
* *
68491 TCAGTTCAAGGCTTGGTTCCATCCAAGCTGCAGCGGCTTTTCCACAAGCCAAACTCGTTTCCATA
66 TCAGTTCAAGCCTTGGTTCCATCCAAGCTGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATA
68556 CGAGTCAGT
131 CGAGTCAGT
* *
68565 TCAAACTTTGGTTCCATCCAAGTAC-T-CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
1 TCAAGCTTTGGTTCCATCCAA--ACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
*
68628 AGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCA
64 AGTCAGTTCAAGCCTTGGTTCCATCCAAGCTGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCA
* *
68693 CACGAGTCAAT
129 TACGAGTCAGT
* * * * * *
68704 TTAGGCTTT-GTTCCATCCAAGCA-GTAAGGGCTTTTCCACTAGCCAAACTCGTTTCCATATGAG
1 TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
* * *
68767 TTAGTT-TAGCCTTGGTTCCATCCAA---GCAGGGGCTTTTCCATAAGCCAA
66 TCAGTTCAAGCCTTGGTTCCATCCAAGCTGCAGGGGCTTTTCCACAAGCCAA
68815 GTTAATTTCC
Statistics
Matches: 351, Mismatches: 32, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
133 22 0.06
136 19 0.05
137 40 0.11
138 12 0.03
139 171 0.49
140 85 0.24
141 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (139 bp):
TCAAGCTTTGGTTCCATCCAAACATGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG
TCAGTTCAAGCCTTGGTTCCATCCAAGCTGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATA
CGAGTCAGT
Found at i:69062 original size:19 final size:20
Alignment explanation
Indices: 69038--69080 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
69028 AGTCCTTTAA
69038 AAAAAAGGAAAAAGAAA-TG
1 AAAAAAGGAAAAAGAAAGTG
* *
69057 AAAAAATGAAAATGAAAGTG
1 AAAAAAGGAAAAAGAAAGTG
69077 AAAA
1 AAAA
69081 TGAATGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (20 bp):
AAAAAAGGAAAAAGAAAGTG
Found at i:71600 original size:22 final size:22
Alignment explanation
Indices: 71567--71620 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
71557 CCATTCATGA
*
71567 GAGAGAGGGAGAATCCAAGTGT
1 GAGAGAGTGAGAATCCAAGTGT
*
71589 GAGCGAGTGAGAATCCAAGTGT
1 GAGAGAGTGAGAATCCAAGTGT
71611 GAGAGAGTGA
1 GAGAGAGTGA
71621 TGAGGAATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.09, G:0.41, T:0.15
Consensus pattern (22 bp):
GAGAGAGTGAGAATCCAAGTGT
Found at i:73319 original size:27 final size:27
Alignment explanation
Indices: 73270--73361 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
73260 AAATGACCTG
* *
73270 AATGCCCCCTAAATGCAAGAATGACAAA
1 AATG-CCCCTAAATGTAAAAATGACAAA
*
73298 AATGCCCCTAAATGTAAAAATGAAAAA
1 AATGCCCCTAAATGTAAAAATGACAAA
* * *
73325 AATGCCCCTGAATGTAAAATTGACCAA
1 AATGCCCCTAAATGTAAAAATGACAAA
73352 AATGCCCCTA
1 AATGCCCCTA
73362 GGTGACCTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 52 0.93
28 4 0.07
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (27 bp):
AATGCCCCTAAATGTAAAAATGACAAA
Done.