Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017902.1 Corchorus olitorius cultivar O-4 contig17935, 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: 62648
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:53 original size:18 final size:18
Alignment explanation
Indices: 42--86 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
32 TTTTAGATTT
42 TCTTTTAATTTTATTTTA
1 TCTTTTAATTTTATTTTA
60 TCTTTTAATTTTATTTTA
1 TCTTTTAATTTTATTTTA
78 TCTTTTAAT
1 TCTTTTAAT
87 AAGTATTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTTTAATTTTATTTTA
Found at i:59 original size:31 final size:29
Alignment explanation
Indices: 19--77 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
9 TTTCTGCGCT
* *
19 TTTTTTTTTATCTTTTTAGATTTTCTTTTAA
1 TTTTATTTTATC-TTTTA-ATTTTATTTTAA
50 TTTTATTTTATCTTTTAATTTTATTTTA
1 TTTTATTTTATCTTTTAATTTTATTTTA
78 TCTTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 5 0.19
31 11 0.42
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTTATTTTATCTTTTAATTTTATTTTAA
Found at i:1463 original size:434 final size:434
Alignment explanation
Indices: 650--1654 Score: 1181
Period size: 434 Copynumber: 2.3 Consensus size: 434
640 TTTCAAAAGT
* * * * *
650 ATTTTTTAGAATTGAAATATAAAAATTAGCTTTTGAGTCTTTCATGAAAGTTGTAGACCATCAAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTC-TTCATAAAAGTTGTAGATCATGAAA
* * * * **
715 TTACTTTTTAATAGACACCTGAATTATCTTAATTAGACAAATAGAATAAAGAAAATAAAAAAAAT
65 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAATAAAG-AAAT--AAAAAAT
* *
780 GAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATATAAAATAGAAA
127 GAAGCGTTAAATCGAGTAAAATAGAATTTATAAAGGACTAAGTAG------ATATAAAATAGAAA
* * * *
845 AGTATGAGAGTCATTTGATAACTAATTCAAATAAGAAAATATTTCTTAATCGATATCTTGAAACA
186 AATATGAGAGTCATTTGATAAATAATTCAAATAAGAAAATATTTCTCAATCGAGATCTT-AAACA
* * * *
910 TAAAAATTCCCTTTTGAATCCTTCATGAAACTCATAGATCAAATTAACTTTCGAGTTCTTCATGA
250 TAAAAACTCCCGTTTGAACCCTTCATGAAACTCATAGATCAAATTAACTTTCGAGTCCTTCATGA
* * * *
975 AAGTCGTAGATCATACAGTAACCTTTTAACCGACACTTGAATAATTATAATCGGACATGTGGATC
315 AAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAATTACAATCGGACATGTGGA-C
* * * * * *
1040 -GAAAATTATATGGTATTAAATAGACCAACAATTAAAACGACTAAATTTAGGAAGC
379 AAAAAATTATACGATATTAAATAGACCAACAAATAAAACCACAAAATTTAGGAAGC
* * * *
1095 ATTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCGTTCATAAAAGTCGTAGATTATGAAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTC-TTCATAAAAGTTGTAGATCATGAAA
* *
1160 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAATAAAG-AAT-AAAAGTTAA
65 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAATAAAGAAATAAAAAATGAA
* *
1223 GTC-TTAAA-CGTTAGATTAAAATATAATTTATGAAGGACTAAGTAG-TATAAAATAGAAAAATA
130 G-CGTTAAATCG--AG--TAAAATAGAATTTATAAAGGACTAAGTAGATATAAAATAGAAAAATA
* * * *
1285 TGAGGGTCATTTGATAAATAA-TCTAAATAAGAAAATGTTTGTCAATGGAGATCTT-AACATAAA
190 TGAGAGTCATTTGATAAATAATTC-AAATAAGAAAATATTTCTCAATCGAGATCTTAAACATAAA
* ** *
1348 AACTCCCGTTTGAACCCTTCATGAAACTCGTAGATC-AATGTAGTTTTCGGGTCCTTCATGAAAG
254 AACTCCCGTTTGAACCCTTCATGAAACTCATAGATCAAAT-TAACTTTCGAGTCCTTCATGAAAG
*
1412 TCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTT-CAATCGGACATGTGGACAAA
318 TCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAA-TTACAATCGGACATGTGGACAAA
* ** *
1476 AAATTATACGATATTAAATTGACCGGCAAATAAAACCACAAAATTTTGGAAGC
382 AAATTATACGATATTAAATAGACCAACAAATAAAACCACAAAATTTAGGAAGC
* * *
1529 ATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAA-TTGTAGATCATGAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAG-TCTTCAT-AAAAGTTGTAGATCATGAA
* * *
1593 ATTACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGGA-AAA-AAATACAAAAAT
64 ATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAATAAAGAAATA-AAAAAT
1655 AAATGGGAAC
Statistics
Matches: 483, Mismatches: 63, Indels: 38
0.83 0.11 0.07
Matches are distributed among these distances:
433 10 0.02
434 251 0.52
435 15 0.03
436 61 0.13
439 2 0.00
440 13 0.03
441 3 0.01
443 28 0.06
445 100 0.21
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (434 bp):
ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCTTCATAAAAGTTGTAGATCATGAAAT
TACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAATAAAGAAATAAAAAATGAAG
CGTTAAATCGAGTAAAATAGAATTTATAAAGGACTAAGTAGATATAAAATAGAAAAATATGAGAG
TCATTTGATAAATAATTCAAATAAGAAAATATTTCTCAATCGAGATCTTAAACATAAAAACTCCC
GTTTGAACCCTTCATGAAACTCATAGATCAAATTAACTTTCGAGTCCTTCATGAAAGTCGTAAAT
CATACAATAACCTTTTAACCGACACTTCAATAATTACAATCGGACATGTGGACAAAAAATTATAC
GATATTAAATAGACCAACAAATAAAACCACAAAATTTAGGAAGC
Found at i:3657 original size:22 final size:22
Alignment explanation
Indices: 3632--3688 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
3622 AATTGAATGG
3632 GACAAATTTGCAACTTAATGAA
1 GACAAATTTGCAACTTAATGAA
*
3654 GACAAATTTACAACTTAATGAA
1 GACAAATTTGCAACTTAATGAA
* *
3676 TACAGATTTGCAA
1 GACAAATTTGCAA
3689 TTCATTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (22 bp):
GACAAATTTGCAACTTAATGAA
Found at i:5528 original size:12 final size:13
Alignment explanation
Indices: 5513--5545 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5503 GGCTAAAACT
*
5513 AAAAGAAAAA-TG
1 AAAAGAAAAATTA
5525 AAAAGAAAAATTA
1 AAAAGAAAAATTA
5538 AAAAGAAA
1 AAAAGAAA
5546 GGAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (13 bp):
AAAAGAAAAATTA
Found at i:7332 original size:19 final size:19
Alignment explanation
Indices: 7308--7345 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7298 GAGAAAGAGT
*
7308 AAACACAAAATTATAAAAA
1 AAACACAAAAATATAAAAA
7327 AAACACAAAAATATAAAAA
1 AAACACAAAAATATAAAAA
7346 GTGTCTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (19 bp):
AAACACAAAAATATAAAAA
Found at i:8722 original size:43 final size:45
Alignment explanation
Indices: 8668--8755 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
8658 CATATTTTAG
* *
8668 ATCTTTTCTCTTTGTTT-C-TTTTTCTTATTTCTATAGTGGAGAT
1 ATCTTTCCTCTTTCTTTCCTTTTTTCTTATTTCTATAGTGGAGAT
*
8711 ATCTTTCCTCTTTCTTTCCTTTTTTTTTTATTTCTATAGTGGAGA
1 ATCTTTCCTCTTTCTTTCC-TTTTTTCTTATTTCTATAGTGGAGA
8756 ATGACAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 15 0.38
44 1 0.03
46 23 0.59
ACGTcount: A:0.14, C:0.16, G:0.10, T:0.60
Consensus pattern (45 bp):
ATCTTTCCTCTTTCTTTCCTTTTTTCTTATTTCTATAGTGGAGAT
Found at i:9650 original size:6 final size:6
Alignment explanation
Indices: 9641--9684 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
9631 GCTGAAGCAG
* * *
9641 AGGCTA AGGCTC AGGCAA AAGCTA AGGCTA AGGCTA AGGCTA AG
1 AGGCTA AGGCTA AGGCTA AGGCTA AGGCTA AGGCTA AGGCTA AG
9685 CCTCGCAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.32, T:0.14
Consensus pattern (6 bp):
AGGCTA
Found at i:10057 original size:27 final size:27
Alignment explanation
Indices: 10027--10097 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 27
10017 ATTCAAAACA
*
10027 AGGACGGTGTCGAATGTACTGATGACG
1 AGGACGGTGTCGAATGTACTGAAGACG
* *
10054 AGGACGGTGTTGAATCATGTACTGAAGAGG
1 AGGACGGTGTCG-A--ATGTACTGAAGACG
*
10084 AGGACTGTGTCGAA
1 AGGACGGTGTCGAA
10098 AGCATTGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
27 12 0.33
28 1 0.03
29 1 0.03
30 22 0.61
ACGTcount: A:0.28, C:0.13, G:0.37, T:0.23
Consensus pattern (27 bp):
AGGACGGTGTCGAATGTACTGAAGACG
Found at i:12615 original size:19 final size:20
Alignment explanation
Indices: 12573--12619 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
12563 TTTAATCTAA
12573 GATTA-AAAAAAACTATAAT
1 GATTATAAAAAAACTATAAT
* *
12592 GATTATAAAAAAAGTATAGT
1 GATTATAAAAAAACTATAAT
12612 -ATTATAAA
1 GATTATAAA
12620 CTACTATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
GATTATAAAAAAACTATAAT
Found at i:12835 original size:100 final size:100
Alignment explanation
Indices: 12656--12858 Score: 325
Period size: 100 Copynumber: 2.0 Consensus size: 100
12646 TTGGTTATCA
** *
12656 AATCAAATTTCTTACTTATAGTTATGCAGTAAATAACTTTCATCAATGATCAAGGTTATCAATTT
1 AATCAAATTTCTTACTTATAGTTACACAGTAAATAACTTTCATCAATGATCAAAGTTATCAATTT
*
12721 TTTATCTAAGGGGGGGGGGGACCTAACACTAAATT
66 TTTATCTAAGGGGGGGGGGGAACTAACACTAAATT
* *
12756 AATCAAATTTCTTACTTATAGTTACACAGTAAATAACTTTCATCAGTGATCAAATTTATCAATTT
1 AATCAAATTTCTTACTTATAGTTACACAGTAAATAACTTTCATCAATGATCAAAGTTATCAATTT
12821 TTTATCGTAAGGGGGGGGGGGGGAACTAACACTAAATT
66 TTTATC-TAA--GGGGGGGGGGGAACTAACACTAAATT
12859 TCAATACAGG
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
100 66 0.70
101 3 0.03
103 25 0.27
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (100 bp):
AATCAAATTTCTTACTTATAGTTACACAGTAAATAACTTTCATCAATGATCAAAGTTATCAATTT
TTTATCTAAGGGGGGGGGGGAACTAACACTAAATT
Found at i:16043 original size:39 final size:39
Alignment explanation
Indices: 15999--16076 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
15989 GACTACAAGA
*
15999 TTTTTCAATATTTCTAACATATATTTAATGGTGGAAAAT
1 TTTTTCAATAGTTCTAACATATATTTAATGGTGGAAAAT
*
16038 TTTTTCAATAGTTCTAACATATATTTAATGGTGGTAAAT
1 TTTTTCAATAGTTCTAACATATATTTAATGGTGGAAAAT
16077 ATAACGCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (39 bp):
TTTTTCAATAGTTCTAACATATATTTAATGGTGGAAAAT
Found at i:16412 original size:106 final size:99
Alignment explanation
Indices: 16227--16428 Score: 314
Period size: 106 Copynumber: 2.0 Consensus size: 99
16217 ATAATAAAGA
*
16227 ATCAAATTTTACATTTATGATCCATTTAATAGGAGTATTCCTGTTGATTTTTTAAAATATTAATC
1 ATCAAATTTTACATTTATGATACATTTAATAGGAGTATTCCTGTTGATTTTTTAAAATATTAATC
*
16292 CTAGATTAAGTTACAAAAGGGTGTAAAAAGTTGG
66 CTAGATTAAGTTACAAAAGAGTGTAAAAAGTTGG
16326 ATCAAATTTTACATTTATGATACATTTAATAGGAGTATTCAATCTAACTGTTGATTTTTTAAAAT
1 ATCAAATTTTACATTTATGATACATTTAATAGGAGTA-T---TC---CTGTTGATTTTTTAAAAT
*
16391 ATTAATCCTAGGTTAAGTTACAAAAGAGTGTAAAAAGT
59 ATTAATCCTAGATTAAGTTACAAAAGAGTGTAAAAAGT
16429 CTTAAATCTA
Statistics
Matches: 93, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
99 36 0.39
100 1 0.01
103 2 0.02
106 54 0.58
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (99 bp):
ATCAAATTTTACATTTATGATACATTTAATAGGAGTATTCCTGTTGATTTTTTAAAATATTAATC
CTAGATTAAGTTACAAAAGAGTGTAAAAAGTTGG
Found at i:19927 original size:2 final size:2
Alignment explanation
Indices: 19920--19948 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19910 AATAAAAACT
19920 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
19949 TATAGTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:34903 original size:8 final size:7
Alignment explanation
Indices: 34881--34921 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
34871 ATGCAAATAT
*
34881 AAAAGAT
1 AAAAGAA
34888 AAAAGAA
1 AAAAGAA
34895 AATAAG-A
1 AA-AAGAA
34902 AAAAGAA
1 AAAAGAA
34909 AAAAGAA
1 AAAAGAA
34916 AAAAGA
1 AAAAGA
34922 GAGGAGGGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (7 bp):
AAAAGAA
Found at i:34906 original size:21 final size:20
Alignment explanation
Indices: 34881--34921 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
34871 ATGCAAATAT
*
34881 AAAAGATAAAAGAAAATAAGA
1 AAAAGAAAAAAGAAAA-AAGA
34902 AAAAGAAAAAAGAAAAAAGA
1 AAAAGAAAAAAGAAAAAAGA
34922 GAGGAGGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAAAGAAAAAAGA
Found at i:43463 original size:59 final size:59
Alignment explanation
Indices: 43382--43497 Score: 223
Period size: 59 Copynumber: 2.0 Consensus size: 59
43372 AATTTACTGA
43382 TTGGGCTTTATAAGTGTCTTCTTAATGGGCCTCAACAAATACTTTGGAAATTTGGAAAT
1 TTGGGCTTTATAAGTGTCTTCTTAATGGGCCTCAACAAATACTTTGGAAATTTGGAAAT
*
43441 TTGGGCTTTATAAGTGTTTTCTTAATGGGCCTCAACAAATACTTTGGAAATTTGGAA
1 TTGGGCTTTATAAGTGTCTTCTTAATGGGCCTCAACAAATACTTTGGAAATTTGGAA
43498 TTTTTTTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (59 bp):
TTGGGCTTTATAAGTGTCTTCTTAATGGGCCTCAACAAATACTTTGGAAATTTGGAAAT
Found at i:46690 original size:12 final size:12
Alignment explanation
Indices: 46669--46730 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
46659 TGTTAAAATG
46669 ATTCAAAAGATC
1 ATTCAAAAGATC
* *
46681 ATTTAAAAGATA
1 ATTCAAAAGATC
* *
46693 ATACAAAAGATG
1 ATTCAAAAGATC
* *
46705 ATTTAAAAGATG
1 ATTCAAAAGATC
*
46717 GTTCAAAAGATC
1 ATTCAAAAGATC
46729 AT
1 AT
46731 GGGATCATTG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (12 bp):
ATTCAAAAGATC
Found at i:46701 original size:24 final size:24
Alignment explanation
Indices: 46672--46730 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
46662 TAAAATGATT
46672 CAAAAGATCATTTAAAAGATAATA
1 CAAAAGATCATTTAAAAGATAATA
* ** *
46696 CAAAAGATGATTTAAAAGATGGTT
1 CAAAAGATCATTTAAAAGATAATA
46720 CAAAAGATCAT
1 CAAAAGATCAT
46731 GGGATCATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (24 bp):
CAAAAGATCATTTAAAAGATAATA
Found at i:50670 original size:3 final size:3
Alignment explanation
Indices: 50662--50718 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
50652 TTTGAGACAA
50662 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
50710 ATT A-T ATT A
1 ATT ATT ATT A
50719 AGGTAGTCCC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:51681 original size:17 final size:17
Alignment explanation
Indices: 51659--51692 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
51649 ATTCATCCAC
51659 TAATTAAATATACGCTA
1 TAATTAAATATACGCTA
* *
51676 TAATTAAGTATATGCTA
1 TAATTAAATATACGCTA
51693 AACTTTGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
TAATTAAATATACGCTA
Found at i:53020 original size:203 final size:202
Alignment explanation
Indices: 52403--53018 Score: 1196
Period size: 202 Copynumber: 3.0 Consensus size: 202
52393 TGAATCATGA
*
52403 TTAATGAAAGGGTAATTATTTGATACACCGGTGGTGTAAATTTTGGACTCCACAAGCGGGTTGTG
1 TTAATGAAAGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTG
52468 GAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGG
66 GAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGG
52533 ACACATGTCACCCTTGAAAACCCGCTTGTGTAGTCTGCTAAACTCCACAGCCGGTGTATTGTATA
131 ACACATGTCACCCTTGAAAACCCGCTTGTGTAGTCTGCTAAACTCCACAGCCGGTGTATTGTATA
52598 ATTTGCC
196 ATTTGCC
52605 TTAATGAAAGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTG
1 TTAATGAAAGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTG
52670 GAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGG
66 GAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGG
52735 ACACATGTCACCCTTGAAAACCCGCTTGTGTAGTCTGCTAAACTCCACAGCCGGTGTATTGTATA
131 ACACATGTCACCCTTGAAAACCCGCTTGTGTAGTCTGCTAAACTCCACAGCCGGTGTATTGTATA
52800 ATTTGCC
196 ATTTGCC
52807 TTAATGAAAAGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGT
1 TTAATG-AAAGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGT
52872 GGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAG
65 GGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAG
* *
52937 GACACATGTCACCATTGAAAACCCGCTTGTGTAGTCTGCTAAACTCCACAGCCGATGTATTGTAT
130 GACACATGTCACCCTTGAAAACCCGCTTGTGTAGTCTGCTAAACTCCACAGCCGGTGTATTGTAT
53002 AATTTGCC
195 AATTTGCC
53010 TTAATGAAA
1 TTAATGAAA
53019 AGCCAAGTTT
Statistics
Matches: 410, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
202 210 0.51
203 200 0.49
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (202 bp):
TTAATGAAAGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTG
GAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGG
ACACATGTCACCCTTGAAAACCCGCTTGTGTAGTCTGCTAAACTCCACAGCCGGTGTATTGTATA
ATTTGCC
Found at i:55571 original size:104 final size:103
Alignment explanation
Indices: 55373--55577 Score: 297
Period size: 104 Copynumber: 2.0 Consensus size: 103
55363 AATATCTTTA
* * * *
55373 TAACTATTTTATTTTTATCATTTTACTATTTTAATAAAAAAACTTAGATATATTAGATTTTCTTA
1 TAACTACTTTATTTTTACCATTTTACTATTTTAATAAAAAAACTTAGATATATTAAAATTTCTTA
*
55438 AATATATTTCTTAAATGACATTGTATAAACTTTTACGT
66 AATATATTTCTTAAATGACATTATATAAACTTTTACGT
*
55476 TAACTACTTTATTTTTACCATTTTACTATATTTTTAATTAAAAAACTTAGAT-TATTAAAATTT-
1 TAACTACTTTATTTTTACCATTTTAC--TA-TTTTAATAAAAAAACTTAGATATATTAAAATTTC
**
55539 TTAAATATATTTCTTAAATGGTATTATATAAACTTTTAC
63 TTAAATATATTTCTTAAATGACATTATATAAACTTTTAC
55578 AGTTTTATTC
Statistics
Matches: 91, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
103 24 0.26
104 36 0.40
105 11 0.12
106 20 0.22
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.50
Consensus pattern (103 bp):
TAACTACTTTATTTTTACCATTTTACTATTTTAATAAAAAAACTTAGATATATTAAAATTTCTTA
AATATATTTCTTAAATGACATTATATAAACTTTTACGT
Found at i:56263 original size:22 final size:21
Alignment explanation
Indices: 56238--56789 Score: 230
Period size: 22 Copynumber: 25.3 Consensus size: 21
56228 ATTTCTTATG
56238 ACCTCCTTATGAAATTTTGATA
1 ACCTCC-TATGAAATTTTGATA
* *
56260 ACCTTCTTATGAAATTTTAATA
1 ACC-TCCTATGAAATTTTGATA
* * * *
56282 ACGATACTAT-AGAATTTCGAGA
1 AC-CTCCTATGA-AATTTTGATA
** * **
56304 ACCTTTTTATAAAATTTTTTTA
1 ACC-TCCTATGAAATTTTGATA
* *
56326 ACCCTCTTATGAAATTTTGTTA
1 A-CCTCCTATGAAATTTTGATA
* *
56348 ACCTCCCTAAGGAATTTTGA-A
1 ACCT-CCTATGAAATTTTGATA
56369 GACCTCACTATGAAATTTTGATA
1 -ACCTC-CTATGAAATTTTGATA
** * *
56392 ACAAACACTATGAGATGTTGATA
1 AC-CTC-CTATGAAATTTTGATA
* *
56415 ACCTCCATATGATATATTGATA
1 ACCTCC-TATGAAATTTTGATA
* * * * *
56437 ACCACGTTATGAAAATTTAAAA
1 ACCTC-CTATGAAATTTTGATA
56459 ACCTCCATATG-AATTGTT-AGTA
1 ACCTCC-TATGAAATT-TTGA-TA
* *
56481 A-TTACACTCTGAAATTTTGATA
1 ACCT-C-CTATGAAATTTTGATA
* *
56503 ATCTCGCTATGAAATTGTGATA
1 ACCTC-CTATGAAATTTTGATA
* *
56525 ACCTCGTTATGAAATTTCGATCA
1 ACCTC-CTATGAAATTTTGAT-A
* *
56548 ACCTTCCTATAAAATTGTGATAA
1 ACC-TCCTATGAAATTTTGAT-A
*
56571 ACCTCACTATAAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
*
56593 ACCTCCTTATGAAATTTTGTTA
1 ACCTCC-TATGAAATTTTGATA
* *
56615 ATCTCCCTATGAAATTTTGATCT
1 ACCT-CCTATGAAATTTTGAT-A
* * *
56638 ACATACTATGAAATTCTGATA
1 ACCTCCTATGAAATTTTGATA
*
56659 ACCCTCTTATGAAATTTTGA-A
1 A-CCTCCTATGAAATTTTGATA
* *
56680 AACTAAACTATGAAATTTTGATA
1 ACCT--CCTATGAAATTTTGATA
* * * *
56703 TCCT-CTCTGATATTTTGATT
1 ACCTCCTATGAAATTTTGATA
* *
56723 A-CTCCATAATAAAATTTTAATA
1 ACCTCC-T-ATGAAATTTTGATA
* *
56745 ACCTACC--T--AA-TTCGGTA
1 ACCT-CCTATGAAATTTTGATA
*
56762 ACCATACTATGAAATTTTGATA
1 ACC-TCCTATGAAATTTTGATA
56784 ACCTCC
1 ACCTCC
56790 AGAAATACCA
Statistics
Matches: 394, Mismatches: 94, Indels: 85
0.69 0.16 0.15
Matches are distributed among these distances:
17 8 0.02
18 3 0.01
19 3 0.01
20 17 0.04
21 21 0.05
22 265 0.67
23 73 0.19
24 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
ACCTCCTATGAAATTTTGATA
Found at i:57139 original size:44 final size:43
Alignment explanation
Indices: 57077--57287 Score: 151
Period size: 44 Copynumber: 4.7 Consensus size: 43
57067 AAATTGAGAC
*
57077 TTTTA-TAACCTTCATATGAAATTTTGATAACCTCCCCATGAAA
1 TTTTAGTAACC-TCCTATGAAATTTTGATAACCTCCCCATGAAA
* ** *
57120 TTTTAGTAACCTCCTTATGAAATTTTGTTTAATAACTTGATTCTATGAAA
1 TTTTAGTAACCTCC-TATGAAATTTTG----ATAACCT--CCCCATGAAA
* * * **
57170 TTTTGGTAACCACACTATGAAATTTTGATAACTTCCATATGAAA
1 TTTTAGTAACCTC-CTATGAAATTTTGATAACCTCCCCATGAAA
* * *
57214 TTTTGGTAACCACGCTATGGAATTTTGATAACCT---CATGAAA
1 TTTTAGTAACCTC-CTATGAAATTTTGATAACCTCCCCATGAAA
* * *
57255 TTATAATAACCATCTTATGAAATTTTGATAACC
1 TTTTAGTAACC-TCCTATGAAATTTTGATAACC
57288 ACATAGAGAC
Statistics
Matches: 138, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
41 31 0.22
42 1 0.01
43 7 0.05
44 55 0.40
46 7 0.05
48 6 0.04
50 30 0.22
51 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (43 bp):
TTTTAGTAACCTCCTATGAAATTTTGATAACCTCCCCATGAAA
Found at i:57265 original size:41 final size:42
Alignment explanation
Indices: 57176--57287 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 42
57166 GAAATTTTGG
* * **
57176 TAACCACACTATGAAATTTTGATAACTTCCATATGAAATTTTGG
1 TAACCAC-CTATGAAATTTTGATAACCTCCA-ATGAAATTATAA
*
57220 TAACCACGCTATGGAATTTTGATAACCT-C-ATGAAATTATAA
1 TAACCAC-CTATGAAATTTTGATAACCTCCAATGAAATTATAA
*
57261 TAACCATCTTATGAAATTTTGATAACC
1 TAACCA-CCTATGAAATTTTGATAACC
57288 ACATAGAGAC
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
41 32 0.54
42 1 0.02
43 1 0.02
44 25 0.42
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (42 bp):
TAACCACCTATGAAATTTTGATAACCTCCAATGAAATTATAA
Found at i:57288 original size:22 final size:22
Alignment explanation
Indices: 56801--57288 Score: 117
Period size: 22 Copynumber: 21.9 Consensus size: 22
56791 GAAATACCAC
* *
56801 TATGAAATTTTGGTAATCA-CGT
1 TATGAAATTTTGATAACCATC-T
* *
56823 TTTGAAAATTTGATAACC-TCTT
1 TATGAAATTTTGATAACCATC-T
* *
56845 TAAGAAATTTTGATAACC-TTT
1 TATGAAATTTTGATAACCATCT
* * * *
56866 CTATAAAATTTTGTTGACC-CCT
1 -TATGAAATTTTGATAACCATCT
*
56888 CTATGAAATTTTGATAATCA-CAT
1 -TATGAAATTTTGATAACCATC-T
56911 TAT-ATAATTTTGATAACC-TCGCT
1 TATGA-AATTTTGATAACCAT--CT
56934 T-TGAAATTTTGATAACAACA-C-
1 TATGAAATTTTGATAAC--CATCT
* * * *
56955 TATGAAATTTTAATAATCTTCC
1 TATGAAATTTTGATAACCATCT
* *
56977 TAT-AAATTTTGATGATTCAATCTT
1 TATGAAATTTTGAT-A-ACCATC-T
* *
57001 TATGAAATTTCGATAATCA-CT
1 TATGAAATTTTGATAACCATCT
** *
57022 CTATGGGA-TTTGATAACCTTC-
1 -TATGAAATTTTGATAACCATCT
* * * * **
57043 TATCAACTTTTGGTACTCCTTATAA
1 TATGAAATTTTGATA-ACC--ATCT
* * * *
57068 AATTGAGACTTTT-ATAACCTTCA
1 TA-TGA-AATTTTGATAACCATCT
*
57091 TATGAAATTTTGATAACC-TCCC
1 TATGAAATTTTGATAACCAT-CT
*
57113 CATGAAATTTT-AGTAACC-TCCT
1 TATGAAATTTTGA-TAACCAT-CT
*
57135 TATGAAATTTTGTTTAATAACTTGAT-T
1 TATGAAATTTTG----ATAAC--CATCT
* *
57162 CTATGAAATTTTGGTAACCA-CAC
1 -TATGAAATTTTGATAACCATC-T
* *
57185 TATGAAATTTTGATAA-CTTCCA
1 TATGAAATTTTGATAACCAT-CT
* *
57207 TATGAAATTTTGGTAACCA-CGC
1 TATGAAATTTTGATAACCATC-T
*
57229 TATGGAATTTTGATAACC-TC-
1 TATGAAATTTTGATAACCATCT
* *
57249 -ATGAAATTATAATAACCATCT
1 TATGAAATTTTGATAACCATCT
57270 TATGAAATTTTGATAACCA
1 TATGAAATTTTGATAACCA
57289 CATAGAGACA
Statistics
Matches: 341, Mismatches: 75, Indels: 100
0.66 0.15 0.19
Matches are distributed among these distances:
19 14 0.04
20 6 0.02
21 37 0.11
22 220 0.65
23 12 0.04
24 11 0.03
25 12 0.04
26 8 0.02
27 8 0.02
28 12 0.04
29 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATCT
Found at i:58061 original size:53 final size:53
Alignment explanation
Indices: 57981--58402 Score: 552
Period size: 53 Copynumber: 8.1 Consensus size: 53
57971 TGTTTATTCA
* * *
57981 ATTGAACCTATTAAATAAGAATACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
58034 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
58087 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
*
58140 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGGACT
1 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
* * ** * * *** ***** * * * *
58193 ATTGGA--T-TTAAAGAAAAATACA-AGCACCCAAT-TGTGTTG--TTTATTCA
1 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGA-ACT
* * * *
58240 ATTGAACCTATTAAATAAGAACACATAGCAAATAATACAAAATACAATGAACT
1 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
58293 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
58346 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
58399 ATTG
1 ATTG
58403 GATTTAAAGA
Statistics
Matches: 317, Mismatches: 44, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
46 1 0.00
47 6 0.02
48 2 0.01
49 7 0.02
50 23 0.07
51 8 0.03
52 1 0.00
53 267 0.84
54 2 0.01
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.26
Consensus pattern (53 bp):
ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:58295 original size:206 final size:206
Alignment explanation
Indices: 58034--58426 Score: 741
Period size: 206 Copynumber: 1.9 Consensus size: 206
58024 GCAATGAACT
* * *
58034 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATT
1 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATACAATGAACTATTGAATCTATT
58099 AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATTAAATAAGCACAC
66 AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATTAAATAAGCACAC
*
58164 ATACCAAATAATACAAAATGCAATGGACTATTGGATTTAAAGAAAAATACAAGCACCCAATTGTG
131 ATACCAAATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCCAATTGTG
58229 TTGTTTATTCA
196 TTGTTTATTCA
*
58240 ATTGAACCTATTAAATAAGAACACATAGCAAATAATACAAAATACAATGAACTATTGAATCTATT
1 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATACAATGAACTATTGAATCTATT
58305 AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATTAAATAAGCACAC
66 AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATTAAATAAGCACAC
58370 ATACCAAATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
131 ATACCAAATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
58427 AAAATGACTA
Statistics
Matches: 182, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
206 182 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (206 bp):
ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATACAATGAACTATTGAATCTATT
AAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGAATCTATTAAATAAGCACAC
ATACCAAATAATACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCCAATTGTG
TTGTTTATTCA
Found at i:61309 original size:66 final size:67
Alignment explanation
Indices: 61211--61338 Score: 188
Period size: 66 Copynumber: 1.9 Consensus size: 67
61201 ATAAGGATAT
* *
61211 TAGATTTAATTAAATAAAGATGGAGTTTTTAGTTGAGTAAAATTATAAAAGTTTAAACAATGACA
1 TAGATCTAATTAAATAAAGATGGAGTTTTTAGTAGAGTAAAATTATAAAAGTTTAAACAATGACA
61276 TA
66 TA
* * *
61278 TAGATCTAATTTAAA-AAA-ATTGAGTTTTTAGTAGAGTAAAATTGTAACAGTTTAAACAATG
1 TAGATCTAA-TTAAATAAAGATGGAGTTTTTAGTAGAGTAAAATTATAAAAGTTTAAACAATG
61339 GCAGTTTAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
66 39 0.71
67 11 0.20
68 5 0.09
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (67 bp):
TAGATCTAATTAAATAAAGATGGAGTTTTTAGTAGAGTAAAATTATAAAAGTTTAAACAATGACA
TA
Done.