Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1681
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: 62074
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:5779 original size:18 final size:18
Alignment explanation
Indices: 5756--5790 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5746 ATAAGTTGAG
*
5756 GGCGTCACCCACTGAACT
1 GGCGTCAACCACTGAACT
5774 GGCGTCAACCACTGAAC
1 GGCGTCAACCACTGAAC
5791 AAATACCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.23, T:0.14
Consensus pattern (18 bp):
GGCGTCAACCACTGAACT
Found at i:9995 original size:37 final size:37
Alignment explanation
Indices: 9954--10033 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
9944 TCCTCATATG
*
9954 TGTTGTAGGACTTATGTCTCGTGACTTTCATACTCAA
1 TGTTGTAGGACTTATGCCTCGTGACTTTCATACTCAA
9991 TGTTGTAGGACTTATGCCTCGTGACTTTCATACTCAA
1 TGTTGTAGGACTTATGCCTCGTGACTTTCATACTCAA
10028 TGTTGT
1 TGTTGT
10034 GAGGGTATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (37 bp):
TGTTGTAGGACTTATGCCTCGTGACTTTCATACTCAA
Found at i:14386 original size:23 final size:23
Alignment explanation
Indices: 14355--14400 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
14345 TATTGTTTTA
14355 AATAATTTAAT-ATAATAAATATT
1 AATAATTT-ATGATAATAAATATT
* *
14378 AATATTTTATGATAATTAATATT
1 AATAATTTATGATAATAAATATT
14401 TTATTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATAATTTATGATAATAAATATT
Found at i:17594 original size:20 final size:21
Alignment explanation
Indices: 17569--17607 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
17559 AAATTAGATC
17569 CATTCAAGGCCGG-GCTTGAA
1 CATTCAAGGCCGGAGCTTGAA
17589 CATTCAAGGCCGGAGCTTG
1 CATTCAAGGCCGGAGCTTG
17608 GTTTAGTCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.21
Consensus pattern (21 bp):
CATTCAAGGCCGGAGCTTGAA
Found at i:18698 original size:26 final size:26
Alignment explanation
Indices: 18668--18717 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
18658 ATTTTACATG
*
18668 TTATAGAAGTGTTATAATATATTTAT
1 TTATAAAAGTGTTATAATATATTTAT
18694 TTATAAAAGTGTTATAATATATTT
1 TTATAAAAGTGTTATAATATATTT
18718 TACATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (26 bp):
TTATAAAAGTGTTATAATATATTTAT
Found at i:19559 original size:16 final size:15
Alignment explanation
Indices: 19538--19569 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
19528 CTAATATATG
19538 AAAAAGGAAAAAGAAA
1 AAAAAGGAAAAA-AAA
19554 AAAAAGGAAAAAAAA
1 AAAAAGGAAAAAAAA
19569 A
1 A
19570 TTTTGGTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGGAAAAAAAA
Found at i:19884 original size:116 final size:117
Alignment explanation
Indices: 19743--20128 Score: 545
Period size: 116 Copynumber: 3.4 Consensus size: 117
19733 AAAATTGAAA
* *
19743 TTTTTTTTCGTGTCAGAATTAGATATAAATATACGAAAAAAGTATAAAAAAAAATTTT-GATGCT
1 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTATAAAAAAAAATTTTGGGTGCT
* *
19807 GGCCTGTCAATGGTCGGCACCCAACCGTAAAATTTTTTTTTAAAATTTTTCT
66 GGCCTGTCAATGGCCGGCACCCAACAGTAAAATTTTTTTTTAAAATTTTTCT
19859 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTA-AAAAAAAAATTTTGGGTGCT
1 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTATAAAAAAAAATTTTGGGTGCT
* * * * *
19923 GGCCTGTCAATGGCCGACACCCAACAATAAATTTTTTTTTTGAATTTTTTCTT
66 GGCCTGTCAATGGCCGGCACCCAACAGTAAAATTTTTTTTTAAAATTTTTC-T
19976 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAG--TAAAAAAAAATTTTGGGTGCT
1 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTATAAAAAAAAATTTTGGGTGCT
* *****
20039 AGCCTGTCAATGGCCGGCACCCAACAGTAAAA-AAAAATTT--AATTTTT-T
66 GGCCTGTCAATGGCCGGCACCCAACAGTAAAATTTTTTTTTAAAATTTTTCT
* *
20087 TCTTTTTTTCGTGTTAGAATCAAATATAAATATACGAAAAAA
1 T-TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAA
20129 AATCTTTTTT
Statistics
Matches: 245, Mismatches: 21, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
111 2 0.01
112 38 0.16
113 6 0.02
115 16 0.07
116 140 0.57
117 43 0.18
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (117 bp):
TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTATAAAAAAAAATTTTGGGTGCT
GGCCTGTCAATGGCCGGCACCCAACAGTAAAATTTTTTTTTAAAATTTTTCT
Found at i:20534 original size:13 final size:13
Alignment explanation
Indices: 20516--20540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20506 GAAAAAAAAG
20516 AAAAAATTTTTAA
1 AAAAAATTTTTAA
20529 AAAAAATTTTTA
1 AAAAAATTTTTA
20541 CGGTTGGGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAAATTTTTAA
Found at i:20551 original size:115 final size:116
Alignment explanation
Indices: 20132--20713 Score: 792
Period size: 115 Copynumber: 5.1 Consensus size: 116
20122 GAAAAAAAAT
* * *
20132 CTTTTTTCGTATATTTATATTTGATTCTGACATGAAAAAAAAAGAAAAAAAAATTTT--AAACAA
1 CTTTTTTCGTATATTTATATCTGATTCTGACACG-AAAAAAAAG--AAAAAAATTTTAAAAAAAA
*
20195 ATTTTACTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTTA
63 ATTTTACTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTA
* * * *****
20249 CTTTTTTCGTATATTTATATCTGATTTTAACAC-AAAAAAAAG-AAAAAA--TT-CAATTTTTTT
1 CTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAATTTTAAAAAAAAATT
20309 TTACTGTTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAATTTTTTTTTA
66 TTACTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTA
*
20359 CTTTTTTCGTATATTTATATCTGATTCTTACAC-AAAAAAAA-AAGAAAAATTTTAAAAAAAAAT
1 CTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAA-AAAAATTTTAAAAAAAAAT
*
20422 TTTACTGTTGGGTGCCGGCCATTGAC-GGCCCGCACCCAAAATTTTTTTTTA
65 TTTACTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTA
* *
20473 CTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAAAAATTTTTAAAAAAAATTT
1 CTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAATTTTAAAAAAAAATT
* *
20538 TTACGGTTGGGTGCCGACCATTGACAGGCCAGCA-CCAAAATTTTTTTTTA
66 TTACTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTA
* * * *
20588 CTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAAAGAAAAAATTCAAAAAAAAAA
1 CTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAA-AAAAATTTTAAAAAAAAAT
* * *
20653 TTTACTGTTGGGTGCCGGCCATTGATAGGCCAGCACCCCCAAATTTTTTTTTTC
65 TTTACTGTTGGGTGCCGGCCATTGACAGGCCAGCA--CCCAAAATTTTTTTTTA
20707 CTTTTTT
1 CTTTTTT
20714 TTTCTTTTTC
Statistics
Matches: 415, Mismatches: 36, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
110 54 0.13
111 46 0.11
112 6 0.01
113 12 0.03
114 74 0.18
115 118 0.28
116 55 0.13
117 29 0.07
119 21 0.05
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (116 bp):
CTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAATTTTAAAAAAAAATT
TTACTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTA
Found at i:20721 original size:17 final size:16
Alignment explanation
Indices: 20696--20729 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
20686 CACCCCCAAA
20696 TTTTTTTTTTCCTTTT
1 TTTTTTTTTTCCTTTT
20712 TTTTTCTTTTTCCTTTT
1 TTTTT-TTTTTCCTTTT
20729 T
1 T
20730 CGTATATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTTCCTTTT
Found at i:23286 original size:30 final size:28
Alignment explanation
Indices: 23245--23303 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
23235 AAACTATAAT
* *
23245 TGGTATTCAAATAAGCCCTTAATCTTTAAC
1 TGGTATCCAAATAAG-CCTTAA-CCTTAAC
23275 TGGTATCCAAATAAGCCTTAACCTTAAC
1 TGGTATCCAAATAAGCCTTAACCTTAAC
23303 T
1 T
23304 TATACCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 6 0.22
30 14 0.52
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (28 bp):
TGGTATCCAAATAAGCCTTAACCTTAAC
Found at i:27405 original size:5 final size:5
Alignment explanation
Indices: 27391--27433 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
27381 CTATATGAAT
* * *
27391 ATAAA ATAAA GTAAA ATAAA ATAAA AT-AA ATGAA AGAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
27434 GCAAAAGGGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:27411 original size:15 final size:15
Alignment explanation
Indices: 27391--27433 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
27381 CTATATGAAT
*
27391 ATAAAATAAAGTAAA
1 ATAAAATAAAATAAA
27406 ATAAAATAAAAT-AA
1 ATAAAATAAAATAAA
* *
27420 ATGAAAGAAAATAA
1 ATAAAATAAAATAA
27434 GCAAAAGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (15 bp):
ATAAAATAAAATAAA
Found at i:28615 original size:18 final size:17
Alignment explanation
Indices: 28594--28628 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28584 TTATTATTAA
*
28594 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28612 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28629 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28767 original size:157 final size:157
Alignment explanation
Indices: 28481--28797 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
28471 CTAAATACTC
* *
28481 TTAGCATAAATTTGTTTTGGTTAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
28546 TTATCAAGAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAAGAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
28611 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
28638 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
28703 ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
66 ATATCAAGAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
28768 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
28795 TTA
1 TTA
28798 ATCTTCTTAT
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAAGAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:28831 original size:61 final size:60
Alignment explanation
Indices: 28766--28953 Score: 179
Period size: 61 Copynumber: 3.1 Consensus size: 60
28756 TTATAATTAA
28766 AATATATAATTTAATAAAATTCTTAATAATTAATCTTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAAT-TTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * * *
28827 AATATATGATACT-GTAAAA-TATAAATTAACATAA-TTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAA-TTAATTTCTTATATGAATTTACTCA-AATCAT
28886 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAAT-TTCTTATATGAATTTACTCAAATCAT
28947 AATATAT
1 AATATAT
28954 GATACTATAA
Statistics
Matches: 93, Mismatches: 24, Indels: 20
0.68 0.18 0.15
Matches are distributed among these distances:
58 6 0.06
59 27 0.29
60 20 0.22
61 34 0.37
62 6 0.06
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATTTCTTATATGAATTTACTCAAATCAT
Found at i:28869 original size:120 final size:121
Alignment explanation
Indices: 28729--29026 Score: 453
Period size: 120 Copynumber: 2.5 Consensus size: 121
28719 ATTTAATCAT
* *
28729 ATTTAAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
28794 ATTAATCTTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
28851 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
28914 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * * * *
28970 ATTTGAA-ATAATTAATA-CATCATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTA-AATATATTATAATTAAAATATATAATTTAATAAAATT
29027 TAAAATAATT
Statistics
Matches: 164, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
119 8 0.05
120 151 0.92
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:28899 original size:14 final size:15
Alignment explanation
Indices: 28850--28901 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28840 GTAAAATATA
28850 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
28865 TATTAAATATATTAT
1 AATTAAATATATTAT
28880 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
28893 AATTTAATA
1 AATTAAATA
28902 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:29113 original size:24 final size:25
Alignment explanation
Indices: 29067--29114 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
29057 TATGAATTTG
29067 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
29093 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
29115 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:29118 original size:92 final size:92
Alignment explanation
Indices: 29022--29250 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
29012 TGATTTAATA
* * *
29022 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
29084 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
29114 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
29179 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
29204 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
29251 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:32554 original size:12 final size:12
Alignment explanation
Indices: 32537--32563 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
32527 TTAATAATTA
32537 TTATCAAATTTT
1 TTATCAAATTTT
32549 TTATCAAATTTT
1 TTATCAAATTTT
32561 TTA
1 TTA
32564 CTAATCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATCAAATTTT
Found at i:35922 original size:20 final size:22
Alignment explanation
Indices: 35890--35942 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
35880 AACACATACT
35890 TAATATGAGAAATAATA-AAAAAA
1 TAATAT-A-AAATAATATAAAAAA
* *
35913 TAA-ATAAAATGATATAAAAGA
1 TAATATAAAATAATATAAAAAA
35934 TAATATAAA
1 TAATATAAA
35943 TAAACACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.27
21 9 0.35
22 7 0.27
23 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (22 bp):
TAATATAAAATAATATAAAAAA
Found at i:37249 original size:17 final size:19
Alignment explanation
Indices: 37222--37258 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
37212 AATTGGTTTG
37222 ATTTAAAAAATATT-AAAA
1 ATTTAAAAAATATTCAAAA
37240 ATTT-AAAAATATTCAAAA
1 ATTTAAAAAATATTCAAAA
37258 A
1 A
37259 AAGAGTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTTAAAAAATATTCAAAA
Found at i:38258 original size:31 final size:30
Alignment explanation
Indices: 38167--38259 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
38157 AGTACCTAAA
* * *
38167 TTATACATGAACTTTT-ATCTAATGTACAATG
1 TTATACATGAA-TTTTAATTTGATGT-CAATT
*
38198 TTATACATGAATTTTAATTTTATGT-AATT
1 TTATACATGAATTTTAATTTGATGTCAATT
*
38227 TTATACATGAAAATTTTGATTTGAT-TCAATT
1 TTATACATG--AATTTTAATTTGATGTCAATT
38258 TT
1 TT
38260 CATAAATCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
29 12 0.23
30 5 0.09
31 36 0.68
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (30 bp):
TTATACATGAATTTTAATTTGATGTCAATT
Found at i:38822 original size:23 final size:21
Alignment explanation
Indices: 38789--38835 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
38779 CTCTTTCAAT
38789 AAAAAATATAAAAAAATAAAA
1 AAAAAATATAAAAAAATAAAA
* *
38810 AAAAAATTCATAAAAGAATTAAA
1 AAAAAA-T-ATAAAAAAATAAAA
38833 AAA
1 AAA
38836 GAACAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
23 15 0.68
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAAAATATAAAAAAATAAAA
Found at i:38903 original size:26 final size:26
Alignment explanation
Indices: 38874--38923 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
38864 TATAAAACTC
*
38874 TAAAAAATATATAAAAATGA-AAATTT
1 TAAAAAA-AAATAAAAATGATAAATTT
*
38900 TAAAAAAAAATTAAAATGATAAAT
1 TAAAAAAAAATAAAAATGATAAAT
38924 AATTATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (26 bp):
TAAAAAAAAATAAAAATGATAAATTT
Found at i:43070 original size:17 final size:18
Alignment explanation
Indices: 43048--43082 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43038 GGAGAAACAT
*
43048 AATTTGC-ATAAATATAA
1 AATTTGCAATAAAGATAA
43065 AATTTGCAATAAAGATAA
1 AATTTGCAATAAAGATAA
43083 TTTACATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTTGCAATAAAGATAA
Found at i:45786 original size:14 final size:13
Alignment explanation
Indices: 45765--45813 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
45755 AAGGTAACCA
45765 AATATTTAAATAT
1 AATATTTAAATAT
45778 AATTATTT-AA-A-
1 AA-TATTTAAATAT
45789 AATATTTAAATAT
1 AATATTTAAATAT
* *
45802 AAAATATAAATA
1 AATATTTAAATA
45814 ATCCTTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 5 0.17
11 4 0.13
12 2 0.07
13 14 0.47
14 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATTTAAATAT
Done.