Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2496
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: 51830
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Found at i:846 original size:40 final size:40
Alignment explanation
Indices: 802--1012 Score: 322
Period size: 40 Copynumber: 5.4 Consensus size: 40
792 AACCCAATTA
* * ** *
802 CCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
842 CCTTCGGGACTTAACCC-GAAATAGCAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
881 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
921 CCTTCGGGACTTAACCCGG-AATAACAA-CAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
* *
959 CCTTC-GGACTTAACCCAGAAATAACAACCAGCATGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
998 CCTTCGGGACTTAAC
1 CCTTCGGGACTTAAC
1013 GGATATAATC
Statistics
Matches: 158, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
37 12 0.08
38 24 0.15
39 58 0.37
40 64 0.41
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
Found at i:874 original size:39 final size:40
Alignment explanation
Indices: 824--1012 Score: 305
Period size: 39 Copynumber: 4.8 Consensus size: 40
814 AGCCCGGATG
*
824 TAACAACCAGCACAAATGCCTTCGGGACTTAACCC-GAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCAGAAA
* *
863 TAGCAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCAGAAA
*
903 TAACAACCAGCACGAATGCCTTCGGGACTTAACCC-GGAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCAGAAA
942 TAACAA-CAGCACGAATGCCTTC-GGACTTAACCCAGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCAGAAA
*
980 TAACAACCAGCATGAATGCCTTCGGGACTTAAC
1 TAACAACCAGCACGAATGCCTTCGGGACTTAAC
1013 GGATATAATC
Statistics
Matches: 140, Mismatches: 6, Indels: 7
0.92 0.04 0.05
Matches are distributed among these distances:
37 11 0.08
38 25 0.18
39 57 0.41
40 47 0.34
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (40 bp):
TAACAACCAGCACGAATGCCTTCGGGACTTAACCCAGAAA
Found at i:933 original size:79 final size:78
Alignment explanation
Indices: 802--1012 Score: 325
Period size: 79 Copynumber: 2.7 Consensus size: 78
792 AACCCAATTA
* * ** * *
802 CCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAATGCCTTCGGGACTTAACCCGAAATAGC
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGCCTTCGGGACTTAACCCGAAATAAC
867 AACCAGCACGAATG
66 AA-CAGCACGAATG
*
881 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAATAAC
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGCCTTCGGGACTTAACCCGAAATAAC
946 AACAGCACGAATG
66 AACAGCACGAATG
* *
959 CCTTC-GGACTTAACCCAGAAATAACAACCAGCATGAATGCCTTCGGGACTTAAC
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGCCTTCGGGACTTAAC
1013 GGATATAATC
Statistics
Matches: 123, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
77 47 0.38
78 16 0.13
79 60 0.49
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (78 bp):
CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGCCTTCGGGACTTAACCCGAAATAAC
AACAGCACGAATG
Found at i:7506 original size:79 final size:79
Alignment explanation
Indices: 7373--7532 Score: 266
Period size: 79 Copynumber: 2.0 Consensus size: 79
7363 TAATTTAGGA
* * * * *
7373 GTAGATTTAATTTATTTTCTTTTCGGGTTTTCAATAATTTCTTGTTTTCTTCTTGACATAGGTTT
1 GTAGATTTAATTTATTTTCTTTTCAGCTTTTCAATAATTTCTTATTTTCATCTTGACATAAGTTT
7438 TTATTCAAGAGTTT
66 TTATTCAAGAGTTT
*
7452 GTAGATTTAATTTATTTTCTTTTCAGCTTTTCAATACTTTCTTATTTTCATCTTGACATAAGTTT
1 GTAGATTTAATTTATTTTCTTTTCAGCTTTTCAATAATTTCTTATTTTCATCTTGACATAAGTTT
7517 TTATTCAAGAGTTT
66 TTATTCAAGAGTTT
7531 GT
1 GT
7533 TTATATAATT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.55
Consensus pattern (79 bp):
GTAGATTTAATTTATTTTCTTTTCAGCTTTTCAATAATTTCTTATTTTCATCTTGACATAAGTTT
TTATTCAAGAGTTT
Found at i:12825 original size:19 final size:20
Alignment explanation
Indices: 12801--12838 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12791 GGTACCACCA
12801 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
12820 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
12839 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:13179 original size:93 final size:93
Alignment explanation
Indices: 13068--13238 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
13058 GCCCCTAAGT
* *
13068 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATAAACTCGAACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGAACTCAACTCAA
13133 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * * * *
13161 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGAACTCAACTCAA
13226 CGAGTTCGGATGC
66 CGAGTTCGGATGC
13239 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:13223 original size:46 final size:46
Alignment explanation
Indices: 13063--13235 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
13053 AACCCGCCCC
* * * *
13063 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * * *
13109 TAAATAAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
13157 TCA-CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
13202 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
13236 TGCTCAACCA
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 56 0.55
47 26 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:13254 original size:46 final size:44
Alignment explanation
Indices: 13115--13254 Score: 115
Period size: 46 Copynumber: 3.0 Consensus size: 44
13105 TCCATAAATA
* *
13115 AACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTCA-CG
1 AACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AGTG
* * * *
13162 AACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCAT-AAGTG
1 AACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTAGTG
13208 AACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAGTG
13254 A
1 A
13255 CATGTCACTT
Statistics
Matches: 75, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.43
47 28 0.37
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.23
Consensus pattern (44 bp):
AACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAGTG
Found at i:15029 original size:48 final size:47
Alignment explanation
Indices: 14977--15128 Score: 187
Period size: 48 Copynumber: 3.2 Consensus size: 47
14967 CAAATTGCTA
** * * * *
14977 ATATCATGGCTCATAGCCAAATCAGTGGAGCTCGCACCCGAAGTGCCG
1 ATATCATGGCTCA-AGCCAAATCAAAGTAACTCACACCCGAAGTGTCG
* * *
15025 ATATCATGACCCAAAGCCCAATCAAAGTAACTCACACCCGAAGTGTCG
1 ATATCATGGCTC-AAGCCAAATCAAAGTAACTCACACCCGAAGTGTCG
*
15073 ATATCATGGCTCGAAGCCAAATCAAAGTAACTCACACCCAAAGTGTCG
1 ATATCATGGCTC-AAGCCAAATCAAAGTAACTCACACCCGAAGTGTCG
15121 ATATCATG
1 ATATCATG
15129 TCCCCCGAAG
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 88 0.99
49 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.19
Consensus pattern (47 bp):
ATATCATGGCTCAAGCCAAATCAAAGTAACTCACACCCGAAGTGTCG
Found at i:27134 original size:22 final size:23
Alignment explanation
Indices: 27089--27132 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
27079 ACTGTAAACA
*
27089 TTTTTCCTAGTTACCTTTGAAAT
1 TTTTTCCCAGTTACCTTTGAAAT
27112 TTTTTCCCAGTTACCTTTGAA
1 TTTTTCCCAGTTACCTTTGAA
27133 TTCTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTTTCCCAGTTACCTTTGAAAT
Found at i:38532 original size:23 final size:23
Alignment explanation
Indices: 38502--38570 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 23
38492 ACAAGCTGCT
38502 CGTTGTGGTCAAACCACTCAATA-
1 CGTTGTGG-CAAACCACTCAATAG
38525 CGTTGTGGCAAAGCCACTCAATAG
1 CGTTGTGGCAAA-CCACTCAATAG
* *
38549 CATTGTGGACAAATCACTCAAT
1 CGTTGTGG-CAAACCACTCAAT
38571 TTTTCAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
22 4 0.10
23 18 0.44
24 15 0.37
25 4 0.10
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (23 bp):
CGTTGTGGCAAACCACTCAATAG
Found at i:41427 original size:40 final size:40
Alignment explanation
Indices: 41382--41493 Score: 188
Period size: 40 Copynumber: 2.8 Consensus size: 40
41372 ATAACCACAA
* * *
41382 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
41422 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
41462 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
41494 CACTCATAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:41564 original size:56 final size:54
Alignment explanation
Indices: 41464--41574 Score: 147
Period size: 56 Copynumber: 2.0 Consensus size: 54
41454 ATCAACTCGC
*
41464 ACAAATGCCTTCGGGTCTTAGCCCGGATATCACTCATAAATGCCTTCGGG-CTT
1 ACAAATGCCTTCGGGACTTAGCCCGGATATCACTCATAAATGCCTTCGGGACTT
41517 ACAAATGCCTT-GGGACTTAGCCC-GATAAAATCACTAGCATAAATGCCTTCGGGACTT
1 ACAAATGCCTTCGGGACTTAGCCCGGAT---ATCACT--CATAAATGCCTTCGGGACTT
41574 A
1 A
41575 TGCCCTTAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
51 3 0.06
52 11 0.22
53 11 0.22
54 6 0.12
56 16 0.31
57 4 0.08
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (54 bp):
ACAAATGCCTTCGGGACTTAGCCCGGATATCACTCATAAATGCCTTCGGGACTT
Found at i:41598 original size:44 final size:43
Alignment explanation
Indices: 41540--41622 Score: 157
Period size: 44 Copynumber: 1.9 Consensus size: 43
41530 GACTTAGCCC
41540 GATAAAATCACTAGCATAAATGCCTTCGGGACTTATGCCCTTAG
1 GATAAAATCACTAGCATAAATGCCTTCGGGACTTA-GCCCTTAG
41584 GATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCC
1 GATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCC
41623 GGATATCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
43 4 0.10
44 35 0.90
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (43 bp):
GATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCTTAG
Found at i:49648 original size:39 final size:40
Alignment explanation
Indices: 49605--49690 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 40
49595 ATAACCACAA
49605 GCACAATTGCCTTCGGGTCTTAACCCGG-TATAGCAACTC
1 GCACAATTGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * * *
49644 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
1 GCACAATTGCCTTCGGGTCTTAACCCGGATATAGCAACTC
49684 GCACAAT
1 GCACAAT
49691 GCTCTTAGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 26 0.63
40 15 0.37
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:49802 original size:110 final size:110
Alignment explanation
Indices: 49585--49802 Score: 235
Period size: 110 Copynumber: 2.0 Consensus size: 110
49575 TCTTCGGAAT
* * * * * *
49585 TTAGCCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGTATAGCAACTCGCACAA
1 TTAGCCCGATAAAACCACAAGCACAAATGCCTTCGGGTCTTAACCCGATAAAGCAACTAGCACAA
* * * * *
49650 ATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAATGCTC
66 ATGCCTTCGGGACTTAGCCCGGATAAATCAACTAGCAAAATGCTC
* * * * * *
49695 TTAGCCCGATAAAATCACTAGCATAAATGCCTTCGGGTCTTAGCCCGATAAAATC-ACTAGCATA
1 TTAGCCCGATAAAACCACAAGCACAAATGCCTTCGGGTCTTAACCCGAT-AAAGCAACTAGCACA
49759 AATGCCTTC-GGACTTAGCCCGGATAAAATC-ACTAGCATAAATGC
65 AATGCCTTCGGGACTTAGCCCGGAT-AAATCAACTAGCA-AAATGC
49803 CTTCGGGACT
Statistics
Matches: 88, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
109 19 0.22
110 66 0.75
111 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (110 bp):
TTAGCCCGATAAAACCACAAGCACAAATGCCTTCGGGTCTTAACCCGATAAAGCAACTAGCACAA
ATGCCTTCGGGACTTAGCCCGGATAAATCAACTAGCAAAATGCTC
Found at i:49823 original size:40 final size:39
Alignment explanation
Indices: 49694--49819 Score: 227
Period size: 39 Copynumber: 3.2 Consensus size: 39
49684 GCACAATGCT
*
49694 CTTAGCCCGATAAAATCACTAGCATAAATGCCTTCGGGT
1 CTTAGCCCGATAAAATCACTAGCATAAATGCCTTCGGGA
49733 CTTAGCCCGATAAAATCACTAGCATAAATGCCTTC-GGA
1 CTTAGCCCGATAAAATCACTAGCATAAATGCCTTCGGGA
49771 CTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGA
1 CTTAGCCC-GATAAAATCACTAGCATAAATGCCTTCGGGA
49811 CTTAGCCCG
1 CTTAGCCCG
49820 GATATCATTC
Statistics
Matches: 84, Mismatches: 1, Indels: 4
0.94 0.01 0.04
Matches are distributed among these distances:
38 10 0.12
39 63 0.75
40 11 0.13
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (39 bp):
CTTAGCCCGATAAAATCACTAGCATAAATGCCTTCGGGA
Done.