Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1309
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: 45510
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:3214 original size:30 final size:29
Alignment explanation
Indices: 3174--3276 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
3164 CGAGTTTAAA
*
3174 CTAAAATGAGCTAAGCTTTAGCTCGTGAG
1 CTAAAGTGAGCTAAGCTTTAGCTCGTGAG
* * * * *
3203 CTAAAGCTGAGCTGAGGC-TAAACTCCTAAG
1 CTAAAG-TGAGCT-AAGCTTTAGCTCGTGAG
*
3233 CTAAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CTAAAG-TGAGCTAAGCTTTAGCTCGTGAG
*
3263 TTGAAAGTGAGCTA
1 CT-AAAGTGAGCTA
3277 GGAGTGAGCT
Statistics
Matches: 56, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
29 7 0.12
30 42 0.75
31 7 0.12
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (29 bp):
CTAAAGTGAGCTAAGCTTTAGCTCGTGAG
Found at i:5206 original size:11 final size:12
Alignment explanation
Indices: 5174--5206 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5164 GAGCTGTAGC
5174 AAACTTAATTAT
1 AAACTTAATTAT
*
5186 AAACTAAATTA-
1 AAACTTAATTAT
5197 AAACTTAATT
1 AAACTTAATT
5207 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:9876 original size:79 final size:81
Alignment explanation
Indices: 9708--9892 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
9698 GCTACTCGTT
* * *
9708 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGTACAAATGCCTTCTGGACTTAACCCA
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCTGGACTTAACCCA
* *
9772 GATTTAGTAACTCGCAC
65 GATATAGTAACTAGCAC
* ** *
9789 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCTGGA-CTTAACCCA
* *
9851 GATATGGTCACTTAGCA-
65 GATATAGTAAC-TAGCAC
9868 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
9893 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 57 0.65
80 25 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCTGGACTTAACCCAG
ATATAGTAACTAGCAC
Found at i:9892 original size:40 final size:40
Alignment explanation
Indices: 9689--9892 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
9679 CGGAATTTAA
** *
9689 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
9729 CCGGTTATAGTAACTCGTACAAATGCCTTCTGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
9769 CCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
9808 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
9848 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
9888 CCGGA
1 CCGGA
9893 CATCATTCGA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 91 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:11793 original size:16 final size:16
Alignment explanation
Indices: 11772--11802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11762 AAAATTCAGG
*
11772 ATTTCGGGATTTTTGA
1 ATTTCGAGATTTTTGA
11788 ATTTCGAGATTTTTG
1 ATTTCGAGATTTTTG
11803 GGGCGTTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (16 bp):
ATTTCGAGATTTTTGA
Found at i:14768 original size:21 final size:20
Alignment explanation
Indices: 14725--14780 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
14715 AGTTCCCATC
* *
14725 AGCTCACTTGAGCTCGTTTT
1 AGCTCATTTGAGCTCGATTT
*
14745 AGCTCGTTTGAGCTCGAATTT
1 AGCTCATTTGAGCTCG-ATTT
*
14766 AGCTCATTTCAGCTC
1 AGCTCATTTGAGCTC
14781 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.38
Consensus pattern (20 bp):
AGCTCATTTGAGCTCGATTT
Found at i:15023 original size:13 final size:13
Alignment explanation
Indices: 15005--15033 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
14995 AATAGTTGTG
15005 TGTTATTTAATTA
1 TGTTATTTAATTA
15018 TGTTATTTAATTA
1 TGTTATTTAATTA
15031 TGT
1 TGT
15034 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:19681 original size:13 final size:13
Alignment explanation
Indices: 19663--19691 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19653 AATAGTTGTG
19663 TGTTATTTAATTA
1 TGTTATTTAATTA
19676 TGTTATTTAATTA
1 TGTTATTTAATTA
19689 TGT
1 TGT
19692 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:26956 original size:27 final size:27
Alignment explanation
Indices: 26925--26997 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
26915 TCTTCTTCAA
26925 CATCTTTTTCTTTTTCAATTTT-TTCT
1 CATCTTTTTCTTTTTCAATTTTCTTCT
* *
26951 CAATCTCAATTTCTTTTTCAATTTTCTTTT
1 C-ATCT--TTTTCTTTTTCAATTTTCTTCT
* *
26981 CTTCATTTTCTTTTTCA
1 CATCTTTTTCTTTTTCA
26998 CTCACTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.39
29 18 0.47
30 4 0.11
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (27 bp):
CATCTTTTTCTTTTTCAATTTTCTTCT
Found at i:26961 original size:17 final size:18
Alignment explanation
Indices: 26939--26972 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26929 TTTTTCTTTT
26939 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
26956 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
26973 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:27918 original size:30 final size:31
Alignment explanation
Indices: 27867--27931 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
27857 TTTAACTTGA
27867 TTTTTTTTGCTCACCCTTTTTTTC-CTTTTCT
1 TTTTTTTTGCTCACCCTTTTTTTCACTTTT-T
*
27898 TTTTTTTTGCTCGA-TC-TTTTTTCACTTTTT
1 TTTTTTTTGCTC-ACCCTTTTTTTCACTTTTT
27928 TTTT
1 TTTT
27932 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 12 0.39
31 18 0.58
32 1 0.03
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.71
Consensus pattern (31 bp):
TTTTTTTTGCTCACCCTTTTTTTCACTTTTT
Found at i:27955 original size:16 final size:15
Alignment explanation
Indices: 27936--27975 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
27926 TTTTTTGAAT
*
27936 TTTTTTTTTCAATCAA
1 TTTTTTTTTCAA-AAA
27952 TTTTTTTTTCAAAAA
1 TTTTTTTTTCAAAAA
27967 TTTTTTTTT
1 TTTTTTTTT
27976 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTTTTTCAAAAA
Found at i:35493 original size:45 final size:46
Alignment explanation
Indices: 35428--35601 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
35418 TGTAACCCGC
35428 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
35474 CCAT-AGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCGTTCGCAT
* *** * * *
35519 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
35566 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
35602 ATGCCCAAAT
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
45 36 0.34
46 37 0.35
47 34 0.32
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:35606 original size:93 final size:92
Alignment explanation
Indices: 35436--35606 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 92
35426 GCCCATAAGT
* *
35436 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
35501 GAGCTCGGATGCCTAGTTACATCTCTC
66 GAGCTCGGATGCCTAGTTACATCTCTC
*
35528 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
*
35593 CGAGTTCGGATGCC
65 CGAGCTCGGATGCC
35607 CAAATATCCT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 39 0.53
93 35 0.47
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTC
Found at i:38018 original size:15 final size:14
Alignment explanation
Indices: 37975--38021 Score: 76
Period size: 14 Copynumber: 3.3 Consensus size: 14
37965 CAAAGATAAC
*
37975 AAGAAAACCGAATA
1 AAGAAATCCGAATA
37989 AAGAAATCCGAATA
1 AAGAAATCCGAATA
38003 AAGAAATCCAGAATA
1 AAGAAATCC-GAATA
38018 AAGA
1 AAGA
38022 TCCAGATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 22 0.71
15 9 0.29
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.11
Consensus pattern (14 bp):
AAGAAATCCGAATA
Found at i:38031 original size:27 final size:27
Alignment explanation
Indices: 37975--38035 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 27
37965 CAAAGATAAC
37975 AAGAAAACCGAATAAAGAAATCCGAATA
1 AAGAAAACCGAATAAAG-AATCCGAATA
*
38003 AAGAAATCCAGAATAAAG-ATCC-AGATA
1 AAGAAAACC-GAATAAAGAATCCGA-ATA
38030 AAGAAA
1 AAGAAA
38036 CCCAAGATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 13 0.43
28 8 0.27
29 8 0.27
ACGTcount: A:0.61, C:0.13, G:0.15, T:0.11
Consensus pattern (27 bp):
AAGAAAACCGAATAAAGAATCCGAATA
Found at i:38032 original size:12 final size:13
Alignment explanation
Indices: 37984--38033 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
37974 CAAGAAAACC
37984 GAATAAAGAAATCC-
1 GAATAAAG--ATCCA
37998 GAATAAAGAAATCCA
1 GAATAAAG--ATCCA
38013 GAATAAAGATCCA
1 GAATAAAGATCCA
38026 G-ATAAAGA
1 GAATAAAGA
38034 AACCCAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.20
13 6 0.17
14 14 0.40
15 8 0.23
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (13 bp):
GAATAAAGATCCA
Found at i:41064 original size:95 final size:95
Alignment explanation
Indices: 40949--41122 Score: 321
Period size: 95 Copynumber: 1.8 Consensus size: 95
40939 GCCCATAAGT
* *
40949 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41014 CGAGTTCGGATGCCTAGTTACATCTCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCTCAC
*
41044 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41109 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
41123 AAATATCCTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (95 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCTCAC
Found at i:41118 original size:46 final size:46
Alignment explanation
Indices: 40941--41118 Score: 227
Period size: 46 Copynumber: 3.8 Consensus size: 46
40931 TGTAACCCGC
* * *
40941 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40987 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
41037 CTC-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
41082 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41119 TGCCAAATAT
Statistics
Matches: 114, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
44 3 0.03
45 7 0.06
46 65 0.57
49 30 0.26
50 6 0.05
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:45272 original size:19 final size:19
Alignment explanation
Indices: 45248--45287 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
45238 AGCTCCTATG
45248 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
45267 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
45286 TA
1 TA
45288 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Done.