Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold380_ERROPOS5882787+
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: 97473
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:14158 original size:19 final size:20
Alignment explanation
Indices: 14112--14162 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
14102 CTAGAGCCAC
*
14112 TTCATTTACTTACTTTTCAT
1 TTCATTTACTTACTTCTCAT
*
14132 TCCATTTACTTACTTCT-AT
1 TTCATTTACTTACTTCTCAT
14151 TTCATTTACTTA
1 TTCATTTACTTA
14163 GCTTAAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (20 bp):
TTCATTTACTTACTTCTCAT
Found at i:16057 original size:23 final size:22
Alignment explanation
Indices: 16031--16075 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
16021 AAATGGTTTA
16031 TTTA-CCAGTTAAGTCCATTTAAT
1 TTTATCCA-TTAAG-CCATTTAAT
*
16054 TTTATTCATTAAGCCATTTAAT
1 TTTATCCATTAAGCCATTTAAT
16076 CATTCAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 9 0.45
24 2 0.10
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (22 bp):
TTTATCCATTAAGCCATTTAAT
Found at i:20636 original size:37 final size:37
Alignment explanation
Indices: 20586--20670 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
20576 ATCAATGACA
*
20586 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTTATC
1 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
* *
20623 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
*
20660 AGTGACAAGTG
1 AGTGATAAGTG
20671 ACAAGTGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
Found at i:27103 original size:51 final size:51
Alignment explanation
Indices: 27020--27136 Score: 198
Period size: 51 Copynumber: 2.3 Consensus size: 51
27010 ACTTCTAATC
* * *
27020 AGTGACAAGTGATAACTGGTAGCCTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAACTGGTAGCCTCAACTACACTTATCTAATCAGTGACA
*
27071 AGTGACAAGTGATAAGTGGTAGCCTCAACTACACTTATCTAATCAGTGACA
1 AGTGACAAGTGATAACTGGTAGCCTCAACTACACTTATCTAATCAGTGACA
27122 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
27137 ATGTGATCTG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (51 bp):
AGTGACAAGTGATAACTGGTAGCCTCAACTACACTTATCTAATCAGTGACA
Found at i:30904 original size:32 final size:33
Alignment explanation
Indices: 30834--30905 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
30824 ACAAGGCAAA
* **
30834 TAAAAAAATTAAAATTTTAAATATTTAATTAAC
1 TAAAAAAATCAAAATTCAAAATATTTAATTAAC
* **
30867 AAAAAAAATCAAAA-TCAAAATATTTAATTATG
1 TAAAAAAATCAAAATTCAAAATATTTAATTAAC
30899 TAAAAAA
1 TAAAAAA
30906 TCACAAACAC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (33 bp):
TAAAAAAATCAAAATTCAAAATATTTAATTAAC
Found at i:39055 original size:60 final size:61
Alignment explanation
Indices: 38984--39097 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 61
38974 TTAATATTTA
* **
38984 TTTTTTCATACAATTTTTAAATTACCCATC-CAACTTTTAAATAAAAAGATAATGTACTTG
1 TTTTTTCATACAATTTTTAAATTACCCACCTCAACCATTAAATAAAAAGATAATGTACTTG
* *
39044 TTTTTTTATACAATTTTTAAATTACTCACCTCAACCATTAAATAAAAAGATAAT
1 TTTTTTCATACAATTTTTAAATTACCCACCTCAACCATTAAATAAAAAGATAAT
39098 ATATTTTAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 27 0.56
61 21 0.44
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41
Consensus pattern (61 bp):
TTTTTTCATACAATTTTTAAATTACCCACCTCAACCATTAAATAAAAAGATAATGTACTTG
Found at i:52535 original size:28 final size:28
Alignment explanation
Indices: 52504--52557 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
52494 ATCACACGAC
52504 CGTGTCACTGCCCGAGGTATGAGCACGT
1 CGTGTCACTGCCCGAGGTATGAGCACGT
* * * *
52532 CGTGTCGCTGTCTGTGGTATGAGCAC
1 CGTGTCACTGCCCGAGGTATGAGCAC
52558 AGCCTAAGGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.33, T:0.26
Consensus pattern (28 bp):
CGTGTCACTGCCCGAGGTATGAGCACGT
Found at i:56670 original size:20 final size:21
Alignment explanation
Indices: 56645--56684 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
56635 CCCACGTTGA
56645 CCCATTTTCTC-CT-TTTTTAG
1 CCCA-TTTCTCGCTCTTTTTAG
56665 CCCATTTCTCGCTCTTTTTA
1 CCCATTTCTCGCTCTTTTTA
56685 CTCTCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.10, C:0.33, G:0.05, T:0.53
Consensus pattern (21 bp):
CCCATTTCTCGCTCTTTTTAG
Found at i:58786 original size:75 final size:76
Alignment explanation
Indices: 58656--58822 Score: 259
Period size: 75 Copynumber: 2.2 Consensus size: 76
58646 TAAACCCACA
* *
58656 TTAAATGTTACTTAAACCATTAAAGGGTTTTAAAGAAATTAAGTAACTCATAATAATGA-AAAAT
1 TTAAATGTTACTTAAACCATTAAAGGCTTTTAAAGAAATTAAGTAACTCAAAATAATGACAAAA-
58720 TTACTTAATTTC
65 TTACTTAATTTC
* *
58732 TTAAATGTTACATAAA-CATTAAAGGACTTTTAAA-AAATTAAGTAACTTAAAATAATGACAAAA
1 TTAAATGTTACTTAAACCATTAAAGG-CTTTTAAAGAAATTAAGTAACTCAAAATAATGACAAAA
58795 TTACTTAATTTC
65 TTACTTAATTTC
58807 TTAAATGTTACTTAAA
1 TTAAATGTTACTTAAA
58823 ATATTAAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
75 58 0.69
76 26 0.31
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (76 bp):
TTAAATGTTACTTAAACCATTAAAGGCTTTTAAAGAAATTAAGTAACTCAAAATAATGACAAAAT
TACTTAATTTC
Found at i:58863 original size:23 final size:24
Alignment explanation
Indices: 58837--58884 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
58827 TAAAAATTCC
58837 TAAATCTT-GCTAAATTACTTAAT
1 TAAATCTTGGCTAAATTACTTAAT
* *
58860 TAAATCTTGGGTAATTTACTTAAT
1 TAAATCTTGGCTAAATTACTTAAT
58884 T
1 T
58885 TCTTAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.46
Consensus pattern (24 bp):
TAAATCTTGGCTAAATTACTTAAT
Found at i:60940 original size:28 final size:25
Alignment explanation
Indices: 60882--60940 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 25
60872 GGATTTTTAG
*
60882 TTTATTTAATATTAATATATTTATA
1 TTTATTTAATATTAATATATTTAAA
60907 TTTATTTAATATTAATATTAAATTTAAA
1 TTTATTTAATATTAATA-T--ATTTAAA
60935 TTTATT
1 TTTATT
60941 ATTATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 17 0.57
26 1 0.03
28 12 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTATTTAATATTAATATATTTAAA
Found at i:61016 original size:22 final size:21
Alignment explanation
Indices: 60969--61025 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
60959 TTTTTTTATT
**
60969 TTTATATATATTTTAAAATTTA
1 TTTATATAT-TTTTAAAAAATA
60991 -TTATTATATTTTTAAAAAATA
1 TTTA-TATATTTTTAAAAAATA
*
61012 TTTATGTATTTTTA
1 TTTATATATTTTTA
61026 TATATTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTATATATTTTTAAAAAATA
Found at i:66137 original size:37 final size:34
Alignment explanation
Indices: 66087--66158 Score: 81
Period size: 37 Copynumber: 2.0 Consensus size: 34
66077 AGTGTGCCGT
* *
66087 TTTTTCTGACCATCTTCCCTCCTCCTCCTTTCTTTTC
1 TTTTTCTCACCATC-TACCTCCTCCT-C-TTCTTTTC
* *
66124 TTTTTCTCTCCATCTACCTTCTCCTCTTCTTTTC
1 TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
66158 T
1 T
66159 CCATAGGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 9 0.29
35 1 0.03
36 9 0.29
37 12 0.39
ACGTcount: A:0.06, C:0.39, G:0.01, T:0.54
Consensus pattern (34 bp):
TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
Found at i:76383 original size:21 final size:21
Alignment explanation
Indices: 76344--76383 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
76334 GAGGTGATGG
*
76344 AGAATCAGGTGGGATAGGTGA
1 AGAATCAGGTGGGAAAGGTGA
* *
76365 AGAATTAGGTGGTAAAGGT
1 AGAATCAGGTGGGAAAGGT
76384 AGGTTATTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.40, T:0.23
Consensus pattern (21 bp):
AGAATCAGGTGGGAAAGGTGA
Found at i:86984 original size:40 final size:39
Alignment explanation
Indices: 86922--87175 Score: 388
Period size: 40 Copynumber: 6.4 Consensus size: 39
86912 AAACCAAGTA
* * *
86922 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAG-TAACTCGCACAAATG
**
86961 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
87001 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
87041 CCTTCGGGACTTAGCCC-GAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG
87079 CCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
87119 CCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
87159 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
87176 CGTTATCATC
Statistics
Matches: 204, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
38 36 0.18
39 18 0.09
40 150 0.74
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG
Found at i:87156 original size:118 final size:119
Alignment explanation
Indices: 86922--87175 Score: 399
Period size: 118 Copynumber: 2.1 Consensus size: 119
86912 AAACCAAGTA
* * * *
86922 CCTTCGGGATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
86987 AGTTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
66 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
87041 CCTTCGGGACTTAGCCCGA-ATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATTA
1 CCTTCGGGACTTAGCCCGATATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TA
87103 GTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
64 GTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
87159 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
87176 CGTTATCATC
Statistics
Matches: 126, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
117 3 0.02
118 107 0.85
119 16 0.13
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (119 bp):
CCTTCGGGACTTAGCCCGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:95054 original size:40 final size:39
Alignment explanation
Indices: 94992--95247 Score: 381
Period size: 40 Copynumber: 6.5 Consensus size: 39
94982 AAACCAAGTA
* * *
94992 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAG-TAACTCGCACAAATG
**
95031 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
95071 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
95111 CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG
95150 CCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
* *
95190 CCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
95230 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
95248 TTATCATCCG
Statistics
Matches: 205, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
39 53 0.26
40 152 0.74
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG
Found at i:95151 original size:79 final size:79
Alignment explanation
Indices: 94992--95247 Score: 392
Period size: 79 Copynumber: 3.2 Consensus size: 79
94982 AAACCAAGTA
* * *
94992 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATA
**
95055 GTAGTTCGCACAAATG
64 GTAACTCGCACAAATG
95071 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATAGT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATAGT
95136 AACTCGCACAAATG
66 AACTCGCACAAATG
95150 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA-TA
* *
95214 GTCACTAGCACAAATG
64 GTAACTCGCACAAATG
95230 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
95248 TTATCATCCG
Statistics
Matches: 166, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
78 1 0.01
79 89 0.54
80 76 0.46
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATAGT
AACTCGCACAAATG
Found at i:95203 original size:119 final size:120
Alignment explanation
Indices: 94992--95247 Score: 387
Period size: 119 Copynumber: 2.1 Consensus size: 120
94982 AAACCAAGTA
* * *
94992 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
** *
95056 TAGTTCGCACAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAACTCGCACAAATG
66 TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTAGCACAAATG
95111 CCTTCGGGACTTAGCCCGGA-ATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATT
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-T
*
95173 AGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATG
64 AGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAATG
95230 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
95248 TTATCATCCG
Statistics
Matches: 126, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
118 2 0.02
119 117 0.93
120 7 0.06
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (120 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAATG
Done.