Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2627
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: 29418
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Found at i:1904 original size:79 final size:81
Alignment explanation
Indices: 1768--1952 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
1758 TTGAATGATG
*
1768 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
1832 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
1847 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
1909 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
1927 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1953 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:1966 original size:40 final size:40
Alignment explanation
Indices: 1769--1952 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
1759 TGAATGATGT
* * * *
1769 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
1809 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
1849 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
1887 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
1928 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
1953 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:1974 original size:79 final size:79
Alignment explanation
Indices: 1769--1985 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
1759 TGAATGATGT
** * * * **
1769 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
1832 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
1849 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
1914 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
1928 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
1986 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:9847 original size:79 final size:81
Alignment explanation
Indices: 9711--9895 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
9701 TTGAATGATG
*
9711 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
9775 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
9790 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
9852 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
9870 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
9896 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:9909 original size:40 final size:40
Alignment explanation
Indices: 9712--9895 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
9702 TGAATGATGT
* * * *
9712 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
9752 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
9792 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
9830 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
9871 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
9896 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:9917 original size:79 final size:79
Alignment explanation
Indices: 9712--9928 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
9702 TGAATGATGT
** * * * **
9712 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
9775 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
9792 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
9857 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
9871 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
9929 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:15372 original size:50 final size:50
Alignment explanation
Indices: 15297--15534 Score: 223
Period size: 50 Copynumber: 4.7 Consensus size: 50
15287 CGAAGCTTTC
* *
15297 TGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAATT
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAATT
* * *
15347 TGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGATC-A--AAGTTT
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAA--TT
* * * * *
15396 TCGGGTACACATACTAGCTTGCACTTAGTACTACACATGCGACCTATCAATC
1 T--GGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAATT
* * * * * *
15448 TAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCT
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAAT-T
** * *
15499 T-AAACACATAGTAGCCTGCACATAGTACTACACATG
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATG
15535 TGTTCTCACA
Statistics
Matches: 153, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
47 2 0.01
49 4 0.03
50 107 0.70
51 35 0.23
52 3 0.02
54 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (50 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAATT
Found at i:15473 original size:101 final size:101
Alignment explanation
Indices: 15293--15487 Score: 318
Period size: 101 Copynumber: 1.9 Consensus size: 101
15283 TAACCGAAGC
* * * * * * *
15293 TTTCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAATTTGGTACATGTA
1 TTTCGGGTACACATACTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTA
15358 GTAGCCTGCACTTAGTACTACACACGTGATCAAAGT
66 GTAGCCTGCACTTAGTACTACACACGTGATCAAAGT
*
15394 TTTCGGGTACACATACTAGCTTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTA
1 TTTCGGGTACACATACTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTA
15459 GTAGCCTGCACTTAGTACTACACACGTGA
66 GTAGCCTGCACTTAGTACTACACACGTGA
15488 CCTAACCATC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (101 bp):
TTTCGGGTACACATACTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTA
GTAGCCTGCACTTAGTACTACACACGTGATCAAAGT
Found at i:15915 original size:19 final size:20
Alignment explanation
Indices: 15887--15933 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
15877 AAGAACATGT
15887 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
15908 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
15927 TATATAT
1 TATATAT
15934 ACTTACAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:20102 original size:29 final size:29
Alignment explanation
Indices: 20039--20106 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
20029 TAATCAACCA
20039 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
20068 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
20097 CGCACACTTA
1 CGCACACTTA
20107 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:20247 original size:29 final size:30
Alignment explanation
Indices: 20208--20286 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
20198 CTTAATAATC
20208 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
20238 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
20267 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
20287 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:28170 original size:29 final size:29
Alignment explanation
Indices: 28107--28174 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
28097 TAATCAACCA
28107 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
28136 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
28165 CGCACACTTA
1 CGCACACTTA
28175 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:28315 original size:29 final size:30
Alignment explanation
Indices: 28276--28354 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
28266 CTTAATAATC
28276 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
28306 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
28335 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28355 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:28346 original size:174 final size:172
Alignment explanation
Indices: 27998--28348 Score: 533
Period size: 174 Copynumber: 2.0 Consensus size: 172
27988 AACTCAAGGT
* *
27998 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
28063 GAAATATATACTGGGTTGCACACATAATGTTTAGTAATCAACCACGCACACTTAGTGCCATGCAC
66 GAAATATATACTGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCAC
* ***
28128 TTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 TTTAAACTCACACACTTAGTGCCATACATTTCAAACCCGCAC
28170 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* * * *
28235 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 G-AAATATATACTGGGTT-GCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGC
* **
28300 ACTTTAAACTCGCACACTTAGTGCTGTACAATTT-AAACCCGCAC
129 ACTTTAAACTCACACACTTAGTGCCATAC-ATTTCAAACCCGCAC
28344 ACTTA
1 ACTTA
28349 GTGCCAATCT
Statistics
Matches: 161, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
172 64 0.40
173 15 0.09
174 78 0.48
175 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (172 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAATATATACTGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCAC
TTTAAACTCACACACTTAGTGCCATACATTTCAAACCCGCAC
Done.