Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2304
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: 36781
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:6846 original size:20 final size:19
Alignment explanation
Indices: 6821--6863 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
6811 GTTGAGGGCT
6821 TGGGGT-GGTTGGTGGGGCGG
1 TGGGGTGGGTTGG-GGGG-GG
6841 TGGGGTGGGTTGGGGGGGG
1 TGGGGTGGGTTGGGGGGGG
6860 TGGG
1 TGGG
6864 TGTGCTGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.00, C:0.02, G:0.74, T:0.23
Consensus pattern (19 bp):
TGGGGTGGGTTGGGGGGGG
Found at i:12926 original size:39 final size:39
Alignment explanation
Indices: 12830--13011 Score: 199
Period size: 39 Copynumber: 4.6 Consensus size: 39
12820 TTGAATGCTG
* * *
12830 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTA-TAAT
**
12869 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATAAT
* * *
12909 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATAAT
* * *
12948 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAT-AAT
12988 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
13012 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
38 1 0.01
39 64 0.52
40 50 0.41
41 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATAAT
Found at i:12992 original size:79 final size:80
Alignment explanation
Indices: 12830--13008 Score: 224
Period size: 79 Copynumber: 2.3 Consensus size: 80
12820 TTGAATGCTG
* * *
12830 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
* *
12894 TGTGCGAGTTATAAT
66 CGTGCGAGTTATAAA
**
12909 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACAAT-TCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACAATATCCGGACTAAGAT-CCGAAGGCA
*
12970 TTCGTGCGAGTTTTAAAA
64 TTCGTGCGAGTTAT-AAA
12988 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
13009 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
77 1 0.01
78 30 0.34
79 48 0.55
80 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTATAAA
Found at i:13032 original size:39 final size:39
Alignment explanation
Indices: 12883--13057 Score: 124
Period size: 39 Copynumber: 4.5 Consensus size: 39
12873 GGACTAAGAT
** * *
12883 CCGAAGGCATTTGTGCGAGTTAT-AATTCCGGGTTAAGTC
1 CCGAAGGCA-TTGAACGAGTTCTAAAATCCGGGTTAAGTC
* ** * *
12922 CCGAAGGCCTTTGTGCGAG--ATACAATTCCGGGTTAAGTC
1 CCGAAGG-CATTGAACGAGTTCTA-AAATCCGGGTTAAGTC
** *
12961 CCGAAGGCATTCGTGCGAGTTTTAAAATCCGGGTTAAGTC
1 CCGAAGGCATT-GAACGAGTTCTAAAATCCGGGTTAAGTC
* ** * *
13001 CCGAAGGCATTGAATGAGTTACTATGA-CCGGGCTATGTC
1 CCGAAGGCATTGAACGAGTT-CTAAAATCCGGGTTAAGTC
13040 CCGAAGGCATTGAACGAG
1 CCGAAGGCATTGAACGAG
13058 GAGCTATATC
Statistics
Matches: 116, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
37 2 0.02
38 3 0.03
39 79 0.68
40 30 0.26
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTGAACGAGTTCTAAAATCCGGGTTAAGTC
Found at i:13032 original size:79 final size:78
Alignment explanation
Indices: 12883--13050 Score: 203
Period size: 79 Copynumber: 2.1 Consensus size: 78
12873 GGACTAAGAT
* * * **
12883 CCGAAGGCATTTGTGCGAGTTATAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACAAT
1 CCGAAGGCATTCGTGCGAGTTATAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAAT
* *
12948 TCCGGGTTAAGTC
66 ACCGGGCTAAGTC
* * * *
12961 CCGAAGGCATTCGTGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGG-CATTGAATGAGTTACTA
1 CCGAAGGCATTCGTGCGAGTTAT-AAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
*
13025 TGACCGGGCTATGTC
65 T-ACCGGGCTAAGTC
13040 CCGAAGGCATT
1 CCGAAGGCATT
13051 GAACGAGGAG
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
78 33 0.43
79 43 0.57
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (78 bp):
CCGAAGGCATTCGTGCGAGTTATAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAAT
ACCGGGCTAAGTC
Found at i:20249 original size:40 final size:40
Alignment explanation
Indices: 20131--20309 Score: 165
Period size: 40 Copynumber: 4.5 Consensus size: 40
20121 TTGAATGCTG
* *
20131 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTA-AGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGA-T-ACTAAT
** * *
20170 ATCCGGACTAAGAT-CCGAAGG--TTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCCTTTGTGCGAGATACTAAT
20209 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
* * ** *
20249 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
20289 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
20310 ATTGAATGAG
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
37 1 0.01
38 18 0.15
39 13 0.11
40 86 0.72
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
Found at i:20266 original size:78 final size:80
Alignment explanation
Indices: 20131--20309 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
20121 TTGAATGCTG
* * *
20131 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGG-TTT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGATTC
*
20194 GTGCGAGTTATT-AAT
66 GTGCGAGTT-TTAAAA
**
20209 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGG-
20270 ATTCGTGCGAGTTTTAAAA
62 ATTCGTGCGAGTTTTAAAA
20289 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
20310 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
77 2 0.02
78 41 0.47
79 11 0.12
80 34 0.39
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGATTC
GTGCGAGTTTTAAAA
Found at i:20310 original size:40 final size:39
Alignment explanation
Indices: 20194--20312 Score: 166
Period size: 40 Copynumber: 3.0 Consensus size: 39
20184 CCGAAGGTTT
* *
20194 GTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTT
1 GTGCGAGTT-TTAATTCCGGGTTAAGTCCCGAAGGCATTC
**
20234 GTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTC
1 GTGCGAG-TTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
*
20274 GTGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATT
1 GTGCGAGTTTT-AATTCCGGGTTAAGTCCCGAAGGCATT
20313 GAATGAGTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.03
40 67 0.96
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
GTGCGAGTTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
Found at i:20366 original size:39 final size:39
Alignment explanation
Indices: 20131--20371 Score: 120
Period size: 40 Copynumber: 6.1 Consensus size: 39
20121 TTGAATGCTG
* ** *
20131 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTGAAC-GAGTGACTATA
* * ** * *
20171 TCCGGACTAAGAT-CCGAAGG-TTTGTGCGAGTTATTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTGAACGAGTGACTATA
* * **
20208 TTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGAT-ACTA-A
1 -TCCGGGCTAAGTCCCGAAGG-CATTGAACGAG-TGACTATA
* ** ** *
20248 TTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 -TCCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACT-ATA
* * *
20289 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATA
*
20328 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATA
20367 TCCGG
1 TCCGG
20372 TTAAATTCCG
Statistics
Matches: 168, Mismatches: 20, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
37 2 0.01
38 42 0.25
39 32 0.19
40 89 0.53
41 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATA
Found at i:26568 original size:40 final size:41
Alignment explanation
Indices: 26501--26594 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
26491 CGACTATGAT
*
26501 TGGCACTAAGTGTGCGGTTTAATATAGCTTCGGCTATA-AA
1 TGGCACTAAGTGTGCGGTTTAACATAGCTTCGGCTATATAA
** *
26541 TGGCACTAAGTGTGCGAG-TTGGCATAGCTTCGGTTATATAA
1 TGGCACTAAGTGTGCG-GTTTAACATAGCTTCGGCTATATAA
*
26582 -GGCAGTAAGTGTG
1 TGGCACTAAGTGTG
26595 TGATACCGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 44 0.94
41 3 0.06
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.31
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGGTTTAACATAGCTTCGGCTATATAA
Found at i:29757 original size:18 final size:18
Alignment explanation
Indices: 29734--29822 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 18
29724 GAACGATTAT
* *
29734 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAATCAA
*
29752 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
29770 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
*
29788 TTATTCAGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
29807 TTATTCAGTAACAATC
1 TTATTCAGTAACAATC
29823 GATCTTTCCA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
18 42 0.72
19 16 0.28
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:29775 original size:36 final size:37
Alignment explanation
Indices: 29734--29822 Score: 126
Period size: 36 Copynumber: 2.4 Consensus size: 37
29724 GAACGATTAT
* * *
29734 TTATTCAGTAACAGTCAGTTATTCGGTAACAA-TCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATTAAA
* *
29770 TTATTCAATAATAATCAGTTATTCAGTAACAATTAAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATTAAA
29807 TTATTCAGTAACAATC
1 TTATTCAGTAACAATC
29823 GATCTTTCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 28 0.62
37 17 0.38
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (37 bp):
TTATTCAGTAACAATCAGTTATTCAGTAACAATTAAA
Found at i:30016 original size:47 final size:47
Alignment explanation
Indices: 29947--30063 Score: 164
Period size: 47 Copynumber: 2.5 Consensus size: 47
29937 CAGTAACAGT
* * * *
29947 AACAGTAGCAATACGGTACACAGAGTACCTCATCGGTACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
*
29994 AACAGTGACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
*
30041 AATAGTAACAGTAACGGTA-ACAG
1 AACAGTAACAGT-ACGGTACACAG
30064 TAACAATATC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 56 0.90
48 6 0.10
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.16
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:31898 original size:31 final size:32
Alignment explanation
Indices: 31842--31904 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
31832 AACACTTGTC
*
31842 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
31874 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
31905 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:32044 original size:6 final size:6
Alignment explanation
Indices: 32023--32054 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
32013 ATTTATTTCA
32023 TAATA- TAATA- TAATAT TAATAT TAATAT TAAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAAT
32055 TAATAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:32050 original size:12 final size:11
Alignment explanation
Indices: 32022--32059 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
32012 AATTTATTTC
32022 ATAATA-TAAT
1 ATAATATTAAT
32032 ATAATATTAAT
1 ATAATATTAAT
32043 ATTAATATTAAT
1 A-TAATATTAAT
32055 -TAATA
1 ATAATA
32060 ATTATAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 11 0.42
11 5 0.19
12 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATAATATTAAT
Found at i:34635 original size:30 final size:29
Alignment explanation
Indices: 34596--34660 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
34586 GTCACCATCT
* * *
34596 CTTTCCATAATTTGATAGCCGAAGCTATCC
1 CTTTTCATAATTTGACAGCCGAAGATAT-C
34626 CTTTTCATAATTTGACAGCCGAAGATATC
1 CTTTTCATAATTTGACAGCCGAAGATATC
34655 CTTTTC
1 CTTTTC
34661 CATTAGTCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (29 bp):
CTTTTCATAATTTGACAGCCGAAGATATC
Found at i:34750 original size:12 final size:12
Alignment explanation
Indices: 34733--34788 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
34723 CAATAATAAC
34733 ATTTAAAACA-T
1 ATTTAAAACACT
34744 AATTTAAAACACT
1 -ATTTAAAACACT
34757 ATTT-AAACGTA-T
1 ATTTAAAAC--ACT
34769 AATTTAAAACACT
1 -ATTTAAAACACT
34782 ATTTAAA
1 ATTTAAA
34789 CGTACGAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
11 4 0.11
12 23 0.61
13 7 0.18
14 4 0.11
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36
Consensus pattern (12 bp):
ATTTAAAACACT
Found at i:34773 original size:25 final size:25
Alignment explanation
Indices: 34742--34792 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
34732 CATTTAAAAC
34742 ATAATTTAAAACACTATTTAAACGT
1 ATAATTTAAAACACTATTTAAACGT
34767 ATAATTTAAAACACTATTTAAACGT
1 ATAATTTAAAACACTATTTAAACGT
34792 A
1 A
34793 CGAACTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (25 bp):
ATAATTTAAAACACTATTTAAACGT
Done.