Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2301
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: 29956
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:2960 original size:31 final size:32
Alignment explanation
Indices: 2915--2981 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
2905 ACATGCATGC
*
2915 ACCTTGCTAAAATGAATCTCCA-A-ATTCGGCTA
1 ACCTTGCTAAAATG-ATC-CCACACATTCGGCCA
*
2947 ACCTTG-TTAAATGATCCCACACATTCGGCCA
1 ACCTTGCTAAAATGATCCCACACATTCGGCCA
2978 ACCT
1 ACCT
2982 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 18 0.58
32 6 0.19
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (32 bp):
ACCTTGCTAAAATGATCCCACACATTCGGCCA
Found at i:3310 original size:30 final size:30
Alignment explanation
Indices: 3252--3310 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3242 TTGAAAATGT
* *
3252 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
3282 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
3311 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:6931 original size:36 final size:37
Alignment explanation
Indices: 6884--6961 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 37
6874 TTATTACGAA
* *
6884 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATC-G
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
6920 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
6957 GTCTT
1 GTCTT
6962 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 29 0.78
37 8 0.22
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:7158 original size:47 final size:47
Alignment explanation
Indices: 7080--7723 Score: 1193
Period size: 47 Copynumber: 13.7 Consensus size: 47
7070 CCCTTCGGGA
* * * * * *
7080 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7127 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7174 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7221 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7268 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7315 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7362 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7409 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7456 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7503 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7550 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7597 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7644 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7691 CTTATCACATATAT-CA-TTTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
7724 AGATCCTAAA
Statistics
Matches: 586, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
45 16 0.03
46 2 0.00
47 568 0.97
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11167 original size:24 final size:25
Alignment explanation
Indices: 11126--11175 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
11116 AAGGAATTCG
11126 CACACACACAGTGCCTCTAATTATT
1 CACACACACAGTGCCTCTAATTATT
* * *
11151 CACATACATAGTG-CTCTTATTATT
1 CACACACACAGTGCCTCTAATTATT
11175 C
1 C
11176 GTTAATACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (25 bp):
CACACACACAGTGCCTCTAATTATT
Found at i:11496 original size:38 final size:39
Alignment explanation
Indices: 11354--11603 Score: 320
Period size: 38 Copynumber: 6.5 Consensus size: 39
11344 AGCATGATTA
** *
11354 CTCTTCGGGTTTAGCACGGATATAT-ACTAGCACGAATG
1 CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
*
11392 CTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGG-ACTTAGCCCGGATATATCACTAGCACGAATG
11432 CTC-TCGGACTTAG-CCGGATATATCACTAGCACGAATG
1 CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
11469 CTC-TCGGACTTAGCCCGGATATATCACTAGCACGAATG
1 CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
*
11507 CTC-TCGGGACTTAG-CCGGATACATCACTAGCACGAATG
1 CTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAATG
* * *
11545 C-CTTCGGACTTAGTCCGGATATGGTCACTTAGCAC-AAAG
1 CTCTTCGGACTTAGCCCGGATAT-ATCAC-TAGCACGAATG
11584 C-CTTCGGGACTTAGCCCGGA
1 CTCTTC-GGACTTAGCCCGGA
11604 CATCATTCAA
Statistics
Matches: 193, Mismatches: 10, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
37 45 0.23
38 76 0.39
39 37 0.19
40 35 0.18
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:11948 original size:29 final size:29
Alignment explanation
Indices: 11909--11987 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
11899 CTTAATAATC
*
11909 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
11939 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
11968 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
11988 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:12030 original size:43 final size:43
Alignment explanation
Indices: 11969--12071 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
11959 TGCATTTCAA
11969 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
12012 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
12055 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
12072 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:13984 original size:37 final size:37
Alignment explanation
Indices: 13934--14012 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
13924 TTATTACGAA
* *
13934 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
13971 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
14008 GTCTT
1 GTCTT
14013 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:14209 original size:47 final size:47
Alignment explanation
Indices: 14131--14538 Score: 707
Period size: 47 Copynumber: 8.8 Consensus size: 47
14121 CCCTTCGGGA
* * * * * * *
14131 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
14178 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14225 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14272 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14319 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14365 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14412 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14459 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14506 CTTATCAC--ATATACACTTTCACATT-ATCACATC
1 CTTATCACATATATACACTTTCACATTCATCACATC
14539 CATTATCCAA
Statistics
Matches: 349, Mismatches: 11, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
44 8 0.02
45 17 0.05
46 46 0.13
47 278 0.80
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:14447 original size:187 final size:188
Alignment explanation
Indices: 14131--14538 Score: 707
Period size: 187 Copynumber: 2.2 Consensus size: 188
14121 CCCTTCGGGA
* * * * * * *
14131 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
14196 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
14261 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
14319 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
14383 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
14448 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14506 CTTATCAC--ATATACACTTTCACATT-ATCACATC
1 CTTATCACATATATACACTTTCACATTCATCACATC
14539 CATTATCCAA
Statistics
Matches: 211, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
184 8 0.04
185 17 0.08
187 153 0.73
188 33 0.16
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:22040 original size:16 final size:16
Alignment explanation
Indices: 22019--22052 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
22009 CTGTAACGCC
22019 CTAAAAATCCCAAAAT
1 CTAAAAATCCCAAAAT
*
22035 CTAAAAATCCTAAAAT
1 CTAAAAATCCCAAAAT
22051 CT
1 CT
22053 TGAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
CTAAAAATCCCAAAAT
Found at i:23604 original size:29 final size:28
Alignment explanation
Indices: 23545--23659 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 28
23535 GTGAGCATGA
* **
23545 ATATGAATGTGATTGGGCCTAACAGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
*
23573 ATATAAATGTGAGTTGGGCCTAATGGGTC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* *
23602 ATATATAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* *
23631 ATATGAATATGATT-GGCCTTAATGGGCC
1 ATATAAATGTGATTGGGCC-TAATGGGCC
23659 A
1 A
23660 GATATAGGTA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
27 4 0.05
28 23 0.32
29 46 0.63
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:23665 original size:57 final size:57
Alignment explanation
Indices: 23553--23668 Score: 146
Period size: 58 Copynumber: 2.0 Consensus size: 57
23543 GAATATGAAT
* * *
23553 GTGATTGGGCCTAACAGGCCATATAAATGTGAGTTGGGCCTAATGGGTCATATATAG
1 GTGATTGGGCCTAACAGGCCATATAAATATGAGTTGGGCCTAATGGGCCAGATATAG
** *
23610 GTGATTTGGGCCTAATGGGCCATATGAATATGA-TT-GGCCTTAATGGGCCAGATATAG
1 GTGA-TTGGGCCTAACAGGCCATATAAATATGAGTTGGGCC-TAATGGGCCAGATATAG
23667 GT
1 GT
23669 ATGTGAATTC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
56 4 0.08
57 23 0.45
58 24 0.47
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (57 bp):
GTGATTGGGCCTAACAGGCCATATAAATATGAGTTGGGCCTAATGGGCCAGATATAG
Done.