Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2858
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: 24412
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Found at i:1515 original size:44 final size:44
Alignment explanation
Indices: 1371--1533 Score: 169
Period size: 44 Copynumber: 3.7 Consensus size: 44
1361 TGTAACCCGC
* *
1371 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TCGGCATTCGCAT
* *
1416 CCA-AAGTGAACTCGGACTCAAC-CAACGATTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTCGGCATTCGC-A--T
* *
1459 ACACTCA--GAACTCGGACTCAACTCAACGAGT-GGACATTCGCAT
1 CCA-TAAGTGAACTCGGACTCAACTCAACGAGTCGG-CATTCGCAT
1502 CCATAAGTGAACTCGGACTCAACTCAACGAGT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGT
1534 TCGGATGCTC
Statistics
Matches: 97, Mismatches: 10, Indels: 23
0.75 0.08 0.18
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 6 0.06
43 29 0.30
44 49 0.51
45 8 0.08
46 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTCGGCATTCGCAT
Found at i:8971 original size:93 final size:93
Alignment explanation
Indices: 8859--9030 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
8849 CGCCCATAAG
* *
8859 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
8924 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
8952 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
9017 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
9031 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:9027 original size:46 final size:46
Alignment explanation
Indices: 8852--9027 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
8842 TGTAACCCGC
* * *
8852 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
8898 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
8948 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
8991 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
9028 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:17807 original size:37 final size:37
Alignment explanation
Indices: 17747--17824 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
17737 TATTACGAAG
* * *
17747 TCTTACCCGGACATAATCTCCACACGAAGTTATCGGA
1 TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGA
* *
17784 TCTTACCCGGACAAAATCCCCACACGTAGTCATCGGG
1 TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGA
17821 TCTT
1 TCTT
17825 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (37 bp):
TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGA
Found at i:18012 original size:47 final size:47
Alignment explanation
Indices: 17943--18263 Score: 509
Period size: 47 Copynumber: 6.7 Consensus size: 47
17933 CCCTTCGGGA
* * * * *
17943 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17990 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18037 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18086 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18135 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18182 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
18229 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
18264 AGAATCCTAA
Statistics
Matches: 262, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 165 0.63
49 96 0.37
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:18147 original size:96 final size:94
Alignment explanation
Indices: 17943--18263 Score: 509
Period size: 96 Copynumber: 3.4 Consensus size: 94
17933 CCCTTCGGGA
* * * *
17943 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
18008 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
18037 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
18102 ACACTTTCACATTCATCACATCGGCCATTAGGC
62 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
18135 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
18200 TTTCACATTCATCACATCAGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
18229 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATCCATCACAT
18264 AGAATCCTAA
Statistics
Matches: 213, Mismatches: 9, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
93 1 0.00
94 76 0.36
96 89 0.42
98 47 0.22
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:20404 original size:85 final size:85
Alignment explanation
Indices: 20283--20453 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
20273 TGCCCATTCC
20283 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
1 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
20348 ACATCTTGTCCACCCATGCT
66 ACATCTTGTCCACCCATGCT
20368 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
1 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
20433 ACATCTTGTCCACCCATGCT
66 ACATCTTGTCCACCCATGCT
20453 C
1 C
20454 ATGGCCGGCC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (85 bp):
CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
ACATCTTGTCCACCCATGCT
Found at i:22108 original size:40 final size:39
Alignment explanation
Indices: 22076--22375 Score: 471
Period size: 40 Copynumber: 7.6 Consensus size: 39
22066 CCAGCATGAT
* * *
22076 TGCTCTTCGAGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCG-GACTTAGCCCGGATATATCACTAGCACGAA
** *
22116 TGCTCTTCGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
22155 TGCTC-TCGGTACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATATATCACTAGCACGAA
22194 TGCTCTTCGGACTTAGCCCGG--ATATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
22231 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
*
22270 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAA
22310 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAA
22350 TGCTCTTCGGGACTTAGCCCGGATAT
1 TGCTCTTC-GGACTTAGCCCGGATAT
22376 GCTCTTCGGG
Statistics
Matches: 244, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
37 37 0.15
38 4 0.02
39 94 0.39
40 109 0.45
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:22258 original size:76 final size:78
Alignment explanation
Indices: 22076--22372 Score: 467
Period size: 76 Copynumber: 3.8 Consensus size: 78
22066 CCAGCATGAT
* * * * *
22076 TGCTCTTCGAGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGG-TTTAGCACGGATA
1 TGCTCTTCG-GACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGA-A
22140 TATCACTAGCACGAA
64 TATCACTAGCACGAA
22155 TGCTC-TCGGTACTTAGCCCGGATATATCACTAGCACGAATGCTCTTC-GGACTTAGCCCGG-AT
1 TGCTCTTCGG-ACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAAT
22217 ATCACTAGCACGAA
65 ATCACTAGCACGAA
*
22231 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATAT
1 TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGA-AT
22296 ATCACTAGCACGAA
65 ATCACTAGCACGAA
22310 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGA
1 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGA
22373 TATGCTCTTC
Statistics
Matches: 204, Mismatches: 7, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
76 57 0.28
77 20 0.10
78 45 0.22
79 29 0.14
80 53 0.26
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (78 bp):
TGCTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAATA
TCACTAGCACGAA
Found at i:22377 original size:25 final size:25
Alignment explanation
Indices: 22349--22400 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
22339 ACTAGCACGA
22349 ATGCTCTTCGGGACTTAGCCCGGAT
1 ATGCTCTTCGGGACTTAGCCCGGAT
22374 ATGCTCTTCGGGACTTAGCCCGGAT
1 ATGCTCTTCGGGACTTAGCCCGGAT
22399 AT
1 AT
22401 ATCACTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (25 bp):
ATGCTCTTCGGGACTTAGCCCGGAT
Found at i:23670 original size:37 final size:37
Alignment explanation
Indices: 23611--23682 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
23601 ATTACGAAGT
* * *
23611 CTTACCCGGACATAATCTCCACACGAAGTTATCGGTG
1 CTTACCCGGACAAAATCCCCACACGAAGTCATCGGTG
*
23648 CTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 CTTACCCGGACAAAATCCCCACACGAAGTCATCGG
23683 GTCTTTAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (37 bp):
CTTACCCGGACAAAATCCCCACACGAAGTCATCGGTG
Found at i:24014 original size:95 final size:94
Alignment explanation
Indices: 23804--24218 Score: 608
Period size: 95 Copynumber: 4.4 Consensus size: 94
23794 CCCTTCGGGA
* * * *
23804 CTTATCACATTTATACACTTTCA-A-CCATCACATCTGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
23867 TTTCACATTCATCACACATCGGCCATATTAGGC
66 TTTCACATTCAT--CACATCGGCC--ATTAGGC
*
23900 CTTATCACATATATACACTTTCACTTTCATCACATCGGCCATTAGGCCTTATCACATAATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT-ATATACA
23965 CTTTCACATTCATCACATCGGCCATTAGGC
65 CTTTCACATTCATCACATCGGCCATTAGGC
23995 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATTATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA-TATACA
24060 CTTTCACATTCATCACATCGGCCATTAGGC
65 CTTTCACATTCATCACATCGGCCATTAGGC
24090 CTTAT-AC-TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
24153 TTTCAACAGTCAATCACACGCGGCC-TTAGGC
66 TTTC-ACATTC-ATCACA-TCGGCCATTAGGC
* * *
24184 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
24219 AGAATCCTAA
Statistics
Matches: 298, Mismatches: 11, Indels: 20
0.91 0.03 0.06
Matches are distributed among these distances:
92 11 0.04
93 54 0.18
94 20 0.07
95 111 0.37
96 44 0.15
97 10 0.03
98 28 0.09
99 20 0.07
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:24027 original size:47 final size:47
Alignment explanation
Indices: 23804--24218 Score: 608
Period size: 48 Copynumber: 8.7 Consensus size: 47
23794 CCCTTCGGGA
* * * *
23804 CTTATCACATTTATACACTTTCA-A-CCATCACATCTGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23849 CTTATCACATATATACACTTTCACATTCATCACACATCGGCCATATTAGGC
1 CTTATCACATATATACACTTTCACATTCAT--CACATCGGCC--ATTAGGC
*
23900 CTTATCACATATATACACTTTCACTTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23947 CTTATCACATAATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACAT-ATATACACTTTCACATTCATCACATCGGCCATTAGGC
23995 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24042 CTTATCACATATTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATA-TATACACTTTCACATTCATCACATCGGCCATTAGGC
24090 CTTAT-AC-TATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
24135 CTTATCACATATATACACTTTCAACAGTCAATCACACGCGGCC-TTAGGC
1 CTTATCACATATATACACTTTC-ACATTC-ATCACA-TCGGCCATTAGGC
* * *
24184 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
24219 AGAATCCTAA
Statistics
Matches: 343, Mismatches: 13, Indels: 27
0.90 0.03 0.07
Matches are distributed among these distances:
45 63 0.18
46 5 0.01
47 89 0.26
48 97 0.28
49 48 0.14
50 5 0.01
51 36 0.10
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.