Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3386
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: 35146
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:6080 original size:40 final size:40
Alignment explanation
Indices: 6033--6316 Score: 362
Period size: 40 Copynumber: 7.1 Consensus size: 40
6023 CGGGCTTTAA
* * * *
6033 CCGGATATAGCCACTCGCTCAAATGCCTTCGGGACTTTGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGC
* * ** *
6073 CCGGATATAGT-AGTTTGCACAAATATCTTCAGGACTTAGC
1 CCGGATATAGTCA-CTAGCACAAATGCCTTCGGGACTTAGC
* *
6113 CCGGATATAGTAACTCGCACAAATGCC-TCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGC
* *
6152 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGC
6192 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTCACTAGCACAAATGCCTTCGGGACTTAGC
*
6232 CCGGA-ATTAGTCAATAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTCACTAGCACAAATGCCTTCGGGACTTAGC
*
6272 CTGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTCACTAGCACAAATGCCTTCGGGACTTAGC
6312 CCGGA
1 CCGGA
6317 ATTATCATCC
Statistics
Matches: 221, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
39 40 0.18
40 180 0.81
41 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGC
Found at i:6252 original size:119 final size:120
Alignment explanation
Indices: 6033--6320 Score: 381
Period size: 119 Copynumber: 2.4 Consensus size: 120
6023 CGGGCTTTAA
* * * * *
6033 CCGGATATAGCCACTCGCTCAAATGCCTTCGGGACTTTGCCCGG-ATATAGTAGTTTGCACAAAT
1 CCGGATATAGTCACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAGCTAGCACAAAT
* *
6097 ATCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATGCC-TCGGGACTTAGC
65 ACCTTCAGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGC
*
6152 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCA-CTAGCACAAAT
1 CCGGATATAGTCACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT-AGCTAGCACAAAT
* *
6216 GCCTTCGGGACTTAGCCCGGA-ATTAGTCAA-TAGCACAAATGCCTTCGGGACTTAGC
65 ACCTTCAGGACTTAGCCCGGATA-TAGT-AACTAGCACAAATGCCTTCGGGACTTAGC
* *
6272 CTGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
1 CCGGATA-TAGTCACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
6321 TCATCCGAAT
Statistics
Matches: 150, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
118 1 0.01
119 88 0.59
120 61 0.41
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (120 bp):
CCGGATATAGTCACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAGCTAGCACAAATA
CCTTCAGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGC
Found at i:10107 original size:103 final size:102
Alignment explanation
Indices: 9928--10132 Score: 401
Period size: 103 Copynumber: 2.0 Consensus size: 102
9918 TAAGGCCGAG
9928 CACTAATTGCCTTCTGGATTACTGCAATCGGTGAAAATTCCACTATGGAAGTGGGAGAGAGTAAC
1 CACTAATTGCCTTCTGGATTACTGCAATCGGTGAAAATTCCACTATGGAAGTGGGAGAGAGTAAC
9993 TATGGACTTTGTGAGTGGGCTACCTTTGACACCCACCA
66 TATGGACTTTGTG-GTGGGCTACCTTTGACACCCACCA
10031 CACTAATTGCCTTCTGGATTACTGCAATCGGTGAAAATTCCACTATGGAAGTGGGAGAGAGTAAC
1 CACTAATTGCCTTCTGGATTACTGCAATCGGTGAAAATTCCACTATGGAAGTGGGAGAGAGTAAC
10096 TATGGACTTTGTGGTGGGCTACCTTTGACACCCACCA
66 TATGGACTTTGTGGTGGGCTACCTTTGACACCCACCA
10133 AGAAAGATTA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 24 0.24
103 78 0.76
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (102 bp):
CACTAATTGCCTTCTGGATTACTGCAATCGGTGAAAATTCCACTATGGAAGTGGGAGAGAGTAAC
TATGGACTTTGTGGTGGGCTACCTTTGACACCCACCA
Found at i:12877 original size:22 final size:21
Alignment explanation
Indices: 12846--12886 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12836 CATGTTTGAC
12846 TGTTACTATTTACTGCATGCCA
1 TGTTACTATTTACTG-ATGCCA
* *
12868 TGTTATTATTTTCTGATGC
1 TGTTACTATTTACTGATGC
12887 ATGGGACTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (21 bp):
TGTTACTATTTACTGATGCCA
Found at i:13196 original size:21 final size:20
Alignment explanation
Indices: 13154--13213 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
13144 AGCTCCAATC
13154 AGCTCACTTGAGCTCGATTT
1 AGCTCACTTGAGCTCGATTT
*
13174 AGCTCGCTTGAGCTCGAATTT
1 AGCTCACTTGAGCTCG-ATTT
* *
13195 AGCTCATTTCAGCTC-ATTT
1 AGCTCACTTGAGCTCGATTT
13214 CTTCTTCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.11
20 15 0.43
21 16 0.46
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (20 bp):
AGCTCACTTGAGCTCGATTT
Found at i:13442 original size:13 final size:13
Alignment explanation
Indices: 13424--13457 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
13414 TTATATGAAA
*
13424 AATTATTTTATTT
1 AATTATGTTATTT
13437 AATTATGTTATTT
1 AATTATGTTATTT
13450 AATTATGT
1 AATTATGT
13458 AGGTTAGCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
AATTATGTTATTT
Found at i:16432 original size:11 final size:11
Alignment explanation
Indices: 16418--16449 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
16408 ATATATCATA
16418 GCATATCATGT
1 GCATATCATGT
16429 GCATATCATGT
1 GCATATCATGT
16440 -CATATCATGT
1 GCATATCATGT
16450 ATATCAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (11 bp):
GCATATCATGT
Found at i:16434 original size:21 final size:21
Alignment explanation
Indices: 16410--16449 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
16400 TATAGTGAAT
16410 ATATCATAG-CATATCATGTGC
1 ATATCAT-GTCATATCATGTGC
16431 ATATCATGTCATATCATGT
1 ATATCATGTCATATCATGT
16450 ATATCAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATCATGTCATATCATGTGC
Found at i:16459 original size:10 final size:10
Alignment explanation
Indices: 16410--16455 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
16400 TATAGTGAAT
16410 ATATCATAG-C
1 ATATCAT-GTC
16420 ATATCATGTGC
1 ATATCATGT-C
16431 ATATCATGTC
1 ATATCATGTC
16441 ATATCATGT-
1 ATATCATGTC
16450 ATATCA
1 ATATCA
16456 ATGTTTCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.21
10 17 0.50
11 10 0.29
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (10 bp):
ATATCATGTC
Found at i:23166 original size:43 final size:43
Alignment explanation
Indices: 23008--23166 Score: 130
Period size: 43 Copynumber: 3.7 Consensus size: 43
22998 TGTGTTATCG
* *
23008 TGTAAGACCATGTCTAGGACCTTGGCATTGACT-TCT-ATTTTACGA
1 TGTAAGACCATGTCTGGGACGTTGGCATTGA-TATCTGA--TTAC-A
* * *
23053 -GTAAGACCATGTCTGGGACATTGGCA-TCATATCTGATTTCA
1 TGTAAGACCATGTCTGGGACGTTGGCATTGATATCTGATTACA
* * * * * *
23094 TGTAAGACCCTATTTGGGACAG-TGACATTGATGTTTGATTACA
1 TGTAAGACCATGTCTGGGAC-GTTGGCATTGATATCTGATTACA
*
23137 TGTTAGACCATGTCTGGGACGTTGGCATTG
1 TGTAAGACCATGTCTGGGACGTTGGCATTG
23167 TATAAGCTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
41 1 0.01
42 25 0.28
43 39 0.43
44 25 0.28
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCATTGATATCTGATTACA
Found at i:25027 original size:27 final size:27
Alignment explanation
Indices: 24997--25201 Score: 241
Period size: 27 Copynumber: 7.6 Consensus size: 27
24987 ATATTAAGTC
* * *
24997 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * *
25024 CGCACACTTAGTGCCACGTAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
25052 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
25079 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
25106 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
25133 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
*
25160 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
25187 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25202 GTACAATTTA
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 131 0.84
28 25 0.16
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:25136 original size:54 final size:54
Alignment explanation
Indices: 24997--25200 Score: 266
Period size: 54 Copynumber: 3.8 Consensus size: 54
24987 ATATTAAGTC
* * * * *
24997 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * *
25052 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
25106 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATAGTCAAAT
*
25160 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
25201 TGTACAATTT
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 82 0.64
55 46 0.36
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:32908 original size:27 final size:27
Alignment explanation
Indices: 32877--33054 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
32867 TATATTAGTC
* * * *
32877 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
32904 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
32931 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
32959 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
32986 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
33013 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
33040 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
33055 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:33016 original size:82 final size:81
Alignment explanation
Indices: 32898--33053 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
32888 TGCTATATAA
* *
32898 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
32963 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
32980 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
33044 CACTTAGTGC
65 CACTTAGTGC
33054 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.