Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2974
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: 25407
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:572 original size:46 final size:46
Alignment explanation
Indices: 516--691 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
506 GATGGTTGAG
*
516 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * * * * * *
562 TATCTGAACTCGTTGAGTTGAGTCCGAGTTCGA--GAGTGTA-ACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTA-TGGATGCGA-A
* *
608 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** *
654 CGCCCGAGCTCGTTGAGTTGAGTCCGA-TTCACTTATGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
692 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 20, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
45 15 0.14
46 85 0.82
47 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:2930 original size:42 final size:42
Alignment explanation
Indices: 2884--2966 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
2874 AGGCTTGAGG
* * *
2884 GAGCAATTAAGGTACGTTTTTGACTCGTTTTTAATGATTTCA
1 GAGCAATTAAGGAACGATTTTGACTCATTTTTAATGATTTCA
*
2926 GAGCAATTAAGGAACGATTTTGATTCATTTTTAATGATTTC
1 GAGCAATTAAGGAACGATTTTGACTCATTTTTAATGATTTC
2967 TACGTTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (42 bp):
GAGCAATTAAGGAACGATTTTGACTCATTTTTAATGATTTCA
Found at i:8174 original size:45 final size:44
Alignment explanation
Indices: 8109--8311 Score: 240
Period size: 45 Copynumber: 4.7 Consensus size: 44
8099 ATCGTACACC
** * *
8109 ACTATTCAAGCCTTTGAGCCTAGCAGGCTATGATGCCTGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATG-CGGTGAAAT
*
8154 ACTATTCGGGCCTTCAAGCCTAGCAGGCTATGATGCCGGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATG-CGGTGAAAT
*
8199 ACTATTCGGGCCTTCGAGCCTAGCAGGC--T-AT-CGGTGAGAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCGGTGAAAT
* *
8239 ACTATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCTGGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGC-GGTGAAAT
*
8284 GA-TA-TCGGG-CTTCGAGCCTAGTAGGCTA
1 -ACTATTCGGGCCTTCGAGCCTAGCAGGCTA
8312 AATGCCGGTG
Statistics
Matches: 143, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
40 35 0.24
42 3 0.02
43 22 0.15
44 6 0.04
45 76 0.53
46 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (44 bp):
ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCGGTGAAAT
Found at i:8267 original size:85 final size:83
Alignment explanation
Indices: 8147--8311 Score: 242
Period size: 85 Copynumber: 2.0 Consensus size: 83
8137 TATGATGCCT
*
8147 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATGATGCCGGTGAAAT-ACTATTCGGGCC
1 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCGGG-C
8211 TTCGAGCCTAGCAGGCTATCG
63 TTCGAGCCTAGCAGGCTATCG
* * * *
8232 GTGAGATACTATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCTGGTGAAATGATATCGGGCTTC
1 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTC
*
8297 GAGCCTAGTAGGCTA
66 GAGCCTAGCAGGCTA
8312 AATGCCGGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 18 0.25
84 5 0.07
85 49 0.67
86 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (83 bp):
GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTC
GAGCCTAGCAGGCTATCG
Found at i:13191 original size:12 final size:13
Alignment explanation
Indices: 13163--13195 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
13153 TTATTTCTTT
13163 TTCTCCATCTACC
1 TTCTCCATCTACC
*
13176 TTCTCC-TCTTCC
1 TTCTCCATCTACC
13188 TTCTCCAT
1 TTCTCCAT
13196 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:14345 original size:27 final size:28
Alignment explanation
Indices: 14246--14365 Score: 188
Period size: 28 Copynumber: 4.3 Consensus size: 28
14236 ATTTACTAGA
14246 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
14274 ATACCCCTATATATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
14302 ATACCCCTATGTATGCAAAATTATCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* * *
14330 AT-CCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
14357 ATACCCCTA
1 ATACCCCTA
14366 GGGTTAATTT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 23 0.27
28 61 0.73
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:14514 original size:28 final size:27
Alignment explanation
Indices: 14481--14552 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
14471 CTGGTGGCTA
*
14481 TGCCACAAATTATCTGTTCTAGTGGCCC
1 TGCCACAAA-TATCTGTTCTAGTGGCAC
**
14509 TGCCACGTATATCTGTTCTAGTGGCAC
1 TGCCACAAATATCTGTTCTAGTGGCAC
*
14536 AGCCACAAAATATCTGT
1 TGCCAC-AAATATCTGT
14553 ATCTGGTGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (27 bp):
TGCCACAAATATCTGTTCTAGTGGCAC
Found at i:15566 original size:16 final size:17
Alignment explanation
Indices: 15545--15577 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
15535 CACATTGAAG
15545 TGTTTT-TTGAAAACCT
1 TGTTTTATTGAAAACCT
15561 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
15578 CTTCTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTTTATTGAAAACCT
Found at i:16194 original size:11 final size:11
Alignment explanation
Indices: 16178--16203 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16168 CGAAGCCCAC
16178 ATCACAATAAT
1 ATCACAATAAT
16189 ATCACAATAAT
1 ATCACAATAAT
16200 ATCA
1 ATCA
16204 AACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Done.