Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1211
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: 19081
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Found at i:1163 original size:47 final size:47
Alignment explanation
Indices: 1087--1264 Score: 225
Period size: 51 Copynumber: 3.7 Consensus size: 47
1077 ACTATTGTGA
1087 GGTC-ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATT
1 GGTCGATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATT
* * * *
1133 GGTCGATATGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCGATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGATAA-T-T
* *
1183 GATC-ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATT
1 GGTCGA--TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GATAATT
1232 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCG-ATGTGTAGTACTAAGTGCAGGCTACTA
1265 TGCGTACCAG
Statistics
Matches: 112, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
46 4 0.04
47 30 0.27
48 6 0.05
49 32 0.29
50 7 0.06
51 33 0.29
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (47 bp):
GGTCGATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATT
Found at i:1262 original size:49 final size:49
Alignment explanation
Indices: 1090--1277 Score: 245
Period size: 49 Copynumber: 3.8 Consensus size: 49
1080 ATTGTGAGGT
*
1090 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GATAATTGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCG
* * * * * *
1138 -ATATGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-T-TGGTCG
* * *
1188 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCG
*
1237 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
1278 GCTTCGGCTA
Statistics
Matches: 117, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
47 32 0.27
48 4 0.03
49 42 0.36
50 5 0.04
51 34 0.29
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCG
Found at i:4204 original size:14 final size:14
Alignment explanation
Indices: 4182--4239 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
4172 GTATCGTATC
*
4182 TTGGGTTTCTTTAT
1 TTGGATTTCTTTAT
4196 TTGGATTTCTTTAT
1 TTGGATTTCTTTAT
* *
4210 TCTGGGTTT-TCTAT
1 T-TGGATTTCTTTAT
4224 CTTGGATTTCTTTAT
1 -TTGGATTTCTTTAT
4239 T
1 T
4240 CTTTTCTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.62
Consensus pattern (14 bp):
TTGGATTTCTTTAT
Found at i:4228 original size:29 final size:29
Alignment explanation
Indices: 4183--4241 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
4173 TATCGTATCT
*
4183 TGGGTTTCTTTATTTGGATTTCTTTATTC
1 TGGGTTTCTCTATTTGGATTTCTTTATTC
4212 TGGGTTT-TCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTCTAT-TTGGATTTCTTTATTC
4241 T
1 T
4242 TTTCTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.10, C:0.12, G:0.17, T:0.61
Consensus pattern (29 bp):
TGGGTTTCTCTATTTGGATTTCTTTATTC
Found at i:6356 original size:51 final size:49
Alignment explanation
Indices: 6234--6423 Score: 247
Period size: 49 Copynumber: 3.8 Consensus size: 49
6224 ATTGTGAGGT
* *
6234 CATGTGTAGTACTAAGTGCATGG-TACTACGTGTACCGGATAATTGGTCG
1 CATGTGTAGTACTAAGTGCA-GGCTACTACGCGTACCAGATAATTGGTCG
* * * * *
6283 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-T-TGGTCG
* * *
6334 CATGTGTAGTACTAAGTTCAGGCTACTACGTGTACCAGATTATTGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCG
*
6383 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
6424 GCTTCGGCCA
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
48 2 0.02
49 76 0.63
50 2 0.02
51 40 0.33
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCG
Found at i:6399 original size:100 final size:100
Alignment explanation
Indices: 6234--6418 Score: 327
Period size: 100 Copynumber: 1.9 Consensus size: 100
6224 ATTGTGAGGT
*
6234 CATGTGTAGTACTAAGTGCATGGTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAAG
1 CATGTGTAGTACTAAGTGCATGGTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACTAAG
6299 TGCAGGCTACTATGCGTACCCGAAAACTGTGATCA
66 TGCAGGCTACTATGCGTACCCGAAAACTGTGATCA
* *
6334 CATGTGTAGTACTAAGTTCA-GGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACTAA
1 CATGTGTAGTACTAAGTGCATGG-TACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACTAA
6398 GTGCAGGCTACTATGCGTACC
65 GTGCAGGCTACTATGCGTACC
6419 AGATAGCTTC
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
99 2 0.02
100 79 0.98
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (100 bp):
CATGTGTAGTACTAAGTGCATGGTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACTAAG
TGCAGGCTACTATGCGTACCCGAAAACTGTGATCA
Found at i:10846 original size:40 final size:40
Alignment explanation
Indices: 10699--10921 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
10689 TTGAATGCTG
* * * *
10699 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
** *
10739 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
10778 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
10817 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
10857 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
10896 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
10922 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
38 22 0.14
39 56 0.36
40 68 0.43
41 10 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:10883 original size:79 final size:78
Alignment explanation
Indices: 10699--10919 Score: 241
Period size: 79 Copynumber: 2.8 Consensus size: 78
10689 TTGAATGCTG
* * * * *
10699 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGA-T-ACTAAATCCGGGCTAAG-TCCCGAAGGCAT
* *
10762 TTGTGCGAGATACAAT
63 TCGTGCGAGATACAAA
*
10778 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTC
* *
10842 GTGCGAGTTATTAAA
65 GTGCGAGATA-CAAA
* * * * *
10857 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATT
10920 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 41 0.34
79 70 0.58
80 9 0.07
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACAAA
Found at i:10939 original size:79 final size:80
Alignment explanation
Indices: 10778--10954 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
10768 GAGATACAAT
* * *
10778 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
10842 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
10857 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
10921 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
10936 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
10955 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:18826 original size:39 final size:39
Alignment explanation
Indices: 18614--18833 Score: 212
Period size: 40 Copynumber: 5.6 Consensus size: 39
18604 TTGAATGCTG
* * * * * *
18614 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
18654 TCCGGACTAAGAT-CCGAAGGCATT-TGCGAGATAC-AAT
1 TCCGGGTTAAG-TCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
18691 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
18731 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
18771 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
18810 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
18834 TGAACGAGGA
Statistics
Matches: 150, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
37 17 0.11
38 6 0.04
39 49 0.33
40 77 0.51
41 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:18854 original size:79 final size:80
Alignment explanation
Indices: 18691--18841 Score: 196
Period size: 79 Copynumber: 1.9 Consensus size: 80
18681 GAGATACAAT
* * * *
18691 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
18756 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
18771 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
18835 GAACGAG
66 GAACGAG
18842 GAGCTATATC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 42 0.69
80 19 0.31
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Done.