Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2314
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: 37079
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2595 original size:93 final size:93
Alignment explanation
Indices: 2482--2653 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
2472 CGCCCATAAG
* *
2482 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
2547 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
2575 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
2640 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
2654 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:2650 original size:46 final size:46
Alignment explanation
Indices: 2475--2650 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
2465 TGTAACCCGC
* * *
2475 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
2521 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
2571 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
2614 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
2651 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:10152 original size:46 final size:48
Alignment explanation
Indices: 10030--10159 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 48
10020 TGTAACCCGC
10030 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * *
10080 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGGA-C-A-TTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT-ACAT
*
10123 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
10160 TGCTCAACCA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 2 0.03
45 2 0.03
46 28 0.40
47 29 0.41
48 2 0.03
49 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (48 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:10178 original size:46 final size:44
Alignment explanation
Indices: 10038--10178 Score: 126
Period size: 46 Copynumber: 3.0 Consensus size: 44
10028 GCCCATAAGC
*
10038 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AGT
* * * *
10085 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTAGT
10131 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAGT
10177 GA
1 GA
10179 CATGTCACTT
Statistics
Matches: 77, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.42
47 30 0.39
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (44 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAGT
Found at i:12219 original size:28 final size:24
Alignment explanation
Indices: 12165--12215 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
12155 AAACAACTCC
*
12165 TAAAAAAAACTCAAGAGCAATTCT
1 TAAAAAAAACTCAAGAGCAATTAT
12189 TAAAGAAAAACTCAAAGAGC-ATTAT
1 TAAA-AAAAACTC-AAGAGCAATTAT
12214 TA
1 TA
12216 TTAACTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 14 0.58
26 6 0.25
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.22
Consensus pattern (24 bp):
TAAAAAAAACTCAAGAGCAATTAT
Found at i:17107 original size:26 final size:26
Alignment explanation
Indices: 17061--17135 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
17051 TCTCATCCCT
* * *
17061 ATTTTACCC-CAACAAAATTTTGGCA
1 ATTTTACCCTTAATAAAATTTTGACA
* * *
17086 ATTTTACCTTTGATAAAATTTTGACG
1 ATTTTACCCTTAATAAAATTTTGACA
*
17112 ATTTTCCCCTTAATAAAATTTTGA
1 ATTTTACCCTTAATAAAATTTTGA
17136 TGACTTTGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 8 0.20
26 32 0.80
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.41
Consensus pattern (26 bp):
ATTTTACCCTTAATAAAATTTTGACA
Found at i:17158 original size:26 final size:26
Alignment explanation
Indices: 17098--17148 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
17088 TTTACCTTTG
*
17098 ATAAAATTTTGACGATTTTCCCCTTA
1 ATAAAATTTTGACGATTTGCCCCTTA
*
17124 ATAAAATTTTGATGACTTTGCCCCT
1 ATAAAATTTTGACGA-TTTGCCCCT
17149 GGTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (26 bp):
ATAAAATTTTGACGATTTGCCCCTTA
Found at i:17323 original size:12 final size:12
Alignment explanation
Indices: 17306--17330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17296 TGCAAACGGA
17306 TCATTTCCATTT
1 TCATTTCCATTT
17318 TCATTTCCATTT
1 TCATTTCCATTT
17330 T
1 T
17331 TTGGAAACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:19407 original size:23 final size:26
Alignment explanation
Indices: 19381--19432 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
19371 GGGATAATAA
*
19381 TTTTT-AA-TTAATATTCAACTGATT
1 TTTTTGAAGTTAATATTCAACTAATT
19405 TTTTTGAAGTTAATATTCAACTAATT
1 TTTTTGAAGTTAATATTCAACTAATT
19431 TT
1 TT
19433 GAAAACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 2 0.08
26 18 0.72
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.54
Consensus pattern (26 bp):
TTTTTGAAGTTAATATTCAACTAATT
Found at i:23709 original size:34 final size:34
Alignment explanation
Indices: 23665--23785 Score: 134
Period size: 34 Copynumber: 3.5 Consensus size: 34
23655 GGGGCCTAAA
* * **
23665 CCCATATCAGTAACAGTGGCAATCTGGGCATTAG
1 CCCATTTCAGTAACAGTAGCAATCTGGGTTTTAG
** *
23699 CCCATTTCAGTAACAGTAGCAGCCTGGGTTTTAA
1 CCCATTTCAGTAACAGTAGCAATCTGGGTTTTAG
* * *
23733 CCCATTTCAGTAATAGTAATCAATCTAGGTTTTAG
1 CCCATTTCAGTAACAGT-AGCAATCTGGGTTTTAG
*
23768 CCCATTTCAGTAATAGTA
1 CCCATTTCAGTAACAGTA
23786 ATCAGTGCAG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
34 44 0.60
35 29 0.40
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (34 bp):
CCCATTTCAGTAACAGTAGCAATCTGGGTTTTAG
Found at i:23772 original size:35 final size:35
Alignment explanation
Indices: 23695--23789 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
23685 AATCTGGGCA
* * * *
23695 TTAGCCCATTTCAGTAACAGT-AGCAGCCTGGGTT
1 TTAGCCCATTTCAGTAATAGTAATCAACCTAGGTT
* *
23729 TTAACCCATTTCAGTAATAGTAATCAATCTAGGTT
1 TTAGCCCATTTCAGTAATAGTAATCAACCTAGGTT
23764 TTAGCCCATTTCAGTAATAGTAATCA
1 TTAGCCCATTTCAGTAATAGTAATCA
23790 GTGCAGTAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 19 0.36
35 34 0.64
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (35 bp):
TTAGCCCATTTCAGTAATAGTAATCAACCTAGGTT
Found at i:23798 original size:18 final size:18
Alignment explanation
Indices: 23775--23833 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
23765 TAGCCCATTT
*
23775 CAGTAATAGTAATCAGTG
1 CAGTAACAGTAATCAGTG
* *
23793 CAGTAACCA-TGATCAATG
1 CAGTAA-CAGTAATCAGTG
23811 CAGTAACAGTAATCAGTG
1 CAGTAACAGTAATCAGTG
23829 CAGTA
1 CAGTA
23834 TGCAAACAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.06
18 31 0.91
19 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (18 bp):
CAGTAACAGTAATCAGTG
Found at i:24260 original size:27 final size:27
Alignment explanation
Indices: 24230--24302 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
24220 GGGTATTTCG
24230 GTCATTTTATCACATAAGGGAAAAATC
1 GTCATTTTATCACATAAGGGAAAAATC
*
24257 GTCATTTTATCACATAAGGGTAAAATC
1 GTCATTTTATCACATAAGGGAAAAATC
* *
24284 ATCATTTTACCACATAAGG
1 GTCATTTTATCACATAAGG
24303 TGATACGGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (27 bp):
GTCATTTTATCACATAAGGGAAAAATC
Found at i:25154 original size:12 final size:13
Alignment explanation
Indices: 25137--25165 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25127 TTAAACTAAG
25137 TAAATAAAT-AAA
1 TAAATAAATAAAA
25149 TAAATAAATAAAA
1 TAAATAAATAAAA
25162 TAAA
1 TAAA
25166 AATAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:26570 original size:23 final size:22
Alignment explanation
Indices: 26518--26570 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
26508 TCCACGTCTT
*
26518 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
26540 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
26563 TTTCTTTT
1 TTTCTTTT
26571 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:29378 original size:27 final size:27
Alignment explanation
Indices: 29102--29370 Score: 387
Period size: 27 Copynumber: 10.0 Consensus size: 27
29092 TGACTCGTAT
* * *
29102 CATAAGGGAAAAATTGTCATTTTATCG
1 CATAAGGGCAAAATCGTCATTTTATCA
* * *
29129 CCTAAAGGTAAAATCGTCATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
*
29156 CCTAAGGGCAAAATCGTCATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
*
29183 CATGAGGGCAAAATCGTCATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
29210 CATAAGGGCAAAATCGTCATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
* ** * *
29237 CTTAAGGTAAAAATCATAATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
*
29264 CATGAGGGCAAAATCGTCATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
*
29291 CATAAAGGCAAAATCGTCATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
*
29318 C-TAAGGGCAAAATCATCATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
29344 CATAAGGGCAAAATCGTCATTTTATCA
1 CATAAGGGCAAAATCGTCATTTTATCA
29371 AATGAGGGTT
Statistics
Matches: 215, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
26 24 0.11
27 191 0.89
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (27 bp):
CATAAGGGCAAAATCGTCATTTTATCA
Found at i:31350 original size:39 final size:39
Alignment explanation
Indices: 31146--31368 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
31136 TTGAATGCTG
* * * * * *
31146 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
31186 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
31226 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
31266 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
31306 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
31345 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
31369 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:31388 original size:79 final size:80
Alignment explanation
Indices: 31226--31403 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
31216 AGATACAAGT
* * * *
31226 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
31291 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
31306 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
31370 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
31385 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
31404 TATGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Done.