Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2341
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: 38585
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:5645 original size:13 final size:13
Alignment explanation
Indices: 5627--5656 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5617 TTTTCGATGC
5627 TCAAATGATTAAA
1 TCAAATGATTAAA
5640 TCAAATGATTAAA
1 TCAAATGATTAAA
5653 TCAA
1 TCAA
5657 TTATTTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (13 bp):
TCAAATGATTAAA
Found at i:6038 original size:40 final size:39
Alignment explanation
Indices: 5954--6138 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
5944 TTGAATGATG
* * * *
5954 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
5994 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
6034 TCCGGGCTAAGCCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
6073 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
6114 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
6139 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:6090 original size:79 final size:79
Alignment explanation
Indices: 5954--6171 Score: 239
Period size: 79 Copynumber: 2.7 Consensus size: 79
5944 TTGAATGATG
* * * * **
5954 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTATATCCGGGTTAAG-TCCGAAGGCATT
6018 TGTGCGAGATACTA-A
64 TGTGCGAGATACTATA
*
6033 TTCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGGGTTAAGT-CCGAAGGCATT
*
6097 TGTGCGAGTTACTATA
64 TGTGCGAGATACTATA
* * * *
6113 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTA-CTATATCCGGGTT-AAGTCCGAAGG
6172 TACGTGATTT
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
78 1 0.01
79 71 0.60
80 47 0.39
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGGGTTAAGTCCGAAGGCATTTG
TGCGAGATACTATA
Found at i:8213 original size:27 final size:26
Alignment explanation
Indices: 8165--8216 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
8155 ACGAGGCTGC
*
8165 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
8191 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
8217 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:11967 original size:58 final size:58
Alignment explanation
Indices: 11877--11992 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
11867 AACATCATTG
11877 GTTTTAATTCAAATTGGGTTGCCTCAATATCTGGCCTTCTAATTCCTAGATTTACCTC
1 GTTTTAATTCAAATTGGGTTGCCTCAATATCTGGCCTTCTAATTCCTAGATTTACCTC
11935 GTTTTAATTCAAATTGGGTTGCCTCAATATCTGGCCTTCTAATTCCTAGATTTACCTC
1 GTTTTAATTCAAATTGGGTTGCCTCAATATCTGGCCTTCTAATTCCTAGATTTACCTC
11993 ACTGAAAAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.41
Consensus pattern (58 bp):
GTTTTAATTCAAATTGGGTTGCCTCAATATCTGGCCTTCTAATTCCTAGATTTACCTC
Found at i:19978 original size:27 final size:27
Alignment explanation
Indices: 19948--20125 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
19938 ATATTGAGTC
* * * *
19948 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
19975 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
20002 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
20030 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
20057 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
20084 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
20111 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20126 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:20087 original size:82 final size:81
Alignment explanation
Indices: 19969--20124 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19959 TGCTATATAA
* *
19969 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
20034 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
20051 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
20115 CACTTAGTGC
65 CACTTAGTGC
20125 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
Found at i:28148 original size:27 final size:27
Alignment explanation
Indices: 28109--28287 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
28099 GTATTGAGTC
* * *
28109 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * *
28136 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
28163 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
** * *
28191 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
28218 CGCACACTTAGTGC-ATCATATTCATTCT
1 CGCACACTTAGTGCTA-CATAGTCA-ACT
* *
28246 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
28273 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28288 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 82 0.64
28 45 0.35
29 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:28201 original size:55 final size:55
Alignment explanation
Indices: 28109--28287 Score: 218
Period size: 55 Copynumber: 3.3 Consensus size: 55
28099 GTATTGAGTC
* * * * *
28109 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
28163 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
28218 CGCACACTTAGTGC-ATCATATTCATTCTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAAT
28273 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28288 GTACAATTTA
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
54 21 0.20
55 85 0.80
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAAT
Done.