Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 61599
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3031 original size:39 final size:39
Alignment explanation
Indices: 2947--3057 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 39
2937 AGATACTAAT
** *
2947 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
2987 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
3027 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
3058 GAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 25 0.42
40 35 0.58
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:10884 original size:39 final size:39
Alignment explanation
Indices: 10800--10910 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 39
10790 AGATACTAAT
** *
10800 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
10840 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
10880 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
10911 GAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 25 0.42
40 35 0.58
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:15243 original size:22 final size:21
Alignment explanation
Indices: 15218--15259 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15208 TTAAATATAA
15218 ATTATAAAATTCATAAAAAAAC
1 ATTA-AAAATTCATAAAAAAAC
* *
15240 ATTAGAAATTTATAAAAAAA
1 ATTAAAAATTCATAAAAAAA
15260 TTTAAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (21 bp):
ATTAAAAATTCATAAAAAAAC
Found at i:31026 original size:27 final size:27
Alignment explanation
Indices: 30996--31173 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
30986 ATATTGAGTC
* * * *
30996 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31023 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31050 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31078 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31105 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31132 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31159 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31174 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:31135 original size:82 final size:81
Alignment explanation
Indices: 31017--31172 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31007 TGCTATATAA
* *
31017 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31082 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31099 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31163 CACTTAGTGC
65 CACTTAGTGC
31173 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:39210 original size:27 final size:27
Alignment explanation
Indices: 39180--39357 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39170 ATATTGAGTC
* * * *
39180 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39207 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39234 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39262 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39289 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39316 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39343 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39358 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:39319 original size:82 final size:81
Alignment explanation
Indices: 39201--39356 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39191 TGCTATATAA
* *
39201 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39266 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39283 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39347 CACTTAGTGC
65 CACTTAGTGC
39357 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:41894 original size:25 final size:25
Alignment explanation
Indices: 41864--41993 Score: 67
Period size: 25 Copynumber: 5.2 Consensus size: 25
41854 TTAGCTCTTA
41864 TGAGCTTCTCGATTATGGCTCTTCG
1 TGAGCTTCTCGATTATGGCTCTTCG
*
41889 TGAGCTTC-CTG-TTAATTAGCTCTAT-G
1 TGAGCTTCTC-GATT-A-TGGCTCT-TCG
* *
41915 TGAGCTTCTCGA-TATGGCT-TGCT
1 TGAGCTTCTCGATTATGGCTCTTCG
* * * * *
41938 TGAACTTCCCGTTATATGGCTATCCG
1 TGAGCTTCTCGAT-TATGGCTCTTCG
* *
41964 -GAGCTCCTTGATTATTGGCTCTTCG
1 TGAGCTTCTCGATTA-TGGCTCTTCG
41989 -GAGCT
1 TGAGCT
41994 ACCTATTATA
Statistics
Matches: 78, Mismatches: 16, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
23 10 0.13
24 9 0.12
25 38 0.49
26 19 0.24
27 2 0.03
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (25 bp):
TGAGCTTCTCGATTATGGCTCTTCG
Found at i:44747 original size:42 final size:42
Alignment explanation
Indices: 44688--44811 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
44678 ATTAGGGTTA
44688 ATGAGACTACGTGTAAGACCATATTTGGGATATGGCATCAAC
1 ATGAGACTACGTGTAAGACCATATTTGGGATATGGCATCAAC
* * * * *
44730 ATGAGACTGCGTGTAAGACCATATTTAGGACATGGCATCGAT
1 ATGAGACTACGTGTAAGACCATATTTGGGATATGGCATCAAC
* * * * * *
44772 ATGAAACTTCGTATAAAACCATAGTTGGGCTATTGGCATC
1 ATGAGACTACGTGTAAGACCATATTTGGGATA-TGGCATC
44812 GAAACGAGAT
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 61 0.90
43 7 0.10
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (42 bp):
ATGAGACTACGTGTAAGACCATATTTGGGATATGGCATCAAC
Found at i:46965 original size:46 final size:46
Alignment explanation
Indices: 46912--47019 Score: 182
Period size: 46 Copynumber: 2.3 Consensus size: 46
46902 GTTGAGTCCA
46912 AGTTGAGTCCGAGTTCACTTATGGATGCGAACATT-CGAACTCGTTG
1 AGTTGAGTCCGAGTTCACTTATGGATGCGAAC-TTCCGAACTCGTTG
*
46958 AGTTGAGTCCGAGTTCACTTATGGATGTGAACTTCCGAACTCGTTG
1 AGTTGAGTCCGAGTTCACTTATGGATGCGAACTTCCGAACTCGTTG
*
47004 AGTTGAGTTCGAGTTC
1 AGTTGAGTCCGAGTTC
47020 GTGAAATGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
45 2 0.03
46 57 0.97
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (46 bp):
AGTTGAGTCCGAGTTCACTTATGGATGCGAACTTCCGAACTCGTTG
Found at i:52177 original size:46 final size:46
Alignment explanation
Indices: 52115--52237 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 46
52105 GATATTTGGG
* *
52115 CATCCAAAATCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAA
1 CATCCAAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAA
* *
52161 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCAAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAA
** * *
52207 TGTCCAAACTCGTTGAGTTGAGTCTGAGTTC
1 CATCCAAACTCATTGAGTTGAGTCCGAGTTC
52238 GTGAAATGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (46 bp):
CATCCAAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAA
Found at i:55657 original size:79 final size:80
Alignment explanation
Indices: 55489--55673 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 80
55479 GCTACTCGTT
* * *
55489 CAAATGCCTTCGGGACATAGGCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
1 CAAA-GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
* *
55553 GATTTAGTAACTCGCAC
64 GATATAGTAACTAGCAC
* ** *
55570 CAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 CAAAGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCAG
* *
55633 ATATGGTCACTTAGCA-
65 ATATAGTAAC-TAGCAC
55649 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
55674 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 57 0.65
80 25 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGA
TATAGTAACTAGCAC
Found at i:55673 original size:40 final size:40
Alignment explanation
Indices: 55470--55673 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
55460 CGGAATTTAA
** * *
55470 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGG
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55510 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
55550 CCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
55589 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
55629 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
55669 CCGGA
1 CCGGA
55674 CATCATTCGA
Statistics
Matches: 138, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 92 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.