Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3153
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: 41451
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:4105 original size:79 final size:82
Alignment explanation
Indices: 3994--4178 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
3984 GCTACTCGTT
* * *
3994 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
4057 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
4074 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
4137 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
4154 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
4179 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:4178 original size:40 final size:40
Alignment explanation
Indices: 3975--4178 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
3965 CGGAATTTAA
** *
3975 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
4015 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
4055 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
4094 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
4134 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
4174 CCGGA
1 CCGGA
4179 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:21219 original size:49 final size:49
Alignment explanation
Indices: 21159--21341 Score: 231
Period size: 49 Copynumber: 3.7 Consensus size: 49
21149 ATCTGGTACG
*
21159 ATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACAC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACAC
* * *
21208 GTAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGGACAC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACAC
* * * * * * *
21257 ATAGTAGCATGCACTTAGTACTACACACGTGATCAAAGTTTTCGGGTACGC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTACAC
**
21308 ATAGTAGCCTGTGCTTAGTACTACACATGCGACC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACC
21342 TCACAATAGA
Statistics
Matches: 114, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
49 74 0.65
50 4 0.04
51 36 0.32
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (49 bp):
ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACAC
Found at i:21330 original size:100 final size:98
Alignment explanation
Indices: 21159--21341 Score: 240
Period size: 100 Copynumber: 1.8 Consensus size: 98
21149 ATCTGGTACG
* * * *
21159 ATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTT
1 ATAGTAGCATGCACATAGTACTACACACGCGACAAATTATCCGGTACACATAGTAGCCTGCACTT
*
21224 AGTACTACACATGTGACCAATTATCCGGGACAC
66 AGTACTACACATGCGACCAATTATCCGGGACAC
* * * * * **
21257 ATAGTAGCATGCACTTAGTACTACACACGTGATCAAAGTTTTCGGGTACGCATAGTAGCCTGTGC
1 ATAGTAGCATGCACATAGTACTACACACGCGA-CAAA-TTATCCGGTACACATAGTAGCCTGCAC
21322 TTAGTACTACACATGCGACC
64 TTAGTACTACACATGCGACC
21342 TCACAATAGA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 28 0.39
99 3 0.04
100 40 0.56
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (98 bp):
ATAGTAGCATGCACATAGTACTACACACGCGACAAATTATCCGGTACACATAGTAGCCTGCACTT
AGTACTACACATGCGACCAATTATCCGGGACAC
Found at i:24534 original size:24 final size:23
Alignment explanation
Indices: 24482--24536 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
24472 CAACCGAATT
*
24482 TGCACACATAGTGCTCATCACAC
1 TGCACACATAGTGCTCATCAAAC
*
24505 TCGCACACATAGTGC-CATAGTAAAC
1 T-GCACACATAGTGCTCAT--CAAAC
24530 TGCACAC
1 TGCACAC
24537 TCAGTGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.15
24 19 0.70
25 4 0.15
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.20
Consensus pattern (23 bp):
TGCACACATAGTGCTCATCAAAC
Found at i:26768 original size:27 final size:27
Alignment explanation
Indices: 26714--26768 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
26704 CATAAGGAAG
* *
26714 GAATAGCCTTTGTGGAAAACTATGAAA
1 GAATAGCCTTCGTGGAAAACTATAAAA
*
26741 GAATAGCCTTCGTGGAAAACTTTAAAA
1 GAATAGCCTTCGTGGAAAACTATAAAA
26768 G
1 G
26769 GAATCCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (27 bp):
GAATAGCCTTCGTGGAAAACTATAAAA
Found at i:26782 original size:27 final size:26
Alignment explanation
Indices: 26714--26784 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
26704 CATAAGGAAG
*
26714 GAATAGCCTTTGTGGAAAACTATGAAA
1 GAATA-CCTTTGTGGAAAACTATAAAA
* *
26741 GAATAGCCTTCGTGGAAAACTTTAAAA
1 GAATA-CCTTTGTGGAAAACTATAAAA
26768 GGAAT-CCATTTGTGGAA
1 -GAATACC-TTTGTGGAA
26785 TATTTTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.05
27 32 0.84
28 4 0.11
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (26 bp):
GAATACCTTTGTGGAAAACTATAAAA
Found at i:30732 original size:38 final size:40
Alignment explanation
Indices: 30642--30852 Score: 262
Period size: 38 Copynumber: 5.5 Consensus size: 40
30632 CGGATGATAA
* * *
30642 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
30682 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-T-TAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
30720 CCGGGCTAAGTCCCGAAGGCA-TT-TGCGAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
30757 CCGGGCTAAGT-CCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
30796 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
30835 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
30853 TACTTGGCTT
Statistics
Matches: 153, Mismatches: 10, Indels: 18
0.85 0.06 0.10
Matches are distributed among these distances:
35 2 0.01
36 16 0.10
37 18 0.12
38 43 0.28
39 34 0.22
40 40 0.26
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:38706 original size:40 final size:40
Alignment explanation
Indices: 38651--38827 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
38641 TGGATGATAA
* * *
38651 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
38691 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
38731 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
38771 CCGGGCTATGTCCCGAAGGCA-TTGAGTGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
38810 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
38828 TACTTGGCTT
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
38 15 0.12
39 15 0.12
40 94 0.76
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.