Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4455
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: 14766
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Found at i:2088 original size:30 final size:32
Alignment explanation
Indices: 2027--2091 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
2017 TTCAATCTCA
*
2027 ACATATACTGGGCCGAAGCCTCTTCATAATTC
1 ACATATACTGGGCCAAAGCCTCTTCATAATTC
*
2059 ACAT-TACTGGGCCAAAGCCT-TTTATAATTC
1 ACATATACTGGGCCAAAGCCTCTTCATAATTC
2089 ACA
1 ACA
2092 ACTCATATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 12 0.39
31 15 0.48
32 4 0.13
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (32 bp):
ACATATACTGGGCCAAAGCCTCTTCATAATTC
Found at i:3730 original size:40 final size:40
Alignment explanation
Indices: 3647--3869 Score: 204
Period size: 40 Copynumber: 5.6 Consensus size: 40
3637 TTGAATGCTG
* * * * *
3647 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-T-ACTAAA
* * *
3687 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGATACTAAA
* * **
3727 TCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
**
3767 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGA-ATTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-TACTAAA
* * *
3807 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
* *
3846 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3870 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 20, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
39 34 0.22
40 112 0.71
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
Found at i:3784 original size:80 final size:79
Alignment explanation
Indices: 3647--3871 Score: 229
Period size: 80 Copynumber: 2.8 Consensus size: 79
3637 TTGAATGCTG
* * * * * * * * *
3647 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTATGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
3711 TGTGCGAGA-TACTAAA
64 TGTGCGA-ATTACTAAA
** *
3727 TCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-ATGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
**
3792 GTGCGAATTGTTAAA
65 GTGCGAATTACTAAA
* * * * *
3807 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTATGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
3872 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 36 0.30
80 82 0.68
81 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTATGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
TGCGAATTACTAAA
Found at i:3889 original size:79 final size:80
Alignment explanation
Indices: 3722--3904 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
3712 GTGCGAGATA
** *
3722 CTAAATCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
** **
3787 CATTCGTGCGAATTG
66 CATTCGAACGAAGAG
* * * * *
3802 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
* *
3866 CATTTGAACGAGGAG
66 CATTCGAACGAAGAG
* *
3881 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
3905 TACGTGATTT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.16
79 44 0.52
80 27 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
CATTCGAACGAAGAG
Found at i:3889 original size:119 final size:119
Alignment explanation
Indices: 3647--3904 Score: 274
Period size: 119 Copynumber: 2.2 Consensus size: 119
3637 TTGAATGCTG
* * * * *
3647 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTTT
1 TCCGGGTTAAGTCCCGAAGGCTTCGTGCGAAGTGAATAAATCCGGATTAAGATCCGAAGGCCATT
* ** *
3712 GTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTTGTTAAA
66 GTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATT-ATGCGAGGAGCTAAA
* * * *
3767 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTG-TTAAATCCGGGTTATG-TCCCGAAGG-CA
1 TCCGGGTTAAGTCCCGAAGGC-TTCGTGCGAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCCA
* * * *
3829 TTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATT-TGAACGAGGAGCTATA
64 TTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTATG--CGAGGAGCTAAA
*
3886 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
3905 TACGTGATTT
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
117 2 0.02
118 15 0.13
119 50 0.43
120 39 0.34
121 10 0.09
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTCGTGCGAAGTGAATAAATCCGGATTAAGATCCGAAGGCCATT
GTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTATGCGAGGAGCTAAA
Found at i:11233 original size:40 final size:39
Alignment explanation
Indices: 11137--11394 Score: 190
Period size: 40 Copynumber: 6.7 Consensus size: 39
11127 TTGAATGCTG
* * * *
11137 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAA-T-ACTAAA
* *
11177 TCC-GGATAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGA-ATACTAAA
* * **
11216 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATACTAAA
* * **
11256 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGATTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATACTAAA
** ** *
11295 TCCGGGTT-AGT-CCGAAGGCATTCATGCGAATTGTTAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATACTAAA
* * *
11332 T-CGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATACTAAA
* *
11370 TCC-GGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
11395 AACGAGGAGC
Statistics
Matches: 184, Mismatches: 24, Indels: 21
0.80 0.10 0.09
Matches are distributed among these distances:
36 6 0.03
37 29 0.16
38 34 0.18
39 42 0.23
40 72 0.39
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATACTAAA
Found at i:11370 original size:75 final size:78
Alignment explanation
Indices: 11189--11392 Score: 256
Period size: 75 Copynumber: 2.6 Consensus size: 78
11179 CGGATAAGAT
* * * *
11189 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGG-CATTGTGCGAGTTACTAAATCCGGGTT-AGTCCCGAAGGCATTCATGCGAATTGTTA
11254 AATCCGGGTTAAGTC
64 AATCCGGGTTAAGTC
**
11269 CCGAAGGCATTCGTGCGA-TTGTTAAATCCGGGTTAGT-CCGAAGGCATTCATGCGAATTGTT-A
1 CCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTAGTCCCGAAGGCATTCATGCGAATTGTTAA
*
11331 AT-CGGGTTATGTC
65 ATCCGGGTTAAGTC
* *
11344 CCGAAGGCATTGTGTGAGTTACTAAATCC-GGCTATGTCCCGAAGGCATT
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTA-GTCCCGAAGGCATT
11393 TGAACGAGGA
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
74 9 0.08
75 32 0.29
76 14 0.13
77 22 0.20
78 3 0.03
79 16 0.15
80 13 0.12
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (78 bp):
CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAGTCCCGAAGGCATTCATGCGAATTGTTAAA
TCCGGGTTAAGTC
Found at i:11380 original size:38 final size:39
Alignment explanation
Indices: 11189--11392 Score: 202
Period size: 40 Copynumber: 5.3 Consensus size: 39
11179 CGGATAAGAT
* * * *
11189 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCC-GGTTATGTC
** *
11229 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCC-GGTTATGTC
**
11269 CCGAAGGCATTCGTGCGA-TTGTTAAATCCGGGTTA-GT-
1 CCGAAGGCATTCGTGCGAGTTACTAAATCC-GGTTATGTC
* * * * *
11306 CCGAAGGCATTCATGCGAATT-GTTAATCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGTTATGTC
* *
11344 CCGAAGGCATT-GTGTGAGTTACTAAATCCGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGTTATGTC
11382 CCGAAGGCATT
1 CCGAAGGCATT
11393 TGAACGAGGA
Statistics
Matches: 144, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
36 5 0.03
37 30 0.21
38 39 0.27
39 17 0.12
40 53 0.37
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGTTATGTC
Done.