Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1875
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: 27002
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:1027 original size:29 final size:29
Alignment explanation
Indices: 991--1070 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
981 TCATGAGATT
*
991 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA-AGTACA
*
1021 -GCACTAAGTGTGCGAGTTTAAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAAGTACA
1049 TGGCACTAAGGTGTGCCGGGTT
1 -GGCACTAA-GTGTG-CGGGTT
1071 GGATTATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 21 0.49
30 7 0.16
31 5 0.12
32 5 0.12
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (29 bp):
GGCACTAAGTGTGCGGGTTTAAAAGTACA
Found at i:1341 original size:179 final size:181
Alignment explanation
Indices: 1021--1350 Score: 512
Period size: 180 Copynumber: 1.8 Consensus size: 181
1011 AAATTGTACA
*
1021 GCACTAAGTGTGCGAGTTTAAAAGTACATGGCACTAAGGTGTGCCGGGTTGGATTATTAAGCACT
1 GCACTAAGTGTGCGAGTTTAAAAGTACATGGCACTAAGGTGTGCCGCGTTGGATTATTAAGCACT
*
1086 ATGTTGTGCGAACCCAATTATATATTTTCTATAAATTATTTACATTAAGGGTTGCGACCTTACCG
66 ATGTTGTGCGAACCCAATTATATATTTTCTATAAATTATTTACATGAAGGGTTGCGACCTTACCG
*
1151 AGTCGATTTTGGGACAGCGGAAAAGGTTAGTGTGCGAACTTGAAATGCATGG
131 AGTCAATTTT-GGACAGCGGAAAAGGTTAGTGTGCGAACTTGAAATGCATGG
* *
1203 GCACTAAGTGTGTGAGTTT-AAAGTGCATGGCACTAA-GTGTGCCGCGTT-GATTATTATAGCAC
1 GCACTAAGTGTGCGAGTTTAAAAGTACATGGCACTAAGGTGTGCCGCGTTGGATTATTA-AGCAC
*
1265 TATG-TGTGCGAAACCCAA-TATATATTTTTCT-TAAAATTATTTACATGAAGGG-TGCGACTTT
65 TATGTTGTGCG-AACCCAATTATATA-TTTTCTAT-AAATTATTTACATGAAGGGTTGCGACCTT
1326 ACCGAGTCAATTTTGGACAGCGGAA
127 ACCGAGTCAATTTTGGACAGCGGAA
1351 TTAAAGGTAT
Statistics
Matches: 138, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
178 11 0.08
179 42 0.30
180 51 0.37
181 16 0.12
182 18 0.13
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (181 bp):
GCACTAAGTGTGCGAGTTTAAAAGTACATGGCACTAAGGTGTGCCGCGTTGGATTATTAAGCACT
ATGTTGTGCGAACCCAATTATATATTTTCTATAAATTATTTACATGAAGGGTTGCGACCTTACCG
AGTCAATTTTGGACAGCGGAAAAGGTTAGTGTGCGAACTTGAAATGCATGG
Found at i:9143 original size:29 final size:28
Alignment explanation
Indices: 9100--9177 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
9090 TCATGAGATT
9100 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
9130 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
9157 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
9178 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:9443 original size:174 final size:175
Alignment explanation
Indices: 9130--9459 Score: 547
Period size: 174 Copynumber: 1.9 Consensus size: 175
9120 AAATTGTACA
* *
9130 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
9195 TGTGCGAACCCAATATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTC
66 CGTGCGAACCC-ATATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTC
*
9260 GATTTTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATG
130 AATTTTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
9307 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
9372 CGTGC-AACCC-TATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCA
66 CGTGCGAACCCATATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCA
9435 ATTTTGGACAGCGGAAAAGGTAAGT
131 ATTTTGGACAGCGGAAAAGGTAAGT
9460 ATCTTGAGTT
Statistics
Matches: 144, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
173 11 0.08
174 65 0.45
176 5 0.03
177 63 0.44
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (175 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
CGTGCGAACCCATATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCA
ATTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:17465 original size:29 final size:28
Alignment explanation
Indices: 17422--17499 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
17412 TCATGAGATT
17422 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
17452 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
17479 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
17500 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:17765 original size:174 final size:175
Alignment explanation
Indices: 17452--17773 Score: 531
Period size: 174 Copynumber: 1.8 Consensus size: 175
17442 AAATTGTACA
* *
17452 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
17517 TGTGCGAACCCAATATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTC
66 CGTGCGAACCC-ATATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTC
*
17582 GATTTTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATG
130 AATTTTGGACAGC-GAAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
17629 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
17694 CGTGC-AACCC-TATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCA
66 CGTGCGAACCCATATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCA
17757 ATTTTGGACAGCGAAAA
131 ATTTTGGACAGCGAAAA
17774 GTAAGTATCT
Statistics
Matches: 136, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
173 5 0.04
174 63 0.46
176 5 0.04
177 63 0.46
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (175 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
CGTGCGAACCCATATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCA
ATTTTGGACAGCGAAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:25601 original size:29 final size:28
Alignment explanation
Indices: 25558--25635 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
25548 TCATGAGATT
25558 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
25588 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
25615 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
25636 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:25853 original size:174 final size:173
Alignment explanation
Indices: 25588--25914 Score: 539
Period size: 174 Copynumber: 1.9 Consensus size: 173
25578 AAATTGTACA
* *
25588 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* * *
25653 TGTGCGAACCCAATATATATTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGAT
66 CGTGCGAACCCAATATATATTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
25718 TTTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
25762 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
25827 CGTGC-AACCCTATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 CGTGCGAACCCAATATATA-TTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
25891 TTTTGGACAGCGGAAAAGGTAAGT
130 TTTTGGACAGCGGAAAAGGTAAGT
25915 ATCTTGAGTT
Statistics
Matches: 142, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
173 23 0.16
174 119 0.84
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (173 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
CGTGCGAACCCAATATATATTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Done.