Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3316
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: 42817
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:22056 original size:20 final size:21
Alignment explanation
Indices: 22033--22077 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
22023 AGGTGAGATT
*
22033 CTAAA-TTTTTATTGATTAAA
1 CTAAACTTTTTATTCATTAAA
22053 CTAAACTTTTTATTCATTAAA
1 CTAAACTTTTTATTCATTAAA
22074 CTAA
1 CTAA
22078 GTGAGTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (21 bp):
CTAAACTTTTTATTCATTAAA
Found at i:26929 original size:23 final size:23
Alignment explanation
Indices: 26897--27105 Score: 158
Period size: 22 Copynumber: 9.1 Consensus size: 23
26887 TATGTAAAGA
26897 GTAT-ATTGGTTGTGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
26919 GTATAGTTGGTTGTGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* * * * *
26942 TTATATATATGGTGGTATTTTGCA-A
1 GTATA-AT-TGGTTGT-GTTTGGAGG
* * * * **
26967 GTACATTTGATTATGTTCAGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
26990 GTA-AATTGGTTGTGTTTGGAAG
1 GTATAATTGGTTGTGTTTGGAGG
* *
27012 GTATACTTGGTTGTGTTCGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
27035 TTATATATATGGTTGTGTTTGGAGG
1 GTATA-AT-TGGTTGTGTTTGGAGG
* *
27060 GTA-AATTGGTTGTGTTTCGAGA
1 GTATAATTGGTTGTGTTTGGAGG
* *
27082 GTA-AATTGGTTTTGTTTGGGGG
1 GTATAATTGGTTGTGTTTGGAGG
27104 GT
1 GT
27106 GATAGCTTTA
Statistics
Matches: 142, Mismatches: 37, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
22 57 0.40
23 50 0.35
24 4 0.03
25 26 0.18
26 5 0.04
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44
Consensus pattern (23 bp):
GTATAATTGGTTGTGTTTGGAGG
Found at i:31324 original size:23 final size:23
Alignment explanation
Indices: 31278--31442 Score: 147
Period size: 23 Copynumber: 7.2 Consensus size: 23
31268 GATATGTTGA
*
31278 AGGGTAT-ATTGATTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
* *
31300 AGGGTATAGTTGGTTGTGTTCGG
1 AGGGTATAATTGGTTGTGTTTGG
* * *
31323 AGGTTATATATATGGTTTTGTTTTG
1 AGGGTATA-AT-TGGTTGTGTTTGG
* * *
31348 AGGGTACATTTGGTTGTGTTCGG
1 AGGGTATAATTGGTTGTGTTTGG
*
31371 AGGGTA-AATTAGTTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
* ** *
31393 AGGCTATGTTTTGTTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
*
31416 AGGGTA-AATTGGTTGTATTTGG
1 AGGGTATAATTGGTTGTGTTTGG
*
31438 TGGGT
1 AGGGT
31443 GATAGATTTA
Statistics
Matches: 112, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
22 41 0.37
23 53 0.47
24 2 0.02
25 16 0.14
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (23 bp):
AGGGTATAATTGGTTGTGTTTGG
Found at i:31411 original size:45 final size:45
Alignment explanation
Indices: 31278--31442 Score: 170
Period size: 45 Copynumber: 3.6 Consensus size: 45
31268 GATATGTTGA
* *
31278 AGGGTATATTGATTGTGTTTGGAGGGTATAG-TTGGTTGTGTTCGG
1 AGGGTAAATTGGTTGTGTTTGGAGGGTAT-GTTTGGTTGTGTTCGG
* * * **
31323 AGGTTATATATATGGTTTTGTTTTGAGGGTACATTTGGTTGTGTTCGG
1 AGGGTA-A-AT-TGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
* * * *
31371 AGGGTAAATTAGTTGTGTTTGGAGGCTATGTTTTGTTGTGTTTGG
1 AGGGTAAATTGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
* *
31416 AGGGTAAATTGGTTGTATTTGGTGGGT
1 AGGGTAAATTGGTTGTGTTTGGAGGGT
31443 GATAGATTTA
Statistics
Matches: 96, Mismatches: 20, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
45 56 0.58
46 2 0.02
47 3 0.03
48 35 0.36
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (45 bp):
AGGGTAAATTGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
Found at i:34493 original size:27 final size:27
Alignment explanation
Indices: 34450--34728 Score: 353
Period size: 27 Copynumber: 10.3 Consensus size: 27
34440 TGCGATTTGT
* *
34450 GGTAAAATGATCAAAATACCCTTGAAG
1 GGTAAAATGATCGAAATACCCTCGAAG
* * *
34477 GTTAAAATGACCGAAATACGCTCGAAG
1 GGTAAAATGATCGAAATACCCTCGAAG
* *
34504 GGTAAAATAACCGAAATACCCTCGAAG
1 GGTAAAATGATCGAAATACCCTCGAAG
* *
34531 GGTAAAATAACCGAAATACCCTCGAAG
1 GGTAAAATGATCGAAATACCCTCGAAG
*
34558 GGTAAAATGATCGAAATACCCTCCAAG
1 GGTAAAATGATCGAAATACCCTCGAAG
* *
34585 GGTAAAATGAAT-AAAACACCCTCGAAG
1 GGTAAAATG-ATCGAAATACCCTCGAAG
*
34612 GGTAAAATGACCGAAATACCCTCGAAG
1 GGTAAAATGATCGAAATACCCTCGAAG
*
34639 GGTAAAATGATTGAAATACCCTCGAAG
1 GGTAAAATGATCGAAATACCCTCGAAG
* * * *
34666 AGTAAAATGATAGAAATACCCCCGATG
1 GGTAAAATGATCGAAATACCCTCGAAG
* * *
34693 TGTAAAATGATCGAAATACCCCCAAAG
1 GGTAAAATGATCGAAATACCCTCGAAG
34720 GGTAAAATG
1 GGTAAAATG
34729 TCTGTATACC
Statistics
Matches: 222, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.00
27 219 0.99
28 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (27 bp):
GGTAAAATGATCGAAATACCCTCGAAG
Found at i:34973 original size:25 final size:25
Alignment explanation
Indices: 34914--35009 Score: 113
Period size: 25 Copynumber: 3.8 Consensus size: 25
34904 TACTGTTACC
* * * *
34914 GGCAGCTTTACTGCGTTACTGTTATT
1 GGCAGCTTTGCTGCGTTATTATT-CT
34940 GGCAGCTTTGCTGCGTTATTATTCT
1 GGCAGCTTTGCTGCGTTATTATTCT
34965 GGCAGCTTT-CTTGCGTTATTATTCT
1 GGCAGCTTTGC-TGCGTTATTATTCT
* *
34990 GGTAGCTTTGCTGCGATATT
1 GGCAGCTTTGCTGCGTTATT
35010 GGTGTGTTGG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
24 1 0.02
25 40 0.65
26 21 0.34
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.44
Consensus pattern (25 bp):
GGCAGCTTTGCTGCGTTATTATTCT
Found at i:35374 original size:20 final size:21
Alignment explanation
Indices: 35349--35397 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
35339 ACAACTAAAC
*
35349 TAAACTAAAC-TTTTATTGAT
1 TAAACTAAACTTTTTATTCAT
35369 TAAACTAAACTTTTTATTCAT
1 TAAACTAAACTTTTTATTCAT
35390 TAAACTAA
1 TAAACTAA
35398 GTGAGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAACTAAACTTTTTATTCAT
Found at i:39714 original size:20 final size:21
Alignment explanation
Indices: 39691--39735 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
39681 AGGTGAGATT
* *
39691 CTAAA-TTTTTATTGATTAAA
1 CTAAACTTTGTATTCATTAAA
39711 CTAAACTTTGTATTCATTAAA
1 CTAAACTTTGTATTCATTAAA
39732 CTAA
1 CTAA
39736 GTGAGTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (21 bp):
CTAAACTTTGTATTCATTAAA
Done.