Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3158
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: 19955
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:2201 original size:33 final size:32
Alignment explanation
Indices: 2164--2297 Score: 145
Period size: 33 Copynumber: 4.3 Consensus size: 32
2154 GTCTGCTTTA
*
2164 TGTTTCTCTATTTTCTGTTTCTGTACCGTGTTT
1 TGTTTCTCTATTTTCTG-TTCTGTACCATGTTT
*
2197 TGTTTCTTTATTTTCTGTTTCTGTACCATGTTT
1 TGTTTCTCTATTTTCTG-TTCTGTACCATGTTT
* **
2230 TGTTCCTCTATTTTCTGTAGTGGT----T-TTT
1 TGTTTCTCTATTTTCTGTTCT-GTACCATGTTT
2258 T-TTTCTCTATTTTCTGTTCTGTACCATGTTT
1 TGTTTCTCTATTTTCTGTTCTGTACCATGTTT
*
2289 TGTTCCTCT
1 TGTTTCTCT
2298 TGCCATTTGC
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
26 2 0.02
27 16 0.19
28 4 0.05
29 1 0.01
30 1 0.01
31 4 0.05
32 8 0.10
33 48 0.57
ACGTcount: A:0.07, C:0.18, G:0.13, T:0.61
Consensus pattern (32 bp):
TGTTTCTCTATTTTCTGTTCTGTACCATGTTT
Found at i:2202 original size:18 final size:17
Alignment explanation
Indices: 2179--2233 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
2169 CTCTATTTTC
2179 TGTTTCTGTACCGTGTTT
1 TGTTTCTGTACC-TGTTT
*
2197 TGTTTCTTTA--T-TTT
1 TGTTTCTGTACCTGTTT
2211 CTGTTTCTGTACCATGTTT
1 -TGTTTCTGTACC-TGTTT
2230 TGTT
1 TGTT
2234 CCTCTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
18 14 0.47
19 3 0.10
ACGTcount: A:0.07, C:0.15, G:0.16, T:0.62
Consensus pattern (17 bp):
TGTTTCTGTACCTGTTT
Found at i:3286 original size:22 final size:21
Alignment explanation
Indices: 3233--3287 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3223 AGTTTCCCCG
* *
3233 TTGCCAGTGGCTATACATTGT
1 TTGCCAGTGGCTATAAATTAT
3254 TTGCCAGTGGCTATATAATTTAT
1 TTGCCAGTGGCTATA-AA-TTAT
3277 TTG-CAGTGGCT
1 TTGCCAGTGGCT
3288 CCATTGCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 15 0.50
22 9 0.30
23 6 0.20
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (21 bp):
TTGCCAGTGGCTATAAATTAT
Found at i:4692 original size:38 final size:38
Alignment explanation
Indices: 4624--4697 Score: 91
Period size: 38 Copynumber: 1.9 Consensus size: 38
4614 ATTTAAGGTA
*
4624 TATTAAATATATTAAAATCATTATTATATT-ATATTTT
1 TATTAAATATATTAAAATCATTATGATATTAATATTTT
4661 TATTGAAATATAATT-AAATCATT-TGATTATTAATATT
1 TATT-AAATAT-ATTAAAATCATTATGA-TATTAATATT
4698 ATATAACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 6 0.19
38 18 0.56
39 8 0.25
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
TATTAAATATATTAAAATCATTATGATATTAATATTTT
Found at i:6475 original size:11 final size:11
Alignment explanation
Indices: 6459--6485 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6449 TAGAAATTAG
6459 TTTGTGAAACT
1 TTTGTGAAACT
6470 TTTGTGAAACT
1 TTTGTGAAACT
6481 TTTGT
1 TTTGT
6486 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:7903 original size:15 final size:14
Alignment explanation
Indices: 7883--7912 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
7873 ATATATCACT
7883 ATATAATTATATTTA
1 ATATAATTAT-TTTA
7898 ATATAATTATTTTA
1 ATATAATTATTTTA
7912 A
1 A
7913 ATTGTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATAATTATTTTA
Found at i:7990 original size:11 final size:11
Alignment explanation
Indices: 7968--8003 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
7958 AATTATATAT
7968 TATTATAAATTA
1 TATTA-AAATTA
7980 TATTAAAATTA
1 TATTAAAATTA
*
7991 TATTTAAATTA
1 TATTAAAATTA
8002 TA
1 TA
8004 CAAATCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:8197 original size:15 final size:15
Alignment explanation
Indices: 8162--8294 Score: 59
Period size: 15 Copynumber: 8.9 Consensus size: 15
8152 TTAAGAATTT
*
8162 TATTAAATTAT-ATA
1 TATTTAATTATAATA
8176 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
8190 TATTTAATAATAACT-
1 TATTTAATTATAA-TA
8205 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
8219 T-TTTACAGTATCATA
1 TATTTA-ATTATAATA
*
8234 TATTATGATTTGAGTAA-A
1 TATT-T-AATT-A-TAATA
* *
8252 TCATATAAATAT-ATA
1 T-ATTTAATTATAATA
8267 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
8281 TATTTAATAATAAT
1 TATTTAATTATAAT
8295 TATGTTTAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 33
0.66 0.10 0.24
Matches are distributed among these distances:
12 3 0.03
13 19 0.21
14 13 0.15
15 32 0.36
16 9 0.10
17 4 0.04
18 5 0.06
19 4 0.04
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:8244 original size:121 final size:114
Alignment explanation
Indices: 8042--8256 Score: 290
Period size: 121 Copynumber: 1.8 Consensus size: 114
8032 ATAATAATTA
* *
8042 AATTTTATTAAATCATATATTAATTAAATCATATTAATATTAATTATTTGAAATTTCTTTATAGT
1 AATTTTATTAAATCATATATTAATTAAATCATATTAATAATAATTATTTGAAATTTCTTTACAGT
8107 ATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
66 ATCATATATTATGATTTGAGTAAA-TCATAGAAGAATTTTATTTATTAAG
* * *
8157 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAACTTATGTT-AATTTATAT
1 AATTTTATTAAATCATATA--TTAATTA-AATCATA-TTAATAATAA-TTAT-TTGAAATT-T-C
8220 TTTACAGTATCATATATTATGATTTGAGTAAATCATA
58 TTTACAGTATCATATATTATGATTTGAGTAAATCATA
8257 TAAATATATA
Statistics
Matches: 87, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
115 18 0.21
117 10 0.11
118 12 0.14
119 8 0.09
120 8 0.09
121 31 0.36
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (114 bp):
AATTTTATTAAATCATATATTAATTAAATCATATTAATAATAATTATTTGAAATTTCTTTACAGT
ATCATATATTATGATTTGAGTAAATCATAGAAGAATTTTATTTATTAAG
Found at i:8283 original size:16 final size:16
Alignment explanation
Indices: 8262--8303 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
8252 TCATATAAAT
*
8262 ATATATTTTAATTATA
1 ATATATTTTAATAATA
8278 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
8293 AT-TATGTTTAA
1 ATATAT-TTTAA
8304 ATATGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:8431 original size:18 final size:17
Alignment explanation
Indices: 8403--8437 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
8393 ATTATTAAGA
*
8403 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
8420 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
8438 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Done.