Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2080
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: 40918
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:1165 original size:14 final size:15
Alignment explanation
Indices: 1142--1183 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
1132 ATTACCATAT
*
1142 AAATAAAATATAATTC
1 AAATAATATAT-ATTC
1158 AAATAATA-ATATTC
1 AAATAATATATATTC
*
1172 GAATAATATATA
1 AAATAATATATA
1184 AATAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.48
15 5 0.22
16 7 0.30
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (15 bp):
AAATAATATATATTC
Found at i:4116 original size:30 final size:29
Alignment explanation
Indices: 4082--4157 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
4072 ATTTAAGTTG
4082 ATTAAAATTTATTTTATTATTTGTTATATT-
1 ATTAAAATTTATTTTATTATTT-TTAT-TTA
4112 ATTAAAATATTATTTTA-TATTTTTATTTA
1 ATTAAAAT-TTATTTTATTATTTTTATTTA
* *
4141 AATAAAAATTATTTTAT
1 ATTAAAATTTATTTTAT
4158 GATTAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 10 0.24
29 10 0.24
30 13 0.32
31 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (29 bp):
ATTAAAATTTATTTTATTATTTTTATTTA
Found at i:4129 original size:28 final size:28
Alignment explanation
Indices: 4084--4157 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 28
4074 TTAAGTTGAT
* *
4084 TAAAATTTATTTTATTATTTGTTATATT-AT
1 TAAAAATTATTTTA-TA-TTGTTAT-TTAAA
*
4114 TAAAATATTATTTTATATTTTTATTTAAA
1 TAAAA-ATTATTTTATATTGTTATTTAAA
4143 TAAAAATTATTTTAT
1 TAAAAATTATTTTAT
4158 GATTAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 12 0.31
29 12 0.31
30 7 0.18
31 8 0.21
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
TAAAAATTATTTTATATTGTTATTTAAA
Found at i:5545 original size:16 final size:16
Alignment explanation
Indices: 5520--5550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5510 TAATCAATCA
5520 AAATTAAAAATAATTT
1 AAATTAAAAATAATTT
*
5536 AAATTTAAAATAATT
1 AAATTAAAAATAATT
5551 CGAACTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTAAAAATAATTT
Found at i:7093 original size:19 final size:18
Alignment explanation
Indices: 7049--7093 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
7039 ATAAGTAAAT
*
7049 ATTTTTTTTGAGAAATTA
1 ATTTTTTTTAAGAAATTA
* *
7067 ATCATTTTCTAAGAAATTA
1 AT-TTTTTTTAAGAAATTA
7086 ATTTTTTT
1 ATTTTTTT
7094 ATATATAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (18 bp):
ATTTTTTTTAAGAAATTA
Found at i:7973 original size:3 final size:3
Alignment explanation
Indices: 7956--7989 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
7946 ACTTTTAATT
7956 TTA TTA TCTA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TT
7990 GCAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.83
4 4 0.14
5 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9220 original size:19 final size:18
Alignment explanation
Indices: 9186--9222 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
9176 ATATTTTTAC
*
9186 TTAAATTTAATTTAAAAT
1 TTAAATTTAATATAAAAT
9204 TTAAATATTAATATAAAAT
1 TTAAAT-TTAATATAAAAT
9223 AATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAATTTAATATAAAAT
Found at i:11928 original size:15 final size:15
Alignment explanation
Indices: 11893--11934 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
11883 ACGAGATTTG
11893 AATAAAAATATAAATT
1 AATAAAAA-ATAAATT
*
11909 -TTAAAAAATAAATT
1 AATAAAAAATAAATT
11923 AATAAAAAATAA
1 AATAAAAAATAA
11935 TAAAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAAAAATAAATT
Found at i:15006 original size:2 final size:2
Alignment explanation
Indices: 14999--15027 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14989 TTTCTACATT
14999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15028 TTACATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15944 original size:2 final size:2
Alignment explanation
Indices: 15937--15969 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15927 TCACATTAAA
15937 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
15970 TTATGCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16176 original size:15 final size:14
Alignment explanation
Indices: 16165--16194 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16155 GACTTTTTCT
16165 AAAAGAAATTTTATC
1 AAAA-AAATTTTATC
16180 AAAAAAATTTTATC
1 AAAAAAATTTTATC
16194 A
1 A
16195 CTGTAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (14 bp):
AAAAAAATTTTATC
Found at i:16352 original size:19 final size:20
Alignment explanation
Indices: 16314--16351 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16304 TGTCATAGAA
*
16314 AATTTTTAGTGATTAAAAAT
1 AATTTTTAGCGATTAAAAAT
*
16334 AATTTTTAGCGATGAAAA
1 AATTTTTAGCGATTAAAA
16352 TTTCATTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (20 bp):
AATTTTTAGCGATTAAAAAT
Found at i:16491 original size:15 final size:15
Alignment explanation
Indices: 16466--16503 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
16456 AAATTATCAT
*
16466 AATAAAGATATAAAA
1 AATAAATATATAAAA
*
16481 TATAAATATATAAAA
1 AATAAATATATAAAA
16496 AATAAATA
1 AATAAATA
16504 AAATATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AATAAATATATAAAA
Found at i:16509 original size:20 final size:20
Alignment explanation
Indices: 16478--16547 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
16468 TAAAGATATA
16478 AAATATAAATATATAAAAAAT
1 AAATA-AAATATATAAAAAAT
**
16499 AAATAAAATATA-ATTAAAT
1 AAATAAAATATATAAAAAAT
* *
16518 AAGTGAAAATATATTAAAAAT
1 AAAT-AAAATATATAAAAAAT
16539 AAATAAAAT
1 AAATAAAAT
16548 TGTATATACA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.20
20 20 0.50
21 12 0.30
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AAATAAAATATATAAAAAAT
Found at i:20694 original size:20 final size:20
Alignment explanation
Indices: 20653--20695 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
20643 AAATAAATAA
* *
20653 AAATTTTAATTTTTATATTT
1 AAATTTTAATTTTGATAATT
20673 AAATTTATAA-TTTGATAATT
1 AAATTT-TAATTTTGATAATT
20693 AAA
1 AAA
20696 AGTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATTTTAATTTTGATAATT
Found at i:20776 original size:24 final size:24
Alignment explanation
Indices: 20749--20795 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
20739 CTTTCTATTG
20749 ATTTTATTATATTT-ATATTTTTAA
1 ATTTTATTAT-TTTAATATTTTTAA
20773 ATTTTATTATTTTAAATATTTTT
1 ATTTTATTATTTT-AATATTTTT
20796 TTAACAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 10 0.48
25 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTATTATTTTAATATTTTTAA
Found at i:23116 original size:23 final size:24
Alignment explanation
Indices: 23079--23135 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 24
23069 TACTCATTAA
23079 TTATTTTTTTAAAAAAAATTATTT
1 TTATTTTTTTAAAAAAAATTATTT
*
23103 TTATTTTTTT-AAAAATATTATTT
1 TTATTTTTTTAAAAAAAATTATTT
23126 TTATTTTTTT
1 TTATTTTTTT
23136 TAACTAGCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATTTTTTTAAAAAAAATTATTT
Found at i:23492 original size:2 final size:2
Alignment explanation
Indices: 23485--23516 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23475 AATGGACTTG
23485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23517 TAATTATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23716 original size:2 final size:2
Alignment explanation
Indices: 23709--23736 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23699 ACAAAATCTT
23709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23737 GTTCAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24517 original size:2 final size:2
Alignment explanation
Indices: 24510--24537 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24500 CTACTTTGTT
24510 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24538 AACCAGCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26252 original size:23 final size:24
Alignment explanation
Indices: 26224--26276 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
26214 TATAATTTTG
26224 AATATGATATAAAAAATAAT-TAA
1 AATATGATATAAAAAATAATATAA
*
26247 AATATGATATAAAAATTAATATAA
1 AATATGATATAAAAAATAATATAA
26271 ATATAT
1 A-ATAT
26277 AAAATGTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 19 0.70
24 4 0.15
25 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
AATATGATATAAAAAATAATATAA
Found at i:26265 original size:19 final size:19
Alignment explanation
Indices: 26241--26308 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
26231 TATAAAAAAT
*
26241 AATTAAAATATGATATAAA
1 AATTAAAATATAATATAAA
*
26260 AATTAATATA-AATATATAA
1 AATTAAAATATAATATA-AA
* *
26279 AATGTCAAAAT-TTACATAAA
1 AAT-T-AAAATATAATATAAA
26299 AA-TAAAATAT
1 AATTAAAATAT
26309 TAACATATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.13
18 7 0.18
19 14 0.36
20 5 0.13
21 8 0.21
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AATTAAAATATAATATAAA
Found at i:27401 original size:28 final size:28
Alignment explanation
Indices: 27370--27425 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
27360 AAAAAATTGT
27370 GAGATAAAATTATAGAACTCATTGATCA
1 GAGATAAAATTATAGAACTCATTGATCA
*
27398 GAGATATAATTATAGAACTCATTGATCA
1 GAGATAAAATTATAGAACTCATTGATCA
27426 AAGAGAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (28 bp):
GAGATAAAATTATAGAACTCATTGATCA
Found at i:34048 original size:18 final size:20
Alignment explanation
Indices: 34025--34067 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
34015 GTGAGTCAAG
34025 TATTTATA-TTTATAAAA-T
1 TATTTATATTTTATAAAATT
*
34043 TATTTATATTTTTTAAAATT
1 TATTTATATTTTATAAAATT
34063 TATTT
1 TATTT
34068 TTTAATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 8 0.36
20 6 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTATATTTTATAAAATT
Found at i:35909 original size:2 final size:2
Alignment explanation
Indices: 35902--35944 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
35892 TAATGGCGCC
35902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35944 T
1 T
35945 CCTTAATATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36215 original size:16 final size:16
Alignment explanation
Indices: 36194--36228 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
36184 ACCTTAGATG
36194 AAATATAATGGATAAC
1 AAATATAATGGATAAC
36210 AAATATAATGGATAAC
1 AAATATAATGGATAAC
36226 AAA
1 AAA
36229 GATTACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (16 bp):
AAATATAATGGATAAC
Found at i:39150 original size:14 final size:14
Alignment explanation
Indices: 39131--39158 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39121 ATATAAAAAC
39131 AGTCTTTTGTTCAT
1 AGTCTTTTGTTCAT
39145 AGTCTTTTGTTCAT
1 AGTCTTTTGTTCAT
39159 TTGAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
AGTCTTTTGTTCAT
Found at i:40029 original size:15 final size:16
Alignment explanation
Indices: 40009--40038 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39999 AAATATTATT
40009 TTTATTA-ATTTTTAA
1 TTTATTATATTTTTAA
40024 TTTATTATATTTTTA
1 TTTATTATATTTTTA
40039 TTAATTAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTATATTTTTAA
Found at i:40442 original size:16 final size:17
Alignment explanation
Indices: 40410--40453 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
40400 TATTAAAAGT
*
40410 AAAATTATTATATATT-A
1 AAAATT-TTAAATATTAA
*
40427 ATAATTTTAAATATTAA
1 AAAATTTTAAATATTAA
40444 AAAATTTTAA
1 AAAATTTTAA
40454 TCAAACTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTTTAAATATTAA
Found at i:40578 original size:23 final size:24
Alignment explanation
Indices: 40550--40595 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
40540 CTTAAAAATT
40550 TTAAATA-TATTTTAAA-ATTAAAA
1 TTAAATATTA-TTTAAATATTAAAA
40573 TTAAATATTATTTAAATATTAAA
1 TTAAATATTATTTAAATATTAAA
40596 TTATTAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAAATATTATTTAAATATTAAAA
Found at i:40762 original size:17 final size:17
Alignment explanation
Indices: 40694--40762 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 17
40684 ATAATCAAAT
40694 TTTTA-TTTTTAGA-TTA
1 TTTTATTTTTTA-ATTTA
40710 TTTTATTTTTTTACAATTTA
1 TTTTA-TTTTTT--AATTTA
**
40730 TTGAATTTATTT-ATTTA
1 TTTTATTT-TTTAATTTA
40747 TTTTATTTTTTAATTT
1 TTTTATTTTTTAATTT
40763 TAAAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
16 8 0.19
17 15 0.36
18 5 0.12
19 4 0.10
20 10 0.24
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTATTTTTTAATTTA
Done.