Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2121
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: 17362
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:1706 original size:26 final size:24
Alignment explanation
Indices: 1661--1710 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
1651 TATACGAATA
*
1661 TTTTAAAATTTATATAATATAAAT
1 TTTTAAAATTTAGATAATATAAAT
*
1685 TTTTAATATATTTAGATTATATAAAT
1 TTTTAA-A-ATTTAGATAATATAAAT
1711 ATAAAATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 1 0.05
26 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTAAAATTTAGATAATATAAAT
Found at i:2529 original size:2 final size:2
Alignment explanation
Indices: 2522--2549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2512 CTTTTTAATA
2522 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
2550 CACAGAAGAT
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):
AT
Found at i:3073 original size:21 final size:21
Alignment explanation
Indices: 3014--3095 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 21
3004 ATAATTATCA
* *
3014 AAATA-AAAAATTTAAATTCAT
1 AAATATAAAATTTTAAATT-TT
* **
3035 GAATATGAAAATCATAAATTTT
1 AAATAT-AAAATTTTAAATTTT
*
3057 AAATATAAAATTTTAAAATTT
1 AAATATAAAATTTTAAATTTT
*
3078 AAAT-TCAAA-TTTAAATTT
1 AAATATAAAATTTTAAATTT
3096 AAGTTTTCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
19 8 0.17
20 4 0.08
21 20 0.42
22 6 0.12
23 10 0.21
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATATAAAATTTTAAATTTT
Found at i:3081 original size:14 final size:13
Alignment explanation
Indices: 3049--3095 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3039 ATGAAAATCA
3049 TAAATTTTAAATAT
1 TAAATTTTAAAT-T
*
3063 AAAATTTTAAAATT
1 TAAATTTT-AAATT
*
3077 TAAA-TTCAAATT
1 TAAATTTTAAATT
3089 TAAATTT
1 TAAATTT
3096 AAGTTTTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 9 0.32
13 4 0.14
14 11 0.39
15 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATTTTAAATT
Found at i:3495 original size:20 final size:18
Alignment explanation
Indices: 3447--3495 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
3437 TTAATTTTTA
3447 TTTAAATTCAAATCAAAT
1 TTTAAATTCAAATCAAAT
*
3465 CTTAATTATTCAAATACAAAAT
1 TTTAA--ATTCAAAT-C-AAAT
3487 TTTAAATTC
1 TTTAAATTC
3496 GTGAATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 4 0.16
20 12 0.48
21 1 0.04
22 8 0.32
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAAATTCAAATCAAAT
Found at i:4275 original size:11 final size:11
Alignment explanation
Indices: 4241--4278 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
4231 TGAATATAAT
4241 TATAATAAAAA
1 TATAATAAAAA
*
4252 AATAATATAAAA
1 TATAATA-AAAA
4264 TATAATAAAAA
1 TATAATAAAAA
4275 TATA
1 TATA
4279 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:4448 original size:8 final size:8
Alignment explanation
Indices: 4435--4503 Score: 50
Period size: 8 Copynumber: 8.0 Consensus size: 8
4425 TTGGTTGTTG
4435 TTTTTATT
1 TTTTTATT
4443 TTTTTATT
1 TTTTTATT
4451 TTTTGTATT
1 TTTT-TATT
*
4460 TTAATTATT
1 TT-TTTATT
4469 TATTTT-TT
1 T-TTTTATT
* *
4477 AGTTTTAAT
1 -TTTTTATT
4486 TTTTTATCT
1 TTTTTAT-T
4495 TTATTTATT
1 TT-TTTATT
4504 ATTGCAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
8 23 0.48
9 18 0.38
10 7 0.15
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (8 bp):
TTTTTATT
Found at i:4452 original size:7 final size:7
Alignment explanation
Indices: 4435--4506 Score: 56
Period size: 7 Copynumber: 10.1 Consensus size: 7
4425 TTGGTTGTTG
4435 TTTTTATT
1 TTTTTA-T
4443 TTTTTAT
1 TTTTTAT
*
4450 TTTTTGT
1 TTTTTAT
*
4457 ATTTTAAT
1 -TTTTTAT
*
4465 TATTTAT
1 TTTTTAT
*
4472 TTTTTAG
1 TTTTTAT
*
4479 TTTTAAT
1 TTTTTAT
4486 TTTTTA-
1 TTTTTAT
*
4492 TCTTTAT
1 TTTTTAT
*
4499 TTATTAT
1 TTTTTAT
4506 T
1 T
4507 GCAAAAACAT
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
6 5 0.10
7 33 0.67
8 11 0.22
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTTAT
Found at i:4456 original size:21 final size:21
Alignment explanation
Indices: 4432--4490 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
4422 GGCTTGGTTG
4432 TTGTTTTTATTTTTTTATTTT
1 TTGTTTTTATTTTTTTATTTT
* *
4453 TTGTATTTTAATTATTTATTTT
1 TTGT-TTTTATTTTTTTATTTT
*
4475 TTAGTTTTAATTTTTT
1 TT-GTTTTTATTTTTT
4491 ATCTTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 4 0.13
22 25 0.81
23 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (21 bp):
TTGTTTTTATTTTTTTATTTT
Found at i:4753 original size:13 final size:13
Alignment explanation
Indices: 4735--4784 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
4725 TCAAACCCAA
*
4735 TTATTATATGTAT
1 TTATTATATATAT
*
4748 TTATTATATATTTT
1 TTATTATATA-TAT
*
4762 TTGTTATATATAT
1 TTATTATATATAT
4775 TTATTATATA
1 TTATTATATA
4785 AAATTAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTATTATATATAT
Found at i:4990 original size:16 final size:18
Alignment explanation
Indices: 4950--4988 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
4940 TTTACTGTTT
4950 AAAATATTATTAAAAATTA
1 AAAATATTATT-AAAATTA
*
4969 AAAATATTATTAAATTTA
1 AAAATATTATTAAAATTA
4987 AA
1 AA
4989 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATTATTAAAATTA
Found at i:7234 original size:24 final size:23
Alignment explanation
Indices: 7205--7256 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
7195 AATCTTTCTA
*
7205 AAATTATTTTATTCATCAAATTT
1 AAATTATTTTACTCATCAAATTT
7228 CAAATTATTTTACTCATCAAATTT
1 -AAATTATTTTACTCATCAAATTT
7252 AAATT
1 AAATT
7257 TTAAATTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTATTTTACTCATCAAATTT
Found at i:8131 original size:20 final size:20
Alignment explanation
Indices: 8106--8156 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
8096 TTTTGAAGCA
*
8106 ATGTATCGATACAAT-TCGTC
1 ATGTATCGATACAATGT-GCC
*
8126 ATGTATCAATACAATGTGCC
1 ATGTATCGATACAATGTGCC
8146 ATGTATCGATA
1 ATGTATCGATA
8157 TAAACAGTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:8213 original size:20 final size:20
Alignment explanation
Indices: 8188--8262 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
8178 CTGCCAGTTT
8188 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
*
8208 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTGTC
**
8228 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTC
*
8247 TATGTATCGATACAAT
1 CATGTATCGATACAAT
8263 GTATCGATAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
19 15 0.31
20 34 0.69
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:8266 original size:13 final size:13
Alignment explanation
Indices: 8248--8274 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8238 TACAATGAAT
8248 ATGTATCGATACA
1 ATGTATCGATACA
8261 ATGTATCGATACA
1 ATGTATCGATACA
8274 A
1 A
8275 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:8270 original size:32 final size:33
Alignment explanation
Indices: 8229--8291 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
8219 ACAATTATCC
*
8229 ATGTATCGATACAATGAAT-ATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
*
8261 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGAATAATGTATCGATA
8292 GATCTGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:10635 original size:33 final size:33
Alignment explanation
Indices: 10576--10640 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
10566 TACAAGCCAA
* *
10576 TGTATCGATACAATTTTTTGTATATCGATACAT
1 TGTATCGATACAATCTTTGGTATATCGATACAT
*
10609 TGTATCGATAC-ATACTTTGGTGTATCGATACA
1 TGTATCGATACAAT-CTTTGGTATATCGATACA
10641 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTATATCGATACAT
Found at i:11340 original size:12 final size:12
Alignment explanation
Indices: 11323--11347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11313 TAAGGTAATT
11323 TTAGCAAATTTA
1 TTAGCAAATTTA
11335 TTAGCAAATTTA
1 TTAGCAAATTTA
11347 T
1 T
11348 GCATCCTCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTAGCAAATTTA
Found at i:11426 original size:23 final size:23
Alignment explanation
Indices: 11394--11439 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
11384 TCAAGTAATT
11394 CATATAAAAAATTTATTTGCACA
1 CATATAAAAAATTTATTTGCACA
*
11417 CATATCAAAAATTTATTTGCACA
1 CATATAAAAAATTTATTTGCACA
11440 TACATCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (23 bp):
CATATAAAAAATTTATTTGCACA
Found at i:12763 original size:21 final size:20
Alignment explanation
Indices: 12734--12776 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12724 GGCTAGTATG
* *
12734 GGGACTGCCCTGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
12755 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
12775 GG
1 GG
12777 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.30, G:0.42, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:13235 original size:13 final size:13
Alignment explanation
Indices: 13219--13255 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
13209 AATCCCCCTA
*
13219 TATCGATACAGTG
1 TATCGATACAATG
*
13232 TATCGATATAATG
1 TATCGATACAATG
13245 TATCGATACAA
1 TATCGATACAA
13256 AGAAAAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Done.