Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2079
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: 29504
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2103 original size:20 final size:21
Alignment explanation
Indices: 2078--2128 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2068 CCCTCAATTC
2078 TATCGATACA-CATGGT-AATG
1 TATCGATACATCAT-GTAAATG
*
2098 TATCGATACATTATGTAAATG
1 TATCGATACATCATGTAAATG
2119 TATCGATACA
1 TATCGATACA
2129 AGTCATTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
TATCGATACATCATGTAAATG
Found at i:4318 original size:15 final size:15
Alignment explanation
Indices: 4271--4323 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
4261 CGAATCATAA
*
4271 TTATAATATTTAAAT
1 TTATAATAATTAAAT
4286 TTA-AATATTATCTAAAT
1 TTATAATA--AT-TAAAT
4303 TTATAATAATTAAAT
1 TTATAATAATTAAAT
4318 TTATAA
1 TTATAA
4324 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 4 0.12
15 14 0.42
16 3 0.09
17 8 0.24
18 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATAATAATTAAAT
Found at i:4334 original size:32 final size:32
Alignment explanation
Indices: 4271--4334 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
4261 CGAATCATAA
* * **
4271 TTATAATATTTAAATTTAAATATTATCTAAAT
1 TTATAATAATTAAATTTAAAAAAAATCTAAAT
4303 TTATAATAATTAAATTTATAAAAAAAT-TAAAT
1 TTATAATAATTAAATTTA-AAAAAAATCTAAAT
4335 AATTATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (32 bp):
TTATAATAATTAAATTTAAAAAAAATCTAAAT
Found at i:5184 original size:13 final size:14
Alignment explanation
Indices: 5152--5182 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5142 TAAACTCGAT
5152 ATTTATAAAAAATA
1 ATTTATAAAAAATA
5166 ATTTATAAAAAATA
1 ATTTATAAAAAATA
5180 ATT
1 ATT
5183 ATCAAACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTTATAAAAAATA
Found at i:5653 original size:35 final size:34
Alignment explanation
Indices: 5614--5694 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
5604 TAATCTTTAA
* * *
5614 TTATTATTTAATATGAATATAGTTTTAATATACT-T
1 TTATTATTTAATAT-AAAATAATTTCAATATA-TGT
5649 TTATTATTTAATATAAAATAATTTCAATATATGT
1 TTATTATTTAATATAAAATAATTTCAATATATGT
5683 TTAATTATTTAA
1 TT-ATTATTTAA
5695 AACAAATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 1 0.02
34 17 0.41
35 23 0.56
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (34 bp):
TTATTATTTAATATAAAATAATTTCAATATATGT
Found at i:7984 original size:21 final size:21
Alignment explanation
Indices: 7960--8003 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7950 ATTAAAAAAT
7960 TATTTTATA-TTAATATCTAAA
1 TATTTTATAGTTAA-ATCTAAA
*
7981 TATTTTATAGTTAAATTTAAA
1 TATTTTATAGTTAAATCTAAA
8002 TA
1 TA
8004 AAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTTTATAGTTAAATCTAAA
Found at i:9560 original size:28 final size:28
Alignment explanation
Indices: 9490--9564 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
9480 TTCTATATAC
* *
9490 AAAATTTAAATAAATAATTATTATTTAAT
1 AAAATTTAATTTAA-AATTATTATTTAAT
*
9519 AAAATTTAATTTAAAATTAATTTTTTAAT
1 AAAATTTAATTTAAAATT-ATTATTTAAT
9548 AATAA-TTAA-TTAAAATT
1 AA-AATTTAATTTAAAATT
9565 TATAAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.29
29 27 0.66
30 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AAAATTTAATTTAAAATTATTATTTAAT
Found at i:10719 original size:10 final size:10
Alignment explanation
Indices: 10693--10730 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
10683 TTTAAATTAA
10693 AAATATAGT-T
1 AAATATA-TAT
*
10703 AATTATATAT
1 AAATATATAT
10713 AAATATATAT
1 AAATATATAT
10723 AAATATAT
1 AAATATAT
10731 TTAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 1 0.04
10 24 0.96
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (10 bp):
AAATATATAT
Found at i:10739 original size:13 final size:13
Alignment explanation
Indices: 10721--10772 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
10711 ATAAATATAT
10721 ATAAATATATTTA
1 ATAAATATATTTA
*
10734 ATAAATAT-TTAA
1 ATAAATATATTTA
*
10746 ATAAATA-ATTTT
1 ATAAATATATTTA
*
10758 ATATAATATAATTA
1 ATA-AATATATTTA
10772 A
1 A
10773 AATTATAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 15 0.48
13 12 0.39
14 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAATATATTTA
Found at i:10758 original size:25 final size:27
Alignment explanation
Indices: 10705--10773 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 27
10695 ATATAGTTAA
*
10705 TTATAT-ATA-AATATATATAAATATAT
1 TTATATAATATAAT-TAAATAAATATAT
*
10731 TTA-ATAA-ATATTTAAATAAATA-ATT
1 TTATATAATATAATTAAATAAATATA-T
10756 TTATATAATATAATTAAA
1 TTATATAATATAATTAAA
10774 ATTATAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
24 1 0.03
25 16 0.46
26 10 0.29
27 8 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTATATAATATAATTAAATAAATATAT
Found at i:11238 original size:21 final size:20
Alignment explanation
Indices: 11212--11251 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
11202 TATATTAATA
11212 TTTATATAAAATTTATGATAT
1 TTTATATAAAA-TTATGATAT
11233 TTTATATAAAATTATGATA
1 TTTATATAAAATTATGATA
11252 GAAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTATATAAAATTATGATAT
Found at i:13148 original size:13 final size:13
Alignment explanation
Indices: 13107--13168 Score: 80
Period size: 13 Copynumber: 5.2 Consensus size: 13
13097 CCGTTACAAG
13107 CAATGTATCGATA
1 CAATGTATCGATA
13120 CAAT-T-TC-AT-
1 CAATGTATCGATA
13129 C-ATGTATCGATA
1 CAATGTATCGATA
13141 CAATGTATCGATA
1 CAATGTATCGATA
*
13154 CAATGTATTGATA
1 CAATGTATCGATA
13167 CA
1 CA
13169 TTGTCCCATG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
8 2 0.05
9 2 0.05
10 4 0.09
11 4 0.09
12 2 0.05
13 29 0.67
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:13262 original size:19 final size:20
Alignment explanation
Indices: 13219--13272 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
13209 TGCCAATTTT
* **
13219 ATGTATTGATACAATTGTCC
1 ATGTATCGATACAATTGAAC
13239 ATGTATCGATACAATT-AAC
1 ATGTATCGATACAATTGAAC
13258 ATGTATCGATACAAT
1 ATGTATCGATACAAT
13273 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:13276 original size:13 final size:13
Alignment explanation
Indices: 13258--13284 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13248 TACAATTAAC
13258 ATGTATCGATACA
1 ATGTATCGATACA
13271 ATGTATCGATACA
1 ATGTATCGATACA
13284 A
1 A
13285 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:21476 original size:13 final size:13
Alignment explanation
Indices: 21435--21483 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
21425 CCGTTACAAG
21435 CAATGTATCGATA
1 CAATGTATCGATA
21448 CAAT-T-TC-AT-
1 CAATGTATCGATA
*
21457 C-ATGTATCGGTA
1 CAATGTATCGATA
21469 CAATGTATCGATA
1 CAATGTATCGATA
21482 CA
1 CA
21484 TTGTCCCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 4 0.14
11 3 0.10
12 2 0.07
13 16 0.55
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:21476 original size:34 final size:33
Alignment explanation
Indices: 21435--21504 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
21425 CCGTTACAAG
* *
21435 CAATGTATCGATACAATT-TCATCATGTATCGGTA
1 CAATGTATCGATAC-ATTGTC-CCATGTATCGATA
21469 CAATGTATCGATACATTGTCCCATGTATCGATA
1 CAATGTATCGATACATTGTCCCATGTATCGATA
21502 CAA
1 CAA
21505 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACATTGTCCCATGTATCGATA
Found at i:21577 original size:19 final size:20
Alignment explanation
Indices: 21533--21586 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
21523 CTGCCAATCT
**
21533 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
21553 CATGTATCGATACAATT-AA
1 CATGTATCGATACAATTGAA
21572 CATGTATCGATACAA
1 CATGTATCGATACAA
21587 AGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:22017 original size:20 final size:20
Alignment explanation
Indices: 21992--22045 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
21982 GTATCGATAC
**
21992 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
22012 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
22032 AATGTATCGATACA
1 AATGTATCGATACA
22046 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:22141 original size:33 final size:32
Alignment explanation
Indices: 22077--22144 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
22067 GTAGCTAAAT
* *
22077 TTGTATCGATACATACAATATGTATCGATACA
1 TTGTATCAATACATACAAAATGTATCGATACA
* *
22109 TTGTATCAATACATCATAAAATTTATCGATACA
1 TTGTATCAATACAT-ACAAAATGTATCGATACA
22142 TTG
1 TTG
22145 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (32 bp):
TTGTATCAATACATACAAAATGTATCGATACA
Found at i:28286 original size:13 final size:13
Alignment explanation
Indices: 28267--28305 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
28257 ACATCATTCT
28267 CTGTATCGATACA
1 CTGTATCGATACA
*
28280 TTGTATCGATACA
1 CTGTATCGATACA
28293 CTGTATCGATACA
1 CTGTATCGATACA
28306 AGGGCATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:28480 original size:22 final size:21
Alignment explanation
Indices: 28437--28477 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28427 CAAATTTCTT
28437 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
28459 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
28478 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Done.