Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1158
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: 40033
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:818 original size:18 final size:18
Alignment explanation
Indices: 780--818 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
770 TTGCTATCGG
**
780 TTATGCTCGAGACTATCA
1 TTATGCTCGAGACTAGAA
798 TTATGCTCGAGACTAGAA
1 TTATGCTCGAGACTAGAA
816 TTA
1 TTA
819 CTAAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (18 bp):
TTATGCTCGAGACTAGAA
Found at i:5623 original size:44 final size:44
Alignment explanation
Indices: 5564--5647 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
5554 ATTTTTATCA
*
5564 AGGGGGAGAGCCTTAACTATTTTATAAAGGGGGGAAAAACTTTT
1 AGGGGGAGAGCCTTAACTATTTTATAAAGGGGAGAAAAACTTTT
5608 AGGGGGAGAGCCTTAACTATTTTATAAAGGGGAGAAAAAC
1 AGGGGGAGAGCCTTAACTATTTTATAAAGGGGAGAAAAAC
5648 GAAACTTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.37, C:0.10, G:0.30, T:0.24
Consensus pattern (44 bp):
AGGGGGAGAGCCTTAACTATTTTATAAAGGGGAGAAAAACTTTT
Found at i:6216 original size:19 final size:18
Alignment explanation
Indices: 6191--6248 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
6181 TTGTATCGAT
*
6191 ACATTGTATCGATATATG
1 ACATTGTATCGATACATG
6209 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
6229 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
6248 A
1 A
6249 AACTGGCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.50
20 17 0.47
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:6237 original size:20 final size:20
Alignment explanation
Indices: 6192--6247 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
6182 TGTATCGATA
*
6192 CATTGTATCGATATAT-GAT
1 CATTGTATCGATACATGGAT
6211 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
6230 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
6248 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:7333 original size:13 final size:13
Alignment explanation
Indices: 7315--7341 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7305 CAATTTTTTG
7315 TGTATCGATACAT
1 TGTATCGATACAT
7328 TGTATCGATACAT
1 TGTATCGATACAT
7341 T
1 T
7342 CTTGCTGTAT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7356 original size:32 final size:33
Alignment explanation
Indices: 7295--7358 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
7285 TACAAGCCAA
*
7295 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTTCTTGTGTATCGATACAT
7328 TGTATCGATAC-A-TTCTTGCTGTATCGATACA
1 TGTATCGATACAATTTCTTG-TGTATCGATACA
7359 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 5 0.17
32 13 0.45
33 11 0.38
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATTTCTTGTGTATCGATACAT
Found at i:7425 original size:20 final size:20
Alignment explanation
Indices: 7400--7472 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
7390 CAACTTTTTT
7400 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
7420 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
7441 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
7461 ATGTATCGATAC
1 ATGTATCGATAC
7473 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:7438 original size:41 final size:41
Alignment explanation
Indices: 7379--7472 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
7369 CTGCCAAGAA
*
7379 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
7420 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
7461 ATGTATCGATAC
1 ATGTATCGATAC
7473 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:7454 original size:21 final size:21
Alignment explanation
Indices: 7379--7454 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
7369 CTGCCAAGAA
* *
7379 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
7400 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
7420 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
7441 ATGTATCGATACAT
1 ATGTATCGATACAT
7455 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:9933 original size:13 final size:13
Alignment explanation
Indices: 9915--9952 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
9905 ATAATCACCC
9915 TGTATCGATACAG
1 TGTATCGATACAG
*
9928 TGTATCGATACAT
1 TGTATCGATACAG
9941 TGTATCGATACA
1 TGTATCGATACA
9953 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:9966 original size:20 final size:20
Alignment explanation
Indices: 9941--10017 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
9931 ATCGATACAT
9941 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
9961 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
9986 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
10006 TGTATCGATACA
1 TGTATCGATACA
10018 TTTTAGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:12043 original size:15 final size:15
Alignment explanation
Indices: 12023--12053 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12013 ATTTCGTTTG
*
12023 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
12038 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
12053 G
1 G
12054 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:16120 original size:20 final size:20
Alignment explanation
Indices: 16095--16146 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
16085 TACAAGCCAA
*
16095 TGTATCGATACAATTTTTTG-
1 TGTATCGATACAA-TTCTTGC
16115 TGTATCGATAC-ATTCTTGC
1 TGTATCGATACAATTCTTGC
16134 TGTATCGATACAA
1 TGTATCGATACAA
16147 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.17
19 12 0.41
20 12 0.41
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATTCTTGC
Found at i:16212 original size:20 final size:20
Alignment explanation
Indices: 16187--16259 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
16177 CAACTTTTTT
16187 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
16207 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
16228 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
16248 ATGTATCGATAC
1 ATGTATCGATAC
16260 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:16225 original size:41 final size:41
Alignment explanation
Indices: 16166--16259 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
16156 CTGCCAAGAA
*
16166 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
16207 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
16248 ATGTATCGATAC
1 ATGTATCGATAC
16260 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:16241 original size:21 final size:21
Alignment explanation
Indices: 16166--16241 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
16156 CTGCCAAGAA
* *
16166 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
16187 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
16207 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
16228 ATGTATCGATACAT
1 ATGTATCGATACAT
16242 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:18443 original size:13 final size:13
Alignment explanation
Indices: 18425--18463 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
18415 GCCAAGGAAA
18425 TGTATCGATACAT
1 TGTATCGATACAT
18438 TGTATCGATACAT
1 TGTATCGATACAT
18451 TGTATCGATACAT
1 TGTATCGATACAT
18464 GGATCTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25064 original size:14 final size:15
Alignment explanation
Indices: 25044--25108 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 15
25034 ATTTCACGAT
*
25044 TTTTTTTATTTTTGA
1 TTTTATTATTTTTGA
25059 TTTT-TTA--TTTGA
1 TTTTATTATTTTTGA
25071 TTATTATTATTTTTTTG-
1 TT-TTATTA--TTTTTGA
*
25088 TTTTATTATTTTTAA
1 TTTTATTATTTTTGA
25103 TTTTAT
1 TTTTAT
25109 ATAAAAAATC
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
12 7 0.17
13 2 0.05
14 11 0.26
15 10 0.24
16 6 0.14
17 2 0.05
18 4 0.10
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTTATTATTTTTGA
Found at i:25074 original size:22 final size:21
Alignment explanation
Indices: 25049--25106 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
25039 ACGATTTTTT
25049 TTATTTTTGATTTTTTATTTGA
1 TTATTTTT-ATTTTTTATTTGA
* * *
25071 TTATTATTATTTTTTTGTTTTA
1 TTATTTTTA-TTTTTTATTTGA
*
25093 TTATTTTTAATTTT
1 TTATTTTTATTTTT
25107 ATATAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (21 bp):
TTATTTTTATTTTTTATTTGA
Found at i:26910 original size:13 final size:13
Alignment explanation
Indices: 26892--26916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26882 CATGGCGCGT
26892 TGTATCGATACAA
1 TGTATCGATACAA
26905 TGTATCGATACA
1 TGTATCGATACA
26917 TGATGAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:34366 original size:17 final size:17
Alignment explanation
Indices: 34346--34384 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
34336 AAAGTAGAGG
34346 GAAAAAAAAAGAGAAAA
1 GAAAAAAAAAGAGAAAA
*
34363 GAAAGAAAAAGAGAAAA
1 GAAAAAAAAAGAGAAAA
34380 -AAAAA
1 GAAAAA
34385 GAGAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAAGAGAAAA
Found at i:34393 original size:12 final size:12
Alignment explanation
Indices: 34362--34395 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34352 AAAAGAGAAA
*
34362 AGAAAGAAAAAG
1 AGAAAAAAAAAG
34374 AGAAAAAAAAAG
1 AGAAAAAAAAAG
34386 AGAGAAAAAA
1 AGA-AAAAAA
34396 TTAAGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:37131 original size:99 final size:100
Alignment explanation
Indices: 37001--37220 Score: 327
Period size: 99 Copynumber: 2.2 Consensus size: 100
36991 TTTTTTATTG
* *
37001 AAAAA-GGGGTTGAAGTATCCCCTCAGAGGAATGGGGCTAGAGTATCCCCGATGATGACAATTCA
1 AAAAATGGGGTTGGAGTATCCCCTCAGAGGAATGGGGCTAGAGTATCCCCGATGAAGACAATTCA
*
37065 AGTGAAAATAATATTTAAATCTTGACAAG-TTTTA
66 AGTGAAAATAAGATTTAAATCTTGACAAGTTTTTA
* * * * * * *
37099 AAAAATGGGGTTGGAGTATCCTCTCGGTGGAATGGGGTTAGAGTGTCCCCGATGAAGATAATTTA
1 AAAAATGGGGTTGGAGTATCCCCTCAGAGGAATGGGGCTAGAGTATCCCCGATGAAGACAATTCA
37164 AGTGAAAATAAGATTTAAATCTTGACAAGTTTTTA
66 AGTGAAAATAAGATTTAAATCTTGACAAGTTTTTA
*
37199 AAAAATAGGGTTGGAGTATCCC
1 AAAAATGGGGTTGGAGTATCCC
37221 GAATGAATAA
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
98 5 0.05
99 78 0.72
100 25 0.23
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (100 bp):
AAAAATGGGGTTGGAGTATCCCCTCAGAGGAATGGGGCTAGAGTATCCCCGATGAAGACAATTCA
AGTGAAAATAAGATTTAAATCTTGACAAGTTTTTA
Found at i:39499 original size:51 final size:51
Alignment explanation
Indices: 39384--39500 Score: 155
Period size: 53 Copynumber: 2.3 Consensus size: 51
39374 AATTAACTAG
* * * *
39384 ATGTATCGATACATTGAAAAATGTATCGATACATTTGGGTGAAAAAAACATA
1 ATGTATCGATACATTAAAAAATATATCGATACATCTGGGT-AAAAAAACAGA
* *
39436 ATATATCGATACATTAAAAAAATATATCGATACATCTGGGT-AAAACACAGA
1 ATGTATCGATACATT-AAAAAATATATCGATACATCTGGGTAAAAAAACAGA
39487 ATGTATCGATACAT
1 ATGTATCGATACAT
39501 GTACTATTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
51 21 0.37
52 14 0.25
53 22 0.39
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAAAAAAACAGA
Found at i:40024 original size:13 final size:13
Alignment explanation
Indices: 40006--40033 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39996 TTTCAAATTT
40006 AAGTCTAAATTAA
1 AAGTCTAAATTAA
40019 AAGTCTAAATTAA
1 AAGTCTAAATTAA
40032 AA
1 AA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
AAGTCTAAATTAA
Done.