Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1172
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: 46899
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9968 original size:19 final size:21
Alignment explanation
Indices: 9941--9989 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
9931 TCAATCTCAA
9941 TCTCATTTTCTTTGTTT-TTC
1 TCTCATTTTCTTTGTTTCTTC
9961 TCTC-TTTTCTTTGTTTCTTC
1 TCTCATTTTCTTTGTTTCTTC
9981 TCTCGATTT
1 TCTC-ATTT
9990 CATTCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.46
20 11 0.42
22 3 0.12
ACGTcount: A:0.04, C:0.22, G:0.06, T:0.67
Consensus pattern (21 bp):
TCTCATTTTCTTTGTTTCTTC
Found at i:10060 original size:17 final size:17
Alignment explanation
Indices: 10031--10077 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
10021 CTTTTCTTGC
*
10031 CTCTCTTTTCTTTTGAT
1 CTCTCTTTTCTTTTCAT
10048 CTCT-TTTTGCTTTTCAT
1 CTCTCTTTT-CTTTTCAT
10065 CTTCTTCTTTTCT
1 C-TC-TCTTTTCT
10078 CACTTGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 12 0.48
18 2 0.08
19 3 0.12
20 4 0.16
ACGTcount: A:0.04, C:0.26, G:0.04, T:0.66
Consensus pattern (17 bp):
CTCTCTTTTCTTTTCAT
Found at i:12690 original size:18 final size:19
Alignment explanation
Indices: 12667--12705 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
12657 TTTATCTCAA
*
12667 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
12685 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
12704 TT
1 TT
12706 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:12761 original size:24 final size:22
Alignment explanation
Indices: 12698--12777 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 22
12688 CTTGTTCACA
*
12698 TTCTTTTTCTCTCTCAAACTTTTT
1 TTCTTTTTC-CTCTCAATC-TTTT
* * * *
12722 TTCATTCTCTTTTCAATCTTATT
1 TTCTTTTTCCTCTCAATCTT-TT
12745 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTTTC-CTCTCAATCT-TTT
12769 TTCTTTTTC
1 TTCTTTTTC
12778 TTTCATTTCT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.05
23 15 0.34
24 26 0.59
25 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (22 bp):
TTCTTTTTCCTCTCAATCTTTT
Found at i:14339 original size:56 final size:55
Alignment explanation
Indices: 14223--14340 Score: 150
Period size: 55 Copynumber: 2.1 Consensus size: 55
14213 TGCATGCTTT
* * * *
14223 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
* *
14277 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTTATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
14333 CATTAAAT
1 CATTAAAT
14341 CAGCAAGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 3 0.06
55 27 0.50
56 24 0.44
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:14989 original size:20 final size:20
Alignment explanation
Indices: 14964--15018 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
14954 ACGAGTTAAA
* *
14964 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
14984 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
15004 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
15019 TTGAGCCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:17232 original size:20 final size:20
Alignment explanation
Indices: 17186--17233 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
17176 GGTAAGCTAG
*
17186 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACAAGCTGA
*** *
17206 AACGAGCTCAAATAAGCTGA
1 GTTGAGCTCAAACAAGCTGA
17226 GTTGAGCT
1 GTTGAGCT
17234 GGACGAAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACAAGCTGA
Found at i:19017 original size:30 final size:30
Alignment explanation
Indices: 18983--19079 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
18973 AAAACTAAAA
18983 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
19013 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
19043 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
19072 ATGAGCTA
1 -TGAGCTA
19080 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:27561 original size:23 final size:22
Alignment explanation
Indices: 27509--27561 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
27499 TCCACGTCTT
*
27509 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
27531 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
27554 TTTCTTTT
1 TTTCTTTT
27562 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:31443 original size:30 final size:30
Alignment explanation
Indices: 31409--31506 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
31399 AGCTCACTCC
31409 TAGCTCATATTCAGCTCACGAGCTAAAACT
1 TAGCTCATATTCAGCTCACGAGCTAAAACT
** * * * * *
31439 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAAACT
* * *
31469 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAAACT
*
31499 TACCTCAT
1 TAGCTCAT
31507 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 17, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAAACT
Found at i:33247 original size:30 final size:30
Alignment explanation
Indices: 33213--33309 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
33203 TAAACTAAAA
33213 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33243 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
33273 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
33302 ATGAGCTA
1 -TGAGCTA
33310 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:35031 original size:4 final size:4
Alignment explanation
Indices: 35022--35049 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
35012 AAGTTTTATT
35022 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
35050 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:38820 original size:12 final size:13
Alignment explanation
Indices: 38798--38826 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
38788 AAGTTTTATT
38798 TTTATTTTATTTA
1 TTTATTTTATTTA
38811 TTTA-TTTATTTA
1 TTTATTTTATTTA
38823 TTTA
1 TTTA
38827 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:40272 original size:12 final size:12
Alignment explanation
Indices: 40257--40287 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
40247 TTCTTTTTGC
40257 TTTTCAAAGGCT
1 TTTTCAAAGGCT
40269 TTTTCAAAGGCT
1 TTTTCAAAGGCT
40281 TTTTCAA
1 TTTTCAA
40288 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:40345 original size:5 final size:5
Alignment explanation
Indices: 40335--40397 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
40325 CTCTTGCCTC
*
40335 TCTTT TCTTT T-TATT TCATTT TCTTTT TCTTC TCTTGCT T-TTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTT--T TCTTT TCTTT
40383 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
40398 GTTTTCTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
4 3 0.06
5 33 0.67
6 11 0.22
7 2 0.04
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:40393 original size:16 final size:16
Alignment explanation
Indices: 40335--40397 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
40325 CTCTTGCCTC
*
40335 TCTTTTCTTTTT-ATT
1 TCTTTTCTTTTTCTTT
*
40350 TCATTTTCTTTTTCTTC
1 TC-TTTTCTTTTTCTTT
*
40367 TC-TTGCTTTTTTCTTT
1 TCTTTTC-TTTTTCTTT
40383 TCTTTTC-TTTTCTTT
1 TCTTTTCTTTTTCTTT
40398 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
15 13 0.33
16 20 0.51
17 6 0.15
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (16 bp):
TCTTTTCTTTTTCTTT
Found at i:41335 original size:10 final size:10
Alignment explanation
Indices: 41320--41366 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
41310 TTAACTCGAT
41320 TTTTTTTCAC
1 TTTTTTTCAC
41330 TTTTTTTC-C
1 TTTTTTTCAC
*
41339 TTTTTTTCGAT
1 TTTTTTTC-AC
* *
41350 TTTTTTTGAA
1 TTTTTTTCAC
41360 TTTTTTT
1 TTTTTTT
41367 TTCTGAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 9 0.28
10 16 0.50
11 7 0.22
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.77
Consensus pattern (10 bp):
TTTTTTTCAC
Found at i:41366 original size:14 final size:15
Alignment explanation
Indices: 41349--41386 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
41339 TTTTTTTCGA
41349 TTTTTTTTGAATTT-
1 TTTTTTTTGAATTTC
*
41363 TTTTTTCTGAATTTC
1 TTTTTTTTGAATTTC
41378 TTCTTTTTT
1 TT-TTTTTT
41387 TTTAAATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 2 0.10
16 5 0.25
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTTTTTTGAATTTC
Found at i:46714 original size:22 final size:20
Alignment explanation
Indices: 46673--46716 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
46663 ACCAGCTCAC
46673 TTGAGCTTGTTTAAGCTCGT
1 TTGAGCTTGTTTAAGCTCGT
*
46693 TTGAGCTTTGATTTTAGCTCGT
1 TTGAGC-TTG-TTTAAGCTCGT
46715 TT
1 TT
46717 CAGCCTGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 3 0.14
22 12 0.57
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTGAGCTTGTTTAAGCTCGT
Done.