Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2497
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: 38084
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2122 original size:17 final size:16
Alignment explanation
Indices: 2102--2141 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2092 ATACTCACTC
2102 TCTTTTCAATTTTCTTT
1 TCTTTTCAA-TTTCTTT
*
2119 TCTTGATCAATTTCTTT
1 TCTT-TTCAATTTCTTT
2136 TCTTTT
1 TCTTTT
2142 TCTCATTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.12, C:0.17, G:0.03, T:0.68
Consensus pattern (16 bp):
TCTTTTCAATTTCTTT
Found at i:3140 original size:30 final size:31
Alignment explanation
Indices: 3106--3202 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
3096 AGCTCACTTC
*
3106 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
3136 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
3166 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
3196 TAGCTCA
1 TAGCTCA
3203 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:4087 original size:22 final size:20
Alignment explanation
Indices: 4055--4103 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
4045 GCCGAATTTA
4055 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATTA-TG
* *
4078 TGAACATTTTTATTATTATG
1 TGAACATTTTAATCATTATG
4098 TGAACA
1 TGAACA
4104 CCTTGATACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 4 0.17
22 7 0.29
23 5 0.21
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTATG
Found at i:4268 original size:20 final size:20
Alignment explanation
Indices: 4222--4268 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4212 AGCTCGTTTC
*
4222 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
4242 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
4262 CAGCTCA
1 CAGCTCA
4269 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:7941 original size:48 final size:47
Alignment explanation
Indices: 7862--7967 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
7852 GAGTGTCATG
*
7862 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
7910 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
7958 GAAAAAGAAA
1 GAAAAAGAAA
7968 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:9678 original size:20 final size:20
Alignment explanation
Indices: 9622--9678 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
9612 AGCTCCGTTT
* *
9622 AGCTCATTTCCAGCTCACTCG
1 AGCTCAATT-CAGCTCACTCA
* *
9643 AGCTCAAGTCAACTCACTCA
1 AGCTCAATTCAGCTCACTCA
9663 AGCTCAATTCAGCTCA
1 AGCTCAATTCAGCTCA
9679 ATCTTAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.28, C:0.35, G:0.12, T:0.25
Consensus pattern (20 bp):
AGCTCAATTCAGCTCACTCA
Found at i:21296 original size:30 final size:30
Alignment explanation
Indices: 21262--21358 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
21252 TAAACTAAAA
21262 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
21292 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
21322 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
21352 TGAGCTA
1 TGAGCTA
21359 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:24683 original size:23 final size:22
Alignment explanation
Indices: 24631--24683 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
24621 TCCACGTCTT
*
24631 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
24653 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
24676 TTTCTTTT
1 TTTCTTTT
24684 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:29904 original size:17 final size:17
Alignment explanation
Indices: 29868--29900 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29858 GATTGAGAGT
*
29868 GAAAAGGAATGTGAAAA
1 GAAAAGAAATGTGAAAA
29885 GAAAAGAAAT-TGAAAA
1 GAAAAGAAATGTGAAAA
29901 AGAATTGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (17 bp):
GAAAAGAAATGTGAAAA
Found at i:29922 original size:28 final size:28
Alignment explanation
Indices: 29867--29920 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
29857 AGATTGAGAG
*
29867 TGAAAAGGAATGTGAAAAGAAAAGAAAT
1 TGAAAAAGAATGTGAAAAGAAAAGAAAT
* *
29895 TGAAAAAGAAT-TGAGAAGAAGAGAAA
1 TGAAAAAGAATGTGAAAAGAAAAGAAA
29921 ATGAGTTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (28 bp):
TGAAAAAGAATGTGAAAAGAAAAGAAAT
Done.