Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2903
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: 40585
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3924 original size:16 final size:17
Alignment explanation
Indices: 3903--3934 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3893 TATTGGAGTA
3903 TCAAAAAAA-TCAAAAT
1 TCAAAAAAATTCAAAAT
3919 TCAAAAAAATTCAAAA
1 TCAAAAAAATTCAAAA
3935 AAAAAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (17 bp):
TCAAAAAAATTCAAAAT
Found at i:3960 original size:14 final size:14
Alignment explanation
Indices: 3943--3991 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
3933 AAAAAAAGTG
*
3943 AAAAAAATTGAGCA
1 AAAAAAAGTGAGCA
** *
3957 AAAAAAAGAAAGAA
1 AAAAAAAGTGAGCA
3971 AAAAAAAGTGAGCA
1 AAAAAAAGTGAGCA
3985 AAAAAAA
1 AAAAAAA
3992 TCAAGTTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.76, C:0.04, G:0.14, T:0.06
Consensus pattern (14 bp):
AAAAAAAGTGAGCA
Found at i:3962 original size:28 final size:28
Alignment explanation
Indices: 3931--4010 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
3921 AAAAAAATTC
* *
3931 AAAAAAAAAGTGAAAAAAATTGAGCAAA
1 AAAAAAAAAGTAAAAAAAAGTGAGCAAA
* *
3959 AAAAAGAAAGAAAAAAAAAGTGAGCAAA
1 AAAAAAAAAGTAAAAAAAAGTGAGCAAA
**
3987 AAAAATCAAGTTAAAAAAAAGTGA
1 AAAAAAAAAG-TAAAAAAAAGTGA
4011 AAAGTCTTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 32 0.73
29 12 0.27
ACGTcount: A:0.71, C:0.04, G:0.15, T:0.10
Consensus pattern (28 bp):
AAAAAAAAAGTAAAAAAAAGTGAGCAAA
Found at i:4903 original size:18 final size:18
Alignment explanation
Indices: 4882--4916 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4872 AGAAAAGAAA
4882 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
4900 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
4917 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:7603 original size:12 final size:11
Alignment explanation
Indices: 7586--7618 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
7576 GTTCGTAACG
7586 AAAAAAAAAGTC
1 AAAAAAAAA-TC
7598 AAAAAAAAATC
1 AAAAAAAAATC
7609 AAAAAAAAAT
1 AAAAAAAAAT
7619 TTTTGAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:8885 original size:48 final size:47
Alignment explanation
Indices: 8806--8911 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
8796 GAGTGTCATG
*
8806 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
8854 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
8902 GAAAAAGAAA
1 GAAAAAGAAA
8912 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:10625 original size:20 final size:20
Alignment explanation
Indices: 10579--10625 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
10569 AGCTCGTTTC
*
10579 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
10599 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
10619 CAGCTCA
1 CAGCTCA
10626 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:12339 original size:20 final size:20
Alignment explanation
Indices: 12316--12362 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
12306 GGGTTAAGAT
*
12316 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
12336 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
12356 TGAGCTG
1 TGAGCTG
12363 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:13601 original size:10 final size:10
Alignment explanation
Indices: 13585--13642 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
13575 CAACACCGAC
13585 CAGCTCAATT
1 CAGCTCAATT
* *
13595 GAGCTCATTT
1 CAGCTCAATT
13605 CAGCTCAA-T
1 CAGCTCAATT
13614 CGAGCTCAATT
1 C-AGCTCAATT
*
13625 TAGCTACAATT
1 CAGCT-CAATT
13636 CAGCTCA
1 CAGCTCA
13643 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:13608 original size:20 final size:20
Alignment explanation
Indices: 13585--13645 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
13575 CAACACCGAC
13585 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
13605 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
13626 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
13646 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:17311 original size:19 final size:20
Alignment explanation
Indices: 17282--17320 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
17272 GAAACAGTAA
*
17282 TAAAGGAGCTGCTGGTGCAT
1 TAAAGGAGCTGCTAGTGCAT
17302 TAAA-GAGCTGCTAGTGCAT
1 TAAAGGAGCTGCTAGTGCAT
17321 GAACAGCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (20 bp):
TAAAGGAGCTGCTAGTGCAT
Found at i:17383 original size:54 final size:54
Alignment explanation
Indices: 17297--17407 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 54
17287 GAGCTGCTGG
* *
17297 TGCATTAAAGAGCTGCTAGTGCATGAACAGCCTAGGAGCATGAAATGTGATTAA
1 TGCATTAAAGAGCTGCTAGTGCATGAACAGCCTAGGAGCAAGAAACGTGATTAA
* *
17351 TGCATTAAAGAGCTGCTGGTGCATGAATAGCCTAGGAGCAAGAAACGTGATTAA
1 TGCATTAAAGAGCTGCTAGTGCATGAACAGCCTAGGAGCAAGAAACGTGATTAA
17405 TGC
1 TGC
17408 TAGAAGGCTG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.23
Consensus pattern (54 bp):
TGCATTAAAGAGCTGCTAGTGCATGAACAGCCTAGGAGCAAGAAACGTGATTAA
Found at i:19041 original size:80 final size:80
Alignment explanation
Indices: 18850--19181 Score: 405
Period size: 80 Copynumber: 4.1 Consensus size: 80
18840 TTACACTACA
* * * * * * *
18850 AGGGTATTTCGATAATTTTA-TACTACAAGGATATTTCGATAATTTTACAAATTGAGGGTGTTTC
1 AGGGTATTTCAATAATTTTACAAAT-CGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTC
** *
18914 GGTAATTTTACAAATCG
65 AATAATTTCAC-AATCG
*
18931 AGGGTATTTCAATAATTTTACAAATTGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
1 AGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
18996 ATAATTTCACAATCG
66 ATAATTTCACAATCG
* * * *
19011 AGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGGTAATTTTATAAATTGAGGGTATTTTA
1 AGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
* *
19076 GTAATTTCACAATTG
66 ATAATTTCACAATCG
* * * * * *
19091 AGGGTTTTTCGATAATTTTATAAATCGGGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCG
1 AGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
*
19156 ATAATTTCATAAATCG
66 ATAATTTCA-CAATCG
*
19172 GGGGTATTTC
1 AGGGTATTTC
19182 GGTAATTTCT
Statistics
Matches: 216, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
80 141 0.65
81 73 0.34
82 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (80 bp):
AGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
ATAATTTCACAATCG
Found at i:19190 original size:27 final size:27
Alignment explanation
Indices: 18850--19189 Score: 400
Period size: 27 Copynumber: 12.7 Consensus size: 27
18840 TTACACTACA
* * *
18850 AGGGTATTTCGATAATTTTA-TACTACA
1 AGGGTATTTCGATAATTTTACAAAT-CG
* *
18877 AGGATATTTCGATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
18904 AGGGTGTTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
18931 AGGGTATTTCAATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
18958 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
18985 AGGGTATTTCAATAATTTCAC-AATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
19011 AGGGTATTTCAATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
19038 AGGGTATTTCGGTAATTTTATAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
19065 AGGGTATTT-TAGTAATTTCAC-AATTG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
19091 AGGGTTTTTCGATAATTTTATAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
19118 GGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
19145 AGGGTGTTTCGATAATTTCATAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
19172 GGGGTATTTCGGTAATTT
1 AGGGTATTTCGATAATTT
19190 CTTTTTATTA
Statistics
Matches: 267, Mismatches: 41, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
26 45 0.17
27 220 0.82
28 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:27831 original size:17 final size:17
Alignment explanation
Indices: 27802--27836 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27792 TTAAGAGCTG
27802 TAACTAAATTAATTAAT
1 TAACTAAATTAATTAAT
27819 TAACTTAAA-TAATTAAT
1 TAAC-TAAATTAATTAAT
27836 T
1 T
27837 TATTCCAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TAACTAAATTAATTAAT
Found at i:30908 original size:12 final size:11
Alignment explanation
Indices: 30882--30907 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30872 CTTCAAAAAA
30882 TTTTGAATTTT
1 TTTTGAATTTT
30893 TTTTGAATTTT
1 TTTTGAATTTT
30904 TTTT
1 TTTT
30908 TTCAATTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTGAATTTT
Found at i:33520 original size:15 final size:16
Alignment explanation
Indices: 33500--33529 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33490 TTTCTATTGA
33500 ATCACTC-TCTTTTTT
1 ATCACTCATCTTTTTT
33515 ATCACTCATCTTTTT
1 ATCACTCATCTTTTT
33530 GTTTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
ATCACTCATCTTTTTT
Found at i:36471 original size:23 final size:22
Alignment explanation
Indices: 36419--36471 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
36409 TCCACGTCTT
*
36419 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
36441 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
36464 TTTCTTTT
1 TTTCTTTT
36472 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
Done.