Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3632
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: 13577
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:3817 original size:24 final size:20
Alignment explanation
Indices: 3799--3852 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
3789 CAAATGAGAG
*
3799 AAAAGAAAAGAACGAAAAT-AC
1 AAAAGAAAAGAA--AAAATGAA
3820 AAAAGAAAAG-AAAAATGAA
1 AAAAGAAAAGAAAAAATGAA
3839 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
3853 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 11 0.37
20 4 0.13
21 10 0.33
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAGAAAAAATGAA
Found at i:3859 original size:19 final size:19
Alignment explanation
Indices: 3820--3861 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3810 ACGAAAATAC
*
3820 AAAAGAAAAGAAAAATGAA
1 AAAAGAAAAGAAAAATCAA
*
3839 AAAAGAAAAGAAAATTCAA
1 AAAAGAAAAGAAAAATCAA
3858 AAAA
1 AAAA
3862 AGAGAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAGAAAAGAAAAATCAA
Found at i:8209 original size:20 final size:19
Alignment explanation
Indices: 8186--8250 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
8176 AAGCTCAAAC
8186 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
8206 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
8226 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
8246 GAGCT
1 GAGCT
8251 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:10063 original size:33 final size:33
Alignment explanation
Indices: 10025--10087 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
10015 GATTACTCAC
10025 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
10058 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
10088 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:10114 original size:21 final size:21
Alignment explanation
Indices: 10085--10140 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
10075 CAAGCTCTCT
*
10085 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
10106 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
10127 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
10141 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:10133 original size:14 final size:14
Alignment explanation
Indices: 10084--10140 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
10074 TCAAGCTCTC
10084 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
10097 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
10111 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
10125 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
10139 TT
1 TT
10141 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:10168 original size:18 final size:18
Alignment explanation
Indices: 10147--10204 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
10137 TTTTCTCTCA
10147 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
10165 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
10183 C-TTTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
10200 GTTTT
1 CTTTT
10205 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:10193 original size:11 final size:11
Alignment explanation
Indices: 10174--10208 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
10164 TCTTTTGCAA
*
10174 TTTCTTTTTCT
1 TTTCGTTTTCT
10185 TTTCGTTTTCT
1 TTTCGTTTTCT
*
10196 TTTTGTTTTCT
1 TTTCGTTTTCT
10207 TT
1 TT
10209 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTCGTTTTCT
Found at i:10221 original size:6 final size:6
Alignment explanation
Indices: 10102--10208 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
10092 TCTTTTTTCG
* * * **
10102 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
10153 CGATTT CTTTTT CTTTTG CAATTT CTTTTT C-TTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
10200 -GTTTT CTTT
1 CTTTTT CTTT
10209 CAATTTCTTT
Statistics
Matches: 73, Mismatches: 24, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
5 9 0.12
6 52 0.71
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:11299 original size:30 final size:28
Alignment explanation
Indices: 11221--11304 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 28
11211 GCAAGACTTT
**
11221 TCACTTTTTTTTAAACTTGATTTTTTTTGC
1 TCACTTTTTTTT--ACTTTTTTTTTTTTGC
*
11251 TCACCTTTTTTTTTCTTTTCTTTTTTTTGC
1 TCA-CTTTTTTTTACTTTT-TTTTTTTTGC
11281 TCGA-TTTTTTTTCACTTTTTTTTT
1 TC-ACTTTTTTTT-ACTTTTTTTTT
11305 GAATTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
29 16 0.35
30 20 0.43
31 10 0.22
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.70
Consensus pattern (28 bp):
TCACTTTTTTTTACTTTTTTTTTTTTGC
Found at i:11300 original size:12 final size:12
Alignment explanation
Indices: 11285--11342 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
11275 TTTTGCTCGA
*
11285 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
11297 TTTTTTTTGAAT
1 TTTTTTTTCAAT
*
11309 TTTTTTTCAATCAAA
1 TTTTTTT---TCAAT
*
11324 TTTTTTTTGAAT
1 TTTTTTTTCAAT
11336 TTTTTTT
1 TTTTTTT
11343 ATTTTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 27 0.73
15 10 0.27
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:11315 original size:27 final size:27
Alignment explanation
Indices: 11285--11347 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
11275 TTTTGCTCGA
**
11285 TTTTTTTTCACTTTTTTTTTGAATTTT
1 TTTTTTTTCAAATTTTTTTTGAATTTT
***
11312 TTTTCAATCAAATTTTTTTTGAATTTT
1 TTTTTTTTCAAATTTTTTTTGAATTTT
11339 TTTTATTTT
1 TTTT-TTTT
11348 TTTTTTGTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.73
Consensus pattern (27 bp):
TTTTTTTTCAAATTTTTTTTGAATTTT
Found at i:12968 original size:20 final size:19
Alignment explanation
Indices: 12945--13009 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
12935 AAGCTCAAAC
12945 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
12965 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
12985 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
13005 GAGCT
1 GAGCT
13010 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:13424 original size:18 final size:18
Alignment explanation
Indices: 13403--13437 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13393 TTTTTCTTTT
13403 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
13421 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
13438 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:13455 original size:14 final size:15
Alignment explanation
Indices: 13436--13465 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13426 TTCTTTTTCA
13436 ATTTTC-TTTTCTTC
1 ATTTTCTTTTTCTTC
13450 ATTTTCTTTTTCTTC
1 ATTTTCTTTTTCTTC
13465 A
1 A
13466 CTATTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTCTTTTTCTTC
Done.