Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3672
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: 38092
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:7086 original size:15 final size:15
Alignment explanation
Indices: 7066--7102 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
7056 TTGAGCGAGA
**
7066 AAAAGAAAAAGAGTG
1 AAAAGAAAAAGAAAG
7081 AAAAGAAAAAGAAAG
1 AAAAGAAAAAGAAAG
7096 AAAAGAA
1 AAAAGAA
7103 TGAGGAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAGAAAG
Found at i:14056 original size:13 final size:13
Alignment explanation
Indices: 14038--14063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14028 ACCTGAAAGC
14038 AATTTAATTCATA
1 AATTTAATTCATA
14051 AATTTAATTCATA
1 AATTTAATTCATA
14064 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:14477 original size:20 final size:21
Alignment explanation
Indices: 14452--14490 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14442 CTCAAAAAGC
14452 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
14472 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
14491 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:15763 original size:17 final size:17
Alignment explanation
Indices: 15743--15796 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
15733 CTTCACTCGT
15743 TTTCTTTTCAAACTCTC
1 TTTCTTTTCAAACTCTC
*
15760 TTTCTTTTTCAATCTCAT-
1 TTTC-TTTTCAAACTC-TC
15778 TTTGCTTTTC--ACTCTC
1 TTT-CTTTTCAAACTCTC
15794 TTT
1 TTT
15797 TGTTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 4 0.13
18 18 0.58
19 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTCTTTTCAAACTCTC
Found at i:15786 original size:18 final size:18
Alignment explanation
Indices: 15765--15816 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
15755 CTCTCTTTCT
15765 TTTTCAATCTCATTTTGC
1 TTTTCAATCTCATTTTGC
* *
15783 TTTTCACTCTC-TTTTGT
1 TTTTCAATCTCATTTTGC
*
15800 TTTTGAAATCTCATTTT
1 TTTT-CAATCTCATTTT
15817 CATATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTCAATCTCATTTTGC
Found at i:15830 original size:6 final size:6
Alignment explanation
Indices: 15821--15918 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
15811 CATTTTCATA
* * * **
15821 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * **
15872 GTTTTC -TTTTC TTTTT- TGTTTTC TTTTTC TTCTTC ACTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
15919 GAATTCATTA
Statistics
Matches: 69, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
5 6 0.09
6 50 0.72
7 10 0.14
8 3 0.04
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.72
Consensus pattern (6 bp):
TTTTTC
Found at i:16891 original size:19 final size:18
Alignment explanation
Indices: 16866--16914 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
16856 TCAATCCACG
16866 AATTTTTTTTACTTTTTTT
1 AATTTTTTTTA-TTTTTTT
* *
16885 TATTTTTTTCGATTTTTTT
1 AATTTTTTT-TATTTTTTT
16904 AATTTTTTTTA
1 AATTTTTTTTA
16915 ATCACTTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (18 bp):
AATTTTTTTTATTTTTTT
Found at i:16915 original size:10 final size:10
Alignment explanation
Indices: 16866--16916 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
16856 TCAATCCACG
16866 AATTTTTTTT
1 AATTTTTTTT
*
16876 ACTTTTTTTT
1 AATTTTTTTT
*
16886 -ATTTTTTTC
1 AATTTTTTTT
*
16895 GA-TTTTTTT
1 AATTTTTTTT
16904 AATTTTTTTT
1 AATTTTTTTT
16914 AAT
1 AAT
16917 CACTTACTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 14 0.41
10 20 0.59
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (10 bp):
AATTTTTTTT
Found at i:18036 original size:13 final size:13
Alignment explanation
Indices: 18018--18043 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18008 ACCTAAAAGC
18018 AATTTAATTCATA
1 AATTTAATTCATA
18031 AATTTAATTCATA
1 AATTTAATTCATA
18044 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:18458 original size:20 final size:21
Alignment explanation
Indices: 18433--18471 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18423 TCAAACAAGC
18433 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
18453 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
18472 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:19310 original size:22 final size:22
Alignment explanation
Indices: 19259--19324 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
19249 GGTATTTGGG
*
19259 AATTGGCT-CGAAATGATATGG-
1 AATTGG-TACGAAATGGTATGGT
19280 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
19302 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
19325 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 1 0.03
21 18 0.46
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:21486 original size:23 final size:22
Alignment explanation
Indices: 21434--21486 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
21424 TCCACGTCTT
*
21434 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
21456 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
21479 TTTCTTTT
1 TTTCTTTT
21487 TCACTTTCAA
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:33103 original size:18 final size:18
Alignment explanation
Indices: 33082--33116 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33072 TTTTTCTTTT
33082 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
33100 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
33117 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:33170 original size:18 final size:18
Alignment explanation
Indices: 33149--33186 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
33139 TCTCTCACTA
33149 TTTTGATTTCTTTTTCTT
1 TTTTGATTTCTTTTTCTT
* *
33167 TTTTGTTTTCTTTTTGTT
1 TTTTGATTTCTTTTTCTT
33185 TT
1 TT
33187 CTTTCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.82
Consensus pattern (18 bp):
TTTTGATTTCTTTTTCTT
Found at i:33177 original size:12 final size:12
Alignment explanation
Indices: 33160--33190 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
33150 TTTGATTTCT
33160 TTTTCTTTTTTG
1 TTTTCTTTTTTG
33172 TTTTC-TTTTTG
1 TTTTCTTTTTTG
33183 TTTTCTTT
1 TTTTCTTT
33191 CAATTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTG
Found at i:34241 original size:12 final size:10
Alignment explanation
Indices: 34202--34254 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
34192 TTTTTAACTC
34202 GATTTTTTTGT
1 GATTTTTTT-T
*
34213 CACTTTTTTTT
1 GA-TTTTTTTT
**
34224 TCTTTTTTTT
1 GATTTTTTTT
34234 GATTTTTTTT
1 GATTTTTTTT
34244 GAATTTTTTTT
1 G-ATTTTTTTT
34255 TGAATTTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 17 0.49
11 11 0.31
12 7 0.20
ACGTcount: A:0.09, C:0.06, G:0.08, T:0.77
Consensus pattern (10 bp):
GATTTTTTTT
Found at i:34255 original size:12 final size:12
Alignment explanation
Indices: 34226--34276 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
34216 TTTTTTTTTC
34226 TTTTTTTTG-A-
1 TTTTTTTTGAAT
34236 TTTTTTTTGAAT
1 TTTTTTTTGAAT
34248 TTTTTTTTGAAT
1 TTTTTTTTGAAT
34260 TTCTTCTCTTTGAAT
1 TT-TT-T-TTTGAAT
34275 TT
1 TT
34277 CTTCTCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
12 14 0.39
13 2 0.06
14 1 0.03
15 9 0.25
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.73
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:34271 original size:15 final size:15
Alignment explanation
Indices: 34241--34285 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
34231 TTTGATTTTT
34241 TTTGAATTT-TT-T-
1 TTTGAATTTCTTCTC
34253 TTTGAATTTCTTCTC
1 TTTGAATTTCTTCTC
34268 TTTGAATTTCTTCTC
1 TTTGAATTTCTTCTC
34283 TTT
1 TTT
34286 TTTAAATCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.30
13 2 0.07
14 1 0.03
15 18 0.60
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTGAATTTCTTCTC
Found at i:34365 original size:11 final size:11
Alignment explanation
Indices: 34349--34377 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
34339 CCAACTCAAA
34349 TTTTTTTTGA-
1 TTTTTTTTGAC
34359 TTTTTTTTGAC
1 TTTTTTTTGAC
34370 TTTTTTTT
1 TTTTTTTT
34378 TTACGAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:35651 original size:11 final size:10
Alignment explanation
Indices: 35626--35686 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
35616 ACCAATAAAA
35626 TAAA-TGAGC
1 TAAATTGAGC
*
35635 TGAATTGTAGC
1 TAAATTG-AGC
35646 TAAATTGAGC
1 TAAATTGAGC
**
35656 TCGATTGAGC
1 TAAATTGAGC
35666 TGAAA-TGAGC
1 T-AAATTGAGC
*
35676 TCAATTGAGC
1 TAAATTGAGC
35686 T
1 T
35687 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:35687 original size:20 final size:20
Alignment explanation
Indices: 35627--35687 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
35617 CCAATAAAAT
*
35627 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
35647 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
35668 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
35688 GTCGGAGTTG
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:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Done.