Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1631
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: 101004
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:6378 original size:10 final size:10
Alignment explanation
Indices: 6363--6388 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6353 GAATAACAAT
6363 AAAGAATAAA
1 AAAGAATAAA
6373 AAAGAATAAA
1 AAAGAATAAA
6383 AAAGAA
1 AAAGAA
6389 ATCTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAGAATAAA
Found at i:8037 original size:22 final size:22
Alignment explanation
Indices: 8010--8053 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
8000 AAGGTTCCGT
8010 TTTGGTTT-AAGCTAAAAGAATG
1 TTTGGTTTGAA-CTAAAAGAATG
*
8032 TTTGGTTTGAATTAAAAGAATG
1 TTTGGTTTGAACTAAAAGAATG
8054 AGGCCTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (22 bp):
TTTGGTTTGAACTAAAAGAATG
Found at i:13226 original size:25 final size:24
Alignment explanation
Indices: 13184--13234 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
13174 AAAAAGAATC
* *
13184 TTTATTATTTATCGTTTTATTTAA
1 TTTATTAATTATCCTTTTATTTAA
13208 TTTATTTAATTATCCTTTTATTTAA
1 TTTA-TTAATTATCCTTTTATTTAA
13233 TT
1 TT
13235 AGTTCGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTATTAATTATCCTTTTATTTAA
Found at i:13386 original size:21 final size:24
Alignment explanation
Indices: 13362--13407 Score: 71
Period size: 21 Copynumber: 2.0 Consensus size: 24
13352 TTTATTATTA
13362 TCATTT-TCATT-TTTTA-ATGAT
1 TCATTTCTCATTCTTTTATATGAT
13383 TCATTTCTCATTCTTTTATATGAT
1 TCATTTCTCATTCTTTTATATGAT
13407 T
1 T
13408 TATGATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 5 0.23
24 6 0.27
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.61
Consensus pattern (24 bp):
TCATTTCTCATTCTTTTATATGAT
Found at i:13768 original size:21 final size:21
Alignment explanation
Indices: 13744--13783 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
13734 TTAATATTAT
13744 AAATTGAATATTATAAAAAAG
1 AAATTGAATATTATAAAAAAG
13765 AAATTGAATATTATAAAAA
1 AAATTGAATATTATAAAAA
13784 TAACAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
AAATTGAATATTATAAAAAAG
Found at i:24515 original size:32 final size:32
Alignment explanation
Indices: 24474--24534 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
24464 ATCTATTTTC
24474 ATTGTTCAACTCTTTGACAACACGAAAAACCT
1 ATTGTTCAACTCTTTGACAACACGAAAAACCT
*
24506 ATTGTTCAACTCTTTGACAACATGAAAAA
1 ATTGTTCAACTCTTTGACAACACGAAAAA
24535 ACCAAAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (32 bp):
ATTGTTCAACTCTTTGACAACACGAAAAACCT
Found at i:28664 original size:21 final size:21
Alignment explanation
Indices: 28638--28677 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28628 TAATTTGTTA
28638 TTTTTATAATATTCAATTTCT
1 TTTTTATAATATTCAATTTCT
28659 TTTTTATAATATTCAATTT
1 TTTTTATAATATTCAATTT
28678 ATAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTATAATATTCAATTTCT
Found at i:29059 original size:21 final size:24
Alignment explanation
Indices: 29014--29059 Score: 71
Period size: 21 Copynumber: 2.0 Consensus size: 24
29004 AAAAATCATA
29014 AATCATATAAAAGAATGAGAAATG
1 AATCATATAAAAGAATGAGAAATG
29038 AATCAT-TAAAA-AATGA-AAATG
1 AATCATATAAAAGAATGAGAAATG
29059 A
1 A
29060 TAATAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 5 0.23
24 6 0.27
ACGTcount: A:0.61, C:0.04, G:0.13, T:0.22
Consensus pattern (24 bp):
AATCATATAAAAGAATGAGAAATG
Found at i:29215 original size:25 final size:24
Alignment explanation
Indices: 29187--29237 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
29177 TTGACGAACT
* *
29187 AATTAAATAAAAGGATAATTAAATA
1 AATTAAATAAAACGATAAAT-AATA
29212 AATTAAATAAAACGATAAATAATA
1 AATTAAATAAAACGATAAATAATA
29236 AA
1 AA
29238 GATTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (24 bp):
AATTAAATAAAACGATAAATAATA
Found at i:36048 original size:10 final size:10
Alignment explanation
Indices: 36033--36058 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
36023 AAAAAAAGAT
36033 TTCTTTTTTA
1 TTCTTTTTTA
36043 TTCTTTTTTA
1 TTCTTTTTTA
36053 TTCTTT
1 TTCTTT
36059 ATTGTTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (10 bp):
TTCTTTTTTA
Found at i:42922 original size:22 final size:22
Alignment explanation
Indices: 42893--42938 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
42883 GAGGATGTCT
42893 TATATATATTAAGATTATATTAAA
1 TATATATA-T-AGATTATATTAAA
*
42917 TATATATATAGATTCTATTAAA
1 TATATATATAGATTATATTAAA
42939 AAGATGGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 1 0.05
24 8 0.38
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATATATAGATTATATTAAA
Found at i:48204 original size:14 final size:14
Alignment explanation
Indices: 48185--48212 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48175 TATATTAGTA
48185 TTTTCTATTCTATT
1 TTTTCTATTCTATT
48199 TTTTCTATTCTATT
1 TTTTCTATTCTATT
48213 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:48224 original size:5 final size:6
Alignment explanation
Indices: 48209--48259 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
48199 TTTTCTATTC
* *
48209 TATTAG TATTAG -ATTAG TA-TAC TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
48253 TATTAG T
1 TATTAG T
48260 TAGTGATCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 19 0.49
6 20 0.51
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (6 bp):
TATTAG
Found at i:48233 original size:27 final size:27
Alignment explanation
Indices: 48203--48255 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
48193 TCTATTTTTT
48203 CTATTCTATTAGTATTAGATTAGTATA
1 CTATTCTATTAGTATTAGATTAGTATA
48230 CTATTCTATTAGTATTAGATTAGTAT
1 CTATTCTATTAGTATTAGATTAGTAT
48256 TAGTTAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (27 bp):
CTATTCTATTAGTATTAGATTAGTATA
Found at i:56987 original size:14 final size:14
Alignment explanation
Indices: 56968--56995 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56958 TATATTAGTA
56968 TTTTCTATTCTATT
1 TTTTCTATTCTATT
56982 TTTTCTATTCTATT
1 TTTTCTATTCTATT
56996 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:57007 original size:5 final size:6
Alignment explanation
Indices: 56992--57042 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
56982 TTTTCTATTC
* *
56992 TATTAG TATTAG -ATTAG TA-TAC TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
57036 TATTAG T
1 TATTAG T
57043 TAGTGATCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 19 0.49
6 20 0.51
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (6 bp):
TATTAG
Found at i:57016 original size:27 final size:27
Alignment explanation
Indices: 56986--57038 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
56976 TCTATTTTTT
56986 CTATTCTATTAGTATTAGATTAGTATA
1 CTATTCTATTAGTATTAGATTAGTATA
57013 CTATTCTATTAGTATTAGATTAGTAT
1 CTATTCTATTAGTATTAGATTAGTAT
57039 TAGTTAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (27 bp):
CTATTCTATTAGTATTAGATTAGTATA
Found at i:65244 original size:32 final size:32
Alignment explanation
Indices: 65203--65263 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
65193 ATCTATTTTC
65203 ATTGTTCAACTCTTTGACAACACGAAAAACCT
1 ATTGTTCAACTCTTTGACAACACGAAAAACCT
*
65235 ATTGTTCAACTCTTTGACAACATGAAAAA
1 ATTGTTCAACTCTTTGACAACACGAAAAA
65264 ACCAAAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (32 bp):
ATTGTTCAACTCTTTGACAACACGAAAAACCT
Found at i:75806 original size:10 final size:10
Alignment explanation
Indices: 75791--75816 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
75781 GAATAACAAT
75791 AAAGAATAAA
1 AAAGAATAAA
75801 AAAGAATAAA
1 AAAGAATAAA
75811 AAAGAA
1 AAAGAA
75817 ATCTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAGAATAAA
Found at i:77465 original size:22 final size:22
Alignment explanation
Indices: 77438--77481 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
77428 AAGGTTCCGT
77438 TTTGGTTT-AAGCTAAAAGAATG
1 TTTGGTTTGAA-CTAAAAGAATG
*
77460 TTTGGTTTGAATTAAAAGAATG
1 TTTGGTTTGAACTAAAAGAATG
77482 AGGCCTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (22 bp):
TTTGGTTTGAACTAAAAGAATG
Found at i:82654 original size:25 final size:24
Alignment explanation
Indices: 82612--82662 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
82602 AAAAAGAATC
* *
82612 TTTATTATTTATCGTTTTATTTAA
1 TTTATTAATTATCCTTTTATTTAA
82636 TTTATTTAATTATCCTTTTATTTAA
1 TTTA-TTAATTATCCTTTTATTTAA
82661 TT
1 TT
82663 AGTTCGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTATTAATTATCCTTTTATTTAA
Found at i:82814 original size:21 final size:24
Alignment explanation
Indices: 82790--82835 Score: 71
Period size: 21 Copynumber: 2.0 Consensus size: 24
82780 TTTATTATTA
82790 TCATTT-TCATT-TTTTA-ATGAT
1 TCATTTCTCATTCTTTTATATGAT
82811 TCATTTCTCATTCTTTTATATGAT
1 TCATTTCTCATTCTTTTATATGAT
82835 T
1 T
82836 TATGATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 5 0.23
24 6 0.27
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.61
Consensus pattern (24 bp):
TCATTTCTCATTCTTTTATATGAT
Found at i:83196 original size:21 final size:21
Alignment explanation
Indices: 83172--83211 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
83162 TTAATATTAT
83172 AAATTGAATATTATAAAAAAG
1 AAATTGAATATTATAAAAAAG
83193 AAATTGAATATTATAAAAA
1 AAATTGAATATTATAAAAA
83212 TAACAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
AAATTGAATATTATAAAAAAG
Found at i:87358 original size:32 final size:32
Alignment explanation
Indices: 87315--87375 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
87305 AGCTTTTGGT
87315 TTTTTCATGTTGTCAAAGAGTTGAACAATAGG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATAGG
*
87347 TTTTTCGTGTTGTCAAAGAGTTGAACAAT
1 TTTTTCATGTTGTCAAAGAGTTGAACAAT
87376 GAAAATAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATAGG
Found at i:95575 original size:27 final size:27
Alignment explanation
Indices: 95537--95589 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
95527 TCACTAACTA
95537 ATACTAATCTAATACTAATAGAATAGT
1 ATACTAATCTAATACTAATAGAATAGT
95564 ATACTAATCTAATACTAATAGAATAG
1 ATACTAATCTAATACTAATAGAATAG
95590 AAAAAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (27 bp):
ATACTAATCTAATACTAATAGAATAGT
Found at i:95576 original size:5 final size:6
Alignment explanation
Indices: 95533--95583 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
95523 GGGATCACTA
* *
95533 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT AGT-AT ACTAAT -CTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
95577 ACTAAT A
1 ACTAAT A
95584 GAATAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 18 0.47
6 20 0.53
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (6 bp):
ACTAAT
Found at i:95599 original size:14 final size:14
Alignment explanation
Indices: 95580--95607 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
95570 ATCTAATACT
95580 AATAGAATAGAAAA
1 AATAGAATAGAAAA
95594 AATAGAATAGAAAA
1 AATAGAATAGAAAA
95608 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:100880 original size:22 final size:24
Alignment explanation
Indices: 100854--100899 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
100844 TGTCCATCTT
100854 TTTAATAGAATC-T-ATATATATA
1 TTTAATAGAATCTTAATATATATA
*
100876 TTTAATATAATCTTAATATATATA
1 TTTAATAGAATCTTAATATATATA
100900 AGACATCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 9 0.43
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTAATAGAATCTTAATATATATA
Done.