Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3263
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: 29998
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1117 original size:51 final size:52
Alignment explanation
Indices: 1055--1164 Score: 181
Period size: 52 Copynumber: 2.1 Consensus size: 52
1045 ACTCACTCTG
1055 TATGAGTTGA-TTTTG-AAAACAAAAATTAAAAGG-TTCAACTCACTCTCGCAA
1 TATGAGTTGATTTTTGAAAAAC-AAAATTAAAAGGCTT-AACTCACTCTCGCAA
1106 TATGAGTTGATTTTTGAAAAACAAAATTAAAAGGCTTAACTCACTCTCGCAA
1 TATGAGTTGATTTTTGAAAAACAAAATTAAAAGGCTTAACTCACTCTCGCAA
1158 TATGAGT
1 TATGAGT
1165 CAATTTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
51 10 0.18
52 39 0.70
53 7 0.12
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (52 bp):
TATGAGTTGATTTTTGAAAAACAAAATTAAAAGGCTTAACTCACTCTCGCAA
Found at i:1232 original size:171 final size:169
Alignment explanation
Indices: 917--1255 Score: 408
Period size: 171 Copynumber: 2.0 Consensus size: 169
907 TGTCTGAGGC
*
917 TCAACTCACCTCTCGCAATATAAGTTGATTTTGAAAAAGAAATTGAAAAGGTTCAACTCACTCGC
1 TCAACTCACCTCTCGCAATATAAGTTGATTTTGAAAAAAAAATTGAAAAGGTTCAACTCACTCGC
* * * **
982 AATATGAGTTGATTTTGAAACAAGAAACAGATTGAAATTACCTCAGGCATGTGCCGAGGCTCAAC
66 AATATGAGTTCAATTTAAAACAAGAAACAGA-T-AAATTACCTCAGGCATGCCCCGAGGCTCAAC
1047 TCACTCTGTATGAGTTGATTTTGAAAACAAAAATTAAAAGGT
129 TCACTCTGTATGAGTTGATTTTGAAAA-AAAAATTAAAAGGT
*
1089 TCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAACAAAATT-AAAAGGCTT-AACTCACT
1 TCAACTCACCTCTCGCAATATAAGTTGA-TTTTGAAAAA-AAAATTGAAAAGG-TTCAACTCA--
* *
1151 CTCGCAATATGAG-TCAATTTAAAAC-ATAAACTA-A-AAA-TACCTC-GGCGTGCCCCGAGGCT
61 CTCGCAATATGAGTTCAATTTAAAACAAGAAAC-AGATAAATTACCTCAGGCATGCCCCGAGGCT
*
1210 CAACTCACTCTCGCAATATGAGTTGATTTTTAAAAAAAAATTAAAA
125 CAACTCACTCT-G---TATGAGTTGATTTTGAAAAAAAAATTAAAA
1256 TACCTCAGCG
Statistics
Matches: 147, Mismatches: 10, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
167 24 0.16
168 7 0.05
169 3 0.02
170 11 0.07
171 36 0.24
172 36 0.24
173 17 0.12
174 13 0.09
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (169 bp):
TCAACTCACCTCTCGCAATATAAGTTGATTTTGAAAAAAAAATTGAAAAGGTTCAACTCACTCGC
AATATGAGTTCAATTTAAAACAAGAAACAGATAAATTACCTCAGGCATGCCCCGAGGCTCAACTC
ACTCTGTATGAGTTGATTTTGAAAAAAAAATTAAAAGGT
Found at i:1256 original size:68 final size:68
Alignment explanation
Indices: 1137--1299 Score: 215
Period size: 68 Copynumber: 2.4 Consensus size: 68
1127 CAAAATTAAA
* * *
1137 AGGCTTAACTCACTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACTCTCGCAATATGAGTTCAATTTAAAACATAAAATAAAAATACCTCAGCGTG-
*
1201 CCCG
65 ACCG
* * *
1205 AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTAAAA-A-AAAATTAAAATACCTCAGCGTG
1 AGGCTCAACTCACTCTCGCAATATGAGTTCA-ATTTAAAACATAAAATAAAAATACCTCAGCGTG
*
1268 ACTG
65 ACCG
1272 AGGCTCAACTCACTCTCGCAATATGAGT
1 AGGCTCAACTCACTCTCGCAATATGAGT
1300 CATTTTCCTT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
67 30 0.35
68 45 0.53
69 3 0.04
70 7 0.08
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (68 bp):
AGGCTCAACTCACTCTCGCAATATGAGTTCAATTTAAAACATAAAATAAAAATACCTCAGCGTGA
CCG
Found at i:9547 original size:15 final size:16
Alignment explanation
Indices: 9522--9552 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9512 AGTATGGGAT
9522 ATGCAATGAATGAATG
1 ATGCAATGAATGAATG
9538 ATGC-ATGAATGAATG
1 ATGCAATGAATGAATG
9553 CATGAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
ATGCAATGAATGAATG
Found at i:13552 original size:3 final size:3
Alignment explanation
Indices: 13544--13631 Score: 51
Period size: 3 Copynumber: 30.0 Consensus size: 3
13534 ATGAATAAAG
* ** *
13544 ATA ATA ATA CTA ATA ATA ATA ATA ATA A-A ATA CGA AGA AGT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* * *
13588 TATA AT- ATA ATA ATA ATA TTA A-A AT- ACA ATA ATTA AAA ATA ATA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
13632 TTATATATAA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
2 8 0.12
3 51 0.78
4 6 0.09
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:13644 original size:26 final size:26
Alignment explanation
Indices: 13584--13648 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
13574 TACGAAGAAG
* *
13584 TATATATAATATAATAATAATATTAA
1 TATAAATAATATAAAAATAATATTAA
*
13610 AATACAATAAT-TAAAAATAATATTATA
1 TATA-AATAATATAAAAATAATATTA-A
13637 TATAAAT-ATATA
1 TATAAATAATATA
13649 CAATATTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 2 0.06
26 21 0.66
27 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TATAAATAATATAAAAATAATATTAA
Found at i:20753 original size:20 final size:20
Alignment explanation
Indices: 20728--20767 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20718 TTCAAAGTCT
20728 GAATCTGAACATGAGCAACA
1 GAATCTGAACATGAGCAACA
20748 GAATCTGAACATGAGCAACA
1 GAATCTGAACATGAGCAACA
20768 TCTTCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (20 bp):
GAATCTGAACATGAGCAACA
Found at i:22988 original size:7 final size:7
Alignment explanation
Indices: 22976--23000 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22966 AGTAAATAGA
22976 TATTTAT
1 TATTTAT
22983 TATTTAT
1 TATTTAT
22990 TATTTAT
1 TATTTAT
22997 TATT
1 TATT
23001 AGTAAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:23011 original size:34 final size:37
Alignment explanation
Indices: 22951--23018 Score: 106
Period size: 34 Copynumber: 1.9 Consensus size: 37
22941 ATGGATTTAA
22951 ATTACTTATTATTTAAGTAAATAGATATTTATTATTT
1 ATTACTTATTATTTAAGTAAATAGATATTTATTATTT
*
22988 ATTATTTATTA-TT-AGTAAA-AGATATTTATTA
1 ATTACTTATTATTTAAGTAAATAGATATTTATTA
23019 GTTAAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 12 0.40
35 6 0.20
36 2 0.07
37 10 0.33
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (37 bp):
ATTACTTATTATTTAAGTAAATAGATATTTATTATTT
Found at i:23035 original size:34 final size:34
Alignment explanation
Indices: 22958--23035 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
22948 TAAATTACTT
* *
22958 ATTAT-TTAAGTAAATAGATATTTATTATTTATTA
1 ATTATATT-AGTAAATAGATATTTATTATTAAATA
*
22992 TTTATTATTAGTAAA-AGATATTTATTAGTTAAATA
1 ATTA-TATTAGTAAATAGATATTTATTA-TTAAATA
23027 ATTATATTA
1 ATTATATTA
23036 TAAGATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
34 20 0.54
35 15 0.41
36 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.51
Consensus pattern (34 bp):
ATTATATTAGTAAATAGATATTTATTATTAAATA
Found at i:24246 original size:18 final size:18
Alignment explanation
Indices: 24220--24286 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
24210 TAAACTACTG
*
24220 TACTAAATAATTGATAGT
1 TACTGAATAATTGATAGT
** *
24238 TACTGAATAACTAAATTACT
1 TACTGAATAA-TTGA-TAGT
*
24258 GTATTGAATAATTGATAGT
1 -TACTGAATAATTGATAGT
*
24277 TATTGAATAA
1 TACTGAATAA
24287 CTAAACTACT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 19 0.50
19 5 0.13
20 5 0.13
21 9 0.24
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (18 bp):
TACTGAATAATTGATAGT
Found at i:24258 original size:39 final size:39
Alignment explanation
Indices: 24210--24356 Score: 204
Period size: 39 Copynumber: 3.8 Consensus size: 39
24200 TTAATAGGGG
* *
24210 TAAACTACTGTACTAAATAATTGATAGTTACTGAATAAC
1 TAAACTACTGTATTGAATAATTGATAGTTACTGAATAAC
* *
24249 TAAATTACTGTATTGAATAATTGATAGTTATTGAATAAC
1 TAAACTACTGTATTGAATAATTGATAGTTACTGAATAAC
* * *
24288 TAAACTACTGCAATGAATATTTGATAGTTACTGAATAAC
1 TAAACTACTGTATTGAATAATTGATAGTTACTGAATAAC
* * *
24327 TAAATTACTGTATTGAATAACTGATTGTTA
1 TAAACTACTGTATTGAATAATTGATAGTTA
24357 TTGATTAAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (39 bp):
TAAACTACTGTATTGAATAATTGATAGTTACTGAATAAC
Found at i:24314 original size:78 final size:78
Alignment explanation
Indices: 24210--24360 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
24200 TTAATAGGGG
* * *
24210 TAAACTACTGTACTAAATAATTGATAGTTACTGAATAACTAAATTACTGTATTGAATAATTGATA
1 TAAACTACTGCAATAAATAATTGATAGTTACTGAATAACTAAATTACTGTATTGAATAACTGATA
24275 GTTATTGAATAAC
66 GTTATTGAATAAC
* * *
24288 TAAACTACTGCAATGAATATTTGATAGTTACTGAATAACTAAATTACTGTATTGAATAACTGATT
1 TAAACTACTGCAATAAATAATTGATAGTTACTGAATAACTAAATTACTGTATTGAATAACTGATA
24353 GTTATTGA
66 GTTATTGA
24361 TTAAATATGA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (78 bp):
TAAACTACTGCAATAAATAATTGATAGTTACTGAATAACTAAATTACTGTATTGAATAACTGATA
GTTATTGAATAAC
Found at i:26536 original size:26 final size:26
Alignment explanation
Indices: 26476--26540 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
26466 TACGAAGAAG
* *
26476 TATATATAATATAATAATAATATTAA
1 TATAAATAATATAAAAATAATATTAA
*
26502 AATACAATAAT-TAAAAATAATATTATA
1 TATA-AATAATATAAAAATAATATTA-A
26529 TATAAAT-ATATA
1 TATAAATAATATA
26541 CAATATTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 2 0.06
26 21 0.66
27 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TATAAATAATATAAAAATAATATTAA
Found at i:27166 original size:33 final size:34
Alignment explanation
Indices: 27127--27196 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
27117 TCCTTTTACA
27127 AGCAGCTGAAT-TCCATCGGATTTGGTGTCCAGC
1 AGCAGCTGAATCTCCATCGGATTTGGTGTCCAGC
27160 AGCAGCTGAATCTCCATCGGATTTGGTGTCCAGC
1 AGCAGCTGAATCTCCATCGGATTTGGTGTCCAGC
27194 AGC
1 AGC
27197 GCGCAAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 11 0.31
34 25 0.69
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (34 bp):
AGCAGCTGAATCTCCATCGGATTTGGTGTCCAGC
Found at i:28689 original size:55 final size:55
Alignment explanation
Indices: 28601--28736 Score: 192
Period size: 54 Copynumber: 2.5 Consensus size: 55
28591 TTTTAAATTG
*
28601 ACTCATATTGCGAGA-ATGAGTT-AAGCCTTTTAATTCCTGTTTTTCAAAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTGAAGCCTTTTAATTCCTGTTTTTC-AAAAATCA
*
28655 ACTCATATTGCGAGAGGTGAGTTGAA-CCTTTTAATTTCTGTTTTTCAAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTGAAGCCTTTTAATTCCTGTTTTTCAAAAATCA
* *
28709 ACTCATAATAC-AGAGGTGAGTTG-AGCCT
1 ACTCATATTGCGAGAGGTGAGTTGAAGCCT
28737 CGGGCCACAT
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
52 1 0.01
53 15 0.20
54 32 0.43
55 25 0.33
56 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (55 bp):
ACTCATATTGCGAGAGGTGAGTTGAAGCCTTTTAATTCCTGTTTTTCAAAAATCA
Found at i:28959 original size:73 final size:71
Alignment explanation
Indices: 28785--29177 Score: 401
Period size: 68 Copynumber: 5.5 Consensus size: 71
28775 AAATTCTGTG
* * * * * *
28785 TTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGT-ATTTCTTT
1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA-GTAATTTC---
*
28848 TAAATTTTTGTT
62 --AATTTTTTTT
28860 TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
1 TTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA-GTAATTTCAA
28925 TTTTTTTT
64 TTTTTTTT
** * ** *
28933 TTCCAAATTTCAACTCATGTTGCGAGAAATGGGTTGAGCCTCAGGACACGCTGAGTAATTTCAA-
1 TT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGTAATTTCAAT
*
28997 TTTGTTT
65 TTTTTTT
*
29004 TT--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAAT
1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA-GTAATTTCAAT
*
29067 TTATGTTT
65 TT-TTTTT
* * *
29075 TTC-AAAATCAACTCATA-TGCGA-AGGTGAGTTGAGCCTC-GGGCACGCCGAGTATTTTCAA-T
1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGTAATTTCAATT
* **
29135 TCTACT
66 TTTTTT
*
29141 TTCAAAAAATCAACTCATATTGCGAGAGGTGGGTTGA
1 TTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
29178 ACCTTTTAAT
Statistics
Matches: 276, Mismatches: 30, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
66 4 0.01
67 2 0.01
68 65 0.24
69 23 0.08
70 28 0.10
71 20 0.07
72 24 0.09
73 55 0.20
74 1 0.00
75 3 0.01
76 17 0.06
77 29 0.11
78 5 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (71 bp):
TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGTAATTTCAATT
TTTTTT
Done.