Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3580
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: 30277
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:3634 original size:14 final size:16
Alignment explanation
Indices: 3617--3651 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
3607 ATATTAGAAT
3617 AATAAAAAA-A-TAAA
1 AATAAAAAATAGTAAA
3631 AATAAAAAATAGTAAA
1 AATAAAAAATAGTAAA
3647 AATAA
1 AATAA
3652 CATCAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 1 0.05
16 9 0.47
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AATAAAAAATAGTAAA
Found at i:9647 original size:19 final size:19
Alignment explanation
Indices: 9623--9671 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
9613 GAGCTTTTTT
9623 TTTAAAGATATAA-AGATAA
1 TTTAAA-ATATAATAGATAA
9642 TTTAAAATTATAATAGATAA
1 TTTAAAA-TATAATAGATAA
*
9662 ATTAAAATAT
1 TTTAAAATAT
9672 TTAAATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 12 0.44
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (19 bp):
TTTAAAATATAATAGATAA
Found at i:9661 original size:20 final size:19
Alignment explanation
Indices: 9631--9669 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
9621 TTTTTAAAGA
*
9631 TATAAAGATAATTTAAAAT
1 TATAAAGATAAATTAAAAT
9650 TATAATAGATAAATTAAAAT
1 TATAA-AGATAAATTAAAAT
9670 ATTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
TATAAAGATAAATTAAAAT
Found at i:9665 original size:14 final size:14
Alignment explanation
Indices: 9646--9684 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
9636 AGATAATTTA
9646 AAATTATAATAGAT
1 AAATTATAATAGAT
* **
9660 AAATTAAAATATTT
1 AAATTATAATAGAT
9674 AAATTATAATA
1 AAATTATAATA
9685 CACCCTATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
AAATTATAATAGAT
Found at i:11844 original size:16 final size:16
Alignment explanation
Indices: 11823--11858 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
11813 TTGGGCCCTA
*
11823 AACCAAACAACCCACT
1 AACCAAACAACCCAAT
11839 AACCAAACAACCCAAT
1 AACCAAACAACCCAAT
11855 AACC
1 AACC
11859 CGTCAGCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.42, G:0.00, T:0.06
Consensus pattern (16 bp):
AACCAAACAACCCAAT
Found at i:13050 original size:3 final size:3
Alignment explanation
Indices: 13042--13083 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
13032 TGTATTTTCA
13042 TAT TAT TAT TAT TAT TAT TAT ATAT T-T TAT ATAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT
13084 ATGCATATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.11
3 25 0.71
4 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:26300 original size:251 final size:251
Alignment explanation
Indices: 25896--26502 Score: 909
Period size: 251 Copynumber: 2.5 Consensus size: 251
25886 TTTTTAATTT
* * * *
25896 TTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCAT--GCTGAGGT-ATTTC
1 TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGG-ATACGATGAGGTAATTTC
* * * ** **
25958 ----T-AGTTTT--AAATT-GACTCATATTGCGAGAGGTGAGTTAAGCCTTTTCATTTTTGTTTT
65 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTCCTACTTT
26015 TCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTT
130 TCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTT
*
26080 CTGTTTGTCAAGAATCAACTCATATTGCGAGAGGT-GTTGAACCTTTTAATTCCTAC
195 CTGTCTGTCAAGAATCAACTCATATTGCGAGAGGTGGTTGAACCTTTTAATTCCTAC
* *
26136 TTTTTCAAAATCAACTCATATTGCTAGATGTGAGTTGAGCCTGAGGATACGATGAGGTAATTTCA
1 TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCA
*
26201 ATTTCTGTTTGTCAAGAA-TCAACTCATATTGCGAGAGGTGGGTTGAA-CCTTTTAATTCCTACT
66 ATTTCTGTTT-TCAA-AATTCAACTCATATTGCGAGAGGTGAGTT-AAGCCTTTTAATTCCTACT
26264 TTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAAT
128 TTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAAT
26329 TTCTGTCTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTCCTAC
193 TTCTGTCTGTCAAGAATCAACTCATATTGCGAGAGGT-GGTTGAACCTTTTAATTCCTAC
26389 TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCA
1 TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCA
** *
26454 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
66 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCCT
26503 CAAGACTCAT
Statistics
Matches: 329, Mismatches: 20, Indels: 24
0.88 0.05 0.06
Matches are distributed among these distances:
239 2 0.01
240 42 0.13
241 7 0.02
242 5 0.02
246 1 0.00
247 4 0.01
248 1 0.00
250 2 0.01
251 139 0.42
252 32 0.10
253 94 0.29
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (251 bp):
TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCA
ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTCCTACTTTT
CAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTC
TGTCTGTCAAGAATCAACTCATATTGCGAGAGGTGGTTGAACCTTTTAATTCCTAC
Found at i:26326 original size:126 final size:127
Alignment explanation
Indices: 25971--26488 Score: 897
Period size: 126 Copynumber: 4.1 Consensus size: 127
25961 TTTTAAATTG
* * * **
25971 ACTCATATTGCGAGAGGTGAGTT-AAGCCTTTTCATT-TTTGTTTTTCAAAATCAACTCATATTG
1 ACTCATATTGCGAGAGGTGGGTTGAA-CCTTTTAATTCCTACTTTTTCAAAATCAACTCATATTG
26034 CTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAATCA
65 CTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAATCA
26097 ACTCATATTGCGAGAGGT--GTTGAACCTTTTAATTCCTACTTTTTCAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTCCTACTTTTTCAAAATCAACTCATATTGC
* *
26160 TAGATGTGAGTTGAGCCTGAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAATCA
66 TAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAATCA
26222 ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTCCTAC-TTTTCAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTCCTACTTTTTCAAAATCAACTCATATTGC
*
26286 TAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTCTGTCAAGAATCA
66 TAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAATCA
26348 ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTCCTACTTTTTCAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTCCTACTTTTTCAAAATCAACTCATATTGC
26413 TAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTT-TCAA-AATTCA
66 TAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAA-TCA
26474 ACTCATATTGCGAGA
1 ACTCATATTGCGAGA
26489 AATGAGTTGA
Statistics
Matches: 376, Mismatches: 10, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
124 12 0.03
125 107 0.28
126 163 0.43
127 94 0.25
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (127 bp):
ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTCCTACTTTTTCAAAATCAACTCATATTGC
TAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAATCA
Found at i:26517 original size:72 final size:72
Alignment explanation
Indices: 26390--26541 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 72
26380 AATTCCTACT
* ** *
26390 TTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAA
1 TTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGATACGATGAGGTAATTTCAA
**
26455 TTTCTG-
66 AATCTGC
*
26461 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACT-C-ATTGAGGTATTTT
1 TTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA-TACGA-TGAGGTAATTT
26524 CAAAATCTGC
63 CAAAATCTGC
26534 TTTTCAAA
1 TTTTCAAA
26542 TTAAGTTTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
71 10 0.14
72 51 0.73
73 9 0.13
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (72 bp):
TTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGATACGATGAGGTAATTTCAA
AATCTGC
Found at i:27224 original size:16 final size:17
Alignment explanation
Indices: 27203--27235 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
27193 ATTTTGGGCC
27203 CTAAACCAAAC-ACCCA
1 CTAAACCAAACAACCCA
27219 CTAAACCAAACAACCCA
1 CTAAACCAAACAACCCA
27236 ATAACCCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.52, C:0.42, G:0.00, T:0.06
Consensus pattern (17 bp):
CTAAACCAAACAACCCA
Found at i:27241 original size:16 final size:16
Alignment explanation
Indices: 27204--27239 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
27194 TTTTGGGCCC
*
27204 TAAACCAAACACCCAC
1 TAAACCAAACACCCAA
27220 TAAACCAAACAACCCAA
1 TAAACCAAAC-ACCCAA
27237 TAA
1 TAA
27240 CCCGTCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (16 bp):
TAAACCAAACACCCAA
Found at i:28264 original size:3 final size:3
Alignment explanation
Indices: 28256--28310 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
28246 TATATTTTCA
* *
28256 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT CAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28303 TAT T-T TAT
1 TAT TAT TAT
28311 ATGTATATCA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Done.