Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold869
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: 27776
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Found at i:308 original size:20 final size:20
Alignment explanation
Indices: 254--308 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
244 TAAAAAAATT
254 AAAAT-ATAAA-ATTATAATA
1 AAAATAATAAATA-TATAATA
*
273 AAAATAATACGA-ATATAATA
1 AAAATAATA-AATATATAATA
*
293 TAAATAATAAATATAT
1 AAAATAATAAATATAT
309 CAAAATGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.20
20 22 0.73
21 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATAATAAATATATAATA
Found at i:584 original size:21 final size:21
Alignment explanation
Indices: 560--599 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
550 ATATTGTTTT
560 TAAAT-TTAATTATAAAATATA
1 TAAATATT-ATTATAAAATATA
581 TAAATATTATTATAAAATA
1 TAAATATTATTATAAAATA
600 ACATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTATTATAAAATATA
Found at i:624 original size:19 final size:18
Alignment explanation
Indices: 596--631 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
586 ATTATTATAA
*
596 AATAACATTTTAATATTTT
1 AATAAAATTTTAA-ATTTT
615 AATAAAATTTTAAATTT
1 AATAAAATTTTAAATTT
632 AAAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAAAATTTTAAATTTT
Found at i:1028 original size:41 final size:44
Alignment explanation
Indices: 958--1041 Score: 113
Period size: 41 Copynumber: 2.0 Consensus size: 44
948 TTTAAAAAAA
*
958 TTATGATTAATTTATTATTTTTTAAAATTTTAA-AAAATATTTT
1 TTATGATTAATTTATTATTTTTTAAAATTTAAATAAAATATTTT
*
1001 TTATG-TT-ATTTATT-TTTTTTATTAATTTAAATAAAATATTT
1 TTATGATTAATTTATTATTTTTTA-AAATTTAAATAAAATATTT
1042 ATTTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
40 7 0.19
41 14 0.38
42 11 0.30
43 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (44 bp):
TTATGATTAATTTATTATTTTTTAAAATTTAAATAAAATATTTT
Found at i:1054 original size:41 final size:41
Alignment explanation
Indices: 957--1051 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
947 TTTTAAAAAA
*
957 ATTATGATTAATTTATTATTTTTTAAAATTTTAAAAAATATTT
1 ATTATG-TT-ATTTATTATTTTTTAAAATTTAAAAAAATATTT
* *
1000 TTTATGTTATTTATT-TTTTTTATTAATTTAAATAAAATATTT
1 ATTATGTTATTTATTATTTTTTA-AAATTTAAA-AAAATATTT
1042 ATT-T-TTATTT
1 ATTATGTTATTT
1052 TATATAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 13 0.28
41 15 0.33
42 13 0.28
43 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (41 bp):
ATTATGTTATTTATTATTTTTTAAAATTTAAAAAAATATTT
Found at i:1067 original size:30 final size:30
Alignment explanation
Indices: 1007--1065 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
997 TTTTTTATGT
* *
1007 TATTTATTTTTTTTATTAATTTAAATAAAA
1 TATTTATTTTTATTATTAATATAAATAAAA
1037 TATTTATTTTTATT-TT-ATATAAATTAAAA
1 TATTTATTTTTATTATTAATATAAA-TAAAA
1066 ATTGAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 6 0.23
29 7 0.27
30 13 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTTATTTTTATTATTAATATAAATAAAA
Found at i:1497 original size:18 final size:18
Alignment explanation
Indices: 1474--1514 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1464 ATTAACTCAA
1474 AATATAA-AAAATAATATG
1 AATATAATAAAATAA-ATG
*
1492 AATATAATATAATAAATG
1 AATATAATAAAATAAATG
1510 AATAT
1 AATAT
1515 GTTAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AATATAATAAAATAAATG
Found at i:1671 original size:15 final size:15
Alignment explanation
Indices: 1631--1667 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1621 ATATTATCAA
*
1631 ATTTATATATCATAT
1 ATTTATATATAATAT
1646 ATTTATATATAATAT
1 ATTTATATATAATAT
1661 -TTTATAT
1 ATTTATAT
1668 TATATCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATATATAATAT
Found at i:1672 original size:12 final size:13
Alignment explanation
Indices: 1631--1672 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 13
1621 ATATTATCAA
1631 ATTTATATATCATAT
1 ATTTATATAT--TAT
*
1646 ATTTATATATAAT
1 ATTTATATATTAT
1659 ATTT-TATATTAT
1 ATTTATATATTAT
1671 AT
1 AT
1673 CTAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.36
13 6 0.24
15 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTATATATTAT
Found at i:2813 original size:2 final size:2
Alignment explanation
Indices: 2808--2841 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2798 AAAAAATAAA
2808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2842 TCATTCTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3797 original size:39 final size:39
Alignment explanation
Indices: 3743--3818 Score: 136
Period size: 39 Copynumber: 1.9 Consensus size: 39
3733 TTTTAAAGTC
3743 AAACTCAGTTCAAGATTAAAATTAAACTATTTGAGTTTT
1 AAACTCAGTTCAAGATTAAAATTAAACTATTTGAGTTTT
3782 AAACTC-GATTCAAGATTAAAATTAAACTATTTGAGTT
1 AAACTCAG-TTCAAGATTAAAATTAAACTATTTGAGTT
3819 CACTTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (39 bp):
AAACTCAGTTCAAGATTAAAATTAAACTATTTGAGTTTT
Found at i:5215 original size:3 final size:3
Alignment explanation
Indices: 5207--5237 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5197 CCCTCTTGCA
5207 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5238 CACAAAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:7617 original size:33 final size:32
Alignment explanation
Indices: 7574--7635 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
7564 TGAAACCAGT
7574 TTTTCCCTACTAATAAAAGTGGTTCCTGTCAG
1 TTTTCCCTACTAATAAAAGTGGTTCCTGTCAG
* *
7606 TTTTCCACTACTACTGAAAGTGGTTCCTGT
1 TTTTCC-CTACTAATAAAAGTGGTTCCTGT
7636 TTTTCTGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (32 bp):
TTTTCCCTACTAATAAAAGTGGTTCCTGTCAG
Found at i:13148 original size:10 final size:10
Alignment explanation
Indices: 13129--13161 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
13119 TATGAATATA
13129 TTTA-ATTTT
1 TTTATATTTT
13138 TTTATATTTT
1 TTTATATTTT
*
13148 TTTATATATT
1 TTTATATTTT
13158 TTTA
1 TTTA
13162 AAAGATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTATATTTT
Found at i:16082 original size:34 final size:34
Alignment explanation
Indices: 16044--16141 Score: 151
Period size: 34 Copynumber: 2.9 Consensus size: 34
16034 GTGAAGCATG
*
16044 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATA
1 TTAGGTGTGTTAGGTAATGTATTTGGTGAGAATA
*
16078 TTAGGTGTGTTAGGTAATGTATTTGGTGAAAATA
1 TTAGGTGTGTTAGGTAATGTATTTGGTGAGAATA
* * *
16112 TTATGTGTGTTAGGTAATGTGTTAGGTGAG
1 TTAGGTGTGTTAGGTAATGTATTTGGTGAG
16142 TAAGATATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.42
Consensus pattern (34 bp):
TTAGGTGTGTTAGGTAATGTATTTGGTGAGAATA
Found at i:16581 original size:22 final size:22
Alignment explanation
Indices: 16553--16605 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
16543 CTCGTGCATA
16553 GTTTGGAACTGTGAGTTCATCG
1 GTTTGGAACTGTGAGTTCATCG
16575 GTTTGGAACTGTGAGTTCATCG
1 GTTTGGAACTGTGAGTTCATCG
16597 GTTTGGAAC
1 GTTTGGAAC
16606 CAGAATTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.36
Consensus pattern (22 bp):
GTTTGGAACTGTGAGTTCATCG
Found at i:20960 original size:34 final size:34
Alignment explanation
Indices: 20890--21056 Score: 266
Period size: 34 Copynumber: 5.0 Consensus size: 34
20880 TAGGTGAAGC
20890 ATGTTAGGTGTGTTAGGTGATGTATTT-GTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
20923 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
20957 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
*
20991 ATGTTAGGTGTGTTAGGTGATATA-TTGGTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
* * * * *
21024 ATATTAGATGTGTTAGGTAATGTGTTAGGTGAG
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAG
21057 TAAGATATTT
Statistics
Matches: 125, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
33 55 0.44
34 70 0.56
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.41
Consensus pattern (34 bp):
ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
Found at i:20996 original size:25 final size:25
Alignment explanation
Indices: 20900--21000 Score: 71
Period size: 22 Copynumber: 4.4 Consensus size: 25
20890 ATGTTAGGTG
20900 TGTTAGGTGATGTATTT-GTGAGAA
1 TGTTAGGTGATGTATTTGGTGAGAA
* *
20924 TGTTAGGTG-TG--TTAGGTGATGTA
1 TGTTAGGTGATGTATTTGGTGA-GAA
*
20947 T-TT-GGTGA-GAATGTTAGGT--G--
1 TGTTAGGTGATGTAT-TT-GGTGAGAA
20967 TGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGATGTATTTGGTGAGAA
20992 TGTTAGGTG
1 TGTTAGGTG
21001 TGTTAGGTGA
Statistics
Matches: 59, Mismatches: 4, Indels: 27
0.66 0.04 0.30
Matches are distributed among these distances:
20 1 0.02
21 12 0.20
22 14 0.24
23 10 0.17
24 10 0.17
25 12 0.20
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.42
Consensus pattern (25 bp):
TGTTAGGTGATGTATTTGGTGAGAA
Found at i:21019 original size:67 final size:68
Alignment explanation
Indices: 20890--21056 Score: 266
Period size: 67 Copynumber: 2.5 Consensus size: 68
20880 TAGGTGAAGC
*
20890 ATGTTAGGTGTGTTAGGTGATGTATTT-GTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTG
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATATATTTGGTG
20954 AGA
66 AGA
20957 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATATA-TTGGTG
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATATATTTGGTG
21021 AGA
66 AGA
* * * * *
21024 ATATTAGATGTGTTAGGTAATGTGTTAGGTGAG
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAG
21057 TAAGATATTT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
67 64 0.69
68 29 0.31
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.41
Consensus pattern (68 bp):
ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATATATTTGGTG
AGA
Found at i:23036 original size:2 final size:2
Alignment explanation
Indices: 23029--23066 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
23019 CAAGCAAAAC
23029 GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
23067 GGTTTGCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23172 original size:2 final size:2
Alignment explanation
Indices: 23167--23202 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
23157 TTTTTTTTCT
*
23167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23203 ATCTTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26505 original size:2 final size:2
Alignment explanation
Indices: 26498--26533 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
26488 ATCAGAAACA
*
26498 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26534 TATTAATCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.