Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold415
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: 50751
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:10629 original size:23 final size:23
Alignment explanation
Indices: 10603--10700 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
10593 ATAAGTGCCA
10603 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
10626 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
10649 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
10671 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
10694 CACTGAT
1 CACTGAT
10701 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:10668 original size:45 final size:45
Alignment explanation
Indices: 10610--10698 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
10600 CCACACTGAT
* *
10610 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
10655 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
10699 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:15349 original size:18 final size:19
Alignment explanation
Indices: 15326--15386 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
15316 TCTTTAGAAT
15326 TTTTTAAAACTAT-TATAA
1 TTTTTAAAACTATATATAA
15344 TTTTTAAATA-TATATATAA
1 TTTTTAAA-ACTATATATAA
* *
15363 ATTTTGAAACT-TATATATA
1 TTTTTAAAACTATATATA-A
15382 TTTTT
1 TTTTT
15387 CATTTCTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 18 0.50
19 18 0.50
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTTTAAAACTATATATAA
Found at i:15365 original size:20 final size:20
Alignment explanation
Indices: 15326--15381 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
15316 TCTTTAGAAT
15326 TTTTTAAA-ACTAT-TAT-AA
1 TTTTTAAATA-TATATATAAA
15344 TTTTTAAATATATATATAAA
1 TTTTTAAATATATATATAAA
*
15364 TTTTGAAACT-TATATATA
1 TTTTTAAA-TATATATATA
15382 TTTTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 11 0.33
19 4 0.12
20 17 0.52
21 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTTAAATATATATATAAA
Found at i:20880 original size:21 final size:22
Alignment explanation
Indices: 20849--20892 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
20839 TCATACTTCT
20849 ATTTTTCTTATAAATTTATATG
1 ATTTTTCTTATAAATTTATATG
* *
20871 ATTTTT-TTATAATTTTGTATG
1 ATTTTTCTTATAAATTTATATG
20892 A
1 A
20893 ATTCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTCTTATAAATTTATATG
Found at i:30257 original size:10 final size:11
Alignment explanation
Indices: 30229--30256 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
30219 TATTCTATTG
30229 AAAAAAATTAC
1 AAAAAAATTAC
30240 AAAAAAATTAC
1 AAAAAAATTAC
30251 AAAAAA
1 AAAAAA
30257 TGTTCAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTAC
Found at i:36719 original size:26 final size:25
Alignment explanation
Indices: 36671--36733 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
36661 ATATTTTATA
* *
36671 AATTATATTTTGAATGTAATAAT-T
1 AATTATATTTTAAATATAATAATAT
36695 AATTATACTTTTAAAATATAATAATAT
1 AATTATA-TTTT-AAATATAATAATAT
*
36722 AATATAAATTTT
1 AAT-TATATTTT
36734 CATAAAGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 7 0.22
25 4 0.12
26 10 0.31
27 8 0.25
28 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (25 bp):
AATTATATTTTAAATATAATAATAT
Found at i:37036 original size:23 final size:23
Alignment explanation
Indices: 37009--37059 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
36999 ATTTATAAAA
37009 AAATT-ATTATTTATTAT-ATTACT
1 AAATTGATT-TTTATT-TCATTACT
*
37032 AAATTGATTTTTATTTCATTATT
1 AAATTGATTTTTATTTCATTACT
37055 AAATT
1 AAATT
37060 TTGAATATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 21 0.84
24 3 0.12
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATTGATTTTTATTTCATTACT
Found at i:38560 original size:27 final size:27
Alignment explanation
Indices: 38498--38560 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
38488 CTTTTAATTG
*
38498 TAATAATTATAGTAAAATATAATTTAT
1 TAATAATTATAGTAAAATATAATTTAA
* *
38525 TATTTATTATAGTAAAA-A-AATTTCAAA
1 TAATAATTATAGTAAAATATAATTT--AA
38552 TAATAATTA
1 TAATAATTA
38561 GAATATTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 5 0.17
26 1 0.03
27 23 0.79
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (27 bp):
TAATAATTATAGTAAAATATAATTTAA
Found at i:40206 original size:17 final size:17
Alignment explanation
Indices: 40164--40210 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
40154 AATTTAATTT
40164 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
40180 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
40198 TAATATAAATAAT
1 TAATATAAATAAT
40211 ATAAAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 13 0.48
18 8 0.30
19 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:40707 original size:21 final size:21
Alignment explanation
Indices: 40668--40707 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
40658 GGGGAAAGTG
*
40668 GGAAGAAGTAAAAGTTTTGAA
1 GGAAGAAGTAAAAATTTTGAA
40689 GGAA-AAGTAAAAATATTTG
1 GGAAGAAGTAAAAAT-TTTG
40708 GAAATTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (21 bp):
GGAAGAAGTAAAAATTTTGAA
Found at i:45798 original size:40 final size:40
Alignment explanation
Indices: 45681--45959 Score: 405
Period size: 40 Copynumber: 7.2 Consensus size: 40
45671 CGGATGATAA
45681 CGAAGGCATTTGTGCGAG--ACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
45719 CGAAGGCATTTGTGCGAGTTAC--TATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* *
45757 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
*
45797 CGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
45837 CGAAGGCATTTGTGCGAGTTACTATA-CCCGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
45876 CG-AGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
45915 CGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
45954 CGAAGG
1 CGAAGG
45960 TACTTGGTTT
Statistics
Matches: 221, Mismatches: 11, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 76 0.34
39 45 0.20
40 99 0.45
41 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:45907 original size:118 final size:117
Alignment explanation
Indices: 45681--45959 Score: 424
Period size: 118 Copynumber: 2.4 Consensus size: 117
45671 CGGATGATAA
45681 CGAAGGCATTTGTGCGAG-ACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATC
1 CGAAGGCATTTGTGCGAGTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATC
* *
45745 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCC
66 CCGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCC
*
45797 CGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
1 CGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
45862 ACCCGGCTAAGTCCCG-AGGCATTTGTGCGAGCT-ACT-ATATCCGGGCTAAGTCC
65 -CCCGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACTAAT-TCCGGGCTAAGTCC
* * *
45915 CGAAGGCATTTGAGCGAGTAGCTATATCC-GGTTAAATCCCGAAGG
1 CGAAGGCATTTGTGCGAGTA-CTATATCCGGGCTAAGTCCCGAAGG
45960 TACTTGGTTT
Statistics
Matches: 150, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
116 17 0.11
117 18 0.12
118 100 0.67
119 15 0.10
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (117 bp):
CGAAGGCATTTGTGCGAGTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATC
CCGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCC
Found at i:45932 original size:78 final size:78
Alignment explanation
Indices: 45681--45959 Score: 395
Period size: 78 Copynumber: 3.6 Consensus size: 78
45671 CGGATGATAA
*
45681 CGAAGGCATTTGTGCGAG-ACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC--TA
1 CGAAGGCATTTGTGCGAGTACTATA-CCCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
45743 TCCGGGCTAAGTCC
65 TCCGGGCTAAGTCC
* * * *
45757 CGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT
1 CGAAGGCATTTGTGCGAGT-ACT-ATACCCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
45822 ATCCGGGCTAAGTCC
64 ATCCGGGCTAAGTCC
*
45837 CGAAGGCATTTGTGCGAGTTACTATACCCGGCTAAGTCCCG-AGGCATTTGTGCGAGCTACTATA
1 CGAAGGCATTTGTGCGAG-TACTATACCCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
45901 TCCGGGCTAAGTCC
65 TCCGGGCTAAGTCC
* * * *
45915 CGAAGGCATTTGAGCGAGTAGCTATATCCGGTTAAATCCCGAAGG
1 CGAAGGCATTTGTGCGAGTA-CTATACCCGGCTAAGTCCCGAAGG
45960 TACTTGGTTT
Statistics
Matches: 183, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
76 17 0.09
77 2 0.01
78 106 0.58
79 21 0.11
80 36 0.20
81 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (78 bp):
CGAAGGCATTTGTGCGAGTACTATACCCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
CCGGGCTAAGTCC
Done.