Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold938
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: 43612
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:426 original size:31 final size:30
Alignment explanation
Indices: 364--434 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
354 TTAAGAGAGA
**
364 AAATTTGAGAGATTTTTGAGAGTTGATTGAG
1 AAATTTGAGAGATTTAAGAGAGTTGA-TGAG
395 AAATTTGAGAGATTTAAGAGAGAATTG-TGAG
1 AAATTTGAGAGATTTAAGAGAG--TTGATGAG
*
426 AAATGTGAG
1 AAATTTGAG
435 TGAGAAAGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 32 0.91
33 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (30 bp):
AAATTTGAGAGATTTAAGAGAGTTGATGAG
Found at i:1117 original size:29 final size:30
Alignment explanation
Indices: 1066--1127 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
1056 CCTTATTTTA
1066 TTGTTAATTTTGTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTGTTATTATTTTATAA-GCAT
1096 TTGTTAATTTT-TTATTATTTTATAAGCAT
1 TTGTTAATTTTGTTATTATTTTATAAGCAT
1125 TTG
1 TTG
1128 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTATAAGCAT
Found at i:7121 original size:20 final size:20
Alignment explanation
Indices: 7096--7134 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7086 AGTTGAATGA
7096 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
7116 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
7135 AATAGCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:13796 original size:20 final size:20
Alignment explanation
Indices: 13771--13809 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13761 AAAATTTCAA
13771 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
13791 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
13810 AATAGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:14986 original size:3 final size:3
Alignment explanation
Indices: 14978--15040 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
14968 TTCTAACACA
14978 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
15026 CTT ATT CTT CTT CTT
1 CTT CTT CTT CTT CTT
15041 TCTAAGACCT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:16129 original size:30 final size:31
Alignment explanation
Indices: 16095--16157 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
16085 ACTTATTTTA
16095 TTGTTAA-TTTTGTTACTATTTTAAAGGCAT
1 TTGTTAATTTTTGTTACTATTTTAAAGGCAT
* *
16125 TTGTTAATTTTTTTTATTATTTTAAAGGCAT
1 TTGTTAATTTTTGTTACTATTTTAAAGGCAT
16156 TT
1 TT
16158 TCTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTGTTACTATTTTAAAGGCAT
Found at i:19329 original size:13 final size:13
Alignment explanation
Indices: 19311--19335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19301 TAATGGTATA
19311 TTGAATCCATGAT
1 TTGAATCCATGAT
19324 TTGAATCCATGA
1 TTGAATCCATGA
19336 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:20959 original size:47 final size:47
Alignment explanation
Indices: 20850--21017 Score: 223
Period size: 47 Copynumber: 3.6 Consensus size: 47
20840 TATTTGAATA
20850 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
20899 AATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * * *
20944 AATGTGAAAGTGTATATATGTGACAGGGTCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
20991 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
21018 TCCCGAAGGG
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
45 44 0.42
47 53 0.50
49 9 0.08
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:22832 original size:40 final size:40
Alignment explanation
Indices: 22478--22820 Score: 510
Period size: 40 Copynumber: 8.6 Consensus size: 40
22468 GAGTGAAATG
*
22478 TCCGGGCTAAATCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
*
22518 TCCGGACTAAGT-TCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCT-CGAAGAGCATTCGTGCTAGTGATGTA
*
22558 TCCAGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
22598 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
22638 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
22678 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
* *
22718 TCCGGACTAAGT-TCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCT-CGAAGAGCATTCGTGCTAGTGATGTA
* ** * * * * * *
22758 TCCGTGCTAAACCCCAAAGAGCATTTGTGCTGGTGTTATA
1 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
* *
22798 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGGCTAAGTCTCGAAGAGCA
22821 ATCATGCTGG
Statistics
Matches: 278, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
39 2 0.01
40 275 0.99
41 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:25031 original size:13 final size:13
Alignment explanation
Indices: 25013--25037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25003 TAATGGTATA
25013 TTGAATCCATGAT
1 TTGAATCCATGAT
25026 TTGAATCCATGA
1 TTGAATCCATGA
25038 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:26599 original size:22 final size:22
Alignment explanation
Indices: 26571--26644 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
26561 GTGTATATAT
26571 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* ** ****
26593 ATGTGATGAATGTGTAA-GTATAT
1 ATGTGAT-AAGGCCTAATG-GCCG
26616 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
26638 ATGTGAT
1 ATGTGAT
26645 GAATGTGAAA
Statistics
Matches: 35, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 21 0.60
23 14 0.40
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:26661 original size:47 final size:47
Alignment explanation
Indices: 26552--26719 Score: 223
Period size: 47 Copynumber: 3.6 Consensus size: 47
26542 TATTTGAATA
26552 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
26601 AATGTGTAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
26646 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
26693 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
26720 TCCCGAAGGG
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
45 43 0.41
47 54 0.51
49 8 0.08
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:33709 original size:40 final size:40
Alignment explanation
Indices: 33533--33755 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
33523 TCCTCGTTCA
* * * * *
33533 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
33572 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
33612 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
33652 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
33692 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
33732 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
33756 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42979 original size:39 final size:38
Alignment explanation
Indices: 42931--43106 Score: 131
Period size: 39 Copynumber: 4.5 Consensus size: 38
42921 CTGTCCGGGC
* * *
42931 TAAGGCCGAAGGCTTTGTGCTA-ATGAATATATCCGGAT
1 TAAGTCCGAAGGCTTTGTGCGAGAT-AATAAATCCGGAT
* *
42969 TAAGATCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAG-TCCGAAGG-CTTTGTGCGAGATAATAAATCCGGAT
* * *
43009 TAAGTCCGAAGGCATTCGTGCGAGTTATTAAATCCGG-T
1 TAAGTCCGAAGGC-TTTGTGCGAGATAATAAATCCGGAT
* * * ** *
43047 TAAGTCCCGAAGGCAGTCGTGGCGAGTTGTTAAATCCGGGT
1 TAAGT-CCGAAGGC-TTTGT-GCGAGATAATAAATCCGGAT
* *
43088 TATGTCCGAAGGCATTGTG
1 TAAGTCCGAAGGCTTTGTG
43107 TGAGTTACTA
Statistics
Matches: 118, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
38 12 0.10
39 51 0.43
40 48 0.41
41 7 0.06
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (38 bp):
TAAGTCCGAAGGCTTTGTGCGAGATAATAAATCCGGAT
Found at i:43057 original size:78 final size:78
Alignment explanation
Indices: 42924--43143 Score: 212
Period size: 78 Copynumber: 2.8 Consensus size: 78
42914 TTGAATGCTG
* * * * * * * * *
42924 TCCGGGCTAAGGCCGAAGGCTTTGTGCTAATGAATATATCCGGATTAAGAT-CCGAAGGCCTTTG
1 TCCGGGTTAAGTCCGAAGGCATTGTGCGAGTTACTAAATCCGG-TTAAG-TCCCGAAGGCATTTG
42988 T-GCGAGATACTAAA
64 TGGCGAGATACTAAA
* * *
43002 TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAATCCGGTTAAGTCCCGAAGGCAGTCGT
1 TCCGGGTTAAGTCCGAAGGCATT-GTGCGAGTTACTAAATCCGGTTAAGTCCCGAAGGCATTTGT
* **
43067 GGCGAGTTGTTAAA
65 GGCGAGATACTAAA
* * * *
43081 TCCGGGTTATGTCCGAAGGCATTGTGTGAGTTACTAAA-CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCGAAGGCATTGTGCGAGTTACTAAATCC-GGTTAAGTCCCGAAGGCATTTG
43144 AACGAGGAGC
Statistics
Matches: 117, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
77 3 0.03
78 67 0.57
79 47 0.40
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (78 bp):
TCCGGGTTAAGTCCGAAGGCATTGTGCGAGTTACTAAATCCGGTTAAGTCCCGAAGGCATTTGTG
GCGAGATACTAAA
Found at i:43083 original size:40 final size:39
Alignment explanation
Indices: 42961--43139 Score: 175
Period size: 39 Copynumber: 4.6 Consensus size: 39
42951 TAATGAATAT
* ** * * *
42961 ATCCGGATTAAGATCCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCGAAGGCAGTCGTGCGAGTTATTAA
*
43001 ATCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCGAAGGCAGTCGTGCGAGTTATTAA
*
43040 ATCC-GGTTAAGTCCCGAAGGCAGTCGTGGCGAGTTGTTAA
1 ATCCGGGTTAAGT-CCGAAGGCAGTCGT-GCGAGTTATTAA
* * * *
43080 ATCCGGGTTATGTCCGAAGGCA-TTGTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCGAAGGCAGTCGTGCGAGTTATTAA
* *
43118 A-CCGGGCTATGTCCCGAAGGCA
1 ATCCGGGTTAAGT-CCGAAGGCA
43140 TTTGAACGAG
Statistics
Matches: 122, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
37 10 0.08
38 27 0.22
39 43 0.35
40 35 0.29
41 7 0.06
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (39 bp):
ATCCGGGTTAAGTCCGAAGGCAGTCGTGCGAGTTATTAA
Done.