Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1862
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: 22483
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2730 original size:22 final size:22
Alignment explanation
Indices: 2702--2752 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
2692 AGTGTAGTAT
2702 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
2724 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
2746 ATGTGAT
1 ATGTGAT
2753 GAATGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:2739 original size:70 final size:72
Alignment explanation
Indices: 2653--2803 Score: 243
Period size: 70 Copynumber: 2.1 Consensus size: 72
2643 GAGAGTGTAT
* *
2653 ATGTGTATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA-G-TATATGTGATAAGGCCT
1 ATGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATGATATATGTAATAAGGCCT
*
2716 AATGGCCG
65 AATAGCCG
2724 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATGTATATATGTAATAAGGCCT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATG-ATATATGTAATAAGGCCT
2789 AATAGCCG
65 AATAGCCG
2797 ATGTGAT
1 ATGTGAT
2804 GAATGTGAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
70 38 0.51
71 6 0.08
73 30 0.41
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (72 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATGATATATGTAATAAGGCCTA
ATAGCCG
Found at i:2837 original size:47 final size:47
Alignment explanation
Indices: 2724--2968 Score: 409
Period size: 47 Copynumber: 5.1 Consensus size: 47
2714 CTAATGGCCG
2724 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG----TGTATAT
* *
2775 ATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
2822 GTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
2869 ATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
2916 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
2963 ATGTGA
1 ATGTGA
2969 CAGGGCCGAG
Statistics
Matches: 186, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
47 148 0.80
51 38 0.20
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
Found at i:3189 original size:36 final size:37
Alignment explanation
Indices: 3135--3211 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
3125 CCGAGCTCTA
* * *
3135 AAGA-CCGATGACTACGTGTGGGGATTTTGT-CGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
3170 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
3207 AAGAC
1 AAGAC
3212 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 4 0.11
36 22 0.61
37 10 0.28
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:10951 original size:26 final size:26
Alignment explanation
Indices: 10922--10980 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
10912 TATCCCTAAC
10922 AAAATTTTAACGATTTTACCCTTAGA-
1 AAAATTTTAACGATTTTACCCTT-GAT
* * * *
10948 AAAAATTTGATGATTTTGCCCTTGAT
1 AAAATTTTAACGATTTTACCCTTGAT
10974 AAAATTT
1 AAAATTT
10981 CAAGAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATTTTAACGATTTTACCCTTGAT
Found at i:13103 original size:20 final size:20
Alignment explanation
Indices: 13078--13125 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
13068 TTAGAACAAT
13078 TGAAACATGCGAGATATGTA
1 TGAAACATGCGAGATATGTA
13098 TGAAACATGCGAGATATGTA
1 TGAAACATGCGAGATATGTA
13118 TGAAACAT
1 TGAAACAT
13126 AAATTGATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (20 bp):
TGAAACATGCGAGATATGTA
Found at i:15642 original size:40 final size:40
Alignment explanation
Indices: 15572--15869 Score: 401
Period size: 40 Copynumber: 7.5 Consensus size: 40
15562 AAACCAAGTA
* *
15572 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
15611 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
15651 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
15691 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
15731 CCTTTAGGG-CTTAGCTCGGA-ATTAGTCACTAGCACAAATG
1 CC-TTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
15771 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
15811 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
15851 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
15870 TTATCATCCG
Statistics
Matches: 230, Mismatches: 20, Indels: 17
0.86 0.07 0.06
Matches are distributed among these distances:
39 22 0.10
40 201 0.87
41 7 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:15704 original size:80 final size:80
Alignment explanation
Indices: 15605--15869 Score: 485
Period size: 80 Copynumber: 3.3 Consensus size: 80
15595 GCTACTCGCT
15605 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGGCTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGGCTTAGCCCGG
*
15670 AATTAGTCACTCGCA
66 AATTAGTCACTAGCA
** *
15685 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTTAGGGCTTAGCTCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGGCTTAGCCCGG
15750 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
*
15765 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGGCTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGGCTTAGCCCGG
15830 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
15845 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
15870 TTATCATCCG
Statistics
Matches: 176, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 176 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGGCTTAGCCCGG
AATTAGTCACTAGCA
Done.