Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold243
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: 30504
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:2162 original size:17 final size:17
Alignment explanation
Indices: 2140--2173 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2130 CACTAACATG
*
2140 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
2157 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
2174 TATTTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:2641 original size:15 final size:15
Alignment explanation
Indices: 2618--2651 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2608 GCAACTTCTT
*
2618 CTTCTTCAGCAACAA
1 CTTCATCAGCAACAA
2633 CTTCATCAGCAACAA
1 CTTCATCAGCAACAA
2648 CTTC
1 CTTC
2652 CTTCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.26
Consensus pattern (15 bp):
CTTCATCAGCAACAA
Found at i:6755 original size:43 final size:43
Alignment explanation
Indices: 6707--6790 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
6697 AAGATATGTG
*
6707 GCATCCGAGCTCGTTGAAAGGT-TCGAGTTCATTATGGATGCAA
1 GCATCCGAGCTCGTTGAAAGGTAT-GAGTTCATGATGGATGCAA
* *
6750 GCATCCGAGCTCGTTGAGAGGTATGAGTTCATGGTGGATGC
1 GCATCCGAGCTCGTTGAAAGGTATGAGTTCATGATGGATGC
6791 GATTCATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAAAGGTATGAGTTCATGATGGATGCAA
Found at i:8176 original size:13 final size:13
Alignment explanation
Indices: 8158--8182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8148 AGGCCATGTG
8158 AAGGACACGGGCC
1 AAGGACACGGGCC
8171 AAGGACACGGGC
1 AAGGACACGGGC
8183 ATGTGTTCGG
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:0.28, G:0.40, T:0.00
Consensus pattern (13 bp):
AAGGACACGGGCC
Found at i:11504 original size:79 final size:81
Alignment explanation
Indices: 11395--11577 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
11385 TACTCGTTCA
* *
11395 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
11458 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
11475 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
11538 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
11554 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
11578 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:11577 original size:40 final size:40
Alignment explanation
Indices: 11374--11577 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
11364 CGGAATTTAA
** *
11374 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
11414 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
11454 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
11493 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
11533 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
11573 CCGGA
1 CCGGA
11578 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:15695 original size:22 final size:22
Alignment explanation
Indices: 15670--15715 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
15660 TTCTGAAAAC
15670 TTCAATCTTTTGAGCATCGCAT
1 TTCAATCTTTTGAGCATCGCAT
15692 TTCAATCTTTTGAGCATCGCAT
1 TTCAATCTTTTGAGCATCGCAT
15714 TT
1 TT
15716 ATGTCATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (22 bp):
TTCAATCTTTTGAGCATCGCAT
Found at i:15902 original size:19 final size:18
Alignment explanation
Indices: 15886--15925 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
15876 GATAAAAATG
15886 AAAAAAACACAAGAAAACT
1 AAAAAAACACAA-AAAACT
*
15905 AAAAAACCACAAAAAAC-
1 AAAAAAACACAAAAAACT
15922 AAAA
1 AAAA
15926 CAAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 5 0.25
19 11 0.55
ACGTcount: A:0.78, C:0.17, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAAAAACACAAAAAACT
Found at i:19736 original size:40 final size:41
Alignment explanation
Indices: 19601--19786 Score: 218
Period size: 41 Copynumber: 4.6 Consensus size: 41
19591 TACTCGAATG
* *
19601 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGACTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* *
19642 ACATCCGGACTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGACTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* *
19683 ACATCCGGACTAAGAT-CTGAAGGCATTTGTGCT-AGCGACT
1 ATATCCGGACTAAG-TCCCGAAGGCATTTGTGCTAAGCGACT
* * *
19723 ATATCC-GAGCTAAGTCCCGAAGGCATTTATGCT-AGTGACC
1 ATATCCGGA-CTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
** *
19763 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGACTAAGTCCCGAAGGC
19787 CTTGTGCGAG
Statistics
Matches: 129, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
39 3 0.02
40 56 0.43
41 69 0.53
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (41 bp):
ATATCCGGACTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
Found at i:22595 original size:47 final size:47
Alignment explanation
Indices: 22529--23000 Score: 761
Period size: 47 Copynumber: 10.1 Consensus size: 47
22519 GAAATGATAG
22529 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
22576 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
22623 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
22670 TAAGGCC-AAAGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
22716 TAAGGCCTAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
22764 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
22811 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
22857 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
22904 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
22950 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
22997 TAAG
1 TAAG
23001 TCCCGAAGGG
Statistics
Matches: 402, Mismatches: 19, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
46 130 0.32
47 226 0.56
48 46 0.11
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:22711 original size:23 final size:23
Alignment explanation
Indices: 22639--22712 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
22629 CTAATGGCCG
22639 ATGTGATGAATGTGAAAGTGTAT
1 ATGTGATGAATGTGAAAGTGTAT
* ***
22662 ATGTG-TGATAAG-GCCAAAG-GCCG
1 ATGTGATGA-ATGTG--AAAGTGTAT
22685 ATGTGATGAATGTGAAAGTGTAT
1 ATGTGATGAATGTGAAAGTGTAT
22708 ATGTG
1 ATGTG
22713 TGATAAGGCC
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
22 8 0.22
23 21 0.57
24 8 0.22
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.30
Consensus pattern (23 bp):
ATGTGATGAATGTGAAAGTGTAT
Found at i:22715 original size:25 final size:25
Alignment explanation
Indices: 22640--22716 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
22630 TAATGGCCGA
22640 TGTGATGAATGTGAAAGTGTATATG
1 TGTGATGAATGTGAAAGTGTATATG
* ** ***
22665 TGTGAT-AAGGCCAAAG-GCCGA--
1 TGTGATGAATGTGAAAGTGTATATG
22686 TGTGATGAATGTGAAAGTGTATATG
1 TGTGATGAATGTGAAAGTGTATATG
22711 TGTGAT
1 TGTGAT
22717 AAGGCCTAAA
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
21 6 0.17
22 7 0.19
23 4 0.11
24 7 0.19
25 12 0.33
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.31
Consensus pattern (25 bp):
TGTGATGAATGTGAAAGTGTATATG
Found at i:22899 original size:93 final size:94
Alignment explanation
Indices: 22529--23000 Score: 761
Period size: 93 Copynumber: 5.0 Consensus size: 94
22519 GAAATGATAG
*
22529 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
22594 GTGATGAATGTGAAAGTGTATATGTGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* *
22623 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCC-AAAGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
22687 GTGATGAATGTGAAAGTGTATATGTGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* *
22716 TAAGGCCTAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGA
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGA
22781 TGTGATGAATGTGAAAGTGTATATATGTGA
65 TGTGATGAATGTGAAAGTGTATATATGTGA
*
22811 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT-ATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
22875 GTGATGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* * * * * *
22904 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * *
22968 GTGATGGATGTGAAAGTGCATAAATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
22997 TAAG
1 TAAG
23001 TCCCGAAGGG
Statistics
Matches: 356, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
92 23 0.06
93 155 0.44
94 134 0.38
95 44 0.12
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (94 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGA
Found at i:23175 original size:37 final size:37
Alignment explanation
Indices: 23119--23197 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
23109 CCGAGCTCTA
* * *
23119 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
23156 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
23193 AAGAC
1 AAGAC
23198 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Done.