Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2670
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: 33894
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Found at i:380 original size:19 final size:19
Alignment explanation
Indices: 356--392 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
346 CATAATTCAT
* *
356 TTCATATAAACTAAAATAC
1 TTCATAAAAACCAAAATAC
375 TTCATAAAAACCAAAATA
1 TTCATAAAAACCAAAATA
393 GATAGGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (19 bp):
TTCATAAAAACCAAAATAC
Found at i:1913 original size:40 final size:37
Alignment explanation
Indices: 1868--1971 Score: 86
Period size: 40 Copynumber: 2.6 Consensus size: 37
1858 ATAGCCCGTT
*
1868 ATTAGTAACTCGCACAATTGCCTTCGGGGACTTAACCGGA
1 ATTAGTAACTCGCACAA-TGCCTTC-AGG-CTTAACCGGA
* *
1908 TTTAGTTAA-TCGCCACAAAATGCCTTCAGGCTTACCCGGA
1 ATTAG-TAACTCG-CAC--AATGCCTTCAGGCTTAACCGGA
*
1948 ATTAGTATC-CGCACACATGCCTTC
1 ATTAGTAACTCGCACA-ATGCCTTC
1972 TGATCTTAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
36 1 0.02
37 8 0.15
38 3 0.06
39 4 0.08
40 20 0.38
41 8 0.15
42 7 0.13
43 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (37 bp):
ATTAGTAACTCGCACAATGCCTTCAGGCTTAACCGGA
Found at i:9927 original size:41 final size:40
Alignment explanation
Indices: 9862--10046 Score: 209
Period size: 41 Copynumber: 4.6 Consensus size: 40
9852 GCTACTCGTT
*
9862 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
9902 CAAATTGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAA-TGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
9943 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * *
9982 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
10023 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
10047 ACATCATTCA
Statistics
Matches: 124, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 42 0.34
41 47 0.38
42 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:9974 original size:80 final size:82
Alignment explanation
Indices: 9862--10047 Score: 231
Period size: 80 Copynumber: 2.3 Consensus size: 82
9852 GCTACTCGTT
* *
9862 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATTGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAA-TGCCTTC-GGATCTTAACC
* *
9925 CGGATTTAGTAAC-TCGCA
64 CGGATATAGTAACTTAGCA
* **
9943 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
10006 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
10023 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
10048 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
78 3 0.03
79 31 0.34
80 43 0.47
81 15 0.16
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:17853 original size:79 final size:82
Alignment explanation
Indices: 17742--17926 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
17732 GCTACTCGTT
* * *
17742 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
17805 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
17822 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
17885 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
17902 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17927 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:17926 original size:40 final size:40
Alignment explanation
Indices: 17723--17926 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
17713 CGGAATTTAA
** *
17723 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
17763 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
17803 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
17842 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
17882 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
17922 CCGGA
1 CCGGA
17927 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:20514 original size:53 final size:53
Alignment explanation
Indices: 20434--20546 Score: 199
Period size: 53 Copynumber: 2.1 Consensus size: 53
20424 GTAGTATACA
20434 GGTGTGTGATCGACGAACCAGGCAGTGCGCGCGTGACACAGGTGTATGACACG
1 GGTGTGTGATCGACGAACCAGGCAGTGCGCGCGTGACACAGGTGTATGACACG
* *
20487 GGTGTGTGATCGACGAATCAGGCAGTGCGCGCTTGACACAGGTGTATGACACG
1 GGTGTGTGATCGACGAACCAGGCAGTGCGCGCGTGACACAGGTGTATGACACG
*
20540 GGCGTGT
1 GGTGTGT
20547 AAGGATTGGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.19
Consensus pattern (53 bp):
GGTGTGTGATCGACGAACCAGGCAGTGCGCGCGTGACACAGGTGTATGACACG
Found at i:28041 original size:80 final size:79
Alignment explanation
Indices: 27940--28165 Score: 271
Period size: 80 Copynumber: 2.8 Consensus size: 79
27930 GCTCCTCGTT
* *
27940 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
28005 ATTTAGTAACTCGCA
65 ATTTAGTAACTCACA
* *
28020 CAAATGCCTTCGGGACTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAGCCC
*
28083 GGATTTAGTATCTCACA
63 GGATTTAGTAACTCACA
* * * *
28100 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
28163 GGA
63 GGA
28166 CATCATTCAA
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
79 9 0.07
80 104 0.83
81 12 0.10
82 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
TTTAGTAACTCACA
Found at i:28149 original size:120 final size:120
Alignment explanation
Indices: 27940--28165 Score: 291
Period size: 120 Copynumber: 1.9 Consensus size: 120
27930 GCTCCTCGTT
*
27940 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCACACAAATGCCTTCGGGACTTAACCCGG
* *
28005 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
66 ATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * **
28060 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGT-ATCTCACACAAATGCCTTC-GGATCTTAGT
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAAT-TCACACAAATGCCTTCGGGA-CTTAAC
* *
28121 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
62 CCGGATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAGCCCGGA
28166 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
119 8 0.09
120 74 0.80
121 10 0.11
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCACACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:28165 original size:40 final size:40
Alignment explanation
Indices: 27940--28165 Score: 241
Period size: 40 Copynumber: 5.7 Consensus size: 40
27930 GCTCCTCGTT
* * *
27940 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
* *
27980 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
28020 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
* * *
28060 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTA-TCTCACA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTACT-TCGCA
* * *
28100 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-ACTTCGCA
28141 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28166 CATCATTCAA
Statistics
Matches: 162, Mismatches: 15, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
39 4 0.02
40 145 0.90
41 12 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
Done.