Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1925
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: 26557
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:113 original size:27 final size:26
Alignment explanation
Indices: 81--163 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 26
71 TCACATACTG
81 TATATGGCCCACTAGGCCCATCACATT
1 TATATGGCCCA-TAGGCCCATCACATT
*
108 TATATGGCCCATTAGGCCCA-AATCATT
1 TATATGGCCCA-TAGGCCCATCA-CATT
*
135 TATATGGCCTATCAGGCCCATTCACATT
1 TATATGGCCCAT-AGGCCCA-TCACATT
163 T
1 T
164 TTAGTCATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.04
27 40 0.83
28 5 0.10
29 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (26 bp):
TATATGGCCCATAGGCCCATCACATT
Found at i:8774 original size:52 final size:53
Alignment explanation
Indices: 8679--8781 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 53
8669 TGCAAGCGAA
*
8679 TAATGTCCCTAAAGAAAATATTAGAAATATGAACGGCACCGTCAGTCTTTGAC
1 TAATGTCCCTAAAGAAAAGATTAGAAATATGAACGGCACCGTCAGTCTTTGAC
* *
8732 TAATGTCCCTAAAG-AAAGATTGGAAATATGAACGGCATCGTCAGTCTTTG
1 TAATGTCCCTAAAGAAAAGATTAGAAATATGAACGGCACCGTCAGTCTTTG
8782 TACAAGCAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 33 0.70
53 14 0.30
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (53 bp):
TAATGTCCCTAAAGAAAAGATTAGAAATATGAACGGCACCGTCAGTCTTTGAC
Found at i:12245 original size:39 final size:39
Alignment explanation
Indices: 12064--12245 Score: 185
Period size: 40 Copynumber: 4.7 Consensus size: 39
12054 GCTACTCGTT
* * * *
12064 CAAATGCCTTCGGAACATAGCCCGGTTATAGTAACTCCCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
12104 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
* * *
12144 CCAATTCCTTCGGG-CTTAGCCCGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
* * *
12182 CAAATGCCTTC-GGATCTTA-TCCGGA-TATGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTA-GTAAC-TCGCA
12221 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12246 CATCATTCGA
Statistics
Matches: 119, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
37 4 0.03
38 40 0.34
39 29 0.24
40 45 0.38
41 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:12844 original size:24 final size:24
Alignment explanation
Indices: 12816--12863 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
12806 ACAAATGGCA
*
12816 TACATTTTACTAA-TCAATACGCAT
1 TACATATTA-TAACTCAATACGCAT
12840 TACATATTATAACTCAATACGCAT
1 TACATATTATAACTCAATACGCAT
12864 CCATCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (24 bp):
TACATATTATAACTCAATACGCAT
Found at i:16662 original size:21 final size:21
Alignment explanation
Indices: 16621--16728 Score: 69
Period size: 22 Copynumber: 5.0 Consensus size: 21
16611 TATTTTCACT
*
16621 TTCTTTTTCTTTTTCTTTTTC
1 TTCTTTTTCATTTTCTTTTTC
16642 TTCTTTTCTCATTTTC-TTTTC
1 TTCTTTT-TCATTTTCTTTTTC
* * ** *
16663 -GCTTTTTTAGCTACTTTTTC
1 TTCTTTTTCATTTTCTTTTTC
*
16683 TTTCTTTTTCACATTTCTCATTTTTT
1 -TTCTTTTT--CATTT-TC-TTTTTC
*
16709 TTCATTTTC-TTTTCTTTTTC
1 TTCTTTTTCATTTTCTTTTTC
16729 AACTTCATTC
Statistics
Matches: 65, Mismatches: 14, Indels: 17
0.68 0.15 0.18
Matches are distributed among these distances:
19 4 0.06
20 15 0.23
21 14 0.22
22 16 0.25
23 1 0.02
24 2 0.03
25 8 0.12
26 5 0.08
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCTTTTTCATTTTCTTTTTC
Found at i:16714 original size:17 final size:17
Alignment explanation
Indices: 16678--16743 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
16668 TTTAGCTACT
16678 TTTTC-TTTCTTTTTCACA
1 TTTTCATTTCTTTTT--CA
16696 TTTCTCATTT-TTTTTCA
1 TTT-TCATTTCTTTTTCA
*
16713 TTTTCTTTTCTTTTTCA
1 TTTTCATTTCTTTTTCA
**
16730 ACTTCA-TTCTTTTT
1 TTTTCATTTCTTTTT
16744 TCTTTCAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 13 0.32
17 15 0.37
18 3 0.07
19 7 0.17
20 3 0.07
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTCATTTCTTTTTCA
Found at i:21103 original size:24 final size:24
Alignment explanation
Indices: 21076--21123 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21066 TCTTTAGTCC
* * * *
21076 TAGGCTTTTTTAGTTTAGGGTTTT
1 TAGGATTTTTAAGGTTAAGGTTTT
21100 TAGGATTTTTAAGGTTAAGGTTTT
1 TAGGATTTTTAAGGTTAAGGTTTT
21124 ATTAAAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.25, T:0.54
Consensus pattern (24 bp):
TAGGATTTTTAAGGTTAAGGTTTT
Found at i:21513 original size:126 final size:126
Alignment explanation
Indices: 21378--21754 Score: 424
Period size: 126 Copynumber: 3.0 Consensus size: 126
21368 CTATTTTTAC
* * **
21378 CTTGAAAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTTAAAAACGCTTCAAAAAGGA
1 CTTG-AAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTAAAAAATGCTTCAAGCAGGA
* * * *
21443 TGCATTATCAGTAAAATTACTGAAAAAAGCTCACACGTAAACGCTCTTTTTCTATGGTAGTT
65 TGCATTATCAGTAAAATTACTGAAAAAAGCTCCCACATGAACGCTCTTTTTCTATAGTAGTT
** * * *
21505 CTTGAAAAAATAATTTTGAGAAGATGTTTTTGAACAAATAGTGTCAAAAATGCTTTAAGCAGGAT
1 CTTGAAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTAAAAAATGCTTCAAGCAGGAT
* * * * * * * *
21570 GCACTGTCAGTAAAAGTACTGAAAAATGCTCCCACATGGAA-GCTATTTTTCTACAATAGCT
66 GCATTATCAGTAAAATTACTGAAAAAAGCTCCCACAT-GAACGCTCTTTTTCTATAGTAGTT
* * * *
21631 CCTGAAAAAA-AATTTTCAGAAGACATTTCTG-A-AAA-AGCGTAAAAAAATTGCTTCAAGCAGC
1 CTTGAAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGT-AAAAAA-TGCTTCAAGCAGG
* * *
21692 ATGCATTATCAGCAAAATTTCTG-AAAAAGCTCCCACATGGACGCTCTTTTTCTATAGTAGTT
64 ATGCATTATCAGTAAAATTACTGAAAAAAGCTCCCACATGAACGCTCTTTTTCTATAGTAGTT
21754 C
1 C
21755 ATGTTTGGCC
Statistics
Matches: 206, Mismatches: 40, Indels: 12
0.80 0.16 0.05
Matches are distributed among these distances:
122 6 0.03
123 39 0.19
124 30 0.15
125 17 0.08
126 108 0.52
127 6 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (126 bp):
CTTGAAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTAAAAAATGCTTCAAGCAGGAT
GCATTATCAGTAAAATTACTGAAAAAAGCTCCCACATGAACGCTCTTTTTCTATAGTAGTT
Done.