Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3056
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: 40004
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:2847 original size:117 final size:118
Alignment explanation
Indices: 2667--2887 Score: 297
Period size: 117 Copynumber: 1.9 Consensus size: 118
2657 TCCTCGTTCA
*
2667 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
2732 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCC
* * **
2785 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
2847 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
2888 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
116 4 0.04
117 66 0.73
118 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (118 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCC
Found at i:2887 original size:40 final size:40
Alignment explanation
Indices: 2665--2887 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
2655 GCTCCTCGTT
* *
2665 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2705 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2745 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGC-
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
2784 C-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
2822 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
2863 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2888 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
37 20 0.12
38 15 0.09
39 10 0.06
40 105 0.65
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:9507 original size:14 final size:14
Alignment explanation
Indices: 9490--9523 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
9480 AAAAAATGAA
9490 AAAATGTGATCTAC
1 AAAATGTGATCTAC
*
9504 AAAATGTTATCTAC
1 AAAATGTGATCTAC
9518 AAAATG
1 AAAATG
9524 AAAAAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (14 bp):
AAAATGTGATCTAC
Found at i:9905 original size:36 final size:36
Alignment explanation
Indices: 9812--9914 Score: 111
Period size: 36 Copynumber: 2.8 Consensus size: 36
9802 TGAGCTTCAC
*
9812 TCAGTATAACAATAGAATTTGCTCGATTGAACATCAT
1 TCAGTATAACAATA-AATTTGCTCGATTGAACACCAT
** *
9849 TCAGTATAACGGTAAGATTTGCTC-AGTT-AAGACCAT
1 TCAGTATAACAATAA-ATTTGCTCGA-TTGAACACCAT
*
9885 TCAGTATAACAATATAATTTGCTTGATTGA
1 TCAGTATAACAATA-AATTTGCTCGATTGA
9915 GCTTTAGTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
36 29 0.54
37 25 0.46
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (36 bp):
TCAGTATAACAATAAATTTGCTCGATTGAACACCAT
Found at i:17156 original size:21 final size:20
Alignment explanation
Indices: 17108--17156 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
17098 TTATTTCATT
17108 TTTTTATTTTTCTTTATTTA
1 TTTTTATTTTTCTTTATTTA
*
17128 TTTCTATTTTTCCTTTATTTA
1 TTTTTATTTTT-CTTTATTTA
17149 TTTTTATT
1 TTTTTATT
17157 CCATCAACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTATTTTTCTTTATTTA
Found at i:19357 original size:18 final size:19
Alignment explanation
Indices: 19320--19365 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
19310 GTCTCGTTTT
19320 ATGCTTTTATCACACTCACA
1 ATGCTTTTA-CACACTCACA
*
19340 ATGCTTTTA-ACCCTCACA
1 ATGCTTTTACACACTCACA
19358 ATGCTTTT
1 ATGCTTTT
19366 GTTCCCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.64
20 9 0.36
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.39
Consensus pattern (19 bp):
ATGCTTTTACACACTCACA
Found at i:20012 original size:22 final size:24
Alignment explanation
Indices: 19976--20023 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
19966 TATACCTATT
19976 AAATTAAAAAAATCTAA-TCTTAA
1 AAATTAAAAAAATCTAAGTCTTAA
*
19999 AAATT-AAAATATCTAAGTCTTAA
1 AAATTAAAAAAATCTAAGTCTTAA
20022 AA
1 AA
20024 TAAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATTAAAAAAATCTAAGTCTTAA
Found at i:20032 original size:23 final size:21
Alignment explanation
Indices: 19974--20032 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
19964 AATATACCTA
* *
19974 TTAAATTAAAAAAATCTAATC
1 TTAAAATAAAAATATCTAATC
*
19995 TTAAAAATTAAAATATCTAAGTC
1 TT-AAAATAAAAATATCTAA-TC
20018 TTAAAATAAATAATA
1 TTAAAATAAA-AATA
20033 ATAAGGAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 21 0.68
23 8 0.26
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.34
Consensus pattern (21 bp):
TTAAAATAAAAATATCTAATC
Found at i:35982 original size:24 final size:24
Alignment explanation
Indices: 35955--36000 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35945 AGAACAATCC
* *
35955 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
35979 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
36001 AAAAGATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Done.