Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2935
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: 40194
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:965 original size:40 final size:40
Alignment explanation
Indices: 928--1057 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
918 GCTACTCGTT
*
928 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
968 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * *
1008 CCAATGCCTTC-GG-CTTAGCCC-GAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
1045 CAAATGCCTTCGG
1 CAAATGCCTTCGG
1058 ATCTTAGTCC
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
37 24 0.30
38 8 0.10
39 2 0.02
40 45 0.56
41 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:9218 original size:79 final size:81
Alignment explanation
Indices: 9103--9285 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
9093 TACTCGTTCA
* *
9103 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
9166 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
9183 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
9246 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
9262 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
9286 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:9285 original size:40 final size:40
Alignment explanation
Indices: 9082--9285 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
9072 TTCAATTTAA
** *
9082 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9122 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9162 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9201 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
9241 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
9281 CCGGA
1 CCGGA
9286 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:13369 original size:28 final size:27
Alignment explanation
Indices: 13337--13391 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 27
13327 GAGAAATGTC
13337 ATATCTATACTGATCATA-AAAG-TCTGAA
1 ATATCTA-A-TGA-CATAGAAAGATCTGAA
13365 ATATCTAATGACATAGAAAGATCTGAA
1 ATATCTAATGACATAGAAAGATCTGAA
13392 TTTGAGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.16
26 7 0.28
27 7 0.28
28 7 0.28
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (27 bp):
ATATCTAATGACATAGAAAGATCTGAA
Found at i:16507 original size:46 final size:47
Alignment explanation
Indices: 16409--16538 Score: 145
Period size: 46 Copynumber: 2.8 Consensus size: 47
16399 TATGTGAATA
* * ** *
16409 ATACCTTGATTTGGCTACGGGCCATGATATAGGTATTTTAAGAGGAG
1 ATACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAAGAGAAG
** *
16456 ATACCTTGATTTGGCTA-GGGCCATGGTATAGGTACTCCGGGATAAG
1 ATACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAAGAGAAG
* * * *
16502 TTACCTTGATTTAGCTATGGGCCATAGTATAGGTACT
1 ATACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
16539 TATCGATTGT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
46 36 0.51
47 35 0.49
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (47 bp):
ATACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAAGAGAAG
Found at i:20441 original size:6 final size:6
Alignment explanation
Indices: 20396--20425 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
20386 TAATTCTAAG
*
20396 AAATAA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA
20426 GTGGTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:23797 original size:21 final size:22
Alignment explanation
Indices: 23772--23812 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
23762 TTAGTGGAAA
*
23772 TAGATTAA-TTAGGCTTAATCT
1 TAGATTAAGTAAGGCTTAATCT
23793 TAGATTAAGTAAGGCTTAAT
1 TAGATTAAGTAAGGCTTAAT
23813 TAAGAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (22 bp):
TAGATTAAGTAAGGCTTAATCT
Found at i:24679 original size:37 final size:38
Alignment explanation
Indices: 24616--24693 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 38
24606 CTAGAAGTAC
24616 GCTCAATCGAGCCAAATTATACCGTTATACTAAATGAA
1 GCTCAATCGAGCCAAATTATACCGTTATACTAAATGAA
* * *
24654 GCTCAATCGAG-CAAATTATATCGTTATACTGAATGGA
1 GCTCAATCGAGCCAAATTATACCGTTATACTAAATGAA
24691 GCT
1 GCT
24694 TAACTAAGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 26 0.70
38 11 0.30
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (38 bp):
GCTCAATCGAGCCAAATTATACCGTTATACTAAATGAA
Found at i:24704 original size:37 final size:37
Alignment explanation
Indices: 24616--24770 Score: 116
Period size: 37 Copynumber: 4.2 Consensus size: 37
24606 CTAGAAGTAC
*
24616 GCTCAATCGAGCCAAATTATACCGTTATACTAAATGAA
1 GCTCAATCAAG-CAAATTATACCGTTATACTAAATGAA
* * * *
24654 GCTCAATCGAGCAAATTATATCGTTATACTGAATGGA
1 GCTCAATCAAGCAAATTATACCGTTATACTAAATGAA
* * * * * *
24691 GCTTAA-CTAAGCAAATCT-TACTGTTGTATTGAATGAT
1 GCTCAATC-AAGCAAAT-TATACCGTTATACTAAATGAA
* * ** * *
24728 GCTCAATCAAGAAAATTCTACTATTATACTGAGTGAA
1 GCTCAATCAAGCAAATTATACCGTTATACTAAATGAA
24765 GCTCAA
1 GCTCAA
24771 ATGAGTAGAA
Statistics
Matches: 95, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
36 2 0.02
37 80 0.84
38 13 0.14
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (37 bp):
GCTCAATCAAGCAAATTATACCGTTATACTAAATGAA
Found at i:27173 original size:104 final size:104
Alignment explanation
Indices: 27062--27272 Score: 395
Period size: 104 Copynumber: 2.0 Consensus size: 104
27052 AAATGTTATC
*
27062 TAACCATAATGATTTATTAGTAACATGAATTTATTATTTGTTATATTTAATATATGTTTTATTTA
1 TAACCATAATGATTTATTAGTAACATGAATTTATTATTTGTTATATTTAACATATGTTTTATTTA
27127 TACCTATTCACTTTATTATTATATGAATAAATAAAATTT
66 TACCTATTCACTTTATTATTATATGAATAAATAAAATTT
*
27166 TAACCATAATGATTTATTAGTAACATGAATTTATTATTTGTTATGTTTAACATATGTTTTATTTA
1 TAACCATAATGATTTATTAGTAACATGAATTTATTATTTGTTATATTTAACATATGTTTTATTTA
*
27231 TACCTATTCATTTTATTATTATATGAATAAATAAAATTT
66 TACCTATTCACTTTATTATTATATGAATAAATAAAATTT
27270 TAA
1 TAA
27273 AAGATCAGAA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (104 bp):
TAACCATAATGATTTATTAGTAACATGAATTTATTATTTGTTATATTTAACATATGTTTTATTTA
TACCTATTCACTTTATTATTATATGAATAAATAAAATTT
Found at i:36379 original size:29 final size:29
Alignment explanation
Indices: 36340--36418 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
36330 CTTAATAATC
*
36340 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
36370 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
36399 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
36419 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Done.