Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1112
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: 26296
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:4800 original size:40 final size:40
Alignment explanation
Indices: 4763--4845 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
4753 GCTACTCGTT
*
4763 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
4803 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
4843 CAA
1 CAA
4846 CCCATTAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:4903 original size:39 final size:40
Alignment explanation
Indices: 4849--4927 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
4839 CGCACAACCC
*
4849 ATTAGTAACTCGCACAAATGCCTTCG-GGCTTAGTCCGGA
1 ATTAGTAACTCGCACAAATGCCTTCGAAGCTTAGTCCGGA
* *
4888 ATTAGTATCTCGCACAAATGCCTTCGAATCTTAGTCCGGA
1 ATTAGTAACTCGCACAAATGCCTTCGAAGCTTAGTCCGGA
4928 TATGGTCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 25 0.69
40 11 0.31
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (40 bp):
ATTAGTAACTCGCACAAATGCCTTCGAAGCTTAGTCCGGA
Found at i:4961 original size:40 final size:40
Alignment explanation
Indices: 4849--4967 Score: 113
Period size: 40 Copynumber: 3.0 Consensus size: 40
4839 CGCACAACCC
* *
4849 ATTAGTAACTCGCACAAATGCCTTCGGG-CTTAGTCCGGA
1 ATTAGTATCTAGCACAAATGCCTTCGGGACTTAGTCCGGA
* *
4888 ATTAGTATCTCGCACAAATGCCTTC-GAATCTTAGTCCGG-
1 ATTAGTATCTAGCACAAATGCCTTCGGGA-CTTAGTCCGGA
* *
4927 ATATGGTCA-CTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AT-TAGT-ATC-TAGCACAAATGCCTTCGGGACTTAGTCCGGA
4968 CATCATTCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
38 1 0.01
39 26 0.39
40 29 0.43
41 11 0.16
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
ATTAGTATCTAGCACAAATGCCTTCGGGACTTAGTCCGGA
Found at i:8516 original size:39 final size:40
Alignment explanation
Indices: 8300--8516 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
8290 TATTCGAATG
8300 ATATCCGGGCTAAGTCCCGAA--CA-TTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
8337 ATAT-CGGGCTAAGTCCC-AAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
8375 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
8415 AAATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
8455 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
8495 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
8517 TACTTGGGTT
Statistics
Matches: 166, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
35 2 0.01
36 13 0.08
37 6 0.04
38 17 0.10
39 27 0.16
40 99 0.60
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:16785 original size:40 final size:40
Alignment explanation
Indices: 16700--16920 Score: 340
Period size: 40 Copynumber: 5.6 Consensus size: 40
16690 TATTCGAATG
16700 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
16739 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
16779 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * *
16819 AAATACAGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
16859 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
16899 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
16921 TACTTGGGTT
Statistics
Matches: 168, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 39 0.23
40 127 0.76
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:25217 original size:39 final size:40
Alignment explanation
Indices: 25163--25381 Score: 358
Period size: 39 Copynumber: 5.6 Consensus size: 40
25153 TATTCGAATG
25163 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
25202 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
25242 A-ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
25281 A-ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
25320 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
25360 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
25382 TACTTGGGTT
Statistics
Matches: 171, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
39 116 0.68
40 53 0.31
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:25294 original size:78 final size:80
Alignment explanation
Indices: 25163--25381 Score: 358
Period size: 79 Copynumber: 2.8 Consensus size: 80
25153 TATTCGAATG
25163 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
25227 TTTGTGCTAGTGACT
66 TTTGTGCTAGTGACT
*
25242 A-ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATCCGGGCTAAGTCCCGAAGGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
25305 TTTGTGCTAGTGACT
66 TTTGTGCTAGTGACT
* * *
25320 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGG
25382 TACTTGGGTT
Statistics
Matches: 132, Mismatches: 4, Indels: 8
0.92 0.03 0.06
Matches are distributed among these distances:
78 61 0.46
79 65 0.49
80 6 0.05
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCTAGTGACT
Found at i:25377 original size:118 final size:117
Alignment explanation
Indices: 25165--25381 Score: 357
Period size: 118 Copynumber: 1.8 Consensus size: 117
25155 TTCGAATGAT
*
25165 ATCCGGGCTAAGTCCCGAAGGCATTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTT
1 ATCCGGGCTAAGTCCCGAAGGCATTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATTT
* *
25230 GTGCTAGTGACTAATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA
66 GTGCGAGTGACTAATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACTA
*
25282 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGC-ATTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATT
25347 TGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAGG
65 TGTGCGAG-TGACTA-ATCCGGGCTAAATCCCGAAGG
25382 TACTTGGGTT
Statistics
Matches: 93, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
117 22 0.24
118 65 0.70
119 6 0.06
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (117 bp):
ATCCGGGCTAAGTCCCGAAGGCATTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGTGACTAATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACTA
Done.