Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3264
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: 45640
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1718 original size:39 final size:38
Alignment explanation
Indices: 1682--1862 Score: 177
Period size: 38 Copynumber: 4.6 Consensus size: 38
1672 GCTACTCGTT
*
1682 CAATGCCTTCGGGTCATAGCCCGG-TTATAGTAACTCGCA
1 CAATGCCTTCGGG-CTTAGCCCGGATT-TAGTAACTCGCA
*
1721 CAATGCCTTCGGGACTTA-ACCGGATTTAGTAACTCGCA
1 CAATGCCTTCGGG-CTTAGCCCGGATTTAGTAACTCGCA
* * *
1759 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
1797 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 C-AATGCCTTCGG-GCTTAGCCCGGATTTAGTAAC-TCGCA
*
1838 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAATGCCTTCGGG-CTTAGCCCGGA
1863 CATCATTCGA
Statistics
Matches: 117, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
37 4 0.03
38 45 0.38
39 29 0.25
40 34 0.29
41 5 0.04
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (38 bp):
CAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
Found at i:3078 original size:55 final size:56
Alignment explanation
Indices: 2977--3095 Score: 231
Period size: 55 Copynumber: 2.1 Consensus size: 56
2967 TATTAGTTTA
2977 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
3033 TTGCCCATGCTTCTTATTTTATT-TTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
3088 TTGCCCAT
1 TTGCCCAT
3096 CACCCTTGTC
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 40 0.63
56 23 0.37
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:8964 original size:79 final size:82
Alignment explanation
Indices: 8853--9037 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
8843 GCTACTCGTT
* *
8853 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
8916 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
8933 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
8996 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
9013 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9038 CATCATTCGA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:9037 original size:40 final size:40
Alignment explanation
Indices: 8834--9037 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
8824 CGGAATTTAA
** *
8834 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
8874 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
8914 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
8953 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
8993 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
9033 CCGGA
1 CCGGA
9038 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
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:10227 original size:56 final size:56
Alignment explanation
Indices: 10160--10279 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
10150 TATTAGTTTA
10160 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
10216 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
10272 TTGCCCAT
1 TTGCCCAT
10280 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:11901 original size:46 final size:44
Alignment explanation
Indices: 11803--11970 Score: 151
Period size: 46 Copynumber: 3.6 Consensus size: 44
11793 TATGAGAGCT
* * * *
11803 AGTGTAAGACTGTGTCTGGGACATGGCATCAGC-ATTGAGATGAGAGCT
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCTA-CGAGATGA-A-CC
* *
11851 AGTGTAAGACATGCCTAGGACATGCATCGGCCT-CGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATG-AA-CC
* * *
11897 AGTGTAAGACATGTTTGGGACATGCAGCGGCTACGAGATGCACC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAACC
11941 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
11971 TGTAACAGCC
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
44 11 0.11
45 16 0.16
46 52 0.51
47 12 0.12
48 10 0.10
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAACC
Found at i:13210 original size:43 final size:43
Alignment explanation
Indices: 13125--13248 Score: 171
Period size: 43 Copynumber: 2.9 Consensus size: 43
13115 TTGAATTTGA
* *
13125 GGCACTAAGTGTTCGATA-AATGAAATAG-CTACGGCTAATTAATT
1 GGCACTAAGTGTGCGATACAAT--TATAGCCT-CGGCTAATTAATT
*
13169 GGCACTAAGTGTGCGATACAATTATAGCCTGGGCTAATTAATT
1 GGCACTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATT
*
13212 GGTACTAAGTGTGCGATACAATTATAGCCTCGGCTAA
1 GGCACTAAGTGTGCGATACAATTATAGCCTCGGCTAA
13249 GTGTGCGATA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
43 51 0.70
44 19 0.26
45 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (43 bp):
GGCACTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATT
Found at i:13249 original size:29 final size:29
Alignment explanation
Indices: 13216--13277 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
13206 TTAATTGGTA
13216 CTAAGTGTGCGATACAATTATAGCCTCGG
1 CTAAGTGTGCGATACAATTATAGCCTCGG
*
13245 CTAAGTGTGCGATACAATTTTAGCCTCGG
1 CTAAGTGTGCGATACAATTATAGCCTCGG
13274 CTAA
1 CTAA
13278 TTAATTGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (29 bp):
CTAAGTGTGCGATACAATTATAGCCTCGG
Found at i:13291 original size:72 final size:72
Alignment explanation
Indices: 13173--13320 Score: 260
Period size: 72 Copynumber: 2.1 Consensus size: 72
13163 TTAATTGGCA
* * *
13173 CTAAGTGTGCGATACAATTATAGCCTGGGCTAATTAATTGGTACTAAGTGTGCGATACAATTATA
1 CTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATTGGCACTAAGTGTGCAATACAATTATA
13238 GCCTCGG
66 GCCTCGG
*
13245 CTAAGTGTGCGATACAATTTTAGCCTCGGCTAATTAATTGGCACTAAGTGTGCAATACAATTATA
1 CTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATTGGCACTAAGTGTGCAATACAATTATA
13310 GCCTCGG
66 GCCTCGG
13317 CTAA
1 CTAA
13321 TTAATTGGCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (72 bp):
CTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATTGGCACTAAGTGTGCAATACAATTATA
GCCTCGG
Found at i:13294 original size:43 final size:43
Alignment explanation
Indices: 13245--13386 Score: 194
Period size: 43 Copynumber: 3.3 Consensus size: 43
13235 ATAGCCTCGG
*
13245 CTAAGTGTGCGATACAATTTTAGCCTCGGCTAATTAATTGGCA
1 CTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATTGGCA
*
13288 CTAAGTGTGCAATACAATTATAGCCTCGGCTAATTAATTGGCA
1 CTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATTGGCA
* * * * ** *
13331 CTAATTGTGTGATACAATTCTAGCTTTAGCTAATTAATCGGCA
1 CTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATTGGCA
*
13374 CTACGTGTGCGAT
1 CTAAGTGTGCGAT
13387 TTCGTTGAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (43 bp):
CTAAGTGTGCGATACAATTATAGCCTCGGCTAATTAATTGGCA
Found at i:13363 original size:115 final size:115
Alignment explanation
Indices: 13156--13363 Score: 335
Period size: 115 Copynumber: 1.8 Consensus size: 115
13146 GAAATAGCTA
* * *
13156 CGGCTAATTAATTGGCACTAAGTGTGCGATACAATTATAGCCTGGGCTAATTAATTGGTACTAAG
1 CGGCTAATTAATTGGCACTAAGTGTGCAATACAATTATAGCCTCGGCTAATTAATTGGCACTAAG
*
13221 TGTGCGATACAATTATAGCCTCGGCTAAGTGTGCGATACAATTTTAGCCT
66 TGTGCGATACAATTATAGCCTCAGCTAAGTGTGCGATACAATTTTAGCCT
*
13271 CGGCTAATTAATTGGCACTAAGTGTGCAATACAATTATAGCCTCGGCTAATTAATTGGCACTAAT
1 CGGCTAATTAATTGGCACTAAGTGTGCAATACAATTATAGCCTCGGCTAATTAATTGGCACTAAG
* * * *
13336 TGTGTGATACAATTCTAGCTTTAGCTAA
66 TGTGCGATACAATTATAGCCTCAGCTAA
13364 TTAATCGGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 84 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (115 bp):
CGGCTAATTAATTGGCACTAAGTGTGCAATACAATTATAGCCTCGGCTAATTAATTGGCACTAAG
TGTGCGATACAATTATAGCCTCAGCTAAGTGTGCGATACAATTTTAGCCT
Found at i:17643 original size:30 final size:30
Alignment explanation
Indices: 17585--17645 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
17575 TTCCCCAGCC
*
17585 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATCCAAAAGTT
* * * *
17615 TAGGGGCAAAATTGTAATTTTCCCAAAGTT
1 TAGGGGCAAAAGTGTAAATATCCAAAAGTT
17645 T
1 T
17646 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATCCAAAAGTT
Found at i:20369 original size:20 final size:20
Alignment explanation
Indices: 20303--20369 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
20293 ATTTTAGTAA
* *
20303 ACATGGTATGTATGATATGT
1 ACATGATATGTATGATATGC
* * *
20323 ACATGACATGTTTGCTATGC
1 ACATGATATGTATGATATGC
20343 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
20363 ACATGAT
1 ACATGAT
20370 GTATTCATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:20450 original size:23 final size:23
Alignment explanation
Indices: 20420--20468 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
20410 AGGAAGGGCA
20420 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
20443 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
20466 AAA
1 AAA
20469 TAGAGGCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:28242 original size:33 final size:33
Alignment explanation
Indices: 28173--28270 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
28163 CTATACCCAT
* * *
28173 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
28210 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
28243 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
28271 ATACATATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:28589 original size:41 final size:41
Alignment explanation
Indices: 28487--28592 Score: 203
Period size: 41 Copynumber: 2.6 Consensus size: 41
28477 ACCGGCTCTT
*
28487 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28528 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
28569 AGCCTGCTAGACTTATAGTCTGAA
1 AGCCTGCTAGACTTATAGTCTGAA
28593 TAATTTCACT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:35834 original size:33 final size:33
Alignment explanation
Indices: 35765--35862 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
35755 CTATACCCAT
* * *
35765 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
35802 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
35835 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
35863 ACATATCTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:36179 original size:41 final size:41
Alignment explanation
Indices: 36077--36182 Score: 203
Period size: 41 Copynumber: 2.6 Consensus size: 41
36067 ACCGGCTCTT
*
36077 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
36118 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
36159 AGCCTGCTAGACTTATAGTCTGAA
1 AGCCTGCTAGACTTATAGTCTGAA
36183 TATTTCACTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:39548 original size:41 final size:41
Alignment explanation
Indices: 39457--39561 Score: 144
Period size: 42 Copynumber: 2.6 Consensus size: 41
39447 AGTGAAATTA
39457 TTCA-ACTATAAGTCTAGGGCAGGCTTAATGCCGGTGACACAT
1 TTCAGACTATAAGTCTA--GCAGGCTTAATGCCGGTGACACAT
39499 TTCAGACTATAATGTCTAGCAGGCTTAATGCC-GTGACACAT
1 TTCAGACTATAA-GTCTAGCAGGCTTAATGCCGGTGACACAT
**
39540 TTTGGACTAT-AGTCTAGCAGGC
1 TTCAGACTATAAGTCTAGCAGGC
39562 CTAAGAGCCG
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
39 11 0.19
40 1 0.02
41 17 0.29
42 18 0.31
43 7 0.12
44 5 0.08
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (41 bp):
TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
Done.