Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1672
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: 21290
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Found at i:1400 original size:40 final size:40
Alignment explanation
Indices: 1363--1447 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
1353 GCTACTCGTT
*
1363 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
1403 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
1443 CAAAT
1 CAAAT
1448 TTAGTAACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 40 0.95
41 2 0.05
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:1506 original size:39 final size:38
Alignment explanation
Indices: 1448--1565 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 38
1438 TCGCACAAAT
*
1448 TTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAA
1 TTAGT-ACTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
* *
1487 TTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG-A
1 TTAGTA-CTCGCACAAATGCCTTCGG-GCTTAGCCCGGAA
* *
1526 TATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 T-TAGT-AC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1566 CATCATTCGA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
38 1 0.02
39 25 0.38
40 30 0.46
41 9 0.14
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (38 bp):
TTAGTACTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
Found at i:2793 original size:55 final size:56
Alignment explanation
Indices: 2692--2810 Score: 231
Period size: 55 Copynumber: 2.1 Consensus size: 56
2682 TATTAGTTTA
2692 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
2748 TTGCCCATGCTTCTTATTTTATT-TTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
2803 TTGCCCAT
1 TTGCCCAT
2811 CATCCCTTGT
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:9308 original size:39 final size:40
Alignment explanation
Indices: 9234--9457 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
9224 GCTACTCGTT
*
9234 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
9274 CAAATGCCTTCGGGACTTA-CCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
9313 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
9353 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
9392 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
9433 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9458 CATCATTCGA
Statistics
Matches: 164, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 68 0.41
40 83 0.51
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:9337 original size:79 final size:80
Alignment explanation
Indices: 9234--9457 Score: 296
Period size: 79 Copynumber: 2.8 Consensus size: 80
9224 GCTACTCGTT
*
9234 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTA-CCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
9298 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* *
9313 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
9376 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
* * * * *
9392 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
9455 GGA
64 GGA
9458 CATCATTCGA
Statistics
Matches: 127, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
78 8 0.06
79 99 0.78
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:10652 original size:56 final size:56
Alignment explanation
Indices: 10585--10704 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
10575 TATTAGTTTA
10585 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
10641 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
10697 TTGCCCAT
1 TTGCCCAT
10705 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:12376 original size:46 final size:45
Alignment explanation
Indices: 12309--12479 Score: 213
Period size: 46 Copynumber: 3.7 Consensus size: 45
12299 AACCCGCCCC
*
12309 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCA
*
12355 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCA
* * * *
12403 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCA
12447 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
12480 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
42 5 0.05
43 1 0.01
44 3 0.03
45 28 0.26
46 32 0.30
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCA
Found at i:12472 original size:92 final size:93
Alignment explanation
Indices: 12314--12483 Score: 306
Period size: 92 Copynumber: 1.8 Consensus size: 93
12304 GCCCCTAAGT
* *
12314 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
12379 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
12407 GAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
12471 CGAGTTCGGATGC
66 CGAGTTCGGATGC
12484 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 44 0.59
93 30 0.41
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19900 original size:93 final size:93
Alignment explanation
Indices: 19790--19960 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
19780 GCCCCTAAGT
* *
19790 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
19855 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
19883 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
19948 CGAGTTCGGATGC
66 CGAGTTCGGATGC
19961 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19957 original size:46 final size:46
Alignment explanation
Indices: 19785--19957 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
19775 AACCCGCCCC
* * * *
19785 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
19831 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
19879 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
19924 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
19958 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Done.