Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4732.1
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: 46557
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:374 original size:57 final size:57
Alignment explanation
Indices: 312--426 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
302 ACAATGATTT
*
312 CCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGGTAATCAATGACAAG
1 CCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGGTAACCAATGACAAG
369 CCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGGTAACCAATGACAAG
1 CCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGGTAACCAATGACAAG
426 C
1 C
427 TCGTAATCTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (57 bp):
CCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGGTAACCAATGACAAG
Found at i:5430 original size:65 final size:64
Alignment explanation
Indices: 5355--5484 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 64
5345 AGTCCCATAC
5355 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACA-TCAAACATGCATTCAGGTCAACCTT
* *
5420 ATCAGATAATAATAACATGGCATGTAGTAAATAGTAACATCAAACATGCATTTAGGTCAACCTT
1 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACATCAAACATGCATTCAGGTCAACCTT
5484 A
1 A
5485 ACCCTAGGGG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 25 0.40
65 38 0.60
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (64 bp):
ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACATCAAACATGCATTCAGGTCAACCTT
Found at i:7335 original size:47 final size:47
Alignment explanation
Indices: 7271--7439 Score: 206
Period size: 47 Copynumber: 3.6 Consensus size: 47
7261 ATCCATAAGT
*
7271 GAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
* *
7318 GAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACATC-CATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACATCTC-T---C
*
7364 GAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
*
7411 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGCTCGGA
7440 CATTCACATC
Statistics
Matches: 103, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
42 3 0.03
43 7 0.07
44 1 0.01
46 27 0.26
47 54 0.52
49 1 0.01
50 7 0.07
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:7337 original size:93 final size:93
Alignment explanation
Indices: 7225--7488 Score: 483
Period size: 93 Copynumber: 2.8 Consensus size: 93
7215 GCCCATAAGT
* * * *
7225 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
7290 TGAGCTCGGATGCCTAGTTACATCTCTC
66 TGAGCTCGGATGCCTAGTTACATCTCTC
7318 GAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
7383 TGAGCTCGGATGCCTAGTTACATCTCTC
66 TGAGCTCGGATGCCTAGTTACATCTCTC
7411 GAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
7476 TGAGTTCGGATGC
66 TGAGCTCGGATGC
7489 TCAACCATCC
Statistics
Matches: 166, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 166 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
TGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:7485 original size:46 final size:46
Alignment explanation
Indices: 7217--7485 Score: 261
Period size: 46 Copynumber: 5.8 Consensus size: 46
7207 TGTAACCCGC
* * *
7217 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACAT
*
7263 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCACAT
* *
7313 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACAT
*
7356 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCACAT
* *
7406 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACAT
* *
7449 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
7486 TGCTCAACCA
Statistics
Matches: 186, Mismatches: 15, Indels: 44
0.76 0.06 0.18
Matches are distributed among these distances:
42 6 0.03
43 14 0.08
44 2 0.01
46 90 0.48
47 54 0.29
49 2 0.01
50 12 0.06
51 6 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACAT
Found at i:10342 original size:19 final size:18
Alignment explanation
Indices: 10305--10348 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
10295 ATACATACAG
10305 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
10322 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
10341 TACTAATT
1 TAATAATT
10349 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:14130 original size:32 final size:32
Alignment explanation
Indices: 14094--14160 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
14084 ACGGGCGTGC
*
14094 CCCACGGCCGTATGCCCCAAAATCTATATAAA
1 CCCACGCCCGTATGCCCCAAAATCTATATAAA
*
14126 CCCACGCCCGTGTGCCCCAAAATCTATATAAA
1 CCCACGCCCGTATGCCCCAAAATCTATATAAA
14158 CCC
1 CCC
14161 CTCACTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.39, G:0.12, T:0.18
Consensus pattern (32 bp):
CCCACGCCCGTATGCCCCAAAATCTATATAAA
Found at i:18333 original size:48 final size:48
Alignment explanation
Indices: 18261--18355 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
18251 TATGAACTAA
* ** * * *
18261 ACCCCCTAAATACCTAAGGGGAATGAAACCTAATACGGATCTTGTTAG
1 ACCCCCTAAATACCAAAGAAGAATGAAACCTAAGACAGATATTGTTAG
*
18309 ACCCCCTAAATACCAAAGAAGAATGAAATCTAAGACAGATATTGTTA
1 ACCCCCTAAATACCAAAGAAGAATGAAACCTAAGACAGATATTGTTA
18356 TTATTATCTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (48 bp):
ACCCCCTAAATACCAAAGAAGAATGAAACCTAAGACAGATATTGTTAG
Found at i:20994 original size:40 final size:40
Alignment explanation
Indices: 20964--21191 Score: 187
Period size: 40 Copynumber: 5.6 Consensus size: 40
20954 GCTACTCGTT
* **
20964 CAAATGCCTTCGGGTCATAGCCCGGTTATAGTAACCTACTCGTT
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGT-A---ACTCGCA
*
21008 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
* *
21048 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
* * * *
21088 CAAATGCCTTCGGG-CTTAGCCCAG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAACTCGCA
* * * * * *
21127 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAGCCCGGTTATAGTAAC-TCGCA
* *
21168 CAAA-GCCTTCGGCACTTAGCCCGG
1 CAAATGCCTTCGGGACATAGCCCGG
21192 ACATCATTCG
Statistics
Matches: 156, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 79 0.51
41 13 0.08
43 1 0.01
44 31 0.20
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
Found at i:21003 original size:44 final size:44
Alignment explanation
Indices: 20955--21082 Score: 167
Period size: 44 Copynumber: 3.0 Consensus size: 44
20945 CCGGATATAG
*
20955 CTACTCGTTCAAATGCCTTCGGGTCATAGCCCGGTTATAGTAAC
1 CTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAAC
20999 CTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAA-
1 CTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAAC
** * *
21042 -T--TCGCACAAATGCCTTCGGGACTTAACCCGGATT-TAGTAAC
1 CTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAC
21083 TCGCACAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
40 32 0.42
41 2 0.03
42 1 0.01
44 42 0.55
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (44 bp):
CTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAAC
Found at i:21152 original size:79 final size:80
Alignment explanation
Indices: 21008--21190 Score: 196
Period size: 79 Copynumber: 2.3 Consensus size: 80
20998 CCTACTCGTT
* **
21008 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
21073 ATTTAGTAAC-TCGCA
65 ATATAGTAACTTAGCA
**
21088 CAAATGCCTTCGGGCTTAGCCCAGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGCTTAGCCC-GAATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACCC
* *
21150 GGATATGGTCACTTAGCA
63 GGATATAGTAACTTAGCA
*
21168 CAAA-GCCTTCGGCACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCG
21191 GACATCATTC
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
78 5 0.06
79 51 0.58
80 32 0.36
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCA
Found at i:22427 original size:59 final size:56
Alignment explanation
Indices: 22322--22500 Score: 322
Period size: 56 Copynumber: 3.1 Consensus size: 56
22312 TATTAGTTTA
*
22322 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
22378 TTGCCCATGCTTCTTATTTTATTTTTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTA---TTTTTCCATTAACACAACATGTTTCATGACATGTT
22437 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
22493 TTGCCCAT
1 TTGCCCAT
22501 CATCCCTTGT
Statistics
Matches: 119, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
56 64 0.54
59 55 0.46
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:26315 original size:48 final size:48
Alignment explanation
Indices: 26244--26341 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
26234 AACTATGAAC
26244 TAAACCCCCTAAATACCTAAGGGGAATGAAACCTAAGACGGATCTTGT
1 TAAACCCCCTAAATACCTAAGGGGAATGAAACCTAAGACGGATCTTGT
*
26292 TAAACCCCCTAAATACCTAAGGGGAATGAAACCTAAGATGGATCTTGT
1 TAAACCCCCTAAATACCTAAGGGGAATGAAACCTAAGACGGATCTTGT
26340 TA
1 TA
26342 TTATTATCTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (48 bp):
TAAACCCCCTAAATACCTAAGGGGAATGAAACCTAAGACGGATCTTGT
Found at i:37380 original size:25 final size:24
Alignment explanation
Indices: 37293--37356 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
37283 AAGGCTATGC
** *
37293 GGCACTATGTGTGCGAGATTACAT
1 GGCACTATGTGTGCGAGAAAACGT
37317 GGCACTATGTGTGCGAGAAAACGT
1 GGCACTATGTGTGCGAGAAAACGT
37341 GGCACTATGTGTGCGA
1 GGCACTATGTGTGCGA
37357 ATAAGTAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (24 bp):
GGCACTATGTGTGCGAGAAAACGT
Found at i:39964 original size:40 final size:40
Alignment explanation
Indices: 39933--40063 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 40
39923 GGACTAAGAT
39933 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
39973 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* *
40013 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC
40053 CCGAAGGCATT
1 CCGAAGGCATT
40064 GTATGAGTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 81 0.99
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
Found at i:40084 original size:39 final size:38
Alignment explanation
Indices: 39933--40100 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 38
39923 GGACTAAGAT
* *
39933 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCA-TTGTGCGAGTTACTAA-ACCGGGTTAAGTC
* * *
39973 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGTTACTAA-ACCGGGTTAAGTC
*
40013 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATT-GTGCGAGTTACT-AAA-CCGGGTTAAGTC
** *
40053 CCGAAGGCATTGTATGAGTTACTATAACCGGGCTATA-TC
1 CCGAAGGCATTGTGCGAGTTACTA-AACCGGGTTA-AGTC
40092 CCGAAGGCA
1 CCGAAGGCA
40101 CTTGAACGAG
Statistics
Matches: 110, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
39 30 0.27
40 79 0.72
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (38 bp):
CCGAAGGCATTGTGCGAGTTACTAAACCGGGTTAAGTC
Done.