Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1335
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: 39192
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:13802 original size:40 final size:40
Alignment explanation
Indices: 13728--13938 Score: 230
Period size: 40 Copynumber: 5.3 Consensus size: 40
13718 TCTTCGAGAT
** * *
13728 TTAG-CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * * *
13766 TTATCCCGGATATGGTCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* *
13806 TTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGGTA
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * * *
13846 TTAGCCTGGATATAG-CAACTCGCACAAATGCCTTCAGATC
1 TTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGTC
* * * *
13886 TTAGTCCGGATATAGTCACTAGCATAAAAGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
13926 TTAGCCCGGATAT
1 TTAGCCCGGATAT
13939 CATTCGAATA
Statistics
Matches: 140, Mismatches: 29, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
38 3 0.02
39 16 0.11
40 120 0.86
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
Found at i:15796 original size:40 final size:41
Alignment explanation
Indices: 15748--15932 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 41
15738 GCTACTCGTT
* *
15748 CAAATGCCTTCGGGACATAGCCCGG-TTATGGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCA
*
15788 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCA
* * *
15828 CCAATGCCTTCGGG-CTTAGCCAGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCA
* * *
15867 CAAATGCCTTC-GGATCTTAGTCCGGA-TATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTATAGTAAC-TCGCA
15908 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
15933 CATCATTCGA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 78 0.62
41 13 0.10
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCA
Found at i:15868 original size:79 final size:80
Alignment explanation
Indices: 15748--15928 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 80
15738 GCTACTCGTT
* *
15748 CAAATGCCTTCGGGACATAGCCCGG--TTATGGTAACTCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAA-GCCTTCGGGACTTAGCCAGGAATTA--GTAACTCGCACAAATGCCTTC-GGATCTTAACC
* *
15810 CGGATTTAGTAAC-TCGCA
62 CGGATATAGTAACTTAGCA
* **
15828 CCAATGCCTTCGGG-CTTAGCCAGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 -CAAAGCCTTCGGGACTTAGCCAGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
*
15892 ATATAGTCACTTAGCA
65 ATATAGTAACTTAGCA
15908 CAAAGCCTTCGGGACTTAGCC
1 CAAAGCCTTCGGGACTTAGCC
15929 CGGACATCAT
Statistics
Matches: 86, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
78 3 0.03
79 57 0.66
80 20 0.23
81 6 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCAGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:22316 original size:47 final size:47
Alignment explanation
Indices: 22198--22366 Score: 176
Period size: 46 Copynumber: 3.7 Consensus size: 47
22188 GGATGGTTGA
*
22198 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGAAT
* *
22246 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGAA-T
*
22289 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGAAT
* *
22338 -C-GCCGAGCTCGTTGAGTTGAGT-CGAGTTC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
22367 GCTTATGGGC
Statistics
Matches: 104, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 7 0.07
45 22 0.21
46 30 0.29
47 29 0.28
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGAAT
Found at i:29553 original size:119 final size:120
Alignment explanation
Indices: 29369--29593 Score: 305
Period size: 119 Copynumber: 1.9 Consensus size: 120
29359 GCTCCTCGTT
*
29369 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
29434 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
29489 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
29551 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
29594 CATCATTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
118 4 0.04
119 66 0.72
120 22 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:29593 original size:40 final size:40
Alignment explanation
Indices: 29369--29593 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
29359 GCTCCTCGTT
* *
29369 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
29409 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
29449 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
29489 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
29528 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
29569 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29594 CATCATTCAA
Statistics
Matches: 166, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 120 0.72
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:35707 original size:46 final size:46
Alignment explanation
Indices: 35657--35830 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 46
35647 GTTGAGCATC
35657 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
* * * *
35703 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TT
* *
35750 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
* * * *
35796 CGAGCTCATTGAGTTGAGTTCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
35831 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 58 0.55
47 28 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
Found at i:35811 original size:93 final size:93
Alignment explanation
Indices: 35652--35823 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
35642 GGATGGTTGA
* * *
35652 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAACTCATTGAGT
35717 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
35745 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAACTCATTGAGT
*
35810 TGAGTTCGAGTTCG
66 TGAGTCCGAGTTCG
35824 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.