Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1591
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: 27108
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:5508 original size:79 final size:78
Alignment explanation
Indices: 5406--5628 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 78
5396 GCTCCTCGTT
* *
5406 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
5471 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
5486 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
5549 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
5564 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
5627 GA
63 GA
5629 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:5523 original size:39 final size:40
Alignment explanation
Indices: 5406--5628 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
5396 GCTCCTCGTT
* *
5406 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
5446 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
5486 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
5525 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
5564 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
5605 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5629 CATCATTCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:13758 original size:22 final size:22
Alignment explanation
Indices: 13730--13775 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13720 TTCGACAAAT
13730 AATTCTGAAGCTCCCTAATTAC
1 AATTCTGAAGCTCCCTAATTAC
13752 AATTCTGAAGCTCCCTAATTAC
1 AATTCTGAAGCTCCCTAATTAC
13774 AA
1 AA
13776 CTACCTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (22 bp):
AATTCTGAAGCTCCCTAATTAC
Found at i:16736 original size:40 final size:40
Alignment explanation
Indices: 16654--16874 Score: 191
Period size: 40 Copynumber: 5.5 Consensus size: 40
16644 CTCAAGAAAT
* *
16654 CTTCGGGAT-TTAG-CCGGATATAA-CTACTTGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAATC-ACTAGCACAAATGC
* ** *
16692 CTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCACAAATGC
* *
16732 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCACAAATGC
* * * *
16772 CTTCGGGTCTTAGCCCGAATAT-AGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCACAAATGC
* * * * * *
16812 CTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGA
1 CTTCGGGTCTTAGCCCGGATATAATCA-CTAGCACAAATGC
* *
16853 CTTCGGGACTTATCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
16875 CATTCGAATA
Statistics
Matches: 143, Mismatches: 33, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
37 1 0.01
38 11 0.08
39 15 0.10
40 89 0.62
41 27 0.19
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAATCACTAGCACAAATGC
Found at i:19779 original size:46 final size:46
Alignment explanation
Indices: 19729--19997 Score: 284
Period size: 46 Copynumber: 5.8 Consensus size: 46
19719 TGGTTGAGCA
19729 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
19775 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
19820 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
19868 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
19913 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
19961 CCCGAGCTCGTTGAGTTGAGTCCAAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19998 GCGGGTTACA
Statistics
Matches: 186, Mismatches: 19, Indels: 36
0.77 0.08 0.15
Matches are distributed among these distances:
42 4 0.02
43 10 0.05
45 6 0.03
46 90 0.48
47 57 0.31
48 6 0.03
50 9 0.05
51 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:19885 original size:93 final size:93
Alignment explanation
Indices: 19726--19990 Score: 485
Period size: 93 Copynumber: 2.8 Consensus size: 93
19716 GGATGGTTGA
19726 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
19791 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
19819 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
19884 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
19912 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
*
19977 TGAGTCCAAGTTCG
66 TGAGTCCGAGTTCG
19991 CTTATGGGCG
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 167 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.