Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1335
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: 32559
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Found at i:7778 original size:40 final size:40
Alignment explanation
Indices: 7678--7942 Score: 263
Period size: 40 Copynumber: 6.7 Consensus size: 40
7668 GCTCCTCGTT
* * * * *
7678 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* ** *
7718 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* *
7757 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* *
7797 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTATCTCGCA
*
7837 CAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTATCTCGCA
** * * *
7877 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-ATC-TCGCA
*
7918 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
7943 CAGCATTCAA
Statistics
Matches: 196, Mismatches: 22, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
39 39 0.20
40 141 0.72
41 16 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
Found at i:7951 original size:41 final size:41
Alignment explanation
Indices: 7874--7951 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
7864 TTTGTATCTC
* * *
7874 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
7915 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
7952 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:17586 original size:40 final size:40
Alignment explanation
Indices: 17524--17781 Score: 378
Period size: 40 Copynumber: 6.5 Consensus size: 40
17514 AAGCCAAGTA
* * *
17524 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACGAATG
*
17563 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
17603 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
17643 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* *
17683 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* * * * *
17723 CCTTCGGGACTTAGCCC-GAAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACGAATG
17763 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
17782 TTATCATCCA
Statistics
Matches: 203, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 15 0.07
40 187 0.92
41 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
Found at i:25759 original size:40 final size:40
Alignment explanation
Indices: 25682--25898 Score: 287
Period size: 40 Copynumber: 5.5 Consensus size: 40
25672 AAGCCAAGTA
* * * *
25682 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACGAATG
* *
25721 CCTTCGGGACATAGCCCAGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
*
25761 CCTTCGGGACTTAGCCCGGATATAGTAACTCTCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
*
25801 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* * * *
25841 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACGAATG
25881 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
25899 ATTATCATCC
Statistics
Matches: 161, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 13 0.08
40 148 0.92
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
Found at i:29563 original size:52 final size:52
Alignment explanation
Indices: 29506--29683 Score: 155
Period size: 52 Copynumber: 3.4 Consensus size: 52
29496 ATGTCTTGAC
* * *
29506 TGGTCTTACGTGGTATCCTTG-CTTATG-AACTCACCATTGTCATGCCTTGGCA
1 TGGTCTTACATGGTATCCTTGCCTTATGAAAATTACCA-TG-CATGCCTTGGCA
* * * ** * * *
29558 TGGTCTTACATGGGATCTTTGCCTTATCGTAGTTTATCATGCCATGTCTTGACA
1 TGGTCTTACATGGTATCCTTGCCTTAT-GAAAATTACCATG-CATGCCTTGGCA
* * *
29612 TGGTCTTACATGATTTCC-TGCCTTGTGAAAATTACCAATGCATGCCTTGGCA
1 TGGTCTTACATGGTATCCTTGCCTTATGAAAATTACC-ATGCATGCCTTGGCA
*
29664 TGGTCTTACTTGGTATCCTT
1 TGGTCTTACATGGTATCCTT
29684 AAACCCTAAT
Statistics
Matches: 97, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
52 49 0.51
53 16 0.16
54 27 0.28
55 5 0.05
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (52 bp):
TGGTCTTACATGGTATCCTTGCCTTATGAAAATTACCATGCATGCCTTGGCA
Found at i:31437 original size:44 final size:44
Alignment explanation
Indices: 31385--31528 Score: 148
Period size: 44 Copynumber: 3.3 Consensus size: 44
31375 TATCCTAGAT
* ** * * *
31385 ATGGTCTTACATGTTATCACATATCGATGCCGAT-GTCCCAGGC
1 ATGGTCTTACACGAAATCACATAACGATGCCAATGGTCCCAGAC
*
31428 ATGGTTCTTACACGAAATCTCATAACGATGCCAATGGTCCCAGAC
1 ATGG-TCTTACACGAAATCACATAACGATGCCAATGGTCCCAGAC
* * * *
31473 ATGGTCTTATACGAAATCACAAATATGATGCCAAT-GTTCCAGAC
1 ATGGTCTTACACGAAATCACATA-ACGATGCCAATGGTCCCAGAC
*
31517 ATGGTTTTACAC
1 ATGGTCTTACAC
31529 ACAATCTCAT
Statistics
Matches: 84, Mismatches: 14, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
43 4 0.05
44 58 0.69
45 22 0.26
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
ATGGTCTTACACGAAATCACATAACGATGCCAATGGTCCCAGAC
Done.