Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold542
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: 42118
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:530 original size:19 final size:19
Alignment explanation
Indices: 502--556 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
492 ACATACTATG
*
502 TTATATTATTTGATATTT-C
1 TTATAATATTT-ATATTTAC
521 TTATAATATTTAT-TTTAC
1 TTATAATATTTATATTTAC
*
539 TTATATATCTTTATATTT
1 TTATA-ATATTTATATTT
557 TATTATACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 3 0.10
18 8 0.26
19 17 0.55
20 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATAATATTTATATTTAC
Found at i:6078 original size:38 final size:37
Alignment explanation
Indices: 6013--6095 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 37
6003 ACCTTCATCG
* *
6013 TTTCTTCTCTCTTCTTCCATCCTCTTTTCTTCTTC-T
1 TTTCTTTTCTCTTCTTCCATCCTCTTTTCCTCTTCTT
6049 TTTCTTTTCTTCTTCTCTCCAT-CTACTTTTCCTCTTCTT
1 TTTCTTTTC-TCTTCT-TCCATCCT-CTTTTCCTCTTCTT
6088 TTTCTTTT
1 TTTCTTTT
6096 TTGCTCTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
36 8 0.20
37 8 0.20
38 16 0.39
39 9 0.22
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.64
Consensus pattern (37 bp):
TTTCTTTTCTCTTCTTCCATCCTCTTTTCCTCTTCTT
Found at i:7727 original size:27 final size:26
Alignment explanation
Indices: 7687--7798 Score: 98
Period size: 27 Copynumber: 4.2 Consensus size: 26
7677 GAGGAACGTC
7687 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCAC-ATTATCTGAT
* *
7714 CTGGTGGCTTTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAT-TATCTGAT
* * *
7741 CTAGTGGCTCTGCCACGATTATCTGCTT
1 CTGGTGGCTATGCCAC-ATTATCTG-AT
* * * * *
7769 TTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACATTATCTGAT
7795 CTGG
1 CTGG
7799 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.10
27 50 0.68
28 16 0.22
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTATGCCACATTATCTGAT
Found at i:7791 original size:54 final size:54
Alignment explanation
Indices: 7690--7796 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
7680 GAACGTCCTG
* *
7690 GTGGCTATGCCACAATTATCTGATCTGGTGGCTTTGCCACATATATCTGTTCTA
1 GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTA
* * * * *
7744 GTGGCTCTGCCACGATTATCTGCTTTTGGTGACTCTGTCACAT-TATCTGTTCT
1 GTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTTCT
7797 GGCAGCCATG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 30 0.67
55 15 0.33
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (54 bp):
GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTA
Found at i:11166 original size:38 final size:38
Alignment explanation
Indices: 11115--11280 Score: 262
Period size: 38 Copynumber: 4.3 Consensus size: 38
11105 ATGATTAAAT
*
11115 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCTGC
1 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
*
11153 AGGCTTAATGCTGGTATTATATCCGGGTTAAATCCCGC
1 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
11191 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
1 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
*
11229 AGGCTTAATGCTGGTATTATATTCGGGTTTATAGTTCCC-C
1 AGGCTTAATGCTGGTATTATATCCGGG-TTA-AG-TCCCGC
*
11269 AGGCTTTATGCT
1 AGGCTTAATGCT
11281 AGTAATTGGA
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
38 99 0.82
39 3 0.03
40 14 0.12
41 4 0.03
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (38 bp):
AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
Found at i:18768 original size:38 final size:38
Alignment explanation
Indices: 18717--18882 Score: 296
Period size: 38 Copynumber: 4.3 Consensus size: 38
18707 ATGATTAAAT
18717 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
1 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
*
18755 AGGCTTAATGCTGGTATTATATCCGGGTTAAATCCCGC
1 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
18793 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
1 AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
18831 AGGCTTAATGCTGGTATTATATCCGGGTTTAAAGTCCCGC
1 AGGCTTAATGCTGGTATTATATCCGGG-TT-AAGTCCCGC
*
18871 AGGCTTTATGCT
1 AGGCTTAATGCT
18883 AGTAATTGTA
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
38 101 0.82
39 2 0.02
40 20 0.16
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (38 bp):
AGGCTTAATGCTGGTATTATATCCGGGTTAAGTCCCGC
Found at i:19292 original size:46 final size:46
Alignment explanation
Indices: 19239--19332 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
19229 TTTTTTTTGT
19239 GACATGTTTTAACTATTTGAAATTGCTTAAACTTACTAAGCCTCGA
1 GACATGTTTTAACTATTTGAAATTGCTTAAACTTACTAAGCCTCGA
19285 GACATGTTTTAACTATTTGAAATTGCTTAAACTTACTAAGCCTCGA
1 GACATGTTTTAACTATTTGAAATTGCTTAAACTTACTAAGCCTCGA
19331 GA
1 GA
19333 GCTTACTCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (46 bp):
GACATGTTTTAACTATTTGAAATTGCTTAAACTTACTAAGCCTCGA
Found at i:26669 original size:21 final size:21
Alignment explanation
Indices: 26645--26689 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
26635 GATAATAGTA
26645 ATAGTAATAA-AAGTGAAAATG
1 ATAGTAATAATAAG-GAAAATG
*
26666 ATAGTAATAATAAGGACAATG
1 ATAGTAATAATAAGGAAAATG
26687 ATA
1 ATA
26690 TATAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.56, C:0.02, G:0.18, T:0.24
Consensus pattern (21 bp):
ATAGTAATAATAAGGAAAATG
Found at i:27151 original size:21 final size:20
Alignment explanation
Indices: 27117--27155 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
27107 TGTGTGTTAG
*
27117 AAAATGTATACATAATATATA
1 AAAATATATACAT-ATATATA
*
27138 AAAATATATGCATATATA
1 AAAATATATACATATATA
27156 GTATTTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATATATACATATATATA
Found at i:34441 original size:45 final size:46
Alignment explanation
Indices: 34377--34469 Score: 179
Period size: 45 Copynumber: 2.0 Consensus size: 46
34367 CAGAGTAAGC
34377 TCTCGAGGCTTAGTAAGTTTAAGCAA-TTCAAATAGTTAAAACATG
1 TCTCGAGGCTTAGTAAGTTTAAGCAATTTCAAATAGTTAAAACATG
34422 TCTCGAGGCTTAGTAAGTTTAAGCAATTTCAAATAGTTAAAACATG
1 TCTCGAGGCTTAGTAAGTTTAAGCAATTTCAAATAGTTAAAACATG
34468 TC
1 TC
34470 ACAAAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 26 0.55
46 21 0.45
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (46 bp):
TCTCGAGGCTTAGTAAGTTTAAGCAATTTCAAATAGTTAAAACATG
Found at i:34900 original size:38 final size:38
Alignment explanation
Indices: 34826--34991 Score: 287
Period size: 38 Copynumber: 4.3 Consensus size: 38
34816 TACAATTACT
*
34826 AGCATAAAGCCTGCGGGACTTTAAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGAC-TT-AACCCGGATATAATACC
*
34866 AGCATTAAGCCTGCGGAACTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
*
34904 AGCATTAAGCCTGCGGGATTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
34942 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
34980 AGCATTAAGCCT
1 AGCATTAAGCCT
34992 ATTTAATCAT
Statistics
Matches: 121, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
38 102 0.84
39 2 0.02
40 17 0.14
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (38 bp):
AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
Found at i:40287 original size:38 final size:38
Alignment explanation
Indices: 40214--40379 Score: 262
Period size: 38 Copynumber: 4.3 Consensus size: 38
40204 TCCAATTACT
* *
40214 AGCATAAAGCCTG-GGGAACTATAAACCCGAATATAATACC
1 AGCATTAAGCCTGCGGG-ACT-T-AACCCGGATATAATACC
40254 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
*
40292 AGCATTAAGCCTGCGGGATTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
*
40330 AGCATTAAGCCTGCAGGACTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
40368 AGCATTAAGCCT
1 AGCATTAAGCCT
40380 ATTTAATCAT
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
38 101 0.84
39 1 0.01
40 15 0.12
41 3 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (38 bp):
AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
Done.