Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3130
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: 14962
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Found at i:5710 original size:39 final size:37
Alignment explanation
Indices: 5643--5735 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
5633 ACCAGAATGG
* *
5643 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
5682 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
5719 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
5736 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:5930 original size:24 final size:26
Alignment explanation
Indices: 5879--5939 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 26
5869 ACATATATTC
5879 TCAATTCAATCACACTTTTTCACACTT
1 TCAATTCAAT-ACACTTTTTCACACTT
5906 TCAATTCAAT-CA-TTTTTC-CACCTT
1 TCAATTCAATACACTTTTTCACA-CTT
5930 TCAA-TCAATA
1 TCAATTCAATA
5940 ATTAATCCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.22
24 13 0.41
25 2 0.06
27 10 0.31
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (26 bp):
TCAATTCAATACACTTTTTCACACTT
Found at i:6132 original size:18 final size:18
Alignment explanation
Indices: 6090--6133 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
6080 ATTCCCACTC
*
6090 ATAATAATAATACTAATA
1 ATAATACTAATACTAATA
6108 ATAATACTAATACTAATA
1 ATAATACTAATACTAATA
*
6126 TTAATACT
1 ATAATACT
6134 TACCTCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATACTAATACTAATA
Found at i:6133 original size:12 final size:12
Alignment explanation
Indices: 6091--6131 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
6081 TTCCCACTCA
6091 TAATAATAATAC
1 TAATAATAATAC
6103 TAATAATAATAC
1 TAATAATAATAC
* *
6115 TAATACTAATAT
1 TAATAATAATAC
6127 TAATA
1 TAATA
6132 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:6855 original size:16 final size:16
Alignment explanation
Indices: 6836--6870 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6826 TTCTTTGTTC
6836 TTTCTATTCTGTTTCT
1 TTTCTATTCTGTTTCT
* *
6852 TTTCTGTTTTGTTTCT
1 TTTCTATTCTGTTTCT
6868 TTT
1 TTT
6871 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTCTATTCTGTTTCT
Found at i:6944 original size:28 final size:29
Alignment explanation
Indices: 6873--6936 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
6863 TTTCTTTTAT
*
6873 ATATAATAATATAATATTTATAATGTAATTA
1 ATATAATAATAT-A-CTTTATAATGTAATTA
* *
6904 ATTTAATAATATACTTTATAAT-TAATTT
1 ATATAATAATATACTTTATAATGTAATTA
6932 ATATA
1 ATATA
6937 TTTATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 9 0.31
29 8 0.28
30 1 0.03
31 11 0.38
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
ATATAATAATATACTTTATAATGTAATTA
Found at i:11893 original size:21 final size:21
Alignment explanation
Indices: 11851--11893 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
11841 TTCACTATAC
*
11851 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
11872 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
11893 A
1 A
11894 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:12998 original size:39 final size:37
Alignment explanation
Indices: 12931--13023 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
12921 ACCAGAATGG
* *
12931 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
12970 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
13007 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
13024 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:13218 original size:24 final size:26
Alignment explanation
Indices: 13167--13227 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 26
13157 ACATATATTC
13167 TCAATTCAATCACACTTTTTCACACTT
1 TCAATTCAAT-ACACTTTTTCACACTT
13194 TCAATTCAAT-CA-TTTTTC-CACCTT
1 TCAATTCAATACACTTTTTCACA-CTT
13218 TCAA-TCAATA
1 TCAATTCAATA
13228 ATTAATCCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.22
24 13 0.41
25 2 0.06
27 10 0.31
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (26 bp):
TCAATTCAATACACTTTTTCACACTT
Found at i:13419 original size:12 final size:12
Alignment explanation
Indices: 13378--13417 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
13368 TTCCCACTCA
13378 TAATAATAATAC
1 TAATAATAATAC
13390 TAATAAT-ATAC
1 TAATAATAATAC
* *
13401 TAATACTAATAT
1 TAATAATAATAC
13413 TAATA
1 TAATA
13418 CTTACCTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:14142 original size:16 final size:16
Alignment explanation
Indices: 14123--14157 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
14113 TTCTTTGTTC
14123 TTTCTATTCTGTTTCT
1 TTTCTATTCTGTTTCT
* *
14139 TTTCTGTTTTGTTTCT
1 TTTCTATTCTGTTTCT
14155 TTT
1 TTT
14158 TATATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTCTATTCTGTTTCT
Found at i:14228 original size:28 final size:28
Alignment explanation
Indices: 14156--14221 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
14146 TTTGTTTCTT
14156 TTTATATATAATATAAATTTATAATGTAA
1 TTTATATATAATAT-AATTTATAATGTAA
* * *
14185 TTAATTTAATAATATACTTTATAAT-TAA
1 TTTATAT-ATAATATAATTTATAATGTAA
14213 TTTATATAT
1 TTTATATAT
14222 TTATATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 2 0.06
28 8 0.26
29 14 0.45
30 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TTTATATATAATATAATTTATAATGTAA
Found at i:14234 original size:21 final size:20
Alignment explanation
Indices: 14196--14234 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
14186 TAATTTAATA
*
14196 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
14216 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
14235 ATAAAAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:14626 original size:23 final size:23
Alignment explanation
Indices: 14577--14626 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
14567 TCATGATTAT
* *
14577 TATTGTGTTTATTTTACTACTAT
1 TATTGTATTTATTTTACTACTAG
*
14600 TATTGTATTTATTATTAGTA-TAG
1 TATTGTATTTATT-TTACTACTAG
14623 TATT
1 TATT
14627 ATAATTACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.26, C:0.04, G:0.10, T:0.60
Consensus pattern (23 bp):
TATTGTATTTATTTTACTACTAG
Found at i:14862 original size:27 final size:29
Alignment explanation
Indices: 14809--14871 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
14799 GTGTATGTAT
* *
14809 TATATATATTTTTTAATACTATATTTATG
1 TATATATATATATTAATACTATATTTATG
*
14838 TATATATATATATTAAT-TTAT-TTTATG
1 TATATATATATATTAATACTATATTTATG
14865 TATATAT
1 TATATAT
14872 TTTAATATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 13 0.42
28 3 0.10
29 15 0.48
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
TATATATATATATTAATACTATATTTATG
Done.