Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold586
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: 37018
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:5612 original size:26 final size:27
Alignment explanation
Indices: 5557--5634 Score: 95
Period size: 26 Copynumber: 2.9 Consensus size: 27
5547 GTGACAGAGT
** *
5557 CACCAGATACAGATATTTTTGGCAGTGC
1 CACCAGA-ACAGATATTAGTGGCAGGGC
5585 CACCAGAACAGATA-TAGTGGCAGGGC
1 CACCAGAACAGATATTAGTGGCAGGGC
*
5611 CACCAGAACAGATAATTTGTGGCA
1 CACCAGAACAGAT-ATTAGTGGCA
5635 TAGCCACCGA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 22 0.50
27 8 0.18
28 14 0.32
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (27 bp):
CACCAGAACAGATATTAGTGGCAGGGC
Found at i:5641 original size:28 final size:26
Alignment explanation
Indices: 5557--5646 Score: 94
Period size: 26 Copynumber: 3.3 Consensus size: 26
5547 GTGACAGAGT
*
5557 CACCAGATACAGATATTTTTGGCAGTGC
1 CACCAGA-ACAGATATTTGTGGCA-TGC
* *
5585 CACCAGAACAGATA-TAGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCA-TGC
5611 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGAT-ATTTGTGGCAT-GC
5639 CACC-GAAC
1 CACCAGAAC
5647 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
26 22 0.41
27 12 0.22
28 20 0.37
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.19
Consensus pattern (26 bp):
CACCAGAACAGATATTTGTGGCATGC
Found at i:5807 original size:27 final size:30
Alignment explanation
Indices: 5756--5837 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 30
5746 TAACCCTGGG
*
5756 ATATAA-GGTCATTTTGCATACATAGGGGT
1 ATATAATGGTAATTTTGCATACATAGGGGT
5785 AT-TAATGG-AATTTTGC-TACATA-GGGT
1 ATATAATGGTAATTTTGCATACATAGGGGT
*
5811 TTATAATGGTAA-TTTGCATACATAGGG
1 ATATAATGGTAATTTTGCATACATAGGG
5838 TACTCTAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
26 5 0.11
27 17 0.37
28 18 0.39
29 6 0.13
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.37
Consensus pattern (30 bp):
ATATAATGGTAATTTTGCATACATAGGGGT
Found at i:13419 original size:27 final size:27
Alignment explanation
Indices: 13367--13456 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
13357 GTGACAGAGT
13367 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
13396 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
13423 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
13451 CACCAG
1 CACCAG
13457 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:13650 original size:28 final size:27
Alignment explanation
Indices: 13563--13651 Score: 142
Period size: 27 Copynumber: 3.2 Consensus size: 27
13553 AATTAACCCT
* *
13563 GGGGTATAAAGGTCATTTGCATACATA
1 GGGGTATAATGGTAATTTGCATACATA
13590 GGGGTATAATGGTAATTTGCATACATA
1 GGGGTATAATGGTAATTTGCATACATA
13617 GGGGGTATAATGGTAATTTTGCATACATA
1 -GGGGTATAATGGTAA-TTTGCATACATA
13646 GGGGTA
1 GGGGTA
13652 CTCTAGTACA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
27 25 0.43
28 21 0.36
29 12 0.21
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.31
Consensus pattern (27 bp):
GGGGTATAATGGTAATTTGCATACATA
Found at i:17314 original size:17 final size:17
Alignment explanation
Indices: 17292--17338 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
17282 GTAGTCTTTT
17292 TTATGTTATATGCAAAC
1 TTATGTTATATGCAAAC
*
17309 TTATGTTGTTATGCAAAC
1 TTATGTT-ATATGCAAAC
* *
17327 CTATGCTATATG
1 TTATGTTATATG
17339 TGAACCCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (17 bp):
TTATGTTATATGCAAAC
Found at i:21655 original size:22 final size:22
Alignment explanation
Indices: 21627--21670 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
21617 ATGTACATGC
21627 CACAATTCTGAGCTTAATCAAG
1 CACAATTCTGAGCTTAATCAAG
21649 CACAATTCTGAGCTTAATCAAG
1 CACAATTCTGAGCTTAATCAAG
21671 AAAAAGTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (22 bp):
CACAATTCTGAGCTTAATCAAG
Found at i:25660 original size:27 final size:28
Alignment explanation
Indices: 25630--25697 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 28
25620 ATATTAAGTC
*
25630 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
25657 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
25685 CGCACACTTAGTG
1 CGCACACTTAGTG
25698 ATGAACAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:29751 original size:9 final size:9
Alignment explanation
Indices: 29739--29795 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
29729 TTTGATAAAC
29739 ATGATATGT
1 ATGATATGT
*
29748 ATGATATGCAC
1 ATGATATG--T
*
29759 ATGACATGT
1 ATGATATGT
*
29768 ATGATATGCAC
1 ATGATATG--T
29779 ATGATATGT
1 ATGATATGT
29788 ATGATATG
1 ATGATATG
29796 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:29762 original size:20 final size:20
Alignment explanation
Indices: 29737--29799 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
29727 ATTTTGATAA
29737 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
29757 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
29777 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
29797 ACA
1 ACA
29800 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:29967 original size:25 final size:24
Alignment explanation
Indices: 29856--29971 Score: 148
Period size: 23 Copynumber: 4.8 Consensus size: 24
29846 AAGTGCAAAT
29856 GGGCTTATGCCCCAGTTATTAAAA
1 GGGCTTATGCCCCAGTTATTAAAA
29880 GGGCTTATGCCCCAGTTATT-AAA
1 GGGCTTATGCCCCAGTTATTAAAA
* *
29903 GGGCTTATGCCCTAGTTTTTAAAAAA
1 GGGCTTATGCCCCAGTTATT--AAAA
29929 GGGCTT-TGCCCCAGTTATTAAAA
1 GGGCTTATGCCCCAGTTATTAAAA
*
29952 GAGGC-TAGGCCTCCAGTTAT
1 G-GGCTTATGCC-CCAGTTAT
29972 ATGATAAAGC
Statistics
Matches: 81, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
23 27 0.33
24 26 0.32
25 19 0.23
26 9 0.11
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (24 bp):
GGGCTTATGCCCCAGTTATTAAAA
Found at i:30202 original size:31 final size:31
Alignment explanation
Indices: 30164--30227 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
30154 CGTTTACCGT
30164 AAAGGCTTCGGCCCAGTAATATGAAGTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAGTATGA
* ** *
30195 AAAGGCTTTGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAGTATGA
30226 AA
1 AA
30228 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAGTATGA
Done.