Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2311
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: 38636
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:189 original size:36 final size:35
Alignment explanation
Indices: 91--194 Score: 120
Period size: 35 Copynumber: 2.9 Consensus size: 35
81 AAAAGCAATC
*
91 TGAAGACTTAAAATTTCCATTAATAAAACC-AAAA
1 TGAAGACCTAAAATTTCCATTAATAAAACCAAAAA
* ** *
125 TCAAAGAAGTAAAATTTCCATGAATAAAACCAAAAA
1 T-GAAGACCTAAAATTTCCATTAATAAAACCAAAAA
*
161 TGAAGACCTAAATTTTCCATTAATTAAAAGCCAA
1 TGAAGACCTAAAATTTCCATTAA-TAAAA-CCAA
195 GTCAGACTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
34 1 0.02
35 42 0.74
36 10 0.18
37 4 0.07
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (35 bp):
TGAAGACCTAAAATTTCCATTAATAAAACCAAAAA
Found at i:4185 original size:8 final size:9
Alignment explanation
Indices: 4158--4186 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4148 ATCCTAGTTC
4158 AATTGTTAA
1 AATTGTTAA
4167 AATTGTTAA
1 AATTGTTAA
4176 AATT-TTAA
1 AATTGTTAA
4184 AAT
1 AAT
4187 AGTTTGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (9 bp):
AATTGTTAA
Found at i:9884 original size:3 final size:3
Alignment explanation
Indices: 9870--9963 Score: 109
Period size: 3 Copynumber: 31.7 Consensus size: 3
9860 TTAATATTTA
* *
9870 ATT ATT ACT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** * * *
9918 ATT ATT ATT ATT ACT GCT ACT ATT A-T ATT ATT AGT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9964 CAATTTATCT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:11782 original size:18 final size:19
Alignment explanation
Indices: 11744--11785 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11734 TTTGGGTTAA
*
11744 AAGTTTTTTTACACTGCAG
1 AAGTGTTTTTACACTGCAG
*
11763 AAGTGTTTTTCCACTG-AG
1 AAGTGTTTTTACACTGCAG
11781 AAGTG
1 AAGTG
11786 ATGAAGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (19 bp):
AAGTGTTTTTACACTGCAG
Found at i:11908 original size:12 final size:12
Alignment explanation
Indices: 11893--11921 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11883 AAAGGTACAT
11893 AAAAAATTTTAA
1 AAAAAATTTTAA
11905 AAAAAATTTTAA
1 AAAAAATTTTAA
11917 AAAAA
1 AAAAA
11922 GAGCATTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAAAATTTTAA
Found at i:12939 original size:17 final size:18
Alignment explanation
Indices: 12911--12945 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
12901 TATGCAAAAA
12911 AATTTCAAAGTAAATAAT
1 AATTTCAAAGTAAATAAT
12929 AATTT-AAAGTAAATAAT
1 AATTTCAAAGTAAATAAT
12946 TTATAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
AATTTCAAAGTAAATAAT
Found at i:13148 original size:24 final size:25
Alignment explanation
Indices: 13128--13215 Score: 72
Period size: 27 Copynumber: 3.5 Consensus size: 25
13118 TTAAAATGAC
13128 TAATATATAAAA-AATTTAAATAAA
1 TAATATATAAAACAATTTAAATAAA
* *
13152 TAGTATGTAAAACAATTTAAAATAAA
1 TAATATATAAAACAATTT-AAATAAA
* * * * *
13178 TGATAAATAAAAAAAACTTAAAACAAA
1 TAATATAT-AAAACAA-TTTAAATAAA
13205 TAATA-ATAAAA
1 TAATATATAAAA
13216 GAGTTTTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
24 10 0.20
25 9 0.18
26 13 0.26
27 16 0.32
28 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (25 bp):
TAATATATAAAACAATTTAAATAAA
Found at i:13178 original size:26 final size:25
Alignment explanation
Indices: 13117--13215 Score: 85
Period size: 24 Copynumber: 3.9 Consensus size: 25
13107 CATATAATGG
* *
13117 TTTAAAATGACTAATATATAAAAAA
1 TTTAAAATAAATAATATATAAAAAA
* *
13142 TTT-AAATAAATAGTATGTAAAACAA
1 TTTAAAATAAATAATATATAAAA-AA
* *
13167 TTTAAAATAAATGATAAATAAAAAAAA
1 TTTAAAATAAAT-A-ATATATAAAAAA
* *
13194 CTTAAAACAAATAATA-ATAAAA
1 TTTAAAATAAATAATATATAAAA
13216 GAGTTTTTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 9
0.73 0.15 0.11
Matches are distributed among these distances:
24 20 0.34
25 10 0.17
26 9 0.16
27 13 0.22
28 6 0.10
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (25 bp):
TTTAAAATAAATAATATATAAAAAA
Found at i:13184 original size:22 final size:22
Alignment explanation
Indices: 13129--13178 Score: 57
Period size: 26 Copynumber: 2.1 Consensus size: 22
13119 TAAAATGACT
13129 AATA-TATAAAAAATTTAAATA
1 AATAGTATAAAAAATTTAAATA
13150 AATAGTATGTAAAACAATTTAAAATA
1 AATAGTA--TAAAA-AATTT-AAATA
13176 AAT
1 AAT
13179 GATAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.17
22 2 0.08
24 5 0.21
25 5 0.21
26 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AATAGTATAAAAAATTTAAATA
Found at i:20777 original size:91 final size:91
Alignment explanation
Indices: 20622--20790 Score: 293
Period size: 91 Copynumber: 1.9 Consensus size: 91
20612 GGAGATGTCC
* * * *
20622 GGGGTGTTTCGATTTCAAATGTTTTCTGTAGACTGGTGATTGATTGGAGGCTTATCGTTGAGCTC
1 GGGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATCGATAGGAGGCTTATCGTTGAGCTC
*
20687 ACTTATGATGATGTATGATGTATGAA
66 ACTTATAATGATGTATGATGTATGAA
20713 GGGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATCGATAGGAGGCTTATCGTTGAGCTC
1 GGGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATCGATAGGAGGCTTATCGTTGAGCTC
20778 ACTTATAATGATG
66 ACTTATAATGATG
20791 GTACATTCGT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 73 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (91 bp):
GGGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATCGATAGGAGGCTTATCGTTGAGCTC
ACTTATAATGATGTATGATGTATGAA
Found at i:33127 original size:19 final size:21
Alignment explanation
Indices: 33103--33148 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
33093 ATTTTTATGA
33103 GATAAAAAAT-A-ATTATAAC
1 GATAAAAAATGATATTATAAC
33122 GATAAAAAATGATATTATAA-
1 GATAAAAAATGATATTATAAC
33142 G-TAAAAA
1 GATAAAAA
33149 TACATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 16 0.64
20 2 0.08
21 7 0.28
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (21 bp):
GATAAAAAATGATATTATAAC
Found at i:33138 original size:21 final size:18
Alignment explanation
Indices: 33097--33148 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
33087 TATTGAATTT
*
33097 TTATGAGATAAAAAATAA
1 TTATAAGATAAAAAATAA
33115 TTATAACGATAAAAAATGATA
1 TTATAA-GATAAAAAAT-A-A
33136 TTATAAG-TAAAAA
1 TTATAAGATAAAAA
33149 TACATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 16 0.53
20 2 0.07
21 7 0.23
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (18 bp):
TTATAAGATAAAAAATAA
Found at i:37802 original size:18 final size:19
Alignment explanation
Indices: 37775--37816 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
37765 TTTGGGTTAA
37775 AAGTGTTTTTACACTGCAG
1 AAGTGTTTTTACACTGCAG
*
37794 AAGTG-TTTTCCACTGCAG
1 AAGTGTTTTTACACTGCAG
37812 AAGTG
1 AAGTG
37817 ATGAACAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (19 bp):
AAGTGTTTTTACACTGCAG
Found at i:37988 original size:31 final size:32
Alignment explanation
Indices: 37945--38019 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
37935 AATTTATATT
37945 TTATATATTATTATATTAAATTGTTT-AAATC
1 TTATATATTATTATATTAAATTGTTTCAAATC
* * * *
37976 TTATTTATTATTATATTTAATTTTTTCAAATAT
1 TTATATATTATTATATTAAATTGTTTCAAAT-C
38009 TTATATATTAT
1 TTATATATTAT
38020 CAATTTTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 23 0.62
32 4 0.11
33 10 0.27
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (32 bp):
TTATATATTATTATATTAAATTGTTTCAAATC
Found at i:38158 original size:20 final size:20
Alignment explanation
Indices: 38133--38175 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
38123 TTGAAAAAAA
38133 ATATTATCAATTCCACTGAT
1 ATATTATCAATTCCACTGAT
38153 ATATTATCAATTCCACTGAT
1 ATATTATCAATTCCACTGAT
38173 ATA
1 ATA
38176 AAGCTCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATTATCAATTCCACTGAT
Done.