Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1745
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: 29617
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:3051 original size:29 final size:29
Alignment explanation
Indices: 2985--3052 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
2975 AAAAATTTAA
*
2985 TTTT-AAATTTTTATAACTTTTTTTATGT
1 TTTTAAAATTTTTATAACTTTTTTTATAT
* * *
3013 TGTTATAATTTTTATGA-TTTTTTTAATAT
1 TTTTAAAATTTTTATAACTTTTTTT-ATAT
3042 TTTTAAAATTT
1 TTTTAAAATTT
3053 AAAAAAGACA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (29 bp):
TTTTAAAATTTTTATAACTTTTTTTATAT
Found at i:3390 original size:16 final size:15
Alignment explanation
Indices: 3365--3394 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3355 GTACCGTTTA
3365 AACTTAAATAAATCG
1 AACTTAAATAAATCG
3380 AACTCTAAATAAATC
1 AACT-TAAATAAATC
3395 TATTTAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.27
Consensus pattern (15 bp):
AACTTAAATAAATCG
Found at i:4639 original size:18 final size:17
Alignment explanation
Indices: 4618--4653 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
4608 TTTCTGTGTT
4618 TTTTTTTTCTGGTTCTTG
1 TTTTTTTTCTGGTT-TTG
4636 TTTTTTTTCTGGTTTTG
1 TTTTTTTTCTGGTTTTG
4653 T
1 T
4654 AATGGTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.00, C:0.08, G:0.17, T:0.75
Consensus pattern (17 bp):
TTTTTTTTCTGGTTTTG
Found at i:20591 original size:348 final size:351
Alignment explanation
Indices: 19931--20640 Score: 1210
Period size: 348 Copynumber: 2.0 Consensus size: 351
19921 TTCCAGTTTT
* *
19931 TCCGGCTACAGTTTCAGTTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
1 TCCGGCAACAGTTTCAGCTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
19996 TTGTTATAAATTCAGCCATGATCACATTACTGCAAGTAATATCATTTTCATATCATTTTTTACAA
66 TTGTTATAAATTCAGCCATGATCACATTACTGCAAG----ATCA---T-ATATCATTTTTTACAA
* * * *
20061 CGCCACCTAGGCTGAATCTGAAAAAAGTTATAGTGGTGGGCGAAAACTTCAGTTGTTAAGTCTAT
123 CGCCACCTAGGCTGAATCTGAAAAAAGTTACAGTGGTGGGCGAAAACTTCAATTGTTAACTCTAC
20126 GGAGAGCAAACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGG
188 GGAGAGCAAACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGG
*
20191 GTTTATATCTTGGGTAAGAAACTAGAAATGAATCAAGTGGGAACCTTTTTTTTTTTTAAATCAGA
253 GTTTATATCTTGGGTAAGAAACTAGAAATGAATCAAGTGGGAACCATTTTTTTTTTTAAATCAGA
20256 TTATAAGATTGTAAACAGATATAAACCTTCCATC
318 TTATAAGATTGTAAACAGATATAAACCTTCCATC
20290 TCCGGCAACAGTTTCAGCTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
1 TCCGGCAACAGTTTCAGCTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
*
20355 TTGTTATAACTTCAGCCATGATCACATTACTGCAAG-T-A-ATATCATTTTTTACAACGCCACCT
66 TTGTTATAAATTCAGCCATGATCACATTACTGCAAGATCATATATCATTTTTTACAACGCCACCT
* * *
20417 AGGCTGAATCTGAAAAAGGTTACAGTGGTGGGTGAAAACTTTAATTGTTAACTCTACGGAGAGCA
131 AGGCTGAATCTGAAAAAAGTTACAGTGGTGGGCGAAAACTTCAATTGTTAACTCTACGGAGAGCA
20482 AACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGGGTTTATAT
196 AACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGGGTTTATAT
*
20547 CTTGGGTAAGAAACTAGAAATGAATCAAGTTGGAACCATTTTTTTTTTTAAATCAGATTATAAGA
261 CTTGGGTAAGAAACTAGAAATGAATCAAGTGGGAACCATTTTTTTTTTTAAATCAGATTATAAGA
*
20612 TTGTAAACAGGTATAAACCTTCCATC
326 TTGTAAACAGATATAAACCTTCCATC
20638 TCC
1 TCC
20641 AGCAGAAGCC
Statistics
Matches: 338, Mismatches: 13, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
348 238 0.70
353 1 0.00
354 1 0.00
359 98 0.29
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (351 bp):
TCCGGCAACAGTTTCAGCTTCACCAGAACTACAAGACAAAAATAGAAAATAGAGGTCATCAATAA
TTGTTATAAATTCAGCCATGATCACATTACTGCAAGATCATATATCATTTTTTACAACGCCACCT
AGGCTGAATCTGAAAAAAGTTACAGTGGTGGGCGAAAACTTCAATTGTTAACTCTACGGAGAGCA
AACAACAGTGTAAAGTAATAGACTAAAGAACTATACATAAAAAGGCTATTCCATAGGGTTTATAT
CTTGGGTAAGAAACTAGAAATGAATCAAGTGGGAACCATTTTTTTTTTTAAATCAGATTATAAGA
TTGTAAACAGATATAAACCTTCCATC
Found at i:21410 original size:3 final size:3
Alignment explanation
Indices: 21402--21429 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
21392 AACGTTAAAT
21402 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
21430 AAAATACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:22780 original size:30 final size:30
Alignment explanation
Indices: 22744--22800 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
22734 GCTCCCCTAA
22744 ATTCGCCCCTGAA-TAGGATCTAGTTAATAG
1 ATTCGCCCCT-AACTAGGATCTAGTTAATAG
22774 ATTCGCCCCTAACTAGGATCTAGTTAA
1 ATTCGCCCCTAACTAGGATCTAGTTAA
22801 GCCATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (30 bp):
ATTCGCCCCTAACTAGGATCTAGTTAATAG
Found at i:28212 original size:9 final size:9
Alignment explanation
Indices: 28198--28225 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28188 TCACTTAGGC
28198 TAGCACATT
1 TAGCACATT
28207 TAGCACATT
1 TAGCACATT
28216 TAGCACATT
1 TAGCACATT
28225 T
1 T
28226 TTGTGCCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (9 bp):
TAGCACATT
Done.