Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold22
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: 1926927
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.27
Warning! 314813 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:1890891 original size:13 final size:13
Alignment explanation
Indices: 1890873--1890937 Score: 85
Period size: 13 Copynumber: 5.0 Consensus size: 13
1890863 AAAACTCAGA
1890873 TGTATCGATACAT
1 TGTATCGATACAT
** *
1890886 TGTATCGACGCAA
1 TGTATCGATACAT
1890899 TGTATCGATACAT
1 TGTATCGATACAT
* *
1890912 TGTATCGATGCAA
1 TGTATCGATACAT
1890925 TGTATCGATACAT
1 TGTATCGATACAT
1890938 GGGTTACTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1890908 original size:26 final size:26
Alignment explanation
Indices: 1890872--1890937 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
1890862 AAAAACTCAG
1890872 ATGTATCGATACATTGTATCGACGCA
1 ATGTATCGATACATTGTATCGACGCA
*
1890898 ATGTATCGATACATTGTATCGATGCA
1 ATGTATCGATACATTGTATCGACGCA
1890924 ATGTATCGATACAT
1 ATGTATCGATACAT
1890938 GGGTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (26 bp):
ATGTATCGATACATTGTATCGACGCA
Found at i:1893356 original size:13 final size:13
Alignment explanation
Indices: 1893338--1893364 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1893328 ACATTATGCT
1893338 TTGTATCGATACA
1 TTGTATCGATACA
1893351 TTGTATCGATACA
1 TTGTATCGATACA
1893364 T
1 T
1893365 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1900871 original size:20 final size:20
Alignment explanation
Indices: 1900842--1900880 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1900832 AAAGCCAAAA
1900842 ACCTAAAAGTATCGATACAG
1 ACCTAAAAGTATCGATACAG
*
1900862 ACCTAGAAGTATCGATACA
1 ACCTAAAAGTATCGATACA
1900881 TATTGCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (20 bp):
ACCTAAAAGTATCGATACAG
Found at i:1900931 original size:32 final size:33
Alignment explanation
Indices: 1900872--1900933 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1900862 ACCTAGAAGT
*
1900872 ATCGATACATATTGCTTTGTATCGATACACTGC
1 ATCGATACATATTGCTTGGTATCGATACACTGC
1900905 ATCGATACATGA-T-CTTGGTATCGATACAC
1 ATCGATACAT-ATTGCTTGGTATCGATACAC
1900934 AGCAAATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 15 0.56
33 11 0.41
34 1 0.04
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (33 bp):
ATCGATACATATTGCTTGGTATCGATACACTGC
Found at i:1902979 original size:21 final size:19
Alignment explanation
Indices: 1902937--1902989 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
1902927 TTTTAAAAAA
*
1902937 TTCATTTATTTTCATAAGTTT
1 TTCATTT-TTTTCATAA-ATT
*
1902958 TTCATTTTTTTCTTTAAATT
1 TTCATTTTTTTC-ATAAATT
*
1902978 TTCCTTTTTTTC
1 TTCATTTTTTTC
1902990 GAAAAATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (19 bp):
TTCATTTTTTTCATAAATT
Found at i:1903227 original size:156 final size:159
Alignment explanation
Indices: 1902937--1903232 Score: 393
Period size: 156 Copynumber: 1.9 Consensus size: 159
1902927 TTTTAAAAAA
* * * *
1902937 TTCATTTATTTTCATAAGTTTTTCATTTTTTTCTTTAAATTTTCCTTTTTTTCGAAAAATCAAGT
1 TTCATTTATTTTCATAAGTTTTTCA-TTTTTTCTTGAAA-TTCCCTATATTTCGAAAAATCAAGT
*
1903002 TTTCTAGTCCATAAATATTTTCGAAGGGATTTTTCTCGACTTAAAATCTTTAAAATTCATCCAAC
64 TCTCTAGTCCATAAATATTTTCGAAGGGATTTTTCTCGACTTAAAATCTTTAAAATTCATCCAAC
1903067 ATTGTCATTAGACTCCCTGTAAACCAATTTG
129 ATTGTCATTAGACTCCCTGTAAACCAATTTG
*
1903098 TTCATTTATTTTCATAAGTTTTTCA-TTTTT-TTGAAA-TCCCTATATTTCTGAAAAATCGAGTT
1 TTCATTTATTTTCATAAGTTTTTCATTTTTTCTTGAAATTCCCTATATTTC-GAAAAATCAAGTT
* * * * ** * * * *
1903160 CTCTATTCCATAAATGTTTTCG-GGGGATTTTTCTTGGTTTAAAATTTTTAAGATTCATCTAATA
65 CTCTAGTCCATAAATATTTTCGAAGGGATTTTTCTCGACTTAAAATCTTTAAAATTCATCCAACA
1903224 TTGTCATTA
130 TTGTCATTA
1903233 AATTCAAATT
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
156 52 0.44
157 31 0.26
158 5 0.04
159 5 0.04
161 25 0.21
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (159 bp):
TTCATTTATTTTCATAAGTTTTTCATTTTTTCTTGAAATTCCCTATATTTCGAAAAATCAAGTTC
TCTAGTCCATAAATATTTTCGAAGGGATTTTTCTCGACTTAAAATCTTTAAAATTCATCCAACAT
TGTCATTAGACTCCCTGTAAACCAATTTG
Found at i:1903449 original size:5 final size:5
Alignment explanation
Indices: 1903439--1903464 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1903429 GATTTTTGGA
1903439 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
1903465 TTTCCAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:1903799 original size:12 final size:12
Alignment explanation
Indices: 1903782--1903818 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
1903772 GGCAAGTGAG
1903782 AAAAAAGAGAG-
1 AAAAAAGAGAGA
1903793 AAAAAA-AGAGA
1 AAAAAAGAGAGA
1903804 AAAAAAGAGA-A
1 AAAAAAGAGAGA
1903815 AAAA
1 AAAA
1903819 TTAAGCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.17
11 17 0.71
12 3 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAAAGAGAGA
Found at i:1903802 original size:10 final size:10
Alignment explanation
Indices: 1903779--1903818 Score: 71
Period size: 10 Copynumber: 3.9 Consensus size: 10
1903769 TTTGGCAAGT
1903779 GAGAAAAAAGA
1 GAGAAAAAA-A
1903790 GAGAAAAAAA
1 GAGAAAAAAA
1903800 GAGAAAAAAA
1 GAGAAAAAAA
1903810 GAGAAAAAA
1 GAGAAAAAA
1903819 TTAAGCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
GAGAAAAAAA
Found at i:1911993 original size:22 final size:22
Alignment explanation
Indices: 1911968--1912015 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1911958 GAAAAAGCAC
*
1911968 AAAAACATG-AAAAG-AAGAATA
1 AAAAAAATGCAAAAGCAA-AATA
*
1911989 AAAAAAGTGCAAAAGCAAAATA
1 AAAAAAATGCAAAAGCAAAATA
1912011 AAAAA
1 AAAAA
1912016 GGGGAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 14 0.61
23 2 0.09
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.08
Consensus pattern (22 bp):
AAAAAAATGCAAAAGCAAAATA
Found at i:1913134 original size:33 final size:33
Alignment explanation
Indices: 1913097--1913163 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1913087 TTCAACGATT
1913097 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1913130 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1913163 T
1 T
1913164 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1913135 original size:13 final size:13
Alignment explanation
Indices: 1913117--1913141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1913107 CATAAAATGT
1913117 TGTATCGATACAA
1 TGTATCGATACAA
1913130 TGTATCGATACA
1 TGTATCGATACA
1913142 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1913222 original size:13 final size:13
Alignment explanation
Indices: 1913204--1913228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1913194 ATTACTCAAA
1913204 TGTATCGATACAT
1 TGTATCGATACAT
1913217 TGTATCGATACA
1 TGTATCGATACA
1913229 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1913330 original size:52 final size:52
Alignment explanation
Indices: 1913237--1913360 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1913227 CACTGATCTT
*
1913237 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1913288 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1913340 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1913361 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1917494 original size:10 final size:10
Alignment explanation
Indices: 1917479--1917505 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1917469 TGCTAACTAA
1917479 GTTTTTGTTT
1 GTTTTTGTTT
1917489 GTTTTTGTTT
1 GTTTTTGTTT
1917499 GTTTTTG
1 GTTTTTG
1917506 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Done.