Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5298.1
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: 26981
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.21
Warning! 7556 characters in sequence are not A, C, G, or T
Found at i:1945 original size:12 final size:12
Alignment explanation
Indices: 1928--1968 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1918 TTCATGATTG
*
1928 GCATTCATTTAT
1 GCATTCATTCAT
1940 GCATTCATTCAT
1 GCATTCATTCAT
*
1952 TCATTCATTCATT
1 GCATTCATTCA-T
1965 GCAT
1 GCAT
1969 ATCCCATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (12 bp):
GCATTCATTCAT
Found at i:1948 original size:4 final size:4
Alignment explanation
Indices: 1929--1964 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1919 TCATGATTGG
* *
1929 CATT CATT TATG CATT CATT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT
1965 GCATATCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.22, G:0.03, T:0.50
Consensus pattern (4 bp):
CATT
Found at i:8660 original size:77 final size:77
Alignment explanation
Indices: 8533--8687 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
8523 CCCCAAAAGC
8533 TTCTAATGGACACCGGTTCATTTTTGTGGTCATTGATTACTTCACAAAATGGATAGAAGCCGCTT
1 TTCTAATGGACACCGGTTCATTTTTGTGGTCATTGATTACTTCACAAAATGGATAGAAGCCGCTT
8598 CGTTTGCCAATG
66 CGTTTGCCAATG
*
8610 TTCTAATGGACACTGGTTCATTTTTGTGGTCATTGATTACTTCACAAAATGGATAGAAGCCGCTT
1 TTCTAATGGACACCGGTTCATTTTTGTGGTCATTGATTACTTCACAAAATGGATAGAAGCCGCTT
8675 CGTTTGCCAATG
66 CGTTTGCCAATG
8687 T
1 T
8688 GACAAAGACT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (77 bp):
TTCTAATGGACACCGGTTCATTTTTGTGGTCATTGATTACTTCACAAAATGGATAGAAGCCGCTT
CGTTTGCCAATG
Found at i:9369 original size:57 final size:57
Alignment explanation
Indices: 9293--9406 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
9283 GGAAAATGGG
9293 CACCAAATTGGGAAGGACCATACGTCGTGAAGAAAGCATTCTCGGGAGGAGCTTTGA
1 CACCAAATTGGGAAGGACCATACGTCGTGAAGAAAGCATTCTCGGGAGGAGCTTTGA
*
9350 CACCAAATTGGGAAGGACCATACGTCGTGAAGAAAGCATTCTCGGGTGGAGCTTTGA
1 CACCAAATTGGGAAGGACCATACGTCGTGAAGAAAGCATTCTCGGGAGGAGCTTTGA
9407 TTCTCACTGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (57 bp):
CACCAAATTGGGAAGGACCATACGTCGTGAAGAAAGCATTCTCGGGAGGAGCTTTGA
Found at i:10443 original size:54 final size:54
Alignment explanation
Indices: 10355--10463 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
10345 TATTTTGATG
**
10355 TTTTAATTTCTATTTTTCAAAAATCAACTTATATTGCAAGAGGTGAGTTAAGCC
1 TTTTAATTTCTATTTTTCAAAAATCAACACATATTGCAAGAGGTGAGTTAAGCC
* * *
10409 TTTTAATTTCTGTTTTTCAAAAATCAACACATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTATTTTTCAAAAATCAACACATATTGCAAGAGGTGAGTTAAGCC
10463 T
1 T
10464 CGAGACATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (54 bp):
TTTTAATTTCTATTTTTCAAAAATCAACACATATTGCAAGAGGTGAGTTAAGCC
Found at i:10757 original size:90 final size:90
Alignment explanation
Indices: 10585--10757 Score: 190
Period size: 90 Copynumber: 1.9 Consensus size: 90
10575 AGGTCTGTTT
* ** * **
10585 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGCTGAGGTTTTTTCAAATTCTGTTT
1 TCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAGGATACGCCAAGGTATTTTCAAATTCTGTAC
** *
10650 TTTCAGTTTATATTTTTTTCAAAAA
66 TTTCAAATTATAGTTTTTTCAAAAA
* *
10675 TCAACTCATATTGAGAGAGGTGAGTTGAGCC-CTGGGTCACATGCCAAGGTATTTTCAAATTCTG
1 TCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAGGAT-AC--GCCAAGGTATTTTCAAATTCTG
*
10739 -ACTTTCAAATTCT-GTTTTT
63 TACTTTCAAATTATAGTTTTT
10758 AATTTCTACT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
89 4 0.06
90 37 0.54
91 8 0.12
92 19 0.28
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (90 bp):
TCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAGGATACGCCAAGGTATTTTCAAATTCTGTAC
TTTCAAATTATAGTTTTTTCAAAAA
Found at i:10987 original size:60 final size:61
Alignment explanation
Indices: 10894--11018 Score: 243
Period size: 60 Copynumber: 2.1 Consensus size: 61
10884 GCTCACGTGT
10894 TGAGCCACTTTCAATTTCTGTTTTTAATGTCTGTTTTTAAATCAACTCATATTGCGAGA-G
1 TGAGCCACTTTCAATTTCTGTTTTTAATGTCTGTTTTTAAATCAACTCATATTGCGAGAGG
10954 TGAGCCACTTTCAATTTCTGTTTTTAATGTCTGTTTTTAAATCAACTCATATTGCGAGAGG
1 TGAGCCACTTTCAATTTCTGTTTTTAATGTCTGTTTTTAAATCAACTCATATTGCGAGAGG
11015 TGAG
1 TGAG
11019 TTAAGCCTCG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 59 0.92
61 5 0.08
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (61 bp):
TGAGCCACTTTCAATTTCTGTTTTTAATGTCTGTTTTTAAATCAACTCATATTGCGAGAGG
Found at i:11142 original size:13 final size:13
Alignment explanation
Indices: 11124--11156 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
11114 ATGTGTTGAG
11124 CTATTTTTAATTT
1 CTATTTTTAATTT
*
11137 CTATTTTTACTTT
1 CTATTTTTAATTT
11150 CTATTTT
1 CTATTTT
11157 AAAGAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (13 bp):
CTATTTTTAATTT
Found at i:13216 original size:42 final size:39
Alignment explanation
Indices: 13170--13268 Score: 92
Period size: 44 Copynumber: 2.4 Consensus size: 39
13160 GTTATATATG
13170 TTTTTGTAT-TATGTATATATTTTAAATATTATATACTAAGTA
1 TTTTTGTATCTAT-TAT-TATTTTAAATATTAT-TACTAA-TA
* * *
13212 TTTTTAATATCCCTATTATTATTTTAAATATTATTAGTTATA
1 TTTTT-GTAT--CTATTATTATTTTAAATATTATTACTAATA
*
13254 TTTTTGTATATATTA
1 TTTTTGTATCTATTA
13269 CTCTATGTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
39 5 0.10
41 3 0.06
42 12 0.25
43 7 0.15
44 15 0.31
45 3 0.06
46 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (39 bp):
TTTTTGTATCTATTATTATTTTAAATATTATTACTAATA
Found at i:13255 original size:21 final size:22
Alignment explanation
Indices: 13187--13257 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 22
13177 ATTATGTATA
* *
13187 TATTTTAAATATTATATACTAAG
1 TATTTTAAATATTAT-TAGTTAG
* *** *
13210 TATTTTTAATATCCCTA-TTAT
1 TATTTTAAATATTATTAGTTAG
13231 TATTTTAAATATTATTAGTTA-
1 TATTTTAAATATTATTAGTTAG
13252 TATTTT
1 TATTTT
13258 TGTATATATT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 21 0.57
22 5 0.14
23 11 0.30
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (22 bp):
TATTTTAAATATTATTAGTTAG
Found at i:24910 original size:34 final size:34
Alignment explanation
Indices: 24867--24934 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
24857 TGAAAAAGTC
24867 CTTTTACAGTTTGAAACAGTCACCAAGACAGTGG
1 CTTTTACAGTTTGAAACAGTCACCAAGACAGTGG
24901 CTTTTACAGTTTGAAACAGTCACCAAGACAGTGG
1 CTTTTACAGTTTGAAACAGTCACCAAGACAGTGG
24935 TACAAGAGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (34 bp):
CTTTTACAGTTTGAAACAGTCACCAAGACAGTGG
Found at i:24947 original size:34 final size:34
Alignment explanation
Indices: 24872--24948 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
24862 AAGTCCTTTT
***
24872 ACAGTTTGAAACAGTCACCAAGACAGTGGCTTTT
1 ACAGTTTGAAACAGTCACCAAGACAGTGGCTACA
24906 ACAGTTTGAAACAGTCACCAAGACAGTGG-TACA
1 ACAGTTTGAAACAGTCACCAAGACAGTGGCTACA
*
24939 AGAGGTTTGA
1 ACA-GTTTGA
24949 TTCCTTTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 3 0.08
34 35 0.92
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (34 bp):
ACAGTTTGAAACAGTCACCAAGACAGTGGCTACA
Found at i:26544 original size:38 final size:38
Alignment explanation
Indices: 26486--26561 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
26476 TATTTTATTT
* *
26486 TATTTTATTTTTTCTCAAATTGGTATCCGAGCTTCCGG
1 TATTTTATTTTTTCACAAATTGGTATCAGAGCTTCCGG
26524 NTATTTTA-TTTTTCACAAATTGGTATCAGAGCTTCCGG
1 -TATTTTATTTTTTCACAAATTGGTATCAGAGCTTCCGG
26562 GTTATTCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 28 0.80
39 7 0.20
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.45
Consensus pattern (38 bp):
TATTTTATTTTTTCACAAATTGGTATCAGAGCTTCCGG
Done.