Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1431
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: 24270
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:4271 original size:39 final size:40
Alignment explanation
Indices: 4122--4382 Score: 328
Period size: 40 Copynumber: 6.7 Consensus size: 40
4112 GCTCCTCGTT
* *
4122 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
4162 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
4202 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
4242 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
4281 CAAATGCCTTCGGG-CTTAGCCCGGAA-TAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
4319 C-AATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
4359 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
4383 CATCATTCAA
Statistics
Matches: 203, Mismatches: 9, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
36 2 0.01
37 9 0.04
38 23 0.11
39 72 0.35
40 95 0.47
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:12169 original size:39 final size:40
Alignment explanation
Indices: 12052--12273 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
12042 GCTCCTCGTT
* *
12052 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
12092 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
12132 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
12171 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
12210 CAAATGCCTTC-GGATCTTAGTCCGG-A-TATGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAATTA-GT-ATC-TCGCA
12250 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12274 CATCATTCAA
Statistics
Matches: 164, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
38 19 0.12
39 82 0.50
40 61 0.37
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:14206 original size:46 final size:46
Alignment explanation
Indices: 14139--14260 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
14129 TGAGCATCCG
* * *
14139 AACTCGTTGAGTTGAGTCCGAGTTCACTTATATATGTGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGCCCA
* *
14185 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGCCCA
* *
14231 AGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
14261 GGGGCGGGTT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGCCCA
Found at i:16777 original size:15 final size:15
Alignment explanation
Indices: 16757--16785 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16747 ATTTTGTGTG
16757 ATGTTTTATTATAAA
1 ATGTTTTATTATAAA
16772 ATGTTTTATTATAA
1 ATGTTTTATTATAA
16786 GATGAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
ATGTTTTATTATAAA
Found at i:19314 original size:40 final size:40
Alignment explanation
Indices: 19259--19530 Score: 454
Period size: 40 Copynumber: 6.8 Consensus size: 40
19249 ATTTGAATAC
*
19259 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
19299 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
19339 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGACATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG--ATAT
19381 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* *
19421 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* *
19461 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* * *
19501 ACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
19531 TTGTGGTTAT
Statistics
Matches: 219, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
40 179 0.82
42 40 0.18
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
Found at i:19476 original size:122 final size:122
Alignment explanation
Indices: 19251--19530 Score: 467
Period size: 122 Copynumber: 2.3 Consensus size: 122
19241 GCATGAGCAT
*
19251 TTGA-ATACATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
* * *
19315 GAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
66 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
*
19372 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
19437 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
66 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
* * *
19494 TTG-C-TATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
19531 TTGTGGTTAT
Statistics
Matches: 150, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 30 0.20
121 5 0.03
122 115 0.77
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (122 bp):
TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
Done.