Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3473
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: 24144
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:6872 original size:3 final size:3
Alignment explanation
Indices: 6864--6894 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6854 AAAGCTCCAG
6864 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
6895 TGTTCTTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10161 original size:88 final size:85
Alignment explanation
Indices: 10066--10362 Score: 267
Period size: 89 Copynumber: 3.4 Consensus size: 85
10056 ACCAGTATGG
* * ** * *
10066 GAAGATAAAATATGTATATTCGATCCCCTTCGCTACC-GATATAGGGAGACAGGACCTGCTATCT
1 GAAGATAAAATATGTTTCTTCGATCTACTTCGC-ACCAG-TAT-GGGAGACAAGATCTG-TATCT
10130 TTGATCTACTTCACGCCAGTACAT
62 TTGATCTACTTCACGCCAGTACAT
* * * * * *
10154 GAAGATAAGATCTAT-TTTCTTCAATTTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCT
1 GAAGATAA-A-ATATGTTTCTTCGATCTACTTC-GCACCAGTAT-GGGAGACAAGATCTGTATCT
*
10218 TTGATCTACTTCATGCCAGTACAT
62 TTGATCTACTTCACGCCAGTACAT
* * * *
10242 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGACACCAGTATGGGAAGATAAGATCTGGTATCT
1 GAAGATAAAATATG-TTTCTTCGATCTACTTCG-CACCAGTATGGG-AGACAAGATCT-GTATCT
*
10307 TTGATCTACTTCACGCTAGTACAT
62 TTGATCTACTTCACGCCAGTACAT
* *
10331 GAAGACAATATCA-GCTTTCTTCGATCTACTTC
1 GAAGATAAAAT-ATG-TTTCTTCGATCTACTTC
10363 ACGCCAATAC
Statistics
Matches: 170, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
86 2 0.01
87 3 0.02
88 75 0.44
89 85 0.50
90 5 0.03
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (85 bp):
GAAGATAAAATATGTTTCTTCGATCTACTTCGCACCAGTATGGGAGACAAGATCTGTATCTTTGA
TCTACTTCACGCCAGTACAT
Found at i:10282 original size:133 final size:132
Alignment explanation
Indices: 10127--10416 Score: 330
Period size: 133 Copynumber: 2.2 Consensus size: 132
10117 GGACCTGCTA
* * * * * *
10127 TCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTCTTCAATTTACTCCACCACC
1 TCTTCGATCTACTTCACACCAGTACAGGAAGATAAGATCTAGTATCTTCAATCTACTCCA-CACC
** * * * * *
10192 AGTATGGGGAGACAAGATCTG-TTTCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTG
65 AGTACAGGAAGACAAGATCAGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
10256 TTT
130 TTT
** * ** * * *
10259 TCTTCGATCTACTTCGACACCAGTATGGGAAGATAAGATCTGGTATCTTTGATCTACTTCACGCT
1 TCTTCGATCTACTTC-ACACCAGTACAGGAAGATAAGATCTAGTATCTTCAATCTACTCCACACC
* *
10324 AGTACATGAAGACAATATCAGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
65 AGTACAGGAAGACAAGATCAGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
10389 TTT
130 TTT
*
10392 TCTTCGATCTACTCCACCACCAGTA
1 TCTTCGATCTACTTCA-CACCAGTA
10417 TGGGGAGACA
Statistics
Matches: 131, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
132 32 0.24
133 99 0.76
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (132 bp):
TCTTCGATCTACTTCACACCAGTACAGGAAGATAAGATCTAGTATCTTCAATCTACTCCACACCA
GTACAGGAAGACAAGATCAGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGT
TT
Found at i:10417 original size:133 final size:133
Alignment explanation
Indices: 10213--10495 Score: 406
Period size: 133 Copynumber: 2.1 Consensus size: 133
10203 ACAAGATCTG
* * * *
10213 TTTCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGACA
1 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCCACA
* * * * * *
10278 CCAGTATGGGAAGATAAGATCTGGTATCTTTGATCTACTTCACGCTAGTACATGAAGACAATATC
66 CCAGTATGGGAAGACAAGATCTGCTATATTCGATCTACTTCACGCCAATACATGAAGACAATATC
10343 AGC
131 AGC
10346 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTAC-TCCACC
1 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCCA-C
* * *
10410 ACCAGTATGGGGAGACAAGATCTGCTTTATTCGATCTACTTCGCGCCAATACATGAAGACAATAT
65 ACCAGTATGGGAAGACAAGATCTGCTATATTCGATCTACTTCACGCCAATACATGAAGACAATAT
***
10475 CTTT
130 CAGC
10479 TTTCTTCGATCTACTTC
1 TTTCTTCGATCTACTTC
10496 GCCACCAGTA
Statistics
Matches: 133, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
132 3 0.02
133 130 0.98
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.34
Consensus pattern (133 bp):
TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCCACA
CCAGTATGGGAAGACAAGATCTGCTATATTCGATCTACTTCACGCCAATACATGAAGACAATATC
AGC
Found at i:10457 original size:89 final size:88
Alignment explanation
Indices: 10201--10521 Score: 329
Period size: 89 Copynumber: 3.6 Consensus size: 88
10191 CAGTATGGGG
* ** * *
10201 AGACAAGATCTG-TTTCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGTTTTCTTCG
1 AGACAAGATCTGTTTTCTTCGATCTACTTCACACCAGTACAGGAAGACAAGATCTGCTTTCTTCG
* * ***
10265 ATCTACTTCGACACCAGTATGGGA
66 ATCTACTTCG-CGCCAATACATGA
* * * * * * * * *
10289 AGATAAGATCTGGTATCTTTGATCTACTTCACGCTAGTACATGAAGACAATATCAGCTTTCTTCG
1 AGACAAGATCTGTTTTCTTCGATCTACTTCACACCAGTACAGGAAGACAAGATCTGCTTTCTTCG
*
10354 ATCTACTTCACGCCAATACATGA
66 ATCTACTTCGCGCCAATACATGA
* ** * *
10377 AGACAAGATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGCTTTATTC
1 AGACAAGATCTGTTTTCTTCGATCTACTTCA-CACCAGTACAGGAAGACAAGATCTGCTTTCTTC
10442 GATCTACTTCGCGCCAATACATGA
65 GATCTACTTCGCGCCAATACATGA
* * * ** *
10466 AGACAATATCTTTTTTCTTCGATCTACTTCGCCACCAGTATGGGAATACAAGATCT
1 AGACAAGATCTGTTTTCTTCGATCTACTTC-ACACCAGTACAGGAAGACAAGATCT
10522 ACTGCTTGTC
Statistics
Matches: 196, Mismatches: 34, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
88 45 0.23
89 151 0.77
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (88 bp):
AGACAAGATCTGTTTTCTTCGATCTACTTCACACCAGTACAGGAAGACAAGATCTGCTTTCTTCG
ATCTACTTCGCGCCAATACATGA
Found at i:10497 original size:44 final size:44
Alignment explanation
Indices: 10127--10495 Score: 362
Period size: 44 Copynumber: 8.3 Consensus size: 44
10117 GGACCTGCTA
* * *
10127 TCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
* * * * *** *
10171 TCTTCAATTTACTCCACCACCAGTATGGGGAGACAAGATCTG-TT
1 TCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTTT
* *
10215 TCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
* *** * * *
10259 TCTTCGATCTACTTCGACACCAGTATGGGAAGATAAGATCTGGTA
1 TCTTCGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTT
* * * * *
10304 TCTTTGATCTACTTCACGCTAGTACATGAAGACAATATCAGCTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
*
10348 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
* * *** * *
10392 TCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGCTT
1 TCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTTT
* * * * *
10437 TATTCGATCTACTTCGCGCCAATACATGAAGACAATATCTTTTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
10481 TCTTCGATCTACTTC
1 TCTTCGATCTACTTC
10496 GCCACCAGTA
Statistics
Matches: 253, Mismatches: 68, Indels: 8
0.77 0.21 0.02
Matches are distributed among these distances:
43 19 0.08
44 147 0.58
45 87 0.34
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
Found at i:11838 original size:20 final size:21
Alignment explanation
Indices: 11787--11839 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
11777 TTTCTTTTCT
11787 TTTTC-CATTTTTATTTCTTA
1 TTTTCACATTTTTATTTCTTA
*
11807 TTTTCACTTTTTTATTT-TTA
1 TTTTCACATTTTTATTTCTTA
11827 -TTTCATCATTTTT
1 TTTTCA-CATTTTT
11840 TACGACTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 5 0.17
20 14 0.48
21 10 0.34
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCACATTTTTATTTCTTA
Found at i:13615 original size:22 final size:22
Alignment explanation
Indices: 13565--13638 Score: 121
Period size: 23 Copynumber: 3.3 Consensus size: 22
13555 GTGTTATTGA
*
13565 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTAC-AT
13588 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
13610 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
13632 ATCAGTG
1 -TCAGTG
13639 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 23 0.47
23 26 0.53
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (22 bp):
TCAGTGGTAGCTTCGGCTACAT
Found at i:20690 original size:17 final size:17
Alignment explanation
Indices: 20668--20705 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20658 TTTTATAAAT
*
20668 TGTGAATTTAT-TTGATA
1 TGTGAATTAATATTGA-A
20685 TGTGAATTAATATTGAA
1 TGTGAATTAATATTGAA
20702 TGTG
1 TGTG
20706 GAAGGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
TGTGAATTAATATTGAA
Found at i:20755 original size:13 final size:13
Alignment explanation
Indices: 20737--20761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20727 TATTCAAGTG
20737 ATAAAGTGTTAAA
1 ATAAAGTGTTAAA
20750 ATAAAGTGTTAA
1 ATAAAGTGTTAA
20762 GTGTAAATTC
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
ATAAAGTGTTAAA
Found at i:20981 original size:22 final size:22
Alignment explanation
Indices: 20931--21004 Score: 121
Period size: 23 Copynumber: 3.3 Consensus size: 22
20921 GTGTTATTGA
*
20931 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTAC-AT
20954 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
20976 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
20998 ATCAGTG
1 -TCAGTG
21005 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 23 0.47
23 26 0.53
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (22 bp):
TCAGTGGTAGCTTCGGCTACAT
Done.