Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold869
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: 26348
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:2388 original size:40 final size:40
Alignment explanation
Indices: 2333--2556 Score: 279
Period size: 40 Copynumber: 5.5 Consensus size: 40
2323 TATTCGGATG
* *
2333 ATATCTGGGCTAAGTCCCGAAGTCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
2373 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
2416 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * *
2456 ATATCCGGGCTAAGTCCCGAAAGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
2496 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
2536 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
2557 ATACTTGGGT
Statistics
Matches: 161, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 13 0.08
40 110 0.68
41 1 0.01
43 37 0.23
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:2482 original size:83 final size:80
Alignment explanation
Indices: 2339--2555 Score: 278
Period size: 83 Copynumber: 2.7 Consensus size: 80
2329 GATGATATCT
* * * **
2339 GGGCTAAGTCCCGAAGTCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAAGCATTCATG
2404 CGAGTAGTTG-CTATACCC
66 C---TAG-TGACTATACCC
*
2422 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAAGCATTCATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAAGCATTCATG
*
2487 CTAGTGACTATATCC
66 CTAGTGACTATACCC
* * *
2502 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAA
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAA
2556 GATACTTGGG
Statistics
Matches: 122, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
79 15 0.12
80 45 0.37
81 2 0.02
83 60 0.49
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (80 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAAGCATTCATG
CTAGTGACTATACCC
Found at i:5354 original size:79 final size:81
Alignment explanation
Indices: 5245--5427 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
5235 TACTCGTTCA
* *
5245 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
5308 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
5325 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
5388 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
5404 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
5428 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:5427 original size:40 final size:40
Alignment explanation
Indices: 5224--5427 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
5214 CGGAATTTAA
** *
5224 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5264 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5304 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5343 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5383 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5423 CCGGA
1 CCGGA
5428 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12144 original size:40 final size:40
Alignment explanation
Indices: 12070--12253 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
12060 GCTACTCGTT
*
12070 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
12109 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
12149 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
12188 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
12229 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12254 CATCATTCGA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 43 0.35
40 66 0.53
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:12169 original size:79 final size:79
Alignment explanation
Indices: 12072--12253 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 79
12062 TACTCGTTCA
* * *
12072 AATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGA
* *
12135 TTTAGTAAC-TCGCACC
64 TATAGTAACTTAGCA-C
* **
12151 AATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATA
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
* *
12216 TGGTCACTTAGCAC
66 TAGTAACTTAGCAC
*
12230 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGG-CTTAGCCCGGA
12254 CATCATTCGA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 69 0.78
80 16 0.18
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
TAGTAACTTAGCAC
Found at i:20822 original size:40 final size:40
Alignment explanation
Indices: 20767--20989 Score: 279
Period size: 40 Copynumber: 5.5 Consensus size: 40
20757 TATTCGGATG
*
20767 ATATCCGGGCTAAGTCCCGAAGTCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
20807 ATATCCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
20850 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
20890 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
20930 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
20970 ATAT-C-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
20990 ATACTTGGGT
Statistics
Matches: 161, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
38 13 0.08
39 1 0.01
40 110 0.68
41 1 0.01
43 36 0.22
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:20912 original size:83 final size:80
Alignment explanation
Indices: 20771--20989 Score: 275
Period size: 83 Copynumber: 2.7 Consensus size: 80
20761 CGGATGATAT
* * * **
20771 CCGGGCTAAGTCCCGAAGTCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCTGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
20836 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
20854 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
20919 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
20934 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT-C-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
20990 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
78 14 0.11
79 3 0.02
80 43 0.35
81 2 0.02
83 62 0.50
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:25884 original size:42 final size:40
Alignment explanation
Indices: 25814--25957 Score: 149
Period size: 42 Copynumber: 3.7 Consensus size: 40
25804 TGCAAGATAC
25814 TAAATCCGGGTTAAGT-CCGAAGGCCATTCGTGCGAGTTATT
1 TAAATCCGGG-TAAGTCCCGAAGG-CATTCGTGCGAGTTATT
* *
25855 TAAATCGCAGTGTAAGTCCCGAAGGCATTCGTGCGAGTT-GT
1 TAAATC-C-GGGTAAGTCCCGAAGGCATTCGTGCGAGTTATT
* *
25896 TAAATCCGGGTATGTCCCGAAGGCATT-GTGTGAGTTA--
1 TAAATCCGGGTAAGTCCCGAAGGCATTCGTGCGAGTTATT
* *
25933 TAAA-CCGGGCATGT-CCGAAGGCATT
1 TAAATCCGGGTAAGTCCCGAAGGCATT
25958 TGAACGAGAG
Statistics
Matches: 93, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
35 11 0.12
36 9 0.10
37 4 0.04
38 8 0.09
39 18 0.19
40 1 0.01
41 13 0.14
42 20 0.22
43 9 0.10
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.27
Consensus pattern (40 bp):
TAAATCCGGGTAAGTCCCGAAGGCATTCGTGCGAGTTATT
Done.