Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2303
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: 20184
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:8608 original size:40 final size:40
Alignment explanation
Indices: 8509--8730 Score: 317
Period size: 40 Copynumber: 5.6 Consensus size: 40
8499 TGGATGATAA
* * * * **
8509 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
8549 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
8588 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
8628 CCGGGCTAAGTCCCGAAAGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
8668 CCGGG-TAAGT-CCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
*
8706 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
8731 AGCAAGTAGC
Statistics
Matches: 166, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
38 27 0.16
39 44 0.27
40 95 0.57
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:8677 original size:79 final size:80
Alignment explanation
Indices: 8509--8730 Score: 317
Period size: 79 Copynumber: 2.8 Consensus size: 80
8499 TGGATGATAA
* * * * **
8509 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTTCCGGGC-AAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
8573 TGCGAGTTACTAAAT
66 TGCGAGTTACTAAAT
*
8588 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAAGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
8653 TGCGAGTTACTAAAT
66 TGCGAGTTACTAAAT
* * *
8668 CCGGG-TAAGT-CCGAAGGCAATTGTGCGAGTTACTCTAA-CCGGGCTATGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAATCCGGGCTAAGTCCCGAAGGCATTT
8730 G
65 G
8731 AGCAAGTAGC
Statistics
Matches: 130, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
78 46 0.35
79 47 0.36
80 37 0.28
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTAAAT
Found at i:8720 original size:78 final size:80
Alignment explanation
Indices: 8509--8730 Score: 310
Period size: 78 Copynumber: 2.8 Consensus size: 80
8499 TGGATGATAA
* * * **
8509 CCGGGCTAAGTCCCGAAGGC-ATCTGCGCTAGTGACTAGTTCCGGGC-AAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCAAT-TGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
8572 GTGCGAGTTACTAAAT
65 GTGCGAGTTACTAAAT
* *
8588 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAAGCATTTG
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
8653 TGCGAGTTACTAAAT
66 TGCGAGTTACTAAAT
* *
8668 CCGGG-TAAGT-CCGAAGGCAATTGTGCGAGTTACTCTAA-CCGGGCTATGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AAATCCGGGCTAAGTCCCGAAGGCATTT
8730 G
65 G
8731 AGCAAGTAGC
Statistics
Matches: 129, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
78 46 0.36
79 45 0.35
80 38 0.29
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTAAAT
Found at i:8749 original size:118 final size:119
Alignment explanation
Indices: 8509--8737 Score: 318
Period size: 118 Copynumber: 1.9 Consensus size: 119
8499 TGGATGATAA
* * ** *
8509 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTTCCGGGCAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAAGCATCTGCGCGAGTGACTAAATCCGGGCAAGTCCCGAAGGCAATTGT
* *
8574 GCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
66 GCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACTAAAT
* * * *
8628 CCGGGCTAAGTCCCGAAAGCATTTGTGCGAGTTACTAAATCCGGGTAAGT-CCGAAGGCAATTGT
1 CCGGGCTAAGTCCCGAAAGCATCTGCGCGAGTGACTAAATCCGGGCAAGTCCCGAAGGCAATTGT
* *
8692 GCGAGTTACTCTAA-CCGGGCTATGTCCCGAAGGCATTTGAGCAAGT
66 GCGAGTTACT-AAATCCGGGCTAAGTCCCGAAGGCATTTGAGCAAGT
8738 AGCTATATCC
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
118 52 0.54
119 44 0.46
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (119 bp):
CCGGGCTAAGTCCCGAAAGCATCTGCGCGAGTGACTAAATCCGGGCAAGTCCCGAAGGCAATTGT
GCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACTAAAT
Found at i:10397 original size:78 final size:78
Alignment explanation
Indices: 10265--10456 Score: 262
Period size: 78 Copynumber: 2.4 Consensus size: 78
10255 ATTTGGATGA
* * ** * *
10265 TAACCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTCACTAGTTTCGGGCTAAGTCCCGAAGGTAT
1 TAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCAT
10330 T-TGTCGAGTTA-C
66 TGTG-CGAGTTACC
* *
10342 TAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCA
1 TAA-CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCA
10407 TTGTGCGAGTTACTC
65 TTGTGCGAGTTAC-C
*
10422 TAACCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 TAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
10457 AGCTATATCC
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
77 3 0.03
78 63 0.62
79 32 0.31
80 4 0.04
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (78 bp):
TAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCAT
TGTGCGAGTTACC
Found at i:10411 original size:39 final size:39
Alignment explanation
Indices: 10268--10456 Score: 224
Period size: 40 Copynumber: 4.8 Consensus size: 39
10258 TGGATGATAA
* **
10268 CCGGGCTAAGTCCCGAAGGCATT-TGCGCTAGTCACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCG--AGTTACTAAAT
* *
10308 TCGGGCTAAGTCCCGAAGGTATT-TGTCGAGTTACT-AAT
1 CCGGGCTAAGTCCCGAAGGCATTGTG-CGAGTTACTAAAT
10346 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAAT
*
10386 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACT-AAAT
* *
10425 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGT
10457 AGCTATATCC
Statistics
Matches: 133, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
38 20 0.15
39 51 0.38
40 60 0.45
41 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAT
Found at i:10480 original size:78 final size:75
Alignment explanation
Indices: 10265--10482 Score: 249
Period size: 78 Copynumber: 2.8 Consensus size: 75
10255 ATTTGGATGA
* * * * *
10265 TAACCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTCACTAGTTTCGGGCTAAGTCCCGAAGGTAT
1 TAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT-ACTA-TATCCGGCTAAGTCCCGAAGGCAT
10330 TTGTCGAGTTAC
64 TTGTCGAGTTAC
* *
10342 TAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCA
1 TAA-CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TACTATATCC-GGCTAAGTCCCGAAGGCA
10407 -TTGTGCGAGTTACTC
63 TTTGT-CGAGTTA--C
* * * *
10422 TAACCGGGCTATGTCCCGAAGGCATTTGAGCGAGTAGCTATATCCGGTTAAATTCCGAAGG
1 TAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTA-CTATATCCGGCTAAGTCCCGAAGG
10483 TACGTGATTT
Statistics
Matches: 122, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
77 9 0.07
78 72 0.59
79 37 0.30
80 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (75 bp):
TAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTACTATATCCGGCTAAGTCCCGAAGGCATTT
GTCGAGTTAC
Found at i:18379 original size:40 final size:40
Alignment explanation
Indices: 18280--18510 Score: 349
Period size: 40 Copynumber: 5.8 Consensus size: 40
18270 TGGATGATAA
* * * * **
18280 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
18320 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
18359 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
18399 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
18439 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
18479 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
18511 AGCTATATCC
Statistics
Matches: 178, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 33 0.19
40 143 0.80
41 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:20083 original size:40 final size:40
Alignment explanation
Indices: 20028--20178 Score: 144
Period size: 40 Copynumber: 3.8 Consensus size: 40
20018 TGGATGATAA
* * **
20028 CCGGGCTAAGTCCCGAAGGCTTTTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAAAT
* * *
20068 CCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAAAT
* * * * *
20108 CTGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACT-AAAT
* * *
20148 CCGGGCTATGTCTCGAA-GCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGT
20179 AGCTAT
Statistics
Matches: 94, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 12 0.13
40 80 0.85
41 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAAAT
Done.