Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3156
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: 19968
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Found at i:2369 original size:37 final size:39
Alignment explanation
Indices: 2328--2463 Score: 145
Period size: 37 Copynumber: 3.5 Consensus size: 39
2318 TGATGTACGG
*
2328 AAGTCCGAAGGCTTTGTGCTAAGTGACCAT-T-TGGACT
1 AAGTCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACT
*
2365 AAGTCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACT
1 AAGTCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACT
* * * *
2404 AAGATCCGAAGGCATTTGTGC-GAGTTACTA-ATTCCGGGCT
1 AAG-TCCGAAGGC-TTTGTGCTAAGTGACCATA-TCCGGACT
*
2444 AAGCCCGAAGGCATTTGTGC
1 AAGTCCGAAGGC-TTTGTGC
2464 GAGTTACTAA
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
37 29 0.33
38 1 0.01
39 25 0.28
40 26 0.30
41 7 0.08
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
AAGTCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACT
Found at i:2386 original size:20 final size:20
Alignment explanation
Indices: 2328--2388 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
2318 TGATGTACGG
2328 AAGTCCGAAGGCTTTGTGCT
1 AAGTCCGAAGGCTTTGTGCT
*
2348 AAGT--G-A-CCATTTG-GACT
1 AAGTCCGAAGGC-TTTGTG-CT
2365 AAGTCCGAAGGCTTTGTGCT
1 AAGTCCGAAGGCTTTGTGCT
2385 AAGT
1 AAGT
2389 GACTATATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
16 2 0.06
17 11 0.34
18 1 0.03
19 1 0.03
20 15 0.47
21 2 0.06
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (20 bp):
AAGTCCGAAGGCTTTGTGCT
Found at i:2440 original size:40 final size:39
Alignment explanation
Indices: 2360--2500 Score: 169
Period size: 39 Copynumber: 3.6 Consensus size: 39
2350 GTGACCATTT
* *
2360 GGACTAAGTCCGAAGGC-TTTGTGCTAAGTGACT-ATATCC
1 GGACTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAT-TCC
2399 GGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGACTAAG-TCCGAAGGCATTTGTGCGAGTTACTAATTCC
* * *
2439 GGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGACTAAGTCCGAAGGCATTTGTGCGAGTTACTAATTCC
**
2478 GGGTTAAGTCCCGAAGGCATTTG
1 GGACTAAGT-CCGAAGGCATTTG
2501 CGTTTAGCTA
Statistics
Matches: 91, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
39 44 0.48
40 38 0.42
41 9 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
GGACTAAGTCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:2457 original size:39 final size:40
Alignment explanation
Indices: 2369--2500 Score: 162
Period size: 40 Copynumber: 3.3 Consensus size: 40
2359 TGGACTAAGT
* * * *
2369 CCGAAGGC-TTTGTGCTAAGTGACT-ATATCCGGACTAAGAT
1 CCGAAGGCATTTGTGC-GAGTTACTAAT-TCCGGGCTAAGAC
2409 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGAC
* * *
2448 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGAC
2488 CCGAAGGCATTTG
1 CCGAAGGCATTTG
2501 CGTTTAGCTA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
39 36 0.43
40 38 0.46
41 9 0.11
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGAC
Found at i:9265 original size:15 final size:15
Alignment explanation
Indices: 9245--9274 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9235 TTTGGGAAAG
9245 AAATAAAAAATAAAA
1 AAATAAAAAATAAAA
*
9260 AAATAACAAATAAAA
1 AAATAAAAAATAAAA
9275 TCCCTATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAATAAAAAATAAAA
Found at i:9338 original size:17 final size:18
Alignment explanation
Indices: 9316--9353 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
9306 AACAAATCAA
*
9316 CCACTCAGACT-TTAAAG
1 CCACTCAAACTCTTAAAG
*
9333 CCACTCAAACTCTTTAAG
1 CCACTCAAACTCTTAAAG
9351 CCA
1 CCA
9354 ACCGAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.34, G:0.08, T:0.24
Consensus pattern (18 bp):
CCACTCAAACTCTTAAAG
Found at i:12242 original size:15 final size:15
Alignment explanation
Indices: 12222--12251 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12212 AACTATGGTA
*
12222 ATGAAATATTGATAT
1 ATGAAATAATGATAT
12237 ATGAAATAATGATAT
1 ATGAAATAATGATAT
12252 GTGTTTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (15 bp):
ATGAAATAATGATAT
Found at i:17934 original size:46 final size:46
Alignment explanation
Indices: 17884--18051 Score: 193
Period size: 46 Copynumber: 3.6 Consensus size: 46
17874 TGATTGAGCA
17884 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
17930 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
17975 CATCCGAACTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
18023 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTC
18052 GCTCATGGGC
Statistics
Matches: 102, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 53 0.52
47 28 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:18040 original size:93 final size:93
Alignment explanation
Indices: 17881--18052 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
17871 GGATGATTGA
*
17881 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
17946 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
17974 GCATCCGAACTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
18038 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
18053 CTCATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.