Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_246 ID=scaffold_246-JGI_221_v2.0
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: 9003
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:80 original size:17 final size:16
Alignment explanation
Indices: 58--92 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
48 TACAACATCC
*
58 AAACAAGTAAAATATAA
1 AAACAAATAAAAT-TAA
75 AAACAAATAAAATTAA
1 AAACAAATAAAATTAA
91 AA
1 AA
93 CCTTCACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (16 bp):
AAACAAATAAAATTAA
Found at i:260 original size:2 final size:2
Alignment explanation
Indices: 253--325 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
243 ATTCACGTGA
253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
326 CAAAAGTATA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1313 original size:8 final size:8
Alignment explanation
Indices: 1300--1341 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1290 GTGTAAATGT
1300 AAATAAAA
1 AAATAAAA
*
1308 AAATAACA
1 AAATAAAA
*
1316 AAATAACA
1 AAATAAAA
*
1324 AAA-AAGA
1 AAATAAAA
1331 AAATAAAA
1 AAATAAAA
1339 AAA
1 AAA
1342 GATGAAGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (8 bp):
AAATAAAA
Found at i:2060 original size:44 final size:43
Alignment explanation
Indices: 1943--2061 Score: 166
Period size: 44 Copynumber: 2.7 Consensus size: 43
1933 TCCACTGCAT
* * * *
1943 CTTGTCGCTTCGATCCACTTCCTTGCAACCTCTGAGAGATTCGA
1 CTTGTAGCTTCAATCCACTT-ATTGCAACTTCTGAGAGATTCGA
*
1987 CTTGTAGCTCCAATCCACTTTATTGCAACTTCTGAGAGATTCGA
1 CTTGTAGCTTCAATCCAC-TTATTGCAACTTCTGAGAGATTCGA
2031 CTTGTAGCTTCAATCCACTCTATTGCAACTT
1 CTTGTAGCTTCAATCCACT-TATTGCAACTT
2062 TAGGGGGACG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
43 1 0.01
44 64 0.96
45 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (43 bp):
CTTGTAGCTTCAATCCACTTATTGCAACTTCTGAGAGATTCGA
Found at i:2426 original size:44 final size:44
Alignment explanation
Indices: 2378--2491 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 44
2368 TTTTAATCCT
* * *
2378 CTCCACTGCAACTTTAGGGAGATAGGA-TTAGTAGCTTCAGTCT-G
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GTAGCTTCA-ACTGG
* *
2422 CTCCACTGTAACTTCAGGGAGATAAGACTTGTATCTTCAACTGG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACTGG
*
2466 CCCCACTGCAACTTCAGGGAGATAAG
1 CTCCACTGCAACTTCAGGGAGATAAG
2492 GTTTGATATG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
43 2 0.03
44 57 0.93
45 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACTGG
Found at i:2833 original size:89 final size:89
Alignment explanation
Indices: 2716--3022 Score: 461
Period size: 89 Copynumber: 3.4 Consensus size: 89
2706 AGGACTAGTT
* * * *
2716 TTCGATTTGCTTCACTGCCAGTATAGGAAGACAAGATCTGCTGCTTTTAGTCTACTCCGCTGCAA
1 TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTGCAA
2781 ACTCAGGGAGGTCAGGCTTGTGTC
66 ACTCAGGGAGGTCAGGCTTGTGTC
** * * *
2805 TTCGATCTGCTTTGCTACCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTGCTCCACTGCAA
1 TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTGCAA
2870 ACTCAGGGAGGTCAGGCTTGTGTC
66 ACTCAGGGAGGTCAGGCTTGTGTC
* * *
2894 TTCGATCTGCTTCCCTGCCGGTACAGGAAGACAAGATCTGCTACTTATAGTCTGCTCCGCTGCAA
1 TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTGCAA
* * * *
2959 ACTTAGGGAGATCAGGCTGGTGCC
66 ACTCAGGGAGGTCAGGCTTGTGTC
*
2983 TTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTG
1 TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTG
3023 TTGCTTCTAT
Statistics
Matches: 198, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 198 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (89 bp):
TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTGCAA
ACTCAGGGAGGTCAGGCTTGTGTC
Found at i:4415 original size:17 final size:17
Alignment explanation
Indices: 4393--4439 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
4383 TTGGCCTCTC
4393 TTTTTTCTTTTTCTTCT
1 TTTTTTCTTTTTCTTCT
*
4410 TTTTTT-TATTTTCTTTT
1 TTTTTTCT-TTTTCTTCT
4427 TTATTTTCTTTTT
1 TT-TTTTCTTTTT
4440 GTTTTTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 16 0.62
18 8 0.31
19 1 0.04
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTCT
Found at i:4426 original size:12 final size:12
Alignment explanation
Indices: 4411--4439 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4401 TTTTCTTCTT
4411 TTTTTTATTTTC
1 TTTTTTATTTTC
4423 TTTTTTATTTTC
1 TTTTTTATTTTC
4435 TTTTT
1 TTTTT
4440 GTTTTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTATTTTC
Found at i:4444 original size:17 final size:16
Alignment explanation
Indices: 4395--4446 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
4385 GGCCTCTCTT
*
4395 TTTTCTTTTTCTTCTTTT
1 TTTTCTTTTT-TT-TTTA
*
4413 TTTTATTTTCTTTTTTA
1 TTTTCTTTT-TTTTTTA
4430 TTTTCTTTTTGTTTTTA
1 TTTTCTTTTT-TTTTTA
4447 ACATTCTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.03
17 17 0.59
18 10 0.34
19 1 0.03
ACGTcount: A:0.06, C:0.10, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTTTTTTA
Found at i:4445 original size:12 final size:11
Alignment explanation
Indices: 4393--4445 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
4383 TTGGCCTCTC
4393 TTTTTTCTTTT
1 TTTTTTCTTTT
4404 TCTTCTTT-TTTT
1 T-TT-TTTCTTTT
*
4416 TATTTTCTTTT
1 TTTTTTCTTTT
4427 TTATTTTCTTTT
1 TT-TTTTCTTTT
4439 TGTTTTT
1 T-TTTTT
4446 AACATTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.09
11 7 0.20
12 21 0.60
13 4 0.11
ACGTcount: A:0.04, C:0.09, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTT
Done.