Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_268 ID=scaffold_268-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: 9088
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.31
Warning! 301 characters in sequence are not A, C, G, or T
Found at i:1774 original size:88 final size:88
Alignment explanation
Indices: 1703--2213 Score: 640
Period size: 88 Copynumber: 5.8 Consensus size: 88
1693 TCTTTGATCT
* *
1703 GCTCCA-CTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGAAGGAA
1 GCTCCATC-ACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
*
1767 GGCAAGATCTGTTGTCTTCAACCA
65 GGCAAGATCTTTTGTCTTCAACCA
* * *
1791 GCTCCATCACAACTGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAG
* *
1856 GCAAGATCTATTGTCTTCGACCA
66 GCAAGATCTTTTGTCTTCAACCA
* * * *
1879 GCTCCATCACAACCGAGAGAGGCAAGGTTTGCGTCTTCGACCTACTTCGCTGTCAATGCAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAG
1944 GCAAGATCTTTTGTCTTCAACCA
66 GCAAGATCTTTTGTCTTCAACCA
* * * * *
1967 GCTCCATCACAACCGAGAGAGGAAAGGTTTGTGTCTTTGATCTGCTTCGTTGTTAATGCAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAG
*
2032 GCAAGATCTTTTGTCTTTAACCA
66 GCAAGATCTTTTGTCTTCAACCA
* * * *
2055 GCTCCA-CTGCAACCAATGA-AGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 GCTCCATC-ACAACCGA-GAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* ** *
2117 GGGCAAGATCTGCT-TCTTTAACCA
64 AGGCAAGATCTTTTGTCTTCAACCA
* ** * * * *
2141 GCTCCACCGTAACCAATGA-AGGCAAGGCTT-TGTTTTCGATCTGCTTCGTTGTTAATGCAGGAA
1 GCTCCATCACAACCGA-GAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
2204 GGCAAGATCT
65 GGCAAGATCT
2214 GCTTCTTTAA
Statistics
Matches: 386, Mismatches: 33, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
86 78 0.20
87 42 0.11
88 263 0.68
89 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (88 bp):
GCTCCATCACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAG
GCAAGATCTTTTGTCTTCAACCA
Found at i:1814 original size:44 final size:44
Alignment explanation
Indices: 1766--1988 Score: 158
Period size: 44 Copynumber: 5.1 Consensus size: 44
1756 CAATGAAGGA
*
1766 AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACTGAGAG
1 AGGCAAGATCTGTTGTCTTCGACCAGCTCCATCACAACTGAGAG
* * * **
1810 AGGCAAGGTTTG-TGTCTTCGACCTGCTTCGC-TGTCAA-TGCAG-G
1 AGGCAAGATCTGTTGTCTTCGACCAGC-TC-CATCACAACTG-AGAG
* *
1853 AAGGCAAGATCTATTGTCTTCGACCAGCTCCATCACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCGACCAGCTCCATCACAACTGAGAG
* * * **
1898 AGGCAAGGTTTG-CGTCTTCGACCTA-CTTCGC-TGTCAA-TGCAG-G
1 AGGCAAGATCTGTTGTCTTCGACC-AGC-TC-CATCACAACTG-AGAG
* * *
1941 AAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCGACCAGCTCCATCACAACTGAGAG
1986 AGG
1 AGG
1989 AAAGGTTTGT
Statistics
Matches: 133, Mismatches: 28, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
43 30 0.23
44 74 0.56
45 29 0.22
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (44 bp):
AGGCAAGATCTGTTGTCTTCGACCAGCTCCATCACAACTGAGAG
Found at i:3479 original size:21 final size:20
Alignment explanation
Indices: 3455--3525 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
3445 TTAGCCTCTC
3455 CATTTTTACTTTTTCATTTTT
1 CATTTTT-CTTTTTCATTTTT
3476 CATTTTT-TTTCATTCATTTTTT
1 CATTTTTCTTT--TTCA-TTTTT
**
3498 CATTTTTCTTCTTTTTTTTTT
1 CATTTTTCTT-TTTCATTTTT
3519 CATTTTT
1 CATTTTT
3526 TGTTTGAGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
19 3 0.07
21 23 0.53
22 14 0.33
23 2 0.05
24 1 0.02
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (20 bp):
CATTTTTCTTTTTCATTTTT
Found at i:3496 original size:22 final size:21
Alignment explanation
Indices: 3467--3526 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
3457 TTTTTACTTT
3467 TTCA-TTTTTCATTTTTTTTC
1 TTCATTTTTTCATTTTTTTTC
*
3487 ATTCATTTTTTCATTTTTCTTC
1 -TTCATTTTTTCATTTTTTTTC
**
3509 TTTTTTTTTTCATTTTTT
1 TTCATTTTTTCATTTTTT
3527 GTTTGAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (21 bp):
TTCATTTTTTCATTTTTTTTC
Found at i:3505 original size:29 final size:29
Alignment explanation
Indices: 3464--3526 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
3454 CCATTTTTAC
3464 TTTTTCATTTTTCATT-TTTTTTCATTCAT
1 TTTTTCATTTTTC-TTCTTTTTTCATTCAT
**
3493 TTTTTCATTTTTCTTCTTTTTTTTTTCAT
1 TTTTTCATTTTTCTTCTTTTTTCATTCAT
3522 TTTTT
1 TTTTT
3527 GTTTGAGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 2 0.06
29 29 0.94
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTTCATTTTTCTTCTTTTTTCATTCAT
Found at i:4442 original size:20 final size:19
Alignment explanation
Indices: 4419--4487 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
4409 TTCTTTCTTT
*
4419 TTTTCTTATTTTGACTTTGA
1 TTTT-TTATTTTGATTTTGA
*
4439 TTTTTTGATTTTTATTTTGA
1 TTTTTT-ATTTTGATTTTGA
4459 -TTTTT-TTTT-ATTTTGA
1 TTTTTTATTTTGATTTTGA
4475 TTTTTTATTTTGA
1 TTTTTTATTTTGA
4488 GTCGGAACTC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 7 0.16
17 9 0.21
18 4 0.09
19 8 0.19
20 15 0.35
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (19 bp):
TTTTTTATTTTGATTTTGA
Found at i:4468 original size:16 final size:16
Alignment explanation
Indices: 4447--4480 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4437 GATTTTTTGA
4447 TTTTTATTTTGATTTT
1 TTTTTATTTTGATTTT
4463 TTTTTATTTTGATTTT
1 TTTTTATTTTGATTTT
4479 TT
1 TT
4481 ATTTTGAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTATTTTGATTTT
Found at i:4479 original size:12 final size:12
Alignment explanation
Indices: 4441--4478 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
4431 GACTTTGATT
4441 TTTTGATTTTTA
1 TTTTGATTTTTA
4453 TTTTGATTTTT-
1 TTTTGATTTTTA
*
4464 TTTT-ATTTTGA
1 TTTTGATTTTTA
4475 TTTT
1 TTTT
4479 TTATTTTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 5 0.21
11 8 0.33
12 11 0.46
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (12 bp):
TTTTGATTTTTA
Found at i:7116 original size:19 final size:20
Alignment explanation
Indices: 7087--7135 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
7077 CACTTCGTGA
* *
7087 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
7106 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
7126 AAATG-AATGC
1 AAATGTAATGC
7136 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Done.