Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_64 ID=scaffold_64-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: 18604
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.34
Warning! 713 characters in sequence are not A, C, G, or T
Found at i:980 original size:252 final size:250
Alignment explanation
Indices: 535--1035 Score: 885
Period size: 252 Copynumber: 2.0 Consensus size: 250
525 TTTTCTCAAC
* *
535 CTCTGAAATATGAACTTTTATTGGCTTTTGAATCTAGTTTCTCTCTTGCTCTATTTGCATATTTT
1 CTCTGAAATATGAACTTTTATTGGCTTATGAATCTAGTTTCTCTCTTGCTCCATTTGCATATTTT
* * *
600 CCTTATGAAATATGTCTTCAAGAGAGTAAGGGAGATCTAGATTCATAACCCAGCAAAAGTCATCA
66 CCTTATGAAATATGGCTTCAAGAGAGCAAGGGAGACCTAGATTCATAACCCAGCAAAAGTCATCA
* * *
665 ACTTGACTCTAGTCTCTTCCTAATGTTTTTGTAGGGTTAAGAGAAGGTGTTGCAGACACTTTAGA
131 ACTTGACTCTAATCTCTTCCTAATATTTGTGTAGGGTTAAGAGAAGGTGTTGCAGACACTTTAGA
730 TGTTTGAAACTTTTAAGTTTCAAACTCAATGAATGCCATCCTTTTCACGTCTAAT
196 TGTTTGAAACTTTTAAGTTTCAAACTCAATGAATGCCATCCTTTTCACGTCTAAT
* *
785 CTCTGAAATATGAACTTTTATTGGCTTATGAATCTAGTTTCTCTCTTGCTCCATTTTTCATTTTT
1 CTCTGAAATATGAACTTTTATTGGCTTATGAATCTAGTTTCTCTCTTGCTCCA-TTTGCATATTT
850 TCCTTATGAAAATATGGCTTCAAGAGAGCAAGGGAGACCTAGATTCATAACCCAGCAAAAGTCAT
65 TCCTTATG-AAATATGGCTTCAAGAGAGCAAGGGAGACCTAGATTCATAACCCAGCAAAAGTCAT
*
915 CAACTTGACTCTAATCTCTTCCTAATATTTGTGTAGGGTTAAGAGAAGGTGTTGCAGATACTTTA
129 CAACTTGACTCTAATCTCTTCCTAATATTTGTGTAGGGTTAAGAGAAGGTGTTGCAGACACTTTA
980 GATGTTTGAAACTTTTAAGTTTCAAACTCAATGAATGCCATCCTTTTCACGTCTAA
194 GATGTTTGAAACTTTTAAGTTTCAAACTCAATGAATGCCATCCTTTTCACGTCTAA
1036 GCTAAGATGA
Statistics
Matches: 238, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
250 51 0.21
251 17 0.07
252 170 0.71
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (250 bp):
CTCTGAAATATGAACTTTTATTGGCTTATGAATCTAGTTTCTCTCTTGCTCCATTTGCATATTTT
CCTTATGAAATATGGCTTCAAGAGAGCAAGGGAGACCTAGATTCATAACCCAGCAAAAGTCATCA
ACTTGACTCTAATCTCTTCCTAATATTTGTGTAGGGTTAAGAGAAGGTGTTGCAGACACTTTAGA
TGTTTGAAACTTTTAAGTTTCAAACTCAATGAATGCCATCCTTTTCACGTCTAAT
Found at i:1724 original size:50 final size:50
Alignment explanation
Indices: 1644--1738 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
1634 TTGCAACTTG
*
1644 GTTCTCTTATCTAATGTTCGTAGAGCATGTTTGGTTGGCATGAATGGTAA
1 GTTCTCTTATCTAATGTTCGTAGAGAATGTTTGGTTGGCATGAATGGTAA
1694 GTTCTCTTATCTAATGTT-GTTAGAGAATGTTTGGTTGGCATGAAT
1 GTTCTCTTATCTAATGTTCG-TAGAGAATGTTTGGTTGGCATGAAT
1739 AATCAGACCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
49 1 0.02
50 42 0.98
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (50 bp):
GTTCTCTTATCTAATGTTCGTAGAGAATGTTTGGTTGGCATGAATGGTAA
Found at i:12053 original size:18 final size:19
Alignment explanation
Indices: 12030--12073 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
12020 ATTTCCTCTA
*
12030 TTCTCTTTAATTT-TTCCT
1 TTCTCTTTAATTTCTCCCT
*
12048 TTCTCTTTTATTTCTCCCT
1 TTCTCTTTAATTTCTCCCT
12067 TT-TCTTT
1 TTCTCTTT
12074 CTATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTCTTTAATTTCTCCCT
Found at i:15937 original size:17 final size:17
Alignment explanation
Indices: 15911--15946 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15901 GTGTGTTTTG
*
15911 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
*
15928 TTTTGACTGCATGGCAT
1 TTTTGACTGCATGACAT
15945 TT
1 TT
15947 CATCATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Done.