Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013118.1 Corchorus olitorius cultivar O-4 contig13151, whole genome shotgun sequence
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: 11023
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:6538 original size:16 final size:16
Alignment explanation
Indices: 6507--6538 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6497 AATAAATATG
*
6507 CAAAAAAAAACCAAAA
1 CAAAAAAAAACAAAAA
6523 CAAAAAAAAACAAAAA
1 CAAAAAAAAACAAAAA
6539 ATTCAGTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAACAAAAA
Found at i:8156 original size:145 final size:144
Alignment explanation
Indices: 7809--8454 Score: 928
Period size: 145 Copynumber: 4.5 Consensus size: 144
7799 TACTCAGAGA
* *
7809 TTTGCATTTTTAAGACCTCCGGGCACCATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCT
1 TTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTACGGGTATTAATTCTGATAAATCCT
* * * * *
7874 CCGGGTATCATTTCATTTTATCGAGTTTTTAATCAAAGCTGTGTTTAAGTTT----A-AAAACCT
66 CCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATAAAACCT
7934 TGCTCAAGGTTGAG
131 TGCTCAAGGTTGAG
* * *
7948 TTTGCATTCGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCT
1 TTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTACGGGTATTAATTCTGATAAATCCT
*
8013 CCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCATTTAAATTTCAAAATTAAAACC
66 CCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAA-TAAAACC
*
8078 TTGCTCAAGGTTGAT
130 TTGCTCAAGGTTGAG
* *
8093 TTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAGCCTACGGGTATTAATTATGATAAATCCT
1 TTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTACGGGTATTAATTCTGATAAATCCT
*
8158 CCGGGTATGATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAAATCAAAAC
66 CCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTC-AAAAT-AAAAC
8223 CTTGCTCAAGGTTGAG
129 CTTGCTCAAGGTTGAG
* *
8239 TTTGCAATTGTAAGACCTCCGGGCACCATTTCAGAAGCCTACGGGTATTAATTCTGATAAATCC-
1 TTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTACGGGTATTAATTCTGATAAATCCT
* * * *
8303 CCGGGTATGATTTCATTTCATCAAGCTTTTAATCAAAGTTGCGTTTAAGTTTCAAAACCAAAAAA
66 CCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTC-AAA--ATAAAA
8368 CCTTGCTCAAGGTTGAG
128 CCTTGCTCAAGGTTGAG
** * * * * *
8385 TTTGCATCCGTAAGACCTCCGGACACAATTTCAGAAACCT-CTTGGTATTAATTCTGACAAGTCC
1 TTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTAC-GGGTATTAATTCTGATAAATCC
8449 TCCGGG
65 TCCGGG
8455 CATTCCATAT
Statistics
Matches: 463, Mismatches: 32, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
139 108 0.23
143 1 0.00
145 188 0.41
146 160 0.35
147 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (144 bp):
TTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTACGGGTATTAATTCTGATAAATCCT
CCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATAAAACCT
TGCTCAAGGTTGAG
Found at i:8602 original size:40 final size:40
Alignment explanation
Indices: 8555--9136 Score: 782
Period size: 40 Copynumber: 14.6 Consensus size: 40
8545 AGTCAATTTT
8555 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
8595 AACCCTGCTCAGGATCATTGCTATATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
8635 AA-CACTGCTCAAGATCATTGCTATATCAAATTAATTTCAA
1 AATC-CTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * ** *
8675 AACCCTGCTCAAGATCATTGCTTTATCGTATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
8715 AATCCTGCTCAGGATCATCT-TTTTATCGAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
*
8755 AATCCTGCTCAGGATCATCT-TTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
** * *
8795 AGCCCTGCTCAGAATCATTGCTTTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
8835 AATCCTACTCAGGATCATCT-TTTTATCAAATTAATTTCAC
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* *
8875 AACCCTGCTCAGGATCATCGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
8915 AATCCTGCTCAGAATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
8955 AATCCTGCTCAGGATCA-T-CTTT-TTAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
8992 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
9032 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
** * * * * *
9072 AATCCTATTCAGGATTATTACTTTATTAGATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
9112 AATCCTGCTCAGGATCATTTCTTTA
1 AATCCTGCTCAGGATCATTGCTTTA
9137 CCAATCAATC
Statistics
Matches: 487, Mismatches: 46, Indels: 18
0.88 0.08 0.03
Matches are distributed among these distances:
37 31 0.06
38 5 0.01
39 7 0.01
40 441 0.91
41 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (40 bp):
AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
Found at i:9349 original size:27 final size:27
Alignment explanation
Indices: 9268--9343 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
9258 TCAGATAAAA
9268 TTCTGAATCCTATTTAGGATCATTGCTT
1 TTCTGAATCCTATTTAGGATCATTG-TT
* *
9296 TT-AGAATCCTATTCAGGATCATTGTT
1 TTCTGAATCCTATTTAGGATCATTGTT
*
9322 TTCTGAATCTTATTTAGGATCA
1 TTCTGAATCCTATTTAGGATCA
9344 AAGTTTATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.10
27 36 0.86
28 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (27 bp):
TTCTGAATCCTATTTAGGATCATTGTT
Found at i:10580 original size:44 final size:44
Alignment explanation
Indices: 10523--10606 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
10513 GCTCACACTC
*
10523 ATCACACACTGTATTTCTGCATTTACTACAAATCATTTCACATA
1 ATCACACAATGTATTTCTGCATTTACTACAAATCATTTCACATA
* *
10567 ATCACACAATGTATTTCTGCATTTAGTATAAATCATTTCA
1 ATCACACAATGTATTTCTGCATTTACTACAAATCATTTCA
10607 TATACACACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (44 bp):
ATCACACAATGTATTTCTGCATTTACTACAAATCATTTCACATA
Done.