Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018909.1 Corchorus olitorius cultivar O-4 contig18942, 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: 8861
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:237 original size:31 final size:31
Alignment explanation
Indices: 200--272 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
190 CTACAAAAAC
* * *
200 TGTCAATTTAGCCCCTCTA-TTTACAATTTGG
1 TGTCAATTGAGCCCCTCTACTTGACAAATT-G
* *
231 TGTCAATTGAGTCCTTCTACTTGACAAATTG
1 TGTCAATTGAGCCCCTCTACTTGACAAATTG
262 TGTCAATTGAG
1 TGTCAATTGAG
273 TAAATTACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 28 0.78
32 8 0.22
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (31 bp):
TGTCAATTGAGCCCCTCTACTTGACAAATTG
Found at i:395 original size:22 final size:19
Alignment explanation
Indices: 344--395 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
334 TGACACGTGG
344 AAAATAAAAAAATATTTTCC
1 AAAA-AAAAAAATATTTTCC
*
364 AAAAATAAAAAAGTAATTTTGC
1 AAAAA-AAAAAA-T-ATTTTCC
*
386 AAAGAAAAAA
1 AAAAAAAAAA
396 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 10 0.37
21 6 0.22
22 10 0.37
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (19 bp):
AAAAAAAAAAATATTTTCC
Found at i:1588 original size:17 final size:17
Alignment explanation
Indices: 1566--1614 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
1556 AAGAAATACA
1566 TTTCAATTCCAGAAAAT
1 TTTCAATTCCAGAAAAT
1583 TTTCAATTCCAGAAAAT
1 TTTCAATTCCAGAAAAT
1600 TTTCAATTCCAGAAA
1 TTTCAATTCCAGAAA
1615 CTACAACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
TTTCAATTCCAGAAAAT
Found at i:3505 original size:43 final size:43
Alignment explanation
Indices: 3444--3776 Score: 346
Period size: 43 Copynumber: 7.9 Consensus size: 43
3434 CCAATAACTA
*
3444 AAAGTCCCCAAACACATTTATAACACAGGGGCACTTCTATTCC
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACTTCTATTCC
*
3487 AAAGTCCTCAAACACATTTATAACACAGAGGCAC--CTATAT-C
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACTTCTAT-TCC
* * *
3528 AAAGTCCCCAAACACAATTATAACACATGGGCATCTT-TATTCC
1 AAAGTCCTCAAACACATTTATAACACAGGGGCA-CTTCTATTCC
*
3571 AAAGTCCTCAAACACATTTATAACACAGAGGCA--TCTATAT-C
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACTTCTAT-TCC
* * * * * *
3612 AAAGTCCCCAAACACAATTATAACACATGGGCAATTCT-CTCTA
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACTTCTATTC-C
* * * * *
3655 AAAGTCCTCAAACACATTTATAACACA-GAG-ACATCCATACT
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACTTCTATTCC
* * *
3696 AAAGTCC-CAAAACACATTTATAACACAGGGGTACCTCTATTTC
1 AAAGTCCTC-AAACACATTTATAACACAGGGGCACTTCTATTCC
* *
3739 AAAGTCCTCAAACACATTTATAACACAGAGGCATTTCT
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACTTCT
3777 CTTTATGGCA
Statistics
Matches: 239, Mismatches: 35, Indels: 32
0.78 0.11 0.10
Matches are distributed among these distances:
40 2 0.01
41 96 0.40
42 9 0.04
43 131 0.55
44 1 0.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (43 bp):
AAAGTCCTCAAACACATTTATAACACAGGGGCACTTCTATTCC
Found at i:3540 original size:84 final size:84
Alignment explanation
Indices: 3444--3771 Score: 475
Period size: 84 Copynumber: 3.9 Consensus size: 84
3434 CCAATAACTA
*
3444 AAAGTCCCCAAACACATTTATAACACAGGGGCACTTCTATTCCAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCACTTCTATTCCAAAGTCCTCAAACACATTTATA
3509 ACACAGAGGCACCTATATC
66 ACACAGAGGCACCTATATC
*
3528 AAAGTCCCCAAACACAATTATAACACATGGGCATCTT-TATTCCAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCA-CTTCTATTCCAAAGTCCTCAAACACATTTAT
*
3592 AACACAGAGGCATCTATATC
65 AACACAGAGGCACCTATATC
* * * *
3612 AAAGTCCCCAAACACAATTATAACACATGGGCAATTCT-CTCTAAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCACTTCTATTC-CAAAGTCCTCAAACACATTTAT
*
3676 AACACAGAGACATCC-ATA-C
65 AACACAGAGGCA-CCTATATC
* * * * *
3695 TAAAGTCCCAAAACACATTTATAACACAGGGGTACCTCTATTTCAAAGTCCTCAAACACATTTAT
1 -AAAGTCCCCAAACACAATTATAACACAGGGGCACTTCTATTCCAAAGTCCTCAAACACATTTAT
3760 AACACAGAGGCA
65 AACACAGAGGCA
3772 TTTCTCTTTA
Statistics
Matches: 220, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
83 5 0.02
84 210 0.95
85 5 0.02
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (84 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCACTTCTATTCCAAAGTCCTCAAACACATTTATA
ACACAGAGGCACCTATATC
Done.