Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024426.1 Corchorus olitorius cultivar O-4 contig24459, 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: 37123
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:16938 original size:11 final size:11
Alignment explanation
Indices: 16922--16952 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16912 CAAACCTTGG
16922 ACCCGGCCCGA
1 ACCCGGCCCGA
*
16933 ACCCGGCCTGA
1 ACCCGGCCCGA
16944 ACCCGGCCC
1 ACCCGGCCC
16953 ATGAACACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.16, C:0.55, G:0.26, T:0.03
Consensus pattern (11 bp):
ACCCGGCCCGA
Found at i:19614 original size:23 final size:26
Alignment explanation
Indices: 19570--19619 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
19560 CTCGACAAGT
* *
19570 TAAAGAAGAATATGAGATGAAGGAGA
1 TAAAGAAGAATATGAGAGGAAGAAGA
19596 TAAAGAAGAATA-G-G-GGAAGAAGA
1 TAAAGAAGAATATGAGAGGAAGAAGA
19619 T
1 T
19620 GGAAGAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 1 0.05
25 1 0.05
26 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.32, T:0.14
Consensus pattern (26 bp):
TAAAGAAGAATATGAGAGGAAGAAGA
Found at i:19831 original size:27 final size:27
Alignment explanation
Indices: 19756--19820 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
19746 AAATATATAT
19756 ATATATATTTAATTAGTAAAAAGATAA
1 ATATATATTTAATTAGTAAAAAGATAA
19783 ATATATATTTAATTAGTAAAAAGATAA
1 ATATATATTTAATTAGTAAAAAGATAA
19810 ATATATATTTA
1 ATATATATTTA
19821 TTTGCAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (27 bp):
ATATATATTTAATTAGTAAAAAGATAA
Found at i:23683 original size:156 final size:156
Alignment explanation
Indices: 23399--23747 Score: 644
Period size: 156 Copynumber: 2.2 Consensus size: 156
23389 AAGTTCAAGT
23399 TTTCACTTCAAATCCAGAACATATATTTATCAATTTAATTGAGTTCAAATTAATTTCCATTGACT
1 TTTCACTTCAAATCCAGAACATATATTTATCAATTTAATTGAGTTCAAATTAATTTCCATTGACT
**
23464 TAAATTATTAAATTCTATAATTTTGAAGTGAAATTTCTGCTCAACTTACAGAACAATTATTTATC
66 TAAATTATTAAACCCTATAATTTTGAAGTGAAATTTCTGCTCAACTTACAGAACAATTATTTATC
*
23529 AAGAACATATATTTATAGAACATAGA
131 AAGAACATATATTTACAGAACATAGA
*
23555 TTTCACTTCAAATACAGAACATATATTTATCAATTTAATTGAGTTCAAATTAATTTCCATTGACT
1 TTTCACTTCAAATCCAGAACATATATTTATCAATTTAATTGAGTTCAAATTAATTTCCATTGACT
23620 TAAATTATTAAACCCTATAATTTTGAAGTGAAATTTCTGCTCAACTTACAGAACAATTATTTATC
66 TAAATTATTAAACCCTATAATTTTGAAGTGAAATTTCTGCTCAACTTACAGAACAATTATTTATC
*
23685 AAGAACATATATTTACAGAACATATA
131 AAGAACATATATTTACAGAACATAGA
*
23711 TTTCACTTCAAATCCAGAACATATATATATCAATTTA
1 TTTCACTTCAAATCCAGAACATATATTTATCAATTTA
23748 CAAAAAGTTT
Statistics
Matches: 186, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
156 186 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (156 bp):
TTTCACTTCAAATCCAGAACATATATTTATCAATTTAATTGAGTTCAAATTAATTTCCATTGACT
TAAATTATTAAACCCTATAATTTTGAAGTGAAATTTCTGCTCAACTTACAGAACAATTATTTATC
AAGAACATATATTTACAGAACATAGA
Found at i:23706 original size:15 final size:15
Alignment explanation
Indices: 23665--23713 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
23655 TCTGCTCAAC
23665 TTACAGAACA-ATTAT
1 TTACAGAACATA-TAT
23680 TTATCAAGAACATATAT
1 TTA-C-AGAACATATAT
23697 TTACAGAACATATAT
1 TTACAGAACATATAT
23712 TT
1 TT
23714 CACTTCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 16 0.52
16 2 0.06
17 12 0.39
18 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (15 bp):
TTACAGAACATATAT
Found at i:25355 original size:17 final size:18
Alignment explanation
Indices: 25325--25365 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
25315 TAGTTATTTT
25325 ATTATTTGACTATAATTA
1 ATTATTTGACTATAATTA
25343 ATTATTT-ACTATAATTA
1 ATTATTTGACTATAATTA
*
25360 TTTATT
1 ATTATT
25366 ATTGTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATTTGACTATAATTA
Found at i:31955 original size:21 final size:21
Alignment explanation
Indices: 31925--31970 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31915 GTGAAAATTG
* *
31925 ATAATTAAATAGATAATGATA-
1 ATAATGAAATAG-TAATAATAT
31946 ATAATGAAATAGTAATAATAT
1 ATAATGAAATAGTAATAATAT
31967 ATAA
1 ATAA
31971 CATAAAAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (21 bp):
ATAATGAAATAGTAATAATAT
Done.