Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016243.1 Corchorus olitorius cultivar O-4 contig16276, 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: 62246
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7943 original size:61 final size:61
Alignment explanation
Indices: 7848--7966 Score: 211
Period size: 61 Copynumber: 2.0 Consensus size: 61
7838 TTATGCCATC
* *
7848 TGATGCAAGTTGCGAAGATATTGAGGTGCTTTCAAATTGCATTTCTTTTGGTTAATTAGTT
1 TGATGCAAGTTGCGAAGATATTGAGGTGCTTTCAAATTGCATTCCTTTTGCTTAATTAGTT
*
7909 TGATGCAAGTTGTGAAGATATTGAGGTGCTTTCAAATTGCATTCCTTTTGCTTAATTA
1 TGATGCAAGTTGCGAAGATATTGAGGTGCTTTCAAATTGCATTCCTTTTGCTTAATTA
7967 TGGCCTCCCT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (61 bp):
TGATGCAAGTTGCGAAGATATTGAGGTGCTTTCAAATTGCATTCCTTTTGCTTAATTAGTT
Found at i:10418 original size:17 final size:19
Alignment explanation
Indices: 10396--10437 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
10386 ATAGCTACCT
10396 ACAAACCAAA-TAC-ACAA
1 ACAAACCAAATTACTACAA
10413 ACAAA-CAAATTACTACAA
1 ACAAACCAAATTACTACAA
10431 ATCAAAC
1 A-CAAAC
10438 TCACATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 8 0.38
18 5 0.24
19 4 0.19
ACGTcount: A:0.62, C:0.26, G:0.00, T:0.12
Consensus pattern (19 bp):
ACAAACCAAATTACTACAA
Found at i:14891 original size:39 final size:39
Alignment explanation
Indices: 14846--14925 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
14836 CCTTACCAAC
14846 TCAACAAACCTCAATTGGCCCTTGCTCCCTGTCTCTGTG
1 TCAACAAACCTCAATTGGCCCTTGCTCCCTGTCTCTGTG
14885 TCAACAAACCTCAATTGGCCCTTGCTCCCTGTCTCTGTG
1 TCAACAAACCTCAATTGGCCCTTGCTCCCTGTCTCTGTG
14924 TC
1 TC
14926 TTTGGTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.17, C:0.36, G:0.15, T:0.31
Consensus pattern (39 bp):
TCAACAAACCTCAATTGGCCCTTGCTCCCTGTCTCTGTG
Found at i:14980 original size:15 final size:15
Alignment explanation
Indices: 14960--14993 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
14950 TAAGTAATTG
14960 CATTTGCATTGGGAT
1 CATTTGCATTGGGAT
*
14975 CATTTGCATTTGGAT
1 CATTTGCATTGGGAT
14990 CATT
1 CATT
14994 GGGGGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (15 bp):
CATTTGCATTGGGAT
Found at i:20337 original size:44 final size:44
Alignment explanation
Indices: 20274--20361 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
20264 TTGACCACTG
20274 TACTAAAAACATCAATTTTCAAAAATTCATTCTAGAATAAGATC
1 TACTAAAAACATCAATTTTCAAAAATTCATTCTAGAATAAGATC
*
20318 TACTAAAAACATCAATTTTCAAAAATTCATTTTAGAATAAGATC
1 TACTAAAAACATCAATTTTCAAAAATTCATTCTAGAATAAGATC
20362 AAAACTCTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (44 bp):
TACTAAAAACATCAATTTTCAAAAATTCATTCTAGAATAAGATC
Found at i:22404 original size:29 final size:29
Alignment explanation
Indices: 22362--22418 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
22352 GTCTTGAATA
22362 TTGATTGCAGACGAAGAAGAAAAGAAGTG
1 TTGATTGCAGACGAAGAAGAAAAGAAGTG
22391 TTGATTGCAGACGAAGAAGAAAAGAAGT
1 TTGATTGCAGACGAAGAAGAAAAGAAGT
22419 TCAACAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.30, T:0.18
Consensus pattern (29 bp):
TTGATTGCAGACGAAGAAGAAAAGAAGTG
Found at i:33899 original size:16 final size:16
Alignment explanation
Indices: 33878--33914 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
33868 CTATAAAATT
33878 ATATTAAAAAATTCTA
1 ATATTAAAAAATTCTA
*
33894 ATATTAAGAAATTCTA
1 ATATTAAAAAATTCTA
33910 ATATT
1 ATATT
33915 TACGTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (16 bp):
ATATTAAAAAATTCTA
Found at i:35004 original size:86 final size:82
Alignment explanation
Indices: 34905--35074 Score: 214
Period size: 82 Copynumber: 2.0 Consensus size: 82
34895 ATATATATTT
*** * *
34905 AAAAATTATAATATATATCTAAGTTTTGCAATTAAAATAGTTTGATGGTAGAAATAAAATAGTTA
1 AAAAATTAT-A-ATATATCT-A-TTTTGCAATTAAAATAGTAAAATGGTAAAAACAAAATAGTTA
34970 TAAAGAGATTAAATTTAATTA
62 TAAAGAGATTAAATTTAATTA
* ** *
34991 AAAAATTCTAATATATCTATTTTTTAATTAAAATAGTAAAATTGTAAAAACAAAATAGTTATAAA
1 AAAAATTATAATATATCTATTTTGCAATTAAAATAGTAAAATGGTAAAAACAAAATAGTTATAAA
*
35056 GAGATTAGATTTAATTA
66 GAGATTAAATTTAATTA
35073 AA
1 AA
35075 TAAAAATATA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 56 0.76
83 1 0.01
84 8 0.11
85 1 0.01
86 8 0.11
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (82 bp):
AAAAATTATAATATATCTATTTTGCAATTAAAATAGTAAAATGGTAAAAACAAAATAGTTATAAA
GAGATTAAATTTAATTA
Found at i:38227 original size:12 final size:12
Alignment explanation
Indices: 38195--38230 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
38185 TCGGTGCTTC
*
38195 CCAAATCCAAAT
1 CCAAATCCGAAT
38207 CCAAATCCGAAT
1 CCAAATCCGAAT
*
38219 CCGAATCCGAAT
1 CCAAATCCGAAT
38231 TCTAACCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (12 bp):
CCAAATCCGAAT
Found at i:45164 original size:28 final size:27
Alignment explanation
Indices: 45132--45186 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
45122 CAATTAGTTC
*
45132 AATTTTTTTTGAGAAACATCAAATACTA
1 AATTTTTTTGGAG-AACATCAAATACTA
* *
45160 AATTTTTTTGGTGAATATCAAATACTA
1 AATTTTTTTGGAGAACATCAAATACTA
45187 TCTACTGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (27 bp):
AATTTTTTTGGAGAACATCAAATACTA
Found at i:48011 original size:18 final size:17
Alignment explanation
Indices: 47988--48024 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
47978 CTATGGTTTT
47988 CTATGATCCACCAGAGTA
1 CTATGATCCACCAG-GTA
*
48006 CTATGATGCACCAGGTA
1 CTATGATCCACCAGGTA
48023 CT
1 CT
48025 TTTCTGCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (17 bp):
CTATGATCCACCAGGTA
Found at i:55465 original size:18 final size:18
Alignment explanation
Indices: 55403--55466 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
55393 CCATGGTGTC
55403 CACCATGGGCACCATAGG
1 CACCATGGGCACCATAGG
* *
55421 CACCGTGGACACCATAGG
1 CACCATGGGCACCATAGG
* * *
55439 CACCGTGGGCTCCATGGG
1 CACCATGGGCACCATAGG
55457 CACCATGGGC
1 CACCATGGGC
55467 GACATGATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.22, C:0.34, G:0.31, T:0.12
Consensus pattern (18 bp):
CACCATGGGCACCATAGG
Found at i:55472 original size:9 final size:9
Alignment explanation
Indices: 55403--55466 Score: 74
Period size: 9 Copynumber: 7.1 Consensus size: 9
55393 CCATGGTGTC
55403 CACCATGGG
1 CACCATGGG
*
55412 CACCATAGG
1 CACCATGGG
* *
55421 CACCGTGGA
1 CACCATGGG
*
55430 CACCATAGG
1 CACCATGGG
*
55439 CACCGTGGG
1 CACCATGGG
*
55448 CTCCATGGG
1 CACCATGGG
55457 CACCATGGG
1 CACCATGGG
55466 C
1 C
55467 GACATGATGA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.22, C:0.34, G:0.31, T:0.12
Consensus pattern (9 bp):
CACCATGGG
Done.