Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021234.1 Corchorus olitorius cultivar O-4 contig21267, 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: 27660
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:10217 original size:30 final size:30
Alignment explanation
Indices: 10183--10243 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
10173 TCCACATGAA
*
10183 AATGAAAATGAAAACCCTTACATTACATGC
1 AATGAAAATGAAAACCCTTAAATTACATGC
10213 AATGAAAATGAAAACCCTTAAATTACATGC
1 AATGAAAATGAAAACCCTTAAATTACATGC
10243 A
1 A
10244 CACACTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.23
Consensus pattern (30 bp):
AATGAAAATGAAAACCCTTAAATTACATGC
Found at i:17446 original size:57 final size:56
Alignment explanation
Indices: 17358--17472 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 56
17348 TATCCGTTTC
17358 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTAT-CCCCCTATCTCTACTTAATTATT
17415 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
17471 CT
1 CT
17473 ACAAAATAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 25 0.43
57 33 0.57
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:17485 original size:57 final size:57
Alignment explanation
Indices: 17367--17478 Score: 183
Period size: 56 Copynumber: 2.0 Consensus size: 57
17357 CCTTTCACAC
* * *
17367 AATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTCTTTCACAC
1 AATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTCTTACAAAA
17424 AATAAATGTTATAATAAATCCTAT-CCCCCTATCTCTACTTAATTATTC-TACAAAA
1 AATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTCTTACAAAA
17479 TAAATAATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 4 0.08
56 24 0.46
57 24 0.46
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (57 bp):
AATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTCTTACAAAA
Found at i:22562 original size:16 final size:16
Alignment explanation
Indices: 22541--22571 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
22531 AAGACCTGAA
22541 TTCCATATGTAATGAG
1 TTCCATATGTAATGAG
22557 TTCCATATGTAATGA
1 TTCCATATGTAATGA
22572 AGTATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (16 bp):
TTCCATATGTAATGAG
Found at i:24317 original size:20 final size:20
Alignment explanation
Indices: 24292--24330 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
24282 AATTACGATT
*
24292 TAGGTAAATATAGGGTTATC
1 TAGGTAAATATAAGGTTATC
24312 TAGGTAAATATAAGGTTAT
1 TAGGTAAATATAAGGTTAT
24331 GCTGGCAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (20 bp):
TAGGTAAATATAAGGTTATC
Found at i:25203 original size:49 final size:46
Alignment explanation
Indices: 25098--25242 Score: 182
Period size: 49 Copynumber: 3.0 Consensus size: 46
25088 GAGCGTGCCA
* * * *
25098 ATCAATTTTGTTGAAAAATTGATAAAAAGTACAGTGAAAATTAAAAG
1 ATCAATTTTGTTTAAAAATTGAGAAAAAGTGCAGT-AAAAATAAAAG
25145 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGT-TTAAAAATTGAGAAAAAG-TGC-AGTAAAAATAAAAG
* * *
25194 TTCAATTTTGTAATAAAAATTGAGAAAAAGTGCAGTAAAAGTAAAAG
1 ATCAATTTTGT-TTAAAAATTGAGAAAAAGTGCAGTAAAAATAAAAG
25241 AT
1 AT
25243 TGCTTGGAGT
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
47 25 0.29
48 19 0.22
49 39 0.45
50 3 0.03
ACGTcount: A:0.52, C:0.05, G:0.15, T:0.28
Consensus pattern (46 bp):
ATCAATTTTGTTTAAAAATTGAGAAAAAGTGCAGTAAAAATAAAAG
Found at i:26548 original size:9 final size:8
Alignment explanation
Indices: 26518--26559 Score: 66
Period size: 8 Copynumber: 5.0 Consensus size: 8
26508 TTAATTCATT
26518 TAATTTCC
1 TAATTTCC
26526 TAATTTCC
1 TAATTTCC
26534 TAATTTCC
1 TAATTTCC
26542 ATAATTTCCC
1 -TAATTT-CC
26552 TAATTTCC
1 TAATTTCC
26560 ATAAGTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 18 0.56
9 12 0.38
10 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (8 bp):
TAATTTCC
Found at i:26555 original size:18 final size:17
Alignment explanation
Indices: 26518--26563 Score: 76
Period size: 18 Copynumber: 2.7 Consensus size: 17
26508 TTAATTCATT
26518 TAATTTCC-TAATTTCC
1 TAATTTCCATAATTTCC
26534 TAATTTCCATAATTTCCC
1 TAATTTCCATAATTT-CC
26552 TAATTTCCATAA
1 TAATTTCCATAA
26564 GTAATTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
18 14 0.50
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTTCCATAATTTCC
Found at i:27174 original size:14 final size:14
Alignment explanation
Indices: 27149--27182 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
27139 AGTATAATAC
27149 AGATAGACATAGAT
1 AGATAGACATAGAT
* *
27163 ATATAGATATAGAT
1 AGATAGACATAGAT
27177 AGATAG
1 AGATAG
27183 GTGCTGATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (14 bp):
AGATAGACATAGAT
Found at i:27605 original size:20 final size:20
Alignment explanation
Indices: 27580--27634 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
27570 CGCGAATCTT
27580 TCTCTCTCCTCTTCCCTCTC
1 TCTCTCTCCTCTTCCCTCTC
*
27600 TCTCTCT-CTCTTTCCCTTTC
1 TCTCTCTCCTC-TTCCCTCTC
*
27620 TCTTTCTCTCTCTTC
1 TCTCTCTC-CTCTTC
27635 GAAAGTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.10
20 21 0.70
21 3 0.10
22 3 0.10
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (20 bp):
TCTCTCTCCTCTTCCCTCTC
Done.