Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007838.1 Corchorus capsularis cultivar CVL-1 contig07859, 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: 7914
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:463 original size:31 final size:30
Alignment explanation
Indices: 393--464 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
383 GACACCTTGC
*
393 TACAGGTAATACCCACGTGGTTACACATGT
1 TACAGGTAATACCCACGTGGTTACACACGT
* * * *
423 TATAAGTAATACCCCACTTGGTTACATACGT
1 TACAGGTAATA-CCCACGTGGTTACACACGT
454 TACAGGTAATA
1 TACAGGTAATA
465 TACTCTGTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (30 bp):
TACAGGTAATACCCACGTGGTTACACACGT
Found at i:497 original size:16 final size:16
Alignment explanation
Indices: 476--536 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
466 ACTCTGTAAC
476 TGGTAATACATGTTGT
1 TGGTAATACATGTTGT
* *
492 TGGTAATACCT-TATGAC
1 TGGTAATACATGT-TG-T
509 TGGTAATACATATTGTTGT
1 TGGTAATAC--A-TGTTGT
528 TGGTAATAC
1 TGGTAATAC
537 CCTGTGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
15 1 0.03
16 12 0.34
17 9 0.26
19 9 0.26
20 3 0.09
21 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (16 bp):
TGGTAATACATGTTGT
Found at i:1234 original size:41 final size:44
Alignment explanation
Indices: 1138--1238 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 44
1128 CTATTAACCA
* * *
1138 TATTATCCATATATATTTAAGAGATAATTATGGTGATTATTATAT
1 TATTAACCATAT-TATTCAAGAGATAAATATGGTGATTATTATAT
* *
1183 AATTACCCATATTATTCATAGAGATAAATAT-G-GATTA-TAT-T
1 TATTAACCATATTATTCA-AGAGATAAATATGGTGATTATTATAT
1224 TATTAACCATATTAT
1 TATTAACCATATTAT
1239 CTACATAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 14 0.29
42 3 0.06
43 5 0.10
44 6 0.12
45 21 0.43
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.44
Consensus pattern (44 bp):
TATTAACCATATTATTCAAGAGATAAATATGGTGATTATTATAT
Found at i:4369 original size:7 final size:7
Alignment explanation
Indices: 4357--4388 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
4347 AATTGCAACT
4357 TTTTTTG
1 TTTTTTG
4364 -TTTTT-
1 TTTTTTG
4369 TTTTTTG
1 TTTTTTG
4376 TTTTTTG
1 TTTTTTG
4383 TTTTTT
1 TTTTTT
4389 TTACGGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 10 0.43
7 13 0.57
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (7 bp):
TTTTTTG
Found at i:4373 original size:12 final size:12
Alignment explanation
Indices: 4356--4387 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
4346 GAATTGCAAC
4356 TTTTTTTGTTTT
1 TTTTTTTGTTTT
4368 TTTTTTTGTTTT
1 TTTTTTTGTTTT
4380 TTGTTTTT
1 TT-TTTTT
4388 TTTACGGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTTGTTTT
Done.