Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003772.1 Corchorus capsularis cultivar CVL-1 contig03780, 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, 657
Length: 1095
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Found at i:350 original size:22 final size:21
Alignment explanation
Indices: 317--437 Score: 84
Period size: 22 Copynumber: 5.5 Consensus size: 21
307 CACATTTTGA
* *
317 AAATTTGGTAACATCATTATG
1 AAATTTGATAACATCACTATG
* *
338 AAATTTCGATAACCTCCCTATG
1 AAATTT-GATAACATCACTATG
*
360 AAAATTTGATAACCA-CACTGTG
1 -AAATTTGATAA-CATCACTATG
*
382 AAATTTTGGTAACCAT-ACTATG
1 AAA-TTTGATAA-CATCACTATG
* * *
404 AAATTTCGATAACCTCAGTGTG
1 AAATTT-GATAACATCACTATG
426 AAATTTTGATAA
1 AAA-TTTGATAA
438 TCCGCCTATA
Statistics
Matches: 79, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
21 14 0.18
22 55 0.70
23 10 0.13
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (21 bp):
AAATTTGATAACATCACTATG
Found at i:371 original size:66 final size:66
Alignment explanation
Indices: 293--437 Score: 193
Period size: 66 Copynumber: 2.2 Consensus size: 66
283 CTCCAATGTA
* * * *
293 AAAATATTGATAACCACATTTTGAAAATTTGGTAA-CATCATTATGAAATTTCGATAACCTCCCT
1 AAAAT-TTGATAACCACACTGTGAAAATTTGGTAACCAT-ACTATGAAATTTCGATAACCTCACT
357 ATG
64 ATG
* * *
360 AAAATTTGATAACCACACTGTGAAATTTTGGTAACCATACTATGAAATTTCGATAACCTCAGTGT
1 AAAATTTGATAACCACACTGTGAAAATTTGGTAACCATACTATGAAATTTCGATAACCTCACTAT
425 G
66 G
*
426 AAATTTTGATAA
1 AAAATTTGATAA
438 TCCGCCTATA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
66 61 0.88
67 8 0.12
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (66 bp):
AAAATTTGATAACCACACTGTGAAAATTTGGTAACCATACTATGAAATTTCGATAACCTCACTAT
G
Found at i:384 original size:44 final size:43
Alignment explanation
Indices: 314--453 Score: 133
Period size: 44 Copynumber: 3.2 Consensus size: 43
304 AACCACATTT
* * * *
314 TGAAAATTTGGTAA-CATCATTATGAAATTTCGATAACCTCCCTA
1 TGAAAATTTGATAACCA-CACTGTGAAATTTTGATAACCT-CCTA
* *
358 TGAAAATTTGATAACCACACTGTGAAATTTTGGTAACCATACTA
1 TGAAAATTTGATAACCACACTGTGAAATTTTGATAACC-TCCTA
* * *
402 TG-AAATTTCGATAACCTCAGTGTGAAATTTTGATAATCCGCCTA
1 TGAAAATTT-GATAACCACACTGTGAAATTTTGATAA-CCTCCTA
446 T-AAAATTT
1 TGAAAATTT
454 TAATAATCAC
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.08
44 69 0.86
45 5 0.06
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (43 bp):
TGAAAATTTGATAACCACACTGTGAAATTTTGATAACCTCCTA
Found at i:452 original size:66 final size:66
Alignment explanation
Indices: 293--549 Score: 181
Period size: 66 Copynumber: 3.9 Consensus size: 66
283 CTCCAATGTA
* * * *
293 AAAATATTGATAACCACATTTTGAAAA-TTTGGTAACATCATTATGAAATTTCGATAACCTCCCT
1 AAAAT-TTGATAACCACACTAT-AAAATTTTGGTAACATCACTATGAAATTTCGATAACCTCACT
357 ATG
64 ATG
* * * *
360 AAAATTTGATAACCACACTGTGAAATTTTGGTAACCAT-ACTATGAAATTTCGATAACCTCAGTG
1 AAAATTTGATAACCACACTATAAAATTTTGGTAA-CATCACTATGAAATTTCGATAACCTCACTA
424 TG
65 TG
* * ** * * * *
426 AAATTTTGATAATCCGC-CTATAAAATTTTAATAATCA-CACTAAAT-AAAATT-GGTGACCGCA
1 AAAATTTGATAA-CCACACTATAAAATTTTGGTAA-CATCACT--ATGAAATTTCGATAACCTCA
*
487 ATATG
62 CTATG
* * * * *
492 AAAATTTTGATAA-C-C-TTATAAAATTTTGATAACAACACCATGATATTTCGATAACCTC
1 AAAA-TTTGATAACCACACTATAAAATTTTGGTAACATCACTATGAAATTTCGATAACCTC
550 CCTCTGAGAA
Statistics
Matches: 151, Mismatches: 29, Indels: 23
0.74 0.14 0.11
Matches are distributed among these distances:
62 2 0.01
63 6 0.04
64 25 0.17
65 4 0.03
66 88 0.58
67 24 0.16
68 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (66 bp):
AAAATTTGATAACCACACTATAAAATTTTGGTAACATCACTATGAAATTTCGATAACCTCACTAT
G
Found at i:619 original size:22 final size:22
Alignment explanation
Indices: 589--646 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
579 ATATGTATTT
* *
589 TTTTTATAACCTCTCC-ATAACA
1 TTTTCATAACCTC-CCTATAAAA
611 TTTTCATAACCTCCCTATAAAA
1 TTTTCATAACCTCCCTATAAAA
**
633 TTTTGTTAACCTCC
1 TTTTCATAACCTCC
647 ATAGGAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.29, C:0.28, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTTCATAACCTCCCTATAAAA
Found at i:756 original size:22 final size:22
Alignment explanation
Indices: 694--763 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
684 CCTCCCTATG
* * *
694 TTTTGGTAACCTCTAAATGAAA
1 TTTTGATAACTTCTATATGAAA
* * ** *
716 TTTTGATAAGTACCCTATGAAG
1 TTTTGATAACTTCTATATGAAA
738 TTTTGATAACTTCTATATGAAA
1 TTTTGATAACTTCTATATGAAA
760 TTTT
1 TTTT
764 CGTAACCACA
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (22 bp):
TTTTGATAACTTCTATATGAAA
Done.