Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020920.1 Corchorus olitorius cultivar O-4 contig20953, 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: 13497
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:91 original size:2 final size:2
Alignment explanation
Indices: 84--111 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
74 CTTTAACTAG
84 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
112 ATTTACACGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:324 original size:2 final size:2
Alignment explanation
Indices: 317--343 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
307 TTCTTCGAGG
317 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
344 ATTACGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:546 original size:87 final size:90
Alignment explanation
Indices: 448--626 Score: 258
Period size: 93 Copynumber: 2.0 Consensus size: 90
438 TTGTTTAAAT
*
448 TTTTATAG-TTT-T-CTAAAAACTTTATTTTTATTTAATTAAATCTAATATCCTTATAAC-TATT
1 TTTTATAGTTTTATACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-ACGTATT
* *
509 TTATTTTTACCATTTTACTATTTTAG
65 TTATATTTACCATATTACTATTTTAG
535 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACGTA
1 TTTTATAGTTTTA-T--ACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACGTA
*
600 TTTTATATTTACGATATTACTATTTTA
63 TTTTATATTTACCATATTACTATTTTA
627 ATTAAAAGCT
Statistics
Matches: 81, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
87 8 0.10
88 3 0.04
90 1 0.01
92 2 0.02
93 67 0.83
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.54
Consensus pattern (90 bp):
TTTTATAGTTTTATACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACGTATTT
TATATTTACCATATTACTATTTTAG
Found at i:1288 original size:16 final size:16
Alignment explanation
Indices: 1263--1294 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1253 TTTGGCCTTA
1263 GGTCACTCGGGTTTTG
1 GGTCACTCGGGTTTTG
*
1279 GGTCATTCGGGTTTTG
1 GGTCACTCGGGTTTTG
1295 AGTTTTTCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.38, T:0.41
Consensus pattern (16 bp):
GGTCACTCGGGTTTTG
Found at i:5224 original size:25 final size:25
Alignment explanation
Indices: 5196--5250 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5186 AATTTAATAT
5196 ATTTAA-AATTAAAAAACTATAATTA
1 ATTTAAGAATTAAAAAA-TATAATTA
* *
5221 ATTTAAGATTTAAAGAATATAATTA
1 ATTTAAGAATTAAAAAATATAATTA
5246 ATTTA
1 ATTTA
5251 TTTAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTAAGAATTAAAAAATATAATTA
Found at i:7593 original size:2 final size:2
Alignment explanation
Indices: 7586--7625 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
7576 ATGGAGTAGT
7586 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7626 GTGTGGCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8597 original size:22 final size:21
Alignment explanation
Indices: 8506--8606 Score: 69
Period size: 22 Copynumber: 4.6 Consensus size: 21
8496 TCATAATTAG
* *
8506 GTTATCATAATTTCATATGG-A
1 GTTATCAAAATTTAATA-GGTA
*
8527 GTTTATCACAATTTAATAGGTAA
1 G-TTATCAAAATTTAATAGGT-A
* ** ** *
8550 ATTATCAAAATTCCATAACATG
1 GTTATCAAAATTTAAT-AGGTA
8572 GTTATCAAAATTTAATAGGGTA
1 GTTATCAAAATTTAATA-GGTA
8594 GTTATCAAAATTT
1 GTTATCAAAATTT
8607 CATAAAAATA
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
21 4 0.07
22 53 0.88
23 3 0.05
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
GTTATCAAAATTTAATAGGTA
Found at i:9748 original size:14 final size:14
Alignment explanation
Indices: 9729--9778 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
9719 TTCTCACATG
9729 ATATATATATCTAT
1 ATATATATATCTAT
9743 ATATATATAT-TAT
1 ATATATATATCTAT
9756 -T-T-TATATCTAT
1 ATATATATATCTAT
9767 ACTATAGTATAT
1 A-TATA-TATAT
9779 AAAAGCCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
10 5 0.17
11 4 0.13
12 1 0.03
13 4 0.13
14 11 0.37
16 5 0.17
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (14 bp):
ATATATATATCTAT
Done.