Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021099.1 Corchorus olitorius cultivar O-4 contig21132, 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: 16423
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1119 original size:12 final size:12
Alignment explanation
Indices: 1067--1122 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
1057 CCCGTTGAGG
*
1067 AAATGTTTTATT
1 AAATGTTTTAAT
*
1079 ACA-GTTTTACAT
1 AAATGTTTTA-AT
1091 AAATGATTTT-A-
1 AAATG-TTTTAAT
1102 AAATGTTTTAAT
1 AAATGTTTTAAT
1114 AAATGTTTT
1 AAATGTTTT
1123 GGGTGCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
10 4 0.11
11 12 0.33
12 15 0.42
13 1 0.03
14 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.50
Consensus pattern (12 bp):
AAATGTTTTAAT
Found at i:2413 original size:21 final size:22
Alignment explanation
Indices: 2379--2424 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2369 AAAAAATTAC
2379 AGGGAGATTAACAAAATATCAT
1 AGGGAGATTAACAAAATATCAT
* *
2401 AGGGAGGTT-ACAAAATTTCAT
1 AGGGAGATTAACAAAATATCAT
2422 AGG
1 AGG
2425 AATGTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (22 bp):
AGGGAGATTAACAAAATATCAT
Found at i:2445 original size:44 final size:44
Alignment explanation
Indices: 2381--2491 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 44
2371 AAAATTACAG
* * *
2381 GGAGATTAACAAAATATCATAGGGAGGTT-ACAAAATTTCATA-
1 GGAGTTTATCAAAATTTCATAGGGAGGTTGACAAAATTTCATAT
* ** *
2423 GGAATGTTTATTAAAATTTCATAGTTAGGTTGTCAAAATTTCATAT
1 GG-A-GTTTATCAAAATTTCATAGGGAGGTTGACAAAATTTCATAT
*
2469 GGAGTTTATCACAATTTCATAGG
1 GGAGTTTATCAAAATTTCATAGG
2492 TAATTATCAG
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
42 2 0.04
43 1 0.02
44 37 0.67
45 13 0.24
46 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (44 bp):
GGAGTTTATCAAAATTTCATAGGGAGGTTGACAAAATTTCATAT
Found at i:2522 original size:22 final size:21
Alignment explanation
Indices: 2385--2532 Score: 86
Period size: 22 Copynumber: 6.8 Consensus size: 21
2375 TTACAGGGAG
* * *
2385 ATTAACAAAATATCATAGGGA
1 ATTATCAAAATTTCATAGGTA
*
2406 GGTTA-CAAAATTTCATAGG-A
1 -ATTATCAAAATTTCATAGGTA
* *
2426 ATGTTTATTAAAATTTCATAGTTA
1 A---TTATCAAAATTTCATAGGTA
* *
2450 GGTTGTCAAAATTTCATATGG-A
1 -ATTATCAAAATTTCATA-GGTA
* *
2472 GTTTATCACAATTTCATAGGTA
1 -ATTATCAAAATTTCATAGGTA
* * *
2494 ATTATCAGAATTTTATAGCGTG
1 ATTATCAAAATTTCATAG-GTA
2516 ATTATCAAAATTTCATA
1 ATTATCAAAATTTCATA
2533 AAAATATTCA
Statistics
Matches: 99, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 30 0.30
22 54 0.55
23 13 0.13
24 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
ATTATCAAAATTTCATAGGTA
Found at i:10121 original size:1 final size:1
Alignment explanation
Indices: 10077--10105 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
10067 CCATATCGCG
10077 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10106 CTCTTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12030 original size:30 final size:31
Alignment explanation
Indices: 11965--12038 Score: 105
Period size: 32 Copynumber: 2.4 Consensus size: 31
11955 CGATCATAAA
*
11965 AAGTATGACTCGTAATTCACCAAAAAAAATGG
1 AAGTATGACTCGTAATACACCAAAAAAAA-GG
* *
11997 AAGTATGACTTGTAATACACCCAAAAAAA-G
1 AAGTATGACTCGTAATACACCAAAAAAAAGG
12027 AAGTATGACTCG
1 AAGTATGACTCG
12039 CATGTAGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 12 0.32
32 26 0.68
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (31 bp):
AAGTATGACTCGTAATACACCAAAAAAAAGG
Found at i:12588 original size:42 final size:44
Alignment explanation
Indices: 12537--12630 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
12527 AGTGCATTAT
12537 CTAA-ATTCTACT-T-CATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTATCCATCTCTAGATAATTCATCAAAATAAAG
* *
12578 CTAATATTCTACTCATCCATCTCTAGATAATTCATCCAAATTAAG
1 CTAATATTCTACT-ATCCATCTCTAGATAATTCATCAAAATAAAG
12623 CTAATATT
1 CTAATATT
12631 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 34 0.72
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTATCCATCTCTAGATAATTCATCAAAATAAAG
Done.