Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014762.1 Corchorus capsularis cultivar CVL-1 contig14783, 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: 28689
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:12945 original size:14 final size:14
Alignment explanation
Indices: 12915--12952 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
12905 GAAGAACAAA
12915 AAAGAAGAGAAAGG
1 AAAGAAGAGAAAGG
*
12929 AAATAAGA-AAAGAG
1 AAAGAAGAGAAAG-G
12943 AAAGAAGAGA
1 AAAGAAGAGA
12953 GAAAAGGGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 4 0.20
14 15 0.75
15 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (14 bp):
AAAGAAGAGAAAGG
Found at i:13507 original size:28 final size:28
Alignment explanation
Indices: 13475--13532 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
13465 GGACAATCCT
13475 ACTGCAGACTCAAATTATTAAATTCTGA
1 ACTGCAGACTCAAATTATTAAATTCTGA
*
13503 ACTGCAGACTCAAATTATTAAATTTTGA
1 ACTGCAGACTCAAATTATTAAATTCTGA
13531 AC
1 AC
13533 AATCCTACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (28 bp):
ACTGCAGACTCAAATTATTAAATTCTGA
Found at i:13584 original size:36 final size:36
Alignment explanation
Indices: 13507--13584 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
13497 TTCTGAACTG
* *
13507 CAGACTCAAATTATTAAATTTTGAACAATCCTACTC
1 CAGACTCAAATTATTAAATTTTGAACAATCATACAC
*
13543 CAGACTCAAATTATTAAATTTTGAATAATCATACAC
1 CAGACTCAAATTATTAAATTTTGAACAATCATACAC
*
13579 TAGACT
1 CAGACT
13585 TTTAATTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
CAGACTCAAATTATTAAATTTTGAACAATCATACAC
Found at i:21763 original size:2 final size:2
Alignment explanation
Indices: 21756--21781 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21746 TTTTCATAAC
21756 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
21782 TTGGCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23399 original size:1 final size:1
Alignment explanation
Indices: 23395--23428 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
23385 TTCTGCCTTG
*
23395 TTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23429 AAATTTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:28336 original size:3 final size:3
Alignment explanation
Indices: 28328--28384 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
28318 AATAGTAGGT
28328 ATA ATA AT- ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
28373 AT- ATA GTA ATA A
1 ATA ATA ATA ATA A
28385 CACCTGCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:28667 original size:2 final size:2
Alignment explanation
Indices: 28660--28687 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28650 ATTGTAGGCA
28660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28688 CC
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):
AT
Done.