Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019385.1 Corchorus olitorius cultivar O-4 contig19418, 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: 34096
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--52 Score: 86
Period size: 2 Copynumber: 25.5 Consensus size: 2
*
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43 AT ACT AT AT A
1 AT A-T AT AT A
53 AGTCTAAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:431 original size:28 final size:28
Alignment explanation
Indices: 374--431 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
364 TTTTGAATTT
*** *
374 TTAACGTGATGTATACTTTTTTTACCAA
1 TTAACGTGATGTATACTTTAAATAACAA
*
402 TTAACGTGATGTATACTTTAAATAATAA
1 TTAACGTGATGTATACTTTAAATAACAA
430 TT
1 TT
432 TTCATTAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (28 bp):
TTAACGTGATGTATACTTTAAATAACAA
Found at i:2459 original size:24 final size:24
Alignment explanation
Indices: 2414--2462 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2404 ATAAACTAAT
*
2414 AAAATTAAAAAAAAATTATTTAGA
1 AAAATTAAAAAAAAAGTATTTAGA
*
2438 AAAATTAAATTAAAAAGT-TTTAGA
1 AAAATTAAA-AAAAAAGTATTTAGA
2462 A
1 A
2463 GTTATTAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (24 bp):
AAAATTAAAAAAAAAGTATTTAGA
Found at i:6047 original size:21 final size:21
Alignment explanation
Indices: 6010--6051 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
6000 TGTTCTGTCT
*
6010 TTCTTTTTATTTATTTTTTTA
1 TTCTTTTTACTTATTTTTTTA
*
6031 TTCTTGTTTACTTTTTTTTTT
1 TTCTT-TTTACTTATTTTTTT
6052 TTTCGAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.81
Consensus pattern (21 bp):
TTCTTTTTACTTATTTTTTTA
Found at i:11677 original size:17 final size:17
Alignment explanation
Indices: 11657--11690 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11647 GTTTTACAAT
11657 GAAAAAATCCATAAATC
1 GAAAAAATCCATAAATC
*
11674 GAAAAAATCCGTAAATC
1 GAAAAAATCCATAAATC
11691 CTCAAAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.18
Consensus pattern (17 bp):
GAAAAAATCCATAAATC
Found at i:25430 original size:1 final size:1
Alignment explanation
Indices: 25424--25449 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
25414 TCTTGTGGCC
25424 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
25450 CTCGAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26878 original size:23 final size:23
Alignment explanation
Indices: 26852--26900 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
26842 TATATAGTAT
26852 CCACCCTTATTTGAATTGAGTGC
1 CCACCCTTATTTGAATTGAGTGC
26875 CCACCCTTATTTGAATTGAGTGC
1 CCACCCTTATTTGAATTGAGTGC
26898 CCA
1 CCA
26901 TTCTCAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (23 bp):
CCACCCTTATTTGAATTGAGTGC
Found at i:26911 original size:23 final size:23
Alignment explanation
Indices: 26852--26912 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
26842 TATATAGTAT
* *
26852 CCACCCTTATTTGAATTGAGTGC
1 CCACCCTCAATTGAATTGAGTGC
* *
26875 CCACCCTTATTTGAATTGAGTGC
1 CCACCCTCAATTGAATTGAGTGC
**
26898 CCATTCTCAATTGAA
1 CCACCCTCAATTGAA
26913 AAATTCATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (23 bp):
CCACCCTCAATTGAATTGAGTGC
Found at i:30720 original size:26 final size:24
Alignment explanation
Indices: 30690--30761 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
30680 ATTTGGCCCC
*
30690 TCCATAATTTTTATTTTCTAATTTAG
1 TCCATAATTTTTATTTT-GAATTT-G
30716 TCCAT--TTTTT-TTTTGAATTTG
1 TCCATAATTTTTATTTTGAATTTG
30737 TCCCATAAATTTTTATTTT-AATTTG
1 T-CCAT-AATTTTTATTTTGAATTTG
30762 GCCCATTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
21 2 0.05
22 9 0.22
23 4 0.10
24 5 0.12
25 11 0.28
26 9 0.22
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.60
Consensus pattern (24 bp):
TCCATAATTTTTATTTTGAATTTG
Found at i:31234 original size:2 final size:2
Alignment explanation
Indices: 31227--31251 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31217 TTCAAATGTT
31227 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31252 GTTGCGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.