Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021702.1 Corchorus olitorius cultivar O-4 contig21735, 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: 12674
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:98 original size:51 final size:50
Alignment explanation
Indices: 10--136 Score: 164
Period size: 50 Copynumber: 2.5 Consensus size: 50
1 AATCTAGCT
* * *
10 CTTTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGCAATCAATCCAG
1 CTTTTTTAAATTGGGAAAGTTCCCACAAGTTTCCAAAGCAATCAATCCAG
* * *
60 CTTTTTTAAATTGGGAAAGTTCCCATCAAGTTTCCAAAGTATTCAATCTAG
1 CTTTTTTAAATTGGGAAAGTTCCCA-CAAGTTTCCAAAGCAATCAATCCAG
*
111 CTCTTTTTAATTTAGGGAAAGTTCCC
1 CT-TTTTTAAATT-GGGAAAGTTCCC
137 GTCATTTTCG
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 24 0.36
51 22 0.33
52 9 0.13
53 12 0.18
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (50 bp):
CTTTTTTAAATTGGGAAAGTTCCCACAAGTTTCCAAAGCAATCAATCCAG
Found at i:5746 original size:14 final size:14
Alignment explanation
Indices: 5703--5746 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5693 ATATAAAAAG
5703 ATTATGGTATTTTT
1 ATTATGGTATTTTT
*
5717 ATTAT--TATTATT
1 ATTATGGTATTTTT
5729 -TTATGGTATTTTT
1 ATTATGGTATTTTT
5742 ATTAT
1 ATTAT
5747 CAATGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.16
12 6 0.24
13 6 0.24
14 9 0.36
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (14 bp):
ATTATGGTATTTTT
Found at i:6741 original size:8 final size:8
Alignment explanation
Indices: 6728--6753 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6718 TTTTATATAG
6728 TAGTAAGA
1 TAGTAAGA
6736 TAGTAAGA
1 TAGTAAGA
6744 TAGTAAGA
1 TAGTAAGA
6752 TA
1 TA
6754 AGATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (8 bp):
TAGTAAGA
Found at i:9209 original size:18 final size:18
Alignment explanation
Indices: 9166--9221 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
9156 GATAATGATG
9166 TGAAAATTTGATAACATCATTA
1 TGAAAATTTGATAAC--C--TA
9188 TG-AAATTTCGATAACCTA
1 TGAAAATTT-GATAACCTA
9206 TGAAAATTTGATAACC
1 TGAAAATTTGATAACC
9222 ACTCTGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 11 0.34
19 6 0.19
20 1 0.03
21 6 0.19
22 8 0.25
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (18 bp):
TGAAAATTTGATAACCTA
Found at i:9264 original size:22 final size:22
Alignment explanation
Indices: 9201--9278 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
9191 AATTTCGATA
*
9201 ACCTATGAAAATTTGATAA-CC
1 ACCTATGAAATTTTGATAATCC
* *
9222 ACTCTGTGAAATTTTGATAATCT
1 AC-CTATGAAATTTTGATAATCC
*
9245 TCCTATGAAATTTTGATAAT-C
1 ACCTATGAAATTTTGATAATCC
*
9266 ACACTATAAAATT
1 AC-CTATGAAATT
9279 GGTAAGCGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.07
22 41 0.89
23 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (22 bp):
ACCTATGAAATTTTGATAATCC
Found at i:9464 original size:24 final size:23
Alignment explanation
Indices: 9368--9492 Score: 82
Period size: 22 Copynumber: 5.6 Consensus size: 23
9358 CTCTTTATCT
* * *
9368 AATTTTGATAACATCTCC-ATCA
1 AATTTTGATAACCTCCCCAATGA
*
9390 AATTTTTG-TAACCT-TCCAATGA
1 AA-TTTTGATAACCTCCCCAATGA
* *
9412 AATTTTGTTAACCTCCCTAA-GA
1 AATTTTGATAACCTCCCCAATGA
* **
9434 AACTTTGATAATTTCCCCCAATGA
1 AATTTTGATAACCT-CCCCAATGA
* * *
9458 AATTTTGATAACC-ACACTAT-A
1 AATTTTGATAACCTCCCCAATGA
9479 AATTTTGATAACCT
1 AATTTTGATAACCT
9493 TCTTATACAA
Statistics
Matches: 81, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
21 22 0.27
22 34 0.42
23 13 0.16
24 12 0.15
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTTTGATAACCTCCCCAATGA
Found at i:9553 original size:22 final size:22
Alignment explanation
Indices: 9454--9645 Score: 99
Period size: 22 Copynumber: 8.7 Consensus size: 22
9444 ATTTCCCCCA
*
9454 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACTCT
*
9476 AT-AAATTTTGATAACC-TTCTT
1 ATGAAATTTTGATAACCACTC-T
*
9497 AT-ACAATTTTGTTAACGACACTCT
1 ATGA-AATTTTGATAAC--CACTCT
* * ** *
9521 AAGAAAATTTGATAACCTTTTT
1 ATGAAATTTTGATAACCACTCT
* *
9543 ATGAAATTTTGGTAACGC-CTGT
1 ATGAAATTTTGATAAC-CACTCT
* * * *
9565 ATAAAATTTTTATAACTACACT
1 ATGAAATTTTGATAACCACTCT
** *
9587 ATGACGTTTTGATAACCTC-CAT
1 ATGAAATTTTGATAACCACTC-T
*
9609 ATGAAATTTT-AGTAACCACACT
1 ATGAAATTTTGA-TAACCACTCT
* *
9631 ATGAAAATTTCATAA
1 ATGAAATTTTGATAA
9646 TCTTCCTATG
Statistics
Matches: 127, Mismatches: 31, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
20 1 0.01
21 20 0.16
22 87 0.69
23 3 0.02
24 13 0.10
25 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACTCT
Done.