Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013300.1 Corchorus olitorius cultivar O-4 contig13333, 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: 26145
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:482 original size:25 final size:24
Alignment explanation
Indices: 454--510 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
444 GTGGATTGTA
*
454 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
* *
479 AAATAAATTTAAGAATTAAATATT
1 AAATAAATTGAAGAATTAAACATT
503 AAA-AAATT
1 AAATAAATT
511 CAAGGCTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 7 0.24
25 17 0.59
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:645 original size:16 final size:16
Alignment explanation
Indices: 626--680 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
616 AACCCAGCAA
626 ACCTGAGACCCGAATG
1 ACCTGAGACCCGAATG
**
642 ACCTGA-ACCAAAATG
1 ACCTGAGACCCGAATG
*
657 AGCC-GAAACCCGAATG
1 A-CCTGAGACCCGAATG
*
673 ACCCGAGA
1 ACCTGAGA
681 AAATTACCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.38, C:0.31, G:0.22, T:0.09
Consensus pattern (16 bp):
ACCTGAGACCCGAATG
Found at i:1543 original size:2 final size:2
Alignment explanation
Indices: 1536--1565 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1526 TTCATACTTT
1536 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
1566 ATCGAAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2716 original size:3 final size:3
Alignment explanation
Indices: 2708--2734 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2698 ATTTATATAT
2708 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
2735 TTGTTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:2921 original size:2 final size:2
Alignment explanation
Indices: 2914--2943 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2904 GTAACTAGTC
2914 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
2944 ATCTAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11303 original size:11 final size:10
Alignment explanation
Indices: 11287--11333 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
11277 AAACTCGTGT
11287 TTGAAGACTCA
1 TTGAAGA-TCA
*
11298 TTGAAGATAA
1 TTGAAGATCA
11308 TTTGAAGAT--
1 -TTGAAGATCA
11317 TTGAAGATCA
1 TTGAAGATCA
11327 TTGAAGA
1 TTGAAGA
11334 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:11322 original size:19 final size:18
Alignment explanation
Indices: 11298--11333 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11288 TGAAGACTCA
11298 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
11317 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
11334 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:23610 original size:17 final size:17
Alignment explanation
Indices: 23590--23628 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
23580 AATTTTCTGA
23590 TTTTTCCATTTTTCCAT
1 TTTTTCCATTTTTCCAT
**
23607 TTTTTCTTTTTTTCCAT
1 TTTTTCCATTTTTCCAT
23624 TTTTT
1 TTTTT
23629 TTTTTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCCATTTTTCCAT
Found at i:23633 original size:17 final size:17
Alignment explanation
Indices: 23598--23644 Score: 66
Period size: 15 Copynumber: 3.0 Consensus size: 17
23588 GATTTTTCCA
23598 TTTTTCCATTTTTTCTT
1 TTTTTCCATTTTTTCTT
23615 TTTTTCCA--TTTT-TT
1 TTTTTCCATTTTTTCTT
23629 TTTTT-CATTTTTTCTT
1 TTTTTCCATTTTTTCTT
23645 CAACTTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.07
14 7 0.26
15 8 0.30
16 2 0.07
17 8 0.30
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCCATTTTTTCTT
Found at i:23639 original size:8 final size:8
Alignment explanation
Indices: 23589--23642 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
23579 TAATTTTCTG
*
23589 ATTTTTCC
1 ATTTTTTC
*
23597 ATTTTTCC
1 ATTTTTTC
23605 ATTTTTTC
1 ATTTTTTC
*
23613 TTTTTTTCC
1 ATTTTTT-C
23622 A-TTTTT-
1 ATTTTTTC
23628 -TTTTTTC
1 ATTTTTTC
23635 ATTTTTTC
1 ATTTTTTC
23643 TTCAACTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 5 0.13
8 33 0.85
9 1 0.03
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTTC
Done.