Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002078.1 Corchorus olitorius cultivar O-4 contig02078, 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: 7031
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Found at i:19 original size:2 final size:2
Alignment explanation
Indices: 7--44 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 AGTACT
7 TA TA TA GTA TA TA 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 TA TA TA TA TA TA T
45 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4366 original size:22 final size:22
Alignment explanation
Indices: 4310--4372 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
4300 GTCCCAGGCT
*
4310 ATAATCACATTATGAAATTGTG
1 ATAATCACACTATGAAATTGTG
* *
4332 ATAACCTTC-CTATGAAATTGTG
1 ATAATC-ACACTATGAAATTGTG
*
4354 ATAATCACACTATGGAATT
1 ATAATCACACTATGAAATT
4373 TTAATCCCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (22 bp):
ATAATCACACTATGAAATTGTG
Found at i:4705 original size:18 final size:20
Alignment explanation
Indices: 4660--4706 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
4650 TTAACCTTCT
4660 TATGAAAATTTGAACTACACA
1 TATGAAAATTTGAAC-ACACA
4681 TTATGAAAATTTGAAC-CAC-
1 -TATGAAAATTTGAACACACA
4700 TATGAAA
1 TATGAAA
4707 TTCTAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.28
20 3 0.12
22 15 0.60
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (20 bp):
TATGAAAATTTGAACACACA
Found at i:4746 original size:22 final size:21
Alignment explanation
Indices: 4721--4793 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 21
4711 AAAAACTAAA
*
4721 CTATGAAATTTCAATAACCTCC
1 CTATGAAATTTTAATAA-CTCC
* * *
4743 CTATAAAATTTTGATAACTTC
1 CTATGAAATTTTAATAACTCC
*
4764 ATATGAAATTTTAATAAGCTCC
1 CTATGAAATTTTAATAA-CTCC
*
4786 CTTTGAAA
1 CTATGAAA
4794 GTTTGGTTAC
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 17 0.43
22 23 0.57
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (21 bp):
CTATGAAATTTTAATAACTCC
Found at i:4993 original size:22 final size:21
Alignment explanation
Indices: 4908--5123 Score: 128
Period size: 22 Copynumber: 10.1 Consensus size: 21
4898 TAATCACGAC
* * *
4908 ATTTTGATACCTCTCAATGAA
1 ATTTTGATAACACTCTATGAA
*
4929 ATTTTGATAACCACACTAT-AA
1 ATTTTGATAA-CACTCTATGAA
4950 ATTTTG-TAA-ACTGCATATGAA
1 ATTTTGATAACACT-C-TATGAA
4971 ATTTTGATAACATCTCTATGAA
1 ATTTTGATAACA-CTCTATGAA
* * * *
4993 AATTTGATATCACACCATGAA
1 ATTTTGATAACACTCTATGAA
*
5014 ATTTTGATAACCACT-T-TGAG
1 ATTTTGATAA-CACTCTATGAA
5034 ATTTTGA-AAC-CTCCTTATGAA
1 ATTTTGATAACACT-C-TATGAA
* *
5055 ATTTTTATAACCACAT-TATAAA
1 ATTTTGATAA-CAC-TCTATGAA
* *
5077 ATTCTGATAAC-CTCCGTATAAA
1 ATTTTGATAACACT-C-TATGAA
5099 ATTTTGATAA-ACTCCTTATGAA
1 ATTTTGATAACACT-C-TATGAA
5121 ATT
1 ATT
5124 GAGATTTTTA
Statistics
Matches: 153, Mismatches: 22, Indels: 39
0.71 0.10 0.18
Matches are distributed among these distances:
17 2 0.01
18 3 0.02
19 4 0.03
20 18 0.12
21 50 0.33
22 69 0.45
23 3 0.02
24 3 0.02
25 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
ATTTTGATAACACTCTATGAA
Found at i:5054 original size:41 final size:44
Alignment explanation
Indices: 4924--5108 Score: 147
Period size: 44 Copynumber: 4.3 Consensus size: 44
4914 ATACCTCTCA
* * * * *
4924 ATGAAATTTTGATAACCACACTAT-AAATTTTG-TAAACTGCAT
1 ATGAAATTTTGATAACCACATTATAAAATTCTGATAACCTCCGT
* *
4966 ATGAAATTTTGATAA-CATC-TCTATGAAAATT-TGATATCACACC--
1 ATGAAATTTTGATAACCA-CAT-TAT-AAAATTCTGATAAC-CTCCGT
* * * *
5009 ATGAAATTTTGATAACCAC-TT-TGAGATTTTGA-AACCTCCTT
1 ATGAAATTTTGATAACCACATTATAAAATTCTGATAACCTCCGT
*
5050 ATGAAATTTTTATAACCACATTATAAAATTCTGATAACCTCCGT
1 ATGAAATTTTGATAACCACATTATAAAATTCTGATAACCTCCGT
*
5094 ATAAAATTTTGATAA
1 ATGAAATTTTGATAA
5109 ACTCCTTATG
Statistics
Matches: 114, Mismatches: 16, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
39 3 0.03
40 6 0.05
41 24 0.21
42 22 0.19
43 27 0.24
44 30 0.26
45 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (44 bp):
ATGAAATTTTGATAACCACATTATAAAATTCTGATAACCTCCGT
Done.