Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019940.1 Corchorus olitorius cultivar O-4 contig19973, 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: 14870
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:116 original size:15 final size:16
Alignment explanation
Indices: 91--120 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
81 AATTTGCTAA
91 AATTCATTATATGAAC
1 AATTCATTATATGAAC
107 AATT-ATTATATGAA
1 AATTCATTATATGAA
121 TAAATACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
AATTCATTATATGAAC
Found at i:461 original size:42 final size:43
Alignment explanation
Indices: 410--502 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
400 AGAGCAATAT
*
410 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATC-AAATAAAG
*
451 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAATAAAG
1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAATAAAG
495 CTAATATT
1 CTAATATT
503 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
41 3 0.07
42 8 0.18
43 2 0.04
44 15 0.33
45 17 0.38
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAATAAAG
Found at i:1651 original size:22 final size:22
Alignment explanation
Indices: 1622--1702 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
1612 TGAATATTTT
1622 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAACTATCC
* * *
1644 TATTAAATTTTGATAACCA-CGT
1 TATGAAATTTTGATAACTATC-C
*
1666 TATGAAATTTTGATAA-TAACC
1 TATGAAATTTTGATAACTATCC
*
1687 TATGAAATTGTGATAA
1 TATGAAATTTTGATAA
1703 ACTCCATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 17 0.34
22 33 0.66
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACTATCC
Found at i:1763 original size:21 final size:22
Alignment explanation
Indices: 1739--1793 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
1729 ACTATTAATA
1739 AACCTTCCTATGAAATTTTG-T
1 AACCTTCCTATGAAATTTTGAT
* *
1760 AACCTTTCTATG-AGTTTTGAT
1 AACCTTCCTATGAAATTTTGAT
1781 AACC-TCACTATGA
1 AACCTTC-CTATGA
1794 GATCGGTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (22 bp):
AACCTTCCTATGAAATTTTGAT
Found at i:3565 original size:11 final size:11
Alignment explanation
Indices: 3541--3575 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3531 TTGACAGCGC
3541 AACAAAAACAA
1 AACAAAAACAA
* *
3552 AACGAAAACGA
1 AACAAAAACAA
3563 AACAAAAACAA
1 AACAAAAACAA
3574 AA
1 AA
3576 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:3988 original size:10 final size:10
Alignment explanation
Indices: 3973--4005 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3963 GGGTTGGTCA
3973 ATAATAATAT
1 ATAATAATAT
3983 ATAATAATAT
1 ATAATAATAT
*
3993 AT-ATAAAAT
1 ATAATAATAT
4002 ATAA
1 ATAA
4006 AAGTCTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAATAATAT
Found at i:4695 original size:27 final size:26
Alignment explanation
Indices: 4646--4697 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
4636 TTTTCATTAT
4646 TTTAATAATGAAATAATTAAAATATTG
1 TTTAATAATGAAAT-ATTAAAATATTG
4673 TTTAATAATGACAAT-TTAGAAATAT
1 TTTAATAATGA-AATATTA-AAATAT
4698 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.13
27 17 0.74
28 3 0.13
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (26 bp):
TTTAATAATGAAATATTAAAATATTG
Found at i:4851 original size:71 final size:72
Alignment explanation
Indices: 4754--4893 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 72
4744 TTCATACTTT
4754 TATATATAGTATAGATAAAGCTTCTTGGGTAGTAGTAATAATTAATTCTACTGCAACTCTTCTTG
1 TATATATAGTATAGATAAAGCTTCTTGGGTAGTAGTAATAATTAATTCTACTGCAACTCTTCTTG
4819 GGTTATA
66 GGTTATA
*
4826 TATATATA-TATATATAAAGCTTCTTGGGTAGTAGTAATAATTAATTCTACTGCAACTCTTCTTG
1 TATATATAGTATAGATAAAGCTTCTTGGGTAGTAGTAATAATTAATTCTACTGCAACTCTTCTTG
4890 GGTT
66 GGTT
4894 TCCTTTTAAG
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 59 0.88
72 8 0.12
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (72 bp):
TATATATAGTATAGATAAAGCTTCTTGGGTAGTAGTAATAATTAATTCTACTGCAACTCTTCTTG
GGTTATA
Found at i:10342 original size:2 final size:2
Alignment explanation
Indices: 10335--10361 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10325 CACCAAATCC
10335 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
10362 GTGTAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11433 original size:25 final size:25
Alignment explanation
Indices: 11405--11485 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
11395 ACCAATTGAT
11405 TCTAATTAGATAGCTAGTGTCGTCA
1 TCTAATTAGATAGCTAGTGTCGTCA
* *
11430 TCTAATTAGTATA-CTAAT-TAGT-A
1 TCTAATTAG-ATAGCTAGTGTCGTCA
*
11453 -CTAATTAGCTAGCTAGTGTCGTCA
1 TCTAATTAGATAGCTAGTGTCGTCA
11477 TCTAATTAG
1 TCTAATTAG
11486 TTGATGACCC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
21 2 0.04
22 12 0.26
23 4 0.09
24 4 0.09
25 21 0.46
26 3 0.07
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (25 bp):
TCTAATTAGATAGCTAGTGTCGTCA
Done.