Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021563.1 Corchorus olitorius cultivar O-4 contig21596, 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: 8838
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:866 original size:2 final size:2
Alignment explanation
Indices: 859--883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
849 TCTTTACTAG
859 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
884 TTCTTTTCTT
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
Found at i:3112 original size:21 final size:22
Alignment explanation
Indices: 3087--3130 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3077 CACAACAATA
3087 ATTTAGTTA-AAAAATGAATTG
1 ATTTAGTTAGAAAAATGAATTG
3108 ATTTAGTTAGAAAAATGAATTG
1 ATTTAGTTAGAAAAATGAATTG
3130 A
1 A
3131 ATGACAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (22 bp):
ATTTAGTTAGAAAAATGAATTG
Found at i:4579 original size:22 final size:21
Alignment explanation
Indices: 4554--4652 Score: 101
Period size: 22 Copynumber: 4.6 Consensus size: 21
4544 TATTTTTATG
*
4554 AAATTTTGATAATTACCCTATT
1 AAATTTTGATAA-TACCCTATA
4576 AAATTTTGATAAGTACCCTATA
1 AAATTTTGATAA-TACCCTATA
* *
4598 AAATTTTGATAATAACCTATG
1 AAATTTTGATAATACCCTATA
* *
4619 AAATTGTGATAA-ACTCCATATG
1 AAATTTTGATAATAC-CC-TATA
*
4641 AAACTTTGATAA
1 AAATTTTGATAA
4653 CCTAACTATG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.01
21 20 0.30
22 46 0.69
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.37
Consensus pattern (21 bp):
AAATTTTGATAATACCCTATA
Found at i:4616 original size:21 final size:22
Alignment explanation
Indices: 4554--4630 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
4544 TATTTTTATG
* *
4554 AAATTTTGATAATTACCCTATT
1 AAATTTTGATAAGTACCCTATA
4576 AAATTTTGATAAGTACCCTATA
1 AAATTTTGATAAGTACCCTATA
* *
4598 AAATTTTGATAA-TAACCTATG
1 AAATTTTGATAAGTACCCTATA
*
4619 AAATTGTGATAA
1 AAATTTTGATAA
4631 ACTCCATATG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 18 0.36
22 32 0.64
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAAGTACCCTATA
Found at i:4662 original size:22 final size:23
Alignment explanation
Indices: 4593--4693 Score: 79
Period size: 22 Copynumber: 4.6 Consensus size: 23
4583 GATAAGTACC
*
4593 CTATAAAATTTTGAT-AA--TAA
1 CTATGAAATTTTGATAAACCTAA
* *
4613 CCTATGAAATTGTGATAAA-CT-C
1 -CTATGAAATTTTGATAAACCTAA
*
4635 CATATGAAACTTTGAT-AACCTAA
1 C-TATGAAATTTTGATAAACCTAA
* **
4658 CTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTTGATAAACCTAA
4681 CTATGAAATTTTG
1 CTATGAAATTTTG
4694 TAATCTTCCT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
21 16 0.25
22 28 0.44
23 19 0.30
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (23 bp):
CTATGAAATTTTGATAAACCTAA
Found at i:4675 original size:44 final size:44
Alignment explanation
Indices: 4592--4697 Score: 112
Period size: 44 Copynumber: 2.4 Consensus size: 44
4582 TGATAAGTAC
* * *
4592 CCTATAAAATTTTGATAATAACCTATGAAATTGTGATAAA-C-T
1 CCTATGAAACTTTGATAATAACCTATGAAATTGTAATAAACCTT
*
4634 CCATATGAAACTTTGATAACCTAA-CTATGAAATTTTAATAAACCTT
1 CC-TATGAAACTTTGATAA--TAACCTATGAAATTGTAATAAACCTT
*
4680 CCTATGAAATTTTG-TAAT
1 CCTATGAAACTTTGATAAT
4698 CTTCCTATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
42 3 0.06
43 14 0.26
44 19 0.35
45 15 0.28
46 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (44 bp):
CCTATGAAACTTTGATAATAACCTATGAAATTGTAATAAACCTT
Found at i:4684 original size:23 final size:23
Alignment explanation
Indices: 4613--4717 Score: 96
Period size: 22 Copynumber: 4.8 Consensus size: 23
4603 TTGATAATAA
*
4613 CCTATGAAATTGTGATAAA-C-T
1 CCTATGAAATTTTGATAAACCTT
* *
4634 CCATATGAAACTTTGAT-AACCTA
1 CC-TATGAAATTTTGATAAACCTT
* *
4657 ACTATGAAATTTTAATAAACCTT
1 CCTATGAAATTTTGATAAACCTT
*
4680 CCTATGAAATTTTG-T-AATCTT
1 CCTATGAAATTTTGATAAACCTT
*
4701 CCTATG-ATTTTTGATAA
1 CCTATGAAATTTTGATAA
4718 CCTCCTTGTG
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
20 6 0.09
21 16 0.24
22 27 0.40
23 18 0.27
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (23 bp):
CCTATGAAATTTTGATAAACCTT
Found at i:4706 original size:44 final size:44
Alignment explanation
Indices: 4612--4707 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
4602 TTTGATAATA
*
4612 ACCTATGAAATTGTGATAAACTCCATATGAAACTTTGATAACCT
1 ACCTATGAAATTGTAATAAACTCCATATGAAACTTTGATAACCT
* * * *
4656 AACTATGAAATTTTAATAAACCTTCC-TATGAAATTTTG-TAATCT
1 ACCTATGAAATTGTAATAAA-C-TCCATATGAAACTTTGATAACCT
*
4700 TCCTATGA
1 ACCTATGA
4708 TTTTTGATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 28 0.65
45 12 0.28
46 3 0.07
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (44 bp):
ACCTATGAAATTGTAATAAACTCCATATGAAACTTTGATAACCT
Found at i:4720 original size:42 final size:43
Alignment explanation
Indices: 4674--4755 Score: 98
Period size: 42 Copynumber: 1.9 Consensus size: 43
4664 AATTTTAATA
*
4674 AACCTTCC-TATGAAATTTTG-TAATCTTCC-TATGATTTTTGAT
1 AACC-TCCTTATGAAATTTTGTTAATC-TCCTTATAATTTTTGAT
* *
4716 AACCTCCTTGTGAGATTTTGTTAATCTCCTTATAATTTTT
1 AACCTCCTTATGAAATTTTGTTAATCTCCTTATAATTTTT
4756 TACTATAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 3 0.09
42 17 0.50
43 14 0.41
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (43 bp):
AACCTCCTTATGAAATTTTGTTAATCTCCTTATAATTTTTGAT
Found at i:5684 original size:35 final size:35
Alignment explanation
Indices: 5627--5694 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
5617 TTAAACTTTG
*
5627 TAAACACCTTAAGACCCCACTAACTTCAATATCCC
1 TAAACACCTTAAGACCCCACTAACTCCAATATCCC
* * *
5662 TAAATACCTTAAGATCCTACTAACTCCAATATC
1 TAAACACCTTAAGACCCCACTAACTCCAATATC
5695 AAAGAGGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.26
Consensus pattern (35 bp):
TAAACACCTTAAGACCCCACTAACTCCAATATCCC
Done.