Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015289.1 Corchorus olitorius cultivar O-4 contig15322, 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: 21642
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:502 original size:83 final size:83
Alignment explanation
Indices: 404--568 Score: 321
Period size: 83 Copynumber: 2.0 Consensus size: 83
394 AAAGTAAAAA
404 TTAAATAATTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAGTA
1 TTAAATAATTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAGTA
469 TAAAAGTTTAAATAATGG
66 TAAAAGTTTAAATAATGG
*
487 TTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAGTA
1 TTAAATAATTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAGTA
552 TAAAAGTTTAAATAATG
66 TAAAAGTTTAAATAATG
569 ACATTTAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.38
Consensus pattern (83 bp):
TTAAATAATTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAGTA
TAAAAGTTTAAATAATGG
Found at i:5552 original size:14 final size:14
Alignment explanation
Indices: 5533--5559 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5523 TGTCTATGAT
5533 ATGAATAAATATTA
1 ATGAATAAATATTA
5547 ATGAATAAATATT
1 ATGAATAAATATT
5560 GAATTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
ATGAATAAATATTA
Found at i:5900 original size:25 final size:26
Alignment explanation
Indices: 5865--5915 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
5855 TAATAAATTA
*
5865 ATAATGGCAATTT-AAATATATTTTG
1 ATAATGACAATTTAAAATATATTTTG
5890 ATAATGACAATTTAGAAATATATTTT
1 ATAATGACAATTTA-AAATATATTTT
5916 AAAAAAGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
27 11 0.48
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (26 bp):
ATAATGACAATTTAAAATATATTTTG
Found at i:6752 original size:3 final size:3
Alignment explanation
Indices: 6746--6773 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6736 ATAATAATAA
6746 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6774 GGCCAACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:7709 original size:22 final size:22
Alignment explanation
Indices: 7684--7883 Score: 156
Period size: 22 Copynumber: 9.1 Consensus size: 22
7674 TCAAAAAATT
* *
7684 ATAGGGAGATTAACAAAATTTC
1 ATAGGGAGGTTATCAAAATTTC
**
7706 ATAGGGAGGTTAT-AAAAAATC
1 ATAGGGAGGTTATCAAAATTTC
* *
7727 ATAAGAAGGTTA-CAAAATTTC
1 ATAGGGAGGTTATCAAAATTTC
* *
7748 ATAAGGAGGGTTTATTAAAATTTC
1 ATAGGGA-GG-TTATCAAAATTTC
*** *
7772 ATATTTAGGTTATCAAAGTTTC
1 ATAGGGAGGTTATCAAAATTTC
* * *
7794 ATATGGAGTTTATCAAGATTTC
1 ATAGGGAGGTTATCAAAATTTC
* *
7816 ATAGGTA-ATTATCAAAATTTC
1 ATAGGGAGGTTATCAAAATTTC
* * *
7837 ATAGCGTGGTTATCAAAATTTA
1 ATAGGGAGGTTATCAAAATTTC
*
7859 ATAGGGTA-ATTATCAAAATTTC
1 ATAGGG-AGGTTATCAAAATTTC
7881 ATA
1 ATA
7884 AAAATATTCA
Statistics
Matches: 139, Mismatches: 33, Indels: 12
0.76 0.18 0.07
Matches are distributed among these distances:
21 44 0.32
22 78 0.56
23 5 0.04
24 12 0.09
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.35
Consensus pattern (22 bp):
ATAGGGAGGTTATCAAAATTTC
Found at i:7723 original size:43 final size:44
Alignment explanation
Indices: 7676--7883 Score: 156
Period size: 43 Copynumber: 4.8 Consensus size: 44
7666 CTATAATATC
* *
7676 AAAAAATT-ATAGGGAGATTAACAAAATTTCATAGGGAGGTTAT
1 AAAAATTTCATAGGGAGATTATCAAAATTTCATAGGGAGGTTAT
* * * * *
7719 AAAAA-ATCATAAGAAGGTTA-CAAAATTTCATAAGGAGGGTTTAT
1 AAAAATTTCATAGGGAGATTATCAAAATTTCATAGGGA-GG-TTAT
* *** * * * *
7763 TAAAATTTCATATTTAGGTTATCAAAGTTTCATATGGAGTTTAT
1 AAAAATTTCATAGGGAGATTATCAAAATTTCATAGGGAGGTTAT
* * * * *
7807 CAAGATTTCATAGGTA-ATTATCAAAATTTCATAGCGTGGTTAT
1 AAAAATTTCATAGGGAGATTATCAAAATTTCATAGGGAGGTTAT
* *
7850 CAAAATTTAATAGGGTA-ATTATCAAAATTTCATA
1 AAAAATTTCATAGGG-AGATTATCAAAATTTCATA
7884 AAAATATTCA
Statistics
Matches: 133, Mismatches: 26, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
42 16 0.12
43 49 0.37
44 42 0.32
45 12 0.09
46 14 0.11
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (44 bp):
AAAAATTTCATAGGGAGATTATCAAAATTTCATAGGGAGGTTAT
Found at i:7728 original size:21 final size:20
Alignment explanation
Indices: 7676--7743 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
7666 CTATAATATC
* *
7676 AAAAAATTATAGGGAGATTA
1 AAAAAATCATAGGGAGGTTA
*
7696 ACAAAATTTCATAGGGAGGTTA
1 A-AAAA-ATCATAGGGAGGTTA
* *
7718 TAAAAAATCATAAGAAGGTTA
1 -AAAAAATCATAGGGAGGTTA
7739 CAAAA
1 -AAAA
7744 TTTCATAAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.03
21 20 0.53
22 16 0.42
23 1 0.03
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (20 bp):
AAAAAATCATAGGGAGGTTA
Found at i:7749 original size:21 final size:21
Alignment explanation
Indices: 7696--7752 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
7686 AGGGAGATTA
* *
7696 ACAAAATTTCATAGGGAGGTT
1 ACAAAATTTCATAAGAAGGTT
* **
7717 ATAAAAAATCATAAGAAGGTT
1 ACAAAATTTCATAAGAAGGTT
7738 ACAAAATTTCATAAG
1 ACAAAATTTCATAAG
7753 GAGGGTTTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (21 bp):
ACAAAATTTCATAAGAAGGTT
Found at i:8729 original size:52 final size:54
Alignment explanation
Indices: 8651--8773 Score: 187
Period size: 52 Copynumber: 2.3 Consensus size: 54
8641 AGGGTCATTC
* *
8651 AGGGGTATTTTGGTCATTTTTACACTAGGGGTATTTTGATCATTTTT-ATA-CT
1 AGGGGCATTTTGGTCATTTTTACACTAGGGGCATTTTGATCATTTTTCATATCT
* *
8703 AGGGGCATTTTGGTCATTTTTACACTAGGGGCATTTTGGTCATTTTTCATATTT
1 AGGGGCATTTTGGTCATTTTTACACTAGGGGCATTTTGATCATTTTTCATATCT
*
8757 AGGGGCGTTTTGGTCAT
1 AGGGGCATTTTGGTCAT
8774 CTTGCATACT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 44 0.69
53 3 0.05
54 17 0.27
ACGTcount: A:0.19, C:0.11, G:0.24, T:0.46
Consensus pattern (54 bp):
AGGGGCATTTTGGTCATTTTTACACTAGGGGCATTTTGATCATTTTTCATATCT
Found at i:8768 original size:28 final size:26
Alignment explanation
Indices: 8651--8773 Score: 165
Period size: 26 Copynumber: 4.7 Consensus size: 26
8641 AGGGTCATTC
*
8651 AGGGGTATTTTGGTCATTTTTACACT
1 AGGGGCATTTTGGTCATTTTTACACT
* * *
8677 AGGGGTATTTTGATCATTTTTATACT
1 AGGGGCATTTTGGTCATTTTTACACT
8703 AGGGGCATTTTGGTCATTTTTACACT
1 AGGGGCATTTTGGTCATTTTTACACT
* *
8729 AGGGGCATTTTGGTCATTTTTCATATTT
1 AGGGGCATTTTGGTCATTTTT-ACA-CT
*
8757 AGGGGCGTTTTGGTCAT
1 AGGGGCATTTTGGTCAT
8774 CTTGCATACT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
26 68 0.78
27 2 0.02
28 17 0.20
ACGTcount: A:0.19, C:0.11, G:0.24, T:0.46
Consensus pattern (26 bp):
AGGGGCATTTTGGTCATTTTTACACT
Found at i:8781 original size:28 final size:28
Alignment explanation
Indices: 8702--8781 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
8692 ATTTTTATAC
** * *
8702 TAGGGGCATTTTGGTCAT-TTTTACA-C
1 TAGGGGCATTTTGGTCATCTTGCATATT
* *
8728 TAGGGGCATTTTGGTCATTTTTCATATT
1 TAGGGGCATTTTGGTCATCTTGCATATT
*
8756 TAGGGGCGTTTTGGTCATCTTGCATA
1 TAGGGGCATTTTGGTCATCTTGCATA
8782 CTCAGGGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 18 0.39
27 5 0.11
28 23 0.50
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.44
Consensus pattern (28 bp):
TAGGGGCATTTTGGTCATCTTGCATATT
Found at i:8788 original size:28 final size:26
Alignment explanation
Indices: 8651--8788 Score: 141
Period size: 26 Copynumber: 5.2 Consensus size: 26
8641 AGGGTCATTC
* * *
8651 AGGGGTATTTTGGTCATTTTTACACT
1 AGGGGCATTTTGGTCATTTTCATACT
* * *
8677 AGGGGTATTTTGATCATTTTTATACT
1 AGGGGCATTTTGGTCATTTTCATACT
* *
8703 AGGGGCATTTTGGTCATTTTTACACT
1 AGGGGCATTTTGGTCATTTTCATACT
*
8729 AGGGGCATTTTGGTCATTTTTCATATTT
1 AGGGGCATTTTGGTCA-TTTTCATA-CT
* *
8757 AGGGGCGTTTTGGTCATCTTGCATACT
1 AGGGGCATTTTGGTCAT-TTTCATACT
8784 CAGGG
1 -AGGG
8789 TTTTTCTTTG
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
26 63 0.65
27 8 0.08
28 26 0.27
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (26 bp):
AGGGGCATTTTGGTCATTTTCATACT
Found at i:19914 original size:2 final size:2
Alignment explanation
Indices: 19907--19937 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19897 TCGGCTTGGT
19907 CA CA CA CA CA CA CA CA CA CA CA -A CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19938 TATAGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.