Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015955.1 Corchorus capsularis cultivar CVL-1 contig15976, 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: 18102
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2693 original size:98 final size:98
Alignment explanation
Indices: 2524--2724 Score: 393
Period size: 98 Copynumber: 2.1 Consensus size: 98
2514 ACCCCTCCCC
*
2524 ATTTGCTCTTGAATTCATGGATTGCATTGGTTAGATTTGTTTTTTTGTATTTTCCATTTTCCATT
1 ATTTGCTCTTGAATTCATGGATTGCATTGGTTAGATTGGTTTTTTTGTATTTTCCATTTTCCATT
2589 CTTCCTATTATTGTTTGTTATGTTATGTTTGTT
66 CTTCCTATTATTGTTTGTTATGTTATGTTTGTT
2622 ATTTGCTCTTGAATTCATGGATTGCATTGGTTAGATTGGTTTTTTTGTATTTTCCATTTTCCATT
1 ATTTGCTCTTGAATTCATGGATTGCATTGGTTAGATTGGTTTTTTTGTATTTTCCATTTTCCATT
2687 CTTCCTATTATTGTTTGTTATGTTATGTTTGTT
66 CTTCCTATTATTGTTTGTTATGTTATGTTTGTT
2720 ATTTG
1 ATTTG
2725 TTATAATGTT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 102 1.00
ACGTcount: A:0.15, C:0.11, G:0.16, T:0.58
Consensus pattern (98 bp):
ATTTGCTCTTGAATTCATGGATTGCATTGGTTAGATTGGTTTTTTTGTATTTTCCATTTTCCATT
CTTCCTATTATTGTTTGTTATGTTATGTTTGTT
Found at i:2738 original size:12 final size:13
Alignment explanation
Indices: 2720--2758 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
2710 TATGTTTGTT
2720 ATTTGTTATAAT-
1 ATTTGTTATAATA
*
2732 GTTTGTTAT-ATA
1 ATTTGTTATAATA
2744 ATTTGTTATAATA
1 ATTTGTTATAATA
2757 AT
1 AT
2759 AAGTTCGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 2 0.09
12 16 0.70
13 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (13 bp):
ATTTGTTATAATA
Found at i:3055 original size:25 final size:25
Alignment explanation
Indices: 3016--3099 Score: 118
Period size: 25 Copynumber: 3.4 Consensus size: 25
3006 TTCAAACCCT
*
3016 AAACTTCATTCCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACTTCTTC
* *
3041 AAAGTTCATTTCTAACAACTTCTCC
1 AAACTTCATTTCTAACAACTTCTTC
*
3066 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACTTCTTC
3090 AAAC-TCATTT
1 AAACTTCATTT
3100 TCCTTCATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.11
24 8 0.15
25 39 0.74
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACTTCTTC
Found at i:3392 original size:15 final size:15
Alignment explanation
Indices: 3372--3408 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3362 TAGTTTGGTT
**
3372 ATTAGTTTATGTTTA
1 ATTAGTTTATAATTA
3387 ATTAGTTTATAATTA
1 ATTAGTTTATAATTA
3402 ATTAGTT
1 ATTAGTT
3409 CATTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (15 bp):
ATTAGTTTATAATTA
Found at i:3623 original size:15 final size:14
Alignment explanation
Indices: 3571--3650 Score: 71
Period size: 14 Copynumber: 5.9 Consensus size: 14
3561 TTGATGATTA
3571 ATTTTAATTAGTTT
1 ATTTTAATTAGTTT
**
3585 ATTAAAATTAGTTT
1 ATTTTAATTAGTTT
*
3599 -GTTT-ATTAGTTT
1 ATTTTAATTAGTTT
3611 ATGTTTAATTAG--T
1 AT-TTTAATTAGTTT
3624 A-TTTAATTAGTTT
1 ATTTTAATTAGTTT
*
3637 ATAATTAATTAGTT
1 AT-TTTAATTAGTT
3651 CATTATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
11 9 0.17
12 8 0.15
13 5 0.10
14 15 0.29
15 15 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (14 bp):
ATTTTAATTAGTTT
Found at i:3644 original size:26 final size:26
Alignment explanation
Indices: 3573--3649 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
3563 GATGATTAAT
*
3573 TTTAATTAGTTTATTAA--AATTAGTT
1 TTTAATTAGTTTA-TAATTAATTAGTA
* **
3598 TGTTTATTAGTTTATGTTTAATTAGTA
1 T-TTAATTAGTTTATAATTAATTAGTA
3625 TTTAATTAGTTTATAATTAATTAGT
1 TTTAATTAGTTTATAATTAATTAGT
3650 TCATTATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 2 0.05
26 32 0.76
27 8 0.19
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.57
Consensus pattern (26 bp):
TTTAATTAGTTTATAATTAATTAGTA
Found at i:3947 original size:24 final size:27
Alignment explanation
Indices: 3914--4009 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 27
3904 CTCCGCCCGT
*
3914 AGGGACAGAGAGG-AGCATT-TG-CAG
1 AGGGAGAGAGAGGCAGCATTCTGCCAG
3938 AGGGAGAGAGAGGCAGCAATTGCTGCTCAG
1 AGGGAGAGAGAGGCAGC-ATT-CTGC-CAG
*
3968 AGGGAGAGAGAGGCAGCAGCTGCTGCTCAG
1 AGGGAGAGAGAGGCAGCA--TTCTGC-CAG
3998 AGGGAGAGAGAG
1 AGGGAGAGAGAG
4010 CTTGCTGCTG
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
24 12 0.19
25 3 0.05
26 3 0.05
28 2 0.03
29 1 0.02
30 40 0.65
31 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.44, T:0.10
Consensus pattern (27 bp):
AGGGAGAGAGAGGCAGCATTCTGCCAG
Found at i:4024 original size:30 final size:30
Alignment explanation
Indices: 3935--4009 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
3925 GGAGCATTTG
**
3935 CAGAGGGAGAGAGAGGCAGCAATTGCTGCT
1 CAGAGGGAGAGAGAGGCAGCAGCTGCTGCT
3965 CAGAGGGAGAGAGAGGCAGCAGCTGCTGCT
1 CAGAGGGAGAGAGAGGCAGCAGCTGCTGCT
3995 CAGAGGGAGAGAGAG
1 CAGAGGGAGAGAGAG
4010 CTTGCTGCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.44, T:0.09
Consensus pattern (30 bp):
CAGAGGGAGAGAGAGGCAGCAGCTGCTGCT
Found at i:9793 original size:15 final size:15
Alignment explanation
Indices: 9706--9787 Score: 64
Period size: 15 Copynumber: 5.5 Consensus size: 15
9696 TATCATTAAT
9706 TAATTAATCATAAAC
1 TAATTAATCATAAAC
9721 TAATTAA--AT--AC
1 TAATTAATCATAAAC
*
9732 TAATTAAACATAAAC
1 TAATTAATCATAAAC
* * **
9747 TAATAAACTAAGTAATTT
1 TAATTAA-TCA-TAA-AC
9765 TAATTAATCATAAAC
1 TAATTAATCATAAAC
9780 TAATTAAT
1 TAATTAAT
9788 ATTAAAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
11 9 0.18
13 4 0.08
15 23 0.45
16 4 0.08
17 5 0.10
18 6 0.12
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (15 bp):
TAATTAATCATAAAC
Found at i:9832 original size:27 final size:26
Alignment explanation
Indices: 9776--9831 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
9766 AATTAATCAT
9776 AAACTAATTAATATTAAAAAAATTAAA
1 AAACTAATTAATA-TAAAAAAATTAAA
*
9803 AAACTAATTAGTA-AAAAAAATTCAAA
1 AAACTAATTAATATAAAAAAATT-AAA
9829 AAA
1 AAA
9832 ATCTTGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.33
26 6 0.22
27 12 0.44
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (26 bp):
AAACTAATTAATATAAAAAAATTAAA
Found at i:12831 original size:42 final size:41
Alignment explanation
Indices: 12729--12843 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 41
12719 ATGTAGAGAA
* ** * *
12729 AATTGCCCTTGTGTTGCATGTGTTT-AGGGACTTTAGTATAG
1 AATTGCCCCTGTGTTATATGTGTTTGA-GGACTTTAGAAGAG
*
12770 -A-TGCCTCTGTGTTATATGTGTTTGAGGACTTTAGAAGGAG
1 AATTGCCCCTGTGTTATATGTGTTTGAGGACTTTAGAA-GAG
*
12810 AATTGCCCCTGTGTTATATGTGTTTGGGGACTTT
1 AATTGCCCCTGTGTTATATGTGTTTGAGGACTTT
12844 GGGGAGAGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
39 28 0.45
40 4 0.06
41 1 0.02
42 29 0.47
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.41
Consensus pattern (41 bp):
AATTGCCCCTGTGTTATATGTGTTTGAGGACTTTAGAAGAG
Found at i:17539 original size:27 final size:27
Alignment explanation
Indices: 17509--17588 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
17499 GCATTAGGGT
* *
17509 CACCCAAGGGTATTTTGGTCATTTTTG
1 CACCCAGGGGCATTTTGGTCATTTTTG
17536 CACCCAGGGGCATTTTGGTCATTTTTG
1 CACCCAGGGGCATTTTGGTCATTTTTG
* * *
17563 TACTCAGGGGCATTTTAGTCATTTTT
1 CACCCAGGGGCATTTTGGTCATTTTT
17589 AGGTGCACCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (27 bp):
CACCCAGGGGCATTTTGGTCATTTTTG
Found at i:18055 original size:20 final size:19
Alignment explanation
Indices: 18027--18077 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
18017 TACATTCAGC
18027 ATAAGCAAAAAAAAGTAATA
1 ATAAGCAAAAAAAA-TAATA
* *
18047 ATAATCAAAATAAATAATA
1 ATAAGCAAAAAAAATAATA
*
18066 AAATAGCAAAAA
1 ATA-AGCAAAAA
18078 TAAGAAGATG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (19 bp):
ATAAGCAAAAAAAATAATA
Found at i:18077 original size:21 final size:23
Alignment explanation
Indices: 18030--18080 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 23
18020 ATTCAGCATA
18030 AGCAAAAA-AAAGTAATAATAAT
1 AGCAAAAATAAAGTAATAATAAT
18052 --C-AAAATAAA-TAATAA-AAT
1 AGCAAAAATAAAGTAATAATAAT
18070 AGCAAAAATAA
1 AGCAAAAATAA
18081 GAAGATGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
18 3 0.12
19 10 0.40
20 5 0.20
21 7 0.28
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (23 bp):
AGCAAAAATAAAGTAATAATAAT
Done.