Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016844.1 Corchorus olitorius cultivar O-4 contig16877, 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: 5397
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Found at i:2467 original size:17 final size:18
Alignment explanation
Indices: 2428--2469 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2418 AACTTAACCT
*
2428 AAAAAAGAAAGAGGTTAG
1 AAAAAAGAAAGAAGTTAG
2446 AAAAAA-AAAGAAG-TAG
1 AAAAAAGAAAGAAGTTAG
2462 ATAAAAAG
1 A-AAAAAG
2470 GAGGGGTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (18 bp):
AAAAAAGAAAGAAGTTAG
Found at i:3448 original size:38 final size:39
Alignment explanation
Indices: 3367--3498 Score: 117
Period size: 39 Copynumber: 3.4 Consensus size: 39
3357 TTATCCTAGC
* * * * *
3367 AAACCTGCTTAGGTCCCCT-TTCAGAATTGC-CATTTATGC
1 AAACCTGCTTAGGT-CTCTGTTTAGAAAT-CTCATTTAAGA
* *
3406 AAACCTGTTTAGGTCTGTGTTTAG-AATCTCATTTAAGA
1 AAACCTGCTTAGGTCTCTGTTTAGAAATCTCATTTAAGA
* * * *
3444 AAACCCGCTTAGGTCTCTGTTTAGAAATTTCGTTTAAGT
1 AAACCTGCTTAGGTCTCTGTTTAGAAATCTCATTTAAGA
*
3483 GAACCTGCTTAGGTCT
1 AAACCTGCTTAGGTCT
3499 ACGTTCATGA
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
37 1 0.01
38 32 0.43
39 42 0.56
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (39 bp):
AAACCTGCTTAGGTCTCTGTTTAGAAATCTCATTTAAGA
Found at i:3493 original size:39 final size:38
Alignment explanation
Indices: 3406--3984 Score: 258
Period size: 39 Copynumber: 15.4 Consensus size: 38
3396 CCATTTATGC
* * * * *
3406 AAACCTGTTTAGGTCTGTGTTTAGAATCTCATTTAAGA
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTCGTTTAAGT
*
3444 AAACCCGCTTAGGTCTCTGTTTAGAAATTTCGTTTAAGT
1 AAACCTGCTTAGGTCTCTGTTTAG-AATTTCGTTTAAGT
* * * *
3483 GAACCTGCTTAGGTCTAC-GTTCATGAGTTTCGTTTAATCT
1 AAACCTGCTTAGGTCT-CTGTTTA-GAATTTCGTTTAA-GT
*** * *
3523 TCGCCTGCTTAGGTC-CTTGTGTAAAATTTTCGTTTAAGT
1 AAACCTGCTTAGGTCTC-TGTTTAGAA-TTTCGTTTAAGT
* * * *
3562 GAACCTGCTTAGGTCTATGTTTATGAGTTTCGTTTAATCT
1 AAACCTGCTTAGGTCTCTGTTTA-GAATTTCGTTTAA-GT
*** * * *
3602 TCGCCTGCTTAGGTC-CTTGTGTAAAATTTCCGTTTAAGA
1 AAACCTGCTTAGGTCTC-TGTTTAGAATTT-CGTTTAAGT
* *
3641 AAACCTGCTTAGAG---C--TTT-G-A--TC---AAAGC
1 AAACCTGCTTAG-GTCTCTGTTTAGAATTTCGTTTAAGT
* *
3668 AAACCGGCTTAGGTC-CTTGTTTAGAATTTTCGTTTAAGC
1 AAACCTGCTTAGGTCTC-TGTTTAGAA-TTTCGTTTAAGT
*
3707 AAACCTGCTTAGGTC-CTTGTTTAGAATTTTCGTTTAAGC
1 AAACCTGCTTAGGTCTC-TGTTTAGAA-TTTCGTTTAAGT
* * ** * * *
3746 AAACCTGCTTAGATCTCCGCGTAGAGTCTCGTTCAAGT
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTCGTTTAAGT
* *
3784 AAACCTGCTTAGG--TC-G-TT-G-ACTT-GTTTAAAT
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTCGTTTAAGT
* * ** * *
3815 GAACCTGCTTAGGATCTCTGCTTAGGGCTTT-GATCAAGT
1 AAACCTGCTTAGG-TCTCTGTTTA-GAATTTCGTTTAAGT
* * * * *
3854 AAACCTGCTTAGGTCCCTATATA-AAGTTGCCATTTAAGT
1 AAACCTGCTTAGGTCTCTGTTTAGAA-TT-TCGTTTAAGT
** * *
3893 AAACCTGCTTAGGTCTAGGTTTAGAATTTCATTTAAGA
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTCGTTTAAGT
* **
3931 AAACCTGCTTAGGTC-CTCGTTTAGAATTTTTGTTTAACC
1 AAACCTGCTTAGGTCTCT-GTTTAGAA-TTTCGTTTAAGT
*
3970 GAACCTGCTTAGGTC
1 AAACCTGCTTAGGTC
3985 CCTCTTTACA
Statistics
Matches: 408, Mismatches: 92, Indels: 81
0.70 0.16 0.14
Matches are distributed among these distances:
26 1 0.00
27 14 0.03
28 1 0.00
30 1 0.00
31 22 0.05
32 2 0.00
33 3 0.01
34 3 0.01
35 4 0.01
36 6 0.01
37 2 0.00
38 82 0.20
39 209 0.51
40 58 0.14
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (38 bp):
AAACCTGCTTAGGTCTCTGTTTAGAATTTCGTTTAAGT
Found at i:3537 original size:40 final size:39
Alignment explanation
Indices: 3486--3616 Score: 140
Period size: 40 Copynumber: 3.3 Consensus size: 39
3476 TTTAAGTGAA
*
3486 CCTGCTTAGGTCTACGTTCATGAGTTTCGTTTAATCTTCG
1 CCTGCTTAGGTCTATGTT-ATGAGTTTCGTTTAATCTTCG
** * * ***
3526 CCTGCTTAGGTCCT-TGTGTAAAATTTTCGTTTAA-GTGAA
1 CCTGCTTAGGT-CTATGT-TATGAGTTTCGTTTAATCTTCG
3565 CCTGCTTAGGTCTATGTTTATGAGTTTCGTTTAATCTTCG
1 CCTGCTTAGGTCTATG-TTATGAGTTTCGTTTAATCTTCG
3605 CCTGCTTAGGTC
1 CCTGCTTAGGTC
3617 CTTGTGTAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
38 2 0.03
39 27 0.38
40 39 0.55
41 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.43
Consensus pattern (39 bp):
CCTGCTTAGGTCTATGTTATGAGTTTCGTTTAATCTTCG
Found at i:3554 original size:79 final size:79
Alignment explanation
Indices: 3450--3652 Score: 320
Period size: 79 Copynumber: 2.6 Consensus size: 79
3440 AAGAAAACCC
*
3450 GCTTAGGT-CTCTGTTTAGAAA-TTTCGTTTAAGTGAACCTGCTTAGGTCTACGTTCATGAGTTT
1 GCTTAGGTCCT-TGTGTA-AAATTTTCGTTTAAGTGAACCTGCTTAGGTCTACGTTCATGAGTTT
3513 CGTTTAATCTTCGCCT
64 CGTTTAATCTTCGCCT
* *
3529 GCTTAGGTCCTTGTGTAAAATTTTCGTTTAAGTGAACCTGCTTAGGTCTATGTTTATGAGTTTCG
1 GCTTAGGTCCTTGTGTAAAATTTTCGTTTAAGTGAACCTGCTTAGGTCTACGTTCATGAGTTTCG
3594 TTTAATCTTCGCCT
66 TTTAATCTTCGCCT
* **
3608 GCTTAGGTCCTTGTGTAAAATTTCCGTTTAAGAAAACCTGCTTAG
1 GCTTAGGTCCTTGTGTAAAATTTTCGTTTAAGTGAACCTGCTTAG
3653 AGCTTTGATC
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
78 3 0.03
79 111 0.96
80 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (79 bp):
GCTTAGGTCCTTGTGTAAAATTTTCGTTTAAGTGAACCTGCTTAGGTCTACGTTCATGAGTTTCG
TTTAATCTTCGCCT
Found at i:3636 original size:40 final size:39
Alignment explanation
Indices: 3510--3638 Score: 145
Period size: 40 Copynumber: 3.3 Consensus size: 39
3500 CGTTCATGAG
3510 TTTCGTTTAATCTTCGCCTGCTTAGGTCCTTGTGTAAAA
1 TTTCGTTTAATCTTCGCCTGCTTAGGTCCTTGTGTAAAA
* *** * * *
3549 TTTTCGTTTAA-GTGAACCTGCTTAGGT-CTATGTTTATGAG
1 -TTTCGTTTAATCTTCGCCTGCTTAGGTCCT-TGTGTA-AAA
3589 TTTCGTTTAATCTTCGCCTGCTTAGGTCCTTGTGTAAAA
1 TTTCGTTTAATCTTCGCCTGCTTAGGTCCTTGTGTAAAA
3628 TTTCCGTTTAA
1 TTT-CGTTTAA
3639 GAAAACCTGC
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
38 2 0.03
39 31 0.44
40 35 0.50
41 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.45
Consensus pattern (39 bp):
TTTCGTTTAATCTTCGCCTGCTTAGGTCCTTGTGTAAAA
Found at i:3935 original size:38 final size:38
Alignment explanation
Indices: 3884--3959 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
3874 ATAAAGTTGC
* *
3884 CATTTAAGTAAACCTGCTTAGGT-CTAGGTTTAGAATTT
1 CATTTAAGAAAACCTGCTTAGGTCCT-CGTTTAGAATTT
3922 CATTTAAGAAAACCTGCTTAGGTCCTCGTTTAGAATTT
1 CATTTAAGAAAACCTGCTTAGGTCCTCGTTTAGAATTT
3960 TTGTTTAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (38 bp):
CATTTAAGAAAACCTGCTTAGGTCCTCGTTTAGAATTT
Found at i:4765 original size:23 final size:24
Alignment explanation
Indices: 4735--4784 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
4725 ATTGAATTGA
4735 AAAAAAAAG-AAAGAAGAAAAGTC
1 AAAAAAAAGAAAAGAAGAAAAGTC
4758 AAAAAAAAGAAAAAGAAGAAAAGTC
1 AAAAAAAAG-AAAAGAAGAAAAGTC
4783 AA
1 AA
4785 GTTCCATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 9 0.36
25 16 0.64
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (24 bp):
AAAAAAAAGAAAAGAAGAAAAGTC
Done.