Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005279.1 Corchorus capsularis cultivar CVL-1 contig05297, 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: 3423
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Found at i:420 original size:11 final size:11
Alignment explanation
Indices: 404--450 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
394 AGAGAGTGAT
404 ATGACAAACAA
1 ATGACAAACAA
*
415 ATGACAGAGAGAA
1 ATGACA-A-ACAA
*
428 AT-ACACACAA
1 ATGACAAACAA
438 ATGACAAACAA
1 ATGACAAACAA
449 AT
1 AT
451 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
10 5 0.17
11 15 0.52
12 4 0.14
13 5 0.17
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.11
Consensus pattern (11 bp):
ATGACAAACAA
Found at i:661 original size:138 final size:138
Alignment explanation
Indices: 487--765 Score: 549
Period size: 138 Copynumber: 2.0 Consensus size: 138
477 TTGGTGCTAA
487 CTAGAAGCAACCCATTTTAGTATATTCTCTTTTATTATTATTATGTAATAAAACCCAACACCACC
1 CTAGAAGCAACCCATTTTAGTATATTCTCTTTTATTATTATTATGTAATAAAACCCAACACCACC
552 ATGATACTTCTAGTTAATTAAAGAGTAGTAAACCTTATGTGACGATGTAATCCAACTAGAAGATT
66 ATGATACTTCTAGTTAATTAAAGAGTAGTAAACCTTATGTGACGATGTAATCCAACTAGAAGATT
617 TAGCAAAT
131 TAGCAAAT
*
625 CTAGAAGCAGCCCATTTTAGTATATTCTCTTTTATTATTATTATGTAATAAAACCCAACACCACC
1 CTAGAAGCAACCCATTTTAGTATATTCTCTTTTATTATTATTATGTAATAAAACCCAACACCACC
690 ATGATACTTCTAGTTAATTAAAGAGTAGTAAACCTTATGTGACGATGTAATCCAACTAGAAGATT
66 ATGATACTTCTAGTTAATTAAAGAGTAGTAAACCTTATGTGACGATGTAATCCAACTAGAAGATT
755 TAGCAAAT
131 TAGCAAAT
763 CTA
1 CTA
766 AAGGACATGG
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (138 bp):
CTAGAAGCAACCCATTTTAGTATATTCTCTTTTATTATTATTATGTAATAAAACCCAACACCACC
ATGATACTTCTAGTTAATTAAAGAGTAGTAAACCTTATGTGACGATGTAATCCAACTAGAAGATT
TAGCAAAT
Found at i:2500 original size:22 final size:22
Alignment explanation
Indices: 2475--3052 Score: 245
Period size: 22 Copynumber: 26.6 Consensus size: 22
2465 ATGACGTCCT
2475 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** *** *
2497 TATGAAATTTCAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
2519 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
2541 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
*
2563 TATGAAATTTT-ATTAACCTCCC
1 TATGAAATTTTGA-TAACCTTCC
* *
2585 TAAGGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATA-ACCTTC-C
*
2607 TATGAAGTTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* **
2628 AAATGAAATTTTGATAACCAACAC
1 -TATGAAATTTTGATAACCTTC-C
*
2652 TAT-AAGATGTTGATAACC-TCC
1 TATGAA-ATTTTGATAACCTTCC
* * * *
2673 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * * *
2696 TACGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
2717 ATATG-AATTGTCAGTAATC-ACAC
1 -TATGAAATTTTGA-TAACCTTC-C
* * * *
2740 TCTGAAATTTTGATAATCATAC
1 TATGAAATTTTGATAACCTTCC
*
2762 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
2784 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
2807 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
*
2830 TATAAAATTTTGATAACC-T-C
1 TATGAAATTTTGATAACCTTCC
*
2850 -ATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
2866 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
**
2887 TATGATTTTTTGATAACC-TCAC
1 TATGAAATTTTGATAACCTTC-C
* * *
2909 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
2931 TATAAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
*
2953 TATGAAATTTTGATAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * **
2975 TACGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
2997 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* *
3019 TATGAAATTTTAATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
3040 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
3053 TACTCTATAA
Statistics
Matches: 412, Mismatches: 108, Indels: 74
0.69 0.18 0.12
Matches are distributed among these distances:
16 12 0.03
17 1 0.00
19 13 0.03
20 12 0.03
21 25 0.06
22 273 0.66
23 73 0.18
24 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:2521 original size:62 final size:62
Alignment explanation
Indices: 2354--2513 Score: 259
Period size: 62 Copynumber: 2.6 Consensus size: 62
2344 ATATTCATAC
* * *
2354 GAAATTATGATAACCTTCCTATTAAATTATGATAATTACACTATTTTTGATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGATGACGTCCTTAT
* *
2416 GAAATTTTGATAACCTTGCTATGAAATTATAATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGATGACGTCCTTAT
2478 GAAATTTTGATAACCTTCCTATGAAATT-TCAATAAT
1 GAAATTTTGATAACCTTCCTATGAAATTAT-AATAAT
2514 GATACTATGG
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
61 1 0.01
62 90 0.99
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGATGACGTCCTTAT
Found at i:2877 original size:16 final size:18
Alignment explanation
Indices: 2834--2881 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
2824 TCTCCCTATA
*
2834 AAATTTTGATAACCTCATG
1 AAATTTTGATAA-CTCATC
*
2853 AAATCTTGATAACT-A-C
1 AAATTTTGATAACTCATC
2869 AAATTTTGATAAC
1 AAATTTTGATAAC
2882 CTCCCTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 2 0.08
19 11 0.42
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (18 bp):
AAATTTTGATAACTCATC
Found at i:3247 original size:22 final size:22
Alignment explanation
Indices: 3134--3278 Score: 91
Period size: 22 Copynumber: 6.6 Consensus size: 22
3124 GAAATACCAC
*
3134 TATGAAATTTTGGTAATCAT-AT
1 TATGAAATTTTGATAATC-TCAT
* * * *
3156 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCTCAT
*
3178 TATGAAATTTTGATAACCTC-T
1 TATGAAATTTTGATAATCTCAT
* * * * * *
3199 CTGTAAAATTTTGTTGA-CCCCT
1 -TATGAAATTTTGATAATCTCAT
*
3221 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAATCTCAT
* *
3244 TATGTAATTTTGATAATCTCGCT
1 TATGAAATTTTGATAATCTC-AT
3267 T-TGAAATTTTGA
1 TATGAAATTTTGA
3279 AATTGGATCC
Statistics
Matches: 96, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
21 4 0.04
22 87 0.91
23 5 0.05
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTCAT
Found at i:3253 original size:44 final size:44
Alignment explanation
Indices: 3133--3278 Score: 118
Period size: 44 Copynumber: 3.3 Consensus size: 44
3123 AGAAATACCA
* * * * * *
3133 CTATGAAATTTTGGTAATCATATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCCCT
* * * *
3177 TTATGAAATTTTGATAA-C-C-TCTCTGTAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGT--AATTTTGATAACCCCT
* * *
3221 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAATCTCG
1 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCCCT
*
3265 CTTTGAAATTTTGA
1 CTATGAAATTTTGA
3279 AATTGGATCC
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
41 1 0.01
42 3 0.04
43 1 0.01
44 67 0.85
45 1 0.01
46 5 0.06
47 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCCCT
Done.