Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011334.1 Corchorus capsularis cultivar CVL-1 contig11355, 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: 3012
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:660 original size:9 final size:9
Alignment explanation
Indices: 646--684 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
636 CCTTACAACC
646 TTAATAAGT
1 TTAATAAGT
655 TTAATAAGT
1 TTAATAAGT
* *
664 TTAGTAACT
1 TTAATAAGT
673 TTAATAAGT
1 TTAATAAGT
682 TTA
1 TTA
685 GTAACTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (9 bp):
TTAATAAGT
Found at i:677 original size:18 final size:18
Alignment explanation
Indices: 654--691 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
644 CCTTAATAAG
654 TTTAATAAGTTTAGTAAC
1 TTTAATAAGTTTAGTAAC
672 TTTAATAAGTTTAGTAAC
1 TTTAATAAGTTTAGTAAC
690 TT
1 TT
692 ATTAAACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTAATAAGTTTAGTAAC
Found at i:703 original size:27 final size:27
Alignment explanation
Indices: 642--709 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
632 GTTACCTTAC
*
642 AACCTTAATAAGTTTAATAAGTTTAGT
1 AACCTTAATAAGTTTAATAAGCTTAGT
* * *
669 AACTTTAATAAGTTTAGTAA-CTTATT
1 AACCTTAATAAGTTTAATAAGCTTAGT
695 AAACCTTAATAAGTT
1 -AACCTTAATAAGTT
710 ACCTTACAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 4 0.11
27 31 0.89
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (27 bp):
AACCTTAATAAGTTTAATAAGCTTAGT
Found at i:2163 original size:30 final size:30
Alignment explanation
Indices: 2072--2550 Score: 584
Period size: 30 Copynumber: 15.7 Consensus size: 30
2062 TTAAATCTCC
* * *
2072 ATTGACACCAGAAGTTGTCAATGGTGTTATA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
* * *
2103 ATTGACACCAGAAATTGTCAATAATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
* * *
2134 AATGACACCAGAAGTTGTCATGGTCTTACA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
*
2164 AATGACACCAGAAGTTGTCATGATTTTACA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
* *
2194 ATTAACACCAGAAGTTGTCAATAATTTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
*
2225 AATGACACCAGAAGTTGTCATGATTTTACA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
* *
2255 ATTGACACCAGAAGTTGTCAATAATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
* *
2286 AATGACACCAGAAGTTGTCATGACTTTACA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
* * *
2316 ATTGACACCAGAAGTTGTCAATAATCTTATA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
* * *
2347 A-TGACACCAAAAGTTGTCATGGTCTTACGA
1 ATTGACACCAGAAGTTGTCATGATTTTAC-A
*
2377 A-TGACACCAGAAGTTGTCATGATTTTTGCA
1 ATTGACACCAGAAGTTGTCATGA-TTTTACA
*
2407 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
*
2437 ATTGACACCAGAAGTTGTCATGATTTTTGCA
1 ATTGACACCAGAAGTTGTCATGA-TTTTACA
*
2468 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
** *
2498 ATTGACACTTGAAGATGTCATGATTTTATTCA
1 ATTGACACCAGAAGTTGTCATGATTTTA--CA
2530 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
2551 ATACACCATG
Statistics
Matches: 395, Mismatches: 44, Indels: 17
0.87 0.10 0.04
Matches are distributed among these distances:
29 7 0.02
30 208 0.53
31 160 0.41
32 20 0.05
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATTTTACA
Found at i:2182 original size:61 final size:61
Alignment explanation
Indices: 2038--2550 Score: 583
Period size: 61 Copynumber: 8.4 Consensus size: 61
2028 TCAAAGTCTC
* * * *
2038 CAAATGACGCCAGAAGTTGTCATG-TTAAATCT-CCATTGACACCAGAAGTTGTCAATGGTGTTA
1 CAAATGACACCAGAAGTTGTCATGATT---T-TACAATTGACACCAGAAGTTGTCAATGATTTTA
* * * * * * * *
2101 TAATTGACACCAGAAATTGTCAATAATCTTACAAATGACACCAGAAGTTGTC-ATGGTCTTA
1 CAAATGACACCAGAAGTTGTC-ATGATTTTACAATTGACACCAGAAGTTGTCAATGATTTTA
* *
2162 CAAATGACACCAGAAGTTGTCATGATTTTACAATTAACACCAGAAGTTGTCAATAATTTTA
1 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATGATTTTA
* *
2223 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATAATCTTA
1 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATGATTTTA
* * *
2284 CAAATGACACCAGAAGTTGTCATGACTTTACAATTGACACCAGAAGTTGTCAATAATCTTA
1 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATGATTTTA
* * * * *
2345 -TAATGACACCAAAAGTTGTCATGGTCTTACGAA-TGACACCAGAAGTTGTC-ATGATTTTTG
1 CAAATGACACCAGAAGTTGTCATGATTTTAC-AATTGACACCAGAAGTTGTCAATGA-TTTTA
* * *
2405 CAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTC-ATGATTTTTG
1 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATGA-TTTTA
* * ** *
2466 CAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACTTGAAGATGTC-ATGATTTTA
1 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATGATTTTA
*
2526 TTCAATTGACACCAGAAGTTGTCAT
1 --CAAATGACACCAGAAGTTGTCAT
2551 ATACACCATG
Statistics
Matches: 400, Mismatches: 40, Indels: 21
0.87 0.09 0.05
Matches are distributed among these distances:
59 3 0.01
60 77 0.19
61 257 0.64
62 43 0.11
63 17 0.04
64 2 0.00
65 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (61 bp):
CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATGATTTTA
Found at i:2224 original size:91 final size:90
Alignment explanation
Indices: 2072--2550 Score: 575
Period size: 91 Copynumber: 5.2 Consensus size: 90
2062 TTAAATCTCC
* * * * * *
2072 ATTGACACCAGAAGTTGTCAATGGTGTTATAATTGACACCAGAAATTGTCAATAATCTTACAAAT
1 ATTGACACCAGAAGTTGTC-ATGATCTTACAATTGACACCAGAAGTTGTC-ATAATTTTACAATT
* *
2137 GACACCAGAAGTTGTCATGGTCTTACA
64 GACACCAGAAGTTGTCATGATTTTACA
* * * *
2164 AATGACACCAGAAGTTGTCATGATTTTACAATTAACACCAGAAGTTGTCAATAATTTTACAAATG
1 ATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC-ATAATTTTACAATTG
2229 ACACCAGAAGTTGTCATGATTTTACA
65 ACACCAGAAGTTGTCATGATTTTACA
* * * *
2255 ATTGACACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGACTTTACAATTG
1 ATTGACACCAGAAGTTGTC-ATGATCTTACAATTGACACCAGAAGTTGTCATAATTTTACAATTG
* * *
2320 ACACCAGAAGTTGTCAATAATCTTATA
65 ACACCAGAAGTTGTC-ATGATTTTACA
* * * *
2347 A-TGACACCAAAAGTTGTCATGGTCTTACGAA-TGACACCAGAAGTTGTCATGATTTTTGCAATT
1 ATTGACACCAGAAGTTGTCATGATCTTAC-AATTGACACCAGAAGTTGTCAT-AATTTTACAATT
*
2410 GACACCAGAAGTTGTCATGATTTTGCA
64 GACACCAGAAGTTGTCATGATTTTACA
* * * *
2437 ATTGACACCAGAAGTTGTCATGATTTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAATTG
1 ATTGACACCAGAAGTTGTCATGA-TCTTACAATTGACACCAGAAGTTGTCATAATTTTACAATTG
** *
2502 ACACTTGAAGATGTCATGATTTTATTCA
65 ACACCAGAAGTTGTCATGATTTTA--CA
2530 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
2551 ATACACCATG
Statistics
Matches: 337, Mismatches: 41, Indels: 17
0.85 0.10 0.04
Matches are distributed among these distances:
90 35 0.10
91 203 0.60
92 76 0.23
93 23 0.07
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (90 bp):
ATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATAATTTTACAATTGA
CACCAGAAGTTGTCATGATTTTACA
Found at i:2580 original size:45 final size:45
Alignment explanation
Indices: 2530--2641 Score: 224
Period size: 45 Copynumber: 2.5 Consensus size: 45
2520 ATTTTATTCA
2530 ATTGACACCAGAAGTTGTCATATACACCATGAATTTTAAATCGTT
1 ATTGACACCAGAAGTTGTCATATACACCATGAATTTTAAATCGTT
2575 ATTGACACCAGAAGTTGTCATATACACCATGAATTTTAAATCGTT
1 ATTGACACCAGAAGTTGTCATATACACCATGAATTTTAAATCGTT
2620 ATTGACACCAGAAGTTGTCATA
1 ATTGACACCAGAAGTTGTCATA
2642 ACTAATTCCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (45 bp):
ATTGACACCAGAAGTTGTCATATACACCATGAATTTTAAATCGTT
Found at i:2857 original size:118 final size:118
Alignment explanation
Indices: 2649--2886 Score: 449
Period size: 118 Copynumber: 2.0 Consensus size: 118
2639 ATAACTAATT
*
2649 CCCATTTGACACTAGAAGTTGTCATTGTGTTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
1 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
*
2714 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCCATCTTTCCTGGGAATTTA
66 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCCATCTTTCCTAGGAATTTA
*
2767 CCCATTTGACACTAGAGGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
1 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
2832 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCCATCTTTCCTAGGAATTTA
66 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCCATCTTTCCTAGGAATTTA
2885 CC
1 CC
2887 TGGTGTAATT
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (118 bp):
CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCCATCTTTCCTAGGAATTTA
Done.