Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011667.1 Corchorus capsularis cultivar CVL-1 contig11688, 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: 9400
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:651 original size:71 final size:71
Alignment explanation
Indices: 559--729 Score: 216
Period size: 71 Copynumber: 2.4 Consensus size: 71
549 CCGACTGAGT
* * * *
559 TGAAGAACAATCACCCCCGATCATTCCGACACAAATTGGAGAAAGACCACCCTGGGTCAAATGAA
1 TGAAGAACGATCACCCTCGATCATTCCGACACAAACTGAAGAAAGACCACCCTGGGTCAAATGAA
*
624 ATAAGC
66 ATAAAC
* ** * * * * *
630 TGAAGAATGATCACCCTCGATCATTTTGATACAAACTGAAGGAAGACCGCCTTGGGTCAACTGAA
1 TGAAGAACGATCACCCTCGATCATTCCGACACAAACTGAAGAAAGACCACCCTGGGTCAAATGAA
695 ATAAAC
66 ATAAAC
*
701 TGAAGAACGACCACCCTCGATCATTCCGA
1 TGAAGAACGATCACCCTCGATCATTCCGA
730 TCTGGACTGT
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 83 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (71 bp):
TGAAGAACGATCACCCTCGATCATTCCGACACAAACTGAAGAAAGACCACCCTGGGTCAAATGAA
ATAAAC
Found at i:783 original size:35 final size:35
Alignment explanation
Indices: 743--809 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
733 GGACTGTATC
* * *
743 ATTGAAGTAAATTGAAGAATGATCGCCCTGGACCA
1 ATTGAAATAAACTGAAGAAAGATCGCCCTGGACCA
*
778 ATTGAAATTAACTGAAGAAAGATCGCCCTGGA
1 ATTGAAATAAACTGAAGAAAGATCGCCCTGGA
810 TCGAGTAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (35 bp):
ATTGAAATAAACTGAAGAAAGATCGCCCTGGACCA
Found at i:968 original size:34 final size:35
Alignment explanation
Indices: 925--1016 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 35
915 ATGATTGGAG
* * * *
925 AATTGAAGAAAGACCGCCCTGTATC-ATTGAAGTA
1 AATTGAAGAAAGATCGCCCTGGACCAATTGAAATA
* *
959 AATTGAAGAATGATCGCCCTGGACCAATTGAAATT
1 AATTGAAGAAAGATCGCCCTGGACCAATTGAAATA
*
994 AACTGAAGAAAGATCGCCCTGGA
1 AATTGAAGAAAGATCGCCCTGGA
1017 TCGAGTAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 21 0.43
35 28 0.57
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (35 bp):
AATTGAAGAAAGATCGCCCTGGACCAATTGAAATA
Found at i:2310 original size:1 final size:1
Alignment explanation
Indices: 2304--2329 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2294 CACCCTAGAG
2304 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
2330 GCATCTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2643 original size:17 final size:18
Alignment explanation
Indices: 2609--2643 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2599 TTTGCTCCAT
2609 CTTTTACCTTCATTTTTC
1 CTTTTACCTTCATTTTTC
*
2627 CTTTTACTTTC-TTTTTC
1 CTTTTACCTTCATTTTTC
2644 AATTTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (18 bp):
CTTTTACCTTCATTTTTC
Found at i:7299 original size:35 final size:35
Alignment explanation
Indices: 7253--7344 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 35
7243 AACAATTATT
7253 TTAATTACCCTGAATTAAGTTGA-TTACTGACTTAC
1 TTAATTACCCTGAATTAAGTT-ACTTACTGACTTAC
*
7288 TTAATTACCCTGAATTAAGTTACTTA-T---TGAC
1 TTAATTACCCTGAATTAAGTTACTTACTGACTTAC
* *
7319 TTAATTACTCTGAATTAAATTACTTA
1 TTAATTACCCTGAATTAAGTTACTTA
7345 TTACTGATTC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
31 27 0.51
34 2 0.04
35 24 0.45
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (35 bp):
TTAATTACCCTGAATTAAGTTACTTACTGACTTAC
Done.