Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005106.1 Corchorus capsularis cultivar CVL-1 contig05124, 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: 5882
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Found at i:1680 original size:84 final size:84
Alignment explanation
Indices: 1440--1668 Score: 354
Period size: 85 Copynumber: 2.7 Consensus size: 84
1430 TAAATCTTTG
* * * * *
1440 TAAAATATCTCCTAAACCTTCCACAATTTGACAAGATTCAGAAAATATTCCCTTTACAAATGAAA
1 TAAAATATTTCCTAAACCTTCCACAATTTGGCAAGATTAAGAAAATATTCTC-TTACAAATTAAA
*
1505 TCTTTATAATTTTTATTTCT
65 TCTTTATAATTTTTATTTAT
*
1525 TAAAATATTTCCTAAACCTTCCACAATTTGGCAAGATTAAGAAAATATTCTATTTACAAATTAAA
1 TAAAATATTTCCTAAACCTTCCACAATTTGGCAAGATTAAGAAAATATTCT-CTTACAAATTAAA
1590 TCTTTATAA-TTTTATTTAT
65 TCTTTATAATTTTTATTTAT
*
1609 TAAAATATTTCCTAAACCTTCCACAA-TTGGCAAGATTTAGAAAATATTCTCTTACAAATT
1 TAAAATATTTCCTAAACCTTCCACAATTTGGCAAGATTAAGAAAATATTCTCTTACAAATT
1669 TTATTATTTT
Statistics
Matches: 134, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
82 9 0.07
83 23 0.17
84 35 0.26
85 67 0.50
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (84 bp):
TAAAATATTTCCTAAACCTTCCACAATTTGGCAAGATTAAGAAAATATTCTCTTACAAATTAAAT
CTTTATAATTTTTATTTAT
Found at i:1965 original size:2 final size:2
Alignment explanation
Indices: 1954--1984 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1944 AACCAAAGGC
1954 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1985 CTAATTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3130 original size:35 final size:35
Alignment explanation
Indices: 2794--3122 Score: 417
Period size: 35 Copynumber: 9.4 Consensus size: 35
2784 AACTCCTCTG
* * * * *
2794 GATCAACTCTGATCATCGGAAATTTCTTG-AAATGA
1 GATCAACTCTGATCGTTGGAAAATAC-TGAAAATGC
* * * * *
2829 GATCACCTATGATTGTTGGAAACTACTGAAAATGT
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
* * * *
2864 TATTAACTCTGATCGTTGGAAACTACTGAAAATAC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
*
2899 GATCAACTCTGATCGTTGCAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
* *
2934 GATCAACTTTGATCGTTGGAAAATACTGGAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
* * *
2969 GATCAACTCTGATCGTTGGAAACTTCTGAAAATGT
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
* * *
3004 AATCAACTCTGATCATTGGAGAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
* *
3039 GATCAACTTTGATCGTTGGAGAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
3074 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
3109 GATCAACTCTGATC
1 GATCAACTCTGATC
3123 ATCGGAAACT
Statistics
Matches: 254, Mismatches: 39, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
34 2 0.01
35 252 0.99
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (35 bp):
GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
Found at i:3148 original size:35 final size:35
Alignment explanation
Indices: 3104--3558 Score: 669
Period size: 35 Copynumber: 12.9 Consensus size: 35
3094 AAATACTGAA
* * * *
3104 AATGCGATCAACTCTGATCATC-GGAAACTTTTTGG
1 AATGAGATCAACTCTGA-CCTCTGAAAACTTCTTGG
3139 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
* *
3174 AATGAGATCAACTCTGACCTCTTAAAACTTCTTGC
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
3209 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
* *
3244 AATGAGATCAACTCTGACCTCTCAAAACCTCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
* *
3279 AATGAGAACAACTCTGACCTCCGAAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
3314 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
* **
3349 AATGAGATCAACCCTGACCTCTGAAAACTTCTTTAA
1 AATGAGATCAACTCTGACCTCTGAAAACTTC-TTGG
* * **
3385 AATGAGATCAATTCTGACCTCTAAAAACTTCTTTAA
1 AATGAGATCAACTCTGACCTCTGAAAACTTC-TTGG
* *
3421 AATGAGATCAACTCTCACCTCTGAAAACTTTTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
3456 AATGAGATCAACTCTGACCTCTTAAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
3491 AATGAGATCAACTCTGACCTCGGAAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
3526 AATGAGATCAACTCTGACCTCTGAAAACTTCTT
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTT
3559 AAAAGTGACT
Statistics
Matches: 383, Mismatches: 35, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
34 3 0.01
35 317 0.83
36 63 0.16
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (35 bp):
AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
Found at i:3183 original size:105 final size:107
Alignment explanation
Indices: 2794--3555 Score: 505
Period size: 105 Copynumber: 7.2 Consensus size: 107
2784 AACTCCTCTG
* * * * * * *
2794 GATCAACTCTGATCATCGGAAA-TTTCTTGAAATGAGATCACCTATGA-TTGTTGGAAACTAC-T
1 GATCAACTCTGATCATCGAAAACTTT-TTGAAATGAGATCAACTCTGACCT-CTGAAAACTTCTT
* ** * *
2856 GAAAATGTTATTAACTCTGATCGTTGG-AAACTAC-TGAAAAT-A
64 G-GAATGAGATCAACTCTGATCGTTGGAAAACTTCTTGAAAATGA
* * ** * * * *
2898 CGATCAACTCTGATCGTTGCAAAA--TACTGAAAATGCGATCAACTTTGATCGT-TGGAAAA-TA
1 -GATCAACTCTGATCATCG-AAAACTTTTTG-AAATGAGATCAACTCTGA-CCTCT-GAAAACTT
*
2959 C-TGGAAATGCGATCAACTCTGATCGTTGG-AAACTTC-TGAAAATGTA
61 CTTGG-AATGAGATCAACTCTGATCGTTGGAAAACTTCTTGAAAATG-A
* * ** * * * * *
3005 -ATCAACTCTGATCATTGGAGAA--TACTGAAAATGCGATCAACTTTGATCGT-TGGAGAA-TAC
1 GATCAACTCTGATCA-TCGAAAACTTTTTG-AAATGAGATCAACTCTGA-CCTCT-GAAAACTTC
* * * *
3065 -TGAAAATGCGATCAACTCTGATCGTTGGAAAA-TAC-TGAAAATGC
62 TTG-GAATGAGATCAACTCTGATCGTTGGAAAACTTCTTGAAAATGA
* *
3109 GATCAACTCTGATCATCGGAAACTTTTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
1 GATCAACTCTGATCATCGAAAACTTTTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
3174 AATGAGATCAACTCTGACCTC-TT--AAAACTTCTTG-CAATGA
66 AATGAGATCAACTCTGA--TCGTTGGAAAACTTCTTGAAAATGA
* * * *
3214 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTCAAAACCTCTTG
1 GATCAACTCTGATCATC-GAAAACTTTTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* * ** *
3278 GAATGAGAACAACTCTGA-CCTCCGAAAACTTCTTG-GAATGA
65 GAATGAGATCAACTCTGATCGTTGGAAAACTTCTTGAAAATGA
* * *
3319 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGATCAACCCTGACCTCTGAAAACTTCTTT
1 GATCAACTCTGATCATC-GAAAACTTTTTGAAATGAGATCAACTCTGACCTCTGAAAACTTC-TT
** * * * *
3383 AAAATGAGATCAATTCTGA-CCTCT-AAAAACTTCTTTAAAATGA
64 GGAATGAGATCAACTCTGATCGT-TGGAAAACTTCTTGAAAATGA
* * * *
3426 GATCAACTCTCA-CCTCTGAAAACTTTTTGGAATGAGATCAACTCTGACCTCTTAAAACTTCTTG
1 GATCAACTCTGATCATC-GAAAACTTTTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* * *
3490 GAATGAGATCAACTCTGA-CCTCGGAAAACTTCTTG-GAATGA
65 GAATGAGATCAACTCTGATCGTTGGAAAACTTCTTGAAAATGA
*
3531 GATCAACTCTGA-CCTCTGAAAACTT
1 GATCAACTCTGATCATC-GAAAACTT
3556 CTTAAAAGTG
Statistics
Matches: 557, Mismatches: 71, Indels: 58
0.81 0.10 0.08
Matches are distributed among these distances:
102 1 0.00
103 1 0.00
104 19 0.03
105 389 0.70
106 82 0.15
107 65 0.12
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (107 bp):
GATCAACTCTGATCATCGAAAACTTTTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
AATGAGATCAACTCTGATCGTTGGAAAACTTCTTGAAAATGA
Done.