Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014191.1 Corchorus capsularis cultivar CVL-1 contig14212, 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: 8779
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Found at i:2038 original size:30 final size:31
Alignment explanation
Indices: 1998--2071 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
1988 GGGTTGTGCT
** *
1998 CGGTCTTGTGCGATTGGC-CCATGCCATGGC
1 CGGTCTTGTGCGATTCCCTCCATGCAATGGC
* *
2028 CGGTCATGTGC-AATCCCTCCATGCAATGGC
1 CGGTCTTGTGCGATTCCCTCCATGCAATGGC
2058 CGGTCTTGTGCGAT
1 CGGTCTTGTGCGAT
2072 GGCATCCTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 3 0.09
30 31 0.89
31 1 0.03
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.27
Consensus pattern (31 bp):
CGGTCTTGTGCGATTCCCTCCATGCAATGGC
Found at i:2448 original size:37 final size:37
Alignment explanation
Indices: 2407--2499 Score: 150
Period size: 37 Copynumber: 2.5 Consensus size: 37
2397 AAGTTATCAA
*
2407 AAGTCGACTAGAAACAGGTCATTCTCAACAGTCATCG
1 AAGTCGACTGGAAACAGGTCATTCTCAACAGTCATCG
* *
2444 AAGTCGACTGGAAACAGGTCATTTTCAACAGTCATTG
1 AAGTCGACTGGAAACAGGTCATTCTCAACAGTCATCG
*
2481 AAGTTGACTGGAAACAGGT
1 AAGTCGACTGGAAACAGGT
2500 TGTCTTTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (37 bp):
AAGTCGACTGGAAACAGGTCATTCTCAACAGTCATCG
Found at i:2522 original size:38 final size:37
Alignment explanation
Indices: 2407--2523 Score: 144
Period size: 37 Copynumber: 3.1 Consensus size: 37
2397 AAGTTATCAA
* * *
2407 AAGTCGACTAGAAACAGGTCATTCTCAACAGTCATCG
1 AAGTTGACTGGAAACAGGTCATTTTCAACAGTCATCG
* *
2444 AAGTCGACTGGAAACAGGTCATTTTCAACAGTCATTG
1 AAGTTGACTGGAAACAGGTCATTTTCAACAGTCATCG
** * *
2481 AAGTTGACTGGAAACAGGTTGTCTTTCAATAGTTATCG
1 AAGTTGACTGGAAACAGGTCAT-TTTCAACAGTCATCG
2519 AAGTT
1 AAGTT
2524 ATCTTTCAGC
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
37 53 0.76
38 17 0.24
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (37 bp):
AAGTTGACTGGAAACAGGTCATTTTCAACAGTCATCG
Found at i:2698 original size:38 final size:38
Alignment explanation
Indices: 2596--2881 Score: 266
Period size: 38 Copynumber: 7.7 Consensus size: 38
2586 ATCATCTTTC
* * * *
2596 AGATCAACTGGAAATAGGCCATCTTTCAAAAG-TATCA
1 AGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCA
* * * *
2633 AAATCGACTGGAAACAGGACGTTTTTCAACAGTTATCGA
1 AGATCGACTGGAAACAGGTCATCTTTCAACAGTTATC-A
*
2672 A-ATTGACTGGAAACAGGTCATCTTT---CAG--ATCGA
1 AGATCGACTGGAAACAGGTCATCTTTCAACAGTTATC-A
* * * *
2705 AG-TTGACTGGAAACAGGTAATCTTTCAATAATTATCA
1 AGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCA
* * * *
2742 AGATCGACTGGAAACAGATCATCTTTCAGCAGTTGTTA
1 AGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCA
* * * *
2780 AGATCGACTAGAAACATGTCATCTTTCAGCAGTTGTCA
1 AGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCA
**
2818 AGATCGACTAAAAACAGGTCATCTTTCATA-AGTTATCA
1 AGATCGACTGGAAACAGGTCATCTTTCA-ACAGTTATCA
*
2856 AGATTGACTGGAAACAGGTCATCTTT
1 AGATCGACTGGAAACAGGTCATCTTT
2882 TCGACTGGAA
Statistics
Matches: 206, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
33 28 0.14
35 3 0.01
36 1 0.00
37 28 0.14
38 144 0.70
39 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (38 bp):
AGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCA
Found at i:2711 original size:33 final size:33
Alignment explanation
Indices: 2667--2731 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2657 TTCAACAGTT
*
2667 ATCGAAATTGACTGGAAACAGGTCATCTTTCAG
1 ATCGAAATTGACTGGAAACAGGTAATCTTTCAG
*
2700 ATCGAAGTTGACTGGAAACAGGTAATCTTTCA
1 ATCGAAATTGACTGGAAACAGGTAATCTTTCA
2732 ATAATTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (33 bp):
ATCGAAATTGACTGGAAACAGGTAATCTTTCAG
Found at i:5199 original size:30 final size:30
Alignment explanation
Indices: 5163--5221 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5153 TGTCTTCAAG
*
5163 TCCATGATAAGTCCTT-GGCGTATCATTCCT
1 TCCATGATAAG-CCTTGGGCGCATCATTCCT
5193 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATGATAAGCCTTGGGCGCATCATTCC
5222 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.32
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCT
Done.