Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007104.1 Corchorus capsularis cultivar CVL-1 contig07125, 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: 17575
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5178 original size:21 final size:23
Alignment explanation
Indices: 5153--5199 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5143 AAACTAATCC
5153 TAAAG-TTCTAATCCCTCTA-AT
1 TAAAGATTCTAATCCCTCTATAT
*
5174 TAAAGATTTTTAATCCCTCTATAT
1 TAAAGA-TTCTAATCCCTCTATAT
5198 TA
1 TA
5200 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAAGATTCTAATCCCTCTATAT
Found at i:6075 original size:25 final size:24
Alignment explanation
Indices: 6029--6075 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6019 TAAGATTAGT
* * *
6029 AAAAAAGTTGTGAAGATTATTATA
1 AAAAAAGTTGCGAAAATGATTATA
6053 AAAAAAGTTGACGAAAATGATTA
1 AAAAAAGTTG-CGAAAATGATTA
6076 AAAGTAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.28
Consensus pattern (24 bp):
AAAAAAGTTGCGAAAATGATTATA
Found at i:12700 original size:66 final size:66
Alignment explanation
Indices: 12578--12701 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
12568 TATCAAAATG
* * *
12578 TCATAGCGATGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATTAGTAGGTTACTAATAT
1 TCATAGCGAGGTTATAAGAATTTCATAGGGTGGTTAACAAAATTTCATTAGAAGGTTACTAATAT
12643 T
66 T
* * *
12644 TCATAGGGAGGTTATCAA-AATTTTATAGGGTGGTTATCAAAATTTCA-TATGAAGGTTA
1 TCATAGCGAGGTTAT-AAGAATTTCATAGGGTGGTTAACAAAATTTCATTA-GAAGGTTA
12702 TAAAACTCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
65 2 0.04
66 46 0.92
67 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (66 bp):
TCATAGCGAGGTTATAAGAATTTCATAGGGTGGTTAACAAAATTTCATTAGAAGGTTACTAATAT
T
Found at i:12908 original size:22 final size:22
Alignment explanation
Indices: 12560--12936 Score: 134
Period size: 22 Copynumber: 17.0 Consensus size: 22
12550 AAAGGTTATC
* *
12560 AAAGAGATTATCAAAATGTCAT
1 AAAGAGGTTATCAAAATTTCAT
** *
12582 AGCGATGTTAT-AAGAATTTCAT
1 AAAGAGGTTATCAA-AATTTCAT
** * *
12604 AGTGTGGTTAACAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* *
12626 -TAGTAGGTTA-CTAATATTTCAT
1 AAAG-AGGTTATC-AAAATTTCAT
** *
12648 AGGGAGGTTATCAAAATTTTAT
1 AAAGAGGTTATCAAAATTTCAT
** *
12670 AGGGTGGTTATCAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* *
12692 -ATGAAGGTTATAAAACTCTCAATTTCAT
1 AAAG-AGGTTAT-CAA-----AATTTCAT
* * *
12720 AAGGA-G-TACCAAAATTTGAT
1 AAAGAGGTTATCAAAATTTCAT
* *
12740 AGA-AGGTTATC-AAATCTCAT
1 AAAGAGGTTATCAAAATTTCAT
* * * *
12760 AGAGTGATTATCGAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* *
12782 AGAGATCGGATTATCAAAA-TTAAT
1 AAAGA--GG-TTATCAAAATTTCAT
12806 AGGAAGA--TTATCAAAATTTCA-
1 A--AAGAGGTTATCAAAATTTCAT
* * *
12827 AAGCGATGTTATCAAAATTACA-
1 AA-AGAGGTTATCAAAATTTCAT
* * *
12849 AAATGTGATTATCAGAATTTCAT
1 AAA-GAGGTTATCAAAATTTCAT
* * *
12872 AGAAG-GGTCAACAAAATTTTAT
1 A-AAGAGGTTATCAAAATTTCAT
12894 AAAGAGGTTATCAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
*
12916 AAAGAGGTTATCAAATTTTCA
1 AAAGAGGTTATCAAAATTTCA
12937 AAATGTGATT
Statistics
Matches: 266, Mismatches: 58, Indels: 62
0.69 0.15 0.16
Matches are distributed among these distances:
19 2 0.01
20 21 0.08
21 27 0.10
22 173 0.65
23 8 0.03
24 8 0.03
25 10 0.04
26 5 0.02
27 1 0.00
28 9 0.03
29 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (22 bp):
AAAGAGGTTATCAAAATTTCAT
Found at i:12954 original size:44 final size:44
Alignment explanation
Indices: 12729--12961 Score: 135
Period size: 44 Copynumber: 5.3 Consensus size: 44
12719 TAAGGAGTAC
* * *
12729 CAAAATTTGATAGAA-GGTTATCAAA-TCTCATAGA-GTGATTAT
1 CAAAATTTCATAGAAGGGTTATCAAATTTTCA-AAATGTGATTAT
* * * * * *
12771 CGAAATTTCATAGAGATCGGATTATCAAA-ATT-AATAGGAAGATTAT
1 CAAAATTTCATAGA-A--GGGTTATCAAATTTTCAAAATG-TGATTAT
* * * * *
12817 CAAAATTTCAAAG-CGATGTTATCAAAATTACAAAATGTGATTAT
1 CAAAATTTCATAGAAG-GGTTATCAAATTTTCAAAATGTGATTAT
* * * * *
12861 CAGAATTTCATAGAAGGGTCAACAAAATTTT-ATAAA-GAGGTTAT
1 CAAAATTTCATAGAAGGGTTATC-AAATTTTCA-AAATGTGATTAT
12905 CAAAATTTCATA-AAGAGGTTATCAAATTTTCAAAATGTGATTA-
1 CAAAATTTCATAGAAG-GGTTATCAAATTTTCAAAATGTGATTAT
12948 CAAAAATTTCATAG
1 C-AAAATTTCATAG
12962 TGGTATTTCT
Statistics
Matches: 142, Mismatches: 32, Indels: 31
0.69 0.16 0.15
Matches are distributed among these distances:
42 13 0.09
43 23 0.16
44 64 0.45
45 15 0.11
46 27 0.19
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (44 bp):
CAAAATTTCATAGAAGGGTTATCAAATTTTCAAAATGTGATTAT
Found at i:13262 original size:23 final size:22
Alignment explanation
Indices: 13042--13602 Score: 193
Period size: 22 Copynumber: 25.7 Consensus size: 22
13032 TTATGGAGTA
13042 ATCAAAATTTCAGTAAGGA---T
1 ATCAAAATTTCA-TAAGGAGGTT
* *
13062 ATCAAAATTTCATATA-AAGATT
1 ATCAAAATTTCATA-AGGAGGTT
*
13084 ATCAAAATTTCAT-AGTTTA-GTT
1 ATCAAAATTTCATAAG--GAGGTT
*
13106 TTCAAAATTTCATAA-GAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * *
13128 ATCAAAATTTCAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
* *
13150 ATCAATATTTCATATGGAGAGGTT
1 ATCAAAATTTCATA-AG-GAGGTT
** * *
13174 ATCAAAAAATCATAGGGAGCTT
1 ATCAAAATTTCATAAGGAGGTT
*
13196 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
13212 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAAGGAGGTT
*
13234 ATCAAAATTTTATAAGGAGGTTT
1 ATCAAAATTTCATAAGGAGG-TT
* *
13257 ATCAAAATTTTAT-AGGAAGATTT
1 ATCAAAATTTCATAAGG-AG-GTT
*
13280 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
13302 ATCACAATTTCAT-AGTGTA-ATT
1 ATCAAAATTTCATAAG-G-AGGTT
* * *
13324 ATCAAAATTTCA-GAGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
*
13346 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAAGGAGGTT
* * * * *
13368 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
13390 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
13412 ATCAACATCTCAT-AGTGTTGATT
1 ATCAAAATTTCATAAG-G-AGGTT
* *
13435 ATCAAAATTTCAT-TGAGAAGTT
1 ATCAAAATTTCATAAG-GAGGTT
** *
13457 ATCAAAATTTCATATTGAGATCT
1 ATCAAAATTTCATAAGGAGGT-T
* * *
13480 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
13501 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
** * **
13523 AAAAAAAATT-ATAAAAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * ***
13544 CTCGAAATTCCAT-AGTGTCATT
1 ATCAAAATTTCATAAG-GAGGTT
*
13566 ATTAAAATTTCAT-AGGAAGGTT
1 ATCAAAATTTCATAAGG-AGGTT
13588 ATCAAAATTTCATAA
1 ATCAAAATTTCATAA
13603 TGGGATCATA
Statistics
Matches: 397, Mismatches: 101, Indels: 83
0.68 0.17 0.14
Matches are distributed among these distances:
16 8 0.02
17 4 0.01
19 5 0.01
20 15 0.04
21 27 0.07
22 261 0.66
23 60 0.15
24 14 0.04
25 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:13293 original size:106 final size:106
Alignment explanation
Indices: 13101--13311 Score: 228
Period size: 106 Copynumber: 2.0 Consensus size: 106
13091 TTTCATAGTT
* ** * * *
13101 TAGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAGATCAATATTTCATATG
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATATG
**
13166 GAGAGGTTATCAAAAAATCATAGGGAGCTTATCAAAATTTG
66 GAGAGGTTATCAAAAAATCATAACGAGCTTATCAAAATTTG
* * ** *
13207 TAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAAGGAGGTTTATCAAAATTTTATA-
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCAT-AGGAGGTAGATCAAAATTTCATAT
* ** * *
13271 GGA-AGATTTATCAAAATTTCATAACGAGGTTATCACAATTT
65 GGAGAG-GTTATCAAAAAATCATAACGAGCTTATCAAAATTT
13312 CATAGTGTAA
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
105 2 0.02
106 66 0.78
107 17 0.20
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (106 bp):
TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATATG
GAGAGGTTATCAAAAAATCATAACGAGCTTATCAAAATTTG
Found at i:17510 original size:2 final size:2
Alignment explanation
Indices: 17503--17575 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
17493 CATTAGAAGG
17503 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17545 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.