Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006043.1 Corchorus olitorius cultivar O-4 contig06068, 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, 615
Length: 1025
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Found at i:36 original size:22 final size:21
Alignment explanation
Indices: 9--142 Score: 65
Period size: 22 Copynumber: 6.1 Consensus size: 21
1 AACGAAAT
9 TTTATAAGGAGATTATAAAAAA
1 TTTATAAGGAGATTAT-AAAAA
* * *
31 TTTATAGGGATATTATCAAAA
1 TTTATAAGGAGATTATAAAAA
* *
52 TTTCATAA-GATGGTTATCAAAA
1 TTT-ATAAGGA-GATTATAAAAA
* * * *
74 TTTCATAAGGTGGTTTTCAAAA
1 TTT-ATAAGGAGATTATAAAAA
* * *
96 TTCA-AATGGAGGTTTATCAAAA
1 TTTATAA-GGA-GATTATAAAAA
* *
118 TTTATAGGGAAGTTTATAAAAA
1 TTTATAAGG-AGATTATAAAAA
140 TTT
1 TTT
143 CATAGTGAGC
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
20 2 0.02
21 12 0.13
22 73 0.81
23 3 0.03
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (21 bp):
TTTATAAGGAGATTATAAAAA
Found at i:94 original size:44 final size:44
Alignment explanation
Indices: 43--318 Score: 167
Period size: 43 Copynumber: 6.3 Consensus size: 44
33 TATAGGGATA
*
43 TTATCAAAATTTCATAA-GATGGTTATCAAAATTTCATAAGGTGG
1 TTATCAAAATTTCATAATG-TGGTTATCAAAATTTCATAAGGAGG
* * * *
87 TTTTCAAAA-TTCA-AATGGAGGTTTATCAAAATTT-ATAGGGAAGT
1 TTATCAAAATTTCATAAT-GTGG-TTATCAAAATTTCATAAGG-AGG
* * * *
131 TTATAAAAATTTCAT-A-GTGAGCTATCACAATTT--TATGGTATGG
1 TTATCAAAATTTCATAATGTG-GTTATCAAAATTTCATAAGG-A-GG
* * * * * *
174 TTATCAGAATTTCATAATGTGATTACCAATATTTTAT-CGGAAGG
1 TTATCAAAATTTCATAATGTGGTTATCAAAATTTCATAAGG-AGG
* * * **
218 TTATCAAAATATCATAATGTGCGCTTAACAACATTTCATTGGGAGG
1 TTATCAAAATTTCATAATGTG-G-TTATCAAAATTTCATAAGGAGG
* * * *
264 CTATCAAAATTTCAT-AGGTGGTTATCAAAATTTCATTAGGTGG
1 TTATCAAAATTTCATAATGTGGTTATCAAAATTTCATAAGGAGG
*
307 TTATTAAAATTT
1 TTATCAAAATTT
319 TTATAGGGAT
Statistics
Matches: 179, Mismatches: 38, Indels: 31
0.72 0.15 0.12
Matches are distributed among these distances:
42 7 0.04
43 65 0.36
44 61 0.34
45 15 0.08
46 29 0.16
47 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGTGGTTATCAAAATTTCATAAGGAGG
Found at i:279 original size:46 final size:44
Alignment explanation
Indices: 175--279 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 44
165 ATGGTATGGT
* * * * *
175 TATCAGAATTTCATAATGTGATTACCAATATTTTATCGGAAGGT
1 TATCAAAATTTCATAATGTGATTAACAACATTTCATCGGAAGGC
* * * *
219 TATCAAAATATCATAATGTGCGCTTAACAACATTTCATTGGGAGGC
1 TATCAAAATTTCATAATGT--GATTAACAACATTTCATCGGAAGGC
265 TATCAAAATTTCATA
1 TATCAAAATTTCATA
280 GGTGGTTATC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
44 17 0.35
46 32 0.65
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (44 bp):
TATCAAAATTTCATAATGTGATTAACAACATTTCATCGGAAGGC
Found at i:316 original size:43 final size:43
Alignment explanation
Indices: 43--318 Score: 163
Period size: 44 Copynumber: 6.3 Consensus size: 43
33 TATAGGGATA
*
43 TTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAAGGTGG
1 TTATCAAAATTTCATAAGGTGGTTATCAAAATTTCAT-AGGTGG
* *
87 TTTTCAAAA-TTCA-AATGGAGGTTTATCAAAATTT-ATAGG-GAAG
1 TTATCAAAATTTCATAA-GGTGG-TTATCAAAATTTCATAGGTG--G
* * * *
130 TTTATAAAAATTTCAT-A-GTGAGCTATCACAATTTTAT-GGTATGG
1 -TTATCAAAATTTCATAAGGTG-GTTATCAAAATTTCATAGG--TGG
* * * * * * * *
174 TTATCAGAATTTCATAATGTGATTACCAATATTTTATCGGAAGG
1 TTATCAAAATTTCATAAGGTGGTTATCAAAATTTCATAGG-TGG
* * * * * *
218 TTATCAAAATATCATAATGTGCGCTTAACAACATTTCATTGGGAGG
1 TTATCAAAATTTCATAAGGTG-G-TTATCAAAATTTCA-TAGGTGG
*
264 CTATCAAAATTTCAT-AGGTGGTTATCAAAATTTCATTAGGTGG
1 TTATCAAAATTTCATAAGGTGGTTATCAAAATTTCA-TAGGTGG
*
307 TTATTAAAATTT
1 TTATCAAAATTT
319 TTATAGGGAT
Statistics
Matches: 182, Mismatches: 32, Indels: 37
0.73 0.13 0.15
Matches are distributed among these distances:
41 1 0.01
42 5 0.03
43 65 0.36
44 66 0.36
45 14 0.08
46 28 0.15
47 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (43 bp):
TTATCAAAATTTCATAAGGTGGTTATCAAAATTTCATAGGTGG
Found at i:325 original size:22 final size:21
Alignment explanation
Indices: 43--318 Score: 148
Period size: 22 Copynumber: 12.6 Consensus size: 21
33 TATAGGGATA
*
43 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCAT-AGGTGG
65 TTATCAAAATTTCATAAGGTGG
1 TTATCAAAATTTCAT-AGGTGG
* * *
87 TTTTCAAAA-TTCAAATGGAGG
1 TTATCAAAATTTCATA-GGTGG
108 TTTATCAAAATTT-ATAGG-GAAG
1 -TTATCAAAATTTCATAGGTG--G
*
130 TTTATAAAAATTTCATA-GTGAG
1 -TTATCAAAATTTCATAGGTG-G
* * *
152 CTATCACAATTTTAT-GGTATGG
1 TTATCAAAATTTCATAGG--TGG
* * *
174 TTATCAGAATTTCATAATGTGA
1 TTATCAAAATTTCAT-AGGTGG
* * * * *
196 TTACCAATATTTTATCGGAAGG
1 TTATCAAAATTTCATAGG-TGG
* *
218 TTATCAAAATATCATAATGTGCG
1 TTATCAAAATTTCAT-AGGTG-G
* * * *
241 CTTAACAACATTTCATTGGGAGG
1 -TTATCAAAATTTCA-TAGGTGG
*
264 CTATCAAAATTTCATAGGTGG
1 TTATCAAAATTTCATAGGTGG
285 TTATCAAAATTTCATTAGGTGG
1 TTATCAAAATTTCA-TAGGTGG
*
307 TTATTAAAATTT
1 TTATCAAAATTT
319 TTATAGGGAT
Statistics
Matches: 192, Mismatches: 44, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
20 2 0.01
21 41 0.21
22 123 0.64
23 11 0.06
24 14 0.07
25 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGG
Found at i:432 original size:22 final size:21
Alignment explanation
Indices: 340--473 Score: 69
Period size: 22 Copynumber: 6.2 Consensus size: 21
330 TGAATTGTAA
* *
340 CAAAATTTTATAGGGAAGTTAA
1 CAAAATTTTATAGTGAA-TTAT
* *
362 CAAAATTTCATA-TGGAGATTCT
1 CAAAATTTTATAGT-GA-ATTAT
* * *
384 CGAAATTCTATAGT-ATCATCAT
1 CAAAATTTTATAGTGA--ATTAT
* *
406 AAAAACTTTATAGTGTAATTAT
1 CAAAATTTTATAGTG-AATTAT
* *
428 CAAAATTTTATA-TGGAGGTTAG
1 CAAAATTTTATAGT-GA-ATTAT
450 CAAAATTTTATAGTG-ATTAT
1 CAAAATTTTATAGTGAATTAT
470 CAAA
1 CAAA
474 TTTCATAAAA
Statistics
Matches: 82, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
20 7 0.09
21 3 0.04
22 68 0.83
23 3 0.04
24 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (21 bp):
CAAAATTTTATAGTGAATTAT
Done.