Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006128.1 Corchorus olitorius cultivar O-4 contig06153, 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: 2392
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Found at i:360 original size:20 final size:21
Alignment explanation
Indices: 323--385 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
313 AGGGAGATTA
* *
323 ACAAAATTTCATAGGAAGG-T
1 ACAAAATATCATAAGAAGGTT
343 ATCAAAA-ATCATAAGAAGGTT
1 A-CAAAATATCATAAGAAGGTT
*
364 ACAAAATTTCATAAGGAAGGTT
1 ACAAAATATCATAA-GAAGGTT
386 TATTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 16 0.44
21 13 0.36
22 7 0.19
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (21 bp):
ACAAAATATCATAAGAAGGTT
Found at i:396 original size:24 final size:23
Alignment explanation
Indices: 324--488 Score: 111
Period size: 22 Copynumber: 7.6 Consensus size: 23
314 GGGAGATTAA
324 CAAAATTTCAT-AGGAAGG-TAT
1 CAAAATTTCATAAGGAAGGTTAT
*
345 CAAAA-ATCATAA-GAAGGTTA-
1 CAAAATTTCATAAGGAAGGTTAT
365 CAAAATTTCATAAGGAAGGTTTAT
1 CAAAATTTCATAAGGAAGG-TTAT
* ***
389 TAAAATTTCAT-ATTTAGGTTAT
1 CAAAATTTCATAAGGAAGGTTAT
* * *
411 CAAAGTTTCATATGG-AGTTTAT
1 CAAAATTTCATAAGGAAGGTTAT
**
433 CACGATTTCAT-AGGTAA--TTAT
1 CAAAATTTCATAAGG-AAGGTTAT
* *
454 CAAAATTTTAT-AGCG-TGGTTAT
1 CAAAATTTCATAAG-GAAGGTTAT
476 CAAAATTTCATAA
1 CAAAATTTCATAA
489 AAATATTCAA
Statistics
Matches: 110, Mismatches: 21, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
20 14 0.13
21 30 0.27
22 47 0.43
23 9 0.08
24 10 0.09
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (23 bp):
CAAAATTTCATAAGGAAGGTTAT
Found at i:1843 original size:45 final size:45
Alignment explanation
Indices: 1779--1871 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
1769 ATTTTTCAAA
1779 GGAGTTGAATTTGTAAACGTATAATCATACT-ATAAGAACTAAACC
1 GGAGTTGAATTTGTAAACGTATAATCATA-TAATAAGAACTAAACC
* **
1824 GGAGTTGAATTTTTAAACGTATAATCATATAATAAGAGTTAAACC
1 GGAGTTGAATTTGTAAACGTATAATCATATAATAAGAACTAAACC
1869 GGA
1 GGA
1872 TTAGATTGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (45 bp):
GGAGTTGAATTTGTAAACGTATAATCATATAATAAGAACTAAACC
Found at i:2134 original size:22 final size:22
Alignment explanation
Indices: 2100--2244 Score: 80
Period size: 22 Copynumber: 6.6 Consensus size: 22
2090 ACTATAGTAT
* * *
2100 CAAAAAATTATAGGGAGATTAA
1 CAAAATATCATAGGGAGGTTAA
*
2122 CAAAATATCATAGGGGGGTTATA
1 CAAAATATCATAGGGAGGTTA-A
*
2145 -AAAA-ATCATAGGAAGGTT-A
1 CAAAATATCATAGGGAGGTTAA
* * *
2164 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATATCATAGGGAGG-TTAA
* * ** *
2187 TAAAATTTCATAGTTAGGTTAT
1 CAAAATATCATAGGGAGGTTAA
* * * *
2209 CAAAATTTCATATGGAGTTTAT
1 CAAAATATCATAGGGAGGTTAA
* *
2231 CACAATTTCATAGG
1 CAAAATATCATAGG
2245 TAATTATCTG
Statistics
Matches: 100, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.01
20 4 0.04
21 23 0.23
22 56 0.56
23 16 0.16
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (22 bp):
CAAAATATCATAGGGAGGTTAA
Found at i:2162 original size:21 final size:20
Alignment explanation
Indices: 2101--2183 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 20
2091 CTATAGTATC
* * *
2101 AAAAAATTATAGGGAGATTA
1 AAAAAATCATAGGAAGGTTA
**
2121 ACAAAATATCATAGGGGGGTTA
1 A-AAAA-ATCATAGGAAGGTTA
2143 TAAAAAATCATAGGAAGGTTA
1 -AAAAAATCATAGGAAGGTTA
**
2164 CAAAATTTCATAGGAAGGTT
1 -AAAAAATCATAGGAAGGTT
2184 TATTAAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.02
21 34 0.65
22 16 0.31
23 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (20 bp):
AAAAAATCATAGGAAGGTTA
Found at i:2195 original size:23 final size:22
Alignment explanation
Indices: 2122--2307 Score: 134
Period size: 22 Copynumber: 8.5 Consensus size: 22
2112 GGGAGATTAA
* **
2122 CAAAATATCATAGGGGGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
**
2144 -AAAAAATCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
2164 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
2187 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
2209 CAAAATTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGAAGGTTAT
*
2231 CACAATTTCATAGGTAA--TTAT
1 CAAAATTTCATAGG-AAGGTTAT
** * *
2252 CTGAATTTCATAGCG-TGATTAT
1 CAAAATTTCATAG-GAAGGTTAT
* *
2274 CAAAATTTAATAGGATA-ATTAT
1 CAAAATTTCATAGGA-AGGTTAT
2296 CAAAATTTCATA
1 CAAAATTTCATA
2308 AAAATATTCA
Statistics
Matches: 133, Mismatches: 20, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
21 50 0.38
22 66 0.50
23 17 0.13
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:2372 original size:2 final size:2
Alignment explanation
Indices: 2365--2390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2355 GCTAAAACTA
2365 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2391 CT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.