Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016006.1 Corchorus capsularis cultivar CVL-1 contig16027, 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: 27085
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Found at i:3464 original size:36 final size:35
Alignment explanation
Indices: 3417--3487 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
3407 ATTGCCGAAG
3417 CAAGATTACACCTTGTAAAAACAAGGGTGAATGAAA
1 CAAGATTACACCTTGTAAAAACAAGGGTG-ATGAAA
3453 CAAGATTACACCTTGTAAAAACAAGGGTGATGAAA
1 CAAGATTACACCTTGTAAAAACAAGGGTGATGAAA
3488 AGTAAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 6 0.17
36 29 0.83
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (35 bp):
CAAGATTACACCTTGTAAAAACAAGGGTGATGAAA
Found at i:9326 original size:41 final size:41
Alignment explanation
Indices: 9273--9403 Score: 117
Period size: 41 Copynumber: 3.1 Consensus size: 41
9263 ATTCTCTCTA
9273 AAAGTCAT-CAAGCACATTTATAACACAGAAGCATCCATATC
1 AAAGTC-TCCAAGCACATTTATAACACAGAAGCATCCATATC
** * * *
9314 AAAGTCTCCAAGCACAAATATAACATAGAGGCACCTCTC-TTTC
1 AAAGTCTCCAAGCACATTTATAACACAGAAGCA--TC-CATATC
* *
9357 AAATTC-CTCAAGCACATTTATAACACAG-AGACATCTATATC
1 AAAGTCTC-CAAGCACATTTATAACACAGAAG-CATCCATATC
9398 AAAGTC
1 AAAGTC
9404 CCTAAACACA
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
40 1 0.01
41 37 0.53
42 2 0.03
43 29 0.41
44 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (41 bp):
AAAGTCTCCAAGCACATTTATAACACAGAAGCATCCATATC
Found at i:9336 original size:84 final size:81
Alignment explanation
Indices: 9225--9438 Score: 216
Period size: 84 Copynumber: 2.6 Consensus size: 81
9215 GGGCAAATCT
*
9225 ATATCAAAGTCCCCAAAAACAATTATAACACAAGGGCAATTCTCTCTAAAAGTCATCAAGCACAT
1 ATATCAAAGT-CCC--AAACAAATATAACACAAGGGCAATTCTCTCTAAAAGTCATCAAGCACAT
9290 TTATAACACAGA-AGCATCC
63 TTATAACACAGAGA-CATCC
* ** * * * *
9309 ATATCAAAGTCTCCAAGCACAAATATAACA-TAGAGGCACCTCTCTTTCAAATTCCTCAAGCACA
1 ATATCAAAGTC-CCAA--ACAAATATAACACAAG-GGCAATTCTCTCTAAAAGTCATCAAGCACA
*
9373 TTTATAACACAGAGACATCT
62 TTTATAACACAGAGACATCC
* * * *
9393 ATATCAAAGTCCCTAAACACATGTAACACAAGGACAATTTTCTCTA
1 ATATCAAAGTCCC-AAACAAATATAACACAAGGGCAATTCTCTCTA
9439 TGTGGCAAAG
Statistics
Matches: 105, Mismatches: 18, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
82 20 0.19
83 7 0.07
84 77 0.73
85 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24
Consensus pattern (81 bp):
ATATCAAAGTCCCAAACAAATATAACACAAGGGCAATTCTCTCTAAAAGTCATCAAGCACATTTA
TAACACAGAGACATCC
Found at i:9414 original size:41 final size:41
Alignment explanation
Indices: 9184--9414 Score: 112
Period size: 43 Copynumber: 5.5 Consensus size: 41
9174 TTACCCAATA
* * * * *
9184 ATCAAAGTCCCCAAATACATTTATAAAACAGGGGCAAATCTAT
1 ATCAAAGTCCCTAAACACATTTATAACACA-GAG-ACATCTAT
* * * * *
9227 ATCAAAGTCCCCAAAAACAATTATAACACA-AGGGCAATTCTCT
1 ATCAAAGTCCCTAAACACATTTATAACACAGA-GAC-A-TCTAT
* * * * *
9270 CTAAAAGT-CATCAAGCACATTTATAACACAGA-AGCATCCAT
1 ATCAAAGTCCCT-AAACACATTTATAACACAGAGA-CATCTAT
* ** * * *
9311 ATCAAAGTCTCC-AAGCACAAATATAACATAGAGGCACCTCTCT
1 ATCAAAGTC-CCTAAACACATTTATAACACAGA-G-ACATCTAT
* * *
9354 TTCAAA-TTCCTCAAGCACATTTATAACACAGAGACATCTAT
1 ATCAAAGTCCCT-AAACACATTTATAACACAGAGACATCTAT
9395 ATCAAAGTCCCTAAACACAT
1 ATCAAAGTCCCTAAACACAT
9415 GTAACACAAG
Statistics
Matches: 138, Mismatches: 36, Indels: 30
0.68 0.18 0.15
Matches are distributed among these distances:
41 46 0.33
42 10 0.07
43 80 0.58
44 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (41 bp):
ATCAAAGTCCCTAAACACATTTATAACACAGAGACATCTAT
Found at i:11381 original size:4 final size:4
Alignment explanation
Indices: 11372--11406 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
11362 CTTGAGGAGC
*
11372 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTTT TTG
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTG
11407 GTTTTTTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:23359 original size:18 final size:18
Alignment explanation
Indices: 23336--23371 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
23326 AATAAAAGCT
23336 TACTCAAAAGGTAGGCAA
1 TACTCAAAAGGTAGGCAA
23354 TACTCAAAAGGTAGGCAA
1 TACTCAAAAGGTAGGCAA
23372 CTTCCAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (18 bp):
TACTCAAAAGGTAGGCAA
Done.