Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014383.1 Corchorus capsularis cultivar CVL-1 contig14404, 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: 19932
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Found at i:5410 original size:102 final size:102
Alignment explanation
Indices: 5231--5437 Score: 288
Period size: 102 Copynumber: 2.0 Consensus size: 102
5221 TAAATCCCTC
* * * *
5231 GTTGATCTCTCTTAATCCCCAGTGACTCCATTACGAGGGGCACACCTGCGGGCAGTATTGGGGTG
1 GTTGATATCTCTTAATCCCAAGTGACTCCATGACGAGGGGCACACCTGCGGGCAGTATTGAGGTG
* * * * * *
5296 TGTCATGGATCTTAACATAGTGTGGAAACATATAAGA
66 TGCCATGAATCTTAACACAATGTAGAAACAGATAAGA
* * *
5333 GTTGATATCTCTTAATCCCAAGTGACTTCATGGCGAGGGGTACACCTGCGGGCAGTATTGAGGTG
1 GTTGATATCTCTTAATCCCAAGTGACTCCATGACGAGGGGCACACCTGCGGGCAGTATTGAGGTG
*
5398 TGCCATGAATCTTAACACAATGTAGAAACAGGTAAGA
66 TGCCATGAATCTTAACACAATGTAGAAACAGATAAGA
5435 GTT
1 GTT
5438 TATGTAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (102 bp):
GTTGATATCTCTTAATCCCAAGTGACTCCATGACGAGGGGCACACCTGCGGGCAGTATTGAGGTG
TGCCATGAATCTTAACACAATGTAGAAACAGATAAGA
Found at i:11274 original size:71 final size:71
Alignment explanation
Indices: 11059--11381 Score: 371
Period size: 71 Copynumber: 4.4 Consensus size: 71
11049 ACATATTATG
*
11059 AGTTTAAGTTTTGTAAATAGAAGAAATAGACGGTGAAAAGAGATTCTCCGATATCCCTTACATAC
1 AGTTTAAGTTTTGTAAATAGAGGAAATAGACGGTGAAAAGAGATTCTCCGATATCCCTTACA-AC
11124 ATATCTA
65 ATATCTA
** * *
11131 AACTTAAGTTTTGTAAATAAAAGAAAAGGAAATAGACGGTGAAAAGGGATTCTCCAATAT-CCTT
1 AGTTTAAGTTTTGTAAAT---AG---AGGAAATAGACGGTGAAAAGAGATTCTCCGATATCCCTT
11195 ACATACATATCTA
60 ACA-ACATATCTA
** * *
11208 AGTTTAAGTTTTGTAAATAGAGGAAATAGACTATGAAAAGAAGAGATTCTTCGATATCCCTCACA
1 AGTTTAAGTTTTGTAAATAGAGGAAATAGACGGTG--AA-AAGAGATTCTCCGATATCCCTTACA
11273 TACATATCTA
63 -ACATATCTA
* * * * * *
11283 AGTTTAAGTTTTGTAAATAAAGAAAATAAACTGTGAAAA-AGATTCTCTGATATCCCTTGCATAC
1 AGTTTAAGTTTTGTAAATAGAGGAAATAGACGGTGAAAAGAGATTCTCCGATATCCCTTACA-AC
11347 ATATCTA
65 ATATCTA
*
11354 AGCTTAAGTTTTGTAAATAGAGGAAATA
1 AGTTTAAGTTTTGTAAATAGAGGAAATA
11382 TAGACTGAAA
Statistics
Matches: 217, Mismatches: 24, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
71 66 0.30
72 18 0.08
73 4 0.02
74 16 0.07
75 49 0.23
77 33 0.15
78 31 0.14
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (71 bp):
AGTTTAAGTTTTGTAAATAGAGGAAATAGACGGTGAAAAGAGATTCTCCGATATCCCTTACAACA
TATCTA
Found at i:11391 original size:146 final size:147
Alignment explanation
Indices: 11062--11394 Score: 424
Period size: 146 Copynumber: 2.2 Consensus size: 147
11052 TATTATGAGT
* * ** *
11062 TTAAGTTTTGTAAATAGAAGAAATAGACGGTGAA-AAGAGATTCTCCGATATCCCTTACATACAT
1 TTAAGTTTTGTAAATAGAGGAAATAGACTGAAAAGAAGAGATTCTCCGATATCCCTCACATACAT
* *
11126 ATCTAAACTTAAGTTTTGTAAATAAAAGAAAAGGAAATAGACGGTGAAAAGGGATTCTCCAATAT
66 ATCTAAACTTAAGTTTTGTAAATAAAAG--AA-GAAATAAACGGTGAAAAGAGATTCTCCAATAT
*
11191 CCTTACATACATATCTAAGT
128 CCTTACATACATATCTAAGC
*
11211 TTAAGTTTTGTAAATAGAGGAAATAGACTATGAAAAGAAGAGATTCTTCGATATCCCTCACATAC
1 TTAAGTTTTGTAAATAGAGGAAATAGAC--TGAAAAGAAGAGATTCTCCGATATCCCTCACATAC
** * **
11276 ATATCTAAGTTTAAGTTTTGTAAAT-AAAG-A-AAATAAACTGTGAAAA-AGATTCTCTGATATC
64 ATATCTAAACTTAAGTTTTGTAAATAAAAGAAGAAATAAACGGTGAAAAGAGATTCTCCAATAT-
*
11337 CCTTGCATACATATCTAAGC
128 CCTTACATACATATCTAAGC
11357 TTAAGTTTTGTAAATAGAGGAAATATAGACTGAAAAGA
1 TTAAGTTTTGTAAATAGAGG-AA-ATAGACTGAAAAGA
11395 TTCTCTTATT
Statistics
Matches: 163, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
145 11 0.07
146 60 0.37
147 2 0.01
148 7 0.04
149 27 0.17
151 7 0.04
152 49 0.30
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (147 bp):
TTAAGTTTTGTAAATAGAGGAAATAGACTGAAAAGAAGAGATTCTCCGATATCCCTCACATACAT
ATCTAAACTTAAGTTTTGTAAATAAAAGAAGAAATAAACGGTGAAAAGAGATTCTCCAATATCCT
TACATACATATCTAAGC
Found at i:16572 original size:21 final size:21
Alignment explanation
Indices: 16546--16672 Score: 173
Period size: 21 Copynumber: 6.0 Consensus size: 21
16536 CATGCTGGCT
*
16546 TCCCTTGATTCAGGCATTCGC
1 TCCCTTGAATCAGGCATTCGC
** *
16567 TCCCTTGGTTCAGGCATTCGT
1 TCCCTTGAATCAGGCATTCGC
**
16588 TCCCTTGGGTCAGGCATTCGC
1 TCCCTTGAATCAGGCATTCGC
* *
16609 TCCCTCGAATCAGGCATTCGT
1 TCCCTTGAATCAGGCATTCGC
*
16630 TCCCTCGAATCAGGCATTCGC
1 TCCCTTGAATCAGGCATTCGC
16651 TCCCTTGAATCAGGCATTCGC
1 TCCCTTGAATCAGGCATTCGC
16672 T
1 T
16673 GTCGTGACTC
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 96 1.00
ACGTcount: A:0.15, C:0.33, G:0.21, T:0.31
Consensus pattern (21 bp):
TCCCTTGAATCAGGCATTCGC
Done.