Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009646.1 Corchorus olitorius cultivar O-4 contig09678, 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: 9204
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:3211 original size:41 final size:42
Alignment explanation
Indices: 3089--3211 Score: 153
Period size: 41 Copynumber: 3.0 Consensus size: 42
3079 TTTACTTTAA
*
3089 CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTA-GCTTT-TC
1 CCAGTTTGCCCTTCCTCATCGGGAGGTGTTGTTACG-TTTGTC
* * * *
3130 CCAATTTGCCCTTCCTGATCGGGAGGTGTTGTTGCCTTTGT-
1 CCAGTTTGCCCTTCCTCATCGGGAGGTGTTGTTACGTTTGTC
* *
3171 CGAGTTTACCCTTCCTCATCGGGAGGTGTTGTTACGTTTGT
1 CCAGTTTGCCCTTCCTCATCGGGAGGTGTTGTTACGTTTGT
3212 ACAAAGTTGT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 68 0.99
42 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.39
Consensus pattern (42 bp):
CCAGTTTGCCCTTCCTCATCGGGAGGTGTTGTTACGTTTGTC
Found at i:3282 original size:40 final size:39
Alignment explanation
Indices: 3233--3663 Score: 256
Period size: 40 Copynumber: 10.7 Consensus size: 39
3223 TACTTCCTGT
*
3233 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATGCTTGG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCAT-CTTGA
* * ** *
3273 TTTTCCCTTCCTCATCGGGAGGTGTTGTTGGCAT-TTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATCTT---GA
*
3314 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATCCTCGA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCAT-CTTGA
*
3354 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAACATTTCTCT-A
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA--TCT-TGA
* * * *
3395 ATTGCCCTTCCTCATCGGAAGGTGTTGTTA--AGTTTATCA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA-TCT-TGA
* * ** *
3434 GTTTGCCCTTCCTCATCAGAAGGTGTTGTTAAGTTTACTAG-
1 -TTTGCCCTTCCTCATCGGAAGGTGTTG-TCAGCAT-CTTGA
* * **
3475 TTTGCCCTTACTCATCGGAAGGTGTTGTTAAGTTCA-CCAG-
1 TTTGCCCTTCCTCATCGGAAGGTGTTG-TCAG--CATCTTGA
* * **
3515 TTTGCCCTTCCTCATCGGAAAGTGTTGTTAAGTTCA-CCAG-
1 TTTGCCCTTCCTCATCGGAAGGTGTTG-TCAG--CATCTTGA
* **
3555 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTCA-CCAG-
1 TTTGCCCTTCCTCATCGGAAGGTGTTG-TCAG--CATCTTGA
* * *
3595 TTTGCCCTTCCTCATCGGAAGGTGTTTTCTA-CATTTCTCA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTC-AGCATCT-TGA
* *
3635 GTTTGCCCTCCCTCATCGGGAGGTGTTGT
1 -TTTGCCCTTCCTCATCGGAAGGTGTTGT
3664 TTCTATTCCT
Statistics
Matches: 327, Mismatches: 43, Indels: 41
0.80 0.10 0.10
Matches are distributed among these distances:
37 2 0.01
38 5 0.02
39 3 0.01
40 225 0.69
41 88 0.27
42 2 0.01
43 2 0.01
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (39 bp):
TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATCTTGA
Found at i:3503 original size:80 final size:80
Alignment explanation
Indices: 3233--3664 Score: 461
Period size: 81 Copynumber: 5.4 Consensus size: 80
3223 TACTTCCTGT
* ** * *
3233 TTTGCCCTTCCTCATCGGAAGGTGTTG-TCAG--CATGCTTGGTTTTCCCTTCCTCATCGGGAGG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTCA--C-CAGTTTGCCCTTCCTCATCGGAAGG
* * *
3295 TGTTGTT-GGCATTTACCAA
63 TGTTGTTAAG--TTTACTAG
* *
3314 TTTGCCCTTCCTCATCGGAAGGTGTTG-TCAG--CATCCTCGATTTGCCCTTCCTCATCGGAAGG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTCA-CC-AG-TTTGCCCTTCCTCATCGGAAGG
* * *
3376 TGTTGTCAACATTTCTCTA-
63 TGTTGTTAA-GTTT-ACTAG
* * * *
3395 ATTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTTATCAGTTTGCCCTTCCTCATCAGAAGGTGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTCACCAGTTTGCCCTTCCTCATCGGAAGGTGT
3460 TGTTAAGTTTACTAG
66 TGTTAAGTTTACTAG
* *
3475 TTTGCCCTTACTCATCGGAAGGTGTTGTTAAGTTCACCAGTTTGCCCTTCCTCATCGGAAAGTGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTCACCAGTTTGCCCTTCCTCATCGGAAGGTGT
* *
3540 TGTTAAGTTCACCAG
66 TGTTAAGTTTACTAG
3555 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTCACCAGTTTGCCCTTCCTCATCGGAAGGTGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTCACCAGTTTGCCCTTCCTCATCGGAAGGTGT
*
3620 TTTCTACA-TTT-CTCAG
66 TGT-TA-AGTTTACT-AG
* *
3636 TTTGCCCTCCCTCATCGGGAGGTGTTGTT
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTT
3665 TCTATTCCTG
Statistics
Matches: 305, Mismatches: 34, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
79 3 0.01
80 143 0.47
81 150 0.49
82 7 0.02
83 1 0.00
84 1 0.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (80 bp):
TTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTTCACCAGTTTGCCCTTCCTCATCGGAAGGTGT
TGTTAAGTTTACTAG
Done.