Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007010.1 Corchorus capsularis cultivar CVL-1 contig07031, 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: 3540
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Found at i:607 original size:321 final size:321
Alignment explanation
Indices: 1--737 Score: 1190
Period size: 321 Copynumber: 2.3 Consensus size: 321
* *
1 AACAAGAATCAGATGCTTGTAAGAAAAAAAAATCCTTAAATCCATTGTGGCTGAGATTTGTTTTG
1 AACAAGATTCAGATGCTCGT---AAAAAAAAATCCTTAAATCCATTGTGGCTGAGATTTGTTTTG
* * * * *
66 ATGAATAAAGATATTACAGGGAATCTTTCTCCCAAAAATCATGCAAAACTGAGGCGGTGCGCCGA
63 ATGAATACAGATATTACAAGGAATCTTTCTCCCAAAAATCATGCAAAACAGAGCCAGTGCGCCGA
*
131 ATTGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACACGAAAA
128 AATGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACACGAAAA
*
196 TTTTATTTCTCAATTTTTGCCAGAATACTAAAAAAAATTTATTATTCATCACCAAAAAAATTAAG
193 TTTTATTTCTCAATTTTTCCCAGAATACTAAAAAAAATTTATTATTCATCACCAAAAAAATTAAG
* *
261 AGTTTTTCCATGCTTCTAATATGATTTTTCCATTTTTATTCCGAATTTATTTCAAATTATATCGA
258 AGTTTTTCCATGCTTCTAATATGA-TTTTCCATTTCTATTCCGAATATATTTCAAATTATATCGA
*
326 AACAAGATTCAGATGCTCGT-AAAAAAAATCCTTAAATCCATTGTGGCTGAGATTTGTTTTCATG
1 AACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCATTGTGGCTGAGATTTGTTTTGATG
* * *
390 AATACAGATATTACAAGGAGTCTTTCTGCCAAAAATCATGCAAAACAGAGCCAGTGTGCCGAAAT
66 AATACAGATATTACAAGGAATCTTTCTCCCAAAAATCATGCAAAACAGAGCCAGTGCGCCGAAAT
** *
455 GCATTTTTATTCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTT
131 GCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACACGAAAATTT
520 TATTTCTCAATTTTTTCCCAGAATACTAAAAAAAATTTATTATTCATCACCAAAAAAATTAAGAG
196 TATTTCTCAA-TTTTTCCCAGAATACTAAAAAAAATTTATTATTCATCACCAAAAAAATTAAGAG
585 TTTTT-CATGCTTCTAATATGATTTTCCATTTCTATTCCGAATATATTTCAAATTATATCGA
260 TTTTTCCATGCTTCTAATATGATTTTCCATTTCTATTCCGAATATATTTCAAATTATATCGA
* * *
646 AATAAGATTCAGATGCTCGTAAAAAAAAAATCCTTAAATCCTTTGTGGCTGAGATTTCTTTTGAT
1 AACAAGATTCAGATGCTCGT-AAAAAAAAATCCTTAAATCCATTGTGGCTGAGATTTGTTTTGAT
* **
711 GAATACAGATATTCCAAATAATCTTTC
65 GAATACAGATATTACAAGGAATCTTTC
738 AGCCATAAAA
Statistics
Matches: 383, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
320 57 0.15
321 187 0.49
322 121 0.32
325 18 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (321 bp):
AACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCATTGTGGCTGAGATTTGTTTTGATG
AATACAGATATTACAAGGAATCTTTCTCCCAAAAATCATGCAAAACAGAGCCAGTGCGCCGAAAT
GCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACACGAAAATTT
TATTTCTCAATTTTTCCCAGAATACTAAAAAAAATTTATTATTCATCACCAAAAAAATTAAGAGT
TTTTCCATGCTTCTAATATGATTTTCCATTTCTATTCCGAATATATTTCAAATTATATCGA
Found at i:928 original size:244 final size:243
Alignment explanation
Indices: 499--967 Score: 798
Period size: 244 Copynumber: 1.9 Consensus size: 243
489 CGATTTCGGC
* *
499 TAAAAACTGACCCGAAAATTTTATTTCTCAATTTTTTCCCAGAATACTAAAAAAAATTTATTATT
1 TAAAAACTGACACGAAAATTTTATTTCTCAATTTTTTCCCAGAATACTAAAAAAAAGTTATTATT
564 CATCACCAAAAAAATTAAGAGTTTTTCATGCTTCTAATATGATTTTCCATTTCTATTCCGAATAT
66 CATCACCAAAAAAATTAAGAGTTTTTCATGCTTCTAATATGATTTTCCATTTCTATTCCGAATAT
* **
629 ATTTCAAATTATATCGAAATAAGATTCAGATGCTCGTAAAAAAAAAATCCTTAAATCCTTTGTGG
131 ATTTCAAATTATATCGAAACAAGATTCAGATGCTCGT-AAAAAAAAATCCTTAAATCCACTGTGG
694 CTGAGATTTCTTTTGATGAATACAGATATTCCAAATAATCTTTCAGCCA
195 CTGAGATTTCTTTTGATGAATACAGATATTCCAAATAATCTTTCAGCCA
*
743 TAAAAACTGACACGAAAATTTTATTTCTCAATTTTTTGCCAGAATACTCAAAAAAAAGTTATTAT
1 TAAAAACTGACACGAAAATTTTATTTCTCAATTTTTTCCCAGAATACT-AAAAAAAAGTTATTAT
*
808 TCATCACC-AAAAAATTAAGAGTTTTTCATGCTTCTAATATGATTTTTTCCATTTTTATTCCGAA
65 TCATCACCAAAAAAATTAAGAGTTTTTCATGCTTCTAATATGA--TTTTCCATTTCTATTCCGAA
* *
872 TTTATTTCAAATTATATCGAAACAAGATTTAGATGCTCGT-AAAAAAAATCCTTAAATCCACTGT
128 TATATTTCAAATTATATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCACTGT
*
936 GGCTGAGATTTGTTTTGATGAATACAGATATT
193 GGCTGAGATTTCTTTTGATGAATACAGATATT
968 ACAAGGAGTC
Statistics
Matches: 212, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
244 133 0.63
245 23 0.11
246 56 0.26
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (243 bp):
TAAAAACTGACACGAAAATTTTATTTCTCAATTTTTTCCCAGAATACTAAAAAAAAGTTATTATT
CATCACCAAAAAAATTAAGAGTTTTTCATGCTTCTAATATGATTTTCCATTTCTATTCCGAATAT
ATTTCAAATTATATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCACTGTGGC
TGAGATTTCTTTTGATGAATACAGATATTCCAAATAATCTTTCAGCCA
Found at i:3260 original size:27 final size:27
Alignment explanation
Indices: 3205--3262 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3195 TGGCCTCTAG
* *
3205 GGGCAAAACTGTAATTTTAGCCTAATA
1 GGGCAAAAATGTAATTTTAGCATAATA
*
3232 GGGCAAAAATGGTAATTTT-GCATATTA
1 GGGCAAAAAT-GTAATTTTAGCATAATA
3259 GGGC
1 GGGC
3263 TATCACAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (27 bp):
GGGCAAAAATGTAATTTTAGCATAATA
Done.