Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010871.1 Corchorus capsularis cultivar CVL-1 contig10892, 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: 21751
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:12203 original size:16 final size:16
Alignment explanation
Indices: 12182--12212 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12172 GACATGTGCT
*
12182 AGAGTACTTGTGGTAA
1 AGAGTACTAGTGGTAA
12198 AGAGTACTAGTGGTA
1 AGAGTACTAGTGGTA
12213 GACCAGAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.29
Consensus pattern (16 bp):
AGAGTACTAGTGGTAA
Found at i:20968 original size:323 final size:321
Alignment explanation
Indices: 20076--21741 Score: 2015
Period size: 323 Copynumber: 5.1 Consensus size: 321
20066 ATTAATTTAC
* * **
20076 TTTCCGAATTAATTTATAATTTAAATCGAAACAAGATT-AGGATGCTTGAAAAGTCAAATCTTTA
1 TTTCCGAATTAATTTCTAA-TTAAATCGAAACAAGATTGA-GATGCTCGAAAAAACAAATCTTTA
* * * * *
20140 TATTCATTATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAA
64 TATCCAATATGGCTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAA
* * * * * * *
20205 TCTTGCAAAACCTGAGCCGGGGC-CCTGGAAAGCGTTTTTAGTCATAAACCGTGACAAACGATTT
129 TCATGCAAAA-TTGAGCCGGGGCTCC-GGAACGCGTTTTTAGCCAAAAACCGTG----ATG-GTT
* * * * ** * * *
20269 CGAATAAAATTTTGC-AAAAATTGATCCGAAAA-TTTTTTCCTCAATTCTTT-CCACAATACCCA
187 AGTACACAATTCAGCTAAAAACTGATCCGAAAAGTTTTTT-CTCAATTTTTTGCCACAATACTCA
* * * * * * *
20331 GAAAAAATATATAATTCAATCCCGAAAATATTAAAGGGTTTTT-AAGCTTCTAATATCGTTGTTC
251 GAAAAAATATATAATTCAATGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTC
20395 CAAAATTTTTTT
316 C---A---TTTT
* * * * *
20407 TTTCTGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATA
1 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCTTTATA
* * * * * * *
20472 TCCAATGTGGCTGACATTTGGTTCGATG-AATTAGATATTTCATGGAGCCTTTGCGCTAAAAATA
66 TCCAATATGGCTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAATC
** *
20536 ATGCAAAATTGAGCCGGGGCTCTAGAACGCGTTTTTAGCC-AAAACCGTGATGGTTAGTACACGT
131 ATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC-A
* * *
20600 TTTCAGCTAAAAACTGATCCGAAAAGTTTTATCTCAATATTTTGCCACAATACTCAGAAAAAATA
195 ATTCAGCTAAAAACTGATCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATA
* *
20665 TATAATTCAATGCCAAAAAGATTAATGGGTTTTTCACGCTTCTAATATTGTTTTTCCATTTT
260 TATAATTCAATGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* * *
20727 TTTCCGAATCAATTTCTAATTAAATCGAAACAAGATTGGGATGCTCGAAAAAATAAATCTTTATA
1 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCTTTATA
* * *
20792 TCCAATATGGCTGAAATTTGGTTCAATGAAAATAGATATTTGAAGGAGTCTTTGCGCCAAAAAAT
66 TCCAATATGGCTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCC-AAAAAT
* * *
20857 CATACAAATTTGAGCCGAGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACC
130 CATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA-C
20922 AATTCAGCTAAAAACTGATCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAT
194 AATTCAGCTAAAAACTGATCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAT
** ** * *
20987 ATATAATTCAACACCAAAAAGATTGACAGGCTTTTAACGCTTCTAATATCGTTTTTCC-TTTT
259 ATATAATTCAATGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* * * * *
21049 TTTTCTAATTAATTTCTAATTAAGTCGAAACAAGATTGAAATGCTCAAAAAAAACAAAT-TATTA
1 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTC-GAAAAAACAAATCT-TTA
* ** * *
21113 TCTCCAATATGATTGAGATTTGGTTCAATGAATAA-AGATATTTCAAAGAGTCTTTGCGCCAAAA
64 TATCCAATATGGCTGAGATTTGGTTCGATGAA-AATAGATATTTCAAGGAGTCTTTGCGCCAAAA
* * * * * **
21177 ATCATGAAAAATTTAGCCGGGGCTCCGGAACGCATTTTTAGGCAAAAACCGTAATAATTAGTACA
128 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* * * * * *
21242 TGATTATCGGCTAGAAACTGATCCGAAAAGTTTTATCTCAATTTTTTTGTCACAATACTCAGAAA
193 -CAAT-TCAGCTAAAAACTGATCCGAAAAGTTTTTTCTCAA-TTTTTTGCCACAATACTCAGAAA
*
21307 AAATATATAATTTAATGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-T
255 AAATATATAATTCAATGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATT
21371 TT
320 TT
* *
21373 TTTCCGAATCAATTTCTAATTAAATCGAAACAAGATTGCGATGCTCGAAAAAACAAATCTTTATA
1 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCTTTATA
*
21438 TCCAATATGGCTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCAAAAAATC
66 TCCAATATGGCTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAATC
* *
21503 ATGCAAAATTGAGTCGGGGCTCCGGAACGCGGTTTTAGCCAAAAACCGTGATGGGTTAGTACACA
131 ATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-GGTTAGTACACA
* * * *
21568 ATTTCGGCTAAAAACTGATTCGAAAAGTTTTTTCTCAATTTTTTGCCAGAATACTCACAAAAAAT
195 A-TTCAGCTAAAAACTGATCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAT
* * *
21633 ATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTTT
259 ATATAATTCAATGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTT
** * * * *
21697 TTTATGAATTAAATTCTAATTAAGTCAAAACAAGATTGCGATGCT
1 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCT
21742 AAAAAAAAAA
Statistics
Matches: 1151, Mismatches: 161, Indels: 53
0.84 0.12 0.04
Matches are distributed among these distances:
320 86 0.07
321 24 0.02
322 233 0.20
323 385 0.33
324 200 0.17
325 55 0.05
326 19 0.02
327 8 0.01
328 25 0.02
329 36 0.03
330 62 0.05
331 18 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (321 bp):
TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCTTTATA
TCCAATATGGCTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAATC
ATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAA
TTCAGCTAAAAACTGATCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATAT
ATAATTCAATGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
Done.