Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014317.1 Corchorus olitorius cultivar O-4 contig14350, 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: 3867
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Found at i:1811 original size:32 final size:32
Alignment explanation
Indices: 1770--1834 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1760 AGCCGCGTGT
* *
1770 CTGGTTATGGTAGGTAAGTCTATCAATGGGGG
1 CTGGTTATGGTAGGTAAATCTACCAATGGGGG
1802 CTGGTTATGGTAGGTAAATCTACCAATGGGGG
1 CTGGTTATGGTAGGTAAATCTACCAATGGGGG
1834 C
1 C
1835 AGCTGCGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.29
Consensus pattern (32 bp):
CTGGTTATGGTAGGTAAATCTACCAATGGGGG
Found at i:3782 original size:417 final size:416
Alignment explanation
Indices: 2996--3867 Score: 1390
Period size: 417 Copynumber: 2.1 Consensus size: 416
2986 GCATTTTTAG
*
2996 AATCAAAACATTAAAATTGGCTTCTGATTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTT
1 AATCAAAACATTAAAATTGGCTTCTGATTTCTTCATGAAAGTTGAAGATCATGAAATTACCTTTT
* *
3061 AATAGACACTTGAATCACCTTAATTAGACAAATAGAAAAAAATACAAAAAAAAAGCCGACGCGTT
66 AATAGACACTAGAATCACCTTAATCAGACAAATAGAAAAAAATACAAAAAAAAAGCCGACGCGTT
**
3126 AAATCGTCCAACCCATAATTATAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGAGGATCAT
131 AAATCGTCCAACAAATAATTATAAAGGATTAAATAGCATAAAGCATAAAAGTAT-AGAGGATCAT
** * *
3191 TCGATAAATAATCCAACAAAAAAATATTTCTTTGTGGAGAATGGGTCCCACGGAGGGTAACCTTT
195 TCGATAAATAATCCAACAAAAAAATATTTCTTTACGGAGAATGGGTCCCACAGAGAGTAACCTTT
* *
3256 TTGCAAACATCCCAAAACACCCTCGGTCCTTAATCAAAATAACAAAAAAACCGAGTATGAAAACC
260 TTGCAAACATCCCAAAACACCCTCGGTCCTTAATCAAAATAACAAAAAAACCGAGTACGAAAAAC
* * * *
3321 CGAAATACCCTTGACAATTTGTTTTTGGGTGAATGTAGTGCATCTTATAGCTGGACAAAAGGGTA
325 CGAAATACCCCTGACAATTTGTTCTTGGGTAAATGTAATGCATCTTATAGCTGGACAAAAGGGTA
*
3386 ATTTCCTTTCCAACTTTAATATATGTT
390 ATTCCCTTTCCAACTTTAATATATGTT
* *
3413 AATCAAAACATTAAAATTGCCTTCTGATTTCTTCATGAAAGTTGAAGATCTTGAAATTACCTTTT
1 AATCAAAACATTAAAATTGGCTTCTGATTTCTTCATGAAAGTTGAAGATCATGAAATTACCTTTT
* *
3478 AATAGACACTAGAATCACCTTAATCGGACAAATAGAACAAAAAATACAAAAAAAAA-CCGACGTG
66 AATAGACACTAGAATCACCTTAATCAGACAAATAG-A-AAAAAATACAAAAAAAAAGCCGACGCG
* *
3542 TTAAATCGTCGAACAAATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTAT-GAGGATCA
129 TTAAATCGTCCAACAAATAATTATAAAGGATTAAATAGCATAAAGCATAAAAGTATAGAGGATCA
* * *
3606 TTTGATAAATAATTCAACAAAAAAATATTTCTTTACGGAGAATGGGTCCCATAGAGAGTAA-CTG
194 TTCGATAAATAATCCAACAAAAAAATATTTCTTTACGGAGAATGGGTCCCACAGAGAGTAACCT-
* ** * *
3670 TTTTGCAAACTTCCCAAAATGCCTTCGGTCCTTAATCAAAATAACAAAAAAATCGAGTACGAAAA
258 TTTTGCAAACATCCCAAAACACCCTCGGTCCTTAATCAAAATAACAAAAAAACCGAGTACGAAAA
3735 TACCGAAATACCCCTGACAATTTGTTCTTGGGTAAATGTAATGCATCTTATAGCTGGACAAAAGG
323 -ACCGAAATACCCCTGACAATTTGTTCTTGGGTAAATGTAATGCATCTTATAGCTGGACAAAAGG
3800 GTAATTCCCTTTCCAACTTTAATATATGTT
387 GTAATTCCCTTTCCAACTTTAATATATGTT
* *
3830 AATCTAAACATTAAAATTGGTTTCTGATTTCTTCATGA
1 AATCAAAACATTAAAATTGGCTTCTGATTTCTTCATGA
Statistics
Matches: 418, Mismatches: 33, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
415 2 0.00
416 121 0.29
417 217 0.52
418 60 0.14
419 18 0.04
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (416 bp):
AATCAAAACATTAAAATTGGCTTCTGATTTCTTCATGAAAGTTGAAGATCATGAAATTACCTTTT
AATAGACACTAGAATCACCTTAATCAGACAAATAGAAAAAAATACAAAAAAAAAGCCGACGCGTT
AAATCGTCCAACAAATAATTATAAAGGATTAAATAGCATAAAGCATAAAAGTATAGAGGATCATT
CGATAAATAATCCAACAAAAAAATATTTCTTTACGGAGAATGGGTCCCACAGAGAGTAACCTTTT
TGCAAACATCCCAAAACACCCTCGGTCCTTAATCAAAATAACAAAAAAACCGAGTACGAAAAACC
GAAATACCCCTGACAATTTGTTCTTGGGTAAATGTAATGCATCTTATAGCTGGACAAAAGGGTAA
TTCCCTTTCCAACTTTAATATATGTT
Done.