Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007646.1 Corchorus olitorius cultivar O-4 contig07672, 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, 988
Length: 1648
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:614 original size:335 final size:333
Alignment explanation
Indices: 1--916 Score: 1356
Period size: 335 Copynumber: 2.7 Consensus size: 333
*
1 CGAAATCGTGTACTAACCATCACATGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCTGACTCAGT
1 CGAAATCGTGTACTAACCATCAC-GGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCTGACTCAGT
*
66 TTTGGCATAA-TTTTGGCAAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGC
65 TTT-GCATAATTTTTGGCAGAAGACTTCTCGAAATATCTATATTCATCTAATCAAA--TCTCAGC
*
130 CACAATGCATTTACGGATTTATTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAAATA
127 CACAATGCATTTACGGATTTATTTTTAAGAGTATCTGAATCTTGTTTCGATTTAATTAG-AAATA
* * ** *
195 AAATCAGAAAAAAATGGAAAAA-AGATATTTGAAGCGTGAAAAATTCTGAAATATTTTTGGCGTT
191 AATTCAGAAAAAAATGGAAAAACA-ATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTT
259 GAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTTG
255 GAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTT-
324 TTGCAAAATTTTAGC
319 TTGCAAAATTTTAGC
*
339 CGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCTGACTTAGTT
1 CGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCTGACTCAGTT
* * * * *
404 TTGCATAAATTTTTGGCAGGAAGACTT-TCCGAAATATCTATATTCTTATGACCAAATCTCAGCT
66 TTGCAT-AATTTTTGGCA-GAAGACTTCT-CGAAATATCTATATTCATCTAATCAAATCTCAGCC
* * * * * * **
468 ACATTG-GTTTATGGATTTCTTTTTACGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAA
128 ACAATGCATTTACGGATTTATTTTTAAGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
532 TTCAGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAA
193 TTCAGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAA
* * *
597 TTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGATAAACTTTTTGGGTCAGTTTTTTGC
258 TTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTTTTGC
662 AAAATTTTAGC
323 AAAATTTTAGC
* * * *
673 CGAAATCGTGTACTAACCATCACGG-TTTTTGGCTACAAATGCGTTTCGGGGTCCTGGCTCAGTT
1 CGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCTGACTCAGTT
* *
737 TTGCATGATTTTTGGCAGAATGACTTCTCAAAATATCTATATTCATCTAATCAAATCTCTTAGCC
66 TTGCATAATTTTTGGCAGAA-GACTTCTCGAAATATCTATATTCATCTAATCAAATCTC--AGCC
* *
802 ACAATGCATTTACGGATTTATTTTTAAAAGTATCTAAATCTTGTTTCGATTTAATTAGAAATAAA
128 ACAATGCATTTACGGATTTATTTTTAAGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
*
867 TTCAGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAA
193 TTCAG--AAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAACCCTAAA
917 TGTTATTAGT
Statistics
Matches: 519, Mismatches: 47, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
331 3 0.01
332 41 0.08
333 41 0.08
334 48 0.09
335 177 0.34
336 49 0.09
337 98 0.19
338 32 0.06
339 30 0.06
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (333 bp):
CGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGGCCTGACTCAGTT
TTGCATAATTTTTGGCAGAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCAGCCACA
ATGCATTTACGGATTTATTTTTAAGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
AGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTA
TATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTTTTGCAAA
ATTTTAGC
Done.