Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014340.1 Corchorus olitorius cultivar O-4 contig14373, 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: 7969
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7749 original size:964 final size:965
Alignment explanation
Indices: 5316--7941 Score: 4587
Period size: 968 Copynumber: 2.7 Consensus size: 965
5306 AAGCCTAATC
*
5316 CAAGCTCTTATGCATATCGATTGCAAGTAAGGTGATGATCTTGGAACTAATGGATGAATGATTGC
1 CAAGCTCTTATGCATATCGATTGCAAGTAAGGTGATGATCTTGGAACTAATGGATGAATGCTTGC
* *
5381 TCAAATCATCACCAAAGCTCTTTAATGGTGCGTCAATGACTTTCATATCATCTAAATGACTTCGA
66 TCAAATCATCACCAAAGCTC-TTAATGGCGCATCAATGACTTTCATATCATCTAAATGACTTCGA
* *
5446 ACAAGGCCCATGAGTACATCCTTGAATCTCTTAGCTCTTGCTGTTGTCGTGAGACCATTAGGCAT
130 ACAAGGCCCATGAGTACATCCTTGAA-CTCTTAGCTCTTGCTGTTGTCATGAGACCAATAGGCAT
5511 CTCTAATGGATCAAATGGCTTCTTCTTGGTGCTTGGAACATGCTCAACGATATCTCCTTGATCTT
194 CTCTAATGGATCAAATGGCTTCTTCTTGGTGCTTGGAACATGCTCAACGATATCTCCTTGATCTT
*
5576 CATGCTTCTCCATGCTTCCTTGCACTCCATGCTCATCCTTTCCATGATCTCCATTGTCATCTTCA
259 CATGCTTCTCCATGCTTCCTTGCACTCCATGCTCATCCTTTCCATGATCTCCATTGTCATATTCA
5641 TGTCCATAATAAGCCCTTGGCGCATCATGATACCAATTGATACGAATCTAGTTGTATTAGATTCA
324 TGTCCATAATAAGCCCTTGGCGCATCATGATACCAATTGATACGAATCTAGTTGTATTAGATTCA
* *
5706 AATCTACCCTTGAATTCCTCCAAAGATCAACTTAAAACTTCAACTTCTAGATTTGATGTAGATCG
389 AATCTACCCTTGAATTCCTCCAAAGATCAACTTGAAACTTCAACTTCTAGATTTGACGTAGATCG
* * * *
5771 ATTTCCCTAGCTAGCTCTTCTTCTTGGTTCGTCGCCTCTAGATGAATATTTAGACCTGCAATTAT
454 ATTTCCCTAGCTAGCTCTTCTTCTTCGTTCGTCGCCTCAAGATGGATAATTAGACCTGCAATTAT
*
5836 CAATCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGACTCT
519 CAATCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGACTAT
** *
5901 ACAAGAAAGAAAAACCCTAAAGTATGCTCAAACTAGAACAATGAAGCTAAATTATCAATTGGATG
584 ACAAGATTGAAGAACCCTAAAGTATGCTCAAACTAGAACAATGAAGCTAAATTATCAATTGGATG
5966 AATAAACCTCAACTTTTATTGAAAACTTAACATGGTTTACAAAGGGGGGGAGGTCGATGTCCTTA
649 AATAAACCTCAACTTTTATTGAAAACTTAACATGGTTTACAAAGGGGGGGAGGTCGATGTCCTTA
* *
6031 TATAGGCAAAGGGTCGACCAAAACTATCAAAAAGTGAGCCCTCTAGGCGGTTTACAATGCCTTGG
714 TATAGGCAAAGGGTCGACCAAAACTATCAAAAAGTAAGCCATCTAGGCGGTTTACAATGCCTTGG
6096 TCGACAATCTTAAGGAAAGGACAAGGAAATAACCTAATCCAAGTCCAACTAGGAATAATAAAATA
779 TCGACAATCTTAAGGAAAGGACAAGGAAATAACCTAATCCAAGTCCAACTAGGAATAATAAAATA
*
6161 ACAAGGAATAAATAAACAAGGATTGAACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTGAAC
844 ACAAGGAATAAATAAACAAGGATTGAACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTAAAC
* *
6226 ATAAATATAAACTAATCTAAGATAGAATAAAGCCCACAATGGCCTAAATAACACATT
909 ATAAAGATAAACTAATCTAAGATAGAACAAAGCCCACAATGGCCTAAATAACACATT
*
6283 CAAGCTCTAATGCATATCGATTGCAAGTAAGGTGATGATCTTGGAACTAATGGATGAATGCTTGC
1 CAAGCTCTTATGCATATCGATTGCAAGTAAGGTGATGATCTTGGAACTAATGGATGAATGCTTGC
* *
6348 TCAAATCATCGCCAAAGCTCTTCATTGGCGCATCAATGACTTTCATATCATCTAAATGACTTCGA
66 TCAAATCATCACCAAAGCTCTT-AATGGCGCATCAATGACTTTCATATCATCTAAATGACTTCGA
* *
6413 ACAAGGCCCATGGGTGCATCCTTGAATCTCTTAGCTCTTGCTGTTGTCATAGAGACCAATAGGCA
130 ACAAGGCCCATGAGTACATCCTTGAA-CTCTTAGCTCTTGCTGTTGTCAT-GAGACCAATAGGCA
6478 TCTCTAATGGATCAAATGGCTTCTTCTTGGTGCTTGGAACATGCTCAACGATATCTCCTTGATCT
193 TCTCTAATGGATCAAATGGCTTCTTCTTGGTGCTTGGAACATGCTCAACGATATCTCCTTGATCT
*
6543 TCATGCTTCTCCATGCTTCCTTCCACTCCATGCTCATCCTTTCCATGATCTCCATTGTCATATTC
258 TCATGCTTCTCCATGCTTCCTTGCACTCCATGCTCATCCTTTCCATGATCTCCATTGTCATATTC
* *
6608 ATGTCCATTATAAGCCCTTGGCGCATAATGATACCAATTGATACGAATCTAGTTGTATTAGATTC
323 ATGTCCATAATAAGCCCTTGGCGCATCATGATACCAATTGATACGAATCTAGTTGTATTAGATTC
* *
6673 AAATCTACCCTTGAATTCCTCCAAAGATCAACTCGAAACTTCAACTTCTAGATTTGACGTAGATT
388 AAATCTACCCTTGAATTCCTCCAAAGATCAACTTGAAACTTCAACTTCTAGATTTGACGTAGATC
*
6738 GATTTCCCTAGCTAGCTCTTCTTCTTCGTTCGTCGCCTCAGGATGGATAATTAGACCTGCAATTA
453 GATTTCCCTAGCTAGCTCTTCTTCTTCGTTCGTCGCCTCAAGATGGATAATTAGACCTGCAATTA
6803 TCAATCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGACTA
518 TCAATCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGACTA
*
6868 TACAAGATTGAAGAACCCTAAAGTATGCTCAAACTAGAACAATGAAGCTAAATTATCAATTGGGT
583 TACAAGATTGAAGAACCCTAAAGTATGCTCAAACTAGAACAATGAAGCTAAATTATCAATTGGAT
6933 GAATAAACCTCAACTTTTATTGAAAACTTAACATGGTTTACAAAGGGGGGGAGGTCGATGTCCTT
648 GAATAAACCTCAACTTTTATTGAAAACTTAACATGGTTTACAAAGGGGGGGAGGTCGATGTCCTT
* * *
6998 ATATAGGCAGAGGGTCGACCAAAACTATCCAAAAA-TAAGCTATCTAGGCGGTTTACGATGCCTT
713 ATATAGGCAAAGGGTCGACCAAAACTAT-CAAAAAGTAAGCCATCTAGGCGGTTTACAATGCCTT
* * * *
7062 GGGTTG-CAATCTTCAGGAAAGGACAAGGAAATAGCCTAATCCAAGTCCAACTAGGAA-AATTAA
777 -GGTCGACAATCTTAAGGAAAGGACAAGGAAATAACCTAATCCAAGTCCAACTAGGAATAATAAA
* * *
7125 ATAATAAGGAATAAATAAACAAGGATTGGACTTAGTCAAGCAAGGCCCAATCCTAATGTCATCTA
841 ATAACAAGGAATAAATAAACAAGGATTGAACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTA
*
7190 AACATAAAGATAAAGTAATCTAAGATAGAACAAAGCCCACAATGGCCTAAATAACACATT
906 AACATAAAGATAAACTAATCTAAGATAGAACAAAGCCCACAATGGCCTAAATAACACATT
7250 CAAGCTCTTATGCATATCGATTGCAAGTAAGGTGATGATCTTGGAACTAATGGATGAATGCTTGC
1 CAAGCTCTTATGCATATCGATTGCAAGTAAGGTGATGATCTTGGAACTAATGGATGAATGCTTGC
*
7315 TCAAATCATCACCAAAGCTCGTTAATGGCACATCAATGACTTTCATATCATCTAAATGACTTCGA
66 TCAAATCATCACCAAAGCTC-TTAATGGCGCATCAATGACTTTCATATCATCTAAATGACTTCGA
* *
7380 ACAAGGCTCATGATTACATCCTTGAA-TCTTAGCTCTTGCTGTTGTCATGAGACCAATAGGCATC
130 ACAAGGCCCATGAGTACATCCTTGAACTCTTAGCTCTTGCTGTTGTCATGAGACCAATAGGCATC
* * *
7444 TCTAATGTATCAAATGGCTTCTTTTTGGTGCTTGGAACATGCTCAACGATATCTCCTTGATCTTT
195 TCTAATGGATCAAATGGCTTCTTCTTGGTGCTTGGAACATGCTCAACGATATCTCCTTGATCTTC
*
7509 ATGATTCTCCATGCTTCCTTGCACTCCATGCTCATCCTTTCCATGATCTCCATTGTCATATTCAT
260 ATGCTTCTCCATGCTTCCTTGCACTCCATGCTCATCCTTTCCATGATCTCCATTGTCATATTCAT
*
7574 GTCCAAAATAAGCCCTTGGCGCATCATGATACCAATTGATACGAATCTAGTTGTATTAGATTCAA
325 GTCCATAATAAGCCCTTGGCGCATCATGATACCAATTGATACGAATCTAGTTGTATTAGATTCAA
7639 ATCTACCCTTGAATTCCTCCAAAGATCAACTTGAAACTTCAACTTCTAGATTTGACGTAGATCGA
390 ATCTACCCTTGAATTCCTCCAAAGATCAACTTGAAACTTCAACTTCTAGATTTGACGTAGATCGA
* *
7704 TTTCCCTAACTAGCTCTTCTTCTTCGTTCGTCGCCTCAAGATGGATAATT-GCACCTACAATTAT
455 TTTCCCTAGCTAGCTCTTCTTCTTCGTTCGTCGCCTCAAGATGGATAATTAG-ACCTGCAATTAT
*
7768 CAATCTAAGATCACAAGATTCACAAACAATTAAGCAATCAGAACCTAATTGTTTGCTAGGACTAT
519 CAATCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGACTAT
* * *
7833 ATAGGATTGAAGAACCCTAAAGTATGCTCAAACTAGAACAATGAAGCTAAATTATCAATTGGTTG
584 ACAAGATTGAAGAACCCTAAAGTATGCTCAAACTAGAACAATGAAGCTAAATTATCAATTGGATG
* *
7898 AATAAACCTTAACTTTTATTGAAAACTTAACTTGGTTTTACAAA
649 AATAAACCTCAACTTTTATTGAAAACTTAACATGG-TTTACAAA
7942 AAGGGCGGGG
Statistics
Matches: 1581, Mismatches: 71, Indels: 16
0.95 0.04 0.01
Matches are distributed among these distances:
963 1 0.00
964 484 0.31
965 30 0.02
966 2 0.00
967 436 0.28
968 618 0.39
969 10 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (965 bp):
CAAGCTCTTATGCATATCGATTGCAAGTAAGGTGATGATCTTGGAACTAATGGATGAATGCTTGC
TCAAATCATCACCAAAGCTCTTAATGGCGCATCAATGACTTTCATATCATCTAAATGACTTCGAA
CAAGGCCCATGAGTACATCCTTGAACTCTTAGCTCTTGCTGTTGTCATGAGACCAATAGGCATCT
CTAATGGATCAAATGGCTTCTTCTTGGTGCTTGGAACATGCTCAACGATATCTCCTTGATCTTCA
TGCTTCTCCATGCTTCCTTGCACTCCATGCTCATCCTTTCCATGATCTCCATTGTCATATTCATG
TCCATAATAAGCCCTTGGCGCATCATGATACCAATTGATACGAATCTAGTTGTATTAGATTCAAA
TCTACCCTTGAATTCCTCCAAAGATCAACTTGAAACTTCAACTTCTAGATTTGACGTAGATCGAT
TTCCCTAGCTAGCTCTTCTTCTTCGTTCGTCGCCTCAAGATGGATAATTAGACCTGCAATTATCA
ATCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGACTATAC
AAGATTGAAGAACCCTAAAGTATGCTCAAACTAGAACAATGAAGCTAAATTATCAATTGGATGAA
TAAACCTCAACTTTTATTGAAAACTTAACATGGTTTACAAAGGGGGGGAGGTCGATGTCCTTATA
TAGGCAAAGGGTCGACCAAAACTATCAAAAAGTAAGCCATCTAGGCGGTTTACAATGCCTTGGTC
GACAATCTTAAGGAAAGGACAAGGAAATAACCTAATCCAAGTCCAACTAGGAATAATAAAATAAC
AAGGAATAAATAAACAAGGATTGAACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTAAACAT
AAAGATAAACTAATCTAAGATAGAACAAAGCCCACAATGGCCTAAATAACACATT
Done.