Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018367.1 Corchorus olitorius cultivar O-4 contig18400, 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, 694
Length: 1158
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:612 original size:334 final size:334
Alignment explanation
Indices: 4--1158 Score: 1921
Period size: 334 Copynumber: 3.5 Consensus size: 334
1 ATT
* * *
4 TTTTTTCTGATGAAATTTCTAATTATATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTC
1 TTTTTTCTGATTAAATTTCTAATTAAATCGAAACAAGATTCAAAGGCTCGTAAAAACAAATCCTC
** * **
69 AATTGCTACATGGCTAAGTTTTTATTAGAAGAATATAGATATTTCAAGGAGTCTTGACGCCAATG
66 AAACGCTACATGGCTAAGTTTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAA
*
134 ATCAAGCAAAACTGAGTCC-GGTCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTAC
131 ATCATGCAAAACTGAG-CCGGGTCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTAC
* * * *
198 ACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTTCCTCAAGTTTTGGATAAAA
195 ACGATTTTGGCTAAAATTTTGCAAAAAACGACCACGAAAATTTTTTCCTCAATTTTTGGATAAAA
*
263 TACTCATAAAATATATATAACTAAACACCAAAAAGATTCGAGGACTTTTAACGCTTTTAATATCG
260 TACTCATAAAATATATATAACTAAACGCCAAAAAGATTCGAGGACTTTTAACGCTTTTAATATCG
328 TTTTAT-ATA
325 TTTTATCATA
337 TTTTTTTCTGATTAAATTTCTAATTAAATCGAAACAAGATTCAAAGGCTCGTAAAAACAAATCCT
1 -TTTTTTCTGATTAAATTTCTAATTAAATCGAAACAAGATTCAAAGGCTCGTAAAAACAAATCCT
*
402 TAAACGCTACATGGCTAAGTTTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAA
65 CAAACGCTACATGGCTAAGTTTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAA
*
467 AATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCACAAACCGTGATGGTTAGTAC
130 AATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTAC
532 ACGATTTTGGCTAAAATTTTGCAAAAAACGACCACGAAAATTTTTTCCTCAATTTTTGGATAAAA
195 ACGATTTTGGCTAAAATTTTGCAAAAAACGACCACGAAAATTTTTTCCTCAATTTTTGGATAAAA
* * *
597 TACTCAGAAAATATATATAATTTAAA-GCCAAAAATATTCGAGGACTTTTAACGCTTTTAATATC
260 TACTCATAAAATATATATAA-CTAAACGCCAAAAAGATTCGAGGACTTTTAACGCTTTTAATATC
661 GTTTTATCATA
324 GTTTTATCATA
*
672 TTTTTTCTGAATT-AATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
1 TTTTTTCTG-ATTAAATTTCTAATTAAATCGAAACAAGATTCAAAGGCTCGTAAAAACAAATCCT
*
736 CAAATGCTACATGGCTAAGTTTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAA
65 CAAACGCTACATGGCTAAGTTTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAA
* *
801 AATCATGCAAAACTGAGCCGGGTCTCCGAAACGCGTTTTTAACCAAAAACCGTGATGGTTAGTAC
130 AATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTAC
*
866 ACGATTTTGGCTAAAATTTTGCAAAAAAACGACCATGAAAATTTTTTCCTCAATTTTTGGATAAA
195 ACGATTTTGGCTAAAATTTTGC-AAAAAACGACCACGAAAATTTTTTCCTCAATTTTTGGATAAA
931 ATACTCATAAAATATATATAACTAAACGCCAAAAAGATTCGAGGACTTTTCAA-GCTTTTAATAT
259 ATACTCATAAAATATATATAACTAAACGCCAAAAAGATTCGAGGACTTTT-AACGCTTTTAATAT
995 CGTTTT-TCATA
323 CGTTTTATCATA
* * *
1006 TTTTTTCTGATTTAATTTCTAATTAAATCGAAACAAGATTAAAAGGCTCGTAAAAACAAATCCTT
1 TTTTTTCTGATTAAATTTCTAATTAAATCGAAACAAGATTCAAAGGCTCGTAAAAACAAATCCTC
* *
1071 AAACGCAACATGGCTAAG-TTTTATTAGATGAATATAGATATTTCAAGGAGTCTTCACGCCAAAA
66 AAACGCTACATGGCTAAGTTTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAA
*
1135 ATCAGGCAAAGA-TGAGCCGGGTCC
131 ATCATGCAAA-ACTGAGCCGGGTCC
Statistics
Matches: 775, Mismatches: 37, Indels: 19
0.93 0.04 0.02
Matches are distributed among these distances:
333 70 0.09
334 593 0.77
335 110 0.14
336 2 0.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (334 bp):
TTTTTTCTGATTAAATTTCTAATTAAATCGAAACAAGATTCAAAGGCTCGTAAAAACAAATCCTC
AAACGCTACATGGCTAAGTTTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAA
ATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
CGATTTTGGCTAAAATTTTGCAAAAAACGACCACGAAAATTTTTTCCTCAATTTTTGGATAAAAT
ACTCATAAAATATATATAACTAAACGCCAAAAAGATTCGAGGACTTTTAACGCTTTTAATATCGT
TTTATCATA
Done.