Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017849.1 Corchorus olitorius cultivar O-4 contig17882, 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, 978
Length: 1631
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Found at i:1413 original size:687 final size:661
Alignment explanation
Indices: 1--1630 Score: 1949
Period size: 687 Copynumber: 2.4 Consensus size: 661
* * * * *
1 AATTTAATGCCAAAAAAATTGAAGGA--TTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTCCG
1 AATTCAATGCCAAAAAAATTAAATGATGTTTTCACGCTTCTAATATCGTTTTTCATTTTTTCCCG
* * * *
64 AATTTATTTCTAATTAAATCTAAACAAAGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAT
66 AATTTATTTCTAATTAAATCAAAACAAAGATTCAAATGCGCGTAAAAACAAATCCTTAAATCCAT
*
129 TATGTCTGAGATTTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
131 TATGGCTGAGATTTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
* * *
194 AAAACTGAGCCGGGGCCCGAAACTCGTTTTTAGCCAAAAACCGTGATGGTTAGCACATGATTTCA
196 AAAACTAAGCCGGGGCCCGAAACGCGTTTTTAGCCAAAAACCGTAATGGTTAGCACATGATTTCA
*
259 GCTAAAAACTAACCCAAAAAGTTTTTAACAATTTTTTGCAAAATATTTAGAAAAAATATATAATT
261 GCTAAAAACTAACCCAAAAAGTTTTTAACAATTTTTTGCAAAATATTCAGAAAAAATATATAATT
** * *
324 CAACGCCAAAAAAATTGACGGGTTTTTCACGCTTTTAATATTGTTTTTCCATTTTTTTCGGAATT
326 CAACGCCAAAAAAATTGACGGCCTTTTCACGCTTCTAATATTGTTTTTCCATTTTTTTCCGAATT
* * * * *
389 AATTTCTAATTAAATCAAAATAAGATTAAGATGCTTGTAAAAACAAATCCTTATATACAATGTGG
391 AATTTCTAATTAAATCAAAACAAGATTAAGATACTCGTAAAAACAAATCCTTATATACAAAGTCG
* *
454 CTGAGGTTTCGTTCGATGAATACAGATATTTCAAGGAGTCCTCACGCCAAAAATCATGCAAAATT
456 CTGAGATTACGTTCGATGAATACAGATATTTCAAGGAGTCCTCACGCCAAAAATCATGCAAAATT
519 GAGCCGGGACTCCGGAACGCGTTTTTAGCCAAAAAAAACCATGATAGTTAGTACACGATTTCGTT
521 GAGCCGGGACTCCGGAACGCGTTTTTAG---------ACCA-GATA--TAGTACACGA-TTCGTT
* ** * * *
584 AGCAAAAAAAAAAGTACACGATTTTGGCTAAAATTTTGCAAAAATTGACTCAAAAGGTTTTTCCT
573 AG---------AAG-ACAAGATTTCAGCTAAAATTTTGCAAAAACTGACTCAAAAAGTTTTTCCC
* *
649 CAATTTTTTTCCACAATACTCATAAAAAATATAT
628 CAATTTTTTGCCACAATACTCAGAAAAAATATAT
*
683 AATTCAATGCCAAAAAAATTAAATGGTGTTTTCACGCTTCTAATATCGTTTTTTCAATTTTTTCC
1 AATTCAATGCCAAAAAAATTAAATGATGTTTTCACGCTTCTAATATCG-TTTTTC-ATTTTTTCC
* *
748 TCGAATTTATTTCTAATTAAATCAAAATAAAGATTCAAATGCGCGTAAAATCAAATCCTTAAATC
64 -CGAATTTATTTCTAATTAAATCAAAACAAAGATTCAAATGCGCGTAAAAACAAATCCTTAAATC
*
813 CATTGTGGCTGAGA-TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT-A
128 CATTATGGCTGAGATTTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCA
* * *
876 TTC-AAACTAAGCCGGGGCCATGAAACGCGTTTTTAG-CAAAAACCGTAATGGTTAGTACATGAT
193 TGCAAAACTAAGCCGGGGCC-CGAAACGCGTTTTTAGCCAAAAACCGTAATGGTTAGCACATGAT
* ** **
939 TTC-GACTAAAAACTGACCTGAAAAGTTTTTTCTCAATTTTTTGCAAAATATTCAGAAAAAATAT
257 TTCAG-CTAAAAACTAACCCAAAAAG-TTTTTAACAATTTTTTGCAAAATATTCAGAAAAAATAT
* *
1003 ATAATTCAACGCCAAAAAGATTGACGGCCTTTTCATGCTTCTAATATTGTTTTTCCATTATATTT
320 ATAATTCAACGCCAAAAAAATTGACGGCCTTTTCACGCTTCTAATATTGTTTTTCCA-T-T-TTT
* * * *
1068 TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAGCAAATTCTTATAT
382 TTCCGAATTAATTTCTAATTAAATCAAAACAAGATTAAGATACTCGTAAAAACAAATCCTTATAT
* * * * * *** *
1133 ACAAAGTCGTTGAGATTAGGTTCGATGAATATAGATATTTCAATGAGT-TTTTGGCCAAAAATTA
447 ACAAAGTCGCTGAGATTACGTTCGATGAATACAGATATTTCAAGGAGTCCTCACGCCAAAAATCA
* ** * *
1197 TGCAAAATTGAGCCGGGGCTCCTTAACGCGTTTTTAG-CCA-A-A-AGT-CATGA-TGGTTAG-A
512 TGCAAAATTGAGCCGGGACTCCGGAACGCGTTTTTAGACCAGATATAGTACACGATTCGTTAGAA
1255 -ACAAGATTTCAGCTAAAATTTTGC-AAAACTGAC-CAGAAAAGTTTTTCCCCAATTTTTTGCCA
577 GACAAGATTTCAGCTAAAATTTTGCAAAAACTGACTCA-AAAAGTTTTTCCCCAATTTTTTGCCA
1317 CAATACTCAGAAAAAATATAT
641 CAATACTCAGAAAAAATATAT
* * * * * *
1338 AATTTAATGCCAAAAAAATTGAAGGA--TTTTCACACTTCTAATATCGTTTATCATTTTTT-CCT
1 AATTCAATGCCAAAAAAATTAAATGATGTTTTCACGCTTCTAATATCGTTTTTCATTTTTTCCCG
* * * * * *
1400 AATTTATTTCTAATTAAATCGAAACAAAGATTGAGATGCTCGTAAAAACCAATCCTTAAATCCAA
66 AATTTATTTCTAATTAAATCAAAACAAAGATTCAAATGCGCGTAAAAACAAATCCTTAAATCCAT
* * * *
1465 TGTGTCTGAGA-TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAATTATGC
131 TATGGCTGAGATTTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
* * * * **
1529 AAAACTGAGCCGGGACCCGAAACAG-GTTTTTAGCCAAAAACCGTGATGATTAGCACACAATTTC
196 AAAACTAAGCCGGGGCCCGAAAC-GCGTTTTTAGCCAAAAACCGTAATGGTTAGCACATGATTTC
* * * **
1593 GGCGTAAAAA-GAACCCGAAAAGTTTTTCTCAATTTTTT
260 AGC-TAAAAACTAACCCAAAAAGTTTTTAACAATTTTTT
1631 T
Statistics
Matches: 836, Mismatches: 94, Indels: 68
0.84 0.09 0.07
Matches are distributed among these distances:
649 115 0.14
650 33 0.04
651 57 0.07
652 12 0.01
653 19 0.02
654 2 0.00
655 73 0.09
656 21 0.03
658 1 0.00
668 6 0.01
670 4 0.00
671 3 0.00
674 1 0.00
675 1 0.00
677 3 0.00
682 22 0.03
683 1 0.00
684 80 0.10
685 110 0.13
686 56 0.07
687 116 0.14
688 100 0.12
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (661 bp):
AATTCAATGCCAAAAAAATTAAATGATGTTTTCACGCTTCTAATATCGTTTTTCATTTTTTCCCG
AATTTATTTCTAATTAAATCAAAACAAAGATTCAAATGCGCGTAAAAACAAATCCTTAAATCCAT
TATGGCTGAGATTTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
AAAACTAAGCCGGGGCCCGAAACGCGTTTTTAGCCAAAAACCGTAATGGTTAGCACATGATTTCA
GCTAAAAACTAACCCAAAAAGTTTTTAACAATTTTTTGCAAAATATTCAGAAAAAATATATAATT
CAACGCCAAAAAAATTGACGGCCTTTTCACGCTTCTAATATTGTTTTTCCATTTTTTTCCGAATT
AATTTCTAATTAAATCAAAACAAGATTAAGATACTCGTAAAAACAAATCCTTATATACAAAGTCG
CTGAGATTACGTTCGATGAATACAGATATTTCAAGGAGTCCTCACGCCAAAAATCATGCAAAATT
GAGCCGGGACTCCGGAACGCGTTTTTAGACCAGATATAGTACACGATTCGTTAGAAGACAAGATT
TCAGCTAAAATTTTGCAAAAACTGACTCAAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAG
AAAAAATATAT
Done.