Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012692.1 Kokia drynarioides strain JFW-HI SEQ_127703, 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: 1956
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1771 original size:602 final size:552
Alignment explanation
Indices: 627--1780 Score: 1554
Period size: 602 Copynumber: 2.0 Consensus size: 552
617 TGGGTACTCG
627 ATTGAACTTTAGTACAGCATATCATCCTCAGACAGATGGACAGTCAGAAAGGGTGATTCAGATTT
1 ATTGAACTTTAGTACAGCATATCATCCTCAGACAGATGGACAGTCAGAAAGGGTGATTCAGATTT
*
692 TGGAAGACATGTTGAGAAGCTGTATTATTGAGTTTGAAGGAAATTGGGAAAGGTATTTACCGTTG
66 TGAAAGACATGTTGAGAAGCTGTATTATTGAGTTTGAAGGAAATTGGGAAAGGTATTTACCGTTG
*
757 ATTGAATTTACTTATAATAATAGTTATCAGTCAAATATTCAGATGGCACCGTATGAAGCATTGTA
131 ATTGAATTTACTTATAATAACAGTTATCAGTCAAATATTCAGATGGCACCGTATGAAGCATTGTA
822 CGGAAGAAAGTGTAGGACTCCTGTATGTTGGACAGAGTTAAGTGAACAGAAGCTTGTGGGTCCTG
196 CGGAAGAAAGTGTAGGACTCCTGTATGTTGGACAGAGTTAAGTGAACAGAAGCTTGTGGGTCCTG
*
887 ATCTGATTCGAGAAACTGAAGAAAAAGTAAAGTTGATCCGAGAGCGATTAAAGGCTGCTTCAGAT
261 ATCTGATTCGAGAAACTGAAGAAAAAGTAAAGTTGATCCGAGAGCGATTAAAGGCTGCTTCAAAT
952 AGACAGAAGTCCTATGCGGATTTGAAAAGGAAAGATATAGAGTTCAATGTTGGTGAAAAGGTTTT
326 AGACAGAAGTCCTATGCGGATTTGAAAAGGAAAGATATAGAGTTCAATGTTGGTGAAAAGGTTTT
1017 CTTAAAAGTGTCTCCGTGGAAGAAAGTTCTCCGATTTGGCAAAAAGGGGAAATTGAGCCCAAGAT
391 CTTAAAAGTGTCTCCGTGGAAGAAAGTTCTCCGATTTGGCAAAAAGGGGAAATTGAGCCCAAGAT
1082 TTATCGGGCCATATGAGATATTGGAAAGAATTGGTCCAGTTGCTTATCGATTGGCTCTTCCACCA
456 TTATCGGGCCATATGAGATATTGGAAAGAATTGGTCCAGTTGCTTATCGATTGGCTCTTCCACCA
1147 GAATTAGATAAGATTCATAATGTTTTTCATGT
521 GAATTAGATAAGATTCATAATGTTTTTCATGT
****************** * * * *
1179 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAT-TGAACTTTAGTA
1 --------------------------------ATTGAACTTTAGTACAGCATATCATCCTCAG-A
1243 CAGCATATCATCCTCAGACAGATGGACAGTCAGAAAGGGTGATTCAGATTTTGAAAGACATGTTG
33 C------------------AGATGGACAGTCAGAAAGGGTGATTCAGATTTTGAAAGACATGTTG
* * **
1308 AGAAGTTGTATTATTGAGTTTGAAGGTAATTGGGAAAGGTATTTGTCGTTGATTGAATTTACTTA
80 AGAAGCTGTATTATTGAGTTTGAAGGAAATTGGGAAAGGTATTTACCGTTGATTGAATTTACTTA
* *
1373 TAATAACAGTTATCAGTCAAGTATTCAGATGGCATCGTATGAAGCATTGTACGGAAGAAAGTGTA
145 TAATAACAGTTATCAGTCAAATATTCAGATGGCACCGTATGAAGCATTGTACGGAAGAAAGTGTA
*
1438 GGACTCCTGTGTGTTGGACAGAGTTAAGTGAACAGAAGCTTGTGGGTCCTGATCTGATTCGAGAA
210 GGACTCCTGTATGTTGGACAGAGTTAAGTGAACAGAAGCTTGTGGGTCCTGATCTGATTCGAGAA
1503 ACTGAAGAAAAAGTAAAGTTGATCCGAGAGCGATTAAAGGCTGCTTCAAATAGACAGAAGTCCTA
275 ACTGAAGAAAAAGTAAAGTTGATCCGAGAGCGATTAAAGGCTGCTTCAAATAGACAGAAGTCCTA
1568 TGCGGATTTGAAAAGGAAAGATATAGAGTTCAATGTTGGTGAAAAGGTTTTCTTAAAAGTGTCTC
340 TGCGGATTTGAAAAGGAAAGATATAGAGTTCAATGTTGGTGAAAAGGTTTTCTTAAAAGTGTCTC
1633 CGTGGAAGAAAGTTCTCCGATTTGGCAAAAAGGGGAAATTGAGCCCAAGATTTATCGGGCCATAT
405 CGTGGAAGAAAGTTCTCCGATTTGGCAAAAAGGGGAAATTGAGCCCAAGATTTATCGGGCCATAT
1698 GAGATATTGGAAAGAATTGGTCCAGTTGCTTATCGATTGGCTCTTCCACCAGAATTAGATAAGAT
470 GAGATATTGGAAAGAATTGGTCCAGTTGCTTATCGATTGGCTCTTCCACCAGAATTAGATAAGAT
1763 TCATAATGTTTTTCATGT
535 TCATAATGTTTTTCATGT
1781 GTCTATGCTA
Statistics
Matches: 519, Mismatches: 32, Indels: 20
0.91 0.06 0.04
Matches are distributed among these distances:
583 6 0.01
584 4 0.01
602 509 0.98
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.28
Consensus pattern (552 bp):
ATTGAACTTTAGTACAGCATATCATCCTCAGACAGATGGACAGTCAGAAAGGGTGATTCAGATTT
TGAAAGACATGTTGAGAAGCTGTATTATTGAGTTTGAAGGAAATTGGGAAAGGTATTTACCGTTG
ATTGAATTTACTTATAATAACAGTTATCAGTCAAATATTCAGATGGCACCGTATGAAGCATTGTA
CGGAAGAAAGTGTAGGACTCCTGTATGTTGGACAGAGTTAAGTGAACAGAAGCTTGTGGGTCCTG
ATCTGATTCGAGAAACTGAAGAAAAAGTAAAGTTGATCCGAGAGCGATTAAAGGCTGCTTCAAAT
AGACAGAAGTCCTATGCGGATTTGAAAAGGAAAGATATAGAGTTCAATGTTGGTGAAAAGGTTTT
CTTAAAAGTGTCTCCGTGGAAGAAAGTTCTCCGATTTGGCAAAAAGGGGAAATTGAGCCCAAGAT
TTATCGGGCCATATGAGATATTGGAAAGAATTGGTCCAGTTGCTTATCGATTGGCTCTTCCACCA
GAATTAGATAAGATTCATAATGTTTTTCATGT
Done.