Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003108.1 Kokia drynarioides strain JFW-HI SEQ_115678, 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: 4550
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1025 original size:330 final size:336
Alignment explanation
Indices: 358--1026 Score: 861
Period size: 330 Copynumber: 2.0 Consensus size: 336
348 TGGTTTCGAT
** * *
358 TGAGTCAAACATTTTCAAATATATTTTAACCATTTTCAAACAAGTTAGAATTGCTCCGGTACAAA
1 TGAGTCAAACATTTTCAAATATATTTTAACCATTTAAAAAAAAATTAGAATTGCTCCGGTACAAA
* * *
423 CAGTATCGGTACTTTTTTGTCTTAGTATCGATATTTTACAAGATATTAATACCCCTCTGATAAAC
66 CAGTATCAGTACTTTTTTGTCTTAGTATCGATATTTTACAAGATATCAACACCCCTCTGATAAAC
*
488 GATACAAAATGAGCATTTTGTTTTACCAAACCCTAGGAAGTATCGATCTGATATCGATACCTTAA
131 GATACAAAATGAGCATTCTGTTTTACCAAACCCTAGGAAGTATCGATCT-ATAT--ATA-C-TAA
* * * * * *
553 GTAACGTATCGAGAAAATCTAATGTTTATCTATATTCCTGCTACAGCGGTCATTGAAATCTACGT
191 GTAAC-TATCGAGAAAATCCAATGTGTATCTATATTCCTGCTACAACGATCACTGAAATCTACAT
* * *
618 TAATTAAATAAAATACCGATACCCATTTAGTAGGTATCGATAATCGTTGCTGCAGGAGTAATTAA
255 TAATTAAAGAAAATACCGATAACCATTTAGTAGGTATCGATAATCGTTGCTACAGGAGTAATTAA
683 TGAGCTGGTATTTCAAA
320 TGAGCTGGTATTTCAAA
* * * * *
700 TGAGTTAAACATTTTTAAATATGTTTTAACCATTTAAAAAAAAATTAGAATTGTTCCAGG-GCAA
1 TGAGTCAAACATTTTCAAATATATTTTAACCATTTAAAAAAAAATTAGAATTGCTCC-GGTACAA
* *
764 ACAGTATCAGTGC-TTTTTGTCTTAGTATCGATATTTTACAAGATATCAACACCCCTGTGATAAA
65 ACAGTATCAGTACTTTTTTGTCTTAGTATCGATATTTTACAAGATATCAACACCCCTCTGATAAA
* *
828 CGATACCAAATGAGCATTCTGTTTTACCGAACCCTAGGAAGTATCGATACCT-T-T-TA-T-AG-
130 CGATACAAAATGAGCATTCTGTTTTACCAAACCCTAGGAAGTATCGAT--CTATATATACTAAGT
* * * * * *
887 GA-TATCGATAAAATCCAATGTGTCTCTATATTCCTGTTCCAACGATCACTGAAATCTGCATTAA
193 AACTATCGAGAAAATCCAATGTGTATCTATATTCCTGCTACAACGATCACTGAAATCTACATTAA
* * * * *
951 TTACAGAAAATATCGATAACCTTTTAGTAGGTATCGATACTCGTTGCTACAGGTGTAATTAATGA
258 TTAAAGAAAATACCGATAACCATTTAGTAGGTATCGATAATCGTTGCTACAGGAGTAATTAATGA
1016 GCTGGTATTTC
323 GCTGGTATTTC
1027 TTCCCCAACG
Statistics
Matches: 287, Mismatches: 37, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
330 119 0.41
332 1 0.00
333 2 0.01
334 1 0.00
337 2 0.01
340 1 0.00
341 94 0.33
342 63 0.22
343 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (336 bp):
TGAGTCAAACATTTTCAAATATATTTTAACCATTTAAAAAAAAATTAGAATTGCTCCGGTACAAA
CAGTATCAGTACTTTTTTGTCTTAGTATCGATATTTTACAAGATATCAACACCCCTCTGATAAAC
GATACAAAATGAGCATTCTGTTTTACCAAACCCTAGGAAGTATCGATCTATATATACTAAGTAAC
TATCGAGAAAATCCAATGTGTATCTATATTCCTGCTACAACGATCACTGAAATCTACATTAATTA
AAGAAAATACCGATAACCATTTAGTAGGTATCGATAATCGTTGCTACAGGAGTAATTAATGAGCT
GGTATTTCAAA
Done.