Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005085.1 Kokia drynarioides strain JFW-HI SEQ_118898, 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: 10148
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Found at i:5211 original size:6 final size:6
Alignment explanation
Indices: 5200--5250 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
5190 TAATCAAAAT
* * *
5200 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
5248 TGA
1 TGA
5251 TATGAATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:9306 original size:210 final size:209
Alignment explanation
Indices: 8983--9715 Score: 1173
Period size: 210 Copynumber: 3.5 Consensus size: 209
8973 TGTTAAGCTC
* *
8983 TCCAATTTGTCACAATCACCAATTGATGGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGAAT
1 TCCAATTTGTCACAATAACCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGAAT
*
9048 GGAAGTTAAATTAGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTGGATAATCCGT
66 GGAAGTTAAATTAGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGT
9113 CTCCAATCTTGCTTAATTTTTTGCAAGAGAAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCT
131 CTCCAATCTTGCTTAATTTTTTGCAAGAGAAAATCT-AAGCTTTTCAAGAGATGAACATCCTCCT
*
9178 GTCCATGGAAGAACT
195 GTCAATGGAAGAACT
*
9193 TCCAATTTGCCACAATAACCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGAAT
1 TCCAATTTGTCACAATAACCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGAAT
* * * *
9258 GGACGTTAAATTAGAACAATATCTTAGTCCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGT
66 GGAAGTTAAATTAGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGT
** *** *
9323 CTCCAATCTTGCTTAATTTTGCGCATCCGAAAATGCTAAACTTTTCAAGAGATGAACATCCTCCT
131 CTCCAATCTTGCTTAATTTTTTGCAAGAGAAAAT-CTAAGCTTTTCAAGAGATGAACATCCTCCT
9388 GTCAATGGAAGAACT
195 GTCAATGGAAGAACT
** *
9403 TCCAATTTGTTGCAGACAGA--AATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGA
1 TCCAATTTGTCACA-ATA-ACCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGA
** * *
9466 ATGGAAGTTAAATTAGCGCAAAACATTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCC
64 ATGGAAGTTAAATTAGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCC
9531 GTCTCCAATCTTGCTTAATTTTTTGCAAGAGAAAATCTCAAGCTTTTCAAGAGATGAACATCCTC
129 GTCTCCAATCTTGCTTAATTTTTTGCAAGAGAAAATCT-AAGCTTTTCAAGAGATGAACATCCTC
9596 CTGTCAATGGAAGAACT
193 CTGTCAATGGAAGAACT
**
9613 TCCAATTTGTCACAATCTCCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGAAT
1 TCCAATTTGTCACAATAACCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGAAT
**
9678 GGAAGTTAAATTAGCGCAAGACCTTAGTTCTAATTCTT
66 GGAAGTTAAATTAGAACAAGACCTTAGTTCTAATTCTT
9716 CCAAGCAAGG
Statistics
Matches: 478, Mismatches: 39, Indels: 12
0.90 0.07 0.02
Matches are distributed among these distances:
209 3 0.01
210 470 0.98
211 4 0.01
212 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (209 bp):
TCCAATTTGTCACAATAACCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGGAAT
GGAAGTTAAATTAGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGT
CTCCAATCTTGCTTAATTTTTTGCAAGAGAAAATCTAAGCTTTTCAAGAGATGAACATCCTCCTG
TCAATGGAAGAACT
Done.