Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000626.1 Kokia drynarioides strain JFW-HI SEQ_111583, 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, 602
Length: 1004
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Found at i:783 original size:215 final size:215
Alignment explanation
Indices: 1--1004 Score: 1010
Period size: 215 Copynumber: 4.6 Consensus size: 215
* *
1 CAAGATGATCCATTCCTTCGACCAATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGG
1 CAAGACGATCCATTCCTTCGACCAATTTTTCGAGCATTCCATTATCAGGAAATCGTATCATTTGG
* *
66 TCTAAATAGTTTGTCATTTCGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGGGA
66 TCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATT-AAAACTTTTTTACGTGAGA
* * *
131 ATTGTTTCTCTATTTGTTCTTGGACGAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATA
130 ATTGTTTCTCTATTGGTTCTTGGACGAACTATCGAACACGTCAAACATTTTAGAGTTCTTTTATA
196 ACTTCGATTCCTGAGAGTATT
195 ACTTCGATTCCTGAGAGTATT
* * * *
217 AAAGACGATCCATTCCTTC-AGCCAATTTTTCGAACATTCCATTA-CCGTGAAATCGCT-TCGTT
1 CAAGACGATCCATTCCTTCGA-CCAATTTTTCGAGCATTCCATTATCAG-GAAATCG-TATCATT
* * * * * *
279 TGATTTAAATAGTTTATCATTTTGTATA-AATTTTTAGTCTTTGATGAACATATGAACTAGTCAA
63 TGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTC-TT--TG---A-AT----TA---AA
* * * * * *
343 ACTTTTCAATACTTGAGAATTATTTCCCTCTTGGTTCTTGGATGAACATAT-GAACTA-GTCAAA
114 ACTTTT--TTACGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAAC-TATCGAAC-ACGTCAAA
* *
406 C-TTTTACAAGTTCTTTTATAACTTCGGTTCCTGAGAGTATT
175 CATTTTA-GAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
* * * *
447 CAAGACGATCCAATT-CTTTGACCAATTTTTTGAAG-ATTCCATTAT-AGAGAAATCGCAGCATT
1 CAAGACGATCC-ATTCCTTCGACCAATTTTTCG-AGCATTCCATTATCAG-GAAATCGTATCATT
** * * * * * * *
509 TGGTAAAAATAGTTTGCCA-TTTGTAAATAAATTTTGCTCTTTGAATTAAAATTTTTTTTACATT
63 TGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA-CTTTTTTACGTG
* * * ** *
573 AGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCAAACA-TTTATTAGTTCTTT
127 AGAATTGTTTCTCTATTGGTTCTTGGACGAACTATCGAACACGTCAAACATTTTA-GAGTTCTTT
* **
637 TACAACTTCGATTCCTGAGAGTAGC
191 TATAACTTCGATTCCTGAGAGTATT
* *
662 CAAGATGATCCATTCCTTCGACCAATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGG
1 CAAGACGATCCATTCCTTCGACCAATTTTTCGAGCATTCCATTATCAGGAAATCGTATCATTTGG
* * *
727 TCGAAATCGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAACTTTTTTACGTGGGAA
66 TCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAACTTTTTTACGTGAGAA
* * * *
792 TTGTTTCTCTATTTGTTCTTGGACAAACTTTCAAACACGTCAAACATTTTAGAGTTCTTTTATAA
131 TTGTTTCTCTATTGGTTCTTGGACGAACTATCGAACACGTCAAACATTTTAGAGTTCTTTTATAA
857 CTTCGATTCCTGAGAGTATT
196 CTTCGATTCCTGAGAGTATT
* * * * * *
877 AAACACGATCCATTCCTTC-AGCCAATTTTTCGAACATTCCATTACCGGGAAATCGCT-TCGTTT
1 CAAGACGATCCATTCCTTCGA-CCAATTTTTCGAGCATTCCATTATCAGGAAATCG-TATCATTT
* * * * * * *
940 GATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGA
64 GGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA-ACTTTTTTACGTGA
Statistics
Matches: 642, Mismatches: 106, Indels: 80
0.78 0.13 0.10
Matches are distributed among these distances:
214 9 0.01
215 321 0.50
216 125 0.19
217 5 0.01
218 2 0.00
219 2 0.00
221 1 0.00
222 2 0.00
223 2 0.00
224 1 0.00
225 1 0.00
226 1 0.00
227 2 0.00
228 8 0.01
229 13 0.02
230 139 0.22
231 8 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (215 bp):
CAAGACGATCCATTCCTTCGACCAATTTTTCGAGCATTCCATTATCAGGAAATCGTATCATTTGG
TCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAACTTTTTTACGTGAGAA
TTGTTTCTCTATTGGTTCTTGGACGAACTATCGAACACGTCAAACATTTTAGAGTTCTTTTATAA
CTTCGATTCCTGAGAGTATT
Done.