Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011545.1 Kokia drynarioides strain JFW-HI SEQ_126531, 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, 883
Length: 1472
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.37
Warning! 75 characters in sequence are not A, C, G, or T
Found at i:570 original size:216 final size:215
Alignment explanation
Indices: 1--790 Score: 955
Period size: 216 Copynumber: 3.7 Consensus size: 215
1 GTCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAAC
1 GTCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAAC
* * * * *
66 TTATTTACGTGAGAATTGTATCTCTCTTGGTTGATGGATGAGCTTACGAAATTATGAAACTTTTA
66 TTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGATGAACTTACGAAATTGTCAAACTTTTA
* * * *
131 CGAGTTGTTTTTTAAATCTGGTTCCTGAAAGTGTTCAAGACGATCCATTCCTTCGAGTAATTTTC
131 CGAGTTCTTTTATAAATCTGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTTGAG-AATTTTC
* * *
196 GGAACATTCCATGC-GATGAAA
195 GGAACATTACATGCTG-GGGAA
* * * * * * * **
217 ATCGCATCATTTGGTTTAAATAGTTTTTCATTTTATGAACATGTTTTTGATCTTTGAATTAAAAA
1 GTCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAAG-TTTTGGCCTTTGAATTAAAAA
* ** * * **
282 CTTATTTATGTGAGAATTGTTTCTCTCTTGGTACTTGGATGAAATTTCGAACA-TGTTGAACTTT
65 CTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGATGAACTTACGAA-ATTGTCAAACTTT
* ** * * * *
346 TACGAGTTCATTTATAGCT-TCGGTTCCTTAAAGTATGCAAGACGATCCAATCCTTTGTGCAATT
129 TACGAGTTCTTTTATAAATCT-GGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTTGAG-AA-T
410 TTTC-GAACATTACATGCTGGGGAA
191 TTTCGGAACATTACATGCTGGGGAA
* * *
434 GTAGCATCATTTGGTCTAAAAGGTTTGTCATTTTGTAAACAAGTTTTTGCCTTTGAATTAAAAAC
1 GTCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAAC
*
499 TTATTTACGTGAGAATTGTTTCTCTCCTGGTTGTTGGATGAACTTACGAAATTGTCAAACTTTTA
66 TTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGATGAACTTACGAAATTGTCAAACTTTTA
* * *
564 CGAGTTCTTTTATAAATCTGATTCCATAAAGTGTTC-AGAACGATCCATTGC-TTGAAGAAATTT
131 CGAGTTCTTTTATAAATCTGGTTCCTTAAAGTGTTCAAG-ACGATCCATTCCTTTG-AG-AATTT
* * *
627 TCTGAACGTTACATGCTCGGGAA
193 TCGGAACATTACATGCTGGGGAA
*
650 GTCGCATCGTTTGGTCTAAAAAGTTTGTCATTTTGTAAA-AATGTTTTGGCCTTTGAATTAAAAA
1 GTCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAA-GTTTTGGCCTTTGAATTAAAAA
* * * * **
714 CTTATTTACGTGAGAATTGATTCTCTCTTGGTCGTTGGATGTACTTCCGATCTTGTCAAACTTTT
65 CTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGATGAACTTACGAAATTGTCAAACTTTT
*
779 ACTAGTTCTTTT
130 ACGAGTTCTTTT
791 TCAAATCNNN
Statistics
Matches: 483, Mismatches: 80, Indels: 22
0.83 0.14 0.04
Matches are distributed among these distances:
215 13 0.03
216 295 0.61
217 168 0.35
218 7 0.01
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (215 bp):
GTCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAAC
TTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGATGAACTTACGAAATTGTCAAACTTTTA
CGAGTTCTTTTATAAATCTGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTTGAGAATTTTCG
GAACATTACATGCTGGGGAA
Found at i:1263 original size:216 final size:214
Alignment explanation
Indices: 908--1467 Score: 592
Period size: 216 Copynumber: 2.6 Consensus size: 214
898 GAATTATTTC
* * * * * * * * * * * *
908 TCTCTTGGTTCTTGGATGAACATACGAACTTGCCGAACTTTTATGACTTCTTTTATAGCTTCGGT
1 TCTCTT-GCTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTTTTTTATAACTCCAGT
* * *
973 TCCTTAAAGTATGCAAGACGATACAATACTTCGAGCAATTTTCCGAACATTACATGCACGGGAAG
65 TCCTTAAAGTATTCAAGACGATCCAATACTTCGAGCAATTTT-CGAACATTACATGCACGGGAAA
** *
1038 TCACATCATTTCGTCT-AATAGGTTTGTCATTTTGTAAACAAGTTTTTGCCTTTGAATTAAAAAC
129 TCACATCATTTCGTCTAAATA-GTTTGTCATTTTGTAAACAAGTTTTAACCTTTGAATTAAAAAA
* *
1102 TTATTTACA-TGACAATTGTTTA
193 TTATTTA-AGTGACAAATGTGTA
* * *
1124 TCTCTTGGT-TGGTGGATGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTT-TAAAC-CC
1 TCTCTTGCTCT--TGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTT-TTTTTAT-AACTCC
* * * * *
1186 AGTTCCTTAAAGTGTTCAAGACGATCCATTTCTTCGAGTAATTTATCGAACATTCCATGCGA-GG
62 AGTTCCTTAAAGTATTCAAGACGATCCAATACTTCGAGCAATTT-TCGAACATTACATGC-ACGG
* * * *
1250 GAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTAATCTTTGAATTAAA
125 GAAATCACATCATTTCGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTAACCTTTGAATTAAA
** *
1315 AAATTATTTAAGTGTGAAATGTGTC
190 AAATTATTTAAGTGACAAATGTGTA
* * * * *
1340 TCTCTTGCTCTTGGACGAACTTTCGAACTTGTCGAACTTTTACGAGTTTTTTTATAGCTTCGGTT
1 TCTCTTGCTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTTTTTTATAACTCCAGTT
* * *
1405 CCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTTGAACATTACATGCTCGGGAA
66 CCTTAAAGTATTCAAGACGATCCAATACTTCGAGCAA-TTTTCGAACATTACATGCACGGGAA
1468 GTCGC
Statistics
Matches: 284, Mismatches: 47, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
214 8 0.03
215 92 0.32
216 171 0.60
217 13 0.05
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (214 bp):
TCTCTTGCTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTTTTTTATAACTCCAGTT
CCTTAAAGTATTCAAGACGATCCAATACTTCGAGCAATTTTCGAACATTACATGCACGGGAAATC
ACATCATTTCGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTAACCTTTGAATTAAAAAATTA
TTTAAGTGACAAATGTGTA
Done.