Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002327.1 Kokia drynarioides strain JFW-HI SEQ_114374, 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, 831
Length: 1385
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Found at i:842 original size:422 final size:422
Alignment explanation
Indices: 98--1383 Score: 1281
Period size: 422 Copynumber: 3.0 Consensus size: 422
88 ATTTTGTTGA
* * * * * *
98 TTGAATTAAAAACTTATTTACGAGAGAATTGTTTCTCTATTTTTGTTCTTGGCCGAACTTTCGAA
1 TTGAATTAAAAACTTATTTAAGTGAGAATCGTTTCTC--TCTTGGTTCTTGGACGAACTTTCGAA
* * * * * *
163 CTTGTCAAACTTTTACGAGTTCTTTCACAAGTTTGGTTCCTTAAAGTATTCAAAACT-A--C-C-
64 CTTGTCAAACTCTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACTCATCCTCG
* * * * ** ** * * * * *
223 --C-ATTCCTTCGAGCA-ACTTTTTTCGAGAAATAGCAACACTTGATCAAAATAGTTCT-TCATT
129 AGCAATT-TTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTT-TGTCATT
* * * *
283 TTG-GAACAAGTTTTGGTCTTTGAATCAAAAACTTATTT-CGTGAGAATTGTTTCTC-TTGGTTC
192 TTGTAAACAAATTTTGGTTTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTGGTTC
** *
345 TTGGACGAACCTTCGAACTTGTCAAACTTTTACGAGTTCTTCAATAACTTCGGTTCCTTACAGTA
257 TTGGACGAA-CTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC-GTTCCATACAGTA
* * *
410 TTCAAGATGATCCATTCCTTCAAGCAATTTTCTAAACATTACATGCTCGGGAAATGGCATCATTT
320 TTC-AGATGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGGGAAATCGCATCATTT
* **
475 -TGTATAAATAGTGCGTCATTATGTAAATAA-TTTTTTTTCT
384 GT-TATAAATAGTGCG-CATTATGTAAA-AAGGTTTGGTTCT
* * * * *
515 TTGGATTAAACACTTA-TTACGTGAGAATCGTTTCTCTCTTGGTTCTTTGACGAACTTTTGAACT
1 TTGAATTAAAAACTTATTTAAGTGAGAATCGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACT
* * *
579 TTTCAAACTCTTACGAGTTCTTTTATAACTTCGGTTTCTTAGAGTATTCAAGAC-C-T-C-CGAG
66 TGTCAAACTCTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACTCATCCTCGAG
**
640 CAATTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT
131 CAATTTTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT
* *
705 AAACAACTTTTGGTTTTTGAATTAAATACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTG
196 AAACAAATTTTGGTTTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTC-TTTGGTTCTTG
* * * * * *
770 GATGAACTTCCCAACTTGTCAAAATTTTATGAGTTCTTTTATAATTTCTGTTCCATACAGTGTTC
260 GACGAACTT-CGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC-GTTCCATACAGTATTC
* * *
835 TAGATGATCCATTCCTTTGAGCAATTTT-TCGAACTTTCCATGCTCGGGAAATCGCATCATTTGT
323 -AGATGATCCATTCCTTCGAGCAATTTTCT-AAACATTCCATGCTCGGGAAATCGCATCATTTGT
* ** * *
899 TTTAAATAGTTTGCATTTTGTAAAAAGGTTTGGTTGT
386 TATAAATAGTGCGCATTATGTAAAAAGGTTTGGTTCT
*
936 TTGAATTAAAAACTTATTTAAGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACT
1 TTGAATTAAAAACTTATTTAAGTGAGAATCGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACT
* *
1001 TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATTCATTCCT
66 TGTCAAACTCTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGAC---TCA-TCC-
* * * * * *
1066 TCTAGTAATTTTTCAAACATTCTATGCTCGAGATATCACATCATTTAGTCTAAATAGTTTGTCAT
126 TCGAGCAATTTTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT
* * * * *
1131 TTTGTAAAAAAAGTTTCGTTGTTTGAATTAAAAACTTATTTACGTGAGAATTTTTTGTC-TTGGT
191 TTTGTAAACAAATTTTGGTT-TTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTGGT
* * * *
1195 TCTTGGACGAACTTTCGAACTTTTCCAACTTTTACGAGTTC-TTTATAACTTCGATTCCAGAAAG
255 TCTTGGACGAAC-TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG-TTCCATACAG
* * ** * * **
1259 TATTCACGACGATCCTTTAATTCGAGCAATATTCTAAACATTCCATGCTCAGGAAATCATATCAT
318 TATTCA-GATGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGGGAAATCGCATCAT
* * * ** *
1324 TTGGTCTAAATTGTTTGTCACTT-TGTAAAAAAGTTTTGG-TCT
382 TTGTTATAAATAGTGCG-CA-TTATGT-AAAAAGGTTTGGTTCT
*
1366 TTGCATTAAAAACTTATT
1 TTGAATTAAAAACTTATT
1384 CC
Statistics
Matches: 721, Mismatches: 114, Indels: 55
0.81 0.13 0.06
Matches are distributed among these distances:
414 70 0.10
416 18 0.02
417 22 0.03
418 40 0.06
419 30 0.04
420 19 0.03
421 34 0.05
422 217 0.30
423 1 0.00
426 1 0.00
428 3 0.00
429 82 0.11
430 62 0.09
431 87 0.12
432 35 0.05
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (422 bp):
TTGAATTAAAAACTTATTTAAGTGAGAATCGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACT
TGTCAAACTCTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACTCATCCTCGAG
CAATTTTTCAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT
AAACAAATTTTGGTTTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTGGTTCTTGG
ACGAACTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGTTCCATACAGTATTCAGA
TGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGGGAAATCGCATCATTTGTTATAA
ATAGTGCGCATTATGTAAAAAGGTTTGGTTCT
Found at i:1021 original size:215 final size:215
Alignment explanation
Indices: 268--1383 Score: 1245
Period size: 215 Copynumber: 5.2 Consensus size: 215
258 CACTTGATCA
* * *
268 AAATAGTTCT-TCATTTTGGAACAAGTTTTGG-TCTTTGAATCAAAAACTTATTT-CGTGAGAAT
1 AAATAGTT-TGTCATTTTGTAAAAAGTTTTGGTTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* **
330 TG-TT-TCTCTTGGTTCTTGGACGAACCTTCGAACTTGTCAAACTTTTACGAGTTCTTCAATAAC
65 TGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
* * * *
393 TTCGGTTCCTTACAGTATTCAAGATGATCCATTCCTTCAAGCAA-TTTTCTAAACATTACATGCT
130 TTCGGTTCCTTAAAGTATTC-AGACGATCCATTCCTTCGAGCAATTTTTC-AAACATTCCATGCT
* * *
457 CGGGAAATGGCATCATTTTGTAT
193 CGGGAAATCGCATCATTTGGTCT
** * ** * *
480 AAATAGTGCGTCATTATGTAAATAA-TTTTTTTTCTTTGGATTAAACACTTA-TTACGTGAGAAT
1 AAATAGTTTGTCATTTTGTAAA-AAGTTTTGGTTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * * * *
543 CGTTTCTCTCTTGGTTCTTTGACGAACTTTTGAACTTTTCAAACTCTTACGAGTTCTTTTATAAC
65 TGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
* * **
608 TTCGGTTTCTTAGAGTATTCA-A-GA-CC--T-C--CGAGCAATTTTTTGAACATTCCATGCTCG
130 TTCGGTTCCTTAAAGTATTCAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCG
*
665 AGAAATCGCATCATTTGGTCT
195 GGAAATCGCATCATTTGGTCT
* *
686 AAATAGTTTGTCATTTTGTAAACAACTTTTGGTT-TTTGAATTAAATACTTATTTACGTGAGAAT
1 AAATAGTTTGTCATTTTGTAAA-AAGTTTTGGTTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * * * * * *
750 TGTTTCTCTTTTGGTTCTTGGATGAACTTCCCAACTTGTCAAAATTTTATGAGTTCTTTTATAAT
65 TGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
* * * * * * * *
815 TTCTGTTCCATACAGTGTTCTAGATGATCCATTCCTTTGAGCAATTTTTCGAACTTTCCATGCTC
130 TTCGGTTCCTTAAAGTATTC-AGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTC
* *
880 GGGAAATCGCATCATTTGTTTT
194 GGGAAATCGCATCATTTGGTCT
* * *
902 AAATAGTTTG-CATTTTGTAAAAAGGTTTGGTTGTTTGAATTAAAAACTTATTTAAGTGAGAATT
1 AAATAGTTTGTCATTTTGTAAAAAGTTTTGGTTCTTTGAATTAAAAACTTATTTACGTGAGAATT
966 GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACT
66 GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACT
* * * * *
1031 TTGGTTCCTTAAAGTATTCAAGACGATTCATTCCTTCTAGTAATTTTTCAAACATTCTATGCTCG
131 TCGGTTCCTTAAAGTATTC-AGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCG
* * * *
1096 AGATATCACATCATTTAGTCT
195 GGAAATCGCATCATTTGGTCT
* *
1117 AAATAGTTTGTCATTTTGTAAAAAAAG-TTTCGTTGTTTGAATTAAAAACTTATTTACGTGAGAA
1 AAATAGTTTGTCATTTTGT--AAAAAGTTTTGGTTCTTTGAATTAAAAACTTATTTACGTGAGAA
* * *
1181 TT-TTT-TGTCTTGGTTCTTGGACGAACTTTCGAACTTTTCCAACTTTTACGAGTTC-TTTATAA
64 TTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAA
* ** * ** *
1243 CTTCGATTCCAGAAAGTATTCACGACGATCCTTTAATTCGAGCAA-TATTCTAAACATTCCATGC
129 CTTCGGTTCCTTAAAGTATTCA-GACGATCCATTCCTTCGAGCAATTTTTC-AAACATTCCATGC
* **
1307 TCAGGAAATCATATCATTTGGTCT
192 TCGGGAAATCGCATCATTTGGTCT
* * *
1331 AAATTGTTTGTCACTTTGTAAAAAAGTTTTGG-TCTTTGCATTAAAAACTTATT
1 AAATAGTTTGTCATTTTGT-AAAAAGTTTTGGTTCTTTGAATTAAAAACTTATT
1384 CC
Statistics
Matches: 762, Mismatches: 117, Indels: 49
0.82 0.13 0.05
Matches are distributed among these distances:
206 73 0.10
207 90 0.12
208 2 0.00
209 2 0.00
210 2 0.00
211 4 0.01
212 24 0.03
213 61 0.08
214 105 0.14
215 291 0.38
216 65 0.09
217 37 0.05
218 6 0.01
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (215 bp):
AAATAGTTTGTCATTTTGTAAAAAGTTTTGGTTCTTTGAATTAAAAACTTATTTACGTGAGAATT
GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACT
TCGGTTCCTTAAAGTATTCAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGG
GAAATCGCATCATTTGGTCT
Done.