Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004910.1 Kokia drynarioides strain JFW-HI SEQ_118605, 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, 827
Length: 1379
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:544 original size:216 final size:213
Alignment explanation
Indices: 8--1072 Score: 1176
Period size: 216 Copynumber: 4.9 Consensus size: 213
1 GAACATC
* * * *
8 CGAACTTGTCAAACTTTTACTGAA--TCTTTTATAAATTCGATTCCTTAAAATATTCAA-TAGAT
1 CGAACTTGTCAAACTTTTAC--AAGTTATTTTATAACTTCGA-TCCTTAAAGTATTCAAGAAGAT
* * * * * *
70 CCATTCCTTTGAGCAATATTCCGAACATTCCA-GACTCGGCAAATCACATAATTTGGTCTAAATA
63 CCATT-CTTAGAGCAATTTTTCGAACATTCCATG-CTCGGGAAATCGCATCATTTGGTCTAAATA
* * ** * * *
134 GTTTGTCTTTTTGCAAACAAGTTTCAGTCTTTGAGTTAAAAATTTA-TTACTTGAGAATTGTTTC
126 GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
*
198 TCTCTTTGTTCATGGACGAACTTT
191 TCTCTTTGTTCTTGGACGAAC-TT
* * *
222 CGAACTTATCAAACTTTTACAAGTTATTTT-TAACTTCGGTTCCCTT-AAGTATTCAACAAGATC
1 CGAACTTGTCAAACTTTTACAAGTTATTTTATAACTTC-GAT-CCTTAAAGTATTCAAGAAGATC
* * ** *
285 CAATTTTTAGAGCAA-TTTTCTGAACATTCCATCCTTAGGAAATCGCATCATTTTGTCTAAATAG
64 C-ATTCTTAGAGCAATTTTTC-GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAG
* * * * *
349 TTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTCAGAACTTATTTACGTGAGAATGGTATCT
127 TTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCT
* * * *
414 CTCTTTCTTCTTAGATGAACGT
192 CTCTTTGTTCTTGGACGAACTT
* ** * *
436 CTAAGCTTGTCAAACTTTTACTTGTTATTTTATAATTTCGGATCCTTAAAGTATTCAAGACGATC
1 CGAA-CTTGTCAAACTTTTACAAGTTATTTTATAACTTC-GATCCTTAAAGTATTCAAGAAGATC
* * * *
501 CATTCCTTCGAGCAATTTTTCAAACATTCCATTCTCGGGAAATCGCATTATTTGGTCTAAATAGT
64 CATT-CTTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGT
* * *
566 TTGTCATTTTGCT-AACAAGTTTTGGTCTTTAAATTAAAAACTTATTCACGTGAAAATTGTTTCT
128 TTGTCATTTTG-TAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCT
** *
630 CTCTTTAATCTTGGGCGAACTCT
192 CTCTTTGTTCTTGGACGAACT-T
* * * * *
653 CGAACTTGCCAAACTTTTACGAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAATAAGATCC
1 CGAACTTGTCAAACTTTTACAAGTTATTTTATAACTTCGA-TCCTTAAAGTATTCAAGAAGATCC
* * * * * *
718 ATTTCTTAGAGCATTTTTTTGAACATTCCATGCTCGAGAAATCACAGCATTTGGTCTAAATAGCT
65 A-TTCTTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTT
* *
783 TGTCATTTTGTGAACAAGTTTTAGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
129 TGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
848 CTTTGTTCTTGGACGAACTT
194 CTTTGTTCTTGGACGAACTT
* * * * * * *
868 CCGAACTTGTCAAACTATTAAAAGTTCTTTTATAACTTCCGATCCTTAAATTATTCTAGACGATT
1 -CGAACTTGTCAAACTTTTACAAGTTATTTTATAACTT-CGATCCTTAAAGTATTCAAGAAGATC
* * * * *
933 TATTCTTACGAGCAATTTTTTGAACATTCCATGCTAGGGAAATCGTATCGTTTGGTCTAAATAGT
64 CATTCTTA-GAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGT
* * * *
998 TTGTCATTTTGCAAACATGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTA
128 TTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTC
1063 TCTTTGTTCT
193 TCTTTGTTCT
1073 CGGATCCTTA
Statistics
Matches: 712, Mismatches: 117, Indels: 42
0.82 0.13 0.05
Matches are distributed among these distances:
212 2 0.00
213 19 0.03
214 118 0.17
215 75 0.11
216 483 0.68
217 15 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (213 bp):
CGAACTTGTCAAACTTTTACAAGTTATTTTATAACTTCGATCCTTAAAGTATTCAAGAAGATCCA
TTCTTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTG
TCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
TTGTTCTTGGACGAACTT
Found at i:812 original size:432 final size:428
Alignment explanation
Indices: 1--1067 Score: 1334
Period size: 432 Copynumber: 2.5 Consensus size: 428
* * *
1 GAACATCCGAACTTGTCAAACTTTTACTGAATCTTTTATAAATTCGATTCCTTAAAATATTCAAT
1 GAACGTCCGAACTTGTCAAACTTTTACTG-TTCTTTTATAAATTCGA-TCCTTAAAATATTCAAG
* * * * * *
66 A-GATCCATTCCTTTGAGCAATATTCCGAACATTCCAGACTCGGCAAATCACATAATTTGGTCTA
64 ACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATACTCGGGAAATCGCATAATTTGGTCTA
* ** * * *
130 AATAGTTTGTCTTTTTGCAAACAAGTTTCAGTCTTTGAGTTAAAAATTTATTACTTGAGAATTGT
129 AATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTACGTGAGAATTGT
** * *
195 TTCTCTCTTTGTTCATGGACGAACTTTCGAACTTATCAAACTTTTACAAGTTATTTTTAACTTCG
194 TTCTCTCTTTAATCATGGACGAACTCTCGAACTTACCAAACTTTTACAAGTTATTTTTAACTTCG
* * *
260 GTTCCCTTAAGTATTCAACAAGATCCAATTTTTAGAGCAATTTTCTGAACATTCCATCCTTAGGA
259 ATTCCCTAAAGTATTCAACAAGATCCAATTTTTAGAGCAATTTTCTGAACATTCCATCCTGAGGA
* * * * * * *
325 AATCGCATCATTTTGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTCAGAA
324 AATCACAGCATTTGGTCTAAATAGCTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAA
*
390 CTTATTTACGTGAGAATGGTATCTCTCTTTCTTCTTAGAT
389 CTTATTTACGTGAGAATGGTATCTCTCTTTCTTCTTAGAC
* * * *
430 GAACGT-CTAAGCTTGTCAAACTTTTACTTGTTATTTTATAATTTCGGATCCTTAAAGTATTCAA
1 GAACGTCCGAA-CTTGTCAAACTTTTAC-TGTTCTTTTATAAATTC-GATCCTTAAAATATTCAA
* * *
494 GACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATTCTCGGGAAATCGCATTATTTGGTCT
63 GACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATACTCGGGAAATCGCATAATTTGGTCT
* * *
559 AAATAGTTTGTCATTTTGCTAACAAGTTTTGGTCTTTAAATTAAAAACTTATTCACGTGAAAATT
128 AAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT-ACGTGAGAATT
* * * *
624 GTTTCTCTCTTTAATCTTGGGCGAACTCTCGAACTTGCCAAACTTTTACGAGTTATTTTTTAACT
192 GTTTCTCTCTTTAATCATGGACGAACTCTCGAACTTACCAAACTTTTACAAGTTA-TTTTTAACT
* * * *
689 TCGATTCCCTAAAGTATTCAATAAGATCC-ATTTCTTAGAGCATTTTTTTGAACATTCCATGCTC
256 TCGATTCCCTAAAGTATTCAACAAGATCCAATTT-TTAGAGCAATTTTCTGAACATTCCATCCT-
* *
753 GA-GAAATCACAGCATTTGGTCTAAATAGCTTGTCATTTTGTGAACAAGTTTTAGTCTTTGAATT
319 GAGGAAATCACAGCATTTGGTCTAAATAGCTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATT
* * * *
817 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGAC
384 AAAAACTTATTTACGTGAGAATGGTATCTCTCTTTCTTCTTAGAC
* * ** * * *
862 GAACTTCCGAACTTGTCAAACTATTAAAAGTTCTTTTATAACTTCCGATCCTTAAATTATTCTAG
1 GAACGTCCGAACTTGTCAAACT-TTTACTGTTCTTTTATAAATT-CGATCCTTAAAATATTCAAG
** * * * * **
927 ACGATTTATT-CTTACGAGCAATTTTTTGAACATTCCATGCTAGGGAAATCGTATCGTTTGGTCT
64 ACGATCCATTCCTT-CGAGCAATTTTTCGAACATTCCATACTCGGGAAATCGCATAATTTGGTCT
* *
991 AAATAGTTTGTCATTTTGCAAACATGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATT
128 AAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTA-TTACGTGAGAATT
*
1056 GTTTCTATCTTT
192 GTTTCTCTCTTT
1068 GTTCTCGGAT
Statistics
Matches: 547, Mismatches: 78, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
428 3 0.01
429 49 0.09
430 103 0.19
431 63 0.12
432 319 0.58
433 10 0.02
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (428 bp):
GAACGTCCGAACTTGTCAAACTTTTACTGTTCTTTTATAAATTCGATCCTTAAAATATTCAAGAC
GATCCATTCCTTCGAGCAATTTTTCGAACATTCCATACTCGGGAAATCGCATAATTTGGTCTAAA
TAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTACGTGAGAATTGTTT
CTCTCTTTAATCATGGACGAACTCTCGAACTTACCAAACTTTTACAAGTTATTTTTAACTTCGAT
TCCCTAAAGTATTCAACAAGATCCAATTTTTAGAGCAATTTTCTGAACATTCCATCCTGAGGAAA
TCACAGCATTTGGTCTAAATAGCTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACT
TATTTACGTGAGAATGGTATCTCTCTTTCTTCTTAGAC
Found at i:1207 original size:76 final size:76
Alignment explanation
Indices: 1081--1236 Score: 233
Period size: 76 Copynumber: 2.1 Consensus size: 76
1071 CTCGGATCCT
*
1081 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAAAATTCCATGCTCG-GAAAATCT
1 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAAAATTCCATGCTCGAG-AAATCG
1145 CATCATTTGGTC
65 CATCATTTGGTC
* * * ** *
1157 TAAAGTATTCGAGACGATCTATTCTTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGC
1 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAAAATTCCATGCTCGAGAAATCGC
1222 ATCATTTGGTC
66 ATCATTTGGTC
1233 TAAA
1 TAAA
1237 TAGTTTGTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
76 71 0.99
77 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (76 bp):
TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAAAATTCCATGCTCGAGAAATCGC
ATCATTTGGTC
Done.