Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003052.1 Kokia drynarioides strain JFW-HI SEQ_115580, 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, 841
Length: 1402
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Found at i:458 original size:216 final size:216
Alignment explanation
Indices: 39--1402 Score: 1382
Period size: 216 Copynumber: 6.4 Consensus size: 216
29 GGTTCCCTAA
*
39 ATCCATTCCTTAGAGCAATTTT-TCGAACATTCCATGCTCGGGAAATCGCATCATTTGATCTAAA
1 ATCCATTCCTTAGAGCAATTTTCT-GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
* * *
103 TA---TGTCATTTTGCAAACAAGTTTT-GCTCTTTGAATTAAAAACTTCTTTGC-ATGAGAATTG
65 TAGTTTGTCATTTTGTAAACAAGTTTTAG-TCTTTGAATTAAAAACTTATTTACGA-GAGAATTG
* * * * * *
163 TTTCTCTCTTTGTTTTTGGACGAACTTTCGGAGTTGTCAAACTTTTATGAGTTATTTTTTAACTT
128 TTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTTTAACTT
*** * *
228 CGGTTCCCTAAAGTATTCAATAAG
193 AACTTCCTTAAAGTATTCAAGAAG
** * *
252 ATCCATTCCTTAGAGCAATTTTCTGAACATTTTATACTCGGGAAATCGAATCATTTGGTCTAAAT
1 ATCCATTCCTTAGAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
* *
317 AGTTTGTCATTTTGTAAACAAGTTTTAGACTTTGAATTAAAAACTTATTTACGAGAGAATTGTAT
66 AGTTTGTCATTTTGTAAACAAGTTTTAGTCTTTGAATTAAAAACTTATTTACGAGAGAATTGTTT
* * * * * * * * * * * *
382 CACTCTTGGTCCATGGACGAACTCCCGAACTTATCCAACTTTGAGGAGATCTTTTATAGCTTAAC
131 CTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTTTAACTTAAC
*
447 TTCCTTAAAGTATTCAAGACG
196 TTCCTTAAAGTATTCAAGAAG
* *
468 A-CTCATTCCTTTGAGCATTTTTCTGAACATTCCATGCTCGGGAAA-CTGCATCATTTGGTCTAA
1 ATC-CATTCCTTAGAGCAATTTTCTGAACATTCCATGCTCGGGAAATC-GCATCATTTGGTCTAA
* ** * ** *
531 ATAGTATGTCATTTCCTAAACAAGTTTTAGTCTTGGAATTAAAAACTTATTTGTGTGAGAATTGT
64 ATAGTTTGTCATTTTGTAAACAAGTTTTAGTCTTTGAATTAAAAACTTATTTACGAGAGAATTGT
* * * * * * * *
596 TTCTCACTTTCTTCTTGGAAGAACTTTCGAACGTGTCAAACTTTTACAACTTCTTTTTTAACTTC
129 TTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTTTAACTTA
** * **
661 TGTTCCTTAAAGAATTCAAGGCG
194 ACTTCCTTAAAGTATTCAAGAAG
* * ** * ** * *
684 ATCCATTCCTTCGAGCAGTTTTCCAAACATTCCTTGCTCAAGAAATCGTATCATTTGGTCAAAAT
1 ATCCATTCCTTAGAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
* * *
749 AGATTGTCATTTTGTAAACAAGTTTTAGTCGTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
66 AGTTTGTCATTTTGTAAACAAGTTTTAGTCTTTGAATTAAAAACTTATTTACGAGAGAATTGTTT
* * * * * * *
814 CCCTCTTTCTTCTTGGACAAACTTCCAAACTGGTTAAACTTTTACGAG-T-TATTTT---TTAAC
131 CTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTTTAACTTAAC
* ***
874 -T--TT---G-GTTCCCTAA-
196 TTCCTTAAAGTATTCAAGAAG
*
887 ATCCATTCCTTAGAGCAATTTT-TCGAACATTCCATGCTCGGGAAATCGCATCATTTGATCTAAA
1 ATCCATTCCTTAGAGCAATTTTCT-GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
* * *
951 TA---TGTCATTTTGCAAACAAGTTTT-GCTCTTTGAATTAAAAACTTCTTTGC-ATGAGAATTG
65 TAGTTTGTCATTTTGTAAACAAGTTTTAG-TCTTTGAATTAAAAACTTATTTACGA-GAGAATTG
* * * * *
1011 TTTCTCTCTTTGTTCTTGGACGAACTTTCGGAGTTGTCAAACTTTTATGAGTTATTTTTTAACTT
128 TTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTTTAACTT
*** * *
1076 CGGTTCCCTAAAGTATTCAATAAG
193 AACTTCCTTAAAGTATTCAAGAAG
** * *
1100 ATCCATTCCTTAGAGCAATTTTCTGAACATTTTATACTCGGGAAATCGCATCATTTGGTCTAAGT
1 ATCCATTCCTTAGAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
* *
1165 AGTTTGTCATTTTGTAAACAAGTTTTAGACTTTGAATTAAAAACTTATTTACGAGAGAATTGTAT
66 AGTTTGTCATTTTGTAAACAAGTTTTAGTCTTTGAATTAAAAACTTATTTACGAGAGAATTGTTT
* * * * * * * * * * * *
1230 CACTCTTGGTCCATGGACGAACTCCCGAACTTATCCAACTTTGAGGAGATCTTTTATAGCTTAAC
131 CTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTTTAACTTAAC
*
1295 TTCCTTAAAGTATTCAAGACG
196 TTCCTTAAAGTATTCAAGAAG
* *
1316 A-CTCATTCCTTTGAGCATTTTTCTGAACATTCCATGCTCGGGAAA-CTGCATCATTTGGTCTAA
1 ATC-CATTCCTTAGAGCAATTTTCTGAACATTCCATGCTCGGGAAATC-GCATCATTTGGTCTAA
* **
1379 ATAGTATGTCATTTCCTAAACAAG
64 ATAGTTTGTCATTTTGTAAACAAG
Statistics
Matches: 933, Mismatches: 184, Indels: 65
0.79 0.16 0.05
Matches are distributed among these distances:
199 1 0.00
200 91 0.10
201 1 0.00
202 5 0.01
203 55 0.06
204 3 0.00
205 3 0.00
206 1 0.00
208 3 0.00
210 1 0.00
211 3 0.00
212 6 0.01
213 118 0.13
214 7 0.01
215 5 0.01
216 624 0.67
217 6 0.01
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (216 bp):
ATCCATTCCTTAGAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
AGTTTGTCATTTTGTAAACAAGTTTTAGTCTTTGAATTAAAAACTTATTTACGAGAGAATTGTTT
CTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTTTAACTTAAC
TTCCTTAAAGTATTCAAGAAG
Found at i:1326 original size:632 final size:637
Alignment explanation
Indices: 39--1402 Score: 1502
Period size: 632 Copynumber: 2.1 Consensus size: 637
29 GGTTCCCTAA
* *
39 ATCCATTCCTTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGATCTAAAT
1 ATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
* * * *
104 --A-TGTCATTTTGCAAACAAGTTTTGCTCTTTGAATTAAAAACTTCTTTGCATGAGAATTGTTT
66 AGATTGTCATTTTGTAAACAAGTTTTGCTCGTTGAATTAAAAACTTATTTACATGAGAATTGTTT
* * * * * ** * * *
166 CTCTCTTTGTTTTTGGACGAACTTTCGGAGTTGTCAAACTTTTATGAGTTATTTTTTAACTTCGG
131 CCCTCTTTCTTCTTGGACAAACTTCCAAACTGGTCAAACTTTTACGAGTTATTTTTTAACTTCGG
**
231 TTCCCTAAAGTATTCAATAAGATCCATTCCTTAGAGCAATTTTCTGAACATTTTATACTCGGGAA
196 TTCCC------A--C-ATAAGATCCATTCCTTAGAGCAATTTTCTGAACATTCCATACTCGGGAA
* *
296 ATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTAGACTTTGAATTAAAAAC
252 ATCGAATCATTTGATCTAAATA--TTGTCATTTTGCAAACAAGTTTTAGACTTTGAATTAAAAAC
*
361 TTATTTACGAGAGAATTGTATCACTCTTGGTCCATGGACGAACTCCCGAACTTATCCAACTTTGA
315 TTATTTACGAGAGAATTGTATCACTCTTGGTCCATGGACGAACTCCCGAACTTATCAAACTTTGA
* * * * * *
426 GGAGATCTTTTATAGCTTAACTTCCTTAAAGTATTCAAGACGACTCATTCCTTTGAGCATTTTTC
380 GGAGATATTTTATAACTTAACTTCCCTAAAGTATTCAAGAAGACTCATTCCTTAGAGCAATTTTC
*
491 TGAACATTCCATGCTCGGGAAACTGCATCATTTGGTCTAAATAGTATGTCATTTCCTAAACAAGT
445 TGAACATTCCATACTCGGGAAACTGCATCATTTGGTCTAAATAGTATGTCATTTCCTAAACAAGT
* ** * * * * * *
556 TTTAGTCTTGGAATTAAAAACTTATTTGTGTGAGAATTGTTTCTCACTTTCTTCTTGGAAGAACT
510 TTTAGACTTGGAATTAAAAACTTATTTACGAGAGAATTGTATCACACTTGCTCCATGGAAGAACT
** * * * * *** *
621 TTCGAACGTGTCAAACTTTTACAACTTCTTTTTTAACTTCTGTTCCTTAAAGAATTCAAGGCG
575 CCCGAACGTATCAAACTTTGACAACATCTTTTATAACTTAACTTCCTTAAAGAATTCAAGACG
* * * * ** * *
684 ATCCATTCCTTCGAGCAGTTTTCCAAACATTCCTTGCTCAAGAAATCGTATCATTTGGTCAAAAT
1 ATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
*
749 AGATTGTCATTTTGTAAACAAGTTTTAG-TCGTTGAATTAAAAACTTATTTACGTGAGAATTGTT
66 AGATTGTCATTTTGTAAACAAGTTTT-GCTCGTTGAATTAAAAACTTATTTACATGAGAATTGTT
* *
813 TCCCTCTTTCTTCTTGGACAAACTTCCAAACTGGTTAAACTTTTACGAGTTATTTTTTAACTTTG
130 TCCCTCTTTCTTCTTGGACAAACTTCCAAACTGGTCAAACTTTTACGAGTTATTTTTTAACTTCG
* *
878 GTT-CC-C-TAA-ATCCATTCCTTAGAGCAATTTT-TCGAACATTCCATGCTCGGGAAATCGCAT
195 GTTCCCACATAAGATCCATTCCTTAGAGCAATTTTCT-GAACATTCCATACTCGGGAAATCGAAT
* * *
938 CATTTGATCTAAATA-TGTCATTTTGCAAACAAGTTTT-GCTCTTTGAATTAAAAACTTCTTTGC
259 CATTTGATCTAAATATTGTCATTTTGCAAACAAGTTTTAG-ACTTTGAATTAAAAACTTATTTAC
* * * * * ** * * * * * *
1001 -ATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGGAGTTGTCAAACTTTTATGAGTTA
323 GA-GAGAATTGTATCACTCTTGGTCCATGGACGAACTCCCGAACTTATCAAACTTTGAGGAGATA
* *** *
1065 TTTTTTAACTTCGGTTCCCTAAAGTATTCAATAAGA-TCCATTCCTTAGAGCAATTTTCTGAACA
387 TTTTATAACTTAACTTCCCTAAAGTATTCAAGAAGACT-CATTCCTTAGAGCAATTTTCTGAACA
** * * **
1129 TTTTATACTCGGGAAA-TCGCATCATTTGGTCTAAGTAGTTTGTCATTTTGTAAACAAGTTTTAG
451 TTCCATACTCGGGAAACT-GCATCATTTGGTCTAAATAGTATGTCATTTCCTAAACAAGTTTTAG
* * * *
1193 ACTTTGAATTAAAAACTTATTTACGAGAGAATTGTATCACTCTTGGTCCATGGACGAACTCCCGA
515 ACTTGGAATTAAAAACTTATTTACGAGAGAATTGTATCACACTTGCTCCATGGAAGAACTCCCGA
* * ** * * *
1258 ACTTATCCAACTTTGAGGAGATCTTTTATAGCTTAACTTCCTTAAAGTATTCAAGACG
580 ACGTATCAAACTTTGACAACATCTTTTATAACTTAACTTCCTTAAAGAATTCAAGACG
* * *
1316 A-CTCATTCCTTTGAGCATTTTTCTGAACATTCCATGCTCGGGAAA-CTGCATCATTTGGTCTAA
1 ATC-CATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGGAAATC-GCATCATTTGGTCTAA
**
1379 ATAG-TATGTCATTTCCTAAACAAG
64 ATAGAT-TGTCATTTTGTAAACAAG
Statistics
Matches: 598, Mismatches: 109, Indels: 37
0.80 0.15 0.05
Matches are distributed among these distances:
631 7 0.01
632 359 0.60
634 1 0.00
635 59 0.10
636 3 0.01
638 1 0.00
645 55 0.09
647 3 0.01
648 109 0.18
649 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (637 bp):
ATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
AGATTGTCATTTTGTAAACAAGTTTTGCTCGTTGAATTAAAAACTTATTTACATGAGAATTGTTT
CCCTCTTTCTTCTTGGACAAACTTCCAAACTGGTCAAACTTTTACGAGTTATTTTTTAACTTCGG
TTCCCACATAAGATCCATTCCTTAGAGCAATTTTCTGAACATTCCATACTCGGGAAATCGAATCA
TTTGATCTAAATATTGTCATTTTGCAAACAAGTTTTAGACTTTGAATTAAAAACTTATTTACGAG
AGAATTGTATCACTCTTGGTCCATGGACGAACTCCCGAACTTATCAAACTTTGAGGAGATATTTT
ATAACTTAACTTCCCTAAAGTATTCAAGAAGACTCATTCCTTAGAGCAATTTTCTGAACATTCCA
TACTCGGGAAACTGCATCATTTGGTCTAAATAGTATGTCATTTCCTAAACAAGTTTTAGACTTGG
AATTAAAAACTTATTTACGAGAGAATTGTATCACACTTGCTCCATGGAAGAACTCCCGAACGTAT
CAAACTTTGACAACATCTTTTATAACTTAACTTCCTTAAAGAATTCAAGACG
Done.