Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001195.1 Kokia drynarioides strain JFW-HI SEQ_112538, 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, 737
Length: 1229
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Found at i:852 original size:437 final size:432
Alignment explanation
Indices: 151--1109 Score: 1094
Period size: 436 Copynumber: 2.2 Consensus size: 432
141 AAATTTTTCT
* * * * * * *
151 AACATTCCATGCTCGAGAAATTGCATCTTTTGGTCTAAATAGTTGTCAT-TT-TGAAAACCAAGT
1 AACATTCCATGCTCGAGAAATCGCATCATTCGGTCAAAATATTTGCCATCTTCT-AAAA--AACT
* * * ** *
214 TTTGGTC-TTCAAACTAAAAACTTATTTACGTG-AGAATTGTTACTCCTTTGGTTCTTTGACAAC
63 TTTGGTCACT-GAATTAAAAACTTATTTATTTGTA-AATTGTTACTCCTTTGGTTCTTGGACAAC
** * *
277 CTTCTGAACTAGTCAAACTTTTTACGAGTTCTTTTATAACTTTGGTTCATTAAAGTATTCAAGAC
126 CTTCTGAACTAGGAAAACTTTTTACGAGTTCTGTTATAACTTCGGTTCATTAAAGTATTCAAGAC
* * *
342 GATCCATTCCTTCGATCAATATTCCGAACATTCCATGCATGGGAAATAGCATCATCCGGTCTAAA
191 GATCCATTCCTTCGAGCAATATTACGAACATTCCATGCATGAGAAATAGCATCATCCGGTCTAAA
*
407 TAGTTTTTCATTTTGCAAACAACTTTTTGGTCCTTGAATTAAAAACATATTTATGAAAGAATTAT
256 TAGTTTTTCATTTCGCAAACAAC-TTTTGGTCCTTGAATTAAAAACATATTTATGAAAGAATTAT
* * * *
472 TTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACTATTTCTTCTATGATAAC
320 TTCTCTCTTGATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACGAGTTCTTCTATG-GAA-
* * *
537 TTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATATT-CG
383 TT-GGTTCCTTAAACTATCCAAGATGATCCAATCCTTCAACCAATATTCCA
*
587 AACATTCCATGCTCGGGAAATCGCATCATTCGGTCAAAATAGTTTGCCA-CTTCGTAAAAAAAAC
1 AACATTCCATGCTCGAGAAATCGCATCATTCGGTCAAAATA-TTTGCCATCTTC-T--AAAAAAC
* * *
651 TTTTGGTCACTGAATTAAATACTTATTTATTTGTAAATTGTTTCTCTTTTGGTTCTTGGACGAA-
62 TTTTGGTCACTGAATTAAAAACTTATTTATTTGTAAATTGTTACTCCTTTGGTTCTTGGAC-AAC
* * * * *
715 CTTTTGAACTAGGAAAAC-TTTTACTATTTCTGTTATAACTTCGGTTCCTTAAAGTATTCAAGAT
126 CTTCTGAACTAGGAAAACTTTTTACGAGTTCTGTTATAACTTCGGTTCATTAAAGTATTCAAGAC
* * * * *
779 GATCCATTTCTTCGAGCAACT-TTATGAACATTCCATGC-TCGATAAATTGCATCA-CTTGGTCT
191 GATCCATTCCTTCGAGCAA-TATTACGAACATTCCATGCAT-GAGAAATAGCATCATC-CGGTCT
* * * * * **
841 ATATTGTTTTTCATTTCGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATT
253 AAATAGTTTTTCATTTCGCAAACAACTTTTGGTCCTTGAATTAAAAACATATTTATGAAAGAATT
* * * * * *
906 GTTTCTCTCTTGGTTCTTAGACGAACTTCTGAACTTTTCAAGCTTTTACGAGTTCTTTTATGGCA
318 ATTTCTCTCTTGATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACGAGTTCTTCTATGGAA
* * * * *
971 TTGGTTCCTTAAAGTATTCAAGGTGATCCATTCTTTCAACCAATATTCCA
383 TTGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCAACCAATATTCCA
* * * *
1021 AACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTGTCATTTTCTAAACAACTTTT
1 AACATTCCATGCTCGAGAAATCGCATCATTCGGTCAAAATATTTGCCATCTTCTAAAAAACTTTT
**
1086 GGTCTTTGAATTAAAAACTTATTT
66 GGTCACTGAATTAAAAACTTATTT
1110 GCATGAGAAT
Statistics
Matches: 441, Mismatches: 69, Indels: 31
0.82 0.13 0.06
Matches are distributed among these distances:
431 31 0.07
433 45 0.10
434 45 0.10
435 1 0.00
436 127 0.29
437 117 0.27
438 66 0.15
439 5 0.01
440 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (432 bp):
AACATTCCATGCTCGAGAAATCGCATCATTCGGTCAAAATATTTGCCATCTTCTAAAAAACTTTT
GGTCACTGAATTAAAAACTTATTTATTTGTAAATTGTTACTCCTTTGGTTCTTGGACAACCTTCT
GAACTAGGAAAACTTTTTACGAGTTCTGTTATAACTTCGGTTCATTAAAGTATTCAAGACGATCC
ATTCCTTCGAGCAATATTACGAACATTCCATGCATGAGAAATAGCATCATCCGGTCTAAATAGTT
TTTCATTTCGCAAACAACTTTTGGTCCTTGAATTAAAAACATATTTATGAAAGAATTATTTCTCT
CTTGATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACGAGTTCTTCTATGGAATTGGTTCC
TTAAACTATCCAAGATGATCCAATCCTTCAACCAATATTCCA
Found at i:908 original size:216 final size:215
Alignment explanation
Indices: 1--1179 Score: 1203
Period size: 216 Copynumber: 5.4 Consensus size: 215
* * * * *
1 GGTCTTTGAATTAAAAACTTATTTATGTGAAAATT-TTCTCCCTCTTGGTTCTTGGACGAACTAC
1 GGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTT-TCTCTTTTGGTTCTTAGACGAACTTC
* * * * * **
65 CGAACTTGTAAAACTTTTACAAGTTATTTTATAACTTCGGTTCATTAAAGTATTCAAGACCATCC
65 TGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCC
* * * * * * *
130 GTTTC-TCTGAGAAATTTTTCTAACATTCCATGCTCGAGAAATTGCATCTTTTGGTCTAAATAG-
130 ATTTCTTC-GAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATC-ATTGGTCTAAATAGT
* * *
193 TTGTCATTTTGAAAACCAAGTTTT
193 TTGTCATTTCGTAAA-CAACTTTT
** * * * * *
217 GGTCTTCAAACTAAAAACTTATTTACGTGAGAATTGTTACTCCTTTGGTTCTTTGAC-AACCTTC
1 GGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTTTTGGTTCTTAGACGAA-CTTC
* * * *
281 TGAACTAGTCAAACTTTTTACGAGTTCTTTTATAACTTTGGTTCATTAAAGTATTCAAGACGATC
65 TGAACTTGTCAAAC-TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATC
* * * * *
346 CATTCCTTCGATCAATATTCCGAACATTCCATGCAT-GGGAAATAGCATCATCCGGTCTAAATAG
129 CATTTCTTCGAGCAATATTCCGAACATTCCATGC-TCGAGAAATCGCATCAT-TGGTCTAAATAG
* * *
410 TTTTTCATTTTGCAAACAACTTTTT
192 TTTGTCATTTCGTAAACAAC-TTTT
* * ** * * *
435 GGTCCTTGAATTAAAAACATATTTATGAAAGAATTATTTCTCTTTTGATTCTTAGACAAACTTCT
1 GGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTTTTGGTTCTTAGACGAACTTCT
* * * * *
500 GAACTTGTCAAGCTTTTACTATTTCTTCTATGATAACTTCGGTTCCTTAAACTATCCAAGATGAT
66 GAACTTGTCAAACTTTTACGAGTTCTT-T-T-ATAACTTCGGTTCCTTAAAGTATTCAAGATGAT
* * * *
565 CCAATCCTTCGAGCAATATT-CGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCAAAATAG
128 CCATTTCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATT-GGTCTAAATAG
* * *
629 TTTGCCACTTCGTAAAAAAAACTTTT
192 TTTGTCATTTCGT--AAACAACTTTT
** * * * *
655 GGTCACTGAATTAAATACTTATTTATTTGTA-AATTGTTTCTCTTTTGGTTCTTGGACGAACTTT
1 GGTCTTTGAATTAAAAACTTATTTATGTG-AGAATTGTTTCTCTTTTGGTTCTTAGACGAACTTC
* ** * * *
719 TGAACTAGGAAAACTTTTACTATTTCTGTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCC
65 TGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCC
** * * * *
784 ATTTCTTCGAGCAACT-TTATGAACATTCCATGCTCGATAAATTGCATCACTTGGTCTATATTGT
130 ATTTCTTCGAGCAA-TATTCCGAACATTCCATGCTCGAGAAATCGCATCA-TTGGTCTAAATAGT
*
848 TTTTCATTTCGTAAACAACTTTT
193 TTGTCATTTCGTAAACAACTTTT
*
871 GGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTAGACGAACTTCT
1 GGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTTTTGGTTCTTAGACGAACTTCT
* * ** *
936 GAACTTTTCAAGCTTTTACGAGTTCTTTTATGGCATT-GGTTCCTTAAAGTATTCAAGGTGATCC
66 GAACTTGTCAAACTTTTACGAGTTCTTTTATAAC-TTCGGTTCCTTAAAGTATTCAAGATGATCC
* * *
1000 A-TTCTTTCAACCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATA-T
130 ATTTC-TTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATT-GGTCTAAATAGT
1063 TTGTCATTTTC-TAAACAACTTTT
193 TTGTCA-TTTCGTAAACAACTTTT
*** * ** * * *
1086 GGTCTTTGAATTAAAAACTTATTTGCATGAGAATTGTTTCTCTCTAAGTTCTTAGATGATCTTCC
1 GGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTTTTGGTTCTTAGACGAACTTCT
1151 GAACTTGTCAAACTTTTACGAGTTCTTTT
66 GAACTTGTCAAACTTTTACGAGTTCTTTT
1180 GAAACATAGG
Statistics
Matches: 802, Mismatches: 135, Indels: 53
0.81 0.14 0.05
Matches are distributed among these distances:
215 111 0.14
216 223 0.28
217 158 0.20
218 128 0.16
219 52 0.06
220 123 0.15
221 7 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (215 bp):
GGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTTTTGGTTCTTAGACGAACTTCT
GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCA
TTTCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTGGTCTAAATAGTTTG
TCATTTCGTAAACAACTTTT
Done.