Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006486.1 Kokia drynarioides strain JFW-HI SEQ_121069, 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, 687
Length: 1145
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Found at i:454 original size:215 final size:211
Alignment explanation
Indices: 1--1143 Score: 962
Period size: 216 Copynumber: 5.3 Consensus size: 211
* * * *
1 AACTTGTCAAGCTTTTACTATTTCTTCTATAATAACTTCGCTTCCTTAAACTATTCAAGATGATC
1 AACTTGTCAAACTTTTACTAGTTCTT-T-T-ATAACTTCGGTTCCTTAAAGTATTCAAGAT-ATC
* * * * * * * *
66 CAATGCTTCGAGCAATATTCTGAGCATTCCATGCTCGGGAAATCGAATCATTCTGTCAAAATAGT
62 CATTTCTTCGAGCAATTTTC-GAACATTCCATGCTC-AGAAATCGCATCATT-GGTCTAAATAGT
* * ** * * * *
131 TTGCCATTTCT-TAAAAAAACTTTTGGTCACTGAATTAAATACTTATTTATGTGTA-AATTATTT
124 TTGTCATTT-TGT-AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGT-AAGAATTGTTT
*
194 CTCTCTTGGTTCTTGGATGAACCTTCG
186 CTCTCTTGGTTCTTGGACGAA-CTTCG
* * * *
221 AAATATG-AAAACTTTTACTATTTCTGTTATAACTTCGGTTCCTTAAAGTATTCAAGATATCCAT
1 AACT-TGTCAAACTTTTACTAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATATCCAT
*
285 TTCTTCGAGCAATTTTGCGAACATTCCATGCTCAAGAAATTGCATCACTTGGTCTAAATAGTTTG
65 TTCTTCGAGCAATTTT-CGAACATTCCATGCTC-AGAAATCGCATCA-TTGGTCTAAATAGTTTG
* * *
350 TCATTTTGTAAACAACTTTTAGTCTTTGATTTAAAAACTTATTTACGTAAGAACTGTTTCTCTCT
127 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCT
** *
415 CAGTTCTTAGACGAACTTCTG
192 TGGTTCTTGGACGAACTTC-G
* * * * **
436 AACTTTTGAAGCTTTTACTAGTTCTTTTATAGCATT-GGTTCCTTAAAGTATTCAAGGCGATCCA
1 AACTTGTCAAACTTTTACTAGTTCTTTTATAAC-TTCGGTTCCTTAAAGTATTCAA-GATATCCA
* * * * *
500 TTAT-TTCAAGCAATATTCCAAACATTTCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTT
64 TT-TCTTCGAGCAAT-TTTCGAACATTCCATGCTC-AGAAATCGCATCATT-GGTCTAAATAGTT
* * * *
564 TGTCATTCTGTAAACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAGAATTGTTTCCCT
125 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCT
* * *
629 CGTAGTTCTTGGATGAACTTCCG
190 CTTGGTTCTTGGACGAACTT-CG
* * * * * *
652 CATTTGTCAAGCTTTTAC-AGGTTCTTTTACAACTTAC-GTTCCTTAAAGCATTCTATGCA-ATC
1 AACTTGTCAAACTTTTACTA-GTTCTTTTATAACTT-CGGTTCCTTAAAGTATTC-AAG-ATATC
* * * * *
714 CATTCCTTCTA-CAAATTTTCGAACATTCAATGTTCAGAAAATCGCATCATTTGATCTAAATAGT
62 CATTTCTTCGAGC-AATTTTCGAACATTCCATGCTCAG-AAATCGCATCA-TTGGTCTAAATAGT
* * ** *
778 TTGTCATTTTGTGAACAACTTTTGGTCTTTGAATTAAAAACTTATTGACGTGGGATTTGTTTCTC
124 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTC
* *
843 TCTTGGTTCTTGGACGAACCTCC
189 TCTTGGTTCTTGGACGAACTTCG
* * * * * *
866 AGACTTGTCAAACTTTTACAAGTCCTTTTAAAACTTCGGTTCCTTGAAGTGTATTATATATAAAT
1 A-ACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGGTTCCTT-AA-AGTA-T-T-CA-AGAT
* * * * * * * *
931 GATCCACTACATCGAG-AAATTTCGAACATTCCACTG-TCCGAAAATCGAAT-ATTTTGGTTTAT
59 -ATCCATTTCTTCGAGCAATTTTCGAACATTCCA-TGCTCAG-AAATCGCATCA--TTGGTCTAA
* * * *
993 ACAGTTTGCCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAA-AATTG
119 ATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGT-AAGAATTG
* * * *
1057 TCTCTCTCTTGGTTATTGGACGAGCTACCG
183 TTTCTCTCTTGGTTCTTGGACGAACT-TCG
* * *
1087 AACTTGTAAAACTTTTACGAGTTATTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
1 AACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
1144 CT
Statistics
Matches: 753, Mismatches: 132, Indels: 82
0.78 0.14 0.08
Matches are distributed among these distances:
214 12 0.02
215 252 0.33
216 255 0.34
217 39 0.05
218 5 0.01
219 7 0.01
220 167 0.22
221 16 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (211 bp):
AACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATATCCATT
TCTTCGAGCAATTTTCGAACATTCCATGCTCAGAAATCGCATCATTGGTCTAAATAGTTTGTCAT
TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGT
TCTTGGACGAACTTCG
Found at i:585 original size:216 final size:213
Alignment explanation
Indices: 9--1142 Score: 874
Period size: 215 Copynumber: 5.2 Consensus size: 213
1 AACTTGTC
* * * * ** *
9 AAGCTTTTACTATTTCTTCTATAATAACTTCGCTTCCTTAAACTATTCAAGATGATCCAATGCTT
1 AAGCTTTTACTAGTTCTT-T-T-ATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCC-ATTCTT
* * * * * * *
74 CGAGCAATATTCTGAGCATTCCATGCTCGGGAAATCGAATCATTCTGTCAAAATAGTTTGCCATT
62 CGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGTTTGTCA-T
* ** * * * *
139 TCT-TAAAAAAACTTTTGGTCACTGAATTAAATACTTATTTATGTGTA-AATTATTTCTCTCTTG
126 TCTGT-AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTG-AGAATTGTTTCTCTCTTA
* * *
202 GTTCTTGGATGAACCTTCGAAATATG
189 GTTCTTGGACGAA-CTTCGAATTTTG
* * * * **
228 AAAACTTTTACTATTTCTGTTATAACTTCGGTTCCTTAAAGTATTCAA-GATATCCATTTCTTCG
1 -AAGCTTTTACTAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCA-TTCTTCG
* * * * *
292 AGCAATTTTGCGAACATTCCATGCTCAAGAAATTGCATCACTT-GGTCTAAATAGTTTGTCATTT
64 AGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCA-TTCGGTCTAAATAGTTTGTCATTC
* * * * *
356 TGTAAACAACTTTTAGTCTTTGATTTAAAAACTTATTTACGTAAGAACTGTTTCTCTCTCAGTTC
128 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTC
*
421 TTAGACGAACTTCTGAACTTTTG
193 TTGGACGAACTTC-GAA-TTTTG
* * *
444 AAGCTTTTACTAGTTCTTTTATAGCATT-GGTTCCTTAAAGTATTCAAGGCGATCCATTATTTCA
1 AAGCTTTTACTAGTTCTTTTATAAC-TTAGGTTCCTTAAAGTATTCAAGGCGATCCATT-CTTCG
* * *
508 AGCAATATTCCAAACATTTCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTTGTCATTCT
64 AGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGTTTGTCATTCT
* * *
573 GTAAACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAGAATTGTTTCCCTCGTAGTTCT
129 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCT
* * *
638 TGGATGAACTTCCGCATTTGTC
194 TGGACGAACTT-CGAATTT-TG
* * * * * * *
660 AAGCTTTTAC-AGGTTCTTTTACAACTTACGTTCCTTAAAGCATTCTATGCAATCCATTCCTTCT
1 AAGCTTTTACTA-GTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCATT-CTTCG
* * * * *
724 A-CAA-ATTTTCGAACATTCAATGTTC-AGAAAATCGCATCATTTGATCTAAATAGTTTGTCATT
64 AGCAATA-TTCCGAACATTCCATGCTCGAG-AAATCGCATCATTCGGTCTAAATAGTTTGTCATT
* * * * * *
786 TTGTGAACAACTTTTGGTCTTTGAATTAAAAACTTATTGACGTGGGATTTGTTTCTCTCTTGGTT
127 CTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTT
* * * *
851 CTTGGACGAACCTCCAGACTTGTC
192 CTTGGACGAA-CTTC-GAATTTTG
* * * * * * * *** *
875 AAACTTTTACAAGTCCTTTTAAAACTTCGGTTCCTTGAAGTGTATTATATATAAATGATCCACTA
1 AAGCTTTTACTAGTTCTTTTATAACTTAGGTTCCTT-AA-AGTA-T-T-CA-AGGCGATCCA-TT
* * * * * * *
940 CATCGAG-AA-ATTTCGAACATTCCACTG-TCCGA-AAATCGAAT-ATTTTGGTTTATACAGTTT
59 CTTCGAGCAATATTCCGAACATTCCA-TGCT-CGAGAAATCGCATCA-TTCGGTCTAAATAGTTT
* * * * * *
1000 GCCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAAAATTGTCTCTCTC
121 GTCATTCTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
* * * * * *
1065 TTGGTTATTGGACGAGCTACCGAACTTGTA
186 TTAGTTCTTGGACGAACT-TCGAA-TTTTG
* * * *
1095 AAACTTTTACGAGTTATTTTATAACTTCGGTTCCTTAAAGTATTCAAG
1 AAGCTTTTACTAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAG
1143 ACT
Statistics
Matches: 743, Mismatches: 138, Indels: 72
0.78 0.14 0.08
Matches are distributed among these distances:
214 9 0.01
215 258 0.35
216 254 0.34
217 31 0.04
218 5 0.01
219 9 0.01
220 159 0.21
221 16 0.02
222 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (213 bp):
AAGCTTTTACTAGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAGGCGATCCATTCTTCGAG
CAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGTTTGTCATTCTGT
AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTG
GACGAACTTCGAATTTTG
Found at i:884 original size:431 final size:432
Alignment explanation
Indices: 1--910 Score: 1000
Period size: 431 Copynumber: 2.1 Consensus size: 432
* *
1 AACTTGTCAAGCTTTTACTATTTCTTCTATAATAACTTCGCTTCCTTAAACTATTCAAGATGATC
1 AACTTGTCAAGCTTTTACTAGTTCTT-T-T-ATAACTTCGCTTCCTTAAACTATTCAAGACGATC
* * ** * * *
66 CAATGCTTCGAGCAATATTCTGAGCATTCCATGCTCGGGAAATCGAATCATTCTGTCAAAATAGT
63 CAATACTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGAATCATTCGGTCAAAATAGT
* * * *
131 TTGCCATTTCTTAAAAAAACTTTTGGTCACTGAATTAAATACTTATTTATGTGTAAATTATTTCT
128 TTGCCATTTCTTAAAAAAACTTTTGGTCACTGAATTAAAAACCTATTTACGTGTAAATTATTTCC
* * * *
196 CTCTTGGTTCTTGGATGAACCTTCGAAATATGAAAACTTTTACTATTTCTGTTATAACTTCGGTT
193 CTCGTAGTTCTTGGATGAACCTTCGAAATATGAAAACTTTTACTAGTTCTGTTACAACTTCGGTT
* * * *
261 CCTTAAAGTATTCAAGATATCCATTTCTTCGAGCAATTTTGCGAACATTCCATGCTCAAGAAATT
258 CCTTAAAGCATTCAAGATATCCATTCCTTCGAGCAATTTTGCGAACATTCAATGCTCAAGAAATC
* *
326 GCATCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTAGTCTTTGATTTAAAAACTTA
323 GCATCACTTGATCTAAATAGTTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACTTA
* * *
391 TTTACGTAAGAACTGTTTCTCTCTCAGTTCTTAGACGAACTTCTG
388 TTGACGTAAGAACTGTTTCTCTCTCAGTTCTTAGACGAACTCCAG
* * * * * *
436 AACTTTTGAAGCTTTTACTAGTTCTTTTATAGCATT-GGTTCCTTAAAGTATTCAAGGCGATCCA
1 AACTTGTCAAGCTTTTACTAGTTCTTTTATAAC-TTCGCTTCCTTAAACTATTCAAGACGATCCA
* * * * * *
500 TTATTTCAAGCAATATTCCAAACATTTCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTT
65 ATACTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGAATCATTCGGTCAAAATAGTTT
* * ** *
565 GTCA-TTCTGT-AAACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTG-AGAATTGTTTCC
130 GCCATTTCT-TAAAAAAACTTTTGGTCACTGAATTAAAAACCTATTTACGTGTA-AATTATTTCC
* * * * *
627 CTCGTAGTTCTTGGATGAA-CTTCCG-CATTTGTCAAGCTTTTAC-AGGTTCTTTTACAACTTAC
193 CTCGTAGTTCTTGGATGAACCTT-CGAAATATG-AAAACTTTTACTA-GTTCTGTTACAACTT-C
* * *
689 -GTTCCTTAAAGCATTCTATGCA-ATCCATTCCTTCTA-CAAATTTT-CGAACATTCAATGTTC-
254 GGTTCCTTAAAGCATTC-AAG-ATATCCATTCCTTCGAGC-AATTTTGCGAACATTCAATGCTCA
* * *
749 AGAAAATCGCATCATTTGATCTAAATAGTTTGTCATTTTGTGAACAACTTTTGGTCTTTGAATTA
316 AG-AAATCGCATCACTTGATCTAAATAGTTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATTA
** ** ** *
814 AAAACTTATTGACGTGGGATTTGTTTCTCTCTTGGTTCTTGGACGAACCTCCAG
380 AAAACTTATTGACGTAAGAACTGTTTCTCTCTCAGTTCTTAGACGAA-CTCCAG
* * * * *
868 -ACTTGTCAAACTTTTACAAGTCCTTTTAAAACTTCGGTTCCTT
1 AACTTGTCAAGCTTTTACTAGTTCTTTTATAACTTCGCTTCCTT
911 GAAGTGTATT
Statistics
Matches: 394, Mismatches: 68, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
430 13 0.03
431 244 0.62
432 109 0.28
433 4 0.01
434 1 0.00
435 23 0.06
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (432 bp):
AACTTGTCAAGCTTTTACTAGTTCTTTTATAACTTCGCTTCCTTAAACTATTCAAGACGATCCAA
TACTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGAATCATTCGGTCAAAATAGTTTG
CCATTTCTTAAAAAAACTTTTGGTCACTGAATTAAAAACCTATTTACGTGTAAATTATTTCCCTC
GTAGTTCTTGGATGAACCTTCGAAATATGAAAACTTTTACTAGTTCTGTTACAACTTCGGTTCCT
TAAAGCATTCAAGATATCCATTCCTTCGAGCAATTTTGCGAACATTCAATGCTCAAGAAATCGCA
TCACTTGATCTAAATAGTTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACTTATTG
ACGTAAGAACTGTTTCTCTCTCAGTTCTTAGACGAACTCCAG
Done.