Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006487.1 Kokia drynarioides strain JFW-HI SEQ_121070, 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, 1000
Length: 1783
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Found at i:468 original size:215 final size:215
Alignment explanation
Indices: 1--1404 Score: 1221
Period size: 216 Copynumber: 6.5 Consensus size: 215
* * * *
1 AACTTGTCAAGCTTTTACTATTTCTTCTATAATAACTTCGCTTCCTTAAACTATTCAAGATGATC
1 AACTTGTCAAGCTTTTACGAGTTCTT-T-T-ATAACTTCGGTTCCTTAAAGTATTCAAGAT-ATC
* * * * * * *
66 CAATGCTTCGAGCAATATTCTGAGCATTCCATGCTCGGGAAATCGAATCATTCT-GTCAAAATAG
62 CATTTCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATT-TGGTCTAAATAG
* * ** * * *
130 TTTGCCATTTCT-TAAAAAAACTTTTGGTCACTGAATTAAATACTTATTTATGTGTA-AATTATT
126 TTTGTCATTT-TGT-AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTG-AGAATTGTT
*
193 TCTCTCTTGGTTCTTGGATGAACCTT-CG
188 TCTCTCTTGGTTCTTGGACGAA-CTTCCG
* * * * * *
221 AAATATG-AAAACTTTTACTATTTCTGTTATAACTTCGGTTCCTTAAAGTATTCAAGATATCCAT
1 AACT-TGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATATCCAT
* * * * *
285 TTCTTCGAGCAATTTTGCGAACATTCCATGCTCAAGAAATTGCATCACTTGGTCTAAATAGTTTG
65 TTCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* * * *
350 TCATTTTGTAAACAACTTTTAGTCTTTGATTTAAAAACTTATTTACGTAAGAACTGTTTCTCTCT
130 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
** * *
415 CAGTTCTTAGACGAACTTCTG
195 TGGTTCTTGGACGAACTTCCG
* * ** *
436 AACTTTTCAAGCTTTTACGAGTTCTTTTATAACATCGGTTCCTTAAAGTATTCAAGGCGAACCA-
1 AACTTGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA-GATATCCAT
* * * *
500 TTCTTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTT
65 TTC-TTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
* * *
565 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTGACAATTGTTTCCCTC
129 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
* * *
630 GTAGTTCTTGGATGAACTTCCG
194 TTGGTTCTTGGACGAACTTCCG
* * * * * *
652 CATTTGTCAAGCTTTTAC-AGGTTCTTTTACAACTTAGGTTCCTTAAAGCATTCTATGCA-ATCC
1 AACTTGTCAAGCTTTTACGA-GTTCTTTTATAACTTCGGTTCCTTAAAGTATTC-AAG-ATATCC
* * * * * *
715 ATTCCTTCTA-CAA-ATTTTCGAACATTCAATGTTCG-GAAAATCGCATCATTTGATCTAAATAG
63 ATTTCTTCGAGCAATA-TTCCGAACATTCCATGCTCGAG-AAATCGCATCATTTGGTCTAAATAG
* * * *
777 TTTGTCATTTTGTGAACAACTTTTGGTCTTTGAATTAAAAACTTATTGACGTGGGATTTGTTTCT
126 TTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCT
* *
842 CTCTTGGTTCTTGGACGAGCTACCG
191 CTCTTGGTTCTTGGACGAACTTCCG
* * * * * * *
867 AACTTGTCAAACTTTTACAAGTCCTTTTAAAACTTCGGTTCCTTGAAGTGTATTATATATAAATG
1 AACTTGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTT-AA-AGTA-T-T-CA-AGAT-
* * * *
932 ATCCACTTCATCGAGCAA-ATTTCCGAA-A----A---TC--G-AAT--C-T--TTTGGT-TTAT
59 ATCCATTTCTTCGAGCAATA-TTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAA
* * * * *
979 TCAGTTTGCCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTAGTTATGTGAAAATTGT
123 T-AGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * * *
1044 CTCTCTCTTGGTTATTGGACGAGCTACCG
187 TTCTCTCTTGGTTCTTGGACGAACTTCCG
* * * * *
1073 AACTTGTAAAACTTTTACGAGTTGTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACCATCCGT
1 AACTTGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA-TATCCAT
* * * * *
1138 TTCTACGAGCGATATTCCAAACATTCCATGCTCGAGAAATTGCATCTTTTGGTCTAAATAGTTTG
65 TTCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* * *** * * *
1203 TCATTTTGAAAACCAAGTTTTGGTCTCCAAACTAAAAACTTATTTACGTGAGAGTTGTATCTC-C
130 TCATTTTGTAAA-CAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
** *
1267 TTTGGTTCTCAGACGAACTTCTG
194 -TTGGTTCTTGGACGAACTTCCG
* * * * *
1290 AACTAGCCAAGCTTTTTACGAGTTCTTTTATAATTTTGGTTCCTTAAAGTATTCAAGAAGATCCA
1 AACTTGTCAAGC-TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAG-ATATCCA
* * * * *
1355 TTCCTCCGATCAATATCCCGAACATTCCATGCTCGAGAAATAGCATCATT
64 TTTCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATT
1405 CCGATCCATT
Statistics
Matches: 958, Mismatches: 178, Indels: 98
0.78 0.14 0.08
Matches are distributed among these distances:
200 21 0.02
201 3 0.00
202 1 0.00
203 1 0.00
204 3 0.00
205 6 0.01
206 125 0.13
208 3 0.00
209 1 0.00
210 1 0.00
211 6 0.01
213 2 0.00
214 10 0.01
215 262 0.27
216 274 0.29
217 102 0.11
218 89 0.09
219 5 0.01
220 19 0.02
221 13 0.01
222 11 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (215 bp):
AACTTGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATATCCATT
TCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGT
CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
GGTTCTTGGACGAACTTCCG
Found at i:593 original size:216 final size:216
Alignment explanation
Indices: 1--915 Score: 925
Period size: 215 Copynumber: 4.2 Consensus size: 216
* * * * *
1 AACTTGTCAAGCTTTTACTATTTCTTCTATAATAACTTCGCTTCCTTAAACTATTCAAGATGATC
1 AACTTGTCAAGCTTTTACGAGTTCTT-T-T-ATAACTTCGGTTCCTTAAAGTATTCAAGACGATC
* * * * * * * *
66 CAATGCTTCGAGCAATATTCTGAGCATTCCATGCTCGGGAAATCGAATCATTCTGTCAAAATAGT
63 CATTCCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGT
* * ** * * *
131 TTGCCATTTCT-TAAAAAAACTTTTGGTCACTGAATTAAATACTTATTTATGTGTA-AATTATTT
128 TTGTCATTT-TGT-AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTG-AGAATTGTTT
*
194 CTCTCTTGGTTCTTGGATGAACCTT-CG
190 CTCTCTTGGTTCTTGGACGAA-CTTCCG
* * * * * * *
221 AAATATG-AAAACTTTTACTATTTCTGTTATAACTTCGGTTCCTTAAAGTATTCAAGA-TATCCA
1 AACT-TGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCA
* * * * *
284 TTTCTTCGAGCAATTTTGCGAACATTCCATGCTCAAGAAATTGCATCACTT-GGTCTAAATAGTT
65 TTCCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCA-TTCGGTCTAAATAGTT
* * * *
348 TGTCATTTTGTAAACAACTTTTAGTCTTTGATTTAAAAACTTATTTACGTAAGAACTGTTTCTCT
129 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
** * *
413 CTCAGTTCTTAGACGAACTTCTG
194 CTTGGTTCTTGGACGAACTTCCG
* * * *
436 AACTTTTCAAGCTTTTACGAGTTCTTTTATAACATCGGTTCCTTAAAGTATTCAAGGCGAACCAT
1 AACTTGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
* * * *
501 TCTTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTTG
66 TCCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGTTTG
* * * *
566 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTGACAATTGTTTCCCTCG
131 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* *
631 TAGTTCTTGGATGAACTTCCG
196 TGGTTCTTGGACGAACTTCCG
* * * * * * *
652 CATTTGTCAAGCTTTTAC-AGGTTCTTTTACAACTTAGGTTCCTTAAAGCATTCTATG-CAATCC
1 AACTTGTCAAGCTTTTACGA-GTTCTTTTATAACTTCGGTTCCTTAAAGTATTC-AAGACGATCC
* * * * * *
715 ATTCCTTCTA-CAA-ATTTTCGAACATTCAATGTTCG-GAAAATCGCATCATTTGATCTAAATAG
64 ATTCCTTCGAGCAATA-TTCCGAACATTCCATGCTCGAG-AAATCGCATCATTCGGTCTAAATAG
* * * *
777 TTTGTCATTTTGTGAACAACTTTTGGTCTTTGAATTAAAAACTTATTGACGTGGGATTTGTTTCT
127 TTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCT
* *
842 CTCTTGGTTCTTGGACGAGCTACCG
192 CTCTTGGTTCTTGGACGAACTTCCG
* * * * *
867 AACTTGTCAAACTTTTACAAGTCCTTTTAAAACTTCGGTTCCTTGAAGT
1 AACTTGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGT
916 GTATTATATA
Statistics
Matches: 576, Mismatches: 106, Indels: 31
0.81 0.15 0.04
Matches are distributed among these distances:
214 7 0.01
215 264 0.46
216 251 0.44
217 31 0.05
218 1 0.00
219 1 0.00
220 19 0.03
221 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (216 bp):
AACTTGTCAAGCTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
TCCTTCGAGCAATATTCCGAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATAGTTTG
TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
TGGTTCTTGGACGAACTTCCG
Found at i:884 original size:431 final size:432
Alignment explanation
Indices: 1--915 Score: 1033
Period size: 431 Copynumber: 2.1 Consensus size: 432
* * * * * *
1 AACTTGTCAAGCTTTTACTATTTCTTCTATAATAACTTCGCTTCCTTAAACTATTCAAGATGATC
1 AACTTGTCAAGCTTTTACAAGTTCTT-T-T-ATAACTTCGGTTCCTTAAAGTATTCAAGACGAAC
* ** * * *
66 CAATGCTTCGAGCAATATTCTGAGCATTCCATGCTCGGGAAATCGAATCATTCTGTCAAAATAGT
63 CAATGCTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGAATCATTCGGTCAAAATAGT
* * * *
131 TTGCCATTTCTTAAAAAAACTTTTGGTCACTGAATTAAATACTTATTTATGTGTAAATTATTTCT
128 TTGCCATTTCTTAAAAAAACTTTTGGTCACTGAATTAAAAACCTATTTACGTGTAAATTATTTCC
* * * * *
196 CTCTTGGTTCTTGGATGAACCTTCGAAATATGAAAACTTTTACTATTTCTGTTATAACTTCGGTT
193 CTCGTAGTTCTTGGATGAACCTTCGAAATATGAAAACTTTTACTAGTTCTGTTACAACTTAGGTT
* * * *
261 CCTTAAAGTATTCAAGATATCCATTTCTTCGAGCAATTTTGCGAACATTCCATGCTCAAGAAATT
258 CCTTAAAGCATTCAAGATATCCATTCCTTCGAGCAATTTTGCGAACATTCAATGCTCAAGAAATC
* *
326 GCATCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTAGTCTTTGATTTAAAAACTTA
323 GCATCACTTGATCTAAATAGTTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACTTA
* * *
391 TTTACGTAAGAACTGTTTCTCTCTCAGTTCTTAGACGAACTTCTG
388 TTGACGTAAGAACTGTTTCTCTCTCAGTTCTTAGACGAACTACCG
* * * *
436 AACTTTTCAAGCTTTTACGAGTTCTTTTATAACATCGGTTCCTTAAAGTATTCAAGGCGAACC-A
1 AACTTGTCAAGCTTTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAACCAA
* * * *
500 TTCTTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGCATCATTCGGTCTAAATATTTT
66 TGC-TTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGAATCATTCGGTCAAAATAGTTT
* * ** *
565 GTCATTT-TGT-AAACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTG-ACAATTGTTTCC
130 GCCATTTCT-TAAAAAAACTTTTGGTCACTGAATTAAAAACCTATTTACGTGTA-AATTATTTCC
* * * * *
627 CTCGTAGTTCTTGGATGAA-CTTCCG-CATTTGTCAAGCTTTTAC-AGGTTCTTTTACAACTTAG
193 CTCGTAGTTCTTGGATGAACCTT-CGAAATATG-AAAACTTTTACTA-GTTCTGTTACAACTTAG
* * * *
689 GTTCCTTAAAGCATTCTATGCA-ATCCATTCCTTCTA-CAAATTTT-CGAACATTCAATGTTC-G
255 GTTCCTTAAAGCATTC-AAG-ATATCCATTCCTTCGAGC-AATTTTGCGAACATTCAATGCTCAA
* * *
750 GAAAATCGCATCATTTGATCTAAATAGTTTGTCATTTTGTGAACAACTTTTGGTCTTTGAATTAA
317 G-AAATCGCATCACTTGATCTAAATAGTTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATTAA
** ** ** * *
815 AAACTTATTGACGTGGGATTTGTTTCTCTCTTGGTTCTTGGACGAGCTACCG
381 AAACTTATTGACGTAAGAACTGTTTCTCTCTCAGTTCTTAGACGAACTACCG
* * * *
867 AACTTGTCAAACTTTTACAAGTCCTTTTAAAACTTCGGTTCCTTGAAGT
1 AACTTGTCAAGCTTTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGT
916 GTATTATATA
Statistics
Matches: 401, Mismatches: 69, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
430 10 0.02
431 257 0.64
432 108 0.27
433 2 0.00
434 1 0.00
435 23 0.06
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (432 bp):
AACTTGTCAAGCTTTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAACCAA
TGCTTCAAGCAATATTCCAAACATTCCATGCTCGAGAAATCGAATCATTCGGTCAAAATAGTTTG
CCATTTCTTAAAAAAACTTTTGGTCACTGAATTAAAAACCTATTTACGTGTAAATTATTTCCCTC
GTAGTTCTTGGATGAACCTTCGAAATATGAAAACTTTTACTAGTTCTGTTACAACTTAGGTTCCT
TAAAGCATTCAAGATATCCATTCCTTCGAGCAATTTTGCGAACATTCAATGCTCAAGAAATCGCA
TCACTTGATCTAAATAGTTTGTCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACTTATTG
ACGTAAGAACTGTTTCTCTCTCAGTTCTTAGACGAACTACCG
Done.