Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007094.1 Kokia drynarioides strain JFW-HI SEQ_121703, 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, 822
Length: 1371
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Found at i:740 original size:216 final size:216
Alignment explanation
Indices: 174--1368 Score: 1496
Period size: 216 Copynumber: 5.5 Consensus size: 216
164 AGTTTGTCAG
* * * **
174 TTTGCTCTTTGAATTAAAAACTGATTTACATGAGAATTACTTCTCTCTTGGTTCTTGGACGAACT
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACT
* ** * *
239 TCCGAACTAGTCAAACTTTTACGAGTTCTTAGATAACTT-AGTTTCCTTAAAGTATTCAAGACAA
66 TCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCTG-TTCCTTAAAGTATTCAAGACGA
* * * * *
303 TCCATTCCTTCGAGAAATTTTCT-AAGCATTCCATGCTCGGGAAATCTCATGATTTGTTCCAAAT
130 TCCATTCCTTCGAGCAATTTTTTGAA-CATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAAT
*
367 AGTTTGTCATTTTGTAAGCAACT
194 AGTTTGTCATTTTGTAAACAACT
* * * *
390 TTTGGTCTTTAAAATAAAAAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAAC
1 TTTGGTCTTT-GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC
* * * * * *
455 TTCTGAACTTCTCATACTTTTACGAGTTCTTTGATAACTT-TGGTTCCTTAGAGTATTCAAGAAG
65 TTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCT-GTTCCTTAAAGTATTCAAGACG
* ** * *
519 ATCCATTCTTTCGAGCAATTTTTTGAACATTCCATGCTCGAAAAAACGCATCATTTGCTCCAAAT
129 ATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAAT
*
584 AGTTTGTCATTTTGTAAATAACT
194 AGTTTGTCATTTTGTAAACAACT
* * * *
607 TTTGGTGTTTGAATTAAAGACTTATTGACGTGAGAATTGTTTCTCT-TTCGATTCTTGGACGAAC
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT-GGTTCTTGGACGAAC
* * * * *
671 -ACTCAAACTTGCCAAACATTTACGAGTTCTTTTATAACTTCTGCTCCTTAAAGTATTCAAGACG
65 TTC-CGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCTGTTCCTTAAAGTATTCAAGACG
* * * * * *
735 ATCCATTCCTTCAAGCAATTTTCTGAAGATTTCATGCTCAGGAAATTGCATCATTT-GTCCAAAT
129 ATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAAT
799 AGTTTGTCATTTTGTAAACAACT
194 AGTTTGTCATTTTGTAAACAACT
*
822 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACT
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACT
* * * * * * *
887 TCCGAAATTTTTAAACTGTTACGAGTTCTTTTATAACATCGGTTCCTTAAAGTATTCAAGATGAT
66 TCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCTGTTCCTTAAAGTATTCAAGACGAT
* *
952 CGATTCCTTCGAGCAATTTTTTGAACATTCC-TGGCTCGGGAAATCGCATCATCTGGTCCAAATA
131 CCATTCCTTCGAGCAATTTTTTGAACATTCCAT-GCTCGGGAAATCGCATCATTTGGTCCAAATA
1016 GTTTGTCATTTTGTAAACAACT
195 GTTTGTCATTTTGTAAACAACT
* ** * *
1038 TTGGGTCTTTGAATTAAAAACTTCCTTAGGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACT
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACT
* * * *
1103 TACGAAGTTGTCAAACTTTTACGAGTTATTTTATAACTTC-GATTCCTTAAAGTATTCAAGACAA
66 TCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCTG-TTCCTTAAAGTATTCAAGACGA
* * * *
1167 TCCATTCCGTCAAACAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCCAAATA
130 TCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATA
*
1232 GTTTGTCATTTTATAAACAACT
195 GTTTGTCATTTTGTAAACAACT
* * * * * * *
1254 TTTGCTCTTTGAAATAAAAACTTATTTACCTGAGAAATGTTTCTCTATTGGTTCTT-CACCAAAC
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGA-CGAAC
* *
1318 TTCCGAACATGTCAAACTTTTAAGAGTT-TTTTATAACTT-TGTTTCC-TAAAG
65 TTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCTG-TTCCTTAAAG
1369 GTA
Statistics
Matches: 841, Mismatches: 124, Indels: 30
0.85 0.12 0.03
Matches are distributed among these distances:
214 6 0.01
215 201 0.24
216 447 0.53
217 184 0.22
218 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (216 bp):
TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACT
TCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCTGTTCCTTAAAGTATTCAAGACGAT
CCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAG
TTTGTCATTTTGTAAACAACT
Found at i:1002 original size:431 final size:427
Alignment explanation
Indices: 1--1368 Score: 1587
Period size: 431 Copynumber: 3.2 Consensus size: 427
* * * * *
1 GTGAGAATTATTTCTCTCTTGGTTCTTCGACAAACTTTC-AAACTTGTCAAACTTTTACAAGTTC
1 GTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAAA-TTCTCAAACTTTTACGAGTTC
* * * * *
65 TTTTATAACTTTGGTTCCTTAAAGTATTCAAGTTTATTCATTCTTTCGA-CCACTTTTCGAACAT
65 TTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGA-TCATTCTTTCGAGCAATTTTTTGAACA-
** * * *
129 TTAATGCTCTGGAAATTGCATCATTT-CGTCCAAATAGTTTGTCA----G--------TTTGCTC
128 TTCCTGCTCGGGAAATCGCATCATTTGC-TCCAAATAGTTTGTCATTTTGTAAAAACTTTTGGTC
* * ** *
181 TTTGAATTAAAAACTGATTTACATGAGAATTACTTCTCTCTTGGTTCTTGGACGAACTTCCGAAC
192 TTTGAATTAAAAACTTA-TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTACGAAC
* ** * *
246 TAGTCAAACTTTTACGAGTTCTTAGATAACTTAGTTTCCTTAAAGTATTCAAGACAATCCATTCC
256 TTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACAATCCATTCC
* * *
311 TTCGAGAAATTTTCT-AAGCATTCCATGCTCGGGAAATCT-CATGATTTGTTCCAAATAGTTTGT
321 TTCAAGCAATTTTCTGAAG-ATTCCATGCTCGGGAAAT-TGCATCATTTG-TCCAAATAGTTTGT
* * * *
374 CATTTTGTAAGCAACTTTTGGTCTTTAAAATAAAAAACTTATATAC
383 CATTTTGTAAACAACTTTTGGTCTTT-GAATTAAAAACTTATTTAC
* * * * *
420 GTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTCTGAACTTCTCATACTTTTACGAGTTCT
1 GTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAAATTCTCAAACTTTTACGAGTTCT
* * *
485 TTGATAACTTTGGTTCCTTAGAGTATTCAAGAAGATCCATTCTTTCGAGCAATTTTTTGAACATT
66 TTTATAACTTTGGTTCCTTAAAGTATTCAAGATGAT-CATTCTTTCGAGCAATTTTTTGAACATT
** * *
550 CCATGCTCGAAAAAACGCATCATTTGCTCCAAATAGTTTGTCATTTTGTAAATAACTTTTGGTGT
130 CC-TGCTCGGGAAATCGCATCATTTGCTCCAAATAGTTTGTCATTTTGTAAA-AACTTTTGGTCT
* * * *
615 TTGAATTAAAGACTTATTGACGTGAGAATTGTTTCTCT-TTCGATTCTTGGACGAACACT-CAAA
193 TTGAATTAAAAACTTATT-ACGTGAGAATTGTTTCTCTCTT-GGTTCTTGGACGAAC-TTACGAA
* * * *
678 CTTGCCAAACATTTACGAGTTCTTTTATAACTTCTG-CTCCTTAAAGTATTCAAGACGATCCATT
255 CTTGTCAAACTTTTACGAGTTCTTTTATAACTTC-GATTCCTTAAAGTATTCAAGACAATCCATT
* *
742 CCTTCAAGCAATTTTCTGAAGATTTCATGCTCAGGAAATTGCATCATTTGTCCAAATAGTTTGTC
319 CCTTCAAGCAATTTTCTGAAGATTCCATGCTCGGGAAATTGCATCATTTGTCCAAATAGTTTGTC
807 ATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAC
384 ATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAC
* * *
851 GTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAAATTTTTAAACTGTTACGAGTTCT
1 GTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAAATTCTCAAACTTTTACGAGTTCT
* * *
916 TTTATAACATCGGTTCCTTAAAGTATTCAAGATGATCGATTCCTTCGAGCAATTTTTTGAACATT
66 TTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATC-ATTCTTTCGAGCAATTTTTTGAACATT
* * *
981 CCTGGCTCGGGAAATCGCATCATCTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTGGGTCT
130 CCT-GCTCGGGAAATCGCATCATTTGCTCCAAATAGTTTGTCATTTTGTAAA-AACTTTTGGTCT
* * * *
1046 TTGAATTAAAAACTTCCTTAGGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTACGAAGT
193 TTGAATTAAAAACTT-ATTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTACGAACT
* *
1111 TGTCAAACTTTTACGAGTTATTTTATAACTTCGATTCCTTAAAGTATTCAAGACAATCCATTCCG
257 TGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACAATCCATTCCT
* * * * *
1176 TCAAACAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCAT
322 TCAAGCAATTTTCTGAAGATTCCATGCTCGGGAAATTGCATCATTT-GTCCAAATAGTTTGTCAT
* * *
1241 TTTATAAACAACTTTTGCTCTTTGAAATAAAAACTTATTTAC
386 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAC
* * * * * * * *
1283 CTGAGAAATGTTTCTCTATTGGTTCTT-CACCAAACTTCCGAACA-TGTCAAACTTTTAAGAGTT
1 GTGAGAATTATTTCTCTCTTGGTTCTTGGA-CGAACTTCCGAA-ATTCTCAAACTTTTACGAGTT
*
1346 -TTTTATAACTTTGTTTCC-TAAAG
64 CTTTTATAACTTTGGTTCCTTAAAG
1369 GTA
Statistics
Matches: 805, Mismatches: 111, Indels: 55
0.83 0.11 0.06
Matches are distributed among these distances:
418 1 0.00
419 95 0.12
420 46 0.06
421 1 0.00
424 1 0.00
430 9 0.01
431 346 0.43
432 154 0.19
433 147 0.18
434 5 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (427 bp):
GTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAAATTCTCAAACTTTTACGAGTTCT
TTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCATTCTTTCGAGCAATTTTTTGAACATTC
CTGCTCGGGAAATCGCATCATTTGCTCCAAATAGTTTGTCATTTTGTAAAAACTTTTGGTCTTTG
AATTAAAAACTTATTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTACGAACTTGTC
AAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACAATCCATTCCTTCAA
GCAATTTTCTGAAGATTCCATGCTCGGGAAATTGCATCATTTGTCCAAATAGTTTGTCATTTTGT
AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAC
Found at i:1257 original size:647 final size:635
Alignment explanation
Indices: 1--1310 Score: 1648
Period size: 647 Copynumber: 2.0 Consensus size: 635
* * ** * *
1 GTGAGAATTATTTCTCTCTTGGTTCTTCGACAAACTTTCAAACTTGTCAAACTTTTACAAGTTCT
1 GTGAGAATTGTTTCTCTCTTGATTCTTCGACAAACACTCAAACTTGCCAAACATTTACAAGTTCT
* *** * * * *
66 TTTATAACTTTGGTTCCTTAAAGTATTCAAGTTTATTCATTCTTTCGACCACTTTTCGAACATTT
66 TTTATAACTTTGGCTCCTTAAAGTATTCAAGACGATCCATTCCTTCAACCAATTTTCGAACATTT
*
131 AATGCTCTGGAAATTGCATCATTTCGTCCAAATAGTTTGTCAGTTTGCTCTTTGAATTAAAAACT
131 AATGCTCAGGAAATTGCATCATTTCGTCCAAATAGTTTGTCAGTTTGCTCTTTGAATTAAAAACT
* *
196 GATTTACATGAGAATTACTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTAGTCAAACTTTTAC
196 GATTTACATGAGAATTACTTCTCTCTTGGTTCTTGGACGAACTTCCGAAATAGTCAAACTGTTAC
* *
261 GAGTTCTTAGATAACTTAGTTTCCTTAAAGTATTCAAGACAATCCATTCCTTCGAGAAATTTTCT
261 GAGTTCTTAGATAACATAGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCGAGAAATTTTCT
* * * * *
326 AAGCATTCCATGCTCGGGAAATCTCATGATTTGTTCCAAATAGTTTGTCATTTTGTAAGCAACTT
326 AAGCATTCCATGCTCGGGAAATCGCATCATCTGGTCCAAATAGTTTGTCATTTTGTAAACAACTT
*
391 TTGGTCTTTAAAATAAAAAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACT
391 TGGGTCTTTAAAATAAAAAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACT
* * * * *
456 TCTGAACTTCTCATACTTTTACGAGTTCTTTGATAACTTTGGTTCCTTAGAGTATTCAAGAAGAT
456 TCTGAACTTCTCAAACTTTTACGAGTTATTTGATAACTTCGATTCCTTAAAGTATTCAAGAAGAT
** * *
521 CCATTCTTTCGAGCAATTTTTTGAACATTCCATGCTCGAAAAAACGCATCATTTGCTCCAAATAG
521 CCATTCCGTCAAACAATTTTTTGAACATTCCATGCTCGAAAAAACGCATCATTTGCTCCAAATAG
* * * * * *
586 TTTGTCATTTTGTAAATAACTTTTGGTGTTTGAATTAAAGACTTATTGAC
586 TTTGTCATTTTATAAACAACTTTTGCTCTTTGAAATAAAAACTTATTGAC
* * *
636 GTGAGAATTGTTTCTCT-TTCGATTCTTGGACGAACACTCAAACTTGCCAAACATTTACGAGTTC
1 GTGAGAATTGTTTCTCTCTT-GATTCTTCGACAAACACTCAAACTTGCCAAACATTTACAAGTTC
* *
700 TTTTATAACTTCT-GCTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTCTGAAGA
65 TTTTATAACTT-TGGCTCCTTAAAGTATTCAAGACGATCCATTCCTTCAACCAATTTTC-GAACA
* *
764 TTTCATGCTCAGGAAATTGCATCATTT-GTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGT
128 TTTAATGCTCAGGAAATTGCATCATTTCGTCCAAATAGTTTGTCA----G---------TTTGCT
* * *
828 CTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAA
180 CTTTGAATTAAAAACTGATTTACATGAGAATTACTTCTCTCTTGGTTCTTGGACGAACTTCCGAA
** * ** * ** *
893 ATTTTTAAACTGTTACGAGTTCTTTTATAACATCGGTTCCTTAAAGTATTCAAGATGATCGATTC
245 ATAGTCAAACTGTTACGAGTTCTTAGATAACATAGGTTCCTTAAAGTATTCAAGACAATCCATTC
* *
958 CTTCGAGCAATTTTTTGAA-CATTCC-TGGCTCGGGAAATCGCATCATCTGGTCCAAATAGTTTG
310 CTTCGAGAAATTTTCT-AAGCATTCCAT-GCTCGGGAAATCGCATCATCTGGTCCAAATAGTTTG
* * * *
1021 TCATTTTGTAAACAACTTTGGGTCTTT-GAATTAAAAACTTCCT-TAGGTGAGAATTGTTTCTCT
373 TCATTTTGTAAACAACTTTGGGTCTTTAAAATAAAAAACTT-ATATACGTGAGAATTGTTTCTCT
* * * * *
1084 CTTGGTTCTTGGCCGAACTTAC-GAAGTTGTCAAACTTTTACGAGTTATTTTATAACTTCGATTC
437 CTTGGTTCTCGGACGAACTT-CTGAACTTCTCAAACTTTTACGAGTTATTTGATAACTTCGATTC
* ** *
1148 CTTAAAGTATTCAAGACA-ATCCATTCCGTCAAACAATTTTTTGAACATTCCATGCTTGGGAAAT
501 CTTAAAGTATTCAAGA-AGATCCATTCCGTCAAACAATTTTTTGAACATTCCATGCTCGAAAAAA
*
1212 CGCATCATTTGGTCCAAATAGTTTGTCATTTTATAAACAACTTTTGCTCTTTGAAATAAAAACTT
565 CGCATCATTTGCTCCAAATAGTTTGTCATTTTATAAACAACTTTTGCTCTTTGAAATAAAAACTT
*
1277 ATTTAC
630 ATTGAC
* * * *
1283 CTGAGAAATGTTTCTCTATTGGTTCTTC
1 GTGAGAATTGTTTCTCTCTTGATTCTTC
1311 ACCAAACTTC
Statistics
Matches: 573, Mismatches: 80, Indels: 32
0.84 0.12 0.05
Matches are distributed among these distances:
634 2 0.00
635 116 0.20
636 30 0.05
639 1 0.00
647 221 0.39
648 201 0.35
649 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (635 bp):
GTGAGAATTGTTTCTCTCTTGATTCTTCGACAAACACTCAAACTTGCCAAACATTTACAAGTTCT
TTTATAACTTTGGCTCCTTAAAGTATTCAAGACGATCCATTCCTTCAACCAATTTTCGAACATTT
AATGCTCAGGAAATTGCATCATTTCGTCCAAATAGTTTGTCAGTTTGCTCTTTGAATTAAAAACT
GATTTACATGAGAATTACTTCTCTCTTGGTTCTTGGACGAACTTCCGAAATAGTCAAACTGTTAC
GAGTTCTTAGATAACATAGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCGAGAAATTTTCT
AAGCATTCCATGCTCGGGAAATCGCATCATCTGGTCCAAATAGTTTGTCATTTTGTAAACAACTT
TGGGTCTTTAAAATAAAAAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACT
TCTGAACTTCTCAAACTTTTACGAGTTATTTGATAACTTCGATTCCTTAAAGTATTCAAGAAGAT
CCATTCCGTCAAACAATTTTTTGAACATTCCATGCTCGAAAAAACGCATCATTTGCTCCAAATAG
TTTGTCATTTTATAAACAACTTTTGCTCTTTGAAATAAAAACTTATTGAC
Done.