Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000443.1 Kokia drynarioides strain JFW-HI SEQ_111291, 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, 995
Length: 1659
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Found at i:633 original size:216 final size:213
Alignment explanation
Indices: 102--1646 Score: 1385
Period size: 216 Copynumber: 7.2 Consensus size: 213
92 TTTGGTAATG
* * * ** *** * * *
102 AAAAACTTATTTACATGAGAATTGTTTCTCAATTGGAAATTGGACGAACTTCTATATTTGACAAA
1 AAAAACCTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGAC-AA
* * * *
167 CTTTAACGAGTTCTTCTATAACTTTA-ATCTTTAAAGTATTCAT-ACGATCCATTCCTTCGAGCA
65 CTTTTACGAGTTCTTCTATAACTTCATTTC-TTAAAGTATTCATGACAATCCATTCCTTCGAGCA
* * * ** *
230 ATTTTCTGAACATTCCATG---GGGAAATCACATCATTTGTCTACATAGTTTGTCATTTGGTATA
129 ATTTTCCGAACATTCCATGCTCGAGAAATCACATCATTTGTCTAAATAGTTTGTCATTTTCTAAA
* *
292 CAAATTTTGGTCATTT-AGTT
194 CAACTTTTGGTC-TTTGAATT
* * * * * * *
312 AAAAACTTATTTACGTGAGAATT-TATTATCTCTTGGATCATGGACAAACTTCCTAACTTCG-CA
1 AAAAACCTATTTACGTGAGAGTTGT-TTCTCTCTTGGTTCTTGGACGAACTTCCAAACTT-GAC-
* * * *
375 AACTCTTACTAGTTGTT-TAATAACTTTCA-TCCATTAAAGTATTCATGA-AGATCCATTCCTTC
63 AACTTTTACGAGTTCTTCT-ATAAC-TTCATTTC-TTAAAGTATTCATGACA-ATCCATTCCTTC
* * * ** *
437 TAGCAATTTTCCGAACATTCCAGGCACGAGAAATCGTATCATTATGTCTAAACAGTTTGTCATTT
124 GAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACATCATT-TGTCTAAATAGTTTGTCATTT
*
502 TCTAAACAACTTTTGGTCCTTGAATT
188 TCTAAACAACTTTTGGTCTTTGAATT
* * * * *
528 TAAAACCTATTTATGTGAGAGTTGTTTCTCTTTTGGCTCTTAGACGAACTTCCAAACTTGACATA
1 AAAAACCTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACA-A
* * * *
593 CTTTTACGAGTTCTTCTATAACTGTGATTTCTTGAAGTATTCAAGACAATCCATTCCTTAGAGCA
65 CTTTTACGAGTTCTTCTATAACT-TCATTTCTTAAAGTATTCATGACAATCCATTCCTTCGAGCA
** * *
658 ATTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGTTCTAAATACTTTGTCATTTTCTAA
129 ATTTTCCGAACATTCCATGCTCGAGAAATCACATCATTTG-TCTAAATAGTTTGTCATTTTCTAA
** * *
723 ATGACTTTTAGTCTTTGAATG
193 ACAACTTTTGGTCTTTGAATT
* * *** * *
744 AAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACAAACTTTTGAACTTTTAAAA
1 AAAAACCTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAAC-TTGACAA
* * * * *
809 CTTTTGTC-AGTTCATCTATCACTTTCATTCCTT-AAGTATTCATGACAATCCATTCCTTCAAGC
65 CTTTT-ACGAGTTCTTCTATAAC-TTCATTTCTTAAAGTATTCATGACAATCCATTCCTTCGAGC
* * * *
872 AATTTTCCGAACGTTCCATGCTCGAGAAATAACATCATTTGATCTAAATAGTTTGCCATTTTGTA
128 AATTTTCCGAACATTCCATGCTCGAGAAATCACATCATTTG-TCTAAATAGTTTGTCATTTTCTA
*
937 AACAACTTTTGGTCTTTAAATT
192 AACAACTTTTGGTCTTTGAATT
* * * * * * * *
959 AAAATCTTATTTACATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGATGAA
1 AAAAACCTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGA-CAA
* * * * *
1024 GTTTTACAAGTTCTTTTAAAACTTCAGTTCCTTAAAGTATTCATGACAATCCATTCCTTCGAGCA
65 CTTTTACGAGTTCTTCTATAACTTCA-TTTCTTAAAGTATTCATGACAATCCATTCCTTCGAGCA
* * * * **
1089 ATTTTCCGAGCATTCCATGCAC-AGCAAATCGCATCATTTTATCTAAATAGTTTGTCATTTGGTA
129 ATTTTCCGAACATTCCATGCTCGAG-AAATCACATCA-TTTGTCTAAATAGTTTGTCATTTTCTA
1153 AACAACTTTTGGTCTTTGAATT
192 AACAACTTTTGGTCTTTGAATT
* * * *
1175 AAAAACCTATTTACGTGAGAGTTTTTTTTTCTCTTGGTTCTTAGATGAACTTCCAAACTTGACGA
1 AAAAACCTATTTACGTGAGAG-TTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGAC-A
* * * * * *
1240 ACTTTTACGAGTTCTTCAATAACTTCGGTTTCTTAAAGTATTAAGGACAACCCATT-CTTAGAGC
64 ACTTTTACGAGTTCTTCTATAACTTC-ATTTCTTAAAGTATTCATGACAATCCATTCCTTCGAGC
** * * * *
1304 AATTTTTTGAACATTACATACTCGGGAAATCACATCATTTGGTCTAAATACTTTGTCATTTTCTA
128 AATTTTCCGAACATTCCATGCTCGAGAAATCACATCATTT-GTCTAAATAGTTTGTCATTTTCTA
* *
1369 AACTACTTTTGGTCTTTGAATG
192 AACAACTTTTGGTCTTTGAATT
* * * * ** *
1391 AAAAAACTTTCTTACGTGAGAGTTGTTTCTATCTTGGTTCTTGGACGATCTTCTGAACTTGGCAA
1 AAAAACCTAT-TTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAA
* * * * *
1456 GCTTTTTACGATTTCTTTTATAACTTCAGTTCAATAAAGTATTCATGACGATCCATTCCTTCGAG
65 -C-TTTTACGAGTTCTTCTATAACTTCATTTC-TTAAAGTATTCATGACAATCCATTCCTTCGAG
* * * * ** * * * *
1521 AAATTTTTCAAAAATTTAATGCTTGGGAAATCGCATCATTTTTTTTCTAAACTA-TTTGTCATTT
127 CAATTTTCCGAACATTCCATGCTCGAGAAATCACATCA---TTTGTCTAAA-TAGTTTGTCATTT
** * * *
1585 GGTAAGCAACTTTTGGGCTTTGAATG
188 TCTAAACAACTTTTGGTCTTTGAATT
** * *
1611 AAAAAGTTATTTACATGAGAATTGTTTCTCTCTTGG
1 AAAAACCTATTTACGTGAGAGTTGTTTCTCTCTTGG
1647 ATATTGGATG
Statistics
Matches: 1088, Mismatches: 205, Indels: 75
0.80 0.15 0.05
Matches are distributed among these distances:
209 2 0.00
210 65 0.06
211 18 0.02
212 34 0.03
214 8 0.01
215 200 0.18
216 509 0.47
217 145 0.13
218 35 0.03
219 23 0.02
220 44 0.04
221 5 0.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (213 bp):
AAAAACCTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAC
TTTTACGAGTTCTTCTATAACTTCATTTCTTAAAGTATTCATGACAATCCATTCCTTCGAGCAAT
TTTCCGAACATTCCATGCTCGAGAAATCACATCATTTGTCTAAATAGTTTGTCATTTTCTAAACA
ACTTTTGGTCTTTGAATT
Found at i:941 original size:431 final size:428
Alignment explanation
Indices: 103--1646 Score: 1449
Period size: 431 Copynumber: 3.6 Consensus size: 428
93 TTGGTAATGA
* * * ** *** * * *
103 AAAACTTATTTACATGAGAATTGTTTCTCAATTGGAAATTGGACGAACTTCTATATTTGACAAAC
1 AAAACCTATTTACGTGAGAGTTGTTTCTCTTTTGGTTCTTGGACGAACTTCCAAACTTGAC-AAC
* * * * *
168 TTTAACGAGTTCTTCTATAACTTTA-ATCTTTAAAGTATTC-ATACGATCCATTCCTTCGAGCAA
65 TTTTACGAGTTCTTCTATAACTTCATTTC-TTAAAGTATTCAAGACAATCCATTCCTTCGAGCAA
* * * * *
231 TTTTCTGAACATTCCATG---GGGAAATCACATCATTTG-TCTACATAGTTTGTCATTTGGTATA
129 TTTTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGTTCTAAATAGTTTGTCATTTGGTAAA
* * * * * *
292 CAAATTTTGGTCATTT-AGTTAAAAACTTATTTACGTGAGAATT-TATTATCTCTTGGATCATGG
194 CAACTTTTGGTC-TTTGAATGAAAAACTTATTTACGTGAGAATTGT-TTCTCTCTTGGTTCTTGG
* * * * * *
355 ACAAACTTCCTAACTTCGCAAACTCTTACTAGTT-GTTTAATAACTTTCA-TCCATTAAAGTATT
257 ACAAACTT-CTAACTTTGAAAACTTTTACGAGTTCATCT-ATAACTTTCATTCC-TTAAAGTATT
* * * **
418 CATGA-AGATCCATTCCTTCTAGCAATTTTCCGAACATTCCAGGCACGAGAAATCGTATCATTAT
319 CATGACA-ATCCATTCCTTCAAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACATCATT-T
*
482 GTCTAAACAGTTTGTCATTTTCTAAACAACTTTTGGTCCTTGAATTT
382 GTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCCTTGAATTT
* * *
529 AAAACCTATTTATGTGAGAGTTGTTTCTCTTTTGGCTCTTAGACGAACTTCCAAACTTGACATAC
1 AAAACCTATTTACGTGAGAGTTGTTTCTCTTTTGGTTCTTGGACGAACTTCCAAACTTGACA-AC
* * *
594 TTTTACGAGTTCTTCTATAACTGTGATTTCTTGAAGTATTCAAGACAATCCATTCCTTAGAGCAA
65 TTTTACGAGTTCTTCTATAACT-TCATTTCTTAAAGTATTCAAGACAATCCATTCCTTCGAGCAA
** * **
659 TTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGTTCTAAATACTTTGTCATTTTCTAAA
129 TTTTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGTTCTAAATAGTTTGTCATTTGGTAAA
** * *
724 TGACTTTTAGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGAC
194 CAACTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAC
* * * *
789 AAACTTTTGAACTTTTAAAACTTTTGTC-AGTTCATCTATCACTTTCATTCCTT-AAGTATTCAT
259 AAACTTCT-AACTTTGAAAACTTTT-ACGAGTTCATCTATAACTTTCATTCCTTAAAGTATTCAT
* *
852 GACAATCCATTCCTTCAAGCAATTTTCCGAACGTTCCATGCTCGAGAAATAACATCATTTGATCT
322 GACAATCCATTCCTTCAAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACATCATTTG-TCT
* * * *
917 AAATAGTTTGCCATTTTGTAAACAACTTTTGGT-CTTTAAATT
386 AAATAGTTTGTCATTTTCTAAACAACTTTTGGTCCTTGAATTT
* * * * * *
959 AAAATCTTATTTACATGAGAATTGTTTCTCTCTTT-GTTCTTGGACGAACTTTCGAACTTGATGA
1 AAAA-CCTATTTACGTGAGAGTTGTTTCTCT-TTTGGTTCTTGGACGAACTTCCAAACTTGA-CA
* * * * * *
1023 AGTTTTACAAGTTCTTTTAAAACTTCAGTTCCTTAAAGTATTCATGACAATCCATTCCTTCGAGC
63 ACTTTTACGAGTTCTTCTATAACTTCA-TTTCTTAAAGTATTCAAGACAATCCATTCCTTCGAGC
* *
1088 AATTTTCCGAGCATTCCATGCAC-AGCAAATCGCATCATTT-TATCTAAATAGTTTGTCATTTGG
127 AATTTTCCGAACATTCCATGCTCGAG-AAATCGCATCATTTGT-TCTAAATAGTTTGTCATTTGG
* * * * *
1151 TAAACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAGAGTTTTTTTTTCTCTTGGTTCT
190 TAAACAACTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGA-ATTGTTTCTCTCTTGGTTCT
* ** * * * * * *
1216 TAGATGAACTTCCAAAC-TTGACGAACTTTTACGAGTTCTTCAATAAC-TTCGGTTTCTTAAAGT
254 TGGACAAACTT-CTAACTTTGA-AAACTTTTACGAGTTCATCTATAACTTTC-ATTCCTTAAAGT
* * * ** * * *
1279 ATTAAGGACAACCCATT-CTT-AGAGCAATTTTTTGAACATTACATACTCGGGAAATCACATCAT
316 ATTCATGACAATCCATTCCTTCA-AGCAATTTTCCGAACATTCCATGCTCGAGAAATCACATCAT
* * * **
1342 TTGGTCTAAATACTTTGTCATTTTCTAAACTACTTTTGGTCTTTGAATGA
380 TT-GTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCCTTGAATTT
* * * * * ** *
1392 AAAAACTTTCTTACGTGAGAGTTGTTTCTATCTTGGTTCTTGGACGATCTTCTGAACTTGGCAAG
1 AAAACCTAT-TTACGTGAGAGTTGTTTCTCTTTTGGTTCTTGGACGAACTTCCAAACTTGACAA-
* * * * * * *
1457 CTTTTTACGATTTCTTTTATAACTTCAGTTCAATAAAGTATTCATGACGATCCATTCCTTCGAGA
64 C-TTTTACGAGTTCTTCTATAACTTCATTTC-TTAAAGTATTCAAGACAATCCATTCCTTCGAGC
* * * ** * * *
1522 AATTTTTCAAAAATTTAATGCTTGGGAAATCGCATCATTTTTTTTCTAAACTA-TTTGTCATTTG
127 AATTTTCCGAACATTCCATGCTCGAGAAATCGCATCA--TTTGTTCTAAA-TAGTTTGTCATTTG
* * * *
1586 GTAAGCAACTTTTGGGCTTTGAATGAAAAAGTTATTTACATGAGAATTGTTTCTCTCTTGG
189 GTAAACAACTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGG
1647 ATATTGGATG
Statistics
Matches: 914, Mismatches: 163, Indels: 73
0.79 0.14 0.06
Matches are distributed among these distances:
425 1 0.00
426 71 0.08
427 12 0.01
428 39 0.04
430 18 0.02
431 308 0.34
432 235 0.26
433 76 0.08
434 78 0.09
435 14 0.02
436 59 0.06
437 3 0.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (428 bp):
AAAACCTATTTACGTGAGAGTTGTTTCTCTTTTGGTTCTTGGACGAACTTCCAAACTTGACAACT
TTTACGAGTTCTTCTATAACTTCATTTCTTAAAGTATTCAAGACAATCCATTCCTTCGAGCAATT
TTCCGAACATTCCATGCTCGAGAAATCGCATCATTTGTTCTAAATAGTTTGTCATTTGGTAAACA
ACTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAA
ACTTCTAACTTTGAAAACTTTTACGAGTTCATCTATAACTTTCATTCCTTAAAGTATTCATGACA
ATCCATTCCTTCAAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACATCATTTGTCTAAATA
GTTTGTCATTTTCTAAACAACTTTTGGTCCTTGAATTT
Done.