Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005360.1 Kokia drynarioides strain JFW-HI SEQ_119342, 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, 600
Length: 1001
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.27
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:382 original size:215 final size:215
Alignment explanation
Indices: 11--1001 Score: 1037
Period size: 215 Copynumber: 4.7 Consensus size: 215
1 TGAATATTTC
* *
11 AAGGAACCAAAGTTATAACAGAACTCGTAAAAGTTTCACAAGTTCATAAGTTCATCCAAGAACCA
1 AAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGCTCATAAGTTCATCCAAGAACCA
* * * *
76 AAAGAGAAACAATATGACGTAAATAAGTTTTAAATTCAAAGACGAAAAGTTGTTTACAAAATGAC
66 AAAGAGAAACAATCTGATGCAAATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
* * * *
141 AAAGCATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATGGCTCGAAGGAA
131 AAACCATTTGGACCAAATGATGCGATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCGAAGGAA
* * *
206 TGGATCGTCATGAATACGTT
196 TGGATCGTCTTGAACACTTT
* *
226 AAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCATAAGTTCGTCCAAGAACCA
1 AAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGCTCATAAGTTCATCCAAGAACCA
*
291 AAAGAGAAACAATCTGATGCAAATAAGTTTTAAATTCAAAGGCCAAAAGTT-TTTACAAAAATGA
66 AAAGAGAAACAATCTGATGCAAATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTAC-AAAATGA
* *
355 CAAACCGTTTGGACCAAATGATGCGATTTCCCGAGCATCGAATGCTCGAAATATTGCTC-----A
130 CAAACCATTTGGACCAAATGATGCGATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCGAAGGA
*
415 A--G-T--T-TTGAACATTTT
195 ATGGATCGTCTTGAACACTTT
* * ** * * *
430 AAGGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTATCCAAGAACCA
1 AAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGCTCATAAGTTCATCCAAGAACCA
* * * * * * *
495 AAAGAGAAACAAGTCTTACT-TAAATAATTTTTTTAGTTTAAAAACCAAAAGTTGTTTAC-AAAT
66 AAAGAGAAACAA-TCTGA-TGCAAATAA-GTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAAT
* * * * * * * *
558 AACAAACTATTTGGACCAAATGATGCGATCTCCCAAGCATGGAATGTTTGAAAAATTACTCGAAG
128 GACAAACCATTTGGACCAAATGATGCGATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCGAAG
*
623 GAATGGATCGTCTTGAATACTTT
193 GAATGGATCGTCTTGAACACTTT
******************
646 AAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTNNNNNNNNNNNNNNNNNNTCCAAGAACCA
1 AAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGCTCATAAGTTCATCCAAGAACCA
*
711 AAAGAGAAACAATCTGATGCAAATAAGTTTTAAATTCAAAGGCCAAAAGTT-TTTACAAAAATGA
66 AAAGAGAAACAATCTGATGCAAATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTAC-AAAATGA
* * * * *
775 CAAACCGTTTGGATCAAATGATGCGATTTCCCGAGCATCGAATGCTCGAAATATTGCTCAAATGA
130 CAAACCATTTGGACCAAATGATGCGATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCGAAGGA
*
840 ATGGATCGTTTTGAACACTTT
195 ATGGATCGTCTTGAACACTTT
* * * ** * * * **
861 ATGGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTATTTAAGAACCA
1 AAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGCTCATAAGTTCATCCAAGAACCA
* * * * *
926 AAAGAGAAACAAGTCTCACT-TATATAAGTTCTT-AATTTAAAAACCAAAAGTTGTTTAC-AAAT
66 AAAGAGAAACAA-TCTGA-TGCAAATAAGTT-TTAAATTCAAAGACCAAAAGTTGTTTACAAAAT
*
988 GACAAACTATTTGG
128 GACAAACCATTTGG
Statistics
Matches: 627, Mismatches: 126, Indels: 46
0.78 0.16 0.06
Matches are distributed among these distances:
204 75 0.12
205 66 0.11
206 20 0.03
207 6 0.01
208 1 0.00
210 4 0.01
212 1 0.00
213 6 0.01
214 25 0.04
215 324 0.52
216 91 0.15
217 8 0.01
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.27
Consensus pattern (215 bp):
AAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGCTCATAAGTTCATCCAAGAACCA
AAAGAGAAACAATCTGATGCAAATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
AAACCATTTGGACCAAATGATGCGATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCGAAGGAA
TGGATCGTCTTGAACACTTT
Found at i:798 original size:420 final size:422
Alignment explanation
Indices: 1--1001 Score: 1382
Period size: 420 Copynumber: 2.4 Consensus size: 422
* * * * * ** * * * *
1 TGAATATTTCAAGGAACCAAAGTTATAACAGAACTCGTAAAAGTTTCACAAGTTCATAAGTTCAT
1 TGAACATTTTAAGGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTAT
* * * * * * *
66 CCAAGAACCAAAAGAGAAACAA-TATGACGTAAATAAGTTTTAAATTCAAAGACGAAAAGTTGTT
66 CCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAAGTTTTTAATTTAAAAACCAAAAGTTGTT
* *
130 TACAAAATGACAAAGC-ATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAAT
131 TAC-AAATGACAAA-CTATTTGGACCAAATGATGCGATCTCCCAAGCATGGAATGTTCGAAAAAT
*
194 GGCTCGAAGGAATGGATCGTCATGAATACGTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAG
194 GACTCGAAGGAATGGATCGTCATGAATACGTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAG
259 TTTCACAAGTTCATAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTGATGCAAATAAGTTTTAA
259 TTTCACAAGTTCATAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTGATGCAAATAAGTTTTAA
324 ATTCAAAGGCCAAAAGTTTTTACAAAAATGACAAACCGTTTGGACCAAATGATGCGATTTCCCGA
324 ATTCAAAGGCCAAAAGTTTTTACAAAAATGACAAACCGTTTGGACCAAATGATGCGATTTCCCGA
389 GCATCGAATGCTCGAAATATTGCTC-A-A-GTTT
389 GCATCGAATGCTCGAAATATTGCTCAAGACGTTT
420 TGAACATTTTAAGGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTAT
1 TGAACATTTTAAGGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTAT
* * *
485 CCAAGAACCAAAAGAGAAACAAGTCTTACTTAAATAATTTTTTTAGTTTAAAAACCAAAAGTTGT
66 CCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAA-GTTTTTAATTTAAAAACCAAAAGTTGT
* * *
550 TTACAAATAACAAACTATTTGGACCAAATGATGCGATCTCCCAAGCATGGAATGTTTGAAAAATT
130 TTACAAATGACAAACTATTTGGACCAAATGATGCGATCTCCCAAGCATGGAATGTTCGAAAAATG
* *
615 ACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGT
195 ACTCGAAGGAATGGATCGTCATGAATACGTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGT
******************
680 TTNNNNNNNNNNNNNNNNNNTCCAAGAACCAAAAGAGAAACAATCTGATGCAAATAAGTTTTAAA
260 TTCACAAGTTCATAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTGATGCAAATAAGTTTTAAA
*
745 TTCAAAGGCCAAAAGTTTTTACAAAAATGACAAACCGTTTGGATCAAATGATGCGATTTCCCGAG
325 TTCAAAGGCCAAAAGTTTTTACAAAAATGACAAACCGTTTGGACCAAATGATGCGATTTCCCGAG
810 CATCGAATGCTCGAAATATTGCTCAAATGAATGGATCGTTT
390 CATCGAATGCTCGAAATATTGCTC-----AA--GA-CGTTT
* *
851 TGAACACTTTATGGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTAT
1 TGAACATTTTAAGGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTAT
** * *
916 TTAAGAACCAAAAGAGAAACAAGTCTCACTTATATAAGTTCTTAATTTAAAAACCAAAAGTTGTT
66 CCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAAGTTTTTAATTTAAAAACCAAAAGTTGTT
981 TACAAATGACAAACTATTTGG
131 TACAAATGACAAACTATTTGG
Statistics
Matches: 511, Mismatches: 57, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
419 77 0.15
420 262 0.51
421 25 0.05
426 1 0.00
429 1 0.00
430 45 0.09
431 100 0.20
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.27
Consensus pattern (422 bp):
TGAACATTTTAAGGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTAT
CCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAAGTTTTTAATTTAAAAACCAAAAGTTGTT
TACAAATGACAAACTATTTGGACCAAATGATGCGATCTCCCAAGCATGGAATGTTCGAAAAATGA
CTCGAAGGAATGGATCGTCATGAATACGTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTT
TCACAAGTTCATAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTGATGCAAATAAGTTTTAAAT
TCAAAGGCCAAAAGTTTTTACAAAAATGACAAACCGTTTGGACCAAATGATGCGATTTCCCGAGC
ATCGAATGCTCGAAATATTGCTCAAGACGTTT
Done.