Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010484.1 Kokia drynarioides strain JFW-HI SEQ_125387, 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: 1863
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Found at i:406 original size:216 final size:216
Alignment explanation
Indices: 1--1860 Score: 2018
Period size: 215 Copynumber: 8.7 Consensus size: 216
* * * *
1 GAACAAACAGAGAAACAATTCTCACGTAAATAAGTATTTAATTCAAAGACAAAAACTTGTTTGCA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
* ** *
66 AAAAGACAAACTATTTAGACCAAATGATGTGATTTGTCGAGCATGGAATGTT-AGAAAAATAGCT
66 AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCG-AAAATAGCT
* * ** ** * * *
130 CGAAGGAGTGGATCGCCTTGAATACTTTATTGATCCGAAGTTATAAAAGACCTAGTAAAAGTTTG
130 CTAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGAAGTTAAAAAAGAACTCGTAAAAGTTTG
*
195 ACAAGTTGGAAAGTTCGTCCAA
195 ACAAGTTCGAAAGTTCGTCCAA
* * *
217 GAACGAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAATTTGTTTACA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
* * * * * * **
282 AAATTATAAACTATTTAGACCAAATAATTTGATTTCCCGACCATGGAATGTTCCGAAATTTTCTC
66 AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCGAAAATAGCTC
* * * * *
347 TAAGGAATGGATCTTGTTGAATACTGTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTGA
131 TAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGAAGTTAAAAAAGAACTCGTAAAAGTTTGA
*
412 CAAGTTTGAAAGTTCGTCCAA
196 CAAGTTCGAAAGTTCGTCCAA
* * * *
433 GAACAAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTATTTCAAAGACCAAAACTTGTTTGCG
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
* * * * * * *
498 AAATGATAAACTATTTAAACCAAATGATGCGATTTCACAAGCATGGAATGTT-CGAAAAATTGTT
66 AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCG-AAAATAGCT
* * * * * * * * * * *
562 CGAA-GAATTGTTCGTCTTGAATATTTTAAGTATCCGATGTTATAGAAGAACTAGTAAAAGTTTG
130 CTAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGAAGTTAAAAAAGAACTCGTAAAAGTTTG
*
626 ACAAGTTCGGAAGTTCGTCCAA
195 ACAAGTTCGAAAGTTCGTCCAA
* * * *
648 GAACAAAGAGAGAAACAATTATCACGTAAATAAGTATTTAATTCGAAGACCAAAACTTGTTTGCA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
* * * *
713 AAAAGACAAACTATTTAGACCAAATGATGCGATTTGCCGAGCATGGAATGTTCGGAAAATAGCTC
66 AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCGAAAATAGCTC
* * * * * * *
778 AAAGAAATGGATCGTCTTGAATACTTTATGGATCC-AGAGTTATAAAAG-AC-C--AAAATTTTC
131 TAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGA-AGTTAAAAAAGAACTCGTAAAAGTTTG
* * *
838 ACAAGTACGGAAGTTCGTCTAA
195 ACAAGTTCGAAAGTTCGTCCAA
* * * * *
860 GAAC-GA-AGAGAAACAATTCTCACATATATAAGTTTTTAATTCGAAGACCAAAATTTGTTTACA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
* * * * * *
923 AAATAACAAACTATTTAGACCAAATGATTTGATTTCCCGAGGATGGAATGTTCGGAAATTTGCTC
66 AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCGAAAATAGCTC
* * ** * * * * * *
988 TAATGAATGGATCTTGTTGAATACTTTACAGAGCCAAATTTAAAAAATAGCTCGTAAAATTTTGA
131 TAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGAAGTTAAAAAAGAACTCGTAAAAGTTTGA
* *
1053 CAAGTTTGAATGTTCGTCCAGA
196 CAAGTTCGAAAGTTCGTCCA-A
* * * * * * *
1075 AAACAAAGAGAGAAACAATTCTCACATAAATAAGGTTTTAGTACAAAGACCAAAGCTTGTTTGCA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
* * * * * *
1140 AAATGATAAACAATATAGACCAAATGATGCGATTTTCCAAGCATGGAATGTT-CGAAAGA-A---
66 AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCGAAA-ATAGCT
* * * * * * * * *
1200 -T-A-G-ATCG-TCTTC---AATACTTTAAGTATCTGATGGTATAGAAGAACTAGTAAAAGTTTG
130 CTAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGAAGTTAAAAAAGAACTCGTAAAAGTTTG
*
1257 ACAAGTTCAAAAGTTCGTCCAA
195 ACAAGTTCGAAAGTTCGTCCAA
* * * *
1279 GAACAAAAAGAGAAACAATTCTGACGTAAATAAGTATTTAATTCAAAGAACAAAACTTGTTTACA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
* * *
1344 AAATTACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAGTGTT-CGTAAAATAGCT
66 AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCG-AAAATAGCT
* * * * *
1408 CTAAGGAATGGATCTTGTTGAATACTTTCGGGAACCGAA-TTTAAAAAGAAACTCATAAAAGATT
130 CTAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGAAGTTAAAAAAG-AACTCGTAAAAG-TT
*
1472 TG-CAA-TTCGAAAGTTCTTCCAA
193 TGACAAGTTCGAAAGTTCGTCCAA
*
1494 GATCAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
*
1559 AAATGACAAACTATTTAGACCAAATGATGCT-ATTTCCCGAGCAT-GAAGTGTTCGGAAAATAGC
66 AAATGACAAACTATTTAGACCAAATGATG-TGATTTCCCGAGCATGGAA-TGTTCCGAAAATAGC
* * ** * *
1622 TCTAAGGAATGGATCTTTTTGAATACTTTTGGGAAACGAATTTAAAAAATAACTCGTAAAAGATT
129 TCTAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGAAGTTAAAAAAGAACTCGTAAAAG-TT
*
1687 TG-CAA-TTCGAAAGTTCATCCAA
193 TGACAAGTTCGAAAGTTCGTCCAA
* *
1709 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGACCAAAACTTGTTGACA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
* * * * * * *
1774 AAATGACAAACTATTTAGACCAAATGATTTGATTTCTCGAGCGTGGAATGTTCAGAAATTTGCCC
66 AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCGAAAATAGCTC
*
1839 TAAGGAATGGATCTTGTTGAAT
131 TAAGGAATGGATCTTCTTGAAT
1861 TCT
Statistics
Matches: 1374, Mismatches: 235, Indels: 71
0.82 0.14 0.04
Matches are distributed among these distances:
204 103 0.07
205 52 0.04
208 4 0.00
209 4 0.00
210 145 0.11
211 5 0.00
212 36 0.03
213 4 0.00
214 27 0.02
215 529 0.39
216 368 0.27
217 97 0.07
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
AAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCCGAAAATAGCTC
TAAGGAATGGATCTTCTTGAATACTTTAGGGATCCGAAGTTAAAAAAGAACTCGTAAAAGTTTGA
CAAGTTCGAAAGTTCGTCCAA
Found at i:563 original size:12 final size:12
Alignment explanation
Indices: 546--575 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
536 AAGCATGGAA
546 TGTTCGAAAAAT
1 TGTTCGAAAAAT
*
558 TGTTCGAAGAAT
1 TGTTCGAAAAAT
570 TGTTCG
1 TGTTCG
576 TCTTGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (12 bp):
TGTTCGAAAAAT
Done.