Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011993.1 Kokia drynarioides strain JFW-HI SEQ_126991, 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: 2505
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.22
Warning! 520 characters in sequence are not A, C, G, or T
Found at i:378 original size:216 final size:216
Alignment explanation
Indices: 1--778 Score: 824
Period size: 216 Copynumber: 3.6 Consensus size: 216
* * * * *
1 CACGTAAATAAGTTTTTAATTCGAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCA
1 CACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGACAAACTATTTAGACCA
* * ** * * * **
66 AATGATGCGACTTCCCGAGCA-TGTAATGCTCGGAGTATTGCTTGAAAGTTTGGATCGTCTTGAA
66 AATGATGCGACTTCCCTAGCATTG-AATGTTCGGAAAATTACTCGAAGGAATGGATCGTCTTGAA
* * * * * * **
130 TACTTTAAGGAACCGATGTTGTAAAAGAACTCGTAAAAGTTGGACAAGTTCGGAAGTTCGTCCAA
130 CACTTTAATGAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTAAGAAGTTCGTCCAA
* *
195 GAACAAAGAGAGACACAATTCT
195 GAACCAAGAGAGAAACAATTCT
* * * * *
217 CAAGTAAATATGTTTTTAATTCAAAGATCAAAACATGTTTCCAAAATGTA-AAACTATTTACACC
1 CACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATG-ACAAACTATTTAGACC
* * *
281 AAATGATGCGATTTCCCTCGCATTGAATGTTCGGAAAATTACTCGAAGGAATGGATCGTCTTGGA
65 AAATGATGCGACTTCCCTAGCATTGAATGTTCGGAAAATTACTCGAAGGAATGGATCGTCTTGAA
* ** * *
346 CACTTTAATGAACCGAAGCTATAAAAGAACTCGTAAAAGTTTGTTAATTTAAGAATTTCGTCCAA
130 CACTTTAATGAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTAAGAAGTTCGTCCAA
*
411 GAACCAAGAGAGAAACGATTCT
195 GAACCAAGAGAGAAACAATTCT
* * *
433 CACGTAAATAAGTTTTTAATTCAAAGGCCAAAACCTGTTTACAAAATGACAAACTTTTTAGACCA
1 CACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGACAAACTATTTAGACCA
* * * * *
498 AATGATGCGACTTCCCAAACATAT-AATGTTC-GAAATATTGCTCGACGGATTGGATCGTCTTGA
66 AATGATGCGACTTCCCTAGCAT-TGAATGTTCGGAAA-ATTACTCGAAGGAATGGATCGTCTTGA
* * * ***** *
561 ATAC-TTCATGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTTCGACANNNNNNA-AAGTTCATC
129 ACACTTTAAT-GAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACA-AGTTAAGAAGTTCGTC
* *
624 CAAGAGCCAAGAGA-AAACAATTCC
192 CAAGAACCAAGAGAGAAACAATTCT
* * *
648 CACGTAAATAAGTTTTTAATTAAAAGATCAAAACATGTTTACAAAATGA-AAA--A--CAGACCA
1 CACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGACAAACTATTTAGACCA
* * ** * *
708 AATGATGCGATTTCCCTCGCAAGGAATGTTCGAAAAATTACTCAAAGGAATGGATCGTCTTGAAC
66 AATGATGCGACTTCCCTAGCATTGAATGTTCGGAAAATTACTCGAAGGAATGGATCGTCTTGAAC
773 ACTTTA
131 ACTTTA
779 TGGAACCNNN
Statistics
Matches: 464, Mismatches: 88, Indels: 25
0.80 0.15 0.04
Matches are distributed among these distances:
210 56 0.12
211 5 0.01
214 3 0.01
215 62 0.13
216 333 0.72
217 5 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (216 bp):
CACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGACAAACTATTTAGACCA
AATGATGCGACTTCCCTAGCATTGAATGTTCGGAAAATTACTCGAAGGAATGGATCGTCTTGAAC
ACTTTAATGAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTAAGAAGTTCGTCCAAG
AACCAAGAGAGAAACAATTCT
Found at i:1324 original size:215 final size:215
Alignment explanation
Indices: 837--1396 Score: 705
Period size: 215 Copynumber: 2.6 Consensus size: 215
827 NNNNNNNNNC
* * *
837 CAAAATGTAAAACTATTTACACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGGAAAATTAC
1 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCAAGGAATGTTC-GAAAATTAC
*
902 TCGAAGGAATGGATCGTCTTGGACACTTTAAT-GAACCGAAGCTATAAAAGAACTCGTAAAAGTT
65 TCGAAGGAATGGATCGTCTTGAACAC-TTAATGGAACCGAAGCTATAAAAGAACTCGTAAAAGTT
* ** * * * * *
966 TGTTAATTTAAGAATTTCGTCCAAGAACCAAGAGAGAAACGATTCTCACGTAAATAAGTTTTTAA
129 CGACAATTCAAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCCCACGTAAATAAGTTTTTAA
* * *
1031 TTCAAAGGCCAAAACCTGTTTA
194 TTAAAAGACCAAAACATGTTTA
* * * *** * *
1053 CAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCAAACATA-TAATGTTCGAAATATTG
1 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCA-AGGAATGTTCGAAA-ATTA
* * * * *
1117 CTCGACGGATTGGATCGTCTTGAATACTTCATGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTT
64 CTCGAAGGAATGGATCGTCTTGAACACTTAATGGAACCGAAGCTATAAAAGAACTCGTAAAAGTT
* *
1182 CGACAAGTTCGA-AAGTTCATCCAAGAGCCAAGAGA-AAACAATTCCCACGTAAATAAGTTTTTA
129 CGACAA-TTCAAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCCCACGTAAATAAGTTTTTA
*
1245 ATTAAAAGATCAAAACATGTTTA
193 ATTAAAAGACCAAAACATGTTTA
1268 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCAAGGAATGTTCGAAAAATTAC
1 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCAAGGAATGTTCG-AAAATTAC
* * * ** *
1333 TCAAAGGAATGGATCGTCTTGAACACTTTATGGAACCGGATTTAAAAAAGAACTCGTAAAAGTT
65 TCGAAGGAATGGATCGTCTTGAACACTTAATGGAACCGAAGCTATAAAAGAACTCGTAAAAGTT
1397 TGANNNNNNN
Statistics
Matches: 289, Mismatches: 49, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
214 1 0.00
215 158 0.55
216 127 0.44
217 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (215 bp):
CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCAAGGAATGTTCGAAAATTACT
CGAAGGAATGGATCGTCTTGAACACTTAATGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTCG
ACAATTCAAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCCCACGTAAATAAGTTTTTAATT
AAAAGACCAAAACATGTTTA
Found at i:2412 original size:216 final size:216
Alignment explanation
Indices: 2030--2459 Score: 520
Period size: 216 Copynumber: 2.0 Consensus size: 216
2020 NNNNNGTTTG
* * *
2030 ACAAGTTCGAAAGTTCATCCAACAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
1 ACAAGTTCGAAAGTTCATCCAACAACAAAGACAGAAACAATTCTCAAGTAAATAAGTTTTTAATT
* * * * * * *
2095 CGAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATTATGCGACTTCCCGAGCA
66 CAAAGACCAAAACATGTTTACAAAATGACAAACTATTTACACCAAATGATGCGACTTCCCGAGCA
* ** * * ** * * *
2160 TGTAATGCTCGGAGTATTGCTTGAAAGTTTGGATCGTCTTGAATACTTTAAGGAACCGATGTTAT
131 TGGAATGCTCGGAAAATTACTCGAAAGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTAT
2225 AAAAGAACTCGTAAAAGTTGC
196 AAAAGAACTCGTAAAAGTTGC
* * * * ** *
2246 ACAAGTTTGGAAGTTCGTCCAATAACAAAGACAGGCACAATTCTCAAGTAAATATGTTTTTAATT
1 ACAAGTTCGAAAGTTCATCCAACAACAAAGACAGAAACAATTCTCAAGTAAATAAGTTTTTAATT
* * * **
2311 CAAAGATCAAAACATGTTTCCAAAATGTA-AAACTATTTACACCAAATGATGCGATTTCCCTCGC
66 CAAAGACCAAAACATGTTTACAAAATG-ACAAACTATTTACACCAAATGATGCGACTTCCCGAGC
* * * *
2375 ATGGAATGTTCGGAAAATTACTCGAAGGAATGGATCGTCTTGGACACTTTAATGAACCGAAGCTA
130 ATGGAATGCTCGGAAAATTACTCGAAAGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTA
2440 TAAAAGAACTCGTAAAAGTT
195 TAAAAGAACTCGTAAAAGTT
2460 TGTTAATTTA
Statistics
Matches: 177, Mismatches: 36, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
216 176 0.99
217 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (216 bp):
ACAAGTTCGAAAGTTCATCCAACAACAAAGACAGAAACAATTCTCAAGTAAATAAGTTTTTAATT
CAAAGACCAAAACATGTTTACAAAATGACAAACTATTTACACCAAATGATGCGACTTCCCGAGCA
TGGAATGCTCGGAAAATTACTCGAAAGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGCTAT
AAAAGAACTCGTAAAAGTTGC
Done.