Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008160.1 Kokia drynarioides strain JFW-HI SEQ_122819, 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: 1821
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Found at i:1495 original size:215 final size:216
Alignment explanation
Indices: 14--1821 Score: 1778
Period size: 216 Copynumber: 8.4 Consensus size: 216
4 ATATTCTCAA
* * * * * * *
14 GAACCAAAGTTATAAAAGAACTCGTAATTGTTTGACAAGTTTGAAAG-TT-CCCAAGAACCAAAA
1 GAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA
* * * * *
77 GAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCACAAGTTATTTACAAAATAACAA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACAA
* * * * * * * * *
142 ACTTTTTGGACCAAGTGATACTATTTCCTGAGCATGGAATATTCTG-AAAATTGGACGAAGAAAT
131 ACTATTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTC-GAAAAATTGGTCGAAGGAAT
* *
206 GGATCATCTTGAACACTTTAAG
195 GGATCGTCTTGAATACTTTAAG
* * * ** * *
228 GAACCGAAGATATAAAAGAACTCAAAAATGTTTGACAAGTTCAGAAGTTCATCCAAGATCCAACA
1 GAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA
* * * **
293 AAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAGAGTCATTTACAAAATGACAA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACAA
* * * ** * *
358 ACTTTTTAGACCAAATGATGCAA-ATCCTGAGCATATAATGTTCGGAAAATTGGTCGAGGGAATG
131 ACTATTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATG
* * *
422 GATCGCCTTGAACT-CTCTCAG
196 GATCGTCTTGAA-TACTTTAAG
* * * * ** * * *
443 GAACCAAAGTTATAAAAGAACTCGTAAAATGTTTGACAATTTTGGGTGTTCGTTCAAGAATCAAG
1 GAACCGAAGTTATAAAAGAACTCAT-AAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAG
* *
508 AGAGAAACAATTATCACGTAAATAA----TTAATTCAAAGAA-CAAAAGTTGTTTACAAAATGAG
65 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA-AACCAAAAGTTGTTTACAAAATGAC
* * * * * * * * *
568 AAACTATATAGATCAAATGATGCGACTTCCCAAGCATGGAATGCTCGAAAAATTGCTCAAAGAAA
129 AAACTATTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
633 TGGATCGTCATT-AATACTTTAAG
194 TGGATCGTC-TTGAATACTTTAAG
* *** * * *
656 GTATTTAAGTTATAAAAGAACTCATAAATTTTTGACAAGATCGAAAGTTTGTCCAAGATA-CAAG
1 GAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGA-ACCAAG
* * * *
720 AGAGAAATAATTCTCACGTAAATAAGTTTTAAATTCAAAAACCAAAAGTTGTTTACAAGATGAAA
65 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACA
* * * * * * *
785 AACTACTTT-GACCAAATGATGCGATTTCTCAAGAATGGAATGCTCAAAAAATTGGTCAAAGGAA
130 AACTA-TTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
* *
849 TGGATCGTCTTGAATACTCTCAG
194 TGGATCGTCTTGAATACTTTAAG
* * * * *
872 AAACCGAAGTTAGAAAAGAACTCATAAATGTTTGACAAGTTCAGAAATTTGTCCAAGAACCAATA
1 GAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA
* * * * *
937 GAGAAACAATTCTCATGTAAATAAGTTTTAAATTCAAAGACGAAAAGTTGTTTAC-AGATGGA-A
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAAT-GACA
** * * * * *
1000 AACTATTTTTACCAAATGATTCCATTTTACCGAGAATGGAATGTTCGAAAAATTGGTCAAAGGAA
130 AACTATTTAGACCAAATGA-TGCAATTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
* * *
1065 TGGATCTTCTTAAATA-TTCTCTA-
194 TGGATCGTCTTGAATACTT-T-AAG
* * * * * * * * *
1088 GAATCAAAGTTATAAACA-AACTCCTATATGTTTGAGAGGTTCAGAAGTTCGTCCAAGAACCAAA
1 GAACCGAAGTTATAAA-AGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAG
* * * * ** *
1152 AAAGAAATAATTCTCATGTAAATAAGTTTTTAATTGAAGCACCACAAGTTGTTTACAAAATGACA
65 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACA
* * * * * * *
1217 AACTTTTTAGACCAAATGATGCGATTTCCTGATCATGGAATGTTCAAAAAACTAGAT-GAAGGAA
130 AACTATTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTCGAAAAA-TTGGTCGAAGGAA
* *
1281 TGGTTCGTCTTGAATGCTTTAAG
194 TGGATCGTCTTGAATACTTTAAG
* * * * *
1304 GAATCGAAGTTATAAAAGAACTCAAAAATGTTTGACATGTTCGGAAGTTTGTCAAAGAACCAATA
1 GAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA
* *
1369 -ATGAAACAATTCTCACGTAAA-AAGTTTTTAATTCAAAAACCAAAAGCTATTTACAAAATGACA
66 GA-GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACA
* *
1432 AACTATTTAGACCAAATAATGCAACTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAAT
130 AACTATTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAAT
* *
1497 GGATCATCTTGAATACTCTCAA-
195 GGATCGTCTTGAATACT-TTAAG
* * * * *
1519 GAACCGAAGTTATAAAAGAACTCTTAAATGTTTAACAAGTTCAGAAGTTTGCCCAAGAA-AAAGA
1 GAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA
** * * *
1583 GAGAAACAATTCTCACCAAAATAAGTTTTTAATTTAAAGACTAAAAGTT-TTATACAAAATGACA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTT-TACAAAATGACA
* * * * *
1647 AACTATTTAGA-CAAATGCTGCGAA-TTACCGAGAATGGAATGTTCAAAAAATTGTTCGAAGGAA
130 AACTATTTAGACCAAATGATGC-AATTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAA
* * *
1710 TGGATTGCCTTGAATACTTTAAA
194 TGGATCGTCTTGAATACTTTAAG
** * * * * *
1733 GAATTGAAGTTTTAAAAGAACTCGTAAATGTTTGACATGTTCGGAAGTTCGTCCAAGAACAAAGA
1 GAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA
*
1798 GAGAAACAATTCTAACGTAAATAA
66 GAGAAACAATTCTCACGTAAATAA
Statistics
Matches: 1316, Mismatches: 239, Indels: 77
0.81 0.15 0.05
Matches are distributed among these distances:
212 101 0.08
213 69 0.05
214 178 0.14
215 325 0.25
216 614 0.47
217 29 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (216 bp):
GAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA
GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACAA
ACTATTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATG
GATCGTCTTGAATACTTTAAG
Done.