Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003379.1 Kokia drynarioides strain JFW-HI SEQ_116107, 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, 795
Length: 1325
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Found at i:386 original size:216 final size:215
Alignment explanation
Indices: 6--460 Score: 563
Period size: 216 Copynumber: 2.1 Consensus size: 215
1 CTAGG
* * ** * * * *
6 AAATGTTTGACAAGTTCGGCACTTCATCCAAGAACCGAGAGAGAAACAATTCTCACGTAATAAAG
1 AAATGTTTGACAAGTTCGGAAGTTTGTTCGAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAG
* * * * *
71 TTTTTAATCCAAAGGCTAAATGTTGTTTATAAAATGACACACTTTTTAGACCAAATGATGCGATT
66 TTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATT
* * ** * * * * *
136 TCCCAAGCATGGAATGTTCAAGAAATTGGTCGAAGGAATGGATCGTATTGAATACTCTTATGAAC
131 TCCCAAGAATGAAATGTTCAAGAAATAAGTCGAAGGAATGGAACGCATT-AAAACTCTCAGGAAC
201 CAAAGTTATAAAAGAACTCAT
195 CAAAGTTATAAAAGAACTCAT
* *
222 AAATGTTTGACAAGTTTGGAAGTTTGTTCGAGAACCAAGAGAGAACCAATTCTCACGTAAAAAAG
1 AAATGTTTGACAAGTTCGGAAGTTTGTTCGAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAG
* * * *
287 TTTTTAAAT-CAAAGACCAAAAGTTTTTTACAACAT-ACCAAACTTTTTAGGCCAAGTGATGCGA
66 TTTTT-AATCCAAAGACCAAAAGTTGTTTACAAAATGA-CAAACTTTTTAGACCAAATGATGCGA
* **
350 TTTCCCGAGAATGAAATGTTCGGGAAATAAGTCGAAGGAATGGAACGCATTAAAACTCTCAGGAA
129 TTTCCCAAGAATGAAATGTTCAAGAAATAAGTCGAAGGAATGGAACGCATTAAAACTCTCAGGAA
** *
415 CTGAAGTTATAAAAGAACTCGT
194 CCAAAGTTATAAAAGAACTCAT
437 AAATGTTTGACAAGTTCGGAAGTT
1 AAATGTTTGACAAGTTCGGAAGTT
461 CGTCCAAGAA
Statistics
Matches: 202, Mismatches: 35, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
215 54 0.27
216 145 0.72
217 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (215 bp):
AAATGTTTGACAAGTTCGGAAGTTTGTTCGAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAG
TTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATT
TCCCAAGAATGAAATGTTCAAGAAATAAGTCGAAGGAATGGAACGCATTAAAACTCTCAGGAACC
AAAGTTATAAAAGAACTCAT
Found at i:886 original size:213 final size:214
Alignment explanation
Indices: 516--1325 Score: 1020
Period size: 213 Copynumber: 3.8 Consensus size: 214
506 AATTCAAAAT
* * * * * *
516 AAACTATTTTGACCAAATGATGCGATTTCCCGATCATGGAATATTCGAAAAATAGGTC-AAGGAA
1 AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAATTGGTCAAAGAAA
* * * * * * *
580 TGGATCATCTTGAATACTCTTAGGAACAGATGTTATAAAAGAATTCGTAAATGTTTAACAAGTTC
66 TGGATCGTCTTGACTACTC--AGGAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTC
* * * * * *
645 GGAAGTTCATCCAAGAACTAATAGAGAAACAAGTCTCACGTTAAAAAGTTTTTAATTCAAAGTCC
129 GGAACTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACC
710 AAAAGTTGTTTACAAAATGAC
194 AAAAGTTGTTTACAAAATGAC
* *
731 TAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAATTGGACAAAGAAA
1 AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAATTGGTCAAAGAAA
* *
796 TGGATCGTCTTGACTAC-CAGGAATCGAAGTTATAAAAGATTTAGTAAATGTTTGATAAGTTCGG
66 TGGATCGTCTTGACTACTCAGGAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTCGG
*
860 AACTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAAAGACCAA
131 AACTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAA
925 AAGCTT-TTTACAAAATGAC
196 AAG-TTGTTTACAAAATGAC
* * * * * *
944 AAACGT-TTTAGACAAAATGATGCGATTTTCCGATCATGGAATCTTCAAAACAA-TGGTCAACGG
1 AAAC-TATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAA-AATTGGTCAAAGA
* * * * *
1007 AATGGATCGTCTTGAATGCT-CTCAGGAACCGAAGTTGTAATAGAACTT-GTAAAAGTTTGACTA
64 AATGGATCGTCTTG-A--CTACTCAGGAACCGAAGTTATAAAAG-ATTTAGTAAATGTTTGACAA
* * * *
1070 GTTC-GTA--T-GTCC--G-TCCAAGA-AGGAAACAATTCTCACGTAAAAAAGTATTTAATTCAA
125 GTTCGGAACTTCATCCAAGAACCAAGAGA-GAAACAATTCTCACGTAAAAAAGTTTTTAATTCAA
*
1127 AGACCAAAGGTTGTTTACAAAATGAC
189 AGACCAAAAGTTGTTTACAAAATGAC
* *
1153 AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCGAAAAATTGGTCGAAGAAA
1 AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAATTGGTCAAAGAAA
*
1218 TGGATCGTCTTGACTACTATCAGAAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTC
66 TGGATCGTCTTGACTAC--TCAGGAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTC
1283 GGAACTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAA
129 GGAACTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAA
Statistics
Matches: 508, Mismatches: 62, Indels: 49
0.82 0.10 0.08
Matches are distributed among these distances:
206 2 0.00
207 1 0.00
208 10 0.02
209 161 0.32
210 3 0.01
212 4 0.01
213 181 0.36
214 6 0.01
215 56 0.11
216 80 0.16
217 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (214 bp):
AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAATTGGTCAAAGAAA
TGGATCGTCTTGACTACTCAGGAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTCGG
AACTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAA
AAGTTGTTTACAAAATGAC
Found at i:1156 original size:209 final size:208
Alignment explanation
Indices: 516--1283 Score: 854
Period size: 209 Copynumber: 3.6 Consensus size: 208
506 AATTCAAAAT
* * * * *
516 AAACTATTTTGACCAAATGATGCGATTTCCCGATCATGGAATATTCGAAAAATAGGTCAAGGAAT
1 AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAAT-GGTCAAGAAAT
* * * * * * *
581 GGATCATCTTGAATACTCTTAGGAACAGATGTTATAAAAGAATTCGTAAATGTTTAACAAGTTCG
65 GGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTC-
* * * * * *
646 GAA-GTTCATCCAAGAACTAATAGAGAAACAAGTCTCACGTTAAAAAGTTTTTAATTCAAAGTCC
129 GAATGTCCGTCCAAG-----A-AGAGAAACAATTCTCACGTAAAAAAGTATTTAATTCAAAGACC
*
710 AAAAGTTGTTTACAAAATGAC
188 AAAGGTTGTTTACAAAATGAC
* *
731 TAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAATTGGACAAAGAAA
1 AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAA-TGGTC-AAGAAA
* * *
796 TGGATCGTCTTGACTA--C-CAGGAATCGAAGTTATAAAAGATTTAGTAAATGTTTGATAAGTTC
64 TGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTC
* *
858 GGAACTTCATCCAAGAACCAAG-AGAGAAACAATTCTCACGTAAAAAAG-ATTTTAATTCAAAGA
129 -GAA--T-GTCC--G-TCCAAGAAGAGAAACAATTCTCACGTAAAAAAGTA-TTTAATTCAAAGA
*
921 CCAAAAGCTT-TTTACAAAATGAC
186 CC-AAAGGTTGTTTACAAAATGAC
* * * * *
944 AAACGT-TTTAGACAAAATGATGCGATTTTCCGATCATGGAATCTTCAAAACAATGGTCAACGGA
1 AAAC-TATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAA-AATGGTCAA-GAA
* * * * * *
1008 ATGGATCGTCTTGAATGCTCTCAGGAACCGAAGTTGTAATAGAACTT-GTAAAAGTTTGACTAGT
63 ATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAG-ATTTAGTAAATGTTTGACAAGT
*
1072 TCGTATGTCCGTCCAAGAAG-GAAACAATTCTCACGTAAAAAAGTATTTAATTCAAAGACCAAAG
127 TCGAATGTCCGTCCAAGAAGAGAAACAATTCTCACGTAAAAAAGTATTTAATTCAAAGACCAAAG
1136 GTTGTTTACAAAATGAC
192 GTTGTTTACAAAATGAC
*
1153 AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCGAAAAATTGGTCGAAGAAA
1 AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTC-AAAAAATGGTC-AAGAAA
* * *
1218 TGGATCGTCTTGACTACTATCAGAAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTC
64 TGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTC
1283 G
129 G
1284 GAACTTCATC
Statistics
Matches: 466, Mismatches: 62, Indels: 56
0.80 0.11 0.10
Matches are distributed among these distances:
208 10 0.02
209 158 0.34
210 10 0.02
212 5 0.01
213 157 0.34
214 9 0.02
215 53 0.11
216 54 0.12
217 5 0.01
220 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (208 bp):
AAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTCAAAAAATGGTCAAGAAATG
GATCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTCGA
ATGTCCGTCCAAGAAGAGAAACAATTCTCACGTAAAAAAGTATTTAATTCAAAGACCAAAGGTTG
TTTACAAAATGAC
Done.