Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000239.1 Kokia drynarioides strain JFW-HI SEQ_110966, 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: 2036
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Found at i:422 original size:216 final size:216
Alignment explanation
Indices: 8--2032 Score: 1961
Period size: 216 Copynumber: 9.4 Consensus size: 216
1 AGTTTAG
* * * ** * * *
8 AAGTTCATCCAATATCCAAGAGAGGAACAATTCTCATGTAAATAAGTTTTTCATTCAAAGACCAA
1 AAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
*** * * * *
73 AAGTTGTTTACCCAATGA-AAAATAGTTTAGAAAAAATGATGCGATTTCCCAAGCACGAAATGTT
66 AAGTTGTTTAGAAAATGACAAACTA-TTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGTT
* * * * * * *
137 CGAAAAATTGGTCGAAGGAATGGATGGTCATGTATACTTTATGGAACTGAAGTTAGAAAAGAACT
130 CGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAACT
* *
202 CGTAATAGTTTGCCAAGTTTGA
195 CGTAAAAGTTTGTCAAGTTTGA
* * * * *
224 AAGTTCGTCTAAGAACCAAGATAAAAACAACTCTCACGTGAATAAGTTTTTCATTCAAAGACTAA
1 AAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
** * * *
289 AAGTAATTTAGAAAATGACAAAGTATTTAGACTAAATTATGCGATTTCCCAAGCATGGAATGTTC
66 AAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGTTC
* * * * * *
354 -AACAAATTGCTCTAAGGAATGGATTGTCCTGAATACTTTAAGAAACCAAAGTTATTGAAGAACT
131 GAA-AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAACT
*
418 CGTAAAAGTTTGTCAAGCTTGA
195 CGTAAAAGTTTGTCAAGTTTGA
* ** * ** * * **
440 AAGTTTATCTAAGATGCAAGAGAAAGACAACTCTCGTGTAATTAGGTTTTTAATTCAAAGATAAA
1 AAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* * * * ** * * *
505 AAGTTGTTTAGAAAATGACAAACAATTTAGGCATAATGATACGA-TTCCCGTGCTTGGATTGTTT
66 AAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGTTC
* * * * * *
569 GGAAAATTGCTCGTAGGAATGGATCATCATGAATACTTTAAGGAACTGAAGTTTTAGAAGAACTT
131 GAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAACTC
** * * *
634 GTAAAACATCGTCAAGTTCGG
196 GTAAAAGTTTGTCAAGTTTGA
* * * * * * *
655 AAGTTCGTCCAAGAA-CAATGAGAGAAACAACTCTCACGTAAATAACTTTTAAATTTATAGACCA
1 AAGTTCATCTAAGAACCAA-GAGAAAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * * * * * ** *
719 AAAGTTGTTTAGAAAATGAAAAACTATTTAGGCAGAATAATGCGGTTCCCCGTGCTTGGAATGTT
65 AAAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGTT
* * * * * *
784 CGTAAAATTACTCGAAGGAAAT-GATCGTCATGAATACTTTAATGAACCAATGTTATAGAACAAC
130 CGAAAAATTGCTCGAAGG-AATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAAC
*
848 TGGTAAAAGTTTGT-ACAGTTTGA
194 TCGTAAAAGTTTGTCA-AGTTTGA
* * * * * * * *
871 AAGTTTATCCATGATCCAAGAGATAATA-AATTCTCACGTAAATAAGTTTTTAATGCAATGACCA
1 AAGTTCATCTAAGAACCAAGAGA-AAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* ** * *
935 AAAGTTGTATACCAAATGACAAA-TAGTTTAGAAAAAATGATGTGATTTCCCAAGCA-GGAACTG
65 AAAGTTGTTTAGAAAATGACAAACTA-TTTAGACAAAATGATGCGATTTCCCAAGCATGGAA-TG
* * *
998 TTCGAAAAATTGCTCGAAGGAA--G---GTCATGAATACTTTATGGAACTGAAGTTATAAAAGAA
128 TTCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAA
*
1058 CTCGTAAAAGTTTGCCAAGTTTGA
193 CTCGTAAAAGTTTGTCAAGTTTGA
* * * * *
1082 AAGTTCGTCTAAGAACCAAGATAAAAACAACTCTCACGTGAATAAGTTTTTCATTCAAAGACTAA
1 AAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
** * *
1147 AAGTAATTTAGAAAATGACAAAGTATTTAGACTAAATGATGCGATTTCCCAAGCATGGAATGTTC
66 AAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGTTC
* * * * * *
1212 -AACAAATTGCTCTAAGGAATGGATTGTCCTGAATACTTTAAGAAACAAAAGTTATTGAAGAACT
131 GAA-AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAACT
*
1276 CGTAAAAGTTTGTCAAGCTTGA
195 CGTAAAAGTTTGTCAAGTTTGA
* * * **
1298 AAGTTCATCTAAGAAGCAAGAGAAAGACAACTCT-A-GTATAAATAGGTTTTTAATTCAAAGATA
1 AAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACG--TAAATAAGTTTTTAATTCAAAGACC
* * **
1361 AAAAGTTGTTTAGAAAATGACAAACAATTTAGACAAAATGATGCGATTTCTCGTGCATGGAATGT
64 AAAAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGT
* ** * *
1426 TCGGAAAATTGCTATAAGGAACGGATCGTCATGAATACTTTAAGGAACTAAAGTTTTAGAAGAAC
129 TCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAAC
* * *
1491 TCGTAAAACTTCGTCAAGTTCGA
194 TCGTAAAAGTTTGTCAAGTTTGA
* * * * * *
1514 AAGTTCAT-TCAAGAA-CAATGAGAGAAACAACACTCACTTAAATAACTTTTTAATTTATAGACC
1 AAGTTCATCT-AAGAACCAA-GAGAAAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * * * * ** *
1577 AAAAGTTGTTTAGAAAATGAAAAACTATTTAGGCAGAATGATGCGGTTCCCCGTGCTTGGAATGT
64 AAAAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGT
* * * * * * *
1642 TCGAAAAATTGTTCGAAGGAAAGGATCGTCATGAGTACTTTAATGAACCAAAGTTATAGAACAAT
129 TCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAAC
* * *
1707 TGGTAAAAGTTTGTAAAGTTCGA
194 TCGTAAAAGTTTGTCAAGTTTGA
** * * * * * *
1730 AAGTTTGTCCATGATCCAAGAGATAATA-AATTCTCACGTAAATAAGTTTTTAATTCAATGACCA
1 AAGTTCATCTAAGAACCAAGAGA-AAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* ** * *
1794 AAAGTTGTATACCAAATGACAAACTATTTAGAGAAAATGATGTGATTTCCCAAGCATGGAATGTT
65 AAAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGTT
* * * *
1859 C-AGAAAATTGCTCGAAGGAATGGATCGCCATGAATACTTTAAAGAGCTGAAGTTATAGAAGAAC
130 CGA-AAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAAC
*
1923 TCGTCAAAGTTTGTCAAGTTT-A
194 TCGTAAAAGTTTGTCAAGTTTGA
* * *** ** * * *
1945 GAAGTTCTTCCAATTTCCAAGAGAGGAACAATTCTCATGTAAATAAGTTTTTCATTCAAAGACCA
1 -AAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* **
2010 GAAGTTGTTTACCAAATGACAAA
65 AAAGTTGTTTAGAAAATGACAAA
2033 TAGT
Statistics
Matches: 1465, Mismatches: 310, Indels: 68
0.79 0.17 0.04
Matches are distributed among these distances:
210 5 0.00
211 162 0.11
212 7 0.00
213 1 0.00
214 5 0.00
215 183 0.12
216 1082 0.74
217 20 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (216 bp):
AAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
AAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGGAATGTTC
GAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACTAAAGTTATAGAAGAACTC
GTAAAAGTTTGTCAAGTTTGA
Found at i:1868 original size:859 final size:858
Alignment explanation
Indices: 36--2007 Score: 3153
Period size: 859 Copynumber: 2.3 Consensus size: 858
26 AGAGAGGAAC
* * * * * *
36 AATTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTTGTTTACCCAATGAAAAATAGTTT
1 AATTCTCACGTAAATAAGTTTTTAATTCAATGACCAAAAGTTGTATACCAAATGACAAATAGTTT
* * *
101 AGAAAAAATGATGCGATTTCCCAAGCACGAAATGTTCGAAAAATTGGTCGAAGGAATGGATGGTC
66 AGAAAAAATGATGTGATTTCCCAAGCA-GGAATGTTCGAAAAATTGCTCGAAGG-A---ATGGTC
* * *
166 ATGTATACTTTATGGAACTGAAGTTAGAAAAGAACTCGTAATAGTTTGCCAAGTTTGAAAGTTCG
126 ATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTTTGAAAGTTCG
231 TCTAAGAACCAAGATAAAAACAACTCTCACGTGAATAAGTTTTTCATTCAAAGACTAAAAGTAAT
191 TCTAAGAACCAAGATAAAAACAACTCTCACGTGAATAAGTTTTTCATTCAAAGACTAAAAGTAAT
*
296 TTAGAAAATGACAAAGTATTTAGACTAAATTATGCGATTTCCCAAGCATGGAATGTTCAACAAAT
256 TTAGAAAATGACAAAGTATTTAGACTAAATGATGCGATTTCCCAAGCATGGAATGTTCAACAAAT
*
361 TGCTCTAAGGAATGGATTGTCCTGAATACTTTAAGAAACCAAAGTTATTGAAGAACTCGTAAAAG
321 TGCTCTAAGGAATGGATTGTCCTGAATACTTTAAGAAACAAAAGTTATTGAAGAACTCGTAAAAG
* * * * *
426 TTTGTCAAGCTTGAAAGTTTATCTAAGATGCAAGAGAAAGACAACTCTCGTGTAATTAGGTTTTT
386 TTTGTCAAGCTTGAAAGTTCATCTAAGAAGCAAGAGAAAGACAACTCTAGTATAAATAGGTTTTT
* *
491 AATTCAAAGATAAAAAGTTGTTTAGAAAATGACAAACAATTTAGGCATAATGATACGATTCCCGT
451 AATTCAAAGATAAAAAGTTGTTTAGAAAATGACAAACAATTTAGACAAAATGATACGATTCCCGT
* * * * * *
556 GCTTGGATTGTTTGGAAAATTGCTCGTAGGAATGGATCATCATGAATACTTTAAGGAACTGAAGT
516 GCATGGAATGTTCGGAAAATTGCTCATAGGAACGGATCATCATGAATACTTTAAGGAACTAAAGT
* * *
621 TTTAGAAGAACTTGTAAAACATCGTCAAGTTCGGAAGTTCGTCCAAGAACAATGAGAGAAACAAC
581 TTTAGAAGAACTCGTAAAACATCGTCAAGTTCGAAAGTTCATCCAAGAACAATGAGAGAAACAAC
*
686 TCTCACGTAAATAACTTTTAAATTTATAGACCAAAAGTTGTTTAGAAAATGAAAAACTATTTAGG
646 ACTCACGTAAATAACTTTTAAATTTATAGACCAAAAGTTGTTTAGAAAATGAAAAACTATTTAGG
* *
751 CAGAATAATGCGGTTCCCCGTGCTTGGAATGTTCGTAAAATTACTCGAAGGAAATGATCGTCATG
711 CAGAATAATGCGGTTCCCCGTGCTTGGAATGTTCGAAAAATTACTCGAAGGAAAGGATCGTCATG
* * *
816 AATACTTTAATGAACCAATGTTATAGAACAACTGGTAAAAGTTTGTACAGTTTGAAAGTTTATCC
776 AATACTTTAATGAACCAAAGTTATAGAACAACTGGTAAAAGTTTGTAAAGTTCGAAAGTTTATCC
881 ATGATCCAAGAGATAATA
841 ATGATCCAAGAGATAATA
*
899 AATTCTCACGTAAATAAGTTTTTAATGCAATGACCAAAAGTTGTATACCAAATGACAAATAGTTT
1 AATTCTCACGTAAATAAGTTTTTAATTCAATGACCAAAAGTTGTATACCAAATGACAAATAGTTT
964 AGAAAAAATGATGTGATTTCCCAAGCAGGAACTGTTCGAAAAATTGCTCGAAGGAA-GGTCATGA
66 AGAAAAAATGATGTGATTTCCCAAGCAGGAA-TGTTCGAAAAATTGCTCGAAGGAATGGTCATGA
1028 ATACTTTATGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTTTGAAAGTTCGTCTA
130 ATACTTTATGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTTTGAAAGTTCGTCTA
1093 AGAACCAAGATAAAAACAACTCTCACGTGAATAAGTTTTTCATTCAAAGACTAAAAGTAATTTAG
195 AGAACCAAGATAAAAACAACTCTCACGTGAATAAGTTTTTCATTCAAAGACTAAAAGTAATTTAG
1158 AAAATGACAAAGTATTTAGACTAAATGATGCGATTTCCCAAGCATGGAATGTTCAACAAATTGCT
260 AAAATGACAAAGTATTTAGACTAAATGATGCGATTTCCCAAGCATGGAATGTTCAACAAATTGCT
1223 CTAAGGAATGGATTGTCCTGAATACTTTAAGAAACAAAAGTTATTGAAGAACTCGTAAAAGTTTG
325 CTAAGGAATGGATTGTCCTGAATACTTTAAGAAACAAAAGTTATTGAAGAACTCGTAAAAGTTTG
1288 TCAAGCTTGAAAGTTCATCTAAGAAGCAAGAGAAAGACAACTCTAGTATAAATAGGTTTTTAATT
390 TCAAGCTTGAAAGTTCATCTAAGAAGCAAGAGAAAGACAACTCTAGTATAAATAGGTTTTTAATT
* *
1353 CAAAGATAAAAAGTTGTTTAGAAAATGACAAACAATTTAGACAAAATGATGCGATTTCTCGTGCA
455 CAAAGATAAAAAGTTGTTTAGAAAATGACAAACAATTTAGACAAAATGATACGA-TTCCCGTGCA
*
1418 TGGAATGTTCGGAAAATTGCT-ATAAGGAACGGATCGTCATGAATACTTTAAGGAACTAAAGTTT
519 TGGAATGTTCGGAAAATTGCTCAT-AGGAACGGATCATCATGAATACTTTAAGGAACTAAAGTTT
* *
1482 TAGAAGAACTCGTAAAACTTCGTCAAGTTCGAAAGTTCATTCAAGAACAATGAGAGAAACAACAC
583 TAGAAGAACTCGTAAAACATCGTCAAGTTCGAAAGTTCATCCAAGAACAATGAGAGAAACAACAC
* *
1547 TCACTTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGAAAAACTATTTAGGCA
648 TCACGTAAATAACTTTTAAATTTATAGACCAAAAGTTGTTTAGAAAATGAAAAACTATTTAGGCA
* ** *
1612 GAATGATGCGGTTCCCCGTGCTTGGAATGTTCGAAAAATTGTTCGAAGGAAAGGATCGTCATGAG
713 GAATAATGCGGTTCCCCGTGCTTGGAATGTTCGAAAAATTACTCGAAGGAAAGGATCGTCATGAA
* *
1677 TACTTTAATGAACCAAAGTTATAGAACAATTGGTAAAAGTTTGTAAAGTTCGAAAGTTTGTCCAT
778 TACTTTAATGAACCAAAGTTATAGAACAACTGGTAAAAGTTTGTAAAGTTCGAAAGTTTATCCAT
1742 GATCCAAGAGATAATA
843 GATCCAAGAGATAATA
1758 AATTCTCACGTAAATAAGTTTTTAATTCAATGACCAAAAGTTGTATACCAAATGACAAACTA-TT
1 AATTCTCACGTAAATAAGTTTTTAATTCAATGACCAAAAGTTGTATACCAAATGACAAA-TAGTT
*
1822 TAGAGAAAATGATGTGATTTCCCAAGCATGGAATGTTC-AGAAAATTGCTCGAAGGAATGGATCG
65 TAGAAAAAATGATGTGATTTCCCAAGCA-GGAATGTTCGA-AAAATTGCTCGAAGGAATGG-T--
** * * * *
1886 CCATGAATACTTTAAAGAGCTGAAGTTATAGAAGAACTCGTCAAAGTTTGTCAAGTTT-AGAAGT
125 -CATGAATACTTTATGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTTTGA-AAGT
* * *** * ** * * *
1950 TCTTCCAATTTCCAAGAGAGGAACAATTCTCATGTAAATAAGTTTTTCATTCAAAGAC
188 TCGTCTAAGAACCAAGATAAAAACAACTCTCACGTGAATAAGTTTTTCATTCAAAGAC
2008 CAGAAGTTGT
Statistics
Matches: 1028, Mismatches: 69, Indels: 23
0.92 0.06 0.02
Matches are distributed among these distances:
858 376 0.37
859 431 0.42
860 8 0.01
861 1 0.00
862 4 0.00
863 106 0.10
864 102 0.10
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (858 bp):
AATTCTCACGTAAATAAGTTTTTAATTCAATGACCAAAAGTTGTATACCAAATGACAAATAGTTT
AGAAAAAATGATGTGATTTCCCAAGCAGGAATGTTCGAAAAATTGCTCGAAGGAATGGTCATGAA
TACTTTATGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTTTGAAAGTTCGTCTAA
GAACCAAGATAAAAACAACTCTCACGTGAATAAGTTTTTCATTCAAAGACTAAAAGTAATTTAGA
AAATGACAAAGTATTTAGACTAAATGATGCGATTTCCCAAGCATGGAATGTTCAACAAATTGCTC
TAAGGAATGGATTGTCCTGAATACTTTAAGAAACAAAAGTTATTGAAGAACTCGTAAAAGTTTGT
CAAGCTTGAAAGTTCATCTAAGAAGCAAGAGAAAGACAACTCTAGTATAAATAGGTTTTTAATTC
AAAGATAAAAAGTTGTTTAGAAAATGACAAACAATTTAGACAAAATGATACGATTCCCGTGCATG
GAATGTTCGGAAAATTGCTCATAGGAACGGATCATCATGAATACTTTAAGGAACTAAAGTTTTAG
AAGAACTCGTAAAACATCGTCAAGTTCGAAAGTTCATCCAAGAACAATGAGAGAAACAACACTCA
CGTAAATAACTTTTAAATTTATAGACCAAAAGTTGTTTAGAAAATGAAAAACTATTTAGGCAGAA
TAATGCGGTTCCCCGTGCTTGGAATGTTCGAAAAATTACTCGAAGGAAAGGATCGTCATGAATAC
TTTAATGAACCAAAGTTATAGAACAACTGGTAAAAGTTTGTAAAGTTCGAAAGTTTATCCATGAT
CCAAGAGATAATA
Done.