Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001038.1 Kokia drynarioides strain JFW-HI SEQ_112267, 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: 2141
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.28
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:894 original size:220 final size:216
Alignment explanation
Indices: 609--2046 Score: 1102
Period size: 220 Copynumber: 6.6 Consensus size: 216
599 NNNNNNGTCC
** * *** *
609 AAGAACCAGGAGAGAAACAATT-TACACATAAATAAGTATTTAATTCAGTGACCGAAAGTTTTTT
1 AAGAACCAAAAGAGAAACAATTCT-CACATAAATAAGTTTTTAATTCAAACACCAAAAG-TTTTT
*
673 TGAGAAATGGA-AAACTACTTT-GACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGG-ATT
64 TGA-AAAT-GACAAACTA-TTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGGAATA
* * *
735 TTGCTCGAAGGATTGGATCATCTTGAATACTTTACGGAACCATAGTTATTATAGAAGAAACAGTA
126 TTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATTA-A-AAGAAACAGTA
*
800 AAAGCTTGACAAGTTCAGAAGTTTTTTCT
189 AAAGCTTGACAAGTTCAGAAG-TTTGTCT
* *
829 AAGAATCAAAAGAGAAATAATTCTCACATAAATATA-TTTTTAATTCAAACACCAAAAAGTTTTT
1 AAGAACCAAAAGAGAAACAATTCTCACATAAATA-AGTTTTTAATTCAAACACC-AAAAGTTTTT
*
893 TGCAAAATGACAAACTATTTAGACCGAATGATGCTG-TTTACCGAGCATGGAATGTTCGGAATAT
64 TG-AAAATGACAAACTATTTAGACCGAATGATGC-GATTTCCCGAGCATGGAATGTTCGGAATAT
* * * * *
957 TGATCGAAGGAATGCATCGTCTTGAATACTTTAAGGAAGCAAAGTTA-TAAAAG-AACTCGTAAA
127 TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATTAAAAGAAAC-AGT-AA
* *
1020 AAGCTTGA-ATAGTTCAAAAGTTCGTCT
190 AAGCTTGACA-AGTTCAGAAGTTTGTCT
* * * * *
1047 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACT
1 AAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTTA-ATTCAA-A-C---ACCAAAAGT
** * * * * *
1112 TGGTTTTCTAAATGACAAACTATTTAGACCAAAAGATGCAATTTCTCGAGCATGGAATGTTTGGA
60 T--TTTTGAAAATGACAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
* * * * * * *
1177 AAATTGCTCGTA-GAAGCGGATGATCTTGAATACTTTAAGGAACCGAAGTTA-TAATAGAAATAG
123 ATATTGCTCGAAGGAA-TGGATCATCTTGAATACTTTAAGGAACCAAAGTTATTAAAAGAAACAG
** ** ** *
1240 TAAAATATTTCCTCGTTC-GAAAGTTTGTCC
187 TAAAAGCTTGACAAGTTCAG-AAGTTTGTCT
** * *** *
1270 AAGAACCAGGAGAGAAACAATT-TACACATAAATAAGTATTTAATTCAGTGACCGAAAGTTTTTT
1 AAGAACCAAAAGAGAAACAATTCT-CACATAAATAAGTTTTTAATTCAAACACCAAAAG-TTTTT
* *
1334 TGAGAAATGGCAAACTATTTTGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGG-ATATT
64 TGA-AAATGACAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGGAATATT
* * *
1398 GCTCTAAGGATTGGATCATCTTGAATACTTTACGGAACCAAAGTTATTATAGAAGAAACAGTAAA
128 GCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATTA-A-AAGAAACAGTAAA
*
1463 AGCTTGACAAGTTCAGAAGTTTTTTCT
191 AGCTTGACAAGTTCAGAAG-TTTGTCT
* *
1490 AAGAATCAAAAGAGAAATAATTCTCACATAAATATA-TTTTTAATTCAAACACCAAAAAGTTTTT
1 AAGAACCAAAAGAGAAACAATTCTCACATAAATA-AGTTTTTAATTCAAACACC-AAAAGTTTTT
* *
1554 TGCAAAATGACAAACTATTTAGACCGAATGATTCTG-TTTACCGAGCATGGAATGTTCGGAATAT
64 TG-AAAATGACAAACTATTTAGACCGAATGATGC-GATTTCCCGAGCATGGAATGTTCGGAATAT
* * *
1618 TGAC-CGAAGGAATGGATCGTCTTGAATACTTTAAGTAACCAAAGTTA-TAAAAG-AACTCGTAA
127 TG-CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATTAAAAGAAAC-AGT-A
*
1680 AAAACTTG--AA--T----AG--T-TC-
189 AAAGCTTGACAAGTTCAGAAGTTTGTCT
* * * * *
1696 AA-AATC----GAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACT
1 AAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTTA-ATTCAA-A-C---ACCAAAAGT
* * ** * * * *
1756 TGGTTTTCAAAATGACAAACTATTTAGACCAAAACATACAATTTCTCGAGCATGGAATGTTTGGA
60 T--TTTTGAAAATGACAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
* * * * ** * * * *
1821 AAATTGCTCGCAGAAACGGATGGTCTTGAATACTTTAAGTAACCGAAGTTA-TAAAA-TAACTCG
123 ATATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATTAAAAGAAAC-AG
* * * * * * ** *
1884 TAAAAGTTTTAGAAGTTCGGTAGATCATCC
187 TAAAAGCTTGACAAGTTCAGAAGTTTGTCT
* * * * * * * *
1914 AAGAACCAAGAGAGAGATAATTGTCACACAAATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTA
1 AAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAACACCAAAAGTT-TTTT
* * * * * * * *
1979 CAAAATGACAAACTATTTAAACCAAAAGACT-AGATTTCCGGAGAATGGAATGTTC-GAAAATTG
65 GAAAATGACAAACTATTTAGACCGAATGA-TGCGATTTCCCGAGCATGGAATGTTCGGAATATTG
2042 CTCGA
129 CTCGA
2047 TTGAGTTGAT
Statistics
Matches: 985, Mismatches: 160, Indels: 151
0.76 0.12 0.12
Matches are distributed among these distances:
200 1 0.00
201 27 0.03
202 4 0.00
203 1 0.00
204 1 0.00
205 4 0.00
206 15 0.02
207 108 0.11
208 7 0.01
210 1 0.00
211 2 0.00
214 2 0.00
215 13 0.01
216 93 0.09
217 79 0.08
218 57 0.06
219 63 0.06
220 201 0.20
221 105 0.11
222 9 0.01
223 89 0.09
224 97 0.10
225 6 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (216 bp):
AAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAACACCAAAAGTTTTTTG
AAAATGACAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGGAATATTGCT
CGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATTAAAAGAAACAGTAAAAGCTT
GACAAGTTCAGAAGTTTGTCT
Found at i:1272 original size:661 final size:660
Alignment explanation
Indices: 2--1874 Score: 2675
Period size: 661 Copynumber: 2.9 Consensus size: 660
1 A
* * *
2 AAAGTTTTTTTAAGAAATGGCAAACTACTTTGACCGAATGATGCGATTTCCAGAGAATGGAATGT
1 AAAGTTTTTTTGAGAAATGGCAAACTACTTTGACCGAATGATGCGATTTCCCGAGCATGGAATGT
** * *
67 TCGGAATATTGCTCGAATAATTGGATCATCTTGAATAGTTTAAGGAACCGAAGTTATTATAGAAG
66 TCGG-ATATTGCTCGAAGGATTGGATCATCTTGAATACTTTACGGAACC-AAGTTATTATAGAAG
* *
132 AAATAGTAAAAGCTTGACAAGTTCAGAAG-TTTGTCTAAGAATCAAAAGAGAAATAATTCTCACA
129 AAACAGTAAAAGCTTGACAAGTTCAGAAGTTTTTTCTAAGAATCAAAAGAGAAATAATTCTCACA
* * *
196 TAAATATGTTTTTAATTCAAACACCAAAAAGTTGTTTGCAAAATGACAAACTATTAAGACCGAAT
194 TAAATATATTTTTAATTCAAACACCAAAAAGTTTTTTGCAAAATGACAAACTATTTAGACCGAAT
*
261 GATGCTGTTTCCCGAGCATGGAATGTTCGGAATATTGATCGAAGGAATGCATCGTCTTGAATACT
259 GATGCTGTTTACCGAGCATGGAATGTTCGGAATATTGATCGAAGGAATGCATCGTCTTGAATACT
*
326 TTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAAGCTTGACTAGTTCAAAAGTTCGTCTAAGAA
324 TTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAAGCTTGAATAGTTCAAAAGTTCGTCTAAGAA
*
391 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACATGGTT
389 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACTTGGTT
456 TTCAAAATGACAAACTATTTAGACCAAAAGATGCAATTTCTCGAGCATGGAATGTTTGGAAAATT
454 TTCAAAATGACAAACTATTTAGACCAAAAGATGCAATTTCTCGAGCATGGAATGTTTGGAAAATT
**************************************************
521 GCTCGTAGAAGCGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
519 GCTCGTAGAAGCGGATGATCTTGAATACTTTAAGGAACCGAAGTTATAATAGAAATAGTAAAATA
*******************
586 NNNNNNNNNNNNNNNNNNNGTCCAAGAACCAGGAGAGAAACAATTTACACATAAATAAGTATTTA
584 TTTCCTCGTTCGAAAGTTTGTCCAAGAACCAGGAGAGAAACAATTTACACATAAATAAGTATTTA
651 ATTCAGTGACCG
649 ATTCAGTGACCG
*
663 AAAGTTTTTTTGAGAAATGGAAAACTACTTTGACCGAATGATGCGATTTCCCGAGCATGGAATGT
1 AAAGTTTTTTTGAGAAATGGCAAACTACTTTGACCGAATGATGCGATTTCCCGAGCATGGAATGT
*
728 TCGGATTTTGCTCGAAGGATTGGATCATCTTGAATACTTTACGGAACCATAGTTATTATAGAAGA
66 TCGGATATTGCTCGAAGGATTGGATCATCTTGAATACTTTACGGAACCA-AGTTATTATAGAAGA
793 AACAGTAAAAGCTTGACAAGTTCAGAAGTTTTTTCTAAGAATCAAAAGAGAAATAATTCTCACAT
130 AACAGTAAAAGCTTGACAAGTTCAGAAGTTTTTTCTAAGAATCAAAAGAGAAATAATTCTCACAT
858 AAATATATTTTTAATTCAAACACCAAAAAGTTTTTTGCAAAATGACAAACTATTTAGACCGAATG
195 AAATATATTTTTAATTCAAACACCAAAAAGTTTTTTGCAAAATGACAAACTATTTAGACCGAATG
923 ATGCTGTTTACCGAGCATGGAATGTTCGGAATATTGATCGAAGGAATGCATCGTCTTGAATACTT
260 ATGCTGTTTACCGAGCATGGAATGTTCGGAATATTGATCGAAGGAATGCATCGTCTTGAATACTT
*
988 TAAGGAAGCAAAGTTATAAAAGAACTCGTAAAAAGCTTGAATAGTTCAAAAGTTCGTCTAAGAAC
325 TAAGGAACCAAAGTTATAAAAGAACTCGTAAAAAGCTTGAATAGTTCAAAAGTTCGTCTAAGAAC
1053 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACTTGGTTT
390 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACTTGGTTT
*
1118 TCTAAATGACAAACTATTTAGACCAAAAGATGCAATTTCTCGAGCATGGAATGTTTGGAAAATTG
455 TCAAAATGACAAACTATTTAGACCAAAAGATGCAATTTCTCGAGCATGGAATGTTTGGAAAATTG
1183 CTCGTAGAAGCGGATGATCTTGAATACTTTAAGGAACCGAAGTTATAATAGAAATAGTAAAATAT
520 CTCGTAGAAGCGGATGATCTTGAATACTTTAAGGAACCGAAGTTATAATAGAAATAGTAAAATAT
1248 TTCCTCGTTCGAAAGTTTGTCCAAGAACCAGGAGAGAAACAATTTACACATAAATAAGTATTTAA
585 TTCCTCGTTCGAAAGTTTGTCCAAGAACCAGGAGAGAAACAATTTACACATAAATAAGTATTTAA
1313 TTCAGTGACCG
650 TTCAGTGACCG
*
1324 AAAGTTTTTTTGAGAAATGGCAAACTATTTTGACCGAATGATGCGATTTCCCGAGCATGGAATGT
1 AAAGTTTTTTTGAGAAATGGCAAACTACTTTGACCGAATGATGCGATTTCCCGAGCATGGAATGT
*
1389 TCGGATATTGCTCTAAGGATTGGATCATCTTGAATACTTTACGGAACCAAAGTTATTATAGAAGA
66 TCGGATATTGCTCGAAGGATTGGATCATCTTGAATACTTTACGGAACC-AAGTTATTATAGAAGA
1454 AACAGTAAAAGCTTGACAAGTTCAGAAGTTTTTTCTAAGAATCAAAAGAGAAATAATTCTCACAT
130 AACAGTAAAAGCTTGACAAGTTCAGAAGTTTTTTCTAAGAATCAAAAGAGAAATAATTCTCACAT
1519 AAATATATTTTTAATTCAAACACCAAAAAGTTTTTTGCAAAATGACAAACTATTTAGACCGAATG
195 AAATATATTTTTAATTCAAACACCAAAAAGTTTTTTGCAAAATGACAAACTATTTAGACCGAATG
* * *
1584 ATTCTGTTTACCGAGCATGGAATGTTCGGAATATTGACCGAAGGAATGGATCGTCTTGAATACTT
260 ATGCTGTTTACCGAGCATGGAATGTTCGGAATATTGATCGAAGGAATGCATCGTCTTGAATACTT
* *
1649 TAAGTAACCAAAGTTATAAAAGAACTCGTAAAAAACTTGAATAGTTCAAAA-------T------
325 TAAGGAACCAAAGTTATAAAAGAACTCGTAAAAAGCTTGAATAGTTCAAAAGTTCGTCTAAGAAC
1701 C----GAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACTTGGTTT
390 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACTTGGTTT
* *
1762 TCAAAATGACAAACTATTTAGACCAAAACATACAATTTCTCGAGCATGGAATGTTTGGAAAATTG
455 TCAAAATGACAAACTATTTAGACCAAAAGATGCAATTTCTCGAGCATGGAATGTTTGGAAAATTG
* * * *
1827 CTCGCAGAAACGGATGGTCTTGAATACTTTAAGTAACCGAAGTTATAA
520 CTCGTAGAAGCGGATGATCTTGAATACTTTAAGGAACCGAAGTTATAA
1875 AATAACTCGT
Statistics
Matches: 1104, Mismatches: 105, Indels: 23
0.90 0.09 0.02
Matches are distributed among these distances:
644 166 0.15
648 1 0.00
654 1 0.00
659 1 0.00
660 81 0.07
661 853 0.77
662 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.28
Consensus pattern (660 bp):
AAAGTTTTTTTGAGAAATGGCAAACTACTTTGACCGAATGATGCGATTTCCCGAGCATGGAATGT
TCGGATATTGCTCGAAGGATTGGATCATCTTGAATACTTTACGGAACCAAGTTATTATAGAAGAA
ACAGTAAAAGCTTGACAAGTTCAGAAGTTTTTTCTAAGAATCAAAAGAGAAATAATTCTCACATA
AATATATTTTTAATTCAAACACCAAAAAGTTTTTTGCAAAATGACAAACTATTTAGACCGAATGA
TGCTGTTTACCGAGCATGGAATGTTCGGAATATTGATCGAAGGAATGCATCGTCTTGAATACTTT
AAGGAACCAAAGTTATAAAAGAACTCGTAAAAAGCTTGAATAGTTCAAAAGTTCGTCTAAGAACC
AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAGACCAAAACTTGGTTTT
CAAAATGACAAACTATTTAGACCAAAAGATGCAATTTCTCGAGCATGGAATGTTTGGAAAATTGC
TCGTAGAAGCGGATGATCTTGAATACTTTAAGGAACCGAAGTTATAATAGAAATAGTAAAATATT
TCCTCGTTCGAAAGTTTGTCCAAGAACCAGGAGAGAAACAATTTACACATAAATAAGTATTTAAT
TCAGTGACCG
Done.