Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012167.1 Kokia drynarioides strain JFW-HI SEQ_127168, 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: 2888
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Found at i:385 original size:73 final size:72
Alignment explanation
Indices: 261--395 Score: 200
Period size: 73 Copynumber: 1.9 Consensus size: 72
251 GATCGGCTTG
* *
261 AATAATTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-AGAAGTTCATC
1 AATAATTTAAGGAACCAAAGTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGA-AAGTTCATC
325 CAAAAGTA
65 CAAAAGTA
** *
333 AATAAGTTTAAGGAACTGAGGTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGAAAGTTCA
1 AATAA-TTTAAGGAACCAAAGTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGAAAGTTCA
396 GCGAAGAACA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
72 5 0.09
73 50 0.89
74 1 0.02
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (72 bp):
AATAATTTAAGGAACCAAAGTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGAAAGTTCATCC
AAAAGTA
Found at i:560 original size:289 final size:289
Alignment explanation
Indices: 41--618 Score: 1102
Period size: 289 Copynumber: 2.0 Consensus size: 289
31 TTTCCGAAGC
41 GTAAATAAGTTTAAGGAACTGAGGTTATAAAAGAACTCATAAAAACTTGACAAGTTCGAAAGTTC
1 GTAAATAAGTTTAAGGAACTGAGGTTATAAAAGAACTCATAAAAACTTGACAAGTTCGAAAGTTC
106 AGCCAAGAACAAAGAGAGAAACAGTTCGCACGTAAATAAGTTTTTAATTCAAAGAGCAAAAGTTG
66 AGCCAAGAACAAAGAGAGAAACAGTTCGCACGTAAATAAGTTTTTAATTCAAAGAGCAAAAGTTG
*
171 TTTACGAAATGACAAACTATTTAGACCAAATAATGCGATTTTTCGAGCATTGAATGTTCGAAAAA
131 TTTACGAAATGACAAACTATTTAGACCAAAAAATGCGATTTTTCGAGCATTGAATGTTCGAAAAA
* *
236 CAGGTCGAAGGATTGGATCGGCTTGAATAATTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAA
196 CAGGTCGAAGGATAGGATCGGCTTGAAAAATTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAA
301 GTTTGACAAGTTCAGAAGTTCATCCAAAA
261 GTTTGACAAGTTCAGAAGTTCATCCAAAA
*
330 GTAAATAAGTTTAAGGAACTGAGGTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGAAAGTTC
1 GTAAATAAGTTTAAGGAACTGAGGTTATAAAAGAACTCATAAAAACTTGACAAGTTCGAAAGTTC
*
395 AGCGAAGAACAAAGAGAGAAACAGTTCGCACGTAAATAAGTTTTTAATTCAAAGAGCAAAAGTTG
66 AGCCAAGAACAAAGAGAGAAACAGTTCGCACGTAAATAAGTTTTTAATTCAAAGAGCAAAAGTTG
460 TTTACGAAATGACAAACTATTTAGACCAAAAAATGCGATTTTTCGAGCATTGAATGTTCGAAAAA
131 TTTACGAAATGACAAACTATTTAGACCAAAAAATGCGATTTTTCGAGCATTGAATGTTCGAAAAA
*
525 CTGGTCGAAGGATAGGATCGGCTTGAAAAATTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAA
196 CAGGTCGAAGGATAGGATCGGCTTGAAAAATTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAA
590 GTTTGACAAGTTCAGAAGTTCATCCAAAA
261 GTTTGACAAGTTCAGAAGTTCATCCAAAA
619 ACCAAGAGAG
Statistics
Matches: 283, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
289 283 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (289 bp):
GTAAATAAGTTTAAGGAACTGAGGTTATAAAAGAACTCATAAAAACTTGACAAGTTCGAAAGTTC
AGCCAAGAACAAAGAGAGAAACAGTTCGCACGTAAATAAGTTTTTAATTCAAAGAGCAAAAGTTG
TTTACGAAATGACAAACTATTTAGACCAAAAAATGCGATTTTTCGAGCATTGAATGTTCGAAAAA
CAGGTCGAAGGATAGGATCGGCTTGAAAAATTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAA
GTTTGACAAGTTCAGAAGTTCATCCAAAA
Found at i:1346 original size:216 final size:216
Alignment explanation
Indices: 353--2666 Score: 2130
Period size: 216 Copynumber: 10.7 Consensus size: 216
343 AGGAACTGAG
* * * * * *
353 GTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGAAAGTTCAGCGAAGAACAAAGAGAGAAACA
1 GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACA
* * *
418 GTTCGCACGTAAATAAGTTTTTAATTCAAAGAGC-AAAAGTTGTTTACGAAATGACAAACTATTT
66 ATTCTCACGTAAATAAGTTTTTAATTCAAAGA-CAAAAAGTTGTTTACAAAATGACAAACTATTT
** * * * * *
482 AGACCAAAAAATGCGATTTTTCGAGCATTGAATGTTCGAAAAACTGGTCGAAGG-ATAGGATCGG
130 AGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCGAAAAATTGGTCAAAGGAAT-GGATCGT
* * *
546 CTTGAAAAATTTAAGGAACCAAA
194 CTTGAATACTTTCAGGAACCAAA
* * *
569 GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAAAACCAAGAGAGATACA
1 GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACA
* * * * * *
634 ATTCTCACGTAAATTAGTTTTCAATTCAAAGACCAAAAGTTGTTTAGAAAATTAAAAAAAC-ATT
66 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAA-T-GACAAACTATT
*** * * * * * * * * *
698 TAGAATGAATGATGTGATTTCCCGAGCCTGGAATGCTCGAAAAGTTAGTCGAAGGAATGGGTCAT
129 TAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGT
* * * * *
763 CTTTAATGCTCTCAGAAACCGAA
194 CTTGAATACTTTCAGGAACCAAA
* **
786 GTTATAAAAGAACTGGTAAATA-TTTGACAAGTTCTAAAGTTCATCCAAGAACCAAGAGAGAAAC
1 GTTATAAAAGAACTCGTAAA-AGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAAC
* * *
850 AATCCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAAGGTT-TTTACAAAATGACAAACTATT
65 AATTCTCACGTAAATAAGTTTTTAATTCAAAGA-CAAAAAGTTGTTTACAAAATGACAAACTATT
* * * **
914 TAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTTGAAAAATTGCACAAAGGAATGGATCGT
129 TAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGT
* * *
979 CTTTAATACTCTCAAGAACCAAA
194 CTTGAATACTTTCAGGAACCAAA
* ** * * * * *
1002 GTTATAATAAAAGAACTTGTAAATTTTTGAAAAGTTTGAAAGTTAATCCAAGAACCAGGAGAGAA
1 G-T-T-ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAA
* * * * * * * * * *
1067 A-ATATTCTCATGCAAAAAAATTTTAAATTCAAACACCAAAAGTTGTTTACCATATTACAAACTA
63 ACA-ATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTA
* ** * ** *
1131 TTTTGACCAAATGATGAAATTTTCCGAGAATGGAATGTTCGAAAAATTGGTTGAAGGAATGCATC
127 TTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATC
* * *
1196 TTCTTAAATAC-TACTAGGAACCAAA
192 GTCTTGAATACTTTC-AGGAACCAAA
** ** * * ****
1221 GTTATAAAAGAACTTTTAAATTTTTGAAAAGTTCGGAAGTTCATCCGAGAATTGGGAGAGAAACA
1 GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACA
* *
1286 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTCACAAAATGTCAAACTATTTA
66 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATTTA
* * * * *
1351 GACCAAATGATGTGATTTAT-CGAGCATGGAATGTTCGGAAAA-TGGCCCAAATGAATGGATAGT
131 GACCAAATGATGCGATTT-TCCGAGCATGGAATGTTCGAAAAATTGG-TCAAAGGAATGGATCGT
* *
1414 CTTGAGTACTTTGAGGAACCAAA
194 CTTGAATACTTTCAGGAACCAAA
* * *
1437 GTTATAAAAGAACTCGTAAAAGTTTGACTAGTTCGTAAGTTCATCCGAGAACCACA-AGAGAAAC
1 GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCA-AGAGAGAAAC
* * * * * * * * *
1501 AATTATCACGTAAATAGGTTTTTGAATTCGAAGACTAAATGTTGTTAACATAATGACAAAGTTTT
65 AATTCTCACGTAAATAAGTTTTT-AATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATT
* * * * * * * *
1566 TAGACCGAATGATGCGA-TTTCTCGAGCAAGGAATGCTAGAAAAA-AGGCTCAAATGAACGGATA
129 TAGACCAAATGATGCGATTTTC-CGAGCATGGAATGTTCGAAAAATTGG-TCAAAGGAATGGATC
*
1629 GTCTTGAATACTTTAAGGAACCAAA
192 GTCTTGAATACTTTCAGGAACCAAA
* * * * * *
1654 GTTGTAAAAGAACTCGTAAAAGTTTTACTAGTTCGTAAGTTCGTCCGAGAACCAAGAGAGAAACA
1 GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACA
* * * * *
1719 ATTCTCATGTAAATAAGTTTTTAATTTAAAGACCAAAATTTGTTTACAAAATCACAAACTATTTA
66 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATTTA
* * * * *
1784 GA-CAAAAGATGCGATTTTCGGAGCATGGAATGCTC-AGAAAA-CGGCTCAAAGGAATGGATAGT
131 GACCAAATGATGCGATTTTCCGAGCATGGAATGTTCGA-AAAATTGG-TCAAAGGAATGGATCGT
*
1846 CTTGAATACTTTGAGGAACCAAA
194 CTTGAATACTTTCAGGAACCAAA
* * * * * *
1869 GTTATAAAAGAACTCGTAAAAGTTCGACTAGTTCGTAAGTTCGTCCGAGAACCACA-AGAGAAGC
1 GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCA-AGAGAGAAAC
* * * * * * *
1933 AATTCTCACGTAAATACGTTTTTGAATTCGAAGACTAAATGTTGTTTACATAATGACAAATTTTT
65 AATTCTCACGTAAATAAGTTTTT-AATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATT
* * * * * * *
1998 TAGATCGAATGATGCGA-TTTCCGAAGCATGAAAAGTTCGAAAAATTGGTCGAAGGAATGAATAG
129 TAGACCAAATGATGCGATTTTCCG-AGCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCG
* *
2062 TCTTGAATACTTTGAAGAACCAAA
193 TCTTGAATACTTTCAGGAACCAAA
* * * *
2086 GTTATAAAAGAACTCGTAAAAGTTCGATC-AGTTCGTAAGTTCGTCCTAGAACCACA-AGAGAAA
1 GTTATAAAAGAACTCGTAAAAGTTTGA-CAAGTTCGGAAGTTCATCCAAGAACCA-AGAGAGAAA
* * * * * * *
2149 CAATTCTCACGTAAATAGGTTTTTAATTCGAAGACTAAAAGTTGTTTACATAATGACATAGTTTT
64 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATT
* * * * * *
2214 TAGACCGAATGATACGA-TTCCCGAGCATGGAAAGTTTGAAAAATTGGTCAAATGAATGGATCGT
129 TAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGT
* **
2278 CTTGAATACTCTCAGGAACTTAA
194 CTTGAATACTTTCAGGAACCAAA
* * ** * * * * * * *
2301 GTTACAAAAGAGCTATTAAATGTTCCG-CTAGTACGGAAGTTCGA-ACAAAAACCATGAGAGAAA
1 GTTATAAAAGAACTCGTAAAAGTT-TGACAAGTTCGGAAGTTC-ATCCAAGAACCAAGAGAGAAA
* * *
2364 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAA-TTGTTTAGAAAATGATAACCTAT
64 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-CAAAAAGTTGTTTACAAAATGACAAACTAT
* **
2428 TTAGACCAAATGATGTC-A-TTTCTCGAGCATGGAAAGCTT-GAAAAATTGCACAAAGGAATGGA
128 TTAGACCAAATGATG-CGATTTTC-CGAGCATGGAATG-TTCGAAAAATTGGTCAAAGGAATGGA
** * * * *
2490 TCACCTTTAATAGTTTAAAAGGAACCGAA
190 TCGTCTTGAATACTTT--CAGGAACCAAA
* * ** *
2519 GTTATAAAGGAACT-GATAAAAAGTTTGAAAAGTTTAGAAGTTCGTCCAAGAACCAAGAGAGAAA
1 GTTATAAAAGAACTCG-T-AAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAA
* * * * * *
2583 CAATTGTCATGTAAAT-A-TTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGAAAAATTATT
64 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATT
*
2646 TAGACCAAACGATGCGATTTT
129 TAGACCAAATGATGCGATTTT
2667 GGAAGCGTAA
Statistics
Matches: 1744, Mismatches: 305, Indels: 96
0.81 0.14 0.04
Matches are distributed among these distances:
214 2 0.00
215 318 0.18
216 615 0.35
217 541 0.31
218 55 0.03
219 213 0.12
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (216 bp):
GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACA
ATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATTTA
GACCAAATGATGCGATTTTCCGAGCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGTCT
TGAATACTTTCAGGAACCAAA
Found at i:2763 original size:176 final size:181
Alignment explanation
Indices: 2501--2844 Score: 436
Period size: 178 Copynumber: 1.9 Consensus size: 181
2491 CACCTTTAAT
* * * *
2501 AGTTTAAAAGGAACCGAAGTTATAAAGGAACTGATAAAAAGTTTGAAAAGTTTAGAAGTTCGTCC
1 AGTTTAAAAGGAACCGAAGTTATAAAAGAACTCATAAAAAGCTTGAAAAGTTGAGAAGTTCGTCC
* * * * *
2566 AAGAACCAAGAGAGAAACAATTGTCATGTAAAT-A-TTTTTAATTCAAAGA-CGAAAAGTTGAT-
66 AAGAACAAAGAGAGAAACAATTCTCACGAAAATAAGTTTTTAATTCAAAGAGC-AAAAGCTG-TC
* *
2627 TACAAAATGAAAAATTATTTAGACCAAACGATGCGATTTTGGAAGCGTAAATA
129 TACAAAATGAAAAACTATTTAGACCAAACAATGCGATTTTGGAAGCGTAAATA
* *
2680 AGTTT-AAA-GAACTGAAGTTATAAAAGAACTCAT-AAAAGCTTGACAAGTTCGA-AAGTTCAG-
1 AGTTTAAAAGGAACCGAAGTTATAAAAGAACTCATAAAAAGCTTGAAAAGTT-GAGAAGTTC-GT
*
2740 CCAAGAATAAAGAGAGAAACAATTCTCACGAAAATAAGTTTTTAATTCAAAGAGCAAAAGCTGTC
64 CCAAGAACAAAGAGAGAAACAATTCTCACGAAAATAAGTTTTTAATTCAAAGAGCAAAAGCTGTC
* * *
2805 TACGAAATGACAAACTATTTAGACCAAATAATGCGATTTT
129 TACAAAATGAAAAACTATTTAGACCAAACAATGCGATTTT
2845 TCGAGCATTG
Statistics
Matches: 142, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
176 50 0.35
177 26 0.18
178 60 0.42
179 6 0.04
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (181 bp):
AGTTTAAAAGGAACCGAAGTTATAAAAGAACTCATAAAAAGCTTGAAAAGTTGAGAAGTTCGTCC
AAGAACAAAGAGAGAAACAATTCTCACGAAAATAAGTTTTTAATTCAAAGAGCAAAAGCTGTCTA
CAAAATGAAAAACTATTTAGACCAAACAATGCGATTTTGGAAGCGTAAATA
Done.