Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012719.1 Kokia drynarioides strain JFW-HI SEQ_127730, 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: 9427
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:805 original size:5 final size:5
Alignment explanation
Indices: 795--843 Score: 57
Period size: 5 Copynumber: 10.2 Consensus size: 5
785 TTCTATTTGG
* * *
795 AAGAA AAGAA AATAA ATGAA ATG-A AA-AA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
843 A
1 A
844 CCAAACAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 5 0.13
5 33 0.87
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (5 bp):
AAGAA
Found at i:6111 original size:2 final size:2
Alignment explanation
Indices: 6106--6131 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6096 TATATATATA
6106 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
6132 ATGCAAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:6524 original size:74 final size:74
Alignment explanation
Indices: 6398--6547 Score: 257
Period size: 74 Copynumber: 2.0 Consensus size: 74
6388 TGGAGGGATA
6398 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATAGCT
1 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATAGCT
6463 ATTCACATT
66 ATTCACATT
*
6472 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTA-GTAATGATGAATGATGGC
1 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATG-AATGATGAATGATAGC
* *
6536 TGTTCACTTT
65 TATTCACATT
6546 CA
1 CA
6548 TTTTGTAAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
73 1 0.01
74 71 0.99
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (74 bp):
CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATAGCT
ATTCACATT
Found at i:6796 original size:74 final size:74
Alignment explanation
Indices: 6670--6819 Score: 257
Period size: 74 Copynumber: 2.0 Consensus size: 74
6660 NNNNNNNNNN
6670 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATAGCT
1 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATAGCT
6735 ATTCACATT
66 ATTCACATT
*
6744 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTA-GTAATGATGAATGATGGC
1 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATG-AATGATGAATGATAGC
* *
6808 TGTTCACTTT
65 TATTCACATT
6818 CA
1 CA
6820 TTTTGTAAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
73 1 0.01
74 71 0.99
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (74 bp):
CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATAGCT
ATTCACATT
Found at i:7863 original size:214 final size:215
Alignment explanation
Indices: 7292--8577 Score: 1288
Period size: 214 Copynumber: 6.0 Consensus size: 215
7282 TAATCATATT
* * * * * * *
7292 AGAAACAATATAGAAATAATTCTCACGTAAATGAGTTTTAAATTCAAAGATCAAAATTTGTTTAC
1 AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
* *
7357 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCTTTTGTGCATGGAATGTTC-GAAAAATT
66 AAAATGACAAACTATTTAGACCAAATGATGCGATTTC--CTGAGCATGGAATGTTCAG-AAAATT
* * * * *
7421 GCTCGAATGAATGGATCATCTTGAATGCTTAAAGGAACCAAAGTTATAAAAAGAACTCGTAAAAG
128 GCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTAT-AAGA-AACTCGTAAAAG
* *
7486 TTTCTA-AAGTTTGAAAGCTCGTCGCA
191 TTT-GACAAGTTTGAAAGTTCGTC-CA
* * * * *
7512 A-AACCAATAGAGAAACAATTCTCACATAAATAAGTTTTTAATTTAAACACTAAAACCTGTTTAC
1 AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
** * *
7576 AAAATTCCAAACTATTTAGACCAAATGATTCGATTACCCT-AGCATGGAATGTTCAGAAAATTGC
66 AAAATGACAAACTATTTAGACCAAATGATGCGATT-TCCTGAGCATGGAATGTTCAGAAAATTGC
** *
7640 TCGAAGGAATGGATTGTCTTGAATACTTTAAGGAACCGAAGTTATAACGAAACTCATAAAAGTTT
130 TCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAA-GAAACTCGTAAAAGTTT
*
7705 GACAAGTTTGAAAGTTTGTCCA
194 GACAAGTTTGAAAGTTCGTCCA
* * *
7727 AGTACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-C-AAACTTTTTTAC
1 AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
* * *
7790 AAAATGACATACTATTTAGACCAAATGATGCGATTTCATGAGAATGGAATGTTCAGAAAATTGCT
66 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTGCT
** * *
7855 AAAAGGAATTGAT-AGTCTTGAATACTTTAAGGTACC-----------AAA---GTAAAAGTTTG
131 CGAAGGAATGGATCA-TCTTGAATACTTTAAGGAACCGAAGTTATAAGAAACTCGTAAAAGTTTG
** *
7905 ACAAGTTCAAAAGTTCGTCCT
195 ACAAGTTTGAAAGTTCGTCCA
* ** *
7926 AGAACCAATAGAGAAACAATTCTCACGTAAATGAGTTTTTAATTCAAAGATGAAAACATGTTTAC
1 AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
* * * * *** * * * *
7991 AGAATGAAAAAAATATTTAGACAAAATGATTTAATTTCCCGAGAATGGAATGTTCGGAAAATTGT
66 AAAATG-ACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTGC
* * * * * *
8056 TTGAAAGAATGG-TCATCTTGAATACTTTTAAAGAACCGAAGTAATAAAGGATCTCGTAAAAGTT
130 TCGAAGGAATGGATCATCTTGAATAC-TTTAAGGAACCGAAGTTAT-AAGAAACTCGTAAAAGTT
* *
8120 TTACTAGTTCTG-AAGTTCGTCCA
193 TGACAAGTT-TGAAAGTTCGTCCA
* * * * *
8143 AGAACC-A-AGAGAAACAATTCTCACTTAAATATGTGTTTAATTCAAAGACCAAAACTTGTGTAG
1 AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
* * * * * * * *
8206 AAAATGGCAAAATATTTAGACCATATGATGCAATCTCTTGTGCATGGAATGTT-TGAAAAATTGC
66 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCAG-AAAATTGC
* * * *
8270 TCGAATGAATAGATCATCTTGAATACATTAAGGAACCGAAGTTATAACGAAACTCATAAAAGTTT
130 TCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAA-GAAACTCGTAAAAGTTT
8335 GACAAGTTTGAAAGTTCGTCCA
194 GACAAGTTTGAAAGTTCGTCCA
* * * * * *
8357 AGAA-CATAAACAGAAACAATTCTCACGTAAATAAG---TT-ATTCAAATACCAAAAGTTGCTAA
1 AGAACCA-ATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * *
8417 CAAAATGAAAAACTATTTAGACCAAACT-ATGTGATTTCCCGAGCATGGAATGTTCAGAAAATTG
65 CAAAATGACAAACTATTTAGACCAAA-TGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTG
* * * * *
8481 CTCGAAGGAATGGATCGTCTTCAATATTTTAAGGAACCGAAATTATAAAAGAACTCGTAAAAGTT
129 CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAGA-AACTCGTAAAAGTT
*
8546 TGACAAGTTCGAAAGTTCGTCTC-
193 TGACAAGTTTGAAAGTTCGTC-CA
8569 AGAACCAAT
1 AGAACCAAT
8578 TGATACGATC
Statistics
Matches: 876, Mismatches: 150, Indels: 88
0.79 0.13 0.08
Matches are distributed among these distances:
199 74 0.08
201 26 0.03
202 68 0.08
211 1 0.00
212 145 0.17
213 15 0.02
214 199 0.23
215 70 0.08
216 98 0.11
217 93 0.11
218 2 0.00
219 83 0.09
220 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (215 bp):
AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTGCT
CGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAGAAACTCGTAAAAGTTTGA
CAAGTTTGAAAGTTCGTCCA
Found at i:8255 original size:416 final size:418
Alignment explanation
Indices: 7303--8576 Score: 1172
Period size: 416 Copynumber: 3.0 Consensus size: 418
7293 GAAACAATAT
* * * *
7303 AGAAATAATTCTCACGTAAATGAGT-TTTAAATTCAAAGATCAAAATTTGTTTACAAAATGACAA
1 AGAAACAATTCTCACGTAAATAAGTGTTT-AATTCAAAGA-C-AAACTTGTGTACAAAATGACAA
* * ** * * * ** *
7367 ACTATTTAGACCAAATGATGCGATTTCTTTTGTGCATGGAATGTTCGAAAAATTGCTCGAATGAA
63 AATATTTAGACCAAATGATGC-A-ATCTCATGAGAATGGAATGTTAGAAAAATTGCTAAAAGGAA
* * * *
7432 TGGATCATCTTGAATGC-TTAAAGGAACCAAAGTTATAAAAAGAACTCGTAAAAGTTTCTA-AAG
126 TAGATCATCTTGAATACATT-AAGGAACC--A---AT--AACG-A----TAAAAGTTT-GACAAG
** * * *
7495 TTTGAAAGCTCGTCGCAA-AACCAATAGAGAAACAATTCTCACATAAATAAGTTTTTAATTTAAA
177 TTCAAAAGTTCGTC-CAAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* *** * * * *
7559 CACTAAAACCTGTTTACAAAATTCCAAACTATTTAGACCAAATGATTCGATTACCCTAGCATGGA
241 CA-TAAAACATGTTTACAAAATGAAAAACTATTTAGACAAAATGATTTGATTTCCCGAGCATGGA
* *
7624 ATGTTCAGAAAATTGCTCGAAGGAATGGATTGTCTTGAATAC-TTTAAGGAACCGAAGTTATAAC
305 ATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTTAAGGAACCGAAGTTATAAA
* * * *
7688 GAAACTCATAAAAGTTTGACAAGTT-TGAAAGTTTGTCCAAGTACCAAGAG
370 GGAACTCGTAAAAGTTTGACAAGTTCTGAAAGTTCGTCCAAGAACC-A-AG
* * * * *
7738 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAACTTTTTTACAAAATGACATACT
1 AGAAACAATTCTCACGTAAATAAGTGTTTAATTCAAAGACAAACTTGTGTACAAAATGACAAAAT
* * *
7803 ATTTAGACCAAATGATGCGATTTCATGAGAATGGAATGTTCAG-AAAATTGCTAAAAGGAATTGA
66 ATTTAGACCAAATGATGCAATCTCATGAGAATGGAATGTT-AGAAAAATTGCTAAAAGGAATAGA
* * *
7867 T-AGTCTTGAATACTTTAAGGTACC-A-AA-G-TAAAAGTTTGACAAGTTCAAAAGTTCGTCCTA
130 TCA-TCTTGAATACATTAAGGAACCAATAACGATAAAAGTTTGACAAGTTCAAAAGTTCGTCCAA
* *
7927 GAACCAATAGAGAAACAATTCTCACGTAAATGAGTTTTTAATTCAAAGATGAAAACATGTTTACA
194 GAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAACAT-AAAACATGTTTACA
* * * * * *
7992 GAATGAAAAAAATATTTAGACAAAATGATTTAATTTCCCGAGAATGGAATGTTCGGAAAATTGTT
258 AAATG-AAAAACTATTTAGACAAAATGATTTGATTTCCCGAGCATGGAATGTTCAGAAAATTGCT
* * * * * *
8057 TGAAAGAATGG-TCATCTTGAATACTTTTAAAGAACCGAAGTAATAAAGGATCTCGTAAAAGTTT
322 CGAAGGAATGGATCGTCTTGAATACTTTTAAGGAACCGAAGTTATAAAGGAACTCGTAAAAGTTT
* *
8121 TACTAGTTCTG-AAGTTCGTCCAAGAACCAAG
387 GACAAGTTCTGAAAGTTCGTCCAAGAACCAAG
* * * *
8152 AGAAACAATTCTCACTTAAATATGTGTTTAATTCAAAGACCAAAACTTGTGTAGAAAATGGCAAA
1 AGAAACAATTCTCACGTAAATAAGTGTTTAATTCAAAGA-C-AAACTTGTGTACAAAATGACAAA
* * * * * ** *
8217 ATATTTAGACCATATGATGCAATCTCTTGTGCATGGAATGTTTGAAAAATTGCTCGAATGAATAG
64 ATATTTAGACCAAATGATGCAATCTCATGAGAATGGAATGTTAGAAAAATTGCTAAAAGGAATAG
**
8282 ATCATCTTGAATACATTAAGGAACCGAAGTTATAACGAAACTCATAAAAGTTTGACAAGTTTGAA
129 ATCATCTTGAATACATTAAGGAACC--A---ATAACG------ATAAAAGTTTGACAAGTTCAAA
* * * *
8347 AGTTCGTCCAAGAA-CATAAACAGAAACAATTCTCACGTAAATAAG---TT-ATTCAAATACCAA
183 AGTTCGTCCAAGAACCA-ATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAACA-TAA
** * * * *
8407 AAGTTGCTAACAAAATGAAAAACTATTTAGACCAAACT-ATGTGATTTCCCGAGCATGGAATGTT
246 AACATGTTTACAAAATGAAAAACTATTTAGA-CAAAATGATTTGATTTCCCGAGCATGGAATGTT
* * *
8471 CAGAAAATTGCTCGAAGGAATGGATCGTCTTCAATA-TTTTAAGGAACCGAAATTATAAAAGAAC
310 CAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTTAAGGAACCGAAGTTATAAAGGAAC
8535 TCGTAAAAGTTTGACAAGTTC-GAAAGTTCGTCTC-AGAACCAA
375 TCGTAAAAGTTTGACAAGTTCTGAAAGTTCGTC-CAAGAACCAA
8577 TTGATACGAT
Statistics
Matches: 695, Mismatches: 109, Indels: 79
0.79 0.12 0.09
Matches are distributed among these distances:
414 42 0.06
415 97 0.14
416 201 0.29
417 3 0.00
421 1 0.00
422 3 0.00
423 2 0.00
424 1 0.00
425 2 0.00
426 114 0.16
427 38 0.05
428 2 0.00
430 3 0.00
431 106 0.15
432 3 0.00
433 40 0.06
434 1 0.00
435 33 0.05
436 3 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (418 bp):
AGAAACAATTCTCACGTAAATAAGTGTTTAATTCAAAGACAAACTTGTGTACAAAATGACAAAAT
ATTTAGACCAAATGATGCAATCTCATGAGAATGGAATGTTAGAAAAATTGCTAAAAGGAATAGAT
CATCTTGAATACATTAAGGAACCAATAACGATAAAAGTTTGACAAGTTCAAAAGTTCGTCCAAGA
ACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAACATAAAACATGTTTACAAAA
TGAAAAACTATTTAGACAAAATGATTTGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAA
GGAATGGATCGTCTTGAATACTTTTAAGGAACCGAAGTTATAAAGGAACTCGTAAAAGTTTGACA
AGTTCTGAAAGTTCGTCCAAGAACCAAG
Found at i:8467 original size:212 final size:209
Alignment explanation
Indices: 7894--8566 Score: 665
Period size: 212 Copynumber: 3.1 Consensus size: 209
7884 AGGTACCAAA
* * * *
7894 GTAAAAGTTTGACAAGTTCAAAAGTTCGTCCTAGAACCAATAGAGAAACAATTCTCACGTAAATG
1 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAA-CAAAAGAGAAACAATTCTCACGTAAATA
** * * * *
7959 AGTTTTTAATTCAAAGATGAAAACATGTTTACAGAATGAAAAAAATATTTAGACAAAATGATTTA
65 AG--TTTAATTCAAAGACCAAAACTTG-TTACAAAATG--AAAAATATTTAGACCAAATGATGTA
* * * * * * *
8024 ATTTCCCGAGAATGGAATGTTCGGAAAATTGTTTGAAAGAATGGTCATCTTGAATACTTTTAAAG
125 ATTTCCCGAGCATGGAATGTTTGAAAAATTGCTCGAAAGAATGATCATCTTGAATAC-TTTAAGG
* * *
8089 AACCGAAGTAATAAAGGATCTC
189 AACCGAAGTTAT-AAGAAACTC
* * * *
8111 GTAAAAGTTTTACTAGTTCTG-AAGTTCGTCCAAGAAC-CAAGAGAAACAATTCTCACTTAAATA
1 GTAAAAGTTTGACAAGTTC-GAAAGTTCGTCCAAGAACAAAAGAGAAACAATTCTCACGTAAATA
* * * * *
8174 TGTGTTTAATTCAAAGACCAAAACTTGTGTAGAAAATGGCAAAATATTTAGACCATATGATGCAA
65 --AGTTTAATTCAAAGACCAAAACTTGT-TACAAAAT-GAAAAATATTTAGACCAAATGATGTAA
* ** * * *
8239 TCTCTTGTGCATGGAATGTTTGAAAAATTGCTCGAATGAATAGATCATCTTGAATACATTAAGGA
126 TTTCCCGAGCATGGAATGTTTGAAAAATTGCTCGAAAGAAT-GATCATCTTGAATACTTTAAGGA
8304 ACCGAAGTTATAACGAAACTC
190 ACCGAAGTTATAA-GAAACTC
* * *
8325 ATAAAAGTTTGACAAGTTTGAAAGTTCGTCCAAGAACATAAACAGAAACAATTCTCACGTAAATA
1 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACA-AAAGAGAAACAATTCTCACGTAAATA
* * * *
8390 AG-TT-ATTCAAATACCAAAAGTTGCTAACAAAATGAAAAACTATTTAGACCAAACT-ATGTGAT
65 AGTTTAATTCAAAGACCAAAACTTG-TTACAAAATGAAAAA-TATTTAGACCAAA-TGATGTAAT
* * * * *
8452 TTCCCGAGCATGGAATG-TTCAGAAAATTGCTCGAAGGAATGGATCGTCTTCAATATTTTAAGGA
127 TTCCCGAGCATGGAATGTTTGA-AAAATTGCTCGAAAGAAT-GATCATCTTGAATACTTTAAGGA
* *
8516 ACCGAAATTATAAAAGAACTC
190 ACCGAAGTTATAAGA-AACTC
8537 GTAAAAGTTTGACAAGTTCGAAAGTTCGTC
1 GTAAAAGTTTGACAAGTTCGAAAGTTCGTC
8567 TCAGAACCAA
Statistics
Matches: 375, Mismatches: 66, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
211 9 0.02
212 134 0.36
213 7 0.02
214 106 0.28
215 62 0.17
216 25 0.07
217 32 0.09
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (209 bp):
GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAAGAGAAACAATTCTCACGTAAATAA
GTTTAATTCAAAGACCAAAACTTGTTACAAAATGAAAAATATTTAGACCAAATGATGTAATTTCC
CGAGCATGGAATGTTTGAAAAATTGCTCGAAAGAATGATCATCTTGAATACTTTAAGGAACCGAA
GTTATAAGAAACTC
Done.