Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003869.1 Kokia drynarioides strain JFW-HI SEQ_116903, 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: 1949
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Found at i:380 original size:216 final size:215
Alignment explanation
Indices: 1--704 Score: 1070
Period size: 216 Copynumber: 3.3 Consensus size: 215
1 AATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAGTAACTCGTAA
1 AATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAA-TAACTCGTAA
* *
66 AAGTTTGACAAGTTCGAAAATTCGTACAAAGACAAAGAGAGAAACAATTATCACGTAAATAAGTT
65 AAGTTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTT
131 TTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATTTTAACCAAATGATGCGATTTC
130 TTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATTTTAACCAAATGATGCGATTTC
196 CCAAGTATGGAAAATTCGAAA
195 CCAAGTATGGAAAATTCGAAA
* *
217 AATTGCTCAAAGGAATGGATCTTGTTGAATAGTTTAGGGAACTGAAGTTAAGAAATAACTCGTAA
1 AATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAA-AAATAACTCGTAA
* * * **
282 AAGTTTGAAAAGTTCGAGAGTTCGT-CGAAGAACAAAGAGAGAAACAATTCTCACAAAAATAAGT
65 AAGTTTGACAAGTTCGAAAGTTCGTACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGT
* * * * * * *
346 TTTTAATTCAAAGTCCAAAACTTATTTGCAAAATGACGAATTATTTAAACCAAATGATGCGATTT
129 TTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATTTTAACCAAATGATGCGATTT
* * **
411 CCCGAGCATGGAATGTTCGAAA
194 CCCAAGTATGGAAAATTCGAAA
* *
433 AATTGCTCTAAGAAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAATATAACTCGTAA
1 AATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAA-ATAACTCGTAA
*
498 AAGTTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAATT
65 AAGTTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * *
563 TTTAATTCAAAGACAAAAACTTGTGTACAAAATGACAAACTA-TTTAGACCAAATGAAGGGATTT
130 TTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATTTTA-ACCAAATGATGCGATTT
* *
627 TCCAAGTATGGAAAATTTGAAA
194 CCCAAGTATGGAAAATTCGAAA
* *
649 AATTGCTCAAAGGAGTGGATCTTGTTGAATACTTTAGGGAACTGAAGTTACAAAAT
1 AATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTA-AAAAT
705 GACAAACTAT
Statistics
Matches: 432, Mismatches: 50, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
215 9 0.02
216 413 0.96
217 10 0.02
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (215 bp):
AATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAATAACTCGTAAA
AGTTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTT
TTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATTTTAACCAAATGATGCGATTTCC
CAAGTATGGAAAATTCGAAA
Found at i:779 original size:109 final size:109
Alignment explanation
Indices: 588--811 Score: 324
Period size: 109 Copynumber: 2.1 Consensus size: 109
578 AAAACTTGTG
* * * * * ***
588 TACAAAATGACAAACTATTTAGACCAAATGAAGGGATTTTCCAAGTATGGAAAATTTGAAAAATT
1 TACAAAATGACAAACTATATAAACCAAATGAAGCGATTTCCCAAGCATGGAAAATCCAAAAAATT
* *
653 GCTCAAAGGAGTGGATCTTGTTGAATACTTTAGGGAACTGAAGT
66 GCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGT
* * *
697 TACAAAATGACAAACTATATAAACCAAATGATGCGATTTCCCGAGCATGGAATATCCAAAAAATT
1 TACAAAATGACAAACTATATAAACCAAATGAAGCGATTTCCCAAGCATGGAAAATCCAAAAAATT
762 GCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGT
66 GCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGT
806 TA-AAAA
1 TACAAAA
812 GTAACTTGTA
Statistics
Matches: 102, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 4 0.04
109 98 0.96
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (109 bp):
TACAAAATGACAAACTATATAAACCAAATGAAGCGATTTCCCAAGCATGGAAAATCCAAAAAATT
GCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGT
Found at i:978 original size:325 final size:325
Alignment explanation
Indices: 374--981 Score: 1011
Period size: 325 Copynumber: 1.9 Consensus size: 325
364 AACTTATTTG
* * * * * *
374 CAAAATGACGAATTATTTAAACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGC
1 CAAAATGACAAACTATATAAACCAAATGATGCGATTTCCCGAGCATGGAATATCCAAAAAATTGC
*
439 TCTAAGAAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAATATAACTCGTAAAAGTTT
66 TCAAAGAAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAATATAACTCGTAAAAGTTT
504 GACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAAT
131 GACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAAT
* * *
569 TCAAAGACAAAAACTTGTGTACAAAATGACAAACTATTTAGACCAAATGAAGGGATTTTCCAAGT
196 TCAAAGACAAAAACTTGTGTACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTCCCAAGC
*
634 ATGGAAAATTTGAAAAATTGCTCAAAGGAGTGGATCTTGTTGAATACTTTAGGGAACTGAAGTTA
261 ATGGAAAATTCGAAAAATTGCTCAAAGGAGTGGATCTTGTTGAATACTTTAGGGAACTGAAGTTA
699 CAAAATGACAAACTATATAAACCAAATGATGCGATTTCCCGAGCATGGAATATCCAAAAAATTGC
1 CAAAATGACAAACTATATAAACCAAATGATGCGATTTCCCGAGCATGGAATATCCAAAAAATTGC
* *
764 TCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAA-AGTAACTTGTAAAAGTT
66 TCAAAGAAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAATA-TAACTCGTAAAAGTT
*
828 TGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA
130 TGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAA
* * * *
893 TTCAAAGACATAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAG
195 TTCAAAGACAAAAACTTGTGTACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTCCCAAG
** *
958 CATGGAATGTTCGGAAAATTGCTC
260 CATGGAAAATTCGAAAAATTGCTC
982 GAAGCAATGA
Statistics
Matches: 261, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
324 1 0.00
325 260 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (325 bp):
CAAAATGACAAACTATATAAACCAAATGATGCGATTTCCCGAGCATGGAATATCCAAAAAATTGC
TCAAAGAAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAATATAACTCGTAAAAGTTT
GACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAAT
TCAAAGACAAAAACTTGTGTACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTCCCAAGC
ATGGAAAATTCGAAAAATTGCTCAAAGGAGTGGATCTTGTTGAATACTTTAGGGAACTGAAGTTA
Found at i:1080 original size:215 final size:214
Alignment explanation
Indices: 696--1949 Score: 1676
Period size: 215 Copynumber: 5.8 Consensus size: 214
686 GGAACTGAAG
* * * *
696 TTACAAAATGACAAACTATATAAACCAAATGATGCGATTTCCCGAGCATGGAATATCCAAAAAAT
1 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATATTCGAAAAAT
*
761 TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAGTAACTTGTAAAAG
66 TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAG-AACTCGTAAAAG
826 TTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
130 TTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
891 AATTCAAAGACATAAACTTGT
195 AATTCAAAGACA-AAACTTGT
* *
912 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAAT
1 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATATTCGAAAAAT
* * * * * * * *
977 TGCTCGAAGCAAT-GATCATCTTGAATACTTGAAGGATCCGAAGTTATAAAAGAACTAGTAAAAG
66 TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTA-AAAAGAACTCGTAAAAG
* * * *
1041 TTTGACAAGTTCGAAAGTTCGT-CCAGGAACAAAGAGAGAAACAATTCTCACATAAATAAATTTT
130 TTTGACAAGTTCGAAAGTTCGTACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
1105 TAATTCAAAGACAAAAACTTGT
194 TAATTCAAAGAC-AAAACTTGT
* * * ** * * * * *
1127 TTTCAAAATGACAAACTATTTAGACCAAATGAAGCGATTTTCAAAGTATGAAAAATTTGAAAATT
1 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATATTCGAAAAAT
* *
1192 TACTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCG-AGTTAAAAAGTAACTCGTAAATG
66 TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAG-AACTCGTAAAAG
1256 TTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
130 TTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
1321 AATTCAAAGACCAAAACTTGT
195 AATTCAAAGA-CAAAACTTGT
* * * * * * *
1342 TTGCAAAATGACAAACTAATTAGGCCAAATGATGCGATCTCCCGAGCATGAAATGTTTGAAAAAT
1 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATATTCGAAAAAT
* * * * * *
1407 TGCTCGAAA-GAATGGATCGTCTTGAATTCTTTAAGGATCCGAAGTTATAAAAGAACTAGTAAAA
66 TGCTC-AAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTA-AAAAGAACTCGTAAAA
* * *
1471 GTTTAACAAGTTCGAAAGTTCGT-CCAGGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTT
129 GTTTGACAAGTTCGAAAGTTCGTACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTT
*
1535 TTAATTCAAAGACAAAAACTTGG
193 TTAATTCAAAGAC-AAAACTTGT
* * *** * * *
1558 ATACAAAATGACAAACTATTTAGACGAAATGAAATGATTTCCCAAGGATGGAATATTAGAAAAAT
1 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATATTCGAAAAAT
* * *
1623 TGCTCAAAGGAATGGATCTTGTTAAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAG
66 TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTT-AAAAAGAACTCGTAAAAG
* * *
1688 TTTGACAAGTTCGAAAGTT--TGCCAAGAACAAAGAGAGAAACAATTCTCATGTAAATAAGTTTT
130 TTTGACAAGTTCGAAAGTTCGTACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
*
1751 TAATTCAAAGTGCAAAACTTGT
194 TAATTCAAAG-ACAAAACTTGT
* * * * *
1773 TTACAAAATGACAAATTAATTAGACCAAATGATACGATTTCCCGAGCATGGAATGTTCGGAAAAT
1 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATATTCGAAAAAT
* * *
1838 TGCTCGAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACCCGTAAAAG
66 TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTT-AAAAAGAACTCGTAAAAG
*
1903 TTTGACAAGTTCGAAAGTTAGTACAAAGACAAAGAGAGAAACAATTC
130 TTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTC
Statistics
Matches: 907, Mismatches: 113, Indels: 36
0.86 0.11 0.03
Matches are distributed among these distances:
214 9 0.01
215 552 0.61
216 335 0.37
217 11 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (214 bp):
TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATATTCGAAAAAT
TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAGAACTCGTAAAAGT
TTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA
ATTCAAAGACAAAACTTGT
Found at i:1508 original size:431 final size:431
Alignment explanation
Indices: 697--1949 Score: 1890
Period size: 431 Copynumber: 2.9 Consensus size: 431
687 GAACTGAAGT
* * * * *
697 TACAAAATGACAAACTATATAAACCAAATGATGCGATTTCCCGAGCATGGAATATCCA-AAAAAT
1 TACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTCCCAAGCATGGAATAT-TAGAAAAAT
*
761 TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAGTAACTTGTAAAAG
65 TGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAGTAACTCGTAAAAG
826 TTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
130 TTTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
*
891 AATTCAAAGACATAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCG
195 AATTCAAAGACA-AAACTTGTTTACAAAATGACAAACTAATTAGACCAAATGATGCGATTTCCCG
*
956 AGCATGGAATGTTCGGAAAATTGCTCG-AAGCAAT-GATCATCTTGAATACTTGAAGGATCCGAA
259 AGCATGGAATGTTCGGAAAATTGCTCGAAAG-AATGGATCATCTTGAATACTTTAAGGATCCGAA
1019 GTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAGGAACAAAGAGAGAAACA
323 GTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAGGAACAAAGAGAGAAACA
**
1084 ATTCTCACATAAATAAATTTTTAATTCAAAGACAAAAACTTGTT
388 ATTCTCACATAAATAAATTTTTAATTCAAAGACAAAAACTTGGA
* * * * * * * *
1128 TTCAAAATGACAAACTATTTAGACCAAATGAAGCGATTTTCAAAGTATGAAAAATTTGAAAATTT
1 TACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTCCCAAGCATGGAATATTAGAAAAATT
* *
1193 ACTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCG-AGTTAAAAAGTAACTCGTAAATGT
66 GCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAGTAACTCGTAAAAGT
1257 TTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA
131 TTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA
* * *
1322 ATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTAATTAGGCCAAATGATGCGATCTCCCGA
196 ATTCAAAGA-CAAAACTTGTTTACAAAATGACAAACTAATTAGACCAAATGATGCGATTTCCCGA
* * * * *
1387 GCATGAAATGTTTGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATTCTTTAAGGATCCGAAGT
260 GCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCATCTTGAATACTTTAAGGATCCGAAGT
*
1452 TATAAAAGAACTAGTAAAAGTTTAACAAGTTCGAAAGTTCGTCCAGGAACAAAGAGAGAAACAAT
325 TATAAAAGAACTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAGGAACAAAGAGAGAAACAAT
* *
1517 TCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGGA
390 TCTCACATAAATAAATTTTTAATTCAAAGACAAAAACTTGGA
* ** *
1559 TACAAAATGACAAACTATTTAGACGAAATGAAATGATTTCCCAAGGATGGAATATTAGAAAAATT
1 TACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTCCCAAGCATGGAATATTAGAAAAATT
* * *
1624 GCTCAAAGGAATGGATCTTGTTAAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGT
66 GCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAGTAACTCGTAAAAGT
* * *
1689 TTGACAAGTTCGAAAGTT--TGCCAAGAACAAAGAGAGAAACAATTCTCATGTAAATAAGTTTTT
131 TTGACAAGTTCGAAAGTTCGTACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * *
1752 AATTCAAAGTGCAAAACTTGTTTACAAAATGACAAATTAATTAGACCAAATGATACGATTTCCCG
195 AATTCAAAG-ACAAAACTTGTTTACAAAATGACAAACTAATTAGACCAAATGATGCGATTTCCCG
* * * * *
1817 AGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAG
259 AGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCATCTTGAATACTTTAAGGATCCGAAG
* * ** * * *
1882 TTAAAAAATAACCCGTAAAAGTTTGACAAGTTCGAAAGTTAGTACA-AAGACAAAGAGAGAAACA
324 TTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAGGA-ACAAAGAGAGAAACA
1946 ATTC
388 ATTC
Statistics
Matches: 741, Mismatches: 73, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
430 177 0.24
431 524 0.71
432 40 0.05
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (431 bp):
TACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTCCCAAGCATGGAATATTAGAAAAATT
GCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAGTAACTCGTAAAAGT
TTGACAAGTTCGAAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA
ATTCAAAGACAAAACTTGTTTACAAAATGACAAACTAATTAGACCAAATGATGCGATTTCCCGAG
CATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCATCTTGAATACTTTAAGGATCCGAAGTT
ATAAAAGAACTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAGGAACAAAGAGAGAAACAATT
CTCACATAAATAAATTTTTAATTCAAAGACAAAAACTTGGA
Done.