Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000849.1 Kokia drynarioides strain JFW-HI SEQ_111951, 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: 1854
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Found at i:502 original size:196 final size:196
Alignment explanation
Indices: 151--521 Score: 444
Period size: 196 Copynumber: 1.9 Consensus size: 196
141 ACAAAATGGC
** * * * *
151 AAACTATTTAGACCAAATGATTTGATTTCTCGAGCGTGGAATGTTCAGAAATTTGCCCTAAGGAA
1 AAACTATTTAGACCAAATGATGGGATTTCTCGAGCATGGAATGTTCAGAAAATTGCCCAAAAGAA
* * * * * *
216 TGGATCTTGTTGAATTCTTTAGGGAATCGAAGTTAAAAAATAACTCGTAAAAGTTTAACAAGTTC
66 TGGATCGTCTTGAATACTTTAAGGAATCGAAGTTAAAAAAGAACTCGCAAAAGTTTAACAAGTTC
*
281 GAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTTAAAGGCC
131 GAAAGATCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTTAAAGGCC
346 A
196 A
* * * *
347 AAACTCTTTAGATCAAATGATGGGATTTGC-CGAGCATGGAATGTTCGGAAAATTGCTCAAAAGA
1 AAACTATTTAGACCAAATGATGGGATTT-CTCGAGCATGGAATGTTCAGAAAATTGCCCAAAAGA
* ** *
411 ATGGATCGTCTTGAATACTTTAAGGAAGT-TAAGTTATGAAAGATCTC-CACAAAG-TTAGACAA
65 ATGGATCGTCTTGAATACTTTAAGGAA-TCGAAGTTAAAAAAGAACTCGCA-AAAGTTTA-ACAA
* * * * *
473 GTTCGATAGATCGTCCATGAACCAAGAGAGATACAATTCTCTCGTAAAT
127 GTTCGAAAGATCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAAT
522 TTTTAATTCA
Statistics
Matches: 145, Mismatches: 26, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
195 4 0.03
196 139 0.96
197 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (196 bp):
AAACTATTTAGACCAAATGATGGGATTTCTCGAGCATGGAATGTTCAGAAAATTGCCCAAAAGAA
TGGATCGTCTTGAATACTTTAAGGAATCGAAGTTAAAAAAGAACTCGCAAAAGTTTAACAAGTTC
GAAAGATCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTTAAAGGCC
A
Found at i:999 original size:215 final size:216
Alignment explanation
Indices: 347--1846 Score: 1718
Period size: 215 Copynumber: 7.0 Consensus size: 216
337 TTAAAGGCCA
* * * * * *
347 AAACTCTTTAGATCAAATGATGGGATTTGCCGAGCATGGAATGTTCGGAAAATTGCTCAAAAGAA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCTAAGGAA
* * * *** ** * * *
412 TGGATCGTCTTGAATACTTTAAGGAAGTTAAGTTATGAAAGATCTC-CACAAAG-TTAGACAAGT
66 TGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA-AAAGTTTAG-CAAGT
* * * * * *
475 TCGATAGATCGTCCATGAACCAAGAGAGATACAATTCTCTCGT--A-AA-TTTTTAATTCAAAGA
129 TCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * **
536 CTAATACTTGTTCGCAAAATGAC
194 CCAAAACTTGTTTACAAAATGAC
* * * * * *
559 AAAATATTTAGACCAAATGATGCGATTTCCCGCGCATTGAATGTTAGGAAAATTGCTTTAAGGAT
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCTAAGGAA
* * *
624 TGGATCTTATTGAATACTGTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTACCAAGTTC
66 TGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTAGCAAGTTC
* * * * *
689 GAAAGTACGTCCAAGAACAAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAACTCAAAAAAC
131 GAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
*
754 AAAACTTGTTTACAAAATGGC
196 AAAACTTGTTTACAAAATGAC
* * * *
775 ATACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAGTGTTCGGAAAATAGCTCTGAGGAA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCTAAGGAA
* * * * *
840 TTGATCTTGTTGAAAACTTTAGGGAACCGAAGTTAAAAAAGAACTCGTAAAAGTTTTGCAA-TTC
66 TGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTAGCAAGTTC
* * *
904 AAAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACC
131 GAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
*
969 AAAACTTGTTTACAAAATTAC
196 AAAACTTGTTTACAAAATGAC
* * *
990 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAGTGGTCGGAAAATAGCTCTAAGGAA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCTAAGGAA
* * * *
1055 TGGATCTTTTTGAATACTTTTGGGAAACGAATTTAAAAAATAACTCGTAAAAGATTT-GCAA-TT
66 TGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAG-TTTAGCAAGTT
* *
1118 CGAAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGAC
130 CGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
*
1183 CAAAACTTGTTGACAAAATGAC
195 CAAAACTTGTTTACAAAATGAC
** * * * * *
1205 AAACTATTTAGACCAAATGATTTGATTTCTCGAGCGTGGAATGTTCAGAAATTTGCCCTAAGGAA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCTAAGGAA
* * * * *
1270 TGGATCTTGTTGAATTCTTTAGGGAATCGAAGTTAAAAAATAACTTGTAAAAGTTTAACAAGTTC
66 TGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTAGCAAGTTC
* * * *
1335 GAAAGTTTGTCCAACAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGGCC
131 GAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * *
1400 AGAACTTGTTTGCGAAATGAC
196 AAAACTTGTTTACAAAATGAC
* * * * *
1421 AAACTCTTTAGATCAAATGATGCGATTTGCCGAGCATAGAATGTTCGGAAAATTGCTCAAAGGAA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCTAAGGAA
* * * *** ** * * * *
1486 TGGATCGTCTTGAATACTTTAAGGAAGTTAAGTTATGAAAGATCTC-CACGAAG-TTAGACAAGT
66 TGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA-AAAGTTTAG-CAAGT
* * * * * *
1549 TCGATAGATCGTCCATGAACCAAGAGAGATACAATTCTCTCGT--A-AA-TTTTTAATTCAAAGA
129 TCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * **
1610 CTAATACTTGTTCGCAAAATGAC
194 CCAAAACTTGTTTACAAAATGAC
* * * * * *
1633 AAAATATTTAGACCAAATGATGCGATTTCCCGCGCATTGAATGTTAGGAAAATTGCTTTAAGGAT
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCTAAGGAA
* * * *
1698 TGGATCTTATTGAATACTGTAGGGAACCAAAGTTAAAAAATAACTTGTAAAAGTTTACCAAGTTC
66 TGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTAGCAAGTTC
* * *
1763 GAAAGTAT-GTCCAAGAACAAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAACTCAAAGAA
131 GAAAGT-TCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
1827 CAAAACTTGTTTACAAAATG
195 CAAAACTTGTTTACAAAATG
1847 GCATACTA
Statistics
Matches: 1082, Mismatches: 188, Indels: 32
0.83 0.14 0.02
Matches are distributed among these distances:
212 297 0.27
213 11 0.01
214 6 0.01
215 388 0.36
216 380 0.35
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (216 bp):
AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCTAAGGAA
TGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTAGCAAGTTC
GAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
AAAACTTGTTTACAAAATGAC
Found at i:1392 original size:431 final size:430
Alignment explanation
Indices: 347--1846 Score: 1696
Period size: 431 Copynumber: 3.5 Consensus size: 430
337 TTAAAGGCCA
* * * * * * *
347 AAACTCTTTAGATCAAATGATGGGATTTGCCGAGCATGGAATGTTCGGAAAATTGCTCAAAAGAA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCTAAGGAA
* * * *** ** * * **
412 TGGATCGTCTTGAATACTTTAAGGAAGTTAAGTTATGAAAGATC-TCCACAAAG-TTAGACAAGT
66 TGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTTGTA-AAAGTTTA-ACAAGT
* * * * * * *
475 TCGATAGATCGTCCATGAACCAAGAGAGATACAATTCTCTCG----TAAATTTTTAATTCAAAGA
129 TCGAAAGTTTGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGA
* * ** * * *
536 CTAATACTTGTTCGCAAAATGACAAAATATTTAGACCAAATGATGCGATTTCCCGCGCATTGAAT
194 CCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAAT
* * * * *
601 GTTAGGAAAATTGCTTTAAGGATTGGATCTTATTGAATACTGTAGGGAACCAAAGTTAAAAAATA
259 GTTCGGAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTTAGGGAAACAAAGTTAAAAAATA
* *
666 ACTCGTAAAAGTTTACCAAGTTCGAAAGTACGTCCAAGAACAAAGAGAGAAACAATTCTCACGTG
324 ACTCGTAAAAGTTT-GCAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGT-
* * * * *
731 AATAAGTTTTTAACTCAAAAAACAAAACTTGTTTACAAAATGGC
387 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTGACAAAATGAC
* * * * *
775 ATACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAGTGTTCGGAAAATAGCTCTGAGGAA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCTAAGGAA
* * * * **
840 TTGATCTTGTTGAAAACTTTAGGGAACCGAAGTTAAAAAAGAACTCGTAAAAGTTTTGCAA-TTC
66 TGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTTGTAAAAGTTTAACAAGTTC
* ** * *
904 AAAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACC
131 GAAAGTTTGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGACC
* * * *
969 AAAACTTGTTTACAAAATTACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAGTGG
196 AAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGT
* * * * *
1034 TCGGAAAATAGCTCTAAGGAATGGATCTTTTTGAATACTTTTGGGAAACGAATTTAAAAAATAAC
261 TCGGAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTTAGGGAAACAAAGTTAAAAAATAAC
*
1099 TCGTAAAAGATTTGCAA-TTCGAAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAA
326 TCGTAAAAG-TTTGCAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGT-AA
*
1163 TAAGTTTTTAATTGAAAGACCAAAACTTGTTGACAAAATGAC
389 TAAGTTTTTAATTCAAAGACCAAAACTTGTTGACAAAATGAC
** * * * *
1205 AAACTATTTAGACCAAATGATTTGATTTCTCGAGCGTGGAATGTTCAGAAATTTGCCCTAAGGAA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCTAAGGAA
* *
1270 TGGATCTTGTTGAATTCTTTAGGGAATCGAAGTTAAAAAATAACTTGTAAAAGTTTAACAAGTTC
66 TGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTTGTAAAAGTTTAACAAGTTC
* *
1335 GAAAGTTTGTCCAACAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGGCC
131 GAAAGTTTGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGACC
* * * * * *
1400 AGAACTTGTTTGCGAAATGACAAACTCTTTAGATCAAATGATGCGATTTGCCGAGCATAGAATGT
196 AAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGT
* * * * *** ** * *
1465 TCGGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAAGTTAAGTTATGAAAGATC
261 TCGGAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTTAGGGAAACAAAGTTAAAAAATAAC
* * * * * * * * *
1530 TC-CACGAAGTTAGACAAGTTCGATAGATCGTCCATGAACCAAGAGAGATACAATTCTCTCGT-A
326 TCGTA-AAAGTTTG-CAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAA
* *
1593 -AA-TTTTTAATTCAAAGACTAATACTTGTTCG-CAAAATGAC
389 TAAGTTTTTAATTCAAAGACCAAAACTTGTT-GACAAAATGAC
* * * *
1633 AAAATATTTAGACCAAATGATGCGATTTCCCGCGCATTGAATGTT-AGGAAAATTGCTTTAAGGA
1 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCA-GAAAATTGCTCTAAGGA
* * * * *
1697 TTGGATCTTATTGAATACTGTAGGGAACCAAAGTTAAAAAATAACTTGTAAAAGTTTACCAAGTT
65 ATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTTGTAAAAGTTTAACAAGTT
* * * * *
1762 CGAAAGTATGTCCAAGAACAAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAACTCAAAGAA
130 CGAAAGTTTGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGAC
1827 CAAAACTTGTTTACAAAATG
195 CAAAACTTGTTTACAAAATG
1847 GCATACTA
Statistics
Matches: 903, Mismatches: 156, Indels: 26
0.83 0.14 0.02
Matches are distributed among these distances:
427 35 0.04
428 313 0.35
429 6 0.01
430 192 0.21
431 317 0.35
432 40 0.04
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (430 bp):
AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCTAAGGAA
TGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTTGTAAAAGTTTAACAAGTTC
GAAAGTTTGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGACC
AAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGT
TCGGAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTTAGGGAAACAAAGTTAAAAAATAAC
TCGTAAAAGTTTGCAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAATA
AGTTTTTAATTCAAAGACCAAAACTTGTTGACAAAATGAC
Done.