Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000431.1 Kokia drynarioides strain JFW-HI SEQ_111264, 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, 842
Length: 1404
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Found at i:402 original size:215 final size:214
Alignment explanation
Indices: 1--1397 Score: 1368
Period size: 215 Copynumber: 6.6 Consensus size: 214
* *
1 AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAACCAAAGTTATAAAAGAAATCGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
* *
66 AAAAGTTTGTCAAGTT-TAAAGTTCGGCCGAGAACTAAGAAAGAAACAATTCTCA-CATAAATAA
66 AAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACCA-AAA-AA
* * * *
129 TTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAACGATAACTATTTAGACCAAATGATGAGA-T
129 ATTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATT
* *
193 TCCCTGAGCTTGGAATGTTCAG
194 TCCC-AAGCATGGAATGTTCAG
* * * * * ** *
215 AAAATTACTCGAAGGAATGGTTTGTCTTGATTACTGTAAGGAACTGAAGTTATAAAAGAACACGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
* * * * * * *
280 AAAAGCTTGTCAACTTCGGAAGTTTGGCCTAGAAACAAGAAAGAAACTATTCTCACCAAAAAAAG
66 AAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACCAAAAAAA-
* * * * * * *
345 TTTTTAATTCAGAGACCAAAAGTTGTTTACATAATGGCAATTATTTACACTAAATGATGCGAGTT
130 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATTT
* * **
410 -CTAGAGCATAGAAT-TCTCTT
195 CCCA-AGCATGGAATGT-TCAG
* * *
430 AAAATTTCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCAAAATTAT-AAAGTAACTCG
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAG-AACTCG
* * * * * *
494 TAAAAGTTTTTCAAGTTCGGAAGTTCGACCGAGAACCAA-AAGAAAAACAATTCTCAACTAAATA
65 TAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAA-AGAAACAATTCTC-ACCAAAAA
* * * * * *
558 AATTTTTAATT-AGAAGTCCAGAAGTAGTTTAAAAAATGACAACTATTTAGACCTAATGATGTGA
128 AATTTTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGA
* *
622 TTTCCCAAGCATGGACTGTACAG
192 TTTCCCAAGCATGGAATGTTCAG
* * * * * *
645 AAAATTACTCGAAAGAATCGATCGTCTTGAATACTTTAACGAACAAAAGTTATAAAAGTACTCGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
* * * * * *
710 AAAA-CTT-T---GTT---AAGTTCGGCTGAGAACGAATAGAGAAACAATTCTCACCTAAATAAA
66 AAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACC-AAAAAAA
* ** * * * * * *
767 TTTTTAATTGAAA-ACTGAAAGTAGTTTACAAAATGACAACAATTTGGACCTAATAATGTGATTT
130 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATTT
* * *
831 CCCAAGCACGGACTGTACA-
195 CCCAAGCATGGAATGTTCAG
* * * * * *
850 ATATATTGCT-GAAGGAATGAAAT-GTCTTGAATACTTTAATGAACAAAATTTATAAAAGAACTT
1 A-AAATTGCTCGAAGGAATG-GATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC
* * * * *
913 G-AAAATTTTGTCAAGTT-TAAAATTTGGCCGAGAACCAAGAAAGAAACAATTCTCACCTAAAGA
64 GTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACC-AAAAA
* * * *
976 ATTTTTTAATTCAAAGGCCAAATGTTGTTTACAAAATGACAACTATTTAAACCAAATGATGCGAT
128 AATTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGAT
* *
1041 TT-CCAAGCATGGAAAGTTCGG
193 TTCCCAAGCATGGAATGTTCAG
* *
1062 AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAACCAAAGTTATAAAAGAA-ACGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
* * * ** * *
1126 AAAAGTTTGTCAACTTCGAAAGTTCGGCCCAGAACCAAGAGAGAAATTATTCTCACCTAAATAAG
66 AAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACC-AAAAAAA
* * * *
1191 TTTTTAATTCAAAGATCAAAAGTTGTTTACATAATAACAACTATTTAGACCAAATGGTGCGATTT
130 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATTT
* * *
1256 CTCGAGCATGAAATGTTCCA-
195 CCCAAGCATGGAATGTT-CAG
* * * * * * *
1276 TAAATTGCTCGAAGGAATAGATCGTCTTCATTACTTTAAAGAACCGAAGTTATAAAAGAACTCTT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
* * * * * *
1341 AAAAGTTAGTTAGGTTCGAAAGTTTGGCCGAGAACCAAGAGAGAAATAATTCTCACC
66 AAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACC
1398 TAAATAA
Statistics
Matches: 969, Mismatches: 180, Indels: 67
0.80 0.15 0.06
Matches are distributed among these distances:
204 4 0.00
205 47 0.05
206 72 0.07
207 46 0.05
208 2 0.00
209 3 0.00
210 3 0.00
211 73 0.08
212 97 0.10
213 98 0.10
214 147 0.15
215 358 0.37
216 19 0.02
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (214 bp):
AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
AAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCACCAAAAAAAT
TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATTTC
CCAAGCATGGAATGTTCAG
Found at i:1236 original size:631 final size:637
Alignment explanation
Indices: 1--1358 Score: 1518
Period size: 631 Copynumber: 2.1 Consensus size: 637
* * *
1 AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAACCAAAGTTATAAAAGAAATCGT
1 AAAATTGCTCGAAGGAATAGATCGTCTTAAATACTTTAAAGAACCAAAGTTATAAAAGAACTCGT
* * *
66 AAAAGTTTGTCAAGTTTAAAGTTCGGCCGAGAACTAAGAAAGAAACAATTCTCACATAAATAATT
66 AAAA-CTT-T---G-TT-AAGTTCGGCCGAGAACGAAGAAAGAAACAATTCTCACATAAATAAAT
* * * *
131 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAACGATAACTATTTAGACCAAATGATGAGATTCC
124 TTTTAATTCAAAGACCAAAAGTAGTTTACAAAACGACAACAATTTAGACCAAATAATGAGATTCC
* ** * *** * **
196 CTGAGCTTGGAATGTTCAGAAAATTACTCGAAGGAATGGTTTGTCTTGATTACTGTAAGGAACTG
189 CTAAGCACGGAATGTACAGAAAATTACTCGAAGGAATGAAATGTCTTGAATACTGTAAGGAACAA
* * *
261 AAGTTATAAAAGAACACGTAAAAGCTTGTCAACTTCGGAAGTTTGGCCTAGAAACAAGAAAGAAA
254 AAGTTATAAAAGAACACGTAAAAGCTTGTCAACTTCGAAAATTTGGCCGAGAAACAAGAAAGAAA
* * * * *
326 CTATTCTCACCAAAAAAAGTTTTTAATTCAGAGACCAAAAGTTGTTTACATAATGGCAATTATTT
319 CAATTCTCACCAAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTT
* * * * ** *
391 ACACTAAATGATGCGAGTTCTAGAGCATAGAATTCTCTTAAAATTTCTCGAAGGAATGGATCGTC
384 AAACCAAATGATGCGAGTTCCAGAGCATAGAAGTCTCGGAAAATTGCTCGAAGGAATGGATCGTC
* * * * * *
456 TTGAATACTTTAAGGAATCAAAATTATAAAGTAACTCGTAAAAGTTTTTCAAGTTCGGAAGTTCG
449 TTAAATACTTTAAGGAACCAAAATTATAAAGTAACACGTAAAAGTTTGTCAACTTCGAAAGTTCG
* *
521 ACCGAGAACCAAAAGAAAAACAATTCTCAACTAAATAAATTTTTAATTAGAAGTCCAGAAGTAGT
514 ACCCAGAACCAAAAGAAAAACAATTCTCAACTAAATAAATTTTTAATTAGAAGTCCAAAAGTAGT
* * * * *
586 TTAAAAAATGACAACTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTG-TACA
579 TTAAAAAATAACAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGAAATGTTACA
* * * * * * *
644 GAAAATTACTCGAAAGAATCGATCGTCTTGAATACTTTAACGAACAAAAGTTATAAAAGTACTCG
1 -AAAATTGCTCGAAGGAATAGATCGTCTTAAATACTTTAAAGAACCAAAGTTATAAAAGAACTCG
* * * *
709 TAAAACTTTGTTAAGTTCGGCTGAGAACGAATAGAGAAACAATTCTCACCTAAATAAATTTTTAA
65 TAAAACTTTGTTAAGTTCGGCCGAGAACGAAGAAAGAAACAATTCTCACATAAATAAATTTTTAA
* ** * * * *
774 TTGAAA-ACTGAAAGTAGTTTACAAAATGACAACAATTTGGACCTAATAATGTGATTTCCC-AAG
130 TTCAAAGACCAAAAGTAGTTTACAAAACGACAACAATTTAGACCAAATAATGAGA-TTCCCTAAG
* * * * * *
837 CACGGACTGTACA-ATATATTGCT-GAAGGAATGAAATGTCTTGAATACTTTAATGAACAAAATT
194 CACGGAATGTACAGA-AAATTACTCGAAGGAATGAAATGTCTTGAATACTGTAAGGAACAAAAGT
** ** * * *
900 TATAAAAGAACTTG-AAAATTTTGTCAAGTT-TAAAATTTGGCCGAGAACCAAGAAAGAAACAAT
258 TATAAAAGAACACGTAAAAGCTTGTCAACTTCGAAAATTTGGCCGAGAAACAAGAAAGAAACAAT
* * * * *
963 TCTCACCTAAAGAATTTTTTAATTCAAAGGCCAAATGTTGTTTACAAAATGACAACTATTTAAAC
323 TCTCACCAAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAAC
* *
1028 CAAATGATGCGATTTCCA-AGCATGGAAAGT-TCGGAAAATTGCTCGAAGGAATGGATCGTCTTA
388 CAAATGATGCGAGTTCCAGAGCATAG-AAGTCTCGGAAAATTGCTCGAAGGAATGGATCGTCTTA
* *
1091 AATACTTTAAGGAACCAAAGTTATAAAAG-AA-ACGTAAAAGTTTGTCAACTTCGAAAGTTCGGC
452 AATACTTTAAGGAACCAAAATTAT-AAAGTAACACGTAAAAGTTTGTCAACTTCGAAAGTTCGAC
* * ** * * *
1154 CCAGAACCAAGAGAGAAATTATTCTCACCTAAATAAGTTTTTAATTCA-AAGAT-CAAAAGTTGT
516 CCAGAACCAAAAGAAAAACAATTCTCAACTAAATAAATTTTTAATT-AGAAG-TCCAAAAGTAGT
* * * * * *
1217 TTACATAATAACAACTATTTAGACCAAATGGTGCGATTTCTCGAGCATGAAATGTTCCA
579 TTAAAAAATAACAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGAAATGTTACA
* * * * *
1276 TAAATTGCTCGAAGGAATAGATCGTCTTCATTACTTTAAAGAACCGAAGTTATAAAAGAACTCTT
1 AAAATTGCTCGAAGGAATAGATCGTCTTAAATACTTTAAAGAACCAAAGTTATAAAAGAACTCGT
* * *
1341 AAAAGTTAGTTAGGTTCG
66 AAAACTTTGTTAAGTTCG
1359 AAAGTTTGGC
Statistics
Matches: 594, Mismatches: 113, Indels: 27
0.81 0.15 0.04
Matches are distributed among these distances:
631 190 0.32
632 64 0.11
633 104 0.18
634 13 0.02
635 44 0.07
636 55 0.09
637 57 0.10
638 2 0.00
639 1 0.00
642 1 0.00
643 2 0.00
644 61 0.10
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (637 bp):
AAAATTGCTCGAAGGAATAGATCGTCTTAAATACTTTAAAGAACCAAAGTTATAAAAGAACTCGT
AAAACTTTGTTAAGTTCGGCCGAGAACGAAGAAAGAAACAATTCTCACATAAATAAATTTTTAAT
TCAAAGACCAAAAGTAGTTTACAAAACGACAACAATTTAGACCAAATAATGAGATTCCCTAAGCA
CGGAATGTACAGAAAATTACTCGAAGGAATGAAATGTCTTGAATACTGTAAGGAACAAAAGTTAT
AAAAGAACACGTAAAAGCTTGTCAACTTCGAAAATTTGGCCGAGAAACAAGAAAGAAACAATTCT
CACCAAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAA
ATGATGCGAGTTCCAGAGCATAGAAGTCTCGGAAAATTGCTCGAAGGAATGGATCGTCTTAAATA
CTTTAAGGAACCAAAATTATAAAGTAACACGTAAAAGTTTGTCAACTTCGAAAGTTCGACCCAGA
ACCAAAAGAAAAACAATTCTCAACTAAATAAATTTTTAATTAGAAGTCCAAAAGTAGTTTAAAAA
ATAACAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGAAATGTTACA
Done.