Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004773.1 Kokia drynarioides strain JFW-HI SEQ_118383, 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, 675
Length: 1125
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Found at i:296 original size:63 final size:62
Alignment explanation
Indices: 213--401 Score: 247
Period size: 62 Copynumber: 3.0 Consensus size: 62
203 ATCGTAAAAG
* * *
213 TTTGACAAGTTCAGATGTTCGTCCAAGAACAAAGAGAGAAACAATTCTTACAT-AAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTC-T-CATGTAAATAAGTT
* *
276 TTTGACAAGTTCGGAAGTTCGTCCAAGAACTAAGAGA-AAAGCAATTCTCATGTAAACAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAA-CAATTCTCATGTAAATAAGTT
* * * * *
338 TTCGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAACCAATTCTCATGTAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCATGTAAATAAGTT
400 TT
1 TT
402 AAATTTTGCG
Statistics
Matches: 112, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
61 3 0.03
62 67 0.60
63 42 0.38
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (62 bp):
TTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCATGTAAATAAGTT
Found at i:639 original size:62 final size:62
Alignment explanation
Indices: 561--739 Score: 250
Period size: 62 Copynumber: 2.9 Consensus size: 62
551 AAGTTTGAAT
* * *
561 AGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTATCACGTAAATAAGTTTTTGACA
1 AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACA
*
623 AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGATA
1 AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACA
* * *** * * *
685 AGTTTGGAAATTCGTCCCAGAACTGGGAGAGAAATAATTCTTACGTAACTAAGTT
1 AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
740 ATTAATTAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 105 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (62 bp):
AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACA
Found at i:819 original size:340 final size:340
Alignment explanation
Indices: 1--954 Score: 1088
Period size: 340 Copynumber: 2.8 Consensus size: 340
* * * *
1 AAGTTC-AGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAATTC
1 AAGTTCGA-AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTAAATTT
* * * *
65 AA-AGACCAAAA-TAT-TTTTCAGAATGACAAAAAACTATTTAGACCAAATGATGCGATTTCCCG
65 AACA-ACCAAAACT-TGTTTACAGAAAGAC---AAACAATTTAGACCAAATTATGCGATTTCCCG
* * * ** * * * *
127 AGCAAGGAAGGTTTGGAAAA-TAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAACCGAA
125 AGCACGAAATG-TTCAAAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTCAGGAACTGAA
* *
191 GTTATAAAAGAAATCGTAAAAGTTTGACAAGTTCAGATGTTCGTCCAAGAACAAAGAGAGAAACA
189 GTTATAAAAGAAATCGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACA
* *
256 ATTCTTACATAAAATAAGTTTTTGACAAGTTCGGAAGTTCGTCCAAGAACTAAGAGAAAAGCAAT
254 ATTCTTACGT-AAATAAGTTTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAAAAGCAAT
*
321 TCTCATGTAAACAAGTTTTCGAC
318 TCTCACGTAAACAAGTTTTCGAC
* * *
344 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAACCAATTCTCATGTAAATAAGTTTTAAATTTT
1 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTAAATTTA
* * * *
409 GCGACCAAAACTTGTTTACAGAAAGACAAACTATTTAGACCAAATTATGCGATTTCCCGAGCATG
66 ACAACCAAAACTTGTTTACAGAAAGACAAACAATTTAGACCAAATTATGCGATTTCCCGAGCACG
* *
474 AAATGTTCAAAAATTTGCTCAAAGGATTGGATCCTCTTGAATACTTTCAGGAACTGAAGTTATAA
131 AAATGTTCAAAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTCAGGAACTGAAGTTATAA
* * *
539 AAAAAATCGTAAAAGTTTGA-ATAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTATC
196 AAGAAATCGTAAAAGTTTGACA-AGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTT
*
603 ACGTAAATAAGTTTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAA-CAATTCTCAC
260 ACGTAAATAAGTTTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGA-AAAGCAATTCTCAC
* * *
667 GTAAATAAGTTTTTGAT
324 GTAAACAAGTTTTCGAC
* * * *** * * *
684 AAGTTTGGAAA-TTCGTCCCAGAACTGGGAGAGAAATAATTCTTACGTAACTAAGTTATT-AA-T
1 AAG-TTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT-TTAAATT
* * * * *
746 TAACAATCCAAAAGTTGTTTACA-AAATGACAAACAATTTTA-ACCAACTTGTGTGATTTCTCGA
64 TAACAA-CCAAAACTTGTTTACAGAAA-GACAAACAA-TTTAGACCAAATTATGCGATTTCCCGA
*** * * **
809 GCACGAAATGTTTGGAAATTTGCTCAAAGGAAT-GATCGTCTTGAATACTTTAAGGAACTTAAAA
126 GCACGAAATGTTCAAAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTCAGGAACTGAAGT
* * * * * *
873 TATAAAAGAACTAGTGAAAGTTTGACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAGAAACAAT
191 TATAAAAGAAATCGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAAT
*
938 TCTTACGTAACTAAGTT
256 TCTTACGTAAATAAGTT
955 ATTAATTAAC
Statistics
Matches: 523, Mismatches: 75, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
339 103 0.20
340 184 0.35
341 159 0.30
343 64 0.12
344 13 0.02
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (340 bp):
AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTAAATTTA
ACAACCAAAACTTGTTTACAGAAAGACAAACAATTTAGACCAAATTATGCGATTTCCCGAGCACG
AAATGTTCAAAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTCAGGAACTGAAGTTATAA
AAGAAATCGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTA
CGTAAATAAGTTTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAAAAGCAATTCTCACGT
AAACAAGTTTTCGAC
Found at i:1055 original size:215 final size:216
Alignment explanation
Indices: 678--1125 Score: 711
Period size: 215 Copynumber: 2.1 Consensus size: 216
668 TAAATAAGTT
* * *** *
678 TTTGATAAGTTTGGAAA-TTCGTCCCAGAACTGGGAGAGAAATAATTCTTACGTAACTAAGTTAT
1 TTTGACAAGTTT-GAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAACTAAGTTAT
* *
742 TAATTAACAATCCAAAAGTTGTTTACAAAATGACAAACAATTTTAACCAACTTGTGTGATTTCTC
65 TAATTAACAATCCAAAAGTTGTTTACAAAATGACAAACAATTTTAACCAAATGGTGTGATTTCTC
*
807 GAGCACGAAATGTTTGGAAATTTGCTCAAAGGAAT-GATCGTCTTGAATACTTTAAGGAACTTAA
130 GAGCACGAAATGTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAA
871 AATATAAAAGAACTAGTGAAAG
195 AATATAAAAGAACTAGTGAAAG
893 TTTGACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAACTAAGTTATT
1 TTTGACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAACTAAGTTATT
* * *
958 AATTAACAGTCCAAAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGGTGTGATTTCTCG
66 AATTAACAATCCAAAAGTTGTTTACAAAATGACAAACAATTTTAACCAAATGGTGTGATTTCTCG
* * * *
1023 AGCACGGAATGTTTGGAATTTTGCTCAAAGGAATGGATCGTCTTGTATACTTTAAGGAACCTAAG
131 AGCACGAAATGTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAA
*
1088 TTATAAAAGAACTAGTGAAAG
196 ATATAAAAGAACTAGTGAAAG
*
1109 TTTGACAAGTTCGAAAG
1 TTTGACAAGTTTGAAAG
Statistics
Matches: 213, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
214 4 0.02
215 146 0.69
216 63 0.30
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (216 bp):
TTTGACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAACTAAGTTATT
AATTAACAATCCAAAAGTTGTTTACAAAATGACAAACAATTTTAACCAAATGGTGTGATTTCTCG
AGCACGAAATGTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAA
ATATAAAAGAACTAGTGAAAG
Done.