Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011149.1 Kokia drynarioides strain JFW-HI SEQ_126123, 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: 7083
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:760 original size:45 final size:45
Alignment explanation
Indices: 563--1200 Score: 501
Period size: 45 Copynumber: 13.9 Consensus size: 45
553 GCTTTCTATA
* * * * * *
563 GCTTCAATTTACCCCTCTGGATTTAATGGGTATAAGAATTGAAGTGGTA
1 GCTTCAATCTACCCCTCTAGA-TT-AGGGGTAAAAG-ATTGGA-TGGTG
** * *
612 GCTTCAATCTGTCCCTCTAGATTTAGGGGTATAAGATTGGATGTGGTA
1 GCTTCAATCTACCCCTCTAGA-TTAGGGGTAAAAGATTGGA--TGGTG
* * * * * *
660 GCTTCAATATGCCTCTATGGATTTAGGGGTAAAAGATTGGATGATG
1 GCTTCAATCTACCCCTCTAGA-TTAGGGGTAAAAGATTGGATGGTG
* * *
706 GCTTTAATCTACCCCTCTAGATTAAGGGCAAAAGATTGGATGGTG
1 GCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGGATGGTG
* * * **
751 GCGTCAATCTGCCCCTCTAGATTAAGGGTAAAAGATTATATGGTG
1 GCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGGATGGTG
* * *
796 GCTTCAATCTGCTCCTCTAGATTAGAGGTAAAAGATTGGATGGTG
1 GCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGGATGGTG
* * * * * * *
841 GCTTCAATTTTCCCCTCTAAAGTAGGGGTAAACGATTGGACGGGG
1 GCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGGATGGTG
* * * * * *
886 GCTTCAAT-TGGCCCTTTTGGATTTAGGGATAAAAGGTTGGATGGTG
1 GCTTCAATCT-ACCCCTCTAGA-TTAGGGGTAAAAGATTGGATGGTG
** * * * *
932 GCTTTGATCTACCTCTTCATA-TTTAGGGGTAAAATATTGAATGGTG
1 GCTTCAATCTACC-CCTC-TAGATTAGGGGTAAAAGATTGGATGGTG
* * *
978 GCTTCAATTTGCCCCTCTAGATTAGGGGTAAAAGATTGAATGGTG
1 GCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGGATGGTG
* *
1023 GCTTCAATCTATCCTTCT-GTATTTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTACCCCTCTAG-A-TTAGGGGTAAAAGATTGGATGGTG
* * *
1069 ACTTCAATCTATCCTTCT-GTATTTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTACCCCTCTAG-A-TTAGGGGTAAAAGATTGGATGGTG
* * * * * *
1115 GTTTAAATTTGCCCCTCTGGATTTAGGGAGTAAAAGATTAGATGGTG
1 GCTTCAATCTACCCCTCTAGA-TTAGGG-GTAAAAGATTGGATGGTG
* * * * *
1162 GTTTTAATCTGCCTCTCTAGATTAGGGGTAAAAGGTTGG
1 GCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGG
1201 GTGTTACAGC
Statistics
Matches: 486, Mismatches: 92, Indels: 26
0.80 0.15 0.04
Matches are distributed among these distances:
44 4 0.01
45 200 0.41
46 166 0.34
47 44 0.09
48 52 0.11
49 20 0.04
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (45 bp):
GCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGGATGGTG
Found at i:984 original size:137 final size:137
Alignment explanation
Indices: 612--1132 Score: 448
Period size: 137 Copynumber: 3.8 Consensus size: 137
602 TGAAGTGGTA
* * * * * *
612 GCTTCAATCTGTCCC-TCTAGATTTAGGGGTATAAGATTGGAT-GTGGTAGCTTCAATAT-GCC-
1 GCTTCAATCT-ACCCTTCTGGATTTAGGGATAAAAGATTGGATGGT-G-A-CTTCAATCTACCCT
* * * * * * * *
673 TCTATGGATTTAGGGGTAAAAGATTGGATGATGGCTTTAATCTACCCCTCTAGATTAAGGGCAAA
62 TCTAT--ATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAAAGTAGGGGTAAA
* * *
738 AGATTGGATGGTG
125 AGATTGAACGGGG
* * * * * ** * *
751 GCGTCAATCTGCCCCTCTAGATTAAGGG-TAAAAGATTATATGGTGGCTTCAATCTGCTCC-TCT
1 GCTTCAATCTACCCTTCTGGATTTAGGGATAAAAGATTGGATGGTGACTTCAATCTAC-CCTTCT
* * * *
814 AGA-TTAGAGGTAAAAGATTGGATGGTGGCTTCAATTTTCCCCTCTAAAGTAGGGGTAAACGATT
65 ATATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAAAGTAGGGGTAAAAGATT
*
878 GGACGGGG
130 GAACGGGG
* * * * **
886 GCTTCAAT-TGGCCCTTTTGGATTTAGGGATAAAAGGTTGGATGGTGGCTTTGATCTACCTCTTC
1 GCTTCAATCT-ACCCTTCTGGATTTAGGGATAAAAGATTGGATGGTGACTTCAATCTACC-CTTC
* * * *
950 -ATATTTAGGGGTAAAATATTGAATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGGTAAAAGAT
64 TATATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAAAGTAGGGGTAAAAGAT
* *
1014 TGAATGGTG
129 TGAACGGGG
* * * * *
1023 GCTTCAATCTATCCTTCTGTATTTAGGGGTAAAAGATTGGATGGTGACTTCAATCTATCCTTCTG
1 GCTTCAATCTACCCTTCTGGATTTAGGGATAAAAGATTGGATGGTGACTTCAATCTACCCTTCTA
* *
1088 TATTTAGGGGTAAAAGATTGGATGGTGGTTTAAATTTGCCCCTCT
66 TATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCT
1133 GGATTTAGGG
Statistics
Matches: 312, Mismatches: 59, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
134 1 0.00
135 79 0.25
136 39 0.12
137 149 0.48
138 21 0.07
139 23 0.07
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (137 bp):
GCTTCAATCTACCCTTCTGGATTTAGGGATAAAAGATTGGATGGTGACTTCAATCTACCCTTCTA
TATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAAAGTAGGGGTAAAAGATTG
AACGGGG
Done.