Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002146.1 Kokia drynarioides strain JFW-HI SEQ_114093, 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, 715
Length: 1192
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Found at i:580 original size:205 final size:205
Alignment explanation
Indices: 224--746 Score: 913
Period size: 205 Copynumber: 2.6 Consensus size: 205
214 GATTATCCAT
224 AAAC-AACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
1 AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
*
288 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAA
*
353 AAGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAG
131 AAGGTTAGCTTCCTGATGAGATACTAAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAGAG
*
418 AAGTGAAATG
196 AAGCGAAATG
* *
428 AAACAAACGACGTAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACTCACGCTC
1 AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
*
493 GATGTGAGCAAATCTTCGAACCCCAGTTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAA
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAA
* * * * *
558 AATGTTAGCTTCCTGATGAGATATTGAGAAATGGACCAAATTCGTCTTTCTGATGAGATATAGAG
131 AAGGTTAGCTTCCTGATGAGATACTAAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAGAG
*
623 AAGCGAATTG
196 AAGCGAAATG
*
633 AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACTAAATCAAACTCACGCTC
1 AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
*
698 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGATATACTGAGAAG
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
747 TGGACCAAAT
Statistics
Matches: 301, Mismatches: 17, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
204 4 0.01
205 297 0.99
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (205 bp):
AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAA
AAGGTTAGCTTCCTGATGAGATACTAAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAGAG
AAGCGAAATG
Found at i:904 original size:158 final size:158
Alignment explanation
Indices: 564--904 Score: 538
Period size: 158 Copynumber: 2.2 Consensus size: 158
554 ATAAAATGTT
* * * * *
564 AGCTTCCTGATGAGATATTGAGAAATGGACCAAATTCGTCTTTCTGATGAGATATAGAGAAGCGA
1 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGA
* *
629 ATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACTAAATCAAACTCAC
66 ATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
694 GCTCGATGTGAGCAAATCTTCGAACCCC
131 GCTCGATGTGAGCAAATCTTCGAACCCC
* * * *
722 AGCTTCCTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGTGG
1 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGA
* * *
787 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTGAAACCCAC
66 ATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
852 GCTCGATGTGAGCAAATCTTCGAACCCC
131 GCTCGATGTGAGCAAATCTTCGAACCCC
* *
880 AGCTTCCTGATGAGACACCGAGAAG
1 AGCTTCCTGATGAGATACTGAGAAG
905 CAGGTCGATG
Statistics
Matches: 166, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
158 166 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (158 bp):
AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGA
ATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
GCTCGATGTGAGCAAATCTTCGAACCCC
Found at i:1099 original size:208 final size:206
Alignment explanation
Indices: 722--1154 Score: 552
Period size: 208 Copynumber: 2.1 Consensus size: 206
712 TTCGAACCCC
* * * *
722 AGCTTCCTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGTGG
1 AGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGA
* * * * * *
787 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTGAAACCCAC
66 ACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACCCAC
* * *
852 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGATGTG
131 GCTCAATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGA---A
917 AGAATAAAATG-TT
193 AGAATAAAATGATT
*
930 AGCTTCTTGATGAGATA-TGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCT
1 AGCTTCTTGATGAGATACT-GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAG-T
*
994 -AACTAAAACAAATGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACCC
64 GAACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACCC
* * ****
1058 -CTTCTCAAT-TCGAGCGAATCTTCGAACCCCAACTTCCTGATGAGATGTTGAGAAGCAGGTCGA
129 AC-GCTCAATGT-GAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGA
*
1121 AATAATAAAATGAATT
192 AAGAATAAAATG-ATT
*
1137 AGCTTCTTGATGAAATAC
1 AGCTTCTTGATGAGATAC
1155 GGGGAAGTAA
Statistics
Matches: 195, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
205 10 0.05
207 21 0.11
208 163 0.84
209 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (206 bp):
AGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGA
ACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACCCAC
GCTCAATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGAAAGA
ATAAAATGATT
Found at i:1112 original size:366 final size:363
Alignment explanation
Indices: 361--1112 Score: 1114
Period size: 363 Copynumber: 2.1 Consensus size: 363
351 AAAAGGTTAG
* *
361 CTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAAA
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGAAA
* *
426 TGAAACAAACGACGTAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACTCACGC
66 TGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
* * *
491 TCGATGTGAGCAAATCTTCGAACCCCAGTTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAAT
131 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGCAAAGCAAT
* * *
556 AAAATGTTAGCTTCCTGATGAGATATTGAGAAATGGACCAAATTCGTCTTTCTGATGAGATATAG
196 AAAATGTTAGCTTCCTGATGAGATATGGAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAG
* * * *
621 AGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACTAAATC
261 AGAAGCGAACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATC
* *
686 AAACTCACGCTCGATGTGAGCAAATCTTCGAACCCCAG
326 AAACTCACGCTCAATGTGAGCAAATCTTCGAACCCCAA
* * * *
724 CTTCCTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGTGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGAAA
* * * *
789 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTGAAACCCACGC
66 TGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
* *
854 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGATGTGAG
131 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGC-A---AAG
* *
919 -AATAAAATGTTAGCTTCTTGATGAGATATGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
192 CAATAAAATGTTAGCTTCCTGATGAGATATGGAGAAATGGACCAAATTCGTCTTCCTGATGAGAT
* *
983 ACAGAGAAGCTAACTAAAACAAATGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCA
257 ACAGAGAAGCGAACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCA
* * *
1048 AATCAAAC-CCCTTCTCAAT-TCGAGCGAATCTTCGAACCCCAA
322 AATCAAACTCAC-GCTCAATGT-GAGCAAATCTTCGAACCCCAA
**
1090 CTTCCTGATGAGATGTTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
1113 CAGGTCGAAA
Statistics
Matches: 347, Mismatches: 36, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
363 171 0.49
364 1 0.00
365 3 0.01
366 170 0.49
367 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (363 bp):
CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGAAA
TGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGCAAAGCAAT
AAAATGTTAGCTTCCTGATGAGATATGGAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAG
AGAAGCGAACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATC
AAACTCACGCTCAATGTGAGCAAATCTTCGAACCCCAA
Found at i:1179 original size:366 final size:356
Alignment explanation
Indices: 361--1112 Score: 979
Period size: 366 Copynumber: 2.1 Consensus size: 356
351 AAAAGGTTAG
* * * *
361 CTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAAA
1 CTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAAATACAAAGAAGTG--A
* *
426 TGAAACAAACGACGTAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACTCACGC
64 T-AAACAAAC-AC--CG-CATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
* * *
491 TCGATGTGAGCAAATCTTCGAACCCCAGTTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAAT
124 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGCAAAGCAAT
* * *
556 AAAATGTTAGCTTCCTGATGAGATATTGAGAAATGGACCAAATTCGTCTTTCTGATGAGATATAG
189 AAAATGTTAGCTTCCTGATGAGATATGGAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAG
* * * *
621 AGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACTAAATC
254 AGAAGCGAACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATC
* *
686 AAACTCACGCTCGATGTGAGCAAATCTTCGAACCCCAG
319 AAACTCACGCTCAATGTGAGCAAATCTTCGAACCCCAA
* * **
724 CTTCCTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGTGGAT
1 CTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAAATACAAAGAAGT-GA-
* * *
789 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTGAAACCCACGC
64 T-AAACAAAC-AC-C-G-CATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
* *
854 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGATGTGAG
124 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGC-A---AAG
* *
919 -AATAAAATGTTAGCTTCTTGATGAGATATGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
185 CAATAAAATGTTAGCTTCCTGATGAGATATGGAGAAATGGACCAAATTCGTCTTCCTGATGAGAT
* *
983 ACAGAGAAGCTAACTAAAACAAATGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCA
250 ACAGAGAAGCGAACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCA
* * *
1048 AATCAAAC-CCCTTCTCAAT-TCGAGCGAATCTTCGAACCCCAA
315 AATCAAACTCAC-GCTCAATGT-GAGCAAATCTTCGAACCCCAA
**
1090 CTTCCTGATGAGATGTTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
1113 CAGGTCGAAA
Statistics
Matches: 346, Mismatches: 34, Indels: 15
0.88 0.09 0.04
Matches are distributed among these distances:
362 1 0.00
363 168 0.49
364 2 0.01
365 3 0.01
366 170 0.49
367 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (356 bp):
CTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAAATACAAAGAAGTGATA
AACAAACACCGCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGCTCGATGT
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGCAAAGCAATAAAATGT
TAGCTTCCTGATGAGATATGGAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
AACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACTCA
CGCTCAATGTGAGCAAATCTTCGAACCCCAA
Done.