Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002609.1 Kokia drynarioides strain JFW-HI SEQ_114824, 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: 1805
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Found at i:146 original size:86 final size:85
Alignment explanation
Indices: 1--206 Score: 205
Period size: 86 Copynumber: 2.4 Consensus size: 85
* * * * * *
1 GGCCTAAGTTGTCGATGGTGTTCGATACTCTCGTACATCGAAGGTACCAAAGTACCGATACTTTC
1 GGCCTAA-TTGTCGATGGTGTCCGATACTCCCGCAAATCGAAGGCACCAAAGTACCGATACTTCC
* ** *
66 CAATGGTCTCGTACCATCATC
65 CAATGGTCCCCCACCACCATC
* ** *
87 GGCCTCAATTGTCGATGGTGTCCGATGCTCCCGCAAATCGAAGGCACCATGGTGCCGATACTTCC
1 GGCCT-AATTGTCGATGGTGTCCGATACTCCCGCAAATCGAAGGCACCAAAGTACCGATACTTCC
*
152 CGATGGTCCCCCACCACCATC
65 CAATGGTCCCCCACCACCATC
* * * *
173 GGCCTTAATTGCCAATAGTGTCTGATACATCCCG
1 GGCC-TAATTGTCGATGGTGTCCGATAC-TCCCG
207 ATGGTCCCGT
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
86 89 0.92
87 8 0.08
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (85 bp):
GGCCTAATTGTCGATGGTGTCCGATACTCCCGCAAATCGAAGGCACCAAAGTACCGATACTTCCC
AATGGTCCCCCACCACCATC
Found at i:206 original size:53 final size:53
Alignment explanation
Indices: 143--247 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
133 CCATGGTGCC
* * * *
143 GATACTTCCCGATGGTCCCCCACCACCATCGGCCTTAATTGCCAATAGTGTCT
1 GATACATCCCGATGGTCCCCCACCACCATCGACCTAAATTACCAATAGTGTCT
** * *
196 GATACATCCCGATGGTCCCGTACCTCCATCGACCTAAATTACCGATAGTGTC
1 GATACATCCCGATGGTCCCCCACCACCATCGACCTAAATTACCAATAGTGTC
248 CGATGCTCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (53 bp):
GATACATCCCGATGGTCCCCCACCACCATCGACCTAAATTACCAATAGTGTCT
Found at i:284 original size:139 final size:139
Alignment explanation
Indices: 68--333 Score: 340
Period size: 139 Copynumber: 1.9 Consensus size: 139
58 ATACTTTCCA
* * * ** *
68 ATGGTCTCGTACCATCATCGGCCTCAATTGTCGATGGTGTCCGATGCTCCCGCAAATCGAAGGCA
1 ATGGTCCCGTACCATCATCGACCTAAATTACCGATAGTGTCCGATGCTCCCGCAAATCGAAGGCA
* * *
133 CCATGGTGCCGATACTTCCCGATGGTCCCCCACCACCATCGGCCTTAA-TTGCCAATAGTGTCTG
66 CCATGGTACCGATACATCCCGATGGTCCCCCACCACCATCGGCC-TAAGTTACCAATAGTGTCTG
197 ATACATCCCG
130 ATACATCCCG
* * * *
207 ATGGTCCCGTACC-TCCATCGACCTAAATTACCGATAGTGTCCGATGCTCTCGTACATCTAAGGC
1 ATGGTCCCGTACCAT-CATCGACCTAAATTACCGATAGTGTCCGATGCTCCCGCAAATCGAAGGC
** *
271 ACCAAT-GTACCGATGGATCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTGTC
65 ACC-ATGGTACCGATACATCCCGATGGTCCCCCACCACCATCGGCCTAAGTTACCAATAGTGTC
334 CAATGCTCTC
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
138 4 0.04
139 102 0.94
140 2 0.02
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.24
Consensus pattern (139 bp):
ATGGTCCCGTACCATCATCGACCTAAATTACCGATAGTGTCCGATGCTCCCGCAAATCGAAGGCA
CCATGGTACCGATACATCCCGATGGTCCCCCACCACCATCGGCCTAAGTTACCAATAGTGTCTGA
TACATCCCG
Found at i:318 original size:86 final size:86
Alignment explanation
Indices: 196--498 Score: 347
Period size: 86 Copynumber: 3.5 Consensus size: 86
186 AATAGTGTCT
* * * * *
196 GATACATCCCGATGGTCCCGTACCTCCATCGACCTAAATTACCGATAGTGTCCGATGCTCTCGTA
1 GATACATCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATAGTGTCCAATGCTCTCGCA
*
261 CATCTAAGGCACCAATGTACC
66 CATCGAAGGCACCAATGTACC
** * *
282 GATGGATCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTGTCCAATGCTCTCGCA
1 GATACATCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATAGTGTCCAATGCTCTCGCA
* *
347 CATCGAAGGCACCAAGGTGCC
66 CATCGAAGGCACCAATGTACC
* * * ** * * *
368 GATACTTCCCGATGGTCCCGCACCACCATCGGCCTCAGTTGTCGATGGTGTCCAACGCTCCCGCA
1 GATACATCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATAGTGTCCAATGCTCTCGCA
*
433 CATAGAAGGCACC-ATGGTACC
66 CATCGAAGGCACCAAT-GTACC
*** * * *
454 GATTTTTCCTGATGGTCCCACACCACCATCGACCTTAGTTACCGA
1 GATACATCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGA
499 CGATGTCCGA
Statistics
Matches: 183, Mismatches: 33, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
85 1 0.01
86 182 0.99
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (86 bp):
GATACATCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATAGTGTCCAATGCTCTCGCA
CATCGAAGGCACCAATGTACC
Found at i:516 original size:53 final size:53
Alignment explanation
Indices: 459--565 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 53
449 GTACCGATTT
* * *
459 TTCCTGATGGTCCCACACCACCATCGACCTTAGTTACCGACGA-TGTCCGATGC
1 TTCCTGATGGTCCCAAACCACCATCAACCTAAGTTACCGA-GAGTGTCCGATGC
* *
512 TTCCTGATGGTCTCAAACCACCATCAACCTAAGTTACCGATAGTGTCCGATGC
1 TTCCTGATGGTCCCAAACCACCATCAACCTAAGTTACCGAGAGTGTCCGATGC
565 T
1 T
566 CTCACACATC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 1 0.02
53 47 0.98
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (53 bp):
TTCCTGATGGTCCCAAACCACCATCAACCTAAGTTACCGAGAGTGTCCGATGC
Found at i:523 original size:225 final size:225
Alignment explanation
Indices: 291--820 Score: 623
Period size: 225 Copynumber: 2.4 Consensus size: 225
281 CGATGGATCC
** * * * *
291 CGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTGTCCAATGCTCTCGCACATCGAAGG
1 CGATGGTCCCAAACCACCATCAGCCTAAGTTACCGATAGTGTCCGATGCTCTCGCACATCCAAGG
* * * ** * * *
356 CACCAAGGTGCCGATACTTCCCGATGGTCCCGCACCACCATCGGCCTCAGTTGTCGATGGTGTCC
66 CACCAAGGTACCGATACATCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTATCC
* * ** *
421 AACGCTCCCGCACATAGAAGGCACCATGGTACCGATTTTTCCTGATGGTCCCACACCACCATCGA
131 AACGCTCCCGCACATACAAGGCACCAAGGTACCGATGCTTCCTGATAGTCCCACACCACCATCGA
* *
486 CCTTAGTTACCGACGATGTCCGATGCTTC-
196 CCTAAGTTACCGACGATGTCCGATCCTTCT
* * * *
515 CTGATGGTCTCAAACCACCATCAACCTAAGTTACCGATAGTGTCCGATGCTCTCACACATCTAAG
1 C-GATGGTCCCAAACCACCATCAGCCTAAGTTACCGATAGTGTCCGATGCTCTCGCACATCCAAG
** * *
580 GC-CCTAAGGTATTGATAGATCCCGATGGTCCCGCACCACCGTCGGCCTAAGTTACCAATAGTAT
65 GCACC-AAGGTACCGATACATCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTAT
* * * * * ** * * *
644 CCGATGCTCTCGCACATCCAAGGTACCAAGGTGTCGATGCTTCCTGATAGTCTCGCACTACCATC
129 CCAACGCTCCCGCACATACAAGGCACCAAGGTACCGATGCTTCCTGATAGTCCCACACCACCATC
* * * *
709 GGCCTAAGTTACCGATGGTGTCCGGTCCTTCT
194 GACCTAAGTTACCGACGATGTCCGATCCTTCT
* *
741 CGATGGTCCCATACCACCATCAGCCTAAGTTACCGATGGTGTCCGATGCTCTCGCACATCCAAGG
1 CGATGGTCCCAAACCACCATCAGCCTAAGTTACCGATAGTGTCCGATGCTCTCGCACATCCAAGG
806 CACCAAGGTACCGAT
66 CACCAAGGTACCGAT
821 TGTCCCGTAC
Statistics
Matches: 252, Mismatches: 50, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
224 3 0.01
225 246 0.98
226 3 0.01
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (225 bp):
CGATGGTCCCAAACCACCATCAGCCTAAGTTACCGATAGTGTCCGATGCTCTCGCACATCCAAGG
CACCAAGGTACCGATACATCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTATCC
AACGCTCCCGCACATACAAGGCACCAAGGTACCGATGCTTCCTGATAGTCCCACACCACCATCGA
CCTAAGTTACCGACGATGTCCGATCCTTCT
Found at i:564 original size:311 final size:311
Alignment explanation
Indices: 28--731 Score: 908
Period size: 311 Copynumber: 2.3 Consensus size: 311
18 GTGTTCGATA
* * * * * * *
28 CTCTCGTACATCGAAGGTACCAAAGTACCGATACTTTCCAATGGTCTCGTACCATCATCGGCCTC
1 CTCTCGCACATCGAAGGTACCAAGGTGCCGATACTTCCCGATGGTCTCGCACCACCATCGGCCTC
* * * * *
93 AATTGTCGATGGTGTCCGATGCTCCCGCAAATCGAAGGCACCATGGTGCCGATACTTCCCGATGG
66 AGTTGTCGATGGTGTCCAACGCTCCCGCAAATAGAAGGCACCATGGTACCGATACTTCCCGATGG
* * * * * ** *
158 TCCCCCACCACCATCGGCCTTAATTGCCAATAGTGTCTGATACATCCCGATGGTCCCGTACCTCC
131 TCCCACACCACCATCGACCTTAATTACCAAGAGTGTCCGATACATCCCGATGGTCCCAAACCACC
* ** * *
223 ATCGACCTAAATTACCGATAGTGTCCGATGCTCTCGTACATCTAAGGCACC-AATGTACCGATGG
196 ATCAACCTAAATTACCGATAGTGTCCGATGCTCTCACACATCTAAGGC-CCTAAGGTACCGATAG
*
287 ATCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTGTCCAATG
260 ATCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTATCCAATG
* *
339 CTCTCGCACATCGAAGGCACCAAGGTGCCGATACTTCCCGATGGTCCCGCACCACCATCGGCCTC
1 CTCTCGCACATCGAAGGTACCAAGGTGCCGATACTTCCCGATGGTCTCGCACCACCATCGGCCTC
* ** *
404 AGTTGTCGATGGTGTCCAACGCTCCCGCACATAGAAGGCACCATGGTACCGATTTTTCCTGATGG
66 AGTTGTCGATGGTGTCCAACGCTCCCGCAAATAGAAGGCACCATGGTACCGATACTTCCCGATGG
* * * * * *
469 TCCCACACCACCATCGACCTTAGTTACCGACGA-TGTCCGATGCTTCCTGATGGTCTCAAACCAC
131 TCCCACACCACCATCGACCTTAATTACC-AAGAGTGTCCGATACATCCCGATGGTCCCAAACCAC
* **
533 CATCAACCTAAGTTACCGATAGTGTCCGATGCTCTCACACATCTAAGGCCCTAAGGTATTGATAG
195 CATCAACCTAAATTACCGATAGTGTCCGATGCTCTCACACATCTAAGGCCCTAAGGTACCGATAG
* *
598 ATCCCGATGGTCCCGCACCACCGTCGGCCTAAGTTACCAATAGTATCCGATG
260 ATCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTATCCAATG
* * * * * * *
650 CTCTCGCACATCCAAGGTACCAAGGTGTCGATGCTTCCTGATAGTCTCGCACTACCATCGGCCTA
1 CTCTCGCACATCGAAGGTACCAAGGTGCCGATACTTCCCGATGGTCTCGCACCACCATCGGCCTC
**
715 AGTTACCGATGGTGTCC
66 AGTTGTCGATGGTGTCC
732 GGTCCTTCTC
Statistics
Matches: 337, Mismatches: 54, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
310 2 0.01
311 333 0.99
312 2 0.01
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (311 bp):
CTCTCGCACATCGAAGGTACCAAGGTGCCGATACTTCCCGATGGTCTCGCACCACCATCGGCCTC
AGTTGTCGATGGTGTCCAACGCTCCCGCAAATAGAAGGCACCATGGTACCGATACTTCCCGATGG
TCCCACACCACCATCGACCTTAATTACCAAGAGTGTCCGATACATCCCGATGGTCCCAAACCACC
ATCAACCTAAATTACCGATAGTGTCCGATGCTCTCACACATCTAAGGCCCTAAGGTACCGATAGA
TCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCAATAGTATCCAATG
Found at i:675 original size:86 final size:86
Alignment explanation
Indices: 528--721 Score: 221
Period size: 86 Copynumber: 2.3 Consensus size: 86
518 ATGGTCTCAA
** * * * * *
528 ACCACCATCAACCTAAGTTACCGATAGTGTCCGATGCTCTCACACATCTAAGGCCCTAAGGTATT
1 ACCACCATCGGCCTAAGTTACCAATAGTATCCGATGCTCTCACACATCCAAGGACCTAAGGTATC
*
593 GATAG-ATCCCGATGGTCCCGC
66 GAT-GCATCCCGATAGTCCCGC
* * *
614 ACCACCGTCGGCCTAAGTTACCAATAGTATCCGATGCTCTCGCACATCCAAGGTACC-AAGGTGT
1 ACCACCATCGGCCTAAGTTACCAATAGTATCCGATGCTCTCACACATCCAAGG-ACCTAAGGTAT
* * *
678 CGATGCTTCCTGATAGTCTCGC
65 CGATGCATCCCGATAGTCCCGC
*
700 ACTACCATCGGCCTAAGTTACC
1 ACCACCATCGGCCTAAGTTACC
722 GATGGTGTCC
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
85 1 0.01
86 87 0.97
87 2 0.02
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (86 bp):
ACCACCATCGGCCTAAGTTACCAATAGTATCCGATGCTCTCACACATCCAAGGACCTAAGGTATC
GATGCATCCCGATAGTCCCGC
Found at i:876 original size:76 final size:76
Alignment explanation
Indices: 741--886 Score: 222
Period size: 76 Copynumber: 1.9 Consensus size: 76
731 CGGTCCTTCT
* *
741 CGATGGTCCCATACCACCATCAGCCTAAGTTACCGATGGTGTCCGATGCTCTCGCACATCCAAGG
1 CGATGGTCCCATACCACCATCAGCCTAAGTTACCGATGGTGTCCGATGCTCCCGAACATCCAAGG
806 CACCAAGGTAC
66 CACCAAGGTAC
* * **
817 CGATTGTCCCGTACCACCATC-GACCTAAGTTACCGATGGTGTCCGATGCTCCCGAACATCGTAG
1 CGATGGTCCCATACCACCATCAG-CCTAAGTTACCGATGGTGTCCGATGCTCCCGAACATCCAAG
881 GCACCA
65 GCACCA
887 TGGTGCTGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 1 0.02
76 62 0.98
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (76 bp):
CGATGGTCCCATACCACCATCAGCCTAAGTTACCGATGGTGTCCGATGCTCCCGAACATCCAAGG
CACCAAGGTAC
Found at i:1046 original size:85 final size:84
Alignment explanation
Indices: 829--1133 Score: 310
Period size: 86 Copynumber: 3.6 Consensus size: 84
819 ATTGTCCCGT
* * *
829 ACCACCATCGACCTAAGTTACCGATGGTGTCCGATGCTCCCGAACATCGTAGGCACCATGGTGCT
1 ACCACCATCGACCTAAGTTGCCGATGGTGTCCGATGCTCCTGCACATCG-AGGCACCATGGTGCT
* * *
894 GATACTTCCTGATGGTTTCGC
65 GATACTTCCCGATGG-TCCCC
* * * * * * *
915 ACCACCATCGGCCTCAGTTACTGATGGAGTCTGATGCTCCCT-CACATCGAAGGCACCATGGT-T
1 ACCACCATCGACCTAAGTTGCCGATGGTGTCCGATGCT-CCTGCACATCG-AGGCACCATGGTGC
978 TCGATACTTCCCGATGGTCCCC
64 T-GATACTTCCCGATGGTCCCC
* * * *
1000 ACCACCATCGACCTCAGTTGTCGATGGTGTCCGATGCTCTTGCACATCCGAGGCACCAAGGTGCT
1 ACCACCATCGACCTAAGTTGCCGATGGTGTCCGATGCTCCTGCACAT-CGAGGCACCATGGTGCT
* * *
1065 GATGA-TTCTCGATAGTCCCGT
65 GAT-ACTTCCCGATGGTCCC-C
* * *
1086 ACCACCATCGACCTAAGCTGCCGATGGTGTCCGATGATCCAGCACATC
1 ACCACCATCGACCTAAGTTGCCGATGGTGTCCGATGCTCCTGCACATC
1134 TAGGGTATTA
Statistics
Matches: 182, Mismatches: 30, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
84 2 0.01
85 68 0.37
86 110 0.60
87 2 0.01
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.24
Consensus pattern (84 bp):
ACCACCATCGACCTAAGTTGCCGATGGTGTCCGATGCTCCTGCACATCGAGGCACCATGGTGCTG
ATACTTCCCGATGGTCCCC
Found at i:1371 original size:3 final size:3
Alignment explanation
Indices: 1363--1399 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1353 CCTTCAAATT
* *
1363 TAA TAA TAA TAG TAA TAA TAA TAA TAA CAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1400 TTTGCTTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Done.