Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012702.1 Kokia drynarioides strain JFW-HI SEQ_127713, 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: 1819
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.27
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:590 original size:18 final size:20
Alignment explanation
Indices: 550--590 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
540 AAATAGAAAA
*
550 TTTGAAATTTTATTAAATAT
1 TTTGAAATTTTATAAAATAT
*
570 TTTG-AATTTTA-AAAATGT
1 TTTGAAATTTTATAAAATAT
588 TTT
1 TTT
591 TGAGCACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTGAAATTTTATAAAATAT
Found at i:757 original size:86 final size:86
Alignment explanation
Indices: 609--1167 Score: 487
Period size: 86 Copynumber: 6.5 Consensus size: 86
599 ATCAGACACA
* * * * * * *
609 ATCGGCACGTTGGTGCC-CTGGATGTGCTGGATCATCGGACAACA-TCGGTAGCTTAGGCCGATG
1 ATCGGCACCTTGGTGCCTC-GGATGTACGGGAGCATCGGACACCACT-GGCAACTTAGGCCGATG
672 GTGGTGCGAGACCATCGGGAATC
64 GTGGTGCGAGACCATCGGGAATC
* * * *
695 ATCGGCTCCTTGGTGCCTCGGATGTACGGGAGCATCGGACACCACTGACAACTAAGGTCGATGGT
1 ATCGGCACCTTGGTGCCTCGGATGTACGGGAGCATCGGACACCACTGGCAACTTAGGCCGATGGT
*
760 GGTTCGAGACCATCGGGAAGT-
66 GGTGCGAGACCATCGGGAA-TC
* * * *
781 ATCGGAACCATGGTGCCTTGGATGTACGGGAGCATCGGACACCA-TCGGTAA-TTGAGGCCGATG
1 ATCGGCACCTTGGTGCCTCGGATGTACGGGAGCATCGGACACCACT-GGCAACTT-AGGCCGATG
*
844 GTGGTGCGGGACCATCGGGAAGT-
64 GTGGTGCGAGACCATCGGGAA-TC
* * * * *
867 ATCGGTACCATGGTGCCTTC-GATGTGCGGGAGCATCGGACACCACCGGCTACTTAGGCCGATGG
1 ATCGGCACCTTGGTGCC-TCGGATGTACGGGAGCATCGGACACCACTGGCAACTTAGGCCGATGG
* * * *
931 TGGTACGGGACAATTGGG-ATCC
65 TGGTGCGAGACCATCGGGAAT-C
* * * * * *
953 ATCGGTACCTTGGTGCCTTGGATGTGCGAGAGCATCGGACACCA-TCGGCAGCTTAGGGCGATGG
1 ATCGGCACCTTGGTGCCTCGGATGTACGGGAGCATCGGACACCACT-GGCAACTTAGGCCGATGG
*
1017 TGGTGC-AGGACTATCGGG-ATCC
65 TGGTGCGA-GACCATCGGGAAT-C
* * * * * * *
1039 ATCGGCACCTTGCTACCTTGGATGTGCGAGAGCATCGGACACCA-TCGGTAAATTAGGCCGATGG
1 ATCGGCACCTTGGTGCCTCGGATGTACGGGAGCATCGGACACCACT-GGCAACTTAGGCCGATGG
** * *
1103 TGGT-ATAGGACCATCGAGAAGC
65 TGGTGCGA-GACCATCGGGAATC
* * *
1125 ATCGGCACCTTGGTACCTCGGATGTATGGGAGCATCGGGCACC
1 ATCGGCACCTTGGTGCCTCGGATGTACGGGAGCATCGGACACC
1168 NNNNNNNNNN
Statistics
Matches: 399, Mismatches: 59, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
84 1 0.00
85 4 0.01
86 387 0.97
87 7 0.02
ACGTcount: A:0.21, C:0.24, G:0.34, T:0.21
Consensus pattern (86 bp):
ATCGGCACCTTGGTGCCTCGGATGTACGGGAGCATCGGACACCACTGGCAACTTAGGCCGATGGT
GGTGCGAGACCATCGGGAATC
Found at i:817 original size:43 final size:43
Alignment explanation
Indices: 770--904 Score: 118
Period size: 43 Copynumber: 3.1 Consensus size: 43
760 GGTTCGAGAC
*
770 CATCGGGAAGTATCGGAACCATGGTGCCTTGGATGTACGGGAG
1 CATCGGGAAGTATCGGAACCATGGTGCCTTGGATGTGCGGGAG
** * * *
813 CATC-GGACACCATCGGTAA--TTGAG-GCCGATGG-TGGTGCGGGAC
1 CATCGGGA-AGTATCGG-AACCATG-GTGCC-TTGGAT-GTGCGGGAG
* *
856 CATCGGGAAGTATCGGTACCATGGTGCCTTCGATGTGCGGGAG
1 CATCGGGAAGTATCGGAACCATGGTGCCTTGGATGTGCGGGAG
899 CATCGG
1 CATCGG
905 ACACCACCGG
Statistics
Matches: 69, Mismatches: 13, Indels: 20
0.68 0.13 0.20
Matches are distributed among these distances:
42 10 0.14
43 48 0.70
44 11 0.16
ACGTcount: A:0.21, C:0.21, G:0.37, T:0.21
Consensus pattern (43 bp):
CATCGGGAAGTATCGGAACCATGGTGCCTTGGATGTGCGGGAG
Found at i:905 original size:172 final size:170
Alignment explanation
Indices: 609--1167 Score: 586
Period size: 172 Copynumber: 3.3 Consensus size: 170
599 ATCAGACACA
* * * * * * *
609 ATCGGCACGTTGGTGCCCTGGATGTGCTGGATCATCGGACAACATCGGTAGCTTAGGCCGATGGT
1 ATCGGAACCTTGGTGCCTTGGATGTACGGGAGCATCGGACACCATCGGTAGCTTAGGCCGATGGT
* *
674 GGTGCGAGACCATCGGGAATCATCGGCT-CCTTGGTGCC-TCGGATGTACGGGAGCATCGGACAC
66 GGTGCGGGACCATCGGGAAT-ATCGG-TACCTTGGTGCCTTC-GATGTGCGGGAGCATCGGACAC
* * * *
737 CACTGACAACTAAGGTCGATGGTGGTTCGAGACCATCGGGAAGT
128 CACCGACAACTTAGGCCGATGGTGGTTCG-GACCATCGGGAAGC
* *
781 ATCGGAACCATGGTGCCTTGGATGTACGGGAGCATCGGACACCATCGGTA-ATTGAGGCCGATGG
1 ATCGGAACCTTGGTGCCTTGGATGTACGGGAGCATCGGACACCATCGGTAGCTT-AGGCCGATGG
*
845 TGGTGCGGGACCATCGGGAAGTATCGGTACCATGGTGCCTTCGATGTGCGGGAGCATCGGACACC
65 TGGTGCGGGACCATCGGGAA-TATCGGTACCTTGGTGCCTTCGATGTGCGGGAGCATCGGACACC
* * * * * **
910 ACCGGCTACTTAGGCCGATGGTGGTACGGGACAATTGGGATCC
129 ACCGACAACTTAGGCCGATGGTGGTTC-GGACCATCGGGAAGC
* * * * *
953 ATCGGTACCTTGGTGCCTTGGATGTGCGAGAGCATCGGACACCATCGGCAGCTTAGGGCGATGGT
1 ATCGGAACCTTGGTGCCTTGGATGTACGGGAGCATCGGACACCATCGGTAGCTTAGGCCGATGGT
* * * * * * *
1018 GGTGCAGGACTATCGGG-ATCCATCGGCACCTTGCTACCTTGGATGTGCGAGAGCATCGGACACC
66 GGTGCGGGACCATCGGGAAT--ATCGGTACCTTGGTGCCTTCGATGTGCGGGAGCATCGGACACC
* ** * * *
1082 ATCGGTAAATTAGGCCGATGGTGGTATAGGACCATCGAGAAGC
129 ACCGACAACTTAGGCCGATGGTGGT-TCGGACCATCGGGAAGC
* * * * *
1125 ATCGGCACCTTGGTACCTCGGATGTATGGGAGCATCGGGCACC
1 ATCGGAACCTTGGTGCCTTGGATGTACGGGAGCATCGGACACC
1168 NNNNNNNNNN
Statistics
Matches: 322, Mismatches: 56, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
170 1 0.00
171 4 0.01
172 311 0.97
173 6 0.02
ACGTcount: A:0.21, C:0.24, G:0.34, T:0.21
Consensus pattern (170 bp):
ATCGGAACCTTGGTGCCTTGGATGTACGGGAGCATCGGACACCATCGGTAGCTTAGGCCGATGGT
GGTGCGGGACCATCGGGAATATCGGTACCTTGGTGCCTTCGATGTGCGGGAGCATCGGACACCAC
CGACAACTTAGGCCGATGGTGGTTCGGACCATCGGGAAGC
Found at i:1076 original size:258 final size:257
Alignment explanation
Indices: 609--1167 Score: 635
Period size: 258 Copynumber: 2.2 Consensus size: 257
599 ATCAGACACA
** * * * * *
609 ATCGGCACGTTGGTGCCCTGGATGTGCTGGATCATCGGACAACATCGGTAGCTTAGGCCGATGGT
1 ATCGGCACCATGGTG-CCTCGATGTGCGGGAGCATCGGACACCACCGGTAGCTTAGGCCGATGGT
* * *
674 GGTGCGAGACCATCGGGAATCATCGGCTCCTTGGTGCCTCGGATGTACGGGAGCATCGGACACCA
65 GGTACGAGACAATCGGGAATCATCGGCTCCTTGGTGCCTCGGATGTACGAGAGCATCGGACACCA
* * ** * *
739 CTGACAACTAAGGTCGATGGTGGTTCGAGACCATCGGGAAGTATCGGAACCATGGTGCCTTGGAT
130 CTGACAACTAAGGGCGATGGTGGTGCGAGACCATCGGGAACCATCGGAACCATGCTACCTTGGAT
* * * * *
804 GTACGGGAGCATCGGACACCATCGGT-AATTGAGGCCGATGGTGGTGCGGGACCATCGGGAAGT
195 GTACGAGAGCATCGGACACCATCGGTAAATT-AGGCCGATGGTGGTACAGGACCATCGAGAAGC
*
867 ATCGGTACCATGGTGCCTTCGATGTGCGGGAGCATCGGACACCACCGGCTA-CTTAGGCCGATGG
1 ATCGGCACCATGGTGCC-TCGATGTGCGGGAGCATCGGACACCACCGG-TAGCTTAGGCCGATGG
* * * *
931 TGGTACGGGACAATTGGG-ATCCATCGG-TACCTTGGTGCCTTGGATGTGCGAGAGCATCGGACA
64 TGGTACGAGACAATCGGGAAT-CATCGGCT-CCTTGGTGCCTCGGATGTACGAGAGCATCGGACA
* * * * * * *
994 CCA-TCGGCAGCTTAGGGCGATGGTGGTGC-AGGACTATCGGGATCCATCGGCACCTTGCTACCT
127 CCACT-GACAACTAAGGGCGATGGTGGTGCGA-GACCATCGGGAACCATCGGAACCATGCTACCT
* *
1057 TGGATGTGCGAGAGCATCGGACACCATCGGTAAATTAGGCCGATGGTGGTATAGGACCATCGAGA
190 TGGATGTACGAGAGCATCGGACACCATCGGTAAATTAGGCCGATGGTGGTACAGGACCATCGAGA
1122 AGC
255 AGC
* * ** *
1125 ATCGGCACCTTGGTACCTCGGATGTATGGGAGCATCGGGCACC
1 ATCGGCACCATGGTGCCTC-GATGTGCGGGAGCATCGGACACC
1168 NNNNNNNNNN
Statistics
Matches: 252, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
257 9 0.04
258 237 0.94
259 6 0.02
ACGTcount: A:0.21, C:0.24, G:0.34, T:0.21
Consensus pattern (257 bp):
ATCGGCACCATGGTGCCTCGATGTGCGGGAGCATCGGACACCACCGGTAGCTTAGGCCGATGGTG
GTACGAGACAATCGGGAATCATCGGCTCCTTGGTGCCTCGGATGTACGAGAGCATCGGACACCAC
TGACAACTAAGGGCGATGGTGGTGCGAGACCATCGGGAACCATCGGAACCATGCTACCTTGGATG
TACGAGAGCATCGGACACCATCGGTAAATTAGGCCGATGGTGGTACAGGACCATCGAGAAGC
Found at i:1084 original size:43 final size:42
Alignment explanation
Indices: 951--1086 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 42
941 CAATTGGGAT
*
951 CCATCGGTACCTTGGTGCCTTGGATGTGCGAGAGCATCGGACA
1 CCATCGGCACCTT-GTGCCTTGGATGTGCGAGAGCATCGGACA
* * ** *
994 CCATCGGCAGCTTAGGGCGATGG-TGGTGC-AG-GACTATCGGGA-T
1 CCATCGGCACCTT-GTGCCTTGGAT-GTGCGAGAG-C-ATC-GGACA
*
1037 CCATCGGCACCTTGCTACCTTGGATGTGCGAGAGCATCGGACA
1 CCATCGGCACCTTG-TGCCTTGGATGTGCGAGAGCATCGGACA
1080 CCATCGG
1 CCATCGG
1087 TAAATTAGGC
Statistics
Matches: 71, Mismatches: 13, Indels: 18
0.70 0.13 0.18
Matches are distributed among these distances:
41 1 0.01
42 8 0.11
43 54 0.76
44 7 0.10
45 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.21
Consensus pattern (42 bp):
CCATCGGCACCTTGTGCCTTGGATGTGCGAGAGCATCGGACA
Found at i:1392 original size:43 final size:43
Alignment explanation
Indices: 1265--1394 Score: 113
Period size: 43 Copynumber: 3.0 Consensus size: 43
1255 AATTATCGAC
*
1265 ACCATGGTGCCTTCGATGTGCGGGAGCATCGGACACCATCGGT
1 ACCATGGTGCCTTTGATGTGCGGGAGCATCGGACACCATCGGT
* * ** * * * **
1308 AACTTAGGT--CGATGGTGGTACGGGACCATCGGGA-AGTATCGGT
1 ACCAT-GGTGCCTTTGAT-GTGCGGGAGCATC-GGACACCATCGGT
*
1351 ACCATGGTGCCTTTGATGTGCGGAAGCATCGGACACCATCGGT
1 ACCATGGTGCCTTTGATGTGCGGGAGCATCGGACACCATCGGT
1394 A
1 A
1395 ACTTAGGCCG
Statistics
Matches: 61, Mismatches: 20, Indels: 12
0.66 0.22 0.13
Matches are distributed among these distances:
42 9 0.15
43 42 0.69
44 10 0.16
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (43 bp):
ACCATGGTGCCTTTGATGTGCGGGAGCATCGGACACCATCGGT
Found at i:1435 original size:86 final size:86
Alignment explanation
Indices: 1218--1439 Score: 309
Period size: 86 Copynumber: 2.6 Consensus size: 86
1208 NNNNNNNNNN
* ** * *
1218 CGGTAACTAAGGCCGATGGTGGTGCGGGACCATTGAAAATTATCGACACCATGGTGCCTTCGATG
1 CGGTAACTTAGGCCGATGGTGGTGCGGGACCATTGGGAAGTATCGGCACCATGGTGCCTTCGATG
*
1283 TGCGGGAGCATCGGACACCAT
66 TGCGGAAGCATCGGACACCAT
* * * * *
1304 CGGTAACTTAGGTCGATGGTGGTACGGGACCATCGGGAAGTATCGGTACCATGGTGCCTTTGATG
1 CGGTAACTTAGGCCGATGGTGGTGCGGGACCATTGGGAAGTATCGGCACCATGGTGCCTTCGATG
1369 TGCGGAAGCATCGGACACCAT
66 TGCGGAAGCATCGGACACCAT
* * **
1390 CGGTAACTTAGGCCGATGGTGGTGTGAGACCATTGGGAANCATCGGCACC
1 CGGTAACTTAGGCCGATGGTGGTGCGGGACCATTGGGAAGTATCGGCACC
1440 TTGCATGTAC
Statistics
Matches: 117, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 117 1.00
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (86 bp):
CGGTAACTTAGGCCGATGGTGGTGCGGGACCATTGGGAAGTATCGGCACCATGGTGCCTTCGATG
TGCGGAAGCATCGGACACCAT
Done.