Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014161.1 Kokia drynarioides strain JFW-HI SEQ_129194, 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: 3821
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Found at i:231 original size:49 final size:48
Alignment explanation
Indices: 150--613 Score: 189
Period size: 49 Copynumber: 9.5 Consensus size: 48
140 CAGTACTTCA
* * * * *
150 AAGA-ATGAAGGGAAAGATCTAAGCCGTAACGGCAAATCCATTACCATG
1 AAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAATCCAGTACC-TG
* * * *
198 AAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCGTGTACCTCAG
1 AAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAATCC-AGTACCT--G
* * * * *
248 AAG-CATAAAGGGAAAGGTTTAAGTCACAATGG-AAAACCTAGTACCTC
1 AAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAATCC-AGTACCTG
* * ** * *
295 AGAGACATGAAGGGAAAGATTTAATTCGCAACGGTGAATCTAGTACCGTA
1 A-AGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAATCCAGTACC-TG
* * *
345 AAGACATG-AGGAGAAAGGTTTAAGTCGTAACGGCGAA-CCTTA-TACCTC
1 AAGACATGAAGG-GAAAGGTTTAAGTCGCAACGGCAAATCC--AGTACCTG
* * * * * ** * *
393 AAAAGCATAAAAGGAAAGATTTAAGTCGTAACGGTGAATCTAGTATCATG
1 AAGA-CATGAAGGGAAAGGTTTAAGTCGCAACGGCAAATCCAGTA-CCTG
* * *** *
443 AAGACATGAAGGGAAAGATTTAAG-CTGTAACGATGAATCTAGTACC-G
1 AAGACATGAAGGGAAAGGTTTAAGTC-GCAACGGCAAATCCAGTACCTG
** * * *
490 CCAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTAGAACCTCAG
1 --AAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAATCC-AGTACCT--G
* * * *** * *
542 AAG-CATAAAGTGAAAGATTTAAG-CTGCAACGATGAATCTAGTACCACG
1 AAGACATGAAGGGAAAGGTTTAAGTC-GCAACGGCAAATCCAGTACC-TG
590 AAGACATGAAGGG-AAGGATTTAAG
1 AAGACATGAAGGGAAAGG-TTTAAG
614 CTGCTACCAC
Statistics
Matches: 320, Mismatches: 66, Indels: 59
0.72 0.15 0.13
Matches are distributed among these distances:
47 2 0.01
48 31 0.10
49 263 0.82
50 23 0.07
52 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (48 bp):
AAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAATCCAGTACCTG
Found at i:384 original size:98 final size:97
Alignment explanation
Indices: 207--613 Score: 296
Period size: 98 Copynumber: 4.2 Consensus size: 97
197 GAAGATATGG
* * * *
207 AGGGAAAGGTTTAAGTCGCAACGGCGAACCGT-GTACC-TCAGAAG-CATAAAGGGAAAGGTTTA
1 AGGGAAAGATTTAAGTCGCAACGGTGAATC-TAGTACCAT-A-AAGACATGAAGGGAAAGGTTTA
** * * *
269 AGTCACAATGGAAAACCTAGTACCTCAGAGACATGA
63 AGTCGTAACGGAGAACCTAGTACCTCA-AGACATAA
* *
305 AGGGAAAGATTTAATTCGCAACGGTGAATCTAGTACCGTAAAGACATG-AGGAGAAAGGTTTAAG
1 AGGGAAAGATTTAAGTCGCAACGGTGAATCTAGTACCATAAAGACATGAAGG-GAAAGGTTTAAG
* *
369 TCGTAACGGCGAACCTTA-TACCTCAAAAGCATAA
65 TCGTAACGGAGAACC-TAGTACCTCAAGA-CATAA
* * * * *
403 AAGGAAAGATTTAAGTCGTAACGGTGAATCTAGTATCATGAAGACATGAAGGGAAAGATTTAAG-
1 AGGGAAAGATTTAAGTCGCAACGGTGAATCTAGTACCATAAAGACATGAAGGGAAAGGTTTAAGT
* * *
467 CTGTAAC-GATGAATCTAGTACCGCCAAGACACAA
66 C-GTAACGGA-GAACCTAGTACC-TCAAGACATAA
* * * * * * * *
501 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGAACC-TCAGAAG-CATAAAGTGAAAGATTTAA
1 AGGGAAAGATTTAAGTCGCAACGGTGAATCTAGTACCAT-A-AAGACATGAAGGGAAAGGTTTAA
* * * *
564 G-CTGCAAC-GATGAATCTAGTACCACGAAGACATGA
64 GTC-GTAACGGA-GAACCTAGTACCTC-AAGACATAA
*
599 AGGGAAGGATTTAAG
1 AGGGAAAGATTTAAG
614 CTGCTACCAC
Statistics
Matches: 254, Mismatches: 41, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
97 15 0.06
98 226 0.89
99 13 0.05
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (97 bp):
AGGGAAAGATTTAAGTCGCAACGGTGAATCTAGTACCATAAAGACATGAAGGGAAAGGTTTAAGT
CGTAACGGAGAACCTAGTACCTCAAGACATAA
Found at i:436 original size:147 final size:147
Alignment explanation
Indices: 206--617 Score: 489
Period size: 147 Copynumber: 2.8 Consensus size: 147
196 TGAAGATATG
* * *
206 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTCAGAAGCATAAAGGGAAAGGTTTAAG
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATAAAAGGAAAGATTTAAG
* * ** * * *
271 TCACAATGGAAAACCTAGTACCTCAG-AGACATGAAGGGAAAGATTTAA-TTCGCAACGGTGAAT
65 TCGCAACGGTGAATCTAGTACCTCAGAAGACATGAAGGGAAAGATTTAAGCT-GCAACGATGAAT
* *
334 CTAGTACCGTAAAGACA-T
129 CTAGTACCGCAAAGACACA
* *
352 GAGGAGAAAGGTTTAAGTCGTAACGGCGAACCTTATACCTCAAAAGCATAAAAGGAAAGATTTAA
1 GAGG-GAAAGGTTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATAAAAGGAAAGATTTAA
* *
417 GTCGTAACGGTGAATCTAGTA--TCATGAAGACATGAAGGGAAAGATTTAAGCTGTAACGATGAA
64 GTCGCAACGGTGAATCTAGTACCTCA-GAAGACATGAAGGGAAAGATTTAAGCTGCAACGATGAA
*
480 TCTAGTACCGCCAAGACACA
128 TCTAGTACCGCAAAGACACA
* * *
500 AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGAACCTCAGAAGCAT-AAAGTGAAAGATTTAA
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTA-TACCTCAGAAGCATAAAAG-GAAAGATTTAA
* * *
564 G-CTGCAACGATGAATCTAGTACCAC-GAAGACATGAAGGGAAGGATTTAAGCTGC
64 GTC-GCAACGGTGAATCTAGTACCTCAGAAGACATGAAGGGAAAGATTTAAGCTGC
618 TACCACCAAG
Statistics
Matches: 228, Mismatches: 28, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
145 3 0.01
146 12 0.05
147 208 0.91
148 4 0.02
149 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (147 bp):
GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTATACCTCAGAAGCATAAAAGGAAAGATTTAAGT
CGCAACGGTGAATCTAGTACCTCAGAAGACATGAAGGGAAAGATTTAAGCTGCAACGATGAATCT
AGTACCGCAAAGACACA
Found at i:629 original size:35 final size:35
Alignment explanation
Indices: 583--649 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
573 ATGAATCTAG
* * *
583 TACCACGAAGACATGAAGGGAAGGATTTAAGCTGC
1 TACCACCAAGACATAAAGGGAAAGATTTAAGCTGC
618 TACCACCAAGACATAAAGGGAAAGATTTAAGC
1 TACCACCAAGACATAAAGGGAAAGATTTAAGC
650 CGCAACGGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (35 bp):
TACCACCAAGACATAAAGGGAAAGATTTAAGCTGC
Found at i:1186 original size:17 final size:17
Alignment explanation
Indices: 1164--1245 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
1154 TGGGCCTAAC
1164 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
1181 AAATTTAAATATATATT
1 AAATTTAAATTTATTTT
** *
1198 AAATTTAAATCCATTTG
1 AAATTTAAATTTATTTT
* *
1215 GAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
*
1232 AAATATTAAGTTTA
1 AAAT-TTAAATTTA
1246 AATTTATTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 43 0.84
18 8 0.16
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:1888 original size:3 final size:3
Alignment explanation
Indices: 1880--1953 Score: 98
Period size: 3 Copynumber: 25.3 Consensus size: 3
1870 CAAATAGCAT
* **
1880 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TTT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1928 TAA TAT TAA TAA TAA TAA -AA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1954 TTGAAAGGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3092 original size:59 final size:59
Alignment explanation
Indices: 2966--3242 Score: 239
Period size: 59 Copynumber: 4.7 Consensus size: 59
2956 CCCGAATTTG
* * *
2966 CAAAATTCCA-TTTTAACCTTGAACTTTT-TAAAAA-TACATTTTAACCCCTGAACTTTC
1 CAAAATTCCATTTTTAACCTTGAA-TTTTCCAAAAATTACATTTTTACCCCTAAACTTTC
* * *
3023 TAAAATTCCATTGTTAACCTTGAATTTTCCAAAAATTACATTTTTA-CTCTCAAACTTTC
1 CAAAATTCCATTTTTAACCTTGAATTTTCCAAAAATTACATTTTTACCCCT-AAACTTTC
* * * * *
3082 CAAAAATCCATTTTTAACCTCGATTTTTCCACAAATTACCTTTTTACCCCTAAACTTTC
1 CAAAATTCCATTTTTAACCTTGAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTC
* * * * * *
3141 CAAAATTCTATTTTTGA-CTTCGATTTTTCC-AAAATTAC-TATTTTACCCCCATA-TGTC
1 CAAAATTCCATTTTTAACCTT-GAATTTTCCAAAAATTACAT-TTTTACCCCTAAACTTTC
* * ** *
3198 AAAAAATTCCATTTTAAACCACGAACTTTCC-AAAATTACTATTTT
1 -CAAAATTCCATTTTTAACCTTGAATTTTCCAAAAATTAC-ATTTT
3243 ATCCTCGAAT
Statistics
Matches: 179, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
57 17 0.09
58 68 0.38
59 90 0.50
60 4 0.02
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (59 bp):
CAAAATTCCATTTTTAACCTTGAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTC
Found at i:3110 original size:29 final size:28
Alignment explanation
Indices: 2958--3301 Score: 126
Period size: 29 Copynumber: 11.8 Consensus size: 28
2948 TGGAGGTCCC
* *
2958 CGAA-TTTGCAAAATTCCATTTTAACCT
1 CGAATTTTCCAAAATTCCATTTTTACCT
* * * * * *
2985 TGAACTTTT-TAAAAATACATTTTAACCC
1 CGAA-TTTTCCAAAATTCCATTTTTACCT
* * *
3013 CTGAACTTTCTAAAATTCCATTGTTAACCT
1 C-GAATTTTCCAAAATTCCATT-TTTACCT
* *
3043 TGAATTTTCCAAAAATTACATTTTTACTCT
1 CGAATTTTCC-AAAATTCCATTTTTAC-CT
* * *
3073 CAAACTTTCCAAAAATCCATTTTTAACCT
1 CGAATTTTCCAAAATTCCATTTTT-ACCT
* *
3102 CGATTTTTCCACAAATTACC-TTTTTACCC
1 CGAATTTTCCA-AAATT-CCATTTTTACCT
* * * *
3131 CTAAACTTTCCAAAATTCTATTTTTGACTT
1 C-GAATTTTCCAAAATTCCATTTTT-ACCT
* *
3161 CGATTTTTCCAAAATTAC-TATTTTACC-
1 CGAATTTTCCAAAATTCCAT-TTTTACCT
** * * * *
3188 CCCATATGTCAAAAAATTCCATTTTAAACCA
1 CGAAT-TTTC-CAAAATTCCATTTT-TACCT
* *
3219 CGAACTTTCCAAAATTAC-TATTTTATCCT
1 CGAATTTTCCAAAATTCCAT-TTTTA-CCT
* * *
3248 CGAA-TGTCTAAAAATTCTATTTTTGACCT
1 CGAATTTTC-CAAAATTCCATTTTT-ACCT
* *
3277 CGAACCTTCCCAAAATTACCATTTT
1 CGAA-TTTTCCAAAATT-CCATTTT
3302 GCCCTCGGGT
Statistics
Matches: 230, Mismatches: 60, Indels: 50
0.68 0.18 0.15
Matches are distributed among these distances:
27 5 0.02
28 30 0.13
29 122 0.53
30 61 0.27
31 12 0.05
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (28 bp):
CGAATTTTCCAAAATTCCATTTTTACCT
Found at i:3204 original size:58 final size:56
Alignment explanation
Indices: 3024--3279 Score: 194
Period size: 58 Copynumber: 4.4 Consensus size: 56
3014 TGAACTTTCT
* * * * * *
3024 AAAATTCCATTGTTAACCTTGAATTTTCCAAAAATTAC-ATTTTTACTCTCAAACTTTCCA
1 AAAATTCCATTTTTAACCTCGATTTTTCC-AAAATTACTA-TTTTAC-CCCCAA-TGT-CA
* * *
3084 AAAA-TCCATTTTTAACCTCGATTTTTCCACAAATTACCT-TTTTACCCCTAAACTTTCC
1 AAAATTCCATTTTTAACCTCGATTTTTCCA-AAATTA-CTATTTTACCCC-CAA-TGTCA
* * *
3142 AAAATTCTATTTTTGACTTCGATTTTTCCAAAATTACTATTTTACCCCCATATGTCAA
1 AAAATTCCATTTTTAACCTCGATTTTTCCAAAATTACTATTTTACCCCCA-ATGTC-A
* * ** * *
3200 AAAATTCCATTTTAAACCACGAACTTTCCAAAATTACTATTTTATCCTCGAATGTCTA
1 AAAATTCCATTTTTAACCTCGATTTTTCCAAAATTACTATTTTA-CCCCCAATGTC-A
* *
3258 AAAATTCTATTTTTGACCTCGA
1 AAAATTCCATTTTTAACCTCGA
3280 ACCTTCCCAA
Statistics
Matches: 162, Mismatches: 25, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
57 6 0.04
58 85 0.52
59 66 0.41
60 5 0.03
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (56 bp):
AAAATTCCATTTTTAACCTCGATTTTTCCAAAATTACTATTTTACCCCCAATGTCA
Found at i:3281 original size:58 final size:58
Alignment explanation
Indices: 3142--3301 Score: 187
Period size: 58 Copynumber: 2.7 Consensus size: 58
3132 TAAACTTTCC
* **
3142 AAAATTCTATTTTTGACTTCGATTTTTCCAAAATTACTATTTTACCCCCATATGTCAA
1 AAAATTCTATTTTTGACCTCGAACTTTCCAAAATTACTATTTTACCCCCATATGTCAA
* ** * * * *
3200 AAAATTCCATTTTAAACCACGAACTTTCCAAAATTACTATTTTATCCTCGA-ATGTCTA
1 AAAATTCTATTTTTGACCTCGAACTTTCCAAAATTACTATTTTA-CCCCCATATGTCAA
* *
3258 AAAATTCTATTTTTGACCTCGAACCTTCCCAAAATTACCATTTT
1 AAAATTCTATTTTTGACCTCGAA-CTTTCCAAAATTACTATTTT
3302 GCCCTCGGGT
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
58 62 0.74
59 22 0.26
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (58 bp):
AAAATTCTATTTTTGACCTCGAACTTTCCAAAATTACTATTTTACCCCCATATGTCAA
Found at i:3320 original size:59 final size:58
Alignment explanation
Indices: 3049--3330 Score: 144
Period size: 58 Copynumber: 4.8 Consensus size: 58
3039 ACCTTGAATT
* * * * * * **
3049 TTCCAAAAATTA-CATTTTTACTCTCAAACTTTCCAAAAA-TCCATTTTTAACCTCGATT
1 TTCCCAAAATTACCA-TTTTACCCTCGAA-TATCCAAAAATTCTATTTTTAACCACGAAC
* * * * * ** **
3107 TTTCCACAAATTACCTTTTTACCC-CTAAACTTTCC-AAAATTCTATTTTTGACTTCGATT
1 TTCCCA-AAATTACCATTTTACCCTC-GAA-TATCCAAAAATTCTATTTTTAACCACGAAC
* * * * * * *
3166 TTTCCAAAATTACTATTTTACCC-CCATATGTCAAAAAATTCCATTTTAAACCACGAAC
1 TTCCCAAAATTACCATTTTACCCTCGA-ATATCCAAAAATTCTATTTTTAACCACGAAC
* * * * * * *
3224 TTTCCAAAATTACTATTTTATCCTCGAATGTCTAAAAATTCTATTTTTGACCTCGAACC
1 TTCCCAAAATTACCATTTTACCCTCGAATATCCAAAAATTCTATTTTTAACCACGAA-C
* **
3283 TTCCCAAAATTACCATTTTGCCCTCGGGTATCCAAAAA-TCTCATTTTT
1 TTCCCAAAATTACCATTTTACCCTCGAATATCCAAAAATTCT-ATTTTT
3331 TACTCCGATT
Statistics
Matches: 181, Mismatches: 34, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
57 4 0.02
58 93 0.51
59 83 0.46
60 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.39
Consensus pattern (58 bp):
TTCCCAAAATTACCATTTTACCCTCGAATATCCAAAAATTCTATTTTTAACCACGAAC
Done.