Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007740.1 Kokia drynarioides strain JFW-HI SEQ_122373, 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: 3544
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:299 original size:172 final size:172
Alignment explanation
Indices: 2--324 Score: 560
Period size: 172 Copynumber: 1.9 Consensus size: 172
1 A
* *
2 TCTTCTTGATGAGATACAGAGAAGCATACCAAATTAATGAAACAAAGTTCAATGTGAGTGAAACT
1 TCTTCCTGATGAGATACAGAGAAGCATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACT
67 TCGAATCCCAGCTTCCGGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTCGTCTTCTT
66 TCGAATCCCAGCTTCCGGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTCGTCTTCTT
132 GATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCC
131 GATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCC
*
174 TCTTCCTGATGAGATACAGAGAAGTATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACT
1 TCTTCCTGATGAGATACAGAGAAGCATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACT
* * *
239 TCGAA-CCCTAGCTTCCTGATGAGGTACTGAG-AGACAGGTCGAAGCAATAAAGCTGTCGTCTTC
66 TCGAATCCC-AGCTTCCGGATGAGATACTGAGAAG-CAGGTCGAAGCAATAAAGCGGTCGTCTTC
302 TTGATGAGATACAGAGAAGTGGA
129 TTGATGAGATACAGAGAAGTGGA
325 CCAAATCCGT
Statistics
Matches: 143, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
171 5 0.03
172 138 0.97
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (172 bp):
TCTTCCTGATGAGATACAGAGAAGCATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACT
TCGAATCCCAGCTTCCGGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTCGTCTTCTT
GATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCC
Found at i:703 original size:208 final size:207
Alignment explanation
Indices: 122--841 Score: 944
Period size: 209 Copynumber: 3.4 Consensus size: 207
112 AATAAAGCGG
* * * *
122 TCGTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCCTCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAG
* *
187 ATACAGAGAAGTATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCTAGCT
66 ATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCTAGCT
* * * *
252 TCCTGATGAGGTACTGAG-AGACAGGTCGAAGCAATAAAGCTGTCGTCTTCTTGATGAGATACAG
131 T-CTGATGAGATACTGAGAAG-CAGGTCGAAGCAATAAA-ATGTCATCTTCCTGATGAGATACAG
316 AGAAGTGGACCAAAT
193 AGAAGTGGACCAAAT
* **
331 CCGTCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAGTGA-G-GTAGTCATCTTCCTGATG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG-A-TCATCTTCCTGATG
** * *
394 AGATATGGAGAAGTATACCAAATCAATGAAGCAAAGCTCGATGTGAGCGAAACTTCGAACCCTAG
64 AGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCTAG
* ** *
459 CTTACTGATGAGATACTGAGAAGCATGTTAAAGCAATAAAATGATCAACTTCCTGATGAGATACA
129 CTT-CTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATG-TCATCTTCCTGATGAGATACA
*
524 GAGAAGTGAACCAAAT
192 GAGAAGTGGACCAAAT
* * *
540 TCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAAC-AGTGATGCGATCATCTTCCTAATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAG
* * * * * * * * *
604 ATATAGAGAAGAATACCAAATCAACGAAATAAAGCTTAATATGAGCGAAACTCCAAACCCCAGCT
66 ATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCTAGCT
* ** *
669 TCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGACACAGA
131 TC-TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA-ATGTCATCTTCCTGATGAGATACAGA
734 GAAGTGGACCAAAT
194 GAAGTGGACCAAAT
* * *
748 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAAGAAGTAATGCGGTCATCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAG
*
813 ATACAGAGAAGTAGACCAAATCAAATGAA
66 ATACAGAGAAGTATACCAAATC-AATGAA
842 GGAAAATGTG
Statistics
Matches: 444, Mismatches: 57, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
207 2 0.00
208 178 0.40
209 256 0.58
210 8 0.02
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (207 bp):
TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAG
ATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCTAGCT
TCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGTCATCTTCCTGATGAGATACAGAGA
AGTGGACCAAAT
Found at i:807 original size:86 final size:85
Alignment explanation
Indices: 667--833 Score: 237
Period size: 86 Copynumber: 2.0 Consensus size: 85
657 CAAACCCCAG
* * **
667 CTTCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGACACA
1 CTTCCTGATGAGATACAGAGAAGCGGGTAAAAGCAATAAAGCGGTCATCTTCCTGATGAGACACA
*
732 GAGAAGTGGACCAAATTCGT
66 GAGAAGTAGACCAAATTCGT
* * *
752 CTTCCTGATGAGATACAGAGAAGCGGATTAAAAG-AAGTAATGCGGTCATCTTCCTGATGAGATA
1 CTTCCTGATGAGATACAGAGAAGCGG-GTAAAAGCAA-TAAAGCGGTCATCTTCCTGATGAGACA
816 CAGAGAAGTAGACCAAAT
64 CAGAGAAGTAGACCAAAT
834 CAAATGAAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
85 26 0.36
86 46 0.64
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGCGGGTAAAAGCAATAAAGCGGTCATCTTCCTGATGAGACACA
GAGAAGTAGACCAAATTCGT
Found at i:910 original size:208 final size:205
Alignment explanation
Indices: 122--946 Score: 913
Period size: 209 Copynumber: 4.0 Consensus size: 205
112 AATAAAGCGG
* * *
122 TCGTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCCTCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
* * * *
187 ATACAGAGAAGTATACCAAAT-TAATGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCTAGC
66 ATACAGAGAAGTATACCAAATCAAATGAAGC-AA----AATGTGAGCGAAACTTCAAACCCTAGC
* * *
251 TTCCTGATGAGGTACTGAG-AGACAGGTCGAAGCAATAAAGCTG-TCGTCTTCTTGATGAGATAC
126 TTCCTGATGAGATACTGAGAAG-CAGGTCGAAGCAATAAAGC-GATCATCTTCCTGATGAGATAC
314 AGAGAAGTGGACCAAAT
189 AGAGAAGTGGACCAAAT
* ** * **
331 CCGTCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAGTGAGGTAGTCATCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
** *
396 ATATGGAGAAGTATACCAAATC-AATGAAGCAAAGCTCGATGTGAGCGAAACTTCGAACCCTAGC
66 ATACAGAGAAGTATACCAAATCAAATGAAGCAAA-----ATGTGAGCGAAACTTCAAACCCTAGC
* * ** ** *
460 TTACTGATGAGATACTGAGAAGCATGTTAAAGCAATAAAATGATCAACTTCCTGATGAGATACAG
126 TTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATCATCTTCCTGATGAGATACAG
*
525 AGAAGTGAACCAAAT
191 AGAAGTGGACCAAAT
* * * *
540 TCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAAC-AGTGATGCGATCATCTTCCTAATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
* * * ** * * *
604 ATATAGAGAAGAATACCAAATCAACGAAATAAAGCTTAATATGAGCGAAACTCCAAACCCCAGCT
66 ATACAGAGAAGTATACCAAAT---C-AAATGAAGCAAAATGTGAGCGAAACTTCAAACCCTAGCT
* * * *
669 TCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGACACAGA
127 TCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGA
734 GAAGTGGACCAAAT
192 GAAGTGGACCAAAT
* *
748 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAAGAAGTAATGCGGTCATCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
* * * * **
813 ATACAGAGAAGTAGACCAAATCAAATGAAGGAAAATGTGAGTGAAGCTTCAAAAACCCCTATTTT
66 ATACAGAGAAGTATACCAAATCAAATGAAGCAAAATGTGAGCGAAACTTC--AAA-CCCTAGCTT
* * ** * * * *
878 CCTGATAAGATACAGAGAAGTGGGTTGAAGCAATAAATCGATCATCTTCTTGGTGAGATACAGAG
128 CCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGAG
943 AAGT
193 AAGT
947 AGACTGAGAG
Statistics
Matches: 516, Mismatches: 83, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
204 1 0.00
205 20 0.04
206 1 0.00
207 3 0.01
208 233 0.45
209 247 0.48
210 2 0.00
211 1 0.00
213 8 0.02
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (205 bp):
TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
ATACAGAGAAGTATACCAAATCAAATGAAGCAAAATGTGAGCGAAACTTCAAACCCTAGCTTCCT
GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGAGAAG
TGGACCAAAT
Found at i:3052 original size:30 final size:31
Alignment explanation
Indices: 2908--3119 Score: 187
Period size: 30 Copynumber: 7.1 Consensus size: 31
2898 AAAAATCATG
* * *
2908 TTTTGACCCCCGAACTT-TCCAAAAAA-TGCA
1 TTTTGACCCTCAAACTTCT-CAAAAAATTACA
2938 TTTTGACCCTCAAACTTCTCAAAAAA-TACA
1 TTTTGACCCTCAAACTTCTCAAAAAATTACA
*
2968 TTTTGACCCTCGAACTTCTC-AAAAATTACA
1 TTTTGACCCTCAAACTTCTCAAAAAATTACA
* *
2998 TTTTAACCCTCAAACTT-TCCAAAAATTACA
1 TTTTGACCCTCAAACTTCTCAAAAAATTACA
* * *
3028 TTTTGACCCTTAAGCTTAT-AAAAAATTACA
1 TTTTGACCCTCAAACTTCTCAAAAAATTACA
* * *
3058 TGTT-ACCC-CTGAACTT-TC-AAAAATCACA
1 TTTTGACCCTC-AAACTTCTCAAAAAATTACA
* *
3086 TTTTTACCCTCAAACATC-C-AAAAATTACCA
1 TTTTGACCCTCAAACTTCTCAAAAAATTA-CA
3116 TTTT
1 TTTT
3120 TATTCCGAAC
Statistics
Matches: 153, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
28 13 0.08
29 31 0.20
30 107 0.70
31 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.33
Consensus pattern (31 bp):
TTTTGACCCTCAAACTTCTCAAAAAATTACA
Found at i:3120 original size:30 final size:29
Alignment explanation
Indices: 2924--3149 Score: 179
Period size: 30 Copynumber: 7.6 Consensus size: 29
2914 CCCCCGAACT
* * *
2924 TTCCAAAAAATGCATTTTGACCCTCAAAC
1 TTCCAAAAATTACATTTTTACCCTCAAAC
* * *
2953 TTCTCAAAAAATACATTTTGACCCTCGAAC
1 TTC-CAAAAATTACATTTTTACCCTCAAAC
*
2983 TTCTCAAAAATTACATTTTAACCCTCAAAC
1 TTC-CAAAAATTACATTTTTACCCTCAAAC
* * *
3013 TTTCCAAAAATTACATTTTGACCCTTAAGC
1 -TTCCAAAAATTACATTTTTACCCTCAAAC
** * *
3043 TTATAAAAAATTACA-TGTTACCC-CTGAAC
1 TT-CCAAAAATTACATTTTTACCCTC-AAAC
* *
3072 TTTCAAAAATCACATTTTTACCCTCAAAC
1 TTCCAAAAATTACATTTTTACCCTCAAAC
* ** *
3101 ATCCAAAAATTACCATTTTTATTC-CGAAC
1 TTCCAAAAATTA-CATTTTTACCCTCAAAC
3130 TTTCCAAAAATTACCATTTT
1 -TTCCAAAAATTA-CATTTT
3150 ACTCTCGAGT
Statistics
Matches: 163, Mismatches: 26, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
28 10 0.06
29 38 0.23
30 112 0.69
31 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTCAAAC
Found at i:3130 original size:58 final size:58
Alignment explanation
Indices: 3068--3180 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 58
3058 TGTTACCCCT
3068 GAACTTT-CAAAAATCA-CATTTTTACCCTCAAACATCCAAAAATTACCATTTTTATTCC
1 GAACTTTCCAAAAATCACCA-TTTTACCCTCAAACATCC-AAAATTACCATTTTTATTCC
* * * **
3126 GAACTTTCCAAAAATTACCATTTTACTCTCGAGTATCCAAAATTACCATTTTTAT
1 GAACTTTCCAAAAATCACCATTTTACCCTCAAACATCCAAAATTACCATTTTTAT
3181 CCCCGGACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 24 0.50
59 22 0.46
60 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (58 bp):
GAACTTTCCAAAAATCACCATTTTACCCTCAAACATCCAAAATTACCATTTTTATTCC
Found at i:3176 original size:28 final size:29
Alignment explanation
Indices: 3101--3177 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
3091 ACCCTCAAAC
*
3101 ATCCAAAAATTACCATTTTTATTCCGAACT
1 ATCCAAAAATTACCA-TTTTACTCCGAACT
* *
3131 TTCCAAAAATTACCATTTTACTCTCG-AGT
1 ATCCAAAAATTACCATTTTACTC-CGAACT
3160 ATCC-AAAATTACCATTTT
1 ATCCAAAAATTACCATTTT
3178 TATCCCCGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.33
29 12 0.29
30 16 0.38
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (29 bp):
ATCCAAAAATTACCATTTTACTCCGAACT
Found at i:3178 original size:29 final size:30
Alignment explanation
Indices: 3075--3205 Score: 105
Period size: 29 Copynumber: 4.5 Consensus size: 30
3065 CCTGAACTTT
* * *
3075 CAAAAATCA-CATTTTTACCCTCAAAC-ATC
1 CAAAAATTACCATTTTTACTC-CGAACTATC
* *
3104 CAAAAATTACCATTTTTATTCCGAACTTTC
1 CAAAAATTACCATTTTTACTCCGAACTATC
*
3134 CAAAAATTACCA-TTTTACTCTCG-AGTATC
1 CAAAAATTACCATTTTTACTC-CGAACTATC
* *
3163 C-AAAATTACCATTTTTATCCCCGGAC-ATC
1 CAAAAATTACCATTTTTA-CTCCGAACTATC
*
3192 C-AAAATTACAATTT
1 CAAAAATTACCATTT
3206 GGCCTCAAAC
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
28 10 0.12
29 47 0.55
30 28 0.33
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.34
Consensus pattern (30 bp):
CAAAAATTACCATTTTTACTCCGAACTATC
Done.