Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010648.1 Kokia drynarioides strain JFW-HI SEQ_125591, 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, 652
Length: 1088
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.17
Warning! 114 characters in sequence are not A, C, G, or T
Found at i:104 original size:54 final size:54
Alignment explanation
Indices: 37--207 Score: 178
Period size: 54 Copynumber: 3.3 Consensus size: 54
27 TGATGGGATC
37 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACTAGCAA
1 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACTAGCAA
* * * ** * * * *
91 ATATTCCTGATGAGATACAGAGAA-ACGGATCGAAAC-AGTGAT-GGAA-T--C--
1 ATCTTCCTGATGAGACACTGAGAAGA-AAACCCAAACAAG-GCTCGAAACTAGCAA
*
139 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAA
1 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACTAGCAA
193 ATCTTCCTGATGAGA
1 ATCTTCCTGATGAGA
208 TACGAAGAAG
Statistics
Matches: 88, Mismatches: 19, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
48 29 0.33
49 6 0.07
50 1 0.01
52 2 0.02
53 6 0.07
54 44 0.50
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (54 bp):
ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACTAGCAA
Found at i:175 original size:48 final size:48
Alignment explanation
Indices: 21--175 Score: 134
Period size: 48 Copynumber: 3.1 Consensus size: 48
11 AAACGGATCG
*
21 AAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCC
1 AAACAGTGATGGAATCATCTTCCTGATGAGACACTGAGAAGAAAACCC
* * * * * ** * *
69 AAACAAG-GCTCGAAACTAGCAAATATTCCTGATGAGATACAGAGAA-ACGGATCG
1 AAAC-AGTGAT-GGAA-T--C--ATCTTCCTGATGAGACACTGAGAAGA-AAACCC
123 AAACAGTGATGGAATCATCTTCCTGATGAGACACTGAGAAGAAAACCC
1 AAACAGTGATGGAATCATCTTCCTGATGAGACACTGAGAAGAAAACCC
171 AAACA
1 AAACA
176 AGGCTCGAAA
Statistics
Matches: 78, Mismatches: 19, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
48 34 0.44
49 5 0.06
50 2 0.03
52 2 0.03
53 6 0.08
54 29 0.37
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.17
Consensus pattern (48 bp):
AAACAGTGATGGAATCATCTTCCTGATGAGACACTGAGAAGAAAACCC
Found at i:177 original size:102 final size:102
Alignment explanation
Indices: 1--210 Score: 393
Period size: 102 Copynumber: 2.1 Consensus size: 102
*
1 AGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAA
1 AGATACAGAGAAACGGATCGAAACAGTGATGGAATCATCTTCCTGATGAGACACTGAGAAGAAAA
*
66 CCCAAACAAGGCTCGAAACTAGCAAATATTCCTGATG
66 CCCAAACAAGGCTCGAAACGAGCAAATATTCCTGATG
103 AGATACAGAGAAACGGATCGAAACAGTGATGGAATCATCTTCCTGATGAGACACTGAGAAGAAAA
1 AGATACAGAGAAACGGATCGAAACAGTGATGGAATCATCTTCCTGATGAGACACTGAGAAGAAAA
*
168 CCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATG
66 CCCAAACAAGGCTCGAAACGAGCAAATATTCCTGATG
205 AGATAC
1 AGATAC
211 GAAGAAGTGN
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 105 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (102 bp):
AGATACAGAGAAACGGATCGAAACAGTGATGGAATCATCTTCCTGATGAGACACTGAGAAGAAAA
CCCAAACAAGGCTCGAAACGAGCAAATATTCCTGATG
Found at i:600 original size:139 final size:136
Alignment explanation
Indices: 348--723 Score: 458
Period size: 139 Copynumber: 2.7 Consensus size: 136
338 TCGAAGCAGT
348 GATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAA-ACGAGCAAA
1 GATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAGA-GAGCAAA
** * * * *
412 TCTTCCAGATTCGATACCGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACAGG
65 TCTTCCAGATGAGATA-TGAGAAGTGAACCAAATTCATCTTCCTAATGAGATACAGAAAAAC-GG
477 -TAGAAACA
128 ATAGAAACA
485 GCGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAGAGAGCAA
1 --GATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAGAGAGCAA
* *
550 ATCTTCCTGATGAGATATGGAGAAGTGAACCAGATTCATCTTCCTAATGAGATACAGAAAAACGG
64 ATCTTCCAGATGAGATAT-GAGAAGTGAACCAAATTCATCTTCCTAATGAGATACAGAAAAACGG
*
615 ATTGAAACA
128 ATAGAAACA
* * * * * * * *
624 G-T--GAGCATCTTCCCGATGAGACGCTGAGAAGGAGACCCAAATGAGGCTTGAAGCA-AGCAGA
1 GATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAG-AGAGCAAA
* *
685 TCTTCCAAGATGAGGTACTGAGAAGTGAAACAAATTCAT
65 TCTTCC-AGATGAGATA-TGAGAAGTGAACCAAATTCAT
724 AAGCGAATTG
Statistics
Matches: 210, Mismatches: 21, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
134 55 0.26
135 27 0.13
136 2 0.01
137 1 0.00
138 2 0.01
139 122 0.58
140 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (136 bp):
GATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAGAGAGCAAAT
CTTCCAGATGAGATATGAGAAGTGAACCAAATTCATCTTCCTAATGAGATACAGAAAAACGGATA
GAAACA
Done.