Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003530.1 Kokia drynarioides strain JFW-HI SEQ_116374, 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: 12403
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:1128 original size:4 final size:4
Alignment explanation
Indices: 1119--1153 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1109 AAATAAACGG
*
1119 GAAA GAAA GAAA GAAA GAAA G-AA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1154 TGTAATGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:4165 original size:7 final size:7
Alignment explanation
Indices: 4155--4236 Score: 87
Period size: 7 Copynumber: 11.7 Consensus size: 7
4145 ATGTATAGGA
4155 TTTAAGG
1 TTTAAGG
4162 TTTAAGG
1 TTTAAGG
4169 TTTCAA-G
1 TTT-AAGG
* *
4176 TCTAGGG
1 TTTAAGG
*
4183 TTTACGG
1 TTTAAGG
4190 TTTAAGG
1 TTTAAGG
*
4197 TTTCAA-A
1 TTT-AAGG
4204 TTTAAGG
1 TTTAAGG
4211 TTTAAGG
1 TTTAAGG
*
4218 TTTAAGT
1 TTTAAGG
4225 TTTAAGG
1 TTTAAGG
4232 TTTAA
1 TTTAA
4237 TGTTATGAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
6 3 0.05
7 55 0.89
8 4 0.06
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (7 bp):
TTTAAGG
Found at i:4181 original size:28 final size:27
Alignment explanation
Indices: 4140--4223 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 27
4130 TTTTTAAAAT
*
4140 GTTTCATGTATAGGATTTAAGGTTTAAG
1 GTTTCAAGTATAGG-TTTAAGGTTTAAG
* *
4168 GTTTCAAGTCTAGGGTTTACGGTTTAAG
1 GTTTCAAGTATA-GGTTTAAGGTTTAAG
* *
4196 GTTTCAAATTTAAGGTTTAAGGTTTAAG
1 GTTTCAAGTAT-AGGTTTAAGGTTTAAG
4224 TTTTAAGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 45 0.94
29 3 0.06
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (27 bp):
GTTTCAAGTATAGGTTTAAGGTTTAAG
Found at i:4235 original size:28 final size:28
Alignment explanation
Indices: 4155--4236 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
4145 ATGTATAGGA
* *
4155 TTTAAGGTTTAAGGTTTCAAGTCTAGGG
1 TTTAAGGTTTAAGGTTTCAAGTTTAAGG
* *
4183 TTTACGGTTTAAGGTTTCAAATTTAAGG
1 TTTAAGGTTTAAGGTTTCAAGTTTAAGG
*
4211 TTTAAGGTTTAA-GTTTTAAGGTTTAA
1 TTTAAGGTTTAAGGTTTCAA-GTTTAA
4237 TGTTATGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 6 0.13
28 40 0.87
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (28 bp):
TTTAAGGTTTAAGGTTTCAAGTTTAAGG
Found at i:8404 original size:112 final size:112
Alignment explanation
Indices: 8219--8422 Score: 293
Period size: 112 Copynumber: 1.8 Consensus size: 112
8209 GAGGGAAAAA
* * * ***
8219 GAGATTTCTGACCTGAGTTAAAACTTCTTTACCTTACTACCTTCGGGTTCTTAGTTCGGCAATGG
1 GAGATTCCTGACCTGAGTTAAAACTTCCTTACCTTACTACCTTCGGGATCTTAGTTCGGCAACAA
* * *
8284 TGGCGTGCAAAAATAATCTATACTAATAATAAAACGAGACGGAAAGG
66 TGGAGTGCAAAAATAAACCATACTAATAATAAAACGAGACGGAAAGG
* *
8331 GAGATTCCTGACCTGAGTTAAAACTTCCTT-CCTTTACTACCTTTGGGATCTTAGTTTGGCAACA
1 GAGATTCCTGACCTGAGTTAAAACTTCCTTACC-TTACTACCTTCGGGATCTTAGTTCGGCAACA
8395 ATGGAGTGCAAAAATAAACCATACTAAT
65 ATGGAGTGCAAAAATAAACCATACTAAT
8423 TGTTAGAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 2 0.03
112 78 0.98
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (112 bp):
GAGATTCCTGACCTGAGTTAAAACTTCCTTACCTTACTACCTTCGGGATCTTAGTTCGGCAACAA
TGGAGTGCAAAAATAAACCATACTAATAATAAAACGAGACGGAAAGG
Found at i:9039 original size:125 final size:125
Alignment explanation
Indices: 8775--9040 Score: 365
Period size: 126 Copynumber: 2.1 Consensus size: 125
8765 ATTTTATCAC
* * * *
8775 TAATATCTTAAAAAACGAAAATAAAATGAGAGGGAAAGAGAGATTCCTAACTTGAAGTAAAACTT
1 TAATATC-CAAAAAACGAAAATAAAATGAAAAGGAAAGAGAGATTCCCAACTTGAAGTAAAACTT
* * * *
8840 CCTTCCTTCCTACCTTCGGGCTCTTAGTTTGGAAACATTAGACTGCAAAAATAAACTATAT
65 CCTTCCTTACTACCTTCGAGCTCTTAGTTCGAAAACATTAGACTGCAAAAATAAACTATAT
* *
8901 TAATATCCAAAAAACGAAAATAAAATGAAAAGGAAAGGGAGATTCCCGACTTG-AGTTAAAACTT
1 TAATATCCAAAAAACGAAAATAAAATGAAAAGGAAAGAGAGATTCCCAACTTGAAG-TAAAACTT
* *
8965 CCTTCCCTTACTA-CTGTCGAGTTCTTAGTTCGAAAACATTAGAGTGCAAAAATAAACTATAT
65 CCTT-CCTTACTACCT-TCGAGCTCTTAGTTCGAAAACATTAGACTGCAAAAATAAACTATAT
*
9027 TAATATCGAAAAAA
1 TAATATCCAAAAAA
9041 ATAAGAGGGA
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
124 2 0.02
125 54 0.44
126 68 0.55
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (125 bp):
TAATATCCAAAAAACGAAAATAAAATGAAAAGGAAAGAGAGATTCCCAACTTGAAGTAAAACTTC
CTTCCTTACTACCTTCGAGCTCTTAGTTCGAAAACATTAGACTGCAAAAATAAACTATAT
Done.