Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001111.1 Kokia drynarioides strain JFW-HI SEQ_112392, 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: 16341
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Found at i:4896 original size:97 final size:98
Alignment explanation
Indices: 4702--4896 Score: 218
Period size: 97 Copynumber: 2.0 Consensus size: 98
4692 AACTATGGAA
* * * **
4702 AAGGATATTTGATTATCTTGATTTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCGTAAATTTTC
1 AAGGATATTCGATTATCTTGATTTTGAAGAAAAATAGCACCTAGTAAGTTAAGGCACAAATTTTC
* * * *
4767 AGAATCAGAGATAAAGAAACATTGTCTTGATTT
66 AAAATCAAAGATAAAGAAACATTGCCTCGATTT
* * *
4800 AAGGGTATTCGATTAT-TTCGA-TTTGAGGAAAAATAGCACCTAGTAAGTTAAGGTACAAATTTT
1 AAGGATATTCGATTATCTT-GATTTTGAAGAAAAATAGCACCTAGTAAGTTAAGGCACAAATTTT
*
4863 CAAAACTCAAAAGA-AAAG-AATATTGCCTCGATTT
65 CAAAA-TC-AAAGATAAAGAAACATTGCCTCGATTT
4897 TAAAGTTTTC
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
97 55 0.68
98 22 0.27
99 4 0.05
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (98 bp):
AAGGATATTCGATTATCTTGATTTTGAAGAAAAATAGCACCTAGTAAGTTAAGGCACAAATTTTC
AAAATCAAAGATAAAGAAACATTGCCTCGATTT
Found at i:5236 original size:29 final size:29
Alignment explanation
Indices: 5136--5296 Score: 104
Period size: 30 Copynumber: 5.4 Consensus size: 29
5126 ATTCGGGGGT
* *
5136 AAAATGGTAATTTTTTA-AAATT-GAGGTAA
1 AAAATGG-AATTTTTGAGAAATTAG-GGTTA
* *
5165 AAAATGAAATTTTTG-GAAGTTTAAGGGTT-
1 AAAATGGAATTTTTGAGAA-ATT-AGGGTTA
5194 -AAATGGTAATTTTTTGAGAAATTAGGGTTA
1 AAAATGG-AA-TTTTTGAGAAATTAGGGTTA
*
5224 AAAATGGAA-TTTTG-GAAAGTTCGAGGGGTA
1 AAAATGGAATTTTTGAGAAA-TT--AGGGTTA
*
5254 AAAATGTAATTTTTGGAGAAATT-GGTGTTA
1 AAAATGGAATTTTT-GAGAAATTAGG-GTTA
*
5284 AAAATGGTATTTT
1 AAAATGGAATTTT
5297 GGAAAGTTTG
Statistics
Matches: 105, Mismatches: 11, Indels: 31
0.71 0.07 0.21
Matches are distributed among these distances:
27 4 0.04
28 21 0.20
29 18 0.17
30 41 0.39
31 14 0.13
32 3 0.03
33 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGAGAAATTAGGGTTA
Found at i:5307 original size:29 final size:30
Alignment explanation
Indices: 5222--5421 Score: 123
Period size: 29 Copynumber: 6.8 Consensus size: 30
5212 AAATTAGGGT
*
5222 TAAAAATGG-AATTTTGGAAAGTTCGAGGGG
1 TAAAAATGGTAATTTTGGAAAGTTTG-GGGG
* * *
5252 TAAAAAT-GTAATTTTTGGAGAA-ATTGGTGT
1 TAAAAATGGTAA-TTTTGGA-AAGTTTGGGGG
5282 TAAAAATGGT-ATTTTGGAAAGTTTGGGGG
1 TAAAAATGGTAATTTTGGAAAGTTTGGGGG
* ** * *
5311 T-AAAATGGTAATTTTAAGAAA-AATCGAGG
1 TAAAAATGGTAATTTT-GGAAAGTTTGGGGG
* * *
5340 TCAAAAATGG-AATTTTGAAAAGTTCGGCGG
1 T-AAAAATGGTAATTTTGGAAAGTTTGGGGG
* * *
5370 TAAAAAT-GTAATTTCT-AAAAATTTAGGGG
1 TAAAAATGGTAATTT-TGGAAAGTTTGGGGG
**
5399 TCGAAATGG-AATTTTGGAAAGTT
1 TAAAAATGGTAATTTTGGAAAGTT
5422 CAGAGGTTAA
Statistics
Matches: 129, Mismatches: 27, Indels: 29
0.70 0.15 0.16
Matches are distributed among these distances:
28 12 0.09
29 62 0.48
30 35 0.27
31 18 0.14
32 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.32
Consensus pattern (30 bp):
TAAAAATGGTAATTTTGGAAAGTTTGGGGG
Found at i:5372 original size:59 final size:59
Alignment explanation
Indices: 5071--5422 Score: 249
Period size: 59 Copynumber: 6.0 Consensus size: 59
5061 TTAGACACTT
* * ** ** * * *
5071 GGGGGCAAAACGGTAATTTTGGGAAAGTTTGAGGTCAAAAATAGAATTTTTAGATA-TTC
1 GGGGGTAAAATGGTAATTTTAAGAAAAATTGAGGTCAAAAATGGAA-TTTTGGAAAGTTC
** * * *
5130 GGGGGTAAAATGGTAATTTT--TTAAAATTGAGGTAAAAAATGAAATTTTTGG-AAGTTT
1 GGGGGTAAAATGGTAATTTTAAGAAAAATTGAGGTCAAAAATGGAA-TTTTGGAAAGTTC
** * ** * *
5187 AAGGGTTAAATGGTAATTTTTTGAGAAATT-AGGGTTAAAAATGGAATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTAAGAAAAATTGA-GGTCAAAAATGGAATTTTGGAAAGTTC
** * * * *
5246 GAGGGGTAAAAAT-GTAATTTTTGGAGAAATTG-GTGTTAAAAATGGTATTTTGGAAAGTTT
1 G-GGGGT-AAAATGGTAATTTTAAGAAAAATTGAG-GTCAAAAATGGAATTTTGGAAAGTTC
* *
5306 GGGGGTAAAATGGTAATTTTAAGAAAAATCGAGGTCAAAAATGGAATTTTGAAAAGTTC
1 GGGGGTAAAATGGTAATTTTAAGAAAAATTGAGGTCAAAAATGGAATTTTGGAAAGTTC
* * * *
5365 GGCGGTAAAAAT-GTAATTTCT-A-AAAATTTAGGGGTC-GAAATGGAATTTTGGAAAGTTC
1 GGGGGT-AAAATGGTAATTT-TAAGAAAAATT-GAGGTCAAAAATGGAATTTTGGAAAGTTC
5423 AGAGGTTAAA
Statistics
Matches: 238, Mismatches: 41, Indels: 29
0.77 0.13 0.09
Matches are distributed among these distances:
56 1 0.00
57 42 0.18
58 37 0.16
59 101 0.42
60 53 0.22
61 4 0.02
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTAAGAAAAATTGAGGTCAAAAATGGAATTTTGGAAAGTTC
Found at i:7330 original size:10 final size:11
Alignment explanation
Indices: 7315--7343 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
7305 AGCAAATTTA
7315 AATTTAAACC-
1 AATTTAAACCT
7325 AATTTAAACCT
1 AATTTAAACCT
7336 AATTTAAA
1 AATTTAAA
7344 ACCGAAGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTTAAACCT
Found at i:7332 original size:16 final size:16
Alignment explanation
Indices: 7276--7328 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
7266 GTTTTAAATC
**
7276 AATTCAAATTTAATTA
1 AATTCAAATTTAAACA
7292 AATTCAAATTTAAAGCA
1 AATTCAAATTTAAA-CA
* *
7309 AATTTAAATTTAAACC
1 AATTCAAATTTAAACA
7325 AATT
1 AATT
7329 TAAACCTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTCAAATTTAAACA
Found at i:7831 original size:49 final size:49
Alignment explanation
Indices: 7735--8153 Score: 398
Period size: 49 Copynumber: 8.6 Consensus size: 49
7725 TAGATTTGCT
* * * * * *
7735 GTTGCCGCTTCAATCTTTCCCCTCGTAT-TTTCGTGGTATTGGATTCGCC
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTTT-GTGGTACTGGATTCGCC
* * ** * *
7784 ATTGCGGATTAAATCTTTCCCTTCATGTCTCCGAGGTACTGGGTTCGCC
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGATTCGCC
* * * * * *
7833 ATTGCGACTTAAACCTTTCCCTTCGTGTCTTTGTGGTA-TTGAATCTGCC
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGATTC-GCC
* * * ***
7882 GTTGTGGCTTAGATC-TTCCCTTCATGTCTTCGTGGTACTGGATTTTTC
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGATTCGCC
**
7930 GTTGCGGCTTAAATC-TTCCCTTTGTGTCTTTGTGGTACTGGATTCGCC
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGATTCGCC
* * * * * *
7978 ATTGCGGCCTAAATCTTTCCCTTTACGTCTCTGTGGTACCGGATTCGCC
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGATTCGCC
* * * *
8027 GTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACAAGG-TTCGTC
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTT-TGTGGTAC-TGGATTCGCC
* * * * *
8077 GTTGCGACTTAAACCTTTCCCTCCATGTCTTCGTGGTACTGGATTCACC
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGATTCGCC
8126 GTTGCGGCTTAAATCTTTCCCTTCATGT
1 GTTGCGGCTTAAATCTTTCCCTTCATGT
8154 TTCGCGGTAC
Statistics
Matches: 294, Mismatches: 69, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
48 80 0.27
49 172 0.59
50 40 0.14
51 2 0.01
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.39
Consensus pattern (49 bp):
GTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGATTCGCC
Found at i:7921 original size:97 final size:98
Alignment explanation
Indices: 7735--8149 Score: 412
Period size: 97 Copynumber: 4.2 Consensus size: 98
7725 TAGATTTGCT
* * * * * * *
7735 GTTGCCGCTTCAATCTTTCCCCTCGTAT-TTTCGTGGTATTGGAT-TCGCCATTGCGGATTAAAT
1 GTTGCGGCTTAAATCTTTCCCTTCGTGTCTTT-GTGGTAATGGATCT-GCCGTTGCGGCTTAAAT
* * *
7798 CTTTCCCTTCATGTCTCCGAGGTACTGGGTTCGCC
64 CTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCC
* * * * * * *
7833 ATTGCGACTTAAACCTTTCCCTTCGTGTCTTTGTGGTATTGAATCTGCCGTTGTGGCTTAGATC-
1 GTTGCGGCTTAAATCTTTCCCTTCGTGTCTTTGTGGTAATGGATCTGCCGTTGCGGCTTAAATCT
***
7897 TTCCCTTCATGTCTTCGTGGTACTGGATTTTTC
66 TTCCCTTCATGTCTTCGTGGTACTGGATTCGCC
* * * *
7930 GTTGCGGCTTAAATC-TTCCCTTTGTGTCTTTGTGGTACTGGAT-TCGCCATTGCGGCCTAAATC
1 GTTGCGGCTTAAATCTTTCCCTTCGTGTCTTTGTGGTAATGGATCT-GCCGTTGCGGCTTAAATC
* * *
7993 TTTCCCTTTACGTC-TCTGTGGTACCGGATTCGCC
65 TTTCCCTTCATGTCTTC-GTGGTACTGGATTCGCC
* * * * * *
8027 GTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACAAGGTTC-GTCGTTGCGACTTAAAC
1 GTTGCGGCTTAAATCTTTCCCTTCGTGTCTT-TGTGGTA-ATGGATCTGCCGTTGCGGCTTAAAT
* *
8091 CTTTCCCTCCATGTCTTCGTGGTACTGGATTCACC
64 CTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCC
8126 GTTGCGGCTTAAATCTTTCCCTTC
1 GTTGCGGCTTAAATCTTTCCCTTC
8150 ATGTTTCGCG
Statistics
Matches: 258, Mismatches: 49, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
95 1 0.00
96 41 0.16
97 78 0.30
98 60 0.23
99 73 0.28
100 5 0.02
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.39
Consensus pattern (98 bp):
GTTGCGGCTTAAATCTTTCCCTTCGTGTCTTTGTGGTAATGGATCTGCCGTTGCGGCTTAAATCT
TTCCCTTCATGTCTTCGTGGTACTGGATTCGCC
Done.