Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012405.1 Kokia drynarioides strain JFW-HI SEQ_127409, 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: 9209
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1811 original size:17 final size:18
Alignment explanation
Indices: 1788--1886 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 18
1778 CCAAACTCAT
1788 TTTAAATTTATTTTAATA
1 TTTAAATTTATTTTAATA
* *
1806 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAATA
1823 TTTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAATA
*
1840 TTTAAATTTAATTTAAT-
1 TTTAAATTTATTTTAATA
*
1857 CTTAAATTTATTTTCAA-A
1 TTTAAATTTATTTT-AATA
*
1875 TTTAAAATTATT
1 TTTAAATTTATT
1887 ATAAATATAA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
17 43 0.62
18 26 0.38
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAATA
Found at i:1827 original size:35 final size:33
Alignment explanation
Indices: 1788--1880 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 33
1778 CCAAACTCAT
**
1788 TTTAAATTTATTTT-AATATTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAT-TTAAATTTAATTT--AA
1823 TTTAAATTTATTTTAAATTTAAATTTAATTTAA
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAA
1856 TCTTAAATTTATTTTCAAATTTAAA
1 T-TTAAATTTATTTT-AAATTTAAA
1881 ATTATTATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
33 3 0.06
34 13 0.25
35 34 0.64
36 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (33 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAA
Found at i:1831 original size:6 final size:6
Alignment explanation
Indices: 1820--1880 Score: 58
Period size: 6 Copynumber: 10.5 Consensus size: 6
1810 ATTTGTTTTA
*
1820 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT -AATCTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAAT-TT AAATTT
*
1866 -ATTTT CAAATTT AAA
1 AAATTT -AAATTT AAA
1881 ATTATTATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
5 16 0.35
6 23 0.50
7 7 0.15
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:1855 original size:52 final size:52
Alignment explanation
Indices: 1788--1897 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
1778 CCAAACTCAT
* * * *
1788 TTTAAATTTATTTTAATATTAAATTTGTTTTAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAATATTAAATTTATTTTAAAATTTAAAATTATTATAAA
* *
1840 TTTAAATTTAATTTAATCTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAATATTAAATTTATTTTAAAATTTAAAATTATTATAAA
*
1892 TATAAA
1 TTTAAA
1898 ATAAATAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.54
Consensus pattern (52 bp):
TTTAAATTTAATTTAATATTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:7049 original size:95 final size:96
Alignment explanation
Indices: 6871--7050 Score: 231
Period size: 95 Copynumber: 1.9 Consensus size: 96
6861 GAAAAGGATG
* ** *
6871 TTCGATTATCCCGATTTGATGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCGA
1 TTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAAAATCGA
*
6936 AGATAAGGAAACATTGCCTCAATTAAGGGTA
66 AGATAAAGAAACATTGCCTCAATTAAGGGTA
** **
6967 TTCGATTATTTCGATTTGAAGAAAAATTACACCTAG-AAGTTAAGGCGTAAATTTTCAAAACTCG
1 TTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAAAA-TCG
*
7031 AA-ATAAA-AGAATATTGCCTC
65 AAGATAAAGA-AACATTGCCTC
7051 GATTTTAAAG
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
94 1 0.01
95 36 0.50
96 35 0.49
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (96 bp):
TTCGATTATCCCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAAAATCGA
AGATAAAGAAACATTGCCTCAATTAAGGGTA
Found at i:7382 original size:29 final size:29
Alignment explanation
Indices: 7313--7629 Score: 316
Period size: 29 Copynumber: 10.8 Consensus size: 29
7303 ATTCTTGGGT
* * **
7313 TAAAAATGGTAATTTTGGGAAAATTTGAGGTA
1 TAAAAATGG-AATTTTTGG-AAGTTTG-GGGG
* ** *
7345 TAAAAATGGAATTTTTAGCTGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTGGGGG
*
7374 TAAAAATGGGATTTTTGGAAGTTTGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTGGGGG
*
7403 TAAAAATAGAATTTTTGGAAGTTTGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTGGGGG
**
7432 TAAAAATGGAA-TTTTGGAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTGGGGG
* * * *
7460 TCAAAAGTGGGATTTTTGGAAGTTTGAGTG
1 T-AAAAATGGAATTTTTGGAAGTTTGGGGG
* ** *
7490 T-AAAATGGAATTGTTGGAAGTTACGAGG
1 TAAAAATGGAATTTTTGGAAGTTTGGGGG
* *
7518 TCAAAAGTGGGATTTTTGGAAGTTTGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTGGGGG
* *
7548 T-AAAATGGAATTTTTGGAAGTTTTTGGGT
1 TAAAAATGGAATTTTTGGAAG-TTTGGGGG
* * *
7577 TAAAAGTGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTGGGGG
7606 TAAAAATGGAATTTTTGGAAGTTT
1 TAAAAATGGAATTTTTGGAAGTTT
7630 TAGGGTCAAA
Statistics
Matches: 231, Mismatches: 48, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
28 53 0.23
29 104 0.45
30 58 0.25
31 7 0.03
32 9 0.04
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTGGGGG
Found at i:7418 original size:58 final size:58
Alignment explanation
Indices: 7369--7662 Score: 371
Period size: 58 Copynumber: 5.1 Consensus size: 58
7359 TTAGCTGTTC
* * * * *
7369 GGGGGTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGGAAGTTT
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAGTGGGATTTTTGGAAGTTT
*
7427 GGGGGTAAAAATGGAA-TTTTGGAAGTTTTAGGGTCAAAAGTGGGATTTTTGGAAGTTT
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGT-AAAAGTGGGATTTTTGGAAGTTT
* * * ** *
7485 GAGTGT-AAAATGGAATTGTTGGAAGTTACGAGGTCAAAAGTGGGATTTTTGGAAGTTT
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGT-AAAAGTGGGATTTTTGGAAGTTT
* *
7543 GGGGGT-AAAATGGAATTTTTGGAAGTTTTTGGGTTAAAAGTGGGATTTTTGGAAGTTC
1 GGGGGTAAAAATGGAATTTTTGGAAG-TTTTGGGGTAAAAGTGGGATTTTTGGAAGTTT
* * *
7601 GGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAGTGAGA-TTTTGGAAGTTC
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGT-AAAAGTGGGATTTTTGGAAGTTT
7659 GGGG
1 GGGG
7663 TCAAAAGGAA
Statistics
Matches: 207, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
57 25 0.12
58 149 0.72
59 33 0.16
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.34
Consensus pattern (58 bp):
GGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAGTGGGATTTTTGGAAGTTT
Found at i:8694 original size:27 final size:27
Alignment explanation
Indices: 8664--8715 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
8654 AAAAAAACTG
* *
8664 TTTATTATTATTAATGTCATTAATATA
1 TTTATTATTATAAATATCATTAATATA
*
8691 TTTATTATTATAAATATTATTAATA
1 TTTATTATTATAAATATCATTAATA
8716 GCACATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTATTATTATAAATATCATTAATATA
Done.