Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011160.1 Kokia drynarioides strain JFW-HI SEQ_126134, 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: 19463
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Found at i:2135 original size:3 final size:3
Alignment explanation
Indices: 2129--2156 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2119 TATTATTATT
2129 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
2157 AGGATAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:3523 original size:58 final size:58
Alignment explanation
Indices: 3383--3745 Score: 374
Period size: 59 Copynumber: 6.2 Consensus size: 58
3373 AATGGTAATC
** * * ** *
3383 TTTGGAAAATTCGAGGTTAAAAAT-GGATTTTTTGGAAGTTTCGAGATTAAAAAT-GGAAT
1 TTTGGAAGTTTCGAGG-TCAAAATGGGA-TTTTTAGAAG-TTCGAGGGTAAAAATGGGATT
* * *
3442 TTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAGTGGGATT
1 TTTGGAAGTTTCGAGGTC-AAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATT
* * *
3501 TTTGGAAGTTTCGAGGTCAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGGATT
1 TTTGGAAGTTTCGAGGTCAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATT
* * * * *
3559 TTTGAAAGTTTTGGGGTCAAAGTGGGATTTTTAGAAGTTC-AGGGGTAAAAACGGGATT
1 TTTGGAAGTTTCGAGGTCAAAATGGGATTTTTAGAAGTTCGA-GGGTAAAAATGGGATT
* * * *
3617 TTTAGAAGTTTCAAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATT
1 TTTGGAAGTTTCGAGGTC-AAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATT
* * * * *
3676 TTTGGAAGTTTTGGGGTTAAAAATGAGATTTTTAGAAGTT-TAGGGTTAAAAATGGGATT
1 TTTGGAAGTTTCGAGG-TCAAAATGGGATTTTTAGAAGTTCGAGGG-TAAAAATGGGATT
*
3735 TTTTGAAGTTT
1 TTTGGAAGTTT
3746 AGGGACCCTC
Statistics
Matches: 253, Mismatches: 43, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
58 113 0.45
59 137 0.54
60 3 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (58 bp):
TTTGGAAGTTTCGAGGTCAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATT
Found at i:3746 original size:29 final size:29
Alignment explanation
Indices: 3397--3749 Score: 309
Period size: 29 Copynumber: 12.1 Consensus size: 29
3387 GAAAATTCGA
*
3397 GGTTAAAAAT-GGATTTTTTGGAAGTTTCG
1 GGTTAAAAATGGGA-TTTTTGGAAGTTTAG
* * *
3426 AGATTAAAAAT-GGAATTTTGGAAGTTTCGG
1 -GGTTAAAAATGGGATTTTTGGAAGTTT-AG
* * * *
3456 GGTCAAAAATGAGATTTTTAGAAGTTCGAG
1 GGTTAAAAATGGGATTTTTGGAAGTT-TAG
* *
3486 GG-TAAAAGTGGGATTTTTGGAAGTTTCG
1 GGTTAAAAATGGGATTTTTGGAAGTTTAG
* **
3514 AGG-TCAAAATGGGATTTTTGGAAGTTCGG
1 -GGTTAAAAATGGGATTTTTGGAAGTTTAG
* * * *
3543 GGGTAAAAATAGGATTTTTGAAAGTTTTG
1 GGTTAAAAATGGGATTTTTGGAAGTTTAG
* * * * *
3572 GGGTCAAAGTGGGATTTTTAGAAGTTCAG
1 GGTTAAAAATGGGATTTTTGGAAGTTTAG
* * * *
3601 GGGTAAAAACGGGATTTTTAGAAGTTTCAA
1 GGTTAAAAATGGGATTTTTGGAAGTTT-AG
* **
3631 GGTCAAAAATGGGATTTTTGGAAGTTCGG
1 GGTTAAAAATGGGATTTTTGGAAGTTTAG
* *
3660 GGGTAAAAATGGGATTTTTGGAAGTTTTGG
1 GGTTAAAAATGGGATTTTTGGAAG-TTTAG
* *
3690 GGTTAAAAATGAGATTTTTAGAAGTTTAG
1 GGTTAAAAATGGGATTTTTGGAAGTTTAG
*
3719 GGTTAAAAATGGGATTTTTTGAAGTTTAG
1 GGTTAAAAATGGGATTTTTGGAAGTTTAG
3748 GG
1 GG
3750 ACCCTCGGGG
Statistics
Matches: 263, Mismatches: 53, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.01
29 184 0.70
30 76 0.29
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (29 bp):
GGTTAAAAATGGGATTTTTGGAAGTTTAG
Found at i:4858 original size:3 final size:3
Alignment explanation
Indices: 4852--4912 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
4842 ATTATTAAAA
* * *
4852 ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
* *
4898 A-T ATA AAT ATT ATT A
1 ATT ATT ATT ATT ATT A
4913 ATAATATAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:4888 original size:27 final size:24
Alignment explanation
Indices: 4841--4914 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
4831 TCATTAATGC
* *
4841 TATTATTA-AAAATTATTATTAGT
1 TATTATTATATAATTATTATTAAT
*
4864 GTCATTATTATTATTATTATTATTAAT
1 -T-ATTATTA-TATAATTATTATTAAT
*
4891 TATTATTATATAAATATTATTAAT
1 TATTATTATATAATTATTATTAAT
4915 AATATAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
24 15 0.36
25 14 0.33
26 1 0.02
27 12 0.29
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (24 bp):
TATTATTATATAATTATTATTAAT
Found at i:4930 original size:24 final size:24
Alignment explanation
Indices: 4881--4933 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4871 TTATTATTAT
* *
4881 TATTATTAATTATTATTATATAAA
1 TATTATTAATAATTAATATATAAA
*
4905 TATTATTAATAATATAATA-ATCAA
1 TATTATTAATAAT-TAATATATAAA
4929 TATTA
1 TATTA
4934 ACTTTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTATTAATAATTAATATATAAA
Found at i:7202 original size:45 final size:45
Alignment explanation
Indices: 7116--7202 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
7106 TTGGTTCCAG
** *
7116 GACGCCCTTTGCGAGTTTTCATCCTGAACCCTTTTTTTTTTTTGA
1 GACGCCCTTTGCGAGTTTTCATCCTGAACCCCCTTTGTTTTTTGA
* * *
7161 GACGCCCTTTGTGGGTTTTCAT-CTTAATCCCCCTTTGTTTTT
1 GACGCCCTTTGCGAGTTTTCATCCTGAA-CCCCCTTTGTTTTT
7203 AGGCGAAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 4 0.11
45 31 0.89
ACGTcount: A:0.11, C:0.25, G:0.16, T:0.47
Consensus pattern (45 bp):
GACGCCCTTTGCGAGTTTTCATCCTGAACCCCCTTTGTTTTTTGA
Found at i:18095 original size:31 final size:30
Alignment explanation
Indices: 18060--18333 Score: 93
Period size: 30 Copynumber: 9.3 Consensus size: 30
18050 GAAACGGTAA
* *
18060 TTTTGGAAAAATTTGGGGTTAAAAAAGGATT
1 TTTTGG-AAAATTTGGGGTCAAAAAAGGAAT
** *
18091 TTTTGGAAGTTTTGGGGTCAAAAATGGAAT
1 TTTTGGAAAATTTGGGGTCAAAAAAGGAAT
** * * *
18121 TTTT-GAAGTTTTAGGGTC-AAAATGGGAT
1 TTTTGGAAAATTTGGGGTCAAAAAAGGAAT
* * *
18149 TTTTTG-AAGTTTAGGGGT--AAAAATGAGAT
1 TTTTGGAAAATTT-GGGGTCAAAAAAGGA-AT
* * * *
18178 TTTTGG-AAGTTTCGGGGTTAAAAATGGGAT
1 TTTTGGAAAATTT-GGGGTCAAAAAAGGAAT
* * ** *
18208 TTTTGG-AAGTTCGAGGGT-AAAATTGGGAT
1 TTTTGGAAAATTTG-GGGTCAAAAAAGGAAT
** * *
18237 TTTTGGAAGTTTTGGGGTCAAAAATGGGAT
1 TTTTGGAAAATTTGGGGTCAAAAAAGGAAT
* * *
18267 TTTTTG-AAGTTTAGGGGT--AAAAATGAGAT
1 TTTTGGAAAATTT-GGGGTCAAAAAAGGA-AT
* ** * * *
18296 TTTTTGAAGTTTTGGGGTTAAAAATGGGAT
1 TTTTGGAAAATTTGGGGTCAAAAAAGGAAT
18326 TTTTGGAA
1 TTTTGGAA
18334 GTTTAGGGAC
Statistics
Matches: 194, Mismatches: 36, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
28 27 0.14
29 74 0.38
30 77 0.40
31 16 0.08
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.38
Consensus pattern (30 bp):
TTTTGGAAAATTTGGGGTCAAAAAAGGAAT
Found at i:18113 original size:29 final size:28
Alignment explanation
Indices: 18071--18337 Score: 286
Period size: 29 Copynumber: 9.1 Consensus size: 28
18061 TTTGGAAAAA
*
18071 TTTGGGGTTAAAAAAGGATTTTTTGGAAGT
1 TTTGGGG-TAAAAATGGA-TTTTTGGAAGT
18101 TTTGGGGTCAAAAATGGAATTTTT-GAAGT
1 TTTGGGGT-AAAAATGG-ATTTTTGGAAGT
* * *
18130 TTTAGGGTCAAAATGGGATTTTTTGAAGT
1 TTTGGGGTAAAAAT-GGATTTTTGGAAGT
*
18159 TTAGGGGTAAAAATGAGATTTTTGGAAGT
1 TTTGGGGTAAAAATG-GATTTTTGGAAGT
*
18188 TTCGGGGTTAAAAATGGGATTTTTGGAAG-
1 TTTGGGG-TAAAAAT-GGATTTTTGGAAGT
* *
18217 TTCGAGGGTAAAATTGGGATTTTTGGAAGT
1 TTTG-GGGTAAAAAT-GGATTTTTGGAAGT
*
18247 TTTGGGGTCAAAAATGGGATTTTTTGAAGT
1 TTTGGGGT-AAAAAT-GGATTTTTGGAAGT
* *
18277 TTAGGGGTAAAAATGAGATTTTTTGAAGT
1 TTTGGGGTAAAAATG-GATTTTTGGAAGT
18306 TTTGGGGTTAAAAATGGGATTTTTGGAAGT
1 TTTGGGG-TAAAAAT-GGATTTTTGGAAGT
18336 TT
1 TT
18338 AGGGACCCTC
Statistics
Matches: 209, Mismatches: 15, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.06
29 102 0.49
30 91 0.44
31 3 0.01
ACGTcount: A:0.29, C:0.02, G:0.30, T:0.39
Consensus pattern (28 bp):
TTTGGGGTAAAAATGGATTTTTGGAAGT
Found at i:18149 original size:59 final size:60
Alignment explanation
Indices: 18071--18341 Score: 346
Period size: 59 Copynumber: 4.6 Consensus size: 60
18061 TTTGGAAAAA
* *
18071 TTTGGGGTTAAAAA-AGGATTTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTT-GAAGT
1 TTTGGGGTTAAAAATGGGATTTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTGGAAGT
* *
18130 TTTAGGG-TCAAAATGGGATTTTTT-GAAGTTTAGGGGTAAAAAT-GAGATTTTTGGAAGT
1 TTTGGGGTTAAAAATGGGATTTTTTGGAAGTTTAGGGGTAAAAATGGA-ATTTTTGGAAGT
* * * *
18188 TTCGGGGTTAAAAATGGGA-TTTTTGGAAG-TTCGAGGGTAAAATTGGGATTTTTGGAAGT
1 TTTGGGGTTAAAAATGGGATTTTTTGGAAGTTTAG-GGGTAAAAATGGAATTTTTGGAAGT
* *
18247 TTTGGGGTCAAAAATGGGATTTTTT-GAAGTTTAGGGGTAAAAAT-GAGATTTTTTGAAGT
1 TTTGGGGTTAAAAATGGGATTTTTTGGAAGTTTAGGGGTAAAAATGGA-ATTTTTGGAAGT
18306 TTTGGGGTTAAAAATGGGA-TTTTTGGAAGTTTAGGG
1 TTTGGGGTTAAAAATGGGATTTTTTGGAAGTTTAGGG
18342 ACCCTCGGGG
Statistics
Matches: 184, Mismatches: 17, Indels: 22
0.83 0.08 0.10
Matches are distributed among these distances:
56 2 0.01
57 12 0.07
58 41 0.22
59 120 0.65
60 9 0.05
ACGTcount: A:0.29, C:0.02, G:0.31, T:0.38
Consensus pattern (60 bp):
TTTGGGGTTAAAAATGGGATTTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGT
Done.