Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004149.1 Kokia drynarioides strain JFW-HI SEQ_117353, 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: 50202
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:14437 original size:55 final size:55
Alignment explanation
Indices: 14353--14481 Score: 172
Period size: 55 Copynumber: 2.3 Consensus size: 55
14343 ATTAGACGTG
* * * *
14353 TTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCA-A-CATAATAATCGA
1 TTTAAACATATAAACAATTGATTCAAAAGAAACAATA-T-CATACCATAACAATCGA
*
14408 TTTAAACATATAAACAATTGATTCAAAAGAAACAATATCATACCATAACAATTGA
1 TTTAAACATATAAACAATTGATTCAAAAGAAACAATATCATACCATAACAATCGA
*
14463 TTTAAACATATAAATAATT
1 TTTAAACATATAAACAATT
14482 TTTTGGGAGG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
53 2 0.03
54 2 0.03
55 62 0.94
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (55 bp):
TTTAAACATATAAACAATTGATTCAAAAGAAACAATATCATACCATAACAATCGA
Found at i:19841 original size:14 final size:15
Alignment explanation
Indices: 19817--19848 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
19807 ATATTATGTT
19817 AAAGAAAAAAGAAAG
1 AAAGAAAAAAGAAAG
19832 AAAG-AAAAAGAAAG
1 AAAGAAAAAAGAAAG
19846 AAA
1 AAA
19849 CCCTACTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAG
Found at i:21125 original size:54 final size:54
Alignment explanation
Indices: 21067--21175 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
21057 CTTTCATAAT
21067 TTTTTTCAATTTTTGCTCTTCCATTTAAATAAAAATTGTGTATTTTATGTTTTC
1 TTTTTTCAATTTTTGCTCTTCCATTTAAATAAAAATTGTGTATTTTATGTTTTC
21121 TTTTTTCAATTTTTGCTCTTCCATTTAAATAAAAATTGTGTATTTTATGTTTTC
1 TTTTTTCAATTTTTGCTCTTCCATTTAAATAAAAATTGTGTATTTTATGTTTTC
21175 T
1 T
21176 AATTAAATTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (54 bp):
TTTTTTCAATTTTTGCTCTTCCATTTAAATAAAAATTGTGTATTTTATGTTTTC
Found at i:23892 original size:16 final size:16
Alignment explanation
Indices: 23856--23892 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
23846 ATCAGGCTTT
23856 AATTTCTAAACTTCTA
1 AATTTCTAAACTTCTA
* *
23872 GATTTCTAAACTTGTA
1 AATTTCTAAACTTCTA
23888 AATTT
1 AATTT
23893 GTGTAGAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTCTAAACTTCTA
Found at i:28084 original size:22 final size:19
Alignment explanation
Indices: 28062--28132 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 19
28052 ATTATATTGT
28062 TGTTTTGGTGTTTTTTTGC
1 TGTTTTGGTGTTTTTTTGC
28081 TGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGG-TG-T-TTTTTTGC
*
28103 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTG-TTTTTTTGC
28123 TGTTTTGGTG
1 TGTTTTGGTG
28133 CTATTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.17
20 19 0.40
21 4 0.09
22 16 0.34
ACGTcount: A:0.03, C:0.06, G:0.25, T:0.66
Consensus pattern (19 bp):
TGTTTTGGTGTTTTTTTGC
Found at i:28139 original size:22 final size:22
Alignment explanation
Indices: 28072--28162 Score: 107
Period size: 22 Copynumber: 4.2 Consensus size: 22
28062 TGTTTTGGTG
*
28072 TTTTTTTGCTGTTTTGGTTGCTA
1 TTTTTTTACTGTTTTGG-TGCTA
*
28095 -TTTTTTGCTGTTTTGGTG-T-
1 TTTTTTTACTGTTTTGGTGCTA
28114 TTTTTTTACTGTTTTGGTGCTA
1 TTTTTTTACTGTTTTGGTGCTA
* *
28136 TTTTTTTTACTATTTTTGTGCTA
1 -TTTTTTTACTGTTTTGGTGCTA
28159 TTTT
1 TTTT
28163 AATTGTTATT
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
20 18 0.30
21 3 0.05
22 20 0.33
23 20 0.33
ACGTcount: A:0.07, C:0.08, G:0.18, T:0.68
Consensus pattern (22 bp):
TTTTTTTACTGTTTTGGTGCTA
Found at i:28142 original size:42 final size:41
Alignment explanation
Indices: 28062--28141 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
28052 ATTATATTGT
*
28062 TGTTTTGGTGTTTTTTTGCTGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGGTGTTTTTTTACTGTTTTGGTTGCTATTTTTTGC
28103 TGTTTTGGTGTTTTTTTTACTGTTTTGG-TGCTATTTTTT
1 TGTTTTGGTG-TTTTTTTACTGTTTTGGTTGCTATTTTTT
28142 TTACTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
41 21 0.57
42 16 0.43
ACGTcount: A:0.04, C:0.06, G:0.23, T:0.68
Consensus pattern (41 bp):
TGTTTTGGTGTTTTTTTACTGTTTTGGTTGCTATTTTTTGC
Found at i:28143 original size:23 final size:23
Alignment explanation
Indices: 28072--28162 Score: 102
Period size: 23 Copynumber: 4.1 Consensus size: 23
28062 TGTTTTGGTG
*
28072 TTTTTTTGCTGTTTTGGTTGCTA-
1 TTTTTTTACTGTTTTGG-TGCTAT
*
28095 -TTTTTTGCTGTTTTGGTG---T
1 TTTTTTTACTGTTTTGGTGCTAT
28114 TTTTTTTACTGTTTTGGTGCTAT
1 TTTTTTTACTGTTTTGGTGCTAT
* *
28137 TTTTTTTACTATTTTTGTGCTAT
1 TTTTTTTACTGTTTTGGTGCTAT
28160 TTT
1 TTT
28163 AATTGTTATT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
20 17 0.28
21 2 0.03
22 16 0.27
23 25 0.42
ACGTcount: A:0.07, C:0.08, G:0.18, T:0.68
Consensus pattern (23 bp):
TTTTTTTACTGTTTTGGTGCTAT
Found at i:28152 original size:24 final size:24
Alignment explanation
Indices: 28113--28210 Score: 83
Period size: 24 Copynumber: 4.2 Consensus size: 24
28103 TGTTTTGGTG
*
28113 TTTTTTTTACT-GTTTTGGTGCTA
1 TTTTTTTTACTATTTTTGGTGCTA
28136 TTTTTTTTACTATTTTT-GTGCTA
1 TTTTTTTTACTATTTTTGGTGCTA
** ** * *
28159 TTTTAATTGTTATTTTTGTTGTTA
1 TTTTTTTTACTATTTTTGGTGCTA
* * * *
28183 TTTTTTCTATTATTTTTGCTGTTA
1 TTTTTTTTACTATTTTTGGTGCTA
28207 TTTT
1 TTTT
28211 GATTGTTTGG
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
23 30 0.49
24 31 0.51
ACGTcount: A:0.12, C:0.06, G:0.11, T:0.70
Consensus pattern (24 bp):
TTTTTTTTACTATTTTTGGTGCTA
Found at i:28187 original size:12 final size:12
Alignment explanation
Indices: 28146--28210 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
28136 TTTTTTTTAC
*
28146 TATTTTTG-TGC
1 TATTTTTGTTGT
**
28157 TATTTTAATTGT
1 TATTTTTGTTGT
28169 TATTTTTGTTGT
1 TATTTTTGTTGT
*
28181 TATTTTT-TCTAT
1 TATTTTTGT-TGT
*
28193 TATTTTTGCTGT
1 TATTTTTGTTGT
28205 TATTTT
1 TATTTT
28211 GATTGTTTGG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
11 7 0.16
12 36 0.84
ACGTcount: A:0.14, C:0.05, G:0.11, T:0.71
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:46156 original size:29 final size:30
Alignment explanation
Indices: 46107--46163 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
46097 GGATTGGATT
* *
46107 AAATCAAAATTTCATTTATAAAATTACATA
1 AAATCAAAATTCCATGTATAAAATTACATA
46137 AAATCAAAA-TCCATGTATAAAATTACA
1 AAATCAAAATTCCATGTATAAAATTACA
46164 CATTAGATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTCCATGTATAAAATTACATA
Found at i:46877 original size:21 final size:22
Alignment explanation
Indices: 46853--46904 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 22
46843 ACTTTTCTTC
* *
46853 ATATGATATAAAT-CATATAAT
1 ATATGATATAAATAAAAATAAT
* *
46874 ATATAAAATAAATGAAAAATAAT
1 ATATGATATAAAT-AAAAATAAT
46897 ATATGATA
1 ATATGATA
46905 AACTTGAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 11 0.48
23 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (22 bp):
ATATGATATAAATAAAAATAAT
Found at i:49546 original size:36 final size:36
Alignment explanation
Indices: 49499--49571 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
49489 AACTTACTGC
49499 GTCAGAGGTTGTTGAGCCAAAGAGACAAAATGATAT
1 GTCAGAGGTTGTTGAGCCAAAGAGACAAAATGATAT
49535 GTCAGAGGTTGTTGAGCCAAAGAGACAAAATGATAT
1 GTCAGAGGTTGTTGAGCCAAAGAGACAAAATGATAT
49571 G
1 G
49572 ACATTCATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (36 bp):
GTCAGAGGTTGTTGAGCCAAAGAGACAAAATGATAT
Done.