Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001023.1 Kokia drynarioides strain JFW-HI SEQ_112238, 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: 73564
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:5223 original size:17 final size:19
Alignment explanation
Indices: 5178--5223 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
5168 GTAATGGCAT
5178 TAATAATTATGTTATTATA
1 TAATAATTATGTTATTATA
* *
5197 TAAGATTTAT-TT-TTATA
1 TAATAATTATGTTATTATA
5214 TAATAATTAT
1 TAATAATTAT
5224 AAACTTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
TAATAATTATGTTATTATA
Found at i:5253 original size:20 final size:20
Alignment explanation
Indices: 5189--5258 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 20
5179 AATAATTATG
* *
5189 TTATTATATAAGATTTATTT
1 TTATTATATAATATATATTT
*
5209 TTA-TATAATAATTATAAACTTT
1 TTATTAT-ATAA-TATATA-TTT
5231 TTATTATGATAA-ATATATTT
1 TTATTAT-ATAATATATATTT
5251 TTAATTAT
1 TT-ATTAT
5259 TCAAAAGATA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.08
20 12 0.30
21 12 0.30
22 6 0.15
23 7 0.17
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (20 bp):
TTATTATATAATATATATTT
Found at i:5674 original size:3 final size:3
Alignment explanation
Indices: 5666--5694 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5656 ATATATACAC
5666 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
5695 ATATACCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:5949 original size:20 final size:20
Alignment explanation
Indices: 5912--5950 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5902 TTAACCAAAC
*
5912 AAATAAATTATAATTATAAA
1 AAATAAATTATAAGTATAAA
* *
5932 AAATAAATTGTACGTATAA
1 AAATAAATTATAAGTATAA
5951 TGTTTGCTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATAAATTATAAGTATAAA
Found at i:21155 original size:22 final size:23
Alignment explanation
Indices: 21121--21164 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
21111 GTATAAATTT
21121 TAAATTATTTT-TAAATAATTAATA
1 TAAATTATTTTAT-AA-AATTAATA
21145 TAAATTA-TTTATAAAATTAA
1 TAAATTATTTTATAAAATTAA
21165 ATTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATTATTTTATAAAATTAATA
Found at i:21203 original size:31 final size:31
Alignment explanation
Indices: 21151--21230 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
21141 AATATAAATT
* *
21151 ATTTATAA-AATTAAATTTAATAATAAATGTG-
1 ATTTA-AATAATTTAATATAATAATAAATG-GA
* *
21182 ATTTAAATAGTTTAATATAATAATAGATGGA
1 ATTTAAATAATTTAATATAATAATAAATGGA
21213 TATTTAAATAATTTAATA
1 -ATTTAAATAATTTAATA
21231 CATTGATCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 3 0.07
31 22 0.54
32 16 0.39
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTTAAATAATTTAATATAATAATAAATGGA
Found at i:22736 original size:6 final size:6
Alignment explanation
Indices: 22725--22751 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
22715 CGATTAGCTG
22725 CTATGC CTATGC CTATGC CTATGC CTA
1 CTATGC CTATGC CTATGC CTATGC CTA
22752 CATATCATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (6 bp):
CTATGC
Found at i:24404 original size:7 final size:6
Alignment explanation
Indices: 24395--24422 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
24385 TGAAAAAGTA
24395 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
24423 GCATAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:24942 original size:28 final size:30
Alignment explanation
Indices: 24895--24953 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
24885 CCCTAATTTA
24895 TAAATTTTTTTCTGTCTTTT-TT-AATCAT
1 TAAATTTTTTTCTGTCTTTTGTTAAATCAT
* * *
24923 TAAATTTTTTTTTTTTTTTTGTTAAATCAT
1 TAAATTTTTTTCTGTCTTTTGTTAAATCAT
24953 T
1 T
24954 TCAAAATGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.65
29 2 0.08
30 7 0.27
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (30 bp):
TAAATTTTTTTCTGTCTTTTGTTAAATCAT
Found at i:25034 original size:9 final size:9
Alignment explanation
Indices: 25022--25050 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
25012 TCATTTAATT
25022 AATTTTAAA
1 AATTTTAAA
25031 AATTTTAAA
1 AATTTTAAA
25040 AA-TTTAAA
1 AATTTTAAA
25048 AAT
1 AAT
25051 ATTATAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTTTAAA
Found at i:27857 original size:2 final size:2
Alignment explanation
Indices: 27850--27874 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27840 ATAAAGAATA
27850 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27875 AATCAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28297 original size:17 final size:16
Alignment explanation
Indices: 28256--28305 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
28246 ATAATGAAAA
*
28256 TATAA-TTTTATTATT
1 TATAATTTTTATTTTT
*
28271 T-TAATATTTATGTTTT
1 TATAATTTTTAT-TTTT
28287 TATAATTTTTATATTTT
1 TATAATTTTTAT-TTTT
28304 TA
1 TA
28306 GAAGGATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.11
15 6 0.21
16 4 0.14
17 15 0.54
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATAATTTTTATTTTT
Found at i:30306 original size:3 final size:3
Alignment explanation
Indices: 30298--30360 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
30288 TTTCAGTTTT
* *
30298 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA -AA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30345 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
30361 CAAATATTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 1 0.02
3 54 0.98
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:54835 original size:46 final size:46
Alignment explanation
Indices: 54762--54852 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
54752 TTTTACATTG
54762 ATGATGTGCTTGAGCGGAAAAAGGGAAGGATAGAATGAGAGAATTA
1 ATGATGTGCTTGAGCGGAAAAAGGGAAGGATAGAATGAGAGAATTA
* * *
54808 ATGATGTGC-TGAAGCGG-AGAAGTGGAAGGATAGAGTGTGAGAATT
1 ATGATGTGCTTG-AGCGGAAAAAG-GGAAGGATAGAATGAGAGAATT
54853 GAAAAAGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
45 6 0.15
46 34 0.85
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.21
Consensus pattern (46 bp):
ATGATGTGCTTGAGCGGAAAAAGGGAAGGATAGAATGAGAGAATTA
Found at i:55062 original size:30 final size:30
Alignment explanation
Indices: 55026--55085 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
55016 AATCTTCATA
*
55026 ATTTTTAAAAAATTAAATTAAAATTTTATT
1 ATTTTTAAAAAATAAAATTAAAATTTTATT
* *
55056 ATTTTTAAAAGATAAAATTACAATTTTATT
1 ATTTTTAAAAAATAAAATTAAAATTTTATT
55086 TTTACAATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTTTTAAAAAATAAAATTAAAATTTTATT
Found at i:65179 original size:26 final size:26
Alignment explanation
Indices: 65149--65199 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
65139 TTTTTATAAT
65149 TTTTTAAAAAAATATAAAATTTTAAC
1 TTTTTAAAAAAATATAAAATTTTAAC
* * * *
65175 TTTTTATAAATATTTTAAATTTTAA
1 TTTTTAAAAAAATATAAAATTTTAA
65200 AAGTATTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTTAAAAAAATATAAAATTTTAAC
Found at i:65182 original size:18 final size:19
Alignment explanation
Indices: 65161--65237 Score: 79
Period size: 18 Copynumber: 4.1 Consensus size: 19
65151 TTTAAAAAAA
*
65161 TATAAA-ATTTTAACTTTT
1 TATAAATATTTTAAATTTT
65179 TATAAATATTTTAAA-TTT
1 TATAAATATTTTAAATTTT
65197 TA-AAAGTATTTTGAAATTTT
1 TATAAA-TATTTT-AAATTTT
* *
65217 GAAAAATATTTTAAATCTTT
1 TATAAATATTTTAAAT-TTT
65237 T
1 T
65238 TTTTATAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
17 3 0.06
18 17 0.34
19 14 0.28
20 13 0.26
21 3 0.06
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:72714 original size:5 final size:5
Alignment explanation
Indices: 72704--72745 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
72694 ACAAATGGCT
72704 GATGA GATGA GATGA GATGA GATGA GATGA GATGA GATGA GA
1 GATGA GATGA GATGA GATGA GATGA GATGA GATGA GATGA GA
72746 CTTCAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.19
Consensus pattern (5 bp):
GATGA
Done.