Multiple sequence alignment - TraesCS2D01G042700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G042700 chr2D 100.000 3120 0 0 1 3120 15374438 15371319 0.000000e+00 5762.0
1 TraesCS2D01G042700 chr2D 93.023 43 3 0 704 746 15383239 15383197 2.600000e-06 63.9
2 TraesCS2D01G042700 chr2A 91.371 1692 90 26 566 2240 17442150 17440498 0.000000e+00 2265.0
3 TraesCS2D01G042700 chr2A 92.611 1218 66 12 1039 2240 17482275 17481066 0.000000e+00 1729.0
4 TraesCS2D01G042700 chr2A 88.729 834 35 22 194 977 17483119 17482295 0.000000e+00 965.0
5 TraesCS2D01G042700 chr2A 86.852 829 83 17 2214 3031 102402775 102403588 0.000000e+00 904.0
6 TraesCS2D01G042700 chr2A 80.826 751 93 29 984 1718 17448077 17447362 2.740000e-150 542.0
7 TraesCS2D01G042700 chr2A 88.158 380 30 5 194 570 17442861 17442494 3.690000e-119 438.0
8 TraesCS2D01G042700 chr2A 83.810 105 8 1 457 552 17491980 17491876 1.190000e-14 91.6
9 TraesCS2D01G042700 chr2A 93.023 43 3 0 704 746 17443349 17443307 2.600000e-06 63.9
10 TraesCS2D01G042700 chr2B 90.387 1498 48 37 699 2140 27530782 27529325 0.000000e+00 1881.0
11 TraesCS2D01G042700 chr2B 85.619 904 109 12 2224 3117 24857344 24858236 0.000000e+00 929.0
12 TraesCS2D01G042700 chr2B 87.801 664 73 7 2276 2939 772233717 772234372 0.000000e+00 771.0
13 TraesCS2D01G042700 chr2B 91.877 357 13 5 194 540 27531176 27530826 4.680000e-133 484.0
14 TraesCS2D01G042700 chr2B 85.017 287 32 6 1431 1715 27537040 27536763 6.590000e-72 281.0
15 TraesCS2D01G042700 chr2B 78.680 394 53 17 984 1361 27537600 27537222 1.870000e-57 233.0
16 TraesCS2D01G042700 chr2B 100.000 30 0 0 652 681 27530810 27530781 4.350000e-04 56.5
17 TraesCS2D01G042700 chr7D 87.610 912 91 11 2230 3120 592973481 592972571 0.000000e+00 1038.0
18 TraesCS2D01G042700 chr7D 96.410 195 6 1 1 194 64543607 64543801 1.400000e-83 320.0
19 TraesCS2D01G042700 chr7D 96.392 194 6 1 1 193 5001122 5000929 5.020000e-83 318.0
20 TraesCS2D01G042700 chr7D 91.781 73 5 1 587 659 90038603 90038532 1.980000e-17 100.0
21 TraesCS2D01G042700 chr7B 87.185 913 94 11 2222 3120 648547656 648548559 0.000000e+00 1016.0
22 TraesCS2D01G042700 chr7B 94.030 67 4 0 587 653 154818590 154818656 5.500000e-18 102.0
23 TraesCS2D01G042700 chr6D 85.572 901 111 14 2231 3119 297258234 297257341 0.000000e+00 926.0
24 TraesCS2D01G042700 chr5B 88.227 722 78 5 2225 2942 297900783 297900065 0.000000e+00 856.0
25 TraesCS2D01G042700 chr5B 81.958 715 105 16 2419 3120 511047481 511048184 4.480000e-163 584.0
26 TraesCS2D01G042700 chr5B 85.768 267 25 10 2864 3120 261930766 261930503 1.430000e-68 270.0
27 TraesCS2D01G042700 chr5B 83.459 133 12 3 2997 3120 297900059 297899928 7.070000e-22 115.0
28 TraesCS2D01G042700 chr5B 77.778 144 18 8 2977 3120 2062959 2062830 3.340000e-10 76.8
29 TraesCS2D01G042700 chr1B 85.749 814 99 15 2227 3037 623238319 623239118 0.000000e+00 845.0
30 TraesCS2D01G042700 chr1B 94.030 67 4 0 587 653 161207012 161207078 5.500000e-18 102.0
31 TraesCS2D01G042700 chr1B 92.647 68 5 0 587 654 503670048 503669981 7.120000e-17 99.0
32 TraesCS2D01G042700 chr4A 86.623 770 87 11 2271 3031 689259830 689260592 0.000000e+00 837.0
33 TraesCS2D01G042700 chr4B 80.626 831 116 32 2227 3039 113598321 113597518 4.450000e-168 601.0
34 TraesCS2D01G042700 chr1D 84.910 444 57 8 2686 3120 370135824 370136266 1.030000e-119 440.0
35 TraesCS2D01G042700 chr1D 91.414 198 15 2 1 197 7189796 7189992 1.430000e-68 270.0
36 TraesCS2D01G042700 chr1D 91.237 194 16 1 1 193 22689699 22689892 2.390000e-66 263.0
37 TraesCS2D01G042700 chr1A 94.330 194 10 1 1 193 524460734 524460927 2.350000e-76 296.0
38 TraesCS2D01G042700 chr1A 91.327 196 13 4 1 193 67644088 67643894 6.630000e-67 265.0
39 TraesCS2D01G042700 chr1A 91.534 189 15 1 6 193 578409252 578409440 3.090000e-65 259.0
40 TraesCS2D01G042700 chr5D 91.753 194 15 1 1 193 530318594 530318787 5.130000e-68 268.0
41 TraesCS2D01G042700 chr5D 82.069 145 9 4 2976 3120 347279584 347279711 1.180000e-19 108.0
42 TraesCS2D01G042700 chr6B 91.371 197 14 3 1 194 698571527 698571723 1.840000e-67 267.0
43 TraesCS2D01G042700 chr6B 92.105 76 5 1 587 661 171967194 171967269 4.260000e-19 106.0
44 TraesCS2D01G042700 chr3B 93.939 66 4 0 588 653 798286530 798286465 1.980000e-17 100.0
45 TraesCS2D01G042700 chr3D 91.549 71 5 1 587 657 22092942 22092873 2.560000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G042700 chr2D 15371319 15374438 3119 True 5762.000000 5762 100.000000 1 3120 1 chr2D.!!$R1 3119
1 TraesCS2D01G042700 chr2A 17481066 17483119 2053 True 1347.000000 1729 90.670000 194 2240 2 chr2A.!!$R4 2046
2 TraesCS2D01G042700 chr2A 17440498 17443349 2851 True 922.300000 2265 90.850667 194 2240 3 chr2A.!!$R3 2046
3 TraesCS2D01G042700 chr2A 102402775 102403588 813 False 904.000000 904 86.852000 2214 3031 1 chr2A.!!$F1 817
4 TraesCS2D01G042700 chr2A 17447362 17448077 715 True 542.000000 542 80.826000 984 1718 1 chr2A.!!$R1 734
5 TraesCS2D01G042700 chr2B 24857344 24858236 892 False 929.000000 929 85.619000 2224 3117 1 chr2B.!!$F1 893
6 TraesCS2D01G042700 chr2B 27529325 27531176 1851 True 807.166667 1881 94.088000 194 2140 3 chr2B.!!$R1 1946
7 TraesCS2D01G042700 chr2B 772233717 772234372 655 False 771.000000 771 87.801000 2276 2939 1 chr2B.!!$F2 663
8 TraesCS2D01G042700 chr2B 27536763 27537600 837 True 257.000000 281 81.848500 984 1715 2 chr2B.!!$R2 731
9 TraesCS2D01G042700 chr7D 592972571 592973481 910 True 1038.000000 1038 87.610000 2230 3120 1 chr7D.!!$R3 890
10 TraesCS2D01G042700 chr7B 648547656 648548559 903 False 1016.000000 1016 87.185000 2222 3120 1 chr7B.!!$F2 898
11 TraesCS2D01G042700 chr6D 297257341 297258234 893 True 926.000000 926 85.572000 2231 3119 1 chr6D.!!$R1 888
12 TraesCS2D01G042700 chr5B 511047481 511048184 703 False 584.000000 584 81.958000 2419 3120 1 chr5B.!!$F1 701
13 TraesCS2D01G042700 chr5B 297899928 297900783 855 True 485.500000 856 85.843000 2225 3120 2 chr5B.!!$R3 895
14 TraesCS2D01G042700 chr1B 623238319 623239118 799 False 845.000000 845 85.749000 2227 3037 1 chr1B.!!$F2 810
15 TraesCS2D01G042700 chr4A 689259830 689260592 762 False 837.000000 837 86.623000 2271 3031 1 chr4A.!!$F1 760
16 TraesCS2D01G042700 chr4B 113597518 113598321 803 True 601.000000 601 80.626000 2227 3039 1 chr4B.!!$R1 812

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
131 132 0.032267 GGTCGCTAGTGTCCATAGGC 59.968 60.0 13.80 0.0 0.00 3.93 F
132 133 0.317938 GTCGCTAGTGTCCATAGGCG 60.318 60.0 2.66 0.0 43.22 5.52 F
256 552 0.897621 ATCGAGACCACTGTCATGCA 59.102 50.0 0.00 0.0 44.33 3.96 F
1073 1827 1.253044 GAAACAAACGCGCTCACACG 61.253 55.0 5.73 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1025 1777 0.621571 AGCTGGGGTGGATCTAAGCA 60.622 55.000 3.68 0.0 33.08 3.91 R
1364 2135 2.028930 ACTAGTGCTTCGCAGTTAGCTT 60.029 45.455 0.00 0.0 39.37 3.74 R
1929 2837 2.243221 CCAGGAGGAGGAACAATGGATT 59.757 50.000 0.00 0.0 36.89 3.01 R
2712 3656 0.258194 GGGAGTAGGAGGAGGTCGAA 59.742 60.000 0.00 0.0 0.00 3.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.821031 ACGTCTCACAAATAGTCTCTAAGT 57.179 37.500 0.00 0.00 0.00 2.24
25 26 7.216973 ACGTCTCACAAATAGTCTCTAAGTT 57.783 36.000 0.00 0.00 0.00 2.66
26 27 8.332996 ACGTCTCACAAATAGTCTCTAAGTTA 57.667 34.615 0.00 0.00 0.00 2.24
27 28 8.790718 ACGTCTCACAAATAGTCTCTAAGTTAA 58.209 33.333 0.00 0.00 0.00 2.01
28 29 9.790389 CGTCTCACAAATAGTCTCTAAGTTAAT 57.210 33.333 0.00 0.00 0.00 1.40
58 59 9.948964 AATTAAATGCTTATTTTCTTGAAGGCT 57.051 25.926 0.00 0.00 0.00 4.58
62 63 9.948964 AAATGCTTATTTTCTTGAAGGCTAATT 57.051 25.926 0.00 0.00 0.00 1.40
79 80 9.860898 AAGGCTAATTATAAGAAAAAGCTTGTG 57.139 29.630 0.00 0.00 0.00 3.33
80 81 8.470002 AGGCTAATTATAAGAAAAAGCTTGTGG 58.530 33.333 0.00 0.00 0.00 4.17
82 83 7.759433 GCTAATTATAAGAAAAAGCTTGTGGCA 59.241 33.333 0.00 0.00 44.79 4.92
83 84 7.889589 AATTATAAGAAAAAGCTTGTGGCAC 57.110 32.000 11.55 11.55 44.79 5.01
84 85 6.648879 TTATAAGAAAAAGCTTGTGGCACT 57.351 33.333 19.83 0.00 44.79 4.40
86 87 1.683385 AGAAAAAGCTTGTGGCACTCC 59.317 47.619 19.83 6.90 44.79 3.85
87 88 1.408702 GAAAAAGCTTGTGGCACTCCA 59.591 47.619 19.83 1.84 44.79 3.86
88 89 1.708341 AAAAGCTTGTGGCACTCCAT 58.292 45.000 19.83 0.00 45.62 3.41
91 92 2.584835 AGCTTGTGGCACTCCATAAA 57.415 45.000 19.83 2.30 45.62 1.40
92 93 2.162681 AGCTTGTGGCACTCCATAAAC 58.837 47.619 19.83 0.00 45.62 2.01
93 94 1.135689 GCTTGTGGCACTCCATAAACG 60.136 52.381 19.83 0.00 45.62 3.60
94 95 2.151202 CTTGTGGCACTCCATAAACGT 58.849 47.619 19.83 0.00 45.62 3.99
95 96 1.803334 TGTGGCACTCCATAAACGTC 58.197 50.000 19.83 0.00 45.62 4.34
96 97 1.346395 TGTGGCACTCCATAAACGTCT 59.654 47.619 19.83 0.00 45.62 4.18
97 98 2.224426 TGTGGCACTCCATAAACGTCTT 60.224 45.455 19.83 0.00 45.62 3.01
99 100 3.998341 GTGGCACTCCATAAACGTCTTAA 59.002 43.478 11.13 0.00 45.62 1.85
100 101 4.092968 GTGGCACTCCATAAACGTCTTAAG 59.907 45.833 11.13 0.00 45.62 1.85
101 102 4.020928 TGGCACTCCATAAACGTCTTAAGA 60.021 41.667 0.00 0.00 37.47 2.10
102 103 4.933400 GGCACTCCATAAACGTCTTAAGAA 59.067 41.667 6.78 0.00 0.00 2.52
104 105 5.446073 GCACTCCATAAACGTCTTAAGAAGC 60.446 44.000 17.03 0.94 0.00 3.86
105 106 4.863131 ACTCCATAAACGTCTTAAGAAGCG 59.137 41.667 17.03 14.64 35.30 4.68
106 107 4.813027 TCCATAAACGTCTTAAGAAGCGT 58.187 39.130 17.03 15.24 40.88 5.07
107 108 4.860907 TCCATAAACGTCTTAAGAAGCGTC 59.139 41.667 18.14 1.50 39.22 5.19
108 109 4.863131 CCATAAACGTCTTAAGAAGCGTCT 59.137 41.667 18.14 9.83 39.22 4.18
109 110 5.347907 CCATAAACGTCTTAAGAAGCGTCTT 59.652 40.000 18.87 18.87 46.18 3.01
110 111 6.128634 CCATAAACGTCTTAAGAAGCGTCTTT 60.129 38.462 20.02 13.28 41.55 2.52
111 112 7.062605 CCATAAACGTCTTAAGAAGCGTCTTTA 59.937 37.037 20.02 10.40 41.55 1.85
112 113 6.449448 AAACGTCTTAAGAAGCGTCTTTAG 57.551 37.500 20.02 19.17 41.55 1.85
114 115 4.022503 ACGTCTTAAGAAGCGTCTTTAGGT 60.023 41.667 22.37 15.63 41.55 3.08
115 116 4.558080 CGTCTTAAGAAGCGTCTTTAGGTC 59.442 45.833 22.37 16.17 41.55 3.85
116 117 4.558080 GTCTTAAGAAGCGTCTTTAGGTCG 59.442 45.833 22.37 4.40 41.55 4.79
117 118 1.711206 AAGAAGCGTCTTTAGGTCGC 58.289 50.000 9.25 0.00 41.55 5.19
123 124 1.135460 GCGTCTTTAGGTCGCTAGTGT 60.135 52.381 2.66 0.00 45.29 3.55
125 126 2.477525 CGTCTTTAGGTCGCTAGTGTCC 60.478 54.545 11.15 11.15 0.00 4.02
126 127 2.490903 GTCTTTAGGTCGCTAGTGTCCA 59.509 50.000 19.62 5.27 0.00 4.02
127 128 3.130693 GTCTTTAGGTCGCTAGTGTCCAT 59.869 47.826 19.62 8.88 0.00 3.41
128 129 4.337555 GTCTTTAGGTCGCTAGTGTCCATA 59.662 45.833 19.62 8.05 0.00 2.74
130 131 1.693627 AGGTCGCTAGTGTCCATAGG 58.306 55.000 19.62 0.00 0.00 2.57
131 132 0.032267 GGTCGCTAGTGTCCATAGGC 59.968 60.000 13.80 0.00 0.00 3.93
132 133 0.317938 GTCGCTAGTGTCCATAGGCG 60.318 60.000 2.66 0.00 43.22 5.52
134 135 0.949397 CGCTAGTGTCCATAGGCGTA 59.051 55.000 0.00 0.00 38.20 4.42
136 137 2.228059 GCTAGTGTCCATAGGCGTAGA 58.772 52.381 0.00 0.00 0.00 2.59
137 138 2.226912 GCTAGTGTCCATAGGCGTAGAG 59.773 54.545 0.00 0.00 0.00 2.43
138 139 2.730934 AGTGTCCATAGGCGTAGAGA 57.269 50.000 0.00 0.00 0.00 3.10
139 140 2.299521 AGTGTCCATAGGCGTAGAGAC 58.700 52.381 10.24 10.24 0.00 3.36
158 159 4.710528 GACGAATAAAATAGCGTCCCAG 57.289 45.455 0.00 0.00 45.16 4.45
159 160 4.365723 GACGAATAAAATAGCGTCCCAGA 58.634 43.478 0.00 0.00 45.16 3.86
160 161 4.761975 ACGAATAAAATAGCGTCCCAGAA 58.238 39.130 0.00 0.00 30.15 3.02
162 163 5.644636 ACGAATAAAATAGCGTCCCAGAAAA 59.355 36.000 0.00 0.00 30.15 2.29
163 164 6.149807 ACGAATAAAATAGCGTCCCAGAAAAA 59.850 34.615 0.00 0.00 30.15 1.94
165 166 3.850122 AAATAGCGTCCCAGAAAAAGC 57.150 42.857 0.00 0.00 0.00 3.51
169 170 1.866925 CGTCCCAGAAAAAGCGACC 59.133 57.895 0.00 0.00 0.00 4.79
171 172 1.534729 GTCCCAGAAAAAGCGACCAT 58.465 50.000 0.00 0.00 0.00 3.55
172 173 2.706890 GTCCCAGAAAAAGCGACCATA 58.293 47.619 0.00 0.00 0.00 2.74
173 174 2.418976 GTCCCAGAAAAAGCGACCATAC 59.581 50.000 0.00 0.00 0.00 2.39
175 176 2.073816 CCAGAAAAAGCGACCATACGT 58.926 47.619 0.00 0.00 35.59 3.57
176 177 2.159707 CCAGAAAAAGCGACCATACGTG 60.160 50.000 0.00 0.00 35.59 4.49
206 502 4.530710 TTGTAGTGACGAAGCCAACTAT 57.469 40.909 0.00 0.00 0.00 2.12
256 552 0.897621 ATCGAGACCACTGTCATGCA 59.102 50.000 0.00 0.00 44.33 3.96
264 560 1.938577 CCACTGTCATGCATGCTAGAC 59.061 52.381 26.53 26.03 0.00 2.59
529 843 3.934457 AACTAACAAAATTCCCCTGCG 57.066 42.857 0.00 0.00 0.00 5.18
577 1240 9.857656 TCTACTCCCTCGTTTCTAAATATAAGA 57.142 33.333 0.00 0.00 0.00 2.10
606 1269 3.689649 AGATTTTGCTCCGTATGTGGTTC 59.310 43.478 0.00 0.00 0.00 3.62
617 1280 6.411376 TCCGTATGTGGTTCATAGTGAAATT 58.589 36.000 0.00 0.00 38.22 1.82
619 1282 7.392113 TCCGTATGTGGTTCATAGTGAAATTTT 59.608 33.333 0.00 0.00 38.22 1.82
801 1467 1.274167 GTGGGAGTATGACCGTGTTGA 59.726 52.381 0.00 0.00 0.00 3.18
803 1469 3.131577 GTGGGAGTATGACCGTGTTGATA 59.868 47.826 0.00 0.00 0.00 2.15
804 1470 3.964688 TGGGAGTATGACCGTGTTGATAT 59.035 43.478 0.00 0.00 0.00 1.63
913 1644 3.902086 GACCCTCGGTCGCTAGCC 61.902 72.222 9.66 0.00 43.14 3.93
1018 1770 8.682936 ATCTCATGTATAAAATGTGACCTTCC 57.317 34.615 0.00 0.00 32.19 3.46
1025 1777 4.974438 TGTGACCTTCCCCCGCCT 62.974 66.667 0.00 0.00 0.00 5.52
1060 1814 3.557898 CCCAGCTAGCTTCAGAGAAACAA 60.558 47.826 16.46 0.00 0.00 2.83
1073 1827 1.253044 GAAACAAACGCGCTCACACG 61.253 55.000 5.73 0.00 0.00 4.49
1247 2015 2.517638 TCGCCGCCGAGATCCTAA 60.518 61.111 0.00 0.00 38.82 2.69
1347 2118 2.425592 CACTGAGACAACCCGGCA 59.574 61.111 0.00 0.00 0.00 5.69
1364 2135 2.811431 CGGCACAAAAGAAGGTACATCA 59.189 45.455 0.00 0.00 0.00 3.07
1373 2144 7.041098 ACAAAAGAAGGTACATCAAGCTAACTG 60.041 37.037 0.00 0.00 0.00 3.16
1772 2674 2.028112 TCAAGATCCTCGACTTTGGGTG 60.028 50.000 0.00 0.00 0.00 4.61
1929 2837 2.282958 AGCTCCTCCACCGACGAA 60.283 61.111 0.00 0.00 0.00 3.85
2011 2922 4.466828 CAACTGCTCCTTTGATTACGTTG 58.533 43.478 0.00 0.00 0.00 4.10
2197 3110 2.606272 GCAGTTTGTACGTACCTATGCC 59.394 50.000 22.43 8.84 0.00 4.40
2199 3112 2.159198 AGTTTGTACGTACCTATGCCGG 60.159 50.000 22.43 0.00 0.00 6.13
2267 3181 4.581868 TGTAAAAGTCGGATCCGGAAAAT 58.418 39.130 32.79 18.79 40.25 1.82
2295 3217 1.859703 CAGTTCGCTGCAGATCAGATC 59.140 52.381 20.43 1.64 45.72 2.75
2329 3251 2.125391 GCGCTGCAGATCAGACCA 60.125 61.111 20.43 0.00 45.72 4.02
2335 3257 2.806818 GCTGCAGATCAGACCACATATG 59.193 50.000 20.43 0.00 45.72 1.78
2500 3440 2.893398 GTGCAGCGTACCCTAGCT 59.107 61.111 0.00 0.00 45.74 3.32
2726 3670 2.119655 GCGCTTCGACCTCCTCCTA 61.120 63.158 0.00 0.00 0.00 2.94
2737 3681 2.279073 CCTCCTACTCCCTCGCCA 59.721 66.667 0.00 0.00 0.00 5.69
2754 3698 1.822613 CAAGCGCTCCATGATGGCT 60.823 57.895 12.06 0.00 37.47 4.75
2939 3885 4.517934 TCCCCGCGGTAGAGGAGG 62.518 72.222 26.12 16.31 39.96 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.821031 ACTTAGAGACTATTTGTGAGACGT 57.179 37.500 0.00 0.00 0.00 4.34
2 3 9.790389 ATTAACTTAGAGACTATTTGTGAGACG 57.210 33.333 0.00 0.00 0.00 4.18
36 37 9.948964 AATTAGCCTTCAAGAAAATAAGCATTT 57.051 25.926 0.00 0.00 35.84 2.32
54 55 8.470002 CCACAAGCTTTTTCTTATAATTAGCCT 58.530 33.333 0.00 0.00 0.00 4.58
55 56 7.222805 GCCACAAGCTTTTTCTTATAATTAGCC 59.777 37.037 0.00 0.00 38.99 3.93
57 58 9.076596 GTGCCACAAGCTTTTTCTTATAATTAG 57.923 33.333 0.00 0.00 44.23 1.73
58 59 8.802267 AGTGCCACAAGCTTTTTCTTATAATTA 58.198 29.630 0.00 0.00 44.23 1.40
59 60 7.670364 AGTGCCACAAGCTTTTTCTTATAATT 58.330 30.769 0.00 0.00 44.23 1.40
60 61 7.232118 AGTGCCACAAGCTTTTTCTTATAAT 57.768 32.000 0.00 0.00 44.23 1.28
61 62 6.294508 GGAGTGCCACAAGCTTTTTCTTATAA 60.295 38.462 0.00 0.00 44.23 0.98
62 63 5.183140 GGAGTGCCACAAGCTTTTTCTTATA 59.817 40.000 0.00 0.00 44.23 0.98
63 64 4.021981 GGAGTGCCACAAGCTTTTTCTTAT 60.022 41.667 0.00 0.00 44.23 1.73
64 65 3.317993 GGAGTGCCACAAGCTTTTTCTTA 59.682 43.478 0.00 0.00 44.23 2.10
65 66 2.101415 GGAGTGCCACAAGCTTTTTCTT 59.899 45.455 0.00 0.00 44.23 2.52
66 67 1.683385 GGAGTGCCACAAGCTTTTTCT 59.317 47.619 0.00 0.00 44.23 2.52
67 68 1.408702 TGGAGTGCCACAAGCTTTTTC 59.591 47.619 0.00 0.00 44.23 2.29
68 69 1.484038 TGGAGTGCCACAAGCTTTTT 58.516 45.000 0.00 0.00 44.23 1.94
69 70 3.205815 TGGAGTGCCACAAGCTTTT 57.794 47.368 0.00 0.00 44.23 2.27
79 80 4.501071 TCTTAAGACGTTTATGGAGTGCC 58.499 43.478 0.00 0.00 0.00 5.01
80 81 5.446073 GCTTCTTAAGACGTTTATGGAGTGC 60.446 44.000 4.18 0.00 0.00 4.40
82 83 4.863131 CGCTTCTTAAGACGTTTATGGAGT 59.137 41.667 4.18 0.00 0.00 3.85
83 84 4.863131 ACGCTTCTTAAGACGTTTATGGAG 59.137 41.667 13.62 3.57 37.77 3.86
84 85 4.813027 ACGCTTCTTAAGACGTTTATGGA 58.187 39.130 13.62 0.00 37.77 3.41
86 87 6.390987 AAGACGCTTCTTAAGACGTTTATG 57.609 37.500 18.68 4.83 40.54 1.90
87 88 7.275123 CCTAAAGACGCTTCTTAAGACGTTTAT 59.725 37.037 18.68 11.79 41.56 1.40
88 89 6.583806 CCTAAAGACGCTTCTTAAGACGTTTA 59.416 38.462 18.68 13.88 41.56 2.01
91 92 4.022503 ACCTAAAGACGCTTCTTAAGACGT 60.023 41.667 17.95 17.95 41.56 4.34
92 93 4.483311 ACCTAAAGACGCTTCTTAAGACG 58.517 43.478 4.18 9.25 41.56 4.18
93 94 4.558080 CGACCTAAAGACGCTTCTTAAGAC 59.442 45.833 4.18 0.00 41.56 3.01
94 95 4.730657 CGACCTAAAGACGCTTCTTAAGA 58.269 43.478 5.81 0.00 41.56 2.10
104 105 2.477525 GGACACTAGCGACCTAAAGACG 60.478 54.545 0.00 0.00 0.00 4.18
105 106 2.490903 TGGACACTAGCGACCTAAAGAC 59.509 50.000 1.10 0.00 0.00 3.01
106 107 2.799017 TGGACACTAGCGACCTAAAGA 58.201 47.619 1.10 0.00 0.00 2.52
107 108 3.802948 ATGGACACTAGCGACCTAAAG 57.197 47.619 1.10 0.00 0.00 1.85
108 109 3.635373 CCTATGGACACTAGCGACCTAAA 59.365 47.826 1.10 0.00 0.00 1.85
109 110 3.220110 CCTATGGACACTAGCGACCTAA 58.780 50.000 1.10 0.00 0.00 2.69
110 111 2.860009 CCTATGGACACTAGCGACCTA 58.140 52.381 1.10 0.00 0.00 3.08
111 112 1.693627 CCTATGGACACTAGCGACCT 58.306 55.000 1.10 0.00 0.00 3.85
112 113 0.032267 GCCTATGGACACTAGCGACC 59.968 60.000 0.00 0.00 0.00 4.79
114 115 0.750546 ACGCCTATGGACACTAGCGA 60.751 55.000 15.49 0.00 0.00 4.93
115 116 0.949397 TACGCCTATGGACACTAGCG 59.051 55.000 9.27 9.27 0.00 4.26
116 117 2.226912 CTCTACGCCTATGGACACTAGC 59.773 54.545 0.00 0.00 0.00 3.42
117 118 3.499157 GTCTCTACGCCTATGGACACTAG 59.501 52.174 0.00 0.00 0.00 2.57
118 119 3.474600 GTCTCTACGCCTATGGACACTA 58.525 50.000 0.00 0.00 0.00 2.74
119 120 2.299521 GTCTCTACGCCTATGGACACT 58.700 52.381 0.00 0.00 0.00 3.55
132 133 5.628606 GGGACGCTATTTTATTCGTCTCTAC 59.371 44.000 12.32 0.00 45.76 2.59
134 135 4.618965 GGGACGCTATTTTATTCGTCTCT 58.381 43.478 12.32 0.00 45.76 3.10
138 139 4.395959 TCTGGGACGCTATTTTATTCGT 57.604 40.909 0.00 0.00 37.92 3.85
139 140 5.728351 TTTCTGGGACGCTATTTTATTCG 57.272 39.130 0.00 0.00 0.00 3.34
140 141 6.472486 GCTTTTTCTGGGACGCTATTTTATTC 59.528 38.462 0.00 0.00 0.00 1.75
141 142 6.330278 GCTTTTTCTGGGACGCTATTTTATT 58.670 36.000 0.00 0.00 0.00 1.40
142 143 5.448632 CGCTTTTTCTGGGACGCTATTTTAT 60.449 40.000 0.00 0.00 0.00 1.40
144 145 3.365969 CGCTTTTTCTGGGACGCTATTTT 60.366 43.478 0.00 0.00 0.00 1.82
145 146 2.161609 CGCTTTTTCTGGGACGCTATTT 59.838 45.455 0.00 0.00 0.00 1.40
147 148 1.066430 TCGCTTTTTCTGGGACGCTAT 60.066 47.619 0.00 0.00 0.00 2.97
148 149 0.319083 TCGCTTTTTCTGGGACGCTA 59.681 50.000 0.00 0.00 0.00 4.26
149 150 1.070786 TCGCTTTTTCTGGGACGCT 59.929 52.632 0.00 0.00 0.00 5.07
150 151 1.206831 GTCGCTTTTTCTGGGACGC 59.793 57.895 0.00 0.00 37.57 5.19
151 152 0.882927 TGGTCGCTTTTTCTGGGACG 60.883 55.000 0.00 0.00 44.78 4.79
153 154 2.706890 GTATGGTCGCTTTTTCTGGGA 58.293 47.619 0.00 0.00 0.00 4.37
154 155 1.396996 CGTATGGTCGCTTTTTCTGGG 59.603 52.381 0.00 0.00 0.00 4.45
155 156 2.073816 ACGTATGGTCGCTTTTTCTGG 58.926 47.619 0.00 0.00 0.00 3.86
157 158 2.073816 CCACGTATGGTCGCTTTTTCT 58.926 47.619 0.00 0.00 41.64 2.52
158 159 2.520686 CCACGTATGGTCGCTTTTTC 57.479 50.000 0.00 0.00 41.64 2.29
182 183 3.942748 AGTTGGCTTCGTCACTACAAAAA 59.057 39.130 0.00 0.00 0.00 1.94
183 184 3.537580 AGTTGGCTTCGTCACTACAAAA 58.462 40.909 0.00 0.00 0.00 2.44
184 185 3.188159 AGTTGGCTTCGTCACTACAAA 57.812 42.857 0.00 0.00 0.00 2.83
186 187 3.508402 TGATAGTTGGCTTCGTCACTACA 59.492 43.478 0.00 0.00 0.00 2.74
187 188 4.106029 TGATAGTTGGCTTCGTCACTAC 57.894 45.455 0.00 0.00 0.00 2.73
188 189 4.794278 TTGATAGTTGGCTTCGTCACTA 57.206 40.909 0.00 0.00 0.00 2.74
189 190 3.678056 TTGATAGTTGGCTTCGTCACT 57.322 42.857 0.00 0.00 0.00 3.41
190 191 4.651994 CATTTGATAGTTGGCTTCGTCAC 58.348 43.478 0.00 0.00 0.00 3.67
192 193 3.126858 TGCATTTGATAGTTGGCTTCGTC 59.873 43.478 0.00 0.00 0.00 4.20
206 502 3.814283 GCTCCATTTGGTTTTGCATTTGA 59.186 39.130 0.00 0.00 36.34 2.69
256 552 2.822637 CCATGGGCGGGTCTAGCAT 61.823 63.158 2.85 0.00 36.08 3.79
264 560 1.338769 GCTACTAATACCATGGGCGGG 60.339 57.143 18.09 4.64 0.00 6.13
577 1240 7.305474 CACATACGGAGCAAAATCTTTAAAGT 58.695 34.615 14.74 0.22 0.00 2.66
583 1246 3.686016 ACCACATACGGAGCAAAATCTT 58.314 40.909 0.00 0.00 0.00 2.40
617 1280 7.221838 CGTTCCTAAATGCAAGTCTTTGAAAAA 59.778 33.333 0.00 0.00 36.36 1.94
619 1282 6.205784 CGTTCCTAAATGCAAGTCTTTGAAA 58.794 36.000 0.00 0.00 36.36 2.69
621 1284 4.215399 CCGTTCCTAAATGCAAGTCTTTGA 59.785 41.667 0.00 0.00 36.36 2.69
801 1467 8.175069 CACGCGCCATTTTATTTCATACTATAT 58.825 33.333 5.73 0.00 0.00 0.86
803 1469 6.370593 CACGCGCCATTTTATTTCATACTAT 58.629 36.000 5.73 0.00 0.00 2.12
804 1470 5.743467 CACGCGCCATTTTATTTCATACTA 58.257 37.500 5.73 0.00 0.00 1.82
915 1646 1.000955 CCGGTTGCCAGCTATAGGTAG 59.999 57.143 3.68 0.00 0.00 3.18
916 1647 1.045407 CCGGTTGCCAGCTATAGGTA 58.955 55.000 3.68 0.00 0.00 3.08
917 1648 1.830145 CCGGTTGCCAGCTATAGGT 59.170 57.895 0.00 0.00 0.00 3.08
1008 1760 4.974438 AGGCGGGGGAAGGTCACA 62.974 66.667 0.00 0.00 0.00 3.58
1018 1770 2.427753 GGATCTAAGCAGGCGGGG 59.572 66.667 0.00 0.00 0.00 5.73
1025 1777 0.621571 AGCTGGGGTGGATCTAAGCA 60.622 55.000 3.68 0.00 33.08 3.91
1073 1827 2.273776 GGGCTGCTTTCTCCCTCC 59.726 66.667 0.00 0.00 37.08 4.30
1347 2118 6.998673 AGTTAGCTTGATGTACCTTCTTTTGT 59.001 34.615 0.00 0.00 0.00 2.83
1364 2135 2.028930 ACTAGTGCTTCGCAGTTAGCTT 60.029 45.455 0.00 0.00 39.37 3.74
1656 2558 2.363147 GGAGGGTCGTGCTCCTCT 60.363 66.667 8.95 0.00 46.51 3.69
1929 2837 2.243221 CCAGGAGGAGGAACAATGGATT 59.757 50.000 0.00 0.00 36.89 3.01
2028 2939 5.062934 TGCTATCGGTACAAAAATGTCTTCG 59.937 40.000 0.00 0.00 0.00 3.79
2197 3110 5.108385 AGAACACTAACAAGAAAATGCCG 57.892 39.130 0.00 0.00 0.00 5.69
2199 3112 5.691754 CCCAAGAACACTAACAAGAAAATGC 59.308 40.000 0.00 0.00 0.00 3.56
2295 3217 1.154225 GCACGAATTCAACCCGCAG 60.154 57.895 6.22 0.00 0.00 5.18
2302 3224 1.207339 CTGCAGCGCACGAATTCAA 59.793 52.632 11.47 0.00 33.79 2.69
2371 3298 4.630894 TGAATGTCGTTGCAAGTTTCTT 57.369 36.364 0.00 0.00 0.00 2.52
2470 3410 4.292145 TGCACGGCCCCCAAATCA 62.292 61.111 0.00 0.00 0.00 2.57
2500 3440 3.201266 ACCCATCGATTTTGGTAGCCTAA 59.799 43.478 8.83 0.00 31.99 2.69
2557 3499 0.528470 GACTCCAACGAGGACTGAGG 59.472 60.000 0.00 0.00 43.07 3.86
2712 3656 0.258194 GGGAGTAGGAGGAGGTCGAA 59.742 60.000 0.00 0.00 0.00 3.71
2716 3660 1.924352 CGAGGGAGTAGGAGGAGGT 59.076 63.158 0.00 0.00 0.00 3.85
2737 3681 1.525535 GAGCCATCATGGAGCGCTT 60.526 57.895 13.26 0.00 40.96 4.68
2944 3899 4.148825 GAGCTCGCCATCCACCGT 62.149 66.667 0.00 0.00 0.00 4.83
2968 3923 2.627004 CGCGAGCTCGACGAGTAT 59.373 61.111 38.74 14.67 43.02 2.12


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.