Multiple sequence alignment - TraesCS4A01G240500

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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 TraesCS4A01G240500 chr4A 100.000 3326 0 0 1 3326 550081585 550084910 0.000000e+00 6143
1 TraesCS4A01G240500 chr4D 92.892 2884 135 26 1 2827 47661398 47658528 0.000000e+00 4126
2 TraesCS4A01G240500 chr4D 90.435 345 19 8 2989 3326 47657424 47657087 3.050000e-120 442
3 TraesCS4A01G240500 chr4B 93.847 2129 93 17 710 2825 69891677 69889574 0.000000e+00 3171
4 TraesCS4A01G240500 chr4B 89.459 351 22 8 2986 3325 69889575 69889229 2.370000e-116 429
5 TraesCS4A01G240500 chr4B 88.031 259 17 7 434 691 69893785 69893540 9.020000e-76 294
6 TraesCS4A01G240500 chr2A 97.041 169 5 0 2821 2989 745301946 745301778 5.430000e-73 285
7 TraesCS4A01G240500 chr2A 97.576 165 4 0 2824 2988 319037619 319037455 1.950000e-72 283
8 TraesCS4A01G240500 chr3D 95.480 177 7 1 2815 2990 79558532 79558708 7.030000e-72 281
9 TraesCS4A01G240500 chr3D 78.448 348 44 21 2992 3325 538853365 538853695 7.280000e-47 198
10 TraesCS4A01G240500 chr5B 94.505 182 7 3 2817 2995 162720171 162719990 9.090000e-71 278
11 TraesCS4A01G240500 chr6D 94.915 177 7 2 2814 2988 406391534 406391358 3.270000e-70 276
12 TraesCS4A01G240500 chr3A 94.886 176 7 2 2814 2987 727378386 727378561 1.180000e-69 274
13 TraesCS4A01G240500 chr1B 94.886 176 8 1 2814 2988 519817797 519817972 1.180000e-69 274
14 TraesCS4A01G240500 chr7A 93.478 184 9 3 2815 2995 320981163 320981346 1.520000e-68 270
15 TraesCS4A01G240500 chr6B 92.063 189 14 1 2819 3007 624802226 624802039 7.080000e-67 265


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 TraesCS4A01G240500 chr4A 550081585 550084910 3325 False 6143 6143 100.000000 1 3326 1 chr4A.!!$F1 3325
1 TraesCS4A01G240500 chr4D 47657087 47661398 4311 True 2284 4126 91.663500 1 3326 2 chr4D.!!$R1 3325
2 TraesCS4A01G240500 chr4B 69889229 69893785 4556 True 1298 3171 90.445667 434 3325 3 chr4B.!!$R1 2891

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
347 367 0.038159 CCTGACTCGTGGAGTTGTCC 60.038 60.0 0.0 0.0 43.53 4.02 F
992 2890 0.179089 CCTTGCTGACCTCCATCTCG 60.179 60.0 0.0 0.0 0.00 4.04 F
1393 3291 0.729690 GCACGGGAAGAAGCAGATTC 59.270 55.0 0.0 0.0 38.28 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 3251 0.107831 TGCAGTTGAGGTACCGCTTT 59.892 50.000 17.09 0.0 0.00 3.51 R
1941 3839 1.021202 TGAACTCAAGGTTGCCAACG 58.979 50.000 0.74 0.0 38.41 4.10 R
2420 4326 1.269102 CCCCGATTATATAGGAGCGCG 60.269 57.143 0.00 0.0 0.00 6.86 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
92 93 7.325821 CACTATCTAAGCAAGAGACATTCGATC 59.674 40.741 0.00 0.00 37.74 3.69
130 131 3.317993 ACAAGGAAAACAATCAACGGAGG 59.682 43.478 0.00 0.00 0.00 4.30
149 169 6.490721 ACGGAGGATAGGTAAATAGAGTTCTG 59.509 42.308 0.00 0.00 0.00 3.02
173 193 0.249699 TGTACGCCCTAATGCATCGG 60.250 55.000 0.00 3.61 0.00 4.18
206 226 8.545472 ACCTTCTATAACCAGTGCTACATAAAA 58.455 33.333 0.00 0.00 0.00 1.52
207 227 9.561069 CCTTCTATAACCAGTGCTACATAAAAT 57.439 33.333 0.00 0.00 0.00 1.82
209 229 8.902540 TCTATAACCAGTGCTACATAAAATGG 57.097 34.615 0.00 0.00 33.60 3.16
210 230 8.491134 TCTATAACCAGTGCTACATAAAATGGT 58.509 33.333 0.00 0.00 41.19 3.55
211 231 9.772973 CTATAACCAGTGCTACATAAAATGGTA 57.227 33.333 0.00 0.00 38.58 3.25
213 233 5.190677 ACCAGTGCTACATAAAATGGTACC 58.809 41.667 4.43 4.43 37.79 3.34
214 234 5.189928 CCAGTGCTACATAAAATGGTACCA 58.810 41.667 18.99 18.99 33.60 3.25
319 339 5.072040 TCACGAGCTTCATCATAACTTGA 57.928 39.130 0.00 0.00 39.12 3.02
330 350 3.698289 TCATAACTTGACGAGTCTCCCT 58.302 45.455 4.78 0.00 37.72 4.20
343 363 0.112606 TCTCCCTGACTCGTGGAGTT 59.887 55.000 11.52 0.00 43.53 3.01
347 367 0.038159 CCTGACTCGTGGAGTTGTCC 60.038 60.000 0.00 0.00 43.53 4.02
352 372 3.018149 GACTCGTGGAGTTGTCCTCTAT 58.982 50.000 0.00 0.00 43.53 1.98
356 376 4.533815 TCGTGGAGTTGTCCTCTATACAT 58.466 43.478 0.00 0.00 44.30 2.29
379 399 8.758829 ACATTGTAATCCTCTGTATTCTACACA 58.241 33.333 0.00 0.00 34.46 3.72
380 400 9.770097 CATTGTAATCCTCTGTATTCTACACAT 57.230 33.333 0.00 0.00 34.46 3.21
381 401 9.770097 ATTGTAATCCTCTGTATTCTACACATG 57.230 33.333 0.00 0.00 34.46 3.21
382 402 8.306313 TGTAATCCTCTGTATTCTACACATGT 57.694 34.615 0.00 0.00 34.46 3.21
402 423 5.878406 TGTTTTATCTTTTTGGAGGCCAA 57.122 34.783 5.01 0.00 42.29 4.52
417 438 4.562963 GGAGGCCAAAACCTAGGTATATCG 60.563 50.000 16.67 3.21 41.32 2.92
425 446 8.179615 CCAAAACCTAGGTATATCGTGTTTTTC 58.820 37.037 16.67 0.00 33.56 2.29
432 453 9.577110 CTAGGTATATCGTGTTTTTCTGTGTTA 57.423 33.333 0.00 0.00 0.00 2.41
466 487 2.686915 CCCTGATTTCCTCACTTGATGC 59.313 50.000 0.00 0.00 0.00 3.91
469 490 1.672881 GATTTCCTCACTTGATGCCCG 59.327 52.381 0.00 0.00 0.00 6.13
482 503 2.070783 GATGCCCGTTCGACTACAAAA 58.929 47.619 0.00 0.00 0.00 2.44
489 510 3.143279 CGTTCGACTACAAAATTCACGC 58.857 45.455 0.00 0.00 0.00 5.34
503 524 6.893958 AAATTCACGCAATGTCTCTAGTAG 57.106 37.500 0.00 0.00 0.00 2.57
504 525 5.584253 ATTCACGCAATGTCTCTAGTAGT 57.416 39.130 0.00 0.00 0.00 2.73
506 527 5.481200 TCACGCAATGTCTCTAGTAGTAC 57.519 43.478 0.00 0.00 0.00 2.73
508 529 5.413523 TCACGCAATGTCTCTAGTAGTACAA 59.586 40.000 2.52 0.00 0.00 2.41
509 530 6.095021 TCACGCAATGTCTCTAGTAGTACAAT 59.905 38.462 2.52 2.51 0.00 2.71
510 531 7.281549 TCACGCAATGTCTCTAGTAGTACAATA 59.718 37.037 2.52 0.00 0.00 1.90
511 532 8.076781 CACGCAATGTCTCTAGTAGTACAATAT 58.923 37.037 2.52 1.44 0.00 1.28
543 565 9.833917 TCACCCAACAATATAAAACGTCATATA 57.166 29.630 0.00 0.00 0.00 0.86
632 654 3.251487 CCGTGTTAACCTGTTAAGGGTTG 59.749 47.826 17.97 5.71 42.81 3.77
645 687 3.297134 AAGGGTTGTGACTTGTGACAT 57.703 42.857 0.00 0.00 0.00 3.06
649 691 4.072131 GGGTTGTGACTTGTGACATACAT 58.928 43.478 0.00 0.00 39.48 2.29
668 712 5.959652 ACATACTTTGTTTTTGTTTCGGC 57.040 34.783 0.00 0.00 33.74 5.54
685 729 1.672854 GGCTAAAATGGAACCGGGCC 61.673 60.000 6.32 7.66 0.00 5.80
810 2700 3.518992 TTTTCCTCCCGGTCAAATCTT 57.481 42.857 0.00 0.00 0.00 2.40
850 2740 1.374947 CCCACATCCCACGTCAAGT 59.625 57.895 0.00 0.00 0.00 3.16
870 2760 4.557205 AGTTACGGACAACAGATGAGAAC 58.443 43.478 0.00 0.00 0.00 3.01
906 2796 4.562082 GGCGGCTACATATACATACACAA 58.438 43.478 0.00 0.00 0.00 3.33
953 2851 3.357079 GGTCACTGGCTGCAACCG 61.357 66.667 0.85 0.00 0.00 4.44
992 2890 0.179089 CCTTGCTGACCTCCATCTCG 60.179 60.000 0.00 0.00 0.00 4.04
1119 3017 3.730761 CACAAGGCAGCAGCGACC 61.731 66.667 0.00 0.00 43.41 4.79
1393 3291 0.729690 GCACGGGAAGAAGCAGATTC 59.270 55.000 0.00 0.00 38.28 2.52
1449 3347 4.966965 AGTGACCAAGTACATCTACTCG 57.033 45.455 0.00 0.00 31.42 4.18
1458 3356 0.757188 ACATCTACTCGGCCCCTGAG 60.757 60.000 0.00 0.00 39.40 3.35
1497 3395 4.577677 TGCCGTCCCTGCAGCAAA 62.578 61.111 8.66 0.00 34.05 3.68
1533 3431 4.796231 GTGGCCGTCGCGTCAGAT 62.796 66.667 5.77 0.00 35.02 2.90
1535 3433 2.103538 GGCCGTCGCGTCAGATAA 59.896 61.111 5.77 0.00 35.02 1.75
1715 3613 1.162698 CTCTACACCTCCGACAACGA 58.837 55.000 0.00 0.00 42.66 3.85
1721 3619 3.103911 CTCCGACAACGACACCGC 61.104 66.667 0.00 0.00 42.66 5.68
1920 3818 1.378382 TGCAATCCCCATCACGGTG 60.378 57.895 0.56 0.56 0.00 4.94
2041 3939 2.350895 CCAAGATGCCCGGTGTCA 59.649 61.111 0.00 0.00 0.00 3.58
2055 3953 2.338500 GGTGTCATCTTCAACGAGACC 58.662 52.381 0.00 0.00 36.13 3.85
2190 4088 6.358178 ACACGATCTGGAGGTATATATCGAT 58.642 40.000 2.16 2.16 38.72 3.59
2249 4147 0.685131 TCCTCGGCGAATAGGGTTCA 60.685 55.000 12.13 0.00 33.40 3.18
2250 4148 0.249489 CCTCGGCGAATAGGGTTCAG 60.249 60.000 12.13 0.00 0.00 3.02
2264 4162 4.899502 AGGGTTCAGTCTATGTTTGAGTG 58.100 43.478 0.00 0.00 36.50 3.51
2330 4228 1.595489 CGCGCTAGGAATTTGATGTGC 60.595 52.381 5.56 0.00 0.00 4.57
2420 4326 3.852286 TGAAATTGTGAATCATGCAGCC 58.148 40.909 0.00 0.00 0.00 4.85
2425 4331 3.580193 GAATCATGCAGCCGCGCT 61.580 61.111 5.56 0.00 42.97 5.92
2540 4451 9.684448 GACGGGACATATGAAGATATATACATG 57.316 37.037 10.38 0.00 0.00 3.21
2648 4560 8.425237 TGTATGTACCAATATTAGGATTCCGA 57.575 34.615 9.93 0.00 0.00 4.55
2785 4697 8.854979 TGATTTTAATTCGCATTTACCATCAG 57.145 30.769 0.00 0.00 0.00 2.90
2828 4740 9.987272 TGTAGAAAAGGTTTTAAGTACTACTCC 57.013 33.333 0.00 0.00 30.29 3.85
2830 4742 8.272659 AGAAAAGGTTTTAAGTACTACTCCCT 57.727 34.615 0.00 0.00 0.00 4.20
2832 4744 6.617782 AAGGTTTTAAGTACTACTCCCTCC 57.382 41.667 0.00 0.00 0.00 4.30
2833 4745 4.708909 AGGTTTTAAGTACTACTCCCTCCG 59.291 45.833 0.00 0.00 0.00 4.63
2834 4746 4.464244 GGTTTTAAGTACTACTCCCTCCGT 59.536 45.833 0.00 0.00 0.00 4.69
2836 4748 5.904362 TTTAAGTACTACTCCCTCCGTTC 57.096 43.478 0.00 0.00 0.00 3.95
2838 4750 1.637553 AGTACTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.00 0.00 3.53
2839 4751 2.042162 AGTACTACTCCCTCCGTTCCAA 59.958 50.000 0.00 0.00 0.00 3.53
2840 4752 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2841 4753 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
2842 4754 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2843 4755 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2844 4756 4.720273 ACTACTCCCTCCGTTCCAAAATAT 59.280 41.667 0.00 0.00 0.00 1.28
2848 4760 4.668636 TCCCTCCGTTCCAAAATATTTGT 58.331 39.130 0.39 0.00 0.00 2.83
2849 4761 4.703093 TCCCTCCGTTCCAAAATATTTGTC 59.297 41.667 0.39 0.00 0.00 3.18
2850 4762 4.705023 CCCTCCGTTCCAAAATATTTGTCT 59.295 41.667 0.39 0.00 0.00 3.41
2851 4763 5.185056 CCCTCCGTTCCAAAATATTTGTCTT 59.815 40.000 0.39 0.00 0.00 3.01
2852 4764 6.295067 CCCTCCGTTCCAAAATATTTGTCTTT 60.295 38.462 0.39 0.00 0.00 2.52
2853 4765 7.151976 CCTCCGTTCCAAAATATTTGTCTTTT 58.848 34.615 0.39 0.00 0.00 2.27
2854 4766 7.655732 CCTCCGTTCCAAAATATTTGTCTTTTT 59.344 33.333 0.39 0.00 0.00 1.94
2857 4769 9.471084 CCGTTCCAAAATATTTGTCTTTTTAGT 57.529 29.630 0.39 0.00 0.00 2.24
2870 4782 7.945033 TGTCTTTTTAGTGATTTCAAATGGC 57.055 32.000 0.00 0.00 0.00 4.40
2872 4784 8.855110 TGTCTTTTTAGTGATTTCAAATGGCTA 58.145 29.630 0.00 0.00 0.00 3.93
2874 4786 8.303876 TCTTTTTAGTGATTTCAAATGGCTACC 58.696 33.333 0.00 0.00 0.00 3.18
2875 4787 7.531857 TTTTAGTGATTTCAAATGGCTACCA 57.468 32.000 0.00 0.00 38.19 3.25
2877 4789 4.406456 AGTGATTTCAAATGGCTACCACA 58.594 39.130 0.00 0.00 35.80 4.17
2878 4790 5.018809 AGTGATTTCAAATGGCTACCACAT 58.981 37.500 0.00 0.00 35.80 3.21
2880 4792 6.095440 AGTGATTTCAAATGGCTACCACATAC 59.905 38.462 0.00 0.00 35.80 2.39
2881 4793 4.955925 TTTCAAATGGCTACCACATACG 57.044 40.909 0.00 0.00 35.80 3.06
2882 4794 2.912771 TCAAATGGCTACCACATACGG 58.087 47.619 0.00 0.00 35.80 4.02
2884 4796 3.135712 TCAAATGGCTACCACATACGGAT 59.864 43.478 0.00 0.00 35.80 4.18
2885 4797 2.839486 ATGGCTACCACATACGGATG 57.161 50.000 5.94 5.94 35.80 3.51
2887 4799 2.668625 TGGCTACCACATACGGATGTA 58.331 47.619 14.23 0.00 44.82 2.29
2888 4800 3.236047 TGGCTACCACATACGGATGTAT 58.764 45.455 14.23 7.46 44.82 2.29
2889 4801 4.409187 TGGCTACCACATACGGATGTATA 58.591 43.478 14.23 8.27 44.82 1.47
2892 4804 6.320418 TGGCTACCACATACGGATGTATATAG 59.680 42.308 14.23 15.27 44.82 1.31
2893 4805 6.544931 GGCTACCACATACGGATGTATATAGA 59.455 42.308 14.23 0.00 44.82 1.98
2894 4806 7.416022 GCTACCACATACGGATGTATATAGAC 58.584 42.308 14.23 7.98 44.82 2.59
2895 4807 7.066645 GCTACCACATACGGATGTATATAGACA 59.933 40.741 14.23 2.07 44.82 3.41
2896 4808 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2898 4810 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2927 4839 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2928 4840 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2929 4841 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2930 4842 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2932 4844 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2933 4845 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2934 4846 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2935 4847 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2936 4848 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2937 4849 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2939 4851 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2940 4852 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2941 4853 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2942 4854 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2943 4855 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2945 4857 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2947 4859 5.047872 TGCTCCGTATGTAGTCACTTGTTAA 60.048 40.000 0.00 0.00 0.00 2.01
2950 4862 7.064253 GCTCCGTATGTAGTCACTTGTTAAAAT 59.936 37.037 0.00 0.00 0.00 1.82
2952 4864 8.308931 TCCGTATGTAGTCACTTGTTAAAATCT 58.691 33.333 0.00 0.00 0.00 2.40
2953 4865 8.592998 CCGTATGTAGTCACTTGTTAAAATCTC 58.407 37.037 0.00 0.00 0.00 2.75
2954 4866 9.355215 CGTATGTAGTCACTTGTTAAAATCTCT 57.645 33.333 0.00 0.00 0.00 3.10
2982 4894 9.961265 GAAAAATAAATATTTAGGAACGGAGGG 57.039 33.333 13.15 0.00 35.00 4.30
2983 4895 9.703677 AAAAATAAATATTTAGGAACGGAGGGA 57.296 29.630 13.15 0.00 35.00 4.20
2984 4896 8.919777 AAATAAATATTTAGGAACGGAGGGAG 57.080 34.615 13.15 0.00 34.36 4.30
2986 4898 8.731591 ATAAATATTTAGGAACGGAGGGAGTA 57.268 34.615 13.15 0.00 0.00 2.59
3011 5865 4.944048 ACAAAACAGCTCAAATGGTTACC 58.056 39.130 0.00 0.00 0.00 2.85
3023 5877 6.754193 TCAAATGGTTACCTGAATTTGGTTC 58.246 36.000 19.04 4.48 39.42 3.62
3052 5906 5.359860 GGTATACAAAGTTGGAGATTTGGGG 59.640 44.000 5.01 0.00 40.05 4.96
3069 5923 1.814394 GGGGGTCAATGTTACGAAACC 59.186 52.381 0.00 0.00 34.49 3.27
3074 5928 5.180271 GGGTCAATGTTACGAAACCTCATA 58.820 41.667 0.00 0.00 34.49 2.15
3109 5963 9.703892 TCCATTTTGTGAACAACCTATTATTTG 57.296 29.630 0.00 0.00 35.28 2.32
3169 6030 6.435904 GCATATATTAGGGTTACCATGCCAAA 59.564 38.462 2.98 0.00 40.13 3.28
3175 6036 7.741554 TTAGGGTTACCATGCCAAAATTAAT 57.258 32.000 2.98 0.00 40.13 1.40
3179 6040 7.609918 AGGGTTACCATGCCAAAATTAATTTTC 59.390 33.333 20.71 12.66 37.25 2.29
3261 6128 1.134371 GGGTCTACCATGGAACTCAGC 60.134 57.143 21.47 6.66 39.85 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.792757 TTGGAGGGCACATTGGAGCT 61.793 55.000 0.00 0.00 0.00 4.09
36 37 6.840527 TCTTCATGGGTTGATATTGCTATCA 58.159 36.000 0.00 0.00 41.55 2.15
92 93 2.226437 CCTTGTCCCTTCATGTTGTTCG 59.774 50.000 0.00 0.00 0.00 3.95
130 131 7.988028 ACAAAGGCAGAACTCTATTTACCTATC 59.012 37.037 0.00 0.00 0.00 2.08
149 169 0.380733 GCATTAGGGCGTACAAAGGC 59.619 55.000 0.00 0.00 35.74 4.35
173 193 4.576463 CACTGGTTATAGAAGGTTCCATGC 59.424 45.833 0.00 0.00 0.00 4.06
206 226 2.849943 TCTACATTGCCCTTGGTACCAT 59.150 45.455 17.17 0.00 0.00 3.55
207 227 2.270858 TCTACATTGCCCTTGGTACCA 58.729 47.619 11.60 11.60 0.00 3.25
209 229 3.279434 CCTTCTACATTGCCCTTGGTAC 58.721 50.000 0.00 0.00 0.00 3.34
210 230 2.241176 CCCTTCTACATTGCCCTTGGTA 59.759 50.000 0.00 0.00 0.00 3.25
211 231 1.005924 CCCTTCTACATTGCCCTTGGT 59.994 52.381 0.00 0.00 0.00 3.67
213 233 2.755103 GTTCCCTTCTACATTGCCCTTG 59.245 50.000 0.00 0.00 0.00 3.61
214 234 2.291605 GGTTCCCTTCTACATTGCCCTT 60.292 50.000 0.00 0.00 0.00 3.95
330 350 0.959553 GAGGACAACTCCACGAGTCA 59.040 55.000 0.00 0.00 42.59 3.41
343 363 7.785028 ACAGAGGATTACAATGTATAGAGGACA 59.215 37.037 0.00 0.00 0.00 4.02
374 394 7.375053 GCCTCCAAAAAGATAAAACATGTGTA 58.625 34.615 0.00 0.00 0.00 2.90
375 395 6.223120 GCCTCCAAAAAGATAAAACATGTGT 58.777 36.000 0.00 0.00 0.00 3.72
376 396 5.639082 GGCCTCCAAAAAGATAAAACATGTG 59.361 40.000 0.00 0.00 0.00 3.21
377 397 5.306678 TGGCCTCCAAAAAGATAAAACATGT 59.693 36.000 3.32 0.00 0.00 3.21
378 398 5.792741 TGGCCTCCAAAAAGATAAAACATG 58.207 37.500 3.32 0.00 0.00 3.21
379 399 6.432403 TTGGCCTCCAAAAAGATAAAACAT 57.568 33.333 3.32 0.00 40.92 2.71
380 400 5.878406 TTGGCCTCCAAAAAGATAAAACA 57.122 34.783 3.32 0.00 40.92 2.83
402 423 8.098912 ACAGAAAAACACGATATACCTAGGTTT 58.901 33.333 22.11 15.40 0.00 3.27
417 438 7.753132 TCTTGAACACATAACACAGAAAAACAC 59.247 33.333 0.00 0.00 0.00 3.32
425 446 5.122869 CAGGGATCTTGAACACATAACACAG 59.877 44.000 0.00 0.00 0.00 3.66
432 453 4.952335 GGAAATCAGGGATCTTGAACACAT 59.048 41.667 4.89 0.00 0.00 3.21
466 487 3.422603 CGTGAATTTTGTAGTCGAACGGG 60.423 47.826 0.00 0.00 0.00 5.28
469 490 4.123276 TGCGTGAATTTTGTAGTCGAAC 57.877 40.909 0.00 0.00 0.00 3.95
482 503 5.584253 ACTACTAGAGACATTGCGTGAAT 57.416 39.130 0.00 0.00 0.00 2.57
511 532 9.233649 ACGTTTTATATTGTTGGGTGATCTTTA 57.766 29.630 0.00 0.00 0.00 1.85
515 536 7.079182 TGACGTTTTATATTGTTGGGTGATC 57.921 36.000 0.00 0.00 0.00 2.92
543 565 9.560860 AAGAAATCACCCCCTCTAATTTAAAAT 57.439 29.630 0.00 0.00 0.00 1.82
544 566 8.966155 AAGAAATCACCCCCTCTAATTTAAAA 57.034 30.769 0.00 0.00 0.00 1.52
545 567 9.695155 CTAAGAAATCACCCCCTCTAATTTAAA 57.305 33.333 0.00 0.00 0.00 1.52
546 568 9.064602 TCTAAGAAATCACCCCCTCTAATTTAA 57.935 33.333 0.00 0.00 0.00 1.52
609 631 1.808343 CCCTTAACAGGTTAACACGGC 59.192 52.381 8.10 0.00 38.79 5.68
632 654 7.421530 ACAAAGTATGTATGTCACAAGTCAC 57.578 36.000 0.00 0.00 41.63 3.67
645 687 6.797454 AGCCGAAACAAAAACAAAGTATGTA 58.203 32.000 0.00 0.00 42.99 2.29
649 691 8.596380 CATTTTAGCCGAAACAAAAACAAAGTA 58.404 29.630 0.00 0.00 0.00 2.24
668 712 1.551452 TTGGCCCGGTTCCATTTTAG 58.449 50.000 12.77 0.00 32.92 1.85
828 2718 3.682292 GACGTGGGATGTGGGGAGC 62.682 68.421 0.00 0.00 0.00 4.70
850 2740 3.322541 TGGTTCTCATCTGTTGTCCGTAA 59.677 43.478 0.00 0.00 0.00 3.18
924 2822 4.813161 CAGCCAGTGACCAATAATCAGTAG 59.187 45.833 0.00 0.00 0.00 2.57
956 2854 3.420893 CAAGGGAATGGTTTGCTGACTA 58.579 45.455 0.00 0.00 0.00 2.59
1140 3038 2.144738 AACAGCAGTGGGTACGGGT 61.145 57.895 0.00 0.00 32.98 5.28
1353 3251 0.107831 TGCAGTTGAGGTACCGCTTT 59.892 50.000 17.09 0.00 0.00 3.51
1458 3356 2.362889 CCCATTGGCAGGGTCACC 60.363 66.667 3.65 0.00 41.61 4.02
1715 3613 2.914908 GCGGTGAATTTGGCGGTGT 61.915 57.895 0.00 0.00 0.00 4.16
1721 3619 2.360600 TCCCGGCGGTGAATTTGG 60.361 61.111 26.32 6.71 0.00 3.28
1941 3839 1.021202 TGAACTCAAGGTTGCCAACG 58.979 50.000 0.74 0.00 38.41 4.10
1980 3878 2.642254 CCGGAGTACCTTGACGCCA 61.642 63.158 0.00 0.00 39.09 5.69
2054 3952 1.623542 CCCTCCCAGAACCCTAACGG 61.624 65.000 0.00 0.00 37.81 4.44
2055 3953 1.905512 CCCTCCCAGAACCCTAACG 59.094 63.158 0.00 0.00 0.00 3.18
2057 3955 1.993391 CGCCCTCCCAGAACCCTAA 60.993 63.158 0.00 0.00 0.00 2.69
2160 4058 1.819288 ACCTCCAGATCGTGTACACAG 59.181 52.381 24.98 17.08 0.00 3.66
2190 4088 4.078571 TCCTTAGGGATCTTTAGGAGCTGA 60.079 45.833 0.00 0.00 36.57 4.26
2237 4135 6.338146 TCAAACATAGACTGAACCCTATTCG 58.662 40.000 0.00 0.00 0.00 3.34
2249 4147 3.834813 TCTCCAGCACTCAAACATAGACT 59.165 43.478 0.00 0.00 0.00 3.24
2250 4148 4.193826 TCTCCAGCACTCAAACATAGAC 57.806 45.455 0.00 0.00 0.00 2.59
2264 4162 1.440476 GCCATTTGCCATCTCCAGC 59.560 57.895 0.00 0.00 0.00 4.85
2330 4228 7.703298 ATCAAATTATGCATTGACAAATCGG 57.297 32.000 3.54 0.00 38.29 4.18
2420 4326 1.269102 CCCCGATTATATAGGAGCGCG 60.269 57.143 0.00 0.00 0.00 6.86
2425 4331 6.981737 TCTCTTCATCCCCGATTATATAGGA 58.018 40.000 0.00 0.00 0.00 2.94
2512 4423 4.720649 ATATCTTCATATGTCCCGTCGG 57.279 45.455 3.60 3.60 0.00 4.79
2645 4557 7.894376 TTAGTAAACTTACCAATGAGTTCGG 57.106 36.000 0.00 0.00 33.72 4.30
2755 4667 9.814899 TGGTAAATGCGAATTAAAATCATCATT 57.185 25.926 0.00 0.00 0.00 2.57
2756 4668 9.985730 ATGGTAAATGCGAATTAAAATCATCAT 57.014 25.926 0.00 0.00 0.00 2.45
2827 4739 4.705023 AGACAAATATTTTGGAACGGAGGG 59.295 41.667 0.00 0.00 0.00 4.30
2828 4740 5.897377 AGACAAATATTTTGGAACGGAGG 57.103 39.130 0.00 0.00 0.00 4.30
2830 4742 9.685828 CTAAAAAGACAAATATTTTGGAACGGA 57.314 29.630 0.00 0.00 29.76 4.69
2844 4756 8.825745 GCCATTTGAAATCACTAAAAAGACAAA 58.174 29.630 0.00 0.00 0.00 2.83
2848 4760 8.303876 GGTAGCCATTTGAAATCACTAAAAAGA 58.696 33.333 0.00 0.00 0.00 2.52
2849 4761 8.087750 TGGTAGCCATTTGAAATCACTAAAAAG 58.912 33.333 0.00 0.00 0.00 2.27
2850 4762 7.870445 GTGGTAGCCATTTGAAATCACTAAAAA 59.130 33.333 0.00 0.00 35.28 1.94
2851 4763 7.014711 TGTGGTAGCCATTTGAAATCACTAAAA 59.985 33.333 6.69 0.00 35.28 1.52
2852 4764 6.491745 TGTGGTAGCCATTTGAAATCACTAAA 59.508 34.615 6.69 0.00 35.28 1.85
2853 4765 6.007076 TGTGGTAGCCATTTGAAATCACTAA 58.993 36.000 6.69 0.00 35.28 2.24
2854 4766 5.565509 TGTGGTAGCCATTTGAAATCACTA 58.434 37.500 6.69 1.15 35.28 2.74
2857 4769 5.065859 CGTATGTGGTAGCCATTTGAAATCA 59.934 40.000 2.01 0.00 35.28 2.57
2858 4770 5.505654 CCGTATGTGGTAGCCATTTGAAATC 60.506 44.000 2.01 0.00 35.28 2.17
2859 4771 4.338118 CCGTATGTGGTAGCCATTTGAAAT 59.662 41.667 2.01 0.00 35.28 2.17
2861 4773 3.055021 TCCGTATGTGGTAGCCATTTGAA 60.055 43.478 2.01 0.00 35.28 2.69
2862 4774 2.502130 TCCGTATGTGGTAGCCATTTGA 59.498 45.455 2.01 0.00 35.28 2.69
2863 4775 2.912771 TCCGTATGTGGTAGCCATTTG 58.087 47.619 2.01 0.00 35.28 2.32
2864 4776 3.118038 ACATCCGTATGTGGTAGCCATTT 60.118 43.478 0.00 0.00 44.79 2.32
2865 4777 2.438021 ACATCCGTATGTGGTAGCCATT 59.562 45.455 0.00 0.00 44.79 3.16
2869 4781 7.066645 TGTCTATATACATCCGTATGTGGTAGC 59.933 40.741 3.56 2.02 45.99 3.58
2870 4782 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
2872 4784 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2905 4817 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2907 4819 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2909 4821 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2911 4823 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2912 4824 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2913 4825 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2916 4828 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2917 4829 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2918 4830 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2920 4832 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2921 4833 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2922 4834 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2924 4836 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2926 4838 8.308931 AGATTTTAACAAGTGACTACATACGGA 58.691 33.333 0.00 0.00 0.00 4.69
2927 4839 8.475331 AGATTTTAACAAGTGACTACATACGG 57.525 34.615 0.00 0.00 0.00 4.02
2928 4840 9.355215 AGAGATTTTAACAAGTGACTACATACG 57.645 33.333 0.00 0.00 0.00 3.06
2956 4868 9.961265 CCCTCCGTTCCTAAATATTTATTTTTC 57.039 33.333 8.34 0.00 37.16 2.29
2958 4870 9.350951 CTCCCTCCGTTCCTAAATATTTATTTT 57.649 33.333 8.34 0.00 37.16 1.82
2960 4872 8.042286 ACTCCCTCCGTTCCTAAATATTTATT 57.958 34.615 8.34 0.00 0.00 1.40
2964 4876 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2966 4878 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2967 4879 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2968 4880 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2969 4881 3.266772 TGTACTACTCCCTCCGTTCCTAA 59.733 47.826 0.00 0.00 0.00 2.69
2971 4883 1.637553 TGTACTACTCCCTCCGTTCCT 59.362 52.381 0.00 0.00 0.00 3.36
2972 4884 2.134789 TGTACTACTCCCTCCGTTCC 57.865 55.000 0.00 0.00 0.00 3.62
2973 4885 4.240888 GTTTTGTACTACTCCCTCCGTTC 58.759 47.826 0.00 0.00 0.00 3.95
2974 4886 3.642848 TGTTTTGTACTACTCCCTCCGTT 59.357 43.478 0.00 0.00 0.00 4.44
2975 4887 3.233507 TGTTTTGTACTACTCCCTCCGT 58.766 45.455 0.00 0.00 0.00 4.69
2976 4888 3.846360 CTGTTTTGTACTACTCCCTCCG 58.154 50.000 0.00 0.00 0.00 4.63
2978 4890 4.021368 TGAGCTGTTTTGTACTACTCCCTC 60.021 45.833 0.00 0.00 32.02 4.30
2979 4891 3.901844 TGAGCTGTTTTGTACTACTCCCT 59.098 43.478 0.00 0.00 32.02 4.20
2981 4893 6.348540 CCATTTGAGCTGTTTTGTACTACTCC 60.349 42.308 0.00 0.00 32.02 3.85
2982 4894 6.204882 ACCATTTGAGCTGTTTTGTACTACTC 59.795 38.462 0.00 0.00 32.99 2.59
2983 4895 6.062095 ACCATTTGAGCTGTTTTGTACTACT 58.938 36.000 0.00 0.00 0.00 2.57
2984 4896 6.313744 ACCATTTGAGCTGTTTTGTACTAC 57.686 37.500 0.00 0.00 0.00 2.73
2986 4898 5.852282 AACCATTTGAGCTGTTTTGTACT 57.148 34.783 0.00 0.00 0.00 2.73
3011 5865 1.616159 ACCACCCGAACCAAATTCAG 58.384 50.000 0.00 0.00 37.12 3.02
3023 5877 3.055675 TCTCCAACTTTGTATACCACCCG 60.056 47.826 0.00 0.00 0.00 5.28
3052 5906 5.293569 CCTATGAGGTTTCGTAACATTGACC 59.706 44.000 7.25 0.00 35.92 4.02
3069 5923 7.730084 TCACAAAATGGACTATCTCCTATGAG 58.270 38.462 0.00 0.00 40.26 2.90
3074 5928 6.126863 TGTTCACAAAATGGACTATCTCCT 57.873 37.500 0.00 0.00 37.74 3.69
3243 6109 4.434520 GTTAGCTGAGTTCCATGGTAGAC 58.565 47.826 12.58 9.40 0.00 2.59
3252 6119 5.885912 TGGATTAAATGGTTAGCTGAGTTCC 59.114 40.000 0.00 0.00 0.00 3.62
3261 6128 6.256321 GTGCTGCAAATGGATTAAATGGTTAG 59.744 38.462 2.77 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.