Multiple sequence alignment - TraesCS2A01G519500

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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 TraesCS2A01G519500 chr2A 100.000 3311 0 0 1 3311 742720912 742717602 0.000000e+00 6115.0
1 TraesCS2A01G519500 chr2D 89.068 2479 188 36 854 3257 609775122 609772652 0.000000e+00 3000.0
2 TraesCS2A01G519500 chr2D 94.417 806 33 6 1 798 609775951 609775150 0.000000e+00 1229.0
3 TraesCS2A01G519500 chr2B 90.460 2285 141 31 853 3081 744166546 744164283 0.000000e+00 2940.0
4 TraesCS2A01G519500 chr2B 95.392 803 32 2 1 798 744167375 744166573 0.000000e+00 1273.0
5 TraesCS2A01G519500 chr5B 86.000 200 22 3 996 1189 61352837 61352638 3.350000e-50 209.0
6 TraesCS2A01G519500 chr6B 98.000 50 0 1 804 853 75029843 75029795 5.890000e-13 86.1


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 TraesCS2A01G519500 chr2A 742717602 742720912 3310 True 6115.0 6115 100.0000 1 3311 1 chr2A.!!$R1 3310
1 TraesCS2A01G519500 chr2D 609772652 609775951 3299 True 2114.5 3000 91.7425 1 3257 2 chr2D.!!$R1 3256
2 TraesCS2A01G519500 chr2B 744164283 744167375 3092 True 2106.5 2940 92.9260 1 3081 2 chr2B.!!$R1 3080

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
729 739 0.543277 TTGATGCCTCTGCCACCTAG 59.457 55.0 0.0 0.0 36.33 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2588 2652 0.179 AGGTCCATCATCAACTCGGC 59.821 55.0 0.0 0.0 0.0 5.54 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
108 109 0.599558 CGGTTTCGTCCAGGACAGTA 59.400 55.000 20.13 1.20 32.09 2.74
219 220 1.336755 GTTCAGCACACATTCCGGTTT 59.663 47.619 0.00 0.00 0.00 3.27
225 226 2.412325 GCACACATTCCGGTTTTACTCG 60.412 50.000 0.00 0.00 0.00 4.18
231 232 0.669318 TCCGGTTTTACTCGCAGCAG 60.669 55.000 0.00 0.00 0.00 4.24
240 241 2.917227 TCGCAGCAGTGGAGGACA 60.917 61.111 0.00 0.00 0.00 4.02
324 325 2.042435 CGGAGGGAAGAGGAGGCT 60.042 66.667 0.00 0.00 0.00 4.58
491 495 1.289109 CCAGATTTTGGCGTCGACGT 61.289 55.000 35.48 17.63 40.87 4.34
601 605 3.798337 ACAAAATTCAAAAGACAGCAGCG 59.202 39.130 0.00 0.00 0.00 5.18
694 698 4.981806 TGTTTCAGTTTTGCTACTTGCT 57.018 36.364 0.00 0.00 43.37 3.91
707 711 1.484038 ACTTGCTGGTTGCCTGAAAA 58.516 45.000 0.00 0.00 42.00 2.29
729 739 0.543277 TTGATGCCTCTGCCACCTAG 59.457 55.000 0.00 0.00 36.33 3.02
749 759 0.607489 AGTTGCACATCACTGAGCCC 60.607 55.000 0.00 0.00 38.09 5.19
759 771 0.883833 CACTGAGCCCAAAAATCGCT 59.116 50.000 0.00 0.00 34.97 4.93
798 811 6.528826 CAAGACTGTGACGACATCAAAATAG 58.471 40.000 0.00 0.00 39.72 1.73
799 812 6.025749 AGACTGTGACGACATCAAAATAGA 57.974 37.500 0.00 0.00 39.72 1.98
800 813 6.634805 AGACTGTGACGACATCAAAATAGAT 58.365 36.000 0.00 0.00 39.72 1.98
802 815 6.398095 ACTGTGACGACATCAAAATAGATGA 58.602 36.000 10.59 0.00 46.51 2.92
803 816 7.044181 ACTGTGACGACATCAAAATAGATGAT 58.956 34.615 10.59 0.00 46.51 2.45
804 817 7.550551 ACTGTGACGACATCAAAATAGATGATT 59.449 33.333 10.59 0.00 46.51 2.57
805 818 8.267620 TGTGACGACATCAAAATAGATGATTT 57.732 30.769 10.59 0.00 46.51 2.17
806 819 8.729756 TGTGACGACATCAAAATAGATGATTTT 58.270 29.630 10.59 0.00 46.60 1.82
841 854 3.092334 GAGCTTCTCTCTCCGATTTCC 57.908 52.381 0.00 0.00 38.78 3.13
842 855 2.428890 GAGCTTCTCTCTCCGATTTCCA 59.571 50.000 0.00 0.00 38.78 3.53
843 856 3.037549 AGCTTCTCTCTCCGATTTCCAT 58.962 45.455 0.00 0.00 0.00 3.41
844 857 3.454082 AGCTTCTCTCTCCGATTTCCATT 59.546 43.478 0.00 0.00 0.00 3.16
845 858 4.651503 AGCTTCTCTCTCCGATTTCCATTA 59.348 41.667 0.00 0.00 0.00 1.90
846 859 5.129485 AGCTTCTCTCTCCGATTTCCATTAA 59.871 40.000 0.00 0.00 0.00 1.40
847 860 5.235401 GCTTCTCTCTCCGATTTCCATTAAC 59.765 44.000 0.00 0.00 0.00 2.01
851 864 6.154534 TCTCTCTCCGATTTCCATTAACAGAA 59.845 38.462 0.00 0.00 0.00 3.02
968 984 3.728385 AAGAGGTTTCAGGATTCAGGG 57.272 47.619 0.00 0.00 0.00 4.45
969 985 2.637165 AGAGGTTTCAGGATTCAGGGT 58.363 47.619 0.00 0.00 0.00 4.34
971 987 1.279271 AGGTTTCAGGATTCAGGGTCG 59.721 52.381 0.00 0.00 0.00 4.79
1737 1781 0.039798 ACATCGTCGCGTACAACACT 60.040 50.000 5.77 0.00 0.00 3.55
1801 1845 1.775385 TCGGATGTACAGGCAGATGA 58.225 50.000 0.33 0.00 0.00 2.92
1806 1850 4.649692 GGATGTACAGGCAGATGATTGAT 58.350 43.478 0.33 0.00 0.00 2.57
1808 1852 3.812262 TGTACAGGCAGATGATTGATGG 58.188 45.455 0.00 0.00 0.00 3.51
1809 1853 3.200605 TGTACAGGCAGATGATTGATGGT 59.799 43.478 0.00 0.00 0.00 3.55
1824 1868 3.670377 GGTGGTTGCAGGCCGAAC 61.670 66.667 0.00 1.55 0.00 3.95
1941 1985 0.543749 AGCCCAATGAGCTCACCTAC 59.456 55.000 20.97 8.01 34.91 3.18
2082 2126 2.856988 TGGGGTTTCCTTCGCCCT 60.857 61.111 0.00 0.00 42.01 5.19
2175 2219 1.551883 GATGCATTGCTGGAAAAGGGT 59.448 47.619 10.49 0.00 0.00 4.34
2196 2240 3.756082 ATGGTGGATTTGGCTAGGAAA 57.244 42.857 0.00 0.00 0.00 3.13
2229 2273 4.560856 CTCGCGAAGGGCCTCTCG 62.561 72.222 24.43 24.43 41.64 4.04
2281 2325 0.540923 GCCAGGAGCAGATTCTGACT 59.459 55.000 17.87 13.10 42.97 3.41
2380 2424 4.074259 CACTGGTTGTCATTGGATCAGAA 58.926 43.478 0.00 0.00 0.00 3.02
2381 2425 4.155462 CACTGGTTGTCATTGGATCAGAAG 59.845 45.833 0.00 0.00 0.00 2.85
2400 2444 6.716173 TCAGAAGGTGATTGAAACAATGATGA 59.284 34.615 1.64 0.00 0.00 2.92
2401 2445 7.395206 TCAGAAGGTGATTGAAACAATGATGAT 59.605 33.333 1.64 0.00 0.00 2.45
2405 2457 5.747197 GGTGATTGAAACAATGATGATGCTC 59.253 40.000 1.64 0.00 0.00 4.26
2408 2460 4.365899 TGAAACAATGATGATGCTCTGC 57.634 40.909 0.00 0.00 0.00 4.26
2413 2465 2.034104 ATGATGATGCTCTGCGTTGT 57.966 45.000 0.00 0.00 0.00 3.32
2417 2469 1.236616 TGATGCTCTGCGTTGTTGGG 61.237 55.000 0.00 0.00 0.00 4.12
2428 2480 2.752903 GCGTTGTTGGGGATCTAATGTT 59.247 45.455 0.00 0.00 0.00 2.71
2438 2490 4.338400 GGGGATCTAATGTTAGTTTGTGCC 59.662 45.833 0.00 0.00 32.61 5.01
2468 2521 6.058183 CACTGGAGGAAAATAGAATGGGTAG 58.942 44.000 0.00 0.00 0.00 3.18
2474 2527 7.027874 AGGAAAATAGAATGGGTAGTGTTGA 57.972 36.000 0.00 0.00 0.00 3.18
2483 2536 4.846779 TGGGTAGTGTTGAATTTTCTGC 57.153 40.909 0.00 0.00 0.00 4.26
2500 2553 3.921119 CTGCCAACTTTCATGCAGTTA 57.079 42.857 9.15 0.00 44.69 2.24
2506 2559 4.381932 CCAACTTTCATGCAGTTATTCCCC 60.382 45.833 9.15 0.00 32.48 4.81
2508 2561 3.278574 CTTTCATGCAGTTATTCCCCGA 58.721 45.455 0.00 0.00 0.00 5.14
2511 2565 3.013921 TCATGCAGTTATTCCCCGAAAC 58.986 45.455 0.00 0.00 0.00 2.78
2520 2574 2.350057 TTCCCCGAAACAACATGTGA 57.650 45.000 0.00 0.00 0.00 3.58
2526 2580 3.066064 CCCGAAACAACATGTGAAAGTGA 59.934 43.478 0.00 0.00 0.00 3.41
2532 2586 4.473444 ACAACATGTGAAAGTGAAGGGAT 58.527 39.130 0.00 0.00 0.00 3.85
2533 2587 4.279169 ACAACATGTGAAAGTGAAGGGATG 59.721 41.667 0.00 0.00 0.00 3.51
2535 2589 4.473444 ACATGTGAAAGTGAAGGGATGTT 58.527 39.130 0.00 0.00 0.00 2.71
2536 2590 4.895297 ACATGTGAAAGTGAAGGGATGTTT 59.105 37.500 0.00 0.00 0.00 2.83
2537 2591 5.363580 ACATGTGAAAGTGAAGGGATGTTTT 59.636 36.000 0.00 0.00 0.00 2.43
2538 2592 5.261209 TGTGAAAGTGAAGGGATGTTTTG 57.739 39.130 0.00 0.00 0.00 2.44
2541 2595 3.733443 AAGTGAAGGGATGTTTTGCAC 57.267 42.857 0.00 0.00 0.00 4.57
2542 2596 1.608590 AGTGAAGGGATGTTTTGCACG 59.391 47.619 0.00 0.00 0.00 5.34
2543 2597 0.313672 TGAAGGGATGTTTTGCACGC 59.686 50.000 0.00 0.00 0.00 5.34
2544 2598 0.313672 GAAGGGATGTTTTGCACGCA 59.686 50.000 0.00 0.00 0.00 5.24
2545 2599 0.749649 AAGGGATGTTTTGCACGCAA 59.250 45.000 0.00 0.00 0.00 4.85
2547 2601 1.070038 GGGATGTTTTGCACGCAATG 58.930 50.000 5.11 0.00 35.70 2.82
2568 2632 1.605232 CACTTGCTGATGTGTTGCTCA 59.395 47.619 0.00 0.00 0.00 4.26
2572 2636 3.082698 TGCTGATGTGTTGCTCAAAAC 57.917 42.857 0.00 0.00 0.00 2.43
2576 2640 3.820467 CTGATGTGTTGCTCAAAACCCTA 59.180 43.478 0.88 0.00 0.00 3.53
2601 2665 1.742761 CTGTTGGCCGAGTTGATGAT 58.257 50.000 0.00 0.00 0.00 2.45
2620 2684 2.009681 TGGACCTGAGTGCTGAGTTA 57.990 50.000 0.00 0.00 34.93 2.24
2649 2721 2.568956 AGCCTGCTTCTACACTGAATGA 59.431 45.455 0.00 0.00 0.00 2.57
2650 2722 3.199508 AGCCTGCTTCTACACTGAATGAT 59.800 43.478 0.00 0.00 0.00 2.45
2651 2723 3.311871 GCCTGCTTCTACACTGAATGATG 59.688 47.826 0.00 0.00 0.00 3.07
2669 2741 2.698855 TGTATTTCTGAGAGCTGGGC 57.301 50.000 0.00 0.00 0.00 5.36
2683 2755 4.413520 AGAGCTGGGCAGGAAGATTAATAA 59.586 41.667 0.00 0.00 0.00 1.40
2710 2784 5.045869 CAGGTTTAGATGACCCTTTACTCCA 60.046 44.000 0.00 0.00 37.93 3.86
2712 2786 5.823045 GGTTTAGATGACCCTTTACTCCATG 59.177 44.000 0.00 0.00 0.00 3.66
2793 2875 9.079367 ACAACCTTGTCTTGAATGGACATTCAG 62.079 40.741 22.39 17.47 46.18 3.02
2844 2932 9.838339 CCAGTTATAGTGGTCTTTCTCATATTT 57.162 33.333 0.00 0.00 33.97 1.40
2853 2941 5.163612 GGTCTTTCTCATATTTTCACTGGGC 60.164 44.000 0.00 0.00 0.00 5.36
2878 2973 2.026822 TCTCTGAGGAAACCATGGAAGC 60.027 50.000 21.47 6.34 0.00 3.86
2903 2998 2.614057 GGCAGGAAATCTAATGTCACGG 59.386 50.000 0.00 0.00 0.00 4.94
2904 2999 2.032178 GCAGGAAATCTAATGTCACGGC 59.968 50.000 0.00 0.00 0.00 5.68
2905 3000 2.614057 CAGGAAATCTAATGTCACGGCC 59.386 50.000 0.00 0.00 0.00 6.13
2909 3004 4.097892 GGAAATCTAATGTCACGGCCAAAT 59.902 41.667 2.24 0.00 0.00 2.32
2930 3026 9.013229 CCAAATCTTAAATAGCAGCATACCATA 57.987 33.333 0.00 0.00 0.00 2.74
2980 3076 7.605410 ACAAATTACAGGTAAATGTACTCGG 57.395 36.000 10.43 0.00 35.44 4.63
2989 3085 1.726853 AATGTACTCGGCAGTTCTGC 58.273 50.000 15.41 15.41 33.62 4.26
2997 3093 6.654975 TACTCGGCAGTTCTGCTATTGCAA 62.655 45.833 21.46 0.00 40.41 4.08
3028 3124 9.276590 GTTTCCATTCCTTTGAATTTTGATTCT 57.723 29.630 1.41 0.00 39.20 2.40
3052 3153 8.304596 TCTAGTACCATGCTATGCTTGTATTAC 58.695 37.037 0.00 0.00 32.83 1.89
3070 3171 8.384607 TGTATTACTGTTGCATTACAGACAAA 57.615 30.769 22.33 13.95 46.72 2.83
3072 3173 6.935741 TTACTGTTGCATTACAGACAAAGT 57.064 33.333 22.33 2.46 46.72 2.66
3073 3174 5.173774 ACTGTTGCATTACAGACAAAGTG 57.826 39.130 22.33 0.00 46.72 3.16
3094 3195 6.542821 AGTGTCCAGTTCCTAATTCATTCAA 58.457 36.000 0.00 0.00 0.00 2.69
3096 3197 8.328758 AGTGTCCAGTTCCTAATTCATTCAATA 58.671 33.333 0.00 0.00 0.00 1.90
3126 3227 6.057533 TCTATTAGTCCTTGATGTGGCAATG 58.942 40.000 0.00 0.00 0.00 2.82
3127 3228 2.592102 AGTCCTTGATGTGGCAATGT 57.408 45.000 0.00 0.00 0.00 2.71
3131 3232 3.989817 GTCCTTGATGTGGCAATGTTTTC 59.010 43.478 0.00 0.00 0.00 2.29
3132 3233 3.640498 TCCTTGATGTGGCAATGTTTTCA 59.360 39.130 0.00 0.00 0.00 2.69
3139 3241 5.731599 TGTGGCAATGTTTTCAAATTGAC 57.268 34.783 0.00 0.00 41.39 3.18
3154 3256 2.260844 TTGACTTCTCACCCAGCTTG 57.739 50.000 0.00 0.00 0.00 4.01
3159 3261 2.093973 ACTTCTCACCCAGCTTGATACG 60.094 50.000 0.00 0.00 0.00 3.06
3160 3262 1.847328 TCTCACCCAGCTTGATACGA 58.153 50.000 0.00 0.00 0.00 3.43
3204 3306 8.729805 ATAGCTTCTTAAACATCCTTTCTCTG 57.270 34.615 0.00 0.00 0.00 3.35
3215 3317 1.477558 CCTTTCTCTGGTGCAGGTTGT 60.478 52.381 0.00 0.00 31.51 3.32
3218 3320 1.717032 TCTCTGGTGCAGGTTGTACT 58.283 50.000 0.00 0.00 33.35 2.73
3227 3329 6.535540 TGGTGCAGGTTGTACTTTTATCTAA 58.464 36.000 0.00 0.00 33.35 2.10
3228 3330 7.172342 TGGTGCAGGTTGTACTTTTATCTAAT 58.828 34.615 0.00 0.00 33.35 1.73
3229 3331 8.322828 TGGTGCAGGTTGTACTTTTATCTAATA 58.677 33.333 0.00 0.00 33.35 0.98
3261 3363 9.819267 GTACCTATCATCTTTAGGCATATAACC 57.181 37.037 0.00 0.00 39.98 2.85
3262 3364 8.686739 ACCTATCATCTTTAGGCATATAACCT 57.313 34.615 3.39 3.39 39.98 3.50
3263 3365 9.117223 ACCTATCATCTTTAGGCATATAACCTT 57.883 33.333 3.20 0.00 39.98 3.50
3267 3369 8.848474 TCATCTTTAGGCATATAACCTTAAGC 57.152 34.615 14.58 0.00 41.54 3.09
3268 3370 8.436778 TCATCTTTAGGCATATAACCTTAAGCA 58.563 33.333 14.58 7.92 41.54 3.91
3269 3371 9.236006 CATCTTTAGGCATATAACCTTAAGCAT 57.764 33.333 14.58 9.20 41.54 3.79
3296 3398 9.643693 AATTAAAATTATTGTGAGACCAAGCTG 57.356 29.630 0.00 0.00 0.00 4.24
3297 3399 5.649782 AAATTATTGTGAGACCAAGCTGG 57.350 39.130 0.00 0.00 45.02 4.85
3298 3400 2.787473 TATTGTGAGACCAAGCTGGG 57.213 50.000 5.25 5.25 43.37 4.45
3299 3401 0.038744 ATTGTGAGACCAAGCTGGGG 59.961 55.000 13.11 7.69 43.37 4.96
3300 3402 1.059584 TTGTGAGACCAAGCTGGGGA 61.060 55.000 13.11 0.00 43.37 4.81
3301 3403 1.059584 TGTGAGACCAAGCTGGGGAA 61.060 55.000 13.11 0.00 43.37 3.97
3302 3404 0.110486 GTGAGACCAAGCTGGGGAAA 59.890 55.000 13.11 0.00 43.37 3.13
3303 3405 0.850100 TGAGACCAAGCTGGGGAAAA 59.150 50.000 13.11 0.00 43.37 2.29
3304 3406 1.428912 TGAGACCAAGCTGGGGAAAAT 59.571 47.619 13.11 0.00 43.37 1.82
3305 3407 2.095461 GAGACCAAGCTGGGGAAAATC 58.905 52.381 13.11 0.00 43.37 2.17
3306 3408 1.186200 GACCAAGCTGGGGAAAATCC 58.814 55.000 13.11 0.00 43.37 3.01
3307 3409 0.611896 ACCAAGCTGGGGAAAATCCG 60.612 55.000 13.11 0.00 43.37 4.18
3308 3410 0.611896 CCAAGCTGGGGAAAATCCGT 60.612 55.000 0.00 0.00 37.43 4.69
3309 3411 1.256812 CAAGCTGGGGAAAATCCGTT 58.743 50.000 0.00 0.00 37.43 4.44
3310 3412 1.202348 CAAGCTGGGGAAAATCCGTTC 59.798 52.381 0.00 0.00 37.43 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 0.173708 CGACCTCGCTAAGAGCCTTT 59.826 55.000 0.00 0.00 45.54 3.11
219 220 0.898326 TCCTCCACTGCTGCGAGTAA 60.898 55.000 4.79 0.00 0.00 2.24
225 226 1.748122 CCATGTCCTCCACTGCTGC 60.748 63.158 0.00 0.00 0.00 5.25
231 232 2.592308 GCTCCCCATGTCCTCCAC 59.408 66.667 0.00 0.00 0.00 4.02
240 241 1.535685 GATGAAGCAGGCTCCCCAT 59.464 57.895 0.00 0.00 0.00 4.00
399 403 4.753662 CGGTGGACTCCCCGGAGA 62.754 72.222 17.73 0.00 44.53 3.71
491 495 1.840630 TTGTTAGTCCGCGTCGTCGA 61.841 55.000 4.92 0.00 39.71 4.20
694 698 3.814283 GCATCAAAATTTTCAGGCAACCA 59.186 39.130 6.57 0.00 37.17 3.67
707 711 1.188863 GGTGGCAGAGGCATCAAAAT 58.811 50.000 0.00 0.00 43.71 1.82
729 739 0.801251 GGCTCAGTGATGTGCAACTC 59.199 55.000 5.34 0.00 38.04 3.01
749 759 1.764851 TTTCGGCACAGCGATTTTTG 58.235 45.000 0.00 0.00 0.00 2.44
759 771 1.266718 GTCTTGCAGATTTTCGGCACA 59.733 47.619 1.79 0.00 46.55 4.57
821 834 2.428890 TGGAAATCGGAGAGAGAAGCTC 59.571 50.000 0.00 0.00 43.63 4.09
822 835 2.461695 TGGAAATCGGAGAGAGAAGCT 58.538 47.619 0.00 0.00 43.63 3.74
823 836 2.969628 TGGAAATCGGAGAGAGAAGC 57.030 50.000 0.00 0.00 43.63 3.86
824 837 6.341316 TGTTAATGGAAATCGGAGAGAGAAG 58.659 40.000 0.00 0.00 43.63 2.85
825 838 6.154534 TCTGTTAATGGAAATCGGAGAGAGAA 59.845 38.462 0.00 0.00 43.63 2.87
826 839 5.656859 TCTGTTAATGGAAATCGGAGAGAGA 59.343 40.000 0.00 0.00 43.63 3.10
827 840 5.907207 TCTGTTAATGGAAATCGGAGAGAG 58.093 41.667 0.00 0.00 43.63 3.20
828 841 5.932619 TCTGTTAATGGAAATCGGAGAGA 57.067 39.130 0.00 0.00 43.63 3.10
829 842 6.985188 TTTCTGTTAATGGAAATCGGAGAG 57.015 37.500 2.92 0.00 43.63 3.20
830 843 7.938140 AATTTCTGTTAATGGAAATCGGAGA 57.062 32.000 14.56 0.00 40.06 3.71
831 844 8.028938 ACAAATTTCTGTTAATGGAAATCGGAG 58.971 33.333 14.56 9.79 40.06 4.63
832 845 7.891561 ACAAATTTCTGTTAATGGAAATCGGA 58.108 30.769 14.56 0.00 40.06 4.55
833 846 8.434661 CAACAAATTTCTGTTAATGGAAATCGG 58.565 33.333 14.56 12.65 40.06 4.18
834 847 9.190858 TCAACAAATTTCTGTTAATGGAAATCG 57.809 29.630 14.56 12.28 40.06 3.34
845 858 9.447157 TTTCCAGAATTTCAACAAATTTCTGTT 57.553 25.926 15.59 0.00 41.47 3.16
846 859 9.617523 ATTTCCAGAATTTCAACAAATTTCTGT 57.382 25.926 15.59 0.00 41.47 3.41
904 917 6.096705 TGAAACTTCTTCAAATCTCAGCCAAA 59.903 34.615 0.00 0.00 0.00 3.28
905 918 5.593909 TGAAACTTCTTCAAATCTCAGCCAA 59.406 36.000 0.00 0.00 0.00 4.52
906 919 5.132502 TGAAACTTCTTCAAATCTCAGCCA 58.867 37.500 0.00 0.00 0.00 4.75
919 932 4.455606 CTTGACCTGACCTGAAACTTCTT 58.544 43.478 0.00 0.00 0.00 2.52
1707 1751 2.036731 ACGATGTCCACCGGGAGA 59.963 61.111 6.32 0.00 46.12 3.71
1801 1845 1.259840 GGCCTGCAACCACCATCAAT 61.260 55.000 0.00 0.00 0.00 2.57
1806 1850 4.196778 TTCGGCCTGCAACCACCA 62.197 61.111 0.00 0.00 0.00 4.17
1808 1852 2.904866 TGTTCGGCCTGCAACCAC 60.905 61.111 0.00 0.00 0.00 4.16
1809 1853 2.904866 GTGTTCGGCCTGCAACCA 60.905 61.111 0.00 0.00 0.00 3.67
1824 1868 1.010125 CGTGTTGAAAGTGGCGGTG 60.010 57.895 0.00 0.00 0.00 4.94
1938 1982 4.080863 AGGTACTGGAAGAAGCAATGGTAG 60.081 45.833 0.00 0.00 37.18 3.18
1941 1985 3.356529 AGGTACTGGAAGAAGCAATGG 57.643 47.619 0.00 0.00 37.18 3.16
2049 2093 1.903404 CCAGCGCCCAAACCTCTTT 60.903 57.895 2.29 0.00 0.00 2.52
2082 2126 3.680490 TGTCTTCCACACAAAGAACACA 58.320 40.909 0.00 0.00 34.68 3.72
2175 2219 4.871871 TTTCCTAGCCAAATCCACCATA 57.128 40.909 0.00 0.00 0.00 2.74
2229 2273 1.881903 GCTCTTTCCTTGGCTTGGGC 61.882 60.000 0.00 0.00 37.82 5.36
2274 2318 7.066163 CCACTTAATGCATTATCACAGTCAGAA 59.934 37.037 19.51 1.69 0.00 3.02
2281 2325 5.942826 TCACACCACTTAATGCATTATCACA 59.057 36.000 19.51 4.30 0.00 3.58
2340 2384 5.118990 CCAGTGGGTAGATGAACATGTTAG 58.881 45.833 11.95 0.00 0.00 2.34
2343 2387 3.634397 CCAGTGGGTAGATGAACATGT 57.366 47.619 0.00 0.00 0.00 3.21
2380 2424 5.421056 AGCATCATCATTGTTTCAATCACCT 59.579 36.000 0.00 0.00 0.00 4.00
2381 2425 5.657474 AGCATCATCATTGTTTCAATCACC 58.343 37.500 0.00 0.00 0.00 4.02
2386 2430 4.673320 CGCAGAGCATCATCATTGTTTCAA 60.673 41.667 0.00 0.00 37.82 2.69
2400 2444 1.973281 CCCCAACAACGCAGAGCAT 60.973 57.895 0.00 0.00 0.00 3.79
2401 2445 2.410322 ATCCCCAACAACGCAGAGCA 62.410 55.000 0.00 0.00 0.00 4.26
2405 2457 2.107950 TTAGATCCCCAACAACGCAG 57.892 50.000 0.00 0.00 0.00 5.18
2408 2460 5.183228 ACTAACATTAGATCCCCAACAACG 58.817 41.667 5.66 0.00 34.84 4.10
2413 2465 5.417580 GCACAAACTAACATTAGATCCCCAA 59.582 40.000 5.66 0.00 34.84 4.12
2417 2469 6.759497 AAGGCACAAACTAACATTAGATCC 57.241 37.500 5.66 0.00 34.84 3.36
2438 2490 4.335416 TCTATTTTCCTCCAGTGCCAAAG 58.665 43.478 0.00 0.00 0.00 2.77
2449 2501 7.110155 TCAACACTACCCATTCTATTTTCCTC 58.890 38.462 0.00 0.00 0.00 3.71
2468 2521 5.580297 TGAAAGTTGGCAGAAAATTCAACAC 59.420 36.000 7.83 1.60 41.14 3.32
2474 2527 4.706035 TGCATGAAAGTTGGCAGAAAATT 58.294 34.783 0.00 0.00 0.00 1.82
2483 2536 4.381932 GGGGAATAACTGCATGAAAGTTGG 60.382 45.833 19.17 0.00 38.32 3.77
2498 2551 4.399219 TCACATGTTGTTTCGGGGAATAA 58.601 39.130 0.00 0.00 0.00 1.40
2500 2553 2.870175 TCACATGTTGTTTCGGGGAAT 58.130 42.857 0.00 0.00 0.00 3.01
2506 2559 4.734854 CCTTCACTTTCACATGTTGTTTCG 59.265 41.667 0.00 0.00 0.00 3.46
2508 2561 4.709397 TCCCTTCACTTTCACATGTTGTTT 59.291 37.500 0.00 0.00 0.00 2.83
2511 2565 4.279169 ACATCCCTTCACTTTCACATGTTG 59.721 41.667 0.00 0.00 0.00 3.33
2520 2574 3.490761 CGTGCAAAACATCCCTTCACTTT 60.491 43.478 0.00 0.00 0.00 2.66
2526 2580 0.749649 TTGCGTGCAAAACATCCCTT 59.250 45.000 4.52 0.00 32.44 3.95
2543 2597 2.717580 ACACATCAGCAAGTGCATTG 57.282 45.000 6.00 0.00 45.16 2.82
2544 2598 2.864882 GCAACACATCAGCAAGTGCATT 60.865 45.455 6.00 0.00 45.16 3.56
2545 2599 1.336517 GCAACACATCAGCAAGTGCAT 60.337 47.619 6.00 0.00 45.16 3.96
2547 2601 0.313043 AGCAACACATCAGCAAGTGC 59.687 50.000 0.00 0.00 39.30 4.40
2548 2602 1.605232 TGAGCAACACATCAGCAAGTG 59.395 47.619 0.00 0.00 41.40 3.16
2549 2603 1.971481 TGAGCAACACATCAGCAAGT 58.029 45.000 0.00 0.00 0.00 3.16
2588 2652 0.179000 AGGTCCATCATCAACTCGGC 59.821 55.000 0.00 0.00 0.00 5.54
2591 2655 3.529533 CACTCAGGTCCATCATCAACTC 58.470 50.000 0.00 0.00 0.00 3.01
2601 2665 1.895798 CTAACTCAGCACTCAGGTCCA 59.104 52.381 0.00 0.00 0.00 4.02
2638 2702 7.708322 GCTCTCAGAAATACATCATTCAGTGTA 59.292 37.037 0.00 0.00 35.49 2.90
2649 2721 2.507058 TGCCCAGCTCTCAGAAATACAT 59.493 45.455 0.00 0.00 0.00 2.29
2650 2722 1.908619 TGCCCAGCTCTCAGAAATACA 59.091 47.619 0.00 0.00 0.00 2.29
2651 2723 2.559440 CTGCCCAGCTCTCAGAAATAC 58.441 52.381 1.25 0.00 0.00 1.89
2683 2755 7.147532 GGAGTAAAGGGTCATCTAAACCTGTAT 60.148 40.741 0.00 0.00 36.97 2.29
2759 2834 3.513515 TCAAGACAAGGTTGTTTGCCTTT 59.486 39.130 0.00 0.00 43.24 3.11
2795 2877 9.653287 CTGGTTTCATTTCACTGTAGAACTATA 57.347 33.333 0.00 0.00 0.00 1.31
2798 2880 6.357367 ACTGGTTTCATTTCACTGTAGAACT 58.643 36.000 0.00 0.00 0.00 3.01
2799 2881 6.619801 ACTGGTTTCATTTCACTGTAGAAC 57.380 37.500 0.00 0.00 0.00 3.01
2800 2882 8.918202 ATAACTGGTTTCATTTCACTGTAGAA 57.082 30.769 0.00 0.00 0.00 2.10
2802 2884 9.436957 ACTATAACTGGTTTCATTTCACTGTAG 57.563 33.333 0.00 0.00 0.00 2.74
2803 2885 9.214957 CACTATAACTGGTTTCATTTCACTGTA 57.785 33.333 0.00 0.00 0.00 2.74
2804 2886 7.174946 CCACTATAACTGGTTTCATTTCACTGT 59.825 37.037 0.00 0.00 0.00 3.55
2805 2887 7.174946 ACCACTATAACTGGTTTCATTTCACTG 59.825 37.037 0.00 0.00 39.07 3.66
2844 2932 1.345741 CTCAGAGAACAGCCCAGTGAA 59.654 52.381 0.00 0.00 0.00 3.18
2853 2941 3.008375 TCCATGGTTTCCTCAGAGAACAG 59.992 47.826 12.58 0.00 25.32 3.16
2878 2973 4.037208 GTGACATTAGATTTCCTGCCCATG 59.963 45.833 0.00 0.00 0.00 3.66
2882 2977 2.614057 CCGTGACATTAGATTTCCTGCC 59.386 50.000 0.00 0.00 0.00 4.85
2903 2998 6.152379 GGTATGCTGCTATTTAAGATTTGGC 58.848 40.000 0.00 0.00 0.00 4.52
2904 2999 7.275888 TGGTATGCTGCTATTTAAGATTTGG 57.724 36.000 0.00 0.00 0.00 3.28
2905 3000 9.831737 GTATGGTATGCTGCTATTTAAGATTTG 57.168 33.333 0.00 0.00 0.00 2.32
2909 3004 6.472887 GGGTATGGTATGCTGCTATTTAAGA 58.527 40.000 0.00 0.00 0.00 2.10
2989 3085 6.870769 AGGAATGGAAACTTCATTGCAATAG 58.129 36.000 12.53 9.65 42.72 1.73
2997 3093 9.059260 CAAAATTCAAAGGAATGGAAACTTCAT 57.941 29.630 0.00 0.00 42.87 2.57
3028 3124 8.088365 CAGTAATACAAGCATAGCATGGTACTA 58.912 37.037 6.80 0.00 40.65 1.82
3034 3130 5.911280 GCAACAGTAATACAAGCATAGCATG 59.089 40.000 0.00 0.00 33.24 4.06
3052 3153 5.173774 ACACTTTGTCTGTAATGCAACAG 57.826 39.130 11.61 11.61 46.78 3.16
3070 3171 6.126863 TGAATGAATTAGGAACTGGACACT 57.873 37.500 0.00 0.00 41.52 3.55
3072 3173 9.342308 GATATTGAATGAATTAGGAACTGGACA 57.658 33.333 0.00 0.00 41.52 4.02
3073 3174 8.787852 GGATATTGAATGAATTAGGAACTGGAC 58.212 37.037 0.00 0.00 41.52 4.02
3096 3197 7.512992 CCACATCAAGGACTAATAGAAAGGAT 58.487 38.462 0.00 0.00 0.00 3.24
3106 3207 4.032960 ACATTGCCACATCAAGGACTAA 57.967 40.909 0.00 0.00 32.67 2.24
3108 3209 2.592102 ACATTGCCACATCAAGGACT 57.408 45.000 0.00 0.00 32.67 3.85
3109 3210 3.665745 AAACATTGCCACATCAAGGAC 57.334 42.857 0.00 0.00 32.67 3.85
3126 3227 5.901552 TGGGTGAGAAGTCAATTTGAAAAC 58.098 37.500 0.00 0.00 33.27 2.43
3127 3228 5.451798 GCTGGGTGAGAAGTCAATTTGAAAA 60.452 40.000 0.00 0.00 33.27 2.29
3131 3232 3.152341 AGCTGGGTGAGAAGTCAATTTG 58.848 45.455 0.00 0.00 33.27 2.32
3132 3233 3.515602 AGCTGGGTGAGAAGTCAATTT 57.484 42.857 0.00 0.00 33.27 1.82
3139 3241 2.166459 TCGTATCAAGCTGGGTGAGAAG 59.834 50.000 0.00 0.00 0.00 2.85
3181 3283 5.942826 CCAGAGAAAGGATGTTTAAGAAGCT 59.057 40.000 0.00 0.00 0.00 3.74
3196 3298 1.972872 ACAACCTGCACCAGAGAAAG 58.027 50.000 0.00 0.00 32.44 2.62
3204 3306 7.625828 ATTAGATAAAAGTACAACCTGCACC 57.374 36.000 0.00 0.00 0.00 5.01
3270 3372 9.643693 CAGCTTGGTCTCACAATAATTTTAATT 57.356 29.630 0.00 0.00 0.00 1.40
3271 3373 8.253113 CCAGCTTGGTCTCACAATAATTTTAAT 58.747 33.333 0.00 0.00 31.35 1.40
3272 3374 7.309744 CCCAGCTTGGTCTCACAATAATTTTAA 60.310 37.037 0.00 0.00 35.17 1.52
3273 3375 6.152661 CCCAGCTTGGTCTCACAATAATTTTA 59.847 38.462 0.00 0.00 35.17 1.52
3274 3376 5.047092 CCCAGCTTGGTCTCACAATAATTTT 60.047 40.000 0.00 0.00 35.17 1.82
3275 3377 4.463891 CCCAGCTTGGTCTCACAATAATTT 59.536 41.667 0.00 0.00 35.17 1.82
3276 3378 4.019174 CCCAGCTTGGTCTCACAATAATT 58.981 43.478 0.00 0.00 35.17 1.40
3277 3379 3.624777 CCCAGCTTGGTCTCACAATAAT 58.375 45.455 0.00 0.00 35.17 1.28
3278 3380 2.290896 CCCCAGCTTGGTCTCACAATAA 60.291 50.000 2.68 0.00 35.17 1.40
3279 3381 1.281867 CCCCAGCTTGGTCTCACAATA 59.718 52.381 2.68 0.00 35.17 1.90
3280 3382 0.038744 CCCCAGCTTGGTCTCACAAT 59.961 55.000 2.68 0.00 35.17 2.71
3281 3383 1.059584 TCCCCAGCTTGGTCTCACAA 61.060 55.000 2.68 0.00 35.17 3.33
3282 3384 1.059584 TTCCCCAGCTTGGTCTCACA 61.060 55.000 2.68 0.00 35.17 3.58
3283 3385 0.110486 TTTCCCCAGCTTGGTCTCAC 59.890 55.000 2.68 0.00 35.17 3.51
3284 3386 0.850100 TTTTCCCCAGCTTGGTCTCA 59.150 50.000 2.68 0.00 35.17 3.27
3285 3387 2.095461 GATTTTCCCCAGCTTGGTCTC 58.905 52.381 2.68 0.00 35.17 3.36
3286 3388 1.272704 GGATTTTCCCCAGCTTGGTCT 60.273 52.381 2.68 0.00 35.17 3.85
3287 3389 1.186200 GGATTTTCCCCAGCTTGGTC 58.814 55.000 2.68 0.00 35.17 4.02
3288 3390 0.611896 CGGATTTTCCCCAGCTTGGT 60.612 55.000 2.68 0.00 35.17 3.67
3289 3391 0.611896 ACGGATTTTCCCCAGCTTGG 60.612 55.000 0.00 0.00 37.25 3.61
3290 3392 1.202348 GAACGGATTTTCCCCAGCTTG 59.798 52.381 0.00 0.00 31.13 4.01
3291 3393 1.545841 GAACGGATTTTCCCCAGCTT 58.454 50.000 0.00 0.00 31.13 3.74
3292 3394 3.266240 GAACGGATTTTCCCCAGCT 57.734 52.632 0.00 0.00 31.13 4.24


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

AutoCloner maintained by Alex Coulton.