Multiple sequence alignment - TraesCS2B01G547500

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 TraesCS2B01G547500 chr2B 100.000 3320 0 0 1 3320 744167381 744164062 0.000000e+00 6131
1 TraesCS2B01G547500 chr2D 91.830 3158 179 32 1 3103 609775957 609772824 0.000000e+00 4329
2 TraesCS2B01G547500 chr2D 82.819 227 26 6 3098 3320 609772783 609772566 1.220000e-44 191
3 TraesCS2B01G547500 chr2A 90.460 2285 141 31 836 3099 742720060 742717832 0.000000e+00 2940
4 TraesCS2B01G547500 chr2A 95.426 809 32 2 1 809 742720918 742720115 0.000000e+00 1284
5 TraesCS2B01G547500 chr5B 82.819 227 26 5 972 1192 61352857 61352638 1.220000e-44 191


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 TraesCS2B01G547500 chr2B 744164062 744167381 3319 True 6131 6131 100.0000 1 3320 1 chr2B.!!$R1 3319
1 TraesCS2B01G547500 chr2D 609772566 609775957 3391 True 2260 4329 87.3245 1 3320 2 chr2D.!!$R1 3319
2 TraesCS2B01G547500 chr2A 742717832 742720918 3086 True 2112 2940 92.9430 1 3099 2 chr2A.!!$R1 3098

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
802 810 0.661552 GCGGAGACTGCGACTACATA 59.338 55.000 21.39 0.0 30.86 2.29 F
953 992 2.572104 AGAGGTTTCAGGATTAAGGCGT 59.428 45.455 0.00 0.0 0.00 5.68 F
1864 1905 0.179240 CAACACGATCGTCAAGCTGC 60.179 55.000 19.84 0.0 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1905 0.111253 AACCTCCCTTCCTTGCACAG 59.889 55.000 0.00 0.0 0.0 3.66 R
2269 2310 0.397675 TCAGACTCCGATCCTGGCAT 60.398 55.000 0.00 0.0 0.0 4.40 R
2882 2966 1.208293 TGCGCATACTTACATGGACCA 59.792 47.619 5.66 0.0 0.0 4.02 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
120 121 1.374758 GTCCAGGACAGTGAAGGCG 60.375 63.158 15.43 0.00 32.09 5.52
527 531 3.547413 GCGGACTAACAAAAACAGACCAC 60.547 47.826 0.00 0.00 0.00 4.16
732 738 1.250328 CTTTTGATGCCTCTGCCACA 58.750 50.000 0.00 0.00 36.33 4.17
733 739 1.822990 CTTTTGATGCCTCTGCCACAT 59.177 47.619 0.00 0.00 36.33 3.21
734 740 2.804986 TTTGATGCCTCTGCCACATA 57.195 45.000 0.00 0.00 36.33 2.29
735 741 2.804986 TTGATGCCTCTGCCACATAA 57.195 45.000 0.00 0.00 36.33 1.90
736 742 3.301794 TTGATGCCTCTGCCACATAAT 57.698 42.857 0.00 0.00 36.33 1.28
760 768 0.801251 GTTGCACATCACTGAGCCTC 59.199 55.000 0.00 0.00 38.09 4.70
767 775 3.754850 CACATCACTGAGCCTCAAAATCA 59.245 43.478 0.00 0.00 0.00 2.57
774 782 2.157738 GAGCCTCAAAATCACAGTGCT 58.842 47.619 0.00 0.00 0.00 4.40
777 785 2.095364 GCCTCAAAATCACAGTGCTGAG 60.095 50.000 6.17 11.80 0.00 3.35
802 810 0.661552 GCGGAGACTGCGACTACATA 59.338 55.000 21.39 0.00 30.86 2.29
811 819 9.472361 GGAGACTGCGACTACATAAAAATATTA 57.528 33.333 0.00 0.00 0.00 0.98
831 867 3.959535 ACCGCAATGATGAAATGGTTT 57.040 38.095 0.00 0.00 0.00 3.27
905 943 3.390639 AGATCGGCTGAGATTTGGAGAAT 59.609 43.478 0.00 0.00 0.00 2.40
906 944 4.590647 AGATCGGCTGAGATTTGGAGAATA 59.409 41.667 0.00 0.00 0.00 1.75
907 945 4.753516 TCGGCTGAGATTTGGAGAATAA 57.246 40.909 0.00 0.00 0.00 1.40
947 986 3.268595 GGGGGAAAGAGGTTTCAGGATTA 59.731 47.826 0.66 0.00 43.52 1.75
953 992 2.572104 AGAGGTTTCAGGATTAAGGCGT 59.428 45.455 0.00 0.00 0.00 5.68
981 1020 4.640855 ACGGTCGCACCACACTCG 62.641 66.667 6.21 0.00 38.47 4.18
986 1025 2.801162 CGCACCACACTCGTCTCG 60.801 66.667 0.00 0.00 0.00 4.04
999 1040 3.138128 TCTCGGCTCGATTGCGGA 61.138 61.111 6.71 6.71 39.41 5.54
1864 1905 0.179240 CAACACGATCGTCAAGCTGC 60.179 55.000 19.84 0.00 0.00 5.25
2088 2129 2.032071 CGCTGGGGTTTCCTTCGT 59.968 61.111 0.00 0.00 36.20 3.85
2091 2132 1.375523 CTGGGGTTTCCTTCGTCCG 60.376 63.158 0.00 0.00 36.20 4.79
2208 2249 3.785887 TGGTGGATTTGGCTAGGAAGTAT 59.214 43.478 0.00 0.00 0.00 2.12
2226 2267 1.387295 ATGACGAGGAGATGCTCGCA 61.387 55.000 21.47 19.24 45.79 5.10
2262 2303 0.915364 AGCCAAGGAAAGAGCTAGGG 59.085 55.000 0.00 0.00 32.73 3.53
2266 2307 3.375699 CCAAGGAAAGAGCTAGGGACTA 58.624 50.000 0.00 0.00 41.75 2.59
2269 2310 5.280521 CCAAGGAAAGAGCTAGGGACTAAAA 60.281 44.000 0.00 0.00 42.17 1.52
2278 2319 3.181439 GCTAGGGACTAAAATGCCAGGAT 60.181 47.826 0.00 0.00 42.17 3.24
2280 2321 2.158755 AGGGACTAAAATGCCAGGATCG 60.159 50.000 0.00 0.00 36.02 3.69
2310 2351 5.066375 TGACAGTGATAATGCATTAAGTGGC 59.934 40.000 22.37 20.39 0.00 5.01
2385 2426 3.565307 ACACACTGGTTGTCATTGGATT 58.435 40.909 0.00 0.00 35.67 3.01
2401 2442 7.335422 GTCATTGGATTAGAGTGTGACTGAAAT 59.665 37.037 0.00 0.00 33.57 2.17
2406 2447 7.770433 TGGATTAGAGTGTGACTGAAATAATGG 59.230 37.037 0.00 0.00 0.00 3.16
2410 2451 7.004555 AGAGTGTGACTGAAATAATGGTGTA 57.995 36.000 0.00 0.00 0.00 2.90
2412 2453 8.103305 AGAGTGTGACTGAAATAATGGTGTAAT 58.897 33.333 0.00 0.00 0.00 1.89
2414 2455 7.882791 AGTGTGACTGAAATAATGGTGTAATGA 59.117 33.333 0.00 0.00 0.00 2.57
2446 2487 6.053632 TGTGTTGATGGAGATCTAATGTGT 57.946 37.500 0.00 0.00 0.00 3.72
2448 2489 4.877823 TGTTGATGGAGATCTAATGTGTGC 59.122 41.667 0.00 0.00 0.00 4.57
2483 2525 4.440663 GCACTGAAGGAAAATAGAATGGGC 60.441 45.833 0.00 0.00 0.00 5.36
2524 2566 1.891150 CTTTCATGCAGCTGTTCCCTT 59.109 47.619 16.64 0.00 0.00 3.95
2544 2587 4.370917 CTTGAAAAACATGTGGAAGTGGG 58.629 43.478 0.00 0.00 0.00 4.61
2546 2589 2.470057 AAAACATGTGGAAGTGGGGT 57.530 45.000 0.00 0.00 0.00 4.95
2618 2679 2.654863 CCAAGTTGTTGAAGGACCTGT 58.345 47.619 0.00 0.00 35.46 4.00
2628 2689 0.394565 AAGGACCTGTGTGCTGAGTC 59.605 55.000 0.00 0.00 43.06 3.36
2654 2715 2.289547 TGTTAGCCTGCTTGAACGTTTC 59.710 45.455 0.46 0.00 0.00 2.78
2655 2716 2.248280 TAGCCTGCTTGAACGTTTCA 57.752 45.000 0.46 0.00 38.04 2.69
2667 2728 2.774439 ACGTTTCAACACTGAATGGC 57.226 45.000 0.00 0.00 41.22 4.40
2668 2729 2.020720 ACGTTTCAACACTGAATGGCA 58.979 42.857 0.00 0.00 41.22 4.92
2673 2734 5.512788 CGTTTCAACACTGAATGGCATATTC 59.487 40.000 0.00 0.00 41.22 1.75
2674 2735 6.623549 CGTTTCAACACTGAATGGCATATTCT 60.624 38.462 0.00 0.00 41.22 2.40
2675 2736 7.413988 CGTTTCAACACTGAATGGCATATTCTA 60.414 37.037 0.00 1.75 41.22 2.10
2684 2746 5.072193 TGAATGGCATATTCTAAGAGCTGGA 59.928 40.000 0.00 0.00 0.00 3.86
2694 2756 5.606348 TCTAAGAGCTGGAAAGGAAGATC 57.394 43.478 0.00 0.00 0.00 2.75
2696 2758 3.910568 AGAGCTGGAAAGGAAGATCAG 57.089 47.619 0.00 0.00 31.20 2.90
2699 2761 1.742268 GCTGGAAAGGAAGATCAGCAC 59.258 52.381 8.50 0.00 46.92 4.40
2730 2792 1.480954 GATGAGTCCCTTTGCTCCGTA 59.519 52.381 0.00 0.00 0.00 4.02
2731 2793 0.606604 TGAGTCCCTTTGCTCCGTAC 59.393 55.000 0.00 0.00 0.00 3.67
2744 2806 5.601583 TGCTCCGTACTTTTACCATATGA 57.398 39.130 3.65 0.00 0.00 2.15
2755 2817 8.682936 ACTTTTACCATATGATCATTCTGACC 57.317 34.615 14.65 0.00 0.00 4.02
2765 2828 1.980765 TCATTCTGACCACCTGAAGCT 59.019 47.619 0.00 0.00 36.40 3.74
2805 2875 5.336690 GCAAATAGCCTTGTCTTGAATGGAA 60.337 40.000 0.00 0.00 37.23 3.53
2810 2894 6.272822 AGCCTTGTCTTGAATGGAAATTAC 57.727 37.500 0.00 0.00 0.00 1.89
2879 2963 3.395941 ACTGGGTTGTTCTCTGAGGAAAT 59.604 43.478 4.59 0.00 0.00 2.17
2880 2964 4.006319 CTGGGTTGTTCTCTGAGGAAATC 58.994 47.826 4.59 0.00 0.00 2.17
2881 2965 3.394274 TGGGTTGTTCTCTGAGGAAATCA 59.606 43.478 4.59 0.00 36.21 2.57
2882 2966 4.043310 TGGGTTGTTCTCTGAGGAAATCAT 59.957 41.667 4.59 0.00 37.28 2.45
2883 2967 4.397417 GGGTTGTTCTCTGAGGAAATCATG 59.603 45.833 4.59 0.00 37.28 3.07
2884 2968 4.397417 GGTTGTTCTCTGAGGAAATCATGG 59.603 45.833 4.59 0.00 37.28 3.66
2885 2969 4.916041 TGTTCTCTGAGGAAATCATGGT 57.084 40.909 4.59 0.00 37.28 3.55
2891 2975 3.524789 TCTGAGGAAATCATGGTCCATGT 59.475 43.478 27.50 14.63 41.98 3.21
2911 2995 4.119862 TGTAAGTATGCGCAGGAAATCTC 58.880 43.478 18.32 2.85 0.00 2.75
2912 2996 1.858091 AGTATGCGCAGGAAATCTCG 58.142 50.000 18.32 0.00 0.00 4.04
2918 3002 1.645034 CGCAGGAAATCTCGTGTCAT 58.355 50.000 0.00 0.00 39.24 3.06
2922 3006 4.371786 GCAGGAAATCTCGTGTCATGATA 58.628 43.478 0.00 0.00 39.24 2.15
2926 3010 7.404985 CAGGAAATCTCGTGTCATGATAAAAG 58.595 38.462 0.00 0.00 33.61 2.27
2949 3033 4.999950 GCTTAGAATAGCAGCATACCATGT 59.000 41.667 0.00 0.00 40.89 3.21
2957 3041 0.179045 AGCATACCATGTCCGGAAGC 60.179 55.000 5.23 0.00 0.00 3.86
2965 3049 2.569059 CATGTCCGGAAGCTTCATGAT 58.431 47.619 27.02 8.95 38.35 2.45
3025 3109 4.973168 TCTGGTATTGCAGTGAAGTTTCT 58.027 39.130 0.00 0.00 0.00 2.52
3106 3241 5.046910 ACAACGCATCCAGTTATTTTCAG 57.953 39.130 0.00 0.00 0.00 3.02
3107 3242 4.759693 ACAACGCATCCAGTTATTTTCAGA 59.240 37.500 0.00 0.00 0.00 3.27
3109 3244 5.741388 ACGCATCCAGTTATTTTCAGATC 57.259 39.130 0.00 0.00 0.00 2.75
3112 3247 5.557136 CGCATCCAGTTATTTTCAGATCGAC 60.557 44.000 0.00 0.00 0.00 4.20
3115 3250 7.414540 GCATCCAGTTATTTTCAGATCGACTTT 60.415 37.037 0.00 0.00 0.00 2.66
3124 3259 2.632996 TCAGATCGACTTTTCACCCAGT 59.367 45.455 0.00 0.00 0.00 4.00
3127 3262 3.815401 AGATCGACTTTTCACCCAGTTTG 59.185 43.478 0.00 0.00 0.00 2.93
3133 3268 5.008217 CGACTTTTCACCCAGTTTGATACAA 59.992 40.000 0.00 0.00 0.00 2.41
3209 3344 6.785488 TGCACTTTATCTAGTGTTCTTGTG 57.215 37.500 5.75 0.00 45.76 3.33
3211 3346 5.179368 GCACTTTATCTAGTGTTCTTGTGCA 59.821 40.000 0.00 0.00 45.76 4.57
3212 3347 6.619446 GCACTTTATCTAGTGTTCTTGTGCAG 60.619 42.308 0.00 0.00 45.76 4.41
3213 3348 6.425114 CACTTTATCTAGTGTTCTTGTGCAGT 59.575 38.462 0.00 0.00 40.48 4.40
3215 3350 7.499232 ACTTTATCTAGTGTTCTTGTGCAGTTT 59.501 33.333 0.00 0.00 0.00 2.66
3216 3351 5.931441 ATCTAGTGTTCTTGTGCAGTTTC 57.069 39.130 0.00 0.00 0.00 2.78
3217 3352 4.127171 TCTAGTGTTCTTGTGCAGTTTCC 58.873 43.478 0.00 0.00 0.00 3.13
3218 3353 3.004752 AGTGTTCTTGTGCAGTTTCCT 57.995 42.857 0.00 0.00 0.00 3.36
3219 3354 3.356290 AGTGTTCTTGTGCAGTTTCCTT 58.644 40.909 0.00 0.00 0.00 3.36
3220 3355 4.523083 AGTGTTCTTGTGCAGTTTCCTTA 58.477 39.130 0.00 0.00 0.00 2.69
3221 3356 4.576463 AGTGTTCTTGTGCAGTTTCCTTAG 59.424 41.667 0.00 0.00 0.00 2.18
3222 3357 3.882888 TGTTCTTGTGCAGTTTCCTTAGG 59.117 43.478 0.00 0.00 0.00 2.69
3225 3360 3.391296 TCTTGTGCAGTTTCCTTAGGAGT 59.609 43.478 0.00 0.00 31.21 3.85
3229 3364 6.614694 TGTGCAGTTTCCTTAGGAGTATAA 57.385 37.500 0.00 0.00 31.21 0.98
3230 3365 6.403878 TGTGCAGTTTCCTTAGGAGTATAAC 58.596 40.000 0.00 3.25 31.21 1.89
3231 3366 5.816258 GTGCAGTTTCCTTAGGAGTATAACC 59.184 44.000 9.26 0.00 31.21 2.85
3232 3367 5.724854 TGCAGTTTCCTTAGGAGTATAACCT 59.275 40.000 9.26 5.30 41.05 3.50
3233 3368 6.214819 TGCAGTTTCCTTAGGAGTATAACCTT 59.785 38.462 9.26 0.00 38.76 3.50
3236 3371 9.819267 CAGTTTCCTTAGGAGTATAACCTTAAG 57.181 37.037 9.26 0.00 38.76 1.85
3237 3372 9.779951 AGTTTCCTTAGGAGTATAACCTTAAGA 57.220 33.333 3.36 0.00 38.76 2.10
3240 3375 9.551339 TTCCTTAGGAGTATAACCTTAAGAACA 57.449 33.333 3.36 0.00 38.76 3.18
3241 3376 9.551339 TCCTTAGGAGTATAACCTTAAGAACAA 57.449 33.333 3.36 0.00 38.76 2.83
3261 3396 9.533253 AGAACAATTTATTTTGAGACCAAACTG 57.467 29.630 0.00 0.00 41.54 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 0.462759 ATGCCTCAACCTCGCTAAGC 60.463 55.000 0.00 0.00 0.00 3.09
204 205 0.889186 ACCGGAATGTGTGCTGAACC 60.889 55.000 9.46 0.00 0.00 3.62
527 531 2.496899 AGCACAGGTAATTCCCAGTG 57.503 50.000 8.07 8.07 42.16 3.66
732 738 7.253422 GCTCAGTGATGTGCAACTTTAATTAT 58.747 34.615 0.00 0.00 38.04 1.28
733 739 6.349280 GGCTCAGTGATGTGCAACTTTAATTA 60.349 38.462 5.34 0.00 38.04 1.40
734 740 5.464168 GCTCAGTGATGTGCAACTTTAATT 58.536 37.500 0.00 0.00 38.04 1.40
735 741 4.082571 GGCTCAGTGATGTGCAACTTTAAT 60.083 41.667 5.34 0.00 38.04 1.40
736 742 3.253188 GGCTCAGTGATGTGCAACTTTAA 59.747 43.478 5.34 0.00 38.04 1.52
760 768 5.391449 CAGATTCTCAGCACTGTGATTTTG 58.609 41.667 12.86 4.05 33.75 2.44
767 775 0.390866 CCGCAGATTCTCAGCACTGT 60.391 55.000 0.00 0.00 33.57 3.55
774 782 0.174389 GCAGTCTCCGCAGATTCTCA 59.826 55.000 0.00 0.00 0.00 3.27
777 785 1.139734 TCGCAGTCTCCGCAGATTC 59.860 57.895 0.00 0.00 0.00 2.52
785 793 7.948278 ATATTTTTATGTAGTCGCAGTCTCC 57.052 36.000 0.00 0.00 0.00 3.71
802 810 9.044150 CCATTTCATCATTGCGGTAATATTTTT 57.956 29.630 0.00 0.00 0.00 1.94
811 819 3.257873 TCAAACCATTTCATCATTGCGGT 59.742 39.130 0.00 0.00 0.00 5.68
887 923 4.446371 ACTTATTCTCCAAATCTCAGCCG 58.554 43.478 0.00 0.00 0.00 5.52
905 943 2.637872 CCCTGACCTGACCTGAAACTTA 59.362 50.000 0.00 0.00 0.00 2.24
906 944 1.421646 CCCTGACCTGACCTGAAACTT 59.578 52.381 0.00 0.00 0.00 2.66
907 945 1.059913 CCCTGACCTGACCTGAAACT 58.940 55.000 0.00 0.00 0.00 2.66
966 1005 2.733593 GACGAGTGTGGTGCGACC 60.734 66.667 0.00 0.00 39.22 4.79
967 1006 1.729838 GAGACGAGTGTGGTGCGAC 60.730 63.158 0.00 0.00 0.00 5.19
981 1020 2.884087 TTCCGCAATCGAGCCGAGAC 62.884 60.000 3.76 0.00 39.91 3.36
986 1025 2.110734 GAGCATTCCGCAATCGAGCC 62.111 60.000 0.00 0.00 46.13 4.70
999 1040 2.270205 CGCACCAGGGAGAGCATT 59.730 61.111 0.00 0.00 0.00 3.56
1719 1760 4.124351 GCGACGATGTCCACCGGA 62.124 66.667 9.46 0.00 0.00 5.14
1737 1778 1.410737 CGTGGATCGCGGTGTTGTAG 61.411 60.000 6.13 0.00 33.47 2.74
1791 1832 0.250038 CCATCTGCCTGTACATCCGG 60.250 60.000 0.00 0.00 0.00 5.14
1864 1905 0.111253 AACCTCCCTTCCTTGCACAG 59.889 55.000 0.00 0.00 0.00 3.66
2046 2087 2.306341 ACCTCTTGATGAGCATGACG 57.694 50.000 0.00 0.00 41.35 4.35
2088 2129 0.542333 TCCACACAAAGAACACCGGA 59.458 50.000 9.46 0.00 0.00 5.14
2091 2132 3.013921 TGTCTTCCACACAAAGAACACC 58.986 45.455 0.00 0.00 34.68 4.16
2226 2267 1.770324 CTTGGGTGAGAGGCCCTTT 59.230 57.895 0.00 0.00 46.22 3.11
2262 2303 3.134458 CTCCGATCCTGGCATTTTAGTC 58.866 50.000 0.00 0.00 0.00 2.59
2266 2307 1.561542 AGACTCCGATCCTGGCATTTT 59.438 47.619 0.00 0.00 0.00 1.82
2269 2310 0.397675 TCAGACTCCGATCCTGGCAT 60.398 55.000 0.00 0.00 0.00 4.40
2278 2319 3.181486 GCATTATCACTGTCAGACTCCGA 60.181 47.826 6.91 0.00 0.00 4.55
2280 2321 4.128925 TGCATTATCACTGTCAGACTCC 57.871 45.455 6.91 0.00 0.00 3.85
2310 2351 1.329906 GCTGCCAGAATTCAGATCACG 59.670 52.381 8.44 0.00 32.26 4.35
2360 2401 3.748048 CCAATGACAACCAGTGTGTAGAG 59.252 47.826 0.00 0.00 41.96 2.43
2366 2407 5.221925 ACTCTAATCCAATGACAACCAGTGT 60.222 40.000 0.00 0.00 45.74 3.55
2385 2426 7.004555 ACACCATTATTTCAGTCACACTCTA 57.995 36.000 0.00 0.00 0.00 2.43
2401 2442 6.095300 CACAAAGCCTCATCATTACACCATTA 59.905 38.462 0.00 0.00 0.00 1.90
2406 2447 5.048782 TCAACACAAAGCCTCATCATTACAC 60.049 40.000 0.00 0.00 0.00 2.90
2410 2451 4.081862 CCATCAACACAAAGCCTCATCATT 60.082 41.667 0.00 0.00 0.00 2.57
2412 2453 2.821378 CCATCAACACAAAGCCTCATCA 59.179 45.455 0.00 0.00 0.00 3.07
2414 2455 3.087031 CTCCATCAACACAAAGCCTCAT 58.913 45.455 0.00 0.00 0.00 2.90
2455 2496 4.985538 TCTATTTTCCTTCAGTGCCAAGT 58.014 39.130 0.00 0.00 0.00 3.16
2456 2497 5.964958 TTCTATTTTCCTTCAGTGCCAAG 57.035 39.130 0.00 0.00 0.00 3.61
2483 2525 4.624015 AGTTGACAGGAAATGCAACATTG 58.376 39.130 0.00 0.00 42.96 2.82
2524 2566 2.697751 CCCCACTTCCACATGTTTTTCA 59.302 45.455 0.00 0.00 0.00 2.69
2606 2667 0.836606 TCAGCACACAGGTCCTTCAA 59.163 50.000 0.00 0.00 0.00 2.69
2618 2679 1.468506 TAACAGCCCGACTCAGCACA 61.469 55.000 0.00 0.00 0.00 4.57
2646 2707 3.042887 GCCATTCAGTGTTGAAACGTTC 58.957 45.455 0.00 0.00 45.82 3.95
2649 2710 2.772568 TGCCATTCAGTGTTGAAACG 57.227 45.000 0.00 0.00 45.82 3.60
2654 2715 7.558161 TCTTAGAATATGCCATTCAGTGTTG 57.442 36.000 9.94 0.00 0.00 3.33
2655 2716 6.261826 GCTCTTAGAATATGCCATTCAGTGTT 59.738 38.462 9.94 0.00 0.00 3.32
2667 2728 7.504403 TCTTCCTTTCCAGCTCTTAGAATATG 58.496 38.462 0.00 0.00 0.00 1.78
2668 2729 7.682787 TCTTCCTTTCCAGCTCTTAGAATAT 57.317 36.000 0.00 0.00 0.00 1.28
2673 2734 5.350504 TGATCTTCCTTTCCAGCTCTTAG 57.649 43.478 0.00 0.00 0.00 2.18
2674 2735 4.383552 GCTGATCTTCCTTTCCAGCTCTTA 60.384 45.833 0.00 0.00 44.75 2.10
2675 2736 3.621958 GCTGATCTTCCTTTCCAGCTCTT 60.622 47.826 0.00 0.00 44.75 2.85
2684 2746 3.584848 ACCTGTAGTGCTGATCTTCCTTT 59.415 43.478 0.00 0.00 0.00 3.11
2694 2756 5.078411 ACTCATCTAAACCTGTAGTGCTG 57.922 43.478 0.00 0.00 0.00 4.41
2696 2758 4.434520 GGACTCATCTAAACCTGTAGTGC 58.565 47.826 0.00 0.00 0.00 4.40
2697 2759 4.712337 AGGGACTCATCTAAACCTGTAGTG 59.288 45.833 0.00 0.00 0.00 2.74
2699 2761 5.941555 AAGGGACTCATCTAAACCTGTAG 57.058 43.478 0.00 0.00 38.49 2.74
2755 2817 1.542492 AGGCATCAAAGCTTCAGGTG 58.458 50.000 0.00 3.39 34.17 4.00
2786 2856 6.945435 TGTAATTTCCATTCAAGACAAGGCTA 59.055 34.615 0.00 0.00 0.00 3.93
2788 2858 6.024552 TGTAATTTCCATTCAAGACAAGGC 57.975 37.500 0.00 0.00 0.00 4.35
2805 2875 9.480053 CTGGTTTCATTTCACTTCAATGTAATT 57.520 29.630 0.00 0.00 36.63 1.40
2879 2963 3.727726 CGCATACTTACATGGACCATGA 58.272 45.455 35.91 19.19 43.81 3.07
2880 2964 2.224079 GCGCATACTTACATGGACCATG 59.776 50.000 29.36 29.36 46.18 3.66
2881 2965 2.158827 TGCGCATACTTACATGGACCAT 60.159 45.455 5.66 0.00 0.00 3.55
2882 2966 1.208293 TGCGCATACTTACATGGACCA 59.792 47.619 5.66 0.00 0.00 4.02
2883 2967 1.867233 CTGCGCATACTTACATGGACC 59.133 52.381 12.24 0.00 0.00 4.46
2884 2968 1.867233 CCTGCGCATACTTACATGGAC 59.133 52.381 12.24 0.00 0.00 4.02
2885 2969 1.760029 TCCTGCGCATACTTACATGGA 59.240 47.619 12.24 8.00 0.00 3.41
2891 2975 3.181479 ACGAGATTTCCTGCGCATACTTA 60.181 43.478 12.24 0.00 0.00 2.24
2911 2995 8.006590 GCTATTCTAAGCTTTTATCATGACACG 58.993 37.037 3.20 0.00 39.50 4.49
2912 2996 8.830580 TGCTATTCTAAGCTTTTATCATGACAC 58.169 33.333 3.20 0.00 43.19 3.67
2918 3002 8.993121 GTATGCTGCTATTCTAAGCTTTTATCA 58.007 33.333 3.20 0.00 43.19 2.15
2922 3006 6.122277 TGGTATGCTGCTATTCTAAGCTTTT 58.878 36.000 3.20 0.00 43.19 2.27
2926 3010 4.999950 ACATGGTATGCTGCTATTCTAAGC 59.000 41.667 0.00 0.00 43.08 3.09
2949 3033 1.833630 ACAGATCATGAAGCTTCCGGA 59.166 47.619 23.42 19.59 0.00 5.14
3106 3241 3.813166 TCAAACTGGGTGAAAAGTCGATC 59.187 43.478 0.00 0.00 0.00 3.69
3107 3242 3.815809 TCAAACTGGGTGAAAAGTCGAT 58.184 40.909 0.00 0.00 0.00 3.59
3109 3244 4.513692 TGTATCAAACTGGGTGAAAAGTCG 59.486 41.667 0.00 0.00 0.00 4.18
3112 3247 7.925483 TCATTTTGTATCAAACTGGGTGAAAAG 59.075 33.333 10.84 0.00 0.00 2.27
3115 3250 6.968263 TCATTTTGTATCAAACTGGGTGAA 57.032 33.333 10.84 0.00 0.00 3.18
3154 3289 8.527810 CACTAGAGAAGAGATGTTTAAGAAGGT 58.472 37.037 0.00 0.00 0.00 3.50
3155 3290 7.491048 GCACTAGAGAAGAGATGTTTAAGAAGG 59.509 40.741 0.00 0.00 0.00 3.46
3200 3335 3.882888 CCTAAGGAAACTGCACAAGAACA 59.117 43.478 0.00 0.00 42.68 3.18
3209 3344 6.236558 AGGTTATACTCCTAAGGAAACTGC 57.763 41.667 0.00 0.00 42.68 4.40
3211 3346 9.779951 TCTTAAGGTTATACTCCTAAGGAAACT 57.220 33.333 1.85 0.00 36.81 2.66
3215 3350 9.551339 TTGTTCTTAAGGTTATACTCCTAAGGA 57.449 33.333 1.85 0.00 34.56 3.36
3236 3371 8.764287 CCAGTTTGGTCTCAAAATAAATTGTTC 58.236 33.333 0.00 0.00 43.56 3.18
3237 3372 7.714813 CCCAGTTTGGTCTCAAAATAAATTGTT 59.285 33.333 0.00 0.00 43.56 2.83
3238 3373 7.070571 TCCCAGTTTGGTCTCAAAATAAATTGT 59.929 33.333 0.00 0.00 43.56 2.71
3239 3374 7.441017 TCCCAGTTTGGTCTCAAAATAAATTG 58.559 34.615 0.00 0.00 43.56 2.32
3240 3375 7.610580 TCCCAGTTTGGTCTCAAAATAAATT 57.389 32.000 0.00 0.00 43.56 1.82
3241 3376 7.610580 TTCCCAGTTTGGTCTCAAAATAAAT 57.389 32.000 0.00 0.00 43.56 1.40
3242 3377 7.425224 TTTCCCAGTTTGGTCTCAAAATAAA 57.575 32.000 0.00 0.00 43.56 1.40
3243 3378 7.425224 TTTTCCCAGTTTGGTCTCAAAATAA 57.575 32.000 0.00 0.00 43.56 1.40


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

AutoCloner maintained by Alex Coulton.