Multiple sequence alignment - TraesCS5B01G413200

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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 TraesCS5B01G413200 chr5B 100.000 3582 0 0 1 3582 588393850 588397431 0.000000e+00 6615
1 TraesCS5B01G413200 chr5B 92.330 352 26 1 489 840 700390630 700390980 1.920000e-137 499
2 TraesCS5B01G413200 chr5A 91.145 2778 161 44 851 3582 598815296 598818034 0.000000e+00 3688
3 TraesCS5B01G413200 chr5D 92.695 1451 57 20 855 2267 480342729 480344168 0.000000e+00 2047
4 TraesCS5B01G413200 chr5D 92.069 1324 71 22 2271 3582 480344297 480345598 0.000000e+00 1832
5 TraesCS5B01G413200 chr7A 94.591 832 35 3 2 833 17847557 17846736 0.000000e+00 1279


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 TraesCS5B01G413200 chr5B 588393850 588397431 3581 False 6615.0 6615 100.000 1 3582 1 chr5B.!!$F1 3581
1 TraesCS5B01G413200 chr5A 598815296 598818034 2738 False 3688.0 3688 91.145 851 3582 1 chr5A.!!$F1 2731
2 TraesCS5B01G413200 chr5D 480342729 480345598 2869 False 1939.5 2047 92.382 855 3582 2 chr5D.!!$F1 2727
3 TraesCS5B01G413200 chr7A 17846736 17847557 821 True 1279.0 1279 94.591 2 833 1 chr7A.!!$R1 831

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
263 264 0.596577 TGTCAGTCTTCGGAGTTCGG 59.403 55.0 0.00 0.00 39.77 4.30 F
743 744 0.665835 GGAGACTCGCTGATCATCGT 59.334 55.0 17.63 0.31 0.00 3.73 F
1492 1522 0.443869 CTCGGCAATTGTGACCTTCG 59.556 55.0 7.40 1.20 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 1242 0.659957 GCGGTTGAAGAGATGATGGC 59.340 55.0 0.0 0.0 0.00 4.40 R
2037 2075 0.961019 GAATTGGTTGCTCACAGGCA 59.039 50.0 0.0 0.0 40.74 4.75 R
2692 2880 1.322442 AAGCAAGACTGGAGGCAAAC 58.678 50.0 0.0 0.0 0.00 2.93 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
63 64 7.648142 TCAGGTGTTGTTAGACAAAAATGATC 58.352 34.615 0.00 0.00 40.15 2.92
130 131 3.822594 TTTACGTGATGATTGTGTGCC 57.177 42.857 0.00 0.00 0.00 5.01
196 197 2.026641 TGGGTACGAGAGGGAATTACG 58.973 52.381 0.00 0.00 0.00 3.18
197 198 2.301346 GGGTACGAGAGGGAATTACGA 58.699 52.381 0.00 0.00 0.00 3.43
224 225 3.960755 TGTCACTGGATGATCGGACTAAT 59.039 43.478 0.00 0.00 40.28 1.73
258 259 2.333014 GCTCTTTGTCAGTCTTCGGAG 58.667 52.381 0.00 0.00 0.00 4.63
259 260 2.288518 GCTCTTTGTCAGTCTTCGGAGT 60.289 50.000 0.00 0.00 0.00 3.85
260 261 3.800604 GCTCTTTGTCAGTCTTCGGAGTT 60.801 47.826 0.00 0.00 0.00 3.01
261 262 3.978687 TCTTTGTCAGTCTTCGGAGTTC 58.021 45.455 0.00 0.00 0.00 3.01
262 263 2.417339 TTGTCAGTCTTCGGAGTTCG 57.583 50.000 0.00 0.00 40.90 3.95
263 264 0.596577 TGTCAGTCTTCGGAGTTCGG 59.403 55.000 0.00 0.00 39.77 4.30
264 265 0.879765 GTCAGTCTTCGGAGTTCGGA 59.120 55.000 0.00 0.00 39.77 4.55
265 266 1.135632 GTCAGTCTTCGGAGTTCGGAG 60.136 57.143 0.00 0.00 45.64 4.63
273 274 1.000506 TCGGAGTTCGGAGAACCAAAG 59.999 52.381 9.05 0.55 45.90 2.77
286 287 1.153086 CCAAAGCCTCGGGATCAGG 60.153 63.158 0.00 0.00 0.00 3.86
293 294 2.044352 TCGGGATCAGGCGAGTGA 60.044 61.111 0.00 0.00 0.00 3.41
372 373 2.285743 GCCTTCCTCCCAGGGACT 60.286 66.667 3.01 0.00 43.88 3.85
423 424 3.261354 CACCAGGGTGGGGTTCTT 58.739 61.111 10.67 0.00 43.37 2.52
431 432 1.241990 GGTGGGGTTCTTTTCTCCGC 61.242 60.000 0.00 0.00 35.26 5.54
450 451 3.160047 AGCAGGGCGATGAGGGAG 61.160 66.667 0.00 0.00 0.00 4.30
455 456 2.268920 GGCGATGAGGGAGTGCAA 59.731 61.111 0.00 0.00 0.00 4.08
456 457 2.109126 GGCGATGAGGGAGTGCAAC 61.109 63.158 0.00 0.00 0.00 4.17
481 482 1.349026 CTGTGGAAGAAGCAGAGGGAA 59.651 52.381 0.00 0.00 32.39 3.97
493 494 3.911719 GAGGGAAATGCCATCCTGT 57.088 52.632 0.00 0.00 41.61 4.00
512 513 1.880027 GTTGGGGATCACAACACTGTC 59.120 52.381 20.95 0.58 45.62 3.51
523 524 0.685097 AACACTGTCGGCCATGTACT 59.315 50.000 2.24 0.00 0.00 2.73
576 577 4.590222 AGTTTGATTGCAAAGGAACTGGAT 59.410 37.500 18.17 0.00 44.12 3.41
648 649 1.812571 AGCACGGCGAGAAATTTCAAT 59.187 42.857 19.99 0.00 0.00 2.57
707 708 2.594013 GGCCCATGAGCTAGCTGC 60.594 66.667 24.99 18.54 43.29 5.25
708 709 2.594013 GCCCATGAGCTAGCTGCC 60.594 66.667 24.99 9.47 44.23 4.85
743 744 0.665835 GGAGACTCGCTGATCATCGT 59.334 55.000 17.63 0.31 0.00 3.73
813 814 5.408880 TGTAGATGGTTCGTGTATTTGGA 57.591 39.130 0.00 0.00 0.00 3.53
860 861 3.571571 TCGACAAACACATTCGGAGTAG 58.428 45.455 0.00 0.00 33.50 2.57
912 913 5.310451 TGTTCTTCATAAAGCGGGTTTAGT 58.690 37.500 16.38 4.31 34.01 2.24
1076 1078 3.706373 GGCAACGCCTCCTCTCCA 61.706 66.667 0.00 0.00 46.69 3.86
1180 1182 4.361971 TCCTCGCCCTCGTCCTGT 62.362 66.667 0.00 0.00 36.96 4.00
1278 1280 3.305314 GGTCATGGCTACCGTCCA 58.695 61.111 0.00 0.00 38.09 4.02
1490 1520 1.880027 GTTCTCGGCAATTGTGACCTT 59.120 47.619 7.40 0.00 0.00 3.50
1491 1521 1.808411 TCTCGGCAATTGTGACCTTC 58.192 50.000 7.40 0.00 0.00 3.46
1492 1522 0.443869 CTCGGCAATTGTGACCTTCG 59.556 55.000 7.40 1.20 0.00 3.79
1493 1523 1.154225 CGGCAATTGTGACCTTCGC 60.154 57.895 7.40 0.00 0.00 4.70
1494 1524 1.851021 CGGCAATTGTGACCTTCGCA 61.851 55.000 7.40 0.00 34.72 5.10
1746 1777 2.112380 TGATTCTGAAGAATGCCGCA 57.888 45.000 10.23 0.00 44.14 5.69
1815 1846 3.804873 GCCTTGCAGAGCTAATACAGTAC 59.195 47.826 2.97 0.00 0.00 2.73
1913 1951 7.518731 TTTTATGGCAAAATTGATCGTTAGC 57.481 32.000 0.00 0.00 0.00 3.09
2067 2106 4.831107 AGCAACCAATTCTGTGTGTTTTT 58.169 34.783 0.00 0.00 0.00 1.94
2188 2237 4.702131 GCTAGTTCAGGTGATGGTTTCAAT 59.298 41.667 0.00 0.00 35.70 2.57
2241 2299 7.545965 CCCATAGGTCTTATGTATCGTCAATTC 59.454 40.741 1.70 0.00 37.96 2.17
2243 2301 4.982916 AGGTCTTATGTATCGTCAATTCGC 59.017 41.667 0.00 0.00 0.00 4.70
2255 2313 1.811965 TCAATTCGCCATCACAGGTTG 59.188 47.619 0.00 0.00 0.00 3.77
2267 2450 6.311200 GCCATCACAGGTTGTTTTCATATTTC 59.689 38.462 0.00 0.00 0.00 2.17
2269 2452 7.543172 CCATCACAGGTTGTTTTCATATTTCTG 59.457 37.037 0.00 0.00 0.00 3.02
2392 2579 6.348540 CCATTCCTCGACTTTCCTTACAAAAG 60.349 42.308 0.00 0.00 39.20 2.27
2631 2819 2.075338 CTCTGAAGCAACTCTTGAGGC 58.925 52.381 2.55 0.00 36.77 4.70
2634 2822 3.324846 TCTGAAGCAACTCTTGAGGCTTA 59.675 43.478 11.95 0.00 45.81 3.09
2649 2837 8.299570 TCTTGAGGCTTAAAATCATTTCAGAAC 58.700 33.333 0.00 0.00 0.00 3.01
2651 2839 7.950512 TGAGGCTTAAAATCATTTCAGAACAA 58.049 30.769 0.00 0.00 0.00 2.83
2653 2841 7.154656 AGGCTTAAAATCATTTCAGAACAACC 58.845 34.615 0.00 0.00 0.00 3.77
2655 2843 7.440856 GGCTTAAAATCATTTCAGAACAACCAA 59.559 33.333 0.00 0.00 0.00 3.67
2656 2844 8.992073 GCTTAAAATCATTTCAGAACAACCAAT 58.008 29.630 0.00 0.00 0.00 3.16
2688 2876 1.985159 TGCTTCCATCTGTGGTAAGGT 59.015 47.619 0.00 0.00 46.16 3.50
2692 2880 4.321230 GCTTCCATCTGTGGTAAGGTTTTG 60.321 45.833 0.00 0.00 46.16 2.44
2693 2881 4.447138 TCCATCTGTGGTAAGGTTTTGT 57.553 40.909 0.00 0.00 46.16 2.83
2694 2882 4.798882 TCCATCTGTGGTAAGGTTTTGTT 58.201 39.130 0.00 0.00 46.16 2.83
2696 2884 5.068460 TCCATCTGTGGTAAGGTTTTGTTTG 59.932 40.000 0.00 0.00 46.16 2.93
2697 2885 4.379339 TCTGTGGTAAGGTTTTGTTTGC 57.621 40.909 0.00 0.00 0.00 3.68
2699 2887 3.100671 TGTGGTAAGGTTTTGTTTGCCT 58.899 40.909 0.00 0.00 31.29 4.75
2700 2888 3.131400 TGTGGTAAGGTTTTGTTTGCCTC 59.869 43.478 0.00 0.00 31.29 4.70
2702 2890 2.696187 GGTAAGGTTTTGTTTGCCTCCA 59.304 45.455 0.00 0.00 0.00 3.86
2704 2892 2.159179 AGGTTTTGTTTGCCTCCAGT 57.841 45.000 0.00 0.00 0.00 4.00
2705 2893 2.031870 AGGTTTTGTTTGCCTCCAGTC 58.968 47.619 0.00 0.00 0.00 3.51
2706 2894 2.031870 GGTTTTGTTTGCCTCCAGTCT 58.968 47.619 0.00 0.00 0.00 3.24
2708 2896 3.447742 GTTTTGTTTGCCTCCAGTCTTG 58.552 45.455 0.00 0.00 0.00 3.02
2709 2897 1.032014 TTGTTTGCCTCCAGTCTTGC 58.968 50.000 0.00 0.00 0.00 4.01
2711 2899 1.322442 GTTTGCCTCCAGTCTTGCTT 58.678 50.000 0.00 0.00 0.00 3.91
2712 2900 2.158682 TGTTTGCCTCCAGTCTTGCTTA 60.159 45.455 0.00 0.00 0.00 3.09
2713 2901 3.084786 GTTTGCCTCCAGTCTTGCTTAT 58.915 45.455 0.00 0.00 0.00 1.73
2714 2902 2.698855 TGCCTCCAGTCTTGCTTATC 57.301 50.000 0.00 0.00 0.00 1.75
2715 2903 1.908619 TGCCTCCAGTCTTGCTTATCA 59.091 47.619 0.00 0.00 0.00 2.15
2716 2904 2.093288 TGCCTCCAGTCTTGCTTATCAG 60.093 50.000 0.00 0.00 0.00 2.90
2717 2905 2.093235 GCCTCCAGTCTTGCTTATCAGT 60.093 50.000 0.00 0.00 0.00 3.41
2718 2906 3.529533 CCTCCAGTCTTGCTTATCAGTG 58.470 50.000 0.00 0.00 0.00 3.66
2719 2907 2.935201 CTCCAGTCTTGCTTATCAGTGC 59.065 50.000 0.00 0.00 0.00 4.40
2720 2908 2.012673 CCAGTCTTGCTTATCAGTGCC 58.987 52.381 0.00 0.00 0.00 5.01
2725 2914 4.457257 AGTCTTGCTTATCAGTGCCTTTTC 59.543 41.667 0.00 0.00 0.00 2.29
2794 2983 5.925509 AGTAAATAGAATTGCTCGCCCTAA 58.074 37.500 0.00 0.00 0.00 2.69
2795 2984 6.534634 AGTAAATAGAATTGCTCGCCCTAAT 58.465 36.000 0.00 0.00 0.00 1.73
2796 2985 7.676947 AGTAAATAGAATTGCTCGCCCTAATA 58.323 34.615 0.00 0.00 0.00 0.98
2797 2986 8.154856 AGTAAATAGAATTGCTCGCCCTAATAA 58.845 33.333 0.00 0.00 0.00 1.40
2838 3027 8.541133 AACAAGAGTTATTACAGAGCTTCTTC 57.459 34.615 0.00 0.00 35.85 2.87
2839 3028 7.100409 ACAAGAGTTATTACAGAGCTTCTTCC 58.900 38.462 0.00 0.00 0.00 3.46
2840 3029 6.859112 AGAGTTATTACAGAGCTTCTTCCA 57.141 37.500 0.00 0.00 0.00 3.53
2841 3030 7.430760 AGAGTTATTACAGAGCTTCTTCCAT 57.569 36.000 0.00 0.00 0.00 3.41
2842 3031 7.496747 AGAGTTATTACAGAGCTTCTTCCATC 58.503 38.462 0.00 0.00 0.00 3.51
2843 3032 7.124901 AGAGTTATTACAGAGCTTCTTCCATCA 59.875 37.037 0.00 0.00 0.00 3.07
2844 3033 7.271511 AGTTATTACAGAGCTTCTTCCATCAG 58.728 38.462 0.00 0.00 0.00 2.90
2845 3034 5.690464 ATTACAGAGCTTCTTCCATCAGT 57.310 39.130 0.00 0.00 0.00 3.41
2846 3035 3.331478 ACAGAGCTTCTTCCATCAGTG 57.669 47.619 0.00 0.00 0.00 3.66
2854 3043 6.893583 AGCTTCTTCCATCAGTGTATATGTT 58.106 36.000 0.00 0.00 0.00 2.71
2862 3051 7.952671 TCCATCAGTGTATATGTTACTTCCTC 58.047 38.462 0.00 0.00 0.00 3.71
2887 3076 8.474025 TCCAATGTTTTCTATCTGTTGTGTTTT 58.526 29.630 0.00 0.00 0.00 2.43
2888 3077 9.743057 CCAATGTTTTCTATCTGTTGTGTTTTA 57.257 29.630 0.00 0.00 0.00 1.52
2904 3094 9.983431 GTTGTGTTTTATTACTTCGTTTAATGC 57.017 29.630 0.00 0.00 0.00 3.56
2930 3120 7.439157 TTCTATCTCTTGTGTTCCACATTTG 57.561 36.000 0.00 0.00 44.16 2.32
2935 3125 6.005823 TCTCTTGTGTTCCACATTTGATCAT 58.994 36.000 0.00 0.00 44.16 2.45
2984 3175 3.519107 TCCATGCATCTCCTTTAGTGTGA 59.481 43.478 0.00 0.00 0.00 3.58
2990 3181 4.626287 GCATCTCCTTTAGTGTGATTCCCA 60.626 45.833 0.00 0.00 0.00 4.37
3068 3264 4.307032 ACTGTGATTGCTTGGAAGGTAT 57.693 40.909 0.00 0.00 0.00 2.73
3121 3318 2.435372 AAAGTGCACCTTTCAGTCCA 57.565 45.000 14.63 0.00 39.17 4.02
3131 3328 4.572389 CACCTTTCAGTCCAAGATAATCCG 59.428 45.833 0.00 0.00 0.00 4.18
3157 3354 9.195411 GCAAAATCTTGTCAGTGAAAAATATCA 57.805 29.630 0.00 0.00 34.79 2.15
3205 3402 2.604174 GGGTTTGAGTGCGACCGTG 61.604 63.158 0.00 0.00 34.22 4.94
3229 3426 6.600822 TGCTCTCCAAATAATCAGAGGAAAAG 59.399 38.462 0.00 0.00 34.14 2.27
3235 3432 7.831193 TCCAAATAATCAGAGGAAAAGGAAGAG 59.169 37.037 0.00 0.00 0.00 2.85
3236 3433 7.067981 CCAAATAATCAGAGGAAAAGGAAGAGG 59.932 40.741 0.00 0.00 0.00 3.69
3268 3465 0.806868 AAACAGCGATCCAGTGCATG 59.193 50.000 0.00 0.00 0.00 4.06
3287 3484 6.094881 GTGCATGTAAAGCCTTATAAAGTGGA 59.905 38.462 0.00 0.00 0.00 4.02
3288 3485 6.661377 TGCATGTAAAGCCTTATAAAGTGGAA 59.339 34.615 0.00 0.00 0.00 3.53
3327 3524 4.095036 GCAGAGGCTTCCACTAAATACAAC 59.905 45.833 0.00 0.00 36.96 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.077169 TGAAGCCAGTCTCTCCCAGTA 59.923 52.381 0.00 0.00 0.00 2.74
63 64 7.961351 AGTAGTATTTTGATCCTCATCTCTGG 58.039 38.462 0.00 0.00 0.00 3.86
83 84 1.067776 GCACGCCACAGTAGAAGTAGT 60.068 52.381 0.00 0.00 0.00 2.73
130 131 6.477033 CGATACTGTTTCTTTACCCTCATGAG 59.523 42.308 16.24 16.24 0.00 2.90
143 144 3.489398 GCACCGATCTCGATACTGTTTCT 60.489 47.826 0.22 0.00 43.02 2.52
147 148 1.335182 CTGCACCGATCTCGATACTGT 59.665 52.381 0.22 0.00 43.02 3.55
149 150 1.681538 ACTGCACCGATCTCGATACT 58.318 50.000 0.22 0.00 43.02 2.12
196 197 3.806521 CCGATCATCCAGTGACAGATTTC 59.193 47.826 0.00 0.00 40.28 2.17
197 198 3.452264 TCCGATCATCCAGTGACAGATTT 59.548 43.478 0.00 0.00 40.28 2.17
224 225 0.112995 AAGAGCCACTGCATTTCCCA 59.887 50.000 0.00 0.00 41.13 4.37
258 259 1.157585 GAGGCTTTGGTTCTCCGAAC 58.842 55.000 0.00 0.00 33.84 3.95
259 260 0.320421 CGAGGCTTTGGTTCTCCGAA 60.320 55.000 0.00 0.00 35.91 4.30
260 261 1.292223 CGAGGCTTTGGTTCTCCGA 59.708 57.895 0.00 0.00 36.30 4.55
261 262 1.741770 CCGAGGCTTTGGTTCTCCG 60.742 63.158 0.00 0.00 36.30 4.63
262 263 1.377333 CCCGAGGCTTTGGTTCTCC 60.377 63.158 0.72 0.00 0.00 3.71
263 264 0.253327 ATCCCGAGGCTTTGGTTCTC 59.747 55.000 0.72 0.00 0.00 2.87
264 265 0.253327 GATCCCGAGGCTTTGGTTCT 59.747 55.000 0.72 0.00 0.00 3.01
265 266 0.035439 TGATCCCGAGGCTTTGGTTC 60.035 55.000 0.72 6.66 0.00 3.62
286 287 3.068873 AGAAGGGATGTATCTTCACTCGC 59.931 47.826 0.00 0.00 41.16 5.03
322 323 7.435488 TGTGTTTATTTTTATCACACCAAACGG 59.565 33.333 0.00 0.00 37.53 4.44
336 337 3.258123 AGGCCGCATCTGTGTTTATTTTT 59.742 39.130 0.00 0.00 0.00 1.94
340 341 2.017049 GAAGGCCGCATCTGTGTTTAT 58.983 47.619 0.00 0.00 0.00 1.40
423 424 4.760047 GCCCTGCTCGCGGAGAAA 62.760 66.667 6.13 0.00 0.00 2.52
431 432 4.598894 CCCTCATCGCCCTGCTCG 62.599 72.222 0.00 0.00 0.00 5.03
450 451 3.386768 TCTTCCACAGAGTAGTTGCAC 57.613 47.619 0.00 0.00 0.00 4.57
455 456 3.501349 TCTGCTTCTTCCACAGAGTAGT 58.499 45.455 0.00 0.00 35.58 2.73
481 482 0.638292 ATCCCCAACAGGATGGCATT 59.362 50.000 0.00 0.00 45.25 3.56
493 494 1.542328 CGACAGTGTTGTGATCCCCAA 60.542 52.381 0.00 0.00 37.76 4.12
510 511 0.104304 CACCCTAGTACATGGCCGAC 59.896 60.000 0.00 0.00 0.00 4.79
512 513 0.104304 GTCACCCTAGTACATGGCCG 59.896 60.000 0.00 0.00 0.00 6.13
648 649 1.274167 ACCGCTTTGATCCTGAACGTA 59.726 47.619 0.00 0.00 0.00 3.57
708 709 3.474570 CCCTCTCGCCTTCCCCAG 61.475 72.222 0.00 0.00 0.00 4.45
833 834 6.017770 ACTCCGAATGTGTTTGTCGATTTTTA 60.018 34.615 0.00 0.00 36.92 1.52
834 835 5.176407 TCCGAATGTGTTTGTCGATTTTT 57.824 34.783 0.00 0.00 36.92 1.94
835 836 4.274950 ACTCCGAATGTGTTTGTCGATTTT 59.725 37.500 0.00 0.00 36.92 1.82
836 837 3.813166 ACTCCGAATGTGTTTGTCGATTT 59.187 39.130 0.00 0.00 36.92 2.17
837 838 3.399330 ACTCCGAATGTGTTTGTCGATT 58.601 40.909 0.00 0.00 36.92 3.34
838 839 3.040147 ACTCCGAATGTGTTTGTCGAT 57.960 42.857 0.00 0.00 36.92 3.59
839 840 2.519377 ACTCCGAATGTGTTTGTCGA 57.481 45.000 0.00 0.00 36.92 4.20
840 841 3.314553 ACTACTCCGAATGTGTTTGTCG 58.685 45.455 0.00 0.00 34.58 4.35
841 842 4.557205 AGACTACTCCGAATGTGTTTGTC 58.443 43.478 0.00 0.00 0.00 3.18
842 843 4.602340 AGACTACTCCGAATGTGTTTGT 57.398 40.909 0.00 0.00 0.00 2.83
843 844 7.416154 TTTTAGACTACTCCGAATGTGTTTG 57.584 36.000 0.00 0.00 0.00 2.93
844 845 6.147328 GCTTTTAGACTACTCCGAATGTGTTT 59.853 38.462 0.00 0.00 0.00 2.83
845 846 5.638234 GCTTTTAGACTACTCCGAATGTGTT 59.362 40.000 0.00 0.00 0.00 3.32
846 847 5.169295 GCTTTTAGACTACTCCGAATGTGT 58.831 41.667 0.00 0.00 0.00 3.72
847 848 5.062308 GTGCTTTTAGACTACTCCGAATGTG 59.938 44.000 0.00 0.00 0.00 3.21
848 849 5.169295 GTGCTTTTAGACTACTCCGAATGT 58.831 41.667 0.00 0.00 0.00 2.71
849 850 5.168569 TGTGCTTTTAGACTACTCCGAATG 58.831 41.667 0.00 0.00 0.00 2.67
850 851 5.401531 TGTGCTTTTAGACTACTCCGAAT 57.598 39.130 0.00 0.00 0.00 3.34
851 852 4.859304 TGTGCTTTTAGACTACTCCGAA 57.141 40.909 0.00 0.00 0.00 4.30
852 853 4.859304 TTGTGCTTTTAGACTACTCCGA 57.141 40.909 0.00 0.00 0.00 4.55
853 854 4.989168 AGTTTGTGCTTTTAGACTACTCCG 59.011 41.667 0.00 0.00 0.00 4.63
1240 1242 0.659957 GCGGTTGAAGAGATGATGGC 59.340 55.000 0.00 0.00 0.00 4.40
1272 1274 0.900647 AGAAGAGTGAGGGTGGACGG 60.901 60.000 0.00 0.00 0.00 4.79
1278 1280 2.224646 GGAAAGCAAGAAGAGTGAGGGT 60.225 50.000 0.00 0.00 0.00 4.34
1322 1324 3.121030 CGCAGCAACTCCTTCGGG 61.121 66.667 0.00 0.00 0.00 5.14
1438 1440 7.639378 ACCAAATTAGGAGGATAAACTAAGCA 58.361 34.615 0.00 0.00 31.02 3.91
1492 1522 1.469126 CGAAGCTGCATTGCGATTGC 61.469 55.000 1.02 0.00 43.20 3.56
1493 1523 0.864377 CCGAAGCTGCATTGCGATTG 60.864 55.000 1.02 0.00 38.13 2.67
1494 1524 1.026182 TCCGAAGCTGCATTGCGATT 61.026 50.000 1.02 4.05 38.13 3.34
1495 1525 1.434622 CTCCGAAGCTGCATTGCGAT 61.435 55.000 1.02 0.00 38.13 4.58
1815 1846 3.681417 TCTTGAGATGTCTGCAATGAACG 59.319 43.478 0.00 0.00 0.00 3.95
1871 1909 9.059260 GCCATAAAAATAGACCCGATAAGTTTA 57.941 33.333 0.00 0.00 0.00 2.01
1872 1910 7.558444 TGCCATAAAAATAGACCCGATAAGTTT 59.442 33.333 0.00 0.00 0.00 2.66
1875 1913 7.504924 TTGCCATAAAAATAGACCCGATAAG 57.495 36.000 0.00 0.00 0.00 1.73
1876 1914 7.883391 TTTGCCATAAAAATAGACCCGATAA 57.117 32.000 0.00 0.00 0.00 1.75
1887 1925 8.603181 GCTAACGATCAATTTTGCCATAAAAAT 58.397 29.630 0.00 0.00 40.60 1.82
1893 1931 4.989279 AGCTAACGATCAATTTTGCCAT 57.011 36.364 0.00 0.00 0.00 4.40
1913 1951 5.293814 CAGAGAATGATCTGCACAAGGTTAG 59.706 44.000 0.00 0.00 40.26 2.34
2037 2075 0.961019 GAATTGGTTGCTCACAGGCA 59.039 50.000 0.00 0.00 40.74 4.75
2039 2077 2.030540 CACAGAATTGGTTGCTCACAGG 60.031 50.000 0.00 0.00 0.00 4.00
2041 2079 2.358582 CACACAGAATTGGTTGCTCACA 59.641 45.455 0.00 0.00 0.00 3.58
2042 2080 2.358898 ACACACAGAATTGGTTGCTCAC 59.641 45.455 0.00 0.00 0.00 3.51
2043 2081 2.653726 ACACACAGAATTGGTTGCTCA 58.346 42.857 0.00 0.00 0.00 4.26
2044 2082 3.715628 AACACACAGAATTGGTTGCTC 57.284 42.857 0.00 0.00 0.00 4.26
2046 2084 4.629200 TCAAAAACACACAGAATTGGTTGC 59.371 37.500 0.00 0.00 0.00 4.17
2067 2106 7.727578 TGAACACCTGTAATAAGACCTATCA 57.272 36.000 0.00 0.00 0.00 2.15
2143 2192 6.639563 AGCAAGTTGAAAAAGTGGTTACATT 58.360 32.000 7.16 0.00 0.00 2.71
2241 2299 1.336440 TGAAAACAACCTGTGATGGCG 59.664 47.619 0.00 0.00 0.00 5.69
2243 2301 7.543172 CAGAAATATGAAAACAACCTGTGATGG 59.457 37.037 0.00 0.00 0.00 3.51
2267 2450 9.278734 GAAAAGACTTTTCACAGTAAAGAACAG 57.721 33.333 28.05 0.00 46.34 3.16
2435 2622 2.234908 AGCTTACGAAGACTCCAAGCAT 59.765 45.455 7.30 0.00 43.15 3.79
2634 2822 9.563748 AATGATTGGTTGTTCTGAAATGATTTT 57.436 25.926 0.00 0.00 0.00 1.82
2677 2865 3.132111 AGGCAAACAAAACCTTACCACAG 59.868 43.478 0.00 0.00 0.00 3.66
2688 2876 2.159114 GCAAGACTGGAGGCAAACAAAA 60.159 45.455 0.00 0.00 0.00 2.44
2692 2880 1.322442 AAGCAAGACTGGAGGCAAAC 58.678 50.000 0.00 0.00 0.00 2.93
2693 2881 2.949177 TAAGCAAGACTGGAGGCAAA 57.051 45.000 0.00 0.00 0.00 3.68
2694 2882 2.305635 TGATAAGCAAGACTGGAGGCAA 59.694 45.455 0.00 0.00 0.00 4.52
2696 2884 2.093235 ACTGATAAGCAAGACTGGAGGC 60.093 50.000 0.00 0.00 0.00 4.70
2697 2885 3.529533 CACTGATAAGCAAGACTGGAGG 58.470 50.000 0.00 0.00 0.00 4.30
2699 2887 2.355108 GGCACTGATAAGCAAGACTGGA 60.355 50.000 0.00 0.00 0.00 3.86
2700 2888 2.012673 GGCACTGATAAGCAAGACTGG 58.987 52.381 0.00 0.00 0.00 4.00
2702 2890 3.710209 AAGGCACTGATAAGCAAGACT 57.290 42.857 0.00 0.00 40.86 3.24
2704 2892 4.655963 AGAAAAGGCACTGATAAGCAAGA 58.344 39.130 0.00 0.00 40.86 3.02
2705 2893 5.159209 CAAGAAAAGGCACTGATAAGCAAG 58.841 41.667 0.00 0.00 40.86 4.01
2706 2894 4.584325 ACAAGAAAAGGCACTGATAAGCAA 59.416 37.500 0.00 0.00 40.86 3.91
2708 2896 4.773323 ACAAGAAAAGGCACTGATAAGC 57.227 40.909 0.00 0.00 40.86 3.09
2709 2897 6.317789 TGAACAAGAAAAGGCACTGATAAG 57.682 37.500 0.00 0.00 40.86 1.73
2711 2899 6.899393 ATTGAACAAGAAAAGGCACTGATA 57.101 33.333 0.00 0.00 40.86 2.15
2712 2900 5.796424 ATTGAACAAGAAAAGGCACTGAT 57.204 34.783 0.00 0.00 40.86 2.90
2713 2901 5.592282 TGTATTGAACAAGAAAAGGCACTGA 59.408 36.000 0.00 0.00 34.35 3.41
2714 2902 5.830912 TGTATTGAACAAGAAAAGGCACTG 58.169 37.500 0.00 0.00 34.35 3.66
2715 2903 5.594317 ACTGTATTGAACAAGAAAAGGCACT 59.406 36.000 0.00 0.00 37.95 4.40
2716 2904 5.831997 ACTGTATTGAACAAGAAAAGGCAC 58.168 37.500 0.00 0.00 37.74 5.01
2717 2905 6.463995 AACTGTATTGAACAAGAAAAGGCA 57.536 33.333 0.00 0.00 37.74 4.75
2718 2906 6.756542 ACAAACTGTATTGAACAAGAAAAGGC 59.243 34.615 8.86 0.00 37.74 4.35
2719 2907 9.965824 ATACAAACTGTATTGAACAAGAAAAGG 57.034 29.630 8.86 0.00 40.40 3.11
2768 2957 7.241042 AGGGCGAGCAATTCTATTTACTATA 57.759 36.000 0.00 0.00 0.00 1.31
2795 2984 9.528489 ACTCTTGTTATTTCTTTTGCCCTATTA 57.472 29.630 0.00 0.00 0.00 0.98
2796 2985 8.422577 ACTCTTGTTATTTCTTTTGCCCTATT 57.577 30.769 0.00 0.00 0.00 1.73
2797 2986 8.422577 AACTCTTGTTATTTCTTTTGCCCTAT 57.577 30.769 0.00 0.00 34.15 2.57
2826 3015 2.636893 ACACTGATGGAAGAAGCTCTGT 59.363 45.455 0.00 0.00 0.00 3.41
2827 3016 3.331478 ACACTGATGGAAGAAGCTCTG 57.669 47.619 0.00 0.00 0.00 3.35
2828 3017 6.326064 ACATATACACTGATGGAAGAAGCTCT 59.674 38.462 0.00 0.00 0.00 4.09
2829 3018 6.520272 ACATATACACTGATGGAAGAAGCTC 58.480 40.000 0.00 0.00 0.00 4.09
2830 3019 6.491714 ACATATACACTGATGGAAGAAGCT 57.508 37.500 0.00 0.00 0.00 3.74
2831 3020 7.928706 AGTAACATATACACTGATGGAAGAAGC 59.071 37.037 0.00 0.00 0.00 3.86
2832 3021 9.823647 AAGTAACATATACACTGATGGAAGAAG 57.176 33.333 0.00 0.00 0.00 2.85
2833 3022 9.817809 GAAGTAACATATACACTGATGGAAGAA 57.182 33.333 0.00 0.00 0.00 2.52
2835 3024 8.424918 AGGAAGTAACATATACACTGATGGAAG 58.575 37.037 0.00 0.00 0.00 3.46
2836 3025 8.319057 AGGAAGTAACATATACACTGATGGAA 57.681 34.615 0.00 0.00 0.00 3.53
2837 3026 7.015292 GGAGGAAGTAACATATACACTGATGGA 59.985 40.741 0.00 0.00 0.00 3.41
2838 3027 7.155328 GGAGGAAGTAACATATACACTGATGG 58.845 42.308 0.00 0.00 0.00 3.51
2839 3028 7.726216 TGGAGGAAGTAACATATACACTGATG 58.274 38.462 0.00 0.00 0.00 3.07
2840 3029 7.914427 TGGAGGAAGTAACATATACACTGAT 57.086 36.000 0.00 0.00 0.00 2.90
2841 3030 7.727578 TTGGAGGAAGTAACATATACACTGA 57.272 36.000 0.00 0.00 0.00 3.41
2842 3031 7.987458 ACATTGGAGGAAGTAACATATACACTG 59.013 37.037 0.00 0.00 0.00 3.66
2843 3032 8.090788 ACATTGGAGGAAGTAACATATACACT 57.909 34.615 0.00 0.00 0.00 3.55
2844 3033 8.732746 AACATTGGAGGAAGTAACATATACAC 57.267 34.615 0.00 0.00 0.00 2.90
2845 3034 9.747898 AAAACATTGGAGGAAGTAACATATACA 57.252 29.630 0.00 0.00 0.00 2.29
2854 3043 7.918076 ACAGATAGAAAACATTGGAGGAAGTA 58.082 34.615 0.00 0.00 0.00 2.24
2862 3051 8.647143 AAAACACAACAGATAGAAAACATTGG 57.353 30.769 0.00 0.00 0.00 3.16
2893 3083 8.443160 CACAAGAGATAGAAAGCATTAAACGAA 58.557 33.333 0.00 0.00 0.00 3.85
2976 3167 3.627395 AAGCGATGGGAATCACACTAA 57.373 42.857 0.00 0.00 0.00 2.24
2984 3175 2.290641 TGGTACACAAAGCGATGGGAAT 60.291 45.455 0.80 0.00 0.00 3.01
3041 3237 4.508461 TCCAAGCAATCACAGTTCATTG 57.492 40.909 0.00 0.00 33.77 2.82
3068 3264 7.397892 TTGCCGGTTCTTCATCAATTTATAA 57.602 32.000 1.90 0.00 0.00 0.98
3076 3272 2.091541 GGATTTGCCGGTTCTTCATCA 58.908 47.619 1.90 0.00 0.00 3.07
3078 3274 2.493278 CAAGGATTTGCCGGTTCTTCAT 59.507 45.455 1.90 0.00 43.43 2.57
3087 3283 3.119531 TGCACTTTATCAAGGATTTGCCG 60.120 43.478 0.00 0.00 43.43 5.69
3121 3318 6.375455 ACTGACAAGATTTTGCGGATTATCTT 59.625 34.615 7.82 7.82 37.72 2.40
3131 3328 9.195411 TGATATTTTTCACTGACAAGATTTTGC 57.805 29.630 0.00 0.00 37.85 3.68
3168 3365 7.888021 TCAAACCCAGATGTGACTTTGTATAAT 59.112 33.333 10.18 0.00 0.00 1.28
3169 3366 7.227873 TCAAACCCAGATGTGACTTTGTATAA 58.772 34.615 10.18 0.00 0.00 0.98
3205 3402 6.039159 CCTTTTCCTCTGATTATTTGGAGAGC 59.961 42.308 0.00 0.00 32.17 4.09
3229 3426 7.436376 GCTGTTTGAAATAATTATGCCTCTTCC 59.564 37.037 0.00 0.00 0.00 3.46
3235 3432 6.363357 GGATCGCTGTTTGAAATAATTATGCC 59.637 38.462 0.00 0.00 0.00 4.40
3236 3433 6.917477 TGGATCGCTGTTTGAAATAATTATGC 59.083 34.615 0.00 0.00 0.00 3.14
3268 3465 9.120538 TGATCATTCCACTTTATAAGGCTTTAC 57.879 33.333 4.45 0.00 0.00 2.01
3287 3484 4.202377 CCTCTGCTTCTCCAGATGATCATT 60.202 45.833 10.14 0.00 40.77 2.57
3288 3485 3.325425 CCTCTGCTTCTCCAGATGATCAT 59.675 47.826 8.25 8.25 40.77 2.45


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

AutoCloner maintained by Alex Coulton.