Multiple sequence alignment - TraesCS3A01G229500

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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 TraesCS3A01G229500 chr3A 100.000 2760 0 0 1 2760 429483380 429480621 0.000000e+00 5097.0
1 TraesCS3A01G229500 chr3A 93.182 88 4 2 2675 2760 212025783 212025696 8.020000e-26 128.0
2 TraesCS3A01G229500 chr3A 97.297 37 1 0 1280 1316 72897686 72897650 2.290000e-06 63.9
3 TraesCS3A01G229500 chr3D 90.699 2731 153 46 19 2689 305321166 305323855 0.000000e+00 3542.0
4 TraesCS3A01G229500 chr3D 81.481 81 13 2 1280 1359 63460724 63460645 6.380000e-07 65.8
5 TraesCS3A01G229500 chr3B 89.409 1794 111 36 1 1765 416515332 416513589 0.000000e+00 2187.0
6 TraesCS3A01G229500 chr3B 86.324 797 79 9 1908 2692 416513395 416512617 0.000000e+00 841.0
7 TraesCS3A01G229500 chr3B 90.566 53 5 0 1815 1867 416513462 416513410 1.370000e-08 71.3
8 TraesCS3A01G229500 chr6A 96.386 83 1 2 2678 2760 295085845 295085925 4.790000e-28 135.0
9 TraesCS3A01G229500 chr6A 97.333 75 2 0 2686 2760 94134369 94134295 8.020000e-26 128.0
10 TraesCS3A01G229500 chr6A 83.544 79 11 2 1281 1358 1126508 1126585 3.810000e-09 73.1
11 TraesCS3A01G229500 chr1B 98.684 76 1 0 2685 2760 110749344 110749269 4.790000e-28 135.0
12 TraesCS3A01G229500 chr1B 96.296 81 2 1 2680 2760 245789453 245789532 6.200000e-27 132.0
13 TraesCS3A01G229500 chr1B 88.073 109 6 6 2657 2760 545744142 545744036 3.730000e-24 122.0
14 TraesCS3A01G229500 chr6B 96.341 82 1 2 2681 2760 33217447 33217366 1.720000e-27 134.0
15 TraesCS3A01G229500 chr2B 97.436 78 2 0 2683 2760 397227447 397227370 1.720000e-27 134.0
16 TraesCS3A01G229500 chr7A 94.118 85 5 0 2676 2760 316127971 316127887 2.230000e-26 130.0
17 TraesCS3A01G229500 chr1D 81.250 96 16 2 1284 1378 8997436 8997342 2.950000e-10 76.8


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 TraesCS3A01G229500 chr3A 429480621 429483380 2759 True 5097.0 5097 100.000000 1 2760 1 chr3A.!!$R3 2759
1 TraesCS3A01G229500 chr3D 305321166 305323855 2689 False 3542.0 3542 90.699000 19 2689 1 chr3D.!!$F1 2670
2 TraesCS3A01G229500 chr3B 416512617 416515332 2715 True 1033.1 2187 88.766333 1 2692 3 chr3B.!!$R1 2691

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
772 796 0.036765 CATGTTGCAAATGCCAGGCT 60.037 50.0 14.15 0.0 41.18 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2730 2917 0.041833 AGCTAGGACCTTGCCTCTCA 59.958 55.0 22.23 0.0 39.5 3.27 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
56 60 2.967459 TGCGTGCATTAGTGAACTTG 57.033 45.000 0.00 0.00 31.11 3.16
68 72 2.505819 AGTGAACTTGAACCCAGTGAGT 59.494 45.455 0.00 0.00 0.00 3.41
92 96 5.168569 TGGTTCTAGCACACGAATTCTAAG 58.831 41.667 3.52 0.00 0.00 2.18
96 100 6.144078 TCTAGCACACGAATTCTAAGCATA 57.856 37.500 3.52 0.00 0.00 3.14
97 101 5.977725 TCTAGCACACGAATTCTAAGCATAC 59.022 40.000 3.52 0.00 0.00 2.39
101 105 3.797256 ACACGAATTCTAAGCATACGAGC 59.203 43.478 3.52 0.00 0.00 5.03
105 109 4.617645 CGAATTCTAAGCATACGAGCTACC 59.382 45.833 3.52 0.00 45.89 3.18
115 119 1.226717 CGAGCTACCCTCAACTCGC 60.227 63.158 0.00 0.00 44.56 5.03
116 120 1.226717 GAGCTACCCTCAACTCGCG 60.227 63.158 0.00 0.00 40.45 5.87
126 130 0.673333 TCAACTCGCGCCATGTTCAT 60.673 50.000 0.00 0.00 0.00 2.57
135 139 1.468565 CGCCATGTTCATTTCAGCTGG 60.469 52.381 15.13 0.00 0.00 4.85
189 193 2.333581 CACCGGAAAAACGTGCCC 59.666 61.111 9.46 0.00 0.00 5.36
215 219 1.415659 GGCCTCACAGCACATCTATCT 59.584 52.381 0.00 0.00 0.00 1.98
223 227 7.294017 TCACAGCACATCTATCTATCAATCA 57.706 36.000 0.00 0.00 0.00 2.57
224 228 7.729116 TCACAGCACATCTATCTATCAATCAA 58.271 34.615 0.00 0.00 0.00 2.57
225 229 8.373220 TCACAGCACATCTATCTATCAATCAAT 58.627 33.333 0.00 0.00 0.00 2.57
226 230 8.657729 CACAGCACATCTATCTATCAATCAATC 58.342 37.037 0.00 0.00 0.00 2.67
227 231 7.823310 ACAGCACATCTATCTATCAATCAATCC 59.177 37.037 0.00 0.00 0.00 3.01
228 232 7.822822 CAGCACATCTATCTATCAATCAATCCA 59.177 37.037 0.00 0.00 0.00 3.41
229 233 7.823310 AGCACATCTATCTATCAATCAATCCAC 59.177 37.037 0.00 0.00 0.00 4.02
230 234 7.823310 GCACATCTATCTATCAATCAATCCACT 59.177 37.037 0.00 0.00 0.00 4.00
231 235 9.368674 CACATCTATCTATCAATCAATCCACTC 57.631 37.037 0.00 0.00 0.00 3.51
240 249 0.320374 TCAATCCACTCCACGGTGAC 59.680 55.000 10.28 0.00 39.34 3.67
424 433 1.081556 CGATCGTTCCATCGCCAACA 61.082 55.000 7.03 0.00 39.32 3.33
451 460 2.434884 AGCGCACATTCACTCGGG 60.435 61.111 11.47 0.00 0.00 5.14
492 501 2.106511 CTCTCCTCTGGTTTGGTTTGGA 59.893 50.000 0.00 0.00 0.00 3.53
493 502 2.158667 TCTCCTCTGGTTTGGTTTGGAC 60.159 50.000 0.00 0.00 0.00 4.02
532 542 3.387397 GTTACAGCTGTACGTGTCCTTT 58.613 45.455 26.02 0.00 0.00 3.11
533 543 1.865865 ACAGCTGTACGTGTCCTTTG 58.134 50.000 20.16 0.00 0.00 2.77
552 562 2.027024 TCACCGTCGAGTGTGCAC 59.973 61.111 10.75 10.75 38.91 4.57
633 643 5.791666 AGTTTCTTCTTCTAGTTAACCCGG 58.208 41.667 0.88 0.00 0.00 5.73
637 648 5.324409 TCTTCTTCTAGTTAACCCGGTGTA 58.676 41.667 0.00 0.00 0.00 2.90
664 680 2.020131 GCACTTGCGATCCATGAGG 58.980 57.895 0.00 0.00 0.00 3.86
667 683 2.086869 CACTTGCGATCCATGAGGTTT 58.913 47.619 0.00 0.00 35.89 3.27
671 687 1.103398 GCGATCCATGAGGTTTGGGG 61.103 60.000 0.00 0.00 34.85 4.96
714 737 6.824704 CCCAAATGGAAGCACATCAAAATAAT 59.175 34.615 0.00 0.00 37.39 1.28
772 796 0.036765 CATGTTGCAAATGCCAGGCT 60.037 50.000 14.15 0.00 41.18 4.58
781 805 1.180029 AATGCCAGGCTAACAGCAAG 58.820 50.000 14.15 0.00 44.75 4.01
807 831 2.224305 GGGCACGTGGCTCTAATCTAAT 60.224 50.000 36.61 0.00 41.00 1.73
808 832 3.006537 GGGCACGTGGCTCTAATCTAATA 59.993 47.826 36.61 0.00 41.00 0.98
809 833 3.988517 GGCACGTGGCTCTAATCTAATAC 59.011 47.826 32.54 2.50 44.01 1.89
810 834 4.262079 GGCACGTGGCTCTAATCTAATACT 60.262 45.833 32.54 0.00 44.01 2.12
811 835 4.918583 GCACGTGGCTCTAATCTAATACTC 59.081 45.833 18.88 0.00 40.25 2.59
812 836 5.462405 CACGTGGCTCTAATCTAATACTCC 58.538 45.833 7.95 0.00 0.00 3.85
820 844 9.689501 GGCTCTAATCTAATACTCCTACTACAT 57.310 37.037 0.00 0.00 0.00 2.29
940 969 1.153939 CTCAGCTTCACCGAGGACG 60.154 63.158 0.00 0.00 39.43 4.79
943 972 1.901948 AGCTTCACCGAGGACGACA 60.902 57.895 0.00 0.00 42.66 4.35
982 1011 1.128200 TCCCGAGAGAGAGAGAGAGG 58.872 60.000 0.00 0.00 0.00 3.69
990 1037 5.261216 GAGAGAGAGAGAGAGGGAGAAAAA 58.739 45.833 0.00 0.00 0.00 1.94
1178 1225 6.297080 TCAACATTGATTAATTGCCATGGT 57.703 33.333 14.67 0.00 31.01 3.55
1211 1258 1.667236 TGCTGCCAGTTGAATATCGG 58.333 50.000 0.00 0.00 0.00 4.18
1237 1285 8.789743 GTCGAAGCTTATAAAGATTTCTTTTGC 58.210 33.333 10.58 10.06 43.07 3.68
1464 1512 3.323979 GTCAAGAACTACTGGAGGACCAA 59.676 47.826 0.00 0.00 46.32 3.67
1483 1531 2.038837 GGTACACAAGAAGGCGCCC 61.039 63.158 26.15 9.10 0.00 6.13
1484 1532 2.047655 TACACAAGAAGGCGCCCG 60.048 61.111 26.15 9.46 0.00 6.13
1485 1533 3.599285 TACACAAGAAGGCGCCCGG 62.599 63.158 26.15 10.96 0.00 5.73
1639 1714 1.884004 CGACCACCACGAAACGGTT 60.884 57.895 0.00 0.00 33.25 4.44
1756 1831 0.317479 ACCCAGTGTACGAAGCACTC 59.683 55.000 7.94 0.00 44.43 3.51
1867 2023 5.508489 GGACTTGATCAATTATGCATGGTGG 60.508 44.000 10.16 0.00 0.00 4.61
1868 2024 4.202182 ACTTGATCAATTATGCATGGTGGC 60.202 41.667 10.16 2.01 0.00 5.01
1916 2091 3.395639 TGTAAACTGGTCGATGAACCAC 58.604 45.455 0.00 0.00 44.40 4.16
2147 2322 0.908198 AAGAGCCTTCCTGCCTAGTG 59.092 55.000 0.00 0.00 0.00 2.74
2153 2328 2.324541 CCTTCCTGCCTAGTGCTATCT 58.675 52.381 5.06 0.00 42.00 1.98
2191 2366 4.827692 TCAATAGCTACATTTCGTGTGGT 58.172 39.130 0.00 0.00 42.24 4.16
2224 2399 3.075005 TACGGCTGGGCTCCTCAC 61.075 66.667 0.00 0.00 0.00 3.51
2247 2433 9.930693 TCACATGCCAATTATATGTTATACGTA 57.069 29.630 0.00 0.00 33.06 3.57
2269 2455 0.034337 GGCAAACGGTCTGGTCAGTA 59.966 55.000 0.00 0.00 0.00 2.74
2285 2471 4.312443 GTCAGTAACCGGTCAAGAAATCA 58.688 43.478 8.04 0.00 0.00 2.57
2309 2495 2.157942 ACCCAGCTATCCCATATCCAGT 60.158 50.000 0.00 0.00 0.00 4.00
2314 2500 4.964897 CAGCTATCCCATATCCAGTCCATA 59.035 45.833 0.00 0.00 0.00 2.74
2317 2503 5.843421 GCTATCCCATATCCAGTCCATATCT 59.157 44.000 0.00 0.00 0.00 1.98
2318 2504 7.013220 GCTATCCCATATCCAGTCCATATCTA 58.987 42.308 0.00 0.00 0.00 1.98
2321 2507 5.499852 TCCCATATCCAGTCCATATCTAGGA 59.500 44.000 0.00 0.00 0.00 2.94
2332 2518 1.938585 TATCTAGGAAGGCCCGGATG 58.061 55.000 0.73 0.00 40.87 3.51
2399 2586 6.479660 CCATCACAAATTTAATCAAATCCCCG 59.520 38.462 0.00 0.00 33.09 5.73
2401 2588 5.717178 TCACAAATTTAATCAAATCCCCGGA 59.283 36.000 0.73 0.00 33.09 5.14
2417 2604 2.517609 GGACCTAGCCCGATCAACT 58.482 57.895 0.00 0.00 0.00 3.16
2428 2615 3.870299 GCCCGATCAACTCTTTTCCTCTT 60.870 47.826 0.00 0.00 0.00 2.85
2433 2620 6.127591 CCGATCAACTCTTTTCCTCTTCTCTA 60.128 42.308 0.00 0.00 0.00 2.43
2438 2625 8.875168 TCAACTCTTTTCCTCTTCTCTATTCTT 58.125 33.333 0.00 0.00 0.00 2.52
2449 2636 0.661552 TCTATTCTTCCTCGTCGGCG 59.338 55.000 1.15 1.15 39.92 6.46
2471 2658 2.060980 CCCCTCCTCTAGCTGCGTT 61.061 63.158 0.00 0.00 0.00 4.84
2481 2668 0.970640 TAGCTGCGTTGTCACCCTAA 59.029 50.000 0.00 0.00 0.00 2.69
2527 2714 1.303724 CCGCCACCACCACCATAAA 60.304 57.895 0.00 0.00 0.00 1.40
2545 2732 1.140312 AAACTCCTCCTTGCCAGTCA 58.860 50.000 0.00 0.00 0.00 3.41
2547 2734 0.764369 ACTCCTCCTTGCCAGTCACA 60.764 55.000 0.00 0.00 0.00 3.58
2559 2746 4.612412 GTCACACCGCCCCGAACA 62.612 66.667 0.00 0.00 0.00 3.18
2567 2754 2.046700 GCCCCGAACATCGTTGGA 60.047 61.111 9.03 0.00 38.40 3.53
2571 2758 1.138266 CCCCGAACATCGTTGGAGTAT 59.862 52.381 0.00 0.00 38.40 2.12
2613 2800 1.064758 ACCTTGCCTTCTGTGTGTTCA 60.065 47.619 0.00 0.00 0.00 3.18
2615 2802 2.624838 CCTTGCCTTCTGTGTGTTCAAT 59.375 45.455 0.00 0.00 0.00 2.57
2661 2848 5.759506 TTCTTTTGTAGGCAAAACGATGA 57.240 34.783 0.00 0.00 46.12 2.92
2662 2849 5.957842 TCTTTTGTAGGCAAAACGATGAT 57.042 34.783 0.00 0.00 46.12 2.45
2664 2851 7.441890 TCTTTTGTAGGCAAAACGATGATTA 57.558 32.000 0.00 0.00 46.12 1.75
2689 2876 0.179134 GGTTCGTCGGATGAGGAGTG 60.179 60.000 0.00 0.00 39.90 3.51
2692 2879 1.062685 CGTCGGATGAGGAGTGTCG 59.937 63.158 0.00 0.00 31.63 4.35
2693 2880 1.645704 CGTCGGATGAGGAGTGTCGT 61.646 60.000 0.00 0.00 31.63 4.34
2694 2881 0.179161 GTCGGATGAGGAGTGTCGTG 60.179 60.000 0.00 0.00 0.00 4.35
2695 2882 1.139734 CGGATGAGGAGTGTCGTGG 59.860 63.158 0.00 0.00 0.00 4.94
2696 2883 1.595993 CGGATGAGGAGTGTCGTGGT 61.596 60.000 0.00 0.00 0.00 4.16
2697 2884 0.608640 GGATGAGGAGTGTCGTGGTT 59.391 55.000 0.00 0.00 0.00 3.67
2698 2885 1.404315 GGATGAGGAGTGTCGTGGTTC 60.404 57.143 0.00 0.00 0.00 3.62
2699 2886 0.608640 ATGAGGAGTGTCGTGGTTCC 59.391 55.000 0.00 0.00 0.00 3.62
2700 2887 0.757561 TGAGGAGTGTCGTGGTTCCA 60.758 55.000 0.00 0.00 32.02 3.53
2701 2888 0.391597 GAGGAGTGTCGTGGTTCCAA 59.608 55.000 0.00 0.00 32.02 3.53
2702 2889 0.393077 AGGAGTGTCGTGGTTCCAAG 59.607 55.000 0.00 0.00 32.02 3.61
2703 2890 1.228657 GGAGTGTCGTGGTTCCAAGC 61.229 60.000 0.11 0.00 0.00 4.01
2704 2891 1.227853 AGTGTCGTGGTTCCAAGCC 60.228 57.895 0.11 0.00 0.00 4.35
2705 2892 1.227853 GTGTCGTGGTTCCAAGCCT 60.228 57.895 0.11 0.00 0.00 4.58
2706 2893 1.227823 TGTCGTGGTTCCAAGCCTG 60.228 57.895 0.11 0.00 0.00 4.85
2707 2894 1.070786 GTCGTGGTTCCAAGCCTGA 59.929 57.895 0.11 0.00 0.00 3.86
2708 2895 1.070786 TCGTGGTTCCAAGCCTGAC 59.929 57.895 0.11 0.00 0.00 3.51
2709 2896 1.227823 CGTGGTTCCAAGCCTGACA 60.228 57.895 0.00 0.00 0.00 3.58
2710 2897 1.230635 CGTGGTTCCAAGCCTGACAG 61.231 60.000 0.00 0.00 0.00 3.51
2711 2898 0.179018 GTGGTTCCAAGCCTGACAGT 60.179 55.000 0.93 0.00 0.00 3.55
2712 2899 1.071699 GTGGTTCCAAGCCTGACAGTA 59.928 52.381 0.93 0.00 0.00 2.74
2713 2900 1.347707 TGGTTCCAAGCCTGACAGTAG 59.652 52.381 0.93 0.00 0.00 2.57
2714 2901 1.623811 GGTTCCAAGCCTGACAGTAGA 59.376 52.381 0.93 0.00 0.00 2.59
2715 2902 2.354203 GGTTCCAAGCCTGACAGTAGAG 60.354 54.545 0.93 0.00 0.00 2.43
2716 2903 2.300437 GTTCCAAGCCTGACAGTAGAGT 59.700 50.000 0.93 0.00 0.00 3.24
2717 2904 1.895798 TCCAAGCCTGACAGTAGAGTG 59.104 52.381 0.93 0.00 0.00 3.51
2718 2905 1.066573 CCAAGCCTGACAGTAGAGTGG 60.067 57.143 0.93 0.00 0.00 4.00
2719 2906 1.066573 CAAGCCTGACAGTAGAGTGGG 60.067 57.143 0.93 0.00 0.00 4.61
2720 2907 0.616111 AGCCTGACAGTAGAGTGGGG 60.616 60.000 0.93 0.00 0.00 4.96
2721 2908 1.617947 GCCTGACAGTAGAGTGGGGG 61.618 65.000 0.93 0.00 0.00 5.40
2737 2924 1.057471 GGGGGTAGGTATTGAGAGGC 58.943 60.000 0.00 0.00 0.00 4.70
2738 2925 1.694693 GGGGGTAGGTATTGAGAGGCA 60.695 57.143 0.00 0.00 0.00 4.75
2739 2926 2.124411 GGGGTAGGTATTGAGAGGCAA 58.876 52.381 0.00 0.00 41.53 4.52
2740 2927 2.104963 GGGGTAGGTATTGAGAGGCAAG 59.895 54.545 0.00 0.00 40.42 4.01
2741 2928 2.104963 GGGTAGGTATTGAGAGGCAAGG 59.895 54.545 0.00 0.00 40.42 3.61
2742 2929 2.772515 GGTAGGTATTGAGAGGCAAGGT 59.227 50.000 0.00 0.00 40.42 3.50
2743 2930 3.181464 GGTAGGTATTGAGAGGCAAGGTC 60.181 52.174 0.00 0.00 40.42 3.85
2744 2931 1.840635 AGGTATTGAGAGGCAAGGTCC 59.159 52.381 0.00 0.00 40.42 4.46
2745 2932 1.840635 GGTATTGAGAGGCAAGGTCCT 59.159 52.381 0.00 0.00 40.42 3.85
2746 2933 3.039011 GGTATTGAGAGGCAAGGTCCTA 58.961 50.000 0.00 0.00 40.42 2.94
2747 2934 3.070302 GGTATTGAGAGGCAAGGTCCTAG 59.930 52.174 0.00 0.00 40.42 3.02
2748 2935 0.905357 TTGAGAGGCAAGGTCCTAGC 59.095 55.000 0.00 0.00 36.38 3.42
2749 2936 0.041833 TGAGAGGCAAGGTCCTAGCT 59.958 55.000 0.00 0.00 36.38 3.32
2750 2937 1.288037 TGAGAGGCAAGGTCCTAGCTA 59.712 52.381 0.00 0.00 36.38 3.32
2751 2938 2.091055 TGAGAGGCAAGGTCCTAGCTAT 60.091 50.000 0.00 0.00 36.38 2.97
2752 2939 2.298729 GAGAGGCAAGGTCCTAGCTATG 59.701 54.545 0.00 0.00 36.38 2.23
2753 2940 1.346068 GAGGCAAGGTCCTAGCTATGG 59.654 57.143 0.00 0.00 36.38 2.74
2754 2941 1.062121 AGGCAAGGTCCTAGCTATGGA 60.062 52.381 7.59 7.59 33.95 3.41
2755 2942 1.346068 GGCAAGGTCCTAGCTATGGAG 59.654 57.143 10.98 3.25 33.78 3.86
2756 2943 2.320781 GCAAGGTCCTAGCTATGGAGA 58.679 52.381 10.98 0.00 33.78 3.71
2757 2944 2.298729 GCAAGGTCCTAGCTATGGAGAG 59.701 54.545 10.98 4.83 33.78 3.20
2758 2945 2.896685 CAAGGTCCTAGCTATGGAGAGG 59.103 54.545 10.98 2.28 33.78 3.69
2759 2946 2.148702 AGGTCCTAGCTATGGAGAGGT 58.851 52.381 10.98 0.00 33.78 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.821033 ACTGGGTTCAAGTTCACTAATGC 59.179 43.478 0.00 0.00 0.00 3.56
68 72 4.002906 AGAATTCGTGTGCTAGAACCAA 57.997 40.909 0.00 0.00 0.00 3.67
92 96 1.409427 AGTTGAGGGTAGCTCGTATGC 59.591 52.381 0.00 0.00 0.00 3.14
96 100 2.181584 CGAGTTGAGGGTAGCTCGT 58.818 57.895 0.00 0.00 43.50 4.18
101 105 2.202756 GGCGCGAGTTGAGGGTAG 60.203 66.667 12.10 0.00 0.00 3.18
105 109 1.970917 GAACATGGCGCGAGTTGAGG 61.971 60.000 12.10 0.00 0.00 3.86
115 119 1.468565 CCAGCTGAAATGAACATGGCG 60.469 52.381 17.39 0.00 0.00 5.69
116 120 1.134907 CCCAGCTGAAATGAACATGGC 60.135 52.381 17.39 0.00 0.00 4.40
126 130 3.744660 GAAAGAGACTTCCCAGCTGAAA 58.255 45.455 17.39 8.31 0.00 2.69
135 139 1.406970 CGCTCGCGAAAGAGACTTCC 61.407 60.000 11.33 0.00 42.83 3.46
168 172 1.946267 CACGTTTTTCCGGTGGGAG 59.054 57.895 0.00 0.00 44.98 4.30
215 219 3.454447 ACCGTGGAGTGGATTGATTGATA 59.546 43.478 0.00 0.00 0.00 2.15
223 227 1.677552 GGTCACCGTGGAGTGGATT 59.322 57.895 0.00 0.00 38.34 3.01
224 228 2.291043 GGGTCACCGTGGAGTGGAT 61.291 63.158 0.00 0.00 38.34 3.41
225 229 2.920912 GGGTCACCGTGGAGTGGA 60.921 66.667 0.00 0.00 38.34 4.02
226 230 4.016706 GGGGTCACCGTGGAGTGG 62.017 72.222 0.00 0.00 38.34 4.00
227 231 2.923035 AGGGGTCACCGTGGAGTG 60.923 66.667 0.00 0.00 46.96 3.51
228 232 2.603776 GAGGGGTCACCGTGGAGT 60.604 66.667 0.00 0.00 46.96 3.85
229 233 3.391382 GGAGGGGTCACCGTGGAG 61.391 72.222 0.00 0.00 46.96 3.86
240 249 3.073599 ATGCCGGATTTGGGAGGGG 62.074 63.158 5.05 0.00 30.60 4.79
304 313 1.372128 CTTGCTGCTTGCCCGAAAC 60.372 57.895 0.00 0.00 42.00 2.78
451 460 5.271598 AGAGGATAGATCTCATCCCATCAC 58.728 45.833 19.46 7.78 42.63 3.06
492 501 4.657824 CCGTCGCGTCCACCAAGT 62.658 66.667 5.77 0.00 0.00 3.16
532 542 2.725641 CACACTCGACGGTGACCA 59.274 61.111 19.06 0.00 40.13 4.02
533 543 2.733593 GCACACTCGACGGTGACC 60.734 66.667 19.06 0.00 40.13 4.02
552 562 1.509644 TTTTCGCCTCACTGCTGCAG 61.510 55.000 27.02 27.02 37.52 4.41
633 643 2.279136 CGCAAGTGCTACGAATCTACAC 59.721 50.000 1.21 0.00 39.32 2.90
637 648 2.464865 GATCGCAAGTGCTACGAATCT 58.535 47.619 1.21 0.00 39.56 2.40
661 677 1.173913 GTGCATGTACCCCAAACCTC 58.826 55.000 1.96 0.00 0.00 3.85
664 680 0.802494 CGAGTGCATGTACCCCAAAC 59.198 55.000 10.59 0.00 0.00 2.93
667 683 2.267642 GCGAGTGCATGTACCCCA 59.732 61.111 10.59 0.00 42.15 4.96
671 687 1.521681 GGAGGGCGAGTGCATGTAC 60.522 63.158 5.71 5.71 45.35 2.90
753 777 0.036765 AGCCTGGCATTTGCAACATG 60.037 50.000 22.65 7.87 44.36 3.21
772 796 1.609580 CGTGCCCCTAACTTGCTGTTA 60.610 52.381 3.61 3.61 39.89 2.41
781 805 1.610554 TAGAGCCACGTGCCCCTAAC 61.611 60.000 10.91 0.00 42.71 2.34
807 831 3.428452 GCACGTGCAATGTAGTAGGAGTA 60.428 47.826 34.52 0.00 41.59 2.59
808 832 2.674177 GCACGTGCAATGTAGTAGGAGT 60.674 50.000 34.52 0.00 41.59 3.85
809 833 1.927174 GCACGTGCAATGTAGTAGGAG 59.073 52.381 34.52 0.00 41.59 3.69
810 834 1.404986 GGCACGTGCAATGTAGTAGGA 60.405 52.381 38.60 0.00 44.36 2.94
811 835 1.006832 GGCACGTGCAATGTAGTAGG 58.993 55.000 38.60 0.00 44.36 3.18
812 836 2.010145 AGGCACGTGCAATGTAGTAG 57.990 50.000 38.60 0.00 44.36 2.57
820 844 3.945436 CGTAGAAGGCACGTGCAA 58.055 55.556 38.60 17.33 44.36 4.08
940 969 0.603975 GAGGAGCCCAGTGTTGTGTC 60.604 60.000 0.00 0.00 0.00 3.67
943 972 1.056700 ACAGAGGAGCCCAGTGTTGT 61.057 55.000 0.00 0.00 0.00 3.32
982 1011 3.084786 CCATCCTGGTCAGTTTTTCTCC 58.915 50.000 0.00 0.00 31.35 3.71
1175 1222 3.715495 CAGCAATGCACTACAAAAACCA 58.285 40.909 8.35 0.00 0.00 3.67
1178 1225 2.102084 TGGCAGCAATGCACTACAAAAA 59.898 40.909 8.35 0.00 36.33 1.94
1211 1258 8.789743 GCAAAAGAAATCTTTATAAGCTTCGAC 58.210 33.333 0.00 0.00 44.69 4.20
1237 1285 4.493057 CGAATCGACACATCATCACAAAGG 60.493 45.833 0.00 0.00 0.00 3.11
1385 1433 2.283173 GGCCCACTTGTTCCCCAG 60.283 66.667 0.00 0.00 0.00 4.45
1426 1474 2.595463 ACCTCGTTGTCGGTCCGA 60.595 61.111 10.71 10.71 37.69 4.55
1464 1512 1.003718 GGCGCCTTCTTGTGTACCT 60.004 57.895 22.15 0.00 0.00 3.08
1483 1531 4.711949 AGCTGCTTCTGGTGCCCG 62.712 66.667 0.00 0.00 0.00 6.13
1484 1532 2.282745 AAGCTGCTTCTGGTGCCC 60.283 61.111 9.53 0.00 0.00 5.36
1485 1533 2.338785 GGAAGCTGCTTCTGGTGCC 61.339 63.158 33.75 18.47 40.07 5.01
1567 1642 1.857853 CGTCTGCGTGTACTCGTCG 60.858 63.158 17.63 13.14 0.00 5.12
1756 1831 5.066634 TGCAGAATAAAGAGGACGAGTCTAG 59.933 44.000 3.09 0.00 0.00 2.43
1825 1980 1.408474 CCGCGTAGTGCCGTTTCTAC 61.408 60.000 4.92 0.00 42.08 2.59
1826 1981 1.153978 CCGCGTAGTGCCGTTTCTA 60.154 57.895 4.92 0.00 42.08 2.10
1867 2023 6.653740 ACAACTTCTTGTAAATACCCTACTGC 59.346 38.462 0.00 0.00 38.95 4.40
1868 2024 7.360946 GCACAACTTCTTGTAAATACCCTACTG 60.361 40.741 0.00 0.00 38.66 2.74
1871 2027 6.653320 CAGCACAACTTCTTGTAAATACCCTA 59.347 38.462 0.00 0.00 38.66 3.53
1873 2029 5.240844 ACAGCACAACTTCTTGTAAATACCC 59.759 40.000 0.00 0.00 38.66 3.69
2018 2193 2.076863 CGAGGAAGTCGCCAAATTTCT 58.923 47.619 0.00 0.00 43.03 2.52
2118 2293 4.741342 CAGGAAGGCTCTTTAATTTGCTG 58.259 43.478 0.00 0.00 32.36 4.41
2175 2350 0.802494 CCCACCACACGAAATGTAGC 59.198 55.000 0.00 0.00 40.64 3.58
2191 2366 0.738975 CGTAGATGCTCGAAGTCCCA 59.261 55.000 0.00 0.00 0.00 4.37
2224 2399 8.325282 CCGTACGTATAACATATAATTGGCATG 58.675 37.037 15.21 0.00 0.00 4.06
2230 2405 8.711457 GTTTGCCCGTACGTATAACATATAATT 58.289 33.333 15.21 0.00 0.00 1.40
2231 2406 7.062138 CGTTTGCCCGTACGTATAACATATAAT 59.938 37.037 15.21 0.00 33.33 1.28
2247 2433 3.819877 GACCAGACCGTTTGCCCGT 62.820 63.158 0.00 0.00 0.00 5.28
2269 2455 2.140717 GTCGTGATTTCTTGACCGGTT 58.859 47.619 9.42 0.00 0.00 4.44
2278 2464 2.103263 GGATAGCTGGGTCGTGATTTCT 59.897 50.000 0.00 0.00 0.00 2.52
2279 2465 2.484889 GGATAGCTGGGTCGTGATTTC 58.515 52.381 0.00 0.00 0.00 2.17
2285 2471 2.180276 GATATGGGATAGCTGGGTCGT 58.820 52.381 0.00 0.00 0.00 4.34
2309 2495 1.552486 CCGGGCCTTCCTAGATATGGA 60.552 57.143 0.84 0.00 0.00 3.41
2314 2500 0.104934 ACATCCGGGCCTTCCTAGAT 60.105 55.000 0.84 0.00 0.00 1.98
2317 2503 2.742116 GCACATCCGGGCCTTCCTA 61.742 63.158 0.84 0.00 0.00 2.94
2318 2504 4.115199 GCACATCCGGGCCTTCCT 62.115 66.667 0.84 0.00 0.00 3.36
2353 2539 0.895530 TCCTGTCTGTCGGATCCAAC 59.104 55.000 13.41 3.67 0.00 3.77
2399 2586 0.389757 GAGTTGATCGGGCTAGGTCC 59.610 60.000 0.00 0.00 0.00 4.46
2401 2588 1.867363 AAGAGTTGATCGGGCTAGGT 58.133 50.000 0.00 0.00 0.00 3.08
2412 2599 8.429237 AGAATAGAGAAGAGGAAAAGAGTTGA 57.571 34.615 0.00 0.00 0.00 3.18
2417 2604 7.147983 CGAGGAAGAATAGAGAAGAGGAAAAGA 60.148 40.741 0.00 0.00 0.00 2.52
2428 2615 1.948145 GCCGACGAGGAAGAATAGAGA 59.052 52.381 0.00 0.00 45.00 3.10
2433 2620 2.202756 GCGCCGACGAGGAAGAAT 60.203 61.111 0.00 0.00 45.00 2.40
2449 2636 2.041405 AGCTAGAGGAGGGGTGGC 60.041 66.667 0.00 0.00 0.00 5.01
2452 2639 2.443016 CGCAGCTAGAGGAGGGGT 60.443 66.667 0.00 0.00 0.00 4.95
2460 2647 1.185618 AGGGTGACAACGCAGCTAGA 61.186 55.000 0.00 0.00 41.58 2.43
2471 2658 1.053424 GTGGTGGAGTTAGGGTGACA 58.947 55.000 0.00 0.00 0.00 3.58
2481 2668 2.446994 TTGGGACGGTGGTGGAGT 60.447 61.111 0.00 0.00 0.00 3.85
2520 2707 2.378547 TGGCAAGGAGGAGTTTTATGGT 59.621 45.455 0.00 0.00 0.00 3.55
2527 2714 0.398318 GTGACTGGCAAGGAGGAGTT 59.602 55.000 0.00 0.00 0.00 3.01
2545 2732 4.752879 CGATGTTCGGGGCGGTGT 62.753 66.667 0.00 0.00 36.00 4.16
2547 2734 4.011517 AACGATGTTCGGGGCGGT 62.012 61.111 1.69 0.00 45.59 5.68
2556 2743 2.494471 TCGGACATACTCCAACGATGTT 59.506 45.455 0.00 0.00 39.39 2.71
2559 2746 2.358267 GAGTCGGACATACTCCAACGAT 59.642 50.000 11.27 0.00 39.39 3.73
2567 2754 7.720074 TGTAATATGAGAAGAGTCGGACATACT 59.280 37.037 11.27 4.00 0.00 2.12
2571 2758 5.067413 GGTGTAATATGAGAAGAGTCGGACA 59.933 44.000 11.27 0.00 0.00 4.02
2615 2802 9.620660 GAATAAGAAAACTGCTCGGAAAATTTA 57.379 29.630 0.00 0.00 0.00 1.40
2661 2848 1.784358 TCCGACGAACCCTCCATAAT 58.216 50.000 0.00 0.00 0.00 1.28
2662 2849 1.411246 CATCCGACGAACCCTCCATAA 59.589 52.381 0.00 0.00 0.00 1.90
2664 2851 0.686441 TCATCCGACGAACCCTCCAT 60.686 55.000 0.00 0.00 0.00 3.41
2689 2876 1.070786 TCAGGCTTGGAACCACGAC 59.929 57.895 0.00 0.00 0.00 4.34
2692 2879 0.179018 ACTGTCAGGCTTGGAACCAC 60.179 55.000 4.53 0.00 0.00 4.16
2693 2880 1.347707 CTACTGTCAGGCTTGGAACCA 59.652 52.381 4.53 0.00 0.00 3.67
2694 2881 1.623811 TCTACTGTCAGGCTTGGAACC 59.376 52.381 4.53 0.00 0.00 3.62
2695 2882 2.300437 ACTCTACTGTCAGGCTTGGAAC 59.700 50.000 4.53 0.00 0.00 3.62
2696 2883 2.300152 CACTCTACTGTCAGGCTTGGAA 59.700 50.000 4.53 0.00 0.00 3.53
2697 2884 1.895798 CACTCTACTGTCAGGCTTGGA 59.104 52.381 4.53 0.00 0.00 3.53
2698 2885 1.066573 CCACTCTACTGTCAGGCTTGG 60.067 57.143 4.53 0.00 0.00 3.61
2699 2886 1.066573 CCCACTCTACTGTCAGGCTTG 60.067 57.143 4.53 0.00 0.00 4.01
2700 2887 1.270907 CCCACTCTACTGTCAGGCTT 58.729 55.000 4.53 0.00 0.00 4.35
2701 2888 0.616111 CCCCACTCTACTGTCAGGCT 60.616 60.000 4.53 0.00 0.00 4.58
2702 2889 1.617947 CCCCCACTCTACTGTCAGGC 61.618 65.000 4.53 0.00 0.00 4.85
2703 2890 2.596776 CCCCCACTCTACTGTCAGG 58.403 63.158 4.53 0.00 0.00 3.86
2718 2905 1.057471 GCCTCTCAATACCTACCCCC 58.943 60.000 0.00 0.00 0.00 5.40
2719 2906 1.802553 TGCCTCTCAATACCTACCCC 58.197 55.000 0.00 0.00 0.00 4.95
2720 2907 2.104963 CCTTGCCTCTCAATACCTACCC 59.895 54.545 0.00 0.00 33.57 3.69
2721 2908 2.772515 ACCTTGCCTCTCAATACCTACC 59.227 50.000 0.00 0.00 33.57 3.18
2722 2909 3.181464 GGACCTTGCCTCTCAATACCTAC 60.181 52.174 0.00 0.00 33.57 3.18
2723 2910 3.039011 GGACCTTGCCTCTCAATACCTA 58.961 50.000 0.00 0.00 33.57 3.08
2724 2911 1.840635 GGACCTTGCCTCTCAATACCT 59.159 52.381 0.00 0.00 33.57 3.08
2725 2912 1.840635 AGGACCTTGCCTCTCAATACC 59.159 52.381 0.00 0.00 30.76 2.73
2726 2913 3.493524 GCTAGGACCTTGCCTCTCAATAC 60.494 52.174 16.20 0.00 39.50 1.89
2727 2914 2.700897 GCTAGGACCTTGCCTCTCAATA 59.299 50.000 16.20 0.00 39.50 1.90
2728 2915 1.488393 GCTAGGACCTTGCCTCTCAAT 59.512 52.381 16.20 0.00 39.50 2.57
2729 2916 0.905357 GCTAGGACCTTGCCTCTCAA 59.095 55.000 16.20 0.00 39.50 3.02
2730 2917 0.041833 AGCTAGGACCTTGCCTCTCA 59.958 55.000 22.23 0.00 39.50 3.27
2731 2918 2.074729 TAGCTAGGACCTTGCCTCTC 57.925 55.000 22.23 0.00 39.50 3.20
2732 2919 2.324541 CATAGCTAGGACCTTGCCTCT 58.675 52.381 22.23 8.59 39.50 3.69
2733 2920 1.346068 CCATAGCTAGGACCTTGCCTC 59.654 57.143 22.23 0.00 39.50 4.70
2734 2921 1.062121 TCCATAGCTAGGACCTTGCCT 60.062 52.381 22.23 13.04 42.15 4.75
2735 2922 1.346068 CTCCATAGCTAGGACCTTGCC 59.654 57.143 22.23 6.76 33.03 4.52
2736 2923 2.298729 CTCTCCATAGCTAGGACCTTGC 59.701 54.545 18.95 18.95 32.79 4.01
2737 2924 2.896685 CCTCTCCATAGCTAGGACCTTG 59.103 54.545 7.04 0.00 0.00 3.61
2738 2925 2.520549 ACCTCTCCATAGCTAGGACCTT 59.479 50.000 7.04 0.00 33.16 3.50
2739 2926 2.148702 ACCTCTCCATAGCTAGGACCT 58.851 52.381 7.04 0.00 33.16 3.85
2740 2927 2.687003 ACCTCTCCATAGCTAGGACC 57.313 55.000 7.04 0.00 33.16 4.46


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

AutoCloner maintained by Alex Coulton.