Multiple sequence alignment - TraesCS3D01G299400

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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 TraesCS3D01G299400 chr3D 100.000 3239 0 0 1 3239 414628248 414631486 0.000000e+00 5982
1 TraesCS3D01G299400 chr3B 96.324 2666 63 11 1 2636 540455775 540458435 0.000000e+00 4348
2 TraesCS3D01G299400 chr3B 92.208 231 9 6 3010 3239 540458549 540458771 5.210000e-83 318
3 TraesCS3D01G299400 chr3A 95.207 2733 76 13 2 2690 535824938 535822217 0.000000e+00 4270
4 TraesCS3D01G299400 chr3A 89.352 216 5 7 3025 3239 535821741 535821543 4.150000e-64 255
5 TraesCS3D01G299400 chr1A 79.589 681 116 14 1575 2236 563784156 563784832 1.760000e-127 466
6 TraesCS3D01G299400 chr1A 78.523 596 105 16 987 1573 563791371 563791952 1.420000e-98 370
7 TraesCS3D01G299400 chr1A 76.481 557 109 16 1024 1574 563769721 563770261 1.900000e-72 283
8 TraesCS3D01G299400 chr1A 79.747 316 61 1 1927 2239 563799417 563799732 3.250000e-55 226
9 TraesCS3D01G299400 chr1B 79.351 678 123 14 1575 2239 652570490 652571163 8.190000e-126 460
10 TraesCS3D01G299400 chr1B 78.655 684 121 16 1576 2236 653238011 653237330 6.420000e-117 431
11 TraesCS3D01G299400 chr1B 78.000 700 118 18 1575 2241 652519177 652519873 1.080000e-109 407
12 TraesCS3D01G299400 chr1B 78.116 690 116 22 1575 2236 652633676 652634358 3.890000e-109 405
13 TraesCS3D01G299400 chr1B 78.804 552 103 11 1024 1573 652569981 652570520 3.070000e-95 359
14 TraesCS3D01G299400 chr1B 78.674 558 95 19 1024 1574 652467745 652468285 1.850000e-92 350
15 TraesCS3D01G299400 chr1B 77.241 580 115 12 1003 1574 652459751 652460321 1.120000e-84 324
16 TraesCS3D01G299400 chr1B 77.184 561 101 21 1024 1574 652518665 652519208 5.250000e-78 302
17 TraesCS3D01G299400 chr1D 79.039 687 113 22 1576 2236 470524807 470524126 2.970000e-120 442
18 TraesCS3D01G299400 chr1D 81.038 559 90 9 1575 2119 470190649 470191205 6.420000e-117 431
19 TraesCS3D01G299400 chr1D 79.928 553 102 8 1023 1574 470081112 470081656 6.510000e-107 398
20 TraesCS3D01G299400 chr1D 77.326 688 123 23 1576 2236 470198955 470199636 3.050000e-100 375
21 TraesCS3D01G299400 chr1D 81.424 323 54 5 1926 2243 470181481 470181802 3.210000e-65 259
22 TraesCS3D01G299400 chr2D 83.333 384 56 5 995 1377 502574200 502574576 6.650000e-92 348
23 TraesCS3D01G299400 chr4A 86.562 320 31 9 2693 3008 670212989 670213300 3.090000e-90 342
24 TraesCS3D01G299400 chr5A 86.120 317 37 5 2693 3008 572406464 572406774 5.180000e-88 335
25 TraesCS3D01G299400 chr2A 82.552 384 59 8 995 1377 648027284 648027660 6.700000e-87 331
26 TraesCS3D01G299400 chr2B 88.298 282 24 7 2728 3008 544757722 544757995 2.410000e-86 329
27 TraesCS3D01G299400 chr2B 82.292 384 60 6 995 1377 590228442 590228818 3.120000e-85 326
28 TraesCS3D01G299400 chr6A 86.071 280 34 2 2734 3008 593691947 593691668 2.440000e-76 296
29 TraesCS3D01G299400 chr6D 82.684 231 37 1 2781 3008 446845090 446844860 5.480000e-48 202


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 TraesCS3D01G299400 chr3D 414628248 414631486 3238 False 5982.0 5982 100.0000 1 3239 1 chr3D.!!$F1 3238
1 TraesCS3D01G299400 chr3B 540455775 540458771 2996 False 2333.0 4348 94.2660 1 3239 2 chr3B.!!$F1 3238
2 TraesCS3D01G299400 chr3A 535821543 535824938 3395 True 2262.5 4270 92.2795 2 3239 2 chr3A.!!$R1 3237
3 TraesCS3D01G299400 chr1A 563784156 563784832 676 False 466.0 466 79.5890 1575 2236 1 chr1A.!!$F2 661
4 TraesCS3D01G299400 chr1A 563791371 563791952 581 False 370.0 370 78.5230 987 1573 1 chr1A.!!$F3 586
5 TraesCS3D01G299400 chr1A 563769721 563770261 540 False 283.0 283 76.4810 1024 1574 1 chr1A.!!$F1 550
6 TraesCS3D01G299400 chr1B 653237330 653238011 681 True 431.0 431 78.6550 1576 2236 1 chr1B.!!$R1 660
7 TraesCS3D01G299400 chr1B 652569981 652571163 1182 False 409.5 460 79.0775 1024 2239 2 chr1B.!!$F5 1215
8 TraesCS3D01G299400 chr1B 652633676 652634358 682 False 405.0 405 78.1160 1575 2236 1 chr1B.!!$F3 661
9 TraesCS3D01G299400 chr1B 652518665 652519873 1208 False 354.5 407 77.5920 1024 2241 2 chr1B.!!$F4 1217
10 TraesCS3D01G299400 chr1B 652467745 652468285 540 False 350.0 350 78.6740 1024 1574 1 chr1B.!!$F2 550
11 TraesCS3D01G299400 chr1B 652459751 652460321 570 False 324.0 324 77.2410 1003 1574 1 chr1B.!!$F1 571
12 TraesCS3D01G299400 chr1D 470524126 470524807 681 True 442.0 442 79.0390 1576 2236 1 chr1D.!!$R1 660
13 TraesCS3D01G299400 chr1D 470190649 470191205 556 False 431.0 431 81.0380 1575 2119 1 chr1D.!!$F3 544
14 TraesCS3D01G299400 chr1D 470081112 470081656 544 False 398.0 398 79.9280 1023 1574 1 chr1D.!!$F1 551
15 TraesCS3D01G299400 chr1D 470198955 470199636 681 False 375.0 375 77.3260 1576 2236 1 chr1D.!!$F4 660

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
463 481 0.196118 AGGGAGAGAAACAGGGGGAA 59.804 55.0 0.0 0.0 0.0 3.97 F
829 880 0.839277 CCTATGACATCTGGTGCCCA 59.161 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1443 1.879380 CCATTTCTGGACTGCGTTTGA 59.121 47.619 0.0 0.0 46.37 2.69 R
2787 2891 0.106918 TGGTGAAAGAAACAGCGGGT 60.107 50.000 0.0 0.0 38.39 5.28 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
80 81 1.475034 GCATGGCTTACGATGGAGGAA 60.475 52.381 0.00 0.00 0.00 3.36
227 228 4.675029 CGGTCGAACGCCTGGGTT 62.675 66.667 11.19 0.00 0.00 4.11
349 353 2.181021 GGAGTCGTCGCGGTCATT 59.819 61.111 6.13 0.00 0.00 2.57
433 451 4.778415 CAGGACGCCCGACAGACG 62.778 72.222 0.00 0.00 42.18 4.18
460 478 1.275421 GGGAGGGAGAGAAACAGGGG 61.275 65.000 0.00 0.00 0.00 4.79
461 479 1.275421 GGAGGGAGAGAAACAGGGGG 61.275 65.000 0.00 0.00 0.00 5.40
462 480 0.252742 GAGGGAGAGAAACAGGGGGA 60.253 60.000 0.00 0.00 0.00 4.81
463 481 0.196118 AGGGAGAGAAACAGGGGGAA 59.804 55.000 0.00 0.00 0.00 3.97
657 705 1.185315 CGGCCCATTTCTCCAAACAT 58.815 50.000 0.00 0.00 0.00 2.71
829 880 0.839277 CCTATGACATCTGGTGCCCA 59.161 55.000 0.00 0.00 0.00 5.36
889 940 0.971386 TCTAAACTCCGGTGGTGGAC 59.029 55.000 8.63 0.00 33.48 4.02
898 949 1.760479 CGGTGGTGGACTGGTGGTAA 61.760 60.000 0.00 0.00 0.00 2.85
926 977 4.322385 GGAACCGTGCACGCCAAC 62.322 66.667 33.17 21.29 38.18 3.77
1626 1691 4.409218 TCGTGGTCAGTACGCGCC 62.409 66.667 5.73 0.00 41.08 6.53
1998 2096 1.465188 TGTGGGGGATGACCAGGTT 60.465 57.895 0.00 0.00 42.91 3.50
2282 2383 0.595095 CTGTTCCAGCTGCTTCCAAC 59.405 55.000 8.66 3.83 0.00 3.77
2311 2412 3.580895 TGGTGATCAGTAGTTACCAAGCA 59.419 43.478 0.00 0.00 38.39 3.91
2394 2496 5.703592 TGGTTACTATGGTGCAAGTTGTTAG 59.296 40.000 4.48 1.98 0.00 2.34
2442 2546 4.833478 AGATCCTAAACTGCATGACTGT 57.167 40.909 0.00 0.00 0.00 3.55
2465 2569 8.032952 TGTTTATCTGTCAATTGTCTTAGCAG 57.967 34.615 5.13 6.07 0.00 4.24
2594 2698 2.305635 TGTGAGCCTACATGATGGTTGT 59.694 45.455 0.00 0.00 0.00 3.32
2692 2796 9.643693 GAATGTTTGCAATATCCAATATTAGGG 57.356 33.333 0.00 0.00 33.86 3.53
2694 2798 8.408043 TGTTTGCAATATCCAATATTAGGGAG 57.592 34.615 0.00 0.00 36.45 4.30
2695 2799 8.224025 TGTTTGCAATATCCAATATTAGGGAGA 58.776 33.333 0.00 0.00 36.45 3.71
2696 2800 9.077885 GTTTGCAATATCCAATATTAGGGAGAA 57.922 33.333 0.00 0.00 36.45 2.87
2697 2801 9.653516 TTTGCAATATCCAATATTAGGGAGAAA 57.346 29.630 0.00 0.00 36.45 2.52
2698 2802 9.653516 TTGCAATATCCAATATTAGGGAGAAAA 57.346 29.630 0.00 0.00 36.45 2.29
2699 2803 9.827198 TGCAATATCCAATATTAGGGAGAAAAT 57.173 29.630 1.46 0.00 36.45 1.82
2714 2818 6.455360 GGAGAAAATCAATTCTACCATGCA 57.545 37.500 0.00 0.00 39.70 3.96
2715 2819 6.268566 GGAGAAAATCAATTCTACCATGCAC 58.731 40.000 0.00 0.00 39.70 4.57
2716 2820 5.883661 AGAAAATCAATTCTACCATGCACG 58.116 37.500 0.00 0.00 37.88 5.34
2717 2821 4.637483 AAATCAATTCTACCATGCACGG 57.363 40.909 0.00 0.00 0.00 4.94
2718 2822 2.036958 TCAATTCTACCATGCACGGG 57.963 50.000 2.80 3.91 0.00 5.28
2719 2823 1.557371 TCAATTCTACCATGCACGGGA 59.443 47.619 12.94 0.00 0.00 5.14
2720 2824 1.942657 CAATTCTACCATGCACGGGAG 59.057 52.381 4.09 4.09 38.52 4.30
2722 2826 0.535335 TTCTACCATGCACGGGAGTC 59.465 55.000 11.61 0.00 44.67 3.36
2723 2827 1.144057 CTACCATGCACGGGAGTCC 59.856 63.158 1.79 0.00 44.67 3.85
2724 2828 2.311688 CTACCATGCACGGGAGTCCC 62.312 65.000 19.37 19.37 44.67 4.46
2740 2844 2.187946 CCGTGCATGGGAGAGTCC 59.812 66.667 17.90 0.00 35.23 3.85
2741 2845 2.362369 CCGTGCATGGGAGAGTCCT 61.362 63.158 17.90 0.00 36.57 3.85
2742 2846 1.599047 CGTGCATGGGAGAGTCCTT 59.401 57.895 0.00 0.00 36.57 3.36
2743 2847 0.742281 CGTGCATGGGAGAGTCCTTG 60.742 60.000 0.00 0.00 36.57 3.61
2744 2848 0.615331 GTGCATGGGAGAGTCCTTGA 59.385 55.000 0.00 0.00 36.57 3.02
2745 2849 1.211457 GTGCATGGGAGAGTCCTTGAT 59.789 52.381 0.00 0.00 36.57 2.57
2746 2850 1.918262 TGCATGGGAGAGTCCTTGATT 59.082 47.619 0.00 0.00 36.57 2.57
2747 2851 2.309755 TGCATGGGAGAGTCCTTGATTT 59.690 45.455 0.00 0.00 36.57 2.17
2748 2852 2.686915 GCATGGGAGAGTCCTTGATTTG 59.313 50.000 0.00 0.00 36.57 2.32
2750 2854 1.988107 TGGGAGAGTCCTTGATTTGCT 59.012 47.619 0.00 0.00 36.57 3.91
2752 2856 3.181429 TGGGAGAGTCCTTGATTTGCTTT 60.181 43.478 0.00 0.00 36.57 3.51
2753 2857 3.192212 GGGAGAGTCCTTGATTTGCTTTG 59.808 47.826 0.00 0.00 36.57 2.77
2757 2861 5.568392 AGAGTCCTTGATTTGCTTTGAGAT 58.432 37.500 0.00 0.00 0.00 2.75
2758 2862 5.647225 AGAGTCCTTGATTTGCTTTGAGATC 59.353 40.000 0.00 0.00 0.00 2.75
2759 2863 4.704057 AGTCCTTGATTTGCTTTGAGATCC 59.296 41.667 0.00 0.00 0.00 3.36
2760 2864 3.691118 TCCTTGATTTGCTTTGAGATCCG 59.309 43.478 0.00 0.00 0.00 4.18
2761 2865 3.181493 CCTTGATTTGCTTTGAGATCCGG 60.181 47.826 0.00 0.00 0.00 5.14
2762 2866 3.348647 TGATTTGCTTTGAGATCCGGA 57.651 42.857 6.61 6.61 0.00 5.14
2763 2867 3.684908 TGATTTGCTTTGAGATCCGGAA 58.315 40.909 9.01 0.00 0.00 4.30
2764 2868 4.078537 TGATTTGCTTTGAGATCCGGAAA 58.921 39.130 9.01 0.00 0.00 3.13
2765 2869 3.915437 TTTGCTTTGAGATCCGGAAAC 57.085 42.857 9.01 6.01 0.00 2.78
2766 2870 2.559698 TGCTTTGAGATCCGGAAACA 57.440 45.000 9.01 6.35 0.00 2.83
2767 2871 3.071874 TGCTTTGAGATCCGGAAACAT 57.928 42.857 9.01 0.00 0.00 2.71
2769 2873 2.478539 GCTTTGAGATCCGGAAACATGC 60.479 50.000 9.01 12.23 0.00 4.06
2770 2874 2.488204 TTGAGATCCGGAAACATGCA 57.512 45.000 9.01 3.42 0.00 3.96
2772 2876 3.836365 TGAGATCCGGAAACATGCATA 57.164 42.857 9.01 0.00 0.00 3.14
2773 2877 3.732212 TGAGATCCGGAAACATGCATAG 58.268 45.455 9.01 0.00 0.00 2.23
2776 2880 5.163353 TGAGATCCGGAAACATGCATAGTTA 60.163 40.000 9.01 1.26 0.00 2.24
2777 2881 5.057149 AGATCCGGAAACATGCATAGTTAC 58.943 41.667 9.01 4.75 0.00 2.50
2781 2885 4.634004 CCGGAAACATGCATAGTTACTCAA 59.366 41.667 12.78 0.00 0.00 3.02
2782 2886 5.123186 CCGGAAACATGCATAGTTACTCAAA 59.877 40.000 12.78 0.00 0.00 2.69
2783 2887 6.348950 CCGGAAACATGCATAGTTACTCAAAA 60.349 38.462 12.78 0.00 0.00 2.44
2784 2888 7.250569 CGGAAACATGCATAGTTACTCAAAAT 58.749 34.615 12.78 0.00 0.00 1.82
2786 2890 8.863049 GGAAACATGCATAGTTACTCAAAATTG 58.137 33.333 12.78 0.00 0.00 2.32
2787 2891 9.624697 GAAACATGCATAGTTACTCAAAATTGA 57.375 29.630 12.78 0.00 35.57 2.57
2789 2893 7.538575 ACATGCATAGTTACTCAAAATTGACC 58.461 34.615 0.00 0.00 32.90 4.02
2790 2894 6.509418 TGCATAGTTACTCAAAATTGACCC 57.491 37.500 0.00 0.00 32.90 4.46
2791 2895 5.123186 TGCATAGTTACTCAAAATTGACCCG 59.877 40.000 0.00 0.00 32.90 5.28
2796 2900 2.306847 ACTCAAAATTGACCCGCTGTT 58.693 42.857 0.00 0.00 32.90 3.16
2798 2902 3.243401 ACTCAAAATTGACCCGCTGTTTC 60.243 43.478 0.00 0.00 32.90 2.78
2800 2904 3.383185 TCAAAATTGACCCGCTGTTTCTT 59.617 39.130 0.00 0.00 31.01 2.52
2801 2905 4.119136 CAAAATTGACCCGCTGTTTCTTT 58.881 39.130 0.00 0.00 0.00 2.52
2802 2906 3.643159 AATTGACCCGCTGTTTCTTTC 57.357 42.857 0.00 0.00 0.00 2.62
2803 2907 2.045561 TTGACCCGCTGTTTCTTTCA 57.954 45.000 0.00 0.00 0.00 2.69
2804 2908 1.305201 TGACCCGCTGTTTCTTTCAC 58.695 50.000 0.00 0.00 0.00 3.18
2805 2909 0.591659 GACCCGCTGTTTCTTTCACC 59.408 55.000 0.00 0.00 0.00 4.02
2806 2910 0.106918 ACCCGCTGTTTCTTTCACCA 60.107 50.000 0.00 0.00 0.00 4.17
2807 2911 0.310854 CCCGCTGTTTCTTTCACCAC 59.689 55.000 0.00 0.00 0.00 4.16
2808 2912 1.021202 CCGCTGTTTCTTTCACCACA 58.979 50.000 0.00 0.00 0.00 4.17
2811 2915 2.397549 GCTGTTTCTTTCACCACATGC 58.602 47.619 0.00 0.00 0.00 4.06
2814 2918 4.044336 TGTTTCTTTCACCACATGCAAG 57.956 40.909 0.00 0.00 33.26 4.01
2815 2919 3.181477 TGTTTCTTTCACCACATGCAAGG 60.181 43.478 0.00 0.00 32.88 3.61
2816 2920 2.655090 TCTTTCACCACATGCAAGGA 57.345 45.000 9.85 0.00 32.88 3.36
2818 2922 1.955778 CTTTCACCACATGCAAGGACA 59.044 47.619 9.85 0.00 28.77 4.02
2820 2924 0.473755 TCACCACATGCAAGGACACT 59.526 50.000 9.85 0.00 0.00 3.55
2821 2925 0.594602 CACCACATGCAAGGACACTG 59.405 55.000 9.85 0.00 0.00 3.66
2822 2926 0.183492 ACCACATGCAAGGACACTGT 59.817 50.000 9.85 0.00 0.00 3.55
2823 2927 1.321474 CCACATGCAAGGACACTGTT 58.679 50.000 0.00 0.00 0.00 3.16
2824 2928 1.267806 CCACATGCAAGGACACTGTTC 59.732 52.381 0.00 0.00 0.00 3.18
2825 2929 1.948834 CACATGCAAGGACACTGTTCA 59.051 47.619 0.00 0.00 0.00 3.18
2826 2930 2.031420 CACATGCAAGGACACTGTTCAG 60.031 50.000 0.00 0.00 0.00 3.02
2827 2931 1.068748 CATGCAAGGACACTGTTCAGC 60.069 52.381 0.00 0.00 0.00 4.26
2831 2935 2.417933 GCAAGGACACTGTTCAGCTATG 59.582 50.000 0.00 0.00 0.00 2.23
2832 2936 2.393271 AGGACACTGTTCAGCTATGC 57.607 50.000 0.00 0.00 0.00 3.14
2833 2937 1.625315 AGGACACTGTTCAGCTATGCA 59.375 47.619 0.00 0.00 0.00 3.96
2834 2938 2.005451 GGACACTGTTCAGCTATGCAG 58.995 52.381 8.47 8.47 35.31 4.41
2851 2955 4.126524 GCCTTACGCTCCACCATC 57.873 61.111 0.00 0.00 0.00 3.51
2852 2956 1.523938 GCCTTACGCTCCACCATCC 60.524 63.158 0.00 0.00 0.00 3.51
2853 2957 1.146263 CCTTACGCTCCACCATCCC 59.854 63.158 0.00 0.00 0.00 3.85
2854 2958 1.622607 CCTTACGCTCCACCATCCCA 61.623 60.000 0.00 0.00 0.00 4.37
2855 2959 0.179073 CTTACGCTCCACCATCCCAG 60.179 60.000 0.00 0.00 0.00 4.45
2856 2960 0.616395 TTACGCTCCACCATCCCAGA 60.616 55.000 0.00 0.00 0.00 3.86
2857 2961 1.327690 TACGCTCCACCATCCCAGAC 61.328 60.000 0.00 0.00 0.00 3.51
2858 2962 2.592308 GCTCCACCATCCCAGACC 59.408 66.667 0.00 0.00 0.00 3.85
2859 2963 1.997874 GCTCCACCATCCCAGACCT 60.998 63.158 0.00 0.00 0.00 3.85
2860 2964 1.566298 GCTCCACCATCCCAGACCTT 61.566 60.000 0.00 0.00 0.00 3.50
2861 2965 0.995024 CTCCACCATCCCAGACCTTT 59.005 55.000 0.00 0.00 0.00 3.11
2862 2966 1.355720 CTCCACCATCCCAGACCTTTT 59.644 52.381 0.00 0.00 0.00 2.27
2863 2967 1.354368 TCCACCATCCCAGACCTTTTC 59.646 52.381 0.00 0.00 0.00 2.29
2864 2968 1.075374 CCACCATCCCAGACCTTTTCA 59.925 52.381 0.00 0.00 0.00 2.69
2865 2969 2.291800 CCACCATCCCAGACCTTTTCAT 60.292 50.000 0.00 0.00 0.00 2.57
2866 2970 3.019564 CACCATCCCAGACCTTTTCATC 58.980 50.000 0.00 0.00 0.00 2.92
2867 2971 2.922283 ACCATCCCAGACCTTTTCATCT 59.078 45.455 0.00 0.00 0.00 2.90
2868 2972 3.334881 ACCATCCCAGACCTTTTCATCTT 59.665 43.478 0.00 0.00 0.00 2.40
2869 2973 4.540099 ACCATCCCAGACCTTTTCATCTTA 59.460 41.667 0.00 0.00 0.00 2.10
2870 2974 5.194537 ACCATCCCAGACCTTTTCATCTTAT 59.805 40.000 0.00 0.00 0.00 1.73
2871 2975 6.131961 CCATCCCAGACCTTTTCATCTTATT 58.868 40.000 0.00 0.00 0.00 1.40
2872 2976 6.608808 CCATCCCAGACCTTTTCATCTTATTT 59.391 38.462 0.00 0.00 0.00 1.40
2873 2977 7.201857 CCATCCCAGACCTTTTCATCTTATTTC 60.202 40.741 0.00 0.00 0.00 2.17
2874 2978 7.032598 TCCCAGACCTTTTCATCTTATTTCT 57.967 36.000 0.00 0.00 0.00 2.52
2875 2979 8.158025 TCCCAGACCTTTTCATCTTATTTCTA 57.842 34.615 0.00 0.00 0.00 2.10
2876 2980 8.611257 TCCCAGACCTTTTCATCTTATTTCTAA 58.389 33.333 0.00 0.00 0.00 2.10
2877 2981 8.897752 CCCAGACCTTTTCATCTTATTTCTAAG 58.102 37.037 0.00 0.00 36.46 2.18
2878 2982 9.454859 CCAGACCTTTTCATCTTATTTCTAAGT 57.545 33.333 0.00 0.00 36.51 2.24
2948 3052 9.702494 TTGTTTGCATATTTGTGTTTATGATGA 57.298 25.926 0.00 0.00 0.00 2.92
2949 3053 9.872721 TGTTTGCATATTTGTGTTTATGATGAT 57.127 25.926 0.00 0.00 0.00 2.45
2951 3055 8.874744 TTGCATATTTGTGTTTATGATGATGG 57.125 30.769 0.00 0.00 0.00 3.51
2952 3056 8.235359 TGCATATTTGTGTTTATGATGATGGA 57.765 30.769 0.00 0.00 0.00 3.41
2953 3057 8.354426 TGCATATTTGTGTTTATGATGATGGAG 58.646 33.333 0.00 0.00 0.00 3.86
2954 3058 8.570488 GCATATTTGTGTTTATGATGATGGAGA 58.430 33.333 0.00 0.00 0.00 3.71
2955 3059 9.888878 CATATTTGTGTTTATGATGATGGAGAC 57.111 33.333 0.00 0.00 0.00 3.36
2956 3060 9.857656 ATATTTGTGTTTATGATGATGGAGACT 57.142 29.630 0.00 0.00 0.00 3.24
2957 3061 8.585471 ATTTGTGTTTATGATGATGGAGACTT 57.415 30.769 0.00 0.00 0.00 3.01
2958 3062 8.408043 TTTGTGTTTATGATGATGGAGACTTT 57.592 30.769 0.00 0.00 0.00 2.66
2959 3063 9.513906 TTTGTGTTTATGATGATGGAGACTTTA 57.486 29.630 0.00 0.00 0.00 1.85
2960 3064 9.513906 TTGTGTTTATGATGATGGAGACTTTAA 57.486 29.630 0.00 0.00 0.00 1.52
2961 3065 9.513906 TGTGTTTATGATGATGGAGACTTTAAA 57.486 29.630 0.00 0.00 0.00 1.52
2964 3068 9.490663 GTTTATGATGATGGAGACTTTAAAACG 57.509 33.333 0.00 0.00 0.00 3.60
2965 3069 6.683974 ATGATGATGGAGACTTTAAAACGG 57.316 37.500 0.00 0.00 0.00 4.44
2966 3070 4.941263 TGATGATGGAGACTTTAAAACGGG 59.059 41.667 0.00 0.00 0.00 5.28
2967 3071 4.627284 TGATGGAGACTTTAAAACGGGA 57.373 40.909 0.00 0.00 0.00 5.14
2968 3072 4.320870 TGATGGAGACTTTAAAACGGGAC 58.679 43.478 0.00 0.00 0.00 4.46
2969 3073 3.130280 TGGAGACTTTAAAACGGGACC 57.870 47.619 0.00 0.00 0.00 4.46
2970 3074 2.438763 TGGAGACTTTAAAACGGGACCA 59.561 45.455 0.00 0.00 0.00 4.02
2971 3075 2.810274 GGAGACTTTAAAACGGGACCAC 59.190 50.000 0.00 0.00 0.00 4.16
2972 3076 3.495629 GGAGACTTTAAAACGGGACCACT 60.496 47.826 0.00 0.00 0.00 4.00
2973 3077 4.132336 GAGACTTTAAAACGGGACCACTT 58.868 43.478 0.00 0.00 0.00 3.16
2974 3078 4.529897 AGACTTTAAAACGGGACCACTTT 58.470 39.130 0.00 0.00 0.00 2.66
2975 3079 4.951715 AGACTTTAAAACGGGACCACTTTT 59.048 37.500 0.00 0.00 0.00 2.27
2976 3080 6.121590 AGACTTTAAAACGGGACCACTTTTA 58.878 36.000 0.00 0.00 0.00 1.52
2977 3081 6.602803 AGACTTTAAAACGGGACCACTTTTAA 59.397 34.615 11.58 11.58 30.90 1.52
2978 3082 7.122501 AGACTTTAAAACGGGACCACTTTTAAA 59.877 33.333 19.84 19.84 37.16 1.52
2979 3083 7.784037 ACTTTAAAACGGGACCACTTTTAAAT 58.216 30.769 20.62 13.41 38.08 1.40
2980 3084 8.911965 ACTTTAAAACGGGACCACTTTTAAATA 58.088 29.630 20.62 9.00 38.08 1.40
2981 3085 9.917129 CTTTAAAACGGGACCACTTTTAAATAT 57.083 29.630 20.62 0.00 38.08 1.28
2985 3089 9.470399 AAAACGGGACCACTTTTAAATATATCT 57.530 29.630 0.00 0.00 0.00 1.98
3040 3444 4.853743 GCATAGTAAGCTTTTTGTGCAGTC 59.146 41.667 19.56 0.00 0.00 3.51
3079 3483 5.300752 CAATACCCAGTACTGAATAGGCAG 58.699 45.833 24.68 4.54 41.63 4.85
3081 3485 3.182152 ACCCAGTACTGAATAGGCAGTT 58.818 45.455 24.68 0.00 46.42 3.16
3082 3486 4.359105 ACCCAGTACTGAATAGGCAGTTA 58.641 43.478 24.68 0.00 46.42 2.24
3085 3489 4.372656 CAGTACTGAATAGGCAGTTAGGC 58.627 47.826 18.45 0.00 46.42 3.93
3086 3490 4.030913 AGTACTGAATAGGCAGTTAGGCA 58.969 43.478 0.00 0.00 46.42 4.75
3087 3491 3.268023 ACTGAATAGGCAGTTAGGCAC 57.732 47.619 0.00 0.00 46.42 5.01
3089 3493 4.030913 ACTGAATAGGCAGTTAGGCACTA 58.969 43.478 0.00 0.00 46.42 2.74
3090 3494 4.141914 ACTGAATAGGCAGTTAGGCACTAC 60.142 45.833 0.00 0.00 46.42 2.73
3091 3495 4.030913 TGAATAGGCAGTTAGGCACTACT 58.969 43.478 0.00 0.00 42.67 2.57
3092 3496 5.205821 TGAATAGGCAGTTAGGCACTACTA 58.794 41.667 0.00 0.00 42.67 1.82
3093 3497 5.839063 TGAATAGGCAGTTAGGCACTACTAT 59.161 40.000 0.00 0.00 42.67 2.12
3094 3498 5.730296 ATAGGCAGTTAGGCACTACTATG 57.270 43.478 0.00 0.00 42.67 2.23
3095 3499 3.375699 AGGCAGTTAGGCACTACTATGT 58.624 45.455 0.00 0.00 42.67 2.29
3096 3500 3.775316 AGGCAGTTAGGCACTACTATGTT 59.225 43.478 0.00 0.00 42.67 2.71
3220 3625 1.668751 TGACAACGACTTCACCAAAGC 59.331 47.619 0.00 0.00 38.67 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
349 353 2.281484 GGAAGCTGTGCCCGAACA 60.281 61.111 0.00 0.00 0.00 3.18
433 451 1.075600 CTCTCCCTCCCACTCTCCC 60.076 68.421 0.00 0.00 0.00 4.30
460 478 0.537653 CTCGTTCCTTCCTCCCTTCC 59.462 60.000 0.00 0.00 0.00 3.46
461 479 1.478916 CTCTCGTTCCTTCCTCCCTTC 59.521 57.143 0.00 0.00 0.00 3.46
462 480 1.562783 CTCTCGTTCCTTCCTCCCTT 58.437 55.000 0.00 0.00 0.00 3.95
463 481 0.324830 CCTCTCGTTCCTTCCTCCCT 60.325 60.000 0.00 0.00 0.00 4.20
651 679 2.560861 CGGGCCGTGTGATGTTTG 59.439 61.111 19.97 0.00 0.00 2.93
829 880 1.333177 GCATACCGGATCTCAGAGGT 58.667 55.000 9.46 0.00 40.52 3.85
898 949 0.108329 CACGGTTCCGCAGATAAGGT 60.108 55.000 11.32 0.00 0.00 3.50
901 952 1.017177 GTGCACGGTTCCGCAGATAA 61.017 55.000 11.32 0.00 39.20 1.75
902 953 1.447140 GTGCACGGTTCCGCAGATA 60.447 57.895 11.32 0.00 39.20 1.98
909 960 4.322385 GTTGGCGTGCACGGTTCC 62.322 66.667 37.47 29.57 40.23 3.62
1146 1208 3.241530 TGCAGGCGGAGGAACTGT 61.242 61.111 0.00 0.00 41.55 3.55
1347 1412 3.999297 GACGCGGGAGAGAGGAGGT 62.999 68.421 12.47 0.00 0.00 3.85
1378 1443 1.879380 CCATTTCTGGACTGCGTTTGA 59.121 47.619 0.00 0.00 46.37 2.69
1626 1691 5.647589 TCATAAAGCCTACACTTGTCGTAG 58.352 41.667 0.00 0.00 36.83 3.51
1998 2096 2.487265 GCACCTTCTCCCAAGAAACAGA 60.487 50.000 0.00 0.00 40.95 3.41
2282 2383 6.127168 TGGTAACTACTGATCACCATACCAAG 60.127 42.308 14.20 0.00 38.76 3.61
2394 2496 2.490509 AGGCACGGTAAACCAATTAAGC 59.509 45.455 0.00 0.00 35.14 3.09
2442 2546 6.599244 CCCTGCTAAGACAATTGACAGATAAA 59.401 38.462 13.59 0.00 0.00 1.40
2465 2569 3.425162 ACAAAAGGTCAGAGATCACCC 57.575 47.619 0.00 0.00 32.45 4.61
2642 2746 4.763793 AGTTAGGTGTCGTCTAGTAGCAAA 59.236 41.667 0.00 0.00 0.00 3.68
2690 2794 5.360714 TGCATGGTAGAATTGATTTTCTCCC 59.639 40.000 0.00 0.00 37.20 4.30
2691 2795 6.268566 GTGCATGGTAGAATTGATTTTCTCC 58.731 40.000 0.00 0.00 37.20 3.71
2692 2796 5.967674 CGTGCATGGTAGAATTGATTTTCTC 59.032 40.000 0.00 0.00 37.20 2.87
2694 2798 5.036737 CCGTGCATGGTAGAATTGATTTTC 58.963 41.667 17.42 0.00 0.00 2.29
2695 2799 4.142182 CCCGTGCATGGTAGAATTGATTTT 60.142 41.667 23.39 0.00 0.00 1.82
2696 2800 3.381272 CCCGTGCATGGTAGAATTGATTT 59.619 43.478 23.39 0.00 0.00 2.17
2697 2801 2.951642 CCCGTGCATGGTAGAATTGATT 59.048 45.455 23.39 0.00 0.00 2.57
2698 2802 2.172505 TCCCGTGCATGGTAGAATTGAT 59.827 45.455 23.39 0.00 0.00 2.57
2699 2803 1.557371 TCCCGTGCATGGTAGAATTGA 59.443 47.619 23.39 8.83 0.00 2.57
2701 2805 1.559682 ACTCCCGTGCATGGTAGAATT 59.440 47.619 23.25 0.00 0.00 2.17
2704 2808 1.327690 GGACTCCCGTGCATGGTAGA 61.328 60.000 23.25 13.34 0.00 2.59
2705 2809 1.144057 GGACTCCCGTGCATGGTAG 59.856 63.158 23.39 19.50 0.00 3.18
2707 2811 3.717294 GGGACTCCCGTGCATGGT 61.717 66.667 23.39 5.14 32.13 3.55
2723 2827 1.903877 AAGGACTCTCCCATGCACGG 61.904 60.000 0.00 0.00 37.19 4.94
2724 2828 0.742281 CAAGGACTCTCCCATGCACG 60.742 60.000 0.00 0.00 37.19 5.34
2729 2833 2.579860 AGCAAATCAAGGACTCTCCCAT 59.420 45.455 0.00 0.00 37.19 4.00
2730 2834 1.988107 AGCAAATCAAGGACTCTCCCA 59.012 47.619 0.00 0.00 37.19 4.37
2731 2835 2.797177 AGCAAATCAAGGACTCTCCC 57.203 50.000 0.00 0.00 37.19 4.30
2732 2836 4.074970 TCAAAGCAAATCAAGGACTCTCC 58.925 43.478 0.00 0.00 36.58 3.71
2733 2837 4.999950 TCTCAAAGCAAATCAAGGACTCTC 59.000 41.667 0.00 0.00 0.00 3.20
2734 2838 4.978099 TCTCAAAGCAAATCAAGGACTCT 58.022 39.130 0.00 0.00 0.00 3.24
2735 2839 5.163673 GGATCTCAAAGCAAATCAAGGACTC 60.164 44.000 0.00 0.00 0.00 3.36
2736 2840 4.704057 GGATCTCAAAGCAAATCAAGGACT 59.296 41.667 0.00 0.00 0.00 3.85
2737 2841 4.437930 CGGATCTCAAAGCAAATCAAGGAC 60.438 45.833 0.00 0.00 0.00 3.85
2739 2843 3.181493 CCGGATCTCAAAGCAAATCAAGG 60.181 47.826 0.00 0.00 0.00 3.61
2740 2844 3.691118 TCCGGATCTCAAAGCAAATCAAG 59.309 43.478 0.00 0.00 0.00 3.02
2741 2845 3.684908 TCCGGATCTCAAAGCAAATCAA 58.315 40.909 0.00 0.00 0.00 2.57
2742 2846 3.348647 TCCGGATCTCAAAGCAAATCA 57.651 42.857 0.00 0.00 0.00 2.57
2743 2847 4.082787 TGTTTCCGGATCTCAAAGCAAATC 60.083 41.667 4.15 0.00 0.00 2.17
2744 2848 3.826157 TGTTTCCGGATCTCAAAGCAAAT 59.174 39.130 4.15 0.00 0.00 2.32
2745 2849 3.218453 TGTTTCCGGATCTCAAAGCAAA 58.782 40.909 4.15 0.00 0.00 3.68
2746 2850 2.857483 TGTTTCCGGATCTCAAAGCAA 58.143 42.857 4.15 0.00 0.00 3.91
2747 2851 2.559698 TGTTTCCGGATCTCAAAGCA 57.440 45.000 4.15 0.00 0.00 3.91
2748 2852 2.478539 GCATGTTTCCGGATCTCAAAGC 60.479 50.000 4.15 9.95 0.00 3.51
2750 2854 2.789213 TGCATGTTTCCGGATCTCAAA 58.211 42.857 4.15 0.00 0.00 2.69
2752 2856 2.715749 ATGCATGTTTCCGGATCTCA 57.284 45.000 4.15 5.53 0.00 3.27
2753 2857 3.733337 ACTATGCATGTTTCCGGATCTC 58.267 45.455 10.16 0.00 0.00 2.75
2757 2861 4.081365 TGAGTAACTATGCATGTTTCCGGA 60.081 41.667 10.16 0.00 0.00 5.14
2758 2862 4.188462 TGAGTAACTATGCATGTTTCCGG 58.812 43.478 10.16 0.00 0.00 5.14
2759 2863 5.794687 TTGAGTAACTATGCATGTTTCCG 57.205 39.130 10.16 0.00 0.00 4.30
2760 2864 8.863049 CAATTTTGAGTAACTATGCATGTTTCC 58.137 33.333 10.16 6.41 0.00 3.13
2761 2865 9.624697 TCAATTTTGAGTAACTATGCATGTTTC 57.375 29.630 10.16 9.51 32.50 2.78
2762 2866 9.410556 GTCAATTTTGAGTAACTATGCATGTTT 57.589 29.630 10.16 4.63 37.98 2.83
2763 2867 8.028938 GGTCAATTTTGAGTAACTATGCATGTT 58.971 33.333 10.16 13.66 37.98 2.71
2764 2868 7.362920 GGGTCAATTTTGAGTAACTATGCATGT 60.363 37.037 10.16 2.51 37.98 3.21
2765 2869 6.974622 GGGTCAATTTTGAGTAACTATGCATG 59.025 38.462 10.16 1.82 37.98 4.06
2766 2870 6.183360 CGGGTCAATTTTGAGTAACTATGCAT 60.183 38.462 3.79 3.79 37.98 3.96
2767 2871 5.123186 CGGGTCAATTTTGAGTAACTATGCA 59.877 40.000 0.00 0.00 37.98 3.96
2769 2873 5.354234 AGCGGGTCAATTTTGAGTAACTATG 59.646 40.000 0.00 0.00 37.98 2.23
2770 2874 5.354234 CAGCGGGTCAATTTTGAGTAACTAT 59.646 40.000 0.00 0.00 37.98 2.12
2772 2876 3.502211 CAGCGGGTCAATTTTGAGTAACT 59.498 43.478 0.00 0.00 37.98 2.24
2773 2877 3.252458 ACAGCGGGTCAATTTTGAGTAAC 59.748 43.478 0.00 0.00 37.98 2.50
2776 2880 1.981256 ACAGCGGGTCAATTTTGAGT 58.019 45.000 0.00 0.00 37.98 3.41
2777 2881 3.004734 AGAAACAGCGGGTCAATTTTGAG 59.995 43.478 0.00 0.00 37.98 3.02
2781 2885 3.383185 TGAAAGAAACAGCGGGTCAATTT 59.617 39.130 0.00 0.00 0.00 1.82
2782 2886 2.955660 TGAAAGAAACAGCGGGTCAATT 59.044 40.909 0.00 0.00 0.00 2.32
2783 2887 2.293399 GTGAAAGAAACAGCGGGTCAAT 59.707 45.455 0.00 0.00 0.00 2.57
2784 2888 1.673920 GTGAAAGAAACAGCGGGTCAA 59.326 47.619 0.00 0.00 0.00 3.18
2786 2890 0.591659 GGTGAAAGAAACAGCGGGTC 59.408 55.000 0.00 0.00 0.00 4.46
2787 2891 0.106918 TGGTGAAAGAAACAGCGGGT 60.107 50.000 0.00 0.00 38.39 5.28
2789 2893 1.021202 TGTGGTGAAAGAAACAGCGG 58.979 50.000 0.00 0.00 38.39 5.52
2790 2894 2.653890 CATGTGGTGAAAGAAACAGCG 58.346 47.619 0.00 0.00 38.39 5.18
2791 2895 2.223782 TGCATGTGGTGAAAGAAACAGC 60.224 45.455 0.00 0.00 36.48 4.40
2796 2900 2.622942 GTCCTTGCATGTGGTGAAAGAA 59.377 45.455 0.00 0.00 45.07 2.52
2798 2902 1.955778 TGTCCTTGCATGTGGTGAAAG 59.044 47.619 0.00 0.00 42.35 2.62
2800 2904 1.133823 AGTGTCCTTGCATGTGGTGAA 60.134 47.619 0.00 0.00 0.00 3.18
2801 2905 0.473755 AGTGTCCTTGCATGTGGTGA 59.526 50.000 0.00 0.00 0.00 4.02
2802 2906 0.594602 CAGTGTCCTTGCATGTGGTG 59.405 55.000 0.00 0.00 0.00 4.17
2803 2907 0.183492 ACAGTGTCCTTGCATGTGGT 59.817 50.000 0.00 0.00 0.00 4.16
2804 2908 1.267806 GAACAGTGTCCTTGCATGTGG 59.732 52.381 0.00 0.00 0.00 4.17
2805 2909 1.948834 TGAACAGTGTCCTTGCATGTG 59.051 47.619 0.00 0.00 0.00 3.21
2806 2910 2.224606 CTGAACAGTGTCCTTGCATGT 58.775 47.619 0.00 0.00 0.00 3.21
2807 2911 1.068748 GCTGAACAGTGTCCTTGCATG 60.069 52.381 0.00 0.00 0.00 4.06
2808 2912 1.202855 AGCTGAACAGTGTCCTTGCAT 60.203 47.619 0.00 0.00 0.00 3.96
2811 2915 2.417933 GCATAGCTGAACAGTGTCCTTG 59.582 50.000 0.00 0.00 0.00 3.61
2814 2918 2.005451 CTGCATAGCTGAACAGTGTCC 58.995 52.381 0.00 0.00 0.00 4.02
2815 2919 1.396301 GCTGCATAGCTGAACAGTGTC 59.604 52.381 0.00 0.00 46.57 3.67
2816 2920 1.446907 GCTGCATAGCTGAACAGTGT 58.553 50.000 0.00 0.00 46.57 3.55
2834 2938 1.523938 GGATGGTGGAGCGTAAGGC 60.524 63.158 0.00 0.00 44.05 4.35
2835 2939 1.146263 GGGATGGTGGAGCGTAAGG 59.854 63.158 0.00 0.00 38.28 2.69
2836 2940 0.179073 CTGGGATGGTGGAGCGTAAG 60.179 60.000 0.00 0.00 43.44 2.34
2837 2941 0.616395 TCTGGGATGGTGGAGCGTAA 60.616 55.000 0.00 0.00 0.00 3.18
2838 2942 1.001120 TCTGGGATGGTGGAGCGTA 59.999 57.895 0.00 0.00 0.00 4.42
2840 2944 2.187946 GTCTGGGATGGTGGAGCG 59.812 66.667 0.00 0.00 0.00 5.03
2842 2946 0.995024 AAAGGTCTGGGATGGTGGAG 59.005 55.000 0.00 0.00 0.00 3.86
2843 2947 1.354368 GAAAAGGTCTGGGATGGTGGA 59.646 52.381 0.00 0.00 0.00 4.02
2844 2948 1.075374 TGAAAAGGTCTGGGATGGTGG 59.925 52.381 0.00 0.00 0.00 4.61
2845 2949 2.584835 TGAAAAGGTCTGGGATGGTG 57.415 50.000 0.00 0.00 0.00 4.17
2846 2950 2.922283 AGATGAAAAGGTCTGGGATGGT 59.078 45.455 0.00 0.00 0.00 3.55
2847 2951 3.659183 AGATGAAAAGGTCTGGGATGG 57.341 47.619 0.00 0.00 0.00 3.51
2848 2952 7.559170 AGAAATAAGATGAAAAGGTCTGGGATG 59.441 37.037 0.00 0.00 0.00 3.51
2849 2953 7.646884 AGAAATAAGATGAAAAGGTCTGGGAT 58.353 34.615 0.00 0.00 0.00 3.85
2850 2954 7.032598 AGAAATAAGATGAAAAGGTCTGGGA 57.967 36.000 0.00 0.00 0.00 4.37
2851 2955 8.807948 TTAGAAATAAGATGAAAAGGTCTGGG 57.192 34.615 0.00 0.00 0.00 4.45
2852 2956 9.454859 ACTTAGAAATAAGATGAAAAGGTCTGG 57.545 33.333 2.19 0.00 0.00 3.86
2922 3026 9.702494 TCATCATAAACACAAATATGCAAACAA 57.298 25.926 0.00 0.00 31.11 2.83
2923 3027 9.872721 ATCATCATAAACACAAATATGCAAACA 57.127 25.926 0.00 0.00 31.11 2.83
2925 3029 9.315525 CCATCATCATAAACACAAATATGCAAA 57.684 29.630 0.00 0.00 31.11 3.68
2926 3030 8.693625 TCCATCATCATAAACACAAATATGCAA 58.306 29.630 0.00 0.00 31.11 4.08
2927 3031 8.235359 TCCATCATCATAAACACAAATATGCA 57.765 30.769 0.00 0.00 31.11 3.96
2928 3032 8.570488 TCTCCATCATCATAAACACAAATATGC 58.430 33.333 0.00 0.00 31.11 3.14
2929 3033 9.888878 GTCTCCATCATCATAAACACAAATATG 57.111 33.333 0.00 0.00 0.00 1.78
2930 3034 9.857656 AGTCTCCATCATCATAAACACAAATAT 57.142 29.630 0.00 0.00 0.00 1.28
2931 3035 9.685276 AAGTCTCCATCATCATAAACACAAATA 57.315 29.630 0.00 0.00 0.00 1.40
2932 3036 8.585471 AAGTCTCCATCATCATAAACACAAAT 57.415 30.769 0.00 0.00 0.00 2.32
2933 3037 8.408043 AAAGTCTCCATCATCATAAACACAAA 57.592 30.769 0.00 0.00 0.00 2.83
2934 3038 9.513906 TTAAAGTCTCCATCATCATAAACACAA 57.486 29.630 0.00 0.00 0.00 3.33
2935 3039 9.513906 TTTAAAGTCTCCATCATCATAAACACA 57.486 29.630 0.00 0.00 0.00 3.72
2938 3042 9.490663 CGTTTTAAAGTCTCCATCATCATAAAC 57.509 33.333 0.00 0.00 0.00 2.01
2939 3043 8.673711 CCGTTTTAAAGTCTCCATCATCATAAA 58.326 33.333 0.00 0.00 0.00 1.40
2940 3044 7.282224 CCCGTTTTAAAGTCTCCATCATCATAA 59.718 37.037 0.00 0.00 0.00 1.90
2941 3045 6.765989 CCCGTTTTAAAGTCTCCATCATCATA 59.234 38.462 0.00 0.00 0.00 2.15
2942 3046 5.590259 CCCGTTTTAAAGTCTCCATCATCAT 59.410 40.000 0.00 0.00 0.00 2.45
2943 3047 4.941263 CCCGTTTTAAAGTCTCCATCATCA 59.059 41.667 0.00 0.00 0.00 3.07
2944 3048 5.064834 GTCCCGTTTTAAAGTCTCCATCATC 59.935 44.000 0.00 0.00 0.00 2.92
2945 3049 4.941873 GTCCCGTTTTAAAGTCTCCATCAT 59.058 41.667 0.00 0.00 0.00 2.45
2946 3050 4.320870 GTCCCGTTTTAAAGTCTCCATCA 58.679 43.478 0.00 0.00 0.00 3.07
2947 3051 3.688185 GGTCCCGTTTTAAAGTCTCCATC 59.312 47.826 0.00 0.00 0.00 3.51
2948 3052 3.073356 TGGTCCCGTTTTAAAGTCTCCAT 59.927 43.478 0.00 0.00 0.00 3.41
2949 3053 2.438763 TGGTCCCGTTTTAAAGTCTCCA 59.561 45.455 0.00 0.00 0.00 3.86
2950 3054 2.810274 GTGGTCCCGTTTTAAAGTCTCC 59.190 50.000 0.00 0.00 0.00 3.71
2951 3055 3.736720 AGTGGTCCCGTTTTAAAGTCTC 58.263 45.455 0.00 0.00 0.00 3.36
2952 3056 3.851458 AGTGGTCCCGTTTTAAAGTCT 57.149 42.857 0.00 0.00 0.00 3.24
2953 3057 4.906065 AAAGTGGTCCCGTTTTAAAGTC 57.094 40.909 0.00 0.00 0.00 3.01
2954 3058 6.772360 TTAAAAGTGGTCCCGTTTTAAAGT 57.228 33.333 12.61 0.00 34.35 2.66
2955 3059 9.917129 ATATTTAAAAGTGGTCCCGTTTTAAAG 57.083 29.630 22.78 0.00 43.52 1.85
2959 3063 9.470399 AGATATATTTAAAAGTGGTCCCGTTTT 57.530 29.630 0.00 4.25 0.00 2.43
3002 3106 9.396022 AGCTTACTATGCACATAACTTATTTGT 57.604 29.630 0.00 0.00 0.00 2.83
3008 3112 8.576442 ACAAAAAGCTTACTATGCACATAACTT 58.424 29.630 0.00 0.00 0.00 2.66
3014 3118 4.037327 TGCACAAAAAGCTTACTATGCACA 59.963 37.500 18.94 7.71 36.94 4.57
3079 3483 7.325694 TCCTTTACAACATAGTAGTGCCTAAC 58.674 38.462 0.00 0.00 0.00 2.34
3081 3485 7.484993 TTCCTTTACAACATAGTAGTGCCTA 57.515 36.000 0.00 0.00 0.00 3.93
3082 3486 6.368779 TTCCTTTACAACATAGTAGTGCCT 57.631 37.500 0.00 0.00 0.00 4.75
3085 3489 7.707035 CCTAGCTTCCTTTACAACATAGTAGTG 59.293 40.741 0.00 0.00 0.00 2.74
3086 3490 7.633116 GCCTAGCTTCCTTTACAACATAGTAGT 60.633 40.741 0.00 0.00 0.00 2.73
3087 3491 6.702282 GCCTAGCTTCCTTTACAACATAGTAG 59.298 42.308 0.00 0.00 0.00 2.57
3089 3493 5.189934 AGCCTAGCTTCCTTTACAACATAGT 59.810 40.000 0.00 0.00 33.89 2.12
3090 3494 5.675538 AGCCTAGCTTCCTTTACAACATAG 58.324 41.667 0.00 0.00 33.89 2.23
3091 3495 5.693769 AGCCTAGCTTCCTTTACAACATA 57.306 39.130 0.00 0.00 33.89 2.29
3092 3496 4.576330 AGCCTAGCTTCCTTTACAACAT 57.424 40.909 0.00 0.00 33.89 2.71
3093 3497 4.367039 AAGCCTAGCTTCCTTTACAACA 57.633 40.909 0.00 0.00 46.77 3.33


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

AutoCloner maintained by Alex Coulton.