Multiple sequence alignment - TraesCS2B01G196400

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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 TraesCS2B01G196400 chr2B 100.000 4838 0 0 492 5329 174588144 174592981 0.000000e+00 8935
1 TraesCS2B01G196400 chr2B 100.000 84 0 0 2491 2574 174590070 174590153 7.150000e-34 156
2 TraesCS2B01G196400 chr2B 100.000 84 0 0 2418 2501 174590143 174590226 7.150000e-34 156
3 TraesCS2B01G196400 chr2B 100.000 75 0 0 1 75 174587653 174587727 7.200000e-29 139
4 TraesCS2B01G196400 chr2A 89.320 2060 121 28 492 2501 125247320 125249330 0.000000e+00 2494
5 TraesCS2B01G196400 chr2A 90.582 1890 99 35 2491 4340 125249249 125251099 0.000000e+00 2431
6 TraesCS2B01G196400 chr2A 87.139 1003 55 33 4340 5326 125251376 125252320 0.000000e+00 1070
7 TraesCS2B01G196400 chr2A 82.766 882 128 19 4461 5326 125458000 125458873 0.000000e+00 765
8 TraesCS2B01G196400 chr2A 95.946 74 3 0 1 74 125234401 125234474 2.610000e-23 121
9 TraesCS2B01G196400 chr2D 90.863 1587 83 18 492 2061 121055979 121057520 0.000000e+00 2071
10 TraesCS2B01G196400 chr2D 93.684 1045 50 11 2491 3530 121058115 121059148 0.000000e+00 1550
11 TraesCS2B01G196400 chr2D 89.658 1054 56 17 4291 5326 121059856 121060874 0.000000e+00 1293
12 TraesCS2B01G196400 chr2D 84.120 869 122 14 4469 5329 121354419 121355279 0.000000e+00 826
13 TraesCS2B01G196400 chr2D 87.443 661 38 20 3710 4336 121059190 121059839 0.000000e+00 719
14 TraesCS2B01G196400 chr2D 94.619 446 22 2 2056 2501 121057754 121058197 0.000000e+00 689
15 TraesCS2B01G196400 chr2D 100.000 74 0 0 2 75 121055754 121055827 2.590000e-28 137


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 TraesCS2B01G196400 chr2B 174587653 174592981 5328 False 2346.500000 8935 100.000000 1 5329 4 chr2B.!!$F1 5328
1 TraesCS2B01G196400 chr2A 125247320 125252320 5000 False 1998.333333 2494 89.013667 492 5326 3 chr2A.!!$F3 4834
2 TraesCS2B01G196400 chr2A 125458000 125458873 873 False 765.000000 765 82.766000 4461 5326 1 chr2A.!!$F2 865
3 TraesCS2B01G196400 chr2D 121055754 121060874 5120 False 1076.500000 2071 92.711167 2 5326 6 chr2D.!!$F2 5324
4 TraesCS2B01G196400 chr2D 121354419 121355279 860 False 826.000000 826 84.120000 4469 5329 1 chr2D.!!$F1 860

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
767 769 0.179086 CGTGCTGGCCCAAACTTTTT 60.179 50.000 0.00 0.00 0.00 1.94 F
824 826 1.075659 GGCCCAGGCTCTTTCTGTT 59.924 57.895 8.89 0.00 41.60 3.16 F
830 832 1.081840 GGCTCTTTCTGTTGCGCAC 60.082 57.895 11.12 6.28 0.00 5.34 F
974 990 1.153329 AAGAACCCGCACGACACAA 60.153 52.632 0.00 0.00 0.00 3.33 F
2524 2828 0.241749 ACGACCTTCATCAACGCGTA 59.758 50.000 14.46 0.00 0.00 4.42 F
3217 3530 0.820074 CCAGCGTAGGTCTCGAGGAT 60.820 60.000 13.56 1.26 33.74 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 2736 0.241749 TACGCGTTGATGAAGGTCGT 59.758 50.000 20.78 10.45 35.47 4.34 R
2504 2808 0.599204 ACGCGTTGATGAAGGTCGTT 60.599 50.000 5.58 0.00 30.81 3.85 R
2505 2809 0.241749 TACGCGTTGATGAAGGTCGT 59.758 50.000 20.78 10.45 35.47 4.34 R
2894 3206 1.272490 CCGTAGCAACTGTGAAGGAGA 59.728 52.381 0.00 0.00 0.00 3.71 R
4245 4606 0.034896 ACGGATGAGCAGGTTCGTTT 59.965 50.000 0.00 0.00 0.00 3.60 R
4349 5044 0.108585 AGGTTCCGCACTGTGTCATT 59.891 50.000 9.86 0.00 0.00 2.57 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
519 520 1.378762 CCACCCCACACCTCGAATT 59.621 57.895 0.00 0.00 0.00 2.17
525 526 2.436417 CCCACACCTCGAATTGTCAAT 58.564 47.619 0.00 0.00 0.00 2.57
540 541 1.283321 GTCAATCCTCCTCCTTGCCTT 59.717 52.381 0.00 0.00 0.00 4.35
547 548 2.747855 CTCCTTGCCTTCACCCGC 60.748 66.667 0.00 0.00 0.00 6.13
561 562 4.953868 CCGCGACACCACGACCAA 62.954 66.667 8.23 0.00 35.09 3.67
566 567 1.153329 GACACCACGACCAACCACA 60.153 57.895 0.00 0.00 0.00 4.17
591 592 4.873129 TCGCGCCGGCTCATTCTC 62.873 66.667 26.68 3.46 36.88 2.87
600 601 2.811101 CTCATTCTCGGCGAGCCT 59.189 61.111 31.01 17.63 0.00 4.58
602 603 0.460987 CTCATTCTCGGCGAGCCTTT 60.461 55.000 31.01 12.78 0.00 3.11
654 655 2.946762 GAACGCTGCGCCTTCTTT 59.053 55.556 23.51 7.56 0.00 2.52
666 667 3.360758 GCGCCTTCTTTTACAATTTGACG 59.639 43.478 2.79 0.00 0.00 4.35
675 676 8.554835 TCTTTTACAATTTGACGTATCCATCA 57.445 30.769 2.79 0.00 0.00 3.07
755 757 1.006102 GATATCGGGACCGTGCTGG 60.006 63.158 10.90 0.00 46.41 4.85
756 758 3.165160 ATATCGGGACCGTGCTGGC 62.165 63.158 10.90 0.00 43.94 4.85
761 763 4.966787 GGACCGTGCTGGCCCAAA 62.967 66.667 0.00 0.00 40.75 3.28
762 764 3.670377 GACCGTGCTGGCCCAAAC 61.670 66.667 0.00 0.00 43.94 2.93
763 765 4.204028 ACCGTGCTGGCCCAAACT 62.204 61.111 0.00 0.00 43.94 2.66
764 766 2.912025 CCGTGCTGGCCCAAACTT 60.912 61.111 0.00 0.00 0.00 2.66
765 767 2.498056 CCGTGCTGGCCCAAACTTT 61.498 57.895 0.00 0.00 0.00 2.66
766 768 1.441311 CGTGCTGGCCCAAACTTTT 59.559 52.632 0.00 0.00 0.00 2.27
767 769 0.179086 CGTGCTGGCCCAAACTTTTT 60.179 50.000 0.00 0.00 0.00 1.94
806 808 7.591426 CCAAACTCTTCTTATTTTGAGAAACCG 59.409 37.037 0.00 0.00 33.10 4.44
824 826 1.075659 GGCCCAGGCTCTTTCTGTT 59.924 57.895 8.89 0.00 41.60 3.16
830 832 1.081840 GGCTCTTTCTGTTGCGCAC 60.082 57.895 11.12 6.28 0.00 5.34
851 853 2.046314 CACGACAATCGGGGGCTT 60.046 61.111 2.97 0.00 45.59 4.35
974 990 1.153329 AAGAACCCGCACGACACAA 60.153 52.632 0.00 0.00 0.00 3.33
1070 1086 4.819761 GAGCGGCGATGTCTGGCA 62.820 66.667 12.98 0.00 0.00 4.92
1221 1237 3.083997 AAATCGAGCTCCGCCCCT 61.084 61.111 8.47 0.00 38.37 4.79
1258 1278 2.105128 CCTGGCTCCGTGACGATC 59.895 66.667 6.54 0.00 0.00 3.69
1460 1480 1.871080 ATCATCTCGTGATTTCGGGC 58.129 50.000 0.00 0.00 45.25 6.13
1605 1629 3.011566 GAGGTGACTGATCCTCTCTGA 57.988 52.381 4.24 0.00 44.68 3.27
1641 1665 7.201705 CCGTCAGTTCTAATCTCATGTGTACTA 60.202 40.741 0.00 0.00 0.00 1.82
1665 1689 2.354539 GCCGTGCACGCAATTTGT 60.355 55.556 33.17 0.00 38.18 2.83
1684 1708 6.739331 TTTGTTCCCACTGGTGATTAATTT 57.261 33.333 1.93 0.00 0.00 1.82
1703 1727 1.154150 GCACCTGCATTGCGACTTC 60.154 57.895 3.84 0.00 41.59 3.01
1727 1751 3.380637 GCAGATCGAGTAGGACTTTACCA 59.619 47.826 0.00 0.00 0.00 3.25
1729 1753 5.341617 CAGATCGAGTAGGACTTTACCAAC 58.658 45.833 0.00 0.00 0.00 3.77
1734 1758 2.233186 AGTAGGACTTTACCAACGGAGC 59.767 50.000 0.00 0.00 0.00 4.70
1751 1775 2.035321 GGAGCGTTTTGTTTTCCATCCA 59.965 45.455 0.00 0.00 0.00 3.41
1752 1776 3.306019 GGAGCGTTTTGTTTTCCATCCAT 60.306 43.478 0.00 0.00 0.00 3.41
1814 1839 5.645497 GTGCACTTCTGGATACTTTGAAGAT 59.355 40.000 10.32 0.00 39.58 2.40
1844 1869 8.717821 GGAGTAATTTTAATTTTTCAGGTTGGC 58.282 33.333 0.00 0.00 0.00 4.52
1898 1940 7.799081 GGTCTAAAACCTTGGGTATACAGTAT 58.201 38.462 5.01 0.00 45.45 2.12
2016 2064 8.470805 TCTATCTGACTAGTTTTGATCCTTGTC 58.529 37.037 0.00 0.00 35.10 3.18
2114 2417 5.125578 CCTGGCCCTTAATCTGAACTTTAAC 59.874 44.000 0.00 0.00 0.00 2.01
2133 2436 8.850156 ACTTTAACTCTCAAACAACTGCATATT 58.150 29.630 0.00 0.00 0.00 1.28
2146 2449 7.620880 ACAACTGCATATTCCTTAAGTACAGA 58.379 34.615 0.97 0.00 0.00 3.41
2223 2526 7.168219 TGCCATTTTATCTGTCTACTTCTGTT 58.832 34.615 0.00 0.00 0.00 3.16
2242 2546 4.230657 TGTTTTATTGACGGGCATTTTCG 58.769 39.130 0.00 0.00 0.00 3.46
2435 2739 4.512198 TCGCCTGAGAACATTTAAAAACGA 59.488 37.500 0.00 0.00 0.00 3.85
2445 2749 8.410141 AGAACATTTAAAAACGACCTTCATCAA 58.590 29.630 0.00 0.00 0.00 2.57
2479 2783 6.990341 TCAGTTGTCATGTTGAAGATATGG 57.010 37.500 0.00 0.00 0.00 2.74
2480 2784 5.882000 TCAGTTGTCATGTTGAAGATATGGG 59.118 40.000 0.00 0.00 0.00 4.00
2481 2785 5.882000 CAGTTGTCATGTTGAAGATATGGGA 59.118 40.000 0.00 0.00 0.00 4.37
2482 2786 6.375174 CAGTTGTCATGTTGAAGATATGGGAA 59.625 38.462 0.00 0.00 0.00 3.97
2483 2787 6.600822 AGTTGTCATGTTGAAGATATGGGAAG 59.399 38.462 0.00 0.00 0.00 3.46
2484 2788 6.312141 TGTCATGTTGAAGATATGGGAAGA 57.688 37.500 0.00 0.00 0.00 2.87
2485 2789 6.351711 TGTCATGTTGAAGATATGGGAAGAG 58.648 40.000 0.00 0.00 0.00 2.85
2486 2790 6.156775 TGTCATGTTGAAGATATGGGAAGAGA 59.843 38.462 0.00 0.00 0.00 3.10
2487 2791 7.147426 TGTCATGTTGAAGATATGGGAAGAGAT 60.147 37.037 0.00 0.00 0.00 2.75
2488 2792 7.172875 GTCATGTTGAAGATATGGGAAGAGATG 59.827 40.741 0.00 0.00 0.00 2.90
2489 2793 6.813293 TGTTGAAGATATGGGAAGAGATGA 57.187 37.500 0.00 0.00 0.00 2.92
2490 2794 7.384524 TGTTGAAGATATGGGAAGAGATGAT 57.615 36.000 0.00 0.00 0.00 2.45
2491 2795 7.222161 TGTTGAAGATATGGGAAGAGATGATG 58.778 38.462 0.00 0.00 0.00 3.07
2492 2796 7.071572 TGTTGAAGATATGGGAAGAGATGATGA 59.928 37.037 0.00 0.00 0.00 2.92
2493 2797 7.242322 TGAAGATATGGGAAGAGATGATGAG 57.758 40.000 0.00 0.00 0.00 2.90
2494 2798 7.015064 TGAAGATATGGGAAGAGATGATGAGA 58.985 38.462 0.00 0.00 0.00 3.27
2495 2799 7.511714 TGAAGATATGGGAAGAGATGATGAGAA 59.488 37.037 0.00 0.00 0.00 2.87
2496 2800 7.243604 AGATATGGGAAGAGATGATGAGAAC 57.756 40.000 0.00 0.00 0.00 3.01
2497 2801 6.786461 AGATATGGGAAGAGATGATGAGAACA 59.214 38.462 0.00 0.00 0.00 3.18
2498 2802 5.908562 ATGGGAAGAGATGATGAGAACAT 57.091 39.130 0.00 0.00 39.67 2.71
2499 2803 5.705397 TGGGAAGAGATGATGAGAACATT 57.295 39.130 0.00 0.00 36.82 2.71
2500 2804 6.070951 TGGGAAGAGATGATGAGAACATTT 57.929 37.500 0.00 0.00 36.82 2.32
2501 2805 7.199167 TGGGAAGAGATGATGAGAACATTTA 57.801 36.000 0.00 0.00 36.82 1.40
2502 2806 7.632861 TGGGAAGAGATGATGAGAACATTTAA 58.367 34.615 0.00 0.00 36.82 1.52
2503 2807 8.108999 TGGGAAGAGATGATGAGAACATTTAAA 58.891 33.333 0.00 0.00 36.82 1.52
2504 2808 8.960591 GGGAAGAGATGATGAGAACATTTAAAA 58.039 33.333 0.00 0.00 36.82 1.52
2507 2811 9.831737 AAGAGATGATGAGAACATTTAAAAACG 57.168 29.630 0.00 0.00 36.82 3.60
2508 2812 9.219603 AGAGATGATGAGAACATTTAAAAACGA 57.780 29.630 0.00 0.00 36.82 3.85
2509 2813 9.267096 GAGATGATGAGAACATTTAAAAACGAC 57.733 33.333 0.00 0.00 36.82 4.34
2510 2814 8.237267 AGATGATGAGAACATTTAAAAACGACC 58.763 33.333 0.00 0.00 36.82 4.79
2511 2815 7.504924 TGATGAGAACATTTAAAAACGACCT 57.495 32.000 0.00 0.00 36.82 3.85
2512 2816 7.936584 TGATGAGAACATTTAAAAACGACCTT 58.063 30.769 0.00 0.00 36.82 3.50
2513 2817 8.073768 TGATGAGAACATTTAAAAACGACCTTC 58.926 33.333 0.00 0.00 36.82 3.46
2514 2818 7.323049 TGAGAACATTTAAAAACGACCTTCA 57.677 32.000 0.00 0.00 0.00 3.02
2515 2819 7.936584 TGAGAACATTTAAAAACGACCTTCAT 58.063 30.769 0.00 0.00 0.00 2.57
2516 2820 8.073768 TGAGAACATTTAAAAACGACCTTCATC 58.926 33.333 0.00 0.00 0.00 2.92
2517 2821 7.936584 AGAACATTTAAAAACGACCTTCATCA 58.063 30.769 0.00 0.00 0.00 3.07
2518 2822 8.410141 AGAACATTTAAAAACGACCTTCATCAA 58.590 29.630 0.00 0.00 0.00 2.57
2519 2823 7.924103 ACATTTAAAAACGACCTTCATCAAC 57.076 32.000 0.00 0.00 0.00 3.18
2520 2824 6.635239 ACATTTAAAAACGACCTTCATCAACG 59.365 34.615 0.00 0.00 0.00 4.10
2521 2825 2.681152 AAAACGACCTTCATCAACGC 57.319 45.000 0.00 0.00 0.00 4.84
2522 2826 0.511221 AAACGACCTTCATCAACGCG 59.489 50.000 3.53 3.53 0.00 6.01
2523 2827 0.599204 AACGACCTTCATCAACGCGT 60.599 50.000 5.58 5.58 0.00 6.01
2524 2828 0.241749 ACGACCTTCATCAACGCGTA 59.758 50.000 14.46 0.00 0.00 4.42
2525 2829 1.135199 ACGACCTTCATCAACGCGTAT 60.135 47.619 14.46 0.00 0.00 3.06
2526 2830 1.924524 CGACCTTCATCAACGCGTATT 59.075 47.619 14.46 0.00 0.00 1.89
2527 2831 2.347452 CGACCTTCATCAACGCGTATTT 59.653 45.455 14.46 0.00 0.00 1.40
2528 2832 3.548668 CGACCTTCATCAACGCGTATTTA 59.451 43.478 14.46 0.00 0.00 1.40
2529 2833 4.208460 CGACCTTCATCAACGCGTATTTAT 59.792 41.667 14.46 0.30 0.00 1.40
2530 2834 5.609696 CGACCTTCATCAACGCGTATTTATC 60.610 44.000 14.46 0.89 0.00 1.75
2531 2835 5.113383 ACCTTCATCAACGCGTATTTATCA 58.887 37.500 14.46 0.00 0.00 2.15
2532 2836 5.234329 ACCTTCATCAACGCGTATTTATCAG 59.766 40.000 14.46 3.58 0.00 2.90
2533 2837 5.234329 CCTTCATCAACGCGTATTTATCAGT 59.766 40.000 14.46 0.00 0.00 3.41
2534 2838 6.238103 CCTTCATCAACGCGTATTTATCAGTT 60.238 38.462 14.46 0.00 0.00 3.16
2535 2839 6.031549 TCATCAACGCGTATTTATCAGTTG 57.968 37.500 14.46 2.47 39.94 3.16
2536 2840 5.579119 TCATCAACGCGTATTTATCAGTTGT 59.421 36.000 14.46 0.00 39.66 3.32
2537 2841 5.444586 TCAACGCGTATTTATCAGTTGTC 57.555 39.130 14.46 0.00 39.66 3.18
2538 2842 4.924462 TCAACGCGTATTTATCAGTTGTCA 59.076 37.500 14.46 0.00 39.66 3.58
2539 2843 5.579119 TCAACGCGTATTTATCAGTTGTCAT 59.421 36.000 14.46 0.00 39.66 3.06
2540 2844 5.389642 ACGCGTATTTATCAGTTGTCATG 57.610 39.130 11.67 0.00 0.00 3.07
2541 2845 4.868171 ACGCGTATTTATCAGTTGTCATGT 59.132 37.500 11.67 0.00 0.00 3.21
2542 2846 5.350365 ACGCGTATTTATCAGTTGTCATGTT 59.650 36.000 11.67 0.00 0.00 2.71
2543 2847 5.672426 CGCGTATTTATCAGTTGTCATGTTG 59.328 40.000 0.00 0.00 0.00 3.33
2544 2848 6.454981 CGCGTATTTATCAGTTGTCATGTTGA 60.455 38.462 0.00 0.00 0.00 3.18
2545 2849 7.240674 GCGTATTTATCAGTTGTCATGTTGAA 58.759 34.615 0.00 0.00 0.00 2.69
2546 2850 7.426456 GCGTATTTATCAGTTGTCATGTTGAAG 59.574 37.037 0.00 0.00 0.00 3.02
2547 2851 8.655970 CGTATTTATCAGTTGTCATGTTGAAGA 58.344 33.333 0.00 0.00 0.00 2.87
2581 2888 5.357314 AGATGATGAGAACATTTTCTGCCAG 59.643 40.000 0.00 0.00 42.53 4.85
2592 2903 3.788333 TTTCTGCCAGATATTGCTTGC 57.212 42.857 0.00 0.00 0.00 4.01
2652 2963 7.277981 AGCTATATGTACACTTTCCTTTGTTCG 59.722 37.037 0.00 0.00 0.00 3.95
2759 3070 2.894257 AAGTCCGCACCCAGCATGA 61.894 57.895 0.00 0.00 46.13 3.07
2967 3279 4.125703 CAGAGCTCTTTACATGTGATCCC 58.874 47.826 15.27 0.00 0.00 3.85
3076 3388 9.661187 CATGTTCTGCTGATGATTAGTTATTTC 57.339 33.333 0.00 0.00 0.00 2.17
3077 3389 8.791327 TGTTCTGCTGATGATTAGTTATTTCA 57.209 30.769 0.00 0.00 0.00 2.69
3078 3390 8.668353 TGTTCTGCTGATGATTAGTTATTTCAC 58.332 33.333 0.00 0.00 0.00 3.18
3212 3525 1.805945 GCAACCAGCGTAGGTCTCG 60.806 63.158 1.37 0.00 42.25 4.04
3217 3530 0.820074 CCAGCGTAGGTCTCGAGGAT 60.820 60.000 13.56 1.26 33.74 3.24
3262 3575 2.202919 GCAATGGCGGGCAATTCC 60.203 61.111 8.78 0.00 0.00 3.01
3336 3649 6.208988 ACAGTATTATCGAAGAGCAGACAA 57.791 37.500 0.00 0.00 43.63 3.18
3338 3651 7.268586 ACAGTATTATCGAAGAGCAGACAAAT 58.731 34.615 0.00 0.00 43.63 2.32
3339 3652 7.766278 ACAGTATTATCGAAGAGCAGACAAATT 59.234 33.333 0.00 0.00 43.63 1.82
3340 3653 8.607459 CAGTATTATCGAAGAGCAGACAAATTT 58.393 33.333 0.00 0.00 43.63 1.82
3341 3654 9.167311 AGTATTATCGAAGAGCAGACAAATTTT 57.833 29.630 0.00 0.00 43.63 1.82
3397 3716 7.722949 AACACAGATAAAAATGATGGTCCAT 57.277 32.000 3.26 3.26 0.00 3.41
3458 3777 6.313905 CCTGTAGCTCGTTCAGTTGATTTATT 59.686 38.462 0.00 0.00 0.00 1.40
3535 3859 1.003118 AGCAGGCCGTCAACTATTTCA 59.997 47.619 0.00 0.00 0.00 2.69
3596 3920 3.978687 AGTATCGGCAGTTGTATAGCAC 58.021 45.455 0.00 0.00 0.00 4.40
3600 3924 3.605634 TCGGCAGTTGTATAGCACATTT 58.394 40.909 0.00 0.00 36.90 2.32
3603 3927 4.662145 GGCAGTTGTATAGCACATTTGTC 58.338 43.478 0.00 0.00 36.90 3.18
3604 3928 4.155826 GGCAGTTGTATAGCACATTTGTCA 59.844 41.667 0.00 0.00 36.90 3.58
3605 3929 5.327091 GCAGTTGTATAGCACATTTGTCAG 58.673 41.667 0.00 0.00 36.90 3.51
3607 3931 5.643348 CAGTTGTATAGCACATTTGTCAGGA 59.357 40.000 0.00 0.00 36.90 3.86
3608 3932 5.643777 AGTTGTATAGCACATTTGTCAGGAC 59.356 40.000 0.00 0.00 36.90 3.85
3609 3933 5.159273 TGTATAGCACATTTGTCAGGACA 57.841 39.130 0.00 0.00 33.78 4.02
3621 3947 6.537453 TTTGTCAGGACATTTTTCTTCCAA 57.463 33.333 2.52 0.00 41.52 3.53
3624 3950 5.163561 TGTCAGGACATTTTTCTTCCAACAC 60.164 40.000 0.00 0.00 36.21 3.32
3679 4005 7.042950 TGGATTCTCATGTTTTTATTGGCATG 58.957 34.615 0.00 0.00 39.81 4.06
3684 4010 9.941325 TTCTCATGTTTTTATTGGCATGTTTAT 57.059 25.926 0.00 0.00 39.54 1.40
3698 4024 5.473039 GCATGTTTATATGCCTCCATTTCC 58.527 41.667 0.48 0.00 45.93 3.13
3699 4025 5.010922 GCATGTTTATATGCCTCCATTTCCA 59.989 40.000 0.48 0.00 45.93 3.53
3700 4026 6.462768 GCATGTTTATATGCCTCCATTTCCAA 60.463 38.462 0.48 0.00 45.93 3.53
3701 4027 7.499292 CATGTTTATATGCCTCCATTTCCAAA 58.501 34.615 0.00 0.00 32.85 3.28
3702 4028 7.487822 TGTTTATATGCCTCCATTTCCAAAA 57.512 32.000 0.00 0.00 32.85 2.44
3703 4029 7.911651 TGTTTATATGCCTCCATTTCCAAAAA 58.088 30.769 0.00 0.00 32.85 1.94
3745 4071 7.062605 GGCATCTTGAACTCATGTTGTTAATTG 59.937 37.037 6.79 3.87 36.39 2.32
3784 4110 1.101049 CACAGTTTGGTTCCCTGCGT 61.101 55.000 0.00 0.00 0.00 5.24
3820 4147 2.840651 AGCTGGCCTATTTGACTGTAGT 59.159 45.455 3.32 0.00 0.00 2.73
3854 4181 1.338484 TGAATCAGCTCAGTGGCACTC 60.338 52.381 19.13 6.97 34.17 3.51
3871 4199 3.355378 CACTCCAAGCCCATTGTGATTA 58.645 45.455 0.00 0.00 37.17 1.75
3971 4299 6.498304 ACATCGAGGTAATGCAATTGAAATC 58.502 36.000 10.34 0.00 36.99 2.17
4070 4423 5.046591 AGTTGTCAGGAAGAATTATCCGACA 60.047 40.000 20.61 20.61 42.78 4.35
4237 4598 1.250328 TTTCAATCAGGCAGCCACAG 58.750 50.000 15.80 2.88 0.00 3.66
4241 4602 0.964358 AATCAGGCAGCCACAGAAGC 60.964 55.000 15.80 0.00 0.00 3.86
4245 4606 1.601759 GGCAGCCACAGAAGCTCAA 60.602 57.895 6.55 0.00 38.95 3.02
4249 4610 0.947244 AGCCACAGAAGCTCAAAACG 59.053 50.000 0.00 0.00 34.91 3.60
4366 5061 1.225855 TGAATGACACAGTGCGGAAC 58.774 50.000 0.00 0.00 0.00 3.62
4408 5115 3.734463 TCGCTTTATTATTCCGATGGCA 58.266 40.909 0.00 0.00 0.00 4.92
4424 5131 4.617959 GATGGCAATGGATGATGAAACTG 58.382 43.478 0.00 0.00 0.00 3.16
4454 5162 0.036671 AACTAGGAAGAAACCGCCGG 60.037 55.000 0.00 0.00 34.73 6.13
4540 5248 1.198637 CGAAGAAGAGGTAACCGTCGT 59.801 52.381 0.00 0.00 37.17 4.34
4541 5249 2.593257 GAAGAAGAGGTAACCGTCGTG 58.407 52.381 0.00 0.00 37.17 4.35
4776 5495 2.735134 GCAACCAAGAATTACGAGACGT 59.265 45.455 0.00 0.00 44.35 4.34
5002 5744 3.369147 CAGCTCACAGAATTAACTGGTCG 59.631 47.826 0.00 0.00 41.59 4.79
5009 5751 4.631813 ACAGAATTAACTGGTCGCTTGATC 59.368 41.667 0.00 0.00 41.59 2.92
5045 5812 3.910817 AGCAAGACTGAGACTGCAG 57.089 52.632 13.48 13.48 41.63 4.41
5046 5813 1.336131 AGCAAGACTGAGACTGCAGA 58.664 50.000 23.35 0.00 39.20 4.26
5047 5814 1.000731 AGCAAGACTGAGACTGCAGAC 59.999 52.381 23.35 15.44 39.20 3.51
5048 5815 1.000731 GCAAGACTGAGACTGCAGACT 59.999 52.381 23.35 20.86 41.43 3.24
5049 5816 2.674954 CAAGACTGAGACTGCAGACTG 58.325 52.381 23.33 12.16 40.00 3.51
5050 5817 2.284754 AGACTGAGACTGCAGACTGA 57.715 50.000 23.33 14.22 38.96 3.41
5051 5818 2.161855 AGACTGAGACTGCAGACTGAG 58.838 52.381 25.56 25.56 38.96 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
509 510 2.939103 GGAGGATTGACAATTCGAGGTG 59.061 50.000 1.39 0.00 0.00 4.00
519 520 0.620556 GGCAAGGAGGAGGATTGACA 59.379 55.000 0.00 0.00 32.01 3.58
525 526 1.201429 GGTGAAGGCAAGGAGGAGGA 61.201 60.000 0.00 0.00 0.00 3.71
547 548 2.107343 TGGTTGGTCGTGGTGTCG 59.893 61.111 0.00 0.00 0.00 4.35
579 580 4.207281 TCGCCGAGAATGAGCCGG 62.207 66.667 0.00 0.00 45.51 6.13
586 587 2.109126 GCAAAGGCTCGCCGAGAAT 61.109 57.895 20.05 1.41 41.95 2.40
600 601 2.975799 GGCGACGTCCTTGGCAAA 60.976 61.111 10.58 0.00 0.00 3.68
773 775 5.921962 AATAAGAAGAGTTTGGGCATTCC 57.078 39.130 0.00 0.00 0.00 3.01
774 776 7.378181 TCAAAATAAGAAGAGTTTGGGCATTC 58.622 34.615 0.00 0.00 32.91 2.67
775 777 7.233348 TCTCAAAATAAGAAGAGTTTGGGCATT 59.767 33.333 0.00 0.00 32.57 3.56
776 778 6.721208 TCTCAAAATAAGAAGAGTTTGGGCAT 59.279 34.615 0.00 0.00 32.57 4.40
777 779 6.068010 TCTCAAAATAAGAAGAGTTTGGGCA 58.932 36.000 0.00 0.00 32.57 5.36
806 808 1.075659 AACAGAAAGAGCCTGGGCC 59.924 57.895 8.11 0.00 43.17 5.80
824 826 4.874977 TTGTCGTGGACGTGCGCA 62.875 61.111 20.73 5.66 40.80 6.09
830 832 2.508439 CCCCGATTGTCGTGGACG 60.508 66.667 0.00 0.00 39.86 4.79
851 853 0.178967 TCACCTGATTGCAGCCCAAA 60.179 50.000 0.00 0.00 40.91 3.28
1070 1086 3.858868 TTCTGCTTTCGCCGACGCT 62.859 57.895 8.71 0.00 39.84 5.07
1258 1278 1.734477 CGACGGACAGCACAGGAAG 60.734 63.158 0.00 0.00 0.00 3.46
1399 1419 4.932789 GCATTCGGCAGTACTGGA 57.067 55.556 23.95 11.08 43.97 3.86
1410 1430 2.305853 CCCGATCGAGCAGCATTCG 61.306 63.158 18.66 0.00 39.33 3.34
1456 1476 1.597663 GAAATCACCGATTACTGCCCG 59.402 52.381 0.00 0.00 31.46 6.13
1460 1480 2.930040 AGCACGAAATCACCGATTACTG 59.070 45.455 0.00 0.00 31.46 2.74
1522 1546 0.251297 TGGAACAGGTGCATGAAGGG 60.251 55.000 0.00 0.00 0.00 3.95
1641 1665 0.242286 TTGCGTGCACGGCATTAATT 59.758 45.000 37.47 0.00 41.91 1.40
1665 1689 4.021544 GTGCAAATTAATCACCAGTGGGAA 60.022 41.667 15.21 0.46 38.05 3.97
1703 1727 1.025812 AAGTCCTACTCGATCTGCGG 58.974 55.000 0.00 0.00 41.33 5.69
1706 1730 5.341617 GTTGGTAAAGTCCTACTCGATCTG 58.658 45.833 0.00 0.00 32.22 2.90
1729 1753 2.315901 GATGGAAAACAAAACGCTCCG 58.684 47.619 0.00 0.00 0.00 4.63
1734 1758 7.590279 AGTACTTATGGATGGAAAACAAAACG 58.410 34.615 0.00 0.00 0.00 3.60
1751 1775 7.241042 TCAAGGTGTTCTAGCAAGTACTTAT 57.759 36.000 8.04 2.75 0.00 1.73
1752 1776 6.659745 TCAAGGTGTTCTAGCAAGTACTTA 57.340 37.500 8.04 0.00 0.00 2.24
1814 1839 7.452189 ACCTGAAAAATTAAAATTACTCCCGGA 59.548 33.333 0.73 0.00 0.00 5.14
1898 1940 5.499004 AATTAAAGACCTGGCTGACAGTA 57.501 39.130 10.12 0.00 46.06 2.74
1935 1983 7.715265 AAAGATCACGATTCACGCTAATAAT 57.285 32.000 0.00 0.00 46.94 1.28
2016 2064 6.968904 GGTACTAAATCAACAGTGCAATCATG 59.031 38.462 0.00 0.00 0.00 3.07
2114 2417 6.506500 AAGGAATATGCAGTTGTTTGAGAG 57.493 37.500 0.00 0.00 0.00 3.20
2133 2436 9.013229 TGTTCTACGTAATTCTGTACTTAAGGA 57.987 33.333 7.53 0.00 0.00 3.36
2146 2449 3.259876 TGGCCTCAGTGTTCTACGTAATT 59.740 43.478 3.32 0.00 0.00 1.40
2242 2546 1.552337 TCTCCCATCAGCTTCAGTGAC 59.448 52.381 0.00 0.00 0.00 3.67
2373 2677 3.914605 CTGTGCTGCCTGCGTCGTA 62.915 63.158 0.00 0.00 46.63 3.43
2432 2736 0.241749 TACGCGTTGATGAAGGTCGT 59.758 50.000 20.78 10.45 35.47 4.34
2435 2739 5.113383 TGATAAATACGCGTTGATGAAGGT 58.887 37.500 20.78 0.00 0.00 3.50
2445 2749 4.868171 ACATGACAACTGATAAATACGCGT 59.132 37.500 19.17 19.17 0.00 6.01
2475 2779 7.384524 AATGTTCTCATCATCTCTTCCCATA 57.615 36.000 0.00 0.00 32.56 2.74
2476 2780 5.908562 ATGTTCTCATCATCTCTTCCCAT 57.091 39.130 0.00 0.00 0.00 4.00
2477 2781 5.705397 AATGTTCTCATCATCTCTTCCCA 57.295 39.130 0.00 0.00 32.56 4.37
2478 2782 8.511604 TTTAAATGTTCTCATCATCTCTTCCC 57.488 34.615 0.00 0.00 32.56 3.97
2481 2785 9.831737 CGTTTTTAAATGTTCTCATCATCTCTT 57.168 29.630 0.00 0.00 32.56 2.85
2482 2786 9.219603 TCGTTTTTAAATGTTCTCATCATCTCT 57.780 29.630 0.00 0.00 32.56 3.10
2483 2787 9.267096 GTCGTTTTTAAATGTTCTCATCATCTC 57.733 33.333 0.00 0.00 32.56 2.75
2484 2788 8.237267 GGTCGTTTTTAAATGTTCTCATCATCT 58.763 33.333 0.00 0.00 32.56 2.90
2485 2789 8.237267 AGGTCGTTTTTAAATGTTCTCATCATC 58.763 33.333 0.00 0.00 32.56 2.92
2486 2790 8.110860 AGGTCGTTTTTAAATGTTCTCATCAT 57.889 30.769 0.00 0.00 32.56 2.45
2487 2791 7.504924 AGGTCGTTTTTAAATGTTCTCATCA 57.495 32.000 0.00 0.00 32.56 3.07
2488 2792 8.073768 TGAAGGTCGTTTTTAAATGTTCTCATC 58.926 33.333 0.00 0.00 32.56 2.92
2489 2793 7.936584 TGAAGGTCGTTTTTAAATGTTCTCAT 58.063 30.769 0.00 0.00 35.59 2.90
2490 2794 7.323049 TGAAGGTCGTTTTTAAATGTTCTCA 57.677 32.000 0.00 0.00 0.00 3.27
2491 2795 8.073768 TGATGAAGGTCGTTTTTAAATGTTCTC 58.926 33.333 0.00 0.00 0.00 2.87
2492 2796 7.936584 TGATGAAGGTCGTTTTTAAATGTTCT 58.063 30.769 0.00 0.00 0.00 3.01
2493 2797 8.476925 GTTGATGAAGGTCGTTTTTAAATGTTC 58.523 33.333 0.00 0.00 0.00 3.18
2494 2798 7.166804 CGTTGATGAAGGTCGTTTTTAAATGTT 59.833 33.333 0.00 0.00 0.00 2.71
2495 2799 6.635239 CGTTGATGAAGGTCGTTTTTAAATGT 59.365 34.615 0.00 0.00 0.00 2.71
2496 2800 6.398517 GCGTTGATGAAGGTCGTTTTTAAATG 60.399 38.462 0.00 0.00 0.00 2.32
2497 2801 5.627780 GCGTTGATGAAGGTCGTTTTTAAAT 59.372 36.000 0.00 0.00 0.00 1.40
2498 2802 4.971220 GCGTTGATGAAGGTCGTTTTTAAA 59.029 37.500 0.00 0.00 0.00 1.52
2499 2803 4.529446 GCGTTGATGAAGGTCGTTTTTAA 58.471 39.130 0.00 0.00 0.00 1.52
2500 2804 3.363182 CGCGTTGATGAAGGTCGTTTTTA 60.363 43.478 0.00 0.00 0.00 1.52
2501 2805 2.601266 CGCGTTGATGAAGGTCGTTTTT 60.601 45.455 0.00 0.00 0.00 1.94
2502 2806 1.070175 CGCGTTGATGAAGGTCGTTTT 60.070 47.619 0.00 0.00 0.00 2.43
2503 2807 0.511221 CGCGTTGATGAAGGTCGTTT 59.489 50.000 0.00 0.00 0.00 3.60
2504 2808 0.599204 ACGCGTTGATGAAGGTCGTT 60.599 50.000 5.58 0.00 30.81 3.85
2505 2809 0.241749 TACGCGTTGATGAAGGTCGT 59.758 50.000 20.78 10.45 35.47 4.34
2506 2810 1.556564 ATACGCGTTGATGAAGGTCG 58.443 50.000 20.78 1.53 0.00 4.79
2507 2811 5.233476 TGATAAATACGCGTTGATGAAGGTC 59.767 40.000 20.78 5.43 0.00 3.85
2508 2812 5.113383 TGATAAATACGCGTTGATGAAGGT 58.887 37.500 20.78 0.00 0.00 3.50
2509 2813 5.234329 ACTGATAAATACGCGTTGATGAAGG 59.766 40.000 20.78 5.68 0.00 3.46
2510 2814 6.274001 ACTGATAAATACGCGTTGATGAAG 57.726 37.500 20.78 10.35 0.00 3.02
2511 2815 6.091577 ACAACTGATAAATACGCGTTGATGAA 59.908 34.615 20.78 0.00 36.26 2.57
2512 2816 5.579119 ACAACTGATAAATACGCGTTGATGA 59.421 36.000 20.78 0.00 36.26 2.92
2513 2817 5.795766 ACAACTGATAAATACGCGTTGATG 58.204 37.500 20.78 5.24 36.26 3.07
2514 2818 5.579119 TGACAACTGATAAATACGCGTTGAT 59.421 36.000 20.78 1.77 36.26 2.57
2515 2819 4.924462 TGACAACTGATAAATACGCGTTGA 59.076 37.500 20.78 0.00 36.26 3.18
2516 2820 5.198116 TGACAACTGATAAATACGCGTTG 57.802 39.130 20.78 8.02 38.10 4.10
2517 2821 5.350365 ACATGACAACTGATAAATACGCGTT 59.650 36.000 20.78 0.76 0.00 4.84
2518 2822 4.868171 ACATGACAACTGATAAATACGCGT 59.132 37.500 19.17 19.17 0.00 6.01
2519 2823 5.389642 ACATGACAACTGATAAATACGCG 57.610 39.130 3.53 3.53 0.00 6.01
2520 2824 6.771076 TCAACATGACAACTGATAAATACGC 58.229 36.000 0.00 0.00 0.00 4.42
2521 2825 8.655970 TCTTCAACATGACAACTGATAAATACG 58.344 33.333 0.00 0.00 0.00 3.06
2526 2830 9.112725 CCATATCTTCAACATGACAACTGATAA 57.887 33.333 0.00 0.00 0.00 1.75
2527 2831 7.716560 CCCATATCTTCAACATGACAACTGATA 59.283 37.037 0.00 1.06 0.00 2.15
2528 2832 6.544931 CCCATATCTTCAACATGACAACTGAT 59.455 38.462 0.00 0.00 0.00 2.90
2529 2833 5.882000 CCCATATCTTCAACATGACAACTGA 59.118 40.000 0.00 0.00 0.00 3.41
2530 2834 5.882000 TCCCATATCTTCAACATGACAACTG 59.118 40.000 0.00 0.00 0.00 3.16
2531 2835 6.065976 TCCCATATCTTCAACATGACAACT 57.934 37.500 0.00 0.00 0.00 3.16
2532 2836 6.599244 TCTTCCCATATCTTCAACATGACAAC 59.401 38.462 0.00 0.00 0.00 3.32
2533 2837 6.720309 TCTTCCCATATCTTCAACATGACAA 58.280 36.000 0.00 0.00 0.00 3.18
2534 2838 6.156775 TCTCTTCCCATATCTTCAACATGACA 59.843 38.462 0.00 0.00 0.00 3.58
2535 2839 6.586344 TCTCTTCCCATATCTTCAACATGAC 58.414 40.000 0.00 0.00 0.00 3.06
2536 2840 6.813293 TCTCTTCCCATATCTTCAACATGA 57.187 37.500 0.00 0.00 0.00 3.07
2537 2841 7.222161 TCATCTCTTCCCATATCTTCAACATG 58.778 38.462 0.00 0.00 0.00 3.21
2538 2842 7.384524 TCATCTCTTCCCATATCTTCAACAT 57.615 36.000 0.00 0.00 0.00 2.71
2539 2843 6.813293 TCATCTCTTCCCATATCTTCAACA 57.187 37.500 0.00 0.00 0.00 3.33
2540 2844 7.448420 TCATCATCTCTTCCCATATCTTCAAC 58.552 38.462 0.00 0.00 0.00 3.18
2541 2845 7.511714 TCTCATCATCTCTTCCCATATCTTCAA 59.488 37.037 0.00 0.00 0.00 2.69
2542 2846 7.015064 TCTCATCATCTCTTCCCATATCTTCA 58.985 38.462 0.00 0.00 0.00 3.02
2543 2847 7.479352 TCTCATCATCTCTTCCCATATCTTC 57.521 40.000 0.00 0.00 0.00 2.87
2544 2848 7.291885 TGTTCTCATCATCTCTTCCCATATCTT 59.708 37.037 0.00 0.00 0.00 2.40
2545 2849 6.786461 TGTTCTCATCATCTCTTCCCATATCT 59.214 38.462 0.00 0.00 0.00 1.98
2546 2850 7.002250 TGTTCTCATCATCTCTTCCCATATC 57.998 40.000 0.00 0.00 0.00 1.63
2547 2851 7.571071 ATGTTCTCATCATCTCTTCCCATAT 57.429 36.000 0.00 0.00 0.00 1.78
2581 2888 8.370493 TCTGATACTAAAGTGCAAGCAATATC 57.630 34.615 0.00 0.00 0.00 1.63
2592 2903 9.081997 CAGAAAGTAAGCTCTGATACTAAAGTG 57.918 37.037 0.00 0.00 41.38 3.16
2652 2963 3.568007 TGAATGAAGTGTGCCAAGTTACC 59.432 43.478 0.00 0.00 0.00 2.85
2759 3070 3.110705 ACTCTGTAAGGTCTCATGCCAT 58.889 45.455 0.00 0.00 0.00 4.40
2894 3206 1.272490 CCGTAGCAACTGTGAAGGAGA 59.728 52.381 0.00 0.00 0.00 3.71
2967 3279 2.328099 GCCAAGGACTTGTCCAGCG 61.328 63.158 20.36 8.84 38.85 5.18
3069 3381 8.507249 ACATTACTGCTTGAGAAGTGAAATAAC 58.493 33.333 1.74 0.00 34.09 1.89
3076 3388 4.318332 TCCACATTACTGCTTGAGAAGTG 58.682 43.478 1.74 0.00 34.09 3.16
3077 3389 4.623932 TCCACATTACTGCTTGAGAAGT 57.376 40.909 0.00 0.00 37.72 3.01
3078 3390 4.334759 CCATCCACATTACTGCTTGAGAAG 59.665 45.833 0.00 0.00 0.00 2.85
3159 3472 6.078456 ACATCAGGGAATCCAGTTATTCAA 57.922 37.500 0.09 0.00 37.56 2.69
3169 3482 1.696884 GGAGAGGACATCAGGGAATCC 59.303 57.143 0.00 0.00 0.00 3.01
3212 3525 3.153919 ACTCGATAGCTTCCTGATCCTC 58.846 50.000 0.00 0.00 0.00 3.71
3217 3530 4.640789 GAGAAACTCGATAGCTTCCTGA 57.359 45.455 0.00 0.00 0.00 3.86
3262 3575 6.040166 CCATGGTTTCCTGGAATGATAAAGAG 59.960 42.308 10.45 0.00 34.24 2.85
3305 3618 8.817100 TGCTCTTCGATAATACTGTTAATGTTG 58.183 33.333 0.00 0.00 0.00 3.33
3371 3684 8.642935 TGGACCATCATTTTTATCTGTGTTTA 57.357 30.769 0.00 0.00 0.00 2.01
3397 3716 7.782049 AGACATTAGGAAATACGATCAACTCA 58.218 34.615 0.00 0.00 0.00 3.41
3496 3815 6.683110 GCCTGCTGTCTGCTTTATTAGTAGTA 60.683 42.308 3.20 0.00 43.37 1.82
3497 3816 5.665459 CCTGCTGTCTGCTTTATTAGTAGT 58.335 41.667 3.20 0.00 43.37 2.73
3498 3817 4.509600 GCCTGCTGTCTGCTTTATTAGTAG 59.490 45.833 3.20 0.00 43.37 2.57
3505 3829 1.375908 CGGCCTGCTGTCTGCTTTA 60.376 57.895 0.00 0.00 43.37 1.85
3535 3859 3.818773 CGGAAACCACAAGTAGGAACAAT 59.181 43.478 0.00 0.00 0.00 2.71
3596 3920 6.514947 TGGAAGAAAAATGTCCTGACAAATG 58.485 36.000 3.79 0.00 45.41 2.32
3600 3924 4.952957 TGTTGGAAGAAAAATGTCCTGACA 59.047 37.500 1.93 1.93 46.44 3.58
3603 3927 5.520376 AGTGTTGGAAGAAAAATGTCCTG 57.480 39.130 0.00 0.00 32.28 3.86
3604 3928 4.275936 CGAGTGTTGGAAGAAAAATGTCCT 59.724 41.667 0.00 0.00 32.28 3.85
3605 3929 4.036380 ACGAGTGTTGGAAGAAAAATGTCC 59.964 41.667 0.00 0.00 0.00 4.02
3607 3931 4.638421 TCACGAGTGTTGGAAGAAAAATGT 59.362 37.500 2.97 0.00 0.00 2.71
3608 3932 5.168526 TCACGAGTGTTGGAAGAAAAATG 57.831 39.130 2.97 0.00 0.00 2.32
3609 3933 5.357032 ACTTCACGAGTGTTGGAAGAAAAAT 59.643 36.000 7.19 0.00 39.20 1.82
3621 3947 2.244651 GCCGCAACTTCACGAGTGT 61.245 57.895 2.97 0.00 39.00 3.55
3624 3950 2.671177 CCAGCCGCAACTTCACGAG 61.671 63.158 0.00 0.00 0.00 4.18
3704 4030 2.040330 TGCCGCTGCACAGATTTTT 58.960 47.368 0.00 0.00 44.23 1.94
3705 4031 3.762293 TGCCGCTGCACAGATTTT 58.238 50.000 0.00 0.00 44.23 1.82
3719 4045 4.510038 AACAACATGAGTTCAAGATGCC 57.490 40.909 0.00 0.00 35.28 4.40
3751 4077 8.691661 AACCAAACTGTGACTTATAGACAAAT 57.308 30.769 0.00 0.00 0.00 2.32
3784 4110 2.681976 GCCAGCTCTGCTATCTTGGAAA 60.682 50.000 0.00 0.00 36.40 3.13
3820 4147 5.380043 AGCTGATTCAGGAAAACTTTGAGA 58.620 37.500 15.28 0.00 31.21 3.27
3854 4181 5.452356 GGAAGATTAATCACAATGGGCTTGG 60.452 44.000 17.56 0.00 39.30 3.61
3871 4199 5.073691 TCTGGAAAACCAAGAGAGGAAGATT 59.926 40.000 0.00 0.00 0.00 2.40
3971 4299 8.313227 CGCAAAATACTGCTACAACATTAATTG 58.687 33.333 0.00 0.00 40.33 2.32
4070 4423 2.146342 CGCCTCAACACAGTTCTGAAT 58.854 47.619 6.83 0.00 0.00 2.57
4168 4521 6.567602 ACTAGGAGAAATTGCAGTCCTATT 57.432 37.500 2.59 0.00 40.22 1.73
4198 4551 0.035739 TGAGACCCCACGCTAAAACC 59.964 55.000 0.00 0.00 0.00 3.27
4237 4598 1.604278 AGCAGGTTCGTTTTGAGCTTC 59.396 47.619 0.00 0.00 0.00 3.86
4241 4602 2.160417 GGATGAGCAGGTTCGTTTTGAG 59.840 50.000 0.00 0.00 0.00 3.02
4245 4606 0.034896 ACGGATGAGCAGGTTCGTTT 59.965 50.000 0.00 0.00 0.00 3.60
4249 4610 1.519455 CCGACGGATGAGCAGGTTC 60.519 63.158 8.64 0.00 0.00 3.62
4349 5044 0.108585 AGGTTCCGCACTGTGTCATT 59.891 50.000 9.86 0.00 0.00 2.57
4380 5075 3.493503 CGGAATAATAAAGCGAGGTCACC 59.506 47.826 0.00 0.00 0.00 4.02
4382 5077 4.659111 TCGGAATAATAAAGCGAGGTCA 57.341 40.909 0.00 0.00 0.00 4.02
4385 5080 3.125316 GCCATCGGAATAATAAAGCGAGG 59.875 47.826 0.00 0.00 0.00 4.63
4386 5081 3.745975 TGCCATCGGAATAATAAAGCGAG 59.254 43.478 0.00 0.00 0.00 5.03
4387 5082 3.734463 TGCCATCGGAATAATAAAGCGA 58.266 40.909 0.00 0.00 0.00 4.93
4390 5085 6.573664 TCCATTGCCATCGGAATAATAAAG 57.426 37.500 0.00 0.00 0.00 1.85
4408 5115 3.941483 GACGGTCAGTTTCATCATCCATT 59.059 43.478 2.62 0.00 0.00 3.16
4424 5131 3.883669 TCTTCCTAGTTCCTAGACGGTC 58.116 50.000 0.00 0.00 36.26 4.79
4776 5495 4.832248 ACCATCTATCTGACGAAAAGCAA 58.168 39.130 0.00 0.00 0.00 3.91
4982 5724 2.094417 GCGACCAGTTAATTCTGTGAGC 59.906 50.000 0.00 0.00 34.02 4.26
5002 5744 0.663688 CAGCAGCTCCATGATCAAGC 59.336 55.000 9.45 9.45 36.27 4.01
5009 5751 3.518998 GCAGGCAGCAGCTCCATG 61.519 66.667 11.98 3.76 44.79 3.66
5039 5806 3.147553 TCACTCTACTCAGTCTGCAGT 57.852 47.619 14.67 2.90 0.00 4.40
5040 5807 3.505680 ACTTCACTCTACTCAGTCTGCAG 59.494 47.826 7.63 7.63 0.00 4.41
5041 5808 3.254411 CACTTCACTCTACTCAGTCTGCA 59.746 47.826 0.00 0.00 0.00 4.41
5042 5809 3.832276 CACTTCACTCTACTCAGTCTGC 58.168 50.000 0.00 0.00 0.00 4.26
5043 5810 3.254411 TGCACTTCACTCTACTCAGTCTG 59.746 47.826 0.00 0.00 0.00 3.51
5044 5811 3.491342 TGCACTTCACTCTACTCAGTCT 58.509 45.455 0.00 0.00 0.00 3.24
5045 5812 3.366883 CCTGCACTTCACTCTACTCAGTC 60.367 52.174 0.00 0.00 0.00 3.51
5046 5813 2.560542 CCTGCACTTCACTCTACTCAGT 59.439 50.000 0.00 0.00 0.00 3.41
5047 5814 2.094286 CCCTGCACTTCACTCTACTCAG 60.094 54.545 0.00 0.00 0.00 3.35
5048 5815 1.895798 CCCTGCACTTCACTCTACTCA 59.104 52.381 0.00 0.00 0.00 3.41
5049 5816 1.404851 GCCCTGCACTTCACTCTACTC 60.405 57.143 0.00 0.00 0.00 2.59
5050 5817 0.610687 GCCCTGCACTTCACTCTACT 59.389 55.000 0.00 0.00 0.00 2.57
5051 5818 0.737715 CGCCCTGCACTTCACTCTAC 60.738 60.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.