Multiple sequence alignment - TraesCS1A01G092500

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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 TraesCS1A01G092500 chr1A 100.000 2954 0 0 1 2954 85007560 85004607 0.000000e+00 5456.0
1 TraesCS1A01G092500 chr1A 94.860 1576 58 14 795 2355 84796876 84795309 0.000000e+00 2440.0
2 TraesCS1A01G092500 chr1A 80.797 552 52 30 1 507 84797628 84797086 1.660000e-102 383.0
3 TraesCS1A01G092500 chr1A 96.190 105 3 1 408 511 85007070 85006966 1.410000e-38 171.0
4 TraesCS1A01G092500 chr1A 96.190 105 3 1 491 595 85007153 85007050 1.410000e-38 171.0
5 TraesCS1A01G092500 chr1D 92.385 1602 68 23 795 2353 88282777 88281187 0.000000e+00 2233.0
6 TraesCS1A01G092500 chr1D 93.208 1222 57 4 795 1991 87903450 87904670 0.000000e+00 1773.0
7 TraesCS1A01G092500 chr1D 94.681 658 27 7 795 1444 88244509 88243852 0.000000e+00 1014.0
8 TraesCS1A01G092500 chr1D 87.879 792 39 11 1558 2302 88243854 88243073 0.000000e+00 878.0
9 TraesCS1A01G092500 chr1D 88.199 322 30 8 206 522 88275932 88275614 7.730000e-101 377.0
10 TraesCS1A01G092500 chr1D 78.676 544 65 24 1 511 87902664 87903189 6.150000e-82 315.0
11 TraesCS1A01G092500 chr1D 85.113 309 29 9 491 788 88275731 88275429 1.720000e-77 300.0
12 TraesCS1A01G092500 chr1D 86.081 273 21 8 492 752 87903085 87903352 8.060000e-71 278.0
13 TraesCS1A01G092500 chr1D 88.793 116 9 4 410 522 87896864 87896978 3.970000e-29 139.0
14 TraesCS1A01G092500 chr1D 92.857 42 2 1 755 795 88244584 88244543 3.180000e-05 60.2
15 TraesCS1A01G092500 chr1D 92.857 42 2 1 755 795 88282852 88282811 3.180000e-05 60.2
16 TraesCS1A01G092500 chr4D 89.585 1613 79 43 795 2355 464798147 464796572 0.000000e+00 1965.0
17 TraesCS1A01G092500 chr1B 90.781 1486 64 17 795 2232 142134702 142133242 0.000000e+00 1917.0
18 TraesCS1A01G092500 chr1B 88.649 1621 106 31 795 2355 141844781 141846383 0.000000e+00 1903.0
19 TraesCS1A01G092500 chr1B 92.781 1219 59 12 795 1989 142037290 142038503 0.000000e+00 1736.0
20 TraesCS1A01G092500 chr1B 92.043 1219 68 12 795 1989 142093550 142094763 0.000000e+00 1687.0
21 TraesCS1A01G092500 chr1B 91.573 1068 88 2 924 1991 142086376 142087441 0.000000e+00 1472.0
22 TraesCS1A01G092500 chr1B 80.367 545 63 25 1 513 142036494 142037026 1.000000e-99 374.0
23 TraesCS1A01G092500 chr1B 86.275 306 32 10 213 513 141844215 141844515 1.020000e-84 324.0
24 TraesCS1A01G092500 chr1B 85.621 306 32 11 213 511 142025876 142026176 7.950000e-81 311.0
25 TraesCS1A01G092500 chr1B 85.662 272 21 10 491 752 142026073 142026336 1.350000e-68 270.0
26 TraesCS1A01G092500 chr1B 85.714 273 19 12 491 752 142036921 142037184 1.350000e-68 270.0
27 TraesCS1A01G092500 chr1B 79.221 308 34 14 491 795 142135016 142134736 1.400000e-43 187.0
28 TraesCS1A01G092500 chr3B 93.880 964 59 0 1028 1991 535705558 535704595 0.000000e+00 1454.0
29 TraesCS1A01G092500 chr3B 89.478 1131 95 17 795 1925 535563163 535562057 0.000000e+00 1408.0


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 TraesCS1A01G092500 chr1A 85004607 85007560 2953 True 1932.666667 5456 97.460000 1 2954 3 chr1A.!!$R2 2953
1 TraesCS1A01G092500 chr1A 84795309 84797628 2319 True 1411.500000 2440 87.828500 1 2355 2 chr1A.!!$R1 2354
2 TraesCS1A01G092500 chr1D 88281187 88282852 1665 True 1146.600000 2233 92.621000 755 2353 2 chr1D.!!$R3 1598
3 TraesCS1A01G092500 chr1D 87902664 87904670 2006 False 788.666667 1773 85.988333 1 1991 3 chr1D.!!$F2 1990
4 TraesCS1A01G092500 chr1D 88243073 88244584 1511 True 650.733333 1014 91.805667 755 2302 3 chr1D.!!$R1 1547
5 TraesCS1A01G092500 chr1D 88275429 88275932 503 True 338.500000 377 86.656000 206 788 2 chr1D.!!$R2 582
6 TraesCS1A01G092500 chr4D 464796572 464798147 1575 True 1965.000000 1965 89.585000 795 2355 1 chr4D.!!$R1 1560
7 TraesCS1A01G092500 chr1B 142093550 142094763 1213 False 1687.000000 1687 92.043000 795 1989 1 chr1B.!!$F2 1194
8 TraesCS1A01G092500 chr1B 142086376 142087441 1065 False 1472.000000 1472 91.573000 924 1991 1 chr1B.!!$F1 1067
9 TraesCS1A01G092500 chr1B 141844215 141846383 2168 False 1113.500000 1903 87.462000 213 2355 2 chr1B.!!$F3 2142
10 TraesCS1A01G092500 chr1B 142133242 142135016 1774 True 1052.000000 1917 85.001000 491 2232 2 chr1B.!!$R1 1741
11 TraesCS1A01G092500 chr1B 142036494 142038503 2009 False 793.333333 1736 86.287333 1 1989 3 chr1B.!!$F5 1988
12 TraesCS1A01G092500 chr3B 535704595 535705558 963 True 1454.000000 1454 93.880000 1028 1991 1 chr3B.!!$R2 963
13 TraesCS1A01G092500 chr3B 535562057 535563163 1106 True 1408.000000 1408 89.478000 795 1925 1 chr3B.!!$R1 1130

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
978 1147 0.179116 TTGCTCTGATCTGCTCTCGC 60.179 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2893 3194 0.11734 ACCTCTGGCTCTGGTTACCT 59.883 55.0 2.07 0.0 0.0 3.08 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
162 164 7.504922 TTCATGAAAACAAATGTATTAGCGC 57.495 32.000 5.45 0.00 0.00 5.92
163 165 6.616017 TCATGAAAACAAATGTATTAGCGCA 58.384 32.000 11.47 0.00 0.00 6.09
176 178 7.733046 TGTATTAGCGCATGTTAAAAATGTG 57.267 32.000 11.47 8.07 38.33 3.21
177 179 7.530863 TGTATTAGCGCATGTTAAAAATGTGA 58.469 30.769 11.47 0.00 37.67 3.58
181 183 3.423867 GCGCATGTTAAAAATGTGAACGT 59.576 39.130 0.30 0.00 37.67 3.99
182 184 4.660414 GCGCATGTTAAAAATGTGAACGTG 60.660 41.667 0.30 0.00 41.14 4.49
204 207 7.760794 ACGTGTGCATTCAAAAATATTCATCAT 59.239 29.630 0.00 0.00 0.00 2.45
286 323 4.385358 AAAAGAAGTGTCCACGCATTTT 57.615 36.364 0.00 0.00 36.20 1.82
292 329 5.746721 AGAAGTGTCCACGCATTTTAAAAAC 59.253 36.000 4.44 0.00 36.20 2.43
411 459 8.533569 TTCATACAGAAAAGGGAAAAAGAAGT 57.466 30.769 0.00 0.00 32.05 3.01
412 460 7.940850 TCATACAGAAAAGGGAAAAAGAAGTG 58.059 34.615 0.00 0.00 0.00 3.16
413 461 7.559897 TCATACAGAAAAGGGAAAAAGAAGTGT 59.440 33.333 0.00 0.00 0.00 3.55
414 462 6.605471 ACAGAAAAGGGAAAAAGAAGTGTT 57.395 33.333 0.00 0.00 0.00 3.32
415 463 6.631016 ACAGAAAAGGGAAAAAGAAGTGTTC 58.369 36.000 0.00 0.00 0.00 3.18
416 464 6.210584 ACAGAAAAGGGAAAAAGAAGTGTTCA 59.789 34.615 0.00 0.00 0.00 3.18
417 465 6.531594 CAGAAAAGGGAAAAAGAAGTGTTCAC 59.468 38.462 0.00 0.00 0.00 3.18
418 466 5.993748 AAAGGGAAAAAGAAGTGTTCACA 57.006 34.783 5.74 0.00 0.00 3.58
419 467 4.983671 AGGGAAAAAGAAGTGTTCACAC 57.016 40.909 1.53 1.53 46.77 3.82
710 770 5.674933 AAAGAGAGAGAAAACGCGAAAAT 57.325 34.783 15.93 0.00 0.00 1.82
711 771 6.780706 AAAGAGAGAGAAAACGCGAAAATA 57.219 33.333 15.93 0.00 0.00 1.40
753 852 3.006940 CGGATGGATCGGAAAGAAAACA 58.993 45.455 0.00 0.00 0.00 2.83
793 892 4.974591 GGGTGACGAAGAGATTTGAAATG 58.025 43.478 0.00 0.00 0.00 2.32
832 968 2.892425 GTCTGAATCCCGCGCCAG 60.892 66.667 0.00 1.68 0.00 4.85
878 1015 0.947244 GCCCATAAACAGCCTCGATG 59.053 55.000 0.00 0.00 0.00 3.84
906 1050 3.119673 CGTCCTCGATCCTTATCATCCTG 60.120 52.174 0.00 0.00 39.71 3.86
948 1116 2.431771 TCCCGACGCACACGAATG 60.432 61.111 0.00 0.00 43.93 2.67
960 1129 4.489771 CGAATGCCCGCCCCTCTT 62.490 66.667 0.00 0.00 0.00 2.85
978 1147 0.179116 TTGCTCTGATCTGCTCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
2273 2551 9.056005 TGTTTATGCATGGACTAAATAGATGTC 57.944 33.333 10.16 0.00 0.00 3.06
2355 2656 1.016130 CATCAGTTCGGAGCAACGCT 61.016 55.000 0.00 0.00 43.88 5.07
2370 2671 6.995511 AGCAACGCTCTTATAACCAATAAA 57.004 33.333 0.00 0.00 30.62 1.40
2371 2672 7.385778 AGCAACGCTCTTATAACCAATAAAA 57.614 32.000 0.00 0.00 30.62 1.52
2372 2673 7.822658 AGCAACGCTCTTATAACCAATAAAAA 58.177 30.769 0.00 0.00 30.62 1.94
2373 2674 7.753580 AGCAACGCTCTTATAACCAATAAAAAC 59.246 33.333 0.00 0.00 30.62 2.43
2374 2675 7.753580 GCAACGCTCTTATAACCAATAAAAACT 59.246 33.333 0.00 0.00 29.59 2.66
2375 2676 9.620660 CAACGCTCTTATAACCAATAAAAACTT 57.379 29.630 0.00 0.00 29.59 2.66
2437 2738 7.215719 AGGTCTGTTATTAGCAAAAACTTCC 57.784 36.000 0.00 0.00 0.00 3.46
2438 2739 7.004691 AGGTCTGTTATTAGCAAAAACTTCCT 58.995 34.615 0.00 0.00 0.00 3.36
2439 2740 8.161425 AGGTCTGTTATTAGCAAAAACTTCCTA 58.839 33.333 0.00 0.00 0.00 2.94
2440 2741 8.957466 GGTCTGTTATTAGCAAAAACTTCCTAT 58.043 33.333 0.00 0.00 0.00 2.57
2496 2797 8.945195 ATTGCATAGGAAGATAATGAAATGGA 57.055 30.769 0.00 0.00 29.46 3.41
2497 2798 8.765488 TTGCATAGGAAGATAATGAAATGGAA 57.235 30.769 0.00 0.00 0.00 3.53
2498 2799 8.765488 TGCATAGGAAGATAATGAAATGGAAA 57.235 30.769 0.00 0.00 0.00 3.13
2499 2800 9.370930 TGCATAGGAAGATAATGAAATGGAAAT 57.629 29.630 0.00 0.00 0.00 2.17
2513 2814 8.821686 TGAAATGGAAATTCATGTATGGTAGT 57.178 30.769 0.00 0.00 32.10 2.73
2514 2815 9.253832 TGAAATGGAAATTCATGTATGGTAGTT 57.746 29.630 0.00 0.00 32.10 2.24
2516 2817 9.874205 AAATGGAAATTCATGTATGGTAGTTTG 57.126 29.630 0.00 0.00 0.00 2.93
2517 2818 6.862209 TGGAAATTCATGTATGGTAGTTTGC 58.138 36.000 0.00 0.00 0.00 3.68
2518 2819 6.663093 TGGAAATTCATGTATGGTAGTTTGCT 59.337 34.615 0.00 0.00 0.00 3.91
2519 2820 7.831690 TGGAAATTCATGTATGGTAGTTTGCTA 59.168 33.333 0.00 0.00 0.00 3.49
2520 2821 8.682710 GGAAATTCATGTATGGTAGTTTGCTAA 58.317 33.333 0.00 0.00 0.00 3.09
2521 2822 9.722056 GAAATTCATGTATGGTAGTTTGCTAAG 57.278 33.333 0.00 0.00 0.00 2.18
2522 2823 9.461312 AAATTCATGTATGGTAGTTTGCTAAGA 57.539 29.630 0.00 0.00 0.00 2.10
2523 2824 8.668510 ATTCATGTATGGTAGTTTGCTAAGAG 57.331 34.615 0.00 0.00 0.00 2.85
2524 2825 6.582636 TCATGTATGGTAGTTTGCTAAGAGG 58.417 40.000 0.00 0.00 0.00 3.69
2525 2826 4.766375 TGTATGGTAGTTTGCTAAGAGGC 58.234 43.478 0.00 0.00 0.00 4.70
2526 2827 4.469945 TGTATGGTAGTTTGCTAAGAGGCT 59.530 41.667 0.00 0.00 0.00 4.58
2527 2828 3.334583 TGGTAGTTTGCTAAGAGGCTG 57.665 47.619 0.00 0.00 0.00 4.85
2528 2829 2.903784 TGGTAGTTTGCTAAGAGGCTGA 59.096 45.455 0.00 0.00 0.00 4.26
2529 2830 3.519510 TGGTAGTTTGCTAAGAGGCTGAT 59.480 43.478 0.00 0.00 0.00 2.90
2530 2831 4.019321 TGGTAGTTTGCTAAGAGGCTGATT 60.019 41.667 0.00 0.00 0.00 2.57
2531 2832 4.333926 GGTAGTTTGCTAAGAGGCTGATTG 59.666 45.833 0.00 0.00 0.00 2.67
2532 2833 4.292186 AGTTTGCTAAGAGGCTGATTGA 57.708 40.909 0.00 0.00 0.00 2.57
2533 2834 4.260170 AGTTTGCTAAGAGGCTGATTGAG 58.740 43.478 0.00 0.00 0.00 3.02
2534 2835 2.996249 TGCTAAGAGGCTGATTGAGG 57.004 50.000 0.00 0.00 0.00 3.86
2535 2836 2.470990 TGCTAAGAGGCTGATTGAGGA 58.529 47.619 0.00 0.00 0.00 3.71
2536 2837 3.044156 TGCTAAGAGGCTGATTGAGGAT 58.956 45.455 0.00 0.00 0.00 3.24
2537 2838 3.181457 TGCTAAGAGGCTGATTGAGGATG 60.181 47.826 0.00 0.00 0.00 3.51
2538 2839 3.806507 GCTAAGAGGCTGATTGAGGATGG 60.807 52.174 0.00 0.00 0.00 3.51
2539 2840 1.138568 AGAGGCTGATTGAGGATGGG 58.861 55.000 0.00 0.00 0.00 4.00
2540 2841 0.536915 GAGGCTGATTGAGGATGGGC 60.537 60.000 0.00 0.00 0.00 5.36
2541 2842 1.530183 GGCTGATTGAGGATGGGCC 60.530 63.158 0.00 0.00 0.00 5.80
2542 2843 1.228228 GCTGATTGAGGATGGGCCA 59.772 57.895 9.61 9.61 40.02 5.36
2543 2844 0.396139 GCTGATTGAGGATGGGCCAA 60.396 55.000 11.89 0.00 40.02 4.52
2544 2845 1.961435 GCTGATTGAGGATGGGCCAAA 60.961 52.381 11.89 0.00 40.02 3.28
2545 2846 2.029623 CTGATTGAGGATGGGCCAAAG 58.970 52.381 11.89 0.00 40.02 2.77
2546 2847 1.640149 TGATTGAGGATGGGCCAAAGA 59.360 47.619 11.89 0.00 40.02 2.52
2547 2848 2.042842 TGATTGAGGATGGGCCAAAGAA 59.957 45.455 11.89 0.00 40.02 2.52
2548 2849 1.923356 TTGAGGATGGGCCAAAGAAC 58.077 50.000 11.89 2.02 40.02 3.01
2549 2850 1.075601 TGAGGATGGGCCAAAGAACT 58.924 50.000 11.89 4.23 40.02 3.01
2550 2851 1.004745 TGAGGATGGGCCAAAGAACTC 59.995 52.381 11.89 14.08 40.02 3.01
2551 2852 1.004745 GAGGATGGGCCAAAGAACTCA 59.995 52.381 11.89 0.00 40.02 3.41
2552 2853 1.177401 GGATGGGCCAAAGAACTCAC 58.823 55.000 11.89 0.00 36.34 3.51
2553 2854 1.547675 GGATGGGCCAAAGAACTCACA 60.548 52.381 11.89 0.00 36.34 3.58
2554 2855 2.238521 GATGGGCCAAAGAACTCACAA 58.761 47.619 11.89 0.00 0.00 3.33
2555 2856 1.398692 TGGGCCAAAGAACTCACAAC 58.601 50.000 2.13 0.00 0.00 3.32
2556 2857 1.064017 TGGGCCAAAGAACTCACAACT 60.064 47.619 2.13 0.00 0.00 3.16
2557 2858 2.173782 TGGGCCAAAGAACTCACAACTA 59.826 45.455 2.13 0.00 0.00 2.24
2558 2859 3.181434 TGGGCCAAAGAACTCACAACTAT 60.181 43.478 2.13 0.00 0.00 2.12
2559 2860 3.826729 GGGCCAAAGAACTCACAACTATT 59.173 43.478 4.39 0.00 0.00 1.73
2560 2861 4.280929 GGGCCAAAGAACTCACAACTATTT 59.719 41.667 4.39 0.00 0.00 1.40
2561 2862 5.461526 GGCCAAAGAACTCACAACTATTTC 58.538 41.667 0.00 0.00 0.00 2.17
2562 2863 5.009610 GGCCAAAGAACTCACAACTATTTCA 59.990 40.000 0.00 0.00 0.00 2.69
2563 2864 5.915196 GCCAAAGAACTCACAACTATTTCAC 59.085 40.000 0.00 0.00 0.00 3.18
2564 2865 6.136071 CCAAAGAACTCACAACTATTTCACG 58.864 40.000 0.00 0.00 0.00 4.35
2565 2866 6.018262 CCAAAGAACTCACAACTATTTCACGA 60.018 38.462 0.00 0.00 0.00 4.35
2566 2867 7.307989 CCAAAGAACTCACAACTATTTCACGAT 60.308 37.037 0.00 0.00 0.00 3.73
2567 2868 6.952935 AGAACTCACAACTATTTCACGATC 57.047 37.500 0.00 0.00 0.00 3.69
2568 2869 5.573282 AGAACTCACAACTATTTCACGATCG 59.427 40.000 14.88 14.88 0.00 3.69
2569 2870 4.806330 ACTCACAACTATTTCACGATCGT 58.194 39.130 16.60 16.60 0.00 3.73
2570 2871 4.621460 ACTCACAACTATTTCACGATCGTG 59.379 41.667 36.47 36.47 46.64 4.35
2588 2889 8.963725 ACGATCGTGATATTATAAATAGGTCCA 58.036 33.333 22.06 0.00 0.00 4.02
2589 2890 9.452065 CGATCGTGATATTATAAATAGGTCCAG 57.548 37.037 7.03 0.00 0.00 3.86
2627 2928 9.920946 AGATAGGTGGCAGAATAAAATTAGAAA 57.079 29.630 0.00 0.00 0.00 2.52
2629 2930 9.920946 ATAGGTGGCAGAATAAAATTAGAAAGA 57.079 29.630 0.00 0.00 0.00 2.52
2630 2931 8.286191 AGGTGGCAGAATAAAATTAGAAAGAG 57.714 34.615 0.00 0.00 0.00 2.85
2631 2932 8.109634 AGGTGGCAGAATAAAATTAGAAAGAGA 58.890 33.333 0.00 0.00 0.00 3.10
2632 2933 8.907885 GGTGGCAGAATAAAATTAGAAAGAGAT 58.092 33.333 0.00 0.00 0.00 2.75
2645 2946 7.630242 TTAGAAAGAGATACAATGCCAAAGG 57.370 36.000 0.00 0.00 0.00 3.11
2646 2947 5.574188 AGAAAGAGATACAATGCCAAAGGT 58.426 37.500 0.00 0.00 0.00 3.50
2647 2948 6.721318 AGAAAGAGATACAATGCCAAAGGTA 58.279 36.000 0.00 0.00 0.00 3.08
2648 2949 7.349598 AGAAAGAGATACAATGCCAAAGGTAT 58.650 34.615 0.00 0.00 0.00 2.73
2649 2950 6.949352 AAGAGATACAATGCCAAAGGTATG 57.051 37.500 0.00 0.00 0.00 2.39
2650 2951 6.006275 AGAGATACAATGCCAAAGGTATGT 57.994 37.500 0.00 0.00 0.00 2.29
2651 2952 6.058183 AGAGATACAATGCCAAAGGTATGTC 58.942 40.000 0.00 0.00 37.00 3.06
2652 2953 5.754782 AGATACAATGCCAAAGGTATGTCA 58.245 37.500 0.00 0.00 0.00 3.58
2653 2954 5.590259 AGATACAATGCCAAAGGTATGTCAC 59.410 40.000 0.00 0.00 0.00 3.67
2690 2991 8.635765 AAAAACTCTATAACCATGTGACACAT 57.364 30.769 15.48 15.48 39.91 3.21
2700 3001 3.986996 ATGTGACACATGATCACCTGA 57.013 42.857 20.21 11.67 44.91 3.86
2701 3002 3.767902 TGTGACACATGATCACCTGAA 57.232 42.857 23.20 9.26 44.91 3.02
2702 3003 3.667360 TGTGACACATGATCACCTGAAG 58.333 45.455 23.20 0.00 44.91 3.02
2703 3004 3.324556 TGTGACACATGATCACCTGAAGA 59.675 43.478 23.20 8.47 44.91 2.87
2704 3005 3.931468 GTGACACATGATCACCTGAAGAG 59.069 47.826 18.42 0.00 40.56 2.85
2705 3006 2.935201 GACACATGATCACCTGAAGAGC 59.065 50.000 0.00 0.00 0.00 4.09
2706 3007 2.286872 CACATGATCACCTGAAGAGCC 58.713 52.381 0.00 0.00 0.00 4.70
2707 3008 1.134580 ACATGATCACCTGAAGAGCCG 60.135 52.381 0.00 0.00 0.00 5.52
2708 3009 1.137675 CATGATCACCTGAAGAGCCGA 59.862 52.381 0.00 0.00 0.00 5.54
2709 3010 1.266178 TGATCACCTGAAGAGCCGAA 58.734 50.000 0.00 0.00 0.00 4.30
2710 3011 1.623311 TGATCACCTGAAGAGCCGAAA 59.377 47.619 0.00 0.00 0.00 3.46
2711 3012 2.237143 TGATCACCTGAAGAGCCGAAAT 59.763 45.455 0.00 0.00 0.00 2.17
2712 3013 2.859165 TCACCTGAAGAGCCGAAATT 57.141 45.000 0.00 0.00 0.00 1.82
2713 3014 2.426522 TCACCTGAAGAGCCGAAATTG 58.573 47.619 0.00 0.00 0.00 2.32
2714 3015 2.038426 TCACCTGAAGAGCCGAAATTGA 59.962 45.455 0.00 0.00 0.00 2.57
2715 3016 2.160417 CACCTGAAGAGCCGAAATTGAC 59.840 50.000 0.00 0.00 0.00 3.18
2716 3017 2.224523 ACCTGAAGAGCCGAAATTGACA 60.225 45.455 0.00 0.00 0.00 3.58
2717 3018 2.160417 CCTGAAGAGCCGAAATTGACAC 59.840 50.000 0.00 0.00 0.00 3.67
2718 3019 2.807967 CTGAAGAGCCGAAATTGACACA 59.192 45.455 0.00 0.00 0.00 3.72
2719 3020 2.548057 TGAAGAGCCGAAATTGACACAC 59.452 45.455 0.00 0.00 0.00 3.82
2720 3021 2.254546 AGAGCCGAAATTGACACACA 57.745 45.000 0.00 0.00 0.00 3.72
2721 3022 2.783135 AGAGCCGAAATTGACACACAT 58.217 42.857 0.00 0.00 0.00 3.21
2722 3023 3.937814 AGAGCCGAAATTGACACACATA 58.062 40.909 0.00 0.00 0.00 2.29
2723 3024 3.684788 AGAGCCGAAATTGACACACATAC 59.315 43.478 0.00 0.00 0.00 2.39
2724 3025 3.407698 AGCCGAAATTGACACACATACA 58.592 40.909 0.00 0.00 0.00 2.29
2725 3026 4.009675 AGCCGAAATTGACACACATACAT 58.990 39.130 0.00 0.00 0.00 2.29
2726 3027 4.094887 AGCCGAAATTGACACACATACATC 59.905 41.667 0.00 0.00 0.00 3.06
2727 3028 4.094887 GCCGAAATTGACACACATACATCT 59.905 41.667 0.00 0.00 0.00 2.90
2728 3029 5.293324 GCCGAAATTGACACACATACATCTA 59.707 40.000 0.00 0.00 0.00 1.98
2729 3030 6.510157 GCCGAAATTGACACACATACATCTAG 60.510 42.308 0.00 0.00 0.00 2.43
2730 3031 6.535150 CCGAAATTGACACACATACATCTAGT 59.465 38.462 0.00 0.00 0.00 2.57
2731 3032 7.064609 CCGAAATTGACACACATACATCTAGTT 59.935 37.037 0.00 0.00 0.00 2.24
2732 3033 9.083080 CGAAATTGACACACATACATCTAGTTA 57.917 33.333 0.00 0.00 0.00 2.24
2736 3037 9.982651 ATTGACACACATACATCTAGTTATACC 57.017 33.333 0.00 0.00 0.00 2.73
2737 3038 8.762481 TGACACACATACATCTAGTTATACCT 57.238 34.615 0.00 0.00 0.00 3.08
2738 3039 9.197306 TGACACACATACATCTAGTTATACCTT 57.803 33.333 0.00 0.00 0.00 3.50
2748 3049 9.745880 ACATCTAGTTATACCTTAATCGTGTTG 57.254 33.333 0.00 0.00 0.00 3.33
2749 3050 9.961265 CATCTAGTTATACCTTAATCGTGTTGA 57.039 33.333 0.00 0.00 0.00 3.18
2767 3068 9.263538 TCGTGTTGAATGTAAGTATACTTTTGT 57.736 29.630 22.66 6.92 37.40 2.83
2790 3091 8.956446 TGTAGAGATATGGAAATACCTCATGA 57.044 34.615 0.00 0.00 39.86 3.07
2791 3092 9.379770 TGTAGAGATATGGAAATACCTCATGAA 57.620 33.333 0.00 0.00 39.86 2.57
2800 3101 9.699410 ATGGAAATACCTCATGAAAATACTGAA 57.301 29.630 0.00 0.00 39.86 3.02
2801 3102 9.699410 TGGAAATACCTCATGAAAATACTGAAT 57.301 29.630 0.00 0.00 39.86 2.57
2802 3103 9.956720 GGAAATACCTCATGAAAATACTGAATG 57.043 33.333 0.00 0.00 35.41 2.67
2805 3106 8.682936 ATACCTCATGAAAATACTGAATGACC 57.317 34.615 0.00 0.00 0.00 4.02
2806 3107 6.484288 ACCTCATGAAAATACTGAATGACCA 58.516 36.000 0.00 0.00 0.00 4.02
2807 3108 6.375455 ACCTCATGAAAATACTGAATGACCAC 59.625 38.462 0.00 0.00 0.00 4.16
2808 3109 6.375174 CCTCATGAAAATACTGAATGACCACA 59.625 38.462 0.00 0.00 0.00 4.17
2809 3110 7.067859 CCTCATGAAAATACTGAATGACCACAT 59.932 37.037 0.00 0.00 38.50 3.21
2810 3111 9.112725 CTCATGAAAATACTGAATGACCACATA 57.887 33.333 0.00 0.00 35.50 2.29
2811 3112 9.460019 TCATGAAAATACTGAATGACCACATAA 57.540 29.630 0.00 0.00 35.50 1.90
2861 3162 9.738832 AAAATACGCAAAACACAAATAGTAAGT 57.261 25.926 0.00 0.00 0.00 2.24
2862 3163 9.738832 AAATACGCAAAACACAAATAGTAAGTT 57.261 25.926 0.00 0.00 0.00 2.66
2863 3164 8.944212 ATACGCAAAACACAAATAGTAAGTTC 57.056 30.769 0.00 0.00 0.00 3.01
2864 3165 7.023197 ACGCAAAACACAAATAGTAAGTTCT 57.977 32.000 0.00 0.00 0.00 3.01
2865 3166 7.130269 ACGCAAAACACAAATAGTAAGTTCTC 58.870 34.615 0.00 0.00 0.00 2.87
2866 3167 7.012044 ACGCAAAACACAAATAGTAAGTTCTCT 59.988 33.333 0.00 0.00 0.00 3.10
2867 3168 7.855904 CGCAAAACACAAATAGTAAGTTCTCTT 59.144 33.333 0.00 0.00 37.65 2.85
2868 3169 8.958043 GCAAAACACAAATAGTAAGTTCTCTTG 58.042 33.333 0.00 0.00 35.36 3.02
2869 3170 8.958043 CAAAACACAAATAGTAAGTTCTCTTGC 58.042 33.333 0.00 0.00 36.72 4.01
2870 3171 8.451908 AAACACAAATAGTAAGTTCTCTTGCT 57.548 30.769 4.32 4.32 45.67 3.91
2871 3172 9.555727 AAACACAAATAGTAAGTTCTCTTGCTA 57.444 29.630 7.87 7.87 46.78 3.49
2881 3182 9.415008 AGTAAGTTCTCTTGCTATATGAGAAGA 57.585 33.333 5.09 0.00 45.07 2.87
2886 3187 9.123709 GTTCTCTTGCTATATGAGAAGATAACG 57.876 37.037 5.09 0.00 45.07 3.18
2887 3188 7.309177 TCTCTTGCTATATGAGAAGATAACGC 58.691 38.462 0.00 0.00 36.84 4.84
2888 3189 7.175816 TCTCTTGCTATATGAGAAGATAACGCT 59.824 37.037 0.00 0.00 36.84 5.07
2889 3190 7.661968 TCTTGCTATATGAGAAGATAACGCTT 58.338 34.615 0.00 0.00 0.00 4.68
2890 3191 8.144478 TCTTGCTATATGAGAAGATAACGCTTT 58.856 33.333 0.00 0.00 0.00 3.51
2891 3192 7.875316 TGCTATATGAGAAGATAACGCTTTC 57.125 36.000 0.00 0.00 0.00 2.62
2892 3193 7.661968 TGCTATATGAGAAGATAACGCTTTCT 58.338 34.615 0.00 0.00 0.00 2.52
2893 3194 8.793592 TGCTATATGAGAAGATAACGCTTTCTA 58.206 33.333 0.00 0.00 0.00 2.10
2894 3195 9.284594 GCTATATGAGAAGATAACGCTTTCTAG 57.715 37.037 0.00 0.00 0.00 2.43
2895 3196 9.781834 CTATATGAGAAGATAACGCTTTCTAGG 57.218 37.037 0.00 0.00 0.00 3.02
2896 3197 5.916661 TGAGAAGATAACGCTTTCTAGGT 57.083 39.130 0.00 0.00 0.00 3.08
2897 3198 7.584122 ATGAGAAGATAACGCTTTCTAGGTA 57.416 36.000 0.00 0.00 0.00 3.08
2898 3199 7.400599 TGAGAAGATAACGCTTTCTAGGTAA 57.599 36.000 0.00 0.00 0.00 2.85
2899 3200 7.256286 TGAGAAGATAACGCTTTCTAGGTAAC 58.744 38.462 0.00 0.00 0.00 2.50
2900 3201 6.571605 AGAAGATAACGCTTTCTAGGTAACC 58.428 40.000 0.00 0.00 37.17 2.85
2901 3202 5.927281 AGATAACGCTTTCTAGGTAACCA 57.073 39.130 0.00 0.00 37.17 3.67
2902 3203 5.903810 AGATAACGCTTTCTAGGTAACCAG 58.096 41.667 0.00 0.00 37.17 4.00
2903 3204 5.655532 AGATAACGCTTTCTAGGTAACCAGA 59.344 40.000 0.00 0.00 37.17 3.86
2904 3205 3.870633 ACGCTTTCTAGGTAACCAGAG 57.129 47.619 0.00 0.00 37.17 3.35
2905 3206 2.094130 ACGCTTTCTAGGTAACCAGAGC 60.094 50.000 0.00 0.00 37.17 4.09
2906 3207 2.738964 CGCTTTCTAGGTAACCAGAGCC 60.739 54.545 0.00 0.00 37.17 4.70
2907 3208 2.236395 GCTTTCTAGGTAACCAGAGCCA 59.764 50.000 0.00 0.00 37.17 4.75
2908 3209 3.680196 GCTTTCTAGGTAACCAGAGCCAG 60.680 52.174 0.00 0.00 37.17 4.85
2909 3210 3.468071 TTCTAGGTAACCAGAGCCAGA 57.532 47.619 0.00 0.00 37.17 3.86
2910 3211 3.019799 TCTAGGTAACCAGAGCCAGAG 57.980 52.381 0.00 0.00 37.17 3.35
2911 3212 2.035632 CTAGGTAACCAGAGCCAGAGG 58.964 57.143 0.00 0.00 37.17 3.69
2912 3213 0.117340 AGGTAACCAGAGCCAGAGGT 59.883 55.000 0.00 0.00 37.20 3.85
2913 3214 1.361543 AGGTAACCAGAGCCAGAGGTA 59.638 52.381 0.00 0.00 34.63 3.08
2914 3215 2.185387 GGTAACCAGAGCCAGAGGTAA 58.815 52.381 0.00 0.00 34.63 2.85
2915 3216 2.570302 GGTAACCAGAGCCAGAGGTAAA 59.430 50.000 0.00 0.00 34.63 2.01
2916 3217 3.369576 GGTAACCAGAGCCAGAGGTAAAG 60.370 52.174 0.00 0.00 34.63 1.85
2917 3218 0.615850 ACCAGAGCCAGAGGTAAAGC 59.384 55.000 0.00 0.00 32.92 3.51
2918 3219 0.908198 CCAGAGCCAGAGGTAAAGCT 59.092 55.000 0.00 0.00 38.56 3.74
2919 3220 2.111384 CCAGAGCCAGAGGTAAAGCTA 58.889 52.381 0.00 0.00 35.23 3.32
2920 3221 2.501723 CCAGAGCCAGAGGTAAAGCTAA 59.498 50.000 0.00 0.00 35.23 3.09
2921 3222 3.135530 CCAGAGCCAGAGGTAAAGCTAAT 59.864 47.826 0.00 0.00 35.23 1.73
2922 3223 4.384647 CCAGAGCCAGAGGTAAAGCTAATT 60.385 45.833 0.00 0.00 35.23 1.40
2923 3224 4.574013 CAGAGCCAGAGGTAAAGCTAATTG 59.426 45.833 0.00 0.00 35.23 2.32
2924 3225 3.282885 AGCCAGAGGTAAAGCTAATTGC 58.717 45.455 0.00 0.00 43.29 3.56
2925 3226 3.016736 GCCAGAGGTAAAGCTAATTGCA 58.983 45.455 0.00 0.00 45.94 4.08
2926 3227 3.633986 GCCAGAGGTAAAGCTAATTGCAT 59.366 43.478 0.00 0.00 45.94 3.96
2927 3228 4.261363 GCCAGAGGTAAAGCTAATTGCATC 60.261 45.833 0.00 0.00 45.94 3.91
2928 3229 5.128919 CCAGAGGTAAAGCTAATTGCATCT 58.871 41.667 0.00 0.00 45.94 2.90
2929 3230 5.591877 CCAGAGGTAAAGCTAATTGCATCTT 59.408 40.000 1.34 0.00 45.94 2.40
2930 3231 6.096001 CCAGAGGTAAAGCTAATTGCATCTTT 59.904 38.462 1.34 0.00 45.94 2.52
2931 3232 7.363268 CCAGAGGTAAAGCTAATTGCATCTTTT 60.363 37.037 1.34 0.00 45.94 2.27
2932 3233 8.677300 CAGAGGTAAAGCTAATTGCATCTTTTA 58.323 33.333 1.34 0.00 45.94 1.52
2933 3234 8.897752 AGAGGTAAAGCTAATTGCATCTTTTAG 58.102 33.333 0.00 0.00 45.94 1.85
2934 3235 8.807948 AGGTAAAGCTAATTGCATCTTTTAGA 57.192 30.769 9.24 0.00 45.94 2.10
2935 3236 9.243105 AGGTAAAGCTAATTGCATCTTTTAGAA 57.757 29.630 9.24 0.00 45.94 2.10
2947 3248 7.923888 TGCATCTTTTAGAATCATAACTCAGC 58.076 34.615 0.00 0.00 0.00 4.26
2948 3249 7.553760 TGCATCTTTTAGAATCATAACTCAGCA 59.446 33.333 0.00 0.00 0.00 4.41
2949 3250 8.566260 GCATCTTTTAGAATCATAACTCAGCAT 58.434 33.333 0.00 0.00 0.00 3.79
2951 3252 9.842775 ATCTTTTAGAATCATAACTCAGCATCA 57.157 29.630 0.00 0.00 0.00 3.07
2952 3253 9.671279 TCTTTTAGAATCATAACTCAGCATCAA 57.329 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 150 9.622366 CATTTTTAACATGCGCTAATACATTTG 57.378 29.630 9.73 0.00 0.00 2.32
149 151 9.364989 ACATTTTTAACATGCGCTAATACATTT 57.635 25.926 9.73 0.00 0.00 2.32
155 157 6.033407 CGTTCACATTTTTAACATGCGCTAAT 59.967 34.615 9.73 0.00 0.00 1.73
159 161 3.423867 ACGTTCACATTTTTAACATGCGC 59.576 39.130 0.00 0.00 0.00 6.09
162 164 5.230936 TGCACACGTTCACATTTTTAACATG 59.769 36.000 0.00 0.00 0.00 3.21
163 165 5.344066 TGCACACGTTCACATTTTTAACAT 58.656 33.333 0.00 0.00 0.00 2.71
176 178 7.332003 TGAATATTTTTGAATGCACACGTTC 57.668 32.000 0.00 0.00 41.42 3.95
177 179 7.598118 TGATGAATATTTTTGAATGCACACGTT 59.402 29.630 0.00 0.00 0.00 3.99
392 440 6.531594 GTGAACACTTCTTTTTCCCTTTTCTG 59.468 38.462 0.00 0.00 0.00 3.02
474 522 9.440784 GTGAACACTTCGTAAAAATTACATGAA 57.559 29.630 0.00 0.00 0.00 2.57
475 523 8.613482 TGTGAACACTTCGTAAAAATTACATGA 58.387 29.630 0.00 0.00 0.00 3.07
476 524 8.678510 GTGTGAACACTTCGTAAAAATTACATG 58.321 33.333 6.33 0.00 43.25 3.21
477 525 8.399425 TGTGTGAACACTTCGTAAAAATTACAT 58.601 29.630 14.28 0.00 46.55 2.29
478 526 7.749808 TGTGTGAACACTTCGTAAAAATTACA 58.250 30.769 14.28 0.00 46.55 2.41
479 527 8.776680 ATGTGTGAACACTTCGTAAAAATTAC 57.223 30.769 14.28 0.00 46.55 1.89
480 528 9.790389 AAATGTGTGAACACTTCGTAAAAATTA 57.210 25.926 14.28 0.00 46.55 1.40
481 529 8.696410 AAATGTGTGAACACTTCGTAAAAATT 57.304 26.923 14.28 0.70 46.55 1.82
482 530 9.790389 TTAAATGTGTGAACACTTCGTAAAAAT 57.210 25.926 14.28 0.00 46.55 1.82
483 531 9.622004 TTTAAATGTGTGAACACTTCGTAAAAA 57.378 25.926 14.28 4.29 46.55 1.94
484 532 9.622004 TTTTAAATGTGTGAACACTTCGTAAAA 57.378 25.926 14.28 15.87 46.55 1.52
485 533 9.622004 TTTTTAAATGTGTGAACACTTCGTAAA 57.378 25.926 14.28 12.13 46.55 2.01
690 748 6.969828 ATTATTTTCGCGTTTTCTCTCTCT 57.030 33.333 5.77 0.00 0.00 3.10
710 770 6.711194 TCCGGCCGTTCATCATTTATTTATTA 59.289 34.615 26.12 0.00 0.00 0.98
711 771 5.533154 TCCGGCCGTTCATCATTTATTTATT 59.467 36.000 26.12 0.00 0.00 1.40
753 852 2.019951 CGCAAGCCAACTCGTACGT 61.020 57.895 16.05 0.00 0.00 3.57
832 968 3.470567 CAGCACGCGTCTCCGAAC 61.471 66.667 9.86 0.00 35.63 3.95
906 1050 2.560981 GAGGAAGGAAGGATCGAGGATC 59.439 54.545 0.00 0.00 38.25 3.36
1651 1820 1.210931 CAAGCGCCCACATGTCAAG 59.789 57.895 2.29 0.00 0.00 3.02
2251 2529 8.432013 ACTTGACATCTATTTAGTCCATGCATA 58.568 33.333 0.00 0.00 0.00 3.14
2273 2551 6.695245 CATTTGTTTTTCTTCGTTGGACTTG 58.305 36.000 0.00 0.00 0.00 3.16
2411 2712 8.789762 GGAAGTTTTTGCTAATAACAGACCTAA 58.210 33.333 7.97 0.00 0.00 2.69
2412 2713 8.161425 AGGAAGTTTTTGCTAATAACAGACCTA 58.839 33.333 0.00 0.00 32.70 3.08
2413 2714 7.004691 AGGAAGTTTTTGCTAATAACAGACCT 58.995 34.615 0.00 0.00 32.70 3.85
2414 2715 7.215719 AGGAAGTTTTTGCTAATAACAGACC 57.784 36.000 7.97 0.00 32.70 3.85
2471 2772 8.945195 TCCATTTCATTATCTTCCTATGCAAT 57.055 30.769 0.00 0.00 0.00 3.56
2472 2773 8.765488 TTCCATTTCATTATCTTCCTATGCAA 57.235 30.769 0.00 0.00 0.00 4.08
2473 2774 8.765488 TTTCCATTTCATTATCTTCCTATGCA 57.235 30.769 0.00 0.00 0.00 3.96
2487 2788 9.425248 ACTACCATACATGAATTTCCATTTCAT 57.575 29.630 0.00 0.00 42.95 2.57
2488 2789 8.821686 ACTACCATACATGAATTTCCATTTCA 57.178 30.769 0.00 0.00 37.49 2.69
2490 2791 9.874205 CAAACTACCATACATGAATTTCCATTT 57.126 29.630 0.00 0.00 0.00 2.32
2491 2792 7.981225 GCAAACTACCATACATGAATTTCCATT 59.019 33.333 0.00 0.00 0.00 3.16
2492 2793 7.342799 AGCAAACTACCATACATGAATTTCCAT 59.657 33.333 0.00 0.00 0.00 3.41
2493 2794 6.663093 AGCAAACTACCATACATGAATTTCCA 59.337 34.615 0.00 0.00 0.00 3.53
2494 2795 7.100458 AGCAAACTACCATACATGAATTTCC 57.900 36.000 0.00 0.00 0.00 3.13
2495 2796 9.722056 CTTAGCAAACTACCATACATGAATTTC 57.278 33.333 0.00 0.00 0.00 2.17
2496 2797 9.461312 TCTTAGCAAACTACCATACATGAATTT 57.539 29.630 0.00 0.00 0.00 1.82
2497 2798 9.113838 CTCTTAGCAAACTACCATACATGAATT 57.886 33.333 0.00 0.00 0.00 2.17
2498 2799 7.716998 CCTCTTAGCAAACTACCATACATGAAT 59.283 37.037 0.00 0.00 0.00 2.57
2499 2800 7.047891 CCTCTTAGCAAACTACCATACATGAA 58.952 38.462 0.00 0.00 0.00 2.57
2500 2801 6.582636 CCTCTTAGCAAACTACCATACATGA 58.417 40.000 0.00 0.00 0.00 3.07
2501 2802 5.237344 GCCTCTTAGCAAACTACCATACATG 59.763 44.000 0.00 0.00 0.00 3.21
2502 2803 5.131142 AGCCTCTTAGCAAACTACCATACAT 59.869 40.000 0.00 0.00 34.23 2.29
2503 2804 4.469945 AGCCTCTTAGCAAACTACCATACA 59.530 41.667 0.00 0.00 34.23 2.29
2504 2805 4.811557 CAGCCTCTTAGCAAACTACCATAC 59.188 45.833 0.00 0.00 34.23 2.39
2505 2806 4.714802 TCAGCCTCTTAGCAAACTACCATA 59.285 41.667 0.00 0.00 34.23 2.74
2506 2807 3.519510 TCAGCCTCTTAGCAAACTACCAT 59.480 43.478 0.00 0.00 34.23 3.55
2507 2808 2.903784 TCAGCCTCTTAGCAAACTACCA 59.096 45.455 0.00 0.00 34.23 3.25
2508 2809 3.611766 TCAGCCTCTTAGCAAACTACC 57.388 47.619 0.00 0.00 34.23 3.18
2509 2810 5.178797 TCAATCAGCCTCTTAGCAAACTAC 58.821 41.667 0.00 0.00 34.23 2.73
2510 2811 5.420725 TCAATCAGCCTCTTAGCAAACTA 57.579 39.130 0.00 0.00 34.23 2.24
2511 2812 4.260170 CTCAATCAGCCTCTTAGCAAACT 58.740 43.478 0.00 0.00 34.23 2.66
2512 2813 3.376546 CCTCAATCAGCCTCTTAGCAAAC 59.623 47.826 0.00 0.00 34.23 2.93
2513 2814 3.264193 TCCTCAATCAGCCTCTTAGCAAA 59.736 43.478 0.00 0.00 34.23 3.68
2514 2815 2.840038 TCCTCAATCAGCCTCTTAGCAA 59.160 45.455 0.00 0.00 34.23 3.91
2515 2816 2.470990 TCCTCAATCAGCCTCTTAGCA 58.529 47.619 0.00 0.00 34.23 3.49
2516 2817 3.401182 CATCCTCAATCAGCCTCTTAGC 58.599 50.000 0.00 0.00 0.00 3.09
2517 2818 3.244491 CCCATCCTCAATCAGCCTCTTAG 60.244 52.174 0.00 0.00 0.00 2.18
2518 2819 2.707791 CCCATCCTCAATCAGCCTCTTA 59.292 50.000 0.00 0.00 0.00 2.10
2519 2820 1.493871 CCCATCCTCAATCAGCCTCTT 59.506 52.381 0.00 0.00 0.00 2.85
2520 2821 1.138568 CCCATCCTCAATCAGCCTCT 58.861 55.000 0.00 0.00 0.00 3.69
2521 2822 0.536915 GCCCATCCTCAATCAGCCTC 60.537 60.000 0.00 0.00 0.00 4.70
2522 2823 1.535685 GCCCATCCTCAATCAGCCT 59.464 57.895 0.00 0.00 0.00 4.58
2523 2824 1.530183 GGCCCATCCTCAATCAGCC 60.530 63.158 0.00 0.00 0.00 4.85
2524 2825 0.396139 TTGGCCCATCCTCAATCAGC 60.396 55.000 0.00 0.00 35.26 4.26
2525 2826 2.029623 CTTTGGCCCATCCTCAATCAG 58.970 52.381 0.00 0.00 35.26 2.90
2526 2827 1.640149 TCTTTGGCCCATCCTCAATCA 59.360 47.619 0.00 0.00 35.26 2.57
2527 2828 2.428530 GTTCTTTGGCCCATCCTCAATC 59.571 50.000 0.00 0.00 35.26 2.67
2528 2829 2.043526 AGTTCTTTGGCCCATCCTCAAT 59.956 45.455 0.00 0.00 35.26 2.57
2529 2830 1.428912 AGTTCTTTGGCCCATCCTCAA 59.571 47.619 0.00 0.00 35.26 3.02
2530 2831 1.004745 GAGTTCTTTGGCCCATCCTCA 59.995 52.381 0.00 0.00 35.26 3.86
2531 2832 1.004745 TGAGTTCTTTGGCCCATCCTC 59.995 52.381 0.00 0.00 35.26 3.71
2532 2833 1.075601 TGAGTTCTTTGGCCCATCCT 58.924 50.000 0.00 0.00 35.26 3.24
2533 2834 1.177401 GTGAGTTCTTTGGCCCATCC 58.823 55.000 0.00 0.00 0.00 3.51
2534 2835 1.909700 TGTGAGTTCTTTGGCCCATC 58.090 50.000 0.00 0.00 0.00 3.51
2535 2836 1.963515 GTTGTGAGTTCTTTGGCCCAT 59.036 47.619 0.00 0.00 0.00 4.00
2536 2837 1.064017 AGTTGTGAGTTCTTTGGCCCA 60.064 47.619 0.00 0.00 0.00 5.36
2537 2838 1.692411 AGTTGTGAGTTCTTTGGCCC 58.308 50.000 0.00 0.00 0.00 5.80
2538 2839 5.009610 TGAAATAGTTGTGAGTTCTTTGGCC 59.990 40.000 0.00 0.00 0.00 5.36
2539 2840 5.915196 GTGAAATAGTTGTGAGTTCTTTGGC 59.085 40.000 0.00 0.00 0.00 4.52
2540 2841 6.018262 TCGTGAAATAGTTGTGAGTTCTTTGG 60.018 38.462 0.00 0.00 0.00 3.28
2541 2842 6.943981 TCGTGAAATAGTTGTGAGTTCTTTG 58.056 36.000 0.00 0.00 0.00 2.77
2542 2843 7.359264 CGATCGTGAAATAGTTGTGAGTTCTTT 60.359 37.037 7.03 0.00 0.00 2.52
2543 2844 6.089551 CGATCGTGAAATAGTTGTGAGTTCTT 59.910 38.462 7.03 0.00 0.00 2.52
2544 2845 5.573282 CGATCGTGAAATAGTTGTGAGTTCT 59.427 40.000 7.03 0.00 0.00 3.01
2545 2846 5.345202 ACGATCGTGAAATAGTTGTGAGTTC 59.655 40.000 22.06 0.00 0.00 3.01
2546 2847 5.227908 ACGATCGTGAAATAGTTGTGAGTT 58.772 37.500 22.06 0.00 0.00 3.01
2547 2848 4.806330 ACGATCGTGAAATAGTTGTGAGT 58.194 39.130 22.06 0.00 0.00 3.41
2561 2862 9.234384 GGACCTATTTATAATATCACGATCGTG 57.766 37.037 36.47 36.47 46.64 4.35
2562 2863 8.963725 TGGACCTATTTATAATATCACGATCGT 58.036 33.333 16.60 16.60 0.00 3.73
2563 2864 9.452065 CTGGACCTATTTATAATATCACGATCG 57.548 37.037 14.88 14.88 0.00 3.69
2601 2902 9.920946 TTTCTAATTTTATTCTGCCACCTATCT 57.079 29.630 0.00 0.00 0.00 1.98
2603 2904 9.920946 TCTTTCTAATTTTATTCTGCCACCTAT 57.079 29.630 0.00 0.00 0.00 2.57
2604 2905 9.396022 CTCTTTCTAATTTTATTCTGCCACCTA 57.604 33.333 0.00 0.00 0.00 3.08
2605 2906 8.109634 TCTCTTTCTAATTTTATTCTGCCACCT 58.890 33.333 0.00 0.00 0.00 4.00
2606 2907 8.281212 TCTCTTTCTAATTTTATTCTGCCACC 57.719 34.615 0.00 0.00 0.00 4.61
2619 2920 8.689972 CCTTTGGCATTGTATCTCTTTCTAATT 58.310 33.333 0.00 0.00 0.00 1.40
2620 2921 7.836183 ACCTTTGGCATTGTATCTCTTTCTAAT 59.164 33.333 0.00 0.00 0.00 1.73
2621 2922 7.175104 ACCTTTGGCATTGTATCTCTTTCTAA 58.825 34.615 0.00 0.00 0.00 2.10
2622 2923 6.721318 ACCTTTGGCATTGTATCTCTTTCTA 58.279 36.000 0.00 0.00 0.00 2.10
2623 2924 5.574188 ACCTTTGGCATTGTATCTCTTTCT 58.426 37.500 0.00 0.00 0.00 2.52
2624 2925 5.904362 ACCTTTGGCATTGTATCTCTTTC 57.096 39.130 0.00 0.00 0.00 2.62
2625 2926 6.891908 ACATACCTTTGGCATTGTATCTCTTT 59.108 34.615 0.00 0.00 0.00 2.52
2626 2927 6.426587 ACATACCTTTGGCATTGTATCTCTT 58.573 36.000 0.00 0.00 0.00 2.85
2627 2928 6.006275 ACATACCTTTGGCATTGTATCTCT 57.994 37.500 0.00 0.00 0.00 3.10
2628 2929 5.822519 TGACATACCTTTGGCATTGTATCTC 59.177 40.000 0.00 0.00 26.74 2.75
2629 2930 5.590259 GTGACATACCTTTGGCATTGTATCT 59.410 40.000 0.00 0.00 36.90 1.98
2630 2931 5.221048 GGTGACATACCTTTGGCATTGTATC 60.221 44.000 0.00 0.00 46.51 2.24
2631 2932 4.644685 GGTGACATACCTTTGGCATTGTAT 59.355 41.667 0.00 0.00 46.51 2.29
2632 2933 4.013728 GGTGACATACCTTTGGCATTGTA 58.986 43.478 0.00 0.00 46.51 2.41
2633 2934 2.825532 GGTGACATACCTTTGGCATTGT 59.174 45.455 0.00 0.00 46.51 2.71
2634 2935 3.508744 GGTGACATACCTTTGGCATTG 57.491 47.619 0.00 0.00 46.51 2.82
2665 2966 8.635765 ATGTGTCACATGGTTATAGAGTTTTT 57.364 30.769 17.74 0.00 37.45 1.94
2680 2981 3.986996 TCAGGTGATCATGTGTCACAT 57.013 42.857 24.68 12.87 45.99 3.21
2681 2982 3.324556 TCTTCAGGTGATCATGTGTCACA 59.675 43.478 24.68 8.40 45.99 3.58
2682 2983 3.930336 TCTTCAGGTGATCATGTGTCAC 58.070 45.455 19.13 19.13 44.01 3.67
2683 2984 3.618263 GCTCTTCAGGTGATCATGTGTCA 60.618 47.826 0.00 0.00 0.00 3.58
2684 2985 2.935201 GCTCTTCAGGTGATCATGTGTC 59.065 50.000 0.00 0.00 0.00 3.67
2685 2986 2.355513 GGCTCTTCAGGTGATCATGTGT 60.356 50.000 0.00 0.00 0.00 3.72
2686 2987 2.286872 GGCTCTTCAGGTGATCATGTG 58.713 52.381 0.00 0.00 0.00 3.21
2687 2988 1.134580 CGGCTCTTCAGGTGATCATGT 60.135 52.381 0.00 0.00 0.00 3.21
2688 2989 1.137675 TCGGCTCTTCAGGTGATCATG 59.862 52.381 0.00 0.00 0.00 3.07
2689 2990 1.489481 TCGGCTCTTCAGGTGATCAT 58.511 50.000 0.00 0.00 0.00 2.45
2690 2991 1.266178 TTCGGCTCTTCAGGTGATCA 58.734 50.000 0.00 0.00 0.00 2.92
2691 2992 2.386661 TTTCGGCTCTTCAGGTGATC 57.613 50.000 0.00 0.00 0.00 2.92
2692 2993 3.012518 CAATTTCGGCTCTTCAGGTGAT 58.987 45.455 0.00 0.00 0.00 3.06
2693 2994 2.038426 TCAATTTCGGCTCTTCAGGTGA 59.962 45.455 0.00 0.00 0.00 4.02
2694 2995 2.160417 GTCAATTTCGGCTCTTCAGGTG 59.840 50.000 0.00 0.00 0.00 4.00
2695 2996 2.224523 TGTCAATTTCGGCTCTTCAGGT 60.225 45.455 0.00 0.00 0.00 4.00
2696 2997 2.160417 GTGTCAATTTCGGCTCTTCAGG 59.840 50.000 0.00 0.00 0.00 3.86
2697 2998 2.807967 TGTGTCAATTTCGGCTCTTCAG 59.192 45.455 0.00 0.00 0.00 3.02
2698 2999 2.548057 GTGTGTCAATTTCGGCTCTTCA 59.452 45.455 0.00 0.00 0.00 3.02
2699 3000 2.548057 TGTGTGTCAATTTCGGCTCTTC 59.452 45.455 0.00 0.00 0.00 2.87
2700 3001 2.571212 TGTGTGTCAATTTCGGCTCTT 58.429 42.857 0.00 0.00 0.00 2.85
2701 3002 2.254546 TGTGTGTCAATTTCGGCTCT 57.745 45.000 0.00 0.00 0.00 4.09
2702 3003 3.435327 TGTATGTGTGTCAATTTCGGCTC 59.565 43.478 0.00 0.00 0.00 4.70
2703 3004 3.407698 TGTATGTGTGTCAATTTCGGCT 58.592 40.909 0.00 0.00 0.00 5.52
2704 3005 3.822594 TGTATGTGTGTCAATTTCGGC 57.177 42.857 0.00 0.00 0.00 5.54
2705 3006 5.801350 AGATGTATGTGTGTCAATTTCGG 57.199 39.130 0.00 0.00 0.00 4.30
2706 3007 7.525688 ACTAGATGTATGTGTGTCAATTTCG 57.474 36.000 0.00 0.00 0.00 3.46
2710 3011 9.982651 GGTATAACTAGATGTATGTGTGTCAAT 57.017 33.333 0.00 0.00 0.00 2.57
2711 3012 9.197306 AGGTATAACTAGATGTATGTGTGTCAA 57.803 33.333 0.00 0.00 0.00 3.18
2712 3013 8.762481 AGGTATAACTAGATGTATGTGTGTCA 57.238 34.615 0.00 0.00 0.00 3.58
2722 3023 9.745880 CAACACGATTAAGGTATAACTAGATGT 57.254 33.333 0.00 0.00 0.00 3.06
2723 3024 9.961265 TCAACACGATTAAGGTATAACTAGATG 57.039 33.333 0.00 0.00 0.00 2.90
2741 3042 9.263538 ACAAAAGTATACTTACATTCAACACGA 57.736 29.630 18.31 0.00 34.61 4.35
2764 3065 9.379770 TCATGAGGTATTTCCATATCTCTACAA 57.620 33.333 0.00 0.00 41.98 2.41
2765 3066 8.956446 TCATGAGGTATTTCCATATCTCTACA 57.044 34.615 0.00 0.00 41.98 2.74
2774 3075 9.699410 TTCAGTATTTTCATGAGGTATTTCCAT 57.301 29.630 0.00 0.00 39.02 3.41
2775 3076 9.699410 ATTCAGTATTTTCATGAGGTATTTCCA 57.301 29.630 0.00 0.00 39.02 3.53
2776 3077 9.956720 CATTCAGTATTTTCATGAGGTATTTCC 57.043 33.333 0.00 0.00 0.00 3.13
2779 3080 9.125026 GGTCATTCAGTATTTTCATGAGGTATT 57.875 33.333 0.00 0.00 0.00 1.89
2780 3081 8.274322 TGGTCATTCAGTATTTTCATGAGGTAT 58.726 33.333 0.00 0.00 0.00 2.73
2781 3082 7.552687 GTGGTCATTCAGTATTTTCATGAGGTA 59.447 37.037 0.00 0.00 0.00 3.08
2782 3083 6.375455 GTGGTCATTCAGTATTTTCATGAGGT 59.625 38.462 0.00 0.00 0.00 3.85
2783 3084 6.375174 TGTGGTCATTCAGTATTTTCATGAGG 59.625 38.462 0.00 0.00 0.00 3.86
2784 3085 7.381766 TGTGGTCATTCAGTATTTTCATGAG 57.618 36.000 0.00 0.00 0.00 2.90
2785 3086 7.943079 ATGTGGTCATTCAGTATTTTCATGA 57.057 32.000 0.00 0.00 0.00 3.07
2835 3136 9.738832 ACTTACTATTTGTGTTTTGCGTATTTT 57.261 25.926 0.00 0.00 0.00 1.82
2836 3137 9.738832 AACTTACTATTTGTGTTTTGCGTATTT 57.261 25.926 0.00 0.00 0.00 1.40
2837 3138 9.389570 GAACTTACTATTTGTGTTTTGCGTATT 57.610 29.630 0.00 0.00 0.00 1.89
2838 3139 8.780249 AGAACTTACTATTTGTGTTTTGCGTAT 58.220 29.630 0.00 0.00 0.00 3.06
2839 3140 8.145316 AGAACTTACTATTTGTGTTTTGCGTA 57.855 30.769 0.00 0.00 0.00 4.42
2840 3141 7.012044 AGAGAACTTACTATTTGTGTTTTGCGT 59.988 33.333 0.00 0.00 0.00 5.24
2841 3142 7.352739 AGAGAACTTACTATTTGTGTTTTGCG 58.647 34.615 0.00 0.00 0.00 4.85
2842 3143 8.958043 CAAGAGAACTTACTATTTGTGTTTTGC 58.042 33.333 0.00 0.00 34.70 3.68
2843 3144 8.958043 GCAAGAGAACTTACTATTTGTGTTTTG 58.042 33.333 0.00 0.00 34.70 2.44
2844 3145 8.903820 AGCAAGAGAACTTACTATTTGTGTTTT 58.096 29.630 0.00 0.00 34.70 2.43
2845 3146 8.451908 AGCAAGAGAACTTACTATTTGTGTTT 57.548 30.769 0.00 0.00 34.70 2.83
2846 3147 9.726438 ATAGCAAGAGAACTTACTATTTGTGTT 57.274 29.630 0.00 0.00 38.70 3.32
2855 3156 9.415008 TCTTCTCATATAGCAAGAGAACTTACT 57.585 33.333 0.00 0.00 41.88 2.24
2860 3161 9.123709 CGTTATCTTCTCATATAGCAAGAGAAC 57.876 37.037 12.75 12.75 41.88 3.01
2861 3162 7.810282 GCGTTATCTTCTCATATAGCAAGAGAA 59.190 37.037 0.00 0.00 43.82 2.87
2862 3163 7.175816 AGCGTTATCTTCTCATATAGCAAGAGA 59.824 37.037 0.00 0.00 36.68 3.10
2863 3164 7.312154 AGCGTTATCTTCTCATATAGCAAGAG 58.688 38.462 0.00 0.00 30.21 2.85
2864 3165 7.220741 AGCGTTATCTTCTCATATAGCAAGA 57.779 36.000 0.00 0.00 0.00 3.02
2865 3166 7.881643 AAGCGTTATCTTCTCATATAGCAAG 57.118 36.000 0.00 0.00 0.00 4.01
2866 3167 8.144478 AGAAAGCGTTATCTTCTCATATAGCAA 58.856 33.333 0.00 0.00 0.00 3.91
2867 3168 7.661968 AGAAAGCGTTATCTTCTCATATAGCA 58.338 34.615 0.00 0.00 0.00 3.49
2868 3169 9.284594 CTAGAAAGCGTTATCTTCTCATATAGC 57.715 37.037 0.00 0.00 0.00 2.97
2869 3170 9.781834 CCTAGAAAGCGTTATCTTCTCATATAG 57.218 37.037 0.00 0.00 0.00 1.31
2870 3171 9.298250 ACCTAGAAAGCGTTATCTTCTCATATA 57.702 33.333 0.00 0.00 0.00 0.86
2871 3172 8.184304 ACCTAGAAAGCGTTATCTTCTCATAT 57.816 34.615 0.00 0.00 0.00 1.78
2872 3173 7.584122 ACCTAGAAAGCGTTATCTTCTCATA 57.416 36.000 0.00 0.00 0.00 2.15
2873 3174 6.472686 ACCTAGAAAGCGTTATCTTCTCAT 57.527 37.500 0.00 0.00 0.00 2.90
2874 3175 5.916661 ACCTAGAAAGCGTTATCTTCTCA 57.083 39.130 0.00 0.00 0.00 3.27
2875 3176 6.696583 GGTTACCTAGAAAGCGTTATCTTCTC 59.303 42.308 0.00 0.00 0.00 2.87
2876 3177 6.154021 TGGTTACCTAGAAAGCGTTATCTTCT 59.846 38.462 2.07 0.00 0.00 2.85
2877 3178 6.335777 TGGTTACCTAGAAAGCGTTATCTTC 58.664 40.000 2.07 0.00 0.00 2.87
2878 3179 6.154021 TCTGGTTACCTAGAAAGCGTTATCTT 59.846 38.462 2.07 0.00 0.00 2.40
2879 3180 5.655532 TCTGGTTACCTAGAAAGCGTTATCT 59.344 40.000 2.07 0.00 0.00 1.98
2880 3181 5.899299 TCTGGTTACCTAGAAAGCGTTATC 58.101 41.667 2.07 0.00 0.00 1.75
2881 3182 5.681695 GCTCTGGTTACCTAGAAAGCGTTAT 60.682 44.000 2.07 0.00 0.00 1.89
2882 3183 4.381292 GCTCTGGTTACCTAGAAAGCGTTA 60.381 45.833 2.07 0.00 0.00 3.18
2883 3184 3.616802 GCTCTGGTTACCTAGAAAGCGTT 60.617 47.826 2.07 0.00 0.00 4.84
2884 3185 2.094130 GCTCTGGTTACCTAGAAAGCGT 60.094 50.000 2.07 0.00 0.00 5.07
2885 3186 2.541556 GCTCTGGTTACCTAGAAAGCG 58.458 52.381 2.07 0.00 0.00 4.68
2886 3187 2.236395 TGGCTCTGGTTACCTAGAAAGC 59.764 50.000 2.07 4.46 0.00 3.51
2887 3188 3.769844 TCTGGCTCTGGTTACCTAGAAAG 59.230 47.826 2.07 2.44 0.00 2.62
2888 3189 3.769844 CTCTGGCTCTGGTTACCTAGAAA 59.230 47.826 2.07 0.00 0.00 2.52
2889 3190 3.366396 CTCTGGCTCTGGTTACCTAGAA 58.634 50.000 2.07 0.00 0.00 2.10
2890 3191 2.358300 CCTCTGGCTCTGGTTACCTAGA 60.358 54.545 2.07 3.33 0.00 2.43
2891 3192 2.035632 CCTCTGGCTCTGGTTACCTAG 58.964 57.143 2.07 1.38 0.00 3.02
2892 3193 1.361543 ACCTCTGGCTCTGGTTACCTA 59.638 52.381 2.07 0.00 0.00 3.08
2893 3194 0.117340 ACCTCTGGCTCTGGTTACCT 59.883 55.000 2.07 0.00 0.00 3.08
2894 3195 1.861982 TACCTCTGGCTCTGGTTACC 58.138 55.000 0.00 0.00 35.48 2.85
2895 3196 3.863041 CTTTACCTCTGGCTCTGGTTAC 58.137 50.000 0.00 0.00 35.48 2.50
2896 3197 2.236395 GCTTTACCTCTGGCTCTGGTTA 59.764 50.000 0.00 0.00 35.48 2.85
2897 3198 1.003696 GCTTTACCTCTGGCTCTGGTT 59.996 52.381 0.00 0.00 35.48 3.67
2898 3199 0.615850 GCTTTACCTCTGGCTCTGGT 59.384 55.000 0.00 0.00 37.83 4.00
2899 3200 0.908198 AGCTTTACCTCTGGCTCTGG 59.092 55.000 0.00 0.00 0.00 3.86
2900 3201 3.895232 TTAGCTTTACCTCTGGCTCTG 57.105 47.619 0.00 0.00 36.40 3.35
2901 3202 4.775236 CAATTAGCTTTACCTCTGGCTCT 58.225 43.478 0.00 0.00 36.40 4.09
2902 3203 3.313803 GCAATTAGCTTTACCTCTGGCTC 59.686 47.826 0.00 0.00 41.15 4.70
2903 3204 3.282885 GCAATTAGCTTTACCTCTGGCT 58.717 45.455 0.00 0.00 41.15 4.75
2904 3205 3.016736 TGCAATTAGCTTTACCTCTGGC 58.983 45.455 0.00 0.00 45.94 4.85
2905 3206 5.128919 AGATGCAATTAGCTTTACCTCTGG 58.871 41.667 0.00 0.00 45.94 3.86
2906 3207 6.690194 AAGATGCAATTAGCTTTACCTCTG 57.310 37.500 0.00 0.00 45.94 3.35
2907 3208 7.709149 AAAAGATGCAATTAGCTTTACCTCT 57.291 32.000 0.00 0.00 45.94 3.69
2908 3209 8.893727 TCTAAAAGATGCAATTAGCTTTACCTC 58.106 33.333 0.00 0.00 45.94 3.85
2909 3210 8.807948 TCTAAAAGATGCAATTAGCTTTACCT 57.192 30.769 0.00 0.00 45.94 3.08
2921 3222 8.400947 GCTGAGTTATGATTCTAAAAGATGCAA 58.599 33.333 0.00 0.00 0.00 4.08
2922 3223 7.553760 TGCTGAGTTATGATTCTAAAAGATGCA 59.446 33.333 0.00 0.00 0.00 3.96
2923 3224 7.923888 TGCTGAGTTATGATTCTAAAAGATGC 58.076 34.615 0.00 0.00 0.00 3.91
2925 3226 9.842775 TGATGCTGAGTTATGATTCTAAAAGAT 57.157 29.630 0.00 0.00 0.00 2.40
2926 3227 9.671279 TTGATGCTGAGTTATGATTCTAAAAGA 57.329 29.630 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.