Multiple sequence alignment - TraesCS2B01G186600

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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 TraesCS2B01G186600 chr2B 100.000 5548 0 0 1 5548 161419152 161413605 0.000000e+00 10246.0
1 TraesCS2B01G186600 chr2B 95.439 285 13 0 1315 1599 161417745 161417461 6.550000e-124 455.0
2 TraesCS2B01G186600 chr2B 95.439 285 13 0 1408 1692 161417838 161417554 6.550000e-124 455.0
3 TraesCS2B01G186600 chr2B 93.750 192 12 0 1315 1506 161417652 161417461 7.030000e-74 289.0
4 TraesCS2B01G186600 chr2B 93.750 192 12 0 1501 1692 161417838 161417647 7.030000e-74 289.0
5 TraesCS2B01G186600 chr2B 95.763 118 2 3 2824 2941 134367327 134367441 2.640000e-43 187.0
6 TraesCS2B01G186600 chr2B 97.222 108 3 0 2826 2933 766568270 766568163 3.410000e-42 183.0
7 TraesCS2B01G186600 chr2B 94.949 99 5 0 1594 1692 161417838 161417740 7.440000e-34 156.0
8 TraesCS2B01G186600 chr2B 98.333 60 0 1 5145 5203 398971966 398972025 2.730000e-18 104.0
9 TraesCS2B01G186600 chr2D 94.056 2877 89 28 1 2828 111336103 111333260 0.000000e+00 4290.0
10 TraesCS2B01G186600 chr2D 94.644 2222 71 17 2930 5136 111333263 111331075 0.000000e+00 3400.0
11 TraesCS2B01G186600 chr2D 96.140 285 11 0 1408 1692 111334766 111334482 3.030000e-127 466.0
12 TraesCS2B01G186600 chr2D 95.088 285 14 0 1315 1599 111334673 111334389 3.050000e-122 449.0
13 TraesCS2B01G186600 chr2D 94.271 192 11 0 1315 1506 111334580 111334389 1.510000e-75 294.0
14 TraesCS2B01G186600 chr2D 93.229 192 13 0 1501 1692 111334766 111334575 3.270000e-72 283.0
15 TraesCS2B01G186600 chr2D 98.182 110 2 0 2827 2936 352204161 352204270 5.670000e-45 193.0
16 TraesCS2B01G186600 chr2D 93.939 99 6 0 1594 1692 111334766 111334668 3.460000e-32 150.0
17 TraesCS2B01G186600 chr2A 94.466 1825 72 12 2930 4748 111422735 111420934 0.000000e+00 2784.0
18 TraesCS2B01G186600 chr2A 97.540 1423 33 1 1408 2828 111424154 111422732 0.000000e+00 2433.0
19 TraesCS2B01G186600 chr2A 92.857 1624 75 17 1 1599 111425477 111423870 0.000000e+00 2318.0
20 TraesCS2B01G186600 chr2A 91.379 406 23 7 4734 5136 111420915 111420519 3.780000e-151 545.0
21 TraesCS2B01G186600 chr2A 93.229 192 13 0 1315 1506 111424061 111423870 3.270000e-72 283.0
22 TraesCS2B01G186600 chr2A 93.229 192 13 0 1501 1692 111424154 111423963 3.270000e-72 283.0
23 TraesCS2B01G186600 chr2A 81.931 321 45 6 5227 5537 111418172 111417855 5.510000e-65 259.0
24 TraesCS2B01G186600 chr2A 94.949 99 5 0 1315 1413 111423968 111423870 7.440000e-34 156.0
25 TraesCS2B01G186600 chr2A 93.939 99 6 0 1594 1692 111424154 111424056 3.460000e-32 150.0
26 TraesCS2B01G186600 chr2A 95.312 64 1 2 5142 5203 524753102 524753039 3.540000e-17 100.0
27 TraesCS2B01G186600 chr3A 87.184 515 50 8 2320 2819 687993552 687993039 6.240000e-159 571.0
28 TraesCS2B01G186600 chr3A 82.152 381 43 14 2972 3349 687993009 687992651 2.510000e-78 303.0
29 TraesCS2B01G186600 chr3A 86.047 86 7 5 5119 5203 571806141 571806060 2.750000e-13 87.9
30 TraesCS2B01G186600 chr4A 86.911 191 23 2 3490 3680 255591598 255591410 4.350000e-51 213.0
31 TraesCS2B01G186600 chr4A 95.312 64 1 2 5142 5203 92300340 92300403 3.540000e-17 100.0
32 TraesCS2B01G186600 chr4A 95.312 64 1 2 5142 5203 99889834 99889771 3.540000e-17 100.0
33 TraesCS2B01G186600 chr4A 87.013 77 8 2 3362 3437 255591746 255591671 9.900000e-13 86.1
34 TraesCS2B01G186600 chr4D 90.062 161 16 0 3520 3680 274221106 274221266 5.630000e-50 209.0
35 TraesCS2B01G186600 chr4D 80.734 109 21 0 3329 3437 274220897 274221005 9.900000e-13 86.1
36 TraesCS2B01G186600 chr4B 86.387 191 24 2 3490 3680 240826723 240826911 2.030000e-49 207.0
37 TraesCS2B01G186600 chr4B 95.312 64 1 2 5145 5207 102209703 102209765 3.540000e-17 100.0
38 TraesCS2B01G186600 chr4B 80.909 110 19 2 3329 3437 240826542 240826650 9.900000e-13 86.1
39 TraesCS2B01G186600 chr6B 96.581 117 3 1 2827 2942 714337001 714337117 5.670000e-45 193.0
40 TraesCS2B01G186600 chr5B 97.345 113 3 0 2824 2936 659470646 659470534 5.670000e-45 193.0
41 TraesCS2B01G186600 chr5B 95.726 117 4 1 2824 2939 281433783 281433899 2.640000e-43 187.0
42 TraesCS2B01G186600 chr7B 96.522 115 4 0 2823 2937 174674014 174674128 2.040000e-44 191.0
43 TraesCS2B01G186600 chr3B 95.000 120 4 2 2819 2936 48886463 48886582 2.640000e-43 187.0
44 TraesCS2B01G186600 chr1A 93.651 126 7 1 2816 2940 343396813 343396688 2.640000e-43 187.0
45 TraesCS2B01G186600 chr1A 93.750 64 2 2 5142 5203 531183160 531183097 1.650000e-15 95.3
46 TraesCS2B01G186600 chr6A 95.312 64 1 2 5142 5203 424317109 424317172 3.540000e-17 100.0
47 TraesCS2B01G186600 chr7A 89.333 75 6 2 5149 5222 116123092 116123165 5.920000e-15 93.5


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 TraesCS2B01G186600 chr2B 161413605 161419152 5547 True 1981.666667 10246 95.554500 1 5548 6 chr2B.!!$R2 5547
1 TraesCS2B01G186600 chr2D 111331075 111336103 5028 True 1333.142857 4290 94.481000 1 5136 7 chr2D.!!$R1 5135
2 TraesCS2B01G186600 chr2A 111417855 111425477 7622 True 1023.444444 2784 92.613222 1 5537 9 chr2A.!!$R2 5536
3 TraesCS2B01G186600 chr3A 687992651 687993552 901 True 437.000000 571 84.668000 2320 3349 2 chr3A.!!$R2 1029

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
514 521 0.030235 GTTCGGGTGTTTCTTGTGGC 59.970 55.000 0.00 0.00 0.00 5.01 F
531 538 0.178068 GGCTTCGGTATGCTCTGGAA 59.822 55.000 0.00 0.00 0.00 3.53 F
576 606 0.321021 TTTGTGTGCATGAATGGCCC 59.679 50.000 0.00 0.00 0.00 5.80 F
580 610 0.615261 TGTGCATGAATGGCCCATGT 60.615 50.000 18.24 0.00 42.39 3.21 F
1842 1890 0.935898 CATCTCCACAAGCTGATCGC 59.064 55.000 0.00 1.92 39.57 4.58 F
2436 2484 1.482182 GGGACCCCATTGCAAGAAATC 59.518 52.381 4.94 0.00 35.81 2.17 F
3297 3364 0.882042 CAGCGCCATGTGGATACTCC 60.882 60.000 2.29 0.00 37.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2058 0.108615 GTGACGCACTAGCATCAGGT 60.109 55.000 3.2 0.0 44.46 4.00 R
2013 2061 1.066929 ACATGTGACGCACTAGCATCA 60.067 47.619 0.0 0.0 41.20 3.07 R
2225 2273 5.297776 AGAACACACTTGATTTGAGAACCTG 59.702 40.000 0.0 0.0 0.00 4.00 R
2249 2297 6.936335 AGTTGATATATTGTCATGCGGAATCA 59.064 34.615 0.0 0.0 0.00 2.57 R
2904 2967 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.0 0.0 35.93 5.19 R
4255 4323 0.398696 TTCCGCTTGTTGGAAGGCTA 59.601 50.000 0.0 0.0 40.51 3.93 R
5088 5204 0.031585 TGGTCGATATGCGTGGCTAC 59.968 55.000 0.0 0.0 41.80 3.58 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
42 46 4.840005 CTCCCGCCCGCTCCTTTC 62.840 72.222 0.00 0.00 0.00 2.62
88 94 3.125573 GAGGTTTTCGGCGCTCCC 61.126 66.667 7.64 0.00 0.00 4.30
273 280 3.764466 CGAGGCTCGCTGAAGGGT 61.764 66.667 25.31 0.00 31.14 4.34
275 282 4.400961 AGGCTCGCTGAAGGGTGC 62.401 66.667 11.64 11.64 43.67 5.01
280 287 2.435586 CGCTGAAGGGTGCTCTGG 60.436 66.667 0.00 0.00 0.00 3.86
388 395 1.605500 CGTGCGATTTGGACATTGTG 58.394 50.000 0.00 0.00 39.19 3.33
394 401 3.065233 GCGATTTGGACATTGTGCAGATA 59.935 43.478 13.17 3.88 34.96 1.98
421 428 3.429085 GCATTAACACGCTGGATTTGAG 58.571 45.455 0.00 0.00 0.00 3.02
444 451 4.326600 GGGGGTTTATGAAGGGTTTAGT 57.673 45.455 0.00 0.00 0.00 2.24
455 462 1.823610 AGGGTTTAGTCGTAGGTCTGC 59.176 52.381 0.00 0.00 0.00 4.26
457 464 2.233186 GGGTTTAGTCGTAGGTCTGCTT 59.767 50.000 0.00 0.00 0.00 3.91
468 475 1.622811 AGGTCTGCTTTGTGAGAGGAG 59.377 52.381 0.00 0.00 34.30 3.69
474 481 5.523188 GTCTGCTTTGTGAGAGGAGATTATG 59.477 44.000 0.00 0.00 42.38 1.90
507 514 3.103007 CGTTTTTCTGTTCGGGTGTTTC 58.897 45.455 0.00 0.00 0.00 2.78
514 521 0.030235 GTTCGGGTGTTTCTTGTGGC 59.970 55.000 0.00 0.00 0.00 5.01
531 538 0.178068 GGCTTCGGTATGCTCTGGAA 59.822 55.000 0.00 0.00 0.00 3.53
538 545 6.426937 GCTTCGGTATGCTCTGGAATAAATTA 59.573 38.462 0.00 0.00 0.00 1.40
576 606 0.321021 TTTGTGTGCATGAATGGCCC 59.679 50.000 0.00 0.00 0.00 5.80
580 610 0.615261 TGTGCATGAATGGCCCATGT 60.615 50.000 18.24 0.00 42.39 3.21
606 636 6.798315 TTTTGTTTTATGGTGCATGAATGG 57.202 33.333 0.00 0.00 0.00 3.16
607 637 5.480642 TTGTTTTATGGTGCATGAATGGT 57.519 34.783 0.00 0.00 0.00 3.55
608 638 5.070770 TGTTTTATGGTGCATGAATGGTC 57.929 39.130 0.00 0.00 0.00 4.02
609 639 4.771577 TGTTTTATGGTGCATGAATGGTCT 59.228 37.500 0.00 0.00 0.00 3.85
610 640 5.948758 TGTTTTATGGTGCATGAATGGTCTA 59.051 36.000 0.00 0.00 0.00 2.59
664 695 6.529829 TGCAATTGACAGTTTTTCACACTTAC 59.470 34.615 10.34 0.00 0.00 2.34
667 698 5.712217 TGACAGTTTTTCACACTTACGAG 57.288 39.130 0.00 0.00 0.00 4.18
668 699 5.412640 TGACAGTTTTTCACACTTACGAGA 58.587 37.500 0.00 0.00 0.00 4.04
672 703 8.603242 ACAGTTTTTCACACTTACGAGATATT 57.397 30.769 0.00 0.00 0.00 1.28
689 720 4.813161 AGATATTACACAGATGCACAGTGC 59.187 41.667 19.37 19.37 45.29 4.40
700 747 1.592400 GCACAGTGCACATGGAGCAT 61.592 55.000 21.22 5.32 44.79 3.79
877 925 7.582667 ATTTGGTAACTGCAACTTAAGAAGT 57.417 32.000 10.09 4.46 40.20 3.01
1026 1074 3.722147 GACGTATCCTGTGCTGAATGAT 58.278 45.455 0.00 0.00 0.00 2.45
1150 1198 7.348274 TCTTTGAGGAACTTCAGGGTGATATAT 59.652 37.037 0.00 0.00 41.55 0.86
1161 1209 5.071788 TCAGGGTGATATATTTGGTGGAGAC 59.928 44.000 0.00 0.00 0.00 3.36
1210 1258 5.003692 TGATGATCTCAAAGAGGACGAAG 57.996 43.478 0.00 0.00 0.00 3.79
1284 1332 2.834549 TGATGAAGGTCCTTCTCAGGTC 59.165 50.000 28.02 18.40 40.73 3.85
1333 1381 3.357203 TCTGTTACAGAGGCTAGTGAGG 58.643 50.000 11.42 0.00 35.39 3.86
1379 1427 6.821388 AGGTTATTCAGGATGCTGTAGTTAG 58.179 40.000 14.43 0.00 34.76 2.34
1397 1445 7.661437 TGTAGTTAGTACCGAAGAAGTTAGTCA 59.339 37.037 0.00 0.00 0.00 3.41
1430 1478 1.346395 TGCGGAGGCTAGTGAGAAAAA 59.654 47.619 0.00 0.00 40.82 1.94
1434 1482 2.685388 GGAGGCTAGTGAGAAAAATGCC 59.315 50.000 0.00 0.00 39.19 4.40
1545 1593 2.099263 TGCCGATGCTACTACAGAAGTC 59.901 50.000 0.00 0.00 36.02 3.01
1757 1805 4.461781 AGCTGATGAAATTTCTCCAAGTGG 59.538 41.667 18.64 6.43 0.00 4.00
1842 1890 0.935898 CATCTCCACAAGCTGATCGC 59.064 55.000 0.00 1.92 39.57 4.58
1867 1915 7.440198 CCATAGTGAGATTATTGCAGAGAAGA 58.560 38.462 0.00 0.00 0.00 2.87
2013 2061 5.741383 GCAAGATGCAGTATCATCACTACCT 60.741 44.000 0.91 0.00 44.26 3.08
2249 2297 5.297776 CAGGTTCTCAAATCAAGTGTGTTCT 59.702 40.000 0.00 0.00 0.00 3.01
2436 2484 1.482182 GGGACCCCATTGCAAGAAATC 59.518 52.381 4.94 0.00 35.81 2.17
2556 2618 5.220931 GGATGTGATGGAAAGTAAGCATGTC 60.221 44.000 0.00 0.00 0.00 3.06
2744 2807 5.768164 GGAAACTTGGAGGTTTGTCTTCATA 59.232 40.000 0.00 0.00 39.20 2.15
2819 2882 9.607285 GAATATCTTGAGCGTTTTTGTTTTCTA 57.393 29.630 0.00 0.00 0.00 2.10
2823 2886 9.959749 ATCTTGAGCGTTTTTGTTTTCTATTAA 57.040 25.926 0.00 0.00 0.00 1.40
2826 2889 9.575783 TTGAGCGTTTTTGTTTTCTATTAAAGT 57.424 25.926 0.00 0.00 0.00 2.66
2835 2898 9.511272 TTTGTTTTCTATTAAAGTACTCCCTCC 57.489 33.333 0.00 0.00 0.00 4.30
2837 2900 7.038799 TGTTTTCTATTAAAGTACTCCCTCCGT 60.039 37.037 0.00 0.00 0.00 4.69
2838 2901 7.486407 TTTCTATTAAAGTACTCCCTCCGTT 57.514 36.000 0.00 0.00 0.00 4.44
2839 2902 6.705863 TCTATTAAAGTACTCCCTCCGTTC 57.294 41.667 0.00 0.00 0.00 3.95
2840 2903 4.750021 ATTAAAGTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
2841 2904 2.019807 AAAGTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
2842 2905 2.019807 AAGTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2843 2906 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2844 2907 2.547990 AGTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
2845 2908 2.910977 AGTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
2846 2909 4.098894 AGTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
2847 2910 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2848 2911 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2849 2912 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2850 2913 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2851 2914 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2852 2915 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2853 2916 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2854 2917 2.228582 TCCGTTCCAAATTACTCGTCGA 59.771 45.455 0.00 0.00 0.00 4.20
2855 2918 3.119388 TCCGTTCCAAATTACTCGTCGAT 60.119 43.478 0.00 0.00 0.00 3.59
2856 2919 3.000078 CCGTTCCAAATTACTCGTCGATG 60.000 47.826 0.00 0.00 0.00 3.84
2857 2920 3.855379 CGTTCCAAATTACTCGTCGATGA 59.145 43.478 7.21 7.21 0.00 2.92
2858 2921 4.325204 CGTTCCAAATTACTCGTCGATGAA 59.675 41.667 8.98 0.00 0.00 2.57
2859 2922 5.164031 CGTTCCAAATTACTCGTCGATGAAA 60.164 40.000 8.98 1.36 0.00 2.69
2860 2923 6.455113 CGTTCCAAATTACTCGTCGATGAAAT 60.455 38.462 8.98 3.84 0.00 2.17
2861 2924 6.344572 TCCAAATTACTCGTCGATGAAATG 57.655 37.500 8.98 0.00 0.00 2.32
2862 2925 5.293324 TCCAAATTACTCGTCGATGAAATGG 59.707 40.000 8.98 10.29 0.00 3.16
2863 2926 5.293324 CCAAATTACTCGTCGATGAAATGGA 59.707 40.000 8.98 0.00 0.00 3.41
2864 2927 6.017934 CCAAATTACTCGTCGATGAAATGGAT 60.018 38.462 8.98 0.00 32.34 3.41
2865 2928 6.530913 AATTACTCGTCGATGAAATGGATG 57.469 37.500 8.98 0.00 39.16 3.51
2866 2929 3.526931 ACTCGTCGATGAAATGGATGT 57.473 42.857 8.98 0.00 38.92 3.06
2867 2930 4.649088 ACTCGTCGATGAAATGGATGTA 57.351 40.909 8.98 0.00 38.92 2.29
2868 2931 5.201713 ACTCGTCGATGAAATGGATGTAT 57.798 39.130 8.98 0.00 38.92 2.29
2869 2932 5.601662 ACTCGTCGATGAAATGGATGTATT 58.398 37.500 8.98 0.00 38.92 1.89
2870 2933 6.049149 ACTCGTCGATGAAATGGATGTATTT 58.951 36.000 8.98 0.00 38.92 1.40
2871 2934 7.207383 ACTCGTCGATGAAATGGATGTATTTA 58.793 34.615 8.98 0.00 38.92 1.40
2872 2935 7.382488 ACTCGTCGATGAAATGGATGTATTTAG 59.618 37.037 8.98 0.00 38.92 1.85
2873 2936 7.430441 TCGTCGATGAAATGGATGTATTTAGA 58.570 34.615 4.45 0.00 38.92 2.10
2874 2937 7.923878 TCGTCGATGAAATGGATGTATTTAGAA 59.076 33.333 4.45 0.00 38.92 2.10
2875 2938 8.004344 CGTCGATGAAATGGATGTATTTAGAAC 58.996 37.037 0.00 0.00 33.91 3.01
2876 2939 9.046296 GTCGATGAAATGGATGTATTTAGAACT 57.954 33.333 0.00 0.00 32.34 3.01
2905 2968 5.955488 ACATCTAGATACATCCATACGTGC 58.045 41.667 4.54 0.00 0.00 5.34
2906 2969 4.680171 TCTAGATACATCCATACGTGCG 57.320 45.455 0.00 0.00 0.00 5.34
2907 2970 4.320870 TCTAGATACATCCATACGTGCGA 58.679 43.478 0.00 0.00 0.00 5.10
2908 2971 3.284323 AGATACATCCATACGTGCGAC 57.716 47.619 0.00 0.00 0.00 5.19
2909 2972 2.621526 AGATACATCCATACGTGCGACA 59.378 45.455 0.00 0.00 0.00 4.35
2910 2973 2.943449 TACATCCATACGTGCGACAA 57.057 45.000 0.00 0.00 0.00 3.18
2911 2974 1.640428 ACATCCATACGTGCGACAAG 58.360 50.000 0.00 0.00 0.00 3.16
2912 2975 1.067142 ACATCCATACGTGCGACAAGT 60.067 47.619 0.00 0.00 0.00 3.16
2913 2976 2.164827 ACATCCATACGTGCGACAAGTA 59.835 45.455 0.00 7.72 33.49 2.24
2914 2977 3.183754 CATCCATACGTGCGACAAGTAA 58.816 45.455 0.00 0.00 32.82 2.24
2915 2978 3.513680 TCCATACGTGCGACAAGTAAT 57.486 42.857 0.00 0.00 32.82 1.89
2916 2979 3.852286 TCCATACGTGCGACAAGTAATT 58.148 40.909 0.00 0.00 32.82 1.40
2917 2980 3.861113 TCCATACGTGCGACAAGTAATTC 59.139 43.478 0.00 0.00 32.82 2.17
2918 2981 3.301579 CCATACGTGCGACAAGTAATTCG 60.302 47.826 0.00 0.00 32.82 3.34
2919 2982 1.065358 ACGTGCGACAAGTAATTCGG 58.935 50.000 0.00 0.00 35.73 4.30
2920 2983 1.336148 ACGTGCGACAAGTAATTCGGA 60.336 47.619 0.00 0.00 35.73 4.55
2921 2984 1.722464 CGTGCGACAAGTAATTCGGAA 59.278 47.619 0.00 0.00 37.32 4.30
2922 2985 2.471749 CGTGCGACAAGTAATTCGGAAC 60.472 50.000 0.00 0.00 37.32 3.62
3059 3123 5.119125 GGTAAATCTTGCATGAAACAGTTGC 59.881 40.000 6.36 0.00 36.91 4.17
3255 3322 3.375782 AAATGCAGACCAAGAAGTTGC 57.624 42.857 0.00 0.00 35.42 4.17
3265 3332 1.135859 CAAGAAGTTGCTGCGGATGAC 60.136 52.381 0.00 0.00 0.00 3.06
3297 3364 0.882042 CAGCGCCATGTGGATACTCC 60.882 60.000 2.29 0.00 37.39 3.85
3306 3373 5.203528 CCATGTGGATACTCCCAAAATTCT 58.796 41.667 0.00 0.00 38.06 2.40
3378 3445 2.356135 TCGGCCTGCTCTAAAACATTC 58.644 47.619 0.00 0.00 0.00 2.67
3426 3493 1.768275 TGGAGGTTCTCACAAAGAGCA 59.232 47.619 0.00 0.00 44.35 4.26
3703 3770 8.015087 TGTCGCTAACTTCATTGTCTTATTTTG 58.985 33.333 0.00 0.00 0.00 2.44
3758 3825 3.181397 CATTTGTTTGCGCCTTCTATGG 58.819 45.455 4.18 0.00 0.00 2.74
3818 3885 9.405587 GTGTTACAGCTAAAATTTGCTAAATGA 57.594 29.630 2.95 0.00 37.15 2.57
4117 4185 3.375299 GCTACCAGGAATGCTGTTTACAG 59.625 47.826 5.52 5.52 46.40 2.74
4255 4323 4.307032 AGGATACAACTCCAAATGCAGT 57.693 40.909 0.00 0.00 37.81 4.40
4260 4328 2.224867 ACAACTCCAAATGCAGTAGCCT 60.225 45.455 0.00 0.00 41.13 4.58
4274 4342 0.398696 TAGCCTTCCAACAAGCGGAA 59.601 50.000 0.00 0.00 40.26 4.30
4351 4419 3.265791 CTCCACAGCCTCATACAAAGTC 58.734 50.000 0.00 0.00 0.00 3.01
4352 4420 2.637382 TCCACAGCCTCATACAAAGTCA 59.363 45.455 0.00 0.00 0.00 3.41
4460 4528 1.079543 CTTCAGGAGGACACAGGCG 60.080 63.158 0.00 0.00 0.00 5.52
4551 4619 1.558294 GAAATTGGAGACGGTAGGGGT 59.442 52.381 0.00 0.00 0.00 4.95
4591 4659 1.547675 CCTGGTATGTTGGTGCCTTGT 60.548 52.381 0.00 0.00 0.00 3.16
4601 4669 2.507484 TGGTGCCTTGTTCATCTCTTG 58.493 47.619 0.00 0.00 0.00 3.02
4610 4678 3.819368 TGTTCATCTCTTGTTCAGGCAA 58.181 40.909 0.00 0.00 0.00 4.52
4615 4683 3.011566 TCTCTTGTTCAGGCAAAACCA 57.988 42.857 0.00 0.00 43.14 3.67
4627 4695 4.892965 AAACCAGCGTGGCCAGCA 62.893 61.111 23.46 0.00 42.67 4.41
4643 4711 2.950309 CCAGCAGATTCTCTTCCCAATG 59.050 50.000 0.00 0.00 0.00 2.82
4702 4770 5.230323 TGTGGTTACTGCTTGTAATGGTA 57.770 39.130 6.25 0.00 42.36 3.25
4716 4784 6.952773 TGTAATGGTAGGTGATATTTTGCC 57.047 37.500 0.00 0.00 0.00 4.52
4736 4807 2.050077 GCTTTGCACGGTCTTGGC 60.050 61.111 0.00 0.00 0.00 4.52
4758 4864 4.094146 GCCTTGAACTCTTGATAACTGAGC 59.906 45.833 0.00 0.00 0.00 4.26
4784 4890 8.144478 CAGTCCTATTGTAAATTGAGCTAGCTA 58.856 37.037 19.38 2.78 0.00 3.32
4821 4927 2.684881 GCCTAGCTGTTAACATGCACAT 59.315 45.455 23.12 11.49 0.00 3.21
4823 4929 2.642139 AGCTGTTAACATGCACATGC 57.358 45.000 23.12 15.65 42.39 4.06
4920 5034 2.284190 GCTTATGAGTCCTGCTGGTTC 58.716 52.381 9.73 9.29 34.23 3.62
4962 5076 5.877012 AGTCAGCATTTCTCATGTAATCGTT 59.123 36.000 0.00 0.00 0.00 3.85
4973 5087 7.033791 TCTCATGTAATCGTTAGTTTCAGTCC 58.966 38.462 0.00 0.00 0.00 3.85
4975 5089 8.058667 TCATGTAATCGTTAGTTTCAGTCCTA 57.941 34.615 0.00 0.00 0.00 2.94
5055 5171 3.629398 GGAGGGAGTAATGCTCAAATGTG 59.371 47.826 0.02 0.00 45.88 3.21
5096 5212 4.162096 CTGTAATAGCCTAGTAGCCACG 57.838 50.000 0.00 0.00 0.00 4.94
5136 5252 4.584743 CAGGGATATGACTACTGTAGCACA 59.415 45.833 14.55 14.45 0.00 4.57
5138 5254 5.661312 AGGGATATGACTACTGTAGCACAAA 59.339 40.000 14.55 4.62 0.00 2.83
5140 5256 5.986135 GGATATGACTACTGTAGCACAAAGG 59.014 44.000 14.55 0.00 0.00 3.11
5141 5257 6.183360 GGATATGACTACTGTAGCACAAAGGA 60.183 42.308 14.55 4.34 0.00 3.36
5143 5259 4.820897 TGACTACTGTAGCACAAAGGATG 58.179 43.478 14.55 0.00 0.00 3.51
5160 6425 3.467803 GGATGTGTATCCCTCCTTTTCG 58.532 50.000 0.00 0.00 46.03 3.46
5161 6426 3.467803 GATGTGTATCCCTCCTTTTCGG 58.532 50.000 0.00 0.00 0.00 4.30
5165 6430 4.286549 TGTGTATCCCTCCTTTTCGGTTTA 59.713 41.667 0.00 0.00 0.00 2.01
5167 6432 6.156602 TGTGTATCCCTCCTTTTCGGTTTATA 59.843 38.462 0.00 0.00 0.00 0.98
5168 6433 7.049754 GTGTATCCCTCCTTTTCGGTTTATAA 58.950 38.462 0.00 0.00 0.00 0.98
5170 6435 5.106876 TCCCTCCTTTTCGGTTTATAAGG 57.893 43.478 0.00 0.00 38.78 2.69
5174 6439 6.117488 CCTCCTTTTCGGTTTATAAGGCTTA 58.883 40.000 9.79 9.79 37.62 3.09
5180 6445 8.795842 TTTTCGGTTTATAAGGCTTATCTCAA 57.204 30.769 22.39 9.63 0.00 3.02
5181 6446 8.795842 TTTCGGTTTATAAGGCTTATCTCAAA 57.204 30.769 22.39 14.69 0.00 2.69
5182 6447 8.795842 TTCGGTTTATAAGGCTTATCTCAAAA 57.204 30.769 22.39 14.37 0.00 2.44
5184 6449 9.403583 TCGGTTTATAAGGCTTATCTCAAAATT 57.596 29.630 22.39 0.00 0.00 1.82
5231 6496 8.928448 AGATATATGTTGTCATTGGACTAGTGT 58.072 33.333 0.00 0.00 44.61 3.55
5232 6497 9.547753 GATATATGTTGTCATTGGACTAGTGTT 57.452 33.333 0.00 0.00 44.61 3.32
5245 7617 4.776308 GGACTAGTGTTTAGGGAAAGGAGA 59.224 45.833 0.00 0.00 0.00 3.71
5255 7627 1.339151 GGGAAAGGAGAACATGCTCGT 60.339 52.381 0.00 0.00 35.74 4.18
5257 7629 3.596214 GGAAAGGAGAACATGCTCGTTA 58.404 45.455 8.19 0.00 40.82 3.18
5261 7633 1.403780 GGAGAACATGCTCGTTACCGT 60.404 52.381 0.00 0.00 35.74 4.83
5267 7639 2.288334 ACATGCTCGTTACCGTTGTACA 60.288 45.455 0.00 0.00 35.01 2.90
5273 7645 1.192980 CGTTACCGTTGTACAAGCACC 59.807 52.381 8.98 0.00 0.00 5.01
5276 7648 2.170036 CGTTGTACAAGCACCGCG 59.830 61.111 8.98 0.00 0.00 6.46
5277 7649 2.554272 GTTGTACAAGCACCGCGG 59.446 61.111 26.86 26.86 0.00 6.46
5279 7651 1.004320 TTGTACAAGCACCGCGGAT 60.004 52.632 35.90 14.84 0.00 4.18
5280 7652 1.295357 TTGTACAAGCACCGCGGATG 61.295 55.000 35.90 25.95 0.00 3.51
5335 7707 4.838486 CCTCCTGCTCGTCGTCGC 62.838 72.222 0.00 0.00 36.96 5.19
5372 7744 3.402681 ATGAGCCGACCAGGGGTG 61.403 66.667 0.00 0.00 41.48 4.61
5373 7745 3.924013 ATGAGCCGACCAGGGGTGA 62.924 63.158 0.00 0.00 41.48 4.02
5374 7746 4.083862 GAGCCGACCAGGGGTGAC 62.084 72.222 0.00 0.00 41.48 3.67
5390 7764 0.827089 TGACAAACACATGGGGCAGG 60.827 55.000 0.00 0.00 0.00 4.85
5424 7799 4.324991 GGGCTTTGTCCCGACGGT 62.325 66.667 13.94 0.00 36.38 4.83
5425 7800 3.047877 GGCTTTGTCCCGACGGTG 61.048 66.667 13.94 4.52 0.00 4.94
5447 7822 1.489560 AAGGAGGAGGTGGTTTCCCG 61.490 60.000 0.00 0.00 35.20 5.14
5455 7835 1.673337 GTGGTTTCCCGGTGTAGGC 60.673 63.158 0.00 0.00 0.00 3.93
5460 7840 0.979187 TTTCCCGGTGTAGGCTAGGG 60.979 60.000 9.74 9.74 43.32 3.53
5464 7844 0.686769 CCGGTGTAGGCTAGGGTTCT 60.687 60.000 0.00 0.00 0.00 3.01
5469 7849 1.121378 GTAGGCTAGGGTTCTCCACC 58.879 60.000 0.00 0.00 46.46 4.61
5481 7861 1.568504 TCTCCACCCTTATCGCTTGT 58.431 50.000 0.00 0.00 0.00 3.16
5496 7878 0.385223 CTTGTGCAGCGAAACAGAGC 60.385 55.000 0.00 0.00 0.00 4.09
5499 7881 2.738521 GCAGCGAAACAGAGCCGA 60.739 61.111 0.00 0.00 0.00 5.54
5501 7883 2.002127 CAGCGAAACAGAGCCGATC 58.998 57.895 0.00 0.00 0.00 3.69
5515 7897 4.333926 AGAGCCGATCAATTTTAGCAAGTC 59.666 41.667 0.00 0.00 0.00 3.01
5518 7900 4.094887 GCCGATCAATTTTAGCAAGTCAGA 59.905 41.667 0.00 0.00 0.00 3.27
5523 7905 8.127327 CGATCAATTTTAGCAAGTCAGATTGAT 58.873 33.333 8.02 8.02 42.29 2.57
5529 7911 3.668447 AGCAAGTCAGATTGATGAACGT 58.332 40.909 0.00 0.00 31.55 3.99
5533 7915 5.669848 GCAAGTCAGATTGATGAACGTCTTC 60.670 44.000 0.00 0.00 31.55 2.87
5537 7919 6.375736 AGTCAGATTGATGAACGTCTTCTAGA 59.624 38.462 0.00 0.00 0.00 2.43
5538 7920 7.030165 GTCAGATTGATGAACGTCTTCTAGAA 58.970 38.462 4.81 4.81 0.00 2.10
5539 7921 7.542477 GTCAGATTGATGAACGTCTTCTAGAAA 59.458 37.037 6.63 0.00 0.00 2.52
5540 7922 8.088365 TCAGATTGATGAACGTCTTCTAGAAAA 58.912 33.333 6.63 0.00 0.00 2.29
5541 7923 8.712363 CAGATTGATGAACGTCTTCTAGAAAAA 58.288 33.333 6.63 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.299297 CGGGCGGGAGAATCTAAACTAT 59.701 50.000 0.00 0.00 33.73 2.12
18 19 1.745320 GAGCGGGCGGGAGAATCTAA 61.745 60.000 0.00 0.00 33.73 2.10
184 191 4.560716 GCCACAAAACCCTACTGGAATTTC 60.561 45.833 0.00 0.00 38.00 2.17
388 395 4.318831 GCGTGTTAATGCCTAACTATCTGC 60.319 45.833 7.18 0.00 40.62 4.26
394 401 2.027561 TCCAGCGTGTTAATGCCTAACT 60.028 45.455 7.18 0.00 40.62 2.24
444 451 2.229062 CTCTCACAAAGCAGACCTACGA 59.771 50.000 0.00 0.00 0.00 3.43
455 462 5.121811 CCACCATAATCTCCTCTCACAAAG 58.878 45.833 0.00 0.00 0.00 2.77
457 464 3.118261 GCCACCATAATCTCCTCTCACAA 60.118 47.826 0.00 0.00 0.00 3.33
468 475 2.297701 ACGACAATGGCCACCATAATC 58.702 47.619 8.16 0.00 44.40 1.75
474 481 1.339929 AGAAAAACGACAATGGCCACC 59.660 47.619 8.16 0.00 0.00 4.61
507 514 1.009829 GAGCATACCGAAGCCACAAG 58.990 55.000 0.00 0.00 0.00 3.16
514 521 6.867662 AATTTATTCCAGAGCATACCGAAG 57.132 37.500 0.00 0.00 0.00 3.79
531 538 6.977213 GGCATACCGAAACCACATAATTTAT 58.023 36.000 0.00 0.00 0.00 1.40
557 587 0.321021 GGGCCATTCATGCACACAAA 59.679 50.000 4.39 0.00 30.65 2.83
576 606 8.933807 TCATGCACCATAAAACAAAATTACATG 58.066 29.630 0.00 0.00 0.00 3.21
580 610 8.944029 CCATTCATGCACCATAAAACAAAATTA 58.056 29.630 0.00 0.00 0.00 1.40
606 636 9.620259 AAACTGAAAATTCTGGATAGGATAGAC 57.380 33.333 5.26 0.00 0.00 2.59
607 637 9.618890 CAAACTGAAAATTCTGGATAGGATAGA 57.381 33.333 5.26 0.00 0.00 1.98
608 638 9.618890 TCAAACTGAAAATTCTGGATAGGATAG 57.381 33.333 5.26 0.00 0.00 2.08
609 639 9.618890 CTCAAACTGAAAATTCTGGATAGGATA 57.381 33.333 5.26 0.00 0.00 2.59
610 640 7.559170 CCTCAAACTGAAAATTCTGGATAGGAT 59.441 37.037 5.26 0.00 0.00 3.24
664 695 5.174579 CACTGTGCATCTGTGTAATATCTCG 59.825 44.000 13.98 0.00 39.86 4.04
667 698 5.088141 GCACTGTGCATCTGTGTAATATC 57.912 43.478 26.70 0.00 44.26 1.63
689 720 3.504906 AGTCAAGTGAAATGCTCCATGTG 59.495 43.478 0.00 0.00 0.00 3.21
700 747 9.016438 GGTGGGTAAAATTATAGTCAAGTGAAA 57.984 33.333 0.00 0.00 0.00 2.69
852 900 8.685838 ACTTCTTAAGTTGCAGTTACCAAATA 57.314 30.769 1.63 0.00 39.04 1.40
1026 1074 3.084039 GTTCCACTGATCAATTGGCTGA 58.916 45.455 15.52 4.56 0.00 4.26
1150 1198 3.172106 TGGCCCGTCTCCACCAAA 61.172 61.111 0.00 0.00 0.00 3.28
1161 1209 2.438434 GATCCACCAACTGGCCCG 60.438 66.667 0.00 0.00 40.39 6.13
1284 1332 1.543429 GGATATCCTTCCAGGGTTGCG 60.543 57.143 14.97 0.00 35.59 4.85
1333 1381 2.860735 CTGTAGTAGCATCGGCACTTTC 59.139 50.000 0.00 0.00 44.61 2.62
1379 1427 5.368256 TGTCTGACTAACTTCTTCGGTAC 57.632 43.478 9.51 0.00 0.00 3.34
1430 1478 1.615883 CCTCTGTAGTAGCATCGGCAT 59.384 52.381 0.00 0.00 44.61 4.40
1434 1482 6.073327 TGAATAACCTCTGTAGTAGCATCG 57.927 41.667 0.00 0.00 0.00 3.84
1545 1593 4.727507 ACTAACTACAGCATCCTGACTG 57.272 45.455 0.00 0.00 41.77 3.51
1697 1745 5.221722 ACAAGAGGAGCATCACTAACTTCAA 60.222 40.000 0.00 0.00 36.25 2.69
1768 1816 1.112113 TCTAGGTGATCTCCGTTGGC 58.888 55.000 8.14 0.00 0.00 4.52
1842 1890 7.384660 GTCTTCTCTGCAATAATCTCACTATGG 59.615 40.741 0.00 0.00 0.00 2.74
1867 1915 1.280421 GATGGTGCCTTCTTCTGGAGT 59.720 52.381 0.00 0.00 0.00 3.85
2009 2057 1.134367 GTGACGCACTAGCATCAGGTA 59.866 52.381 3.20 0.00 44.46 3.08
2010 2058 0.108615 GTGACGCACTAGCATCAGGT 60.109 55.000 3.20 0.00 44.46 4.00
2013 2061 1.066929 ACATGTGACGCACTAGCATCA 60.067 47.619 0.00 0.00 41.20 3.07
2088 2136 7.124750 TCACTCAAATCTATCACAGGAATCAGA 59.875 37.037 0.00 0.00 0.00 3.27
2225 2273 5.297776 AGAACACACTTGATTTGAGAACCTG 59.702 40.000 0.00 0.00 0.00 4.00
2249 2297 6.936335 AGTTGATATATTGTCATGCGGAATCA 59.064 34.615 0.00 0.00 0.00 2.57
2436 2484 9.056005 TCCAAGATCATATTGGTTTTAGATTCG 57.944 33.333 10.90 0.00 46.11 3.34
2744 2807 1.066430 CAACACTGTATGCGTAGGGGT 60.066 52.381 0.00 0.00 0.00 4.95
2819 2882 4.098894 TGGAACGGAGGGAGTACTTTAAT 58.901 43.478 0.00 0.00 0.00 1.40
2820 2883 3.509442 TGGAACGGAGGGAGTACTTTAA 58.491 45.455 0.00 0.00 0.00 1.52
2821 2884 3.173953 TGGAACGGAGGGAGTACTTTA 57.826 47.619 0.00 0.00 0.00 1.85
2822 2885 2.019807 TGGAACGGAGGGAGTACTTT 57.980 50.000 0.00 0.00 0.00 2.66
2823 2886 2.019807 TTGGAACGGAGGGAGTACTT 57.980 50.000 0.00 0.00 0.00 2.24
2825 2888 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
2826 2889 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2827 2890 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2828 2891 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2829 2892 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2830 2893 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2831 2894 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2832 2895 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2833 2896 2.228582 TCGACGAGTAATTTGGAACGGA 59.771 45.455 0.00 0.00 0.00 4.69
2834 2897 2.598589 TCGACGAGTAATTTGGAACGG 58.401 47.619 0.00 0.00 0.00 4.44
2835 2898 3.855379 TCATCGACGAGTAATTTGGAACG 59.145 43.478 3.01 0.00 0.00 3.95
2837 2900 6.183360 CCATTTCATCGACGAGTAATTTGGAA 60.183 38.462 3.01 0.00 0.00 3.53
2838 2901 5.293324 CCATTTCATCGACGAGTAATTTGGA 59.707 40.000 3.01 0.00 0.00 3.53
2839 2902 5.293324 TCCATTTCATCGACGAGTAATTTGG 59.707 40.000 3.01 9.94 0.00 3.28
2840 2903 6.344572 TCCATTTCATCGACGAGTAATTTG 57.655 37.500 3.01 0.00 0.00 2.32
2841 2904 6.538742 ACATCCATTTCATCGACGAGTAATTT 59.461 34.615 3.01 0.00 0.00 1.82
2842 2905 6.049149 ACATCCATTTCATCGACGAGTAATT 58.951 36.000 3.01 0.00 0.00 1.40
2843 2906 5.601662 ACATCCATTTCATCGACGAGTAAT 58.398 37.500 3.01 0.09 0.00 1.89
2844 2907 5.006153 ACATCCATTTCATCGACGAGTAA 57.994 39.130 3.01 0.00 0.00 2.24
2845 2908 4.649088 ACATCCATTTCATCGACGAGTA 57.351 40.909 3.01 0.00 0.00 2.59
2846 2909 3.526931 ACATCCATTTCATCGACGAGT 57.473 42.857 3.01 0.00 0.00 4.18
2847 2910 6.530913 AAATACATCCATTTCATCGACGAG 57.469 37.500 3.01 0.00 0.00 4.18
2848 2911 7.430441 TCTAAATACATCCATTTCATCGACGA 58.570 34.615 0.00 0.00 30.84 4.20
2849 2912 7.637709 TCTAAATACATCCATTTCATCGACG 57.362 36.000 0.00 0.00 30.84 5.12
2850 2913 9.046296 AGTTCTAAATACATCCATTTCATCGAC 57.954 33.333 0.00 0.00 30.84 4.20
2879 2942 8.191446 GCACGTATGGATGTATCTAGATGTATT 58.809 37.037 15.79 0.00 29.44 1.89
2880 2943 7.467403 CGCACGTATGGATGTATCTAGATGTAT 60.467 40.741 15.79 9.11 29.44 2.29
2881 2944 6.183360 CGCACGTATGGATGTATCTAGATGTA 60.183 42.308 15.79 4.44 29.44 2.29
2882 2945 5.392057 CGCACGTATGGATGTATCTAGATGT 60.392 44.000 15.79 1.25 30.36 3.06
2883 2946 5.030936 CGCACGTATGGATGTATCTAGATG 58.969 45.833 15.79 0.00 0.00 2.90
2884 2947 4.941873 TCGCACGTATGGATGTATCTAGAT 59.058 41.667 10.73 10.73 0.00 1.98
2885 2948 4.153655 GTCGCACGTATGGATGTATCTAGA 59.846 45.833 0.00 0.00 0.00 2.43
2886 2949 4.083484 TGTCGCACGTATGGATGTATCTAG 60.083 45.833 0.00 0.00 0.00 2.43
2887 2950 3.816523 TGTCGCACGTATGGATGTATCTA 59.183 43.478 0.00 0.00 0.00 1.98
2888 2951 2.621526 TGTCGCACGTATGGATGTATCT 59.378 45.455 0.00 0.00 0.00 1.98
2889 2952 3.007979 TGTCGCACGTATGGATGTATC 57.992 47.619 0.00 0.00 0.00 2.24
2890 2953 3.181479 ACTTGTCGCACGTATGGATGTAT 60.181 43.478 0.00 0.00 0.00 2.29
2891 2954 2.164827 ACTTGTCGCACGTATGGATGTA 59.835 45.455 0.00 0.00 0.00 2.29
2892 2955 1.067142 ACTTGTCGCACGTATGGATGT 60.067 47.619 0.00 0.00 0.00 3.06
2893 2956 1.640428 ACTTGTCGCACGTATGGATG 58.360 50.000 0.00 0.00 0.00 3.51
2894 2957 3.513680 TTACTTGTCGCACGTATGGAT 57.486 42.857 0.00 0.00 0.00 3.41
2895 2958 3.513680 ATTACTTGTCGCACGTATGGA 57.486 42.857 0.00 0.00 0.00 3.41
2896 2959 3.301579 CGAATTACTTGTCGCACGTATGG 60.302 47.826 0.00 0.00 0.00 2.74
2897 2960 3.301579 CCGAATTACTTGTCGCACGTATG 60.302 47.826 0.00 0.00 35.93 2.39
2898 2961 2.855963 CCGAATTACTTGTCGCACGTAT 59.144 45.455 0.00 0.00 35.93 3.06
2899 2962 2.095314 TCCGAATTACTTGTCGCACGTA 60.095 45.455 0.00 0.00 35.93 3.57
2900 2963 1.065358 CCGAATTACTTGTCGCACGT 58.935 50.000 0.00 0.00 35.93 4.49
2901 2964 1.342555 TCCGAATTACTTGTCGCACG 58.657 50.000 0.00 0.00 35.93 5.34
2902 2965 2.471749 CGTTCCGAATTACTTGTCGCAC 60.472 50.000 0.00 0.00 35.93 5.34
2903 2966 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
2904 2967 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2905 2968 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
2906 2969 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2907 2970 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2908 2971 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2909 2972 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2910 2973 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2911 2974 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2912 2975 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2913 2976 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
2914 2977 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
2915 2978 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
2916 2979 2.374504 AGATATACTCCCTCCGTTCCGA 59.625 50.000 0.00 0.00 0.00 4.55
2917 2980 2.792878 AGATATACTCCCTCCGTTCCG 58.207 52.381 0.00 0.00 0.00 4.30
2918 2981 5.548181 AAAAGATATACTCCCTCCGTTCC 57.452 43.478 0.00 0.00 0.00 3.62
2919 2982 6.702282 CAGAAAAAGATATACTCCCTCCGTTC 59.298 42.308 0.00 0.00 0.00 3.95
2920 2983 6.156429 ACAGAAAAAGATATACTCCCTCCGTT 59.844 38.462 0.00 0.00 0.00 4.44
2921 2984 5.661759 ACAGAAAAAGATATACTCCCTCCGT 59.338 40.000 0.00 0.00 0.00 4.69
2922 2985 5.986135 CACAGAAAAAGATATACTCCCTCCG 59.014 44.000 0.00 0.00 0.00 4.63
2923 2986 6.987404 GTCACAGAAAAAGATATACTCCCTCC 59.013 42.308 0.00 0.00 0.00 4.30
2924 2987 7.556844 TGTCACAGAAAAAGATATACTCCCTC 58.443 38.462 0.00 0.00 0.00 4.30
2925 2988 7.496346 TGTCACAGAAAAAGATATACTCCCT 57.504 36.000 0.00 0.00 0.00 4.20
2926 2989 8.738645 AATGTCACAGAAAAAGATATACTCCC 57.261 34.615 0.00 0.00 0.00 4.30
3059 3123 6.584184 CGTACAAGAGCAGAATATATGAGGTG 59.416 42.308 0.00 0.00 0.00 4.00
3182 3249 9.090692 CATGATTTCTCCATTTAAACCATTGAC 57.909 33.333 0.00 0.00 0.00 3.18
3265 3332 3.039202 GCGCTGACGTTTGATGGGG 62.039 63.158 0.00 0.00 42.83 4.96
3297 3364 8.140677 TGATGTTTGTTGCTTAAGAATTTTGG 57.859 30.769 6.67 0.00 0.00 3.28
3378 3445 2.189594 TGAATCAGACCTGCCAACAG 57.810 50.000 0.00 0.00 44.05 3.16
3426 3493 1.757699 GCCGAGAAACCTCACCTATCT 59.242 52.381 0.00 0.00 0.00 1.98
3703 3770 4.274459 CCTCTAACAATATTCTGCACAGGC 59.726 45.833 0.00 0.00 41.68 4.85
3818 3885 6.475402 GCTAAAGCACAAACTGTTGTTGTTAT 59.525 34.615 0.00 0.00 46.01 1.89
4225 4293 2.420687 GGAGTTGTATCCTTGCTGAGGG 60.421 54.545 6.83 0.00 46.31 4.30
4255 4323 0.398696 TTCCGCTTGTTGGAAGGCTA 59.601 50.000 0.00 0.00 40.51 3.93
4260 4328 1.877443 GTTAGCTTCCGCTTGTTGGAA 59.123 47.619 0.00 0.00 46.47 3.53
4274 4342 2.171003 GGAAGCATGGTTTGGTTAGCT 58.829 47.619 12.13 0.00 45.76 3.32
4351 4419 3.009473 CCTGGGGTTAGATGTGGGATATG 59.991 52.174 0.00 0.00 0.00 1.78
4352 4420 3.260205 CCTGGGGTTAGATGTGGGATAT 58.740 50.000 0.00 0.00 0.00 1.63
4460 4528 4.320641 GGCAAGTAGTAGATCATCGGAGAC 60.321 50.000 0.00 0.00 42.51 3.36
4551 4619 1.293498 GCGAGCAGGAGGTTTGAGA 59.707 57.895 0.00 0.00 0.00 3.27
4573 4641 2.235016 GAACAAGGCACCAACATACCA 58.765 47.619 0.00 0.00 0.00 3.25
4591 4659 4.037923 GGTTTTGCCTGAACAAGAGATGAA 59.962 41.667 0.00 0.00 0.00 2.57
4601 4669 0.594796 CACGCTGGTTTTGCCTGAAC 60.595 55.000 0.00 0.00 38.33 3.18
4610 4678 4.892965 TGCTGGCCACGCTGGTTT 62.893 61.111 22.36 0.00 40.46 3.27
4615 4683 2.437359 GAATCTGCTGGCCACGCT 60.437 61.111 22.36 7.35 0.00 5.07
4643 4711 2.888998 GCAACACCAACGGTCGGAC 61.889 63.158 0.00 0.00 31.02 4.79
4702 4770 4.824289 CAAAGCTTGGCAAAATATCACCT 58.176 39.130 0.00 0.00 0.00 4.00
4716 4784 0.318107 CCAAGACCGTGCAAAGCTTG 60.318 55.000 0.00 10.98 36.58 4.01
4736 4807 5.240891 TGCTCAGTTATCAAGAGTTCAAGG 58.759 41.667 0.00 0.00 0.00 3.61
4758 4864 6.989169 AGCTAGCTCAATTTACAATAGGACTG 59.011 38.462 12.68 0.00 0.00 3.51
4784 4890 3.561725 GCTAGGCAGACAAGCGAAAATAT 59.438 43.478 0.00 0.00 34.64 1.28
4821 4927 1.513622 TCGGTGATCGAAATCCGCA 59.486 52.632 16.75 6.96 45.86 5.69
4920 5034 2.673368 GACTTGATACCGCAACAAGAGG 59.327 50.000 12.04 0.00 42.12 3.69
4975 5089 8.462016 CCTCGAAAAGAAATTTCAGAACCATAT 58.538 33.333 19.99 0.00 46.42 1.78
4997 5111 2.841442 AAAGAGACCAAGTTCCCTCG 57.159 50.000 0.00 0.00 0.00 4.63
5086 5202 1.538512 GGTCGATATGCGTGGCTACTA 59.461 52.381 0.00 0.00 41.80 1.82
5087 5203 0.314302 GGTCGATATGCGTGGCTACT 59.686 55.000 0.00 0.00 41.80 2.57
5088 5204 0.031585 TGGTCGATATGCGTGGCTAC 59.968 55.000 0.00 0.00 41.80 3.58
5089 5205 0.031585 GTGGTCGATATGCGTGGCTA 59.968 55.000 0.00 0.00 41.80 3.93
5090 5206 1.227263 GTGGTCGATATGCGTGGCT 60.227 57.895 0.00 0.00 41.80 4.75
5091 5207 2.585869 CGTGGTCGATATGCGTGGC 61.586 63.158 0.00 0.00 41.80 5.01
5092 5208 1.065109 TCGTGGTCGATATGCGTGG 59.935 57.895 0.00 0.00 41.35 4.94
5093 5209 4.702020 TCGTGGTCGATATGCGTG 57.298 55.556 0.00 0.00 41.35 5.34
5113 5229 4.584743 TGTGCTACAGTAGTCATATCCCTG 59.415 45.833 9.42 0.00 0.00 4.45
5138 5254 5.967806 CCGAAAAGGAGGGATACACATCCT 61.968 50.000 3.79 0.00 46.01 3.24
5140 5256 3.118371 ACCGAAAAGGAGGGATACACATC 60.118 47.826 0.00 0.00 45.00 3.06
5141 5257 2.844348 ACCGAAAAGGAGGGATACACAT 59.156 45.455 0.00 0.00 45.00 3.21
5143 5259 3.345508 AACCGAAAAGGAGGGATACAC 57.654 47.619 0.00 0.00 45.00 2.90
5145 5261 6.709397 CCTTATAAACCGAAAAGGAGGGATAC 59.291 42.308 0.00 0.00 45.00 2.24
5148 5264 4.627013 GCCTTATAAACCGAAAAGGAGGGA 60.627 45.833 4.19 0.00 45.00 4.20
5149 5265 3.630769 GCCTTATAAACCGAAAAGGAGGG 59.369 47.826 4.19 0.00 45.00 4.30
5150 5266 4.524053 AGCCTTATAAACCGAAAAGGAGG 58.476 43.478 4.19 0.00 45.00 4.30
5151 5267 7.715686 AGATAAGCCTTATAAACCGAAAAGGAG 59.284 37.037 0.00 0.00 45.00 3.69
5152 5268 7.571025 AGATAAGCCTTATAAACCGAAAAGGA 58.429 34.615 0.00 0.00 45.00 3.36
5157 6422 8.795842 TTTTGAGATAAGCCTTATAAACCGAA 57.204 30.769 0.00 0.00 0.00 4.30
5206 6471 9.547753 AACACTAGTCCAATGACAACATATATC 57.452 33.333 0.00 0.00 44.33 1.63
5207 6472 9.905713 AAACACTAGTCCAATGACAACATATAT 57.094 29.630 0.00 0.00 44.33 0.86
5210 6475 7.822334 CCTAAACACTAGTCCAATGACAACATA 59.178 37.037 0.00 0.00 44.33 2.29
5212 6477 5.995282 CCTAAACACTAGTCCAATGACAACA 59.005 40.000 0.00 0.00 44.33 3.33
5213 6478 5.411669 CCCTAAACACTAGTCCAATGACAAC 59.588 44.000 0.00 0.00 44.33 3.32
5216 6481 5.416271 TCCCTAAACACTAGTCCAATGAC 57.584 43.478 0.00 0.00 42.09 3.06
5220 6485 4.909088 TCCTTTCCCTAAACACTAGTCCAA 59.091 41.667 0.00 0.00 0.00 3.53
5221 6486 4.495565 TCCTTTCCCTAAACACTAGTCCA 58.504 43.478 0.00 0.00 0.00 4.02
5222 6487 4.776308 TCTCCTTTCCCTAAACACTAGTCC 59.224 45.833 0.00 0.00 0.00 3.85
5223 6488 5.997384 TCTCCTTTCCCTAAACACTAGTC 57.003 43.478 0.00 0.00 0.00 2.59
5227 6492 5.316987 CATGTTCTCCTTTCCCTAAACACT 58.683 41.667 0.00 0.00 30.26 3.55
5228 6493 4.082733 GCATGTTCTCCTTTCCCTAAACAC 60.083 45.833 0.00 0.00 30.26 3.32
5230 6495 4.336280 AGCATGTTCTCCTTTCCCTAAAC 58.664 43.478 0.00 0.00 0.00 2.01
5231 6496 4.589908 GAGCATGTTCTCCTTTCCCTAAA 58.410 43.478 1.76 0.00 0.00 1.85
5232 6497 3.369471 CGAGCATGTTCTCCTTTCCCTAA 60.369 47.826 8.01 0.00 0.00 2.69
5255 7627 1.500108 CGGTGCTTGTACAACGGTAA 58.500 50.000 3.59 0.00 46.85 2.85
5257 7629 4.036977 CGGTGCTTGTACAACGGT 57.963 55.556 3.59 0.00 46.85 4.83
5261 7633 1.004320 ATCCGCGGTGCTTGTACAA 60.004 52.632 27.15 8.28 0.00 2.41
5335 7707 4.885270 TGGTGTTGGCGTGTGGGG 62.885 66.667 0.00 0.00 0.00 4.96
5372 7744 0.827507 ACCTGCCCCATGTGTTTGTC 60.828 55.000 0.00 0.00 0.00 3.18
5373 7745 0.480690 TACCTGCCCCATGTGTTTGT 59.519 50.000 0.00 0.00 0.00 2.83
5374 7746 0.887933 GTACCTGCCCCATGTGTTTG 59.112 55.000 0.00 0.00 0.00 2.93
5422 7797 2.352805 CACCTCCTCCTTGCCACC 59.647 66.667 0.00 0.00 0.00 4.61
5424 7799 1.360393 AAACCACCTCCTCCTTGCCA 61.360 55.000 0.00 0.00 0.00 4.92
5425 7800 0.609406 GAAACCACCTCCTCCTTGCC 60.609 60.000 0.00 0.00 0.00 4.52
5447 7822 1.121378 GGAGAACCCTAGCCTACACC 58.879 60.000 0.00 0.00 0.00 4.16
5460 7840 2.280628 CAAGCGATAAGGGTGGAGAAC 58.719 52.381 0.00 0.00 0.00 3.01
5464 7844 0.392461 GCACAAGCGATAAGGGTGGA 60.392 55.000 0.00 0.00 0.00 4.02
5481 7861 2.786539 ATCGGCTCTGTTTCGCTGCA 62.787 55.000 0.00 0.00 32.64 4.41
5496 7878 5.801350 TCTGACTTGCTAAAATTGATCGG 57.199 39.130 0.00 0.00 0.00 4.18
5499 7881 8.963725 TCATCAATCTGACTTGCTAAAATTGAT 58.036 29.630 0.00 0.00 40.91 2.57
5501 7883 8.857216 GTTCATCAATCTGACTTGCTAAAATTG 58.143 33.333 0.00 0.00 0.00 2.32
5515 7897 7.818493 TTTCTAGAAGACGTTCATCAATCTG 57.182 36.000 5.12 0.00 34.82 2.90


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

AutoCloner maintained by Alex Coulton.