Multiple sequence alignment - TraesCS6B01G094200

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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 TraesCS6B01G094200 chr6B 100.000 4599 0 0 1 4599 70572593 70567995 0.000000e+00 8493.0
1 TraesCS6B01G094200 chr6B 80.938 640 109 12 2037 2668 70756413 70755779 1.150000e-135 494.0
2 TraesCS6B01G094200 chr6B 74.785 932 186 25 1000 1905 69720083 69719175 1.560000e-99 374.0
3 TraesCS6B01G094200 chr6B 97.778 180 4 0 3020 3199 281231346 281231167 1.240000e-80 311.0
4 TraesCS6B01G094200 chr6B 81.944 72 11 2 3808 3879 69956674 69956605 4.970000e-05 60.2
5 TraesCS6B01G094200 chr6D 93.563 2206 132 10 819 3016 33312680 33310477 0.000000e+00 3278.0
6 TraesCS6B01G094200 chr6D 95.419 895 36 3 3195 4088 33310497 33309607 0.000000e+00 1421.0
7 TraesCS6B01G094200 chr6D 78.216 2029 358 61 907 2917 34323814 34321852 0.000000e+00 1221.0
8 TraesCS6B01G094200 chr6D 78.374 1845 321 57 1013 2808 33253332 33251517 0.000000e+00 1125.0
9 TraesCS6B01G094200 chr6D 84.272 1030 146 13 936 1958 34297653 34296633 0.000000e+00 990.0
10 TraesCS6B01G094200 chr6D 80.623 1027 185 12 935 1958 34306034 34305019 0.000000e+00 782.0
11 TraesCS6B01G094200 chr6D 91.731 520 32 3 4087 4599 33309560 33309045 0.000000e+00 712.0
12 TraesCS6B01G094200 chr6D 83.500 600 78 17 2007 2592 33304573 33303981 1.460000e-149 540.0
13 TraesCS6B01G094200 chr6D 78.178 889 158 27 2037 2912 34296586 34295721 6.770000e-148 534.0
14 TraesCS6B01G094200 chr6D 76.598 970 186 32 1013 1957 33305607 33304654 3.200000e-136 496.0
15 TraesCS6B01G094200 chr6D 81.944 72 11 2 3808 3879 33244070 33244001 4.970000e-05 60.2
16 TraesCS6B01G094200 chr6A 90.647 1700 126 12 1335 3019 38111512 38109831 0.000000e+00 2228.0
17 TraesCS6B01G094200 chr6A 93.230 901 34 17 3195 4088 38109854 38108974 0.000000e+00 1301.0
18 TraesCS6B01G094200 chr6A 77.841 2103 363 65 870 2917 38461815 38459761 0.000000e+00 1206.0
19 TraesCS6B01G094200 chr6A 78.791 1853 305 60 1012 2808 37845608 37843788 0.000000e+00 1164.0
20 TraesCS6B01G094200 chr6A 83.408 1115 117 30 819 1915 38403539 38402475 0.000000e+00 972.0
21 TraesCS6B01G094200 chr6A 91.860 516 35 3 4087 4599 38108927 38108416 0.000000e+00 713.0
22 TraesCS6B01G094200 chr6A 84.507 710 97 9 1255 1958 38447196 38446494 0.000000e+00 689.0
23 TraesCS6B01G094200 chr6A 77.864 899 154 30 2037 2912 38446447 38445571 2.450000e-142 516.0
24 TraesCS6B01G094200 chr6A 74.946 930 188 26 994 1902 37708472 37707567 7.220000e-103 385.0
25 TraesCS6B01G094200 chr6A 97.253 182 5 0 3018 3199 605361584 605361403 4.470000e-80 309.0
26 TraesCS6B01G094200 chr6A 88.479 217 24 1 829 1045 38112919 38112704 1.270000e-65 261.0
27 TraesCS6B01G094200 chr3D 87.890 801 85 7 1 789 101541944 101542744 0.000000e+00 931.0
28 TraesCS6B01G094200 chr3D 97.778 180 4 0 3019 3198 153512402 153512223 1.240000e-80 311.0
29 TraesCS6B01G094200 chr3A 87.229 783 99 1 4 785 535575818 535575036 0.000000e+00 891.0
30 TraesCS6B01G094200 chr4A 74.873 1974 405 62 1070 3005 647340321 647338401 0.000000e+00 813.0
31 TraesCS6B01G094200 chr4A 94.819 193 10 0 3007 3199 143502321 143502129 7.480000e-78 302.0
32 TraesCS6B01G094200 chr2A 79.099 1110 201 22 822 1909 766995003 766993903 0.000000e+00 736.0
33 TraesCS6B01G094200 chr2A 97.238 181 4 1 3019 3199 639066125 639065946 5.780000e-79 305.0
34 TraesCS6B01G094200 chr2D 81.633 784 132 11 9 786 507465052 507465829 1.400000e-179 640.0
35 TraesCS6B01G094200 chr1A 90.291 412 39 1 324 734 351888443 351888032 5.240000e-149 538.0
36 TraesCS6B01G094200 chr1A 88.520 331 32 1 4 328 351890496 351890166 3.330000e-106 396.0
37 TraesCS6B01G094200 chr1A 97.778 180 4 0 3019 3198 82526062 82525883 1.240000e-80 311.0
38 TraesCS6B01G094200 chr3B 75.095 791 169 21 12 787 201879206 201878429 1.230000e-90 344.0
39 TraesCS6B01G094200 chr3B 93.564 202 13 0 3012 3213 91431069 91430868 7.480000e-78 302.0
40 TraesCS6B01G094200 chr3B 81.792 346 58 5 444 785 141074324 141074668 7.530000e-73 285.0
41 TraesCS6B01G094200 chr3B 100.000 30 0 0 4409 4438 729379148 729379177 6.430000e-04 56.5
42 TraesCS6B01G094200 chr7B 97.253 182 5 0 3016 3197 46028674 46028493 4.470000e-80 309.0
43 TraesCS6B01G094200 chr7B 77.087 515 109 8 276 786 713278818 713278309 5.820000e-74 289.0
44 TraesCS6B01G094200 chr7B 100.000 30 0 0 4409 4438 2923415 2923444 6.430000e-04 56.5
45 TraesCS6B01G094200 chr2B 95.789 190 8 0 3009 3198 121669703 121669514 1.610000e-79 307.0
46 TraesCS6B01G094200 chr2B 100.000 30 0 0 4409 4438 694883391 694883420 6.430000e-04 56.5
47 TraesCS6B01G094200 chr5B 74.041 782 180 18 12 780 608345757 608344986 9.670000e-77 298.0
48 TraesCS6B01G094200 chr7D 73.924 790 166 28 926 1704 40646489 40647249 9.740000e-72 281.0
49 TraesCS6B01G094200 chr7A 74.952 519 112 17 278 787 637953975 637953466 5.990000e-54 222.0
50 TraesCS6B01G094200 chr7A 71.843 792 204 13 3 785 654470908 654471689 4.660000e-50 209.0
51 TraesCS6B01G094200 chr4B 83.077 65 7 4 4409 4472 552773991 552773930 6.430000e-04 56.5
52 TraesCS6B01G094200 chr1B 83.077 65 7 4 4409 4472 454915922 454915861 6.430000e-04 56.5


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 TraesCS6B01G094200 chr6B 70567995 70572593 4598 True 8493.00 8493 100.0000 1 4599 1 chr6B.!!$R3 4598
1 TraesCS6B01G094200 chr6B 70755779 70756413 634 True 494.00 494 80.9380 2037 2668 1 chr6B.!!$R4 631
2 TraesCS6B01G094200 chr6B 69719175 69720083 908 True 374.00 374 74.7850 1000 1905 1 chr6B.!!$R1 905
3 TraesCS6B01G094200 chr6D 33303981 33312680 8699 True 1289.40 3278 88.1622 819 4599 5 chr6D.!!$R5 3780
4 TraesCS6B01G094200 chr6D 34321852 34323814 1962 True 1221.00 1221 78.2160 907 2917 1 chr6D.!!$R4 2010
5 TraesCS6B01G094200 chr6D 33251517 33253332 1815 True 1125.00 1125 78.3740 1013 2808 1 chr6D.!!$R2 1795
6 TraesCS6B01G094200 chr6D 34305019 34306034 1015 True 782.00 782 80.6230 935 1958 1 chr6D.!!$R3 1023
7 TraesCS6B01G094200 chr6D 34295721 34297653 1932 True 762.00 990 81.2250 936 2912 2 chr6D.!!$R6 1976
8 TraesCS6B01G094200 chr6A 38459761 38461815 2054 True 1206.00 1206 77.8410 870 2917 1 chr6A.!!$R4 2047
9 TraesCS6B01G094200 chr6A 37843788 37845608 1820 True 1164.00 1164 78.7910 1012 2808 1 chr6A.!!$R2 1796
10 TraesCS6B01G094200 chr6A 38108416 38112919 4503 True 1125.75 2228 91.0540 829 4599 4 chr6A.!!$R6 3770
11 TraesCS6B01G094200 chr6A 38402475 38403539 1064 True 972.00 972 83.4080 819 1915 1 chr6A.!!$R3 1096
12 TraesCS6B01G094200 chr6A 38445571 38447196 1625 True 602.50 689 81.1855 1255 2912 2 chr6A.!!$R7 1657
13 TraesCS6B01G094200 chr6A 37707567 37708472 905 True 385.00 385 74.9460 994 1902 1 chr6A.!!$R1 908
14 TraesCS6B01G094200 chr3D 101541944 101542744 800 False 931.00 931 87.8900 1 789 1 chr3D.!!$F1 788
15 TraesCS6B01G094200 chr3A 535575036 535575818 782 True 891.00 891 87.2290 4 785 1 chr3A.!!$R1 781
16 TraesCS6B01G094200 chr4A 647338401 647340321 1920 True 813.00 813 74.8730 1070 3005 1 chr4A.!!$R2 1935
17 TraesCS6B01G094200 chr2A 766993903 766995003 1100 True 736.00 736 79.0990 822 1909 1 chr2A.!!$R2 1087
18 TraesCS6B01G094200 chr2D 507465052 507465829 777 False 640.00 640 81.6330 9 786 1 chr2D.!!$F1 777
19 TraesCS6B01G094200 chr1A 351888032 351890496 2464 True 467.00 538 89.4055 4 734 2 chr1A.!!$R2 730
20 TraesCS6B01G094200 chr3B 201878429 201879206 777 True 344.00 344 75.0950 12 787 1 chr3B.!!$R2 775
21 TraesCS6B01G094200 chr7B 713278309 713278818 509 True 289.00 289 77.0870 276 786 1 chr7B.!!$R2 510
22 TraesCS6B01G094200 chr5B 608344986 608345757 771 True 298.00 298 74.0410 12 780 1 chr5B.!!$R1 768
23 TraesCS6B01G094200 chr7D 40646489 40647249 760 False 281.00 281 73.9240 926 1704 1 chr7D.!!$F1 778
24 TraesCS6B01G094200 chr7A 637953466 637953975 509 True 222.00 222 74.9520 278 787 1 chr7A.!!$R1 509
25 TraesCS6B01G094200 chr7A 654470908 654471689 781 False 209.00 209 71.8430 3 785 1 chr7A.!!$F1 782

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
404 2155 0.392461 TTACCTGGGTTCATCAGCGC 60.392 55.0 0.00 0.00 0.00 5.92 F
803 2558 0.524414 AAAACCTATTTGGCGGTCGC 59.476 50.0 6.83 6.83 40.22 5.19 F
1422 4147 0.685097 TCCACCTAGACAACCTGCAC 59.315 55.0 0.00 0.00 0.00 4.57 F
3030 5870 0.116541 ATAGTATAGGGCAGCCGGGT 59.883 55.0 5.00 0.00 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 4146 1.554160 CCAGATGCTGAGAGACAAGGT 59.446 52.381 0.00 0.00 32.44 3.50 R
2072 4861 2.161211 GGCAGTGTTTCAGATCTCTTGC 59.839 50.000 0.00 0.00 0.00 4.01 R
3159 5999 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35 R
4195 7090 0.378257 AACGCACTGTCTGCTTGTTG 59.622 50.000 0.00 0.00 44.64 3.33 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
20 21 3.421919 AAGCAATGGTTTCCCAAATGG 57.578 42.857 0.00 0.00 46.04 3.16
43 44 4.371786 CTGATAATCTGGAAGCTAACGCA 58.628 43.478 0.00 0.00 39.10 5.24
115 116 7.345691 TCACAAGGATGGTGATTACATTATGT 58.654 34.615 2.58 2.58 0.00 2.29
178 179 4.584874 TCTTTCAAAGTCCACAACAGACA 58.415 39.130 0.00 0.00 36.68 3.41
243 244 2.028930 ACACTTCGAGGGAACATCAGAC 60.029 50.000 0.00 0.00 0.00 3.51
306 330 0.539051 CCCCTTAGTGGCTCTGTGAG 59.461 60.000 0.00 0.00 0.00 3.51
404 2155 0.392461 TTACCTGGGTTCATCAGCGC 60.392 55.000 0.00 0.00 0.00 5.92
440 2192 3.517296 TTATTGACCCACTGGCTTTGA 57.483 42.857 0.00 0.00 33.59 2.69
442 2194 2.151502 TTGACCCACTGGCTTTGAAA 57.848 45.000 0.00 0.00 33.59 2.69
457 2209 2.346099 TGAAAACTTATGCTTGCCGC 57.654 45.000 0.00 0.00 39.77 6.53
541 2293 9.685276 TGTCAAGAAGTGGTGAATGATATTAAT 57.315 29.630 0.00 0.00 0.00 1.40
553 2306 6.215431 TGAATGATATTAATCGGGGACTGGAT 59.785 38.462 0.00 0.00 34.60 3.41
673 2426 3.888323 TCACAATCTTGCCAAGTTTGCTA 59.112 39.130 22.16 11.62 40.29 3.49
685 2438 4.380655 CCAAGTTTGCTAGTACGCTAGACT 60.381 45.833 5.89 0.00 45.77 3.24
686 2439 4.358494 AGTTTGCTAGTACGCTAGACTG 57.642 45.455 5.89 0.00 45.77 3.51
715 2468 3.973305 ACATGTTTGGTTGGGAAATCCTT 59.027 39.130 0.00 0.00 36.20 3.36
767 2522 9.768662 AATTGTCTTGAATGAATAAATATGGCC 57.231 29.630 0.00 0.00 0.00 5.36
803 2558 0.524414 AAAACCTATTTGGCGGTCGC 59.476 50.000 6.83 6.83 40.22 5.19
816 2571 3.343421 GTCGCCGCCAACGAGTTT 61.343 61.111 0.00 0.00 43.93 2.66
817 2572 3.039588 TCGCCGCCAACGAGTTTC 61.040 61.111 0.00 0.00 43.93 2.78
857 2613 3.470567 CGTGACGAGCCGACTTGC 61.471 66.667 0.00 0.00 0.00 4.01
914 2685 1.592669 CGTCAGGCATCCATCCGAC 60.593 63.158 0.00 0.00 0.00 4.79
941 2712 2.363018 CTCCACCCTCTCCTCGCA 60.363 66.667 0.00 0.00 0.00 5.10
1116 3022 2.530151 TTCCTCCCAGTGCAGGCT 60.530 61.111 0.00 0.00 0.00 4.58
1206 3654 1.226974 CCGCCTTGACGACGATGAT 60.227 57.895 0.00 0.00 34.06 2.45
1208 3656 0.802222 CGCCTTGACGACGATGATGT 60.802 55.000 0.00 0.00 34.06 3.06
1211 3659 2.881074 CCTTGACGACGATGATGTCTT 58.119 47.619 0.00 0.00 36.71 3.01
1249 3700 2.093500 CGGAAGTTCATGGACCATCTGA 60.093 50.000 3.21 0.00 0.00 3.27
1251 3702 4.202253 CGGAAGTTCATGGACCATCTGATA 60.202 45.833 3.21 0.00 0.00 2.15
1421 4146 0.976641 CTCCACCTAGACAACCTGCA 59.023 55.000 0.00 0.00 0.00 4.41
1422 4147 0.685097 TCCACCTAGACAACCTGCAC 59.315 55.000 0.00 0.00 0.00 4.57
1992 4778 7.735326 AGTTATGTATAACCTCCAGTTGAGT 57.265 36.000 10.33 0.00 42.71 3.41
2072 4861 7.372451 TGTATTTCTACCCAGTTCATTTTCG 57.628 36.000 0.00 0.00 0.00 3.46
2150 4939 2.237392 GAGTATTGGTGTGAGGCTCCTT 59.763 50.000 12.86 0.00 0.00 3.36
2403 5198 6.770785 AGCACCTTAACATAGTTGAAGTCAAA 59.229 34.615 0.00 0.00 37.63 2.69
2668 5478 9.546428 CAAAAGGGAAAACCAATATAATCCATC 57.454 33.333 0.00 0.00 43.89 3.51
2739 5553 6.169557 AGTGTAACAGAACATGTGGTCTTA 57.830 37.500 0.00 0.00 39.48 2.10
2853 5682 6.567959 TGAATTGTAACTCAAATGTGTGCAA 58.432 32.000 0.00 7.70 39.62 4.08
2969 5809 3.974719 TGGGCTAAATTATTCAGCACCA 58.025 40.909 0.00 3.41 37.94 4.17
3010 5850 6.989155 TCACTTTGTTCCTAGGAAGTCTTA 57.011 37.500 24.91 7.83 34.49 2.10
3011 5851 7.369551 TCACTTTGTTCCTAGGAAGTCTTAA 57.630 36.000 24.91 11.72 34.49 1.85
3012 5852 7.974504 TCACTTTGTTCCTAGGAAGTCTTAAT 58.025 34.615 24.91 4.77 34.49 1.40
3013 5853 9.096823 TCACTTTGTTCCTAGGAAGTCTTAATA 57.903 33.333 24.91 4.77 34.49 0.98
3014 5854 9.372369 CACTTTGTTCCTAGGAAGTCTTAATAG 57.628 37.037 24.91 14.31 34.49 1.73
3015 5855 9.102453 ACTTTGTTCCTAGGAAGTCTTAATAGT 57.898 33.333 24.91 14.86 34.49 2.12
3022 5862 8.114743 TCCTAGGAAGTCTTAATAGTATAGGGC 58.885 40.741 9.71 0.00 0.00 5.19
3023 5863 7.894364 CCTAGGAAGTCTTAATAGTATAGGGCA 59.106 40.741 1.05 0.00 0.00 5.36
3024 5864 7.784470 AGGAAGTCTTAATAGTATAGGGCAG 57.216 40.000 0.00 0.00 0.00 4.85
3025 5865 6.211785 AGGAAGTCTTAATAGTATAGGGCAGC 59.788 42.308 0.00 0.00 0.00 5.25
3026 5866 6.361768 AAGTCTTAATAGTATAGGGCAGCC 57.638 41.667 1.26 1.26 0.00 4.85
3027 5867 4.463186 AGTCTTAATAGTATAGGGCAGCCG 59.537 45.833 5.00 0.00 0.00 5.52
3028 5868 3.767673 TCTTAATAGTATAGGGCAGCCGG 59.232 47.826 5.00 0.00 0.00 6.13
3029 5869 1.276622 AATAGTATAGGGCAGCCGGG 58.723 55.000 5.00 0.00 0.00 5.73
3030 5870 0.116541 ATAGTATAGGGCAGCCGGGT 59.883 55.000 5.00 0.00 0.00 5.28
3031 5871 0.830444 TAGTATAGGGCAGCCGGGTG 60.830 60.000 29.14 29.14 0.00 4.61
3032 5872 3.556306 TATAGGGCAGCCGGGTGC 61.556 66.667 43.07 43.07 43.19 5.01
3038 5878 3.204827 GCAGCCGGGTGCATGTAG 61.205 66.667 44.63 16.66 43.41 2.74
3039 5879 3.204827 CAGCCGGGTGCATGTAGC 61.205 66.667 22.48 4.21 44.83 3.58
3040 5880 3.402681 AGCCGGGTGCATGTAGCT 61.403 61.111 4.72 1.17 45.94 3.32
3041 5881 2.897350 GCCGGGTGCATGTAGCTC 60.897 66.667 12.77 2.62 45.94 4.09
3045 5885 2.897350 GGTGCATGTAGCTCCGGC 60.897 66.667 5.68 0.00 45.89 6.13
3069 5909 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
3076 5916 3.626394 GGGGAAGGGTCCGACTAC 58.374 66.667 0.00 0.00 46.04 2.73
3077 5917 1.001376 GGGGAAGGGTCCGACTACT 59.999 63.158 0.00 0.00 46.04 2.57
3078 5918 0.616964 GGGGAAGGGTCCGACTACTT 60.617 60.000 8.22 8.22 46.04 2.24
3079 5919 1.273759 GGGAAGGGTCCGACTACTTT 58.726 55.000 9.39 0.00 46.04 2.66
3080 5920 1.066358 GGGAAGGGTCCGACTACTTTG 60.066 57.143 9.39 0.00 46.04 2.77
3081 5921 1.066358 GGAAGGGTCCGACTACTTTGG 60.066 57.143 9.39 0.00 33.05 3.28
3082 5922 0.981943 AAGGGTCCGACTACTTTGGG 59.018 55.000 0.00 0.00 0.00 4.12
3083 5923 0.178912 AGGGTCCGACTACTTTGGGT 60.179 55.000 0.00 0.00 0.00 4.51
3084 5924 0.248565 GGGTCCGACTACTTTGGGTC 59.751 60.000 0.00 0.00 0.00 4.46
3085 5925 1.264295 GGTCCGACTACTTTGGGTCT 58.736 55.000 0.00 0.00 0.00 3.85
3086 5926 2.450476 GGTCCGACTACTTTGGGTCTA 58.550 52.381 0.00 0.00 0.00 2.59
3087 5927 3.029570 GGTCCGACTACTTTGGGTCTAT 58.970 50.000 0.00 0.00 0.00 1.98
3088 5928 4.210331 GGTCCGACTACTTTGGGTCTATA 58.790 47.826 0.00 0.00 0.00 1.31
3089 5929 4.277921 GGTCCGACTACTTTGGGTCTATAG 59.722 50.000 0.00 0.00 0.00 1.31
3090 5930 4.886489 GTCCGACTACTTTGGGTCTATAGT 59.114 45.833 0.00 0.00 0.00 2.12
3091 5931 6.058183 GTCCGACTACTTTGGGTCTATAGTA 58.942 44.000 0.00 0.00 0.00 1.82
3092 5932 6.017523 GTCCGACTACTTTGGGTCTATAGTAC 60.018 46.154 0.00 0.00 0.00 2.73
3093 5933 5.049818 CCGACTACTTTGGGTCTATAGTACG 60.050 48.000 0.00 0.00 0.00 3.67
3094 5934 5.559799 CGACTACTTTGGGTCTATAGTACGC 60.560 48.000 0.00 6.13 0.00 4.42
3095 5935 5.195940 ACTACTTTGGGTCTATAGTACGCA 58.804 41.667 13.98 13.98 37.94 5.24
3096 5936 4.650754 ACTTTGGGTCTATAGTACGCAG 57.349 45.455 16.00 11.29 40.36 5.18
3097 5937 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
3098 5938 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
3099 5939 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
3100 5940 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
3101 5941 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
3102 5942 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
3103 5943 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
3104 5944 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
3105 5945 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
3106 5946 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
3107 5947 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
3108 5948 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
3109 5949 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
3110 5950 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3111 5951 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
3112 5952 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3113 5953 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3114 5954 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3115 5955 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
3116 5956 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
3117 5957 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
3118 5958 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
3119 5959 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
3131 5971 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
3132 5972 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
3133 5973 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
3134 5974 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
3135 5975 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
3136 5976 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
3137 5977 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
3138 5978 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
3139 5979 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3140 5980 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3141 5981 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3142 5982 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
3143 5983 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
3144 5984 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
3145 5985 0.841289 TTCCAGGACTTGAACCCGTT 59.159 50.000 0.00 0.00 0.00 4.44
3146 5986 1.719529 TCCAGGACTTGAACCCGTTA 58.280 50.000 0.00 0.00 0.00 3.18
3147 5987 1.345415 TCCAGGACTTGAACCCGTTAC 59.655 52.381 0.00 0.00 0.00 2.50
3148 5988 1.609841 CCAGGACTTGAACCCGTTACC 60.610 57.143 0.00 0.00 0.00 2.85
3149 5989 1.346722 CAGGACTTGAACCCGTTACCT 59.653 52.381 0.00 0.00 0.00 3.08
3150 5990 1.622312 AGGACTTGAACCCGTTACCTC 59.378 52.381 0.00 0.00 0.00 3.85
3151 5991 1.345415 GGACTTGAACCCGTTACCTCA 59.655 52.381 0.00 0.00 0.00 3.86
3152 5992 2.027469 GGACTTGAACCCGTTACCTCAT 60.027 50.000 0.00 0.00 0.00 2.90
3153 5993 3.000727 GACTTGAACCCGTTACCTCATG 58.999 50.000 0.00 0.00 0.00 3.07
3154 5994 2.290071 ACTTGAACCCGTTACCTCATGG 60.290 50.000 0.00 0.00 39.83 3.66
3156 5996 1.276989 TGAACCCGTTACCTCATGGTC 59.723 52.381 0.00 0.00 44.78 4.02
3157 5997 1.276989 GAACCCGTTACCTCATGGTCA 59.723 52.381 0.00 0.00 44.78 4.02
3158 5998 0.611714 ACCCGTTACCTCATGGTCAC 59.388 55.000 0.00 0.00 44.78 3.67
3159 5999 0.611200 CCCGTTACCTCATGGTCACA 59.389 55.000 0.00 0.00 44.78 3.58
3160 6000 1.002659 CCCGTTACCTCATGGTCACAA 59.997 52.381 0.00 0.00 44.78 3.33
3161 6001 2.346803 CCGTTACCTCATGGTCACAAG 58.653 52.381 0.00 0.00 44.78 3.16
3162 6002 2.346803 CGTTACCTCATGGTCACAAGG 58.653 52.381 0.00 0.00 44.78 3.61
3163 6003 2.084546 GTTACCTCATGGTCACAAGGC 58.915 52.381 0.00 0.00 44.78 4.35
3164 6004 1.357137 TACCTCATGGTCACAAGGCA 58.643 50.000 0.00 0.00 44.78 4.75
3165 6005 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
3166 6006 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
3167 6007 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
3168 6008 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
3169 6009 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
3170 6010 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
3171 6011 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
3172 6012 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
3173 6013 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
3174 6014 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
3175 6015 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
3176 6016 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
3177 6017 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
3178 6018 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
3179 6019 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
3183 6023 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
3184 6024 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
3185 6025 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
3186 6026 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
3187 6027 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
3188 6028 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
3189 6029 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
3190 6030 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
3337 6177 2.823196 TGCTAATGACATTTTCCGCG 57.177 45.000 5.89 0.00 0.00 6.46
3463 6303 5.631119 AGATAAGTTGCACCTGGTAAAGTT 58.369 37.500 15.09 15.09 0.00 2.66
3553 6393 7.801716 TTTACTTCTGCAGATACAACAAAGT 57.198 32.000 19.04 16.92 0.00 2.66
3606 6446 5.018809 AGGATTCAATTTCTAGCAAAGGCA 58.981 37.500 0.00 0.00 44.61 4.75
3639 6479 3.006110 GGTTGATGGTTCATATGCCATGG 59.994 47.826 16.84 7.63 44.73 3.66
3663 6503 5.105997 GCTTGACTATTCAGAAATGCAAGGT 60.106 40.000 14.85 0.00 34.23 3.50
3743 6583 3.576982 TGAGTTCTTTCCGTGTATGGTCT 59.423 43.478 0.00 0.00 0.00 3.85
3747 6587 2.236146 TCTTTCCGTGTATGGTCTGCAT 59.764 45.455 0.00 0.00 0.00 3.96
3748 6588 2.309528 TTCCGTGTATGGTCTGCATC 57.690 50.000 0.00 0.00 0.00 3.91
3750 6590 1.762370 TCCGTGTATGGTCTGCATCAT 59.238 47.619 0.00 0.00 0.00 2.45
3751 6591 2.962421 TCCGTGTATGGTCTGCATCATA 59.038 45.455 0.00 0.00 0.00 2.15
3803 6650 2.100197 GTGGGGCTTGGTTTCCTATTC 58.900 52.381 0.00 0.00 0.00 1.75
3902 6749 6.092748 GTGCATTAACTTGTTCTGTTATGGG 58.907 40.000 0.00 0.00 31.13 4.00
3913 6760 5.251932 TGTTCTGTTATGGGGTGATCCTTTA 59.748 40.000 0.00 0.00 35.33 1.85
4088 6935 3.246226 GCAGCTCTGAACATATGTTACCG 59.754 47.826 20.83 11.93 38.56 4.02
4089 6936 4.433615 CAGCTCTGAACATATGTTACCGT 58.566 43.478 20.83 0.00 38.56 4.83
4090 6937 4.268644 CAGCTCTGAACATATGTTACCGTG 59.731 45.833 20.83 12.99 38.56 4.94
4158 7053 2.429478 TCTCCACACTATTGACGTCGA 58.571 47.619 8.21 8.21 0.00 4.20
4189 7084 2.203294 GTTGTCCCCAACGGCAGT 60.203 61.111 0.00 0.00 41.41 4.40
4190 7085 1.071814 GTTGTCCCCAACGGCAGTA 59.928 57.895 0.00 0.00 41.41 2.74
4194 7089 1.117150 GTCCCCAACGGCAGTATAGA 58.883 55.000 0.00 0.00 0.00 1.98
4195 7090 1.117150 TCCCCAACGGCAGTATAGAC 58.883 55.000 0.00 0.00 0.00 2.59
4196 7091 0.828022 CCCCAACGGCAGTATAGACA 59.172 55.000 0.00 0.00 0.00 3.41
4202 7097 2.618053 ACGGCAGTATAGACAACAAGC 58.382 47.619 0.00 0.00 0.00 4.01
4225 7120 2.280797 GTGCGTTGGCCTCTCACA 60.281 61.111 3.32 0.00 38.85 3.58
4255 7150 2.628657 CGGGTGATAGCTACTAGGCTTT 59.371 50.000 0.00 0.00 42.97 3.51
4274 7169 1.344953 TGCCTCCTCGTGCCCATATT 61.345 55.000 0.00 0.00 0.00 1.28
4362 7260 5.536161 AGATCACACCTGCAACAACTTTTAT 59.464 36.000 0.00 0.00 0.00 1.40
4391 7289 5.730550 TGAATCAAGTAATTACCTGCTCGT 58.269 37.500 12.05 0.00 0.00 4.18
4404 7302 2.233922 CCTGCTCGTATACCAATAGGGG 59.766 54.545 0.00 0.00 42.91 4.79
4448 7346 3.803340 TGGATTCTAGGGTCCAAAGTCT 58.197 45.455 12.77 0.00 41.36 3.24
4472 7370 4.258702 TGAGTTCTCAGACCTGCTTTAC 57.741 45.455 0.00 0.00 0.00 2.01
4529 7434 4.437682 AGTTGTTGGGAGTGATCTGAAA 57.562 40.909 0.00 0.00 0.00 2.69
4541 7446 4.067896 GTGATCTGAAAGTCCTGAAAGCA 58.932 43.478 0.00 0.00 33.76 3.91
4586 7491 4.031611 AGTTAGGTCCCAACAGAGGATAC 58.968 47.826 2.89 0.00 35.38 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.185391 GCGTTAGCTTCCAGATTATCAGC 59.815 47.826 0.00 0.00 41.01 4.26
43 44 1.831580 GCTCAAACAGCCAGATCCTT 58.168 50.000 0.00 0.00 43.17 3.36
145 146 8.514594 TGTGGACTTTGAAAGATTGATTCATAC 58.485 33.333 12.53 2.25 36.72 2.39
178 179 5.518848 TGAAGTTGTTGACAAAGCATGAT 57.481 34.783 0.00 0.00 37.63 2.45
299 323 6.686378 GCACCATCTACATTAATCCTCACAGA 60.686 42.308 0.00 0.00 0.00 3.41
306 330 5.368145 TCACTGCACCATCTACATTAATCC 58.632 41.667 0.00 0.00 0.00 3.01
423 2175 2.151502 TTTCAAAGCCAGTGGGTCAA 57.848 45.000 15.65 5.31 36.17 3.18
442 2194 3.452681 GCTTCGCGGCAAGCATAAGTT 62.453 52.381 23.11 0.00 46.93 2.66
541 2293 4.731853 TGGGCATCCAGTCCCCGA 62.732 66.667 0.00 0.00 43.21 5.14
542 2294 2.572333 ATTTGGGCATCCAGTCCCCG 62.572 60.000 0.00 0.00 43.21 5.73
553 2306 2.339348 CAACGCAGCATTTGGGCA 59.661 55.556 0.00 0.00 43.14 5.36
673 2426 3.197333 TGTCTACCTCAGTCTAGCGTACT 59.803 47.826 0.00 0.00 0.00 2.73
685 2438 3.497763 CCCAACCAAACATGTCTACCTCA 60.498 47.826 0.00 0.00 0.00 3.86
686 2439 3.081804 CCCAACCAAACATGTCTACCTC 58.918 50.000 0.00 0.00 0.00 3.85
715 2468 5.489637 ACATAGGTACAAGGTTTGGGTCATA 59.510 40.000 0.00 0.00 34.12 2.15
799 2554 3.291167 GAAACTCGTTGGCGGCGAC 62.291 63.158 19.10 19.10 38.89 5.19
800 2555 3.039588 GAAACTCGTTGGCGGCGA 61.040 61.111 12.98 0.00 38.89 5.54
801 2556 4.424430 CGAAACTCGTTGGCGGCG 62.424 66.667 0.51 0.51 38.89 6.46
802 2557 1.908066 AATCGAAACTCGTTGGCGGC 61.908 55.000 0.00 0.00 41.35 6.53
803 2558 0.094730 GAATCGAAACTCGTTGGCGG 59.905 55.000 0.00 0.00 41.35 6.13
804 2559 1.059264 GAGAATCGAAACTCGTTGGCG 59.941 52.381 6.49 0.00 41.35 5.69
805 2560 2.789569 GAGAATCGAAACTCGTTGGC 57.210 50.000 6.49 0.00 41.35 4.52
941 2712 3.690460 AGCAAAGGAAGGATCAAACGAT 58.310 40.909 0.00 0.00 0.00 3.73
976 2753 4.814294 GAGTAGGTGGCGGGCGTG 62.814 72.222 0.00 0.00 0.00 5.34
1272 3723 2.462456 TGATCTCAACAGTGTCCAGC 57.538 50.000 0.00 0.00 0.00 4.85
1421 4146 1.554160 CCAGATGCTGAGAGACAAGGT 59.446 52.381 0.00 0.00 32.44 3.50
1422 4147 1.554160 ACCAGATGCTGAGAGACAAGG 59.446 52.381 0.00 0.00 32.44 3.61
1515 4241 7.092079 TGATTTCGCAATCATTCATTTTCAGT 58.908 30.769 6.37 0.00 43.32 3.41
1945 4708 9.727627 AACTTACTAAATACGTAGATAGTGCAC 57.272 33.333 23.27 9.40 31.46 4.57
1986 4772 7.487829 GTGAGATCTGATCTAAGAACACTCAAC 59.512 40.741 19.57 4.05 40.38 3.18
1992 4778 8.303780 AGAATGTGAGATCTGATCTAAGAACA 57.696 34.615 19.57 19.16 40.38 3.18
2039 4826 7.991084 ACTGGGTAGAAATACAAAAGGTAAC 57.009 36.000 0.00 0.00 35.14 2.50
2049 4838 6.128117 TGCGAAAATGAACTGGGTAGAAATAC 60.128 38.462 0.00 0.00 0.00 1.89
2051 4840 4.764823 TGCGAAAATGAACTGGGTAGAAAT 59.235 37.500 0.00 0.00 0.00 2.17
2072 4861 2.161211 GGCAGTGTTTCAGATCTCTTGC 59.839 50.000 0.00 0.00 0.00 4.01
2127 4916 2.622436 GAGCCTCACACCAATACTCAC 58.378 52.381 0.00 0.00 0.00 3.51
2150 4939 2.771372 TGCATGCTAGTGGATCCAAGTA 59.229 45.455 18.20 11.54 0.00 2.24
2403 5198 3.587061 TCCTCTTGTCCACCACATTACAT 59.413 43.478 0.00 0.00 33.90 2.29
2670 5480 7.710475 CGGTTAAATGAAATATCCTTTGCCAAT 59.290 33.333 0.00 0.00 0.00 3.16
2739 5553 5.256474 CCCACAAGACCAGAACTAATCAAT 58.744 41.667 0.00 0.00 0.00 2.57
2853 5682 9.959749 AACACAACGAGTCAAATATTGTTTTAT 57.040 25.926 0.00 0.00 31.25 1.40
3010 5850 1.276622 CCCGGCTGCCCTATACTATT 58.723 55.000 14.12 0.00 0.00 1.73
3011 5851 0.116541 ACCCGGCTGCCCTATACTAT 59.883 55.000 14.12 0.00 0.00 2.12
3012 5852 0.830444 CACCCGGCTGCCCTATACTA 60.830 60.000 14.12 0.00 0.00 1.82
3013 5853 2.140792 CACCCGGCTGCCCTATACT 61.141 63.158 14.12 0.00 0.00 2.12
3014 5854 2.426023 CACCCGGCTGCCCTATAC 59.574 66.667 14.12 0.00 0.00 1.47
3015 5855 3.556306 GCACCCGGCTGCCCTATA 61.556 66.667 14.12 0.00 40.25 1.31
3020 5860 4.794648 TACATGCACCCGGCTGCC 62.795 66.667 18.95 9.11 45.15 4.85
3021 5861 3.204827 CTACATGCACCCGGCTGC 61.205 66.667 15.10 15.10 45.15 5.25
3022 5862 3.204827 GCTACATGCACCCGGCTG 61.205 66.667 0.00 0.00 45.15 4.85
3023 5863 3.391665 GAGCTACATGCACCCGGCT 62.392 63.158 0.00 5.89 45.94 5.52
3024 5864 2.897350 GAGCTACATGCACCCGGC 60.897 66.667 0.00 0.00 45.94 6.13
3025 5865 2.203070 GGAGCTACATGCACCCGG 60.203 66.667 0.00 0.00 45.00 5.73
3028 5868 2.897350 GCCGGAGCTACATGCACC 60.897 66.667 5.05 0.00 46.82 5.01
3052 5892 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
3057 5897 3.667217 TAGTCGGACCCTTCCCCGG 62.667 68.421 4.14 0.00 45.36 5.73
3058 5898 2.043652 TAGTCGGACCCTTCCCCG 60.044 66.667 4.14 0.00 46.57 5.73
3059 5899 0.616964 AAGTAGTCGGACCCTTCCCC 60.617 60.000 4.14 0.00 38.99 4.81
3060 5900 1.066358 CAAAGTAGTCGGACCCTTCCC 60.066 57.143 4.14 0.00 38.99 3.97
3061 5901 1.066358 CCAAAGTAGTCGGACCCTTCC 60.066 57.143 4.14 0.00 38.77 3.46
3062 5902 1.066358 CCCAAAGTAGTCGGACCCTTC 60.066 57.143 4.14 0.00 0.00 3.46
3063 5903 0.981943 CCCAAAGTAGTCGGACCCTT 59.018 55.000 4.14 4.76 0.00 3.95
3064 5904 0.178912 ACCCAAAGTAGTCGGACCCT 60.179 55.000 4.14 0.00 0.00 4.34
3065 5905 0.248565 GACCCAAAGTAGTCGGACCC 59.751 60.000 4.14 0.00 0.00 4.46
3066 5906 1.264295 AGACCCAAAGTAGTCGGACC 58.736 55.000 4.14 0.00 38.08 4.46
3067 5907 4.886489 ACTATAGACCCAAAGTAGTCGGAC 59.114 45.833 6.78 0.00 38.08 4.79
3068 5908 5.121380 ACTATAGACCCAAAGTAGTCGGA 57.879 43.478 6.78 0.00 38.08 4.55
3069 5909 5.049818 CGTACTATAGACCCAAAGTAGTCGG 60.050 48.000 6.78 0.00 38.08 4.79
3070 5910 5.559799 GCGTACTATAGACCCAAAGTAGTCG 60.560 48.000 6.78 0.00 38.08 4.18
3071 5911 5.297776 TGCGTACTATAGACCCAAAGTAGTC 59.702 44.000 6.78 0.00 0.00 2.59
3072 5912 5.195940 TGCGTACTATAGACCCAAAGTAGT 58.804 41.667 6.78 0.00 0.00 2.73
3073 5913 5.759963 CTGCGTACTATAGACCCAAAGTAG 58.240 45.833 6.78 0.00 0.00 2.57
3074 5914 4.037208 GCTGCGTACTATAGACCCAAAGTA 59.963 45.833 6.78 0.00 0.00 2.24
3075 5915 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
3076 5916 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
3077 5917 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
3078 5918 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
3079 5919 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
3080 5920 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
3081 5921 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
3082 5922 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
3083 5923 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
3084 5924 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
3085 5925 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
3086 5926 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
3087 5927 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
3088 5928 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
3089 5929 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
3090 5930 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3091 5931 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
3092 5932 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3093 5933 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3094 5934 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
3095 5935 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
3096 5936 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
3097 5937 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
3098 5938 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
3099 5939 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
3100 5940 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
3101 5941 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
3102 5942 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
3103 5943 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
3104 5944 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
3105 5945 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
3106 5946 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
3107 5947 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
3108 5948 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
3109 5949 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
3123 5963 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
3124 5964 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
3125 5965 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
3126 5966 0.841289 AACGGGTTCAAGTCCTGGAA 59.159 50.000 0.00 0.00 35.79 3.53
3127 5967 1.345415 GTAACGGGTTCAAGTCCTGGA 59.655 52.381 0.00 0.00 35.79 3.86
3128 5968 1.609841 GGTAACGGGTTCAAGTCCTGG 60.610 57.143 0.00 0.00 35.79 4.45
3129 5969 1.346722 AGGTAACGGGTTCAAGTCCTG 59.653 52.381 0.00 0.00 46.39 3.86
3130 5970 1.622312 GAGGTAACGGGTTCAAGTCCT 59.378 52.381 0.00 0.00 46.39 3.85
3131 5971 1.345415 TGAGGTAACGGGTTCAAGTCC 59.655 52.381 0.00 0.00 46.39 3.85
3132 5972 2.825861 TGAGGTAACGGGTTCAAGTC 57.174 50.000 0.00 0.00 46.39 3.01
3133 5973 2.290071 CCATGAGGTAACGGGTTCAAGT 60.290 50.000 0.00 0.00 46.39 3.16
3134 5974 2.356135 CCATGAGGTAACGGGTTCAAG 58.644 52.381 0.00 0.00 46.39 3.02
3135 5975 2.483014 CCATGAGGTAACGGGTTCAA 57.517 50.000 0.00 0.00 46.39 2.69
3147 5987 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
3148 5988 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
3149 5989 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
3150 5990 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
3151 5991 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
3152 5992 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
3153 5993 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
3154 5994 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
3155 5995 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
3156 5996 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
3157 5997 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
3158 5998 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
3159 5999 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
3160 6000 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
3161 6001 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
3166 6006 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
3167 6007 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
3168 6008 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
3169 6009 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
3170 6010 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
3171 6011 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
3172 6012 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
3180 6020 4.803908 GGAAGGGGAGCCTTGGCG 62.804 72.222 5.95 0.00 0.00 5.69
3181 6021 1.988982 CTAGGAAGGGGAGCCTTGGC 61.989 65.000 2.97 2.97 35.73 4.52
3182 6022 1.348775 CCTAGGAAGGGGAGCCTTGG 61.349 65.000 1.05 0.00 40.01 3.61
3183 6023 2.225792 CCTAGGAAGGGGAGCCTTG 58.774 63.158 1.05 0.00 39.48 3.61
3184 6024 4.840545 CCTAGGAAGGGGAGCCTT 57.159 61.111 1.05 0.00 39.48 4.35
3192 6032 4.828963 ACTATTAAGACCCCCTAGGAAGG 58.171 47.826 11.48 13.36 43.25 3.46
3193 6033 4.839550 GGACTATTAAGACCCCCTAGGAAG 59.160 50.000 11.48 3.07 39.89 3.46
3194 6034 4.235873 TGGACTATTAAGACCCCCTAGGAA 59.764 45.833 11.48 0.00 36.81 3.36
3195 6035 3.801317 TGGACTATTAAGACCCCCTAGGA 59.199 47.826 11.48 0.00 36.81 2.94
3196 6036 3.902467 GTGGACTATTAAGACCCCCTAGG 59.098 52.174 0.06 0.06 36.81 3.02
3197 6037 4.553678 TGTGGACTATTAAGACCCCCTAG 58.446 47.826 0.00 0.00 36.81 3.02
3198 6038 4.630382 TGTGGACTATTAAGACCCCCTA 57.370 45.455 0.00 0.00 36.81 3.53
3199 6039 3.502051 TGTGGACTATTAAGACCCCCT 57.498 47.619 0.00 0.00 36.81 4.79
3200 6040 5.605488 TCTTATGTGGACTATTAAGACCCCC 59.395 44.000 0.00 0.00 36.81 5.40
3201 6041 6.742559 TCTTATGTGGACTATTAAGACCCC 57.257 41.667 0.00 0.00 36.81 4.95
3202 6042 9.628500 AAAATCTTATGTGGACTATTAAGACCC 57.372 33.333 0.00 0.00 36.81 4.46
3249 6089 7.229707 CACTACTAGTCCTAGACATGCTTATGT 59.770 40.741 0.00 0.00 36.97 2.29
3337 6177 5.710567 AGTTAAACTGCTCCCTAATTGGAAC 59.289 40.000 0.00 0.00 38.35 3.62
3463 6303 9.793259 AACAAAGTTCAGAAAGTATGGAGATTA 57.207 29.630 0.00 0.00 0.00 1.75
3606 6446 3.884037 ACCATCAACCCAAGTCTTCTT 57.116 42.857 0.00 0.00 0.00 2.52
3639 6479 5.105997 ACCTTGCATTTCTGAATAGTCAAGC 60.106 40.000 0.00 0.00 31.88 4.01
3663 6503 5.629435 CACTCTCGCGACATATATGCTTAAA 59.371 40.000 3.71 0.00 0.00 1.52
3743 6583 9.219603 GTATAAAGTTCATAGGCTTATGATGCA 57.780 33.333 18.18 2.26 43.82 3.96
3747 6587 6.872020 GCGGTATAAAGTTCATAGGCTTATGA 59.128 38.462 14.08 14.08 42.97 2.15
3748 6588 6.092259 GGCGGTATAAAGTTCATAGGCTTATG 59.908 42.308 9.49 9.49 38.41 1.90
3750 6590 5.511888 GGGCGGTATAAAGTTCATAGGCTTA 60.512 44.000 0.00 0.00 0.00 3.09
3751 6591 4.386711 GGCGGTATAAAGTTCATAGGCTT 58.613 43.478 0.00 0.00 0.00 4.35
3902 6749 7.164803 CAGGGAGATAGAATTAAAGGATCACC 58.835 42.308 0.00 0.00 0.00 4.02
3913 6760 7.444703 AAGCTCTTAACAGGGAGATAGAATT 57.555 36.000 0.00 0.00 0.00 2.17
4088 6935 4.866486 GGACCATTTGATTTCAGAATGCAC 59.134 41.667 0.00 0.00 34.76 4.57
4089 6936 4.527427 TGGACCATTTGATTTCAGAATGCA 59.473 37.500 0.00 0.00 34.76 3.96
4090 6937 5.075858 TGGACCATTTGATTTCAGAATGC 57.924 39.130 0.00 0.00 34.76 3.56
4158 7053 1.000955 GGACAACTGAGACCGTGACAT 59.999 52.381 0.00 0.00 0.00 3.06
4183 7078 2.604914 CTGCTTGTTGTCTATACTGCCG 59.395 50.000 0.00 0.00 0.00 5.69
4187 7082 5.473931 CACTGTCTGCTTGTTGTCTATACT 58.526 41.667 0.00 0.00 0.00 2.12
4189 7084 4.245660 GCACTGTCTGCTTGTTGTCTATA 58.754 43.478 0.00 0.00 43.33 1.31
4190 7085 3.070018 GCACTGTCTGCTTGTTGTCTAT 58.930 45.455 0.00 0.00 43.33 1.98
4194 7089 0.744414 ACGCACTGTCTGCTTGTTGT 60.744 50.000 0.00 0.00 44.64 3.32
4195 7090 0.378257 AACGCACTGTCTGCTTGTTG 59.622 50.000 0.00 0.00 44.64 3.33
4196 7091 0.378257 CAACGCACTGTCTGCTTGTT 59.622 50.000 0.00 0.00 44.64 2.83
4202 7097 2.281070 AGGCCAACGCACTGTCTG 60.281 61.111 5.01 0.00 36.38 3.51
4212 7107 1.541588 GGTTGATTGTGAGAGGCCAAC 59.458 52.381 5.01 0.00 34.75 3.77
4225 7120 0.814010 GCTATCACCCGCGGTTGATT 60.814 55.000 37.96 23.52 31.02 2.57
4255 7150 1.344953 AATATGGGCACGAGGAGGCA 61.345 55.000 0.00 0.00 0.00 4.75
4265 7160 2.100584 GCAAACATTCGGAATATGGGCA 59.899 45.455 2.35 0.00 0.00 5.36
4274 7169 2.177394 TACTGCAGCAAACATTCGGA 57.823 45.000 15.27 0.00 0.00 4.55
4362 7260 9.851686 AGCAGGTAATTACTTGATTCATATTGA 57.148 29.630 26.73 0.00 35.55 2.57
4373 7271 6.509656 TGGTATACGAGCAGGTAATTACTTG 58.490 40.000 20.29 20.29 36.49 3.16
4374 7272 6.720112 TGGTATACGAGCAGGTAATTACTT 57.280 37.500 15.05 4.91 0.00 2.24
4391 7289 3.144125 AGACTGCTCCCCCTATTGGTATA 59.856 47.826 0.00 0.00 0.00 1.47
4448 7346 3.845781 AGCAGGTCTGAGAACTCAAAA 57.154 42.857 0.00 0.00 39.39 2.44
4472 7370 5.297776 CCTCCTATGCTGGTTTCTAACATTG 59.702 44.000 0.00 0.00 0.00 2.82
4569 7474 1.486726 CAGGTATCCTCTGTTGGGACC 59.513 57.143 0.00 0.00 35.51 4.46


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

AutoCloner maintained by Alex Coulton.