Multiple sequence alignment - TraesCS3B01G343200

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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 TraesCS3B01G343200 chr3B 100.000 6781 0 0 1 6781 551519499 551512719 0.000000e+00 12523.0
1 TraesCS3B01G343200 chr3B 97.222 108 2 1 5355 5461 22055097 22054990 1.500000e-41 182.0
2 TraesCS3B01G343200 chr3B 93.913 115 6 1 5347 5460 15806510 15806624 9.040000e-39 172.0
3 TraesCS3B01G343200 chr3D 95.989 4537 118 22 833 5336 422961825 422957320 0.000000e+00 7312.0
4 TraesCS3B01G343200 chr3D 88.670 812 48 16 5992 6781 422956730 422955941 0.000000e+00 950.0
5 TraesCS3B01G343200 chr3D 86.772 824 74 21 1 792 529119666 529120486 0.000000e+00 885.0
6 TraesCS3B01G343200 chr3D 89.524 525 17 8 5458 5967 422957309 422956808 1.240000e-176 630.0
7 TraesCS3B01G343200 chr3D 86.260 131 13 5 5520 5648 476994922 476994795 3.300000e-28 137.0
8 TraesCS3B01G343200 chr3A 89.417 1389 81 28 988 2343 565788607 565787252 0.000000e+00 1690.0
9 TraesCS3B01G343200 chr3A 92.254 1007 39 6 4315 5284 565784945 565783941 0.000000e+00 1391.0
10 TraesCS3B01G343200 chr3A 92.340 953 50 14 2764 3709 565786720 565785784 0.000000e+00 1334.0
11 TraesCS3B01G343200 chr3A 91.509 636 29 10 3706 4322 565785683 565785054 0.000000e+00 852.0
12 TraesCS3B01G343200 chr3A 92.966 526 34 3 2342 2866 565787216 565786693 0.000000e+00 763.0
13 TraesCS3B01G343200 chr3A 79.387 587 118 3 1 586 360861242 360861826 1.760000e-110 411.0
14 TraesCS3B01G343200 chr3A 83.904 292 20 5 5613 5886 565783786 565783504 3.140000e-63 254.0
15 TraesCS3B01G343200 chr3A 93.220 118 7 1 5992 6108 565783405 565783288 9.040000e-39 172.0
16 TraesCS3B01G343200 chr3A 86.452 155 11 3 833 978 565789158 565789005 1.960000e-35 161.0
17 TraesCS3B01G343200 chr3A 95.652 69 1 2 5289 5357 565783908 565783842 7.190000e-20 110.0
18 TraesCS3B01G343200 chr3A 97.917 48 1 0 5458 5505 565783845 565783798 4.360000e-12 84.2
19 TraesCS3B01G343200 chr2B 98.243 797 14 0 1 797 549035241 549036037 0.000000e+00 1395.0
20 TraesCS3B01G343200 chr2B 82.642 651 107 6 1 647 704322401 704321753 7.630000e-159 571.0
21 TraesCS3B01G343200 chr2B 97.222 108 2 1 5354 5460 99152093 99152200 1.500000e-41 182.0
22 TraesCS3B01G343200 chr2B 94.737 114 4 2 5349 5460 766568276 766568163 6.990000e-40 176.0
23 TraesCS3B01G343200 chr2B 97.826 92 2 0 5523 5614 41963942 41963851 7.040000e-35 159.0
24 TraesCS3B01G343200 chr1A 88.434 830 60 8 1 795 373324868 373324040 0.000000e+00 968.0
25 TraesCS3B01G343200 chr1A 74.642 489 113 10 60 544 416678978 416679459 8.910000e-49 206.0
26 TraesCS3B01G343200 chr6A 91.345 647 56 0 1 647 612181983 612181337 0.000000e+00 885.0
27 TraesCS3B01G343200 chr6A 89.286 140 11 4 5355 5492 499205117 499204980 9.040000e-39 172.0
28 TraesCS3B01G343200 chr5D 89.799 647 66 0 1 647 495298778 495298132 0.000000e+00 830.0
29 TraesCS3B01G343200 chr5D 95.918 98 1 3 5526 5622 526559563 526559658 9.110000e-34 156.0
30 TraesCS3B01G343200 chr5D 89.286 112 10 2 683 794 495298065 495297956 9.170000e-29 139.0
31 TraesCS3B01G343200 chr5D 89.286 112 8 4 5503 5612 434549287 434549396 3.300000e-28 137.0
32 TraesCS3B01G343200 chr6D 81.029 622 112 6 4 622 472211955 472212573 2.200000e-134 490.0
33 TraesCS3B01G343200 chr2A 79.770 608 117 6 18 622 731206534 731205930 2.900000e-118 436.0
34 TraesCS3B01G343200 chr2A 77.955 626 132 5 1 623 617653891 617654513 2.970000e-103 387.0
35 TraesCS3B01G343200 chr2A 90.769 130 8 4 5351 5477 575602133 575602005 3.250000e-38 171.0
36 TraesCS3B01G343200 chr2A 87.903 124 9 6 5503 5623 51498663 51498543 2.550000e-29 141.0
37 TraesCS3B01G343200 chr2D 79.392 592 118 4 3 592 382465451 382466040 1.360000e-111 414.0
38 TraesCS3B01G343200 chr2D 88.983 118 8 5 5503 5617 49201103 49200988 2.550000e-29 141.0
39 TraesCS3B01G343200 chr1B 95.652 115 3 2 5348 5461 624663031 624662918 4.180000e-42 183.0
40 TraesCS3B01G343200 chr5B 94.068 118 6 1 5354 5470 281433785 281433902 1.940000e-40 178.0
41 TraesCS3B01G343200 chr5B 94.000 100 5 1 5523 5622 264876297 264876395 4.240000e-32 150.0
42 TraesCS3B01G343200 chr4A 92.000 125 7 3 5349 5471 239632819 239632696 9.040000e-39 172.0
43 TraesCS3B01G343200 chr7B 97.802 91 2 0 5525 5615 740996243 740996153 2.530000e-34 158.0
44 TraesCS3B01G343200 chrUn 94.845 97 5 0 5528 5624 301350026 301349930 1.180000e-32 152.0
45 TraesCS3B01G343200 chr7A 93.204 103 4 3 5526 5628 77709535 77709436 1.520000e-31 148.0


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 TraesCS3B01G343200 chr3B 551512719 551519499 6780 True 12523.00 12523 100.000000 1 6781 1 chr3B.!!$R2 6780
1 TraesCS3B01G343200 chr3D 422955941 422961825 5884 True 2964.00 7312 91.394333 833 6781 3 chr3D.!!$R2 5948
2 TraesCS3B01G343200 chr3D 529119666 529120486 820 False 885.00 885 86.772000 1 792 1 chr3D.!!$F1 791
3 TraesCS3B01G343200 chr3A 565783288 565789158 5870 True 681.12 1690 91.563100 833 6108 10 chr3A.!!$R1 5275
4 TraesCS3B01G343200 chr3A 360861242 360861826 584 False 411.00 411 79.387000 1 586 1 chr3A.!!$F1 585
5 TraesCS3B01G343200 chr2B 549035241 549036037 796 False 1395.00 1395 98.243000 1 797 1 chr2B.!!$F2 796
6 TraesCS3B01G343200 chr2B 704321753 704322401 648 True 571.00 571 82.642000 1 647 1 chr2B.!!$R2 646
7 TraesCS3B01G343200 chr1A 373324040 373324868 828 True 968.00 968 88.434000 1 795 1 chr1A.!!$R1 794
8 TraesCS3B01G343200 chr6A 612181337 612181983 646 True 885.00 885 91.345000 1 647 1 chr6A.!!$R2 646
9 TraesCS3B01G343200 chr5D 495297956 495298778 822 True 484.50 830 89.542500 1 794 2 chr5D.!!$R1 793
10 TraesCS3B01G343200 chr6D 472211955 472212573 618 False 490.00 490 81.029000 4 622 1 chr6D.!!$F1 618
11 TraesCS3B01G343200 chr2A 731205930 731206534 604 True 436.00 436 79.770000 18 622 1 chr2A.!!$R3 604
12 TraesCS3B01G343200 chr2A 617653891 617654513 622 False 387.00 387 77.955000 1 623 1 chr2A.!!$F1 622
13 TraesCS3B01G343200 chr2D 382465451 382466040 589 False 414.00 414 79.392000 3 592 1 chr2D.!!$F1 589

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
819 856 0.250038 TCACTTCTGCTGGCTCACAC 60.250 55.0 0.0 0.0 0.00 3.82 F
1395 1849 0.180406 AGTCCACTTTGCAACCGTCT 59.820 50.0 0.0 0.0 0.00 4.18 F
1971 2428 0.460987 GGACATTCAGGAGGTCTGCG 60.461 60.0 0.0 0.0 43.06 5.18 F
1972 2429 0.460987 GACATTCAGGAGGTCTGCGG 60.461 60.0 0.0 0.0 43.06 5.69 F
2205 2663 2.289002 GCTGGATGCAAGAAAGGTATCG 59.711 50.0 0.0 0.0 42.31 2.92 F
3951 4646 0.040204 AAATCACCTGGCTCCTTGGG 59.960 55.0 0.0 0.0 0.00 4.12 F
5236 6101 0.877071 CTGCAATGGACGCACTTCTT 59.123 50.0 0.0 0.0 35.08 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 2177 0.539051 AGTTGGCTCCTCCTCAATCG 59.461 55.000 0.00 0.0 35.26 3.34 R
3085 3669 1.632422 GCAACATGCAGATTTTCCCG 58.368 50.000 0.00 0.0 44.26 5.14 R
3591 4181 2.572104 ACCTCATGTTTACAGGGGAGAC 59.428 50.000 0.00 0.0 27.66 3.36 R
3951 4646 3.181526 CCCAGATCAGGGCAAGAAC 57.818 57.895 10.72 0.0 43.10 3.01 R
4014 4715 0.468226 ACACGAGGAGAAAAGGCACA 59.532 50.000 0.00 0.0 0.00 4.57 R
5448 6340 0.333993 TAAGCTGGTACTCCCTCCGT 59.666 55.000 0.00 0.0 0.00 4.69 R
6570 7550 0.400213 TGAATTTGGCGTGGAGGAGT 59.600 50.000 0.00 0.0 0.00 3.85 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
407 408 1.228306 AATTTCGCCGGGTTCCACA 60.228 52.632 2.18 0.00 0.00 4.17
410 411 2.888464 TTTCGCCGGGTTCCACACAA 62.888 55.000 2.18 0.00 0.00 3.33
555 556 2.372504 CCTCCTCCTCATGCAGATTCAT 59.627 50.000 0.00 0.00 0.00 2.57
596 597 1.842381 CGTCTCCTTCCCCTGCCTTT 61.842 60.000 0.00 0.00 0.00 3.11
798 835 2.025589 CGCCTTAGGGGAGAGAAAAC 57.974 55.000 9.98 0.00 37.91 2.43
799 836 1.555533 CGCCTTAGGGGAGAGAAAACT 59.444 52.381 9.98 0.00 37.91 2.66
800 837 2.027100 CGCCTTAGGGGAGAGAAAACTT 60.027 50.000 9.98 0.00 37.91 2.66
801 838 3.611970 GCCTTAGGGGAGAGAAAACTTC 58.388 50.000 0.00 0.00 37.23 3.01
802 839 3.009143 GCCTTAGGGGAGAGAAAACTTCA 59.991 47.826 0.00 0.00 37.23 3.02
803 840 4.580868 CCTTAGGGGAGAGAAAACTTCAC 58.419 47.826 0.00 0.00 37.23 3.18
804 841 4.287326 CCTTAGGGGAGAGAAAACTTCACT 59.713 45.833 0.00 0.00 37.23 3.41
805 842 5.221945 CCTTAGGGGAGAGAAAACTTCACTT 60.222 44.000 0.00 0.00 37.23 3.16
806 843 4.359434 AGGGGAGAGAAAACTTCACTTC 57.641 45.455 0.00 0.00 30.55 3.01
807 844 3.977326 AGGGGAGAGAAAACTTCACTTCT 59.023 43.478 0.00 0.00 34.58 2.85
808 845 4.068599 GGGGAGAGAAAACTTCACTTCTG 58.931 47.826 0.00 0.00 32.01 3.02
809 846 3.500299 GGGAGAGAAAACTTCACTTCTGC 59.500 47.826 0.00 0.00 32.01 4.26
810 847 4.384940 GGAGAGAAAACTTCACTTCTGCT 58.615 43.478 0.00 0.00 32.01 4.24
811 848 4.213059 GGAGAGAAAACTTCACTTCTGCTG 59.787 45.833 0.00 0.00 32.01 4.41
812 849 4.133078 AGAGAAAACTTCACTTCTGCTGG 58.867 43.478 0.00 0.00 32.01 4.85
813 850 2.620585 AGAAAACTTCACTTCTGCTGGC 59.379 45.455 0.00 0.00 30.67 4.85
814 851 2.355010 AAACTTCACTTCTGCTGGCT 57.645 45.000 0.00 0.00 0.00 4.75
815 852 1.889545 AACTTCACTTCTGCTGGCTC 58.110 50.000 0.00 0.00 0.00 4.70
816 853 0.761187 ACTTCACTTCTGCTGGCTCA 59.239 50.000 0.00 0.00 0.00 4.26
817 854 1.155042 CTTCACTTCTGCTGGCTCAC 58.845 55.000 0.00 0.00 0.00 3.51
818 855 0.469494 TTCACTTCTGCTGGCTCACA 59.531 50.000 0.00 0.00 0.00 3.58
819 856 0.250038 TCACTTCTGCTGGCTCACAC 60.250 55.000 0.00 0.00 0.00 3.82
820 857 1.072159 ACTTCTGCTGGCTCACACC 59.928 57.895 0.00 0.00 0.00 4.16
821 858 1.374190 CTTCTGCTGGCTCACACCT 59.626 57.895 0.00 0.00 0.00 4.00
822 859 0.954449 CTTCTGCTGGCTCACACCTG 60.954 60.000 0.00 0.00 0.00 4.00
823 860 2.359602 CTGCTGGCTCACACCTGG 60.360 66.667 0.00 0.00 0.00 4.45
824 861 4.648626 TGCTGGCTCACACCTGGC 62.649 66.667 0.00 0.00 0.00 4.85
825 862 4.341783 GCTGGCTCACACCTGGCT 62.342 66.667 0.00 0.00 0.00 4.75
826 863 2.046507 CTGGCTCACACCTGGCTC 60.047 66.667 0.00 0.00 0.00 4.70
827 864 2.848679 TGGCTCACACCTGGCTCA 60.849 61.111 0.00 0.00 0.00 4.26
828 865 2.401699 CTGGCTCACACCTGGCTCAA 62.402 60.000 0.00 0.00 0.00 3.02
829 866 1.228245 GGCTCACACCTGGCTCAAA 60.228 57.895 0.00 0.00 0.00 2.69
830 867 0.823356 GGCTCACACCTGGCTCAAAA 60.823 55.000 0.00 0.00 0.00 2.44
831 868 0.595095 GCTCACACCTGGCTCAAAAG 59.405 55.000 0.00 0.00 0.00 2.27
840 877 6.206634 CACACCTGGCTCAAAAGATAGTTTTA 59.793 38.462 0.00 0.00 0.00 1.52
858 895 4.805140 TTTATTAGTCCATGGGCCATGA 57.195 40.909 41.10 26.30 43.81 3.07
971 1017 4.842091 CCCGGACGGCGTTACTCG 62.842 72.222 16.19 15.55 43.12 4.18
1098 1531 2.670592 TCGTCGGAGGAGTTCGCA 60.671 61.111 0.00 0.00 0.00 5.10
1151 1584 1.857965 ACTGCTCTGCACCTCATCTA 58.142 50.000 0.00 0.00 33.79 1.98
1165 1598 0.958091 CATCTACTCCCAGCTCTCCG 59.042 60.000 0.00 0.00 0.00 4.63
1180 1613 1.900486 TCTCCGTTCCTTCCTTCCTTC 59.100 52.381 0.00 0.00 0.00 3.46
1201 1634 1.002134 CGTGCCCCCTTCTGATGTT 60.002 57.895 0.00 0.00 0.00 2.71
1214 1647 0.537143 TGATGTTCCCGTGCTTGCTT 60.537 50.000 0.00 0.00 0.00 3.91
1247 1681 7.070629 GGAAACCCCAATATTTAGGTATTCCA 58.929 38.462 23.17 0.00 38.30 3.53
1250 1684 5.370289 ACCCCAATATTTAGGTATTCCACGA 59.630 40.000 4.62 0.00 35.89 4.35
1366 1804 6.547880 CCTGTACAGTTCATACTAGGAGACAT 59.452 42.308 21.18 0.00 31.96 3.06
1395 1849 0.180406 AGTCCACTTTGCAACCGTCT 59.820 50.000 0.00 0.00 0.00 4.18
1627 2082 6.702282 GCTGACACTAGGTATATTGTTCCTTC 59.298 42.308 0.00 0.00 33.34 3.46
1663 2118 2.100252 CCCATTCTCCACATTCATGCAC 59.900 50.000 0.00 0.00 0.00 4.57
1722 2177 4.889409 TGGTGATTCATCCAAAGATAAGGC 59.111 41.667 5.75 0.00 0.00 4.35
1728 2183 5.034852 TCATCCAAAGATAAGGCGATTGA 57.965 39.130 0.00 0.00 0.00 2.57
1767 2222 3.453717 TCAGAGGAAATGTGCTCAGCTAT 59.546 43.478 7.22 0.00 44.36 2.97
1770 2225 4.057432 GAGGAAATGTGCTCAGCTATCTC 58.943 47.826 0.00 0.00 41.66 2.75
1780 2235 3.255642 GCTCAGCTATCTCGGAGAATTCT 59.744 47.826 12.40 7.95 34.09 2.40
1829 2285 0.613012 GCCTTTTGCACCCTCCTGAT 60.613 55.000 0.00 0.00 40.77 2.90
1830 2286 1.340991 GCCTTTTGCACCCTCCTGATA 60.341 52.381 0.00 0.00 40.77 2.15
1831 2287 2.883888 GCCTTTTGCACCCTCCTGATAA 60.884 50.000 0.00 0.00 40.77 1.75
1832 2288 2.755103 CCTTTTGCACCCTCCTGATAAC 59.245 50.000 0.00 0.00 0.00 1.89
1951 2408 8.379457 AGATGCTCGTTAGAAGTTTTAAAAGT 57.621 30.769 0.00 1.03 0.00 2.66
1971 2428 0.460987 GGACATTCAGGAGGTCTGCG 60.461 60.000 0.00 0.00 43.06 5.18
1972 2429 0.460987 GACATTCAGGAGGTCTGCGG 60.461 60.000 0.00 0.00 43.06 5.69
2026 2483 5.877012 TCTATTCATGACTTCCAAGCTTCAC 59.123 40.000 0.00 0.00 0.00 3.18
2183 2641 2.615493 CCATAACCTTCTCTGCGTGGTT 60.615 50.000 0.00 0.00 44.03 3.67
2205 2663 2.289002 GCTGGATGCAAGAAAGGTATCG 59.711 50.000 0.00 0.00 42.31 2.92
2423 2928 5.811399 TTGAGATATTGGTTTTGTAGCGG 57.189 39.130 0.00 0.00 0.00 5.52
2924 3507 4.437682 TCATCATACCATTCTGAACCCC 57.562 45.455 0.00 0.00 0.00 4.95
3016 3599 3.452264 TGCTAGCATAGTGTGACATCCTT 59.548 43.478 14.93 0.00 41.93 3.36
3156 3744 3.493524 GCTCTGCTAAGTATCCTCCAACC 60.494 52.174 0.00 0.00 0.00 3.77
3194 3782 9.209175 GGATAGCTAATACATCTTACACTTTGG 57.791 37.037 0.00 0.00 0.00 3.28
3591 4181 5.375417 TGAAGTGCATGTTCAATGGTTAG 57.625 39.130 11.03 0.00 30.89 2.34
3598 4188 3.713826 TGTTCAATGGTTAGTCTCCCC 57.286 47.619 0.00 0.00 0.00 4.81
3897 4592 7.987649 TGGTAGTACAAAACTTTCGTTTCATT 58.012 30.769 2.06 0.00 42.28 2.57
3951 4646 0.040204 AAATCACCTGGCTCCTTGGG 59.960 55.000 0.00 0.00 0.00 4.12
3987 4682 8.727149 TGATCTGGGGATTTTAACTAGATGATT 58.273 33.333 0.00 0.00 31.46 2.57
3991 4692 8.025270 TGGGGATTTTAACTAGATGATTCGTA 57.975 34.615 0.00 0.00 0.00 3.43
4014 4715 0.888619 TCTGCGTGCAGTAGTTAGCT 59.111 50.000 20.33 0.00 43.96 3.32
4399 5228 6.090358 ACAACGAGGTTAAAAGTCATGATACG 59.910 38.462 0.00 0.00 0.00 3.06
4749 5606 1.685765 TGCCATAGCACGTCTCCCT 60.686 57.895 0.00 0.00 46.52 4.20
5171 6036 4.993584 GCTGTTGACTATCATGATACAGGG 59.006 45.833 25.96 14.66 0.00 4.45
5174 6039 5.838521 TGTTGACTATCATGATACAGGGCTA 59.161 40.000 11.49 0.00 0.00 3.93
5236 6101 0.877071 CTGCAATGGACGCACTTCTT 59.123 50.000 0.00 0.00 35.08 2.52
5363 6255 7.421087 AACTAGTTAAGAATGTACTCCCTCC 57.579 40.000 6.26 0.00 0.00 4.30
5364 6256 5.593502 ACTAGTTAAGAATGTACTCCCTCCG 59.406 44.000 0.00 0.00 0.00 4.63
5365 6257 4.351127 AGTTAAGAATGTACTCCCTCCGT 58.649 43.478 0.00 0.00 0.00 4.69
5366 6258 4.776308 AGTTAAGAATGTACTCCCTCCGTT 59.224 41.667 0.00 0.00 0.00 4.44
5367 6259 3.889520 AAGAATGTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
5368 6260 2.108970 AGAATGTACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
5369 6261 1.829222 GAATGTACTCCCTCCGTTCCA 59.171 52.381 0.00 0.00 0.00 3.53
5370 6262 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
5371 6263 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
5372 6264 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
5373 6265 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
5374 6266 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
5375 6267 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
5376 6268 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
5377 6269 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
5378 6270 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
5379 6271 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
5380 6272 3.119029 CCCTCCGTTCCAAATTACTCGTA 60.119 47.826 0.00 0.00 0.00 3.43
5381 6273 4.110482 CCTCCGTTCCAAATTACTCGTAG 58.890 47.826 0.00 0.00 0.00 3.51
5382 6274 3.514645 TCCGTTCCAAATTACTCGTAGC 58.485 45.455 0.00 0.00 0.00 3.58
5383 6275 3.194116 TCCGTTCCAAATTACTCGTAGCT 59.806 43.478 0.00 0.00 0.00 3.32
5384 6276 3.306166 CCGTTCCAAATTACTCGTAGCTG 59.694 47.826 0.00 0.00 0.00 4.24
5385 6277 4.171005 CGTTCCAAATTACTCGTAGCTGA 58.829 43.478 0.00 0.00 0.00 4.26
5386 6278 4.624024 CGTTCCAAATTACTCGTAGCTGAA 59.376 41.667 0.00 0.00 0.00 3.02
5387 6279 5.119588 CGTTCCAAATTACTCGTAGCTGAAA 59.880 40.000 0.00 0.00 0.00 2.69
5388 6280 6.183360 CGTTCCAAATTACTCGTAGCTGAAAT 60.183 38.462 0.00 0.00 0.00 2.17
5389 6281 6.662414 TCCAAATTACTCGTAGCTGAAATG 57.338 37.500 0.00 0.00 0.00 2.32
5390 6282 5.584649 TCCAAATTACTCGTAGCTGAAATGG 59.415 40.000 0.00 0.00 0.00 3.16
5391 6283 5.584649 CCAAATTACTCGTAGCTGAAATGGA 59.415 40.000 0.00 0.00 0.00 3.41
5392 6284 6.260936 CCAAATTACTCGTAGCTGAAATGGAT 59.739 38.462 0.00 0.00 0.00 3.41
5393 6285 6.851222 AATTACTCGTAGCTGAAATGGATG 57.149 37.500 0.00 0.00 0.00 3.51
5394 6286 3.895232 ACTCGTAGCTGAAATGGATGT 57.105 42.857 0.00 0.00 0.00 3.06
5395 6287 6.459670 TTACTCGTAGCTGAAATGGATGTA 57.540 37.500 0.00 0.00 0.00 2.29
5396 6288 5.537300 ACTCGTAGCTGAAATGGATGTAT 57.463 39.130 0.00 0.00 0.00 2.29
5397 6289 5.533482 ACTCGTAGCTGAAATGGATGTATC 58.467 41.667 0.00 0.00 0.00 2.24
5398 6290 5.303078 ACTCGTAGCTGAAATGGATGTATCT 59.697 40.000 0.00 0.00 0.00 1.98
5399 6291 6.490381 ACTCGTAGCTGAAATGGATGTATCTA 59.510 38.462 0.00 0.00 0.00 1.98
5400 6292 6.914259 TCGTAGCTGAAATGGATGTATCTAG 58.086 40.000 0.00 0.00 0.00 2.43
5401 6293 6.715264 TCGTAGCTGAAATGGATGTATCTAGA 59.285 38.462 0.00 0.00 0.00 2.43
5402 6294 7.230712 TCGTAGCTGAAATGGATGTATCTAGAA 59.769 37.037 0.00 0.00 0.00 2.10
5403 6295 7.327275 CGTAGCTGAAATGGATGTATCTAGAAC 59.673 40.741 0.00 0.00 0.00 3.01
5404 6296 7.372260 AGCTGAAATGGATGTATCTAGAACT 57.628 36.000 0.00 0.00 0.00 3.01
5405 6297 8.484214 AGCTGAAATGGATGTATCTAGAACTA 57.516 34.615 0.00 0.00 0.00 2.24
5406 6298 8.928448 AGCTGAAATGGATGTATCTAGAACTAA 58.072 33.333 0.00 0.00 0.00 2.24
5407 6299 9.547753 GCTGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
5425 6317 9.656323 AGAACTAAATACATCTAGGTACATCCA 57.344 33.333 0.00 0.00 39.02 3.41
5432 6324 6.042638 ACATCTAGGTACATCCATATGTGC 57.957 41.667 1.24 0.00 45.99 4.57
5433 6325 4.783764 TCTAGGTACATCCATATGTGCG 57.216 45.455 1.24 0.00 46.32 5.34
5434 6326 4.403734 TCTAGGTACATCCATATGTGCGA 58.596 43.478 1.24 0.00 46.32 5.10
5435 6327 3.386768 AGGTACATCCATATGTGCGAC 57.613 47.619 1.24 0.00 46.32 5.19
5436 6328 2.698274 AGGTACATCCATATGTGCGACA 59.302 45.455 1.24 0.00 46.32 4.35
5437 6329 3.133901 AGGTACATCCATATGTGCGACAA 59.866 43.478 1.24 0.00 46.32 3.18
5438 6330 3.494626 GGTACATCCATATGTGCGACAAG 59.505 47.826 1.24 0.00 46.32 3.16
5439 6331 3.266510 ACATCCATATGTGCGACAAGT 57.733 42.857 1.24 0.00 44.79 3.16
5440 6332 4.400529 ACATCCATATGTGCGACAAGTA 57.599 40.909 1.24 0.00 44.79 2.24
5441 6333 4.765273 ACATCCATATGTGCGACAAGTAA 58.235 39.130 1.24 0.00 44.79 2.24
5442 6334 5.368145 ACATCCATATGTGCGACAAGTAAT 58.632 37.500 1.24 0.00 44.79 1.89
5443 6335 5.822519 ACATCCATATGTGCGACAAGTAATT 59.177 36.000 1.24 0.00 44.79 1.40
5444 6336 5.984233 TCCATATGTGCGACAAGTAATTC 57.016 39.130 1.24 0.00 0.00 2.17
5445 6337 4.506288 TCCATATGTGCGACAAGTAATTCG 59.494 41.667 1.24 0.00 38.31 3.34
5446 6338 4.318760 CCATATGTGCGACAAGTAATTCGG 60.319 45.833 1.24 0.00 35.73 4.30
5447 6339 2.442212 TGTGCGACAAGTAATTCGGA 57.558 45.000 0.00 0.00 35.73 4.55
5448 6340 2.756829 TGTGCGACAAGTAATTCGGAA 58.243 42.857 0.00 0.00 37.32 4.30
5449 6341 2.477375 TGTGCGACAAGTAATTCGGAAC 59.523 45.455 0.00 0.00 37.32 3.62
5513 6405 2.221055 GTCCAACGTGTCAATGTCTCAC 59.779 50.000 0.00 0.00 0.00 3.51
5530 6422 2.164624 CTCACGGAGCTAAGCAACTACT 59.835 50.000 0.00 0.00 0.00 2.57
5588 6480 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
5589 6481 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
5590 6482 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
5591 6483 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
5619 6511 9.866655 TTTCTTTACGGAGGGAGTAATATAGTA 57.133 33.333 0.00 0.00 34.50 1.82
5705 6597 2.093306 TGTCATGGAGCTAACCAACG 57.907 50.000 0.00 0.00 43.47 4.10
5717 6627 5.310451 AGCTAACCAACGAGTTTTTATCCA 58.690 37.500 0.00 0.00 0.00 3.41
5781 6691 2.596904 TGTTGATCGGCCTAGCTAAC 57.403 50.000 0.00 1.15 0.00 2.34
5825 6735 5.163216 GGATTGGAGGATAGATCATGGATCC 60.163 48.000 4.20 4.20 39.66 3.36
5860 6770 0.391228 TGCCTAGAGTTGCGTTGTCA 59.609 50.000 0.00 0.00 0.00 3.58
5883 6793 1.576421 GAAGCTTGCTGTGGGTTCG 59.424 57.895 2.10 0.00 31.87 3.95
5895 6805 4.261867 GCTGTGGGTTCGGAATTTACTTTT 60.262 41.667 0.00 0.00 0.00 2.27
5906 6816 8.638629 TCGGAATTTACTTTTTGAAAGGGATA 57.361 30.769 5.52 0.00 0.00 2.59
5930 6840 1.588861 GGATTCGTTCGAGCTGCTAAC 59.411 52.381 0.15 3.47 0.00 2.34
5932 6842 0.731514 TTCGTTCGAGCTGCTAACCG 60.732 55.000 0.15 1.97 0.00 4.44
5951 6861 2.353704 CCGGACTAGTGCAACATGAGAA 60.354 50.000 15.20 0.00 41.43 2.87
5984 6909 5.920312 GTGTCACTATCAACACTGTCAATG 58.080 41.667 0.00 0.00 41.97 2.82
5985 6910 4.452114 TGTCACTATCAACACTGTCAATGC 59.548 41.667 0.00 0.00 0.00 3.56
5987 6912 5.180117 GTCACTATCAACACTGTCAATGCTT 59.820 40.000 0.00 0.00 0.00 3.91
5988 6913 5.764686 TCACTATCAACACTGTCAATGCTTT 59.235 36.000 0.00 0.00 0.00 3.51
5989 6914 5.854866 CACTATCAACACTGTCAATGCTTTG 59.145 40.000 5.99 5.99 0.00 2.77
6075 7041 2.633481 AGTACTTCCAGTGACTTGGTCC 59.367 50.000 0.00 0.00 39.35 4.46
6123 7089 2.289072 TGAAGCTTGCTGGTCACTAGTC 60.289 50.000 2.10 0.00 0.00 2.59
6144 7110 1.675641 ACATCCTGTTTCCGGCAGC 60.676 57.895 0.00 0.00 32.93 5.25
6163 7129 2.916502 CTTGGTACGCCATAGCCGCA 62.917 60.000 0.00 0.00 45.56 5.69
6164 7130 2.030562 GGTACGCCATAGCCGCAT 59.969 61.111 0.00 0.00 34.57 4.73
6165 7131 2.027625 GGTACGCCATAGCCGCATC 61.028 63.158 0.00 0.00 34.57 3.91
6166 7132 1.300620 GTACGCCATAGCCGCATCA 60.301 57.895 0.00 0.00 34.57 3.07
6167 7133 1.300620 TACGCCATAGCCGCATCAC 60.301 57.895 0.00 0.00 34.57 3.06
6168 7134 2.022240 TACGCCATAGCCGCATCACA 62.022 55.000 0.00 0.00 34.57 3.58
6169 7135 1.962822 CGCCATAGCCGCATCACAT 60.963 57.895 0.00 0.00 34.57 3.21
6171 7137 0.239347 GCCATAGCCGCATCACATTC 59.761 55.000 0.00 0.00 0.00 2.67
6172 7138 1.596603 CCATAGCCGCATCACATTCA 58.403 50.000 0.00 0.00 0.00 2.57
6202 7168 7.398024 AGATAAAAGTGTAAACTGAGAGGCAT 58.602 34.615 0.00 0.00 0.00 4.40
6203 7169 5.695851 AAAAGTGTAAACTGAGAGGCATG 57.304 39.130 0.00 0.00 0.00 4.06
6226 7192 1.353694 AGCCTGCAAGACATTCTCCTT 59.646 47.619 0.00 0.00 34.07 3.36
6233 7199 4.202040 TGCAAGACATTCTCCTTTGTTGTG 60.202 41.667 0.00 0.00 0.00 3.33
6234 7200 4.202050 GCAAGACATTCTCCTTTGTTGTGT 60.202 41.667 0.00 0.00 0.00 3.72
6235 7201 5.008613 GCAAGACATTCTCCTTTGTTGTGTA 59.991 40.000 0.00 0.00 0.00 2.90
6236 7202 6.294176 GCAAGACATTCTCCTTTGTTGTGTAT 60.294 38.462 0.00 0.00 0.00 2.29
6253 7219 8.920174 TGTTGTGTATATAGCAGGTACAATAGT 58.080 33.333 0.00 0.00 30.87 2.12
6267 7233 3.046374 ACAATAGTGGGAGGGTATGTCC 58.954 50.000 0.00 0.00 0.00 4.02
6313 7279 5.913137 AGTGGTTCATGTTTCTCACAAAA 57.087 34.783 0.00 0.00 39.50 2.44
6314 7280 5.650543 AGTGGTTCATGTTTCTCACAAAAC 58.349 37.500 0.00 0.00 39.50 2.43
6394 7360 7.871853 ACTTCATTTTACTTGTCATGTGTACC 58.128 34.615 1.71 0.00 0.00 3.34
6410 7376 4.926832 TGTGTACCATCAATGTAGTGAACG 59.073 41.667 0.00 0.00 0.00 3.95
6427 7393 9.136952 GTAGTGAACGAAACATTCTAACTGTAT 57.863 33.333 0.00 0.00 0.00 2.29
6465 7435 6.067263 ACAAAACAATACAATACGCACAGT 57.933 33.333 0.00 0.00 0.00 3.55
6479 7449 0.592637 CACAGTCGCTTGCCATTCAA 59.407 50.000 0.00 0.00 0.00 2.69
6516 7486 4.011966 TCAGAGAAATGCAGAGCTCAAA 57.988 40.909 17.77 0.41 0.00 2.69
6535 7513 1.774110 ATTGCACCCAACAAGTGACA 58.226 45.000 0.00 0.00 37.42 3.58
6538 7516 0.814457 GCACCCAACAAGTGACACAA 59.186 50.000 8.59 0.00 37.42 3.33
6556 7536 7.752239 GTGACACAAAGACAAAGATAATGATGG 59.248 37.037 0.00 0.00 0.00 3.51
6567 7547 7.173907 ACAAAGATAATGATGGAATAGAAGGCG 59.826 37.037 0.00 0.00 0.00 5.52
6570 7550 7.453393 AGATAATGATGGAATAGAAGGCGAAA 58.547 34.615 0.00 0.00 0.00 3.46
6574 7554 3.261981 TGGAATAGAAGGCGAAACTCC 57.738 47.619 0.00 0.00 0.00 3.85
6580 7560 1.004918 AAGGCGAAACTCCTCCACG 60.005 57.895 0.00 0.00 32.45 4.94
6643 7623 7.989170 TGCATCTATGATGTTGTAGTGAAAGAT 59.011 33.333 8.98 0.00 0.00 2.40
6650 7630 9.857656 ATGATGTTGTAGTGAAAGATATGGAAT 57.142 29.630 0.00 0.00 0.00 3.01
6663 7646 9.472361 GAAAGATATGGAATTTGATGTTCATGG 57.528 33.333 0.00 0.00 0.00 3.66
6674 7657 1.532523 TGTTCATGGATGCAGCGAAA 58.467 45.000 0.00 0.00 0.00 3.46
6706 7689 6.791303 TCCAACTGTACAAACTTTGATTGAC 58.209 36.000 8.55 2.13 0.00 3.18
6709 7692 5.821204 ACTGTACAAACTTTGATTGACAGC 58.179 37.500 19.23 0.00 38.29 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
407 408 2.513395 TGGGGACATGCGTGTTGT 59.487 55.556 13.92 0.00 39.09 3.32
555 556 2.158813 ACGGAGGAACTTCTTGCAAGAA 60.159 45.455 33.65 33.65 41.55 2.52
596 597 1.001633 GGCGGAAACAAGTACTCAGGA 59.998 52.381 0.00 0.00 0.00 3.86
797 834 0.761187 TGAGCCAGCAGAAGTGAAGT 59.239 50.000 0.00 0.00 0.00 3.01
798 835 1.155042 GTGAGCCAGCAGAAGTGAAG 58.845 55.000 0.00 0.00 0.00 3.02
799 836 0.469494 TGTGAGCCAGCAGAAGTGAA 59.531 50.000 0.00 0.00 0.00 3.18
800 837 0.250038 GTGTGAGCCAGCAGAAGTGA 60.250 55.000 0.00 0.00 0.00 3.41
801 838 1.233285 GGTGTGAGCCAGCAGAAGTG 61.233 60.000 0.00 0.00 41.31 3.16
802 839 1.072159 GGTGTGAGCCAGCAGAAGT 59.928 57.895 0.00 0.00 41.31 3.01
803 840 0.954449 CAGGTGTGAGCCAGCAGAAG 60.954 60.000 0.00 0.00 44.16 2.85
804 841 1.071987 CAGGTGTGAGCCAGCAGAA 59.928 57.895 0.00 0.00 44.16 3.02
805 842 2.745698 CAGGTGTGAGCCAGCAGA 59.254 61.111 0.00 0.00 44.16 4.26
806 843 2.359602 CCAGGTGTGAGCCAGCAG 60.360 66.667 0.00 0.00 44.16 4.24
807 844 4.648626 GCCAGGTGTGAGCCAGCA 62.649 66.667 0.00 0.00 44.16 4.41
808 845 4.341783 AGCCAGGTGTGAGCCAGC 62.342 66.667 0.00 0.00 42.00 4.85
809 846 2.046507 GAGCCAGGTGTGAGCCAG 60.047 66.667 0.00 0.00 0.00 4.85
810 847 1.993701 TTTGAGCCAGGTGTGAGCCA 61.994 55.000 0.00 0.00 0.00 4.75
811 848 0.823356 TTTTGAGCCAGGTGTGAGCC 60.823 55.000 0.00 0.00 0.00 4.70
812 849 0.595095 CTTTTGAGCCAGGTGTGAGC 59.405 55.000 0.00 0.00 0.00 4.26
813 850 2.260844 TCTTTTGAGCCAGGTGTGAG 57.739 50.000 0.00 0.00 0.00 3.51
814 851 2.957402 ATCTTTTGAGCCAGGTGTGA 57.043 45.000 0.00 0.00 0.00 3.58
815 852 3.679389 ACTATCTTTTGAGCCAGGTGTG 58.321 45.455 0.00 0.00 0.00 3.82
816 853 4.373156 AACTATCTTTTGAGCCAGGTGT 57.627 40.909 0.00 0.00 0.00 4.16
817 854 5.712152 AAAACTATCTTTTGAGCCAGGTG 57.288 39.130 0.00 0.00 0.00 4.00
818 855 9.178758 CTAATAAAACTATCTTTTGAGCCAGGT 57.821 33.333 0.00 0.00 0.00 4.00
819 856 9.178758 ACTAATAAAACTATCTTTTGAGCCAGG 57.821 33.333 0.00 0.00 0.00 4.45
821 858 9.174166 GGACTAATAAAACTATCTTTTGAGCCA 57.826 33.333 0.00 0.00 0.00 4.75
822 859 9.174166 TGGACTAATAAAACTATCTTTTGAGCC 57.826 33.333 0.00 0.00 0.00 4.70
827 864 8.914011 GCCCATGGACTAATAAAACTATCTTTT 58.086 33.333 15.22 0.00 0.00 2.27
828 865 7.505923 GGCCCATGGACTAATAAAACTATCTTT 59.494 37.037 15.22 0.00 0.00 2.52
829 866 7.004691 GGCCCATGGACTAATAAAACTATCTT 58.995 38.462 15.22 0.00 0.00 2.40
830 867 6.102615 TGGCCCATGGACTAATAAAACTATCT 59.897 38.462 15.22 0.00 0.00 1.98
831 868 6.303839 TGGCCCATGGACTAATAAAACTATC 58.696 40.000 15.22 0.00 0.00 2.08
840 877 1.145738 GGTCATGGCCCATGGACTAAT 59.854 52.381 23.20 0.00 41.66 1.73
858 895 0.846693 AAGTGAAGCTTGGTCCAGGT 59.153 50.000 2.10 0.00 35.80 4.00
870 907 2.159028 GCCTAGCCTCCTGTAAGTGAAG 60.159 54.545 0.00 0.00 0.00 3.02
871 908 1.831736 GCCTAGCCTCCTGTAAGTGAA 59.168 52.381 0.00 0.00 0.00 3.18
1151 1584 1.985116 GGAACGGAGAGCTGGGAGT 60.985 63.158 0.00 0.00 0.00 3.85
1165 1598 0.035343 CGGGGAAGGAAGGAAGGAAC 60.035 60.000 0.00 0.00 0.00 3.62
1201 1634 3.936203 ACGGAAGCAAGCACGGGA 61.936 61.111 0.00 0.00 0.00 5.14
1247 1681 0.319083 TGACCCATTAAGCACGTCGT 59.681 50.000 0.00 0.00 0.00 4.34
1250 1684 0.676782 GGCTGACCCATTAAGCACGT 60.677 55.000 0.00 0.00 38.73 4.49
1395 1849 6.435591 TGAATGAACAGGGTAAATGTTGCATA 59.564 34.615 0.00 0.00 40.86 3.14
1554 2008 7.121315 ACAGCATAATTTAGGACTTCCAAGTTC 59.879 37.037 0.00 0.00 39.88 3.01
1627 2082 6.183361 TGGAGAATGGGATAGAAACCTACATG 60.183 42.308 0.00 0.00 0.00 3.21
1663 2118 2.648059 CCCAGGTAAGATTTGCAGGAG 58.352 52.381 0.00 0.00 0.00 3.69
1722 2177 0.539051 AGTTGGCTCCTCCTCAATCG 59.461 55.000 0.00 0.00 35.26 3.34
1728 2183 1.072965 CTGAACAAGTTGGCTCCTCCT 59.927 52.381 7.96 0.00 35.26 3.69
1767 2222 2.828520 AGTTGCTCAGAATTCTCCGAGA 59.171 45.455 21.24 9.32 0.00 4.04
1770 2225 3.244033 AGAGTTGCTCAGAATTCTCCG 57.756 47.619 4.57 0.42 32.06 4.63
1780 2235 3.190079 CTGCGCTAAATAGAGTTGCTCA 58.810 45.455 9.73 0.00 32.06 4.26
1824 2280 8.399425 CACTACAGTCACTACTTAGTTATCAGG 58.601 40.741 0.00 0.00 33.46 3.86
1831 2287 9.730705 TGTATAACACTACAGTCACTACTTAGT 57.269 33.333 0.00 0.00 36.90 2.24
1951 2408 0.615331 GCAGACCTCCTGAATGTCCA 59.385 55.000 0.00 0.00 45.78 4.02
1971 2428 4.259770 CGCATGAAAAACAAACACAGTTCC 60.260 41.667 0.00 0.00 0.00 3.62
1972 2429 4.560819 TCGCATGAAAAACAAACACAGTTC 59.439 37.500 0.00 0.00 0.00 3.01
2270 2734 6.279513 ACCAACACATGAAACTCAAAGAAA 57.720 33.333 0.00 0.00 0.00 2.52
2345 2850 7.847564 GTGAAAAGATCATGAAACAAAAGTTGC 59.152 33.333 0.00 0.00 40.97 4.17
2962 3545 9.481340 TGAGCTTCTCACATATATCAAATGTAC 57.519 33.333 0.00 0.00 35.39 2.90
3085 3669 1.632422 GCAACATGCAGATTTTCCCG 58.368 50.000 0.00 0.00 44.26 5.14
3194 3782 6.177610 TGGTGATACCTGTTAAATGAACTCC 58.822 40.000 0.00 0.00 39.58 3.85
3436 4024 3.244112 ACGTGAACTGAAGGAAACTAGGG 60.244 47.826 0.00 0.00 42.68 3.53
3591 4181 2.572104 ACCTCATGTTTACAGGGGAGAC 59.428 50.000 0.00 0.00 27.66 3.36
3598 4188 8.279970 TGATATGGAAAACCTCATGTTTACAG 57.720 34.615 0.00 0.00 46.39 2.74
3897 4592 6.127758 ACAGCACACTTGAGTATTTTCAAACA 60.128 34.615 0.00 0.00 36.69 2.83
3951 4646 3.181526 CCCAGATCAGGGCAAGAAC 57.818 57.895 10.72 0.00 43.10 3.01
3987 4682 3.342370 CTGCACGCAGAGGCTACGA 62.342 63.158 13.87 0.00 46.30 3.43
3991 4692 1.821061 AACTACTGCACGCAGAGGCT 61.821 55.000 25.09 5.61 46.30 4.58
4014 4715 0.468226 ACACGAGGAGAAAAGGCACA 59.532 50.000 0.00 0.00 0.00 4.57
4242 4955 9.658799 CAAATAGTCAATAGAAGTTTGGAGAGA 57.341 33.333 0.00 0.00 0.00 3.10
4399 5228 0.944386 TTGCGCCTTTCTTGTCAGAC 59.056 50.000 4.18 0.00 0.00 3.51
4732 5589 0.107654 AAAGGGAGACGTGCTATGGC 60.108 55.000 0.00 0.00 39.26 4.40
5139 6004 7.785033 TCATGATAGTCAACAGCTTAGAATCA 58.215 34.615 0.00 0.00 0.00 2.57
5171 6036 8.030106 AGTGTAGAATGTCTTGTAGAACTTAGC 58.970 37.037 0.00 0.00 0.00 3.09
5174 6039 6.647067 GCAGTGTAGAATGTCTTGTAGAACTT 59.353 38.462 0.00 0.00 0.00 2.66
5236 6101 8.221944 TGGAAAGAAAACAGTTCCTTCCTATTA 58.778 33.333 14.48 0.00 41.26 0.98
5357 6249 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
5358 6250 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5359 6251 2.968675 ACGAGTAATTTGGAACGGAGG 58.031 47.619 0.00 0.00 0.00 4.30
5360 6252 3.550678 GCTACGAGTAATTTGGAACGGAG 59.449 47.826 0.00 0.00 35.24 4.63
5361 6253 3.194116 AGCTACGAGTAATTTGGAACGGA 59.806 43.478 0.00 0.00 0.00 4.69
5362 6254 3.306166 CAGCTACGAGTAATTTGGAACGG 59.694 47.826 0.00 0.00 0.00 4.44
5363 6255 4.171005 TCAGCTACGAGTAATTTGGAACG 58.829 43.478 0.00 0.00 0.00 3.95
5364 6256 6.476243 TTTCAGCTACGAGTAATTTGGAAC 57.524 37.500 0.00 0.00 0.00 3.62
5365 6257 6.093495 CCATTTCAGCTACGAGTAATTTGGAA 59.907 38.462 0.00 0.00 0.00 3.53
5366 6258 5.584649 CCATTTCAGCTACGAGTAATTTGGA 59.415 40.000 0.00 0.00 0.00 3.53
5367 6259 5.584649 TCCATTTCAGCTACGAGTAATTTGG 59.415 40.000 0.00 0.00 0.00 3.28
5368 6260 6.662414 TCCATTTCAGCTACGAGTAATTTG 57.338 37.500 0.00 0.00 0.00 2.32
5369 6261 6.823689 ACATCCATTTCAGCTACGAGTAATTT 59.176 34.615 0.00 0.00 0.00 1.82
5370 6262 6.349300 ACATCCATTTCAGCTACGAGTAATT 58.651 36.000 0.00 0.00 0.00 1.40
5371 6263 5.918608 ACATCCATTTCAGCTACGAGTAAT 58.081 37.500 0.00 0.00 0.00 1.89
5372 6264 5.339008 ACATCCATTTCAGCTACGAGTAA 57.661 39.130 0.00 0.00 0.00 2.24
5373 6265 6.490381 AGATACATCCATTTCAGCTACGAGTA 59.510 38.462 0.00 0.00 0.00 2.59
5374 6266 3.895232 ACATCCATTTCAGCTACGAGT 57.105 42.857 0.00 0.00 0.00 4.18
5375 6267 5.777802 AGATACATCCATTTCAGCTACGAG 58.222 41.667 0.00 0.00 0.00 4.18
5376 6268 5.791336 AGATACATCCATTTCAGCTACGA 57.209 39.130 0.00 0.00 0.00 3.43
5377 6269 6.914259 TCTAGATACATCCATTTCAGCTACG 58.086 40.000 0.00 0.00 0.00 3.51
5378 6270 8.364142 AGTTCTAGATACATCCATTTCAGCTAC 58.636 37.037 0.00 0.00 0.00 3.58
5379 6271 8.484214 AGTTCTAGATACATCCATTTCAGCTA 57.516 34.615 0.00 0.00 0.00 3.32
5380 6272 7.372260 AGTTCTAGATACATCCATTTCAGCT 57.628 36.000 0.00 0.00 0.00 4.24
5381 6273 9.547753 TTTAGTTCTAGATACATCCATTTCAGC 57.452 33.333 0.00 0.00 0.00 4.26
5399 6291 9.656323 TGGATGTACCTAGATGTATTTAGTTCT 57.344 33.333 0.00 0.00 39.86 3.01
5406 6298 8.260818 GCACATATGGATGTACCTAGATGTATT 58.739 37.037 7.80 0.00 44.82 1.89
5407 6299 7.416777 CGCACATATGGATGTACCTAGATGTAT 60.417 40.741 7.80 0.00 44.82 2.29
5408 6300 6.127730 CGCACATATGGATGTACCTAGATGTA 60.128 42.308 7.80 0.00 44.82 2.29
5409 6301 5.336770 CGCACATATGGATGTACCTAGATGT 60.337 44.000 7.80 0.00 44.82 3.06
5410 6302 5.105063 CGCACATATGGATGTACCTAGATG 58.895 45.833 7.80 0.00 44.82 2.90
5411 6303 5.016831 TCGCACATATGGATGTACCTAGAT 58.983 41.667 7.80 0.00 44.82 1.98
5412 6304 4.217767 GTCGCACATATGGATGTACCTAGA 59.782 45.833 7.80 0.00 44.82 2.43
5413 6305 4.022329 TGTCGCACATATGGATGTACCTAG 60.022 45.833 7.80 0.00 44.82 3.02
5414 6306 3.892588 TGTCGCACATATGGATGTACCTA 59.107 43.478 7.80 0.00 44.82 3.08
5415 6307 2.698274 TGTCGCACATATGGATGTACCT 59.302 45.455 7.80 0.00 44.82 3.08
5416 6308 3.106242 TGTCGCACATATGGATGTACC 57.894 47.619 7.80 0.00 44.82 3.34
5417 6309 4.119862 ACTTGTCGCACATATGGATGTAC 58.880 43.478 7.80 1.72 44.82 2.90
5418 6310 4.400529 ACTTGTCGCACATATGGATGTA 57.599 40.909 7.80 0.00 44.82 2.29
5420 6312 5.929697 ATTACTTGTCGCACATATGGATG 57.070 39.130 7.80 0.00 39.16 3.51
5421 6313 5.177511 CGAATTACTTGTCGCACATATGGAT 59.822 40.000 7.80 0.00 0.00 3.41
5422 6314 4.506288 CGAATTACTTGTCGCACATATGGA 59.494 41.667 7.80 0.00 0.00 3.41
5423 6315 4.318760 CCGAATTACTTGTCGCACATATGG 60.319 45.833 7.80 0.00 35.93 2.74
5424 6316 4.506288 TCCGAATTACTTGTCGCACATATG 59.494 41.667 0.00 0.00 35.93 1.78
5425 6317 4.689071 TCCGAATTACTTGTCGCACATAT 58.311 39.130 0.00 0.00 35.93 1.78
5426 6318 4.112716 TCCGAATTACTTGTCGCACATA 57.887 40.909 0.00 0.00 35.93 2.29
5427 6319 2.967362 TCCGAATTACTTGTCGCACAT 58.033 42.857 0.00 0.00 35.93 3.21
5428 6320 2.442212 TCCGAATTACTTGTCGCACA 57.558 45.000 0.00 0.00 35.93 4.57
5429 6321 2.471749 CGTTCCGAATTACTTGTCGCAC 60.472 50.000 0.00 0.00 35.93 5.34
5430 6322 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
5431 6323 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
5432 6324 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
5433 6325 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5434 6326 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5435 6327 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5436 6328 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
5437 6329 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
5438 6330 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
5439 6331 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
5440 6332 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
5441 6333 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
5442 6334 0.967380 GGTACTCCCTCCGTTCCGAA 60.967 60.000 0.00 0.00 0.00 4.30
5443 6335 1.379044 GGTACTCCCTCCGTTCCGA 60.379 63.158 0.00 0.00 0.00 4.55
5444 6336 1.664321 CTGGTACTCCCTCCGTTCCG 61.664 65.000 0.00 0.00 0.00 4.30
5445 6337 1.957765 GCTGGTACTCCCTCCGTTCC 61.958 65.000 0.00 0.00 0.00 3.62
5446 6338 0.971447 AGCTGGTACTCCCTCCGTTC 60.971 60.000 0.00 0.00 0.00 3.95
5447 6339 0.544595 AAGCTGGTACTCCCTCCGTT 60.545 55.000 0.00 0.00 0.00 4.44
5448 6340 0.333993 TAAGCTGGTACTCCCTCCGT 59.666 55.000 0.00 0.00 0.00 4.69
5449 6341 1.705873 ATAAGCTGGTACTCCCTCCG 58.294 55.000 0.00 0.00 0.00 4.63
5450 6342 4.161102 ACATATAAGCTGGTACTCCCTCC 58.839 47.826 0.00 0.00 0.00 4.30
5451 6343 5.810080 AACATATAAGCTGGTACTCCCTC 57.190 43.478 0.00 0.00 0.00 4.30
5452 6344 7.292591 ACAATAACATATAAGCTGGTACTCCCT 59.707 37.037 0.00 0.00 0.00 4.20
5453 6345 7.450903 ACAATAACATATAAGCTGGTACTCCC 58.549 38.462 0.00 0.00 0.00 4.30
5454 6346 8.774586 CAACAATAACATATAAGCTGGTACTCC 58.225 37.037 0.00 0.00 0.00 3.85
5455 6347 9.326413 ACAACAATAACATATAAGCTGGTACTC 57.674 33.333 0.00 0.00 0.00 2.59
5456 6348 9.326413 GACAACAATAACATATAAGCTGGTACT 57.674 33.333 0.00 0.00 0.00 2.73
5513 6405 1.202428 GGGAGTAGTTGCTTAGCTCCG 60.202 57.143 5.60 0.00 44.81 4.63
5530 6422 7.857456 TGCTCTTATATTTGTTTACAGAGGGA 58.143 34.615 0.00 0.00 0.00 4.20
5577 6469 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
5578 6470 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
5579 6471 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
5580 6472 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
5581 6473 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
5582 6474 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
5583 6475 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
5584 6476 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
5585 6477 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
5586 6478 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
5592 6484 9.377238 ACTATATTACTCCCTCCGTAAAGAAAT 57.623 33.333 0.00 0.00 31.36 2.17
5593 6485 8.773033 ACTATATTACTCCCTCCGTAAAGAAA 57.227 34.615 0.00 0.00 31.36 2.52
5594 6486 9.866655 TTACTATATTACTCCCTCCGTAAAGAA 57.133 33.333 0.00 0.00 31.36 2.52
5682 6574 2.107366 TGGTTAGCTCCATGACATCGA 58.893 47.619 0.00 0.00 31.96 3.59
5705 6597 5.391312 ACACCTGCATTGGATAAAAACTC 57.609 39.130 0.00 0.00 0.00 3.01
5717 6627 1.143684 ACACTCTGGAACACCTGCATT 59.856 47.619 0.00 0.00 0.00 3.56
5781 6691 0.996462 ATGCATTCGTCCGTAACACG 59.004 50.000 0.00 0.00 42.11 4.49
5860 6770 0.883833 CCCACAGCAAGCTTCGATTT 59.116 50.000 0.00 0.00 0.00 2.17
5895 6805 5.630415 ACGAATCCTCATATCCCTTTCAA 57.370 39.130 0.00 0.00 0.00 2.69
5906 6816 1.804372 GCAGCTCGAACGAATCCTCAT 60.804 52.381 0.00 0.00 0.00 2.90
5930 6840 1.204704 TCTCATGTTGCACTAGTCCGG 59.795 52.381 0.00 0.00 0.00 5.14
5932 6842 4.507710 TGATTCTCATGTTGCACTAGTCC 58.492 43.478 0.00 0.00 0.00 3.85
5951 6861 7.261325 GTGTTGATAGTGACACTACTGATGAT 58.739 38.462 17.46 0.87 42.13 2.45
5969 6893 4.555313 CGACAAAGCATTGACAGTGTTGAT 60.555 41.667 8.96 0.00 38.94 2.57
5983 6908 7.541783 CCTCAAAATAATTCAATCGACAAAGCA 59.458 33.333 0.00 0.00 0.00 3.91
5984 6909 7.542130 ACCTCAAAATAATTCAATCGACAAAGC 59.458 33.333 0.00 0.00 0.00 3.51
5985 6910 8.970691 ACCTCAAAATAATTCAATCGACAAAG 57.029 30.769 0.00 0.00 0.00 2.77
6164 7130 9.942850 TTACACTTTTATCTCTGATGAATGTGA 57.057 29.630 23.94 13.10 32.78 3.58
6169 7135 9.996554 TCAGTTTACACTTTTATCTCTGATGAA 57.003 29.630 0.00 0.00 0.00 2.57
6171 7137 9.645059 TCTCAGTTTACACTTTTATCTCTGATG 57.355 33.333 0.00 0.00 0.00 3.07
6172 7138 9.868277 CTCTCAGTTTACACTTTTATCTCTGAT 57.132 33.333 0.00 0.00 0.00 2.90
6226 7192 9.758651 CTATTGTACCTGCTATATACACAACAA 57.241 33.333 0.00 0.00 0.00 2.83
6233 7199 7.147880 CCTCCCACTATTGTACCTGCTATATAC 60.148 44.444 0.00 0.00 0.00 1.47
6234 7200 6.895756 CCTCCCACTATTGTACCTGCTATATA 59.104 42.308 0.00 0.00 0.00 0.86
6235 7201 5.721960 CCTCCCACTATTGTACCTGCTATAT 59.278 44.000 0.00 0.00 0.00 0.86
6236 7202 5.084519 CCTCCCACTATTGTACCTGCTATA 58.915 45.833 0.00 0.00 0.00 1.31
6267 7233 1.538512 CCTGCACACAAGAGAACATGG 59.461 52.381 0.00 0.00 0.00 3.66
6279 7245 0.663153 GAACCACTTCACCTGCACAC 59.337 55.000 0.00 0.00 0.00 3.82
6313 7279 7.075741 GCAAACACGATAAAGTAATGACTTGT 58.924 34.615 0.00 0.00 45.50 3.16
6314 7280 6.246332 CGCAAACACGATAAAGTAATGACTTG 59.754 38.462 0.00 0.00 39.68 3.16
6324 7290 2.570169 CCACACGCAAACACGATAAAG 58.430 47.619 0.00 0.00 36.70 1.85
6336 7302 5.039524 ACAAAACTTGTATGCCACACGCA 62.040 43.478 0.00 0.00 43.91 5.24
6393 7359 5.605564 TGTTTCGTTCACTACATTGATGG 57.394 39.130 0.00 0.00 0.00 3.51
6394 7360 7.521529 AGAATGTTTCGTTCACTACATTGATG 58.478 34.615 0.00 0.00 40.29 3.07
6444 7414 5.379003 CGACTGTGCGTATTGTATTGTTTT 58.621 37.500 0.00 0.00 0.00 2.43
6445 7415 4.668177 GCGACTGTGCGTATTGTATTGTTT 60.668 41.667 0.00 0.00 0.00 2.83
6465 7435 0.672889 TTGCTTTGAATGGCAAGCGA 59.327 45.000 3.88 0.00 42.45 4.93
6516 7486 1.408702 GTGTCACTTGTTGGGTGCAAT 59.591 47.619 0.00 0.00 34.97 3.56
6556 7536 3.118738 TGGAGGAGTTTCGCCTTCTATTC 60.119 47.826 0.00 0.00 32.83 1.75
6567 7547 1.534729 ATTTGGCGTGGAGGAGTTTC 58.465 50.000 0.00 0.00 0.00 2.78
6570 7550 0.400213 TGAATTTGGCGTGGAGGAGT 59.600 50.000 0.00 0.00 0.00 3.85
6574 7554 3.976169 TCTTTTTGAATTTGGCGTGGAG 58.024 40.909 0.00 0.00 0.00 3.86
6580 7560 7.857389 GGAATTCACTTTCTTTTTGAATTTGGC 59.143 33.333 7.93 0.00 45.58 4.52
6616 7596 6.908870 TTCACTACAACATCATAGATGCAC 57.091 37.500 6.90 0.00 0.00 4.57
6617 7597 7.330262 TCTTTCACTACAACATCATAGATGCA 58.670 34.615 6.90 0.00 0.00 3.96
6622 7602 9.987272 TCCATATCTTTCACTACAACATCATAG 57.013 33.333 0.00 0.00 0.00 2.23
6643 7623 6.324254 TGCATCCATGAACATCAAATTCCATA 59.676 34.615 0.00 0.00 0.00 2.74
6650 7630 2.159352 CGCTGCATCCATGAACATCAAA 60.159 45.455 0.00 0.00 0.00 2.69
6682 7665 6.375736 TGTCAATCAAAGTTTGTACAGTTGGA 59.624 34.615 15.08 0.00 0.00 3.53
6683 7666 6.559810 TGTCAATCAAAGTTTGTACAGTTGG 58.440 36.000 15.08 0.00 0.00 3.77
6684 7667 6.197096 GCTGTCAATCAAAGTTTGTACAGTTG 59.803 38.462 25.58 18.77 36.16 3.16
6685 7668 6.127758 TGCTGTCAATCAAAGTTTGTACAGTT 60.128 34.615 25.58 12.14 36.16 3.16
6688 7671 5.826601 TGCTGTCAATCAAAGTTTGTACA 57.173 34.783 15.08 13.22 0.00 2.90
6689 7672 6.033341 TGTTGCTGTCAATCAAAGTTTGTAC 58.967 36.000 15.08 9.90 34.29 2.90
6690 7673 6.201226 TGTTGCTGTCAATCAAAGTTTGTA 57.799 33.333 15.08 3.20 34.29 2.41
6692 7675 6.592798 ATTGTTGCTGTCAATCAAAGTTTG 57.407 33.333 9.44 9.44 34.29 2.93
6693 7676 7.715657 TCTATTGTTGCTGTCAATCAAAGTTT 58.284 30.769 5.24 0.00 36.92 2.66
6694 7677 7.275888 TCTATTGTTGCTGTCAATCAAAGTT 57.724 32.000 5.24 0.00 36.92 2.66
6695 7678 6.882610 TCTATTGTTGCTGTCAATCAAAGT 57.117 33.333 5.24 0.00 36.92 2.66
6696 7679 8.482429 GTTTTCTATTGTTGCTGTCAATCAAAG 58.518 33.333 5.24 0.48 36.92 2.77
6706 7689 5.221224 TGGGAAGTGTTTTCTATTGTTGCTG 60.221 40.000 0.00 0.00 0.00 4.41
6709 7692 6.142818 TGTGGGAAGTGTTTTCTATTGTTG 57.857 37.500 0.00 0.00 0.00 3.33
6738 7721 4.142337 TGCACCTATTGTTCGATCGAGTTA 60.142 41.667 18.54 7.69 0.00 2.24
6753 7738 3.815401 GAGAAACAACTGTGTGCACCTAT 59.185 43.478 15.69 0.00 38.27 2.57


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

AutoCloner maintained by Alex Coulton.