Multiple sequence alignment - TraesCS7A01G459900

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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 TraesCS7A01G459900 chr7A 100.000 2501 0 0 1 2501 655420337 655417837 0.000000e+00 4619.0
1 TraesCS7A01G459900 chr7A 95.819 861 34 1 943 1801 655406161 655405301 0.000000e+00 1389.0
2 TraesCS7A01G459900 chr7A 97.082 514 15 0 1 514 176994434 176993921 0.000000e+00 867.0
3 TraesCS7A01G459900 chr7A 96.887 514 15 1 1 514 671204633 671204121 0.000000e+00 859.0
4 TraesCS7A01G459900 chr7A 97.460 433 10 1 514 945 655410958 655410526 0.000000e+00 737.0
5 TraesCS7A01G459900 chr7A 97.260 219 5 1 573 790 655410793 655410575 1.090000e-98 370.0
6 TraesCS7A01G459900 chr7A 96.347 219 7 1 678 896 655410898 655410681 2.370000e-95 359.0
7 TraesCS7A01G459900 chr7A 95.434 219 9 1 573 790 655419660 655419442 5.120000e-92 348.0
8 TraesCS7A01G459900 chr7A 95.434 219 9 1 678 896 655419765 655419548 5.120000e-92 348.0
9 TraesCS7A01G459900 chr7A 96.460 113 3 1 784 896 655410898 655410787 4.250000e-43 185.0
10 TraesCS7A01G459900 chr7A 88.356 146 17 0 2041 2186 41465881 41465736 2.560000e-40 176.0
11 TraesCS7A01G459900 chr7A 88.356 146 17 0 2041 2186 617597403 617597548 2.560000e-40 176.0
12 TraesCS7A01G459900 chr7A 94.690 113 5 1 784 896 655419765 655419654 9.200000e-40 174.0
13 TraesCS7A01G459900 chr7D 94.686 1148 35 13 678 1809 568032187 568031050 0.000000e+00 1759.0
14 TraesCS7A01G459900 chr7D 98.195 277 5 0 514 790 568032246 568031970 3.740000e-133 484.0
15 TraesCS7A01G459900 chr7D 97.345 113 2 1 573 684 568032082 568031970 9.130000e-45 191.0
16 TraesCS7A01G459900 chr7D 93.805 113 6 1 784 896 568032187 568032076 4.280000e-38 169.0
17 TraesCS7A01G459900 chr7D 84.354 147 22 1 1199 1344 568235535 568235389 2.590000e-30 143.0
18 TraesCS7A01G459900 chr7B 93.385 1028 59 8 784 1809 622687908 622686888 0.000000e+00 1513.0
19 TraesCS7A01G459900 chr7B 93.481 859 48 7 953 1809 622674980 622674128 0.000000e+00 1269.0
20 TraesCS7A01G459900 chr7B 93.702 524 32 1 784 1307 622788143 622787621 0.000000e+00 784.0
21 TraesCS7A01G459900 chr7B 92.802 514 30 4 1300 1809 622765467 622764957 0.000000e+00 737.0
22 TraesCS7A01G459900 chr7B 97.093 172 4 1 514 684 622687968 622687797 3.150000e-74 289.0
23 TraesCS7A01G459900 chr7B 97.093 172 4 1 514 684 622788203 622788032 3.150000e-74 289.0
24 TraesCS7A01G459900 chr7B 99.248 133 0 1 514 645 622675131 622674999 3.210000e-59 239.0
25 TraesCS7A01G459900 chr7B 96.460 113 3 1 678 790 622788143 622788032 4.250000e-43 185.0
26 TraesCS7A01G459900 chr7B 94.690 113 5 1 678 790 622687908 622687797 9.200000e-40 174.0
27 TraesCS7A01G459900 chr7B 84.615 156 23 1 1190 1344 623270640 623270485 1.200000e-33 154.0
28 TraesCS7A01G459900 chr7B 85.034 147 21 1 1199 1344 623372736 623372590 5.570000e-32 148.0
29 TraesCS7A01G459900 chr7B 86.567 134 18 0 1199 1332 623537062 623536929 5.570000e-32 148.0
30 TraesCS7A01G459900 chr1A 96.710 699 22 1 1803 2501 504398179 504398876 0.000000e+00 1162.0
31 TraesCS7A01G459900 chr1A 94.737 570 29 1 1932 2501 525144012 525143444 0.000000e+00 885.0
32 TraesCS7A01G459900 chr1A 95.638 298 13 0 2204 2501 523369590 523369293 1.740000e-131 479.0
33 TraesCS7A01G459900 chr1A 91.697 277 22 1 1932 2208 523378462 523378187 1.400000e-102 383.0
34 TraesCS7A01G459900 chr3D 95.688 603 22 2 1898 2500 43583841 43583243 0.000000e+00 966.0
35 TraesCS7A01G459900 chr3D 86.182 275 25 8 2238 2501 381985036 381985308 4.070000e-73 285.0
36 TraesCS7A01G459900 chr4A 97.978 544 10 1 1958 2501 312733045 312732503 0.000000e+00 942.0
37 TraesCS7A01G459900 chr4A 94.444 162 8 1 1807 1968 304840009 304839849 5.340000e-62 248.0
38 TraesCS7A01G459900 chr6A 97.665 514 12 0 1 514 549429632 549430145 0.000000e+00 883.0
39 TraesCS7A01G459900 chr6A 95.745 47 1 1 1823 1869 581906397 581906442 9.590000e-10 75.0
40 TraesCS7A01G459900 chr6A 82.500 80 10 3 1800 1879 608304344 608304269 1.610000e-07 67.6
41 TraesCS7A01G459900 chr2B 96.538 520 16 2 1 518 644566335 644566854 0.000000e+00 859.0
42 TraesCS7A01G459900 chr3A 96.838 506 16 0 1 506 641821964 641822469 0.000000e+00 846.0
43 TraesCS7A01G459900 chr3A 85.455 275 27 8 2238 2501 505216112 505216384 8.810000e-70 274.0
44 TraesCS7A01G459900 chr3A 97.541 122 3 0 393 514 65783090 65782969 2.520000e-50 209.0
45 TraesCS7A01G459900 chr5B 95.543 516 18 2 1 514 606639229 606638717 0.000000e+00 821.0
46 TraesCS7A01G459900 chr5B 86.654 547 53 11 1956 2501 275021148 275020621 2.770000e-164 588.0
47 TraesCS7A01G459900 chr2D 95.720 514 8 2 1 514 174231400 174230901 0.000000e+00 815.0
48 TraesCS7A01G459900 chr5A 96.195 473 18 0 1 473 561673467 561672995 0.000000e+00 774.0
49 TraesCS7A01G459900 chr5D 90.909 517 42 4 1 514 369284809 369285323 0.000000e+00 689.0
50 TraesCS7A01G459900 chr3B 85.502 269 26 8 2238 2495 497704523 497704789 4.100000e-68 268.0
51 TraesCS7A01G459900 chrUn 99.248 133 0 1 514 645 381284223 381284091 3.210000e-59 239.0
52 TraesCS7A01G459900 chr2A 88.356 146 17 0 2041 2186 756523370 756523515 2.560000e-40 176.0
53 TraesCS7A01G459900 chr1D 89.344 122 13 0 2041 2162 62893259 62893380 1.200000e-33 154.0


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 TraesCS7A01G459900 chr7A 655417837 655420337 2500 True 1372.250000 4619 96.389500 1 2501 4 chr7A.!!$R6 2500
1 TraesCS7A01G459900 chr7A 655405301 655406161 860 True 1389.000000 1389 95.819000 943 1801 1 chr7A.!!$R3 858
2 TraesCS7A01G459900 chr7A 176993921 176994434 513 True 867.000000 867 97.082000 1 514 1 chr7A.!!$R2 513
3 TraesCS7A01G459900 chr7A 671204121 671204633 512 True 859.000000 859 96.887000 1 514 1 chr7A.!!$R4 513
4 TraesCS7A01G459900 chr7D 568031050 568032246 1196 True 650.750000 1759 96.007750 514 1809 4 chr7D.!!$R2 1295
5 TraesCS7A01G459900 chr7B 622674128 622675131 1003 True 754.000000 1269 96.364500 514 1809 2 chr7B.!!$R5 1295
6 TraesCS7A01G459900 chr7B 622764957 622765467 510 True 737.000000 737 92.802000 1300 1809 1 chr7B.!!$R1 509
7 TraesCS7A01G459900 chr7B 622686888 622687968 1080 True 658.666667 1513 95.056000 514 1809 3 chr7B.!!$R6 1295
8 TraesCS7A01G459900 chr7B 622787621 622788203 582 True 419.333333 784 95.751667 514 1307 3 chr7B.!!$R7 793
9 TraesCS7A01G459900 chr1A 504398179 504398876 697 False 1162.000000 1162 96.710000 1803 2501 1 chr1A.!!$F1 698
10 TraesCS7A01G459900 chr1A 525143444 525144012 568 True 885.000000 885 94.737000 1932 2501 1 chr1A.!!$R3 569
11 TraesCS7A01G459900 chr3D 43583243 43583841 598 True 966.000000 966 95.688000 1898 2500 1 chr3D.!!$R1 602
12 TraesCS7A01G459900 chr4A 312732503 312733045 542 True 942.000000 942 97.978000 1958 2501 1 chr4A.!!$R2 543
13 TraesCS7A01G459900 chr6A 549429632 549430145 513 False 883.000000 883 97.665000 1 514 1 chr6A.!!$F1 513
14 TraesCS7A01G459900 chr2B 644566335 644566854 519 False 859.000000 859 96.538000 1 518 1 chr2B.!!$F1 517
15 TraesCS7A01G459900 chr3A 641821964 641822469 505 False 846.000000 846 96.838000 1 506 1 chr3A.!!$F2 505
16 TraesCS7A01G459900 chr5B 606638717 606639229 512 True 821.000000 821 95.543000 1 514 1 chr5B.!!$R2 513
17 TraesCS7A01G459900 chr5B 275020621 275021148 527 True 588.000000 588 86.654000 1956 2501 1 chr5B.!!$R1 545
18 TraesCS7A01G459900 chr5D 369284809 369285323 514 False 689.000000 689 90.909000 1 514 1 chr5D.!!$F1 513

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
700 814 1.026182 TTAGCTTGCACCCATCTGCG 61.026 55.0 0.0 0.0 40.31 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2013 0.168128 GTTTTTGTCCCGGCGATCTG 59.832 55.0 9.3 0.0 0.0 2.9 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
158 162 7.630082 ACTATTACTTGCTTGGGTCTTTATGA 58.370 34.615 0.00 0.00 0.00 2.15
191 195 7.683578 TCAAATAGCAATCTATCATAGGCAGT 58.316 34.615 0.00 0.00 34.53 4.40
636 750 7.418337 TTGATACAAGAACTAGATGTGCCTA 57.582 36.000 0.00 0.00 0.00 3.93
637 751 6.806751 TGATACAAGAACTAGATGTGCCTAC 58.193 40.000 0.00 0.00 0.00 3.18
638 752 6.379988 TGATACAAGAACTAGATGTGCCTACA 59.620 38.462 0.00 0.00 41.89 2.74
656 770 9.463443 GTGCCTACATTAAATGAAAACATATCC 57.537 33.333 0.00 0.00 0.00 2.59
657 771 9.194972 TGCCTACATTAAATGAAAACATATCCA 57.805 29.630 0.00 0.00 0.00 3.41
684 798 9.892130 AGTTATCTTGAGGGTTCAGTTAATTAG 57.108 33.333 0.00 0.00 34.15 1.73
685 799 8.613482 GTTATCTTGAGGGTTCAGTTAATTAGC 58.387 37.037 0.00 0.00 34.15 3.09
686 800 6.374417 TCTTGAGGGTTCAGTTAATTAGCT 57.626 37.500 0.00 0.00 34.15 3.32
687 801 6.779860 TCTTGAGGGTTCAGTTAATTAGCTT 58.220 36.000 0.00 0.00 34.15 3.74
688 802 6.655003 TCTTGAGGGTTCAGTTAATTAGCTTG 59.345 38.462 0.00 0.00 34.15 4.01
689 803 4.700213 TGAGGGTTCAGTTAATTAGCTTGC 59.300 41.667 0.00 0.00 0.00 4.01
690 804 4.662278 AGGGTTCAGTTAATTAGCTTGCA 58.338 39.130 0.00 0.00 0.00 4.08
691 805 4.459337 AGGGTTCAGTTAATTAGCTTGCAC 59.541 41.667 0.00 0.00 0.00 4.57
692 806 4.380550 GGGTTCAGTTAATTAGCTTGCACC 60.381 45.833 0.00 6.06 0.00 5.01
693 807 4.380550 GGTTCAGTTAATTAGCTTGCACCC 60.381 45.833 0.00 0.00 0.00 4.61
694 808 4.027674 TCAGTTAATTAGCTTGCACCCA 57.972 40.909 0.00 0.00 0.00 4.51
695 809 4.599041 TCAGTTAATTAGCTTGCACCCAT 58.401 39.130 0.00 0.00 0.00 4.00
696 810 4.640201 TCAGTTAATTAGCTTGCACCCATC 59.360 41.667 0.00 0.00 0.00 3.51
697 811 4.641989 CAGTTAATTAGCTTGCACCCATCT 59.358 41.667 0.00 0.00 0.00 2.90
698 812 4.641989 AGTTAATTAGCTTGCACCCATCTG 59.358 41.667 0.00 0.00 0.00 2.90
699 813 1.396653 ATTAGCTTGCACCCATCTGC 58.603 50.000 0.00 0.00 37.70 4.26
700 814 1.026182 TTAGCTTGCACCCATCTGCG 61.026 55.000 0.00 0.00 40.31 5.18
701 815 2.184020 TAGCTTGCACCCATCTGCGT 62.184 55.000 0.00 0.00 40.31 5.24
702 816 1.745115 GCTTGCACCCATCTGCGTA 60.745 57.895 0.00 0.00 40.31 4.42
703 817 1.097547 GCTTGCACCCATCTGCGTAT 61.098 55.000 0.00 0.00 40.31 3.06
704 818 1.810031 GCTTGCACCCATCTGCGTATA 60.810 52.381 0.00 0.00 40.31 1.47
705 819 1.867233 CTTGCACCCATCTGCGTATAC 59.133 52.381 0.00 0.00 40.31 1.47
706 820 1.119684 TGCACCCATCTGCGTATACT 58.880 50.000 0.56 0.00 40.31 2.12
707 821 1.068588 TGCACCCATCTGCGTATACTC 59.931 52.381 0.56 0.00 40.31 2.59
708 822 1.341531 GCACCCATCTGCGTATACTCT 59.658 52.381 0.56 0.00 0.00 3.24
709 823 2.557056 GCACCCATCTGCGTATACTCTA 59.443 50.000 0.56 0.00 0.00 2.43
710 824 3.193691 GCACCCATCTGCGTATACTCTAT 59.806 47.826 0.56 0.00 0.00 1.98
711 825 4.675671 GCACCCATCTGCGTATACTCTATC 60.676 50.000 0.56 0.00 0.00 2.08
712 826 4.702612 CACCCATCTGCGTATACTCTATCT 59.297 45.833 0.56 0.00 0.00 1.98
713 827 4.702612 ACCCATCTGCGTATACTCTATCTG 59.297 45.833 0.56 0.00 0.00 2.90
714 828 4.439426 CCCATCTGCGTATACTCTATCTGC 60.439 50.000 0.56 0.00 0.00 4.26
715 829 4.156739 CCATCTGCGTATACTCTATCTGCA 59.843 45.833 0.56 0.53 0.00 4.41
716 830 5.331098 CATCTGCGTATACTCTATCTGCAG 58.669 45.833 7.63 7.63 42.84 4.41
717 831 4.390264 TCTGCGTATACTCTATCTGCAGT 58.610 43.478 14.67 3.75 42.44 4.40
718 832 4.822350 TCTGCGTATACTCTATCTGCAGTT 59.178 41.667 14.67 8.22 42.44 3.16
719 833 5.299531 TCTGCGTATACTCTATCTGCAGTTT 59.700 40.000 14.67 5.37 42.44 2.66
720 834 5.281727 TGCGTATACTCTATCTGCAGTTTG 58.718 41.667 14.67 6.75 0.00 2.93
721 835 5.067283 TGCGTATACTCTATCTGCAGTTTGA 59.933 40.000 14.67 10.96 0.00 2.69
722 836 6.153067 GCGTATACTCTATCTGCAGTTTGAT 58.847 40.000 14.67 2.22 0.00 2.57
723 837 7.040686 TGCGTATACTCTATCTGCAGTTTGATA 60.041 37.037 14.67 3.40 0.00 2.15
724 838 7.271653 GCGTATACTCTATCTGCAGTTTGATAC 59.728 40.741 14.67 10.12 0.00 2.24
725 839 8.290325 CGTATACTCTATCTGCAGTTTGATACA 58.710 37.037 14.67 1.09 0.00 2.29
726 840 9.967346 GTATACTCTATCTGCAGTTTGATACAA 57.033 33.333 14.67 0.00 0.00 2.41
728 842 7.175347 ACTCTATCTGCAGTTTGATACAAGA 57.825 36.000 14.67 2.55 0.00 3.02
729 843 7.615403 ACTCTATCTGCAGTTTGATACAAGAA 58.385 34.615 14.67 0.00 0.00 2.52
730 844 7.547370 ACTCTATCTGCAGTTTGATACAAGAAC 59.453 37.037 14.67 0.00 0.00 3.01
731 845 7.615403 TCTATCTGCAGTTTGATACAAGAACT 58.385 34.615 14.67 0.00 34.14 3.01
732 846 8.749354 TCTATCTGCAGTTTGATACAAGAACTA 58.251 33.333 14.67 0.00 32.69 2.24
733 847 7.840342 ATCTGCAGTTTGATACAAGAACTAG 57.160 36.000 14.67 0.00 32.69 2.57
734 848 6.993079 TCTGCAGTTTGATACAAGAACTAGA 58.007 36.000 14.67 0.00 32.69 2.43
735 849 7.615403 TCTGCAGTTTGATACAAGAACTAGAT 58.385 34.615 14.67 0.00 32.69 1.98
736 850 7.547019 TCTGCAGTTTGATACAAGAACTAGATG 59.453 37.037 14.67 0.00 32.69 2.90
737 851 7.161404 TGCAGTTTGATACAAGAACTAGATGT 58.839 34.615 0.00 0.00 32.69 3.06
738 852 7.118245 TGCAGTTTGATACAAGAACTAGATGTG 59.882 37.037 0.00 0.00 32.69 3.21
739 853 7.459486 CAGTTTGATACAAGAACTAGATGTGC 58.541 38.462 0.00 0.00 32.69 4.57
740 854 6.595716 AGTTTGATACAAGAACTAGATGTGCC 59.404 38.462 0.00 0.00 32.22 5.01
741 855 5.939764 TGATACAAGAACTAGATGTGCCT 57.060 39.130 0.00 0.00 0.00 4.75
794 908 8.561738 TCTTGAGGGTTTAGTTAATTAGCTTG 57.438 34.615 7.17 0.00 0.00 4.01
795 909 6.753107 TGAGGGTTTAGTTAATTAGCTTGC 57.247 37.500 7.17 0.00 0.00 4.01
796 910 6.242396 TGAGGGTTTAGTTAATTAGCTTGCA 58.758 36.000 7.17 0.00 0.00 4.08
797 911 6.150474 TGAGGGTTTAGTTAATTAGCTTGCAC 59.850 38.462 7.17 2.67 0.00 4.57
798 912 5.417894 AGGGTTTAGTTAATTAGCTTGCACC 59.582 40.000 7.17 10.38 0.00 5.01
799 913 5.393787 GGGTTTAGTTAATTAGCTTGCACCC 60.394 44.000 19.04 19.04 32.53 4.61
800 914 5.184287 GGTTTAGTTAATTAGCTTGCACCCA 59.816 40.000 7.17 0.00 0.00 4.51
801 915 6.127451 GGTTTAGTTAATTAGCTTGCACCCAT 60.127 38.462 7.17 0.00 0.00 4.00
802 916 6.693315 TTAGTTAATTAGCTTGCACCCATC 57.307 37.500 7.17 0.00 0.00 3.51
803 917 4.860022 AGTTAATTAGCTTGCACCCATCT 58.140 39.130 0.00 0.00 0.00 2.90
804 918 6.001449 AGTTAATTAGCTTGCACCCATCTA 57.999 37.500 0.00 0.00 0.00 1.98
805 919 6.423182 AGTTAATTAGCTTGCACCCATCTAA 58.577 36.000 0.00 0.00 0.00 2.10
806 920 6.543831 AGTTAATTAGCTTGCACCCATCTAAG 59.456 38.462 0.00 0.00 0.00 2.18
807 921 4.510167 ATTAGCTTGCACCCATCTAAGT 57.490 40.909 0.00 0.00 0.00 2.24
808 922 5.630415 ATTAGCTTGCACCCATCTAAGTA 57.370 39.130 0.00 0.00 0.00 2.24
809 923 5.630415 TTAGCTTGCACCCATCTAAGTAT 57.370 39.130 0.00 0.00 0.00 2.12
810 924 6.740944 TTAGCTTGCACCCATCTAAGTATA 57.259 37.500 0.00 0.00 0.00 1.47
811 925 4.962155 AGCTTGCACCCATCTAAGTATAC 58.038 43.478 0.00 0.00 0.00 1.47
812 926 4.656112 AGCTTGCACCCATCTAAGTATACT 59.344 41.667 0.00 0.00 0.00 2.12
813 927 4.991687 GCTTGCACCCATCTAAGTATACTC 59.008 45.833 5.70 0.00 0.00 2.59
814 928 5.221541 GCTTGCACCCATCTAAGTATACTCT 60.222 44.000 5.70 0.00 0.00 3.24
815 929 6.015350 GCTTGCACCCATCTAAGTATACTCTA 60.015 42.308 5.70 0.82 0.00 2.43
816 930 7.310113 GCTTGCACCCATCTAAGTATACTCTAT 60.310 40.741 5.70 0.00 0.00 1.98
817 931 7.704578 TGCACCCATCTAAGTATACTCTATC 57.295 40.000 5.70 0.00 0.00 2.08
818 932 7.471041 TGCACCCATCTAAGTATACTCTATCT 58.529 38.462 5.70 0.00 0.00 1.98
819 933 7.394641 TGCACCCATCTAAGTATACTCTATCTG 59.605 40.741 5.70 1.26 0.00 2.90
820 934 7.629652 GCACCCATCTAAGTATACTCTATCTGC 60.630 44.444 5.70 2.97 0.00 4.26
821 935 7.394641 CACCCATCTAAGTATACTCTATCTGCA 59.605 40.741 5.70 0.00 0.00 4.41
822 936 7.613801 ACCCATCTAAGTATACTCTATCTGCAG 59.386 40.741 7.63 7.63 0.00 4.41
823 937 7.613801 CCCATCTAAGTATACTCTATCTGCAGT 59.386 40.741 14.67 3.75 0.00 4.40
824 938 9.019656 CCATCTAAGTATACTCTATCTGCAGTT 57.980 37.037 14.67 8.22 0.00 3.16
827 941 9.628500 TCTAAGTATACTCTATCTGCAGTTTGA 57.372 33.333 14.67 10.96 0.00 2.69
831 945 9.355916 AGTATACTCTATCTGCAGTTTGATACA 57.644 33.333 14.67 1.09 0.00 2.29
832 946 9.967346 GTATACTCTATCTGCAGTTTGATACAA 57.033 33.333 14.67 0.00 0.00 2.41
834 948 7.175347 ACTCTATCTGCAGTTTGATACAAGA 57.825 36.000 14.67 2.55 0.00 3.02
835 949 7.615403 ACTCTATCTGCAGTTTGATACAAGAA 58.385 34.615 14.67 0.00 0.00 2.52
836 950 7.547370 ACTCTATCTGCAGTTTGATACAAGAAC 59.453 37.037 14.67 0.00 0.00 3.01
837 951 7.615403 TCTATCTGCAGTTTGATACAAGAACT 58.385 34.615 14.67 0.00 34.14 3.01
838 952 8.749354 TCTATCTGCAGTTTGATACAAGAACTA 58.251 33.333 14.67 0.00 32.69 2.24
839 953 7.840342 ATCTGCAGTTTGATACAAGAACTAG 57.160 36.000 14.67 0.00 32.69 2.57
840 954 6.993079 TCTGCAGTTTGATACAAGAACTAGA 58.007 36.000 14.67 0.00 32.69 2.43
841 955 7.615403 TCTGCAGTTTGATACAAGAACTAGAT 58.385 34.615 14.67 0.00 32.69 1.98
842 956 7.547019 TCTGCAGTTTGATACAAGAACTAGATG 59.453 37.037 14.67 0.00 32.69 2.90
843 957 7.161404 TGCAGTTTGATACAAGAACTAGATGT 58.839 34.615 0.00 0.00 32.69 3.06
844 958 7.118245 TGCAGTTTGATACAAGAACTAGATGTG 59.882 37.037 0.00 0.00 32.69 3.21
845 959 7.459486 CAGTTTGATACAAGAACTAGATGTGC 58.541 38.462 0.00 0.00 32.69 4.57
846 960 6.595716 AGTTTGATACAAGAACTAGATGTGCC 59.404 38.462 0.00 0.00 32.22 5.01
847 961 5.939764 TGATACAAGAACTAGATGTGCCT 57.060 39.130 0.00 0.00 0.00 4.75
848 962 7.418337 TTGATACAAGAACTAGATGTGCCTA 57.582 36.000 0.00 0.00 0.00 3.93
849 963 6.806751 TGATACAAGAACTAGATGTGCCTAC 58.193 40.000 0.00 0.00 0.00 3.18
850 964 6.379988 TGATACAAGAACTAGATGTGCCTACA 59.620 38.462 0.00 0.00 41.89 2.74
864 978 5.880054 GTGCCTACACTAAATGACAACAT 57.120 39.130 0.00 0.00 43.85 2.71
865 979 6.978343 GTGCCTACACTAAATGACAACATA 57.022 37.500 0.00 0.00 43.85 2.29
866 980 7.553881 GTGCCTACACTAAATGACAACATAT 57.446 36.000 0.00 0.00 43.85 1.78
867 981 7.630924 GTGCCTACACTAAATGACAACATATC 58.369 38.462 0.00 0.00 43.85 1.63
868 982 6.765989 TGCCTACACTAAATGACAACATATCC 59.234 38.462 0.00 0.00 35.50 2.59
869 983 6.765989 GCCTACACTAAATGACAACATATCCA 59.234 38.462 0.00 0.00 35.50 3.41
870 984 7.282224 GCCTACACTAAATGACAACATATCCAA 59.718 37.037 0.00 0.00 35.50 3.53
871 985 8.830580 CCTACACTAAATGACAACATATCCAAG 58.169 37.037 0.00 0.00 35.50 3.61
872 986 9.383519 CTACACTAAATGACAACATATCCAAGT 57.616 33.333 0.00 0.00 35.50 3.16
873 987 8.635765 ACACTAAATGACAACATATCCAAGTT 57.364 30.769 0.00 0.00 35.50 2.66
874 988 9.733556 ACACTAAATGACAACATATCCAAGTTA 57.266 29.630 0.00 0.00 35.50 2.24
880 994 9.685276 AATGACAACATATCCAAGTTATCTTGA 57.315 29.630 13.98 2.59 43.03 3.02
881 995 9.334947 ATGACAACATATCCAAGTTATCTTGAG 57.665 33.333 13.98 5.66 42.57 3.02
1006 1121 4.891756 CCATTTCACATAAGAAGATGGCCT 59.108 41.667 3.32 0.00 33.59 5.19
1117 1232 5.684030 GCGGATAAAAGTAAGGTGATGAGGA 60.684 44.000 0.00 0.00 0.00 3.71
1176 1291 1.139095 CCTTCTACACGGGAGCGTC 59.861 63.158 0.00 0.00 0.00 5.19
1524 1649 2.787473 TCATTGTAAGGGCTGTCTGG 57.213 50.000 0.00 0.00 0.00 3.86
1541 1666 6.374333 GCTGTCTGGTAATGTGGAGAAATAAA 59.626 38.462 0.00 0.00 0.00 1.40
1617 1744 9.394767 GGATGCAAATAATAAAAGGAAAATGGT 57.605 29.630 0.00 0.00 0.00 3.55
1688 1818 2.047274 CAGTCCGCATTCCACCGT 60.047 61.111 0.00 0.00 0.00 4.83
1801 1935 5.205517 TGGGAAATGTATTTCATGACCCT 57.794 39.130 16.58 0.00 46.03 4.34
1818 1952 9.265862 TCATGACCCTCATAATTAAAACCATTT 57.734 29.630 0.00 0.00 34.28 2.32
1824 1958 8.695456 CCCTCATAATTAAAACCATTTAGCTGT 58.305 33.333 0.00 0.00 32.80 4.40
1832 1966 4.870123 AACCATTTAGCTGTGCATCAAA 57.130 36.364 0.00 0.00 0.00 2.69
1843 1977 2.830370 CATCAAAGGCGCCTCCCC 60.830 66.667 32.93 0.00 34.51 4.81
1865 1999 1.824852 TGATAGCCACGTCATCACAGT 59.175 47.619 0.00 0.00 0.00 3.55
1872 2006 1.794701 CACGTCATCACAGTGTGGAAG 59.205 52.381 22.79 16.45 33.87 3.46
1873 2007 1.686587 ACGTCATCACAGTGTGGAAGA 59.313 47.619 22.79 14.75 33.87 2.87
1874 2008 2.061773 CGTCATCACAGTGTGGAAGAC 58.938 52.381 22.79 22.65 33.87 3.01
1875 2009 2.545742 CGTCATCACAGTGTGGAAGACA 60.546 50.000 27.29 11.66 32.83 3.41
1876 2010 3.466836 GTCATCACAGTGTGGAAGACAA 58.533 45.455 22.79 2.10 35.91 3.18
1877 2011 3.876914 GTCATCACAGTGTGGAAGACAAA 59.123 43.478 22.79 1.33 35.91 2.83
1878 2012 4.335315 GTCATCACAGTGTGGAAGACAAAA 59.665 41.667 22.79 0.56 35.91 2.44
1879 2013 4.335315 TCATCACAGTGTGGAAGACAAAAC 59.665 41.667 22.79 0.00 35.91 2.43
1880 2014 3.680490 TCACAGTGTGGAAGACAAAACA 58.320 40.909 22.79 0.00 35.91 2.83
1881 2015 3.689161 TCACAGTGTGGAAGACAAAACAG 59.311 43.478 22.79 0.00 35.91 3.16
1882 2016 3.689161 CACAGTGTGGAAGACAAAACAGA 59.311 43.478 15.86 0.00 35.91 3.41
1883 2017 4.336433 CACAGTGTGGAAGACAAAACAGAT 59.664 41.667 15.86 0.00 35.91 2.90
1884 2018 4.576463 ACAGTGTGGAAGACAAAACAGATC 59.424 41.667 0.00 0.00 35.91 2.75
1885 2019 3.809832 AGTGTGGAAGACAAAACAGATCG 59.190 43.478 0.00 0.00 35.91 3.69
1886 2020 2.548057 TGTGGAAGACAAAACAGATCGC 59.452 45.455 0.00 0.00 0.00 4.58
1887 2021 2.095718 GTGGAAGACAAAACAGATCGCC 60.096 50.000 0.00 0.00 0.00 5.54
1888 2022 1.128692 GGAAGACAAAACAGATCGCCG 59.871 52.381 0.00 0.00 0.00 6.46
1889 2023 1.128692 GAAGACAAAACAGATCGCCGG 59.871 52.381 0.00 0.00 0.00 6.13
1890 2024 0.673644 AGACAAAACAGATCGCCGGG 60.674 55.000 2.18 0.00 0.00 5.73
1891 2025 0.672401 GACAAAACAGATCGCCGGGA 60.672 55.000 2.18 0.00 0.00 5.14
1892 2026 0.953960 ACAAAACAGATCGCCGGGAC 60.954 55.000 2.18 0.00 0.00 4.46
1893 2027 0.953471 CAAAACAGATCGCCGGGACA 60.953 55.000 2.18 0.00 0.00 4.02
1894 2028 0.250553 AAAACAGATCGCCGGGACAA 60.251 50.000 2.18 0.00 0.00 3.18
1895 2029 0.250553 AAACAGATCGCCGGGACAAA 60.251 50.000 2.18 0.00 0.00 2.83
1907 2041 3.851098 CCGGGACAAAAACAAAACAGAA 58.149 40.909 0.00 0.00 0.00 3.02
1909 2043 3.302170 CGGGACAAAAACAAAACAGAACG 59.698 43.478 0.00 0.00 0.00 3.95
2106 2263 3.306595 CTCAGCCGCTTCTCCTGCA 62.307 63.158 0.00 0.00 0.00 4.41
2119 2276 0.341258 TCCTGCATCTTCTCCTCCCT 59.659 55.000 0.00 0.00 0.00 4.20
2405 2563 3.570550 CCCCAGTTTTTACCATTTCGTCA 59.429 43.478 0.00 0.00 0.00 4.35
2480 2638 1.347707 TGAACTCGGAGCAAGTGGAAT 59.652 47.619 4.58 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 7.518188 AGCAAGTAATAGTAATAGCCCATGTT 58.482 34.615 0.00 0.00 0.00 2.71
139 143 4.666512 ACATCATAAAGACCCAAGCAAGT 58.333 39.130 0.00 0.00 0.00 3.16
158 162 8.929260 TGATAGATTGCTATTTGATTGGACAT 57.071 30.769 0.00 0.00 37.45 3.06
499 506 1.848388 TGTAGGACTAGATCGGGACCA 59.152 52.381 0.00 0.00 0.00 4.02
658 772 9.892130 CTAATTAACTGAACCCTCAAGATAACT 57.108 33.333 0.00 0.00 0.00 2.24
659 773 8.613482 GCTAATTAACTGAACCCTCAAGATAAC 58.387 37.037 0.00 0.00 0.00 1.89
660 774 8.548877 AGCTAATTAACTGAACCCTCAAGATAA 58.451 33.333 0.00 0.00 0.00 1.75
661 775 8.090788 AGCTAATTAACTGAACCCTCAAGATA 57.909 34.615 0.00 0.00 0.00 1.98
662 776 6.963322 AGCTAATTAACTGAACCCTCAAGAT 58.037 36.000 0.00 0.00 0.00 2.40
663 777 6.374417 AGCTAATTAACTGAACCCTCAAGA 57.626 37.500 0.00 0.00 0.00 3.02
664 778 6.623767 GCAAGCTAATTAACTGAACCCTCAAG 60.624 42.308 0.00 0.00 0.00 3.02
665 779 5.183140 GCAAGCTAATTAACTGAACCCTCAA 59.817 40.000 0.00 0.00 0.00 3.02
666 780 4.700213 GCAAGCTAATTAACTGAACCCTCA 59.300 41.667 0.00 0.00 0.00 3.86
667 781 4.700213 TGCAAGCTAATTAACTGAACCCTC 59.300 41.667 0.00 0.00 0.00 4.30
668 782 4.459337 GTGCAAGCTAATTAACTGAACCCT 59.541 41.667 0.00 0.00 0.00 4.34
669 783 4.380550 GGTGCAAGCTAATTAACTGAACCC 60.381 45.833 0.00 0.00 0.00 4.11
670 784 4.380550 GGGTGCAAGCTAATTAACTGAACC 60.381 45.833 1.28 1.28 0.00 3.62
671 785 4.217550 TGGGTGCAAGCTAATTAACTGAAC 59.782 41.667 0.00 0.00 0.00 3.18
672 786 4.402829 TGGGTGCAAGCTAATTAACTGAA 58.597 39.130 0.00 0.00 0.00 3.02
673 787 4.027674 TGGGTGCAAGCTAATTAACTGA 57.972 40.909 0.00 0.00 0.00 3.41
674 788 4.641989 AGATGGGTGCAAGCTAATTAACTG 59.358 41.667 0.00 0.00 0.00 3.16
675 789 4.641989 CAGATGGGTGCAAGCTAATTAACT 59.358 41.667 0.00 0.00 0.00 2.24
676 790 4.734695 GCAGATGGGTGCAAGCTAATTAAC 60.735 45.833 0.00 0.00 43.41 2.01
677 791 3.381272 GCAGATGGGTGCAAGCTAATTAA 59.619 43.478 0.00 0.00 43.41 1.40
678 792 2.951642 GCAGATGGGTGCAAGCTAATTA 59.048 45.455 0.00 0.00 43.41 1.40
679 793 1.753073 GCAGATGGGTGCAAGCTAATT 59.247 47.619 0.00 0.00 43.41 1.40
680 794 1.396653 GCAGATGGGTGCAAGCTAAT 58.603 50.000 0.00 0.00 43.41 1.73
681 795 1.026182 CGCAGATGGGTGCAAGCTAA 61.026 55.000 0.00 0.00 44.21 3.09
682 796 1.450134 CGCAGATGGGTGCAAGCTA 60.450 57.895 0.00 0.00 44.21 3.32
683 797 2.184020 TACGCAGATGGGTGCAAGCT 62.184 55.000 12.32 0.00 44.21 3.74
684 798 1.097547 ATACGCAGATGGGTGCAAGC 61.098 55.000 12.32 0.00 44.21 4.01
685 799 1.867233 GTATACGCAGATGGGTGCAAG 59.133 52.381 12.32 0.00 44.21 4.01
686 800 1.484653 AGTATACGCAGATGGGTGCAA 59.515 47.619 12.32 0.00 44.21 4.08
687 801 1.068588 GAGTATACGCAGATGGGTGCA 59.931 52.381 12.32 0.00 44.21 4.57
688 802 1.341531 AGAGTATACGCAGATGGGTGC 59.658 52.381 12.32 3.57 41.49 5.01
689 803 4.702612 AGATAGAGTATACGCAGATGGGTG 59.297 45.833 12.32 0.00 41.49 4.61
690 804 4.702612 CAGATAGAGTATACGCAGATGGGT 59.297 45.833 9.39 7.71 43.82 4.51
691 805 4.439426 GCAGATAGAGTATACGCAGATGGG 60.439 50.000 9.39 0.00 0.00 4.00
692 806 4.156739 TGCAGATAGAGTATACGCAGATGG 59.843 45.833 9.39 0.00 0.00 3.51
693 807 5.106357 ACTGCAGATAGAGTATACGCAGATG 60.106 44.000 23.35 12.55 42.05 2.90
694 808 5.007034 ACTGCAGATAGAGTATACGCAGAT 58.993 41.667 23.35 11.93 42.05 2.90
695 809 4.390264 ACTGCAGATAGAGTATACGCAGA 58.610 43.478 23.35 8.24 42.05 4.26
696 810 4.757799 ACTGCAGATAGAGTATACGCAG 57.242 45.455 23.35 19.00 43.65 5.18
697 811 5.067283 TCAAACTGCAGATAGAGTATACGCA 59.933 40.000 23.35 4.51 0.00 5.24
698 812 5.520632 TCAAACTGCAGATAGAGTATACGC 58.479 41.667 23.35 0.00 0.00 4.42
699 813 8.290325 TGTATCAAACTGCAGATAGAGTATACG 58.710 37.037 23.35 0.00 0.00 3.06
700 814 9.967346 TTGTATCAAACTGCAGATAGAGTATAC 57.033 33.333 23.35 16.56 0.00 1.47
702 816 8.918116 TCTTGTATCAAACTGCAGATAGAGTAT 58.082 33.333 23.35 6.78 0.00 2.12
703 817 8.293699 TCTTGTATCAAACTGCAGATAGAGTA 57.706 34.615 23.35 3.15 0.00 2.59
704 818 7.175347 TCTTGTATCAAACTGCAGATAGAGT 57.825 36.000 23.35 4.16 0.00 3.24
705 819 7.763528 AGTTCTTGTATCAAACTGCAGATAGAG 59.236 37.037 23.35 8.77 32.22 2.43
706 820 7.615403 AGTTCTTGTATCAAACTGCAGATAGA 58.385 34.615 23.35 14.51 32.22 1.98
707 821 7.840342 AGTTCTTGTATCAAACTGCAGATAG 57.160 36.000 23.35 9.20 32.22 2.08
708 822 8.749354 TCTAGTTCTTGTATCAAACTGCAGATA 58.251 33.333 23.35 4.88 35.08 1.98
709 823 7.615403 TCTAGTTCTTGTATCAAACTGCAGAT 58.385 34.615 23.35 5.41 35.08 2.90
710 824 6.993079 TCTAGTTCTTGTATCAAACTGCAGA 58.007 36.000 23.35 0.00 35.08 4.26
711 825 7.332926 ACATCTAGTTCTTGTATCAAACTGCAG 59.667 37.037 13.48 13.48 35.08 4.41
712 826 7.118245 CACATCTAGTTCTTGTATCAAACTGCA 59.882 37.037 0.00 0.00 35.08 4.41
713 827 7.459486 CACATCTAGTTCTTGTATCAAACTGC 58.541 38.462 0.00 0.00 35.08 4.40
714 828 7.413438 GGCACATCTAGTTCTTGTATCAAACTG 60.413 40.741 0.00 0.00 35.08 3.16
715 829 6.595716 GGCACATCTAGTTCTTGTATCAAACT 59.404 38.462 0.00 0.00 37.10 2.66
716 830 6.595716 AGGCACATCTAGTTCTTGTATCAAAC 59.404 38.462 0.00 0.00 0.00 2.93
717 831 6.711277 AGGCACATCTAGTTCTTGTATCAAA 58.289 36.000 0.00 0.00 0.00 2.69
718 832 6.299805 AGGCACATCTAGTTCTTGTATCAA 57.700 37.500 0.00 0.00 0.00 2.57
719 833 5.939764 AGGCACATCTAGTTCTTGTATCA 57.060 39.130 0.00 0.00 0.00 2.15
720 834 6.806751 TGTAGGCACATCTAGTTCTTGTATC 58.193 40.000 0.00 0.00 0.00 2.24
721 835 6.791867 TGTAGGCACATCTAGTTCTTGTAT 57.208 37.500 0.00 0.00 0.00 2.29
722 836 6.791867 ATGTAGGCACATCTAGTTCTTGTA 57.208 37.500 0.00 0.00 41.75 2.41
723 837 5.683876 ATGTAGGCACATCTAGTTCTTGT 57.316 39.130 0.00 0.00 41.75 3.16
724 838 8.492673 TTTAATGTAGGCACATCTAGTTCTTG 57.507 34.615 3.61 0.00 44.83 3.02
725 839 9.113838 CATTTAATGTAGGCACATCTAGTTCTT 57.886 33.333 0.00 0.00 44.83 2.52
726 840 8.486210 TCATTTAATGTAGGCACATCTAGTTCT 58.514 33.333 4.77 0.00 44.83 3.01
727 841 8.552034 GTCATTTAATGTAGGCACATCTAGTTC 58.448 37.037 4.77 0.00 44.83 3.01
728 842 8.046708 TGTCATTTAATGTAGGCACATCTAGTT 58.953 33.333 4.77 0.00 44.83 2.24
729 843 7.564793 TGTCATTTAATGTAGGCACATCTAGT 58.435 34.615 4.77 0.00 44.83 2.57
730 844 8.338259 GTTGTCATTTAATGTAGGCACATCTAG 58.662 37.037 4.77 0.00 44.83 2.43
731 845 7.826744 TGTTGTCATTTAATGTAGGCACATCTA 59.173 33.333 4.77 0.00 44.83 1.98
732 846 6.658816 TGTTGTCATTTAATGTAGGCACATCT 59.341 34.615 4.77 0.00 44.83 2.90
733 847 6.851609 TGTTGTCATTTAATGTAGGCACATC 58.148 36.000 4.77 2.29 44.83 3.06
734 848 8.518430 TATGTTGTCATTTAATGTAGGCACAT 57.482 30.769 4.77 9.45 39.86 3.21
735 849 6.832520 ATGTTGTCATTTAATGTAGGCACA 57.167 33.333 4.77 0.00 39.52 4.57
736 850 8.076178 GGATATGTTGTCATTTAATGTAGGCAC 58.924 37.037 4.77 0.00 35.70 5.01
737 851 7.777440 TGGATATGTTGTCATTTAATGTAGGCA 59.223 33.333 4.77 2.04 35.70 4.75
738 852 8.165239 TGGATATGTTGTCATTTAATGTAGGC 57.835 34.615 4.77 0.00 35.70 3.93
780 894 6.001449 AGATGGGTGCAAGCTAATTAACTA 57.999 37.500 0.00 0.00 0.00 2.24
783 897 6.423182 ACTTAGATGGGTGCAAGCTAATTAA 58.577 36.000 0.00 0.00 0.00 1.40
784 898 6.001449 ACTTAGATGGGTGCAAGCTAATTA 57.999 37.500 0.00 0.00 0.00 1.40
785 899 4.860022 ACTTAGATGGGTGCAAGCTAATT 58.140 39.130 0.00 0.00 0.00 1.40
786 900 4.510167 ACTTAGATGGGTGCAAGCTAAT 57.490 40.909 0.00 0.00 0.00 1.73
787 901 5.630415 ATACTTAGATGGGTGCAAGCTAA 57.370 39.130 0.00 0.00 0.00 3.09
788 902 5.839063 AGTATACTTAGATGGGTGCAAGCTA 59.161 40.000 0.00 0.00 0.00 3.32
789 903 4.656112 AGTATACTTAGATGGGTGCAAGCT 59.344 41.667 0.00 0.00 0.00 3.74
790 904 4.962155 AGTATACTTAGATGGGTGCAAGC 58.038 43.478 0.00 0.00 0.00 4.01
791 905 6.412362 AGAGTATACTTAGATGGGTGCAAG 57.588 41.667 6.88 0.00 0.00 4.01
792 906 7.950684 AGATAGAGTATACTTAGATGGGTGCAA 59.049 37.037 6.88 0.00 0.00 4.08
793 907 7.394641 CAGATAGAGTATACTTAGATGGGTGCA 59.605 40.741 6.88 0.00 0.00 4.57
794 908 7.629652 GCAGATAGAGTATACTTAGATGGGTGC 60.630 44.444 6.88 5.87 0.00 5.01
795 909 7.394641 TGCAGATAGAGTATACTTAGATGGGTG 59.605 40.741 6.88 0.00 0.00 4.61
796 910 7.471041 TGCAGATAGAGTATACTTAGATGGGT 58.529 38.462 6.88 0.00 0.00 4.51
797 911 7.613801 ACTGCAGATAGAGTATACTTAGATGGG 59.386 40.741 23.35 0.00 0.00 4.00
798 912 8.574251 ACTGCAGATAGAGTATACTTAGATGG 57.426 38.462 23.35 0.00 0.00 3.51
801 915 9.628500 TCAAACTGCAGATAGAGTATACTTAGA 57.372 33.333 23.35 0.00 0.00 2.10
805 919 9.355916 TGTATCAAACTGCAGATAGAGTATACT 57.644 33.333 23.35 4.68 0.00 2.12
806 920 9.967346 TTGTATCAAACTGCAGATAGAGTATAC 57.033 33.333 23.35 16.56 0.00 1.47
808 922 8.918116 TCTTGTATCAAACTGCAGATAGAGTAT 58.082 33.333 23.35 6.78 0.00 2.12
809 923 8.293699 TCTTGTATCAAACTGCAGATAGAGTA 57.706 34.615 23.35 3.15 0.00 2.59
810 924 7.175347 TCTTGTATCAAACTGCAGATAGAGT 57.825 36.000 23.35 4.16 0.00 3.24
811 925 7.763528 AGTTCTTGTATCAAACTGCAGATAGAG 59.236 37.037 23.35 8.77 32.22 2.43
812 926 7.615403 AGTTCTTGTATCAAACTGCAGATAGA 58.385 34.615 23.35 14.51 32.22 1.98
813 927 7.840342 AGTTCTTGTATCAAACTGCAGATAG 57.160 36.000 23.35 9.20 32.22 2.08
814 928 8.749354 TCTAGTTCTTGTATCAAACTGCAGATA 58.251 33.333 23.35 4.88 35.08 1.98
815 929 7.615403 TCTAGTTCTTGTATCAAACTGCAGAT 58.385 34.615 23.35 5.41 35.08 2.90
816 930 6.993079 TCTAGTTCTTGTATCAAACTGCAGA 58.007 36.000 23.35 0.00 35.08 4.26
817 931 7.332926 ACATCTAGTTCTTGTATCAAACTGCAG 59.667 37.037 13.48 13.48 35.08 4.41
818 932 7.118245 CACATCTAGTTCTTGTATCAAACTGCA 59.882 37.037 0.00 0.00 35.08 4.41
819 933 7.459486 CACATCTAGTTCTTGTATCAAACTGC 58.541 38.462 0.00 0.00 35.08 4.40
820 934 7.413438 GGCACATCTAGTTCTTGTATCAAACTG 60.413 40.741 0.00 0.00 35.08 3.16
821 935 6.595716 GGCACATCTAGTTCTTGTATCAAACT 59.404 38.462 0.00 0.00 37.10 2.66
822 936 6.595716 AGGCACATCTAGTTCTTGTATCAAAC 59.404 38.462 0.00 0.00 0.00 2.93
823 937 6.711277 AGGCACATCTAGTTCTTGTATCAAA 58.289 36.000 0.00 0.00 0.00 2.69
824 938 6.299805 AGGCACATCTAGTTCTTGTATCAA 57.700 37.500 0.00 0.00 0.00 2.57
825 939 5.939764 AGGCACATCTAGTTCTTGTATCA 57.060 39.130 0.00 0.00 0.00 2.15
826 940 6.697892 GTGTAGGCACATCTAGTTCTTGTATC 59.302 42.308 0.00 0.00 44.64 2.24
827 941 6.574350 GTGTAGGCACATCTAGTTCTTGTAT 58.426 40.000 0.00 0.00 44.64 2.29
828 942 5.962433 GTGTAGGCACATCTAGTTCTTGTA 58.038 41.667 0.00 0.00 44.64 2.41
829 943 4.822026 GTGTAGGCACATCTAGTTCTTGT 58.178 43.478 0.00 0.00 44.64 3.16
839 953 7.279981 TATGTTGTCATTTAGTGTAGGCACATC 59.720 37.037 0.51 0.00 40.23 3.06
840 954 7.109501 TATGTTGTCATTTAGTGTAGGCACAT 58.890 34.615 0.51 0.00 40.23 3.21
841 955 6.468543 TATGTTGTCATTTAGTGTAGGCACA 58.531 36.000 0.51 0.00 40.23 4.57
842 956 5.880054 ATGTTGTCATTTAGTGTAGGCAC 57.120 39.130 0.00 0.00 45.57 5.01
843 957 6.765989 GGATATGTTGTCATTTAGTGTAGGCA 59.234 38.462 0.00 0.00 35.70 4.75
844 958 6.765989 TGGATATGTTGTCATTTAGTGTAGGC 59.234 38.462 0.00 0.00 35.70 3.93
845 959 8.731275 TTGGATATGTTGTCATTTAGTGTAGG 57.269 34.615 0.00 0.00 35.70 3.18
846 960 9.383519 ACTTGGATATGTTGTCATTTAGTGTAG 57.616 33.333 0.00 0.00 35.70 2.74
847 961 9.733556 AACTTGGATATGTTGTCATTTAGTGTA 57.266 29.630 0.00 0.00 35.70 2.90
848 962 8.635765 AACTTGGATATGTTGTCATTTAGTGT 57.364 30.769 0.00 0.00 35.70 3.55
874 988 9.627123 TCATTTAATTAATCGAACCCTCAAGAT 57.373 29.630 0.00 0.00 0.00 2.40
875 989 8.889717 GTCATTTAATTAATCGAACCCTCAAGA 58.110 33.333 0.00 0.00 0.00 3.02
876 990 8.129211 GGTCATTTAATTAATCGAACCCTCAAG 58.871 37.037 0.00 0.00 0.00 3.02
877 991 7.612244 TGGTCATTTAATTAATCGAACCCTCAA 59.388 33.333 0.00 0.00 0.00 3.02
878 992 7.113437 TGGTCATTTAATTAATCGAACCCTCA 58.887 34.615 0.00 0.00 0.00 3.86
879 993 7.562454 TGGTCATTTAATTAATCGAACCCTC 57.438 36.000 0.00 0.00 0.00 4.30
880 994 7.948034 TTGGTCATTTAATTAATCGAACCCT 57.052 32.000 0.00 0.00 0.00 4.34
881 995 8.989653 TTTTGGTCATTTAATTAATCGAACCC 57.010 30.769 0.00 0.00 0.00 4.11
882 996 9.083080 CCTTTTGGTCATTTAATTAATCGAACC 57.917 33.333 0.00 5.84 34.07 3.62
883 997 8.592155 GCCTTTTGGTCATTTAATTAATCGAAC 58.408 33.333 0.00 2.51 42.99 3.95
884 998 7.486551 CGCCTTTTGGTCATTTAATTAATCGAA 59.513 33.333 0.00 0.00 42.99 3.71
885 999 6.970043 CGCCTTTTGGTCATTTAATTAATCGA 59.030 34.615 0.00 0.00 42.99 3.59
886 1000 6.970043 TCGCCTTTTGGTCATTTAATTAATCG 59.030 34.615 0.00 0.00 42.99 3.34
887 1001 8.592155 GTTCGCCTTTTGGTCATTTAATTAATC 58.408 33.333 0.00 0.00 42.99 1.75
888 1002 7.274686 CGTTCGCCTTTTGGTCATTTAATTAAT 59.725 33.333 0.00 0.00 42.99 1.40
1006 1121 7.362574 GCATAAAACTCCTATTGCCTTAACACA 60.363 37.037 0.00 0.00 0.00 3.72
1090 1205 4.191033 TCACCTTACTTTTATCCGCGAA 57.809 40.909 8.23 0.00 0.00 4.70
1117 1232 2.181975 CCCAATGTTCCTCCAGCATTT 58.818 47.619 0.00 0.00 31.31 2.32
1235 1350 3.776969 ACTGATCCTAGCCAGTTCATCAA 59.223 43.478 5.25 0.00 40.40 2.57
1801 1935 8.526978 TGCACAGCTAAATGGTTTTAATTATGA 58.473 29.630 0.00 0.00 0.00 2.15
1818 1952 1.647545 GCGCCTTTGATGCACAGCTA 61.648 55.000 0.00 0.00 0.00 3.32
1824 1958 2.751436 GGAGGCGCCTTTGATGCA 60.751 61.111 33.34 0.00 0.00 3.96
1832 1966 4.853142 TATCACGGGGAGGCGCCT 62.853 66.667 33.48 33.48 36.66 5.52
1855 1989 3.111853 TGTCTTCCACACTGTGATGAC 57.888 47.619 15.86 14.07 35.23 3.06
1865 1999 2.548057 GCGATCTGTTTTGTCTTCCACA 59.452 45.455 0.00 0.00 0.00 4.17
1872 2006 0.672401 TCCCGGCGATCTGTTTTGTC 60.672 55.000 9.30 0.00 0.00 3.18
1873 2007 0.953960 GTCCCGGCGATCTGTTTTGT 60.954 55.000 9.30 0.00 0.00 2.83
1874 2008 0.953471 TGTCCCGGCGATCTGTTTTG 60.953 55.000 9.30 0.00 0.00 2.44
1875 2009 0.250553 TTGTCCCGGCGATCTGTTTT 60.251 50.000 9.30 0.00 0.00 2.43
1876 2010 0.250553 TTTGTCCCGGCGATCTGTTT 60.251 50.000 9.30 0.00 0.00 2.83
1877 2011 0.250553 TTTTGTCCCGGCGATCTGTT 60.251 50.000 9.30 0.00 0.00 3.16
1878 2012 0.250553 TTTTTGTCCCGGCGATCTGT 60.251 50.000 9.30 0.00 0.00 3.41
1879 2013 0.168128 GTTTTTGTCCCGGCGATCTG 59.832 55.000 9.30 0.00 0.00 2.90
1880 2014 0.250553 TGTTTTTGTCCCGGCGATCT 60.251 50.000 9.30 0.00 0.00 2.75
1881 2015 0.594110 TTGTTTTTGTCCCGGCGATC 59.406 50.000 9.30 0.00 0.00 3.69
1882 2016 1.033574 TTTGTTTTTGTCCCGGCGAT 58.966 45.000 9.30 0.00 0.00 4.58
1883 2017 0.815734 TTTTGTTTTTGTCCCGGCGA 59.184 45.000 9.30 0.00 0.00 5.54
1884 2018 0.924777 GTTTTGTTTTTGTCCCGGCG 59.075 50.000 0.00 0.00 0.00 6.46
1885 2019 1.930503 CTGTTTTGTTTTTGTCCCGGC 59.069 47.619 0.00 0.00 0.00 6.13
1886 2020 3.512033 TCTGTTTTGTTTTTGTCCCGG 57.488 42.857 0.00 0.00 0.00 5.73
1887 2021 3.302170 CGTTCTGTTTTGTTTTTGTCCCG 59.698 43.478 0.00 0.00 0.00 5.14
1888 2022 3.061563 GCGTTCTGTTTTGTTTTTGTCCC 59.938 43.478 0.00 0.00 0.00 4.46
1889 2023 3.924073 AGCGTTCTGTTTTGTTTTTGTCC 59.076 39.130 0.00 0.00 0.00 4.02
1890 2024 4.201580 CCAGCGTTCTGTTTTGTTTTTGTC 60.202 41.667 0.00 0.00 38.66 3.18
1891 2025 3.677596 CCAGCGTTCTGTTTTGTTTTTGT 59.322 39.130 0.00 0.00 38.66 2.83
1892 2026 3.061965 CCCAGCGTTCTGTTTTGTTTTTG 59.938 43.478 0.00 0.00 38.66 2.44
1893 2027 3.056465 TCCCAGCGTTCTGTTTTGTTTTT 60.056 39.130 0.00 0.00 38.66 1.94
1894 2028 2.494073 TCCCAGCGTTCTGTTTTGTTTT 59.506 40.909 0.00 0.00 38.66 2.43
1895 2029 2.096248 TCCCAGCGTTCTGTTTTGTTT 58.904 42.857 0.00 0.00 38.66 2.83
1907 2041 2.028930 TGTTTTGTTTTTGTCCCAGCGT 60.029 40.909 0.00 0.00 0.00 5.07
1909 2043 3.855858 TCTGTTTTGTTTTTGTCCCAGC 58.144 40.909 0.00 0.00 0.00 4.85
2106 2263 2.023113 AGAGAAGCAGGGAGGAGAAGAT 60.023 50.000 0.00 0.00 0.00 2.40
2119 2276 1.560146 TCGACTAGGAGGAGAGAAGCA 59.440 52.381 0.00 0.00 0.00 3.91
2202 2359 1.621814 CAGTGTACGGGAAGGAAGGAA 59.378 52.381 0.00 0.00 0.00 3.36
2405 2563 0.843309 TGGCGTGGGATGGTAATCAT 59.157 50.000 0.00 0.00 39.13 2.45
2480 2638 3.916359 GAAAAACTTCCCCAACCCAAA 57.084 42.857 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.