Multiple sequence alignment - TraesCS5B01G232000

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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 TraesCS5B01G232000 chr5B 100.000 5169 0 0 1 5169 409054473 409059641 0.000000e+00 9546.0
1 TraesCS5B01G232000 chr5B 87.156 109 12 1 650 756 565891174 565891282 7.030000e-24 122.0
2 TraesCS5B01G232000 chr5B 93.056 72 5 0 759 830 522847069 522847140 7.080000e-19 106.0
3 TraesCS5B01G232000 chr5B 89.041 73 6 2 759 830 470522613 470522542 7.130000e-14 89.8
4 TraesCS5B01G232000 chr5A 93.593 4027 156 39 858 4836 448830965 448834937 0.000000e+00 5914.0
5 TraesCS5B01G232000 chr5A 92.988 328 16 3 4846 5169 448834996 448835320 6.060000e-129 472.0
6 TraesCS5B01G232000 chr5A 79.292 565 83 15 1 537 448830364 448830922 1.060000e-96 364.0
7 TraesCS5B01G232000 chr5A 85.455 110 13 2 650 756 569789263 569789372 1.520000e-20 111.0
8 TraesCS5B01G232000 chr5A 90.164 61 6 0 765 825 635388235 635388295 4.290000e-11 80.5
9 TraesCS5B01G232000 chr5D 95.798 3498 110 14 1686 5169 348742572 348746046 0.000000e+00 5611.0
10 TraesCS5B01G232000 chr5D 93.569 793 33 9 858 1639 348741787 348742572 0.000000e+00 1166.0
11 TraesCS5B01G232000 chr5D 89.516 248 19 3 1 243 348741041 348741286 1.810000e-79 307.0
12 TraesCS5B01G232000 chr5D 82.569 327 25 14 242 551 348741376 348741687 5.130000e-65 259.0
13 TraesCS5B01G232000 chr5D 86.207 58 6 1 278 333 450946878 450946821 1.550000e-05 62.1
14 TraesCS5B01G232000 chr5D 100.000 28 0 0 279 306 44496647 44496620 9.000000e-03 52.8
15 TraesCS5B01G232000 chr3D 86.486 111 12 2 649 756 85839202 85839312 9.090000e-23 119.0
16 TraesCS5B01G232000 chr3D 84.404 109 15 1 650 756 506036759 506036867 7.080000e-19 106.0
17 TraesCS5B01G232000 chr6A 85.321 109 14 1 650 756 520879249 520879141 1.520000e-20 111.0
18 TraesCS5B01G232000 chr6A 84.404 109 15 1 650 756 596231347 596231239 7.080000e-19 106.0
19 TraesCS5B01G232000 chr3A 85.321 109 14 1 650 756 709042068 709042176 1.520000e-20 111.0
20 TraesCS5B01G232000 chr2B 85.455 110 13 2 650 756 617954233 617954124 1.520000e-20 111.0
21 TraesCS5B01G232000 chr2B 89.231 65 7 0 760 824 717681237 717681301 1.190000e-11 82.4
22 TraesCS5B01G232000 chr1D 83.784 111 15 2 648 756 80632773 80632664 9.160000e-18 102.0
23 TraesCS5B01G232000 chr1D 100.000 28 0 0 277 304 64431270 64431297 9.000000e-03 52.8
24 TraesCS5B01G232000 chr3B 91.045 67 6 0 762 828 785201457 785201391 1.980000e-14 91.6
25 TraesCS5B01G232000 chrUn 89.394 66 7 0 759 824 19194163 19194228 3.320000e-12 84.2
26 TraesCS5B01G232000 chrUn 84.615 65 4 5 269 333 303233728 303233670 5.590000e-05 60.2
27 TraesCS5B01G232000 chrUn 100.000 30 0 0 278 307 101887428 101887457 7.230000e-04 56.5
28 TraesCS5B01G232000 chr4B 88.060 67 5 3 759 824 438598469 438598533 5.550000e-10 76.8
29 TraesCS5B01G232000 chr2A 90.909 55 5 0 770 824 90589143 90589197 2.000000e-09 75.0
30 TraesCS5B01G232000 chr4D 84.615 65 4 5 269 333 499893775 499893833 5.590000e-05 60.2
31 TraesCS5B01G232000 chr2D 90.909 44 4 0 782 825 544672015 544671972 5.590000e-05 60.2
32 TraesCS5B01G232000 chr6B 94.595 37 1 1 270 305 545275946 545275982 7.230000e-04 56.5
33 TraesCS5B01G232000 chr1A 100.000 30 0 0 278 307 558299855 558299884 7.230000e-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 TraesCS5B01G232000 chr5B 409054473 409059641 5168 False 9546.00 9546 100.000000 1 5169 1 chr5B.!!$F1 5168
1 TraesCS5B01G232000 chr5A 448830364 448835320 4956 False 2250.00 5914 88.624333 1 5169 3 chr5A.!!$F3 5168
2 TraesCS5B01G232000 chr5D 348741041 348746046 5005 False 1835.75 5611 90.363000 1 5169 4 chr5D.!!$F1 5168

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
706 826 0.106708 ACGCGCATACATTCATCCCT 59.893 50.0 5.73 0.00 0.00 4.20 F
1073 1193 0.174617 CAGTCCTCGCTTCTCTTCCC 59.825 60.0 0.00 0.00 0.00 3.97 F
1222 1342 0.892755 TGCCGTTTCATACTCCTCGT 59.107 50.0 0.00 0.00 0.00 4.18 F
2163 2306 1.323271 TGCAAAAAGGCCGAACACCA 61.323 50.0 0.00 0.00 0.00 4.17 F
3414 3574 0.030638 AGACCAACGTGTTTGCATGC 59.969 50.0 11.82 11.82 35.09 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 2533 0.543410 TCCAGCCCCTACGAAGAACA 60.543 55.000 0.00 0.0 0.00 3.18 R
2610 2764 4.119862 GGAAACAGATTGCAGCGTATCTA 58.880 43.478 8.98 0.0 30.20 1.98 R
2833 2991 4.991056 GGGTTTTCTTTTGGAGATTTCTGC 59.009 41.667 0.00 0.0 33.49 4.26 R
3592 3752 0.610687 AGCTGCCTCCTACACACTTC 59.389 55.000 0.00 0.0 0.00 3.01 R
4510 4678 0.625849 AGAGTAGGTGGCCCAAATGG 59.374 55.000 0.00 0.0 37.09 3.16 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
101 103 7.083230 CACATAAAACATAGTGTGAACATGCA 58.917 34.615 0.00 0.00 43.41 3.96
130 132 3.985925 GGCCTTAGGAAACGATATACACG 59.014 47.826 0.69 0.00 0.00 4.49
133 135 4.980434 CCTTAGGAAACGATATACACGTGG 59.020 45.833 21.57 2.84 43.16 4.94
168 170 4.201851 GCAATATGCGAGTGATCACAACTT 60.202 41.667 27.02 15.17 31.71 2.66
169 171 5.006649 GCAATATGCGAGTGATCACAACTTA 59.993 40.000 27.02 16.59 31.71 2.24
197 199 3.736996 TTGCCAGCTGGGTGCAAGT 62.737 57.895 33.46 0.00 45.94 3.16
206 208 0.687920 TGGGTGCAAGTTCGGTCATA 59.312 50.000 0.00 0.00 0.00 2.15
207 209 1.280710 TGGGTGCAAGTTCGGTCATAT 59.719 47.619 0.00 0.00 0.00 1.78
208 210 1.670811 GGGTGCAAGTTCGGTCATATG 59.329 52.381 0.00 0.00 0.00 1.78
209 211 1.064060 GGTGCAAGTTCGGTCATATGC 59.936 52.381 0.00 0.00 0.00 3.14
210 212 1.064060 GTGCAAGTTCGGTCATATGCC 59.936 52.381 0.00 1.98 33.01 4.40
283 377 3.804036 CCGTGCCAAAATAGATACTCCA 58.196 45.455 0.00 0.00 0.00 3.86
286 380 5.300752 CGTGCCAAAATAGATACTCCATCT 58.699 41.667 0.00 0.00 46.19 2.90
357 465 4.038271 TCTTTCTCCTGTTCATGCCATT 57.962 40.909 0.00 0.00 0.00 3.16
395 513 4.755123 AGTTTATTCGGACTTGGAGTTGTG 59.245 41.667 0.00 0.00 0.00 3.33
403 521 3.632145 GGACTTGGAGTTGTGTTTGTCAT 59.368 43.478 0.00 0.00 0.00 3.06
404 522 4.261197 GGACTTGGAGTTGTGTTTGTCATC 60.261 45.833 0.00 0.00 0.00 2.92
407 525 2.869801 TGGAGTTGTGTTTGTCATCGAC 59.130 45.455 0.00 0.00 0.00 4.20
408 526 2.869801 GGAGTTGTGTTTGTCATCGACA 59.130 45.455 0.00 0.00 41.09 4.35
412 530 1.855978 TGTGTTTGTCATCGACACGTC 59.144 47.619 0.00 0.00 44.95 4.34
427 545 2.083774 CACGTCTGGGCATGTTGTTAT 58.916 47.619 0.00 0.00 0.00 1.89
430 548 2.095853 CGTCTGGGCATGTTGTTATGAC 59.904 50.000 0.00 0.00 35.26 3.06
432 550 3.375299 GTCTGGGCATGTTGTTATGACTC 59.625 47.826 0.00 0.00 36.31 3.36
435 553 3.008923 TGGGCATGTTGTTATGACTCTCA 59.991 43.478 0.00 0.00 36.31 3.27
438 556 5.121811 GGCATGTTGTTATGACTCTCATCT 58.878 41.667 0.00 0.00 38.26 2.90
442 560 8.668353 GCATGTTGTTATGACTCTCATCTTTTA 58.332 33.333 0.00 0.00 38.26 1.52
504 622 4.553330 TTGAACCCATTAGACTCTGGTC 57.447 45.455 3.90 0.00 42.41 4.02
602 722 7.771183 TCTCAAAATTAATAACATGGCAGTCC 58.229 34.615 0.00 0.00 0.00 3.85
603 723 7.615365 TCTCAAAATTAATAACATGGCAGTCCT 59.385 33.333 0.00 0.00 0.00 3.85
604 724 7.771183 TCAAAATTAATAACATGGCAGTCCTC 58.229 34.615 0.00 0.00 0.00 3.71
605 725 7.615365 TCAAAATTAATAACATGGCAGTCCTCT 59.385 33.333 0.00 0.00 0.00 3.69
606 726 7.961326 AAATTAATAACATGGCAGTCCTCTT 57.039 32.000 0.00 0.00 0.00 2.85
607 727 7.573968 AATTAATAACATGGCAGTCCTCTTC 57.426 36.000 0.00 0.00 0.00 2.87
608 728 4.574674 AATAACATGGCAGTCCTCTTCA 57.425 40.909 0.00 0.00 0.00 3.02
609 729 2.957402 AACATGGCAGTCCTCTTCAA 57.043 45.000 0.00 0.00 0.00 2.69
610 730 3.446442 AACATGGCAGTCCTCTTCAAT 57.554 42.857 0.00 0.00 0.00 2.57
611 731 2.996631 ACATGGCAGTCCTCTTCAATC 58.003 47.619 0.00 0.00 0.00 2.67
612 732 1.938577 CATGGCAGTCCTCTTCAATCG 59.061 52.381 0.00 0.00 0.00 3.34
614 734 2.176045 TGGCAGTCCTCTTCAATCGTA 58.824 47.619 0.00 0.00 0.00 3.43
615 735 2.766263 TGGCAGTCCTCTTCAATCGTAT 59.234 45.455 0.00 0.00 0.00 3.06
619 739 5.234543 GGCAGTCCTCTTCAATCGTATTTAC 59.765 44.000 0.00 0.00 0.00 2.01
620 740 6.043411 GCAGTCCTCTTCAATCGTATTTACT 58.957 40.000 0.00 0.00 0.00 2.24
622 742 7.064728 GCAGTCCTCTTCAATCGTATTTACTTT 59.935 37.037 0.00 0.00 0.00 2.66
623 743 9.582431 CAGTCCTCTTCAATCGTATTTACTTTA 57.418 33.333 0.00 0.00 0.00 1.85
678 798 3.314553 ACATTAGTACAGACACACACGC 58.685 45.455 0.00 0.00 0.00 5.34
680 800 2.983402 TAGTACAGACACACACGCTC 57.017 50.000 0.00 0.00 0.00 5.03
681 801 1.029681 AGTACAGACACACACGCTCA 58.970 50.000 0.00 0.00 0.00 4.26
683 803 2.817844 AGTACAGACACACACGCTCATA 59.182 45.455 0.00 0.00 0.00 2.15
684 804 3.444034 AGTACAGACACACACGCTCATAT 59.556 43.478 0.00 0.00 0.00 1.78
685 805 4.638865 AGTACAGACACACACGCTCATATA 59.361 41.667 0.00 0.00 0.00 0.86
686 806 4.655762 ACAGACACACACGCTCATATAT 57.344 40.909 0.00 0.00 0.00 0.86
687 807 5.767816 ACAGACACACACGCTCATATATA 57.232 39.130 0.00 0.00 0.00 0.86
688 808 5.520632 ACAGACACACACGCTCATATATAC 58.479 41.667 0.00 0.00 0.00 1.47
689 809 4.613031 CAGACACACACGCTCATATATACG 59.387 45.833 1.63 1.63 0.00 3.06
690 810 3.305964 ACACACACGCTCATATATACGC 58.694 45.455 2.81 0.03 0.00 4.42
697 817 3.359654 CGCTCATATATACGCGCATACA 58.640 45.455 5.73 0.00 39.11 2.29
698 818 3.975035 CGCTCATATATACGCGCATACAT 59.025 43.478 5.73 0.00 39.11 2.29
699 819 4.441087 CGCTCATATATACGCGCATACATT 59.559 41.667 5.73 0.00 39.11 2.71
700 820 5.386424 CGCTCATATATACGCGCATACATTC 60.386 44.000 5.73 0.00 39.11 2.67
701 821 5.458779 GCTCATATATACGCGCATACATTCA 59.541 40.000 5.73 0.00 0.00 2.57
702 822 6.144563 GCTCATATATACGCGCATACATTCAT 59.855 38.462 5.73 0.00 0.00 2.57
703 823 7.618139 GCTCATATATACGCGCATACATTCATC 60.618 40.741 5.73 0.00 0.00 2.92
704 824 6.640907 TCATATATACGCGCATACATTCATCC 59.359 38.462 5.73 0.00 0.00 3.51
705 825 1.790755 TACGCGCATACATTCATCCC 58.209 50.000 5.73 0.00 0.00 3.85
706 826 0.106708 ACGCGCATACATTCATCCCT 59.893 50.000 5.73 0.00 0.00 4.20
707 827 1.343142 ACGCGCATACATTCATCCCTA 59.657 47.619 5.73 0.00 0.00 3.53
708 828 2.028112 ACGCGCATACATTCATCCCTAT 60.028 45.455 5.73 0.00 0.00 2.57
709 829 2.349580 CGCGCATACATTCATCCCTATG 59.650 50.000 8.75 0.00 0.00 2.23
710 830 3.599343 GCGCATACATTCATCCCTATGA 58.401 45.455 0.30 0.00 40.43 2.15
716 836 2.986311 TTCATCCCTATGAACGCGC 58.014 52.632 5.73 0.00 45.17 6.86
717 837 0.874175 TTCATCCCTATGAACGCGCG 60.874 55.000 30.96 30.96 45.17 6.86
718 838 2.661866 ATCCCTATGAACGCGCGC 60.662 61.111 32.58 23.91 0.00 6.86
719 839 3.439513 ATCCCTATGAACGCGCGCA 62.440 57.895 32.58 21.73 0.00 6.09
720 840 3.925238 CCCTATGAACGCGCGCAC 61.925 66.667 32.58 23.88 0.00 5.34
721 841 3.185365 CCTATGAACGCGCGCACA 61.185 61.111 32.58 28.72 0.00 4.57
722 842 2.020016 CTATGAACGCGCGCACAC 59.980 61.111 32.58 20.38 0.00 3.82
723 843 2.725699 CTATGAACGCGCGCACACA 61.726 57.895 32.58 25.17 0.00 3.72
724 844 2.863655 CTATGAACGCGCGCACACAC 62.864 60.000 32.58 16.76 0.00 3.82
726 846 4.702826 GAACGCGCGCACACACTC 62.703 66.667 32.58 13.11 0.00 3.51
728 848 3.834447 AACGCGCGCACACACTCTA 62.834 57.895 32.58 0.00 0.00 2.43
729 849 2.880879 CGCGCGCACACACTCTAT 60.881 61.111 32.61 0.00 0.00 1.98
730 850 2.849966 CGCGCGCACACACTCTATC 61.850 63.158 32.61 0.00 0.00 2.08
731 851 2.517450 GCGCGCACACACTCTATCC 61.517 63.158 29.10 0.00 0.00 2.59
732 852 1.153842 CGCGCACACACTCTATCCA 60.154 57.895 8.75 0.00 0.00 3.41
733 853 0.528466 CGCGCACACACTCTATCCAT 60.528 55.000 8.75 0.00 0.00 3.41
734 854 1.269051 CGCGCACACACTCTATCCATA 60.269 52.381 8.75 0.00 0.00 2.74
735 855 2.608016 CGCGCACACACTCTATCCATAT 60.608 50.000 8.75 0.00 0.00 1.78
736 856 2.733552 GCGCACACACTCTATCCATATG 59.266 50.000 0.30 0.00 0.00 1.78
737 857 3.552890 GCGCACACACTCTATCCATATGA 60.553 47.826 0.30 0.00 0.00 2.15
738 858 4.233005 CGCACACACTCTATCCATATGAG 58.767 47.826 3.65 0.00 0.00 2.90
739 859 3.993081 GCACACACTCTATCCATATGAGC 59.007 47.826 3.65 0.00 0.00 4.26
740 860 4.502087 GCACACACTCTATCCATATGAGCA 60.502 45.833 3.65 0.00 0.00 4.26
741 861 4.987285 CACACACTCTATCCATATGAGCAC 59.013 45.833 3.65 0.00 0.00 4.40
742 862 4.651045 ACACACTCTATCCATATGAGCACA 59.349 41.667 3.65 0.00 0.00 4.57
743 863 5.306419 ACACACTCTATCCATATGAGCACAT 59.694 40.000 3.65 1.31 40.16 3.21
744 864 6.183361 ACACACTCTATCCATATGAGCACATT 60.183 38.462 3.65 0.00 37.87 2.71
745 865 6.368243 CACACTCTATCCATATGAGCACATTC 59.632 42.308 3.65 0.00 37.87 2.67
746 866 5.575995 CACTCTATCCATATGAGCACATTCG 59.424 44.000 3.65 0.00 37.87 3.34
747 867 5.478332 ACTCTATCCATATGAGCACATTCGA 59.522 40.000 3.65 0.00 37.87 3.71
748 868 6.015095 ACTCTATCCATATGAGCACATTCGAA 60.015 38.462 3.65 0.00 37.87 3.71
749 869 6.758254 TCTATCCATATGAGCACATTCGAAA 58.242 36.000 0.00 0.00 37.87 3.46
750 870 5.936686 ATCCATATGAGCACATTCGAAAG 57.063 39.130 0.00 0.00 37.87 2.62
751 871 5.022282 TCCATATGAGCACATTCGAAAGA 57.978 39.130 7.49 0.00 37.87 2.52
752 872 4.811024 TCCATATGAGCACATTCGAAAGAC 59.189 41.667 7.49 0.00 41.84 3.01
753 873 4.813161 CCATATGAGCACATTCGAAAGACT 59.187 41.667 7.49 4.01 41.84 3.24
754 874 5.277202 CCATATGAGCACATTCGAAAGACTG 60.277 44.000 7.49 0.84 45.23 3.51
755 875 3.385193 TGAGCACATTCGAAAGACTGA 57.615 42.857 7.49 0.00 42.73 3.41
756 876 3.930336 TGAGCACATTCGAAAGACTGAT 58.070 40.909 7.49 0.00 42.73 2.90
757 877 4.318332 TGAGCACATTCGAAAGACTGATT 58.682 39.130 7.49 0.00 42.73 2.57
758 878 4.152938 TGAGCACATTCGAAAGACTGATTG 59.847 41.667 7.49 0.00 42.73 2.67
759 879 4.318332 AGCACATTCGAAAGACTGATTGA 58.682 39.130 7.49 0.00 42.73 2.57
760 880 4.940046 AGCACATTCGAAAGACTGATTGAT 59.060 37.500 7.49 0.00 42.73 2.57
761 881 5.413833 AGCACATTCGAAAGACTGATTGATT 59.586 36.000 7.49 0.00 42.73 2.57
762 882 6.072286 AGCACATTCGAAAGACTGATTGATTT 60.072 34.615 7.49 0.00 42.73 2.17
763 883 7.119699 AGCACATTCGAAAGACTGATTGATTTA 59.880 33.333 7.49 0.00 42.73 1.40
764 884 7.750458 GCACATTCGAAAGACTGATTGATTTAA 59.250 33.333 7.49 0.00 42.73 1.52
765 885 9.611284 CACATTCGAAAGACTGATTGATTTAAA 57.389 29.630 7.49 0.00 42.73 1.52
766 886 9.612620 ACATTCGAAAGACTGATTGATTTAAAC 57.387 29.630 7.49 0.00 42.73 2.01
767 887 9.611284 CATTCGAAAGACTGATTGATTTAAACA 57.389 29.630 0.00 0.00 42.73 2.83
768 888 9.612620 ATTCGAAAGACTGATTGATTTAAACAC 57.387 29.630 0.00 0.00 41.84 3.32
769 889 8.378172 TCGAAAGACTGATTGATTTAAACACT 57.622 30.769 0.00 0.00 33.31 3.55
770 890 8.282592 TCGAAAGACTGATTGATTTAAACACTG 58.717 33.333 0.00 0.00 33.31 3.66
771 891 8.282592 CGAAAGACTGATTGATTTAAACACTGA 58.717 33.333 0.00 0.00 0.00 3.41
773 893 9.903682 AAAGACTGATTGATTTAAACACTGATG 57.096 29.630 0.00 0.00 0.00 3.07
774 894 8.048534 AGACTGATTGATTTAAACACTGATGG 57.951 34.615 0.00 0.00 0.00 3.51
775 895 7.121759 AGACTGATTGATTTAAACACTGATGGG 59.878 37.037 0.00 0.00 0.00 4.00
776 896 5.964758 TGATTGATTTAAACACTGATGGGC 58.035 37.500 0.00 0.00 0.00 5.36
777 897 5.716228 TGATTGATTTAAACACTGATGGGCT 59.284 36.000 0.00 0.00 0.00 5.19
778 898 5.389859 TTGATTTAAACACTGATGGGCTG 57.610 39.130 0.00 0.00 0.00 4.85
779 899 3.763360 TGATTTAAACACTGATGGGCTGG 59.237 43.478 0.00 0.00 0.00 4.85
780 900 2.214376 TTAAACACTGATGGGCTGGG 57.786 50.000 0.00 0.00 0.00 4.45
781 901 0.331278 TAAACACTGATGGGCTGGGG 59.669 55.000 0.00 0.00 0.00 4.96
782 902 1.434513 AAACACTGATGGGCTGGGGA 61.435 55.000 0.00 0.00 0.00 4.81
783 903 1.217057 AACACTGATGGGCTGGGGAT 61.217 55.000 0.00 0.00 0.00 3.85
784 904 0.327480 ACACTGATGGGCTGGGGATA 60.327 55.000 0.00 0.00 0.00 2.59
785 905 1.070604 CACTGATGGGCTGGGGATAT 58.929 55.000 0.00 0.00 0.00 1.63
786 906 1.004044 CACTGATGGGCTGGGGATATC 59.996 57.143 0.00 0.00 0.00 1.63
787 907 1.365293 CTGATGGGCTGGGGATATCA 58.635 55.000 4.83 0.00 0.00 2.15
788 908 1.004044 CTGATGGGCTGGGGATATCAC 59.996 57.143 4.83 0.00 0.00 3.06
789 909 1.067295 GATGGGCTGGGGATATCACA 58.933 55.000 7.40 3.31 0.00 3.58
790 910 1.004044 GATGGGCTGGGGATATCACAG 59.996 57.143 17.64 17.64 35.40 3.66
791 911 0.327480 TGGGCTGGGGATATCACAGT 60.327 55.000 20.90 0.00 34.79 3.55
792 912 0.398318 GGGCTGGGGATATCACAGTC 59.602 60.000 20.90 19.49 36.17 3.51
793 913 0.398318 GGCTGGGGATATCACAGTCC 59.602 60.000 20.90 18.51 34.79 3.85
802 922 5.367945 GGATATCACAGTCCCTTTAACCA 57.632 43.478 4.83 0.00 0.00 3.67
803 923 5.941788 GGATATCACAGTCCCTTTAACCAT 58.058 41.667 4.83 0.00 0.00 3.55
804 924 5.998363 GGATATCACAGTCCCTTTAACCATC 59.002 44.000 4.83 0.00 0.00 3.51
805 925 3.713826 TCACAGTCCCTTTAACCATCC 57.286 47.619 0.00 0.00 0.00 3.51
806 926 2.983192 TCACAGTCCCTTTAACCATCCA 59.017 45.455 0.00 0.00 0.00 3.41
807 927 3.396276 TCACAGTCCCTTTAACCATCCAA 59.604 43.478 0.00 0.00 0.00 3.53
808 928 4.044065 TCACAGTCCCTTTAACCATCCAAT 59.956 41.667 0.00 0.00 0.00 3.16
809 929 4.399303 CACAGTCCCTTTAACCATCCAATC 59.601 45.833 0.00 0.00 0.00 2.67
810 930 4.044065 ACAGTCCCTTTAACCATCCAATCA 59.956 41.667 0.00 0.00 0.00 2.57
811 931 4.399303 CAGTCCCTTTAACCATCCAATCAC 59.601 45.833 0.00 0.00 0.00 3.06
812 932 4.044065 AGTCCCTTTAACCATCCAATCACA 59.956 41.667 0.00 0.00 0.00 3.58
813 933 4.399303 GTCCCTTTAACCATCCAATCACAG 59.601 45.833 0.00 0.00 0.00 3.66
814 934 4.290985 TCCCTTTAACCATCCAATCACAGA 59.709 41.667 0.00 0.00 0.00 3.41
815 935 5.044179 TCCCTTTAACCATCCAATCACAGAT 60.044 40.000 0.00 0.00 0.00 2.90
816 936 5.658190 CCCTTTAACCATCCAATCACAGATT 59.342 40.000 0.00 0.00 0.00 2.40
817 937 6.406177 CCCTTTAACCATCCAATCACAGATTG 60.406 42.308 11.73 11.73 0.00 2.67
818 938 6.377996 CCTTTAACCATCCAATCACAGATTGA 59.622 38.462 18.51 7.53 39.11 2.57
855 975 7.876896 TTTTAAATCCGTAATTGTCTTTGCC 57.123 32.000 0.00 0.00 0.00 4.52
856 976 6.576662 TTAAATCCGTAATTGTCTTTGCCA 57.423 33.333 0.00 0.00 0.00 4.92
898 1018 3.950397 ACCATACGATTTCCATGTGTGT 58.050 40.909 0.00 0.00 0.00 3.72
954 1074 2.125673 CGTCGCGGGTCTGGATTT 60.126 61.111 6.13 0.00 0.00 2.17
1073 1193 0.174617 CAGTCCTCGCTTCTCTTCCC 59.825 60.000 0.00 0.00 0.00 3.97
1177 1297 1.062488 AACCCACAGGACTCAGGCTT 61.062 55.000 0.00 0.00 36.73 4.35
1178 1298 1.062488 ACCCACAGGACTCAGGCTTT 61.062 55.000 0.00 0.00 36.73 3.51
1212 1332 3.286751 GCCTGTGCTGCCGTTTCA 61.287 61.111 0.00 0.00 33.53 2.69
1222 1342 0.892755 TGCCGTTTCATACTCCTCGT 59.107 50.000 0.00 0.00 0.00 4.18
1245 1365 2.094659 CGCGGCAGAAGGTACTGTG 61.095 63.158 0.00 0.00 40.86 3.66
1256 1377 6.821665 GCAGAAGGTACTGTGGTAATCAAATA 59.178 38.462 0.00 0.00 40.86 1.40
1292 1421 3.503363 TGGCTTGAGCTCTTGTAATTGTG 59.497 43.478 16.19 0.00 41.70 3.33
1353 1495 2.281970 CTGGTGCTGGAGCTTGCA 60.282 61.111 6.00 6.00 42.66 4.08
1407 1549 5.861869 TCCTCTATGGTACCAGGTCTGGC 62.862 56.522 21.41 1.89 44.95 4.85
1444 1586 3.641437 TGTTCCAATGCTGTTTACTGC 57.359 42.857 4.97 4.97 40.61 4.40
1529 1671 5.607119 TGAATTCGCTAGTTTGGAGTTTC 57.393 39.130 0.04 0.00 0.00 2.78
1579 1721 4.449743 TGCGATGTACTAGTTGTTTTGGAC 59.550 41.667 0.00 0.00 0.00 4.02
1680 1823 8.420374 TCTAGTTGCTTGTAAATATAGTGCAC 57.580 34.615 9.40 9.40 0.00 4.57
1681 1824 6.106877 AGTTGCTTGTAAATATAGTGCACG 57.893 37.500 12.01 0.00 0.00 5.34
1816 1959 8.189119 TCTTTGGCAAAAGAGTTAATTATGGT 57.811 30.769 12.46 0.00 45.44 3.55
2056 2199 3.576550 TGGCGCAATATCTACCTGTCATA 59.423 43.478 10.83 0.00 0.00 2.15
2163 2306 1.323271 TGCAAAAAGGCCGAACACCA 61.323 50.000 0.00 0.00 0.00 4.17
2389 2533 8.967552 TTTGAACGTTTTGTACTTGTACAATT 57.032 26.923 21.99 15.13 39.39 2.32
2397 2541 8.730427 GTTTTGTACTTGTACAATTGTTCTTCG 58.270 33.333 21.99 6.87 39.39 3.79
2684 2841 9.678941 CACTGCAATCTATTAACTAGTAATCGA 57.321 33.333 0.00 0.00 34.18 3.59
2686 2843 9.678941 CTGCAATCTATTAACTAGTAATCGACA 57.321 33.333 0.00 0.00 34.18 4.35
2833 2991 8.092687 GGATCATTTTCATTTCCATGGGATAAG 58.907 37.037 13.02 0.00 0.00 1.73
3039 3197 2.639327 GGGTGGCAGTGCATTGACC 61.639 63.158 18.61 15.61 0.00 4.02
3275 3434 4.320608 TTTGGTTTGTTGCTCCTGAATC 57.679 40.909 0.00 0.00 0.00 2.52
3277 3436 3.149196 TGGTTTGTTGCTCCTGAATCTC 58.851 45.455 0.00 0.00 0.00 2.75
3285 3444 8.442632 TTGTTGCTCCTGAATCTCTAATTATG 57.557 34.615 0.00 0.00 0.00 1.90
3292 3451 6.767902 TCCTGAATCTCTAATTATGTTGTGGC 59.232 38.462 0.00 0.00 0.00 5.01
3414 3574 0.030638 AGACCAACGTGTTTGCATGC 59.969 50.000 11.82 11.82 35.09 4.06
3473 3633 6.023603 TCCTCCAGAAGTAATGTCTTTACCT 58.976 40.000 5.28 0.00 41.01 3.08
3592 3752 1.007271 CGGTGAGCTAGTATGCCCG 60.007 63.158 0.00 0.00 0.00 6.13
3646 3806 2.791347 TATTGGCATTGTACCCACGT 57.209 45.000 0.00 0.00 0.00 4.49
3844 4004 4.521256 TGCTGTTACCGCCTTATTTTTCTT 59.479 37.500 0.00 0.00 0.00 2.52
3845 4005 5.093457 GCTGTTACCGCCTTATTTTTCTTC 58.907 41.667 0.00 0.00 0.00 2.87
4006 4170 5.221382 GGCTGATATTGTGATCCAAATGCTT 60.221 40.000 1.49 0.00 36.44 3.91
4033 4197 4.202253 ACAGATTATGCTAGGATCGTGCAA 60.202 41.667 0.00 0.00 40.24 4.08
4116 4281 1.286501 TTGATGCATACGTCGCCTTC 58.713 50.000 0.00 5.50 34.28 3.46
4157 4322 4.769688 TCGGTCGTGTTACCTAGAATCTA 58.230 43.478 0.00 0.00 37.39 1.98
4158 4323 5.371526 TCGGTCGTGTTACCTAGAATCTAT 58.628 41.667 0.00 0.00 37.39 1.98
4187 4352 2.836372 TGACCAGAGCAGAATCATCACT 59.164 45.455 0.00 0.00 0.00 3.41
4210 4375 3.404773 AGCCTAACTGGGTGCTCC 58.595 61.111 0.00 0.00 46.19 4.70
4253 4418 5.600069 AGCTCCATAGTGTACATTCTGATCA 59.400 40.000 0.00 0.00 0.00 2.92
4274 4439 1.951130 CAGATCATTCCCGGTCGCG 60.951 63.158 0.00 0.00 0.00 5.87
4283 4448 3.524606 CCGGTCGCGGTACTCCAT 61.525 66.667 6.13 0.00 0.00 3.41
4296 4461 0.176680 ACTCCATGGTAAGCTCTGCG 59.823 55.000 12.58 0.00 0.00 5.18
4411 4576 0.178998 AGGCCCATAGCTGCTTCATG 60.179 55.000 7.79 6.45 43.05 3.07
4450 4615 4.919754 GTGAAGCTTAGGAAAAACAGCATG 59.080 41.667 0.00 0.00 46.00 4.06
4510 4678 4.806247 ACTTGACAAATAGCTCACGATAGC 59.194 41.667 0.00 5.76 43.11 2.97
4583 4751 0.884704 CTTCACACTTCCACGGGGTG 60.885 60.000 2.12 0.00 37.05 4.61
4743 4914 6.155910 ACCAGCCATCCATATATCTTAGACAG 59.844 42.308 0.00 0.00 0.00 3.51
4792 4963 3.867549 CACCCTGTGCTGATCATCA 57.132 52.632 0.00 0.00 0.00 3.07
4887 5107 7.969536 TTTGCTTAGGACATAAGATATCTGC 57.030 36.000 10.96 1.79 43.17 4.26
4888 5108 6.670695 TGCTTAGGACATAAGATATCTGCA 57.329 37.500 10.96 4.54 43.17 4.41
4910 5130 1.477553 ATTTGCCTCGCCATCAACAT 58.522 45.000 0.00 0.00 0.00 2.71
4911 5131 1.255882 TTTGCCTCGCCATCAACATT 58.744 45.000 0.00 0.00 0.00 2.71
4913 5133 0.810648 TGCCTCGCCATCAACATTTC 59.189 50.000 0.00 0.00 0.00 2.17
5015 5235 5.008613 GTGTGCAAAGTTTCAATAGGAGACA 59.991 40.000 0.00 0.00 33.18 3.41
5079 5303 3.701040 AGGATGCATGGTCCATTGTTTAC 59.299 43.478 2.46 0.00 38.25 2.01
5089 5313 2.009774 CCATTGTTTACAGAGCTCGGG 58.990 52.381 18.37 12.40 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.519419 GGTTGCGAAATTTTGACATTTAATGC 59.481 34.615 9.75 0.00 0.00 3.56
44 45 9.671279 CTTGAATTGGCTTTAGGGAAATAAATT 57.329 29.630 0.00 0.00 0.00 1.82
53 54 5.221422 TGTTGTTCTTGAATTGGCTTTAGGG 60.221 40.000 0.00 0.00 0.00 3.53
67 68 8.957028 CACACTATGTTTTATGTGTTGTTCTTG 58.043 33.333 0.00 0.00 41.04 3.02
101 103 0.036294 GTTTCCTAAGGCCACGCTCT 60.036 55.000 5.01 0.00 0.00 4.09
130 132 1.325355 ATTGCTGCATGATAGGCCAC 58.675 50.000 5.01 0.00 0.00 5.01
133 135 2.477357 CGCATATTGCTGCATGATAGGC 60.477 50.000 16.72 16.72 42.25 3.93
184 186 2.281761 CCGAACTTGCACCCAGCT 60.282 61.111 0.00 0.00 45.94 4.24
186 188 0.606401 ATGACCGAACTTGCACCCAG 60.606 55.000 0.00 0.00 0.00 4.45
208 210 2.203209 CTAGGGTTGGCATCCGGC 60.203 66.667 8.45 0.00 43.74 6.13
209 211 1.632018 TTCCTAGGGTTGGCATCCGG 61.632 60.000 9.46 0.00 0.00 5.14
210 212 0.463833 GTTCCTAGGGTTGGCATCCG 60.464 60.000 9.46 0.00 0.00 4.18
247 251 0.179048 CACGGCCATGGAGCTCATAA 60.179 55.000 18.40 0.14 34.12 1.90
249 253 2.191375 CACGGCCATGGAGCTCAT 59.809 61.111 18.40 4.42 36.31 2.90
283 377 6.533012 CGAGCGACAATTAATATGGATCAGAT 59.467 38.462 0.00 0.00 0.00 2.90
286 380 5.405269 CACGAGCGACAATTAATATGGATCA 59.595 40.000 0.00 0.00 0.00 2.92
333 427 5.378230 TGGCATGAACAGGAGAAAGATAT 57.622 39.130 0.00 0.00 0.00 1.63
334 428 4.842531 TGGCATGAACAGGAGAAAGATA 57.157 40.909 0.00 0.00 0.00 1.98
357 465 7.040340 TCCGAATAAACTTATTGTTTCCTTGCA 60.040 33.333 0.00 0.00 44.81 4.08
381 499 3.013921 TGACAAACACAACTCCAAGTCC 58.986 45.455 0.00 0.00 0.00 3.85
395 513 1.455786 CCAGACGTGTCGATGACAAAC 59.544 52.381 0.00 0.00 44.49 2.93
403 521 2.094757 AACATGCCCAGACGTGTCGA 62.095 55.000 0.00 0.00 38.84 4.20
404 522 1.667830 AACATGCCCAGACGTGTCG 60.668 57.895 0.00 0.00 38.84 4.35
407 525 1.518325 TAACAACATGCCCAGACGTG 58.482 50.000 0.00 0.00 0.00 4.49
408 526 2.083774 CATAACAACATGCCCAGACGT 58.916 47.619 0.00 0.00 0.00 4.34
412 530 3.614092 AGAGTCATAACAACATGCCCAG 58.386 45.455 0.00 0.00 0.00 4.45
578 698 7.775120 AGGACTGCCATGTTATTAATTTTGAG 58.225 34.615 0.00 0.00 36.29 3.02
580 700 7.775120 AGAGGACTGCCATGTTATTAATTTTG 58.225 34.615 0.00 0.00 36.29 2.44
590 710 2.957402 TTGAAGAGGACTGCCATGTT 57.043 45.000 0.00 0.00 36.29 2.71
591 711 2.679059 CGATTGAAGAGGACTGCCATGT 60.679 50.000 0.00 0.00 36.29 3.21
592 712 1.938577 CGATTGAAGAGGACTGCCATG 59.061 52.381 0.00 0.00 36.29 3.66
593 713 1.556911 ACGATTGAAGAGGACTGCCAT 59.443 47.619 0.00 0.00 36.29 4.40
594 714 0.976641 ACGATTGAAGAGGACTGCCA 59.023 50.000 0.00 0.00 36.29 4.92
595 715 2.961526 TACGATTGAAGAGGACTGCC 57.038 50.000 0.00 0.00 0.00 4.85
596 716 6.043411 AGTAAATACGATTGAAGAGGACTGC 58.957 40.000 0.00 0.00 0.00 4.40
651 771 8.329583 CGTGTGTGTCTGTACTAATGTTAAAAA 58.670 33.333 0.00 0.00 0.00 1.94
652 772 7.517101 GCGTGTGTGTCTGTACTAATGTTAAAA 60.517 37.037 0.00 0.00 0.00 1.52
653 773 6.074195 GCGTGTGTGTCTGTACTAATGTTAAA 60.074 38.462 0.00 0.00 0.00 1.52
654 774 5.403166 GCGTGTGTGTCTGTACTAATGTTAA 59.597 40.000 0.00 0.00 0.00 2.01
655 775 4.919168 GCGTGTGTGTCTGTACTAATGTTA 59.081 41.667 0.00 0.00 0.00 2.41
657 777 3.005472 AGCGTGTGTGTCTGTACTAATGT 59.995 43.478 0.00 0.00 0.00 2.71
658 778 3.575630 AGCGTGTGTGTCTGTACTAATG 58.424 45.455 0.00 0.00 0.00 1.90
659 779 3.254903 TGAGCGTGTGTGTCTGTACTAAT 59.745 43.478 0.00 0.00 0.00 1.73
661 781 2.223745 TGAGCGTGTGTGTCTGTACTA 58.776 47.619 0.00 0.00 0.00 1.82
662 782 1.029681 TGAGCGTGTGTGTCTGTACT 58.970 50.000 0.00 0.00 0.00 2.73
663 783 2.065993 ATGAGCGTGTGTGTCTGTAC 57.934 50.000 0.00 0.00 0.00 2.90
664 784 5.767816 ATATATGAGCGTGTGTGTCTGTA 57.232 39.130 0.00 0.00 0.00 2.74
666 786 4.613031 CGTATATATGAGCGTGTGTGTCTG 59.387 45.833 0.00 0.00 0.00 3.51
667 787 4.784329 CGTATATATGAGCGTGTGTGTCT 58.216 43.478 0.00 0.00 0.00 3.41
668 788 3.361053 GCGTATATATGAGCGTGTGTGTC 59.639 47.826 6.12 0.00 0.00 3.67
669 789 3.305964 GCGTATATATGAGCGTGTGTGT 58.694 45.455 6.12 0.00 0.00 3.72
670 790 2.338520 CGCGTATATATGAGCGTGTGTG 59.661 50.000 21.05 1.38 46.48 3.82
678 798 7.148902 GGATGAATGTATGCGCGTATATATGAG 60.149 40.741 22.86 3.76 0.00 2.90
680 800 6.128822 GGGATGAATGTATGCGCGTATATATG 60.129 42.308 22.86 0.00 0.00 1.78
681 801 5.926542 GGGATGAATGTATGCGCGTATATAT 59.073 40.000 19.79 18.88 0.00 0.86
683 803 4.119862 GGGATGAATGTATGCGCGTATAT 58.880 43.478 19.79 12.93 0.00 0.86
684 804 3.194755 AGGGATGAATGTATGCGCGTATA 59.805 43.478 13.13 13.13 0.00 1.47
685 805 2.028112 AGGGATGAATGTATGCGCGTAT 60.028 45.455 15.52 15.52 0.00 3.06
686 806 1.343142 AGGGATGAATGTATGCGCGTA 59.657 47.619 8.43 4.92 0.00 4.42
687 807 0.106708 AGGGATGAATGTATGCGCGT 59.893 50.000 8.43 7.55 0.00 6.01
688 808 2.078849 TAGGGATGAATGTATGCGCG 57.921 50.000 0.00 0.00 0.00 6.86
689 809 3.599343 TCATAGGGATGAATGTATGCGC 58.401 45.455 0.00 0.00 39.20 6.09
699 819 1.299850 CGCGCGTTCATAGGGATGA 60.300 57.895 24.19 0.00 40.45 2.92
700 820 2.943345 GCGCGCGTTCATAGGGATG 61.943 63.158 32.35 0.00 0.00 3.51
701 821 2.661866 GCGCGCGTTCATAGGGAT 60.662 61.111 32.35 0.00 0.00 3.85
702 822 4.136511 TGCGCGCGTTCATAGGGA 62.137 61.111 32.35 0.47 0.00 4.20
703 823 3.925238 GTGCGCGCGTTCATAGGG 61.925 66.667 32.35 0.00 0.00 3.53
704 824 3.185365 TGTGCGCGCGTTCATAGG 61.185 61.111 32.35 0.04 0.00 2.57
705 825 2.020016 GTGTGCGCGCGTTCATAG 59.980 61.111 32.35 0.92 0.00 2.23
706 826 2.735100 TGTGTGCGCGCGTTCATA 60.735 55.556 32.35 23.57 0.00 2.15
707 827 4.368808 GTGTGTGCGCGCGTTCAT 62.369 61.111 32.35 0.00 0.00 2.57
709 829 4.702826 GAGTGTGTGCGCGCGTTC 62.703 66.667 32.35 23.40 0.00 3.95
710 830 3.834447 TAGAGTGTGTGCGCGCGTT 62.834 57.895 32.35 7.59 0.00 4.84
711 831 3.626680 ATAGAGTGTGTGCGCGCGT 62.627 57.895 32.35 9.50 0.00 6.01
712 832 2.849966 GATAGAGTGTGTGCGCGCG 61.850 63.158 28.44 28.44 0.00 6.86
713 833 2.517450 GGATAGAGTGTGTGCGCGC 61.517 63.158 27.26 27.26 0.00 6.86
714 834 0.528466 ATGGATAGAGTGTGTGCGCG 60.528 55.000 0.00 0.00 0.00 6.86
715 835 2.509052 TATGGATAGAGTGTGTGCGC 57.491 50.000 0.00 0.00 0.00 6.09
716 836 4.233005 CTCATATGGATAGAGTGTGTGCG 58.767 47.826 2.13 0.00 0.00 5.34
717 837 3.993081 GCTCATATGGATAGAGTGTGTGC 59.007 47.826 2.13 0.00 0.00 4.57
718 838 4.987285 GTGCTCATATGGATAGAGTGTGTG 59.013 45.833 2.13 0.00 0.00 3.82
719 839 4.651045 TGTGCTCATATGGATAGAGTGTGT 59.349 41.667 2.13 0.00 0.00 3.72
720 840 5.205759 TGTGCTCATATGGATAGAGTGTG 57.794 43.478 2.13 0.00 0.00 3.82
721 841 6.430962 AATGTGCTCATATGGATAGAGTGT 57.569 37.500 2.13 0.00 33.49 3.55
722 842 5.575995 CGAATGTGCTCATATGGATAGAGTG 59.424 44.000 2.13 0.00 33.49 3.51
723 843 5.478332 TCGAATGTGCTCATATGGATAGAGT 59.522 40.000 2.13 0.00 33.49 3.24
724 844 5.958955 TCGAATGTGCTCATATGGATAGAG 58.041 41.667 2.13 0.00 33.49 2.43
725 845 5.982890 TCGAATGTGCTCATATGGATAGA 57.017 39.130 2.13 0.00 33.49 1.98
726 846 6.870439 TCTTTCGAATGTGCTCATATGGATAG 59.130 38.462 10.48 5.14 33.49 2.08
727 847 6.646653 GTCTTTCGAATGTGCTCATATGGATA 59.353 38.462 10.48 0.00 33.49 2.59
728 848 5.468072 GTCTTTCGAATGTGCTCATATGGAT 59.532 40.000 10.48 0.00 33.49 3.41
729 849 4.811024 GTCTTTCGAATGTGCTCATATGGA 59.189 41.667 10.48 0.00 33.49 3.41
730 850 4.813161 AGTCTTTCGAATGTGCTCATATGG 59.187 41.667 10.48 0.00 33.49 2.74
731 851 5.521372 TCAGTCTTTCGAATGTGCTCATATG 59.479 40.000 10.48 0.00 36.65 1.78
732 852 5.664457 TCAGTCTTTCGAATGTGCTCATAT 58.336 37.500 10.48 0.00 36.65 1.78
733 853 5.072040 TCAGTCTTTCGAATGTGCTCATA 57.928 39.130 10.48 0.00 36.65 2.15
734 854 3.930336 TCAGTCTTTCGAATGTGCTCAT 58.070 40.909 10.48 0.00 36.65 2.90
735 855 3.385193 TCAGTCTTTCGAATGTGCTCA 57.615 42.857 10.48 0.00 36.65 4.26
736 856 4.389992 TCAATCAGTCTTTCGAATGTGCTC 59.610 41.667 10.48 1.98 36.65 4.26
737 857 4.318332 TCAATCAGTCTTTCGAATGTGCT 58.682 39.130 10.48 7.69 36.65 4.40
738 858 4.668576 TCAATCAGTCTTTCGAATGTGC 57.331 40.909 10.48 5.81 36.65 4.57
739 859 9.611284 TTTAAATCAATCAGTCTTTCGAATGTG 57.389 29.630 10.48 3.64 36.65 3.21
740 860 9.612620 GTTTAAATCAATCAGTCTTTCGAATGT 57.387 29.630 10.48 0.00 36.65 2.71
741 861 9.611284 TGTTTAAATCAATCAGTCTTTCGAATG 57.389 29.630 0.00 0.78 36.62 2.67
742 862 9.612620 GTGTTTAAATCAATCAGTCTTTCGAAT 57.387 29.630 0.00 0.00 0.00 3.34
743 863 8.836413 AGTGTTTAAATCAATCAGTCTTTCGAA 58.164 29.630 0.00 0.00 0.00 3.71
744 864 8.282592 CAGTGTTTAAATCAATCAGTCTTTCGA 58.717 33.333 0.00 0.00 0.00 3.71
745 865 8.282592 TCAGTGTTTAAATCAATCAGTCTTTCG 58.717 33.333 0.00 0.00 0.00 3.46
747 867 9.903682 CATCAGTGTTTAAATCAATCAGTCTTT 57.096 29.630 0.00 0.00 0.00 2.52
748 868 8.517878 CCATCAGTGTTTAAATCAATCAGTCTT 58.482 33.333 0.00 0.00 0.00 3.01
749 869 7.121759 CCCATCAGTGTTTAAATCAATCAGTCT 59.878 37.037 0.00 0.00 0.00 3.24
750 870 7.253422 CCCATCAGTGTTTAAATCAATCAGTC 58.747 38.462 0.00 0.00 0.00 3.51
751 871 6.350445 GCCCATCAGTGTTTAAATCAATCAGT 60.350 38.462 0.00 0.00 0.00 3.41
752 872 6.038356 GCCCATCAGTGTTTAAATCAATCAG 58.962 40.000 0.00 0.00 0.00 2.90
753 873 5.716228 AGCCCATCAGTGTTTAAATCAATCA 59.284 36.000 0.00 0.00 0.00 2.57
754 874 6.038356 CAGCCCATCAGTGTTTAAATCAATC 58.962 40.000 0.00 0.00 0.00 2.67
755 875 5.105228 CCAGCCCATCAGTGTTTAAATCAAT 60.105 40.000 0.00 0.00 0.00 2.57
756 876 4.220382 CCAGCCCATCAGTGTTTAAATCAA 59.780 41.667 0.00 0.00 0.00 2.57
757 877 3.763360 CCAGCCCATCAGTGTTTAAATCA 59.237 43.478 0.00 0.00 0.00 2.57
758 878 3.131046 CCCAGCCCATCAGTGTTTAAATC 59.869 47.826 0.00 0.00 0.00 2.17
759 879 3.099141 CCCAGCCCATCAGTGTTTAAAT 58.901 45.455 0.00 0.00 0.00 1.40
760 880 2.524306 CCCAGCCCATCAGTGTTTAAA 58.476 47.619 0.00 0.00 0.00 1.52
761 881 1.272425 CCCCAGCCCATCAGTGTTTAA 60.272 52.381 0.00 0.00 0.00 1.52
762 882 0.331278 CCCCAGCCCATCAGTGTTTA 59.669 55.000 0.00 0.00 0.00 2.01
763 883 1.077265 CCCCAGCCCATCAGTGTTT 59.923 57.895 0.00 0.00 0.00 2.83
764 884 1.217057 ATCCCCAGCCCATCAGTGTT 61.217 55.000 0.00 0.00 0.00 3.32
765 885 0.327480 TATCCCCAGCCCATCAGTGT 60.327 55.000 0.00 0.00 0.00 3.55
766 886 1.004044 GATATCCCCAGCCCATCAGTG 59.996 57.143 0.00 0.00 0.00 3.66
767 887 1.366319 GATATCCCCAGCCCATCAGT 58.634 55.000 0.00 0.00 0.00 3.41
768 888 1.004044 GTGATATCCCCAGCCCATCAG 59.996 57.143 0.00 0.00 0.00 2.90
769 889 1.067295 GTGATATCCCCAGCCCATCA 58.933 55.000 0.00 0.00 0.00 3.07
770 890 1.004044 CTGTGATATCCCCAGCCCATC 59.996 57.143 0.00 0.00 0.00 3.51
771 891 1.070604 CTGTGATATCCCCAGCCCAT 58.929 55.000 0.00 0.00 0.00 4.00
772 892 0.327480 ACTGTGATATCCCCAGCCCA 60.327 55.000 15.72 0.00 0.00 5.36
773 893 0.398318 GACTGTGATATCCCCAGCCC 59.602 60.000 15.72 7.60 0.00 5.19
774 894 0.398318 GGACTGTGATATCCCCAGCC 59.602 60.000 15.72 14.01 0.00 4.85
780 900 5.367945 TGGTTAAAGGGACTGTGATATCC 57.632 43.478 0.00 0.00 40.86 2.59
781 901 5.998363 GGATGGTTAAAGGGACTGTGATATC 59.002 44.000 0.00 0.00 40.86 1.63
782 902 5.431731 TGGATGGTTAAAGGGACTGTGATAT 59.568 40.000 0.00 0.00 40.86 1.63
783 903 4.785914 TGGATGGTTAAAGGGACTGTGATA 59.214 41.667 0.00 0.00 40.86 2.15
784 904 3.591527 TGGATGGTTAAAGGGACTGTGAT 59.408 43.478 0.00 0.00 40.86 3.06
785 905 2.983192 TGGATGGTTAAAGGGACTGTGA 59.017 45.455 0.00 0.00 40.86 3.58
786 906 3.433306 TGGATGGTTAAAGGGACTGTG 57.567 47.619 0.00 0.00 40.86 3.66
787 907 4.044065 TGATTGGATGGTTAAAGGGACTGT 59.956 41.667 0.00 0.00 40.86 3.55
788 908 4.399303 GTGATTGGATGGTTAAAGGGACTG 59.601 45.833 0.00 0.00 40.86 3.51
790 910 4.340617 TGTGATTGGATGGTTAAAGGGAC 58.659 43.478 0.00 0.00 0.00 4.46
791 911 4.290985 TCTGTGATTGGATGGTTAAAGGGA 59.709 41.667 0.00 0.00 0.00 4.20
792 912 4.599041 TCTGTGATTGGATGGTTAAAGGG 58.401 43.478 0.00 0.00 0.00 3.95
793 913 6.377996 TCAATCTGTGATTGGATGGTTAAAGG 59.622 38.462 16.98 0.00 0.00 3.11
794 914 7.395190 TCAATCTGTGATTGGATGGTTAAAG 57.605 36.000 16.98 0.00 0.00 1.85
795 915 7.959658 ATCAATCTGTGATTGGATGGTTAAA 57.040 32.000 16.98 0.00 45.13 1.52
830 950 7.926555 TGGCAAAGACAATTACGGATTTAAAAA 59.073 29.630 0.00 0.00 0.00 1.94
831 951 7.434492 TGGCAAAGACAATTACGGATTTAAAA 58.566 30.769 0.00 0.00 0.00 1.52
832 952 6.982852 TGGCAAAGACAATTACGGATTTAAA 58.017 32.000 0.00 0.00 0.00 1.52
833 953 6.576662 TGGCAAAGACAATTACGGATTTAA 57.423 33.333 0.00 0.00 0.00 1.52
834 954 6.767524 ATGGCAAAGACAATTACGGATTTA 57.232 33.333 0.00 0.00 0.00 1.40
835 955 5.659440 ATGGCAAAGACAATTACGGATTT 57.341 34.783 0.00 0.00 0.00 2.17
836 956 5.659440 AATGGCAAAGACAATTACGGATT 57.341 34.783 0.00 0.00 0.00 3.01
837 957 5.410067 CAAATGGCAAAGACAATTACGGAT 58.590 37.500 0.00 0.00 0.00 4.18
838 958 4.804108 CAAATGGCAAAGACAATTACGGA 58.196 39.130 0.00 0.00 0.00 4.69
839 959 3.367630 GCAAATGGCAAAGACAATTACGG 59.632 43.478 0.00 0.00 43.97 4.02
840 960 4.566659 GCAAATGGCAAAGACAATTACG 57.433 40.909 0.00 0.00 43.97 3.18
853 973 1.676615 CCCAGTTTCATGGCAAATGGC 60.677 52.381 15.64 0.00 39.17 4.40
854 974 1.901159 TCCCAGTTTCATGGCAAATGG 59.099 47.619 14.62 14.62 39.17 3.16
855 975 3.681593 TTCCCAGTTTCATGGCAAATG 57.318 42.857 0.00 0.00 39.17 2.32
856 976 4.388485 GTTTTCCCAGTTTCATGGCAAAT 58.612 39.130 0.00 0.00 39.17 2.32
898 1018 2.555325 CCTGTATAAGATACGGCCACGA 59.445 50.000 2.24 0.00 44.60 4.35
1177 1297 2.203938 AGGGAGAACGGGCTGGAA 60.204 61.111 0.00 0.00 0.00 3.53
1178 1298 3.003173 CAGGGAGAACGGGCTGGA 61.003 66.667 0.00 0.00 0.00 3.86
1208 1328 2.846039 GCTCGACGAGGAGTATGAAA 57.154 50.000 25.31 0.00 36.41 2.69
1245 1365 2.623416 GCACAGCCCCTATTTGATTACC 59.377 50.000 0.00 0.00 0.00 2.85
1256 1377 4.982701 GCCAACAGCACAGCCCCT 62.983 66.667 0.00 0.00 42.97 4.79
1292 1421 2.757314 CCTTCATCCCCTTCAAAAGCTC 59.243 50.000 0.00 0.00 0.00 4.09
1353 1495 2.992114 AGCAGCTCCTCGTCGGTT 60.992 61.111 0.00 0.00 0.00 4.44
1444 1586 7.840342 AACAATCAGTTATCTCAGTGCTAAG 57.160 36.000 0.00 0.00 39.09 2.18
1579 1721 2.158914 ACCAAAAGAGGCAGCCAAAAAG 60.159 45.455 15.80 0.00 0.00 2.27
1668 1811 9.595823 ACTACTTTGTAATCGTGCACTATATTT 57.404 29.630 16.19 3.82 0.00 1.40
1671 1814 9.507280 GTTACTACTTTGTAATCGTGCACTATA 57.493 33.333 16.19 2.12 35.27 1.31
1672 1815 7.219535 CGTTACTACTTTGTAATCGTGCACTAT 59.780 37.037 16.19 6.67 35.27 2.12
1673 1816 6.524239 CGTTACTACTTTGTAATCGTGCACTA 59.476 38.462 16.19 3.92 35.27 2.74
1674 1817 5.344128 CGTTACTACTTTGTAATCGTGCACT 59.656 40.000 16.19 0.00 35.27 4.40
1675 1818 5.535616 CGTTACTACTTTGTAATCGTGCAC 58.464 41.667 6.82 6.82 35.27 4.57
1676 1819 4.090354 GCGTTACTACTTTGTAATCGTGCA 59.910 41.667 0.00 0.00 35.27 4.57
1677 1820 4.325472 AGCGTTACTACTTTGTAATCGTGC 59.675 41.667 0.00 0.00 35.27 5.34
1678 1821 7.378804 GTTAGCGTTACTACTTTGTAATCGTG 58.621 38.462 0.00 0.00 35.27 4.35
1679 1822 6.528072 GGTTAGCGTTACTACTTTGTAATCGT 59.472 38.462 0.00 0.00 35.27 3.73
1680 1823 6.290748 CGGTTAGCGTTACTACTTTGTAATCG 60.291 42.308 0.00 0.00 35.27 3.34
1681 1824 6.506984 GCGGTTAGCGTTACTACTTTGTAATC 60.507 42.308 5.55 0.00 33.97 1.75
1816 1959 6.556974 ATTCACAGATCTGATCCTCTTTGA 57.443 37.500 29.27 15.86 0.00 2.69
1952 2095 5.747565 TCAGTCAGCACAATAAAGAAAACG 58.252 37.500 0.00 0.00 0.00 3.60
2163 2306 5.534207 TCATCCAAAGCAACAACAGAAAT 57.466 34.783 0.00 0.00 0.00 2.17
2258 2401 4.021368 GCCTACTTGACTGACCTTAGAACA 60.021 45.833 0.00 0.00 0.00 3.18
2310 2454 9.670442 TCTACAGGGTAATTAATCTAATCAGGT 57.330 33.333 0.00 0.00 0.00 4.00
2361 2505 8.967552 TGTACAAGTACAAAACGTTCAAAAAT 57.032 26.923 10.42 0.00 42.49 1.82
2389 2533 0.543410 TCCAGCCCCTACGAAGAACA 60.543 55.000 0.00 0.00 0.00 3.18
2461 2605 5.584649 TGCACTACATAATTTACTGGAGCAC 59.415 40.000 0.00 0.00 0.00 4.40
2545 2689 5.147767 GGGCATCCTTATACTTCCCAAATT 58.852 41.667 0.00 0.00 32.68 1.82
2610 2764 4.119862 GGAAACAGATTGCAGCGTATCTA 58.880 43.478 8.98 0.00 30.20 1.98
2833 2991 4.991056 GGGTTTTCTTTTGGAGATTTCTGC 59.009 41.667 0.00 0.00 33.49 4.26
3039 3197 6.106877 ACCGATTCATAGATTGTTTTCACG 57.893 37.500 0.00 0.00 0.00 4.35
3275 3434 4.319766 GCGATGGCCACAACATAATTAGAG 60.320 45.833 8.16 0.00 0.00 2.43
3277 3436 3.565482 AGCGATGGCCACAACATAATTAG 59.435 43.478 8.16 0.00 41.24 1.73
3285 3444 2.813179 CGCTAGCGATGGCCACAAC 61.813 63.158 32.98 0.00 42.83 3.32
3292 3451 2.001812 ATCTATTGCGCTAGCGATGG 57.998 50.000 39.52 25.36 46.46 3.51
3473 3633 0.699399 TAATCGGCCACCCTGGAAAA 59.301 50.000 2.24 0.00 40.96 2.29
3525 3685 1.275666 TTACCTGCCTAGCTGCAAGA 58.724 50.000 1.02 0.00 41.51 3.02
3575 3735 0.750850 TTCGGGCATACTAGCTCACC 59.249 55.000 0.00 0.00 33.54 4.02
3592 3752 0.610687 AGCTGCCTCCTACACACTTC 59.389 55.000 0.00 0.00 0.00 3.01
3689 3849 3.209410 CCCTGCATACATTCAAGAGGAC 58.791 50.000 0.00 0.00 0.00 3.85
3844 4004 8.588472 CATGGTGTAAGATAGATATTGACAGGA 58.412 37.037 0.00 0.00 0.00 3.86
3845 4005 8.588472 TCATGGTGTAAGATAGATATTGACAGG 58.412 37.037 0.00 0.00 0.00 4.00
4006 4170 3.511540 CGATCCTAGCATAATCTGTCCCA 59.488 47.826 0.00 0.00 0.00 4.37
4116 4281 2.796383 CGAGTGAGCCGAATCTGTAAGG 60.796 54.545 0.00 0.00 0.00 2.69
4157 4322 4.564782 TCTGCTCTGGTCATTCTTCAAT 57.435 40.909 0.00 0.00 0.00 2.57
4158 4323 4.356405 TTCTGCTCTGGTCATTCTTCAA 57.644 40.909 0.00 0.00 0.00 2.69
4187 4352 0.400213 CACCCAGTTAGGCTTGTCCA 59.600 55.000 0.00 0.00 37.29 4.02
4205 4370 1.847328 TGGTAGACAAGATCGGAGCA 58.153 50.000 0.00 0.00 0.00 4.26
4206 4371 3.460857 AATGGTAGACAAGATCGGAGC 57.539 47.619 0.00 0.00 0.00 4.70
4210 4375 4.938080 AGCTGTAATGGTAGACAAGATCG 58.062 43.478 0.00 0.00 0.00 3.69
4253 4418 1.144057 GACCGGGAATGATCTGCGT 59.856 57.895 6.32 0.00 0.00 5.24
4274 4439 2.483889 GCAGAGCTTACCATGGAGTACC 60.484 54.545 21.47 2.34 0.00 3.34
4296 4461 5.163622 TGTTATCTATGCTCTGCAAAAAGCC 60.164 40.000 11.59 0.00 43.62 4.35
4411 4576 3.989817 GCTTCACAATCAAATTCCCACAC 59.010 43.478 0.00 0.00 0.00 3.82
4450 4615 3.214328 ACACAGTTTCAATCCTGACACC 58.786 45.455 0.00 0.00 33.46 4.16
4510 4678 0.625849 AGAGTAGGTGGCCCAAATGG 59.374 55.000 0.00 0.00 37.09 3.16
4583 4751 1.804151 TGCATGTTCTACAACTTCGGC 59.196 47.619 0.00 0.00 33.17 5.54
4743 4914 4.430137 AATGCGATGCAACCATATCATC 57.570 40.909 0.00 0.00 43.62 2.92
4814 4985 1.132588 GATACTGCTCCGATGAACGC 58.867 55.000 0.00 0.00 41.07 4.84
4860 5080 9.553064 CAGATATCTTATGTCCTAAGCAAAACT 57.447 33.333 1.33 0.00 37.36 2.66
4887 5107 3.181488 TGTTGATGGCGAGGCAAATATTG 60.181 43.478 2.86 0.00 0.00 1.90
4888 5108 3.023119 TGTTGATGGCGAGGCAAATATT 58.977 40.909 2.86 0.00 0.00 1.28
4900 5120 1.895131 ACCAGTGGAAATGTTGATGGC 59.105 47.619 18.40 0.00 0.00 4.40
4910 5130 2.392662 TGCCAAAATCACCAGTGGAAA 58.607 42.857 18.40 3.09 32.54 3.13
4911 5131 2.079170 TGCCAAAATCACCAGTGGAA 57.921 45.000 18.40 3.51 32.54 3.53
4913 5133 1.270252 GGTTGCCAAAATCACCAGTGG 60.270 52.381 7.91 7.91 0.00 4.00
4966 5186 2.094182 ACCTCGCGTTCTCACATGTAAT 60.094 45.455 5.77 0.00 0.00 1.89
5015 5235 2.366533 CTCATTCACAGCATGGCTCTT 58.633 47.619 0.00 0.00 43.62 2.85
5079 5303 1.943116 CTGGTGAGACCCGAGCTCTG 61.943 65.000 12.85 4.96 37.50 3.35


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

AutoCloner maintained by Alex Coulton.