Multiple sequence alignment - TraesCS1B01G113400

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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 TraesCS1B01G113400 chr1B 100.000 5783 0 0 1 5783 132932806 132938588 0.000000e+00 10680.0
1 TraesCS1B01G113400 chr1B 88.286 350 29 7 5434 5783 133032480 133032817 5.390000e-110 409.0
2 TraesCS1B01G113400 chr1B 94.239 243 13 1 5435 5676 133075666 133075908 2.550000e-98 370.0
3 TraesCS1B01G113400 chr1B 95.556 135 5 1 4091 4224 453762758 453762624 1.260000e-51 215.0
4 TraesCS1B01G113400 chr1B 90.984 122 10 1 141 261 577977062 577977183 4.640000e-36 163.0
5 TraesCS1B01G113400 chr1A 95.244 3280 114 18 831 4095 99014169 99017421 0.000000e+00 5155.0
6 TraesCS1B01G113400 chr1A 91.279 1399 68 19 4412 5783 99017576 99018947 0.000000e+00 1858.0
7 TraesCS1B01G113400 chr1A 88.401 319 27 7 5361 5676 99071033 99071344 5.470000e-100 375.0
8 TraesCS1B01G113400 chr1A 85.637 369 37 11 5419 5783 99048751 99049107 1.970000e-99 374.0
9 TraesCS1B01G113400 chr1D 95.788 2944 86 16 831 3769 80443755 80446665 0.000000e+00 4715.0
10 TraesCS1B01G113400 chr1D 93.014 1546 71 20 4244 5783 80447129 80448643 0.000000e+00 2222.0
11 TraesCS1B01G113400 chr1D 96.721 427 11 2 3669 4095 80446667 80447090 0.000000e+00 708.0
12 TraesCS1B01G113400 chr1D 89.375 320 21 9 5359 5676 80540915 80541223 1.950000e-104 390.0
13 TraesCS1B01G113400 chr1D 90.980 255 19 3 5419 5672 80537065 80537316 2.000000e-89 340.0
14 TraesCS1B01G113400 chr1D 96.875 128 4 0 4094 4221 127143402 127143275 1.260000e-51 215.0
15 TraesCS1B01G113400 chr1D 85.616 146 19 1 143 288 453639411 453639268 1.000000e-32 152.0
16 TraesCS1B01G113400 chr1D 90.000 70 7 0 5714 5783 80537383 80537452 2.220000e-14 91.6
17 TraesCS1B01G113400 chr5A 88.966 725 46 17 1 703 437401492 437400780 0.000000e+00 865.0
18 TraesCS1B01G113400 chr5A 95.489 133 6 0 4094 4226 521007341 521007473 4.540000e-51 213.0
19 TraesCS1B01G113400 chr2B 89.365 677 42 12 1 649 682176829 682176155 0.000000e+00 824.0
20 TraesCS1B01G113400 chr2B 88.341 223 21 4 599 818 727670322 727670542 4.440000e-66 263.0
21 TraesCS1B01G113400 chr2B 88.608 158 15 2 141 298 503435360 503435514 7.650000e-44 189.0
22 TraesCS1B01G113400 chr2B 94.186 86 5 0 141 226 655609031 655609116 1.310000e-26 132.0
23 TraesCS1B01G113400 chr5B 91.099 382 19 5 2542 2922 692360566 692360933 2.410000e-138 503.0
24 TraesCS1B01G113400 chr5B 90.541 222 17 4 599 818 579151216 579150997 2.040000e-74 291.0
25 TraesCS1B01G113400 chr5B 88.158 228 19 7 597 818 704258002 704257777 1.240000e-66 265.0
26 TraesCS1B01G113400 chr5B 91.736 121 10 0 141 261 679373097 679372977 9.970000e-38 169.0
27 TraesCS1B01G113400 chr5B 90.909 121 11 0 141 261 381064643 381064523 4.640000e-36 163.0
28 TraesCS1B01G113400 chrUn 88.947 380 24 9 2544 2922 47692020 47691658 2.460000e-123 453.0
29 TraesCS1B01G113400 chr7B 95.146 206 10 0 5445 5650 95337271 95337476 5.590000e-85 326.0
30 TraesCS1B01G113400 chr7B 95.556 135 6 0 4094 4228 84643483 84643349 3.510000e-52 217.0
31 TraesCS1B01G113400 chr7B 83.193 119 16 4 536 652 450683547 450683663 7.930000e-19 106.0
32 TraesCS1B01G113400 chr5D 90.179 224 16 5 599 818 503528781 503529002 2.640000e-73 287.0
33 TraesCS1B01G113400 chr3A 88.393 224 23 3 599 820 13488986 13489208 3.440000e-67 267.0
34 TraesCS1B01G113400 chr4A 88.288 222 23 3 599 818 30766713 30766493 4.440000e-66 263.0
35 TraesCS1B01G113400 chr4A 87.892 223 23 3 599 818 625127780 625127559 5.750000e-65 259.0
36 TraesCS1B01G113400 chr6B 88.000 225 22 4 597 818 53630824 53630602 1.600000e-65 261.0
37 TraesCS1B01G113400 chr4B 88.000 225 19 7 599 818 603150945 603150724 5.750000e-65 259.0
38 TraesCS1B01G113400 chr6D 96.875 128 4 0 4094 4221 126108388 126108261 1.260000e-51 215.0
39 TraesCS1B01G113400 chr6D 93.056 144 8 2 4093 4235 52696763 52696621 5.870000e-50 209.0
40 TraesCS1B01G113400 chr4D 96.875 128 4 0 4094 4221 391290423 391290296 1.260000e-51 215.0
41 TraesCS1B01G113400 chr4D 93.706 143 7 2 4079 4220 614512 614653 4.540000e-51 213.0
42 TraesCS1B01G113400 chr7A 95.455 132 6 0 4089 4220 615329612 615329743 1.630000e-50 211.0
43 TraesCS1B01G113400 chr2D 83.193 238 27 10 141 367 93263415 93263180 7.600000e-49 206.0
44 TraesCS1B01G113400 chr2A 77.027 370 69 9 1074 1432 775689423 775689059 1.270000e-46 198.0
45 TraesCS1B01G113400 chr7D 78.277 267 46 9 3143 3400 13676383 13676120 1.670000e-35 161.0


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 TraesCS1B01G113400 chr1B 132932806 132938588 5782 False 10680.000000 10680 100.000000 1 5783 1 chr1B.!!$F1 5782
1 TraesCS1B01G113400 chr1A 99014169 99018947 4778 False 3506.500000 5155 93.261500 831 5783 2 chr1A.!!$F3 4952
2 TraesCS1B01G113400 chr1D 80443755 80448643 4888 False 2548.333333 4715 95.174333 831 5783 3 chr1D.!!$F1 4952
3 TraesCS1B01G113400 chr1D 80537065 80541223 4158 False 273.866667 390 90.118333 5359 5783 3 chr1D.!!$F2 424
4 TraesCS1B01G113400 chr5A 437400780 437401492 712 True 865.000000 865 88.966000 1 703 1 chr5A.!!$R1 702
5 TraesCS1B01G113400 chr2B 682176155 682176829 674 True 824.000000 824 89.365000 1 649 1 chr2B.!!$R1 648

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
721 767 0.106894 GGTCATTCCAGGGGTCGATC 59.893 60.000 0.00 0.0 35.97 3.69 F
742 788 0.107214 GACGCCCCAGATCCAATCAA 60.107 55.000 0.00 0.0 0.00 2.57 F
746 792 0.259647 CCCCAGATCCAATCAAGCCA 59.740 55.000 0.00 0.0 0.00 4.75 F
781 827 0.393537 AGGAAGCCCAAATCGCTGAG 60.394 55.000 0.00 0.0 36.47 3.35 F
1224 1272 0.818296 CCTTCCTCGAGGTCAACGAT 59.182 55.000 30.17 0.0 39.02 3.73 F
2394 2452 1.004745 TGATTCCCCTCTGCTTTGGTC 59.995 52.381 0.00 0.0 0.00 4.02 F
2477 2535 3.104766 CACCAGCTTGCCTATGCG 58.895 61.111 0.00 0.0 41.78 4.73 F
3993 4155 3.256879 TCAAAGTCGAGTGAAGATCTGCT 59.743 43.478 1.43 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2257 1.474498 CCAAGTATAGAACCCCCACGC 60.474 57.143 0.00 0.0 0.00 5.34 R
2693 2751 2.543641 GCTTTTGCTGCTTTCAGTTGT 58.456 42.857 0.00 0.0 42.29 3.32 R
2837 2895 5.471456 ACGCTTGAAGAAGTCATTCTCAAAT 59.529 36.000 0.00 0.0 45.25 2.32 R
2876 2934 1.064017 ACCTGAAGTTGGCCTGAAACA 60.064 47.619 3.32 0.0 0.00 2.83 R
3121 3179 1.271102 GCACGGTTCATTAAGGCCAAA 59.729 47.619 5.01 0.0 0.00 3.28 R
4095 4257 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.0 0.00 4.30 R
4096 4258 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.0 0.00 4.20 R
5128 5314 0.591659 GAAAGAAACTGGGGCACGAC 59.408 55.000 0.00 0.0 0.00 4.34 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
31 33 4.918810 AAACGAAAAGCCAGAACTGAAT 57.081 36.364 3.19 0.00 0.00 2.57
148 150 3.567797 GCGCTCATGGGAAGACGC 61.568 66.667 0.00 0.00 39.49 5.19
234 236 4.779966 TCGTCCTCCTCGCGCTCT 62.780 66.667 5.56 0.00 0.00 4.09
265 267 1.353091 GTGGTTCTCCTTCTCACCCT 58.647 55.000 0.00 0.00 34.23 4.34
269 271 2.292323 GGTTCTCCTTCTCACCCTCCTA 60.292 54.545 0.00 0.00 0.00 2.94
348 375 1.530323 GGCGGCTCTAAAGTTTGGAA 58.470 50.000 0.00 0.00 0.00 3.53
384 420 2.586357 GGTCATCCTTCTCGCGCC 60.586 66.667 0.00 0.00 0.00 6.53
530 575 4.882396 GAAGAGGAGAGGGCGCGC 62.882 72.222 25.94 25.94 0.00 6.86
616 661 2.029470 TGTGAAATGACGAAAATGCCCC 60.029 45.455 0.00 0.00 0.00 5.80
619 664 0.322997 AATGACGAAAATGCCCCCGA 60.323 50.000 0.00 0.00 0.00 5.14
637 682 1.100510 GACGGGGCAAGGAAATTACC 58.899 55.000 0.00 0.00 0.00 2.85
657 702 4.973055 CGGTGGCACGAAACGGGA 62.973 66.667 12.17 0.00 35.47 5.14
658 703 3.047877 GGTGGCACGAAACGGGAG 61.048 66.667 12.17 0.00 28.17 4.30
660 705 1.005867 GTGGCACGAAACGGGAGTA 60.006 57.895 0.00 0.00 46.69 2.59
671 716 5.809051 ACGAAACGGGAGTAACTATTCATTC 59.191 40.000 0.00 0.00 46.69 2.67
672 717 5.233689 CGAAACGGGAGTAACTATTCATTCC 59.766 44.000 0.00 0.00 46.69 3.01
679 724 6.183360 GGGAGTAACTATTCATTCCAGCAGTA 60.183 42.308 0.00 0.00 0.00 2.74
682 727 9.331282 GAGTAACTATTCATTCCAGCAGTAATT 57.669 33.333 0.00 0.00 0.00 1.40
683 728 9.686683 AGTAACTATTCATTCCAGCAGTAATTT 57.313 29.630 0.00 0.00 0.00 1.82
704 750 1.176527 TTTTATCCGACGGACGAGGT 58.823 50.000 21.02 5.32 45.77 3.85
706 752 0.392863 TTATCCGACGGACGAGGTCA 60.393 55.000 21.02 0.00 45.77 4.02
707 753 0.179037 TATCCGACGGACGAGGTCAT 60.179 55.000 21.02 2.82 45.77 3.06
708 754 1.035932 ATCCGACGGACGAGGTCATT 61.036 55.000 21.02 0.00 45.77 2.57
709 755 1.226603 CCGACGGACGAGGTCATTC 60.227 63.158 8.64 0.00 45.77 2.67
710 756 1.226603 CGACGGACGAGGTCATTCC 60.227 63.158 0.00 0.00 45.77 3.01
711 757 1.888018 GACGGACGAGGTCATTCCA 59.112 57.895 0.00 0.00 39.02 3.53
713 759 1.141881 CGGACGAGGTCATTCCAGG 59.858 63.158 0.00 0.00 39.02 4.45
714 760 1.522569 GGACGAGGTCATTCCAGGG 59.477 63.158 0.00 0.00 39.02 4.45
716 762 1.229529 ACGAGGTCATTCCAGGGGT 60.230 57.895 0.00 0.00 39.02 4.95
717 763 1.265454 ACGAGGTCATTCCAGGGGTC 61.265 60.000 0.00 0.00 39.02 4.46
719 765 0.976073 GAGGTCATTCCAGGGGTCGA 60.976 60.000 0.00 0.00 39.02 4.20
720 766 0.326618 AGGTCATTCCAGGGGTCGAT 60.327 55.000 0.00 0.00 39.02 3.59
721 767 0.106894 GGTCATTCCAGGGGTCGATC 59.893 60.000 0.00 0.00 35.97 3.69
722 768 0.106894 GTCATTCCAGGGGTCGATCC 59.893 60.000 6.02 6.02 0.00 3.36
723 769 1.069765 CATTCCAGGGGTCGATCCG 59.930 63.158 9.04 0.00 37.00 4.18
724 770 1.075525 ATTCCAGGGGTCGATCCGA 60.076 57.895 9.04 0.00 37.00 4.55
732 778 4.570663 GTCGATCCGACGCCCCAG 62.571 72.222 3.69 0.00 46.56 4.45
733 779 4.807631 TCGATCCGACGCCCCAGA 62.808 66.667 0.00 0.00 0.00 3.86
734 780 3.606662 CGATCCGACGCCCCAGAT 61.607 66.667 0.00 0.00 0.00 2.90
736 782 3.227792 GATCCGACGCCCCAGATCC 62.228 68.421 0.00 0.00 30.97 3.36
737 783 4.770362 TCCGACGCCCCAGATCCA 62.770 66.667 0.00 0.00 0.00 3.41
739 785 2.505982 CGACGCCCCAGATCCAAT 59.494 61.111 0.00 0.00 0.00 3.16
741 787 1.526887 GACGCCCCAGATCCAATCA 59.473 57.895 0.00 0.00 0.00 2.57
742 788 0.107214 GACGCCCCAGATCCAATCAA 60.107 55.000 0.00 0.00 0.00 2.57
744 790 1.450531 CGCCCCAGATCCAATCAAGC 61.451 60.000 0.00 0.00 0.00 4.01
745 791 1.111715 GCCCCAGATCCAATCAAGCC 61.112 60.000 0.00 0.00 0.00 4.35
746 792 0.259647 CCCCAGATCCAATCAAGCCA 59.740 55.000 0.00 0.00 0.00 4.75
747 793 1.396653 CCCAGATCCAATCAAGCCAC 58.603 55.000 0.00 0.00 0.00 5.01
748 794 1.396653 CCAGATCCAATCAAGCCACC 58.603 55.000 0.00 0.00 0.00 4.61
749 795 1.396653 CAGATCCAATCAAGCCACCC 58.603 55.000 0.00 0.00 0.00 4.61
750 796 1.002069 AGATCCAATCAAGCCACCCA 58.998 50.000 0.00 0.00 0.00 4.51
752 798 2.023695 AGATCCAATCAAGCCACCCAAT 60.024 45.455 0.00 0.00 0.00 3.16
753 799 1.851304 TCCAATCAAGCCACCCAATC 58.149 50.000 0.00 0.00 0.00 2.67
754 800 0.826062 CCAATCAAGCCACCCAATCC 59.174 55.000 0.00 0.00 0.00 3.01
757 803 1.560505 ATCAAGCCACCCAATCCAAC 58.439 50.000 0.00 0.00 0.00 3.77
759 805 1.606313 AAGCCACCCAATCCAACGG 60.606 57.895 0.00 0.00 0.00 4.44
760 806 3.758931 GCCACCCAATCCAACGGC 61.759 66.667 0.00 0.00 0.00 5.68
761 807 3.068064 CCACCCAATCCAACGGCC 61.068 66.667 0.00 0.00 0.00 6.13
764 810 2.755469 CCCAATCCAACGGCCAGG 60.755 66.667 2.24 0.60 0.00 4.45
766 812 1.304052 CCAATCCAACGGCCAGGAA 60.304 57.895 12.10 0.00 37.48 3.36
767 813 1.315257 CCAATCCAACGGCCAGGAAG 61.315 60.000 12.10 8.24 37.48 3.46
768 814 1.678970 AATCCAACGGCCAGGAAGC 60.679 57.895 12.10 0.00 37.48 3.86
777 823 3.068729 GCCAGGAAGCCCAAATCGC 62.069 63.158 0.00 0.00 33.88 4.58
781 827 0.393537 AGGAAGCCCAAATCGCTGAG 60.394 55.000 0.00 0.00 36.47 3.35
782 828 1.379642 GGAAGCCCAAATCGCTGAGG 61.380 60.000 0.00 0.00 36.47 3.86
784 830 0.393537 AAGCCCAAATCGCTGAGGAG 60.394 55.000 0.00 0.00 36.47 3.69
785 831 2.476320 GCCCAAATCGCTGAGGAGC 61.476 63.158 0.00 0.00 42.37 4.70
786 832 1.821332 CCCAAATCGCTGAGGAGCC 60.821 63.158 0.00 0.00 42.91 4.70
787 833 2.176273 CCAAATCGCTGAGGAGCCG 61.176 63.158 0.00 0.00 42.91 5.52
789 835 3.391665 AAATCGCTGAGGAGCCGGG 62.392 63.158 2.18 0.00 42.91 5.73
790 836 4.841617 ATCGCTGAGGAGCCGGGA 62.842 66.667 2.18 0.00 42.91 5.14
815 861 6.162777 GGATCCTCCTGATTCTTATTTCTCG 58.837 44.000 3.84 0.00 32.41 4.04
816 862 6.015010 GGATCCTCCTGATTCTTATTTCTCGA 60.015 42.308 3.84 0.00 32.41 4.04
817 863 6.985653 TCCTCCTGATTCTTATTTCTCGAT 57.014 37.500 0.00 0.00 0.00 3.59
818 864 7.366847 TCCTCCTGATTCTTATTTCTCGATT 57.633 36.000 0.00 0.00 0.00 3.34
820 866 7.288852 TCCTCCTGATTCTTATTTCTCGATTCT 59.711 37.037 0.00 0.00 0.00 2.40
821 867 7.930865 CCTCCTGATTCTTATTTCTCGATTCTT 59.069 37.037 0.00 0.00 0.00 2.52
822 868 9.973450 CTCCTGATTCTTATTTCTCGATTCTTA 57.027 33.333 0.00 0.00 0.00 2.10
888 936 1.080230 CCCTCATCGCAGCCTATCG 60.080 63.158 0.00 0.00 0.00 2.92
901 949 3.151710 TATCGACCGGGCCACCAG 61.152 66.667 6.32 0.00 36.13 4.00
911 959 4.603535 GCCACCAGCCCACCAAGT 62.604 66.667 0.00 0.00 34.35 3.16
1062 1110 3.934962 GCCGCCTCCATCTCCTCC 61.935 72.222 0.00 0.00 0.00 4.30
1224 1272 0.818296 CCTTCCTCGAGGTCAACGAT 59.182 55.000 30.17 0.00 39.02 3.73
1470 1518 2.338984 GACTTCGTCCACCTGCGT 59.661 61.111 0.00 0.00 0.00 5.24
1594 1642 3.547054 AACCAGAACTTTCCGTGTACA 57.453 42.857 0.00 0.00 0.00 2.90
1636 1684 4.757149 GTGTTTGCTCATTTCTACTCACCT 59.243 41.667 0.00 0.00 0.00 4.00
1695 1743 5.134202 AGTGTTTTGGCCTTTGTTATAGC 57.866 39.130 3.32 0.00 0.00 2.97
1729 1777 4.876107 TGATTCTTAGAATCCGCAGTTTCC 59.124 41.667 26.29 4.68 0.00 3.13
1784 1834 2.837233 AGGCTTACCCCTGGAATTACCA 60.837 50.000 0.00 0.00 41.31 3.25
1816 1866 8.691661 AGGCTGTCTTTTTGTATCTTCTTTTA 57.308 30.769 0.00 0.00 0.00 1.52
1889 1939 9.482175 AATGAGTAGTTTCAGTCTTACCTCTAT 57.518 33.333 0.00 0.00 0.00 1.98
2119 2171 2.352127 GCTGGATTTTCTTGGCTGTGAC 60.352 50.000 0.00 0.00 0.00 3.67
2200 2257 6.347969 CCACATATGCAATCGGACTATTTCAG 60.348 42.308 1.58 0.00 0.00 3.02
2219 2276 1.485066 AGCGTGGGGGTTCTATACTTG 59.515 52.381 0.00 0.00 0.00 3.16
2226 2283 3.446161 GGGGGTTCTATACTTGGTTTTGC 59.554 47.826 0.00 0.00 0.00 3.68
2344 2402 7.750229 TCTGCAGTAATGAGAAAGAAACATT 57.250 32.000 14.67 0.00 37.82 2.71
2394 2452 1.004745 TGATTCCCCTCTGCTTTGGTC 59.995 52.381 0.00 0.00 0.00 4.02
2477 2535 3.104766 CACCAGCTTGCCTATGCG 58.895 61.111 0.00 0.00 41.78 4.73
2837 2895 4.095211 TCAAGGATGATGGGAAAATTGCA 58.905 39.130 0.00 0.00 0.00 4.08
3251 3309 4.787551 TGGTTAAACATGTGGACAAGACT 58.212 39.130 0.00 0.00 0.00 3.24
3295 3353 4.141892 TGTTTCCTCTACTCCGTTTGAACA 60.142 41.667 0.00 0.00 0.00 3.18
3793 3955 8.786898 TGATTCATGCCTTAAATCTATAGTTGC 58.213 33.333 0.00 0.00 31.99 4.17
3815 3977 5.407387 TGCGATCACTTACTTTTTGAGTACC 59.593 40.000 0.00 0.00 40.51 3.34
3908 4070 4.708726 AGCATCACCTAAATTTGACTGC 57.291 40.909 0.00 3.24 31.71 4.40
3909 4071 4.081406 AGCATCACCTAAATTTGACTGCA 58.919 39.130 0.00 0.00 32.90 4.41
3993 4155 3.256879 TCAAAGTCGAGTGAAGATCTGCT 59.743 43.478 1.43 0.00 0.00 4.24
4054 4216 3.454812 ACCCTGTTGTTAGAGAGTTGTGT 59.545 43.478 0.00 0.00 0.00 3.72
4102 4264 4.143986 GCTTATGGCATATACTCCCTCC 57.856 50.000 8.24 0.00 41.35 4.30
4103 4265 3.430929 GCTTATGGCATATACTCCCTCCG 60.431 52.174 8.24 0.00 41.35 4.63
4104 4266 2.327325 ATGGCATATACTCCCTCCGT 57.673 50.000 0.00 0.00 0.00 4.69
4105 4267 1.629043 TGGCATATACTCCCTCCGTC 58.371 55.000 0.00 0.00 0.00 4.79
4106 4268 0.896226 GGCATATACTCCCTCCGTCC 59.104 60.000 0.00 0.00 0.00 4.79
4107 4269 0.896226 GCATATACTCCCTCCGTCCC 59.104 60.000 0.00 0.00 0.00 4.46
4108 4270 1.826042 GCATATACTCCCTCCGTCCCA 60.826 57.143 0.00 0.00 0.00 4.37
4109 4271 2.605257 CATATACTCCCTCCGTCCCAA 58.395 52.381 0.00 0.00 0.00 4.12
4110 4272 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
4111 4273 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4112 4274 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4113 4275 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4114 4276 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4115 4277 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4116 4278 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4117 4279 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
4118 4280 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
4119 4281 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
4120 4282 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
4121 4283 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
4122 4284 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
4123 4285 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
4124 4286 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
4125 4287 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
4126 4288 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
4127 4289 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4128 4290 8.726988 CGTCCCAAAATTCTTGTCTTAGATTTA 58.273 33.333 0.00 0.00 0.00 1.40
4153 4315 8.865420 ATCTAGATACGGATGTATGTAACACT 57.135 34.615 2.53 0.00 41.37 3.55
4154 4316 9.955102 ATCTAGATACGGATGTATGTAACACTA 57.045 33.333 2.53 0.00 41.37 2.74
4155 4317 9.783081 TCTAGATACGGATGTATGTAACACTAA 57.217 33.333 0.00 0.00 41.37 2.24
4195 4357 9.095065 ACATCCGTATGTAAACAAATCTAAGAC 57.905 33.333 0.00 0.00 44.66 3.01
4196 4358 9.093970 CATCCGTATGTAAACAAATCTAAGACA 57.906 33.333 0.00 0.00 0.00 3.41
4197 4359 9.661563 ATCCGTATGTAAACAAATCTAAGACAA 57.338 29.630 0.00 0.00 0.00 3.18
4198 4360 9.146984 TCCGTATGTAAACAAATCTAAGACAAG 57.853 33.333 0.00 0.00 0.00 3.16
4199 4361 9.146984 CCGTATGTAAACAAATCTAAGACAAGA 57.853 33.333 0.00 0.00 0.00 3.02
4207 4369 9.546428 AAACAAATCTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.04 4.12
4208 4370 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4209 4371 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
4210 4372 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
4211 4373 5.860611 TCTAAGACAAGAATTTTGGGACGA 58.139 37.500 0.00 0.00 0.00 4.20
4212 4374 6.292923 TCTAAGACAAGAATTTTGGGACGAA 58.707 36.000 0.00 0.00 0.00 3.85
4213 4375 5.438761 AAGACAAGAATTTTGGGACGAAG 57.561 39.130 0.00 0.00 0.00 3.79
4214 4376 3.821033 AGACAAGAATTTTGGGACGAAGG 59.179 43.478 0.00 0.00 0.00 3.46
4215 4377 2.890945 ACAAGAATTTTGGGACGAAGGG 59.109 45.455 0.00 0.00 0.00 3.95
4216 4378 3.153919 CAAGAATTTTGGGACGAAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
4217 4379 3.073274 AGAATTTTGGGACGAAGGGAG 57.927 47.619 0.00 0.00 0.00 4.30
4218 4380 2.375509 AGAATTTTGGGACGAAGGGAGT 59.624 45.455 0.00 0.00 0.00 3.85
4219 4381 3.585732 AGAATTTTGGGACGAAGGGAGTA 59.414 43.478 0.00 0.00 0.00 2.59
4325 4502 0.818938 TGCATCATCCCAACATGCAC 59.181 50.000 1.71 0.00 46.22 4.57
4345 4522 6.245408 TGCACTATGGTTTTGGTTCTCTAAT 58.755 36.000 0.00 0.00 0.00 1.73
4346 4523 7.398829 TGCACTATGGTTTTGGTTCTCTAATA 58.601 34.615 0.00 0.00 0.00 0.98
4347 4524 7.885922 TGCACTATGGTTTTGGTTCTCTAATAA 59.114 33.333 0.00 0.00 0.00 1.40
4348 4525 8.736244 GCACTATGGTTTTGGTTCTCTAATAAA 58.264 33.333 0.00 0.00 0.00 1.40
4366 4543 9.587772 TCTAATAAAACACTAGCAATCTGAGAC 57.412 33.333 0.00 0.00 0.00 3.36
4367 4544 9.593134 CTAATAAAACACTAGCAATCTGAGACT 57.407 33.333 0.00 0.00 0.00 3.24
4574 4752 6.882610 TGTTTCTTTATGACATGTGAGCTT 57.117 33.333 1.15 0.00 0.00 3.74
4594 4772 4.435651 GCTTACTGCGTAACATCTTGTTCC 60.436 45.833 0.00 0.00 40.22 3.62
4632 4810 1.338655 GATCTTCCTCTGGAGCCGTAC 59.661 57.143 0.00 0.00 31.21 3.67
4719 4897 0.657840 GGATGATCCTTTTCGCCACG 59.342 55.000 3.71 0.00 32.53 4.94
4746 4924 5.396548 CCTGGAGAACATCAGAGATGTCATT 60.397 44.000 12.53 0.00 33.11 2.57
4918 5096 8.978564 ATATCATTTGATATGTCTCGTGTCTC 57.021 34.615 11.36 0.00 43.85 3.36
4927 5105 1.068748 GTCTCGTGTCTCGGCTTGTTA 60.069 52.381 0.00 0.00 40.32 2.41
5001 5179 9.717942 AGTATTATTGGTCATTAGCATCTTCTC 57.282 33.333 0.00 0.00 32.06 2.87
5050 5229 4.457603 TGTTTGTATCTTATGCCGCAAACT 59.542 37.500 15.66 0.00 43.24 2.66
5079 5258 6.715347 ACTGTTTTGAAGATGCCTTAGTTT 57.285 33.333 0.00 0.00 31.62 2.66
5126 5312 0.679640 TTCGCCCACAATAGCCCAAG 60.680 55.000 0.00 0.00 0.00 3.61
5128 5314 1.758122 GCCCACAATAGCCCAAGGG 60.758 63.158 0.00 0.00 39.33 3.95
5131 5317 0.748005 CCACAATAGCCCAAGGGTCG 60.748 60.000 7.05 0.00 37.65 4.79
5279 5487 4.386711 TCATAGTACGACGATGTGGATCT 58.613 43.478 0.00 0.00 33.69 2.75
5326 5534 4.280494 AAGCAGTGACGCGTCGGT 62.280 61.111 31.88 21.14 36.85 4.69
5358 5566 3.454371 ACCAACTCCGCTATGTGTATC 57.546 47.619 0.00 0.00 0.00 2.24
5372 5580 1.398041 GTGTATCAGCGCAATCAAGCA 59.602 47.619 11.47 0.00 35.48 3.91
5409 5617 0.173481 CGTCCATCTCCAAGAAGCGA 59.827 55.000 0.00 0.00 0.00 4.93
5678 5887 4.843516 ACTTCCATCAACCTCTCTTCTCTT 59.156 41.667 0.00 0.00 0.00 2.85
5679 5888 5.046663 ACTTCCATCAACCTCTCTTCTCTTC 60.047 44.000 0.00 0.00 0.00 2.87
5680 5889 4.682563 TCCATCAACCTCTCTTCTCTTCT 58.317 43.478 0.00 0.00 0.00 2.85
5684 5893 3.837146 TCAACCTCTCTTCTCTTCTGCAT 59.163 43.478 0.00 0.00 0.00 3.96
5685 5894 3.891422 ACCTCTCTTCTCTTCTGCATG 57.109 47.619 0.00 0.00 0.00 4.06
5686 5895 2.500910 ACCTCTCTTCTCTTCTGCATGG 59.499 50.000 0.00 0.00 0.00 3.66
5687 5896 2.765135 CCTCTCTTCTCTTCTGCATGGA 59.235 50.000 0.00 0.00 0.00 3.41
5688 5897 3.197333 CCTCTCTTCTCTTCTGCATGGAA 59.803 47.826 0.00 0.00 0.00 3.53
5689 5898 4.323333 CCTCTCTTCTCTTCTGCATGGAAA 60.323 45.833 0.00 0.00 0.00 3.13
5690 5899 5.233083 TCTCTTCTCTTCTGCATGGAAAA 57.767 39.130 0.00 0.00 0.00 2.29
5691 5900 4.999950 TCTCTTCTCTTCTGCATGGAAAAC 59.000 41.667 0.00 0.00 0.00 2.43
5692 5901 4.978099 TCTTCTCTTCTGCATGGAAAACT 58.022 39.130 0.00 0.00 0.00 2.66
5693 5902 5.380043 TCTTCTCTTCTGCATGGAAAACTT 58.620 37.500 0.00 0.00 0.00 2.66
5694 5903 5.240183 TCTTCTCTTCTGCATGGAAAACTTG 59.760 40.000 0.00 0.00 0.00 3.16
5695 5904 4.464008 TCTCTTCTGCATGGAAAACTTGT 58.536 39.130 0.00 0.00 0.00 3.16
5696 5905 5.620206 TCTCTTCTGCATGGAAAACTTGTA 58.380 37.500 0.00 0.00 0.00 2.41
5697 5906 6.240894 TCTCTTCTGCATGGAAAACTTGTAT 58.759 36.000 0.00 0.00 0.00 2.29
5698 5907 7.394016 TCTCTTCTGCATGGAAAACTTGTATA 58.606 34.615 0.00 0.00 0.00 1.47
5699 5908 7.334421 TCTCTTCTGCATGGAAAACTTGTATAC 59.666 37.037 0.00 0.00 0.00 1.47
5700 5909 5.794687 TCTGCATGGAAAACTTGTATACG 57.205 39.130 0.00 0.00 0.00 3.06
5701 5910 5.242434 TCTGCATGGAAAACTTGTATACGT 58.758 37.500 0.00 0.00 0.00 3.57
5702 5911 6.399743 TCTGCATGGAAAACTTGTATACGTA 58.600 36.000 0.00 0.00 0.00 3.57
5703 5912 6.311935 TCTGCATGGAAAACTTGTATACGTAC 59.688 38.462 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 15 3.748048 TCTCATTCAGTTCTGGCTTTTCG 59.252 43.478 0.00 0.00 0.00 3.46
31 33 0.114364 TAGAGGTGCTGGTGGTCTCA 59.886 55.000 0.00 0.00 0.00 3.27
148 150 4.148825 CCGCTTCCTCCACCTCCG 62.149 72.222 0.00 0.00 0.00 4.63
200 202 2.045634 ACCCCGACGTCGAGATCA 60.046 61.111 37.65 0.00 43.02 2.92
265 267 2.124736 GCAAGCCCATGCGTAGGA 60.125 61.111 0.00 0.00 44.33 2.94
348 375 2.600731 CTCGCCTCTCTCCCTCCT 59.399 66.667 0.00 0.00 0.00 3.69
532 577 3.003173 CGCTCCTCCCCCACTTGA 61.003 66.667 0.00 0.00 0.00 3.02
616 661 0.393267 TAATTTCCTTGCCCCGTCGG 60.393 55.000 3.60 3.60 0.00 4.79
619 664 3.276281 GGTAATTTCCTTGCCCCGT 57.724 52.632 0.00 0.00 33.75 5.28
628 673 2.767445 GCCACCGCGGGTAATTTCC 61.767 63.158 31.76 4.57 32.11 3.13
630 675 2.034376 TGCCACCGCGGGTAATTT 59.966 55.556 31.76 3.35 38.08 1.82
652 697 4.443034 GCTGGAATGAATAGTTACTCCCGT 60.443 45.833 0.00 0.00 0.00 5.28
653 698 4.058817 GCTGGAATGAATAGTTACTCCCG 58.941 47.826 0.00 0.00 0.00 5.14
657 702 9.686683 AAATTACTGCTGGAATGAATAGTTACT 57.313 29.630 1.23 0.00 0.00 2.24
684 729 1.545582 ACCTCGTCCGTCGGATAAAAA 59.454 47.619 18.75 0.78 40.32 1.94
688 733 0.179037 ATGACCTCGTCCGTCGGATA 60.179 55.000 18.75 8.17 40.32 2.59
701 747 0.326618 ATCGACCCCTGGAATGACCT 60.327 55.000 0.00 0.00 39.86 3.85
702 748 0.106894 GATCGACCCCTGGAATGACC 59.893 60.000 0.00 0.00 39.54 4.02
704 750 1.399744 CGGATCGACCCCTGGAATGA 61.400 60.000 0.00 0.00 34.64 2.57
706 752 1.075525 TCGGATCGACCCCTGGAAT 60.076 57.895 0.00 0.00 34.64 3.01
707 753 2.361375 TCGGATCGACCCCTGGAA 59.639 61.111 0.00 0.00 34.64 3.53
716 762 4.807631 TCTGGGGCGTCGGATCGA 62.808 66.667 0.00 0.00 0.00 3.59
717 763 3.559657 GATCTGGGGCGTCGGATCG 62.560 68.421 10.94 0.00 39.05 3.69
719 765 3.234730 GGATCTGGGGCGTCGGAT 61.235 66.667 0.00 1.20 35.61 4.18
720 766 4.770362 TGGATCTGGGGCGTCGGA 62.770 66.667 0.00 0.00 0.00 4.55
721 767 2.996168 GATTGGATCTGGGGCGTCGG 62.996 65.000 0.00 0.00 0.00 4.79
722 768 1.595382 GATTGGATCTGGGGCGTCG 60.595 63.158 0.00 0.00 0.00 5.12
723 769 0.107214 TTGATTGGATCTGGGGCGTC 60.107 55.000 0.00 0.00 0.00 5.19
724 770 0.107017 CTTGATTGGATCTGGGGCGT 60.107 55.000 0.00 0.00 0.00 5.68
725 771 1.450531 GCTTGATTGGATCTGGGGCG 61.451 60.000 0.00 0.00 0.00 6.13
726 772 1.111715 GGCTTGATTGGATCTGGGGC 61.112 60.000 0.00 0.00 0.00 5.80
728 774 1.396653 GTGGCTTGATTGGATCTGGG 58.603 55.000 0.00 0.00 0.00 4.45
729 775 1.396653 GGTGGCTTGATTGGATCTGG 58.603 55.000 0.00 0.00 0.00 3.86
730 776 1.341285 TGGGTGGCTTGATTGGATCTG 60.341 52.381 0.00 0.00 0.00 2.90
731 777 1.002069 TGGGTGGCTTGATTGGATCT 58.998 50.000 0.00 0.00 0.00 2.75
732 778 1.851304 TTGGGTGGCTTGATTGGATC 58.149 50.000 0.00 0.00 0.00 3.36
733 779 2.391678 GATTGGGTGGCTTGATTGGAT 58.608 47.619 0.00 0.00 0.00 3.41
734 780 1.619432 GGATTGGGTGGCTTGATTGGA 60.619 52.381 0.00 0.00 0.00 3.53
736 782 1.559368 TGGATTGGGTGGCTTGATTG 58.441 50.000 0.00 0.00 0.00 2.67
737 783 1.901833 GTTGGATTGGGTGGCTTGATT 59.098 47.619 0.00 0.00 0.00 2.57
739 785 0.893270 CGTTGGATTGGGTGGCTTGA 60.893 55.000 0.00 0.00 0.00 3.02
741 787 1.606313 CCGTTGGATTGGGTGGCTT 60.606 57.895 0.00 0.00 0.00 4.35
742 788 2.035626 CCGTTGGATTGGGTGGCT 59.964 61.111 0.00 0.00 0.00 4.75
744 790 3.068064 GGCCGTTGGATTGGGTGG 61.068 66.667 0.00 0.00 0.00 4.61
745 791 2.282816 TGGCCGTTGGATTGGGTG 60.283 61.111 0.00 0.00 0.00 4.61
746 792 2.035626 CTGGCCGTTGGATTGGGT 59.964 61.111 0.00 0.00 0.00 4.51
747 793 2.755469 CCTGGCCGTTGGATTGGG 60.755 66.667 0.00 0.00 0.00 4.12
748 794 1.304052 TTCCTGGCCGTTGGATTGG 60.304 57.895 11.92 0.00 31.76 3.16
749 795 1.937546 GCTTCCTGGCCGTTGGATTG 61.938 60.000 11.92 9.51 31.76 2.67
750 796 1.678970 GCTTCCTGGCCGTTGGATT 60.679 57.895 11.92 0.00 31.76 3.01
752 798 4.344865 GGCTTCCTGGCCGTTGGA 62.345 66.667 7.73 7.73 42.82 3.53
759 805 3.068729 GCGATTTGGGCTTCCTGGC 62.069 63.158 0.00 0.00 40.96 4.85
760 806 1.379044 AGCGATTTGGGCTTCCTGG 60.379 57.895 0.00 0.00 37.50 4.45
761 807 0.677731 TCAGCGATTTGGGCTTCCTG 60.678 55.000 0.00 0.00 39.08 3.86
764 810 0.392998 TCCTCAGCGATTTGGGCTTC 60.393 55.000 0.00 0.00 39.08 3.86
766 812 1.222936 CTCCTCAGCGATTTGGGCT 59.777 57.895 0.00 0.00 42.61 5.19
767 813 2.476320 GCTCCTCAGCGATTTGGGC 61.476 63.158 0.00 0.00 35.39 5.36
768 814 3.819188 GCTCCTCAGCGATTTGGG 58.181 61.111 0.00 0.00 35.39 4.12
777 823 2.123077 ATCCTCCCGGCTCCTCAG 60.123 66.667 0.00 0.00 0.00 3.35
781 827 2.920384 GAGGATCCTCCCGGCTCC 60.920 72.222 28.84 3.71 44.40 4.70
794 840 6.985653 ATCGAGAAATAAGAATCAGGAGGA 57.014 37.500 0.00 0.00 0.00 3.71
795 841 7.441017 AGAATCGAGAAATAAGAATCAGGAGG 58.559 38.462 0.00 0.00 0.00 4.30
796 842 8.885494 AAGAATCGAGAAATAAGAATCAGGAG 57.115 34.615 0.00 0.00 0.00 3.69
808 854 7.655328 AGCATCGAGAAATAAGAATCGAGAAAT 59.345 33.333 2.50 0.00 46.16 2.17
809 855 6.980978 AGCATCGAGAAATAAGAATCGAGAAA 59.019 34.615 2.50 0.00 46.16 2.52
810 856 6.419116 CAGCATCGAGAAATAAGAATCGAGAA 59.581 38.462 2.50 0.00 46.16 2.87
811 857 5.917447 CAGCATCGAGAAATAAGAATCGAGA 59.083 40.000 2.50 0.00 46.16 4.04
812 858 5.917447 TCAGCATCGAGAAATAAGAATCGAG 59.083 40.000 2.50 0.00 46.16 4.04
813 859 5.831997 TCAGCATCGAGAAATAAGAATCGA 58.168 37.500 0.00 0.00 46.90 3.59
814 860 6.183360 GGATCAGCATCGAGAAATAAGAATCG 60.183 42.308 0.00 0.00 36.54 3.34
815 861 6.183360 CGGATCAGCATCGAGAAATAAGAATC 60.183 42.308 0.00 0.00 0.00 2.52
816 862 5.636965 CGGATCAGCATCGAGAAATAAGAAT 59.363 40.000 0.00 0.00 0.00 2.40
817 863 4.984785 CGGATCAGCATCGAGAAATAAGAA 59.015 41.667 0.00 0.00 0.00 2.52
818 864 4.278419 TCGGATCAGCATCGAGAAATAAGA 59.722 41.667 0.00 0.00 0.00 2.10
820 866 4.299155 GTCGGATCAGCATCGAGAAATAA 58.701 43.478 0.00 0.00 33.41 1.40
821 867 3.609409 CGTCGGATCAGCATCGAGAAATA 60.609 47.826 0.00 0.00 33.41 1.40
822 868 2.748605 GTCGGATCAGCATCGAGAAAT 58.251 47.619 0.00 0.00 33.41 2.17
823 869 1.533965 CGTCGGATCAGCATCGAGAAA 60.534 52.381 0.00 0.00 33.41 2.52
824 870 0.029433 CGTCGGATCAGCATCGAGAA 59.971 55.000 0.00 0.00 33.41 2.87
825 871 1.649267 CGTCGGATCAGCATCGAGA 59.351 57.895 0.00 0.00 33.41 4.04
827 873 2.721859 CCGTCGGATCAGCATCGA 59.278 61.111 4.91 0.00 0.00 3.59
828 874 3.032609 GCCGTCGGATCAGCATCG 61.033 66.667 17.49 0.00 0.00 3.84
829 875 1.953138 CAGCCGTCGGATCAGCATC 60.953 63.158 17.49 0.00 0.00 3.91
901 949 1.377333 GGACTGCTACTTGGTGGGC 60.377 63.158 0.00 0.00 0.00 5.36
903 951 0.976641 TCTGGACTGCTACTTGGTGG 59.023 55.000 0.00 0.00 0.00 4.61
904 952 1.670087 CGTCTGGACTGCTACTTGGTG 60.670 57.143 0.00 0.00 0.00 4.17
905 953 0.603569 CGTCTGGACTGCTACTTGGT 59.396 55.000 0.00 0.00 0.00 3.67
907 955 1.073216 CGCGTCTGGACTGCTACTTG 61.073 60.000 0.00 0.00 0.00 3.16
910 958 2.881352 GCGCGTCTGGACTGCTAC 60.881 66.667 8.43 4.86 0.00 3.58
911 959 4.476410 CGCGCGTCTGGACTGCTA 62.476 66.667 24.19 0.00 0.00 3.49
1224 1272 4.608514 TTCCCCTGGCAGGACCCA 62.609 66.667 34.84 12.58 37.67 4.51
1516 1564 7.225145 CGTCCAAAATCCAATTCAATGCATAAT 59.775 33.333 0.00 0.00 0.00 1.28
1517 1565 6.534436 CGTCCAAAATCCAATTCAATGCATAA 59.466 34.615 0.00 0.00 0.00 1.90
1518 1566 6.041511 CGTCCAAAATCCAATTCAATGCATA 58.958 36.000 0.00 0.00 0.00 3.14
1558 1606 7.397221 AGTTCTGGTTTCATATGAATCACTCA 58.603 34.615 18.61 12.78 38.81 3.41
1594 1642 2.035193 CACTACATCAGCGGATACAGCT 59.965 50.000 0.00 0.00 45.07 4.24
1636 1684 5.559770 TGGACTGTCTCAATAATCAGCAAA 58.440 37.500 7.85 0.00 0.00 3.68
1695 1743 7.096271 CGGATTCTAAGAATCAACTTCATCGAG 60.096 40.741 0.20 0.00 36.24 4.04
1729 1777 9.896645 ATAAATGGATACTGGCATTACTATCAG 57.103 33.333 0.00 0.00 37.61 2.90
1784 1834 8.814038 AGATACAAAAAGACAGCCTATCATTT 57.186 30.769 0.00 0.00 0.00 2.32
1819 1869 7.656412 TGAAGCAAGATAAACAGCATAACAAA 58.344 30.769 0.00 0.00 0.00 2.83
1823 1873 8.306038 ACAAATGAAGCAAGATAAACAGCATAA 58.694 29.630 0.00 0.00 0.00 1.90
1889 1939 3.181447 TGGGGAATTGCAAAATGAAAGCA 60.181 39.130 1.71 0.00 36.32 3.91
1929 1979 4.156739 GCTGCAAACTCCATAGCTTTAACT 59.843 41.667 0.00 0.00 0.00 2.24
2200 2257 1.474498 CCAAGTATAGAACCCCCACGC 60.474 57.143 0.00 0.00 0.00 5.34
2219 2276 4.742438 TTCACGATGTAAGAGCAAAACC 57.258 40.909 0.00 0.00 0.00 3.27
2394 2452 8.034058 AGCAAGTGTTAAGCTAATTCTTACAG 57.966 34.615 0.00 0.00 36.73 2.74
2693 2751 2.543641 GCTTTTGCTGCTTTCAGTTGT 58.456 42.857 0.00 0.00 42.29 3.32
2837 2895 5.471456 ACGCTTGAAGAAGTCATTCTCAAAT 59.529 36.000 0.00 0.00 45.25 2.32
2876 2934 1.064017 ACCTGAAGTTGGCCTGAAACA 60.064 47.619 3.32 0.00 0.00 2.83
3121 3179 1.271102 GCACGGTTCATTAAGGCCAAA 59.729 47.619 5.01 0.00 0.00 3.28
3251 3309 1.300971 GCTCCAGACGCTCAATTGCA 61.301 55.000 0.00 0.00 0.00 4.08
3295 3353 6.186957 TCCACAGCCTTTGTATATGAAATGT 58.813 36.000 0.00 0.00 38.16 2.71
3473 3533 5.491070 TCACCTCAGTCAAATACCTTCATG 58.509 41.667 0.00 0.00 0.00 3.07
3793 3955 7.596749 ATGGTACTCAAAAAGTAAGTGATCG 57.403 36.000 0.00 0.00 42.11 3.69
3815 3977 7.915397 CGATTAATTCACCAACCTAGGAAAATG 59.085 37.037 17.98 8.57 0.00 2.32
3908 4070 6.459257 GTCACTGAGACACAAAATAGTCTG 57.541 41.667 0.00 0.00 44.61 3.51
4054 4216 8.570068 AAAACAAACAACTCAGGTAGAAAGTA 57.430 30.769 0.00 0.00 0.00 2.24
4095 4257 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4096 4258 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4097 4259 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
4098 4260 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
4099 4261 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
4100 4262 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
4101 4263 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
4102 4264 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
4127 4289 9.955102 AGTGTTACATACATCCGTATCTAGATA 57.045 33.333 8.44 8.44 39.39 1.98
4128 4290 8.865420 AGTGTTACATACATCCGTATCTAGAT 57.135 34.615 10.73 10.73 39.39 1.98
4129 4291 9.783081 TTAGTGTTACATACATCCGTATCTAGA 57.217 33.333 0.00 0.00 39.39 2.43
4170 4332 9.093970 TGTCTTAGATTTGTTTACATACGGATG 57.906 33.333 5.94 5.94 39.16 3.51
4171 4333 9.661563 TTGTCTTAGATTTGTTTACATACGGAT 57.338 29.630 0.00 0.00 0.00 4.18
4172 4334 9.146984 CTTGTCTTAGATTTGTTTACATACGGA 57.853 33.333 0.00 0.00 0.00 4.69
4173 4335 9.146984 TCTTGTCTTAGATTTGTTTACATACGG 57.853 33.333 0.00 0.00 0.00 4.02
4181 4343 9.546428 CCCAAAATTCTTGTCTTAGATTTGTTT 57.454 29.630 0.00 0.00 28.79 2.83
4182 4344 8.923270 TCCCAAAATTCTTGTCTTAGATTTGTT 58.077 29.630 0.00 0.00 28.79 2.83
4183 4345 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
4184 4346 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
4185 4347 7.447238 TCGTCCCAAAATTCTTGTCTTAGATTT 59.553 33.333 0.00 0.00 0.00 2.17
4186 4348 6.940298 TCGTCCCAAAATTCTTGTCTTAGATT 59.060 34.615 0.00 0.00 0.00 2.40
4187 4349 6.472887 TCGTCCCAAAATTCTTGTCTTAGAT 58.527 36.000 0.00 0.00 0.00 1.98
4188 4350 5.860611 TCGTCCCAAAATTCTTGTCTTAGA 58.139 37.500 0.00 0.00 0.00 2.10
4189 4351 6.348540 CCTTCGTCCCAAAATTCTTGTCTTAG 60.349 42.308 0.00 0.00 0.00 2.18
4190 4352 5.472137 CCTTCGTCCCAAAATTCTTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
4191 4353 4.278419 CCTTCGTCCCAAAATTCTTGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
4192 4354 3.821033 CCTTCGTCCCAAAATTCTTGTCT 59.179 43.478 0.00 0.00 0.00 3.41
4193 4355 3.057526 CCCTTCGTCCCAAAATTCTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
4194 4356 2.890945 CCCTTCGTCCCAAAATTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
4195 4357 3.153919 TCCCTTCGTCCCAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
4196 4358 3.181433 ACTCCCTTCGTCCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
4197 4359 2.375509 ACTCCCTTCGTCCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
4198 4360 2.791655 ACTCCCTTCGTCCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
4199 4361 2.971901 ACTCCCTTCGTCCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
4200 4362 4.586306 AATACTCCCTTCGTCCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
4201 4363 5.427481 AGATAATACTCCCTTCGTCCCAAAA 59.573 40.000 0.00 0.00 0.00 2.44
4202 4364 4.966805 AGATAATACTCCCTTCGTCCCAAA 59.033 41.667 0.00 0.00 0.00 3.28
4203 4365 4.553678 AGATAATACTCCCTTCGTCCCAA 58.446 43.478 0.00 0.00 0.00 4.12
4204 4366 4.194678 AGATAATACTCCCTTCGTCCCA 57.805 45.455 0.00 0.00 0.00 4.37
4205 4367 5.774184 ACTAAGATAATACTCCCTTCGTCCC 59.226 44.000 0.00 0.00 0.00 4.46
4206 4368 6.897706 ACTAAGATAATACTCCCTTCGTCC 57.102 41.667 0.00 0.00 0.00 4.79
4207 4369 9.032420 CAAAACTAAGATAATACTCCCTTCGTC 57.968 37.037 0.00 0.00 0.00 4.20
4208 4370 8.537858 ACAAAACTAAGATAATACTCCCTTCGT 58.462 33.333 0.00 0.00 0.00 3.85
4209 4371 8.943909 ACAAAACTAAGATAATACTCCCTTCG 57.056 34.615 0.00 0.00 0.00 3.79
4345 4522 9.944376 AAATAGTCTCAGATTGCTAGTGTTTTA 57.056 29.630 0.00 0.00 0.00 1.52
4346 4523 8.854614 AAATAGTCTCAGATTGCTAGTGTTTT 57.145 30.769 0.00 0.00 0.00 2.43
4347 4524 8.854614 AAAATAGTCTCAGATTGCTAGTGTTT 57.145 30.769 0.00 0.00 0.00 2.83
4348 4525 9.372369 GTAAAATAGTCTCAGATTGCTAGTGTT 57.628 33.333 0.00 0.00 0.00 3.32
4574 4752 4.260139 TGGAACAAGATGTTACGCAGTA 57.740 40.909 1.34 0.00 44.06 2.74
4594 4772 1.244816 TCGGCGTCCAGTATCCTATG 58.755 55.000 6.85 0.00 0.00 2.23
4611 4789 1.361993 CGGCTCCAGAGGAAGATCG 59.638 63.158 0.00 0.00 0.00 3.69
4632 4810 1.321074 GGAGGTCCAGGTACCACTCG 61.321 65.000 15.94 0.00 42.40 4.18
4699 4877 0.657840 GTGGCGAAAAGGATCATCCG 59.342 55.000 0.00 0.00 42.75 4.18
4719 4897 0.179936 CTCTGATGTTCTCCAGGCCC 59.820 60.000 0.00 0.00 0.00 5.80
4746 4924 2.135189 CCAGGGTATCTTGGGAATGGA 58.865 52.381 0.00 0.00 0.00 3.41
4833 5011 3.432252 ACACTTCTCCAAAATCGCTAACG 59.568 43.478 0.00 0.00 42.01 3.18
5033 5211 4.185394 TCGAAAGTTTGCGGCATAAGATA 58.815 39.130 2.28 0.00 0.00 1.98
5050 5229 4.338118 AGGCATCTTCAAAACAGTTCGAAA 59.662 37.500 0.00 0.00 0.00 3.46
5079 5258 4.080582 ACACCGATTTAACATCCTCCATGA 60.081 41.667 0.00 0.00 36.21 3.07
5128 5314 0.591659 GAAAGAAACTGGGGCACGAC 59.408 55.000 0.00 0.00 0.00 4.34
5131 5317 4.341235 ACTTTAAGAAAGAAACTGGGGCAC 59.659 41.667 5.98 0.00 41.02 5.01
5279 5487 2.212900 CTGACCGACGATGCAGTCCA 62.213 60.000 0.00 0.00 37.85 4.02
5321 5529 3.255969 TGGTTAAATAGGCAGACCGAC 57.744 47.619 0.00 0.00 42.76 4.79
5326 5534 3.869065 CGGAGTTGGTTAAATAGGCAGA 58.131 45.455 0.00 0.00 0.00 4.26
5358 5566 1.071019 CTGCTTGCTTGATTGCGCTG 61.071 55.000 9.73 0.00 35.36 5.18
5372 5580 3.341043 CGTGTGTGCGCTCTGCTT 61.341 61.111 9.73 0.00 46.63 3.91
5409 5617 3.492102 TTGCTCTGTTCTACTGGCTTT 57.508 42.857 0.00 0.00 0.00 3.51
5414 5622 3.058639 GCTTGGTTTGCTCTGTTCTACTG 60.059 47.826 0.00 0.00 0.00 2.74
5421 5630 1.035139 CCTTGCTTGGTTTGCTCTGT 58.965 50.000 0.00 0.00 0.00 3.41
5678 5887 5.242434 ACGTATACAAGTTTTCCATGCAGA 58.758 37.500 3.32 0.00 0.00 4.26
5679 5888 5.545658 ACGTATACAAGTTTTCCATGCAG 57.454 39.130 3.32 0.00 0.00 4.41
5680 5889 5.062433 CGTACGTATACAAGTTTTCCATGCA 59.938 40.000 7.22 0.00 0.00 3.96
5684 5893 5.341993 CGTTCGTACGTATACAAGTTTTCCA 59.658 40.000 16.05 0.00 42.72 3.53
5685 5894 5.764862 CGTTCGTACGTATACAAGTTTTCC 58.235 41.667 16.05 0.00 42.72 3.13
5700 5909 8.385789 TGAGATTGTTAATAACTCGTTCGTAC 57.614 34.615 4.67 0.00 0.00 3.67
5701 5910 8.969121 TTGAGATTGTTAATAACTCGTTCGTA 57.031 30.769 4.67 0.00 0.00 3.43
5702 5911 7.878477 TTGAGATTGTTAATAACTCGTTCGT 57.122 32.000 4.67 0.00 0.00 3.85
5703 5912 9.755064 AATTTGAGATTGTTAATAACTCGTTCG 57.245 29.630 4.67 0.00 0.00 3.95
5724 5933 1.136252 CGACTCTGCGTGTGGAATTTG 60.136 52.381 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.