Multiple sequence alignment - TraesCS4D01G169300

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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 TraesCS4D01G169300 chr4D 100.000 8222 0 0 1 8222 294341253 294349474 0.000000e+00 15184.0
1 TraesCS4D01G169300 chr4D 87.072 263 26 7 4960 5215 402546414 402546675 2.900000e-74 291.0
2 TraesCS4D01G169300 chr4D 87.109 256 25 6 4968 5218 65537974 65537722 4.860000e-72 283.0
3 TraesCS4D01G169300 chr4B 97.650 6341 107 10 854 7183 362139883 362146192 0.000000e+00 10846.0
4 TraesCS4D01G169300 chr4B 91.264 435 13 8 7810 8222 362146481 362146912 3.330000e-158 569.0
5 TraesCS4D01G169300 chr4B 86.770 257 26 7 4965 5215 498391507 498391761 6.280000e-71 279.0
6 TraesCS4D01G169300 chr4B 92.982 114 8 0 7180 7293 362146351 362146464 5.100000e-37 167.0
7 TraesCS4D01G169300 chr4B 95.238 42 2 0 687 728 404564673 404564632 5.330000e-07 67.6
8 TraesCS4D01G169300 chr4A 96.555 2874 92 5 1818 4688 215254257 215251388 0.000000e+00 4752.0
9 TraesCS4D01G169300 chr4A 95.532 2395 99 3 4902 7296 215251385 215248999 0.000000e+00 3823.0
10 TraesCS4D01G169300 chr4A 97.436 975 20 3 850 1820 215255309 215254336 0.000000e+00 1657.0
11 TraesCS4D01G169300 chr4A 91.367 417 10 8 7829 8222 215248974 215248561 1.560000e-151 547.0
12 TraesCS4D01G169300 chr4A 86.932 176 23 0 6778 6953 215249592 215249417 1.810000e-46 198.0
13 TraesCS4D01G169300 chr4A 85.714 70 8 2 12 81 652174365 652174298 1.140000e-08 73.1
14 TraesCS4D01G169300 chr6D 94.664 506 26 1 7303 7807 20126328 20125823 0.000000e+00 784.0
15 TraesCS4D01G169300 chr6D 92.759 511 32 4 7303 7808 467999190 467999700 0.000000e+00 734.0
16 TraesCS4D01G169300 chr6D 84.808 757 80 21 1 730 356803292 356804040 0.000000e+00 728.0
17 TraesCS4D01G169300 chr6D 88.079 302 35 1 375 676 454784595 454784295 2.820000e-94 357.0
18 TraesCS4D01G169300 chr6D 83.418 392 46 10 6 381 51970823 51971211 6.110000e-91 346.0
19 TraesCS4D01G169300 chr3D 93.898 508 29 2 7301 7808 147470269 147469764 0.000000e+00 765.0
20 TraesCS4D01G169300 chr3D 80.055 727 78 26 16 679 404006106 404006828 2.080000e-130 477.0
21 TraesCS4D01G169300 chr3D 79.777 717 95 15 1 676 347448307 347447600 7.470000e-130 475.0
22 TraesCS4D01G169300 chr3D 81.405 484 62 14 221 678 302053951 302054432 3.620000e-98 370.0
23 TraesCS4D01G169300 chr3D 87.925 265 26 4 4955 5213 178651803 178652067 2.880000e-79 307.0
24 TraesCS4D01G169300 chr3D 79.476 458 66 17 9 442 512253857 512253404 4.820000e-77 300.0
25 TraesCS4D01G169300 chr7D 93.083 506 32 3 7306 7808 208652075 208652580 0.000000e+00 737.0
26 TraesCS4D01G169300 chr7D 92.520 508 36 1 7303 7808 536979631 536980138 0.000000e+00 726.0
27 TraesCS4D01G169300 chr7D 92.644 503 33 4 7306 7806 178124428 178124928 0.000000e+00 721.0
28 TraesCS4D01G169300 chr7D 92.323 508 37 2 7303 7808 399827893 399828400 0.000000e+00 721.0
29 TraesCS4D01G169300 chr7D 79.442 394 70 8 1 385 600890098 600889707 1.360000e-67 268.0
30 TraesCS4D01G169300 chr7D 100.000 29 0 0 698 726 517336467 517336439 4.000000e-03 54.7
31 TraesCS4D01G169300 chr2B 92.913 508 35 1 7302 7808 622655385 622655892 0.000000e+00 737.0
32 TraesCS4D01G169300 chr2B 77.616 688 106 22 1 669 296292337 296292995 2.800000e-99 374.0
33 TraesCS4D01G169300 chr3B 92.505 507 36 2 7303 7808 9861712 9861207 0.000000e+00 725.0
34 TraesCS4D01G169300 chr3B 79.896 766 95 27 19 729 167776962 167777723 2.650000e-139 507.0
35 TraesCS4D01G169300 chr3B 87.547 265 27 4 4955 5213 257098933 257099197 1.340000e-77 302.0
36 TraesCS4D01G169300 chr3B 95.652 46 2 0 683 728 32378373 32378328 3.180000e-09 75.0
37 TraesCS4D01G169300 chr3B 91.304 46 4 0 683 728 694790089 694790134 6.890000e-06 63.9
38 TraesCS4D01G169300 chr7A 80.261 765 104 15 1 731 620930382 620929631 4.370000e-147 532.0
39 TraesCS4D01G169300 chr7A 79.974 779 97 31 1 728 166481150 166480380 3.400000e-143 520.0
40 TraesCS4D01G169300 chr7A 100.000 29 0 0 698 726 485495599 485495627 4.000000e-03 54.7
41 TraesCS4D01G169300 chr6A 82.903 620 74 20 67 659 541244572 541243958 5.650000e-146 529.0
42 TraesCS4D01G169300 chr6A 81.564 537 52 15 234 731 551626998 551627526 4.620000e-107 399.0
43 TraesCS4D01G169300 chr7B 77.664 685 105 22 4 669 637910615 637909960 2.800000e-99 374.0
44 TraesCS4D01G169300 chr5B 81.148 488 56 14 222 678 421722465 421721983 7.850000e-95 359.0
45 TraesCS4D01G169300 chr6B 76.865 657 110 24 2 626 512569635 512570281 4.760000e-87 333.0
46 TraesCS4D01G169300 chr3A 87.925 265 26 4 4955 5213 221274967 221275231 2.880000e-79 307.0
47 TraesCS4D01G169300 chr5D 87.984 258 26 3 4963 5215 267617436 267617693 4.820000e-77 300.0
48 TraesCS4D01G169300 chr2D 89.091 55 5 1 683 736 135280681 135280627 5.330000e-07 67.6
49 TraesCS4D01G169300 chr2A 100.000 32 0 0 698 729 657507365 657507334 8.910000e-05 60.2


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 TraesCS4D01G169300 chr4D 294341253 294349474 8221 False 15184.000000 15184 100.000000 1 8222 1 chr4D.!!$F1 8221
1 TraesCS4D01G169300 chr4B 362139883 362146912 7029 False 3860.666667 10846 93.965333 854 8222 3 chr4B.!!$F2 7368
2 TraesCS4D01G169300 chr4A 215248561 215255309 6748 True 2195.400000 4752 93.564400 850 8222 5 chr4A.!!$R2 7372
3 TraesCS4D01G169300 chr6D 20125823 20126328 505 True 784.000000 784 94.664000 7303 7807 1 chr6D.!!$R1 504
4 TraesCS4D01G169300 chr6D 467999190 467999700 510 False 734.000000 734 92.759000 7303 7808 1 chr6D.!!$F3 505
5 TraesCS4D01G169300 chr6D 356803292 356804040 748 False 728.000000 728 84.808000 1 730 1 chr6D.!!$F2 729
6 TraesCS4D01G169300 chr3D 147469764 147470269 505 True 765.000000 765 93.898000 7301 7808 1 chr3D.!!$R1 507
7 TraesCS4D01G169300 chr3D 404006106 404006828 722 False 477.000000 477 80.055000 16 679 1 chr3D.!!$F3 663
8 TraesCS4D01G169300 chr3D 347447600 347448307 707 True 475.000000 475 79.777000 1 676 1 chr3D.!!$R2 675
9 TraesCS4D01G169300 chr7D 208652075 208652580 505 False 737.000000 737 93.083000 7306 7808 1 chr7D.!!$F2 502
10 TraesCS4D01G169300 chr7D 536979631 536980138 507 False 726.000000 726 92.520000 7303 7808 1 chr7D.!!$F4 505
11 TraesCS4D01G169300 chr7D 178124428 178124928 500 False 721.000000 721 92.644000 7306 7806 1 chr7D.!!$F1 500
12 TraesCS4D01G169300 chr7D 399827893 399828400 507 False 721.000000 721 92.323000 7303 7808 1 chr7D.!!$F3 505
13 TraesCS4D01G169300 chr2B 622655385 622655892 507 False 737.000000 737 92.913000 7302 7808 1 chr2B.!!$F2 506
14 TraesCS4D01G169300 chr2B 296292337 296292995 658 False 374.000000 374 77.616000 1 669 1 chr2B.!!$F1 668
15 TraesCS4D01G169300 chr3B 9861207 9861712 505 True 725.000000 725 92.505000 7303 7808 1 chr3B.!!$R1 505
16 TraesCS4D01G169300 chr3B 167776962 167777723 761 False 507.000000 507 79.896000 19 729 1 chr3B.!!$F1 710
17 TraesCS4D01G169300 chr7A 620929631 620930382 751 True 532.000000 532 80.261000 1 731 1 chr7A.!!$R2 730
18 TraesCS4D01G169300 chr7A 166480380 166481150 770 True 520.000000 520 79.974000 1 728 1 chr7A.!!$R1 727
19 TraesCS4D01G169300 chr6A 541243958 541244572 614 True 529.000000 529 82.903000 67 659 1 chr6A.!!$R1 592
20 TraesCS4D01G169300 chr6A 551626998 551627526 528 False 399.000000 399 81.564000 234 731 1 chr6A.!!$F1 497
21 TraesCS4D01G169300 chr7B 637909960 637910615 655 True 374.000000 374 77.664000 4 669 1 chr7B.!!$R1 665
22 TraesCS4D01G169300 chr6B 512569635 512570281 646 False 333.000000 333 76.865000 2 626 1 chr6B.!!$F1 624

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
804 892 0.114954 TTTTTCCTCAGCCAGCCCAT 59.885 50.000 0.00 0.0 0.00 4.00 F
805 893 0.323725 TTTTCCTCAGCCAGCCCATC 60.324 55.000 0.00 0.0 0.00 3.51 F
2246 2424 0.253044 ATGGCACGCACTGAGGTATT 59.747 50.000 0.00 0.0 0.00 1.89 F
3189 3370 1.360393 TTTCCTGTGGCCCCACTTCT 61.360 55.000 17.57 0.0 46.30 2.85 F
4155 4337 1.466167 GCTTGTAGTGATGTGTGCCAG 59.534 52.381 0.00 0.0 0.00 4.85 F
4724 4906 0.892755 ACGTGAATCCGAGGTAAGCA 59.107 50.000 0.00 0.0 0.00 3.91 F
5534 5716 3.304257 GCATATCAAGGAAACTGCATCCG 60.304 47.826 0.00 0.0 42.68 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 2088 1.376424 ACAATGAGCAGCCTCCACG 60.376 57.895 0.00 0.00 37.29 4.94 R
2251 2429 3.383185 ACAAAAAGATCAAACCGCCTTGA 59.617 39.130 0.00 0.56 39.56 3.02 R
4155 4337 5.471116 TCATATTTATCAGCATGGCACTGTC 59.529 40.000 5.18 0.00 36.50 3.51 R
4380 4562 4.488126 TTCTTTTGCTCTGAATCCAACG 57.512 40.909 0.00 0.00 0.00 4.10 R
5534 5716 1.476471 CCCACAAGATGCCTCTGATCC 60.476 57.143 0.00 0.00 0.00 3.36 R
6601 6783 0.249676 ACTCTCAGGTGATGCAGCAG 59.750 55.000 4.06 0.00 33.95 4.24 R
7438 7785 1.464376 GCTGCATCTACCTAGCCCGA 61.464 60.000 0.00 0.00 0.00 5.14 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
158 167 1.267806 GTCACTTACCACGACGGAGAA 59.732 52.381 0.00 0.00 38.63 2.87
248 283 2.129555 GAGGGTGGCCAAGCTCAAGA 62.130 60.000 7.24 0.00 0.00 3.02
311 358 1.534235 ATCCCCGATTCCTCCTCCG 60.534 63.158 0.00 0.00 0.00 4.63
312 359 2.313749 ATCCCCGATTCCTCCTCCGT 62.314 60.000 0.00 0.00 0.00 4.69
340 387 1.513158 CGACTCCAACTGCTCCGAT 59.487 57.895 0.00 0.00 0.00 4.18
420 490 4.930405 GCTCGCCCTCTCCTTTTATATAAC 59.070 45.833 0.00 0.00 0.00 1.89
421 491 5.510861 GCTCGCCCTCTCCTTTTATATAACA 60.511 44.000 0.00 0.00 0.00 2.41
422 492 5.850614 TCGCCCTCTCCTTTTATATAACAC 58.149 41.667 0.00 0.00 0.00 3.32
605 679 7.140705 ACGTTGCATGAATTTATATGGACATG 58.859 34.615 0.00 0.00 38.33 3.21
606 680 7.013178 ACGTTGCATGAATTTATATGGACATGA 59.987 33.333 0.00 0.00 37.77 3.07
612 686 6.604171 TGAATTTATATGGACATGAGGTGCT 58.396 36.000 0.00 0.00 38.87 4.40
626 700 3.834813 TGAGGTGCTGGATATGAGATACC 59.165 47.826 0.00 0.00 0.00 2.73
627 701 4.093011 GAGGTGCTGGATATGAGATACCT 58.907 47.826 0.00 0.00 39.82 3.08
649 723 1.612199 GGTGTGGAGGCGTGGATTTAA 60.612 52.381 0.00 0.00 0.00 1.52
659 733 1.763968 GTGGATTTAAGGAGTGCCCC 58.236 55.000 0.00 0.00 34.66 5.80
661 735 1.101635 GGATTTAAGGAGTGCCCCGC 61.102 60.000 0.00 0.00 34.66 6.13
709 797 2.893489 GAGGGGTCAGATTTGCAAAGTT 59.107 45.455 18.19 0.87 0.00 2.66
731 819 2.159099 CGGTTGTAGATGCTCTTAGGCA 60.159 50.000 0.00 0.00 46.63 4.75
732 820 3.462021 GGTTGTAGATGCTCTTAGGCAG 58.538 50.000 2.33 0.00 45.75 4.85
738 826 2.488952 GATGCTCTTAGGCAGCTAACC 58.511 52.381 4.24 0.00 45.75 2.85
739 827 1.573108 TGCTCTTAGGCAGCTAACCT 58.427 50.000 11.92 11.92 41.57 3.50
740 828 1.208052 TGCTCTTAGGCAGCTAACCTG 59.792 52.381 16.05 2.53 44.67 4.00
741 829 1.208293 GCTCTTAGGCAGCTAACCTGT 59.792 52.381 16.05 0.00 43.71 4.00
742 830 2.431057 GCTCTTAGGCAGCTAACCTGTA 59.569 50.000 16.05 5.01 43.71 2.74
743 831 3.070302 GCTCTTAGGCAGCTAACCTGTAT 59.930 47.826 16.05 0.00 43.71 2.29
744 832 4.281182 GCTCTTAGGCAGCTAACCTGTATA 59.719 45.833 16.05 0.00 43.71 1.47
745 833 5.774630 CTCTTAGGCAGCTAACCTGTATAC 58.225 45.833 16.05 0.00 43.71 1.47
746 834 5.205821 TCTTAGGCAGCTAACCTGTATACA 58.794 41.667 16.05 5.25 43.71 2.29
747 835 5.659525 TCTTAGGCAGCTAACCTGTATACAA 59.340 40.000 16.05 2.49 43.71 2.41
748 836 4.837093 AGGCAGCTAACCTGTATACAAA 57.163 40.909 7.06 0.00 43.71 2.83
749 837 4.514401 AGGCAGCTAACCTGTATACAAAC 58.486 43.478 7.06 0.00 43.71 2.93
750 838 3.626217 GGCAGCTAACCTGTATACAAACC 59.374 47.826 7.06 0.00 43.71 3.27
751 839 4.258543 GCAGCTAACCTGTATACAAACCA 58.741 43.478 7.06 0.00 43.71 3.67
752 840 4.094442 GCAGCTAACCTGTATACAAACCAC 59.906 45.833 7.06 0.00 43.71 4.16
753 841 4.634443 CAGCTAACCTGTATACAAACCACC 59.366 45.833 7.06 0.00 36.79 4.61
754 842 4.287585 AGCTAACCTGTATACAAACCACCA 59.712 41.667 7.06 0.00 0.00 4.17
755 843 5.005094 GCTAACCTGTATACAAACCACCAA 58.995 41.667 7.06 0.00 0.00 3.67
756 844 5.474189 GCTAACCTGTATACAAACCACCAAA 59.526 40.000 7.06 0.00 0.00 3.28
757 845 5.777850 AACCTGTATACAAACCACCAAAC 57.222 39.130 7.06 0.00 0.00 2.93
758 846 5.056553 ACCTGTATACAAACCACCAAACT 57.943 39.130 7.06 0.00 0.00 2.66
759 847 6.190346 ACCTGTATACAAACCACCAAACTA 57.810 37.500 7.06 0.00 0.00 2.24
760 848 6.786122 ACCTGTATACAAACCACCAAACTAT 58.214 36.000 7.06 0.00 0.00 2.12
761 849 7.920227 ACCTGTATACAAACCACCAAACTATA 58.080 34.615 7.06 0.00 0.00 1.31
762 850 8.554011 ACCTGTATACAAACCACCAAACTATAT 58.446 33.333 7.06 0.00 0.00 0.86
763 851 8.836413 CCTGTATACAAACCACCAAACTATATG 58.164 37.037 7.06 0.00 0.00 1.78
764 852 8.215926 TGTATACAAACCACCAAACTATATGC 57.784 34.615 2.20 0.00 0.00 3.14
765 853 7.829706 TGTATACAAACCACCAAACTATATGCA 59.170 33.333 2.20 0.00 0.00 3.96
766 854 5.643379 ACAAACCACCAAACTATATGCAG 57.357 39.130 0.00 0.00 0.00 4.41
767 855 5.321102 ACAAACCACCAAACTATATGCAGA 58.679 37.500 0.00 0.00 0.00 4.26
768 856 5.772672 ACAAACCACCAAACTATATGCAGAA 59.227 36.000 0.00 0.00 0.00 3.02
769 857 6.071952 ACAAACCACCAAACTATATGCAGAAG 60.072 38.462 0.00 0.00 0.00 2.85
770 858 5.435686 ACCACCAAACTATATGCAGAAGA 57.564 39.130 0.00 0.00 0.00 2.87
771 859 6.006275 ACCACCAAACTATATGCAGAAGAT 57.994 37.500 0.00 0.00 0.00 2.40
772 860 5.824624 ACCACCAAACTATATGCAGAAGATG 59.175 40.000 0.00 0.00 0.00 2.90
773 861 6.057533 CCACCAAACTATATGCAGAAGATGA 58.942 40.000 0.00 0.00 0.00 2.92
774 862 6.713903 CCACCAAACTATATGCAGAAGATGAT 59.286 38.462 0.00 0.00 0.00 2.45
775 863 7.230108 CCACCAAACTATATGCAGAAGATGATT 59.770 37.037 0.00 0.00 0.00 2.57
776 864 8.627403 CACCAAACTATATGCAGAAGATGATTT 58.373 33.333 0.00 0.00 0.00 2.17
777 865 9.851686 ACCAAACTATATGCAGAAGATGATTTA 57.148 29.630 0.00 0.00 0.00 1.40
782 870 9.829507 ACTATATGCAGAAGATGATTTATAGGC 57.170 33.333 0.00 0.00 30.80 3.93
784 872 8.734218 ATATGCAGAAGATGATTTATAGGCTG 57.266 34.615 0.00 0.00 0.00 4.85
785 873 5.933617 TGCAGAAGATGATTTATAGGCTGT 58.066 37.500 0.00 0.00 0.00 4.40
786 874 6.359804 TGCAGAAGATGATTTATAGGCTGTT 58.640 36.000 0.00 0.00 0.00 3.16
787 875 6.830324 TGCAGAAGATGATTTATAGGCTGTTT 59.170 34.615 0.00 0.00 0.00 2.83
788 876 7.340232 TGCAGAAGATGATTTATAGGCTGTTTT 59.660 33.333 0.00 0.00 0.00 2.43
789 877 8.193438 GCAGAAGATGATTTATAGGCTGTTTTT 58.807 33.333 0.00 0.00 0.00 1.94
790 878 9.727627 CAGAAGATGATTTATAGGCTGTTTTTC 57.272 33.333 0.00 0.00 0.00 2.29
791 879 8.907885 AGAAGATGATTTATAGGCTGTTTTTCC 58.092 33.333 0.00 0.00 0.00 3.13
792 880 8.829373 AAGATGATTTATAGGCTGTTTTTCCT 57.171 30.769 0.00 0.00 36.51 3.36
793 881 8.457238 AGATGATTTATAGGCTGTTTTTCCTC 57.543 34.615 0.00 0.00 34.02 3.71
794 882 8.055181 AGATGATTTATAGGCTGTTTTTCCTCA 58.945 33.333 0.00 0.00 34.02 3.86
795 883 7.630242 TGATTTATAGGCTGTTTTTCCTCAG 57.370 36.000 0.00 0.00 34.02 3.35
801 889 0.600057 CTGTTTTTCCTCAGCCAGCC 59.400 55.000 0.00 0.00 0.00 4.85
802 890 0.827507 TGTTTTTCCTCAGCCAGCCC 60.828 55.000 0.00 0.00 0.00 5.19
803 891 0.827507 GTTTTTCCTCAGCCAGCCCA 60.828 55.000 0.00 0.00 0.00 5.36
804 892 0.114954 TTTTTCCTCAGCCAGCCCAT 59.885 50.000 0.00 0.00 0.00 4.00
805 893 0.323725 TTTTCCTCAGCCAGCCCATC 60.324 55.000 0.00 0.00 0.00 3.51
806 894 1.210204 TTTCCTCAGCCAGCCCATCT 61.210 55.000 0.00 0.00 0.00 2.90
807 895 0.326522 TTCCTCAGCCAGCCCATCTA 60.327 55.000 0.00 0.00 0.00 1.98
808 896 0.326522 TCCTCAGCCAGCCCATCTAA 60.327 55.000 0.00 0.00 0.00 2.10
809 897 0.548031 CCTCAGCCAGCCCATCTAAA 59.452 55.000 0.00 0.00 0.00 1.85
810 898 1.064463 CCTCAGCCAGCCCATCTAAAA 60.064 52.381 0.00 0.00 0.00 1.52
811 899 2.621407 CCTCAGCCAGCCCATCTAAAAA 60.621 50.000 0.00 0.00 0.00 1.94
812 900 3.294214 CTCAGCCAGCCCATCTAAAAAT 58.706 45.455 0.00 0.00 0.00 1.82
813 901 3.290710 TCAGCCAGCCCATCTAAAAATC 58.709 45.455 0.00 0.00 0.00 2.17
814 902 3.025978 CAGCCAGCCCATCTAAAAATCA 58.974 45.455 0.00 0.00 0.00 2.57
815 903 3.026694 AGCCAGCCCATCTAAAAATCAC 58.973 45.455 0.00 0.00 0.00 3.06
816 904 2.760092 GCCAGCCCATCTAAAAATCACA 59.240 45.455 0.00 0.00 0.00 3.58
817 905 3.385755 GCCAGCCCATCTAAAAATCACAT 59.614 43.478 0.00 0.00 0.00 3.21
818 906 4.738541 GCCAGCCCATCTAAAAATCACATG 60.739 45.833 0.00 0.00 0.00 3.21
819 907 4.365723 CAGCCCATCTAAAAATCACATGC 58.634 43.478 0.00 0.00 0.00 4.06
820 908 4.025360 AGCCCATCTAAAAATCACATGCA 58.975 39.130 0.00 0.00 0.00 3.96
821 909 4.467082 AGCCCATCTAAAAATCACATGCAA 59.533 37.500 0.00 0.00 0.00 4.08
822 910 5.129815 AGCCCATCTAAAAATCACATGCAAT 59.870 36.000 0.00 0.00 0.00 3.56
835 923 3.377434 CATGCAATGCAACCAAAATCG 57.623 42.857 13.45 0.00 43.62 3.34
836 924 2.808523 TGCAATGCAACCAAAATCGA 57.191 40.000 5.01 0.00 34.76 3.59
837 925 3.316071 TGCAATGCAACCAAAATCGAT 57.684 38.095 5.01 0.00 34.76 3.59
838 926 2.994578 TGCAATGCAACCAAAATCGATG 59.005 40.909 5.01 0.00 34.76 3.84
839 927 2.222863 GCAATGCAACCAAAATCGATGC 60.223 45.455 0.00 0.00 37.52 3.91
840 928 3.255725 CAATGCAACCAAAATCGATGCT 58.744 40.909 0.00 0.00 37.86 3.79
841 929 4.422840 CAATGCAACCAAAATCGATGCTA 58.577 39.130 0.00 0.00 37.86 3.49
842 930 4.717233 ATGCAACCAAAATCGATGCTAA 57.283 36.364 0.00 0.00 37.86 3.09
843 931 4.511617 TGCAACCAAAATCGATGCTAAA 57.488 36.364 0.00 0.00 37.86 1.85
844 932 4.233789 TGCAACCAAAATCGATGCTAAAC 58.766 39.130 0.00 0.00 37.86 2.01
845 933 4.233789 GCAACCAAAATCGATGCTAAACA 58.766 39.130 0.00 0.00 34.29 2.83
846 934 4.089923 GCAACCAAAATCGATGCTAAACAC 59.910 41.667 0.00 0.00 34.29 3.32
847 935 4.434713 ACCAAAATCGATGCTAAACACC 57.565 40.909 0.00 0.00 0.00 4.16
848 936 4.079253 ACCAAAATCGATGCTAAACACCT 58.921 39.130 0.00 0.00 0.00 4.00
1011 1105 4.124351 GACGGTGATGTCGGCGGA 62.124 66.667 7.21 0.00 0.00 5.54
1345 1439 3.785189 ATTCCGATCCCGCGTTCCG 62.785 63.158 4.92 2.76 0.00 4.30
1423 1517 1.237954 CGCTCGCCTATCAGCTCCTA 61.238 60.000 0.00 0.00 33.09 2.94
2187 2362 4.706962 GGGGTTATGAGCACTGAAGAAATT 59.293 41.667 0.00 0.00 0.00 1.82
2246 2424 0.253044 ATGGCACGCACTGAGGTATT 59.747 50.000 0.00 0.00 0.00 1.89
2249 2427 1.867233 GGCACGCACTGAGGTATTATG 59.133 52.381 0.00 0.00 0.00 1.90
2250 2428 2.483013 GGCACGCACTGAGGTATTATGA 60.483 50.000 0.00 0.00 0.00 2.15
2251 2429 3.393800 GCACGCACTGAGGTATTATGAT 58.606 45.455 0.00 0.00 0.00 2.45
2261 2439 4.102524 TGAGGTATTATGATCAAGGCGGTT 59.897 41.667 0.00 0.00 0.00 4.44
2336 2514 4.343231 TGACATAGCATGTTTCCATTGGT 58.657 39.130 1.86 0.00 45.03 3.67
2341 2519 6.437162 ACATAGCATGTTTCCATTGGTTTACT 59.563 34.615 1.86 0.00 41.63 2.24
2593 2772 6.109359 CCTGAAGGAGTTACTGGACTATTTG 58.891 44.000 0.00 0.00 37.39 2.32
2594 2773 5.488341 TGAAGGAGTTACTGGACTATTTGC 58.512 41.667 0.00 0.00 0.00 3.68
2711 2890 5.984926 AGTATTCCATGCTTTTGTTGTTGTG 59.015 36.000 0.00 0.00 0.00 3.33
2793 2973 4.133796 GGCCATGTTCAAGCGGGC 62.134 66.667 0.00 0.00 43.86 6.13
3189 3370 1.360393 TTTCCTGTGGCCCCACTTCT 61.360 55.000 17.57 0.00 46.30 2.85
3194 3375 2.557452 CCTGTGGCCCCACTTCTTAAAT 60.557 50.000 17.57 0.00 46.30 1.40
4155 4337 1.466167 GCTTGTAGTGATGTGTGCCAG 59.534 52.381 0.00 0.00 0.00 4.85
4380 4562 3.561725 GTGAAGCTCATATGGTGGCTTAC 59.438 47.826 21.85 17.50 41.39 2.34
4397 4579 3.188460 GCTTACGTTGGATTCAGAGCAAA 59.812 43.478 0.00 0.00 0.00 3.68
4724 4906 0.892755 ACGTGAATCCGAGGTAAGCA 59.107 50.000 0.00 0.00 0.00 3.91
4758 4940 7.129457 TCTGAGTAGGAAAGCAACATATGAT 57.871 36.000 10.38 0.00 0.00 2.45
4763 4945 6.713903 AGTAGGAAAGCAACATATGATGGATG 59.286 38.462 10.38 1.78 33.60 3.51
4777 4959 4.910195 TGATGGATGCTGTTTCTACTGTT 58.090 39.130 0.00 0.00 0.00 3.16
4814 4996 4.408270 ACTCTGATGATCAGTTGCACCTAT 59.592 41.667 20.82 0.00 44.58 2.57
4858 5040 4.993584 CACAGTAGATGTTTCTGCTTCTGT 59.006 41.667 0.00 0.00 41.57 3.41
4861 5043 6.015010 ACAGTAGATGTTTCTGCTTCTGTACT 60.015 38.462 0.00 0.00 41.57 2.73
5208 5390 9.362151 ACCTAGAACTTCAATTATTTTGGAACA 57.638 29.630 0.00 0.00 0.00 3.18
5534 5716 3.304257 GCATATCAAGGAAACTGCATCCG 60.304 47.826 0.00 0.00 42.68 4.18
5804 5986 4.330250 CTGTCTTCCTTCACATGGTTGAT 58.670 43.478 0.00 0.00 0.00 2.57
6601 6783 1.443828 GGGATTCTCCTCCAGCGAC 59.556 63.158 0.00 0.00 36.57 5.19
6637 6819 0.415429 AGTGACCCTGAGGAGGATGT 59.585 55.000 0.00 0.00 42.93 3.06
6639 6821 2.035632 GTGACCCTGAGGAGGATGTAG 58.964 57.143 0.00 0.00 42.93 2.74
6774 6959 4.142513 GGAAGAGAGCTAATGCAAACCAAG 60.143 45.833 0.00 0.00 42.74 3.61
6888 7073 3.132111 GTCTGATGGAGAAGAGGAGGAAC 59.868 52.174 0.00 0.00 30.26 3.62
6997 7182 0.886563 AGGCAGCAATCAGAAAGCAC 59.113 50.000 0.00 0.00 0.00 4.40
7016 7201 4.402793 AGCACAAGTCATACTCGTAGGAAT 59.597 41.667 0.00 0.00 0.00 3.01
7048 7233 8.251721 AGCAATACTCGTAGATAGTTTTGAACT 58.748 33.333 9.59 0.00 45.40 3.01
7072 7257 5.477291 TGTTTCTGTTGGTTAACCTGTTGAA 59.523 36.000 24.78 18.85 35.92 2.69
7156 7341 7.447374 TCTCATGAATTTTAACACGAACCAT 57.553 32.000 0.00 0.00 0.00 3.55
7239 7586 5.723672 TTAGTCCTTCCTGTCTTACTGTG 57.276 43.478 0.00 0.00 0.00 3.66
7245 7592 4.564406 CCTTCCTGTCTTACTGTGCTTCAT 60.564 45.833 0.00 0.00 0.00 2.57
7248 7595 3.686726 CCTGTCTTACTGTGCTTCATTCC 59.313 47.826 0.00 0.00 0.00 3.01
7249 7596 3.325870 TGTCTTACTGTGCTTCATTCCG 58.674 45.455 0.00 0.00 0.00 4.30
7256 7603 0.527565 GTGCTTCATTCCGTGCCAAT 59.472 50.000 0.00 0.00 0.00 3.16
7258 7605 2.358898 GTGCTTCATTCCGTGCCAATAT 59.641 45.455 0.00 0.00 0.00 1.28
7296 7643 8.589335 TTGAAACGACTTGAGATATATTAGCC 57.411 34.615 0.00 0.00 0.00 3.93
7297 7644 7.952671 TGAAACGACTTGAGATATATTAGCCT 58.047 34.615 0.00 0.00 0.00 4.58
7298 7645 7.867909 TGAAACGACTTGAGATATATTAGCCTG 59.132 37.037 0.00 0.00 0.00 4.85
7299 7646 7.526142 AACGACTTGAGATATATTAGCCTGA 57.474 36.000 0.00 0.00 0.00 3.86
7300 7647 6.915349 ACGACTTGAGATATATTAGCCTGAC 58.085 40.000 0.00 0.00 0.00 3.51
7301 7648 6.717540 ACGACTTGAGATATATTAGCCTGACT 59.282 38.462 0.00 0.00 0.00 3.41
7438 7785 4.271816 CGTCGGCGGCAGCTAGAT 62.272 66.667 13.62 0.00 44.37 1.98
7444 7791 3.610669 CGGCAGCTAGATCGGGCT 61.611 66.667 9.16 9.16 39.60 5.19
7538 7885 2.345244 CTGGTTGAGGAGCACGCT 59.655 61.111 0.00 0.00 0.00 5.07
7588 7935 2.352805 CTGGTTGGGACCTCAGGC 59.647 66.667 0.00 0.00 46.66 4.85
7616 7963 0.978151 TTAGGTTTGGCTGCGAGGTA 59.022 50.000 0.00 0.00 0.00 3.08
7665 8012 2.224621 CGCCCCTTCATCAACTGGATAT 60.225 50.000 0.00 0.00 33.95 1.63
7699 8051 1.301716 TTGCTCAGACGGTGGCTTC 60.302 57.895 0.00 0.00 0.00 3.86
7926 8300 0.725784 GTTTCTGATGGTTGCGCACG 60.726 55.000 11.12 0.00 0.00 5.34
7995 8370 1.684869 CCCAACACAACACAGGTTCCT 60.685 52.381 0.00 0.00 34.21 3.36
8043 8419 3.371063 GAGTCGACTCCACCGCCA 61.371 66.667 31.24 0.00 37.02 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 2.746277 GGGCACCGACATCACACC 60.746 66.667 0.00 0.00 40.86 4.16
175 184 1.377202 GCTTGGCGTTGATCCTCCA 60.377 57.895 0.00 0.00 0.00 3.86
248 283 1.174712 ACAATGCGGTCTTGCTTGCT 61.175 50.000 0.00 0.00 35.36 3.91
320 367 2.266055 GGAGCAGTTGGAGTCGGG 59.734 66.667 0.00 0.00 0.00 5.14
329 376 1.215647 GGTCGACATCGGAGCAGTT 59.784 57.895 18.91 0.00 40.29 3.16
332 379 2.678580 TGGGTCGACATCGGAGCA 60.679 61.111 18.91 0.00 40.29 4.26
340 387 0.611062 CAGTAGGAGGTGGGTCGACA 60.611 60.000 18.91 0.00 0.00 4.35
420 490 9.856488 ACATTGTAACTACATACTAGAACTGTG 57.144 33.333 0.00 0.00 35.89 3.66
421 491 9.856488 CACATTGTAACTACATACTAGAACTGT 57.144 33.333 0.00 0.00 35.89 3.55
422 492 8.808529 GCACATTGTAACTACATACTAGAACTG 58.191 37.037 0.00 0.00 35.89 3.16
595 669 2.411583 TCCAGCACCTCATGTCCATAT 58.588 47.619 0.00 0.00 0.00 1.78
602 676 4.554960 ATCTCATATCCAGCACCTCATG 57.445 45.455 0.00 0.00 0.00 3.07
605 679 4.081752 CAGGTATCTCATATCCAGCACCTC 60.082 50.000 0.00 0.00 32.91 3.85
606 680 3.837146 CAGGTATCTCATATCCAGCACCT 59.163 47.826 0.00 0.00 35.56 4.00
612 686 3.903714 CACACCCAGGTATCTCATATCCA 59.096 47.826 0.00 0.00 0.00 3.41
626 700 4.704833 CCACGCCTCCACACCCAG 62.705 72.222 0.00 0.00 0.00 4.45
659 733 3.403057 CGTTCGTGGACACTGGCG 61.403 66.667 0.56 0.00 0.00 5.69
661 735 3.403057 CGCGTTCGTGGACACTGG 61.403 66.667 0.00 0.00 0.00 4.00
696 784 4.819630 TCTACAACCGAACTTTGCAAATCT 59.180 37.500 13.23 2.34 0.00 2.40
731 819 4.287585 TGGTGGTTTGTATACAGGTTAGCT 59.712 41.667 5.56 0.00 0.00 3.32
732 820 4.581868 TGGTGGTTTGTATACAGGTTAGC 58.418 43.478 5.56 5.34 0.00 3.09
733 821 6.713450 AGTTTGGTGGTTTGTATACAGGTTAG 59.287 38.462 5.56 0.00 0.00 2.34
734 822 6.603224 AGTTTGGTGGTTTGTATACAGGTTA 58.397 36.000 5.56 0.00 0.00 2.85
735 823 5.451354 AGTTTGGTGGTTTGTATACAGGTT 58.549 37.500 5.56 0.00 0.00 3.50
736 824 5.056553 AGTTTGGTGGTTTGTATACAGGT 57.943 39.130 5.56 0.00 0.00 4.00
737 825 8.836413 CATATAGTTTGGTGGTTTGTATACAGG 58.164 37.037 5.56 0.00 0.00 4.00
738 826 8.342634 GCATATAGTTTGGTGGTTTGTATACAG 58.657 37.037 5.56 0.00 0.00 2.74
739 827 7.829706 TGCATATAGTTTGGTGGTTTGTATACA 59.170 33.333 0.08 0.08 0.00 2.29
740 828 8.215926 TGCATATAGTTTGGTGGTTTGTATAC 57.784 34.615 0.00 0.00 0.00 1.47
741 829 8.268605 TCTGCATATAGTTTGGTGGTTTGTATA 58.731 33.333 0.00 0.00 0.00 1.47
742 830 7.116075 TCTGCATATAGTTTGGTGGTTTGTAT 58.884 34.615 0.00 0.00 0.00 2.29
743 831 6.477253 TCTGCATATAGTTTGGTGGTTTGTA 58.523 36.000 0.00 0.00 0.00 2.41
744 832 5.321102 TCTGCATATAGTTTGGTGGTTTGT 58.679 37.500 0.00 0.00 0.00 2.83
745 833 5.895636 TCTGCATATAGTTTGGTGGTTTG 57.104 39.130 0.00 0.00 0.00 2.93
746 834 6.245408 TCTTCTGCATATAGTTTGGTGGTTT 58.755 36.000 0.00 0.00 0.00 3.27
747 835 5.815581 TCTTCTGCATATAGTTTGGTGGTT 58.184 37.500 0.00 0.00 0.00 3.67
748 836 5.435686 TCTTCTGCATATAGTTTGGTGGT 57.564 39.130 0.00 0.00 0.00 4.16
749 837 6.057533 TCATCTTCTGCATATAGTTTGGTGG 58.942 40.000 0.00 0.00 0.00 4.61
750 838 7.741027 ATCATCTTCTGCATATAGTTTGGTG 57.259 36.000 0.00 0.00 0.00 4.17
751 839 8.757982 AAATCATCTTCTGCATATAGTTTGGT 57.242 30.769 0.00 0.00 0.00 3.67
756 844 9.829507 GCCTATAAATCATCTTCTGCATATAGT 57.170 33.333 0.00 0.00 0.00 2.12
758 846 9.828039 CAGCCTATAAATCATCTTCTGCATATA 57.172 33.333 0.00 0.00 0.00 0.86
759 847 8.327271 ACAGCCTATAAATCATCTTCTGCATAT 58.673 33.333 0.00 0.00 0.00 1.78
760 848 7.683578 ACAGCCTATAAATCATCTTCTGCATA 58.316 34.615 0.00 0.00 0.00 3.14
761 849 6.540995 ACAGCCTATAAATCATCTTCTGCAT 58.459 36.000 0.00 0.00 0.00 3.96
762 850 5.933617 ACAGCCTATAAATCATCTTCTGCA 58.066 37.500 0.00 0.00 0.00 4.41
763 851 6.874288 AACAGCCTATAAATCATCTTCTGC 57.126 37.500 0.00 0.00 0.00 4.26
764 852 9.727627 GAAAAACAGCCTATAAATCATCTTCTG 57.272 33.333 0.00 0.00 0.00 3.02
765 853 8.907885 GGAAAAACAGCCTATAAATCATCTTCT 58.092 33.333 0.00 0.00 0.00 2.85
766 854 8.907885 AGGAAAAACAGCCTATAAATCATCTTC 58.092 33.333 0.00 0.00 31.31 2.87
767 855 8.829373 AGGAAAAACAGCCTATAAATCATCTT 57.171 30.769 0.00 0.00 31.31 2.40
768 856 8.055181 TGAGGAAAAACAGCCTATAAATCATCT 58.945 33.333 0.00 0.00 33.84 2.90
769 857 8.225603 TGAGGAAAAACAGCCTATAAATCATC 57.774 34.615 0.00 0.00 33.84 2.92
770 858 8.230472 CTGAGGAAAAACAGCCTATAAATCAT 57.770 34.615 0.00 0.00 33.84 2.45
771 859 7.630242 CTGAGGAAAAACAGCCTATAAATCA 57.370 36.000 0.00 0.00 33.84 2.57
782 870 0.600057 GGCTGGCTGAGGAAAAACAG 59.400 55.000 0.00 0.00 37.22 3.16
783 871 0.827507 GGGCTGGCTGAGGAAAAACA 60.828 55.000 0.00 0.00 0.00 2.83
784 872 0.827507 TGGGCTGGCTGAGGAAAAAC 60.828 55.000 0.00 0.00 0.00 2.43
785 873 0.114954 ATGGGCTGGCTGAGGAAAAA 59.885 50.000 0.00 0.00 0.00 1.94
786 874 0.323725 GATGGGCTGGCTGAGGAAAA 60.324 55.000 0.00 0.00 0.00 2.29
787 875 1.210204 AGATGGGCTGGCTGAGGAAA 61.210 55.000 0.00 0.00 0.00 3.13
788 876 0.326522 TAGATGGGCTGGCTGAGGAA 60.327 55.000 0.00 0.00 0.00 3.36
789 877 0.326522 TTAGATGGGCTGGCTGAGGA 60.327 55.000 0.00 0.00 0.00 3.71
790 878 0.548031 TTTAGATGGGCTGGCTGAGG 59.452 55.000 0.00 0.00 0.00 3.86
791 879 2.425143 TTTTAGATGGGCTGGCTGAG 57.575 50.000 0.00 0.00 0.00 3.35
792 880 2.897271 TTTTTAGATGGGCTGGCTGA 57.103 45.000 0.00 0.00 0.00 4.26
793 881 3.025978 TGATTTTTAGATGGGCTGGCTG 58.974 45.455 0.00 0.00 0.00 4.85
794 882 3.026694 GTGATTTTTAGATGGGCTGGCT 58.973 45.455 0.00 0.00 0.00 4.75
795 883 2.760092 TGTGATTTTTAGATGGGCTGGC 59.240 45.455 0.00 0.00 0.00 4.85
796 884 4.738541 GCATGTGATTTTTAGATGGGCTGG 60.739 45.833 0.00 0.00 0.00 4.85
797 885 4.142116 TGCATGTGATTTTTAGATGGGCTG 60.142 41.667 0.00 0.00 0.00 4.85
798 886 4.025360 TGCATGTGATTTTTAGATGGGCT 58.975 39.130 0.00 0.00 0.00 5.19
799 887 4.389890 TGCATGTGATTTTTAGATGGGC 57.610 40.909 0.00 0.00 0.00 5.36
800 888 5.235616 GCATTGCATGTGATTTTTAGATGGG 59.764 40.000 3.15 0.00 0.00 4.00
801 889 5.813157 TGCATTGCATGTGATTTTTAGATGG 59.187 36.000 7.38 0.00 31.71 3.51
802 890 6.895607 TGCATTGCATGTGATTTTTAGATG 57.104 33.333 7.38 0.00 31.71 2.90
803 891 6.314400 GGTTGCATTGCATGTGATTTTTAGAT 59.686 34.615 12.95 0.00 38.76 1.98
804 892 5.638657 GGTTGCATTGCATGTGATTTTTAGA 59.361 36.000 12.95 0.00 38.76 2.10
805 893 5.408909 TGGTTGCATTGCATGTGATTTTTAG 59.591 36.000 12.95 0.00 38.76 1.85
806 894 5.303165 TGGTTGCATTGCATGTGATTTTTA 58.697 33.333 12.95 0.00 38.76 1.52
807 895 4.135306 TGGTTGCATTGCATGTGATTTTT 58.865 34.783 12.95 0.00 38.76 1.94
808 896 3.741249 TGGTTGCATTGCATGTGATTTT 58.259 36.364 12.95 0.00 38.76 1.82
809 897 3.404224 TGGTTGCATTGCATGTGATTT 57.596 38.095 12.95 0.00 38.76 2.17
810 898 3.404224 TTGGTTGCATTGCATGTGATT 57.596 38.095 12.95 0.00 38.76 2.57
811 899 3.404224 TTTGGTTGCATTGCATGTGAT 57.596 38.095 12.95 0.00 38.76 3.06
812 900 2.904697 TTTGGTTGCATTGCATGTGA 57.095 40.000 12.95 0.00 38.76 3.58
813 901 3.423776 CGATTTTGGTTGCATTGCATGTG 60.424 43.478 12.95 0.00 38.76 3.21
814 902 2.737783 CGATTTTGGTTGCATTGCATGT 59.262 40.909 12.95 0.00 38.76 3.21
815 903 2.994578 TCGATTTTGGTTGCATTGCATG 59.005 40.909 12.95 0.00 38.76 4.06
816 904 3.316071 TCGATTTTGGTTGCATTGCAT 57.684 38.095 12.95 0.00 38.76 3.96
817 905 2.808523 TCGATTTTGGTTGCATTGCA 57.191 40.000 7.38 7.38 36.47 4.08
818 906 2.222863 GCATCGATTTTGGTTGCATTGC 60.223 45.455 0.46 0.46 33.58 3.56
819 907 3.255725 AGCATCGATTTTGGTTGCATTG 58.744 40.909 7.57 0.00 35.79 2.82
820 908 3.598019 AGCATCGATTTTGGTTGCATT 57.402 38.095 7.57 0.00 35.79 3.56
821 909 4.717233 TTAGCATCGATTTTGGTTGCAT 57.283 36.364 7.57 0.00 35.79 3.96
822 910 4.233789 GTTTAGCATCGATTTTGGTTGCA 58.766 39.130 7.57 0.00 35.79 4.08
823 911 4.089923 GTGTTTAGCATCGATTTTGGTTGC 59.910 41.667 0.00 0.00 0.00 4.17
824 912 4.621034 GGTGTTTAGCATCGATTTTGGTTG 59.379 41.667 0.00 0.00 0.00 3.77
825 913 4.522789 AGGTGTTTAGCATCGATTTTGGTT 59.477 37.500 0.00 0.00 32.28 3.67
826 914 4.079253 AGGTGTTTAGCATCGATTTTGGT 58.921 39.130 0.00 0.00 32.28 3.67
827 915 4.438744 GGAGGTGTTTAGCATCGATTTTGG 60.439 45.833 0.00 0.00 32.28 3.28
828 916 4.396166 AGGAGGTGTTTAGCATCGATTTTG 59.604 41.667 0.00 0.00 32.28 2.44
829 917 4.589908 AGGAGGTGTTTAGCATCGATTTT 58.410 39.130 0.00 0.00 32.28 1.82
830 918 4.222124 AGGAGGTGTTTAGCATCGATTT 57.778 40.909 0.00 0.00 32.28 2.17
831 919 3.914426 AGGAGGTGTTTAGCATCGATT 57.086 42.857 0.00 0.00 32.28 3.34
832 920 5.353394 TTTAGGAGGTGTTTAGCATCGAT 57.647 39.130 0.00 0.00 32.28 3.59
833 921 4.382685 CCTTTAGGAGGTGTTTAGCATCGA 60.383 45.833 0.00 0.00 40.95 3.59
834 922 3.871594 CCTTTAGGAGGTGTTTAGCATCG 59.128 47.826 0.00 0.00 40.95 3.84
847 935 3.853355 ATGATCCTGCACCTTTAGGAG 57.147 47.619 2.06 0.00 45.65 3.69
848 936 4.228210 AGAAATGATCCTGCACCTTTAGGA 59.772 41.667 2.06 0.00 46.43 2.94
1405 1499 0.242555 GTAGGAGCTGATAGGCGAGC 59.757 60.000 0.00 0.00 37.29 5.03
1423 1517 2.943978 CGGTTTGGAGGCGAGGAGT 61.944 63.158 0.00 0.00 0.00 3.85
1913 2088 1.376424 ACAATGAGCAGCCTCCACG 60.376 57.895 0.00 0.00 37.29 4.94
2187 2362 4.827692 ACGACTTGAGCATATTAACACCA 58.172 39.130 0.00 0.00 0.00 4.17
2246 2424 4.422073 AGATCAAACCGCCTTGATCATA 57.578 40.909 26.47 0.13 46.84 2.15
2249 2427 4.440839 AAAAGATCAAACCGCCTTGATC 57.559 40.909 21.29 21.29 46.84 2.92
2250 2428 4.039124 ACAAAAAGATCAAACCGCCTTGAT 59.961 37.500 9.27 9.27 46.38 2.57
2251 2429 3.383185 ACAAAAAGATCAAACCGCCTTGA 59.617 39.130 0.00 0.56 39.56 3.02
2261 2439 4.541705 TGACTCCCCAACAAAAAGATCAA 58.458 39.130 0.00 0.00 0.00 2.57
2593 2772 5.106791 CGATATCTTGTCATTCATGAAGGGC 60.107 44.000 17.38 17.38 38.75 5.19
2594 2773 6.146837 GTCGATATCTTGTCATTCATGAAGGG 59.853 42.308 19.21 11.30 38.75 3.95
2711 2890 3.885297 CCACAATCATCATACCCCAGTTC 59.115 47.826 0.00 0.00 0.00 3.01
3236 3417 7.278461 TCTATAGTATCAAGTGGACAGAAGC 57.722 40.000 0.00 0.00 0.00 3.86
4155 4337 5.471116 TCATATTTATCAGCATGGCACTGTC 59.529 40.000 5.18 0.00 36.50 3.51
4380 4562 4.488126 TTCTTTTGCTCTGAATCCAACG 57.512 40.909 0.00 0.00 0.00 4.10
4397 4579 6.015940 GTGTTCTTCTTGAATCCACCATTCTT 60.016 38.462 0.00 0.00 41.58 2.52
4555 4737 8.907829 TCATATCCTCTATATTTGAAGGAGCT 57.092 34.615 0.00 0.00 0.00 4.09
4724 4906 8.034313 TGCTTTCCTACTCAGATTACCATTAT 57.966 34.615 0.00 0.00 0.00 1.28
4758 4940 6.058833 TGTAAAACAGTAGAAACAGCATCCA 58.941 36.000 0.00 0.00 0.00 3.41
4796 4978 5.528690 TGCTAAATAGGTGCAACTGATCATC 59.471 40.000 16.44 0.00 36.74 2.92
4814 4996 8.849168 ACTGTGCATTATGCTTATTATGCTAAA 58.151 29.630 18.44 0.00 45.31 1.85
4846 5028 6.942532 AAATGAACAGTACAGAAGCAGAAA 57.057 33.333 0.00 0.00 0.00 2.52
4861 5043 9.202273 GTGCAAATATTTCCAACTAAATGAACA 57.798 29.630 0.00 0.00 31.63 3.18
5534 5716 1.476471 CCCACAAGATGCCTCTGATCC 60.476 57.143 0.00 0.00 0.00 3.36
5804 5986 6.830324 CCCATTCCAGTTCAATAAGAGATGAA 59.170 38.462 0.00 0.00 33.37 2.57
6601 6783 0.249676 ACTCTCAGGTGATGCAGCAG 59.750 55.000 4.06 0.00 33.95 4.24
6637 6819 3.775316 GGGAACATCTGGACCTTCTTCTA 59.225 47.826 0.00 0.00 0.00 2.10
6639 6821 2.678190 CGGGAACATCTGGACCTTCTTC 60.678 54.545 0.00 0.00 0.00 2.87
6774 6959 4.253685 TCGGATTCAGAATCTTGGACAAC 58.746 43.478 20.41 3.08 38.01 3.32
6888 7073 1.819288 TCTCTTCCTCCGTGCTAACAG 59.181 52.381 0.00 0.00 0.00 3.16
7048 7233 5.010933 TCAACAGGTTAACCAACAGAAACA 58.989 37.500 26.26 0.00 38.89 2.83
7156 7341 8.421784 AGTATATGTCTCGCTCCAAAAGAAATA 58.578 33.333 0.00 0.00 0.00 1.40
7164 7349 5.131067 ACAGTAGTATATGTCTCGCTCCAA 58.869 41.667 0.00 0.00 0.00 3.53
7239 7586 2.618241 TCATATTGGCACGGAATGAAGC 59.382 45.455 0.00 0.00 0.00 3.86
7245 7592 2.288666 GAAGCTCATATTGGCACGGAA 58.711 47.619 0.00 0.00 0.00 4.30
7248 7595 1.600957 CAGGAAGCTCATATTGGCACG 59.399 52.381 0.00 0.00 0.00 5.34
7249 7596 2.648059 ACAGGAAGCTCATATTGGCAC 58.352 47.619 0.00 0.00 0.00 5.01
7256 7603 5.810587 GTCGTTTCAATACAGGAAGCTCATA 59.189 40.000 0.00 0.00 0.00 2.15
7258 7605 3.994392 GTCGTTTCAATACAGGAAGCTCA 59.006 43.478 0.00 0.00 0.00 4.26
7293 7640 3.950395 GGCAAGATAAATCAAGTCAGGCT 59.050 43.478 0.00 0.00 0.00 4.58
7296 7643 6.095860 TCAATGGGCAAGATAAATCAAGTCAG 59.904 38.462 0.00 0.00 0.00 3.51
7297 7644 5.951148 TCAATGGGCAAGATAAATCAAGTCA 59.049 36.000 0.00 0.00 0.00 3.41
7298 7645 6.455360 TCAATGGGCAAGATAAATCAAGTC 57.545 37.500 0.00 0.00 0.00 3.01
7299 7646 6.608405 TCATCAATGGGCAAGATAAATCAAGT 59.392 34.615 0.00 0.00 0.00 3.16
7300 7647 6.921857 GTCATCAATGGGCAAGATAAATCAAG 59.078 38.462 0.00 0.00 0.00 3.02
7301 7648 6.459985 CGTCATCAATGGGCAAGATAAATCAA 60.460 38.462 0.00 0.00 0.00 2.57
7438 7785 1.464376 GCTGCATCTACCTAGCCCGA 61.464 60.000 0.00 0.00 0.00 5.14
7444 7791 4.023980 AGTTGTACTGCTGCATCTACCTA 58.976 43.478 1.31 0.00 0.00 3.08
7588 7935 3.378427 GCAGCCAAACCTAACATCTAAGG 59.622 47.826 0.00 0.00 38.93 2.69
7616 7963 7.512746 TGATAGTCTAGGCCTAATACCAAACAT 59.487 37.037 14.85 4.20 0.00 2.71
7665 8012 1.546029 AGCAACATCTGTCGCTACTCA 59.454 47.619 0.00 0.00 31.60 3.41
7686 8038 0.034059 AAGACTGAAGCCACCGTCTG 59.966 55.000 5.81 0.00 36.88 3.51
7808 8163 4.096382 CACTTTGTACTGGGACAATATGCC 59.904 45.833 0.00 0.00 39.04 4.40
7893 8248 0.460284 AGAAACATCAGCTACCGCCG 60.460 55.000 0.00 0.00 36.60 6.46
7926 8300 1.329906 CAGATTCAGATGTTGCCGAGC 59.670 52.381 0.00 0.00 0.00 5.03
7995 8370 2.656646 CGCACCAGCACTAGGTCA 59.343 61.111 0.00 0.00 42.27 4.02
8043 8419 6.573289 CGAAAGAGTGAGGCATATATAGGCTT 60.573 42.308 18.06 11.47 42.47 4.35


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

AutoCloner maintained by Alex Coulton.