Multiple sequence alignment - TraesCS6B01G451700

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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 TraesCS6B01G451700 chr6B 100.000 3822 0 0 1 3822 710227528 710231349 0.000000e+00 7059.0
1 TraesCS6B01G451700 chr6B 92.983 2095 104 24 997 3050 710151672 710149580 0.000000e+00 3014.0
2 TraesCS6B01G451700 chr6B 96.696 787 14 4 3047 3822 710144892 710144107 0.000000e+00 1299.0
3 TraesCS6B01G451700 chr6B 78.136 279 38 16 635 909 710152091 710151832 5.110000e-34 156.0
4 TraesCS6B01G451700 chr6B 90.000 70 6 1 814 882 646010656 646010587 5.260000e-14 89.8
5 TraesCS6B01G451700 chr2B 93.939 561 27 6 1 555 13353404 13353963 0.000000e+00 841.0
6 TraesCS6B01G451700 chr2B 88.988 563 47 10 1 555 794739640 794739085 0.000000e+00 682.0
7 TraesCS6B01G451700 chr1B 92.446 556 33 8 7 555 289298411 289297858 0.000000e+00 785.0
8 TraesCS6B01G451700 chr5B 92.196 551 31 9 1 544 207158518 207159063 0.000000e+00 769.0
9 TraesCS6B01G451700 chr5B 89.362 564 43 12 3 555 17560080 17559523 0.000000e+00 693.0
10 TraesCS6B01G451700 chr3B 89.483 561 47 9 1 555 74729737 74730291 0.000000e+00 699.0
11 TraesCS6B01G451700 chr3B 81.169 154 22 7 749 900 197794651 197794503 2.410000e-22 117.0
12 TraesCS6B01G451700 chrUn 89.343 563 43 14 1 555 17435825 17436378 0.000000e+00 691.0
13 TraesCS6B01G451700 chr7B 89.247 558 48 9 1 555 474478374 474478922 0.000000e+00 688.0
14 TraesCS6B01G451700 chr4B 88.929 560 51 10 1 555 106796954 106796401 0.000000e+00 680.0
15 TraesCS6B01G451700 chr6D 86.239 218 26 2 684 901 462839025 462839238 2.300000e-57 233.0
16 TraesCS6B01G451700 chr6D 89.189 148 14 2 767 913 465967382 465967236 2.350000e-42 183.0
17 TraesCS6B01G451700 chr6D 89.583 144 15 0 752 895 466328586 466328729 2.350000e-42 183.0
18 TraesCS6B01G451700 chr6A 87.692 195 22 2 720 913 612109853 612109660 3.840000e-55 226.0
19 TraesCS6B01G451700 chr6A 87.857 140 16 1 752 890 612299510 612299649 3.060000e-36 163.0
20 TraesCS6B01G451700 chr6A 84.314 153 24 0 730 882 573635797 573635949 2.380000e-32 150.0
21 TraesCS6B01G451700 chr6A 95.714 70 2 1 826 895 612290792 612290860 1.120000e-20 111.0
22 TraesCS6B01G451700 chr6A 79.874 159 14 5 730 888 612588735 612588875 2.430000e-17 100.0
23 TraesCS6B01G451700 chr4A 88.587 184 16 2 734 913 594050131 594049949 6.430000e-53 219.0


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 TraesCS6B01G451700 chr6B 710227528 710231349 3821 False 7059 7059 100.0000 1 3822 1 chr6B.!!$F1 3821
1 TraesCS6B01G451700 chr6B 710149580 710152091 2511 True 1585 3014 85.5595 635 3050 2 chr6B.!!$R3 2415
2 TraesCS6B01G451700 chr6B 710144107 710144892 785 True 1299 1299 96.6960 3047 3822 1 chr6B.!!$R2 775
3 TraesCS6B01G451700 chr2B 13353404 13353963 559 False 841 841 93.9390 1 555 1 chr2B.!!$F1 554
4 TraesCS6B01G451700 chr2B 794739085 794739640 555 True 682 682 88.9880 1 555 1 chr2B.!!$R1 554
5 TraesCS6B01G451700 chr1B 289297858 289298411 553 True 785 785 92.4460 7 555 1 chr1B.!!$R1 548
6 TraesCS6B01G451700 chr5B 207158518 207159063 545 False 769 769 92.1960 1 544 1 chr5B.!!$F1 543
7 TraesCS6B01G451700 chr5B 17559523 17560080 557 True 693 693 89.3620 3 555 1 chr5B.!!$R1 552
8 TraesCS6B01G451700 chr3B 74729737 74730291 554 False 699 699 89.4830 1 555 1 chr3B.!!$F1 554
9 TraesCS6B01G451700 chrUn 17435825 17436378 553 False 691 691 89.3430 1 555 1 chrUn.!!$F1 554
10 TraesCS6B01G451700 chr7B 474478374 474478922 548 False 688 688 89.2470 1 555 1 chr7B.!!$F1 554
11 TraesCS6B01G451700 chr4B 106796401 106796954 553 True 680 680 88.9290 1 555 1 chr4B.!!$R1 554

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
570 594 0.104934 GGGGAGAGATGCCCTTAGGA 60.105 60.0 0.00 0.0 45.30 2.94 F
835 873 0.105224 TTTCTTGTCGCAGTCCGGAA 59.895 50.0 5.23 0.0 37.59 4.30 F
950 1063 0.178953 AGCCACCAGCCAACAGATTT 60.179 50.0 0.00 0.0 45.47 2.17 F
2179 2332 0.393808 ACTGTGGCAGGTGTTTCGTT 60.394 50.0 0.00 0.0 35.51 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2040 0.249657 GGGCATGACCAACGCAAAAA 60.250 50.000 14.59 0.0 42.05 1.94 R
2161 2314 0.307760 GAACGAAACACCTGCCACAG 59.692 55.000 0.00 0.0 0.00 3.66 R
2380 2533 0.395173 AACAAACTTGGGCGGTCACT 60.395 50.000 0.00 0.0 0.00 3.41 R
3113 3266 3.118408 AGCATAAATTACCAGCGACTCCA 60.118 43.478 0.00 0.0 0.00 3.86 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
92 93 2.045926 GCGCCAGGACTCCATTGT 60.046 61.111 0.00 0.00 0.00 2.71
166 167 4.577246 GCTTCGAGGAGCGCCGAT 62.577 66.667 2.29 0.00 40.61 4.18
220 221 3.568907 GACAGCGACGACGACGACA 62.569 63.158 22.94 0.00 42.66 4.35
287 297 1.878656 CGCGTCAAGGAGGAGAAGGT 61.879 60.000 0.00 0.00 0.00 3.50
318 328 0.391661 ATGGCAGCGACGACTTCAAT 60.392 50.000 0.00 0.00 0.00 2.57
428 444 4.250464 TCTTTGTCATAACTTCGCCGAAT 58.750 39.130 0.00 0.00 0.00 3.34
564 588 3.174265 CCCTGGGGAGAGATGCCC 61.174 72.222 4.27 0.00 45.25 5.36
565 589 2.040043 CCTGGGGAGAGATGCCCT 60.040 66.667 6.38 0.00 45.30 5.19
566 590 1.695597 CCTGGGGAGAGATGCCCTT 60.696 63.158 6.38 0.00 45.30 3.95
567 591 0.400525 CCTGGGGAGAGATGCCCTTA 60.401 60.000 6.38 0.00 45.30 2.69
568 592 1.055040 CTGGGGAGAGATGCCCTTAG 58.945 60.000 6.38 0.00 45.30 2.18
569 593 0.400525 TGGGGAGAGATGCCCTTAGG 60.401 60.000 6.38 0.00 45.30 2.69
570 594 0.104934 GGGGAGAGATGCCCTTAGGA 60.105 60.000 0.00 0.00 45.30 2.94
571 595 1.695989 GGGGAGAGATGCCCTTAGGAA 60.696 57.143 0.00 0.00 45.30 3.36
572 596 1.696884 GGGAGAGATGCCCTTAGGAAG 59.303 57.143 0.00 0.00 42.56 3.46
573 597 2.683768 GGAGAGATGCCCTTAGGAAGA 58.316 52.381 0.00 0.00 33.47 2.87
574 598 3.041946 GGAGAGATGCCCTTAGGAAGAA 58.958 50.000 0.00 0.00 33.47 2.52
575 599 3.070878 GGAGAGATGCCCTTAGGAAGAAG 59.929 52.174 0.00 0.00 33.47 2.85
576 600 3.044894 AGAGATGCCCTTAGGAAGAAGG 58.955 50.000 0.00 0.00 44.96 3.46
582 606 2.570386 CCTTAGGAAGAAGGGGGAGA 57.430 55.000 0.00 0.00 42.12 3.71
583 607 2.403561 CCTTAGGAAGAAGGGGGAGAG 58.596 57.143 0.00 0.00 42.12 3.20
584 608 2.022918 CCTTAGGAAGAAGGGGGAGAGA 60.023 54.545 0.00 0.00 42.12 3.10
585 609 2.850695 TAGGAAGAAGGGGGAGAGAC 57.149 55.000 0.00 0.00 0.00 3.36
586 610 1.097722 AGGAAGAAGGGGGAGAGACT 58.902 55.000 0.00 0.00 0.00 3.24
587 611 1.199615 GGAAGAAGGGGGAGAGACTG 58.800 60.000 0.00 0.00 0.00 3.51
588 612 1.199615 GAAGAAGGGGGAGAGACTGG 58.800 60.000 0.00 0.00 0.00 4.00
589 613 0.252927 AAGAAGGGGGAGAGACTGGG 60.253 60.000 0.00 0.00 0.00 4.45
590 614 1.690985 GAAGGGGGAGAGACTGGGG 60.691 68.421 0.00 0.00 0.00 4.96
591 615 3.274550 AAGGGGGAGAGACTGGGGG 62.275 68.421 0.00 0.00 0.00 5.40
592 616 4.026357 GGGGGAGAGACTGGGGGT 62.026 72.222 0.00 0.00 0.00 4.95
593 617 2.689034 GGGGAGAGACTGGGGGTG 60.689 72.222 0.00 0.00 0.00 4.61
594 618 2.450243 GGGAGAGACTGGGGGTGA 59.550 66.667 0.00 0.00 0.00 4.02
595 619 1.687493 GGGAGAGACTGGGGGTGAG 60.687 68.421 0.00 0.00 0.00 3.51
596 620 1.388531 GGAGAGACTGGGGGTGAGA 59.611 63.158 0.00 0.00 0.00 3.27
597 621 0.686112 GGAGAGACTGGGGGTGAGAG 60.686 65.000 0.00 0.00 0.00 3.20
598 622 0.333312 GAGAGACTGGGGGTGAGAGA 59.667 60.000 0.00 0.00 0.00 3.10
599 623 1.014804 AGAGACTGGGGGTGAGAGAT 58.985 55.000 0.00 0.00 0.00 2.75
600 624 1.118838 GAGACTGGGGGTGAGAGATG 58.881 60.000 0.00 0.00 0.00 2.90
601 625 0.980231 AGACTGGGGGTGAGAGATGC 60.980 60.000 0.00 0.00 0.00 3.91
602 626 2.303549 GACTGGGGGTGAGAGATGCG 62.304 65.000 0.00 0.00 0.00 4.73
603 627 3.746949 CTGGGGGTGAGAGATGCGC 62.747 68.421 0.00 0.00 0.00 6.09
604 628 4.554036 GGGGGTGAGAGATGCGCC 62.554 72.222 4.18 0.00 35.19 6.53
605 629 4.899239 GGGGTGAGAGATGCGCCG 62.899 72.222 4.18 0.00 36.79 6.46
606 630 4.899239 GGGTGAGAGATGCGCCGG 62.899 72.222 4.18 0.00 36.79 6.13
626 650 2.870372 GCGGTGTGCCATTGTCTC 59.130 61.111 0.00 0.00 37.76 3.36
627 651 2.690778 GCGGTGTGCCATTGTCTCC 61.691 63.158 0.00 0.00 37.76 3.71
628 652 2.040544 CGGTGTGCCATTGTCTCCC 61.041 63.158 0.00 0.00 34.09 4.30
629 653 1.678970 GGTGTGCCATTGTCTCCCC 60.679 63.158 0.00 0.00 34.09 4.81
630 654 2.040544 GTGTGCCATTGTCTCCCCG 61.041 63.158 0.00 0.00 0.00 5.73
631 655 3.134127 GTGCCATTGTCTCCCCGC 61.134 66.667 0.00 0.00 0.00 6.13
632 656 4.776322 TGCCATTGTCTCCCCGCG 62.776 66.667 0.00 0.00 0.00 6.46
633 657 4.467084 GCCATTGTCTCCCCGCGA 62.467 66.667 8.23 0.00 0.00 5.87
634 658 2.202932 CCATTGTCTCCCCGCGAG 60.203 66.667 8.23 0.00 40.30 5.03
635 659 2.892425 CATTGTCTCCCCGCGAGC 60.892 66.667 8.23 0.00 38.62 5.03
636 660 4.162690 ATTGTCTCCCCGCGAGCC 62.163 66.667 8.23 0.00 38.62 4.70
651 675 0.602372 GAGCCTCCGCATGAGAATCC 60.602 60.000 0.00 0.00 44.42 3.01
665 689 0.807496 GAATCCAGTGGTGCTTGAGC 59.193 55.000 9.54 0.00 42.50 4.26
681 705 2.796651 GCAGAGGCGCCAAATCAG 59.203 61.111 31.54 15.66 0.00 2.90
682 706 1.746615 GCAGAGGCGCCAAATCAGA 60.747 57.895 31.54 0.00 0.00 3.27
687 725 1.078143 GGCGCCAAATCAGAGGAGT 60.078 57.895 24.80 0.00 0.00 3.85
695 733 2.746362 CAAATCAGAGGAGTTGCAGTCC 59.254 50.000 8.80 8.80 41.50 3.85
716 754 1.673337 AATCGAAGCAGCAGCAGCA 60.673 52.632 12.92 0.00 45.49 4.41
717 755 1.645704 AATCGAAGCAGCAGCAGCAG 61.646 55.000 12.92 3.23 45.49 4.24
728 766 4.521075 GCAGCAGCTCCGTAATCA 57.479 55.556 0.00 0.00 37.91 2.57
729 767 2.767536 GCAGCAGCTCCGTAATCAA 58.232 52.632 0.00 0.00 37.91 2.57
730 768 0.654683 GCAGCAGCTCCGTAATCAAG 59.345 55.000 0.00 0.00 37.91 3.02
731 769 0.654683 CAGCAGCTCCGTAATCAAGC 59.345 55.000 0.00 0.00 36.27 4.01
732 770 0.250234 AGCAGCTCCGTAATCAAGCA 59.750 50.000 0.00 0.00 38.51 3.91
733 771 0.654683 GCAGCTCCGTAATCAAGCAG 59.345 55.000 0.00 0.00 38.51 4.24
734 772 0.654683 CAGCTCCGTAATCAAGCAGC 59.345 55.000 0.00 0.00 38.51 5.25
735 773 0.539051 AGCTCCGTAATCAAGCAGCT 59.461 50.000 0.00 0.00 38.51 4.24
736 774 0.933796 GCTCCGTAATCAAGCAGCTC 59.066 55.000 0.00 0.00 36.06 4.09
737 775 1.472376 GCTCCGTAATCAAGCAGCTCT 60.472 52.381 0.00 0.00 36.06 4.09
738 776 2.200067 CTCCGTAATCAAGCAGCTCTG 58.800 52.381 0.00 0.00 0.00 3.35
765 803 3.680156 GCAACCGGCAATCCAAGA 58.320 55.556 0.00 0.00 43.97 3.02
766 804 1.963679 GCAACCGGCAATCCAAGAA 59.036 52.632 0.00 0.00 43.97 2.52
767 805 0.316841 GCAACCGGCAATCCAAGAAA 59.683 50.000 0.00 0.00 43.97 2.52
768 806 1.066929 GCAACCGGCAATCCAAGAAAT 60.067 47.619 0.00 0.00 43.97 2.17
780 818 1.457346 CAAGAAATCAAGCGGCTCCT 58.543 50.000 1.45 0.00 0.00 3.69
814 852 3.577313 GCAATCGAAGCGGCTCCC 61.577 66.667 1.45 0.00 0.00 4.30
819 857 0.744771 ATCGAAGCGGCTCCCTTTTC 60.745 55.000 1.45 0.00 0.00 2.29
820 858 1.376037 CGAAGCGGCTCCCTTTTCT 60.376 57.895 1.45 0.00 0.00 2.52
821 859 0.955919 CGAAGCGGCTCCCTTTTCTT 60.956 55.000 1.45 0.00 0.00 2.52
825 863 1.912371 GCGGCTCCCTTTTCTTGTCG 61.912 60.000 0.00 0.00 0.00 4.35
828 866 0.519077 GCTCCCTTTTCTTGTCGCAG 59.481 55.000 0.00 0.00 0.00 5.18
835 873 0.105224 TTTCTTGTCGCAGTCCGGAA 59.895 50.000 5.23 0.00 37.59 4.30
850 888 1.740025 CCGGAATCAAAGCAGTCCTTC 59.260 52.381 0.00 0.00 31.99 3.46
851 889 1.740025 CGGAATCAAAGCAGTCCTTCC 59.260 52.381 0.00 0.00 31.99 3.46
852 890 2.095461 GGAATCAAAGCAGTCCTTCCC 58.905 52.381 0.00 0.00 31.99 3.97
855 893 1.675641 CAAAGCAGTCCTTCCCGGG 60.676 63.158 16.85 16.85 31.99 5.73
856 894 3.569200 AAAGCAGTCCTTCCCGGGC 62.569 63.158 18.49 0.00 37.80 6.13
868 906 0.830648 TCCCGGGCTACAATCAGAAG 59.169 55.000 18.49 0.00 0.00 2.85
873 911 1.065126 GGGCTACAATCAGAAGCAGGT 60.065 52.381 0.00 0.00 38.01 4.00
889 927 2.160417 GCAGGTCCTGTTTCGAATTCAG 59.840 50.000 20.24 18.07 33.43 3.02
891 929 3.433615 CAGGTCCTGTTTCGAATTCAGTC 59.566 47.826 21.14 15.76 0.00 3.51
901 939 4.252971 TCGAATTCAGTCTCCGAGTTTT 57.747 40.909 6.22 0.00 0.00 2.43
909 947 3.433615 CAGTCTCCGAGTTTTCATTGGTC 59.566 47.826 0.00 0.00 0.00 4.02
935 1048 4.253685 CAATTTTAAGAGGAGACGAGCCA 58.746 43.478 0.00 0.00 0.00 4.75
936 1049 3.314541 TTTTAAGAGGAGACGAGCCAC 57.685 47.619 0.00 0.00 0.00 5.01
941 1054 4.459089 GGAGACGAGCCACCAGCC 62.459 72.222 0.00 0.00 45.47 4.85
942 1055 3.695606 GAGACGAGCCACCAGCCA 61.696 66.667 0.00 0.00 45.47 4.75
943 1056 3.240134 GAGACGAGCCACCAGCCAA 62.240 63.158 0.00 0.00 45.47 4.52
946 1059 3.052082 CGAGCCACCAGCCAACAG 61.052 66.667 0.00 0.00 45.47 3.16
950 1063 0.178953 AGCCACCAGCCAACAGATTT 60.179 50.000 0.00 0.00 45.47 2.17
955 1068 0.451783 CCAGCCAACAGATTTACGGC 59.548 55.000 0.00 0.00 43.31 5.68
970 1083 4.148825 GGCGACCGGCTGTCAGAT 62.149 66.667 0.00 0.00 44.71 2.90
971 1084 2.583593 GCGACCGGCTGTCAGATC 60.584 66.667 0.00 0.00 44.71 2.75
973 1086 2.761195 CGACCGGCTGTCAGATCGA 61.761 63.158 0.00 0.00 44.71 3.59
982 1095 3.838271 TCAGATCGACGGCCAGGC 61.838 66.667 1.26 1.26 0.00 4.85
983 1096 4.899239 CAGATCGACGGCCAGGCC 62.899 72.222 22.33 22.33 46.75 5.19
993 1106 4.416738 GCCAGGCCACAGTCCTCC 62.417 72.222 5.01 0.00 0.00 4.30
994 1107 3.721706 CCAGGCCACAGTCCTCCC 61.722 72.222 5.01 0.00 0.00 4.30
995 1108 2.608988 CAGGCCACAGTCCTCCCT 60.609 66.667 5.01 0.00 0.00 4.20
1019 1138 0.995024 ATGGGGGTGAGTTCCTCTTG 59.005 55.000 0.00 0.00 0.00 3.02
1054 1175 8.704849 TTTTCAGATAAAGAACAGGGAATCAA 57.295 30.769 0.00 0.00 0.00 2.57
1055 1176 8.704849 TTTCAGATAAAGAACAGGGAATCAAA 57.295 30.769 0.00 0.00 0.00 2.69
1056 1177 8.884124 TTCAGATAAAGAACAGGGAATCAAAT 57.116 30.769 0.00 0.00 0.00 2.32
1057 1178 9.973661 TTCAGATAAAGAACAGGGAATCAAATA 57.026 29.630 0.00 0.00 0.00 1.40
1058 1179 9.973661 TCAGATAAAGAACAGGGAATCAAATAA 57.026 29.630 0.00 0.00 0.00 1.40
1061 1182 9.468532 GATAAAGAACAGGGAATCAAATAATGC 57.531 33.333 0.00 0.00 0.00 3.56
1062 1183 5.505173 AGAACAGGGAATCAAATAATGCG 57.495 39.130 0.00 0.00 0.00 4.73
1064 1185 4.900635 ACAGGGAATCAAATAATGCGTC 57.099 40.909 0.00 0.00 0.00 5.19
1080 1209 5.927954 ATGCGTCAAATTTGCATCTTTTT 57.072 30.435 13.54 0.00 45.68 1.94
1116 1254 3.914426 ACAACAACTTGAGACCAGTCT 57.086 42.857 0.00 0.00 43.78 3.24
1129 1267 6.231211 TGAGACCAGTCTTTAGAAATCAACC 58.769 40.000 1.08 0.00 40.61 3.77
1161 1299 2.580322 TCCATGGTAAATGCAGAAGGGA 59.420 45.455 12.58 0.00 0.00 4.20
1166 1304 2.678336 GGTAAATGCAGAAGGGAAGTCG 59.322 50.000 0.00 0.00 0.00 4.18
1167 1305 1.826385 AAATGCAGAAGGGAAGTCGG 58.174 50.000 0.00 0.00 0.00 4.79
1170 1308 0.909610 TGCAGAAGGGAAGTCGGGAT 60.910 55.000 0.00 0.00 0.00 3.85
1177 1315 1.301009 GGAAGTCGGGATGATCGGC 60.301 63.158 0.00 0.00 0.00 5.54
1215 1353 4.145876 TGACATTTTGCTCAACATCGTC 57.854 40.909 0.00 0.00 0.00 4.20
1227 1365 4.143333 ATCGTCGACCGGCTTGGG 62.143 66.667 10.58 0.00 44.64 4.12
1231 1369 1.376812 GTCGACCGGCTTGGGATTT 60.377 57.895 3.51 0.00 44.64 2.17
1237 1375 1.423845 CGGCTTGGGATTTTCGACG 59.576 57.895 0.00 0.00 0.00 5.12
1293 1431 1.301558 GATCCCTGCCATGCTCTCG 60.302 63.158 0.00 0.00 0.00 4.04
1302 1440 1.004504 GCCATGCTCTCGAAAATCGAC 60.005 52.381 0.00 0.00 44.82 4.20
1306 1444 3.230743 TGCTCTCGAAAATCGACATCA 57.769 42.857 0.00 0.00 44.82 3.07
1307 1445 2.923655 TGCTCTCGAAAATCGACATCAC 59.076 45.455 0.00 0.00 44.82 3.06
1322 1460 1.196808 CATCACGGTTGGTTCCTTTCG 59.803 52.381 0.00 0.00 0.00 3.46
1323 1461 0.533308 TCACGGTTGGTTCCTTTCGG 60.533 55.000 0.00 0.00 0.00 4.30
1328 1466 1.901464 TTGGTTCCTTTCGGCTGGC 60.901 57.895 0.00 0.00 0.00 4.85
1363 1501 1.120714 CGTGACGAGTGACGATGTCG 61.121 60.000 9.49 0.11 42.67 4.35
1386 1524 2.203294 GCCAGTTCCACCACCGTT 60.203 61.111 0.00 0.00 0.00 4.44
1390 1528 0.944386 CAGTTCCACCACCGTTGAAG 59.056 55.000 0.00 0.00 0.00 3.02
1391 1529 0.818040 AGTTCCACCACCGTTGAAGC 60.818 55.000 0.00 0.00 0.00 3.86
1395 1533 1.358759 CACCACCGTTGAAGCAACC 59.641 57.895 4.86 0.00 40.82 3.77
1404 1542 1.815003 GTTGAAGCAACCAGGAGGATG 59.185 52.381 0.00 0.00 38.30 3.51
1426 1564 1.006639 TGGAAAATAGGCCCCCAAGTC 59.993 52.381 0.00 0.00 0.00 3.01
1427 1565 1.688311 GGAAAATAGGCCCCCAAGTCC 60.688 57.143 0.00 0.00 0.00 3.85
1432 1570 0.696485 TAGGCCCCCAAGTCCATACC 60.696 60.000 0.00 0.00 0.00 2.73
1442 1580 1.979809 AGTCCATACCCCATTCACCA 58.020 50.000 0.00 0.00 0.00 4.17
1443 1581 1.564348 AGTCCATACCCCATTCACCAC 59.436 52.381 0.00 0.00 0.00 4.16
1455 1593 2.658679 TTCACCACCTGTCCGTGCAG 62.659 60.000 0.00 0.00 36.31 4.41
1536 1674 1.671845 CAAAAGGTTGGTTCGTCCGAA 59.328 47.619 0.00 0.00 39.52 4.30
1542 1680 1.868498 GTTGGTTCGTCCGAATTCACA 59.132 47.619 6.22 1.06 39.52 3.58
1552 1690 5.050227 TCGTCCGAATTCACAATTTTAACGT 60.050 36.000 6.22 0.00 34.10 3.99
1593 1731 3.220110 CACCTATGATGAATTGGCTGCT 58.780 45.455 0.00 0.00 34.78 4.24
1596 1734 4.823989 ACCTATGATGAATTGGCTGCTTAC 59.176 41.667 0.00 0.00 34.78 2.34
1614 1752 4.154347 GGGAGGCAGCTCAGGTCG 62.154 72.222 0.00 0.00 0.00 4.79
1647 1785 2.671619 CCGGTCGCATTTGGTGGT 60.672 61.111 0.00 0.00 0.00 4.16
1689 1827 0.729116 ATTTGACGCTGGCTCAATCG 59.271 50.000 7.75 0.00 0.00 3.34
1713 1851 6.920817 GGATTTCCCGGAAATATTTGGTATC 58.079 40.000 22.84 9.88 41.56 2.24
1828 1966 6.541278 TGAGATTATCAACTGCAGATTTGAGG 59.459 38.462 23.35 0.00 35.25 3.86
1829 1967 5.826737 AGATTATCAACTGCAGATTTGAGGG 59.173 40.000 23.35 0.00 35.25 4.30
1837 1975 1.963515 GCAGATTTGAGGGTGGTGTTT 59.036 47.619 0.00 0.00 0.00 2.83
1885 2023 3.068165 ACTGCTGACTTTTAAAGGTTGGC 59.932 43.478 9.64 16.05 0.00 4.52
1933 2071 4.437587 ATGCCCCACTGCTCCAGC 62.438 66.667 0.00 0.00 42.50 4.85
2007 2145 0.883833 AGATCCTTGGCAAAGCAACG 59.116 50.000 0.00 0.00 31.51 4.10
2035 2173 6.955364 AGTGATCTCCATCTCAATTTCAGAA 58.045 36.000 0.00 0.00 0.00 3.02
2080 2218 4.018050 ACCTCTTGGTCATGCTAATTTCCT 60.018 41.667 0.00 0.00 44.78 3.36
2094 2232 7.946207 TGCTAATTTCCTTTGTTCATGTTGTA 58.054 30.769 0.00 0.00 0.00 2.41
2096 2234 8.915654 GCTAATTTCCTTTGTTCATGTTGTAAG 58.084 33.333 0.00 0.00 0.00 2.34
2099 2237 9.480053 AATTTCCTTTGTTCATGTTGTAAGATG 57.520 29.630 0.00 0.00 0.00 2.90
2100 2238 7.581213 TTCCTTTGTTCATGTTGTAAGATGT 57.419 32.000 0.00 0.00 32.08 3.06
2103 2241 7.284261 TCCTTTGTTCATGTTGTAAGATGTTCA 59.716 33.333 0.00 1.39 32.08 3.18
2104 2242 7.920151 CCTTTGTTCATGTTGTAAGATGTTCAA 59.080 33.333 0.00 6.15 32.08 2.69
2106 2244 9.814899 TTTGTTCATGTTGTAAGATGTTCAAAT 57.185 25.926 15.08 0.00 33.64 2.32
2107 2245 9.462174 TTGTTCATGTTGTAAGATGTTCAAATC 57.538 29.630 0.00 0.00 32.08 2.17
2137 2290 4.096081 GTCTTCATCTTCTGCAGATTTGGG 59.904 45.833 19.04 6.90 40.67 4.12
2179 2332 0.393808 ACTGTGGCAGGTGTTTCGTT 60.394 50.000 0.00 0.00 35.51 3.85
2190 2343 4.025145 CAGGTGTTTCGTTCACTAAAGGTC 60.025 45.833 0.00 0.00 36.25 3.85
2192 2345 2.540931 TGTTTCGTTCACTAAAGGTCGC 59.459 45.455 0.00 0.00 0.00 5.19
2228 2381 8.577048 AACATTTCTGAAGAATGTGATCTGAT 57.423 30.769 8.13 0.00 33.54 2.90
2253 2406 4.019681 TGGACGTTATTCATTCTCCAAGGT 60.020 41.667 0.00 0.00 0.00 3.50
2306 2459 5.350640 AGGTAAACTGTTTGTAGCTAATCGC 59.649 40.000 15.69 0.00 39.57 4.58
2342 2495 2.825205 AGTTGCAAAAGGTGATGTTGC 58.175 42.857 0.00 0.76 46.21 4.17
2350 2503 2.969821 AGGTGATGTTGCCCTGTTTA 57.030 45.000 0.00 0.00 0.00 2.01
2378 2531 6.798315 ATGATGCACATAGTTTAGATGCTC 57.202 37.500 0.00 0.00 37.46 4.26
2380 2533 4.385358 TGCACATAGTTTAGATGCTCGA 57.615 40.909 0.00 0.00 37.20 4.04
2381 2534 4.363138 TGCACATAGTTTAGATGCTCGAG 58.637 43.478 8.45 8.45 37.20 4.04
2384 2537 5.582550 CACATAGTTTAGATGCTCGAGTGA 58.417 41.667 15.13 1.08 0.00 3.41
2386 2539 3.512033 AGTTTAGATGCTCGAGTGACC 57.488 47.619 15.13 0.00 0.00 4.02
2397 2550 1.841663 CGAGTGACCGCCCAAGTTTG 61.842 60.000 0.00 0.00 0.00 2.93
2408 2561 4.041723 CGCCCAAGTTTGTTTCTTGTAAG 58.958 43.478 0.00 0.00 40.15 2.34
2423 2576 8.403236 GTTTCTTGTAAGAACCTTGTGTAATGT 58.597 33.333 6.56 0.00 44.18 2.71
2458 2611 0.632835 ATGGAATGCAGGTGTGGGAT 59.367 50.000 0.00 0.00 0.00 3.85
2476 2629 7.926018 GTGTGGGATAATGTATGCGATATGATA 59.074 37.037 0.00 0.00 0.00 2.15
2477 2630 8.482128 TGTGGGATAATGTATGCGATATGATAA 58.518 33.333 0.00 0.00 0.00 1.75
2506 2659 1.932511 GAAGAGAGGAAGAAGCATGCG 59.067 52.381 13.01 0.00 0.00 4.73
2534 2687 0.391793 GGAGAGGAAGGACAAAGGCG 60.392 60.000 0.00 0.00 0.00 5.52
2821 2974 1.335132 GGATACACTTCCCGGGCTGA 61.335 60.000 18.49 2.81 0.00 4.26
2839 2992 3.557903 AAGTGCCGAGGTGCTGCAT 62.558 57.895 5.27 0.00 38.99 3.96
2844 2997 1.890979 CCGAGGTGCTGCATGGATC 60.891 63.158 5.27 1.05 0.00 3.36
2861 3014 4.211125 TGGATCAAGCTTGTTGTTGGTAA 58.789 39.130 25.19 3.73 0.00 2.85
2897 3050 2.665165 TCAACTTGCTGGGTTGACAAT 58.335 42.857 12.90 0.00 45.14 2.71
3065 3218 9.482627 GATGGAAATTATGTTCACTCCTACTAG 57.517 37.037 0.00 0.00 0.00 2.57
3074 3227 6.999950 TGTTCACTCCTACTAGCATTTGTTA 58.000 36.000 0.00 0.00 0.00 2.41
3117 3270 6.095432 TGGTGGTGTATTTTGAAATTGGAG 57.905 37.500 0.00 0.00 0.00 3.86
3120 3273 5.856455 GTGGTGTATTTTGAAATTGGAGTCG 59.144 40.000 0.00 0.00 0.00 4.18
3143 3296 5.334414 CGCTGGTAATTTATGCTTCATCCTC 60.334 44.000 0.00 0.00 0.00 3.71
3161 3314 3.149196 CCTCATTTGCCTGTAGTTGTGT 58.851 45.455 0.00 0.00 0.00 3.72
3231 3384 2.435372 TCTGTGTTCAGTTTTGCCCT 57.565 45.000 0.00 0.00 41.91 5.19
3590 3744 5.174943 GCTTTACCTGATTTGTCGGTTTTTG 59.825 40.000 0.00 0.00 32.36 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 4.838152 GGCGCGCCTTCTCCATCA 62.838 66.667 41.71 0.00 0.00 3.07
297 307 1.446099 GAAGTCGTCGCTGCCATCA 60.446 57.895 0.00 0.00 0.00 3.07
343 357 8.327429 CAAATTCGCCCATTTTCATTACATTAC 58.673 33.333 0.00 0.00 0.00 1.89
381 396 8.827177 AGTAGTTAAATTTCGTCTGAACATGA 57.173 30.769 0.00 0.00 32.71 3.07
555 579 3.044894 CCTTCTTCCTAAGGGCATCTCT 58.955 50.000 0.00 0.00 42.08 3.10
556 580 3.483808 CCTTCTTCCTAAGGGCATCTC 57.516 52.381 0.00 0.00 42.08 2.75
563 587 2.022918 TCTCTCCCCCTTCTTCCTAAGG 60.023 54.545 0.00 0.00 44.87 2.69
564 588 3.035363 GTCTCTCCCCCTTCTTCCTAAG 58.965 54.545 0.00 0.00 0.00 2.18
565 589 2.660556 AGTCTCTCCCCCTTCTTCCTAA 59.339 50.000 0.00 0.00 0.00 2.69
566 590 2.023888 CAGTCTCTCCCCCTTCTTCCTA 60.024 54.545 0.00 0.00 0.00 2.94
567 591 1.097722 AGTCTCTCCCCCTTCTTCCT 58.902 55.000 0.00 0.00 0.00 3.36
568 592 1.199615 CAGTCTCTCCCCCTTCTTCC 58.800 60.000 0.00 0.00 0.00 3.46
569 593 1.199615 CCAGTCTCTCCCCCTTCTTC 58.800 60.000 0.00 0.00 0.00 2.87
570 594 0.252927 CCCAGTCTCTCCCCCTTCTT 60.253 60.000 0.00 0.00 0.00 2.52
571 595 1.394151 CCCAGTCTCTCCCCCTTCT 59.606 63.158 0.00 0.00 0.00 2.85
572 596 1.690985 CCCCAGTCTCTCCCCCTTC 60.691 68.421 0.00 0.00 0.00 3.46
573 597 2.456840 CCCCAGTCTCTCCCCCTT 59.543 66.667 0.00 0.00 0.00 3.95
574 598 3.700350 CCCCCAGTCTCTCCCCCT 61.700 72.222 0.00 0.00 0.00 4.79
575 599 4.026357 ACCCCCAGTCTCTCCCCC 62.026 72.222 0.00 0.00 0.00 5.40
576 600 2.689034 CACCCCCAGTCTCTCCCC 60.689 72.222 0.00 0.00 0.00 4.81
577 601 1.687493 CTCACCCCCAGTCTCTCCC 60.687 68.421 0.00 0.00 0.00 4.30
578 602 0.686112 CTCTCACCCCCAGTCTCTCC 60.686 65.000 0.00 0.00 0.00 3.71
579 603 0.333312 TCTCTCACCCCCAGTCTCTC 59.667 60.000 0.00 0.00 0.00 3.20
580 604 1.014804 ATCTCTCACCCCCAGTCTCT 58.985 55.000 0.00 0.00 0.00 3.10
581 605 1.118838 CATCTCTCACCCCCAGTCTC 58.881 60.000 0.00 0.00 0.00 3.36
582 606 0.980231 GCATCTCTCACCCCCAGTCT 60.980 60.000 0.00 0.00 0.00 3.24
583 607 1.524482 GCATCTCTCACCCCCAGTC 59.476 63.158 0.00 0.00 0.00 3.51
584 608 2.362369 CGCATCTCTCACCCCCAGT 61.362 63.158 0.00 0.00 0.00 4.00
585 609 2.503061 CGCATCTCTCACCCCCAG 59.497 66.667 0.00 0.00 0.00 4.45
586 610 3.785859 GCGCATCTCTCACCCCCA 61.786 66.667 0.30 0.00 0.00 4.96
587 611 4.554036 GGCGCATCTCTCACCCCC 62.554 72.222 10.83 0.00 0.00 5.40
588 612 4.899239 CGGCGCATCTCTCACCCC 62.899 72.222 10.83 0.00 0.00 4.95
589 613 4.899239 CCGGCGCATCTCTCACCC 62.899 72.222 10.83 0.00 0.00 4.61
614 638 3.134127 GCGGGGAGACAATGGCAC 61.134 66.667 0.00 0.00 0.00 5.01
615 639 4.776322 CGCGGGGAGACAATGGCA 62.776 66.667 0.00 0.00 0.00 4.92
616 640 4.467084 TCGCGGGGAGACAATGGC 62.467 66.667 6.13 0.00 0.00 4.40
617 641 2.202932 CTCGCGGGGAGACAATGG 60.203 66.667 16.33 0.00 46.23 3.16
618 642 2.892425 GCTCGCGGGGAGACAATG 60.892 66.667 24.34 0.00 46.23 2.82
631 655 0.943359 GATTCTCATGCGGAGGCTCG 60.943 60.000 8.69 5.22 44.19 5.03
632 656 0.602372 GGATTCTCATGCGGAGGCTC 60.602 60.000 5.78 5.78 44.19 4.70
633 657 1.340399 TGGATTCTCATGCGGAGGCT 61.340 55.000 5.48 0.00 44.19 4.58
634 658 0.883814 CTGGATTCTCATGCGGAGGC 60.884 60.000 5.48 0.00 44.19 4.70
635 659 0.467384 ACTGGATTCTCATGCGGAGG 59.533 55.000 5.48 0.00 44.19 4.30
636 660 1.579698 CACTGGATTCTCATGCGGAG 58.420 55.000 0.00 0.00 45.49 4.63
637 661 0.178767 CCACTGGATTCTCATGCGGA 59.821 55.000 0.00 0.00 31.52 5.54
638 662 0.107508 ACCACTGGATTCTCATGCGG 60.108 55.000 0.71 0.00 33.30 5.69
639 663 1.012086 CACCACTGGATTCTCATGCG 58.988 55.000 0.71 0.00 0.00 4.73
640 664 0.737219 GCACCACTGGATTCTCATGC 59.263 55.000 0.71 0.00 0.00 4.06
641 665 2.414994 AGCACCACTGGATTCTCATG 57.585 50.000 0.71 0.00 0.00 3.07
647 671 2.952714 GCTCAAGCACCACTGGATT 58.047 52.632 0.71 0.00 41.59 3.01
665 689 1.094073 CCTCTGATTTGGCGCCTCTG 61.094 60.000 29.70 20.02 0.00 3.35
673 697 2.746362 GACTGCAACTCCTCTGATTTGG 59.254 50.000 0.00 0.00 33.15 3.28
675 699 2.290577 GGGACTGCAACTCCTCTGATTT 60.291 50.000 9.45 0.00 0.00 2.17
678 702 1.194781 GGGGACTGCAACTCCTCTGA 61.195 60.000 9.45 0.00 0.00 3.27
679 703 1.298014 GGGGACTGCAACTCCTCTG 59.702 63.158 9.45 0.00 0.00 3.35
681 705 0.329596 ATTGGGGACTGCAACTCCTC 59.670 55.000 10.26 6.97 0.00 3.71
682 706 0.329596 GATTGGGGACTGCAACTCCT 59.670 55.000 10.26 0.00 0.00 3.69
687 725 0.960364 GCTTCGATTGGGGACTGCAA 60.960 55.000 0.00 0.00 0.00 4.08
695 733 1.989966 CTGCTGCTGCTTCGATTGGG 61.990 60.000 17.00 0.00 40.48 4.12
716 754 3.071580 GCTGCTTGATTACGGAGCT 57.928 52.632 0.35 0.00 40.81 4.09
717 755 0.933796 GAGCTGCTTGATTACGGAGC 59.066 55.000 2.53 0.00 43.80 4.70
719 757 2.299993 CAGAGCTGCTTGATTACGGA 57.700 50.000 2.53 0.00 0.00 4.69
754 792 2.533266 CGCTTGATTTCTTGGATTGCC 58.467 47.619 0.00 0.00 0.00 4.52
760 798 0.453390 GGAGCCGCTTGATTTCTTGG 59.547 55.000 0.00 0.00 0.00 3.61
761 799 1.399791 GAGGAGCCGCTTGATTTCTTG 59.600 52.381 0.00 0.00 0.00 3.02
762 800 1.280421 AGAGGAGCCGCTTGATTTCTT 59.720 47.619 0.00 0.00 0.00 2.52
763 801 0.908198 AGAGGAGCCGCTTGATTTCT 59.092 50.000 0.00 0.00 0.00 2.52
764 802 1.294857 GAGAGGAGCCGCTTGATTTC 58.705 55.000 0.00 0.00 0.00 2.17
765 803 0.107459 GGAGAGGAGCCGCTTGATTT 60.107 55.000 0.00 0.00 0.00 2.17
766 804 1.524482 GGAGAGGAGCCGCTTGATT 59.476 57.895 0.00 0.00 0.00 2.57
767 805 2.790791 CGGAGAGGAGCCGCTTGAT 61.791 63.158 0.00 0.00 42.55 2.57
768 806 3.452786 CGGAGAGGAGCCGCTTGA 61.453 66.667 0.00 0.00 42.55 3.02
809 847 0.519077 CTGCGACAAGAAAAGGGAGC 59.481 55.000 0.00 0.00 0.00 4.70
814 852 0.512952 CCGGACTGCGACAAGAAAAG 59.487 55.000 0.00 0.00 0.00 2.27
819 857 0.389817 TGATTCCGGACTGCGACAAG 60.390 55.000 1.83 0.00 0.00 3.16
820 858 0.034198 TTGATTCCGGACTGCGACAA 59.966 50.000 1.83 1.83 0.00 3.18
821 859 0.034198 TTTGATTCCGGACTGCGACA 59.966 50.000 1.83 0.00 0.00 4.35
825 863 0.449388 CTGCTTTGATTCCGGACTGC 59.551 55.000 1.83 0.00 0.00 4.40
828 866 1.087501 GGACTGCTTTGATTCCGGAC 58.912 55.000 1.83 0.00 0.00 4.79
835 873 0.035056 CCGGGAAGGACTGCTTTGAT 60.035 55.000 0.00 0.00 45.00 2.57
850 888 0.815615 GCTTCTGATTGTAGCCCGGG 60.816 60.000 19.09 19.09 33.67 5.73
851 889 0.107703 TGCTTCTGATTGTAGCCCGG 60.108 55.000 0.00 0.00 38.15 5.73
852 890 1.293924 CTGCTTCTGATTGTAGCCCG 58.706 55.000 0.00 0.00 38.15 6.13
855 893 2.093235 AGGACCTGCTTCTGATTGTAGC 60.093 50.000 0.00 0.00 39.19 3.58
856 894 3.055530 ACAGGACCTGCTTCTGATTGTAG 60.056 47.826 21.95 0.00 34.37 2.74
858 896 1.701847 ACAGGACCTGCTTCTGATTGT 59.298 47.619 21.95 0.00 34.37 2.71
868 906 2.151202 TGAATTCGAAACAGGACCTGC 58.849 47.619 21.95 4.44 34.37 4.85
873 911 3.614150 CGGAGACTGAATTCGAAACAGGA 60.614 47.826 27.10 0.00 36.17 3.86
889 927 2.412089 CGACCAATGAAAACTCGGAGAC 59.588 50.000 12.86 1.18 0.00 3.36
891 929 1.732259 CCGACCAATGAAAACTCGGAG 59.268 52.381 2.83 2.83 45.58 4.63
909 947 2.351726 CGTCTCCTCTTAAAATTGGCCG 59.648 50.000 0.00 0.00 0.00 6.13
917 1007 1.549170 GGTGGCTCGTCTCCTCTTAAA 59.451 52.381 0.00 0.00 0.00 1.52
920 1010 1.228894 TGGTGGCTCGTCTCCTCTT 60.229 57.895 0.00 0.00 0.00 2.85
921 1011 1.680651 CTGGTGGCTCGTCTCCTCT 60.681 63.158 0.00 0.00 0.00 3.69
935 1048 1.821216 CCGTAAATCTGTTGGCTGGT 58.179 50.000 0.00 0.00 0.00 4.00
936 1049 0.451783 GCCGTAAATCTGTTGGCTGG 59.548 55.000 0.00 0.00 42.44 4.85
941 1054 0.368907 CGGTCGCCGTAAATCTGTTG 59.631 55.000 9.69 0.00 42.73 3.33
942 1055 0.738412 CCGGTCGCCGTAAATCTGTT 60.738 55.000 15.38 0.00 46.80 3.16
943 1056 1.153706 CCGGTCGCCGTAAATCTGT 60.154 57.895 15.38 0.00 46.80 3.41
946 1059 2.202837 AGCCGGTCGCCGTAAATC 60.203 61.111 15.38 2.13 46.80 2.17
964 1077 2.105128 CCTGGCCGTCGATCTGAC 59.895 66.667 0.00 7.40 44.53 3.51
966 1079 4.899239 GGCCTGGCCGTCGATCTG 62.899 72.222 24.16 0.00 39.62 2.90
976 1089 4.416738 GGAGGACTGTGGCCTGGC 62.417 72.222 11.05 11.05 35.44 4.85
977 1090 2.822643 TAGGGAGGACTGTGGCCTGG 62.823 65.000 3.32 0.00 35.44 4.45
978 1091 1.306141 TAGGGAGGACTGTGGCCTG 60.306 63.158 3.32 0.00 35.44 4.85
979 1092 1.002274 CTAGGGAGGACTGTGGCCT 59.998 63.158 3.32 0.00 38.81 5.19
982 1095 0.692419 ATGGCTAGGGAGGACTGTGG 60.692 60.000 0.00 0.00 0.00 4.17
983 1096 0.467384 CATGGCTAGGGAGGACTGTG 59.533 60.000 0.00 0.00 0.00 3.66
984 1097 0.692419 CCATGGCTAGGGAGGACTGT 60.692 60.000 0.00 0.00 0.00 3.55
985 1098 2.140405 CCATGGCTAGGGAGGACTG 58.860 63.158 0.00 0.00 0.00 3.51
993 1106 1.281925 AACTCACCCCCATGGCTAGG 61.282 60.000 6.09 9.23 37.83 3.02
994 1107 0.181350 GAACTCACCCCCATGGCTAG 59.819 60.000 6.09 0.00 37.83 3.42
995 1108 1.279025 GGAACTCACCCCCATGGCTA 61.279 60.000 6.09 0.00 37.83 3.93
1041 1162 5.163663 TGACGCATTATTTGATTCCCTGTTC 60.164 40.000 0.00 0.00 0.00 3.18
1047 1168 6.901357 GCAAATTTGACGCATTATTTGATTCC 59.099 34.615 22.31 0.00 39.26 3.01
1054 1175 7.599630 AAAGATGCAAATTTGACGCATTATT 57.400 28.000 22.31 12.91 46.01 1.40
1055 1176 7.599630 AAAAGATGCAAATTTGACGCATTAT 57.400 28.000 22.31 8.22 46.01 1.28
1056 1177 7.418840 AAAAAGATGCAAATTTGACGCATTA 57.581 28.000 22.31 0.00 46.01 1.90
1057 1178 5.927954 AAAAGATGCAAATTTGACGCATT 57.072 30.435 22.31 7.60 46.01 3.56
1098 1236 6.235231 TCTAAAGACTGGTCTCAAGTTGTT 57.765 37.500 2.11 0.00 39.39 2.83
1099 1237 5.871396 TCTAAAGACTGGTCTCAAGTTGT 57.129 39.130 2.11 0.00 39.39 3.32
1100 1238 7.442364 TGATTTCTAAAGACTGGTCTCAAGTTG 59.558 37.037 3.60 0.00 39.39 3.16
1102 1240 7.067496 TGATTTCTAAAGACTGGTCTCAAGT 57.933 36.000 3.60 0.00 39.39 3.16
1103 1241 7.095017 GGTTGATTTCTAAAGACTGGTCTCAAG 60.095 40.741 3.60 5.14 39.39 3.02
1105 1243 6.231211 GGTTGATTTCTAAAGACTGGTCTCA 58.769 40.000 3.60 0.00 39.39 3.27
1161 1299 1.043116 TCAGCCGATCATCCCGACTT 61.043 55.000 0.00 0.00 0.00 3.01
1166 1304 0.883814 CTTGCTCAGCCGATCATCCC 60.884 60.000 0.00 0.00 0.00 3.85
1167 1305 0.179062 ACTTGCTCAGCCGATCATCC 60.179 55.000 0.00 0.00 0.00 3.51
1170 1308 1.300971 GCAACTTGCTCAGCCGATCA 61.301 55.000 6.50 0.00 40.96 2.92
1177 1315 0.674581 TCATCGGGCAACTTGCTCAG 60.675 55.000 14.09 6.77 46.28 3.35
1215 1353 1.800681 GAAAATCCCAAGCCGGTCG 59.199 57.895 1.90 0.00 0.00 4.79
1227 1365 1.525185 GCTCTTGCGACGTCGAAAATC 60.525 52.381 39.74 22.23 43.02 2.17
1231 1369 2.430244 GGCTCTTGCGACGTCGAA 60.430 61.111 39.74 29.65 43.02 3.71
1237 1375 2.817396 GGAGCTGGCTCTTGCGAC 60.817 66.667 19.92 1.27 42.38 5.19
1246 1384 1.228552 TTTTGGACAGGGAGCTGGC 60.229 57.895 0.00 0.00 0.00 4.85
1293 1431 2.482721 ACCAACCGTGATGTCGATTTTC 59.517 45.455 0.00 0.00 0.00 2.29
1302 1440 1.196808 CGAAAGGAACCAACCGTGATG 59.803 52.381 0.00 0.00 34.73 3.07
1322 1460 1.968540 GACCTGTCTTGTGCCAGCC 60.969 63.158 0.00 0.00 0.00 4.85
1323 1461 1.968540 GGACCTGTCTTGTGCCAGC 60.969 63.158 0.00 0.00 0.00 4.85
1328 1466 0.937304 CACGTTGGACCTGTCTTGTG 59.063 55.000 0.00 0.00 0.00 3.33
1363 1501 1.525077 TGGTGGAACTGGCACGAAC 60.525 57.895 0.00 0.00 36.74 3.95
1386 1524 3.963733 CATCCTCCTGGTTGCTTCA 57.036 52.632 0.00 0.00 34.23 3.02
1391 1529 4.651867 CCAGCATCCTCCTGGTTG 57.348 61.111 0.00 0.00 43.86 3.77
1395 1533 3.484407 CCTATTTTCCAGCATCCTCCTG 58.516 50.000 0.00 0.00 0.00 3.86
1404 1542 0.325203 TTGGGGGCCTATTTTCCAGC 60.325 55.000 0.84 0.00 0.00 4.85
1413 1551 0.696485 GGTATGGACTTGGGGGCCTA 60.696 60.000 0.84 0.00 45.52 3.93
1426 1564 0.926293 AGGTGGTGAATGGGGTATGG 59.074 55.000 0.00 0.00 0.00 2.74
1427 1565 1.284785 ACAGGTGGTGAATGGGGTATG 59.715 52.381 0.00 0.00 0.00 2.39
1432 1570 1.377202 CGGACAGGTGGTGAATGGG 60.377 63.158 0.00 0.00 0.00 4.00
1442 1580 1.623811 AGAATAACTGCACGGACAGGT 59.376 47.619 11.10 7.24 42.21 4.00
1443 1581 2.386661 AGAATAACTGCACGGACAGG 57.613 50.000 11.10 0.00 42.21 4.00
1455 1593 7.446001 GATGGAATCATCTCCCAAGAATAAC 57.554 40.000 0.00 0.00 44.70 1.89
1502 1640 2.035832 ACCTTTTGTGTTGCCATAGTGC 59.964 45.455 0.00 0.00 0.00 4.40
1536 1674 8.026607 CCATCCTTGTACGTTAAAATTGTGAAT 58.973 33.333 0.00 0.00 0.00 2.57
1542 1680 5.105917 CCTGCCATCCTTGTACGTTAAAATT 60.106 40.000 0.00 0.00 0.00 1.82
1552 1690 2.378038 GCATTTCCTGCCATCCTTGTA 58.622 47.619 0.00 0.00 45.66 2.41
1585 1723 2.668632 CCTCCCGTAAGCAGCCAA 59.331 61.111 0.00 0.00 0.00 4.52
1593 1731 2.359169 CCTGAGCTGCCTCCCGTAA 61.359 63.158 0.00 0.00 37.29 3.18
1596 1734 4.154347 GACCTGAGCTGCCTCCCG 62.154 72.222 0.00 0.00 37.29 5.14
1614 1752 0.667184 CCGGGCAAGCATCAACAAAC 60.667 55.000 0.00 0.00 0.00 2.93
1638 1776 0.889186 GGCGTGTGAGACCACCAAAT 60.889 55.000 0.00 0.00 42.53 2.32
1689 1827 6.719829 AGATACCAAATATTTCCGGGAAATCC 59.280 38.462 32.38 14.36 40.77 3.01
1698 1836 7.939588 AGCCTCTTACAGATACCAAATATTTCC 59.060 37.037 0.00 0.00 0.00 3.13
1713 1851 2.183679 AGGAACTCCAGCCTCTTACAG 58.816 52.381 0.00 0.00 38.89 2.74
1785 1923 1.202806 TCAAGTTGGCTGAGTTGAGGG 60.203 52.381 2.34 0.00 34.83 4.30
1828 1966 3.763897 AGCCATTTCAGATAAACACCACC 59.236 43.478 0.00 0.00 0.00 4.61
1829 1967 5.163652 GGTAGCCATTTCAGATAAACACCAC 60.164 44.000 0.00 0.00 0.00 4.16
1902 2040 0.249657 GGGCATGACCAACGCAAAAA 60.250 50.000 14.59 0.00 42.05 1.94
1965 2103 5.610398 TCACTTAACTTGAGCATCTTGTGA 58.390 37.500 0.00 0.00 34.92 3.58
2007 2145 8.899427 TGAAATTGAGATGGAGATCACTTATC 57.101 34.615 0.00 0.00 34.52 1.75
2035 2173 0.534203 TCCTCGCAAACCTTTTCGCT 60.534 50.000 0.00 0.00 0.00 4.93
2078 2216 7.424803 TGAACATCTTACAACATGAACAAAGG 58.575 34.615 0.00 0.00 0.00 3.11
2080 2218 9.814899 ATTTGAACATCTTACAACATGAACAAA 57.185 25.926 0.00 0.00 35.47 2.83
2103 2241 9.017509 TGCAGAAGATGAAGACAATTAAGATTT 57.982 29.630 0.00 0.00 0.00 2.17
2104 2242 8.571461 TGCAGAAGATGAAGACAATTAAGATT 57.429 30.769 0.00 0.00 0.00 2.40
2106 2244 7.389232 TCTGCAGAAGATGAAGACAATTAAGA 58.611 34.615 15.67 0.00 38.82 2.10
2107 2245 7.606858 TCTGCAGAAGATGAAGACAATTAAG 57.393 36.000 15.67 0.00 38.82 1.85
2110 2248 7.313646 CAAATCTGCAGAAGATGAAGACAATT 58.686 34.615 22.50 2.26 46.94 2.32
2111 2249 6.127703 CCAAATCTGCAGAAGATGAAGACAAT 60.128 38.462 22.50 0.00 46.94 2.71
2121 2274 4.522789 GGTTTAACCCAAATCTGCAGAAGA 59.477 41.667 22.50 0.00 33.47 2.87
2125 2278 3.826157 TCTGGTTTAACCCAAATCTGCAG 59.174 43.478 12.02 7.63 37.50 4.41
2161 2314 0.307760 GAACGAAACACCTGCCACAG 59.692 55.000 0.00 0.00 0.00 3.66
2179 2332 2.400399 CAAAGTCGCGACCTTTAGTGA 58.600 47.619 34.08 0.00 0.00 3.41
2190 2343 4.092821 TCAGAAATGTTATCCAAAGTCGCG 59.907 41.667 0.00 0.00 0.00 5.87
2192 2345 7.364522 TCTTCAGAAATGTTATCCAAAGTCG 57.635 36.000 0.00 0.00 0.00 4.18
2228 2381 5.414454 CCTTGGAGAATGAATAACGTCCAAA 59.586 40.000 3.40 0.00 42.14 3.28
2304 2457 3.626028 ACTTTAACAAGAGCTTTGGCG 57.374 42.857 11.59 0.00 37.19 5.69
2306 2459 4.681744 TGCAACTTTAACAAGAGCTTTGG 58.318 39.130 11.59 0.00 36.31 3.28
2342 2495 8.632679 ACTATGTGCATCATATTTTAAACAGGG 58.367 33.333 8.72 0.00 38.21 4.45
2350 2503 9.903682 GCATCTAAACTATGTGCATCATATTTT 57.096 29.630 18.82 18.82 41.44 1.82
2378 2531 1.597027 AAACTTGGGCGGTCACTCG 60.597 57.895 0.00 0.00 0.00 4.18
2380 2533 0.395173 AACAAACTTGGGCGGTCACT 60.395 50.000 0.00 0.00 0.00 3.41
2381 2534 0.458260 AAACAAACTTGGGCGGTCAC 59.542 50.000 0.00 0.00 0.00 3.67
2384 2537 1.136110 CAAGAAACAAACTTGGGCGGT 59.864 47.619 0.00 0.00 40.39 5.68
2386 2539 2.577449 ACAAGAAACAAACTTGGGCG 57.423 45.000 0.00 0.00 45.92 6.13
2408 2561 8.760569 CAAAAACCATAACATTACACAAGGTTC 58.239 33.333 0.00 0.00 39.28 3.62
2423 2576 4.982241 TTCCATTGGGCAAAAACCATAA 57.018 36.364 2.09 0.00 37.93 1.90
2476 2629 5.205517 TCTTCCTCTCTTCCTCATCTCTT 57.794 43.478 0.00 0.00 0.00 2.85
2477 2630 4.879295 TCTTCCTCTCTTCCTCATCTCT 57.121 45.455 0.00 0.00 0.00 3.10
2482 2635 2.894731 TGCTTCTTCCTCTCTTCCTCA 58.105 47.619 0.00 0.00 0.00 3.86
2506 2659 2.100989 TCCTTCCTCTCCTCGCTAAAC 58.899 52.381 0.00 0.00 0.00 2.01
2534 2687 1.298014 CCAGTCCTTCCCACTCTGC 59.702 63.158 0.00 0.00 0.00 4.26
2749 2902 0.532573 TCCTCACCGACATCTTCTGC 59.467 55.000 0.00 0.00 0.00 4.26
2821 2974 4.254709 TGCAGCACCTCGGCACTT 62.255 61.111 0.00 0.00 40.89 3.16
2839 2992 2.665165 ACCAACAACAAGCTTGATCCA 58.335 42.857 32.50 0.00 0.00 3.41
2897 3050 4.824479 TGATTATTGCAGTGACCTCAGA 57.176 40.909 0.00 0.00 0.00 3.27
3065 3218 4.439305 TGCTCCAAGTGATAACAAATGC 57.561 40.909 0.00 0.00 0.00 3.56
3074 3227 5.824624 CACCATAGTTATTGCTCCAAGTGAT 59.175 40.000 0.00 0.00 0.00 3.06
3113 3266 3.118408 AGCATAAATTACCAGCGACTCCA 60.118 43.478 0.00 0.00 0.00 3.86
3114 3267 3.467803 AGCATAAATTACCAGCGACTCC 58.532 45.455 0.00 0.00 0.00 3.85
3117 3270 4.875544 TGAAGCATAAATTACCAGCGAC 57.124 40.909 0.00 0.00 0.00 5.19
3120 3273 5.532406 TGAGGATGAAGCATAAATTACCAGC 59.468 40.000 0.00 0.00 0.00 4.85
3143 3296 4.043750 CACAACACAACTACAGGCAAATG 58.956 43.478 0.00 0.00 0.00 2.32
3161 3314 7.042992 CGTCAAGATAATAATCGGCTAACACAA 60.043 37.037 0.00 0.00 37.19 3.33
3614 3768 7.747155 AAACCTTCTAGAACTTCCTAAAAGC 57.253 36.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.