Multiple sequence alignment - TraesCS3B01G538700

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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 TraesCS3B01G538700 chr3B 100.000 2981 0 0 1 2981 778431118 778434098 0.000000e+00 5505.0
1 TraesCS3B01G538700 chr3B 91.186 1509 78 20 1512 2981 778392966 778394458 0.000000e+00 1999.0
2 TraesCS3B01G538700 chr3B 88.738 959 68 12 1476 2415 778443006 778443943 0.000000e+00 1136.0
3 TraesCS3B01G538700 chr3B 95.841 577 19 4 2410 2981 778443963 778444539 0.000000e+00 928.0
4 TraesCS3B01G538700 chr3B 90.071 705 36 6 1 693 778380225 778380907 0.000000e+00 883.0
5 TraesCS3B01G538700 chr3B 98.423 444 7 0 912 1355 778392234 778392677 0.000000e+00 782.0
6 TraesCS3B01G538700 chr3B 96.000 475 19 0 912 1386 778403815 778404289 0.000000e+00 773.0
7 TraesCS3B01G538700 chr3B 92.727 495 32 2 912 1404 778442417 778442909 0.000000e+00 712.0
8 TraesCS3B01G538700 chr3B 88.060 603 57 9 1476 2068 778404485 778405082 0.000000e+00 701.0
9 TraesCS3B01G538700 chr3B 81.250 320 57 3 1691 2008 776120871 776120553 3.810000e-64 255.0
10 TraesCS3B01G538700 chr3B 95.935 123 5 0 686 808 778386104 778386226 1.810000e-47 200.0
11 TraesCS3B01G538700 chr3B 79.286 140 15 5 1806 1944 775972557 775972431 5.290000e-13 86.1
12 TraesCS3B01G538700 chr3B 97.368 38 1 0 1349 1386 778392697 778392734 6.900000e-07 65.8
13 TraesCS3B01G538700 chr3D 76.550 516 102 13 1599 2100 580587230 580586720 6.340000e-67 265.0
14 TraesCS3B01G538700 chr3A 79.439 321 63 3 1689 2007 716097690 716097371 1.080000e-54 224.0
15 TraesCS3B01G538700 chr3A 93.258 89 5 1 816 903 644809206 644809118 2.410000e-26 130.0
16 TraesCS3B01G538700 chr1B 97.531 81 2 0 816 896 657408868 657408948 4.010000e-29 139.0
17 TraesCS3B01G538700 chr1B 97.468 79 2 0 816 894 308586742 308586664 5.180000e-28 135.0
18 TraesCS3B01G538700 chr1B 86.667 120 15 1 515 634 8788288 8788170 6.700000e-27 132.0
19 TraesCS3B01G538700 chr5A 93.407 91 6 0 817 907 68933029 68932939 5.180000e-28 135.0
20 TraesCS3B01G538700 chr2B 97.468 79 2 0 816 894 512174754 512174676 5.180000e-28 135.0
21 TraesCS3B01G538700 chr5B 93.407 91 5 1 816 906 411518850 411518939 1.860000e-27 134.0
22 TraesCS3B01G538700 chr5B 91.753 97 5 2 816 912 703263484 703263391 6.700000e-27 132.0
23 TraesCS3B01G538700 chr2A 93.182 88 6 0 806 893 275932382 275932295 2.410000e-26 130.0
24 TraesCS3B01G538700 chr2D 91.579 95 4 2 816 910 619720623 619720533 8.670000e-26 128.0


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 TraesCS3B01G538700 chr3B 778431118 778434098 2980 False 5505.000000 5505 100.000000 1 2981 1 chr3B.!!$F3 2980
1 TraesCS3B01G538700 chr3B 778392234 778394458 2224 False 948.933333 1999 95.659000 912 2981 3 chr3B.!!$F4 2069
2 TraesCS3B01G538700 chr3B 778442417 778444539 2122 False 925.333333 1136 92.435333 912 2981 3 chr3B.!!$F6 2069
3 TraesCS3B01G538700 chr3B 778380225 778380907 682 False 883.000000 883 90.071000 1 693 1 chr3B.!!$F1 692
4 TraesCS3B01G538700 chr3B 778403815 778405082 1267 False 737.000000 773 92.030000 912 2068 2 chr3B.!!$F5 1156
5 TraesCS3B01G538700 chr3D 580586720 580587230 510 True 265.000000 265 76.550000 1599 2100 1 chr3D.!!$R1 501

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
693 706 0.034896 TCCACGAAAGGAAGAGGTGC 59.965 55.0 0.0 0.0 33.93 5.01 F
694 707 0.035458 CCACGAAAGGAAGAGGTGCT 59.965 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2041 0.321298 GTCCGGCAAGCACTCCTTAA 60.321 55.0 0.0 0.0 31.0 1.85 R
2052 2241 0.396060 CAGCAGCTCCCCCTTATCTC 59.604 60.0 0.0 0.0 0.0 2.75 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 32 7.934855 TCATCTAGTACGGTTTACTTCTTCT 57.065 36.000 0.00 0.00 0.00 2.85
34 35 7.150783 TCTAGTACGGTTTACTTCTTCTTCC 57.849 40.000 0.00 0.00 0.00 3.46
60 61 9.006215 CAGTAACTATAAAATAAAAACGGCAGC 57.994 33.333 0.00 0.00 0.00 5.25
114 127 1.438651 TAGCGAGCCACACAACAATC 58.561 50.000 0.00 0.00 0.00 2.67
127 140 4.747108 ACACAACAATCAGCGATAGATAGC 59.253 41.667 0.00 0.00 39.76 2.97
141 154 2.819115 AGATAGCGAGCATCAACACTG 58.181 47.619 0.00 0.00 33.17 3.66
198 211 8.900511 ATTTCACAATGTTGATGTATTCTTCG 57.099 30.769 0.00 0.00 0.00 3.79
253 266 4.586001 ACTTCAAAGTCACGTACCTTCCTA 59.414 41.667 0.00 0.00 32.86 2.94
336 349 0.745845 ACGCTGATGCATCCAAGGTC 60.746 55.000 23.67 0.00 39.64 3.85
337 350 1.769098 CGCTGATGCATCCAAGGTCG 61.769 60.000 23.67 13.06 39.64 4.79
341 354 0.462581 GATGCATCCAAGGTCGAGCA 60.463 55.000 16.23 5.73 36.34 4.26
360 373 2.287788 GCAGTTGTGTATGTGCTTGCTT 60.288 45.455 0.00 0.00 32.97 3.91
363 376 5.702865 CAGTTGTGTATGTGCTTGCTTTAT 58.297 37.500 0.00 0.00 0.00 1.40
369 382 5.572896 GTGTATGTGCTTGCTTTATCAAACC 59.427 40.000 0.00 0.00 0.00 3.27
376 389 3.644966 TGCTTTATCAAACCGGGAGAT 57.355 42.857 6.32 8.62 0.00 2.75
379 392 5.690865 TGCTTTATCAAACCGGGAGATAAT 58.309 37.500 19.51 4.55 0.00 1.28
380 393 5.763204 TGCTTTATCAAACCGGGAGATAATC 59.237 40.000 19.51 15.81 0.00 1.75
395 408 7.765695 GGAGATAATCCCTGCATAAATGAAA 57.234 36.000 0.00 0.00 43.01 2.69
396 409 8.358582 GGAGATAATCCCTGCATAAATGAAAT 57.641 34.615 0.00 0.00 43.01 2.17
397 410 8.465201 GGAGATAATCCCTGCATAAATGAAATC 58.535 37.037 0.00 0.00 43.01 2.17
398 411 9.240734 GAGATAATCCCTGCATAAATGAAATCT 57.759 33.333 0.00 0.00 0.00 2.40
399 412 9.240734 AGATAATCCCTGCATAAATGAAATCTC 57.759 33.333 0.00 0.00 0.00 2.75
444 457 8.148351 ACTACTACTCTAGAAAATGCAACAACA 58.852 33.333 0.00 0.00 0.00 3.33
445 458 7.986085 ACTACTCTAGAAAATGCAACAACAT 57.014 32.000 0.00 0.00 0.00 2.71
586 599 2.421107 CCATGATGGTAGTTGCAGAGCT 60.421 50.000 2.54 0.00 31.35 4.09
588 601 2.182827 TGATGGTAGTTGCAGAGCTCT 58.817 47.619 11.45 11.45 0.00 4.09
598 611 1.079543 CAGAGCTCTCACCCAACCG 60.080 63.158 14.96 0.00 0.00 4.44
601 614 0.250513 GAGCTCTCACCCAACCGAAT 59.749 55.000 6.43 0.00 0.00 3.34
608 621 1.165270 CACCCAACCGAATCTTCACC 58.835 55.000 0.00 0.00 0.00 4.02
616 629 3.403038 ACCGAATCTTCACCTGAACAAG 58.597 45.455 0.00 0.00 0.00 3.16
624 637 5.192927 TCTTCACCTGAACAAGACAACAAT 58.807 37.500 0.00 0.00 0.00 2.71
627 640 5.132502 TCACCTGAACAAGACAACAATCAT 58.867 37.500 0.00 0.00 0.00 2.45
644 657 2.627945 TCATCAATTACGTGCCTGGAC 58.372 47.619 0.00 0.00 0.00 4.02
659 672 2.158579 CCTGGACCCTAGAGACCTAGAC 60.159 59.091 0.00 0.00 44.00 2.59
678 691 1.065928 CGGCTGGATACGACTCCAC 59.934 63.158 6.62 4.96 40.43 4.02
687 700 3.436496 GATACGACTCCACGAAAGGAAG 58.564 50.000 0.00 0.00 37.20 3.46
693 706 0.034896 TCCACGAAAGGAAGAGGTGC 59.965 55.000 0.00 0.00 33.93 5.01
694 707 0.035458 CCACGAAAGGAAGAGGTGCT 59.965 55.000 0.00 0.00 0.00 4.40
695 708 1.433534 CACGAAAGGAAGAGGTGCTC 58.566 55.000 0.00 0.00 0.00 4.26
696 709 1.001406 CACGAAAGGAAGAGGTGCTCT 59.999 52.381 0.00 0.00 43.37 4.09
697 710 1.273886 ACGAAAGGAAGAGGTGCTCTC 59.726 52.381 0.00 0.32 40.28 3.20
698 711 1.404851 CGAAAGGAAGAGGTGCTCTCC 60.405 57.143 0.00 0.00 40.28 3.71
699 712 1.625818 GAAAGGAAGAGGTGCTCTCCA 59.374 52.381 0.00 0.00 40.28 3.86
700 713 1.734655 AAGGAAGAGGTGCTCTCCAA 58.265 50.000 0.00 0.00 40.28 3.53
701 714 1.734655 AGGAAGAGGTGCTCTCCAAA 58.265 50.000 0.00 0.00 40.28 3.28
702 715 1.349357 AGGAAGAGGTGCTCTCCAAAC 59.651 52.381 0.00 0.00 40.28 2.93
703 716 1.349357 GGAAGAGGTGCTCTCCAAACT 59.651 52.381 0.00 0.00 40.28 2.66
704 717 2.614229 GGAAGAGGTGCTCTCCAAACTC 60.614 54.545 0.00 0.00 40.28 3.01
705 718 2.022718 AGAGGTGCTCTCCAAACTCT 57.977 50.000 4.43 0.00 43.44 3.24
706 719 1.622811 AGAGGTGCTCTCCAAACTCTG 59.377 52.381 0.00 0.00 43.44 3.35
707 720 1.620819 GAGGTGCTCTCCAAACTCTGA 59.379 52.381 0.00 0.00 36.52 3.27
708 721 2.235898 GAGGTGCTCTCCAAACTCTGAT 59.764 50.000 0.00 0.00 36.52 2.90
709 722 2.235898 AGGTGCTCTCCAAACTCTGATC 59.764 50.000 0.00 0.00 0.00 2.92
710 723 2.266554 GTGCTCTCCAAACTCTGATCG 58.733 52.381 0.00 0.00 0.00 3.69
711 724 1.205655 TGCTCTCCAAACTCTGATCGG 59.794 52.381 0.00 0.00 0.00 4.18
712 725 1.472376 GCTCTCCAAACTCTGATCGGG 60.472 57.143 0.62 0.00 0.00 5.14
713 726 2.103373 CTCTCCAAACTCTGATCGGGA 58.897 52.381 0.62 0.00 0.00 5.14
714 727 1.825474 TCTCCAAACTCTGATCGGGAC 59.175 52.381 0.62 0.00 0.00 4.46
715 728 1.827969 CTCCAAACTCTGATCGGGACT 59.172 52.381 0.62 0.00 0.00 3.85
716 729 3.024547 CTCCAAACTCTGATCGGGACTA 58.975 50.000 0.62 0.00 0.00 2.59
717 730 3.437213 TCCAAACTCTGATCGGGACTAA 58.563 45.455 0.62 0.00 0.00 2.24
718 731 3.194968 TCCAAACTCTGATCGGGACTAAC 59.805 47.826 0.62 0.00 0.00 2.34
719 732 3.056107 CCAAACTCTGATCGGGACTAACA 60.056 47.826 0.62 0.00 0.00 2.41
720 733 4.562757 CCAAACTCTGATCGGGACTAACAA 60.563 45.833 0.62 0.00 0.00 2.83
721 734 4.884668 AACTCTGATCGGGACTAACAAA 57.115 40.909 0.62 0.00 0.00 2.83
722 735 4.884668 ACTCTGATCGGGACTAACAAAA 57.115 40.909 0.62 0.00 0.00 2.44
723 736 4.566987 ACTCTGATCGGGACTAACAAAAC 58.433 43.478 0.62 0.00 0.00 2.43
724 737 4.039973 ACTCTGATCGGGACTAACAAAACA 59.960 41.667 0.62 0.00 0.00 2.83
725 738 4.312443 TCTGATCGGGACTAACAAAACAC 58.688 43.478 0.62 0.00 0.00 3.32
726 739 4.039973 TCTGATCGGGACTAACAAAACACT 59.960 41.667 0.62 0.00 0.00 3.55
727 740 4.062293 TGATCGGGACTAACAAAACACTG 58.938 43.478 0.00 0.00 0.00 3.66
728 741 2.215196 TCGGGACTAACAAAACACTGC 58.785 47.619 0.00 0.00 0.00 4.40
729 742 1.944024 CGGGACTAACAAAACACTGCA 59.056 47.619 0.00 0.00 0.00 4.41
730 743 2.032030 CGGGACTAACAAAACACTGCAG 60.032 50.000 13.48 13.48 0.00 4.41
731 744 2.949644 GGGACTAACAAAACACTGCAGT 59.050 45.455 15.25 15.25 0.00 4.40
732 745 3.380320 GGGACTAACAAAACACTGCAGTT 59.620 43.478 18.94 6.15 0.00 3.16
733 746 4.351192 GGACTAACAAAACACTGCAGTTG 58.649 43.478 18.94 15.71 0.00 3.16
734 747 4.095782 GGACTAACAAAACACTGCAGTTGA 59.904 41.667 18.94 0.00 0.00 3.18
735 748 5.235305 ACTAACAAAACACTGCAGTTGAG 57.765 39.130 18.94 9.06 0.00 3.02
736 749 4.941263 ACTAACAAAACACTGCAGTTGAGA 59.059 37.500 18.94 5.76 0.00 3.27
737 750 4.782019 AACAAAACACTGCAGTTGAGAA 57.218 36.364 18.94 0.00 0.00 2.87
738 751 4.096732 ACAAAACACTGCAGTTGAGAAC 57.903 40.909 18.94 0.00 0.00 3.01
739 752 3.505680 ACAAAACACTGCAGTTGAGAACA 59.494 39.130 18.94 0.00 0.00 3.18
740 753 4.022416 ACAAAACACTGCAGTTGAGAACAA 60.022 37.500 18.94 0.00 0.00 2.83
753 766 4.794248 TGAGAACAACTGATTCAACACG 57.206 40.909 0.00 0.00 0.00 4.49
754 767 4.188462 TGAGAACAACTGATTCAACACGT 58.812 39.130 0.00 0.00 0.00 4.49
755 768 4.634004 TGAGAACAACTGATTCAACACGTT 59.366 37.500 0.00 0.00 0.00 3.99
756 769 5.123186 TGAGAACAACTGATTCAACACGTTT 59.877 36.000 0.00 0.00 0.00 3.60
757 770 5.569413 AGAACAACTGATTCAACACGTTTC 58.431 37.500 0.00 0.00 0.00 2.78
758 771 5.354234 AGAACAACTGATTCAACACGTTTCT 59.646 36.000 0.00 0.00 0.00 2.52
759 772 6.537301 AGAACAACTGATTCAACACGTTTCTA 59.463 34.615 0.00 0.00 0.00 2.10
760 773 6.287107 ACAACTGATTCAACACGTTTCTAG 57.713 37.500 0.00 0.00 0.00 2.43
761 774 4.992381 ACTGATTCAACACGTTTCTAGC 57.008 40.909 0.00 0.00 0.00 3.42
762 775 4.377021 ACTGATTCAACACGTTTCTAGCA 58.623 39.130 0.00 0.00 0.00 3.49
763 776 4.997395 ACTGATTCAACACGTTTCTAGCAT 59.003 37.500 0.00 0.00 0.00 3.79
764 777 5.106948 ACTGATTCAACACGTTTCTAGCATG 60.107 40.000 0.00 0.00 0.00 4.06
765 778 4.994217 TGATTCAACACGTTTCTAGCATGA 59.006 37.500 0.00 0.00 0.00 3.07
766 779 4.990543 TTCAACACGTTTCTAGCATGAG 57.009 40.909 0.00 0.00 0.00 2.90
767 780 2.736721 TCAACACGTTTCTAGCATGAGC 59.263 45.455 0.00 0.00 42.56 4.26
785 798 2.900122 GCTCATAGCGTTTCTTTGCA 57.100 45.000 0.00 0.00 0.00 4.08
786 799 2.509870 GCTCATAGCGTTTCTTTGCAC 58.490 47.619 0.00 0.00 0.00 4.57
787 800 2.095768 GCTCATAGCGTTTCTTTGCACA 60.096 45.455 0.00 0.00 0.00 4.57
788 801 3.426695 GCTCATAGCGTTTCTTTGCACAT 60.427 43.478 0.00 0.00 0.00 3.21
789 802 4.337763 CTCATAGCGTTTCTTTGCACATC 58.662 43.478 0.00 0.00 0.00 3.06
790 803 3.126858 TCATAGCGTTTCTTTGCACATCC 59.873 43.478 0.00 0.00 0.00 3.51
791 804 1.317613 AGCGTTTCTTTGCACATCCA 58.682 45.000 0.00 0.00 0.00 3.41
792 805 1.888512 AGCGTTTCTTTGCACATCCAT 59.111 42.857 0.00 0.00 0.00 3.41
793 806 1.987770 GCGTTTCTTTGCACATCCATG 59.012 47.619 0.00 0.00 0.00 3.66
794 807 2.607771 GCGTTTCTTTGCACATCCATGT 60.608 45.455 0.00 0.00 42.84 3.21
795 808 3.641648 CGTTTCTTTGCACATCCATGTT 58.358 40.909 0.00 0.00 39.39 2.71
796 809 3.670055 CGTTTCTTTGCACATCCATGTTC 59.330 43.478 0.00 0.00 39.39 3.18
797 810 3.940209 TTCTTTGCACATCCATGTTCC 57.060 42.857 0.00 0.00 39.39 3.62
798 811 2.170166 TCTTTGCACATCCATGTTCCC 58.830 47.619 0.00 0.00 39.39 3.97
799 812 1.894466 CTTTGCACATCCATGTTCCCA 59.106 47.619 0.00 0.00 39.39 4.37
800 813 1.255882 TTGCACATCCATGTTCCCAC 58.744 50.000 0.00 0.00 39.39 4.61
801 814 0.959867 TGCACATCCATGTTCCCACG 60.960 55.000 0.00 0.00 39.39 4.94
802 815 1.802636 CACATCCATGTTCCCACGC 59.197 57.895 0.00 0.00 39.39 5.34
803 816 0.677731 CACATCCATGTTCCCACGCT 60.678 55.000 0.00 0.00 39.39 5.07
804 817 0.908910 ACATCCATGTTCCCACGCTA 59.091 50.000 0.00 0.00 37.90 4.26
805 818 1.280710 ACATCCATGTTCCCACGCTAA 59.719 47.619 0.00 0.00 37.90 3.09
806 819 2.092429 ACATCCATGTTCCCACGCTAAT 60.092 45.455 0.00 0.00 37.90 1.73
807 820 3.135712 ACATCCATGTTCCCACGCTAATA 59.864 43.478 0.00 0.00 37.90 0.98
808 821 3.188159 TCCATGTTCCCACGCTAATAC 57.812 47.619 0.00 0.00 0.00 1.89
809 822 2.502130 TCCATGTTCCCACGCTAATACA 59.498 45.455 0.00 0.00 0.00 2.29
810 823 3.135712 TCCATGTTCCCACGCTAATACAT 59.864 43.478 0.00 0.00 0.00 2.29
811 824 3.250762 CCATGTTCCCACGCTAATACATG 59.749 47.826 11.42 11.42 41.36 3.21
812 825 2.285083 TGTTCCCACGCTAATACATGC 58.715 47.619 0.00 0.00 0.00 4.06
813 826 2.285083 GTTCCCACGCTAATACATGCA 58.715 47.619 0.00 0.00 0.00 3.96
814 827 1.948104 TCCCACGCTAATACATGCAC 58.052 50.000 0.00 0.00 0.00 4.57
815 828 0.581529 CCCACGCTAATACATGCACG 59.418 55.000 0.00 0.00 0.00 5.34
816 829 1.286501 CCACGCTAATACATGCACGT 58.713 50.000 0.00 0.00 0.00 4.49
817 830 2.465855 CCACGCTAATACATGCACGTA 58.534 47.619 0.00 0.00 31.70 3.57
818 831 3.057019 CCACGCTAATACATGCACGTAT 58.943 45.455 0.00 0.00 33.43 3.06
819 832 3.121279 CCACGCTAATACATGCACGTATC 59.879 47.826 5.81 0.00 30.73 2.24
820 833 3.981416 CACGCTAATACATGCACGTATCT 59.019 43.478 5.81 0.03 30.73 1.98
821 834 5.151389 CACGCTAATACATGCACGTATCTA 58.849 41.667 5.81 1.16 30.73 1.98
822 835 5.283953 CACGCTAATACATGCACGTATCTAG 59.716 44.000 5.81 10.66 30.73 2.43
823 836 5.180680 ACGCTAATACATGCACGTATCTAGA 59.819 40.000 18.09 0.00 30.73 2.43
824 837 5.508573 CGCTAATACATGCACGTATCTAGAC 59.491 44.000 18.09 11.90 30.73 2.59
839 852 8.625023 CGTATCTAGACGTATTTTACTTCGAG 57.375 38.462 0.00 0.00 38.04 4.04
840 853 8.483218 CGTATCTAGACGTATTTTACTTCGAGA 58.517 37.037 0.00 6.49 40.77 4.04
844 857 9.317936 TCTAGACGTATTTTACTTCGAGATACA 57.682 33.333 0.00 0.00 35.12 2.29
847 860 8.838365 AGACGTATTTTACTTCGAGATACATCT 58.162 33.333 0.00 0.00 40.50 2.90
880 893 8.700722 TCCATTTTGATGACAAATATTTTCGG 57.299 30.769 0.00 0.00 43.99 4.30
881 894 8.526978 TCCATTTTGATGACAAATATTTTCGGA 58.473 29.630 0.00 0.00 43.99 4.55
882 895 8.594687 CCATTTTGATGACAAATATTTTCGGAC 58.405 33.333 0.00 0.00 43.99 4.79
883 896 7.789341 TTTTGATGACAAATATTTTCGGACG 57.211 32.000 0.00 0.00 43.99 4.79
884 897 5.478233 TGATGACAAATATTTTCGGACGG 57.522 39.130 0.00 0.00 0.00 4.79
885 898 5.179533 TGATGACAAATATTTTCGGACGGA 58.820 37.500 0.00 0.00 0.00 4.69
886 899 5.293324 TGATGACAAATATTTTCGGACGGAG 59.707 40.000 0.00 0.00 0.00 4.63
887 900 3.936453 TGACAAATATTTTCGGACGGAGG 59.064 43.478 0.00 0.00 0.00 4.30
888 901 3.275999 ACAAATATTTTCGGACGGAGGG 58.724 45.455 0.00 0.00 0.00 4.30
889 902 3.054948 ACAAATATTTTCGGACGGAGGGA 60.055 43.478 0.00 0.00 0.00 4.20
890 903 3.470645 AATATTTTCGGACGGAGGGAG 57.529 47.619 0.00 0.00 0.00 4.30
891 904 1.856629 TATTTTCGGACGGAGGGAGT 58.143 50.000 0.00 0.00 0.00 3.85
892 905 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
893 906 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
894 907 2.734755 TTTCGGACGGAGGGAGTATA 57.265 50.000 0.00 0.00 0.00 1.47
895 908 2.965671 TTCGGACGGAGGGAGTATAT 57.034 50.000 0.00 0.00 0.00 0.86
896 909 2.486472 TCGGACGGAGGGAGTATATC 57.514 55.000 0.00 0.00 0.00 1.63
1023 1036 2.079925 GTGGAACCAGTGAAGCTCATC 58.920 52.381 0.00 0.00 0.00 2.92
1163 1176 1.752198 CCGTCCACAAGAAGGTCCA 59.248 57.895 0.00 0.00 39.15 4.02
1307 1320 3.230134 TCTGGTCCAAATTCTTTGTGGG 58.770 45.455 0.00 0.00 38.98 4.61
1386 1425 4.890581 GGATACTCCTCCGCTCATACATAT 59.109 45.833 0.00 0.00 32.53 1.78
1387 1426 6.062749 GGATACTCCTCCGCTCATACATATA 58.937 44.000 0.00 0.00 32.53 0.86
1388 1427 6.717540 GGATACTCCTCCGCTCATACATATAT 59.282 42.308 0.00 0.00 32.53 0.86
1389 1428 5.843673 ACTCCTCCGCTCATACATATATG 57.156 43.478 11.29 11.29 39.79 1.78
1390 1429 4.646945 ACTCCTCCGCTCATACATATATGG 59.353 45.833 16.96 0.00 39.04 2.74
1392 1431 5.762279 TCCTCCGCTCATACATATATGGTA 58.238 41.667 16.96 7.42 39.04 3.25
1422 1536 5.804473 TGTGTTCATGTGTTTGATGTTGAAC 59.196 36.000 6.65 6.65 41.90 3.18
1425 1539 5.833406 TCATGTGTTTGATGTTGAACTGT 57.167 34.783 0.00 0.00 0.00 3.55
1443 1557 8.267620 TGAACTGTTCTCAACCATACAATATG 57.732 34.615 20.18 0.00 0.00 1.78
1445 1559 7.615582 ACTGTTCTCAACCATACAATATGTG 57.384 36.000 0.00 0.00 0.00 3.21
1556 1713 8.771920 AAATAAGACAAGACGACATGTATTCA 57.228 30.769 6.41 0.00 32.75 2.57
1560 1717 7.757097 AGACAAGACGACATGTATTCAATAC 57.243 36.000 0.00 0.02 36.29 1.89
1584 1741 8.245195 ACTTGTAACCCAATTGAAATACTTGT 57.755 30.769 7.12 6.95 31.20 3.16
1585 1742 9.357161 ACTTGTAACCCAATTGAAATACTTGTA 57.643 29.630 7.12 0.00 31.20 2.41
1610 1772 5.489792 TTCTTCCTCTAGTGCTTGATGTT 57.510 39.130 0.00 0.00 0.00 2.71
1616 1778 4.498241 CTCTAGTGCTTGATGTTGCTGTA 58.502 43.478 0.00 0.00 0.00 2.74
1618 1780 3.131709 AGTGCTTGATGTTGCTGTAGT 57.868 42.857 0.00 0.00 0.00 2.73
1623 1785 2.268762 TGATGTTGCTGTAGTTGGCA 57.731 45.000 0.00 0.00 36.62 4.92
1624 1786 2.794103 TGATGTTGCTGTAGTTGGCAT 58.206 42.857 0.00 0.00 38.30 4.40
1637 1799 1.773856 TTGGCATTGTGGACGGAGGA 61.774 55.000 0.00 0.00 0.00 3.71
1638 1800 1.450312 GGCATTGTGGACGGAGGAG 60.450 63.158 0.00 0.00 0.00 3.69
1639 1801 1.450312 GCATTGTGGACGGAGGAGG 60.450 63.158 0.00 0.00 0.00 4.30
1647 1809 4.144727 ACGGAGGAGGGCGAGGAT 62.145 66.667 0.00 0.00 0.00 3.24
1704 1866 3.729965 CCTAGTGGAGGCGCAGCTG 62.730 68.421 10.11 10.11 46.16 4.24
1755 1917 4.521062 GGCCTCGCTGACATCGCT 62.521 66.667 0.00 0.00 0.00 4.93
1760 1922 2.433145 CGCTGACATCGCTGGTGT 60.433 61.111 0.00 0.00 0.00 4.16
1834 1996 3.971240 CGTGATGACAGACGATGAGTATG 59.029 47.826 4.19 0.00 46.78 2.39
2016 2188 7.038302 AGTCTAATCTGGTAGGTTTTGTCATGA 60.038 37.037 0.00 0.00 0.00 3.07
2096 2285 3.012518 AGTTATTGCTCCATGTCACTGC 58.987 45.455 0.00 0.00 0.00 4.40
2169 2358 2.047655 CGACTAGCAAACGGGCCA 60.048 61.111 4.39 0.00 0.00 5.36
2226 2423 0.830648 TCAACTAGGCCGCAGCTATT 59.169 50.000 7.27 0.00 39.73 1.73
2316 2514 1.000955 CAGTCGTAGCTCAACAAGGGT 59.999 52.381 0.00 0.00 0.00 4.34
2367 2565 7.490962 TGTCTAAAATGACACCTAGTTTGTG 57.509 36.000 0.00 0.00 41.43 3.33
2503 2729 4.472691 ACTTTTTAGCGTTTCCGTAACC 57.527 40.909 0.00 0.00 36.15 2.85
2599 2826 3.996957 TGACCCATGTACTATGGTGGTA 58.003 45.455 17.62 4.70 37.48 3.25
2777 3004 8.939201 TGTGCTGTTTTCATTTTTATTGAGAA 57.061 26.923 0.00 0.00 0.00 2.87
2916 3143 9.748708 GGATATCAAGCATAGAGAATCAGATAC 57.251 37.037 4.83 0.00 37.82 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.491403 ACTGGAAGAAGAAGTAAACCGTACTA 59.509 38.462 0.00 0.00 37.43 1.82
34 35 9.006215 GCTGCCGTTTTTATTTTATAGTTACTG 57.994 33.333 0.00 0.00 0.00 2.74
82 95 3.238441 GGCTCGCTATCTACGATTTCAG 58.762 50.000 0.00 0.00 39.12 3.02
114 127 2.159462 TGATGCTCGCTATCTATCGCTG 60.159 50.000 0.00 0.00 0.00 5.18
127 140 3.123621 GGTTTCTACAGTGTTGATGCTCG 59.876 47.826 8.25 0.00 0.00 5.03
178 191 7.298122 GTGAACGAAGAATACATCAACATTGT 58.702 34.615 0.00 0.00 0.00 2.71
179 192 6.742718 GGTGAACGAAGAATACATCAACATTG 59.257 38.462 0.00 0.00 0.00 2.82
198 211 5.305585 TGTCTGACCTTTAAGATGGTGAAC 58.694 41.667 5.17 0.22 36.59 3.18
318 331 1.769098 CGACCTTGGATGCATCAGCG 61.769 60.000 27.25 15.93 46.23 5.18
326 339 1.081892 CAACTGCTCGACCTTGGATG 58.918 55.000 0.00 0.00 0.00 3.51
336 349 1.432514 AGCACATACACAACTGCTCG 58.567 50.000 0.00 0.00 34.90 5.03
337 350 2.666619 GCAAGCACATACACAACTGCTC 60.667 50.000 0.00 0.00 39.08 4.26
341 354 5.473162 TGATAAAGCAAGCACATACACAACT 59.527 36.000 0.00 0.00 0.00 3.16
376 389 8.000709 ACTGAGATTTCATTTATGCAGGGATTA 58.999 33.333 0.00 0.00 31.68 1.75
379 392 5.759059 ACTGAGATTTCATTTATGCAGGGA 58.241 37.500 0.00 0.00 31.68 4.20
380 393 5.591472 TGACTGAGATTTCATTTATGCAGGG 59.409 40.000 0.00 0.00 31.68 4.45
381 394 6.688637 TGACTGAGATTTCATTTATGCAGG 57.311 37.500 0.00 0.00 31.68 4.85
461 474 9.942850 TCTTCTCATTGTGTTGAGTATTGAATA 57.057 29.630 1.76 0.00 43.02 1.75
496 509 2.039480 TCCTCTGAGCTCTTGCACATTT 59.961 45.455 16.19 0.00 42.74 2.32
586 599 1.974957 TGAAGATTCGGTTGGGTGAGA 59.025 47.619 0.00 0.00 0.00 3.27
588 601 1.271163 GGTGAAGATTCGGTTGGGTGA 60.271 52.381 0.00 0.00 0.00 4.02
598 611 5.296780 TGTTGTCTTGTTCAGGTGAAGATTC 59.703 40.000 0.00 0.00 34.27 2.52
601 614 4.214986 TGTTGTCTTGTTCAGGTGAAGA 57.785 40.909 0.00 0.00 34.27 2.87
608 621 9.121517 GTAATTGATGATTGTTGTCTTGTTCAG 57.878 33.333 0.00 0.00 0.00 3.02
616 629 4.793216 GGCACGTAATTGATGATTGTTGTC 59.207 41.667 0.00 0.00 0.00 3.18
624 637 2.627945 GTCCAGGCACGTAATTGATGA 58.372 47.619 0.00 0.00 0.00 2.92
627 640 0.035820 GGGTCCAGGCACGTAATTGA 60.036 55.000 0.00 0.00 0.00 2.57
644 657 0.537828 GCCGGTCTAGGTCTCTAGGG 60.538 65.000 1.90 0.00 42.42 3.53
659 672 2.125326 TGGAGTCGTATCCAGCCGG 61.125 63.158 0.00 0.00 44.56 6.13
678 691 1.404851 GGAGAGCACCTCTTCCTTTCG 60.405 57.143 6.18 0.00 41.35 3.46
687 700 1.620819 TCAGAGTTTGGAGAGCACCTC 59.379 52.381 0.00 0.00 41.22 3.85
693 706 2.103373 TCCCGATCAGAGTTTGGAGAG 58.897 52.381 0.00 0.00 0.00 3.20
694 707 1.825474 GTCCCGATCAGAGTTTGGAGA 59.175 52.381 0.00 0.00 0.00 3.71
695 708 1.827969 AGTCCCGATCAGAGTTTGGAG 59.172 52.381 0.00 0.00 0.00 3.86
696 709 1.938585 AGTCCCGATCAGAGTTTGGA 58.061 50.000 0.00 0.00 0.00 3.53
697 710 3.056107 TGTTAGTCCCGATCAGAGTTTGG 60.056 47.826 0.00 0.00 0.00 3.28
698 711 4.188247 TGTTAGTCCCGATCAGAGTTTG 57.812 45.455 0.00 0.00 0.00 2.93
699 712 4.884668 TTGTTAGTCCCGATCAGAGTTT 57.115 40.909 0.00 0.00 0.00 2.66
700 713 4.884668 TTTGTTAGTCCCGATCAGAGTT 57.115 40.909 0.00 0.00 0.00 3.01
701 714 4.039973 TGTTTTGTTAGTCCCGATCAGAGT 59.960 41.667 0.00 0.00 0.00 3.24
702 715 4.389077 GTGTTTTGTTAGTCCCGATCAGAG 59.611 45.833 0.00 0.00 0.00 3.35
703 716 4.039973 AGTGTTTTGTTAGTCCCGATCAGA 59.960 41.667 0.00 0.00 0.00 3.27
704 717 4.152402 CAGTGTTTTGTTAGTCCCGATCAG 59.848 45.833 0.00 0.00 0.00 2.90
705 718 4.062293 CAGTGTTTTGTTAGTCCCGATCA 58.938 43.478 0.00 0.00 0.00 2.92
706 719 3.120304 GCAGTGTTTTGTTAGTCCCGATC 60.120 47.826 0.00 0.00 0.00 3.69
707 720 2.812011 GCAGTGTTTTGTTAGTCCCGAT 59.188 45.455 0.00 0.00 0.00 4.18
708 721 2.215196 GCAGTGTTTTGTTAGTCCCGA 58.785 47.619 0.00 0.00 0.00 5.14
709 722 1.944024 TGCAGTGTTTTGTTAGTCCCG 59.056 47.619 0.00 0.00 0.00 5.14
710 723 2.949644 ACTGCAGTGTTTTGTTAGTCCC 59.050 45.455 20.97 0.00 0.00 4.46
711 724 4.095782 TCAACTGCAGTGTTTTGTTAGTCC 59.904 41.667 22.49 0.00 0.00 3.85
712 725 5.064707 TCTCAACTGCAGTGTTTTGTTAGTC 59.935 40.000 22.49 0.00 0.00 2.59
713 726 4.941263 TCTCAACTGCAGTGTTTTGTTAGT 59.059 37.500 22.49 0.00 0.00 2.24
714 727 5.484173 TCTCAACTGCAGTGTTTTGTTAG 57.516 39.130 22.49 9.14 0.00 2.34
715 728 5.182190 TGTTCTCAACTGCAGTGTTTTGTTA 59.818 36.000 22.49 4.81 0.00 2.41
716 729 4.022416 TGTTCTCAACTGCAGTGTTTTGTT 60.022 37.500 22.49 0.00 0.00 2.83
717 730 3.505680 TGTTCTCAACTGCAGTGTTTTGT 59.494 39.130 22.49 0.00 0.00 2.83
718 731 4.095410 TGTTCTCAACTGCAGTGTTTTG 57.905 40.909 22.49 15.12 0.00 2.44
719 732 4.782019 TTGTTCTCAACTGCAGTGTTTT 57.218 36.364 22.49 0.38 0.00 2.43
731 744 4.634004 ACGTGTTGAATCAGTTGTTCTCAA 59.366 37.500 0.00 0.00 0.00 3.02
732 745 4.188462 ACGTGTTGAATCAGTTGTTCTCA 58.812 39.130 0.00 0.00 0.00 3.27
733 746 4.795970 ACGTGTTGAATCAGTTGTTCTC 57.204 40.909 0.00 0.00 0.00 2.87
734 747 5.354234 AGAAACGTGTTGAATCAGTTGTTCT 59.646 36.000 0.00 0.00 0.00 3.01
735 748 5.569413 AGAAACGTGTTGAATCAGTTGTTC 58.431 37.500 0.00 0.00 0.00 3.18
736 749 5.560966 AGAAACGTGTTGAATCAGTTGTT 57.439 34.783 0.00 0.00 0.00 2.83
737 750 5.277345 GCTAGAAACGTGTTGAATCAGTTGT 60.277 40.000 0.00 0.00 0.00 3.32
738 751 5.140177 GCTAGAAACGTGTTGAATCAGTTG 58.860 41.667 0.00 0.00 0.00 3.16
739 752 4.814234 TGCTAGAAACGTGTTGAATCAGTT 59.186 37.500 0.00 0.00 0.00 3.16
740 753 4.377021 TGCTAGAAACGTGTTGAATCAGT 58.623 39.130 0.00 0.00 0.00 3.41
741 754 4.990543 TGCTAGAAACGTGTTGAATCAG 57.009 40.909 0.00 0.00 0.00 2.90
742 755 4.994217 TCATGCTAGAAACGTGTTGAATCA 59.006 37.500 0.00 0.00 0.00 2.57
743 756 5.530519 TCATGCTAGAAACGTGTTGAATC 57.469 39.130 0.00 0.00 0.00 2.52
744 757 4.142816 GCTCATGCTAGAAACGTGTTGAAT 60.143 41.667 0.00 0.00 36.03 2.57
745 758 3.186409 GCTCATGCTAGAAACGTGTTGAA 59.814 43.478 0.00 0.00 36.03 2.69
746 759 2.736721 GCTCATGCTAGAAACGTGTTGA 59.263 45.455 0.00 0.00 36.03 3.18
747 760 3.109230 GCTCATGCTAGAAACGTGTTG 57.891 47.619 0.00 0.00 36.03 3.33
760 773 2.208431 AGAAACGCTATGAGCTCATGC 58.792 47.619 34.48 30.34 39.60 4.06
761 774 4.585364 CAAAGAAACGCTATGAGCTCATG 58.415 43.478 34.48 24.79 39.60 3.07
762 775 3.064545 GCAAAGAAACGCTATGAGCTCAT 59.935 43.478 30.85 30.85 39.60 2.90
763 776 2.416547 GCAAAGAAACGCTATGAGCTCA 59.583 45.455 20.79 20.79 39.60 4.26
764 777 2.416547 TGCAAAGAAACGCTATGAGCTC 59.583 45.455 6.82 6.82 39.60 4.09
765 778 2.160417 GTGCAAAGAAACGCTATGAGCT 59.840 45.455 0.00 0.00 39.60 4.09
766 779 2.095768 TGTGCAAAGAAACGCTATGAGC 60.096 45.455 0.00 0.00 38.02 4.26
767 780 3.811722 TGTGCAAAGAAACGCTATGAG 57.188 42.857 0.00 0.00 0.00 2.90
768 781 3.126858 GGATGTGCAAAGAAACGCTATGA 59.873 43.478 0.00 0.00 0.00 2.15
769 782 3.119884 TGGATGTGCAAAGAAACGCTATG 60.120 43.478 0.00 0.00 0.00 2.23
770 783 3.081061 TGGATGTGCAAAGAAACGCTAT 58.919 40.909 0.00 0.00 0.00 2.97
771 784 2.499197 TGGATGTGCAAAGAAACGCTA 58.501 42.857 0.00 0.00 0.00 4.26
772 785 1.317613 TGGATGTGCAAAGAAACGCT 58.682 45.000 0.00 0.00 0.00 5.07
773 786 1.987770 CATGGATGTGCAAAGAAACGC 59.012 47.619 0.00 0.00 0.00 4.84
774 787 3.287312 ACATGGATGTGCAAAGAAACG 57.713 42.857 0.00 0.00 40.03 3.60
775 788 3.989817 GGAACATGGATGTGCAAAGAAAC 59.010 43.478 0.00 0.00 41.61 2.78
776 789 3.006752 GGGAACATGGATGTGCAAAGAAA 59.993 43.478 0.00 0.00 41.61 2.52
777 790 2.562298 GGGAACATGGATGTGCAAAGAA 59.438 45.455 0.00 0.00 41.61 2.52
778 791 2.170166 GGGAACATGGATGTGCAAAGA 58.830 47.619 0.00 0.00 41.61 2.52
779 792 1.894466 TGGGAACATGGATGTGCAAAG 59.106 47.619 0.00 0.00 41.61 2.77
780 793 1.617850 GTGGGAACATGGATGTGCAAA 59.382 47.619 0.00 0.00 46.14 3.68
781 794 1.255882 GTGGGAACATGGATGTGCAA 58.744 50.000 0.00 0.00 46.14 4.08
782 795 0.959867 CGTGGGAACATGGATGTGCA 60.960 55.000 0.00 0.00 46.14 4.57
783 796 1.802636 CGTGGGAACATGGATGTGC 59.197 57.895 0.00 0.00 46.14 4.57
791 804 2.878406 GCATGTATTAGCGTGGGAACAT 59.122 45.455 0.00 0.00 46.14 2.71
792 805 2.285083 GCATGTATTAGCGTGGGAACA 58.715 47.619 0.00 0.00 38.70 3.18
793 806 2.031683 GTGCATGTATTAGCGTGGGAAC 59.968 50.000 0.00 0.00 0.00 3.62
794 807 2.285083 GTGCATGTATTAGCGTGGGAA 58.715 47.619 0.00 0.00 0.00 3.97
795 808 1.804746 CGTGCATGTATTAGCGTGGGA 60.805 52.381 0.00 0.00 0.00 4.37
796 809 0.581529 CGTGCATGTATTAGCGTGGG 59.418 55.000 0.00 0.00 0.00 4.61
797 810 1.286501 ACGTGCATGTATTAGCGTGG 58.713 50.000 10.57 0.00 0.00 4.94
798 811 3.981416 AGATACGTGCATGTATTAGCGTG 59.019 43.478 27.89 0.00 35.24 5.34
799 812 4.238761 AGATACGTGCATGTATTAGCGT 57.761 40.909 27.89 15.13 35.24 5.07
800 813 5.508573 GTCTAGATACGTGCATGTATTAGCG 59.491 44.000 27.89 17.81 35.24 4.26
801 814 5.508573 CGTCTAGATACGTGCATGTATTAGC 59.491 44.000 27.89 21.37 38.07 3.09
818 831 9.317936 TGTATCTCGAAGTAAAATACGTCTAGA 57.682 33.333 0.00 9.04 40.88 2.43
821 834 8.838365 AGATGTATCTCGAAGTAAAATACGTCT 58.162 33.333 0.00 8.87 41.19 4.18
822 835 9.105206 GAGATGTATCTCGAAGTAAAATACGTC 57.895 37.037 6.16 0.00 43.29 4.34
854 867 9.316730 CCGAAAATATTTGTCATCAAAATGGAT 57.683 29.630 0.39 0.00 44.97 3.41
855 868 8.526978 TCCGAAAATATTTGTCATCAAAATGGA 58.473 29.630 0.39 0.00 44.97 3.41
856 869 8.594687 GTCCGAAAATATTTGTCATCAAAATGG 58.405 33.333 0.39 0.00 44.97 3.16
857 870 8.313227 CGTCCGAAAATATTTGTCATCAAAATG 58.687 33.333 0.39 0.00 44.97 2.32
858 871 7.487829 CCGTCCGAAAATATTTGTCATCAAAAT 59.512 33.333 0.39 0.00 44.97 1.82
859 872 6.804295 CCGTCCGAAAATATTTGTCATCAAAA 59.196 34.615 0.39 0.00 44.97 2.44
860 873 6.149640 TCCGTCCGAAAATATTTGTCATCAAA 59.850 34.615 0.39 0.00 45.71 2.69
861 874 5.644206 TCCGTCCGAAAATATTTGTCATCAA 59.356 36.000 0.39 0.00 0.00 2.57
862 875 5.179533 TCCGTCCGAAAATATTTGTCATCA 58.820 37.500 0.39 0.00 0.00 3.07
863 876 5.277345 CCTCCGTCCGAAAATATTTGTCATC 60.277 44.000 0.39 0.00 0.00 2.92
864 877 4.574828 CCTCCGTCCGAAAATATTTGTCAT 59.425 41.667 0.39 0.00 0.00 3.06
865 878 3.936453 CCTCCGTCCGAAAATATTTGTCA 59.064 43.478 0.39 0.00 0.00 3.58
866 879 3.311596 CCCTCCGTCCGAAAATATTTGTC 59.688 47.826 0.39 1.54 0.00 3.18
867 880 3.054948 TCCCTCCGTCCGAAAATATTTGT 60.055 43.478 0.39 0.00 0.00 2.83
868 881 3.537580 TCCCTCCGTCCGAAAATATTTG 58.462 45.455 0.39 0.00 0.00 2.32
869 882 3.199289 ACTCCCTCCGTCCGAAAATATTT 59.801 43.478 0.00 0.00 0.00 1.40
870 883 2.770232 ACTCCCTCCGTCCGAAAATATT 59.230 45.455 0.00 0.00 0.00 1.28
871 884 2.395619 ACTCCCTCCGTCCGAAAATAT 58.604 47.619 0.00 0.00 0.00 1.28
872 885 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
873 886 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
874 887 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
875 888 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
876 889 2.553904 GGATATACTCCCTCCGTCCGAA 60.554 54.545 0.00 0.00 38.19 4.30
877 890 1.004044 GGATATACTCCCTCCGTCCGA 59.996 57.143 0.00 0.00 38.19 4.55
878 891 1.271762 TGGATATACTCCCTCCGTCCG 60.272 57.143 0.00 0.00 44.23 4.79
879 892 2.599408 TGGATATACTCCCTCCGTCC 57.401 55.000 0.00 0.00 44.23 4.79
880 893 5.485209 AATTTGGATATACTCCCTCCGTC 57.515 43.478 0.00 0.00 44.23 4.79
881 894 7.394816 CATTAATTTGGATATACTCCCTCCGT 58.605 38.462 0.00 0.00 44.23 4.69
882 895 6.823689 CCATTAATTTGGATATACTCCCTCCG 59.176 42.308 0.00 0.00 44.23 4.63
883 896 7.699878 ACCATTAATTTGGATATACTCCCTCC 58.300 38.462 3.10 0.00 44.23 4.30
884 897 8.606830 AGACCATTAATTTGGATATACTCCCTC 58.393 37.037 3.10 0.00 44.23 4.30
885 898 8.525729 AGACCATTAATTTGGATATACTCCCT 57.474 34.615 3.10 0.00 44.23 4.20
886 899 9.892130 CTAGACCATTAATTTGGATATACTCCC 57.108 37.037 3.10 0.00 44.23 4.30
887 900 9.384764 GCTAGACCATTAATTTGGATATACTCC 57.615 37.037 3.10 0.00 45.19 3.85
888 901 9.944376 TGCTAGACCATTAATTTGGATATACTC 57.056 33.333 3.10 0.00 39.25 2.59
891 904 9.214957 CGTTGCTAGACCATTAATTTGGATATA 57.785 33.333 3.10 0.00 39.25 0.86
892 905 7.936847 TCGTTGCTAGACCATTAATTTGGATAT 59.063 33.333 3.10 0.00 39.25 1.63
893 906 7.225931 GTCGTTGCTAGACCATTAATTTGGATA 59.774 37.037 3.10 0.00 39.25 2.59
894 907 6.038271 GTCGTTGCTAGACCATTAATTTGGAT 59.962 38.462 3.10 0.00 39.25 3.41
895 908 5.353123 GTCGTTGCTAGACCATTAATTTGGA 59.647 40.000 3.10 0.00 39.25 3.53
896 909 5.123186 TGTCGTTGCTAGACCATTAATTTGG 59.877 40.000 0.00 0.00 42.82 3.28
897 910 6.021596 GTGTCGTTGCTAGACCATTAATTTG 58.978 40.000 0.00 0.00 37.80 2.32
898 911 5.123344 GGTGTCGTTGCTAGACCATTAATTT 59.877 40.000 0.00 0.00 37.80 1.82
899 912 4.634443 GGTGTCGTTGCTAGACCATTAATT 59.366 41.667 0.00 0.00 37.80 1.40
900 913 4.189231 GGTGTCGTTGCTAGACCATTAAT 58.811 43.478 0.00 0.00 37.80 1.40
901 914 3.007074 TGGTGTCGTTGCTAGACCATTAA 59.993 43.478 0.00 0.00 35.51 1.40
902 915 2.563620 TGGTGTCGTTGCTAGACCATTA 59.436 45.455 0.00 0.00 35.51 1.90
903 916 1.346395 TGGTGTCGTTGCTAGACCATT 59.654 47.619 0.00 0.00 35.51 3.16
904 917 0.973632 TGGTGTCGTTGCTAGACCAT 59.026 50.000 0.00 0.00 35.51 3.55
905 918 0.973632 ATGGTGTCGTTGCTAGACCA 59.026 50.000 0.00 0.00 43.64 4.02
906 919 2.094762 AATGGTGTCGTTGCTAGACC 57.905 50.000 0.00 0.00 37.80 3.85
907 920 2.159627 CCAAATGGTGTCGTTGCTAGAC 59.840 50.000 0.00 0.00 38.98 2.59
908 921 2.037902 TCCAAATGGTGTCGTTGCTAGA 59.962 45.455 0.00 0.00 36.34 2.43
909 922 2.159627 GTCCAAATGGTGTCGTTGCTAG 59.840 50.000 0.00 0.00 36.34 3.42
910 923 2.147958 GTCCAAATGGTGTCGTTGCTA 58.852 47.619 0.00 0.00 36.34 3.49
1163 1176 3.402681 CCCCGTGGAGGAGCACAT 61.403 66.667 0.00 0.00 45.00 3.21
1252 1265 1.550524 CCTTTCATGAGGGTCAGTCGA 59.449 52.381 0.00 0.00 32.94 4.20
1394 1433 5.904941 ACATCAAACACATGAACACAACAT 58.095 33.333 0.00 0.00 32.06 2.71
1396 1435 5.804473 TCAACATCAAACACATGAACACAAC 59.196 36.000 0.00 0.00 32.06 3.32
1397 1436 5.958955 TCAACATCAAACACATGAACACAA 58.041 33.333 0.00 0.00 32.06 3.33
1398 1437 5.573337 TCAACATCAAACACATGAACACA 57.427 34.783 0.00 0.00 32.06 3.72
1399 1438 6.020440 CAGTTCAACATCAAACACATGAACAC 60.020 38.462 16.05 0.00 45.51 3.32
1400 1439 6.035217 CAGTTCAACATCAAACACATGAACA 58.965 36.000 16.05 0.00 45.51 3.18
1401 1440 6.035843 ACAGTTCAACATCAAACACATGAAC 58.964 36.000 0.00 8.06 44.19 3.18
1402 1441 6.206395 ACAGTTCAACATCAAACACATGAA 57.794 33.333 0.00 0.00 32.06 2.57
1404 1443 6.267817 AGAACAGTTCAACATCAAACACATG 58.732 36.000 15.85 0.00 0.00 3.21
1405 1444 6.095300 TGAGAACAGTTCAACATCAAACACAT 59.905 34.615 15.85 0.00 0.00 3.21
1422 1536 7.615582 ACACATATTGTATGGTTGAGAACAG 57.384 36.000 2.42 0.00 36.32 3.16
1533 1690 8.948631 ATTGAATACATGTCGTCTTGTCTTAT 57.051 30.769 0.00 0.00 34.54 1.73
1584 1741 8.484214 ACATCAAGCACTAGAGGAAGAATATA 57.516 34.615 0.00 0.00 0.00 0.86
1585 1742 7.372260 ACATCAAGCACTAGAGGAAGAATAT 57.628 36.000 0.00 0.00 0.00 1.28
1586 1743 6.798427 ACATCAAGCACTAGAGGAAGAATA 57.202 37.500 0.00 0.00 0.00 1.75
1588 1745 5.240891 CAACATCAAGCACTAGAGGAAGAA 58.759 41.667 0.00 0.00 0.00 2.52
1589 1746 4.825422 CAACATCAAGCACTAGAGGAAGA 58.175 43.478 0.00 0.00 0.00 2.87
1590 1747 3.373439 GCAACATCAAGCACTAGAGGAAG 59.627 47.826 0.00 0.00 0.00 3.46
1593 1750 2.676839 CAGCAACATCAAGCACTAGAGG 59.323 50.000 0.00 0.00 0.00 3.69
1594 1751 3.332919 ACAGCAACATCAAGCACTAGAG 58.667 45.455 0.00 0.00 0.00 2.43
1595 1752 3.407424 ACAGCAACATCAAGCACTAGA 57.593 42.857 0.00 0.00 0.00 2.43
1596 1753 4.248859 ACTACAGCAACATCAAGCACTAG 58.751 43.478 0.00 0.00 0.00 2.57
1610 1772 1.202867 TCCACAATGCCAACTACAGCA 60.203 47.619 0.00 0.00 44.45 4.41
1616 1778 0.606401 CTCCGTCCACAATGCCAACT 60.606 55.000 0.00 0.00 0.00 3.16
1618 1780 1.303236 CCTCCGTCCACAATGCCAA 60.303 57.895 0.00 0.00 0.00 4.52
1623 1785 2.670148 GCCCTCCTCCGTCCACAAT 61.670 63.158 0.00 0.00 0.00 2.71
1624 1786 3.319198 GCCCTCCTCCGTCCACAA 61.319 66.667 0.00 0.00 0.00 3.33
1637 1799 1.002274 ACCTTCTGATCCTCGCCCT 59.998 57.895 0.00 0.00 0.00 5.19
1638 1800 1.045911 AGACCTTCTGATCCTCGCCC 61.046 60.000 0.00 0.00 0.00 6.13
1639 1801 0.827368 AAGACCTTCTGATCCTCGCC 59.173 55.000 0.00 0.00 0.00 5.54
1647 1809 4.566004 CGTCCATAACAAAGACCTTCTGA 58.434 43.478 0.00 0.00 0.00 3.27
1755 1917 1.789523 GGGATAGTAGGCTGACACCA 58.210 55.000 0.00 0.00 0.00 4.17
1879 2041 0.321298 GTCCGGCAAGCACTCCTTAA 60.321 55.000 0.00 0.00 31.00 1.85
2016 2188 5.244402 TCTTCATGTTGATTCAAGCCACAAT 59.756 36.000 0.00 0.00 0.00 2.71
2052 2241 0.396060 CAGCAGCTCCCCCTTATCTC 59.604 60.000 0.00 0.00 0.00 2.75
2083 2272 1.134995 TCTAAGCGCAGTGACATGGAG 60.135 52.381 11.47 0.00 0.00 3.86
2096 2285 4.749245 ACAACCAAATCAACTCTAAGCG 57.251 40.909 0.00 0.00 0.00 4.68
2137 2326 0.468226 AGTCGAGGTTGGACTTGCAA 59.532 50.000 0.00 0.00 41.83 4.08
2169 2358 8.630054 TTTGCAACTAGGACAACTACAATTAT 57.370 30.769 0.00 0.00 0.00 1.28
2316 2514 6.945435 ACATCATGTACAACTTTATCCCACAA 59.055 34.615 0.00 0.00 0.00 3.33
2323 2521 9.719355 TTAGACACACATCATGTACAACTTTAT 57.281 29.630 0.00 0.00 40.64 1.40
2327 2525 8.506437 CATTTTAGACACACATCATGTACAACT 58.494 33.333 0.00 0.00 40.64 3.16
2519 2746 9.783256 GTAAAAACATATCACTGGTCCAATTAC 57.217 33.333 0.00 0.00 0.00 1.89
2714 2941 6.661805 CCTGTACAAGCCCCTTAGAAAAATAA 59.338 38.462 0.00 0.00 0.00 1.40
2916 3143 6.577103 TCTCTGCCTTCATCAATACTAACAG 58.423 40.000 0.00 0.00 0.00 3.16
2950 3177 6.697395 TCATCTTCGGACTCAAACATCTTAA 58.303 36.000 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.