Multiple sequence alignment - TraesCS1B01G092500

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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 TraesCS1B01G092500 chr1B 100.000 3710 0 0 643 4352 94233634 94229925 0.000000e+00 6852.0
1 TraesCS1B01G092500 chr1B 82.084 2361 368 36 1051 3399 94327210 94324893 0.000000e+00 1965.0
2 TraesCS1B01G092500 chr1B 100.000 143 0 0 1 143 94234276 94234134 9.280000e-67 265.0
3 TraesCS1B01G092500 chr1D 92.860 2717 161 21 812 3498 58764403 58761690 0.000000e+00 3912.0
4 TraesCS1B01G092500 chr1D 89.056 2458 237 16 966 3403 58628725 58626280 0.000000e+00 3020.0
5 TraesCS1B01G092500 chr1D 83.424 1478 236 9 1865 3338 36623655 36622183 0.000000e+00 1363.0
6 TraesCS1B01G092500 chr1D 83.006 1477 247 4 1864 3338 38559351 38557877 0.000000e+00 1334.0
7 TraesCS1B01G092500 chr1D 82.296 1542 261 12 1864 3399 50023566 50025101 0.000000e+00 1325.0
8 TraesCS1B01G092500 chr1D 81.753 1540 273 8 1864 3399 50008321 50009856 0.000000e+00 1280.0
9 TraesCS1B01G092500 chr1D 96.918 584 12 1 3492 4075 58761654 58761077 0.000000e+00 974.0
10 TraesCS1B01G092500 chr1D 83.255 848 127 10 1036 1871 50059261 50060105 0.000000e+00 765.0
11 TraesCS1B01G092500 chr1D 83.629 788 115 11 1097 1874 36618122 36617339 0.000000e+00 728.0
12 TraesCS1B01G092500 chr1D 97.551 245 3 2 4110 4352 58761081 58760838 2.420000e-112 416.0
13 TraesCS1B01G092500 chr1D 87.500 88 7 4 26 111 438359804 438359889 9.960000e-17 99.0
14 TraesCS1B01G092500 chr1D 80.531 113 16 5 26 135 413790785 413790894 1.000000e-11 82.4
15 TraesCS1B01G092500 chr1A 88.823 2344 243 13 1067 3403 57405790 57403459 0.000000e+00 2859.0
16 TraesCS1B01G092500 chr1A 92.101 1671 125 3 917 2580 57640294 57638624 0.000000e+00 2348.0
17 TraesCS1B01G092500 chr1A 81.056 2291 413 18 1060 3338 37512184 37509903 0.000000e+00 1807.0
18 TraesCS1B01G092500 chr1A 83.333 1470 239 6 1864 3330 37504384 37502918 0.000000e+00 1352.0
19 TraesCS1B01G092500 chr1A 94.714 454 18 1 3575 4028 57638625 57638178 0.000000e+00 701.0
20 TraesCS1B01G092500 chr1A 91.209 91 8 0 812 902 57673782 57673692 1.640000e-24 124.0
21 TraesCS1B01G092500 chr1A 87.209 86 8 2 16 101 34923587 34923669 1.290000e-15 95.3
22 TraesCS1B01G092500 chr3A 85.714 112 12 3 26 135 14856154 14856263 9.890000e-22 115.0
23 TraesCS1B01G092500 chr4D 85.263 95 11 1 26 120 248902627 248902536 1.290000e-15 95.3
24 TraesCS1B01G092500 chr5A 81.818 110 12 7 30 135 675691790 675691685 7.750000e-13 86.1
25 TraesCS1B01G092500 chrUn 88.571 70 5 3 18 85 94218780 94218848 1.000000e-11 82.4
26 TraesCS1B01G092500 chr6B 81.250 112 11 10 28 135 452184113 452184008 1.000000e-11 82.4
27 TraesCS1B01G092500 chr6D 82.609 92 13 3 26 117 313959815 313959727 1.300000e-10 78.7


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 TraesCS1B01G092500 chr1B 94229925 94234276 4351 True 3558.500000 6852 100.000000 1 4352 2 chr1B.!!$R2 4351
1 TraesCS1B01G092500 chr1B 94324893 94327210 2317 True 1965.000000 1965 82.084000 1051 3399 1 chr1B.!!$R1 2348
2 TraesCS1B01G092500 chr1D 58626280 58628725 2445 True 3020.000000 3020 89.056000 966 3403 1 chr1D.!!$R4 2437
3 TraesCS1B01G092500 chr1D 58760838 58764403 3565 True 1767.333333 3912 95.776333 812 4352 3 chr1D.!!$R5 3540
4 TraesCS1B01G092500 chr1D 36622183 36623655 1472 True 1363.000000 1363 83.424000 1865 3338 1 chr1D.!!$R2 1473
5 TraesCS1B01G092500 chr1D 38557877 38559351 1474 True 1334.000000 1334 83.006000 1864 3338 1 chr1D.!!$R3 1474
6 TraesCS1B01G092500 chr1D 50023566 50025101 1535 False 1325.000000 1325 82.296000 1864 3399 1 chr1D.!!$F2 1535
7 TraesCS1B01G092500 chr1D 50008321 50009856 1535 False 1280.000000 1280 81.753000 1864 3399 1 chr1D.!!$F1 1535
8 TraesCS1B01G092500 chr1D 50059261 50060105 844 False 765.000000 765 83.255000 1036 1871 1 chr1D.!!$F3 835
9 TraesCS1B01G092500 chr1D 36617339 36618122 783 True 728.000000 728 83.629000 1097 1874 1 chr1D.!!$R1 777
10 TraesCS1B01G092500 chr1A 57403459 57405790 2331 True 2859.000000 2859 88.823000 1067 3403 1 chr1A.!!$R3 2336
11 TraesCS1B01G092500 chr1A 37509903 37512184 2281 True 1807.000000 1807 81.056000 1060 3338 1 chr1A.!!$R2 2278
12 TraesCS1B01G092500 chr1A 57638178 57640294 2116 True 1524.500000 2348 93.407500 917 4028 2 chr1A.!!$R5 3111
13 TraesCS1B01G092500 chr1A 37502918 37504384 1466 True 1352.000000 1352 83.333000 1864 3330 1 chr1A.!!$R1 1466

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
754 755 0.171007 CCTTTTAGCCGCCATGTGTG 59.829 55.0 0.0 0.0 0.0 3.82 F
1758 1815 0.403655 TGATGCAGCAAGGGGTTGTA 59.596 50.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1963 0.599558 TGCTTCTTCCATGCTTGCAC 59.400 50.000 0.0 0.0 0.00 4.57 R
3668 3776 2.919494 GCCACCGCTTTCACCAAGG 61.919 63.158 0.0 0.0 32.37 3.61 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
136 137 8.908678 TCATATACATTATACACGTTTTCTCGC 58.091 33.333 0.00 0.00 0.00 5.03
137 138 8.696175 CATATACATTATACACGTTTTCTCGCA 58.304 33.333 0.00 0.00 0.00 5.10
138 139 5.849357 ACATTATACACGTTTTCTCGCAA 57.151 34.783 0.00 0.00 0.00 4.85
139 140 6.230849 ACATTATACACGTTTTCTCGCAAA 57.769 33.333 0.00 0.00 0.00 3.68
140 141 6.660722 ACATTATACACGTTTTCTCGCAAAA 58.339 32.000 0.00 0.00 0.00 2.44
141 142 7.133513 ACATTATACACGTTTTCTCGCAAAAA 58.866 30.769 0.00 0.00 0.00 1.94
663 664 2.684374 TGGATGCATGACTTCATTTCGG 59.316 45.455 2.46 0.00 33.61 4.30
664 665 2.684881 GGATGCATGACTTCATTTCGGT 59.315 45.455 2.46 0.00 33.61 4.69
665 666 3.129287 GGATGCATGACTTCATTTCGGTT 59.871 43.478 2.46 0.00 33.61 4.44
666 667 3.557577 TGCATGACTTCATTTCGGTTG 57.442 42.857 0.00 0.00 33.61 3.77
667 668 3.145286 TGCATGACTTCATTTCGGTTGA 58.855 40.909 0.00 0.00 33.61 3.18
668 669 3.758023 TGCATGACTTCATTTCGGTTGAT 59.242 39.130 0.00 0.00 33.61 2.57
669 670 4.218200 TGCATGACTTCATTTCGGTTGATT 59.782 37.500 0.00 0.00 33.61 2.57
670 671 5.163513 GCATGACTTCATTTCGGTTGATTT 58.836 37.500 0.00 0.00 33.61 2.17
671 672 5.287035 GCATGACTTCATTTCGGTTGATTTC 59.713 40.000 0.00 0.00 33.61 2.17
672 673 6.380995 CATGACTTCATTTCGGTTGATTTCA 58.619 36.000 0.00 0.00 33.61 2.69
673 674 6.573664 TGACTTCATTTCGGTTGATTTCAT 57.426 33.333 0.00 0.00 0.00 2.57
674 675 6.980593 TGACTTCATTTCGGTTGATTTCATT 58.019 32.000 0.00 0.00 0.00 2.57
675 676 7.083858 TGACTTCATTTCGGTTGATTTCATTC 58.916 34.615 0.00 0.00 0.00 2.67
676 677 6.980593 ACTTCATTTCGGTTGATTTCATTCA 58.019 32.000 0.00 0.00 0.00 2.57
677 678 7.605449 ACTTCATTTCGGTTGATTTCATTCAT 58.395 30.769 0.00 0.00 0.00 2.57
678 679 7.543172 ACTTCATTTCGGTTGATTTCATTCATG 59.457 33.333 0.00 0.00 0.00 3.07
679 680 7.155655 TCATTTCGGTTGATTTCATTCATGA 57.844 32.000 0.00 0.00 34.44 3.07
680 681 7.252708 TCATTTCGGTTGATTTCATTCATGAG 58.747 34.615 0.00 0.00 38.19 2.90
681 682 6.816134 TTTCGGTTGATTTCATTCATGAGA 57.184 33.333 0.00 0.00 38.19 3.27
682 683 6.816134 TTCGGTTGATTTCATTCATGAGAA 57.184 33.333 0.00 0.00 38.19 2.87
683 684 6.816134 TCGGTTGATTTCATTCATGAGAAA 57.184 33.333 11.31 11.31 38.19 2.52
684 685 6.611381 TCGGTTGATTTCATTCATGAGAAAC 58.389 36.000 11.18 7.34 38.19 2.78
685 686 6.430925 TCGGTTGATTTCATTCATGAGAAACT 59.569 34.615 11.18 3.38 38.19 2.66
686 687 6.525628 CGGTTGATTTCATTCATGAGAAACTG 59.474 38.462 11.18 3.12 38.19 3.16
687 688 6.810182 GGTTGATTTCATTCATGAGAAACTGG 59.190 38.462 11.18 0.00 38.19 4.00
688 689 7.309377 GGTTGATTTCATTCATGAGAAACTGGA 60.309 37.037 11.18 0.00 38.19 3.86
689 690 7.387119 TGATTTCATTCATGAGAAACTGGAG 57.613 36.000 11.18 0.00 38.19 3.86
690 691 7.170277 TGATTTCATTCATGAGAAACTGGAGA 58.830 34.615 11.18 0.00 38.19 3.71
691 692 7.832685 TGATTTCATTCATGAGAAACTGGAGAT 59.167 33.333 11.18 0.00 38.19 2.75
692 693 6.997239 TTCATTCATGAGAAACTGGAGATG 57.003 37.500 0.00 0.00 38.19 2.90
693 694 6.303903 TCATTCATGAGAAACTGGAGATGA 57.696 37.500 0.00 0.00 37.29 2.92
694 695 6.714278 TCATTCATGAGAAACTGGAGATGAA 58.286 36.000 0.00 0.00 37.29 2.57
695 696 7.344134 TCATTCATGAGAAACTGGAGATGAAT 58.656 34.615 0.00 0.00 39.82 2.57
696 697 7.498239 TCATTCATGAGAAACTGGAGATGAATC 59.502 37.037 0.00 0.00 38.08 2.52
697 698 6.556974 TCATGAGAAACTGGAGATGAATCT 57.443 37.500 0.00 0.00 40.50 2.40
698 699 6.955364 TCATGAGAAACTGGAGATGAATCTT 58.045 36.000 0.00 0.00 37.25 2.40
699 700 6.822170 TCATGAGAAACTGGAGATGAATCTTG 59.178 38.462 0.00 0.00 37.25 3.02
700 701 6.364568 TGAGAAACTGGAGATGAATCTTGA 57.635 37.500 0.00 0.00 37.25 3.02
701 702 6.772605 TGAGAAACTGGAGATGAATCTTGAA 58.227 36.000 0.00 0.00 37.25 2.69
702 703 6.877855 TGAGAAACTGGAGATGAATCTTGAAG 59.122 38.462 0.00 0.00 37.25 3.02
703 704 5.647225 AGAAACTGGAGATGAATCTTGAAGC 59.353 40.000 0.00 0.00 37.25 3.86
704 705 4.840716 ACTGGAGATGAATCTTGAAGCT 57.159 40.909 0.00 0.00 37.25 3.74
705 706 4.768583 ACTGGAGATGAATCTTGAAGCTC 58.231 43.478 0.00 0.00 37.25 4.09
706 707 4.224594 ACTGGAGATGAATCTTGAAGCTCA 59.775 41.667 0.00 0.36 37.25 4.26
707 708 5.104444 ACTGGAGATGAATCTTGAAGCTCAT 60.104 40.000 8.69 8.69 37.25 2.90
708 709 5.366460 TGGAGATGAATCTTGAAGCTCATC 58.634 41.667 20.38 20.38 42.92 2.92
709 710 5.104652 TGGAGATGAATCTTGAAGCTCATCA 60.105 40.000 25.46 12.64 44.33 3.07
710 711 5.821470 GGAGATGAATCTTGAAGCTCATCAA 59.179 40.000 25.46 6.00 44.33 2.57
721 722 5.819270 GAAGCTCATCAAGTTTCAAAAGC 57.181 39.130 0.00 0.00 42.86 3.51
722 723 4.924305 AGCTCATCAAGTTTCAAAAGCA 57.076 36.364 0.00 0.00 0.00 3.91
723 724 5.266733 AGCTCATCAAGTTTCAAAAGCAA 57.733 34.783 0.00 0.00 0.00 3.91
724 725 5.045872 AGCTCATCAAGTTTCAAAAGCAAC 58.954 37.500 0.00 0.00 0.00 4.17
725 726 4.085415 GCTCATCAAGTTTCAAAAGCAACG 60.085 41.667 0.00 0.00 0.00 4.10
726 727 5.242069 TCATCAAGTTTCAAAAGCAACGA 57.758 34.783 0.00 0.00 0.00 3.85
727 728 5.034152 TCATCAAGTTTCAAAAGCAACGAC 58.966 37.500 0.00 0.00 0.00 4.34
728 729 4.695217 TCAAGTTTCAAAAGCAACGACT 57.305 36.364 0.00 0.00 0.00 4.18
729 730 5.804692 TCAAGTTTCAAAAGCAACGACTA 57.195 34.783 0.00 0.00 0.00 2.59
730 731 5.806286 TCAAGTTTCAAAAGCAACGACTAG 58.194 37.500 0.00 0.00 0.00 2.57
731 732 5.353123 TCAAGTTTCAAAAGCAACGACTAGT 59.647 36.000 0.00 0.00 0.00 2.57
732 733 5.813080 AGTTTCAAAAGCAACGACTAGTT 57.187 34.783 0.00 0.00 45.45 2.24
733 734 6.190954 AGTTTCAAAAGCAACGACTAGTTT 57.809 33.333 0.00 0.00 42.02 2.66
734 735 7.311364 AGTTTCAAAAGCAACGACTAGTTTA 57.689 32.000 0.00 0.00 42.02 2.01
735 736 7.184779 AGTTTCAAAAGCAACGACTAGTTTAC 58.815 34.615 0.00 0.00 42.02 2.01
736 737 5.662211 TCAAAAGCAACGACTAGTTTACC 57.338 39.130 0.00 0.00 42.02 2.85
737 738 5.362263 TCAAAAGCAACGACTAGTTTACCT 58.638 37.500 0.00 0.00 42.02 3.08
738 739 5.818857 TCAAAAGCAACGACTAGTTTACCTT 59.181 36.000 0.00 0.00 42.02 3.50
739 740 6.316890 TCAAAAGCAACGACTAGTTTACCTTT 59.683 34.615 0.00 0.71 42.02 3.11
740 741 6.688637 AAAGCAACGACTAGTTTACCTTTT 57.311 33.333 0.00 0.00 42.02 2.27
741 742 7.790823 AAAGCAACGACTAGTTTACCTTTTA 57.209 32.000 0.00 0.00 42.02 1.52
742 743 7.417496 AAGCAACGACTAGTTTACCTTTTAG 57.583 36.000 0.00 0.00 42.02 1.85
743 744 5.407691 AGCAACGACTAGTTTACCTTTTAGC 59.592 40.000 0.00 0.00 42.02 3.09
744 745 5.390251 GCAACGACTAGTTTACCTTTTAGCC 60.390 44.000 0.00 0.00 42.02 3.93
745 746 4.488879 ACGACTAGTTTACCTTTTAGCCG 58.511 43.478 0.00 0.00 0.00 5.52
746 747 3.305361 CGACTAGTTTACCTTTTAGCCGC 59.695 47.826 0.00 0.00 0.00 6.53
747 748 3.603532 ACTAGTTTACCTTTTAGCCGCC 58.396 45.455 0.00 0.00 0.00 6.13
748 749 2.572209 AGTTTACCTTTTAGCCGCCA 57.428 45.000 0.00 0.00 0.00 5.69
749 750 3.081710 AGTTTACCTTTTAGCCGCCAT 57.918 42.857 0.00 0.00 0.00 4.40
750 751 2.752903 AGTTTACCTTTTAGCCGCCATG 59.247 45.455 0.00 0.00 0.00 3.66
751 752 2.490509 GTTTACCTTTTAGCCGCCATGT 59.509 45.455 0.00 0.00 0.00 3.21
752 753 1.745232 TACCTTTTAGCCGCCATGTG 58.255 50.000 0.00 0.00 0.00 3.21
753 754 0.251165 ACCTTTTAGCCGCCATGTGT 60.251 50.000 0.00 0.00 0.00 3.72
754 755 0.171007 CCTTTTAGCCGCCATGTGTG 59.829 55.000 0.00 0.00 0.00 3.82
769 770 6.124088 CCATGTGTGGCTCTCTATTTTAAC 57.876 41.667 0.00 0.00 39.01 2.01
770 771 5.882557 CCATGTGTGGCTCTCTATTTTAACT 59.117 40.000 0.00 0.00 39.01 2.24
771 772 6.375455 CCATGTGTGGCTCTCTATTTTAACTT 59.625 38.462 0.00 0.00 39.01 2.66
772 773 7.094205 CCATGTGTGGCTCTCTATTTTAACTTT 60.094 37.037 0.00 0.00 39.01 2.66
773 774 8.946085 CATGTGTGGCTCTCTATTTTAACTTTA 58.054 33.333 0.00 0.00 0.00 1.85
774 775 9.686683 ATGTGTGGCTCTCTATTTTAACTTTAT 57.313 29.630 0.00 0.00 0.00 1.40
775 776 9.515226 TGTGTGGCTCTCTATTTTAACTTTATT 57.485 29.630 0.00 0.00 0.00 1.40
788 789 9.797556 ATTTTAACTTTATTTGTATTCCCGAGC 57.202 29.630 0.00 0.00 0.00 5.03
789 790 5.479716 AACTTTATTTGTATTCCCGAGCG 57.520 39.130 0.00 0.00 0.00 5.03
790 791 4.510571 ACTTTATTTGTATTCCCGAGCGT 58.489 39.130 0.00 0.00 0.00 5.07
791 792 5.663456 ACTTTATTTGTATTCCCGAGCGTA 58.337 37.500 0.00 0.00 0.00 4.42
792 793 6.285990 ACTTTATTTGTATTCCCGAGCGTAT 58.714 36.000 0.00 0.00 0.00 3.06
793 794 6.764560 ACTTTATTTGTATTCCCGAGCGTATT 59.235 34.615 0.00 0.00 0.00 1.89
794 795 7.927629 ACTTTATTTGTATTCCCGAGCGTATTA 59.072 33.333 0.00 0.00 0.00 0.98
795 796 8.659925 TTTATTTGTATTCCCGAGCGTATTAA 57.340 30.769 0.00 0.00 0.00 1.40
796 797 8.659925 TTATTTGTATTCCCGAGCGTATTAAA 57.340 30.769 0.00 0.00 0.00 1.52
797 798 6.981762 TTTGTATTCCCGAGCGTATTAAAA 57.018 33.333 0.00 0.00 0.00 1.52
798 799 6.592798 TTGTATTCCCGAGCGTATTAAAAG 57.407 37.500 0.00 0.00 0.00 2.27
799 800 5.904941 TGTATTCCCGAGCGTATTAAAAGA 58.095 37.500 0.00 0.00 0.00 2.52
800 801 6.339730 TGTATTCCCGAGCGTATTAAAAGAA 58.660 36.000 0.00 0.00 0.00 2.52
801 802 6.817641 TGTATTCCCGAGCGTATTAAAAGAAA 59.182 34.615 0.00 0.00 0.00 2.52
802 803 5.535043 TTCCCGAGCGTATTAAAAGAAAC 57.465 39.130 0.00 0.00 0.00 2.78
803 804 3.613737 TCCCGAGCGTATTAAAAGAAACG 59.386 43.478 0.00 0.00 38.34 3.60
804 805 3.613737 CCCGAGCGTATTAAAAGAAACGA 59.386 43.478 0.00 0.00 37.53 3.85
805 806 4.259690 CCCGAGCGTATTAAAAGAAACGAG 60.260 45.833 0.00 0.00 37.53 4.18
806 807 4.560035 CCGAGCGTATTAAAAGAAACGAGA 59.440 41.667 0.00 0.00 37.53 4.04
807 808 5.470244 CGAGCGTATTAAAAGAAACGAGAC 58.530 41.667 0.00 0.00 37.53 3.36
808 809 5.060077 CGAGCGTATTAAAAGAAACGAGACA 59.940 40.000 0.00 0.00 37.53 3.41
809 810 6.237490 CGAGCGTATTAAAAGAAACGAGACAT 60.237 38.462 0.00 0.00 37.53 3.06
810 811 7.044510 CGAGCGTATTAAAAGAAACGAGACATA 60.045 37.037 0.00 0.00 37.53 2.29
862 863 0.482446 ACCAGGCCTGAATCCAAACA 59.518 50.000 34.91 0.00 0.00 2.83
864 865 1.272092 CCAGGCCTGAATCCAAACAGA 60.272 52.381 34.91 0.00 36.38 3.41
866 867 1.707427 AGGCCTGAATCCAAACAGACT 59.293 47.619 3.11 0.00 36.38 3.24
869 870 1.815003 CCTGAATCCAAACAGACTGCC 59.185 52.381 1.25 0.00 36.38 4.85
873 874 3.896888 TGAATCCAAACAGACTGCCATTT 59.103 39.130 1.25 0.00 0.00 2.32
877 878 2.886523 CCAAACAGACTGCCATTTCTGA 59.113 45.455 9.76 0.00 41.65 3.27
883 884 1.815003 GACTGCCATTTCTGAACCAGG 59.185 52.381 0.00 0.00 31.51 4.45
925 946 6.667558 TTTTACCCGTTTTCCATTTGGTAT 57.332 33.333 0.00 0.00 36.34 2.73
929 950 3.951680 CCCGTTTTCCATTTGGTATAGCT 59.048 43.478 3.20 0.00 36.34 3.32
937 958 5.211973 TCCATTTGGTATAGCTGAGACTCT 58.788 41.667 3.68 0.00 36.34 3.24
950 971 0.958382 AGACTCTTCTCAGTCGCGCT 60.958 55.000 5.56 0.00 46.52 5.92
952 973 1.582424 CTCTTCTCAGTCGCGCTCG 60.582 63.158 5.56 0.00 0.00 5.03
971 995 2.893398 GCCACTCCTACTCCACCG 59.107 66.667 0.00 0.00 0.00 4.94
974 998 1.982395 CACTCCTACTCCACCGGCA 60.982 63.158 0.00 0.00 0.00 5.69
1016 1041 2.124819 CATGGCTCGCCTCTGCTT 60.125 61.111 9.65 0.00 36.94 3.91
1058 1103 3.148279 CCGCCGCTACTCCTCCTT 61.148 66.667 0.00 0.00 0.00 3.36
1068 1113 1.684049 CTCCTCCTTCACCTCGCCT 60.684 63.158 0.00 0.00 0.00 5.52
1322 1376 1.448717 GAGAAGAAGCAGGACCGCC 60.449 63.158 4.93 0.00 0.00 6.13
1464 1518 1.220749 GATTGTCGCCAGCACCCTA 59.779 57.895 0.00 0.00 0.00 3.53
1579 1633 8.744652 CCATCTCATACTCCATAGTACTTAAGG 58.255 40.741 7.53 0.79 40.98 2.69
1758 1815 0.403655 TGATGCAGCAAGGGGTTGTA 59.596 50.000 0.00 0.00 0.00 2.41
1761 1818 1.228429 GCAGCAAGGGGTTGTACCA 60.228 57.895 0.00 0.00 41.02 3.25
1762 1819 1.244019 GCAGCAAGGGGTTGTACCAG 61.244 60.000 0.00 0.00 41.02 4.00
1795 1852 5.295292 ACATATAGCTCCATTATTGATGCGC 59.705 40.000 0.00 0.00 34.25 6.09
1902 1963 4.080919 TGGAACTCATTCATGTACTCCCTG 60.081 45.833 0.00 0.00 36.46 4.45
2041 2102 5.882557 GGATGCCTCACCGATATGATTAATT 59.117 40.000 0.00 0.00 0.00 1.40
2130 2191 6.363882 TGGATATGCTAAATGTGGAATGACA 58.636 36.000 0.00 0.00 0.00 3.58
2148 2209 4.629092 TGACAGATGAAGCTATGCTCATC 58.371 43.478 15.44 15.44 38.25 2.92
2250 2311 1.005097 AGGCTGTCTGATGCAATGGAA 59.995 47.619 0.00 0.00 0.00 3.53
2277 2338 3.746045 AATGAGATGATTGCAATGGGC 57.254 42.857 18.59 2.87 45.13 5.36
2586 2647 2.680805 CGGAGTACTTGATGCCATGGTT 60.681 50.000 14.67 0.59 0.00 3.67
2959 3020 8.288913 TCAATACCATGATTAATGCAATGTACG 58.711 33.333 0.00 0.00 34.67 3.67
2983 3044 4.257731 GGTTAAGGGAAGAGAAGAAGCTG 58.742 47.826 0.00 0.00 0.00 4.24
3405 3471 2.703536 TCAGAAGGTACAGTTTCAGCCA 59.296 45.455 0.00 0.00 0.00 4.75
3431 3497 4.091549 AGGCAAATGACACAATGAGGATT 58.908 39.130 0.00 0.00 0.00 3.01
3668 3776 6.708502 AGTCTCTCTAAAGCAGGAAAGAAAAC 59.291 38.462 0.00 0.00 0.00 2.43
3807 3915 5.810587 CAGCAAGAGCATGAGCATTAAATTT 59.189 36.000 0.00 0.00 45.49 1.82
3838 3946 1.327303 TGGCGAAAAATGTCAAGGCT 58.673 45.000 0.00 0.00 0.00 4.58
3844 3952 4.385748 GCGAAAAATGTCAAGGCTAAAAGG 59.614 41.667 0.00 0.00 0.00 3.11
3884 3992 2.562298 CTGTCTCTCCAGCTCTTCAACT 59.438 50.000 0.00 0.00 0.00 3.16
4043 4151 7.721399 TCTGAAAGGTTTAAAGCTTCTCAAGAT 59.279 33.333 27.71 13.88 45.17 2.40
4044 4152 8.918202 TGAAAGGTTTAAAGCTTCTCAAGATA 57.082 30.769 27.71 11.66 45.17 1.98
4047 4155 6.418946 AGGTTTAAAGCTTCTCAAGATAGGG 58.581 40.000 14.07 0.00 31.69 3.53
4075 4183 1.271163 GGACGGTTGGAGATGGACAAA 60.271 52.381 0.00 0.00 0.00 2.83
4076 4184 1.804748 GACGGTTGGAGATGGACAAAC 59.195 52.381 0.00 0.00 0.00 2.93
4078 4186 1.806542 CGGTTGGAGATGGACAAACAG 59.193 52.381 0.00 0.00 34.02 3.16
4079 4187 2.810400 CGGTTGGAGATGGACAAACAGT 60.810 50.000 0.00 0.00 34.02 3.55
4080 4188 3.556213 CGGTTGGAGATGGACAAACAGTA 60.556 47.826 0.00 0.00 34.02 2.74
4081 4189 4.394729 GGTTGGAGATGGACAAACAGTAA 58.605 43.478 0.00 0.00 34.52 2.24
4082 4190 4.455877 GGTTGGAGATGGACAAACAGTAAG 59.544 45.833 0.00 0.00 34.52 2.34
4083 4191 3.674997 TGGAGATGGACAAACAGTAAGC 58.325 45.455 0.00 0.00 0.00 3.09
4084 4192 3.072330 TGGAGATGGACAAACAGTAAGCA 59.928 43.478 0.00 0.00 0.00 3.91
4085 4193 4.263462 TGGAGATGGACAAACAGTAAGCAT 60.263 41.667 0.00 0.00 0.00 3.79
4086 4194 5.045942 TGGAGATGGACAAACAGTAAGCATA 60.046 40.000 0.00 0.00 0.00 3.14
4087 4195 6.058183 GGAGATGGACAAACAGTAAGCATAT 58.942 40.000 0.00 0.00 0.00 1.78
4088 4196 6.017605 GGAGATGGACAAACAGTAAGCATATG 60.018 42.308 0.00 0.00 0.00 1.78
4089 4197 5.824624 AGATGGACAAACAGTAAGCATATGG 59.175 40.000 4.56 0.00 0.00 2.74
4090 4198 3.694072 TGGACAAACAGTAAGCATATGGC 59.306 43.478 4.56 0.00 45.30 4.40
4105 4213 4.566759 GCATATGGCATGATTCATGATTGC 59.433 41.667 26.94 20.71 43.81 3.56
4106 4214 5.624509 GCATATGGCATGATTCATGATTGCT 60.625 40.000 26.94 10.57 43.81 3.91
4107 4215 3.726291 TGGCATGATTCATGATTGCTG 57.274 42.857 26.94 4.03 43.81 4.41
4108 4216 3.292460 TGGCATGATTCATGATTGCTGA 58.708 40.909 26.94 4.88 43.81 4.26
4109 4217 3.317993 TGGCATGATTCATGATTGCTGAG 59.682 43.478 26.94 1.22 43.81 3.35
4110 4218 3.568430 GGCATGATTCATGATTGCTGAGA 59.432 43.478 26.94 0.00 43.81 3.27
4111 4219 4.537965 GCATGATTCATGATTGCTGAGAC 58.462 43.478 26.94 4.67 43.81 3.36
4112 4220 4.036380 GCATGATTCATGATTGCTGAGACA 59.964 41.667 26.94 0.00 43.81 3.41
4113 4221 5.449999 GCATGATTCATGATTGCTGAGACAA 60.450 40.000 26.94 0.00 43.81 3.18
4114 4222 5.813080 TGATTCATGATTGCTGAGACAAG 57.187 39.130 0.00 0.00 31.96 3.16
4115 4223 5.493809 TGATTCATGATTGCTGAGACAAGA 58.506 37.500 0.00 0.00 31.96 3.02
4116 4224 5.353400 TGATTCATGATTGCTGAGACAAGAC 59.647 40.000 0.00 0.00 31.96 3.01
4158 4266 3.513662 TCGAATTTTGCATGCATTGGAG 58.486 40.909 23.37 11.77 0.00 3.86
4251 4361 6.694411 GCAAGAACATATGCAGAAATTACAGG 59.306 38.462 1.58 0.00 42.12 4.00
4321 4431 5.634118 TCCATTCACTGAAATCAAAGAGGT 58.366 37.500 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 8.908678 GCGAGAAAACGTGTATAATGTATATGA 58.091 33.333 0.00 0.00 35.59 2.15
111 112 8.696175 TGCGAGAAAACGTGTATAATGTATATG 58.304 33.333 0.00 0.00 35.59 1.78
112 113 8.806177 TGCGAGAAAACGTGTATAATGTATAT 57.194 30.769 0.00 0.00 35.59 0.86
113 114 8.631676 TTGCGAGAAAACGTGTATAATGTATA 57.368 30.769 0.00 0.00 35.59 1.47
114 115 7.528481 TTGCGAGAAAACGTGTATAATGTAT 57.472 32.000 0.00 0.00 35.59 2.29
115 116 6.947903 TTGCGAGAAAACGTGTATAATGTA 57.052 33.333 0.00 0.00 35.59 2.29
116 117 5.849357 TTGCGAGAAAACGTGTATAATGT 57.151 34.783 0.00 0.00 35.59 2.71
117 118 7.541743 TTTTTGCGAGAAAACGTGTATAATG 57.458 32.000 0.00 0.00 35.59 1.90
642 643 2.684374 CCGAAATGAAGTCATGCATCCA 59.316 45.455 0.00 0.00 36.56 3.41
643 644 2.684881 ACCGAAATGAAGTCATGCATCC 59.315 45.455 0.00 0.00 36.56 3.51
644 645 4.100529 CAACCGAAATGAAGTCATGCATC 58.899 43.478 0.00 0.00 36.56 3.91
645 646 3.758023 TCAACCGAAATGAAGTCATGCAT 59.242 39.130 0.00 0.00 36.56 3.96
646 647 3.145286 TCAACCGAAATGAAGTCATGCA 58.855 40.909 0.00 0.00 36.56 3.96
647 648 3.829886 TCAACCGAAATGAAGTCATGC 57.170 42.857 0.00 0.00 36.56 4.06
648 649 6.380995 TGAAATCAACCGAAATGAAGTCATG 58.619 36.000 0.00 0.00 36.56 3.07
649 650 6.573664 TGAAATCAACCGAAATGAAGTCAT 57.426 33.333 0.00 0.00 38.41 3.06
650 651 6.573664 ATGAAATCAACCGAAATGAAGTCA 57.426 33.333 0.00 0.00 31.98 3.41
651 652 7.083858 TGAATGAAATCAACCGAAATGAAGTC 58.916 34.615 0.00 0.00 0.00 3.01
652 653 6.980593 TGAATGAAATCAACCGAAATGAAGT 58.019 32.000 0.00 0.00 0.00 3.01
653 654 7.756272 TCATGAATGAAATCAACCGAAATGAAG 59.244 33.333 0.00 0.00 33.08 3.02
654 655 7.600960 TCATGAATGAAATCAACCGAAATGAA 58.399 30.769 0.00 0.00 33.08 2.57
655 656 7.121020 TCTCATGAATGAAATCAACCGAAATGA 59.879 33.333 0.00 0.00 36.18 2.57
656 657 7.252708 TCTCATGAATGAAATCAACCGAAATG 58.747 34.615 0.00 0.00 36.18 2.32
657 658 7.395190 TCTCATGAATGAAATCAACCGAAAT 57.605 32.000 0.00 0.00 36.18 2.17
658 659 6.816134 TCTCATGAATGAAATCAACCGAAA 57.184 33.333 0.00 0.00 36.18 3.46
659 660 6.816134 TTCTCATGAATGAAATCAACCGAA 57.184 33.333 0.00 0.00 36.18 4.30
660 661 6.430925 AGTTTCTCATGAATGAAATCAACCGA 59.569 34.615 11.89 0.00 36.18 4.69
661 662 6.525628 CAGTTTCTCATGAATGAAATCAACCG 59.474 38.462 11.89 0.00 36.18 4.44
662 663 6.810182 CCAGTTTCTCATGAATGAAATCAACC 59.190 38.462 11.89 1.78 36.18 3.77
663 664 7.596494 TCCAGTTTCTCATGAATGAAATCAAC 58.404 34.615 11.89 2.53 36.18 3.18
664 665 7.666804 TCTCCAGTTTCTCATGAATGAAATCAA 59.333 33.333 11.89 1.33 36.18 2.57
665 666 7.170277 TCTCCAGTTTCTCATGAATGAAATCA 58.830 34.615 11.89 0.00 36.18 2.57
666 667 7.621428 TCTCCAGTTTCTCATGAATGAAATC 57.379 36.000 11.89 7.32 36.18 2.17
667 668 7.832685 TCATCTCCAGTTTCTCATGAATGAAAT 59.167 33.333 11.89 0.00 36.18 2.17
668 669 7.170277 TCATCTCCAGTTTCTCATGAATGAAA 58.830 34.615 6.13 6.13 36.18 2.69
669 670 6.714278 TCATCTCCAGTTTCTCATGAATGAA 58.286 36.000 0.00 0.00 36.18 2.57
670 671 6.303903 TCATCTCCAGTTTCTCATGAATGA 57.696 37.500 0.00 0.00 35.16 2.57
671 672 6.997239 TTCATCTCCAGTTTCTCATGAATG 57.003 37.500 0.00 0.00 31.56 2.67
672 673 7.575505 AGATTCATCTCCAGTTTCTCATGAAT 58.424 34.615 0.00 4.94 41.48 2.57
673 674 6.955364 AGATTCATCTCCAGTTTCTCATGAA 58.045 36.000 0.00 0.00 35.35 2.57
674 675 6.556974 AGATTCATCTCCAGTTTCTCATGA 57.443 37.500 0.00 0.00 29.30 3.07
675 676 6.822170 TCAAGATTCATCTCCAGTTTCTCATG 59.178 38.462 0.00 0.00 35.76 3.07
676 677 6.955364 TCAAGATTCATCTCCAGTTTCTCAT 58.045 36.000 0.00 0.00 35.76 2.90
677 678 6.364568 TCAAGATTCATCTCCAGTTTCTCA 57.635 37.500 0.00 0.00 35.76 3.27
678 679 6.183360 GCTTCAAGATTCATCTCCAGTTTCTC 60.183 42.308 0.00 0.00 35.76 2.87
679 680 5.647225 GCTTCAAGATTCATCTCCAGTTTCT 59.353 40.000 0.00 0.00 35.76 2.52
680 681 5.647225 AGCTTCAAGATTCATCTCCAGTTTC 59.353 40.000 0.00 0.00 35.76 2.78
681 682 5.568392 AGCTTCAAGATTCATCTCCAGTTT 58.432 37.500 0.00 0.00 35.76 2.66
682 683 5.176741 AGCTTCAAGATTCATCTCCAGTT 57.823 39.130 0.00 0.00 35.76 3.16
683 684 4.224594 TGAGCTTCAAGATTCATCTCCAGT 59.775 41.667 0.00 0.00 35.76 4.00
684 685 4.767478 TGAGCTTCAAGATTCATCTCCAG 58.233 43.478 0.00 0.00 35.76 3.86
685 686 4.831674 TGAGCTTCAAGATTCATCTCCA 57.168 40.909 0.00 0.00 35.76 3.86
686 687 5.366460 TGATGAGCTTCAAGATTCATCTCC 58.634 41.667 22.70 7.65 43.87 3.71
687 688 6.922247 TTGATGAGCTTCAAGATTCATCTC 57.078 37.500 22.70 7.05 43.87 2.75
697 698 5.750067 GCTTTTGAAACTTGATGAGCTTCAA 59.250 36.000 1.07 1.07 44.50 2.69
698 699 5.163530 TGCTTTTGAAACTTGATGAGCTTCA 60.164 36.000 0.00 0.00 38.38 3.02
699 700 5.284079 TGCTTTTGAAACTTGATGAGCTTC 58.716 37.500 0.00 0.00 32.29 3.86
700 701 5.266733 TGCTTTTGAAACTTGATGAGCTT 57.733 34.783 0.00 0.00 0.00 3.74
701 702 4.924305 TGCTTTTGAAACTTGATGAGCT 57.076 36.364 0.00 0.00 0.00 4.09
702 703 4.085415 CGTTGCTTTTGAAACTTGATGAGC 60.085 41.667 0.00 0.00 35.80 4.26
703 704 5.172053 GTCGTTGCTTTTGAAACTTGATGAG 59.828 40.000 0.00 0.00 35.80 2.90
704 705 5.034152 GTCGTTGCTTTTGAAACTTGATGA 58.966 37.500 0.00 0.00 35.80 2.92
705 706 5.036737 AGTCGTTGCTTTTGAAACTTGATG 58.963 37.500 0.00 0.00 35.80 3.07
706 707 5.248870 AGTCGTTGCTTTTGAAACTTGAT 57.751 34.783 0.00 0.00 35.80 2.57
707 708 4.695217 AGTCGTTGCTTTTGAAACTTGA 57.305 36.364 0.00 0.00 35.80 3.02
708 709 5.569413 ACTAGTCGTTGCTTTTGAAACTTG 58.431 37.500 0.00 0.00 35.80 3.16
709 710 5.813080 ACTAGTCGTTGCTTTTGAAACTT 57.187 34.783 0.00 0.00 35.80 2.66
710 711 5.813080 AACTAGTCGTTGCTTTTGAAACT 57.187 34.783 0.00 0.00 35.80 2.66
711 712 6.412943 GGTAAACTAGTCGTTGCTTTTGAAAC 59.587 38.462 0.00 0.00 35.61 2.78
712 713 6.316890 AGGTAAACTAGTCGTTGCTTTTGAAA 59.683 34.615 0.00 0.00 35.61 2.69
713 714 5.818857 AGGTAAACTAGTCGTTGCTTTTGAA 59.181 36.000 0.00 0.00 35.61 2.69
714 715 5.362263 AGGTAAACTAGTCGTTGCTTTTGA 58.638 37.500 0.00 0.00 35.61 2.69
715 716 5.668558 AGGTAAACTAGTCGTTGCTTTTG 57.331 39.130 0.00 0.00 35.61 2.44
716 717 6.688637 AAAGGTAAACTAGTCGTTGCTTTT 57.311 33.333 0.00 0.00 35.61 2.27
717 718 6.688637 AAAAGGTAAACTAGTCGTTGCTTT 57.311 33.333 0.00 0.00 35.61 3.51
718 719 6.073385 GCTAAAAGGTAAACTAGTCGTTGCTT 60.073 38.462 0.00 0.00 35.61 3.91
719 720 5.407691 GCTAAAAGGTAAACTAGTCGTTGCT 59.592 40.000 0.00 0.00 35.61 3.91
720 721 5.390251 GGCTAAAAGGTAAACTAGTCGTTGC 60.390 44.000 0.00 0.00 35.61 4.17
721 722 5.164022 CGGCTAAAAGGTAAACTAGTCGTTG 60.164 44.000 0.00 0.00 35.36 4.10
722 723 4.925646 CGGCTAAAAGGTAAACTAGTCGTT 59.074 41.667 0.00 0.00 35.36 3.85
723 724 4.488879 CGGCTAAAAGGTAAACTAGTCGT 58.511 43.478 0.00 0.00 35.36 4.34
724 725 3.305361 GCGGCTAAAAGGTAAACTAGTCG 59.695 47.826 0.00 0.00 41.27 4.18
725 726 3.620374 GGCGGCTAAAAGGTAAACTAGTC 59.380 47.826 0.00 0.00 0.00 2.59
726 727 3.008266 TGGCGGCTAAAAGGTAAACTAGT 59.992 43.478 11.43 0.00 0.00 2.57
727 728 3.602483 TGGCGGCTAAAAGGTAAACTAG 58.398 45.455 11.43 0.00 0.00 2.57
728 729 3.699411 TGGCGGCTAAAAGGTAAACTA 57.301 42.857 11.43 0.00 0.00 2.24
729 730 2.572209 TGGCGGCTAAAAGGTAAACT 57.428 45.000 11.43 0.00 0.00 2.66
730 731 2.490509 ACATGGCGGCTAAAAGGTAAAC 59.509 45.455 11.43 0.00 0.00 2.01
731 732 2.490115 CACATGGCGGCTAAAAGGTAAA 59.510 45.455 11.43 0.00 0.00 2.01
732 733 2.088423 CACATGGCGGCTAAAAGGTAA 58.912 47.619 11.43 0.00 0.00 2.85
733 734 1.003812 ACACATGGCGGCTAAAAGGTA 59.996 47.619 11.43 0.00 0.00 3.08
734 735 0.251165 ACACATGGCGGCTAAAAGGT 60.251 50.000 11.43 0.00 0.00 3.50
735 736 0.171007 CACACATGGCGGCTAAAAGG 59.829 55.000 11.43 0.00 0.00 3.11
736 737 0.171007 CCACACATGGCGGCTAAAAG 59.829 55.000 11.43 0.00 39.82 2.27
737 738 2.262183 CCACACATGGCGGCTAAAA 58.738 52.632 11.43 0.00 39.82 1.52
738 739 3.995074 CCACACATGGCGGCTAAA 58.005 55.556 11.43 0.00 39.82 1.85
747 748 6.992063 AGTTAAAATAGAGAGCCACACATG 57.008 37.500 0.00 0.00 0.00 3.21
748 749 9.686683 ATAAAGTTAAAATAGAGAGCCACACAT 57.313 29.630 0.00 0.00 0.00 3.21
749 750 9.515226 AATAAAGTTAAAATAGAGAGCCACACA 57.485 29.630 0.00 0.00 0.00 3.72
762 763 9.797556 GCTCGGGAATACAAATAAAGTTAAAAT 57.202 29.630 0.00 0.00 0.00 1.82
763 764 7.964011 CGCTCGGGAATACAAATAAAGTTAAAA 59.036 33.333 0.00 0.00 0.00 1.52
764 765 7.119553 ACGCTCGGGAATACAAATAAAGTTAAA 59.880 33.333 0.00 0.00 0.00 1.52
765 766 6.594937 ACGCTCGGGAATACAAATAAAGTTAA 59.405 34.615 0.00 0.00 0.00 2.01
766 767 6.108015 ACGCTCGGGAATACAAATAAAGTTA 58.892 36.000 0.00 0.00 0.00 2.24
767 768 4.939439 ACGCTCGGGAATACAAATAAAGTT 59.061 37.500 0.00 0.00 0.00 2.66
768 769 4.510571 ACGCTCGGGAATACAAATAAAGT 58.489 39.130 0.00 0.00 0.00 2.66
769 770 6.780706 ATACGCTCGGGAATACAAATAAAG 57.219 37.500 0.00 0.00 0.00 1.85
770 771 8.659925 TTAATACGCTCGGGAATACAAATAAA 57.340 30.769 0.00 0.00 0.00 1.40
771 772 8.659925 TTTAATACGCTCGGGAATACAAATAA 57.340 30.769 0.00 0.00 0.00 1.40
772 773 8.659925 TTTTAATACGCTCGGGAATACAAATA 57.340 30.769 0.00 0.00 0.00 1.40
773 774 7.496591 TCTTTTAATACGCTCGGGAATACAAAT 59.503 33.333 0.00 0.00 0.00 2.32
774 775 6.817641 TCTTTTAATACGCTCGGGAATACAAA 59.182 34.615 0.00 0.00 0.00 2.83
775 776 6.339730 TCTTTTAATACGCTCGGGAATACAA 58.660 36.000 0.00 0.00 0.00 2.41
776 777 5.904941 TCTTTTAATACGCTCGGGAATACA 58.095 37.500 0.00 0.00 0.00 2.29
777 778 6.833342 TTCTTTTAATACGCTCGGGAATAC 57.167 37.500 0.00 0.00 0.00 1.89
778 779 6.019640 CGTTTCTTTTAATACGCTCGGGAATA 60.020 38.462 0.00 0.00 0.00 1.75
779 780 5.220529 CGTTTCTTTTAATACGCTCGGGAAT 60.221 40.000 0.00 0.00 0.00 3.01
780 781 4.091800 CGTTTCTTTTAATACGCTCGGGAA 59.908 41.667 0.00 0.00 0.00 3.97
781 782 3.613737 CGTTTCTTTTAATACGCTCGGGA 59.386 43.478 0.00 0.00 0.00 5.14
782 783 3.613737 TCGTTTCTTTTAATACGCTCGGG 59.386 43.478 0.00 0.00 34.24 5.14
783 784 4.560035 TCTCGTTTCTTTTAATACGCTCGG 59.440 41.667 0.00 0.00 34.24 4.63
784 785 5.060077 TGTCTCGTTTCTTTTAATACGCTCG 59.940 40.000 0.00 0.00 34.24 5.03
785 786 6.385537 TGTCTCGTTTCTTTTAATACGCTC 57.614 37.500 0.00 0.00 34.24 5.03
786 787 6.963049 ATGTCTCGTTTCTTTTAATACGCT 57.037 33.333 0.00 0.00 34.24 5.07
787 788 7.335491 CCTATGTCTCGTTTCTTTTAATACGC 58.665 38.462 0.00 0.00 34.24 4.42
788 789 7.222224 AGCCTATGTCTCGTTTCTTTTAATACG 59.778 37.037 0.00 0.00 35.46 3.06
789 790 8.421673 AGCCTATGTCTCGTTTCTTTTAATAC 57.578 34.615 0.00 0.00 0.00 1.89
790 791 8.879759 CAAGCCTATGTCTCGTTTCTTTTAATA 58.120 33.333 0.00 0.00 0.00 0.98
791 792 7.606456 TCAAGCCTATGTCTCGTTTCTTTTAAT 59.394 33.333 0.00 0.00 0.00 1.40
792 793 6.932400 TCAAGCCTATGTCTCGTTTCTTTTAA 59.068 34.615 0.00 0.00 0.00 1.52
793 794 6.367969 GTCAAGCCTATGTCTCGTTTCTTTTA 59.632 38.462 0.00 0.00 0.00 1.52
794 795 5.179555 GTCAAGCCTATGTCTCGTTTCTTTT 59.820 40.000 0.00 0.00 0.00 2.27
795 796 4.691216 GTCAAGCCTATGTCTCGTTTCTTT 59.309 41.667 0.00 0.00 0.00 2.52
796 797 4.246458 GTCAAGCCTATGTCTCGTTTCTT 58.754 43.478 0.00 0.00 0.00 2.52
797 798 3.368531 GGTCAAGCCTATGTCTCGTTTCT 60.369 47.826 0.00 0.00 0.00 2.52
798 799 2.930682 GGTCAAGCCTATGTCTCGTTTC 59.069 50.000 0.00 0.00 0.00 2.78
799 800 2.674177 CGGTCAAGCCTATGTCTCGTTT 60.674 50.000 0.00 0.00 34.25 3.60
800 801 1.135083 CGGTCAAGCCTATGTCTCGTT 60.135 52.381 0.00 0.00 34.25 3.85
801 802 0.456221 CGGTCAAGCCTATGTCTCGT 59.544 55.000 0.00 0.00 34.25 4.18
802 803 0.249073 CCGGTCAAGCCTATGTCTCG 60.249 60.000 0.00 0.00 34.25 4.04
803 804 1.067821 CTCCGGTCAAGCCTATGTCTC 59.932 57.143 0.00 0.00 34.25 3.36
804 805 1.115467 CTCCGGTCAAGCCTATGTCT 58.885 55.000 0.00 0.00 34.25 3.41
805 806 0.105039 CCTCCGGTCAAGCCTATGTC 59.895 60.000 0.00 0.00 34.25 3.06
806 807 1.972660 GCCTCCGGTCAAGCCTATGT 61.973 60.000 0.00 0.00 34.25 2.29
807 808 1.227674 GCCTCCGGTCAAGCCTATG 60.228 63.158 0.00 0.00 34.25 2.23
808 809 1.689233 TGCCTCCGGTCAAGCCTAT 60.689 57.895 0.00 0.00 34.25 2.57
809 810 2.284331 TGCCTCCGGTCAAGCCTA 60.284 61.111 0.00 0.00 34.25 3.93
810 811 3.710722 CTGCCTCCGGTCAAGCCT 61.711 66.667 0.00 0.00 34.25 4.58
828 829 0.944311 CTGGTCCAACGACAGAACGG 60.944 60.000 0.00 0.00 41.13 4.44
831 832 1.070786 GCCTGGTCCAACGACAGAA 59.929 57.895 0.00 0.00 41.13 3.02
834 835 2.847234 AGGCCTGGTCCAACGACA 60.847 61.111 3.11 0.00 41.13 4.35
862 863 2.553904 CCTGGTTCAGAAATGGCAGTCT 60.554 50.000 0.00 0.00 32.44 3.24
864 865 1.915141 CCTGGTTCAGAAATGGCAGT 58.085 50.000 0.00 0.00 32.44 4.40
866 867 0.899717 GGCCTGGTTCAGAAATGGCA 60.900 55.000 18.44 0.00 41.86 4.92
869 870 0.322456 TCCGGCCTGGTTCAGAAATG 60.322 55.000 12.46 0.00 39.52 2.32
873 874 2.203788 ACTCCGGCCTGGTTCAGA 60.204 61.111 12.46 0.00 39.52 3.27
877 878 3.322466 CCTCACTCCGGCCTGGTT 61.322 66.667 12.46 0.34 39.52 3.67
950 971 3.138798 GGAGTAGGAGTGGCGCGA 61.139 66.667 12.10 0.00 0.00 5.87
952 973 2.184579 GTGGAGTAGGAGTGGCGC 59.815 66.667 0.00 0.00 0.00 6.53
962 986 2.201708 TGTTCGTGCCGGTGGAGTA 61.202 57.895 1.90 0.00 0.00 2.59
971 995 3.723348 GGCCTTCGTGTTCGTGCC 61.723 66.667 0.00 0.00 38.86 5.01
1058 1103 2.636412 CGTGAAGGAGGCGAGGTGA 61.636 63.158 0.00 0.00 0.00 4.02
1426 1480 2.044555 GGTTTACCTTGAGGCCCGC 61.045 63.158 0.00 0.00 39.32 6.13
1439 1493 1.271108 TGCTGGCGACAATCAGGTTTA 60.271 47.619 0.00 0.00 42.06 2.01
1445 1499 1.549243 TAGGGTGCTGGCGACAATCA 61.549 55.000 0.00 0.00 42.06 2.57
1449 1503 2.603473 AGTAGGGTGCTGGCGACA 60.603 61.111 0.00 0.00 39.59 4.35
1464 1518 0.322277 CATGGCAGAGGCACTTGAGT 60.322 55.000 0.00 0.00 41.55 3.41
1579 1633 3.808728 TCCTGCTATTGTCACATAAGCC 58.191 45.455 8.92 0.00 0.00 4.35
1676 1733 9.342308 CTTCCTTAAAGAAGCCATGTATGATTA 57.658 33.333 0.93 0.00 37.08 1.75
1678 1735 6.774656 CCTTCCTTAAAGAAGCCATGTATGAT 59.225 38.462 8.13 0.00 41.65 2.45
1683 1740 3.564352 CCCCTTCCTTAAAGAAGCCATGT 60.564 47.826 8.13 0.00 41.65 3.21
1770 1827 6.712549 CGCATCAATAATGGAGCTATATGTG 58.287 40.000 0.00 0.00 35.77 3.21
1795 1852 0.896940 ATTGCCCTGACCTTGCACAG 60.897 55.000 0.00 0.00 34.16 3.66
1902 1963 0.599558 TGCTTCTTCCATGCTTGCAC 59.400 50.000 0.00 0.00 0.00 4.57
1942 2003 1.002134 CCTTGGCGGTCATGGAGTT 60.002 57.895 8.75 0.00 41.70 3.01
2041 2102 6.589523 CCATTGCGTTCCATTGAATTAAAGAA 59.410 34.615 0.00 0.00 31.98 2.52
2059 2120 2.682856 AGTTGGCTACAATACCATTGCG 59.317 45.455 1.24 0.00 39.13 4.85
2108 2169 7.734924 TCTGTCATTCCACATTTAGCATATC 57.265 36.000 0.00 0.00 0.00 1.63
2130 2191 6.183361 TGGTAAAGATGAGCATAGCTTCATCT 60.183 38.462 18.77 18.77 45.60 2.90
2148 2209 6.279882 TCCTTGTTCTTGCATTTTGGTAAAG 58.720 36.000 0.00 0.00 0.00 1.85
2250 2311 7.767198 CCCATTGCAATCATCTCATTTAGTTTT 59.233 33.333 9.53 0.00 0.00 2.43
2959 3020 3.263261 CTTCTTCTCTTCCCTTAACCGC 58.737 50.000 0.00 0.00 0.00 5.68
2983 3044 5.653507 TGATATTGCAGCAAACAAATCCTC 58.346 37.500 12.97 1.49 0.00 3.71
3405 3471 4.021719 CCTCATTGTGTCATTTGCCTTCTT 60.022 41.667 0.00 0.00 0.00 2.52
3414 3480 8.086522 CAGAAAAAGAATCCTCATTGTGTCATT 58.913 33.333 0.00 0.00 0.00 2.57
3420 3486 8.868522 TCATACAGAAAAAGAATCCTCATTGT 57.131 30.769 0.00 0.00 0.00 2.71
3421 3487 9.784680 CTTCATACAGAAAAAGAATCCTCATTG 57.215 33.333 0.00 0.00 35.40 2.82
3431 3497 9.442047 GAAGAGGAATCTTCATACAGAAAAAGA 57.558 33.333 12.04 0.00 43.98 2.52
3461 3527 4.039004 CCATCCTCATACAGTCCTCTCAAG 59.961 50.000 0.00 0.00 0.00 3.02
3668 3776 2.919494 GCCACCGCTTTCACCAAGG 61.919 63.158 0.00 0.00 32.37 3.61
3807 3915 3.802948 TTTTCGCCAACTAAGCCAAAA 57.197 38.095 0.00 0.00 29.62 2.44
3838 3946 3.430453 CCAAGGCATCCACTTCCTTTTA 58.570 45.455 0.00 0.00 38.08 1.52
3844 3952 0.813821 GAAGCCAAGGCATCCACTTC 59.186 55.000 14.40 3.41 44.88 3.01
3884 3992 4.714802 TCCTTGTCTAGCTAGCATGGTAAA 59.285 41.667 28.69 18.14 32.21 2.01
4043 4151 2.502538 CCAACCGTCCAACTAATCCCTA 59.497 50.000 0.00 0.00 0.00 3.53
4044 4152 1.280998 CCAACCGTCCAACTAATCCCT 59.719 52.381 0.00 0.00 0.00 4.20
4047 4155 3.604875 TCTCCAACCGTCCAACTAATC 57.395 47.619 0.00 0.00 0.00 1.75
4075 4183 5.379187 TGAATCATGCCATATGCTTACTGT 58.621 37.500 0.00 0.00 42.00 3.55
4076 4184 5.952526 TGAATCATGCCATATGCTTACTG 57.047 39.130 0.00 0.00 42.00 2.74
4078 4186 6.505044 TCATGAATCATGCCATATGCTTAC 57.495 37.500 17.81 0.00 41.18 2.34
4079 4187 7.543756 CAATCATGAATCATGCCATATGCTTA 58.456 34.615 17.81 0.00 41.18 3.09
4080 4188 6.398095 CAATCATGAATCATGCCATATGCTT 58.602 36.000 17.81 0.00 41.18 3.91
4081 4189 5.624509 GCAATCATGAATCATGCCATATGCT 60.625 40.000 17.81 0.00 41.18 3.79
4082 4190 4.566759 GCAATCATGAATCATGCCATATGC 59.433 41.667 17.81 16.84 41.18 3.14
4083 4191 5.807011 CAGCAATCATGAATCATGCCATATG 59.193 40.000 17.81 12.04 41.18 1.78
4084 4192 5.714806 TCAGCAATCATGAATCATGCCATAT 59.285 36.000 17.81 4.02 41.18 1.78
4085 4193 5.074115 TCAGCAATCATGAATCATGCCATA 58.926 37.500 17.81 1.64 41.18 2.74
4086 4194 3.895041 TCAGCAATCATGAATCATGCCAT 59.105 39.130 17.81 5.08 41.18 4.40
4087 4195 3.292460 TCAGCAATCATGAATCATGCCA 58.708 40.909 17.81 2.75 41.18 4.92
4088 4196 3.568430 TCTCAGCAATCATGAATCATGCC 59.432 43.478 17.81 6.63 41.18 4.40
4089 4197 4.036380 TGTCTCAGCAATCATGAATCATGC 59.964 41.667 17.81 8.33 41.18 4.06
4090 4198 5.751243 TGTCTCAGCAATCATGAATCATG 57.249 39.130 16.63 16.63 42.60 3.07
4091 4199 6.038382 GTCTTGTCTCAGCAATCATGAATCAT 59.962 38.462 0.00 0.00 0.00 2.45
4092 4200 5.353400 GTCTTGTCTCAGCAATCATGAATCA 59.647 40.000 0.00 0.00 0.00 2.57
4093 4201 5.353400 TGTCTTGTCTCAGCAATCATGAATC 59.647 40.000 0.00 0.00 0.00 2.52
4094 4202 5.123502 GTGTCTTGTCTCAGCAATCATGAAT 59.876 40.000 0.00 0.00 0.00 2.57
4095 4203 4.453478 GTGTCTTGTCTCAGCAATCATGAA 59.547 41.667 0.00 0.00 0.00 2.57
4096 4204 3.999001 GTGTCTTGTCTCAGCAATCATGA 59.001 43.478 0.00 0.00 0.00 3.07
4097 4205 3.749609 TGTGTCTTGTCTCAGCAATCATG 59.250 43.478 0.00 0.00 0.00 3.07
4098 4206 4.011966 TGTGTCTTGTCTCAGCAATCAT 57.988 40.909 0.00 0.00 0.00 2.45
4099 4207 3.473923 TGTGTCTTGTCTCAGCAATCA 57.526 42.857 0.00 0.00 0.00 2.57
4100 4208 6.674694 ATATTGTGTCTTGTCTCAGCAATC 57.325 37.500 0.00 0.00 0.00 2.67
4101 4209 8.618677 CAATATATTGTGTCTTGTCTCAGCAAT 58.381 33.333 16.03 0.00 33.22 3.56
4102 4210 7.977904 CAATATATTGTGTCTTGTCTCAGCAA 58.022 34.615 16.03 0.00 33.22 3.91
4103 4211 7.543947 CAATATATTGTGTCTTGTCTCAGCA 57.456 36.000 16.03 0.00 33.22 4.41
4251 4361 1.996191 GTTTGAGATGAGCTCCACGTC 59.004 52.381 12.15 4.41 43.26 4.34
4321 4431 6.936900 ACTTTATGCTTTAGTTCAGAAGCTGA 59.063 34.615 9.19 0.00 46.39 4.26


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

AutoCloner maintained by Alex Coulton.