Multiple sequence alignment - TraesCS6A01G014200

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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 TraesCS6A01G014200 chr6A 100.000 3191 0 0 1 3191 6894077 6897267 0.000000e+00 5893.0
1 TraesCS6A01G014200 chr6A 96.975 562 17 0 2630 3191 616872637 616873198 0.000000e+00 944.0
2 TraesCS6A01G014200 chr6A 73.659 410 96 9 1555 1958 594529747 594529344 7.130000e-32 148.0
3 TraesCS6A01G014200 chrUn 94.607 1131 39 9 857 1983 76210526 76211638 0.000000e+00 1731.0
4 TraesCS6A01G014200 chrUn 93.080 578 30 5 2 572 458246604 458247178 0.000000e+00 837.0
5 TraesCS6A01G014200 chrUn 96.958 263 8 0 590 852 460778678 460778940 2.920000e-120 442.0
6 TraesCS6A01G014200 chrUn 89.275 345 15 10 2040 2383 76211632 76211955 2.290000e-111 412.0
7 TraesCS6A01G014200 chrUn 98.077 52 1 0 2410 2461 76211958 76212009 1.220000e-14 91.6
8 TraesCS6A01G014200 chr6B 84.925 1194 146 18 807 1976 12856541 12855358 0.000000e+00 1177.0
9 TraesCS6A01G014200 chr6B 95.737 563 22 2 2630 3191 101934065 101934626 0.000000e+00 905.0
10 TraesCS6A01G014200 chr6B 83.004 506 78 6 1164 1668 12848269 12848767 4.850000e-123 451.0
11 TraesCS6A01G014200 chr6B 84.257 451 63 5 1710 2156 12848765 12849211 1.760000e-117 433.0
12 TraesCS6A01G014200 chr6B 84.146 328 48 4 134 460 4165535 4165211 6.640000e-82 315.0
13 TraesCS6A01G014200 chr6B 75.783 479 107 6 1496 1968 678818860 678818385 1.910000e-57 233.0
14 TraesCS6A01G014200 chr6D 96.418 670 18 2 1963 2632 7219979 7220642 0.000000e+00 1099.0
15 TraesCS6A01G014200 chr6D 72.437 595 138 21 1355 1945 448365741 448366313 1.970000e-37 167.0
16 TraesCS6A01G014200 chr6D 98.734 79 1 0 2 80 7213502 7213580 1.190000e-29 141.0
17 TraesCS6A01G014200 chr6D 77.632 152 34 0 1515 1666 448033877 448033726 3.390000e-15 93.5
18 TraesCS6A01G014200 chr3A 96.441 562 20 0 2630 3191 672860901 672860340 0.000000e+00 928.0
19 TraesCS6A01G014200 chr3A 93.345 556 37 0 2636 3191 27307639 27307084 0.000000e+00 822.0
20 TraesCS6A01G014200 chr3A 86.930 329 40 3 133 460 198839437 198839111 1.810000e-97 366.0
21 TraesCS6A01G014200 chr3A 82.808 349 51 8 114 457 383693137 383693481 1.440000e-78 303.0
22 TraesCS6A01G014200 chr7D 93.060 562 39 0 2630 3191 259305897 259306458 0.000000e+00 822.0
23 TraesCS6A01G014200 chr7D 93.345 556 37 0 2636 3191 557924548 557923993 0.000000e+00 822.0
24 TraesCS6A01G014200 chr5D 93.345 556 37 0 2636 3191 231957036 231956481 0.000000e+00 822.0
25 TraesCS6A01G014200 chr3D 93.060 562 38 1 2630 3191 9063739 9064299 0.000000e+00 821.0
26 TraesCS6A01G014200 chr5B 93.321 554 37 0 2638 3191 12312125 12312678 0.000000e+00 819.0
27 TraesCS6A01G014200 chr4D 86.154 325 43 2 131 455 304362200 304361878 1.820000e-92 350.0
28 TraesCS6A01G014200 chr2A 85.538 325 43 4 134 457 95604387 95604708 1.420000e-88 337.0
29 TraesCS6A01G014200 chr1A 85.139 323 45 3 139 460 62247538 62247218 8.530000e-86 327.0
30 TraesCS6A01G014200 chr1A 79.459 185 38 0 1785 1969 99908267 99908083 7.180000e-27 132.0
31 TraesCS6A01G014200 chr5A 83.824 340 48 7 129 466 581490315 581490649 1.850000e-82 316.0
32 TraesCS6A01G014200 chr7B 83.728 338 43 9 127 462 3885523 3885196 3.090000e-80 309.0
33 TraesCS6A01G014200 chr4A 78.814 354 67 5 1515 1864 697573910 697574259 6.880000e-57 231.0


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 TraesCS6A01G014200 chr6A 6894077 6897267 3190 False 5893.000000 5893 100.000000 1 3191 1 chr6A.!!$F1 3190
1 TraesCS6A01G014200 chr6A 616872637 616873198 561 False 944.000000 944 96.975000 2630 3191 1 chr6A.!!$F2 561
2 TraesCS6A01G014200 chrUn 458246604 458247178 574 False 837.000000 837 93.080000 2 572 1 chrUn.!!$F1 570
3 TraesCS6A01G014200 chrUn 76210526 76212009 1483 False 744.866667 1731 93.986333 857 2461 3 chrUn.!!$F3 1604
4 TraesCS6A01G014200 chr6B 12855358 12856541 1183 True 1177.000000 1177 84.925000 807 1976 1 chr6B.!!$R2 1169
5 TraesCS6A01G014200 chr6B 101934065 101934626 561 False 905.000000 905 95.737000 2630 3191 1 chr6B.!!$F1 561
6 TraesCS6A01G014200 chr6B 12848269 12849211 942 False 442.000000 451 83.630500 1164 2156 2 chr6B.!!$F2 992
7 TraesCS6A01G014200 chr6D 7219979 7220642 663 False 1099.000000 1099 96.418000 1963 2632 1 chr6D.!!$F2 669
8 TraesCS6A01G014200 chr3A 672860340 672860901 561 True 928.000000 928 96.441000 2630 3191 1 chr3A.!!$R3 561
9 TraesCS6A01G014200 chr3A 27307084 27307639 555 True 822.000000 822 93.345000 2636 3191 1 chr3A.!!$R1 555
10 TraesCS6A01G014200 chr7D 259305897 259306458 561 False 822.000000 822 93.060000 2630 3191 1 chr7D.!!$F1 561
11 TraesCS6A01G014200 chr7D 557923993 557924548 555 True 822.000000 822 93.345000 2636 3191 1 chr7D.!!$R1 555
12 TraesCS6A01G014200 chr5D 231956481 231957036 555 True 822.000000 822 93.345000 2636 3191 1 chr5D.!!$R1 555
13 TraesCS6A01G014200 chr3D 9063739 9064299 560 False 821.000000 821 93.060000 2630 3191 1 chr3D.!!$F1 561
14 TraesCS6A01G014200 chr5B 12312125 12312678 553 False 819.000000 819 93.321000 2638 3191 1 chr5B.!!$F1 553

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
764 772 0.029567 CGACGAGAAGGAAGGATCGG 59.97 60.0 0.0 0.0 39.42 4.18 F
767 775 0.029567 CGAGAAGGAAGGATCGGACG 59.97 60.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2158 0.174162 GCATCACCAATTCACCTGGC 59.826 55.000 0.0 0.0 37.48 4.85 R
2746 2822 1.079612 TCATGCAGGCGAGTGAGTG 60.080 57.895 0.0 0.0 0.00 3.51 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
24 25 6.276847 ACAAATTAGCGGATCAGAGAACTAG 58.723 40.000 0.00 0.00 0.00 2.57
76 77 3.087253 CCATACGCCCAGGGTCCA 61.087 66.667 7.55 0.00 0.00 4.02
80 81 1.205460 ATACGCCCAGGGTCCAACTT 61.205 55.000 7.55 0.00 0.00 2.66
91 92 4.016706 CCAACTTCCGCCGGGAGT 62.017 66.667 12.44 12.44 44.98 3.85
103 104 1.299648 CGGGAGTGGATTTCTGGCA 59.700 57.895 0.00 0.00 0.00 4.92
105 106 0.681243 GGGAGTGGATTTCTGGCACC 60.681 60.000 0.00 0.00 0.00 5.01
147 148 9.945904 CCTTCTATAAAAACTAGATGATACCCC 57.054 37.037 0.00 0.00 0.00 4.95
149 150 7.609056 TCTATAAAAACTAGATGATACCCCGC 58.391 38.462 0.00 0.00 0.00 6.13
160 161 2.419011 ATACCCCGCCAGTTGTTGCA 62.419 55.000 0.00 0.00 0.00 4.08
166 167 1.539388 CCGCCAGTTGTTGCAAGAATA 59.461 47.619 12.62 0.00 0.00 1.75
209 210 6.778834 AGAATTGGTTACATGATGCATGAA 57.221 33.333 2.46 0.00 43.81 2.57
338 339 1.409251 TTTGCATGCTGGGGTTGCTT 61.409 50.000 20.33 0.00 37.28 3.91
377 378 2.582052 TGTTGTGGCGGATCTTTCTTT 58.418 42.857 0.00 0.00 0.00 2.52
396 397 9.421806 CTTTCTTTATGCATGTTAAATGGTGAA 57.578 29.630 10.16 0.00 0.00 3.18
400 401 5.981088 ATGCATGTTAAATGGTGAAGTGA 57.019 34.783 0.00 0.00 0.00 3.41
459 460 8.929487 GGGGCTAGCTATTTAGATATAGAACAT 58.071 37.037 15.72 0.00 31.10 2.71
477 483 3.230976 ACATATGTCTCGAGTGCCCATA 58.769 45.455 13.13 13.97 0.00 2.74
486 492 4.832823 TCTCGAGTGCCCATAAATCTCATA 59.167 41.667 13.13 0.00 0.00 2.15
629 637 9.607333 TGTATCTAGTCCATATTGAAATCCTCT 57.393 33.333 0.00 0.00 0.00 3.69
656 664 7.772332 AAAAGGCGTATATGTAGAAACAGAG 57.228 36.000 0.00 0.00 39.49 3.35
657 665 6.710597 AAGGCGTATATGTAGAAACAGAGA 57.289 37.500 0.00 0.00 39.49 3.10
658 666 6.710597 AGGCGTATATGTAGAAACAGAGAA 57.289 37.500 0.00 0.00 39.49 2.87
659 667 7.108841 AGGCGTATATGTAGAAACAGAGAAA 57.891 36.000 0.00 0.00 39.49 2.52
660 668 7.203910 AGGCGTATATGTAGAAACAGAGAAAG 58.796 38.462 0.00 0.00 39.49 2.62
661 669 6.979238 GGCGTATATGTAGAAACAGAGAAAGT 59.021 38.462 0.00 0.00 39.49 2.66
662 670 8.133627 GGCGTATATGTAGAAACAGAGAAAGTA 58.866 37.037 0.00 0.00 39.49 2.24
663 671 9.171701 GCGTATATGTAGAAACAGAGAAAGTAG 57.828 37.037 0.00 0.00 39.49 2.57
669 677 8.582657 TGTAGAAACAGAGAAAGTAGATAGCT 57.417 34.615 0.00 0.00 0.00 3.32
670 678 8.679100 TGTAGAAACAGAGAAAGTAGATAGCTC 58.321 37.037 0.00 0.00 0.00 4.09
671 679 6.791303 AGAAACAGAGAAAGTAGATAGCTCG 58.209 40.000 0.00 0.00 0.00 5.03
672 680 5.508200 AACAGAGAAAGTAGATAGCTCGG 57.492 43.478 0.00 0.00 0.00 4.63
673 681 3.886505 ACAGAGAAAGTAGATAGCTCGGG 59.113 47.826 0.00 0.00 0.00 5.14
674 682 2.888414 AGAGAAAGTAGATAGCTCGGGC 59.112 50.000 0.00 0.00 39.06 6.13
684 692 2.663196 GCTCGGGCTGGTTACACT 59.337 61.111 0.00 0.00 35.22 3.55
685 693 1.448013 GCTCGGGCTGGTTACACTC 60.448 63.158 0.00 0.00 35.22 3.51
686 694 1.218316 CTCGGGCTGGTTACACTCC 59.782 63.158 0.00 0.00 0.00 3.85
687 695 2.125673 CGGGCTGGTTACACTCCG 60.126 66.667 0.00 0.00 33.03 4.63
688 696 2.642254 CGGGCTGGTTACACTCCGA 61.642 63.158 0.00 0.00 38.56 4.55
689 697 1.675219 GGGCTGGTTACACTCCGAA 59.325 57.895 0.00 0.00 0.00 4.30
690 698 0.035739 GGGCTGGTTACACTCCGAAA 59.964 55.000 0.00 0.00 0.00 3.46
691 699 1.339727 GGGCTGGTTACACTCCGAAAT 60.340 52.381 0.00 0.00 0.00 2.17
692 700 2.007608 GGCTGGTTACACTCCGAAATC 58.992 52.381 0.00 0.00 0.00 2.17
693 701 2.007608 GCTGGTTACACTCCGAAATCC 58.992 52.381 0.00 0.00 0.00 3.01
694 702 2.354805 GCTGGTTACACTCCGAAATCCT 60.355 50.000 0.00 0.00 0.00 3.24
695 703 3.118884 GCTGGTTACACTCCGAAATCCTA 60.119 47.826 0.00 0.00 0.00 2.94
696 704 4.443034 GCTGGTTACACTCCGAAATCCTAT 60.443 45.833 0.00 0.00 0.00 2.57
697 705 5.272283 TGGTTACACTCCGAAATCCTATC 57.728 43.478 0.00 0.00 0.00 2.08
698 706 4.960469 TGGTTACACTCCGAAATCCTATCT 59.040 41.667 0.00 0.00 0.00 1.98
699 707 6.131264 TGGTTACACTCCGAAATCCTATCTA 58.869 40.000 0.00 0.00 0.00 1.98
700 708 6.608405 TGGTTACACTCCGAAATCCTATCTAA 59.392 38.462 0.00 0.00 0.00 2.10
701 709 6.922407 GGTTACACTCCGAAATCCTATCTAAC 59.078 42.308 0.00 0.00 0.00 2.34
702 710 5.184340 ACACTCCGAAATCCTATCTAACG 57.816 43.478 0.00 0.00 0.00 3.18
703 711 4.037684 ACACTCCGAAATCCTATCTAACGG 59.962 45.833 0.00 0.00 40.16 4.44
704 712 3.005578 ACTCCGAAATCCTATCTAACGGC 59.994 47.826 0.00 0.00 38.94 5.68
705 713 2.960384 TCCGAAATCCTATCTAACGGCA 59.040 45.455 0.00 0.00 38.94 5.69
706 714 3.005472 TCCGAAATCCTATCTAACGGCAG 59.995 47.826 0.00 0.00 38.94 4.85
707 715 3.318017 CGAAATCCTATCTAACGGCAGG 58.682 50.000 0.00 0.00 0.00 4.85
708 716 3.665190 GAAATCCTATCTAACGGCAGGG 58.335 50.000 0.00 0.00 0.00 4.45
709 717 2.400467 ATCCTATCTAACGGCAGGGT 57.600 50.000 0.00 0.00 0.00 4.34
710 718 1.410004 TCCTATCTAACGGCAGGGTG 58.590 55.000 0.00 0.00 0.00 4.61
711 719 0.249911 CCTATCTAACGGCAGGGTGC 60.250 60.000 0.00 0.00 44.08 5.01
724 732 3.905249 GGTGCATCCCTCCGAAAC 58.095 61.111 0.00 0.00 0.00 2.78
725 733 2.106683 GGTGCATCCCTCCGAAACG 61.107 63.158 0.00 0.00 0.00 3.60
726 734 1.079405 GTGCATCCCTCCGAAACGA 60.079 57.895 0.00 0.00 0.00 3.85
727 735 0.672401 GTGCATCCCTCCGAAACGAA 60.672 55.000 0.00 0.00 0.00 3.85
728 736 0.672401 TGCATCCCTCCGAAACGAAC 60.672 55.000 0.00 0.00 0.00 3.95
729 737 0.672401 GCATCCCTCCGAAACGAACA 60.672 55.000 0.00 0.00 0.00 3.18
730 738 1.803334 CATCCCTCCGAAACGAACAA 58.197 50.000 0.00 0.00 0.00 2.83
731 739 1.732259 CATCCCTCCGAAACGAACAAG 59.268 52.381 0.00 0.00 0.00 3.16
732 740 0.034337 TCCCTCCGAAACGAACAAGG 59.966 55.000 0.00 0.00 0.00 3.61
733 741 0.250166 CCCTCCGAAACGAACAAGGT 60.250 55.000 0.00 0.00 0.00 3.50
734 742 1.001181 CCCTCCGAAACGAACAAGGTA 59.999 52.381 0.00 0.00 0.00 3.08
735 743 2.334838 CCTCCGAAACGAACAAGGTAG 58.665 52.381 0.00 0.00 0.00 3.18
736 744 2.029649 CCTCCGAAACGAACAAGGTAGA 60.030 50.000 0.00 0.00 0.00 2.59
737 745 3.243336 CTCCGAAACGAACAAGGTAGAG 58.757 50.000 0.00 0.00 0.00 2.43
738 746 2.029649 TCCGAAACGAACAAGGTAGAGG 60.030 50.000 0.00 0.00 0.00 3.69
739 747 1.725164 CGAAACGAACAAGGTAGAGGC 59.275 52.381 0.00 0.00 0.00 4.70
740 748 2.609737 CGAAACGAACAAGGTAGAGGCT 60.610 50.000 0.00 0.00 0.00 4.58
741 749 2.457366 AACGAACAAGGTAGAGGCTG 57.543 50.000 0.00 0.00 0.00 4.85
742 750 0.608640 ACGAACAAGGTAGAGGCTGG 59.391 55.000 0.00 0.00 0.00 4.85
743 751 0.608640 CGAACAAGGTAGAGGCTGGT 59.391 55.000 0.00 0.00 0.00 4.00
744 752 1.673033 CGAACAAGGTAGAGGCTGGTG 60.673 57.143 0.00 0.00 0.00 4.17
745 753 0.036875 AACAAGGTAGAGGCTGGTGC 59.963 55.000 0.00 0.00 38.76 5.01
746 754 1.448540 CAAGGTAGAGGCTGGTGCG 60.449 63.158 0.00 0.00 40.82 5.34
747 755 1.609501 AAGGTAGAGGCTGGTGCGA 60.610 57.895 0.00 0.00 40.82 5.10
748 756 1.889530 AAGGTAGAGGCTGGTGCGAC 61.890 60.000 0.00 0.00 40.82 5.19
749 757 2.202623 GTAGAGGCTGGTGCGACG 60.203 66.667 0.00 0.00 40.82 5.12
750 758 2.360726 TAGAGGCTGGTGCGACGA 60.361 61.111 0.00 0.00 40.82 4.20
751 759 2.407428 TAGAGGCTGGTGCGACGAG 61.407 63.158 0.00 0.00 40.82 4.18
752 760 2.814913 TAGAGGCTGGTGCGACGAGA 62.815 60.000 0.00 0.00 40.82 4.04
753 761 3.282745 GAGGCTGGTGCGACGAGAA 62.283 63.158 0.00 0.00 40.82 2.87
754 762 2.811317 GGCTGGTGCGACGAGAAG 60.811 66.667 0.00 0.00 40.82 2.85
755 763 2.811317 GCTGGTGCGACGAGAAGG 60.811 66.667 0.00 0.00 0.00 3.46
756 764 2.962569 CTGGTGCGACGAGAAGGA 59.037 61.111 0.00 0.00 0.00 3.36
757 765 1.289066 CTGGTGCGACGAGAAGGAA 59.711 57.895 0.00 0.00 0.00 3.36
758 766 0.734253 CTGGTGCGACGAGAAGGAAG 60.734 60.000 0.00 0.00 0.00 3.46
759 767 1.446272 GGTGCGACGAGAAGGAAGG 60.446 63.158 0.00 0.00 0.00 3.46
760 768 1.585006 GTGCGACGAGAAGGAAGGA 59.415 57.895 0.00 0.00 0.00 3.36
761 769 0.173708 GTGCGACGAGAAGGAAGGAT 59.826 55.000 0.00 0.00 0.00 3.24
762 770 0.456221 TGCGACGAGAAGGAAGGATC 59.544 55.000 0.00 0.00 0.00 3.36
763 771 0.592754 GCGACGAGAAGGAAGGATCG 60.593 60.000 0.00 0.00 40.86 3.69
764 772 0.029567 CGACGAGAAGGAAGGATCGG 59.970 60.000 0.00 0.00 39.42 4.18
765 773 1.390565 GACGAGAAGGAAGGATCGGA 58.609 55.000 0.00 0.00 39.42 4.55
766 774 1.065851 GACGAGAAGGAAGGATCGGAC 59.934 57.143 0.00 0.00 39.42 4.79
767 775 0.029567 CGAGAAGGAAGGATCGGACG 59.970 60.000 0.00 0.00 0.00 4.79
768 776 1.104630 GAGAAGGAAGGATCGGACGT 58.895 55.000 0.00 0.00 0.00 4.34
769 777 2.295885 GAGAAGGAAGGATCGGACGTA 58.704 52.381 0.00 0.00 0.00 3.57
770 778 2.885894 GAGAAGGAAGGATCGGACGTAT 59.114 50.000 0.00 0.00 0.00 3.06
771 779 2.623889 AGAAGGAAGGATCGGACGTATG 59.376 50.000 0.00 0.00 0.00 2.39
772 780 2.068834 AGGAAGGATCGGACGTATGT 57.931 50.000 0.00 0.00 0.00 2.29
773 781 1.955080 AGGAAGGATCGGACGTATGTC 59.045 52.381 6.53 6.53 44.72 3.06
784 792 3.481112 GACGTATGTCCCGCAAAAATT 57.519 42.857 3.50 0.00 39.30 1.82
785 793 3.168193 GACGTATGTCCCGCAAAAATTG 58.832 45.455 3.50 0.00 39.30 2.32
786 794 2.094957 ACGTATGTCCCGCAAAAATTGG 60.095 45.455 0.00 0.00 0.00 3.16
787 795 2.162608 CGTATGTCCCGCAAAAATTGGA 59.837 45.455 0.00 0.00 0.00 3.53
788 796 2.741759 ATGTCCCGCAAAAATTGGAC 57.258 45.000 3.93 3.93 45.99 4.02
789 797 3.101019 GTCCCGCAAAAATTGGACG 57.899 52.632 0.00 0.00 38.07 4.79
790 798 0.388006 GTCCCGCAAAAATTGGACGG 60.388 55.000 0.00 0.00 43.44 4.79
791 799 4.569341 CCGCAAAAATTGGACGGG 57.431 55.556 0.00 0.00 40.18 5.28
792 800 1.960612 CCGCAAAAATTGGACGGGA 59.039 52.632 0.00 0.00 40.18 5.14
793 801 0.530288 CCGCAAAAATTGGACGGGAT 59.470 50.000 0.00 0.00 40.18 3.85
794 802 1.746220 CCGCAAAAATTGGACGGGATA 59.254 47.619 0.00 0.00 40.18 2.59
795 803 2.478879 CCGCAAAAATTGGACGGGATAC 60.479 50.000 0.00 0.00 40.18 2.24
796 804 2.162608 CGCAAAAATTGGACGGGATACA 59.837 45.455 0.00 0.00 39.74 2.29
797 805 3.366476 CGCAAAAATTGGACGGGATACAA 60.366 43.478 0.00 0.00 34.83 2.41
798 806 4.561105 GCAAAAATTGGACGGGATACAAA 58.439 39.130 0.00 0.00 33.69 2.83
799 807 4.991687 GCAAAAATTGGACGGGATACAAAA 59.008 37.500 0.00 0.00 33.69 2.44
800 808 5.467063 GCAAAAATTGGACGGGATACAAAAA 59.533 36.000 0.00 0.00 33.69 1.94
801 809 6.148645 GCAAAAATTGGACGGGATACAAAAAT 59.851 34.615 0.00 0.00 33.69 1.82
802 810 7.308288 GCAAAAATTGGACGGGATACAAAAATT 60.308 33.333 0.00 0.00 33.69 1.82
803 811 9.209175 CAAAAATTGGACGGGATACAAAAATTA 57.791 29.630 0.00 0.00 33.69 1.40
804 812 8.766000 AAAATTGGACGGGATACAAAAATTAC 57.234 30.769 0.00 0.00 33.69 1.89
805 813 5.548706 TTGGACGGGATACAAAAATTACG 57.451 39.130 0.00 0.00 39.74 3.18
809 817 2.286536 CGGGATACAAAAATTACGCGGG 60.287 50.000 12.47 0.00 39.74 6.13
815 823 6.634035 GGATACAAAAATTACGCGGGATAAAC 59.366 38.462 12.47 0.00 0.00 2.01
845 853 3.379057 TCTTTTCAGAAACCAAACCGGAC 59.621 43.478 9.46 0.00 38.63 4.79
848 856 2.018515 TCAGAAACCAAACCGGACAAC 58.981 47.619 9.46 0.00 38.63 3.32
852 860 4.036971 CAGAAACCAAACCGGACAACAATA 59.963 41.667 9.46 0.00 38.63 1.90
857 865 3.685756 CCAAACCGGACAACAATACGTAT 59.314 43.478 9.46 1.14 36.56 3.06
865 873 4.933400 GGACAACAATACGTATGTGGTTCT 59.067 41.667 9.24 2.57 35.10 3.01
908 925 2.754658 ACGACCGGCCTGGAGTAG 60.755 66.667 18.74 5.78 42.00 2.57
1246 1271 3.735143 TCGACGACGAACAGGTCA 58.265 55.556 7.68 0.00 45.74 4.02
1254 1279 1.071471 CGAACAGGTCACCAAGCCT 59.929 57.895 0.00 0.00 35.04 4.58
1275 1300 1.005037 CAAGGTGCAGCTCCGTGTA 60.005 57.895 20.46 0.00 31.66 2.90
1289 1314 0.520412 CGTGTAAATTTCGCCAGCCG 60.520 55.000 0.00 0.00 38.61 5.52
1308 1333 3.055144 CGTTACTAGGAAACGGCCC 57.945 57.895 19.33 0.00 44.49 5.80
1316 1341 2.686816 GGAAACGGCCCATCACACG 61.687 63.158 0.00 0.00 0.00 4.49
1363 1388 3.181400 ACCAGGAAACAATTGGGGGTATT 60.181 43.478 10.83 0.00 36.28 1.89
1383 1408 3.386768 TCAAAGTTCGTCAAGAGGGAG 57.613 47.619 0.00 0.00 0.00 4.30
1543 1574 1.352156 GCACCTTGGCGACTTACTCG 61.352 60.000 0.00 0.00 45.97 4.18
1605 1636 2.094659 CACTTTCTCCGCGCATCGT 61.095 57.895 8.75 0.00 36.19 3.73
1669 1703 2.409870 GGTGCAATGAAGGAGGGCG 61.410 63.158 0.00 0.00 0.00 6.13
1670 1704 2.045045 TGCAATGAAGGAGGGCGG 60.045 61.111 0.00 0.00 0.00 6.13
1671 1705 3.521796 GCAATGAAGGAGGGCGGC 61.522 66.667 0.00 0.00 0.00 6.53
1774 1808 2.163509 CGGAGACAGAAGAGGAAGACA 58.836 52.381 0.00 0.00 0.00 3.41
1783 1820 0.035458 AGAGGAAGACAACCAAGGCG 59.965 55.000 0.00 0.00 0.00 5.52
2005 2042 3.288308 CTCACCAGCGGCGACTTCT 62.288 63.158 12.98 0.00 0.00 2.85
2010 2047 2.049063 AGCGGCGACTTCTGTCAC 60.049 61.111 12.98 0.00 43.06 3.67
2176 2213 8.097662 AGCTAGTTATGCCTACTAATTTCATCC 58.902 37.037 0.00 0.00 0.00 3.51
2179 2216 8.682936 AGTTATGCCTACTAATTTCATCCTTG 57.317 34.615 0.00 0.00 0.00 3.61
2197 2252 9.993454 TCATCCTTGTCTAGATTTAATCATGAG 57.007 33.333 7.74 2.07 0.00 2.90
2198 2253 9.217278 CATCCTTGTCTAGATTTAATCATGAGG 57.783 37.037 7.74 5.81 0.00 3.86
2199 2254 8.553085 TCCTTGTCTAGATTTAATCATGAGGA 57.447 34.615 7.74 7.74 0.00 3.71
2200 2255 8.992349 TCCTTGTCTAGATTTAATCATGAGGAA 58.008 33.333 7.74 0.00 0.00 3.36
2201 2256 9.270640 CCTTGTCTAGATTTAATCATGAGGAAG 57.729 37.037 7.74 8.83 0.00 3.46
2202 2257 9.829507 CTTGTCTAGATTTAATCATGAGGAAGT 57.170 33.333 7.74 0.00 0.00 3.01
2209 2264 8.997734 AGATTTAATCATGAGGAAGTAAGGTCT 58.002 33.333 7.74 1.06 0.00 3.85
2210 2265 8.970859 ATTTAATCATGAGGAAGTAAGGTCTG 57.029 34.615 0.09 0.00 0.00 3.51
2211 2266 7.733773 TTAATCATGAGGAAGTAAGGTCTGA 57.266 36.000 0.09 0.00 0.00 3.27
2212 2267 6.821616 AATCATGAGGAAGTAAGGTCTGAT 57.178 37.500 0.09 0.00 0.00 2.90
2213 2268 5.604758 TCATGAGGAAGTAAGGTCTGATG 57.395 43.478 0.00 0.00 0.00 3.07
2214 2269 5.272402 TCATGAGGAAGTAAGGTCTGATGA 58.728 41.667 0.00 0.00 0.00 2.92
2224 2279 3.623906 AGGTCTGATGATTCACCACAG 57.376 47.619 9.58 9.58 0.00 3.66
2228 2283 4.318332 GTCTGATGATTCACCACAGTTGA 58.682 43.478 13.28 0.00 0.00 3.18
2246 2301 7.676338 CACAGTTGAAATTGTGAGTTACGAAGT 60.676 37.037 11.96 0.00 45.97 3.01
2247 2302 7.493320 ACAGTTGAAATTGTGAGTTACGAAGTA 59.507 33.333 0.00 0.00 45.11 2.24
2248 2303 8.004344 CAGTTGAAATTGTGAGTTACGAAGTAG 58.996 37.037 0.00 0.00 46.93 2.57
2383 2459 1.476891 GATCAGTCGTCTGCCTAACCA 59.523 52.381 4.68 0.00 41.10 3.67
2384 2460 1.557099 TCAGTCGTCTGCCTAACCAT 58.443 50.000 4.68 0.00 41.10 3.55
2385 2461 1.899814 TCAGTCGTCTGCCTAACCATT 59.100 47.619 4.68 0.00 41.10 3.16
2386 2462 2.002586 CAGTCGTCTGCCTAACCATTG 58.997 52.381 0.00 0.00 34.79 2.82
2387 2463 1.066143 AGTCGTCTGCCTAACCATTGG 60.066 52.381 0.00 0.00 0.00 3.16
2388 2464 0.251916 TCGTCTGCCTAACCATTGGG 59.748 55.000 7.78 0.00 41.29 4.12
2403 2479 4.685924 CCATTGGGTCTCATTATTGTTGC 58.314 43.478 0.00 0.00 0.00 4.17
2404 2480 4.441913 CCATTGGGTCTCATTATTGTTGCC 60.442 45.833 0.00 0.00 0.00 4.52
2405 2481 3.448093 TGGGTCTCATTATTGTTGCCA 57.552 42.857 0.00 0.00 0.00 4.92
2406 2482 3.355378 TGGGTCTCATTATTGTTGCCAG 58.645 45.455 0.00 0.00 0.00 4.85
2407 2483 2.099756 GGGTCTCATTATTGTTGCCAGC 59.900 50.000 0.00 0.00 0.00 4.85
2408 2484 3.019564 GGTCTCATTATTGTTGCCAGCT 58.980 45.455 0.00 0.00 0.00 4.24
2414 2490 1.585267 TATTGTTGCCAGCTGCCGTG 61.585 55.000 8.66 0.00 40.16 4.94
2612 2688 4.204028 AGGGTGGCGCCAACACTT 62.204 61.111 42.82 26.17 38.83 3.16
2760 2836 0.390340 TGAATCACTCACTCGCCTGC 60.390 55.000 0.00 0.00 0.00 4.85
2774 2850 1.202110 CGCCTGCATGACATTCAACTC 60.202 52.381 0.00 0.00 0.00 3.01
2968 3045 9.528489 AGGAGTCATTCTAACTAGAGATAATCC 57.472 37.037 0.00 0.00 33.21 3.01
2970 3047 9.221933 GAGTCATTCTAACTAGAGATAATCCGA 57.778 37.037 0.00 0.00 33.21 4.55
2974 3051 8.568794 CATTCTAACTAGAGATAATCCGACACA 58.431 37.037 0.00 0.00 33.21 3.72
3093 3170 1.218316 GTGGTCCAGGTAGCTTCGG 59.782 63.158 0.00 0.00 0.00 4.30
3141 3218 4.218417 GGAATATGTTCAGCAACTGGTTGT 59.782 41.667 13.85 0.36 38.17 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.035783 GGAAGTTGGACCCTGGGC 59.964 66.667 14.08 5.57 0.00 5.36
76 77 4.016706 CCACTCCCGGCGGAAGTT 62.017 66.667 30.79 4.14 37.86 2.66
80 81 3.006728 AAATCCACTCCCGGCGGA 61.007 61.111 30.79 12.88 36.45 5.54
91 92 1.001020 ATGCGGTGCCAGAAATCCA 60.001 52.632 0.00 0.00 0.00 3.41
147 148 2.987413 TATTCTTGCAACAACTGGCG 57.013 45.000 0.00 0.00 0.00 5.69
149 150 5.919196 GCAAAATATTCTTGCAACAACTGG 58.081 37.500 20.73 0.00 46.78 4.00
227 228 9.158233 CGTATTTATTTTCACCTTTAGTCCTCA 57.842 33.333 0.00 0.00 0.00 3.86
299 300 7.428020 TGCAAACATGCCTGAGAATTTATATC 58.572 34.615 0.00 0.00 0.00 1.63
377 378 6.432472 TGTCACTTCACCATTTAACATGCATA 59.568 34.615 0.00 0.00 0.00 3.14
396 397 7.888250 TCTCTCATCATACAAGTATGTCACT 57.112 36.000 17.14 2.28 42.57 3.41
409 410 8.597167 CCCCACTAACATATTTCTCTCATCATA 58.403 37.037 0.00 0.00 0.00 2.15
413 414 5.456763 GCCCCCACTAACATATTTCTCTCAT 60.457 44.000 0.00 0.00 0.00 2.90
427 428 4.823107 TCTAAATAGCTAGCCCCCACTAA 58.177 43.478 12.13 0.00 0.00 2.24
459 460 4.588951 AGATTTATGGGCACTCGAGACATA 59.411 41.667 21.68 17.21 0.00 2.29
603 611 9.607333 AGAGGATTTCAATATGGACTAGATACA 57.393 33.333 0.00 0.00 0.00 2.29
631 639 8.038944 TCTCTGTTTCTACATATACGCCTTTTT 58.961 33.333 0.00 0.00 32.86 1.94
632 640 7.553334 TCTCTGTTTCTACATATACGCCTTTT 58.447 34.615 0.00 0.00 32.86 2.27
633 641 7.108841 TCTCTGTTTCTACATATACGCCTTT 57.891 36.000 0.00 0.00 32.86 3.11
634 642 6.710597 TCTCTGTTTCTACATATACGCCTT 57.289 37.500 0.00 0.00 32.86 4.35
635 643 6.710597 TTCTCTGTTTCTACATATACGCCT 57.289 37.500 0.00 0.00 32.86 5.52
636 644 6.979238 ACTTTCTCTGTTTCTACATATACGCC 59.021 38.462 0.00 0.00 32.86 5.68
637 645 7.988904 ACTTTCTCTGTTTCTACATATACGC 57.011 36.000 0.00 0.00 32.86 4.42
643 651 9.196139 AGCTATCTACTTTCTCTGTTTCTACAT 57.804 33.333 0.00 0.00 32.86 2.29
644 652 8.582657 AGCTATCTACTTTCTCTGTTTCTACA 57.417 34.615 0.00 0.00 0.00 2.74
645 653 7.853929 CGAGCTATCTACTTTCTCTGTTTCTAC 59.146 40.741 0.00 0.00 0.00 2.59
646 654 7.012515 CCGAGCTATCTACTTTCTCTGTTTCTA 59.987 40.741 0.00 0.00 0.00 2.10
647 655 6.183360 CCGAGCTATCTACTTTCTCTGTTTCT 60.183 42.308 0.00 0.00 0.00 2.52
648 656 5.974751 CCGAGCTATCTACTTTCTCTGTTTC 59.025 44.000 0.00 0.00 0.00 2.78
649 657 5.163499 CCCGAGCTATCTACTTTCTCTGTTT 60.163 44.000 0.00 0.00 0.00 2.83
650 658 4.339814 CCCGAGCTATCTACTTTCTCTGTT 59.660 45.833 0.00 0.00 0.00 3.16
651 659 3.886505 CCCGAGCTATCTACTTTCTCTGT 59.113 47.826 0.00 0.00 0.00 3.41
652 660 3.305064 GCCCGAGCTATCTACTTTCTCTG 60.305 52.174 0.00 0.00 35.50 3.35
653 661 2.888414 GCCCGAGCTATCTACTTTCTCT 59.112 50.000 0.00 0.00 35.50 3.10
654 662 3.291809 GCCCGAGCTATCTACTTTCTC 57.708 52.381 0.00 0.00 35.50 2.87
667 675 1.448013 GAGTGTAACCAGCCCGAGC 60.448 63.158 0.00 0.00 37.80 5.03
668 676 1.218316 GGAGTGTAACCAGCCCGAG 59.782 63.158 0.00 0.00 37.80 4.63
669 677 2.642254 CGGAGTGTAACCAGCCCGA 61.642 63.158 0.00 0.00 38.38 5.14
670 678 2.125673 CGGAGTGTAACCAGCCCG 60.126 66.667 0.00 0.00 37.80 6.13
671 679 0.035739 TTTCGGAGTGTAACCAGCCC 59.964 55.000 0.00 0.00 37.80 5.19
672 680 2.007608 GATTTCGGAGTGTAACCAGCC 58.992 52.381 0.00 0.00 37.80 4.85
673 681 2.007608 GGATTTCGGAGTGTAACCAGC 58.992 52.381 0.00 0.00 37.80 4.85
674 682 3.611766 AGGATTTCGGAGTGTAACCAG 57.388 47.619 0.00 0.00 37.80 4.00
675 683 4.960469 AGATAGGATTTCGGAGTGTAACCA 59.040 41.667 0.00 0.00 37.80 3.67
676 684 5.532664 AGATAGGATTTCGGAGTGTAACC 57.467 43.478 0.00 0.00 37.80 2.85
677 685 6.636044 CGTTAGATAGGATTTCGGAGTGTAAC 59.364 42.308 0.00 0.00 0.00 2.50
678 686 6.238842 CCGTTAGATAGGATTTCGGAGTGTAA 60.239 42.308 0.00 0.00 38.96 2.41
679 687 5.240183 CCGTTAGATAGGATTTCGGAGTGTA 59.760 44.000 0.00 0.00 38.96 2.90
680 688 4.037684 CCGTTAGATAGGATTTCGGAGTGT 59.962 45.833 0.00 0.00 38.96 3.55
681 689 4.547532 CCGTTAGATAGGATTTCGGAGTG 58.452 47.826 0.00 0.00 38.96 3.51
682 690 3.005578 GCCGTTAGATAGGATTTCGGAGT 59.994 47.826 0.00 0.00 38.96 3.85
683 691 3.005472 TGCCGTTAGATAGGATTTCGGAG 59.995 47.826 0.00 0.00 38.96 4.63
684 692 2.960384 TGCCGTTAGATAGGATTTCGGA 59.040 45.455 0.00 0.00 38.96 4.55
685 693 3.318017 CTGCCGTTAGATAGGATTTCGG 58.682 50.000 0.00 0.00 39.52 4.30
686 694 3.318017 CCTGCCGTTAGATAGGATTTCG 58.682 50.000 0.00 0.00 31.91 3.46
687 695 3.071167 ACCCTGCCGTTAGATAGGATTTC 59.929 47.826 0.00 0.00 31.91 2.17
688 696 3.046374 ACCCTGCCGTTAGATAGGATTT 58.954 45.455 0.00 0.00 31.91 2.17
689 697 2.368875 CACCCTGCCGTTAGATAGGATT 59.631 50.000 0.00 0.00 31.91 3.01
690 698 1.971357 CACCCTGCCGTTAGATAGGAT 59.029 52.381 0.00 0.00 31.91 3.24
691 699 1.410004 CACCCTGCCGTTAGATAGGA 58.590 55.000 0.00 0.00 31.91 2.94
692 700 0.249911 GCACCCTGCCGTTAGATAGG 60.250 60.000 0.00 0.00 37.42 2.57
693 701 0.464036 TGCACCCTGCCGTTAGATAG 59.536 55.000 0.00 0.00 44.23 2.08
694 702 1.070134 GATGCACCCTGCCGTTAGATA 59.930 52.381 0.00 0.00 44.23 1.98
695 703 0.179045 GATGCACCCTGCCGTTAGAT 60.179 55.000 0.00 0.00 44.23 1.98
696 704 1.220749 GATGCACCCTGCCGTTAGA 59.779 57.895 0.00 0.00 44.23 2.10
697 705 1.819632 GGATGCACCCTGCCGTTAG 60.820 63.158 0.00 0.00 44.23 2.34
698 706 2.270850 GGATGCACCCTGCCGTTA 59.729 61.111 0.00 0.00 44.23 3.18
707 715 2.106683 CGTTTCGGAGGGATGCACC 61.107 63.158 0.00 0.00 38.08 5.01
708 716 0.672401 TTCGTTTCGGAGGGATGCAC 60.672 55.000 0.00 0.00 0.00 4.57
709 717 0.672401 GTTCGTTTCGGAGGGATGCA 60.672 55.000 0.00 0.00 0.00 3.96
710 718 0.672401 TGTTCGTTTCGGAGGGATGC 60.672 55.000 0.00 0.00 0.00 3.91
711 719 1.732259 CTTGTTCGTTTCGGAGGGATG 59.268 52.381 0.00 0.00 0.00 3.51
712 720 1.338769 CCTTGTTCGTTTCGGAGGGAT 60.339 52.381 0.00 0.00 0.00 3.85
713 721 0.034337 CCTTGTTCGTTTCGGAGGGA 59.966 55.000 0.00 0.00 0.00 4.20
714 722 0.250166 ACCTTGTTCGTTTCGGAGGG 60.250 55.000 0.00 0.00 0.00 4.30
715 723 2.029649 TCTACCTTGTTCGTTTCGGAGG 60.030 50.000 0.00 0.00 0.00 4.30
716 724 3.243336 CTCTACCTTGTTCGTTTCGGAG 58.757 50.000 0.00 0.00 0.00 4.63
717 725 2.029649 CCTCTACCTTGTTCGTTTCGGA 60.030 50.000 0.00 0.00 0.00 4.55
718 726 2.334838 CCTCTACCTTGTTCGTTTCGG 58.665 52.381 0.00 0.00 0.00 4.30
719 727 1.725164 GCCTCTACCTTGTTCGTTTCG 59.275 52.381 0.00 0.00 0.00 3.46
720 728 2.737252 CAGCCTCTACCTTGTTCGTTTC 59.263 50.000 0.00 0.00 0.00 2.78
721 729 2.550208 CCAGCCTCTACCTTGTTCGTTT 60.550 50.000 0.00 0.00 0.00 3.60
722 730 1.002087 CCAGCCTCTACCTTGTTCGTT 59.998 52.381 0.00 0.00 0.00 3.85
723 731 0.608640 CCAGCCTCTACCTTGTTCGT 59.391 55.000 0.00 0.00 0.00 3.85
724 732 0.608640 ACCAGCCTCTACCTTGTTCG 59.391 55.000 0.00 0.00 0.00 3.95
725 733 1.946283 GCACCAGCCTCTACCTTGTTC 60.946 57.143 0.00 0.00 33.58 3.18
726 734 0.036875 GCACCAGCCTCTACCTTGTT 59.963 55.000 0.00 0.00 33.58 2.83
727 735 1.679898 GCACCAGCCTCTACCTTGT 59.320 57.895 0.00 0.00 33.58 3.16
728 736 1.448540 CGCACCAGCCTCTACCTTG 60.449 63.158 0.00 0.00 37.52 3.61
729 737 1.609501 TCGCACCAGCCTCTACCTT 60.610 57.895 0.00 0.00 37.52 3.50
730 738 2.037367 TCGCACCAGCCTCTACCT 59.963 61.111 0.00 0.00 37.52 3.08
731 739 2.184579 GTCGCACCAGCCTCTACC 59.815 66.667 0.00 0.00 37.52 3.18
732 740 2.202623 CGTCGCACCAGCCTCTAC 60.203 66.667 0.00 0.00 37.52 2.59
733 741 2.360726 TCGTCGCACCAGCCTCTA 60.361 61.111 0.00 0.00 37.52 2.43
734 742 3.753434 CTCGTCGCACCAGCCTCT 61.753 66.667 0.00 0.00 37.52 3.69
735 743 3.282745 TTCTCGTCGCACCAGCCTC 62.283 63.158 0.00 0.00 37.52 4.70
736 744 3.288308 CTTCTCGTCGCACCAGCCT 62.288 63.158 0.00 0.00 37.52 4.58
737 745 2.811317 CTTCTCGTCGCACCAGCC 60.811 66.667 0.00 0.00 37.52 4.85
738 746 2.765250 TTCCTTCTCGTCGCACCAGC 62.765 60.000 0.00 0.00 37.42 4.85
739 747 0.734253 CTTCCTTCTCGTCGCACCAG 60.734 60.000 0.00 0.00 0.00 4.00
740 748 1.289066 CTTCCTTCTCGTCGCACCA 59.711 57.895 0.00 0.00 0.00 4.17
741 749 1.446272 CCTTCCTTCTCGTCGCACC 60.446 63.158 0.00 0.00 0.00 5.01
742 750 0.173708 ATCCTTCCTTCTCGTCGCAC 59.826 55.000 0.00 0.00 0.00 5.34
743 751 0.456221 GATCCTTCCTTCTCGTCGCA 59.544 55.000 0.00 0.00 0.00 5.10
744 752 0.592754 CGATCCTTCCTTCTCGTCGC 60.593 60.000 0.00 0.00 0.00 5.19
745 753 0.029567 CCGATCCTTCCTTCTCGTCG 59.970 60.000 0.00 0.00 0.00 5.12
746 754 1.065851 GTCCGATCCTTCCTTCTCGTC 59.934 57.143 0.00 0.00 0.00 4.20
747 755 1.104630 GTCCGATCCTTCCTTCTCGT 58.895 55.000 0.00 0.00 0.00 4.18
748 756 0.029567 CGTCCGATCCTTCCTTCTCG 59.970 60.000 0.00 0.00 0.00 4.04
749 757 1.104630 ACGTCCGATCCTTCCTTCTC 58.895 55.000 0.00 0.00 0.00 2.87
750 758 2.431954 TACGTCCGATCCTTCCTTCT 57.568 50.000 0.00 0.00 0.00 2.85
751 759 2.361438 ACATACGTCCGATCCTTCCTTC 59.639 50.000 0.00 0.00 0.00 3.46
752 760 2.361438 GACATACGTCCGATCCTTCCTT 59.639 50.000 0.00 0.00 36.02 3.36
753 761 1.955080 GACATACGTCCGATCCTTCCT 59.045 52.381 0.00 0.00 36.02 3.36
754 762 2.418983 GACATACGTCCGATCCTTCC 57.581 55.000 0.00 0.00 36.02 3.46
764 772 3.168193 CAATTTTTGCGGGACATACGTC 58.832 45.455 0.00 0.00 41.80 4.34
765 773 2.094957 CCAATTTTTGCGGGACATACGT 60.095 45.455 0.00 0.00 0.00 3.57
766 774 2.162608 TCCAATTTTTGCGGGACATACG 59.837 45.455 0.00 0.00 0.00 3.06
767 775 3.859411 TCCAATTTTTGCGGGACATAC 57.141 42.857 0.00 0.00 0.00 2.39
771 779 0.388006 CCGTCCAATTTTTGCGGGAC 60.388 55.000 0.00 0.00 44.97 4.46
772 780 1.960612 CCGTCCAATTTTTGCGGGA 59.039 52.632 0.00 0.00 38.86 5.14
773 781 4.569341 CCGTCCAATTTTTGCGGG 57.431 55.556 0.00 0.00 38.86 6.13
774 782 0.530288 ATCCCGTCCAATTTTTGCGG 59.470 50.000 0.00 0.00 41.82 5.69
775 783 2.162608 TGTATCCCGTCCAATTTTTGCG 59.837 45.455 0.00 0.00 0.00 4.85
776 784 3.859411 TGTATCCCGTCCAATTTTTGC 57.141 42.857 0.00 0.00 0.00 3.68
777 785 7.665561 ATTTTTGTATCCCGTCCAATTTTTG 57.334 32.000 0.00 0.00 0.00 2.44
778 786 9.210329 GTAATTTTTGTATCCCGTCCAATTTTT 57.790 29.630 0.00 0.00 0.00 1.94
779 787 7.542824 CGTAATTTTTGTATCCCGTCCAATTTT 59.457 33.333 0.00 0.00 0.00 1.82
780 788 7.030768 CGTAATTTTTGTATCCCGTCCAATTT 58.969 34.615 0.00 0.00 0.00 1.82
781 789 6.557110 CGTAATTTTTGTATCCCGTCCAATT 58.443 36.000 0.00 0.00 0.00 2.32
782 790 5.449451 GCGTAATTTTTGTATCCCGTCCAAT 60.449 40.000 0.00 0.00 0.00 3.16
783 791 4.142643 GCGTAATTTTTGTATCCCGTCCAA 60.143 41.667 0.00 0.00 0.00 3.53
784 792 3.374678 GCGTAATTTTTGTATCCCGTCCA 59.625 43.478 0.00 0.00 0.00 4.02
785 793 3.544637 CGCGTAATTTTTGTATCCCGTCC 60.545 47.826 0.00 0.00 0.00 4.79
786 794 3.544637 CCGCGTAATTTTTGTATCCCGTC 60.545 47.826 4.92 0.00 0.00 4.79
787 795 2.352342 CCGCGTAATTTTTGTATCCCGT 59.648 45.455 4.92 0.00 0.00 5.28
788 796 2.286536 CCCGCGTAATTTTTGTATCCCG 60.287 50.000 4.92 0.00 0.00 5.14
789 797 2.944349 TCCCGCGTAATTTTTGTATCCC 59.056 45.455 4.92 0.00 0.00 3.85
790 798 4.823790 ATCCCGCGTAATTTTTGTATCC 57.176 40.909 4.92 0.00 0.00 2.59
791 799 6.355144 CGTTTATCCCGCGTAATTTTTGTATC 59.645 38.462 4.92 0.00 0.00 2.24
792 800 6.193761 CGTTTATCCCGCGTAATTTTTGTAT 58.806 36.000 4.92 0.00 0.00 2.29
793 801 5.558307 CGTTTATCCCGCGTAATTTTTGTA 58.442 37.500 4.92 0.00 0.00 2.41
794 802 4.405196 CGTTTATCCCGCGTAATTTTTGT 58.595 39.130 4.92 0.00 0.00 2.83
795 803 3.238798 GCGTTTATCCCGCGTAATTTTTG 59.761 43.478 4.92 0.00 41.91 2.44
796 804 3.428163 GCGTTTATCCCGCGTAATTTTT 58.572 40.909 4.92 0.00 41.91 1.94
797 805 3.055613 GCGTTTATCCCGCGTAATTTT 57.944 42.857 4.92 0.00 41.91 1.82
798 806 2.742954 GCGTTTATCCCGCGTAATTT 57.257 45.000 4.92 0.00 41.91 1.82
809 817 4.331717 TCTGAAAAGAATCCGGCGTTTATC 59.668 41.667 6.01 0.00 0.00 1.75
815 823 2.414161 GGTTTCTGAAAAGAATCCGGCG 60.414 50.000 4.09 0.00 30.79 6.46
822 830 4.017808 TCCGGTTTGGTTTCTGAAAAGAA 58.982 39.130 4.09 0.00 39.52 2.52
840 848 2.605818 CCACATACGTATTGTTGTCCGG 59.394 50.000 5.03 0.00 0.00 5.14
845 853 7.844169 CGAATAAGAACCACATACGTATTGTTG 59.156 37.037 15.71 11.35 0.00 3.33
848 856 7.459394 ACGAATAAGAACCACATACGTATTG 57.541 36.000 5.03 7.88 0.00 1.90
852 860 5.472148 TGAACGAATAAGAACCACATACGT 58.528 37.500 0.00 0.00 0.00 3.57
857 865 3.500680 GCCTTGAACGAATAAGAACCACA 59.499 43.478 0.00 0.00 0.00 4.17
865 873 2.865079 TGTTGGGCCTTGAACGAATAA 58.135 42.857 4.53 0.00 0.00 1.40
1153 1178 6.653320 GGGTAATAATTGATGAACCAGCGATA 59.347 38.462 0.00 0.00 0.00 2.92
1236 1261 1.071471 AGGCTTGGTGACCTGTTCG 59.929 57.895 2.11 0.00 34.07 3.95
1237 1262 2.633860 CAGGCTTGGTGACCTGTTC 58.366 57.895 2.11 0.00 46.95 3.18
1238 1263 4.907457 CAGGCTTGGTGACCTGTT 57.093 55.556 2.11 0.00 46.95 3.16
1246 1271 1.529244 GCACCTTGACAGGCTTGGT 60.529 57.895 0.00 0.00 45.56 3.67
1254 1279 2.031012 CGGAGCTGCACCTTGACA 59.969 61.111 14.15 0.00 0.00 3.58
1289 1314 1.086067 GGGCCGTTTCCTAGTAACGC 61.086 60.000 17.27 13.52 45.09 4.84
1308 1333 2.588877 GGATCGGCCCGTGTGATG 60.589 66.667 1.63 0.00 0.00 3.07
1316 1341 3.399181 TCCACACAGGATCGGCCC 61.399 66.667 0.00 0.00 43.07 5.80
1363 1388 2.037251 CCTCCCTCTTGACGAACTTTGA 59.963 50.000 0.00 0.00 0.00 2.69
1383 1408 1.039856 GCTCTGATCTCTCCAGGTCC 58.960 60.000 0.00 0.00 32.73 4.46
1774 1808 2.275380 GGAACATGGCGCCTTGGTT 61.275 57.895 36.71 30.36 0.00 3.67
1783 1820 2.338577 AGTAGATGCTGGAACATGGC 57.661 50.000 0.00 0.00 38.20 4.40
1827 1864 4.845580 ATCAGCTTGAGCCGCCCG 62.846 66.667 0.00 0.00 43.38 6.13
2005 2042 1.276421 GCAGCTCCTTCTTAGGTGACA 59.724 52.381 6.48 0.00 43.52 3.58
2010 2047 1.529309 GGGGCAGCTCCTTCTTAGG 59.471 63.158 3.04 0.00 43.46 2.69
2121 2158 0.174162 GCATCACCAATTCACCTGGC 59.826 55.000 0.00 0.00 37.48 4.85
2176 2213 9.829507 ACTTCCTCATGATTAAATCTAGACAAG 57.170 33.333 0.00 0.00 0.00 3.16
2197 2252 5.119694 GGTGAATCATCAGACCTTACTTCC 58.880 45.833 0.00 0.00 35.88 3.46
2198 2253 5.582665 GTGGTGAATCATCAGACCTTACTTC 59.417 44.000 0.00 0.00 35.88 3.01
2199 2254 5.013079 TGTGGTGAATCATCAGACCTTACTT 59.987 40.000 0.00 0.00 35.88 2.24
2200 2255 4.532126 TGTGGTGAATCATCAGACCTTACT 59.468 41.667 0.00 0.00 35.88 2.24
2201 2256 4.832248 TGTGGTGAATCATCAGACCTTAC 58.168 43.478 0.00 0.00 35.88 2.34
2202 2257 4.532126 ACTGTGGTGAATCATCAGACCTTA 59.468 41.667 15.59 0.00 35.88 2.69
2203 2258 3.328931 ACTGTGGTGAATCATCAGACCTT 59.671 43.478 15.59 0.00 35.88 3.50
2204 2259 2.909006 ACTGTGGTGAATCATCAGACCT 59.091 45.455 15.59 0.00 35.88 3.85
2205 2260 3.340814 ACTGTGGTGAATCATCAGACC 57.659 47.619 15.59 1.04 35.88 3.85
2206 2261 4.318332 TCAACTGTGGTGAATCATCAGAC 58.682 43.478 15.59 0.00 35.88 3.51
2207 2262 4.622260 TCAACTGTGGTGAATCATCAGA 57.378 40.909 15.59 6.61 35.88 3.27
2208 2263 5.694231 TTTCAACTGTGGTGAATCATCAG 57.306 39.130 0.00 4.18 35.88 2.90
2209 2264 6.040729 ACAATTTCAACTGTGGTGAATCATCA 59.959 34.615 0.00 0.00 0.00 3.07
2210 2265 6.364165 CACAATTTCAACTGTGGTGAATCATC 59.636 38.462 0.00 0.00 39.42 2.92
2211 2266 6.040729 TCACAATTTCAACTGTGGTGAATCAT 59.959 34.615 1.57 0.00 42.62 2.45
2212 2267 5.359292 TCACAATTTCAACTGTGGTGAATCA 59.641 36.000 1.57 0.00 42.62 2.57
2213 2268 5.830912 TCACAATTTCAACTGTGGTGAATC 58.169 37.500 1.57 0.00 42.62 2.52
2214 2269 5.360714 ACTCACAATTTCAACTGTGGTGAAT 59.639 36.000 1.57 0.00 42.62 2.57
2224 2279 7.848491 ACTACTTCGTAACTCACAATTTCAAC 58.152 34.615 0.00 0.00 0.00 3.18
2246 2301 7.685155 GCACCCCGTGATTCTTACTAATTACTA 60.685 40.741 0.00 0.00 35.23 1.82
2247 2302 6.579865 CACCCCGTGATTCTTACTAATTACT 58.420 40.000 0.00 0.00 35.23 2.24
2248 2303 5.235831 GCACCCCGTGATTCTTACTAATTAC 59.764 44.000 0.00 0.00 35.23 1.89
2314 2369 6.237942 CGAAAAGATCTAGTAGCACCAATGTG 60.238 42.308 0.00 0.00 45.65 3.21
2403 2479 3.869272 GAATCGCACGGCAGCTGG 61.869 66.667 17.12 1.57 0.00 4.85
2404 2480 4.214383 CGAATCGCACGGCAGCTG 62.214 66.667 10.11 10.11 0.00 4.24
2405 2481 4.742201 ACGAATCGCACGGCAGCT 62.742 61.111 1.15 0.00 34.93 4.24
2406 2482 3.308878 AAACGAATCGCACGGCAGC 62.309 57.895 1.15 0.00 34.93 5.25
2407 2483 1.225745 GAAACGAATCGCACGGCAG 60.226 57.895 1.15 0.00 34.93 4.85
2408 2484 1.225376 AAGAAACGAATCGCACGGCA 61.225 50.000 1.15 0.00 34.93 5.69
2414 2490 2.073816 TGAGGGAAAGAAACGAATCGC 58.926 47.619 1.15 0.00 0.00 4.58
2612 2688 6.615316 TCCTATACATGATGGTGGAAGAAAGA 59.385 38.462 0.00 0.00 0.00 2.52
2746 2822 1.079612 TCATGCAGGCGAGTGAGTG 60.080 57.895 0.00 0.00 0.00 3.51
2760 2836 5.006844 GCTCATCTGAGAGTTGAATGTCATG 59.993 44.000 11.34 0.00 44.74 3.07
2774 2850 0.534412 AAGTGTCCGGCTCATCTGAG 59.466 55.000 0.00 2.75 44.75 3.35
2968 3045 2.587956 CATGCCAGTTTCATTGTGTCG 58.412 47.619 0.00 0.00 0.00 4.35
2970 3047 1.619827 CCCATGCCAGTTTCATTGTGT 59.380 47.619 0.00 0.00 0.00 3.72
3093 3170 3.805971 GCAGTACGTGGTGGGTATAAATC 59.194 47.826 0.00 0.00 0.00 2.17
3141 3218 7.038729 TGCAGAAAATTGTTTATCAATACCCCA 60.039 33.333 0.00 0.00 44.85 4.96


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

AutoCloner maintained by Alex Coulton.