Multiple sequence alignment - TraesCS2D01G349400

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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 TraesCS2D01G349400 chr2D 100.000 1702 0 0 457 2158 446931483 446933184 0.000000e+00 3144
1 TraesCS2D01G349400 chr2D 83.036 1008 102 38 1172 2154 446696996 446696033 0.000000e+00 850
2 TraesCS2D01G349400 chr2D 83.036 1008 102 38 1172 2154 446727664 446726701 0.000000e+00 850
3 TraesCS2D01G349400 chr2D 100.000 445 0 0 2592 3036 446933618 446934062 0.000000e+00 822
4 TraesCS2D01G349400 chr2D 84.873 747 86 17 1158 1901 446652999 446652277 0.000000e+00 728
5 TraesCS2D01G349400 chr2D 96.970 198 6 0 2644 2841 284560154 284559957 1.740000e-87 333
6 TraesCS2D01G349400 chr2D 95.588 204 9 0 2644 2847 643768189 643767986 8.120000e-86 327
7 TraesCS2D01G349400 chr2D 93.607 219 9 2 2628 2841 347449728 347449510 3.780000e-84 322
8 TraesCS2D01G349400 chr2D 85.668 307 26 6 866 1170 446728079 446727789 1.060000e-79 307
9 TraesCS2D01G349400 chr2D 85.809 303 26 5 869 1170 446697407 446697121 3.800000e-79 305
10 TraesCS2D01G349400 chr2D 100.000 117 0 0 1 117 446931027 446931143 1.830000e-52 217
11 TraesCS2D01G349400 chr2D 78.378 296 44 10 891 1170 446653410 446653119 1.120000e-39 174
12 TraesCS2D01G349400 chr2A 96.376 1297 40 4 869 2158 590975103 590973807 0.000000e+00 2128
13 TraesCS2D01G349400 chr2A 84.254 978 98 28 1172 2127 590966064 590965121 0.000000e+00 902
14 TraesCS2D01G349400 chr2A 85.067 750 85 20 1157 1901 590817596 590816869 0.000000e+00 739
15 TraesCS2D01G349400 chr2A 88.667 300 25 3 873 1170 590966481 590966189 1.040000e-94 357
16 TraesCS2D01G349400 chr2A 96.465 198 6 1 2840 3036 590973593 590973396 2.920000e-85 326
17 TraesCS2D01G349400 chr2A 94.009 217 8 2 2630 2841 333742191 333742407 1.050000e-84 324
18 TraesCS2D01G349400 chr2A 100.000 40 0 0 2592 2631 590973631 590973592 1.170000e-09 75
19 TraesCS2D01G349400 chr2B 84.243 971 107 30 1172 2117 526734187 526733238 0.000000e+00 904
20 TraesCS2D01G349400 chr2B 85.615 723 81 13 1183 1901 526670723 526670020 0.000000e+00 737
21 TraesCS2D01G349400 chr2B 89.097 321 17 5 869 1179 526734616 526734304 1.710000e-102 383
22 TraesCS2D01G349400 chr2B 94.359 195 6 2 457 646 765758943 765759137 8.230000e-76 294
23 TraesCS2D01G349400 chr2B 77.926 299 43 15 891 1170 526671159 526670865 6.730000e-37 165
24 TraesCS2D01G349400 chr2B 91.379 116 5 2 1 116 765758784 765758894 1.460000e-33 154
25 TraesCS2D01G349400 chr3D 96.535 202 5 2 457 656 300669253 300669052 1.740000e-87 333
26 TraesCS2D01G349400 chr3D 94.009 217 8 2 2630 2841 2720098 2719882 1.050000e-84 324
27 TraesCS2D01G349400 chr4B 92.511 227 12 2 2629 2850 5551638 5551412 1.360000e-83 320
28 TraesCS2D01G349400 chr4B 87.931 116 9 1 1 116 14276339 14276449 6.830000e-27 132
29 TraesCS2D01G349400 chr7D 94.258 209 11 1 2644 2851 161930728 161930936 4.880000e-83 318
30 TraesCS2D01G349400 chr7D 92.147 191 12 3 458 645 10064909 10065099 1.790000e-67 267
31 TraesCS2D01G349400 chr7D 95.690 116 5 0 1 116 10064763 10064878 1.440000e-43 187
32 TraesCS2D01G349400 chr6D 92.793 222 12 1 2627 2844 68629236 68629457 4.880000e-83 318
33 TraesCS2D01G349400 chr6D 92.694 219 15 1 2630 2848 469274601 469274384 6.320000e-82 315
34 TraesCS2D01G349400 chr5A 94.241 191 9 2 457 645 17285577 17285387 1.060000e-74 291
35 TraesCS2D01G349400 chr5A 92.241 116 9 0 1 116 438848736 438848621 6.730000e-37 165
36 TraesCS2D01G349400 chr1D 92.893 197 12 2 457 651 462963416 462963220 4.950000e-73 285
37 TraesCS2D01G349400 chr1D 93.966 116 7 0 1 116 481548216 481548101 3.110000e-40 176
38 TraesCS2D01G349400 chr4D 92.929 198 8 6 457 652 157652027 157651834 1.780000e-72 283
39 TraesCS2D01G349400 chr6A 93.158 190 11 2 458 645 616108055 616108244 8.290000e-71 278
40 TraesCS2D01G349400 chr6A 77.885 416 72 16 1497 1898 398167440 398167031 1.090000e-59 241
41 TraesCS2D01G349400 chr5B 91.878 197 9 3 457 648 588830058 588830252 4.990000e-68 268
42 TraesCS2D01G349400 chr1B 91.045 201 12 3 457 651 16178833 16179033 1.790000e-67 267
43 TraesCS2D01G349400 chr1B 93.966 116 7 0 1 116 16178669 16178784 3.110000e-40 176
44 TraesCS2D01G349400 chr6B 77.184 412 75 16 1497 1894 439076740 439077146 3.940000e-54 222
45 TraesCS2D01G349400 chr7A 95.690 116 5 0 1 116 6958859 6958974 1.440000e-43 187
46 TraesCS2D01G349400 chr3B 93.966 116 7 0 1 116 125782403 125782288 3.110000e-40 176
47 TraesCS2D01G349400 chr1A 91.589 107 4 4 1 107 24351188 24351087 3.160000e-30 143


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 TraesCS2D01G349400 chr2D 446931027 446934062 3035 False 1394.333333 3144 100.000000 1 3036 3 chr2D.!!$F1 3035
1 TraesCS2D01G349400 chr2D 446726701 446728079 1378 True 578.500000 850 84.352000 866 2154 2 chr2D.!!$R6 1288
2 TraesCS2D01G349400 chr2D 446696033 446697407 1374 True 577.500000 850 84.422500 869 2154 2 chr2D.!!$R5 1285
3 TraesCS2D01G349400 chr2D 446652277 446653410 1133 True 451.000000 728 81.625500 891 1901 2 chr2D.!!$R4 1010
4 TraesCS2D01G349400 chr2A 590973396 590975103 1707 True 843.000000 2128 97.613667 869 3036 3 chr2A.!!$R3 2167
5 TraesCS2D01G349400 chr2A 590816869 590817596 727 True 739.000000 739 85.067000 1157 1901 1 chr2A.!!$R1 744
6 TraesCS2D01G349400 chr2A 590965121 590966481 1360 True 629.500000 902 86.460500 873 2127 2 chr2A.!!$R2 1254
7 TraesCS2D01G349400 chr2B 526733238 526734616 1378 True 643.500000 904 86.670000 869 2117 2 chr2B.!!$R2 1248
8 TraesCS2D01G349400 chr2B 526670020 526671159 1139 True 451.000000 737 81.770500 891 1901 2 chr2B.!!$R1 1010

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
679 680 0.033504 TCACTCTGTTTCACCGGAGC 59.966 55.0 9.46 0.0 0.0 4.70 F
680 681 0.034059 CACTCTGTTTCACCGGAGCT 59.966 55.0 9.46 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 1947 1.666888 CGCCACTGTTGATTTTCCTGC 60.667 52.381 0.00 0.00 0.00 4.85 R
2657 2861 2.027469 GTCAAATTGACGACCTAGGGGT 60.027 50.000 14.81 10.74 42.37 4.95 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
42 43 4.598894 CCAGATCTGGGCCGAGCG 62.599 72.222 31.14 5.44 46.81 5.03
43 44 4.598894 CAGATCTGGGCCGAGCGG 62.599 72.222 15.38 4.20 38.57 5.52
101 102 4.933064 CGCCGTCCAGCCGATCTC 62.933 72.222 0.00 0.00 0.00 2.75
102 103 4.593864 GCCGTCCAGCCGATCTCC 62.594 72.222 0.00 0.00 0.00 3.71
103 104 3.917760 CCGTCCAGCCGATCTCCC 61.918 72.222 0.00 0.00 0.00 4.30
104 105 4.271816 CGTCCAGCCGATCTCCCG 62.272 72.222 0.00 0.00 0.00 5.14
105 106 4.593864 GTCCAGCCGATCTCCCGC 62.594 72.222 0.00 0.00 0.00 6.13
503 504 3.154473 CGAGAGGGGAATGGCCGA 61.154 66.667 0.00 0.00 37.63 5.54
504 505 2.825264 GAGAGGGGAATGGCCGAG 59.175 66.667 0.00 0.00 37.63 4.63
505 506 2.770048 AGAGGGGAATGGCCGAGG 60.770 66.667 0.00 0.00 37.63 4.63
506 507 3.878667 GAGGGGAATGGCCGAGGG 61.879 72.222 0.00 0.00 37.63 4.30
580 581 4.548513 CGGGGAGGGGGAGAGAGG 62.549 77.778 0.00 0.00 0.00 3.69
581 582 4.179599 GGGGAGGGGGAGAGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
582 583 3.036959 GGGAGGGGGAGAGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
583 584 2.612251 GGAGGGGGAGAGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
584 585 2.015726 GGAGGGGGAGAGAGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
585 586 1.541672 GAGGGGGAGAGAGGGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
586 587 2.123033 GGGGGAGAGAGGGAGAGC 60.123 72.222 0.00 0.00 0.00 4.09
587 588 2.710826 GGGGGAGAGAGGGAGAGCT 61.711 68.421 0.00 0.00 0.00 4.09
588 589 1.457455 GGGGAGAGAGGGAGAGCTG 60.457 68.421 0.00 0.00 0.00 4.24
589 590 1.457455 GGGAGAGAGGGAGAGCTGG 60.457 68.421 0.00 0.00 0.00 4.85
590 591 2.133641 GGAGAGAGGGAGAGCTGGC 61.134 68.421 0.00 0.00 0.00 4.85
591 592 2.441901 AGAGAGGGAGAGCTGGCG 60.442 66.667 0.00 0.00 0.00 5.69
592 593 3.535962 GAGAGGGAGAGCTGGCGG 61.536 72.222 0.00 0.00 0.00 6.13
593 594 4.067512 AGAGGGAGAGCTGGCGGA 62.068 66.667 0.00 0.00 0.00 5.54
594 595 3.077556 GAGGGAGAGCTGGCGGAA 61.078 66.667 0.00 0.00 0.00 4.30
595 596 3.080121 AGGGAGAGCTGGCGGAAG 61.080 66.667 0.00 0.00 0.00 3.46
596 597 4.168291 GGGAGAGCTGGCGGAAGG 62.168 72.222 0.00 0.00 0.00 3.46
597 598 4.168291 GGAGAGCTGGCGGAAGGG 62.168 72.222 0.00 0.00 0.00 3.95
598 599 4.168291 GAGAGCTGGCGGAAGGGG 62.168 72.222 0.00 0.00 0.00 4.79
599 600 4.722535 AGAGCTGGCGGAAGGGGA 62.723 66.667 0.00 0.00 0.00 4.81
600 601 3.717294 GAGCTGGCGGAAGGGGAA 61.717 66.667 0.00 0.00 0.00 3.97
601 602 3.017581 AGCTGGCGGAAGGGGAAT 61.018 61.111 0.00 0.00 0.00 3.01
602 603 2.517166 GCTGGCGGAAGGGGAATC 60.517 66.667 0.00 0.00 0.00 2.52
603 604 2.203070 CTGGCGGAAGGGGAATCG 60.203 66.667 0.00 0.00 0.00 3.34
604 605 3.757248 CTGGCGGAAGGGGAATCGG 62.757 68.421 0.00 0.00 0.00 4.18
605 606 4.564110 GGCGGAAGGGGAATCGGG 62.564 72.222 0.00 0.00 0.00 5.14
606 607 4.564110 GCGGAAGGGGAATCGGGG 62.564 72.222 0.00 0.00 0.00 5.73
607 608 4.564110 CGGAAGGGGAATCGGGGC 62.564 72.222 0.00 0.00 0.00 5.80
608 609 4.564110 GGAAGGGGAATCGGGGCG 62.564 72.222 0.00 0.00 0.00 6.13
650 651 3.578272 CGGTCGCGAGAGGAGGAG 61.578 72.222 10.24 0.00 43.49 3.69
651 652 2.124653 GGTCGCGAGAGGAGGAGA 60.125 66.667 10.24 0.00 43.49 3.71
652 653 1.749638 GGTCGCGAGAGGAGGAGAA 60.750 63.158 10.24 0.00 43.49 2.87
653 654 1.720694 GGTCGCGAGAGGAGGAGAAG 61.721 65.000 10.24 0.00 43.49 2.85
654 655 1.452289 TCGCGAGAGGAGGAGAAGG 60.452 63.158 3.71 0.00 34.84 3.46
655 656 2.485795 CGCGAGAGGAGGAGAAGGG 61.486 68.421 0.00 0.00 0.00 3.95
656 657 2.791868 GCGAGAGGAGGAGAAGGGC 61.792 68.421 0.00 0.00 0.00 5.19
657 658 1.076339 CGAGAGGAGGAGAAGGGCT 60.076 63.158 0.00 0.00 0.00 5.19
658 659 0.183971 CGAGAGGAGGAGAAGGGCTA 59.816 60.000 0.00 0.00 0.00 3.93
659 660 1.699730 GAGAGGAGGAGAAGGGCTAC 58.300 60.000 0.00 0.00 0.00 3.58
660 661 1.216930 GAGAGGAGGAGAAGGGCTACT 59.783 57.143 0.00 0.00 41.86 2.57
665 666 2.153034 AGGAGAAGGGCTACTCACTC 57.847 55.000 0.00 0.00 29.07 3.51
666 667 1.643811 AGGAGAAGGGCTACTCACTCT 59.356 52.381 0.00 0.00 29.07 3.24
667 668 1.754226 GGAGAAGGGCTACTCACTCTG 59.246 57.143 0.00 0.00 34.84 3.35
668 669 2.452505 GAGAAGGGCTACTCACTCTGT 58.547 52.381 0.00 0.00 33.04 3.41
669 670 2.829120 GAGAAGGGCTACTCACTCTGTT 59.171 50.000 0.00 0.00 33.04 3.16
670 671 3.243724 AGAAGGGCTACTCACTCTGTTT 58.756 45.455 0.00 0.00 0.00 2.83
671 672 3.259625 AGAAGGGCTACTCACTCTGTTTC 59.740 47.826 0.00 0.00 0.00 2.78
672 673 2.609747 AGGGCTACTCACTCTGTTTCA 58.390 47.619 0.00 0.00 0.00 2.69
673 674 2.300437 AGGGCTACTCACTCTGTTTCAC 59.700 50.000 0.00 0.00 0.00 3.18
674 675 2.613223 GGGCTACTCACTCTGTTTCACC 60.613 54.545 0.00 0.00 0.00 4.02
675 676 2.329379 GCTACTCACTCTGTTTCACCG 58.671 52.381 0.00 0.00 0.00 4.94
676 677 2.927014 GCTACTCACTCTGTTTCACCGG 60.927 54.545 0.00 0.00 0.00 5.28
677 678 1.410004 ACTCACTCTGTTTCACCGGA 58.590 50.000 9.46 0.00 0.00 5.14
678 679 1.341531 ACTCACTCTGTTTCACCGGAG 59.658 52.381 9.46 0.00 0.00 4.63
679 680 0.033504 TCACTCTGTTTCACCGGAGC 59.966 55.000 9.46 0.00 0.00 4.70
680 681 0.034059 CACTCTGTTTCACCGGAGCT 59.966 55.000 9.46 0.00 0.00 4.09
681 682 0.034059 ACTCTGTTTCACCGGAGCTG 59.966 55.000 9.46 0.00 0.00 4.24
682 683 0.671781 CTCTGTTTCACCGGAGCTGG 60.672 60.000 9.46 0.00 0.00 4.85
683 684 1.118965 TCTGTTTCACCGGAGCTGGA 61.119 55.000 9.46 0.00 0.00 3.86
684 685 0.951040 CTGTTTCACCGGAGCTGGAC 60.951 60.000 9.46 0.00 0.00 4.02
685 686 1.671379 GTTTCACCGGAGCTGGACC 60.671 63.158 9.46 0.00 0.00 4.46
686 687 2.144078 TTTCACCGGAGCTGGACCA 61.144 57.895 9.46 0.00 0.00 4.02
687 688 2.111999 TTTCACCGGAGCTGGACCAG 62.112 60.000 17.83 17.83 34.12 4.00
700 701 4.243007 CTGGACCAGCCTTTTTACTTTG 57.757 45.455 8.99 0.00 37.63 2.77
701 702 2.962421 TGGACCAGCCTTTTTACTTTGG 59.038 45.455 0.00 0.00 37.63 3.28
702 703 2.963101 GGACCAGCCTTTTTACTTTGGT 59.037 45.455 0.00 0.00 41.35 3.67
703 704 4.238761 GACCAGCCTTTTTACTTTGGTC 57.761 45.455 5.79 5.79 45.22 4.02
704 705 2.963101 ACCAGCCTTTTTACTTTGGTCC 59.037 45.455 0.00 0.00 33.92 4.46
705 706 2.962421 CCAGCCTTTTTACTTTGGTCCA 59.038 45.455 0.00 0.00 0.00 4.02
706 707 3.386402 CCAGCCTTTTTACTTTGGTCCAA 59.614 43.478 0.00 0.00 0.00 3.53
707 708 4.141824 CCAGCCTTTTTACTTTGGTCCAAA 60.142 41.667 16.26 16.26 0.00 3.28
708 709 5.423886 CAGCCTTTTTACTTTGGTCCAAAA 58.576 37.500 17.70 1.55 32.75 2.44
709 710 5.877564 CAGCCTTTTTACTTTGGTCCAAAAA 59.122 36.000 17.70 7.82 32.75 1.94
710 711 6.542005 CAGCCTTTTTACTTTGGTCCAAAAAT 59.458 34.615 17.70 11.39 32.75 1.82
711 712 7.066887 CAGCCTTTTTACTTTGGTCCAAAAATT 59.933 33.333 17.70 8.00 32.75 1.82
712 713 8.268605 AGCCTTTTTACTTTGGTCCAAAAATTA 58.731 29.630 17.70 7.10 32.75 1.40
713 714 9.062524 GCCTTTTTACTTTGGTCCAAAAATTAT 57.937 29.630 17.70 4.64 32.75 1.28
757 758 6.616774 TTTTTGAGCTTTTATGGCTTTTGG 57.383 33.333 0.00 0.00 40.40 3.28
758 759 4.953940 TTGAGCTTTTATGGCTTTTGGT 57.046 36.364 0.00 0.00 40.40 3.67
759 760 4.255833 TGAGCTTTTATGGCTTTTGGTG 57.744 40.909 0.00 0.00 40.40 4.17
760 761 2.995939 GAGCTTTTATGGCTTTTGGTGC 59.004 45.455 0.00 0.00 40.40 5.01
761 762 2.634453 AGCTTTTATGGCTTTTGGTGCT 59.366 40.909 0.00 0.00 36.56 4.40
762 763 2.995939 GCTTTTATGGCTTTTGGTGCTC 59.004 45.455 0.00 0.00 0.00 4.26
763 764 3.588955 CTTTTATGGCTTTTGGTGCTCC 58.411 45.455 0.00 0.00 0.00 4.70
764 765 2.300956 TTATGGCTTTTGGTGCTCCA 57.699 45.000 2.64 2.64 42.66 3.86
850 851 7.665561 AAAAACTGTAAAAGCAGAAGCAAAA 57.334 28.000 0.00 0.00 45.49 2.44
851 852 7.665561 AAAACTGTAAAAGCAGAAGCAAAAA 57.334 28.000 0.00 0.00 45.49 1.94
852 853 7.848223 AAACTGTAAAAGCAGAAGCAAAAAT 57.152 28.000 0.00 0.00 45.49 1.82
853 854 7.468922 AACTGTAAAAGCAGAAGCAAAAATC 57.531 32.000 0.00 0.00 45.49 2.17
854 855 5.985530 ACTGTAAAAGCAGAAGCAAAAATCC 59.014 36.000 0.00 0.00 45.49 3.01
855 856 5.911752 TGTAAAAGCAGAAGCAAAAATCCA 58.088 33.333 0.00 0.00 45.49 3.41
856 857 6.344500 TGTAAAAGCAGAAGCAAAAATCCAA 58.656 32.000 0.00 0.00 45.49 3.53
857 858 6.820656 TGTAAAAGCAGAAGCAAAAATCCAAA 59.179 30.769 0.00 0.00 45.49 3.28
858 859 5.739752 AAAGCAGAAGCAAAAATCCAAAC 57.260 34.783 0.00 0.00 45.49 2.93
859 860 4.405116 AGCAGAAGCAAAAATCCAAACA 57.595 36.364 0.00 0.00 45.49 2.83
860 861 4.768583 AGCAGAAGCAAAAATCCAAACAA 58.231 34.783 0.00 0.00 45.49 2.83
861 862 5.184711 AGCAGAAGCAAAAATCCAAACAAA 58.815 33.333 0.00 0.00 45.49 2.83
862 863 5.065090 AGCAGAAGCAAAAATCCAAACAAAC 59.935 36.000 0.00 0.00 45.49 2.93
863 864 5.163774 GCAGAAGCAAAAATCCAAACAAACA 60.164 36.000 0.00 0.00 41.58 2.83
864 865 6.480285 CAGAAGCAAAAATCCAAACAAACAG 58.520 36.000 0.00 0.00 0.00 3.16
865 866 6.092533 CAGAAGCAAAAATCCAAACAAACAGT 59.907 34.615 0.00 0.00 0.00 3.55
866 867 5.799681 AGCAAAAATCCAAACAAACAGTG 57.200 34.783 0.00 0.00 0.00 3.66
867 868 4.094739 AGCAAAAATCCAAACAAACAGTGC 59.905 37.500 0.00 0.00 0.00 4.40
876 877 3.715628 AACAAACAGTGCCTAAGCTTG 57.284 42.857 9.86 0.00 40.80 4.01
880 881 1.897560 ACAGTGCCTAAGCTTGGAAC 58.102 50.000 11.99 13.73 40.80 3.62
887 888 2.619074 GCCTAAGCTTGGAACCATGACT 60.619 50.000 11.99 4.93 35.50 3.41
937 942 1.201812 CCGCGTGATTCTTTGAACGAG 60.202 52.381 4.92 0.00 38.27 4.18
969 975 0.391263 CTAGTCCAACCTTGACGCCC 60.391 60.000 0.00 0.00 0.00 6.13
1010 1025 7.959733 TCAAACTTGCTGTGTCTATATAAACG 58.040 34.615 0.00 0.00 0.00 3.60
1435 1612 9.577110 CATATACCAACACTAGACGAGTTTAAA 57.423 33.333 0.00 0.00 35.64 1.52
1770 1947 4.493747 GGGGTTCGGCGAGACGAG 62.494 72.222 10.46 0.00 44.47 4.18
1912 2103 1.196946 GATTCTTGATCGACGCGCG 59.803 57.895 30.96 30.96 42.69 6.86
1937 2128 5.395325 AACATTATTTCAGACGATGCTCG 57.605 39.130 0.00 4.36 46.93 5.03
1978 2169 4.262808 CCCTGTGTATTCTGGGATCATCTC 60.263 50.000 0.00 0.00 45.56 2.75
2635 2839 8.617290 TTTTTACTTCAGAAAGTGATACTCCC 57.383 34.615 1.17 0.00 45.37 4.30
2636 2840 7.554959 TTTACTTCAGAAAGTGATACTCCCT 57.445 36.000 1.17 0.00 45.37 4.20
2637 2841 5.669164 ACTTCAGAAAGTGATACTCCCTC 57.331 43.478 0.00 0.00 44.13 4.30
2638 2842 5.337788 ACTTCAGAAAGTGATACTCCCTCT 58.662 41.667 0.00 0.00 44.13 3.69
2639 2843 5.420739 ACTTCAGAAAGTGATACTCCCTCTC 59.579 44.000 0.00 0.00 44.13 3.20
2640 2844 5.199982 TCAGAAAGTGATACTCCCTCTCT 57.800 43.478 0.00 0.00 0.00 3.10
2641 2845 5.197451 TCAGAAAGTGATACTCCCTCTCTC 58.803 45.833 0.00 0.00 0.00 3.20
2642 2846 5.044476 TCAGAAAGTGATACTCCCTCTCTCT 60.044 44.000 0.00 0.00 0.00 3.10
2643 2847 5.299279 CAGAAAGTGATACTCCCTCTCTCTC 59.701 48.000 0.00 0.00 0.00 3.20
2644 2848 4.871871 AAGTGATACTCCCTCTCTCTCA 57.128 45.455 0.00 0.00 0.00 3.27
2645 2849 4.437682 AGTGATACTCCCTCTCTCTCAG 57.562 50.000 0.00 0.00 0.00 3.35
2646 2850 3.138283 AGTGATACTCCCTCTCTCTCAGG 59.862 52.174 0.00 0.00 0.00 3.86
2650 2854 2.043450 CCCTCTCTCTCAGGGCGT 60.043 66.667 0.00 0.00 44.59 5.68
2651 2855 2.422231 CCCTCTCTCTCAGGGCGTG 61.422 68.421 0.00 0.00 44.59 5.34
2652 2856 2.493973 CTCTCTCTCAGGGCGTGC 59.506 66.667 1.51 0.00 0.00 5.34
2653 2857 3.408501 CTCTCTCTCAGGGCGTGCG 62.409 68.421 1.51 0.00 0.00 5.34
2665 2869 4.564116 CGTGCGCGTACCCCTAGG 62.564 72.222 21.71 0.06 40.04 3.02
2667 2871 3.142838 TGCGCGTACCCCTAGGTC 61.143 66.667 8.43 0.00 46.45 3.85
2668 2872 4.261781 GCGCGTACCCCTAGGTCG 62.262 72.222 8.43 8.12 46.45 4.79
2669 2873 2.825836 CGCGTACCCCTAGGTCGT 60.826 66.667 8.29 6.00 46.45 4.34
2670 2874 2.828128 CGCGTACCCCTAGGTCGTC 61.828 68.421 8.29 3.46 46.45 4.20
2671 2875 1.750399 GCGTACCCCTAGGTCGTCA 60.750 63.158 8.29 0.00 46.45 4.35
2672 2876 1.315257 GCGTACCCCTAGGTCGTCAA 61.315 60.000 8.29 0.00 46.45 3.18
2673 2877 1.396653 CGTACCCCTAGGTCGTCAAT 58.603 55.000 8.29 0.00 46.45 2.57
2674 2878 1.753073 CGTACCCCTAGGTCGTCAATT 59.247 52.381 8.29 0.00 46.45 2.32
2675 2879 2.167075 CGTACCCCTAGGTCGTCAATTT 59.833 50.000 8.29 0.00 46.45 1.82
2676 2880 2.781681 ACCCCTAGGTCGTCAATTTG 57.218 50.000 8.29 0.00 46.45 2.32
2677 2881 2.262637 ACCCCTAGGTCGTCAATTTGA 58.737 47.619 8.29 0.00 46.45 2.69
2678 2882 2.027469 ACCCCTAGGTCGTCAATTTGAC 60.027 50.000 17.76 17.76 46.45 3.18
2679 2883 5.201262 ACCCCTAGGTCGTCAATTTGACC 62.201 52.174 20.87 10.15 46.45 4.02
2685 2889 3.701532 GTCGTCAATTTGACCAACCAA 57.298 42.857 20.87 0.99 44.20 3.67
2686 2890 4.035278 GTCGTCAATTTGACCAACCAAA 57.965 40.909 20.87 0.00 44.20 3.28
2687 2891 4.616953 GTCGTCAATTTGACCAACCAAAT 58.383 39.130 20.87 0.00 44.20 2.32
2688 2892 5.764131 GTCGTCAATTTGACCAACCAAATA 58.236 37.500 20.87 0.00 44.20 1.40
2689 2893 5.627780 GTCGTCAATTTGACCAACCAAATAC 59.372 40.000 20.87 5.03 44.20 1.89
2690 2894 5.299531 TCGTCAATTTGACCAACCAAATACA 59.700 36.000 20.87 0.00 44.20 2.29
2691 2895 5.980116 CGTCAATTTGACCAACCAAATACAA 59.020 36.000 20.87 0.00 44.20 2.41
2692 2896 6.477033 CGTCAATTTGACCAACCAAATACAAA 59.523 34.615 20.87 0.00 44.20 2.83
2693 2897 7.170658 CGTCAATTTGACCAACCAAATACAAAT 59.829 33.333 20.87 0.00 44.20 2.32
2694 2898 8.495148 GTCAATTTGACCAACCAAATACAAATC 58.505 33.333 17.07 0.00 43.61 2.17
2695 2899 8.206867 TCAATTTGACCAACCAAATACAAATCA 58.793 29.630 0.00 0.00 43.61 2.57
2696 2900 9.001542 CAATTTGACCAACCAAATACAAATCAT 57.998 29.630 0.00 0.00 43.61 2.45
2748 2952 9.956720 AACTTCAGATGTTCTATTTTCAAACAG 57.043 29.630 0.00 0.00 36.44 3.16
2749 2953 9.125026 ACTTCAGATGTTCTATTTTCAAACAGT 57.875 29.630 0.00 0.00 36.44 3.55
2798 3002 5.669164 TTAGGGTGATAAAATTGGCAACC 57.331 39.130 0.00 0.00 38.39 3.77
2799 3003 3.790126 AGGGTGATAAAATTGGCAACCT 58.210 40.909 0.00 0.00 43.35 3.50
2800 3004 4.941713 AGGGTGATAAAATTGGCAACCTA 58.058 39.130 0.00 0.00 46.13 3.08
2801 3005 4.956075 AGGGTGATAAAATTGGCAACCTAG 59.044 41.667 0.00 0.00 46.13 3.02
2802 3006 4.099419 GGGTGATAAAATTGGCAACCTAGG 59.901 45.833 7.41 7.41 35.26 3.02
2803 3007 4.709886 GGTGATAAAATTGGCAACCTAGGT 59.290 41.667 9.21 9.21 0.00 3.08
2804 3008 5.889289 GGTGATAAAATTGGCAACCTAGGTA 59.111 40.000 16.67 0.00 0.00 3.08
2805 3009 6.549736 GGTGATAAAATTGGCAACCTAGGTAT 59.450 38.462 16.67 0.83 0.00 2.73
2806 3010 7.722285 GGTGATAAAATTGGCAACCTAGGTATA 59.278 37.037 16.67 0.00 0.00 1.47
2807 3011 8.565416 GTGATAAAATTGGCAACCTAGGTATAC 58.435 37.037 16.67 8.74 0.00 1.47
2808 3012 7.442969 TGATAAAATTGGCAACCTAGGTATACG 59.557 37.037 16.67 5.52 0.00 3.06
2809 3013 2.607631 TTGGCAACCTAGGTATACGC 57.392 50.000 16.67 15.11 0.00 4.42
2810 3014 0.386476 TGGCAACCTAGGTATACGCG 59.614 55.000 16.67 3.53 0.00 6.01
2811 3015 0.942884 GGCAACCTAGGTATACGCGC 60.943 60.000 16.67 10.85 0.00 6.86
2812 3016 0.249155 GCAACCTAGGTATACGCGCA 60.249 55.000 16.67 0.00 0.00 6.09
2813 3017 1.767289 CAACCTAGGTATACGCGCAG 58.233 55.000 16.67 2.42 0.00 5.18
2814 3018 0.672342 AACCTAGGTATACGCGCAGG 59.328 55.000 16.67 6.39 0.00 4.85
2815 3019 0.179009 ACCTAGGTATACGCGCAGGA 60.179 55.000 14.41 0.00 0.00 3.86
2816 3020 0.240411 CCTAGGTATACGCGCAGGAC 59.760 60.000 5.73 0.00 0.00 3.85
2817 3021 1.236628 CTAGGTATACGCGCAGGACT 58.763 55.000 5.73 1.68 0.00 3.85
2818 3022 1.607628 CTAGGTATACGCGCAGGACTT 59.392 52.381 5.73 0.00 0.00 3.01
2819 3023 0.102481 AGGTATACGCGCAGGACTTG 59.898 55.000 5.73 0.00 0.00 3.16
2820 3024 0.179119 GGTATACGCGCAGGACTTGT 60.179 55.000 5.73 0.00 0.00 3.16
2821 3025 1.066002 GGTATACGCGCAGGACTTGTA 59.934 52.381 5.73 0.00 0.00 2.41
2822 3026 2.480073 GGTATACGCGCAGGACTTGTAA 60.480 50.000 5.73 0.00 0.00 2.41
2823 3027 2.373540 ATACGCGCAGGACTTGTAAA 57.626 45.000 5.73 0.00 0.00 2.01
2824 3028 1.421382 TACGCGCAGGACTTGTAAAC 58.579 50.000 5.73 0.00 0.00 2.01
2825 3029 0.249741 ACGCGCAGGACTTGTAAACT 60.250 50.000 5.73 0.00 0.00 2.66
2826 3030 0.163788 CGCGCAGGACTTGTAAACTG 59.836 55.000 8.75 0.00 0.00 3.16
2827 3031 1.508632 GCGCAGGACTTGTAAACTGA 58.491 50.000 0.30 0.00 32.86 3.41
2828 3032 1.871039 GCGCAGGACTTGTAAACTGAA 59.129 47.619 0.30 0.00 32.86 3.02
2829 3033 2.289547 GCGCAGGACTTGTAAACTGAAA 59.710 45.455 0.30 0.00 32.86 2.69
2830 3034 3.848554 GCGCAGGACTTGTAAACTGAAAC 60.849 47.826 0.30 0.00 32.86 2.78
2831 3035 3.603857 CGCAGGACTTGTAAACTGAAACG 60.604 47.826 0.00 0.00 32.86 3.60
2832 3036 3.303791 GCAGGACTTGTAAACTGAAACGG 60.304 47.826 0.00 0.00 32.86 4.44
2833 3037 4.124238 CAGGACTTGTAAACTGAAACGGA 58.876 43.478 0.00 0.00 32.86 4.69
2834 3038 4.211374 CAGGACTTGTAAACTGAAACGGAG 59.789 45.833 0.00 0.00 32.86 4.63
2835 3039 3.497262 GGACTTGTAAACTGAAACGGAGG 59.503 47.826 0.00 0.00 0.00 4.30
2836 3040 4.374399 GACTTGTAAACTGAAACGGAGGA 58.626 43.478 0.00 0.00 0.00 3.71
2837 3041 4.773013 ACTTGTAAACTGAAACGGAGGAA 58.227 39.130 0.00 0.00 0.00 3.36
2838 3042 4.814771 ACTTGTAAACTGAAACGGAGGAAG 59.185 41.667 0.00 0.00 0.00 3.46
2839 3043 4.411256 TGTAAACTGAAACGGAGGAAGT 57.589 40.909 0.00 0.00 0.00 3.01
2840 3044 5.534207 TGTAAACTGAAACGGAGGAAGTA 57.466 39.130 0.00 0.00 0.00 2.24
3029 3233 8.642935 TCCAATATTTCATTGTTGTTGTAGGA 57.357 30.769 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.195334 CCTTCGGGCCCCATCTGG 62.195 72.222 18.66 7.92 0.00 3.86
6 7 4.195334 CCCTTCGGGCCCCATCTG 62.195 72.222 18.66 0.58 35.35 2.90
16 17 2.507944 CAGATCTGGGCCCTTCGG 59.492 66.667 25.70 13.94 0.00 4.30
17 18 2.507944 CCAGATCTGGGCCCTTCG 59.492 66.667 31.14 11.77 46.81 3.79
26 27 4.598894 CCGCTCGGCCCAGATCTG 62.599 72.222 16.24 16.24 0.00 2.90
85 86 4.593864 GGAGATCGGCTGGACGGC 62.594 72.222 0.00 0.00 0.00 5.68
86 87 3.917760 GGGAGATCGGCTGGACGG 61.918 72.222 0.00 0.00 0.00 4.79
87 88 4.271816 CGGGAGATCGGCTGGACG 62.272 72.222 0.00 0.00 0.00 4.79
88 89 4.593864 GCGGGAGATCGGCTGGAC 62.594 72.222 0.00 0.00 38.48 4.02
473 474 3.708220 CTCTCGGTTGCTCTCCGGC 62.708 68.421 0.00 0.00 46.82 6.13
474 475 2.492090 CTCTCGGTTGCTCTCCGG 59.508 66.667 12.90 0.00 46.82 5.14
476 477 2.726351 CCCCTCTCGGTTGCTCTCC 61.726 68.421 0.00 0.00 0.00 3.71
477 478 1.258445 TTCCCCTCTCGGTTGCTCTC 61.258 60.000 0.00 0.00 0.00 3.20
478 479 0.618968 ATTCCCCTCTCGGTTGCTCT 60.619 55.000 0.00 0.00 0.00 4.09
479 480 0.462759 CATTCCCCTCTCGGTTGCTC 60.463 60.000 0.00 0.00 0.00 4.26
480 481 1.604378 CATTCCCCTCTCGGTTGCT 59.396 57.895 0.00 0.00 0.00 3.91
481 482 1.452108 CCATTCCCCTCTCGGTTGC 60.452 63.158 0.00 0.00 0.00 4.17
482 483 1.452108 GCCATTCCCCTCTCGGTTG 60.452 63.158 0.00 0.00 0.00 3.77
483 484 2.680370 GGCCATTCCCCTCTCGGTT 61.680 63.158 0.00 0.00 0.00 4.44
484 485 3.090532 GGCCATTCCCCTCTCGGT 61.091 66.667 0.00 0.00 0.00 4.69
485 486 4.241555 CGGCCATTCCCCTCTCGG 62.242 72.222 2.24 0.00 0.00 4.63
486 487 3.154473 TCGGCCATTCCCCTCTCG 61.154 66.667 2.24 0.00 0.00 4.04
487 488 2.812619 CCTCGGCCATTCCCCTCTC 61.813 68.421 2.24 0.00 0.00 3.20
488 489 2.770048 CCTCGGCCATTCCCCTCT 60.770 66.667 2.24 0.00 0.00 3.69
489 490 3.878667 CCCTCGGCCATTCCCCTC 61.879 72.222 2.24 0.00 0.00 4.30
563 564 4.548513 CCTCTCTCCCCCTCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
564 565 4.179599 CCCTCTCTCCCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
565 566 3.036959 TCCCTCTCTCCCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
566 567 2.015726 TCTCCCTCTCTCCCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
567 568 1.541672 CTCTCCCTCTCTCCCCCTC 59.458 68.421 0.00 0.00 0.00 4.30
568 569 2.710826 GCTCTCCCTCTCTCCCCCT 61.711 68.421 0.00 0.00 0.00 4.79
569 570 2.123033 GCTCTCCCTCTCTCCCCC 60.123 72.222 0.00 0.00 0.00 5.40
570 571 1.457455 CAGCTCTCCCTCTCTCCCC 60.457 68.421 0.00 0.00 0.00 4.81
571 572 1.457455 CCAGCTCTCCCTCTCTCCC 60.457 68.421 0.00 0.00 0.00 4.30
572 573 2.133641 GCCAGCTCTCCCTCTCTCC 61.134 68.421 0.00 0.00 0.00 3.71
573 574 2.489275 CGCCAGCTCTCCCTCTCTC 61.489 68.421 0.00 0.00 0.00 3.20
574 575 2.441901 CGCCAGCTCTCCCTCTCT 60.442 66.667 0.00 0.00 0.00 3.10
575 576 3.535962 CCGCCAGCTCTCCCTCTC 61.536 72.222 0.00 0.00 0.00 3.20
576 577 3.608759 TTCCGCCAGCTCTCCCTCT 62.609 63.158 0.00 0.00 0.00 3.69
577 578 3.077556 TTCCGCCAGCTCTCCCTC 61.078 66.667 0.00 0.00 0.00 4.30
578 579 3.080121 CTTCCGCCAGCTCTCCCT 61.080 66.667 0.00 0.00 0.00 4.20
579 580 4.168291 CCTTCCGCCAGCTCTCCC 62.168 72.222 0.00 0.00 0.00 4.30
580 581 4.168291 CCCTTCCGCCAGCTCTCC 62.168 72.222 0.00 0.00 0.00 3.71
581 582 4.168291 CCCCTTCCGCCAGCTCTC 62.168 72.222 0.00 0.00 0.00 3.20
582 583 4.722535 TCCCCTTCCGCCAGCTCT 62.723 66.667 0.00 0.00 0.00 4.09
583 584 2.949705 GATTCCCCTTCCGCCAGCTC 62.950 65.000 0.00 0.00 0.00 4.09
584 585 3.017581 ATTCCCCTTCCGCCAGCT 61.018 61.111 0.00 0.00 0.00 4.24
585 586 2.517166 GATTCCCCTTCCGCCAGC 60.517 66.667 0.00 0.00 0.00 4.85
586 587 2.203070 CGATTCCCCTTCCGCCAG 60.203 66.667 0.00 0.00 0.00 4.85
587 588 3.792736 CCGATTCCCCTTCCGCCA 61.793 66.667 0.00 0.00 0.00 5.69
588 589 4.564110 CCCGATTCCCCTTCCGCC 62.564 72.222 0.00 0.00 0.00 6.13
589 590 4.564110 CCCCGATTCCCCTTCCGC 62.564 72.222 0.00 0.00 0.00 5.54
590 591 4.564110 GCCCCGATTCCCCTTCCG 62.564 72.222 0.00 0.00 0.00 4.30
591 592 4.564110 CGCCCCGATTCCCCTTCC 62.564 72.222 0.00 0.00 0.00 3.46
633 634 3.578272 CTCCTCCTCTCGCGACCG 61.578 72.222 3.71 0.00 0.00 4.79
634 635 1.720694 CTTCTCCTCCTCTCGCGACC 61.721 65.000 3.71 0.00 0.00 4.79
635 636 1.720694 CCTTCTCCTCCTCTCGCGAC 61.721 65.000 3.71 0.00 0.00 5.19
636 637 1.452289 CCTTCTCCTCCTCTCGCGA 60.452 63.158 9.26 9.26 0.00 5.87
637 638 2.485795 CCCTTCTCCTCCTCTCGCG 61.486 68.421 0.00 0.00 0.00 5.87
638 639 2.791868 GCCCTTCTCCTCCTCTCGC 61.792 68.421 0.00 0.00 0.00 5.03
639 640 0.183971 TAGCCCTTCTCCTCCTCTCG 59.816 60.000 0.00 0.00 0.00 4.04
640 641 1.216930 AGTAGCCCTTCTCCTCCTCTC 59.783 57.143 0.00 0.00 0.00 3.20
641 642 1.216930 GAGTAGCCCTTCTCCTCCTCT 59.783 57.143 0.00 0.00 0.00 3.69
642 643 1.063567 TGAGTAGCCCTTCTCCTCCTC 60.064 57.143 0.40 0.00 0.00 3.71
643 644 1.011595 TGAGTAGCCCTTCTCCTCCT 58.988 55.000 0.40 0.00 0.00 3.69
644 645 1.116308 GTGAGTAGCCCTTCTCCTCC 58.884 60.000 0.40 0.00 0.00 4.30
645 646 2.028876 GAGTGAGTAGCCCTTCTCCTC 58.971 57.143 0.40 3.34 0.00 3.71
646 647 1.643811 AGAGTGAGTAGCCCTTCTCCT 59.356 52.381 0.40 0.00 0.00 3.69
647 648 1.754226 CAGAGTGAGTAGCCCTTCTCC 59.246 57.143 0.40 0.00 0.00 3.71
648 649 2.452505 ACAGAGTGAGTAGCCCTTCTC 58.547 52.381 0.00 0.00 0.00 2.87
649 650 2.614134 ACAGAGTGAGTAGCCCTTCT 57.386 50.000 0.00 0.00 0.00 2.85
650 651 3.006967 TGAAACAGAGTGAGTAGCCCTTC 59.993 47.826 0.00 0.00 0.00 3.46
651 652 2.972713 TGAAACAGAGTGAGTAGCCCTT 59.027 45.455 0.00 0.00 0.00 3.95
652 653 2.300437 GTGAAACAGAGTGAGTAGCCCT 59.700 50.000 0.00 0.00 36.32 5.19
653 654 2.613223 GGTGAAACAGAGTGAGTAGCCC 60.613 54.545 0.00 0.00 39.98 5.19
654 655 2.689646 GGTGAAACAGAGTGAGTAGCC 58.310 52.381 0.00 0.00 39.98 3.93
655 656 2.329379 CGGTGAAACAGAGTGAGTAGC 58.671 52.381 0.00 0.00 39.98 3.58
656 657 2.557056 TCCGGTGAAACAGAGTGAGTAG 59.443 50.000 0.00 0.00 39.98 2.57
657 658 2.557056 CTCCGGTGAAACAGAGTGAGTA 59.443 50.000 0.00 0.00 39.98 2.59
658 659 1.341531 CTCCGGTGAAACAGAGTGAGT 59.658 52.381 0.00 0.00 39.98 3.41
659 660 1.937108 GCTCCGGTGAAACAGAGTGAG 60.937 57.143 7.92 0.00 39.94 3.51
660 661 0.033504 GCTCCGGTGAAACAGAGTGA 59.966 55.000 7.92 0.00 39.94 3.41
661 662 0.034059 AGCTCCGGTGAAACAGAGTG 59.966 55.000 7.92 0.00 39.94 3.51
662 663 0.034059 CAGCTCCGGTGAAACAGAGT 59.966 55.000 7.92 0.00 39.94 3.24
663 664 0.671781 CCAGCTCCGGTGAAACAGAG 60.672 60.000 7.92 0.00 40.53 3.35
664 665 1.118965 TCCAGCTCCGGTGAAACAGA 61.119 55.000 7.92 0.00 39.98 3.41
665 666 0.951040 GTCCAGCTCCGGTGAAACAG 60.951 60.000 7.92 0.00 39.98 3.16
666 667 1.070786 GTCCAGCTCCGGTGAAACA 59.929 57.895 7.92 0.00 39.98 2.83
667 668 1.671379 GGTCCAGCTCCGGTGAAAC 60.671 63.158 7.92 0.00 32.22 2.78
668 669 2.111999 CTGGTCCAGCTCCGGTGAAA 62.112 60.000 5.79 0.00 32.22 2.69
669 670 2.525629 TGGTCCAGCTCCGGTGAA 60.526 61.111 7.92 0.00 32.22 3.18
670 671 2.997315 CTGGTCCAGCTCCGGTGA 60.997 66.667 5.79 0.00 32.22 4.02
679 680 3.005791 CCAAAGTAAAAAGGCTGGTCCAG 59.994 47.826 15.15 15.15 37.29 3.86
680 681 2.962421 CCAAAGTAAAAAGGCTGGTCCA 59.038 45.455 0.00 0.00 37.29 4.02
681 682 2.963101 ACCAAAGTAAAAAGGCTGGTCC 59.037 45.455 0.00 0.00 31.52 4.46
682 683 4.238761 GACCAAAGTAAAAAGGCTGGTC 57.761 45.455 3.48 3.48 44.28 4.02
683 684 2.963101 GGACCAAAGTAAAAAGGCTGGT 59.037 45.455 0.00 0.00 39.85 4.00
684 685 2.962421 TGGACCAAAGTAAAAAGGCTGG 59.038 45.455 0.00 0.00 0.00 4.85
685 686 4.664150 TTGGACCAAAGTAAAAAGGCTG 57.336 40.909 3.84 0.00 0.00 4.85
686 687 5.685520 TTTTGGACCAAAGTAAAAAGGCT 57.314 34.783 18.78 0.00 34.72 4.58
687 688 6.935741 ATTTTTGGACCAAAGTAAAAAGGC 57.064 33.333 18.78 0.00 36.02 4.35
734 735 6.038050 CACCAAAAGCCATAAAAGCTCAAAAA 59.962 34.615 0.00 0.00 40.49 1.94
735 736 5.526846 CACCAAAAGCCATAAAAGCTCAAAA 59.473 36.000 0.00 0.00 40.49 2.44
736 737 5.055812 CACCAAAAGCCATAAAAGCTCAAA 58.944 37.500 0.00 0.00 40.49 2.69
737 738 4.630111 CACCAAAAGCCATAAAAGCTCAA 58.370 39.130 0.00 0.00 40.49 3.02
738 739 3.554752 GCACCAAAAGCCATAAAAGCTCA 60.555 43.478 0.00 0.00 40.49 4.26
739 740 2.995939 GCACCAAAAGCCATAAAAGCTC 59.004 45.455 0.00 0.00 40.49 4.09
740 741 2.634453 AGCACCAAAAGCCATAAAAGCT 59.366 40.909 0.00 0.00 44.19 3.74
741 742 2.995939 GAGCACCAAAAGCCATAAAAGC 59.004 45.455 0.00 0.00 0.00 3.51
742 743 3.006752 TGGAGCACCAAAAGCCATAAAAG 59.993 43.478 0.00 0.00 43.91 2.27
743 744 2.968574 TGGAGCACCAAAAGCCATAAAA 59.031 40.909 0.00 0.00 43.91 1.52
744 745 2.603021 TGGAGCACCAAAAGCCATAAA 58.397 42.857 0.00 0.00 43.91 1.40
745 746 2.300956 TGGAGCACCAAAAGCCATAA 57.699 45.000 0.00 0.00 43.91 1.90
747 748 4.950200 TGGAGCACCAAAAGCCAT 57.050 50.000 0.00 0.00 43.91 4.40
826 827 7.665561 TTTTGCTTCTGCTTTTACAGTTTTT 57.334 28.000 0.00 0.00 38.84 1.94
827 828 7.665561 TTTTTGCTTCTGCTTTTACAGTTTT 57.334 28.000 0.00 0.00 38.84 2.43
828 829 7.011389 GGATTTTTGCTTCTGCTTTTACAGTTT 59.989 33.333 0.00 0.00 38.84 2.66
829 830 6.479990 GGATTTTTGCTTCTGCTTTTACAGTT 59.520 34.615 0.00 0.00 38.84 3.16
830 831 5.985530 GGATTTTTGCTTCTGCTTTTACAGT 59.014 36.000 0.00 0.00 38.84 3.55
831 832 5.984926 TGGATTTTTGCTTCTGCTTTTACAG 59.015 36.000 0.00 0.00 40.48 2.74
832 833 5.911752 TGGATTTTTGCTTCTGCTTTTACA 58.088 33.333 0.00 0.00 40.48 2.41
833 834 6.843069 TTGGATTTTTGCTTCTGCTTTTAC 57.157 33.333 0.00 0.00 40.48 2.01
834 835 6.820656 TGTTTGGATTTTTGCTTCTGCTTTTA 59.179 30.769 0.00 0.00 40.48 1.52
835 836 5.647225 TGTTTGGATTTTTGCTTCTGCTTTT 59.353 32.000 0.00 0.00 40.48 2.27
836 837 5.184711 TGTTTGGATTTTTGCTTCTGCTTT 58.815 33.333 0.00 0.00 40.48 3.51
837 838 4.768583 TGTTTGGATTTTTGCTTCTGCTT 58.231 34.783 0.00 0.00 40.48 3.91
838 839 4.405116 TGTTTGGATTTTTGCTTCTGCT 57.595 36.364 0.00 0.00 40.48 4.24
839 840 5.163774 TGTTTGTTTGGATTTTTGCTTCTGC 60.164 36.000 0.00 0.00 40.20 4.26
840 841 6.092533 ACTGTTTGTTTGGATTTTTGCTTCTG 59.907 34.615 0.00 0.00 0.00 3.02
841 842 6.092533 CACTGTTTGTTTGGATTTTTGCTTCT 59.907 34.615 0.00 0.00 0.00 2.85
842 843 6.250089 CACTGTTTGTTTGGATTTTTGCTTC 58.750 36.000 0.00 0.00 0.00 3.86
843 844 5.391843 GCACTGTTTGTTTGGATTTTTGCTT 60.392 36.000 0.00 0.00 0.00 3.91
844 845 4.094739 GCACTGTTTGTTTGGATTTTTGCT 59.905 37.500 0.00 0.00 0.00 3.91
845 846 4.341935 GCACTGTTTGTTTGGATTTTTGC 58.658 39.130 0.00 0.00 0.00 3.68
846 847 4.635324 AGGCACTGTTTGTTTGGATTTTTG 59.365 37.500 0.00 0.00 37.18 2.44
847 848 4.842574 AGGCACTGTTTGTTTGGATTTTT 58.157 34.783 0.00 0.00 37.18 1.94
848 849 4.486125 AGGCACTGTTTGTTTGGATTTT 57.514 36.364 0.00 0.00 37.18 1.82
849 850 5.600696 CTTAGGCACTGTTTGTTTGGATTT 58.399 37.500 0.00 0.00 41.52 2.17
850 851 4.501400 GCTTAGGCACTGTTTGTTTGGATT 60.501 41.667 0.00 0.00 41.52 3.01
851 852 3.005791 GCTTAGGCACTGTTTGTTTGGAT 59.994 43.478 0.00 0.00 41.52 3.41
852 853 2.360801 GCTTAGGCACTGTTTGTTTGGA 59.639 45.455 0.00 0.00 41.52 3.53
853 854 2.362077 AGCTTAGGCACTGTTTGTTTGG 59.638 45.455 0.00 0.00 41.52 3.28
854 855 3.715628 AGCTTAGGCACTGTTTGTTTG 57.284 42.857 0.00 0.00 41.52 2.93
855 856 3.181476 CCAAGCTTAGGCACTGTTTGTTT 60.181 43.478 0.00 0.00 41.52 2.83
856 857 2.362077 CCAAGCTTAGGCACTGTTTGTT 59.638 45.455 0.00 0.00 41.52 2.83
857 858 1.956477 CCAAGCTTAGGCACTGTTTGT 59.044 47.619 0.00 0.00 41.52 2.83
858 859 2.229792 TCCAAGCTTAGGCACTGTTTG 58.770 47.619 0.00 0.00 41.52 2.93
859 860 2.623416 GTTCCAAGCTTAGGCACTGTTT 59.377 45.455 0.00 0.00 41.52 2.83
860 861 2.230660 GTTCCAAGCTTAGGCACTGTT 58.769 47.619 0.00 0.00 41.52 3.16
861 862 1.545651 GGTTCCAAGCTTAGGCACTGT 60.546 52.381 0.00 0.00 41.52 3.55
862 863 1.168714 GGTTCCAAGCTTAGGCACTG 58.831 55.000 0.00 0.00 41.52 3.66
863 864 0.771127 TGGTTCCAAGCTTAGGCACT 59.229 50.000 0.00 0.00 46.37 4.40
864 865 1.474077 CATGGTTCCAAGCTTAGGCAC 59.526 52.381 0.00 3.95 41.70 5.01
865 866 1.354031 TCATGGTTCCAAGCTTAGGCA 59.646 47.619 0.00 0.00 41.70 4.75
866 867 1.745653 GTCATGGTTCCAAGCTTAGGC 59.254 52.381 0.00 0.00 39.06 3.93
867 868 3.054802 AGAGTCATGGTTCCAAGCTTAGG 60.055 47.826 0.00 3.44 0.00 2.69
876 877 2.783135 TCTTTGCAGAGTCATGGTTCC 58.217 47.619 3.90 0.00 0.00 3.62
880 881 4.518211 AGACTTTTCTTTGCAGAGTCATGG 59.482 41.667 3.90 0.00 39.27 3.66
887 888 5.635280 CGACTATCAGACTTTTCTTTGCAGA 59.365 40.000 0.00 0.00 0.00 4.26
937 942 1.829222 TGGACTAGATCAAACCGACCC 59.171 52.381 0.00 0.00 0.00 4.46
969 975 4.810790 AGTTTGATCTTGTGGACGACTAG 58.189 43.478 0.00 0.00 0.00 2.57
1062 1078 0.315251 GTTTGCTTGTTGAGGCCCTC 59.685 55.000 2.98 2.98 0.00 4.30
1770 1947 1.666888 CGCCACTGTTGATTTTCCTGC 60.667 52.381 0.00 0.00 0.00 4.85
1912 2103 7.656404 GAGCATCGTCTGAAATAATGTTTTC 57.344 36.000 0.00 0.00 36.38 2.29
1937 2128 3.633065 CAGGGAGGTAGAGCTGTAAGTAC 59.367 52.174 0.00 0.00 35.30 2.73
2634 2838 3.074999 GCACGCCCTGAGAGAGAGG 62.075 68.421 0.00 0.00 0.00 3.69
2635 2839 2.493973 GCACGCCCTGAGAGAGAG 59.506 66.667 0.00 0.00 0.00 3.20
2636 2840 3.443925 CGCACGCCCTGAGAGAGA 61.444 66.667 0.00 0.00 0.00 3.10
2655 2859 4.916984 GTCAAATTGACGACCTAGGGGTAC 60.917 50.000 14.81 2.61 40.90 3.34
2656 2860 3.196254 GTCAAATTGACGACCTAGGGGTA 59.804 47.826 14.81 0.00 40.90 3.69
2657 2861 2.027469 GTCAAATTGACGACCTAGGGGT 60.027 50.000 14.81 10.74 42.37 4.95
2658 2862 2.629051 GTCAAATTGACGACCTAGGGG 58.371 52.381 14.81 7.16 37.67 4.79
2668 2872 7.778470 TTTGTATTTGGTTGGTCAAATTGAC 57.222 32.000 17.16 17.16 46.23 3.18
2669 2873 8.206867 TGATTTGTATTTGGTTGGTCAAATTGA 58.793 29.630 7.91 0.00 42.63 2.57
2670 2874 8.375608 TGATTTGTATTTGGTTGGTCAAATTG 57.624 30.769 7.91 0.00 42.63 2.32
2722 2926 9.956720 CTGTTTGAAAATAGAACATCTGAAGTT 57.043 29.630 0.00 0.00 33.31 2.66
2723 2927 9.125026 ACTGTTTGAAAATAGAACATCTGAAGT 57.875 29.630 6.55 0.00 33.31 3.01
2772 2976 9.084533 GGTTGCCAATTTTATCACCCTAATATA 57.915 33.333 0.00 0.00 0.00 0.86
2773 2977 7.789349 AGGTTGCCAATTTTATCACCCTAATAT 59.211 33.333 0.00 0.00 0.00 1.28
2774 2978 7.129425 AGGTTGCCAATTTTATCACCCTAATA 58.871 34.615 0.00 0.00 0.00 0.98
2775 2979 5.963865 AGGTTGCCAATTTTATCACCCTAAT 59.036 36.000 0.00 0.00 0.00 1.73
2776 2980 5.337788 AGGTTGCCAATTTTATCACCCTAA 58.662 37.500 0.00 0.00 0.00 2.69
2777 2981 4.941713 AGGTTGCCAATTTTATCACCCTA 58.058 39.130 0.00 0.00 0.00 3.53
2778 2982 3.790126 AGGTTGCCAATTTTATCACCCT 58.210 40.909 0.00 0.00 0.00 4.34
2779 2983 4.099419 CCTAGGTTGCCAATTTTATCACCC 59.901 45.833 0.00 0.00 0.00 4.61
2780 2984 4.709886 ACCTAGGTTGCCAATTTTATCACC 59.290 41.667 9.21 0.00 0.00 4.02
2781 2985 5.914898 ACCTAGGTTGCCAATTTTATCAC 57.085 39.130 9.21 0.00 0.00 3.06
2782 2986 7.442969 CGTATACCTAGGTTGCCAATTTTATCA 59.557 37.037 22.11 0.00 0.00 2.15
2783 2987 7.572539 GCGTATACCTAGGTTGCCAATTTTATC 60.573 40.741 22.11 0.00 0.00 1.75
2784 2988 6.206048 GCGTATACCTAGGTTGCCAATTTTAT 59.794 38.462 22.11 5.71 0.00 1.40
2785 2989 5.528320 GCGTATACCTAGGTTGCCAATTTTA 59.472 40.000 22.11 0.00 0.00 1.52
2786 2990 4.337274 GCGTATACCTAGGTTGCCAATTTT 59.663 41.667 22.11 0.00 0.00 1.82
2787 2991 3.881089 GCGTATACCTAGGTTGCCAATTT 59.119 43.478 22.11 0.00 0.00 1.82
2788 2992 3.473625 GCGTATACCTAGGTTGCCAATT 58.526 45.455 22.11 0.00 0.00 2.32
2789 2993 2.547218 CGCGTATACCTAGGTTGCCAAT 60.547 50.000 22.11 9.64 0.00 3.16
2790 2994 1.202440 CGCGTATACCTAGGTTGCCAA 60.202 52.381 22.11 0.75 0.00 4.52
2791 2995 0.386476 CGCGTATACCTAGGTTGCCA 59.614 55.000 22.11 1.21 0.00 4.92
2792 2996 0.942884 GCGCGTATACCTAGGTTGCC 60.943 60.000 22.11 7.02 0.00 4.52
2793 2997 0.249155 TGCGCGTATACCTAGGTTGC 60.249 55.000 22.11 17.41 0.00 4.17
2794 2998 1.602165 CCTGCGCGTATACCTAGGTTG 60.602 57.143 22.11 9.15 0.00 3.77
2795 2999 0.672342 CCTGCGCGTATACCTAGGTT 59.328 55.000 22.11 10.62 0.00 3.50
2796 3000 0.179009 TCCTGCGCGTATACCTAGGT 60.179 55.000 20.57 20.57 0.00 3.08
2797 3001 0.240411 GTCCTGCGCGTATACCTAGG 59.760 60.000 7.41 7.41 0.00 3.02
2798 3002 1.236628 AGTCCTGCGCGTATACCTAG 58.763 55.000 8.43 0.00 0.00 3.02
2799 3003 1.335810 CAAGTCCTGCGCGTATACCTA 59.664 52.381 8.43 0.00 0.00 3.08
2800 3004 0.102481 CAAGTCCTGCGCGTATACCT 59.898 55.000 8.43 0.00 0.00 3.08
2801 3005 0.179119 ACAAGTCCTGCGCGTATACC 60.179 55.000 8.43 0.00 0.00 2.73
2802 3006 2.480224 TACAAGTCCTGCGCGTATAC 57.520 50.000 8.43 4.74 0.00 1.47
2803 3007 3.119388 AGTTTACAAGTCCTGCGCGTATA 60.119 43.478 8.43 0.00 0.00 1.47
2804 3008 1.997606 GTTTACAAGTCCTGCGCGTAT 59.002 47.619 8.43 0.00 0.00 3.06
2805 3009 1.000060 AGTTTACAAGTCCTGCGCGTA 60.000 47.619 8.43 0.71 0.00 4.42
2806 3010 0.249741 AGTTTACAAGTCCTGCGCGT 60.250 50.000 8.43 0.00 0.00 6.01
2807 3011 0.163788 CAGTTTACAAGTCCTGCGCG 59.836 55.000 0.00 0.00 0.00 6.86
2808 3012 1.508632 TCAGTTTACAAGTCCTGCGC 58.491 50.000 0.00 0.00 0.00 6.09
2809 3013 3.603857 CGTTTCAGTTTACAAGTCCTGCG 60.604 47.826 0.00 0.00 0.00 5.18
2810 3014 3.303791 CCGTTTCAGTTTACAAGTCCTGC 60.304 47.826 0.00 0.00 0.00 4.85
2811 3015 4.124238 TCCGTTTCAGTTTACAAGTCCTG 58.876 43.478 0.00 0.00 0.00 3.86
2812 3016 4.377897 CTCCGTTTCAGTTTACAAGTCCT 58.622 43.478 0.00 0.00 0.00 3.85
2813 3017 3.497262 CCTCCGTTTCAGTTTACAAGTCC 59.503 47.826 0.00 0.00 0.00 3.85
2814 3018 4.374399 TCCTCCGTTTCAGTTTACAAGTC 58.626 43.478 0.00 0.00 0.00 3.01
2815 3019 4.411256 TCCTCCGTTTCAGTTTACAAGT 57.589 40.909 0.00 0.00 0.00 3.16
2816 3020 4.814771 ACTTCCTCCGTTTCAGTTTACAAG 59.185 41.667 0.00 0.00 0.00 3.16
2817 3021 4.773013 ACTTCCTCCGTTTCAGTTTACAA 58.227 39.130 0.00 0.00 0.00 2.41
2818 3022 4.411256 ACTTCCTCCGTTTCAGTTTACA 57.589 40.909 0.00 0.00 0.00 2.41
2819 3023 6.161381 TGATACTTCCTCCGTTTCAGTTTAC 58.839 40.000 0.00 0.00 0.00 2.01
2820 3024 6.349243 TGATACTTCCTCCGTTTCAGTTTA 57.651 37.500 0.00 0.00 0.00 2.01
2821 3025 5.223449 TGATACTTCCTCCGTTTCAGTTT 57.777 39.130 0.00 0.00 0.00 2.66
2822 3026 4.884668 TGATACTTCCTCCGTTTCAGTT 57.115 40.909 0.00 0.00 0.00 3.16
2823 3027 4.884668 TTGATACTTCCTCCGTTTCAGT 57.115 40.909 0.00 0.00 0.00 3.41
2824 3028 8.438676 AATATTTGATACTTCCTCCGTTTCAG 57.561 34.615 0.00 0.00 0.00 3.02
2825 3029 8.801882 AAATATTTGATACTTCCTCCGTTTCA 57.198 30.769 0.00 0.00 0.00 2.69
2826 3030 8.889717 TGAAATATTTGATACTTCCTCCGTTTC 58.110 33.333 5.17 0.00 0.00 2.78
2827 3031 8.801882 TGAAATATTTGATACTTCCTCCGTTT 57.198 30.769 5.17 0.00 0.00 3.60
2828 3032 8.980481 ATGAAATATTTGATACTTCCTCCGTT 57.020 30.769 5.17 0.00 0.00 4.44
2829 3033 8.980481 AATGAAATATTTGATACTTCCTCCGT 57.020 30.769 5.17 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.