Multiple sequence alignment - TraesCS4B01G052400

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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 TraesCS4B01G052400 chr4B 100.000 2382 0 0 1 2382 41196202 41198583 0.000000e+00 4399
1 TraesCS4B01G052400 chr4B 100.000 382 0 0 2616 2997 41198817 41199198 0.000000e+00 706
2 TraesCS4B01G052400 chr4B 100.000 265 0 0 3068 3332 41199269 41199533 1.070000e-134 490
3 TraesCS4B01G052400 chr4D 92.232 2446 90 53 1 2382 28880260 28882669 0.000000e+00 3373
4 TraesCS4B01G052400 chr4D 93.985 266 7 5 3068 3330 28882705 28882964 8.660000e-106 394
5 TraesCS4B01G052400 chr4D 83.333 198 33 0 1514 1711 80836572 80836769 2.040000e-42 183
6 TraesCS4B01G052400 chr4A 91.306 2450 94 67 3 2380 574843009 574840607 0.000000e+00 3234
7 TraesCS4B01G052400 chr4A 90.602 266 7 4 3068 3332 574840569 574840321 1.480000e-88 337
8 TraesCS4B01G052400 chrUn 100.000 382 0 0 2616 2997 88901207 88901588 0.000000e+00 706
9 TraesCS4B01G052400 chr7D 100.000 382 0 0 2616 2997 31446532 31446151 0.000000e+00 706
10 TraesCS4B01G052400 chr7D 100.000 382 0 0 2616 2997 551318687 551318306 0.000000e+00 706
11 TraesCS4B01G052400 chr6B 100.000 382 0 0 2616 2997 24571189 24571570 0.000000e+00 706
12 TraesCS4B01G052400 chr6B 100.000 382 0 0 2616 2997 35020208 35020589 0.000000e+00 706
13 TraesCS4B01G052400 chr6A 100.000 382 0 0 2616 2997 503500280 503500661 0.000000e+00 706
14 TraesCS4B01G052400 chr5B 100.000 382 0 0 2616 2997 6295933 6296314 0.000000e+00 706
15 TraesCS4B01G052400 chr5B 100.000 382 0 0 2616 2997 14984367 14983986 0.000000e+00 706
16 TraesCS4B01G052400 chr1D 100.000 382 0 0 2616 2997 344689244 344689625 0.000000e+00 706
17 TraesCS4B01G052400 chr3B 84.834 211 30 2 1513 1722 258721284 258721075 9.370000e-51 211
18 TraesCS4B01G052400 chr3B 82.741 197 34 0 1513 1709 722590912 722590716 3.420000e-40 176
19 TraesCS4B01G052400 chr3A 84.834 211 30 2 1513 1722 225894569 225894360 9.370000e-51 211
20 TraesCS4B01G052400 chr3D 84.360 211 31 2 1513 1722 180470744 180470535 4.360000e-49 206
21 TraesCS4B01G052400 chr3D 90.845 142 7 5 2083 2224 569929255 569929390 5.680000e-43 185
22 TraesCS4B01G052400 chr3D 82.234 197 35 0 1513 1709 546198932 546198736 1.590000e-38 171
23 TraesCS4B01G052400 chr6D 79.310 174 24 11 1524 1691 142138974 142138807 9.770000e-21 111


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 TraesCS4B01G052400 chr4B 41196202 41199533 3331 False 1865.0 4399 100.0000 1 3332 3 chr4B.!!$F1 3331
1 TraesCS4B01G052400 chr4D 28880260 28882964 2704 False 1883.5 3373 93.1085 1 3330 2 chr4D.!!$F2 3329
2 TraesCS4B01G052400 chr4A 574840321 574843009 2688 True 1785.5 3234 90.9540 3 3332 2 chr4A.!!$R1 3329

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
429 445 0.108662 CTGGCGAGACACTGCACATA 60.109 55.0 0.0 0.0 0.0 2.29 F
754 786 0.254178 TTGCCTCTTCTCATCCTGCC 59.746 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2070 0.036765 GTTCCGGACACACATGGCTA 60.037 55.0 1.83 0.0 32.54 3.93 R
2704 2807 0.167908 CGCGCCTGATGCAAGTTAAA 59.832 50.0 0.00 0.0 41.33 1.52 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
126 130 6.528537 TTGCACCAGCTTAATTAATCACAT 57.471 33.333 0.00 0.00 42.74 3.21
128 132 5.418524 TGCACCAGCTTAATTAATCACATGT 59.581 36.000 0.00 0.00 42.74 3.21
130 134 6.813152 GCACCAGCTTAATTAATCACATGTTT 59.187 34.615 0.00 0.00 37.91 2.83
132 136 9.289303 CACCAGCTTAATTAATCACATGTTTAC 57.711 33.333 0.00 0.00 0.00 2.01
133 137 9.019656 ACCAGCTTAATTAATCACATGTTTACA 57.980 29.630 0.00 0.00 0.00 2.41
249 255 5.679734 ACTCACAAATCAACTGTTGCTAG 57.320 39.130 15.52 7.85 0.00 3.42
250 256 5.126067 ACTCACAAATCAACTGTTGCTAGT 58.874 37.500 15.52 8.43 0.00 2.57
269 276 6.211986 TGCTAGTATAATATAAGCCACCGGTT 59.788 38.462 2.97 0.00 32.14 4.44
302 311 5.484715 TGTCATAGTAGTAAGTTGTTGGCC 58.515 41.667 0.00 0.00 0.00 5.36
375 388 6.458232 ACAAACAGTGTGCTTAATTTGGTA 57.542 33.333 0.00 0.00 39.72 3.25
377 390 8.172352 ACAAACAGTGTGCTTAATTTGGTATA 57.828 30.769 0.00 0.00 39.72 1.47
379 392 9.289303 CAAACAGTGTGCTTAATTTGGTATATC 57.711 33.333 0.00 0.00 0.00 1.63
426 442 0.319555 TAACTGGCGAGACACTGCAC 60.320 55.000 1.44 0.00 0.00 4.57
429 445 0.108662 CTGGCGAGACACTGCACATA 60.109 55.000 0.00 0.00 0.00 2.29
453 476 3.526534 GTTGATCTTGTGGACCTAGCTC 58.473 50.000 0.00 0.00 0.00 4.09
454 477 3.107402 TGATCTTGTGGACCTAGCTCT 57.893 47.619 0.00 0.00 0.00 4.09
455 478 4.251103 TGATCTTGTGGACCTAGCTCTA 57.749 45.455 0.00 0.00 0.00 2.43
529 556 1.536766 GTACAAAACCACCCGTTAGCC 59.463 52.381 0.00 0.00 33.05 3.93
620 647 4.720649 TCAACAATAACGAGAGCTAGCT 57.279 40.909 19.45 19.45 0.00 3.32
754 786 0.254178 TTGCCTCTTCTCATCCTGCC 59.746 55.000 0.00 0.00 0.00 4.85
755 787 1.227497 GCCTCTTCTCATCCTGCCG 60.227 63.158 0.00 0.00 0.00 5.69
756 788 1.680522 GCCTCTTCTCATCCTGCCGA 61.681 60.000 0.00 0.00 0.00 5.54
757 789 1.047002 CCTCTTCTCATCCTGCCGAT 58.953 55.000 0.00 0.00 0.00 4.18
784 816 4.284746 TCTTTGTCTCTTCTCTTCCCTTCC 59.715 45.833 0.00 0.00 0.00 3.46
817 857 2.363018 TCTCTCCAGTGGCCTCGG 60.363 66.667 3.51 6.83 0.00 4.63
823 863 2.105128 CAGTGGCCTCGGATCGAC 59.895 66.667 3.32 0.00 0.00 4.20
875 917 9.840427 TTATTAGTTTATTCTTTTGCTGCTGTC 57.160 29.630 0.00 0.00 0.00 3.51
934 976 2.365635 GGTAGCCAGCTGGAGGGA 60.366 66.667 37.21 14.39 37.39 4.20
935 977 1.768077 GGTAGCCAGCTGGAGGGAT 60.768 63.158 37.21 17.22 37.39 3.85
936 978 1.751563 GTAGCCAGCTGGAGGGATC 59.248 63.158 37.21 17.23 37.39 3.36
977 1020 2.007360 TTTGCTGCTGTTGTTTGTGG 57.993 45.000 0.00 0.00 0.00 4.17
994 1037 1.659098 GTGGTTGGTTGATCGATCGAC 59.341 52.381 30.19 30.19 39.88 4.20
1121 1164 1.152525 AGGGCCGATCAGGTACGAT 60.153 57.895 0.00 0.00 43.70 3.73
1123 1166 0.526662 GGGCCGATCAGGTACGATAG 59.473 60.000 0.00 0.00 43.70 2.08
1126 1169 3.276857 GGCCGATCAGGTACGATAGATA 58.723 50.000 0.00 0.00 43.70 1.98
1127 1170 3.065095 GGCCGATCAGGTACGATAGATAC 59.935 52.174 0.00 0.00 43.70 2.24
1151 1194 5.567138 ATGTATGCATGCATGATCATCAG 57.433 39.130 37.43 1.01 37.82 2.90
1457 1508 0.859232 GTGTCGTTGAAGCACATCGT 59.141 50.000 11.82 0.00 40.95 3.73
1499 1558 5.692115 AATTAACCCATGGAAAATGACCC 57.308 39.130 15.22 0.00 0.00 4.46
1508 1573 1.000717 GGAAAATGACCCGTTGTGTGG 60.001 52.381 0.00 0.00 0.00 4.17
1966 2040 5.796935 CACGAATGAAGGTGAAATGATTGAC 59.203 40.000 0.00 0.00 36.25 3.18
1996 2070 4.804868 TGCATGCATGGTACTGAAATTT 57.195 36.364 27.34 0.00 0.00 1.82
1999 2073 4.741676 GCATGCATGGTACTGAAATTTAGC 59.258 41.667 27.34 3.82 0.00 3.09
2000 2074 4.981806 TGCATGGTACTGAAATTTAGCC 57.018 40.909 0.00 0.00 0.00 3.93
2001 2075 4.339748 TGCATGGTACTGAAATTTAGCCA 58.660 39.130 0.00 0.00 0.00 4.75
2005 2099 5.895636 TGGTACTGAAATTTAGCCATGTG 57.104 39.130 0.00 0.00 0.00 3.21
2010 2104 4.218417 ACTGAAATTTAGCCATGTGTGTCC 59.782 41.667 0.00 0.00 0.00 4.02
2015 2109 0.036765 TAGCCATGTGTGTCCGGAAC 60.037 55.000 5.23 7.82 0.00 3.62
2016 2110 1.302511 GCCATGTGTGTCCGGAACT 60.303 57.895 5.23 0.00 0.00 3.01
2031 2125 6.156602 TGTCCGGAACTAATCAATTAGGGTTA 59.843 38.462 5.23 0.00 43.07 2.85
2032 2126 7.049754 GTCCGGAACTAATCAATTAGGGTTAA 58.950 38.462 5.23 0.00 43.07 2.01
2036 2130 9.730420 CGGAACTAATCAATTAGGGTTAATTTG 57.270 33.333 12.99 0.00 43.07 2.32
2076 2170 3.947910 TCGGTGGAGTTCTACGATTTT 57.052 42.857 0.00 0.00 0.00 1.82
2213 2310 1.630369 CATGGAGGTTGGGACTTCTCA 59.370 52.381 0.00 0.00 32.81 3.27
2217 2314 2.305927 GGAGGTTGGGACTTCTCATCAA 59.694 50.000 0.00 0.00 32.81 2.57
2641 2744 8.798859 ACCGTCATTAGTTCTCTTAGTAGTAA 57.201 34.615 0.00 0.00 0.00 2.24
2642 2745 8.672815 ACCGTCATTAGTTCTCTTAGTAGTAAC 58.327 37.037 0.00 0.00 0.00 2.50
2643 2746 8.891720 CCGTCATTAGTTCTCTTAGTAGTAACT 58.108 37.037 0.00 0.00 39.91 2.24
2662 2765 8.792830 AGTAACTACGTACTACTTGATTACCA 57.207 34.615 6.74 0.00 32.42 3.25
2663 2766 8.669243 AGTAACTACGTACTACTTGATTACCAC 58.331 37.037 6.74 0.00 32.42 4.16
2664 2767 7.452880 AACTACGTACTACTTGATTACCACA 57.547 36.000 0.00 0.00 0.00 4.17
2665 2768 7.636150 ACTACGTACTACTTGATTACCACAT 57.364 36.000 0.00 0.00 0.00 3.21
2666 2769 8.737168 ACTACGTACTACTTGATTACCACATA 57.263 34.615 0.00 0.00 0.00 2.29
2667 2770 9.347240 ACTACGTACTACTTGATTACCACATAT 57.653 33.333 0.00 0.00 0.00 1.78
2670 2773 8.295288 ACGTACTACTTGATTACCACATATAGC 58.705 37.037 0.00 0.00 0.00 2.97
2671 2774 8.294577 CGTACTACTTGATTACCACATATAGCA 58.705 37.037 0.00 0.00 0.00 3.49
2672 2775 9.976511 GTACTACTTGATTACCACATATAGCAA 57.023 33.333 0.00 0.00 0.00 3.91
2674 2777 9.494271 ACTACTTGATTACCACATATAGCAATG 57.506 33.333 0.00 0.00 0.00 2.82
2675 2778 7.206981 ACTTGATTACCACATATAGCAATGC 57.793 36.000 0.00 0.00 0.00 3.56
2676 2779 7.000472 ACTTGATTACCACATATAGCAATGCT 59.000 34.615 13.92 13.92 43.41 3.79
2677 2780 7.503566 ACTTGATTACCACATATAGCAATGCTT 59.496 33.333 14.85 4.05 40.44 3.91
2678 2781 7.822161 TGATTACCACATATAGCAATGCTTT 57.178 32.000 14.85 8.46 40.44 3.51
2679 2782 8.236585 TGATTACCACATATAGCAATGCTTTT 57.763 30.769 14.85 4.20 40.44 2.27
2680 2783 9.348476 TGATTACCACATATAGCAATGCTTTTA 57.652 29.630 14.85 6.55 40.44 1.52
2681 2784 9.612620 GATTACCACATATAGCAATGCTTTTAC 57.387 33.333 14.85 0.00 40.44 2.01
2682 2785 6.060028 ACCACATATAGCAATGCTTTTACG 57.940 37.500 14.85 1.12 40.44 3.18
2683 2786 5.588648 ACCACATATAGCAATGCTTTTACGT 59.411 36.000 14.85 1.80 40.44 3.57
2684 2787 5.909054 CCACATATAGCAATGCTTTTACGTG 59.091 40.000 14.85 13.95 40.44 4.49
2685 2788 5.396362 CACATATAGCAATGCTTTTACGTGC 59.604 40.000 14.85 0.00 40.44 5.34
2686 2789 5.065859 ACATATAGCAATGCTTTTACGTGCA 59.934 36.000 14.85 0.00 40.44 4.57
2687 2790 2.336554 AGCAATGCTTTTACGTGCAG 57.663 45.000 0.00 0.00 42.74 4.41
2688 2791 1.068333 AGCAATGCTTTTACGTGCAGG 60.068 47.619 0.00 4.53 42.74 4.85
2689 2792 1.335872 GCAATGCTTTTACGTGCAGGT 60.336 47.619 17.24 17.24 42.74 4.00
2690 2793 2.862140 GCAATGCTTTTACGTGCAGGTT 60.862 45.455 18.35 2.11 42.74 3.50
2691 2794 2.704725 ATGCTTTTACGTGCAGGTTG 57.295 45.000 18.35 7.18 42.74 3.77
2692 2795 0.665835 TGCTTTTACGTGCAGGTTGG 59.334 50.000 18.35 6.83 34.84 3.77
2693 2796 0.948678 GCTTTTACGTGCAGGTTGGA 59.051 50.000 18.35 1.68 0.00 3.53
2694 2797 1.069227 GCTTTTACGTGCAGGTTGGAG 60.069 52.381 18.35 13.09 0.00 3.86
2695 2798 1.535462 CTTTTACGTGCAGGTTGGAGG 59.465 52.381 18.35 1.21 0.00 4.30
2696 2799 0.250553 TTTACGTGCAGGTTGGAGGG 60.251 55.000 18.35 0.00 0.00 4.30
2697 2800 1.412453 TTACGTGCAGGTTGGAGGGT 61.412 55.000 18.35 0.00 0.00 4.34
2698 2801 1.823169 TACGTGCAGGTTGGAGGGTC 61.823 60.000 18.35 0.00 0.00 4.46
2699 2802 2.836154 GTGCAGGTTGGAGGGTCA 59.164 61.111 0.00 0.00 0.00 4.02
2700 2803 1.380302 GTGCAGGTTGGAGGGTCAT 59.620 57.895 0.00 0.00 0.00 3.06
2701 2804 0.618458 GTGCAGGTTGGAGGGTCATA 59.382 55.000 0.00 0.00 0.00 2.15
2702 2805 0.911769 TGCAGGTTGGAGGGTCATAG 59.088 55.000 0.00 0.00 0.00 2.23
2703 2806 0.181350 GCAGGTTGGAGGGTCATAGG 59.819 60.000 0.00 0.00 0.00 2.57
2704 2807 1.584724 CAGGTTGGAGGGTCATAGGT 58.415 55.000 0.00 0.00 0.00 3.08
2705 2808 1.916181 CAGGTTGGAGGGTCATAGGTT 59.084 52.381 0.00 0.00 0.00 3.50
2706 2809 2.308866 CAGGTTGGAGGGTCATAGGTTT 59.691 50.000 0.00 0.00 0.00 3.27
2707 2810 3.521937 CAGGTTGGAGGGTCATAGGTTTA 59.478 47.826 0.00 0.00 0.00 2.01
2708 2811 4.018779 CAGGTTGGAGGGTCATAGGTTTAA 60.019 45.833 0.00 0.00 0.00 1.52
2709 2812 4.018688 AGGTTGGAGGGTCATAGGTTTAAC 60.019 45.833 0.00 0.00 0.00 2.01
2710 2813 4.018688 GGTTGGAGGGTCATAGGTTTAACT 60.019 45.833 0.00 0.00 0.00 2.24
2711 2814 5.516062 GGTTGGAGGGTCATAGGTTTAACTT 60.516 44.000 0.00 0.00 0.00 2.66
2712 2815 5.174037 TGGAGGGTCATAGGTTTAACTTG 57.826 43.478 0.00 0.00 0.00 3.16
2713 2816 3.945921 GGAGGGTCATAGGTTTAACTTGC 59.054 47.826 0.00 0.00 0.00 4.01
2714 2817 4.566907 GGAGGGTCATAGGTTTAACTTGCA 60.567 45.833 0.00 0.00 0.00 4.08
2715 2818 5.193099 AGGGTCATAGGTTTAACTTGCAT 57.807 39.130 0.00 0.00 0.00 3.96
2716 2819 5.193679 AGGGTCATAGGTTTAACTTGCATC 58.806 41.667 0.00 0.00 0.00 3.91
2717 2820 4.947388 GGGTCATAGGTTTAACTTGCATCA 59.053 41.667 0.00 0.00 0.00 3.07
2718 2821 5.066505 GGGTCATAGGTTTAACTTGCATCAG 59.933 44.000 0.00 0.00 0.00 2.90
2719 2822 5.066505 GGTCATAGGTTTAACTTGCATCAGG 59.933 44.000 0.00 0.00 0.00 3.86
2720 2823 4.640201 TCATAGGTTTAACTTGCATCAGGC 59.360 41.667 0.00 0.00 45.13 4.85
2737 2840 4.134187 CGCGCGCTCGTTTGTCAT 62.134 61.111 30.48 0.00 38.14 3.06
2738 2841 2.571611 GCGCGCTCGTTTGTCATG 60.572 61.111 26.67 0.00 38.14 3.07
2739 2842 2.853210 CGCGCTCGTTTGTCATGT 59.147 55.556 5.56 0.00 0.00 3.21
2740 2843 1.951181 GCGCGCTCGTTTGTCATGTA 61.951 55.000 26.67 0.00 38.14 2.29
2741 2844 0.246757 CGCGCTCGTTTGTCATGTAC 60.247 55.000 5.56 0.00 0.00 2.90
2742 2845 0.246757 GCGCTCGTTTGTCATGTACG 60.247 55.000 0.00 0.00 36.67 3.67
2743 2846 0.246757 CGCTCGTTTGTCATGTACGC 60.247 55.000 0.00 0.00 35.40 4.42
2744 2847 0.787787 GCTCGTTTGTCATGTACGCA 59.212 50.000 0.00 0.00 35.40 5.24
2745 2848 1.393539 GCTCGTTTGTCATGTACGCAT 59.606 47.619 0.00 0.00 35.40 4.73
2746 2849 2.159707 GCTCGTTTGTCATGTACGCATT 60.160 45.455 0.00 0.00 35.40 3.56
2747 2850 3.407252 CTCGTTTGTCATGTACGCATTG 58.593 45.455 0.00 0.00 35.40 2.82
2748 2851 2.803386 TCGTTTGTCATGTACGCATTGT 59.197 40.909 0.00 0.00 35.40 2.71
2749 2852 3.248841 TCGTTTGTCATGTACGCATTGTT 59.751 39.130 0.00 0.00 35.40 2.83
2750 2853 3.597825 CGTTTGTCATGTACGCATTGTTC 59.402 43.478 0.00 0.00 31.99 3.18
2751 2854 3.447752 TTGTCATGTACGCATTGTTCG 57.552 42.857 0.00 0.00 31.99 3.95
2752 2855 2.678324 TGTCATGTACGCATTGTTCGA 58.322 42.857 0.00 0.00 31.99 3.71
2753 2856 2.410392 TGTCATGTACGCATTGTTCGAC 59.590 45.455 0.00 0.00 31.99 4.20
2754 2857 1.996898 TCATGTACGCATTGTTCGACC 59.003 47.619 0.00 0.00 31.99 4.79
2755 2858 0.996462 ATGTACGCATTGTTCGACCG 59.004 50.000 0.00 0.00 29.54 4.79
2756 2859 1.009903 TGTACGCATTGTTCGACCGG 61.010 55.000 0.00 0.00 0.00 5.28
2757 2860 0.733566 GTACGCATTGTTCGACCGGA 60.734 55.000 9.46 0.00 0.00 5.14
2758 2861 0.457166 TACGCATTGTTCGACCGGAG 60.457 55.000 9.46 0.85 0.00 4.63
2759 2862 2.785258 GCATTGTTCGACCGGAGC 59.215 61.111 9.46 0.00 0.00 4.70
2760 2863 3.081133 CATTGTTCGACCGGAGCG 58.919 61.111 9.46 12.28 0.00 5.03
2761 2864 1.736645 CATTGTTCGACCGGAGCGT 60.737 57.895 9.46 0.00 0.00 5.07
2762 2865 0.457166 CATTGTTCGACCGGAGCGTA 60.457 55.000 9.46 2.06 0.00 4.42
2763 2866 0.457337 ATTGTTCGACCGGAGCGTAC 60.457 55.000 9.46 15.73 0.00 3.67
2764 2867 1.794151 TTGTTCGACCGGAGCGTACA 61.794 55.000 21.93 21.93 37.28 2.90
2765 2868 1.081242 GTTCGACCGGAGCGTACAA 60.081 57.895 9.46 0.00 0.00 2.41
2766 2869 0.457337 GTTCGACCGGAGCGTACAAT 60.457 55.000 9.46 0.00 0.00 2.71
2767 2870 1.093972 TTCGACCGGAGCGTACAATA 58.906 50.000 9.46 0.00 0.00 1.90
2768 2871 0.659427 TCGACCGGAGCGTACAATAG 59.341 55.000 9.46 0.00 0.00 1.73
2769 2872 0.317603 CGACCGGAGCGTACAATAGG 60.318 60.000 9.46 0.00 0.00 2.57
2770 2873 0.743097 GACCGGAGCGTACAATAGGT 59.257 55.000 9.46 0.00 0.00 3.08
2771 2874 1.949525 GACCGGAGCGTACAATAGGTA 59.050 52.381 9.46 0.00 0.00 3.08
2772 2875 2.358898 GACCGGAGCGTACAATAGGTAA 59.641 50.000 9.46 0.00 32.72 2.85
2773 2876 2.961062 ACCGGAGCGTACAATAGGTAAT 59.039 45.455 9.46 0.00 32.72 1.89
2774 2877 3.385755 ACCGGAGCGTACAATAGGTAATT 59.614 43.478 9.46 0.00 32.72 1.40
2775 2878 3.985925 CCGGAGCGTACAATAGGTAATTC 59.014 47.826 0.00 0.00 32.72 2.17
2776 2879 4.261909 CCGGAGCGTACAATAGGTAATTCT 60.262 45.833 0.00 0.00 32.72 2.40
2777 2880 4.680110 CGGAGCGTACAATAGGTAATTCTG 59.320 45.833 0.00 0.00 32.72 3.02
2778 2881 4.448060 GGAGCGTACAATAGGTAATTCTGC 59.552 45.833 0.00 0.00 32.72 4.26
2779 2882 4.049186 AGCGTACAATAGGTAATTCTGCG 58.951 43.478 0.00 0.00 32.72 5.18
2780 2883 3.362693 GCGTACAATAGGTAATTCTGCGC 60.363 47.826 0.00 0.00 33.63 6.09
2781 2884 4.049186 CGTACAATAGGTAATTCTGCGCT 58.951 43.478 9.73 0.00 32.72 5.92
2782 2885 4.148348 CGTACAATAGGTAATTCTGCGCTC 59.852 45.833 9.73 0.00 32.72 5.03
2783 2886 4.137116 ACAATAGGTAATTCTGCGCTCA 57.863 40.909 9.73 0.00 0.00 4.26
2784 2887 4.122776 ACAATAGGTAATTCTGCGCTCAG 58.877 43.478 9.73 0.00 41.67 3.35
2785 2888 2.890808 TAGGTAATTCTGCGCTCAGG 57.109 50.000 9.73 0.00 40.69 3.86
2786 2889 0.462759 AGGTAATTCTGCGCTCAGGC 60.463 55.000 9.73 0.00 40.69 4.85
2787 2890 0.462759 GGTAATTCTGCGCTCAGGCT 60.463 55.000 9.73 0.00 40.69 4.58
2788 2891 1.373570 GTAATTCTGCGCTCAGGCTT 58.626 50.000 9.73 0.78 40.69 4.35
2789 2892 2.550978 GTAATTCTGCGCTCAGGCTTA 58.449 47.619 9.73 0.00 40.69 3.09
2790 2893 1.661341 AATTCTGCGCTCAGGCTTAG 58.339 50.000 9.73 0.00 40.69 2.18
2791 2894 0.539051 ATTCTGCGCTCAGGCTTAGT 59.461 50.000 9.73 0.00 40.69 2.24
2792 2895 0.321671 TTCTGCGCTCAGGCTTAGTT 59.678 50.000 9.73 0.00 40.69 2.24
2793 2896 0.321671 TCTGCGCTCAGGCTTAGTTT 59.678 50.000 9.73 0.00 40.69 2.66
2794 2897 1.548719 TCTGCGCTCAGGCTTAGTTTA 59.451 47.619 9.73 0.00 40.69 2.01
2795 2898 1.929836 CTGCGCTCAGGCTTAGTTTAG 59.070 52.381 9.73 0.00 36.68 1.85
2796 2899 0.653114 GCGCTCAGGCTTAGTTTAGC 59.347 55.000 0.00 0.00 40.48 3.09
2797 2900 2.007049 GCGCTCAGGCTTAGTTTAGCA 61.007 52.381 0.00 0.00 43.02 3.49
2798 2901 2.346803 CGCTCAGGCTTAGTTTAGCAA 58.653 47.619 0.00 0.00 43.02 3.91
2799 2902 2.349886 CGCTCAGGCTTAGTTTAGCAAG 59.650 50.000 0.00 0.00 43.02 4.01
2800 2903 2.096657 GCTCAGGCTTAGTTTAGCAAGC 59.903 50.000 0.00 0.00 45.15 4.01
2931 3034 7.778185 TTCTATTCCTTATAGGCAGACTACC 57.222 40.000 0.00 0.00 37.42 3.18
2932 3035 6.254522 TCTATTCCTTATAGGCAGACTACCC 58.745 44.000 0.00 0.00 37.42 3.69
2933 3036 3.985553 TCCTTATAGGCAGACTACCCA 57.014 47.619 0.00 0.00 34.61 4.51
2934 3037 3.573695 TCCTTATAGGCAGACTACCCAC 58.426 50.000 0.00 0.00 34.61 4.61
2935 3038 3.052414 TCCTTATAGGCAGACTACCCACA 60.052 47.826 0.00 0.00 34.61 4.17
2936 3039 3.322254 CCTTATAGGCAGACTACCCACAG 59.678 52.174 0.00 0.00 33.70 3.66
2937 3040 2.552093 ATAGGCAGACTACCCACAGT 57.448 50.000 0.00 0.00 33.70 3.55
2938 3041 1.557099 TAGGCAGACTACCCACAGTG 58.443 55.000 0.00 0.00 0.00 3.66
2939 3042 1.194781 AGGCAGACTACCCACAGTGG 61.195 60.000 13.35 13.35 37.25 4.00
2940 3043 1.192146 GGCAGACTACCCACAGTGGA 61.192 60.000 22.37 0.31 40.96 4.02
2941 3044 0.685097 GCAGACTACCCACAGTGGAA 59.315 55.000 22.37 7.78 40.96 3.53
2942 3045 1.338200 GCAGACTACCCACAGTGGAAG 60.338 57.143 22.37 18.88 40.96 3.46
2943 3046 1.971357 CAGACTACCCACAGTGGAAGT 59.029 52.381 22.37 21.83 40.96 3.01
2944 3047 3.162666 CAGACTACCCACAGTGGAAGTA 58.837 50.000 22.37 14.01 40.96 2.24
2945 3048 3.576982 CAGACTACCCACAGTGGAAGTAA 59.423 47.826 22.37 0.41 40.96 2.24
2946 3049 3.577415 AGACTACCCACAGTGGAAGTAAC 59.423 47.826 22.37 12.11 40.96 2.50
2947 3050 3.311091 ACTACCCACAGTGGAAGTAACA 58.689 45.455 22.37 0.00 40.96 2.41
2948 3051 3.908103 ACTACCCACAGTGGAAGTAACAT 59.092 43.478 22.37 1.92 40.96 2.71
2949 3052 5.088730 ACTACCCACAGTGGAAGTAACATA 58.911 41.667 22.37 0.00 40.96 2.29
2950 3053 5.724854 ACTACCCACAGTGGAAGTAACATAT 59.275 40.000 22.37 0.00 40.96 1.78
2951 3054 6.899075 ACTACCCACAGTGGAAGTAACATATA 59.101 38.462 22.37 0.00 40.96 0.86
2952 3055 6.824958 ACCCACAGTGGAAGTAACATATAT 57.175 37.500 22.37 0.00 40.96 0.86
2953 3056 7.924358 ACCCACAGTGGAAGTAACATATATA 57.076 36.000 22.37 0.00 40.96 0.86
2954 3057 7.963532 ACCCACAGTGGAAGTAACATATATAG 58.036 38.462 22.37 0.44 40.96 1.31
2955 3058 7.016268 ACCCACAGTGGAAGTAACATATATAGG 59.984 40.741 22.37 0.04 40.96 2.57
2956 3059 7.016268 CCCACAGTGGAAGTAACATATATAGGT 59.984 40.741 22.37 0.00 40.96 3.08
2957 3060 9.085645 CCACAGTGGAAGTAACATATATAGGTA 57.914 37.037 15.35 0.00 40.96 3.08
2959 3062 9.878737 ACAGTGGAAGTAACATATATAGGTAGT 57.121 33.333 0.00 0.00 0.00 2.73
2977 3080 7.828508 AGGTAGTAACAATACACATATCCGA 57.171 36.000 0.00 0.00 34.29 4.55
2978 3081 8.241497 AGGTAGTAACAATACACATATCCGAA 57.759 34.615 0.00 0.00 34.29 4.30
2979 3082 8.698210 AGGTAGTAACAATACACATATCCGAAA 58.302 33.333 0.00 0.00 34.29 3.46
2980 3083 9.316730 GGTAGTAACAATACACATATCCGAAAA 57.683 33.333 0.00 0.00 34.29 2.29
2986 3089 8.725405 ACAATACACATATCCGAAAATACACA 57.275 30.769 0.00 0.00 0.00 3.72
2987 3090 8.826710 ACAATACACATATCCGAAAATACACAG 58.173 33.333 0.00 0.00 0.00 3.66
2988 3091 7.962964 ATACACATATCCGAAAATACACAGG 57.037 36.000 0.00 0.00 0.00 4.00
2989 3092 5.984725 ACACATATCCGAAAATACACAGGA 58.015 37.500 0.00 0.00 35.24 3.86
2990 3093 6.049149 ACACATATCCGAAAATACACAGGAG 58.951 40.000 0.00 0.00 34.14 3.69
2991 3094 5.050091 CACATATCCGAAAATACACAGGAGC 60.050 44.000 0.00 0.00 34.14 4.70
2992 3095 2.004583 TCCGAAAATACACAGGAGCG 57.995 50.000 0.00 0.00 0.00 5.03
2993 3096 0.373716 CCGAAAATACACAGGAGCGC 59.626 55.000 0.00 0.00 0.00 5.92
2994 3097 1.359848 CGAAAATACACAGGAGCGCT 58.640 50.000 11.27 11.27 0.00 5.92
2995 3098 1.324736 CGAAAATACACAGGAGCGCTC 59.675 52.381 29.38 29.38 0.00 5.03
2996 3099 1.324736 GAAAATACACAGGAGCGCTCG 59.675 52.381 29.81 19.85 0.00 5.03
3126 3229 3.315470 TCTTCGTGAGATATGGAGAACGG 59.685 47.826 0.00 0.00 41.60 4.44
3254 3359 8.925700 GTTTTAATCAGTCATGGGATGTTTTTC 58.074 33.333 0.00 0.00 0.00 2.29
3255 3360 5.665916 AATCAGTCATGGGATGTTTTTCC 57.334 39.130 0.00 0.00 34.83 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.933577 AGAGATCATTTGTTACTGTCTTTCACA 59.066 33.333 0.00 0.00 0.00 3.58
128 132 4.447290 TCTGTGCTAGCTTGTGTTGTAAA 58.553 39.130 17.23 0.00 0.00 2.01
130 134 3.744238 TCTGTGCTAGCTTGTGTTGTA 57.256 42.857 17.23 0.00 0.00 2.41
132 136 5.049474 TGTTATTCTGTGCTAGCTTGTGTTG 60.049 40.000 17.23 0.00 0.00 3.33
133 137 5.063204 TGTTATTCTGTGCTAGCTTGTGTT 58.937 37.500 17.23 0.00 0.00 3.32
137 141 5.124457 ACCAATGTTATTCTGTGCTAGCTTG 59.876 40.000 17.23 7.08 0.00 4.01
138 142 5.256474 ACCAATGTTATTCTGTGCTAGCTT 58.744 37.500 17.23 0.00 0.00 3.74
249 255 5.106436 GGCAAACCGGTGGCTTATATTATAC 60.106 44.000 25.31 6.44 40.77 1.47
250 256 5.005094 GGCAAACCGGTGGCTTATATTATA 58.995 41.667 25.31 0.00 40.77 0.98
269 276 3.605634 ACTACTATGACATTTGCGGCAA 58.394 40.909 12.11 12.11 0.00 4.52
302 311 2.032894 GTGTGACGTGTCATGGACAAAG 60.033 50.000 5.91 1.62 44.49 2.77
375 388 7.414098 GCTCAACAAACAACATACGGAAGATAT 60.414 37.037 0.00 0.00 0.00 1.63
377 390 5.334879 GCTCAACAAACAACATACGGAAGAT 60.335 40.000 0.00 0.00 0.00 2.40
379 392 4.219033 GCTCAACAAACAACATACGGAAG 58.781 43.478 0.00 0.00 0.00 3.46
426 442 4.697514 AGGTCCACAAGATCAACGATATG 58.302 43.478 0.00 0.00 0.00 1.78
429 445 3.430929 GCTAGGTCCACAAGATCAACGAT 60.431 47.826 0.00 0.00 0.00 3.73
455 478 9.838339 ATGTTAGTTACATGCTATCTAAAGCTT 57.162 29.630 0.00 0.00 45.71 3.74
491 517 3.499537 TGTACGTTAAGCTTCACGAGAGA 59.500 43.478 33.17 18.76 39.76 3.10
498 525 4.035441 GGTGGTTTTGTACGTTAAGCTTCA 59.965 41.667 0.00 0.00 0.00 3.02
529 556 3.994392 AGTTAGTTTGATGCTACGTGTGG 59.006 43.478 0.00 0.00 0.00 4.17
721 753 5.723887 AGAAGAGGCAAGAGAAAGATAAGGA 59.276 40.000 0.00 0.00 0.00 3.36
754 786 5.168526 AGAGAAGAGACAAAGATCGATCG 57.831 43.478 19.33 9.36 0.00 3.69
755 787 5.977129 GGAAGAGAAGAGACAAAGATCGATC 59.023 44.000 17.91 17.91 0.00 3.69
756 788 5.163457 GGGAAGAGAAGAGACAAAGATCGAT 60.163 44.000 0.00 0.00 0.00 3.59
757 789 4.158764 GGGAAGAGAAGAGACAAAGATCGA 59.841 45.833 0.00 0.00 0.00 3.59
784 816 4.465660 TGGAGAGAGATGAACAAAGAGAGG 59.534 45.833 0.00 0.00 0.00 3.69
823 863 3.448686 ACTAATTTCAGACGCAGATCGG 58.551 45.455 0.00 0.00 43.86 4.18
875 917 3.459232 TGTAAGGCTAGCTGCACATAG 57.541 47.619 15.72 0.00 45.15 2.23
918 960 1.751563 GATCCCTCCAGCTGGCTAC 59.248 63.158 28.91 11.52 34.44 3.58
923 965 1.175347 TCGATCGATCCCTCCAGCTG 61.175 60.000 19.51 6.78 0.00 4.24
928 970 2.294074 CCTCTATCGATCGATCCCTCC 58.706 57.143 32.50 0.00 36.17 4.30
934 976 3.125487 CGCTGTAACCTCTATCGATCGAT 59.875 47.826 31.39 31.39 38.54 3.59
935 977 2.479275 CGCTGTAACCTCTATCGATCGA 59.521 50.000 21.86 21.86 0.00 3.59
936 978 2.479275 TCGCTGTAACCTCTATCGATCG 59.521 50.000 9.36 9.36 0.00 3.69
967 1009 3.112580 CGATCAACCAACCACAAACAAC 58.887 45.455 0.00 0.00 0.00 3.32
970 1012 3.666902 CGATCGATCAACCAACCACAAAC 60.667 47.826 24.40 0.00 0.00 2.93
977 1020 0.921347 CGGTCGATCGATCAACCAAC 59.079 55.000 29.92 16.43 33.43 3.77
994 1037 1.153489 CTCTGGTGCACATCCTCGG 60.153 63.158 20.43 5.83 0.00 4.63
1151 1194 4.275689 TCATTAATTCCACACATGATCGGC 59.724 41.667 0.00 0.00 0.00 5.54
1499 1558 1.333619 CTTCCCTGAAACCACACAACG 59.666 52.381 0.00 0.00 0.00 4.10
1508 1573 1.163554 CTGCAGCTCTTCCCTGAAAC 58.836 55.000 0.00 0.00 32.03 2.78
1911 1985 0.977395 ACCCTCCTTGCTACTGTGAC 59.023 55.000 0.00 0.00 0.00 3.67
1983 2057 5.182950 CACACATGGCTAAATTTCAGTACCA 59.817 40.000 0.00 0.00 0.00 3.25
1987 2061 4.218417 GGACACACATGGCTAAATTTCAGT 59.782 41.667 0.00 0.00 32.54 3.41
1990 2064 3.427503 CCGGACACACATGGCTAAATTTC 60.428 47.826 0.00 0.00 32.54 2.17
1991 2065 2.491693 CCGGACACACATGGCTAAATTT 59.508 45.455 0.00 0.00 32.54 1.82
1992 2066 2.091541 CCGGACACACATGGCTAAATT 58.908 47.619 0.00 0.00 32.54 1.82
1995 2069 0.687920 TTCCGGACACACATGGCTAA 59.312 50.000 1.83 0.00 32.54 3.09
1996 2070 0.036765 GTTCCGGACACACATGGCTA 60.037 55.000 1.83 0.00 32.54 3.93
1999 2073 2.465860 TTAGTTCCGGACACACATGG 57.534 50.000 1.83 0.00 0.00 3.66
2000 2074 3.595173 TGATTAGTTCCGGACACACATG 58.405 45.455 1.83 0.00 0.00 3.21
2001 2075 3.973206 TGATTAGTTCCGGACACACAT 57.027 42.857 1.83 2.29 0.00 3.21
2005 2099 4.814771 CCCTAATTGATTAGTTCCGGACAC 59.185 45.833 1.83 6.13 38.41 3.67
2010 2104 9.730420 CAAATTAACCCTAATTGATTAGTTCCG 57.270 33.333 9.28 0.00 37.70 4.30
2031 2125 8.668510 ATCTATTCGTATCTGCAGAACAAATT 57.331 30.769 22.50 5.39 0.00 1.82
2032 2126 7.115520 CGATCTATTCGTATCTGCAGAACAAAT 59.884 37.037 22.50 17.62 43.01 2.32
2036 2130 4.854291 CCGATCTATTCGTATCTGCAGAAC 59.146 45.833 22.50 17.87 46.65 3.01
2037 2131 4.519350 ACCGATCTATTCGTATCTGCAGAA 59.481 41.667 22.50 3.58 46.65 3.02
2038 2132 4.072839 ACCGATCTATTCGTATCTGCAGA 58.927 43.478 20.79 20.79 46.65 4.26
2039 2133 4.162072 CACCGATCTATTCGTATCTGCAG 58.838 47.826 7.63 7.63 46.65 4.41
2076 2170 0.827925 AGCTCACGTTCACCTGGAGA 60.828 55.000 0.00 0.00 0.00 3.71
2125 2219 0.174617 CGGTTCTCCTCTTGCTCCTC 59.825 60.000 0.00 0.00 0.00 3.71
2126 2220 1.261238 CCGGTTCTCCTCTTGCTCCT 61.261 60.000 0.00 0.00 0.00 3.69
2127 2221 1.219393 CCGGTTCTCCTCTTGCTCC 59.781 63.158 0.00 0.00 0.00 4.70
2128 2222 1.219393 CCCGGTTCTCCTCTTGCTC 59.781 63.158 0.00 0.00 0.00 4.26
2129 2223 1.229209 TCCCGGTTCTCCTCTTGCT 60.229 57.895 0.00 0.00 0.00 3.91
2130 2224 1.079057 GTCCCGGTTCTCCTCTTGC 60.079 63.158 0.00 0.00 0.00 4.01
2131 2225 1.215647 CGTCCCGGTTCTCCTCTTG 59.784 63.158 0.00 0.00 0.00 3.02
2132 2226 0.541296 TTCGTCCCGGTTCTCCTCTT 60.541 55.000 0.00 0.00 0.00 2.85
2133 2227 0.966370 CTTCGTCCCGGTTCTCCTCT 60.966 60.000 0.00 0.00 0.00 3.69
2151 2245 0.743701 CTTCAGCTTGCTGATCGCCT 60.744 55.000 23.50 0.00 38.05 5.52
2153 2247 1.712977 CCCTTCAGCTTGCTGATCGC 61.713 60.000 23.50 3.07 39.77 4.58
2166 2263 3.240134 GAGCGACACCTGCCCTTCA 62.240 63.158 0.00 0.00 0.00 3.02
2240 2337 5.922960 AATACTGACCCATAAGGCCATAA 57.077 39.130 5.01 0.00 40.58 1.90
2241 2338 5.922960 AAATACTGACCCATAAGGCCATA 57.077 39.130 5.01 0.00 40.58 2.74
2242 2339 4.814224 AAATACTGACCCATAAGGCCAT 57.186 40.909 5.01 0.00 40.58 4.40
2243 2340 5.192923 AGTTAAATACTGACCCATAAGGCCA 59.807 40.000 5.01 0.00 35.51 5.36
2244 2341 5.691896 AGTTAAATACTGACCCATAAGGCC 58.308 41.667 0.00 0.00 35.51 5.19
2245 2342 6.935208 CCTAGTTAAATACTGACCCATAAGGC 59.065 42.308 0.00 0.00 37.02 4.35
2246 2343 7.450903 CCCTAGTTAAATACTGACCCATAAGG 58.549 42.308 0.00 0.00 37.73 2.69
2247 2344 7.072076 ACCCCTAGTTAAATACTGACCCATAAG 59.928 40.741 0.00 0.00 37.73 1.73
2323 2424 6.494893 TTTGGTGTTAGATTGCTACATGTC 57.505 37.500 0.00 0.00 0.00 3.06
2615 2718 9.890629 TTACTACTAAGAGAACTAATGACGGTA 57.109 33.333 0.00 0.00 0.00 4.02
2616 2719 8.672815 GTTACTACTAAGAGAACTAATGACGGT 58.327 37.037 0.00 0.00 0.00 4.83
2617 2720 8.891720 AGTTACTACTAAGAGAACTAATGACGG 58.108 37.037 0.00 0.00 33.53 4.79
2636 2739 9.884636 TGGTAATCAAGTAGTACGTAGTTACTA 57.115 33.333 16.06 6.08 37.78 1.82
2637 2740 8.669243 GTGGTAATCAAGTAGTACGTAGTTACT 58.331 37.037 8.48 10.57 37.78 2.24
2638 2741 8.450964 TGTGGTAATCAAGTAGTACGTAGTTAC 58.549 37.037 8.48 8.46 37.78 2.50
2639 2742 8.560355 TGTGGTAATCAAGTAGTACGTAGTTA 57.440 34.615 8.48 0.00 37.78 2.24
2640 2743 7.452880 TGTGGTAATCAAGTAGTACGTAGTT 57.547 36.000 8.48 0.00 37.78 2.24
2644 2747 8.295288 GCTATATGTGGTAATCAAGTAGTACGT 58.705 37.037 0.00 0.00 29.18 3.57
2645 2748 8.294577 TGCTATATGTGGTAATCAAGTAGTACG 58.705 37.037 0.00 0.00 29.18 3.67
2646 2749 9.976511 TTGCTATATGTGGTAATCAAGTAGTAC 57.023 33.333 0.00 0.00 0.00 2.73
2648 2751 9.494271 CATTGCTATATGTGGTAATCAAGTAGT 57.506 33.333 0.00 0.00 0.00 2.73
2649 2752 8.446273 GCATTGCTATATGTGGTAATCAAGTAG 58.554 37.037 0.16 0.00 0.00 2.57
2650 2753 8.156820 AGCATTGCTATATGTGGTAATCAAGTA 58.843 33.333 10.00 0.00 36.99 2.24
2651 2754 7.000472 AGCATTGCTATATGTGGTAATCAAGT 59.000 34.615 10.00 0.00 36.99 3.16
2652 2755 7.444629 AGCATTGCTATATGTGGTAATCAAG 57.555 36.000 10.00 0.00 36.99 3.02
2653 2756 7.822161 AAGCATTGCTATATGTGGTAATCAA 57.178 32.000 12.39 0.00 38.25 2.57
2654 2757 7.822161 AAAGCATTGCTATATGTGGTAATCA 57.178 32.000 12.39 0.00 38.25 2.57
2655 2758 9.612620 GTAAAAGCATTGCTATATGTGGTAATC 57.387 33.333 12.39 0.00 38.25 1.75
2656 2759 8.289618 CGTAAAAGCATTGCTATATGTGGTAAT 58.710 33.333 12.39 0.00 38.25 1.89
2657 2760 7.281324 ACGTAAAAGCATTGCTATATGTGGTAA 59.719 33.333 20.13 0.00 38.25 2.85
2658 2761 6.764085 ACGTAAAAGCATTGCTATATGTGGTA 59.236 34.615 20.13 2.68 38.25 3.25
2659 2762 5.588648 ACGTAAAAGCATTGCTATATGTGGT 59.411 36.000 20.13 9.05 38.25 4.16
2660 2763 5.909054 CACGTAAAAGCATTGCTATATGTGG 59.091 40.000 28.43 18.81 40.44 4.17
2661 2764 5.396362 GCACGTAAAAGCATTGCTATATGTG 59.604 40.000 29.96 29.96 43.29 3.21
2662 2765 5.065859 TGCACGTAAAAGCATTGCTATATGT 59.934 36.000 12.39 15.52 38.25 2.29
2663 2766 5.509771 TGCACGTAAAAGCATTGCTATATG 58.490 37.500 12.39 14.94 38.25 1.78
2664 2767 5.277974 CCTGCACGTAAAAGCATTGCTATAT 60.278 40.000 12.39 3.90 38.25 0.86
2665 2768 4.035091 CCTGCACGTAAAAGCATTGCTATA 59.965 41.667 12.39 5.82 38.25 1.31
2666 2769 3.181497 CCTGCACGTAAAAGCATTGCTAT 60.181 43.478 12.39 6.84 38.25 2.97
2667 2770 2.161410 CCTGCACGTAAAAGCATTGCTA 59.839 45.455 12.39 0.00 38.25 3.49
2668 2771 1.068333 CCTGCACGTAAAAGCATTGCT 60.068 47.619 5.03 5.03 42.56 3.91
2669 2772 1.335872 ACCTGCACGTAAAAGCATTGC 60.336 47.619 0.00 0.00 40.42 3.56
2670 2773 2.704725 ACCTGCACGTAAAAGCATTG 57.295 45.000 0.00 0.00 40.42 2.82
2671 2774 2.288152 CCAACCTGCACGTAAAAGCATT 60.288 45.455 0.00 0.00 40.42 3.56
2672 2775 1.269448 CCAACCTGCACGTAAAAGCAT 59.731 47.619 0.00 0.00 40.42 3.79
2673 2776 0.665835 CCAACCTGCACGTAAAAGCA 59.334 50.000 0.00 0.00 39.25 3.91
2674 2777 0.948678 TCCAACCTGCACGTAAAAGC 59.051 50.000 0.00 0.00 0.00 3.51
2675 2778 1.535462 CCTCCAACCTGCACGTAAAAG 59.465 52.381 0.00 0.00 0.00 2.27
2676 2779 1.600023 CCTCCAACCTGCACGTAAAA 58.400 50.000 0.00 0.00 0.00 1.52
2677 2780 0.250553 CCCTCCAACCTGCACGTAAA 60.251 55.000 0.00 0.00 0.00 2.01
2678 2781 1.373435 CCCTCCAACCTGCACGTAA 59.627 57.895 0.00 0.00 0.00 3.18
2679 2782 1.823169 GACCCTCCAACCTGCACGTA 61.823 60.000 0.00 0.00 0.00 3.57
2680 2783 3.168528 ACCCTCCAACCTGCACGT 61.169 61.111 0.00 0.00 0.00 4.49
2681 2784 2.358737 GACCCTCCAACCTGCACG 60.359 66.667 0.00 0.00 0.00 5.34
2682 2785 0.618458 TATGACCCTCCAACCTGCAC 59.382 55.000 0.00 0.00 0.00 4.57
2683 2786 0.911769 CTATGACCCTCCAACCTGCA 59.088 55.000 0.00 0.00 0.00 4.41
2684 2787 0.181350 CCTATGACCCTCCAACCTGC 59.819 60.000 0.00 0.00 0.00 4.85
2685 2788 1.584724 ACCTATGACCCTCCAACCTG 58.415 55.000 0.00 0.00 0.00 4.00
2686 2789 2.361085 AACCTATGACCCTCCAACCT 57.639 50.000 0.00 0.00 0.00 3.50
2687 2790 4.018688 AGTTAAACCTATGACCCTCCAACC 60.019 45.833 0.00 0.00 0.00 3.77
2688 2791 5.175388 AGTTAAACCTATGACCCTCCAAC 57.825 43.478 0.00 0.00 0.00 3.77
2689 2792 5.566469 CAAGTTAAACCTATGACCCTCCAA 58.434 41.667 0.00 0.00 0.00 3.53
2690 2793 4.566907 GCAAGTTAAACCTATGACCCTCCA 60.567 45.833 0.00 0.00 0.00 3.86
2691 2794 3.945921 GCAAGTTAAACCTATGACCCTCC 59.054 47.826 0.00 0.00 0.00 4.30
2692 2795 4.585879 TGCAAGTTAAACCTATGACCCTC 58.414 43.478 0.00 0.00 0.00 4.30
2693 2796 4.650972 TGCAAGTTAAACCTATGACCCT 57.349 40.909 0.00 0.00 0.00 4.34
2694 2797 4.947388 TGATGCAAGTTAAACCTATGACCC 59.053 41.667 0.00 0.00 0.00 4.46
2695 2798 5.066505 CCTGATGCAAGTTAAACCTATGACC 59.933 44.000 0.00 0.00 0.00 4.02
2696 2799 5.449177 GCCTGATGCAAGTTAAACCTATGAC 60.449 44.000 0.00 0.00 40.77 3.06
2697 2800 4.640201 GCCTGATGCAAGTTAAACCTATGA 59.360 41.667 0.00 0.00 40.77 2.15
2698 2801 4.496341 CGCCTGATGCAAGTTAAACCTATG 60.496 45.833 0.00 0.00 41.33 2.23
2699 2802 3.627577 CGCCTGATGCAAGTTAAACCTAT 59.372 43.478 0.00 0.00 41.33 2.57
2700 2803 3.006940 CGCCTGATGCAAGTTAAACCTA 58.993 45.455 0.00 0.00 41.33 3.08
2701 2804 1.812571 CGCCTGATGCAAGTTAAACCT 59.187 47.619 0.00 0.00 41.33 3.50
2702 2805 1.732405 GCGCCTGATGCAAGTTAAACC 60.732 52.381 0.00 0.00 41.33 3.27
2703 2806 1.617740 GCGCCTGATGCAAGTTAAAC 58.382 50.000 0.00 0.00 41.33 2.01
2704 2807 0.167908 CGCGCCTGATGCAAGTTAAA 59.832 50.000 0.00 0.00 41.33 1.52
2705 2808 1.793581 CGCGCCTGATGCAAGTTAA 59.206 52.632 0.00 0.00 41.33 2.01
2706 2809 2.749865 GCGCGCCTGATGCAAGTTA 61.750 57.895 23.24 0.00 41.33 2.24
2707 2810 4.107051 GCGCGCCTGATGCAAGTT 62.107 61.111 23.24 0.00 41.33 2.66
2720 2823 4.134187 ATGACAAACGAGCGCGCG 62.134 61.111 31.62 31.62 42.48 6.86
2721 2824 1.951181 TACATGACAAACGAGCGCGC 61.951 55.000 26.66 26.66 42.48 6.86
2722 2825 0.246757 GTACATGACAAACGAGCGCG 60.247 55.000 8.75 8.75 44.79 6.86
2723 2826 0.246757 CGTACATGACAAACGAGCGC 60.247 55.000 0.00 0.00 38.89 5.92
2724 2827 0.246757 GCGTACATGACAAACGAGCG 60.247 55.000 15.15 0.00 38.89 5.03
2725 2828 0.787787 TGCGTACATGACAAACGAGC 59.212 50.000 15.15 1.61 38.89 5.03
2726 2829 3.120683 ACAATGCGTACATGACAAACGAG 60.121 43.478 15.15 6.90 38.89 4.18
2727 2830 2.803386 ACAATGCGTACATGACAAACGA 59.197 40.909 15.15 4.91 38.89 3.85
2728 2831 3.181826 ACAATGCGTACATGACAAACG 57.818 42.857 0.00 5.03 36.36 3.60
2729 2832 3.597825 CGAACAATGCGTACATGACAAAC 59.402 43.478 0.00 0.00 36.36 2.93
2730 2833 3.495001 TCGAACAATGCGTACATGACAAA 59.505 39.130 0.00 0.00 36.36 2.83
2731 2834 3.060602 TCGAACAATGCGTACATGACAA 58.939 40.909 0.00 0.00 36.36 3.18
2732 2835 2.410392 GTCGAACAATGCGTACATGACA 59.590 45.455 0.00 0.00 36.36 3.58
2733 2836 2.222729 GGTCGAACAATGCGTACATGAC 60.223 50.000 0.00 0.00 36.36 3.06
2734 2837 1.996898 GGTCGAACAATGCGTACATGA 59.003 47.619 0.00 0.00 36.36 3.07
2735 2838 1.266842 CGGTCGAACAATGCGTACATG 60.267 52.381 0.00 0.00 36.36 3.21
2736 2839 0.996462 CGGTCGAACAATGCGTACAT 59.004 50.000 0.00 0.00 38.49 2.29
2737 2840 1.009903 CCGGTCGAACAATGCGTACA 61.010 55.000 0.00 0.00 0.00 2.90
2738 2841 0.733566 TCCGGTCGAACAATGCGTAC 60.734 55.000 0.00 0.00 0.00 3.67
2739 2842 0.457166 CTCCGGTCGAACAATGCGTA 60.457 55.000 0.00 0.00 0.00 4.42
2740 2843 1.736645 CTCCGGTCGAACAATGCGT 60.737 57.895 0.00 0.00 0.00 5.24
2741 2844 3.081133 CTCCGGTCGAACAATGCG 58.919 61.111 0.00 0.00 0.00 4.73
2742 2845 2.785258 GCTCCGGTCGAACAATGC 59.215 61.111 0.00 0.00 0.00 3.56
2743 2846 0.457166 TACGCTCCGGTCGAACAATG 60.457 55.000 21.67 0.00 0.00 2.82
2744 2847 0.457337 GTACGCTCCGGTCGAACAAT 60.457 55.000 21.67 5.35 0.00 2.71
2745 2848 1.081242 GTACGCTCCGGTCGAACAA 60.081 57.895 21.67 5.33 0.00 2.83
2746 2849 1.794151 TTGTACGCTCCGGTCGAACA 61.794 55.000 21.67 9.84 0.00 3.18
2747 2850 0.457337 ATTGTACGCTCCGGTCGAAC 60.457 55.000 21.67 0.00 0.00 3.95
2748 2851 1.064505 CTATTGTACGCTCCGGTCGAA 59.935 52.381 21.67 9.14 0.00 3.71
2749 2852 0.659427 CTATTGTACGCTCCGGTCGA 59.341 55.000 21.67 6.45 0.00 4.20
2750 2853 0.317603 CCTATTGTACGCTCCGGTCG 60.318 60.000 15.21 15.21 0.00 4.79
2751 2854 0.743097 ACCTATTGTACGCTCCGGTC 59.257 55.000 0.00 0.00 0.00 4.79
2752 2855 2.057137 TACCTATTGTACGCTCCGGT 57.943 50.000 0.00 0.00 0.00 5.28
2753 2856 3.655276 ATTACCTATTGTACGCTCCGG 57.345 47.619 0.00 0.00 0.00 5.14
2754 2857 4.680110 CAGAATTACCTATTGTACGCTCCG 59.320 45.833 0.00 0.00 0.00 4.63
2755 2858 4.448060 GCAGAATTACCTATTGTACGCTCC 59.552 45.833 0.00 0.00 0.00 4.70
2756 2859 4.148348 CGCAGAATTACCTATTGTACGCTC 59.852 45.833 0.00 0.00 0.00 5.03
2757 2860 4.049186 CGCAGAATTACCTATTGTACGCT 58.951 43.478 0.00 0.00 0.00 5.07
2758 2861 3.362693 GCGCAGAATTACCTATTGTACGC 60.363 47.826 0.30 0.00 42.59 4.42
2759 2862 4.049186 AGCGCAGAATTACCTATTGTACG 58.951 43.478 11.47 0.00 31.39 3.67
2760 2863 5.047847 TGAGCGCAGAATTACCTATTGTAC 58.952 41.667 11.47 0.00 0.00 2.90
2761 2864 5.270893 TGAGCGCAGAATTACCTATTGTA 57.729 39.130 11.47 0.00 0.00 2.41
2762 2865 4.122776 CTGAGCGCAGAATTACCTATTGT 58.877 43.478 12.68 0.00 45.17 2.71
2763 2866 3.496130 CCTGAGCGCAGAATTACCTATTG 59.504 47.826 19.95 0.00 45.17 1.90
2764 2867 3.733337 CCTGAGCGCAGAATTACCTATT 58.267 45.455 19.95 0.00 45.17 1.73
2765 2868 2.548920 GCCTGAGCGCAGAATTACCTAT 60.549 50.000 19.95 0.00 45.17 2.57
2766 2869 1.202533 GCCTGAGCGCAGAATTACCTA 60.203 52.381 19.95 0.00 45.17 3.08
2767 2870 0.462759 GCCTGAGCGCAGAATTACCT 60.463 55.000 19.95 0.00 45.17 3.08
2768 2871 0.462759 AGCCTGAGCGCAGAATTACC 60.463 55.000 19.95 0.15 45.17 2.85
2769 2872 1.373570 AAGCCTGAGCGCAGAATTAC 58.626 50.000 19.95 2.92 45.17 1.89
2770 2873 2.168521 ACTAAGCCTGAGCGCAGAATTA 59.831 45.455 19.95 14.84 45.17 1.40
2771 2874 1.065854 ACTAAGCCTGAGCGCAGAATT 60.066 47.619 19.95 14.51 45.17 2.17
2772 2875 0.539051 ACTAAGCCTGAGCGCAGAAT 59.461 50.000 19.95 6.91 45.17 2.40
2773 2876 0.321671 AACTAAGCCTGAGCGCAGAA 59.678 50.000 19.95 0.56 45.17 3.02
2774 2877 0.321671 AAACTAAGCCTGAGCGCAGA 59.678 50.000 19.95 0.00 45.17 4.26
2775 2878 1.929836 CTAAACTAAGCCTGAGCGCAG 59.070 52.381 11.47 10.92 46.67 5.18
2776 2879 2.007049 GCTAAACTAAGCCTGAGCGCA 61.007 52.381 11.47 0.00 46.67 6.09
2777 2880 0.653114 GCTAAACTAAGCCTGAGCGC 59.347 55.000 0.00 0.00 46.67 5.92
2778 2881 2.010145 TGCTAAACTAAGCCTGAGCG 57.990 50.000 0.00 0.00 46.67 5.03
2779 2882 2.096657 GCTTGCTAAACTAAGCCTGAGC 59.903 50.000 0.00 0.00 42.57 4.26
2905 3008 9.476928 GGTAGTCTGCCTATAAGGAATAGAATA 57.523 37.037 0.00 0.00 40.16 1.75
2906 3009 7.400627 GGGTAGTCTGCCTATAAGGAATAGAAT 59.599 40.741 6.95 0.00 40.16 2.40
2907 3010 6.724905 GGGTAGTCTGCCTATAAGGAATAGAA 59.275 42.308 6.95 0.00 40.16 2.10
2908 3011 6.183361 TGGGTAGTCTGCCTATAAGGAATAGA 60.183 42.308 6.95 0.00 40.16 1.98
2909 3012 6.017192 TGGGTAGTCTGCCTATAAGGAATAG 58.983 44.000 6.95 0.00 37.67 1.73
2910 3013 5.778750 GTGGGTAGTCTGCCTATAAGGAATA 59.221 44.000 6.95 0.00 37.67 1.75
2911 3014 4.593634 GTGGGTAGTCTGCCTATAAGGAAT 59.406 45.833 6.95 0.00 37.67 3.01
2912 3015 3.965347 GTGGGTAGTCTGCCTATAAGGAA 59.035 47.826 6.95 0.00 37.67 3.36
2913 3016 3.052414 TGTGGGTAGTCTGCCTATAAGGA 60.052 47.826 6.95 0.00 37.67 3.36
2914 3017 3.305720 TGTGGGTAGTCTGCCTATAAGG 58.694 50.000 6.95 0.00 38.80 2.69
2915 3018 3.961408 ACTGTGGGTAGTCTGCCTATAAG 59.039 47.826 6.95 5.82 0.00 1.73
2916 3019 3.704566 CACTGTGGGTAGTCTGCCTATAA 59.295 47.826 6.95 0.00 0.00 0.98
2917 3020 3.296854 CACTGTGGGTAGTCTGCCTATA 58.703 50.000 6.95 0.00 0.00 1.31
2918 3021 2.111384 CACTGTGGGTAGTCTGCCTAT 58.889 52.381 6.95 0.00 0.00 2.57
2919 3022 1.557099 CACTGTGGGTAGTCTGCCTA 58.443 55.000 6.95 0.00 0.00 3.93
2920 3023 1.194781 CCACTGTGGGTAGTCTGCCT 61.195 60.000 19.23 0.00 32.67 4.75
2921 3024 1.192146 TCCACTGTGGGTAGTCTGCC 61.192 60.000 25.67 0.00 38.32 4.85
2922 3025 0.685097 TTCCACTGTGGGTAGTCTGC 59.315 55.000 25.67 0.00 38.32 4.26
2923 3026 1.971357 ACTTCCACTGTGGGTAGTCTG 59.029 52.381 25.67 10.84 38.32 3.51
2924 3027 2.400467 ACTTCCACTGTGGGTAGTCT 57.600 50.000 25.67 7.00 38.32 3.24
2925 3028 3.322828 TGTTACTTCCACTGTGGGTAGTC 59.677 47.826 27.28 18.94 38.32 2.59
2926 3029 3.311091 TGTTACTTCCACTGTGGGTAGT 58.689 45.455 26.90 26.90 38.32 2.73
2927 3030 4.553330 ATGTTACTTCCACTGTGGGTAG 57.447 45.455 25.67 22.86 38.32 3.18
2928 3031 7.924358 ATATATGTTACTTCCACTGTGGGTA 57.076 36.000 25.67 17.47 38.32 3.69
2929 3032 6.824958 ATATATGTTACTTCCACTGTGGGT 57.175 37.500 25.67 18.45 38.32 4.51
2930 3033 7.016268 ACCTATATATGTTACTTCCACTGTGGG 59.984 40.741 25.67 13.63 38.32 4.61
2931 3034 7.963532 ACCTATATATGTTACTTCCACTGTGG 58.036 38.462 20.86 20.86 39.43 4.17
2933 3036 9.878737 ACTACCTATATATGTTACTTCCACTGT 57.121 33.333 0.00 0.00 0.00 3.55
2951 3054 9.524496 TCGGATATGTGTATTGTTACTACCTAT 57.476 33.333 0.00 0.00 0.00 2.57
2952 3055 8.922931 TCGGATATGTGTATTGTTACTACCTA 57.077 34.615 0.00 0.00 0.00 3.08
2953 3056 7.828508 TCGGATATGTGTATTGTTACTACCT 57.171 36.000 0.00 0.00 0.00 3.08
2954 3057 8.876275 TTTCGGATATGTGTATTGTTACTACC 57.124 34.615 0.00 0.00 0.00 3.18
2960 3063 9.168451 TGTGTATTTTCGGATATGTGTATTGTT 57.832 29.630 0.00 0.00 0.00 2.83
2961 3064 8.725405 TGTGTATTTTCGGATATGTGTATTGT 57.275 30.769 0.00 0.00 0.00 2.71
2962 3065 8.282592 CCTGTGTATTTTCGGATATGTGTATTG 58.717 37.037 0.00 0.00 0.00 1.90
2963 3066 8.208224 TCCTGTGTATTTTCGGATATGTGTATT 58.792 33.333 0.00 0.00 0.00 1.89
2964 3067 7.732025 TCCTGTGTATTTTCGGATATGTGTAT 58.268 34.615 0.00 0.00 0.00 2.29
2965 3068 7.114866 TCCTGTGTATTTTCGGATATGTGTA 57.885 36.000 0.00 0.00 0.00 2.90
2966 3069 5.984725 TCCTGTGTATTTTCGGATATGTGT 58.015 37.500 0.00 0.00 0.00 3.72
2967 3070 5.050091 GCTCCTGTGTATTTTCGGATATGTG 60.050 44.000 0.00 0.00 0.00 3.21
2968 3071 5.057149 GCTCCTGTGTATTTTCGGATATGT 58.943 41.667 0.00 0.00 0.00 2.29
2969 3072 4.150627 CGCTCCTGTGTATTTTCGGATATG 59.849 45.833 0.00 0.00 0.00 1.78
2970 3073 4.307432 CGCTCCTGTGTATTTTCGGATAT 58.693 43.478 0.00 0.00 0.00 1.63
2971 3074 3.713288 CGCTCCTGTGTATTTTCGGATA 58.287 45.455 0.00 0.00 0.00 2.59
2972 3075 2.550978 CGCTCCTGTGTATTTTCGGAT 58.449 47.619 0.00 0.00 0.00 4.18
2973 3076 2.004583 CGCTCCTGTGTATTTTCGGA 57.995 50.000 0.00 0.00 0.00 4.55
2974 3077 0.373716 GCGCTCCTGTGTATTTTCGG 59.626 55.000 0.00 0.00 0.00 4.30
2975 3078 1.324736 GAGCGCTCCTGTGTATTTTCG 59.675 52.381 27.22 0.00 0.00 3.46
2976 3079 1.324736 CGAGCGCTCCTGTGTATTTTC 59.675 52.381 30.66 2.96 0.00 2.29
2977 3080 1.359848 CGAGCGCTCCTGTGTATTTT 58.640 50.000 30.66 0.00 0.00 1.82
2978 3081 3.050703 CGAGCGCTCCTGTGTATTT 57.949 52.632 30.66 0.00 0.00 1.40
2979 3082 4.814900 CGAGCGCTCCTGTGTATT 57.185 55.556 30.66 0.00 0.00 1.89
3126 3229 6.515272 TTACAAATGATGAGAGAAAAGCCC 57.485 37.500 0.00 0.00 0.00 5.19
3220 3324 5.104109 CCATGACTGATTAAAACCCTCCCTA 60.104 44.000 0.00 0.00 0.00 3.53
3221 3325 4.325344 CCATGACTGATTAAAACCCTCCCT 60.325 45.833 0.00 0.00 0.00 4.20
3222 3326 3.954258 CCATGACTGATTAAAACCCTCCC 59.046 47.826 0.00 0.00 0.00 4.30
3223 3327 3.954258 CCCATGACTGATTAAAACCCTCC 59.046 47.826 0.00 0.00 0.00 4.30
3224 3328 4.855340 TCCCATGACTGATTAAAACCCTC 58.145 43.478 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.