Multiple sequence alignment - TraesCS2A01G555200

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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 TraesCS2A01G555200 chr2A 100.000 3704 0 0 1 3704 759819517 759823220 0.000000e+00 6841.0
1 TraesCS2A01G555200 chr2A 81.102 127 12 6 597 723 628691006 628690892 1.420000e-14 91.6
2 TraesCS2A01G555200 chr2D 95.606 1866 70 4 943 2797 631950026 631948162 0.000000e+00 2981.0
3 TraesCS2A01G555200 chr2D 91.460 726 53 9 2802 3522 631948209 631947488 0.000000e+00 989.0
4 TraesCS2A01G555200 chr2B 94.257 1898 82 8 923 2797 775338818 775336925 0.000000e+00 2876.0
5 TraesCS2A01G555200 chr2B 91.799 695 43 10 2799 3480 775336975 775336282 0.000000e+00 955.0
6 TraesCS2A01G555200 chr2B 83.193 357 37 10 3 357 707177945 707178280 4.650000e-79 305.0
7 TraesCS2A01G555200 chr2B 80.097 206 19 11 597 802 202495058 202495241 2.320000e-27 134.0
8 TraesCS2A01G555200 chr2B 82.443 131 15 7 811 936 560729953 560730080 1.410000e-19 108.0
9 TraesCS2A01G555200 chr1D 92.300 961 39 10 1 936 75936211 75935261 0.000000e+00 1332.0
10 TraesCS2A01G555200 chr4B 91.354 960 46 11 3 937 3863805 3862858 0.000000e+00 1279.0
11 TraesCS2A01G555200 chr3B 83.520 358 37 9 3 358 119122010 119122347 7.720000e-82 315.0
12 TraesCS2A01G555200 chr3D 84.691 307 39 7 33 337 450573388 450573088 2.160000e-77 300.0
13 TraesCS2A01G555200 chr3D 82.216 343 36 9 3 337 281084011 281084336 4.710000e-69 272.0
14 TraesCS2A01G555200 chr3D 89.583 96 10 0 339 434 250333516 250333421 5.020000e-24 122.0
15 TraesCS2A01G555200 chr4D 83.333 336 38 7 3 337 500038984 500039302 1.010000e-75 294.0
16 TraesCS2A01G555200 chr1A 83.333 336 38 8 3 337 493289870 493290188 1.010000e-75 294.0
17 TraesCS2A01G555200 chr1A 79.126 206 21 11 597 802 44062905 44063088 5.020000e-24 122.0
18 TraesCS2A01G555200 chr5A 82.849 344 39 7 7 350 127454637 127454960 1.300000e-74 291.0
19 TraesCS2A01G555200 chr7D 88.889 99 11 0 336 434 616704990 616705088 5.020000e-24 122.0
20 TraesCS2A01G555200 chr6D 89.583 96 10 0 339 434 448383363 448383268 5.020000e-24 122.0
21 TraesCS2A01G555200 chr6B 83.969 131 16 5 811 937 687966480 687966351 1.810000e-23 121.0
22 TraesCS2A01G555200 chr6B 88.542 96 11 0 339 434 719413187 719413092 2.340000e-22 117.0


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 TraesCS2A01G555200 chr2A 759819517 759823220 3703 False 6841.0 6841 100.000 1 3704 1 chr2A.!!$F1 3703
1 TraesCS2A01G555200 chr2D 631947488 631950026 2538 True 1985.0 2981 93.533 943 3522 2 chr2D.!!$R1 2579
2 TraesCS2A01G555200 chr2B 775336282 775338818 2536 True 1915.5 2876 93.028 923 3480 2 chr2B.!!$R1 2557
3 TraesCS2A01G555200 chr1D 75935261 75936211 950 True 1332.0 1332 92.300 1 936 1 chr1D.!!$R1 935
4 TraesCS2A01G555200 chr4B 3862858 3863805 947 True 1279.0 1279 91.354 3 937 1 chr4B.!!$R1 934

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
904 928 0.035458 AACGCCCCAACTTCTCTCAG 59.965 55.0 0.0 0.0 0.00 3.35 F
940 966 0.109723 GCCCCAACCACTAGTTCACA 59.890 55.0 0.0 0.0 36.18 3.58 F
2028 2075 0.178891 TCAAACTGGGAGAGGGCTCT 60.179 55.0 0.0 0.0 43.78 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2268 0.034337 AACGTGATGTGGTTAGGCGT 59.966 50.0 0.0 0.0 0.0 5.68 R
2543 2590 0.038251 CCTCGACAGCAGCAAGTACA 60.038 55.0 0.0 0.0 0.0 2.90 R
3219 3283 0.250252 TCATCGCCTGTTGTCTGCAA 60.250 50.0 0.0 0.0 0.0 4.08 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
29 30 4.860907 GCAGCAAGGAATGAACATTACAAG 59.139 41.667 11.59 5.20 34.05 3.16
30 31 5.565439 GCAGCAAGGAATGAACATTACAAGT 60.565 40.000 11.59 0.00 34.05 3.16
31 32 6.449698 CAGCAAGGAATGAACATTACAAGTT 58.550 36.000 11.59 0.28 34.05 2.66
32 33 6.925165 CAGCAAGGAATGAACATTACAAGTTT 59.075 34.615 11.59 0.00 34.05 2.66
33 34 8.081633 CAGCAAGGAATGAACATTACAAGTTTA 58.918 33.333 11.59 0.00 34.05 2.01
34 35 8.082242 AGCAAGGAATGAACATTACAAGTTTAC 58.918 33.333 11.59 0.00 34.05 2.01
35 36 7.865385 GCAAGGAATGAACATTACAAGTTTACA 59.135 33.333 11.59 0.00 34.05 2.41
36 37 9.743057 CAAGGAATGAACATTACAAGTTTACAA 57.257 29.630 11.59 0.00 34.05 2.41
130 131 9.269453 TCTACTATGCATCATCATTTTCTTCTG 57.731 33.333 0.19 0.00 0.00 3.02
282 283 3.497884 GAGTTGGTGGGCAGCTGGT 62.498 63.158 17.12 0.00 0.00 4.00
291 292 2.047274 GCAGCTGGTTGTAGCCGA 60.047 61.111 17.12 0.00 44.76 5.54
306 307 0.523072 GCCGAAGCAAGAGCATTCAA 59.477 50.000 0.00 0.00 45.49 2.69
324 325 4.750021 TCAAAGACATGAGCTGCTATCT 57.250 40.909 0.15 0.56 0.00 1.98
330 331 4.588106 AGACATGAGCTGCTATCTGTACAT 59.412 41.667 0.15 0.00 0.00 2.29
368 369 3.386078 TCTGCACTGTCTCTTTGTCTCTT 59.614 43.478 0.00 0.00 0.00 2.85
378 379 8.019656 TGTCTCTTTGTCTCTTTACTACCTTT 57.980 34.615 0.00 0.00 0.00 3.11
433 434 3.417069 TGGTGAGGTTATTGTGAGGTG 57.583 47.619 0.00 0.00 0.00 4.00
434 435 2.976185 TGGTGAGGTTATTGTGAGGTGA 59.024 45.455 0.00 0.00 0.00 4.02
469 491 5.239525 GCATGGTCAGATTTTAGGTGTATCC 59.760 44.000 0.00 0.00 0.00 2.59
530 552 7.285566 TCAGCTATTATTCTCATTTGCTTCCT 58.714 34.615 0.00 0.00 0.00 3.36
552 574 1.284657 TGTGCATTTGGTTTGTTGCG 58.715 45.000 0.00 0.00 37.92 4.85
565 587 0.178301 TGTTGCGGGTCTTACACACA 59.822 50.000 0.00 0.00 0.00 3.72
602 624 3.845781 ATTGCATGGATCCGACTAAGT 57.154 42.857 7.39 0.00 0.00 2.24
616 638 4.322049 CCGACTAAGTCTTCCATGTGTCTT 60.322 45.833 0.00 0.00 0.00 3.01
620 642 6.831976 ACTAAGTCTTCCATGTGTCTTTCTT 58.168 36.000 0.00 0.00 0.00 2.52
755 778 8.554835 TGATGGAAAATTAGTTGTGAACGATA 57.445 30.769 0.00 0.00 36.23 2.92
831 854 6.822667 AAATGCATGTACTTTGAGTGATGA 57.177 33.333 0.00 0.00 0.00 2.92
852 876 5.071370 TGAAATAACACCCGTGGTACAAAT 58.929 37.500 0.00 0.00 44.16 2.32
862 886 4.998672 CCCGTGGTACAAATAAGAAAGTGA 59.001 41.667 0.00 0.00 44.16 3.41
883 907 3.311110 GGGCGTGTCTCCACCTGA 61.311 66.667 0.00 0.00 38.41 3.86
899 923 0.535102 CTGACAACGCCCCAACTTCT 60.535 55.000 0.00 0.00 0.00 2.85
900 924 0.534203 TGACAACGCCCCAACTTCTC 60.534 55.000 0.00 0.00 0.00 2.87
901 925 0.250338 GACAACGCCCCAACTTCTCT 60.250 55.000 0.00 0.00 0.00 3.10
902 926 0.250338 ACAACGCCCCAACTTCTCTC 60.250 55.000 0.00 0.00 0.00 3.20
903 927 0.250295 CAACGCCCCAACTTCTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
904 928 0.035458 AACGCCCCAACTTCTCTCAG 59.965 55.000 0.00 0.00 0.00 3.35
906 930 1.544825 CGCCCCAACTTCTCTCAGGA 61.545 60.000 0.00 0.00 0.00 3.86
913 939 3.423162 CTTCTCTCAGGAGCCCGCG 62.423 68.421 0.00 0.00 39.31 6.46
937 963 1.001269 GGGCCCCAACCACTAGTTC 60.001 63.158 12.23 0.00 36.18 3.01
938 964 1.765074 GGCCCCAACCACTAGTTCA 59.235 57.895 0.00 0.00 36.18 3.18
939 965 0.608308 GGCCCCAACCACTAGTTCAC 60.608 60.000 0.00 0.00 36.18 3.18
940 966 0.109723 GCCCCAACCACTAGTTCACA 59.890 55.000 0.00 0.00 36.18 3.58
941 967 1.271926 GCCCCAACCACTAGTTCACAT 60.272 52.381 0.00 0.00 36.18 3.21
983 1009 0.998226 CGCACAAAACCGCATGACAG 60.998 55.000 0.00 0.00 0.00 3.51
1600 1647 0.755686 GATTCTCTGGCGGAGGATGT 59.244 55.000 21.99 0.00 40.22 3.06
1640 1687 0.389948 GACGGGTTCTCGTTCAGCAT 60.390 55.000 0.00 0.00 43.96 3.79
1801 1848 2.664851 CCGGCAACAGAGCGTTCA 60.665 61.111 1.01 0.00 34.86 3.18
1890 1937 2.825836 GCCAAGGCCATCGGAGTG 60.826 66.667 5.01 0.00 34.56 3.51
1923 1970 0.908910 TGCTCGAAGGAATTAGGCCA 59.091 50.000 5.01 0.00 0.00 5.36
2028 2075 0.178891 TCAAACTGGGAGAGGGCTCT 60.179 55.000 0.00 0.00 43.78 4.09
2221 2268 0.674581 CATGCTTCTGGAAGGCGTCA 60.675 55.000 11.61 2.53 38.80 4.35
2394 2441 2.657355 AGGCAGGCCATATAGAGGAT 57.343 50.000 13.63 0.00 38.92 3.24
2469 2516 2.675056 GCTGCTCGGTGCTTGTCAG 61.675 63.158 3.53 0.00 43.37 3.51
2543 2590 1.104630 GAGAAGGAAGACCCGTCGAT 58.895 55.000 0.00 0.00 46.33 3.59
2544 2591 0.818296 AGAAGGAAGACCCGTCGATG 59.182 55.000 0.00 0.00 46.33 3.84
2548 2595 1.101331 GGAAGACCCGTCGATGTACT 58.899 55.000 3.52 0.00 34.09 2.73
2747 2799 2.274542 TCCTAATGGAAGCACCTGGAA 58.725 47.619 0.00 0.00 39.87 3.53
2748 2800 2.026262 TCCTAATGGAAGCACCTGGAAC 60.026 50.000 0.00 0.00 39.87 3.62
2749 2801 2.369394 CTAATGGAAGCACCTGGAACC 58.631 52.381 0.00 0.00 39.86 3.62
2750 2802 0.251787 AATGGAAGCACCTGGAACCC 60.252 55.000 0.00 0.00 39.86 4.11
2751 2803 1.142688 ATGGAAGCACCTGGAACCCT 61.143 55.000 0.00 0.00 39.86 4.34
2752 2804 1.360393 TGGAAGCACCTGGAACCCTT 61.360 55.000 0.00 0.00 39.86 3.95
2753 2805 0.178961 GGAAGCACCTGGAACCCTTT 60.179 55.000 0.00 0.00 35.41 3.11
2754 2806 1.704641 GAAGCACCTGGAACCCTTTT 58.295 50.000 0.00 0.00 0.00 2.27
2755 2807 1.613925 GAAGCACCTGGAACCCTTTTC 59.386 52.381 0.00 0.00 0.00 2.29
2756 2808 0.853530 AGCACCTGGAACCCTTTTCT 59.146 50.000 0.00 0.00 0.00 2.52
2757 2809 0.961753 GCACCTGGAACCCTTTTCTG 59.038 55.000 0.00 0.00 0.00 3.02
2758 2810 1.620822 CACCTGGAACCCTTTTCTGG 58.379 55.000 0.00 0.00 0.00 3.86
2759 2811 0.178961 ACCTGGAACCCTTTTCTGGC 60.179 55.000 0.00 0.00 0.00 4.85
2760 2812 0.900182 CCTGGAACCCTTTTCTGGCC 60.900 60.000 0.00 0.00 0.00 5.36
2761 2813 0.113190 CTGGAACCCTTTTCTGGCCT 59.887 55.000 3.32 0.00 0.00 5.19
2762 2814 0.178964 TGGAACCCTTTTCTGGCCTG 60.179 55.000 3.32 2.92 0.00 4.85
2763 2815 0.112412 GGAACCCTTTTCTGGCCTGA 59.888 55.000 8.48 8.48 0.00 3.86
2764 2816 1.480498 GGAACCCTTTTCTGGCCTGAA 60.480 52.381 20.15 20.15 0.00 3.02
2765 2817 2.316108 GAACCCTTTTCTGGCCTGAAA 58.684 47.619 28.22 28.22 34.55 2.69
2766 2818 2.001076 ACCCTTTTCTGGCCTGAAAG 57.999 50.000 29.46 22.69 37.27 2.62
2783 2835 4.522971 GGCTTCAGGCTACGAAGG 57.477 61.111 14.34 0.21 40.23 3.46
2784 2836 1.898154 GGCTTCAGGCTACGAAGGA 59.102 57.895 14.34 0.00 40.23 3.36
2785 2837 0.249398 GGCTTCAGGCTACGAAGGAA 59.751 55.000 14.34 0.50 40.23 3.36
2786 2838 1.338769 GGCTTCAGGCTACGAAGGAAA 60.339 52.381 14.34 0.00 40.23 3.13
2787 2839 2.003301 GCTTCAGGCTACGAAGGAAAG 58.997 52.381 14.34 0.00 40.23 2.62
2788 2840 2.613223 GCTTCAGGCTACGAAGGAAAGT 60.613 50.000 14.34 0.00 40.23 2.66
2789 2841 3.368116 GCTTCAGGCTACGAAGGAAAGTA 60.368 47.826 14.34 0.00 40.23 2.24
2790 2842 4.425520 CTTCAGGCTACGAAGGAAAGTAG 58.574 47.826 6.68 0.00 42.23 2.57
2791 2843 2.758979 TCAGGCTACGAAGGAAAGTAGG 59.241 50.000 0.00 0.00 40.32 3.18
2792 2844 2.496470 CAGGCTACGAAGGAAAGTAGGT 59.504 50.000 0.00 0.00 40.32 3.08
2793 2845 3.698040 CAGGCTACGAAGGAAAGTAGGTA 59.302 47.826 0.00 0.00 40.32 3.08
2794 2846 4.341520 CAGGCTACGAAGGAAAGTAGGTAT 59.658 45.833 0.00 0.00 40.32 2.73
2795 2847 4.961099 AGGCTACGAAGGAAAGTAGGTATT 59.039 41.667 0.00 0.00 40.32 1.89
2796 2848 5.424573 AGGCTACGAAGGAAAGTAGGTATTT 59.575 40.000 0.00 0.00 40.32 1.40
2797 2849 6.608808 AGGCTACGAAGGAAAGTAGGTATTTA 59.391 38.462 0.00 0.00 40.32 1.40
2798 2850 7.124750 AGGCTACGAAGGAAAGTAGGTATTTAA 59.875 37.037 0.00 0.00 40.32 1.52
2839 2891 2.351455 GCTTCAGGCTACAGAGGAAAC 58.649 52.381 0.00 0.00 38.06 2.78
2910 2969 6.064060 AGTGAATTGACAGTTTCCTGAATGA 58.936 36.000 0.00 0.00 41.50 2.57
2912 2971 6.638468 GTGAATTGACAGTTTCCTGAATGAAC 59.362 38.462 0.00 0.00 41.50 3.18
2941 3001 4.808414 TGATCCAACTGGTAAGAGTCTG 57.192 45.455 0.00 0.00 36.34 3.51
2968 3028 6.604396 TGTGATCAATGGCTATCAATTCTGTT 59.396 34.615 0.00 0.00 34.06 3.16
2973 3033 3.889815 TGGCTATCAATTCTGTTCAGGG 58.110 45.455 0.00 0.00 0.00 4.45
3172 3236 3.754068 CTGTGCAGCTCAAGCCAA 58.246 55.556 0.00 0.00 43.38 4.52
3219 3283 4.935808 GTGAACCATTACAAGAATCGGTCT 59.064 41.667 0.00 0.00 38.69 3.85
3227 3291 2.839486 AAGAATCGGTCTTGCAGACA 57.161 45.000 15.22 0.51 46.79 3.41
3228 3292 2.839486 AGAATCGGTCTTGCAGACAA 57.161 45.000 15.22 6.07 46.79 3.18
3240 3304 0.376152 GCAGACAACAGGCGATGATG 59.624 55.000 0.00 0.00 37.69 3.07
3244 3308 2.183478 ACAACAGGCGATGATGTCAA 57.817 45.000 0.00 0.00 40.62 3.18
3358 3422 3.878778 CCCGTTCTTGAAGAGGATCAAT 58.121 45.455 2.32 0.00 38.55 2.57
3394 3458 7.490402 CCGTAAACCTTGTACTTCTCGATAATT 59.510 37.037 0.00 0.00 0.00 1.40
3457 3521 6.150332 TCTCCCCTCATATTCCTGTTTCATA 58.850 40.000 0.00 0.00 0.00 2.15
3459 3523 6.841601 TCCCCTCATATTCCTGTTTCATAAG 58.158 40.000 0.00 0.00 0.00 1.73
3480 3545 5.344743 AGAAAATCGCCAACTATCAGAGA 57.655 39.130 0.00 0.00 0.00 3.10
3481 3546 5.923204 AGAAAATCGCCAACTATCAGAGAT 58.077 37.500 0.00 0.00 0.00 2.75
3483 3548 6.926272 AGAAAATCGCCAACTATCAGAGATAC 59.074 38.462 0.00 0.00 0.00 2.24
3484 3549 5.791336 AATCGCCAACTATCAGAGATACA 57.209 39.130 0.00 0.00 0.00 2.29
3485 3550 5.791336 ATCGCCAACTATCAGAGATACAA 57.209 39.130 0.00 0.00 0.00 2.41
3486 3551 5.592104 TCGCCAACTATCAGAGATACAAA 57.408 39.130 0.00 0.00 0.00 2.83
3487 3552 6.161855 TCGCCAACTATCAGAGATACAAAT 57.838 37.500 0.00 0.00 0.00 2.32
3488 3553 6.582636 TCGCCAACTATCAGAGATACAAATT 58.417 36.000 0.00 0.00 0.00 1.82
3489 3554 7.722363 TCGCCAACTATCAGAGATACAAATTA 58.278 34.615 0.00 0.00 0.00 1.40
3490 3555 8.201464 TCGCCAACTATCAGAGATACAAATTAA 58.799 33.333 0.00 0.00 0.00 1.40
3519 3584 8.753497 AACAGACTTCCACTCTAAATTTCTTT 57.247 30.769 0.00 0.00 0.00 2.52
3520 3585 9.847224 AACAGACTTCCACTCTAAATTTCTTTA 57.153 29.630 0.00 0.00 0.00 1.85
3521 3586 9.495572 ACAGACTTCCACTCTAAATTTCTTTAG 57.504 33.333 0.00 0.00 43.47 1.85
3522 3587 8.447053 CAGACTTCCACTCTAAATTTCTTTAGC 58.553 37.037 0.00 0.00 42.35 3.09
3523 3588 8.379331 AGACTTCCACTCTAAATTTCTTTAGCT 58.621 33.333 0.00 0.00 42.35 3.32
3524 3589 8.926092 ACTTCCACTCTAAATTTCTTTAGCTT 57.074 30.769 0.00 0.00 42.35 3.74
3525 3590 9.355916 ACTTCCACTCTAAATTTCTTTAGCTTT 57.644 29.630 0.00 0.00 42.35 3.51
3526 3591 9.833182 CTTCCACTCTAAATTTCTTTAGCTTTC 57.167 33.333 0.00 0.00 42.35 2.62
3527 3592 8.918202 TCCACTCTAAATTTCTTTAGCTTTCA 57.082 30.769 0.00 0.00 42.35 2.69
3528 3593 9.003658 TCCACTCTAAATTTCTTTAGCTTTCAG 57.996 33.333 0.00 0.00 42.35 3.02
3529 3594 7.752686 CCACTCTAAATTTCTTTAGCTTTCAGC 59.247 37.037 0.00 0.00 42.35 4.26
3549 3614 2.838360 TGCTGAGGCCTGCAGAAA 59.162 55.556 26.77 15.68 41.38 2.52
3550 3615 1.151221 TGCTGAGGCCTGCAGAAAA 59.849 52.632 26.77 13.84 41.38 2.29
3551 3616 0.251474 TGCTGAGGCCTGCAGAAAAT 60.251 50.000 26.77 0.00 41.38 1.82
3552 3617 0.893447 GCTGAGGCCTGCAGAAAATT 59.107 50.000 26.77 0.00 37.23 1.82
3553 3618 1.274447 GCTGAGGCCTGCAGAAAATTT 59.726 47.619 26.77 0.00 37.23 1.82
3554 3619 2.289257 GCTGAGGCCTGCAGAAAATTTT 60.289 45.455 26.77 2.28 37.23 1.82
3555 3620 3.582780 CTGAGGCCTGCAGAAAATTTTC 58.417 45.455 21.00 21.00 35.39 2.29
3556 3621 2.299867 TGAGGCCTGCAGAAAATTTTCC 59.700 45.455 24.01 12.50 37.92 3.13
3557 3622 2.299867 GAGGCCTGCAGAAAATTTTCCA 59.700 45.455 24.01 15.88 37.92 3.53
3558 3623 2.908351 AGGCCTGCAGAAAATTTTCCAT 59.092 40.909 24.01 7.04 37.92 3.41
3559 3624 3.004862 GGCCTGCAGAAAATTTTCCATG 58.995 45.455 24.01 18.22 37.92 3.66
3560 3625 2.417586 GCCTGCAGAAAATTTTCCATGC 59.582 45.455 26.41 26.41 38.26 4.06
3561 3626 3.666274 CCTGCAGAAAATTTTCCATGCA 58.334 40.909 30.37 30.37 42.39 3.96
3562 3627 3.434299 CCTGCAGAAAATTTTCCATGCAC 59.566 43.478 29.56 15.12 40.88 4.57
3563 3628 3.401182 TGCAGAAAATTTTCCATGCACC 58.599 40.909 29.56 13.03 40.88 5.01
3564 3629 2.743664 GCAGAAAATTTTCCATGCACCC 59.256 45.455 27.42 8.90 37.91 4.61
3565 3630 3.557686 GCAGAAAATTTTCCATGCACCCT 60.558 43.478 27.42 8.40 37.91 4.34
3566 3631 4.644498 CAGAAAATTTTCCATGCACCCTT 58.356 39.130 24.01 2.25 37.92 3.95
3567 3632 5.792741 CAGAAAATTTTCCATGCACCCTTA 58.207 37.500 24.01 0.00 37.92 2.69
3568 3633 6.229733 CAGAAAATTTTCCATGCACCCTTAA 58.770 36.000 24.01 0.00 37.92 1.85
3569 3634 6.880529 CAGAAAATTTTCCATGCACCCTTAAT 59.119 34.615 24.01 1.18 37.92 1.40
3570 3635 7.391275 CAGAAAATTTTCCATGCACCCTTAATT 59.609 33.333 24.01 0.58 37.92 1.40
3571 3636 7.944000 AGAAAATTTTCCATGCACCCTTAATTT 59.056 29.630 24.01 0.00 37.92 1.82
3572 3637 7.451501 AAATTTTCCATGCACCCTTAATTTG 57.548 32.000 0.00 0.00 0.00 2.32
3573 3638 5.815233 TTTTCCATGCACCCTTAATTTGA 57.185 34.783 0.00 0.00 0.00 2.69
3574 3639 4.799564 TTCCATGCACCCTTAATTTGAC 57.200 40.909 0.00 0.00 0.00 3.18
3575 3640 4.046286 TCCATGCACCCTTAATTTGACT 57.954 40.909 0.00 0.00 0.00 3.41
3576 3641 4.016444 TCCATGCACCCTTAATTTGACTC 58.984 43.478 0.00 0.00 0.00 3.36
3577 3642 4.019174 CCATGCACCCTTAATTTGACTCT 58.981 43.478 0.00 0.00 0.00 3.24
3578 3643 4.096984 CCATGCACCCTTAATTTGACTCTC 59.903 45.833 0.00 0.00 0.00 3.20
3579 3644 4.640771 TGCACCCTTAATTTGACTCTCT 57.359 40.909 0.00 0.00 0.00 3.10
3580 3645 4.985538 TGCACCCTTAATTTGACTCTCTT 58.014 39.130 0.00 0.00 0.00 2.85
3581 3646 5.385198 TGCACCCTTAATTTGACTCTCTTT 58.615 37.500 0.00 0.00 0.00 2.52
3582 3647 5.241506 TGCACCCTTAATTTGACTCTCTTTG 59.758 40.000 0.00 0.00 0.00 2.77
3583 3648 5.335976 GCACCCTTAATTTGACTCTCTTTGG 60.336 44.000 0.00 0.00 0.00 3.28
3584 3649 6.003950 CACCCTTAATTTGACTCTCTTTGGA 58.996 40.000 0.00 0.00 0.00 3.53
3585 3650 6.490040 CACCCTTAATTTGACTCTCTTTGGAA 59.510 38.462 0.00 0.00 0.00 3.53
3586 3651 7.014230 CACCCTTAATTTGACTCTCTTTGGAAA 59.986 37.037 0.00 0.00 0.00 3.13
3587 3652 7.563556 ACCCTTAATTTGACTCTCTTTGGAAAA 59.436 33.333 0.00 0.00 0.00 2.29
3588 3653 8.421002 CCCTTAATTTGACTCTCTTTGGAAAAA 58.579 33.333 0.00 0.00 0.00 1.94
3589 3654 9.468532 CCTTAATTTGACTCTCTTTGGAAAAAG 57.531 33.333 0.00 0.00 0.00 2.27
3593 3658 8.932945 ATTTGACTCTCTTTGGAAAAAGAAAC 57.067 30.769 2.82 0.00 38.23 2.78
3594 3659 7.703058 TTGACTCTCTTTGGAAAAAGAAACT 57.297 32.000 2.82 0.00 38.23 2.66
3595 3660 8.801882 TTGACTCTCTTTGGAAAAAGAAACTA 57.198 30.769 2.82 0.00 38.23 2.24
3596 3661 8.209917 TGACTCTCTTTGGAAAAAGAAACTAC 57.790 34.615 2.82 0.00 38.23 2.73
3597 3662 8.047310 TGACTCTCTTTGGAAAAAGAAACTACT 58.953 33.333 2.82 0.00 38.23 2.57
3598 3663 8.214721 ACTCTCTTTGGAAAAAGAAACTACTG 57.785 34.615 2.82 0.00 38.23 2.74
3599 3664 7.283354 ACTCTCTTTGGAAAAAGAAACTACTGG 59.717 37.037 2.82 0.00 38.23 4.00
3600 3665 6.546034 TCTCTTTGGAAAAAGAAACTACTGGG 59.454 38.462 2.82 0.00 38.23 4.45
3601 3666 6.192044 TCTTTGGAAAAAGAAACTACTGGGT 58.808 36.000 0.00 0.00 35.99 4.51
3602 3667 7.348033 TCTTTGGAAAAAGAAACTACTGGGTA 58.652 34.615 0.00 0.00 35.99 3.69
3603 3668 7.501225 TCTTTGGAAAAAGAAACTACTGGGTAG 59.499 37.037 0.00 3.50 37.67 3.18
3604 3669 5.627135 TGGAAAAAGAAACTACTGGGTAGG 58.373 41.667 9.14 0.00 40.13 3.18
3605 3670 5.133153 TGGAAAAAGAAACTACTGGGTAGGT 59.867 40.000 9.14 0.00 40.13 3.08
3606 3671 5.472478 GGAAAAAGAAACTACTGGGTAGGTG 59.528 44.000 9.14 0.00 40.13 4.00
3607 3672 5.899631 AAAAGAAACTACTGGGTAGGTGA 57.100 39.130 9.14 0.00 40.13 4.02
3608 3673 6.449830 AAAAGAAACTACTGGGTAGGTGAT 57.550 37.500 9.14 0.00 40.13 3.06
3609 3674 6.449830 AAAGAAACTACTGGGTAGGTGATT 57.550 37.500 9.14 0.00 40.13 2.57
3610 3675 5.422214 AGAAACTACTGGGTAGGTGATTG 57.578 43.478 9.14 0.00 40.13 2.67
3611 3676 4.844655 AGAAACTACTGGGTAGGTGATTGT 59.155 41.667 9.14 0.00 40.13 2.71
3612 3677 5.309806 AGAAACTACTGGGTAGGTGATTGTT 59.690 40.000 9.14 0.00 40.13 2.83
3613 3678 4.820894 ACTACTGGGTAGGTGATTGTTC 57.179 45.455 9.14 0.00 40.13 3.18
3614 3679 4.164981 ACTACTGGGTAGGTGATTGTTCA 58.835 43.478 9.14 0.00 40.13 3.18
3631 3696 9.101655 TGATTGTTCACATAGAGTACATTGATG 57.898 33.333 0.00 0.00 0.00 3.07
3632 3697 9.102757 GATTGTTCACATAGAGTACATTGATGT 57.897 33.333 1.84 1.84 44.48 3.06
3633 3698 8.479313 TTGTTCACATAGAGTACATTGATGTC 57.521 34.615 0.00 0.00 41.97 3.06
3634 3699 7.840931 TGTTCACATAGAGTACATTGATGTCT 58.159 34.615 0.00 0.00 41.97 3.41
3635 3700 7.761249 TGTTCACATAGAGTACATTGATGTCTG 59.239 37.037 0.00 0.00 41.97 3.51
3636 3701 7.410120 TCACATAGAGTACATTGATGTCTGT 57.590 36.000 0.00 0.43 41.97 3.41
3637 3702 8.519799 TCACATAGAGTACATTGATGTCTGTA 57.480 34.615 0.00 2.42 41.97 2.74
3638 3703 8.406297 TCACATAGAGTACATTGATGTCTGTAC 58.594 37.037 0.00 5.01 45.15 2.90
3639 3704 8.190784 CACATAGAGTACATTGATGTCTGTACA 58.809 37.037 13.49 0.00 46.50 2.90
3640 3705 8.191446 ACATAGAGTACATTGATGTCTGTACAC 58.809 37.037 13.49 8.36 46.50 2.90
3641 3706 6.590234 AGAGTACATTGATGTCTGTACACA 57.410 37.500 13.49 0.00 46.50 3.72
3642 3707 7.175347 AGAGTACATTGATGTCTGTACACAT 57.825 36.000 13.49 0.00 46.50 3.21
3643 3708 7.615403 AGAGTACATTGATGTCTGTACACATT 58.385 34.615 13.49 0.00 46.50 2.71
3644 3709 7.547019 AGAGTACATTGATGTCTGTACACATTG 59.453 37.037 13.49 0.00 46.50 2.82
3645 3710 5.885230 ACATTGATGTCTGTACACATTGG 57.115 39.130 0.00 0.00 38.78 3.16
3646 3711 4.156556 ACATTGATGTCTGTACACATTGGC 59.843 41.667 0.00 0.00 38.78 4.52
3647 3712 2.710377 TGATGTCTGTACACATTGGCC 58.290 47.619 0.00 0.00 38.78 5.36
3648 3713 2.039613 TGATGTCTGTACACATTGGCCA 59.960 45.455 0.00 0.00 38.78 5.36
3649 3714 2.647683 TGTCTGTACACATTGGCCAA 57.352 45.000 23.00 23.00 0.00 4.52
3650 3715 3.153369 TGTCTGTACACATTGGCCAAT 57.847 42.857 25.73 25.73 0.00 3.16
3651 3716 3.495331 TGTCTGTACACATTGGCCAATT 58.505 40.909 28.68 16.84 0.00 2.32
3652 3717 3.255395 TGTCTGTACACATTGGCCAATTG 59.745 43.478 28.68 27.00 0.00 2.32
3653 3718 3.505680 GTCTGTACACATTGGCCAATTGA 59.494 43.478 30.65 18.31 0.00 2.57
3654 3719 4.158394 GTCTGTACACATTGGCCAATTGAT 59.842 41.667 30.65 21.46 0.00 2.57
3655 3720 4.398988 TCTGTACACATTGGCCAATTGATC 59.601 41.667 30.65 24.20 0.00 2.92
3656 3721 4.085009 TGTACACATTGGCCAATTGATCA 58.915 39.130 30.65 25.53 0.00 2.92
3657 3722 3.880047 ACACATTGGCCAATTGATCAG 57.120 42.857 30.65 21.70 0.00 2.90
3658 3723 2.498481 ACACATTGGCCAATTGATCAGG 59.502 45.455 30.65 21.15 0.00 3.86
3659 3724 2.112998 ACATTGGCCAATTGATCAGGG 58.887 47.619 28.68 16.42 0.00 4.45
3660 3725 2.292389 ACATTGGCCAATTGATCAGGGA 60.292 45.455 28.68 0.00 0.00 4.20
3661 3726 2.148446 TTGGCCAATTGATCAGGGAG 57.852 50.000 16.05 0.00 0.00 4.30
3662 3727 1.002069 TGGCCAATTGATCAGGGAGT 58.998 50.000 0.61 0.00 0.00 3.85
3663 3728 1.358787 TGGCCAATTGATCAGGGAGTT 59.641 47.619 0.61 0.00 0.00 3.01
3664 3729 2.225343 TGGCCAATTGATCAGGGAGTTT 60.225 45.455 0.61 0.00 0.00 2.66
3665 3730 2.833943 GGCCAATTGATCAGGGAGTTTT 59.166 45.455 7.12 0.00 0.00 2.43
3666 3731 3.118992 GGCCAATTGATCAGGGAGTTTTC 60.119 47.826 7.12 0.00 0.00 2.29
3667 3732 3.511146 GCCAATTGATCAGGGAGTTTTCA 59.489 43.478 7.12 0.00 0.00 2.69
3668 3733 4.161001 GCCAATTGATCAGGGAGTTTTCAT 59.839 41.667 7.12 0.00 0.00 2.57
3669 3734 5.657474 CCAATTGATCAGGGAGTTTTCATG 58.343 41.667 7.12 0.00 0.00 3.07
3670 3735 5.419788 CCAATTGATCAGGGAGTTTTCATGA 59.580 40.000 7.12 0.00 0.00 3.07
3671 3736 6.097839 CCAATTGATCAGGGAGTTTTCATGAT 59.902 38.462 7.12 0.00 35.31 2.45
3672 3737 7.364408 CCAATTGATCAGGGAGTTTTCATGATT 60.364 37.037 7.12 0.00 33.76 2.57
3673 3738 6.519679 TTGATCAGGGAGTTTTCATGATTG 57.480 37.500 0.00 0.00 33.76 2.67
3674 3739 4.400251 TGATCAGGGAGTTTTCATGATTGC 59.600 41.667 0.00 0.00 33.76 3.56
3675 3740 4.038271 TCAGGGAGTTTTCATGATTGCT 57.962 40.909 0.00 0.00 0.00 3.91
3676 3741 5.178096 TCAGGGAGTTTTCATGATTGCTA 57.822 39.130 0.00 0.00 0.00 3.49
3677 3742 5.188434 TCAGGGAGTTTTCATGATTGCTAG 58.812 41.667 0.00 0.00 0.00 3.42
3678 3743 4.946157 CAGGGAGTTTTCATGATTGCTAGT 59.054 41.667 0.00 0.00 0.00 2.57
3679 3744 4.946157 AGGGAGTTTTCATGATTGCTAGTG 59.054 41.667 0.00 0.00 0.00 2.74
3680 3745 4.943705 GGGAGTTTTCATGATTGCTAGTGA 59.056 41.667 0.00 0.00 0.00 3.41
3681 3746 5.065731 GGGAGTTTTCATGATTGCTAGTGAG 59.934 44.000 0.00 0.00 0.00 3.51
3682 3747 5.877012 GGAGTTTTCATGATTGCTAGTGAGA 59.123 40.000 0.00 0.00 0.00 3.27
3683 3748 6.183360 GGAGTTTTCATGATTGCTAGTGAGAC 60.183 42.308 0.00 0.00 0.00 3.36
3684 3749 5.645497 AGTTTTCATGATTGCTAGTGAGACC 59.355 40.000 0.00 0.00 0.00 3.85
3685 3750 4.824479 TTCATGATTGCTAGTGAGACCA 57.176 40.909 0.00 0.00 0.00 4.02
3686 3751 4.824479 TCATGATTGCTAGTGAGACCAA 57.176 40.909 0.00 0.00 0.00 3.67
3687 3752 5.363562 TCATGATTGCTAGTGAGACCAAT 57.636 39.130 0.00 0.00 0.00 3.16
3688 3753 5.748402 TCATGATTGCTAGTGAGACCAATT 58.252 37.500 0.00 0.00 0.00 2.32
3689 3754 6.182627 TCATGATTGCTAGTGAGACCAATTT 58.817 36.000 0.00 0.00 0.00 1.82
3690 3755 6.660521 TCATGATTGCTAGTGAGACCAATTTT 59.339 34.615 0.00 0.00 0.00 1.82
3691 3756 6.258230 TGATTGCTAGTGAGACCAATTTTG 57.742 37.500 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.689972 ACATCAAAGAAAATCAAAGAGAGTTGT 58.310 29.630 0.00 0.00 34.27 3.32
34 35 9.525409 AACATCAAAGAAAATCAAAGAGAGTTG 57.475 29.630 0.00 0.00 34.27 3.16
36 37 9.741647 GAAACATCAAAGAAAATCAAAGAGAGT 57.258 29.630 0.00 0.00 0.00 3.24
169 170 7.123847 ACCGAAGTTGTGTCTATTACCTCTAAT 59.876 37.037 0.00 0.00 0.00 1.73
174 175 4.525487 TGACCGAAGTTGTGTCTATTACCT 59.475 41.667 3.73 0.00 0.00 3.08
191 192 5.918426 TTGTACTAACATGGTATGACCGA 57.082 39.130 0.00 0.00 42.58 4.69
225 226 6.015603 TGCAACTGATACATGTTTGGAATTGA 60.016 34.615 2.30 0.00 0.00 2.57
282 283 0.034756 TGCTCTTGCTTCGGCTACAA 59.965 50.000 0.00 0.00 42.37 2.41
291 292 4.521639 TCATGTCTTTGAATGCTCTTGCTT 59.478 37.500 0.00 0.00 40.48 3.91
306 307 4.403752 TGTACAGATAGCAGCTCATGTCTT 59.596 41.667 0.00 0.00 0.00 3.01
330 331 8.651589 ACAGTGCAGAAGCTAATATATACCTA 57.348 34.615 0.00 0.00 42.74 3.08
368 369 5.014534 TGAGTGGGTAGGAAAGGTAGTAA 57.985 43.478 0.00 0.00 0.00 2.24
378 379 2.265367 TCAAAGCATGAGTGGGTAGGA 58.735 47.619 0.00 0.00 33.04 2.94
530 552 3.492383 CGCAACAAACCAAATGCACAATA 59.508 39.130 0.00 0.00 38.69 1.90
552 574 3.069729 AGAAGTGAGTGTGTGTAAGACCC 59.930 47.826 0.00 0.00 0.00 4.46
565 587 6.769822 CCATGCAATATAAGGAAGAAGTGAGT 59.230 38.462 0.00 0.00 0.00 3.41
654 677 7.642082 AGATGAAGCTGAAATGCTAAGAAAT 57.358 32.000 0.00 0.00 43.24 2.17
802 825 7.228507 TCACTCAAAGTACATGCATTTAACACT 59.771 33.333 0.00 0.00 0.00 3.55
831 854 6.941436 TCTTATTTGTACCACGGGTGTTATTT 59.059 34.615 5.90 0.00 36.19 1.40
852 876 2.158726 ACACGCCCCTTTCACTTTCTTA 60.159 45.455 0.00 0.00 0.00 2.10
883 907 0.250338 GAGAGAAGTTGGGGCGTTGT 60.250 55.000 0.00 0.00 0.00 3.32
899 923 3.531207 CATCGCGGGCTCCTGAGA 61.531 66.667 6.13 3.69 35.72 3.27
900 924 4.598894 CCATCGCGGGCTCCTGAG 62.599 72.222 6.13 0.00 0.00 3.35
937 963 5.455849 CGAGGTTTCAGAAGACGTATATGTG 59.544 44.000 1.31 0.00 0.00 3.21
938 964 5.579718 CGAGGTTTCAGAAGACGTATATGT 58.420 41.667 0.00 0.00 0.00 2.29
939 965 4.441415 GCGAGGTTTCAGAAGACGTATATG 59.559 45.833 0.00 0.00 0.00 1.78
940 966 4.338682 AGCGAGGTTTCAGAAGACGTATAT 59.661 41.667 0.00 0.00 0.00 0.86
941 967 3.693085 AGCGAGGTTTCAGAAGACGTATA 59.307 43.478 0.00 0.00 0.00 1.47
1519 1563 1.337821 GTGTTCCACGAGACGATGTC 58.662 55.000 0.00 0.00 0.00 3.06
1520 1564 3.491581 GTGTTCCACGAGACGATGT 57.508 52.632 0.00 0.00 0.00 3.06
1569 1616 0.807667 AGAGAATCCACATGCGCGTC 60.808 55.000 8.43 0.00 33.66 5.19
1668 1715 2.280592 AAACCGCTCACCGTGTCC 60.281 61.111 0.00 0.00 34.38 4.02
1695 1742 1.601759 GCTCTTGACAAGCTGCCCA 60.602 57.895 10.50 0.00 36.80 5.36
1747 1794 2.894765 TCTTCGTGTACATCTCCACCAA 59.105 45.455 0.00 0.00 0.00 3.67
1789 1836 0.603569 ATCTCGGTGAACGCTCTGTT 59.396 50.000 0.00 0.00 45.61 3.16
1790 1837 0.109086 CATCTCGGTGAACGCTCTGT 60.109 55.000 0.00 0.00 43.86 3.41
1801 1848 4.458829 TCTCCGGGGCATCTCGGT 62.459 66.667 0.00 0.00 45.79 4.69
1890 1937 1.596477 GAGCATCATGGGACCGAGC 60.596 63.158 0.00 0.00 33.17 5.03
1923 1970 2.032377 CGTCGCCAATGTGTAGTTGTTT 60.032 45.455 0.00 0.00 0.00 2.83
2012 2059 0.043940 ATCAGAGCCCTCTCCCAGTT 59.956 55.000 0.00 0.00 40.22 3.16
2028 2075 1.553195 CGTTGTTCACGGCGACATCA 61.553 55.000 16.62 4.63 45.89 3.07
2179 2226 2.241880 CGAACACCTTCACGGCGTT 61.242 57.895 11.19 0.00 40.65 4.84
2221 2268 0.034337 AACGTGATGTGGTTAGGCGT 59.966 50.000 0.00 0.00 0.00 5.68
2233 2280 1.215647 GGACGCAGAGGAACGTGAT 59.784 57.895 0.00 0.00 43.71 3.06
2394 2441 1.959848 CGATATCAGCTCCTCGGCA 59.040 57.895 3.12 0.00 34.17 5.69
2431 2478 2.227036 CCTGCCAGACCAGAACCCT 61.227 63.158 0.00 0.00 34.77 4.34
2463 2510 1.179152 CATTGCCATGGAGCTGACAA 58.821 50.000 18.40 9.40 0.00 3.18
2469 2516 3.126528 GCCTCATTGCCATGGAGC 58.873 61.111 18.40 0.45 0.00 4.70
2517 2564 1.213013 GTCTTCCTTCTCGAGCGCA 59.787 57.895 11.47 0.00 0.00 6.09
2543 2590 0.038251 CCTCGACAGCAGCAAGTACA 60.038 55.000 0.00 0.00 0.00 2.90
2544 2591 0.243907 TCCTCGACAGCAGCAAGTAC 59.756 55.000 0.00 0.00 0.00 2.73
2548 2595 2.049156 CGTCCTCGACAGCAGCAA 60.049 61.111 0.00 0.00 39.71 3.91
2731 2783 0.251787 GGGTTCCAGGTGCTTCCATT 60.252 55.000 1.79 0.00 39.02 3.16
2742 2794 0.113190 AGGCCAGAAAAGGGTTCCAG 59.887 55.000 5.01 0.00 0.00 3.86
2747 2799 1.481242 CCTTTCAGGCCAGAAAAGGGT 60.481 52.381 25.10 0.00 37.09 4.34
2748 2800 1.260544 CCTTTCAGGCCAGAAAAGGG 58.739 55.000 25.10 19.41 37.09 3.95
2761 2813 0.973632 TCGTAGCCTGAAGCCTTTCA 59.026 50.000 0.00 0.00 45.47 2.69
2762 2814 2.003301 CTTCGTAGCCTGAAGCCTTTC 58.997 52.381 0.00 0.00 45.47 2.62
2763 2815 1.339151 CCTTCGTAGCCTGAAGCCTTT 60.339 52.381 5.01 0.00 45.47 3.11
2764 2816 0.250513 CCTTCGTAGCCTGAAGCCTT 59.749 55.000 5.01 0.00 45.47 4.35
2765 2817 0.614979 TCCTTCGTAGCCTGAAGCCT 60.615 55.000 5.01 0.00 45.47 4.58
2766 2818 0.249398 TTCCTTCGTAGCCTGAAGCC 59.751 55.000 5.01 0.00 45.47 4.35
2767 2819 2.003301 CTTTCCTTCGTAGCCTGAAGC 58.997 52.381 5.01 0.00 41.16 3.86
2768 2820 3.320673 ACTTTCCTTCGTAGCCTGAAG 57.679 47.619 3.80 3.80 41.95 3.02
2769 2821 3.194968 CCTACTTTCCTTCGTAGCCTGAA 59.805 47.826 0.00 0.00 33.46 3.02
2770 2822 2.758979 CCTACTTTCCTTCGTAGCCTGA 59.241 50.000 0.00 0.00 33.46 3.86
2771 2823 2.496470 ACCTACTTTCCTTCGTAGCCTG 59.504 50.000 0.00 0.00 33.46 4.85
2772 2824 2.817665 ACCTACTTTCCTTCGTAGCCT 58.182 47.619 0.00 0.00 33.46 4.58
2773 2825 4.933505 ATACCTACTTTCCTTCGTAGCC 57.066 45.455 0.00 0.00 33.46 3.93
2774 2826 8.707938 TTTAAATACCTACTTTCCTTCGTAGC 57.292 34.615 0.00 0.00 33.46 3.58
2777 2829 9.901172 ATGATTTAAATACCTACTTTCCTTCGT 57.099 29.630 0.00 0.00 0.00 3.85
2786 2838 9.474313 TGCCAGAAAATGATTTAAATACCTACT 57.526 29.630 0.00 0.00 0.00 2.57
2789 2841 8.980596 TCATGCCAGAAAATGATTTAAATACCT 58.019 29.630 0.00 0.00 0.00 3.08
2790 2842 9.598517 TTCATGCCAGAAAATGATTTAAATACC 57.401 29.630 0.00 0.00 33.01 2.73
2793 2845 9.169592 CCTTTCATGCCAGAAAATGATTTAAAT 57.830 29.630 0.00 0.00 37.09 1.40
2794 2846 7.119553 GCCTTTCATGCCAGAAAATGATTTAAA 59.880 33.333 0.00 0.00 37.09 1.52
2795 2847 6.594937 GCCTTTCATGCCAGAAAATGATTTAA 59.405 34.615 0.00 0.00 37.09 1.52
2796 2848 6.070653 AGCCTTTCATGCCAGAAAATGATTTA 60.071 34.615 0.00 0.00 37.09 1.40
2797 2849 4.939439 GCCTTTCATGCCAGAAAATGATTT 59.061 37.500 2.83 0.00 37.09 2.17
2798 2850 4.224370 AGCCTTTCATGCCAGAAAATGATT 59.776 37.500 2.83 0.00 37.09 2.57
2910 2969 3.087031 CCAGTTGGATCATGCAGAAGTT 58.913 45.455 0.00 0.00 37.39 2.66
2912 2971 2.719739 ACCAGTTGGATCATGCAGAAG 58.280 47.619 4.92 0.00 38.94 2.85
2941 3001 7.040617 ACAGAATTGATAGCCATTGATCACATC 60.041 37.037 0.00 0.00 31.85 3.06
2968 3028 6.696411 CCAATTAATAACTGTTTTGCCCTGA 58.304 36.000 0.00 0.00 0.00 3.86
2973 3033 6.620518 GCAAGGCCAATTAATAACTGTTTTGC 60.621 38.462 5.01 2.08 0.00 3.68
3022 3082 6.905067 ATATCAAGGGCTATCATGAGGATT 57.095 37.500 0.09 0.00 37.44 3.01
3060 3121 8.345565 GGACTATGTATGGCTTTCTTTGTATTG 58.654 37.037 0.00 0.00 0.00 1.90
3068 3130 5.279206 CGATCAGGACTATGTATGGCTTTCT 60.279 44.000 0.00 0.00 0.00 2.52
3116 3179 1.789523 TCCCCACTCCATAGCTGTAC 58.210 55.000 0.00 0.00 0.00 2.90
3119 3182 2.025887 AGTTTTCCCCACTCCATAGCTG 60.026 50.000 0.00 0.00 0.00 4.24
3219 3283 0.250252 TCATCGCCTGTTGTCTGCAA 60.250 50.000 0.00 0.00 0.00 4.08
3227 3291 1.089920 GCTTGACATCATCGCCTGTT 58.910 50.000 0.00 0.00 0.00 3.16
3228 3292 1.086067 CGCTTGACATCATCGCCTGT 61.086 55.000 0.00 0.00 0.00 4.00
3240 3304 2.413453 GAGACCTCAAATGTCGCTTGAC 59.587 50.000 0.00 0.00 43.19 3.18
3244 3308 0.976641 TGGAGACCTCAAATGTCGCT 59.023 50.000 0.00 0.00 37.80 4.93
3334 3398 0.762418 TCCTCTTCAAGAACGGGCAA 59.238 50.000 0.00 0.00 0.00 4.52
3394 3458 2.684374 CGACCATGATGCAAATCCTCAA 59.316 45.455 0.00 0.00 0.00 3.02
3457 3521 5.734720 TCTCTGATAGTTGGCGATTTTCTT 58.265 37.500 0.00 0.00 0.00 2.52
3459 3523 6.701841 TGTATCTCTGATAGTTGGCGATTTTC 59.298 38.462 0.00 0.00 0.00 2.29
3465 3529 6.851222 AATTTGTATCTCTGATAGTTGGCG 57.149 37.500 0.00 0.00 0.00 5.69
3532 3597 0.251474 ATTTTCTGCAGGCCTCAGCA 60.251 50.000 21.00 18.95 42.56 4.41
3533 3598 0.893447 AATTTTCTGCAGGCCTCAGC 59.107 50.000 21.00 15.73 38.76 4.26
3534 3599 3.582780 GAAAATTTTCTGCAGGCCTCAG 58.417 45.455 21.21 20.19 34.41 3.35
3535 3600 2.299867 GGAAAATTTTCTGCAGGCCTCA 59.700 45.455 25.86 3.14 37.35 3.86
3536 3601 2.299867 TGGAAAATTTTCTGCAGGCCTC 59.700 45.455 25.86 10.06 37.35 4.70
3537 3602 2.328319 TGGAAAATTTTCTGCAGGCCT 58.672 42.857 25.86 0.00 37.35 5.19
3538 3603 2.837532 TGGAAAATTTTCTGCAGGCC 57.162 45.000 25.86 12.03 37.35 5.19
3539 3604 2.417586 GCATGGAAAATTTTCTGCAGGC 59.582 45.455 27.42 24.77 37.91 4.85
3540 3605 3.434299 GTGCATGGAAAATTTTCTGCAGG 59.566 43.478 31.97 23.37 44.01 4.85
3541 3606 3.434299 GGTGCATGGAAAATTTTCTGCAG 59.566 43.478 31.97 20.33 44.01 4.41
3542 3607 3.401182 GGTGCATGGAAAATTTTCTGCA 58.599 40.909 29.56 29.56 42.39 4.41
3543 3608 2.743664 GGGTGCATGGAAAATTTTCTGC 59.256 45.455 26.41 26.41 38.26 4.26
3544 3609 4.276058 AGGGTGCATGGAAAATTTTCTG 57.724 40.909 25.86 19.26 37.35 3.02
3545 3610 4.980339 AAGGGTGCATGGAAAATTTTCT 57.020 36.364 25.86 8.60 37.35 2.52
3546 3611 7.686438 AATTAAGGGTGCATGGAAAATTTTC 57.314 32.000 20.51 20.51 36.46 2.29
3547 3612 7.723172 TCAAATTAAGGGTGCATGGAAAATTTT 59.277 29.630 2.28 2.28 0.00 1.82
3548 3613 7.174772 GTCAAATTAAGGGTGCATGGAAAATTT 59.825 33.333 0.00 0.00 0.00 1.82
3549 3614 6.654582 GTCAAATTAAGGGTGCATGGAAAATT 59.345 34.615 0.00 0.00 0.00 1.82
3550 3615 6.013466 AGTCAAATTAAGGGTGCATGGAAAAT 60.013 34.615 0.00 0.00 0.00 1.82
3551 3616 5.306678 AGTCAAATTAAGGGTGCATGGAAAA 59.693 36.000 0.00 0.00 0.00 2.29
3552 3617 4.837860 AGTCAAATTAAGGGTGCATGGAAA 59.162 37.500 0.00 0.00 0.00 3.13
3553 3618 4.415596 AGTCAAATTAAGGGTGCATGGAA 58.584 39.130 0.00 0.00 0.00 3.53
3554 3619 4.016444 GAGTCAAATTAAGGGTGCATGGA 58.984 43.478 0.00 0.00 0.00 3.41
3555 3620 4.019174 AGAGTCAAATTAAGGGTGCATGG 58.981 43.478 0.00 0.00 0.00 3.66
3556 3621 4.946157 AGAGAGTCAAATTAAGGGTGCATG 59.054 41.667 0.00 0.00 0.00 4.06
3557 3622 5.184892 AGAGAGTCAAATTAAGGGTGCAT 57.815 39.130 0.00 0.00 0.00 3.96
3558 3623 4.640771 AGAGAGTCAAATTAAGGGTGCA 57.359 40.909 0.00 0.00 0.00 4.57
3559 3624 5.335976 CCAAAGAGAGTCAAATTAAGGGTGC 60.336 44.000 0.00 0.00 0.00 5.01
3560 3625 6.003950 TCCAAAGAGAGTCAAATTAAGGGTG 58.996 40.000 0.00 0.00 0.00 4.61
3561 3626 6.200878 TCCAAAGAGAGTCAAATTAAGGGT 57.799 37.500 0.00 0.00 0.00 4.34
3562 3627 7.524717 TTTCCAAAGAGAGTCAAATTAAGGG 57.475 36.000 0.00 0.00 0.00 3.95
3563 3628 9.468532 CTTTTTCCAAAGAGAGTCAAATTAAGG 57.531 33.333 0.00 0.00 41.97 2.69
3577 3642 6.192044 ACCCAGTAGTTTCTTTTTCCAAAGA 58.808 36.000 0.00 0.00 45.63 2.52
3578 3643 6.465439 ACCCAGTAGTTTCTTTTTCCAAAG 57.535 37.500 0.00 0.00 40.91 2.77
3579 3644 6.548251 CCTACCCAGTAGTTTCTTTTTCCAAA 59.452 38.462 1.40 0.00 34.62 3.28
3580 3645 6.066032 CCTACCCAGTAGTTTCTTTTTCCAA 58.934 40.000 1.40 0.00 34.62 3.53
3581 3646 5.133153 ACCTACCCAGTAGTTTCTTTTTCCA 59.867 40.000 1.40 0.00 34.62 3.53
3582 3647 5.472478 CACCTACCCAGTAGTTTCTTTTTCC 59.528 44.000 1.40 0.00 34.62 3.13
3583 3648 6.293698 TCACCTACCCAGTAGTTTCTTTTTC 58.706 40.000 1.40 0.00 34.62 2.29
3584 3649 6.256643 TCACCTACCCAGTAGTTTCTTTTT 57.743 37.500 1.40 0.00 34.62 1.94
3585 3650 5.899631 TCACCTACCCAGTAGTTTCTTTT 57.100 39.130 1.40 0.00 34.62 2.27
3586 3651 6.183361 ACAATCACCTACCCAGTAGTTTCTTT 60.183 38.462 1.40 0.00 34.62 2.52
3587 3652 5.309806 ACAATCACCTACCCAGTAGTTTCTT 59.690 40.000 1.40 0.00 34.62 2.52
3588 3653 4.844655 ACAATCACCTACCCAGTAGTTTCT 59.155 41.667 1.40 0.00 34.62 2.52
3589 3654 5.161943 ACAATCACCTACCCAGTAGTTTC 57.838 43.478 1.40 0.00 34.62 2.78
3590 3655 5.072600 TGAACAATCACCTACCCAGTAGTTT 59.927 40.000 1.40 0.00 34.62 2.66
3591 3656 4.595781 TGAACAATCACCTACCCAGTAGTT 59.404 41.667 1.40 0.00 34.62 2.24
3592 3657 4.164981 TGAACAATCACCTACCCAGTAGT 58.835 43.478 1.40 0.00 34.62 2.73
3593 3658 4.819105 TGAACAATCACCTACCCAGTAG 57.181 45.455 0.00 0.00 36.04 2.57
3605 3670 9.101655 CATCAATGTACTCTATGTGAACAATCA 57.898 33.333 0.00 0.00 0.00 2.57
3606 3671 9.102757 ACATCAATGTACTCTATGTGAACAATC 57.897 33.333 0.00 0.00 39.68 2.67
3607 3672 9.102757 GACATCAATGTACTCTATGTGAACAAT 57.897 33.333 7.95 0.00 41.95 2.71
3608 3673 8.314021 AGACATCAATGTACTCTATGTGAACAA 58.686 33.333 7.95 0.00 41.95 2.83
3609 3674 7.761249 CAGACATCAATGTACTCTATGTGAACA 59.239 37.037 7.95 0.00 41.95 3.18
3610 3675 7.761704 ACAGACATCAATGTACTCTATGTGAAC 59.238 37.037 7.95 0.00 41.95 3.18
3611 3676 7.840931 ACAGACATCAATGTACTCTATGTGAA 58.159 34.615 7.95 0.00 41.95 3.18
3612 3677 7.410120 ACAGACATCAATGTACTCTATGTGA 57.590 36.000 7.95 0.00 41.95 3.58
3613 3678 8.567369 GTACAGACATCAATGTACTCTATGTG 57.433 38.462 7.95 0.00 45.33 3.21
3622 3687 5.353956 GCCAATGTGTACAGACATCAATGTA 59.646 40.000 0.00 0.00 41.95 2.29
3623 3688 4.156556 GCCAATGTGTACAGACATCAATGT 59.843 41.667 0.00 0.00 45.16 2.71
3624 3689 4.439153 GGCCAATGTGTACAGACATCAATG 60.439 45.833 0.00 0.00 38.04 2.82
3625 3690 3.696051 GGCCAATGTGTACAGACATCAAT 59.304 43.478 0.00 0.00 38.04 2.57
3626 3691 3.081061 GGCCAATGTGTACAGACATCAA 58.919 45.455 0.00 0.00 38.04 2.57
3627 3692 2.039613 TGGCCAATGTGTACAGACATCA 59.960 45.455 0.61 0.00 38.04 3.07
3628 3693 2.710377 TGGCCAATGTGTACAGACATC 58.290 47.619 0.61 0.00 38.04 3.06
3629 3694 2.877097 TGGCCAATGTGTACAGACAT 57.123 45.000 0.61 0.00 38.04 3.06
3630 3695 2.647683 TTGGCCAATGTGTACAGACA 57.352 45.000 16.05 0.00 0.00 3.41
3631 3696 3.505680 TCAATTGGCCAATGTGTACAGAC 59.494 43.478 31.28 0.00 0.00 3.51
3632 3697 3.760738 TCAATTGGCCAATGTGTACAGA 58.239 40.909 31.28 16.42 0.00 3.41
3633 3698 4.158209 TGATCAATTGGCCAATGTGTACAG 59.842 41.667 31.28 14.59 0.00 2.74
3634 3699 4.085009 TGATCAATTGGCCAATGTGTACA 58.915 39.130 31.28 24.62 0.00 2.90
3635 3700 4.440525 CCTGATCAATTGGCCAATGTGTAC 60.441 45.833 31.28 22.98 0.00 2.90
3636 3701 3.700539 CCTGATCAATTGGCCAATGTGTA 59.299 43.478 31.28 16.74 0.00 2.90
3637 3702 2.498481 CCTGATCAATTGGCCAATGTGT 59.502 45.455 31.28 19.00 0.00 3.72
3638 3703 2.159014 CCCTGATCAATTGGCCAATGTG 60.159 50.000 31.28 26.62 0.00 3.21
3639 3704 2.112998 CCCTGATCAATTGGCCAATGT 58.887 47.619 31.28 19.71 0.00 2.71
3640 3705 2.364324 CTCCCTGATCAATTGGCCAATG 59.636 50.000 31.28 23.00 0.00 2.82
3641 3706 2.023695 ACTCCCTGATCAATTGGCCAAT 60.024 45.455 25.73 25.73 0.00 3.16
3642 3707 1.358787 ACTCCCTGATCAATTGGCCAA 59.641 47.619 23.00 23.00 0.00 4.52
3643 3708 1.002069 ACTCCCTGATCAATTGGCCA 58.998 50.000 0.00 0.00 0.00 5.36
3644 3709 2.149973 AACTCCCTGATCAATTGGCC 57.850 50.000 5.42 0.00 0.00 5.36
3645 3710 3.511146 TGAAAACTCCCTGATCAATTGGC 59.489 43.478 5.42 0.00 0.00 4.52
3646 3711 5.419788 TCATGAAAACTCCCTGATCAATTGG 59.580 40.000 5.42 0.00 0.00 3.16
3647 3712 6.519679 TCATGAAAACTCCCTGATCAATTG 57.480 37.500 0.00 0.00 0.00 2.32
3648 3713 7.553334 CAATCATGAAAACTCCCTGATCAATT 58.447 34.615 0.00 0.00 0.00 2.32
3649 3714 6.406624 GCAATCATGAAAACTCCCTGATCAAT 60.407 38.462 0.00 0.00 0.00 2.57
3650 3715 5.105635 GCAATCATGAAAACTCCCTGATCAA 60.106 40.000 0.00 0.00 0.00 2.57
3651 3716 4.400251 GCAATCATGAAAACTCCCTGATCA 59.600 41.667 0.00 0.00 0.00 2.92
3652 3717 4.643784 AGCAATCATGAAAACTCCCTGATC 59.356 41.667 0.00 0.00 0.00 2.92
3653 3718 4.607239 AGCAATCATGAAAACTCCCTGAT 58.393 39.130 0.00 0.00 0.00 2.90
3654 3719 4.038271 AGCAATCATGAAAACTCCCTGA 57.962 40.909 0.00 0.00 0.00 3.86
3655 3720 4.946157 ACTAGCAATCATGAAAACTCCCTG 59.054 41.667 0.00 0.00 0.00 4.45
3656 3721 4.946157 CACTAGCAATCATGAAAACTCCCT 59.054 41.667 0.00 0.00 0.00 4.20
3657 3722 4.943705 TCACTAGCAATCATGAAAACTCCC 59.056 41.667 0.00 0.00 0.00 4.30
3658 3723 5.877012 TCTCACTAGCAATCATGAAAACTCC 59.123 40.000 0.00 0.00 0.00 3.85
3659 3724 6.183360 GGTCTCACTAGCAATCATGAAAACTC 60.183 42.308 0.00 0.00 0.00 3.01
3660 3725 5.645497 GGTCTCACTAGCAATCATGAAAACT 59.355 40.000 0.00 0.00 0.00 2.66
3661 3726 5.412594 TGGTCTCACTAGCAATCATGAAAAC 59.587 40.000 0.00 0.00 0.00 2.43
3662 3727 5.559770 TGGTCTCACTAGCAATCATGAAAA 58.440 37.500 0.00 0.00 0.00 2.29
3663 3728 5.164620 TGGTCTCACTAGCAATCATGAAA 57.835 39.130 0.00 0.00 0.00 2.69
3664 3729 4.824479 TGGTCTCACTAGCAATCATGAA 57.176 40.909 0.00 0.00 0.00 2.57
3665 3730 4.824479 TTGGTCTCACTAGCAATCATGA 57.176 40.909 0.00 0.00 32.22 3.07
3666 3731 6.446781 AAATTGGTCTCACTAGCAATCATG 57.553 37.500 2.16 0.00 44.52 3.07
3667 3732 6.127535 CCAAAATTGGTCTCACTAGCAATCAT 60.128 38.462 3.95 0.00 44.52 2.45
3668 3733 5.183713 CCAAAATTGGTCTCACTAGCAATCA 59.816 40.000 3.95 0.00 44.52 2.57
3669 3734 5.644644 CCAAAATTGGTCTCACTAGCAATC 58.355 41.667 3.95 0.00 44.52 2.67
3670 3735 5.649782 CCAAAATTGGTCTCACTAGCAAT 57.350 39.130 3.95 0.00 46.58 3.56
3674 3739 9.802468 TGGAACCTCCAAAATTGGTCTCACTAG 62.802 44.444 11.74 0.73 45.00 2.57
3675 3740 8.115069 TGGAACCTCCAAAATTGGTCTCACTA 62.115 42.308 11.74 0.00 45.00 2.74
3676 3741 7.406034 TGGAACCTCCAAAATTGGTCTCACT 62.406 44.000 11.74 0.00 45.00 3.41
3677 3742 5.232705 TGGAACCTCCAAAATTGGTCTCAC 61.233 45.833 11.74 3.35 45.00 3.51
3678 3743 3.117322 TGGAACCTCCAAAATTGGTCTCA 60.117 43.478 11.74 1.35 45.00 3.27
3679 3744 3.496331 TGGAACCTCCAAAATTGGTCTC 58.504 45.455 11.74 5.01 45.00 3.36
3680 3745 3.611025 TGGAACCTCCAAAATTGGTCT 57.389 42.857 11.74 0.00 45.00 3.85


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

AutoCloner maintained by Alex Coulton.