Multiple sequence alignment - TraesCS3B01G475300

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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 TraesCS3B01G475300 chr3B 100.000 2996 0 0 1 2996 723795091 723798086 0.000000e+00 5533
1 TraesCS3B01G475300 chr3B 78.323 489 74 23 8 491 167208068 167208529 1.360000e-73 287
2 TraesCS3B01G475300 chr3B 78.261 437 61 21 58 491 726149134 726149539 1.780000e-62 250
3 TraesCS3B01G475300 chr3A 95.510 1804 68 11 574 2366 683442016 683443817 0.000000e+00 2870
4 TraesCS3B01G475300 chr3A 93.870 571 23 5 1 568 683441200 683441761 0.000000e+00 850
5 TraesCS3B01G475300 chr3D 95.135 1665 44 17 566 2210 546705021 546706668 0.000000e+00 2591
6 TraesCS3B01G475300 chr3D 91.935 558 28 5 1 550 546704319 546704867 0.000000e+00 765
7 TraesCS3B01G475300 chr5A 80.204 490 63 24 8 491 603292989 603292528 1.330000e-88 337


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 TraesCS3B01G475300 chr3B 723795091 723798086 2995 False 5533 5533 100.000 1 2996 1 chr3B.!!$F2 2995
1 TraesCS3B01G475300 chr3A 683441200 683443817 2617 False 1860 2870 94.690 1 2366 2 chr3A.!!$F1 2365
2 TraesCS3B01G475300 chr3D 546704319 546706668 2349 False 1678 2591 93.535 1 2210 2 chr3D.!!$F1 2209

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
635 1035 1.00299 TCTGTGGCTGTGGATGCTG 60.003 57.895 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2821 0.102481 GCAGAAGGCGACGATTAGGA 59.898 55.0 0.0 0.0 0.0 2.94 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
25 26 8.040716 GTTCTAATAACTGGTATGTGCTTTGT 57.959 34.615 0.00 0.00 0.00 2.83
39 40 2.768527 TGCTTTGTAGGAGCTCTGCTAT 59.231 45.455 14.64 0.00 39.88 2.97
104 105 2.133281 ATTGTCAAGCTGCCATGCTA 57.867 45.000 0.00 0.00 43.24 3.49
257 261 6.214208 AGCAGGACATCCTATGATTATTAGCA 59.786 38.462 0.00 0.00 46.65 3.49
350 354 5.227569 AGTTTGTCTATGTGGTGACATGA 57.772 39.130 0.00 0.00 43.03 3.07
352 356 6.946340 AGTTTGTCTATGTGGTGACATGATA 58.054 36.000 0.00 0.00 43.03 2.15
353 357 7.568349 AGTTTGTCTATGTGGTGACATGATAT 58.432 34.615 0.00 0.00 43.03 1.63
355 359 8.677300 GTTTGTCTATGTGGTGACATGATATTT 58.323 33.333 0.00 0.00 43.03 1.40
356 360 8.806429 TTGTCTATGTGGTGACATGATATTTT 57.194 30.769 0.00 0.00 43.03 1.82
357 361 8.212317 TGTCTATGTGGTGACATGATATTTTG 57.788 34.615 0.00 0.00 43.03 2.44
359 363 8.124823 GTCTATGTGGTGACATGATATTTTGTG 58.875 37.037 0.00 0.00 43.03 3.33
360 364 8.046107 TCTATGTGGTGACATGATATTTTGTGA 58.954 33.333 0.00 0.00 43.03 3.58
361 365 6.890979 TGTGGTGACATGATATTTTGTGAA 57.109 33.333 0.00 0.00 46.14 3.18
362 366 6.676950 TGTGGTGACATGATATTTTGTGAAC 58.323 36.000 0.00 0.00 46.14 3.18
363 367 6.264067 TGTGGTGACATGATATTTTGTGAACA 59.736 34.615 0.00 0.00 46.14 3.18
365 369 7.114811 GTGGTGACATGATATTTTGTGAACAAC 59.885 37.037 0.00 0.00 46.14 3.32
366 370 7.014134 TGGTGACATGATATTTTGTGAACAACT 59.986 33.333 0.00 0.00 32.70 3.16
367 371 7.326789 GGTGACATGATATTTTGTGAACAACTG 59.673 37.037 0.00 0.00 35.28 3.16
368 372 8.075574 GTGACATGATATTTTGTGAACAACTGA 58.924 33.333 0.00 0.00 35.28 3.41
369 373 8.795513 TGACATGATATTTTGTGAACAACTGAT 58.204 29.630 0.00 0.00 35.28 2.90
370 374 9.282247 GACATGATATTTTGTGAACAACTGATC 57.718 33.333 0.00 0.49 35.28 2.92
371 375 8.795513 ACATGATATTTTGTGAACAACTGATCA 58.204 29.630 0.00 12.11 35.28 2.92
372 376 9.628746 CATGATATTTTGTGAACAACTGATCAA 57.371 29.630 13.08 0.00 34.11 2.57
373 377 9.630098 ATGATATTTTGTGAACAACTGATCAAC 57.370 29.630 13.08 0.00 34.11 3.18
429 433 6.220930 CGATGGAAGGATTAACCGATCTTTA 58.779 40.000 0.00 0.00 44.74 1.85
634 1034 1.196766 TCTCTGTGGCTGTGGATGCT 61.197 55.000 0.00 0.00 0.00 3.79
635 1035 1.002990 TCTGTGGCTGTGGATGCTG 60.003 57.895 0.00 0.00 0.00 4.41
649 1049 1.947456 GATGCTGATTGATGCTGCTGA 59.053 47.619 0.00 0.00 0.00 4.26
679 1085 4.092968 GCTGTCGAACAAATTAATCCTCGT 59.907 41.667 0.00 0.00 0.00 4.18
700 1106 9.154847 CCTCGTCAAATTCATATATCAGCATTA 57.845 33.333 0.00 0.00 0.00 1.90
815 1221 3.065786 CAGCAGTGGTATGGCAGTAAATG 59.934 47.826 0.00 0.00 0.00 2.32
819 1225 5.277974 GCAGTGGTATGGCAGTAAATGTATG 60.278 44.000 0.00 0.00 0.00 2.39
891 1300 5.221441 GGGTTAAGTTCTTGCCAATTTCTGT 60.221 40.000 9.05 0.00 0.00 3.41
901 1310 2.542411 GCCAATTTCTGTCATGCCGATC 60.542 50.000 0.00 0.00 0.00 3.69
1008 1420 1.212616 CCGAGCGAGAAATGATGTCC 58.787 55.000 0.00 0.00 0.00 4.02
1276 1688 2.347490 GGGAGAAGAAGCACGCCA 59.653 61.111 0.00 0.00 0.00 5.69
1278 1690 1.004440 GGAGAAGAAGCACGCCACT 60.004 57.895 0.00 0.00 0.00 4.00
1452 1864 2.654079 CCAGCTGAAGCCGGACTCT 61.654 63.158 17.39 0.00 41.04 3.24
1541 1958 3.546714 AAGGTAAGCGCCGCCACTT 62.547 57.895 4.98 2.10 0.00 3.16
1547 1964 4.179579 GCGCCGCCACTTCATTCC 62.180 66.667 0.00 0.00 0.00 3.01
1549 1966 2.877691 GCCGCCACTTCATTCCAC 59.122 61.111 0.00 0.00 0.00 4.02
1550 1967 3.039202 GCCGCCACTTCATTCCACG 62.039 63.158 0.00 0.00 0.00 4.94
1551 1968 2.480555 CGCCACTTCATTCCACGC 59.519 61.111 0.00 0.00 0.00 5.34
1552 1969 2.324330 CGCCACTTCATTCCACGCA 61.324 57.895 0.00 0.00 0.00 5.24
1553 1970 1.210155 GCCACTTCATTCCACGCAC 59.790 57.895 0.00 0.00 0.00 5.34
1555 1972 1.167851 CCACTTCATTCCACGCACAT 58.832 50.000 0.00 0.00 0.00 3.21
1556 1973 1.135603 CCACTTCATTCCACGCACATG 60.136 52.381 0.00 0.00 0.00 3.21
1557 1974 0.523072 ACTTCATTCCACGCACATGC 59.477 50.000 0.00 0.00 37.78 4.06
1996 2421 1.352404 GACGTCTCGACCGGATGAG 59.648 63.158 9.46 15.09 0.00 2.90
2009 2434 0.447011 GGATGAGTTCTCGTCGTCGT 59.553 55.000 13.60 0.00 38.33 4.34
2220 2645 8.296713 TGTTTGTTGTCTAGATTAATTCCTTGC 58.703 33.333 0.00 0.00 0.00 4.01
2235 2660 4.202245 TCCTTGCAGGATGTACAACTAC 57.798 45.455 0.00 0.00 40.06 2.73
2242 2667 4.042398 CAGGATGTACAACTACGAATCCG 58.958 47.826 0.00 0.00 42.50 4.18
2257 2682 1.991121 ATCCGTCCAGGTAATCGCTA 58.009 50.000 0.00 0.00 41.99 4.26
2258 2683 1.991121 TCCGTCCAGGTAATCGCTAT 58.009 50.000 0.00 0.00 41.99 2.97
2259 2684 3.144657 TCCGTCCAGGTAATCGCTATA 57.855 47.619 0.00 0.00 41.99 1.31
2299 2724 9.769093 CTAGTGTTATTTATTTTGGGAGAAACG 57.231 33.333 0.00 0.00 0.00 3.60
2310 2735 6.790285 TTTGGGAGAAACGTATTGTTAGAC 57.210 37.500 0.00 0.00 40.84 2.59
2323 2748 9.052759 ACGTATTGTTAGACAAAGTGAGAAATT 57.947 29.630 0.00 0.00 41.96 1.82
2356 2781 8.292448 TCAATTTTCTCTATTTGTGTTGAGAGC 58.708 33.333 0.00 0.00 36.98 4.09
2381 2806 3.907927 TTTTTCGTGACTTGTGGCG 57.092 47.368 0.00 0.00 0.00 5.69
2382 2807 1.370609 TTTTTCGTGACTTGTGGCGA 58.629 45.000 0.00 0.00 0.00 5.54
2383 2808 0.934496 TTTTCGTGACTTGTGGCGAG 59.066 50.000 0.00 0.00 34.78 5.03
2384 2809 0.103390 TTTCGTGACTTGTGGCGAGA 59.897 50.000 0.00 0.00 34.78 4.04
2385 2810 0.318699 TTCGTGACTTGTGGCGAGAG 60.319 55.000 0.00 0.00 34.78 3.20
2408 2833 0.311477 GGAGACCTCCTAATCGTCGC 59.689 60.000 8.76 0.00 46.16 5.19
2409 2834 0.311477 GAGACCTCCTAATCGTCGCC 59.689 60.000 0.00 0.00 0.00 5.54
2410 2835 0.106619 AGACCTCCTAATCGTCGCCT 60.107 55.000 0.00 0.00 0.00 5.52
2411 2836 0.745468 GACCTCCTAATCGTCGCCTT 59.255 55.000 0.00 0.00 0.00 4.35
2412 2837 0.745468 ACCTCCTAATCGTCGCCTTC 59.255 55.000 0.00 0.00 0.00 3.46
2413 2838 1.033574 CCTCCTAATCGTCGCCTTCT 58.966 55.000 0.00 0.00 0.00 2.85
2414 2839 1.269309 CCTCCTAATCGTCGCCTTCTG 60.269 57.143 0.00 0.00 0.00 3.02
2415 2840 0.102481 TCCTAATCGTCGCCTTCTGC 59.898 55.000 0.00 0.00 0.00 4.26
2425 2850 3.180984 GCCTTCTGCGTCGTATAGG 57.819 57.895 7.11 7.11 0.00 2.57
2426 2851 0.384669 GCCTTCTGCGTCGTATAGGT 59.615 55.000 11.43 0.00 0.00 3.08
2427 2852 1.864435 GCCTTCTGCGTCGTATAGGTG 60.864 57.143 11.43 0.00 0.00 4.00
2428 2853 1.404391 CCTTCTGCGTCGTATAGGTGT 59.596 52.381 0.00 0.00 0.00 4.16
2429 2854 2.159282 CCTTCTGCGTCGTATAGGTGTT 60.159 50.000 0.00 0.00 0.00 3.32
2430 2855 2.838386 TCTGCGTCGTATAGGTGTTC 57.162 50.000 0.00 0.00 0.00 3.18
2431 2856 2.086094 TCTGCGTCGTATAGGTGTTCA 58.914 47.619 0.00 0.00 0.00 3.18
2432 2857 2.159476 TCTGCGTCGTATAGGTGTTCAC 60.159 50.000 0.00 0.00 0.00 3.18
2433 2858 1.186030 GCGTCGTATAGGTGTTCACG 58.814 55.000 0.00 0.74 35.78 4.35
2434 2859 1.186030 CGTCGTATAGGTGTTCACGC 58.814 55.000 0.00 0.00 34.50 5.34
2435 2860 1.186030 GTCGTATAGGTGTTCACGCG 58.814 55.000 3.53 3.53 34.50 6.01
2436 2861 0.523968 TCGTATAGGTGTTCACGCGC 60.524 55.000 5.73 0.00 34.50 6.86
2437 2862 1.477030 CGTATAGGTGTTCACGCGCC 61.477 60.000 5.73 0.00 39.22 6.53
2438 2863 1.142314 TATAGGTGTTCACGCGCCC 59.858 57.895 5.73 0.00 39.73 6.13
2439 2864 1.605971 TATAGGTGTTCACGCGCCCA 61.606 55.000 5.73 0.00 39.73 5.36
2440 2865 3.750077 TATAGGTGTTCACGCGCCCAC 62.750 57.143 5.73 7.79 39.73 4.61
2464 2889 3.120385 GCAAATTTGCGCTGGCCC 61.120 61.111 26.15 0.01 45.11 5.80
2465 2890 2.343018 CAAATTTGCGCTGGCCCA 59.657 55.556 9.73 0.00 38.85 5.36
2466 2891 2.028733 CAAATTTGCGCTGGCCCAC 61.029 57.895 9.73 0.00 38.85 4.61
2467 2892 3.238755 AAATTTGCGCTGGCCCACC 62.239 57.895 9.73 0.00 38.85 4.61
2468 2893 4.992740 ATTTGCGCTGGCCCACCA 62.993 61.111 9.73 0.00 46.51 4.17
2479 2904 4.899239 CCCACCAGGCGAGCGATC 62.899 72.222 0.00 0.00 0.00 3.69
2505 2930 4.469883 AGCACTGGTCAGCTGTTG 57.530 55.556 14.67 5.73 40.13 3.33
2506 2931 1.832219 AGCACTGGTCAGCTGTTGA 59.168 52.632 14.67 0.00 40.13 3.18
2515 2940 1.662517 TCAGCTGTTGACTTTTGCGA 58.337 45.000 14.67 0.00 0.00 5.10
2516 2941 2.013400 TCAGCTGTTGACTTTTGCGAA 58.987 42.857 14.67 0.00 0.00 4.70
2517 2942 2.421775 TCAGCTGTTGACTTTTGCGAAA 59.578 40.909 14.67 0.00 0.00 3.46
2518 2943 3.119673 TCAGCTGTTGACTTTTGCGAAAA 60.120 39.130 14.67 0.00 0.00 2.29
2519 2944 3.611986 CAGCTGTTGACTTTTGCGAAAAA 59.388 39.130 5.25 0.38 0.00 1.94
2520 2945 3.612423 AGCTGTTGACTTTTGCGAAAAAC 59.388 39.130 0.00 3.35 0.00 2.43
2521 2946 3.366422 GCTGTTGACTTTTGCGAAAAACA 59.634 39.130 12.46 12.46 0.00 2.83
2522 2947 4.720946 GCTGTTGACTTTTGCGAAAAACAC 60.721 41.667 9.98 5.66 0.00 3.32
2523 2948 4.299155 TGTTGACTTTTGCGAAAAACACA 58.701 34.783 9.98 0.00 0.00 3.72
2524 2949 4.745125 TGTTGACTTTTGCGAAAAACACAA 59.255 33.333 9.98 4.64 0.00 3.33
2525 2950 5.234329 TGTTGACTTTTGCGAAAAACACAAA 59.766 32.000 13.74 0.00 0.00 2.83
2526 2951 5.907197 TGACTTTTGCGAAAAACACAAAA 57.093 30.435 0.00 0.00 40.07 2.44
2531 2956 5.907197 TTTGCGAAAAACACAAAAGAACA 57.093 30.435 0.00 0.00 30.75 3.18
2532 2957 5.907197 TTGCGAAAAACACAAAAGAACAA 57.093 30.435 0.00 0.00 0.00 2.83
2533 2958 5.907197 TGCGAAAAACACAAAAGAACAAA 57.093 30.435 0.00 0.00 0.00 2.83
2534 2959 6.287107 TGCGAAAAACACAAAAGAACAAAA 57.713 29.167 0.00 0.00 0.00 2.44
2535 2960 6.715464 TGCGAAAAACACAAAAGAACAAAAA 58.285 28.000 0.00 0.00 0.00 1.94
2536 2961 6.848296 TGCGAAAAACACAAAAGAACAAAAAG 59.152 30.769 0.00 0.00 0.00 2.27
2537 2962 7.066505 GCGAAAAACACAAAAGAACAAAAAGA 58.933 30.769 0.00 0.00 0.00 2.52
2538 2963 7.584485 GCGAAAAACACAAAAGAACAAAAAGAA 59.416 29.630 0.00 0.00 0.00 2.52
2539 2964 9.592720 CGAAAAACACAAAAGAACAAAAAGAAT 57.407 25.926 0.00 0.00 0.00 2.40
2542 2967 9.877137 AAAACACAAAAGAACAAAAAGAATCAC 57.123 25.926 0.00 0.00 0.00 3.06
2543 2968 8.600449 AACACAAAAGAACAAAAAGAATCACA 57.400 26.923 0.00 0.00 0.00 3.58
2544 2969 8.600449 ACACAAAAGAACAAAAAGAATCACAA 57.400 26.923 0.00 0.00 0.00 3.33
2545 2970 9.050601 ACACAAAAGAACAAAAAGAATCACAAA 57.949 25.926 0.00 0.00 0.00 2.83
2546 2971 9.316859 CACAAAAGAACAAAAAGAATCACAAAC 57.683 29.630 0.00 0.00 0.00 2.93
2547 2972 9.050601 ACAAAAGAACAAAAAGAATCACAAACA 57.949 25.926 0.00 0.00 0.00 2.83
2548 2973 9.875675 CAAAAGAACAAAAAGAATCACAAACAA 57.124 25.926 0.00 0.00 0.00 2.83
2552 2977 9.434420 AGAACAAAAAGAATCACAAACAATTGA 57.566 25.926 13.59 0.00 38.94 2.57
2583 3008 9.881529 AATTTCGTGAATTCAAAATTTTCATGG 57.118 25.926 18.71 0.00 37.12 3.66
2584 3009 8.654230 TTTCGTGAATTCAAAATTTTCATGGA 57.346 26.923 10.35 0.00 37.12 3.41
2585 3010 8.830201 TTCGTGAATTCAAAATTTTCATGGAT 57.170 26.923 10.35 0.00 37.12 3.41
2586 3011 8.830201 TCGTGAATTCAAAATTTTCATGGATT 57.170 26.923 10.35 0.00 37.12 3.01
2587 3012 9.270640 TCGTGAATTCAAAATTTTCATGGATTT 57.729 25.926 10.35 0.00 37.12 2.17
2588 3013 9.320406 CGTGAATTCAAAATTTTCATGGATTTG 57.680 29.630 10.35 0.00 34.32 2.32
2681 3106 7.385778 TCATGGATTAGGAAAAAGTTTACGG 57.614 36.000 0.00 0.00 0.00 4.02
2682 3107 7.169591 TCATGGATTAGGAAAAAGTTTACGGA 58.830 34.615 0.00 0.00 0.00 4.69
2683 3108 7.832187 TCATGGATTAGGAAAAAGTTTACGGAT 59.168 33.333 0.00 0.00 0.00 4.18
2684 3109 8.466798 CATGGATTAGGAAAAAGTTTACGGATT 58.533 33.333 0.00 0.00 0.00 3.01
2685 3110 8.411991 TGGATTAGGAAAAAGTTTACGGATTT 57.588 30.769 0.00 0.00 0.00 2.17
2686 3111 8.862085 TGGATTAGGAAAAAGTTTACGGATTTT 58.138 29.630 0.00 0.00 0.00 1.82
2687 3112 9.135843 GGATTAGGAAAAAGTTTACGGATTTTG 57.864 33.333 0.00 0.00 0.00 2.44
2688 3113 9.902196 GATTAGGAAAAAGTTTACGGATTTTGA 57.098 29.630 0.00 0.00 0.00 2.69
2689 3114 9.687210 ATTAGGAAAAAGTTTACGGATTTTGAC 57.313 29.630 0.00 0.00 0.00 3.18
2690 3115 7.102847 AGGAAAAAGTTTACGGATTTTGACA 57.897 32.000 0.00 0.00 0.00 3.58
2691 3116 7.200455 AGGAAAAAGTTTACGGATTTTGACAG 58.800 34.615 0.00 0.00 0.00 3.51
2692 3117 7.067737 AGGAAAAAGTTTACGGATTTTGACAGA 59.932 33.333 0.00 0.00 0.00 3.41
2693 3118 7.703197 GGAAAAAGTTTACGGATTTTGACAGAA 59.297 33.333 0.00 0.00 0.00 3.02
2694 3119 8.989653 AAAAAGTTTACGGATTTTGACAGAAA 57.010 26.923 0.00 0.00 0.00 2.52
2695 3120 8.989653 AAAAGTTTACGGATTTTGACAGAAAA 57.010 26.923 0.00 0.00 0.00 2.29
2696 3121 8.989653 AAAGTTTACGGATTTTGACAGAAAAA 57.010 26.923 0.00 0.00 33.76 1.94
2697 3122 9.594478 AAAGTTTACGGATTTTGACAGAAAAAT 57.406 25.926 0.00 0.00 41.34 1.82
2698 3123 9.594478 AAGTTTACGGATTTTGACAGAAAAATT 57.406 25.926 0.00 0.00 39.31 1.82
2699 3124 9.594478 AGTTTACGGATTTTGACAGAAAAATTT 57.406 25.926 0.00 0.00 39.31 1.82
2700 3125 9.631639 GTTTACGGATTTTGACAGAAAAATTTG 57.368 29.630 0.00 0.00 39.31 2.32
2701 3126 9.587772 TTTACGGATTTTGACAGAAAAATTTGA 57.412 25.926 0.00 0.00 39.31 2.69
2702 3127 7.698836 ACGGATTTTGACAGAAAAATTTGAG 57.301 32.000 0.00 0.00 39.31 3.02
2703 3128 6.701400 ACGGATTTTGACAGAAAAATTTGAGG 59.299 34.615 0.00 0.00 39.31 3.86
2704 3129 6.922957 CGGATTTTGACAGAAAAATTTGAGGA 59.077 34.615 0.00 0.00 39.31 3.71
2705 3130 7.599998 CGGATTTTGACAGAAAAATTTGAGGAT 59.400 33.333 0.00 0.00 39.31 3.24
2706 3131 9.276590 GGATTTTGACAGAAAAATTTGAGGATT 57.723 29.630 0.00 0.00 39.31 3.01
2709 3134 9.664332 TTTTGACAGAAAAATTTGAGGATTTGA 57.336 25.926 0.00 0.00 30.06 2.69
2710 3135 9.664332 TTTGACAGAAAAATTTGAGGATTTGAA 57.336 25.926 0.00 0.00 30.06 2.69
2711 3136 9.664332 TTGACAGAAAAATTTGAGGATTTGAAA 57.336 25.926 0.00 0.00 30.06 2.69
2712 3137 9.664332 TGACAGAAAAATTTGAGGATTTGAAAA 57.336 25.926 0.00 0.00 30.06 2.29
2758 3183 9.553418 AAAAATCACGAATTTGGAAAAAGTTTG 57.447 25.926 0.00 0.00 37.64 2.93
2759 3184 7.841915 AATCACGAATTTGGAAAAAGTTTGT 57.158 28.000 0.00 0.00 0.00 2.83
2760 3185 6.639671 TCACGAATTTGGAAAAAGTTTGTG 57.360 33.333 7.15 7.15 36.15 3.33
2761 3186 5.578727 TCACGAATTTGGAAAAAGTTTGTGG 59.421 36.000 11.50 0.00 35.74 4.17
2762 3187 5.578727 CACGAATTTGGAAAAAGTTTGTGGA 59.421 36.000 0.00 0.00 32.91 4.02
2763 3188 6.257630 CACGAATTTGGAAAAAGTTTGTGGAT 59.742 34.615 0.00 0.00 32.91 3.41
2764 3189 6.821160 ACGAATTTGGAAAAAGTTTGTGGATT 59.179 30.769 0.00 0.00 0.00 3.01
2765 3190 7.335673 ACGAATTTGGAAAAAGTTTGTGGATTT 59.664 29.630 0.00 0.00 0.00 2.17
2766 3191 8.180920 CGAATTTGGAAAAAGTTTGTGGATTTT 58.819 29.630 0.00 0.00 0.00 1.82
2769 3194 9.898152 ATTTGGAAAAAGTTTGTGGATTTTAGA 57.102 25.926 0.00 0.00 0.00 2.10
2770 3195 9.898152 TTTGGAAAAAGTTTGTGGATTTTAGAT 57.102 25.926 0.00 0.00 0.00 1.98
2814 3239 8.641499 TTTTGTCCATTTGAGTGTATTTGAAC 57.359 30.769 0.00 0.00 0.00 3.18
2815 3240 6.951062 TGTCCATTTGAGTGTATTTGAACA 57.049 33.333 0.00 0.00 0.00 3.18
2816 3241 7.340122 TGTCCATTTGAGTGTATTTGAACAA 57.660 32.000 0.00 0.00 0.00 2.83
2817 3242 7.776107 TGTCCATTTGAGTGTATTTGAACAAA 58.224 30.769 2.48 2.48 34.46 2.83
2818 3243 7.920151 TGTCCATTTGAGTGTATTTGAACAAAG 59.080 33.333 6.18 0.00 33.32 2.77
2819 3244 7.920682 GTCCATTTGAGTGTATTTGAACAAAGT 59.079 33.333 6.18 0.00 33.32 2.66
2820 3245 8.474025 TCCATTTGAGTGTATTTGAACAAAGTT 58.526 29.630 6.18 0.00 33.32 2.66
2821 3246 8.755018 CCATTTGAGTGTATTTGAACAAAGTTC 58.245 33.333 6.18 3.05 33.32 3.01
2822 3247 9.299963 CATTTGAGTGTATTTGAACAAAGTTCA 57.700 29.630 8.39 8.39 33.32 3.18
2824 3249 9.868277 TTTGAGTGTATTTGAACAAAGTTCATT 57.132 25.926 12.75 7.11 33.32 2.57
2825 3250 8.854979 TGAGTGTATTTGAACAAAGTTCATTG 57.145 30.769 12.75 0.00 33.32 2.82
2826 3251 7.920151 TGAGTGTATTTGAACAAAGTTCATTGG 59.080 33.333 12.75 0.00 34.56 3.16
2827 3252 8.006298 AGTGTATTTGAACAAAGTTCATTGGA 57.994 30.769 12.75 0.00 34.56 3.53
2828 3253 8.641541 AGTGTATTTGAACAAAGTTCATTGGAT 58.358 29.630 12.75 8.04 34.56 3.41
2829 3254 9.260002 GTGTATTTGAACAAAGTTCATTGGATT 57.740 29.630 12.75 0.00 34.56 3.01
2830 3255 9.474920 TGTATTTGAACAAAGTTCATTGGATTC 57.525 29.630 12.75 5.20 34.56 2.52
2831 3256 9.474920 GTATTTGAACAAAGTTCATTGGATTCA 57.525 29.630 12.75 0.00 34.56 2.57
2832 3257 8.961294 ATTTGAACAAAGTTCATTGGATTCAA 57.039 26.923 12.75 0.00 35.37 2.69
2833 3258 8.961294 TTTGAACAAAGTTCATTGGATTCAAT 57.039 26.923 12.75 0.00 43.79 2.57
2834 3259 8.961294 TTGAACAAAGTTCATTGGATTCAATT 57.039 26.923 12.75 0.00 41.29 2.32
2835 3260 8.961294 TGAACAAAGTTCATTGGATTCAATTT 57.039 26.923 8.39 0.00 41.29 1.82
2836 3261 9.393512 TGAACAAAGTTCATTGGATTCAATTTT 57.606 25.926 8.39 0.00 41.29 1.82
2839 3264 9.393512 ACAAAGTTCATTGGATTCAATTTTTCA 57.606 25.926 0.00 0.00 41.29 2.69
2840 3265 9.872757 CAAAGTTCATTGGATTCAATTTTTCAG 57.127 29.630 0.00 0.00 41.29 3.02
2841 3266 8.611654 AAGTTCATTGGATTCAATTTTTCAGG 57.388 30.769 0.00 0.00 41.29 3.86
2842 3267 7.965718 AGTTCATTGGATTCAATTTTTCAGGA 58.034 30.769 0.00 0.00 41.29 3.86
2843 3268 8.431222 AGTTCATTGGATTCAATTTTTCAGGAA 58.569 29.630 0.00 0.00 41.29 3.36
2844 3269 9.223099 GTTCATTGGATTCAATTTTTCAGGAAT 57.777 29.630 0.00 0.00 41.29 3.01
2845 3270 9.796180 TTCATTGGATTCAATTTTTCAGGAATT 57.204 25.926 0.00 0.00 41.29 2.17
2846 3271 9.796180 TCATTGGATTCAATTTTTCAGGAATTT 57.204 25.926 0.00 0.00 41.29 1.82
2847 3272 9.834628 CATTGGATTCAATTTTTCAGGAATTTG 57.165 29.630 0.00 0.00 41.29 2.32
2848 3273 9.796180 ATTGGATTCAATTTTTCAGGAATTTGA 57.204 25.926 0.00 0.00 40.42 2.69
2849 3274 9.624373 TTGGATTCAATTTTTCAGGAATTTGAA 57.376 25.926 13.12 13.12 40.33 2.69
2850 3275 9.624373 TGGATTCAATTTTTCAGGAATTTGAAA 57.376 25.926 14.03 1.91 43.32 2.69
2859 3284 7.826260 TTTCAGGAATTTGAAAACAGTTCAC 57.174 32.000 3.35 0.00 42.39 3.18
2860 3285 6.522625 TCAGGAATTTGAAAACAGTTCACA 57.477 33.333 0.00 0.00 0.00 3.58
2861 3286 7.111247 TCAGGAATTTGAAAACAGTTCACAT 57.889 32.000 0.00 0.00 0.00 3.21
2862 3287 6.979817 TCAGGAATTTGAAAACAGTTCACATG 59.020 34.615 0.00 0.00 0.00 3.21
2863 3288 6.757947 CAGGAATTTGAAAACAGTTCACATGT 59.242 34.615 0.00 0.00 0.00 3.21
2864 3289 7.278424 CAGGAATTTGAAAACAGTTCACATGTT 59.722 33.333 0.00 0.00 42.55 2.71
2891 3316 5.845391 AAAAAGGTTCACGGATTTGAAGA 57.155 34.783 0.00 0.00 36.15 2.87
2892 3317 5.845391 AAAAGGTTCACGGATTTGAAGAA 57.155 34.783 0.00 0.00 36.15 2.52
2893 3318 5.845391 AAAGGTTCACGGATTTGAAGAAA 57.155 34.783 0.00 0.00 36.15 2.52
2894 3319 6.405278 AAAGGTTCACGGATTTGAAGAAAT 57.595 33.333 0.00 0.00 36.15 2.17
2895 3320 6.405278 AAGGTTCACGGATTTGAAGAAATT 57.595 33.333 0.00 0.00 36.15 1.82
2896 3321 6.405278 AGGTTCACGGATTTGAAGAAATTT 57.595 33.333 0.00 0.00 36.15 1.82
2897 3322 6.447162 AGGTTCACGGATTTGAAGAAATTTC 58.553 36.000 10.33 10.33 36.15 2.17
2898 3323 5.633601 GGTTCACGGATTTGAAGAAATTTCC 59.366 40.000 14.61 1.15 36.15 3.13
2899 3324 6.212955 GTTCACGGATTTGAAGAAATTTCCA 58.787 36.000 14.61 3.90 36.15 3.53
2900 3325 6.398234 TCACGGATTTGAAGAAATTTCCAA 57.602 33.333 14.61 9.76 31.58 3.53
2901 3326 6.991938 TCACGGATTTGAAGAAATTTCCAAT 58.008 32.000 14.61 8.11 31.58 3.16
2902 3327 6.867816 TCACGGATTTGAAGAAATTTCCAATG 59.132 34.615 14.61 7.66 31.58 2.82
2903 3328 6.646240 CACGGATTTGAAGAAATTTCCAATGT 59.354 34.615 14.61 5.27 31.58 2.71
2904 3329 7.171337 CACGGATTTGAAGAAATTTCCAATGTT 59.829 33.333 14.61 2.01 31.58 2.71
2905 3330 7.714813 ACGGATTTGAAGAAATTTCCAATGTTT 59.285 29.630 14.61 1.28 31.58 2.83
2906 3331 8.558700 CGGATTTGAAGAAATTTCCAATGTTTT 58.441 29.630 14.61 0.55 31.58 2.43
2918 3343 9.804977 AATTTCCAATGTTTTTATCAAATCCCA 57.195 25.926 0.00 0.00 0.00 4.37
2919 3344 8.614469 TTTCCAATGTTTTTATCAAATCCCAC 57.386 30.769 0.00 0.00 0.00 4.61
2920 3345 7.308450 TCCAATGTTTTTATCAAATCCCACA 57.692 32.000 0.00 0.00 0.00 4.17
2921 3346 7.915930 TCCAATGTTTTTATCAAATCCCACAT 58.084 30.769 0.00 0.00 0.00 3.21
2922 3347 9.040259 TCCAATGTTTTTATCAAATCCCACATA 57.960 29.630 0.00 0.00 0.00 2.29
2923 3348 9.835389 CCAATGTTTTTATCAAATCCCACATAT 57.165 29.630 0.00 0.00 0.00 1.78
2988 3413 5.485662 AACACTAGAAGAAAACACACTGC 57.514 39.130 0.00 0.00 0.00 4.40
2989 3414 4.513442 ACACTAGAAGAAAACACACTGCA 58.487 39.130 0.00 0.00 0.00 4.41
2990 3415 4.941263 ACACTAGAAGAAAACACACTGCAA 59.059 37.500 0.00 0.00 0.00 4.08
2991 3416 5.590259 ACACTAGAAGAAAACACACTGCAAT 59.410 36.000 0.00 0.00 0.00 3.56
2992 3417 6.095440 ACACTAGAAGAAAACACACTGCAATT 59.905 34.615 0.00 0.00 0.00 2.32
2993 3418 6.634436 CACTAGAAGAAAACACACTGCAATTC 59.366 38.462 0.00 0.00 0.00 2.17
2994 3419 4.601019 AGAAGAAAACACACTGCAATTCG 58.399 39.130 0.00 0.00 0.00 3.34
2995 3420 4.096382 AGAAGAAAACACACTGCAATTCGT 59.904 37.500 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.403968 CGTAGTCATAGCAGAGCTCCTA 58.596 50.000 10.93 6.12 40.44 2.94
39 40 2.426024 GTTCAGGACATAGCCGTAGTCA 59.574 50.000 0.00 0.00 34.04 3.41
257 261 3.626028 AAATGAGAACGCGCTTCTTTT 57.374 38.095 19.84 15.43 39.53 2.27
338 342 6.264067 TGTTCACAAAATATCATGTCACCACA 59.736 34.615 0.00 0.00 36.78 4.17
350 354 8.849168 TCAGTTGATCAGTTGTTCACAAAATAT 58.151 29.630 0.00 0.00 37.63 1.28
352 356 7.099266 TCAGTTGATCAGTTGTTCACAAAAT 57.901 32.000 0.00 0.00 37.63 1.82
353 357 6.507958 TCAGTTGATCAGTTGTTCACAAAA 57.492 33.333 0.00 0.00 37.63 2.44
355 359 7.984422 ATATCAGTTGATCAGTTGTTCACAA 57.016 32.000 0.00 0.00 36.05 3.33
356 360 7.984422 AATATCAGTTGATCAGTTGTTCACA 57.016 32.000 0.00 0.00 36.05 3.58
357 361 9.121517 CAAAATATCAGTTGATCAGTTGTTCAC 57.878 33.333 0.00 0.00 36.05 3.18
359 363 9.121517 CACAAAATATCAGTTGATCAGTTGTTC 57.878 33.333 0.00 0.00 33.35 3.18
360 364 8.849168 TCACAAAATATCAGTTGATCAGTTGTT 58.151 29.630 0.00 0.00 33.35 2.83
361 365 8.394971 TCACAAAATATCAGTTGATCAGTTGT 57.605 30.769 0.00 5.02 34.66 3.32
362 366 9.121517 GTTCACAAAATATCAGTTGATCAGTTG 57.878 33.333 0.00 0.00 36.05 3.16
363 367 8.849168 TGTTCACAAAATATCAGTTGATCAGTT 58.151 29.630 0.00 0.00 36.05 3.16
365 369 9.121517 GTTGTTCACAAAATATCAGTTGATCAG 57.878 33.333 0.00 0.00 37.63 2.90
366 370 8.849168 AGTTGTTCACAAAATATCAGTTGATCA 58.151 29.630 0.00 0.00 37.63 2.92
367 371 9.121517 CAGTTGTTCACAAAATATCAGTTGATC 57.878 33.333 0.00 0.00 37.63 2.92
368 372 8.849168 TCAGTTGTTCACAAAATATCAGTTGAT 58.151 29.630 0.00 0.00 37.63 2.57
369 373 8.219546 TCAGTTGTTCACAAAATATCAGTTGA 57.780 30.769 0.00 0.00 37.63 3.18
370 374 9.121517 GATCAGTTGTTCACAAAATATCAGTTG 57.878 33.333 0.00 0.00 37.63 3.16
371 375 8.299570 GGATCAGTTGTTCACAAAATATCAGTT 58.700 33.333 0.00 0.00 37.63 3.16
372 376 7.448161 TGGATCAGTTGTTCACAAAATATCAGT 59.552 33.333 0.00 0.00 37.63 3.41
373 377 7.819644 TGGATCAGTTGTTCACAAAATATCAG 58.180 34.615 0.00 0.00 37.63 2.90
429 433 6.403866 TGCAAGGAACACATAAAAATGTCT 57.596 33.333 0.00 0.00 31.37 3.41
568 720 6.171921 CAATGAGACAGACAGGAGAAGAAAT 58.828 40.000 0.00 0.00 0.00 2.17
576 728 1.203287 CGAGCAATGAGACAGACAGGA 59.797 52.381 0.00 0.00 0.00 3.86
577 729 1.203287 TCGAGCAATGAGACAGACAGG 59.797 52.381 0.00 0.00 0.00 4.00
634 1034 3.875134 CAGTATGTCAGCAGCATCAATCA 59.125 43.478 0.00 0.00 0.00 2.57
635 1035 3.303857 GCAGTATGTCAGCAGCATCAATC 60.304 47.826 0.00 0.00 39.31 2.67
649 1049 6.795098 TTAATTTGTTCGACAGCAGTATGT 57.205 33.333 0.00 0.00 39.31 2.29
700 1106 5.091552 TGTACCCAAGAGGAGACATAAACT 58.908 41.667 0.00 0.00 39.89 2.66
701 1107 5.416271 TGTACCCAAGAGGAGACATAAAC 57.584 43.478 0.00 0.00 39.89 2.01
707 1113 1.939980 ACCTGTACCCAAGAGGAGAC 58.060 55.000 3.32 0.00 41.34 3.36
815 1221 6.509418 TGCACCTATCCAAAAAGTTCATAC 57.491 37.500 0.00 0.00 0.00 2.39
819 1225 6.024552 TCATTGCACCTATCCAAAAAGTTC 57.975 37.500 0.00 0.00 0.00 3.01
833 1242 4.394300 GTGCCATCTATATCTCATTGCACC 59.606 45.833 0.00 0.00 40.35 5.01
901 1310 2.562298 TGCTGTTTCCTTGGCCATTAAG 59.438 45.455 6.09 0.00 0.00 1.85
992 1404 0.811616 GGCGGACATCATTTCTCGCT 60.812 55.000 0.00 0.00 42.33 4.93
995 1407 1.062587 CGTTGGCGGACATCATTTCTC 59.937 52.381 0.00 0.00 0.00 2.87
1452 1864 2.042537 AGCTCCATCTCCTCGGCA 60.043 61.111 0.00 0.00 0.00 5.69
1541 1958 0.606130 AGTGCATGTGCGTGGAATGA 60.606 50.000 0.00 0.00 45.83 2.57
1547 1964 2.429571 GGCAAGTGCATGTGCGTG 60.430 61.111 15.79 1.69 45.83 5.34
1549 1966 2.410638 AAGTGGCAAGTGCATGTGCG 62.411 55.000 15.79 0.00 45.83 5.34
1550 1967 0.942410 CAAGTGGCAAGTGCATGTGC 60.942 55.000 14.42 14.42 44.36 4.57
1551 1968 0.942410 GCAAGTGGCAAGTGCATGTG 60.942 55.000 16.42 0.00 44.36 3.21
1552 1969 1.364901 GCAAGTGGCAAGTGCATGT 59.635 52.632 16.42 0.00 44.36 3.21
1553 1970 4.255126 GCAAGTGGCAAGTGCATG 57.745 55.556 16.42 0.00 44.36 4.06
1806 2230 4.100084 TGCCTCCCCATGCTCGTG 62.100 66.667 0.00 0.00 0.00 4.35
1996 2421 4.127726 GGTGACGACGACGAGAAC 57.872 61.111 15.32 8.53 42.66 3.01
2009 2434 2.256117 TCTCTGCTATCGATCGGTGA 57.744 50.000 16.41 0.12 0.00 4.02
2220 2645 4.042398 CGGATTCGTAGTTGTACATCCTG 58.958 47.826 0.00 0.00 32.80 3.86
2235 2660 1.767289 CGATTACCTGGACGGATTCG 58.233 55.000 0.00 0.00 43.02 3.34
2242 2667 6.845669 ATCCAGCTATAGCGATTACCTGGAC 61.846 48.000 24.12 0.00 46.96 4.02
2257 2682 8.713708 ATAACACTAGTAACTGATCCAGCTAT 57.286 34.615 0.00 0.00 34.37 2.97
2258 2683 8.534954 AATAACACTAGTAACTGATCCAGCTA 57.465 34.615 0.00 0.00 34.37 3.32
2259 2684 7.425224 AATAACACTAGTAACTGATCCAGCT 57.575 36.000 0.00 0.00 34.37 4.24
2308 2733 8.633075 TTGATTTGTCAATTTCTCACTTTGTC 57.367 30.769 0.00 0.00 0.00 3.18
2366 2791 0.318699 CTCTCGCCACAAGTCACGAA 60.319 55.000 0.00 0.00 33.61 3.85
2367 2792 1.285950 CTCTCGCCACAAGTCACGA 59.714 57.895 0.00 0.00 0.00 4.35
2368 2793 2.375766 GCTCTCGCCACAAGTCACG 61.376 63.158 0.00 0.00 0.00 4.35
2369 2794 0.671781 ATGCTCTCGCCACAAGTCAC 60.672 55.000 0.00 0.00 34.43 3.67
2370 2795 0.671472 CATGCTCTCGCCACAAGTCA 60.671 55.000 0.00 0.00 34.43 3.41
2371 2796 1.364626 CCATGCTCTCGCCACAAGTC 61.365 60.000 0.00 0.00 34.43 3.01
2372 2797 1.376424 CCATGCTCTCGCCACAAGT 60.376 57.895 0.00 0.00 34.43 3.16
2373 2798 1.078918 TCCATGCTCTCGCCACAAG 60.079 57.895 0.00 0.00 34.43 3.16
2374 2799 1.078918 CTCCATGCTCTCGCCACAA 60.079 57.895 0.00 0.00 34.43 3.33
2375 2800 1.984026 TCTCCATGCTCTCGCCACA 60.984 57.895 0.00 0.00 34.43 4.17
2376 2801 1.520342 GTCTCCATGCTCTCGCCAC 60.520 63.158 0.00 0.00 34.43 5.01
2377 2802 2.725312 GGTCTCCATGCTCTCGCCA 61.725 63.158 0.00 0.00 34.43 5.69
2378 2803 2.107953 GGTCTCCATGCTCTCGCC 59.892 66.667 0.00 0.00 34.43 5.54
2379 2804 1.067250 GAGGTCTCCATGCTCTCGC 59.933 63.158 0.00 0.00 0.00 5.03
2390 2815 0.311477 GGCGACGATTAGGAGGTCTC 59.689 60.000 0.00 0.00 0.00 3.36
2391 2816 0.106619 AGGCGACGATTAGGAGGTCT 60.107 55.000 0.00 0.00 0.00 3.85
2392 2817 0.745468 AAGGCGACGATTAGGAGGTC 59.255 55.000 0.00 0.00 0.00 3.85
2393 2818 0.745468 GAAGGCGACGATTAGGAGGT 59.255 55.000 0.00 0.00 0.00 3.85
2394 2819 1.033574 AGAAGGCGACGATTAGGAGG 58.966 55.000 0.00 0.00 0.00 4.30
2395 2820 1.866063 GCAGAAGGCGACGATTAGGAG 60.866 57.143 0.00 0.00 0.00 3.69
2396 2821 0.102481 GCAGAAGGCGACGATTAGGA 59.898 55.000 0.00 0.00 0.00 2.94
2397 2822 2.594541 GCAGAAGGCGACGATTAGG 58.405 57.895 0.00 0.00 0.00 2.69
2407 2832 0.384669 ACCTATACGACGCAGAAGGC 59.615 55.000 0.00 0.00 39.90 4.35
2408 2833 1.404391 ACACCTATACGACGCAGAAGG 59.596 52.381 0.00 0.00 0.00 3.46
2409 2834 2.846039 ACACCTATACGACGCAGAAG 57.154 50.000 0.00 0.00 0.00 2.85
2410 2835 2.488937 TGAACACCTATACGACGCAGAA 59.511 45.455 0.00 0.00 0.00 3.02
2411 2836 2.086094 TGAACACCTATACGACGCAGA 58.914 47.619 0.00 0.00 0.00 4.26
2412 2837 2.182825 GTGAACACCTATACGACGCAG 58.817 52.381 0.00 0.00 0.00 5.18
2413 2838 1.466192 CGTGAACACCTATACGACGCA 60.466 52.381 0.00 0.00 38.72 5.24
2414 2839 1.186030 CGTGAACACCTATACGACGC 58.814 55.000 0.00 0.00 38.72 5.19
2415 2840 1.186030 GCGTGAACACCTATACGACG 58.814 55.000 0.00 0.00 38.72 5.12
2416 2841 1.186030 CGCGTGAACACCTATACGAC 58.814 55.000 0.00 0.00 38.72 4.34
2417 2842 0.523968 GCGCGTGAACACCTATACGA 60.524 55.000 8.43 0.00 38.72 3.43
2418 2843 1.477030 GGCGCGTGAACACCTATACG 61.477 60.000 8.43 0.00 39.37 3.06
2419 2844 1.149964 GGGCGCGTGAACACCTATAC 61.150 60.000 8.43 0.00 0.00 1.47
2420 2845 1.142314 GGGCGCGTGAACACCTATA 59.858 57.895 8.43 0.00 0.00 1.31
2421 2846 2.125269 GGGCGCGTGAACACCTAT 60.125 61.111 8.43 0.00 0.00 2.57
2422 2847 3.617735 TGGGCGCGTGAACACCTA 61.618 61.111 8.43 0.00 0.00 3.08
2435 2860 4.722855 ATTTGCTTGCGCGTGGGC 62.723 61.111 8.43 10.14 39.65 5.36
2436 2861 1.664333 AAATTTGCTTGCGCGTGGG 60.664 52.632 8.43 0.00 39.65 4.61
2437 2862 1.488093 CAAATTTGCTTGCGCGTGG 59.512 52.632 8.43 0.00 39.65 4.94
2448 2873 2.028733 GTGGGCCAGCGCAAATTTG 61.029 57.895 6.40 14.03 40.51 2.32
2449 2874 2.343387 GTGGGCCAGCGCAAATTT 59.657 55.556 6.40 0.00 40.51 1.82
2450 2875 3.694538 GGTGGGCCAGCGCAAATT 61.695 61.111 21.35 0.00 40.51 1.82
2451 2876 4.992740 TGGTGGGCCAGCGCAAAT 62.993 61.111 28.77 0.00 40.46 2.32
2462 2887 4.899239 GATCGCTCGCCTGGTGGG 62.899 72.222 7.51 4.80 38.36 4.61
2488 2913 1.832219 TCAACAGCTGACCAGTGCT 59.168 52.632 23.35 0.00 40.54 4.40
2489 2914 4.462394 TCAACAGCTGACCAGTGC 57.538 55.556 23.35 0.00 0.00 4.40
2496 2921 1.662517 TCGCAAAAGTCAACAGCTGA 58.337 45.000 23.35 0.00 0.00 4.26
2497 2922 2.473530 TTCGCAAAAGTCAACAGCTG 57.526 45.000 13.48 13.48 0.00 4.24
2498 2923 3.502191 TTTTCGCAAAAGTCAACAGCT 57.498 38.095 0.00 0.00 0.00 4.24
2499 2924 3.366422 TGTTTTTCGCAAAAGTCAACAGC 59.634 39.130 0.00 0.00 32.32 4.40
2500 2925 4.384247 TGTGTTTTTCGCAAAAGTCAACAG 59.616 37.500 0.00 0.00 32.32 3.16
2501 2926 4.299155 TGTGTTTTTCGCAAAAGTCAACA 58.701 34.783 0.00 0.00 32.32 3.33
2502 2927 4.894798 TGTGTTTTTCGCAAAAGTCAAC 57.105 36.364 0.00 0.00 32.32 3.18
2510 2935 5.907197 TTGTTCTTTTGTGTTTTTCGCAA 57.093 30.435 0.00 0.00 43.56 4.85
2511 2936 5.907197 TTTGTTCTTTTGTGTTTTTCGCA 57.093 30.435 0.00 0.00 34.52 5.10
2512 2937 7.066505 TCTTTTTGTTCTTTTGTGTTTTTCGC 58.933 30.769 0.00 0.00 0.00 4.70
2513 2938 8.979817 TTCTTTTTGTTCTTTTGTGTTTTTCG 57.020 26.923 0.00 0.00 0.00 3.46
2516 2941 9.877137 GTGATTCTTTTTGTTCTTTTGTGTTTT 57.123 25.926 0.00 0.00 0.00 2.43
2517 2942 9.050601 TGTGATTCTTTTTGTTCTTTTGTGTTT 57.949 25.926 0.00 0.00 0.00 2.83
2518 2943 8.600449 TGTGATTCTTTTTGTTCTTTTGTGTT 57.400 26.923 0.00 0.00 0.00 3.32
2519 2944 8.600449 TTGTGATTCTTTTTGTTCTTTTGTGT 57.400 26.923 0.00 0.00 0.00 3.72
2520 2945 9.316859 GTTTGTGATTCTTTTTGTTCTTTTGTG 57.683 29.630 0.00 0.00 0.00 3.33
2521 2946 9.050601 TGTTTGTGATTCTTTTTGTTCTTTTGT 57.949 25.926 0.00 0.00 0.00 2.83
2522 2947 9.875675 TTGTTTGTGATTCTTTTTGTTCTTTTG 57.124 25.926 0.00 0.00 0.00 2.44
2526 2951 9.434420 TCAATTGTTTGTGATTCTTTTTGTTCT 57.566 25.926 5.13 0.00 34.32 3.01
2557 2982 9.881529 CCATGAAAATTTTGAATTCACGAAATT 57.118 25.926 18.71 18.71 42.24 1.82
2558 2983 9.270640 TCCATGAAAATTTTGAATTCACGAAAT 57.729 25.926 7.89 9.75 36.03 2.17
2559 2984 8.654230 TCCATGAAAATTTTGAATTCACGAAA 57.346 26.923 7.89 7.69 36.03 3.46
2560 2985 8.830201 ATCCATGAAAATTTTGAATTCACGAA 57.170 26.923 7.89 6.77 36.03 3.85
2561 2986 8.830201 AATCCATGAAAATTTTGAATTCACGA 57.170 26.923 7.89 0.00 36.03 4.35
2562 2987 9.320406 CAAATCCATGAAAATTTTGAATTCACG 57.680 29.630 7.89 0.00 36.03 4.35
2655 3080 8.466798 CCGTAAACTTTTTCCTAATCCATGATT 58.533 33.333 0.00 0.00 36.20 2.57
2656 3081 7.832187 TCCGTAAACTTTTTCCTAATCCATGAT 59.168 33.333 0.00 0.00 0.00 2.45
2657 3082 7.169591 TCCGTAAACTTTTTCCTAATCCATGA 58.830 34.615 0.00 0.00 0.00 3.07
2658 3083 7.385778 TCCGTAAACTTTTTCCTAATCCATG 57.614 36.000 0.00 0.00 0.00 3.66
2659 3084 8.589701 AATCCGTAAACTTTTTCCTAATCCAT 57.410 30.769 0.00 0.00 0.00 3.41
2660 3085 8.411991 AAATCCGTAAACTTTTTCCTAATCCA 57.588 30.769 0.00 0.00 0.00 3.41
2661 3086 9.135843 CAAAATCCGTAAACTTTTTCCTAATCC 57.864 33.333 0.00 0.00 0.00 3.01
2662 3087 9.902196 TCAAAATCCGTAAACTTTTTCCTAATC 57.098 29.630 0.00 0.00 0.00 1.75
2663 3088 9.687210 GTCAAAATCCGTAAACTTTTTCCTAAT 57.313 29.630 0.00 0.00 0.00 1.73
2664 3089 8.684520 TGTCAAAATCCGTAAACTTTTTCCTAA 58.315 29.630 0.00 0.00 0.00 2.69
2665 3090 8.223177 TGTCAAAATCCGTAAACTTTTTCCTA 57.777 30.769 0.00 0.00 0.00 2.94
2666 3091 7.067737 TCTGTCAAAATCCGTAAACTTTTTCCT 59.932 33.333 0.00 0.00 0.00 3.36
2667 3092 7.197703 TCTGTCAAAATCCGTAAACTTTTTCC 58.802 34.615 0.00 0.00 0.00 3.13
2668 3093 8.623310 TTCTGTCAAAATCCGTAAACTTTTTC 57.377 30.769 0.00 0.00 0.00 2.29
2669 3094 8.989653 TTTCTGTCAAAATCCGTAAACTTTTT 57.010 26.923 0.00 0.00 0.00 1.94
2670 3095 8.989653 TTTTCTGTCAAAATCCGTAAACTTTT 57.010 26.923 0.00 0.00 0.00 2.27
2671 3096 8.989653 TTTTTCTGTCAAAATCCGTAAACTTT 57.010 26.923 0.00 0.00 0.00 2.66
2672 3097 9.594478 AATTTTTCTGTCAAAATCCGTAAACTT 57.406 25.926 0.00 0.00 35.67 2.66
2673 3098 9.594478 AAATTTTTCTGTCAAAATCCGTAAACT 57.406 25.926 0.00 0.00 35.67 2.66
2674 3099 9.631639 CAAATTTTTCTGTCAAAATCCGTAAAC 57.368 29.630 0.00 0.00 35.67 2.01
2675 3100 9.587772 TCAAATTTTTCTGTCAAAATCCGTAAA 57.412 25.926 0.00 0.00 35.67 2.01
2676 3101 9.243637 CTCAAATTTTTCTGTCAAAATCCGTAA 57.756 29.630 0.00 0.00 35.67 3.18
2677 3102 7.865385 CCTCAAATTTTTCTGTCAAAATCCGTA 59.135 33.333 0.00 0.00 35.67 4.02
2678 3103 6.701400 CCTCAAATTTTTCTGTCAAAATCCGT 59.299 34.615 0.00 0.00 35.67 4.69
2679 3104 6.922957 TCCTCAAATTTTTCTGTCAAAATCCG 59.077 34.615 0.00 0.00 35.67 4.18
2680 3105 8.837788 ATCCTCAAATTTTTCTGTCAAAATCC 57.162 30.769 0.00 0.00 35.67 3.01
2683 3108 9.664332 TCAAATCCTCAAATTTTTCTGTCAAAA 57.336 25.926 0.00 0.00 0.00 2.44
2684 3109 9.664332 TTCAAATCCTCAAATTTTTCTGTCAAA 57.336 25.926 0.00 0.00 0.00 2.69
2685 3110 9.664332 TTTCAAATCCTCAAATTTTTCTGTCAA 57.336 25.926 0.00 0.00 0.00 3.18
2686 3111 9.664332 TTTTCAAATCCTCAAATTTTTCTGTCA 57.336 25.926 0.00 0.00 0.00 3.58
2732 3157 9.553418 CAAACTTTTTCCAAATTCGTGATTTTT 57.447 25.926 0.00 0.00 35.79 1.94
2733 3158 8.726068 ACAAACTTTTTCCAAATTCGTGATTTT 58.274 25.926 0.00 0.00 35.79 1.82
2734 3159 8.174422 CACAAACTTTTTCCAAATTCGTGATTT 58.826 29.630 0.00 0.00 38.49 2.17
2735 3160 7.201600 CCACAAACTTTTTCCAAATTCGTGATT 60.202 33.333 0.00 0.00 0.00 2.57
2736 3161 6.257630 CCACAAACTTTTTCCAAATTCGTGAT 59.742 34.615 0.00 0.00 0.00 3.06
2737 3162 5.578727 CCACAAACTTTTTCCAAATTCGTGA 59.421 36.000 0.00 0.00 0.00 4.35
2738 3163 5.578727 TCCACAAACTTTTTCCAAATTCGTG 59.421 36.000 0.00 0.00 0.00 4.35
2739 3164 5.725362 TCCACAAACTTTTTCCAAATTCGT 58.275 33.333 0.00 0.00 0.00 3.85
2740 3165 6.843069 ATCCACAAACTTTTTCCAAATTCG 57.157 33.333 0.00 0.00 0.00 3.34
2743 3168 9.898152 TCTAAAATCCACAAACTTTTTCCAAAT 57.102 25.926 0.00 0.00 0.00 2.32
2744 3169 9.898152 ATCTAAAATCCACAAACTTTTTCCAAA 57.102 25.926 0.00 0.00 0.00 3.28
2788 3213 9.260002 GTTCAAATACACTCAAATGGACAAAAT 57.740 29.630 0.00 0.00 0.00 1.82
2789 3214 8.253810 TGTTCAAATACACTCAAATGGACAAAA 58.746 29.630 0.00 0.00 0.00 2.44
2790 3215 7.776107 TGTTCAAATACACTCAAATGGACAAA 58.224 30.769 0.00 0.00 0.00 2.83
2791 3216 7.340122 TGTTCAAATACACTCAAATGGACAA 57.660 32.000 0.00 0.00 0.00 3.18
2792 3217 6.951062 TGTTCAAATACACTCAAATGGACA 57.049 33.333 0.00 0.00 0.00 4.02
2793 3218 7.920682 ACTTTGTTCAAATACACTCAAATGGAC 59.079 33.333 0.00 0.00 0.00 4.02
2794 3219 8.006298 ACTTTGTTCAAATACACTCAAATGGA 57.994 30.769 0.00 0.00 0.00 3.41
2795 3220 8.647143 AACTTTGTTCAAATACACTCAAATGG 57.353 30.769 0.00 0.00 0.00 3.16
2796 3221 9.299963 TGAACTTTGTTCAAATACACTCAAATG 57.700 29.630 10.25 0.00 0.00 2.32
2798 3223 9.868277 AATGAACTTTGTTCAAATACACTCAAA 57.132 25.926 15.61 0.00 31.55 2.69
2799 3224 9.299963 CAATGAACTTTGTTCAAATACACTCAA 57.700 29.630 15.61 0.00 31.55 3.02
2800 3225 7.920151 CCAATGAACTTTGTTCAAATACACTCA 59.080 33.333 15.61 0.00 31.55 3.41
2801 3226 8.134895 TCCAATGAACTTTGTTCAAATACACTC 58.865 33.333 15.61 0.00 31.55 3.51
2802 3227 8.006298 TCCAATGAACTTTGTTCAAATACACT 57.994 30.769 15.61 0.00 31.55 3.55
2803 3228 8.816640 ATCCAATGAACTTTGTTCAAATACAC 57.183 30.769 15.61 0.00 31.55 2.90
2804 3229 9.474920 GAATCCAATGAACTTTGTTCAAATACA 57.525 29.630 15.61 2.31 31.55 2.29
2805 3230 9.474920 TGAATCCAATGAACTTTGTTCAAATAC 57.525 29.630 15.61 6.39 31.55 1.89
2807 3232 8.961294 TTGAATCCAATGAACTTTGTTCAAAT 57.039 26.923 15.61 6.72 32.85 2.32
2808 3233 8.961294 ATTGAATCCAATGAACTTTGTTCAAA 57.039 26.923 15.61 5.19 41.18 2.69
2809 3234 8.961294 AATTGAATCCAATGAACTTTGTTCAA 57.039 26.923 15.61 14.73 41.84 2.69
2810 3235 8.961294 AAATTGAATCCAATGAACTTTGTTCA 57.039 26.923 14.29 14.29 41.84 3.18
2813 3238 9.393512 TGAAAAATTGAATCCAATGAACTTTGT 57.606 25.926 0.00 0.00 41.84 2.83
2814 3239 9.872757 CTGAAAAATTGAATCCAATGAACTTTG 57.127 29.630 0.00 0.00 41.84 2.77
2815 3240 9.059260 CCTGAAAAATTGAATCCAATGAACTTT 57.941 29.630 0.00 0.00 41.84 2.66
2816 3241 8.431222 TCCTGAAAAATTGAATCCAATGAACTT 58.569 29.630 0.00 0.00 41.84 2.66
2817 3242 7.965718 TCCTGAAAAATTGAATCCAATGAACT 58.034 30.769 0.00 0.00 41.84 3.01
2818 3243 8.606040 TTCCTGAAAAATTGAATCCAATGAAC 57.394 30.769 0.00 0.00 41.84 3.18
2819 3244 9.796180 AATTCCTGAAAAATTGAATCCAATGAA 57.204 25.926 0.00 0.00 41.84 2.57
2820 3245 9.796180 AAATTCCTGAAAAATTGAATCCAATGA 57.204 25.926 0.00 0.00 41.84 2.57
2821 3246 9.834628 CAAATTCCTGAAAAATTGAATCCAATG 57.165 29.630 0.00 0.00 41.84 2.82
2822 3247 9.796180 TCAAATTCCTGAAAAATTGAATCCAAT 57.204 25.926 0.00 0.00 44.38 3.16
2823 3248 9.624373 TTCAAATTCCTGAAAAATTGAATCCAA 57.376 25.926 11.53 0.00 32.39 3.53
2824 3249 9.624373 TTTCAAATTCCTGAAAAATTGAATCCA 57.376 25.926 14.25 4.04 41.25 3.41
2835 3260 7.382110 TGTGAACTGTTTTCAAATTCCTGAAA 58.618 30.769 1.91 1.91 42.21 2.69
2836 3261 6.929625 TGTGAACTGTTTTCAAATTCCTGAA 58.070 32.000 0.00 0.00 33.48 3.02
2837 3262 6.522625 TGTGAACTGTTTTCAAATTCCTGA 57.477 33.333 0.00 0.00 0.00 3.86
2838 3263 6.757947 ACATGTGAACTGTTTTCAAATTCCTG 59.242 34.615 0.00 0.00 0.00 3.86
2839 3264 6.877236 ACATGTGAACTGTTTTCAAATTCCT 58.123 32.000 0.00 0.00 0.00 3.36
2840 3265 7.538303 AACATGTGAACTGTTTTCAAATTCC 57.462 32.000 0.00 0.00 33.10 3.01
2869 3294 5.845391 TCTTCAAATCCGTGAACCTTTTT 57.155 34.783 0.00 0.00 33.92 1.94
2870 3295 5.845391 TTCTTCAAATCCGTGAACCTTTT 57.155 34.783 0.00 0.00 33.92 2.27
2871 3296 5.845391 TTTCTTCAAATCCGTGAACCTTT 57.155 34.783 0.00 0.00 33.92 3.11
2872 3297 6.405278 AATTTCTTCAAATCCGTGAACCTT 57.595 33.333 0.00 0.00 33.92 3.50
2873 3298 6.405278 AAATTTCTTCAAATCCGTGAACCT 57.595 33.333 0.00 0.00 33.92 3.50
2874 3299 5.633601 GGAAATTTCTTCAAATCCGTGAACC 59.366 40.000 17.42 0.00 33.92 3.62
2875 3300 6.212955 TGGAAATTTCTTCAAATCCGTGAAC 58.787 36.000 17.42 0.00 33.92 3.18
2876 3301 6.398234 TGGAAATTTCTTCAAATCCGTGAA 57.602 33.333 17.42 0.00 36.15 3.18
2877 3302 6.398234 TTGGAAATTTCTTCAAATCCGTGA 57.602 33.333 17.42 0.00 30.37 4.35
2878 3303 6.646240 ACATTGGAAATTTCTTCAAATCCGTG 59.354 34.615 17.42 10.70 30.37 4.94
2879 3304 6.758254 ACATTGGAAATTTCTTCAAATCCGT 58.242 32.000 17.42 8.05 30.37 4.69
2880 3305 7.656707 AACATTGGAAATTTCTTCAAATCCG 57.343 32.000 17.42 7.56 30.37 4.18
2892 3317 9.804977 TGGGATTTGATAAAAACATTGGAAATT 57.195 25.926 0.00 0.00 0.00 1.82
2893 3318 9.230122 GTGGGATTTGATAAAAACATTGGAAAT 57.770 29.630 0.00 0.00 0.00 2.17
2894 3319 8.213679 TGTGGGATTTGATAAAAACATTGGAAA 58.786 29.630 0.00 0.00 0.00 3.13
2895 3320 7.739825 TGTGGGATTTGATAAAAACATTGGAA 58.260 30.769 0.00 0.00 0.00 3.53
2896 3321 7.308450 TGTGGGATTTGATAAAAACATTGGA 57.692 32.000 0.00 0.00 0.00 3.53
2897 3322 9.835389 ATATGTGGGATTTGATAAAAACATTGG 57.165 29.630 0.00 0.00 0.00 3.16
2963 3388 6.806739 GCAGTGTGTTTTCTTCTAGTGTTTTT 59.193 34.615 0.00 0.00 0.00 1.94
2964 3389 6.072175 TGCAGTGTGTTTTCTTCTAGTGTTTT 60.072 34.615 0.00 0.00 0.00 2.43
2965 3390 5.414454 TGCAGTGTGTTTTCTTCTAGTGTTT 59.586 36.000 0.00 0.00 0.00 2.83
2966 3391 4.941263 TGCAGTGTGTTTTCTTCTAGTGTT 59.059 37.500 0.00 0.00 0.00 3.32
2967 3392 4.513442 TGCAGTGTGTTTTCTTCTAGTGT 58.487 39.130 0.00 0.00 0.00 3.55
2968 3393 5.484173 TTGCAGTGTGTTTTCTTCTAGTG 57.516 39.130 0.00 0.00 0.00 2.74
2969 3394 6.511767 CGAATTGCAGTGTGTTTTCTTCTAGT 60.512 38.462 0.00 0.00 0.00 2.57
2970 3395 5.848036 CGAATTGCAGTGTGTTTTCTTCTAG 59.152 40.000 0.00 0.00 0.00 2.43
2971 3396 5.295787 ACGAATTGCAGTGTGTTTTCTTCTA 59.704 36.000 0.00 0.00 0.00 2.10
2972 3397 4.096382 ACGAATTGCAGTGTGTTTTCTTCT 59.904 37.500 0.00 0.00 0.00 2.85
2973 3398 4.351192 ACGAATTGCAGTGTGTTTTCTTC 58.649 39.130 0.00 0.00 0.00 2.87
2974 3399 4.370364 ACGAATTGCAGTGTGTTTTCTT 57.630 36.364 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.