Multiple sequence alignment - TraesCS3A01G035800

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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 TraesCS3A01G035800 chr3A 100.000 2813 0 0 1 2813 19861762 19864574 0.000000e+00 5195.0
1 TraesCS3A01G035800 chr3A 89.130 46 4 1 222 267 696374381 696374337 3.910000e-04 56.5
2 TraesCS3A01G035800 chr3D 90.312 1600 83 33 543 2092 17012358 17010781 0.000000e+00 2030.0
3 TraesCS3A01G035800 chr3D 89.397 547 30 11 1 543 17012933 17012411 0.000000e+00 664.0
4 TraesCS3A01G035800 chr3D 83.698 411 18 13 2196 2557 17010730 17010320 2.680000e-90 342.0
5 TraesCS3A01G035800 chr3D 93.182 44 1 1 2557 2598 17010305 17010262 2.340000e-06 63.9
6 TraesCS3A01G035800 chr3B 89.765 1534 57 34 626 2090 24410673 24409171 0.000000e+00 1871.0
7 TraesCS3A01G035800 chr3B 91.557 533 37 7 21 547 24411371 24410841 0.000000e+00 728.0
8 TraesCS3A01G035800 chr3B 89.100 211 13 3 2190 2390 24409136 24408926 1.290000e-63 254.0
9 TraesCS3A01G035800 chr2D 88.398 362 30 6 1196 1557 12874389 12874738 2.590000e-115 425.0
10 TraesCS3A01G035800 chr7D 100.000 28 0 0 223 250 18880319 18880346 5.000000e-03 52.8


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 TraesCS3A01G035800 chr3A 19861762 19864574 2812 False 5195.000 5195 100.000000 1 2813 1 chr3A.!!$F1 2812
1 TraesCS3A01G035800 chr3D 17010262 17012933 2671 True 774.975 2030 89.147250 1 2598 4 chr3D.!!$R1 2597
2 TraesCS3A01G035800 chr3B 24408926 24411371 2445 True 951.000 1871 90.140667 21 2390 3 chr3B.!!$R1 2369

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
706 826 0.179161 TCAAACGGCAAAACACACGG 60.179 50.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2383 0.036388 ATTGCAACGGAGGTCGATGT 60.036 50.0 0.0 0.0 42.53 3.06 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
170 171 0.611618 ATTTGTGAAGCGGCCATGGA 60.612 50.000 18.40 0.00 0.00 3.41
288 291 7.544804 AAAGGGGCTAATGGAATTTATCATC 57.455 36.000 0.00 0.00 37.87 2.92
290 293 4.399303 GGGGCTAATGGAATTTATCATCGG 59.601 45.833 0.00 0.00 37.87 4.18
298 301 6.866010 TGGAATTTATCATCGGATGAGTTG 57.134 37.500 23.59 0.00 43.53 3.16
306 309 4.748892 TCATCGGATGAGTTGAAAGAGTC 58.251 43.478 16.44 0.00 33.59 3.36
350 353 8.408043 ACAGATTCCAATACTGTTTTTCATGA 57.592 30.769 0.00 0.00 41.21 3.07
351 354 8.859090 ACAGATTCCAATACTGTTTTTCATGAA 58.141 29.630 3.38 3.38 41.21 2.57
352 355 9.695526 CAGATTCCAATACTGTTTTTCATGAAA 57.304 29.630 16.91 16.91 0.00 2.69
356 359 9.829507 TTCCAATACTGTTTTTCATGAAAATGT 57.170 25.926 29.13 26.34 39.69 2.71
397 423 6.665465 ACCTCGCTACTGAATTGTTTTAAAC 58.335 36.000 0.20 0.20 0.00 2.01
500 527 4.864704 TTGTAAAGAGGGCATGGTTTTC 57.135 40.909 0.00 0.00 0.00 2.29
509 539 2.029470 GGGCATGGTTTTCGTCATCAAA 60.029 45.455 0.00 0.00 0.00 2.69
624 711 5.163622 GGCGATCCATATGTAATGAAATGGG 60.164 44.000 1.24 0.00 39.51 4.00
686 806 2.895039 GTGTACACACCAGTCCACG 58.105 57.895 21.14 0.00 40.85 4.94
703 823 3.314339 CGTCAAACGGCAAAACACA 57.686 47.368 0.00 0.00 38.08 3.72
705 825 0.911184 GTCAAACGGCAAAACACACG 59.089 50.000 0.00 0.00 0.00 4.49
706 826 0.179161 TCAAACGGCAAAACACACGG 60.179 50.000 0.00 0.00 0.00 4.94
715 835 1.815613 CAAAACACACGGCATCCCATA 59.184 47.619 0.00 0.00 0.00 2.74
733 853 9.533253 CATCCCATAATAATCCACAAAGAAAAC 57.467 33.333 0.00 0.00 0.00 2.43
751 882 6.846350 AGAAAACATAAATCAGAGGCGAAAG 58.154 36.000 0.00 0.00 0.00 2.62
1641 1809 0.809385 TCGATGTGAGTTCGTCCCTC 59.191 55.000 0.00 0.00 37.82 4.30
1643 1811 0.179134 GATGTGAGTTCGTCCCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
1670 1839 1.457455 CTCCTCTGCTCCTCCCCTC 60.457 68.421 0.00 0.00 0.00 4.30
1672 1841 2.445654 CTCTGCTCCTCCCCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
1852 2022 1.956477 ACCCAACAGTAAGCAAAGCAG 59.044 47.619 0.00 0.00 0.00 4.24
1877 2052 0.304705 ATTCGCCGATCGCAATTCAC 59.695 50.000 10.32 0.00 37.30 3.18
1878 2053 1.016653 TTCGCCGATCGCAATTCACA 61.017 50.000 10.32 0.00 37.30 3.58
1890 2068 4.922692 TCGCAATTCACAAATCAATTGGTC 59.077 37.500 5.42 0.00 43.66 4.02
1939 2122 8.757982 ATCCATCCATTAATTGGTCATATAGC 57.242 34.615 4.88 0.00 46.52 2.97
1970 2157 5.698104 TGATATGAATCCCAGCATTGAACT 58.302 37.500 0.00 0.00 0.00 3.01
2002 2209 3.242518 CAGCAAGTGCAAGTGATGATTG 58.757 45.455 9.89 0.00 45.16 2.67
2023 2230 7.341512 TGATTGATGACTAGTCAGTGATTCTCT 59.658 37.037 28.29 10.34 43.61 3.10
2024 2231 6.448207 TGATGACTAGTCAGTGATTCTCTG 57.552 41.667 28.29 9.04 43.61 3.35
2026 2233 4.667573 TGACTAGTCAGTGATTCTCTGGT 58.332 43.478 21.74 0.00 34.21 4.00
2030 2237 6.959904 ACTAGTCAGTGATTCTCTGGTAGTA 58.040 40.000 19.37 9.17 34.52 1.82
2031 2238 7.051623 ACTAGTCAGTGATTCTCTGGTAGTAG 58.948 42.308 19.37 16.20 34.52 2.57
2032 2239 4.642885 AGTCAGTGATTCTCTGGTAGTAGC 59.357 45.833 14.07 0.00 34.15 3.58
2044 2251 0.319405 GTAGTAGCGGTGGTTGTGGT 59.681 55.000 0.00 0.00 0.00 4.16
2050 2257 0.952010 GCGGTGGTTGTGGTTCGTAT 60.952 55.000 0.00 0.00 0.00 3.06
2051 2258 1.073177 CGGTGGTTGTGGTTCGTATC 58.927 55.000 0.00 0.00 0.00 2.24
2055 2262 2.347452 GTGGTTGTGGTTCGTATCATCG 59.653 50.000 0.00 0.00 0.00 3.84
2074 2281 1.612146 TCAGCGGATTGGGAGGACA 60.612 57.895 0.00 0.00 0.00 4.02
2091 2298 3.025924 CACAATGTGGTGTGCTCCT 57.974 52.632 5.29 0.00 42.26 3.69
2092 2299 2.183478 CACAATGTGGTGTGCTCCTA 57.817 50.000 5.29 0.00 42.26 2.94
2093 2300 2.503331 CACAATGTGGTGTGCTCCTAA 58.497 47.619 5.29 0.00 42.26 2.69
2094 2301 2.485426 CACAATGTGGTGTGCTCCTAAG 59.515 50.000 5.29 0.00 42.26 2.18
2095 2302 2.106511 ACAATGTGGTGTGCTCCTAAGT 59.893 45.455 0.00 0.00 0.00 2.24
2096 2303 2.479566 ATGTGGTGTGCTCCTAAGTG 57.520 50.000 0.00 0.00 0.00 3.16
2097 2304 0.250295 TGTGGTGTGCTCCTAAGTGC 60.250 55.000 0.00 0.00 0.00 4.40
2098 2305 0.250295 GTGGTGTGCTCCTAAGTGCA 60.250 55.000 0.00 0.00 40.06 4.57
2133 2340 5.046878 TGGTCCACTCAGTACAATCGTTAAT 60.047 40.000 0.00 0.00 0.00 1.40
2134 2341 5.873164 GGTCCACTCAGTACAATCGTTAATT 59.127 40.000 0.00 0.00 0.00 1.40
2136 2343 7.094933 GGTCCACTCAGTACAATCGTTAATTTT 60.095 37.037 0.00 0.00 0.00 1.82
2184 2391 8.123445 AGTACAATCGTTAATTAACATCGACC 57.877 34.615 24.27 9.09 35.99 4.79
2185 2392 7.977853 AGTACAATCGTTAATTAACATCGACCT 59.022 33.333 24.27 10.82 35.99 3.85
2186 2393 7.230466 ACAATCGTTAATTAACATCGACCTC 57.770 36.000 24.27 0.00 35.99 3.85
2187 2394 6.257193 ACAATCGTTAATTAACATCGACCTCC 59.743 38.462 24.27 0.00 35.99 4.30
2188 2395 4.353737 TCGTTAATTAACATCGACCTCCG 58.646 43.478 24.27 9.45 35.99 4.63
2208 2415 3.168963 CGTTGCAATCTCAATGCTTCTG 58.831 45.455 0.59 0.00 44.14 3.02
2229 2436 4.309099 TGCTGTGCATGGAAATTTTTCTC 58.691 39.130 0.00 0.00 33.81 2.87
2236 2443 7.134163 GTGCATGGAAATTTTTCTCCTTTTTG 58.866 34.615 0.00 0.00 37.35 2.44
2307 2525 4.410400 GAGCACGGGGAGGGTTGG 62.410 72.222 0.00 0.00 0.00 3.77
2454 2709 1.979155 CAGTGAGGGCCGAGTGAGA 60.979 63.158 7.47 0.00 0.00 3.27
2512 2770 4.373116 CCCTGTCGTGGTCGTGGG 62.373 72.222 0.00 0.00 37.08 4.61
2534 2792 0.863799 GTTCCCCAAGTTCGTTCGTC 59.136 55.000 0.00 0.00 0.00 4.20
2562 2820 4.389576 GCGCGCTTTGTGGGTGAG 62.390 66.667 26.67 0.00 40.95 3.51
2563 2821 3.726517 CGCGCTTTGTGGGTGAGG 61.727 66.667 5.56 0.00 40.95 3.86
2598 2873 2.224217 CGTCCACGCACGCTCTATG 61.224 63.158 0.00 0.00 31.96 2.23
2599 2874 1.878522 GTCCACGCACGCTCTATGG 60.879 63.158 0.00 0.00 0.00 2.74
2600 2875 2.586079 CCACGCACGCTCTATGGG 60.586 66.667 0.00 0.00 36.17 4.00
2601 2876 3.264897 CACGCACGCTCTATGGGC 61.265 66.667 0.00 0.00 33.49 5.36
2602 2877 3.461773 ACGCACGCTCTATGGGCT 61.462 61.111 0.00 0.00 33.49 5.19
2603 2878 2.125326 ACGCACGCTCTATGGGCTA 61.125 57.895 0.00 0.00 33.49 3.93
2604 2879 1.290324 CGCACGCTCTATGGGCTAT 59.710 57.895 0.00 0.00 0.00 2.97
2605 2880 1.010935 CGCACGCTCTATGGGCTATG 61.011 60.000 0.00 0.00 0.00 2.23
2606 2881 0.671781 GCACGCTCTATGGGCTATGG 60.672 60.000 0.00 0.00 0.00 2.74
2607 2882 0.671781 CACGCTCTATGGGCTATGGC 60.672 60.000 0.00 0.00 37.82 4.40
2608 2883 0.833834 ACGCTCTATGGGCTATGGCT 60.834 55.000 0.00 0.00 38.73 4.75
2609 2884 0.390866 CGCTCTATGGGCTATGGCTG 60.391 60.000 0.00 0.00 38.73 4.85
2610 2885 0.979665 GCTCTATGGGCTATGGCTGA 59.020 55.000 0.00 0.00 38.73 4.26
2611 2886 1.338579 GCTCTATGGGCTATGGCTGAC 60.339 57.143 0.00 0.00 38.73 3.51
2612 2887 1.973515 CTCTATGGGCTATGGCTGACA 59.026 52.381 0.00 0.00 38.73 3.58
2613 2888 1.694150 TCTATGGGCTATGGCTGACAC 59.306 52.381 0.00 0.00 38.73 3.67
2614 2889 1.696336 CTATGGGCTATGGCTGACACT 59.304 52.381 0.00 0.00 38.73 3.55
2615 2890 1.806496 ATGGGCTATGGCTGACACTA 58.194 50.000 0.00 0.00 38.73 2.74
2616 2891 1.123077 TGGGCTATGGCTGACACTAG 58.877 55.000 0.00 0.00 38.73 2.57
2617 2892 0.250081 GGGCTATGGCTGACACTAGC 60.250 60.000 13.31 13.31 42.94 3.42
2618 2893 0.465705 GGCTATGGCTGACACTAGCA 59.534 55.000 19.52 0.00 45.46 3.49
2619 2894 1.071385 GGCTATGGCTGACACTAGCAT 59.929 52.381 19.52 0.00 45.46 3.79
2620 2895 2.300152 GGCTATGGCTGACACTAGCATA 59.700 50.000 19.52 0.00 45.46 3.14
2621 2896 3.583806 GCTATGGCTGACACTAGCATAG 58.416 50.000 15.54 0.00 45.46 2.23
2622 2897 2.540265 ATGGCTGACACTAGCATAGC 57.460 50.000 0.00 0.00 44.39 2.97
2623 2898 1.194218 TGGCTGACACTAGCATAGCA 58.806 50.000 9.96 0.00 44.39 3.49
2624 2899 1.764723 TGGCTGACACTAGCATAGCAT 59.235 47.619 9.96 0.00 44.39 3.79
2625 2900 2.224137 TGGCTGACACTAGCATAGCATC 60.224 50.000 9.96 0.00 44.39 3.91
2626 2901 2.036992 GGCTGACACTAGCATAGCATCT 59.963 50.000 9.96 0.00 44.39 2.90
2627 2902 3.256879 GGCTGACACTAGCATAGCATCTA 59.743 47.826 9.96 0.00 44.39 1.98
2628 2903 4.262207 GGCTGACACTAGCATAGCATCTAA 60.262 45.833 9.96 0.00 44.39 2.10
2629 2904 5.292765 GCTGACACTAGCATAGCATCTAAA 58.707 41.667 0.00 0.00 44.39 1.85
2630 2905 5.404968 GCTGACACTAGCATAGCATCTAAAG 59.595 44.000 0.00 0.00 44.39 1.85
2631 2906 5.847304 TGACACTAGCATAGCATCTAAAGG 58.153 41.667 0.00 0.00 44.39 3.11
2632 2907 5.598417 TGACACTAGCATAGCATCTAAAGGA 59.402 40.000 0.00 0.00 44.39 3.36
2633 2908 6.095432 ACACTAGCATAGCATCTAAAGGAG 57.905 41.667 0.00 0.00 44.39 3.69
2634 2909 5.011533 ACACTAGCATAGCATCTAAAGGAGG 59.988 44.000 0.00 0.00 44.39 4.30
2635 2910 5.011533 CACTAGCATAGCATCTAAAGGAGGT 59.988 44.000 0.00 0.00 44.39 3.85
2636 2911 5.604650 ACTAGCATAGCATCTAAAGGAGGTT 59.395 40.000 0.00 0.00 44.39 3.50
2637 2912 6.782988 ACTAGCATAGCATCTAAAGGAGGTTA 59.217 38.462 0.00 0.00 44.39 2.85
2638 2913 5.859495 AGCATAGCATCTAAAGGAGGTTAC 58.141 41.667 0.00 0.00 0.00 2.50
2639 2914 4.686554 GCATAGCATCTAAAGGAGGTTACG 59.313 45.833 0.00 0.00 0.00 3.18
2640 2915 5.739358 GCATAGCATCTAAAGGAGGTTACGT 60.739 44.000 0.00 0.00 0.00 3.57
2641 2916 4.820894 AGCATCTAAAGGAGGTTACGTT 57.179 40.909 0.00 0.00 0.00 3.99
2642 2917 5.161943 AGCATCTAAAGGAGGTTACGTTT 57.838 39.130 0.00 0.00 0.00 3.60
2643 2918 5.557866 AGCATCTAAAGGAGGTTACGTTTT 58.442 37.500 0.00 0.00 0.00 2.43
2644 2919 6.002082 AGCATCTAAAGGAGGTTACGTTTTT 58.998 36.000 0.00 0.00 0.00 1.94
2671 2946 6.399204 AGCTTAAAATGAGGTTACGTTACG 57.601 37.500 2.19 2.19 0.00 3.18
2672 2947 5.017612 GCTTAAAATGAGGTTACGTTACGC 58.982 41.667 4.09 0.00 0.00 4.42
2674 2949 0.994263 AATGAGGTTACGTTACGCGC 59.006 50.000 5.73 0.00 46.11 6.86
2675 2950 0.171903 ATGAGGTTACGTTACGCGCT 59.828 50.000 5.73 0.00 46.11 5.92
2676 2951 0.454957 TGAGGTTACGTTACGCGCTC 60.455 55.000 5.73 1.29 46.11 5.03
2677 2952 0.454957 GAGGTTACGTTACGCGCTCA 60.455 55.000 5.73 0.00 46.11 4.26
2678 2953 0.039256 AGGTTACGTTACGCGCTCAA 60.039 50.000 5.73 0.00 46.11 3.02
2679 2954 0.364515 GGTTACGTTACGCGCTCAAG 59.635 55.000 5.73 0.00 46.11 3.02
2680 2955 0.246642 GTTACGTTACGCGCTCAAGC 60.247 55.000 5.73 0.00 46.11 4.01
2691 2966 2.930168 GCTCAAGCGCCGTTATTTG 58.070 52.632 2.29 0.12 0.00 2.32
2692 2967 0.168128 GCTCAAGCGCCGTTATTTGT 59.832 50.000 2.29 0.00 0.00 2.83
2693 2968 1.790481 GCTCAAGCGCCGTTATTTGTC 60.790 52.381 2.29 0.00 0.00 3.18
2694 2969 1.463056 CTCAAGCGCCGTTATTTGTCA 59.537 47.619 2.29 0.00 0.00 3.58
2695 2970 2.080693 TCAAGCGCCGTTATTTGTCAT 58.919 42.857 2.29 0.00 0.00 3.06
2696 2971 2.159585 TCAAGCGCCGTTATTTGTCATG 60.160 45.455 2.29 0.00 0.00 3.07
2697 2972 0.732571 AGCGCCGTTATTTGTCATGG 59.267 50.000 2.29 0.00 0.00 3.66
2698 2973 0.730265 GCGCCGTTATTTGTCATGGA 59.270 50.000 0.00 0.00 0.00 3.41
2699 2974 1.333619 GCGCCGTTATTTGTCATGGAT 59.666 47.619 0.00 0.00 0.00 3.41
2700 2975 2.854424 GCGCCGTTATTTGTCATGGATG 60.854 50.000 0.00 0.00 0.00 3.51
2701 2976 2.286950 CGCCGTTATTTGTCATGGATGG 60.287 50.000 0.00 0.00 0.00 3.51
2702 2977 2.687935 GCCGTTATTTGTCATGGATGGT 59.312 45.455 0.00 0.00 0.00 3.55
2703 2978 3.489059 GCCGTTATTTGTCATGGATGGTG 60.489 47.826 0.00 0.00 0.00 4.17
2704 2979 3.489059 CCGTTATTTGTCATGGATGGTGC 60.489 47.826 0.00 0.00 0.00 5.01
2705 2980 3.128415 CGTTATTTGTCATGGATGGTGCA 59.872 43.478 0.00 0.00 0.00 4.57
2706 2981 4.380339 CGTTATTTGTCATGGATGGTGCAA 60.380 41.667 0.00 0.00 0.00 4.08
2707 2982 5.477510 GTTATTTGTCATGGATGGTGCAAA 58.522 37.500 0.00 0.00 33.13 3.68
2708 2983 4.620589 ATTTGTCATGGATGGTGCAAAA 57.379 36.364 0.00 0.00 32.73 2.44
2709 2984 4.412796 TTTGTCATGGATGGTGCAAAAA 57.587 36.364 0.00 0.00 0.00 1.94
2710 2985 4.620589 TTGTCATGGATGGTGCAAAAAT 57.379 36.364 0.00 0.00 0.00 1.82
2711 2986 4.191033 TGTCATGGATGGTGCAAAAATC 57.809 40.909 0.00 0.00 0.00 2.17
2712 2987 3.577415 TGTCATGGATGGTGCAAAAATCA 59.423 39.130 0.00 0.00 0.00 2.57
2713 2988 4.223255 TGTCATGGATGGTGCAAAAATCAT 59.777 37.500 0.00 0.00 0.00 2.45
2714 2989 5.421374 TGTCATGGATGGTGCAAAAATCATA 59.579 36.000 0.00 0.00 0.00 2.15
2715 2990 5.981315 GTCATGGATGGTGCAAAAATCATAG 59.019 40.000 0.00 0.00 0.00 2.23
2716 2991 5.657745 TCATGGATGGTGCAAAAATCATAGT 59.342 36.000 0.00 0.00 0.00 2.12
2717 2992 6.832900 TCATGGATGGTGCAAAAATCATAGTA 59.167 34.615 0.00 0.00 0.00 1.82
2718 2993 6.449635 TGGATGGTGCAAAAATCATAGTAC 57.550 37.500 0.00 0.00 0.00 2.73
2719 2994 6.186957 TGGATGGTGCAAAAATCATAGTACT 58.813 36.000 0.00 0.00 0.00 2.73
2720 2995 6.095300 TGGATGGTGCAAAAATCATAGTACTG 59.905 38.462 5.39 0.00 0.00 2.74
2721 2996 6.095440 GGATGGTGCAAAAATCATAGTACTGT 59.905 38.462 5.39 0.00 0.00 3.55
2722 2997 6.892658 TGGTGCAAAAATCATAGTACTGTT 57.107 33.333 5.39 0.00 0.00 3.16
2723 2998 7.283625 TGGTGCAAAAATCATAGTACTGTTT 57.716 32.000 5.39 0.00 0.00 2.83
2724 2999 7.144661 TGGTGCAAAAATCATAGTACTGTTTG 58.855 34.615 5.39 7.44 0.00 2.93
2725 3000 6.586082 GGTGCAAAAATCATAGTACTGTTTGG 59.414 38.462 5.39 0.00 0.00 3.28
2726 3001 7.367285 GTGCAAAAATCATAGTACTGTTTGGA 58.633 34.615 5.39 5.14 0.00 3.53
2727 3002 7.865385 GTGCAAAAATCATAGTACTGTTTGGAA 59.135 33.333 5.39 0.00 0.00 3.53
2728 3003 7.865385 TGCAAAAATCATAGTACTGTTTGGAAC 59.135 33.333 5.39 0.00 0.00 3.62
2729 3004 7.865385 GCAAAAATCATAGTACTGTTTGGAACA 59.135 33.333 5.39 0.00 39.52 3.18
2738 3013 2.051334 TGTTTGGAACAGGTGTCTGG 57.949 50.000 0.00 0.00 44.99 3.86
2739 3014 1.562008 TGTTTGGAACAGGTGTCTGGA 59.438 47.619 0.00 0.00 44.99 3.86
2740 3015 2.174639 TGTTTGGAACAGGTGTCTGGAT 59.825 45.455 0.00 0.00 44.99 3.41
2741 3016 2.814336 GTTTGGAACAGGTGTCTGGATC 59.186 50.000 0.00 0.00 44.99 3.36
2742 3017 0.608130 TGGAACAGGTGTCTGGATCG 59.392 55.000 0.00 0.00 44.99 3.69
2743 3018 0.895530 GGAACAGGTGTCTGGATCGA 59.104 55.000 0.00 0.00 44.99 3.59
2744 3019 1.275291 GGAACAGGTGTCTGGATCGAA 59.725 52.381 0.00 0.00 44.99 3.71
2745 3020 2.093447 GGAACAGGTGTCTGGATCGAAT 60.093 50.000 0.00 0.00 44.99 3.34
2746 3021 2.969628 ACAGGTGTCTGGATCGAATC 57.030 50.000 0.00 0.00 44.99 2.52
2747 3022 1.135139 ACAGGTGTCTGGATCGAATCG 59.865 52.381 0.00 0.00 44.99 3.34
2748 3023 1.135139 CAGGTGTCTGGATCGAATCGT 59.865 52.381 1.52 0.00 37.36 3.73
2749 3024 1.825474 AGGTGTCTGGATCGAATCGTT 59.175 47.619 1.52 0.00 0.00 3.85
2750 3025 1.927174 GGTGTCTGGATCGAATCGTTG 59.073 52.381 1.52 0.00 0.00 4.10
2751 3026 2.607187 GTGTCTGGATCGAATCGTTGT 58.393 47.619 1.52 0.00 0.00 3.32
2752 3027 2.993899 GTGTCTGGATCGAATCGTTGTT 59.006 45.455 1.52 0.00 0.00 2.83
2753 3028 4.171005 GTGTCTGGATCGAATCGTTGTTA 58.829 43.478 1.52 0.00 0.00 2.41
2754 3029 4.265556 GTGTCTGGATCGAATCGTTGTTAG 59.734 45.833 1.52 0.00 0.00 2.34
2755 3030 4.082408 TGTCTGGATCGAATCGTTGTTAGT 60.082 41.667 1.52 0.00 0.00 2.24
2756 3031 4.499758 GTCTGGATCGAATCGTTGTTAGTC 59.500 45.833 1.52 0.00 0.00 2.59
2757 3032 3.777478 TGGATCGAATCGTTGTTAGTCC 58.223 45.455 1.52 1.67 0.00 3.85
2758 3033 3.193903 TGGATCGAATCGTTGTTAGTCCA 59.806 43.478 1.52 4.08 0.00 4.02
2759 3034 3.550678 GGATCGAATCGTTGTTAGTCCAC 59.449 47.826 1.52 0.00 0.00 4.02
2760 3035 3.646611 TCGAATCGTTGTTAGTCCACA 57.353 42.857 1.52 0.00 0.00 4.17
2761 3036 4.182693 TCGAATCGTTGTTAGTCCACAT 57.817 40.909 1.52 0.00 0.00 3.21
2762 3037 3.924073 TCGAATCGTTGTTAGTCCACATG 59.076 43.478 1.52 0.00 0.00 3.21
2763 3038 3.924073 CGAATCGTTGTTAGTCCACATGA 59.076 43.478 0.00 0.00 0.00 3.07
2764 3039 4.566759 CGAATCGTTGTTAGTCCACATGAT 59.433 41.667 0.00 0.00 0.00 2.45
2765 3040 5.500771 CGAATCGTTGTTAGTCCACATGATG 60.501 44.000 0.00 0.00 0.00 3.07
2766 3041 4.529109 TCGTTGTTAGTCCACATGATGA 57.471 40.909 0.00 0.00 0.00 2.92
2767 3042 4.494484 TCGTTGTTAGTCCACATGATGAG 58.506 43.478 0.00 0.00 0.00 2.90
2768 3043 4.021456 TCGTTGTTAGTCCACATGATGAGT 60.021 41.667 0.00 0.58 0.00 3.41
2769 3044 4.690748 CGTTGTTAGTCCACATGATGAGTT 59.309 41.667 0.00 0.00 0.00 3.01
2770 3045 5.867174 CGTTGTTAGTCCACATGATGAGTTA 59.133 40.000 0.00 0.00 0.00 2.24
2771 3046 6.535150 CGTTGTTAGTCCACATGATGAGTTAT 59.465 38.462 0.00 0.00 0.00 1.89
2772 3047 7.254117 CGTTGTTAGTCCACATGATGAGTTATC 60.254 40.741 0.00 0.00 36.29 1.75
2773 3048 6.273071 TGTTAGTCCACATGATGAGTTATCG 58.727 40.000 0.00 0.00 38.71 2.92
2774 3049 6.127451 TGTTAGTCCACATGATGAGTTATCGT 60.127 38.462 0.00 0.00 38.71 3.73
2780 3055 4.327982 CATGATGAGTTATCGTGGTCCT 57.672 45.455 8.84 0.00 45.21 3.85
2781 3056 4.302455 CATGATGAGTTATCGTGGTCCTC 58.698 47.826 8.84 0.00 45.21 3.71
2782 3057 3.632333 TGATGAGTTATCGTGGTCCTCT 58.368 45.455 0.00 0.00 38.71 3.69
2783 3058 3.381590 TGATGAGTTATCGTGGTCCTCTG 59.618 47.826 0.00 0.00 38.71 3.35
2784 3059 1.476891 TGAGTTATCGTGGTCCTCTGC 59.523 52.381 0.00 0.00 0.00 4.26
2785 3060 1.751924 GAGTTATCGTGGTCCTCTGCT 59.248 52.381 0.00 0.00 0.00 4.24
2786 3061 1.751924 AGTTATCGTGGTCCTCTGCTC 59.248 52.381 0.00 0.00 0.00 4.26
2787 3062 1.751924 GTTATCGTGGTCCTCTGCTCT 59.248 52.381 0.00 0.00 0.00 4.09
2788 3063 1.681538 TATCGTGGTCCTCTGCTCTC 58.318 55.000 0.00 0.00 0.00 3.20
2789 3064 1.040339 ATCGTGGTCCTCTGCTCTCC 61.040 60.000 0.00 0.00 0.00 3.71
2790 3065 2.888863 GTGGTCCTCTGCTCTCCG 59.111 66.667 0.00 0.00 0.00 4.63
2791 3066 2.363018 TGGTCCTCTGCTCTCCGG 60.363 66.667 0.00 0.00 0.00 5.14
2792 3067 2.043852 GGTCCTCTGCTCTCCGGA 60.044 66.667 2.93 2.93 0.00 5.14
2793 3068 2.419739 GGTCCTCTGCTCTCCGGAC 61.420 68.421 0.00 0.00 44.00 4.79
2794 3069 2.043852 TCCTCTGCTCTCCGGACC 60.044 66.667 0.00 0.00 0.00 4.46
2795 3070 3.522731 CCTCTGCTCTCCGGACCG 61.523 72.222 6.99 6.99 0.00 4.79
2796 3071 2.752238 CTCTGCTCTCCGGACCGT 60.752 66.667 13.94 0.00 0.00 4.83
2797 3072 2.750637 TCTGCTCTCCGGACCGTC 60.751 66.667 13.94 0.00 0.00 4.79
2798 3073 2.752238 CTGCTCTCCGGACCGTCT 60.752 66.667 13.94 0.00 0.00 4.18
2799 3074 3.057547 CTGCTCTCCGGACCGTCTG 62.058 68.421 13.94 0.00 0.00 3.51
2800 3075 2.750637 GCTCTCCGGACCGTCTGA 60.751 66.667 13.94 6.83 0.00 3.27
2801 3076 2.122167 GCTCTCCGGACCGTCTGAT 61.122 63.158 13.94 0.00 0.00 2.90
2802 3077 1.668101 GCTCTCCGGACCGTCTGATT 61.668 60.000 13.94 0.00 0.00 2.57
2803 3078 0.818296 CTCTCCGGACCGTCTGATTT 59.182 55.000 13.94 0.00 0.00 2.17
2804 3079 0.530744 TCTCCGGACCGTCTGATTTG 59.469 55.000 13.94 0.00 0.00 2.32
2805 3080 0.460284 CTCCGGACCGTCTGATTTGG 60.460 60.000 13.94 0.00 0.00 3.28
2806 3081 2.106683 CCGGACCGTCTGATTTGGC 61.107 63.158 13.94 0.00 0.00 4.52
2807 3082 1.375396 CGGACCGTCTGATTTGGCA 60.375 57.895 5.48 0.00 0.00 4.92
2808 3083 0.953471 CGGACCGTCTGATTTGGCAA 60.953 55.000 5.48 0.00 0.00 4.52
2809 3084 0.521735 GGACCGTCTGATTTGGCAAC 59.478 55.000 0.00 0.00 0.00 4.17
2810 3085 0.165944 GACCGTCTGATTTGGCAACG 59.834 55.000 0.00 0.00 42.51 4.10
2811 3086 1.501741 CCGTCTGATTTGGCAACGG 59.498 57.895 11.31 11.31 45.79 4.44
2812 3087 2.539003 CGTCTGATTTGGCAACGGA 58.461 52.632 0.00 0.00 42.51 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 9.421806 TCGCAAATCAAATTGATGACTAAAATT 57.578 25.926 9.47 0.00 37.15 1.82
288 291 3.919216 ACTGACTCTTTCAACTCATCCG 58.081 45.455 0.00 0.00 32.21 4.18
290 293 8.594881 TTTCTTACTGACTCTTTCAACTCATC 57.405 34.615 0.00 0.00 32.21 2.92
298 301 9.620660 TTTTTGTGTTTTCTTACTGACTCTTTC 57.379 29.630 0.00 0.00 0.00 2.62
325 328 8.408043 TCATGAAAAACAGTATTGGAATCTGT 57.592 30.769 0.00 0.00 43.04 3.41
349 352 9.523730 GGTTGACGCAAATATTTTTACATTTTC 57.476 29.630 0.00 0.00 0.00 2.29
350 353 9.267084 AGGTTGACGCAAATATTTTTACATTTT 57.733 25.926 0.00 0.00 0.00 1.82
351 354 8.825667 AGGTTGACGCAAATATTTTTACATTT 57.174 26.923 0.00 0.00 0.00 2.32
352 355 7.272515 CGAGGTTGACGCAAATATTTTTACATT 59.727 33.333 0.00 0.00 0.00 2.71
353 356 6.745450 CGAGGTTGACGCAAATATTTTTACAT 59.255 34.615 0.00 0.00 0.00 2.29
354 357 6.081049 CGAGGTTGACGCAAATATTTTTACA 58.919 36.000 0.00 0.00 0.00 2.41
355 358 6.534615 CGAGGTTGACGCAAATATTTTTAC 57.465 37.500 0.00 0.00 0.00 2.01
368 394 2.279582 ATTCAGTAGCGAGGTTGACG 57.720 50.000 0.00 0.00 0.00 4.35
458 484 1.063114 ACCCGGATAGAGGCAGTACTT 60.063 52.381 0.73 0.00 0.00 2.24
509 539 5.220854 GGCAACATACATTTCGCTAGTCAAT 60.221 40.000 0.00 0.00 0.00 2.57
686 806 0.911184 CGTGTGTTTTGCCGTTTGAC 59.089 50.000 0.00 0.00 0.00 3.18
703 823 3.073798 TGTGGATTATTATGGGATGCCGT 59.926 43.478 2.54 2.54 0.00 5.68
705 825 5.774690 TCTTTGTGGATTATTATGGGATGCC 59.225 40.000 0.00 0.00 0.00 4.40
706 826 6.899393 TCTTTGTGGATTATTATGGGATGC 57.101 37.500 0.00 0.00 0.00 3.91
751 882 2.046604 GCGGGGGTATTATCGGGC 60.047 66.667 0.00 0.00 0.00 6.13
755 886 1.275573 GAGTCCAGCGGGGGTATTATC 59.724 57.143 2.05 0.00 37.22 1.75
1643 1811 4.459089 GCAGAGGAGGCACGGGAC 62.459 72.222 0.00 0.00 0.00 4.46
1670 1839 1.230212 GGGGCTGGAATGTAAGGGG 59.770 63.158 0.00 0.00 0.00 4.79
1672 1841 0.753111 GCAGGGGCTGGAATGTAAGG 60.753 60.000 0.00 0.00 36.96 2.69
1702 1872 2.290450 GGAATTACAAACGGGTCCCTGA 60.290 50.000 6.29 0.00 0.00 3.86
1703 1873 2.089201 GGAATTACAAACGGGTCCCTG 58.911 52.381 6.29 0.00 0.00 4.45
1877 2052 0.801836 GGCGGCGACCAATTGATTTG 60.802 55.000 12.98 0.00 34.93 2.32
1878 2053 1.247419 TGGCGGCGACCAATTGATTT 61.247 50.000 11.74 0.00 36.55 2.17
1890 2068 2.906182 TAGAGCTCACAATGGCGGCG 62.906 60.000 17.77 0.51 0.00 6.46
1939 2122 1.673033 GGGATTCATATCAGCCCGACG 60.673 57.143 0.00 0.00 32.09 5.12
1964 2151 2.295070 TGCTGCTACGACTACAGTTCAA 59.705 45.455 0.00 0.00 33.87 2.69
1965 2152 1.883926 TGCTGCTACGACTACAGTTCA 59.116 47.619 0.00 0.00 33.87 3.18
1966 2153 2.631418 TGCTGCTACGACTACAGTTC 57.369 50.000 0.00 0.00 33.87 3.01
1967 2154 2.296471 ACTTGCTGCTACGACTACAGTT 59.704 45.455 0.00 0.00 33.87 3.16
1968 2155 1.887198 ACTTGCTGCTACGACTACAGT 59.113 47.619 0.00 0.00 33.87 3.55
1970 2157 1.668919 GCACTTGCTGCTACGACTACA 60.669 52.381 0.00 0.00 43.33 2.74
1999 2206 7.417683 CCAGAGAATCACTGACTAGTCATCAAT 60.418 40.741 25.35 15.23 36.82 2.57
2002 2209 5.359576 ACCAGAGAATCACTGACTAGTCATC 59.640 44.000 25.35 18.66 36.82 2.92
2023 2230 0.319083 CACAACCACCGCTACTACCA 59.681 55.000 0.00 0.00 0.00 3.25
2024 2231 0.390735 CCACAACCACCGCTACTACC 60.391 60.000 0.00 0.00 0.00 3.18
2026 2233 1.001181 GAACCACAACCACCGCTACTA 59.999 52.381 0.00 0.00 0.00 1.82
2030 2237 2.030490 TACGAACCACAACCACCGCT 62.030 55.000 0.00 0.00 0.00 5.52
2031 2238 0.952010 ATACGAACCACAACCACCGC 60.952 55.000 0.00 0.00 0.00 5.68
2032 2239 1.073177 GATACGAACCACAACCACCG 58.927 55.000 0.00 0.00 0.00 4.94
2044 2251 1.018910 TCCGCTGACGATGATACGAA 58.981 50.000 0.00 0.00 43.93 3.85
2050 2257 1.143838 CCCAATCCGCTGACGATGA 59.856 57.895 0.00 0.00 43.93 2.92
2051 2258 0.877649 CTCCCAATCCGCTGACGATG 60.878 60.000 0.00 0.00 43.93 3.84
2055 2262 1.153349 GTCCTCCCAATCCGCTGAC 60.153 63.158 0.00 0.00 0.00 3.51
2074 2281 2.106511 ACTTAGGAGCACACCACATTGT 59.893 45.455 0.00 0.00 0.00 2.71
2086 2293 0.610687 AGGACAGTGCACTTAGGAGC 59.389 55.000 18.94 4.39 0.00 4.70
2088 2295 0.888619 CGAGGACAGTGCACTTAGGA 59.111 55.000 18.94 0.00 0.00 2.94
2089 2296 0.888619 TCGAGGACAGTGCACTTAGG 59.111 55.000 18.94 9.06 0.00 2.69
2090 2297 2.534298 CATCGAGGACAGTGCACTTAG 58.466 52.381 18.94 9.89 0.00 2.18
2091 2298 1.204704 CCATCGAGGACAGTGCACTTA 59.795 52.381 18.94 0.00 41.22 2.24
2092 2299 0.036952 CCATCGAGGACAGTGCACTT 60.037 55.000 18.94 9.02 41.22 3.16
2093 2300 1.188219 ACCATCGAGGACAGTGCACT 61.188 55.000 15.25 15.25 41.22 4.40
2094 2301 0.737715 GACCATCGAGGACAGTGCAC 60.738 60.000 9.40 9.40 41.22 4.57
2095 2302 1.591703 GACCATCGAGGACAGTGCA 59.408 57.895 0.00 0.00 41.22 4.57
2096 2303 1.153549 GGACCATCGAGGACAGTGC 60.154 63.158 0.00 0.00 41.22 4.40
2097 2304 0.108615 GTGGACCATCGAGGACAGTG 60.109 60.000 0.00 0.00 41.22 3.66
2098 2305 0.251832 AGTGGACCATCGAGGACAGT 60.252 55.000 0.00 2.44 41.22 3.55
2099 2306 0.457851 GAGTGGACCATCGAGGACAG 59.542 60.000 0.00 0.00 41.22 3.51
2100 2307 0.251608 TGAGTGGACCATCGAGGACA 60.252 55.000 0.00 0.00 41.22 4.02
2101 2308 0.457851 CTGAGTGGACCATCGAGGAC 59.542 60.000 0.00 0.00 41.22 3.85
2102 2309 0.039764 ACTGAGTGGACCATCGAGGA 59.960 55.000 0.00 0.00 41.22 3.71
2158 2365 9.236691 GGTCGATGTTAATTAACGATTGTACTA 57.763 33.333 20.51 3.33 39.00 1.82
2159 2366 7.977853 AGGTCGATGTTAATTAACGATTGTACT 59.022 33.333 20.51 15.99 39.00 2.73
2160 2367 8.123445 AGGTCGATGTTAATTAACGATTGTAC 57.877 34.615 20.51 13.79 39.00 2.90
2161 2368 7.436080 GGAGGTCGATGTTAATTAACGATTGTA 59.564 37.037 20.51 5.28 39.00 2.41
2162 2369 6.257193 GGAGGTCGATGTTAATTAACGATTGT 59.743 38.462 20.51 6.75 39.00 2.71
2163 2370 6.561533 CGGAGGTCGATGTTAATTAACGATTG 60.562 42.308 20.51 17.37 42.43 2.67
2164 2371 5.461078 CGGAGGTCGATGTTAATTAACGATT 59.539 40.000 20.51 10.07 42.43 3.34
2165 2372 4.980434 CGGAGGTCGATGTTAATTAACGAT 59.020 41.667 20.51 15.30 42.43 3.73
2166 2373 4.142403 ACGGAGGTCGATGTTAATTAACGA 60.142 41.667 20.51 13.03 42.43 3.85
2167 2374 4.107622 ACGGAGGTCGATGTTAATTAACG 58.892 43.478 20.51 11.12 42.43 3.18
2168 2375 5.725864 GCAACGGAGGTCGATGTTAATTAAC 60.726 44.000 19.44 19.44 42.53 2.01
2169 2376 4.330620 GCAACGGAGGTCGATGTTAATTAA 59.669 41.667 0.00 0.00 42.53 1.40
2170 2377 3.866910 GCAACGGAGGTCGATGTTAATTA 59.133 43.478 0.00 0.00 42.53 1.40
2171 2378 2.676342 GCAACGGAGGTCGATGTTAATT 59.324 45.455 0.00 0.00 42.53 1.40
2172 2379 2.277084 GCAACGGAGGTCGATGTTAAT 58.723 47.619 0.00 0.00 42.53 1.40
2173 2380 1.001068 TGCAACGGAGGTCGATGTTAA 59.999 47.619 0.00 0.00 42.53 2.01
2174 2381 0.604073 TGCAACGGAGGTCGATGTTA 59.396 50.000 0.00 0.00 42.53 2.41
2175 2382 0.250124 TTGCAACGGAGGTCGATGTT 60.250 50.000 0.00 0.00 42.53 2.71
2176 2383 0.036388 ATTGCAACGGAGGTCGATGT 60.036 50.000 0.00 0.00 42.53 3.06
2177 2384 0.652592 GATTGCAACGGAGGTCGATG 59.347 55.000 0.00 0.00 43.26 3.84
2178 2385 0.537188 AGATTGCAACGGAGGTCGAT 59.463 50.000 0.00 0.00 42.43 3.59
2179 2386 0.108804 GAGATTGCAACGGAGGTCGA 60.109 55.000 0.00 0.00 42.43 4.20
2180 2387 0.389817 TGAGATTGCAACGGAGGTCG 60.390 55.000 0.00 0.00 45.88 4.79
2181 2388 1.808411 TTGAGATTGCAACGGAGGTC 58.192 50.000 0.00 0.00 0.00 3.85
2182 2389 2.086869 CATTGAGATTGCAACGGAGGT 58.913 47.619 0.00 0.00 0.00 3.85
2183 2390 1.202222 GCATTGAGATTGCAACGGAGG 60.202 52.381 0.00 0.00 39.90 4.30
2184 2391 1.741706 AGCATTGAGATTGCAACGGAG 59.258 47.619 0.00 0.00 42.62 4.63
2185 2392 1.825090 AGCATTGAGATTGCAACGGA 58.175 45.000 0.00 0.00 42.62 4.69
2186 2393 2.163010 AGAAGCATTGAGATTGCAACGG 59.837 45.455 0.00 0.00 42.62 4.44
2187 2394 3.168963 CAGAAGCATTGAGATTGCAACG 58.831 45.455 0.00 0.00 42.62 4.10
2188 2395 2.921754 GCAGAAGCATTGAGATTGCAAC 59.078 45.455 0.00 0.00 42.62 4.17
2208 2415 3.681417 GGAGAAAAATTTCCATGCACAGC 59.319 43.478 0.00 0.00 37.92 4.40
2229 2436 8.822652 AAACATCTTCTAGAAATGCAAAAAGG 57.177 30.769 19.18 2.50 0.00 3.11
2236 2443 7.115378 CACCAACAAAACATCTTCTAGAAATGC 59.885 37.037 19.18 0.00 0.00 3.56
2244 2451 6.655078 ATTAGCACCAACAAAACATCTTCT 57.345 33.333 0.00 0.00 0.00 2.85
2304 2522 1.073722 CAGACAGCCAGAAGCCCAA 59.926 57.895 0.00 0.00 45.47 4.12
2307 2525 2.749441 GCCAGACAGCCAGAAGCC 60.749 66.667 0.00 0.00 45.47 4.35
2308 2526 3.123620 CGCCAGACAGCCAGAAGC 61.124 66.667 0.00 0.00 44.25 3.86
2309 2527 3.123620 GCGCCAGACAGCCAGAAG 61.124 66.667 0.00 0.00 0.00 2.85
2391 2628 1.153127 AAACAAACAGGCGACGGGA 60.153 52.632 0.00 0.00 0.00 5.14
2392 2629 1.281656 GAAACAAACAGGCGACGGG 59.718 57.895 0.00 0.00 0.00 5.28
2400 2655 2.541588 CGAGCAACCAGGAAACAAACAG 60.542 50.000 0.00 0.00 0.00 3.16
2454 2709 0.478072 TGCCTGTCAACCAACTCCAT 59.522 50.000 0.00 0.00 0.00 3.41
2512 2770 1.848932 GAACGAACTTGGGGAACGGC 61.849 60.000 0.00 0.00 0.00 5.68
2517 2775 1.368579 GGACGAACGAACTTGGGGA 59.631 57.895 0.14 0.00 0.00 4.81
2521 2779 0.595567 TCACCGGACGAACGAACTTG 60.596 55.000 9.46 0.00 35.47 3.16
2557 2815 4.489771 CATGGACCGGGCCTCACC 62.490 72.222 30.93 10.33 37.93 4.02
2594 2869 1.696336 AGTGTCAGCCATAGCCCATAG 59.304 52.381 0.00 0.00 41.25 2.23
2598 2873 0.250081 GCTAGTGTCAGCCATAGCCC 60.250 60.000 0.00 0.00 41.25 5.19
2599 2874 0.465705 TGCTAGTGTCAGCCATAGCC 59.534 55.000 0.00 0.00 41.04 3.93
2600 2875 2.540265 ATGCTAGTGTCAGCCATAGC 57.460 50.000 0.00 0.00 41.04 2.97
2601 2876 3.006217 TGCTATGCTAGTGTCAGCCATAG 59.994 47.826 6.83 6.83 41.04 2.23
2602 2877 2.965147 TGCTATGCTAGTGTCAGCCATA 59.035 45.455 0.00 0.00 41.04 2.74
2603 2878 1.764723 TGCTATGCTAGTGTCAGCCAT 59.235 47.619 0.00 0.00 41.04 4.40
2604 2879 1.194218 TGCTATGCTAGTGTCAGCCA 58.806 50.000 0.00 0.00 41.04 4.75
2605 2880 2.036992 AGATGCTATGCTAGTGTCAGCC 59.963 50.000 0.00 0.00 41.04 4.85
2606 2881 3.383620 AGATGCTATGCTAGTGTCAGC 57.616 47.619 0.00 0.00 42.15 4.26
2607 2882 5.925397 CCTTTAGATGCTATGCTAGTGTCAG 59.075 44.000 0.00 0.00 0.00 3.51
2608 2883 5.598417 TCCTTTAGATGCTATGCTAGTGTCA 59.402 40.000 0.00 0.00 0.00 3.58
2609 2884 6.090483 TCCTTTAGATGCTATGCTAGTGTC 57.910 41.667 0.00 0.00 0.00 3.67
2610 2885 5.011533 CCTCCTTTAGATGCTATGCTAGTGT 59.988 44.000 0.00 0.00 0.00 3.55
2611 2886 5.011533 ACCTCCTTTAGATGCTATGCTAGTG 59.988 44.000 0.00 0.00 0.00 2.74
2612 2887 5.151454 ACCTCCTTTAGATGCTATGCTAGT 58.849 41.667 0.00 0.00 0.00 2.57
2613 2888 5.736951 ACCTCCTTTAGATGCTATGCTAG 57.263 43.478 0.00 0.00 0.00 3.42
2614 2889 6.294564 CGTAACCTCCTTTAGATGCTATGCTA 60.295 42.308 0.00 0.00 0.00 3.49
2615 2890 5.509840 CGTAACCTCCTTTAGATGCTATGCT 60.510 44.000 0.00 0.00 0.00 3.79
2616 2891 4.686554 CGTAACCTCCTTTAGATGCTATGC 59.313 45.833 0.00 0.00 0.00 3.14
2617 2892 5.844004 ACGTAACCTCCTTTAGATGCTATG 58.156 41.667 0.00 0.00 0.00 2.23
2618 2893 6.481434 AACGTAACCTCCTTTAGATGCTAT 57.519 37.500 0.00 0.00 0.00 2.97
2619 2894 5.927281 AACGTAACCTCCTTTAGATGCTA 57.073 39.130 0.00 0.00 0.00 3.49
2620 2895 4.820894 AACGTAACCTCCTTTAGATGCT 57.179 40.909 0.00 0.00 0.00 3.79
2621 2896 5.874895 AAAACGTAACCTCCTTTAGATGC 57.125 39.130 0.00 0.00 0.00 3.91
2645 2920 8.434661 CGTAACGTAACCTCATTTTAAGCTAAA 58.565 33.333 0.00 0.00 0.00 1.85
2646 2921 7.411804 GCGTAACGTAACCTCATTTTAAGCTAA 60.412 37.037 0.00 0.00 0.00 3.09
2647 2922 6.034898 GCGTAACGTAACCTCATTTTAAGCTA 59.965 38.462 0.00 0.00 0.00 3.32
2648 2923 5.163923 GCGTAACGTAACCTCATTTTAAGCT 60.164 40.000 0.00 0.00 0.00 3.74
2649 2924 5.017612 GCGTAACGTAACCTCATTTTAAGC 58.982 41.667 0.00 0.00 0.00 3.09
2650 2925 5.242877 CGCGTAACGTAACCTCATTTTAAG 58.757 41.667 0.00 0.00 36.87 1.85
2651 2926 4.434067 GCGCGTAACGTAACCTCATTTTAA 60.434 41.667 8.43 0.00 46.11 1.52
2652 2927 3.060628 GCGCGTAACGTAACCTCATTTTA 59.939 43.478 8.43 0.00 46.11 1.52
2653 2928 2.159801 GCGCGTAACGTAACCTCATTTT 60.160 45.455 8.43 0.00 46.11 1.82
2654 2929 1.391144 GCGCGTAACGTAACCTCATTT 59.609 47.619 8.43 0.00 46.11 2.32
2655 2930 0.994263 GCGCGTAACGTAACCTCATT 59.006 50.000 8.43 0.00 46.11 2.57
2656 2931 0.171903 AGCGCGTAACGTAACCTCAT 59.828 50.000 8.43 0.00 46.11 2.90
2657 2932 0.454957 GAGCGCGTAACGTAACCTCA 60.455 55.000 8.43 0.00 46.11 3.86
2658 2933 0.454957 TGAGCGCGTAACGTAACCTC 60.455 55.000 8.43 2.57 46.11 3.85
2659 2934 0.039256 TTGAGCGCGTAACGTAACCT 60.039 50.000 8.43 0.00 46.11 3.50
2660 2935 0.364515 CTTGAGCGCGTAACGTAACC 59.635 55.000 8.43 0.00 46.11 2.85
2661 2936 0.246642 GCTTGAGCGCGTAACGTAAC 60.247 55.000 8.43 0.00 46.11 2.50
2662 2937 2.064387 GCTTGAGCGCGTAACGTAA 58.936 52.632 8.43 0.00 46.11 3.18
2663 2938 3.758035 GCTTGAGCGCGTAACGTA 58.242 55.556 8.43 0.00 46.11 3.57
2673 2948 0.168128 ACAAATAACGGCGCTTGAGC 59.832 50.000 6.90 0.00 37.78 4.26
2674 2949 1.463056 TGACAAATAACGGCGCTTGAG 59.537 47.619 6.90 0.00 0.00 3.02
2675 2950 1.514003 TGACAAATAACGGCGCTTGA 58.486 45.000 6.90 0.00 0.00 3.02
2676 2951 2.176369 CATGACAAATAACGGCGCTTG 58.824 47.619 6.90 8.42 0.00 4.01
2677 2952 1.132262 CCATGACAAATAACGGCGCTT 59.868 47.619 6.90 3.13 0.00 4.68
2678 2953 0.732571 CCATGACAAATAACGGCGCT 59.267 50.000 6.90 0.00 0.00 5.92
2679 2954 0.730265 TCCATGACAAATAACGGCGC 59.270 50.000 6.90 0.00 0.00 6.53
2680 2955 2.286950 CCATCCATGACAAATAACGGCG 60.287 50.000 4.80 4.80 0.00 6.46
2681 2956 2.687935 ACCATCCATGACAAATAACGGC 59.312 45.455 0.00 0.00 0.00 5.68
2682 2957 3.489059 GCACCATCCATGACAAATAACGG 60.489 47.826 0.00 0.00 0.00 4.44
2683 2958 3.128415 TGCACCATCCATGACAAATAACG 59.872 43.478 0.00 0.00 0.00 3.18
2684 2959 4.717233 TGCACCATCCATGACAAATAAC 57.283 40.909 0.00 0.00 0.00 1.89
2685 2960 5.735285 TTTGCACCATCCATGACAAATAA 57.265 34.783 0.00 0.00 0.00 1.40
2686 2961 5.735285 TTTTGCACCATCCATGACAAATA 57.265 34.783 0.00 0.00 30.71 1.40
2687 2962 4.620589 TTTTGCACCATCCATGACAAAT 57.379 36.364 0.00 0.00 30.71 2.32
2688 2963 4.412796 TTTTTGCACCATCCATGACAAA 57.587 36.364 0.00 0.00 0.00 2.83
2689 2964 4.040095 TGATTTTTGCACCATCCATGACAA 59.960 37.500 0.00 0.00 0.00 3.18
2690 2965 3.577415 TGATTTTTGCACCATCCATGACA 59.423 39.130 0.00 0.00 0.00 3.58
2691 2966 4.191033 TGATTTTTGCACCATCCATGAC 57.809 40.909 0.00 0.00 0.00 3.06
2692 2967 5.657745 ACTATGATTTTTGCACCATCCATGA 59.342 36.000 0.00 0.00 0.00 3.07
2693 2968 5.909477 ACTATGATTTTTGCACCATCCATG 58.091 37.500 0.00 0.00 0.00 3.66
2694 2969 6.835488 AGTACTATGATTTTTGCACCATCCAT 59.165 34.615 0.00 0.00 0.00 3.41
2695 2970 6.095300 CAGTACTATGATTTTTGCACCATCCA 59.905 38.462 0.00 0.00 0.00 3.41
2696 2971 6.095440 ACAGTACTATGATTTTTGCACCATCC 59.905 38.462 0.00 0.00 0.00 3.51
2697 2972 7.088589 ACAGTACTATGATTTTTGCACCATC 57.911 36.000 0.00 0.00 0.00 3.51
2698 2973 7.466746 AACAGTACTATGATTTTTGCACCAT 57.533 32.000 0.00 0.00 0.00 3.55
2699 2974 6.892658 AACAGTACTATGATTTTTGCACCA 57.107 33.333 0.00 0.00 0.00 4.17
2700 2975 6.586082 CCAAACAGTACTATGATTTTTGCACC 59.414 38.462 0.00 0.00 0.00 5.01
2701 2976 7.367285 TCCAAACAGTACTATGATTTTTGCAC 58.633 34.615 0.00 0.00 0.00 4.57
2702 2977 7.517614 TCCAAACAGTACTATGATTTTTGCA 57.482 32.000 0.00 0.00 0.00 4.08
2703 2978 7.865385 TGTTCCAAACAGTACTATGATTTTTGC 59.135 33.333 0.00 0.00 36.25 3.68
2719 2994 1.562008 TCCAGACACCTGTTCCAAACA 59.438 47.619 0.00 0.00 38.74 2.83
2720 2995 2.341846 TCCAGACACCTGTTCCAAAC 57.658 50.000 0.00 0.00 38.74 2.93
2721 2996 2.549992 CGATCCAGACACCTGTTCCAAA 60.550 50.000 0.00 0.00 38.74 3.28
2722 2997 1.001974 CGATCCAGACACCTGTTCCAA 59.998 52.381 0.00 0.00 38.74 3.53
2723 2998 0.608130 CGATCCAGACACCTGTTCCA 59.392 55.000 0.00 0.00 38.74 3.53
2724 2999 0.895530 TCGATCCAGACACCTGTTCC 59.104 55.000 0.00 0.00 38.74 3.62
2725 3000 2.743636 TTCGATCCAGACACCTGTTC 57.256 50.000 0.00 0.00 38.74 3.18
2726 3001 2.417379 CGATTCGATCCAGACACCTGTT 60.417 50.000 0.00 0.00 38.74 3.16
2727 3002 1.135139 CGATTCGATCCAGACACCTGT 59.865 52.381 0.00 0.00 38.74 4.00
2728 3003 1.135139 ACGATTCGATCCAGACACCTG 59.865 52.381 13.95 0.00 40.09 4.00
2729 3004 1.475403 ACGATTCGATCCAGACACCT 58.525 50.000 13.95 0.00 0.00 4.00
2730 3005 1.927174 CAACGATTCGATCCAGACACC 59.073 52.381 13.95 0.00 0.00 4.16
2731 3006 2.607187 ACAACGATTCGATCCAGACAC 58.393 47.619 13.95 0.00 0.00 3.67
2732 3007 3.313012 AACAACGATTCGATCCAGACA 57.687 42.857 13.95 0.00 0.00 3.41
2733 3008 4.421948 ACTAACAACGATTCGATCCAGAC 58.578 43.478 13.95 0.00 0.00 3.51
2734 3009 4.439700 GGACTAACAACGATTCGATCCAGA 60.440 45.833 13.95 0.00 0.00 3.86
2735 3010 3.797256 GGACTAACAACGATTCGATCCAG 59.203 47.826 13.95 5.63 0.00 3.86
2736 3011 3.193903 TGGACTAACAACGATTCGATCCA 59.806 43.478 13.95 10.16 0.00 3.41
2737 3012 3.550678 GTGGACTAACAACGATTCGATCC 59.449 47.826 13.95 7.96 0.00 3.36
2738 3013 4.171005 TGTGGACTAACAACGATTCGATC 58.829 43.478 13.95 0.00 0.00 3.69
2739 3014 4.182693 TGTGGACTAACAACGATTCGAT 57.817 40.909 13.95 0.00 0.00 3.59
2740 3015 3.646611 TGTGGACTAACAACGATTCGA 57.353 42.857 13.95 0.00 0.00 3.71
2741 3016 3.924073 TCATGTGGACTAACAACGATTCG 59.076 43.478 4.14 4.14 32.81 3.34
2742 3017 5.580691 TCATCATGTGGACTAACAACGATTC 59.419 40.000 0.00 0.00 32.81 2.52
2743 3018 5.487433 TCATCATGTGGACTAACAACGATT 58.513 37.500 0.00 0.00 32.81 3.34
2744 3019 5.084818 TCATCATGTGGACTAACAACGAT 57.915 39.130 0.00 0.00 32.81 3.73
2745 3020 4.021456 ACTCATCATGTGGACTAACAACGA 60.021 41.667 0.00 0.00 32.81 3.85
2746 3021 4.245660 ACTCATCATGTGGACTAACAACG 58.754 43.478 0.00 0.00 32.81 4.10
2747 3022 7.254117 CGATAACTCATCATGTGGACTAACAAC 60.254 40.741 0.00 0.00 32.81 3.32
2748 3023 6.756542 CGATAACTCATCATGTGGACTAACAA 59.243 38.462 0.00 0.00 32.81 2.83
2749 3024 6.127451 ACGATAACTCATCATGTGGACTAACA 60.127 38.462 0.00 0.00 32.71 2.41
2750 3025 6.199154 CACGATAACTCATCATGTGGACTAAC 59.801 42.308 0.00 0.00 32.71 2.34
2751 3026 6.273071 CACGATAACTCATCATGTGGACTAA 58.727 40.000 0.00 0.00 32.71 2.24
2752 3027 5.221244 CCACGATAACTCATCATGTGGACTA 60.221 44.000 2.41 0.00 43.01 2.59
2753 3028 4.442052 CCACGATAACTCATCATGTGGACT 60.442 45.833 2.41 0.00 43.01 3.85
2754 3029 3.804325 CCACGATAACTCATCATGTGGAC 59.196 47.826 2.41 0.00 43.01 4.02
2755 3030 3.450817 ACCACGATAACTCATCATGTGGA 59.549 43.478 14.76 0.00 43.01 4.02
2756 3031 3.797039 ACCACGATAACTCATCATGTGG 58.203 45.455 6.92 6.92 44.55 4.17
2757 3032 3.804325 GGACCACGATAACTCATCATGTG 59.196 47.826 0.00 0.00 32.71 3.21
2758 3033 3.706594 AGGACCACGATAACTCATCATGT 59.293 43.478 0.00 0.00 32.71 3.21
2759 3034 4.038522 AGAGGACCACGATAACTCATCATG 59.961 45.833 0.00 0.00 32.71 3.07
2760 3035 4.038522 CAGAGGACCACGATAACTCATCAT 59.961 45.833 0.00 0.00 32.71 2.45
2761 3036 3.381590 CAGAGGACCACGATAACTCATCA 59.618 47.826 0.00 0.00 32.71 3.07
2762 3037 3.797184 GCAGAGGACCACGATAACTCATC 60.797 52.174 0.00 0.00 0.00 2.92
2763 3038 2.101582 GCAGAGGACCACGATAACTCAT 59.898 50.000 0.00 0.00 0.00 2.90
2764 3039 1.476891 GCAGAGGACCACGATAACTCA 59.523 52.381 0.00 0.00 0.00 3.41
2765 3040 1.751924 AGCAGAGGACCACGATAACTC 59.248 52.381 0.00 0.00 0.00 3.01
2766 3041 1.751924 GAGCAGAGGACCACGATAACT 59.248 52.381 0.00 0.00 0.00 2.24
2767 3042 1.751924 AGAGCAGAGGACCACGATAAC 59.248 52.381 0.00 0.00 0.00 1.89
2768 3043 2.025155 GAGAGCAGAGGACCACGATAA 58.975 52.381 0.00 0.00 0.00 1.75
2769 3044 1.681538 GAGAGCAGAGGACCACGATA 58.318 55.000 0.00 0.00 0.00 2.92
2770 3045 1.040339 GGAGAGCAGAGGACCACGAT 61.040 60.000 0.00 0.00 0.00 3.73
2771 3046 1.679305 GGAGAGCAGAGGACCACGA 60.679 63.158 0.00 0.00 0.00 4.35
2772 3047 2.888863 GGAGAGCAGAGGACCACG 59.111 66.667 0.00 0.00 0.00 4.94
2773 3048 2.716017 CCGGAGAGCAGAGGACCAC 61.716 68.421 0.00 0.00 0.00 4.16
2774 3049 2.363018 CCGGAGAGCAGAGGACCA 60.363 66.667 0.00 0.00 0.00 4.02
2775 3050 2.043852 TCCGGAGAGCAGAGGACC 60.044 66.667 0.00 0.00 0.00 4.46
2776 3051 3.202467 GTCCGGAGAGCAGAGGAC 58.798 66.667 3.06 0.00 45.07 3.85
2777 3052 2.043852 GGTCCGGAGAGCAGAGGA 60.044 66.667 3.06 0.00 40.37 3.71
2778 3053 3.522731 CGGTCCGGAGAGCAGAGG 61.523 72.222 3.06 0.00 40.69 3.69
2779 3054 2.752238 ACGGTCCGGAGAGCAGAG 60.752 66.667 17.28 0.00 40.69 3.35
2780 3055 2.750637 GACGGTCCGGAGAGCAGA 60.751 66.667 17.28 0.00 40.69 4.26
2781 3056 2.752238 AGACGGTCCGGAGAGCAG 60.752 66.667 17.28 0.00 40.69 4.24
2782 3057 2.838748 ATCAGACGGTCCGGAGAGCA 62.839 60.000 17.28 0.00 40.69 4.26
2783 3058 1.668101 AATCAGACGGTCCGGAGAGC 61.668 60.000 17.28 0.00 37.15 4.09
2784 3059 0.818296 AAATCAGACGGTCCGGAGAG 59.182 55.000 17.28 4.07 0.00 3.20
2785 3060 0.530744 CAAATCAGACGGTCCGGAGA 59.469 55.000 17.28 10.49 0.00 3.71
2786 3061 0.460284 CCAAATCAGACGGTCCGGAG 60.460 60.000 17.28 4.85 0.00 4.63
2787 3062 1.594833 CCAAATCAGACGGTCCGGA 59.405 57.895 17.28 0.00 0.00 5.14
2788 3063 2.106683 GCCAAATCAGACGGTCCGG 61.107 63.158 17.28 0.00 0.00 5.14
2789 3064 0.953471 TTGCCAAATCAGACGGTCCG 60.953 55.000 10.48 10.48 0.00 4.79
2790 3065 0.521735 GTTGCCAAATCAGACGGTCC 59.478 55.000 4.14 0.00 0.00 4.46
2791 3066 0.165944 CGTTGCCAAATCAGACGGTC 59.834 55.000 0.00 0.00 0.00 4.79
2792 3067 1.234615 CCGTTGCCAAATCAGACGGT 61.235 55.000 5.16 0.00 45.94 4.83
2793 3068 1.501741 CCGTTGCCAAATCAGACGG 59.498 57.895 0.00 0.00 45.86 4.79
2794 3069 2.539003 TCCGTTGCCAAATCAGACG 58.461 52.632 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.