Multiple sequence alignment - TraesCS2A01G003400

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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 TraesCS2A01G003400 chr2A 100.000 3535 0 0 1 3535 2275709 2272175 0.000000e+00 6529.0
1 TraesCS2A01G003400 chr2A 91.143 971 66 3 1 952 711053168 711054137 0.000000e+00 1299.0
2 TraesCS2A01G003400 chr2A 94.093 728 43 0 1 728 27648743 27648016 0.000000e+00 1107.0
3 TraesCS2A01G003400 chr2B 90.281 1852 115 23 960 2783 8174777 8176591 0.000000e+00 2362.0
4 TraesCS2A01G003400 chr2B 90.043 1858 120 23 960 2789 8010165 8011985 0.000000e+00 2346.0
5 TraesCS2A01G003400 chr2B 92.460 1512 98 2 960 2461 30982049 30983554 0.000000e+00 2146.0
6 TraesCS2A01G003400 chr2B 93.617 1222 75 3 962 2180 7963842 7965063 0.000000e+00 1821.0
7 TraesCS2A01G003400 chr2B 93.372 1222 78 3 962 2180 8132607 8133828 0.000000e+00 1805.0
8 TraesCS2A01G003400 chr2B 90.619 970 70 4 1 952 732866830 732867796 0.000000e+00 1267.0
9 TraesCS2A01G003400 chr2B 88.802 384 36 2 2551 2933 30983610 30983987 6.910000e-127 464.0
10 TraesCS2A01G003400 chr2B 85.442 419 56 3 3076 3493 30984556 30984970 7.010000e-117 431.0
11 TraesCS2A01G003400 chr2B 88.418 354 40 1 3134 3486 41085696 41086049 3.260000e-115 425.0
12 TraesCS2A01G003400 chr2B 84.762 420 57 5 3076 3493 31053496 31053082 7.060000e-112 414.0
13 TraesCS2A01G003400 chr2B 95.455 44 1 1 2227 2269 8133871 8133828 6.330000e-08 69.4
14 TraesCS2A01G003400 chr2B 97.059 34 1 0 2460 2493 30983585 30983618 1.370000e-04 58.4
15 TraesCS2A01G003400 chr1D 93.299 970 46 7 1 952 451113911 451112943 0.000000e+00 1413.0
16 TraesCS2A01G003400 chr1D 91.701 964 61 2 7 952 393396171 393395209 0.000000e+00 1319.0
17 TraesCS2A01G003400 chr1D 91.340 970 65 4 1 952 7883802 7884770 0.000000e+00 1308.0
18 TraesCS2A01G003400 chr1D 89.744 351 17 2 620 952 99577832 99577483 7.010000e-117 431.0
19 TraesCS2A01G003400 chr2D 92.252 968 56 2 3 952 645789591 645790557 0.000000e+00 1354.0
20 TraesCS2A01G003400 chr2D 90.619 970 72 2 1 952 110837280 110836312 0.000000e+00 1269.0
21 TraesCS2A01G003400 chr2D 86.731 309 41 0 3076 3384 11260956 11260648 9.400000e-91 344.0
22 TraesCS2A01G003400 chr7A 91.503 965 62 4 6 952 270272125 270271163 0.000000e+00 1310.0
23 TraesCS2A01G003400 chr5A 90.216 971 73 7 1 952 13531162 13530195 0.000000e+00 1247.0
24 TraesCS2A01G003400 chr5A 84.956 113 17 0 2724 2836 590079437 590079325 8.020000e-22 115.0
25 TraesCS2A01G003400 chr4D 89.897 970 79 8 1 952 469566501 469565533 0.000000e+00 1230.0
26 TraesCS2A01G003400 chr3A 88.912 974 71 17 1 951 80280411 80281370 0.000000e+00 1166.0
27 TraesCS2A01G003400 chr3B 81.415 947 171 3 6 952 672528325 672529266 0.000000e+00 769.0
28 TraesCS2A01G003400 chr7D 88.501 487 37 12 484 952 137846122 137846607 3.960000e-159 571.0
29 TraesCS2A01G003400 chrUn 88.701 354 39 1 3134 3486 163004347 163004700 7.010000e-117 431.0
30 TraesCS2A01G003400 chrUn 88.418 354 40 1 3134 3486 298964472 298964119 3.260000e-115 425.0
31 TraesCS2A01G003400 chrUn 88.418 354 40 1 3134 3486 307971474 307971827 3.260000e-115 425.0
32 TraesCS2A01G003400 chrUn 87.853 354 42 1 3134 3486 162964970 162965323 7.060000e-112 414.0
33 TraesCS2A01G003400 chrUn 87.853 354 42 1 3134 3486 163024311 163024664 7.060000e-112 414.0
34 TraesCS2A01G003400 chrUn 88.108 185 21 1 3303 3486 406085093 406084909 5.940000e-53 219.0
35 TraesCS2A01G003400 chr5B 83.871 124 20 0 2724 2847 576880417 576880294 6.200000e-23 119.0
36 TraesCS2A01G003400 chr1A 89.535 86 9 0 2732 2817 9910569 9910654 3.730000e-20 110.0


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 TraesCS2A01G003400 chr2A 2272175 2275709 3534 True 6529.00 6529 100.00000 1 3535 1 chr2A.!!$R1 3534
1 TraesCS2A01G003400 chr2A 711053168 711054137 969 False 1299.00 1299 91.14300 1 952 1 chr2A.!!$F1 951
2 TraesCS2A01G003400 chr2A 27648016 27648743 727 True 1107.00 1107 94.09300 1 728 1 chr2A.!!$R2 727
3 TraesCS2A01G003400 chr2B 8174777 8176591 1814 False 2362.00 2362 90.28100 960 2783 1 chr2B.!!$F4 1823
4 TraesCS2A01G003400 chr2B 8010165 8011985 1820 False 2346.00 2346 90.04300 960 2789 1 chr2B.!!$F2 1829
5 TraesCS2A01G003400 chr2B 7963842 7965063 1221 False 1821.00 1821 93.61700 962 2180 1 chr2B.!!$F1 1218
6 TraesCS2A01G003400 chr2B 8132607 8133828 1221 False 1805.00 1805 93.37200 962 2180 1 chr2B.!!$F3 1218
7 TraesCS2A01G003400 chr2B 732866830 732867796 966 False 1267.00 1267 90.61900 1 952 1 chr2B.!!$F6 951
8 TraesCS2A01G003400 chr2B 30982049 30984970 2921 False 774.85 2146 90.94075 960 3493 4 chr2B.!!$F7 2533
9 TraesCS2A01G003400 chr1D 451112943 451113911 968 True 1413.00 1413 93.29900 1 952 1 chr1D.!!$R3 951
10 TraesCS2A01G003400 chr1D 393395209 393396171 962 True 1319.00 1319 91.70100 7 952 1 chr1D.!!$R2 945
11 TraesCS2A01G003400 chr1D 7883802 7884770 968 False 1308.00 1308 91.34000 1 952 1 chr1D.!!$F1 951
12 TraesCS2A01G003400 chr2D 645789591 645790557 966 False 1354.00 1354 92.25200 3 952 1 chr2D.!!$F1 949
13 TraesCS2A01G003400 chr2D 110836312 110837280 968 True 1269.00 1269 90.61900 1 952 1 chr2D.!!$R2 951
14 TraesCS2A01G003400 chr7A 270271163 270272125 962 True 1310.00 1310 91.50300 6 952 1 chr7A.!!$R1 946
15 TraesCS2A01G003400 chr5A 13530195 13531162 967 True 1247.00 1247 90.21600 1 952 1 chr5A.!!$R1 951
16 TraesCS2A01G003400 chr4D 469565533 469566501 968 True 1230.00 1230 89.89700 1 952 1 chr4D.!!$R1 951
17 TraesCS2A01G003400 chr3A 80280411 80281370 959 False 1166.00 1166 88.91200 1 951 1 chr3A.!!$F1 950
18 TraesCS2A01G003400 chr3B 672528325 672529266 941 False 769.00 769 81.41500 6 952 1 chr3B.!!$F1 946

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
914 940 0.618458 AATCCTTCGGCCTTGCTGTA 59.382 50.0 0.0 0.0 36.18 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2550 2627 0.193574 ACACAGGAAGGAGGAGGGAA 59.806 55.0 0.0 0.0 0.0 3.97 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
70 71 5.019785 GGATAGATCCAGTAACCAAACGT 57.980 43.478 3.54 0.00 46.38 3.99
72 73 5.878669 GGATAGATCCAGTAACCAAACGTTT 59.121 40.000 7.96 7.96 46.38 3.60
77 78 2.946990 CCAGTAACCAAACGTTTCCTGT 59.053 45.455 11.37 6.07 35.79 4.00
193 195 4.240096 CCAATTCATTTCTGCAGTTCCAC 58.760 43.478 14.67 0.00 0.00 4.02
544 547 7.647827 TGGAAATAGGAATGGAACTGGAATTA 58.352 34.615 0.00 0.00 0.00 1.40
584 587 4.082463 TCGATTTAACTGCAAATTCCCCAC 60.082 41.667 0.00 0.00 0.00 4.61
829 855 2.222886 CACGTGTTGGTACCATTTCCA 58.777 47.619 17.17 7.67 0.00 3.53
914 940 0.618458 AATCCTTCGGCCTTGCTGTA 59.382 50.000 0.00 0.00 36.18 2.74
955 981 9.750783 TTTAGAGTGAAGATACTTACTACCTGT 57.249 33.333 0.00 0.00 0.00 4.00
958 984 9.344772 AGAGTGAAGATACTTACTACCTGTATG 57.655 37.037 0.00 0.00 33.89 2.39
993 1019 7.136822 TGTCTATATAAACCCAGCAACATCT 57.863 36.000 0.00 0.00 0.00 2.90
996 1022 7.386299 GTCTATATAAACCCAGCAACATCTCAG 59.614 40.741 0.00 0.00 0.00 3.35
997 1023 1.915141 AAACCCAGCAACATCTCAGG 58.085 50.000 0.00 0.00 0.00 3.86
1007 1033 3.633525 GCAACATCTCAGGCAATATCCAA 59.366 43.478 0.00 0.00 0.00 3.53
1027 1053 0.463833 GGGTGTAGGCAGGCACATAC 60.464 60.000 0.00 0.00 37.35 2.39
1039 1065 5.056480 GCAGGCACATACAGATACATACAA 58.944 41.667 0.00 0.00 0.00 2.41
1066 1092 4.633175 TGGAATTCGTGCTAACTGTGTTA 58.367 39.130 0.00 0.00 0.00 2.41
1160 1186 3.458872 GGTCAACAGCCGATCATCA 57.541 52.632 0.00 0.00 0.00 3.07
1173 1199 2.145958 ATCATCAAGATCAGCGACCG 57.854 50.000 0.00 0.00 28.20 4.79
1294 1320 1.007271 CAGCGACAACCTCACGTCT 60.007 57.895 0.00 0.00 0.00 4.18
1330 1356 3.818121 TTGGCGTGTTCTCCGGTGG 62.818 63.158 0.00 0.00 0.00 4.61
1338 1364 1.609501 TTCTCCGGTGGACCCTCAG 60.610 63.158 0.00 0.00 0.00 3.35
1560 1589 2.743752 CCATGCGTGACTTGCTCCG 61.744 63.158 7.72 0.00 0.00 4.63
1828 1857 2.729479 CCTGCGCCCTCTCACAGAT 61.729 63.158 4.18 0.00 31.67 2.90
2013 2042 0.578683 CGGCAGATGAAGTACATGCG 59.421 55.000 0.00 0.00 39.56 4.73
2056 2085 3.781307 CTCCACCCGCCGATTCCA 61.781 66.667 0.00 0.00 0.00 3.53
2069 2098 1.855213 GATTCCAGTGTTGCTGCGCA 61.855 55.000 10.98 10.98 43.71 6.09
2105 2134 1.814169 GTCGCCGAAATCCTGGGAC 60.814 63.158 0.00 0.00 35.30 4.46
2182 2211 1.675310 CGGCAGGGACAAGAATGCA 60.675 57.895 0.00 0.00 40.46 3.96
2194 2223 1.224592 GAATGCATGGACGGACCCT 59.775 57.895 0.00 0.00 38.00 4.34
2195 2224 0.815615 GAATGCATGGACGGACCCTC 60.816 60.000 0.00 0.00 38.00 4.30
2199 2228 1.219124 CATGGACGGACCCTCACAG 59.781 63.158 0.00 0.00 38.00 3.66
2206 2235 2.047179 GACCCTCACAGGTTCCGC 60.047 66.667 0.00 0.00 41.42 5.54
2328 2373 2.795973 CTCGCCACCATGCATGTG 59.204 61.111 24.58 20.38 0.00 3.21
2343 2388 0.517316 ATGTGAAAAGCTTCGTCGCC 59.483 50.000 16.73 6.82 33.94 5.54
2495 2572 2.047274 GTAGCCTTCACGCCTGCA 60.047 61.111 0.00 0.00 0.00 4.41
2513 2590 2.067350 GCACCATGCAGGACGTAGTAC 61.067 57.143 0.00 0.00 42.94 2.73
2529 2606 4.314194 CGTAGTACGAATAAGATCGAACGC 59.686 45.833 17.85 0.00 46.05 4.84
2532 2609 2.871133 ACGAATAAGATCGAACGCACA 58.129 42.857 3.47 0.00 45.48 4.57
2533 2610 3.247442 ACGAATAAGATCGAACGCACAA 58.753 40.909 3.47 0.00 45.48 3.33
2534 2611 3.676172 ACGAATAAGATCGAACGCACAAA 59.324 39.130 3.47 0.00 45.48 2.83
2535 2612 4.328983 ACGAATAAGATCGAACGCACAAAT 59.671 37.500 3.47 0.00 45.48 2.32
2536 2613 5.163893 ACGAATAAGATCGAACGCACAAATT 60.164 36.000 3.47 0.00 45.48 1.82
2537 2614 5.732647 CGAATAAGATCGAACGCACAAATTT 59.267 36.000 0.00 0.00 45.48 1.82
2538 2615 6.290026 CGAATAAGATCGAACGCACAAATTTG 60.290 38.462 16.67 16.67 45.48 2.32
2539 2616 2.584791 AGATCGAACGCACAAATTTGC 58.415 42.857 18.12 5.02 39.28 3.68
2540 2617 2.226437 AGATCGAACGCACAAATTTGCT 59.774 40.909 18.12 2.95 40.62 3.91
2541 2618 1.752753 TCGAACGCACAAATTTGCTG 58.247 45.000 18.12 15.22 40.62 4.41
2542 2619 1.064803 TCGAACGCACAAATTTGCTGT 59.935 42.857 18.12 10.88 40.62 4.40
2543 2620 1.187704 CGAACGCACAAATTTGCTGTG 59.812 47.619 18.12 20.52 45.71 3.66
2544 2621 2.192624 GAACGCACAAATTTGCTGTGT 58.807 42.857 22.79 22.79 44.92 3.72
2545 2622 3.367607 GAACGCACAAATTTGCTGTGTA 58.632 40.909 25.86 0.00 44.92 2.90
2546 2623 3.641437 ACGCACAAATTTGCTGTGTAT 57.359 38.095 25.09 11.72 44.92 2.29
2547 2624 3.976169 ACGCACAAATTTGCTGTGTATT 58.024 36.364 25.09 11.25 44.92 1.89
2548 2625 5.114785 ACGCACAAATTTGCTGTGTATTA 57.885 34.783 25.09 0.00 44.92 0.98
2549 2626 5.153513 ACGCACAAATTTGCTGTGTATTAG 58.846 37.500 25.09 10.76 44.92 1.73
2550 2627 5.153513 CGCACAAATTTGCTGTGTATTAGT 58.846 37.500 18.12 0.00 44.92 2.24
2581 2658 5.580998 TCCTTCCTGTGTTATAGTCACTCT 58.419 41.667 10.13 0.00 36.83 3.24
2582 2659 5.652891 TCCTTCCTGTGTTATAGTCACTCTC 59.347 44.000 10.13 0.00 36.83 3.20
2583 2660 5.419155 CCTTCCTGTGTTATAGTCACTCTCA 59.581 44.000 10.13 0.00 36.83 3.27
2584 2661 5.899120 TCCTGTGTTATAGTCACTCTCAC 57.101 43.478 10.13 0.00 36.83 3.51
2585 2662 5.571285 TCCTGTGTTATAGTCACTCTCACT 58.429 41.667 10.13 0.00 36.83 3.41
2586 2663 6.010850 TCCTGTGTTATAGTCACTCTCACTT 58.989 40.000 10.13 0.00 36.83 3.16
2658 2746 8.621532 TCCCTCTGTTCATAAATATAACATGC 57.378 34.615 0.00 0.00 33.01 4.06
2702 2790 7.042797 ACAAGACTACATGCAGTTTGAAATT 57.957 32.000 19.29 3.71 0.00 1.82
2709 2797 8.292448 ACTACATGCAGTTTGAAATTAGTGAAG 58.708 33.333 0.00 0.00 0.00 3.02
2715 2803 8.031864 TGCAGTTTGAAATTAGTGAAGAAACAA 58.968 29.630 0.00 0.00 0.00 2.83
2776 2864 2.037251 TCTTTGCTCTTTGCCGAGTACT 59.963 45.455 0.00 0.00 42.00 2.73
2783 2872 4.678309 GCTCTTTGCCGAGTACTAGAACAT 60.678 45.833 4.34 0.00 35.15 2.71
2789 2878 3.069729 GCCGAGTACTAGAACATGGGATT 59.930 47.826 4.34 0.00 0.00 3.01
2791 2880 4.051922 CGAGTACTAGAACATGGGATTGC 58.948 47.826 0.00 0.00 0.00 3.56
2798 2887 3.426615 AGAACATGGGATTGCGGTAAAA 58.573 40.909 0.00 0.00 0.00 1.52
2822 2911 2.131776 AGTAAGCCGAGTGTAGCTCT 57.868 50.000 0.00 0.00 41.98 4.09
2823 2912 2.448453 AGTAAGCCGAGTGTAGCTCTT 58.552 47.619 0.00 0.00 41.98 2.85
2825 2914 0.969894 AAGCCGAGTGTAGCTCTTGT 59.030 50.000 0.00 0.00 41.98 3.16
2862 2951 1.340017 GCACATGGGAAGCTCTACCAA 60.340 52.381 0.00 0.00 37.89 3.67
2870 2959 3.787001 GCTCTACCAAGCCCCGCT 61.787 66.667 0.00 0.00 42.56 5.52
2871 2960 2.501610 CTCTACCAAGCCCCGCTC 59.498 66.667 0.00 0.00 38.25 5.03
2881 2970 2.496291 GCCCCGCTCGGTACATAGT 61.496 63.158 7.59 0.00 0.00 2.12
2889 2978 3.242944 CGCTCGGTACATAGTCAAACATG 59.757 47.826 0.00 0.00 0.00 3.21
2900 2989 4.336889 AGTCAAACATGAAGGAACTCGA 57.663 40.909 0.00 0.00 38.49 4.04
2904 2993 5.007724 GTCAAACATGAAGGAACTCGACTTT 59.992 40.000 0.00 0.00 38.49 2.66
2933 3022 2.581354 CCGAGAGCCCTGTGGAAG 59.419 66.667 0.00 0.00 0.00 3.46
2934 3023 2.581354 CGAGAGCCCTGTGGAAGG 59.419 66.667 0.00 0.00 46.94 3.46
2959 3048 1.811860 GCAAATAGCAGCCAGGTGG 59.188 57.895 0.00 0.00 44.79 4.61
2977 3066 4.093952 CGAGGCCGTTTGCAGCTG 62.094 66.667 10.11 10.11 43.89 4.24
2978 3067 2.669569 GAGGCCGTTTGCAGCTGA 60.670 61.111 20.43 0.00 43.89 4.26
2979 3068 2.970974 GAGGCCGTTTGCAGCTGAC 61.971 63.158 20.43 9.67 43.89 3.51
2980 3069 4.389576 GGCCGTTTGCAGCTGACG 62.390 66.667 20.43 18.37 43.89 4.35
2983 3072 2.551270 CGTTTGCAGCTGACGGAC 59.449 61.111 20.43 8.79 33.45 4.79
2985 3074 2.281484 TTTGCAGCTGACGGACCC 60.281 61.111 20.43 0.00 0.00 4.46
2986 3075 4.680237 TTGCAGCTGACGGACCCG 62.680 66.667 20.43 6.94 46.03 5.28
2988 3077 4.803426 GCAGCTGACGGACCCGAG 62.803 72.222 20.43 4.15 42.83 4.63
2989 3078 3.062466 CAGCTGACGGACCCGAGA 61.062 66.667 16.07 0.00 42.83 4.04
2990 3079 3.063084 AGCTGACGGACCCGAGAC 61.063 66.667 16.07 6.76 42.83 3.36
2991 3080 4.131088 GCTGACGGACCCGAGACC 62.131 72.222 16.07 2.26 42.83 3.85
2992 3081 2.361357 CTGACGGACCCGAGACCT 60.361 66.667 16.07 0.00 42.83 3.85
2993 3082 2.360852 TGACGGACCCGAGACCTC 60.361 66.667 16.07 2.34 42.83 3.85
3008 3097 4.344448 GAGACCTCGATGAAAGTTACTCG 58.656 47.826 0.00 0.00 0.00 4.18
3009 3098 3.128938 AGACCTCGATGAAAGTTACTCGG 59.871 47.826 0.00 0.00 0.00 4.63
3010 3099 2.194271 CCTCGATGAAAGTTACTCGGC 58.806 52.381 0.00 0.00 0.00 5.54
3011 3100 2.416836 CCTCGATGAAAGTTACTCGGCA 60.417 50.000 0.00 0.00 0.00 5.69
3012 3101 3.250744 CTCGATGAAAGTTACTCGGCAA 58.749 45.455 0.00 0.00 0.00 4.52
3013 3102 3.857052 TCGATGAAAGTTACTCGGCAAT 58.143 40.909 0.00 0.00 0.00 3.56
3014 3103 3.863424 TCGATGAAAGTTACTCGGCAATC 59.137 43.478 0.00 0.00 0.00 2.67
3016 3105 5.041287 CGATGAAAGTTACTCGGCAATCTA 58.959 41.667 0.00 0.00 0.00 1.98
3018 3107 6.346120 CGATGAAAGTTACTCGGCAATCTATG 60.346 42.308 0.00 0.00 0.00 2.23
3019 3108 5.972935 TGAAAGTTACTCGGCAATCTATGA 58.027 37.500 0.00 0.00 0.00 2.15
3020 3109 6.042777 TGAAAGTTACTCGGCAATCTATGAG 58.957 40.000 0.00 0.00 34.65 2.90
3021 3110 4.592485 AGTTACTCGGCAATCTATGAGG 57.408 45.455 0.00 0.00 32.76 3.86
3023 3112 5.138276 AGTTACTCGGCAATCTATGAGGTA 58.862 41.667 0.00 0.00 32.76 3.08
3025 3114 6.267928 AGTTACTCGGCAATCTATGAGGTATT 59.732 38.462 0.00 0.00 32.76 1.89
3027 3116 5.542779 ACTCGGCAATCTATGAGGTATTTC 58.457 41.667 0.00 0.00 32.76 2.17
3029 3118 5.924356 TCGGCAATCTATGAGGTATTTCAA 58.076 37.500 0.00 0.00 0.00 2.69
3030 3119 5.758296 TCGGCAATCTATGAGGTATTTCAAC 59.242 40.000 0.00 0.00 0.00 3.18
3031 3120 5.049405 CGGCAATCTATGAGGTATTTCAACC 60.049 44.000 0.00 0.00 40.06 3.77
3032 3121 5.049405 GGCAATCTATGAGGTATTTCAACCG 60.049 44.000 0.00 0.00 44.77 4.44
3033 3122 5.049405 GCAATCTATGAGGTATTTCAACCGG 60.049 44.000 0.00 0.00 44.77 5.28
3035 3124 2.052782 ATGAGGTATTTCAACCGGCC 57.947 50.000 0.00 0.00 44.77 6.13
3036 3125 0.693622 TGAGGTATTTCAACCGGCCA 59.306 50.000 0.00 0.00 44.77 5.36
3038 3127 1.471287 GAGGTATTTCAACCGGCCAAC 59.529 52.381 0.00 0.00 44.77 3.77
3040 3129 1.471287 GGTATTTCAACCGGCCAACTC 59.529 52.381 0.00 0.00 0.00 3.01
3042 3131 2.871096 ATTTCAACCGGCCAACTCTA 57.129 45.000 0.00 0.00 0.00 2.43
3043 3132 2.178912 TTTCAACCGGCCAACTCTAG 57.821 50.000 0.00 0.00 0.00 2.43
3044 3133 0.321298 TTCAACCGGCCAACTCTAGC 60.321 55.000 0.00 0.00 0.00 3.42
3045 3134 1.745489 CAACCGGCCAACTCTAGCC 60.745 63.158 0.00 0.00 46.17 3.93
3049 3138 2.202756 GGCCAACTCTAGCCGTCG 60.203 66.667 0.00 0.00 39.87 5.12
3050 3139 2.886124 GCCAACTCTAGCCGTCGC 60.886 66.667 0.00 0.00 0.00 5.19
3052 3141 1.226717 CCAACTCTAGCCGTCGCTC 60.227 63.158 0.00 0.00 43.95 5.03
3053 3142 1.226717 CAACTCTAGCCGTCGCTCC 60.227 63.158 0.00 0.00 43.95 4.70
3054 3143 2.416432 AACTCTAGCCGTCGCTCCC 61.416 63.158 0.00 0.00 43.95 4.30
3056 3145 2.123854 TCTAGCCGTCGCTCCCAT 60.124 61.111 0.00 0.00 43.95 4.00
3057 3146 1.739338 CTCTAGCCGTCGCTCCCATT 61.739 60.000 0.00 0.00 43.95 3.16
3058 3147 1.592669 CTAGCCGTCGCTCCCATTG 60.593 63.158 0.00 0.00 43.95 2.82
3060 3149 1.038681 TAGCCGTCGCTCCCATTGTA 61.039 55.000 0.00 0.00 43.95 2.41
3062 3151 0.814010 GCCGTCGCTCCCATTGTATT 60.814 55.000 0.00 0.00 0.00 1.89
3063 3152 1.217882 CCGTCGCTCCCATTGTATTC 58.782 55.000 0.00 0.00 0.00 1.75
3064 3153 1.202533 CCGTCGCTCCCATTGTATTCT 60.203 52.381 0.00 0.00 0.00 2.40
3065 3154 2.128035 CGTCGCTCCCATTGTATTCTC 58.872 52.381 0.00 0.00 0.00 2.87
3066 3155 2.128035 GTCGCTCCCATTGTATTCTCG 58.872 52.381 0.00 0.00 0.00 4.04
3067 3156 2.028876 TCGCTCCCATTGTATTCTCGA 58.971 47.619 0.00 0.00 0.00 4.04
3070 3159 2.398498 CTCCCATTGTATTCTCGAGCG 58.602 52.381 7.81 0.00 0.00 5.03
3071 3160 1.068588 TCCCATTGTATTCTCGAGCGG 59.931 52.381 7.81 0.00 0.00 5.52
3073 3162 1.502231 CATTGTATTCTCGAGCGGGG 58.498 55.000 7.81 0.00 0.00 5.73
3074 3163 1.068588 CATTGTATTCTCGAGCGGGGA 59.931 52.381 7.81 0.00 0.00 4.81
3089 3604 1.320507 GGGGACTAGGCTAGAGTTCG 58.679 60.000 27.59 1.38 0.00 3.95
3090 3605 1.133853 GGGGACTAGGCTAGAGTTCGA 60.134 57.143 27.59 0.00 0.00 3.71
3097 3612 6.461788 GGACTAGGCTAGAGTTCGATGAATTT 60.462 42.308 27.59 0.00 0.00 1.82
3099 3614 8.184304 ACTAGGCTAGAGTTCGATGAATTTAT 57.816 34.615 27.59 0.00 0.00 1.40
3100 3615 8.085296 ACTAGGCTAGAGTTCGATGAATTTATG 58.915 37.037 27.59 0.00 0.00 1.90
3101 3616 7.055667 AGGCTAGAGTTCGATGAATTTATGA 57.944 36.000 0.00 0.00 0.00 2.15
3109 3624 9.307121 GAGTTCGATGAATTTATGAAAGAGAGA 57.693 33.333 0.00 0.00 0.00 3.10
3119 3634 3.131709 TGAAAGAGAGAGTGCCCTTTG 57.868 47.619 0.00 0.00 0.00 2.77
3121 3636 2.557920 AAGAGAGAGTGCCCTTTGTG 57.442 50.000 0.00 0.00 0.00 3.33
3122 3637 1.428869 AGAGAGAGTGCCCTTTGTGT 58.571 50.000 0.00 0.00 0.00 3.72
3125 3640 1.212935 AGAGAGTGCCCTTTGTGTGTT 59.787 47.619 0.00 0.00 0.00 3.32
3126 3641 1.334869 GAGAGTGCCCTTTGTGTGTTG 59.665 52.381 0.00 0.00 0.00 3.33
3129 3644 0.179113 GTGCCCTTTGTGTGTTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
3138 3653 1.021968 GTGTGTTGTGGGGTCACTTC 58.978 55.000 0.00 0.00 43.94 3.01
3144 3659 0.850100 TGTGGGGTCACTTCCAACAT 59.150 50.000 0.00 0.00 43.94 2.71
3150 3665 2.955660 GGGTCACTTCCAACATTGAACA 59.044 45.455 0.00 0.00 0.00 3.18
3151 3666 3.383185 GGGTCACTTCCAACATTGAACAA 59.617 43.478 0.00 0.00 0.00 2.83
3160 3675 4.099266 TCCAACATTGAACAACAGAAAGGG 59.901 41.667 0.00 0.00 0.00 3.95
3161 3676 3.733443 ACATTGAACAACAGAAAGGGC 57.267 42.857 0.00 0.00 0.00 5.19
3162 3677 2.365293 ACATTGAACAACAGAAAGGGCC 59.635 45.455 0.00 0.00 0.00 5.80
3163 3678 2.151502 TTGAACAACAGAAAGGGCCA 57.848 45.000 6.18 0.00 0.00 5.36
3169 3684 1.069049 CAACAGAAAGGGCCAACAAGG 59.931 52.381 6.18 0.00 41.84 3.61
3193 3708 0.035458 GTATGGGAGGCGAAGGATGG 59.965 60.000 0.00 0.00 0.00 3.51
3197 3712 1.153147 GGAGGCGAAGGATGGGTTC 60.153 63.158 0.00 0.00 0.00 3.62
3198 3713 1.602237 GAGGCGAAGGATGGGTTCA 59.398 57.895 0.00 0.00 0.00 3.18
3242 3757 2.630098 ACCGGTGGAGAGATGATATGTG 59.370 50.000 6.12 0.00 0.00 3.21
3247 3762 5.674525 GGTGGAGAGATGATATGTGTTTCA 58.325 41.667 0.00 0.00 0.00 2.69
3252 3767 7.496920 TGGAGAGATGATATGTGTTTCATTGAC 59.503 37.037 0.00 0.00 37.91 3.18
3254 3769 8.434733 AGAGATGATATGTGTTTCATTGACAG 57.565 34.615 0.00 0.00 37.91 3.51
3272 3787 2.267045 GGACCAGTTCCCACAATGC 58.733 57.895 0.00 0.00 38.70 3.56
3274 3789 1.549203 GACCAGTTCCCACAATGCAT 58.451 50.000 0.00 0.00 0.00 3.96
3276 3791 1.203038 ACCAGTTCCCACAATGCATGA 60.203 47.619 0.00 0.00 0.00 3.07
3289 3804 2.445565 TGCATGATGTCTATCTCGCC 57.554 50.000 0.00 0.00 33.18 5.54
3305 3820 0.870307 CGCCGATTCGAACGAGGATT 60.870 55.000 17.68 0.00 0.00 3.01
3321 3836 6.895782 ACGAGGATTACCCATTTCATTCTTA 58.104 36.000 0.00 0.00 37.41 2.10
3322 3837 6.766467 ACGAGGATTACCCATTTCATTCTTAC 59.234 38.462 0.00 0.00 37.41 2.34
3346 3861 4.573900 TCTTCAACAGAAGATTCAGGCTC 58.426 43.478 3.95 0.00 42.01 4.70
3348 3863 2.005451 CAACAGAAGATTCAGGCTCGG 58.995 52.381 0.00 0.00 0.00 4.63
3356 3871 0.602106 ATTCAGGCTCGGCGATGATG 60.602 55.000 11.27 9.54 0.00 3.07
3357 3872 1.675720 TTCAGGCTCGGCGATGATGA 61.676 55.000 11.27 11.89 0.00 2.92
3358 3873 1.664017 CAGGCTCGGCGATGATGAG 60.664 63.158 11.27 0.00 0.00 2.90
3360 3875 1.663074 GGCTCGGCGATGATGAGAC 60.663 63.158 11.27 0.00 31.31 3.36
3362 3877 0.938637 GCTCGGCGATGATGAGACTG 60.939 60.000 11.27 0.00 31.31 3.51
3370 3885 0.760567 ATGATGAGACTGGCCGCCTA 60.761 55.000 11.61 0.00 0.00 3.93
3399 3914 7.817478 TGACATACTACCGCCAAATAATATCTG 59.183 37.037 0.00 0.00 0.00 2.90
3403 3918 6.003950 ACTACCGCCAAATAATATCTGCATT 58.996 36.000 0.00 0.00 0.00 3.56
3408 3923 4.284234 GCCAAATAATATCTGCATTGGGGT 59.716 41.667 12.16 0.00 38.17 4.95
3409 3924 5.480073 GCCAAATAATATCTGCATTGGGGTA 59.520 40.000 12.16 0.00 38.17 3.69
3410 3925 6.572314 GCCAAATAATATCTGCATTGGGGTAC 60.572 42.308 12.16 0.00 38.17 3.34
3430 3946 1.468520 CCATTTGTGACTGGCCTAACG 59.531 52.381 3.32 0.00 0.00 3.18
3445 3961 5.123186 TGGCCTAACGAACACAAATCTTATG 59.877 40.000 3.32 0.00 0.00 1.90
3454 3970 6.359617 CGAACACAAATCTTATGACCAAACAC 59.640 38.462 0.00 0.00 0.00 3.32
3457 3973 5.624900 CACAAATCTTATGACCAAACACGTG 59.375 40.000 15.48 15.48 0.00 4.49
3493 4009 9.535170 TCTCTTAAGTTATATCCATCTAGGTGG 57.465 37.037 16.63 16.63 40.76 4.61
3494 4010 8.666129 TCTTAAGTTATATCCATCTAGGTGGG 57.334 38.462 22.17 5.58 39.80 4.61
3495 4011 8.461854 TCTTAAGTTATATCCATCTAGGTGGGA 58.538 37.037 22.17 10.89 39.80 4.37
3496 4012 9.101325 CTTAAGTTATATCCATCTAGGTGGGAA 57.899 37.037 22.17 10.71 39.80 3.97
3497 4013 7.560796 AAGTTATATCCATCTAGGTGGGAAG 57.439 40.000 22.17 0.00 39.80 3.46
3498 4014 6.635021 AGTTATATCCATCTAGGTGGGAAGT 58.365 40.000 22.17 10.88 39.80 3.01
3499 4015 7.082972 AGTTATATCCATCTAGGTGGGAAGTT 58.917 38.462 22.17 5.77 39.80 2.66
3500 4016 7.235812 AGTTATATCCATCTAGGTGGGAAGTTC 59.764 40.741 22.17 9.15 39.80 3.01
3501 4017 3.199442 TCCATCTAGGTGGGAAGTTCA 57.801 47.619 22.17 0.00 39.80 3.18
3502 4018 2.838202 TCCATCTAGGTGGGAAGTTCAC 59.162 50.000 22.17 0.62 39.80 3.18
3503 4019 2.418746 CCATCTAGGTGGGAAGTTCACG 60.419 54.545 14.89 0.00 36.09 4.35
3504 4020 2.297698 TCTAGGTGGGAAGTTCACGA 57.702 50.000 5.01 0.00 36.09 4.35
3505 4021 2.168496 TCTAGGTGGGAAGTTCACGAG 58.832 52.381 5.01 0.00 36.09 4.18
3506 4022 1.893801 CTAGGTGGGAAGTTCACGAGT 59.106 52.381 5.01 0.00 36.09 4.18
3507 4023 1.129058 AGGTGGGAAGTTCACGAGTT 58.871 50.000 5.01 0.00 36.09 3.01
3508 4024 1.070289 AGGTGGGAAGTTCACGAGTTC 59.930 52.381 5.01 0.00 37.04 3.01
3509 4025 1.070289 GGTGGGAAGTTCACGAGTTCT 59.930 52.381 5.01 0.00 37.74 3.01
3510 4026 2.484947 GGTGGGAAGTTCACGAGTTCTT 60.485 50.000 5.01 0.00 37.74 2.52
3511 4027 2.544267 GTGGGAAGTTCACGAGTTCTTG 59.456 50.000 5.01 0.00 37.74 3.02
3512 4028 2.143925 GGGAAGTTCACGAGTTCTTGG 58.856 52.381 5.01 0.00 37.74 3.61
3513 4029 2.484947 GGGAAGTTCACGAGTTCTTGGT 60.485 50.000 5.01 0.00 37.74 3.67
3514 4030 3.203716 GGAAGTTCACGAGTTCTTGGTT 58.796 45.455 5.01 0.00 37.74 3.67
3515 4031 3.247886 GGAAGTTCACGAGTTCTTGGTTC 59.752 47.826 5.01 0.00 37.74 3.62
3516 4032 2.835027 AGTTCACGAGTTCTTGGTTCC 58.165 47.619 0.00 0.00 0.00 3.62
3517 4033 1.871676 GTTCACGAGTTCTTGGTTCCC 59.128 52.381 0.00 0.00 0.00 3.97
3518 4034 0.395312 TCACGAGTTCTTGGTTCCCC 59.605 55.000 0.00 0.00 0.00 4.81
3519 4035 0.949105 CACGAGTTCTTGGTTCCCCG 60.949 60.000 0.00 0.00 0.00 5.73
3520 4036 1.370064 CGAGTTCTTGGTTCCCCGT 59.630 57.895 0.00 0.00 0.00 5.28
3521 4037 0.669625 CGAGTTCTTGGTTCCCCGTC 60.670 60.000 0.00 0.00 0.00 4.79
3522 4038 0.685660 GAGTTCTTGGTTCCCCGTCT 59.314 55.000 0.00 0.00 0.00 4.18
3523 4039 0.685660 AGTTCTTGGTTCCCCGTCTC 59.314 55.000 0.00 0.00 0.00 3.36
3524 4040 0.321387 GTTCTTGGTTCCCCGTCTCC 60.321 60.000 0.00 0.00 0.00 3.71
3525 4041 0.765135 TTCTTGGTTCCCCGTCTCCA 60.765 55.000 0.00 0.00 0.00 3.86
3526 4042 0.546747 TCTTGGTTCCCCGTCTCCAT 60.547 55.000 0.00 0.00 0.00 3.41
3527 4043 0.107654 CTTGGTTCCCCGTCTCCATC 60.108 60.000 0.00 0.00 0.00 3.51
3528 4044 0.546747 TTGGTTCCCCGTCTCCATCT 60.547 55.000 0.00 0.00 0.00 2.90
3529 4045 0.337082 TGGTTCCCCGTCTCCATCTA 59.663 55.000 0.00 0.00 0.00 1.98
3530 4046 1.041437 GGTTCCCCGTCTCCATCTAG 58.959 60.000 0.00 0.00 0.00 2.43
3531 4047 0.389757 GTTCCCCGTCTCCATCTAGC 59.610 60.000 0.00 0.00 0.00 3.42
3532 4048 1.107538 TTCCCCGTCTCCATCTAGCG 61.108 60.000 0.00 0.00 0.00 4.26
3533 4049 2.565645 CCCCGTCTCCATCTAGCGG 61.566 68.421 0.00 0.00 41.82 5.52
3534 4050 3.043419 CCGTCTCCATCTAGCGGG 58.957 66.667 0.00 0.00 38.86 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.517650 TTTTCAACCGGTTTGGATGC 57.482 45.000 19.55 0.00 40.23 3.91
70 71 1.228644 TCCGACGGAGGACAGGAAA 60.229 57.895 13.88 0.00 34.92 3.13
72 73 2.045242 CTCCGACGGAGGACAGGA 60.045 66.667 32.26 1.55 45.43 3.86
175 177 3.554934 AGTGTGGAACTGCAGAAATGAA 58.445 40.909 23.35 0.00 37.88 2.57
193 195 1.612950 TGTGCTTTATTGTGGGCAGTG 59.387 47.619 0.00 0.00 35.29 3.66
573 576 4.080299 AGCTTACTAGGAGTGGGGAATTTG 60.080 45.833 0.00 0.00 0.00 2.32
615 618 6.127026 GGTAGAGGTCCAGTTATCTCAACAAT 60.127 42.308 0.00 0.00 0.00 2.71
671 674 5.314923 AGAACGCTAGTCGGTAATTGTTA 57.685 39.130 10.53 0.00 38.87 2.41
856 882 0.659957 GATGCGAGTCAAATCAGCCC 59.340 55.000 0.00 0.00 0.00 5.19
900 926 1.234821 CAAGTTACAGCAAGGCCGAA 58.765 50.000 0.00 0.00 0.00 4.30
914 940 6.184789 TCACTCTAAAACTTTGTCCCAAGTT 58.815 36.000 0.00 0.00 40.63 2.66
968 994 7.749666 AGATGTTGCTGGGTTTATATAGACAT 58.250 34.615 5.83 0.00 0.00 3.06
993 1019 1.922447 ACACCCTTGGATATTGCCTGA 59.078 47.619 0.00 0.00 0.00 3.86
996 1022 2.863809 CCTACACCCTTGGATATTGCC 58.136 52.381 0.00 0.00 0.00 4.52
997 1023 2.230660 GCCTACACCCTTGGATATTGC 58.769 52.381 0.00 0.00 0.00 3.56
1007 1033 0.620410 TATGTGCCTGCCTACACCCT 60.620 55.000 0.00 0.00 35.90 4.34
1027 1053 7.012327 ACGAATTCCATGGTTTGTATGTATCTG 59.988 37.037 12.58 0.00 0.00 2.90
1039 1065 3.440173 CAGTTAGCACGAATTCCATGGTT 59.560 43.478 12.58 0.00 0.00 3.67
1066 1092 4.513442 TGCACAACACAAGAGAAAGTAGT 58.487 39.130 0.00 0.00 0.00 2.73
1160 1186 1.067212 GATGGTACGGTCGCTGATCTT 59.933 52.381 0.00 0.00 0.00 2.40
1173 1199 4.944372 CTCGGCGGGCGATGGTAC 62.944 72.222 26.95 0.00 0.00 3.34
1318 1344 1.911766 GAGGGTCCACCGGAGAACA 60.912 63.158 9.46 0.00 46.96 3.18
1320 1346 1.609501 CTGAGGGTCCACCGGAGAA 60.610 63.158 9.46 0.00 46.96 2.87
1408 1434 3.858868 GACGCGGAGGTCAGCAACA 62.859 63.158 12.47 0.00 36.87 3.33
1457 1486 1.226974 CGTTGAGGATGTCGCGGAT 60.227 57.895 6.13 0.00 0.00 4.18
1600 1629 1.807573 CTTCGCCGTCTTGGAGCTC 60.808 63.158 4.71 4.71 42.00 4.09
1747 1776 3.140623 GTCGAGGAGGTGGTCTAGATAC 58.859 54.545 0.00 0.00 0.00 2.24
1787 1816 4.072088 GCCGTCGGCTGTTTCGTG 62.072 66.667 28.98 0.00 46.69 4.35
1828 1857 2.159819 GAAGGCTCACCAGCTCGTCA 62.160 60.000 0.00 0.00 46.03 4.35
1964 1993 4.767255 GGACAGTGCGCCCTCCAG 62.767 72.222 4.18 0.00 0.00 3.86
2182 2211 1.990060 CCTGTGAGGGTCCGTCCAT 60.990 63.158 9.08 0.00 38.11 3.41
2195 2224 4.760047 CTCCGGGCGGAACCTGTG 62.760 72.222 0.00 0.00 44.28 3.66
2257 2286 0.253347 TCTTGATCTCCTTGGGCCCT 60.253 55.000 25.70 0.00 0.00 5.19
2343 2388 2.486322 GAACTCACGTACGAGCGCG 61.486 63.158 24.41 8.75 44.79 6.86
2495 2572 0.454600 CGTACTACGTCCTGCATGGT 59.545 55.000 0.00 0.00 36.74 3.55
2504 2581 5.554456 CGTTCGATCTTATTCGTACTACGTC 59.446 44.000 8.42 0.00 43.14 4.34
2513 2590 3.899835 TTGTGCGTTCGATCTTATTCG 57.100 42.857 0.00 0.00 40.46 3.34
2529 2606 7.523709 AGGGAACTAATACACAGCAAATTTGTG 60.524 37.037 19.03 16.70 45.07 3.33
2532 2609 6.152831 GGAGGGAACTAATACACAGCAAATTT 59.847 38.462 0.00 0.00 44.43 1.82
2533 2610 5.652452 GGAGGGAACTAATACACAGCAAATT 59.348 40.000 0.00 0.00 44.43 1.82
2534 2611 5.044846 AGGAGGGAACTAATACACAGCAAAT 60.045 40.000 0.00 0.00 44.43 2.32
2535 2612 4.288626 AGGAGGGAACTAATACACAGCAAA 59.711 41.667 0.00 0.00 44.43 3.68
2536 2613 3.844211 AGGAGGGAACTAATACACAGCAA 59.156 43.478 0.00 0.00 44.43 3.91
2537 2614 3.450904 AGGAGGGAACTAATACACAGCA 58.549 45.455 0.00 0.00 44.43 4.41
2538 2615 3.181464 GGAGGAGGGAACTAATACACAGC 60.181 52.174 0.00 0.00 44.43 4.40
2539 2616 4.290942 AGGAGGAGGGAACTAATACACAG 58.709 47.826 0.00 0.00 44.43 3.66
2540 2617 4.348020 AGGAGGAGGGAACTAATACACA 57.652 45.455 0.00 0.00 44.43 3.72
2541 2618 4.101274 GGAAGGAGGAGGGAACTAATACAC 59.899 50.000 0.00 0.00 44.43 2.90
2542 2619 4.015541 AGGAAGGAGGAGGGAACTAATACA 60.016 45.833 0.00 0.00 44.43 2.29
2543 2620 4.345547 CAGGAAGGAGGAGGGAACTAATAC 59.654 50.000 0.00 0.00 44.43 1.89
2544 2621 4.015541 ACAGGAAGGAGGAGGGAACTAATA 60.016 45.833 0.00 0.00 44.43 0.98
2545 2622 3.246535 ACAGGAAGGAGGAGGGAACTAAT 60.247 47.826 0.00 0.00 44.43 1.73
2546 2623 2.113777 ACAGGAAGGAGGAGGGAACTAA 59.886 50.000 0.00 0.00 44.43 2.24
2547 2624 1.722851 ACAGGAAGGAGGAGGGAACTA 59.277 52.381 0.00 0.00 44.43 2.24
2549 2626 0.615850 CACAGGAAGGAGGAGGGAAC 59.384 60.000 0.00 0.00 0.00 3.62
2550 2627 0.193574 ACACAGGAAGGAGGAGGGAA 59.806 55.000 0.00 0.00 0.00 3.97
2581 2658 6.581166 CGTACGCAGCAAATCTATATAAGTGA 59.419 38.462 0.52 0.00 0.00 3.41
2582 2659 6.362551 ACGTACGCAGCAAATCTATATAAGTG 59.637 38.462 16.72 0.00 0.00 3.16
2583 2660 6.362551 CACGTACGCAGCAAATCTATATAAGT 59.637 38.462 16.72 0.00 0.00 2.24
2584 2661 6.667621 GCACGTACGCAGCAAATCTATATAAG 60.668 42.308 23.31 0.00 0.00 1.73
2585 2662 5.118050 GCACGTACGCAGCAAATCTATATAA 59.882 40.000 23.31 0.00 0.00 0.98
2586 2663 4.619760 GCACGTACGCAGCAAATCTATATA 59.380 41.667 23.31 0.00 0.00 0.86
2684 2772 8.506437 TCTTCACTAATTTCAAACTGCATGTAG 58.494 33.333 9.50 9.50 0.00 2.74
2690 2778 7.985634 TGTTTCTTCACTAATTTCAAACTGC 57.014 32.000 0.00 0.00 0.00 4.40
2702 2790 8.770828 GTGCTACTATGTTTTGTTTCTTCACTA 58.229 33.333 0.00 0.00 0.00 2.74
2709 2797 7.386848 TCCAGTAGTGCTACTATGTTTTGTTTC 59.613 37.037 11.08 0.00 43.98 2.78
2715 2803 8.863872 AATTTTCCAGTAGTGCTACTATGTTT 57.136 30.769 11.08 0.48 43.98 2.83
2723 2811 4.171005 CGACGAATTTTCCAGTAGTGCTA 58.829 43.478 0.00 0.00 0.00 3.49
2776 2864 3.916359 TTACCGCAATCCCATGTTCTA 57.084 42.857 0.00 0.00 0.00 2.10
2783 2872 0.251386 TGCCTTTTACCGCAATCCCA 60.251 50.000 0.00 0.00 30.46 4.37
2789 2878 1.538075 GCTTACTTGCCTTTTACCGCA 59.462 47.619 0.00 0.00 0.00 5.69
2822 2911 3.007074 TGCCGTATCCTACTGTTTGACAA 59.993 43.478 0.00 0.00 0.00 3.18
2823 2912 2.563620 TGCCGTATCCTACTGTTTGACA 59.436 45.455 0.00 0.00 0.00 3.58
2825 2914 2.563620 TGTGCCGTATCCTACTGTTTGA 59.436 45.455 0.00 0.00 0.00 2.69
2841 2930 0.464554 GGTAGAGCTTCCCATGTGCC 60.465 60.000 0.00 0.00 0.00 5.01
2848 2937 1.224870 GGGCTTGGTAGAGCTTCCC 59.775 63.158 0.00 0.00 42.32 3.97
2862 2951 2.123597 TATGTACCGAGCGGGGCT 60.124 61.111 14.07 0.00 43.88 5.19
2870 2959 5.186215 TCCTTCATGTTTGACTATGTACCGA 59.814 40.000 0.00 0.00 0.00 4.69
2871 2960 5.416083 TCCTTCATGTTTGACTATGTACCG 58.584 41.667 0.00 0.00 0.00 4.02
2881 2970 4.336889 AGTCGAGTTCCTTCATGTTTGA 57.663 40.909 0.00 0.00 0.00 2.69
2889 2978 2.612212 TGTGCAAAAGTCGAGTTCCTTC 59.388 45.455 5.84 0.00 0.00 3.46
2933 3022 2.753849 TGCTATTTGCCGGGTGCC 60.754 61.111 2.18 0.00 42.00 5.01
2934 3023 2.800736 CTGCTATTTGCCGGGTGC 59.199 61.111 2.18 0.00 42.00 5.01
2935 3024 2.774799 GGCTGCTATTTGCCGGGTG 61.775 63.158 2.18 0.00 42.00 4.61
2936 3025 2.440247 GGCTGCTATTTGCCGGGT 60.440 61.111 2.18 0.00 42.00 5.28
2967 3056 2.617274 GGGTCCGTCAGCTGCAAAC 61.617 63.158 9.47 0.74 0.00 2.93
2968 3057 2.281484 GGGTCCGTCAGCTGCAAA 60.281 61.111 9.47 0.00 0.00 3.68
2969 3058 4.680237 CGGGTCCGTCAGCTGCAA 62.680 66.667 9.47 0.00 34.35 4.08
2971 3060 4.803426 CTCGGGTCCGTCAGCTGC 62.803 72.222 9.47 3.23 40.74 5.25
2973 3062 3.063084 GTCTCGGGTCCGTCAGCT 61.063 66.667 9.36 0.00 40.74 4.24
2974 3063 4.131088 GGTCTCGGGTCCGTCAGC 62.131 72.222 9.36 3.46 40.74 4.26
2976 3065 2.360852 GAGGTCTCGGGTCCGTCA 60.361 66.667 9.36 0.00 40.74 4.35
2986 3075 4.344448 CGAGTAACTTTCATCGAGGTCTC 58.656 47.826 0.00 0.00 37.35 3.36
2987 3076 3.128938 CCGAGTAACTTTCATCGAGGTCT 59.871 47.826 0.00 0.00 37.35 3.85
2988 3077 3.436496 CCGAGTAACTTTCATCGAGGTC 58.564 50.000 0.00 0.00 37.35 3.85
2989 3078 2.416972 GCCGAGTAACTTTCATCGAGGT 60.417 50.000 0.00 0.00 37.35 3.85
2990 3079 2.194271 GCCGAGTAACTTTCATCGAGG 58.806 52.381 0.00 0.00 37.35 4.63
2991 3080 2.876091 TGCCGAGTAACTTTCATCGAG 58.124 47.619 0.00 0.00 37.35 4.04
2992 3081 3.306917 TTGCCGAGTAACTTTCATCGA 57.693 42.857 0.00 0.00 37.35 3.59
2993 3082 3.865745 AGATTGCCGAGTAACTTTCATCG 59.134 43.478 0.00 0.00 35.02 3.84
2994 3083 6.701841 TCATAGATTGCCGAGTAACTTTCATC 59.298 38.462 0.00 0.00 0.00 2.92
2995 3084 6.582636 TCATAGATTGCCGAGTAACTTTCAT 58.417 36.000 0.00 0.00 0.00 2.57
2996 3085 5.972935 TCATAGATTGCCGAGTAACTTTCA 58.027 37.500 0.00 0.00 0.00 2.69
2997 3086 5.463724 CCTCATAGATTGCCGAGTAACTTTC 59.536 44.000 0.00 0.00 0.00 2.62
2998 3087 5.104900 ACCTCATAGATTGCCGAGTAACTTT 60.105 40.000 0.00 0.00 0.00 2.66
2999 3088 4.406003 ACCTCATAGATTGCCGAGTAACTT 59.594 41.667 0.00 0.00 0.00 2.66
3000 3089 3.961408 ACCTCATAGATTGCCGAGTAACT 59.039 43.478 0.00 0.00 0.00 2.24
3001 3090 4.323553 ACCTCATAGATTGCCGAGTAAC 57.676 45.455 0.00 0.00 0.00 2.50
3002 3091 6.665992 AATACCTCATAGATTGCCGAGTAA 57.334 37.500 0.00 0.00 0.00 2.24
3003 3092 6.266786 TGAAATACCTCATAGATTGCCGAGTA 59.733 38.462 0.00 0.00 0.00 2.59
3004 3093 5.070446 TGAAATACCTCATAGATTGCCGAGT 59.930 40.000 0.00 0.00 0.00 4.18
3005 3094 5.541845 TGAAATACCTCATAGATTGCCGAG 58.458 41.667 0.00 0.00 0.00 4.63
3008 3097 5.049405 CGGTTGAAATACCTCATAGATTGCC 60.049 44.000 0.00 0.00 35.97 4.52
3009 3098 5.049405 CCGGTTGAAATACCTCATAGATTGC 60.049 44.000 0.00 0.00 35.97 3.56
3010 3099 5.049405 GCCGGTTGAAATACCTCATAGATTG 60.049 44.000 1.90 0.00 35.97 2.67
3011 3100 5.063880 GCCGGTTGAAATACCTCATAGATT 58.936 41.667 1.90 0.00 35.97 2.40
3012 3101 4.505039 GGCCGGTTGAAATACCTCATAGAT 60.505 45.833 1.90 0.00 35.97 1.98
3013 3102 3.181458 GGCCGGTTGAAATACCTCATAGA 60.181 47.826 1.90 0.00 35.97 1.98
3014 3103 3.139077 GGCCGGTTGAAATACCTCATAG 58.861 50.000 1.90 0.00 35.97 2.23
3016 3105 1.283613 TGGCCGGTTGAAATACCTCAT 59.716 47.619 1.90 0.00 35.97 2.90
3018 3107 1.471287 GTTGGCCGGTTGAAATACCTC 59.529 52.381 1.90 0.00 35.97 3.85
3019 3108 1.074889 AGTTGGCCGGTTGAAATACCT 59.925 47.619 1.90 0.00 35.97 3.08
3020 3109 1.471287 GAGTTGGCCGGTTGAAATACC 59.529 52.381 1.90 0.00 34.72 2.73
3021 3110 2.433436 AGAGTTGGCCGGTTGAAATAC 58.567 47.619 1.90 0.00 0.00 1.89
3023 3112 2.711542 CTAGAGTTGGCCGGTTGAAAT 58.288 47.619 1.90 0.00 0.00 2.17
3025 3114 0.321298 GCTAGAGTTGGCCGGTTGAA 60.321 55.000 1.90 0.00 0.00 2.69
3027 3116 1.745489 GGCTAGAGTTGGCCGGTTG 60.745 63.158 1.90 0.00 41.42 3.77
3032 3121 2.202756 CGACGGCTAGAGTTGGCC 60.203 66.667 0.00 0.00 46.76 5.36
3033 3122 2.886124 GCGACGGCTAGAGTTGGC 60.886 66.667 0.00 0.00 35.83 4.52
3043 3132 0.814010 AATACAATGGGAGCGACGGC 60.814 55.000 0.00 0.00 40.37 5.68
3044 3133 1.202533 AGAATACAATGGGAGCGACGG 60.203 52.381 0.00 0.00 0.00 4.79
3045 3134 2.128035 GAGAATACAATGGGAGCGACG 58.872 52.381 0.00 0.00 0.00 5.12
3046 3135 2.128035 CGAGAATACAATGGGAGCGAC 58.872 52.381 0.00 0.00 0.00 5.19
3048 3137 2.398498 CTCGAGAATACAATGGGAGCG 58.602 52.381 6.58 0.00 0.00 5.03
3049 3138 2.139118 GCTCGAGAATACAATGGGAGC 58.861 52.381 18.75 0.00 38.65 4.70
3050 3139 2.398498 CGCTCGAGAATACAATGGGAG 58.602 52.381 18.75 0.00 0.00 4.30
3052 3141 1.502231 CCGCTCGAGAATACAATGGG 58.498 55.000 18.75 0.00 0.00 4.00
3053 3142 1.502231 CCCGCTCGAGAATACAATGG 58.498 55.000 18.75 3.73 0.00 3.16
3054 3143 1.068588 TCCCCGCTCGAGAATACAATG 59.931 52.381 18.75 0.00 0.00 2.82
3056 3145 0.458669 GTCCCCGCTCGAGAATACAA 59.541 55.000 18.75 0.00 0.00 2.41
3057 3146 0.395311 AGTCCCCGCTCGAGAATACA 60.395 55.000 18.75 0.00 0.00 2.29
3058 3147 1.536331 CTAGTCCCCGCTCGAGAATAC 59.464 57.143 18.75 6.18 0.00 1.89
3060 3149 0.824182 CCTAGTCCCCGCTCGAGAAT 60.824 60.000 18.75 0.00 0.00 2.40
3062 3151 2.192443 CCTAGTCCCCGCTCGAGA 59.808 66.667 18.75 0.00 0.00 4.04
3063 3152 2.677765 TAGCCTAGTCCCCGCTCGAG 62.678 65.000 8.45 8.45 34.03 4.04
3064 3153 2.677765 CTAGCCTAGTCCCCGCTCGA 62.678 65.000 0.00 0.00 34.03 4.04
3065 3154 2.203308 TAGCCTAGTCCCCGCTCG 60.203 66.667 0.00 0.00 34.03 5.03
3066 3155 0.891904 CTCTAGCCTAGTCCCCGCTC 60.892 65.000 0.00 0.00 34.03 5.03
3067 3156 1.151908 CTCTAGCCTAGTCCCCGCT 59.848 63.158 0.00 0.00 36.63 5.52
3070 3159 1.133853 TCGAACTCTAGCCTAGTCCCC 60.134 57.143 0.00 0.00 0.00 4.81
3071 3160 2.345124 TCGAACTCTAGCCTAGTCCC 57.655 55.000 0.00 0.00 0.00 4.46
3073 3162 5.699097 ATTCATCGAACTCTAGCCTAGTC 57.301 43.478 0.00 0.00 0.00 2.59
3074 3163 6.472686 AAATTCATCGAACTCTAGCCTAGT 57.527 37.500 0.00 0.00 0.00 2.57
3089 3604 7.255070 GGGCACTCTCTCTTTCATAAATTCATC 60.255 40.741 0.00 0.00 0.00 2.92
3090 3605 6.545298 GGGCACTCTCTCTTTCATAAATTCAT 59.455 38.462 0.00 0.00 0.00 2.57
3097 3612 4.287067 ACAAAGGGCACTCTCTCTTTCATA 59.713 41.667 0.00 0.00 0.00 2.15
3099 3614 2.439507 ACAAAGGGCACTCTCTCTTTCA 59.560 45.455 0.00 0.00 0.00 2.69
3100 3615 2.810852 CACAAAGGGCACTCTCTCTTTC 59.189 50.000 0.00 0.00 0.00 2.62
3101 3616 2.173569 ACACAAAGGGCACTCTCTCTTT 59.826 45.455 0.00 0.00 0.00 2.52
3109 3624 0.817013 CACAACACACAAAGGGCACT 59.183 50.000 0.00 0.00 0.00 4.40
3119 3634 1.021968 GAAGTGACCCCACAACACAC 58.978 55.000 0.00 0.00 45.54 3.82
3121 3636 0.106918 TGGAAGTGACCCCACAACAC 60.107 55.000 0.00 0.00 45.54 3.32
3122 3637 0.626382 TTGGAAGTGACCCCACAACA 59.374 50.000 0.00 0.00 45.54 3.33
3125 3640 0.850100 ATGTTGGAAGTGACCCCACA 59.150 50.000 0.00 0.00 45.54 4.17
3126 3641 1.613437 CAATGTTGGAAGTGACCCCAC 59.387 52.381 0.00 0.00 43.50 4.61
3129 3644 2.955660 TGTTCAATGTTGGAAGTGACCC 59.044 45.455 0.00 0.00 0.00 4.46
3138 3653 4.370917 CCCTTTCTGTTGTTCAATGTTGG 58.629 43.478 0.00 0.00 0.00 3.77
3144 3659 2.151502 TGGCCCTTTCTGTTGTTCAA 57.848 45.000 0.00 0.00 0.00 2.69
3150 3665 1.063266 TCCTTGTTGGCCCTTTCTGTT 60.063 47.619 0.00 0.00 35.26 3.16
3151 3666 0.555769 TCCTTGTTGGCCCTTTCTGT 59.444 50.000 0.00 0.00 35.26 3.41
3160 3675 1.029947 CCATACGGGTCCTTGTTGGC 61.030 60.000 0.00 0.00 35.26 4.52
3161 3676 3.168773 CCATACGGGTCCTTGTTGG 57.831 57.895 0.00 0.00 37.10 3.77
3193 3708 4.084013 CCGTTCTGTGTAATGAACTGAACC 60.084 45.833 15.92 4.41 45.90 3.62
3197 3712 4.150627 CAGACCGTTCTGTGTAATGAACTG 59.849 45.833 1.10 0.00 43.95 3.16
3198 3713 4.307432 CAGACCGTTCTGTGTAATGAACT 58.693 43.478 1.10 0.00 43.95 3.01
3220 3735 2.894126 ACATATCATCTCTCCACCGGTC 59.106 50.000 2.59 0.00 0.00 4.79
3223 3738 4.327982 AACACATATCATCTCTCCACCG 57.672 45.455 0.00 0.00 0.00 4.94
3225 3740 7.496920 TCAATGAAACACATATCATCTCTCCAC 59.503 37.037 0.00 0.00 38.38 4.02
3242 3757 3.253432 GGAACTGGTCCTGTCAATGAAAC 59.747 47.826 3.98 0.00 43.98 2.78
3247 3762 1.073923 GTGGGAACTGGTCCTGTCAAT 59.926 52.381 12.27 0.00 46.92 2.57
3252 3767 1.538047 CATTGTGGGAACTGGTCCTG 58.462 55.000 12.27 0.00 46.92 3.86
3267 3782 3.124806 GGCGAGATAGACATCATGCATTG 59.875 47.826 0.00 0.00 36.07 2.82
3272 3787 2.997485 TCGGCGAGATAGACATCATG 57.003 50.000 4.99 0.00 33.21 3.07
3274 3789 2.095718 CGAATCGGCGAGATAGACATCA 60.096 50.000 17.22 0.00 38.98 3.07
3276 3791 2.152016 TCGAATCGGCGAGATAGACAT 58.848 47.619 17.22 0.00 38.98 3.06
3289 3804 2.223641 TGGGTAATCCTCGTTCGAATCG 60.224 50.000 0.00 7.46 36.20 3.34
3305 3820 8.956426 GTTGAAGATGTAAGAATGAAATGGGTA 58.044 33.333 0.00 0.00 0.00 3.69
3338 3853 1.227350 CATCATCGCCGAGCCTGAA 60.227 57.895 0.00 0.00 0.00 3.02
3343 3858 0.938637 CAGTCTCATCATCGCCGAGC 60.939 60.000 0.00 0.00 0.00 5.03
3346 3861 1.953138 GCCAGTCTCATCATCGCCG 60.953 63.158 0.00 0.00 0.00 6.46
3348 3863 1.953138 CGGCCAGTCTCATCATCGC 60.953 63.158 2.24 0.00 0.00 4.58
3356 3871 1.153549 CAAGTAGGCGGCCAGTCTC 60.154 63.158 23.09 6.32 35.65 3.36
3357 3872 1.609501 TCAAGTAGGCGGCCAGTCT 60.610 57.895 23.09 12.87 38.92 3.24
3358 3873 1.448013 GTCAAGTAGGCGGCCAGTC 60.448 63.158 23.09 10.70 0.00 3.51
3360 3875 0.464036 TATGTCAAGTAGGCGGCCAG 59.536 55.000 23.09 5.47 0.00 4.85
3362 3877 0.464452 AGTATGTCAAGTAGGCGGCC 59.536 55.000 12.11 12.11 0.00 6.13
3370 3885 3.688694 TTTGGCGGTAGTATGTCAAGT 57.311 42.857 0.00 0.00 0.00 3.16
3399 3914 2.094234 GTCACAAATGGTACCCCAATGC 60.094 50.000 10.07 0.00 46.04 3.56
3408 3923 3.681593 GTTAGGCCAGTCACAAATGGTA 58.318 45.455 5.01 0.00 38.91 3.25
3409 3924 2.514803 GTTAGGCCAGTCACAAATGGT 58.485 47.619 5.01 0.00 38.91 3.55
3410 3925 1.468520 CGTTAGGCCAGTCACAAATGG 59.531 52.381 5.01 0.00 39.73 3.16
3412 3927 2.812011 GTTCGTTAGGCCAGTCACAAAT 59.188 45.455 5.01 0.00 0.00 2.32
3413 3928 2.215196 GTTCGTTAGGCCAGTCACAAA 58.785 47.619 5.01 0.00 0.00 2.83
3422 3938 5.353123 TCATAAGATTTGTGTTCGTTAGGCC 59.647 40.000 0.00 0.00 0.00 5.19
3430 3946 6.359617 CGTGTTTGGTCATAAGATTTGTGTTC 59.640 38.462 0.00 0.00 0.00 3.18
3445 3961 3.071479 ACATACCATCACGTGTTTGGTC 58.929 45.455 33.62 0.00 42.65 4.02
3454 3970 8.873215 ATAACTTAAGAGAACATACCATCACG 57.127 34.615 10.09 0.00 0.00 4.35
3493 4009 2.835027 ACCAAGAACTCGTGAACTTCC 58.165 47.619 0.00 0.00 0.00 3.46
3494 4010 3.247886 GGAACCAAGAACTCGTGAACTTC 59.752 47.826 0.00 0.00 0.00 3.01
3495 4011 3.203716 GGAACCAAGAACTCGTGAACTT 58.796 45.455 0.00 0.00 0.00 2.66
3496 4012 2.835027 GGAACCAAGAACTCGTGAACT 58.165 47.619 0.00 0.00 0.00 3.01
3512 4028 0.389757 GCTAGATGGAGACGGGGAAC 59.610 60.000 0.00 0.00 0.00 3.62
3513 4029 1.107538 CGCTAGATGGAGACGGGGAA 61.108 60.000 0.00 0.00 0.00 3.97
3514 4030 1.528542 CGCTAGATGGAGACGGGGA 60.529 63.158 0.00 0.00 0.00 4.81
3515 4031 2.565645 CCGCTAGATGGAGACGGGG 61.566 68.421 0.00 0.00 40.18 5.73
3516 4032 3.043419 CCGCTAGATGGAGACGGG 58.957 66.667 0.00 0.00 40.18 5.28
3517 4033 3.043419 CCCGCTAGATGGAGACGG 58.957 66.667 0.00 0.00 43.44 4.79


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

AutoCloner maintained by Alex Coulton.