Multiple sequence alignment - TraesCS2A01G389700

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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 TraesCS2A01G389700 chr2A 100.000 1880 0 0 787 2666 638320691 638318812 0.000000e+00 3472.0
1 TraesCS2A01G389700 chr2A 92.374 931 29 12 1536 2438 638311406 638310490 0.000000e+00 1288.0
2 TraesCS2A01G389700 chr2A 100.000 494 0 0 1 494 638321477 638320984 0.000000e+00 913.0
3 TraesCS2A01G389700 chr2A 83.030 495 76 6 1 494 668776948 668777435 2.440000e-120 442.0
4 TraesCS2A01G389700 chr2A 76.126 222 49 3 235 455 757888628 757888410 2.170000e-21 113.0
5 TraesCS2A01G389700 chr2A 91.667 48 4 0 2383 2430 754713425 754713472 1.710000e-07 67.6
6 TraesCS2A01G389700 chr2A 84.375 64 7 3 428 490 672110767 672110828 2.870000e-05 60.2
7 TraesCS2A01G389700 chr2D 90.039 1034 55 12 1020 2010 495398788 495399816 0.000000e+00 1295.0
8 TraesCS2A01G389700 chr2D 91.758 364 22 1 2083 2438 495399882 495400245 1.430000e-137 499.0
9 TraesCS2A01G389700 chr2D 97.674 43 1 0 2395 2437 36689406 36689364 1.020000e-09 75.0
10 TraesCS2A01G389700 chr2B 91.513 919 49 5 1020 1933 583062426 583063320 0.000000e+00 1238.0
11 TraesCS2A01G389700 chr2B 85.794 359 21 9 2083 2438 583063438 583063769 1.170000e-93 353.0
12 TraesCS2A01G389700 chr2B 79.121 91 16 2 366 455 763107944 763107856 2.870000e-05 60.2
13 TraesCS2A01G389700 chr2B 96.875 32 1 0 2404 2435 791288766 791288735 1.000000e-03 54.7
14 TraesCS2A01G389700 chr4D 92.245 490 38 0 1 490 383758585 383758096 0.000000e+00 695.0
15 TraesCS2A01G389700 chr4D 95.556 45 1 1 788 832 383758045 383758002 1.320000e-08 71.3
16 TraesCS2A01G389700 chr6D 85.714 406 56 2 1 405 27858558 27858962 6.820000e-116 427.0
17 TraesCS2A01G389700 chr6D 74.130 460 108 11 1 455 262158323 262157870 2.110000e-41 180.0
18 TraesCS2A01G389700 chr3B 95.614 228 10 0 2434 2661 54765988 54765761 1.510000e-97 366.0
19 TraesCS2A01G389700 chr3B 94.737 228 11 1 2434 2661 54776672 54776446 1.170000e-93 353.0
20 TraesCS2A01G389700 chr3B 97.059 34 0 1 2403 2435 236356550 236356517 3.710000e-04 56.5
21 TraesCS2A01G389700 chr5D 73.611 432 102 10 50 477 430514215 430513792 3.550000e-34 156.0
22 TraesCS2A01G389700 chr7D 72.727 495 121 13 1 490 269716293 269716778 1.280000e-33 154.0
23 TraesCS2A01G389700 chr7D 83.544 79 13 0 2359 2437 195308359 195308281 1.020000e-09 75.0
24 TraesCS2A01G389700 chr7D 95.349 43 2 0 788 830 269716821 269716863 4.760000e-08 69.4
25 TraesCS2A01G389700 chr3D 84.444 90 11 3 366 455 50007969 50008055 4.730000e-13 86.1
26 TraesCS2A01G389700 chr3D 95.349 43 1 1 788 830 50008131 50008172 1.710000e-07 67.6
27 TraesCS2A01G389700 chr7B 84.810 79 12 0 2359 2437 159137666 159137588 2.200000e-11 80.5
28 TraesCS2A01G389700 chr7B 95.349 43 2 0 2395 2437 718469085 718469043 4.760000e-08 69.4
29 TraesCS2A01G389700 chr4B 95.238 42 1 1 788 829 29153928 29153888 6.160000e-07 65.8


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 TraesCS2A01G389700 chr2A 638318812 638321477 2665 True 2192.50 3472 100.0000 1 2666 2 chr2A.!!$R3 2665
1 TraesCS2A01G389700 chr2A 638310490 638311406 916 True 1288.00 1288 92.3740 1536 2438 1 chr2A.!!$R1 902
2 TraesCS2A01G389700 chr2D 495398788 495400245 1457 False 897.00 1295 90.8985 1020 2438 2 chr2D.!!$F1 1418
3 TraesCS2A01G389700 chr2B 583062426 583063769 1343 False 795.50 1238 88.6535 1020 2438 2 chr2B.!!$F1 1418
4 TraesCS2A01G389700 chr4D 383758002 383758585 583 True 383.15 695 93.9005 1 832 2 chr4D.!!$R1 831

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
855 856 0.03582 GGTTGGGTGAAGGCGATACA 60.036 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2438 2564 0.034186 TCCACATCTTGTCCATGGCC 60.034 55.0 6.96 0.0 0.0 5.36 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
42 43 3.002348 GTGTTCGCCATGGCTTATCTAAC 59.998 47.826 33.07 23.66 39.32 2.34
48 49 2.368875 CCATGGCTTATCTAACGACCCT 59.631 50.000 0.00 0.00 0.00 4.34
75 76 2.125350 CTCTGCGACCAAGAGGCC 60.125 66.667 0.00 0.00 39.06 5.19
152 153 1.617947 ATTCTCTCCTGGTGTCGCCC 61.618 60.000 0.00 0.00 36.04 6.13
156 157 0.755698 TCTCCTGGTGTCGCCCTATC 60.756 60.000 0.00 0.00 36.04 2.08
204 205 3.649277 CTTCGCCTGGTGGTCCGAG 62.649 68.421 7.51 0.00 36.30 4.63
231 232 2.353610 GGCATCCCCTGGTTGCTTG 61.354 63.158 14.05 0.00 44.92 4.01
240 241 1.251251 CTGGTTGCTTGAGAAAGGGG 58.749 55.000 0.00 0.00 0.00 4.79
257 258 0.179000 GGGCTCAACTCCATCATCGT 59.821 55.000 0.00 0.00 0.00 3.73
259 260 1.406069 GGCTCAACTCCATCATCGTGT 60.406 52.381 0.00 0.00 0.00 4.49
267 268 1.001860 TCCATCATCGTGTTGTCTGCA 59.998 47.619 0.00 0.00 0.00 4.41
270 271 2.168326 TCATCGTGTTGTCTGCATGT 57.832 45.000 0.00 0.00 0.00 3.21
287 288 1.630223 TGTGCCATTTGGAAGCATCA 58.370 45.000 0.00 0.00 39.04 3.07
312 313 1.737838 CAGCTATCTTCAACGGCCAA 58.262 50.000 2.24 0.00 0.00 4.52
313 314 2.292267 CAGCTATCTTCAACGGCCAAT 58.708 47.619 2.24 0.00 0.00 3.16
396 397 1.321074 GCACCACGGGACTAGCTAGT 61.321 60.000 26.35 26.35 39.71 2.57
465 466 1.529010 CCCTGCTCACTTTGCACCA 60.529 57.895 0.00 0.00 36.37 4.17
474 475 1.069703 CACTTTGCACCATCACTGACG 60.070 52.381 0.00 0.00 0.00 4.35
492 493 4.368808 CCGGCTCGTGCACGTTTG 62.369 66.667 35.74 26.37 41.91 2.93
844 845 2.381752 AAAAAGAGGAGGGTTGGGTG 57.618 50.000 0.00 0.00 0.00 4.61
845 846 1.529744 AAAAGAGGAGGGTTGGGTGA 58.470 50.000 0.00 0.00 0.00 4.02
846 847 1.529744 AAAGAGGAGGGTTGGGTGAA 58.470 50.000 0.00 0.00 0.00 3.18
847 848 1.068121 AAGAGGAGGGTTGGGTGAAG 58.932 55.000 0.00 0.00 0.00 3.02
848 849 0.842467 AGAGGAGGGTTGGGTGAAGG 60.842 60.000 0.00 0.00 0.00 3.46
849 850 2.035783 GGAGGGTTGGGTGAAGGC 59.964 66.667 0.00 0.00 0.00 4.35
850 851 2.359975 GAGGGTTGGGTGAAGGCG 60.360 66.667 0.00 0.00 0.00 5.52
851 852 2.852075 AGGGTTGGGTGAAGGCGA 60.852 61.111 0.00 0.00 0.00 5.54
852 853 2.198304 GAGGGTTGGGTGAAGGCGAT 62.198 60.000 0.00 0.00 0.00 4.58
853 854 0.912487 AGGGTTGGGTGAAGGCGATA 60.912 55.000 0.00 0.00 0.00 2.92
854 855 0.746923 GGGTTGGGTGAAGGCGATAC 60.747 60.000 0.00 0.00 0.00 2.24
855 856 0.035820 GGTTGGGTGAAGGCGATACA 60.036 55.000 0.00 0.00 0.00 2.29
856 857 1.612199 GGTTGGGTGAAGGCGATACAA 60.612 52.381 0.00 0.00 0.00 2.41
857 858 1.467342 GTTGGGTGAAGGCGATACAAC 59.533 52.381 0.00 0.00 0.00 3.32
858 859 0.390603 TGGGTGAAGGCGATACAACG 60.391 55.000 0.00 0.00 0.00 4.10
859 860 0.108520 GGGTGAAGGCGATACAACGA 60.109 55.000 0.00 0.00 35.09 3.85
860 861 1.278238 GGTGAAGGCGATACAACGAG 58.722 55.000 0.00 0.00 35.09 4.18
861 862 0.645868 GTGAAGGCGATACAACGAGC 59.354 55.000 0.00 0.00 35.09 5.03
862 863 0.245266 TGAAGGCGATACAACGAGCA 59.755 50.000 0.00 0.00 35.09 4.26
863 864 1.337354 TGAAGGCGATACAACGAGCAA 60.337 47.619 0.00 0.00 35.09 3.91
864 865 1.060698 GAAGGCGATACAACGAGCAAC 59.939 52.381 0.00 0.00 35.09 4.17
865 866 0.246635 AGGCGATACAACGAGCAACT 59.753 50.000 0.00 0.00 35.09 3.16
866 867 0.645868 GGCGATACAACGAGCAACTC 59.354 55.000 0.00 0.00 35.09 3.01
867 868 1.630148 GCGATACAACGAGCAACTCT 58.370 50.000 0.00 0.00 35.09 3.24
868 869 1.584308 GCGATACAACGAGCAACTCTC 59.416 52.381 0.00 0.00 38.47 3.20
882 883 7.901874 GAGCAACTCTCGTTTAATAGTAGAG 57.098 40.000 0.00 0.00 39.65 2.43
883 884 7.627298 AGCAACTCTCGTTTAATAGTAGAGA 57.373 36.000 0.00 0.00 37.66 3.10
884 885 8.228035 AGCAACTCTCGTTTAATAGTAGAGAT 57.772 34.615 0.00 0.00 37.34 2.75
885 886 8.688151 AGCAACTCTCGTTTAATAGTAGAGATT 58.312 33.333 0.00 0.00 37.34 2.40
886 887 8.747666 GCAACTCTCGTTTAATAGTAGAGATTG 58.252 37.037 0.00 0.00 37.34 2.67
887 888 8.747666 CAACTCTCGTTTAATAGTAGAGATTGC 58.252 37.037 0.00 0.00 37.34 3.56
888 889 7.133513 ACTCTCGTTTAATAGTAGAGATTGCG 58.866 38.462 0.00 0.00 37.34 4.85
889 890 7.012138 ACTCTCGTTTAATAGTAGAGATTGCGA 59.988 37.037 0.00 0.00 37.34 5.10
890 891 7.700505 TCTCGTTTAATAGTAGAGATTGCGAA 58.299 34.615 0.00 0.00 33.58 4.70
891 892 8.186163 TCTCGTTTAATAGTAGAGATTGCGAAA 58.814 33.333 0.00 0.00 33.58 3.46
892 893 8.692110 TCGTTTAATAGTAGAGATTGCGAAAA 57.308 30.769 0.00 0.00 0.00 2.29
893 894 9.142515 TCGTTTAATAGTAGAGATTGCGAAAAA 57.857 29.630 0.00 0.00 0.00 1.94
934 935 1.670791 TTTTTGCGGTTCCGAGAAGT 58.329 45.000 15.69 0.00 0.00 3.01
935 936 0.941542 TTTTGCGGTTCCGAGAAGTG 59.058 50.000 15.69 0.00 0.00 3.16
936 937 0.105224 TTTGCGGTTCCGAGAAGTGA 59.895 50.000 15.69 0.00 0.00 3.41
937 938 0.320374 TTGCGGTTCCGAGAAGTGAT 59.680 50.000 15.69 0.00 0.00 3.06
938 939 1.179152 TGCGGTTCCGAGAAGTGATA 58.821 50.000 15.69 0.00 0.00 2.15
939 940 1.134367 TGCGGTTCCGAGAAGTGATAG 59.866 52.381 15.69 0.00 0.00 2.08
940 941 1.841450 CGGTTCCGAGAAGTGATAGC 58.159 55.000 5.19 0.00 0.00 2.97
941 942 1.134367 CGGTTCCGAGAAGTGATAGCA 59.866 52.381 5.19 0.00 0.00 3.49
942 943 2.416836 CGGTTCCGAGAAGTGATAGCAA 60.417 50.000 5.19 0.00 0.00 3.91
943 944 3.596214 GGTTCCGAGAAGTGATAGCAAA 58.404 45.455 0.00 0.00 0.00 3.68
944 945 4.000988 GGTTCCGAGAAGTGATAGCAAAA 58.999 43.478 0.00 0.00 0.00 2.44
945 946 4.142881 GGTTCCGAGAAGTGATAGCAAAAC 60.143 45.833 0.00 0.00 0.00 2.43
946 947 3.596214 TCCGAGAAGTGATAGCAAAACC 58.404 45.455 0.00 0.00 0.00 3.27
947 948 3.007506 TCCGAGAAGTGATAGCAAAACCA 59.992 43.478 0.00 0.00 0.00 3.67
948 949 3.751175 CCGAGAAGTGATAGCAAAACCAA 59.249 43.478 0.00 0.00 0.00 3.67
949 950 4.378459 CCGAGAAGTGATAGCAAAACCAAC 60.378 45.833 0.00 0.00 0.00 3.77
950 951 4.452455 CGAGAAGTGATAGCAAAACCAACT 59.548 41.667 0.00 0.00 0.00 3.16
951 952 5.049405 CGAGAAGTGATAGCAAAACCAACTT 60.049 40.000 0.00 0.00 0.00 2.66
952 953 6.319141 AGAAGTGATAGCAAAACCAACTTC 57.681 37.500 0.00 0.00 33.42 3.01
953 954 5.827797 AGAAGTGATAGCAAAACCAACTTCA 59.172 36.000 13.35 0.00 35.05 3.02
954 955 6.491403 AGAAGTGATAGCAAAACCAACTTCAT 59.509 34.615 13.35 0.00 35.05 2.57
955 956 6.655078 AGTGATAGCAAAACCAACTTCATT 57.345 33.333 0.00 0.00 0.00 2.57
956 957 7.054491 AGTGATAGCAAAACCAACTTCATTT 57.946 32.000 0.00 0.00 0.00 2.32
957 958 7.500141 AGTGATAGCAAAACCAACTTCATTTT 58.500 30.769 0.00 0.00 0.00 1.82
958 959 7.439056 AGTGATAGCAAAACCAACTTCATTTTG 59.561 33.333 4.67 4.67 43.20 2.44
959 960 7.437862 GTGATAGCAAAACCAACTTCATTTTGA 59.562 33.333 11.72 0.00 43.07 2.69
960 961 8.149647 TGATAGCAAAACCAACTTCATTTTGAT 58.850 29.630 11.72 8.37 43.07 2.57
961 962 9.638239 GATAGCAAAACCAACTTCATTTTGATA 57.362 29.630 11.72 10.08 43.96 2.15
962 963 9.995003 ATAGCAAAACCAACTTCATTTTGATAA 57.005 25.926 11.72 0.00 43.42 1.75
963 964 8.141835 AGCAAAACCAACTTCATTTTGATAAC 57.858 30.769 11.72 0.00 43.07 1.89
964 965 7.768120 AGCAAAACCAACTTCATTTTGATAACA 59.232 29.630 11.72 0.00 43.07 2.41
965 966 8.558700 GCAAAACCAACTTCATTTTGATAACAT 58.441 29.630 11.72 0.00 43.07 2.71
1065 1066 1.191489 AAAGTGGGGGCAAAATCGGG 61.191 55.000 0.00 0.00 0.00 5.14
1092 1093 1.269517 ACGCGAATGTGGTTTTGCAAT 60.270 42.857 15.93 0.00 36.03 3.56
1098 1099 4.448395 CGAATGTGGTTTTGCAATTCACAT 59.552 37.500 24.49 24.49 46.85 3.21
1099 1100 5.612925 CGAATGTGGTTTTGCAATTCACATG 60.613 40.000 27.75 18.95 44.96 3.21
1100 1101 3.464907 TGTGGTTTTGCAATTCACATGG 58.535 40.909 19.30 0.00 34.01 3.66
1101 1102 3.118482 TGTGGTTTTGCAATTCACATGGT 60.118 39.130 19.30 0.00 34.01 3.55
1102 1103 3.494251 GTGGTTTTGCAATTCACATGGTC 59.506 43.478 17.02 0.00 0.00 4.02
1103 1104 3.133542 TGGTTTTGCAATTCACATGGTCA 59.866 39.130 0.00 0.00 0.00 4.02
1124 1125 1.961277 AAGCGGCGTCAAGGTTCTG 60.961 57.895 9.37 0.00 0.00 3.02
1125 1126 2.660258 AAGCGGCGTCAAGGTTCTGT 62.660 55.000 9.37 0.00 0.00 3.41
1126 1127 1.373748 GCGGCGTCAAGGTTCTGTA 60.374 57.895 9.37 0.00 0.00 2.74
1714 1744 3.571828 TGAGATCACTGCCAGAGTATAGC 59.428 47.826 0.00 0.00 31.73 2.97
1740 1778 2.501723 GCAGTTGATCTAGGTCTGGGAA 59.498 50.000 4.28 0.00 0.00 3.97
1746 1784 6.325286 AGTTGATCTAGGTCTGGGAAGATAAC 59.675 42.308 4.28 0.00 0.00 1.89
1754 1792 4.322953 GGTCTGGGAAGATAACGTGGTTTA 60.323 45.833 0.00 0.00 0.00 2.01
1811 1850 3.016736 TGTGAGCAGTGATGATCGTAGA 58.983 45.455 0.00 0.00 45.75 2.59
1955 1997 5.752892 AGATCATGACTGAACATTCATGC 57.247 39.130 21.80 13.46 43.76 4.06
1977 2019 1.826720 GCTTCATGGCAAAATCCCAGA 59.173 47.619 0.00 0.00 35.48 3.86
2017 2087 3.718815 GGGCTCATTCTTCTAGGTTACG 58.281 50.000 0.00 0.00 0.00 3.18
2044 2114 7.254421 GGTTCAAGTTTTACAAAGAAATGCCAG 60.254 37.037 0.00 0.00 0.00 4.85
2050 2120 6.723298 TTTACAAAGAAATGCCAGGAGAAA 57.277 33.333 0.00 0.00 0.00 2.52
2051 2121 4.590850 ACAAAGAAATGCCAGGAGAAAC 57.409 40.909 0.00 0.00 0.00 2.78
2052 2122 3.960102 ACAAAGAAATGCCAGGAGAAACA 59.040 39.130 0.00 0.00 0.00 2.83
2053 2123 4.405358 ACAAAGAAATGCCAGGAGAAACAA 59.595 37.500 0.00 0.00 0.00 2.83
2054 2124 4.590850 AAGAAATGCCAGGAGAAACAAC 57.409 40.909 0.00 0.00 0.00 3.32
2055 2125 3.837355 AGAAATGCCAGGAGAAACAACT 58.163 40.909 0.00 0.00 0.00 3.16
2056 2126 4.985538 AGAAATGCCAGGAGAAACAACTA 58.014 39.130 0.00 0.00 0.00 2.24
2057 2127 4.762251 AGAAATGCCAGGAGAAACAACTAC 59.238 41.667 0.00 0.00 0.00 2.73
2058 2128 3.788227 ATGCCAGGAGAAACAACTACA 57.212 42.857 0.00 0.00 0.00 2.74
2059 2129 3.126001 TGCCAGGAGAAACAACTACAG 57.874 47.619 0.00 0.00 0.00 2.74
2060 2130 2.703536 TGCCAGGAGAAACAACTACAGA 59.296 45.455 0.00 0.00 0.00 3.41
2061 2131 3.135712 TGCCAGGAGAAACAACTACAGAA 59.864 43.478 0.00 0.00 0.00 3.02
2062 2132 4.134563 GCCAGGAGAAACAACTACAGAAA 58.865 43.478 0.00 0.00 0.00 2.52
2063 2133 4.214332 GCCAGGAGAAACAACTACAGAAAG 59.786 45.833 0.00 0.00 0.00 2.62
2064 2134 4.214332 CCAGGAGAAACAACTACAGAAAGC 59.786 45.833 0.00 0.00 0.00 3.51
2065 2135 4.214332 CAGGAGAAACAACTACAGAAAGCC 59.786 45.833 0.00 0.00 0.00 4.35
2066 2136 4.134563 GGAGAAACAACTACAGAAAGCCA 58.865 43.478 0.00 0.00 0.00 4.75
2067 2137 4.578928 GGAGAAACAACTACAGAAAGCCAA 59.421 41.667 0.00 0.00 0.00 4.52
2068 2138 5.278022 GGAGAAACAACTACAGAAAGCCAAG 60.278 44.000 0.00 0.00 0.00 3.61
2069 2139 5.437060 AGAAACAACTACAGAAAGCCAAGA 58.563 37.500 0.00 0.00 0.00 3.02
2070 2140 5.529060 AGAAACAACTACAGAAAGCCAAGAG 59.471 40.000 0.00 0.00 0.00 2.85
2071 2141 4.423625 ACAACTACAGAAAGCCAAGAGT 57.576 40.909 0.00 0.00 0.00 3.24
2072 2142 4.781934 ACAACTACAGAAAGCCAAGAGTT 58.218 39.130 0.00 0.00 0.00 3.01
2073 2143 5.193679 ACAACTACAGAAAGCCAAGAGTTT 58.806 37.500 0.00 0.00 0.00 2.66
2074 2144 5.297029 ACAACTACAGAAAGCCAAGAGTTTC 59.703 40.000 0.00 0.00 33.59 2.78
2075 2145 4.390264 ACTACAGAAAGCCAAGAGTTTCC 58.610 43.478 0.00 0.00 33.84 3.13
2076 2146 2.587522 ACAGAAAGCCAAGAGTTTCCC 58.412 47.619 0.00 0.00 33.84 3.97
2077 2147 1.889170 CAGAAAGCCAAGAGTTTCCCC 59.111 52.381 0.00 0.00 33.84 4.81
2078 2148 1.783365 AGAAAGCCAAGAGTTTCCCCT 59.217 47.619 0.00 0.00 33.84 4.79
2079 2149 1.889170 GAAAGCCAAGAGTTTCCCCTG 59.111 52.381 0.00 0.00 0.00 4.45
2080 2150 0.113190 AAGCCAAGAGTTTCCCCTGG 59.887 55.000 0.00 0.00 0.00 4.45
2081 2151 1.068352 AGCCAAGAGTTTCCCCTGGT 61.068 55.000 0.00 0.00 0.00 4.00
2085 2187 1.702957 CAAGAGTTTCCCCTGGTACCA 59.297 52.381 15.39 15.39 0.00 3.25
2315 2425 3.109928 TCCATGATCTCAAGAGGCTGAA 58.890 45.455 0.00 0.00 0.00 3.02
2319 2429 5.309638 CATGATCTCAAGAGGCTGAATGAT 58.690 41.667 0.00 0.00 0.00 2.45
2384 2510 1.821136 ACCCTTCGTCCCTAAACGTAG 59.179 52.381 0.00 0.00 43.08 3.51
2434 2560 8.082242 ACTGCCAAAACATCTTACATTTAGAAC 58.918 33.333 0.00 0.00 0.00 3.01
2438 2564 9.357652 CCAAAACATCTTACATTTAGAACCATG 57.642 33.333 0.00 0.00 0.00 3.66
2439 2565 9.357652 CAAAACATCTTACATTTAGAACCATGG 57.642 33.333 11.19 11.19 0.00 3.66
2440 2566 6.699575 ACATCTTACATTTAGAACCATGGC 57.300 37.500 13.04 0.00 0.00 4.40
2441 2567 5.594317 ACATCTTACATTTAGAACCATGGCC 59.406 40.000 13.04 3.85 0.00 5.36
2442 2568 5.186256 TCTTACATTTAGAACCATGGCCA 57.814 39.130 13.04 8.56 0.00 5.36
2443 2569 5.765510 TCTTACATTTAGAACCATGGCCAT 58.234 37.500 14.09 14.09 0.00 4.40
2444 2570 5.593909 TCTTACATTTAGAACCATGGCCATG 59.406 40.000 34.82 34.82 38.51 3.66
2454 2580 1.771565 CATGGCCATGGACAAGATGT 58.228 50.000 34.31 4.06 36.35 3.06
2455 2581 1.407618 CATGGCCATGGACAAGATGTG 59.592 52.381 34.31 14.70 36.35 3.21
2456 2582 0.323633 TGGCCATGGACAAGATGTGG 60.324 55.000 21.08 0.00 0.00 4.17
2457 2583 0.034186 GGCCATGGACAAGATGTGGA 60.034 55.000 18.40 0.00 31.59 4.02
2458 2584 1.386533 GCCATGGACAAGATGTGGAG 58.613 55.000 18.40 0.00 31.59 3.86
2459 2585 1.386533 CCATGGACAAGATGTGGAGC 58.613 55.000 5.56 0.00 31.59 4.70
2460 2586 1.340308 CCATGGACAAGATGTGGAGCA 60.340 52.381 5.56 0.00 31.59 4.26
2461 2587 2.014857 CATGGACAAGATGTGGAGCAG 58.985 52.381 0.00 0.00 0.00 4.24
2462 2588 0.321919 TGGACAAGATGTGGAGCAGC 60.322 55.000 0.00 0.00 0.00 5.25
2466 2592 4.315588 AGATGTGGAGCAGCTTGC 57.684 55.556 0.00 0.47 41.72 4.01
2467 2593 1.378250 AGATGTGGAGCAGCTTGCC 60.378 57.895 0.00 0.00 46.52 4.52
2468 2594 2.362120 ATGTGGAGCAGCTTGCCC 60.362 61.111 0.00 0.00 46.52 5.36
2469 2595 3.214190 ATGTGGAGCAGCTTGCCCA 62.214 57.895 0.00 0.00 46.52 5.36
2470 2596 2.362120 GTGGAGCAGCTTGCCCAT 60.362 61.111 4.67 0.00 46.52 4.00
2471 2597 2.361992 TGGAGCAGCTTGCCCATG 60.362 61.111 0.00 0.00 46.52 3.66
2472 2598 2.362120 GGAGCAGCTTGCCCATGT 60.362 61.111 0.00 0.00 46.52 3.21
2473 2599 2.413142 GGAGCAGCTTGCCCATGTC 61.413 63.158 0.00 0.00 46.52 3.06
2474 2600 2.362120 AGCAGCTTGCCCATGTCC 60.362 61.111 0.00 0.00 46.52 4.02
2475 2601 2.677524 GCAGCTTGCCCATGTCCA 60.678 61.111 0.00 0.00 37.42 4.02
2476 2602 2.707849 GCAGCTTGCCCATGTCCAG 61.708 63.158 0.00 0.00 37.42 3.86
2477 2603 2.362120 AGCTTGCCCATGTCCAGC 60.362 61.111 0.00 0.00 0.00 4.85
2478 2604 3.818787 GCTTGCCCATGTCCAGCG 61.819 66.667 0.00 0.00 0.00 5.18
2479 2605 3.818787 CTTGCCCATGTCCAGCGC 61.819 66.667 0.00 0.00 0.00 5.92
2484 2610 4.457496 CCATGTCCAGCGCCTCGT 62.457 66.667 2.29 0.00 0.00 4.18
2485 2611 3.190849 CATGTCCAGCGCCTCGTG 61.191 66.667 2.29 0.00 0.00 4.35
2486 2612 4.457496 ATGTCCAGCGCCTCGTGG 62.457 66.667 2.29 5.19 34.87 4.94
2511 2637 4.907034 CCGCGTCCGAGATCCGTG 62.907 72.222 4.92 0.00 36.29 4.94
2514 2640 3.822192 CGTCCGAGATCCGTGCCA 61.822 66.667 0.00 0.00 36.31 4.92
2515 2641 2.815308 GTCCGAGATCCGTGCCAT 59.185 61.111 0.00 0.00 36.31 4.40
2516 2642 1.592669 GTCCGAGATCCGTGCCATG 60.593 63.158 0.00 0.00 36.31 3.66
2517 2643 2.280389 CCGAGATCCGTGCCATGG 60.280 66.667 7.63 7.63 36.31 3.66
2518 2644 2.969238 CGAGATCCGTGCCATGGC 60.969 66.667 30.54 30.54 42.35 4.40
2534 2660 4.100981 GCACGAGCCATCTCTGAC 57.899 61.111 0.00 0.00 37.19 3.51
2535 2661 1.515020 GCACGAGCCATCTCTGACT 59.485 57.895 0.00 0.00 37.19 3.41
2536 2662 0.527385 GCACGAGCCATCTCTGACTC 60.527 60.000 0.00 0.00 37.19 3.36
2537 2663 0.102120 CACGAGCCATCTCTGACTCC 59.898 60.000 0.00 0.00 37.19 3.85
2538 2664 1.040339 ACGAGCCATCTCTGACTCCC 61.040 60.000 0.00 0.00 37.19 4.30
2539 2665 1.739049 GAGCCATCTCTGACTCCCG 59.261 63.158 0.00 0.00 36.42 5.14
2540 2666 1.743321 GAGCCATCTCTGACTCCCGG 61.743 65.000 0.00 0.00 36.42 5.73
2541 2667 2.818132 CCATCTCTGACTCCCGGC 59.182 66.667 0.00 0.00 0.00 6.13
2542 2668 2.801631 CCATCTCTGACTCCCGGCC 61.802 68.421 0.00 0.00 0.00 6.13
2543 2669 1.760086 CATCTCTGACTCCCGGCCT 60.760 63.158 0.00 0.00 0.00 5.19
2544 2670 1.456705 ATCTCTGACTCCCGGCCTC 60.457 63.158 0.00 0.00 0.00 4.70
2545 2671 3.522731 CTCTGACTCCCGGCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
2546 2672 3.997400 CTCTGACTCCCGGCCTCGA 62.997 68.421 0.00 0.00 39.00 4.04
2547 2673 3.827898 CTGACTCCCGGCCTCGAC 61.828 72.222 0.00 0.00 39.00 4.20
2566 2692 3.644861 GGAACGATCCCACCTTGTT 57.355 52.632 0.00 0.00 40.10 2.83
2567 2693 1.165270 GGAACGATCCCACCTTGTTG 58.835 55.000 0.00 0.00 40.10 3.33
2568 2694 1.271163 GGAACGATCCCACCTTGTTGA 60.271 52.381 0.00 0.00 40.10 3.18
2569 2695 1.804748 GAACGATCCCACCTTGTTGAC 59.195 52.381 0.00 0.00 0.00 3.18
2570 2696 0.036306 ACGATCCCACCTTGTTGACC 59.964 55.000 0.00 0.00 0.00 4.02
2571 2697 1.019278 CGATCCCACCTTGTTGACCG 61.019 60.000 0.00 0.00 0.00 4.79
2572 2698 0.036306 GATCCCACCTTGTTGACCGT 59.964 55.000 0.00 0.00 0.00 4.83
2573 2699 0.036306 ATCCCACCTTGTTGACCGTC 59.964 55.000 0.00 0.00 0.00 4.79
2574 2700 1.147376 CCCACCTTGTTGACCGTCA 59.853 57.895 0.00 0.00 0.00 4.35
2575 2701 0.464735 CCCACCTTGTTGACCGTCAA 60.465 55.000 9.99 9.99 33.32 3.18
2583 2709 3.088259 TTGACCGTCAACAAGGTGG 57.912 52.632 9.99 0.00 41.51 4.61
2584 2710 0.253610 TTGACCGTCAACAAGGTGGT 59.746 50.000 9.99 0.00 41.51 4.16
2585 2711 0.462937 TGACCGTCAACAAGGTGGTG 60.463 55.000 0.00 0.00 41.51 4.17
2586 2712 1.153046 ACCGTCAACAAGGTGGTGG 60.153 57.895 0.00 0.00 39.66 4.61
2587 2713 1.153046 CCGTCAACAAGGTGGTGGT 60.153 57.895 0.00 0.00 35.34 4.16
2588 2714 0.107081 CCGTCAACAAGGTGGTGGTA 59.893 55.000 0.00 0.00 35.34 3.25
2589 2715 1.475392 CCGTCAACAAGGTGGTGGTAA 60.475 52.381 0.00 0.00 35.34 2.85
2590 2716 1.871039 CGTCAACAAGGTGGTGGTAAG 59.129 52.381 0.00 0.00 35.34 2.34
2591 2717 2.227194 GTCAACAAGGTGGTGGTAAGG 58.773 52.381 0.00 0.00 35.34 2.69
2592 2718 2.128535 TCAACAAGGTGGTGGTAAGGA 58.871 47.619 0.00 0.00 35.34 3.36
2593 2719 2.714250 TCAACAAGGTGGTGGTAAGGAT 59.286 45.455 0.00 0.00 35.34 3.24
2594 2720 3.081804 CAACAAGGTGGTGGTAAGGATC 58.918 50.000 0.00 0.00 29.70 3.36
2595 2721 2.632537 ACAAGGTGGTGGTAAGGATCT 58.367 47.619 0.00 0.00 0.00 2.75
2596 2722 2.986728 ACAAGGTGGTGGTAAGGATCTT 59.013 45.455 0.00 0.00 0.00 2.40
2597 2723 3.009143 ACAAGGTGGTGGTAAGGATCTTC 59.991 47.826 0.00 0.00 0.00 2.87
2598 2724 3.207044 AGGTGGTGGTAAGGATCTTCT 57.793 47.619 0.00 0.00 0.00 2.85
2599 2725 3.532102 AGGTGGTGGTAAGGATCTTCTT 58.468 45.455 0.00 0.00 0.00 2.52
2600 2726 3.264450 AGGTGGTGGTAAGGATCTTCTTG 59.736 47.826 0.00 0.00 0.00 3.02
2601 2727 3.610911 GTGGTGGTAAGGATCTTCTTGG 58.389 50.000 0.00 0.00 0.00 3.61
2602 2728 2.026262 TGGTGGTAAGGATCTTCTTGGC 60.026 50.000 0.00 0.00 0.00 4.52
2603 2729 2.644676 GTGGTAAGGATCTTCTTGGCC 58.355 52.381 0.00 0.00 0.00 5.36
2604 2730 1.564348 TGGTAAGGATCTTCTTGGCCC 59.436 52.381 0.00 0.00 0.00 5.80
2605 2731 1.475213 GGTAAGGATCTTCTTGGCCCG 60.475 57.143 0.00 0.00 0.00 6.13
2606 2732 0.837272 TAAGGATCTTCTTGGCCCGG 59.163 55.000 0.00 0.00 0.00 5.73
2607 2733 2.517166 GGATCTTCTTGGCCCGGC 60.517 66.667 0.00 0.00 0.00 6.13
2608 2734 2.897350 GATCTTCTTGGCCCGGCG 60.897 66.667 0.00 0.00 0.00 6.46
2624 2750 4.487412 CGCCACTCGTCCCCGTAC 62.487 72.222 0.00 0.00 35.01 3.67
2625 2751 4.487412 GCCACTCGTCCCCGTACG 62.487 72.222 8.69 8.69 44.19 3.67
2626 2752 4.487412 CCACTCGTCCCCGTACGC 62.487 72.222 10.49 0.00 42.56 4.42
2627 2753 3.437795 CACTCGTCCCCGTACGCT 61.438 66.667 10.49 0.00 42.56 5.07
2628 2754 3.437795 ACTCGTCCCCGTACGCTG 61.438 66.667 10.49 2.56 42.56 5.18
2629 2755 3.437795 CTCGTCCCCGTACGCTGT 61.438 66.667 10.49 0.00 42.56 4.40
2630 2756 3.678717 CTCGTCCCCGTACGCTGTG 62.679 68.421 10.49 0.00 42.56 3.66
2631 2757 3.740397 CGTCCCCGTACGCTGTGA 61.740 66.667 10.49 0.00 35.87 3.58
2632 2758 2.652530 GTCCCCGTACGCTGTGAA 59.347 61.111 10.49 0.00 0.00 3.18
2633 2759 1.445582 GTCCCCGTACGCTGTGAAG 60.446 63.158 10.49 0.00 0.00 3.02
2634 2760 2.125673 CCCCGTACGCTGTGAAGG 60.126 66.667 10.49 3.46 0.00 3.46
2635 2761 2.813908 CCCGTACGCTGTGAAGGC 60.814 66.667 10.49 0.00 0.00 4.35
2642 2768 3.470567 GCTGTGAAGGCGACGTCG 61.471 66.667 32.57 32.57 42.22 5.12
2643 2769 2.254350 CTGTGAAGGCGACGTCGA 59.746 61.111 39.74 17.32 42.22 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.235155 TGCAAGCAGGGTCGTTAGATAA 59.765 45.455 0.00 0.00 0.00 1.75
42 43 1.817099 GAGGATGCAAGCAGGGTCG 60.817 63.158 0.00 0.00 0.00 4.79
152 153 2.203015 CCAACGGTGGGGCGATAG 60.203 66.667 13.17 0.00 41.77 2.08
179 180 1.580845 CCACCAGGCGAAGAAGCTTG 61.581 60.000 2.10 0.00 42.84 4.01
180 181 1.302832 CCACCAGGCGAAGAAGCTT 60.303 57.895 0.00 0.00 37.29 3.74
215 216 0.329261 TCTCAAGCAACCAGGGGATG 59.671 55.000 0.00 0.00 0.00 3.51
225 226 0.478072 TGAGCCCCTTTCTCAAGCAA 59.522 50.000 0.00 0.00 37.61 3.91
231 232 0.693049 TGGAGTTGAGCCCCTTTCTC 59.307 55.000 0.00 0.00 0.00 2.87
240 241 2.015736 ACACGATGATGGAGTTGAGC 57.984 50.000 0.00 0.00 0.00 4.26
257 258 4.575180 TGGCACATGCAGACAACA 57.425 50.000 6.15 0.00 44.36 3.33
270 271 1.630223 TGTGATGCTTCCAAATGGCA 58.370 45.000 0.00 0.00 40.32 4.92
287 288 2.679837 CCGTTGAAGATAGCTGCATTGT 59.320 45.455 1.02 0.00 27.13 2.71
294 295 2.292267 CATTGGCCGTTGAAGATAGCT 58.708 47.619 0.00 0.00 0.00 3.32
323 324 0.106894 GGCCTTGGTTAGATCTCCCG 59.893 60.000 0.00 0.00 0.00 5.14
330 331 2.026262 GTCCTTGATGGCCTTGGTTAGA 60.026 50.000 3.32 0.00 35.26 2.10
333 334 0.609131 CGTCCTTGATGGCCTTGGTT 60.609 55.000 3.32 0.00 35.26 3.67
379 380 3.309600 AATACTAGCTAGTCCCGTGGT 57.690 47.619 29.28 6.46 37.73 4.16
383 384 5.711036 ACAGGAATAATACTAGCTAGTCCCG 59.289 44.000 29.28 17.14 37.73 5.14
465 466 4.498520 CGAGCCGGCGTCAGTGAT 62.499 66.667 23.20 0.00 0.00 3.06
786 787 5.762825 AGCAGCGTATCATTTCATTGATT 57.237 34.783 0.00 0.00 37.51 2.57
829 830 0.842467 CCTTCACCCAACCCTCCTCT 60.842 60.000 0.00 0.00 0.00 3.69
830 831 1.685820 CCTTCACCCAACCCTCCTC 59.314 63.158 0.00 0.00 0.00 3.71
831 832 2.539081 GCCTTCACCCAACCCTCCT 61.539 63.158 0.00 0.00 0.00 3.69
832 833 2.035783 GCCTTCACCCAACCCTCC 59.964 66.667 0.00 0.00 0.00 4.30
833 834 2.198304 ATCGCCTTCACCCAACCCTC 62.198 60.000 0.00 0.00 0.00 4.30
834 835 0.912487 TATCGCCTTCACCCAACCCT 60.912 55.000 0.00 0.00 0.00 4.34
835 836 0.746923 GTATCGCCTTCACCCAACCC 60.747 60.000 0.00 0.00 0.00 4.11
836 837 0.035820 TGTATCGCCTTCACCCAACC 60.036 55.000 0.00 0.00 0.00 3.77
837 838 1.467342 GTTGTATCGCCTTCACCCAAC 59.533 52.381 0.00 0.00 0.00 3.77
838 839 1.816074 GTTGTATCGCCTTCACCCAA 58.184 50.000 0.00 0.00 0.00 4.12
839 840 0.390603 CGTTGTATCGCCTTCACCCA 60.391 55.000 0.00 0.00 0.00 4.51
840 841 0.108520 TCGTTGTATCGCCTTCACCC 60.109 55.000 0.00 0.00 0.00 4.61
841 842 1.278238 CTCGTTGTATCGCCTTCACC 58.722 55.000 0.00 0.00 0.00 4.02
842 843 0.645868 GCTCGTTGTATCGCCTTCAC 59.354 55.000 0.00 0.00 0.00 3.18
843 844 0.245266 TGCTCGTTGTATCGCCTTCA 59.755 50.000 0.00 0.00 0.00 3.02
844 845 1.060698 GTTGCTCGTTGTATCGCCTTC 59.939 52.381 0.00 0.00 0.00 3.46
845 846 1.076332 GTTGCTCGTTGTATCGCCTT 58.924 50.000 0.00 0.00 0.00 4.35
846 847 0.246635 AGTTGCTCGTTGTATCGCCT 59.753 50.000 0.00 0.00 0.00 5.52
847 848 0.645868 GAGTTGCTCGTTGTATCGCC 59.354 55.000 0.00 0.00 0.00 5.54
848 849 1.584308 GAGAGTTGCTCGTTGTATCGC 59.416 52.381 0.00 0.00 35.36 4.58
864 865 7.353497 TCGCAATCTCTACTATTAAACGAGAG 58.647 38.462 0.00 0.00 34.59 3.20
865 866 7.255491 TCGCAATCTCTACTATTAAACGAGA 57.745 36.000 0.00 0.00 35.46 4.04
866 867 7.909777 TTCGCAATCTCTACTATTAAACGAG 57.090 36.000 0.00 0.00 0.00 4.18
867 868 8.692110 TTTTCGCAATCTCTACTATTAAACGA 57.308 30.769 0.00 0.00 0.00 3.85
915 916 1.332375 CACTTCTCGGAACCGCAAAAA 59.668 47.619 8.48 0.00 39.59 1.94
916 917 0.941542 CACTTCTCGGAACCGCAAAA 59.058 50.000 8.48 2.19 39.59 2.44
917 918 0.105224 TCACTTCTCGGAACCGCAAA 59.895 50.000 8.48 4.48 39.59 3.68
918 919 0.320374 ATCACTTCTCGGAACCGCAA 59.680 50.000 8.48 3.25 39.59 4.85
919 920 1.134367 CTATCACTTCTCGGAACCGCA 59.866 52.381 8.48 0.00 39.59 5.69
920 921 1.841450 CTATCACTTCTCGGAACCGC 58.159 55.000 8.48 0.00 39.59 5.68
921 922 1.134367 TGCTATCACTTCTCGGAACCG 59.866 52.381 6.94 6.94 41.35 4.44
922 923 2.961526 TGCTATCACTTCTCGGAACC 57.038 50.000 0.00 0.00 0.00 3.62
923 924 4.142881 GGTTTTGCTATCACTTCTCGGAAC 60.143 45.833 0.00 0.00 0.00 3.62
924 925 4.000988 GGTTTTGCTATCACTTCTCGGAA 58.999 43.478 0.00 0.00 0.00 4.30
925 926 3.007506 TGGTTTTGCTATCACTTCTCGGA 59.992 43.478 0.00 0.00 0.00 4.55
926 927 3.334691 TGGTTTTGCTATCACTTCTCGG 58.665 45.455 0.00 0.00 0.00 4.63
927 928 4.452455 AGTTGGTTTTGCTATCACTTCTCG 59.548 41.667 0.00 0.00 0.00 4.04
928 929 5.948992 AGTTGGTTTTGCTATCACTTCTC 57.051 39.130 0.00 0.00 0.00 2.87
929 930 5.827797 TGAAGTTGGTTTTGCTATCACTTCT 59.172 36.000 9.79 0.00 34.10 2.85
930 931 6.072112 TGAAGTTGGTTTTGCTATCACTTC 57.928 37.500 0.00 0.00 33.72 3.01
931 932 6.655078 ATGAAGTTGGTTTTGCTATCACTT 57.345 33.333 0.00 0.00 0.00 3.16
932 933 6.655078 AATGAAGTTGGTTTTGCTATCACT 57.345 33.333 0.00 0.00 0.00 3.41
933 934 7.437862 TCAAAATGAAGTTGGTTTTGCTATCAC 59.562 33.333 13.56 0.00 40.70 3.06
934 935 7.495901 TCAAAATGAAGTTGGTTTTGCTATCA 58.504 30.769 13.56 0.00 40.70 2.15
935 936 7.945033 TCAAAATGAAGTTGGTTTTGCTATC 57.055 32.000 13.56 0.00 40.70 2.08
936 937 9.995003 TTATCAAAATGAAGTTGGTTTTGCTAT 57.005 25.926 13.56 8.40 40.70 2.97
937 938 9.255304 GTTATCAAAATGAAGTTGGTTTTGCTA 57.745 29.630 13.56 8.51 40.70 3.49
938 939 7.768120 TGTTATCAAAATGAAGTTGGTTTTGCT 59.232 29.630 13.56 9.20 40.70 3.91
939 940 7.914465 TGTTATCAAAATGAAGTTGGTTTTGC 58.086 30.769 13.56 5.02 40.70 3.68
1012 1013 8.932791 CGCTATAAAAATCTACCGATGGTAATT 58.067 33.333 0.00 0.00 37.76 1.40
1013 1014 7.548075 CCGCTATAAAAATCTACCGATGGTAAT 59.452 37.037 0.00 0.00 37.76 1.89
1014 1015 6.869913 CCGCTATAAAAATCTACCGATGGTAA 59.130 38.462 0.00 0.00 37.76 2.85
1015 1016 6.015180 ACCGCTATAAAAATCTACCGATGGTA 60.015 38.462 0.00 0.00 37.09 3.25
1016 1017 5.221581 ACCGCTATAAAAATCTACCGATGGT 60.222 40.000 0.00 0.00 40.16 3.55
1017 1018 5.235516 ACCGCTATAAAAATCTACCGATGG 58.764 41.667 0.00 0.00 0.00 3.51
1018 1019 6.645415 AGAACCGCTATAAAAATCTACCGATG 59.355 38.462 0.00 0.00 0.00 3.84
1035 1036 0.537371 CCCCACTTTTCAGAACCGCT 60.537 55.000 0.00 0.00 0.00 5.52
1065 1066 1.425412 ACCACATTCGCGTTGTAGAC 58.575 50.000 15.09 0.00 0.00 2.59
1092 1093 0.950836 CCGCTTGTTGACCATGTGAA 59.049 50.000 0.00 0.00 32.06 3.18
1098 1099 2.970324 GACGCCGCTTGTTGACCA 60.970 61.111 0.00 0.00 0.00 4.02
1099 1100 2.443957 CTTGACGCCGCTTGTTGACC 62.444 60.000 0.00 0.00 0.00 4.02
1100 1101 1.082756 CTTGACGCCGCTTGTTGAC 60.083 57.895 0.00 0.00 0.00 3.18
1101 1102 2.250939 CCTTGACGCCGCTTGTTGA 61.251 57.895 0.00 0.00 0.00 3.18
1102 1103 2.058829 AACCTTGACGCCGCTTGTTG 62.059 55.000 0.00 0.00 0.00 3.33
1103 1104 1.782028 GAACCTTGACGCCGCTTGTT 61.782 55.000 0.00 0.00 0.00 2.83
1124 1125 1.355066 GGCTGCGCACTGAAGAGTAC 61.355 60.000 5.66 0.00 0.00 2.73
1125 1126 1.079819 GGCTGCGCACTGAAGAGTA 60.080 57.895 5.66 0.00 0.00 2.59
1126 1127 2.358003 GGCTGCGCACTGAAGAGT 60.358 61.111 5.66 0.00 0.00 3.24
1179 1182 3.017232 GATGTCTTCGACGTCGCTT 57.983 52.632 32.19 16.12 38.54 4.68
1180 1183 4.767633 GATGTCTTCGACGTCGCT 57.232 55.556 32.19 12.18 38.54 4.93
1350 1353 1.591703 CTCTGAGCTGTGGCCGTAA 59.408 57.895 0.00 0.00 39.73 3.18
1714 1744 3.030291 AGACCTAGATCAACTGCTCCTG 58.970 50.000 0.00 0.00 0.00 3.86
1740 1778 6.034591 CAGAGTCGAATAAACCACGTTATCT 58.965 40.000 0.00 0.00 0.00 1.98
1746 1784 3.834610 AGACAGAGTCGAATAAACCACG 58.165 45.455 0.00 0.00 37.67 4.94
1754 1792 2.946329 ACGCAGATAGACAGAGTCGAAT 59.054 45.455 0.00 0.00 37.67 3.34
1811 1850 4.221703 ACAAGAGTCAAGATCCAGATCGTT 59.778 41.667 2.08 0.00 42.48 3.85
1955 1997 1.551430 TGGGATTTTGCCATGAAGCTG 59.449 47.619 0.00 0.00 30.85 4.24
1977 2019 3.513662 CCCGTTTGTTCCGTTTTTCTTT 58.486 40.909 0.00 0.00 0.00 2.52
2017 2087 6.018262 GGCATTTCTTTGTAAAACTTGAACCC 60.018 38.462 0.00 0.00 0.00 4.11
2044 2114 4.134563 TGGCTTTCTGTAGTTGTTTCTCC 58.865 43.478 0.00 0.00 0.00 3.71
2050 2120 4.423625 ACTCTTGGCTTTCTGTAGTTGT 57.576 40.909 0.00 0.00 0.00 3.32
2051 2121 5.278022 GGAAACTCTTGGCTTTCTGTAGTTG 60.278 44.000 0.00 0.00 0.00 3.16
2052 2122 4.822350 GGAAACTCTTGGCTTTCTGTAGTT 59.178 41.667 0.00 0.00 0.00 2.24
2053 2123 4.390264 GGAAACTCTTGGCTTTCTGTAGT 58.610 43.478 0.00 0.00 0.00 2.73
2054 2124 3.753797 GGGAAACTCTTGGCTTTCTGTAG 59.246 47.826 0.00 0.00 0.00 2.74
2055 2125 3.497942 GGGGAAACTCTTGGCTTTCTGTA 60.498 47.826 0.00 0.00 0.00 2.74
2056 2126 2.587522 GGGAAACTCTTGGCTTTCTGT 58.412 47.619 0.00 0.00 0.00 3.41
2057 2127 1.889170 GGGGAAACTCTTGGCTTTCTG 59.111 52.381 0.00 0.00 0.00 3.02
2058 2128 1.783365 AGGGGAAACTCTTGGCTTTCT 59.217 47.619 0.00 0.00 38.96 2.52
2059 2129 1.889170 CAGGGGAAACTCTTGGCTTTC 59.111 52.381 0.00 0.00 38.96 2.62
2060 2130 1.481242 CCAGGGGAAACTCTTGGCTTT 60.481 52.381 0.00 0.00 38.96 3.51
2061 2131 0.113190 CCAGGGGAAACTCTTGGCTT 59.887 55.000 0.00 0.00 38.96 4.35
2062 2132 1.068352 ACCAGGGGAAACTCTTGGCT 61.068 55.000 0.00 0.00 38.96 4.75
2063 2133 0.696501 TACCAGGGGAAACTCTTGGC 59.303 55.000 0.00 0.00 38.96 4.52
2064 2134 1.004394 GGTACCAGGGGAAACTCTTGG 59.996 57.143 7.15 0.00 38.96 3.61
2065 2135 1.702957 TGGTACCAGGGGAAACTCTTG 59.297 52.381 11.60 0.00 38.96 3.02
2066 2136 1.985895 CTGGTACCAGGGGAAACTCTT 59.014 52.381 31.15 0.00 38.96 2.85
2068 2138 1.555533 CTCTGGTACCAGGGGAAACTC 59.444 57.143 35.94 0.00 43.75 3.01
2069 2139 1.151413 TCTCTGGTACCAGGGGAAACT 59.849 52.381 36.20 0.00 44.30 2.66
2070 2140 1.652947 TCTCTGGTACCAGGGGAAAC 58.347 55.000 36.20 0.00 44.30 2.78
2071 2141 2.478292 GATCTCTGGTACCAGGGGAAA 58.522 52.381 36.20 21.28 44.30 3.13
2072 2142 1.344087 GGATCTCTGGTACCAGGGGAA 60.344 57.143 36.20 21.99 44.30 3.97
2073 2143 0.264955 GGATCTCTGGTACCAGGGGA 59.735 60.000 36.20 31.41 44.30 4.81
2074 2144 0.266152 AGGATCTCTGGTACCAGGGG 59.734 60.000 36.20 28.14 44.30 4.79
2075 2145 2.599677 GTAGGATCTCTGGTACCAGGG 58.400 57.143 35.94 34.46 45.48 4.45
2076 2146 2.231529 CGTAGGATCTCTGGTACCAGG 58.768 57.143 35.94 26.91 43.75 4.45
2077 2147 1.609555 GCGTAGGATCTCTGGTACCAG 59.390 57.143 32.61 32.61 44.86 4.00
2078 2148 1.214673 AGCGTAGGATCTCTGGTACCA 59.785 52.381 15.39 15.39 0.00 3.25
2079 2149 1.881324 GAGCGTAGGATCTCTGGTACC 59.119 57.143 4.43 4.43 0.00 3.34
2080 2150 2.853705 AGAGCGTAGGATCTCTGGTAC 58.146 52.381 0.00 0.00 32.26 3.34
2081 2151 3.579534 AAGAGCGTAGGATCTCTGGTA 57.420 47.619 3.33 0.00 38.12 3.25
2085 2187 2.880963 GCAAAGAGCGTAGGATCTCT 57.119 50.000 3.33 0.00 38.12 3.10
2384 2510 4.751098 TCAAATTGAGCTGCAAAAACATCC 59.249 37.500 1.02 0.00 40.48 3.51
2438 2564 0.034186 TCCACATCTTGTCCATGGCC 60.034 55.000 6.96 0.00 0.00 5.36
2439 2565 1.386533 CTCCACATCTTGTCCATGGC 58.613 55.000 6.96 2.72 0.00 4.40
2440 2566 1.340308 TGCTCCACATCTTGTCCATGG 60.340 52.381 4.97 4.97 0.00 3.66
2441 2567 2.014857 CTGCTCCACATCTTGTCCATG 58.985 52.381 0.00 0.00 0.00 3.66
2442 2568 1.681166 GCTGCTCCACATCTTGTCCAT 60.681 52.381 0.00 0.00 0.00 3.41
2443 2569 0.321919 GCTGCTCCACATCTTGTCCA 60.322 55.000 0.00 0.00 0.00 4.02
2444 2570 0.035630 AGCTGCTCCACATCTTGTCC 60.036 55.000 0.00 0.00 0.00 4.02
2445 2571 1.467734 CAAGCTGCTCCACATCTTGTC 59.532 52.381 1.00 0.00 44.08 3.18
2446 2572 1.531423 CAAGCTGCTCCACATCTTGT 58.469 50.000 1.00 0.00 44.08 3.16
2448 2574 0.964358 GGCAAGCTGCTCCACATCTT 60.964 55.000 1.00 0.00 44.28 2.40
2449 2575 1.378250 GGCAAGCTGCTCCACATCT 60.378 57.895 1.00 0.00 44.28 2.90
2450 2576 2.413142 GGGCAAGCTGCTCCACATC 61.413 63.158 1.00 0.00 44.28 3.06
2451 2577 2.362120 GGGCAAGCTGCTCCACAT 60.362 61.111 1.00 0.00 44.28 3.21
2452 2578 3.214190 ATGGGCAAGCTGCTCCACA 62.214 57.895 10.38 8.90 45.08 4.17
2453 2579 2.362120 ATGGGCAAGCTGCTCCAC 60.362 61.111 10.38 3.40 45.08 4.02
2454 2580 2.361992 CATGGGCAAGCTGCTCCA 60.362 61.111 10.55 10.55 45.08 3.86
2455 2581 2.362120 ACATGGGCAAGCTGCTCC 60.362 61.111 1.00 0.00 45.08 4.70
2456 2582 2.413142 GGACATGGGCAAGCTGCTC 61.413 63.158 1.00 4.85 46.11 4.26
2457 2583 2.362120 GGACATGGGCAAGCTGCT 60.362 61.111 0.00 0.00 44.28 4.24
2458 2584 2.677524 TGGACATGGGCAAGCTGC 60.678 61.111 0.00 0.00 44.08 5.25
2459 2585 2.707849 GCTGGACATGGGCAAGCTG 61.708 63.158 9.31 0.00 0.00 4.24
2460 2586 2.362120 GCTGGACATGGGCAAGCT 60.362 61.111 9.31 0.00 0.00 3.74
2461 2587 3.818787 CGCTGGACATGGGCAAGC 61.819 66.667 7.05 7.05 0.00 4.01
2462 2588 3.818787 GCGCTGGACATGGGCAAG 61.819 66.667 0.00 0.00 41.97 4.01
2467 2593 4.457496 ACGAGGCGCTGGACATGG 62.457 66.667 7.64 0.00 0.00 3.66
2468 2594 3.190849 CACGAGGCGCTGGACATG 61.191 66.667 7.64 0.00 0.00 3.21
2469 2595 4.457496 CCACGAGGCGCTGGACAT 62.457 66.667 7.64 0.00 32.71 3.06
2494 2620 4.907034 CACGGATCTCGGACGCGG 62.907 72.222 12.47 0.00 44.45 6.46
2497 2623 3.138930 ATGGCACGGATCTCGGACG 62.139 63.158 8.20 0.00 44.45 4.79
2498 2624 1.592669 CATGGCACGGATCTCGGAC 60.593 63.158 8.20 1.31 44.45 4.79
2499 2625 2.796193 CCATGGCACGGATCTCGGA 61.796 63.158 0.00 0.00 44.45 4.55
2500 2626 2.280389 CCATGGCACGGATCTCGG 60.280 66.667 0.00 0.09 44.45 4.63
2501 2627 2.969238 GCCATGGCACGGATCTCG 60.969 66.667 32.08 0.00 45.88 4.04
2517 2643 0.527385 GAGTCAGAGATGGCTCGTGC 60.527 60.000 0.00 0.00 45.98 5.34
2518 2644 0.102120 GGAGTCAGAGATGGCTCGTG 59.898 60.000 3.97 0.00 45.98 4.35
2519 2645 1.040339 GGGAGTCAGAGATGGCTCGT 61.040 60.000 3.97 0.00 45.98 4.18
2520 2646 1.739049 GGGAGTCAGAGATGGCTCG 59.261 63.158 3.97 0.00 45.98 5.03
2521 2647 1.739049 CGGGAGTCAGAGATGGCTC 59.261 63.158 1.23 1.23 39.63 4.70
2522 2648 1.760086 CCGGGAGTCAGAGATGGCT 60.760 63.158 0.00 0.00 0.00 4.75
2523 2649 2.818132 CCGGGAGTCAGAGATGGC 59.182 66.667 0.00 0.00 0.00 4.40
2524 2650 2.801631 GGCCGGGAGTCAGAGATGG 61.802 68.421 2.18 0.00 0.00 3.51
2525 2651 1.743321 GAGGCCGGGAGTCAGAGATG 61.743 65.000 2.18 0.00 0.00 2.90
2526 2652 1.456705 GAGGCCGGGAGTCAGAGAT 60.457 63.158 2.18 0.00 0.00 2.75
2527 2653 2.043852 GAGGCCGGGAGTCAGAGA 60.044 66.667 2.18 0.00 0.00 3.10
2528 2654 3.522731 CGAGGCCGGGAGTCAGAG 61.523 72.222 2.18 0.00 0.00 3.35
2529 2655 4.043100 TCGAGGCCGGGAGTCAGA 62.043 66.667 2.18 0.00 36.24 3.27
2530 2656 3.827898 GTCGAGGCCGGGAGTCAG 61.828 72.222 2.18 0.00 36.24 3.51
2538 2664 4.189188 ATCGTTCCGTCGAGGCCG 62.189 66.667 0.00 1.95 43.00 6.13
2539 2665 2.278661 GATCGTTCCGTCGAGGCC 60.279 66.667 0.00 0.00 43.00 5.19
2540 2666 2.278661 GGATCGTTCCGTCGAGGC 60.279 66.667 0.00 0.00 43.00 4.70
2541 2667 2.412112 GGGATCGTTCCGTCGAGG 59.588 66.667 6.44 0.00 43.63 4.63
2542 2668 1.226603 GTGGGATCGTTCCGTCGAG 60.227 63.158 6.44 0.00 43.63 4.04
2543 2669 2.703798 GGTGGGATCGTTCCGTCGA 61.704 63.158 6.44 0.00 43.63 4.20
2544 2670 2.202703 GGTGGGATCGTTCCGTCG 60.203 66.667 6.44 0.00 43.63 5.12
2545 2671 0.739813 CAAGGTGGGATCGTTCCGTC 60.740 60.000 6.44 2.37 43.63 4.79
2546 2672 1.295423 CAAGGTGGGATCGTTCCGT 59.705 57.895 6.44 0.00 43.63 4.69
2547 2673 0.321298 AACAAGGTGGGATCGTTCCG 60.321 55.000 6.44 0.00 43.63 4.30
2548 2674 1.165270 CAACAAGGTGGGATCGTTCC 58.835 55.000 3.76 3.76 41.77 3.62
2549 2675 1.804748 GTCAACAAGGTGGGATCGTTC 59.195 52.381 0.00 0.00 0.00 3.95
2550 2676 1.544759 GGTCAACAAGGTGGGATCGTT 60.545 52.381 0.00 0.00 0.00 3.85
2551 2677 0.036306 GGTCAACAAGGTGGGATCGT 59.964 55.000 0.00 0.00 0.00 3.73
2552 2678 1.019278 CGGTCAACAAGGTGGGATCG 61.019 60.000 0.00 0.00 0.00 3.69
2553 2679 0.036306 ACGGTCAACAAGGTGGGATC 59.964 55.000 0.00 0.00 0.00 3.36
2554 2680 0.036306 GACGGTCAACAAGGTGGGAT 59.964 55.000 2.62 0.00 0.00 3.85
2555 2681 1.338890 TGACGGTCAACAAGGTGGGA 61.339 55.000 8.68 0.00 0.00 4.37
2556 2682 0.464735 TTGACGGTCAACAAGGTGGG 60.465 55.000 19.07 0.00 30.26 4.61
2557 2683 3.088259 TTGACGGTCAACAAGGTGG 57.912 52.632 19.07 0.00 30.26 4.61
2565 2691 0.253610 ACCACCTTGTTGACGGTCAA 59.746 50.000 19.07 19.07 33.32 3.18
2566 2692 0.462937 CACCACCTTGTTGACGGTCA 60.463 55.000 6.76 6.76 0.00 4.02
2567 2693 1.164041 CCACCACCTTGTTGACGGTC 61.164 60.000 0.00 0.00 0.00 4.79
2568 2694 1.153046 CCACCACCTTGTTGACGGT 60.153 57.895 0.00 0.00 0.00 4.83
2569 2695 0.107081 TACCACCACCTTGTTGACGG 59.893 55.000 0.00 0.00 0.00 4.79
2570 2696 1.871039 CTTACCACCACCTTGTTGACG 59.129 52.381 0.00 0.00 0.00 4.35
2571 2697 2.158726 TCCTTACCACCACCTTGTTGAC 60.159 50.000 0.00 0.00 0.00 3.18
2572 2698 2.128535 TCCTTACCACCACCTTGTTGA 58.871 47.619 0.00 0.00 0.00 3.18
2573 2699 2.649531 TCCTTACCACCACCTTGTTG 57.350 50.000 0.00 0.00 0.00 3.33
2574 2700 2.986728 AGATCCTTACCACCACCTTGTT 59.013 45.455 0.00 0.00 0.00 2.83
2575 2701 2.632537 AGATCCTTACCACCACCTTGT 58.367 47.619 0.00 0.00 0.00 3.16
2576 2702 3.264450 AGAAGATCCTTACCACCACCTTG 59.736 47.826 0.00 0.00 0.00 3.61
2577 2703 3.532102 AGAAGATCCTTACCACCACCTT 58.468 45.455 0.00 0.00 0.00 3.50
2578 2704 3.207044 AGAAGATCCTTACCACCACCT 57.793 47.619 0.00 0.00 0.00 4.00
2579 2705 3.610911 CAAGAAGATCCTTACCACCACC 58.389 50.000 0.00 0.00 0.00 4.61
2580 2706 3.610911 CCAAGAAGATCCTTACCACCAC 58.389 50.000 0.00 0.00 0.00 4.16
2581 2707 2.026262 GCCAAGAAGATCCTTACCACCA 60.026 50.000 0.00 0.00 0.00 4.17
2582 2708 2.644676 GCCAAGAAGATCCTTACCACC 58.355 52.381 0.00 0.00 0.00 4.61
2583 2709 2.644676 GGCCAAGAAGATCCTTACCAC 58.355 52.381 0.00 0.00 0.00 4.16
2584 2710 1.564348 GGGCCAAGAAGATCCTTACCA 59.436 52.381 4.39 0.00 0.00 3.25
2585 2711 1.475213 CGGGCCAAGAAGATCCTTACC 60.475 57.143 4.39 0.00 0.00 2.85
2586 2712 1.475213 CCGGGCCAAGAAGATCCTTAC 60.475 57.143 4.39 0.00 0.00 2.34
2587 2713 0.837272 CCGGGCCAAGAAGATCCTTA 59.163 55.000 4.39 0.00 0.00 2.69
2588 2714 1.609783 CCGGGCCAAGAAGATCCTT 59.390 57.895 4.39 0.00 0.00 3.36
2589 2715 3.049080 GCCGGGCCAAGAAGATCCT 62.049 63.158 8.12 0.00 0.00 3.24
2590 2716 2.517166 GCCGGGCCAAGAAGATCC 60.517 66.667 8.12 0.00 0.00 3.36
2591 2717 2.897350 CGCCGGGCCAAGAAGATC 60.897 66.667 14.55 0.00 0.00 2.75
2615 2741 1.445582 CTTCACAGCGTACGGGGAC 60.446 63.158 18.39 0.00 0.00 4.46
2616 2742 2.642254 CCTTCACAGCGTACGGGGA 61.642 63.158 18.39 4.73 0.00 4.81
2617 2743 2.125673 CCTTCACAGCGTACGGGG 60.126 66.667 18.39 1.93 0.00 5.73
2618 2744 2.813908 GCCTTCACAGCGTACGGG 60.814 66.667 18.39 8.73 0.00 5.28
2625 2751 3.470567 CGACGTCGCCTTCACAGC 61.471 66.667 26.59 0.00 0.00 4.40
2626 2752 2.081212 GTCGACGTCGCCTTCACAG 61.081 63.158 32.19 3.93 39.60 3.66
2627 2753 2.050714 GTCGACGTCGCCTTCACA 60.051 61.111 32.19 11.25 39.60 3.58
2628 2754 2.081212 CAGTCGACGTCGCCTTCAC 61.081 63.158 32.19 23.54 39.60 3.18
2629 2755 2.254350 CAGTCGACGTCGCCTTCA 59.746 61.111 32.19 12.84 39.60 3.02
2630 2756 2.504244 CCAGTCGACGTCGCCTTC 60.504 66.667 32.19 20.36 39.60 3.46
2631 2757 4.052229 CCCAGTCGACGTCGCCTT 62.052 66.667 32.19 16.90 39.60 4.35


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

AutoCloner maintained by Alex Coulton.