Multiple sequence alignment - TraesCS4A01G021900

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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 TraesCS4A01G021900 chr4A 100.000 3104 0 0 1 3104 15758518 15761621 0.000000e+00 5733.0
1 TraesCS4A01G021900 chr4A 84.363 761 98 13 1141 1889 15767365 15768116 0.000000e+00 726.0
2 TraesCS4A01G021900 chr4A 89.216 102 7 2 2970 3071 39520456 39520553 1.170000e-24 124.0
3 TraesCS4A01G021900 chr4A 100.000 61 0 0 3011 3071 616959179 616959239 2.530000e-21 113.0
4 TraesCS4A01G021900 chr4A 95.652 69 2 1 3011 3078 82849210 82849278 3.270000e-20 110.0
5 TraesCS4A01G021900 chr4A 95.238 42 0 2 2974 3015 562283937 562283898 7.180000e-07 65.8
6 TraesCS4A01G021900 chr4D 94.600 2000 60 21 987 2976 451277405 451275444 0.000000e+00 3051.0
7 TraesCS4A01G021900 chr4D 84.273 763 95 14 1141 1889 451178147 451177396 0.000000e+00 721.0
8 TraesCS4A01G021900 chr4D 89.655 116 11 1 2778 2892 451275508 451275393 2.490000e-31 147.0
9 TraesCS4A01G021900 chr4B 94.630 1918 67 16 1069 2976 564653516 564651625 0.000000e+00 2939.0
10 TraesCS4A01G021900 chr4B 84.676 1266 127 20 1063 2308 564786111 564784893 0.000000e+00 1201.0
11 TraesCS4A01G021900 chr4B 89.323 768 75 6 60 825 665294582 665293820 0.000000e+00 957.0
12 TraesCS4A01G021900 chr4B 84.757 761 95 11 1141 1889 564395617 564394866 0.000000e+00 743.0
13 TraesCS4A01G021900 chr4B 87.423 652 47 16 2337 2976 564784897 564784269 0.000000e+00 717.0
14 TraesCS4A01G021900 chr6B 88.242 825 87 8 4 825 182117 181300 0.000000e+00 977.0
15 TraesCS4A01G021900 chr6B 89.453 768 74 6 60 825 599981866 599981104 0.000000e+00 963.0
16 TraesCS4A01G021900 chr6B 89.147 774 79 4 53 825 641301623 641300854 0.000000e+00 959.0
17 TraesCS4A01G021900 chr1B 88.932 777 75 10 60 833 94009895 94009127 0.000000e+00 948.0
18 TraesCS4A01G021900 chr3B 87.515 825 89 9 4 825 804316663 804315850 0.000000e+00 941.0
19 TraesCS4A01G021900 chr2B 87.424 827 88 13 4 825 73986817 73986002 0.000000e+00 937.0
20 TraesCS4A01G021900 chr2B 87.030 825 95 9 4 825 102128283 102127468 0.000000e+00 920.0
21 TraesCS4A01G021900 chr2D 87.120 823 95 8 5 825 484881813 484881000 0.000000e+00 922.0
22 TraesCS4A01G021900 chr6D 87.054 672 84 3 155 825 80003587 80002918 0.000000e+00 756.0
23 TraesCS4A01G021900 chrUn 88.660 97 7 3 2975 3071 26701916 26701824 7.030000e-22 115.0
24 TraesCS4A01G021900 chrUn 84.158 101 10 3 2975 3072 255060436 255060339 3.300000e-15 93.5
25 TraesCS4A01G021900 chrUn 84.158 101 10 3 2975 3072 269237442 269237345 3.300000e-15 93.5
26 TraesCS4A01G021900 chr5A 94.118 68 3 1 3011 3078 504784432 504784498 5.480000e-18 102.0
27 TraesCS4A01G021900 chr5A 84.694 98 9 5 2975 3071 410510034 410509942 3.300000e-15 93.5
28 TraesCS4A01G021900 chr7A 95.000 60 3 0 3011 3070 682442487 682442546 9.160000e-16 95.3
29 TraesCS4A01G021900 chr7B 84.536 97 11 2 2975 3071 474550588 474550496 3.300000e-15 93.5
30 TraesCS4A01G021900 chr1A 78.512 121 13 9 2952 3072 16377839 16377732 2.000000e-07 67.6


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 TraesCS4A01G021900 chr4A 15758518 15761621 3103 False 5733 5733 100.0000 1 3104 1 chr4A.!!$F1 3103
1 TraesCS4A01G021900 chr4A 15767365 15768116 751 False 726 726 84.3630 1141 1889 1 chr4A.!!$F2 748
2 TraesCS4A01G021900 chr4D 451275393 451277405 2012 True 1599 3051 92.1275 987 2976 2 chr4D.!!$R2 1989
3 TraesCS4A01G021900 chr4D 451177396 451178147 751 True 721 721 84.2730 1141 1889 1 chr4D.!!$R1 748
4 TraesCS4A01G021900 chr4B 564651625 564653516 1891 True 2939 2939 94.6300 1069 2976 1 chr4B.!!$R2 1907
5 TraesCS4A01G021900 chr4B 564784269 564786111 1842 True 959 1201 86.0495 1063 2976 2 chr4B.!!$R4 1913
6 TraesCS4A01G021900 chr4B 665293820 665294582 762 True 957 957 89.3230 60 825 1 chr4B.!!$R3 765
7 TraesCS4A01G021900 chr4B 564394866 564395617 751 True 743 743 84.7570 1141 1889 1 chr4B.!!$R1 748
8 TraesCS4A01G021900 chr6B 181300 182117 817 True 977 977 88.2420 4 825 1 chr6B.!!$R1 821
9 TraesCS4A01G021900 chr6B 599981104 599981866 762 True 963 963 89.4530 60 825 1 chr6B.!!$R2 765
10 TraesCS4A01G021900 chr6B 641300854 641301623 769 True 959 959 89.1470 53 825 1 chr6B.!!$R3 772
11 TraesCS4A01G021900 chr1B 94009127 94009895 768 True 948 948 88.9320 60 833 1 chr1B.!!$R1 773
12 TraesCS4A01G021900 chr3B 804315850 804316663 813 True 941 941 87.5150 4 825 1 chr3B.!!$R1 821
13 TraesCS4A01G021900 chr2B 73986002 73986817 815 True 937 937 87.4240 4 825 1 chr2B.!!$R1 821
14 TraesCS4A01G021900 chr2B 102127468 102128283 815 True 920 920 87.0300 4 825 1 chr2B.!!$R2 821
15 TraesCS4A01G021900 chr2D 484881000 484881813 813 True 922 922 87.1200 5 825 1 chr2D.!!$R1 820
16 TraesCS4A01G021900 chr6D 80002918 80003587 669 True 756 756 87.0540 155 825 1 chr6D.!!$R1 670

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
461 473 0.033796 CCTGGTTCATGGATGGCAGT 60.034 55.0 0.0 0.0 0.0 4.40 F
1685 1712 0.035458 CTGACGAACCCTTGGAGCTT 59.965 55.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1944 0.384725 CAAGAACGCCGCAGTTTCAG 60.385 55.0 2.85 0.0 34.00 3.02 R
3000 3097 0.516524 CTAAACGCTCAAACGCTCGC 60.517 55.0 0.00 0.0 36.19 5.03 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
44 46 0.914644 CCAGGAGAGGCCATCTTTCA 59.085 55.000 5.01 0.00 38.84 2.69
45 47 1.134159 CCAGGAGAGGCCATCTTTCAG 60.134 57.143 5.01 0.00 38.84 3.02
46 48 0.545646 AGGAGAGGCCATCTTTCAGC 59.454 55.000 5.01 0.00 38.84 4.26
47 49 0.813210 GGAGAGGCCATCTTTCAGCG 60.813 60.000 5.01 0.00 38.84 5.18
106 111 2.375345 GGGGGTGTCGGATCCATGT 61.375 63.158 13.41 0.00 0.00 3.21
125 130 6.493115 TCCATGTGTGTGGATCATTTTTACTT 59.507 34.615 0.00 0.00 43.20 2.24
126 131 6.808212 CCATGTGTGTGGATCATTTTTACTTC 59.192 38.462 0.00 0.00 42.02 3.01
180 185 3.188786 GCTTCGGCAGCGACGATT 61.189 61.111 7.30 0.00 44.78 3.34
207 212 4.034048 GCGCTGAATAAAGATTCTTCGGAA 59.966 41.667 0.00 0.00 41.87 4.30
216 222 2.907042 AGATTCTTCGGAACTTCCCTGT 59.093 45.455 1.97 0.00 36.72 4.00
258 264 1.111277 GGGGATGGATTTGGAAACCG 58.889 55.000 0.00 0.00 0.00 4.44
266 272 2.626266 GGATTTGGAAACCGGTCTGTTT 59.374 45.455 8.04 0.00 40.99 2.83
287 299 1.640917 AGTAAGGATGGTGTGACGGT 58.359 50.000 0.00 0.00 0.00 4.83
288 300 1.275291 AGTAAGGATGGTGTGACGGTG 59.725 52.381 0.00 0.00 0.00 4.94
289 301 0.611200 TAAGGATGGTGTGACGGTGG 59.389 55.000 0.00 0.00 0.00 4.61
290 302 2.746277 GGATGGTGTGACGGTGGC 60.746 66.667 0.00 0.00 0.00 5.01
291 303 3.118454 GATGGTGTGACGGTGGCG 61.118 66.667 0.00 0.00 0.00 5.69
292 304 3.583276 GATGGTGTGACGGTGGCGA 62.583 63.158 0.00 0.00 0.00 5.54
443 455 3.340789 GAACGTGTGCTGGGTTCC 58.659 61.111 0.00 0.00 35.24 3.62
461 473 0.033796 CCTGGTTCATGGATGGCAGT 60.034 55.000 0.00 0.00 0.00 4.40
509 521 1.852157 TGGTGGGGTGCCAGATCTT 60.852 57.895 0.00 0.00 0.00 2.40
565 577 2.147150 TGATTCGTTCAACGGCAATGA 58.853 42.857 10.69 0.00 42.81 2.57
625 637 1.133730 TGCATATCAGCAATGGAGCCA 60.134 47.619 0.00 0.00 42.46 4.75
628 640 0.815213 TATCAGCAATGGAGCCACGC 60.815 55.000 4.94 4.94 34.23 5.34
665 677 4.095036 GGAGGTGATTCGTCATTCTTTTCC 59.905 45.833 0.00 0.00 33.18 3.13
669 681 4.389077 GTGATTCGTCATTCTTTTCCTCGT 59.611 41.667 0.00 0.00 0.00 4.18
675 687 4.000988 GTCATTCTTTTCCTCGTTGGCTA 58.999 43.478 0.00 0.00 35.26 3.93
702 714 3.233980 TGCCAGACGCAGGTGACT 61.234 61.111 0.00 0.00 44.64 3.41
730 742 2.289257 TGGTGTCAAGCTCAGAGATGTG 60.289 50.000 0.00 0.00 0.00 3.21
732 744 1.338484 TGTCAAGCTCAGAGATGTGCC 60.338 52.381 0.00 0.00 0.00 5.01
745 757 3.609853 AGATGTGCCGCTATCTTTTCAA 58.390 40.909 5.27 0.00 29.64 2.69
771 783 4.059511 TGTCATGTCGGTTTTTACGTGAT 58.940 39.130 0.00 0.00 42.06 3.06
774 786 6.202379 TGTCATGTCGGTTTTTACGTGATTTA 59.798 34.615 0.00 0.00 42.06 1.40
817 829 5.972935 TGAATGAGACACGTATAACCATGT 58.027 37.500 0.00 0.00 0.00 3.21
848 860 9.853177 AAATGTCTTATACTTTGATAGGAAGGG 57.147 33.333 0.00 0.00 0.00 3.95
849 861 8.798975 ATGTCTTATACTTTGATAGGAAGGGA 57.201 34.615 0.00 0.00 0.00 4.20
850 862 8.251383 TGTCTTATACTTTGATAGGAAGGGAG 57.749 38.462 0.00 0.00 0.00 4.30
851 863 7.844779 TGTCTTATACTTTGATAGGAAGGGAGT 59.155 37.037 0.00 0.00 0.00 3.85
852 864 9.364653 GTCTTATACTTTGATAGGAAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
853 865 9.364653 TCTTATACTTTGATAGGAAGGGAGTAC 57.635 37.037 0.00 0.00 0.00 2.73
854 866 9.144298 CTTATACTTTGATAGGAAGGGAGTACA 57.856 37.037 0.00 0.00 0.00 2.90
855 867 9.670442 TTATACTTTGATAGGAAGGGAGTACAT 57.330 33.333 0.00 0.00 0.00 2.29
857 869 7.362802 ACTTTGATAGGAAGGGAGTACATAC 57.637 40.000 0.00 0.00 0.00 2.39
858 870 6.326843 ACTTTGATAGGAAGGGAGTACATACC 59.673 42.308 0.00 0.00 0.00 2.73
859 871 5.412617 TGATAGGAAGGGAGTACATACCA 57.587 43.478 0.00 0.00 0.00 3.25
860 872 5.145564 TGATAGGAAGGGAGTACATACCAC 58.854 45.833 0.00 0.00 0.00 4.16
861 873 3.778622 AGGAAGGGAGTACATACCACT 57.221 47.619 0.00 0.00 0.00 4.00
862 874 3.375699 AGGAAGGGAGTACATACCACTG 58.624 50.000 0.00 0.00 0.00 3.66
863 875 3.012502 AGGAAGGGAGTACATACCACTGA 59.987 47.826 0.00 0.00 0.00 3.41
864 876 3.773119 GGAAGGGAGTACATACCACTGAA 59.227 47.826 0.00 0.00 0.00 3.02
865 877 4.382793 GGAAGGGAGTACATACCACTGAAC 60.383 50.000 0.00 0.00 0.00 3.18
866 878 4.062490 AGGGAGTACATACCACTGAACT 57.938 45.455 0.00 0.00 0.00 3.01
867 879 4.426704 AGGGAGTACATACCACTGAACTT 58.573 43.478 0.00 0.00 0.00 2.66
868 880 4.844655 AGGGAGTACATACCACTGAACTTT 59.155 41.667 0.00 0.00 0.00 2.66
869 881 5.309806 AGGGAGTACATACCACTGAACTTTT 59.690 40.000 0.00 0.00 0.00 2.27
870 882 6.002082 GGGAGTACATACCACTGAACTTTTT 58.998 40.000 0.00 0.00 0.00 1.94
871 883 6.148976 GGGAGTACATACCACTGAACTTTTTC 59.851 42.308 0.00 0.00 0.00 2.29
872 884 6.128634 GGAGTACATACCACTGAACTTTTTCG 60.129 42.308 0.00 0.00 34.04 3.46
873 885 6.518493 AGTACATACCACTGAACTTTTTCGA 58.482 36.000 0.00 0.00 34.04 3.71
874 886 5.924475 ACATACCACTGAACTTTTTCGAG 57.076 39.130 0.00 0.00 34.04 4.04
875 887 5.607477 ACATACCACTGAACTTTTTCGAGA 58.393 37.500 0.00 0.00 34.04 4.04
876 888 6.053005 ACATACCACTGAACTTTTTCGAGAA 58.947 36.000 0.00 0.00 34.04 2.87
877 889 6.540914 ACATACCACTGAACTTTTTCGAGAAA 59.459 34.615 0.78 0.78 34.04 2.52
878 890 5.890424 ACCACTGAACTTTTTCGAGAAAA 57.110 34.783 6.89 6.89 38.40 2.29
879 891 6.262193 ACCACTGAACTTTTTCGAGAAAAA 57.738 33.333 18.89 18.89 44.98 1.94
922 934 4.168291 GGAGCAGCGAGGGGGAAG 62.168 72.222 0.00 0.00 0.00 3.46
923 935 4.168291 GAGCAGCGAGGGGGAAGG 62.168 72.222 0.00 0.00 0.00 3.46
947 959 2.915659 CGGCCGTGGCTATCCCTA 60.916 66.667 19.50 0.00 41.60 3.53
948 960 2.741747 GGCCGTGGCTATCCCTAC 59.258 66.667 11.25 0.00 41.60 3.18
949 961 2.741747 GCCGTGGCTATCCCTACC 59.258 66.667 2.98 0.00 38.26 3.18
950 962 2.138179 GCCGTGGCTATCCCTACCA 61.138 63.158 2.98 0.00 38.26 3.25
953 965 2.925078 GTGGCTATCCCTACCACCA 58.075 57.895 0.00 0.00 46.65 4.17
954 966 0.468648 GTGGCTATCCCTACCACCAC 59.531 60.000 0.00 0.00 46.65 4.16
955 967 0.693092 TGGCTATCCCTACCACCACC 60.693 60.000 0.00 0.00 0.00 4.61
956 968 0.693092 GGCTATCCCTACCACCACCA 60.693 60.000 0.00 0.00 0.00 4.17
957 969 0.468648 GCTATCCCTACCACCACCAC 59.531 60.000 0.00 0.00 0.00 4.16
958 970 1.129058 CTATCCCTACCACCACCACC 58.871 60.000 0.00 0.00 0.00 4.61
959 971 0.418245 TATCCCTACCACCACCACCA 59.582 55.000 0.00 0.00 0.00 4.17
960 972 1.205460 ATCCCTACCACCACCACCAC 61.205 60.000 0.00 0.00 0.00 4.16
961 973 2.754375 CCTACCACCACCACCACC 59.246 66.667 0.00 0.00 0.00 4.61
962 974 2.754375 CTACCACCACCACCACCC 59.246 66.667 0.00 0.00 0.00 4.61
963 975 3.243053 TACCACCACCACCACCCG 61.243 66.667 0.00 0.00 0.00 5.28
965 977 4.947147 CCACCACCACCACCCGTG 62.947 72.222 0.00 0.00 42.62 4.94
966 978 3.867783 CACCACCACCACCCGTGA 61.868 66.667 0.00 0.00 46.20 4.35
967 979 3.868985 ACCACCACCACCCGTGAC 61.869 66.667 0.00 0.00 46.20 3.67
968 980 3.556306 CCACCACCACCCGTGACT 61.556 66.667 0.00 0.00 46.20 3.41
969 981 2.211410 CCACCACCACCCGTGACTA 61.211 63.158 0.00 0.00 46.20 2.59
970 982 1.005394 CACCACCACCCGTGACTAC 60.005 63.158 0.00 0.00 46.20 2.73
971 983 2.212110 ACCACCACCCGTGACTACC 61.212 63.158 0.00 0.00 46.20 3.18
972 984 2.660802 CACCACCCGTGACTACCC 59.339 66.667 0.00 0.00 46.20 3.69
973 985 2.993264 ACCACCCGTGACTACCCG 60.993 66.667 0.00 0.00 0.00 5.28
974 986 3.766691 CCACCCGTGACTACCCGG 61.767 72.222 0.00 0.00 43.82 5.73
975 987 4.446413 CACCCGTGACTACCCGGC 62.446 72.222 0.00 0.00 42.87 6.13
980 992 3.468140 GTGACTACCCGGCCCCTC 61.468 72.222 0.00 0.00 0.00 4.30
981 993 4.791069 TGACTACCCGGCCCCTCC 62.791 72.222 0.00 0.00 0.00 4.30
1036 1048 2.689813 CCCAAATCCCACTCCCCC 59.310 66.667 0.00 0.00 0.00 5.40
1670 1697 1.285950 GTTTTTCCGCCTGGCTGAC 59.714 57.895 17.92 0.37 34.14 3.51
1685 1712 0.035458 CTGACGAACCCTTGGAGCTT 59.965 55.000 0.00 0.00 0.00 3.74
1893 1944 2.093816 TGCTCATCATGTCAGTCTGGTC 60.094 50.000 0.00 0.00 0.00 4.02
1937 1988 1.803334 TCCTTCCGTTCGTTTCATGG 58.197 50.000 0.00 0.00 0.00 3.66
1986 2037 0.486879 AATGGCACCCCTTTCCTTCA 59.513 50.000 0.00 0.00 0.00 3.02
2129 2180 3.347216 ACTTTATCTGCATGTGTGTCCC 58.653 45.455 0.00 0.00 0.00 4.46
2249 2300 5.221185 CCTTCTGAATAACATCCATGCCAAG 60.221 44.000 0.00 0.00 0.00 3.61
2274 2329 9.836864 AGCATGACTATCAGAATACAATTAACA 57.163 29.630 0.00 0.00 0.00 2.41
2423 2479 5.350504 TTGCCTGAAAATGGACTTTGAAA 57.649 34.783 0.00 0.00 0.00 2.69
2440 2496 4.487714 TGAAAGGATTGTAAGAGGCGAT 57.512 40.909 0.00 0.00 0.00 4.58
2467 2524 0.030504 TTTGTGCATGAGTTGTGCGG 59.969 50.000 0.00 0.00 45.37 5.69
2472 2529 2.031919 ATGAGTTGTGCGGCGGAA 59.968 55.556 9.78 0.00 0.00 4.30
2547 2612 1.482593 GCTGATGGCTACTGTACCACT 59.517 52.381 10.08 2.94 39.19 4.00
2548 2613 2.739932 GCTGATGGCTACTGTACCACTG 60.740 54.545 10.08 9.42 39.19 3.66
2612 2677 6.068670 TGTAGCCATAGTTGACTAGCATCTA 58.931 40.000 0.00 0.00 34.30 1.98
2645 2713 3.761218 TGACAACACCGCCATATGATTTT 59.239 39.130 3.65 0.00 0.00 1.82
2646 2714 4.219507 TGACAACACCGCCATATGATTTTT 59.780 37.500 3.65 0.00 0.00 1.94
2707 2777 7.257790 TCTAGAAGACATTTTGGGATGAAGA 57.742 36.000 0.00 0.00 0.00 2.87
2752 2822 6.486993 GGAGGGTGTTTTGTTATCTATGGATC 59.513 42.308 0.00 0.00 33.71 3.36
2808 2905 7.920160 TCATTGTTTGCTATCAGATGTGTTA 57.080 32.000 0.00 0.00 0.00 2.41
2866 2963 6.065976 TGATCTGTCAGGTTTGATATGGTT 57.934 37.500 0.00 0.00 35.39 3.67
2923 3020 3.146066 TGAGCCAGTTTGTGTACCATTC 58.854 45.455 0.00 0.00 0.00 2.67
2984 3081 5.793030 ATTCATCTAAACTACTCCCTCCG 57.207 43.478 0.00 0.00 0.00 4.63
2985 3082 4.246712 TCATCTAAACTACTCCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
2986 3083 5.378230 TCATCTAAACTACTCCCTCCGTA 57.622 43.478 0.00 0.00 0.00 4.02
2987 3084 5.759059 TCATCTAAACTACTCCCTCCGTAA 58.241 41.667 0.00 0.00 0.00 3.18
2988 3085 6.189859 TCATCTAAACTACTCCCTCCGTAAA 58.810 40.000 0.00 0.00 0.00 2.01
2989 3086 6.320672 TCATCTAAACTACTCCCTCCGTAAAG 59.679 42.308 0.00 0.00 0.00 1.85
2990 3087 5.819991 TCTAAACTACTCCCTCCGTAAAGA 58.180 41.667 0.00 0.00 0.00 2.52
2991 3088 6.248433 TCTAAACTACTCCCTCCGTAAAGAA 58.752 40.000 0.00 0.00 0.00 2.52
2992 3089 5.813513 AAACTACTCCCTCCGTAAAGAAA 57.186 39.130 0.00 0.00 0.00 2.52
2993 3090 6.370186 AAACTACTCCCTCCGTAAAGAAAT 57.630 37.500 0.00 0.00 0.00 2.17
2994 3091 7.486407 AAACTACTCCCTCCGTAAAGAAATA 57.514 36.000 0.00 0.00 0.00 1.40
2995 3092 7.672122 AACTACTCCCTCCGTAAAGAAATAT 57.328 36.000 0.00 0.00 0.00 1.28
2996 3093 8.773033 AACTACTCCCTCCGTAAAGAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
2997 3094 8.773033 ACTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
2998 3095 8.858094 ACTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
2999 3096 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3000 3097 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3001 3098 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3002 3099 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
3003 3100 6.444633 CCTCCGTAAAGAAATATAAGAGCGA 58.555 40.000 0.00 0.00 0.00 4.93
3004 3101 6.583050 CCTCCGTAAAGAAATATAAGAGCGAG 59.417 42.308 0.00 0.00 0.00 5.03
3005 3102 5.919141 TCCGTAAAGAAATATAAGAGCGAGC 59.081 40.000 0.00 0.00 0.00 5.03
3006 3103 5.164177 CCGTAAAGAAATATAAGAGCGAGCG 60.164 44.000 0.00 0.00 0.00 5.03
3007 3104 5.398711 CGTAAAGAAATATAAGAGCGAGCGT 59.601 40.000 0.00 0.00 0.00 5.07
3008 3105 6.074994 CGTAAAGAAATATAAGAGCGAGCGTT 60.075 38.462 0.00 0.00 0.00 4.84
3009 3106 6.663944 AAAGAAATATAAGAGCGAGCGTTT 57.336 33.333 0.00 0.00 0.00 3.60
3010 3107 5.643339 AGAAATATAAGAGCGAGCGTTTG 57.357 39.130 0.00 0.00 0.00 2.93
3011 3108 5.348986 AGAAATATAAGAGCGAGCGTTTGA 58.651 37.500 0.00 0.00 0.00 2.69
3012 3109 5.460419 AGAAATATAAGAGCGAGCGTTTGAG 59.540 40.000 0.00 0.00 0.00 3.02
3013 3110 1.281899 ATAAGAGCGAGCGTTTGAGC 58.718 50.000 0.00 0.00 37.41 4.26
3014 3111 1.071019 TAAGAGCGAGCGTTTGAGCG 61.071 55.000 0.00 0.00 43.00 5.03
3015 3112 3.106407 GAGCGAGCGTTTGAGCGT 61.106 61.111 0.00 0.00 43.00 5.07
3016 3113 2.658707 GAGCGAGCGTTTGAGCGTT 61.659 57.895 0.00 0.00 43.00 4.84
3017 3114 2.159272 GAGCGAGCGTTTGAGCGTTT 62.159 55.000 0.00 0.00 43.00 3.60
3018 3115 0.942410 AGCGAGCGTTTGAGCGTTTA 60.942 50.000 0.00 0.00 43.00 2.01
3019 3116 0.516524 GCGAGCGTTTGAGCGTTTAG 60.517 55.000 0.00 0.00 43.00 1.85
3020 3117 1.057636 CGAGCGTTTGAGCGTTTAGA 58.942 50.000 0.00 0.00 43.00 2.10
3021 3118 1.654105 CGAGCGTTTGAGCGTTTAGAT 59.346 47.619 0.00 0.00 43.00 1.98
3022 3119 2.850060 CGAGCGTTTGAGCGTTTAGATA 59.150 45.455 0.00 0.00 43.00 1.98
3023 3120 3.302434 CGAGCGTTTGAGCGTTTAGATAA 59.698 43.478 0.00 0.00 43.00 1.75
3024 3121 4.566177 GAGCGTTTGAGCGTTTAGATAAC 58.434 43.478 0.00 0.00 43.00 1.89
3025 3122 4.243270 AGCGTTTGAGCGTTTAGATAACT 58.757 39.130 0.00 0.00 43.00 2.24
3026 3123 5.404946 AGCGTTTGAGCGTTTAGATAACTA 58.595 37.500 0.00 0.00 43.00 2.24
3027 3124 5.865552 AGCGTTTGAGCGTTTAGATAACTAA 59.134 36.000 0.00 0.00 43.00 2.24
3028 3125 6.366877 AGCGTTTGAGCGTTTAGATAACTAAA 59.633 34.615 1.33 1.33 42.19 1.85
3029 3126 6.677411 GCGTTTGAGCGTTTAGATAACTAAAG 59.323 38.462 5.51 2.65 45.42 1.85
3030 3127 7.620806 GCGTTTGAGCGTTTAGATAACTAAAGT 60.621 37.037 5.51 0.00 45.42 2.66
3031 3128 8.853345 CGTTTGAGCGTTTAGATAACTAAAGTA 58.147 33.333 5.51 0.00 45.42 2.24
3033 3130 9.918630 TTTGAGCGTTTAGATAACTAAAGTAGT 57.081 29.630 5.51 0.00 45.42 2.73
3034 3131 8.906636 TGAGCGTTTAGATAACTAAAGTAGTG 57.093 34.615 5.51 0.00 45.42 2.74
3035 3132 8.733458 TGAGCGTTTAGATAACTAAAGTAGTGA 58.267 33.333 5.51 0.00 45.42 3.41
3036 3133 9.733219 GAGCGTTTAGATAACTAAAGTAGTGAT 57.267 33.333 5.51 0.00 45.42 3.06
3037 3134 9.733219 AGCGTTTAGATAACTAAAGTAGTGATC 57.267 33.333 5.51 5.03 45.42 2.92
3045 3142 9.733219 GATAACTAAAGTAGTGATCTAAACGCT 57.267 33.333 5.75 0.00 41.55 5.07
3046 3143 9.733219 ATAACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.39 5.03
3047 3144 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
3048 3145 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
3049 3146 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
3050 3147 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
3057 3154 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
3065 3162 7.772332 ACGCTCTTATATTTGTTTACAGAGG 57.228 36.000 0.00 0.00 0.00 3.69
3066 3163 6.761714 ACGCTCTTATATTTGTTTACAGAGGG 59.238 38.462 8.36 8.36 38.95 4.30
3067 3164 6.984474 CGCTCTTATATTTGTTTACAGAGGGA 59.016 38.462 4.76 0.00 36.40 4.20
3068 3165 7.169982 CGCTCTTATATTTGTTTACAGAGGGAG 59.830 40.741 4.76 0.00 36.40 4.30
3069 3166 7.988028 GCTCTTATATTTGTTTACAGAGGGAGT 59.012 37.037 0.00 0.00 0.00 3.85
3082 3179 5.026121 ACAGAGGGAGTATTGATCTGTCAA 58.974 41.667 0.48 0.00 45.60 3.18
3086 3183 5.983540 AGGGAGTATTGATCTGTCAAGTTC 58.016 41.667 0.00 0.00 46.75 3.01
3087 3184 5.485353 AGGGAGTATTGATCTGTCAAGTTCA 59.515 40.000 0.00 0.00 46.75 3.18
3099 3196 8.862325 ATCTGTCAAGTTCAATATGGTTGTTA 57.138 30.769 0.00 0.00 0.00 2.41
3100 3197 8.684386 TCTGTCAAGTTCAATATGGTTGTTAA 57.316 30.769 0.00 0.00 0.00 2.01
3102 3199 9.345517 CTGTCAAGTTCAATATGGTTGTTAATG 57.654 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.787001 GCTAGGGTTCCAGCCGCT 61.787 66.667 0.00 0.00 41.56 5.52
38 40 1.738350 CTAGAGGACGTCGCTGAAAGA 59.262 52.381 16.89 0.00 34.07 2.52
39 41 1.795889 GCTAGAGGACGTCGCTGAAAG 60.796 57.143 16.89 9.41 0.00 2.62
40 42 0.170561 GCTAGAGGACGTCGCTGAAA 59.829 55.000 16.89 0.27 0.00 2.69
44 46 3.203412 CCGCTAGAGGACGTCGCT 61.203 66.667 6.69 11.82 0.00 4.93
45 47 4.908877 GCCGCTAGAGGACGTCGC 62.909 72.222 17.75 5.88 0.00 5.19
46 48 4.592936 CGCCGCTAGAGGACGTCG 62.593 72.222 17.75 6.28 0.00 5.12
47 49 3.200593 TCGCCGCTAGAGGACGTC 61.201 66.667 17.75 7.13 34.25 4.34
90 95 0.744414 CACACATGGATCCGACACCC 60.744 60.000 7.39 0.00 0.00 4.61
91 96 0.036388 ACACACATGGATCCGACACC 60.036 55.000 7.39 0.00 0.00 4.16
92 97 1.078709 CACACACATGGATCCGACAC 58.921 55.000 7.39 0.00 0.00 3.67
93 98 0.036483 CCACACACATGGATCCGACA 60.036 55.000 7.39 0.00 43.02 4.35
104 109 6.068010 AGGAAGTAAAAATGATCCACACACA 58.932 36.000 0.00 0.00 32.47 3.72
106 111 6.549364 ACAAGGAAGTAAAAATGATCCACACA 59.451 34.615 0.00 0.00 32.47 3.72
125 130 8.488668 ACAACCTAAAAACTTAGACTACAAGGA 58.511 33.333 0.00 0.00 0.00 3.36
126 131 8.672823 ACAACCTAAAAACTTAGACTACAAGG 57.327 34.615 0.00 0.00 0.00 3.61
138 143 6.238648 CCAAGACGATGAACAACCTAAAAACT 60.239 38.462 0.00 0.00 0.00 2.66
180 185 4.054780 AGAATCTTTATTCAGCGCCGTA 57.945 40.909 2.29 0.00 43.44 4.02
207 212 0.329596 GATGGCCTCAACAGGGAAGT 59.670 55.000 3.32 0.00 40.75 3.01
216 222 0.758734 CATAGGACCGATGGCCTCAA 59.241 55.000 3.32 0.00 32.93 3.02
258 264 5.411669 CACACCATCCTTACTTAAACAGACC 59.588 44.000 0.00 0.00 0.00 3.85
266 272 3.056393 CACCGTCACACCATCCTTACTTA 60.056 47.826 0.00 0.00 0.00 2.24
291 303 1.218316 GGTCCACCACGAGGATGTC 59.782 63.158 5.68 0.00 37.52 3.06
292 304 1.229209 AGGTCCACCACGAGGATGT 60.229 57.895 5.68 0.00 37.52 3.06
359 371 1.271379 TGTGCTACTTTCCAAGCTCCC 60.271 52.381 0.00 0.00 39.53 4.30
369 381 0.905357 ATCCGCTCCTGTGCTACTTT 59.095 50.000 0.00 0.00 0.00 2.66
371 383 1.819229 CATCCGCTCCTGTGCTACT 59.181 57.895 0.00 0.00 0.00 2.57
376 388 0.463295 AATCTGCATCCGCTCCTGTG 60.463 55.000 0.00 0.00 39.64 3.66
377 389 0.463295 CAATCTGCATCCGCTCCTGT 60.463 55.000 0.00 0.00 39.64 4.00
443 455 1.843368 AACTGCCATCCATGAACCAG 58.157 50.000 0.00 0.00 0.00 4.00
509 521 1.080093 GGACACGCCATCGAACTCA 60.080 57.895 0.00 0.00 39.41 3.41
665 677 0.670546 CCACCACAGTAGCCAACGAG 60.671 60.000 0.00 0.00 0.00 4.18
669 681 1.228124 GCACCACCACAGTAGCCAA 60.228 57.895 0.00 0.00 0.00 4.52
675 687 2.510906 GTCTGGCACCACCACAGT 59.489 61.111 0.00 0.00 46.36 3.55
702 714 2.904866 GCTTGACACCAACGCCCA 60.905 61.111 0.00 0.00 0.00 5.36
730 742 5.160641 TGACAAAATTGAAAAGATAGCGGC 58.839 37.500 0.00 0.00 0.00 6.53
732 744 7.253092 CGACATGACAAAATTGAAAAGATAGCG 60.253 37.037 0.00 0.00 0.00 4.26
745 757 5.683743 CACGTAAAAACCGACATGACAAAAT 59.316 36.000 0.00 0.00 0.00 1.82
825 837 7.844779 ACTCCCTTCCTATCAAAGTATAAGACA 59.155 37.037 0.00 0.00 0.00 3.41
828 840 9.144298 TGTACTCCCTTCCTATCAAAGTATAAG 57.856 37.037 0.00 0.00 0.00 1.73
831 843 9.091220 GTATGTACTCCCTTCCTATCAAAGTAT 57.909 37.037 0.00 0.00 0.00 2.12
832 844 7.508296 GGTATGTACTCCCTTCCTATCAAAGTA 59.492 40.741 0.00 0.00 0.00 2.24
833 845 6.326843 GGTATGTACTCCCTTCCTATCAAAGT 59.673 42.308 0.00 0.00 0.00 2.66
834 846 6.326583 TGGTATGTACTCCCTTCCTATCAAAG 59.673 42.308 0.00 0.00 0.00 2.77
835 847 6.099269 GTGGTATGTACTCCCTTCCTATCAAA 59.901 42.308 0.00 0.00 0.00 2.69
836 848 5.601313 GTGGTATGTACTCCCTTCCTATCAA 59.399 44.000 0.00 0.00 0.00 2.57
837 849 5.103215 AGTGGTATGTACTCCCTTCCTATCA 60.103 44.000 0.00 0.00 0.00 2.15
838 850 5.244178 CAGTGGTATGTACTCCCTTCCTATC 59.756 48.000 0.00 0.00 0.00 2.08
839 851 5.103215 TCAGTGGTATGTACTCCCTTCCTAT 60.103 44.000 0.00 0.00 0.00 2.57
840 852 4.231195 TCAGTGGTATGTACTCCCTTCCTA 59.769 45.833 0.00 0.00 0.00 2.94
841 853 3.012502 TCAGTGGTATGTACTCCCTTCCT 59.987 47.826 0.00 0.00 0.00 3.36
842 854 3.371965 TCAGTGGTATGTACTCCCTTCC 58.628 50.000 0.00 0.00 0.00 3.46
843 855 4.466726 AGTTCAGTGGTATGTACTCCCTTC 59.533 45.833 0.00 0.00 0.00 3.46
844 856 4.426704 AGTTCAGTGGTATGTACTCCCTT 58.573 43.478 0.00 0.00 0.00 3.95
845 857 4.062490 AGTTCAGTGGTATGTACTCCCT 57.938 45.455 0.00 0.00 0.00 4.20
846 858 4.820894 AAGTTCAGTGGTATGTACTCCC 57.179 45.455 0.00 0.00 30.52 4.30
847 859 6.128634 CGAAAAAGTTCAGTGGTATGTACTCC 60.129 42.308 0.00 0.00 30.52 3.85
848 860 6.643770 TCGAAAAAGTTCAGTGGTATGTACTC 59.356 38.462 0.00 0.00 30.52 2.59
849 861 6.518493 TCGAAAAAGTTCAGTGGTATGTACT 58.482 36.000 0.00 0.00 32.83 2.73
850 862 6.643770 TCTCGAAAAAGTTCAGTGGTATGTAC 59.356 38.462 0.00 0.00 32.89 2.90
851 863 6.751157 TCTCGAAAAAGTTCAGTGGTATGTA 58.249 36.000 0.00 0.00 32.89 2.29
852 864 5.607477 TCTCGAAAAAGTTCAGTGGTATGT 58.393 37.500 0.00 0.00 32.89 2.29
853 865 6.539649 TTCTCGAAAAAGTTCAGTGGTATG 57.460 37.500 0.00 0.00 32.89 2.39
854 866 7.562454 TTTTCTCGAAAAAGTTCAGTGGTAT 57.438 32.000 2.54 0.00 37.35 2.73
855 867 6.988622 TTTTCTCGAAAAAGTTCAGTGGTA 57.011 33.333 2.54 0.00 37.35 3.25
856 868 5.890424 TTTTCTCGAAAAAGTTCAGTGGT 57.110 34.783 2.54 0.00 37.35 4.16
880 892 4.202121 GCCTTCCGGTTTCTTTCTCTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
881 893 3.318275 GCCTTCCGGTTTCTTTCTCTTTT 59.682 43.478 0.00 0.00 0.00 2.27
882 894 2.885266 GCCTTCCGGTTTCTTTCTCTTT 59.115 45.455 0.00 0.00 0.00 2.52
883 895 2.505405 GCCTTCCGGTTTCTTTCTCTT 58.495 47.619 0.00 0.00 0.00 2.85
884 896 1.608283 CGCCTTCCGGTTTCTTTCTCT 60.608 52.381 0.00 0.00 0.00 3.10
885 897 0.796927 CGCCTTCCGGTTTCTTTCTC 59.203 55.000 0.00 0.00 0.00 2.87
886 898 2.928416 CGCCTTCCGGTTTCTTTCT 58.072 52.632 0.00 0.00 0.00 2.52
905 917 4.168291 CTTCCCCCTCGCTGCTCC 62.168 72.222 0.00 0.00 0.00 4.70
906 918 4.168291 CCTTCCCCCTCGCTGCTC 62.168 72.222 0.00 0.00 0.00 4.26
930 942 2.915659 TAGGGATAGCCACGGCCG 60.916 66.667 26.86 26.86 43.17 6.13
931 943 2.741747 GTAGGGATAGCCACGGCC 59.258 66.667 3.95 0.00 43.17 6.13
932 944 2.138179 TGGTAGGGATAGCCACGGC 61.138 63.158 0.00 0.00 42.33 5.68
933 945 1.746517 GTGGTAGGGATAGCCACGG 59.253 63.158 0.00 0.00 42.43 4.94
936 948 0.693092 GGTGGTGGTAGGGATAGCCA 60.693 60.000 0.00 0.00 35.15 4.75
937 949 0.693092 TGGTGGTGGTAGGGATAGCC 60.693 60.000 0.00 0.00 0.00 3.93
938 950 0.468648 GTGGTGGTGGTAGGGATAGC 59.531 60.000 0.00 0.00 0.00 2.97
939 951 1.129058 GGTGGTGGTGGTAGGGATAG 58.871 60.000 0.00 0.00 0.00 2.08
940 952 0.418245 TGGTGGTGGTGGTAGGGATA 59.582 55.000 0.00 0.00 0.00 2.59
941 953 1.162329 TGGTGGTGGTGGTAGGGAT 59.838 57.895 0.00 0.00 0.00 3.85
942 954 1.844289 GTGGTGGTGGTGGTAGGGA 60.844 63.158 0.00 0.00 0.00 4.20
943 955 2.754375 GTGGTGGTGGTGGTAGGG 59.246 66.667 0.00 0.00 0.00 3.53
944 956 2.754375 GGTGGTGGTGGTGGTAGG 59.246 66.667 0.00 0.00 0.00 3.18
945 957 2.754375 GGGTGGTGGTGGTGGTAG 59.246 66.667 0.00 0.00 0.00 3.18
946 958 3.243053 CGGGTGGTGGTGGTGGTA 61.243 66.667 0.00 0.00 0.00 3.25
948 960 4.947147 CACGGGTGGTGGTGGTGG 62.947 72.222 0.00 0.00 43.16 4.61
949 961 3.867783 TCACGGGTGGTGGTGGTG 61.868 66.667 0.00 0.00 46.96 4.17
950 962 2.950617 TAGTCACGGGTGGTGGTGGT 62.951 60.000 0.00 0.00 46.96 4.16
951 963 2.211410 TAGTCACGGGTGGTGGTGG 61.211 63.158 0.00 0.00 46.96 4.61
952 964 1.005394 GTAGTCACGGGTGGTGGTG 60.005 63.158 0.00 0.00 46.96 4.17
953 965 2.212110 GGTAGTCACGGGTGGTGGT 61.212 63.158 0.00 0.00 46.96 4.16
954 966 2.660802 GGTAGTCACGGGTGGTGG 59.339 66.667 0.00 0.00 46.96 4.61
956 968 2.993264 CGGGTAGTCACGGGTGGT 60.993 66.667 0.00 0.00 36.76 4.16
963 975 3.468140 GAGGGGCCGGGTAGTCAC 61.468 72.222 2.18 0.00 0.00 3.67
964 976 4.791069 GGAGGGGCCGGGTAGTCA 62.791 72.222 2.18 0.00 0.00 3.41
1036 1048 3.149981 GAGGTTTTCCCTTTCAGACTGG 58.850 50.000 1.81 0.00 46.51 4.00
1037 1049 2.808543 CGAGGTTTTCCCTTTCAGACTG 59.191 50.000 0.00 0.00 46.51 3.51
1670 1697 1.301677 GCTGAAGCTCCAAGGGTTCG 61.302 60.000 0.00 0.00 43.89 3.95
1685 1712 3.402681 GCTGCAGGTAGGGGCTGA 61.403 66.667 17.12 0.00 0.00 4.26
1715 1760 1.076705 GGTGGCCTTCTTGATCCCC 60.077 63.158 3.32 0.00 0.00 4.81
1893 1944 0.384725 CAAGAACGCCGCAGTTTCAG 60.385 55.000 2.85 0.00 34.00 3.02
1937 1988 0.391263 CCTACGCAACCTCAGGTTCC 60.391 60.000 5.94 0.00 43.05 3.62
1986 2037 6.921914 ACTAGAAGTAGCACAAACGATTAGT 58.078 36.000 0.00 0.00 0.00 2.24
2022 2073 7.713073 GGAAGCAGTAAGAACTTGATAGCTAAT 59.287 37.037 0.00 0.00 31.97 1.73
2023 2074 7.042335 GGAAGCAGTAAGAACTTGATAGCTAA 58.958 38.462 0.00 0.00 31.97 3.09
2024 2075 6.154534 TGGAAGCAGTAAGAACTTGATAGCTA 59.845 38.462 0.00 0.00 31.97 3.32
2025 2076 5.046304 TGGAAGCAGTAAGAACTTGATAGCT 60.046 40.000 0.00 0.00 31.97 3.32
2026 2077 5.178797 TGGAAGCAGTAAGAACTTGATAGC 58.821 41.667 0.00 0.00 31.97 2.97
2027 2078 6.900568 CTGGAAGCAGTAAGAACTTGATAG 57.099 41.667 0.00 0.00 31.97 2.08
2205 2256 6.891908 AGAAGGCCTACACAATAAACATGAAT 59.108 34.615 5.16 0.00 0.00 2.57
2274 2329 6.357367 TGACTCTTTAGAAAAACTGCTCCTT 58.643 36.000 0.00 0.00 0.00 3.36
2423 2479 1.765314 AGCATCGCCTCTTACAATCCT 59.235 47.619 0.00 0.00 0.00 3.24
2440 2496 0.675083 CTCATGCACAAAACCCAGCA 59.325 50.000 0.00 0.00 41.73 4.41
2467 2524 0.951558 AGTGATGTTGTGGTTTCCGC 59.048 50.000 0.00 0.00 34.12 5.54
2472 2529 3.006859 TCGAGATCAGTGATGTTGTGGTT 59.993 43.478 11.20 0.00 0.00 3.67
2547 2612 2.503765 TCACAAAGTGGGACTCAGAACA 59.496 45.455 0.00 0.00 33.87 3.18
2548 2613 3.134458 CTCACAAAGTGGGACTCAGAAC 58.866 50.000 0.00 0.00 35.82 3.01
2612 2677 3.613910 GCGGTGTTGTCAGGCAATTTTAT 60.614 43.478 0.00 0.00 39.55 1.40
2645 2713 2.856720 GCACGAGCATTGAACGGAAAAA 60.857 45.455 0.00 0.00 41.58 1.94
2646 2714 1.334599 GCACGAGCATTGAACGGAAAA 60.335 47.619 0.00 0.00 41.58 2.29
2659 2727 4.913376 ACATATGAAAGAAATGCACGAGC 58.087 39.130 10.38 0.00 42.57 5.03
2752 2822 8.710980 AAACCTAATGTTAGCCAACTTAGGCAG 61.711 40.741 21.44 8.73 46.80 4.85
2923 3020 1.602851 GCAGCACATCTGATAGCAAGG 59.397 52.381 14.24 6.62 45.72 3.61
2973 3070 9.075678 TCTTATATTTCTTTACGGAGGGAGTAG 57.924 37.037 0.00 0.00 0.00 2.57
2976 3073 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
2977 3074 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
2978 3075 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
2979 3076 6.444633 TCGCTCTTATATTTCTTTACGGAGG 58.555 40.000 0.00 0.00 0.00 4.30
2980 3077 6.088350 GCTCGCTCTTATATTTCTTTACGGAG 59.912 42.308 0.00 0.00 0.00 4.63
2981 3078 5.919141 GCTCGCTCTTATATTTCTTTACGGA 59.081 40.000 0.00 0.00 0.00 4.69
2982 3079 5.164177 CGCTCGCTCTTATATTTCTTTACGG 60.164 44.000 0.00 0.00 0.00 4.02
2983 3080 5.398711 ACGCTCGCTCTTATATTTCTTTACG 59.601 40.000 0.00 0.00 0.00 3.18
2984 3081 6.750775 ACGCTCGCTCTTATATTTCTTTAC 57.249 37.500 0.00 0.00 0.00 2.01
2985 3082 7.490079 TCAAACGCTCGCTCTTATATTTCTTTA 59.510 33.333 0.00 0.00 0.00 1.85
2986 3083 6.312918 TCAAACGCTCGCTCTTATATTTCTTT 59.687 34.615 0.00 0.00 0.00 2.52
2987 3084 5.810587 TCAAACGCTCGCTCTTATATTTCTT 59.189 36.000 0.00 0.00 0.00 2.52
2988 3085 5.348986 TCAAACGCTCGCTCTTATATTTCT 58.651 37.500 0.00 0.00 0.00 2.52
2989 3086 5.637104 TCAAACGCTCGCTCTTATATTTC 57.363 39.130 0.00 0.00 0.00 2.17
2990 3087 4.025647 GCTCAAACGCTCGCTCTTATATTT 60.026 41.667 0.00 0.00 0.00 1.40
2991 3088 3.491267 GCTCAAACGCTCGCTCTTATATT 59.509 43.478 0.00 0.00 0.00 1.28
2992 3089 3.053455 GCTCAAACGCTCGCTCTTATAT 58.947 45.455 0.00 0.00 0.00 0.86
2993 3090 2.460918 GCTCAAACGCTCGCTCTTATA 58.539 47.619 0.00 0.00 0.00 0.98
2994 3091 1.281899 GCTCAAACGCTCGCTCTTAT 58.718 50.000 0.00 0.00 0.00 1.73
2995 3092 1.071019 CGCTCAAACGCTCGCTCTTA 61.071 55.000 0.00 0.00 0.00 2.10
2996 3093 2.375766 CGCTCAAACGCTCGCTCTT 61.376 57.895 0.00 0.00 0.00 2.85
2997 3094 2.807045 CGCTCAAACGCTCGCTCT 60.807 61.111 0.00 0.00 0.00 4.09
2998 3095 2.159272 AAACGCTCAAACGCTCGCTC 62.159 55.000 0.00 0.00 36.19 5.03
2999 3096 0.942410 TAAACGCTCAAACGCTCGCT 60.942 50.000 0.00 0.00 36.19 4.93
3000 3097 0.516524 CTAAACGCTCAAACGCTCGC 60.517 55.000 0.00 0.00 36.19 5.03
3001 3098 1.057636 TCTAAACGCTCAAACGCTCG 58.942 50.000 0.00 0.00 36.19 5.03
3002 3099 4.326548 AGTTATCTAAACGCTCAAACGCTC 59.673 41.667 0.00 0.00 36.19 5.03
3003 3100 4.243270 AGTTATCTAAACGCTCAAACGCT 58.757 39.130 0.00 0.00 36.19 5.07
3004 3101 4.579270 AGTTATCTAAACGCTCAAACGC 57.421 40.909 0.00 0.00 36.19 4.84
3005 3102 7.727017 ACTTTAGTTATCTAAACGCTCAAACG 58.273 34.615 2.47 0.00 40.05 3.60
3007 3104 9.918630 ACTACTTTAGTTATCTAAACGCTCAAA 57.081 29.630 2.47 0.00 40.05 2.69
3008 3105 9.350357 CACTACTTTAGTTATCTAAACGCTCAA 57.650 33.333 2.47 0.00 40.05 3.02
3009 3106 8.733458 TCACTACTTTAGTTATCTAAACGCTCA 58.267 33.333 2.47 0.00 40.05 4.26
3010 3107 9.733219 ATCACTACTTTAGTTATCTAAACGCTC 57.267 33.333 2.47 0.00 40.05 5.03
3011 3108 9.733219 GATCACTACTTTAGTTATCTAAACGCT 57.267 33.333 2.47 0.00 40.05 5.07
3012 3109 9.733219 AGATCACTACTTTAGTTATCTAAACGC 57.267 33.333 7.85 0.00 43.99 4.84
3018 3115 9.733219 GCGTTTAGATCACTACTTTAGTTATCT 57.267 33.333 12.46 12.46 46.18 1.98
3019 3116 9.733219 AGCGTTTAGATCACTACTTTAGTTATC 57.267 33.333 0.00 0.95 38.88 1.75
3020 3117 9.733219 GAGCGTTTAGATCACTACTTTAGTTAT 57.267 33.333 0.00 0.00 36.76 1.89
3021 3118 8.954350 AGAGCGTTTAGATCACTACTTTAGTTA 58.046 33.333 0.00 0.00 37.82 2.24
3022 3119 7.828712 AGAGCGTTTAGATCACTACTTTAGTT 58.171 34.615 0.00 0.00 37.82 2.24
3023 3120 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
3024 3121 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
3031 3128 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
3039 3136 8.665685 CCTCTGTAAACAAATATAAGAGCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
3040 3137 7.280205 CCCTCTGTAAACAAATATAAGAGCGTT 59.720 37.037 0.00 0.00 0.00 4.84
3041 3138 6.761714 CCCTCTGTAAACAAATATAAGAGCGT 59.238 38.462 0.00 0.00 0.00 5.07
3042 3139 6.984474 TCCCTCTGTAAACAAATATAAGAGCG 59.016 38.462 0.00 0.00 0.00 5.03
3043 3140 7.988028 ACTCCCTCTGTAAACAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
3050 3147 9.832445 GATCAATACTCCCTCTGTAAACAAATA 57.168 33.333 0.00 0.00 0.00 1.40
3051 3148 8.552296 AGATCAATACTCCCTCTGTAAACAAAT 58.448 33.333 0.00 0.00 0.00 2.32
3052 3149 7.824289 CAGATCAATACTCCCTCTGTAAACAAA 59.176 37.037 0.00 0.00 30.98 2.83
3053 3150 7.038302 ACAGATCAATACTCCCTCTGTAAACAA 60.038 37.037 1.88 0.00 43.42 2.83
3054 3151 6.440647 ACAGATCAATACTCCCTCTGTAAACA 59.559 38.462 1.88 0.00 43.42 2.83
3055 3152 6.879400 ACAGATCAATACTCCCTCTGTAAAC 58.121 40.000 1.88 0.00 43.42 2.01
3056 3153 6.667848 TGACAGATCAATACTCCCTCTGTAAA 59.332 38.462 3.69 0.00 44.79 2.01
3057 3154 6.194967 TGACAGATCAATACTCCCTCTGTAA 58.805 40.000 3.69 0.00 44.79 2.41
3058 3155 5.766590 TGACAGATCAATACTCCCTCTGTA 58.233 41.667 3.69 0.00 44.79 2.74
3059 3156 4.614475 TGACAGATCAATACTCCCTCTGT 58.386 43.478 3.35 3.35 46.78 3.41
3060 3157 5.128499 ACTTGACAGATCAATACTCCCTCTG 59.872 44.000 0.00 0.00 43.92 3.35
3061 3158 5.276440 ACTTGACAGATCAATACTCCCTCT 58.724 41.667 0.00 0.00 43.92 3.69
3062 3159 5.606348 ACTTGACAGATCAATACTCCCTC 57.394 43.478 0.00 0.00 43.92 4.30
3063 3160 5.485353 TGAACTTGACAGATCAATACTCCCT 59.515 40.000 0.00 0.00 43.92 4.20
3064 3161 5.734720 TGAACTTGACAGATCAATACTCCC 58.265 41.667 0.00 0.00 43.92 4.30
3065 3162 7.856145 ATTGAACTTGACAGATCAATACTCC 57.144 36.000 6.06 0.00 45.81 3.85


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

AutoCloner maintained by Alex Coulton.