Multiple sequence alignment - TraesCS7B01G079000

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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 TraesCS7B01G079000 chr7B 100.000 3639 0 0 1 3639 89000021 89003659 0.000000e+00 6721
1 TraesCS7B01G079000 chr7A 93.719 2006 81 21 702 2686 128150683 128148702 0.000000e+00 2964
2 TraesCS7B01G079000 chr7A 81.535 899 143 14 1745 2639 24860022 24859143 0.000000e+00 719
3 TraesCS7B01G079000 chr7A 81.588 907 134 21 1742 2639 24993705 24994587 0.000000e+00 719
4 TraesCS7B01G079000 chr7A 80.662 393 49 12 3257 3639 128148211 128147836 2.770000e-71 279
5 TraesCS7B01G079000 chr7A 87.097 155 13 4 2758 2911 128148414 128148266 6.250000e-38 169
6 TraesCS7B01G079000 chr7A 71.247 786 166 49 1879 2635 25420959 25421713 1.050000e-35 161
7 TraesCS7B01G079000 chr7A 71.247 786 166 49 1879 2635 25635588 25636342 1.050000e-35 161
8 TraesCS7B01G079000 chr7A 86.813 91 12 0 2545 2635 25710231 25710321 6.430000e-18 102
9 TraesCS7B01G079000 chr7D 93.605 1814 88 17 891 2690 127343221 127341422 0.000000e+00 2682
10 TraesCS7B01G079000 chr7D 81.017 885 130 22 1771 2639 24371072 24370210 0.000000e+00 669
11 TraesCS7B01G079000 chr7D 84.916 358 37 2 3282 3639 127340665 127340325 2.690000e-91 346
12 TraesCS7B01G079000 chr7D 82.500 360 53 8 1766 2122 43482681 43483033 1.270000e-79 307
13 TraesCS7B01G079000 chr4D 94.006 684 35 4 1 678 15072281 15071598 0.000000e+00 1031
14 TraesCS7B01G079000 chr4D 93.713 684 37 4 1 678 331024061 331023378 0.000000e+00 1020
15 TraesCS7B01G079000 chr2D 94.015 685 34 5 1 678 380798802 380798118 0.000000e+00 1031
16 TraesCS7B01G079000 chr2D 79.612 309 39 16 2958 3249 564663609 564663308 2.220000e-47 200
17 TraesCS7B01G079000 chr5B 93.750 688 37 4 1 682 669239551 669240238 0.000000e+00 1027
18 TraesCS7B01G079000 chr5B 93.713 684 37 5 1 678 614976039 614976722 0.000000e+00 1020
19 TraesCS7B01G079000 chr5B 79.868 303 49 8 2956 3253 321983643 321983938 1.020000e-50 211
20 TraesCS7B01G079000 chr5D 93.869 685 34 6 1 678 118155377 118154694 0.000000e+00 1026
21 TraesCS7B01G079000 chr6B 93.860 684 35 5 1 678 209196728 209196046 0.000000e+00 1024
22 TraesCS7B01G079000 chr2B 93.713 684 37 4 1 678 200556053 200556736 0.000000e+00 1020
23 TraesCS7B01G079000 chr1B 93.713 684 37 4 1 678 608885269 608885952 0.000000e+00 1020
24 TraesCS7B01G079000 chrUn 81.949 903 132 21 1745 2639 90140482 90139603 0.000000e+00 736
25 TraesCS7B01G079000 chr4A 84.314 306 41 5 2956 3254 604100503 604100808 3.550000e-75 292


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 TraesCS7B01G079000 chr7B 89000021 89003659 3638 False 6721.000000 6721 100.000000 1 3639 1 chr7B.!!$F1 3638
1 TraesCS7B01G079000 chr7A 128147836 128150683 2847 True 1137.333333 2964 87.159333 702 3639 3 chr7A.!!$R2 2937
2 TraesCS7B01G079000 chr7A 24859143 24860022 879 True 719.000000 719 81.535000 1745 2639 1 chr7A.!!$R1 894
3 TraesCS7B01G079000 chr7A 24993705 24994587 882 False 719.000000 719 81.588000 1742 2639 1 chr7A.!!$F1 897
4 TraesCS7B01G079000 chr7D 127340325 127343221 2896 True 1514.000000 2682 89.260500 891 3639 2 chr7D.!!$R2 2748
5 TraesCS7B01G079000 chr7D 24370210 24371072 862 True 669.000000 669 81.017000 1771 2639 1 chr7D.!!$R1 868
6 TraesCS7B01G079000 chr4D 15071598 15072281 683 True 1031.000000 1031 94.006000 1 678 1 chr4D.!!$R1 677
7 TraesCS7B01G079000 chr4D 331023378 331024061 683 True 1020.000000 1020 93.713000 1 678 1 chr4D.!!$R2 677
8 TraesCS7B01G079000 chr2D 380798118 380798802 684 True 1031.000000 1031 94.015000 1 678 1 chr2D.!!$R1 677
9 TraesCS7B01G079000 chr5B 669239551 669240238 687 False 1027.000000 1027 93.750000 1 682 1 chr5B.!!$F3 681
10 TraesCS7B01G079000 chr5B 614976039 614976722 683 False 1020.000000 1020 93.713000 1 678 1 chr5B.!!$F2 677
11 TraesCS7B01G079000 chr5D 118154694 118155377 683 True 1026.000000 1026 93.869000 1 678 1 chr5D.!!$R1 677
12 TraesCS7B01G079000 chr6B 209196046 209196728 682 True 1024.000000 1024 93.860000 1 678 1 chr6B.!!$R1 677
13 TraesCS7B01G079000 chr2B 200556053 200556736 683 False 1020.000000 1020 93.713000 1 678 1 chr2B.!!$F1 677
14 TraesCS7B01G079000 chr1B 608885269 608885952 683 False 1020.000000 1020 93.713000 1 678 1 chr1B.!!$F1 677
15 TraesCS7B01G079000 chrUn 90139603 90140482 879 True 736.000000 736 81.949000 1745 2639 1 chrUn.!!$R1 894

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
693 703 0.183971 TTGCTTTTCCTTCACGGGGA 59.816 50.0 0.00 0.00 0.00 4.81 F
1237 1262 0.249615 TAGCCGTGATGCATGCTCTC 60.250 55.0 20.33 15.64 35.34 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2384 0.107017 CCCTCATGGCGTTCCTGAAT 60.107 55.0 0.00 0.0 0.00 2.57 R
2727 2767 0.107263 TGACAGTGCAAAGCCAGTGA 60.107 50.0 4.19 0.0 39.04 3.41 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
112 113 4.003648 CCGGCAAGTCTCTTTACTCATTT 58.996 43.478 0.00 0.00 0.00 2.32
263 265 2.354203 GCAACCCAACAAACACCTTTGA 60.354 45.455 0.27 0.00 39.43 2.69
271 273 2.758423 ACAAACACCTTTGAAGACACCC 59.242 45.455 0.27 0.00 39.43 4.61
301 303 8.409358 AGCATCTTTATAATCACCCATTTACC 57.591 34.615 0.00 0.00 0.00 2.85
302 304 7.174946 AGCATCTTTATAATCACCCATTTACCG 59.825 37.037 0.00 0.00 0.00 4.02
421 424 5.940192 AGCAATGAAACTGTAACGATCAA 57.060 34.783 0.00 0.00 0.00 2.57
532 538 9.878599 GTTAGGAAACATAACCATATTTGATCG 57.121 33.333 0.00 0.00 35.56 3.69
540 546 4.060038 ACCATATTTGATCGACGAGCTT 57.940 40.909 14.91 2.12 0.00 3.74
556 563 3.932710 CGAGCTTGTCAAGTAAGGCATAA 59.067 43.478 14.03 0.00 0.00 1.90
565 573 5.992217 GTCAAGTAAGGCATAATAGGGACAG 59.008 44.000 0.00 0.00 0.00 3.51
570 578 7.016914 AGTAAGGCATAATAGGGACAGTATGA 58.983 38.462 0.00 0.00 39.69 2.15
690 700 8.702163 ATTTTATTATTGCTTTTCCTTCACGG 57.298 30.769 0.00 0.00 0.00 4.94
691 701 4.718940 ATTATTGCTTTTCCTTCACGGG 57.281 40.909 0.00 0.00 0.00 5.28
692 702 1.256812 ATTGCTTTTCCTTCACGGGG 58.743 50.000 0.00 0.00 0.00 5.73
693 703 0.183971 TTGCTTTTCCTTCACGGGGA 59.816 50.000 0.00 0.00 0.00 4.81
694 704 0.404040 TGCTTTTCCTTCACGGGGAT 59.596 50.000 0.00 0.00 32.41 3.85
695 705 0.811281 GCTTTTCCTTCACGGGGATG 59.189 55.000 0.00 0.00 32.41 3.51
696 706 1.463674 CTTTTCCTTCACGGGGATGG 58.536 55.000 5.84 5.84 41.17 3.51
697 707 0.610785 TTTTCCTTCACGGGGATGGC 60.611 55.000 7.29 0.00 39.96 4.40
698 708 2.813226 TTTCCTTCACGGGGATGGCG 62.813 60.000 7.29 0.00 39.96 5.69
699 709 4.856801 CCTTCACGGGGATGGCGG 62.857 72.222 0.00 0.00 34.42 6.13
719 729 2.270205 CCATCTCCTTGCCGTGCT 59.730 61.111 0.00 0.00 0.00 4.40
730 740 1.375908 GCCGTGCTGGAATCAGTGA 60.376 57.895 0.00 0.00 42.78 3.41
733 743 1.354040 CGTGCTGGAATCAGTGAGAC 58.646 55.000 0.00 0.00 42.78 3.36
739 749 1.123928 GGAATCAGTGAGACGGGGAT 58.876 55.000 0.00 0.00 0.00 3.85
743 753 2.284625 AGTGAGACGGGGATGCCA 60.285 61.111 5.30 0.00 0.00 4.92
754 764 2.109126 GGATGCCAGCTGGACGAAC 61.109 63.158 37.21 18.40 37.39 3.95
755 765 2.434884 ATGCCAGCTGGACGAACG 60.435 61.111 37.21 8.33 37.39 3.95
796 807 1.534235 ACTGTCGGCTCCTCCTTGT 60.534 57.895 0.00 0.00 0.00 3.16
797 808 1.122019 ACTGTCGGCTCCTCCTTGTT 61.122 55.000 0.00 0.00 0.00 2.83
805 816 3.726517 CCTCCTTGTTGCGTGGCG 61.727 66.667 0.00 0.00 0.00 5.69
806 817 2.664851 CTCCTTGTTGCGTGGCGA 60.665 61.111 0.00 0.00 0.00 5.54
833 844 2.507992 CTCCTCCTTGACGCAGCG 60.508 66.667 14.82 14.82 0.00 5.18
882 893 3.557595 CCGGCAGTCATCATTTAGACTTC 59.442 47.826 0.00 0.00 42.87 3.01
988 999 3.047877 CTGGAAACGGCGACACCC 61.048 66.667 16.62 9.64 33.26 4.61
1125 1145 2.331893 GCGCTACATGGTGGTGCAA 61.332 57.895 12.43 0.00 46.84 4.08
1128 1148 1.247567 GCTACATGGTGGTGCAAACT 58.752 50.000 0.00 0.00 0.00 2.66
1165 1185 2.025605 TCAAAATCCATCTGCTCTGGCT 60.026 45.455 0.00 0.00 39.59 4.75
1235 1260 0.516001 CATAGCCGTGATGCATGCTC 59.484 55.000 20.33 13.98 35.34 4.26
1236 1261 0.395686 ATAGCCGTGATGCATGCTCT 59.604 50.000 20.33 6.11 35.34 4.09
1237 1262 0.249615 TAGCCGTGATGCATGCTCTC 60.250 55.000 20.33 15.64 35.34 3.20
1239 1264 1.094073 GCCGTGATGCATGCTCTCTT 61.094 55.000 20.33 0.00 0.00 2.85
1276 1303 2.203070 ACTCCATCCGCGAATGGC 60.203 61.111 20.93 0.00 44.98 4.40
1366 1394 1.146930 GATGCTCCGCTGGGATCAA 59.853 57.895 0.00 0.00 41.50 2.57
1426 1454 4.034258 GACGACGTGCTCGACCCA 62.034 66.667 16.04 0.00 46.14 4.51
1579 1607 2.047655 GCCATCGACACCACCGAA 60.048 61.111 0.00 0.00 39.62 4.30
1606 1634 1.997874 GTGGATCCAGTGCCTCCCT 60.998 63.158 16.81 0.00 0.00 4.20
1611 1639 3.655211 CCAGTGCCTCCCTTGCCT 61.655 66.667 0.00 0.00 0.00 4.75
1679 1707 2.195567 TCAGCAAAGCACCACTGGC 61.196 57.895 0.00 0.00 0.00 4.85
1688 1716 3.665745 AGCACCACTGGCTTTATTTTG 57.334 42.857 0.00 0.00 38.81 2.44
1690 1718 4.148838 AGCACCACTGGCTTTATTTTGTA 58.851 39.130 0.00 0.00 38.81 2.41
1709 1740 7.905604 TTTGTATGTACTGTCTTCTTGATGG 57.094 36.000 0.00 0.00 0.00 3.51
1717 1748 6.611613 ACTGTCTTCTTGATGGAGTAATGA 57.388 37.500 0.00 0.00 0.00 2.57
1726 1757 9.919416 TTCTTGATGGAGTAATGAAATATCCAA 57.081 29.630 0.00 0.00 42.98 3.53
1840 1871 2.722201 GGCCAACTCGACGGGAGAT 61.722 63.158 0.00 0.00 46.23 2.75
1876 1907 0.822164 AGTACAGCGATAACCGGCTT 59.178 50.000 0.00 0.00 39.04 4.35
2179 2219 4.680237 CCGCTGGTCAGGAACGCA 62.680 66.667 0.00 0.00 0.00 5.24
2302 2342 1.227380 GGACTCGAGCGCCATCATT 60.227 57.895 13.61 0.00 0.00 2.57
2427 2467 2.347490 CTTCGTGGGGGTCACCAG 59.653 66.667 0.00 0.00 42.20 4.00
2642 2682 2.667318 CGTGGTGCGTGTTAGCTGG 61.667 63.158 0.00 0.00 38.13 4.85
2680 2720 4.210304 GCTGGCGCACGTTCGATC 62.210 66.667 12.82 3.04 35.78 3.69
2681 2721 3.554692 CTGGCGCACGTTCGATCC 61.555 66.667 12.82 4.42 0.00 3.36
2682 2722 3.989698 CTGGCGCACGTTCGATCCT 62.990 63.158 12.82 0.00 0.00 3.24
2683 2723 3.255379 GGCGCACGTTCGATCCTC 61.255 66.667 12.82 0.00 0.00 3.71
2684 2724 2.202623 GCGCACGTTCGATCCTCT 60.203 61.111 12.82 0.00 0.00 3.69
2685 2725 1.805945 GCGCACGTTCGATCCTCTT 60.806 57.895 12.82 0.00 0.00 2.85
2686 2726 1.352156 GCGCACGTTCGATCCTCTTT 61.352 55.000 12.82 0.00 0.00 2.52
2687 2727 1.068474 CGCACGTTCGATCCTCTTTT 58.932 50.000 0.00 0.00 0.00 2.27
2688 2728 1.459592 CGCACGTTCGATCCTCTTTTT 59.540 47.619 0.00 0.00 0.00 1.94
2717 2757 1.000955 ACAACGTGCTCGATCCTCTTT 59.999 47.619 16.04 0.00 40.62 2.52
2718 2758 1.656095 CAACGTGCTCGATCCTCTTTC 59.344 52.381 16.04 0.00 40.62 2.62
2723 2763 4.174009 CGTGCTCGATCCTCTTTCTTTAA 58.826 43.478 1.00 0.00 39.71 1.52
2726 2766 6.481984 GTGCTCGATCCTCTTTCTTTAAATG 58.518 40.000 0.00 0.00 0.00 2.32
2727 2767 6.092807 GTGCTCGATCCTCTTTCTTTAAATGT 59.907 38.462 0.00 0.00 0.00 2.71
2732 2779 7.331934 TCGATCCTCTTTCTTTAAATGTCACTG 59.668 37.037 0.00 0.00 0.00 3.66
2745 2792 0.308993 GTCACTGGCTTTGCACTGTC 59.691 55.000 0.00 0.00 0.00 3.51
2746 2793 0.107263 TCACTGGCTTTGCACTGTCA 60.107 50.000 0.00 0.00 0.00 3.58
2827 3114 1.132643 AGAGAGTCGTCGTATTGGCAC 59.867 52.381 0.00 0.00 0.00 5.01
2829 3116 0.804933 GAGTCGTCGTATTGGCACCC 60.805 60.000 0.00 0.00 0.00 4.61
2830 3117 2.162754 GTCGTCGTATTGGCACCCG 61.163 63.158 0.00 0.00 0.00 5.28
2831 3118 2.125832 CGTCGTATTGGCACCCGT 60.126 61.111 0.00 0.00 0.00 5.28
2839 3126 1.204146 ATTGGCACCCGTATCTGTCT 58.796 50.000 0.00 0.00 0.00 3.41
2849 3137 2.460918 CGTATCTGTCTAGCCAAACCG 58.539 52.381 0.00 0.00 0.00 4.44
2860 3148 1.683917 AGCCAAACCGCAAACACATTA 59.316 42.857 0.00 0.00 0.00 1.90
2861 3149 2.298729 AGCCAAACCGCAAACACATTAT 59.701 40.909 0.00 0.00 0.00 1.28
2862 3150 3.508012 AGCCAAACCGCAAACACATTATA 59.492 39.130 0.00 0.00 0.00 0.98
2911 3199 2.612972 CCCTGCAAGTAGTACACACCTG 60.613 54.545 2.52 0.00 0.00 4.00
2913 3201 3.494398 CCTGCAAGTAGTACACACCTGTT 60.494 47.826 2.52 0.00 0.00 3.16
2914 3202 4.262292 CCTGCAAGTAGTACACACCTGTTA 60.262 45.833 2.52 0.00 0.00 2.41
2915 3203 5.477607 TGCAAGTAGTACACACCTGTTAT 57.522 39.130 2.52 0.00 0.00 1.89
2916 3204 5.475719 TGCAAGTAGTACACACCTGTTATC 58.524 41.667 2.52 0.00 0.00 1.75
2917 3205 4.561606 GCAAGTAGTACACACCTGTTATCG 59.438 45.833 2.52 0.00 0.00 2.92
2918 3206 5.620654 GCAAGTAGTACACACCTGTTATCGA 60.621 44.000 2.52 0.00 0.00 3.59
2920 3208 5.251764 AGTAGTACACACCTGTTATCGAGT 58.748 41.667 2.52 0.00 0.00 4.18
2921 3209 4.698583 AGTACACACCTGTTATCGAGTC 57.301 45.455 0.00 0.00 0.00 3.36
2926 3214 2.161808 ACACCTGTTATCGAGTCTCACG 59.838 50.000 0.00 0.00 0.00 4.35
2930 3223 3.127203 CCTGTTATCGAGTCTCACGTTCT 59.873 47.826 0.00 0.00 0.00 3.01
2933 3226 4.214758 TGTTATCGAGTCTCACGTTCTCAA 59.785 41.667 0.00 0.00 0.00 3.02
2934 3227 5.106277 TGTTATCGAGTCTCACGTTCTCAAT 60.106 40.000 0.00 0.00 0.00 2.57
2938 3231 5.152097 TCGAGTCTCACGTTCTCAATAAAC 58.848 41.667 0.00 0.00 0.00 2.01
2941 3234 5.154932 AGTCTCACGTTCTCAATAAACTCG 58.845 41.667 0.00 0.00 0.00 4.18
2952 3245 6.263344 TCTCAATAAACTCGGACGAATACAG 58.737 40.000 0.00 0.00 0.00 2.74
2956 3249 3.489180 AACTCGGACGAATACAGTGAG 57.511 47.619 0.00 0.00 0.00 3.51
2957 3250 1.743958 ACTCGGACGAATACAGTGAGG 59.256 52.381 0.00 0.00 0.00 3.86
2958 3251 1.065701 CTCGGACGAATACAGTGAGGG 59.934 57.143 0.00 0.00 0.00 4.30
2959 3252 0.527817 CGGACGAATACAGTGAGGGC 60.528 60.000 0.00 0.00 0.00 5.19
2960 3253 0.179081 GGACGAATACAGTGAGGGCC 60.179 60.000 0.00 0.00 0.00 5.80
2963 3256 1.628846 ACGAATACAGTGAGGGCCTTT 59.371 47.619 7.89 0.00 0.00 3.11
2964 3257 2.039879 ACGAATACAGTGAGGGCCTTTT 59.960 45.455 7.89 0.00 0.00 2.27
2965 3258 3.081804 CGAATACAGTGAGGGCCTTTTT 58.918 45.455 7.89 0.00 0.00 1.94
2966 3259 3.119849 CGAATACAGTGAGGGCCTTTTTG 60.120 47.826 7.89 9.04 0.00 2.44
2967 3260 3.806949 ATACAGTGAGGGCCTTTTTGA 57.193 42.857 7.89 0.00 0.00 2.69
2968 3261 2.683211 ACAGTGAGGGCCTTTTTGAT 57.317 45.000 7.89 0.00 0.00 2.57
2969 3262 2.962859 ACAGTGAGGGCCTTTTTGATT 58.037 42.857 7.89 0.00 0.00 2.57
2970 3263 2.893489 ACAGTGAGGGCCTTTTTGATTC 59.107 45.455 7.89 0.00 0.00 2.52
2971 3264 2.095059 CAGTGAGGGCCTTTTTGATTCG 60.095 50.000 7.89 0.00 0.00 3.34
2972 3265 0.887933 TGAGGGCCTTTTTGATTCGC 59.112 50.000 7.89 0.00 0.00 4.70
2973 3266 0.887933 GAGGGCCTTTTTGATTCGCA 59.112 50.000 7.89 0.00 0.00 5.10
2974 3267 0.890683 AGGGCCTTTTTGATTCGCAG 59.109 50.000 0.00 0.00 0.00 5.18
2975 3268 0.108662 GGGCCTTTTTGATTCGCAGG 60.109 55.000 0.84 0.00 0.00 4.85
2976 3269 0.887933 GGCCTTTTTGATTCGCAGGA 59.112 50.000 0.00 0.00 0.00 3.86
2981 3274 4.143052 GCCTTTTTGATTCGCAGGATTTTG 60.143 41.667 0.00 0.00 0.00 2.44
2982 3275 5.229423 CCTTTTTGATTCGCAGGATTTTGA 58.771 37.500 0.00 0.00 0.00 2.69
2984 3277 6.202570 CCTTTTTGATTCGCAGGATTTTGAAA 59.797 34.615 0.00 0.00 0.00 2.69
2986 3279 3.836949 TGATTCGCAGGATTTTGAAAGC 58.163 40.909 0.00 0.00 0.00 3.51
2988 3281 3.940209 TTCGCAGGATTTTGAAAGCAT 57.060 38.095 0.00 0.00 0.00 3.79
2989 3282 5.125257 TGATTCGCAGGATTTTGAAAGCATA 59.875 36.000 0.00 0.00 0.00 3.14
2990 3283 4.621068 TCGCAGGATTTTGAAAGCATAG 57.379 40.909 0.00 0.00 0.00 2.23
2991 3284 3.378112 TCGCAGGATTTTGAAAGCATAGG 59.622 43.478 0.00 0.00 0.00 2.57
2995 3288 6.238731 CGCAGGATTTTGAAAGCATAGGAATA 60.239 38.462 0.00 0.00 0.00 1.75
2998 3291 8.906867 CAGGATTTTGAAAGCATAGGAATAGAA 58.093 33.333 0.00 0.00 0.00 2.10
3015 3308 9.453830 AGGAATAGAAAAGTATAGGATTGGAGT 57.546 33.333 0.00 0.00 0.00 3.85
3016 3309 9.495572 GGAATAGAAAAGTATAGGATTGGAGTG 57.504 37.037 0.00 0.00 0.00 3.51
3018 3311 5.685728 AGAAAAGTATAGGATTGGAGTGGC 58.314 41.667 0.00 0.00 0.00 5.01
3020 3313 4.423625 AAGTATAGGATTGGAGTGGCAC 57.576 45.455 10.29 10.29 0.00 5.01
3022 3315 3.643792 AGTATAGGATTGGAGTGGCACTC 59.356 47.826 34.21 34.21 44.32 3.51
3023 3316 1.951209 TAGGATTGGAGTGGCACTCA 58.049 50.000 39.54 25.87 46.79 3.41
3024 3317 0.326264 AGGATTGGAGTGGCACTCAC 59.674 55.000 39.54 30.14 46.79 3.51
3037 3330 6.536731 GTGGCACTCACTTGAATCATATAG 57.463 41.667 11.13 0.00 42.86 1.31
3038 3331 5.468072 GTGGCACTCACTTGAATCATATAGG 59.532 44.000 11.13 0.00 42.86 2.57
3039 3332 5.366477 TGGCACTCACTTGAATCATATAGGA 59.634 40.000 0.00 0.00 0.00 2.94
3040 3333 6.043590 TGGCACTCACTTGAATCATATAGGAT 59.956 38.462 0.00 0.00 0.00 3.24
3042 3335 8.097038 GGCACTCACTTGAATCATATAGGATTA 58.903 37.037 12.35 0.00 37.61 1.75
3043 3336 9.664332 GCACTCACTTGAATCATATAGGATTAT 57.336 33.333 12.35 0.00 37.61 1.28
3059 3352 8.915057 ATAGGATTATCCAGAAGTGTTTGATG 57.085 34.615 14.30 0.00 39.61 3.07
3062 3355 2.655090 TCCAGAAGTGTTTGATGCCA 57.345 45.000 0.00 0.00 0.00 4.92
3063 3356 2.229792 TCCAGAAGTGTTTGATGCCAC 58.770 47.619 0.00 0.00 0.00 5.01
3064 3357 1.069022 CCAGAAGTGTTTGATGCCACG 60.069 52.381 0.00 0.00 36.69 4.94
3065 3358 1.069022 CAGAAGTGTTTGATGCCACGG 60.069 52.381 0.00 0.00 36.69 4.94
3066 3359 0.240945 GAAGTGTTTGATGCCACGGG 59.759 55.000 0.00 0.00 36.69 5.28
3067 3360 0.179004 AAGTGTTTGATGCCACGGGA 60.179 50.000 0.00 0.00 36.69 5.14
3068 3361 0.179004 AGTGTTTGATGCCACGGGAA 60.179 50.000 0.00 0.00 36.69 3.97
3069 3362 0.671251 GTGTTTGATGCCACGGGAAA 59.329 50.000 0.00 0.00 0.00 3.13
3070 3363 1.067821 GTGTTTGATGCCACGGGAAAA 59.932 47.619 0.00 0.00 0.00 2.29
3071 3364 1.757118 TGTTTGATGCCACGGGAAAAA 59.243 42.857 0.00 0.00 0.00 1.94
3072 3365 2.131972 GTTTGATGCCACGGGAAAAAC 58.868 47.619 0.00 4.33 0.00 2.43
3073 3366 1.403814 TTGATGCCACGGGAAAAACA 58.596 45.000 0.00 0.00 0.00 2.83
3074 3367 1.403814 TGATGCCACGGGAAAAACAA 58.596 45.000 0.00 0.00 0.00 2.83
3075 3368 1.757118 TGATGCCACGGGAAAAACAAA 59.243 42.857 0.00 0.00 0.00 2.83
3076 3369 2.168521 TGATGCCACGGGAAAAACAAAA 59.831 40.909 0.00 0.00 0.00 2.44
3077 3370 2.762535 TGCCACGGGAAAAACAAAAA 57.237 40.000 0.00 0.00 0.00 1.94
3170 3463 6.777213 AAATCCTACGCGATCTAATCCTAT 57.223 37.500 15.93 0.00 0.00 2.57
3171 3464 5.759506 ATCCTACGCGATCTAATCCTATG 57.240 43.478 15.93 0.00 0.00 2.23
3172 3465 4.840271 TCCTACGCGATCTAATCCTATGA 58.160 43.478 15.93 0.00 0.00 2.15
3173 3466 5.250982 TCCTACGCGATCTAATCCTATGAA 58.749 41.667 15.93 0.00 0.00 2.57
3174 3467 5.886474 TCCTACGCGATCTAATCCTATGAAT 59.114 40.000 15.93 0.00 0.00 2.57
3175 3468 6.038382 TCCTACGCGATCTAATCCTATGAATC 59.962 42.308 15.93 0.00 0.00 2.52
3176 3469 5.644977 ACGCGATCTAATCCTATGAATCA 57.355 39.130 15.93 0.00 0.00 2.57
3177 3470 6.025749 ACGCGATCTAATCCTATGAATCAA 57.974 37.500 15.93 0.00 0.00 2.57
3178 3471 6.455647 ACGCGATCTAATCCTATGAATCAAA 58.544 36.000 15.93 0.00 0.00 2.69
3179 3472 6.587990 ACGCGATCTAATCCTATGAATCAAAG 59.412 38.462 15.93 0.00 0.00 2.77
3180 3473 6.035435 CGCGATCTAATCCTATGAATCAAAGG 59.965 42.308 0.00 0.00 0.00 3.11
3181 3474 7.099764 GCGATCTAATCCTATGAATCAAAGGA 58.900 38.462 0.00 0.00 43.38 3.36
3187 3480 5.635278 TCCTATGAATCAAAGGATCAGCA 57.365 39.130 0.00 0.00 34.46 4.41
3189 3482 7.320384 TCCTATGAATCAAAGGATCAGCATA 57.680 36.000 0.00 0.00 34.46 3.14
3190 3483 7.392418 TCCTATGAATCAAAGGATCAGCATAG 58.608 38.462 0.00 0.00 38.35 2.23
3191 3484 7.236225 TCCTATGAATCAAAGGATCAGCATAGA 59.764 37.037 0.00 0.00 39.43 1.98
3192 3485 7.881751 CCTATGAATCAAAGGATCAGCATAGAA 59.118 37.037 0.00 0.00 39.43 2.10
3193 3486 9.281371 CTATGAATCAAAGGATCAGCATAGAAA 57.719 33.333 0.00 0.00 39.43 2.52
3194 3487 7.943079 TGAATCAAAGGATCAGCATAGAAAA 57.057 32.000 0.00 0.00 31.88 2.29
3195 3488 8.352137 TGAATCAAAGGATCAGCATAGAAAAA 57.648 30.769 0.00 0.00 31.88 1.94
3227 3520 5.587388 GATTGCAATCCTCCAGAAATCAA 57.413 39.130 26.03 0.00 0.00 2.57
3229 3522 6.555463 ATTGCAATCCTCCAGAAATCAAAT 57.445 33.333 5.99 0.00 0.00 2.32
3230 3523 7.664552 ATTGCAATCCTCCAGAAATCAAATA 57.335 32.000 5.99 0.00 0.00 1.40
3232 3525 8.765488 TTGCAATCCTCCAGAAATCAAATATA 57.235 30.769 0.00 0.00 0.00 0.86
3233 3526 8.765488 TGCAATCCTCCAGAAATCAAATATAA 57.235 30.769 0.00 0.00 0.00 0.98
3258 3551 4.756084 CTTTGAATCAAAGGAGCTCGTT 57.244 40.909 23.96 15.73 44.75 3.85
3259 3552 5.113502 CTTTGAATCAAAGGAGCTCGTTT 57.886 39.130 24.83 24.83 44.75 3.60
3280 3878 8.402472 TCGTTTAGAAACAACAACTTCATTCAT 58.598 29.630 6.00 0.00 38.81 2.57
3288 3886 7.301868 ACAACAACTTCATTCATAAATGGGT 57.698 32.000 0.00 0.00 42.19 4.51
3307 3905 6.130298 TGGGTGCGAAAATTAGTCATAATG 57.870 37.500 0.00 0.00 31.81 1.90
3404 4002 3.209097 CGCCCACCGCCTAATTGG 61.209 66.667 0.00 0.00 39.35 3.16
3412 4010 2.833121 GCCTAATTGGGGCCACCG 60.833 66.667 10.21 0.00 44.64 4.94
3456 4062 1.226745 CACGGCGGCGTAGAATACA 60.227 57.895 36.95 0.00 43.24 2.29
3492 4099 1.177895 TGGCTTGAAAATGCGCCTCA 61.178 50.000 4.18 0.00 42.90 3.86
3496 4103 0.665835 TTGAAAATGCGCCTCAACGT 59.334 45.000 4.18 0.00 34.88 3.99
3520 4127 1.148273 TCCCATACCAGCCATTCGC 59.852 57.895 0.00 0.00 37.98 4.70
3577 4184 2.029020 GCTCCATATGCACGTCCATCTA 60.029 50.000 0.00 0.00 0.00 1.98
3581 4188 0.741915 TATGCACGTCCATCTACGCA 59.258 50.000 0.00 0.00 46.71 5.24
3601 4208 1.604378 CCTCCTCGAGGGCAATGTT 59.396 57.895 30.80 0.00 45.43 2.71
3611 4218 0.179156 GGGCAATGTTCATGTGCTCG 60.179 55.000 5.36 0.00 38.36 5.03
3621 4228 0.609131 CATGTGCTCGGAAAAGGGGT 60.609 55.000 0.00 0.00 0.00 4.95
3628 4235 1.198759 TCGGAAAAGGGGTCCAGAGG 61.199 60.000 0.00 0.00 34.56 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 0.176910 TGCGGGATGAAGCATTACGA 59.823 50.000 0.00 0.00 38.59 3.43
263 265 1.853963 AGATGCTCTACGGGTGTCTT 58.146 50.000 0.00 0.00 0.00 3.01
271 273 6.455647 TGGGTGATTATAAAGATGCTCTACG 58.544 40.000 0.00 0.00 0.00 3.51
301 303 2.409752 GTGTGCTATCAAACGTCACACG 60.410 50.000 15.71 0.00 44.97 4.49
302 304 3.169207 GTGTGCTATCAAACGTCACAC 57.831 47.619 15.71 15.71 46.72 3.82
421 424 3.214328 CCCATCCGTTAGCTTAGCATTT 58.786 45.455 7.07 0.00 0.00 2.32
532 538 1.727335 GCCTTACTTGACAAGCTCGTC 59.273 52.381 15.24 0.00 36.40 4.20
540 546 5.427157 TGTCCCTATTATGCCTTACTTGACA 59.573 40.000 0.00 0.00 0.00 3.58
556 563 8.497910 ACATAGACAAATCATACTGTCCCTAT 57.502 34.615 0.00 0.00 42.45 2.57
570 578 9.890629 AGTACATGTGTGAATACATAGACAAAT 57.109 29.630 9.11 0.00 39.17 2.32
666 676 7.093992 CCCGTGAAGGAAAAGCAATAATAAAA 58.906 34.615 0.00 0.00 45.00 1.52
678 688 0.610785 GCCATCCCCGTGAAGGAAAA 60.611 55.000 0.00 0.00 45.00 2.29
682 692 4.856801 CCGCCATCCCCGTGAAGG 62.857 72.222 0.00 0.00 40.63 3.46
705 715 1.841302 ATTCCAGCACGGCAAGGAGA 61.841 55.000 8.99 4.05 36.63 3.71
713 723 0.247460 TCTCACTGATTCCAGCACGG 59.753 55.000 0.00 0.00 44.16 4.94
716 726 0.247460 CCGTCTCACTGATTCCAGCA 59.753 55.000 0.00 0.00 44.16 4.41
719 729 0.252057 TCCCCGTCTCACTGATTCCA 60.252 55.000 0.00 0.00 0.00 3.53
730 740 3.790437 CAGCTGGCATCCCCGTCT 61.790 66.667 5.57 0.00 35.87 4.18
733 743 4.864334 GTCCAGCTGGCATCCCCG 62.864 72.222 28.91 1.49 35.87 5.73
767 778 2.433145 CGACAGTCATGCCACGCT 60.433 61.111 0.41 0.00 0.00 5.07
768 779 3.490759 CCGACAGTCATGCCACGC 61.491 66.667 0.41 0.00 0.00 5.34
776 787 1.228894 AAGGAGGAGCCGACAGTCA 60.229 57.895 0.41 0.00 43.43 3.41
842 853 3.292159 GGGCCAACAACGGTGTCC 61.292 66.667 6.54 3.39 36.80 4.02
882 893 8.979574 CCAGTTAACTAAGACTAAGACTTGTTG 58.020 37.037 8.04 0.00 0.00 3.33
1081 1098 1.110442 CGTTCCTGATCTGCTCCTCT 58.890 55.000 0.00 0.00 0.00 3.69
1144 1164 2.025605 AGCCAGAGCAGATGGATTTTGA 60.026 45.455 6.08 0.00 43.56 2.69
1165 1185 5.590259 GTCTACCTATGTACGTACCCTTGAA 59.410 44.000 22.43 3.40 0.00 2.69
1606 1634 3.089838 CACTGGGGGATGAGGCAA 58.910 61.111 0.00 0.00 0.00 4.52
1611 1639 1.692749 GGGTAGCACTGGGGGATGA 60.693 63.158 0.00 0.00 0.00 2.92
1688 1716 6.868622 ACTCCATCAAGAAGACAGTACATAC 58.131 40.000 0.00 0.00 0.00 2.39
1690 1718 7.482169 TTACTCCATCAAGAAGACAGTACAT 57.518 36.000 0.00 0.00 0.00 2.29
1726 1757 6.205853 TGCTCGACCTGTAATTTTTGTACAAT 59.794 34.615 9.56 0.00 31.27 2.71
1728 1759 5.049954 GTGCTCGACCTGTAATTTTTGTACA 60.050 40.000 0.00 0.00 0.00 2.90
1731 1762 3.252458 GGTGCTCGACCTGTAATTTTTGT 59.748 43.478 0.00 0.00 42.25 2.83
1732 1763 3.666902 CGGTGCTCGACCTGTAATTTTTG 60.667 47.826 0.00 0.00 43.55 2.44
1736 1767 0.108329 CCGGTGCTCGACCTGTAATT 60.108 55.000 0.00 0.00 43.55 1.40
1737 1768 1.515954 CCGGTGCTCGACCTGTAAT 59.484 57.895 0.00 0.00 43.55 1.89
1738 1769 2.967397 CCGGTGCTCGACCTGTAA 59.033 61.111 0.00 0.00 43.55 2.41
1840 1871 0.968901 ACTCGATCCGGTACAGGCAA 60.969 55.000 7.24 0.00 0.00 4.52
1876 1907 0.744057 TCATGTACGTCCCGAGCGTA 60.744 55.000 0.00 0.00 42.85 4.42
2179 2219 0.107081 TGGTCGGGTTGATGACGTTT 59.893 50.000 0.00 0.00 35.95 3.60
2344 2384 0.107017 CCCTCATGGCGTTCCTGAAT 60.107 55.000 0.00 0.00 0.00 2.57
2479 2519 1.071471 CACGGCCAGAAGGTCAAGT 59.929 57.895 2.24 0.00 40.51 3.16
2665 2705 3.982372 GAGGATCGAACGTGCGCCA 62.982 63.158 12.23 0.00 0.00 5.69
2689 2729 3.473093 TCGAGCACGTTGTTTCAAAAA 57.527 38.095 2.86 0.00 40.69 1.94
2690 2730 3.547214 GGATCGAGCACGTTGTTTCAAAA 60.547 43.478 1.84 0.00 40.69 2.44
2691 2731 2.032377 GGATCGAGCACGTTGTTTCAAA 60.032 45.455 1.84 0.00 40.69 2.69
2692 2732 1.529438 GGATCGAGCACGTTGTTTCAA 59.471 47.619 1.84 0.00 40.69 2.69
2693 2733 1.144969 GGATCGAGCACGTTGTTTCA 58.855 50.000 1.84 0.00 40.69 2.69
2694 2734 1.390463 GAGGATCGAGCACGTTGTTTC 59.610 52.381 1.84 0.00 40.69 2.78
2695 2735 1.000955 AGAGGATCGAGCACGTTGTTT 59.999 47.619 1.84 0.00 42.67 2.83
2696 2736 0.603569 AGAGGATCGAGCACGTTGTT 59.396 50.000 1.84 0.00 42.67 2.83
2697 2737 0.603569 AAGAGGATCGAGCACGTTGT 59.396 50.000 1.84 0.00 42.67 3.32
2698 2738 1.656095 GAAAGAGGATCGAGCACGTTG 59.344 52.381 1.84 0.00 42.67 4.10
2699 2739 1.546476 AGAAAGAGGATCGAGCACGTT 59.454 47.619 1.84 0.30 42.67 3.99
2700 2740 1.178276 AGAAAGAGGATCGAGCACGT 58.822 50.000 1.84 0.00 42.67 4.49
2701 2741 2.285827 AAGAAAGAGGATCGAGCACG 57.714 50.000 1.84 0.00 42.67 5.34
2702 2742 6.092807 ACATTTAAAGAAAGAGGATCGAGCAC 59.907 38.462 1.84 0.00 42.67 4.40
2703 2743 6.173339 ACATTTAAAGAAAGAGGATCGAGCA 58.827 36.000 1.84 0.00 42.67 4.26
2708 2748 7.627300 GCCAGTGACATTTAAAGAAAGAGGATC 60.627 40.741 0.00 0.00 0.00 3.36
2717 2757 4.340666 TGCAAAGCCAGTGACATTTAAAGA 59.659 37.500 0.00 0.00 0.00 2.52
2718 2758 4.445385 GTGCAAAGCCAGTGACATTTAAAG 59.555 41.667 0.00 0.00 0.00 1.85
2723 2763 1.338973 CAGTGCAAAGCCAGTGACATT 59.661 47.619 0.00 0.00 38.19 2.71
2726 2766 0.308993 GACAGTGCAAAGCCAGTGAC 59.691 55.000 4.19 0.00 39.04 3.67
2727 2767 0.107263 TGACAGTGCAAAGCCAGTGA 60.107 50.000 4.19 0.00 39.04 3.41
2732 2779 1.656441 CCAGTGACAGTGCAAAGCC 59.344 57.895 4.63 0.00 0.00 4.35
2745 2792 4.881019 AGGATTACATAGCTAGCCAGTG 57.119 45.455 12.13 10.43 0.00 3.66
2746 2793 7.560796 AATTAGGATTACATAGCTAGCCAGT 57.439 36.000 12.13 10.23 0.00 4.00
2817 3104 1.202486 ACAGATACGGGTGCCAATACG 60.202 52.381 0.00 0.00 0.00 3.06
2827 3114 2.483188 GGTTTGGCTAGACAGATACGGG 60.483 54.545 0.00 0.00 0.00 5.28
2829 3116 2.460918 CGGTTTGGCTAGACAGATACG 58.539 52.381 0.00 0.00 0.00 3.06
2830 3117 2.202566 GCGGTTTGGCTAGACAGATAC 58.797 52.381 0.00 0.00 0.00 2.24
2831 3118 1.828595 TGCGGTTTGGCTAGACAGATA 59.171 47.619 0.00 0.00 0.00 1.98
2839 3126 1.323412 ATGTGTTTGCGGTTTGGCTA 58.677 45.000 0.00 0.00 0.00 3.93
2861 3149 9.981114 ACATATGAAGTTCACATTATGACGATA 57.019 29.630 22.86 4.93 36.92 2.92
2862 3150 8.893219 ACATATGAAGTTCACATTATGACGAT 57.107 30.769 22.86 6.17 36.92 3.73
2874 3162 2.754552 GCAGGGCAACATATGAAGTTCA 59.245 45.455 10.38 8.27 39.74 3.18
2875 3163 2.754552 TGCAGGGCAACATATGAAGTTC 59.245 45.455 10.38 0.00 34.76 3.01
2886 3174 1.804748 GTGTACTACTTGCAGGGCAAC 59.195 52.381 0.00 0.00 43.99 4.17
2900 3188 4.333690 AGACTCGATAACAGGTGTGTACT 58.666 43.478 0.00 0.00 35.08 2.73
2902 3190 4.155462 GTGAGACTCGATAACAGGTGTGTA 59.845 45.833 0.00 0.00 35.08 2.90
2905 3193 2.161808 CGTGAGACTCGATAACAGGTGT 59.838 50.000 0.00 0.00 0.00 4.16
2911 3199 4.337985 TGAGAACGTGAGACTCGATAAC 57.662 45.455 0.00 0.00 39.41 1.89
2913 3201 6.673154 TTATTGAGAACGTGAGACTCGATA 57.327 37.500 13.40 13.40 40.03 2.92
2914 3202 5.562506 TTATTGAGAACGTGAGACTCGAT 57.437 39.130 14.72 14.72 41.20 3.59
2915 3203 5.048921 AGTTTATTGAGAACGTGAGACTCGA 60.049 40.000 0.00 0.00 39.41 4.04
2916 3204 5.154932 AGTTTATTGAGAACGTGAGACTCG 58.845 41.667 0.00 0.00 39.41 4.18
2917 3205 5.284188 CGAGTTTATTGAGAACGTGAGACTC 59.716 44.000 0.00 0.00 38.05 3.36
2918 3206 5.154932 CGAGTTTATTGAGAACGTGAGACT 58.845 41.667 0.00 0.00 32.38 3.24
2920 3208 4.216902 TCCGAGTTTATTGAGAACGTGAGA 59.783 41.667 0.00 0.00 32.38 3.27
2921 3209 4.323868 GTCCGAGTTTATTGAGAACGTGAG 59.676 45.833 0.00 0.00 32.38 3.51
2926 3214 6.529125 TGTATTCGTCCGAGTTTATTGAGAAC 59.471 38.462 0.00 0.00 0.00 3.01
2930 3223 5.803461 CACTGTATTCGTCCGAGTTTATTGA 59.197 40.000 0.00 0.00 0.00 2.57
2933 3226 5.450137 CCTCACTGTATTCGTCCGAGTTTAT 60.450 44.000 0.00 0.00 0.00 1.40
2934 3227 4.142534 CCTCACTGTATTCGTCCGAGTTTA 60.143 45.833 0.00 0.00 0.00 2.01
2938 3231 1.065701 CCCTCACTGTATTCGTCCGAG 59.934 57.143 0.00 0.00 0.00 4.63
2941 3234 0.179081 GGCCCTCACTGTATTCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
2952 3245 1.402852 GCGAATCAAAAAGGCCCTCAC 60.403 52.381 0.00 0.00 0.00 3.51
2956 3249 0.108662 CCTGCGAATCAAAAAGGCCC 60.109 55.000 0.00 0.00 0.00 5.80
2957 3250 0.887933 TCCTGCGAATCAAAAAGGCC 59.112 50.000 0.00 0.00 0.00 5.19
2958 3251 2.947448 ATCCTGCGAATCAAAAAGGC 57.053 45.000 0.00 0.00 0.00 4.35
2959 3252 5.229423 TCAAAATCCTGCGAATCAAAAAGG 58.771 37.500 0.00 0.00 0.00 3.11
2960 3253 6.768029 TTCAAAATCCTGCGAATCAAAAAG 57.232 33.333 0.00 0.00 0.00 2.27
2963 3256 4.685628 GCTTTCAAAATCCTGCGAATCAAA 59.314 37.500 0.00 0.00 0.00 2.69
2964 3257 4.236935 GCTTTCAAAATCCTGCGAATCAA 58.763 39.130 0.00 0.00 0.00 2.57
2965 3258 3.255395 TGCTTTCAAAATCCTGCGAATCA 59.745 39.130 0.00 0.00 0.00 2.57
2966 3259 3.836949 TGCTTTCAAAATCCTGCGAATC 58.163 40.909 0.00 0.00 0.00 2.52
2967 3260 3.940209 TGCTTTCAAAATCCTGCGAAT 57.060 38.095 0.00 0.00 0.00 3.34
2968 3261 3.940209 ATGCTTTCAAAATCCTGCGAA 57.060 38.095 0.00 0.00 0.00 4.70
2969 3262 3.378112 CCTATGCTTTCAAAATCCTGCGA 59.622 43.478 0.00 0.00 0.00 5.10
2970 3263 3.378112 TCCTATGCTTTCAAAATCCTGCG 59.622 43.478 0.00 0.00 0.00 5.18
2971 3264 4.989279 TCCTATGCTTTCAAAATCCTGC 57.011 40.909 0.00 0.00 0.00 4.85
2972 3265 8.455903 TCTATTCCTATGCTTTCAAAATCCTG 57.544 34.615 0.00 0.00 0.00 3.86
2973 3266 9.479549 TTTCTATTCCTATGCTTTCAAAATCCT 57.520 29.630 0.00 0.00 0.00 3.24
2989 3282 9.453830 ACTCCAATCCTATACTTTTCTATTCCT 57.546 33.333 0.00 0.00 0.00 3.36
2990 3283 9.495572 CACTCCAATCCTATACTTTTCTATTCC 57.504 37.037 0.00 0.00 0.00 3.01
2991 3284 9.495572 CCACTCCAATCCTATACTTTTCTATTC 57.504 37.037 0.00 0.00 0.00 1.75
2995 3288 5.191722 TGCCACTCCAATCCTATACTTTTCT 59.808 40.000 0.00 0.00 0.00 2.52
2998 3291 4.475016 AGTGCCACTCCAATCCTATACTTT 59.525 41.667 0.00 0.00 0.00 2.66
3005 3298 0.326264 GTGAGTGCCACTCCAATCCT 59.674 55.000 21.57 0.00 44.44 3.24
3015 3308 5.366477 TCCTATATGATTCAAGTGAGTGCCA 59.634 40.000 0.00 0.00 0.00 4.92
3016 3309 5.858381 TCCTATATGATTCAAGTGAGTGCC 58.142 41.667 0.00 0.00 0.00 5.01
3037 3330 5.221126 GGCATCAAACACTTCTGGATAATCC 60.221 44.000 0.00 0.00 36.96 3.01
3038 3331 5.357878 TGGCATCAAACACTTCTGGATAATC 59.642 40.000 0.00 0.00 0.00 1.75
3039 3332 5.126061 GTGGCATCAAACACTTCTGGATAAT 59.874 40.000 0.00 0.00 34.84 1.28
3040 3333 4.458989 GTGGCATCAAACACTTCTGGATAA 59.541 41.667 0.00 0.00 34.84 1.75
3042 3335 2.821969 GTGGCATCAAACACTTCTGGAT 59.178 45.455 0.00 0.00 34.84 3.41
3043 3336 2.229792 GTGGCATCAAACACTTCTGGA 58.770 47.619 0.00 0.00 34.84 3.86
3044 3337 1.069022 CGTGGCATCAAACACTTCTGG 60.069 52.381 0.00 0.00 35.51 3.86
3045 3338 1.069022 CCGTGGCATCAAACACTTCTG 60.069 52.381 0.00 0.00 35.51 3.02
3046 3339 1.238439 CCGTGGCATCAAACACTTCT 58.762 50.000 0.00 0.00 35.51 2.85
3051 3344 1.403814 TTTTCCCGTGGCATCAAACA 58.596 45.000 0.00 0.00 0.00 2.83
3052 3345 2.131972 GTTTTTCCCGTGGCATCAAAC 58.868 47.619 0.00 0.00 0.00 2.93
3053 3346 1.757118 TGTTTTTCCCGTGGCATCAAA 59.243 42.857 0.00 0.00 0.00 2.69
3054 3347 1.403814 TGTTTTTCCCGTGGCATCAA 58.596 45.000 0.00 0.00 0.00 2.57
3057 3350 2.990066 TTTTGTTTTTCCCGTGGCAT 57.010 40.000 0.00 0.00 0.00 4.40
3058 3351 2.762535 TTTTTGTTTTTCCCGTGGCA 57.237 40.000 0.00 0.00 0.00 4.92
3145 3438 5.855045 AGGATTAGATCGCGTAGGATTTTT 58.145 37.500 5.77 0.00 0.00 1.94
3146 3439 5.470047 AGGATTAGATCGCGTAGGATTTT 57.530 39.130 5.77 0.00 0.00 1.82
3147 3440 6.377429 TCATAGGATTAGATCGCGTAGGATTT 59.623 38.462 5.77 0.00 0.00 2.17
3149 3442 5.437946 TCATAGGATTAGATCGCGTAGGAT 58.562 41.667 5.77 0.00 0.00 3.24
3150 3443 4.840271 TCATAGGATTAGATCGCGTAGGA 58.160 43.478 5.77 0.00 0.00 2.94
3151 3444 5.562506 TTCATAGGATTAGATCGCGTAGG 57.437 43.478 5.77 0.00 0.00 3.18
3152 3445 6.786207 TGATTCATAGGATTAGATCGCGTAG 58.214 40.000 5.77 0.00 0.00 3.51
3153 3446 6.753107 TGATTCATAGGATTAGATCGCGTA 57.247 37.500 5.77 0.00 0.00 4.42
3154 3447 5.644977 TGATTCATAGGATTAGATCGCGT 57.355 39.130 5.77 0.00 0.00 6.01
3155 3448 6.035435 CCTTTGATTCATAGGATTAGATCGCG 59.965 42.308 15.80 0.00 35.14 5.87
3157 3450 9.311916 GATCCTTTGATTCATAGGATTAGATCG 57.688 37.037 28.53 3.56 46.76 3.69
3161 3454 7.881751 TGCTGATCCTTTGATTCATAGGATTAG 59.118 37.037 31.71 31.71 46.76 1.73
3162 3455 7.748677 TGCTGATCCTTTGATTCATAGGATTA 58.251 34.615 28.53 24.82 46.76 1.75
3163 3456 6.607970 TGCTGATCCTTTGATTCATAGGATT 58.392 36.000 28.53 17.81 46.76 3.01
3165 3458 5.635278 TGCTGATCCTTTGATTCATAGGA 57.365 39.130 22.92 22.92 43.50 2.94
3166 3459 7.392418 TCTATGCTGATCCTTTGATTCATAGG 58.608 38.462 14.95 14.95 37.10 2.57
3167 3460 8.843885 TTCTATGCTGATCCTTTGATTCATAG 57.156 34.615 0.00 0.00 37.39 2.23
3170 3463 7.943079 TTTTCTATGCTGATCCTTTGATTCA 57.057 32.000 0.00 0.00 0.00 2.57
3205 3498 5.587388 TTGATTTCTGGAGGATTGCAATC 57.413 39.130 27.91 27.91 34.66 2.67
3206 3499 6.555463 ATTTGATTTCTGGAGGATTGCAAT 57.445 33.333 12.83 12.83 0.00 3.56
3239 3532 5.547465 TCTAAACGAGCTCCTTTGATTCAA 58.453 37.500 17.70 0.00 0.00 2.69
3240 3533 5.147330 TCTAAACGAGCTCCTTTGATTCA 57.853 39.130 17.70 0.62 0.00 2.57
3244 3537 4.699637 TGTTTCTAAACGAGCTCCTTTGA 58.300 39.130 17.70 10.81 41.74 2.69
3246 3539 4.879545 TGTTGTTTCTAAACGAGCTCCTTT 59.120 37.500 8.47 11.81 41.74 3.11
3247 3540 4.448210 TGTTGTTTCTAAACGAGCTCCTT 58.552 39.130 8.47 4.51 41.74 3.36
3248 3541 4.067972 TGTTGTTTCTAAACGAGCTCCT 57.932 40.909 8.47 0.00 41.74 3.69
3249 3542 4.272748 AGTTGTTGTTTCTAAACGAGCTCC 59.727 41.667 8.47 0.00 41.74 4.70
3250 3543 5.405331 AGTTGTTGTTTCTAAACGAGCTC 57.595 39.130 2.73 2.73 41.74 4.09
3251 3544 5.353123 TGAAGTTGTTGTTTCTAAACGAGCT 59.647 36.000 0.00 0.00 41.74 4.09
3252 3545 5.565695 TGAAGTTGTTGTTTCTAAACGAGC 58.434 37.500 0.00 0.00 41.74 5.03
3254 3547 7.753659 TGAATGAAGTTGTTGTTTCTAAACGA 58.246 30.769 0.00 0.00 41.74 3.85
3255 3548 7.962934 TGAATGAAGTTGTTGTTTCTAAACG 57.037 32.000 1.46 0.00 41.74 3.60
3280 3878 6.767524 ATGACTAATTTTCGCACCCATTTA 57.232 33.333 0.00 0.00 0.00 1.40
3288 3886 5.293324 AGTCGCATTATGACTAATTTTCGCA 59.707 36.000 0.00 0.00 44.57 5.10
3354 3952 4.081972 CCATATGGCAGCGAGTCTAACTAT 60.082 45.833 9.29 0.00 0.00 2.12
3358 3956 2.820059 CCATATGGCAGCGAGTCTAA 57.180 50.000 9.29 0.00 0.00 2.10
3412 4010 1.002502 GGGTGGAGGTAGTTGTGGC 60.003 63.158 0.00 0.00 0.00 5.01
3444 4050 2.135664 ACATCGCTGTATTCTACGCC 57.864 50.000 0.00 0.00 32.49 5.68
3445 4051 2.218759 CCAACATCGCTGTATTCTACGC 59.781 50.000 0.00 0.00 33.36 4.42
3447 4053 2.544267 GGCCAACATCGCTGTATTCTAC 59.456 50.000 0.00 0.00 33.36 2.59
3456 4062 3.797353 ATCCGGGCCAACATCGCT 61.797 61.111 4.39 0.00 0.00 4.93
3550 4157 1.672363 ACGTGCATATGGAGCAACATG 59.328 47.619 4.56 0.99 44.64 3.21
3551 4158 1.942657 GACGTGCATATGGAGCAACAT 59.057 47.619 4.56 0.00 44.64 2.71
3597 4204 2.489329 CCTTTTCCGAGCACATGAACAT 59.511 45.455 0.00 0.00 0.00 2.71
3601 4208 0.322456 CCCCTTTTCCGAGCACATGA 60.322 55.000 0.00 0.00 0.00 3.07
3611 4218 1.213182 GATCCTCTGGACCCCTTTTCC 59.787 57.143 0.00 0.00 32.98 3.13


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

AutoCloner maintained by Alex Coulton.