Multiple sequence alignment - TraesCS3D01G239600

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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 TraesCS3D01G239600 chr3D 100.000 2711 0 0 1 2711 332152093 332149383 0.000000e+00 5007.0
1 TraesCS3D01G239600 chr3D 75.966 595 99 28 2114 2686 570954161 570953589 1.600000e-67 267.0
2 TraesCS3D01G239600 chr3D 91.837 49 3 1 1884 1932 59910488 59910535 1.740000e-07 67.6
3 TraesCS3D01G239600 chr3D 97.297 37 1 0 1884 1920 538630459 538630495 2.250000e-06 63.9
4 TraesCS3D01G239600 chr3B 90.504 1011 50 18 892 1870 431153101 431152105 0.000000e+00 1293.0
5 TraesCS3D01G239600 chr3B 77.415 735 129 21 1 729 716740107 716739404 1.170000e-108 403.0
6 TraesCS3D01G239600 chr3B 94.175 103 5 1 777 879 431153242 431153141 3.610000e-34 156.0
7 TraesCS3D01G239600 chr3B 93.023 43 3 0 1878 1920 529783687 529783645 2.250000e-06 63.9
8 TraesCS3D01G239600 chr6D 89.888 712 53 7 2018 2711 141924385 141923675 0.000000e+00 898.0
9 TraesCS3D01G239600 chr1D 81.696 743 120 12 1 729 26644240 26644980 2.990000e-169 604.0
10 TraesCS3D01G239600 chr3A 80.653 796 111 23 1 767 124215693 124216474 6.510000e-161 577.0
11 TraesCS3D01G239600 chr3A 87.234 423 41 7 2073 2482 578883226 578883648 1.140000e-128 470.0
12 TraesCS3D01G239600 chr3A 93.605 172 11 0 2539 2710 578928740 578928911 9.630000e-65 257.0
13 TraesCS3D01G239600 chr3A 89.130 92 8 2 1924 2015 578883127 578883216 2.210000e-21 113.0
14 TraesCS3D01G239600 chr7B 80.882 748 118 19 1 731 677362535 677361796 1.410000e-157 566.0
15 TraesCS3D01G239600 chr7B 86.897 145 15 4 2314 2454 3366988 3366844 2.790000e-35 159.0
16 TraesCS3D01G239600 chr7D 84.023 532 57 11 1924 2440 9377711 9377193 1.130000e-133 486.0
17 TraesCS3D01G239600 chr7D 80.031 641 102 21 80 713 595758796 595759417 4.120000e-123 451.0
18 TraesCS3D01G239600 chr7D 84.783 276 25 4 2452 2711 9376788 9376514 7.450000e-66 261.0
19 TraesCS3D01G239600 chr2D 83.398 512 74 5 18 528 568795276 568794775 5.290000e-127 464.0
20 TraesCS3D01G239600 chr2D 97.500 40 0 1 1881 1920 14520919 14520881 1.740000e-07 67.6
21 TraesCS3D01G239600 chr4D 81.970 538 74 15 204 727 42243157 42242629 4.150000e-118 435.0
22 TraesCS3D01G239600 chr4D 75.168 596 102 28 2114 2686 276903045 276902473 3.490000e-59 239.0
23 TraesCS3D01G239600 chr7A 84.120 466 35 15 2268 2711 33427686 33427238 5.400000e-112 414.0
24 TraesCS3D01G239600 chr7A 81.499 427 65 8 31 454 127037398 127037813 3.340000e-89 339.0
25 TraesCS3D01G239600 chr6B 82.046 479 69 11 1 475 619496874 619496409 2.530000e-105 392.0
26 TraesCS3D01G239600 chr6B 95.000 40 1 1 1881 1920 537452615 537452653 8.100000e-06 62.1
27 TraesCS3D01G239600 chr5D 77.200 500 84 14 2179 2656 503053326 503053817 5.760000e-67 265.0
28 TraesCS3D01G239600 chr5D 97.368 38 1 0 1883 1920 247139633 247139670 6.270000e-07 65.8
29 TraesCS3D01G239600 chr5D 100.000 34 0 0 1887 1920 354720614 354720647 2.250000e-06 63.9
30 TraesCS3D01G239600 chr2B 75.439 627 109 24 2116 2711 429460854 429460242 2.070000e-66 263.0
31 TraesCS3D01G239600 chr2A 77.698 417 69 15 328 729 17957563 17957156 1.620000e-57 233.0
32 TraesCS3D01G239600 chr4A 89.313 131 13 1 2544 2674 147645887 147646016 2.160000e-36 163.0
33 TraesCS3D01G239600 chr1B 95.349 43 2 0 1878 1920 162813484 162813526 4.840000e-08 69.4
34 TraesCS3D01G239600 chr6A 97.222 36 1 0 1885 1920 540306679 540306644 8.100000e-06 62.1


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 TraesCS3D01G239600 chr3D 332149383 332152093 2710 True 5007.0 5007 100.0000 1 2711 1 chr3D.!!$R1 2710
1 TraesCS3D01G239600 chr3D 570953589 570954161 572 True 267.0 267 75.9660 2114 2686 1 chr3D.!!$R2 572
2 TraesCS3D01G239600 chr3B 431152105 431153242 1137 True 724.5 1293 92.3395 777 1870 2 chr3B.!!$R3 1093
3 TraesCS3D01G239600 chr3B 716739404 716740107 703 True 403.0 403 77.4150 1 729 1 chr3B.!!$R2 728
4 TraesCS3D01G239600 chr6D 141923675 141924385 710 True 898.0 898 89.8880 2018 2711 1 chr6D.!!$R1 693
5 TraesCS3D01G239600 chr1D 26644240 26644980 740 False 604.0 604 81.6960 1 729 1 chr1D.!!$F1 728
6 TraesCS3D01G239600 chr3A 124215693 124216474 781 False 577.0 577 80.6530 1 767 1 chr3A.!!$F1 766
7 TraesCS3D01G239600 chr3A 578883127 578883648 521 False 291.5 470 88.1820 1924 2482 2 chr3A.!!$F3 558
8 TraesCS3D01G239600 chr7B 677361796 677362535 739 True 566.0 566 80.8820 1 731 1 chr7B.!!$R2 730
9 TraesCS3D01G239600 chr7D 595758796 595759417 621 False 451.0 451 80.0310 80 713 1 chr7D.!!$F1 633
10 TraesCS3D01G239600 chr7D 9376514 9377711 1197 True 373.5 486 84.4030 1924 2711 2 chr7D.!!$R1 787
11 TraesCS3D01G239600 chr2D 568794775 568795276 501 True 464.0 464 83.3980 18 528 1 chr2D.!!$R2 510
12 TraesCS3D01G239600 chr4D 42242629 42243157 528 True 435.0 435 81.9700 204 727 1 chr4D.!!$R1 523
13 TraesCS3D01G239600 chr4D 276902473 276903045 572 True 239.0 239 75.1680 2114 2686 1 chr4D.!!$R2 572
14 TraesCS3D01G239600 chr2B 429460242 429460854 612 True 263.0 263 75.4390 2116 2711 1 chr2B.!!$R1 595

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
614 643 0.03582 GGGGTGCCAATGTTACTCGA 60.036 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 1986 0.038455 TAAAGCGGGGCAAAAGCCTA 59.962 50.0 6.45 0.0 0.0 3.93 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
29 30 9.762933 AAGCAAACACAATTAACAATCATTACT 57.237 25.926 0.00 0.00 0.00 2.24
74 77 1.289109 CCGACACGATGCGAGGTTTT 61.289 55.000 0.00 0.00 0.00 2.43
84 87 6.579292 CACGATGCGAGGTTTTTATTTTTACA 59.421 34.615 0.00 0.00 0.00 2.41
208 211 2.386064 AAAGGCGTTGGCGTAGGACA 62.386 55.000 0.00 0.00 41.24 4.02
421 427 5.179533 GGTCTTCTTCATACCCAAACTCTC 58.820 45.833 0.00 0.00 0.00 3.20
439 451 4.508128 CTTCTTCGGCGGCGGCTA 62.508 66.667 31.73 18.52 39.81 3.93
523 536 3.148084 CTATCCATTCCGGCCGGT 58.852 61.111 41.57 25.15 36.47 5.28
614 643 0.035820 GGGGTGCCAATGTTACTCGA 60.036 55.000 0.00 0.00 0.00 4.04
616 645 1.338769 GGGTGCCAATGTTACTCGACT 60.339 52.381 0.00 0.00 0.00 4.18
623 652 1.929806 ATGTTACTCGACTGCGGCGA 61.930 55.000 12.98 10.80 38.28 5.54
641 670 4.500887 CGGCGAGATGGAGTAAATTTAGGA 60.501 45.833 0.00 0.00 0.00 2.94
645 674 7.148137 GGCGAGATGGAGTAAATTTAGGAAAAA 60.148 37.037 0.00 0.00 0.00 1.94
670 699 2.045885 AGTGGAAATAGGGAGGTGGAGA 59.954 50.000 0.00 0.00 0.00 3.71
714 745 1.562672 AAAGGATGGGCTAGGTGCGT 61.563 55.000 0.00 0.00 44.05 5.24
715 746 2.203070 GGATGGGCTAGGTGCGTG 60.203 66.667 0.00 0.00 44.05 5.34
722 753 1.610554 GGCTAGGTGCGTGGTAAGGA 61.611 60.000 0.00 0.00 44.05 3.36
731 762 3.811497 GTGCGTGGTAAGGAAGTAAAACT 59.189 43.478 0.00 0.00 0.00 2.66
732 763 4.990426 GTGCGTGGTAAGGAAGTAAAACTA 59.010 41.667 0.00 0.00 0.00 2.24
733 764 4.990426 TGCGTGGTAAGGAAGTAAAACTAC 59.010 41.667 0.00 0.00 0.00 2.73
734 765 5.221501 TGCGTGGTAAGGAAGTAAAACTACT 60.222 40.000 0.00 0.00 0.00 2.57
735 766 5.347093 GCGTGGTAAGGAAGTAAAACTACTC 59.653 44.000 0.00 0.00 0.00 2.59
736 767 5.866092 CGTGGTAAGGAAGTAAAACTACTCC 59.134 44.000 0.00 0.00 0.00 3.85
737 768 6.169094 GTGGTAAGGAAGTAAAACTACTCCC 58.831 44.000 0.00 0.00 0.00 4.30
738 769 6.013898 GTGGTAAGGAAGTAAAACTACTCCCT 60.014 42.308 0.00 0.00 0.00 4.20
741 772 8.766476 GGTAAGGAAGTAAAACTACTCCCTTAT 58.234 37.037 11.69 0.00 0.00 1.73
742 773 9.597170 GTAAGGAAGTAAAACTACTCCCTTATG 57.403 37.037 11.69 0.00 0.00 1.90
743 774 7.196637 AGGAAGTAAAACTACTCCCTTATGG 57.803 40.000 0.00 0.00 0.00 2.74
744 775 6.964086 AGGAAGTAAAACTACTCCCTTATGGA 59.036 38.462 0.00 0.00 42.41 3.41
745 776 7.046652 GGAAGTAAAACTACTCCCTTATGGAC 58.953 42.308 0.00 0.00 38.61 4.02
746 777 7.092979 GGAAGTAAAACTACTCCCTTATGGACT 60.093 40.741 0.00 0.00 38.61 3.85
747 778 7.809880 AGTAAAACTACTCCCTTATGGACTT 57.190 36.000 0.00 0.00 38.61 3.01
748 779 8.215954 AGTAAAACTACTCCCTTATGGACTTT 57.784 34.615 0.00 0.00 38.61 2.66
749 780 8.666821 AGTAAAACTACTCCCTTATGGACTTTT 58.333 33.333 0.00 0.00 38.61 2.27
750 781 9.948964 GTAAAACTACTCCCTTATGGACTTTTA 57.051 33.333 0.00 0.00 38.61 1.52
754 785 8.493787 ACTACTCCCTTATGGACTTTTATAGG 57.506 38.462 0.00 0.00 38.61 2.57
755 786 6.765355 ACTCCCTTATGGACTTTTATAGGG 57.235 41.667 0.00 0.00 38.61 3.53
756 787 5.611408 ACTCCCTTATGGACTTTTATAGGGG 59.389 44.000 0.00 0.00 43.79 4.79
757 788 5.806259 TCCCTTATGGACTTTTATAGGGGA 58.194 41.667 9.33 9.33 46.79 4.81
758 789 6.407613 TCCCTTATGGACTTTTATAGGGGAT 58.592 40.000 9.33 0.00 45.18 3.85
759 790 7.559103 TCCCTTATGGACTTTTATAGGGGATA 58.441 38.462 9.33 0.00 45.18 2.59
760 791 7.682890 TCCCTTATGGACTTTTATAGGGGATAG 59.317 40.741 9.33 0.00 45.18 2.08
761 792 7.092399 CCCTTATGGACTTTTATAGGGGATAGG 60.092 44.444 5.73 0.00 44.68 2.57
762 793 7.461363 CCTTATGGACTTTTATAGGGGATAGGT 59.539 40.741 0.00 0.00 34.57 3.08
763 794 8.823810 TTATGGACTTTTATAGGGGATAGGTT 57.176 34.615 0.00 0.00 0.00 3.50
764 795 9.917118 TTATGGACTTTTATAGGGGATAGGTTA 57.083 33.333 0.00 0.00 0.00 2.85
765 796 7.867160 TGGACTTTTATAGGGGATAGGTTAG 57.133 40.000 0.00 0.00 0.00 2.34
766 797 7.607511 TGGACTTTTATAGGGGATAGGTTAGA 58.392 38.462 0.00 0.00 0.00 2.10
767 798 7.733501 TGGACTTTTATAGGGGATAGGTTAGAG 59.266 40.741 0.00 0.00 0.00 2.43
768 799 7.733955 GGACTTTTATAGGGGATAGGTTAGAGT 59.266 40.741 0.00 0.00 0.00 3.24
769 800 9.156940 GACTTTTATAGGGGATAGGTTAGAGTT 57.843 37.037 0.00 0.00 0.00 3.01
770 801 8.935741 ACTTTTATAGGGGATAGGTTAGAGTTG 58.064 37.037 0.00 0.00 0.00 3.16
771 802 6.930068 TTATAGGGGATAGGTTAGAGTTGC 57.070 41.667 0.00 0.00 0.00 4.17
772 803 2.409570 AGGGGATAGGTTAGAGTTGCC 58.590 52.381 0.00 0.00 0.00 4.52
773 804 1.070289 GGGGATAGGTTAGAGTTGCCG 59.930 57.143 0.00 0.00 0.00 5.69
774 805 2.037144 GGGATAGGTTAGAGTTGCCGA 58.963 52.381 0.00 0.00 0.00 5.54
775 806 2.223994 GGGATAGGTTAGAGTTGCCGAC 60.224 54.545 0.00 0.00 0.00 4.79
807 838 4.415332 ACAGCGCGTAGACCACCG 62.415 66.667 8.43 0.00 0.00 4.94
834 865 2.202544 CGGACTCAGAGCACGAGC 60.203 66.667 8.30 0.00 42.56 5.03
859 890 0.597568 TTCATTTCAGCCCACGCTTG 59.402 50.000 0.00 0.00 45.55 4.01
861 892 1.074775 ATTTCAGCCCACGCTTGGA 59.925 52.632 11.54 0.00 45.55 3.53
875 906 1.795286 GCTTGGACTCGCAGCATATAC 59.205 52.381 0.00 0.00 33.45 1.47
876 907 2.546795 GCTTGGACTCGCAGCATATACT 60.547 50.000 0.00 0.00 33.45 2.12
877 908 3.305403 GCTTGGACTCGCAGCATATACTA 60.305 47.826 0.00 0.00 33.45 1.82
878 909 4.619394 GCTTGGACTCGCAGCATATACTAT 60.619 45.833 0.00 0.00 33.45 2.12
879 910 5.468540 TTGGACTCGCAGCATATACTATT 57.531 39.130 0.00 0.00 0.00 1.73
880 911 6.584185 TTGGACTCGCAGCATATACTATTA 57.416 37.500 0.00 0.00 0.00 0.98
903 966 1.270305 TGTGCGGGCTTGCTCTATATC 60.270 52.381 4.09 0.00 35.36 1.63
905 968 1.001293 TGCGGGCTTGCTCTATATCTG 59.999 52.381 4.09 0.00 35.36 2.90
916 979 7.148820 GCTTGCTCTATATCTGATTCGAGAAAC 60.149 40.741 12.00 0.00 0.00 2.78
931 994 2.879026 GAGAAACGAAAAGTCTTGCCCT 59.121 45.455 0.00 0.00 0.00 5.19
932 995 4.062991 GAGAAACGAAAAGTCTTGCCCTA 58.937 43.478 0.00 0.00 0.00 3.53
938 1001 7.730364 AACGAAAAGTCTTGCCCTATATATG 57.270 36.000 0.00 0.00 0.00 1.78
939 1002 5.701290 ACGAAAAGTCTTGCCCTATATATGC 59.299 40.000 0.00 0.00 0.00 3.14
975 1038 4.202524 ACTGAGTAATAACACCCAAAGCCA 60.203 41.667 0.00 0.00 0.00 4.75
979 1042 2.514458 ATAACACCCAAAGCCAGGAG 57.486 50.000 0.00 0.00 0.00 3.69
980 1043 0.251165 TAACACCCAAAGCCAGGAGC 60.251 55.000 0.00 0.00 44.25 4.70
981 1044 2.677875 CACCCAAAGCCAGGAGCC 60.678 66.667 0.00 0.00 45.47 4.70
982 1045 3.984732 ACCCAAAGCCAGGAGCCC 61.985 66.667 0.00 0.00 45.47 5.19
983 1046 3.983420 CCCAAAGCCAGGAGCCCA 61.983 66.667 0.00 0.00 45.47 5.36
984 1047 2.362120 CCAAAGCCAGGAGCCCAG 60.362 66.667 0.00 0.00 45.47 4.45
985 1048 2.362120 CAAAGCCAGGAGCCCAGG 60.362 66.667 0.00 0.00 45.47 4.45
986 1049 2.532715 AAAGCCAGGAGCCCAGGA 60.533 61.111 6.82 0.00 45.47 3.86
987 1050 2.911926 AAAGCCAGGAGCCCAGGAC 61.912 63.158 6.82 0.00 45.47 3.85
1025 1088 3.848830 CACGTACCATGCACCGCG 61.849 66.667 0.00 0.00 0.00 6.46
1030 1093 1.078778 TACCATGCACCGCGTCAAT 60.079 52.632 4.92 0.00 0.00 2.57
1033 1096 1.061411 CATGCACCGCGTCAATCAG 59.939 57.895 4.92 0.00 0.00 2.90
1034 1097 2.108514 ATGCACCGCGTCAATCAGG 61.109 57.895 4.92 0.00 0.00 3.86
1035 1098 4.166011 GCACCGCGTCAATCAGGC 62.166 66.667 4.92 0.00 0.00 4.85
1053 1116 2.040544 CGATCAACCAGTGGCACCC 61.041 63.158 15.27 0.00 0.00 4.61
1057 1120 4.579384 AACCAGTGGCACCCCGTG 62.579 66.667 15.27 5.78 36.51 4.94
1125 1191 1.442688 GACCACCGTTACGTCGTCC 60.443 63.158 0.00 0.00 0.00 4.79
1195 1261 4.159135 GCAAAGAGATCCATGACCACAATT 59.841 41.667 0.00 0.00 0.00 2.32
1202 1268 1.894466 CCATGACCACAATTGCCTCAA 59.106 47.619 5.05 0.00 0.00 3.02
1218 1284 1.876156 CTCAACAAGGTCCAAGAGCAC 59.124 52.381 0.00 0.00 31.89 4.40
1231 1324 1.303561 GAGCACCACCATTGCCTCA 60.304 57.895 0.00 0.00 41.18 3.86
1266 1359 1.026718 CGGAGTGGCACCAAATCTCC 61.027 60.000 15.27 12.43 40.62 3.71
1268 1361 0.321653 GAGTGGCACCAAATCTCCGT 60.322 55.000 15.27 0.00 0.00 4.69
1299 1392 3.925090 CCCCGGTACCAGATCGCC 61.925 72.222 13.54 0.00 0.00 5.54
1564 1657 1.448119 CCTAGCGCGAGAGGTGATGA 61.448 60.000 19.86 0.00 0.00 2.92
1595 1688 1.134965 CGAGAAGCCGAAGAAGGTGAT 60.135 52.381 0.00 0.00 0.00 3.06
1710 1803 0.320073 TCTGCGAACCCCGTGTTTAG 60.320 55.000 0.00 0.00 37.29 1.85
1711 1804 1.908066 CTGCGAACCCCGTGTTTAGC 61.908 60.000 0.00 8.47 37.29 3.09
1730 1823 2.969990 GCTTCTGAAGATGCTCTGTCA 58.030 47.619 21.06 0.00 40.69 3.58
1731 1824 2.931325 GCTTCTGAAGATGCTCTGTCAG 59.069 50.000 21.06 0.00 40.69 3.51
1732 1825 3.368220 GCTTCTGAAGATGCTCTGTCAGA 60.368 47.826 21.06 1.78 40.69 3.27
1735 1828 5.219343 TCTGAAGATGCTCTGTCAGAAAA 57.781 39.130 3.67 0.00 37.53 2.29
1738 1831 4.753610 TGAAGATGCTCTGTCAGAAAACAG 59.246 41.667 3.67 0.00 46.54 3.16
1740 1833 4.712476 AGATGCTCTGTCAGAAAACAGTT 58.288 39.130 3.67 0.00 45.57 3.16
1747 1840 6.422776 TCTGTCAGAAAACAGTTCAAGTTC 57.577 37.500 0.00 0.00 45.57 3.01
1750 1843 3.687212 TCAGAAAACAGTTCAAGTTCGCA 59.313 39.130 0.00 0.00 0.00 5.10
1870 1964 6.238842 CGTTGGATGCTGAAATTAGGATTGAT 60.239 38.462 0.00 0.00 0.00 2.57
1871 1965 7.495055 GTTGGATGCTGAAATTAGGATTGATT 58.505 34.615 0.00 0.00 0.00 2.57
1872 1966 7.664552 TGGATGCTGAAATTAGGATTGATTT 57.335 32.000 0.00 0.00 0.00 2.17
1873 1967 7.494211 TGGATGCTGAAATTAGGATTGATTTG 58.506 34.615 0.00 0.00 0.00 2.32
1874 1968 7.124599 TGGATGCTGAAATTAGGATTGATTTGT 59.875 33.333 0.00 0.00 0.00 2.83
1875 1969 7.983484 GGATGCTGAAATTAGGATTGATTTGTT 59.017 33.333 0.00 0.00 0.00 2.83
1876 1970 8.712285 ATGCTGAAATTAGGATTGATTTGTTG 57.288 30.769 0.00 0.00 0.00 3.33
1877 1971 6.591062 TGCTGAAATTAGGATTGATTTGTTGC 59.409 34.615 0.00 0.00 0.00 4.17
1878 1972 6.591062 GCTGAAATTAGGATTGATTTGTTGCA 59.409 34.615 0.00 0.00 0.00 4.08
1879 1973 7.412237 GCTGAAATTAGGATTGATTTGTTGCAC 60.412 37.037 0.00 0.00 0.00 4.57
1880 1974 7.440198 TGAAATTAGGATTGATTTGTTGCACA 58.560 30.769 0.00 0.00 0.00 4.57
1881 1975 8.095792 TGAAATTAGGATTGATTTGTTGCACAT 58.904 29.630 0.00 0.00 0.00 3.21
1882 1976 8.851541 AAATTAGGATTGATTTGTTGCACATT 57.148 26.923 0.00 0.00 0.00 2.71
1883 1977 8.483307 AATTAGGATTGATTTGTTGCACATTC 57.517 30.769 0.00 0.00 0.00 2.67
1884 1978 5.733620 AGGATTGATTTGTTGCACATTCT 57.266 34.783 0.00 0.00 0.00 2.40
1885 1979 5.717119 AGGATTGATTTGTTGCACATTCTC 58.283 37.500 0.00 0.00 0.00 2.87
1886 1980 5.479375 AGGATTGATTTGTTGCACATTCTCT 59.521 36.000 0.00 0.00 0.00 3.10
1887 1981 5.803967 GGATTGATTTGTTGCACATTCTCTC 59.196 40.000 0.00 0.00 0.00 3.20
1888 1982 4.408993 TGATTTGTTGCACATTCTCTCG 57.591 40.909 0.00 0.00 0.00 4.04
1889 1983 4.064388 TGATTTGTTGCACATTCTCTCGA 58.936 39.130 0.00 0.00 0.00 4.04
1890 1984 4.514816 TGATTTGTTGCACATTCTCTCGAA 59.485 37.500 0.00 0.00 0.00 3.71
1891 1985 4.891627 TTTGTTGCACATTCTCTCGAAA 57.108 36.364 0.00 0.00 31.91 3.46
1892 1986 5.437289 TTTGTTGCACATTCTCTCGAAAT 57.563 34.783 0.00 0.00 31.91 2.17
1893 1987 6.552859 TTTGTTGCACATTCTCTCGAAATA 57.447 33.333 0.00 0.00 31.91 1.40
1894 1988 5.784750 TGTTGCACATTCTCTCGAAATAG 57.215 39.130 0.00 0.00 31.91 1.73
1895 1989 4.631377 TGTTGCACATTCTCTCGAAATAGG 59.369 41.667 0.00 0.00 31.91 2.57
1896 1990 3.198068 TGCACATTCTCTCGAAATAGGC 58.802 45.455 0.00 0.00 31.91 3.93
1897 1991 3.118629 TGCACATTCTCTCGAAATAGGCT 60.119 43.478 0.00 0.00 31.91 4.58
1898 1992 3.873952 GCACATTCTCTCGAAATAGGCTT 59.126 43.478 0.00 0.00 31.91 4.35
1899 1993 4.333926 GCACATTCTCTCGAAATAGGCTTT 59.666 41.667 0.00 0.00 31.91 3.51
1900 1994 5.163713 GCACATTCTCTCGAAATAGGCTTTT 60.164 40.000 0.00 0.00 31.91 2.27
1901 1995 6.253746 CACATTCTCTCGAAATAGGCTTTTG 58.746 40.000 0.00 0.00 31.91 2.44
1902 1996 4.946784 TTCTCTCGAAATAGGCTTTTGC 57.053 40.909 0.00 0.00 46.64 3.68
1914 2008 2.492019 GCTTTTGCCCCGCTTTATAG 57.508 50.000 0.00 0.00 40.15 1.31
1915 2009 2.021457 GCTTTTGCCCCGCTTTATAGA 58.979 47.619 0.00 0.00 40.15 1.98
1916 2010 2.623416 GCTTTTGCCCCGCTTTATAGAT 59.377 45.455 0.00 0.00 40.15 1.98
1917 2011 3.818773 GCTTTTGCCCCGCTTTATAGATA 59.181 43.478 0.00 0.00 40.15 1.98
1918 2012 4.277423 GCTTTTGCCCCGCTTTATAGATAA 59.723 41.667 0.00 0.00 40.15 1.75
1919 2013 5.221165 GCTTTTGCCCCGCTTTATAGATAAA 60.221 40.000 0.00 0.00 40.15 1.40
1920 2014 6.681865 GCTTTTGCCCCGCTTTATAGATAAAA 60.682 38.462 0.00 0.00 40.15 1.52
1921 2015 6.385649 TTTGCCCCGCTTTATAGATAAAAG 57.614 37.500 0.00 0.00 37.08 2.27
1922 2016 5.298989 TGCCCCGCTTTATAGATAAAAGA 57.701 39.130 0.00 0.00 36.27 2.52
1929 2023 8.455682 CCCGCTTTATAGATAAAAGAAAACACA 58.544 33.333 0.00 0.00 36.27 3.72
1951 2045 5.719085 ACATCCTATCTGTAGGCTGATAAGG 59.281 44.000 11.16 0.00 43.73 2.69
1953 2047 5.965486 TCCTATCTGTAGGCTGATAAGGAA 58.035 41.667 0.00 0.00 46.03 3.36
1962 2056 2.716217 GCTGATAAGGAAGCCAGTGTT 58.284 47.619 0.00 0.00 33.12 3.32
1974 2068 5.163632 GGAAGCCAGTGTTAGACTAGTAGAC 60.164 48.000 3.59 0.00 31.73 2.59
1977 2071 4.260170 CCAGTGTTAGACTAGTAGACGGT 58.740 47.826 3.59 0.00 31.73 4.83
1979 2073 4.332268 CAGTGTTAGACTAGTAGACGGTCC 59.668 50.000 3.59 0.00 31.73 4.46
2032 2137 2.922955 TGTGAACCCCATGGATAGGAAA 59.077 45.455 15.22 0.00 34.81 3.13
2036 2141 6.133356 GTGAACCCCATGGATAGGAAATAAA 58.867 40.000 15.22 0.00 34.81 1.40
2087 2193 4.790790 CCCTAATTAAGCTCCCCATATCCT 59.209 45.833 0.00 0.00 0.00 3.24
2134 2240 2.111384 GCACCTCCTAGATCCACTTCA 58.889 52.381 0.00 0.00 0.00 3.02
2139 2245 1.364678 TCCTAGATCCACTTCACCCCA 59.635 52.381 0.00 0.00 0.00 4.96
2154 2260 2.992689 CCAGGCCTTGCATGCACA 60.993 61.111 22.58 11.00 39.11 4.57
2165 2271 2.876581 CATGCACATGCCTTCTCCA 58.123 52.632 0.49 0.00 41.18 3.86
2206 2324 1.032114 GGCCACTTCTTTCCCATCCG 61.032 60.000 0.00 0.00 0.00 4.18
2283 2401 4.258206 CACTGGTGTGGTTGCCTT 57.742 55.556 0.00 0.00 40.33 4.35
2342 2460 2.419297 CCAGAAGCCGTAAGAATCAGCT 60.419 50.000 0.00 0.00 43.02 4.24
2345 2463 2.593346 AGCCGTAAGAATCAGCTCAG 57.407 50.000 0.00 0.00 43.02 3.35
2454 2974 6.612247 TTTCCATGCTTGGTACGTATTATG 57.388 37.500 17.54 0.00 44.06 1.90
2473 2993 1.666700 TGTTTGTGTTTCTTCCCGACG 59.333 47.619 0.00 0.00 0.00 5.12
2497 3018 5.929697 ACAATTCGCCTCATACATACATG 57.070 39.130 0.00 0.00 0.00 3.21
2501 3022 2.368548 TCGCCTCATACATACATGGCTT 59.631 45.455 0.00 0.00 38.33 4.35
2510 3031 9.113838 CTCATACATACATGGCTTTAGTTCTTT 57.886 33.333 0.00 0.00 0.00 2.52
2516 3037 4.694037 ACATGGCTTTAGTTCTTTACCGAC 59.306 41.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.628630 TTGTTGGTGATCAGTAATGATTGTTA 57.371 30.769 7.17 0.00 0.00 2.41
29 30 4.161377 TCCGATAGTGATTGTTGGTGATCA 59.839 41.667 0.00 0.00 0.00 2.92
84 87 2.492881 TGCTCGATGAAATGCCAACAAT 59.507 40.909 0.00 0.00 0.00 2.71
181 184 1.950630 CCAACGCCTTTTGCTGCAC 60.951 57.895 0.00 0.00 38.05 4.57
189 192 1.670083 GTCCTACGCCAACGCCTTT 60.670 57.895 0.00 0.00 45.53 3.11
197 200 4.752879 GCGCCTTGTCCTACGCCA 62.753 66.667 0.00 0.00 45.35 5.69
201 204 3.952628 AAGCGGCGCCTTGTCCTAC 62.953 63.158 30.40 3.21 0.00 3.18
224 227 3.679980 CCGCGAAGAAGAAGATGAAGAAA 59.320 43.478 8.23 0.00 0.00 2.52
438 450 2.030862 GGAAACCACCCACGCGTA 59.969 61.111 13.44 0.00 0.00 4.42
439 451 4.178169 TGGAAACCACCCACGCGT 62.178 61.111 5.58 5.58 0.00 6.01
523 536 4.776322 CTGCCAATGACCGCCGGA 62.776 66.667 11.71 0.00 0.00 5.14
552 581 3.633094 CTGCACTGTCTCCCGTCGG 62.633 68.421 3.60 3.60 0.00 4.79
555 584 4.363990 CGCTGCACTGTCTCCCGT 62.364 66.667 0.00 0.00 0.00 5.28
594 623 1.029947 CGAGTAACATTGGCACCCCC 61.030 60.000 0.00 0.00 0.00 5.40
596 625 1.084289 GTCGAGTAACATTGGCACCC 58.916 55.000 0.00 0.00 0.00 4.61
604 633 1.516386 CGCCGCAGTCGAGTAACAT 60.516 57.895 0.00 0.00 38.10 2.71
606 635 2.177531 TCGCCGCAGTCGAGTAAC 59.822 61.111 0.00 0.00 27.85 2.50
614 643 1.320344 TTACTCCATCTCGCCGCAGT 61.320 55.000 0.00 0.00 0.00 4.40
616 645 0.464036 ATTTACTCCATCTCGCCGCA 59.536 50.000 0.00 0.00 0.00 5.69
641 670 7.180229 CCACCTCCCTATTTCCACTAAATTTTT 59.820 37.037 0.00 0.00 38.71 1.94
645 674 5.043762 TCCACCTCCCTATTTCCACTAAAT 58.956 41.667 0.00 0.00 40.87 1.40
651 680 2.961536 TCTCCACCTCCCTATTTCCA 57.038 50.000 0.00 0.00 0.00 3.53
697 728 2.365635 ACGCACCTAGCCCATCCT 60.366 61.111 0.00 0.00 41.38 3.24
734 765 5.806259 TCCCCTATAAAAGTCCATAAGGGA 58.194 41.667 6.07 0.00 45.89 4.20
735 766 6.720217 ATCCCCTATAAAAGTCCATAAGGG 57.280 41.667 0.00 0.00 31.84 3.95
736 767 7.461363 ACCTATCCCCTATAAAAGTCCATAAGG 59.539 40.741 0.00 0.00 0.00 2.69
737 768 8.450780 ACCTATCCCCTATAAAAGTCCATAAG 57.549 38.462 0.00 0.00 0.00 1.73
738 769 8.823810 AACCTATCCCCTATAAAAGTCCATAA 57.176 34.615 0.00 0.00 0.00 1.90
741 772 7.607511 TCTAACCTATCCCCTATAAAAGTCCA 58.392 38.462 0.00 0.00 0.00 4.02
742 773 7.733955 ACTCTAACCTATCCCCTATAAAAGTCC 59.266 40.741 0.00 0.00 0.00 3.85
743 774 8.724113 ACTCTAACCTATCCCCTATAAAAGTC 57.276 38.462 0.00 0.00 0.00 3.01
744 775 8.935741 CAACTCTAACCTATCCCCTATAAAAGT 58.064 37.037 0.00 0.00 0.00 2.66
745 776 7.878644 GCAACTCTAACCTATCCCCTATAAAAG 59.121 40.741 0.00 0.00 0.00 2.27
746 777 7.202158 GGCAACTCTAACCTATCCCCTATAAAA 60.202 40.741 0.00 0.00 0.00 1.52
747 778 6.271624 GGCAACTCTAACCTATCCCCTATAAA 59.728 42.308 0.00 0.00 0.00 1.40
748 779 5.783875 GGCAACTCTAACCTATCCCCTATAA 59.216 44.000 0.00 0.00 0.00 0.98
749 780 5.339477 GGCAACTCTAACCTATCCCCTATA 58.661 45.833 0.00 0.00 0.00 1.31
750 781 4.168883 GGCAACTCTAACCTATCCCCTAT 58.831 47.826 0.00 0.00 0.00 2.57
751 782 3.584294 GGCAACTCTAACCTATCCCCTA 58.416 50.000 0.00 0.00 0.00 3.53
752 783 2.409570 GGCAACTCTAACCTATCCCCT 58.590 52.381 0.00 0.00 0.00 4.79
753 784 1.070289 CGGCAACTCTAACCTATCCCC 59.930 57.143 0.00 0.00 0.00 4.81
754 785 2.037144 TCGGCAACTCTAACCTATCCC 58.963 52.381 0.00 0.00 0.00 3.85
755 786 2.429610 TGTCGGCAACTCTAACCTATCC 59.570 50.000 0.00 0.00 0.00 2.59
756 787 3.130693 ACTGTCGGCAACTCTAACCTATC 59.869 47.826 0.00 0.00 0.00 2.08
757 788 3.097614 ACTGTCGGCAACTCTAACCTAT 58.902 45.455 0.00 0.00 0.00 2.57
758 789 2.230508 CACTGTCGGCAACTCTAACCTA 59.769 50.000 0.00 0.00 0.00 3.08
759 790 1.000955 CACTGTCGGCAACTCTAACCT 59.999 52.381 0.00 0.00 0.00 3.50
760 791 1.429463 CACTGTCGGCAACTCTAACC 58.571 55.000 0.00 0.00 0.00 2.85
761 792 0.790814 GCACTGTCGGCAACTCTAAC 59.209 55.000 0.00 0.00 0.00 2.34
762 793 0.679505 AGCACTGTCGGCAACTCTAA 59.320 50.000 0.00 0.00 0.00 2.10
763 794 0.243907 GAGCACTGTCGGCAACTCTA 59.756 55.000 7.02 0.00 0.00 2.43
764 795 1.005630 GAGCACTGTCGGCAACTCT 60.006 57.895 7.02 0.00 0.00 3.24
765 796 0.671781 ATGAGCACTGTCGGCAACTC 60.672 55.000 7.27 7.27 0.00 3.01
766 797 0.250467 AATGAGCACTGTCGGCAACT 60.250 50.000 0.00 0.00 0.00 3.16
767 798 1.438651 TAATGAGCACTGTCGGCAAC 58.561 50.000 0.00 0.00 0.00 4.17
768 799 2.076100 CTTAATGAGCACTGTCGGCAA 58.924 47.619 0.00 0.00 0.00 4.52
769 800 1.725641 CTTAATGAGCACTGTCGGCA 58.274 50.000 0.00 0.00 0.00 5.69
807 838 2.159352 GCTCTGAGTCCGAGTAGGTTTC 60.159 54.545 12.51 0.00 41.99 2.78
834 865 1.815003 GTGGGCTGAAATGAACTCTGG 59.185 52.381 0.00 0.00 0.00 3.86
859 890 8.735303 CATATAATAGTATATGCTGCGAGTCC 57.265 38.462 15.18 0.00 41.53 3.85
875 906 3.338249 AGCAAGCCCGCACATATAATAG 58.662 45.455 0.00 0.00 0.00 1.73
876 907 3.007940 AGAGCAAGCCCGCACATATAATA 59.992 43.478 0.00 0.00 0.00 0.98
877 908 2.154462 GAGCAAGCCCGCACATATAAT 58.846 47.619 0.00 0.00 0.00 1.28
878 909 1.140852 AGAGCAAGCCCGCACATATAA 59.859 47.619 0.00 0.00 0.00 0.98
879 910 0.758734 AGAGCAAGCCCGCACATATA 59.241 50.000 0.00 0.00 0.00 0.86
880 911 0.758734 TAGAGCAAGCCCGCACATAT 59.241 50.000 0.00 0.00 0.00 1.78
916 979 5.163953 CGCATATATAGGGCAAGACTTTTCG 60.164 44.000 9.17 0.00 0.00 3.46
922 985 2.280628 GGCGCATATATAGGGCAAGAC 58.719 52.381 10.83 1.07 45.58 3.01
954 1017 4.331968 CTGGCTTTGGGTGTTATTACTCA 58.668 43.478 0.00 0.00 0.00 3.41
984 1047 2.041819 ATCGGAGGAGGTGGGTCC 60.042 66.667 0.00 0.00 36.79 4.46
985 1048 2.435693 CCATCGGAGGAGGTGGGTC 61.436 68.421 0.00 0.00 0.00 4.46
986 1049 2.365635 CCATCGGAGGAGGTGGGT 60.366 66.667 0.00 0.00 0.00 4.51
987 1050 3.866582 GCCATCGGAGGAGGTGGG 61.867 72.222 0.00 0.00 32.35 4.61
995 1058 1.209128 GTACGTGATTGCCATCGGAG 58.791 55.000 0.00 0.00 31.08 4.63
999 1062 1.002468 GCATGGTACGTGATTGCCATC 60.002 52.381 0.00 0.00 39.47 3.51
1025 1088 1.667724 CTGGTTGATCGCCTGATTGAC 59.332 52.381 7.51 0.00 34.09 3.18
1030 1093 1.296392 CCACTGGTTGATCGCCTGA 59.704 57.895 16.19 0.00 0.00 3.86
1033 1096 2.359850 TGCCACTGGTTGATCGCC 60.360 61.111 0.00 0.00 0.00 5.54
1034 1097 2.690778 GGTGCCACTGGTTGATCGC 61.691 63.158 0.00 0.00 0.00 4.58
1035 1098 2.040544 GGGTGCCACTGGTTGATCG 61.041 63.158 0.00 0.00 0.00 3.69
1038 1101 4.263572 CGGGGTGCCACTGGTTGA 62.264 66.667 0.00 0.00 0.00 3.18
1068 1134 2.824041 ATGACAATGTCCGCGGCC 60.824 61.111 23.51 10.90 0.00 6.13
1070 1136 1.449423 TCCATGACAATGTCCGCGG 60.449 57.895 22.12 22.12 31.27 6.46
1078 1144 1.019278 GTGCCGTCGTCCATGACAAT 61.019 55.000 0.00 0.00 38.84 2.71
1080 1146 2.048597 GTGCCGTCGTCCATGACA 60.049 61.111 0.00 0.00 38.84 3.58
1125 1191 0.390866 AGAGCAAGACATCACAGGCG 60.391 55.000 0.00 0.00 0.00 5.52
1218 1284 1.431488 CGACGATGAGGCAATGGTGG 61.431 60.000 0.00 0.00 0.00 4.61
1299 1392 3.691744 GACGCAGAGCTGGAGGACG 62.692 68.421 0.00 0.00 0.00 4.79
1419 1512 4.953868 TTGACGTCGCCACCCACG 62.954 66.667 11.62 0.00 41.90 4.94
1421 1514 4.980805 GCTTGACGTCGCCACCCA 62.981 66.667 11.62 0.00 0.00 4.51
1446 1539 1.978542 CCTCAAGGTTACAGTCGTCG 58.021 55.000 0.00 0.00 0.00 5.12
1564 1657 1.135257 CGGCTTCTCGATGAGAGTGTT 60.135 52.381 0.00 0.00 46.86 3.32
1595 1688 1.748879 GCGGCCCACTTGCTCATTA 60.749 57.895 0.00 0.00 0.00 1.90
1627 1720 1.828660 CGTACCGGATCTGCTCCCT 60.829 63.158 9.46 0.00 41.49 4.20
1636 1729 2.421739 GATGCAGGCGTACCGGAT 59.578 61.111 9.46 0.00 42.76 4.18
1656 1749 2.087009 GTCGAAGGACACGAAGGCG 61.087 63.158 0.00 0.00 42.91 5.52
1726 1819 4.436852 GCGAACTTGAACTGTTTTCTGACA 60.437 41.667 0.00 0.00 0.00 3.58
1728 1821 3.687212 TGCGAACTTGAACTGTTTTCTGA 59.313 39.130 0.00 0.00 0.00 3.27
1729 1822 3.786048 GTGCGAACTTGAACTGTTTTCTG 59.214 43.478 0.00 0.00 0.00 3.02
1730 1823 3.689649 AGTGCGAACTTGAACTGTTTTCT 59.310 39.130 0.00 0.00 0.00 2.52
1731 1824 4.016113 AGTGCGAACTTGAACTGTTTTC 57.984 40.909 0.00 0.00 0.00 2.29
1732 1825 4.434713 AAGTGCGAACTTGAACTGTTTT 57.565 36.364 8.35 0.00 0.00 2.43
1735 1828 5.065988 ACAATTAAGTGCGAACTTGAACTGT 59.934 36.000 19.55 14.66 0.00 3.55
1738 1831 5.398416 GGAACAATTAAGTGCGAACTTGAAC 59.602 40.000 19.55 2.94 0.00 3.18
1740 1833 4.319190 CGGAACAATTAAGTGCGAACTTGA 60.319 41.667 19.55 11.49 0.00 3.02
1747 1840 5.464965 AATCTACGGAACAATTAAGTGCG 57.535 39.130 2.17 1.43 0.00 5.34
1750 1843 9.498176 ACAACTAAATCTACGGAACAATTAAGT 57.502 29.630 0.00 0.00 0.00 2.24
1801 1895 7.013274 CCATATCGGTCCAAGTATTCACATTTT 59.987 37.037 0.00 0.00 0.00 1.82
1837 1931 0.179137 CAGCATCCAACGTCGAGCTA 60.179 55.000 0.00 0.00 0.00 3.32
1882 1976 3.270877 GGCAAAAGCCTATTTCGAGAGA 58.729 45.455 0.00 0.00 39.20 3.10
1883 1977 2.356069 GGGCAAAAGCCTATTTCGAGAG 59.644 50.000 6.45 0.00 0.00 3.20
1884 1978 2.365582 GGGCAAAAGCCTATTTCGAGA 58.634 47.619 6.45 0.00 0.00 4.04
1885 1979 1.405463 GGGGCAAAAGCCTATTTCGAG 59.595 52.381 6.45 0.00 0.00 4.04
1886 1980 1.470051 GGGGCAAAAGCCTATTTCGA 58.530 50.000 6.45 0.00 0.00 3.71
1887 1981 0.100503 CGGGGCAAAAGCCTATTTCG 59.899 55.000 6.45 0.49 0.00 3.46
1888 1982 0.179111 GCGGGGCAAAAGCCTATTTC 60.179 55.000 6.45 0.00 0.00 2.17
1889 1983 0.614697 AGCGGGGCAAAAGCCTATTT 60.615 50.000 6.45 0.00 0.00 1.40
1890 1984 0.614697 AAGCGGGGCAAAAGCCTATT 60.615 50.000 6.45 0.00 0.00 1.73
1891 1985 0.614697 AAAGCGGGGCAAAAGCCTAT 60.615 50.000 6.45 0.00 0.00 2.57
1892 1986 0.038455 TAAAGCGGGGCAAAAGCCTA 59.962 50.000 6.45 0.00 0.00 3.93
1893 1987 0.614697 ATAAAGCGGGGCAAAAGCCT 60.615 50.000 6.45 0.00 0.00 4.58
1894 1988 1.067060 CTATAAAGCGGGGCAAAAGCC 59.933 52.381 0.00 0.00 0.00 4.35
1895 1989 2.021457 TCTATAAAGCGGGGCAAAAGC 58.979 47.619 0.00 0.00 0.00 3.51
1896 1990 6.385649 TTTATCTATAAAGCGGGGCAAAAG 57.614 37.500 0.00 0.00 0.00 2.27
1897 1991 6.603997 TCTTTTATCTATAAAGCGGGGCAAAA 59.396 34.615 0.00 0.00 34.13 2.44
1898 1992 6.123651 TCTTTTATCTATAAAGCGGGGCAAA 58.876 36.000 0.00 0.00 34.13 3.68
1899 1993 5.686753 TCTTTTATCTATAAAGCGGGGCAA 58.313 37.500 0.00 0.00 34.13 4.52
1900 1994 5.298989 TCTTTTATCTATAAAGCGGGGCA 57.701 39.130 0.00 0.00 34.13 5.36
1901 1995 6.628919 TTTCTTTTATCTATAAAGCGGGGC 57.371 37.500 0.00 0.00 34.13 5.80
1902 1996 7.913821 GTGTTTTCTTTTATCTATAAAGCGGGG 59.086 37.037 0.00 0.00 34.13 5.73
1903 1997 8.455682 TGTGTTTTCTTTTATCTATAAAGCGGG 58.544 33.333 0.00 0.00 34.13 6.13
1913 2007 9.965902 ACAGATAGGATGTGTTTTCTTTTATCT 57.034 29.630 0.00 0.00 32.17 1.98
1951 2045 5.447548 CGTCTACTAGTCTAACACTGGCTTC 60.448 48.000 0.00 0.00 37.09 3.86
1953 2047 3.940221 CGTCTACTAGTCTAACACTGGCT 59.060 47.826 0.00 0.00 37.09 4.75
1959 2053 4.679106 CGAGGACCGTCTACTAGTCTAACA 60.679 50.000 0.00 0.00 0.00 2.41
1962 2056 3.291584 TCGAGGACCGTCTACTAGTCTA 58.708 50.000 0.00 0.00 39.75 2.59
1974 2068 3.165058 TCTCAATTGAATCGAGGACCG 57.835 47.619 9.88 0.00 40.25 4.79
1977 2071 4.741837 GCCAGATCTCAATTGAATCGAGGA 60.742 45.833 26.24 16.21 0.00 3.71
1979 2073 3.183976 CGCCAGATCTCAATTGAATCGAG 59.816 47.826 9.88 11.86 0.00 4.04
2015 2109 7.246027 GGTATTTATTTCCTATCCATGGGGTT 58.754 38.462 13.02 0.00 34.93 4.11
2032 2137 5.058490 CGTACGGGATTTGTGGGTATTTAT 58.942 41.667 7.57 0.00 0.00 1.40
2036 2141 1.832998 ACGTACGGGATTTGTGGGTAT 59.167 47.619 21.06 0.00 0.00 2.73
2154 2260 1.198713 ACGATGAGTGGAGAAGGCAT 58.801 50.000 0.00 0.00 0.00 4.40
2220 2338 4.980805 GCACGTGCGGAAGGGTGA 62.981 66.667 26.77 0.00 32.23 4.02
2283 2401 0.916086 ATCCTTCGGGTTGCATGGTA 59.084 50.000 0.00 0.00 36.28 3.25
2309 2427 0.537653 GCTTCTGGTCCTCCCTACAC 59.462 60.000 0.00 0.00 0.00 2.90
2312 2430 1.381327 CGGCTTCTGGTCCTCCCTA 60.381 63.158 0.00 0.00 0.00 3.53
2342 2460 0.039618 GAACATCCAAAGGGGCCTGA 59.960 55.000 0.84 0.00 36.21 3.86
2345 2463 1.644509 AAAGAACATCCAAAGGGGCC 58.355 50.000 0.00 0.00 36.21 5.80
2417 2544 5.607477 AGCATGGAAATTTGGAAGCATATG 58.393 37.500 0.00 0.00 0.00 1.78
2454 2974 1.667212 ACGTCGGGAAGAAACACAAAC 59.333 47.619 0.00 0.00 0.00 2.93
2473 2993 6.128553 CCATGTATGTATGAGGCGAATTGTAC 60.129 42.308 0.00 0.00 0.00 2.90
2497 3018 5.522824 CCATAGTCGGTAAAGAACTAAAGCC 59.477 44.000 0.00 0.00 0.00 4.35
2501 3022 6.369615 GCAAACCATAGTCGGTAAAGAACTAA 59.630 38.462 0.00 0.00 38.76 2.24
2510 3031 3.965379 TGAAGCAAACCATAGTCGGTA 57.035 42.857 0.00 0.00 38.76 4.02
2516 3037 6.974622 GGTGAAACATATGAAGCAAACCATAG 59.025 38.462 10.38 0.00 39.98 2.23


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

AutoCloner maintained by Alex Coulton.