Multiple sequence alignment - TraesCS6B01G013100

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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 TraesCS6B01G013100 chr6B 100.000 3840 0 0 1 3840 8233485 8237324 0.000000e+00 7092.0
1 TraesCS6B01G013100 chr6B 87.064 1175 120 16 1668 2835 704447124 704445975 0.000000e+00 1299.0
2 TraesCS6B01G013100 chr6B 92.228 772 43 9 1 760 8265567 8266333 0.000000e+00 1077.0
3 TraesCS6B01G013100 chr6B 84.663 802 85 20 827 1625 704448084 704447318 0.000000e+00 765.0
4 TraesCS6B01G013100 chr6B 82.469 559 86 8 1693 2241 8140197 8139641 2.680000e-131 479.0
5 TraesCS6B01G013100 chr6B 87.342 316 40 0 987 1302 8140911 8140596 2.820000e-96 363.0
6 TraesCS6B01G013100 chr6B 94.675 169 8 1 2798 2966 8267720 8267887 1.060000e-65 261.0
7 TraesCS6B01G013100 chr6B 82.392 301 47 4 1316 1616 8140537 8140243 1.370000e-64 257.0
8 TraesCS6B01G013100 chr6B 88.406 138 12 4 57 194 8265511 8265644 3.070000e-36 163.0
9 TraesCS6B01G013100 chr5B 89.569 882 70 6 2978 3840 491041573 491040695 0.000000e+00 1099.0
10 TraesCS6B01G013100 chr5B 89.514 658 58 2 3192 3840 569825167 569824512 0.000000e+00 822.0
11 TraesCS6B01G013100 chr5B 83.393 843 101 24 3034 3840 508151100 508151939 0.000000e+00 745.0
12 TraesCS6B01G013100 chr3A 88.093 907 80 17 1691 2582 599580700 599579807 0.000000e+00 1051.0
13 TraesCS6B01G013100 chr3A 87.702 309 37 1 1303 1610 599581038 599580730 3.650000e-95 359.0
14 TraesCS6B01G013100 chr3A 85.538 325 45 2 987 1310 599581398 599581075 4.750000e-89 339.0
15 TraesCS6B01G013100 chr3D 87.500 920 84 19 1701 2605 456647379 456646476 0.000000e+00 1033.0
16 TraesCS6B01G013100 chr3D 85.846 325 44 2 987 1310 456648089 456647766 1.020000e-90 344.0
17 TraesCS6B01G013100 chr3D 86.408 309 41 1 1303 1610 456647729 456647421 1.710000e-88 337.0
18 TraesCS6B01G013100 chr3D 90.323 62 3 3 1610 1671 16057801 16057743 1.140000e-10 78.7
19 TraesCS6B01G013100 chr3B 88.364 868 76 15 1730 2582 603535936 603535079 0.000000e+00 1020.0
20 TraesCS6B01G013100 chr3B 89.700 767 64 8 3031 3789 39651440 39650681 0.000000e+00 965.0
21 TraesCS6B01G013100 chr3B 81.651 436 62 13 883 1310 603536764 603536339 2.840000e-91 346.0
22 TraesCS6B01G013100 chr3B 78.354 559 92 19 3176 3720 167865133 167864590 6.150000e-88 335.0
23 TraesCS6B01G013100 chr7D 86.788 878 89 15 1723 2582 529717982 529717114 0.000000e+00 953.0
24 TraesCS6B01G013100 chr7D 85.947 797 81 17 3029 3799 553822028 553822819 0.000000e+00 822.0
25 TraesCS6B01G013100 chr7D 82.520 635 88 14 999 1611 529718662 529718029 1.570000e-148 536.0
26 TraesCS6B01G013100 chr7B 86.689 879 88 18 1723 2582 567802311 567801443 0.000000e+00 948.0
27 TraesCS6B01G013100 chr7B 79.340 818 112 38 831 1611 567803155 567802358 4.400000e-144 521.0
28 TraesCS6B01G013100 chr7A 86.034 895 98 14 1723 2602 609262682 609263564 0.000000e+00 935.0
29 TraesCS6B01G013100 chr7A 80.200 500 67 22 831 1310 609261387 609261874 2.840000e-91 346.0
30 TraesCS6B01G013100 chr7A 85.235 298 43 1 1314 1611 609261951 609262247 4.820000e-79 305.0
31 TraesCS6B01G013100 chr5D 87.080 774 70 19 3096 3840 539037119 539036347 0.000000e+00 848.0
32 TraesCS6B01G013100 chr4B 86.521 779 77 13 3029 3798 82596868 82596109 0.000000e+00 832.0
33 TraesCS6B01G013100 chr6D 85.150 835 83 18 3034 3840 132055836 132055015 0.000000e+00 817.0
34 TraesCS6B01G013100 chr6D 83.673 686 76 19 1924 2601 4363424 4362767 7.050000e-172 614.0
35 TraesCS6B01G013100 chr6D 81.475 556 66 25 242 787 4364813 4364285 4.590000e-114 422.0
36 TraesCS6B01G013100 chr6D 84.286 350 52 2 1001 1347 4364281 4363932 4.750000e-89 339.0
37 TraesCS6B01G013100 chr6D 84.810 316 45 3 1303 1616 4373376 4373690 8.010000e-82 315.0
38 TraesCS6B01G013100 chr6A 83.966 817 103 13 3035 3840 119192535 119191736 0.000000e+00 758.0
39 TraesCS6B01G013100 chr5A 76.271 590 68 39 1047 1611 705494738 705495280 8.240000e-62 248.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G013100 chr6B 8233485 8237324 3839 False 7092.000000 7092 100.000000 1 3840 1 chr6B.!!$F1 3839
1 TraesCS6B01G013100 chr6B 704445975 704448084 2109 True 1032.000000 1299 85.863500 827 2835 2 chr6B.!!$R2 2008
2 TraesCS6B01G013100 chr6B 8265511 8267887 2376 False 500.333333 1077 91.769667 1 2966 3 chr6B.!!$F2 2965
3 TraesCS6B01G013100 chr6B 8139641 8140911 1270 True 366.333333 479 84.067667 987 2241 3 chr6B.!!$R1 1254
4 TraesCS6B01G013100 chr5B 491040695 491041573 878 True 1099.000000 1099 89.569000 2978 3840 1 chr5B.!!$R1 862
5 TraesCS6B01G013100 chr5B 569824512 569825167 655 True 822.000000 822 89.514000 3192 3840 1 chr5B.!!$R2 648
6 TraesCS6B01G013100 chr5B 508151100 508151939 839 False 745.000000 745 83.393000 3034 3840 1 chr5B.!!$F1 806
7 TraesCS6B01G013100 chr3A 599579807 599581398 1591 True 583.000000 1051 87.111000 987 2582 3 chr3A.!!$R1 1595
8 TraesCS6B01G013100 chr3D 456646476 456648089 1613 True 571.333333 1033 86.584667 987 2605 3 chr3D.!!$R2 1618
9 TraesCS6B01G013100 chr3B 39650681 39651440 759 True 965.000000 965 89.700000 3031 3789 1 chr3B.!!$R1 758
10 TraesCS6B01G013100 chr3B 603535079 603536764 1685 True 683.000000 1020 85.007500 883 2582 2 chr3B.!!$R3 1699
11 TraesCS6B01G013100 chr3B 167864590 167865133 543 True 335.000000 335 78.354000 3176 3720 1 chr3B.!!$R2 544
12 TraesCS6B01G013100 chr7D 553822028 553822819 791 False 822.000000 822 85.947000 3029 3799 1 chr7D.!!$F1 770
13 TraesCS6B01G013100 chr7D 529717114 529718662 1548 True 744.500000 953 84.654000 999 2582 2 chr7D.!!$R1 1583
14 TraesCS6B01G013100 chr7B 567801443 567803155 1712 True 734.500000 948 83.014500 831 2582 2 chr7B.!!$R1 1751
15 TraesCS6B01G013100 chr7A 609261387 609263564 2177 False 528.666667 935 83.823000 831 2602 3 chr7A.!!$F1 1771
16 TraesCS6B01G013100 chr5D 539036347 539037119 772 True 848.000000 848 87.080000 3096 3840 1 chr5D.!!$R1 744
17 TraesCS6B01G013100 chr4B 82596109 82596868 759 True 832.000000 832 86.521000 3029 3798 1 chr4B.!!$R1 769
18 TraesCS6B01G013100 chr6D 132055015 132055836 821 True 817.000000 817 85.150000 3034 3840 1 chr6D.!!$R1 806
19 TraesCS6B01G013100 chr6D 4362767 4364813 2046 True 458.333333 614 83.144667 242 2601 3 chr6D.!!$R2 2359
20 TraesCS6B01G013100 chr6A 119191736 119192535 799 True 758.000000 758 83.966000 3035 3840 1 chr6A.!!$R1 805
21 TraesCS6B01G013100 chr5A 705494738 705495280 542 False 248.000000 248 76.271000 1047 1611 1 chr5A.!!$F1 564

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
938 1005 0.034089 TCAGCTCAGGTCGATCTCCA 60.034 55.0 0.00 0.00 0.0 3.86 F
1516 1710 0.374758 CGTTGTGGCCAAGATCATCG 59.625 55.0 7.24 8.65 0.0 3.84 F
2311 3352 0.543174 AGCTCAAGAAGTCCGAGGGT 60.543 55.0 0.00 0.00 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 3351 0.307760 CACGTTCTTGCACCTGGAAC 59.692 55.0 0.0 9.56 36.83 3.62 R
2624 4696 0.888619 TAGACCTTGTGCTCGACTGG 59.111 55.0 0.0 0.00 0.00 4.00 R
3668 5810 0.039798 CGGAACCTTCGACTTCGTCA 60.040 55.0 0.0 0.00 40.80 4.35 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
37 94 6.704050 TGCAGCGTGTAAATTATCTTGCTATA 59.296 34.615 0.00 0.00 0.00 1.31
39 96 7.689812 GCAGCGTGTAAATTATCTTGCTATATG 59.310 37.037 0.00 0.00 0.00 1.78
189 246 8.784043 GTTATCAGAGGTATGTTTCAACAACTT 58.216 33.333 0.00 0.00 43.03 2.66
228 286 5.710984 AGTTCATGTAGGTACAAAGTCTCG 58.289 41.667 0.00 0.00 39.99 4.04
230 288 4.338012 TCATGTAGGTACAAAGTCTCGGA 58.662 43.478 0.00 0.00 39.99 4.55
293 353 8.653338 CAAAAATAATGCACCTCAAAAGATCAG 58.347 33.333 0.00 0.00 0.00 2.90
418 479 0.320683 GGTGAGTTTGGGCATTTGGC 60.321 55.000 0.00 0.00 43.74 4.52
430 491 3.055602 GGGCATTTGGCTTTGATTTCTCT 60.056 43.478 4.01 0.00 44.01 3.10
532 593 7.064134 CCATTGATTATATGCCATCAATTGCAC 59.936 37.037 13.17 0.00 44.32 4.57
538 599 8.729805 TTATATGCCATCAATTGCACGATATA 57.270 30.769 0.00 1.28 40.88 0.86
539 600 5.963176 ATGCCATCAATTGCACGATATAA 57.037 34.783 0.00 0.00 40.88 0.98
541 602 5.701855 TGCCATCAATTGCACGATATAATG 58.298 37.500 0.00 0.00 31.31 1.90
542 603 5.241285 TGCCATCAATTGCACGATATAATGT 59.759 36.000 0.00 0.00 31.31 2.71
544 605 6.963242 GCCATCAATTGCACGATATAATGTAG 59.037 38.462 0.00 0.00 0.00 2.74
545 606 7.148423 GCCATCAATTGCACGATATAATGTAGA 60.148 37.037 0.00 0.00 0.00 2.59
580 641 4.880426 ACCGCCCGATCCCCATCT 62.880 66.667 0.00 0.00 0.00 2.90
582 643 2.650116 CCGCCCGATCCCCATCTAG 61.650 68.421 0.00 0.00 0.00 2.43
606 672 1.375523 GGCGGTGTGTTCGGATCTT 60.376 57.895 0.00 0.00 0.00 2.40
614 680 5.504337 CGGTGTGTTCGGATCTTTTACAAAA 60.504 40.000 0.00 0.00 0.00 2.44
636 702 3.132863 GGTGTAGTTCGCCGAATGT 57.867 52.632 1.55 0.00 36.95 2.71
637 703 2.282701 GGTGTAGTTCGCCGAATGTA 57.717 50.000 1.55 0.00 36.95 2.29
726 792 1.962100 TGTGCATGATGCTTGGTTGAA 59.038 42.857 19.19 0.00 45.31 2.69
727 793 2.288334 TGTGCATGATGCTTGGTTGAAC 60.288 45.455 19.19 6.16 45.31 3.18
731 797 3.618019 GCATGATGCTTGGTTGAACCATT 60.618 43.478 19.03 3.64 41.24 3.16
740 806 4.555348 TGGTTGAACCATTTACGTTGTC 57.445 40.909 14.05 0.00 44.79 3.18
742 808 3.315749 GGTTGAACCATTTACGTTGTCCA 59.684 43.478 9.98 0.00 38.42 4.02
744 810 5.181622 GGTTGAACCATTTACGTTGTCCATA 59.818 40.000 9.98 0.00 38.42 2.74
745 811 6.127842 GGTTGAACCATTTACGTTGTCCATAT 60.128 38.462 9.98 0.00 38.42 1.78
746 812 6.429791 TGAACCATTTACGTTGTCCATATG 57.570 37.500 0.00 0.00 0.00 1.78
747 813 5.355630 TGAACCATTTACGTTGTCCATATGG 59.644 40.000 16.25 16.25 37.62 2.74
749 815 5.258051 ACCATTTACGTTGTCCATATGGTT 58.742 37.500 21.28 3.34 40.90 3.67
750 816 5.355910 ACCATTTACGTTGTCCATATGGTTC 59.644 40.000 21.28 15.35 40.90 3.62
751 817 5.220970 CCATTTACGTTGTCCATATGGTTCC 60.221 44.000 21.28 11.03 36.34 3.62
752 818 4.829872 TTACGTTGTCCATATGGTTCCT 57.170 40.909 21.28 3.59 36.34 3.36
753 819 2.985896 ACGTTGTCCATATGGTTCCTG 58.014 47.619 21.28 12.03 36.34 3.86
754 820 2.569853 ACGTTGTCCATATGGTTCCTGA 59.430 45.455 21.28 0.00 36.34 3.86
755 821 2.936498 CGTTGTCCATATGGTTCCTGAC 59.064 50.000 21.28 11.37 36.34 3.51
764 830 3.109847 GGTTCCTGACCTTTGTGCA 57.890 52.632 0.00 0.00 45.55 4.57
765 831 1.620822 GGTTCCTGACCTTTGTGCAT 58.379 50.000 0.00 0.00 45.55 3.96
774 840 1.440850 CTTTGTGCATGCCGTGACG 60.441 57.895 16.68 0.00 0.00 4.35
778 844 1.226101 GTGCATGCCGTGACGATTG 60.226 57.895 16.68 1.78 0.00 2.67
780 846 2.021793 CATGCCGTGACGATTGCG 59.978 61.111 6.54 0.00 44.79 4.85
793 859 4.893424 ACGATTGCGGCAAAGTATAATT 57.107 36.364 20.48 0.00 43.17 1.40
794 860 5.994887 ACGATTGCGGCAAAGTATAATTA 57.005 34.783 20.48 0.00 43.17 1.40
795 861 5.744490 ACGATTGCGGCAAAGTATAATTAC 58.256 37.500 20.48 1.25 43.17 1.89
796 862 4.838642 CGATTGCGGCAAAGTATAATTACG 59.161 41.667 20.48 8.61 33.32 3.18
797 863 5.557514 CGATTGCGGCAAAGTATAATTACGT 60.558 40.000 20.48 0.00 33.32 3.57
798 864 4.782252 TGCGGCAAAGTATAATTACGTC 57.218 40.909 0.00 0.00 33.32 4.34
799 865 3.243410 TGCGGCAAAGTATAATTACGTCG 59.757 43.478 0.00 5.27 33.32 5.12
800 866 3.362304 GCGGCAAAGTATAATTACGTCGG 60.362 47.826 10.11 0.00 33.32 4.79
801 867 3.798337 CGGCAAAGTATAATTACGTCGGT 59.202 43.478 0.00 0.00 33.32 4.69
802 868 4.268405 CGGCAAAGTATAATTACGTCGGTT 59.732 41.667 0.00 0.00 33.32 4.44
803 869 5.495502 GGCAAAGTATAATTACGTCGGTTG 58.504 41.667 0.00 0.00 33.32 3.77
804 870 4.959757 GCAAAGTATAATTACGTCGGTTGC 59.040 41.667 0.00 0.00 33.32 4.17
805 871 5.446206 GCAAAGTATAATTACGTCGGTTGCA 60.446 40.000 0.00 0.00 33.32 4.08
806 872 5.707411 AAGTATAATTACGTCGGTTGCAC 57.293 39.130 0.00 0.00 33.32 4.57
807 873 4.746729 AGTATAATTACGTCGGTTGCACA 58.253 39.130 0.00 0.00 33.32 4.57
808 874 5.170021 AGTATAATTACGTCGGTTGCACAA 58.830 37.500 0.00 0.00 33.32 3.33
809 875 2.961522 AATTACGTCGGTTGCACAAG 57.038 45.000 0.00 0.00 0.00 3.16
810 876 0.515564 ATTACGTCGGTTGCACAAGC 59.484 50.000 0.00 2.51 42.57 4.01
816 882 2.904866 GGTTGCACAAGCGTGGGA 60.905 61.111 5.91 0.00 46.23 4.37
817 883 2.331451 GTTGCACAAGCGTGGGAC 59.669 61.111 5.91 0.00 46.23 4.46
818 884 3.276091 TTGCACAAGCGTGGGACG 61.276 61.111 5.91 0.00 46.23 4.79
819 885 3.741830 TTGCACAAGCGTGGGACGA 62.742 57.895 5.91 0.00 46.05 4.20
820 886 2.970324 GCACAAGCGTGGGACGAA 60.970 61.111 5.91 0.00 46.05 3.85
821 887 2.954753 GCACAAGCGTGGGACGAAG 61.955 63.158 5.91 0.00 46.05 3.79
822 888 2.665185 ACAAGCGTGGGACGAAGC 60.665 61.111 4.26 0.00 46.05 3.86
823 889 2.664851 CAAGCGTGGGACGAAGCA 60.665 61.111 0.00 0.00 46.05 3.91
824 890 2.110213 AAGCGTGGGACGAAGCAA 59.890 55.556 0.00 0.00 46.05 3.91
825 891 1.961277 AAGCGTGGGACGAAGCAAG 60.961 57.895 0.00 0.00 46.05 4.01
866 932 1.561542 GAGGGAGGAAGCAAGGAATCA 59.438 52.381 0.00 0.00 0.00 2.57
891 957 1.092921 GTGTCGGGCACAACTTGTCA 61.093 55.000 8.05 0.00 46.91 3.58
912 979 5.509622 GTCATAAAAGCTTCTTCATTGACGC 59.490 40.000 0.00 0.00 0.00 5.19
917 984 1.004504 GCTTCTTCATTGACGCGATCC 60.005 52.381 15.93 1.42 0.00 3.36
929 996 1.445095 GCGATCCATCAGCTCAGGT 59.555 57.895 0.00 0.00 0.00 4.00
930 997 0.599728 GCGATCCATCAGCTCAGGTC 60.600 60.000 0.00 0.00 0.00 3.85
931 998 0.318529 CGATCCATCAGCTCAGGTCG 60.319 60.000 0.00 0.00 0.00 4.79
932 999 1.035923 GATCCATCAGCTCAGGTCGA 58.964 55.000 0.00 0.00 0.00 4.20
933 1000 1.617850 GATCCATCAGCTCAGGTCGAT 59.382 52.381 0.00 0.00 0.00 3.59
934 1001 1.035923 TCCATCAGCTCAGGTCGATC 58.964 55.000 0.00 0.00 0.00 3.69
935 1002 1.039068 CCATCAGCTCAGGTCGATCT 58.961 55.000 0.00 0.00 0.00 2.75
936 1003 1.000385 CCATCAGCTCAGGTCGATCTC 60.000 57.143 0.00 0.00 0.00 2.75
937 1004 1.000385 CATCAGCTCAGGTCGATCTCC 60.000 57.143 0.00 0.00 0.00 3.71
938 1005 0.034089 TCAGCTCAGGTCGATCTCCA 60.034 55.000 0.00 0.00 0.00 3.86
942 1018 1.313772 CTCAGGTCGATCTCCACGAT 58.686 55.000 0.00 0.00 41.62 3.73
968 1044 1.864669 AGCAGAGAAGAGGAAGGAGG 58.135 55.000 0.00 0.00 0.00 4.30
975 1051 2.107366 GAAGAGGAAGGAGGGAGTGAG 58.893 57.143 0.00 0.00 0.00 3.51
989 1070 3.117813 GGGAGTGAGGAGTAGAAGCTAGA 60.118 52.174 0.00 0.00 0.00 2.43
1203 1299 2.746277 GCCACAAGGAACGCCGAT 60.746 61.111 0.00 0.00 39.96 4.18
1263 1359 2.646175 GGACGTGGTGGAGCTGCTA 61.646 63.158 6.82 0.00 0.00 3.49
1264 1360 1.446272 GACGTGGTGGAGCTGCTAC 60.446 63.158 4.51 4.51 0.00 3.58
1500 1694 3.692406 GAGGGCCTCACCGACGTT 61.692 66.667 28.55 0.00 40.62 3.99
1513 1707 0.948623 CGACGTTGTGGCCAAGATCA 60.949 55.000 7.24 0.00 0.00 2.92
1516 1710 0.374758 CGTTGTGGCCAAGATCATCG 59.625 55.000 7.24 8.65 0.00 3.84
1548 1742 0.761323 TCCACGAGAGGTTTGTCCCA 60.761 55.000 0.00 0.00 36.75 4.37
1551 1745 1.276421 CACGAGAGGTTTGTCCCATCT 59.724 52.381 0.00 0.00 36.75 2.90
1560 1754 3.012518 GTTTGTCCCATCTGACTCCATG 58.987 50.000 0.00 0.00 36.21 3.66
1564 1758 0.835276 CCCATCTGACTCCATGAGCA 59.165 55.000 0.00 0.00 32.04 4.26
1573 1767 4.790962 CCATGAGCAGCACCGCCT 62.791 66.667 0.00 0.00 0.00 5.52
1621 1815 7.168804 GCCACATCCGTAAGTAAATTACTACTC 59.831 40.741 6.04 0.07 41.46 2.59
1625 1819 7.573968 TCCGTAAGTAAATTACTACTCCCTC 57.426 40.000 6.04 0.00 41.46 4.30
1626 1820 7.349598 TCCGTAAGTAAATTACTACTCCCTCT 58.650 38.462 6.04 0.00 41.46 3.69
1627 1821 8.494433 TCCGTAAGTAAATTACTACTCCCTCTA 58.506 37.037 6.04 0.00 41.46 2.43
1628 1822 9.125026 CCGTAAGTAAATTACTACTCCCTCTAA 57.875 37.037 6.04 0.00 41.46 2.10
1666 2150 9.838339 AGTTAGGTCATATATTTTGGAACAGAG 57.162 33.333 0.00 0.00 42.39 3.35
1680 2288 1.222936 CAGAGAGGGCCATGTGTCC 59.777 63.158 6.18 0.00 0.00 4.02
1712 2322 3.567530 TGTCCTGTGTCGTGTAATTACG 58.432 45.455 10.92 2.77 44.98 3.18
1721 2336 4.019919 TCGTGTAATTACGACTAGTGGC 57.980 45.455 10.92 0.00 46.94 5.01
1839 2461 2.556287 GGCGCAGAAGAACAACGG 59.444 61.111 10.83 0.00 0.00 4.44
1844 2466 2.110213 AGAAGAACAACGGCCGCA 59.890 55.556 28.58 0.00 0.00 5.69
1871 2493 1.004560 CTGCTGCTGAACCGGAAGA 60.005 57.895 9.46 0.00 0.00 2.87
2010 3042 3.050275 GGACAGCAACGGCAGGAC 61.050 66.667 0.00 0.00 44.61 3.85
2011 3043 2.280797 GACAGCAACGGCAGGACA 60.281 61.111 0.00 0.00 44.61 4.02
2014 3046 3.946201 AGCAACGGCAGGACAGCT 61.946 61.111 0.00 0.00 44.61 4.24
2153 3185 2.167219 GCTGCGCTGTCGAGCATAA 61.167 57.895 16.05 0.00 46.62 1.90
2310 3351 0.610687 AAGCTCAAGAAGTCCGAGGG 59.389 55.000 0.00 0.00 0.00 4.30
2311 3352 0.543174 AGCTCAAGAAGTCCGAGGGT 60.543 55.000 0.00 0.00 0.00 4.34
2328 3369 0.818040 GGTTCCAGGTGCAAGAACGT 60.818 55.000 11.69 0.00 40.62 3.99
2331 3372 2.639286 CAGGTGCAAGAACGTGCC 59.361 61.111 9.80 2.48 44.26 5.01
2358 3399 3.122250 CTCCTCCCGCGTCTTACCG 62.122 68.421 4.92 0.00 0.00 4.02
2370 3411 4.178214 TTACCGGTCGCGGCGTAG 62.178 66.667 22.90 13.94 0.00 3.51
2382 3423 4.840005 GCGTAGTCAGGGCCAGGC 62.840 72.222 6.18 1.26 0.00 4.85
2534 4606 1.256376 CGGCATTCAAGATCTTCGTCG 59.744 52.381 4.57 4.25 0.00 5.12
2605 4677 2.184830 CATGTGGGCATGGCGAGAG 61.185 63.158 13.76 0.00 46.47 3.20
2617 4689 3.522731 CGAGAGCGGGAGTGGGAG 61.523 72.222 0.00 0.00 0.00 4.30
2618 4690 3.844090 GAGAGCGGGAGTGGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
2639 4711 2.743928 GCCCAGTCGAGCACAAGG 60.744 66.667 0.00 0.00 0.00 3.61
2644 4716 1.402984 CCAGTCGAGCACAAGGTCTAC 60.403 57.143 0.00 0.00 40.07 2.59
2652 4724 1.674221 GCACAAGGTCTACCAGCTCAG 60.674 57.143 1.26 0.00 38.89 3.35
2653 4725 0.610687 ACAAGGTCTACCAGCTCAGC 59.389 55.000 1.26 0.00 38.89 4.26
2704 4776 1.734465 CTCACAAATGTCGCCTTCCTC 59.266 52.381 0.00 0.00 0.00 3.71
2713 4785 2.899339 GCCTTCCTCGCCATGCTC 60.899 66.667 0.00 0.00 0.00 4.26
2715 4787 3.267860 CTTCCTCGCCATGCTCGC 61.268 66.667 1.35 0.00 0.00 5.03
2728 4800 1.880340 GCTCGCCTCCTTCATGACG 60.880 63.158 0.00 0.00 0.00 4.35
2748 4820 1.693083 GCCGTCTACATCACCGTTGC 61.693 60.000 0.00 0.00 0.00 4.17
2846 4918 7.346471 CCTTTGGGAAGAGATGTAGGATTTTA 58.654 38.462 0.00 0.00 34.71 1.52
2856 4928 8.744652 AGAGATGTAGGATTTTACGGAGATATG 58.255 37.037 0.00 0.00 0.00 1.78
2875 4947 6.831868 AGATATGTTTACAATACCCAACACCC 59.168 38.462 0.00 0.00 32.10 4.61
2878 4950 5.148502 TGTTTACAATACCCAACACCCAAT 58.851 37.500 0.00 0.00 0.00 3.16
2886 4958 2.359478 AACACCCAATCGTCCGGC 60.359 61.111 0.00 0.00 0.00 6.13
2972 5044 7.584987 ACTTTAGTTGACAAACATGATAGTGC 58.415 34.615 0.00 0.00 38.88 4.40
2973 5045 6.494893 TTAGTTGACAAACATGATAGTGCC 57.505 37.500 0.00 0.00 38.88 5.01
2974 5046 4.655963 AGTTGACAAACATGATAGTGCCT 58.344 39.130 0.00 0.00 38.88 4.75
2975 5047 5.804639 AGTTGACAAACATGATAGTGCCTA 58.195 37.500 0.00 0.00 38.88 3.93
2976 5048 6.237901 AGTTGACAAACATGATAGTGCCTAA 58.762 36.000 0.00 0.00 38.88 2.69
3013 5085 0.749649 AACAGTTTGCAATGCCGGAA 59.250 45.000 5.05 0.00 0.00 4.30
3016 5088 0.171007 AGTTTGCAATGCCGGAATCG 59.829 50.000 5.05 0.00 0.00 3.34
3017 5089 1.153862 TTTGCAATGCCGGAATCGC 60.154 52.632 5.05 0.00 34.56 4.58
3061 5141 0.178068 ATAAAGCATGCCCGAGTCGT 59.822 50.000 15.66 0.00 0.00 4.34
3063 5143 0.889186 AAAGCATGCCCGAGTCGTTT 60.889 50.000 15.66 2.53 0.00 3.60
3072 5152 1.664649 CGAGTCGTTTCAGCAGGCA 60.665 57.895 3.82 0.00 0.00 4.75
3074 5154 0.880278 GAGTCGTTTCAGCAGGCACA 60.880 55.000 0.00 0.00 0.00 4.57
3088 5172 4.831155 AGCAGGCACATTATATTGCATCTT 59.169 37.500 0.00 0.00 40.75 2.40
3090 5174 5.404366 GCAGGCACATTATATTGCATCTTTG 59.596 40.000 0.00 0.00 40.75 2.77
3144 5237 4.435518 CCGATAGTACAAATGTGCACACAC 60.436 45.833 24.37 14.50 45.05 3.82
3168 5262 6.311445 ACAGACTGCTTCTACGATACAAAATG 59.689 38.462 1.25 0.00 31.12 2.32
3169 5263 6.531594 CAGACTGCTTCTACGATACAAAATGA 59.468 38.462 0.00 0.00 31.12 2.57
3254 5365 0.904865 TCTGCCTCGGTGATGTCCTT 60.905 55.000 0.00 0.00 0.00 3.36
3304 5415 2.504244 GCTCGTCGTTGGAGTCCG 60.504 66.667 4.30 0.00 34.00 4.79
3317 5428 2.181021 GTCCGAGGACGACGCATT 59.819 61.111 6.51 0.00 42.66 3.56
3420 5559 1.490574 CCCTCCTCTCCGTGAAGAAT 58.509 55.000 0.00 0.00 0.00 2.40
3551 5693 2.636412 CCTCGTCGGTGAGAAGCCA 61.636 63.158 6.42 0.00 38.28 4.75
3744 5886 3.151710 TAGGTGCCGGACGGATGG 61.152 66.667 15.99 0.00 37.50 3.51
3823 5965 3.371063 GGCGTGTCGGTGGAGAGA 61.371 66.667 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.503741 ACACGCTGCAAACTTGATAATT 57.496 36.364 0.00 0.00 0.00 1.40
1 2 5.621197 TTACACGCTGCAAACTTGATAAT 57.379 34.783 0.00 0.00 0.00 1.28
3 4 5.621197 ATTTACACGCTGCAAACTTGATA 57.379 34.783 0.00 0.00 0.00 2.15
4 5 3.980646 TTTACACGCTGCAAACTTGAT 57.019 38.095 0.00 0.00 0.00 2.57
14 71 8.712363 ACATATAGCAAGATAATTTACACGCTG 58.288 33.333 0.00 0.00 0.00 5.18
117 174 5.950758 TTACACGCCACAAACTTGATAAT 57.049 34.783 0.00 0.00 0.00 1.28
195 252 3.244911 ACCTACATGAACTTTGACCAGGG 60.245 47.826 0.00 0.00 0.00 4.45
210 268 5.889853 TGTATCCGAGACTTTGTACCTACAT 59.110 40.000 0.00 0.00 35.89 2.29
250 308 4.756084 TTTTGCACCAAACAACCAAAAG 57.244 36.364 0.00 0.00 32.79 2.27
377 438 4.031426 CCGACAAACTCAGCGAACTATAAC 59.969 45.833 0.00 0.00 0.00 1.89
430 491 9.952030 AGTGGAACAAAAATAAAAAGAAAGGAA 57.048 25.926 0.00 0.00 44.16 3.36
462 523 4.033358 CCTAATTAATGGATCGCTCGCATC 59.967 45.833 0.00 0.00 0.00 3.91
520 581 8.255394 TCTACATTATATCGTGCAATTGATGG 57.745 34.615 10.34 0.00 0.00 3.51
538 599 4.142381 GCGCTTTTCTCCCATTTCTACATT 60.142 41.667 0.00 0.00 0.00 2.71
539 600 3.378427 GCGCTTTTCTCCCATTTCTACAT 59.622 43.478 0.00 0.00 0.00 2.29
541 602 2.223044 CGCGCTTTTCTCCCATTTCTAC 60.223 50.000 5.56 0.00 0.00 2.59
542 603 2.006888 CGCGCTTTTCTCCCATTTCTA 58.993 47.619 5.56 0.00 0.00 2.10
544 605 0.802494 TCGCGCTTTTCTCCCATTTC 59.198 50.000 5.56 0.00 0.00 2.17
545 606 0.521735 GTCGCGCTTTTCTCCCATTT 59.478 50.000 5.56 0.00 0.00 2.32
548 609 2.358247 GGTCGCGCTTTTCTCCCA 60.358 61.111 5.56 0.00 0.00 4.37
568 629 0.965866 TAGCGCTAGATGGGGATCGG 60.966 60.000 14.45 0.00 0.00 4.18
571 632 1.261238 GCCTAGCGCTAGATGGGGAT 61.261 60.000 39.42 4.75 34.74 3.85
614 680 2.243602 TTCGGCGAACTACACCTTTT 57.756 45.000 19.83 0.00 0.00 2.27
617 683 0.606604 ACATTCGGCGAACTACACCT 59.393 50.000 26.22 3.85 0.00 4.00
618 684 2.190981 CTACATTCGGCGAACTACACC 58.809 52.381 26.22 0.00 0.00 4.16
619 685 1.587034 GCTACATTCGGCGAACTACAC 59.413 52.381 26.22 11.08 0.00 2.90
621 687 2.205307 AGCTACATTCGGCGAACTAC 57.795 50.000 26.22 12.63 0.00 2.73
623 689 2.953466 TAAGCTACATTCGGCGAACT 57.047 45.000 26.22 14.14 0.00 3.01
627 693 5.006358 AGTGTAAATTAAGCTACATTCGGCG 59.994 40.000 0.00 0.00 31.05 6.46
628 694 6.359480 AGTGTAAATTAAGCTACATTCGGC 57.641 37.500 0.00 0.00 31.05 5.54
684 750 7.710273 CACACGTGCACTAAAATTAAAATGAG 58.290 34.615 17.22 0.00 0.00 2.90
726 792 4.850680 ACCATATGGACAACGTAAATGGT 58.149 39.130 28.77 0.00 38.94 3.55
727 793 5.220970 GGAACCATATGGACAACGTAAATGG 60.221 44.000 28.77 0.00 38.94 3.16
731 797 4.223255 TCAGGAACCATATGGACAACGTAA 59.777 41.667 28.77 3.82 38.94 3.18
747 813 1.336240 GCATGCACAAAGGTCAGGAAC 60.336 52.381 14.21 0.00 0.00 3.62
749 815 0.895100 GGCATGCACAAAGGTCAGGA 60.895 55.000 21.36 0.00 0.00 3.86
750 816 1.588082 GGCATGCACAAAGGTCAGG 59.412 57.895 21.36 0.00 0.00 3.86
751 817 1.210931 CGGCATGCACAAAGGTCAG 59.789 57.895 21.36 0.00 0.00 3.51
752 818 1.528076 ACGGCATGCACAAAGGTCA 60.528 52.632 21.36 0.00 0.00 4.02
753 819 1.081242 CACGGCATGCACAAAGGTC 60.081 57.895 21.36 0.00 0.00 3.85
754 820 1.528076 TCACGGCATGCACAAAGGT 60.528 52.632 21.36 4.05 0.00 3.50
755 821 1.081242 GTCACGGCATGCACAAAGG 60.081 57.895 21.36 3.39 0.00 3.11
756 822 1.440850 CGTCACGGCATGCACAAAG 60.441 57.895 21.36 7.38 0.00 2.77
757 823 1.233950 ATCGTCACGGCATGCACAAA 61.234 50.000 21.36 0.00 0.00 2.83
758 824 1.233950 AATCGTCACGGCATGCACAA 61.234 50.000 21.36 0.00 0.00 3.33
759 825 1.670730 AATCGTCACGGCATGCACA 60.671 52.632 21.36 0.00 0.00 4.57
760 826 1.226101 CAATCGTCACGGCATGCAC 60.226 57.895 21.36 7.98 0.00 4.57
761 827 3.037992 GCAATCGTCACGGCATGCA 62.038 57.895 21.36 0.00 33.25 3.96
762 828 2.277501 GCAATCGTCACGGCATGC 60.278 61.111 9.90 9.90 0.00 4.06
763 829 2.021793 CGCAATCGTCACGGCATG 59.978 61.111 0.00 0.00 0.00 4.06
764 830 3.195002 CCGCAATCGTCACGGCAT 61.195 61.111 0.00 0.00 40.55 4.40
774 840 5.744490 ACGTAATTATACTTTGCCGCAATC 58.256 37.500 6.64 0.00 0.00 2.67
778 844 3.362304 CCGACGTAATTATACTTTGCCGC 60.362 47.826 0.00 0.00 0.00 6.53
780 846 5.495502 CAACCGACGTAATTATACTTTGCC 58.504 41.667 0.00 0.00 0.00 4.52
787 853 4.033129 GCTTGTGCAACCGACGTAATTATA 59.967 41.667 0.00 0.00 39.41 0.98
789 855 2.158058 GCTTGTGCAACCGACGTAATTA 59.842 45.455 0.00 0.00 39.41 1.40
790 856 1.069500 GCTTGTGCAACCGACGTAATT 60.069 47.619 0.00 0.00 39.41 1.40
791 857 0.515564 GCTTGTGCAACCGACGTAAT 59.484 50.000 0.00 0.00 39.41 1.89
792 858 1.823260 CGCTTGTGCAACCGACGTAA 61.823 55.000 0.00 0.00 39.64 3.18
793 859 2.304401 CGCTTGTGCAACCGACGTA 61.304 57.895 0.00 0.00 39.64 3.57
794 860 3.636043 CGCTTGTGCAACCGACGT 61.636 61.111 0.00 0.00 39.64 4.34
795 861 3.636043 ACGCTTGTGCAACCGACG 61.636 61.111 6.63 0.00 39.64 5.12
796 862 2.052237 CACGCTTGTGCAACCGAC 60.052 61.111 6.63 0.00 39.64 4.79
797 863 3.276091 CCACGCTTGTGCAACCGA 61.276 61.111 6.63 0.00 42.46 4.69
798 864 4.326766 CCCACGCTTGTGCAACCG 62.327 66.667 0.00 0.00 42.46 4.44
799 865 2.904866 TCCCACGCTTGTGCAACC 60.905 61.111 0.00 0.00 42.46 3.77
800 866 2.331451 GTCCCACGCTTGTGCAAC 59.669 61.111 0.00 0.00 42.46 4.17
801 867 3.276091 CGTCCCACGCTTGTGCAA 61.276 61.111 0.00 0.00 42.46 4.08
802 868 3.741830 TTCGTCCCACGCTTGTGCA 62.742 57.895 0.00 0.00 42.21 4.57
803 869 2.954753 CTTCGTCCCACGCTTGTGC 61.955 63.158 0.00 0.00 42.21 4.57
804 870 2.954753 GCTTCGTCCCACGCTTGTG 61.955 63.158 0.00 0.00 42.21 3.33
805 871 2.665185 GCTTCGTCCCACGCTTGT 60.665 61.111 0.00 0.00 42.21 3.16
806 872 2.175184 CTTGCTTCGTCCCACGCTTG 62.175 60.000 0.00 0.00 42.21 4.01
807 873 1.961277 CTTGCTTCGTCCCACGCTT 60.961 57.895 0.00 0.00 42.21 4.68
808 874 2.357517 CTTGCTTCGTCCCACGCT 60.358 61.111 0.00 0.00 42.21 5.07
809 875 3.423154 CCTTGCTTCGTCCCACGC 61.423 66.667 0.00 0.00 42.21 5.34
810 876 0.673644 ATTCCTTGCTTCGTCCCACG 60.674 55.000 0.00 0.00 44.19 4.94
811 877 2.396590 TATTCCTTGCTTCGTCCCAC 57.603 50.000 0.00 0.00 0.00 4.61
812 878 3.426787 TTTATTCCTTGCTTCGTCCCA 57.573 42.857 0.00 0.00 0.00 4.37
813 879 3.945285 TGATTTATTCCTTGCTTCGTCCC 59.055 43.478 0.00 0.00 0.00 4.46
814 880 5.560966 TTGATTTATTCCTTGCTTCGTCC 57.439 39.130 0.00 0.00 0.00 4.79
815 881 6.693113 GGAATTGATTTATTCCTTGCTTCGTC 59.307 38.462 7.89 0.00 46.62 4.20
816 882 6.564328 GGAATTGATTTATTCCTTGCTTCGT 58.436 36.000 7.89 0.00 46.62 3.85
846 912 1.561542 TGATTCCTTGCTTCCTCCCTC 59.438 52.381 0.00 0.00 0.00 4.30
848 914 2.373224 CTTGATTCCTTGCTTCCTCCC 58.627 52.381 0.00 0.00 0.00 4.30
891 957 4.391830 TCGCGTCAATGAAGAAGCTTTTAT 59.608 37.500 5.77 0.00 40.22 1.40
912 979 0.318529 CGACCTGAGCTGATGGATCG 60.319 60.000 0.00 0.00 32.20 3.69
917 984 1.000385 GGAGATCGACCTGAGCTGATG 60.000 57.143 0.00 0.00 45.13 3.07
932 999 2.363680 CTGCTACCTTGATCGTGGAGAT 59.636 50.000 10.30 0.00 43.51 2.75
933 1000 1.751351 CTGCTACCTTGATCGTGGAGA 59.249 52.381 10.30 0.00 0.00 3.71
934 1001 1.751351 TCTGCTACCTTGATCGTGGAG 59.249 52.381 10.30 0.00 0.00 3.86
935 1002 1.751351 CTCTGCTACCTTGATCGTGGA 59.249 52.381 10.30 0.00 0.00 4.02
936 1003 1.751351 TCTCTGCTACCTTGATCGTGG 59.249 52.381 2.66 2.66 0.00 4.94
937 1004 3.129462 TCTTCTCTGCTACCTTGATCGTG 59.871 47.826 0.00 0.00 0.00 4.35
938 1005 3.357203 TCTTCTCTGCTACCTTGATCGT 58.643 45.455 0.00 0.00 0.00 3.73
942 1018 3.458044 TCCTCTTCTCTGCTACCTTGA 57.542 47.619 0.00 0.00 0.00 3.02
944 1020 3.103742 CCTTCCTCTTCTCTGCTACCTT 58.896 50.000 0.00 0.00 0.00 3.50
968 1044 4.159244 TCTAGCTTCTACTCCTCACTCC 57.841 50.000 0.00 0.00 0.00 3.85
975 1051 5.475564 CCTGTTCCTATCTAGCTTCTACTCC 59.524 48.000 0.00 0.00 0.00 3.85
989 1070 2.412591 CTGGGTCCATCCTGTTCCTAT 58.587 52.381 0.00 0.00 36.25 2.57
1071 1167 3.140814 GAACCAAGGATGCCGGGC 61.141 66.667 13.32 13.32 0.00 6.13
1160 1256 1.592400 CTTGTAGTCCGCACCGAGGA 61.592 60.000 0.00 0.00 34.99 3.71
1169 1265 2.161486 GCGAGCAGCTTGTAGTCCG 61.161 63.158 11.56 2.30 44.04 4.79
1236 1332 1.477685 CCACCACGTCCACCTTACCT 61.478 60.000 0.00 0.00 0.00 3.08
1290 1386 3.768922 GAGTCCTGCGGCTGCTCT 61.769 66.667 20.27 11.50 43.34 4.09
1329 1500 1.588082 CTTGTTGGCCATGAGCACC 59.412 57.895 6.09 0.00 46.50 5.01
1330 1501 1.588082 CCTTGTTGGCCATGAGCAC 59.412 57.895 6.09 0.74 46.50 4.40
1368 1539 4.680237 CCGTGCTTCACCGCCTCA 62.680 66.667 0.00 0.00 0.00 3.86
1492 1686 2.391724 ATCTTGGCCACAACGTCGGT 62.392 55.000 3.88 0.00 32.14 4.69
1500 1694 4.961637 CCGATGATCTTGGCCACA 57.038 55.556 3.88 0.00 0.00 4.17
1548 1742 1.134461 GTGCTGCTCATGGAGTCAGAT 60.134 52.381 16.42 0.00 36.59 2.90
1551 1745 1.297689 GGTGCTGCTCATGGAGTCA 59.702 57.895 0.00 0.00 33.91 3.41
1644 2128 7.420680 CCCTCTCTGTTCCAAAATATATGACCT 60.421 40.741 0.00 0.00 0.00 3.85
1651 2135 3.269381 TGGCCCTCTCTGTTCCAAAATAT 59.731 43.478 0.00 0.00 0.00 1.28
1653 2137 1.428912 TGGCCCTCTCTGTTCCAAAAT 59.571 47.619 0.00 0.00 0.00 1.82
1656 2140 0.329261 CATGGCCCTCTCTGTTCCAA 59.671 55.000 0.00 0.00 0.00 3.53
1657 2141 0.842030 ACATGGCCCTCTCTGTTCCA 60.842 55.000 0.00 0.00 0.00 3.53
1658 2142 0.393537 CACATGGCCCTCTCTGTTCC 60.394 60.000 0.00 0.00 0.00 3.62
1659 2143 0.326264 ACACATGGCCCTCTCTGTTC 59.674 55.000 0.00 0.00 0.00 3.18
1660 2144 0.326264 GACACATGGCCCTCTCTGTT 59.674 55.000 0.00 0.00 0.00 3.16
1661 2145 1.557269 GGACACATGGCCCTCTCTGT 61.557 60.000 0.00 0.00 37.19 3.41
1662 2146 1.222936 GGACACATGGCCCTCTCTG 59.777 63.158 0.00 0.00 37.19 3.35
1663 2147 2.362369 CGGACACATGGCCCTCTCT 61.362 63.158 0.00 0.00 41.34 3.10
1664 2148 2.187946 CGGACACATGGCCCTCTC 59.812 66.667 0.00 0.00 41.34 3.20
1666 2150 3.682292 GACCGGACACATGGCCCTC 62.682 68.421 9.46 0.00 41.34 4.30
1680 2288 0.390340 CACAGGACATGACAGGACCG 60.390 60.000 0.00 1.81 0.00 4.79
1712 2322 2.202623 CGTCGCCAGCCACTAGTC 60.203 66.667 0.00 0.00 0.00 2.59
1771 2393 2.895680 GTCAGCCCGATCTGCTCA 59.104 61.111 3.83 0.00 36.81 4.26
1796 2418 2.733218 CAGCGCGTTGTTCTCGGA 60.733 61.111 15.40 0.00 0.00 4.55
1797 2419 4.430423 GCAGCGCGTTGTTCTCGG 62.430 66.667 23.96 0.00 0.00 4.63
1839 2461 4.487412 GCAGCTTCACCATGCGGC 62.487 66.667 0.00 0.00 42.23 6.53
1871 2493 1.609783 GCTTGTAGGCCAGGTCCAT 59.390 57.895 5.01 0.00 0.00 3.41
2071 3103 4.144727 ATCTCCTCGGGGCGGACT 62.145 66.667 0.00 0.00 0.00 3.85
2147 3179 2.464459 GCAGCGCCGACTTTATGCT 61.464 57.895 2.29 0.00 36.05 3.79
2153 3185 4.749310 CAGGAGCAGCGCCGACTT 62.749 66.667 9.85 0.00 0.00 3.01
2310 3351 0.307760 CACGTTCTTGCACCTGGAAC 59.692 55.000 0.00 9.56 36.83 3.62
2311 3352 1.444119 GCACGTTCTTGCACCTGGAA 61.444 55.000 0.00 0.00 42.49 3.53
2338 3379 3.145551 TAAGACGCGGGAGGAGGC 61.146 66.667 12.47 0.00 0.00 4.70
2341 3382 3.136123 CGGTAAGACGCGGGAGGA 61.136 66.667 12.47 0.00 0.00 3.71
2343 3384 3.407046 GACCGGTAAGACGCGGGAG 62.407 68.421 7.34 0.00 36.63 4.30
2344 3385 3.443045 GACCGGTAAGACGCGGGA 61.443 66.667 7.34 0.00 36.63 5.14
2345 3386 4.842091 CGACCGGTAAGACGCGGG 62.842 72.222 7.34 1.69 36.63 6.13
2358 3399 4.849329 CCTGACTACGCCGCGACC 62.849 72.222 21.79 5.70 0.00 4.79
2412 3468 2.753009 GATCAGTGTGGCCACCAGCA 62.753 60.000 32.62 14.86 46.50 4.41
2518 4590 3.056821 TGGTGACGACGAAGATCTTGAAT 60.057 43.478 14.00 0.00 0.00 2.57
2534 4606 1.522806 TGGCGACAGTGTTGGTGAC 60.523 57.895 12.54 0.00 35.01 3.67
2615 4687 4.200283 CTCGACTGGGCTCCGCTC 62.200 72.222 0.00 0.00 0.00 5.03
2618 4690 4.803426 GTGCTCGACTGGGCTCCG 62.803 72.222 0.00 0.00 0.00 4.63
2619 4691 3.240134 TTGTGCTCGACTGGGCTCC 62.240 63.158 0.00 0.00 0.00 4.70
2620 4692 1.739562 CTTGTGCTCGACTGGGCTC 60.740 63.158 0.00 0.00 0.00 4.70
2622 4694 2.743928 CCTTGTGCTCGACTGGGC 60.744 66.667 0.00 0.00 0.00 5.36
2624 4696 0.888619 TAGACCTTGTGCTCGACTGG 59.111 55.000 0.00 0.00 0.00 4.00
2626 4698 0.889306 GGTAGACCTTGTGCTCGACT 59.111 55.000 0.00 0.00 0.00 4.18
2693 4765 2.892425 CATGGCGAGGAAGGCGAC 60.892 66.667 0.00 0.00 39.82 5.19
2704 4776 4.845580 AAGGAGGCGAGCATGGCG 62.846 66.667 0.00 0.00 42.57 5.69
2713 4785 2.892425 GCCGTCATGAAGGAGGCG 60.892 66.667 29.13 12.53 38.28 5.52
2715 4787 2.202932 CGGCCGTCATGAAGGAGG 60.203 66.667 29.13 16.17 31.21 4.30
2728 4800 1.082117 CAACGGTGATGTAGACGGCC 61.082 60.000 0.00 0.00 0.00 6.13
2846 4918 6.488769 TGGGTATTGTAAACATATCTCCGT 57.511 37.500 0.00 0.00 0.00 4.69
2856 4928 5.620429 CGATTGGGTGTTGGGTATTGTAAAC 60.620 44.000 0.00 0.00 0.00 2.01
2875 4947 1.963855 TGTTGGTGCCGGACGATTG 60.964 57.895 5.05 0.00 0.00 2.67
2878 4950 3.171828 ATGTGTTGGTGCCGGACGA 62.172 57.895 5.05 0.00 0.00 4.20
2918 4990 6.937436 AATCCTCACGTCACTAAACTTTTT 57.063 33.333 0.00 0.00 0.00 1.94
2972 5044 3.975083 TAGCGCGCCGTGTGTTAGG 62.975 63.158 30.33 0.00 0.00 2.69
2973 5045 1.619526 TTTAGCGCGCCGTGTGTTAG 61.620 55.000 30.33 0.00 0.00 2.34
2974 5046 1.220169 TTTTAGCGCGCCGTGTGTTA 61.220 50.000 30.33 8.92 0.00 2.41
2975 5047 2.049475 TTTTTAGCGCGCCGTGTGTT 62.049 50.000 30.33 10.14 0.00 3.32
2976 5048 2.535788 TTTTTAGCGCGCCGTGTGT 61.536 52.632 30.33 11.01 0.00 3.72
2995 5067 0.968405 ATTCCGGCATTGCAAACTGT 59.032 45.000 11.39 0.00 0.00 3.55
3017 5089 4.741781 CGACCGCGCAAAAGCTGG 62.742 66.667 8.75 0.00 37.04 4.85
3061 5141 4.401837 TGCAATATAATGTGCCTGCTGAAA 59.598 37.500 0.00 0.00 40.14 2.69
3063 5143 3.553904 TGCAATATAATGTGCCTGCTGA 58.446 40.909 0.00 0.00 40.14 4.26
3088 5172 6.825284 TGTGTCGAATCGTAGTTAAAACAA 57.175 33.333 1.52 0.00 0.00 2.83
3090 5174 9.962759 AAATATGTGTCGAATCGTAGTTAAAAC 57.037 29.630 1.52 0.00 0.00 2.43
3144 5237 6.531594 TCATTTTGTATCGTAGAAGCAGTCTG 59.468 38.462 0.00 0.00 43.58 3.51
3168 5262 5.763088 TCATACGAGAAGACTATGTGCATC 58.237 41.667 0.00 0.00 0.00 3.91
3169 5263 5.774498 TCATACGAGAAGACTATGTGCAT 57.226 39.130 0.00 0.00 0.00 3.96
3200 5311 7.223582 CGGAGAATGACGAGTAGTAGTAGTTTA 59.776 40.741 0.00 0.00 0.00 2.01
3254 5365 1.300481 CTATGCTCAGACGTCGGAGA 58.700 55.000 38.66 26.55 39.97 3.71
3281 5392 2.049433 CCAACGACGAGCGGTTCT 60.049 61.111 0.00 0.00 46.49 3.01
3304 5415 1.841450 CTAGGAAATGCGTCGTCCTC 58.159 55.000 13.13 0.00 41.01 3.71
3317 5428 2.309528 ATTGAACATCGCGCTAGGAA 57.690 45.000 5.56 0.00 0.00 3.36
3591 5733 2.737252 GGACATGAACTTCCAGAACGTC 59.263 50.000 0.00 0.00 0.00 4.34
3668 5810 0.039798 CGGAACCTTCGACTTCGTCA 60.040 55.000 0.00 0.00 40.80 4.35
3670 5812 0.240411 CTCGGAACCTTCGACTTCGT 59.760 55.000 0.00 0.00 40.80 3.85
3722 5864 3.066190 CGTCCGGCACCTACTCCA 61.066 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.