Multiple sequence alignment - TraesCS3D01G405300

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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 TraesCS3D01G405300 chr3D 100.000 4626 0 0 1 4626 519681049 519685674 0.000000e+00 8543.0
1 TraesCS3D01G405300 chr3D 91.689 746 13 24 1 702 384565133 384565873 0.000000e+00 989.0
2 TraesCS3D01G405300 chr3D 91.553 734 25 17 1 702 511351614 511350886 0.000000e+00 977.0
3 TraesCS3D01G405300 chr3D 90.094 747 25 22 1 708 29616307 29615571 0.000000e+00 924.0
4 TraesCS3D01G405300 chr3D 91.558 308 25 1 1096 1402 519333601 519333908 1.540000e-114 424.0
5 TraesCS3D01G405300 chr3D 87.402 127 6 4 584 702 429640093 429640217 2.240000e-28 137.0
6 TraesCS3D01G405300 chr3D 85.950 121 12 3 583 702 604635501 604635617 1.750000e-24 124.0
7 TraesCS3D01G405300 chr3A 94.089 3231 138 31 869 4072 654781856 654785060 0.000000e+00 4859.0
8 TraesCS3D01G405300 chr3A 87.264 1429 122 21 2375 3795 655085143 655086519 0.000000e+00 1576.0
9 TraesCS3D01G405300 chr3A 87.431 724 71 11 1775 2494 655083676 655084383 0.000000e+00 815.0
10 TraesCS3D01G405300 chr3A 91.919 495 20 5 4149 4626 654785058 654785549 0.000000e+00 675.0
11 TraesCS3D01G405300 chr3A 83.508 667 63 23 945 1598 655083035 655083667 3.100000e-161 579.0
12 TraesCS3D01G405300 chr3A 85.682 440 50 11 1096 1531 654357721 654358151 7.060000e-123 451.0
13 TraesCS3D01G405300 chr3A 89.216 306 29 4 1095 1398 654382611 654382914 3.380000e-101 379.0
14 TraesCS3D01G405300 chr3A 86.822 258 12 10 4221 4459 655087678 655087932 7.630000e-68 268.0
15 TraesCS3D01G405300 chr3A 95.506 89 4 0 4538 4626 655160543 655160631 4.820000e-30 143.0
16 TraesCS3D01G405300 chr3A 93.976 83 5 0 2296 2378 655084382 655084464 4.860000e-25 126.0
17 TraesCS3D01G405300 chr3B 98.107 1321 24 1 2570 3890 684266338 684267657 0.000000e+00 2300.0
18 TraesCS3D01G405300 chr3B 90.608 724 53 12 857 1573 684264964 684265679 0.000000e+00 946.0
19 TraesCS3D01G405300 chr3B 91.757 643 34 7 1640 2265 684265683 684266323 0.000000e+00 876.0
20 TraesCS3D01G405300 chr3B 89.518 477 31 12 945 1418 684248558 684249018 1.850000e-163 586.0
21 TraesCS3D01G405300 chr3B 84.821 560 57 14 3419 3953 684613818 684614374 5.270000e-149 538.0
22 TraesCS3D01G405300 chr3B 84.788 401 50 8 1122 1519 683678768 683679160 4.340000e-105 392.0
23 TraesCS3D01G405300 chr3B 84.615 416 41 13 1095 1506 683758426 683758822 4.340000e-105 392.0
24 TraesCS3D01G405300 chr3B 92.025 163 11 2 3929 4089 684267667 684267829 1.290000e-55 228.0
25 TraesCS3D01G405300 chr7D 92.808 723 25 21 1 702 538343061 538343777 0.000000e+00 1022.0
26 TraesCS3D01G405300 chr7D 91.667 744 17 20 1 703 235517253 235516514 0.000000e+00 989.0
27 TraesCS3D01G405300 chr7D 91.432 747 12 22 1 702 457145950 457146689 0.000000e+00 977.0
28 TraesCS3D01G405300 chr7D 96.154 156 4 1 703 856 33213768 33213613 2.140000e-63 254.0
29 TraesCS3D01G405300 chr7D 82.677 127 11 3 584 699 442687067 442686941 8.190000e-18 102.0
30 TraesCS3D01G405300 chr1D 91.711 748 12 14 1 702 340321814 340321071 0.000000e+00 992.0
31 TraesCS3D01G405300 chr1D 92.329 717 19 19 2 697 7515037 7514336 0.000000e+00 987.0
32 TraesCS3D01G405300 chr1D 91.059 727 31 22 1 702 389225189 389224472 0.000000e+00 952.0
33 TraesCS3D01G405300 chr1D 93.388 121 5 3 584 702 17253478 17253597 4.760000e-40 176.0
34 TraesCS3D01G405300 chr2D 91.084 729 35 14 1 703 6096318 6097042 0.000000e+00 959.0
35 TraesCS3D01G405300 chr2D 89.516 124 8 3 584 702 637835623 637835500 8.020000e-33 152.0
36 TraesCS3D01G405300 chr5D 96.265 589 10 11 1 582 45130905 45131488 0.000000e+00 955.0
37 TraesCS3D01G405300 chr5D 96.875 576 9 9 1 572 89496522 89495952 0.000000e+00 955.0
38 TraesCS3D01G405300 chr5D 96.701 576 9 10 1 572 450114386 450114955 0.000000e+00 950.0
39 TraesCS3D01G405300 chr5D 90.083 121 3 6 584 702 6297028 6296915 1.040000e-31 148.0
40 TraesCS3D01G405300 chr5D 89.256 121 8 5 584 702 544214677 544214560 3.730000e-31 147.0
41 TraesCS3D01G405300 chr4D 95.424 590 15 11 1 585 509077239 509076657 0.000000e+00 929.0
42 TraesCS3D01G405300 chr4D 89.831 59 4 2 799 856 426647705 426647762 1.790000e-09 75.0
43 TraesCS3D01G405300 chr2B 87.315 473 29 15 249 702 759984915 759984455 3.190000e-141 512.0
44 TraesCS3D01G405300 chr1B 90.909 165 13 2 703 865 480843189 480843353 2.170000e-53 220.0
45 TraesCS3D01G405300 chr4B 93.333 135 9 0 721 855 28506696 28506830 2.820000e-47 200.0
46 TraesCS3D01G405300 chr5B 88.535 157 15 3 703 856 586862629 586862473 2.200000e-43 187.0
47 TraesCS3D01G405300 chr6B 87.013 154 15 1 703 856 673948246 673948394 7.960000e-38 169.0
48 TraesCS3D01G405300 chr6B 86.624 157 10 5 546 698 21282916 21282767 3.700000e-36 163.0
49 TraesCS3D01G405300 chr6B 97.826 46 1 0 799 844 391096495 391096450 3.840000e-11 80.5
50 TraesCS3D01G405300 chr6D 90.741 54 5 0 811 864 282092778 282092725 6.420000e-09 73.1
51 TraesCS3D01G405300 chrUn 88.333 60 4 3 799 856 50017930 50017988 8.310000e-08 69.4


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 TraesCS3D01G405300 chr3D 519681049 519685674 4625 False 8543.0 8543 100.00000 1 4626 1 chr3D.!!$F4 4625
1 TraesCS3D01G405300 chr3D 384565133 384565873 740 False 989.0 989 91.68900 1 702 1 chr3D.!!$F1 701
2 TraesCS3D01G405300 chr3D 511350886 511351614 728 True 977.0 977 91.55300 1 702 1 chr3D.!!$R2 701
3 TraesCS3D01G405300 chr3D 29615571 29616307 736 True 924.0 924 90.09400 1 708 1 chr3D.!!$R1 707
4 TraesCS3D01G405300 chr3A 654781856 654785549 3693 False 2767.0 4859 93.00400 869 4626 2 chr3A.!!$F4 3757
5 TraesCS3D01G405300 chr3A 655083035 655087932 4897 False 672.8 1576 87.80020 945 4459 5 chr3A.!!$F5 3514
6 TraesCS3D01G405300 chr3B 684264964 684267829 2865 False 1087.5 2300 93.12425 857 4089 4 chr3B.!!$F5 3232
7 TraesCS3D01G405300 chr3B 684613818 684614374 556 False 538.0 538 84.82100 3419 3953 1 chr3B.!!$F4 534
8 TraesCS3D01G405300 chr7D 538343061 538343777 716 False 1022.0 1022 92.80800 1 702 1 chr7D.!!$F2 701
9 TraesCS3D01G405300 chr7D 235516514 235517253 739 True 989.0 989 91.66700 1 703 1 chr7D.!!$R2 702
10 TraesCS3D01G405300 chr7D 457145950 457146689 739 False 977.0 977 91.43200 1 702 1 chr7D.!!$F1 701
11 TraesCS3D01G405300 chr1D 340321071 340321814 743 True 992.0 992 91.71100 1 702 1 chr1D.!!$R2 701
12 TraesCS3D01G405300 chr1D 7514336 7515037 701 True 987.0 987 92.32900 2 697 1 chr1D.!!$R1 695
13 TraesCS3D01G405300 chr1D 389224472 389225189 717 True 952.0 952 91.05900 1 702 1 chr1D.!!$R3 701
14 TraesCS3D01G405300 chr2D 6096318 6097042 724 False 959.0 959 91.08400 1 703 1 chr2D.!!$F1 702
15 TraesCS3D01G405300 chr5D 45130905 45131488 583 False 955.0 955 96.26500 1 582 1 chr5D.!!$F1 581
16 TraesCS3D01G405300 chr5D 89495952 89496522 570 True 955.0 955 96.87500 1 572 1 chr5D.!!$R2 571
17 TraesCS3D01G405300 chr5D 450114386 450114955 569 False 950.0 950 96.70100 1 572 1 chr5D.!!$F2 571
18 TraesCS3D01G405300 chr4D 509076657 509077239 582 True 929.0 929 95.42400 1 585 1 chr4D.!!$R1 584

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
927 1016 0.035458 CCACCTTCCTCACTCACCAC 59.965 60.000 0.0 0.0 0.00 4.16 F
928 1017 0.035458 CACCTTCCTCACTCACCACC 59.965 60.000 0.0 0.0 0.00 4.61 F
930 1019 0.035458 CCTTCCTCACTCACCACCAC 59.965 60.000 0.0 0.0 0.00 4.16 F
985 1081 1.202769 CCCCGAACCCTAACCCTCAA 61.203 60.000 0.0 0.0 0.00 3.02 F
2214 2358 1.133025 CGCATCCCTGAAATGTTCACC 59.867 52.381 0.0 0.0 35.46 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 1998 2.749076 TCATGAGCATGTTACTGTTGCC 59.251 45.455 10.01 0.00 39.72 4.52 R
1873 2014 3.118261 GGCACAGAGGAATAGGTTCATGA 60.118 47.826 0.00 0.00 36.01 3.07 R
2136 2280 4.655963 AGGAAAAATTCTGCACTCTAGCA 58.344 39.130 0.00 0.00 43.35 3.49 R
2536 3559 6.573094 GCCTGAAAAGCTAACTTCCAAATGAT 60.573 38.462 0.00 0.00 34.05 2.45 R
4095 6063 0.034089 ATGGTAGGGGAGCAAGTTGC 60.034 55.000 20.44 20.44 45.46 4.17 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
30 31 9.233649 TGGAATGAAAGGTTAAACGTGTATAAT 57.766 29.630 0.00 0.00 0.00 1.28
538 558 2.281761 CCCACAGCGAGCCAACTT 60.282 61.111 0.00 0.00 0.00 2.66
721 806 4.675029 CGAGGTCGTGGGCCGTTT 62.675 66.667 0.00 0.00 37.94 3.60
722 807 2.281276 GAGGTCGTGGGCCGTTTT 60.281 61.111 0.00 0.00 37.94 2.43
723 808 1.895231 GAGGTCGTGGGCCGTTTTT 60.895 57.895 0.00 0.00 37.94 1.94
724 809 1.848932 GAGGTCGTGGGCCGTTTTTC 61.849 60.000 0.00 0.00 37.94 2.29
725 810 2.640989 GTCGTGGGCCGTTTTTCC 59.359 61.111 0.00 0.00 37.94 3.13
726 811 1.895231 GTCGTGGGCCGTTTTTCCT 60.895 57.895 0.00 0.00 37.94 3.36
727 812 1.152922 TCGTGGGCCGTTTTTCCTT 60.153 52.632 0.00 0.00 37.94 3.36
728 813 0.752376 TCGTGGGCCGTTTTTCCTTT 60.752 50.000 0.00 0.00 37.94 3.11
729 814 0.103390 CGTGGGCCGTTTTTCCTTTT 59.897 50.000 0.00 0.00 0.00 2.27
730 815 1.471851 CGTGGGCCGTTTTTCCTTTTT 60.472 47.619 0.00 0.00 0.00 1.94
760 845 6.220579 CGAAGCAGTTGTATTATGAGGATG 57.779 41.667 0.00 0.00 0.00 3.51
761 846 5.985530 CGAAGCAGTTGTATTATGAGGATGA 59.014 40.000 0.00 0.00 0.00 2.92
762 847 6.074088 CGAAGCAGTTGTATTATGAGGATGAC 60.074 42.308 0.00 0.00 0.00 3.06
763 848 5.292765 AGCAGTTGTATTATGAGGATGACG 58.707 41.667 0.00 0.00 0.00 4.35
764 849 4.084328 GCAGTTGTATTATGAGGATGACGC 60.084 45.833 0.00 0.00 0.00 5.19
765 850 4.449068 CAGTTGTATTATGAGGATGACGCC 59.551 45.833 0.00 0.00 0.00 5.68
766 851 4.100963 AGTTGTATTATGAGGATGACGCCA 59.899 41.667 0.00 0.00 0.00 5.69
767 852 4.257267 TGTATTATGAGGATGACGCCAG 57.743 45.455 0.00 0.00 0.00 4.85
768 853 3.895041 TGTATTATGAGGATGACGCCAGA 59.105 43.478 0.00 0.00 0.00 3.86
769 854 4.343814 TGTATTATGAGGATGACGCCAGAA 59.656 41.667 0.00 0.00 0.00 3.02
770 855 4.630644 ATTATGAGGATGACGCCAGAAT 57.369 40.909 0.00 0.00 0.00 2.40
771 856 2.540265 ATGAGGATGACGCCAGAATC 57.460 50.000 0.00 0.00 0.00 2.52
772 857 0.103026 TGAGGATGACGCCAGAATCG 59.897 55.000 0.00 0.00 0.00 3.34
773 858 1.218230 GAGGATGACGCCAGAATCGC 61.218 60.000 0.00 0.00 0.00 4.58
774 859 1.521457 GGATGACGCCAGAATCGCA 60.521 57.895 0.00 0.00 0.00 5.10
775 860 0.882042 GGATGACGCCAGAATCGCAT 60.882 55.000 0.00 0.00 0.00 4.73
776 861 0.234106 GATGACGCCAGAATCGCATG 59.766 55.000 0.00 0.00 0.00 4.06
777 862 1.162181 ATGACGCCAGAATCGCATGG 61.162 55.000 0.00 0.00 39.73 3.66
781 866 2.124193 CCAGAATCGCATGGCCCA 60.124 61.111 0.00 0.00 0.00 5.36
782 867 2.484062 CCAGAATCGCATGGCCCAC 61.484 63.158 0.00 0.00 0.00 4.61
783 868 1.750018 CAGAATCGCATGGCCCACA 60.750 57.895 0.00 0.00 0.00 4.17
784 869 1.105167 CAGAATCGCATGGCCCACAT 61.105 55.000 0.00 0.00 41.57 3.21
791 876 3.403624 ATGGCCCACATGACTCGT 58.596 55.556 0.00 0.00 38.70 4.18
792 877 2.602890 ATGGCCCACATGACTCGTA 58.397 52.632 0.00 0.00 38.70 3.43
793 878 1.131638 ATGGCCCACATGACTCGTAT 58.868 50.000 0.00 0.00 38.70 3.06
794 879 0.177836 TGGCCCACATGACTCGTATG 59.822 55.000 0.00 0.00 0.00 2.39
795 880 0.532862 GGCCCACATGACTCGTATGG 60.533 60.000 0.00 0.00 0.00 2.74
796 881 1.160329 GCCCACATGACTCGTATGGC 61.160 60.000 0.00 0.00 0.00 4.40
797 882 0.177836 CCCACATGACTCGTATGGCA 59.822 55.000 0.00 0.00 0.00 4.92
798 883 1.290203 CCACATGACTCGTATGGCAC 58.710 55.000 0.00 0.00 0.00 5.01
825 910 3.351416 GCGACCGGCCGAAACTTT 61.351 61.111 30.73 2.44 34.80 2.66
826 911 2.858158 CGACCGGCCGAAACTTTC 59.142 61.111 30.73 11.44 0.00 2.62
835 920 4.753877 GAAACTTTCGGCCGGCGC 62.754 66.667 27.83 12.82 0.00 6.53
852 937 2.733593 CGCCGGCGCCTATTACTC 60.734 66.667 38.48 4.19 0.00 2.59
853 938 2.357154 GCCGGCGCCTATTACTCC 60.357 66.667 26.68 0.00 0.00 3.85
854 939 2.342648 CCGGCGCCTATTACTCCC 59.657 66.667 26.68 0.00 0.00 4.30
855 940 2.342648 CGGCGCCTATTACTCCCC 59.657 66.667 26.68 0.00 0.00 4.81
856 941 2.342648 GGCGCCTATTACTCCCCG 59.657 66.667 22.15 0.00 0.00 5.73
857 942 2.505167 GGCGCCTATTACTCCCCGT 61.505 63.158 22.15 0.00 0.00 5.28
858 943 1.006454 GCGCCTATTACTCCCCGTC 60.006 63.158 0.00 0.00 0.00 4.79
859 944 1.741327 GCGCCTATTACTCCCCGTCA 61.741 60.000 0.00 0.00 0.00 4.35
860 945 0.748450 CGCCTATTACTCCCCGTCAA 59.252 55.000 0.00 0.00 0.00 3.18
861 946 1.137479 CGCCTATTACTCCCCGTCAAA 59.863 52.381 0.00 0.00 0.00 2.69
879 964 1.102978 AATATTGCCCCACGTTCAGC 58.897 50.000 0.00 0.00 0.00 4.26
888 973 2.022129 CACGTTCAGCTGACCCGAC 61.022 63.158 30.92 20.13 0.00 4.79
894 979 1.216710 CAGCTGACCCGACTCTTCC 59.783 63.158 8.42 0.00 0.00 3.46
905 991 1.887198 CGACTCTTCCACACTACCTGT 59.113 52.381 0.00 0.00 0.00 4.00
916 1005 0.400594 ACTACCTGTTGCCACCTTCC 59.599 55.000 0.00 0.00 0.00 3.46
921 1010 0.109342 CTGTTGCCACCTTCCTCACT 59.891 55.000 0.00 0.00 0.00 3.41
922 1011 0.108585 TGTTGCCACCTTCCTCACTC 59.891 55.000 0.00 0.00 0.00 3.51
923 1012 0.108585 GTTGCCACCTTCCTCACTCA 59.891 55.000 0.00 0.00 0.00 3.41
925 1014 1.003233 GCCACCTTCCTCACTCACC 60.003 63.158 0.00 0.00 0.00 4.02
926 1015 1.768684 GCCACCTTCCTCACTCACCA 61.769 60.000 0.00 0.00 0.00 4.17
927 1016 0.035458 CCACCTTCCTCACTCACCAC 59.965 60.000 0.00 0.00 0.00 4.16
928 1017 0.035458 CACCTTCCTCACTCACCACC 59.965 60.000 0.00 0.00 0.00 4.61
929 1018 0.399949 ACCTTCCTCACTCACCACCA 60.400 55.000 0.00 0.00 0.00 4.17
930 1019 0.035458 CCTTCCTCACTCACCACCAC 59.965 60.000 0.00 0.00 0.00 4.16
985 1081 1.202769 CCCCGAACCCTAACCCTCAA 61.203 60.000 0.00 0.00 0.00 3.02
989 1085 1.350019 CGAACCCTAACCCTCAAACCT 59.650 52.381 0.00 0.00 0.00 3.50
1164 1260 2.310233 CCACAAGCTCGACCACGTG 61.310 63.158 9.08 9.08 40.69 4.49
1251 1347 2.124942 TGGCGCCGCATCAACATA 60.125 55.556 23.90 0.00 0.00 2.29
1354 1450 2.967397 CGTTCTGGGGCGAGTACA 59.033 61.111 0.00 0.00 0.00 2.90
1410 1506 3.075882 ACCAGTGAGATTTTGAATCCCCA 59.924 43.478 0.00 0.00 0.00 4.96
1412 1508 3.445096 CAGTGAGATTTTGAATCCCCACC 59.555 47.826 14.59 4.31 0.00 4.61
1413 1509 2.760650 GTGAGATTTTGAATCCCCACCC 59.239 50.000 10.28 0.00 0.00 4.61
1414 1510 2.654385 TGAGATTTTGAATCCCCACCCT 59.346 45.455 0.00 0.00 0.00 4.34
1419 1517 2.044620 GAATCCCCACCCTCCCCT 59.955 66.667 0.00 0.00 0.00 4.79
1434 1532 3.123273 CTCCCCTCTCCCCTGATTTTAA 58.877 50.000 0.00 0.00 0.00 1.52
1452 1550 7.383843 TGATTTTAAGGGCTTTCGTTTTGATTC 59.616 33.333 0.00 0.00 0.00 2.52
1475 1578 3.932545 TTTGTTTCGCATTGGCTACAT 57.067 38.095 0.00 0.00 38.10 2.29
1476 1579 5.574891 ATTTGTTTCGCATTGGCTACATA 57.425 34.783 0.00 0.00 38.10 2.29
1477 1580 5.574891 TTTGTTTCGCATTGGCTACATAT 57.425 34.783 0.00 0.00 38.10 1.78
1485 1588 5.010617 TCGCATTGGCTACATATCTCTGTTA 59.989 40.000 0.00 0.00 38.10 2.41
1493 1596 3.793559 ACATATCTCTGTTACCGTTGCC 58.206 45.455 0.00 0.00 0.00 4.52
1497 1600 3.134574 TCTCTGTTACCGTTGCCATTT 57.865 42.857 0.00 0.00 0.00 2.32
1498 1601 2.811431 TCTCTGTTACCGTTGCCATTTG 59.189 45.455 0.00 0.00 0.00 2.32
1512 1615 3.264104 GCCATTTGCTGCAATGTATGTT 58.736 40.909 16.77 0.00 36.87 2.71
1513 1616 4.081807 TGCCATTTGCTGCAATGTATGTTA 60.082 37.500 16.77 5.58 42.00 2.41
1525 1635 5.185056 GCAATGTATGTTACCTTTGGGTCTT 59.815 40.000 0.00 0.00 45.98 3.01
1560 1670 5.631512 TGCGGAAAAATTCGGTAGAAATTTG 59.368 36.000 0.00 0.00 38.21 2.32
1573 1691 6.243148 GGTAGAAATTTGGGTCTGTAGGAAA 58.757 40.000 0.00 0.00 0.00 3.13
1574 1692 6.890268 GGTAGAAATTTGGGTCTGTAGGAAAT 59.110 38.462 0.00 0.00 0.00 2.17
1575 1693 8.050930 GGTAGAAATTTGGGTCTGTAGGAAATA 58.949 37.037 0.00 0.00 0.00 1.40
1576 1694 9.457436 GTAGAAATTTGGGTCTGTAGGAAATAA 57.543 33.333 0.00 0.00 0.00 1.40
1577 1695 8.581253 AGAAATTTGGGTCTGTAGGAAATAAG 57.419 34.615 0.00 0.00 0.00 1.73
1578 1696 8.390921 AGAAATTTGGGTCTGTAGGAAATAAGA 58.609 33.333 0.00 0.00 0.00 2.10
1579 1697 8.950007 AAATTTGGGTCTGTAGGAAATAAGAA 57.050 30.769 0.00 0.00 0.00 2.52
1610 1728 7.409697 CAATTTTATCGTGTAATGGAGAGTGG 58.590 38.462 0.00 0.00 0.00 4.00
1626 1744 5.246883 GGAGAGTGGGGTTAGTGTAAACTAA 59.753 44.000 1.04 1.04 0.00 2.24
1662 1780 7.484641 GCTTGCAATTTGAAATACATCTTCGTA 59.515 33.333 0.00 0.00 0.00 3.43
1857 1998 7.272731 GCGAATTTAAGTAGCAAAGGGTAAAAG 59.727 37.037 0.00 0.00 0.00 2.27
1873 2014 4.022329 GGTAAAAGGCAACAGTAACATGCT 60.022 41.667 0.00 0.00 39.94 3.79
1966 2109 3.567530 ACATTGATGTGTGTTTGCATCG 58.432 40.909 0.00 0.00 43.06 3.84
2214 2358 1.133025 CGCATCCCTGAAATGTTCACC 59.867 52.381 0.00 0.00 35.46 4.02
2388 3411 4.020218 CCTCTGTGTCCACCTCTCATTTAA 60.020 45.833 0.00 0.00 0.00 1.52
2672 3695 3.944015 GTGCCAGAGTGCAGAATTTATCT 59.056 43.478 0.00 0.00 43.02 1.98
3254 4277 1.593196 ACGCTCTTTGCAGCTGTTTA 58.407 45.000 16.64 0.00 43.06 2.01
3303 4326 0.971959 GCCATCCTGGACAATTGCCA 60.972 55.000 17.16 17.16 40.96 4.92
3331 4354 1.224592 GTCCCTTGACATCCGCCAT 59.775 57.895 0.00 0.00 41.37 4.40
3523 4546 2.868044 GCTTGGCTCGGATGATTACGAT 60.868 50.000 0.00 0.00 38.56 3.73
3541 4564 2.033424 CGATGACTACTGCGATCCTTCA 59.967 50.000 0.00 0.00 0.00 3.02
3608 4637 1.144503 GGATGATTCTCAGGGGCATGT 59.855 52.381 0.00 0.00 0.00 3.21
3679 4712 4.082571 CGGATGTTCCTCATTTCTTTTGCT 60.083 41.667 0.00 0.00 36.83 3.91
4043 6010 1.206072 GACGTTTGCTGCAGCTCTG 59.794 57.895 36.61 25.11 42.66 3.35
4094 6062 4.802051 CCCTGGCATGGACCCGTG 62.802 72.222 2.14 3.93 36.13 4.94
4095 6063 4.802051 CCTGGCATGGACCCGTGG 62.802 72.222 10.03 0.00 33.81 4.94
4099 6067 3.747976 GCATGGACCCGTGGCAAC 61.748 66.667 10.03 0.00 33.81 4.17
4100 6068 2.034066 CATGGACCCGTGGCAACT 59.966 61.111 0.00 0.00 37.61 3.16
4101 6069 1.603455 CATGGACCCGTGGCAACTT 60.603 57.895 0.00 0.00 37.61 2.66
4102 6070 1.603455 ATGGACCCGTGGCAACTTG 60.603 57.895 0.00 0.00 37.61 3.16
4103 6071 3.670377 GGACCCGTGGCAACTTGC 61.670 66.667 5.08 5.08 44.08 4.01
4104 6072 2.594592 GACCCGTGGCAACTTGCT 60.595 61.111 13.43 0.00 44.28 3.91
4105 6073 2.594592 ACCCGTGGCAACTTGCTC 60.595 61.111 13.43 4.75 44.28 4.26
4106 6074 3.365265 CCCGTGGCAACTTGCTCC 61.365 66.667 13.43 3.83 44.28 4.70
4107 6075 3.365265 CCGTGGCAACTTGCTCCC 61.365 66.667 13.43 0.00 44.28 4.30
4108 6076 3.365265 CGTGGCAACTTGCTCCCC 61.365 66.667 13.43 0.00 44.28 4.81
4109 6077 2.116125 GTGGCAACTTGCTCCCCT 59.884 61.111 13.43 0.00 44.28 4.79
4110 6078 1.378762 GTGGCAACTTGCTCCCCTA 59.621 57.895 13.43 0.00 44.28 3.53
4111 6079 0.960861 GTGGCAACTTGCTCCCCTAC 60.961 60.000 13.43 0.00 44.28 3.18
4112 6080 1.378646 GGCAACTTGCTCCCCTACC 60.379 63.158 13.43 0.00 44.28 3.18
4113 6081 1.378762 GCAACTTGCTCCCCTACCA 59.621 57.895 6.50 0.00 40.96 3.25
4114 6082 0.034089 GCAACTTGCTCCCCTACCAT 60.034 55.000 6.50 0.00 40.96 3.55
4115 6083 1.616994 GCAACTTGCTCCCCTACCATT 60.617 52.381 6.50 0.00 40.96 3.16
4116 6084 2.094675 CAACTTGCTCCCCTACCATTG 58.905 52.381 0.00 0.00 0.00 2.82
4117 6085 0.034089 ACTTGCTCCCCTACCATTGC 60.034 55.000 0.00 0.00 0.00 3.56
4118 6086 0.753111 CTTGCTCCCCTACCATTGCC 60.753 60.000 0.00 0.00 0.00 4.52
4119 6087 2.203209 GCTCCCCTACCATTGCCG 60.203 66.667 0.00 0.00 0.00 5.69
4120 6088 3.043999 GCTCCCCTACCATTGCCGT 62.044 63.158 0.00 0.00 0.00 5.68
4121 6089 1.607612 CTCCCCTACCATTGCCGTT 59.392 57.895 0.00 0.00 0.00 4.44
4122 6090 0.748005 CTCCCCTACCATTGCCGTTG 60.748 60.000 0.00 0.00 0.00 4.10
4123 6091 1.202099 TCCCCTACCATTGCCGTTGA 61.202 55.000 0.00 0.00 0.00 3.18
4124 6092 1.029947 CCCCTACCATTGCCGTTGAC 61.030 60.000 0.00 0.00 0.00 3.18
4125 6093 0.035439 CCCTACCATTGCCGTTGACT 60.035 55.000 0.00 0.00 0.00 3.41
4126 6094 1.208535 CCCTACCATTGCCGTTGACTA 59.791 52.381 0.00 0.00 0.00 2.59
4127 6095 2.158813 CCCTACCATTGCCGTTGACTAT 60.159 50.000 0.00 0.00 0.00 2.12
4128 6096 2.872245 CCTACCATTGCCGTTGACTATG 59.128 50.000 0.00 0.00 0.00 2.23
4129 6097 2.779755 ACCATTGCCGTTGACTATGA 57.220 45.000 0.00 0.00 0.00 2.15
4130 6098 3.281727 ACCATTGCCGTTGACTATGAT 57.718 42.857 0.00 0.00 0.00 2.45
4131 6099 2.945008 ACCATTGCCGTTGACTATGATG 59.055 45.455 0.00 0.00 0.00 3.07
4132 6100 3.205338 CCATTGCCGTTGACTATGATGA 58.795 45.455 0.00 0.00 0.00 2.92
4133 6101 3.817084 CCATTGCCGTTGACTATGATGAT 59.183 43.478 0.00 0.00 0.00 2.45
4134 6102 4.996758 CCATTGCCGTTGACTATGATGATA 59.003 41.667 0.00 0.00 0.00 2.15
4135 6103 5.469760 CCATTGCCGTTGACTATGATGATAA 59.530 40.000 0.00 0.00 0.00 1.75
4136 6104 6.149973 CCATTGCCGTTGACTATGATGATAAT 59.850 38.462 0.00 0.00 0.00 1.28
4137 6105 6.544038 TTGCCGTTGACTATGATGATAATG 57.456 37.500 0.00 0.00 0.00 1.90
4138 6106 4.452114 TGCCGTTGACTATGATGATAATGC 59.548 41.667 0.00 0.00 0.00 3.56
4139 6107 4.692625 GCCGTTGACTATGATGATAATGCT 59.307 41.667 0.00 0.00 0.00 3.79
4140 6108 5.390251 GCCGTTGACTATGATGATAATGCTG 60.390 44.000 0.00 0.00 0.00 4.41
4141 6109 5.121298 CCGTTGACTATGATGATAATGCTGG 59.879 44.000 0.00 0.00 0.00 4.85
4142 6110 5.698089 CGTTGACTATGATGATAATGCTGGT 59.302 40.000 0.00 0.00 0.00 4.00
4143 6111 6.347160 CGTTGACTATGATGATAATGCTGGTG 60.347 42.308 0.00 0.00 0.00 4.17
4144 6112 6.178607 TGACTATGATGATAATGCTGGTGT 57.821 37.500 0.00 0.00 0.00 4.16
4145 6113 6.594744 TGACTATGATGATAATGCTGGTGTT 58.405 36.000 0.00 0.00 0.00 3.32
4146 6114 7.734942 TGACTATGATGATAATGCTGGTGTTA 58.265 34.615 0.00 0.00 0.00 2.41
4147 6115 8.210265 TGACTATGATGATAATGCTGGTGTTAA 58.790 33.333 0.00 0.00 0.00 2.01
4148 6116 9.224267 GACTATGATGATAATGCTGGTGTTAAT 57.776 33.333 0.00 0.00 0.00 1.40
4149 6117 9.224267 ACTATGATGATAATGCTGGTGTTAATC 57.776 33.333 0.00 0.00 0.00 1.75
4150 6118 6.882610 TGATGATAATGCTGGTGTTAATCC 57.117 37.500 0.00 0.00 0.00 3.01
4154 6122 5.822519 TGATAATGCTGGTGTTAATCCTCAC 59.177 40.000 0.00 0.00 0.00 3.51
4198 6166 2.650827 ACTTCCGGGGAATTAAAAGGGA 59.349 45.455 0.00 0.00 33.28 4.20
4201 6169 2.379226 TCCGGGGAATTAAAAGGGAACA 59.621 45.455 0.00 0.00 0.00 3.18
4204 6172 3.057104 CGGGGAATTAAAAGGGAACACAC 60.057 47.826 0.00 0.00 0.00 3.82
4209 6177 0.475044 TAAAAGGGAACACACGGCCT 59.525 50.000 0.00 0.00 0.00 5.19
4210 6178 1.106944 AAAAGGGAACACACGGCCTG 61.107 55.000 0.00 0.21 0.00 4.85
4382 6386 6.095440 AGGATTGAAGTTGTTACATGCATACC 59.905 38.462 0.00 0.00 0.00 2.73
4478 6482 5.968387 AAATGTTAATCGAGTTAGAGGCG 57.032 39.130 0.00 0.00 0.00 5.52
4496 6500 2.566010 CCCCCGCAAACATGAACG 59.434 61.111 0.00 0.00 0.00 3.95
4503 6507 3.100817 CCGCAAACATGAACGAATGATC 58.899 45.455 0.00 0.00 0.00 2.92
4506 6510 4.493350 CGCAAACATGAACGAATGATCTTC 59.507 41.667 0.00 0.00 0.00 2.87
4509 6513 6.583806 GCAAACATGAACGAATGATCTTCTTT 59.416 34.615 0.00 0.00 0.00 2.52
4510 6514 7.750458 GCAAACATGAACGAATGATCTTCTTTA 59.250 33.333 0.00 0.00 0.00 1.85
4511 6515 9.270576 CAAACATGAACGAATGATCTTCTTTAG 57.729 33.333 0.00 0.00 0.00 1.85
4512 6516 7.545362 ACATGAACGAATGATCTTCTTTAGG 57.455 36.000 0.00 0.00 0.00 2.69
4558 6562 8.308207 GGTGCCCTTTTTATCAAGTTAATGTTA 58.692 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.541632 GATCCGGAGCTGGAACATTTTA 58.458 45.455 13.71 0.00 42.46 1.52
536 556 1.372087 GGGCTGATTGCGTCCTGAAG 61.372 60.000 0.00 0.00 44.05 3.02
538 558 2.268920 GGGCTGATTGCGTCCTGA 59.731 61.111 0.00 0.00 44.05 3.86
711 796 2.319136 AAAAAGGAAAAACGGCCCAC 57.681 45.000 0.00 0.00 0.00 4.61
735 820 3.871006 CCTCATAATACAACTGCTTCGCA 59.129 43.478 0.00 0.00 36.92 5.10
736 821 4.119862 TCCTCATAATACAACTGCTTCGC 58.880 43.478 0.00 0.00 0.00 4.70
737 822 5.985530 TCATCCTCATAATACAACTGCTTCG 59.014 40.000 0.00 0.00 0.00 3.79
738 823 6.074088 CGTCATCCTCATAATACAACTGCTTC 60.074 42.308 0.00 0.00 0.00 3.86
739 824 5.755375 CGTCATCCTCATAATACAACTGCTT 59.245 40.000 0.00 0.00 0.00 3.91
740 825 5.292765 CGTCATCCTCATAATACAACTGCT 58.707 41.667 0.00 0.00 0.00 4.24
741 826 4.084328 GCGTCATCCTCATAATACAACTGC 60.084 45.833 0.00 0.00 0.00 4.40
742 827 4.449068 GGCGTCATCCTCATAATACAACTG 59.551 45.833 0.00 0.00 0.00 3.16
743 828 4.100963 TGGCGTCATCCTCATAATACAACT 59.899 41.667 0.00 0.00 0.00 3.16
744 829 4.377021 TGGCGTCATCCTCATAATACAAC 58.623 43.478 0.00 0.00 0.00 3.32
745 830 4.343814 TCTGGCGTCATCCTCATAATACAA 59.656 41.667 0.00 0.00 0.00 2.41
746 831 3.895041 TCTGGCGTCATCCTCATAATACA 59.105 43.478 0.00 0.00 0.00 2.29
747 832 4.521130 TCTGGCGTCATCCTCATAATAC 57.479 45.455 0.00 0.00 0.00 1.89
748 833 5.622233 CGATTCTGGCGTCATCCTCATAATA 60.622 44.000 0.00 0.00 0.00 0.98
749 834 4.573900 GATTCTGGCGTCATCCTCATAAT 58.426 43.478 0.00 0.00 0.00 1.28
750 835 3.552890 CGATTCTGGCGTCATCCTCATAA 60.553 47.826 0.00 0.00 0.00 1.90
751 836 2.029918 CGATTCTGGCGTCATCCTCATA 60.030 50.000 0.00 0.00 0.00 2.15
752 837 1.269988 CGATTCTGGCGTCATCCTCAT 60.270 52.381 0.00 0.00 0.00 2.90
753 838 0.103026 CGATTCTGGCGTCATCCTCA 59.897 55.000 0.00 0.00 0.00 3.86
754 839 1.218230 GCGATTCTGGCGTCATCCTC 61.218 60.000 0.00 0.00 0.00 3.71
755 840 1.227380 GCGATTCTGGCGTCATCCT 60.227 57.895 0.00 0.00 0.00 3.24
756 841 0.882042 ATGCGATTCTGGCGTCATCC 60.882 55.000 0.00 0.00 0.00 3.51
757 842 0.234106 CATGCGATTCTGGCGTCATC 59.766 55.000 0.00 0.00 0.00 2.92
758 843 1.162181 CCATGCGATTCTGGCGTCAT 61.162 55.000 0.00 0.00 0.00 3.06
759 844 1.815003 CCATGCGATTCTGGCGTCA 60.815 57.895 0.00 0.00 0.00 4.35
760 845 3.017323 CCATGCGATTCTGGCGTC 58.983 61.111 0.00 0.00 0.00 5.19
764 849 2.124193 TGGGCCATGCGATTCTGG 60.124 61.111 0.00 0.00 35.53 3.86
765 850 1.105167 ATGTGGGCCATGCGATTCTG 61.105 55.000 10.70 0.00 30.69 3.02
766 851 1.105167 CATGTGGGCCATGCGATTCT 61.105 55.000 10.70 0.00 44.21 2.40
767 852 1.361271 CATGTGGGCCATGCGATTC 59.639 57.895 10.70 0.00 44.21 2.52
768 853 3.528853 CATGTGGGCCATGCGATT 58.471 55.556 10.70 0.00 44.21 3.34
774 859 1.131638 ATACGAGTCATGTGGGCCAT 58.868 50.000 10.70 0.00 0.00 4.40
775 860 0.177836 CATACGAGTCATGTGGGCCA 59.822 55.000 0.00 0.00 0.00 5.36
776 861 0.532862 CCATACGAGTCATGTGGGCC 60.533 60.000 0.00 0.00 0.00 5.80
777 862 1.160329 GCCATACGAGTCATGTGGGC 61.160 60.000 4.07 2.75 35.13 5.36
778 863 0.177836 TGCCATACGAGTCATGTGGG 59.822 55.000 4.07 0.00 0.00 4.61
779 864 1.290203 GTGCCATACGAGTCATGTGG 58.710 55.000 0.00 0.00 0.00 4.17
790 875 3.204827 CTGCCAGCCGTGCCATAC 61.205 66.667 0.00 0.00 0.00 2.39
791 876 4.488136 CCTGCCAGCCGTGCCATA 62.488 66.667 0.00 0.00 0.00 2.74
808 893 3.304764 GAAAGTTTCGGCCGGTCGC 62.305 63.158 26.77 10.51 0.00 5.19
809 894 2.858158 GAAAGTTTCGGCCGGTCG 59.142 61.111 25.52 25.52 0.00 4.79
818 903 4.753877 GCGCCGGCCGAAAGTTTC 62.754 66.667 30.73 5.47 40.02 2.78
835 920 2.733593 GAGTAATAGGCGCCGGCG 60.734 66.667 43.13 43.13 41.24 6.46
836 921 2.357154 GGAGTAATAGGCGCCGGC 60.357 66.667 23.20 19.07 38.90 6.13
837 922 2.342648 GGGAGTAATAGGCGCCGG 59.657 66.667 23.20 0.00 0.00 6.13
838 923 2.342648 GGGGAGTAATAGGCGCCG 59.657 66.667 23.20 0.00 0.00 6.46
839 924 2.342648 CGGGGAGTAATAGGCGCC 59.657 66.667 21.89 21.89 0.00 6.53
840 925 1.006454 GACGGGGAGTAATAGGCGC 60.006 63.158 0.00 0.00 0.00 6.53
841 926 0.748450 TTGACGGGGAGTAATAGGCG 59.252 55.000 0.00 0.00 0.00 5.52
842 927 2.994186 TTTGACGGGGAGTAATAGGC 57.006 50.000 0.00 0.00 0.00 3.93
843 928 5.411669 GCAATATTTGACGGGGAGTAATAGG 59.588 44.000 0.00 0.00 0.00 2.57
844 929 5.411669 GGCAATATTTGACGGGGAGTAATAG 59.588 44.000 0.00 0.00 0.00 1.73
845 930 5.310451 GGCAATATTTGACGGGGAGTAATA 58.690 41.667 0.00 0.00 0.00 0.98
846 931 4.142038 GGCAATATTTGACGGGGAGTAAT 58.858 43.478 0.00 0.00 0.00 1.89
847 932 3.547746 GGCAATATTTGACGGGGAGTAA 58.452 45.455 0.00 0.00 0.00 2.24
848 933 2.158726 GGGCAATATTTGACGGGGAGTA 60.159 50.000 0.00 0.00 40.53 2.59
849 934 1.409661 GGGCAATATTTGACGGGGAGT 60.410 52.381 0.00 0.00 40.53 3.85
850 935 1.318576 GGGCAATATTTGACGGGGAG 58.681 55.000 0.00 0.00 40.53 4.30
851 936 0.106419 GGGGCAATATTTGACGGGGA 60.106 55.000 0.00 0.00 40.53 4.81
852 937 0.396417 TGGGGCAATATTTGACGGGG 60.396 55.000 0.00 0.00 40.53 5.73
853 938 0.744281 GTGGGGCAATATTTGACGGG 59.256 55.000 0.00 0.00 40.53 5.28
854 939 0.380378 CGTGGGGCAATATTTGACGG 59.620 55.000 0.00 0.00 40.53 4.79
855 940 1.091537 ACGTGGGGCAATATTTGACG 58.908 50.000 0.00 0.00 40.53 4.35
856 941 2.490115 TGAACGTGGGGCAATATTTGAC 59.510 45.455 0.00 0.00 38.21 3.18
857 942 2.752354 CTGAACGTGGGGCAATATTTGA 59.248 45.455 0.00 0.00 0.00 2.69
858 943 2.735126 GCTGAACGTGGGGCAATATTTG 60.735 50.000 0.00 0.00 0.00 2.32
859 944 1.476488 GCTGAACGTGGGGCAATATTT 59.524 47.619 0.00 0.00 0.00 1.40
860 945 1.102978 GCTGAACGTGGGGCAATATT 58.897 50.000 0.00 0.00 0.00 1.28
861 946 0.255890 AGCTGAACGTGGGGCAATAT 59.744 50.000 9.03 0.00 0.00 1.28
879 964 0.038159 GTGTGGAAGAGTCGGGTCAG 60.038 60.000 0.00 0.00 0.00 3.51
888 973 2.417719 GCAACAGGTAGTGTGGAAGAG 58.582 52.381 0.00 0.00 40.26 2.85
905 991 0.108585 GTGAGTGAGGAAGGTGGCAA 59.891 55.000 0.00 0.00 0.00 4.52
916 1005 2.750350 GGGGTGGTGGTGAGTGAG 59.250 66.667 0.00 0.00 0.00 3.51
969 1058 1.350019 AGGTTTGAGGGTTAGGGTTCG 59.650 52.381 0.00 0.00 0.00 3.95
985 1081 2.186903 CATCGCGCTGGGTAGGTT 59.813 61.111 5.56 0.00 0.00 3.50
1092 1188 1.533469 CCCAGTTCCTCGTCTCCGTT 61.533 60.000 0.00 0.00 35.01 4.44
1141 1237 1.079750 GGTCGAGCTTGTGGAGGAC 60.080 63.158 7.51 0.00 0.00 3.85
1164 1260 2.517919 GCCCCCATCAGGATGTCC 59.482 66.667 8.35 0.00 38.24 4.02
1354 1450 4.353437 GAAGTCGTGGTCGGCGGT 62.353 66.667 7.21 0.00 46.96 5.68
1410 1506 3.700350 CAGGGGAGAGGGGAGGGT 61.700 72.222 0.00 0.00 0.00 4.34
1412 1508 0.327964 AAATCAGGGGAGAGGGGAGG 60.328 60.000 0.00 0.00 0.00 4.30
1413 1509 1.601248 AAAATCAGGGGAGAGGGGAG 58.399 55.000 0.00 0.00 0.00 4.30
1414 1510 2.982842 TAAAATCAGGGGAGAGGGGA 57.017 50.000 0.00 0.00 0.00 4.81
1434 1532 2.500229 TCGAATCAAAACGAAAGCCCT 58.500 42.857 0.00 0.00 35.62 5.19
1452 1550 1.981254 AGCCAATGCGAAACAAATCG 58.019 45.000 0.00 0.00 45.41 3.34
1475 1578 4.481368 AATGGCAACGGTAACAGAGATA 57.519 40.909 0.00 0.00 42.51 1.98
1476 1579 3.350219 AATGGCAACGGTAACAGAGAT 57.650 42.857 0.00 0.00 42.51 2.75
1477 1580 2.811431 CAAATGGCAACGGTAACAGAGA 59.189 45.455 0.00 0.00 42.51 3.10
1493 1596 5.653507 AGGTAACATACATTGCAGCAAATG 58.346 37.500 12.97 13.79 40.48 2.32
1497 1600 4.082300 CCAAAGGTAACATACATTGCAGCA 60.082 41.667 0.00 0.00 41.41 4.41
1498 1601 4.423732 CCAAAGGTAACATACATTGCAGC 58.576 43.478 0.00 0.00 41.41 5.25
1525 1635 5.627367 CGAATTTTTCCGCAGACAATAAACA 59.373 36.000 0.00 0.00 0.00 2.83
1560 1670 6.205658 GCATGATTCTTATTTCCTACAGACCC 59.794 42.308 0.00 0.00 0.00 4.46
1576 1694 9.454585 CATTACACGATAAAATTGCATGATTCT 57.545 29.630 0.00 0.00 0.00 2.40
1577 1695 8.693504 CCATTACACGATAAAATTGCATGATTC 58.306 33.333 0.00 0.00 0.00 2.52
1578 1696 8.412456 TCCATTACACGATAAAATTGCATGATT 58.588 29.630 0.00 0.00 0.00 2.57
1579 1697 7.939782 TCCATTACACGATAAAATTGCATGAT 58.060 30.769 0.00 0.00 0.00 2.45
1598 1716 3.798515 ACACTAACCCCACTCTCCATTA 58.201 45.455 0.00 0.00 0.00 1.90
1633 1751 7.534085 AGATGTATTTCAAATTGCAAGCATG 57.466 32.000 4.94 3.92 0.00 4.06
1662 1780 7.616150 TCAGTACAGACCTAGAAAGCTATCTTT 59.384 37.037 0.00 0.00 44.67 2.52
1673 1791 5.104610 ACCGTATCTTCAGTACAGACCTAGA 60.105 44.000 0.00 0.00 0.00 2.43
1770 1911 8.887717 CAATCGGAGATGAAACTCTCTTTTATT 58.112 33.333 0.00 0.00 45.12 1.40
1857 1998 2.749076 TCATGAGCATGTTACTGTTGCC 59.251 45.455 10.01 0.00 39.72 4.52
1873 2014 3.118261 GGCACAGAGGAATAGGTTCATGA 60.118 47.826 0.00 0.00 36.01 3.07
1964 2107 7.041440 CCAATTGTATAAGACCAATGCATACGA 60.041 37.037 0.00 0.00 31.89 3.43
1966 2109 7.230510 TCCCAATTGTATAAGACCAATGCATAC 59.769 37.037 0.00 0.00 31.89 2.39
2136 2280 4.655963 AGGAAAAATTCTGCACTCTAGCA 58.344 39.130 0.00 0.00 43.35 3.49
2214 2358 8.893727 AGAATCAATTGTTAGATTTAAGGGACG 58.106 33.333 5.13 0.00 34.79 4.79
2388 3411 7.595819 TGGATGTAAAACTCAACATTCCTTT 57.404 32.000 0.00 0.00 36.48 3.11
2536 3559 6.573094 GCCTGAAAAGCTAACTTCCAAATGAT 60.573 38.462 0.00 0.00 34.05 2.45
3254 4277 2.584835 TTGTTGGTGAGGCTATTGCT 57.415 45.000 0.00 0.00 39.59 3.91
3303 4326 1.128188 GTCAAGGGACTCCAGGTGGT 61.128 60.000 0.00 0.00 38.49 4.16
3331 4354 2.356382 GTCCATGGTGACGTTGAAACAA 59.644 45.455 12.58 0.00 0.00 2.83
3523 4546 1.132453 CGTGAAGGATCGCAGTAGTCA 59.868 52.381 0.00 0.00 35.77 3.41
3608 4637 6.233905 TGGAGCTCACTTAATAAGCATACA 57.766 37.500 17.19 0.00 38.51 2.29
3619 4648 1.032794 ATCGCGATGGAGCTCACTTA 58.967 50.000 23.04 0.00 34.40 2.24
3651 4684 0.552848 AATGAGGAACATCCGGCCAT 59.447 50.000 2.24 0.00 42.75 4.40
4045 6012 3.330720 AAGCTCCAACCTCCGGGG 61.331 66.667 0.00 0.00 41.89 5.73
4089 6057 3.365265 GGAGCAAGTTGCCACGGG 61.365 66.667 24.02 0.00 46.52 5.28
4090 6058 3.365265 GGGAGCAAGTTGCCACGG 61.365 66.667 24.02 0.00 46.52 4.94
4091 6059 2.463589 TAGGGGAGCAAGTTGCCACG 62.464 60.000 24.02 0.00 46.52 4.94
4092 6060 0.960861 GTAGGGGAGCAAGTTGCCAC 60.961 60.000 24.02 17.47 46.52 5.01
4093 6061 1.378762 GTAGGGGAGCAAGTTGCCA 59.621 57.895 24.02 0.29 46.52 4.92
4094 6062 1.378646 GGTAGGGGAGCAAGTTGCC 60.379 63.158 24.02 14.95 46.52 4.52
4095 6063 0.034089 ATGGTAGGGGAGCAAGTTGC 60.034 55.000 20.44 20.44 45.46 4.17
4096 6064 2.094675 CAATGGTAGGGGAGCAAGTTG 58.905 52.381 0.00 0.00 39.49 3.16
4097 6065 1.616994 GCAATGGTAGGGGAGCAAGTT 60.617 52.381 0.00 0.00 39.49 2.66
4098 6066 0.034089 GCAATGGTAGGGGAGCAAGT 60.034 55.000 0.00 0.00 39.49 3.16
4099 6067 0.753111 GGCAATGGTAGGGGAGCAAG 60.753 60.000 0.00 0.00 39.49 4.01
4100 6068 1.306296 GGCAATGGTAGGGGAGCAA 59.694 57.895 0.00 0.00 39.49 3.91
4101 6069 3.006677 GGCAATGGTAGGGGAGCA 58.993 61.111 0.00 0.00 40.58 4.26
4102 6070 2.203209 CGGCAATGGTAGGGGAGC 60.203 66.667 0.00 0.00 0.00 4.70
4103 6071 0.748005 CAACGGCAATGGTAGGGGAG 60.748 60.000 0.00 0.00 0.00 4.30
4104 6072 1.202099 TCAACGGCAATGGTAGGGGA 61.202 55.000 0.00 0.00 0.00 4.81
4105 6073 1.029947 GTCAACGGCAATGGTAGGGG 61.030 60.000 0.00 0.00 0.00 4.79
4106 6074 0.035439 AGTCAACGGCAATGGTAGGG 60.035 55.000 0.00 0.00 0.00 3.53
4107 6075 2.684001 TAGTCAACGGCAATGGTAGG 57.316 50.000 0.00 0.00 0.00 3.18
4108 6076 3.792401 TCATAGTCAACGGCAATGGTAG 58.208 45.455 0.00 0.00 0.00 3.18
4109 6077 3.897141 TCATAGTCAACGGCAATGGTA 57.103 42.857 0.00 0.00 0.00 3.25
4110 6078 2.779755 TCATAGTCAACGGCAATGGT 57.220 45.000 0.00 0.00 0.00 3.55
4111 6079 3.205338 TCATCATAGTCAACGGCAATGG 58.795 45.455 0.00 0.00 0.00 3.16
4112 6080 6.544038 TTATCATCATAGTCAACGGCAATG 57.456 37.500 0.00 0.00 0.00 2.82
4113 6081 6.348786 GCATTATCATCATAGTCAACGGCAAT 60.349 38.462 0.00 0.00 0.00 3.56
4114 6082 5.049474 GCATTATCATCATAGTCAACGGCAA 60.049 40.000 0.00 0.00 0.00 4.52
4115 6083 4.452114 GCATTATCATCATAGTCAACGGCA 59.548 41.667 0.00 0.00 0.00 5.69
4116 6084 4.692625 AGCATTATCATCATAGTCAACGGC 59.307 41.667 0.00 0.00 0.00 5.68
4117 6085 5.121298 CCAGCATTATCATCATAGTCAACGG 59.879 44.000 0.00 0.00 0.00 4.44
4118 6086 5.698089 ACCAGCATTATCATCATAGTCAACG 59.302 40.000 0.00 0.00 0.00 4.10
4119 6087 6.484643 ACACCAGCATTATCATCATAGTCAAC 59.515 38.462 0.00 0.00 0.00 3.18
4120 6088 6.594744 ACACCAGCATTATCATCATAGTCAA 58.405 36.000 0.00 0.00 0.00 3.18
4121 6089 6.178607 ACACCAGCATTATCATCATAGTCA 57.821 37.500 0.00 0.00 0.00 3.41
4122 6090 8.607441 TTAACACCAGCATTATCATCATAGTC 57.393 34.615 0.00 0.00 0.00 2.59
4123 6091 9.224267 GATTAACACCAGCATTATCATCATAGT 57.776 33.333 0.00 0.00 0.00 2.12
4124 6092 8.671921 GGATTAACACCAGCATTATCATCATAG 58.328 37.037 0.00 0.00 0.00 2.23
4125 6093 8.385491 AGGATTAACACCAGCATTATCATCATA 58.615 33.333 3.82 0.00 0.00 2.15
4126 6094 7.236529 AGGATTAACACCAGCATTATCATCAT 58.763 34.615 3.82 0.00 0.00 2.45
4127 6095 6.604171 AGGATTAACACCAGCATTATCATCA 58.396 36.000 3.82 0.00 0.00 3.07
4128 6096 6.712095 TGAGGATTAACACCAGCATTATCATC 59.288 38.462 3.82 0.00 0.00 2.92
4129 6097 6.488006 GTGAGGATTAACACCAGCATTATCAT 59.512 38.462 3.82 0.00 0.00 2.45
4130 6098 5.822519 GTGAGGATTAACACCAGCATTATCA 59.177 40.000 3.82 0.00 0.00 2.15
4131 6099 6.058183 AGTGAGGATTAACACCAGCATTATC 58.942 40.000 0.00 0.00 37.69 1.75
4132 6100 6.006275 AGTGAGGATTAACACCAGCATTAT 57.994 37.500 0.00 0.00 37.69 1.28
4133 6101 5.435686 AGTGAGGATTAACACCAGCATTA 57.564 39.130 0.00 0.00 37.69 1.90
4134 6102 4.307032 AGTGAGGATTAACACCAGCATT 57.693 40.909 0.00 0.00 37.69 3.56
4135 6103 5.636903 ATAGTGAGGATTAACACCAGCAT 57.363 39.130 0.00 0.00 37.69 3.79
4136 6104 5.435686 AATAGTGAGGATTAACACCAGCA 57.564 39.130 0.00 0.00 37.69 4.41
4137 6105 7.715249 TGATTAATAGTGAGGATTAACACCAGC 59.285 37.037 0.00 0.00 37.69 4.85
4138 6106 9.613428 TTGATTAATAGTGAGGATTAACACCAG 57.387 33.333 0.00 0.00 37.69 4.00
4139 6107 9.391006 GTTGATTAATAGTGAGGATTAACACCA 57.609 33.333 0.00 0.00 37.69 4.17
4140 6108 9.614792 AGTTGATTAATAGTGAGGATTAACACC 57.385 33.333 0.00 0.00 37.69 4.16
4146 6114 9.739276 TTTCACAGTTGATTAATAGTGAGGATT 57.261 29.630 7.44 0.00 35.41 3.01
4147 6115 9.911788 ATTTCACAGTTGATTAATAGTGAGGAT 57.088 29.630 7.44 4.96 35.41 3.24
4148 6116 9.166173 CATTTCACAGTTGATTAATAGTGAGGA 57.834 33.333 7.44 3.44 35.41 3.71
4149 6117 9.166173 TCATTTCACAGTTGATTAATAGTGAGG 57.834 33.333 7.44 4.00 35.41 3.86
4204 6172 3.490759 GTCGATGCACACAGGCCG 61.491 66.667 0.00 0.00 0.00 6.13
4209 6177 1.601903 GAAAGTTGGTCGATGCACACA 59.398 47.619 0.00 0.00 0.00 3.72
4210 6178 1.601903 TGAAAGTTGGTCGATGCACAC 59.398 47.619 0.00 0.00 0.00 3.82
4382 6386 7.989741 ACTGTGATTCTAACCTCCAGATTTATG 59.010 37.037 0.00 0.00 0.00 1.90
4478 6482 2.261361 GTTCATGTTTGCGGGGGC 59.739 61.111 0.00 0.00 0.00 5.80
4510 6514 9.343539 GCACCTTATAGACAAATTTAATCTCCT 57.656 33.333 7.28 1.51 0.00 3.69
4511 6515 8.568794 GGCACCTTATAGACAAATTTAATCTCC 58.431 37.037 7.28 0.00 0.00 3.71
4568 6572 8.792830 AACCACACATTAGTATATATGGCATC 57.207 34.615 1.65 0.00 0.00 3.91
4570 6574 7.877612 CAGAACCACACATTAGTATATATGGCA 59.122 37.037 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.