Multiple sequence alignment - TraesCS3D01G383800

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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 TraesCS3D01G383800 chr3D 100.000 2593 0 0 1 2593 499580504 499583096 0.000000e+00 4789.0
1 TraesCS3D01G383800 chr3D 85.795 711 82 12 51 744 418761397 418760689 0.000000e+00 736.0
2 TraesCS3D01G383800 chr3D 82.927 574 71 16 89 644 316822661 316823225 2.320000e-135 492.0
3 TraesCS3D01G383800 chr3B 96.893 1706 40 7 899 2593 660315587 660317290 0.000000e+00 2844.0
4 TraesCS3D01G383800 chr3B 84.457 534 58 19 89 605 128576554 128576029 1.070000e-138 503.0
5 TraesCS3D01G383800 chr3B 80.222 450 65 16 240 673 429527332 429527773 1.500000e-82 316.0
6 TraesCS3D01G383800 chr7D 84.583 720 84 15 44 744 553590540 553591251 0.000000e+00 689.0
7 TraesCS3D01G383800 chr7D 83.357 715 90 13 51 749 186856653 186855952 3.640000e-178 634.0
8 TraesCS3D01G383800 chr5D 84.582 694 90 10 44 722 435191243 435191934 0.000000e+00 673.0
9 TraesCS3D01G383800 chr5D 86.598 582 57 14 89 654 368075815 368076391 7.880000e-175 623.0
10 TraesCS3D01G383800 chr5D 84.000 600 68 20 89 673 215873455 215874041 3.770000e-153 551.0
11 TraesCS3D01G383800 chr5D 81.531 601 62 31 89 673 240080790 240081357 1.420000e-122 449.0
12 TraesCS3D01G383800 chr1B 86.408 618 68 8 51 654 392141639 392142254 0.000000e+00 662.0
13 TraesCS3D01G383800 chr1B 83.628 678 91 10 57 720 652271018 652270347 1.020000e-173 619.0
14 TraesCS3D01G383800 chr1B 80.723 581 83 17 89 654 617807702 617808268 2.380000e-115 425.0
15 TraesCS3D01G383800 chr2D 85.420 631 72 11 58 673 405068673 405069298 2.810000e-179 638.0
16 TraesCS3D01G383800 chr6A 82.966 681 93 14 44 710 577765865 577765194 6.180000e-166 593.0
17 TraesCS3D01G383800 chr6A 100.000 37 0 0 11 47 544757349 544757313 4.630000e-08 69.4
18 TraesCS3D01G383800 chr6A 95.238 42 2 0 7 48 257438266 257438225 1.670000e-07 67.6
19 TraesCS3D01G383800 chr7B 85.135 592 68 10 44 619 531214395 531213808 2.870000e-164 588.0
20 TraesCS3D01G383800 chr4D 81.833 600 83 17 89 673 338022087 338021499 5.020000e-132 481.0
21 TraesCS3D01G383800 chr4D 92.500 40 3 0 8 47 224669251 224669290 1.000000e-04 58.4
22 TraesCS3D01G383800 chr6B 97.368 38 1 0 7 44 597027707 597027670 5.990000e-07 65.8
23 TraesCS3D01G383800 chr6B 97.059 34 1 0 14 47 309666843 309666810 1.000000e-04 58.4
24 TraesCS3D01G383800 chr2B 97.368 38 1 0 11 48 309687665 309687702 5.990000e-07 65.8
25 TraesCS3D01G383800 chr5B 89.362 47 5 0 1 47 419324426 419324472 2.790000e-05 60.2
26 TraesCS3D01G383800 chr3A 94.444 36 2 0 7 42 393209672 393209637 3.600000e-04 56.5
27 TraesCS3D01G383800 chr2A 94.444 36 2 0 7 42 426726164 426726199 3.600000e-04 56.5


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 TraesCS3D01G383800 chr3D 499580504 499583096 2592 False 4789 4789 100.000 1 2593 1 chr3D.!!$F2 2592
1 TraesCS3D01G383800 chr3D 418760689 418761397 708 True 736 736 85.795 51 744 1 chr3D.!!$R1 693
2 TraesCS3D01G383800 chr3D 316822661 316823225 564 False 492 492 82.927 89 644 1 chr3D.!!$F1 555
3 TraesCS3D01G383800 chr3B 660315587 660317290 1703 False 2844 2844 96.893 899 2593 1 chr3B.!!$F2 1694
4 TraesCS3D01G383800 chr3B 128576029 128576554 525 True 503 503 84.457 89 605 1 chr3B.!!$R1 516
5 TraesCS3D01G383800 chr7D 553590540 553591251 711 False 689 689 84.583 44 744 1 chr7D.!!$F1 700
6 TraesCS3D01G383800 chr7D 186855952 186856653 701 True 634 634 83.357 51 749 1 chr7D.!!$R1 698
7 TraesCS3D01G383800 chr5D 435191243 435191934 691 False 673 673 84.582 44 722 1 chr5D.!!$F4 678
8 TraesCS3D01G383800 chr5D 368075815 368076391 576 False 623 623 86.598 89 654 1 chr5D.!!$F3 565
9 TraesCS3D01G383800 chr5D 215873455 215874041 586 False 551 551 84.000 89 673 1 chr5D.!!$F1 584
10 TraesCS3D01G383800 chr5D 240080790 240081357 567 False 449 449 81.531 89 673 1 chr5D.!!$F2 584
11 TraesCS3D01G383800 chr1B 392141639 392142254 615 False 662 662 86.408 51 654 1 chr1B.!!$F1 603
12 TraesCS3D01G383800 chr1B 652270347 652271018 671 True 619 619 83.628 57 720 1 chr1B.!!$R1 663
13 TraesCS3D01G383800 chr1B 617807702 617808268 566 False 425 425 80.723 89 654 1 chr1B.!!$F2 565
14 TraesCS3D01G383800 chr2D 405068673 405069298 625 False 638 638 85.420 58 673 1 chr2D.!!$F1 615
15 TraesCS3D01G383800 chr6A 577765194 577765865 671 True 593 593 82.966 44 710 1 chr6A.!!$R3 666
16 TraesCS3D01G383800 chr7B 531213808 531214395 587 True 588 588 85.135 44 619 1 chr7B.!!$R1 575
17 TraesCS3D01G383800 chr4D 338021499 338022087 588 True 481 481 81.833 89 673 1 chr4D.!!$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
797 839 0.032017 TACCCCCTCTCTTCTCCAGC 60.032 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 1702 1.029681 GGTTGGCCAGACGAACTTTT 58.97 50.0 5.11 0.0 37.18 2.27 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
25 26 4.540735 CGGACGGGCCATGGTACC 62.541 72.222 14.67 15.08 35.94 3.34
26 27 4.185286 GGACGGGCCATGGTACCC 62.185 72.222 14.67 15.31 43.25 3.69
27 28 3.087906 GACGGGCCATGGTACCCT 61.088 66.667 21.42 11.19 44.63 4.34
28 29 3.400599 GACGGGCCATGGTACCCTG 62.401 68.421 21.42 17.25 44.63 4.45
29 30 4.189580 CGGGCCATGGTACCCTGG 62.190 72.222 27.18 27.18 44.63 4.45
30 31 3.021263 GGGCCATGGTACCCTGGT 61.021 66.667 30.13 4.45 43.36 4.00
31 32 2.622447 GGGCCATGGTACCCTGGTT 61.622 63.158 30.13 0.90 43.36 3.67
32 33 1.076995 GGCCATGGTACCCTGGTTC 60.077 63.158 30.13 21.08 34.86 3.62
33 34 1.076995 GCCATGGTACCCTGGTTCC 60.077 63.158 30.13 15.05 36.31 3.62
34 35 1.613061 CCATGGTACCCTGGTTCCC 59.387 63.158 24.19 4.05 35.12 3.97
35 36 1.211567 CCATGGTACCCTGGTTCCCA 61.212 60.000 24.19 9.19 35.12 4.37
36 37 0.034477 CATGGTACCCTGGTTCCCAC 60.034 60.000 10.07 0.00 35.12 4.61
37 38 0.178843 ATGGTACCCTGGTTCCCACT 60.179 55.000 10.07 0.00 35.12 4.00
38 39 1.131303 TGGTACCCTGGTTCCCACTG 61.131 60.000 10.07 0.00 35.12 3.66
39 40 1.683441 GTACCCTGGTTCCCACTGG 59.317 63.158 0.00 0.00 0.00 4.00
40 41 1.540367 TACCCTGGTTCCCACTGGG 60.540 63.158 7.97 7.97 46.11 4.45
41 42 4.366684 CCCTGGTTCCCACTGGGC 62.367 72.222 9.60 0.00 43.94 5.36
42 43 3.260100 CCTGGTTCCCACTGGGCT 61.260 66.667 9.60 0.00 43.94 5.19
43 44 2.034687 CTGGTTCCCACTGGGCTG 59.965 66.667 9.60 0.00 43.94 4.85
44 45 2.449518 TGGTTCCCACTGGGCTGA 60.450 61.111 9.60 0.00 43.94 4.26
45 46 2.034221 GGTTCCCACTGGGCTGAC 59.966 66.667 9.60 7.75 43.94 3.51
46 47 2.829384 GGTTCCCACTGGGCTGACA 61.829 63.158 9.60 0.00 43.94 3.58
47 48 1.150536 GTTCCCACTGGGCTGACAA 59.849 57.895 9.60 0.00 43.94 3.18
48 49 1.150536 TTCCCACTGGGCTGACAAC 59.849 57.895 9.60 0.00 43.94 3.32
49 50 2.669569 CCCACTGGGCTGACAACG 60.670 66.667 0.00 0.00 35.35 4.10
127 128 5.219739 ACCAATCCATCTATGACCACTAGT 58.780 41.667 0.00 0.00 0.00 2.57
249 252 3.504134 CCTACCACATCGACAGATCTAGG 59.496 52.174 0.00 0.00 34.23 3.02
256 259 4.822896 ACATCGACAGATCTAGGTAGAACC 59.177 45.833 0.00 0.00 34.81 3.62
265 268 7.092354 ACAGATCTAGGTAGAACCAGTAGAGAA 60.092 40.741 0.00 0.00 41.95 2.87
267 270 6.003859 TCTAGGTAGAACCAGTAGAGAAGG 57.996 45.833 0.00 0.00 41.95 3.46
281 285 2.573915 AGAGAAGGAGGGTGATTGAACC 59.426 50.000 0.00 0.00 39.71 3.62
370 375 4.351938 CCGCTGTCAACCGGTCGA 62.352 66.667 8.04 0.00 39.67 4.20
416 422 4.812476 CGAAGTGGATCCGCGCCA 62.812 66.667 19.45 0.00 0.00 5.69
444 450 0.250513 GCACGAGAGAGGGGAAATGT 59.749 55.000 0.00 0.00 0.00 2.71
529 549 1.234615 CCCGCCGCTTTTTCAGAGAA 61.235 55.000 0.00 0.00 0.00 2.87
537 564 2.352127 GCTTTTTCAGAGAAGCGCCATT 60.352 45.455 2.29 0.00 38.89 3.16
542 569 1.812922 AGAGAAGCGCCATTGCTCG 60.813 57.895 2.29 0.00 46.60 5.03
562 594 1.762522 CGCCATCTCCCTGCCTACAT 61.763 60.000 0.00 0.00 0.00 2.29
637 670 2.889018 GTCGATTCGGCCGTTCCC 60.889 66.667 27.15 11.93 0.00 3.97
669 702 4.584325 TGGTTGAGCACTGCTTTAAGATTT 59.416 37.500 4.67 0.00 39.88 2.17
675 708 4.580167 AGCACTGCTTTAAGATTTGTGTGA 59.420 37.500 0.00 0.00 33.89 3.58
676 709 5.067674 AGCACTGCTTTAAGATTTGTGTGAA 59.932 36.000 0.00 0.00 33.89 3.18
703 736 0.107703 TTAGATGCGGGTCAGGCAAG 60.108 55.000 0.00 0.00 44.66 4.01
749 791 1.922821 GGCTGGGCCTAATCCAAGA 59.077 57.895 4.53 0.00 46.69 3.02
750 792 0.480252 GGCTGGGCCTAATCCAAGAT 59.520 55.000 4.53 0.00 46.69 2.40
751 793 1.613836 GCTGGGCCTAATCCAAGATG 58.386 55.000 4.53 0.00 33.36 2.90
752 794 1.820877 GCTGGGCCTAATCCAAGATGG 60.821 57.143 4.53 0.00 39.43 3.51
753 795 0.185901 TGGGCCTAATCCAAGATGGC 59.814 55.000 4.53 0.00 42.56 4.40
755 797 2.633860 GCCTAATCCAAGATGGCCG 58.366 57.895 0.00 0.00 37.47 6.13
756 798 0.890996 GCCTAATCCAAGATGGCCGG 60.891 60.000 0.00 0.00 37.47 6.13
757 799 0.890996 CCTAATCCAAGATGGCCGGC 60.891 60.000 21.18 21.18 37.47 6.13
758 800 1.227823 TAATCCAAGATGGCCGGCG 60.228 57.895 22.54 4.85 37.47 6.46
759 801 2.674563 TAATCCAAGATGGCCGGCGG 62.675 60.000 24.35 24.35 37.47 6.13
777 819 2.574929 CGCAGTGCCGGTTAGGTA 59.425 61.111 10.11 0.00 43.70 3.08
778 820 1.143183 CGCAGTGCCGGTTAGGTAT 59.857 57.895 10.11 0.00 43.70 2.73
779 821 0.386476 CGCAGTGCCGGTTAGGTATA 59.614 55.000 10.11 0.00 43.70 1.47
780 822 1.861971 GCAGTGCCGGTTAGGTATAC 58.138 55.000 2.85 0.00 43.70 1.47
781 823 1.539712 GCAGTGCCGGTTAGGTATACC 60.540 57.143 14.54 14.54 43.70 2.73
782 824 1.069668 CAGTGCCGGTTAGGTATACCC 59.930 57.143 18.65 3.15 43.70 3.69
783 825 0.394192 GTGCCGGTTAGGTATACCCC 59.606 60.000 18.65 11.56 43.70 4.95
784 826 0.763986 TGCCGGTTAGGTATACCCCC 60.764 60.000 18.65 14.36 43.70 5.40
785 827 0.472543 GCCGGTTAGGTATACCCCCT 60.473 60.000 18.65 2.71 43.70 4.79
786 828 1.637338 CCGGTTAGGTATACCCCCTC 58.363 60.000 18.65 6.84 36.42 4.30
787 829 1.148656 CCGGTTAGGTATACCCCCTCT 59.851 57.143 18.65 1.93 36.42 3.69
788 830 2.523245 CGGTTAGGTATACCCCCTCTC 58.477 57.143 18.65 3.29 36.42 3.20
789 831 2.109657 CGGTTAGGTATACCCCCTCTCT 59.890 54.545 18.65 0.40 36.42 3.10
790 832 3.437637 CGGTTAGGTATACCCCCTCTCTT 60.438 52.174 18.65 0.00 36.42 2.85
791 833 4.158786 GGTTAGGTATACCCCCTCTCTTC 58.841 52.174 18.65 0.00 36.42 2.87
792 834 4.140734 GGTTAGGTATACCCCCTCTCTTCT 60.141 50.000 18.65 0.00 36.42 2.85
793 835 3.907459 AGGTATACCCCCTCTCTTCTC 57.093 52.381 18.65 0.00 36.42 2.87
794 836 2.451659 AGGTATACCCCCTCTCTTCTCC 59.548 54.545 18.65 0.00 36.42 3.71
795 837 2.179424 GGTATACCCCCTCTCTTCTCCA 59.821 54.545 11.17 0.00 0.00 3.86
796 838 2.785357 ATACCCCCTCTCTTCTCCAG 57.215 55.000 0.00 0.00 0.00 3.86
797 839 0.032017 TACCCCCTCTCTTCTCCAGC 60.032 60.000 0.00 0.00 0.00 4.85
798 840 1.306482 CCCCCTCTCTTCTCCAGCA 60.306 63.158 0.00 0.00 0.00 4.41
799 841 0.693767 CCCCCTCTCTTCTCCAGCAT 60.694 60.000 0.00 0.00 0.00 3.79
800 842 0.758123 CCCCTCTCTTCTCCAGCATC 59.242 60.000 0.00 0.00 0.00 3.91
801 843 1.692121 CCCCTCTCTTCTCCAGCATCT 60.692 57.143 0.00 0.00 0.00 2.90
802 844 1.413445 CCCTCTCTTCTCCAGCATCTG 59.587 57.143 0.00 0.00 0.00 2.90
803 845 2.109774 CCTCTCTTCTCCAGCATCTGT 58.890 52.381 0.00 0.00 0.00 3.41
804 846 2.500910 CCTCTCTTCTCCAGCATCTGTT 59.499 50.000 0.00 0.00 0.00 3.16
805 847 3.430651 CCTCTCTTCTCCAGCATCTGTTC 60.431 52.174 0.00 0.00 0.00 3.18
806 848 3.168292 TCTCTTCTCCAGCATCTGTTCA 58.832 45.455 0.00 0.00 0.00 3.18
807 849 3.580022 TCTCTTCTCCAGCATCTGTTCAA 59.420 43.478 0.00 0.00 0.00 2.69
808 850 3.933955 CTCTTCTCCAGCATCTGTTCAAG 59.066 47.826 0.00 0.00 0.00 3.02
809 851 3.580022 TCTTCTCCAGCATCTGTTCAAGA 59.420 43.478 0.00 0.00 39.94 3.02
811 853 4.564782 TCTCCAGCATCTGTTCAAGATT 57.435 40.909 0.00 0.00 43.52 2.40
812 854 4.259356 TCTCCAGCATCTGTTCAAGATTG 58.741 43.478 0.00 0.00 43.52 2.67
813 855 2.751259 TCCAGCATCTGTTCAAGATTGC 59.249 45.455 0.00 0.00 43.52 3.56
814 856 2.753452 CCAGCATCTGTTCAAGATTGCT 59.247 45.455 0.00 0.00 43.52 3.91
815 857 3.943381 CCAGCATCTGTTCAAGATTGCTA 59.057 43.478 10.07 0.00 43.52 3.49
816 858 4.035324 CCAGCATCTGTTCAAGATTGCTAG 59.965 45.833 10.07 0.00 43.52 3.42
817 859 4.035324 CAGCATCTGTTCAAGATTGCTAGG 59.965 45.833 10.07 0.68 43.52 3.02
818 860 3.944015 GCATCTGTTCAAGATTGCTAGGT 59.056 43.478 0.00 0.00 43.52 3.08
819 861 4.397417 GCATCTGTTCAAGATTGCTAGGTT 59.603 41.667 0.00 0.00 43.52 3.50
820 862 5.105997 GCATCTGTTCAAGATTGCTAGGTTT 60.106 40.000 0.00 0.00 43.52 3.27
821 863 5.947228 TCTGTTCAAGATTGCTAGGTTTG 57.053 39.130 0.00 0.00 0.00 2.93
822 864 4.761739 TCTGTTCAAGATTGCTAGGTTTGG 59.238 41.667 0.00 0.00 0.00 3.28
823 865 4.724399 TGTTCAAGATTGCTAGGTTTGGA 58.276 39.130 0.00 0.00 0.00 3.53
824 866 5.136828 TGTTCAAGATTGCTAGGTTTGGAA 58.863 37.500 0.00 0.00 0.00 3.53
825 867 5.774690 TGTTCAAGATTGCTAGGTTTGGAAT 59.225 36.000 0.00 0.00 0.00 3.01
826 868 6.945435 TGTTCAAGATTGCTAGGTTTGGAATA 59.055 34.615 0.00 0.00 0.00 1.75
827 869 7.121168 TGTTCAAGATTGCTAGGTTTGGAATAG 59.879 37.037 0.00 0.00 0.00 1.73
828 870 6.957631 TCAAGATTGCTAGGTTTGGAATAGA 58.042 36.000 0.00 0.00 0.00 1.98
829 871 7.402054 TCAAGATTGCTAGGTTTGGAATAGAA 58.598 34.615 0.00 0.00 0.00 2.10
830 872 7.336931 TCAAGATTGCTAGGTTTGGAATAGAAC 59.663 37.037 0.00 0.00 0.00 3.01
831 873 6.122964 AGATTGCTAGGTTTGGAATAGAACC 58.877 40.000 0.00 0.00 44.47 3.62
837 879 4.166246 GGTTTGGAATAGAACCTAGGGG 57.834 50.000 14.81 0.00 41.62 4.79
838 880 3.552875 GTTTGGAATAGAACCTAGGGGC 58.447 50.000 14.81 4.23 35.63 5.80
839 881 1.815757 TGGAATAGAACCTAGGGGCC 58.184 55.000 14.81 0.00 35.63 5.80
840 882 1.010294 TGGAATAGAACCTAGGGGCCA 59.990 52.381 14.81 6.56 35.63 5.36
841 883 1.420514 GGAATAGAACCTAGGGGCCAC 59.579 57.143 14.81 0.00 35.63 5.01
842 884 2.124411 GAATAGAACCTAGGGGCCACA 58.876 52.381 14.81 0.00 35.63 4.17
843 885 2.280308 ATAGAACCTAGGGGCCACAA 57.720 50.000 14.81 0.00 35.63 3.33
844 886 1.580059 TAGAACCTAGGGGCCACAAG 58.420 55.000 14.81 0.00 35.63 3.16
845 887 1.378646 GAACCTAGGGGCCACAAGC 60.379 63.158 14.81 0.00 42.60 4.01
846 888 2.137177 GAACCTAGGGGCCACAAGCA 62.137 60.000 14.81 0.00 46.50 3.91
847 889 2.142292 AACCTAGGGGCCACAAGCAG 62.142 60.000 14.81 0.00 46.50 4.24
848 890 2.273449 CTAGGGGCCACAAGCAGG 59.727 66.667 8.31 0.00 46.50 4.85
849 891 2.204074 TAGGGGCCACAAGCAGGA 60.204 61.111 8.31 0.00 46.50 3.86
850 892 2.262774 CTAGGGGCCACAAGCAGGAG 62.263 65.000 8.31 0.00 46.50 3.69
851 893 4.748144 GGGGCCACAAGCAGGAGG 62.748 72.222 4.39 0.00 46.50 4.30
852 894 3.971702 GGGCCACAAGCAGGAGGT 61.972 66.667 4.39 0.00 46.50 3.85
853 895 2.674380 GGCCACAAGCAGGAGGTG 60.674 66.667 0.00 0.00 46.50 4.00
862 904 4.225497 CAGGAGGTGCCCGATTTC 57.775 61.111 0.00 0.00 37.37 2.17
863 905 1.299648 CAGGAGGTGCCCGATTTCA 59.700 57.895 0.00 0.00 37.37 2.69
864 906 0.745845 CAGGAGGTGCCCGATTTCAG 60.746 60.000 0.00 0.00 37.37 3.02
865 907 1.201429 AGGAGGTGCCCGATTTCAGT 61.201 55.000 0.00 0.00 37.37 3.41
866 908 0.322546 GGAGGTGCCCGATTTCAGTT 60.323 55.000 0.00 0.00 0.00 3.16
867 909 1.087501 GAGGTGCCCGATTTCAGTTC 58.912 55.000 0.00 0.00 0.00 3.01
868 910 0.673644 AGGTGCCCGATTTCAGTTCG 60.674 55.000 0.00 0.00 36.38 3.95
869 911 0.672401 GGTGCCCGATTTCAGTTCGA 60.672 55.000 0.00 0.00 38.88 3.71
870 912 1.369625 GTGCCCGATTTCAGTTCGAT 58.630 50.000 0.00 0.00 38.88 3.59
871 913 1.737793 GTGCCCGATTTCAGTTCGATT 59.262 47.619 0.00 0.00 38.88 3.34
872 914 2.006888 TGCCCGATTTCAGTTCGATTC 58.993 47.619 0.00 0.00 38.88 2.52
873 915 1.004927 GCCCGATTTCAGTTCGATTCG 60.005 52.381 0.00 0.00 38.88 3.34
874 916 2.536365 CCCGATTTCAGTTCGATTCGA 58.464 47.619 4.29 4.29 38.88 3.71
875 917 3.123804 CCCGATTTCAGTTCGATTCGAT 58.876 45.455 9.96 0.00 38.88 3.59
876 918 3.182572 CCCGATTTCAGTTCGATTCGATC 59.817 47.826 9.96 9.26 38.88 3.69
877 919 3.182572 CCGATTTCAGTTCGATTCGATCC 59.817 47.826 9.96 3.99 38.88 3.36
878 920 3.796717 CGATTTCAGTTCGATTCGATCCA 59.203 43.478 9.96 0.00 38.88 3.41
879 921 4.267690 CGATTTCAGTTCGATTCGATCCAA 59.732 41.667 9.96 2.79 38.88 3.53
880 922 5.050769 CGATTTCAGTTCGATTCGATCCAAT 60.051 40.000 9.96 7.78 38.88 3.16
881 923 6.510157 CGATTTCAGTTCGATTCGATCCAATT 60.510 38.462 9.96 2.50 38.88 2.32
882 924 6.494893 TTTCAGTTCGATTCGATCCAATTT 57.505 33.333 9.96 0.00 35.23 1.82
883 925 5.718649 TCAGTTCGATTCGATCCAATTTC 57.281 39.130 9.96 0.00 35.23 2.17
884 926 4.267690 TCAGTTCGATTCGATCCAATTTCG 59.732 41.667 9.96 0.00 35.23 3.46
885 927 4.032900 CAGTTCGATTCGATCCAATTTCGT 59.967 41.667 9.96 0.00 37.82 3.85
886 928 4.630069 AGTTCGATTCGATCCAATTTCGTT 59.370 37.500 9.96 0.00 37.82 3.85
887 929 5.121768 AGTTCGATTCGATCCAATTTCGTTT 59.878 36.000 9.96 0.00 37.82 3.60
888 930 6.311935 AGTTCGATTCGATCCAATTTCGTTTA 59.688 34.615 9.96 0.00 37.82 2.01
889 931 6.268797 TCGATTCGATCCAATTTCGTTTAG 57.731 37.500 4.29 0.00 37.82 1.85
890 932 6.037726 TCGATTCGATCCAATTTCGTTTAGA 58.962 36.000 4.29 0.00 37.82 2.10
891 933 6.700081 TCGATTCGATCCAATTTCGTTTAGAT 59.300 34.615 4.29 0.00 37.82 1.98
892 934 7.004225 CGATTCGATCCAATTTCGTTTAGATC 58.996 38.462 0.00 0.00 37.82 2.75
893 935 7.096023 CGATTCGATCCAATTTCGTTTAGATCT 60.096 37.037 0.00 0.00 37.82 2.75
894 936 6.828502 TCGATCCAATTTCGTTTAGATCTG 57.171 37.500 5.18 0.00 37.82 2.90
895 937 6.338146 TCGATCCAATTTCGTTTAGATCTGT 58.662 36.000 5.18 0.00 37.82 3.41
896 938 7.485810 TCGATCCAATTTCGTTTAGATCTGTA 58.514 34.615 5.18 0.00 37.82 2.74
897 939 7.977293 TCGATCCAATTTCGTTTAGATCTGTAA 59.023 33.333 5.18 0.00 37.82 2.41
917 959 2.863401 TACTGGTCGACCATGATTCG 57.137 50.000 36.21 25.01 46.46 3.34
919 961 0.530650 CTGGTCGACCATGATTCGGG 60.531 60.000 36.21 18.79 46.46 5.14
921 963 1.887707 GTCGACCATGATTCGGGCC 60.888 63.158 3.51 0.00 37.09 5.80
926 968 2.281070 CATGATTCGGGCCGGGAG 60.281 66.667 27.98 6.71 0.00 4.30
927 969 4.256180 ATGATTCGGGCCGGGAGC 62.256 66.667 27.98 18.20 42.60 4.70
949 991 1.064357 GAGTCCGACAAGATCTCCGTC 59.936 57.143 12.98 12.98 0.00 4.79
954 996 2.278857 CAAGATCTCCGTCCGGCG 60.279 66.667 10.75 10.75 40.95 6.46
958 1000 3.183776 GATCTCCGTCCGGCGAGAC 62.184 68.421 17.96 13.41 44.77 3.36
972 1015 3.990469 CGGCGAGACTCATATAAATTGCT 59.010 43.478 0.00 0.00 0.00 3.91
974 1017 5.233988 GGCGAGACTCATATAAATTGCTCT 58.766 41.667 2.82 0.00 0.00 4.09
982 1025 6.043012 ACTCATATAAATTGCTCTCAGAGGCT 59.957 38.462 3.18 0.00 0.00 4.58
983 1026 6.835174 TCATATAAATTGCTCTCAGAGGCTT 58.165 36.000 3.18 2.38 0.00 4.35
995 1038 4.097892 TCTCAGAGGCTTTTTGGTTTTGTC 59.902 41.667 0.00 0.00 0.00 3.18
998 1041 4.567959 CAGAGGCTTTTTGGTTTTGTCTTG 59.432 41.667 0.00 0.00 0.00 3.02
1009 1052 3.302415 GGTTTTGTCTTGCAACAAATCGC 60.302 43.478 15.51 9.93 45.70 4.58
1016 1059 1.462616 TGCAACAAATCGCAGGCTAT 58.537 45.000 0.00 0.00 33.34 2.97
1020 1063 3.181501 GCAACAAATCGCAGGCTATTACA 60.182 43.478 0.00 0.00 0.00 2.41
1025 1068 2.373540 TCGCAGGCTATTACAACGTT 57.626 45.000 0.00 0.00 0.00 3.99
1038 1081 3.433709 ACAACGTTTTGATCGATGTCG 57.566 42.857 0.54 2.81 39.34 4.35
1084 1127 2.164422 CGGAAGGCGATGATAGCTGATA 59.836 50.000 0.00 0.00 34.52 2.15
1143 1186 5.248640 CAGCAGAAGGAGGTGATAAAGAAA 58.751 41.667 0.00 0.00 36.64 2.52
1387 1430 2.771688 ACCAGGCTAAAGGGTATGCTA 58.228 47.619 0.00 0.00 31.89 3.49
1658 1702 3.202906 GTTTGTGGACTGCTGTCACTAA 58.797 45.455 23.12 17.57 44.61 2.24
1721 1765 7.665559 GGAGGGATTGTCATTATAAACTATGCA 59.334 37.037 0.00 0.00 0.00 3.96
1766 1811 6.569127 TCATGGTTATATGTGTTGTAGGGT 57.431 37.500 0.00 0.00 0.00 4.34
1818 1863 2.490903 AGTTCGGTGTACTGCTAATCGT 59.509 45.455 0.00 0.00 0.00 3.73
1832 1877 8.276252 ACTGCTAATCGTTTATATTGGTGTTT 57.724 30.769 0.00 0.00 0.00 2.83
1900 1945 7.118723 ACTCAGCCATGTTTGGAAAGATATTA 58.881 34.615 0.00 0.00 46.92 0.98
2187 2232 1.599542 GCTATGATTCTCAACGGGCAC 59.400 52.381 0.00 0.00 0.00 5.01
2287 2332 8.525290 AACAGGAATCATACCCTTTAATCTTG 57.475 34.615 0.00 0.00 0.00 3.02
2302 2347 8.450964 CCTTTAATCTTGTAATACATATGCGGG 58.549 37.037 1.58 0.00 0.00 6.13
2304 2349 4.617253 TCTTGTAATACATATGCGGGCT 57.383 40.909 1.58 0.00 0.00 5.19
2358 2411 7.285172 ACAATGGCATGTAAGCATTGAACTATA 59.715 33.333 14.08 0.00 36.94 1.31
2380 2433 4.145052 AGTGGAAACTTAGAAGCAAAGGG 58.855 43.478 0.00 0.00 0.00 3.95
2381 2434 4.141251 AGTGGAAACTTAGAAGCAAAGGGA 60.141 41.667 0.00 0.00 0.00 4.20
2518 2571 0.991920 AACCGTGAGACATCCCCATT 59.008 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.540735 GGTACCATGGCCCGTCCG 62.541 72.222 13.04 0.00 37.80 4.79
33 34 2.111043 ACGTTGTCAGCCCAGTGG 59.889 61.111 0.63 0.63 0.00 4.00
34 35 2.253758 CCACGTTGTCAGCCCAGTG 61.254 63.158 0.00 0.00 0.00 3.66
35 36 1.768684 ATCCACGTTGTCAGCCCAGT 61.769 55.000 0.00 0.00 0.00 4.00
36 37 1.003355 ATCCACGTTGTCAGCCCAG 60.003 57.895 0.00 0.00 0.00 4.45
37 38 1.302431 CATCCACGTTGTCAGCCCA 60.302 57.895 0.00 0.00 0.00 5.36
38 39 0.392998 ATCATCCACGTTGTCAGCCC 60.393 55.000 0.00 0.00 0.00 5.19
39 40 1.009829 GATCATCCACGTTGTCAGCC 58.990 55.000 0.00 0.00 0.00 4.85
40 41 2.015736 AGATCATCCACGTTGTCAGC 57.984 50.000 0.00 0.00 0.00 4.26
41 42 3.329386 ACAAGATCATCCACGTTGTCAG 58.671 45.455 0.00 0.00 0.00 3.51
42 43 3.401033 ACAAGATCATCCACGTTGTCA 57.599 42.857 0.00 0.00 0.00 3.58
43 44 3.745975 TGAACAAGATCATCCACGTTGTC 59.254 43.478 0.00 0.00 31.04 3.18
44 45 3.738982 TGAACAAGATCATCCACGTTGT 58.261 40.909 0.00 0.00 32.75 3.32
45 46 4.024133 TGTTGAACAAGATCATCCACGTTG 60.024 41.667 0.00 0.00 0.00 4.10
46 47 4.024048 GTGTTGAACAAGATCATCCACGTT 60.024 41.667 0.00 0.00 0.00 3.99
47 48 3.498397 GTGTTGAACAAGATCATCCACGT 59.502 43.478 0.00 0.00 0.00 4.49
48 49 3.748048 AGTGTTGAACAAGATCATCCACG 59.252 43.478 0.00 0.00 36.98 4.94
49 50 5.455392 CAAGTGTTGAACAAGATCATCCAC 58.545 41.667 0.00 0.00 34.38 4.02
147 148 2.608623 AGCATGCTAGGGGTTGTTTTT 58.391 42.857 21.21 0.00 0.00 1.94
249 252 3.955551 CCCTCCTTCTCTACTGGTTCTAC 59.044 52.174 0.00 0.00 0.00 2.59
256 259 4.026744 TCAATCACCCTCCTTCTCTACTG 58.973 47.826 0.00 0.00 0.00 2.74
265 268 2.915869 TGTAGGTTCAATCACCCTCCT 58.084 47.619 0.00 0.00 37.58 3.69
267 270 3.435671 CGTTTGTAGGTTCAATCACCCTC 59.564 47.826 0.00 0.00 37.58 4.30
281 285 1.927174 CTCTTCCGATGGCGTTTGTAG 59.073 52.381 0.00 0.00 35.23 2.74
370 375 2.048503 GCGGTGCAACTACTCCGT 60.049 61.111 12.13 0.00 45.90 4.69
416 422 1.181786 CTCTCTCGTGCTTTCCCTCT 58.818 55.000 0.00 0.00 0.00 3.69
427 433 1.279271 CCAACATTTCCCCTCTCTCGT 59.721 52.381 0.00 0.00 0.00 4.18
444 450 3.291383 CGGCAAAACTCCCGCCAA 61.291 61.111 0.00 0.00 46.60 4.52
476 486 0.456221 CCGCAGTCGCCCTATATAGG 59.544 60.000 20.43 20.43 43.25 2.57
649 682 5.067674 ACACAAATCTTAAAGCAGTGCTCAA 59.932 36.000 20.03 14.37 38.25 3.02
669 702 4.154015 CGCATCTAAATCTTGGTTCACACA 59.846 41.667 0.00 0.00 0.00 3.72
675 708 3.279434 GACCCGCATCTAAATCTTGGTT 58.721 45.455 0.00 0.00 0.00 3.67
676 709 2.238646 TGACCCGCATCTAAATCTTGGT 59.761 45.455 0.00 0.00 0.00 3.67
703 736 1.477105 GCAGTTTTCGGTCTGTTTGC 58.523 50.000 0.00 0.00 34.57 3.68
759 801 2.918230 ATACCTAACCGGCACTGCGC 62.918 60.000 0.00 0.00 41.28 6.09
760 802 0.386476 TATACCTAACCGGCACTGCG 59.614 55.000 0.00 0.00 35.61 5.18
761 803 1.539712 GGTATACCTAACCGGCACTGC 60.540 57.143 15.09 0.00 35.61 4.40
762 804 1.069668 GGGTATACCTAACCGGCACTG 59.930 57.143 21.25 0.00 37.93 3.66
763 805 1.417288 GGGTATACCTAACCGGCACT 58.583 55.000 21.25 0.00 37.93 4.40
764 806 0.394192 GGGGTATACCTAACCGGCAC 59.606 60.000 21.25 1.36 35.31 5.01
765 807 0.763986 GGGGGTATACCTAACCGGCA 60.764 60.000 21.25 0.00 35.31 5.69
766 808 0.472543 AGGGGGTATACCTAACCGGC 60.473 60.000 21.25 2.82 35.31 6.13
767 809 1.148656 AGAGGGGGTATACCTAACCGG 59.851 57.143 21.25 0.00 38.79 5.28
768 810 2.109657 AGAGAGGGGGTATACCTAACCG 59.890 54.545 21.25 0.00 38.79 4.44
769 811 3.919304 AGAGAGGGGGTATACCTAACC 57.081 52.381 21.25 19.16 38.79 2.85
770 812 5.077369 AGAAGAGAGGGGGTATACCTAAC 57.923 47.826 21.25 11.71 38.79 2.34
771 813 4.107636 GGAGAAGAGAGGGGGTATACCTAA 59.892 50.000 21.25 0.00 38.79 2.69
772 814 3.661654 GGAGAAGAGAGGGGGTATACCTA 59.338 52.174 21.25 0.00 38.79 3.08
773 815 2.451659 GGAGAAGAGAGGGGGTATACCT 59.548 54.545 21.25 1.48 42.18 3.08
774 816 2.179424 TGGAGAAGAGAGGGGGTATACC 59.821 54.545 13.99 13.99 39.11 2.73
775 817 3.502356 CTGGAGAAGAGAGGGGGTATAC 58.498 54.545 0.00 0.00 0.00 1.47
776 818 2.158295 GCTGGAGAAGAGAGGGGGTATA 60.158 54.545 0.00 0.00 0.00 1.47
777 819 1.413808 GCTGGAGAAGAGAGGGGGTAT 60.414 57.143 0.00 0.00 0.00 2.73
778 820 0.032017 GCTGGAGAAGAGAGGGGGTA 60.032 60.000 0.00 0.00 0.00 3.69
779 821 1.306568 GCTGGAGAAGAGAGGGGGT 60.307 63.158 0.00 0.00 0.00 4.95
780 822 0.693767 ATGCTGGAGAAGAGAGGGGG 60.694 60.000 0.00 0.00 0.00 5.40
781 823 0.758123 GATGCTGGAGAAGAGAGGGG 59.242 60.000 0.00 0.00 0.00 4.79
782 824 1.413445 CAGATGCTGGAGAAGAGAGGG 59.587 57.143 0.00 0.00 0.00 4.30
783 825 2.109774 ACAGATGCTGGAGAAGAGAGG 58.890 52.381 0.00 0.00 35.51 3.69
784 826 3.195182 TGAACAGATGCTGGAGAAGAGAG 59.805 47.826 0.00 0.00 35.51 3.20
785 827 3.168292 TGAACAGATGCTGGAGAAGAGA 58.832 45.455 0.00 0.00 35.51 3.10
786 828 3.606595 TGAACAGATGCTGGAGAAGAG 57.393 47.619 0.00 0.00 35.51 2.85
787 829 3.580022 TCTTGAACAGATGCTGGAGAAGA 59.420 43.478 0.00 0.00 35.51 2.87
788 830 3.935315 TCTTGAACAGATGCTGGAGAAG 58.065 45.455 0.00 0.00 35.51 2.85
789 831 4.564782 ATCTTGAACAGATGCTGGAGAA 57.435 40.909 0.00 0.00 41.13 2.87
790 832 4.259356 CAATCTTGAACAGATGCTGGAGA 58.741 43.478 0.00 0.00 41.93 3.71
791 833 3.181499 GCAATCTTGAACAGATGCTGGAG 60.181 47.826 0.00 0.00 41.93 3.86
792 834 2.751259 GCAATCTTGAACAGATGCTGGA 59.249 45.455 0.00 0.00 41.93 3.86
793 835 2.753452 AGCAATCTTGAACAGATGCTGG 59.247 45.455 0.00 0.00 41.93 4.85
794 836 4.035324 CCTAGCAATCTTGAACAGATGCTG 59.965 45.833 8.22 0.00 41.93 4.41
795 837 4.197750 CCTAGCAATCTTGAACAGATGCT 58.802 43.478 3.42 3.42 41.93 3.79
796 838 3.944015 ACCTAGCAATCTTGAACAGATGC 59.056 43.478 0.00 0.00 41.93 3.91
797 839 6.320171 CAAACCTAGCAATCTTGAACAGATG 58.680 40.000 0.00 0.00 41.93 2.90
798 840 5.416952 CCAAACCTAGCAATCTTGAACAGAT 59.583 40.000 0.00 0.00 45.03 2.90
799 841 4.761739 CCAAACCTAGCAATCTTGAACAGA 59.238 41.667 0.00 0.00 35.33 3.41
800 842 4.761739 TCCAAACCTAGCAATCTTGAACAG 59.238 41.667 0.00 0.00 0.00 3.16
801 843 4.724399 TCCAAACCTAGCAATCTTGAACA 58.276 39.130 0.00 0.00 0.00 3.18
802 844 5.705609 TTCCAAACCTAGCAATCTTGAAC 57.294 39.130 0.00 0.00 0.00 3.18
803 845 7.402054 TCTATTCCAAACCTAGCAATCTTGAA 58.598 34.615 0.00 0.00 0.00 2.69
804 846 6.957631 TCTATTCCAAACCTAGCAATCTTGA 58.042 36.000 0.00 0.00 0.00 3.02
805 847 7.415653 GGTTCTATTCCAAACCTAGCAATCTTG 60.416 40.741 0.00 0.00 41.44 3.02
806 848 6.603599 GGTTCTATTCCAAACCTAGCAATCTT 59.396 38.462 0.00 0.00 41.44 2.40
807 849 6.122964 GGTTCTATTCCAAACCTAGCAATCT 58.877 40.000 0.00 0.00 41.44 2.40
808 850 6.378710 GGTTCTATTCCAAACCTAGCAATC 57.621 41.667 0.00 0.00 41.44 2.67
816 858 3.687551 GCCCCTAGGTTCTATTCCAAACC 60.688 52.174 8.29 0.00 44.36 3.27
817 859 3.552875 GCCCCTAGGTTCTATTCCAAAC 58.447 50.000 8.29 0.00 34.57 2.93
818 860 2.512476 GGCCCCTAGGTTCTATTCCAAA 59.488 50.000 8.29 0.00 34.57 3.28
819 861 2.132686 GGCCCCTAGGTTCTATTCCAA 58.867 52.381 8.29 0.00 34.57 3.53
820 862 1.010294 TGGCCCCTAGGTTCTATTCCA 59.990 52.381 8.29 1.28 34.57 3.53
821 863 1.420514 GTGGCCCCTAGGTTCTATTCC 59.579 57.143 8.29 0.00 34.57 3.01
822 864 2.124411 TGTGGCCCCTAGGTTCTATTC 58.876 52.381 8.29 0.00 34.57 1.75
823 865 2.280308 TGTGGCCCCTAGGTTCTATT 57.720 50.000 8.29 0.00 34.57 1.73
824 866 2.127708 CTTGTGGCCCCTAGGTTCTAT 58.872 52.381 8.29 0.00 34.57 1.98
825 867 1.580059 CTTGTGGCCCCTAGGTTCTA 58.420 55.000 8.29 0.00 34.57 2.10
826 868 1.853250 GCTTGTGGCCCCTAGGTTCT 61.853 60.000 8.29 0.00 34.57 3.01
827 869 1.378646 GCTTGTGGCCCCTAGGTTC 60.379 63.158 8.29 0.00 34.57 3.62
828 870 2.142292 CTGCTTGTGGCCCCTAGGTT 62.142 60.000 8.29 0.00 40.92 3.50
829 871 2.531685 TGCTTGTGGCCCCTAGGT 60.532 61.111 8.29 0.00 40.92 3.08
830 872 2.273449 CTGCTTGTGGCCCCTAGG 59.727 66.667 0.06 0.06 40.92 3.02
831 873 2.262774 CTCCTGCTTGTGGCCCCTAG 62.263 65.000 0.00 0.00 40.92 3.02
832 874 2.204074 TCCTGCTTGTGGCCCCTA 60.204 61.111 0.00 0.00 40.92 3.53
833 875 3.655211 CTCCTGCTTGTGGCCCCT 61.655 66.667 0.00 0.00 40.92 4.79
834 876 4.748144 CCTCCTGCTTGTGGCCCC 62.748 72.222 0.00 0.00 40.92 5.80
835 877 3.971702 ACCTCCTGCTTGTGGCCC 61.972 66.667 0.00 0.00 40.92 5.80
836 878 2.674380 CACCTCCTGCTTGTGGCC 60.674 66.667 0.00 0.00 40.92 5.36
837 879 3.368571 GCACCTCCTGCTTGTGGC 61.369 66.667 0.00 0.00 43.33 5.01
838 880 2.674380 GGCACCTCCTGCTTGTGG 60.674 66.667 0.00 0.00 46.25 4.17
851 893 1.369625 ATCGAACTGAAATCGGGCAC 58.630 50.000 0.00 0.00 40.59 5.01
852 894 2.006888 GAATCGAACTGAAATCGGGCA 58.993 47.619 0.00 0.00 40.59 5.36
853 895 1.004927 CGAATCGAACTGAAATCGGGC 60.005 52.381 0.00 0.00 40.59 6.13
854 896 2.536365 TCGAATCGAACTGAAATCGGG 58.464 47.619 1.57 0.00 39.26 5.14
855 897 3.182572 GGATCGAATCGAACTGAAATCGG 59.817 47.826 10.12 0.00 39.99 4.18
856 898 3.796717 TGGATCGAATCGAACTGAAATCG 59.203 43.478 10.12 0.00 39.99 3.34
857 899 5.718649 TTGGATCGAATCGAACTGAAATC 57.281 39.130 10.12 0.10 39.99 2.17
858 900 6.683974 AATTGGATCGAATCGAACTGAAAT 57.316 33.333 10.12 6.36 39.99 2.17
859 901 6.494893 AAATTGGATCGAATCGAACTGAAA 57.505 33.333 10.12 4.29 39.99 2.69
860 902 5.220397 CGAAATTGGATCGAATCGAACTGAA 60.220 40.000 10.12 5.03 42.76 3.02
861 903 4.267690 CGAAATTGGATCGAATCGAACTGA 59.732 41.667 10.12 0.39 42.76 3.41
862 904 4.032900 ACGAAATTGGATCGAATCGAACTG 59.967 41.667 16.99 3.21 42.76 3.16
863 905 4.181578 ACGAAATTGGATCGAATCGAACT 58.818 39.130 16.99 0.00 42.76 3.01
864 906 4.516092 ACGAAATTGGATCGAATCGAAC 57.484 40.909 16.99 6.94 42.76 3.95
865 907 5.539582 AAACGAAATTGGATCGAATCGAA 57.460 34.783 16.99 0.00 42.76 3.71
866 908 6.037726 TCTAAACGAAATTGGATCGAATCGA 58.962 36.000 16.99 8.12 42.76 3.59
867 909 6.268797 TCTAAACGAAATTGGATCGAATCG 57.731 37.500 10.69 10.69 42.76 3.34
868 910 8.006590 CAGATCTAAACGAAATTGGATCGAATC 58.993 37.037 3.21 0.00 46.19 2.52
869 911 7.495934 ACAGATCTAAACGAAATTGGATCGAAT 59.504 33.333 5.09 0.00 46.19 3.34
870 912 6.816640 ACAGATCTAAACGAAATTGGATCGAA 59.183 34.615 5.09 0.00 46.19 3.71
871 913 6.338146 ACAGATCTAAACGAAATTGGATCGA 58.662 36.000 5.09 0.00 46.19 3.59
872 914 6.589830 ACAGATCTAAACGAAATTGGATCG 57.410 37.500 15.15 13.32 46.19 3.69
878 920 9.886132 ACCAGTATTACAGATCTAAACGAAATT 57.114 29.630 0.00 0.00 0.00 1.82
879 921 9.530633 GACCAGTATTACAGATCTAAACGAAAT 57.469 33.333 0.00 0.00 0.00 2.17
880 922 7.699391 CGACCAGTATTACAGATCTAAACGAAA 59.301 37.037 0.00 0.00 0.00 3.46
881 923 7.066163 TCGACCAGTATTACAGATCTAAACGAA 59.934 37.037 0.00 0.00 0.00 3.85
882 924 6.539826 TCGACCAGTATTACAGATCTAAACGA 59.460 38.462 0.00 0.00 0.00 3.85
883 925 6.632035 GTCGACCAGTATTACAGATCTAAACG 59.368 42.308 3.51 0.00 0.00 3.60
884 926 6.916932 GGTCGACCAGTATTACAGATCTAAAC 59.083 42.308 29.75 0.00 35.64 2.01
885 927 6.604396 TGGTCGACCAGTATTACAGATCTAAA 59.396 38.462 33.23 3.66 42.01 1.85
886 928 6.124340 TGGTCGACCAGTATTACAGATCTAA 58.876 40.000 33.23 4.05 42.01 2.10
887 929 5.687780 TGGTCGACCAGTATTACAGATCTA 58.312 41.667 33.23 4.47 42.01 1.98
888 930 4.533815 TGGTCGACCAGTATTACAGATCT 58.466 43.478 33.23 0.00 42.01 2.75
889 931 4.913335 TGGTCGACCAGTATTACAGATC 57.087 45.455 33.23 2.32 42.01 2.75
949 991 3.123621 GCAATTTATATGAGTCTCGCCGG 59.876 47.826 0.00 0.00 0.00 6.13
954 996 7.814107 CCTCTGAGAGCAATTTATATGAGTCTC 59.186 40.741 6.17 0.00 33.41 3.36
958 1000 6.465948 AGCCTCTGAGAGCAATTTATATGAG 58.534 40.000 16.74 0.00 0.00 2.90
972 1015 4.023291 ACAAAACCAAAAAGCCTCTGAGA 58.977 39.130 6.17 0.00 0.00 3.27
974 1017 4.023291 AGACAAAACCAAAAAGCCTCTGA 58.977 39.130 0.00 0.00 0.00 3.27
982 1025 6.377327 TTTGTTGCAAGACAAAACCAAAAA 57.623 29.167 13.06 0.00 44.13 1.94
995 1038 0.038892 AGCCTGCGATTTGTTGCAAG 60.039 50.000 0.00 0.00 41.22 4.01
998 1041 2.566952 AATAGCCTGCGATTTGTTGC 57.433 45.000 0.00 0.00 0.00 4.17
1009 1052 5.062934 TCGATCAAAACGTTGTAATAGCCTG 59.937 40.000 0.00 0.00 36.07 4.85
1016 1059 4.680567 TCGACATCGATCAAAACGTTGTAA 59.319 37.500 0.00 0.00 44.22 2.41
1025 1068 3.785486 ATTGAGCTCGACATCGATCAAA 58.215 40.909 18.85 9.09 44.88 2.69
1038 1081 3.129871 CTCCTCGGATGAAATTGAGCTC 58.870 50.000 6.82 6.82 30.48 4.09
1077 1120 1.411246 TCAATTACGGCCGTATCAGCT 59.589 47.619 36.67 17.28 0.00 4.24
1143 1186 5.234543 CCGAAAAGTCTTCTTCTTCGTCTTT 59.765 40.000 13.37 0.00 37.71 2.52
1387 1430 0.320697 GTGACCTCGGCTTGGTAAGT 59.679 55.000 0.00 0.00 38.03 2.24
1508 1551 6.569179 AACATGATGTTTGTACACCTTACC 57.431 37.500 4.72 0.00 37.26 2.85
1658 1702 1.029681 GGTTGGCCAGACGAACTTTT 58.970 50.000 5.11 0.00 37.18 2.27
1682 1726 2.472695 TCCCTCCGAAAATCACACAG 57.527 50.000 0.00 0.00 0.00 3.66
1683 1727 3.081061 CAATCCCTCCGAAAATCACACA 58.919 45.455 0.00 0.00 0.00 3.72
1721 1765 8.880750 CATGAATAAGCGATGAGACAATATCAT 58.119 33.333 0.00 0.00 40.08 2.45
1766 1811 3.370103 GCAGTACACCAATTAGCCTGGTA 60.370 47.826 0.00 0.00 45.67 3.25
1872 1917 6.061022 TCTTTCCAAACATGGCTGAGTATA 57.939 37.500 0.00 0.00 0.00 1.47
2187 2232 2.938451 TGAAGCTAATGCAGATCAACCG 59.062 45.455 0.00 0.00 42.74 4.44
2287 2332 3.435671 GGTTGAGCCCGCATATGTATTAC 59.564 47.826 4.29 0.00 0.00 1.89
2302 2347 1.069227 GTTGATGTCCAACGGTTGAGC 60.069 52.381 21.88 13.63 44.76 4.26
2358 2411 4.141251 TCCCTTTGCTTCTAAGTTTCCACT 60.141 41.667 0.00 0.00 33.11 4.00
2518 2571 9.519191 CTATGGTTTTATGGGATCATGATGTTA 57.481 33.333 14.30 0.00 34.96 2.41


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

AutoCloner maintained by Alex Coulton.