Multiple sequence alignment - TraesCS3B01G200500

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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 TraesCS3B01G200500 chr3B 100.000 3194 0 0 1 3194 229009988 229006795 0.000000e+00 5899.0
1 TraesCS3B01G200500 chr3B 84.138 145 14 3 3050 3194 228983687 228983552 7.190000e-27 132.0
2 TraesCS3B01G200500 chr3D 90.578 1677 76 31 992 2621 157752722 157751081 0.000000e+00 2146.0
3 TraesCS3B01G200500 chr3D 93.808 759 42 5 1 756 556835628 556836384 0.000000e+00 1136.0
4 TraesCS3B01G200500 chr3D 87.523 545 19 12 2678 3194 157751077 157750554 4.590000e-163 584.0
5 TraesCS3B01G200500 chr3A 90.167 1556 80 32 993 2501 170388401 170389930 0.000000e+00 1958.0
6 TraesCS3B01G200500 chr3A 89.394 594 31 17 2611 3194 170389974 170390545 0.000000e+00 719.0
7 TraesCS3B01G200500 chr3A 88.493 365 21 15 2834 3194 170310915 170310568 3.810000e-114 422.0
8 TraesCS3B01G200500 chr3A 98.198 222 4 0 1196 1417 170310315 170310536 3.860000e-104 388.0
9 TraesCS3B01G200500 chr3A 83.562 146 19 5 3050 3194 170485820 170485961 7.190000e-27 132.0
10 TraesCS3B01G200500 chr3A 97.917 48 1 0 2526 2573 170389927 170389974 2.040000e-12 84.2
11 TraesCS3B01G200500 chr6D 89.199 1324 65 25 1029 2336 438531644 438532905 0.000000e+00 1581.0
12 TraesCS3B01G200500 chr6D 90.387 1009 61 15 1029 2019 438524670 438523680 0.000000e+00 1293.0
13 TraesCS3B01G200500 chr6D 88.252 698 14 16 2526 3194 438519699 438519041 0.000000e+00 773.0
14 TraesCS3B01G200500 chr6D 93.542 480 21 2 2054 2526 438523676 438523200 0.000000e+00 706.0
15 TraesCS3B01G200500 chr7D 95.936 689 26 2 1 687 250626086 250625398 0.000000e+00 1116.0
16 TraesCS3B01G200500 chr7D 87.805 82 6 2 1456 1537 327491085 327491008 3.390000e-15 93.5
17 TraesCS3B01G200500 chr4D 93.122 756 47 4 1 754 85013390 85012638 0.000000e+00 1103.0
18 TraesCS3B01G200500 chr7B 90.957 763 60 8 1 758 356756620 356755862 0.000000e+00 1018.0
19 TraesCS3B01G200500 chr7B 92.135 89 5 1 2798 2884 750378817 750378905 1.200000e-24 124.0
20 TraesCS3B01G200500 chr5B 89.036 757 75 7 3 755 610957670 610956918 0.000000e+00 931.0
21 TraesCS3B01G200500 chr1A 88.742 755 77 8 11 760 549579268 549580019 0.000000e+00 917.0
22 TraesCS3B01G200500 chr1B 88.158 760 73 9 3 759 626403733 626404478 0.000000e+00 889.0
23 TraesCS3B01G200500 chr6A 88.655 714 72 6 3 714 216569692 216570398 0.000000e+00 861.0
24 TraesCS3B01G200500 chr6B 95.445 461 20 1 30 489 384824115 384823655 0.000000e+00 734.0
25 TraesCS3B01G200500 chr4A 95.317 363 14 3 394 754 716546179 716546540 9.940000e-160 573.0
26 TraesCS3B01G200500 chrUn 88.808 411 23 8 1029 1417 293323928 293324337 1.720000e-132 483.0
27 TraesCS3B01G200500 chrUn 88.164 414 26 8 1029 1420 287217493 287217081 3.730000e-129 472.0
28 TraesCS3B01G200500 chrUn 88.493 365 21 15 2834 3194 293324716 293324369 3.810000e-114 422.0
29 TraesCS3B01G200500 chrUn 88.493 365 21 15 2834 3194 389791287 389790940 3.810000e-114 422.0
30 TraesCS3B01G200500 chrUn 88.056 360 22 15 2839 3194 287216710 287217052 1.070000e-109 407.0
31 TraesCS3B01G200500 chrUn 88.056 360 22 15 2839 3194 300436158 300435816 1.070000e-109 407.0
32 TraesCS3B01G200500 chrUn 98.198 222 4 0 1196 1417 389790687 389790908 3.860000e-104 388.0
33 TraesCS3B01G200500 chrUn 97.748 222 5 0 1196 1417 300435563 300435784 1.800000e-102 383.0
34 TraesCS3B01G200500 chr5A 94.828 58 3 0 1481 1538 1710949 1710892 1.220000e-14 91.6


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 TraesCS3B01G200500 chr3B 229006795 229009988 3193 True 5899.0 5899 100.000000 1 3194 1 chr3B.!!$R2 3193
1 TraesCS3B01G200500 chr3D 157750554 157752722 2168 True 1365.0 2146 89.050500 992 3194 2 chr3D.!!$R1 2202
2 TraesCS3B01G200500 chr3D 556835628 556836384 756 False 1136.0 1136 93.808000 1 756 1 chr3D.!!$F1 755
3 TraesCS3B01G200500 chr3A 170388401 170390545 2144 False 920.4 1958 92.492667 993 3194 3 chr3A.!!$F3 2201
4 TraesCS3B01G200500 chr6D 438531644 438532905 1261 False 1581.0 1581 89.199000 1029 2336 1 chr6D.!!$F1 1307
5 TraesCS3B01G200500 chr6D 438519041 438524670 5629 True 924.0 1293 90.727000 1029 3194 3 chr6D.!!$R1 2165
6 TraesCS3B01G200500 chr7D 250625398 250626086 688 True 1116.0 1116 95.936000 1 687 1 chr7D.!!$R1 686
7 TraesCS3B01G200500 chr4D 85012638 85013390 752 True 1103.0 1103 93.122000 1 754 1 chr4D.!!$R1 753
8 TraesCS3B01G200500 chr7B 356755862 356756620 758 True 1018.0 1018 90.957000 1 758 1 chr7B.!!$R1 757
9 TraesCS3B01G200500 chr5B 610956918 610957670 752 True 931.0 931 89.036000 3 755 1 chr5B.!!$R1 752
10 TraesCS3B01G200500 chr1A 549579268 549580019 751 False 917.0 917 88.742000 11 760 1 chr1A.!!$F1 749
11 TraesCS3B01G200500 chr1B 626403733 626404478 745 False 889.0 889 88.158000 3 759 1 chr1B.!!$F1 756
12 TraesCS3B01G200500 chr6A 216569692 216570398 706 False 861.0 861 88.655000 3 714 1 chr6A.!!$F1 711

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
856 866 0.035439 ACCAGGAAATACGGTGGCTG 60.035 55.0 0.00 0.0 32.91 4.85 F
938 948 0.250513 GGGAGCACCACACTAGGAAG 59.749 60.0 1.58 0.0 39.85 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1854 1.421410 CTCGAACGCCGCAATAGCTT 61.421 55.0 0.00 0.00 39.10 3.74 R
2300 2356 1.750193 AGAACACCACCAACACTGTG 58.250 50.0 6.19 6.19 34.92 3.66 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
190 195 6.205853 ACTGATTTTATCACGCAACACCTTTA 59.794 34.615 0.00 0.00 35.06 1.85
250 255 0.108585 AACACAATGTGGACTCCGCT 59.891 50.000 18.37 0.00 37.94 5.52
272 277 5.621329 GCTGCCGTCAGGTTTTATTGTTATT 60.621 40.000 0.00 0.00 40.65 1.40
274 279 7.079182 TGCCGTCAGGTTTTATTGTTATTAG 57.921 36.000 0.00 0.00 40.50 1.73
287 292 3.202906 TGTTATTAGTTCGGATGCTGCC 58.797 45.455 0.00 0.00 0.00 4.85
362 367 2.142319 GGAATTTGTGTTGCCGCATTT 58.858 42.857 0.00 0.00 0.00 2.32
472 478 6.805271 CACTTCTCCAATGTGATTTTTGCTAG 59.195 38.462 0.00 0.00 33.95 3.42
494 500 3.406764 AGATTGCCAGTCTCTTGTGAAC 58.593 45.455 0.00 0.00 0.00 3.18
496 502 2.936919 TGCCAGTCTCTTGTGAACAT 57.063 45.000 0.00 0.00 0.00 2.71
508 514 8.119226 GTCTCTTGTGAACATGATTAATGCTAC 58.881 37.037 0.00 0.00 40.22 3.58
554 560 9.866655 ATTGGTACTGTGGTAAATGATATCAAT 57.133 29.630 9.99 0.00 0.00 2.57
640 648 8.424918 AGCTGCTCATATTTTAGCTAAGTCTTA 58.575 33.333 6.24 0.00 42.45 2.10
703 713 4.141688 GGAATGTATCCGGGAGACTCTTTT 60.142 45.833 21.35 10.47 38.79 2.27
704 714 5.429130 GAATGTATCCGGGAGACTCTTTTT 58.571 41.667 21.35 8.33 0.00 1.94
771 781 2.730094 AAAAACCCTGCTGCAGCG 59.270 55.556 32.11 25.08 45.83 5.18
772 782 3.504524 AAAAACCCTGCTGCAGCGC 62.505 57.895 32.11 12.85 45.83 5.92
778 788 4.099170 CTGCTGCAGCGCCAGAAC 62.099 66.667 32.11 5.47 45.83 3.01
781 791 2.979676 CTGCAGCGCCAGAACCAA 60.980 61.111 2.29 0.00 34.77 3.67
782 792 2.974489 CTGCAGCGCCAGAACCAAG 61.974 63.158 2.29 0.00 34.77 3.61
783 793 2.980233 GCAGCGCCAGAACCAAGT 60.980 61.111 2.29 0.00 0.00 3.16
784 794 2.555547 GCAGCGCCAGAACCAAGTT 61.556 57.895 2.29 0.00 0.00 2.66
785 795 1.576421 CAGCGCCAGAACCAAGTTC 59.424 57.895 2.29 0.00 42.25 3.01
795 805 2.835027 GAACCAAGTTCTCGGAGTTGT 58.165 47.619 4.69 0.00 39.23 3.32
796 806 3.986277 GAACCAAGTTCTCGGAGTTGTA 58.014 45.455 4.69 0.00 39.23 2.41
797 807 3.382048 ACCAAGTTCTCGGAGTTGTAC 57.618 47.619 4.69 0.35 0.00 2.90
798 808 2.288030 ACCAAGTTCTCGGAGTTGTACG 60.288 50.000 4.69 0.00 0.00 3.67
799 809 1.719780 CAAGTTCTCGGAGTTGTACGC 59.280 52.381 4.69 0.00 0.00 4.42
800 810 0.243095 AGTTCTCGGAGTTGTACGCC 59.757 55.000 4.69 0.00 34.50 5.68
805 815 4.424566 GGAGTTGTACGCCGCCGA 62.425 66.667 0.00 0.00 38.29 5.54
806 816 3.177249 GAGTTGTACGCCGCCGAC 61.177 66.667 0.00 0.00 38.29 4.79
807 817 4.729856 AGTTGTACGCCGCCGACC 62.730 66.667 0.00 0.00 38.29 4.79
814 824 4.215742 CGCCGCCGACCCAGAATA 62.216 66.667 0.00 0.00 36.29 1.75
815 825 2.588034 GCCGCCGACCCAGAATAC 60.588 66.667 0.00 0.00 0.00 1.89
816 826 2.279252 CCGCCGACCCAGAATACG 60.279 66.667 0.00 0.00 0.00 3.06
817 827 2.493030 CGCCGACCCAGAATACGT 59.507 61.111 0.00 0.00 0.00 3.57
818 828 1.727511 CCGCCGACCCAGAATACGTA 61.728 60.000 0.00 0.00 0.00 3.57
819 829 0.593263 CGCCGACCCAGAATACGTAC 60.593 60.000 0.00 0.00 0.00 3.67
820 830 0.593263 GCCGACCCAGAATACGTACG 60.593 60.000 15.01 15.01 0.00 3.67
821 831 0.734889 CCGACCCAGAATACGTACGT 59.265 55.000 25.98 25.98 0.00 3.57
822 832 1.939934 CCGACCCAGAATACGTACGTA 59.060 52.381 28.62 28.62 34.87 3.57
823 833 2.286418 CCGACCCAGAATACGTACGTAC 60.286 54.545 28.99 17.70 33.01 3.67
824 834 2.351418 CGACCCAGAATACGTACGTACA 59.649 50.000 28.99 12.00 33.01 2.90
825 835 3.544834 CGACCCAGAATACGTACGTACAG 60.545 52.174 28.99 17.88 33.01 2.74
826 836 3.347216 ACCCAGAATACGTACGTACAGT 58.653 45.455 28.99 22.44 33.01 3.55
827 837 4.513442 ACCCAGAATACGTACGTACAGTA 58.487 43.478 28.99 23.60 33.01 2.74
838 848 2.709213 ACGTACAGTACAGGGAGAGAC 58.291 52.381 11.37 0.00 0.00 3.36
839 849 2.015587 CGTACAGTACAGGGAGAGACC 58.984 57.143 11.37 0.00 38.08 3.85
840 850 2.617276 CGTACAGTACAGGGAGAGACCA 60.617 54.545 11.37 0.00 41.20 4.02
841 851 2.223803 ACAGTACAGGGAGAGACCAG 57.776 55.000 0.00 0.00 41.20 4.00
842 852 1.272760 ACAGTACAGGGAGAGACCAGG 60.273 57.143 0.00 0.00 41.20 4.45
843 853 1.006043 CAGTACAGGGAGAGACCAGGA 59.994 57.143 0.00 0.00 41.20 3.86
844 854 1.717077 AGTACAGGGAGAGACCAGGAA 59.283 52.381 0.00 0.00 41.20 3.36
845 855 2.111972 AGTACAGGGAGAGACCAGGAAA 59.888 50.000 0.00 0.00 41.20 3.13
846 856 2.350863 ACAGGGAGAGACCAGGAAAT 57.649 50.000 0.00 0.00 41.20 2.17
847 857 3.491766 ACAGGGAGAGACCAGGAAATA 57.508 47.619 0.00 0.00 41.20 1.40
848 858 3.108376 ACAGGGAGAGACCAGGAAATAC 58.892 50.000 0.00 0.00 41.20 1.89
849 859 2.101582 CAGGGAGAGACCAGGAAATACG 59.898 54.545 0.00 0.00 41.20 3.06
850 860 1.413077 GGGAGAGACCAGGAAATACGG 59.587 57.143 0.00 0.00 41.20 4.02
851 861 2.108970 GGAGAGACCAGGAAATACGGT 58.891 52.381 0.00 0.00 38.79 4.83
852 862 2.159085 GGAGAGACCAGGAAATACGGTG 60.159 54.545 0.00 0.00 38.79 4.94
853 863 1.831736 AGAGACCAGGAAATACGGTGG 59.168 52.381 0.00 0.00 36.05 4.61
854 864 0.252197 AGACCAGGAAATACGGTGGC 59.748 55.000 0.00 0.00 32.91 5.01
855 865 0.252197 GACCAGGAAATACGGTGGCT 59.748 55.000 0.00 0.00 32.91 4.75
856 866 0.035439 ACCAGGAAATACGGTGGCTG 60.035 55.000 0.00 0.00 32.91 4.85
857 867 1.376609 CCAGGAAATACGGTGGCTGC 61.377 60.000 0.00 0.00 0.00 5.25
858 868 1.077716 AGGAAATACGGTGGCTGCC 60.078 57.895 12.87 12.87 0.00 4.85
859 869 1.077716 GGAAATACGGTGGCTGCCT 60.078 57.895 21.03 1.26 0.00 4.75
860 870 1.376609 GGAAATACGGTGGCTGCCTG 61.377 60.000 21.03 12.06 0.00 4.85
861 871 0.676782 GAAATACGGTGGCTGCCTGT 60.677 55.000 21.03 17.10 0.00 4.00
862 872 0.251165 AAATACGGTGGCTGCCTGTT 60.251 50.000 21.03 0.75 0.00 3.16
863 873 0.251165 AATACGGTGGCTGCCTGTTT 60.251 50.000 21.03 8.15 0.00 2.83
864 874 0.251165 ATACGGTGGCTGCCTGTTTT 60.251 50.000 21.03 3.04 0.00 2.43
865 875 0.466555 TACGGTGGCTGCCTGTTTTT 60.467 50.000 21.03 1.94 0.00 1.94
866 876 1.007387 CGGTGGCTGCCTGTTTTTC 60.007 57.895 21.03 1.81 0.00 2.29
867 877 1.455383 CGGTGGCTGCCTGTTTTTCT 61.455 55.000 21.03 0.00 0.00 2.52
868 878 0.752658 GGTGGCTGCCTGTTTTTCTT 59.247 50.000 21.03 0.00 0.00 2.52
869 879 1.138859 GGTGGCTGCCTGTTTTTCTTT 59.861 47.619 21.03 0.00 0.00 2.52
870 880 2.204237 GTGGCTGCCTGTTTTTCTTTG 58.796 47.619 21.03 0.00 0.00 2.77
871 881 2.106566 TGGCTGCCTGTTTTTCTTTGA 58.893 42.857 21.03 0.00 0.00 2.69
872 882 2.699846 TGGCTGCCTGTTTTTCTTTGAT 59.300 40.909 21.03 0.00 0.00 2.57
873 883 3.062042 GGCTGCCTGTTTTTCTTTGATG 58.938 45.455 12.43 0.00 0.00 3.07
874 884 3.062042 GCTGCCTGTTTTTCTTTGATGG 58.938 45.455 0.00 0.00 0.00 3.51
875 885 3.243839 GCTGCCTGTTTTTCTTTGATGGA 60.244 43.478 0.00 0.00 0.00 3.41
876 886 4.740334 GCTGCCTGTTTTTCTTTGATGGAA 60.740 41.667 0.00 0.00 0.00 3.53
877 887 5.350504 TGCCTGTTTTTCTTTGATGGAAA 57.649 34.783 0.00 0.00 0.00 3.13
878 888 5.738909 TGCCTGTTTTTCTTTGATGGAAAA 58.261 33.333 0.00 0.00 39.79 2.29
879 889 6.176183 TGCCTGTTTTTCTTTGATGGAAAAA 58.824 32.000 9.37 9.37 44.83 1.94
880 890 6.315891 TGCCTGTTTTTCTTTGATGGAAAAAG 59.684 34.615 12.57 4.82 46.39 2.27
881 891 6.238456 GCCTGTTTTTCTTTGATGGAAAAAGG 60.238 38.462 12.57 12.22 46.39 3.11
882 892 6.260714 CCTGTTTTTCTTTGATGGAAAAAGGG 59.739 38.462 12.57 13.10 46.39 3.95
883 893 6.951971 TGTTTTTCTTTGATGGAAAAAGGGA 58.048 32.000 12.57 1.38 46.39 4.20
884 894 7.398024 TGTTTTTCTTTGATGGAAAAAGGGAA 58.602 30.769 12.57 0.88 46.39 3.97
885 895 8.052141 TGTTTTTCTTTGATGGAAAAAGGGAAT 58.948 29.630 12.57 0.00 46.39 3.01
886 896 8.902806 GTTTTTCTTTGATGGAAAAAGGGAATT 58.097 29.630 12.57 0.00 46.39 2.17
889 899 9.554395 TTTCTTTGATGGAAAAAGGGAATTAAC 57.446 29.630 0.00 0.00 35.71 2.01
890 900 7.375053 TCTTTGATGGAAAAAGGGAATTAACG 58.625 34.615 0.00 0.00 35.71 3.18
891 901 6.902771 TTGATGGAAAAAGGGAATTAACGA 57.097 33.333 0.00 0.00 0.00 3.85
892 902 6.509418 TGATGGAAAAAGGGAATTAACGAG 57.491 37.500 0.00 0.00 0.00 4.18
893 903 6.242396 TGATGGAAAAAGGGAATTAACGAGA 58.758 36.000 0.00 0.00 0.00 4.04
894 904 5.952526 TGGAAAAAGGGAATTAACGAGAC 57.047 39.130 0.00 0.00 0.00 3.36
895 905 4.763279 TGGAAAAAGGGAATTAACGAGACC 59.237 41.667 0.00 0.00 0.00 3.85
896 906 4.142752 GGAAAAAGGGAATTAACGAGACCG 60.143 45.833 0.00 0.00 42.50 4.79
910 920 4.303086 CGAGACCGTTGGATGTATAACT 57.697 45.455 0.00 0.00 0.00 2.24
911 921 4.288531 CGAGACCGTTGGATGTATAACTC 58.711 47.826 0.00 0.00 0.00 3.01
912 922 4.288531 GAGACCGTTGGATGTATAACTCG 58.711 47.826 0.00 0.00 0.00 4.18
913 923 2.793232 GACCGTTGGATGTATAACTCGC 59.207 50.000 0.00 0.00 0.00 5.03
914 924 1.784856 CCGTTGGATGTATAACTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
915 925 1.784856 CGTTGGATGTATAACTCGCGG 59.215 52.381 6.13 0.00 0.00 6.46
916 926 2.132762 GTTGGATGTATAACTCGCGGG 58.867 52.381 3.27 3.27 0.00 6.13
917 927 1.405872 TGGATGTATAACTCGCGGGT 58.594 50.000 5.36 5.36 0.00 5.28
918 928 1.067974 TGGATGTATAACTCGCGGGTG 59.932 52.381 14.98 2.22 0.00 4.61
919 929 1.604693 GGATGTATAACTCGCGGGTGG 60.605 57.143 14.98 0.00 0.00 4.61
920 930 0.391597 ATGTATAACTCGCGGGTGGG 59.608 55.000 14.98 0.00 0.00 4.61
921 931 1.068585 GTATAACTCGCGGGTGGGG 59.931 63.158 14.98 0.00 0.00 4.96
922 932 1.076118 TATAACTCGCGGGTGGGGA 60.076 57.895 14.98 0.00 36.06 4.81
934 944 3.805928 TGGGGAGCACCACACTAG 58.194 61.111 0.00 0.00 45.65 2.57
935 945 1.918293 TGGGGAGCACCACACTAGG 60.918 63.158 0.00 0.00 45.65 3.02
936 946 1.612442 GGGGAGCACCACACTAGGA 60.612 63.158 1.58 0.00 42.91 2.94
937 947 1.198759 GGGGAGCACCACACTAGGAA 61.199 60.000 1.58 0.00 42.91 3.36
938 948 0.250513 GGGAGCACCACACTAGGAAG 59.749 60.000 1.58 0.00 39.85 3.46
939 949 0.250513 GGAGCACCACACTAGGAAGG 59.749 60.000 0.00 0.00 35.97 3.46
940 950 1.267121 GAGCACCACACTAGGAAGGA 58.733 55.000 0.00 0.00 0.00 3.36
941 951 1.623811 GAGCACCACACTAGGAAGGAA 59.376 52.381 0.00 0.00 0.00 3.36
942 952 1.625818 AGCACCACACTAGGAAGGAAG 59.374 52.381 0.00 0.00 0.00 3.46
943 953 1.339151 GCACCACACTAGGAAGGAAGG 60.339 57.143 0.00 0.00 0.00 3.46
944 954 2.257207 CACCACACTAGGAAGGAAGGA 58.743 52.381 0.00 0.00 0.00 3.36
945 955 2.234908 CACCACACTAGGAAGGAAGGAG 59.765 54.545 0.00 0.00 0.00 3.69
946 956 1.208293 CCACACTAGGAAGGAAGGAGC 59.792 57.143 0.00 0.00 0.00 4.70
947 957 1.208293 CACACTAGGAAGGAAGGAGCC 59.792 57.143 0.00 0.00 0.00 4.70
948 958 0.833949 CACTAGGAAGGAAGGAGCCC 59.166 60.000 0.00 0.00 0.00 5.19
949 959 0.326713 ACTAGGAAGGAAGGAGCCCC 60.327 60.000 0.00 0.00 0.00 5.80
950 960 0.326618 CTAGGAAGGAAGGAGCCCCA 60.327 60.000 0.00 0.00 33.88 4.96
951 961 0.346932 TAGGAAGGAAGGAGCCCCAT 59.653 55.000 0.00 0.00 33.88 4.00
952 962 0.990818 AGGAAGGAAGGAGCCCCATC 60.991 60.000 0.00 0.00 33.88 3.51
955 965 3.426917 GGAAGGAGCCCCATCCAA 58.573 61.111 3.26 0.00 46.87 3.53
956 966 1.076705 GGAAGGAGCCCCATCCAAC 60.077 63.158 3.26 0.00 46.87 3.77
957 967 1.076705 GAAGGAGCCCCATCCAACC 60.077 63.158 0.00 0.00 42.26 3.77
958 968 2.573893 GAAGGAGCCCCATCCAACCC 62.574 65.000 0.00 0.00 42.26 4.11
959 969 4.143301 GGAGCCCCATCCAACCCC 62.143 72.222 0.00 0.00 39.34 4.95
960 970 3.023735 GAGCCCCATCCAACCCCT 61.024 66.667 0.00 0.00 0.00 4.79
961 971 1.696314 GAGCCCCATCCAACCCCTA 60.696 63.158 0.00 0.00 0.00 3.53
962 972 1.230482 AGCCCCATCCAACCCCTAA 60.230 57.895 0.00 0.00 0.00 2.69
963 973 1.076265 GCCCCATCCAACCCCTAAC 60.076 63.158 0.00 0.00 0.00 2.34
964 974 1.618586 CCCCATCCAACCCCTAACC 59.381 63.158 0.00 0.00 0.00 2.85
965 975 1.618586 CCCATCCAACCCCTAACCC 59.381 63.158 0.00 0.00 0.00 4.11
966 976 1.618586 CCATCCAACCCCTAACCCC 59.381 63.158 0.00 0.00 0.00 4.95
967 977 1.618586 CATCCAACCCCTAACCCCC 59.381 63.158 0.00 0.00 0.00 5.40
982 992 4.675303 CCCCTCCCTCCCACCACA 62.675 72.222 0.00 0.00 0.00 4.17
983 993 2.531685 CCCTCCCTCCCACCACAA 60.532 66.667 0.00 0.00 0.00 3.33
984 994 2.160171 CCCTCCCTCCCACCACAAA 61.160 63.158 0.00 0.00 0.00 2.83
985 995 1.074951 CCTCCCTCCCACCACAAAC 59.925 63.158 0.00 0.00 0.00 2.93
986 996 1.074951 CTCCCTCCCACCACAAACC 59.925 63.158 0.00 0.00 0.00 3.27
987 997 2.117423 CCCTCCCACCACAAACCC 59.883 66.667 0.00 0.00 0.00 4.11
988 998 2.117423 CCTCCCACCACAAACCCC 59.883 66.667 0.00 0.00 0.00 4.95
989 999 2.282180 CTCCCACCACAAACCCCG 60.282 66.667 0.00 0.00 0.00 5.73
990 1000 4.589675 TCCCACCACAAACCCCGC 62.590 66.667 0.00 0.00 0.00 6.13
1130 1146 2.926242 TCCACCCTTCCCCGACAC 60.926 66.667 0.00 0.00 0.00 3.67
1653 1702 1.680522 CCACGGAGATACCTGCTGCT 61.681 60.000 0.00 0.00 36.31 4.24
1668 1717 2.997897 GCTGTCGAGGAGGGTGGT 60.998 66.667 0.00 0.00 0.00 4.16
1733 1782 0.905357 CGTGGTGGAAGGAAGAGGAT 59.095 55.000 0.00 0.00 0.00 3.24
1854 1903 2.639327 GGTGATTGCACAGCCACCC 61.639 63.158 12.47 0.00 46.96 4.61
1974 2026 2.828868 AGCTCGGTTGCTGTTCCA 59.171 55.556 0.00 0.00 42.33 3.53
2052 2104 2.600470 GTTGGTCTTGGGGTGGCC 60.600 66.667 0.00 0.00 0.00 5.36
2217 2270 9.407380 TGATTACCTCATATTGTGCTGTAAAAT 57.593 29.630 0.00 0.00 31.71 1.82
2300 2356 2.735126 CGGCATTGGAAAAGGCATACAC 60.735 50.000 0.00 0.00 40.37 2.90
2305 2361 3.222173 TGGAAAAGGCATACACACAGT 57.778 42.857 0.00 0.00 0.00 3.55
2363 2421 1.664151 GGGTCGCTTAGTTGCATGTAC 59.336 52.381 0.00 0.00 0.00 2.90
2364 2422 2.618053 GGTCGCTTAGTTGCATGTACT 58.382 47.619 7.59 7.59 0.00 2.73
2365 2423 2.348666 GGTCGCTTAGTTGCATGTACTG 59.651 50.000 11.44 0.00 0.00 2.74
2428 2489 5.648178 TGGGATGATGATCAAAGTTTGTG 57.352 39.130 15.08 0.00 0.00 3.33
2450 2511 6.591448 TGTGATCACTTGTAGCTCACTTTATG 59.409 38.462 25.55 0.00 37.65 1.90
2480 2553 6.866010 TGCGATATAAGAAATGCAGTGAAT 57.134 33.333 0.00 0.00 0.00 2.57
2663 6240 3.284617 CCAATGCATCCATCTTCTGTGA 58.715 45.455 0.00 0.00 0.00 3.58
2676 6253 6.351711 CCATCTTCTGTGATAGTTCTCCTGTT 60.352 42.308 0.00 0.00 0.00 3.16
2696 6273 6.127897 CCTGTTATCCAGTTTGAGTCAATTCC 60.128 42.308 6.36 0.00 39.74 3.01
3016 6601 1.295101 CACGGCCATACACACTCCA 59.705 57.895 2.24 0.00 0.00 3.86
3112 6728 4.155733 CGTATCCCAGTGGCGGCA 62.156 66.667 7.97 7.97 0.00 5.69
3144 6763 4.280494 ACGCCGTAGCCATAGCCG 62.280 66.667 0.00 0.00 41.25 5.52
3145 6764 4.280494 CGCCGTAGCCATAGCCGT 62.280 66.667 0.00 0.00 41.25 5.68
3146 6765 2.911484 CGCCGTAGCCATAGCCGTA 61.911 63.158 0.00 0.00 41.25 4.02
3147 6766 1.080705 GCCGTAGCCATAGCCGTAG 60.081 63.158 0.00 0.00 41.25 3.51
3148 6767 1.080705 CCGTAGCCATAGCCGTAGC 60.081 63.158 0.00 0.00 41.25 3.58
3149 6768 1.080705 CGTAGCCATAGCCGTAGCC 60.081 63.158 0.00 0.00 41.25 3.93
3150 6769 1.080705 GTAGCCATAGCCGTAGCCG 60.081 63.158 0.00 0.00 41.25 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 182 1.531149 CAGAGGTGTAAAGGTGTTGCG 59.469 52.381 0.00 0.00 0.00 4.85
190 195 3.197333 CCTGATGACAGATTCAGAGGTGT 59.803 47.826 6.18 0.00 46.03 4.16
250 255 5.968528 AATAACAATAAAACCTGACGGCA 57.031 34.783 0.00 0.00 0.00 5.69
287 292 7.790974 CAGACATGTTGATATCTGGAAATACG 58.209 38.462 0.00 0.00 35.87 3.06
472 478 3.325293 TCACAAGAGACTGGCAATCTC 57.675 47.619 17.73 17.73 42.57 2.75
494 500 6.460123 GGTCAAAGGTGGTAGCATTAATCATG 60.460 42.308 0.00 0.00 35.73 3.07
496 502 4.947388 GGTCAAAGGTGGTAGCATTAATCA 59.053 41.667 0.00 0.00 0.00 2.57
508 514 1.165270 GATGGAACGGTCAAAGGTGG 58.835 55.000 1.31 0.00 0.00 4.61
554 560 3.067106 GTCAAAGATCCTCGAAGCAACA 58.933 45.455 0.00 0.00 0.00 3.33
724 734 6.873997 TGAGAGAGAAATGTCGGCTTTATTA 58.126 36.000 0.00 0.00 0.00 0.98
761 771 4.099170 GTTCTGGCGCTGCAGCAG 62.099 66.667 36.03 27.94 42.21 4.24
764 774 2.974489 CTTGGTTCTGGCGCTGCAG 61.974 63.158 10.11 10.11 0.00 4.41
765 775 2.979676 CTTGGTTCTGGCGCTGCA 60.980 61.111 7.64 0.00 0.00 4.41
766 776 2.463675 GAACTTGGTTCTGGCGCTGC 62.464 60.000 7.64 0.00 39.23 5.25
767 777 1.576421 GAACTTGGTTCTGGCGCTG 59.424 57.895 7.64 0.11 39.23 5.18
768 778 4.065110 GAACTTGGTTCTGGCGCT 57.935 55.556 7.64 0.00 39.23 5.92
775 785 2.835027 ACAACTCCGAGAACTTGGTTC 58.165 47.619 1.33 2.57 42.25 3.62
776 786 3.725490 GTACAACTCCGAGAACTTGGTT 58.275 45.455 1.33 0.00 35.57 3.67
777 787 2.288030 CGTACAACTCCGAGAACTTGGT 60.288 50.000 1.33 0.00 35.57 3.67
778 788 2.325761 CGTACAACTCCGAGAACTTGG 58.674 52.381 1.33 1.86 35.37 3.61
779 789 1.719780 GCGTACAACTCCGAGAACTTG 59.280 52.381 1.33 0.00 0.00 3.16
780 790 1.336609 GGCGTACAACTCCGAGAACTT 60.337 52.381 1.33 0.00 0.00 2.66
781 791 0.243095 GGCGTACAACTCCGAGAACT 59.757 55.000 1.33 0.00 0.00 3.01
782 792 2.734379 GGCGTACAACTCCGAGAAC 58.266 57.895 1.33 0.00 0.00 3.01
788 798 4.424566 TCGGCGGCGTACAACTCC 62.425 66.667 31.06 0.00 0.00 3.85
789 799 3.177249 GTCGGCGGCGTACAACTC 61.177 66.667 31.06 9.97 0.00 3.01
790 800 4.729856 GGTCGGCGGCGTACAACT 62.730 66.667 31.06 0.00 0.00 3.16
797 807 4.215742 TATTCTGGGTCGGCGGCG 62.216 66.667 27.15 27.15 0.00 6.46
798 808 2.588034 GTATTCTGGGTCGGCGGC 60.588 66.667 7.21 4.32 0.00 6.53
799 809 1.727511 TACGTATTCTGGGTCGGCGG 61.728 60.000 7.21 0.00 0.00 6.13
800 810 0.593263 GTACGTATTCTGGGTCGGCG 60.593 60.000 0.00 0.00 0.00 6.46
801 811 0.593263 CGTACGTATTCTGGGTCGGC 60.593 60.000 7.22 0.00 0.00 5.54
802 812 0.734889 ACGTACGTATTCTGGGTCGG 59.265 55.000 21.41 0.00 0.00 4.79
803 813 2.351418 TGTACGTACGTATTCTGGGTCG 59.649 50.000 29.05 0.00 32.82 4.79
804 814 3.375299 ACTGTACGTACGTATTCTGGGTC 59.625 47.826 29.05 14.94 32.82 4.46
805 815 3.347216 ACTGTACGTACGTATTCTGGGT 58.653 45.455 29.05 17.68 32.82 4.51
806 816 4.837567 GTACTGTACGTACGTATTCTGGG 58.162 47.826 29.05 17.15 39.15 4.45
816 826 3.620821 GTCTCTCCCTGTACTGTACGTAC 59.379 52.174 18.90 18.90 46.94 3.67
817 827 3.369892 GGTCTCTCCCTGTACTGTACGTA 60.370 52.174 12.87 0.00 0.00 3.57
818 828 2.617532 GGTCTCTCCCTGTACTGTACGT 60.618 54.545 12.87 0.00 0.00 3.57
819 829 2.015587 GGTCTCTCCCTGTACTGTACG 58.984 57.143 12.87 7.87 0.00 3.67
820 830 3.018149 CTGGTCTCTCCCTGTACTGTAC 58.982 54.545 10.98 10.98 34.77 2.90
821 831 2.025226 CCTGGTCTCTCCCTGTACTGTA 60.025 54.545 0.00 0.00 34.77 2.74
822 832 1.272760 CCTGGTCTCTCCCTGTACTGT 60.273 57.143 0.00 0.00 34.77 3.55
823 833 1.006043 TCCTGGTCTCTCCCTGTACTG 59.994 57.143 0.00 0.00 34.77 2.74
824 834 1.383963 TCCTGGTCTCTCCCTGTACT 58.616 55.000 0.00 0.00 34.77 2.73
825 835 2.233305 TTCCTGGTCTCTCCCTGTAC 57.767 55.000 0.00 0.00 34.77 2.90
826 836 3.491766 ATTTCCTGGTCTCTCCCTGTA 57.508 47.619 0.00 0.00 34.77 2.74
827 837 2.350863 ATTTCCTGGTCTCTCCCTGT 57.649 50.000 0.00 0.00 34.77 4.00
828 838 2.101582 CGTATTTCCTGGTCTCTCCCTG 59.898 54.545 0.00 0.00 34.77 4.45
829 839 2.389715 CGTATTTCCTGGTCTCTCCCT 58.610 52.381 0.00 0.00 34.77 4.20
830 840 1.413077 CCGTATTTCCTGGTCTCTCCC 59.587 57.143 0.00 0.00 34.77 4.30
831 841 2.108970 ACCGTATTTCCTGGTCTCTCC 58.891 52.381 0.00 0.00 0.00 3.71
832 842 2.159085 CCACCGTATTTCCTGGTCTCTC 60.159 54.545 0.00 0.00 32.48 3.20
833 843 1.831736 CCACCGTATTTCCTGGTCTCT 59.168 52.381 0.00 0.00 32.48 3.10
834 844 1.742750 GCCACCGTATTTCCTGGTCTC 60.743 57.143 0.00 0.00 32.48 3.36
835 845 0.252197 GCCACCGTATTTCCTGGTCT 59.748 55.000 0.00 0.00 32.48 3.85
836 846 0.252197 AGCCACCGTATTTCCTGGTC 59.748 55.000 0.00 0.00 32.48 4.02
837 847 0.035439 CAGCCACCGTATTTCCTGGT 60.035 55.000 0.00 0.00 36.10 4.00
838 848 1.376609 GCAGCCACCGTATTTCCTGG 61.377 60.000 0.00 0.00 0.00 4.45
839 849 1.376609 GGCAGCCACCGTATTTCCTG 61.377 60.000 6.55 0.00 0.00 3.86
840 850 1.077716 GGCAGCCACCGTATTTCCT 60.078 57.895 6.55 0.00 0.00 3.36
841 851 1.077716 AGGCAGCCACCGTATTTCC 60.078 57.895 15.80 0.00 33.69 3.13
842 852 0.676782 ACAGGCAGCCACCGTATTTC 60.677 55.000 15.80 0.00 33.69 2.17
843 853 0.251165 AACAGGCAGCCACCGTATTT 60.251 50.000 15.80 0.00 33.69 1.40
844 854 0.251165 AAACAGGCAGCCACCGTATT 60.251 50.000 15.80 2.85 33.69 1.89
845 855 0.251165 AAAACAGGCAGCCACCGTAT 60.251 50.000 15.80 0.00 33.69 3.06
846 856 0.466555 AAAAACAGGCAGCCACCGTA 60.467 50.000 15.80 0.00 33.69 4.02
847 857 1.734388 GAAAAACAGGCAGCCACCGT 61.734 55.000 15.80 4.61 33.69 4.83
848 858 1.007387 GAAAAACAGGCAGCCACCG 60.007 57.895 15.80 3.87 33.69 4.94
849 859 0.752658 AAGAAAAACAGGCAGCCACC 59.247 50.000 15.80 0.00 0.00 4.61
850 860 2.159114 TCAAAGAAAAACAGGCAGCCAC 60.159 45.455 15.80 0.00 0.00 5.01
851 861 2.106566 TCAAAGAAAAACAGGCAGCCA 58.893 42.857 15.80 0.00 0.00 4.75
852 862 2.888834 TCAAAGAAAAACAGGCAGCC 57.111 45.000 1.84 1.84 0.00 4.85
853 863 3.062042 CCATCAAAGAAAAACAGGCAGC 58.938 45.455 0.00 0.00 0.00 5.25
854 864 4.589216 TCCATCAAAGAAAAACAGGCAG 57.411 40.909 0.00 0.00 0.00 4.85
855 865 5.350504 TTTCCATCAAAGAAAAACAGGCA 57.649 34.783 0.00 0.00 30.48 4.75
856 866 6.238456 CCTTTTTCCATCAAAGAAAAACAGGC 60.238 38.462 7.19 0.00 44.25 4.85
857 867 6.260714 CCCTTTTTCCATCAAAGAAAAACAGG 59.739 38.462 7.19 8.01 44.25 4.00
858 868 7.047271 TCCCTTTTTCCATCAAAGAAAAACAG 58.953 34.615 7.19 3.32 44.25 3.16
859 869 6.951971 TCCCTTTTTCCATCAAAGAAAAACA 58.048 32.000 7.19 0.00 44.25 2.83
860 870 7.857734 TTCCCTTTTTCCATCAAAGAAAAAC 57.142 32.000 7.19 0.00 44.25 2.43
863 873 9.554395 GTTAATTCCCTTTTTCCATCAAAGAAA 57.446 29.630 0.00 0.00 33.69 2.52
864 874 7.870445 CGTTAATTCCCTTTTTCCATCAAAGAA 59.130 33.333 0.00 0.00 33.69 2.52
865 875 7.231722 TCGTTAATTCCCTTTTTCCATCAAAGA 59.768 33.333 0.00 0.00 33.69 2.52
866 876 7.375053 TCGTTAATTCCCTTTTTCCATCAAAG 58.625 34.615 0.00 0.00 0.00 2.77
867 877 7.231722 TCTCGTTAATTCCCTTTTTCCATCAAA 59.768 33.333 0.00 0.00 0.00 2.69
868 878 6.717540 TCTCGTTAATTCCCTTTTTCCATCAA 59.282 34.615 0.00 0.00 0.00 2.57
869 879 6.150474 GTCTCGTTAATTCCCTTTTTCCATCA 59.850 38.462 0.00 0.00 0.00 3.07
870 880 6.404403 GGTCTCGTTAATTCCCTTTTTCCATC 60.404 42.308 0.00 0.00 0.00 3.51
871 881 5.417894 GGTCTCGTTAATTCCCTTTTTCCAT 59.582 40.000 0.00 0.00 0.00 3.41
872 882 4.763279 GGTCTCGTTAATTCCCTTTTTCCA 59.237 41.667 0.00 0.00 0.00 3.53
873 883 4.142752 CGGTCTCGTTAATTCCCTTTTTCC 60.143 45.833 0.00 0.00 0.00 3.13
874 884 4.966249 CGGTCTCGTTAATTCCCTTTTTC 58.034 43.478 0.00 0.00 0.00 2.29
889 899 4.288531 GAGTTATACATCCAACGGTCTCG 58.711 47.826 0.00 0.00 43.02 4.04
890 900 4.288531 CGAGTTATACATCCAACGGTCTC 58.711 47.826 0.00 0.00 0.00 3.36
891 901 3.490419 GCGAGTTATACATCCAACGGTCT 60.490 47.826 0.00 0.00 0.00 3.85
892 902 2.793232 GCGAGTTATACATCCAACGGTC 59.207 50.000 0.00 0.00 0.00 4.79
893 903 2.797087 CGCGAGTTATACATCCAACGGT 60.797 50.000 0.00 0.00 0.00 4.83
894 904 1.784856 CGCGAGTTATACATCCAACGG 59.215 52.381 0.00 0.00 0.00 4.44
895 905 1.784856 CCGCGAGTTATACATCCAACG 59.215 52.381 8.23 0.00 0.00 4.10
896 906 2.132762 CCCGCGAGTTATACATCCAAC 58.867 52.381 8.23 0.00 0.00 3.77
897 907 1.758280 ACCCGCGAGTTATACATCCAA 59.242 47.619 8.23 0.00 0.00 3.53
898 908 1.067974 CACCCGCGAGTTATACATCCA 59.932 52.381 8.23 0.00 0.00 3.41
899 909 1.604693 CCACCCGCGAGTTATACATCC 60.605 57.143 8.23 0.00 0.00 3.51
900 910 1.604693 CCCACCCGCGAGTTATACATC 60.605 57.143 8.23 0.00 0.00 3.06
901 911 0.391597 CCCACCCGCGAGTTATACAT 59.608 55.000 8.23 0.00 0.00 2.29
902 912 1.678598 CCCCACCCGCGAGTTATACA 61.679 60.000 8.23 0.00 0.00 2.29
903 913 1.068585 CCCCACCCGCGAGTTATAC 59.931 63.158 8.23 0.00 0.00 1.47
904 914 1.076118 TCCCCACCCGCGAGTTATA 60.076 57.895 8.23 0.00 0.00 0.98
905 915 2.364579 TCCCCACCCGCGAGTTAT 60.365 61.111 8.23 0.00 0.00 1.89
906 916 3.072468 CTCCCCACCCGCGAGTTA 61.072 66.667 8.23 0.00 0.00 2.24
917 927 1.918293 CCTAGTGTGGTGCTCCCCA 60.918 63.158 1.59 0.00 0.00 4.96
918 928 1.198759 TTCCTAGTGTGGTGCTCCCC 61.199 60.000 1.59 0.00 0.00 4.81
919 929 0.250513 CTTCCTAGTGTGGTGCTCCC 59.749 60.000 1.59 0.00 0.00 4.30
920 930 0.250513 CCTTCCTAGTGTGGTGCTCC 59.749 60.000 0.00 0.00 0.00 4.70
921 931 1.267121 TCCTTCCTAGTGTGGTGCTC 58.733 55.000 0.00 0.00 0.00 4.26
922 932 1.625818 CTTCCTTCCTAGTGTGGTGCT 59.374 52.381 0.00 0.00 0.00 4.40
923 933 1.339151 CCTTCCTTCCTAGTGTGGTGC 60.339 57.143 0.00 0.00 0.00 5.01
924 934 2.234908 CTCCTTCCTTCCTAGTGTGGTG 59.765 54.545 0.00 0.00 0.00 4.17
925 935 2.541466 CTCCTTCCTTCCTAGTGTGGT 58.459 52.381 0.00 0.00 0.00 4.16
926 936 1.208293 GCTCCTTCCTTCCTAGTGTGG 59.792 57.143 0.00 0.00 0.00 4.17
927 937 1.208293 GGCTCCTTCCTTCCTAGTGTG 59.792 57.143 0.00 0.00 0.00 3.82
928 938 1.574263 GGCTCCTTCCTTCCTAGTGT 58.426 55.000 0.00 0.00 0.00 3.55
929 939 0.833949 GGGCTCCTTCCTTCCTAGTG 59.166 60.000 0.00 0.00 0.00 2.74
930 940 0.326713 GGGGCTCCTTCCTTCCTAGT 60.327 60.000 0.00 0.00 0.00 2.57
931 941 0.326618 TGGGGCTCCTTCCTTCCTAG 60.327 60.000 3.07 0.00 0.00 3.02
932 942 0.346932 ATGGGGCTCCTTCCTTCCTA 59.653 55.000 3.07 0.00 0.00 2.94
933 943 0.990818 GATGGGGCTCCTTCCTTCCT 60.991 60.000 3.07 0.00 32.71 3.36
934 944 1.534203 GATGGGGCTCCTTCCTTCC 59.466 63.158 3.07 0.00 32.71 3.46
939 949 1.076705 GGTTGGATGGGGCTCCTTC 60.077 63.158 10.10 10.10 36.20 3.46
940 950 2.626467 GGGTTGGATGGGGCTCCTT 61.626 63.158 3.07 0.00 36.20 3.36
941 951 3.023735 GGGTTGGATGGGGCTCCT 61.024 66.667 3.07 0.00 36.20 3.69
942 952 4.143301 GGGGTTGGATGGGGCTCC 62.143 72.222 0.00 0.00 35.74 4.70
943 953 1.286305 TTAGGGGTTGGATGGGGCTC 61.286 60.000 0.00 0.00 0.00 4.70
944 954 1.230482 TTAGGGGTTGGATGGGGCT 60.230 57.895 0.00 0.00 0.00 5.19
945 955 1.076265 GTTAGGGGTTGGATGGGGC 60.076 63.158 0.00 0.00 0.00 5.80
946 956 1.618586 GGTTAGGGGTTGGATGGGG 59.381 63.158 0.00 0.00 0.00 4.96
947 957 1.618586 GGGTTAGGGGTTGGATGGG 59.381 63.158 0.00 0.00 0.00 4.00
948 958 1.618586 GGGGTTAGGGGTTGGATGG 59.381 63.158 0.00 0.00 0.00 3.51
949 959 1.618586 GGGGGTTAGGGGTTGGATG 59.381 63.158 0.00 0.00 0.00 3.51
950 960 4.199287 GGGGGTTAGGGGTTGGAT 57.801 61.111 0.00 0.00 0.00 3.41
965 975 4.675303 TGTGGTGGGAGGGAGGGG 62.675 72.222 0.00 0.00 0.00 4.79
966 976 2.160171 TTTGTGGTGGGAGGGAGGG 61.160 63.158 0.00 0.00 0.00 4.30
967 977 1.074951 GTTTGTGGTGGGAGGGAGG 59.925 63.158 0.00 0.00 0.00 4.30
968 978 1.074951 GGTTTGTGGTGGGAGGGAG 59.925 63.158 0.00 0.00 0.00 4.30
969 979 2.466186 GGGTTTGTGGTGGGAGGGA 61.466 63.158 0.00 0.00 0.00 4.20
970 980 2.117423 GGGTTTGTGGTGGGAGGG 59.883 66.667 0.00 0.00 0.00 4.30
971 981 2.117423 GGGGTTTGTGGTGGGAGG 59.883 66.667 0.00 0.00 0.00 4.30
972 982 2.282180 CGGGGTTTGTGGTGGGAG 60.282 66.667 0.00 0.00 0.00 4.30
973 983 4.589675 GCGGGGTTTGTGGTGGGA 62.590 66.667 0.00 0.00 0.00 4.37
1062 1078 3.057548 TCGTTGGAGGCGTCGCTA 61.058 61.111 18.11 0.00 0.00 4.26
1305 1345 1.211969 CGTGTCGTACTGGTGGGAG 59.788 63.158 0.00 0.00 0.00 4.30
1308 1348 2.260434 CCCGTGTCGTACTGGTGG 59.740 66.667 0.00 0.00 0.00 4.61
1642 1691 0.684479 TCCTCGACAGCAGCAGGTAT 60.684 55.000 0.00 0.00 0.00 2.73
1643 1692 1.304134 TCCTCGACAGCAGCAGGTA 60.304 57.895 0.00 0.00 0.00 3.08
1644 1693 2.601666 TCCTCGACAGCAGCAGGT 60.602 61.111 0.00 0.00 0.00 4.00
1653 1702 2.603473 CCACCACCCTCCTCGACA 60.603 66.667 0.00 0.00 0.00 4.35
1733 1782 2.586245 CCTCAATCTCCTGCGCCA 59.414 61.111 4.18 0.00 0.00 5.69
1805 1854 1.421410 CTCGAACGCCGCAATAGCTT 61.421 55.000 0.00 0.00 39.10 3.74
1812 1861 2.430244 GAACTCTCGAACGCCGCA 60.430 61.111 0.00 0.00 38.37 5.69
1974 2026 1.950748 ATCCTAGTCCGGTCTGCCCT 61.951 60.000 11.77 0.00 0.00 5.19
2300 2356 1.750193 AGAACACCACCAACACTGTG 58.250 50.000 6.19 6.19 34.92 3.66
2305 2361 3.576078 ATGAGAAGAACACCACCAACA 57.424 42.857 0.00 0.00 0.00 3.33
2363 2421 6.878317 TCTCTAACCTTATGATGACAACCAG 58.122 40.000 0.00 0.00 0.00 4.00
2364 2422 6.867519 TCTCTAACCTTATGATGACAACCA 57.132 37.500 0.00 0.00 0.00 3.67
2365 2423 7.500992 TCATCTCTAACCTTATGATGACAACC 58.499 38.462 0.00 0.00 38.67 3.77
2428 2489 5.814705 AGCATAAAGTGAGCTACAAGTGATC 59.185 40.000 0.00 0.00 36.73 2.92
2450 2511 5.121298 TGCATTTCTTATATCGCATCAGAGC 59.879 40.000 0.00 0.00 0.00 4.09
2480 2553 6.127366 GCCATAAATCTCCAGATTCAAAACCA 60.127 38.462 2.24 0.00 43.41 3.67
2544 6118 7.800767 TGTTTTCAATTTCATCTCTCTTCTCG 58.199 34.615 0.00 0.00 0.00 4.04
2576 6153 2.917933 TCCAGGCAGCACATGTATTAC 58.082 47.619 0.00 0.00 0.00 1.89
2577 6154 3.278574 GTTCCAGGCAGCACATGTATTA 58.721 45.455 0.00 0.00 0.00 0.98
2578 6155 2.094675 GTTCCAGGCAGCACATGTATT 58.905 47.619 0.00 0.00 0.00 1.89
2676 6253 5.160607 ACGGAATTGACTCAAACTGGATA 57.839 39.130 0.00 0.00 0.00 2.59
2696 6273 2.224549 TGTCAACGGCTTAATCCAAACG 59.775 45.455 0.00 0.00 0.00 3.60
2899 6482 7.827729 TGCTTCAGTCTGTCTATACTAAGTACA 59.172 37.037 0.00 0.00 0.00 2.90
2900 6483 8.211116 TGCTTCAGTCTGTCTATACTAAGTAC 57.789 38.462 0.00 0.00 0.00 2.73
2901 6484 8.982091 ATGCTTCAGTCTGTCTATACTAAGTA 57.018 34.615 0.00 0.00 0.00 2.24
2902 6485 7.558081 TGATGCTTCAGTCTGTCTATACTAAGT 59.442 37.037 0.00 0.00 0.00 2.24
2903 6486 7.935520 TGATGCTTCAGTCTGTCTATACTAAG 58.064 38.462 0.00 0.00 0.00 2.18
2904 6487 7.881775 TGATGCTTCAGTCTGTCTATACTAA 57.118 36.000 0.00 0.00 0.00 2.24
3016 6601 2.495669 GCAAGAGGAGTAAGACTCTGCT 59.504 50.000 6.58 2.17 44.46 4.24
3022 6607 1.552792 AGCCTGCAAGAGGAGTAAGAC 59.447 52.381 0.00 0.00 46.33 3.01
3087 6703 0.249489 CACTGGGATACGCCTGCTAC 60.249 60.000 0.00 0.00 36.66 3.58
3123 6739 3.768185 CTATGGCTACGGCGTGCGT 62.768 63.158 24.86 16.83 39.81 5.24
3147 6766 1.359459 GCCACTACTACAGCAACGGC 61.359 60.000 0.00 0.00 41.61 5.68
3148 6767 0.037697 TGCCACTACTACAGCAACGG 60.038 55.000 0.00 0.00 30.97 4.44
3149 6768 1.350193 CTGCCACTACTACAGCAACG 58.650 55.000 0.00 0.00 34.26 4.10


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

AutoCloner maintained by Alex Coulton.