Multiple sequence alignment - TraesCS1A01G117700

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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 TraesCS1A01G117700 chr1A 100.000 3533 0 0 1 3533 125111590 125108058 0.000000e+00 6525
1 TraesCS1A01G117700 chr1A 95.200 750 35 1 1 749 551668452 551667703 0.000000e+00 1184
2 TraesCS1A01G117700 chr1A 79.509 1425 262 19 1048 2459 569255710 569257117 0.000000e+00 987
3 TraesCS1A01G117700 chr1A 81.471 367 52 15 2982 3338 574506816 574506456 1.600000e-73 287
4 TraesCS1A01G117700 chr1A 80.201 298 47 10 3049 3338 321184657 321184950 2.760000e-51 213
5 TraesCS1A01G117700 chr1D 94.428 1741 60 16 974 2687 114392015 114390285 0.000000e+00 2643
6 TraesCS1A01G117700 chr1D 81.369 1417 247 15 1048 2457 114645771 114647177 0.000000e+00 1138
7 TraesCS1A01G117700 chr1D 81.497 481 63 17 2877 3338 9750771 9750298 4.310000e-99 372
8 TraesCS1A01G117700 chr1D 94.656 131 7 0 849 979 114392181 114392051 1.660000e-48 204
9 TraesCS1A01G117700 chr1B 94.176 1013 38 2 1675 2687 175604815 175603824 0.000000e+00 1524
10 TraesCS1A01G117700 chr1B 80.169 1417 268 12 1048 2459 175661169 175662577 0.000000e+00 1048
11 TraesCS1A01G117700 chr1B 85.123 773 101 10 2770 3533 175603480 175602713 0.000000e+00 778
12 TraesCS1A01G117700 chr3A 95.867 750 29 2 1 749 649849908 649850656 0.000000e+00 1212
13 TraesCS1A01G117700 chr7A 95.346 752 35 0 1 752 724088571 724087820 0.000000e+00 1195
14 TraesCS1A01G117700 chr7A 79.412 204 35 6 3112 3309 2228871 2229073 1.710000e-28 137
15 TraesCS1A01G117700 chr5A 95.340 751 33 2 1 749 640396392 640395642 0.000000e+00 1192
16 TraesCS1A01G117700 chr5A 95.219 753 32 2 1 749 264075449 264074697 0.000000e+00 1188
17 TraesCS1A01G117700 chr5A 95.225 754 31 3 1 749 338928374 338929127 0.000000e+00 1188
18 TraesCS1A01G117700 chr5A 94.954 753 36 2 1 751 631638636 631637884 0.000000e+00 1179
19 TraesCS1A01G117700 chr5A 80.136 1470 266 17 1002 2459 624708281 624706826 0.000000e+00 1074
20 TraesCS1A01G117700 chr2A 95.340 751 33 2 1 749 772452243 772451493 0.000000e+00 1192
21 TraesCS1A01G117700 chr2A 95.333 750 32 3 1 749 382626428 382627175 0.000000e+00 1188
22 TraesCS1A01G117700 chr2A 81.989 372 49 16 2976 3337 66790268 66789905 2.060000e-77 300
23 TraesCS1A01G117700 chr5D 80.417 1440 251 20 1048 2469 545112883 545111457 0.000000e+00 1068
24 TraesCS1A01G117700 chr5D 79.946 369 58 14 2981 3337 232835919 232835555 1.260000e-64 257
25 TraesCS1A01G117700 chr4A 79.930 1425 256 19 1048 2459 624834603 624833196 0.000000e+00 1020
26 TraesCS1A01G117700 chr5B 79.617 1462 264 20 1018 2459 687694730 687696177 0.000000e+00 1018
27 TraesCS1A01G117700 chr5B 81.699 1224 206 7 1018 2232 687469717 687468503 0.000000e+00 1003
28 TraesCS1A01G117700 chr7B 79.912 453 66 14 2876 3309 718149457 718149011 3.430000e-80 309
29 TraesCS1A01G117700 chr2D 82.133 375 52 14 2973 3338 67572849 67573217 1.230000e-79 307


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 TraesCS1A01G117700 chr1A 125108058 125111590 3532 True 6525.0 6525 100.0000 1 3533 1 chr1A.!!$R1 3532
1 TraesCS1A01G117700 chr1A 551667703 551668452 749 True 1184.0 1184 95.2000 1 749 1 chr1A.!!$R2 748
2 TraesCS1A01G117700 chr1A 569255710 569257117 1407 False 987.0 987 79.5090 1048 2459 1 chr1A.!!$F2 1411
3 TraesCS1A01G117700 chr1D 114390285 114392181 1896 True 1423.5 2643 94.5420 849 2687 2 chr1D.!!$R2 1838
4 TraesCS1A01G117700 chr1D 114645771 114647177 1406 False 1138.0 1138 81.3690 1048 2457 1 chr1D.!!$F1 1409
5 TraesCS1A01G117700 chr1B 175602713 175604815 2102 True 1151.0 1524 89.6495 1675 3533 2 chr1B.!!$R1 1858
6 TraesCS1A01G117700 chr1B 175661169 175662577 1408 False 1048.0 1048 80.1690 1048 2459 1 chr1B.!!$F1 1411
7 TraesCS1A01G117700 chr3A 649849908 649850656 748 False 1212.0 1212 95.8670 1 749 1 chr3A.!!$F1 748
8 TraesCS1A01G117700 chr7A 724087820 724088571 751 True 1195.0 1195 95.3460 1 752 1 chr7A.!!$R1 751
9 TraesCS1A01G117700 chr5A 640395642 640396392 750 True 1192.0 1192 95.3400 1 749 1 chr5A.!!$R4 748
10 TraesCS1A01G117700 chr5A 264074697 264075449 752 True 1188.0 1188 95.2190 1 749 1 chr5A.!!$R1 748
11 TraesCS1A01G117700 chr5A 338928374 338929127 753 False 1188.0 1188 95.2250 1 749 1 chr5A.!!$F1 748
12 TraesCS1A01G117700 chr5A 631637884 631638636 752 True 1179.0 1179 94.9540 1 751 1 chr5A.!!$R3 750
13 TraesCS1A01G117700 chr5A 624706826 624708281 1455 True 1074.0 1074 80.1360 1002 2459 1 chr5A.!!$R2 1457
14 TraesCS1A01G117700 chr2A 772451493 772452243 750 True 1192.0 1192 95.3400 1 749 1 chr2A.!!$R2 748
15 TraesCS1A01G117700 chr2A 382626428 382627175 747 False 1188.0 1188 95.3330 1 749 1 chr2A.!!$F1 748
16 TraesCS1A01G117700 chr5D 545111457 545112883 1426 True 1068.0 1068 80.4170 1048 2469 1 chr5D.!!$R2 1421
17 TraesCS1A01G117700 chr4A 624833196 624834603 1407 True 1020.0 1020 79.9300 1048 2459 1 chr4A.!!$R1 1411
18 TraesCS1A01G117700 chr5B 687694730 687696177 1447 False 1018.0 1018 79.6170 1018 2459 1 chr5B.!!$F1 1441
19 TraesCS1A01G117700 chr5B 687468503 687469717 1214 True 1003.0 1003 81.6990 1018 2232 1 chr5B.!!$R1 1214

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
771 777 0.234625 GCACACGCATTTGTCTCGAA 59.765 50.0 0.0 0.0 38.36 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2706 2807 0.037326 ATGACACGCCGTTGACATCT 60.037 50.0 0.0 0.0 27.4 2.9 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
642 643 3.439540 GCCAATTTCGGCGCCTGA 61.440 61.111 26.68 20.38 43.52 3.86
644 645 1.745115 CCAATTTCGGCGCCTGAGA 60.745 57.895 26.68 18.36 0.00 3.27
658 659 3.749064 GAGAGCGACGACTGGGCA 61.749 66.667 0.00 0.00 0.00 5.36
687 689 1.224069 CCCAGCGCTGATTGTATCGG 61.224 60.000 38.06 23.13 38.71 4.18
694 696 0.249447 CTGATTGTATCGGCGGCTCA 60.249 55.000 7.21 0.60 0.00 4.26
720 722 2.869801 CAGGAGGCGATTTTTATGCGTA 59.130 45.455 0.00 0.00 0.00 4.42
726 729 3.064271 GGCGATTTTTATGCGTACTGGAA 59.936 43.478 0.00 0.00 0.00 3.53
729 735 4.569162 CGATTTTTATGCGTACTGGAAGGA 59.431 41.667 0.00 0.00 39.30 3.36
752 758 1.065418 ACGGTTGGAGATGCCCTAAAG 60.065 52.381 0.00 0.00 34.97 1.85
753 759 1.393603 GGTTGGAGATGCCCTAAAGC 58.606 55.000 0.00 0.00 34.97 3.51
760 766 2.112087 TGCCCTAAAGCACACGCA 59.888 55.556 0.00 0.00 42.27 5.24
761 767 1.303236 TGCCCTAAAGCACACGCAT 60.303 52.632 0.00 0.00 42.27 4.73
762 768 0.893270 TGCCCTAAAGCACACGCATT 60.893 50.000 0.00 0.00 42.27 3.56
763 769 0.243636 GCCCTAAAGCACACGCATTT 59.756 50.000 0.00 0.00 42.27 2.32
764 770 1.981254 CCCTAAAGCACACGCATTTG 58.019 50.000 0.00 0.00 42.27 2.32
765 771 1.269448 CCCTAAAGCACACGCATTTGT 59.731 47.619 0.00 0.00 42.27 2.83
766 772 2.584791 CCTAAAGCACACGCATTTGTC 58.415 47.619 0.00 0.00 42.27 3.18
767 773 2.226437 CCTAAAGCACACGCATTTGTCT 59.774 45.455 0.00 0.00 42.27 3.41
768 774 2.405892 AAAGCACACGCATTTGTCTC 57.594 45.000 0.00 0.00 42.27 3.36
769 775 0.235665 AAGCACACGCATTTGTCTCG 59.764 50.000 0.00 0.00 42.27 4.04
770 776 0.599991 AGCACACGCATTTGTCTCGA 60.600 50.000 0.00 0.00 42.27 4.04
771 777 0.234625 GCACACGCATTTGTCTCGAA 59.765 50.000 0.00 0.00 38.36 3.71
772 778 1.333702 GCACACGCATTTGTCTCGAAA 60.334 47.619 0.00 0.00 38.36 3.46
773 779 2.852901 GCACACGCATTTGTCTCGAAAA 60.853 45.455 0.00 0.00 38.36 2.29
774 780 2.713976 CACACGCATTTGTCTCGAAAAC 59.286 45.455 0.00 0.00 0.00 2.43
775 781 2.353269 ACACGCATTTGTCTCGAAAACA 59.647 40.909 0.00 0.00 0.00 2.83
776 782 3.181505 ACACGCATTTGTCTCGAAAACAA 60.182 39.130 8.53 8.53 34.93 2.83
778 784 3.789224 ACGCATTTGTCTCGAAAACAAAC 59.211 39.130 21.43 12.66 46.19 2.93
779 785 3.179599 CGCATTTGTCTCGAAAACAAACC 59.820 43.478 21.43 15.97 46.19 3.27
780 786 3.489416 GCATTTGTCTCGAAAACAAACCC 59.511 43.478 21.43 14.20 46.19 4.11
781 787 4.736464 GCATTTGTCTCGAAAACAAACCCT 60.736 41.667 21.43 8.93 46.19 4.34
782 788 4.625972 TTTGTCTCGAAAACAAACCCTC 57.374 40.909 17.32 0.00 40.64 4.30
783 789 3.269538 TGTCTCGAAAACAAACCCTCA 57.730 42.857 0.00 0.00 0.00 3.86
784 790 2.940410 TGTCTCGAAAACAAACCCTCAC 59.060 45.455 0.00 0.00 0.00 3.51
785 791 2.289820 GTCTCGAAAACAAACCCTCACC 59.710 50.000 0.00 0.00 0.00 4.02
786 792 2.171870 TCTCGAAAACAAACCCTCACCT 59.828 45.455 0.00 0.00 0.00 4.00
787 793 2.949644 CTCGAAAACAAACCCTCACCTT 59.050 45.455 0.00 0.00 0.00 3.50
788 794 2.946990 TCGAAAACAAACCCTCACCTTC 59.053 45.455 0.00 0.00 0.00 3.46
789 795 2.286772 CGAAAACAAACCCTCACCTTCG 60.287 50.000 0.00 0.00 0.00 3.79
790 796 2.721425 AAACAAACCCTCACCTTCGA 57.279 45.000 0.00 0.00 0.00 3.71
791 797 1.963172 AACAAACCCTCACCTTCGAC 58.037 50.000 0.00 0.00 0.00 4.20
792 798 0.249741 ACAAACCCTCACCTTCGACG 60.250 55.000 0.00 0.00 0.00 5.12
793 799 0.249741 CAAACCCTCACCTTCGACGT 60.250 55.000 0.00 0.00 0.00 4.34
794 800 0.249741 AAACCCTCACCTTCGACGTG 60.250 55.000 0.00 5.62 0.00 4.49
795 801 2.095978 AACCCTCACCTTCGACGTGG 62.096 60.000 10.98 0.00 0.00 4.94
796 802 2.432628 CCTCACCTTCGACGTGGC 60.433 66.667 10.98 0.00 0.00 5.01
797 803 2.432628 CTCACCTTCGACGTGGCC 60.433 66.667 10.98 0.00 0.00 5.36
798 804 2.915659 TCACCTTCGACGTGGCCT 60.916 61.111 3.32 0.00 0.00 5.19
799 805 2.432628 CACCTTCGACGTGGCCTC 60.433 66.667 3.32 0.00 0.00 4.70
800 806 4.052229 ACCTTCGACGTGGCCTCG 62.052 66.667 24.76 24.76 0.00 4.63
801 807 4.052229 CCTTCGACGTGGCCTCGT 62.052 66.667 31.20 31.20 46.88 4.18
802 808 2.049433 CTTCGACGTGGCCTCGTT 60.049 61.111 31.24 16.70 44.21 3.85
803 809 2.049802 TTCGACGTGGCCTCGTTC 60.050 61.111 31.24 22.14 44.21 3.95
804 810 3.562779 TTCGACGTGGCCTCGTTCC 62.563 63.158 31.24 19.39 44.21 3.62
805 811 4.052229 CGACGTGGCCTCGTTCCT 62.052 66.667 31.24 10.99 44.21 3.36
806 812 2.342648 GACGTGGCCTCGTTCCTT 59.657 61.111 31.24 10.60 44.21 3.36
807 813 1.737008 GACGTGGCCTCGTTCCTTC 60.737 63.158 31.24 16.03 44.21 3.46
808 814 2.434359 CGTGGCCTCGTTCCTTCC 60.434 66.667 18.86 0.00 0.00 3.46
809 815 2.747686 GTGGCCTCGTTCCTTCCA 59.252 61.111 3.32 0.00 0.00 3.53
810 816 1.299976 GTGGCCTCGTTCCTTCCAT 59.700 57.895 3.32 0.00 0.00 3.41
811 817 0.322546 GTGGCCTCGTTCCTTCCATT 60.323 55.000 3.32 0.00 0.00 3.16
812 818 0.404040 TGGCCTCGTTCCTTCCATTT 59.596 50.000 3.32 0.00 0.00 2.32
813 819 1.095600 GGCCTCGTTCCTTCCATTTC 58.904 55.000 0.00 0.00 0.00 2.17
814 820 1.613255 GGCCTCGTTCCTTCCATTTCA 60.613 52.381 0.00 0.00 0.00 2.69
815 821 2.159382 GCCTCGTTCCTTCCATTTCAA 58.841 47.619 0.00 0.00 0.00 2.69
816 822 2.095212 GCCTCGTTCCTTCCATTTCAAC 60.095 50.000 0.00 0.00 0.00 3.18
817 823 3.412386 CCTCGTTCCTTCCATTTCAACT 58.588 45.455 0.00 0.00 0.00 3.16
818 824 3.437049 CCTCGTTCCTTCCATTTCAACTC 59.563 47.826 0.00 0.00 0.00 3.01
819 825 4.319177 CTCGTTCCTTCCATTTCAACTCT 58.681 43.478 0.00 0.00 0.00 3.24
820 826 4.714632 TCGTTCCTTCCATTTCAACTCTT 58.285 39.130 0.00 0.00 0.00 2.85
821 827 4.515191 TCGTTCCTTCCATTTCAACTCTTG 59.485 41.667 0.00 0.00 0.00 3.02
822 828 4.320494 CGTTCCTTCCATTTCAACTCTTGG 60.320 45.833 0.00 0.00 0.00 3.61
823 829 4.722526 TCCTTCCATTTCAACTCTTGGA 57.277 40.909 0.00 0.00 36.49 3.53
824 830 4.398319 TCCTTCCATTTCAACTCTTGGAC 58.602 43.478 0.00 0.00 37.97 4.02
825 831 3.189287 CCTTCCATTTCAACTCTTGGACG 59.811 47.826 0.00 0.00 37.97 4.79
826 832 3.485463 TCCATTTCAACTCTTGGACGT 57.515 42.857 0.00 0.00 33.40 4.34
827 833 3.399330 TCCATTTCAACTCTTGGACGTC 58.601 45.455 7.13 7.13 33.40 4.34
828 834 3.071023 TCCATTTCAACTCTTGGACGTCT 59.929 43.478 16.46 0.00 33.40 4.18
829 835 4.282449 TCCATTTCAACTCTTGGACGTCTA 59.718 41.667 16.46 6.50 33.40 2.59
830 836 4.389077 CCATTTCAACTCTTGGACGTCTAC 59.611 45.833 16.46 0.00 0.00 2.59
831 837 3.655276 TTCAACTCTTGGACGTCTACC 57.345 47.619 16.46 0.00 0.00 3.18
832 838 2.872732 TCAACTCTTGGACGTCTACCT 58.127 47.619 16.46 0.00 0.00 3.08
833 839 2.818432 TCAACTCTTGGACGTCTACCTC 59.182 50.000 16.46 0.00 0.00 3.85
834 840 1.451067 ACTCTTGGACGTCTACCTCG 58.549 55.000 16.46 2.88 0.00 4.63
835 841 0.733729 CTCTTGGACGTCTACCTCGG 59.266 60.000 16.46 0.00 0.00 4.63
836 842 0.679002 TCTTGGACGTCTACCTCGGG 60.679 60.000 16.46 0.00 0.00 5.14
837 843 0.964358 CTTGGACGTCTACCTCGGGT 60.964 60.000 16.46 1.14 40.16 5.28
838 844 0.962356 TTGGACGTCTACCTCGGGTC 60.962 60.000 16.46 0.00 37.09 4.46
839 845 2.117779 GGACGTCTACCTCGGGTCC 61.118 68.421 16.46 0.00 40.24 4.46
840 846 1.377725 GACGTCTACCTCGGGTCCA 60.378 63.158 8.70 0.00 37.09 4.02
841 847 0.962356 GACGTCTACCTCGGGTCCAA 60.962 60.000 8.70 0.00 37.09 3.53
842 848 1.246737 ACGTCTACCTCGGGTCCAAC 61.247 60.000 0.00 0.00 37.09 3.77
843 849 1.509923 GTCTACCTCGGGTCCAACG 59.490 63.158 0.00 0.00 37.09 4.10
844 850 0.962356 GTCTACCTCGGGTCCAACGA 60.962 60.000 0.00 0.00 37.09 3.85
870 876 3.005050 CACGAGTGGTACTGTACTTTCCA 59.995 47.826 16.79 4.52 0.00 3.53
883 889 1.558294 ACTTTCCAGGTCCGTATTCCC 59.442 52.381 0.00 0.00 0.00 3.97
913 919 4.201910 CCATCGATCGCAATAAAACCTTGT 60.202 41.667 11.09 0.00 0.00 3.16
943 949 2.964978 GGGCCACACAATGCACTC 59.035 61.111 4.39 0.00 0.00 3.51
950 956 2.112928 ACAATGCACTCACCCGCA 59.887 55.556 0.00 0.00 43.45 5.69
995 1043 0.248498 CATCCATCTTTGCAGCTGCG 60.248 55.000 32.11 19.09 45.83 5.18
1251 1312 2.754658 GAGCTCGAGTTCCCGGGA 60.755 66.667 22.63 22.63 30.09 5.14
1921 1997 4.287781 TCGCGCACTTGTTCCCGA 62.288 61.111 8.75 0.00 0.00 5.14
2328 2410 2.435059 GAGAGAGCGGTGGTTGCC 60.435 66.667 0.00 0.00 0.00 4.52
2487 2569 0.735287 GTAAAGACGCCGTGGAGGTC 60.735 60.000 0.00 0.00 43.70 3.85
2518 2600 0.906756 TGACCTCAGGGAGCAGGAAG 60.907 60.000 0.00 0.00 36.25 3.46
2536 2618 5.578727 CAGGAAGAAGAAACTAGTTGATCCG 59.421 44.000 9.34 4.63 0.00 4.18
2564 2647 3.071602 ACAAATAGTGGGGATCGATCAGG 59.928 47.826 25.93 5.78 0.00 3.86
2683 2784 2.780643 CAGCAGATGTCAACGGCG 59.219 61.111 4.80 4.80 34.06 6.46
2687 2788 1.841663 GCAGATGTCAACGGCGTGTT 61.842 55.000 15.70 0.00 43.09 3.32
2688 2789 1.424403 CAGATGTCAACGGCGTGTTA 58.576 50.000 15.70 0.42 39.29 2.41
2689 2790 1.126113 CAGATGTCAACGGCGTGTTAC 59.874 52.381 15.70 12.95 39.29 2.50
2690 2791 1.000506 AGATGTCAACGGCGTGTTACT 59.999 47.619 15.70 6.10 39.29 2.24
2691 2792 1.796459 GATGTCAACGGCGTGTTACTT 59.204 47.619 15.70 10.37 39.29 2.24
2692 2793 1.654317 TGTCAACGGCGTGTTACTTT 58.346 45.000 15.70 0.00 39.29 2.66
2693 2794 1.593933 TGTCAACGGCGTGTTACTTTC 59.406 47.619 15.70 0.00 39.29 2.62
2694 2795 1.593933 GTCAACGGCGTGTTACTTTCA 59.406 47.619 15.70 0.00 39.29 2.69
2695 2796 2.030701 GTCAACGGCGTGTTACTTTCAA 59.969 45.455 15.70 0.00 39.29 2.69
2696 2797 2.676839 TCAACGGCGTGTTACTTTCAAA 59.323 40.909 15.70 0.00 39.29 2.69
2697 2798 3.126514 TCAACGGCGTGTTACTTTCAAAA 59.873 39.130 15.70 0.00 39.29 2.44
2698 2799 3.761311 ACGGCGTGTTACTTTCAAAAA 57.239 38.095 13.76 0.00 0.00 1.94
2729 2830 0.584396 GTCAACGGCGTGTCATCAAA 59.416 50.000 15.70 0.00 0.00 2.69
2730 2831 0.865111 TCAACGGCGTGTCATCAAAG 59.135 50.000 15.70 0.00 0.00 2.77
2733 2836 1.359848 ACGGCGTGTCATCAAAGATC 58.640 50.000 13.76 0.00 0.00 2.75
2786 3184 8.930760 TGGTCATTTACTTTTCAAAACAACTTG 58.069 29.630 0.00 0.00 0.00 3.16
2816 3214 2.188062 ACCCAATTGCCAGCAAAATG 57.812 45.000 9.44 11.13 39.55 2.32
2848 3246 8.964420 TCATTTAAATTCTTTTTCTAGCCGTG 57.036 30.769 0.00 0.00 0.00 4.94
2852 3250 5.391312 AATTCTTTTTCTAGCCGTGCATT 57.609 34.783 0.00 0.00 0.00 3.56
2854 3252 4.939509 TCTTTTTCTAGCCGTGCATTAC 57.060 40.909 0.00 0.00 0.00 1.89
2861 3259 5.777850 TCTAGCCGTGCATTACTGTATTA 57.222 39.130 0.00 0.00 0.00 0.98
2922 3320 1.072159 GCACTCACCTGCCAAGTCT 59.928 57.895 0.00 0.00 0.00 3.24
2923 3321 0.536006 GCACTCACCTGCCAAGTCTT 60.536 55.000 0.00 0.00 0.00 3.01
2924 3322 1.233019 CACTCACCTGCCAAGTCTTG 58.767 55.000 5.53 5.53 0.00 3.02
2926 3324 0.250640 CTCACCTGCCAAGTCTTGCT 60.251 55.000 7.09 0.00 0.00 3.91
2927 3325 0.535780 TCACCTGCCAAGTCTTGCTG 60.536 55.000 7.09 6.92 0.00 4.41
2928 3326 1.900498 ACCTGCCAAGTCTTGCTGC 60.900 57.895 7.09 6.94 0.00 5.25
2929 3327 2.633509 CCTGCCAAGTCTTGCTGCC 61.634 63.158 7.09 0.00 0.00 4.85
2931 3329 1.863662 CTGCCAAGTCTTGCTGCCTG 61.864 60.000 7.09 0.00 0.00 4.85
2934 3332 1.584380 CCAAGTCTTGCTGCCTGCTC 61.584 60.000 7.09 0.00 43.37 4.26
2935 3333 0.887836 CAAGTCTTGCTGCCTGCTCA 60.888 55.000 0.00 0.00 43.37 4.26
2936 3334 0.888285 AAGTCTTGCTGCCTGCTCAC 60.888 55.000 0.00 0.00 43.37 3.51
2937 3335 2.357881 TCTTGCTGCCTGCTCACG 60.358 61.111 0.00 0.00 43.37 4.35
2943 3341 1.094073 GCTGCCTGCTCACGATTCAT 61.094 55.000 0.00 0.00 38.95 2.57
2953 3351 6.074088 CCTGCTCACGATTCATACAATAGTTC 60.074 42.308 0.00 0.00 0.00 3.01
2958 3356 8.365399 TCACGATTCATACAATAGTTCAATCC 57.635 34.615 0.00 0.00 0.00 3.01
2959 3357 7.441157 TCACGATTCATACAATAGTTCAATCCC 59.559 37.037 0.00 0.00 0.00 3.85
2962 3360 4.055360 TCATACAATAGTTCAATCCCGCG 58.945 43.478 0.00 0.00 0.00 6.46
2963 3361 2.396590 ACAATAGTTCAATCCCGCGT 57.603 45.000 4.92 0.00 0.00 6.01
2966 3364 2.225068 ATAGTTCAATCCCGCGTGAG 57.775 50.000 4.92 0.00 0.00 3.51
2968 3366 1.079405 GTTCAATCCCGCGTGAGGA 60.079 57.895 4.92 4.97 37.93 3.71
2971 3369 1.153369 CAATCCCGCGTGAGGACAT 60.153 57.895 4.92 0.00 35.85 3.06
3011 3409 9.634300 TTTTAACGTTTGAAACTTGTGTTTTTC 57.366 25.926 5.91 0.00 45.36 2.29
3012 3410 5.489011 ACGTTTGAAACTTGTGTTTTTCG 57.511 34.783 6.49 0.00 45.36 3.46
3015 3413 5.443955 CGTTTGAAACTTGTGTTTTTCGCAT 60.444 36.000 6.49 0.00 45.36 4.73
3025 3423 5.527951 TGTGTTTTTCGCATCTAAAATGCT 58.472 33.333 8.24 0.00 42.50 3.79
3034 3432 9.900710 TTTCGCATCTAAAATGCTAAGTTTTAA 57.099 25.926 8.24 0.00 42.50 1.52
3036 3434 7.966204 TCGCATCTAAAATGCTAAGTTTTAACC 59.034 33.333 8.24 0.00 42.50 2.85
3037 3435 7.753132 CGCATCTAAAATGCTAAGTTTTAACCA 59.247 33.333 8.24 0.00 42.50 3.67
3197 3598 7.516198 AATGGATCTTATTTAAAGCGCTCAT 57.484 32.000 12.06 5.48 0.00 2.90
3208 3609 1.154413 GCGCTCATGACAAACACGG 60.154 57.895 0.00 0.00 0.00 4.94
3218 3619 6.607689 TCATGACAAACACGGATATGAAAAC 58.392 36.000 0.00 0.00 0.00 2.43
3283 3685 8.425577 TTGAAAATCGACAGGCAAAATAAAAA 57.574 26.923 0.00 0.00 0.00 1.94
3284 3686 8.600449 TGAAAATCGACAGGCAAAATAAAAAT 57.400 26.923 0.00 0.00 0.00 1.82
3285 3687 9.050601 TGAAAATCGACAGGCAAAATAAAAATT 57.949 25.926 0.00 0.00 0.00 1.82
3338 3740 1.369625 GTGCCACAAATACTCTCCCG 58.630 55.000 0.00 0.00 0.00 5.14
3339 3741 0.251916 TGCCACAAATACTCTCCCGG 59.748 55.000 0.00 0.00 0.00 5.73
3342 3744 2.112998 CCACAAATACTCTCCCGGGTA 58.887 52.381 22.86 9.43 0.00 3.69
3351 3753 3.163467 ACTCTCCCGGGTATTATGCTAC 58.837 50.000 22.86 0.00 0.00 3.58
3382 3787 4.992688 AGAAAAACAACATTGTCGAGCAA 58.007 34.783 0.00 3.49 41.31 3.91
3399 3804 5.411053 TCGAGCAAATGTGTCATTTGTATGA 59.589 36.000 25.51 19.63 40.19 2.15
3401 3806 5.404946 AGCAAATGTGTCATTTGTATGAGC 58.595 37.500 25.51 15.76 41.33 4.26
3402 3807 5.184479 AGCAAATGTGTCATTTGTATGAGCT 59.816 36.000 25.51 17.16 41.33 4.09
3409 3814 5.122239 GTGTCATTTGTATGAGCTTGTAGCA 59.878 40.000 1.09 0.00 45.56 3.49
3420 3825 2.092212 AGCTTGTAGCATGTTAGGCCAT 60.092 45.455 5.01 0.00 45.56 4.40
3425 3830 1.396653 AGCATGTTAGGCCATCTTGC 58.603 50.000 5.01 14.09 34.14 4.01
3428 3833 1.679680 CATGTTAGGCCATCTTGCTGG 59.320 52.381 5.01 0.00 39.45 4.85
3436 3841 1.078918 CATCTTGCTGGGCTCGACA 60.079 57.895 0.00 0.00 0.00 4.35
3442 3847 0.036732 TGCTGGGCTCGACATCTTTT 59.963 50.000 0.00 0.00 0.00 2.27
3484 3889 3.198068 TCTGCATCGATTTTCCAGTAGC 58.802 45.455 0.00 0.00 0.00 3.58
3493 3898 6.173339 TCGATTTTCCAGTAGCTGAATTTCT 58.827 36.000 0.00 0.00 32.44 2.52
3494 3899 6.655003 TCGATTTTCCAGTAGCTGAATTTCTT 59.345 34.615 0.00 0.00 32.44 2.52
3501 3906 4.214971 CAGTAGCTGAATTTCTTGTGTGCT 59.785 41.667 0.00 0.00 32.44 4.40
3512 3918 2.290367 TCTTGTGTGCTTTGTCGGAATG 59.710 45.455 0.00 0.00 0.00 2.67
3513 3919 0.950836 TGTGTGCTTTGTCGGAATGG 59.049 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
215 216 4.448210 GTGTCAAACACTGGGTCTTCTTA 58.552 43.478 3.03 0.00 45.27 2.10
250 251 1.233369 GGCTAGAGGACCCTGCCTA 59.767 63.158 8.24 0.00 38.73 3.93
558 559 1.661112 GAATAGGCTCATATTCGGCGC 59.339 52.381 0.00 0.00 33.68 6.53
598 599 0.038343 GCAGCCCAATTTCAGCGAAA 60.038 50.000 6.26 6.26 35.94 3.46
642 643 4.057428 GTGCCCAGTCGTCGCTCT 62.057 66.667 0.00 0.00 0.00 4.09
644 645 2.933878 TTTTGTGCCCAGTCGTCGCT 62.934 55.000 0.00 0.00 0.00 4.93
698 700 1.597937 CGCATAAAAATCGCCTCCTGC 60.598 52.381 0.00 0.00 0.00 4.85
703 705 2.612212 CCAGTACGCATAAAAATCGCCT 59.388 45.455 0.00 0.00 0.00 5.52
720 722 0.179029 CCAACCGTTGTCCTTCCAGT 60.179 55.000 10.34 0.00 0.00 4.00
726 729 0.321653 GCATCTCCAACCGTTGTCCT 60.322 55.000 10.34 0.00 0.00 3.85
729 735 1.303317 GGGCATCTCCAACCGTTGT 60.303 57.895 10.34 0.00 36.21 3.32
752 758 0.234625 TTCGAGACAAATGCGTGTGC 59.765 50.000 0.00 0.00 43.20 4.57
753 759 2.661504 TTTCGAGACAAATGCGTGTG 57.338 45.000 0.00 0.00 0.00 3.82
754 760 2.353269 TGTTTTCGAGACAAATGCGTGT 59.647 40.909 1.69 0.00 0.00 4.49
755 761 2.980586 TGTTTTCGAGACAAATGCGTG 58.019 42.857 1.69 0.00 0.00 5.34
756 762 3.684103 TTGTTTTCGAGACAAATGCGT 57.316 38.095 12.34 0.00 34.32 5.24
757 763 3.179599 GGTTTGTTTTCGAGACAAATGCG 59.820 43.478 23.29 0.00 45.49 4.73
758 764 3.489416 GGGTTTGTTTTCGAGACAAATGC 59.511 43.478 23.29 15.30 45.49 3.56
759 765 4.932146 AGGGTTTGTTTTCGAGACAAATG 58.068 39.130 23.29 0.00 45.49 2.32
760 766 4.642885 TGAGGGTTTGTTTTCGAGACAAAT 59.357 37.500 23.29 13.27 45.49 2.32
761 767 4.011023 TGAGGGTTTGTTTTCGAGACAAA 58.989 39.130 19.18 19.18 42.78 2.83
762 768 3.375922 GTGAGGGTTTGTTTTCGAGACAA 59.624 43.478 11.10 11.10 35.36 3.18
763 769 2.940410 GTGAGGGTTTGTTTTCGAGACA 59.060 45.455 0.14 0.14 0.00 3.41
764 770 2.289820 GGTGAGGGTTTGTTTTCGAGAC 59.710 50.000 0.00 0.00 0.00 3.36
765 771 2.171870 AGGTGAGGGTTTGTTTTCGAGA 59.828 45.455 0.00 0.00 0.00 4.04
766 772 2.572290 AGGTGAGGGTTTGTTTTCGAG 58.428 47.619 0.00 0.00 0.00 4.04
767 773 2.721425 AGGTGAGGGTTTGTTTTCGA 57.279 45.000 0.00 0.00 0.00 3.71
768 774 2.286772 CGAAGGTGAGGGTTTGTTTTCG 60.287 50.000 0.00 0.00 0.00 3.46
769 775 2.946990 TCGAAGGTGAGGGTTTGTTTTC 59.053 45.455 0.00 0.00 0.00 2.29
770 776 2.686405 GTCGAAGGTGAGGGTTTGTTTT 59.314 45.455 0.00 0.00 0.00 2.43
771 777 2.294979 GTCGAAGGTGAGGGTTTGTTT 58.705 47.619 0.00 0.00 0.00 2.83
772 778 1.808891 CGTCGAAGGTGAGGGTTTGTT 60.809 52.381 0.00 0.00 0.00 2.83
773 779 0.249741 CGTCGAAGGTGAGGGTTTGT 60.250 55.000 0.00 0.00 0.00 2.83
774 780 0.249741 ACGTCGAAGGTGAGGGTTTG 60.250 55.000 0.00 0.00 0.00 2.93
775 781 0.249741 CACGTCGAAGGTGAGGGTTT 60.250 55.000 11.38 0.00 36.17 3.27
776 782 1.366366 CACGTCGAAGGTGAGGGTT 59.634 57.895 11.38 0.00 36.17 4.11
777 783 2.571216 CCACGTCGAAGGTGAGGGT 61.571 63.158 16.94 0.00 36.17 4.34
778 784 2.261671 CCACGTCGAAGGTGAGGG 59.738 66.667 16.94 0.04 36.17 4.30
779 785 2.432628 GCCACGTCGAAGGTGAGG 60.433 66.667 16.94 7.92 36.17 3.86
780 786 2.432628 GGCCACGTCGAAGGTGAG 60.433 66.667 16.94 9.60 36.17 3.51
781 787 2.915659 AGGCCACGTCGAAGGTGA 60.916 61.111 16.94 0.00 36.17 4.02
782 788 2.432628 GAGGCCACGTCGAAGGTG 60.433 66.667 5.01 10.15 34.07 4.00
783 789 4.052229 CGAGGCCACGTCGAAGGT 62.052 66.667 15.01 0.00 43.12 3.50
784 790 3.569049 AACGAGGCCACGTCGAAGG 62.569 63.158 28.37 1.22 45.83 3.46
785 791 2.049433 AACGAGGCCACGTCGAAG 60.049 61.111 28.37 0.00 45.83 3.79
786 792 2.049802 GAACGAGGCCACGTCGAA 60.050 61.111 28.37 0.00 45.83 3.71
787 793 4.047059 GGAACGAGGCCACGTCGA 62.047 66.667 28.37 0.00 45.83 4.20
788 794 3.569049 AAGGAACGAGGCCACGTCG 62.569 63.158 28.37 19.50 45.83 5.12
789 795 1.737008 GAAGGAACGAGGCCACGTC 60.737 63.158 28.37 19.85 45.83 4.34
791 797 2.434359 GGAAGGAACGAGGCCACG 60.434 66.667 21.59 21.59 39.31 4.94
792 798 0.322546 AATGGAAGGAACGAGGCCAC 60.323 55.000 5.01 0.00 0.00 5.01
793 799 0.404040 AAATGGAAGGAACGAGGCCA 59.596 50.000 5.01 0.00 0.00 5.36
794 800 1.095600 GAAATGGAAGGAACGAGGCC 58.904 55.000 0.00 0.00 0.00 5.19
795 801 1.821216 TGAAATGGAAGGAACGAGGC 58.179 50.000 0.00 0.00 0.00 4.70
796 802 3.412386 AGTTGAAATGGAAGGAACGAGG 58.588 45.455 0.00 0.00 0.00 4.63
797 803 4.319177 AGAGTTGAAATGGAAGGAACGAG 58.681 43.478 0.00 0.00 0.00 4.18
798 804 4.351874 AGAGTTGAAATGGAAGGAACGA 57.648 40.909 0.00 0.00 0.00 3.85
799 805 4.320494 CCAAGAGTTGAAATGGAAGGAACG 60.320 45.833 0.00 0.00 34.82 3.95
800 806 4.827284 TCCAAGAGTTGAAATGGAAGGAAC 59.173 41.667 0.00 0.00 38.95 3.62
801 807 4.827284 GTCCAAGAGTTGAAATGGAAGGAA 59.173 41.667 0.00 0.00 43.21 3.36
802 808 4.398319 GTCCAAGAGTTGAAATGGAAGGA 58.602 43.478 0.00 0.00 43.21 3.36
803 809 3.189287 CGTCCAAGAGTTGAAATGGAAGG 59.811 47.826 0.00 0.00 43.21 3.46
804 810 3.815401 ACGTCCAAGAGTTGAAATGGAAG 59.185 43.478 5.28 5.28 43.21 3.46
805 811 3.813166 GACGTCCAAGAGTTGAAATGGAA 59.187 43.478 3.51 0.00 43.21 3.53
806 812 3.071023 AGACGTCCAAGAGTTGAAATGGA 59.929 43.478 13.01 0.00 39.57 3.41
807 813 3.403038 AGACGTCCAAGAGTTGAAATGG 58.597 45.455 13.01 0.00 0.00 3.16
808 814 4.389077 GGTAGACGTCCAAGAGTTGAAATG 59.611 45.833 13.01 0.00 0.00 2.32
809 815 4.283722 AGGTAGACGTCCAAGAGTTGAAAT 59.716 41.667 13.01 0.00 0.00 2.17
810 816 3.640029 AGGTAGACGTCCAAGAGTTGAAA 59.360 43.478 13.01 0.00 0.00 2.69
811 817 3.228453 AGGTAGACGTCCAAGAGTTGAA 58.772 45.455 13.01 0.00 0.00 2.69
812 818 2.818432 GAGGTAGACGTCCAAGAGTTGA 59.182 50.000 13.01 0.00 0.00 3.18
813 819 2.414293 CGAGGTAGACGTCCAAGAGTTG 60.414 54.545 13.01 0.00 0.00 3.16
814 820 1.811359 CGAGGTAGACGTCCAAGAGTT 59.189 52.381 13.01 0.00 0.00 3.01
815 821 1.451067 CGAGGTAGACGTCCAAGAGT 58.549 55.000 13.01 0.00 0.00 3.24
816 822 0.733729 CCGAGGTAGACGTCCAAGAG 59.266 60.000 13.01 0.00 0.00 2.85
817 823 0.679002 CCCGAGGTAGACGTCCAAGA 60.679 60.000 13.01 0.00 0.00 3.02
818 824 0.964358 ACCCGAGGTAGACGTCCAAG 60.964 60.000 13.01 0.00 32.11 3.61
819 825 0.962356 GACCCGAGGTAGACGTCCAA 60.962 60.000 13.01 0.00 35.25 3.53
820 826 1.377725 GACCCGAGGTAGACGTCCA 60.378 63.158 13.01 0.00 35.25 4.02
821 827 2.117779 GGACCCGAGGTAGACGTCC 61.118 68.421 13.01 0.00 35.25 4.79
822 828 0.962356 TTGGACCCGAGGTAGACGTC 60.962 60.000 7.70 7.70 35.25 4.34
823 829 1.075482 TTGGACCCGAGGTAGACGT 59.925 57.895 0.00 0.00 35.25 4.34
824 830 1.509923 GTTGGACCCGAGGTAGACG 59.490 63.158 0.00 0.00 35.25 4.18
825 831 0.962356 TCGTTGGACCCGAGGTAGAC 60.962 60.000 0.00 0.00 35.25 2.59
826 832 0.679002 CTCGTTGGACCCGAGGTAGA 60.679 60.000 11.20 0.00 46.09 2.59
827 833 1.807886 CTCGTTGGACCCGAGGTAG 59.192 63.158 11.20 0.00 46.09 3.18
828 834 2.020694 GATCTCGTTGGACCCGAGGTA 61.021 57.143 16.97 3.04 45.23 3.08
832 838 1.888018 GTGATCTCGTTGGACCCGA 59.112 57.895 0.00 0.00 0.00 5.14
833 839 1.516386 CGTGATCTCGTTGGACCCG 60.516 63.158 8.97 0.00 0.00 5.28
834 840 0.179134 CTCGTGATCTCGTTGGACCC 60.179 60.000 16.03 0.00 0.00 4.46
835 841 0.526662 ACTCGTGATCTCGTTGGACC 59.473 55.000 16.03 0.00 0.00 4.46
836 842 1.618861 CACTCGTGATCTCGTTGGAC 58.381 55.000 16.03 0.00 0.00 4.02
837 843 0.526211 CCACTCGTGATCTCGTTGGA 59.474 55.000 24.11 5.70 37.30 3.53
838 844 0.243907 ACCACTCGTGATCTCGTTGG 59.756 55.000 25.47 25.47 39.26 3.77
839 845 2.161808 AGTACCACTCGTGATCTCGTTG 59.838 50.000 16.03 13.65 0.00 4.10
840 846 2.161808 CAGTACCACTCGTGATCTCGTT 59.838 50.000 16.03 3.10 0.00 3.85
841 847 1.738350 CAGTACCACTCGTGATCTCGT 59.262 52.381 16.03 0.29 0.00 4.18
842 848 1.738350 ACAGTACCACTCGTGATCTCG 59.262 52.381 10.84 10.84 0.00 4.04
843 849 3.940221 AGTACAGTACCACTCGTGATCTC 59.060 47.826 7.13 0.00 0.00 2.75
844 850 3.952931 AGTACAGTACCACTCGTGATCT 58.047 45.455 7.13 0.00 0.00 2.75
845 851 4.698583 AAGTACAGTACCACTCGTGATC 57.301 45.455 7.13 0.00 0.00 2.92
846 852 4.082354 GGAAAGTACAGTACCACTCGTGAT 60.082 45.833 7.13 0.00 0.00 3.06
847 853 3.254166 GGAAAGTACAGTACCACTCGTGA 59.746 47.826 7.13 0.00 0.00 4.35
870 876 1.041447 CGAGTGGGGAATACGGACCT 61.041 60.000 0.00 0.00 0.00 3.85
995 1043 1.345176 GTACAGCAAGACATCGCGC 59.655 57.895 0.00 0.00 0.00 6.86
999 1047 1.269166 CGTCCGTACAGCAAGACATC 58.731 55.000 0.00 0.00 0.00 3.06
1839 1915 3.440415 AGCCATGACGCGACGAGA 61.440 61.111 15.93 0.00 0.00 4.04
2115 2197 1.251527 ACTCCAGCGTCGAGTTCCAT 61.252 55.000 0.00 0.00 37.28 3.41
2328 2410 2.190578 GCCCCCTCGTCCATCAAG 59.809 66.667 0.00 0.00 0.00 3.02
2468 2550 0.735287 GACCTCCACGGCGTCTTTAC 60.735 60.000 10.85 0.00 35.61 2.01
2469 2551 1.588082 GACCTCCACGGCGTCTTTA 59.412 57.895 10.85 0.00 35.61 1.85
2487 2569 4.457496 AGGTCAGGCGCGTCATGG 62.457 66.667 15.58 1.27 0.00 3.66
2518 2600 4.865365 CCTGACGGATCAACTAGTTTCTTC 59.135 45.833 5.07 3.21 33.30 2.87
2536 2618 3.741388 CGATCCCCACTATTTGTCCTGAC 60.741 52.174 0.00 0.00 0.00 3.51
2551 2634 4.688966 GCGCCCTGATCGATCCCC 62.689 72.222 22.31 7.20 0.00 4.81
2564 2647 2.504681 CTGCCACGAAAATGCGCC 60.505 61.111 4.18 0.00 33.86 6.53
2609 2692 1.071471 CTGGTTCGAGCCACCTGTT 59.929 57.895 17.98 0.00 35.07 3.16
2702 2803 1.673920 ACACGCCGTTGACATCTTTTT 59.326 42.857 0.00 0.00 0.00 1.94
2703 2804 1.263217 GACACGCCGTTGACATCTTTT 59.737 47.619 0.00 0.00 0.00 2.27
2704 2805 0.865769 GACACGCCGTTGACATCTTT 59.134 50.000 0.00 0.00 0.00 2.52
2705 2806 0.249699 TGACACGCCGTTGACATCTT 60.250 50.000 0.00 0.00 0.00 2.40
2706 2807 0.037326 ATGACACGCCGTTGACATCT 60.037 50.000 0.00 0.00 27.40 2.90
2707 2808 0.370273 GATGACACGCCGTTGACATC 59.630 55.000 12.77 12.77 40.02 3.06
2708 2809 0.320334 TGATGACACGCCGTTGACAT 60.320 50.000 0.00 0.00 35.06 3.06
2709 2810 0.530870 TTGATGACACGCCGTTGACA 60.531 50.000 0.00 0.00 0.00 3.58
2710 2811 0.584396 TTTGATGACACGCCGTTGAC 59.416 50.000 0.00 0.00 0.00 3.18
2711 2812 0.865111 CTTTGATGACACGCCGTTGA 59.135 50.000 0.00 0.00 0.00 3.18
2712 2813 0.865111 TCTTTGATGACACGCCGTTG 59.135 50.000 0.00 0.00 0.00 4.10
2713 2814 1.732259 GATCTTTGATGACACGCCGTT 59.268 47.619 0.00 0.00 0.00 4.44
2714 2815 1.066858 AGATCTTTGATGACACGCCGT 60.067 47.619 0.00 0.00 0.00 5.68
2715 2816 1.645034 AGATCTTTGATGACACGCCG 58.355 50.000 0.00 0.00 0.00 6.46
2716 2817 4.184629 ACTAAGATCTTTGATGACACGCC 58.815 43.478 21.42 0.00 0.00 5.68
2717 2818 4.864806 TGACTAAGATCTTTGATGACACGC 59.135 41.667 21.42 3.54 0.00 5.34
2718 2819 6.587990 AGTTGACTAAGATCTTTGATGACACG 59.412 38.462 21.42 0.48 0.00 4.49
2761 2865 8.931775 ACAAGTTGTTTTGAAAAGTAAATGACC 58.068 29.630 1.64 0.00 0.00 4.02
2771 2875 6.876257 AGCCACAATACAAGTTGTTTTGAAAA 59.124 30.769 32.52 9.90 40.26 2.29
2772 2876 6.402222 AGCCACAATACAAGTTGTTTTGAAA 58.598 32.000 32.52 10.55 40.26 2.69
2786 3184 3.436700 GCAATTGGGTAGCCACAATAC 57.563 47.619 14.60 0.00 36.36 1.89
2845 3243 9.856488 ATAATACTCCTAATACAGTAATGCACG 57.144 33.333 0.00 0.00 0.00 5.34
2847 3245 9.653287 GCATAATACTCCTAATACAGTAATGCA 57.347 33.333 9.40 0.00 38.30 3.96
2848 3246 8.808529 CGCATAATACTCCTAATACAGTAATGC 58.191 37.037 0.00 0.00 36.67 3.56
2852 3250 8.640063 TTCCGCATAATACTCCTAATACAGTA 57.360 34.615 0.00 0.00 0.00 2.74
2854 3252 9.436957 AATTTCCGCATAATACTCCTAATACAG 57.563 33.333 0.00 0.00 0.00 2.74
2911 3309 2.633509 GGCAGCAAGACTTGGCAGG 61.634 63.158 16.80 0.00 0.00 4.85
2924 3322 1.094073 ATGAATCGTGAGCAGGCAGC 61.094 55.000 0.00 0.00 46.19 5.25
2926 3324 1.206849 TGTATGAATCGTGAGCAGGCA 59.793 47.619 0.00 0.00 0.00 4.75
2927 3325 1.939974 TGTATGAATCGTGAGCAGGC 58.060 50.000 0.00 0.00 0.00 4.85
2928 3326 5.292765 ACTATTGTATGAATCGTGAGCAGG 58.707 41.667 0.00 0.00 0.00 4.85
2929 3327 6.476706 TGAACTATTGTATGAATCGTGAGCAG 59.523 38.462 0.00 0.00 0.00 4.24
2931 3329 6.828502 TGAACTATTGTATGAATCGTGAGC 57.171 37.500 0.00 0.00 0.00 4.26
2934 3332 7.569408 CGGGATTGAACTATTGTATGAATCGTG 60.569 40.741 0.00 0.00 0.00 4.35
2935 3333 6.423905 CGGGATTGAACTATTGTATGAATCGT 59.576 38.462 0.00 0.00 0.00 3.73
2936 3334 6.618592 GCGGGATTGAACTATTGTATGAATCG 60.619 42.308 0.00 0.00 0.00 3.34
2937 3335 6.603095 GCGGGATTGAACTATTGTATGAATC 58.397 40.000 0.00 0.00 0.00 2.52
2943 3341 3.119065 TCACGCGGGATTGAACTATTGTA 60.119 43.478 7.15 0.00 0.00 2.41
2953 3351 0.104120 TATGTCCTCACGCGGGATTG 59.896 55.000 13.56 6.60 35.15 2.67
2958 3356 3.093717 ACTTATTATGTCCTCACGCGG 57.906 47.619 12.47 0.00 0.00 6.46
2959 3357 7.594015 ACTTAATACTTATTATGTCCTCACGCG 59.406 37.037 3.53 3.53 33.75 6.01
2988 3386 6.398726 GCGAAAAACACAAGTTTCAAACGTTA 60.399 34.615 0.00 0.00 46.79 3.18
2992 3390 5.257345 TGCGAAAAACACAAGTTTCAAAC 57.743 34.783 0.00 0.00 46.79 2.93
2996 3394 7.444558 TTTAGATGCGAAAAACACAAGTTTC 57.555 32.000 0.00 0.00 46.79 2.78
3012 3410 8.980143 TGGTTAAAACTTAGCATTTTAGATGC 57.020 30.769 0.00 0.00 44.85 3.91
3084 3483 8.573035 GGGGCGACTGATAAAAATCATTATTTA 58.427 33.333 0.00 0.00 34.12 1.40
3085 3484 7.433680 GGGGCGACTGATAAAAATCATTATTT 58.566 34.615 0.00 0.00 36.87 1.40
3093 3492 2.413310 ACGGGGCGACTGATAAAAAT 57.587 45.000 0.00 0.00 0.00 1.82
3094 3493 2.234414 AGTACGGGGCGACTGATAAAAA 59.766 45.455 0.00 0.00 0.00 1.94
3099 3498 1.030457 CTTAGTACGGGGCGACTGAT 58.970 55.000 0.00 0.00 0.00 2.90
3100 3499 0.322816 ACTTAGTACGGGGCGACTGA 60.323 55.000 0.00 0.00 0.00 3.41
3102 3501 1.203287 GAAACTTAGTACGGGGCGACT 59.797 52.381 0.00 0.00 0.00 4.18
3107 3507 3.000727 CTGCTTGAAACTTAGTACGGGG 58.999 50.000 0.00 0.00 0.00 5.73
3172 3572 7.333528 TGAGCGCTTTAAATAAGATCCATTT 57.666 32.000 13.26 7.74 0.00 2.32
3176 3576 6.017934 TGTCATGAGCGCTTTAAATAAGATCC 60.018 38.462 13.26 0.00 0.00 3.36
3186 3587 2.096466 CGTGTTTGTCATGAGCGCTTTA 60.096 45.455 13.26 4.19 35.23 1.85
3197 3598 5.760743 TCTGTTTTCATATCCGTGTTTGTCA 59.239 36.000 0.00 0.00 0.00 3.58
3247 3649 9.997482 GCCTGTCGATTTTCAAAGTTTTATATA 57.003 29.630 0.00 0.00 0.00 0.86
3269 3671 4.082841 GGTGCCCAATTTTTATTTTGCCTG 60.083 41.667 0.00 0.00 0.00 4.85
3272 3674 4.612486 CGTGGTGCCCAATTTTTATTTTGC 60.612 41.667 0.00 0.00 34.18 3.68
3283 3685 0.326595 TCATGTACGTGGTGCCCAAT 59.673 50.000 15.02 0.00 34.18 3.16
3284 3686 0.321210 CTCATGTACGTGGTGCCCAA 60.321 55.000 15.02 0.00 34.18 4.12
3285 3687 1.295101 CTCATGTACGTGGTGCCCA 59.705 57.895 15.02 0.00 0.00 5.36
3294 3696 2.202878 CGGGGGCACTCATGTACG 60.203 66.667 0.00 0.00 0.00 3.67
3296 3698 3.006133 TGCGGGGGCACTCATGTA 61.006 61.111 0.00 0.00 0.00 2.29
3320 3722 0.251916 CCGGGAGAGTATTTGTGGCA 59.748 55.000 0.00 0.00 0.00 4.92
3330 3732 2.400467 AGCATAATACCCGGGAGAGT 57.600 50.000 32.02 16.66 0.00 3.24
3351 3753 9.833894 CGACAATGTTGTTTTTCTATTTGAAAG 57.166 29.630 0.00 0.00 42.32 2.62
3366 3771 3.066621 ACACATTTGCTCGACAATGTTGT 59.933 39.130 9.24 0.00 45.65 3.32
3382 3787 6.579666 ACAAGCTCATACAAATGACACATT 57.420 33.333 0.00 0.00 37.20 2.71
3399 3804 1.281867 TGGCCTAACATGCTACAAGCT 59.718 47.619 3.32 0.00 42.97 3.74
3401 3806 3.813443 AGATGGCCTAACATGCTACAAG 58.187 45.455 3.32 0.00 0.00 3.16
3402 3807 3.931907 AGATGGCCTAACATGCTACAA 57.068 42.857 3.32 0.00 0.00 2.41
3409 3814 1.410648 CCCAGCAAGATGGCCTAACAT 60.411 52.381 3.32 0.00 39.17 2.71
3420 3825 1.219124 GATGTCGAGCCCAGCAAGA 59.781 57.895 0.00 0.00 0.00 3.02
3442 3847 8.876275 GCAGATGCAGAATATAATTTTCCAAA 57.124 30.769 0.00 0.00 41.59 3.28
3468 3873 6.825721 AGAAATTCAGCTACTGGAAAATCGAT 59.174 34.615 0.00 0.00 31.51 3.59
3476 3881 4.756642 CACACAAGAAATTCAGCTACTGGA 59.243 41.667 0.00 0.00 31.51 3.86
3477 3882 4.614535 GCACACAAGAAATTCAGCTACTGG 60.615 45.833 0.00 0.00 31.51 4.00
3484 3889 4.438797 CGACAAAGCACACAAGAAATTCAG 59.561 41.667 0.00 0.00 0.00 3.02
3493 3898 1.336440 CCATTCCGACAAAGCACACAA 59.664 47.619 0.00 0.00 0.00 3.33
3494 3899 0.950836 CCATTCCGACAAAGCACACA 59.049 50.000 0.00 0.00 0.00 3.72
3501 3906 2.869101 TGATGTCCCATTCCGACAAA 57.131 45.000 0.00 0.00 43.16 2.83


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

AutoCloner maintained by Alex Coulton.