Multiple sequence alignment - TraesCS3A01G157100

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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 TraesCS3A01G157100 chr3A 100.000 3929 0 0 1 3929 154029687 154033615 0.000000e+00 7256
1 TraesCS3A01G157100 chr3A 81.119 143 27 0 2423 2565 105112549 105112407 8.920000e-22 115
2 TraesCS3A01G157100 chr3D 95.050 2404 68 12 863 3229 136401243 136403632 0.000000e+00 3733
3 TraesCS3A01G157100 chr3D 91.994 662 35 7 3253 3904 136403698 136404351 0.000000e+00 913
4 TraesCS3A01G157100 chr3D 82.759 464 27 20 255 692 136400800 136401236 8.020000e-97 364
5 TraesCS3A01G157100 chr3D 94.828 116 5 1 1 116 136400607 136400721 3.120000e-41 180
6 TraesCS3A01G157100 chr3D 82.517 143 25 0 2423 2565 88352612 88352754 4.120000e-25 126
7 TraesCS3A01G157100 chr3B 94.038 1912 83 16 2006 3904 194758825 194760718 0.000000e+00 2870
8 TraesCS3A01G157100 chr3B 96.685 1116 30 6 858 1973 194757724 194758832 0.000000e+00 1849
9 TraesCS3A01G157100 chr3B 87.649 753 32 19 1 696 194756977 194757725 0.000000e+00 819
10 TraesCS3A01G157100 chr1A 82.529 435 59 7 2397 2815 186213063 186213496 2.230000e-97 366
11 TraesCS3A01G157100 chr1A 81.793 368 56 8 2410 2770 387029190 387028827 8.250000e-77 298
12 TraesCS3A01G157100 chr1A 96.648 179 4 2 695 872 393948618 393948441 2.970000e-76 296
13 TraesCS3A01G157100 chr1A 78.697 399 81 4 1517 1913 186212226 186212622 3.010000e-66 263
14 TraesCS3A01G157100 chr1D 81.839 435 62 6 2397 2815 127504596 127505029 2.250000e-92 350
15 TraesCS3A01G157100 chr1D 81.250 368 58 8 2410 2770 307832764 307832401 1.790000e-73 287
16 TraesCS3A01G157100 chr1D 95.055 182 7 2 681 861 39871992 39871812 6.430000e-73 285
17 TraesCS3A01G157100 chr1D 79.198 399 79 4 1517 1913 127503755 127504151 1.390000e-69 274
18 TraesCS3A01G157100 chr6D 94.681 188 6 4 689 873 206560445 206560259 4.970000e-74 289
19 TraesCS3A01G157100 chr5A 95.580 181 7 1 694 873 290391862 290391682 4.970000e-74 289
20 TraesCS3A01G157100 chr4B 96.023 176 7 0 693 868 488893288 488893113 1.790000e-73 287
21 TraesCS3A01G157100 chr4B 96.023 176 6 1 690 864 136055331 136055506 6.430000e-73 285
22 TraesCS3A01G157100 chr1B 81.250 368 58 8 2410 2770 416822559 416822196 1.790000e-73 287
23 TraesCS3A01G157100 chr6B 93.750 192 6 6 686 873 320413113 320412924 2.310000e-72 283
24 TraesCS3A01G157100 chr7B 96.450 169 5 1 695 863 482283570 482283403 1.080000e-70 278
25 TraesCS3A01G157100 chr6A 93.617 188 8 4 689 873 276304154 276304340 1.080000e-70 278
26 TraesCS3A01G157100 chr2D 77.865 384 77 8 2423 2802 498228147 498228526 8.490000e-57 231


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 TraesCS3A01G157100 chr3A 154029687 154033615 3928 False 7256.0 7256 100.000000 1 3929 1 chr3A.!!$F1 3928
1 TraesCS3A01G157100 chr3D 136400607 136404351 3744 False 1297.5 3733 91.157750 1 3904 4 chr3D.!!$F2 3903
2 TraesCS3A01G157100 chr3B 194756977 194760718 3741 False 1846.0 2870 92.790667 1 3904 3 chr3B.!!$F1 3903
3 TraesCS3A01G157100 chr1A 186212226 186213496 1270 False 314.5 366 80.613000 1517 2815 2 chr1A.!!$F1 1298
4 TraesCS3A01G157100 chr1D 127503755 127505029 1274 False 312.0 350 80.518500 1517 2815 2 chr1D.!!$F1 1298

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
237 246 0.973632 TATGCCTGTCCGTGACTGTT 59.026 50.000 5.77 0.00 33.15 3.16 F
238 247 0.973632 ATGCCTGTCCGTGACTGTTA 59.026 50.000 5.77 0.00 33.15 2.41 F
239 248 0.973632 TGCCTGTCCGTGACTGTTAT 59.026 50.000 5.77 0.00 33.15 1.89 F
240 249 1.337728 TGCCTGTCCGTGACTGTTATG 60.338 52.381 5.77 0.00 33.15 1.90 F
241 250 1.337823 GCCTGTCCGTGACTGTTATGT 60.338 52.381 5.77 0.00 33.15 2.29 F
1882 1972 1.375140 CTTCGGCAGAAGCAGCTGA 60.375 57.895 20.43 4.23 46.12 4.26 F
1997 2088 1.597195 TCAGTGTTTGTGCGATGACAC 59.403 47.619 5.42 5.42 41.94 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 1972 0.106708 TGCTCGGAGAAGTGCTTGTT 59.893 50.000 9.69 0.0 34.09 2.83 R
1979 2070 1.662517 TGTGTCATCGCACAAACACT 58.337 45.000 9.82 0.0 45.17 3.55 R
2005 2096 8.749026 AAGAGAATTATGATGAGCAATTGAGT 57.251 30.769 10.34 0.0 0.00 3.41 R
2386 2532 2.290367 CGTTGAACTCCATTGTCTGCAA 59.710 45.455 0.00 0.0 39.16 4.08 R
2394 2540 1.298859 GCTCCGCGTTGAACTCCATT 61.299 55.000 4.92 0.0 0.00 3.16 R
2857 3018 0.038709 GTCGACAAGCTGCTCAGAGT 60.039 55.000 11.55 0.0 0.00 3.24 R
3533 3801 0.102663 GCGTCTACCAGCTAGGGTTC 59.897 60.000 0.33 0.0 43.89 3.62 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
72 73 1.138661 TGCATACATGATCAGGCACGA 59.861 47.619 7.40 0.00 0.00 4.35
122 130 8.731275 TGTTATGTTCAGAGAAAGTCAAAAGA 57.269 30.769 0.00 0.00 0.00 2.52
125 133 5.126067 TGTTCAGAGAAAGTCAAAAGAGGG 58.874 41.667 0.00 0.00 0.00 4.30
126 134 3.744660 TCAGAGAAAGTCAAAAGAGGGC 58.255 45.455 0.00 0.00 0.00 5.19
127 135 3.392616 TCAGAGAAAGTCAAAAGAGGGCT 59.607 43.478 0.00 0.00 0.00 5.19
128 136 3.501445 CAGAGAAAGTCAAAAGAGGGCTG 59.499 47.826 0.00 0.00 0.00 4.85
187 195 4.694037 ACTTAAACACCTTCAGATAACGGC 59.306 41.667 0.00 0.00 0.00 5.68
234 243 1.195115 ATGTATGCCTGTCCGTGACT 58.805 50.000 5.77 0.00 33.15 3.41
237 246 0.973632 TATGCCTGTCCGTGACTGTT 59.026 50.000 5.77 0.00 33.15 3.16
238 247 0.973632 ATGCCTGTCCGTGACTGTTA 59.026 50.000 5.77 0.00 33.15 2.41
239 248 0.973632 TGCCTGTCCGTGACTGTTAT 59.026 50.000 5.77 0.00 33.15 1.89
240 249 1.337728 TGCCTGTCCGTGACTGTTATG 60.338 52.381 5.77 0.00 33.15 1.90
241 250 1.337823 GCCTGTCCGTGACTGTTATGT 60.338 52.381 5.77 0.00 33.15 2.29
242 251 2.094390 GCCTGTCCGTGACTGTTATGTA 60.094 50.000 5.77 0.00 33.15 2.29
243 252 3.615592 GCCTGTCCGTGACTGTTATGTAA 60.616 47.826 5.77 0.00 33.15 2.41
244 253 4.755411 CCTGTCCGTGACTGTTATGTAAT 58.245 43.478 5.77 0.00 33.15 1.89
245 254 5.680408 GCCTGTCCGTGACTGTTATGTAATA 60.680 44.000 5.77 0.00 33.15 0.98
246 255 5.747197 CCTGTCCGTGACTGTTATGTAATAC 59.253 44.000 5.77 0.00 33.15 1.89
247 256 5.653507 TGTCCGTGACTGTTATGTAATACC 58.346 41.667 5.77 0.00 33.15 2.73
248 257 5.185442 TGTCCGTGACTGTTATGTAATACCA 59.815 40.000 5.77 0.00 33.15 3.25
249 258 6.127281 TGTCCGTGACTGTTATGTAATACCAT 60.127 38.462 5.77 0.00 33.15 3.55
250 259 6.200286 GTCCGTGACTGTTATGTAATACCATG 59.800 42.308 0.00 0.00 0.00 3.66
251 260 6.097129 TCCGTGACTGTTATGTAATACCATGA 59.903 38.462 0.00 0.00 0.00 3.07
252 261 6.200286 CCGTGACTGTTATGTAATACCATGAC 59.800 42.308 0.00 0.00 33.31 3.06
253 262 6.754675 CGTGACTGTTATGTAATACCATGACA 59.245 38.462 0.00 0.00 38.53 3.58
335 370 3.244526 TGGTCTGTATGTGCATGTTCTGT 60.245 43.478 0.00 0.00 0.00 3.41
447 529 8.568676 TTGTATACAGCTTATTAAGGCAACAA 57.431 30.769 5.56 0.00 41.41 2.83
692 782 5.165961 CTTCCTGGGAAGTTGACTAATGA 57.834 43.478 18.35 0.00 44.65 2.57
696 786 5.187186 TCCTGGGAAGTTGACTAATGACTAC 59.813 44.000 0.00 0.00 0.00 2.73
698 788 6.282199 TGGGAAGTTGACTAATGACTACTC 57.718 41.667 0.00 0.00 0.00 2.59
699 789 5.187186 TGGGAAGTTGACTAATGACTACTCC 59.813 44.000 0.00 0.00 0.00 3.85
700 790 5.395435 GGGAAGTTGACTAATGACTACTCCC 60.395 48.000 0.00 0.00 31.60 4.30
701 791 5.422650 GGAAGTTGACTAATGACTACTCCCT 59.577 44.000 0.00 0.00 0.00 4.20
702 792 6.406065 GGAAGTTGACTAATGACTACTCCCTC 60.406 46.154 0.00 0.00 0.00 4.30
703 793 5.833340 AGTTGACTAATGACTACTCCCTCT 58.167 41.667 0.00 0.00 0.00 3.69
704 794 5.654650 AGTTGACTAATGACTACTCCCTCTG 59.345 44.000 0.00 0.00 0.00 3.35
705 795 5.194473 TGACTAATGACTACTCCCTCTGT 57.806 43.478 0.00 0.00 0.00 3.41
706 796 5.580998 TGACTAATGACTACTCCCTCTGTT 58.419 41.667 0.00 0.00 0.00 3.16
707 797 5.652891 TGACTAATGACTACTCCCTCTGTTC 59.347 44.000 0.00 0.00 0.00 3.18
708 798 4.957327 ACTAATGACTACTCCCTCTGTTCC 59.043 45.833 0.00 0.00 0.00 3.62
709 799 3.767309 ATGACTACTCCCTCTGTTCCT 57.233 47.619 0.00 0.00 0.00 3.36
710 800 4.883021 ATGACTACTCCCTCTGTTCCTA 57.117 45.455 0.00 0.00 0.00 2.94
711 801 4.669866 TGACTACTCCCTCTGTTCCTAA 57.330 45.455 0.00 0.00 0.00 2.69
712 802 5.006896 TGACTACTCCCTCTGTTCCTAAA 57.993 43.478 0.00 0.00 0.00 1.85
713 803 5.590818 TGACTACTCCCTCTGTTCCTAAAT 58.409 41.667 0.00 0.00 0.00 1.40
714 804 6.738635 TGACTACTCCCTCTGTTCCTAAATA 58.261 40.000 0.00 0.00 0.00 1.40
715 805 7.363031 TGACTACTCCCTCTGTTCCTAAATAT 58.637 38.462 0.00 0.00 0.00 1.28
716 806 7.844779 TGACTACTCCCTCTGTTCCTAAATATT 59.155 37.037 0.00 0.00 0.00 1.28
717 807 8.625467 ACTACTCCCTCTGTTCCTAAATATTT 57.375 34.615 5.89 5.89 0.00 1.40
718 808 8.487028 ACTACTCCCTCTGTTCCTAAATATTTG 58.513 37.037 11.05 1.40 0.00 2.32
719 809 7.272144 ACTCCCTCTGTTCCTAAATATTTGT 57.728 36.000 11.05 0.00 0.00 2.83
720 810 7.339482 ACTCCCTCTGTTCCTAAATATTTGTC 58.661 38.462 11.05 0.00 0.00 3.18
721 811 7.182930 ACTCCCTCTGTTCCTAAATATTTGTCT 59.817 37.037 11.05 0.00 0.00 3.41
722 812 7.928873 TCCCTCTGTTCCTAAATATTTGTCTT 58.071 34.615 11.05 0.00 0.00 3.01
723 813 8.390921 TCCCTCTGTTCCTAAATATTTGTCTTT 58.609 33.333 11.05 0.00 0.00 2.52
724 814 9.025041 CCCTCTGTTCCTAAATATTTGTCTTTT 57.975 33.333 11.05 0.00 0.00 2.27
759 849 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
760 850 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
761 851 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
762 852 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
763 853 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
764 854 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
765 855 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
766 856 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
767 857 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
768 858 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
770 860 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
799 889 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
800 890 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
801 891 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
802 892 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
803 893 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
804 894 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
805 895 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
806 896 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
807 897 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
808 898 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
809 899 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
810 900 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
811 901 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
812 902 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
813 903 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
814 904 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
815 905 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
816 906 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
817 907 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
818 908 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
819 909 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
820 910 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
821 911 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
822 912 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
823 913 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
824 914 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
825 915 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
826 916 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
827 917 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
828 918 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
829 919 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
830 920 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
831 921 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
832 922 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
833 923 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
834 924 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
835 925 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
836 926 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
837 927 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
850 940 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
851 941 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
852 942 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
853 943 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
854 944 6.555463 AGACAAATATTTAGGAACGGAGGA 57.445 37.500 0.00 0.00 0.00 3.71
855 945 6.954232 AGACAAATATTTAGGAACGGAGGAA 58.046 36.000 0.00 0.00 0.00 3.36
856 946 7.048512 AGACAAATATTTAGGAACGGAGGAAG 58.951 38.462 0.00 0.00 0.00 3.46
857 947 6.718294 ACAAATATTTAGGAACGGAGGAAGT 58.282 36.000 0.00 0.00 0.00 3.01
858 948 7.854337 ACAAATATTTAGGAACGGAGGAAGTA 58.146 34.615 0.00 0.00 0.00 2.24
859 949 7.985752 ACAAATATTTAGGAACGGAGGAAGTAG 59.014 37.037 0.00 0.00 0.00 2.57
860 950 7.672122 AATATTTAGGAACGGAGGAAGTAGT 57.328 36.000 0.00 0.00 0.00 2.73
861 951 5.595257 ATTTAGGAACGGAGGAAGTAGTC 57.405 43.478 0.00 0.00 0.00 2.59
937 1027 7.865706 TGGTCTTCCAAATTCTATTTCTAGC 57.134 36.000 0.00 0.00 41.25 3.42
1032 1122 4.134563 GGTCATACAACAAACTGGACACT 58.865 43.478 0.00 0.00 0.00 3.55
1424 1514 4.572389 CAGAGGCATGAACAGTAATACACC 59.428 45.833 0.00 0.00 0.00 4.16
1468 1558 2.851263 AACCATTCGTCAAGGTAGCA 57.149 45.000 0.00 0.00 34.63 3.49
1704 1794 3.619733 CGATGAAGGTGATGGACAAGGAA 60.620 47.826 0.00 0.00 0.00 3.36
1707 1797 3.330405 TGAAGGTGATGGACAAGGAATCA 59.670 43.478 0.00 0.00 0.00 2.57
1743 1833 2.334946 GCTGATCAGGGCGCAAACA 61.335 57.895 23.89 0.00 0.00 2.83
1803 1893 2.151202 CCCACGCTGTACACTCATTTT 58.849 47.619 0.00 0.00 0.00 1.82
1882 1972 1.375140 CTTCGGCAGAAGCAGCTGA 60.375 57.895 20.43 4.23 46.12 4.26
1979 2070 3.880047 ATTGGTACTCGATTCGGTTCA 57.120 42.857 6.18 3.56 0.00 3.18
1997 2088 1.597195 TCAGTGTTTGTGCGATGACAC 59.403 47.619 5.42 5.42 41.94 3.67
2386 2532 4.640690 ACCTCAGCCTCCACGGGT 62.641 66.667 0.00 0.00 46.68 5.28
2394 2540 2.425592 CTCCACGGGTTGCAGACA 59.574 61.111 0.00 0.00 0.00 3.41
2442 2588 1.804326 CCGGTCCATGTCGTTCGTC 60.804 63.158 0.00 0.00 0.00 4.20
2520 2666 2.214920 GGACTGGTGGACCTTCGGT 61.215 63.158 0.00 0.00 39.44 4.69
2532 2678 4.140994 TGGACCTTCGGTATCTTCCTCTAT 60.141 45.833 0.00 0.00 35.25 1.98
2553 2699 3.051479 CTGCTGCACGGCATGACA 61.051 61.111 4.30 0.00 41.63 3.58
2670 2831 2.503061 CTCATCCGGGGACTGCTG 59.497 66.667 0.00 0.00 0.00 4.41
2805 2966 3.688159 CCGGACCCCGTCGACTTT 61.688 66.667 14.70 0.00 46.80 2.66
2861 3022 3.177884 TGGCCTTGGCACCACTCT 61.178 61.111 14.04 0.00 31.79 3.24
2871 3032 1.575576 GCACCACTCTGAGCAGCTTG 61.576 60.000 4.19 0.00 0.00 4.01
2875 3036 0.038801 CACTCTGAGCAGCTTGTCGA 60.039 55.000 4.19 0.00 0.00 4.20
2877 3038 1.069924 CTCTGAGCAGCTTGTCGACG 61.070 60.000 11.62 0.00 0.00 5.12
2975 3136 4.596354 TGTAGGACTACTGGACACCATA 57.404 45.455 10.51 0.00 37.00 2.74
2976 3137 4.533815 TGTAGGACTACTGGACACCATAG 58.466 47.826 10.51 0.00 37.00 2.23
2977 3138 4.228895 TGTAGGACTACTGGACACCATAGA 59.771 45.833 10.51 0.00 37.00 1.98
2978 3139 4.544564 AGGACTACTGGACACCATAGAT 57.455 45.455 0.00 0.00 30.82 1.98
2979 3140 5.664815 AGGACTACTGGACACCATAGATA 57.335 43.478 0.00 0.00 30.82 1.98
2980 3141 5.386924 AGGACTACTGGACACCATAGATAC 58.613 45.833 0.00 0.00 30.82 2.24
3002 3169 3.637229 CAGATACAGATACCCCGTGTTCT 59.363 47.826 0.00 0.00 0.00 3.01
3021 3188 9.745880 CGTGTTCTTATATCACTGTATAAACCT 57.254 33.333 0.00 0.00 0.00 3.50
3026 3193 9.656323 TCTTATATCACTGTATAAACCTCCTGT 57.344 33.333 0.00 0.00 0.00 4.00
3042 3209 4.765856 CCTCCTGTACTGTACTGTACTGTT 59.234 45.833 30.96 15.98 42.22 3.16
3211 3413 3.443329 TGTGCACATGACTGAAGTTTTGT 59.557 39.130 17.42 0.00 0.00 2.83
3230 3432 9.051679 AGTTTTGTAATATCCTTTTGTTTTGCC 57.948 29.630 0.00 0.00 0.00 4.52
3259 3517 9.906660 CTTGTTTTTATTTTGCTAGTGGTCATA 57.093 29.630 0.00 0.00 0.00 2.15
3312 3575 1.740025 GGCACTGAAGCTATCAACACC 59.260 52.381 0.00 0.00 37.67 4.16
3399 3667 1.997606 CCAGAAACGGCCTAAACTACG 59.002 52.381 0.00 0.00 0.00 3.51
3417 3685 6.282199 ACTACGACCAATTCATCTACAGTT 57.718 37.500 0.00 0.00 0.00 3.16
3424 3692 7.169308 CGACCAATTCATCTACAGTTATACCAC 59.831 40.741 0.00 0.00 0.00 4.16
3432 3700 1.913419 ACAGTTATACCACCACCCCTG 59.087 52.381 0.00 0.00 0.00 4.45
3526 3794 4.947388 GGTGAATTTAGCAATGGTCAGGTA 59.053 41.667 0.00 0.00 0.00 3.08
3527 3795 5.066505 GGTGAATTTAGCAATGGTCAGGTAG 59.933 44.000 0.00 0.00 0.00 3.18
3528 3796 4.640201 TGAATTTAGCAATGGTCAGGTAGC 59.360 41.667 0.00 0.00 0.00 3.58
3529 3797 2.710096 TTAGCAATGGTCAGGTAGCC 57.290 50.000 0.00 0.00 0.00 3.93
3530 3798 0.837272 TAGCAATGGTCAGGTAGCCC 59.163 55.000 0.00 0.00 0.00 5.19
3531 3799 1.207488 AGCAATGGTCAGGTAGCCCA 61.207 55.000 0.00 0.00 0.00 5.36
3532 3800 0.323360 GCAATGGTCAGGTAGCCCAA 60.323 55.000 0.00 0.00 0.00 4.12
3533 3801 1.755179 CAATGGTCAGGTAGCCCAAG 58.245 55.000 0.00 0.00 0.00 3.61
3534 3802 1.281867 CAATGGTCAGGTAGCCCAAGA 59.718 52.381 0.00 0.00 0.00 3.02
3535 3803 1.668826 ATGGTCAGGTAGCCCAAGAA 58.331 50.000 0.00 0.00 0.00 2.52
3539 3807 0.178873 TCAGGTAGCCCAAGAACCCT 60.179 55.000 0.00 0.00 33.53 4.34
3649 3917 0.602638 GTTCGGTGTGTGCATCCAGA 60.603 55.000 0.00 0.00 0.00 3.86
3839 4107 6.524586 GTGAAAGGCTTGTAAGAATGAATTCG 59.475 38.462 0.00 0.00 41.56 3.34
3862 4130 2.563620 TGGCATGAAGAACAATGCACAT 59.436 40.909 9.59 0.00 41.44 3.21
3873 4141 4.662468 ACAATGCACATGTGGTACAAAA 57.338 36.364 26.55 0.00 44.16 2.44
3908 4176 2.710096 TTTGCTATGTGCTACCTCCC 57.290 50.000 0.00 0.00 43.37 4.30
3909 4177 1.879575 TTGCTATGTGCTACCTCCCT 58.120 50.000 0.00 0.00 43.37 4.20
3910 4178 1.414158 TGCTATGTGCTACCTCCCTC 58.586 55.000 0.00 0.00 43.37 4.30
3911 4179 0.682292 GCTATGTGCTACCTCCCTCC 59.318 60.000 0.00 0.00 38.95 4.30
3912 4180 2.034799 GCTATGTGCTACCTCCCTCCA 61.035 57.143 0.00 0.00 38.95 3.86
3913 4181 2.614259 CTATGTGCTACCTCCCTCCAT 58.386 52.381 0.00 0.00 0.00 3.41
3914 4182 1.898863 ATGTGCTACCTCCCTCCATT 58.101 50.000 0.00 0.00 0.00 3.16
3915 4183 1.204146 TGTGCTACCTCCCTCCATTC 58.796 55.000 0.00 0.00 0.00 2.67
3916 4184 0.470341 GTGCTACCTCCCTCCATTCC 59.530 60.000 0.00 0.00 0.00 3.01
3917 4185 0.343372 TGCTACCTCCCTCCATTCCT 59.657 55.000 0.00 0.00 0.00 3.36
3918 4186 1.578703 TGCTACCTCCCTCCATTCCTA 59.421 52.381 0.00 0.00 0.00 2.94
3919 4187 2.022428 TGCTACCTCCCTCCATTCCTAA 60.022 50.000 0.00 0.00 0.00 2.69
3920 4188 3.046374 GCTACCTCCCTCCATTCCTAAA 58.954 50.000 0.00 0.00 0.00 1.85
3921 4189 3.653352 GCTACCTCCCTCCATTCCTAAAT 59.347 47.826 0.00 0.00 0.00 1.40
3922 4190 4.844655 GCTACCTCCCTCCATTCCTAAATA 59.155 45.833 0.00 0.00 0.00 1.40
3923 4191 5.489278 GCTACCTCCCTCCATTCCTAAATAT 59.511 44.000 0.00 0.00 0.00 1.28
3924 4192 6.672657 GCTACCTCCCTCCATTCCTAAATATA 59.327 42.308 0.00 0.00 0.00 0.86
3925 4193 7.182206 GCTACCTCCCTCCATTCCTAAATATAA 59.818 40.741 0.00 0.00 0.00 0.98
3926 4194 7.575499 ACCTCCCTCCATTCCTAAATATAAG 57.425 40.000 0.00 0.00 0.00 1.73
3927 4195 7.089566 ACCTCCCTCCATTCCTAAATATAAGT 58.910 38.462 0.00 0.00 0.00 2.24
3928 4196 7.237887 ACCTCCCTCCATTCCTAAATATAAGTC 59.762 40.741 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 2.555325 CTGTGTCAAACTGGCATGTGAT 59.445 45.455 0.00 0.00 33.03 3.06
81 89 2.542766 AACAACGCTGTGTCAAACTG 57.457 45.000 0.00 0.00 35.37 3.16
187 195 9.836076 TGTAGAATACGATTATAAATCCGTGAG 57.164 33.333 16.18 0.00 46.99 3.51
234 243 9.679661 ATTTGTCTGTCATGGTATTACATAACA 57.320 29.630 0.00 0.00 36.78 2.41
237 246 9.108284 CACATTTGTCTGTCATGGTATTACATA 57.892 33.333 0.00 0.00 0.00 2.29
238 247 7.611467 ACACATTTGTCTGTCATGGTATTACAT 59.389 33.333 0.00 0.00 0.00 2.29
239 248 6.939730 ACACATTTGTCTGTCATGGTATTACA 59.060 34.615 0.00 0.00 0.00 2.41
240 249 7.377766 ACACATTTGTCTGTCATGGTATTAC 57.622 36.000 0.00 0.00 0.00 1.89
241 250 8.941977 GTTACACATTTGTCTGTCATGGTATTA 58.058 33.333 0.00 0.00 37.15 0.98
242 251 7.665559 AGTTACACATTTGTCTGTCATGGTATT 59.334 33.333 0.00 0.00 37.15 1.89
243 252 7.168219 AGTTACACATTTGTCTGTCATGGTAT 58.832 34.615 0.00 0.00 37.15 2.73
244 253 6.530120 AGTTACACATTTGTCTGTCATGGTA 58.470 36.000 0.00 0.00 37.15 3.25
245 254 5.376625 AGTTACACATTTGTCTGTCATGGT 58.623 37.500 0.00 0.00 37.15 3.55
246 255 5.947228 AGTTACACATTTGTCTGTCATGG 57.053 39.130 0.00 0.00 37.15 3.66
247 256 7.041848 TCAGAAGTTACACATTTGTCTGTCATG 60.042 37.037 0.00 0.00 37.15 3.07
248 257 6.992123 TCAGAAGTTACACATTTGTCTGTCAT 59.008 34.615 0.00 0.00 37.15 3.06
249 258 6.345298 TCAGAAGTTACACATTTGTCTGTCA 58.655 36.000 0.00 0.00 37.15 3.58
250 259 6.564873 GCTCAGAAGTTACACATTTGTCTGTC 60.565 42.308 0.00 0.00 37.15 3.51
251 260 5.237344 GCTCAGAAGTTACACATTTGTCTGT 59.763 40.000 0.00 0.00 37.15 3.41
252 261 5.468072 AGCTCAGAAGTTACACATTTGTCTG 59.532 40.000 0.00 0.00 37.15 3.51
253 262 5.615289 AGCTCAGAAGTTACACATTTGTCT 58.385 37.500 0.00 0.00 37.15 3.41
254 263 5.931441 AGCTCAGAAGTTACACATTTGTC 57.069 39.130 0.00 0.00 37.15 3.18
255 264 5.934625 CCTAGCTCAGAAGTTACACATTTGT 59.065 40.000 0.00 0.00 40.02 2.83
256 265 6.166279 TCCTAGCTCAGAAGTTACACATTTG 58.834 40.000 0.00 0.00 0.00 2.32
257 266 6.014156 ACTCCTAGCTCAGAAGTTACACATTT 60.014 38.462 0.00 0.00 0.00 2.32
258 267 5.482175 ACTCCTAGCTCAGAAGTTACACATT 59.518 40.000 0.00 0.00 0.00 2.71
259 268 5.020132 ACTCCTAGCTCAGAAGTTACACAT 58.980 41.667 0.00 0.00 0.00 3.21
529 616 9.095065 ACCGACAATGTCTAAAGTGATAATAAC 57.905 33.333 11.92 0.00 0.00 1.89
686 776 5.205056 AGGAACAGAGGGAGTAGTCATTAG 58.795 45.833 0.00 0.00 0.00 1.73
692 782 8.487028 CAAATATTTAGGAACAGAGGGAGTAGT 58.513 37.037 0.00 0.00 0.00 2.73
696 786 7.569240 AGACAAATATTTAGGAACAGAGGGAG 58.431 38.462 0.00 0.00 0.00 4.30
698 788 8.581253 AAAGACAAATATTTAGGAACAGAGGG 57.419 34.615 0.00 0.00 0.00 4.30
726 816 9.614792 GTATGTGGTAGTCCATTTAAAATCTCT 57.385 33.333 0.00 0.00 46.20 3.10
727 817 8.548721 CGTATGTGGTAGTCCATTTAAAATCTC 58.451 37.037 0.00 0.00 46.20 2.75
728 818 7.497909 CCGTATGTGGTAGTCCATTTAAAATCT 59.502 37.037 0.00 0.00 46.20 2.40
729 819 7.496591 TCCGTATGTGGTAGTCCATTTAAAATC 59.503 37.037 0.00 0.00 46.20 2.17
730 820 7.340256 TCCGTATGTGGTAGTCCATTTAAAAT 58.660 34.615 0.00 0.00 46.20 1.82
731 821 6.709281 TCCGTATGTGGTAGTCCATTTAAAA 58.291 36.000 0.00 0.00 46.20 1.52
732 822 6.297080 TCCGTATGTGGTAGTCCATTTAAA 57.703 37.500 0.00 0.00 46.20 1.52
733 823 5.936187 TCCGTATGTGGTAGTCCATTTAA 57.064 39.130 0.00 0.00 46.20 1.52
734 824 5.364446 ACATCCGTATGTGGTAGTCCATTTA 59.636 40.000 0.00 0.00 44.79 1.40
735 825 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
736 826 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
737 827 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
738 828 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
739 829 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
740 830 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
741 831 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
742 832 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
744 834 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
777 867 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
778 868 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
779 869 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
780 870 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
781 871 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
782 872 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
783 873 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
784 874 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
785 875 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
786 876 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
787 877 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
788 878 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
789 879 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
790 880 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
791 881 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
792 882 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
793 883 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
794 884 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
795 885 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
796 886 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
797 887 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
798 888 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
799 889 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
800 890 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
801 891 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
803 893 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
804 894 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
805 895 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
806 896 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
807 897 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
808 898 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
809 899 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
810 900 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
811 901 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
824 914 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
825 915 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
826 916 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
827 917 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
828 918 7.551617 TCCTCCGTTCCTAAATATTTGTCTTTC 59.448 37.037 11.05 0.00 0.00 2.62
829 919 7.399634 TCCTCCGTTCCTAAATATTTGTCTTT 58.600 34.615 11.05 0.00 0.00 2.52
830 920 6.954232 TCCTCCGTTCCTAAATATTTGTCTT 58.046 36.000 11.05 0.00 0.00 3.01
831 921 6.555463 TCCTCCGTTCCTAAATATTTGTCT 57.445 37.500 11.05 0.00 0.00 3.41
832 922 6.822170 ACTTCCTCCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
833 923 6.718294 ACTTCCTCCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
834 924 7.985752 ACTACTTCCTCCGTTCCTAAATATTTG 59.014 37.037 11.05 1.40 0.00 2.32
835 925 8.087303 ACTACTTCCTCCGTTCCTAAATATTT 57.913 34.615 5.89 5.89 0.00 1.40
836 926 7.343833 TGACTACTTCCTCCGTTCCTAAATATT 59.656 37.037 0.00 0.00 0.00 1.28
837 927 6.837568 TGACTACTTCCTCCGTTCCTAAATAT 59.162 38.462 0.00 0.00 0.00 1.28
838 928 6.189859 TGACTACTTCCTCCGTTCCTAAATA 58.810 40.000 0.00 0.00 0.00 1.40
839 929 5.021458 TGACTACTTCCTCCGTTCCTAAAT 58.979 41.667 0.00 0.00 0.00 1.40
840 930 4.410099 TGACTACTTCCTCCGTTCCTAAA 58.590 43.478 0.00 0.00 0.00 1.85
841 931 4.038271 TGACTACTTCCTCCGTTCCTAA 57.962 45.455 0.00 0.00 0.00 2.69
842 932 3.726557 TGACTACTTCCTCCGTTCCTA 57.273 47.619 0.00 0.00 0.00 2.94
843 933 2.599408 TGACTACTTCCTCCGTTCCT 57.401 50.000 0.00 0.00 0.00 3.36
844 934 2.758979 TGATGACTACTTCCTCCGTTCC 59.241 50.000 0.00 0.00 0.00 3.62
845 935 4.098044 TCATGATGACTACTTCCTCCGTTC 59.902 45.833 0.00 0.00 0.00 3.95
846 936 4.023980 TCATGATGACTACTTCCTCCGTT 58.976 43.478 0.00 0.00 0.00 4.44
847 937 3.632333 TCATGATGACTACTTCCTCCGT 58.368 45.455 0.00 0.00 0.00 4.69
848 938 4.279420 TGATCATGATGACTACTTCCTCCG 59.721 45.833 14.30 0.00 0.00 4.63
849 939 5.798125 TGATCATGATGACTACTTCCTCC 57.202 43.478 14.30 0.00 0.00 4.30
850 940 7.171167 CACAATGATCATGATGACTACTTCCTC 59.829 40.741 14.30 0.00 0.00 3.71
851 941 6.990939 CACAATGATCATGATGACTACTTCCT 59.009 38.462 14.30 0.00 0.00 3.36
852 942 6.988580 TCACAATGATCATGATGACTACTTCC 59.011 38.462 14.30 0.00 0.00 3.46
853 943 8.429493 TTCACAATGATCATGATGACTACTTC 57.571 34.615 14.30 0.00 0.00 3.01
854 944 8.045507 ACTTCACAATGATCATGATGACTACTT 58.954 33.333 14.30 0.00 0.00 2.24
855 945 7.563020 ACTTCACAATGATCATGATGACTACT 58.437 34.615 14.30 0.00 0.00 2.57
856 946 7.783090 ACTTCACAATGATCATGATGACTAC 57.217 36.000 14.30 0.00 0.00 2.73
857 947 7.825761 ACAACTTCACAATGATCATGATGACTA 59.174 33.333 14.30 7.36 0.00 2.59
858 948 6.657966 ACAACTTCACAATGATCATGATGACT 59.342 34.615 14.30 0.00 0.00 3.41
859 949 6.849502 ACAACTTCACAATGATCATGATGAC 58.150 36.000 14.30 0.00 0.00 3.06
860 950 7.040271 ACAACAACTTCACAATGATCATGATGA 60.040 33.333 14.30 12.93 0.00 2.92
861 951 7.088272 ACAACAACTTCACAATGATCATGATG 58.912 34.615 14.30 10.75 0.00 3.07
937 1027 7.067532 TGTGCAATAGTAGAACCATTTAACG 57.932 36.000 0.00 0.00 0.00 3.18
1032 1122 6.925718 TGTTAAAATCCATTTTGTCATTCGCA 59.074 30.769 7.42 0.00 40.00 5.10
1424 1514 4.499183 AGCGGAATCACTAAGTTTCTCTG 58.501 43.478 0.00 0.00 0.00 3.35
1468 1558 4.740934 GCTGTTACTTCTTGGACTGTCAGT 60.741 45.833 4.81 4.81 0.00 3.41
1506 1596 1.442526 GATGCTTGACATGGCCGGAG 61.443 60.000 5.05 0.00 39.84 4.63
1704 1794 3.607741 CTTGTTCCTGCTGATGAGTGAT 58.392 45.455 0.00 0.00 0.00 3.06
1707 1797 1.350351 AGCTTGTTCCTGCTGATGAGT 59.650 47.619 0.00 0.00 38.21 3.41
1743 1833 0.111639 GGCCGAGTATCTCCCTCTCT 59.888 60.000 0.00 0.00 0.00 3.10
1803 1893 3.005897 GGCAGTAGAACTTGTCTGTCTCA 59.994 47.826 0.00 0.00 37.12 3.27
1882 1972 0.106708 TGCTCGGAGAAGTGCTTGTT 59.893 50.000 9.69 0.00 34.09 2.83
1950 2040 5.579511 CGAATCGAGTACCAATAACAAGGTT 59.420 40.000 0.00 0.00 39.31 3.50
1979 2070 1.662517 TGTGTCATCGCACAAACACT 58.337 45.000 9.82 0.00 45.17 3.55
2005 2096 8.749026 AAGAGAATTATGATGAGCAATTGAGT 57.251 30.769 10.34 0.00 0.00 3.41
2386 2532 2.290367 CGTTGAACTCCATTGTCTGCAA 59.710 45.455 0.00 0.00 39.16 4.08
2394 2540 1.298859 GCTCCGCGTTGAACTCCATT 61.299 55.000 4.92 0.00 0.00 3.16
2442 2588 3.379445 AGGTACTCGTGGGTGCCG 61.379 66.667 1.12 0.00 44.73 5.69
2520 2666 3.257873 GCAGCAGCTCATAGAGGAAGATA 59.742 47.826 0.00 0.00 37.91 1.98
2556 2702 1.299850 GTTGCCGTTGCCCTTGAAC 60.300 57.895 0.00 0.00 36.33 3.18
2670 2831 0.840722 TCTTCTGGGGGTCCTTGGTC 60.841 60.000 0.00 0.00 0.00 4.02
2745 2906 4.681978 ACGAGCGCCCAGTTCACC 62.682 66.667 2.29 0.00 0.00 4.02
2823 2984 0.530288 GCTCTGCCGTCTTCTTCTCT 59.470 55.000 0.00 0.00 0.00 3.10
2857 3018 0.038709 GTCGACAAGCTGCTCAGAGT 60.039 55.000 11.55 0.00 0.00 3.24
2858 3019 1.069924 CGTCGACAAGCTGCTCAGAG 61.070 60.000 17.16 0.00 0.00 3.35
2861 3022 2.049156 CCGTCGACAAGCTGCTCA 60.049 61.111 17.16 0.00 0.00 4.26
2975 3136 5.010933 CACGGGGTATCTGTATCTGTATCT 58.989 45.833 0.00 0.00 32.77 1.98
2976 3137 4.765856 ACACGGGGTATCTGTATCTGTATC 59.234 45.833 0.00 0.00 32.77 2.24
2977 3138 4.737578 ACACGGGGTATCTGTATCTGTAT 58.262 43.478 0.00 0.00 32.77 2.29
2978 3139 4.174704 ACACGGGGTATCTGTATCTGTA 57.825 45.455 0.00 0.00 32.77 2.74
2979 3140 3.028094 ACACGGGGTATCTGTATCTGT 57.972 47.619 0.00 0.00 32.77 3.41
2980 3141 3.637229 AGAACACGGGGTATCTGTATCTG 59.363 47.826 0.00 0.00 32.30 2.90
3021 3188 5.009310 CACAACAGTACAGTACAGTACAGGA 59.991 44.000 25.01 0.00 45.25 3.86
3022 3189 5.009310 TCACAACAGTACAGTACAGTACAGG 59.991 44.000 25.01 19.39 45.25 4.00
3024 3191 6.644248 ATCACAACAGTACAGTACAGTACA 57.356 37.500 25.01 7.83 45.25 2.90
3025 3192 7.115947 GGAAATCACAACAGTACAGTACAGTAC 59.884 40.741 18.11 18.11 43.61 2.73
3026 3193 7.149973 GGAAATCACAACAGTACAGTACAGTA 58.850 38.462 13.37 0.00 0.00 2.74
3027 3194 5.989777 GGAAATCACAACAGTACAGTACAGT 59.010 40.000 13.37 8.19 0.00 3.55
3042 3209 7.958088 TCATCAGGTATATAACGGAAATCACA 58.042 34.615 4.67 0.00 0.00 3.58
3148 3338 8.198109 GGTTAGAAAGATAAGCAGACATGTCTA 58.802 37.037 27.44 13.12 37.98 2.59
3149 3339 7.044798 GGTTAGAAAGATAAGCAGACATGTCT 58.955 38.462 22.89 22.89 41.37 3.41
3150 3340 7.010923 CAGGTTAGAAAGATAAGCAGACATGTC 59.989 40.741 18.47 18.47 35.96 3.06
3211 3413 7.234577 ACAAGGAGGCAAAACAAAAGGATATTA 59.765 33.333 0.00 0.00 0.00 0.98
3221 3423 7.929941 AAATAAAAACAAGGAGGCAAAACAA 57.070 28.000 0.00 0.00 0.00 2.83
3230 3432 7.433680 ACCACTAGCAAAATAAAAACAAGGAG 58.566 34.615 0.00 0.00 0.00 3.69
3259 3517 5.301551 TGTGAATAGAACATGTGCCACTTTT 59.698 36.000 0.00 0.00 0.00 2.27
3336 3599 7.094075 ACGTTATATGTCTACCTCACTTTGTGA 60.094 37.037 0.37 0.37 40.50 3.58
3399 3667 7.441458 GGTGGTATAACTGTAGATGAATTGGTC 59.559 40.741 0.00 0.00 0.00 4.02
3417 3685 0.720232 AGTCCAGGGGTGGTGGTATA 59.280 55.000 0.00 0.00 36.37 1.47
3424 3692 1.685820 GGAAGAAGTCCAGGGGTGG 59.314 63.158 0.00 0.00 46.97 4.61
3432 3700 4.995487 ACACGAAAGTTATGGAAGAAGTCC 59.005 41.667 0.00 0.00 46.40 3.85
3446 3714 5.529430 TGTAAATCACAATCCACACGAAAGT 59.471 36.000 0.00 0.00 38.78 2.66
3526 3794 1.566298 CCAGCTAGGGTTCTTGGGCT 61.566 60.000 0.00 0.00 0.00 5.19
3527 3795 1.077429 CCAGCTAGGGTTCTTGGGC 60.077 63.158 0.00 0.00 0.00 5.36
3528 3796 1.486726 CTACCAGCTAGGGTTCTTGGG 59.513 57.143 0.33 0.00 43.89 4.12
3529 3797 2.168728 GTCTACCAGCTAGGGTTCTTGG 59.831 54.545 0.33 0.00 43.89 3.61
3530 3798 2.159226 CGTCTACCAGCTAGGGTTCTTG 60.159 54.545 0.33 0.00 43.89 3.02
3531 3799 2.100989 CGTCTACCAGCTAGGGTTCTT 58.899 52.381 0.33 0.00 43.89 2.52
3532 3800 1.765230 CGTCTACCAGCTAGGGTTCT 58.235 55.000 0.33 0.00 43.89 3.01
3533 3801 0.102663 GCGTCTACCAGCTAGGGTTC 59.897 60.000 0.33 0.00 43.89 3.62
3534 3802 1.664321 CGCGTCTACCAGCTAGGGTT 61.664 60.000 0.33 0.00 43.89 4.11
3535 3803 2.119655 CGCGTCTACCAGCTAGGGT 61.120 63.158 0.00 0.82 43.89 4.34
3539 3807 1.227639 GAGATCGCGTCTACCAGCTA 58.772 55.000 5.77 0.00 37.29 3.32
3649 3917 2.341846 TTGCCGGTTTCAAGAAGTCT 57.658 45.000 1.90 0.00 0.00 3.24
3839 4107 1.273048 TGCATTGTTCTTCATGCCACC 59.727 47.619 1.84 0.00 39.12 4.61
3862 4130 4.787551 ACATCCTTCAGTTTTGTACCACA 58.212 39.130 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.