Multiple sequence alignment - TraesCS3D01G264300

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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 TraesCS3D01G264300 chr3D 100.000 3473 0 0 1 3473 365930353 365926881 0.000000e+00 6414.0
1 TraesCS3D01G264300 chr3D 98.387 124 2 0 843 966 365929632 365929509 5.840000e-53 219.0
2 TraesCS3D01G264300 chr3D 84.615 221 32 2 626 845 365932475 365932694 5.840000e-53 219.0
3 TraesCS3D01G264300 chr3D 84.163 221 32 3 626 845 365931570 365931788 9.770000e-51 211.0
4 TraesCS3D01G264300 chr3D 86.905 168 22 0 843 1010 365932571 365932738 4.580000e-44 189.0
5 TraesCS3D01G264300 chr3A 96.361 1484 36 5 1026 2503 488109831 488108360 0.000000e+00 2425.0
6 TraesCS3D01G264300 chr3A 86.343 864 91 22 1 845 556167443 556168298 0.000000e+00 917.0
7 TraesCS3D01G264300 chr3A 92.624 583 40 3 2891 3473 488083288 488082709 0.000000e+00 835.0
8 TraesCS3D01G264300 chr3A 84.234 222 31 4 625 845 556166959 556166741 2.720000e-51 213.0
9 TraesCS3D01G264300 chr3A 90.000 150 15 0 864 1013 556166843 556166694 9.840000e-46 195.0
10 TraesCS3D01G264300 chr3A 90.076 131 4 3 2765 2894 488083344 488083222 9.980000e-36 161.0
11 TraesCS3D01G264300 chr3B 92.573 1683 91 20 1014 2678 477329081 477327415 0.000000e+00 2385.0
12 TraesCS3D01G264300 chr3B 92.281 583 32 4 2891 3473 477322716 477322147 0.000000e+00 815.0
13 TraesCS3D01G264300 chr3B 87.755 147 15 3 866 1010 29101040 29101185 5.960000e-38 169.0
14 TraesCS3D01G264300 chr3B 90.678 118 3 2 2765 2882 477322771 477322662 2.160000e-32 150.0
15 TraesCS3D01G264300 chr7D 95.518 647 27 2 199 845 342337698 342337054 0.000000e+00 1033.0
16 TraesCS3D01G264300 chr7D 91.827 208 13 4 1 206 342337858 342337653 1.580000e-73 287.0
17 TraesCS3D01G264300 chr7D 92.147 191 13 2 822 1010 342337200 342337010 5.710000e-68 268.0
18 TraesCS3D01G264300 chr7D 80.906 309 51 6 537 845 342338281 342338581 1.610000e-58 237.0
19 TraesCS3D01G264300 chr7D 87.500 168 21 0 843 1010 342338458 342338625 9.840000e-46 195.0
20 TraesCS3D01G264300 chr2D 92.142 649 28 8 197 843 5259104 5259731 0.000000e+00 894.0
21 TraesCS3D01G264300 chr2D 82.105 475 58 19 1 450 190019158 190018686 7.030000e-102 381.0
22 TraesCS3D01G264300 chr2D 95.906 171 7 0 1 171 5258944 5259114 9.490000e-71 278.0
23 TraesCS3D01G264300 chr5D 90.993 433 37 2 412 843 553795393 553795824 1.800000e-162 582.0
24 TraesCS3D01G264300 chr5D 91.827 208 13 4 1 206 553795076 553795281 1.580000e-73 287.0
25 TraesCS3D01G264300 chr5D 95.152 165 4 3 199 362 553795236 553795397 1.240000e-64 257.0
26 TraesCS3D01G264300 chr5D 83.041 171 26 3 844 1013 553794478 553794310 6.000000e-33 152.0
27 TraesCS3D01G264300 chr2B 83.462 260 37 5 586 845 145861451 145861704 1.610000e-58 237.0
28 TraesCS3D01G264300 chr2B 85.119 168 23 1 843 1010 145861583 145861748 1.660000e-38 171.0
29 TraesCS3D01G264300 chr1D 81.347 193 32 4 821 1010 291328290 291328481 1.670000e-33 154.0
30 TraesCS3D01G264300 chr4D 77.966 118 24 2 2140 2256 14561880 14561996 4.810000e-09 73.1
31 TraesCS3D01G264300 chr6A 90.000 50 5 0 2135 2184 26735331 26735380 8.050000e-07 65.8
32 TraesCS3D01G264300 chr5B 88.889 45 4 1 2153 2196 20170545 20170501 2.000000e-03 54.7


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 TraesCS3D01G264300 chr3D 365926881 365930353 3472 True 3316.500000 6414 99.193500 1 3473 2 chr3D.!!$R1 3472
1 TraesCS3D01G264300 chr3D 365931570 365932738 1168 False 206.333333 219 85.227667 626 1010 3 chr3D.!!$F1 384
2 TraesCS3D01G264300 chr3A 488108360 488109831 1471 True 2425.000000 2425 96.361000 1026 2503 1 chr3A.!!$R1 1477
3 TraesCS3D01G264300 chr3A 556167443 556168298 855 False 917.000000 917 86.343000 1 845 1 chr3A.!!$F1 844
4 TraesCS3D01G264300 chr3A 488082709 488083344 635 True 498.000000 835 91.350000 2765 3473 2 chr3A.!!$R2 708
5 TraesCS3D01G264300 chr3B 477327415 477329081 1666 True 2385.000000 2385 92.573000 1014 2678 1 chr3B.!!$R1 1664
6 TraesCS3D01G264300 chr3B 477322147 477322771 624 True 482.500000 815 91.479500 2765 3473 2 chr3B.!!$R2 708
7 TraesCS3D01G264300 chr7D 342337010 342337858 848 True 529.333333 1033 93.164000 1 1010 3 chr7D.!!$R1 1009
8 TraesCS3D01G264300 chr2D 5258944 5259731 787 False 586.000000 894 94.024000 1 843 2 chr2D.!!$F1 842
9 TraesCS3D01G264300 chr5D 553795076 553795824 748 False 375.333333 582 92.657333 1 843 3 chr5D.!!$F1 842

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
819 1102 0.173481 GCGCTGAGATGGTACTGACA 59.827 55.0 0.0 0.0 0.0 3.58 F
1683 1973 1.123928 CCCTCCTGATTTACGCCTCT 58.876 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2561 0.809385 CGAGTCGGTACACATCCACT 59.191 55.0 4.1 0.0 0.0 4.00 R
3118 3420 0.904865 TGATCACGGGCAAGTCTCCT 60.905 55.0 0.0 0.0 0.0 3.69 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
273 333 5.059833 TCAATATACAACACACACACAGCA 58.940 37.500 0.00 0.00 0.00 4.41
322 382 8.601845 TCTGAAAAGAGATAAACGAAATGTGA 57.398 30.769 0.00 0.00 0.00 3.58
598 659 0.388907 GTCGTTGGTTCGAATCCCGA 60.389 55.000 14.11 14.11 46.94 5.14
667 949 5.922960 TCTGGCAAACAAGGGGTATATAT 57.077 39.130 0.00 0.00 0.00 0.86
719 1002 4.157472 TCGCAAAAGAATATGCCACATCAA 59.843 37.500 0.00 0.00 39.39 2.57
726 1009 1.462616 TATGCCACATCAACACCTGC 58.537 50.000 0.00 0.00 0.00 4.85
732 1015 1.379916 CATCAACACCTGCCAGGGA 59.620 57.895 16.70 2.49 40.58 4.20
733 1016 0.679002 CATCAACACCTGCCAGGGAG 60.679 60.000 16.70 9.82 40.58 4.30
734 1017 1.136329 ATCAACACCTGCCAGGGAGT 61.136 55.000 16.70 10.52 40.58 3.85
735 1018 1.302832 CAACACCTGCCAGGGAGTC 60.303 63.158 16.70 0.00 40.58 3.36
736 1019 2.529744 AACACCTGCCAGGGAGTCC 61.530 63.158 16.70 0.00 40.58 3.85
737 1020 3.721706 CACCTGCCAGGGAGTCCC 61.722 72.222 21.81 21.81 45.90 4.46
755 1038 4.203076 GCCGGTCGGATACAGCGT 62.203 66.667 14.15 0.00 37.05 5.07
756 1039 2.025727 CCGGTCGGATACAGCGTC 59.974 66.667 2.83 0.00 37.05 5.19
757 1040 2.767445 CCGGTCGGATACAGCGTCA 61.767 63.158 2.83 0.00 37.05 4.35
758 1041 1.138036 CGGTCGGATACAGCGTCAA 59.862 57.895 0.00 0.00 35.11 3.18
759 1042 0.248907 CGGTCGGATACAGCGTCAAT 60.249 55.000 0.00 0.00 35.11 2.57
760 1043 1.002142 CGGTCGGATACAGCGTCAATA 60.002 52.381 0.00 0.00 35.11 1.90
761 1044 2.391879 GGTCGGATACAGCGTCAATAC 58.608 52.381 0.00 0.00 0.00 1.89
762 1045 2.223641 GGTCGGATACAGCGTCAATACA 60.224 50.000 0.00 0.00 0.00 2.29
763 1046 2.787680 GTCGGATACAGCGTCAATACAC 59.212 50.000 0.00 0.00 0.00 2.90
764 1047 2.686405 TCGGATACAGCGTCAATACACT 59.314 45.455 0.00 0.00 0.00 3.55
765 1048 2.789339 CGGATACAGCGTCAATACACTG 59.211 50.000 0.00 0.00 40.82 3.66
767 1050 4.181578 GGATACAGCGTCAATACACTGTT 58.818 43.478 4.70 0.00 44.61 3.16
768 1051 5.345702 GGATACAGCGTCAATACACTGTTA 58.654 41.667 4.70 0.00 44.61 2.41
769 1052 5.983720 GGATACAGCGTCAATACACTGTTAT 59.016 40.000 4.70 0.00 44.61 1.89
770 1053 7.143340 GGATACAGCGTCAATACACTGTTATA 58.857 38.462 4.70 0.00 44.61 0.98
771 1054 7.114529 GGATACAGCGTCAATACACTGTTATAC 59.885 40.741 4.70 0.00 44.61 1.47
772 1055 5.716094 ACAGCGTCAATACACTGTTATACA 58.284 37.500 0.00 0.00 44.61 2.29
773 1056 5.575606 ACAGCGTCAATACACTGTTATACAC 59.424 40.000 0.00 0.00 44.61 2.90
774 1057 5.575218 CAGCGTCAATACACTGTTATACACA 59.425 40.000 0.00 0.00 32.25 3.72
775 1058 6.090223 CAGCGTCAATACACTGTTATACACAA 59.910 38.462 0.00 0.00 33.87 3.33
776 1059 6.816640 AGCGTCAATACACTGTTATACACAAT 59.183 34.615 0.00 0.00 33.87 2.71
777 1060 7.333423 AGCGTCAATACACTGTTATACACAATT 59.667 33.333 0.00 0.00 33.87 2.32
778 1061 7.960738 GCGTCAATACACTGTTATACACAATTT 59.039 33.333 0.00 0.00 33.87 1.82
786 1069 9.555727 ACACTGTTATACACAATTTAGACTGTT 57.444 29.630 0.00 0.00 33.87 3.16
802 1085 8.882415 TTAGACTGTTTTCCTATAATTAGGCG 57.118 34.615 0.00 0.00 44.20 5.52
803 1086 5.758784 AGACTGTTTTCCTATAATTAGGCGC 59.241 40.000 0.00 0.00 44.20 6.53
804 1087 5.681639 ACTGTTTTCCTATAATTAGGCGCT 58.318 37.500 7.64 0.00 44.20 5.92
805 1088 5.527582 ACTGTTTTCCTATAATTAGGCGCTG 59.472 40.000 7.64 0.00 44.20 5.18
806 1089 5.676552 TGTTTTCCTATAATTAGGCGCTGA 58.323 37.500 7.64 0.00 44.20 4.26
807 1090 5.758296 TGTTTTCCTATAATTAGGCGCTGAG 59.242 40.000 7.64 0.00 44.20 3.35
808 1091 5.801531 TTTCCTATAATTAGGCGCTGAGA 57.198 39.130 7.64 0.00 44.20 3.27
809 1092 6.360370 TTTCCTATAATTAGGCGCTGAGAT 57.640 37.500 7.64 0.00 44.20 2.75
810 1093 5.330455 TCCTATAATTAGGCGCTGAGATG 57.670 43.478 7.64 0.00 44.20 2.90
811 1094 4.160439 TCCTATAATTAGGCGCTGAGATGG 59.840 45.833 7.64 0.00 44.20 3.51
812 1095 4.081420 CCTATAATTAGGCGCTGAGATGGT 60.081 45.833 7.64 0.00 38.75 3.55
813 1096 5.127194 CCTATAATTAGGCGCTGAGATGGTA 59.873 44.000 7.64 0.00 38.75 3.25
814 1097 2.821991 ATTAGGCGCTGAGATGGTAC 57.178 50.000 7.64 0.00 0.00 3.34
815 1098 1.776662 TTAGGCGCTGAGATGGTACT 58.223 50.000 7.64 0.00 0.00 2.73
816 1099 1.032794 TAGGCGCTGAGATGGTACTG 58.967 55.000 7.64 0.00 0.00 2.74
817 1100 0.684479 AGGCGCTGAGATGGTACTGA 60.684 55.000 7.64 0.00 0.00 3.41
818 1101 0.528684 GGCGCTGAGATGGTACTGAC 60.529 60.000 7.64 0.00 0.00 3.51
819 1102 0.173481 GCGCTGAGATGGTACTGACA 59.827 55.000 0.00 0.00 0.00 3.58
820 1103 1.202463 GCGCTGAGATGGTACTGACAT 60.202 52.381 0.00 0.00 0.00 3.06
821 1104 2.467838 CGCTGAGATGGTACTGACATG 58.532 52.381 0.00 0.00 0.00 3.21
822 1105 2.208431 GCTGAGATGGTACTGACATGC 58.792 52.381 0.00 0.00 0.00 4.06
823 1106 2.419159 GCTGAGATGGTACTGACATGCA 60.419 50.000 0.00 0.00 0.00 3.96
824 1107 3.865446 CTGAGATGGTACTGACATGCAA 58.135 45.455 0.00 0.00 0.00 4.08
825 1108 4.256110 CTGAGATGGTACTGACATGCAAA 58.744 43.478 0.00 0.00 0.00 3.68
826 1109 4.650734 TGAGATGGTACTGACATGCAAAA 58.349 39.130 0.00 0.00 0.00 2.44
827 1110 5.069318 TGAGATGGTACTGACATGCAAAAA 58.931 37.500 0.00 0.00 0.00 1.94
848 1131 7.582667 AAAAATATGACTAATGGTACCTGCC 57.417 36.000 14.36 0.00 0.00 4.85
849 1132 5.904984 AATATGACTAATGGTACCTGCCA 57.095 39.130 14.36 3.21 43.48 4.92
850 1133 3.845781 ATGACTAATGGTACCTGCCAG 57.154 47.619 14.36 7.56 42.47 4.85
851 1134 1.837439 TGACTAATGGTACCTGCCAGG 59.163 52.381 14.36 9.83 42.47 4.45
852 1135 1.141053 GACTAATGGTACCTGCCAGGG 59.859 57.143 16.70 0.00 42.47 4.45
853 1136 1.274184 ACTAATGGTACCTGCCAGGGA 60.274 52.381 16.70 2.57 42.47 4.20
974 1258 9.706691 AATATGACTAATGGTACCAATTCGTAG 57.293 33.333 20.76 16.27 0.00 3.51
998 1282 2.299297 AGGTGCTGAAGTGTGGTACTAC 59.701 50.000 1.77 1.77 39.18 2.73
1018 1302 7.986085 ACTACCATGCAATTAAGTCATATCC 57.014 36.000 0.00 0.00 0.00 2.59
1075 1359 3.046087 CAGCTGCCACGGACACAG 61.046 66.667 0.00 0.00 34.48 3.66
1102 1386 1.280066 TATGACGATGACGACGACGA 58.720 50.000 15.32 0.00 42.66 4.20
1572 1862 2.088763 CCACTACGTGCACTCGCTG 61.089 63.158 16.19 4.97 39.64 5.18
1683 1973 1.123928 CCCTCCTGATTTACGCCTCT 58.876 55.000 0.00 0.00 0.00 3.69
1821 2111 1.449601 CGAGCACCTGCCGGTTATT 60.450 57.895 1.90 0.00 42.13 1.40
2224 2520 4.980805 GAGTGCCGGTCGTTGCCA 62.981 66.667 1.90 0.00 0.00 4.92
2265 2561 2.607635 GAGCATCAACGCGAAATTCCTA 59.392 45.455 15.93 0.00 36.85 2.94
2324 2620 2.815647 GACAAGGGAAGCGCTCCG 60.816 66.667 12.06 4.17 46.51 4.63
2505 2802 2.777494 CGTGCTTCATGTGCATTAGTG 58.223 47.619 16.32 4.71 42.69 2.74
2556 2853 9.995003 AGCATTTAGATCACTAGAGGAAATTAG 57.005 33.333 0.00 0.00 0.00 1.73
2567 2864 9.535878 CACTAGAGGAAATTAGTGATCTAAACC 57.464 37.037 0.00 0.00 46.10 3.27
2568 2865 8.706521 ACTAGAGGAAATTAGTGATCTAAACCC 58.293 37.037 0.00 0.00 39.23 4.11
2569 2866 7.757242 AGAGGAAATTAGTGATCTAAACCCT 57.243 36.000 0.00 0.00 39.23 4.34
2570 2867 8.164057 AGAGGAAATTAGTGATCTAAACCCTT 57.836 34.615 0.00 0.00 39.23 3.95
2571 2868 8.615705 AGAGGAAATTAGTGATCTAAACCCTTT 58.384 33.333 0.00 0.00 39.23 3.11
2572 2869 9.244292 GAGGAAATTAGTGATCTAAACCCTTTT 57.756 33.333 0.00 0.00 39.23 2.27
2590 2887 9.581099 AACCCTTTTATATTTGTTTATCAAGCG 57.419 29.630 0.00 0.00 37.35 4.68
2632 2933 3.056107 TGTCTTATCAGTGTAGTGTGCCC 60.056 47.826 0.00 0.00 0.00 5.36
2660 2961 7.303182 TCCTCTCGTGATGGTCATTATTATT 57.697 36.000 0.00 0.00 0.00 1.40
2670 2971 8.970020 TGATGGTCATTATTATTGCTTTTCACT 58.030 29.630 0.00 0.00 0.00 3.41
2671 2972 9.807649 GATGGTCATTATTATTGCTTTTCACTT 57.192 29.630 0.00 0.00 0.00 3.16
2682 2983 9.897744 TTATTGCTTTTCACTTTCTCATACAAG 57.102 29.630 0.00 0.00 0.00 3.16
2683 2984 6.942532 TGCTTTTCACTTTCTCATACAAGT 57.057 33.333 0.00 0.00 33.29 3.16
2684 2985 7.333528 TGCTTTTCACTTTCTCATACAAGTT 57.666 32.000 0.00 0.00 30.48 2.66
2685 2986 7.771183 TGCTTTTCACTTTCTCATACAAGTTT 58.229 30.769 0.00 0.00 30.48 2.66
2686 2987 8.898761 TGCTTTTCACTTTCTCATACAAGTTTA 58.101 29.630 0.00 0.00 30.48 2.01
2687 2988 9.899226 GCTTTTCACTTTCTCATACAAGTTTAT 57.101 29.630 0.00 0.00 30.48 1.40
2739 3040 9.118236 GCATAATAAGGAAATATCAAAAGTCGC 57.882 33.333 0.00 0.00 0.00 5.19
2742 3043 8.506168 AATAAGGAAATATCAAAAGTCGCTCA 57.494 30.769 0.00 0.00 0.00 4.26
2743 3044 5.803020 AGGAAATATCAAAAGTCGCTCAC 57.197 39.130 0.00 0.00 0.00 3.51
2744 3045 5.491982 AGGAAATATCAAAAGTCGCTCACT 58.508 37.500 0.00 0.00 36.64 3.41
2754 3055 4.521130 AAGTCGCTCACTTTCTCATACA 57.479 40.909 0.00 0.00 43.38 2.29
2755 3056 4.521130 AGTCGCTCACTTTCTCATACAA 57.479 40.909 0.00 0.00 26.56 2.41
2756 3057 5.078411 AGTCGCTCACTTTCTCATACAAT 57.922 39.130 0.00 0.00 26.56 2.71
2757 3058 5.482908 AGTCGCTCACTTTCTCATACAATT 58.517 37.500 0.00 0.00 26.56 2.32
2758 3059 5.934625 AGTCGCTCACTTTCTCATACAATTT 59.065 36.000 0.00 0.00 26.56 1.82
2759 3060 7.097192 AGTCGCTCACTTTCTCATACAATTTA 58.903 34.615 0.00 0.00 26.56 1.40
2760 3061 7.063544 AGTCGCTCACTTTCTCATACAATTTAC 59.936 37.037 0.00 0.00 26.56 2.01
2761 3062 6.312918 TCGCTCACTTTCTCATACAATTTACC 59.687 38.462 0.00 0.00 0.00 2.85
2762 3063 6.313905 CGCTCACTTTCTCATACAATTTACCT 59.686 38.462 0.00 0.00 0.00 3.08
2763 3064 7.467623 GCTCACTTTCTCATACAATTTACCTG 58.532 38.462 0.00 0.00 0.00 4.00
2786 3087 8.956426 CCTGCTGAATTTTATAGTTTGGAGTAA 58.044 33.333 0.00 0.00 0.00 2.24
2864 3166 6.186957 TGGAGTATTTGCATTGTTGGAGTAT 58.813 36.000 0.00 0.00 0.00 2.12
2865 3167 7.342581 TGGAGTATTTGCATTGTTGGAGTATA 58.657 34.615 0.00 0.00 0.00 1.47
2866 3168 7.831690 TGGAGTATTTGCATTGTTGGAGTATAA 59.168 33.333 0.00 0.00 0.00 0.98
2867 3169 8.345565 GGAGTATTTGCATTGTTGGAGTATAAG 58.654 37.037 0.00 0.00 0.00 1.73
2868 3170 9.109393 GAGTATTTGCATTGTTGGAGTATAAGA 57.891 33.333 0.00 0.00 0.00 2.10
2869 3171 9.461312 AGTATTTGCATTGTTGGAGTATAAGAA 57.539 29.630 0.00 0.00 0.00 2.52
2871 3173 8.986477 ATTTGCATTGTTGGAGTATAAGAAAC 57.014 30.769 0.00 0.00 0.00 2.78
2872 3174 7.759489 TTGCATTGTTGGAGTATAAGAAACT 57.241 32.000 0.00 0.00 0.00 2.66
2873 3175 7.759489 TGCATTGTTGGAGTATAAGAAACTT 57.241 32.000 0.00 0.00 0.00 2.66
2874 3176 7.592938 TGCATTGTTGGAGTATAAGAAACTTG 58.407 34.615 0.00 0.00 0.00 3.16
2875 3177 7.230510 TGCATTGTTGGAGTATAAGAAACTTGT 59.769 33.333 0.00 0.00 0.00 3.16
2876 3178 8.082242 GCATTGTTGGAGTATAAGAAACTTGTT 58.918 33.333 0.00 0.00 0.00 2.83
2877 3179 9.612620 CATTGTTGGAGTATAAGAAACTTGTTC 57.387 33.333 0.00 0.00 0.00 3.18
2878 3180 7.739498 TGTTGGAGTATAAGAAACTTGTTCC 57.261 36.000 0.00 0.00 0.00 3.62
2879 3181 7.514721 TGTTGGAGTATAAGAAACTTGTTCCT 58.485 34.615 0.00 0.00 0.00 3.36
2880 3182 7.996644 TGTTGGAGTATAAGAAACTTGTTCCTT 59.003 33.333 0.00 0.00 0.00 3.36
2881 3183 8.847196 GTTGGAGTATAAGAAACTTGTTCCTTT 58.153 33.333 0.00 0.00 0.00 3.11
2882 3184 8.990163 TGGAGTATAAGAAACTTGTTCCTTTT 57.010 30.769 0.00 0.00 0.00 2.27
2883 3185 8.846211 TGGAGTATAAGAAACTTGTTCCTTTTG 58.154 33.333 0.00 0.00 0.00 2.44
2884 3186 7.808381 GGAGTATAAGAAACTTGTTCCTTTTGC 59.192 37.037 0.00 0.00 0.00 3.68
2885 3187 8.465273 AGTATAAGAAACTTGTTCCTTTTGCT 57.535 30.769 0.00 0.00 0.00 3.91
2886 3188 8.568794 AGTATAAGAAACTTGTTCCTTTTGCTC 58.431 33.333 0.00 0.00 0.00 4.26
2887 3189 4.655762 AGAAACTTGTTCCTTTTGCTCC 57.344 40.909 0.00 0.00 0.00 4.70
2888 3190 4.281657 AGAAACTTGTTCCTTTTGCTCCT 58.718 39.130 0.00 0.00 0.00 3.69
2889 3191 4.711846 AGAAACTTGTTCCTTTTGCTCCTT 59.288 37.500 0.00 0.00 0.00 3.36
2890 3192 5.187772 AGAAACTTGTTCCTTTTGCTCCTTT 59.812 36.000 0.00 0.00 0.00 3.11
2891 3193 4.391405 ACTTGTTCCTTTTGCTCCTTTG 57.609 40.909 0.00 0.00 0.00 2.77
2892 3194 4.023291 ACTTGTTCCTTTTGCTCCTTTGA 58.977 39.130 0.00 0.00 0.00 2.69
2893 3195 4.466015 ACTTGTTCCTTTTGCTCCTTTGAA 59.534 37.500 0.00 0.00 0.00 2.69
2894 3196 5.129320 ACTTGTTCCTTTTGCTCCTTTGAAT 59.871 36.000 0.00 0.00 0.00 2.57
2895 3197 5.612725 TGTTCCTTTTGCTCCTTTGAATT 57.387 34.783 0.00 0.00 0.00 2.17
2896 3198 5.988287 TGTTCCTTTTGCTCCTTTGAATTT 58.012 33.333 0.00 0.00 0.00 1.82
2897 3199 5.816777 TGTTCCTTTTGCTCCTTTGAATTTG 59.183 36.000 0.00 0.00 0.00 2.32
2898 3200 4.959723 TCCTTTTGCTCCTTTGAATTTGG 58.040 39.130 0.00 0.00 0.00 3.28
2899 3201 4.653341 TCCTTTTGCTCCTTTGAATTTGGA 59.347 37.500 0.00 0.00 0.00 3.53
2900 3202 5.307716 TCCTTTTGCTCCTTTGAATTTGGAT 59.692 36.000 0.00 0.00 0.00 3.41
2901 3203 5.999600 CCTTTTGCTCCTTTGAATTTGGATT 59.000 36.000 0.00 0.00 0.00 3.01
2902 3204 6.072893 CCTTTTGCTCCTTTGAATTTGGATTG 60.073 38.462 0.00 0.00 0.00 2.67
2903 3205 5.549742 TTGCTCCTTTGAATTTGGATTGT 57.450 34.783 0.00 0.00 0.00 2.71
2904 3206 5.549742 TGCTCCTTTGAATTTGGATTGTT 57.450 34.783 0.00 0.00 0.00 2.83
2905 3207 5.299148 TGCTCCTTTGAATTTGGATTGTTG 58.701 37.500 0.00 0.00 0.00 3.33
2906 3208 4.692155 GCTCCTTTGAATTTGGATTGTTGG 59.308 41.667 0.00 0.00 0.00 3.77
2907 3209 5.511202 GCTCCTTTGAATTTGGATTGTTGGA 60.511 40.000 0.00 0.00 0.00 3.53
2908 3210 6.100404 TCCTTTGAATTTGGATTGTTGGAG 57.900 37.500 0.00 0.00 0.00 3.86
2909 3211 5.602145 TCCTTTGAATTTGGATTGTTGGAGT 59.398 36.000 0.00 0.00 0.00 3.85
2910 3212 6.780031 TCCTTTGAATTTGGATTGTTGGAGTA 59.220 34.615 0.00 0.00 0.00 2.59
2911 3213 7.454380 TCCTTTGAATTTGGATTGTTGGAGTAT 59.546 33.333 0.00 0.00 0.00 2.12
2912 3214 8.096414 CCTTTGAATTTGGATTGTTGGAGTATT 58.904 33.333 0.00 0.00 0.00 1.89
2913 3215 9.492973 CTTTGAATTTGGATTGTTGGAGTATTT 57.507 29.630 0.00 0.00 0.00 1.40
2914 3216 8.830201 TTGAATTTGGATTGTTGGAGTATTTG 57.170 30.769 0.00 0.00 0.00 2.32
2915 3217 6.873076 TGAATTTGGATTGTTGGAGTATTTGC 59.127 34.615 0.00 0.00 0.00 3.68
2916 3218 5.798125 TTTGGATTGTTGGAGTATTTGCA 57.202 34.783 0.00 0.00 0.00 4.08
2917 3219 4.782019 TGGATTGTTGGAGTATTTGCAC 57.218 40.909 0.00 0.00 0.00 4.57
2918 3220 4.406456 TGGATTGTTGGAGTATTTGCACT 58.594 39.130 0.00 0.00 0.00 4.40
2919 3221 4.218200 TGGATTGTTGGAGTATTTGCACTG 59.782 41.667 0.00 0.00 0.00 3.66
2920 3222 4.218417 GGATTGTTGGAGTATTTGCACTGT 59.782 41.667 0.00 0.00 0.00 3.55
2921 3223 5.278957 GGATTGTTGGAGTATTTGCACTGTT 60.279 40.000 0.00 0.00 0.00 3.16
2922 3224 4.566545 TGTTGGAGTATTTGCACTGTTG 57.433 40.909 0.00 0.00 0.00 3.33
2923 3225 3.317711 TGTTGGAGTATTTGCACTGTTGG 59.682 43.478 0.00 0.00 0.00 3.77
2924 3226 3.500448 TGGAGTATTTGCACTGTTGGA 57.500 42.857 0.00 0.00 0.00 3.53
2925 3227 3.411446 TGGAGTATTTGCACTGTTGGAG 58.589 45.455 0.00 0.00 0.00 3.86
2926 3228 3.181445 TGGAGTATTTGCACTGTTGGAGT 60.181 43.478 0.00 0.00 34.02 3.85
2927 3229 4.041075 TGGAGTATTTGCACTGTTGGAGTA 59.959 41.667 0.00 0.00 31.73 2.59
2974 3276 3.291584 TGCAGGTGTTCAACAACCAATA 58.708 40.909 0.59 0.00 36.16 1.90
3054 3356 6.495181 ACTGAGTAAAGATGGAGAAGTTGAGA 59.505 38.462 0.00 0.00 0.00 3.27
3112 3414 2.624838 ACAAGTCTTAGAACCGTCGGAA 59.375 45.455 20.51 0.00 0.00 4.30
3118 3420 5.047802 AGTCTTAGAACCGTCGGAACAATAA 60.048 40.000 20.51 8.36 0.00 1.40
3147 3449 1.135024 GCCCGTGATCAAATTGCACAT 60.135 47.619 0.00 0.00 32.96 3.21
3273 3575 4.965200 AACAACCAGAGCTCTTTCTAGT 57.035 40.909 15.27 6.64 0.00 2.57
3304 3606 3.072476 TGTTATATAGCCCTTCACCAGCC 59.928 47.826 0.00 0.00 0.00 4.85
3310 3612 1.937924 GCCCTTCACCAGCCCCTTAT 61.938 60.000 0.00 0.00 0.00 1.73
3368 3670 6.538021 AGACTCAAGTTCTGCATATTCATGTC 59.462 38.462 0.00 0.00 34.40 3.06
3395 3697 2.463752 AGCAACATTGGAGAATGCCAT 58.536 42.857 0.00 0.00 42.54 4.40
3437 3739 3.108144 GCATAATTGTCCACATTGACGC 58.892 45.455 0.00 0.00 38.11 5.19
3444 3746 0.032815 TCCACATTGACGCGAAGTGA 59.967 50.000 15.93 1.85 43.07 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
273 333 5.647589 TCGTGTTTATTCTTCGAGCACTAT 58.352 37.500 0.00 0.00 0.00 2.12
322 382 9.959775 CATTTTTGTGTGTATACGTTTGTTTTT 57.040 25.926 0.00 0.00 0.00 1.94
528 589 0.652592 GTGCTACATCACACATCGCC 59.347 55.000 0.00 0.00 36.77 5.54
688 971 5.633182 GGCATATTCTTTTGCGAAAAAGACA 59.367 36.000 27.45 19.28 45.37 3.41
719 1002 2.930562 GGACTCCCTGGCAGGTGT 60.931 66.667 30.68 26.75 36.35 4.16
738 1021 4.203076 ACGCTGTATCCGACCGGC 62.203 66.667 0.00 0.00 34.68 6.13
739 1022 2.025727 GACGCTGTATCCGACCGG 59.974 66.667 0.00 0.00 0.00 5.28
740 1023 0.248907 ATTGACGCTGTATCCGACCG 60.249 55.000 0.00 0.00 0.00 4.79
741 1024 2.223641 TGTATTGACGCTGTATCCGACC 60.224 50.000 0.00 0.00 0.00 4.79
742 1025 2.787680 GTGTATTGACGCTGTATCCGAC 59.212 50.000 0.00 0.00 33.03 4.79
743 1026 2.686405 AGTGTATTGACGCTGTATCCGA 59.314 45.455 0.00 0.00 44.84 4.55
744 1027 3.079960 AGTGTATTGACGCTGTATCCG 57.920 47.619 0.00 0.00 44.84 4.18
752 1035 6.397831 TTGTGTATAACAGTGTATTGACGC 57.602 37.500 0.00 0.34 40.74 5.19
760 1043 9.555727 AACAGTCTAAATTGTGTATAACAGTGT 57.444 29.630 0.00 0.00 40.74 3.55
790 1073 5.078411 ACCATCTCAGCGCCTAATTATAG 57.922 43.478 2.29 0.00 0.00 1.31
791 1074 5.715279 AGTACCATCTCAGCGCCTAATTATA 59.285 40.000 2.29 0.00 0.00 0.98
792 1075 4.528596 AGTACCATCTCAGCGCCTAATTAT 59.471 41.667 2.29 0.00 0.00 1.28
793 1076 3.895656 AGTACCATCTCAGCGCCTAATTA 59.104 43.478 2.29 0.00 0.00 1.40
794 1077 2.700897 AGTACCATCTCAGCGCCTAATT 59.299 45.455 2.29 0.00 0.00 1.40
795 1078 2.036475 CAGTACCATCTCAGCGCCTAAT 59.964 50.000 2.29 0.00 0.00 1.73
796 1079 1.409064 CAGTACCATCTCAGCGCCTAA 59.591 52.381 2.29 0.00 0.00 2.69
797 1080 1.032794 CAGTACCATCTCAGCGCCTA 58.967 55.000 2.29 0.00 0.00 3.93
798 1081 0.684479 TCAGTACCATCTCAGCGCCT 60.684 55.000 2.29 0.00 0.00 5.52
799 1082 0.528684 GTCAGTACCATCTCAGCGCC 60.529 60.000 2.29 0.00 0.00 6.53
800 1083 0.173481 TGTCAGTACCATCTCAGCGC 59.827 55.000 0.00 0.00 0.00 5.92
801 1084 2.467838 CATGTCAGTACCATCTCAGCG 58.532 52.381 0.00 0.00 0.00 5.18
802 1085 2.208431 GCATGTCAGTACCATCTCAGC 58.792 52.381 0.00 0.00 0.00 4.26
803 1086 3.531934 TGCATGTCAGTACCATCTCAG 57.468 47.619 0.00 0.00 0.00 3.35
804 1087 3.979101 TTGCATGTCAGTACCATCTCA 57.021 42.857 0.00 0.00 0.00 3.27
805 1088 5.627499 TTTTTGCATGTCAGTACCATCTC 57.373 39.130 0.00 0.00 0.00 2.75
824 1107 7.122715 TGGCAGGTACCATTAGTCATATTTTT 58.877 34.615 15.94 0.00 33.75 1.94
825 1108 6.668645 TGGCAGGTACCATTAGTCATATTTT 58.331 36.000 15.94 0.00 33.75 1.82
826 1109 6.260700 TGGCAGGTACCATTAGTCATATTT 57.739 37.500 15.94 0.00 33.75 1.40
827 1110 5.221925 CCTGGCAGGTACCATTAGTCATATT 60.222 44.000 25.74 0.00 39.54 1.28
828 1111 4.287067 CCTGGCAGGTACCATTAGTCATAT 59.713 45.833 25.74 0.00 39.54 1.78
829 1112 3.646162 CCTGGCAGGTACCATTAGTCATA 59.354 47.826 25.74 0.00 39.54 2.15
830 1113 2.439507 CCTGGCAGGTACCATTAGTCAT 59.560 50.000 25.74 0.00 39.54 3.06
831 1114 1.837439 CCTGGCAGGTACCATTAGTCA 59.163 52.381 25.74 7.68 39.54 3.41
832 1115 1.141053 CCCTGGCAGGTACCATTAGTC 59.859 57.143 30.68 2.93 39.54 2.59
833 1116 1.213296 CCCTGGCAGGTACCATTAGT 58.787 55.000 30.68 0.00 39.54 2.24
834 1117 1.417890 CTCCCTGGCAGGTACCATTAG 59.582 57.143 30.68 13.73 39.54 1.73
835 1118 1.274184 ACTCCCTGGCAGGTACCATTA 60.274 52.381 30.68 7.27 39.54 1.90
836 1119 0.550147 ACTCCCTGGCAGGTACCATT 60.550 55.000 30.68 7.11 39.54 3.16
837 1120 0.983378 GACTCCCTGGCAGGTACCAT 60.983 60.000 30.68 12.29 39.54 3.55
838 1121 1.612442 GACTCCCTGGCAGGTACCA 60.612 63.158 30.68 11.61 38.29 3.25
839 1122 2.368011 GGACTCCCTGGCAGGTACC 61.368 68.421 30.68 22.16 31.93 3.34
840 1123 2.368011 GGGACTCCCTGGCAGGTAC 61.368 68.421 30.68 14.34 41.34 3.34
841 1124 2.040606 GGGACTCCCTGGCAGGTA 59.959 66.667 30.68 16.22 41.34 3.08
852 1135 1.826921 TATCTGACCGGCGGGACTC 60.827 63.158 31.78 19.28 36.97 3.36
853 1136 2.125961 GTATCTGACCGGCGGGACT 61.126 63.158 31.78 9.54 36.97 3.85
912 1195 2.434336 ACCATCTCAGCGCCTAATTGTA 59.566 45.455 2.29 0.00 0.00 2.41
973 1257 0.687354 CCACACTTCAGCACCTACCT 59.313 55.000 0.00 0.00 0.00 3.08
974 1258 0.396811 ACCACACTTCAGCACCTACC 59.603 55.000 0.00 0.00 0.00 3.18
998 1282 5.771666 AGTGGGATATGACTTAATTGCATGG 59.228 40.000 0.00 0.00 0.00 3.66
1030 1314 8.418597 TCAACTACTATTGTCCTACACTCTTT 57.581 34.615 0.00 0.00 0.00 2.52
1075 1359 0.512952 GTCATCGTCATAATGGCGGC 59.487 55.000 0.00 0.00 46.79 6.53
1683 1973 2.171209 CTCGCCACATGTCCTGGTCA 62.171 60.000 0.00 0.00 0.00 4.02
1797 2087 2.512515 GGCAGGTGCTCGCTAAGG 60.513 66.667 1.26 0.00 41.70 2.69
1821 2111 1.758514 GATGAGAGGGCCGACTGGA 60.759 63.158 10.69 0.00 37.49 3.86
2208 2504 4.988598 CTGGCAACGACCGGCACT 62.989 66.667 0.00 0.00 42.51 4.40
2265 2561 0.809385 CGAGTCGGTACACATCCACT 59.191 55.000 4.10 0.00 0.00 4.00
2324 2620 2.865079 TGACCTCCTCGATGGATAGAC 58.135 52.381 6.30 2.91 45.16 2.59
2527 2824 9.692325 ATTTCCTCTAGTGATCTAAATGCTTTT 57.308 29.630 2.86 2.86 0.00 2.27
2528 2825 9.692325 AATTTCCTCTAGTGATCTAAATGCTTT 57.308 29.630 0.00 0.00 0.00 3.51
2530 2827 9.995003 CTAATTTCCTCTAGTGATCTAAATGCT 57.005 33.333 0.00 0.00 0.00 3.79
2531 2828 9.771534 ACTAATTTCCTCTAGTGATCTAAATGC 57.228 33.333 0.00 0.00 0.00 3.56
2541 2838 9.535878 GGTTTAGATCACTAATTTCCTCTAGTG 57.464 37.037 0.00 3.37 44.22 2.74
2542 2839 8.706521 GGGTTTAGATCACTAATTTCCTCTAGT 58.293 37.037 0.00 0.00 38.23 2.57
2543 2840 8.929487 AGGGTTTAGATCACTAATTTCCTCTAG 58.071 37.037 0.00 0.00 38.23 2.43
2544 2841 8.855804 AGGGTTTAGATCACTAATTTCCTCTA 57.144 34.615 0.00 0.00 38.23 2.43
2545 2842 7.757242 AGGGTTTAGATCACTAATTTCCTCT 57.243 36.000 0.00 0.00 38.23 3.69
2546 2843 8.809468 AAAGGGTTTAGATCACTAATTTCCTC 57.191 34.615 0.00 0.00 38.23 3.71
2564 2861 9.581099 CGCTTGATAAACAAATATAAAAGGGTT 57.419 29.630 0.00 0.00 38.08 4.11
2565 2862 8.962679 TCGCTTGATAAACAAATATAAAAGGGT 58.037 29.630 0.00 0.00 38.08 4.34
2566 2863 9.450807 CTCGCTTGATAAACAAATATAAAAGGG 57.549 33.333 0.00 0.00 38.08 3.95
2584 2881 9.817809 AATGAAGATTAAATAGTACTCGCTTGA 57.182 29.630 0.00 0.00 0.00 3.02
2585 2882 9.855361 CAATGAAGATTAAATAGTACTCGCTTG 57.145 33.333 0.00 0.00 0.00 4.01
2586 2883 9.601217 ACAATGAAGATTAAATAGTACTCGCTT 57.399 29.630 0.00 0.00 0.00 4.68
2588 2885 9.250624 AGACAATGAAGATTAAATAGTACTCGC 57.749 33.333 0.00 0.00 0.00 5.03
2616 2913 1.644509 TGAGGGCACACTACACTGAT 58.355 50.000 0.00 0.00 0.00 2.90
2617 2914 1.550524 GATGAGGGCACACTACACTGA 59.449 52.381 0.00 0.00 0.00 3.41
2623 2924 1.781786 GAGAGGATGAGGGCACACTA 58.218 55.000 0.00 0.00 0.00 2.74
2632 2933 2.027385 TGACCATCACGAGAGGATGAG 58.973 52.381 4.07 0.00 43.80 2.90
2660 2961 6.942532 ACTTGTATGAGAAAGTGAAAAGCA 57.057 33.333 0.00 0.00 35.34 3.91
2713 3014 9.118236 GCGACTTTTGATATTTCCTTATTATGC 57.882 33.333 0.00 0.00 0.00 3.14
2716 3017 9.607988 TGAGCGACTTTTGATATTTCCTTATTA 57.392 29.630 0.00 0.00 0.00 0.98
2717 3018 8.398665 GTGAGCGACTTTTGATATTTCCTTATT 58.601 33.333 0.00 0.00 0.00 1.40
2718 3019 7.770897 AGTGAGCGACTTTTGATATTTCCTTAT 59.229 33.333 0.00 0.00 0.00 1.73
2719 3020 7.103641 AGTGAGCGACTTTTGATATTTCCTTA 58.896 34.615 0.00 0.00 0.00 2.69
2720 3021 5.940470 AGTGAGCGACTTTTGATATTTCCTT 59.060 36.000 0.00 0.00 0.00 3.36
2721 3022 5.491982 AGTGAGCGACTTTTGATATTTCCT 58.508 37.500 0.00 0.00 0.00 3.36
2722 3023 5.803020 AGTGAGCGACTTTTGATATTTCC 57.197 39.130 0.00 0.00 0.00 3.13
2734 3035 4.521130 TTGTATGAGAAAGTGAGCGACT 57.479 40.909 0.00 0.00 35.94 4.18
2735 3036 5.786401 AATTGTATGAGAAAGTGAGCGAC 57.214 39.130 0.00 0.00 0.00 5.19
2736 3037 6.312918 GGTAAATTGTATGAGAAAGTGAGCGA 59.687 38.462 0.00 0.00 0.00 4.93
2737 3038 6.313905 AGGTAAATTGTATGAGAAAGTGAGCG 59.686 38.462 0.00 0.00 0.00 5.03
2738 3039 7.467623 CAGGTAAATTGTATGAGAAAGTGAGC 58.532 38.462 0.00 0.00 0.00 4.26
2739 3040 7.335422 AGCAGGTAAATTGTATGAGAAAGTGAG 59.665 37.037 0.00 0.00 0.00 3.51
2740 3041 7.119699 CAGCAGGTAAATTGTATGAGAAAGTGA 59.880 37.037 0.00 0.00 0.00 3.41
2741 3042 7.119699 TCAGCAGGTAAATTGTATGAGAAAGTG 59.880 37.037 0.00 0.00 0.00 3.16
2742 3043 7.168219 TCAGCAGGTAAATTGTATGAGAAAGT 58.832 34.615 0.00 0.00 0.00 2.66
2743 3044 7.615582 TCAGCAGGTAAATTGTATGAGAAAG 57.384 36.000 0.00 0.00 0.00 2.62
2744 3045 7.994425 TTCAGCAGGTAAATTGTATGAGAAA 57.006 32.000 0.00 0.00 0.00 2.52
2745 3046 8.579850 AATTCAGCAGGTAAATTGTATGAGAA 57.420 30.769 0.00 0.00 0.00 2.87
2746 3047 8.579850 AAATTCAGCAGGTAAATTGTATGAGA 57.420 30.769 0.00 0.00 0.00 3.27
2756 3057 9.303116 TCCAAACTATAAAATTCAGCAGGTAAA 57.697 29.630 0.00 0.00 0.00 2.01
2757 3058 8.871629 TCCAAACTATAAAATTCAGCAGGTAA 57.128 30.769 0.00 0.00 0.00 2.85
2758 3059 8.107095 ACTCCAAACTATAAAATTCAGCAGGTA 58.893 33.333 0.00 0.00 0.00 3.08
2759 3060 6.948309 ACTCCAAACTATAAAATTCAGCAGGT 59.052 34.615 0.00 0.00 0.00 4.00
2760 3061 7.396540 ACTCCAAACTATAAAATTCAGCAGG 57.603 36.000 0.00 0.00 0.00 4.85
2763 3064 9.237846 GCATTACTCCAAACTATAAAATTCAGC 57.762 33.333 0.00 0.00 0.00 4.26
2808 3109 9.757227 CCAAATTCAGTTAACATTACTCCAAAA 57.243 29.630 8.61 0.00 0.00 2.44
2809 3110 9.137459 TCCAAATTCAGTTAACATTACTCCAAA 57.863 29.630 8.61 0.00 0.00 3.28
2810 3111 8.698973 TCCAAATTCAGTTAACATTACTCCAA 57.301 30.769 8.61 0.00 0.00 3.53
2864 3166 5.891551 AGGAGCAAAAGGAACAAGTTTCTTA 59.108 36.000 6.90 0.00 37.41 2.10
2865 3167 4.711846 AGGAGCAAAAGGAACAAGTTTCTT 59.288 37.500 0.61 0.61 39.98 2.52
2866 3168 4.281657 AGGAGCAAAAGGAACAAGTTTCT 58.718 39.130 0.00 0.00 0.00 2.52
2867 3169 4.655762 AGGAGCAAAAGGAACAAGTTTC 57.344 40.909 0.00 0.00 0.00 2.78
2868 3170 5.046663 TCAAAGGAGCAAAAGGAACAAGTTT 60.047 36.000 0.00 0.00 0.00 2.66
2869 3171 4.466015 TCAAAGGAGCAAAAGGAACAAGTT 59.534 37.500 0.00 0.00 0.00 2.66
2870 3172 4.023291 TCAAAGGAGCAAAAGGAACAAGT 58.977 39.130 0.00 0.00 0.00 3.16
2871 3173 4.654091 TCAAAGGAGCAAAAGGAACAAG 57.346 40.909 0.00 0.00 0.00 3.16
2872 3174 5.612725 ATTCAAAGGAGCAAAAGGAACAA 57.387 34.783 0.00 0.00 0.00 2.83
2873 3175 5.612725 AATTCAAAGGAGCAAAAGGAACA 57.387 34.783 0.00 0.00 0.00 3.18
2874 3176 5.237127 CCAAATTCAAAGGAGCAAAAGGAAC 59.763 40.000 0.00 0.00 0.00 3.62
2875 3177 5.130145 TCCAAATTCAAAGGAGCAAAAGGAA 59.870 36.000 0.00 0.00 0.00 3.36
2876 3178 4.653341 TCCAAATTCAAAGGAGCAAAAGGA 59.347 37.500 0.00 0.00 0.00 3.36
2877 3179 4.959723 TCCAAATTCAAAGGAGCAAAAGG 58.040 39.130 0.00 0.00 0.00 3.11
2878 3180 6.484308 ACAATCCAAATTCAAAGGAGCAAAAG 59.516 34.615 0.00 0.00 34.40 2.27
2879 3181 6.355747 ACAATCCAAATTCAAAGGAGCAAAA 58.644 32.000 0.00 0.00 34.40 2.44
2880 3182 5.927819 ACAATCCAAATTCAAAGGAGCAAA 58.072 33.333 0.00 0.00 34.40 3.68
2881 3183 5.549742 ACAATCCAAATTCAAAGGAGCAA 57.450 34.783 0.00 0.00 34.40 3.91
2882 3184 5.299148 CAACAATCCAAATTCAAAGGAGCA 58.701 37.500 0.00 0.00 34.40 4.26
2883 3185 4.692155 CCAACAATCCAAATTCAAAGGAGC 59.308 41.667 0.00 0.00 34.40 4.70
2884 3186 6.100404 TCCAACAATCCAAATTCAAAGGAG 57.900 37.500 0.00 0.00 34.40 3.69
2885 3187 5.602145 ACTCCAACAATCCAAATTCAAAGGA 59.398 36.000 0.00 0.00 35.59 3.36
2886 3188 5.857268 ACTCCAACAATCCAAATTCAAAGG 58.143 37.500 0.00 0.00 0.00 3.11
2887 3189 9.492973 AAATACTCCAACAATCCAAATTCAAAG 57.507 29.630 0.00 0.00 0.00 2.77
2888 3190 9.270640 CAAATACTCCAACAATCCAAATTCAAA 57.729 29.630 0.00 0.00 0.00 2.69
2889 3191 7.387397 GCAAATACTCCAACAATCCAAATTCAA 59.613 33.333 0.00 0.00 0.00 2.69
2890 3192 6.873076 GCAAATACTCCAACAATCCAAATTCA 59.127 34.615 0.00 0.00 0.00 2.57
2891 3193 6.873076 TGCAAATACTCCAACAATCCAAATTC 59.127 34.615 0.00 0.00 0.00 2.17
2892 3194 6.650390 GTGCAAATACTCCAACAATCCAAATT 59.350 34.615 0.00 0.00 0.00 1.82
2893 3195 6.014327 AGTGCAAATACTCCAACAATCCAAAT 60.014 34.615 0.00 0.00 0.00 2.32
2894 3196 5.304101 AGTGCAAATACTCCAACAATCCAAA 59.696 36.000 0.00 0.00 0.00 3.28
2895 3197 4.832266 AGTGCAAATACTCCAACAATCCAA 59.168 37.500 0.00 0.00 0.00 3.53
2896 3198 4.218200 CAGTGCAAATACTCCAACAATCCA 59.782 41.667 0.00 0.00 0.00 3.41
2897 3199 4.218417 ACAGTGCAAATACTCCAACAATCC 59.782 41.667 0.00 0.00 0.00 3.01
2898 3200 5.376854 ACAGTGCAAATACTCCAACAATC 57.623 39.130 0.00 0.00 0.00 2.67
2899 3201 5.509501 CCAACAGTGCAAATACTCCAACAAT 60.510 40.000 0.00 0.00 0.00 2.71
2900 3202 4.202101 CCAACAGTGCAAATACTCCAACAA 60.202 41.667 0.00 0.00 0.00 2.83
2901 3203 3.317711 CCAACAGTGCAAATACTCCAACA 59.682 43.478 0.00 0.00 0.00 3.33
2902 3204 3.568007 TCCAACAGTGCAAATACTCCAAC 59.432 43.478 0.00 0.00 0.00 3.77
2903 3205 3.820467 CTCCAACAGTGCAAATACTCCAA 59.180 43.478 0.00 0.00 0.00 3.53
2904 3206 3.181445 ACTCCAACAGTGCAAATACTCCA 60.181 43.478 0.00 0.00 32.26 3.86
2905 3207 3.412386 ACTCCAACAGTGCAAATACTCC 58.588 45.455 0.00 0.00 32.26 3.85
2906 3208 6.426937 TCTTTACTCCAACAGTGCAAATACTC 59.573 38.462 0.00 0.00 36.43 2.59
2907 3209 6.296026 TCTTTACTCCAACAGTGCAAATACT 58.704 36.000 0.00 0.00 36.43 2.12
2908 3210 6.554334 TCTTTACTCCAACAGTGCAAATAC 57.446 37.500 0.00 0.00 36.43 1.89
2909 3211 7.284489 AGTTTCTTTACTCCAACAGTGCAAATA 59.716 33.333 0.00 0.00 36.43 1.40
2910 3212 6.096846 AGTTTCTTTACTCCAACAGTGCAAAT 59.903 34.615 0.00 0.00 36.43 2.32
2911 3213 5.417580 AGTTTCTTTACTCCAACAGTGCAAA 59.582 36.000 0.00 0.00 36.43 3.68
2912 3214 4.947388 AGTTTCTTTACTCCAACAGTGCAA 59.053 37.500 0.00 0.00 36.43 4.08
2913 3215 4.523083 AGTTTCTTTACTCCAACAGTGCA 58.477 39.130 0.00 0.00 36.43 4.57
2914 3216 5.273944 CAAGTTTCTTTACTCCAACAGTGC 58.726 41.667 0.00 0.00 36.43 4.40
2915 3217 5.066505 AGCAAGTTTCTTTACTCCAACAGTG 59.933 40.000 0.00 0.00 36.43 3.66
2916 3218 5.193679 AGCAAGTTTCTTTACTCCAACAGT 58.806 37.500 0.00 0.00 39.41 3.55
2917 3219 5.278022 GGAGCAAGTTTCTTTACTCCAACAG 60.278 44.000 16.76 0.00 39.46 3.16
2918 3220 4.578928 GGAGCAAGTTTCTTTACTCCAACA 59.421 41.667 16.76 0.00 39.46 3.33
2919 3221 4.822350 AGGAGCAAGTTTCTTTACTCCAAC 59.178 41.667 20.65 4.71 41.28 3.77
2920 3222 5.048846 AGGAGCAAGTTTCTTTACTCCAA 57.951 39.130 20.65 0.00 41.28 3.53
2921 3223 4.706842 AGGAGCAAGTTTCTTTACTCCA 57.293 40.909 20.65 0.00 41.28 3.86
2922 3224 6.209361 CAAAAGGAGCAAGTTTCTTTACTCC 58.791 40.000 15.09 15.09 39.80 3.85
2923 3225 5.687730 GCAAAAGGAGCAAGTTTCTTTACTC 59.312 40.000 0.00 0.00 0.00 2.59
2924 3226 5.360999 AGCAAAAGGAGCAAGTTTCTTTACT 59.639 36.000 0.00 0.00 0.00 2.24
2925 3227 5.592054 AGCAAAAGGAGCAAGTTTCTTTAC 58.408 37.500 0.00 0.00 0.00 2.01
2926 3228 5.221244 GGAGCAAAAGGAGCAAGTTTCTTTA 60.221 40.000 0.00 0.00 0.00 1.85
2927 3229 4.442052 GGAGCAAAAGGAGCAAGTTTCTTT 60.442 41.667 0.00 0.00 0.00 2.52
2946 3248 1.032014 TTGAACACCTGCAAAGGAGC 58.968 50.000 0.00 0.00 0.00 4.70
2984 3286 3.598019 AACATGTGCTTATTTGGCAGG 57.402 42.857 0.00 0.00 40.54 4.85
3027 3329 5.413309 ACTTCTCCATCTTTACTCAGTGG 57.587 43.478 0.00 0.00 0.00 4.00
3112 3414 1.628846 ACGGGCAAGTCTCCTTATTGT 59.371 47.619 0.00 0.00 0.00 2.71
3118 3420 0.904865 TGATCACGGGCAAGTCTCCT 60.905 55.000 0.00 0.00 0.00 3.69
3147 3449 2.902486 AGAGACATCAACTTCTGAGCCA 59.098 45.455 0.00 0.00 37.52 4.75
3236 3538 4.707448 TGGTTGTTTTCCTTCTGTTTAGCA 59.293 37.500 0.00 0.00 0.00 3.49
3243 3545 3.217626 AGCTCTGGTTGTTTTCCTTCTG 58.782 45.455 0.00 0.00 0.00 3.02
3273 3575 4.827789 AGGGCTATATAACACCCAGAGAA 58.172 43.478 14.56 0.00 45.45 2.87
3304 3606 6.235231 TGGCTTGAGTAAAGTCTATAAGGG 57.765 41.667 0.00 0.00 41.38 3.95
3310 3612 8.911918 TTGTTAATTGGCTTGAGTAAAGTCTA 57.088 30.769 0.00 0.00 41.38 2.59
3368 3670 2.358957 TCTCCAATGTTGCTTGATCCG 58.641 47.619 0.00 0.00 0.00 4.18
3395 3697 6.117975 TGCTCATATCAATGAATCTAGGCA 57.882 37.500 0.00 0.00 41.57 4.75
3437 3739 7.278646 TCCTTTGAGTCATATCAAATCACTTCG 59.721 37.037 0.00 0.00 45.50 3.79
3444 3746 7.977853 GTGCATTTCCTTTGAGTCATATCAAAT 59.022 33.333 0.00 0.00 45.50 2.32


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

AutoCloner maintained by Alex Coulton.