Multiple sequence alignment - TraesCS5D01G326300

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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 TraesCS5D01G326300 chr5D 100.000 3333 0 0 1 3333 418582018 418585350 0.000000e+00 6156.0
1 TraesCS5D01G326300 chr5D 95.469 309 13 1 622 929 367986774 367987082 2.990000e-135 492.0
2 TraesCS5D01G326300 chr5D 83.598 189 27 4 291 479 365442523 365442707 1.230000e-39 174.0
3 TraesCS5D01G326300 chr5A 96.518 1120 37 2 1318 2437 533343749 533344866 0.000000e+00 1851.0
4 TraesCS5D01G326300 chr5A 87.751 498 42 15 2439 2933 533344916 533345397 6.240000e-157 564.0
5 TraesCS5D01G326300 chr5A 77.670 618 71 39 5 561 533342738 533343349 6.940000e-82 315.0
6 TraesCS5D01G326300 chr5A 83.636 330 28 12 2925 3253 533345803 533346107 1.510000e-73 287.0
7 TraesCS5D01G326300 chr5B 93.648 1165 46 2 1300 2437 506205656 506206819 0.000000e+00 1716.0
8 TraesCS5D01G326300 chr5B 88.372 817 51 20 2439 3253 506206869 506207643 0.000000e+00 942.0
9 TraesCS5D01G326300 chr5B 84.830 646 71 17 1 623 506204142 506204783 2.820000e-175 625.0
10 TraesCS5D01G326300 chr5B 95.225 356 12 5 938 1291 506204772 506205124 2.900000e-155 558.0
11 TraesCS5D01G326300 chr5B 97.561 41 1 0 3261 3301 398069794 398069834 1.660000e-08 71.3
12 TraesCS5D01G326300 chr4A 89.985 649 55 4 1191 1839 244492088 244491450 0.000000e+00 830.0
13 TraesCS5D01G326300 chr4A 75.048 517 69 42 29 499 5704191 5704693 5.680000e-43 185.0
14 TraesCS5D01G326300 chr4A 91.837 49 3 1 3250 3297 697388845 697388893 2.150000e-07 67.6
15 TraesCS5D01G326300 chr4D 94.895 333 16 1 618 949 64046159 64046491 1.370000e-143 520.0
16 TraesCS5D01G326300 chr4D 95.000 320 15 1 623 941 431039942 431039623 4.960000e-138 501.0
17 TraesCS5D01G326300 chr4D 95.455 308 12 2 623 929 20532516 20532210 1.070000e-134 490.0
18 TraesCS5D01G326300 chr4D 94.062 320 17 2 623 941 298121030 298120712 5.000000e-133 484.0
19 TraesCS5D01G326300 chr4D 93.519 324 20 1 623 945 57766721 57767044 6.470000e-132 481.0
20 TraesCS5D01G326300 chr2D 96.117 309 11 1 622 929 509938759 509938451 1.380000e-138 503.0
21 TraesCS5D01G326300 chr2D 80.319 188 26 8 317 500 5317356 5317536 7.500000e-27 132.0
22 TraesCS5D01G326300 chr2D 97.826 46 1 0 3250 3295 218045365 218045410 2.760000e-11 80.5
23 TraesCS5D01G326300 chr3D 94.062 320 18 1 623 941 289990702 289991021 5.000000e-133 484.0
24 TraesCS5D01G326300 chr3D 82.051 156 24 3 2 153 64108008 64107853 2.700000e-26 130.0
25 TraesCS5D01G326300 chr3D 81.657 169 19 10 294 459 188361646 188361487 2.700000e-26 130.0
26 TraesCS5D01G326300 chr1A 93.750 320 19 1 623 941 540286038 540286357 2.330000e-131 479.0
27 TraesCS5D01G326300 chr1A 82.353 153 16 10 24 168 78960047 78959898 4.520000e-24 122.0
28 TraesCS5D01G326300 chr3B 98.529 204 3 0 1209 1412 605678874 605679077 8.790000e-96 361.0
29 TraesCS5D01G326300 chr3B 97.608 209 5 0 1209 1417 602440252 602440044 3.160000e-95 359.0
30 TraesCS5D01G326300 chr3B 96.651 209 7 0 1209 1417 99537647 99537855 6.840000e-92 348.0
31 TraesCS5D01G326300 chr1B 95.673 208 9 0 1210 1417 679125489 679125696 5.330000e-88 335.0
32 TraesCS5D01G326300 chr1B 95.215 209 10 0 1209 1417 223788448 223788240 6.890000e-87 331.0
33 TraesCS5D01G326300 chr1B 93.333 45 2 1 3257 3300 645555369 645555325 7.720000e-07 65.8
34 TraesCS5D01G326300 chr1D 76.762 525 70 35 3 485 438359734 438359220 2.570000e-61 246.0
35 TraesCS5D01G326300 chr2B 90.058 171 2 1 1209 1379 214284103 214283948 1.210000e-49 207.0
36 TraesCS5D01G326300 chr2B 78.744 207 31 13 299 499 144246414 144246613 3.490000e-25 126.0
37 TraesCS5D01G326300 chr2B 95.652 46 2 0 3250 3295 331012762 331012717 1.280000e-09 75.0
38 TraesCS5D01G326300 chr2B 95.000 40 2 0 3250 3289 175632152 175632191 2.780000e-06 63.9
39 TraesCS5D01G326300 chr7B 79.091 330 46 15 1 308 15929334 15929006 4.360000e-49 206.0
40 TraesCS5D01G326300 chr7D 84.360 211 27 6 299 506 54053722 54053515 5.640000e-48 202.0
41 TraesCS5D01G326300 chr7D 83.173 208 25 8 296 499 63706521 63706722 7.350000e-42 182.0
42 TraesCS5D01G326300 chr7D 80.203 197 21 11 52 234 46957875 46957683 7.500000e-27 132.0
43 TraesCS5D01G326300 chr7A 79.808 208 31 7 296 499 66676349 66676549 1.250000e-29 141.0
44 TraesCS5D01G326300 chr6B 85.185 135 14 4 26 156 4853962 4854094 2.090000e-27 134.0
45 TraesCS5D01G326300 chr6B 79.882 169 24 7 34 196 151970702 151970866 7.560000e-22 115.0
46 TraesCS5D01G326300 chr6B 79.032 124 13 10 103 216 41572950 41572830 4.610000e-09 73.1
47 TraesCS5D01G326300 chr3A 91.667 48 4 0 3252 3299 100417804 100417851 2.150000e-07 67.6
48 TraesCS5D01G326300 chr3A 93.333 45 2 1 3257 3300 661983555 661983511 7.720000e-07 65.8
49 TraesCS5D01G326300 chr2A 89.796 49 5 0 3250 3298 127200341 127200389 2.780000e-06 63.9


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 TraesCS5D01G326300 chr5D 418582018 418585350 3332 False 6156.00 6156 100.00000 1 3333 1 chr5D.!!$F3 3332
1 TraesCS5D01G326300 chr5A 533342738 533346107 3369 False 754.25 1851 86.39375 5 3253 4 chr5A.!!$F1 3248
2 TraesCS5D01G326300 chr5B 506204142 506207643 3501 False 960.25 1716 90.51875 1 3253 4 chr5B.!!$F2 3252
3 TraesCS5D01G326300 chr4A 244491450 244492088 638 True 830.00 830 89.98500 1191 1839 1 chr4A.!!$R1 648
4 TraesCS5D01G326300 chr1D 438359220 438359734 514 True 246.00 246 76.76200 3 485 1 chr1D.!!$R1 482

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
847 936 0.033109 AGGGCTTTTACCAGATGGGC 60.033 55.0 3.48 0.0 42.05 5.36 F
883 972 0.398664 AAGTAGGTCCGATGGGAGGG 60.399 60.0 0.00 0.0 44.97 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 2832 0.465824 AGGTACTCCCCGAGATCGTG 60.466 60.0 1.09 0.0 37.74 4.35 R
2709 3401 0.672401 TTCATTGGGACTTCGCCGTC 60.672 55.0 0.00 0.0 0.00 4.79 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
444 503 7.680982 TCTTGATGTATGCGTAAAATGTACAC 58.319 34.615 0.00 0.00 0.00 2.90
485 574 9.554395 TGTAGACATGTGTTGAAGAATAAAAGA 57.446 29.630 1.15 0.00 0.00 2.52
512 601 3.068307 ACGAAGAAAGACGAGATATGGGG 59.932 47.826 0.00 0.00 0.00 4.96
601 690 9.110502 GACTAATTTCTCGATTCCAAAATAGGT 57.889 33.333 0.00 0.00 0.00 3.08
630 719 3.324846 TGCTATATGGCAACTAGTCCTGG 59.675 47.826 11.82 0.00 39.43 4.45
631 720 2.938956 ATATGGCAACTAGTCCTGGC 57.061 50.000 12.88 12.88 38.54 4.85
632 721 0.837272 TATGGCAACTAGTCCTGGCC 59.163 55.000 16.11 16.35 44.82 5.36
633 722 3.077907 GGCAACTAGTCCTGGCCA 58.922 61.111 17.83 4.71 44.01 5.36
634 723 1.609783 GGCAACTAGTCCTGGCCAT 59.390 57.895 5.51 0.00 44.01 4.40
635 724 0.464554 GGCAACTAGTCCTGGCCATC 60.465 60.000 5.51 0.00 44.01 3.51
636 725 0.543749 GCAACTAGTCCTGGCCATCT 59.456 55.000 5.51 8.22 0.00 2.90
637 726 1.474143 GCAACTAGTCCTGGCCATCTC 60.474 57.143 5.51 0.00 0.00 2.75
638 727 1.833630 CAACTAGTCCTGGCCATCTCA 59.166 52.381 5.51 0.00 0.00 3.27
639 728 1.786937 ACTAGTCCTGGCCATCTCAG 58.213 55.000 5.51 2.71 0.00 3.35
680 769 2.520982 GGCCCGGCCCTAAAATCC 60.521 66.667 18.83 0.00 44.06 3.01
681 770 2.277404 GCCCGGCCCTAAAATCCA 59.723 61.111 0.00 0.00 0.00 3.41
682 771 1.828224 GCCCGGCCCTAAAATCCAG 60.828 63.158 0.00 0.00 0.00 3.86
683 772 1.152756 CCCGGCCCTAAAATCCAGG 60.153 63.158 0.00 0.00 0.00 4.45
689 778 2.959465 CCCTAAAATCCAGGGCCTAG 57.041 55.000 5.28 0.00 46.27 3.02
690 779 1.425448 CCCTAAAATCCAGGGCCTAGG 59.575 57.143 5.28 10.90 46.27 3.02
691 780 1.202940 CCTAAAATCCAGGGCCTAGGC 60.203 57.143 26.55 26.55 41.06 3.93
734 823 3.882131 GCTTGGGCCTGAGTTATGA 57.118 52.632 4.53 0.00 0.00 2.15
735 824 1.673168 GCTTGGGCCTGAGTTATGAG 58.327 55.000 4.53 0.00 0.00 2.90
736 825 1.673168 CTTGGGCCTGAGTTATGAGC 58.327 55.000 4.53 0.00 0.00 4.26
737 826 0.255890 TTGGGCCTGAGTTATGAGCC 59.744 55.000 4.53 0.00 43.09 4.70
738 827 4.887615 GGCCTGAGTTATGAGCCC 57.112 61.111 0.00 0.00 37.66 5.19
739 828 1.915228 GGCCTGAGTTATGAGCCCA 59.085 57.895 0.00 0.00 37.66 5.36
740 829 0.464554 GGCCTGAGTTATGAGCCCAC 60.465 60.000 0.00 0.00 37.66 4.61
741 830 0.464554 GCCTGAGTTATGAGCCCACC 60.465 60.000 0.00 0.00 0.00 4.61
742 831 0.911769 CCTGAGTTATGAGCCCACCA 59.088 55.000 0.00 0.00 0.00 4.17
743 832 1.134280 CCTGAGTTATGAGCCCACCAG 60.134 57.143 0.00 0.00 0.00 4.00
744 833 0.253044 TGAGTTATGAGCCCACCAGC 59.747 55.000 0.00 0.00 0.00 4.85
745 834 0.253044 GAGTTATGAGCCCACCAGCA 59.747 55.000 0.00 0.00 34.23 4.41
746 835 0.254178 AGTTATGAGCCCACCAGCAG 59.746 55.000 0.00 0.00 34.23 4.24
747 836 0.749454 GTTATGAGCCCACCAGCAGG 60.749 60.000 0.00 0.00 42.21 4.85
773 862 2.043046 GGGCTTGGGCTTGGCATA 60.043 61.111 0.00 0.00 38.73 3.14
774 863 1.458209 GGGCTTGGGCTTGGCATAT 60.458 57.895 0.00 0.00 38.73 1.78
775 864 1.050421 GGGCTTGGGCTTGGCATATT 61.050 55.000 0.00 0.00 38.73 1.28
776 865 0.105408 GGCTTGGGCTTGGCATATTG 59.895 55.000 0.00 0.00 38.73 1.90
777 866 0.105408 GCTTGGGCTTGGCATATTGG 59.895 55.000 0.00 0.00 35.22 3.16
778 867 0.105408 CTTGGGCTTGGCATATTGGC 59.895 55.000 0.00 0.00 44.03 4.52
791 880 6.160576 GGCATATTGGCATTTTAAGGAAGA 57.839 37.500 0.00 0.00 43.14 2.87
792 881 6.218746 GGCATATTGGCATTTTAAGGAAGAG 58.781 40.000 0.00 0.00 43.14 2.85
793 882 6.218746 GCATATTGGCATTTTAAGGAAGAGG 58.781 40.000 0.00 0.00 0.00 3.69
794 883 4.743057 ATTGGCATTTTAAGGAAGAGGC 57.257 40.909 0.00 0.00 0.00 4.70
795 884 2.456577 TGGCATTTTAAGGAAGAGGCC 58.543 47.619 0.00 0.00 40.51 5.19
796 885 1.757118 GGCATTTTAAGGAAGAGGCCC 59.243 52.381 0.00 0.00 34.17 5.80
797 886 1.405463 GCATTTTAAGGAAGAGGCCCG 59.595 52.381 0.00 0.00 0.00 6.13
798 887 2.024414 CATTTTAAGGAAGAGGCCCGG 58.976 52.381 0.00 0.00 0.00 5.73
799 888 0.323087 TTTTAAGGAAGAGGCCCGGC 60.323 55.000 0.00 0.00 0.00 6.13
815 904 2.516405 GCCCTAAGCCCTAAGCCC 59.484 66.667 0.00 0.00 45.47 5.19
816 905 2.079288 GCCCTAAGCCCTAAGCCCT 61.079 63.158 0.00 0.00 45.47 5.19
817 906 0.767060 GCCCTAAGCCCTAAGCCCTA 60.767 60.000 0.00 0.00 45.47 3.53
818 907 1.815757 CCCTAAGCCCTAAGCCCTAA 58.184 55.000 0.00 0.00 45.47 2.69
819 908 2.132686 CCCTAAGCCCTAAGCCCTAAA 58.867 52.381 0.00 0.00 45.47 1.85
820 909 2.106684 CCCTAAGCCCTAAGCCCTAAAG 59.893 54.545 0.00 0.00 45.47 1.85
821 910 2.106684 CCTAAGCCCTAAGCCCTAAAGG 59.893 54.545 0.00 0.00 45.47 3.11
832 921 1.186200 CCCTAAAGGCTTTTCAGGGC 58.814 55.000 27.02 0.00 39.62 5.19
833 922 1.272704 CCCTAAAGGCTTTTCAGGGCT 60.273 52.381 27.02 2.36 39.62 5.19
839 928 2.248248 AGGCTTTTCAGGGCTTTTACC 58.752 47.619 0.00 0.00 36.12 2.85
840 929 1.967779 GGCTTTTCAGGGCTTTTACCA 59.032 47.619 0.00 0.00 0.00 3.25
841 930 2.029020 GGCTTTTCAGGGCTTTTACCAG 60.029 50.000 0.00 0.00 0.00 4.00
842 931 2.890945 GCTTTTCAGGGCTTTTACCAGA 59.109 45.455 0.00 0.00 0.00 3.86
843 932 3.511540 GCTTTTCAGGGCTTTTACCAGAT 59.488 43.478 0.00 0.00 0.00 2.90
844 933 4.619160 GCTTTTCAGGGCTTTTACCAGATG 60.619 45.833 0.00 0.00 0.00 2.90
845 934 2.806945 TCAGGGCTTTTACCAGATGG 57.193 50.000 0.00 0.00 42.17 3.51
846 935 1.284785 TCAGGGCTTTTACCAGATGGG 59.715 52.381 3.48 0.00 44.81 4.00
847 936 0.033109 AGGGCTTTTACCAGATGGGC 60.033 55.000 3.48 0.00 42.05 5.36
848 937 1.043116 GGGCTTTTACCAGATGGGCC 61.043 60.000 3.48 0.00 42.05 5.80
849 938 1.384222 GGCTTTTACCAGATGGGCCG 61.384 60.000 3.48 0.00 42.05 6.13
850 939 1.384222 GCTTTTACCAGATGGGCCGG 61.384 60.000 0.00 0.00 42.05 6.13
851 940 0.751643 CTTTTACCAGATGGGCCGGG 60.752 60.000 2.18 0.00 42.05 5.73
852 941 2.847366 TTTTACCAGATGGGCCGGGC 62.847 60.000 22.00 22.00 42.05 6.13
853 942 4.815973 TACCAGATGGGCCGGGCT 62.816 66.667 28.80 9.11 42.05 5.19
864 953 2.600173 CCGGGCTTGGGCTTGAAA 60.600 61.111 0.00 0.00 38.73 2.69
865 954 2.206536 CCGGGCTTGGGCTTGAAAA 61.207 57.895 0.00 0.00 38.73 2.29
879 968 3.270877 CTTGAAAAGTAGGTCCGATGGG 58.729 50.000 0.00 0.00 39.70 4.00
880 969 2.542550 TGAAAAGTAGGTCCGATGGGA 58.457 47.619 0.00 0.00 41.08 4.37
881 970 2.500098 TGAAAAGTAGGTCCGATGGGAG 59.500 50.000 0.00 0.00 44.97 4.30
882 971 1.497161 AAAGTAGGTCCGATGGGAGG 58.503 55.000 0.00 0.00 44.97 4.30
883 972 0.398664 AAGTAGGTCCGATGGGAGGG 60.399 60.000 0.00 0.00 44.97 4.30
884 973 2.122989 TAGGTCCGATGGGAGGGC 60.123 66.667 0.00 0.00 44.97 5.19
887 976 3.866582 GTCCGATGGGAGGGCCTG 61.867 72.222 12.95 0.00 44.97 4.85
900 989 3.686760 GCCTGGGCCTCAGTTTTC 58.313 61.111 16.96 3.57 41.83 2.29
901 990 1.075659 GCCTGGGCCTCAGTTTTCT 59.924 57.895 16.96 0.00 41.83 2.52
902 991 1.246737 GCCTGGGCCTCAGTTTTCTG 61.247 60.000 16.96 5.05 41.83 3.02
903 992 1.246737 CCTGGGCCTCAGTTTTCTGC 61.247 60.000 16.96 0.00 46.59 4.26
904 993 1.228552 TGGGCCTCAGTTTTCTGCC 60.229 57.895 4.53 0.00 46.59 4.85
905 994 1.228552 GGGCCTCAGTTTTCTGCCA 60.229 57.895 0.84 0.00 46.59 4.92
906 995 0.613012 GGGCCTCAGTTTTCTGCCAT 60.613 55.000 0.84 0.00 46.59 4.40
907 996 0.529378 GGCCTCAGTTTTCTGCCATG 59.471 55.000 0.00 0.00 46.59 3.66
908 997 0.529378 GCCTCAGTTTTCTGCCATGG 59.471 55.000 7.63 7.63 46.59 3.66
909 998 1.180029 CCTCAGTTTTCTGCCATGGG 58.820 55.000 15.13 0.00 46.59 4.00
920 1009 1.078918 GCCATGGGCTTTTTCAGGC 60.079 57.895 15.13 0.00 46.69 4.85
925 1014 4.069232 GGCTTTTTCAGGCCCGGC 62.069 66.667 0.00 0.00 42.55 6.13
962 1051 2.253758 GCAACTGACTTCCGCAGCA 61.254 57.895 0.00 0.00 36.86 4.41
1013 1103 3.257561 CGCTGCCCGTTGAGATCG 61.258 66.667 0.00 0.00 0.00 3.69
1017 1107 4.508128 GCCCGTTGAGATCGGCGA 62.508 66.667 13.87 13.87 45.71 5.54
1021 1111 1.482621 CCGTTGAGATCGGCGACATG 61.483 60.000 13.76 1.83 41.48 3.21
1023 1113 0.460284 GTTGAGATCGGCGACATGGT 60.460 55.000 13.76 0.00 0.00 3.55
1087 1178 3.348236 CTGCACAAGCTGGTGACC 58.652 61.111 25.91 8.67 41.32 4.02
1292 1383 4.816984 TCCTCTCCGTCCTCCGCC 62.817 72.222 0.00 0.00 34.38 6.13
1459 2073 3.578272 CTCCGGCTCGTCTCCTCG 61.578 72.222 0.00 0.00 0.00 4.63
1988 2602 6.239430 GGCAGAGACATACTTGGAAGATATGA 60.239 42.308 12.21 0.00 31.90 2.15
1996 2610 8.378565 ACATACTTGGAAGATATGATGGGTAAG 58.621 37.037 12.21 0.00 31.90 2.34
2192 2806 5.273674 TGAGGTGATTTTGTTGCAAATGA 57.726 34.783 0.00 0.00 0.00 2.57
2263 2877 1.153066 ATGTTGCGTGGTGTGGTGA 60.153 52.632 0.00 0.00 0.00 4.02
2285 2899 7.094634 GGTGACAGAGATTTAAGAAGCAATCAA 60.095 37.037 0.00 0.00 32.61 2.57
2345 2987 4.405116 AGCCTTGCTGAAAACAAAATGA 57.595 36.364 0.00 0.00 37.57 2.57
2346 2988 4.964593 AGCCTTGCTGAAAACAAAATGAT 58.035 34.783 0.00 0.00 37.57 2.45
2358 3000 8.386606 TGAAAACAAAATGATACAGTGCAAAAC 58.613 29.630 0.00 0.00 0.00 2.43
2359 3001 7.840342 AAACAAAATGATACAGTGCAAAACA 57.160 28.000 0.00 0.00 0.00 2.83
2384 3026 4.706962 GGACCAAGAAGGCATATTTTCTGT 59.293 41.667 0.00 0.00 43.14 3.41
2433 3075 4.646492 ACTTGTTTTGCAAAGGTGAGATCT 59.354 37.500 12.41 0.00 36.53 2.75
2434 3076 4.836125 TGTTTTGCAAAGGTGAGATCTC 57.164 40.909 16.21 16.21 0.00 2.75
2435 3077 4.464008 TGTTTTGCAAAGGTGAGATCTCT 58.536 39.130 22.95 0.38 0.00 3.10
2450 3139 4.348486 AGATCTCTGTACTTGAAGCCAGA 58.652 43.478 12.68 12.68 33.22 3.86
2469 3158 5.121454 GCCAGAACAGACAGAAAAGATAGTG 59.879 44.000 0.00 0.00 0.00 2.74
2587 3276 3.961582 TGCACAGGATCAAGATGCA 57.038 47.368 8.56 8.56 43.70 3.96
2588 3277 2.430248 TGCACAGGATCAAGATGCAT 57.570 45.000 0.00 0.00 41.18 3.96
2653 3345 3.308323 GCGTTCTGCTCAAAGGAAGATAG 59.692 47.826 0.00 0.00 41.73 2.08
2671 3363 6.240549 AGATAGTGGGGCTATATTATGTGC 57.759 41.667 0.00 0.00 40.30 4.57
2699 3391 3.695830 TCCAGTTGGACAGTATGGAAC 57.304 47.619 0.00 0.00 43.62 3.62
2703 3395 2.370849 AGTTGGACAGTATGGAACGGTT 59.629 45.455 0.00 0.00 43.62 4.44
2705 3397 1.695242 TGGACAGTATGGAACGGTTGT 59.305 47.619 0.00 0.00 43.62 3.32
2709 3401 1.724623 CAGTATGGAACGGTTGTCACG 59.275 52.381 0.00 0.00 37.36 4.35
2908 3608 1.274184 TGATAACCAGGGGGCTACTGT 60.274 52.381 7.88 0.00 37.90 3.55
2926 3626 8.630917 GGCTACTGTAGTTGTTATTAGAGATGA 58.369 37.037 15.71 0.00 0.00 2.92
3001 4117 0.181114 TTGACTGCTGAAGCCTGTGT 59.819 50.000 0.00 0.00 41.18 3.72
3032 4148 3.574445 GCAGCGCTGATGCCTGAG 61.574 66.667 40.21 11.64 39.19 3.35
3050 4166 4.370049 CTGAGATCTGAATAGGTGCACAG 58.630 47.826 20.43 6.28 0.00 3.66
3111 4228 2.096417 GCTTTCATTTTTGCTGCTGCTG 60.096 45.455 17.00 6.30 40.48 4.41
3132 4255 3.557185 TGTCGATGATGCTCATTTACTGC 59.443 43.478 0.00 0.00 37.20 4.40
3133 4256 3.557185 GTCGATGATGCTCATTTACTGCA 59.443 43.478 0.00 0.00 37.20 4.41
3134 4257 4.034394 GTCGATGATGCTCATTTACTGCAA 59.966 41.667 0.00 0.00 37.20 4.08
3135 4258 4.034394 TCGATGATGCTCATTTACTGCAAC 59.966 41.667 0.00 0.00 37.20 4.17
3136 4259 4.034858 CGATGATGCTCATTTACTGCAACT 59.965 41.667 0.00 0.00 37.20 3.16
3137 4260 5.448225 CGATGATGCTCATTTACTGCAACTT 60.448 40.000 0.00 0.00 37.20 2.66
3138 4261 6.238184 CGATGATGCTCATTTACTGCAACTTA 60.238 38.462 0.00 0.00 37.20 2.24
3139 4262 7.519488 CGATGATGCTCATTTACTGCAACTTAT 60.519 37.037 0.00 0.00 37.20 1.73
3140 4263 7.395190 TGATGCTCATTTACTGCAACTTATT 57.605 32.000 0.00 0.00 40.24 1.40
3141 4264 7.252708 TGATGCTCATTTACTGCAACTTATTG 58.747 34.615 0.00 0.00 40.24 1.90
3142 4265 6.573664 TGCTCATTTACTGCAACTTATTGT 57.426 33.333 0.00 0.00 38.17 2.71
3143 4266 7.680442 TGCTCATTTACTGCAACTTATTGTA 57.320 32.000 0.00 0.00 38.17 2.41
3155 4278 8.407457 TGCAACTTATTGTAGAATCGAGTTAG 57.593 34.615 11.51 8.82 38.17 2.34
3156 4279 7.491372 TGCAACTTATTGTAGAATCGAGTTAGG 59.509 37.037 11.51 5.18 38.17 2.69
3157 4280 7.705325 GCAACTTATTGTAGAATCGAGTTAGGA 59.295 37.037 11.51 0.00 38.17 2.94
3158 4281 9.021863 CAACTTATTGTAGAATCGAGTTAGGAC 57.978 37.037 11.51 0.00 31.67 3.85
3159 4282 8.289939 ACTTATTGTAGAATCGAGTTAGGACA 57.710 34.615 0.00 0.00 0.00 4.02
3160 4283 8.407064 ACTTATTGTAGAATCGAGTTAGGACAG 58.593 37.037 0.00 0.00 0.00 3.51
3161 4284 8.515695 TTATTGTAGAATCGAGTTAGGACAGA 57.484 34.615 0.00 0.00 0.00 3.41
3162 4285 6.438259 TTGTAGAATCGAGTTAGGACAGAG 57.562 41.667 0.00 0.00 0.00 3.35
3173 4296 1.693627 AGGACAGAGACGTGACAGTT 58.306 50.000 0.00 0.00 0.00 3.16
3179 4302 4.250464 ACAGAGACGTGACAGTTTCAAAA 58.750 39.130 0.00 0.00 35.39 2.44
3192 4315 6.999950 ACAGTTTCAAAAGTAAACAACCCTT 58.000 32.000 0.00 0.00 38.92 3.95
3240 4363 5.007385 AGGTCAGTAGCAAAATACTACCG 57.993 43.478 0.00 0.00 40.77 4.02
3242 4365 4.430908 GTCAGTAGCAAAATACTACCGCT 58.569 43.478 0.00 0.00 40.77 5.52
3246 4369 2.629051 AGCAAAATACTACCGCTGTCC 58.371 47.619 0.00 0.00 0.00 4.02
3253 4376 2.579410 ACTACCGCTGTCCCAAAATT 57.421 45.000 0.00 0.00 0.00 1.82
3254 4377 2.159382 ACTACCGCTGTCCCAAAATTG 58.841 47.619 0.00 0.00 0.00 2.32
3255 4378 2.224670 ACTACCGCTGTCCCAAAATTGA 60.225 45.455 0.00 0.00 0.00 2.57
3256 4379 1.698506 ACCGCTGTCCCAAAATTGAA 58.301 45.000 0.00 0.00 0.00 2.69
3257 4380 1.613437 ACCGCTGTCCCAAAATTGAAG 59.387 47.619 0.00 0.00 0.00 3.02
3258 4381 1.613437 CCGCTGTCCCAAAATTGAAGT 59.387 47.619 0.00 0.00 0.00 3.01
3259 4382 2.607771 CCGCTGTCCCAAAATTGAAGTG 60.608 50.000 0.00 0.00 0.00 3.16
3260 4383 2.407090 GCTGTCCCAAAATTGAAGTGC 58.593 47.619 0.00 0.00 0.00 4.40
3261 4384 2.224018 GCTGTCCCAAAATTGAAGTGCA 60.224 45.455 0.00 0.00 0.00 4.57
3262 4385 3.740764 GCTGTCCCAAAATTGAAGTGCAA 60.741 43.478 0.00 0.00 41.53 4.08
3263 4386 4.440880 CTGTCCCAAAATTGAAGTGCAAA 58.559 39.130 0.00 0.00 40.48 3.68
3264 4387 4.836825 TGTCCCAAAATTGAAGTGCAAAA 58.163 34.783 0.00 0.00 40.48 2.44
3265 4388 5.248640 TGTCCCAAAATTGAAGTGCAAAAA 58.751 33.333 0.00 0.00 40.48 1.94
3266 4389 5.123027 TGTCCCAAAATTGAAGTGCAAAAAC 59.877 36.000 0.00 0.00 40.48 2.43
3267 4390 4.331168 TCCCAAAATTGAAGTGCAAAAACG 59.669 37.500 0.00 0.00 40.48 3.60
3268 4391 4.094146 CCCAAAATTGAAGTGCAAAAACGT 59.906 37.500 0.00 0.00 40.48 3.99
3269 4392 5.254842 CCAAAATTGAAGTGCAAAAACGTC 58.745 37.500 0.00 0.00 40.48 4.34
3270 4393 5.063312 CCAAAATTGAAGTGCAAAAACGTCT 59.937 36.000 0.00 0.00 40.48 4.18
3271 4394 6.402011 CCAAAATTGAAGTGCAAAAACGTCTT 60.402 34.615 0.00 0.00 40.48 3.01
3272 4395 7.201478 CCAAAATTGAAGTGCAAAAACGTCTTA 60.201 33.333 0.00 0.00 40.48 2.10
3273 4396 8.327429 CAAAATTGAAGTGCAAAAACGTCTTAT 58.673 29.630 0.00 0.00 40.48 1.73
3274 4397 9.522804 AAAATTGAAGTGCAAAAACGTCTTATA 57.477 25.926 0.00 0.00 40.48 0.98
3275 4398 9.691362 AAATTGAAGTGCAAAAACGTCTTATAT 57.309 25.926 0.00 0.00 40.48 0.86
3276 4399 9.691362 AATTGAAGTGCAAAAACGTCTTATATT 57.309 25.926 0.00 0.00 40.48 1.28
3277 4400 9.691362 ATTGAAGTGCAAAAACGTCTTATATTT 57.309 25.926 0.00 0.00 40.48 1.40
3278 4401 9.522804 TTGAAGTGCAAAAACGTCTTATATTTT 57.477 25.926 0.00 0.00 32.46 1.82
3279 4402 8.963130 TGAAGTGCAAAAACGTCTTATATTTTG 58.037 29.630 13.82 13.82 42.66 2.44
3280 4403 9.176181 GAAGTGCAAAAACGTCTTATATTTTGA 57.824 29.630 19.73 6.87 42.48 2.69
3281 4404 8.728088 AGTGCAAAAACGTCTTATATTTTGAG 57.272 30.769 19.73 1.12 42.48 3.02
3282 4405 8.564574 AGTGCAAAAACGTCTTATATTTTGAGA 58.435 29.630 19.73 6.88 42.48 3.27
3283 4406 8.627428 GTGCAAAAACGTCTTATATTTTGAGAC 58.373 33.333 19.73 12.97 42.48 3.36
3292 4415 7.714703 GTCTTATATTTTGAGACGGAGGTAGT 58.285 38.462 0.00 0.00 31.54 2.73
3293 4416 8.844244 GTCTTATATTTTGAGACGGAGGTAGTA 58.156 37.037 0.00 0.00 31.54 1.82
3294 4417 8.844244 TCTTATATTTTGAGACGGAGGTAGTAC 58.156 37.037 0.00 0.00 0.00 2.73
3295 4418 8.523915 TTATATTTTGAGACGGAGGTAGTACA 57.476 34.615 2.06 0.00 0.00 2.90
3296 4419 5.934402 ATTTTGAGACGGAGGTAGTACAT 57.066 39.130 2.06 0.00 0.00 2.29
3297 4420 8.701908 ATATTTTGAGACGGAGGTAGTACATA 57.298 34.615 2.06 0.00 0.00 2.29
3298 4421 5.824904 TTTGAGACGGAGGTAGTACATAC 57.175 43.478 2.06 0.00 0.00 2.39
3299 4422 4.767578 TGAGACGGAGGTAGTACATACT 57.232 45.455 2.06 0.00 40.24 2.12
3300 4423 5.108187 TGAGACGGAGGTAGTACATACTT 57.892 43.478 2.06 0.00 37.73 2.24
3301 4424 5.503927 TGAGACGGAGGTAGTACATACTTT 58.496 41.667 2.06 0.00 37.73 2.66
3302 4425 6.653020 TGAGACGGAGGTAGTACATACTTTA 58.347 40.000 2.06 0.00 37.73 1.85
3303 4426 6.540189 TGAGACGGAGGTAGTACATACTTTAC 59.460 42.308 2.06 0.00 37.73 2.01
3304 4427 5.825151 AGACGGAGGTAGTACATACTTTACC 59.175 44.000 2.06 0.20 35.91 2.85
3305 4428 5.760131 ACGGAGGTAGTACATACTTTACCT 58.240 41.667 11.68 11.68 44.13 3.08
3306 4429 5.591877 ACGGAGGTAGTACATACTTTACCTG 59.408 44.000 15.34 7.25 42.45 4.00
3307 4430 5.591877 CGGAGGTAGTACATACTTTACCTGT 59.408 44.000 15.34 0.00 42.45 4.00
3308 4431 6.096001 CGGAGGTAGTACATACTTTACCTGTT 59.904 42.308 15.34 0.00 42.45 3.16
3309 4432 7.283127 CGGAGGTAGTACATACTTTACCTGTTA 59.717 40.741 15.34 0.00 42.45 2.41
3310 4433 8.971073 GGAGGTAGTACATACTTTACCTGTTAA 58.029 37.037 15.34 0.00 42.45 2.01
3312 4435 8.473219 AGGTAGTACATACTTTACCTGTTAAGC 58.527 37.037 11.24 0.00 41.43 3.09
3313 4436 8.253113 GGTAGTACATACTTTACCTGTTAAGCA 58.747 37.037 2.06 0.00 37.73 3.91
3314 4437 9.813446 GTAGTACATACTTTACCTGTTAAGCAT 57.187 33.333 0.00 0.00 37.73 3.79
3315 4438 8.718102 AGTACATACTTTACCTGTTAAGCATG 57.282 34.615 7.39 7.39 32.32 4.06
3316 4439 8.537016 AGTACATACTTTACCTGTTAAGCATGA 58.463 33.333 13.37 0.00 31.22 3.07
3317 4440 7.849804 ACATACTTTACCTGTTAAGCATGAG 57.150 36.000 13.37 0.00 31.22 2.90
3318 4441 6.316390 ACATACTTTACCTGTTAAGCATGAGC 59.684 38.462 13.37 0.00 42.56 4.26
3319 4442 4.651778 ACTTTACCTGTTAAGCATGAGCA 58.348 39.130 0.00 0.00 45.49 4.26
3320 4443 5.256474 ACTTTACCTGTTAAGCATGAGCAT 58.744 37.500 0.00 0.00 45.49 3.79
3321 4444 5.124457 ACTTTACCTGTTAAGCATGAGCATG 59.876 40.000 6.11 6.11 45.49 4.06
3331 4454 2.492019 CATGAGCATGCACATCCTTG 57.508 50.000 25.22 13.76 31.39 3.61
3332 4455 0.744874 ATGAGCATGCACATCCTTGC 59.255 50.000 22.86 0.00 43.31 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 100 9.219603 CATTGTACATTTTCGGTATATCAGGAT 57.780 33.333 0.00 0.00 0.00 3.24
444 503 9.281075 CACATGTCTACATTTTTCATACACATG 57.719 33.333 0.00 0.00 42.72 3.21
512 601 1.242076 CCATGGCCCATTCGAGATTC 58.758 55.000 0.00 0.00 0.00 2.52
541 630 3.719871 TGGCCCATCTTGAGTAGTCTTA 58.280 45.455 0.00 0.00 0.00 2.10
664 753 1.828224 CTGGATTTTAGGGCCGGGC 60.828 63.158 22.00 22.00 0.00 6.13
665 754 1.152756 CCTGGATTTTAGGGCCGGG 60.153 63.158 2.18 0.00 41.55 5.73
666 755 4.579127 CCTGGATTTTAGGGCCGG 57.421 61.111 0.00 0.00 0.00 6.13
671 760 1.202940 GCCTAGGCCCTGGATTTTAGG 60.203 57.143 24.19 10.45 34.56 2.69
672 761 2.278332 GCCTAGGCCCTGGATTTTAG 57.722 55.000 24.19 0.33 34.56 1.85
716 805 1.673168 CTCATAACTCAGGCCCAAGC 58.327 55.000 0.00 0.00 38.76 4.01
717 806 1.673168 GCTCATAACTCAGGCCCAAG 58.327 55.000 0.00 0.00 0.00 3.61
718 807 0.255890 GGCTCATAACTCAGGCCCAA 59.744 55.000 0.00 0.00 37.12 4.12
719 808 1.915228 GGCTCATAACTCAGGCCCA 59.085 57.895 0.00 0.00 37.12 5.36
720 809 4.887615 GGCTCATAACTCAGGCCC 57.112 61.111 0.00 0.00 37.12 5.80
722 811 0.464554 GGTGGGCTCATAACTCAGGC 60.465 60.000 0.00 0.00 34.44 4.85
723 812 0.911769 TGGTGGGCTCATAACTCAGG 59.088 55.000 0.00 0.00 0.00 3.86
724 813 1.745141 GCTGGTGGGCTCATAACTCAG 60.745 57.143 0.00 0.00 0.00 3.35
725 814 0.253044 GCTGGTGGGCTCATAACTCA 59.747 55.000 0.00 0.00 0.00 3.41
726 815 0.253044 TGCTGGTGGGCTCATAACTC 59.747 55.000 0.00 0.00 0.00 3.01
727 816 0.254178 CTGCTGGTGGGCTCATAACT 59.746 55.000 0.00 0.00 0.00 2.24
728 817 0.749454 CCTGCTGGTGGGCTCATAAC 60.749 60.000 0.51 0.00 0.00 1.89
729 818 1.609239 CCTGCTGGTGGGCTCATAA 59.391 57.895 0.51 0.00 0.00 1.90
730 819 2.377810 CCCTGCTGGTGGGCTCATA 61.378 63.158 9.00 0.00 37.99 2.15
731 820 3.736224 CCCTGCTGGTGGGCTCAT 61.736 66.667 9.00 0.00 37.99 2.90
756 845 1.050421 AATATGCCAAGCCCAAGCCC 61.050 55.000 0.00 0.00 41.25 5.19
757 846 0.105408 CAATATGCCAAGCCCAAGCC 59.895 55.000 0.00 0.00 41.25 4.35
758 847 0.105408 CCAATATGCCAAGCCCAAGC 59.895 55.000 0.00 0.00 40.32 4.01
759 848 0.105408 GCCAATATGCCAAGCCCAAG 59.895 55.000 0.00 0.00 0.00 3.61
760 849 0.616964 TGCCAATATGCCAAGCCCAA 60.617 50.000 0.00 0.00 0.00 4.12
761 850 0.398806 ATGCCAATATGCCAAGCCCA 60.399 50.000 0.00 0.00 0.00 5.36
762 851 0.760572 AATGCCAATATGCCAAGCCC 59.239 50.000 0.00 0.00 0.00 5.19
763 852 2.625695 AAATGCCAATATGCCAAGCC 57.374 45.000 0.00 0.00 0.00 4.35
764 853 4.512571 CCTTAAAATGCCAATATGCCAAGC 59.487 41.667 0.00 0.00 0.00 4.01
765 854 5.916318 TCCTTAAAATGCCAATATGCCAAG 58.084 37.500 0.00 0.00 0.00 3.61
766 855 5.946942 TCCTTAAAATGCCAATATGCCAA 57.053 34.783 0.00 0.00 0.00 4.52
767 856 5.660417 TCTTCCTTAAAATGCCAATATGCCA 59.340 36.000 0.00 0.00 0.00 4.92
768 857 6.160576 TCTTCCTTAAAATGCCAATATGCC 57.839 37.500 0.00 0.00 0.00 4.40
769 858 6.218746 CCTCTTCCTTAAAATGCCAATATGC 58.781 40.000 0.00 0.00 0.00 3.14
770 859 6.218746 GCCTCTTCCTTAAAATGCCAATATG 58.781 40.000 0.00 0.00 0.00 1.78
771 860 5.305386 GGCCTCTTCCTTAAAATGCCAATAT 59.695 40.000 0.00 0.00 37.58 1.28
772 861 4.649218 GGCCTCTTCCTTAAAATGCCAATA 59.351 41.667 0.00 0.00 37.58 1.90
773 862 3.452264 GGCCTCTTCCTTAAAATGCCAAT 59.548 43.478 0.00 0.00 37.58 3.16
774 863 2.831526 GGCCTCTTCCTTAAAATGCCAA 59.168 45.455 0.00 0.00 37.58 4.52
775 864 2.456577 GGCCTCTTCCTTAAAATGCCA 58.543 47.619 0.00 0.00 37.58 4.92
776 865 1.757118 GGGCCTCTTCCTTAAAATGCC 59.243 52.381 0.84 0.00 36.92 4.40
777 866 1.405463 CGGGCCTCTTCCTTAAAATGC 59.595 52.381 0.84 0.00 0.00 3.56
778 867 2.024414 CCGGGCCTCTTCCTTAAAATG 58.976 52.381 0.84 0.00 0.00 2.32
779 868 1.685180 GCCGGGCCTCTTCCTTAAAAT 60.685 52.381 8.12 0.00 0.00 1.82
780 869 0.323087 GCCGGGCCTCTTCCTTAAAA 60.323 55.000 8.12 0.00 0.00 1.52
781 870 1.301954 GCCGGGCCTCTTCCTTAAA 59.698 57.895 8.12 0.00 0.00 1.52
782 871 2.676265 GGCCGGGCCTCTTCCTTAA 61.676 63.158 30.86 0.00 46.69 1.85
783 872 3.087906 GGCCGGGCCTCTTCCTTA 61.088 66.667 30.86 0.00 46.69 2.69
798 887 0.767060 TAGGGCTTAGGGCTTAGGGC 60.767 60.000 3.76 3.76 41.46 5.19
799 888 1.815757 TTAGGGCTTAGGGCTTAGGG 58.184 55.000 0.00 0.00 41.46 3.53
800 889 2.106684 CCTTTAGGGCTTAGGGCTTAGG 59.893 54.545 0.00 0.00 41.46 2.69
801 890 3.493767 CCTTTAGGGCTTAGGGCTTAG 57.506 52.381 0.00 0.00 41.46 2.18
814 903 2.222227 AGCCCTGAAAAGCCTTTAGG 57.778 50.000 0.00 0.00 38.53 2.69
815 904 4.607293 AAAAGCCCTGAAAAGCCTTTAG 57.393 40.909 0.00 0.00 0.00 1.85
816 905 4.282449 GGTAAAAGCCCTGAAAAGCCTTTA 59.718 41.667 0.00 0.00 0.00 1.85
817 906 3.071023 GGTAAAAGCCCTGAAAAGCCTTT 59.929 43.478 0.00 0.00 0.00 3.11
818 907 2.632996 GGTAAAAGCCCTGAAAAGCCTT 59.367 45.455 0.00 0.00 0.00 4.35
819 908 2.248248 GGTAAAAGCCCTGAAAAGCCT 58.752 47.619 0.00 0.00 0.00 4.58
820 909 1.967779 TGGTAAAAGCCCTGAAAAGCC 59.032 47.619 0.00 0.00 0.00 4.35
821 910 2.890945 TCTGGTAAAAGCCCTGAAAAGC 59.109 45.455 0.00 0.00 0.00 3.51
822 911 4.082026 CCATCTGGTAAAAGCCCTGAAAAG 60.082 45.833 0.00 0.00 34.19 2.27
823 912 3.831911 CCATCTGGTAAAAGCCCTGAAAA 59.168 43.478 0.00 0.00 34.19 2.29
824 913 3.430453 CCATCTGGTAAAAGCCCTGAAA 58.570 45.455 0.00 0.00 34.19 2.69
825 914 2.291540 CCCATCTGGTAAAAGCCCTGAA 60.292 50.000 0.00 0.00 34.19 3.02
826 915 1.284785 CCCATCTGGTAAAAGCCCTGA 59.715 52.381 0.00 0.00 34.87 3.86
827 916 1.767759 CCCATCTGGTAAAAGCCCTG 58.232 55.000 0.00 0.00 0.00 4.45
828 917 0.033109 GCCCATCTGGTAAAAGCCCT 60.033 55.000 0.00 0.00 36.04 5.19
829 918 1.043116 GGCCCATCTGGTAAAAGCCC 61.043 60.000 0.00 0.00 33.22 5.19
830 919 1.384222 CGGCCCATCTGGTAAAAGCC 61.384 60.000 0.00 4.00 35.16 4.35
831 920 1.384222 CCGGCCCATCTGGTAAAAGC 61.384 60.000 0.00 0.00 36.43 3.51
832 921 0.751643 CCCGGCCCATCTGGTAAAAG 60.752 60.000 0.00 0.00 39.73 2.27
833 922 1.304952 CCCGGCCCATCTGGTAAAA 59.695 57.895 0.00 0.00 39.73 1.52
834 923 3.003230 CCCGGCCCATCTGGTAAA 58.997 61.111 0.00 0.00 39.73 2.01
835 924 3.804329 GCCCGGCCCATCTGGTAA 61.804 66.667 0.00 0.00 39.73 2.85
836 925 4.815973 AGCCCGGCCCATCTGGTA 62.816 66.667 5.55 0.00 39.73 3.25
847 936 2.158561 CTTTTCAAGCCCAAGCCCGG 62.159 60.000 0.00 0.00 41.25 5.73
848 937 1.290009 CTTTTCAAGCCCAAGCCCG 59.710 57.895 0.00 0.00 41.25 6.13
849 938 1.546029 CTACTTTTCAAGCCCAAGCCC 59.454 52.381 0.00 0.00 41.25 5.19
850 939 1.546029 CCTACTTTTCAAGCCCAAGCC 59.454 52.381 0.00 0.00 41.25 4.35
851 940 2.229062 GACCTACTTTTCAAGCCCAAGC 59.771 50.000 0.00 0.00 40.32 4.01
852 941 2.820197 GGACCTACTTTTCAAGCCCAAG 59.180 50.000 0.00 0.00 0.00 3.61
853 942 2.812613 CGGACCTACTTTTCAAGCCCAA 60.813 50.000 0.00 0.00 0.00 4.12
854 943 1.271163 CGGACCTACTTTTCAAGCCCA 60.271 52.381 0.00 0.00 0.00 5.36
855 944 1.002773 TCGGACCTACTTTTCAAGCCC 59.997 52.381 0.00 0.00 0.00 5.19
856 945 2.467566 TCGGACCTACTTTTCAAGCC 57.532 50.000 0.00 0.00 0.00 4.35
857 946 2.678336 CCATCGGACCTACTTTTCAAGC 59.322 50.000 0.00 0.00 0.00 4.01
858 947 3.055385 TCCCATCGGACCTACTTTTCAAG 60.055 47.826 0.00 0.00 31.13 3.02
859 948 2.907696 TCCCATCGGACCTACTTTTCAA 59.092 45.455 0.00 0.00 31.13 2.69
860 949 2.500098 CTCCCATCGGACCTACTTTTCA 59.500 50.000 0.00 0.00 33.32 2.69
861 950 2.158943 CCTCCCATCGGACCTACTTTTC 60.159 54.545 0.00 0.00 33.32 2.29
862 951 1.838077 CCTCCCATCGGACCTACTTTT 59.162 52.381 0.00 0.00 33.32 2.27
863 952 1.497161 CCTCCCATCGGACCTACTTT 58.503 55.000 0.00 0.00 33.32 2.66
864 953 0.398664 CCCTCCCATCGGACCTACTT 60.399 60.000 0.00 0.00 33.32 2.24
865 954 1.233369 CCCTCCCATCGGACCTACT 59.767 63.158 0.00 0.00 33.32 2.57
866 955 2.508751 GCCCTCCCATCGGACCTAC 61.509 68.421 0.00 0.00 33.32 3.18
867 956 2.122989 GCCCTCCCATCGGACCTA 60.123 66.667 0.00 0.00 33.32 3.08
870 959 3.866582 CAGGCCCTCCCATCGGAC 61.867 72.222 0.00 0.00 33.32 4.79
886 975 1.228552 GGCAGAAAACTGAGGCCCA 60.229 57.895 0.00 0.00 38.70 5.36
887 976 0.613012 ATGGCAGAAAACTGAGGCCC 60.613 55.000 0.00 0.00 43.96 5.80
888 977 0.529378 CATGGCAGAAAACTGAGGCC 59.471 55.000 0.00 0.00 44.82 5.19
889 978 0.529378 CCATGGCAGAAAACTGAGGC 59.471 55.000 0.00 0.00 0.00 4.70
890 979 1.180029 CCCATGGCAGAAAACTGAGG 58.820 55.000 6.09 0.00 0.00 3.86
903 992 1.598517 GGCCTGAAAAAGCCCATGG 59.401 57.895 4.14 4.14 43.76 3.66
909 998 4.069232 GGCCGGGCCTGAAAAAGC 62.069 66.667 30.86 7.24 46.69 3.51
932 1021 5.471456 GGAAGTCAGTTGCCATTATATCTGG 59.529 44.000 0.74 0.74 36.81 3.86
933 1022 5.178252 CGGAAGTCAGTTGCCATTATATCTG 59.822 44.000 0.00 0.00 0.00 2.90
934 1023 5.300752 CGGAAGTCAGTTGCCATTATATCT 58.699 41.667 0.00 0.00 0.00 1.98
935 1024 4.083802 GCGGAAGTCAGTTGCCATTATATC 60.084 45.833 0.00 0.00 0.00 1.63
936 1025 3.815401 GCGGAAGTCAGTTGCCATTATAT 59.185 43.478 0.00 0.00 0.00 0.86
937 1026 3.202906 GCGGAAGTCAGTTGCCATTATA 58.797 45.455 0.00 0.00 0.00 0.98
938 1027 2.017049 GCGGAAGTCAGTTGCCATTAT 58.983 47.619 0.00 0.00 0.00 1.28
939 1028 1.271108 TGCGGAAGTCAGTTGCCATTA 60.271 47.619 0.00 0.00 0.00 1.90
940 1029 0.537143 TGCGGAAGTCAGTTGCCATT 60.537 50.000 0.00 0.00 0.00 3.16
962 1051 4.083862 GGAGCGAAGAACCGGGCT 62.084 66.667 6.32 2.64 38.70 5.19
969 1058 1.141881 GGCGAGATGGAGCGAAGAA 59.858 57.895 0.00 0.00 0.00 2.52
994 1083 4.473520 ATCTCAACGGGCAGCGGG 62.474 66.667 0.00 0.00 0.00 6.13
995 1084 2.892425 GATCTCAACGGGCAGCGG 60.892 66.667 0.00 0.00 0.00 5.52
1171 1262 3.223589 GAGAGGCCGAGGAGGAGC 61.224 72.222 0.00 0.00 45.00 4.70
1873 2487 2.671351 GCCACTATCCGTCATATCACCG 60.671 54.545 0.00 0.00 0.00 4.94
1988 2602 2.512476 GTGGTACAATCCCCTTACCCAT 59.488 50.000 0.00 0.00 44.16 4.00
1996 2610 3.119280 CCGAAAAATGTGGTACAATCCCC 60.119 47.826 0.00 0.00 44.16 4.81
2192 2806 2.043953 GCGCCCCCTTCCTTTCAT 60.044 61.111 0.00 0.00 0.00 2.57
2218 2832 0.465824 AGGTACTCCCCGAGATCGTG 60.466 60.000 1.09 0.00 37.74 4.35
2228 2842 3.914426 ACATCATCACAAGGTACTCCC 57.086 47.619 0.00 0.00 38.49 4.30
2263 2877 9.635520 CAAATTGATTGCTTCTTAAATCTCTGT 57.364 29.630 0.00 0.00 34.52 3.41
2285 2899 9.480053 CATCACCAAAAATGAGAAACTACAAAT 57.520 29.630 0.00 0.00 0.00 2.32
2342 2984 4.158394 GGTCCATGTTTTGCACTGTATCAT 59.842 41.667 0.00 0.00 0.00 2.45
2343 2985 3.505680 GGTCCATGTTTTGCACTGTATCA 59.494 43.478 0.00 0.00 0.00 2.15
2345 2987 3.495331 TGGTCCATGTTTTGCACTGTAT 58.505 40.909 0.00 0.00 0.00 2.29
2346 2988 2.937519 TGGTCCATGTTTTGCACTGTA 58.062 42.857 0.00 0.00 0.00 2.74
2358 3000 5.361857 AGAAAATATGCCTTCTTGGTCCATG 59.638 40.000 0.00 0.00 38.35 3.66
2359 3001 5.361857 CAGAAAATATGCCTTCTTGGTCCAT 59.638 40.000 0.00 0.00 38.35 3.41
2367 3009 6.381801 CGTTTTGACAGAAAATATGCCTTCT 58.618 36.000 0.00 0.00 31.99 2.85
2384 3026 1.781025 CTCCGGCAGTTGCGTTTTGA 61.781 55.000 0.00 0.00 43.26 2.69
2433 3075 3.641436 TCTGTTCTGGCTTCAAGTACAGA 59.359 43.478 9.16 9.16 38.44 3.41
2434 3076 3.743396 GTCTGTTCTGGCTTCAAGTACAG 59.257 47.826 0.00 5.22 34.38 2.74
2435 3077 3.133901 TGTCTGTTCTGGCTTCAAGTACA 59.866 43.478 0.00 0.00 0.00 2.90
2450 3139 4.973168 TGGCACTATCTTTTCTGTCTGTT 58.027 39.130 0.00 0.00 0.00 3.16
2469 3158 2.423538 CCTTGCAACCAAGTAGTATGGC 59.576 50.000 0.00 0.00 45.57 4.40
2587 3276 4.670727 ACCAGGTACTAGGATGGACTCTAT 59.329 45.833 1.31 0.00 36.02 1.98
2588 3277 4.052922 ACCAGGTACTAGGATGGACTCTA 58.947 47.826 1.31 0.00 36.02 2.43
2653 3345 3.328382 TCGCACATAATATAGCCCCAC 57.672 47.619 0.00 0.00 0.00 4.61
2694 3386 1.589461 CGTCGTGACAACCGTTCCA 60.589 57.895 0.41 0.00 0.00 3.53
2696 3388 2.935446 GCCGTCGTGACAACCGTTC 61.935 63.158 0.41 0.00 0.00 3.95
2699 3391 4.986587 TCGCCGTCGTGACAACCG 62.987 66.667 0.41 0.00 36.96 4.44
2703 3395 2.050714 GACTTCGCCGTCGTGACA 60.051 61.111 0.41 0.00 36.96 3.58
2705 3397 4.047059 GGGACTTCGCCGTCGTGA 62.047 66.667 0.00 0.00 34.75 4.35
2709 3401 0.672401 TTCATTGGGACTTCGCCGTC 60.672 55.000 0.00 0.00 0.00 4.79
2843 3543 2.754946 TCAGTTTAACGGCTACAGGG 57.245 50.000 0.00 0.00 0.00 4.45
2848 3548 5.391523 GCATCAACATTCAGTTTAACGGCTA 60.392 40.000 0.00 0.00 38.74 3.93
2900 3600 8.630917 TCATCTCTAATAACAACTACAGTAGCC 58.369 37.037 7.57 0.00 0.00 3.93
2908 3608 9.679661 TGCCATTTTCATCTCTAATAACAACTA 57.320 29.630 0.00 0.00 0.00 2.24
2926 3626 0.978151 TGCAATGAGGCTGCCATTTT 59.022 45.000 22.65 7.80 39.13 1.82
3001 4117 0.674581 CGCTGCTCCATCTCCACAAA 60.675 55.000 0.00 0.00 0.00 2.83
3050 4166 3.371168 TGAACGCAAAAGTGAAAGCATC 58.629 40.909 0.00 0.00 0.00 3.91
3132 4255 9.021863 GTCCTAACTCGATTCTACAATAAGTTG 57.978 37.037 0.00 0.00 41.20 3.16
3133 4256 8.746530 TGTCCTAACTCGATTCTACAATAAGTT 58.253 33.333 0.00 0.00 34.62 2.66
3134 4257 8.289939 TGTCCTAACTCGATTCTACAATAAGT 57.710 34.615 0.00 0.00 0.00 2.24
3135 4258 8.622157 TCTGTCCTAACTCGATTCTACAATAAG 58.378 37.037 0.00 0.00 0.00 1.73
3136 4259 8.515695 TCTGTCCTAACTCGATTCTACAATAA 57.484 34.615 0.00 0.00 0.00 1.40
3137 4260 7.991460 TCTCTGTCCTAACTCGATTCTACAATA 59.009 37.037 0.00 0.00 0.00 1.90
3138 4261 6.829298 TCTCTGTCCTAACTCGATTCTACAAT 59.171 38.462 0.00 0.00 0.00 2.71
3139 4262 6.093771 GTCTCTGTCCTAACTCGATTCTACAA 59.906 42.308 0.00 0.00 0.00 2.41
3140 4263 5.585445 GTCTCTGTCCTAACTCGATTCTACA 59.415 44.000 0.00 0.00 0.00 2.74
3141 4264 5.276963 CGTCTCTGTCCTAACTCGATTCTAC 60.277 48.000 0.00 0.00 0.00 2.59
3142 4265 4.809958 CGTCTCTGTCCTAACTCGATTCTA 59.190 45.833 0.00 0.00 0.00 2.10
3143 4266 3.623960 CGTCTCTGTCCTAACTCGATTCT 59.376 47.826 0.00 0.00 0.00 2.40
3144 4267 3.374678 ACGTCTCTGTCCTAACTCGATTC 59.625 47.826 0.00 0.00 0.00 2.52
3145 4268 3.127203 CACGTCTCTGTCCTAACTCGATT 59.873 47.826 0.00 0.00 0.00 3.34
3146 4269 2.678836 CACGTCTCTGTCCTAACTCGAT 59.321 50.000 0.00 0.00 0.00 3.59
3147 4270 2.074576 CACGTCTCTGTCCTAACTCGA 58.925 52.381 0.00 0.00 0.00 4.04
3148 4271 2.074576 TCACGTCTCTGTCCTAACTCG 58.925 52.381 0.00 0.00 0.00 4.18
3149 4272 2.812591 TGTCACGTCTCTGTCCTAACTC 59.187 50.000 0.00 0.00 0.00 3.01
3150 4273 2.814919 CTGTCACGTCTCTGTCCTAACT 59.185 50.000 0.00 0.00 0.00 2.24
3151 4274 2.553172 ACTGTCACGTCTCTGTCCTAAC 59.447 50.000 0.00 0.00 0.00 2.34
3152 4275 2.860009 ACTGTCACGTCTCTGTCCTAA 58.140 47.619 0.00 0.00 0.00 2.69
3153 4276 2.563261 ACTGTCACGTCTCTGTCCTA 57.437 50.000 0.00 0.00 0.00 2.94
3154 4277 1.693627 AACTGTCACGTCTCTGTCCT 58.306 50.000 0.00 0.00 0.00 3.85
3155 4278 2.223735 TGAAACTGTCACGTCTCTGTCC 60.224 50.000 0.00 0.00 0.00 4.02
3156 4279 3.079960 TGAAACTGTCACGTCTCTGTC 57.920 47.619 0.00 0.00 0.00 3.51
3157 4280 3.520290 TTGAAACTGTCACGTCTCTGT 57.480 42.857 0.00 0.00 35.39 3.41
3158 4281 4.330074 ACTTTTGAAACTGTCACGTCTCTG 59.670 41.667 0.00 0.00 35.39 3.35
3159 4282 4.504858 ACTTTTGAAACTGTCACGTCTCT 58.495 39.130 0.00 0.00 35.39 3.10
3160 4283 4.859629 ACTTTTGAAACTGTCACGTCTC 57.140 40.909 0.00 0.00 35.39 3.36
3161 4284 6.148150 TGTTTACTTTTGAAACTGTCACGTCT 59.852 34.615 0.00 0.00 37.62 4.18
3162 4285 6.308675 TGTTTACTTTTGAAACTGTCACGTC 58.691 36.000 0.00 0.00 37.62 4.34
3173 4296 6.378848 AGCTACAAGGGTTGTTTACTTTTGAA 59.621 34.615 0.00 0.00 42.22 2.69
3179 4302 4.596212 ACCTAGCTACAAGGGTTGTTTACT 59.404 41.667 6.00 0.00 42.22 2.24
3192 4315 5.865085 AGAAACAACATCAACCTAGCTACA 58.135 37.500 0.00 0.00 0.00 2.74
3240 4363 2.224018 TGCACTTCAATTTTGGGACAGC 60.224 45.455 0.00 0.00 42.39 4.40
3242 4365 4.478206 TTTGCACTTCAATTTTGGGACA 57.522 36.364 0.00 0.00 34.12 4.02
3246 4369 5.063312 AGACGTTTTTGCACTTCAATTTTGG 59.937 36.000 0.00 0.00 34.12 3.28
3253 4376 8.963130 CAAAATATAAGACGTTTTTGCACTTCA 58.037 29.630 7.67 0.00 33.75 3.02
3254 4377 9.176181 TCAAAATATAAGACGTTTTTGCACTTC 57.824 29.630 13.47 0.00 38.38 3.01
3255 4378 9.180678 CTCAAAATATAAGACGTTTTTGCACTT 57.819 29.630 13.47 3.03 38.38 3.16
3256 4379 8.564574 TCTCAAAATATAAGACGTTTTTGCACT 58.435 29.630 13.47 0.00 38.38 4.40
3257 4380 8.627428 GTCTCAAAATATAAGACGTTTTTGCAC 58.373 33.333 13.47 9.83 38.38 4.57
3258 4381 8.722342 GTCTCAAAATATAAGACGTTTTTGCA 57.278 30.769 13.47 0.00 38.38 4.08
3267 4390 7.714703 ACTACCTCCGTCTCAAAATATAAGAC 58.285 38.462 0.00 0.00 36.82 3.01
3268 4391 7.893124 ACTACCTCCGTCTCAAAATATAAGA 57.107 36.000 0.00 0.00 0.00 2.10
3269 4392 8.627403 TGTACTACCTCCGTCTCAAAATATAAG 58.373 37.037 0.00 0.00 0.00 1.73
3270 4393 8.523915 TGTACTACCTCCGTCTCAAAATATAA 57.476 34.615 0.00 0.00 0.00 0.98
3271 4394 8.701908 ATGTACTACCTCCGTCTCAAAATATA 57.298 34.615 0.00 0.00 0.00 0.86
3272 4395 7.598759 ATGTACTACCTCCGTCTCAAAATAT 57.401 36.000 0.00 0.00 0.00 1.28
3273 4396 7.776969 AGTATGTACTACCTCCGTCTCAAAATA 59.223 37.037 0.00 0.00 34.13 1.40
3274 4397 5.934402 ATGTACTACCTCCGTCTCAAAAT 57.066 39.130 0.00 0.00 0.00 1.82
3275 4398 5.948162 AGTATGTACTACCTCCGTCTCAAAA 59.052 40.000 0.00 0.00 34.13 2.44
3276 4399 5.503927 AGTATGTACTACCTCCGTCTCAAA 58.496 41.667 0.00 0.00 34.13 2.69
3277 4400 5.108187 AGTATGTACTACCTCCGTCTCAA 57.892 43.478 0.00 0.00 34.13 3.02
3278 4401 4.767578 AGTATGTACTACCTCCGTCTCA 57.232 45.455 0.00 0.00 34.13 3.27
3279 4402 6.017523 GGTAAAGTATGTACTACCTCCGTCTC 60.018 46.154 5.32 0.00 34.99 3.36
3280 4403 5.825151 GGTAAAGTATGTACTACCTCCGTCT 59.175 44.000 5.32 0.00 34.99 4.18
3281 4404 5.825151 AGGTAAAGTATGTACTACCTCCGTC 59.175 44.000 8.27 0.00 34.99 4.79
3282 4405 5.591877 CAGGTAAAGTATGTACTACCTCCGT 59.408 44.000 10.37 0.00 35.92 4.69
3283 4406 5.591877 ACAGGTAAAGTATGTACTACCTCCG 59.408 44.000 10.37 5.37 35.92 4.63
3284 4407 7.415592 AACAGGTAAAGTATGTACTACCTCC 57.584 40.000 10.37 4.49 35.92 4.30
3286 4409 8.473219 GCTTAACAGGTAAAGTATGTACTACCT 58.527 37.037 8.27 8.27 38.35 3.08
3287 4410 8.253113 TGCTTAACAGGTAAAGTATGTACTACC 58.747 37.037 4.61 4.61 34.99 3.18
3288 4411 9.813446 ATGCTTAACAGGTAAAGTATGTACTAC 57.187 33.333 0.00 0.00 34.99 2.73
3289 4412 9.811995 CATGCTTAACAGGTAAAGTATGTACTA 57.188 33.333 0.00 0.00 39.51 1.82
3290 4413 8.537016 TCATGCTTAACAGGTAAAGTATGTACT 58.463 33.333 11.23 0.00 42.74 2.73
3291 4414 8.712285 TCATGCTTAACAGGTAAAGTATGTAC 57.288 34.615 11.23 0.00 42.74 2.90
3292 4415 7.494625 GCTCATGCTTAACAGGTAAAGTATGTA 59.505 37.037 11.23 1.48 42.74 2.29
3293 4416 6.316390 GCTCATGCTTAACAGGTAAAGTATGT 59.684 38.462 11.23 0.00 42.74 2.29
3294 4417 6.316140 TGCTCATGCTTAACAGGTAAAGTATG 59.684 38.462 6.77 6.77 43.21 2.39
3295 4418 6.414732 TGCTCATGCTTAACAGGTAAAGTAT 58.585 36.000 0.00 0.00 40.48 2.12
3296 4419 5.800296 TGCTCATGCTTAACAGGTAAAGTA 58.200 37.500 0.00 0.00 40.48 2.24
3297 4420 4.651778 TGCTCATGCTTAACAGGTAAAGT 58.348 39.130 0.00 0.00 40.48 2.66
3298 4421 5.575957 CATGCTCATGCTTAACAGGTAAAG 58.424 41.667 0.00 0.00 40.48 1.85
3299 4422 5.565592 CATGCTCATGCTTAACAGGTAAA 57.434 39.130 0.00 0.00 40.48 2.01
3312 4435 1.536072 GCAAGGATGTGCATGCTCATG 60.536 52.381 33.31 23.15 44.29 3.07
3313 4436 0.744874 GCAAGGATGTGCATGCTCAT 59.255 50.000 29.85 29.85 44.29 2.90
3314 4437 2.186155 GCAAGGATGTGCATGCTCA 58.814 52.632 23.37 23.37 44.29 4.26


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

AutoCloner maintained by Alex Coulton.