Multiple sequence alignment - TraesCS2D01G182900

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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 TraesCS2D01G182900 chr2D 100.000 5224 0 0 1 5224 127118238 127113015 0.000000e+00 9648.0
1 TraesCS2D01G182900 chr2D 86.848 479 50 8 3 468 586906666 586906188 1.670000e-144 523.0
2 TraesCS2D01G182900 chr2D 83.395 542 77 6 41 576 580976208 580976742 1.690000e-134 490.0
3 TraesCS2D01G182900 chr2B 98.038 1682 26 4 3549 5224 180886705 180885025 0.000000e+00 2916.0
4 TraesCS2D01G182900 chr2B 90.783 217 14 4 4897 5108 726050191 726050406 8.560000e-73 285.0
5 TraesCS2D01G182900 chr2B 100.000 43 0 0 5182 5224 180852176 180852134 4.340000e-11 80.5
6 TraesCS2D01G182900 chr2A 96.213 1294 35 5 3190 4469 133985017 133983724 0.000000e+00 2106.0
7 TraesCS2D01G182900 chr2A 95.447 1142 29 6 2055 3193 133986218 133985097 0.000000e+00 1799.0
8 TraesCS2D01G182900 chr2A 93.328 1169 62 7 806 1965 133987382 133986221 0.000000e+00 1712.0
9 TraesCS2D01G182900 chr2A 93.116 276 13 3 4461 4730 133982571 133982296 2.930000e-107 399.0
10 TraesCS2D01G182900 chr2A 89.796 245 18 3 4830 5067 731196335 731196579 1.830000e-79 307.0
11 TraesCS2D01G182900 chr2A 90.991 111 8 1 4722 4832 133981437 133981329 1.170000e-31 148.0
12 TraesCS2D01G182900 chr2A 93.617 47 3 0 5178 5224 133980445 133980399 2.610000e-08 71.3
13 TraesCS2D01G182900 chr2A 100.000 32 0 0 769 800 726163143 726163112 5.650000e-05 60.2
14 TraesCS2D01G182900 chr4D 82.591 741 95 13 3 738 28835479 28834768 1.600000e-174 623.0
15 TraesCS2D01G182900 chr4D 97.143 35 1 0 765 799 325358815 325358781 5.650000e-05 60.2
16 TraesCS2D01G182900 chr3B 82.219 748 98 22 1 735 715004704 715005429 3.460000e-171 612.0
17 TraesCS2D01G182900 chrUn 83.518 631 93 4 16 643 75461861 75462483 3.510000e-161 579.0
18 TraesCS2D01G182900 chr5D 85.000 520 55 13 3 505 22388273 22388786 1.680000e-139 507.0
19 TraesCS2D01G182900 chr5D 87.037 54 5 2 684 735 472431846 472431899 5.650000e-05 60.2
20 TraesCS2D01G182900 chr1D 86.526 475 45 12 7 468 408410601 408411069 6.040000e-139 505.0
21 TraesCS2D01G182900 chr5B 85.146 478 57 9 8 472 63561761 63561285 1.320000e-130 477.0
22 TraesCS2D01G182900 chr5B 84.200 481 59 12 3 468 293460601 293460123 7.980000e-123 451.0
23 TraesCS2D01G182900 chr6A 91.638 287 17 4 4832 5111 263908507 263908793 1.760000e-104 390.0
24 TraesCS2D01G182900 chr6D 91.289 287 18 4 4832 5111 221864004 221864290 8.210000e-103 385.0
25 TraesCS2D01G182900 chr6D 91.556 225 14 3 4860 5082 189733765 189733986 6.570000e-79 305.0
26 TraesCS2D01G182900 chr6B 90.941 287 19 4 4832 5111 345232885 345233171 3.820000e-101 379.0
27 TraesCS2D01G182900 chr6B 88.583 254 18 8 4862 5111 400319592 400319838 1.100000e-76 298.0
28 TraesCS2D01G182900 chr6B 85.965 57 6 1 681 735 623175936 623175992 5.650000e-05 60.2
29 TraesCS2D01G182900 chr7A 85.971 278 17 8 4839 5111 81143379 81143119 1.430000e-70 278.0
30 TraesCS2D01G182900 chr3A 97.222 36 1 0 769 804 22812801 22812766 1.570000e-05 62.1
31 TraesCS2D01G182900 chr3A 94.872 39 2 0 766 804 670654585 670654623 1.570000e-05 62.1
32 TraesCS2D01G182900 chr4A 97.143 35 1 0 765 799 145883949 145883983 5.650000e-05 60.2


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 TraesCS2D01G182900 chr2D 127113015 127118238 5223 True 9648.000000 9648 100.000000 1 5224 1 chr2D.!!$R1 5223
1 TraesCS2D01G182900 chr2D 580976208 580976742 534 False 490.000000 490 83.395000 41 576 1 chr2D.!!$F1 535
2 TraesCS2D01G182900 chr2B 180885025 180886705 1680 True 2916.000000 2916 98.038000 3549 5224 1 chr2B.!!$R2 1675
3 TraesCS2D01G182900 chr2A 133980399 133987382 6983 True 1039.216667 2106 93.785333 806 5224 6 chr2A.!!$R2 4418
4 TraesCS2D01G182900 chr4D 28834768 28835479 711 True 623.000000 623 82.591000 3 738 1 chr4D.!!$R1 735
5 TraesCS2D01G182900 chr3B 715004704 715005429 725 False 612.000000 612 82.219000 1 735 1 chr3B.!!$F1 734
6 TraesCS2D01G182900 chrUn 75461861 75462483 622 False 579.000000 579 83.518000 16 643 1 chrUn.!!$F1 627
7 TraesCS2D01G182900 chr5D 22388273 22388786 513 False 507.000000 507 85.000000 3 505 1 chr5D.!!$F1 502

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
126 131 0.327480 ATCCTAGCCATGTCCCCACA 60.327 55.0 0.00 0.00 36.78 4.17 F
1109 1153 0.325296 TAACTGGCAGATCCGACCCT 60.325 55.0 23.66 0.00 37.80 4.34 F
1603 1647 0.105964 ATGATGCAACATGCCATGGC 59.894 50.0 30.54 30.54 44.23 4.40 F
1978 2027 0.178990 GGTTCTGTGGCCAGGAAACT 60.179 55.0 22.22 0.00 46.44 2.66 F
1983 2032 0.257328 TGTGGCCAGGAAACTCAACA 59.743 50.0 5.11 0.00 40.21 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1145 1189 0.247460 GGAACCCCAGCAAGCAAATC 59.753 55.000 0.0 0.0 0.00 2.17 R
2511 2563 0.249955 TTGATGACGAGCATGAGCCA 59.750 50.000 0.0 0.0 43.56 4.75 R
3516 3659 1.990563 GTGCATTTGTGAGATTGCAGC 59.009 47.619 0.0 0.0 44.99 5.25 R
3806 3949 1.603802 ACGATGCTTAATGGATTGCCG 59.396 47.619 0.0 0.0 36.79 5.69 R
4356 4505 6.730977 AGCCATTAGAAATGCTAGGAGGTATA 59.269 38.462 0.0 0.0 30.97 1.47 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
38 39 3.536917 CGCCCGAGACCATAGCCA 61.537 66.667 0.00 0.00 0.00 4.75
57 58 1.525306 GCTATTTAAGCCGGCCGGT 60.525 57.895 42.53 28.17 46.25 5.28
79 81 2.377810 CCCAGCCCTAGCACATCCA 61.378 63.158 0.00 0.00 43.56 3.41
119 124 1.043816 CCACTCGATCCTAGCCATGT 58.956 55.000 0.00 0.00 0.00 3.21
126 131 0.327480 ATCCTAGCCATGTCCCCACA 60.327 55.000 0.00 0.00 36.78 4.17
129 134 1.540118 TAGCCATGTCCCCACACCA 60.540 57.895 0.00 0.00 34.48 4.17
146 151 1.022735 CCACCGCTACTACACGATCT 58.977 55.000 0.00 0.00 0.00 2.75
239 250 0.693049 TTTCAAGGAGGAGGAGGTGC 59.307 55.000 0.00 0.00 0.00 5.01
242 253 3.239627 AAGGAGGAGGAGGTGCCGA 62.240 63.158 0.00 0.00 43.43 5.54
251 262 2.685380 AGGTGCCGAGGAAGGAGG 60.685 66.667 0.00 0.00 0.00 4.30
252 263 2.683933 GGTGCCGAGGAAGGAGGA 60.684 66.667 0.00 0.00 0.00 3.71
253 264 2.291043 GGTGCCGAGGAAGGAGGAA 61.291 63.158 0.00 0.00 0.00 3.36
308 347 4.761058 AGCCGGCGGAGAAGGAGA 62.761 66.667 33.44 0.00 0.00 3.71
321 360 4.821589 GGAGAAGGAGGCGCCACG 62.822 72.222 31.54 0.00 40.02 4.94
355 394 3.224324 GAGGAGGCACCGGCGATA 61.224 66.667 9.30 0.00 44.74 2.92
370 409 0.465824 CGATAGAGGAGGACGTGGGT 60.466 60.000 0.00 0.00 39.76 4.51
397 436 2.501128 GAGCAGCACGCCATCCTA 59.499 61.111 0.00 0.00 44.04 2.94
463 502 2.334946 GCAACAGATGAAGGCGGCA 61.335 57.895 13.08 0.00 0.00 5.69
468 507 2.268920 GATGAAGGCGGCACAGGA 59.731 61.111 13.08 0.00 0.00 3.86
624 664 7.333528 AGAGATTGAGTATGAGAGACTTGTC 57.666 40.000 0.00 0.00 0.00 3.18
629 669 5.073428 TGAGTATGAGAGACTTGTCTGTGT 58.927 41.667 8.11 0.00 0.00 3.72
644 684 8.375506 ACTTGTCTGTGTAGAAGGAAATATGAA 58.624 33.333 0.00 0.00 34.01 2.57
645 685 9.219603 CTTGTCTGTGTAGAAGGAAATATGAAA 57.780 33.333 0.00 0.00 34.01 2.69
646 686 9.567776 TTGTCTGTGTAGAAGGAAATATGAAAA 57.432 29.630 0.00 0.00 34.01 2.29
650 690 8.918202 TGTGTAGAAGGAAATATGAAAAGTGT 57.082 30.769 0.00 0.00 0.00 3.55
654 694 6.472887 AGAAGGAAATATGAAAAGTGTCCGA 58.527 36.000 0.00 0.00 0.00 4.55
658 698 6.884295 AGGAAATATGAAAAGTGTCCGATCAA 59.116 34.615 0.00 0.00 0.00 2.57
662 702 2.487762 TGAAAAGTGTCCGATCAATGCC 59.512 45.455 0.00 0.00 0.00 4.40
663 703 2.496899 AAAGTGTCCGATCAATGCCT 57.503 45.000 0.00 0.00 0.00 4.75
664 704 3.627395 AAAGTGTCCGATCAATGCCTA 57.373 42.857 0.00 0.00 0.00 3.93
666 706 1.831106 AGTGTCCGATCAATGCCTACA 59.169 47.619 0.00 0.00 0.00 2.74
667 707 2.236146 AGTGTCCGATCAATGCCTACAA 59.764 45.455 0.00 0.00 0.00 2.41
669 709 3.627577 GTGTCCGATCAATGCCTACAAAT 59.372 43.478 0.00 0.00 0.00 2.32
670 710 4.814234 GTGTCCGATCAATGCCTACAAATA 59.186 41.667 0.00 0.00 0.00 1.40
679 719 1.423541 TGCCTACAAATATGCCCGGAT 59.576 47.619 0.73 0.00 0.00 4.18
681 721 2.436417 CCTACAAATATGCCCGGATGG 58.564 52.381 0.73 0.00 37.09 3.51
700 740 2.895865 TGCGTTCGCGGGTTTGAA 60.896 55.556 6.13 0.00 41.67 2.69
714 754 0.829602 TTTGAAGGGCCGGATTTGCA 60.830 50.000 5.05 0.00 0.00 4.08
735 775 1.118838 AGTCCAGCTGTAGATGCTCC 58.881 55.000 13.81 0.00 38.92 4.70
738 778 2.035321 GTCCAGCTGTAGATGCTCCTAC 59.965 54.545 13.81 8.51 38.92 3.18
739 779 1.342819 CCAGCTGTAGATGCTCCTACC 59.657 57.143 13.81 1.07 38.92 3.18
740 780 2.034878 CAGCTGTAGATGCTCCTACCA 58.965 52.381 5.25 2.72 38.92 3.25
741 781 2.035704 CAGCTGTAGATGCTCCTACCAG 59.964 54.545 5.25 10.21 38.92 4.00
742 782 2.091610 AGCTGTAGATGCTCCTACCAGA 60.092 50.000 11.65 0.00 38.53 3.86
743 783 2.295909 GCTGTAGATGCTCCTACCAGAG 59.704 54.545 11.65 5.91 38.53 3.35
744 784 3.561143 CTGTAGATGCTCCTACCAGAGT 58.439 50.000 11.65 0.00 38.53 3.24
745 785 3.556999 TGTAGATGCTCCTACCAGAGTC 58.443 50.000 11.65 0.00 38.53 3.36
746 786 2.836636 AGATGCTCCTACCAGAGTCA 57.163 50.000 0.00 0.00 36.20 3.41
747 787 3.107402 AGATGCTCCTACCAGAGTCAA 57.893 47.619 0.00 0.00 36.20 3.18
748 788 2.763448 AGATGCTCCTACCAGAGTCAAC 59.237 50.000 0.00 0.00 36.20 3.18
749 789 2.009681 TGCTCCTACCAGAGTCAACA 57.990 50.000 0.00 0.00 36.20 3.33
750 790 1.618837 TGCTCCTACCAGAGTCAACAC 59.381 52.381 0.00 0.00 36.20 3.32
751 791 1.066787 GCTCCTACCAGAGTCAACACC 60.067 57.143 0.00 0.00 36.20 4.16
752 792 2.248248 CTCCTACCAGAGTCAACACCA 58.752 52.381 0.00 0.00 0.00 4.17
753 793 2.232452 CTCCTACCAGAGTCAACACCAG 59.768 54.545 0.00 0.00 0.00 4.00
754 794 1.338200 CCTACCAGAGTCAACACCAGC 60.338 57.143 0.00 0.00 0.00 4.85
755 795 0.685097 TACCAGAGTCAACACCAGCC 59.315 55.000 0.00 0.00 0.00 4.85
756 796 1.669115 CCAGAGTCAACACCAGCCG 60.669 63.158 0.00 0.00 0.00 5.52
757 797 2.031163 AGAGTCAACACCAGCCGC 59.969 61.111 0.00 0.00 0.00 6.53
758 798 3.050275 GAGTCAACACCAGCCGCC 61.050 66.667 0.00 0.00 0.00 6.13
759 799 3.825160 GAGTCAACACCAGCCGCCA 62.825 63.158 0.00 0.00 0.00 5.69
760 800 2.904866 GTCAACACCAGCCGCCAA 60.905 61.111 0.00 0.00 0.00 4.52
761 801 2.124109 TCAACACCAGCCGCCAAA 60.124 55.556 0.00 0.00 0.00 3.28
762 802 1.530419 TCAACACCAGCCGCCAAAT 60.530 52.632 0.00 0.00 0.00 2.32
763 803 1.080569 CAACACCAGCCGCCAAATC 60.081 57.895 0.00 0.00 0.00 2.17
764 804 1.530419 AACACCAGCCGCCAAATCA 60.530 52.632 0.00 0.00 0.00 2.57
765 805 0.899717 AACACCAGCCGCCAAATCAT 60.900 50.000 0.00 0.00 0.00 2.45
766 806 1.140161 CACCAGCCGCCAAATCATG 59.860 57.895 0.00 0.00 0.00 3.07
767 807 2.105528 CCAGCCGCCAAATCATGC 59.894 61.111 0.00 0.00 0.00 4.06
777 817 4.509915 GCCAAATCATGCGAATTTTGAG 57.490 40.909 2.59 0.00 32.17 3.02
778 818 3.928375 GCCAAATCATGCGAATTTTGAGT 59.072 39.130 2.59 0.00 32.17 3.41
779 819 4.389687 GCCAAATCATGCGAATTTTGAGTT 59.610 37.500 2.59 0.00 32.17 3.01
780 820 5.106987 GCCAAATCATGCGAATTTTGAGTTT 60.107 36.000 2.59 0.00 32.17 2.66
781 821 6.301108 CCAAATCATGCGAATTTTGAGTTTG 58.699 36.000 2.59 0.00 32.17 2.93
782 822 5.520022 AATCATGCGAATTTTGAGTTTGC 57.480 34.783 0.00 0.00 36.67 3.68
783 823 4.241590 TCATGCGAATTTTGAGTTTGCT 57.758 36.364 0.00 0.00 36.99 3.91
784 824 5.369685 TCATGCGAATTTTGAGTTTGCTA 57.630 34.783 0.00 0.00 36.99 3.49
785 825 5.767269 TCATGCGAATTTTGAGTTTGCTAA 58.233 33.333 0.00 0.00 36.99 3.09
786 826 5.629020 TCATGCGAATTTTGAGTTTGCTAAC 59.371 36.000 2.56 2.56 36.99 2.34
787 827 4.295051 TGCGAATTTTGAGTTTGCTAACC 58.705 39.130 7.43 0.58 36.99 2.85
788 828 4.202060 TGCGAATTTTGAGTTTGCTAACCA 60.202 37.500 7.43 3.14 36.99 3.67
789 829 4.148174 GCGAATTTTGAGTTTGCTAACCAC 59.852 41.667 7.43 3.54 34.71 4.16
790 830 5.277825 CGAATTTTGAGTTTGCTAACCACA 58.722 37.500 7.43 6.00 34.71 4.17
791 831 5.920273 CGAATTTTGAGTTTGCTAACCACAT 59.080 36.000 7.43 0.00 34.71 3.21
792 832 6.129115 CGAATTTTGAGTTTGCTAACCACATG 60.129 38.462 7.43 0.00 34.71 3.21
793 833 5.590530 TTTTGAGTTTGCTAACCACATGT 57.409 34.783 7.43 0.00 34.71 3.21
794 834 6.701145 TTTTGAGTTTGCTAACCACATGTA 57.299 33.333 7.43 0.00 34.71 2.29
795 835 5.682943 TTGAGTTTGCTAACCACATGTAC 57.317 39.130 7.43 0.00 34.71 2.90
796 836 4.069304 TGAGTTTGCTAACCACATGTACC 58.931 43.478 7.43 0.00 34.71 3.34
797 837 4.069304 GAGTTTGCTAACCACATGTACCA 58.931 43.478 7.43 0.00 34.71 3.25
798 838 4.662278 AGTTTGCTAACCACATGTACCAT 58.338 39.130 7.43 0.00 34.71 3.55
799 839 4.458989 AGTTTGCTAACCACATGTACCATG 59.541 41.667 7.43 2.77 34.71 3.66
800 840 2.364632 TGCTAACCACATGTACCATGC 58.635 47.619 0.00 1.63 0.00 4.06
801 841 1.330521 GCTAACCACATGTACCATGCG 59.669 52.381 0.00 0.00 0.00 4.73
802 842 1.939934 CTAACCACATGTACCATGCGG 59.060 52.381 9.19 9.19 38.77 5.69
826 866 1.811965 CAGCCGTCAAATCATGGTTGA 59.188 47.619 8.22 8.22 36.08 3.18
828 868 3.627123 CAGCCGTCAAATCATGGTTGATA 59.373 43.478 13.61 0.00 41.83 2.15
850 890 2.279784 GGATCAGAAGCCGGAGCG 60.280 66.667 5.05 0.00 46.67 5.03
989 1033 4.320788 CGTACTTAATACTCCCATCGGACC 60.321 50.000 0.00 0.00 33.32 4.46
1010 1054 2.548067 CGGGAGAGGATATTTTCGGTGG 60.548 54.545 0.00 0.00 0.00 4.61
1095 1139 3.130516 TCTCGCCAAGGTACATCTAACTG 59.869 47.826 0.00 0.00 0.00 3.16
1109 1153 0.325296 TAACTGGCAGATCCGACCCT 60.325 55.000 23.66 0.00 37.80 4.34
1127 1171 4.089361 ACCCTGAGCCTTTCCATTTTAAG 58.911 43.478 0.00 0.00 0.00 1.85
1128 1172 4.089361 CCCTGAGCCTTTCCATTTTAAGT 58.911 43.478 0.00 0.00 0.00 2.24
1129 1173 4.528206 CCCTGAGCCTTTCCATTTTAAGTT 59.472 41.667 0.00 0.00 0.00 2.66
1130 1174 5.012046 CCCTGAGCCTTTCCATTTTAAGTTT 59.988 40.000 0.00 0.00 0.00 2.66
1167 1211 2.677875 GCTTGCTGGGGTTCCCTG 60.678 66.667 7.87 5.58 45.70 4.45
1179 1223 3.955543 TTCCCTGGGGGCGAAATGC 62.956 63.158 14.00 0.00 43.94 3.56
1254 1298 3.089284 TCCTAAGACTGATCGCTGTTGA 58.911 45.455 0.00 0.00 0.00 3.18
1316 1360 0.679505 GGGAGTGCGCATATGGAGTA 59.320 55.000 15.91 0.00 0.00 2.59
1342 1386 2.822561 TCGGGATGCTATTTGTTTTGCA 59.177 40.909 0.00 0.00 39.83 4.08
1350 1394 5.414360 TGCTATTTGTTTTGCACAACTTGA 58.586 33.333 16.21 3.52 45.54 3.02
1351 1395 5.871524 TGCTATTTGTTTTGCACAACTTGAA 59.128 32.000 16.21 9.10 45.54 2.69
1386 1430 4.217118 GCACCCCTTGACATGAATATCATC 59.783 45.833 0.00 0.00 34.28 2.92
1437 1481 5.752036 TCAGAACCTGAGAAGATTGATGT 57.248 39.130 0.00 0.00 35.39 3.06
1457 1501 9.562583 TTGATGTAATGTTAAGCGTTTATTTCC 57.437 29.630 0.00 0.00 0.00 3.13
1520 1564 6.094325 TGTTGGGCTTAGGAAAATTATGTACG 59.906 38.462 0.00 0.00 0.00 3.67
1522 1566 6.416415 TGGGCTTAGGAAAATTATGTACGAA 58.584 36.000 0.00 0.00 0.00 3.85
1557 1601 6.463995 TTTACTCCTCACAAACAATGCTTT 57.536 33.333 0.00 0.00 0.00 3.51
1571 1615 6.822667 ACAATGCTTTATGTTGAGACATGA 57.177 33.333 0.00 0.00 45.80 3.07
1603 1647 0.105964 ATGATGCAACATGCCATGGC 59.894 50.000 30.54 30.54 44.23 4.40
1715 1759 5.220931 GGTGAGCCTTCTTGTATTAAGCATG 60.221 44.000 0.00 0.00 0.00 4.06
1739 1783 7.969314 TGTTTTTGCTCCTTTAAATTCACAAC 58.031 30.769 0.00 0.00 0.00 3.32
1748 1792 6.266786 TCCTTTAAATTCACAACCTTCTTCCC 59.733 38.462 0.00 0.00 0.00 3.97
1761 1805 1.289160 TCTTCCCTGAAGACCATGGG 58.711 55.000 18.09 0.00 42.78 4.00
1763 1807 2.696864 TCCCTGAAGACCATGGGAC 58.303 57.895 18.09 9.91 43.20 4.46
1777 1821 1.757682 TGGGACAACTGACAACCAAC 58.242 50.000 0.00 0.00 31.92 3.77
1780 1824 1.597663 GGACAACTGACAACCAACTCG 59.402 52.381 0.00 0.00 0.00 4.18
1799 1843 8.886719 CCAACTCGTATAGTCGTATATATGGAA 58.113 37.037 2.10 0.00 37.50 3.53
1828 1872 7.340999 TCCCTTTTTACATTCTTTAGTATGGCC 59.659 37.037 0.00 0.00 0.00 5.36
1836 1884 8.034313 ACATTCTTTAGTATGGCCTTCAGATA 57.966 34.615 3.32 0.00 0.00 1.98
1837 1885 8.494433 ACATTCTTTAGTATGGCCTTCAGATAA 58.506 33.333 3.32 0.00 0.00 1.75
1838 1886 9.342308 CATTCTTTAGTATGGCCTTCAGATAAA 57.658 33.333 3.32 1.62 0.00 1.40
1858 1906 9.343539 AGATAAAATGGTTAGTTGCTCTATTCC 57.656 33.333 0.00 0.00 0.00 3.01
1867 1915 5.033589 AGTTGCTCTATTCCTGATTCTGG 57.966 43.478 3.27 3.27 0.00 3.86
1889 1937 5.181748 GGTAGGATAGCTATTCTTGGCATG 58.818 45.833 19.84 0.00 35.86 4.06
1908 1956 3.804786 TGCAAGGCATGTTCCATAATG 57.195 42.857 0.00 0.00 31.71 1.90
1914 1962 6.400568 CAAGGCATGTTCCATAATGTTCTTT 58.599 36.000 0.00 0.00 0.00 2.52
1915 1963 5.969423 AGGCATGTTCCATAATGTTCTTTG 58.031 37.500 0.00 0.00 0.00 2.77
1944 1992 6.042093 TCACAGTTATCTTCCTGGGTGATATC 59.958 42.308 0.00 0.00 33.73 1.63
1950 1998 5.418692 TCTTCCTGGGTGATATCCTCTTA 57.581 43.478 0.00 0.00 0.00 2.10
1954 2003 7.350921 TCTTCCTGGGTGATATCCTCTTATTTT 59.649 37.037 0.00 0.00 0.00 1.82
1965 2014 5.964958 TCCTCTTATTTTTGCTGGTTCTG 57.035 39.130 0.00 0.00 0.00 3.02
1966 2015 5.385198 TCCTCTTATTTTTGCTGGTTCTGT 58.615 37.500 0.00 0.00 0.00 3.41
1967 2016 5.241506 TCCTCTTATTTTTGCTGGTTCTGTG 59.758 40.000 0.00 0.00 0.00 3.66
1968 2017 5.452078 TCTTATTTTTGCTGGTTCTGTGG 57.548 39.130 0.00 0.00 0.00 4.17
1969 2018 2.531522 ATTTTTGCTGGTTCTGTGGC 57.468 45.000 0.00 0.00 0.00 5.01
1970 2019 0.463620 TTTTTGCTGGTTCTGTGGCC 59.536 50.000 0.00 0.00 0.00 5.36
1971 2020 0.685785 TTTTGCTGGTTCTGTGGCCA 60.686 50.000 0.00 0.00 0.00 5.36
1974 2023 3.160585 CTGGTTCTGTGGCCAGGA 58.839 61.111 5.11 4.66 46.27 3.86
1975 2024 1.455849 CTGGTTCTGTGGCCAGGAA 59.544 57.895 5.11 11.64 46.27 3.36
1976 2025 0.178992 CTGGTTCTGTGGCCAGGAAA 60.179 55.000 18.96 6.15 46.27 3.13
1977 2026 0.467290 TGGTTCTGTGGCCAGGAAAC 60.467 55.000 22.54 22.54 39.31 2.78
1978 2027 0.178990 GGTTCTGTGGCCAGGAAACT 60.179 55.000 22.22 0.00 46.44 2.66
1979 2028 1.239347 GTTCTGTGGCCAGGAAACTC 58.761 55.000 18.96 7.05 40.21 3.01
1980 2029 0.843309 TTCTGTGGCCAGGAAACTCA 59.157 50.000 5.11 0.00 40.21 3.41
1981 2030 0.843309 TCTGTGGCCAGGAAACTCAA 59.157 50.000 5.11 0.00 40.21 3.02
1982 2031 0.954452 CTGTGGCCAGGAAACTCAAC 59.046 55.000 5.11 0.00 40.21 3.18
1983 2032 0.257328 TGTGGCCAGGAAACTCAACA 59.743 50.000 5.11 0.00 40.21 3.33
1984 2033 1.341482 TGTGGCCAGGAAACTCAACAA 60.341 47.619 5.11 0.00 40.21 2.83
1985 2034 1.338020 GTGGCCAGGAAACTCAACAAG 59.662 52.381 5.11 0.00 40.21 3.16
1986 2035 1.214175 TGGCCAGGAAACTCAACAAGA 59.786 47.619 0.00 0.00 40.21 3.02
1987 2036 1.609072 GGCCAGGAAACTCAACAAGAC 59.391 52.381 0.00 0.00 40.21 3.01
1988 2037 2.576615 GCCAGGAAACTCAACAAGACT 58.423 47.619 0.00 0.00 40.21 3.24
1989 2038 3.496160 GGCCAGGAAACTCAACAAGACTA 60.496 47.826 0.00 0.00 40.21 2.59
1990 2039 4.327680 GCCAGGAAACTCAACAAGACTAT 58.672 43.478 0.00 0.00 40.21 2.12
1991 2040 4.393371 GCCAGGAAACTCAACAAGACTATC 59.607 45.833 0.00 0.00 40.21 2.08
1992 2041 4.938226 CCAGGAAACTCAACAAGACTATCC 59.062 45.833 0.00 0.00 40.21 2.59
1993 2042 4.627467 CAGGAAACTCAACAAGACTATCCG 59.373 45.833 0.00 0.00 40.21 4.18
1994 2043 4.527038 AGGAAACTCAACAAGACTATCCGA 59.473 41.667 0.00 0.00 32.90 4.55
1995 2044 5.187967 AGGAAACTCAACAAGACTATCCGAT 59.812 40.000 0.00 0.00 32.90 4.18
1996 2045 6.380274 AGGAAACTCAACAAGACTATCCGATA 59.620 38.462 0.00 0.00 32.90 2.92
1997 2046 6.476053 GGAAACTCAACAAGACTATCCGATAC 59.524 42.308 0.00 0.00 0.00 2.24
1998 2047 6.777213 AACTCAACAAGACTATCCGATACT 57.223 37.500 0.00 0.00 0.00 2.12
1999 2048 6.777213 ACTCAACAAGACTATCCGATACTT 57.223 37.500 0.00 0.00 0.00 2.24
2000 2049 7.171630 ACTCAACAAGACTATCCGATACTTT 57.828 36.000 0.00 0.00 0.00 2.66
2001 2050 7.612677 ACTCAACAAGACTATCCGATACTTTT 58.387 34.615 0.00 0.00 0.00 2.27
2002 2051 8.095169 ACTCAACAAGACTATCCGATACTTTTT 58.905 33.333 0.00 0.00 0.00 1.94
2003 2052 9.582431 CTCAACAAGACTATCCGATACTTTTTA 57.418 33.333 0.00 0.00 0.00 1.52
2004 2053 9.582431 TCAACAAGACTATCCGATACTTTTTAG 57.418 33.333 0.00 0.00 0.00 1.85
2005 2054 9.367444 CAACAAGACTATCCGATACTTTTTAGT 57.633 33.333 0.00 0.00 0.00 2.24
2006 2055 9.939802 AACAAGACTATCCGATACTTTTTAGTT 57.060 29.630 0.00 0.00 0.00 2.24
2125 2174 1.587088 GGCTTTCAATGGCATCGCG 60.587 57.895 0.00 0.00 0.00 5.87
2312 2361 9.865321 TTGTTATGTACCTACTTGTAAGATCAC 57.135 33.333 0.00 0.00 0.00 3.06
2313 2362 9.027202 TGTTATGTACCTACTTGTAAGATCACA 57.973 33.333 0.00 0.00 0.00 3.58
2333 2382 1.488393 AGTCTTCCTGCTAAGCCCATC 59.512 52.381 0.00 0.00 0.00 3.51
2337 2386 0.687757 TCCTGCTAAGCCCATCGACT 60.688 55.000 0.00 0.00 0.00 4.18
2347 2396 6.128526 GCTAAGCCCATCGACTTTATTCATAC 60.129 42.308 0.00 0.00 0.00 2.39
2371 2420 7.597386 ACTTCAATCCTCTTTCTTATGTTTGC 58.403 34.615 0.00 0.00 0.00 3.68
2410 2462 8.969260 TCTAATCATTCAGTTGATGCATACTT 57.031 30.769 0.00 0.00 36.48 2.24
2411 2463 9.399797 TCTAATCATTCAGTTGATGCATACTTT 57.600 29.630 0.00 0.00 36.48 2.66
2417 2469 5.559770 TCAGTTGATGCATACTTTTGAGGA 58.440 37.500 0.00 0.00 0.00 3.71
2421 2473 7.652909 CAGTTGATGCATACTTTTGAGGAAAAA 59.347 33.333 0.00 0.00 36.34 1.94
2511 2563 1.821136 GCTCCAGCCTTATGCAACTTT 59.179 47.619 0.00 0.00 44.83 2.66
2559 2611 9.442047 GGAACTGAGAATCTAATTTTCTTCTCA 57.558 33.333 17.88 17.88 46.84 3.27
2781 2833 6.239629 GGGCTATAGGATATGGTATTGCTACC 60.240 46.154 1.04 0.00 46.65 3.18
2889 2941 6.208797 AGAGTATTTTCCAGGTTACTTTTGCC 59.791 38.462 0.00 0.00 0.00 4.52
2894 2946 2.156098 CCAGGTTACTTTTGCCGCTTA 58.844 47.619 0.00 0.00 0.00 3.09
2955 3007 2.308570 TCTTTATGAGGCCAGGAGCAAA 59.691 45.455 5.01 0.00 46.50 3.68
3023 3075 4.134563 AGGTACTGTACTGCCTGTTTTTG 58.865 43.478 16.79 0.00 37.18 2.44
3082 3134 8.445493 ACGTTACCTTTATTTACATGTTGTAGC 58.555 33.333 2.30 0.00 33.92 3.58
3083 3135 8.662141 CGTTACCTTTATTTACATGTTGTAGCT 58.338 33.333 2.30 0.00 33.92 3.32
3084 3136 9.983804 GTTACCTTTATTTACATGTTGTAGCTC 57.016 33.333 2.30 0.00 33.92 4.09
3085 3137 7.625828 ACCTTTATTTACATGTTGTAGCTCC 57.374 36.000 2.30 0.00 33.92 4.70
3086 3138 7.172342 ACCTTTATTTACATGTTGTAGCTCCA 58.828 34.615 2.30 0.00 33.92 3.86
3087 3139 7.668052 ACCTTTATTTACATGTTGTAGCTCCAA 59.332 33.333 2.30 0.00 33.92 3.53
3088 3140 8.686334 CCTTTATTTACATGTTGTAGCTCCAAT 58.314 33.333 2.30 0.00 33.92 3.16
3090 3142 9.853555 TTTATTTACATGTTGTAGCTCCAATTG 57.146 29.630 2.30 0.00 33.92 2.32
3091 3143 7.701539 ATTTACATGTTGTAGCTCCAATTGA 57.298 32.000 2.30 0.00 33.92 2.57
3092 3144 7.517614 TTTACATGTTGTAGCTCCAATTGAA 57.482 32.000 2.30 0.00 33.92 2.69
3093 3145 5.633830 ACATGTTGTAGCTCCAATTGAAG 57.366 39.130 7.12 0.00 0.00 3.02
3094 3146 5.072741 ACATGTTGTAGCTCCAATTGAAGT 58.927 37.500 7.12 0.00 0.00 3.01
3095 3147 6.237901 ACATGTTGTAGCTCCAATTGAAGTA 58.762 36.000 7.12 0.00 0.00 2.24
3096 3148 6.714810 ACATGTTGTAGCTCCAATTGAAGTAA 59.285 34.615 7.12 0.00 0.00 2.24
3097 3149 7.394359 ACATGTTGTAGCTCCAATTGAAGTAAT 59.606 33.333 7.12 0.00 0.00 1.89
3110 3162 3.261580 TGAAGTAATCATGTCCGTGCTG 58.738 45.455 0.00 0.00 31.50 4.41
3232 3367 3.307550 GGGAAGTTGGAGAGAAAGGTACC 60.308 52.174 2.73 2.73 0.00 3.34
3233 3368 3.326880 GGAAGTTGGAGAGAAAGGTACCA 59.673 47.826 15.94 0.00 0.00 3.25
3235 3370 3.588569 AGTTGGAGAGAAAGGTACCACT 58.411 45.455 15.94 10.25 0.00 4.00
3249 3384 5.855045 AGGTACCACTGAGACACTAAAAAG 58.145 41.667 15.94 0.00 0.00 2.27
3320 3460 6.288941 TCCTATGGTTTTGTATGAAGTCGA 57.711 37.500 0.00 0.00 0.00 4.20
3324 3464 6.817765 ATGGTTTTGTATGAAGTCGACAAT 57.182 33.333 19.50 10.69 33.33 2.71
3342 3485 6.479990 TCGACAATGAATGTTCACTCATATCC 59.520 38.462 0.00 0.00 44.12 2.59
3383 3526 1.834263 AGGTTCTTCGATAAGGCAGCT 59.166 47.619 0.00 0.00 33.22 4.24
3404 3547 5.884792 AGCTGTTATTTCTGATCTTCCCTTG 59.115 40.000 0.00 0.00 0.00 3.61
3516 3659 2.349886 GCGACTGGAGTATTCTTTGCTG 59.650 50.000 0.00 0.00 0.00 4.41
3863 4006 4.467084 TTCGTCATCGCTGGGGCC 62.467 66.667 0.00 0.00 36.96 5.80
4217 4366 6.904463 TTGAAGTGTATATATAGGCCACGA 57.096 37.500 5.01 0.00 0.00 4.35
4356 4505 3.448686 CCGCAAAGAGTGTCGATCTTAT 58.551 45.455 0.37 0.00 35.98 1.73
4521 5831 3.483421 CTGATGGATTGATTAGCTGGCA 58.517 45.455 0.00 0.00 0.00 4.92
4522 5832 4.079970 CTGATGGATTGATTAGCTGGCAT 58.920 43.478 0.00 0.00 0.00 4.40
4751 6934 7.662669 GTCTAACCCAAAACAGTATTAAGTGGA 59.337 37.037 0.00 0.00 0.00 4.02
4834 7017 2.586648 AAATTGGAGAACCGGCTCTT 57.413 45.000 9.15 0.00 39.42 2.85
4947 7130 8.047310 TCTAGAGAGTTTGTGAAAGTTTCCTTT 58.953 33.333 13.01 0.00 43.58 3.11
5038 7221 5.905331 TCTACCACATGGATAGATGTTCCTT 59.095 40.000 4.53 0.00 34.18 3.36
5039 7222 5.041191 ACCACATGGATAGATGTTCCTTC 57.959 43.478 4.53 0.00 34.18 3.46
5164 7347 7.797617 AGGTGGTTAGTGGGGATCTTTATATTA 59.202 37.037 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.536917 CTATGGTCTCGGGCGGCA 61.537 66.667 12.47 0.00 0.00 5.69
79 81 1.554583 GGCGGAGGAAGGAAAGAGGT 61.555 60.000 0.00 0.00 0.00 3.85
108 110 1.082019 TGTGGGGACATGGCTAGGA 59.918 57.895 0.00 0.00 46.14 2.94
119 124 2.444004 TAGTAGCGGTGGTGTGGGGA 62.444 60.000 0.00 0.00 0.00 4.81
126 131 0.737219 GATCGTGTAGTAGCGGTGGT 59.263 55.000 0.00 0.00 0.00 4.16
129 134 1.872313 GCTAGATCGTGTAGTAGCGGT 59.128 52.381 0.00 0.00 0.00 5.68
146 151 0.331954 AGGAGGAAGAGACGGTGCTA 59.668 55.000 0.00 0.00 0.00 3.49
224 229 2.685380 CGGCACCTCCTCCTCCTT 60.685 66.667 0.00 0.00 0.00 3.36
239 250 0.033011 TCCTCTTCCTCCTTCCTCGG 60.033 60.000 0.00 0.00 0.00 4.63
242 253 1.290732 CTCCTCCTCTTCCTCCTTCCT 59.709 57.143 0.00 0.00 0.00 3.36
251 262 0.032615 TCCTGCTCCTCCTCCTCTTC 60.033 60.000 0.00 0.00 0.00 2.87
252 263 0.032217 CTCCTGCTCCTCCTCCTCTT 60.032 60.000 0.00 0.00 0.00 2.85
253 264 1.620259 CTCCTGCTCCTCCTCCTCT 59.380 63.158 0.00 0.00 0.00 3.69
302 341 2.607750 TGGCGCCTCCTTCTCCTT 60.608 61.111 29.70 0.00 35.26 3.36
355 394 1.908793 CACACCCACGTCCTCCTCT 60.909 63.158 0.00 0.00 0.00 3.69
397 436 1.517832 CTCCGAGCGGATGGAGTTT 59.482 57.895 12.54 0.00 45.48 2.66
440 479 0.961019 GCCTTCATCTGTTGCCAACA 59.039 50.000 10.31 10.31 39.52 3.33
443 482 1.675310 CCGCCTTCATCTGTTGCCA 60.675 57.895 0.00 0.00 0.00 4.92
463 502 2.041405 GGAGCCTAGGCCTCCTGT 60.041 66.667 30.18 15.70 43.17 4.00
515 554 4.444838 TTGTCGACGATGCCCGGG 62.445 66.667 19.09 19.09 43.93 5.73
557 597 9.961264 ATGCAGAGTATATAGCTAAGTACTACA 57.039 33.333 16.81 15.40 0.00 2.74
602 642 6.663093 ACAGACAAGTCTCTCATACTCAATCT 59.337 38.462 0.00 0.00 37.98 2.40
604 644 6.210385 ACACAGACAAGTCTCTCATACTCAAT 59.790 38.462 0.00 0.00 37.98 2.57
605 645 5.536538 ACACAGACAAGTCTCTCATACTCAA 59.463 40.000 0.00 0.00 37.98 3.02
609 649 6.745159 TCTACACAGACAAGTCTCTCATAC 57.255 41.667 0.00 0.00 37.98 2.39
619 659 8.777865 TTCATATTTCCTTCTACACAGACAAG 57.222 34.615 0.00 0.00 0.00 3.16
624 664 9.003658 ACACTTTTCATATTTCCTTCTACACAG 57.996 33.333 0.00 0.00 0.00 3.66
629 669 7.617225 TCGGACACTTTTCATATTTCCTTCTA 58.383 34.615 0.00 0.00 0.00 2.10
644 684 2.496899 AGGCATTGATCGGACACTTT 57.503 45.000 0.00 0.00 0.00 2.66
645 685 2.236146 TGTAGGCATTGATCGGACACTT 59.764 45.455 0.00 0.00 0.00 3.16
646 686 1.831106 TGTAGGCATTGATCGGACACT 59.169 47.619 0.00 0.00 0.00 3.55
650 690 4.455533 GCATATTTGTAGGCATTGATCGGA 59.544 41.667 0.00 0.00 0.00 4.55
654 694 3.507233 CGGGCATATTTGTAGGCATTGAT 59.493 43.478 0.00 0.00 0.00 2.57
658 698 1.423541 TCCGGGCATATTTGTAGGCAT 59.576 47.619 0.00 0.00 0.00 4.40
681 721 4.676586 CAAACCCGCGAACGCACC 62.677 66.667 18.69 0.00 42.06 5.01
684 724 2.127383 CTTCAAACCCGCGAACGC 60.127 61.111 8.23 9.20 38.22 4.84
687 727 2.981350 GCCCTTCAAACCCGCGAA 60.981 61.111 8.23 0.00 0.00 4.70
692 732 0.902984 AAATCCGGCCCTTCAAACCC 60.903 55.000 0.00 0.00 0.00 4.11
693 733 0.246360 CAAATCCGGCCCTTCAAACC 59.754 55.000 0.00 0.00 0.00 3.27
700 740 1.228862 ACTTTGCAAATCCGGCCCT 60.229 52.632 13.23 0.00 0.00 5.19
714 754 2.093235 GGAGCATCTACAGCTGGACTTT 60.093 50.000 19.93 0.00 43.58 2.66
721 761 2.091610 TCTGGTAGGAGCATCTACAGCT 60.092 50.000 15.27 0.00 46.82 4.24
735 775 1.338200 GGCTGGTGTTGACTCTGGTAG 60.338 57.143 0.00 0.00 0.00 3.18
738 778 1.669115 CGGCTGGTGTTGACTCTGG 60.669 63.158 0.00 0.00 0.00 3.86
739 779 2.320587 GCGGCTGGTGTTGACTCTG 61.321 63.158 0.00 0.00 0.00 3.35
740 780 2.031163 GCGGCTGGTGTTGACTCT 59.969 61.111 0.00 0.00 0.00 3.24
741 781 3.050275 GGCGGCTGGTGTTGACTC 61.050 66.667 0.00 0.00 0.00 3.36
742 782 2.902423 TTTGGCGGCTGGTGTTGACT 62.902 55.000 11.43 0.00 0.00 3.41
743 783 1.805428 ATTTGGCGGCTGGTGTTGAC 61.805 55.000 11.43 0.00 0.00 3.18
744 784 1.523154 GATTTGGCGGCTGGTGTTGA 61.523 55.000 11.43 0.00 0.00 3.18
745 785 1.080569 GATTTGGCGGCTGGTGTTG 60.081 57.895 11.43 0.00 0.00 3.33
746 786 0.899717 ATGATTTGGCGGCTGGTGTT 60.900 50.000 11.43 0.00 0.00 3.32
747 787 1.304381 ATGATTTGGCGGCTGGTGT 60.304 52.632 11.43 0.00 0.00 4.16
748 788 1.140161 CATGATTTGGCGGCTGGTG 59.860 57.895 11.43 0.00 0.00 4.17
749 789 2.713967 GCATGATTTGGCGGCTGGT 61.714 57.895 11.43 0.00 0.00 4.00
750 790 2.105528 GCATGATTTGGCGGCTGG 59.894 61.111 11.43 0.00 0.00 4.85
756 796 3.928375 ACTCAAAATTCGCATGATTTGGC 59.072 39.130 0.00 0.00 34.39 4.52
757 797 6.301108 CAAACTCAAAATTCGCATGATTTGG 58.699 36.000 0.00 0.00 34.39 3.28
758 798 5.786574 GCAAACTCAAAATTCGCATGATTTG 59.213 36.000 0.00 0.00 34.81 2.32
759 799 5.697633 AGCAAACTCAAAATTCGCATGATTT 59.302 32.000 0.00 0.00 0.00 2.17
760 800 5.232463 AGCAAACTCAAAATTCGCATGATT 58.768 33.333 0.00 0.00 0.00 2.57
761 801 4.813027 AGCAAACTCAAAATTCGCATGAT 58.187 34.783 0.00 0.00 0.00 2.45
762 802 4.241590 AGCAAACTCAAAATTCGCATGA 57.758 36.364 0.00 0.00 0.00 3.07
763 803 5.164061 GGTTAGCAAACTCAAAATTCGCATG 60.164 40.000 0.00 0.00 35.81 4.06
764 804 4.923281 GGTTAGCAAACTCAAAATTCGCAT 59.077 37.500 0.00 0.00 35.81 4.73
765 805 4.202060 TGGTTAGCAAACTCAAAATTCGCA 60.202 37.500 0.00 0.00 35.81 5.10
766 806 4.148174 GTGGTTAGCAAACTCAAAATTCGC 59.852 41.667 0.00 0.00 35.81 4.70
767 807 5.277825 TGTGGTTAGCAAACTCAAAATTCG 58.722 37.500 0.00 0.00 35.81 3.34
768 808 6.701400 ACATGTGGTTAGCAAACTCAAAATTC 59.299 34.615 0.00 0.00 35.81 2.17
769 809 6.581712 ACATGTGGTTAGCAAACTCAAAATT 58.418 32.000 0.00 0.00 35.81 1.82
770 810 6.160576 ACATGTGGTTAGCAAACTCAAAAT 57.839 33.333 0.00 0.00 35.81 1.82
771 811 5.590530 ACATGTGGTTAGCAAACTCAAAA 57.409 34.783 0.00 0.00 35.81 2.44
772 812 5.009210 GGTACATGTGGTTAGCAAACTCAAA 59.991 40.000 9.11 0.00 35.81 2.69
773 813 4.517453 GGTACATGTGGTTAGCAAACTCAA 59.483 41.667 9.11 0.00 35.81 3.02
774 814 4.069304 GGTACATGTGGTTAGCAAACTCA 58.931 43.478 9.11 0.00 35.81 3.41
775 815 4.069304 TGGTACATGTGGTTAGCAAACTC 58.931 43.478 9.11 0.00 35.81 3.01
776 816 4.093472 TGGTACATGTGGTTAGCAAACT 57.907 40.909 9.11 0.00 35.81 2.66
801 841 1.315257 ATGATTTGACGGCTGGCACC 61.315 55.000 0.00 0.00 0.00 5.01
802 842 0.179156 CATGATTTGACGGCTGGCAC 60.179 55.000 0.00 0.00 0.00 5.01
803 843 1.314534 CCATGATTTGACGGCTGGCA 61.315 55.000 0.00 0.00 0.00 4.92
804 844 1.315257 ACCATGATTTGACGGCTGGC 61.315 55.000 0.00 0.00 0.00 4.85
812 852 8.000127 TGATCCATTCTATCAACCATGATTTGA 59.000 33.333 10.93 10.93 43.89 2.69
826 866 3.242867 TCCGGCTTCTGATCCATTCTAT 58.757 45.455 0.00 0.00 0.00 1.98
828 868 1.415659 CTCCGGCTTCTGATCCATTCT 59.584 52.381 0.00 0.00 0.00 2.40
856 896 3.110178 GGAGAAACCACGCGACGG 61.110 66.667 15.93 16.02 38.79 4.79
989 1033 2.548067 CCACCGAAAATATCCTCTCCCG 60.548 54.545 0.00 0.00 0.00 5.14
1010 1054 1.002011 GGTCTGCTTTGGTCCCTCC 60.002 63.158 0.00 0.00 0.00 4.30
1070 1114 5.597182 AGTTAGATGTACCTTGGCGAGAATA 59.403 40.000 2.43 0.00 0.00 1.75
1078 1122 3.197766 TCTGCCAGTTAGATGTACCTTGG 59.802 47.826 0.00 0.00 0.00 3.61
1095 1139 2.818132 CTCAGGGTCGGATCTGCC 59.182 66.667 0.00 1.48 0.00 4.85
1142 1186 0.252375 ACCCCAGCAAGCAAATCCAT 60.252 50.000 0.00 0.00 0.00 3.41
1145 1189 0.247460 GGAACCCCAGCAAGCAAATC 59.753 55.000 0.00 0.00 0.00 2.17
1179 1223 1.068333 CCACCAACAATTTCTGCTCCG 60.068 52.381 0.00 0.00 0.00 4.63
1254 1298 0.255890 ATACAATGTTCCCCAGCGCT 59.744 50.000 2.64 2.64 0.00 5.92
1316 1360 6.701400 GCAAAACAAATAGCATCCCGAAATAT 59.299 34.615 0.00 0.00 0.00 1.28
1350 1394 6.268847 TGTCAAGGGGTGCAATTAACTTAATT 59.731 34.615 1.48 1.48 38.84 1.40
1351 1395 5.777732 TGTCAAGGGGTGCAATTAACTTAAT 59.222 36.000 0.00 0.00 0.00 1.40
1355 1399 3.237268 TGTCAAGGGGTGCAATTAACT 57.763 42.857 0.00 0.00 0.00 2.24
1360 1404 2.307496 TTCATGTCAAGGGGTGCAAT 57.693 45.000 0.00 0.00 0.00 3.56
1386 1430 1.134367 TCAACTGCCCTTCGTCTATCG 59.866 52.381 0.00 0.00 41.41 2.92
1400 1444 7.874940 TCAGGTTCTGAAATTTGTATCAACTG 58.125 34.615 0.00 0.00 37.57 3.16
1437 1481 5.950549 TGGGGGAAATAAACGCTTAACATTA 59.049 36.000 0.00 0.00 0.00 1.90
1457 1501 4.141181 TCCTTGATGAATCCATTACTGGGG 60.141 45.833 0.00 0.00 43.34 4.96
1520 1564 5.934625 TGAGGAGTAAATCAAAGACAGCTTC 59.065 40.000 0.00 0.00 31.82 3.86
1522 1566 5.221722 TGTGAGGAGTAAATCAAAGACAGCT 60.222 40.000 0.00 0.00 0.00 4.24
1557 1601 7.201947 CCTGATAGAAGGTCATGTCTCAACATA 60.202 40.741 0.00 0.00 36.97 2.29
1571 1615 4.164796 TGTTGCATCATCCTGATAGAAGGT 59.835 41.667 0.00 0.00 34.28 3.50
1639 1683 3.186702 CCTCTAGGTTTAAGCTCTGGC 57.813 52.381 0.00 0.00 39.06 4.85
1715 1759 7.279981 AGGTTGTGAATTTAAAGGAGCAAAAAC 59.720 33.333 0.00 0.00 0.00 2.43
1724 1768 6.267699 AGGGAAGAAGGTTGTGAATTTAAAGG 59.732 38.462 0.00 0.00 0.00 3.11
1732 1776 3.458118 TCTTCAGGGAAGAAGGTTGTGAA 59.542 43.478 6.22 0.00 44.37 3.18
1748 1792 2.038952 TCAGTTGTCCCATGGTCTTCAG 59.961 50.000 11.73 0.00 0.00 3.02
1761 1805 2.277084 ACGAGTTGGTTGTCAGTTGTC 58.723 47.619 0.00 0.00 0.00 3.18
1763 1807 5.227908 ACTATACGAGTTGGTTGTCAGTTG 58.772 41.667 0.00 0.00 33.13 3.16
1805 1849 9.788960 GAAGGCCATACTAAAGAATGTAAAAAG 57.211 33.333 5.01 0.00 0.00 2.27
1822 1866 7.582719 ACTAACCATTTTATCTGAAGGCCATA 58.417 34.615 5.01 0.00 0.00 2.74
1826 1870 6.036470 GCAACTAACCATTTTATCTGAAGGC 58.964 40.000 0.00 0.00 0.00 4.35
1828 1872 8.273780 AGAGCAACTAACCATTTTATCTGAAG 57.726 34.615 0.00 0.00 0.00 3.02
1836 1884 7.175104 TCAGGAATAGAGCAACTAACCATTTT 58.825 34.615 14.26 0.00 35.61 1.82
1837 1885 6.721318 TCAGGAATAGAGCAACTAACCATTT 58.279 36.000 14.26 0.03 35.61 2.32
1838 1886 6.313519 TCAGGAATAGAGCAACTAACCATT 57.686 37.500 14.26 1.00 35.61 3.16
1858 1906 7.716799 AGAATAGCTATCCTACCAGAATCAG 57.283 40.000 6.72 0.00 0.00 2.90
1867 1915 4.633565 GCATGCCAAGAATAGCTATCCTAC 59.366 45.833 6.36 0.00 0.00 3.18
1907 1955 8.567948 GGAAGATAACTGTGAAATCAAAGAACA 58.432 33.333 7.59 0.00 34.81 3.18
1908 1956 8.787852 AGGAAGATAACTGTGAAATCAAAGAAC 58.212 33.333 7.59 0.00 34.81 3.01
1914 1962 5.014123 ACCCAGGAAGATAACTGTGAAATCA 59.986 40.000 0.00 0.00 32.90 2.57
1915 1963 5.355350 CACCCAGGAAGATAACTGTGAAATC 59.645 44.000 0.00 0.00 32.90 2.17
1944 1992 5.464168 CACAGAACCAGCAAAAATAAGAGG 58.536 41.667 0.00 0.00 0.00 3.69
1950 1998 1.070601 GGCCACAGAACCAGCAAAAAT 59.929 47.619 0.00 0.00 0.00 1.82
1954 2003 2.600164 TGGCCACAGAACCAGCAA 59.400 55.556 0.00 0.00 0.00 3.91
1965 2014 1.338020 CTTGTTGAGTTTCCTGGCCAC 59.662 52.381 0.00 0.00 0.00 5.01
1966 2015 1.214175 TCTTGTTGAGTTTCCTGGCCA 59.786 47.619 4.71 4.71 0.00 5.36
1967 2016 1.609072 GTCTTGTTGAGTTTCCTGGCC 59.391 52.381 0.00 0.00 0.00 5.36
1968 2017 2.576615 AGTCTTGTTGAGTTTCCTGGC 58.423 47.619 0.00 0.00 0.00 4.85
1969 2018 4.938226 GGATAGTCTTGTTGAGTTTCCTGG 59.062 45.833 0.00 0.00 40.70 4.45
1970 2019 4.627467 CGGATAGTCTTGTTGAGTTTCCTG 59.373 45.833 0.00 0.00 41.29 3.86
1971 2020 4.527038 TCGGATAGTCTTGTTGAGTTTCCT 59.473 41.667 0.00 0.00 41.29 3.36
1972 2021 4.817517 TCGGATAGTCTTGTTGAGTTTCC 58.182 43.478 0.00 0.00 40.57 3.13
1973 2022 7.259161 AGTATCGGATAGTCTTGTTGAGTTTC 58.741 38.462 0.00 0.00 0.00 2.78
1974 2023 7.171630 AGTATCGGATAGTCTTGTTGAGTTT 57.828 36.000 0.00 0.00 0.00 2.66
1975 2024 6.777213 AGTATCGGATAGTCTTGTTGAGTT 57.223 37.500 0.00 0.00 0.00 3.01
1976 2025 6.777213 AAGTATCGGATAGTCTTGTTGAGT 57.223 37.500 5.84 0.00 0.00 3.41
1977 2026 8.480643 AAAAAGTATCGGATAGTCTTGTTGAG 57.519 34.615 5.84 0.00 0.00 3.02
1978 2027 9.582431 CTAAAAAGTATCGGATAGTCTTGTTGA 57.418 33.333 5.84 0.00 0.00 3.18
1979 2028 9.367444 ACTAAAAAGTATCGGATAGTCTTGTTG 57.633 33.333 5.84 3.79 0.00 3.33
1980 2029 9.939802 AACTAAAAAGTATCGGATAGTCTTGTT 57.060 29.630 5.84 7.24 0.00 2.83
2033 2082 9.524106 CTTCTAATGCATGCAAATTTGATCTAA 57.476 29.630 26.68 6.03 0.00 2.10
2034 2083 8.139350 CCTTCTAATGCATGCAAATTTGATCTA 58.861 33.333 26.68 6.36 0.00 1.98
2035 2084 6.984474 CCTTCTAATGCATGCAAATTTGATCT 59.016 34.615 26.68 0.80 0.00 2.75
2036 2085 6.982141 TCCTTCTAATGCATGCAAATTTGATC 59.018 34.615 26.68 5.64 0.00 2.92
2037 2086 6.880484 TCCTTCTAATGCATGCAAATTTGAT 58.120 32.000 26.68 2.56 0.00 2.57
2038 2087 6.283544 TCCTTCTAATGCATGCAAATTTGA 57.716 33.333 26.68 18.05 0.00 2.69
2039 2088 7.924412 AGTATCCTTCTAATGCATGCAAATTTG 59.076 33.333 26.68 16.00 0.00 2.32
2040 2089 7.924412 CAGTATCCTTCTAATGCATGCAAATTT 59.076 33.333 26.68 17.13 0.00 1.82
2041 2090 7.286087 TCAGTATCCTTCTAATGCATGCAAATT 59.714 33.333 26.68 17.91 0.00 1.82
2042 2091 6.774170 TCAGTATCCTTCTAATGCATGCAAAT 59.226 34.615 26.68 18.86 0.00 2.32
2043 2092 6.121590 TCAGTATCCTTCTAATGCATGCAAA 58.878 36.000 26.68 15.04 0.00 3.68
2044 2093 5.683681 TCAGTATCCTTCTAATGCATGCAA 58.316 37.500 26.68 8.38 0.00 4.08
2045 2094 5.294734 TCAGTATCCTTCTAATGCATGCA 57.705 39.130 25.04 25.04 0.00 3.96
2046 2095 6.429078 TCAATCAGTATCCTTCTAATGCATGC 59.571 38.462 11.82 11.82 0.00 4.06
2047 2096 7.660617 AGTCAATCAGTATCCTTCTAATGCATG 59.339 37.037 0.00 0.00 0.00 4.06
2048 2097 7.743749 AGTCAATCAGTATCCTTCTAATGCAT 58.256 34.615 0.00 0.00 0.00 3.96
2049 2098 7.129457 AGTCAATCAGTATCCTTCTAATGCA 57.871 36.000 0.00 0.00 0.00 3.96
2050 2099 9.547753 TTTAGTCAATCAGTATCCTTCTAATGC 57.452 33.333 0.00 0.00 0.00 3.56
2053 2102 9.886132 GGTTTTAGTCAATCAGTATCCTTCTAA 57.114 33.333 0.00 0.00 0.00 2.10
2104 2153 1.847818 CGATGCCATTGAAAGCCATG 58.152 50.000 0.00 0.00 0.00 3.66
2125 2174 5.233689 GCGGATATACACAACTAGGTTTGTC 59.766 44.000 2.06 0.00 37.62 3.18
2313 2362 1.488393 GATGGGCTTAGCAGGAAGACT 59.512 52.381 6.53 0.00 34.59 3.24
2333 2382 8.879342 AGAGGATTGAAGTATGAATAAAGTCG 57.121 34.615 0.00 0.00 0.00 4.18
2347 2396 6.744537 CGCAAACATAAGAAAGAGGATTGAAG 59.255 38.462 0.00 0.00 0.00 3.02
2390 2442 7.362315 CCTCAAAAGTATGCATCAACTGAATGA 60.362 37.037 0.19 7.18 0.00 2.57
2396 2448 6.899393 TTTCCTCAAAAGTATGCATCAACT 57.101 33.333 0.19 0.00 0.00 3.16
2511 2563 0.249955 TTGATGACGAGCATGAGCCA 59.750 50.000 0.00 0.00 43.56 4.75
2559 2611 5.045578 ACCAACAGCAGATAGATACAAACCT 60.046 40.000 0.00 0.00 0.00 3.50
2693 2745 6.652481 AGAAGTAATCACACCAAAGATGACAG 59.348 38.462 0.00 0.00 29.52 3.51
2781 2833 3.403277 GCCAGAGCTATGCACGTG 58.597 61.111 12.28 12.28 35.50 4.49
2889 2941 7.700322 TTCTAAGCTCATGTTCTTATAAGCG 57.300 36.000 7.67 0.00 34.99 4.68
2894 2946 7.718753 CAGGGATTTCTAAGCTCATGTTCTTAT 59.281 37.037 8.91 0.00 0.00 1.73
2955 3007 2.741878 CGGTCCTCTCTTGTGTGTGTTT 60.742 50.000 0.00 0.00 0.00 2.83
3009 3061 7.502895 TGAATAAGTAACCAAAAACAGGCAGTA 59.497 33.333 0.00 0.00 0.00 2.74
3075 3127 7.377766 TGATTACTTCAATTGGAGCTACAAC 57.622 36.000 15.19 0.00 32.39 3.32
3080 3132 5.591877 GGACATGATTACTTCAATTGGAGCT 59.408 40.000 14.03 4.08 38.03 4.09
3081 3133 5.504665 CGGACATGATTACTTCAATTGGAGC 60.505 44.000 14.03 0.00 38.03 4.70
3082 3134 5.586243 ACGGACATGATTACTTCAATTGGAG 59.414 40.000 12.50 12.50 38.03 3.86
3083 3135 5.353956 CACGGACATGATTACTTCAATTGGA 59.646 40.000 5.42 0.00 38.03 3.53
3084 3136 5.572211 CACGGACATGATTACTTCAATTGG 58.428 41.667 5.42 0.00 38.03 3.16
3085 3137 5.030295 GCACGGACATGATTACTTCAATTG 58.970 41.667 0.00 0.00 38.03 2.32
3086 3138 4.943705 AGCACGGACATGATTACTTCAATT 59.056 37.500 0.00 0.00 38.03 2.32
3087 3139 4.333649 CAGCACGGACATGATTACTTCAAT 59.666 41.667 0.00 0.00 38.03 2.57
3088 3140 3.684305 CAGCACGGACATGATTACTTCAA 59.316 43.478 0.00 0.00 38.03 2.69
3089 3141 3.056179 TCAGCACGGACATGATTACTTCA 60.056 43.478 0.00 0.00 39.12 3.02
3090 3142 3.521560 TCAGCACGGACATGATTACTTC 58.478 45.455 0.00 0.00 0.00 3.01
3091 3143 3.055819 ACTCAGCACGGACATGATTACTT 60.056 43.478 0.00 0.00 0.00 2.24
3092 3144 2.497675 ACTCAGCACGGACATGATTACT 59.502 45.455 0.00 0.00 0.00 2.24
3093 3145 2.893637 ACTCAGCACGGACATGATTAC 58.106 47.619 0.00 0.00 0.00 1.89
3094 3146 4.682787 CTTACTCAGCACGGACATGATTA 58.317 43.478 0.00 0.00 0.00 1.75
3095 3147 3.525537 CTTACTCAGCACGGACATGATT 58.474 45.455 0.00 0.00 0.00 2.57
3096 3148 3.170791 CTTACTCAGCACGGACATGAT 57.829 47.619 0.00 0.00 0.00 2.45
3097 3149 2.654749 CTTACTCAGCACGGACATGA 57.345 50.000 0.00 0.00 0.00 3.07
3232 3367 5.468072 ACTGCATCTTTTTAGTGTCTCAGTG 59.532 40.000 0.00 0.00 30.91 3.66
3233 3368 5.615289 ACTGCATCTTTTTAGTGTCTCAGT 58.385 37.500 0.00 0.00 0.00 3.41
3235 3370 8.621532 AATAACTGCATCTTTTTAGTGTCTCA 57.378 30.769 0.00 0.00 0.00 3.27
3249 3384 7.990541 TGCATTGTGATAAAATAACTGCATC 57.009 32.000 0.00 0.00 32.65 3.91
3270 3405 6.016360 AGCAATGACAGTAAAAGTATGTTGCA 60.016 34.615 0.00 0.00 0.00 4.08
3320 3460 6.666678 AGGGATATGAGTGAACATTCATTGT 58.333 36.000 15.61 7.52 38.48 2.71
3324 3464 7.293299 AGGATTAGGGATATGAGTGAACATTCA 59.707 37.037 2.79 2.79 34.20 2.57
3371 3514 4.811024 TCAGAAATAACAGCTGCCTTATCG 59.189 41.667 15.27 4.64 0.00 2.92
3383 3526 6.180472 GTCCAAGGGAAGATCAGAAATAACA 58.820 40.000 0.00 0.00 31.38 2.41
3516 3659 1.990563 GTGCATTTGTGAGATTGCAGC 59.009 47.619 0.00 0.00 44.99 5.25
3806 3949 1.603802 ACGATGCTTAATGGATTGCCG 59.396 47.619 0.00 0.00 36.79 5.69
4356 4505 6.730977 AGCCATTAGAAATGCTAGGAGGTATA 59.269 38.462 0.00 0.00 30.97 1.47
4521 5831 3.926616 ACACTAAAAGAGTACGCTGCAT 58.073 40.909 0.00 0.00 35.64 3.96
4522 5832 3.380479 ACACTAAAAGAGTACGCTGCA 57.620 42.857 0.00 0.00 35.64 4.41
4751 6934 7.118390 GCACTCACTCTTTTCATGTATACAAGT 59.882 37.037 10.14 4.00 0.00 3.16
4834 7017 4.199310 GCCTCAATAACTTCAGTGCCATA 58.801 43.478 0.00 0.00 0.00 2.74
4947 7130 1.066858 GCCTCTCGGTTCTCATGTTCA 60.067 52.381 0.00 0.00 0.00 3.18
5018 7201 4.103785 AGGAAGGAACATCTATCCATGTGG 59.896 45.833 0.00 0.00 39.55 4.17
5128 7311 5.206587 CCCACTAACCACCTAGTACATAGT 58.793 45.833 0.00 0.00 30.77 2.12


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

AutoCloner maintained by Alex Coulton.