Multiple sequence alignment - TraesCS5D01G012800

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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 TraesCS5D01G012800 chr5D 100.000 7210 0 0 1 7210 6998094 7005303 0.000000e+00 13315.0
1 TraesCS5D01G012800 chr5D 97.724 747 14 2 1 747 487588888 487589631 0.000000e+00 1282.0
2 TraesCS5D01G012800 chr5D 90.541 148 8 3 5968 6115 549240291 549240432 2.650000e-44 191.0
3 TraesCS5D01G012800 chr5A 91.167 4834 253 75 2433 7210 2866293 2871008 0.000000e+00 6401.0
4 TraesCS5D01G012800 chr5A 83.371 1329 113 44 763 2066 2864399 2865644 0.000000e+00 1131.0
5 TraesCS5D01G012800 chr5A 91.057 369 8 9 2063 2430 2865887 2866231 6.540000e-130 475.0
6 TraesCS5D01G012800 chrUn 93.769 3531 143 36 2734 6214 65440445 65436942 0.000000e+00 5230.0
7 TraesCS5D01G012800 chrUn 84.153 1180 90 48 894 2023 65442728 65441596 0.000000e+00 1053.0
8 TraesCS5D01G012800 chrUn 87.306 709 52 20 6528 7210 65436686 65435990 0.000000e+00 776.0
9 TraesCS5D01G012800 chrUn 90.305 361 28 2 2433 2786 65440857 65440497 3.940000e-127 466.0
10 TraesCS5D01G012800 chrUn 91.635 263 16 2 2062 2323 65441288 65441031 6.880000e-95 359.0
11 TraesCS5D01G012800 chrUn 89.189 148 9 5 5968 6115 28596814 28596674 2.070000e-40 178.0
12 TraesCS5D01G012800 chrUn 96.226 53 2 0 2734 2786 65440497 65440445 3.580000e-13 87.9
13 TraesCS5D01G012800 chr3D 96.929 749 19 4 1 747 594817219 594816473 0.000000e+00 1253.0
14 TraesCS5D01G012800 chr3D 89.189 148 10 3 5968 6115 510785135 510785276 5.750000e-41 180.0
15 TraesCS5D01G012800 chr6D 97.039 743 21 1 1 742 433304093 433304835 0.000000e+00 1249.0
16 TraesCS5D01G012800 chr6D 95.989 748 26 4 1 747 126848327 126847583 0.000000e+00 1212.0
17 TraesCS5D01G012800 chr4D 96.252 747 22 4 1 747 476863758 476864498 0.000000e+00 1219.0
18 TraesCS5D01G012800 chr1D 95.850 747 29 2 1 747 324704244 324703500 0.000000e+00 1206.0
19 TraesCS5D01G012800 chr2D 96.060 736 29 0 1 736 50495433 50496168 0.000000e+00 1199.0
20 TraesCS5D01G012800 chr2D 96.060 736 29 0 1 736 50520413 50521148 0.000000e+00 1199.0
21 TraesCS5D01G012800 chr2D 90.541 148 8 3 5968 6115 336917031 336916890 2.650000e-44 191.0
22 TraesCS5D01G012800 chr2D 89.865 148 7 5 5968 6115 193917240 193917379 4.440000e-42 183.0
23 TraesCS5D01G012800 chr7A 95.594 749 27 4 1 747 486230128 486230872 0.000000e+00 1195.0
24 TraesCS5D01G012800 chr3B 85.517 290 27 9 6697 6980 801589460 801589180 9.150000e-74 289.0
25 TraesCS5D01G012800 chr3B 80.000 320 37 13 6166 6464 801589783 801589470 2.040000e-50 211.0
26 TraesCS5D01G012800 chr3B 89.726 146 9 3 5968 6113 165341146 165341285 1.600000e-41 182.0
27 TraesCS5D01G012800 chr1A 81.416 339 48 11 3042 3372 566301753 566302084 5.550000e-66 263.0
28 TraesCS5D01G012800 chr7D 89.189 148 10 3 5968 6115 47173380 47173239 5.750000e-41 180.0
29 TraesCS5D01G012800 chr7D 88.514 148 11 3 5968 6115 461079124 461078983 2.670000e-39 174.0


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 TraesCS5D01G012800 chr5D 6998094 7005303 7209 False 13315.00 13315 100.000000 1 7210 1 chr5D.!!$F1 7209
1 TraesCS5D01G012800 chr5D 487588888 487589631 743 False 1282.00 1282 97.724000 1 747 1 chr5D.!!$F2 746
2 TraesCS5D01G012800 chr5A 2864399 2871008 6609 False 2669.00 6401 88.531667 763 7210 3 chr5A.!!$F1 6447
3 TraesCS5D01G012800 chrUn 65435990 65442728 6738 True 1328.65 5230 90.565667 894 7210 6 chrUn.!!$R2 6316
4 TraesCS5D01G012800 chr3D 594816473 594817219 746 True 1253.00 1253 96.929000 1 747 1 chr3D.!!$R1 746
5 TraesCS5D01G012800 chr6D 433304093 433304835 742 False 1249.00 1249 97.039000 1 742 1 chr6D.!!$F1 741
6 TraesCS5D01G012800 chr6D 126847583 126848327 744 True 1212.00 1212 95.989000 1 747 1 chr6D.!!$R1 746
7 TraesCS5D01G012800 chr4D 476863758 476864498 740 False 1219.00 1219 96.252000 1 747 1 chr4D.!!$F1 746
8 TraesCS5D01G012800 chr1D 324703500 324704244 744 True 1206.00 1206 95.850000 1 747 1 chr1D.!!$R1 746
9 TraesCS5D01G012800 chr2D 50495433 50496168 735 False 1199.00 1199 96.060000 1 736 1 chr2D.!!$F1 735
10 TraesCS5D01G012800 chr2D 50520413 50521148 735 False 1199.00 1199 96.060000 1 736 1 chr2D.!!$F2 735
11 TraesCS5D01G012800 chr7A 486230128 486230872 744 False 1195.00 1195 95.594000 1 747 1 chr7A.!!$F1 746
12 TraesCS5D01G012800 chr3B 801589180 801589783 603 True 250.00 289 82.758500 6166 6980 2 chr3B.!!$R1 814

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
542 545 0.674895 CTTGTCGCCAAGGAAGAGGG 60.675 60.000 0.00 0.00 43.62 4.30 F
1332 1400 0.031585 TACTTTCACTGCTCACGCGT 59.968 50.000 5.58 5.58 39.65 6.01 F
1865 1977 0.034896 GACAGTCGGACACCAATGGT 59.965 55.000 11.27 0.00 35.62 3.55 F
2024 2136 0.392193 CCAACTAGAGCCCTGCAGTG 60.392 60.000 13.81 1.33 0.00 3.66 F
2064 2185 1.273781 ACATTGGGGGAATTTCTGGGG 60.274 52.381 0.00 0.00 0.00 4.96 F
2786 3339 1.374505 CAATTTGGGCCAACCGCAG 60.375 57.895 20.79 3.68 44.64 5.18 F
4248 4863 0.749454 AGATTGATGCGTTCCAGGCC 60.749 55.000 0.00 0.00 0.00 5.19 F
4612 5227 0.032813 CCTGGAAGTGGCCATGGATT 60.033 55.000 18.40 3.57 37.30 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 1810 0.104120 TCAATCGGTGTGATAGCCCG 59.896 55.000 0.00 0.00 43.03 6.13 R
2782 3335 2.061028 GCAAGATTTGTTTTCCCTGCG 58.939 47.619 0.00 0.00 0.00 5.18 R
3813 4425 1.077265 CATGGAAGGGGCACAAGGT 59.923 57.895 0.00 0.00 0.00 3.50 R
3814 4426 2.353610 GCATGGAAGGGGCACAAGG 61.354 63.158 0.00 0.00 0.00 3.61 R
4056 4668 1.211457 CCCTGAGATTTGTCAGAGGGG 59.789 57.143 6.31 0.00 46.02 4.79 R
4281 4896 0.179189 GGAAGAAACCAAGCGCGATG 60.179 55.000 12.10 7.99 0.00 3.84 R
5220 5835 1.227943 GCAGCATAGCCCCATCGAA 60.228 57.895 0.00 0.00 0.00 3.71 R
6514 7223 0.040204 CCTGAAGGTTGGGCTGGAAT 59.960 55.000 0.00 0.00 0.00 3.01 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
106 108 1.067142 CGGGTCATCAAGGACGAAGAA 60.067 52.381 0.00 0.00 38.70 2.52
291 293 6.319658 GGCATGATGAATAAGAAGGACTCAAA 59.680 38.462 0.00 0.00 0.00 2.69
395 398 2.816087 GAGAAGCAAGCCAAGATGTTCA 59.184 45.455 0.00 0.00 0.00 3.18
445 448 0.827925 TAGAGATCGAGGCCGCCAAT 60.828 55.000 13.15 1.63 35.37 3.16
542 545 0.674895 CTTGTCGCCAAGGAAGAGGG 60.675 60.000 0.00 0.00 43.62 4.30
604 607 1.333931 GACGAGTGATCTATGGCGTCA 59.666 52.381 16.31 0.00 45.10 4.35
743 751 5.047802 CCAGCATGAACTGTGGTATTTTCTT 60.048 40.000 0.00 0.00 39.69 2.52
744 752 5.860182 CAGCATGAACTGTGGTATTTTCTTG 59.140 40.000 0.00 0.00 39.69 3.02
746 754 6.265196 AGCATGAACTGTGGTATTTTCTTGAA 59.735 34.615 0.00 0.00 0.00 2.69
747 755 6.922957 GCATGAACTGTGGTATTTTCTTGAAA 59.077 34.615 0.00 0.00 0.00 2.69
748 756 7.437862 GCATGAACTGTGGTATTTTCTTGAAAA 59.562 33.333 10.41 10.41 0.00 2.29
749 757 9.311916 CATGAACTGTGGTATTTTCTTGAAAAA 57.688 29.630 11.78 0.00 0.00 1.94
811 819 3.792401 AGTTTGGCATCGTATCATTCGA 58.208 40.909 0.00 0.00 41.45 3.71
831 839 7.801716 TTCGACCCTTATGATATTTTTGGAG 57.198 36.000 0.00 0.00 0.00 3.86
832 840 5.763204 TCGACCCTTATGATATTTTTGGAGC 59.237 40.000 0.00 0.00 0.00 4.70
833 841 5.765182 CGACCCTTATGATATTTTTGGAGCT 59.235 40.000 0.00 0.00 0.00 4.09
835 843 7.352079 ACCCTTATGATATTTTTGGAGCTTG 57.648 36.000 0.00 0.00 0.00 4.01
836 844 6.324770 ACCCTTATGATATTTTTGGAGCTTGG 59.675 38.462 0.00 0.00 0.00 3.61
837 845 6.550854 CCCTTATGATATTTTTGGAGCTTGGA 59.449 38.462 0.00 0.00 0.00 3.53
838 846 7.234166 CCCTTATGATATTTTTGGAGCTTGGAT 59.766 37.037 0.00 0.00 0.00 3.41
839 847 9.300681 CCTTATGATATTTTTGGAGCTTGGATA 57.699 33.333 0.00 0.00 0.00 2.59
842 850 8.945195 ATGATATTTTTGGAGCTTGGATATCA 57.055 30.769 4.83 13.52 38.57 2.15
843 851 8.945195 TGATATTTTTGGAGCTTGGATATCAT 57.055 30.769 4.83 0.00 32.87 2.45
844 852 9.017509 TGATATTTTTGGAGCTTGGATATCATC 57.982 33.333 4.83 0.00 32.87 2.92
845 853 8.945195 ATATTTTTGGAGCTTGGATATCATCA 57.055 30.769 4.83 0.00 0.00 3.07
846 854 7.850935 ATTTTTGGAGCTTGGATATCATCAT 57.149 32.000 4.83 0.00 0.00 2.45
847 855 6.889301 TTTTGGAGCTTGGATATCATCATC 57.111 37.500 4.83 0.00 0.00 2.92
848 856 5.571791 TTGGAGCTTGGATATCATCATCA 57.428 39.130 4.83 0.00 0.00 3.07
849 857 5.774102 TGGAGCTTGGATATCATCATCAT 57.226 39.130 4.83 0.00 0.00 2.45
850 858 5.742063 TGGAGCTTGGATATCATCATCATC 58.258 41.667 4.83 0.00 0.00 2.92
851 859 5.249852 TGGAGCTTGGATATCATCATCATCA 59.750 40.000 4.83 0.00 0.00 3.07
852 860 6.069615 TGGAGCTTGGATATCATCATCATCAT 60.070 38.462 4.83 0.00 0.00 2.45
853 861 6.483974 GGAGCTTGGATATCATCATCATCATC 59.516 42.308 4.83 0.00 0.00 2.92
854 862 6.958767 AGCTTGGATATCATCATCATCATCA 58.041 36.000 4.83 0.00 0.00 3.07
855 863 7.578203 AGCTTGGATATCATCATCATCATCAT 58.422 34.615 4.83 0.00 0.00 2.45
856 864 7.717436 AGCTTGGATATCATCATCATCATCATC 59.283 37.037 4.83 0.00 0.00 2.92
857 865 7.499232 GCTTGGATATCATCATCATCATCATCA 59.501 37.037 4.83 0.00 0.00 3.07
858 866 9.566432 CTTGGATATCATCATCATCATCATCAT 57.434 33.333 4.83 0.00 0.00 2.45
859 867 9.920946 TTGGATATCATCATCATCATCATCATT 57.079 29.630 4.83 0.00 0.00 2.57
860 868 9.342308 TGGATATCATCATCATCATCATCATTG 57.658 33.333 4.83 0.00 0.00 2.82
861 869 8.787852 GGATATCATCATCATCATCATCATTGG 58.212 37.037 4.83 0.00 0.00 3.16
862 870 9.561069 GATATCATCATCATCATCATCATTGGA 57.439 33.333 0.00 0.00 0.00 3.53
925 933 3.339731 TTGCGAAGGAAGTTGCCG 58.660 55.556 0.00 0.00 31.30 5.69
966 974 1.849823 CCCCTCCATCCTCCCCATC 60.850 68.421 0.00 0.00 0.00 3.51
978 987 1.630369 CTCCCCATCTCTCACCAAACA 59.370 52.381 0.00 0.00 0.00 2.83
979 988 1.630369 TCCCCATCTCTCACCAAACAG 59.370 52.381 0.00 0.00 0.00 3.16
993 1002 2.571653 CCAAACAGTCCTCCATCCAGTA 59.428 50.000 0.00 0.00 0.00 2.74
995 1004 2.930109 ACAGTCCTCCATCCAGTACT 57.070 50.000 0.00 0.00 0.00 2.73
996 1005 3.191888 ACAGTCCTCCATCCAGTACTT 57.808 47.619 0.00 0.00 0.00 2.24
997 1006 3.100671 ACAGTCCTCCATCCAGTACTTC 58.899 50.000 0.00 0.00 0.00 3.01
998 1007 2.432510 CAGTCCTCCATCCAGTACTTCC 59.567 54.545 0.00 0.00 0.00 3.46
999 1008 1.763545 GTCCTCCATCCAGTACTTCCC 59.236 57.143 0.00 0.00 0.00 3.97
1000 1009 1.132500 CCTCCATCCAGTACTTCCCC 58.868 60.000 0.00 0.00 0.00 4.81
1001 1010 1.625228 CCTCCATCCAGTACTTCCCCA 60.625 57.143 0.00 0.00 0.00 4.96
1002 1011 2.412591 CTCCATCCAGTACTTCCCCAT 58.587 52.381 0.00 0.00 0.00 4.00
1003 1012 2.370189 CTCCATCCAGTACTTCCCCATC 59.630 54.545 0.00 0.00 0.00 3.51
1004 1013 2.126882 CCATCCAGTACTTCCCCATCA 58.873 52.381 0.00 0.00 0.00 3.07
1005 1014 2.105477 CCATCCAGTACTTCCCCATCAG 59.895 54.545 0.00 0.00 0.00 2.90
1006 1015 1.204146 TCCAGTACTTCCCCATCAGC 58.796 55.000 0.00 0.00 0.00 4.26
1007 1016 0.179073 CCAGTACTTCCCCATCAGCG 60.179 60.000 0.00 0.00 0.00 5.18
1008 1017 0.179073 CAGTACTTCCCCATCAGCGG 60.179 60.000 0.00 0.00 0.00 5.52
1009 1018 1.523938 GTACTTCCCCATCAGCGGC 60.524 63.158 0.00 0.00 0.00 6.53
1010 1019 3.088941 TACTTCCCCATCAGCGGCG 62.089 63.158 0.51 0.51 0.00 6.46
1085 1125 1.445926 GGGCGCGCATCAACAAATT 60.446 52.632 34.42 0.00 0.00 1.82
1088 1128 1.620225 CGCGCATCAACAAATTCGC 59.380 52.632 8.75 0.00 39.26 4.70
1091 1145 0.171007 CGCATCAACAAATTCGCCCT 59.829 50.000 0.00 0.00 0.00 5.19
1094 1148 2.094675 CATCAACAAATTCGCCCTCCT 58.905 47.619 0.00 0.00 0.00 3.69
1120 1174 4.292178 GATCGCGCCCTCCTCCAG 62.292 72.222 0.00 0.00 0.00 3.86
1332 1400 0.031585 TACTTTCACTGCTCACGCGT 59.968 50.000 5.58 5.58 39.65 6.01
1343 1411 2.028766 CTCACGCGTGCCATTGCTAG 62.029 60.000 33.63 19.04 38.71 3.42
1355 1423 0.322456 ATTGCTAGTGCTTCCGCCAA 60.322 50.000 0.00 0.00 40.48 4.52
1380 1448 2.359900 GATTCCGCAAATGTCCTGTCT 58.640 47.619 0.00 0.00 0.00 3.41
1388 1466 2.756760 CAAATGTCCTGTCTTGGGGATG 59.243 50.000 0.00 0.00 33.89 3.51
1456 1541 4.840005 CCCCTCTTTCCCGCTCGC 62.840 72.222 0.00 0.00 0.00 5.03
1459 1544 4.840005 CTCTTTCCCGCTCGCCCC 62.840 72.222 0.00 0.00 0.00 5.80
1553 1640 4.416738 AGAAGAAGGCCGCCCTGC 62.417 66.667 5.55 0.00 41.90 4.85
1600 1690 2.231235 GCCAAACCGGTTGATTGAATCT 59.769 45.455 23.08 0.00 39.87 2.40
1606 1696 2.420022 CCGGTTGATTGAATCTCCACAC 59.580 50.000 6.73 0.00 0.00 3.82
1624 1714 2.820787 ACACGTCACAAAGGGTCAAAAA 59.179 40.909 0.00 0.00 0.00 1.94
1637 1727 6.306643 AGGGTCAAAAATTTTGTTTCCAGA 57.693 33.333 16.83 0.00 0.00 3.86
1692 1800 1.936656 GCATTCAGCTCACACACGAGA 60.937 52.381 0.00 0.00 41.15 4.04
1702 1810 3.334691 TCACACACGAGATCCCATTTTC 58.665 45.455 0.00 0.00 0.00 2.29
1710 1818 3.339141 GAGATCCCATTTTCGGGCTATC 58.661 50.000 0.00 0.00 46.92 2.08
1729 1837 1.208535 TCACACCGATTGATGTACCCC 59.791 52.381 0.00 0.00 0.00 4.95
1754 1862 5.914033 TGATGTGGAAGTATTAGCACCTAC 58.086 41.667 0.00 0.00 0.00 3.18
1773 1881 3.971245 ACCAAACCTTAGCTCAGAGAG 57.029 47.619 0.00 0.00 0.00 3.20
1792 1901 3.017442 GAGCAACCTTTCCCCTGTTATC 58.983 50.000 0.00 0.00 0.00 1.75
1803 1912 4.742012 TCCCCTGTTATCAGTAGGATCTC 58.258 47.826 5.95 0.00 37.33 2.75
1806 1915 4.021544 CCCTGTTATCAGTAGGATCTCTGC 60.022 50.000 0.00 0.00 39.82 4.26
1820 1929 3.542712 TCTCTGCGCAAACAATCTTTC 57.457 42.857 13.05 0.00 0.00 2.62
1865 1977 0.034896 GACAGTCGGACACCAATGGT 59.965 55.000 11.27 0.00 35.62 3.55
1909 2021 1.774110 TTGTTCAGGGCTTCTTTGCA 58.226 45.000 0.00 0.00 34.04 4.08
1964 2076 2.224426 TGAAGGTTTCAAGCTAAGGCGA 60.224 45.455 0.00 0.00 37.95 5.54
2023 2135 0.545309 TCCAACTAGAGCCCTGCAGT 60.545 55.000 13.81 0.00 0.00 4.40
2024 2136 0.392193 CCAACTAGAGCCCTGCAGTG 60.392 60.000 13.81 1.33 0.00 3.66
2064 2185 1.273781 ACATTGGGGGAATTTCTGGGG 60.274 52.381 0.00 0.00 0.00 4.96
2117 2501 5.624159 CATAATCTACTGGGCCAATTGAGA 58.376 41.667 8.04 8.21 0.00 3.27
2338 2730 3.202151 TCCCTCCCCAACATACATTTCTC 59.798 47.826 0.00 0.00 0.00 2.87
2341 2733 4.569653 CCTCCCCAACATACATTTCTCCAA 60.570 45.833 0.00 0.00 0.00 3.53
2344 2736 5.656416 TCCCCAACATACATTTCTCCAATTC 59.344 40.000 0.00 0.00 0.00 2.17
2346 2738 6.155049 CCCCAACATACATTTCTCCAATTCTT 59.845 38.462 0.00 0.00 0.00 2.52
2347 2739 7.310609 CCCCAACATACATTTCTCCAATTCTTT 60.311 37.037 0.00 0.00 0.00 2.52
2348 2740 8.096414 CCCAACATACATTTCTCCAATTCTTTT 58.904 33.333 0.00 0.00 0.00 2.27
2349 2741 9.492973 CCAACATACATTTCTCCAATTCTTTTT 57.507 29.630 0.00 0.00 0.00 1.94
2352 2744 9.696917 ACATACATTTCTCCAATTCTTTTTGAC 57.303 29.630 0.00 0.00 0.00 3.18
2353 2745 9.918630 CATACATTTCTCCAATTCTTTTTGACT 57.081 29.630 0.00 0.00 0.00 3.41
2354 2746 9.918630 ATACATTTCTCCAATTCTTTTTGACTG 57.081 29.630 0.00 0.00 0.00 3.51
2355 2747 8.010733 ACATTTCTCCAATTCTTTTTGACTGA 57.989 30.769 0.00 0.00 0.00 3.41
2356 2748 8.477256 ACATTTCTCCAATTCTTTTTGACTGAA 58.523 29.630 0.00 0.00 0.00 3.02
2357 2749 9.485206 CATTTCTCCAATTCTTTTTGACTGAAT 57.515 29.630 0.00 0.00 32.52 2.57
2359 2751 9.889128 TTTCTCCAATTCTTTTTGACTGAATTT 57.111 25.926 0.00 0.00 38.05 1.82
2360 2752 9.533253 TTCTCCAATTCTTTTTGACTGAATTTC 57.467 29.630 0.00 0.00 38.05 2.17
2361 2753 8.917088 TCTCCAATTCTTTTTGACTGAATTTCT 58.083 29.630 0.00 0.00 38.05 2.52
2362 2754 9.538508 CTCCAATTCTTTTTGACTGAATTTCTT 57.461 29.630 0.00 0.00 38.05 2.52
2363 2755 9.533253 TCCAATTCTTTTTGACTGAATTTCTTC 57.467 29.630 0.00 0.00 38.05 2.87
2364 2756 9.316730 CCAATTCTTTTTGACTGAATTTCTTCA 57.683 29.630 0.00 0.00 38.05 3.02
2473 2962 8.515414 CACGGTACATAATATCATTCTCTCTCA 58.485 37.037 0.00 0.00 0.00 3.27
2475 2964 9.513727 CGGTACATAATATCATTCTCTCTCATG 57.486 37.037 0.00 0.00 0.00 3.07
2507 2996 9.653287 AAACGACAAAAGATATGACTAGATGAA 57.347 29.630 0.00 0.00 0.00 2.57
2540 3036 6.500684 TGAGTCAAGAAATCACATTAAGCC 57.499 37.500 0.00 0.00 0.00 4.35
2556 3052 3.951563 AAGCCTGTAGCCCATTTATGA 57.048 42.857 0.00 0.00 45.47 2.15
2642 3138 7.204604 TGCTGTTATGCTTATCATTTGAATGG 58.795 34.615 4.05 0.00 37.03 3.16
2647 3143 8.632679 GTTATGCTTATCATTTGAATGGGAAGA 58.367 33.333 16.13 7.35 37.03 2.87
2654 3150 6.131972 TCATTTGAATGGGAAGAGTCTTCT 57.868 37.500 27.68 11.78 37.03 2.85
2655 3151 6.176183 TCATTTGAATGGGAAGAGTCTTCTC 58.824 40.000 27.68 25.76 37.67 2.87
2681 3178 4.085733 TGCAACTGGGTAGCAATTACATT 58.914 39.130 0.00 0.00 34.97 2.71
2700 3197 5.478407 ACATTGCTAAAATAACCTTGGTGC 58.522 37.500 0.00 0.00 0.00 5.01
2705 3202 6.529220 TGCTAAAATAACCTTGGTGCATTTT 58.471 32.000 19.84 19.84 34.26 1.82
2741 3238 9.959721 AGTGAGTTCTTAATAGCTAAAATGGAA 57.040 29.630 0.00 0.00 0.00 3.53
2782 3335 5.606348 TGTATATTCAATTTGGGCCAACC 57.394 39.130 20.79 0.00 40.81 3.77
2786 3339 1.374505 CAATTTGGGCCAACCGCAG 60.375 57.895 20.79 3.68 44.64 5.18
2850 3455 9.056005 CATAACAAGCAAGGCTAGATGTAATTA 57.944 33.333 0.00 0.00 38.25 1.40
2853 3458 7.282585 ACAAGCAAGGCTAGATGTAATTATCA 58.717 34.615 0.00 0.00 38.25 2.15
2910 3515 4.036027 GTGTACTGCATGCTAGCATTCATT 59.964 41.667 26.69 23.35 44.68 2.57
2919 3524 3.972537 GCATTCATTGCGCAGTCG 58.027 55.556 11.31 2.97 42.54 4.18
3009 3614 4.377328 GGTTTATTGGTTAACGGTCACGAC 60.377 45.833 0.00 0.00 44.60 4.34
3035 3642 2.555325 TCAGACAAGAAATGGCAAGCTG 59.445 45.455 0.00 0.00 40.75 4.24
3040 3647 2.283145 AGAAATGGCAAGCTGTCTGT 57.717 45.000 0.00 0.00 0.00 3.41
3487 4099 3.036091 GGTAGTGCTACTGGATACCCAA 58.964 50.000 8.96 0.00 42.98 4.12
3603 4215 5.068987 TCAAGGAAATAATTATGTGCAGCCC 59.931 40.000 9.56 0.00 0.00 5.19
4056 4668 3.375299 CAGCTCCAACTGTTTATAGTGGC 59.625 47.826 0.00 0.00 32.78 5.01
4140 4755 5.346281 GTCCAACTTAAGATCACTGAAGTCG 59.654 44.000 10.09 0.00 44.49 4.18
4161 4776 1.153628 GCGGGCAGTCGAACAGTAT 60.154 57.895 0.00 0.00 0.00 2.12
4236 4851 6.057533 TGATAATCTCCGTTGCAAGATTGAT 58.942 36.000 17.74 9.46 41.22 2.57
4248 4863 0.749454 AGATTGATGCGTTCCAGGCC 60.749 55.000 0.00 0.00 0.00 5.19
4281 4896 1.242076 AGCTGCTTCATGACCACAAC 58.758 50.000 0.00 0.00 0.00 3.32
4398 5013 0.957395 AGCAGTTTGGCACGATGAGG 60.957 55.000 0.00 0.00 35.83 3.86
4504 5119 3.676291 ACTTTCTGAGAGAGGCTGTTC 57.324 47.619 4.94 0.00 0.00 3.18
4612 5227 0.032813 CCTGGAAGTGGCCATGGATT 60.033 55.000 18.40 3.57 37.30 3.01
4674 5289 1.815421 CACCTACAGCGCCATGGTC 60.815 63.158 14.67 5.80 0.00 4.02
4854 5469 2.417516 CAGATCGCCGGATTCCGT 59.582 61.111 22.83 4.97 46.80 4.69
4914 5529 1.556911 GGTCACTGTGGTCATCTGGAT 59.443 52.381 8.11 0.00 0.00 3.41
5091 5706 0.682209 CCACCTGCAATTCCCTCCTG 60.682 60.000 0.00 0.00 0.00 3.86
5222 5837 3.470567 CACCGACGCTCACGCTTC 61.471 66.667 0.00 0.00 45.53 3.86
5365 5980 0.741927 CATGATGCACAGCGAGGACA 60.742 55.000 0.00 0.00 0.00 4.02
5397 6012 3.330275 GGCATAATGGACGCCGTC 58.670 61.111 9.15 9.15 35.79 4.79
5487 6102 2.758089 CGTCTACCCGGACTCCGTG 61.758 68.421 16.35 7.60 46.80 4.94
5661 6276 1.305718 GAGGAGGAGCAGGGTCACT 60.306 63.158 0.56 0.00 0.00 3.41
5697 6312 0.809241 GCCAGTCCATCGAGAAGCTG 60.809 60.000 0.00 0.00 0.00 4.24
5727 6342 2.262915 CAGTTCCCGCTCTTCGCT 59.737 61.111 0.00 0.00 36.73 4.93
5852 6491 1.915078 TAGGGCCTGCTTCTGCTTCC 61.915 60.000 18.53 0.00 40.48 3.46
5947 6586 1.069049 GGTGCAGTTTTGTGGAGCAAT 59.931 47.619 0.00 0.00 36.39 3.56
5958 6597 6.409524 TTTGTGGAGCAATCATTCTCTTTT 57.590 33.333 0.00 0.00 36.89 2.27
6016 6655 1.260561 AGCGTGCGTGTGTTAAGAAAG 59.739 47.619 0.00 0.00 0.00 2.62
6023 6662 4.505191 TGCGTGTGTTAAGAAAGTGTAGTC 59.495 41.667 0.00 0.00 0.00 2.59
6025 6664 5.176958 GCGTGTGTTAAGAAAGTGTAGTCAT 59.823 40.000 0.00 0.00 0.00 3.06
6040 6679 7.324178 AGTGTAGTCATGGTTGAGTTCTTATC 58.676 38.462 0.00 0.00 36.84 1.75
6051 6690 7.228706 TGGTTGAGTTCTTATCTTTCCAAACTC 59.771 37.037 6.19 6.19 41.72 3.01
6052 6691 7.445707 GGTTGAGTTCTTATCTTTCCAAACTCT 59.554 37.037 12.61 0.00 41.83 3.24
6053 6692 9.490379 GTTGAGTTCTTATCTTTCCAAACTCTA 57.510 33.333 12.61 4.42 41.83 2.43
6115 6754 6.849502 CATTGTTGCACTCTGAATTAGACAT 58.150 36.000 0.00 0.00 0.00 3.06
6117 6756 6.882610 TGTTGCACTCTGAATTAGACATTT 57.117 33.333 0.00 0.00 0.00 2.32
6119 6758 8.032952 TGTTGCACTCTGAATTAGACATTTAG 57.967 34.615 0.00 0.00 0.00 1.85
6120 6759 7.877612 TGTTGCACTCTGAATTAGACATTTAGA 59.122 33.333 0.00 0.00 0.00 2.10
6121 6760 7.834068 TGCACTCTGAATTAGACATTTAGAC 57.166 36.000 0.00 0.00 0.00 2.59
6122 6761 7.386059 TGCACTCTGAATTAGACATTTAGACA 58.614 34.615 0.00 0.00 0.00 3.41
6124 6763 8.887717 GCACTCTGAATTAGACATTTAGACATT 58.112 33.333 0.00 0.00 0.00 2.71
6126 6765 8.887717 ACTCTGAATTAGACATTTAGACATTGC 58.112 33.333 0.00 0.00 0.00 3.56
6127 6766 8.791327 TCTGAATTAGACATTTAGACATTGCA 57.209 30.769 0.00 0.00 0.00 4.08
6133 6790 8.969121 TTAGACATTTAGACATTGCATTGTTG 57.031 30.769 14.95 11.17 0.00 3.33
6152 6809 3.272574 TGCAATCTAGCCTTCTGGAAG 57.727 47.619 3.57 3.57 33.39 3.46
6178 6837 4.508461 TGCATTGGTCTTCTGATTGTTG 57.492 40.909 0.00 0.00 0.00 3.33
6213 6872 4.321452 GCATCAATTCAGAAGTTTGCTCCA 60.321 41.667 7.67 0.00 0.00 3.86
6219 6878 2.439507 TCAGAAGTTTGCTCCAGGAACT 59.560 45.455 0.00 0.00 43.88 3.01
6220 6879 3.117888 TCAGAAGTTTGCTCCAGGAACTT 60.118 43.478 4.18 4.18 43.95 2.66
6265 6926 8.655651 TTGCTATGATGTGACGATACAATTAA 57.344 30.769 0.00 0.00 33.69 1.40
6308 6982 7.581213 TCTTGGTTGTGTGTAATTTCATCTT 57.419 32.000 0.00 0.00 0.00 2.40
6313 6987 9.689976 TGGTTGTGTGTAATTTCATCTTTTATG 57.310 29.630 0.00 0.00 0.00 1.90
6320 6994 8.583765 GTGTAATTTCATCTTTTATGGTTTCGC 58.416 33.333 0.00 0.00 0.00 4.70
6365 7043 7.758820 TTTATCTGGGAACATTTAGGGACTA 57.241 36.000 0.00 0.00 39.36 2.59
6366 7044 7.758820 TTATCTGGGAACATTTAGGGACTAA 57.241 36.000 0.00 0.00 44.93 2.24
6433 7112 8.352201 TCTATTTGTTTGTGAGAAGGAACATTG 58.648 33.333 0.00 0.00 32.64 2.82
6437 7146 5.528690 TGTTTGTGAGAAGGAACATTGAGAG 59.471 40.000 0.00 0.00 0.00 3.20
6469 7178 8.984891 TTGTTGCATTCTAAATTAGACAATGG 57.015 30.769 13.51 1.13 33.84 3.16
6475 7184 9.822185 GCATTCTAAATTAGACAATGGGAATTT 57.178 29.630 13.51 7.03 35.99 1.82
6491 7200 7.489574 TGGGAATTTTGTTTTATGTTTCAGC 57.510 32.000 0.00 0.00 0.00 4.26
6493 7202 7.011857 TGGGAATTTTGTTTTATGTTTCAGCAC 59.988 33.333 0.00 0.00 0.00 4.40
6495 7204 8.558700 GGAATTTTGTTTTATGTTTCAGCACAT 58.441 29.630 0.00 0.00 40.61 3.21
6520 7229 6.575162 AGGTGTTTTAGCTGTAAATTCCAG 57.425 37.500 0.00 1.65 35.38 3.86
6528 7237 2.807676 CTGTAAATTCCAGCCCAACCT 58.192 47.619 0.00 0.00 0.00 3.50
6541 7250 1.615392 CCCAACCTTCAGGAAAAGCAG 59.385 52.381 0.00 0.00 38.94 4.24
6573 7282 6.938596 CACTGGGCATATTCATCTTCTGATTA 59.061 38.462 0.00 0.00 32.72 1.75
6586 7295 7.712639 TCATCTTCTGATTATTACTGCCAAGTC 59.287 37.037 0.00 0.00 37.88 3.01
6592 7301 7.764443 TCTGATTATTACTGCCAAGTCTACAAC 59.236 37.037 0.00 0.00 37.88 3.32
6640 7349 5.129634 TCTTACTCCACAGCAAAATTGTCA 58.870 37.500 0.00 0.00 0.00 3.58
6698 7407 7.769272 TCTTGGTTATCTTTGCTTGTTTTTG 57.231 32.000 0.00 0.00 0.00 2.44
6735 7469 3.131400 GGACTAGCAGCTAAGCTACACTT 59.869 47.826 3.09 0.00 44.50 3.16
6748 7482 8.557029 GCTAAGCTACACTTTCAGAAGTTTTTA 58.443 33.333 0.00 0.00 43.48 1.52
6772 7510 3.477530 AGTTTGTCAGCCAGTAAGAACC 58.522 45.455 0.00 0.00 0.00 3.62
6869 7608 4.321082 GCTTGCTCTTCTTTGAGAATGCTT 60.321 41.667 13.14 0.00 38.80 3.91
7005 7748 8.137745 AAAGAATTTTAATGGAAGCATCTCCA 57.862 30.769 4.84 4.84 42.55 3.86
7006 7749 8.596293 AAAGAATTTTAATGGAAGCATCTCCAA 58.404 29.630 6.32 0.00 41.93 3.53
7014 7757 5.705609 TGGAAGCATCTCCAAGTTTTTAC 57.294 39.130 0.03 0.00 42.69 2.01
7015 7758 5.385198 TGGAAGCATCTCCAAGTTTTTACT 58.615 37.500 0.03 0.00 42.69 2.24
7018 7761 7.669722 TGGAAGCATCTCCAAGTTTTTACTAAT 59.330 33.333 0.03 0.00 42.69 1.73
7019 7762 8.184848 GGAAGCATCTCCAAGTTTTTACTAATC 58.815 37.037 0.00 0.00 35.36 1.75
7020 7763 7.631717 AGCATCTCCAAGTTTTTACTAATCC 57.368 36.000 0.00 0.00 0.00 3.01
7021 7764 6.316390 AGCATCTCCAAGTTTTTACTAATCCG 59.684 38.462 0.00 0.00 0.00 4.18
7022 7765 6.487103 CATCTCCAAGTTTTTACTAATCCGC 58.513 40.000 0.00 0.00 0.00 5.54
7023 7766 5.801380 TCTCCAAGTTTTTACTAATCCGCT 58.199 37.500 0.00 0.00 0.00 5.52
7024 7767 5.642063 TCTCCAAGTTTTTACTAATCCGCTG 59.358 40.000 0.00 0.00 0.00 5.18
7025 7768 5.310451 TCCAAGTTTTTACTAATCCGCTGT 58.690 37.500 0.00 0.00 0.00 4.40
7026 7769 5.180492 TCCAAGTTTTTACTAATCCGCTGTG 59.820 40.000 0.00 0.00 0.00 3.66
7027 7770 5.390613 CAAGTTTTTACTAATCCGCTGTGG 58.609 41.667 0.00 0.00 40.09 4.17
7039 7782 3.833732 TCCGCTGTGGAGATATCTACTT 58.166 45.455 16.10 0.00 43.74 2.24
7063 7806 1.256812 CCTGAAAATTGAACCCGCCT 58.743 50.000 0.00 0.00 0.00 5.52
7078 7821 3.299977 CCTGTGACCCCGTCGACA 61.300 66.667 17.16 0.00 34.95 4.35
7146 7890 1.269257 GGGTTGCAAGTTCAAGACAGC 60.269 52.381 0.00 0.00 33.68 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 229 2.359850 GTTGGTGGCCGCATCTCA 60.360 61.111 19.98 3.43 0.00 3.27
395 398 2.888863 CTTCTCCGCCTCGAGCTT 59.111 61.111 6.99 0.00 40.39 3.74
542 545 1.014044 TGCATCTTCTCGAACCACGC 61.014 55.000 0.00 0.00 42.26 5.34
788 796 4.982295 TCGAATGATACGATGCCAAACTAG 59.018 41.667 0.00 0.00 34.85 2.57
796 804 2.440539 AGGGTCGAATGATACGATGC 57.559 50.000 0.00 0.00 41.62 3.91
797 805 5.709966 TCATAAGGGTCGAATGATACGATG 58.290 41.667 0.00 0.00 41.62 3.84
811 819 6.324770 CCAAGCTCCAAAAATATCATAAGGGT 59.675 38.462 0.00 0.00 0.00 4.34
831 839 7.499232 TGATGATGATGATGATGATATCCAAGC 59.501 37.037 0.00 0.00 0.00 4.01
832 840 8.964476 TGATGATGATGATGATGATATCCAAG 57.036 34.615 0.00 0.00 0.00 3.61
833 841 9.920946 AATGATGATGATGATGATGATATCCAA 57.079 29.630 0.00 0.00 0.00 3.53
835 843 8.787852 CCAATGATGATGATGATGATGATATCC 58.212 37.037 0.00 0.00 0.00 2.59
836 844 9.561069 TCCAATGATGATGATGATGATGATATC 57.439 33.333 0.00 0.00 0.00 1.63
839 847 9.920946 TTATCCAATGATGATGATGATGATGAT 57.079 29.630 0.00 0.00 32.18 2.45
840 848 9.747898 TTTATCCAATGATGATGATGATGATGA 57.252 29.630 0.00 0.00 32.18 2.92
842 850 9.190317 CCTTTATCCAATGATGATGATGATGAT 57.810 33.333 0.00 0.00 32.18 2.45
843 851 8.387813 TCCTTTATCCAATGATGATGATGATGA 58.612 33.333 0.00 0.00 32.18 2.92
844 852 8.575649 TCCTTTATCCAATGATGATGATGATG 57.424 34.615 0.00 0.00 32.18 3.07
845 853 9.244292 CTTCCTTTATCCAATGATGATGATGAT 57.756 33.333 0.00 0.00 32.18 2.45
846 854 7.176165 GCTTCCTTTATCCAATGATGATGATGA 59.824 37.037 0.00 0.00 32.18 2.92
847 855 7.313646 GCTTCCTTTATCCAATGATGATGATG 58.686 38.462 0.00 0.00 32.18 3.07
848 856 6.150641 CGCTTCCTTTATCCAATGATGATGAT 59.849 38.462 0.00 0.00 32.18 2.45
849 857 5.471116 CGCTTCCTTTATCCAATGATGATGA 59.529 40.000 0.00 0.00 32.18 2.92
850 858 5.240183 ACGCTTCCTTTATCCAATGATGATG 59.760 40.000 0.00 0.00 32.18 3.07
851 859 5.380043 ACGCTTCCTTTATCCAATGATGAT 58.620 37.500 0.00 0.00 32.18 2.45
852 860 4.780815 ACGCTTCCTTTATCCAATGATGA 58.219 39.130 0.00 0.00 32.18 2.92
853 861 4.023707 GGACGCTTCCTTTATCCAATGATG 60.024 45.833 1.07 0.00 39.13 3.07
854 862 4.137543 GGACGCTTCCTTTATCCAATGAT 58.862 43.478 1.07 0.00 39.13 2.45
855 863 3.541632 GGACGCTTCCTTTATCCAATGA 58.458 45.455 1.07 0.00 39.13 2.57
856 864 2.287915 CGGACGCTTCCTTTATCCAATG 59.712 50.000 7.75 0.00 40.23 2.82
857 865 2.169769 TCGGACGCTTCCTTTATCCAAT 59.830 45.455 7.75 0.00 40.23 3.16
858 866 1.551430 TCGGACGCTTCCTTTATCCAA 59.449 47.619 7.75 0.00 40.23 3.53
859 867 1.136305 CTCGGACGCTTCCTTTATCCA 59.864 52.381 7.75 0.00 40.23 3.41
860 868 1.407979 TCTCGGACGCTTCCTTTATCC 59.592 52.381 7.75 0.00 40.23 2.59
861 869 2.865343 TCTCGGACGCTTCCTTTATC 57.135 50.000 7.75 0.00 40.23 1.75
862 870 2.738964 GCTTCTCGGACGCTTCCTTTAT 60.739 50.000 7.75 0.00 40.23 1.40
863 871 1.403780 GCTTCTCGGACGCTTCCTTTA 60.404 52.381 7.75 0.00 40.23 1.85
864 872 0.670854 GCTTCTCGGACGCTTCCTTT 60.671 55.000 7.75 0.00 40.23 3.11
966 974 1.694150 TGGAGGACTGTTTGGTGAGAG 59.306 52.381 0.00 0.00 0.00 3.20
978 987 2.627217 GGGAAGTACTGGATGGAGGACT 60.627 54.545 0.00 0.00 38.96 3.85
979 988 1.763545 GGGAAGTACTGGATGGAGGAC 59.236 57.143 0.00 0.00 0.00 3.85
1076 1116 1.613255 GGAGGAGGGCGAATTTGTTGA 60.613 52.381 0.00 0.00 0.00 3.18
1085 1125 4.144727 GAGGGAGGAGGAGGGCGA 62.145 72.222 0.00 0.00 0.00 5.54
1088 1128 1.228737 GATCGAGGGAGGAGGAGGG 60.229 68.421 0.00 0.00 0.00 4.30
1091 1145 2.203365 GCGATCGAGGGAGGAGGA 60.203 66.667 21.57 0.00 0.00 3.71
1120 1174 2.766229 GGGCTGGAGAGGGAGGAC 60.766 72.222 0.00 0.00 0.00 3.85
1246 1306 0.686112 AGAGAGGAAGGGAAGGCGAG 60.686 60.000 0.00 0.00 0.00 5.03
1278 1344 1.612442 CCTTGAGACGGGAGGGGAA 60.612 63.158 0.00 0.00 0.00 3.97
1332 1400 1.026182 CGGAAGCACTAGCAATGGCA 61.026 55.000 0.00 0.00 45.49 4.92
1355 1423 1.474330 GACATTTGCGGAATCCCCTT 58.526 50.000 0.00 0.00 0.00 3.95
1365 1433 0.523072 CCCAAGACAGGACATTTGCG 59.477 55.000 0.00 0.00 0.00 4.85
1438 1523 4.162690 CGAGCGGGAAAGAGGGGG 62.163 72.222 0.00 0.00 0.00 5.40
1553 1640 5.057149 ACTGGTACTAGCAAGAAAACACAG 58.943 41.667 6.09 0.00 0.00 3.66
1558 1647 4.240096 GCGTACTGGTACTAGCAAGAAAA 58.760 43.478 6.09 0.00 34.04 2.29
1559 1648 3.367703 GGCGTACTGGTACTAGCAAGAAA 60.368 47.826 6.09 0.00 34.04 2.52
1600 1690 0.179067 GACCCTTTGTGACGTGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
1606 1696 5.350091 ACAAAATTTTTGACCCTTTGTGACG 59.650 36.000 24.73 0.00 38.45 4.35
1654 1755 0.966179 GCAAAGGGGGAAACACGATT 59.034 50.000 0.00 0.00 0.00 3.34
1655 1756 0.178975 TGCAAAGGGGGAAACACGAT 60.179 50.000 0.00 0.00 0.00 3.73
1656 1757 0.178975 ATGCAAAGGGGGAAACACGA 60.179 50.000 0.00 0.00 0.00 4.35
1657 1758 0.678950 AATGCAAAGGGGGAAACACG 59.321 50.000 0.00 0.00 0.00 4.49
1660 1761 1.338105 GCTGAATGCAAAGGGGGAAAC 60.338 52.381 0.00 0.00 42.31 2.78
1663 1764 0.323725 GAGCTGAATGCAAAGGGGGA 60.324 55.000 0.00 0.00 45.94 4.81
1702 1810 0.104120 TCAATCGGTGTGATAGCCCG 59.896 55.000 0.00 0.00 43.03 6.13
1705 1813 3.741344 GGTACATCAATCGGTGTGATAGC 59.259 47.826 0.00 0.00 35.84 2.97
1710 1818 1.065782 TGGGGTACATCAATCGGTGTG 60.066 52.381 0.00 0.00 0.00 3.82
1729 1837 5.371526 AGGTGCTAATACTTCCACATCATG 58.628 41.667 0.00 0.00 0.00 3.07
1739 1847 5.774102 AGGTTTGGTAGGTGCTAATACTT 57.226 39.130 0.00 0.00 0.00 2.24
1773 1881 2.755103 CTGATAACAGGGGAAAGGTTGC 59.245 50.000 0.00 0.00 40.14 4.17
1792 1901 1.929836 GTTTGCGCAGAGATCCTACTG 59.070 52.381 11.31 7.51 37.22 2.74
1803 1912 3.058708 TCTCTGAAAGATTGTTTGCGCAG 60.059 43.478 11.31 0.00 45.62 5.18
1806 1915 4.997905 TCTCTCTGAAAGATTGTTTGCG 57.002 40.909 0.00 0.00 45.62 4.85
1820 1929 7.758980 CCTGATCCACGAATATTATTCTCTCTG 59.241 40.741 13.19 1.97 0.00 3.35
1837 1949 0.173708 GTCCGACTGTCCTGATCCAC 59.826 60.000 1.55 0.00 0.00 4.02
1909 2021 3.381272 CCAAAATGGTGATACCGAAGCAT 59.619 43.478 0.00 0.00 42.58 3.79
1964 2076 4.965532 AGTCCATAATCTAGACACCTGCTT 59.034 41.667 0.00 0.00 32.82 3.91
2055 2176 7.294958 AGTGCCTTATATAGTTACCCCAGAAAT 59.705 37.037 0.00 0.00 0.00 2.17
2059 2180 6.183361 ACAAGTGCCTTATATAGTTACCCCAG 60.183 42.308 0.00 0.00 0.00 4.45
2064 2185 8.674607 AGCAAAACAAGTGCCTTATATAGTTAC 58.325 33.333 0.00 0.00 43.27 2.50
2093 2477 4.144297 TCAATTGGCCCAGTAGATTATGC 58.856 43.478 5.42 0.00 0.00 3.14
2117 2501 9.836864 TGTAAATCAAATCAGTAGTAGCATGAT 57.163 29.630 0.00 0.00 35.21 2.45
2338 2730 9.316730 TGAAGAAATTCAGTCAAAAAGAATTGG 57.683 29.630 0.00 0.00 40.11 3.16
2349 2741 9.554724 GCGTAAATAAATGAAGAAATTCAGTCA 57.445 29.630 0.00 0.00 34.02 3.41
2350 2742 9.554724 TGCGTAAATAAATGAAGAAATTCAGTC 57.445 29.630 0.00 0.00 34.02 3.51
2353 2745 8.806634 GCATGCGTAAATAAATGAAGAAATTCA 58.193 29.630 0.00 0.00 35.15 2.57
2354 2746 9.023967 AGCATGCGTAAATAAATGAAGAAATTC 57.976 29.630 13.01 0.00 0.00 2.17
2355 2747 8.810427 CAGCATGCGTAAATAAATGAAGAAATT 58.190 29.630 13.01 0.00 0.00 1.82
2356 2748 7.436080 CCAGCATGCGTAAATAAATGAAGAAAT 59.564 33.333 13.01 0.00 31.97 2.17
2357 2749 6.751425 CCAGCATGCGTAAATAAATGAAGAAA 59.249 34.615 13.01 0.00 31.97 2.52
2358 2750 6.127758 ACCAGCATGCGTAAATAAATGAAGAA 60.128 34.615 13.01 0.00 31.97 2.52
2359 2751 5.356751 ACCAGCATGCGTAAATAAATGAAGA 59.643 36.000 13.01 0.00 31.97 2.87
2360 2752 5.581605 ACCAGCATGCGTAAATAAATGAAG 58.418 37.500 13.01 0.00 31.97 3.02
2361 2753 5.574891 ACCAGCATGCGTAAATAAATGAA 57.425 34.783 13.01 0.00 31.97 2.57
2362 2754 6.685527 TTACCAGCATGCGTAAATAAATGA 57.314 33.333 13.01 0.00 31.80 2.57
2363 2755 6.198216 GGTTTACCAGCATGCGTAAATAAATG 59.802 38.462 24.38 11.15 40.84 2.32
2364 2756 6.096282 AGGTTTACCAGCATGCGTAAATAAAT 59.904 34.615 24.38 13.46 40.84 1.40
2365 2757 5.416326 AGGTTTACCAGCATGCGTAAATAAA 59.584 36.000 24.38 17.24 40.84 1.40
2366 2758 4.944930 AGGTTTACCAGCATGCGTAAATAA 59.055 37.500 24.38 13.52 40.84 1.40
2367 2759 4.519213 AGGTTTACCAGCATGCGTAAATA 58.481 39.130 24.38 9.02 40.84 1.40
2484 2973 8.535592 GTGTTCATCTAGTCATATCTTTTGTCG 58.464 37.037 0.00 0.00 0.00 4.35
2507 2996 7.013559 TGTGATTTCTTGACTCATTTCATGTGT 59.986 33.333 0.00 0.00 39.45 3.72
2517 3013 6.149973 CAGGCTTAATGTGATTTCTTGACTCA 59.850 38.462 0.00 0.00 0.00 3.41
2531 3027 3.669939 AATGGGCTACAGGCTTAATGT 57.330 42.857 2.57 0.00 41.46 2.71
2540 3036 7.170965 AGATATGGTTCATAAATGGGCTACAG 58.829 38.462 0.00 0.00 29.74 2.74
2556 3052 9.301897 AGAAAAAGTTTCAAGCTAGATATGGTT 57.698 29.630 0.00 0.00 0.00 3.67
2630 3126 6.729428 AGAAGACTCTTCCCATTCAAATGAT 58.271 36.000 14.19 0.00 38.70 2.45
2642 3138 4.759183 AGTTGCATTTGAGAAGACTCTTCC 59.241 41.667 14.19 7.52 42.99 3.46
2647 3143 3.152341 CCCAGTTGCATTTGAGAAGACT 58.848 45.455 0.00 0.00 0.00 3.24
2654 3150 2.284754 TGCTACCCAGTTGCATTTGA 57.715 45.000 0.00 0.00 39.07 2.69
2655 3151 3.598019 ATTGCTACCCAGTTGCATTTG 57.402 42.857 4.77 0.00 42.77 2.32
2681 3178 5.736951 AATGCACCAAGGTTATTTTAGCA 57.263 34.783 0.00 1.42 0.00 3.49
2696 3193 7.538575 ACTCACTAATATCAACAAAATGCACC 58.461 34.615 0.00 0.00 0.00 5.01
2782 3335 2.061028 GCAAGATTTGTTTTCCCTGCG 58.939 47.619 0.00 0.00 0.00 5.18
2786 3339 6.405538 TGGATATTGCAAGATTTGTTTTCCC 58.594 36.000 8.18 2.83 0.00 3.97
2825 3430 9.799106 ATAATTACATCTAGCCTTGCTTGTTAT 57.201 29.630 0.00 0.00 40.44 1.89
2910 3515 2.087501 TAAAAGAATCCGACTGCGCA 57.912 45.000 10.98 10.98 35.83 6.09
2919 3524 8.974060 TCAATACTGGTGGTATAAAAGAATCC 57.026 34.615 0.00 0.00 39.94 3.01
3009 3614 5.675575 GCTTGCCATTTCTTGTCTGATACAG 60.676 44.000 0.00 0.00 39.87 2.74
3035 3642 9.926751 CATGAATATTATCAAGTGAACACAGAC 57.073 33.333 7.68 0.00 32.06 3.51
3040 3647 9.112725 CAGGACATGAATATTATCAAGTGAACA 57.887 33.333 0.00 0.00 31.91 3.18
3171 3781 9.727627 GTTCTGCTTTCATAATCTGGATAAAAG 57.272 33.333 0.00 0.00 0.00 2.27
3487 4099 5.564550 AGGAATGACATTAACAGCTTGAGT 58.435 37.500 0.00 0.00 0.00 3.41
3603 4215 2.202987 CTGGCGGCCTGCTTAGAG 60.203 66.667 21.46 2.99 45.43 2.43
3813 4425 1.077265 CATGGAAGGGGCACAAGGT 59.923 57.895 0.00 0.00 0.00 3.50
3814 4426 2.353610 GCATGGAAGGGGCACAAGG 61.354 63.158 0.00 0.00 0.00 3.61
4056 4668 1.211457 CCCTGAGATTTGTCAGAGGGG 59.789 57.143 6.31 0.00 46.02 4.79
4119 4734 6.584954 CAACGACTTCAGTGATCTTAAGTTG 58.415 40.000 1.63 7.37 41.47 3.16
4140 4755 2.954753 CTGTTCGACTGCCCGCAAC 61.955 63.158 0.00 0.00 0.00 4.17
4161 4776 0.534873 TCTGCTGCAGCGTATGGTAA 59.465 50.000 32.11 12.38 45.83 2.85
4236 4851 1.228398 TTGATTGGCCTGGAACGCA 60.228 52.632 3.32 0.00 0.00 5.24
4248 4863 1.540267 AGCAGCTTCAGCACTTGATTG 59.460 47.619 0.75 0.00 45.16 2.67
4281 4896 0.179189 GGAAGAAACCAAGCGCGATG 60.179 55.000 12.10 7.99 0.00 3.84
4398 5013 3.052036 GCTCATCTCATCGAGAAGCTTC 58.948 50.000 19.11 19.11 42.27 3.86
4504 5119 1.680735 CTCCATCTCCTCGAAGACCTG 59.319 57.143 0.00 0.00 0.00 4.00
4612 5227 2.804986 TCTTGCATCCTGCCATACAA 57.195 45.000 0.00 0.00 44.23 2.41
4653 5268 0.676466 CCATGGCGCTGTAGGTGAAA 60.676 55.000 7.64 0.00 0.00 2.69
4854 5469 2.429610 GCTGTAGGTTATCTTGTCGGGA 59.570 50.000 0.00 0.00 0.00 5.14
4914 5529 1.372683 GAACACAGCCTCAGCCTCA 59.627 57.895 0.00 0.00 41.25 3.86
4977 5592 1.557269 CCCAGAGGTCCACCAGAAGG 61.557 65.000 0.00 0.00 38.89 3.46
5220 5835 1.227943 GCAGCATAGCCCCATCGAA 60.228 57.895 0.00 0.00 0.00 3.71
5221 5836 2.427320 GCAGCATAGCCCCATCGA 59.573 61.111 0.00 0.00 0.00 3.59
5365 5980 2.690510 GCCCCTCTTGCTCTCCCT 60.691 66.667 0.00 0.00 0.00 4.20
5397 6012 3.265791 GGACTTGTGCAGGAAGTCTATG 58.734 50.000 26.43 0.42 45.82 2.23
5766 6381 2.919856 AGCCACTGACTGAGCGGT 60.920 61.111 0.00 0.00 0.00 5.68
5947 6586 5.416952 GCTTCCTTCATCCAAAAGAGAATGA 59.583 40.000 0.00 0.00 0.00 2.57
5958 6597 3.265221 AGAACAGATGCTTCCTTCATCCA 59.735 43.478 9.17 0.00 40.79 3.41
6016 6655 7.324178 AGATAAGAACTCAACCATGACTACAC 58.676 38.462 0.00 0.00 0.00 2.90
6023 6662 7.452880 TTGGAAAGATAAGAACTCAACCATG 57.547 36.000 0.00 0.00 0.00 3.66
6025 6664 7.060421 AGTTTGGAAAGATAAGAACTCAACCA 58.940 34.615 0.00 0.00 0.00 3.67
6101 6740 8.886719 TGCAATGTCTAAATGTCTAATTCAGAG 58.113 33.333 0.00 0.00 32.51 3.35
6126 6765 4.439700 CCAGAAGGCTAGATTGCAACAATG 60.440 45.833 0.00 0.00 34.04 2.82
6127 6766 3.698040 CCAGAAGGCTAGATTGCAACAAT 59.302 43.478 0.00 0.00 34.04 2.71
6152 6809 1.820519 TCAGAAGACCAATGCATTGCC 59.179 47.619 30.15 22.98 36.48 4.52
6213 6872 2.378038 TGCTGTGAAGCAAAAGTTCCT 58.622 42.857 0.00 0.00 42.40 3.36
6239 6898 7.734924 AATTGTATCGTCACATCATAGCAAT 57.265 32.000 0.00 0.00 0.00 3.56
6251 6910 7.654568 AGGTACATCGATTAATTGTATCGTCA 58.345 34.615 18.36 6.64 43.91 4.35
6265 6926 5.453903 CCAAGATTCAGGAAGGTACATCGAT 60.454 44.000 0.00 0.00 0.00 3.59
6278 6939 5.964958 ATTACACACAACCAAGATTCAGG 57.035 39.130 0.00 0.00 0.00 3.86
6320 6994 1.779569 AAGTTTCGACACGCTACAGG 58.220 50.000 0.00 0.00 0.00 4.00
6329 7003 7.162761 TGTTCCCAGATAAATAAGTTTCGACA 58.837 34.615 0.00 0.00 0.00 4.35
6394 7072 9.918630 CACAAACAAATAGAAGGAAATTCTCAT 57.081 29.630 0.00 0.00 45.50 2.90
6395 7073 9.130661 TCACAAACAAATAGAAGGAAATTCTCA 57.869 29.630 0.00 0.00 45.50 3.27
6396 7074 9.617975 CTCACAAACAAATAGAAGGAAATTCTC 57.382 33.333 0.00 0.00 45.50 2.87
6399 7077 9.971922 CTTCTCACAAACAAATAGAAGGAAATT 57.028 29.630 0.00 0.00 39.52 1.82
6405 7083 7.930217 TGTTCCTTCTCACAAACAAATAGAAG 58.070 34.615 0.00 0.00 41.73 2.85
6406 7084 7.873719 TGTTCCTTCTCACAAACAAATAGAA 57.126 32.000 0.00 0.00 0.00 2.10
6407 7085 8.352201 CAATGTTCCTTCTCACAAACAAATAGA 58.648 33.333 0.00 0.00 35.46 1.98
6408 7086 8.352201 TCAATGTTCCTTCTCACAAACAAATAG 58.648 33.333 0.00 0.00 35.46 1.73
6414 7092 5.760253 TCTCTCAATGTTCCTTCTCACAAAC 59.240 40.000 0.00 0.00 0.00 2.93
6416 7094 5.551305 TCTCTCAATGTTCCTTCTCACAA 57.449 39.130 0.00 0.00 0.00 3.33
6433 7112 9.798994 ATTTAGAATGCAACAAATCAATCTCTC 57.201 29.630 0.00 0.00 0.00 3.20
6469 7178 7.914465 TGTGCTGAAACATAAAACAAAATTCC 58.086 30.769 0.00 0.00 0.00 3.01
6475 7184 6.183360 ACCTGATGTGCTGAAACATAAAACAA 60.183 34.615 0.00 0.00 40.87 2.83
6476 7185 5.301551 ACCTGATGTGCTGAAACATAAAACA 59.698 36.000 0.00 0.00 40.87 2.83
6493 7202 7.029563 GGAATTTACAGCTAAAACACCTGATG 58.970 38.462 0.00 0.00 0.00 3.07
6495 7204 6.065374 TGGAATTTACAGCTAAAACACCTGA 58.935 36.000 13.79 0.70 0.00 3.86
6510 7219 3.161866 TGAAGGTTGGGCTGGAATTTAC 58.838 45.455 0.00 0.00 0.00 2.01
6511 7220 3.430453 CTGAAGGTTGGGCTGGAATTTA 58.570 45.455 0.00 0.00 0.00 1.40
6512 7221 2.250924 CTGAAGGTTGGGCTGGAATTT 58.749 47.619 0.00 0.00 0.00 1.82
6513 7222 1.550869 CCTGAAGGTTGGGCTGGAATT 60.551 52.381 0.00 0.00 0.00 2.17
6514 7223 0.040204 CCTGAAGGTTGGGCTGGAAT 59.960 55.000 0.00 0.00 0.00 3.01
6515 7224 1.065410 TCCTGAAGGTTGGGCTGGAA 61.065 55.000 0.00 0.00 36.34 3.53
6516 7225 1.065410 TTCCTGAAGGTTGGGCTGGA 61.065 55.000 0.00 0.00 36.34 3.86
6517 7226 0.178964 TTTCCTGAAGGTTGGGCTGG 60.179 55.000 0.00 0.00 36.34 4.85
6518 7227 1.615392 CTTTTCCTGAAGGTTGGGCTG 59.385 52.381 0.00 0.00 36.34 4.85
6519 7228 2.001076 CTTTTCCTGAAGGTTGGGCT 57.999 50.000 0.00 0.00 36.34 5.19
6520 7229 0.318441 GCTTTTCCTGAAGGTTGGGC 59.682 55.000 0.00 0.00 36.34 5.36
6521 7230 1.615392 CTGCTTTTCCTGAAGGTTGGG 59.385 52.381 0.00 0.00 36.34 4.12
6522 7231 2.035066 CACTGCTTTTCCTGAAGGTTGG 59.965 50.000 0.00 0.00 36.34 3.77
6523 7232 2.951642 TCACTGCTTTTCCTGAAGGTTG 59.048 45.455 0.00 0.00 36.34 3.77
6524 7233 3.297134 TCACTGCTTTTCCTGAAGGTT 57.703 42.857 0.00 0.00 36.34 3.50
6525 7234 3.297134 TTCACTGCTTTTCCTGAAGGT 57.703 42.857 0.00 0.00 36.34 3.50
6526 7235 4.170292 CATTCACTGCTTTTCCTGAAGG 57.830 45.455 0.00 0.00 0.00 3.46
6561 7270 7.714377 AGACTTGGCAGTAATAATCAGAAGATG 59.286 37.037 0.00 0.00 30.97 2.90
6573 7282 4.530710 TCGTTGTAGACTTGGCAGTAAT 57.469 40.909 0.00 0.00 31.22 1.89
6586 7295 4.211164 TGAGCAACTTGTGAATCGTTGTAG 59.789 41.667 0.00 0.00 39.98 2.74
6640 7349 4.494350 AACTGTATCGTCGTGTTGTAGT 57.506 40.909 0.00 0.00 0.00 2.73
6647 7356 3.646491 TCGACTAACTGTATCGTCGTG 57.354 47.619 18.90 1.76 46.55 4.35
6698 7407 4.098044 TGCTAGTCCACAGTATTGTAGCTC 59.902 45.833 10.33 0.00 35.75 4.09
6735 7469 9.730420 GCTGACAAACTTATAAAAACTTCTGAA 57.270 29.630 0.00 0.00 0.00 3.02
6748 7482 5.705905 GGTTCTTACTGGCTGACAAACTTAT 59.294 40.000 0.00 0.00 0.00 1.73
6788 7526 4.782691 TGAAATCATGACAAGGAGGGTAGA 59.217 41.667 0.00 0.00 0.00 2.59
6984 7723 7.486407 ACTTGGAGATGCTTCCATTAAAATT 57.514 32.000 6.10 0.00 46.22 1.82
6985 7724 7.486407 AACTTGGAGATGCTTCCATTAAAAT 57.514 32.000 6.10 0.00 46.22 1.82
6989 7732 6.916360 AAAAACTTGGAGATGCTTCCATTA 57.084 33.333 6.10 0.00 46.22 1.90
6990 7733 5.813513 AAAAACTTGGAGATGCTTCCATT 57.186 34.783 6.10 0.00 46.22 3.16
6991 7734 6.012745 AGTAAAAACTTGGAGATGCTTCCAT 58.987 36.000 6.10 0.00 46.22 3.41
6992 7735 5.385198 AGTAAAAACTTGGAGATGCTTCCA 58.615 37.500 1.71 1.71 45.34 3.53
6993 7736 5.966742 AGTAAAAACTTGGAGATGCTTCC 57.033 39.130 0.00 0.00 37.77 3.46
6994 7737 8.184848 GGATTAGTAAAAACTTGGAGATGCTTC 58.815 37.037 0.00 0.00 0.00 3.86
6995 7738 7.148239 CGGATTAGTAAAAACTTGGAGATGCTT 60.148 37.037 0.00 0.00 0.00 3.91
6996 7739 6.316390 CGGATTAGTAAAAACTTGGAGATGCT 59.684 38.462 0.00 0.00 0.00 3.79
6997 7740 6.487103 CGGATTAGTAAAAACTTGGAGATGC 58.513 40.000 0.00 0.00 0.00 3.91
6999 7742 6.316390 CAGCGGATTAGTAAAAACTTGGAGAT 59.684 38.462 0.00 0.00 0.00 2.75
7000 7743 5.642063 CAGCGGATTAGTAAAAACTTGGAGA 59.358 40.000 0.00 0.00 0.00 3.71
7004 7747 5.180492 TCCACAGCGGATTAGTAAAAACTTG 59.820 40.000 0.00 0.00 39.64 3.16
7005 7748 5.310451 TCCACAGCGGATTAGTAAAAACTT 58.690 37.500 0.00 0.00 39.64 2.66
7006 7749 4.901868 TCCACAGCGGATTAGTAAAAACT 58.098 39.130 0.00 0.00 39.64 2.66
7007 7750 4.933400 TCTCCACAGCGGATTAGTAAAAAC 59.067 41.667 0.00 0.00 45.19 2.43
7008 7751 5.155278 TCTCCACAGCGGATTAGTAAAAA 57.845 39.130 0.00 0.00 45.19 1.94
7009 7752 4.811969 TCTCCACAGCGGATTAGTAAAA 57.188 40.909 0.00 0.00 45.19 1.52
7010 7753 6.493802 AGATATCTCCACAGCGGATTAGTAAA 59.506 38.462 0.00 0.00 45.19 2.01
7011 7754 6.010850 AGATATCTCCACAGCGGATTAGTAA 58.989 40.000 0.00 0.00 45.19 2.24
7012 7755 5.571285 AGATATCTCCACAGCGGATTAGTA 58.429 41.667 0.00 0.00 45.19 1.82
7014 7757 5.650266 AGTAGATATCTCCACAGCGGATTAG 59.350 44.000 8.95 0.00 45.19 1.73
7015 7758 5.571285 AGTAGATATCTCCACAGCGGATTA 58.429 41.667 8.95 0.00 45.19 1.75
7018 7761 3.510531 AGTAGATATCTCCACAGCGGA 57.489 47.619 8.95 0.00 43.61 5.54
7019 7762 3.823873 AGAAGTAGATATCTCCACAGCGG 59.176 47.826 8.95 0.00 0.00 5.52
7020 7763 5.446143 AAGAAGTAGATATCTCCACAGCG 57.554 43.478 8.95 0.00 0.00 5.18
7021 7764 6.492087 AGGTAAGAAGTAGATATCTCCACAGC 59.508 42.308 8.95 0.00 0.00 4.40
7022 7765 7.721842 TCAGGTAAGAAGTAGATATCTCCACAG 59.278 40.741 8.95 0.00 0.00 3.66
7023 7766 7.583625 TCAGGTAAGAAGTAGATATCTCCACA 58.416 38.462 8.95 0.00 0.00 4.17
7024 7767 8.466617 TTCAGGTAAGAAGTAGATATCTCCAC 57.533 38.462 8.95 2.80 0.00 4.02
7025 7768 9.488762 TTTTCAGGTAAGAAGTAGATATCTCCA 57.511 33.333 8.95 0.00 0.00 3.86
7039 7782 3.504520 GCGGGTTCAATTTTCAGGTAAGA 59.495 43.478 0.00 0.00 0.00 2.10
7063 7806 0.967662 TTAATGTCGACGGGGTCACA 59.032 50.000 11.62 0.00 32.00 3.58
7078 7821 7.042335 GTGTGATCTTGCTGTAGGTACTTAAT 58.958 38.462 0.00 0.00 41.75 1.40
7146 7890 1.674221 GCAGGAGAGGTAACAGCACAG 60.674 57.143 0.00 0.00 41.41 3.66


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

AutoCloner maintained by Alex Coulton.