Multiple sequence alignment - TraesCS3A01G075000

Loading Multiple Alignment...

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 TraesCS3A01G075000 chr3A 100.000 5825 0 0 1 5825 46828659 46834483 0.000000e+00 10757
1 TraesCS3A01G075000 chr3A 90.510 569 38 9 870 1432 36858466 36857908 0.000000e+00 737
2 TraesCS3A01G075000 chr3D 89.484 3005 193 54 775 3694 36008053 36011019 0.000000e+00 3685
3 TraesCS3A01G075000 chr3D 87.758 1985 146 51 3889 5824 36011251 36013187 0.000000e+00 2230
4 TraesCS3A01G075000 chr3D 91.200 125 9 2 3709 3831 36011130 36011254 1.000000e-37 169
5 TraesCS3A01G075000 chr3B 90.377 2442 151 31 2591 5005 59025915 59028299 0.000000e+00 3131
6 TraesCS3A01G075000 chr3B 89.653 1788 128 29 775 2540 59024007 59025759 0.000000e+00 2224
7 TraesCS3A01G075000 chr3B 85.216 487 18 25 5340 5825 59030717 59031150 8.900000e-123 451
8 TraesCS3A01G075000 chr3B 88.830 188 17 2 5004 5188 59028357 59028543 1.630000e-55 228
9 TraesCS3A01G075000 chrUn 90.370 675 49 9 870 1536 74791608 74792274 0.000000e+00 872
10 TraesCS3A01G075000 chrUn 89.858 424 41 1 319 740 30899858 30899435 1.430000e-150 544
11 TraesCS3A01G075000 chrUn 87.311 331 26 8 5462 5789 359350285 359349968 1.190000e-96 364
12 TraesCS3A01G075000 chr2A 90.222 675 51 11 870 1536 303689235 303688568 0.000000e+00 867
13 TraesCS3A01G075000 chr2A 90.074 675 50 10 870 1536 575785027 575784362 0.000000e+00 859
14 TraesCS3A01G075000 chr2A 86.013 479 60 4 259 735 716503238 716503711 1.870000e-139 507
15 TraesCS3A01G075000 chr2A 91.830 306 24 1 2 307 732990326 732990630 5.400000e-115 425
16 TraesCS3A01G075000 chr7A 89.896 673 52 10 870 1536 627184532 627185194 0.000000e+00 852
17 TraesCS3A01G075000 chr7A 88.791 678 57 10 870 1536 595556303 595556972 0.000000e+00 813
18 TraesCS3A01G075000 chr7A 85.541 740 66 17 8 735 13341562 13340852 0.000000e+00 736
19 TraesCS3A01G075000 chr5D 85.195 743 78 16 2 741 376719386 376720099 0.000000e+00 734
20 TraesCS3A01G075000 chr5D 90.261 421 37 2 319 735 534087505 534087085 1.100000e-151 547
21 TraesCS3A01G075000 chr5D 92.079 303 24 0 2 304 47797307 47797609 1.500000e-115 427
22 TraesCS3A01G075000 chr5D 92.333 300 23 0 8 307 534087788 534087489 1.500000e-115 427
23 TraesCS3A01G075000 chr5D 87.311 331 26 8 5462 5789 553222246 553221929 1.190000e-96 364
24 TraesCS3A01G075000 chr5D 87.311 331 26 8 5462 5789 553256571 553256254 1.190000e-96 364
25 TraesCS3A01G075000 chr6B 83.137 765 73 10 2 742 135310999 135311731 0.000000e+00 647
26 TraesCS3A01G075000 chr6B 85.890 326 27 11 5483 5805 699901425 699901116 4.350000e-86 329
27 TraesCS3A01G075000 chr6B 84.211 323 34 11 5483 5805 699822167 699821862 1.230000e-76 298
28 TraesCS3A01G075000 chr7B 89.189 481 39 8 870 1346 738951947 738952418 6.500000e-164 588
29 TraesCS3A01G075000 chr5A 90.187 428 40 1 319 744 685991327 685990900 1.830000e-154 556
30 TraesCS3A01G075000 chr5A 90.453 419 36 2 319 735 346121088 346120672 3.070000e-152 549
31 TraesCS3A01G075000 chr5A 92.459 305 23 0 2 306 685991616 685991312 2.490000e-118 436
32 TraesCS3A01G075000 chr2D 89.302 430 42 3 319 744 621119918 621120347 2.390000e-148 536
33 TraesCS3A01G075000 chr2D 92.333 300 23 0 8 307 42736676 42736377 1.500000e-115 427
34 TraesCS3A01G075000 chr6D 92.532 308 21 1 2 307 30533851 30534158 1.930000e-119 440
35 TraesCS3A01G075000 chr6D 92.182 307 23 1 2 307 374101996 374101690 3.220000e-117 433
36 TraesCS3A01G075000 chr6A 92.484 306 22 1 2 307 346595935 346595631 2.490000e-118 436
37 TraesCS3A01G075000 chr1D 91.830 306 23 2 2 307 350650813 350651116 5.400000e-115 425
38 TraesCS3A01G075000 chr4A 85.833 120 13 4 5636 5753 220151485 220151602 2.200000e-24 124


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 TraesCS3A01G075000 chr3A 46828659 46834483 5824 False 10757.0 10757 100.000000 1 5825 1 chr3A.!!$F1 5824
1 TraesCS3A01G075000 chr3A 36857908 36858466 558 True 737.0 737 90.510000 870 1432 1 chr3A.!!$R1 562
2 TraesCS3A01G075000 chr3D 36008053 36013187 5134 False 2028.0 3685 89.480667 775 5824 3 chr3D.!!$F1 5049
3 TraesCS3A01G075000 chr3B 59024007 59031150 7143 False 1508.5 3131 88.519000 775 5825 4 chr3B.!!$F1 5050
4 TraesCS3A01G075000 chrUn 74791608 74792274 666 False 872.0 872 90.370000 870 1536 1 chrUn.!!$F1 666
5 TraesCS3A01G075000 chr2A 303688568 303689235 667 True 867.0 867 90.222000 870 1536 1 chr2A.!!$R1 666
6 TraesCS3A01G075000 chr2A 575784362 575785027 665 True 859.0 859 90.074000 870 1536 1 chr2A.!!$R2 666
7 TraesCS3A01G075000 chr7A 627184532 627185194 662 False 852.0 852 89.896000 870 1536 1 chr7A.!!$F2 666
8 TraesCS3A01G075000 chr7A 595556303 595556972 669 False 813.0 813 88.791000 870 1536 1 chr7A.!!$F1 666
9 TraesCS3A01G075000 chr7A 13340852 13341562 710 True 736.0 736 85.541000 8 735 1 chr7A.!!$R1 727
10 TraesCS3A01G075000 chr5D 376719386 376720099 713 False 734.0 734 85.195000 2 741 1 chr5D.!!$F2 739
11 TraesCS3A01G075000 chr5D 534087085 534087788 703 True 487.0 547 91.297000 8 735 2 chr5D.!!$R3 727
12 TraesCS3A01G075000 chr6B 135310999 135311731 732 False 647.0 647 83.137000 2 742 1 chr6B.!!$F1 740
13 TraesCS3A01G075000 chr5A 685990900 685991616 716 True 496.0 556 91.323000 2 744 2 chr5A.!!$R2 742

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
822 862 0.534412 TACGATACCCGCCCGAAAAA 59.466 50.000 0.00 0.00 43.32 1.94 F
1683 1780 0.110192 GCTTGTGCACGGTTAGAAGC 60.110 55.000 18.04 18.04 36.29 3.86 F
2523 2632 0.249741 CACCCTGAGGAAAACGACGT 60.250 55.000 0.00 0.00 36.73 4.34 F
2798 3012 0.467290 TGTTTCAGGACCCTTGCCAC 60.467 55.000 0.00 0.00 0.00 5.01 F
3263 3481 1.202313 TGCAACAAACTTTACACCGGC 60.202 47.619 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2771 2985 1.517242 GGTCCTGAAACAGAGCACAG 58.483 55.0 0.00 0.0 32.44 3.66 R
3324 3542 1.609208 ACTTGCAAGCATTTCGGAGT 58.391 45.0 26.27 0.0 0.00 3.85 R
4247 4599 0.453390 GCTTGCCTCTACACAATGGC 59.547 55.0 0.00 0.0 45.10 4.40 R
4248 4600 0.729116 CGCTTGCCTCTACACAATGG 59.271 55.0 0.00 0.0 0.00 3.16 R
5056 5479 0.101219 GATGCAAAATCCGGGCAGAC 59.899 55.0 0.00 0.0 41.40 3.51 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
30 31 4.371975 GCTGTGTGGGCGAACTAA 57.628 55.556 0.00 0.00 0.00 2.24
45 46 4.453136 GCGAACTAATTTCTACCCACACAA 59.547 41.667 0.00 0.00 31.20 3.33
62 72 0.762418 CAACCACCACCTAGTCCACA 59.238 55.000 0.00 0.00 0.00 4.17
86 96 1.668751 GTGTGGACGAACTGCTTTTCA 59.331 47.619 0.00 0.00 0.00 2.69
95 105 1.101049 ACTGCTTTTCACCCACACGG 61.101 55.000 0.00 0.00 37.81 4.94
112 122 0.935831 CGGCAGTCGTACGTTGTTGA 60.936 55.000 16.05 0.00 0.00 3.18
204 234 3.966215 AACTGCAGTTGCGCGTAT 58.034 50.000 30.66 4.24 45.83 3.06
251 281 4.083217 GGCAATTGTGATTAACCACACGTA 60.083 41.667 0.85 0.00 45.62 3.57
260 290 4.852134 TTAACCACACGTAGCAACTAGA 57.148 40.909 0.00 0.00 0.00 2.43
288 318 7.275888 ACACACATGACAACTATTGTTTGAT 57.724 32.000 0.00 0.00 45.52 2.57
305 335 8.846943 TTGTTTGATCATATGTGACAAGTAGT 57.153 30.769 1.90 0.00 37.14 2.73
306 336 8.846943 TGTTTGATCATATGTGACAAGTAGTT 57.153 30.769 1.90 0.00 37.14 2.24
307 337 9.283768 TGTTTGATCATATGTGACAAGTAGTTT 57.716 29.630 1.90 0.00 37.14 2.66
393 423 7.201732 GCAGCAACTACCATAAATTAGACATGT 60.202 37.037 0.00 0.00 0.00 3.21
412 442 9.436957 AGACATGTCAACTATAGTTAACCAAAG 57.563 33.333 27.02 12.58 36.32 2.77
587 619 2.093869 GGGATGCGTAGTACTTGTTGGA 60.094 50.000 0.00 0.00 0.00 3.53
638 670 4.055360 CGTGTGGACAATTCTACTGTTCA 58.945 43.478 0.00 0.00 34.36 3.18
735 769 1.036707 TGTGATGGATATCGGCGTCA 58.963 50.000 6.85 0.00 36.04 4.35
770 804 3.923017 GTTGCAAACCTTCTACTGCAT 57.077 42.857 0.00 0.00 43.83 3.96
771 805 3.826466 GTTGCAAACCTTCTACTGCATC 58.174 45.455 0.00 0.00 43.83 3.91
772 806 2.076100 TGCAAACCTTCTACTGCATCG 58.924 47.619 0.00 0.00 39.77 3.84
773 807 2.076863 GCAAACCTTCTACTGCATCGT 58.923 47.619 0.00 0.00 34.87 3.73
798 832 2.286713 CGTCACGGAGAAGAGATAGCAG 60.287 54.545 0.00 0.00 0.00 4.24
822 862 0.534412 TACGATACCCGCCCGAAAAA 59.466 50.000 0.00 0.00 43.32 1.94
1073 1123 0.247460 TTCCTGGAGCTGATGTCGTG 59.753 55.000 0.00 0.00 0.00 4.35
1191 1241 2.823154 GGTAAGCTCAGCCGAGATCTAT 59.177 50.000 0.00 0.00 42.34 1.98
1223 1273 1.342819 CCCTCTAGGCATGTACTCTGC 59.657 57.143 11.22 11.22 38.93 4.26
1233 1283 1.116536 TGTACTCTGCCCACGGTTGA 61.117 55.000 0.00 0.00 0.00 3.18
1295 1346 5.847304 TGTATTCTGTCATGGTCTAGATGC 58.153 41.667 0.00 0.00 0.00 3.91
1374 1427 5.396484 CCATTGTATGCTTGTCTCAGTTTG 58.604 41.667 0.00 0.00 0.00 2.93
1381 1434 5.581126 TGCTTGTCTCAGTTTGTTCAAAT 57.419 34.783 1.33 0.00 0.00 2.32
1385 1438 8.196771 TGCTTGTCTCAGTTTGTTCAAATATTT 58.803 29.630 0.00 0.00 0.00 1.40
1402 1469 1.489574 TTTTTCAAGCATGCGCACAG 58.510 45.000 14.90 10.28 42.27 3.66
1435 1519 6.398918 AGATTTCTGCACTACGATGTAAAGT 58.601 36.000 0.00 0.00 0.00 2.66
1507 1593 6.298361 AGCTGCCCTGTTTTTATTTTGAATT 58.702 32.000 0.00 0.00 0.00 2.17
1547 1633 8.598202 TGTACAGGTTCAAGTATTATACAGGA 57.402 34.615 5.11 0.00 0.00 3.86
1598 1694 3.371102 ACATACGAATCCACCATCGAG 57.629 47.619 1.84 0.00 41.43 4.04
1604 1700 2.288457 CGAATCCACCATCGAGCAGTAT 60.288 50.000 0.00 0.00 41.43 2.12
1605 1701 2.827800 ATCCACCATCGAGCAGTATG 57.172 50.000 0.00 0.00 40.87 2.39
1606 1702 1.775385 TCCACCATCGAGCAGTATGA 58.225 50.000 0.00 0.00 39.69 2.15
1607 1703 1.409064 TCCACCATCGAGCAGTATGAC 59.591 52.381 0.00 0.00 39.69 3.06
1610 1706 3.068165 CCACCATCGAGCAGTATGACTTA 59.932 47.826 0.00 0.00 39.69 2.24
1661 1758 1.056660 GGTCTGGTTCAGAACAGGGA 58.943 55.000 15.36 6.78 46.41 4.20
1683 1780 0.110192 GCTTGTGCACGGTTAGAAGC 60.110 55.000 18.04 18.04 36.29 3.86
1687 1784 0.447801 GTGCACGGTTAGAAGCATGG 59.552 55.000 0.00 0.00 36.96 3.66
1690 1787 1.810151 GCACGGTTAGAAGCATGGAAA 59.190 47.619 0.00 0.00 0.00 3.13
1785 1883 1.202830 TGGGGACACGTAATGCAGTTT 60.203 47.619 0.00 0.00 33.40 2.66
1798 1896 2.405892 GCAGTTTGCAGATCAACGTT 57.594 45.000 0.00 0.00 44.26 3.99
1799 1897 3.536158 GCAGTTTGCAGATCAACGTTA 57.464 42.857 0.00 0.00 44.26 3.18
1801 1899 4.091424 GCAGTTTGCAGATCAACGTTATC 58.909 43.478 0.00 5.14 44.26 1.75
1802 1900 4.378356 GCAGTTTGCAGATCAACGTTATCA 60.378 41.667 0.00 0.00 44.26 2.15
1805 1903 6.086765 CAGTTTGCAGATCAACGTTATCAAAC 59.913 38.462 19.62 19.62 41.07 2.93
1849 1947 2.265683 GCAAGGCTTAAGCATTTGAGC 58.734 47.619 31.62 24.86 42.92 4.26
1859 1957 1.376609 GCATTTGAGCCCACTACCCG 61.377 60.000 0.00 0.00 0.00 5.28
1867 1965 2.356780 CCCACTACCCGGTCCACTC 61.357 68.421 0.00 0.00 0.00 3.51
1868 1966 1.608336 CCACTACCCGGTCCACTCA 60.608 63.158 0.00 0.00 0.00 3.41
1882 1980 4.448060 GGTCCACTCAAAGACTTTAACTCG 59.552 45.833 0.00 0.00 33.39 4.18
1893 2001 8.913656 CAAAGACTTTAACTCGAAGTAGTTAGG 58.086 37.037 0.00 0.00 41.63 2.69
1900 2008 6.462552 AACTCGAAGTAGTTAGGGGTTATC 57.537 41.667 0.00 0.00 37.93 1.75
1901 2009 5.513233 ACTCGAAGTAGTTAGGGGTTATCA 58.487 41.667 0.00 0.00 0.00 2.15
1906 2014 6.040616 CGAAGTAGTTAGGGGTTATCAGATGT 59.959 42.308 0.00 0.00 0.00 3.06
1910 2018 8.457757 AGTAGTTAGGGGTTATCAGATGTAGAT 58.542 37.037 0.00 0.00 0.00 1.98
1960 2069 2.234300 TCAACAAGGTTCGGTGTCTC 57.766 50.000 0.00 0.00 0.00 3.36
1961 2070 1.202604 TCAACAAGGTTCGGTGTCTCC 60.203 52.381 0.00 0.00 0.00 3.71
2041 2150 1.119684 GGTGCCCTCAGTTTTGGTTT 58.880 50.000 0.00 0.00 0.00 3.27
2068 2177 4.386424 GGTCTAAGCCCCATAGGATTTTGT 60.386 45.833 0.00 0.00 43.52 2.83
2078 2187 6.040166 CCCCATAGGATTTTGTCTGAATTCTG 59.960 42.308 7.05 6.50 38.24 3.02
2206 2315 4.096984 GCATACTTTCCCTCTGGTGAATTG 59.903 45.833 0.00 0.00 0.00 2.32
2377 2486 8.308207 GTTGCTAGTTTAATTGTTTATTGGGGA 58.692 33.333 0.00 0.00 0.00 4.81
2405 2514 4.286032 TCAGTTTACCTATGCACCTTGACT 59.714 41.667 0.00 0.00 0.00 3.41
2514 2623 2.036733 CGTTTCAAGTACACCCTGAGGA 59.963 50.000 0.00 0.00 36.73 3.71
2523 2632 0.249741 CACCCTGAGGAAAACGACGT 60.250 55.000 0.00 0.00 36.73 4.34
2530 2639 4.380655 CCTGAGGAAAACGACGTCTTAGAT 60.381 45.833 14.70 0.00 0.00 1.98
2540 2649 5.517904 ACGACGTCTTAGATAATGGTAAGC 58.482 41.667 14.70 0.00 0.00 3.09
2541 2650 5.066893 ACGACGTCTTAGATAATGGTAAGCA 59.933 40.000 14.70 0.00 0.00 3.91
2542 2651 5.625721 CGACGTCTTAGATAATGGTAAGCAG 59.374 44.000 14.70 0.00 0.00 4.24
2543 2652 6.512903 CGACGTCTTAGATAATGGTAAGCAGA 60.513 42.308 14.70 0.00 0.00 4.26
2649 2863 3.402628 TTCTGTGGCTCTAGAACAACC 57.597 47.619 0.00 0.00 0.00 3.77
2652 2866 3.135712 TCTGTGGCTCTAGAACAACCAAA 59.864 43.478 0.00 0.00 30.82 3.28
2679 2893 4.772100 CCCTCAAATTTGGTGAAGGTATGT 59.228 41.667 17.90 0.00 0.00 2.29
2693 2907 6.968904 GTGAAGGTATGTGTGATTAATGCTTG 59.031 38.462 0.00 0.00 0.00 4.01
2712 2926 3.812156 TGACTCAACCTTTTCTCGTCA 57.188 42.857 0.00 0.00 0.00 4.35
2713 2927 4.336889 TGACTCAACCTTTTCTCGTCAT 57.663 40.909 0.00 0.00 0.00 3.06
2714 2928 5.462530 TGACTCAACCTTTTCTCGTCATA 57.537 39.130 0.00 0.00 0.00 2.15
2715 2929 6.037786 TGACTCAACCTTTTCTCGTCATAT 57.962 37.500 0.00 0.00 0.00 1.78
2716 2930 7.165460 TGACTCAACCTTTTCTCGTCATATA 57.835 36.000 0.00 0.00 0.00 0.86
2717 2931 7.608153 TGACTCAACCTTTTCTCGTCATATAA 58.392 34.615 0.00 0.00 0.00 0.98
2718 2932 7.759886 TGACTCAACCTTTTCTCGTCATATAAG 59.240 37.037 0.00 0.00 0.00 1.73
2719 2933 7.612677 ACTCAACCTTTTCTCGTCATATAAGT 58.387 34.615 0.00 0.00 0.00 2.24
2720 2934 7.760340 ACTCAACCTTTTCTCGTCATATAAGTC 59.240 37.037 0.00 0.00 0.00 3.01
2721 2935 7.039882 TCAACCTTTTCTCGTCATATAAGTCC 58.960 38.462 0.00 0.00 0.00 3.85
2722 2936 6.540438 ACCTTTTCTCGTCATATAAGTCCA 57.460 37.500 0.00 0.00 0.00 4.02
2723 2937 6.338937 ACCTTTTCTCGTCATATAAGTCCAC 58.661 40.000 0.00 0.00 0.00 4.02
2724 2938 6.070995 ACCTTTTCTCGTCATATAAGTCCACA 60.071 38.462 0.00 0.00 0.00 4.17
2725 2939 6.986817 CCTTTTCTCGTCATATAAGTCCACAT 59.013 38.462 0.00 0.00 0.00 3.21
2771 2985 5.339008 TGTGACAGTTCCATATACTGACC 57.661 43.478 10.44 3.73 44.52 4.02
2795 3009 1.528129 CTCTGTTTCAGGACCCTTGC 58.472 55.000 0.00 0.00 31.51 4.01
2798 3012 0.467290 TGTTTCAGGACCCTTGCCAC 60.467 55.000 0.00 0.00 0.00 5.01
2828 3042 6.232581 AGTCATCTAGCAAGCACTTATTCT 57.767 37.500 0.00 0.00 0.00 2.40
2921 3135 2.584492 AAAAACTGCAGCAACCAGAC 57.416 45.000 15.27 0.00 34.47 3.51
2997 3211 9.681062 TTCAAAATTTACCTGGGAAGTATCTAG 57.319 33.333 0.00 0.00 0.00 2.43
2999 3213 5.827326 ATTTACCTGGGAAGTATCTAGGC 57.173 43.478 0.00 0.00 34.96 3.93
3012 3226 6.274157 AGTATCTAGGCATTTCCATCTACG 57.726 41.667 0.00 0.00 37.29 3.51
3039 3253 9.060347 ACCTGCATTAACATTATCACTAGAATG 57.940 33.333 0.00 0.00 39.66 2.67
3075 3293 4.569719 ATCACCGGAATAGTTTCACCTT 57.430 40.909 9.46 0.00 33.23 3.50
3133 3351 2.246469 CACCCCATGGTTGATTCACAA 58.754 47.619 11.73 0.00 44.75 3.33
3155 3373 8.906867 CACAATCCACATCCTTCATTATAGTTT 58.093 33.333 0.00 0.00 0.00 2.66
3178 3396 8.863049 GTTTTGTTTCAGGAACATATGCATTAG 58.137 33.333 3.54 0.00 46.99 1.73
3263 3481 1.202313 TGCAACAAACTTTACACCGGC 60.202 47.619 0.00 0.00 0.00 6.13
3264 3482 1.749153 CAACAAACTTTACACCGGCG 58.251 50.000 0.00 0.00 0.00 6.46
3309 3527 8.372459 TGTATTTGTACTAGAATGTTCAGGTGT 58.628 33.333 0.00 0.00 0.00 4.16
3324 3542 7.672240 TGTTCAGGTGTTGTACTGTTATGATA 58.328 34.615 0.00 0.00 36.17 2.15
3329 3547 5.747197 GGTGTTGTACTGTTATGATACTCCG 59.253 44.000 0.00 0.00 0.00 4.63
3362 3580 3.963129 AGTAGTCTAGTGCTTCTCTGCT 58.037 45.455 0.00 0.00 0.00 4.24
3374 3592 3.919197 GCTTCTCTGCTCATTTTGCTTTC 59.081 43.478 0.00 0.00 0.00 2.62
3377 3595 5.779529 TCTCTGCTCATTTTGCTTTCTTT 57.220 34.783 0.00 0.00 0.00 2.52
3437 3673 6.639563 TGTGCATCTGACATTAGCTAACTTA 58.360 36.000 8.70 0.00 0.00 2.24
3442 3678 8.066595 GCATCTGACATTAGCTAACTTAACATG 58.933 37.037 8.70 8.73 0.00 3.21
3478 3716 3.136260 TCATGCCTACTCATATTGGTGCA 59.864 43.478 0.00 0.00 0.00 4.57
3505 3743 3.797256 CAGACCTACGCTTTGTATACTGC 59.203 47.826 4.17 5.38 31.20 4.40
3617 3858 4.024218 GCGATCTGCTCAATGCTAAAAGAT 60.024 41.667 0.00 0.00 43.37 2.40
3694 3935 3.510719 GCTTGCGAAAATTCCTAATGCA 58.489 40.909 0.00 0.00 0.00 3.96
3695 3936 3.304293 GCTTGCGAAAATTCCTAATGCAC 59.696 43.478 0.00 0.00 0.00 4.57
3700 3941 4.785341 GCGAAAATTCCTAATGCACCGTAG 60.785 45.833 0.00 0.00 0.00 3.51
3702 3943 5.163794 CGAAAATTCCTAATGCACCGTAGTT 60.164 40.000 0.00 0.00 0.00 2.24
3703 3944 6.584185 AAAATTCCTAATGCACCGTAGTTT 57.416 33.333 0.00 0.00 0.00 2.66
3704 3945 6.584185 AAATTCCTAATGCACCGTAGTTTT 57.416 33.333 0.00 0.00 0.00 2.43
3705 3946 5.813080 ATTCCTAATGCACCGTAGTTTTC 57.187 39.130 0.00 0.00 0.00 2.29
3706 3947 4.274602 TCCTAATGCACCGTAGTTTTCA 57.725 40.909 0.00 0.00 0.00 2.69
3707 3948 4.839121 TCCTAATGCACCGTAGTTTTCAT 58.161 39.130 0.00 0.00 0.00 2.57
3761 4106 4.400251 TGCTATTTGCCTTTCCTGATTCTG 59.600 41.667 0.00 0.00 42.00 3.02
3772 4117 3.849911 TCCTGATTCTGTTTCTACTGCG 58.150 45.455 0.00 0.00 0.00 5.18
3882 4228 9.981460 ATGGAGGTTATTCTTTAGAGTTTCAAT 57.019 29.630 0.00 0.00 0.00 2.57
4105 4456 5.278957 GCCTTCAGGTCAAATTCTGCTTAAA 60.279 40.000 0.00 0.00 37.57 1.52
4111 4462 6.583806 CAGGTCAAATTCTGCTTAAATGTGTC 59.416 38.462 0.00 0.00 0.00 3.67
4133 4484 8.125448 GTGTCTCTGCAGTTATCCATTAAAATC 58.875 37.037 14.67 0.00 0.00 2.17
4138 4489 5.655974 TGCAGTTATCCATTAAAATCTGCCA 59.344 36.000 10.50 0.00 43.95 4.92
4179 4530 7.783090 AATGCACAATAGTCTACATGAGAAG 57.217 36.000 0.00 0.00 35.37 2.85
4240 4592 1.795872 CGGTGAACATTACTGACGCAA 59.204 47.619 0.00 0.00 0.00 4.85
4247 4599 2.160219 ACATTACTGACGCAATGCAGTG 59.840 45.455 10.38 10.38 44.47 3.66
4248 4600 0.516877 TTACTGACGCAATGCAGTGC 59.483 50.000 28.26 28.26 44.47 4.40
4267 4622 0.729116 CCATTGTGTAGAGGCAAGCG 59.271 55.000 0.00 0.00 0.00 4.68
4306 4661 1.683385 GGCAGAAGAAACAAGCCAAGT 59.317 47.619 0.00 0.00 44.59 3.16
4334 4689 1.393883 GCTACGCTTTCTGGTTAGCAC 59.606 52.381 0.00 0.00 37.23 4.40
4342 4697 5.391950 CGCTTTCTGGTTAGCACATTAACAT 60.392 40.000 0.00 0.00 37.23 2.71
4345 4700 6.509418 TTCTGGTTAGCACATTAACATTCC 57.491 37.500 0.00 0.00 35.67 3.01
4347 4702 6.953101 TCTGGTTAGCACATTAACATTCCTA 58.047 36.000 0.00 0.00 35.67 2.94
4349 4704 8.710239 TCTGGTTAGCACATTAACATTCCTATA 58.290 33.333 0.00 0.00 35.67 1.31
4394 4749 2.391389 GCGGTAGCAGCAACACCTC 61.391 63.158 8.69 0.00 44.35 3.85
4454 4809 1.134401 TCATTCAGGATTGGAGGCGTC 60.134 52.381 0.00 0.00 0.00 5.19
4487 4842 0.872021 GCGCCTACCACTTGATCGAG 60.872 60.000 8.54 8.54 0.00 4.04
4628 4983 8.918202 TCAAGTTTTCAAACAGGTCTATATGT 57.082 30.769 5.26 0.00 41.30 2.29
4632 4987 9.396022 AGTTTTCAAACAGGTCTATATGTATGG 57.604 33.333 5.26 0.00 41.30 2.74
4646 5001 9.298250 TCTATATGTATGGTCCTTTACTGACTC 57.702 37.037 0.00 0.00 33.22 3.36
4743 5099 5.535406 AGACATCTACCATTCTTACTACGGG 59.465 44.000 0.00 0.00 0.00 5.28
4831 5187 2.107141 CCGCACTGTAGCTAGCCC 59.893 66.667 12.13 2.72 0.00 5.19
4855 5211 1.000739 ACCGATCCTCCCCGTTGTA 59.999 57.895 0.00 0.00 0.00 2.41
4895 5258 3.120546 AGTTTTGTTGCGATCGACAGATG 60.121 43.478 21.57 0.00 37.84 2.90
4937 5300 2.725815 GCGTGCGGCTGAAAACAC 60.726 61.111 0.00 0.00 39.11 3.32
4971 5334 0.108615 CGTGAGGCTTCTTGATCCGT 60.109 55.000 0.00 0.00 0.00 4.69
4998 5361 6.004928 GCTTTCGGCGTGTTTATTATTTTC 57.995 37.500 6.85 0.00 0.00 2.29
5012 5434 5.722021 ATTATTTTCCGGTTGAGCTGTTT 57.278 34.783 0.00 0.00 0.00 2.83
5016 5438 1.522668 TCCGGTTGAGCTGTTTGATG 58.477 50.000 0.00 0.00 0.00 3.07
5040 5463 0.992802 CGAAAGCTACTGAGAACGGC 59.007 55.000 0.00 0.00 0.00 5.68
5067 5490 1.443407 CAGAATCGTCTGCCCGGAT 59.557 57.895 0.73 0.00 44.74 4.18
5075 5498 0.101219 GTCTGCCCGGATTTTGCATC 59.899 55.000 0.73 0.00 33.97 3.91
5076 5499 1.064621 CTGCCCGGATTTTGCATCG 59.935 57.895 0.73 0.00 33.97 3.84
5079 5502 2.024588 CCGGATTTTGCATCGGCG 59.975 61.111 0.00 0.00 45.35 6.46
5094 5517 2.371923 GGCGTTTGAATTGCGTGCC 61.372 57.895 0.00 0.00 0.00 5.01
5101 5524 1.353103 GAATTGCGTGCCCGATGAG 59.647 57.895 0.00 0.00 35.63 2.90
5127 5550 3.061848 GCGTGTGGTGGGGATTGG 61.062 66.667 0.00 0.00 0.00 3.16
5140 5563 0.749049 GGATTGGGCAAGCTGGATTC 59.251 55.000 0.00 0.00 0.00 2.52
5208 6360 2.786539 TAACTGCCACGAGCTGCTGG 62.787 60.000 7.01 8.90 43.85 4.85
5233 6388 4.148645 TCGCTCACTCGCTCGTCG 62.149 66.667 0.00 0.00 40.15 5.12
5264 6430 1.372251 CCGATCTCGCCAGATTCCG 60.372 63.158 0.00 0.00 39.71 4.30
5268 6434 2.076622 ATCTCGCCAGATTCCGTCCG 62.077 60.000 0.00 0.00 35.67 4.79
5286 6453 2.380081 GGATTCAAACCGATCGCGT 58.620 52.632 10.32 6.50 35.23 6.01
5287 6454 0.026285 GGATTCAAACCGATCGCGTG 59.974 55.000 10.32 7.07 35.23 5.34
5288 6455 0.719465 GATTCAAACCGATCGCGTGT 59.281 50.000 10.32 1.28 35.23 4.49
5289 6456 0.719465 ATTCAAACCGATCGCGTGTC 59.281 50.000 10.32 5.02 35.23 3.67
5290 6457 1.610715 TTCAAACCGATCGCGTGTCG 61.611 55.000 22.90 22.90 38.75 4.35
5336 6503 0.106894 GCCTCCTAATCCAACTCCCG 59.893 60.000 0.00 0.00 0.00 5.14
5408 7874 0.240945 CGGCCATTATTTGATCCGCC 59.759 55.000 2.24 0.00 35.55 6.13
5409 7875 1.620822 GGCCATTATTTGATCCGCCT 58.379 50.000 0.00 0.00 32.09 5.52
5410 7876 1.541588 GGCCATTATTTGATCCGCCTC 59.458 52.381 0.00 0.00 32.09 4.70
5411 7877 1.197721 GCCATTATTTGATCCGCCTCG 59.802 52.381 0.00 0.00 0.00 4.63
5412 7878 1.197721 CCATTATTTGATCCGCCTCGC 59.802 52.381 0.00 0.00 0.00 5.03
5453 7920 3.518998 GCGTCTGCGGCCTAGAGA 61.519 66.667 0.00 0.00 38.78 3.10
5454 7921 3.064987 GCGTCTGCGGCCTAGAGAA 62.065 63.158 0.00 0.00 38.78 2.87
5455 7922 1.226717 CGTCTGCGGCCTAGAGAAC 60.227 63.158 0.00 0.00 0.00 3.01
5456 7923 1.890894 GTCTGCGGCCTAGAGAACA 59.109 57.895 0.00 0.00 0.00 3.18
5457 7924 0.246635 GTCTGCGGCCTAGAGAACAA 59.753 55.000 0.00 0.00 0.00 2.83
5458 7925 0.973632 TCTGCGGCCTAGAGAACAAA 59.026 50.000 0.00 0.00 0.00 2.83
5459 7926 1.555075 TCTGCGGCCTAGAGAACAAAT 59.445 47.619 0.00 0.00 0.00 2.32
5460 7927 2.764010 TCTGCGGCCTAGAGAACAAATA 59.236 45.455 0.00 0.00 0.00 1.40
5547 8014 0.960364 GGATGGTGCGCCTTCTTTCA 60.960 55.000 26.09 2.49 38.56 2.69
5549 8016 1.474077 GATGGTGCGCCTTCTTTCATT 59.526 47.619 21.65 0.00 36.37 2.57
5550 8017 0.597568 TGGTGCGCCTTCTTTCATTG 59.402 50.000 18.96 0.00 35.27 2.82
5551 8018 0.109132 GGTGCGCCTTCTTTCATTGG 60.109 55.000 9.68 0.00 0.00 3.16
5552 8019 0.881118 GTGCGCCTTCTTTCATTGGA 59.119 50.000 4.18 0.00 0.00 3.53
5554 8021 2.094545 GTGCGCCTTCTTTCATTGGATT 60.095 45.455 4.18 0.00 0.00 3.01
5555 8022 2.562298 TGCGCCTTCTTTCATTGGATTT 59.438 40.909 4.18 0.00 0.00 2.17
5556 8023 2.925563 GCGCCTTCTTTCATTGGATTTG 59.074 45.455 0.00 0.00 0.00 2.32
5557 8024 3.367292 GCGCCTTCTTTCATTGGATTTGA 60.367 43.478 0.00 0.00 0.00 2.69
5563 8030 6.984474 CCTTCTTTCATTGGATTTGATGGATG 59.016 38.462 0.00 0.00 0.00 3.51
5587 8054 3.179685 TGGATGGATGGATGGATCTCTC 58.820 50.000 0.00 0.00 0.00 3.20
5625 8092 3.056536 TCTGACCAGTTCGGATCTCTTTG 60.057 47.826 0.00 0.00 34.38 2.77
5626 8093 2.028112 TGACCAGTTCGGATCTCTTTGG 60.028 50.000 0.00 0.00 38.63 3.28
5763 8230 0.103937 CATGGAGGTCCGCTTCTCTC 59.896 60.000 0.00 0.00 39.43 3.20
5764 8231 0.032615 ATGGAGGTCCGCTTCTCTCT 60.033 55.000 0.00 0.00 39.43 3.10
5771 8238 2.159296 GGTCCGCTTCTCTCTTCTCTTC 60.159 54.545 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.175931 TGGTGGTTGTGTGGGTAGAAAT 59.824 45.455 0.00 0.00 0.00 2.17
45 46 1.469335 CGTGTGGACTAGGTGGTGGT 61.469 60.000 0.00 0.00 0.00 4.16
62 72 2.657296 CAGTTCGTCCACACGCGT 60.657 61.111 5.58 5.58 46.28 6.01
95 105 2.411031 CCATTCAACAACGTACGACTGC 60.411 50.000 24.41 0.00 0.00 4.40
123 133 2.171341 TTGCCATGTACGTGCAACTA 57.829 45.000 11.22 0.00 39.86 2.24
204 234 6.039605 CCATGTATGTTTATCTGATTGCCACA 59.960 38.462 0.00 0.00 0.00 4.17
251 281 6.230472 TGTCATGTGTGTTTATCTAGTTGCT 58.770 36.000 0.00 0.00 0.00 3.91
260 290 9.462174 CAAACAATAGTTGTCATGTGTGTTTAT 57.538 29.630 0.00 0.00 44.59 1.40
307 337 8.828751 ACTACTTGTCACATATACCCCTAAAAA 58.171 33.333 0.00 0.00 0.00 1.94
308 338 8.383374 ACTACTTGTCACATATACCCCTAAAA 57.617 34.615 0.00 0.00 0.00 1.52
309 339 7.983166 ACTACTTGTCACATATACCCCTAAA 57.017 36.000 0.00 0.00 0.00 1.85
310 340 7.983166 AACTACTTGTCACATATACCCCTAA 57.017 36.000 0.00 0.00 0.00 2.69
311 341 9.664777 ATTAACTACTTGTCACATATACCCCTA 57.335 33.333 0.00 0.00 0.00 3.53
312 342 7.983166 TTAACTACTTGTCACATATACCCCT 57.017 36.000 0.00 0.00 0.00 4.79
313 343 8.426489 TGATTAACTACTTGTCACATATACCCC 58.574 37.037 0.00 0.00 0.00 4.95
314 344 9.257651 GTGATTAACTACTTGTCACATATACCC 57.742 37.037 0.00 0.00 39.10 3.69
315 345 9.811995 TGTGATTAACTACTTGTCACATATACC 57.188 33.333 2.68 0.00 42.82 2.73
321 351 6.342111 TGTGTGTGATTAACTACTTGTCACA 58.658 36.000 2.68 2.68 44.74 3.58
322 352 6.838198 TGTGTGTGATTAACTACTTGTCAC 57.162 37.500 0.00 0.00 39.58 3.67
323 353 6.819146 TGTTGTGTGTGATTAACTACTTGTCA 59.181 34.615 0.00 0.00 0.00 3.58
324 354 7.241663 TGTTGTGTGTGATTAACTACTTGTC 57.758 36.000 0.00 0.00 0.00 3.18
325 355 7.335924 AGTTGTTGTGTGTGATTAACTACTTGT 59.664 33.333 0.00 0.00 36.30 3.16
326 356 7.693952 AGTTGTTGTGTGTGATTAACTACTTG 58.306 34.615 0.00 0.00 36.30 3.16
327 357 7.859325 AGTTGTTGTGTGTGATTAACTACTT 57.141 32.000 0.00 0.00 36.30 2.24
328 358 8.988934 CATAGTTGTTGTGTGTGATTAACTACT 58.011 33.333 0.00 0.00 40.39 2.57
329 359 8.227791 CCATAGTTGTTGTGTGTGATTAACTAC 58.772 37.037 0.00 0.00 33.56 2.73
330 360 7.934665 ACCATAGTTGTTGTGTGTGATTAACTA 59.065 33.333 0.00 0.00 34.75 2.24
331 361 6.770785 ACCATAGTTGTTGTGTGTGATTAACT 59.229 34.615 0.00 0.00 0.00 2.24
393 423 7.903145 TCTCTGCTTTGGTTAACTATAGTTGA 58.097 34.615 25.27 16.23 38.90 3.18
412 442 4.393062 TGTAAAAGCATAGCAACTCTCTGC 59.607 41.667 0.00 0.00 43.06 4.26
474 506 3.342377 TGACGATTTAGTTGCCATCCA 57.658 42.857 0.00 0.00 0.00 3.41
560 592 1.047034 GTACTACGCATCCCCACCCT 61.047 60.000 0.00 0.00 0.00 4.34
572 604 2.722629 CACACGTCCAACAAGTACTACG 59.277 50.000 11.12 11.12 36.48 3.51
614 646 2.224185 ACAGTAGAATTGTCCACACGCA 60.224 45.455 0.00 0.00 0.00 5.24
615 647 2.413837 ACAGTAGAATTGTCCACACGC 58.586 47.619 0.00 0.00 0.00 5.34
623 655 4.134563 GTGTGGGTGAACAGTAGAATTGT 58.865 43.478 0.00 0.00 0.00 2.71
638 670 4.562425 CACGGGCTGTGTGTGGGT 62.562 66.667 18.40 0.00 43.88 4.51
659 691 2.673523 GCATGAGCAGGGGACAGT 59.326 61.111 0.00 0.00 41.58 3.55
693 725 2.878406 GTGTGGCATAATAGGCATTCGT 59.122 45.455 0.00 0.00 46.23 3.85
744 778 4.097892 CAGTAGAAGGTTTGCAACAAAGGT 59.902 41.667 0.00 0.00 0.00 3.50
745 779 4.610945 CAGTAGAAGGTTTGCAACAAAGG 58.389 43.478 0.00 0.00 0.00 3.11
746 780 4.044426 GCAGTAGAAGGTTTGCAACAAAG 58.956 43.478 0.00 0.00 36.59 2.77
747 781 3.445450 TGCAGTAGAAGGTTTGCAACAAA 59.555 39.130 0.00 0.00 42.96 2.83
748 782 3.020274 TGCAGTAGAAGGTTTGCAACAA 58.980 40.909 0.00 0.00 42.96 2.83
749 783 2.649190 TGCAGTAGAAGGTTTGCAACA 58.351 42.857 0.00 0.00 42.96 3.33
753 787 2.076863 ACGATGCAGTAGAAGGTTTGC 58.923 47.619 0.00 0.00 37.09 3.68
754 788 3.067106 ACACGATGCAGTAGAAGGTTTG 58.933 45.455 0.00 0.00 0.00 2.93
755 789 3.402628 ACACGATGCAGTAGAAGGTTT 57.597 42.857 0.00 0.00 0.00 3.27
756 790 3.326747 GAACACGATGCAGTAGAAGGTT 58.673 45.455 0.00 0.00 0.00 3.50
757 791 2.671351 CGAACACGATGCAGTAGAAGGT 60.671 50.000 0.00 0.00 0.00 3.50
758 792 1.920574 CGAACACGATGCAGTAGAAGG 59.079 52.381 0.00 0.00 0.00 3.46
759 793 2.594654 GACGAACACGATGCAGTAGAAG 59.405 50.000 0.00 0.00 0.00 2.85
760 794 2.030628 TGACGAACACGATGCAGTAGAA 60.031 45.455 0.00 0.00 0.00 2.10
761 795 1.538075 TGACGAACACGATGCAGTAGA 59.462 47.619 0.00 0.00 0.00 2.59
762 796 1.649171 GTGACGAACACGATGCAGTAG 59.351 52.381 0.00 0.00 39.78 2.57
763 797 1.693467 GTGACGAACACGATGCAGTA 58.307 50.000 0.00 0.00 39.78 2.74
764 798 2.517598 GTGACGAACACGATGCAGT 58.482 52.632 0.00 0.00 39.78 4.40
772 806 1.266175 TCTCTTCTCCGTGACGAACAC 59.734 52.381 6.54 0.00 45.11 3.32
773 807 1.601166 TCTCTTCTCCGTGACGAACA 58.399 50.000 6.54 0.00 0.00 3.18
798 832 1.294459 GGGCGGGTATCGTATTCCC 59.706 63.158 0.00 0.00 41.72 3.97
815 849 6.804783 ACTACACTTCTGTTTTTGTTTTTCGG 59.195 34.615 0.00 0.00 0.00 4.30
822 862 4.271776 GCCGTACTACACTTCTGTTTTTGT 59.728 41.667 0.00 0.00 0.00 2.83
967 1013 2.626780 GGCCGTGGAAAGTGAAGGC 61.627 63.158 0.00 0.00 43.47 4.35
1065 1115 2.583593 GGGAGCTCGCACGACATC 60.584 66.667 24.65 0.00 0.00 3.06
1213 1263 0.036388 CAACCGTGGGCAGAGTACAT 60.036 55.000 0.00 0.00 0.00 2.29
1223 1273 0.386731 GCAATTCGTTCAACCGTGGG 60.387 55.000 0.00 0.00 0.00 4.61
1233 1283 0.802494 AGAATTCCGCGCAATTCGTT 59.198 45.000 25.30 10.14 44.40 3.85
1295 1346 1.804372 GCTATGAACAGAGGACAGCCG 60.804 57.143 0.00 0.00 39.96 5.52
1374 1427 5.729424 GCGCATGCTTGAAAAATATTTGAAC 59.271 36.000 17.13 0.00 38.39 3.18
1381 1434 3.057666 TCTGTGCGCATGCTTGAAAAATA 60.058 39.130 15.91 0.00 43.34 1.40
1385 1438 0.040157 GTCTGTGCGCATGCTTGAAA 60.040 50.000 15.91 0.00 43.34 2.69
1402 1469 5.457148 CGTAGTGCAGAAATCTACTGATGTC 59.543 44.000 9.09 0.00 37.23 3.06
1435 1519 7.703058 TTTTTCAAAAATTTGCCACCCTTTA 57.297 28.000 0.98 0.00 38.05 1.85
1507 1593 5.754782 ACCTGTACATATCCTTGCAATTCA 58.245 37.500 0.00 0.00 0.00 2.57
1571 1667 4.837972 TGGTGGATTCGTATGTTGATTGA 58.162 39.130 0.00 0.00 0.00 2.57
1572 1668 5.558844 CGATGGTGGATTCGTATGTTGATTG 60.559 44.000 0.00 0.00 0.00 2.67
1573 1669 4.511454 CGATGGTGGATTCGTATGTTGATT 59.489 41.667 0.00 0.00 0.00 2.57
1574 1670 4.058124 CGATGGTGGATTCGTATGTTGAT 58.942 43.478 0.00 0.00 0.00 2.57
1584 1680 2.890808 TACTGCTCGATGGTGGATTC 57.109 50.000 0.00 0.00 0.00 2.52
1598 1694 6.382869 AATTGCCTTGATAAGTCATACTGC 57.617 37.500 0.00 0.00 33.56 4.40
1752 1850 3.987868 CGTGTCCCCATATTCGTGATTAG 59.012 47.826 0.00 0.00 0.00 1.73
1755 1853 1.760613 ACGTGTCCCCATATTCGTGAT 59.239 47.619 0.00 0.00 0.00 3.06
1798 1896 4.513692 AGTTGCTGTTACAAGCGTTTGATA 59.486 37.500 19.42 4.78 46.65 2.15
1799 1897 3.315191 AGTTGCTGTTACAAGCGTTTGAT 59.685 39.130 19.42 5.74 46.65 2.57
1801 1899 2.783284 CAGTTGCTGTTACAAGCGTTTG 59.217 45.455 10.72 10.72 46.65 2.93
1802 1900 2.794631 GCAGTTGCTGTTACAAGCGTTT 60.795 45.455 0.00 0.00 46.65 3.60
1805 1903 3.077339 GCAGTTGCTGTTACAAGCG 57.923 52.632 0.00 0.00 46.65 4.68
1849 1947 2.284405 AGTGGACCGGGTAGTGGG 60.284 66.667 6.32 0.00 0.00 4.61
1859 1957 4.448060 CGAGTTAAAGTCTTTGAGTGGACC 59.552 45.833 8.14 0.00 33.39 4.46
1867 1965 8.913656 CCTAACTACTTCGAGTTAAAGTCTTTG 58.086 37.037 8.14 0.00 40.51 2.77
1868 1966 8.087136 CCCTAACTACTTCGAGTTAAAGTCTTT 58.913 37.037 2.81 2.81 40.51 2.52
1882 1980 7.362802 ACATCTGATAACCCCTAACTACTTC 57.637 40.000 0.00 0.00 0.00 3.01
1901 2009 4.029520 AGTTGTCAGGCAGATCTACATCT 58.970 43.478 0.00 0.00 40.32 2.90
1906 2014 5.204292 ACATCTAGTTGTCAGGCAGATCTA 58.796 41.667 0.00 0.00 0.00 1.98
1910 2018 3.876274 GACATCTAGTTGTCAGGCAGA 57.124 47.619 23.25 0.00 44.38 4.26
1960 2069 2.422093 GGGTCCCTTTGCTCTTATCAGG 60.422 54.545 0.00 0.00 0.00 3.86
1961 2070 2.239654 TGGGTCCCTTTGCTCTTATCAG 59.760 50.000 10.00 0.00 0.00 2.90
2041 2150 3.194620 TCCTATGGGGCTTAGACCAAAA 58.805 45.455 6.40 0.00 40.73 2.44
2060 2169 4.161333 CACGCAGAATTCAGACAAAATCC 58.839 43.478 8.44 0.00 0.00 3.01
2068 2177 1.532437 CAACTGCACGCAGAATTCAGA 59.468 47.619 25.09 0.00 46.30 3.27
2078 2187 3.730761 CAGCTCCCAACTGCACGC 61.731 66.667 0.00 0.00 0.00 5.34
2167 2276 7.283127 GGAAAGTATGCTGATTGATAAACCTGA 59.717 37.037 0.00 0.00 0.00 3.86
2377 2486 7.232534 TCAAGGTGCATAGGTAAACTGAAATTT 59.767 33.333 0.00 0.00 0.00 1.82
2453 2562 7.545615 GGCAATTTGATCCTTGTTAACCTAAAG 59.454 37.037 2.48 0.21 0.00 1.85
2514 2623 7.009907 GCTTACCATTATCTAAGACGTCGTTTT 59.990 37.037 9.81 6.39 0.00 2.43
2523 2632 8.540507 AAGAGTCTGCTTACCATTATCTAAGA 57.459 34.615 0.00 0.00 0.00 2.10
2612 2826 5.353938 CACAGAATCCATAAAATTGCCCTG 58.646 41.667 0.00 0.00 0.00 4.45
2652 2866 4.907269 ACCTTCACCAAATTTGAGGGAAAT 59.093 37.500 19.86 9.96 41.68 2.17
2679 2893 5.316167 AGGTTGAGTCAAGCATTAATCACA 58.684 37.500 30.80 0.00 43.28 3.58
2693 2907 7.760340 ACTTATATGACGAGAAAAGGTTGAGTC 59.240 37.037 0.00 0.00 0.00 3.36
2742 2956 9.161629 CAGTATATGGAACTGTCACAACAAATA 57.838 33.333 0.00 0.00 39.61 1.40
2743 2957 7.882791 TCAGTATATGGAACTGTCACAACAAAT 59.117 33.333 4.45 0.00 43.88 2.32
2746 2960 6.163476 GTCAGTATATGGAACTGTCACAACA 58.837 40.000 4.45 0.00 43.88 3.33
2747 2961 5.581085 GGTCAGTATATGGAACTGTCACAAC 59.419 44.000 4.45 0.00 43.88 3.32
2771 2985 1.517242 GGTCCTGAAACAGAGCACAG 58.483 55.000 0.00 0.00 32.44 3.66
2795 3009 4.406648 TGCTAGATGACTACCATTGTGG 57.593 45.455 0.00 0.00 45.02 4.17
2798 3012 4.272018 GTGCTTGCTAGATGACTACCATTG 59.728 45.833 0.00 0.00 35.17 2.82
2828 3042 5.005740 ACAATCTTCAATGTAGCAAGAGCA 58.994 37.500 0.00 0.00 45.49 4.26
2831 3045 6.711277 ACCTACAATCTTCAATGTAGCAAGA 58.289 36.000 7.29 0.00 44.86 3.02
2909 3123 2.328099 CCTTCCGTCTGGTTGCTGC 61.328 63.158 0.00 0.00 36.30 5.25
2921 3135 4.142687 CCAAAGCTAAACACATACCTTCCG 60.143 45.833 0.00 0.00 0.00 4.30
2997 3211 2.213499 CAGGTCGTAGATGGAAATGCC 58.787 52.381 0.00 0.00 40.67 4.40
2999 3213 2.905075 TGCAGGTCGTAGATGGAAATG 58.095 47.619 0.00 0.00 40.67 2.32
3012 3226 8.662781 TTCTAGTGATAATGTTAATGCAGGTC 57.337 34.615 0.00 0.00 0.00 3.85
3039 3253 7.619964 TTCCGGTGATTATTTCCTAGAAAAC 57.380 36.000 0.00 0.00 0.00 2.43
3049 3263 7.116736 AGGTGAAACTATTCCGGTGATTATTT 58.883 34.615 0.00 1.95 36.74 1.40
3050 3264 6.659824 AGGTGAAACTATTCCGGTGATTATT 58.340 36.000 0.00 0.00 36.74 1.40
3051 3265 6.248569 AGGTGAAACTATTCCGGTGATTAT 57.751 37.500 0.00 0.00 36.74 1.28
3052 3266 5.687166 AGGTGAAACTATTCCGGTGATTA 57.313 39.130 0.00 0.00 36.74 1.75
3075 3293 2.976589 CAGCATGTGAGGTATGTGACA 58.023 47.619 0.00 0.00 0.00 3.58
3133 3351 9.479549 AACAAAACTATAATGAAGGATGTGGAT 57.520 29.630 0.00 0.00 0.00 3.41
3178 3396 7.116233 CACATGGTAAATGAAAAGGCTTACAAC 59.884 37.037 0.00 0.23 0.00 3.32
3309 3527 7.223971 GCATTTCGGAGTATCATAACAGTACAA 59.776 37.037 0.00 0.00 36.25 2.41
3324 3542 1.609208 ACTTGCAAGCATTTCGGAGT 58.391 45.000 26.27 0.00 0.00 3.85
3329 3547 5.672321 GCACTAGACTACTTGCAAGCATTTC 60.672 44.000 26.27 16.37 32.19 2.17
3362 3580 9.612066 AATAAAACAGGAAAGAAAGCAAAATGA 57.388 25.926 0.00 0.00 0.00 2.57
3374 3592 7.013274 TCTGAGTTGACCAATAAAACAGGAAAG 59.987 37.037 0.00 0.00 0.00 2.62
3377 3595 5.935945 TCTGAGTTGACCAATAAAACAGGA 58.064 37.500 0.00 0.00 0.00 3.86
3442 3678 5.936956 AGTAGGCATGAAGCTATAAAGATGC 59.063 40.000 0.00 0.00 44.79 3.91
3478 3716 3.470645 ACAAAGCGTAGGTCTGTTTCT 57.529 42.857 0.00 0.00 37.06 2.52
3505 3743 2.433838 CAGTGCTCCTCACCTGCG 60.434 66.667 0.00 0.00 46.81 5.18
3566 3807 5.122869 TGAGAACAGAGCTCAAATGCATAAC 59.877 40.000 17.77 0.00 39.29 1.89
3568 3809 4.835678 TGAGAACAGAGCTCAAATGCATA 58.164 39.130 17.77 0.00 39.29 3.14
3617 3858 2.061848 TCCTTGTCCATTCCTGACCAA 58.938 47.619 0.00 0.00 31.60 3.67
3694 3935 6.687081 TCACTGAAAAATGAAAACTACGGT 57.313 33.333 0.00 0.00 0.00 4.83
3695 3936 7.138736 ACATCACTGAAAAATGAAAACTACGG 58.861 34.615 0.00 0.00 0.00 4.02
3700 3941 9.736023 ACTCTTACATCACTGAAAAATGAAAAC 57.264 29.630 0.00 0.00 0.00 2.43
3702 3943 8.902806 ACACTCTTACATCACTGAAAAATGAAA 58.097 29.630 0.00 0.00 0.00 2.69
3703 3944 8.450578 ACACTCTTACATCACTGAAAAATGAA 57.549 30.769 0.00 0.00 0.00 2.57
3704 3945 8.450578 AACACTCTTACATCACTGAAAAATGA 57.549 30.769 0.00 0.00 0.00 2.57
3705 3946 8.562892 AGAACACTCTTACATCACTGAAAAATG 58.437 33.333 0.00 0.00 0.00 2.32
3706 3947 8.562892 CAGAACACTCTTACATCACTGAAAAAT 58.437 33.333 0.00 0.00 0.00 1.82
3707 3948 7.467267 GCAGAACACTCTTACATCACTGAAAAA 60.467 37.037 0.00 0.00 0.00 1.94
3772 4117 1.290203 CCACCGTCATATGACTGCAC 58.710 55.000 28.51 7.72 42.66 4.57
3879 4225 6.503524 ACTTAACTTAGTTGCCACACAATTG 58.496 36.000 8.00 3.24 41.27 2.32
3882 4228 5.433526 AGACTTAACTTAGTTGCCACACAA 58.566 37.500 8.00 0.00 35.33 3.33
4050 4401 2.536928 GGAGCAATTGTACGTCAATCGC 60.537 50.000 7.40 12.71 44.85 4.58
4105 4456 4.767578 ATGGATAACTGCAGAGACACAT 57.232 40.909 23.35 15.33 0.00 3.21
4111 4462 7.137426 GCAGATTTTAATGGATAACTGCAGAG 58.863 38.462 23.35 0.00 45.48 3.35
4196 4547 8.889717 CCGGTAAGCTAATAAAGAGATTTTTGA 58.110 33.333 0.00 0.00 0.00 2.69
4204 4555 6.103997 TGTTCACCGGTAAGCTAATAAAGAG 58.896 40.000 6.87 0.00 0.00 2.85
4219 4570 0.719465 GCGTCAGTAATGTTCACCGG 59.281 55.000 0.00 0.00 0.00 5.28
4240 4592 2.362736 CTCTACACAATGGCACTGCAT 58.637 47.619 2.82 0.00 0.00 3.96
4247 4599 0.453390 GCTTGCCTCTACACAATGGC 59.547 55.000 0.00 0.00 45.10 4.40
4248 4600 0.729116 CGCTTGCCTCTACACAATGG 59.271 55.000 0.00 0.00 0.00 3.16
4267 4622 1.452108 CTGAAATCCCCCGTCTGCC 60.452 63.158 0.00 0.00 0.00 4.85
4342 4697 9.267071 TCAGCCAAATAGCAGTATATATAGGAA 57.733 33.333 0.00 0.00 34.23 3.36
4347 4702 7.768120 GCTTCTCAGCCAAATAGCAGTATATAT 59.232 37.037 0.00 0.00 40.61 0.86
4349 4704 5.936956 GCTTCTCAGCCAAATAGCAGTATAT 59.063 40.000 0.00 0.00 40.61 0.86
4390 4745 5.405269 GCAGCAAACAAATTTTTATCGAGGT 59.595 36.000 0.00 0.00 0.00 3.85
4391 4746 5.163963 GGCAGCAAACAAATTTTTATCGAGG 60.164 40.000 0.00 0.00 0.00 4.63
4394 4749 4.450419 TGGGCAGCAAACAAATTTTTATCG 59.550 37.500 0.00 0.00 0.00 2.92
4454 4809 1.386533 AGGCGCCAATCATCTTCAAG 58.613 50.000 31.54 0.00 0.00 3.02
4504 4859 1.228245 TGGCAGGTGAGCAGAAACC 60.228 57.895 0.00 0.00 36.66 3.27
4571 4926 9.936759 GGTTTTATATTTGGTTGAAATCTTGGA 57.063 29.630 0.00 0.00 35.74 3.53
4572 4927 9.942850 AGGTTTTATATTTGGTTGAAATCTTGG 57.057 29.630 0.00 0.00 35.74 3.61
4627 4982 4.715527 ACGAGTCAGTAAAGGACCATAC 57.284 45.455 0.00 0.00 35.89 2.39
4628 4983 5.733620 AAACGAGTCAGTAAAGGACCATA 57.266 39.130 0.00 0.00 35.89 2.74
4794 5150 2.811514 GGCGATGATCCCCAGCTCA 61.812 63.158 0.00 0.00 0.00 4.26
4831 5187 2.190578 GGGAGGATCGGTGCCTTG 59.809 66.667 0.00 0.00 35.44 3.61
4895 5258 3.498774 ATGGTGGATGGATCTTACAGC 57.501 47.619 0.00 0.00 0.00 4.40
4957 5320 2.517450 CGCGACGGATCAAGAAGCC 61.517 63.158 0.00 0.00 0.00 4.35
4959 5322 1.078759 AAGCGCGACGGATCAAGAAG 61.079 55.000 12.10 0.00 0.00 2.85
4998 5361 1.069022 CACATCAAACAGCTCAACCGG 60.069 52.381 0.00 0.00 0.00 5.28
5012 5434 2.231235 TCAGTAGCTTTCGAGCACATCA 59.769 45.455 0.00 0.00 37.25 3.07
5016 5438 2.638556 TCTCAGTAGCTTTCGAGCAC 57.361 50.000 0.00 0.00 37.25 4.40
5056 5479 0.101219 GATGCAAAATCCGGGCAGAC 59.899 55.000 0.00 0.00 41.40 3.51
5063 5486 0.455972 AAACGCCGATGCAAAATCCG 60.456 50.000 0.00 0.00 37.32 4.18
5067 5490 2.430546 ATTCAAACGCCGATGCAAAA 57.569 40.000 0.00 0.00 37.32 2.44
5075 5498 2.706123 GCACGCAATTCAAACGCCG 61.706 57.895 0.00 0.00 0.00 6.46
5076 5499 2.371923 GGCACGCAATTCAAACGCC 61.372 57.895 0.00 0.00 0.00 5.68
5079 5502 0.109319 ATCGGGCACGCAATTCAAAC 60.109 50.000 1.67 0.00 40.69 2.93
5094 5517 2.885676 CGCGCCATTTCCTCATCGG 61.886 63.158 0.00 0.00 0.00 4.18
5101 5524 3.361977 ACCACACGCGCCATTTCC 61.362 61.111 5.73 0.00 0.00 3.13
5127 5550 3.521796 GCCCGAATCCAGCTTGCC 61.522 66.667 0.00 0.00 0.00 4.52
5152 5578 1.146263 GCTCCCATCTACCCAACCG 59.854 63.158 0.00 0.00 0.00 4.44
5211 6366 4.427661 AGCGAGTGAGCGAGTGGC 62.428 66.667 0.00 0.00 43.00 5.01
5218 6373 2.872001 CACGACGAGCGAGTGAGC 60.872 66.667 0.00 0.00 44.57 4.26
5233 6388 0.381089 AGATCGGATCGTTCGGACAC 59.619 55.000 12.08 4.56 34.45 3.67
5264 6430 0.928229 CGATCGGTTTGAATCCGGAC 59.072 55.000 6.12 0.00 46.82 4.79
5268 6434 0.026285 CACGCGATCGGTTTGAATCC 59.974 55.000 15.93 0.00 40.69 3.01
5285 6452 2.105128 CTCTGCCGGGATCGACAC 59.895 66.667 2.18 0.00 39.00 3.67
5286 6453 1.541310 AAACTCTGCCGGGATCGACA 61.541 55.000 2.18 0.00 39.00 4.35
5287 6454 1.084370 CAAACTCTGCCGGGATCGAC 61.084 60.000 2.18 0.00 39.00 4.20
5288 6455 1.218047 CAAACTCTGCCGGGATCGA 59.782 57.895 2.18 0.00 39.00 3.59
5289 6456 0.673644 AACAAACTCTGCCGGGATCG 60.674 55.000 2.18 0.00 0.00 3.69
5290 6457 0.804989 CAACAAACTCTGCCGGGATC 59.195 55.000 2.18 0.00 0.00 3.36
5291 6458 0.609131 CCAACAAACTCTGCCGGGAT 60.609 55.000 2.18 0.00 0.00 3.85
5292 6459 1.228124 CCAACAAACTCTGCCGGGA 60.228 57.895 2.18 0.00 0.00 5.14
5293 6460 2.919494 GCCAACAAACTCTGCCGGG 61.919 63.158 2.18 0.00 0.00 5.73
5294 6461 2.644992 GCCAACAAACTCTGCCGG 59.355 61.111 0.00 0.00 0.00 6.13
5295 6462 2.133742 CTGGCCAACAAACTCTGCCG 62.134 60.000 7.01 0.00 45.12 5.69
5336 6503 1.527311 GGAAGAAATAGCACGCGGATC 59.473 52.381 12.47 0.00 0.00 3.36
5380 7846 0.465460 AATAATGGCCGCCGATGTGT 60.465 50.000 4.58 0.00 0.00 3.72
5381 7847 0.667993 AAATAATGGCCGCCGATGTG 59.332 50.000 4.58 0.00 0.00 3.21
5442 7909 4.261197 CCATTTATTTGTTCTCTAGGCCGC 60.261 45.833 0.00 0.00 0.00 6.53
5444 7911 5.188327 GCCATTTATTTGTTCTCTAGGCC 57.812 43.478 0.00 0.00 32.50 5.19
5445 7912 4.261197 CGGCCATTTATTTGTTCTCTAGGC 60.261 45.833 2.24 0.00 37.69 3.93
5446 7913 4.275936 CCGGCCATTTATTTGTTCTCTAGG 59.724 45.833 2.24 0.00 0.00 3.02
5447 7914 4.261197 GCCGGCCATTTATTTGTTCTCTAG 60.261 45.833 18.11 0.00 0.00 2.43
5448 7915 3.630312 GCCGGCCATTTATTTGTTCTCTA 59.370 43.478 18.11 0.00 0.00 2.43
5449 7916 2.427095 GCCGGCCATTTATTTGTTCTCT 59.573 45.455 18.11 0.00 0.00 3.10
5450 7917 2.794631 CGCCGGCCATTTATTTGTTCTC 60.795 50.000 23.46 0.00 0.00 2.87
5451 7918 1.134175 CGCCGGCCATTTATTTGTTCT 59.866 47.619 23.46 0.00 0.00 3.01
5452 7919 1.135228 ACGCCGGCCATTTATTTGTTC 60.135 47.619 23.46 0.00 0.00 3.18
5453 7920 0.892063 ACGCCGGCCATTTATTTGTT 59.108 45.000 23.46 0.00 0.00 2.83
5454 7921 0.454196 GACGCCGGCCATTTATTTGT 59.546 50.000 23.46 9.49 0.00 2.83
5455 7922 0.591236 CGACGCCGGCCATTTATTTG 60.591 55.000 23.46 5.65 0.00 2.32
5456 7923 1.725066 CGACGCCGGCCATTTATTT 59.275 52.632 23.46 0.00 0.00 1.40
5457 7924 3.416490 CGACGCCGGCCATTTATT 58.584 55.556 23.46 0.00 0.00 1.40
5501 7968 1.445582 CGACCCAGTTGTAGACGGC 60.446 63.158 0.00 0.00 0.00 5.68
5541 8008 6.196434 TCCATCCATCAAATCCAATGAAAGA 58.804 36.000 0.00 0.00 0.00 2.52
5547 8014 5.082633 TCCATCCATCCATCAAATCCAAT 57.917 39.130 0.00 0.00 0.00 3.16
5549 8016 4.412843 CATCCATCCATCCATCAAATCCA 58.587 43.478 0.00 0.00 0.00 3.41
5550 8017 3.767673 CCATCCATCCATCCATCAAATCC 59.232 47.826 0.00 0.00 0.00 3.01
5551 8018 4.669700 TCCATCCATCCATCCATCAAATC 58.330 43.478 0.00 0.00 0.00 2.17
5552 8019 4.752621 TCCATCCATCCATCCATCAAAT 57.247 40.909 0.00 0.00 0.00 2.32
5554 8021 3.245479 CCATCCATCCATCCATCCATCAA 60.245 47.826 0.00 0.00 0.00 2.57
5555 8022 2.310647 CCATCCATCCATCCATCCATCA 59.689 50.000 0.00 0.00 0.00 3.07
5556 8023 2.579400 TCCATCCATCCATCCATCCATC 59.421 50.000 0.00 0.00 0.00 3.51
5557 8024 2.651190 TCCATCCATCCATCCATCCAT 58.349 47.619 0.00 0.00 0.00 3.41
5563 8030 2.851194 AGATCCATCCATCCATCCATCC 59.149 50.000 0.00 0.00 0.00 3.51
5587 8054 0.318107 CAGACCCAAAGCAAGCAACG 60.318 55.000 0.00 0.00 0.00 4.10
5625 8092 3.989787 CGCCCTGCCAACCAAACC 61.990 66.667 0.00 0.00 0.00 3.27
5626 8093 4.662961 GCGCCCTGCCAACCAAAC 62.663 66.667 0.00 0.00 37.76 2.93
5763 8230 3.904800 GGGGGAAGAAGAGAAGAGAAG 57.095 52.381 0.00 0.00 0.00 2.85
5795 8262 3.368948 GCTAGGAGTCAACTCAAAGAGGG 60.369 52.174 11.99 0.00 44.60 4.30


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

AutoCloner maintained by Alex Coulton.