Multiple sequence alignment - TraesCS3B01G440800

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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 TraesCS3B01G440800 chr3B 100.000 3690 0 0 2857 6546 680421977 680425666 0.000000e+00 6815.0
1 TraesCS3B01G440800 chr3B 100.000 2551 0 0 1 2551 680419121 680421671 0.000000e+00 4711.0
2 TraesCS3B01G440800 chr3B 96.691 544 16 1 1 544 823510405 823510946 0.000000e+00 904.0
3 TraesCS3B01G440800 chr3B 94.624 93 4 1 4175 4266 126580153 126580061 6.840000e-30 143.0
4 TraesCS3B01G440800 chr3B 85.393 89 3 3 2957 3035 187335767 187335679 4.210000e-12 84.2
5 TraesCS3B01G440800 chr3A 94.753 1982 84 12 3031 4998 652028775 652026800 0.000000e+00 3066.0
6 TraesCS3B01G440800 chr3A 94.828 1508 61 10 5044 6546 652026787 652025292 0.000000e+00 2337.0
7 TraesCS3B01G440800 chr3A 92.884 1082 58 7 608 1687 652029893 652028829 0.000000e+00 1554.0
8 TraesCS3B01G440800 chr3A 83.455 550 67 10 1904 2430 217840878 217840330 2.120000e-134 490.0
9 TraesCS3B01G440800 chr3A 95.000 40 2 0 2857 2896 698273233 698273272 5.480000e-06 63.9
10 TraesCS3B01G440800 chr3D 91.938 1873 97 20 4684 6546 516880102 516878274 0.000000e+00 2573.0
11 TraesCS3B01G440800 chr3D 95.606 1593 63 7 3031 4622 516881694 516880108 0.000000e+00 2547.0
12 TraesCS3B01G440800 chr3D 94.917 1082 52 3 608 1687 516882828 516881748 0.000000e+00 1690.0
13 TraesCS3B01G440800 chr1B 96.875 544 14 3 1 544 28492052 28492592 0.000000e+00 907.0
14 TraesCS3B01G440800 chr1B 94.803 558 28 1 1 557 656572951 656572394 0.000000e+00 869.0
15 TraesCS3B01G440800 chr1B 87.692 65 7 1 2971 3035 198732979 198733042 2.530000e-09 75.0
16 TraesCS3B01G440800 chr2B 96.514 545 18 1 1 544 799411192 799411736 0.000000e+00 900.0
17 TraesCS3B01G440800 chr2B 93.680 538 26 4 8 545 379784449 379784978 0.000000e+00 798.0
18 TraesCS3B01G440800 chr2B 84.786 677 72 20 1686 2345 761627972 761627310 0.000000e+00 651.0
19 TraesCS3B01G440800 chr2B 84.786 677 72 20 1686 2345 761653973 761653311 0.000000e+00 651.0
20 TraesCS3B01G440800 chr2B 84.786 677 72 19 1686 2345 761684081 761683419 0.000000e+00 651.0
21 TraesCS3B01G440800 chr2B 84.211 95 4 4 2952 3035 782178848 782178754 1.510000e-11 82.4
22 TraesCS3B01G440800 chr2B 94.872 39 2 0 2857 2895 761616499 761616461 1.970000e-05 62.1
23 TraesCS3B01G440800 chr2B 94.872 39 2 0 2857 2895 761672535 761672497 1.970000e-05 62.1
24 TraesCS3B01G440800 chr6B 95.430 547 21 2 1 544 654179704 654180249 0.000000e+00 869.0
25 TraesCS3B01G440800 chr6B 86.420 81 3 3 2960 3035 657250024 657249947 1.510000e-11 82.4
26 TraesCS3B01G440800 chr4B 95.264 549 23 3 1 548 166767946 166767400 0.000000e+00 867.0
27 TraesCS3B01G440800 chr4B 96.078 51 2 0 2988 3038 399559017 399558967 4.210000e-12 84.2
28 TraesCS3B01G440800 chr7B 94.600 537 26 3 1 536 105475454 105474920 0.000000e+00 828.0
29 TraesCS3B01G440800 chr7B 91.525 59 4 1 2988 3045 119145275 119145333 5.440000e-11 80.5
30 TraesCS3B01G440800 chr5A 92.791 541 38 1 8 547 672025302 672025842 0.000000e+00 782.0
31 TraesCS3B01G440800 chr5A 85.564 762 80 19 1686 2429 487272619 487271870 0.000000e+00 771.0
32 TraesCS3B01G440800 chr5A 95.000 40 2 0 2857 2896 487271735 487271696 5.480000e-06 63.9
33 TraesCS3B01G440800 chr7A 85.621 765 81 18 1685 2432 724116157 724115405 0.000000e+00 776.0
34 TraesCS3B01G440800 chr7A 86.116 569 46 17 1686 2234 689536646 689536091 3.400000e-162 582.0
35 TraesCS3B01G440800 chr7A 96.591 88 3 0 4178 4265 398924432 398924519 5.290000e-31 147.0
36 TraesCS3B01G440800 chr7A 95.000 40 2 0 2857 2896 724115273 724115234 5.480000e-06 63.9
37 TraesCS3B01G440800 chr2A 82.908 901 109 29 1686 2551 277160829 277159939 0.000000e+00 769.0
38 TraesCS3B01G440800 chr2A 82.336 702 82 23 1738 2432 667687769 667688435 7.360000e-159 571.0
39 TraesCS3B01G440800 chr2A 96.703 91 2 1 4174 4263 593655998 593655908 4.090000e-32 150.0
40 TraesCS3B01G440800 chr2A 91.346 104 8 1 4171 4274 4969446 4969548 2.460000e-29 141.0
41 TraesCS3B01G440800 chr4A 83.558 742 74 18 1686 2411 621001822 621002531 0.000000e+00 651.0
42 TraesCS3B01G440800 chr4A 97.674 86 2 0 4180 4265 590111549 590111634 1.470000e-31 148.0
43 TraesCS3B01G440800 chr4A 94.340 53 1 1 2983 3035 734390848 734390798 5.440000e-11 80.5
44 TraesCS3B01G440800 chr4A 93.023 43 3 0 2857 2899 681657990 681658032 5.480000e-06 63.9
45 TraesCS3B01G440800 chr1A 73.672 866 163 49 3275 4093 460333229 460332382 6.470000e-70 276.0
46 TraesCS3B01G440800 chr1A 83.333 84 6 5 2959 3040 33216304 33216227 3.270000e-08 71.3
47 TraesCS3B01G440800 chr1D 87.162 148 19 0 3946 4093 360479489 360479342 1.130000e-37 169.0
48 TraesCS3B01G440800 chr2D 94.565 92 5 0 4171 4262 299891012 299891103 6.840000e-30 143.0
49 TraesCS3B01G440800 chr2D 94.565 92 5 0 4171 4262 557267175 557267266 6.840000e-30 143.0
50 TraesCS3B01G440800 chr2D 92.857 42 3 0 2857 2898 645370871 645370830 1.970000e-05 62.1
51 TraesCS3B01G440800 chr6D 91.935 62 3 2 2992 3051 284394966 284395027 1.170000e-12 86.1
52 TraesCS3B01G440800 chr6A 95.000 40 2 0 2857 2896 49199883 49199922 5.480000e-06 63.9
53 TraesCS3B01G440800 chrUn 94.872 39 2 0 2857 2895 11758850 11758888 1.970000e-05 62.1


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 TraesCS3B01G440800 chr3B 680419121 680425666 6545 False 5763.00 6815 100.000000 1 6546 2 chr3B.!!$F2 6545
1 TraesCS3B01G440800 chr3B 823510405 823510946 541 False 904.00 904 96.691000 1 544 1 chr3B.!!$F1 543
2 TraesCS3B01G440800 chr3A 652025292 652029893 4601 True 2319.00 3066 94.155000 608 6546 3 chr3A.!!$R2 5938
3 TraesCS3B01G440800 chr3A 217840330 217840878 548 True 490.00 490 83.455000 1904 2430 1 chr3A.!!$R1 526
4 TraesCS3B01G440800 chr3D 516878274 516882828 4554 True 2270.00 2573 94.153667 608 6546 3 chr3D.!!$R1 5938
5 TraesCS3B01G440800 chr1B 28492052 28492592 540 False 907.00 907 96.875000 1 544 1 chr1B.!!$F1 543
6 TraesCS3B01G440800 chr1B 656572394 656572951 557 True 869.00 869 94.803000 1 557 1 chr1B.!!$R1 556
7 TraesCS3B01G440800 chr2B 799411192 799411736 544 False 900.00 900 96.514000 1 544 1 chr2B.!!$F2 543
8 TraesCS3B01G440800 chr2B 379784449 379784978 529 False 798.00 798 93.680000 8 545 1 chr2B.!!$F1 537
9 TraesCS3B01G440800 chr2B 761627310 761627972 662 True 651.00 651 84.786000 1686 2345 1 chr2B.!!$R2 659
10 TraesCS3B01G440800 chr2B 761653311 761653973 662 True 651.00 651 84.786000 1686 2345 1 chr2B.!!$R3 659
11 TraesCS3B01G440800 chr2B 761683419 761684081 662 True 651.00 651 84.786000 1686 2345 1 chr2B.!!$R5 659
12 TraesCS3B01G440800 chr6B 654179704 654180249 545 False 869.00 869 95.430000 1 544 1 chr6B.!!$F1 543
13 TraesCS3B01G440800 chr4B 166767400 166767946 546 True 867.00 867 95.264000 1 548 1 chr4B.!!$R1 547
14 TraesCS3B01G440800 chr7B 105474920 105475454 534 True 828.00 828 94.600000 1 536 1 chr7B.!!$R1 535
15 TraesCS3B01G440800 chr5A 672025302 672025842 540 False 782.00 782 92.791000 8 547 1 chr5A.!!$F1 539
16 TraesCS3B01G440800 chr5A 487271696 487272619 923 True 417.45 771 90.282000 1686 2896 2 chr5A.!!$R1 1210
17 TraesCS3B01G440800 chr7A 689536091 689536646 555 True 582.00 582 86.116000 1686 2234 1 chr7A.!!$R1 548
18 TraesCS3B01G440800 chr7A 724115234 724116157 923 True 419.95 776 90.310500 1685 2896 2 chr7A.!!$R2 1211
19 TraesCS3B01G440800 chr2A 277159939 277160829 890 True 769.00 769 82.908000 1686 2551 1 chr2A.!!$R1 865
20 TraesCS3B01G440800 chr2A 667687769 667688435 666 False 571.00 571 82.336000 1738 2432 1 chr2A.!!$F2 694
21 TraesCS3B01G440800 chr4A 621001822 621002531 709 False 651.00 651 83.558000 1686 2411 1 chr4A.!!$F2 725
22 TraesCS3B01G440800 chr1A 460332382 460333229 847 True 276.00 276 73.672000 3275 4093 1 chr1A.!!$R2 818

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
606 618 0.038744 CCCTGAAGCACCTCCATTGT 59.961 55.000 0.00 0.00 0.0 2.71 F
2153 2205 1.063266 AGGCCTTTGACCCAAGAAACA 60.063 47.619 0.00 0.00 0.0 2.83 F
2974 3053 0.124522 ATTTTACCCCCTCCCTCCCA 59.875 55.000 0.00 0.00 0.0 4.37 F
2975 3054 0.124522 TTTTACCCCCTCCCTCCCAT 59.875 55.000 0.00 0.00 0.0 4.00 F
2979 3058 0.403453 ACCCCCTCCCTCCCATAATG 60.403 60.000 0.00 0.00 0.0 1.90 F
2981 3060 1.132201 CCCCCTCCCTCCCATAATGTA 60.132 57.143 0.00 0.00 0.0 2.29 F
3114 3193 1.213013 CTCGCTGACTGGTTACGCT 59.787 57.895 0.00 0.00 0.0 5.07 F
5006 5210 0.187117 TGTTTCAAGCCCCATGGACA 59.813 50.000 15.22 3.64 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 2417 0.827925 TCCACTGTCTGCTCGTTCCT 60.828 55.000 0.00 0.0 0.00 3.36 R
3017 3096 0.033306 AGAACTACTCCCTCCGTCCC 60.033 60.000 0.00 0.0 0.00 4.46 R
4622 4824 2.656947 AAGGGCACTTCAGCAAGTAA 57.343 45.000 0.00 0.0 41.24 2.24 R
4688 4890 2.715046 TGCTGCCCTTTATTCAGACTG 58.285 47.619 0.00 0.0 0.00 3.51 R
4696 4898 3.031013 GGGTAACATTGCTGCCCTTTAT 58.969 45.455 6.01 0.0 36.49 1.40 R
4731 4933 5.591099 TCTCTCAAACAGAAAATTGGTTGC 58.409 37.500 0.00 0.0 43.74 4.17 R
5013 5217 0.106918 ACCGGGTGCTGAAACAAGAA 60.107 50.000 6.32 0.0 0.00 2.52 R
5841 6052 0.040204 AGGGGTGAAAGAGGCAATGG 59.960 55.000 0.00 0.0 0.00 3.16 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
101 102 8.144478 GGGATTGAAAGAGCTTACTTTTCTTTT 58.856 33.333 2.25 0.00 40.27 2.27
489 499 8.267183 GGGTCAAATCCCAAAATATTTTCAGAT 58.733 33.333 10.53 12.08 46.30 2.90
514 526 8.792830 TTAAGGTCAGATCTCGATTTGATTTT 57.207 30.769 0.00 4.78 34.94 1.82
548 560 0.596341 ACACGAAATTTTGCCGCACC 60.596 50.000 5.27 0.00 0.00 5.01
562 574 2.662596 CACCTGGTCAAGCGCCTA 59.337 61.111 2.29 0.00 0.00 3.93
563 575 1.448540 CACCTGGTCAAGCGCCTAG 60.449 63.158 2.29 0.00 0.00 3.02
564 576 2.187946 CCTGGTCAAGCGCCTAGG 59.812 66.667 2.29 3.67 0.00 3.02
565 577 2.359169 CCTGGTCAAGCGCCTAGGA 61.359 63.158 14.75 0.00 30.79 2.94
566 578 1.142748 CTGGTCAAGCGCCTAGGAG 59.857 63.158 14.75 11.38 0.00 3.69
567 579 1.304962 TGGTCAAGCGCCTAGGAGA 60.305 57.895 17.75 0.49 0.00 3.71
568 580 0.902984 TGGTCAAGCGCCTAGGAGAA 60.903 55.000 17.75 0.00 0.00 2.87
569 581 0.249398 GGTCAAGCGCCTAGGAGAAA 59.751 55.000 17.75 0.00 0.00 2.52
570 582 1.338769 GGTCAAGCGCCTAGGAGAAAA 60.339 52.381 17.75 0.00 0.00 2.29
571 583 2.423577 GTCAAGCGCCTAGGAGAAAAA 58.576 47.619 17.75 0.00 0.00 1.94
601 613 1.995376 TTTTTCCCTGAAGCACCTCC 58.005 50.000 0.00 0.00 0.00 4.30
602 614 0.850100 TTTTCCCTGAAGCACCTCCA 59.150 50.000 0.00 0.00 0.00 3.86
603 615 1.075601 TTTCCCTGAAGCACCTCCAT 58.924 50.000 0.00 0.00 0.00 3.41
604 616 1.075601 TTCCCTGAAGCACCTCCATT 58.924 50.000 0.00 0.00 0.00 3.16
605 617 0.329261 TCCCTGAAGCACCTCCATTG 59.671 55.000 0.00 0.00 0.00 2.82
606 618 0.038744 CCCTGAAGCACCTCCATTGT 59.961 55.000 0.00 0.00 0.00 2.71
610 622 3.005554 CTGAAGCACCTCCATTGTACAG 58.994 50.000 0.00 0.00 0.00 2.74
801 814 2.673523 CTCTCCCCCACAGCCAAG 59.326 66.667 0.00 0.00 0.00 3.61
973 986 2.577593 GACGGAGGGAGGGTTTCG 59.422 66.667 0.00 0.00 0.00 3.46
984 997 1.676303 GGGTTTCGCGGGAATTCCA 60.676 57.895 25.67 2.18 37.91 3.53
1220 1233 1.439353 ATTGCGCTGCTTACCATCGG 61.439 55.000 9.73 0.00 33.89 4.18
1356 1369 7.543905 ATTCCAGCTGAAATCCATGTTGGAAT 61.544 38.462 17.39 14.19 41.77 3.01
1370 1383 6.095300 CCATGTTGGAATAGCAGACATGTAAA 59.905 38.462 0.00 0.00 43.61 2.01
1373 1386 5.692115 TGGAATAGCAGACATGTAAAGGA 57.308 39.130 0.00 0.00 0.00 3.36
1395 1408 4.971125 GGGATAGGGTGAGCGCGC 62.971 72.222 26.66 26.66 0.00 6.86
1407 1420 2.434359 GCGCGCCAGAGTTTAGGT 60.434 61.111 23.24 0.00 0.00 3.08
1415 1428 5.054477 GCGCCAGAGTTTAGGTTGATAATA 58.946 41.667 0.00 0.00 0.00 0.98
1421 1434 9.613428 CCAGAGTTTAGGTTGATAATATTGACA 57.387 33.333 0.00 0.00 0.00 3.58
1464 1477 5.675684 TCACATATGCTGGAGTTTGTAGA 57.324 39.130 1.58 0.00 0.00 2.59
1489 1502 2.066262 GGTGCCGTAATGATATCGGTG 58.934 52.381 9.27 0.00 45.11 4.94
1518 1531 7.273381 GCTTTTATTCTGCATTGTTCGTTACAT 59.727 33.333 0.00 0.00 36.44 2.29
1521 1534 2.161410 TCTGCATTGTTCGTTACATGGC 59.839 45.455 0.00 8.64 36.44 4.40
1531 1544 1.393539 CGTTACATGGCTGCACTGTAC 59.606 52.381 11.56 7.65 0.00 2.90
1561 1574 5.258841 TCTCATCTCATTGTTCAGCCAATT 58.741 37.500 0.00 0.00 32.81 2.32
1606 1620 9.049050 TGTACTAGTTCAATTTAGTGGGGAATA 57.951 33.333 0.00 0.00 32.64 1.75
1623 1637 8.626917 TGGGGAATAACCTCACTAGTTAATTA 57.373 34.615 0.00 0.00 45.39 1.40
1634 1648 9.226606 CCTCACTAGTTAATTATTCCAAACACA 57.773 33.333 0.00 0.00 0.00 3.72
1682 1696 4.889409 TGATTTTTGAGAGCTGTTCTTGGT 59.111 37.500 0.00 0.00 35.87 3.67
1737 1751 1.664874 GCGAACTTAAAAAGTGGGCCG 60.665 52.381 0.00 0.00 41.91 6.13
1746 1760 7.567458 ACTTAAAAAGTGGGCCGAATATAGTA 58.433 34.615 0.00 0.00 41.01 1.82
1809 1833 7.935338 AAAGAAGATACAAAGCACAACATTG 57.065 32.000 0.00 0.00 33.18 2.82
1813 1837 7.981225 AGAAGATACAAAGCACAACATTGTTTT 59.019 29.630 0.00 0.00 40.49 2.43
1827 1851 5.189180 ACATTGTTTTTGCCCTAAAAAGCA 58.811 33.333 0.00 0.00 45.95 3.91
1828 1852 5.827267 ACATTGTTTTTGCCCTAAAAAGCAT 59.173 32.000 0.00 0.00 45.95 3.79
1829 1853 6.017192 ACATTGTTTTTGCCCTAAAAAGCATC 60.017 34.615 0.00 0.00 45.95 3.91
1830 1854 5.289083 TGTTTTTGCCCTAAAAAGCATCT 57.711 34.783 0.00 0.00 45.95 2.90
1834 1860 6.859420 TTTTGCCCTAAAAAGCATCTTTTC 57.141 33.333 5.18 0.00 39.11 2.29
1877 1904 3.951775 ATCGGATCTAACTCATCTGCC 57.048 47.619 0.00 0.00 0.00 4.85
1894 1925 5.280654 TCTGCCAGCATTTTCTTCTTTTT 57.719 34.783 0.00 0.00 0.00 1.94
1895 1926 5.291971 TCTGCCAGCATTTTCTTCTTTTTC 58.708 37.500 0.00 0.00 0.00 2.29
1931 1963 9.697250 GTTTTTAGGCAACATTTTACAAGAAAC 57.303 29.630 0.00 0.00 41.41 2.78
1940 1972 6.725246 ACATTTTACAAGAAACGAGTGGAAG 58.275 36.000 0.00 0.00 0.00 3.46
2034 2078 4.344390 GGGTCCTCGTATCCTCAAATAAGT 59.656 45.833 0.00 0.00 0.00 2.24
2043 2088 8.970020 TCGTATCCTCAAATAAGTAACCTGTAA 58.030 33.333 0.00 0.00 0.00 2.41
2102 2154 3.813529 AACAGTACAAAGATCAAGCGC 57.186 42.857 0.00 0.00 0.00 5.92
2110 2162 4.874970 ACAAAGATCAAGCGCAAAAAGAT 58.125 34.783 11.47 4.89 0.00 2.40
2153 2205 1.063266 AGGCCTTTGACCCAAGAAACA 60.063 47.619 0.00 0.00 0.00 2.83
2245 2301 8.037758 AGATGAGAATACTTATAGGCAAATCCG 58.962 37.037 0.00 0.00 40.77 4.18
2262 2318 3.669354 CGTAAGGGAGTGAGATGGC 57.331 57.895 0.00 0.00 0.00 4.40
2317 2379 4.925054 CAGCGGCAATATCCATTAATTTGG 59.075 41.667 1.45 0.00 38.18 3.28
2321 2383 6.072175 GCGGCAATATCCATTAATTTGGTAGA 60.072 38.462 0.00 0.00 38.01 2.59
2355 2417 1.063942 TCGGGAGTAGGAGCAGAATGA 60.064 52.381 0.00 0.00 39.69 2.57
2364 2428 1.285578 GAGCAGAATGAGGAACGAGC 58.714 55.000 0.00 0.00 39.69 5.03
2371 2435 1.261480 ATGAGGAACGAGCAGACAGT 58.739 50.000 0.00 0.00 0.00 3.55
2372 2436 0.315251 TGAGGAACGAGCAGACAGTG 59.685 55.000 0.00 0.00 0.00 3.66
2384 2448 3.118261 AGCAGACAGTGGAAGAAGAAACA 60.118 43.478 0.00 0.00 0.00 2.83
2390 2454 1.673920 GTGGAAGAAGAAACAACGGCA 59.326 47.619 0.00 0.00 0.00 5.69
2412 2476 2.159099 GCTGGTGTTACGAGATGGATCA 60.159 50.000 0.00 0.00 0.00 2.92
2416 2480 6.228616 TGGTGTTACGAGATGGATCAATTA 57.771 37.500 0.00 0.00 0.00 1.40
2432 2496 8.359642 TGGATCAATTAAATCGAAATTGGGATC 58.640 33.333 16.93 13.69 42.17 3.36
2433 2497 8.579863 GGATCAATTAAATCGAAATTGGGATCT 58.420 33.333 16.93 2.76 42.17 2.75
2506 2584 2.477245 TCCTAGCTGATTGGGCTACAA 58.523 47.619 0.00 0.00 44.54 2.41
2518 2597 2.509166 GGCTACAAGTTTAAGGCCCT 57.491 50.000 0.00 0.00 34.19 5.19
2960 3039 5.007034 TGAGCAATGGTTCCGAAGATTTTA 58.993 37.500 0.00 0.00 0.00 1.52
2961 3040 5.106317 TGAGCAATGGTTCCGAAGATTTTAC 60.106 40.000 0.00 0.00 0.00 2.01
2962 3041 4.157840 AGCAATGGTTCCGAAGATTTTACC 59.842 41.667 0.00 0.00 0.00 2.85
2963 3042 4.676986 GCAATGGTTCCGAAGATTTTACCC 60.677 45.833 0.00 0.00 0.00 3.69
2964 3043 3.076079 TGGTTCCGAAGATTTTACCCC 57.924 47.619 0.00 0.00 0.00 4.95
2965 3044 2.291089 TGGTTCCGAAGATTTTACCCCC 60.291 50.000 0.00 0.00 0.00 5.40
2966 3045 2.025605 GGTTCCGAAGATTTTACCCCCT 60.026 50.000 0.00 0.00 0.00 4.79
2967 3046 3.276857 GTTCCGAAGATTTTACCCCCTC 58.723 50.000 0.00 0.00 0.00 4.30
2968 3047 1.841919 TCCGAAGATTTTACCCCCTCC 59.158 52.381 0.00 0.00 0.00 4.30
2969 3048 1.133884 CCGAAGATTTTACCCCCTCCC 60.134 57.143 0.00 0.00 0.00 4.30
2970 3049 1.844497 CGAAGATTTTACCCCCTCCCT 59.156 52.381 0.00 0.00 0.00 4.20
2971 3050 2.158798 CGAAGATTTTACCCCCTCCCTC 60.159 54.545 0.00 0.00 0.00 4.30
2972 3051 1.908643 AGATTTTACCCCCTCCCTCC 58.091 55.000 0.00 0.00 0.00 4.30
2973 3052 0.851469 GATTTTACCCCCTCCCTCCC 59.149 60.000 0.00 0.00 0.00 4.30
2974 3053 0.124522 ATTTTACCCCCTCCCTCCCA 59.875 55.000 0.00 0.00 0.00 4.37
2975 3054 0.124522 TTTTACCCCCTCCCTCCCAT 59.875 55.000 0.00 0.00 0.00 4.00
2976 3055 1.036926 TTTACCCCCTCCCTCCCATA 58.963 55.000 0.00 0.00 0.00 2.74
2977 3056 1.036926 TTACCCCCTCCCTCCCATAA 58.963 55.000 0.00 0.00 0.00 1.90
2978 3057 1.270835 TACCCCCTCCCTCCCATAAT 58.729 55.000 0.00 0.00 0.00 1.28
2979 3058 0.403453 ACCCCCTCCCTCCCATAATG 60.403 60.000 0.00 0.00 0.00 1.90
2980 3059 0.403453 CCCCCTCCCTCCCATAATGT 60.403 60.000 0.00 0.00 0.00 2.71
2981 3060 1.132201 CCCCCTCCCTCCCATAATGTA 60.132 57.143 0.00 0.00 0.00 2.29
2982 3061 2.499218 CCCCCTCCCTCCCATAATGTAT 60.499 54.545 0.00 0.00 0.00 2.29
2983 3062 3.269034 CCCCTCCCTCCCATAATGTATT 58.731 50.000 0.00 0.00 0.00 1.89
2984 3063 3.662642 CCCCTCCCTCCCATAATGTATTT 59.337 47.826 0.00 0.00 0.00 1.40
2985 3064 4.107961 CCCCTCCCTCCCATAATGTATTTT 59.892 45.833 0.00 0.00 0.00 1.82
2986 3065 5.079643 CCCTCCCTCCCATAATGTATTTTG 58.920 45.833 0.00 0.00 0.00 2.44
2987 3066 5.162991 CCCTCCCTCCCATAATGTATTTTGA 60.163 44.000 0.00 0.00 0.00 2.69
2988 3067 5.770162 CCTCCCTCCCATAATGTATTTTGAC 59.230 44.000 0.00 0.00 0.00 3.18
2989 3068 6.334378 TCCCTCCCATAATGTATTTTGACA 57.666 37.500 0.00 0.00 0.00 3.58
2990 3069 6.921412 TCCCTCCCATAATGTATTTTGACAT 58.079 36.000 0.00 0.00 41.92 3.06
3022 3101 5.789710 AAAACGACTTACATTATGGGACG 57.210 39.130 0.00 1.99 0.00 4.79
3023 3102 3.447918 ACGACTTACATTATGGGACGG 57.552 47.619 0.00 0.00 0.00 4.79
3024 3103 3.025978 ACGACTTACATTATGGGACGGA 58.974 45.455 0.00 0.00 0.00 4.69
3025 3104 3.067742 ACGACTTACATTATGGGACGGAG 59.932 47.826 0.00 0.00 0.00 4.63
3026 3105 3.552273 CGACTTACATTATGGGACGGAGG 60.552 52.174 0.00 0.00 0.00 4.30
3027 3106 2.704065 ACTTACATTATGGGACGGAGGG 59.296 50.000 0.00 0.00 0.00 4.30
3028 3107 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3029 3108 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3030 3109 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3038 3117 1.750206 GGACGGAGGGAGTAGTTCTTC 59.250 57.143 0.00 0.00 0.00 2.87
3061 3140 8.677148 TTCAGCTATTTAGTTCTGTTCAACTT 57.323 30.769 0.00 0.00 37.75 2.66
3062 3141 8.677148 TCAGCTATTTAGTTCTGTTCAACTTT 57.323 30.769 0.00 0.00 37.75 2.66
3114 3193 1.213013 CTCGCTGACTGGTTACGCT 59.787 57.895 0.00 0.00 0.00 5.07
3123 3202 3.880490 TGACTGGTTACGCTCAAATTTGT 59.120 39.130 17.47 1.31 0.00 2.83
3443 3532 3.668447 TGCTGACAATTCTGGAAGTCTC 58.332 45.455 0.00 0.00 33.76 3.36
3472 3561 3.093574 TCGAACTAACGTATTTCTCGCG 58.906 45.455 0.00 0.00 34.70 5.87
3527 3616 7.675062 AGGAGAAGCTACATATCTTTGGTATG 58.325 38.462 0.00 0.00 36.01 2.39
3993 4193 5.248477 TCTTGGTATAGCCTTGAAACTGACT 59.752 40.000 0.00 0.00 38.35 3.41
4151 4352 5.533482 AGTGATCGTACTTCAATATCTGCC 58.467 41.667 0.00 0.00 0.00 4.85
4285 4487 6.376248 ACATCTTTAATCTGCCATAATGGGT 58.624 36.000 0.00 0.00 38.19 4.51
4315 4517 9.039870 GGCATGCTATTGATATTAGTATCTGAC 57.960 37.037 18.92 0.00 38.03 3.51
4355 4557 6.975772 TGTTACAAACTTATGCTTGGTGTTTC 59.024 34.615 0.00 0.00 0.00 2.78
4362 4564 5.121768 ACTTATGCTTGGTGTTTCGTACATC 59.878 40.000 0.00 0.00 39.39 3.06
4465 4667 6.373216 TGTTTACATCACTAACAATACTGGCC 59.627 38.462 0.00 0.00 0.00 5.36
4468 4670 4.019321 ACATCACTAACAATACTGGCCAGT 60.019 41.667 38.92 38.92 45.02 4.00
4502 4704 4.709397 TCAAGGTAACATATTTGGGCTTGG 59.291 41.667 0.00 0.00 41.41 3.61
4596 4798 6.938542 CAAGTAGTGCTTGCTTATACTAAGC 58.061 40.000 8.09 11.10 46.68 3.09
4622 4824 5.048782 TGCAGTGAATTGCTTTTAGAATCGT 60.049 36.000 0.00 0.00 44.38 3.73
4637 4839 3.433615 AGAATCGTTACTTGCTGAAGTGC 59.566 43.478 0.00 0.00 42.66 4.40
4644 4846 1.410153 ACTTGCTGAAGTGCCCTTTTG 59.590 47.619 0.00 0.00 41.12 2.44
4662 4864 6.038714 CCCTTTTGGCAGTTATCTTATCTCAC 59.961 42.308 0.00 0.00 38.58 3.51
4688 4890 3.254166 AGTTGGACACAGTGATTGAATGC 59.746 43.478 7.81 0.00 0.00 3.56
4689 4891 2.861274 TGGACACAGTGATTGAATGCA 58.139 42.857 7.81 0.00 0.00 3.96
4696 4898 4.214758 CACAGTGATTGAATGCAGTCTGAA 59.785 41.667 16.05 2.36 32.48 3.02
4724 4926 4.141733 GGGCAGCAATGTTACCCAAATATT 60.142 41.667 0.01 0.00 40.52 1.28
4731 4933 9.612066 AGCAATGTTACCCAAATATTTAATTGG 57.388 29.630 0.00 0.00 44.61 3.16
4835 5037 8.775151 TCACCTATCATGATCTATGCCATATTT 58.225 33.333 12.53 0.00 36.70 1.40
4836 5038 9.404848 CACCTATCATGATCTATGCCATATTTT 57.595 33.333 12.53 0.00 36.70 1.82
4954 5158 1.750778 CCATGGGGCTACACAACATTC 59.249 52.381 2.85 0.00 0.00 2.67
4998 5202 4.853924 TTCATCTTCTTGTTTCAAGCCC 57.146 40.909 4.82 0.00 0.00 5.19
4999 5203 3.157087 TCATCTTCTTGTTTCAAGCCCC 58.843 45.455 4.82 0.00 0.00 5.80
5000 5204 2.746279 TCTTCTTGTTTCAAGCCCCA 57.254 45.000 4.82 0.00 0.00 4.96
5002 5206 2.892852 TCTTCTTGTTTCAAGCCCCATG 59.107 45.455 4.82 0.00 0.00 3.66
5004 5208 1.146774 TCTTGTTTCAAGCCCCATGGA 59.853 47.619 15.22 0.00 0.00 3.41
5005 5209 1.273327 CTTGTTTCAAGCCCCATGGAC 59.727 52.381 15.22 4.77 0.00 4.02
5006 5210 0.187117 TGTTTCAAGCCCCATGGACA 59.813 50.000 15.22 3.64 0.00 4.02
5007 5211 1.337118 GTTTCAAGCCCCATGGACAA 58.663 50.000 15.22 0.00 0.00 3.18
5008 5212 1.000843 GTTTCAAGCCCCATGGACAAC 59.999 52.381 15.22 1.90 0.00 3.32
5009 5213 0.187117 TTCAAGCCCCATGGACAACA 59.813 50.000 15.22 0.00 0.00 3.33
5010 5214 0.251297 TCAAGCCCCATGGACAACAG 60.251 55.000 15.22 0.00 0.00 3.16
5011 5215 0.540365 CAAGCCCCATGGACAACAGT 60.540 55.000 15.22 0.00 0.00 3.55
5012 5216 0.251341 AAGCCCCATGGACAACAGTC 60.251 55.000 15.22 0.00 0.00 3.51
5013 5217 1.136329 AGCCCCATGGACAACAGTCT 61.136 55.000 15.22 0.00 32.81 3.24
5014 5218 0.251341 GCCCCATGGACAACAGTCTT 60.251 55.000 15.22 0.00 32.81 3.01
5015 5219 1.826385 CCCCATGGACAACAGTCTTC 58.174 55.000 15.22 0.00 32.81 2.87
5016 5220 1.352352 CCCCATGGACAACAGTCTTCT 59.648 52.381 15.22 0.00 32.81 2.85
5017 5221 2.224867 CCCCATGGACAACAGTCTTCTT 60.225 50.000 15.22 0.00 32.81 2.52
5018 5222 2.816087 CCCATGGACAACAGTCTTCTTG 59.184 50.000 15.22 0.00 32.81 3.02
5019 5223 3.480470 CCATGGACAACAGTCTTCTTGT 58.520 45.455 5.56 0.00 32.81 3.16
5020 5224 3.885297 CCATGGACAACAGTCTTCTTGTT 59.115 43.478 5.56 0.00 32.81 2.83
5028 5232 2.945668 ACAGTCTTCTTGTTTCAGCACC 59.054 45.455 0.00 0.00 0.00 5.01
5031 5235 0.593128 CTTCTTGTTTCAGCACCCGG 59.407 55.000 0.00 0.00 0.00 5.73
5045 5249 4.511826 CAGCACCCGGTAATCTAATTTCTC 59.488 45.833 0.00 0.00 0.00 2.87
5052 5256 4.025979 CGGTAATCTAATTTCTCGTGCCAC 60.026 45.833 0.00 0.00 0.00 5.01
5081 5285 5.762218 ACTATTATGCCATCTTGAGTTCAGC 59.238 40.000 0.00 0.00 0.00 4.26
5147 5351 9.683069 ACAAATGTTTCTGCTAAACTTGATAAG 57.317 29.630 16.62 0.00 0.00 1.73
5156 5361 1.739067 AACTTGATAAGCTGCCGGTC 58.261 50.000 1.90 0.00 0.00 4.79
5167 5372 1.836383 CTGCCGGTCTTGTCGTATAC 58.164 55.000 1.90 0.00 0.00 1.47
5174 5379 4.033684 CGGTCTTGTCGTATACAGTTAGC 58.966 47.826 3.32 0.00 39.87 3.09
5177 5382 5.505324 GGTCTTGTCGTATACAGTTAGCGAT 60.505 44.000 3.32 0.00 39.87 4.58
5186 5391 6.747739 CGTATACAGTTAGCGATAATGCTCAT 59.252 38.462 3.32 0.00 45.87 2.90
5197 5403 8.531622 AGCGATAATGCTCATGATATTATAGC 57.468 34.615 27.72 27.72 42.95 2.97
5274 5480 3.876914 TGACAGAGATGTGTGGTTTTGTC 59.123 43.478 0.00 0.00 35.48 3.18
5289 5495 8.076351 GTGGTTTTGTCACAATCCTTTCTGGA 62.076 42.308 11.83 0.00 40.79 3.86
5375 5581 7.544622 TCTGGTTTGCACATAGTAACTAGTAG 58.455 38.462 9.13 0.00 32.81 2.57
5377 5583 7.544622 TGGTTTGCACATAGTAACTAGTAGAG 58.455 38.462 3.59 0.00 0.00 2.43
5378 5584 7.177921 TGGTTTGCACATAGTAACTAGTAGAGT 59.822 37.037 3.59 0.00 41.56 3.24
5379 5585 8.680903 GGTTTGCACATAGTAACTAGTAGAGTA 58.319 37.037 3.59 0.00 37.44 2.59
5506 5712 0.465705 TTAGATCCGCTGCTGAAGGG 59.534 55.000 0.00 0.00 38.56 3.95
5643 5849 7.339482 ACTTTAGGGCTCTATAAACAGGAAAG 58.661 38.462 0.00 0.00 0.00 2.62
5804 6015 7.224753 CGGCTATCATCTGTAACTGTTGTATTT 59.775 37.037 2.69 0.00 0.00 1.40
5841 6052 7.649705 GGGAAAGAATCTGAAGAACTCAAAAAC 59.350 37.037 0.00 0.00 32.17 2.43
5846 6058 8.139989 AGAATCTGAAGAACTCAAAAACCATTG 58.860 33.333 0.00 0.00 32.17 2.82
5857 6069 3.751479 AAAACCATTGCCTCTTTCACC 57.249 42.857 0.00 0.00 0.00 4.02
5858 6070 1.632589 AACCATTGCCTCTTTCACCC 58.367 50.000 0.00 0.00 0.00 4.61
5872 6084 0.770499 TCACCCCTGTTGAATCTGCA 59.230 50.000 0.00 0.00 0.00 4.41
5875 6087 1.076024 ACCCCTGTTGAATCTGCACAT 59.924 47.619 0.00 0.00 0.00 3.21
5911 6123 2.223782 TGGTGATGTTCTTTGCTTGTGC 60.224 45.455 0.00 0.00 40.20 4.57
6016 6229 1.401199 GCTTGCTCATTTCAGCTCTCC 59.599 52.381 0.00 0.00 40.39 3.71
6031 6244 2.844966 GCTCTCCCCTTTAACTAACCCT 59.155 50.000 0.00 0.00 0.00 4.34
6040 6253 5.708697 CCCTTTAACTAACCCTGTAACCTTG 59.291 44.000 0.00 0.00 0.00 3.61
6114 6329 2.553086 GCTGAGCATGAAGGAGAAGAG 58.447 52.381 0.00 0.00 0.00 2.85
6126 6341 2.564947 AGGAGAAGAGTACAAGGTGCTG 59.435 50.000 0.00 0.00 0.00 4.41
6129 6344 4.323104 GGAGAAGAGTACAAGGTGCTGATT 60.323 45.833 0.00 0.00 0.00 2.57
6159 6374 1.890041 CAAAGACGCCGGTGAACCA 60.890 57.895 24.59 0.00 35.14 3.67
6171 6386 1.092921 GTGAACCACACCAAGACGCA 61.093 55.000 0.00 0.00 43.05 5.24
6179 6394 1.079819 ACCAAGACGCAGACGATGG 60.080 57.895 0.00 0.76 43.93 3.51
6180 6395 1.079819 CCAAGACGCAGACGATGGT 60.080 57.895 0.00 0.00 43.93 3.55
6228 6443 3.742983 GGTCATGAACCTCGTCCTC 57.257 57.895 0.00 0.00 45.45 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 1.445942 GATCGAGATGGCCCCGAAA 59.554 57.895 0.00 0.00 35.87 3.46
258 267 4.504340 GGGTGTGGACATATATAAACCGCT 60.504 45.833 13.74 0.00 33.09 5.52
444 454 1.243902 CTTTTGCCTACCGCCAAGAA 58.756 50.000 0.00 0.00 36.24 2.52
489 499 8.792830 AAAATCAAATCGAGATCTGACCTTAA 57.207 30.769 0.00 0.00 0.00 1.85
492 504 5.819901 GGAAAATCAAATCGAGATCTGACCT 59.180 40.000 0.00 0.00 0.00 3.85
514 526 2.724454 TCGTGTTTTGACCCTTTTGGA 58.276 42.857 0.00 0.00 44.07 3.53
548 560 1.142748 CTCCTAGGCGCTTGACCAG 59.857 63.158 7.64 0.00 0.00 4.00
582 594 1.216678 TGGAGGTGCTTCAGGGAAAAA 59.783 47.619 0.00 0.00 0.00 1.94
583 595 0.850100 TGGAGGTGCTTCAGGGAAAA 59.150 50.000 0.00 0.00 0.00 2.29
584 596 1.075601 ATGGAGGTGCTTCAGGGAAA 58.924 50.000 0.00 0.00 0.00 3.13
585 597 1.075601 AATGGAGGTGCTTCAGGGAA 58.924 50.000 0.00 0.00 0.00 3.97
586 598 0.329261 CAATGGAGGTGCTTCAGGGA 59.671 55.000 0.00 0.00 0.00 4.20
587 599 0.038744 ACAATGGAGGTGCTTCAGGG 59.961 55.000 0.00 0.00 0.00 4.45
588 600 2.290260 TGTACAATGGAGGTGCTTCAGG 60.290 50.000 0.00 0.00 0.00 3.86
589 601 3.005554 CTGTACAATGGAGGTGCTTCAG 58.994 50.000 0.00 0.00 0.00 3.02
590 602 2.290260 CCTGTACAATGGAGGTGCTTCA 60.290 50.000 0.00 0.00 0.00 3.02
591 603 2.359900 CCTGTACAATGGAGGTGCTTC 58.640 52.381 0.00 0.00 0.00 3.86
592 604 1.614317 GCCTGTACAATGGAGGTGCTT 60.614 52.381 5.35 0.00 0.00 3.91
593 605 0.035056 GCCTGTACAATGGAGGTGCT 60.035 55.000 5.35 0.00 0.00 4.40
594 606 1.032114 GGCCTGTACAATGGAGGTGC 61.032 60.000 5.35 0.00 0.00 5.01
595 607 0.744414 CGGCCTGTACAATGGAGGTG 60.744 60.000 0.00 0.00 0.00 4.00
596 608 0.907704 TCGGCCTGTACAATGGAGGT 60.908 55.000 0.00 0.00 0.00 3.85
597 609 0.469917 ATCGGCCTGTACAATGGAGG 59.530 55.000 0.00 0.00 0.00 4.30
598 610 1.586422 CATCGGCCTGTACAATGGAG 58.414 55.000 0.00 0.00 0.00 3.86
599 611 0.463654 GCATCGGCCTGTACAATGGA 60.464 55.000 0.00 0.00 0.00 3.41
600 612 2.024918 GCATCGGCCTGTACAATGG 58.975 57.895 0.00 0.00 0.00 3.16
1107 1120 0.967887 TGAAGACGCTGGAGGAGAGG 60.968 60.000 0.00 0.00 0.00 3.69
1298 1311 3.490933 GCATAATCAGACACCAGCGTCTA 60.491 47.826 0.00 0.00 44.49 2.59
1356 1369 5.128827 CCCTAACTCCTTTACATGTCTGCTA 59.871 44.000 0.00 0.00 0.00 3.49
1359 1372 5.677319 TCCCTAACTCCTTTACATGTCTG 57.323 43.478 0.00 0.00 0.00 3.51
1360 1373 6.555360 CCTATCCCTAACTCCTTTACATGTCT 59.445 42.308 0.00 0.00 0.00 3.41
1370 1383 2.426561 GCTCACCCTATCCCTAACTCCT 60.427 54.545 0.00 0.00 0.00 3.69
1373 1386 1.705873 CGCTCACCCTATCCCTAACT 58.294 55.000 0.00 0.00 0.00 2.24
1395 1408 9.613428 TGTCAATATTATCAACCTAAACTCTGG 57.387 33.333 0.00 0.00 0.00 3.86
1415 1428 5.365605 TCCCTACATCTAAATCGGTGTCAAT 59.634 40.000 0.00 0.00 0.00 2.57
1421 1434 4.960469 TGAACTCCCTACATCTAAATCGGT 59.040 41.667 0.00 0.00 0.00 4.69
1435 1448 2.437281 CTCCAGCATATGTGAACTCCCT 59.563 50.000 4.29 0.00 0.00 4.20
1479 1492 6.458206 GCAGAATAAAAGCAACACCGATATCA 60.458 38.462 3.12 0.00 0.00 2.15
1483 1496 3.505680 TGCAGAATAAAAGCAACACCGAT 59.494 39.130 0.00 0.00 34.97 4.18
1489 1502 5.402270 ACGAACAATGCAGAATAAAAGCAAC 59.598 36.000 0.00 0.00 42.15 4.17
1518 1531 1.121407 ACCAGAGTACAGTGCAGCCA 61.121 55.000 0.00 0.00 0.00 4.75
1521 1534 2.297315 TGAGAACCAGAGTACAGTGCAG 59.703 50.000 0.00 0.00 0.00 4.41
1531 1544 5.485620 TGAACAATGAGATGAGAACCAGAG 58.514 41.667 0.00 0.00 0.00 3.35
1577 1590 7.402071 TCCCCACTAAATTGAACTAGTACATCT 59.598 37.037 0.00 0.00 0.00 2.90
1606 1620 9.802039 TGTTTGGAATAATTAACTAGTGAGGTT 57.198 29.630 0.00 0.00 0.00 3.50
1634 1648 9.878599 CAAAACGACAGAATGATAACTTTTACT 57.121 29.630 0.00 0.00 39.69 2.24
1785 1809 7.491682 ACAATGTTGTGCTTTGTATCTTCTTT 58.508 30.769 0.00 0.00 41.69 2.52
1786 1810 7.042797 ACAATGTTGTGCTTTGTATCTTCTT 57.957 32.000 0.00 0.00 41.69 2.52
1787 1811 6.639632 ACAATGTTGTGCTTTGTATCTTCT 57.360 33.333 0.00 0.00 41.69 2.85
1809 1833 6.618287 AAAGATGCTTTTTAGGGCAAAAAC 57.382 33.333 0.00 0.00 40.39 2.43
1813 1837 5.806654 AGAAAAGATGCTTTTTAGGGCAA 57.193 34.783 6.60 0.00 41.90 4.52
1870 1897 4.451629 AAGAAGAAAATGCTGGCAGATG 57.548 40.909 20.86 0.00 0.00 2.90
1877 1904 8.614346 TGATTTTGGAAAAAGAAGAAAATGCTG 58.386 29.630 0.00 0.00 0.00 4.41
1894 1925 6.586344 TGTTGCCTAAAAACATGATTTTGGA 58.414 32.000 21.08 7.21 33.94 3.53
1895 1926 6.857777 TGTTGCCTAAAAACATGATTTTGG 57.142 33.333 20.35 17.59 34.51 3.28
1931 1963 4.315803 ACAAATTCAGGTACTTCCACTCG 58.684 43.478 0.00 0.00 34.60 4.18
2110 2162 8.349983 GCCTACAAAGTTCTTGTAATTTCAGAA 58.650 33.333 0.00 0.00 34.84 3.02
2153 2205 2.435372 TTGCAAGTTCCAACAGGACT 57.565 45.000 0.00 0.00 0.00 3.85
2163 2215 2.615912 AGCTCAGTCACTTTGCAAGTTC 59.384 45.455 0.00 0.00 40.46 3.01
2245 2301 1.112113 TCGCCATCTCACTCCCTTAC 58.888 55.000 0.00 0.00 0.00 2.34
2262 2318 3.625764 TCTTTGGTCCACTTTCAGTTTCG 59.374 43.478 0.00 0.00 0.00 3.46
2278 2334 2.096496 CCGCTGTAGCTGATTTCTTTGG 59.904 50.000 0.00 0.00 39.32 3.28
2355 2417 0.827925 TCCACTGTCTGCTCGTTCCT 60.828 55.000 0.00 0.00 0.00 3.36
2364 2428 4.260375 CGTTGTTTCTTCTTCCACTGTCTG 60.260 45.833 0.00 0.00 0.00 3.51
2371 2435 1.946768 CTGCCGTTGTTTCTTCTTCCA 59.053 47.619 0.00 0.00 0.00 3.53
2372 2436 1.335051 GCTGCCGTTGTTTCTTCTTCC 60.335 52.381 0.00 0.00 0.00 3.46
2384 2448 1.959226 CGTAACACCAGCTGCCGTT 60.959 57.895 19.11 19.11 0.00 4.44
2390 2454 1.557099 TCCATCTCGTAACACCAGCT 58.443 50.000 0.00 0.00 0.00 4.24
2478 2556 3.334691 CCAATCAGCTAGGAAACGTTCA 58.665 45.455 0.00 0.00 0.00 3.18
2485 2563 2.477245 TGTAGCCCAATCAGCTAGGAA 58.523 47.619 0.00 0.00 43.26 3.36
2486 2564 2.174685 TGTAGCCCAATCAGCTAGGA 57.825 50.000 0.00 0.00 43.26 2.94
2506 2584 3.069016 CCGAACAAAAAGGGCCTTAAACT 59.931 43.478 21.25 0.00 0.00 2.66
2518 2597 2.766970 GCTACACAGCCGAACAAAAA 57.233 45.000 0.00 0.00 42.37 1.94
2859 2938 2.430367 GGGCAAGAAGGGTGACGT 59.570 61.111 0.00 0.00 0.00 4.34
2864 2943 1.929088 GGGTAGGGGCAAGAAGGGT 60.929 63.158 0.00 0.00 0.00 4.34
2901 2980 6.072893 GGTAGTTTCTCCGCAAATACTTGAAA 60.073 38.462 0.00 0.00 34.14 2.69
2911 2990 2.137523 GTTTCGGTAGTTTCTCCGCAA 58.862 47.619 0.00 0.00 45.44 4.85
2927 3006 0.529378 CCATTGCTCAGGCCAGTTTC 59.471 55.000 5.01 0.00 37.74 2.78
2931 3010 1.318158 GGAACCATTGCTCAGGCCAG 61.318 60.000 5.01 0.00 37.74 4.85
2960 3039 0.403453 CATTATGGGAGGGAGGGGGT 60.403 60.000 0.00 0.00 0.00 4.95
2961 3040 0.403453 ACATTATGGGAGGGAGGGGG 60.403 60.000 0.00 0.00 0.00 5.40
2962 3041 2.433444 TACATTATGGGAGGGAGGGG 57.567 55.000 0.00 0.00 0.00 4.79
2963 3042 5.079643 CAAAATACATTATGGGAGGGAGGG 58.920 45.833 0.00 0.00 0.00 4.30
2964 3043 5.770162 GTCAAAATACATTATGGGAGGGAGG 59.230 44.000 0.00 0.00 0.00 4.30
2965 3044 6.364701 TGTCAAAATACATTATGGGAGGGAG 58.635 40.000 0.00 0.00 0.00 4.30
2966 3045 6.334378 TGTCAAAATACATTATGGGAGGGA 57.666 37.500 0.00 0.00 0.00 4.20
2967 3046 7.601705 AATGTCAAAATACATTATGGGAGGG 57.398 36.000 0.55 0.00 45.84 4.30
2968 3047 9.354673 ACTAATGTCAAAATACATTATGGGAGG 57.645 33.333 9.23 1.61 46.13 4.30
2970 3049 9.693739 ACACTAATGTCAAAATACATTATGGGA 57.306 29.630 9.23 0.00 46.13 4.37
2999 3078 5.122711 CCGTCCCATAATGTAAGTCGTTTTT 59.877 40.000 0.00 0.00 0.00 1.94
3000 3079 4.632688 CCGTCCCATAATGTAAGTCGTTTT 59.367 41.667 0.00 0.00 0.00 2.43
3001 3080 4.081531 TCCGTCCCATAATGTAAGTCGTTT 60.082 41.667 0.00 0.00 0.00 3.60
3002 3081 3.448301 TCCGTCCCATAATGTAAGTCGTT 59.552 43.478 0.00 0.00 0.00 3.85
3003 3082 3.025978 TCCGTCCCATAATGTAAGTCGT 58.974 45.455 0.00 0.00 0.00 4.34
3004 3083 3.552273 CCTCCGTCCCATAATGTAAGTCG 60.552 52.174 0.00 0.00 0.00 4.18
3005 3084 3.244112 CCCTCCGTCCCATAATGTAAGTC 60.244 52.174 0.00 0.00 0.00 3.01
3006 3085 2.704065 CCCTCCGTCCCATAATGTAAGT 59.296 50.000 0.00 0.00 0.00 2.24
3007 3086 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3008 3087 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3009 3088 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3010 3089 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3011 3090 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3012 3091 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3013 3092 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3014 3093 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3015 3094 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3016 3095 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
3017 3096 0.033306 AGAACTACTCCCTCCGTCCC 60.033 60.000 0.00 0.00 0.00 4.46
3018 3097 1.750206 GAAGAACTACTCCCTCCGTCC 59.250 57.143 0.00 0.00 0.00 4.79
3019 3098 2.424246 CTGAAGAACTACTCCCTCCGTC 59.576 54.545 0.00 0.00 0.00 4.79
3020 3099 2.448453 CTGAAGAACTACTCCCTCCGT 58.552 52.381 0.00 0.00 0.00 4.69
3021 3100 1.135333 GCTGAAGAACTACTCCCTCCG 59.865 57.143 0.00 0.00 0.00 4.63
3022 3101 2.462723 AGCTGAAGAACTACTCCCTCC 58.537 52.381 0.00 0.00 0.00 4.30
3023 3102 5.862678 AATAGCTGAAGAACTACTCCCTC 57.137 43.478 0.00 0.00 0.00 4.30
3024 3103 6.898521 ACTAAATAGCTGAAGAACTACTCCCT 59.101 38.462 0.00 0.00 0.00 4.20
3025 3104 7.114866 ACTAAATAGCTGAAGAACTACTCCC 57.885 40.000 0.00 0.00 0.00 4.30
3026 3105 8.471609 AGAACTAAATAGCTGAAGAACTACTCC 58.528 37.037 0.00 0.00 0.00 3.85
3027 3106 9.296400 CAGAACTAAATAGCTGAAGAACTACTC 57.704 37.037 0.00 0.00 0.00 2.59
3028 3107 8.808092 ACAGAACTAAATAGCTGAAGAACTACT 58.192 33.333 0.00 0.00 32.86 2.57
3029 3108 8.989653 ACAGAACTAAATAGCTGAAGAACTAC 57.010 34.615 0.00 0.00 32.86 2.73
3030 3109 9.640963 GAACAGAACTAAATAGCTGAAGAACTA 57.359 33.333 0.00 0.00 32.86 2.24
3114 3193 5.303971 CCCTGCCATAAACAACAAATTTGA 58.696 37.500 24.64 1.13 0.00 2.69
3123 3202 1.133009 ACCAACCCCTGCCATAAACAA 60.133 47.619 0.00 0.00 0.00 2.83
3379 3458 3.450817 TCATTAAGGATCGCACTTCTGGA 59.549 43.478 0.00 0.00 0.00 3.86
3472 3561 4.748679 CTGCAAGAACGGCGCTGC 62.749 66.667 18.15 13.45 34.07 5.25
3527 3616 3.632189 GACACAAAGAACACATCCAAGC 58.368 45.455 0.00 0.00 0.00 4.01
3938 4073 5.109210 CGCTCATGACCTGTCAAGTAAATA 58.891 41.667 3.79 0.00 43.58 1.40
4121 4322 9.197694 GATATTGAAGTACGATCACTAAGCAAT 57.802 33.333 4.18 0.00 33.39 3.56
4315 4517 7.810658 AGTTTGTAACAAGCAGAATCATGTAG 58.189 34.615 0.00 0.00 0.00 2.74
4355 4557 8.328146 CAAACATAGTAGGTTGAATGATGTACG 58.672 37.037 0.13 0.00 0.00 3.67
4362 4564 7.148755 GCAAAAGCAAACATAGTAGGTTGAATG 60.149 37.037 0.13 0.00 0.00 2.67
4465 4667 7.433708 TGTTACCTTGAACATTATGACACTG 57.566 36.000 0.00 0.00 34.40 3.66
4596 4798 6.020916 CGATTCTAAAAGCAATTCACTGCATG 60.021 38.462 0.00 0.00 45.18 4.06
4622 4824 2.656947 AAGGGCACTTCAGCAAGTAA 57.343 45.000 0.00 0.00 41.24 2.24
4637 4839 6.038714 GTGAGATAAGATAACTGCCAAAAGGG 59.961 42.308 0.00 0.00 40.85 3.95
4644 4846 6.116126 ACTTTGGTGAGATAAGATAACTGCC 58.884 40.000 0.00 0.00 0.00 4.85
4679 4881 6.501781 CCCTTTATTCAGACTGCATTCAATC 58.498 40.000 6.84 0.00 0.00 2.67
4688 4890 2.715046 TGCTGCCCTTTATTCAGACTG 58.285 47.619 0.00 0.00 0.00 3.51
4689 4891 3.439857 TTGCTGCCCTTTATTCAGACT 57.560 42.857 0.00 0.00 0.00 3.24
4696 4898 3.031013 GGGTAACATTGCTGCCCTTTAT 58.969 45.455 6.01 0.00 36.49 1.40
4731 4933 5.591099 TCTCTCAAACAGAAAATTGGTTGC 58.409 37.500 0.00 0.00 43.74 4.17
4835 5037 7.660208 GGATTGTCCTAGACTGAAAAACACTAA 59.340 37.037 0.00 0.00 32.53 2.24
4836 5038 7.159372 GGATTGTCCTAGACTGAAAAACACTA 58.841 38.462 0.00 0.00 32.53 2.74
4837 5039 5.998363 GGATTGTCCTAGACTGAAAAACACT 59.002 40.000 0.00 0.00 32.53 3.55
4840 5042 6.877611 TTGGATTGTCCTAGACTGAAAAAC 57.122 37.500 0.00 0.00 37.46 2.43
4844 5046 6.549736 TCGATATTGGATTGTCCTAGACTGAA 59.450 38.462 0.00 0.00 37.46 3.02
4846 5048 6.332735 TCGATATTGGATTGTCCTAGACTG 57.667 41.667 0.00 0.00 37.46 3.51
4973 5177 6.808704 GGGCTTGAAACAAGAAGATGAATTAC 59.191 38.462 14.44 0.00 0.00 1.89
4998 5202 3.480470 ACAAGAAGACTGTTGTCCATGG 58.520 45.455 4.97 4.97 43.91 3.66
4999 5203 5.066375 TGAAACAAGAAGACTGTTGTCCATG 59.934 40.000 4.37 0.00 43.91 3.66
5000 5204 5.192927 TGAAACAAGAAGACTGTTGTCCAT 58.807 37.500 4.37 0.00 43.91 3.41
5002 5206 4.496507 GCTGAAACAAGAAGACTGTTGTCC 60.497 45.833 4.37 1.99 43.91 4.02
5004 5208 4.009675 TGCTGAAACAAGAAGACTGTTGT 58.990 39.130 0.00 0.00 38.56 3.32
5005 5209 4.346129 GTGCTGAAACAAGAAGACTGTTG 58.654 43.478 0.00 0.00 0.00 3.33
5006 5210 3.378427 GGTGCTGAAACAAGAAGACTGTT 59.622 43.478 0.00 0.00 0.00 3.16
5007 5211 2.945668 GGTGCTGAAACAAGAAGACTGT 59.054 45.455 0.00 0.00 0.00 3.55
5008 5212 2.291741 GGGTGCTGAAACAAGAAGACTG 59.708 50.000 0.00 0.00 0.00 3.51
5009 5213 2.576615 GGGTGCTGAAACAAGAAGACT 58.423 47.619 0.00 0.00 0.00 3.24
5010 5214 1.264288 CGGGTGCTGAAACAAGAAGAC 59.736 52.381 0.00 0.00 0.00 3.01
5011 5215 1.593196 CGGGTGCTGAAACAAGAAGA 58.407 50.000 0.00 0.00 0.00 2.87
5012 5216 0.593128 CCGGGTGCTGAAACAAGAAG 59.407 55.000 0.00 0.00 0.00 2.85
5013 5217 0.106918 ACCGGGTGCTGAAACAAGAA 60.107 50.000 6.32 0.00 0.00 2.52
5014 5218 0.759959 TACCGGGTGCTGAAACAAGA 59.240 50.000 10.66 0.00 0.00 3.02
5015 5219 1.600023 TTACCGGGTGCTGAAACAAG 58.400 50.000 10.66 0.00 0.00 3.16
5016 5220 2.156098 GATTACCGGGTGCTGAAACAA 58.844 47.619 10.66 0.00 0.00 2.83
5017 5221 1.349688 AGATTACCGGGTGCTGAAACA 59.650 47.619 10.66 0.00 0.00 2.83
5018 5222 2.109425 AGATTACCGGGTGCTGAAAC 57.891 50.000 10.66 0.00 0.00 2.78
5019 5223 3.985019 TTAGATTACCGGGTGCTGAAA 57.015 42.857 10.66 0.00 0.00 2.69
5020 5224 4.497291 AATTAGATTACCGGGTGCTGAA 57.503 40.909 10.66 0.00 0.00 3.02
5028 5232 3.493503 GGCACGAGAAATTAGATTACCGG 59.506 47.826 0.00 0.00 0.00 5.28
5031 5235 4.025979 CCGTGGCACGAGAAATTAGATTAC 60.026 45.833 38.91 0.00 46.05 1.89
5045 5249 1.858458 CATAATAGTGACCGTGGCACG 59.142 52.381 31.78 31.78 41.04 5.34
5052 5256 4.631131 TCAAGATGGCATAATAGTGACCG 58.369 43.478 0.00 0.00 0.00 4.79
5117 5321 8.031864 TCAAGTTTAGCAGAAACATTTGTTGAA 58.968 29.630 14.48 1.77 38.44 2.69
5134 5338 3.270877 ACCGGCAGCTTATCAAGTTTAG 58.729 45.455 0.00 0.00 0.00 1.85
5147 5351 0.101759 TATACGACAAGACCGGCAGC 59.898 55.000 0.00 0.00 0.00 5.25
5156 5361 7.409449 GCATTATCGCTAACTGTATACGACAAG 60.409 40.741 0.00 0.00 37.70 3.16
5167 5372 7.767745 ATATCATGAGCATTATCGCTAACTG 57.232 36.000 0.09 0.00 44.01 3.16
5197 5403 5.986135 CCTGCAAGCAAGTACTATTAGTAGG 59.014 44.000 3.75 0.61 30.12 3.18
5378 5584 9.609346 GCCAGAAAGTTAGAAGTTACCAATATA 57.391 33.333 0.00 0.00 0.00 0.86
5379 5585 8.107095 TGCCAGAAAGTTAGAAGTTACCAATAT 58.893 33.333 0.00 0.00 0.00 1.28
5380 5586 7.455058 TGCCAGAAAGTTAGAAGTTACCAATA 58.545 34.615 0.00 0.00 0.00 1.90
5381 5587 6.303839 TGCCAGAAAGTTAGAAGTTACCAAT 58.696 36.000 0.00 0.00 0.00 3.16
5506 5712 1.194781 TTGGTGACCTCAGAGGGAGC 61.195 60.000 21.31 15.70 42.62 4.70
5727 5938 5.452077 CCATACCGGTTCCTCAAAAACAAAA 60.452 40.000 15.04 0.00 0.00 2.44
5841 6052 0.040204 AGGGGTGAAAGAGGCAATGG 59.960 55.000 0.00 0.00 0.00 3.16
5846 6058 0.110486 TCAACAGGGGTGAAAGAGGC 59.890 55.000 0.00 0.00 0.00 4.70
5857 6069 5.587388 AATAATGTGCAGATTCAACAGGG 57.413 39.130 13.03 0.00 0.00 4.45
5858 6070 7.318141 AGAAAATAATGTGCAGATTCAACAGG 58.682 34.615 13.03 0.00 0.00 4.00
5872 6084 8.055181 ACATCACCACCTATGAGAAAATAATGT 58.945 33.333 0.00 0.00 0.00 2.71
5875 6087 8.328758 AGAACATCACCACCTATGAGAAAATAA 58.671 33.333 0.00 0.00 0.00 1.40
5887 6099 2.624838 CAAGCAAAGAACATCACCACCT 59.375 45.455 0.00 0.00 0.00 4.00
5911 6123 0.742505 AACGGAGCATTGCCATCATG 59.257 50.000 4.70 0.00 0.00 3.07
5913 6125 0.527113 CAAACGGAGCATTGCCATCA 59.473 50.000 4.70 0.00 0.00 3.07
5914 6126 0.803380 GCAAACGGAGCATTGCCATC 60.803 55.000 4.70 0.00 44.43 3.51
6016 6229 5.509832 AGGTTACAGGGTTAGTTAAAGGG 57.490 43.478 0.00 0.00 0.00 3.95
6031 6244 4.594123 TTGATGAGACGACAAGGTTACA 57.406 40.909 0.00 0.00 0.00 2.41
6040 6253 2.489971 TGTTGGGTTTGATGAGACGAC 58.510 47.619 0.00 0.00 0.00 4.34
6088 6303 1.282738 TCCTTCATGCTCAGCCATTGA 59.717 47.619 0.00 0.00 0.00 2.57
6102 6317 3.006967 GCACCTTGTACTCTTCTCCTTCA 59.993 47.826 0.00 0.00 0.00 3.02
6114 6329 4.871993 CTGATCAATCAGCACCTTGTAC 57.128 45.455 7.05 0.00 46.63 2.90
6126 6341 3.063180 CGTCTTTGCTGGTCTGATCAATC 59.937 47.826 0.00 0.00 0.00 2.67
6129 6344 1.941209 GCGTCTTTGCTGGTCTGATCA 60.941 52.381 0.00 0.00 0.00 2.92
6159 6374 0.667487 CATCGTCTGCGTCTTGGTGT 60.667 55.000 0.00 0.00 39.49 4.16
6171 6386 1.213013 GTCAGCGTCACCATCGTCT 59.787 57.895 0.00 0.00 0.00 4.18
6180 6395 2.643272 GAGGTGTCGTCAGCGTCA 59.357 61.111 6.22 0.00 45.42 4.35


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

AutoCloner maintained by Alex Coulton.