Multiple sequence alignment - TraesCS6B01G458400

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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 TraesCS6B01G458400 chr6B 100.000 4455 0 0 3057 7511 713509340 713513794 0.000000e+00 8227.0
1 TraesCS6B01G458400 chr6B 100.000 2692 0 0 1 2692 713506284 713508975 0.000000e+00 4972.0
2 TraesCS6B01G458400 chr6B 95.954 2867 90 12 4010 6860 713968267 713971123 0.000000e+00 4628.0
3 TraesCS6B01G458400 chr6B 93.769 1685 77 10 1 1668 713964611 713966284 0.000000e+00 2505.0
4 TraesCS6B01G458400 chr6B 95.005 961 44 2 3057 4014 713967281 713968240 0.000000e+00 1506.0
5 TraesCS6B01G458400 chr6B 93.016 673 18 11 6837 7509 713971132 713971775 0.000000e+00 955.0
6 TraesCS6B01G458400 chr6B 82.297 949 164 4 4635 5581 713487741 713488687 0.000000e+00 819.0
7 TraesCS6B01G458400 chr6B 81.723 952 166 8 4637 5584 713783871 713782924 0.000000e+00 787.0
8 TraesCS6B01G458400 chr6B 81.138 949 174 5 4635 5580 713391209 713392155 0.000000e+00 756.0
9 TraesCS6B01G458400 chr6B 79.155 1089 214 11 4500 5581 713701660 713702742 0.000000e+00 741.0
10 TraesCS6B01G458400 chr6B 80.818 954 171 9 4637 5584 713743075 713744022 0.000000e+00 737.0
11 TraesCS6B01G458400 chr6B 78.015 1169 229 23 456 1619 713381290 713382435 0.000000e+00 710.0
12 TraesCS6B01G458400 chr6B 77.975 1185 209 39 477 1641 713956697 713957849 0.000000e+00 695.0
13 TraesCS6B01G458400 chr6B 76.093 1167 233 34 462 1606 713829890 713831032 1.090000e-157 568.0
14 TraesCS6B01G458400 chr6B 93.503 354 18 4 2003 2354 713966367 713966717 8.640000e-144 521.0
15 TraesCS6B01G458400 chr6B 82.150 493 77 7 456 947 713176570 713177052 5.420000e-111 412.0
16 TraesCS6B01G458400 chr6B 91.148 305 22 3 2391 2692 713966934 713967236 7.020000e-110 409.0
17 TraesCS6B01G458400 chr6B 81.762 488 76 9 461 947 713788592 713788117 5.460000e-106 396.0
18 TraesCS6B01G458400 chr6B 75.187 669 159 5 5676 6339 713961826 713962492 7.320000e-80 309.0
19 TraesCS6B01G458400 chr6B 77.323 538 101 17 1111 1641 713923531 713924054 1.580000e-76 298.0
20 TraesCS6B01G458400 chr6B 74.328 670 146 15 5676 6338 713392290 713392940 2.080000e-65 261.0
21 TraesCS6B01G458400 chr6B 73.867 662 155 14 5681 6336 713164565 713165214 1.620000e-61 248.0
22 TraesCS6B01G458400 chr6B 81.467 259 42 3 3540 3798 713786100 713785848 2.750000e-49 207.0
23 TraesCS6B01G458400 chr6B 74.171 422 102 7 5690 6109 713744230 713744646 1.300000e-37 169.0
24 TraesCS6B01G458400 chr6B 74.005 427 96 14 5689 6109 713780056 713779639 7.800000e-35 159.0
25 TraesCS6B01G458400 chr6B 75.000 340 72 10 3526 3862 713841342 713841671 2.180000e-30 145.0
26 TraesCS6B01G458400 chr6B 96.078 51 2 0 2351 2401 713966736 713966786 4.830000e-12 84.2
27 TraesCS6B01G458400 chr6A 94.338 3550 113 23 4010 7509 613985380 613988891 0.000000e+00 5361.0
28 TraesCS6B01G458400 chr6A 96.452 930 30 1 3088 4014 613984424 613985353 0.000000e+00 1531.0
29 TraesCS6B01G458400 chr6A 82.285 954 166 3 4633 5584 613962466 613963418 0.000000e+00 822.0
30 TraesCS6B01G458400 chr6A 90.093 535 49 4 454 986 613982784 613983316 0.000000e+00 691.0
31 TraesCS6B01G458400 chr6A 89.521 334 27 4 60 385 613982455 613982788 4.190000e-112 416.0
32 TraesCS6B01G458400 chr6A 83.631 336 42 8 2359 2688 613984006 613984334 3.410000e-78 303.0
33 TraesCS6B01G458400 chr6A 79.476 229 39 6 3540 3767 613958985 613959206 1.010000e-33 156.0
34 TraesCS6B01G458400 chr6D 95.237 3023 90 17 4010 6989 467911292 467914303 0.000000e+00 4735.0
35 TraesCS6B01G458400 chr6D 94.049 1277 68 7 454 1728 467907837 467909107 0.000000e+00 1930.0
36 TraesCS6B01G458400 chr6D 97.372 837 14 5 3061 3889 467910001 467910837 0.000000e+00 1417.0
37 TraesCS6B01G458400 chr6D 96.130 491 13 1 7025 7509 467914306 467914796 0.000000e+00 797.0
38 TraesCS6B01G458400 chr6D 89.664 387 19 4 1 385 467907474 467907841 2.450000e-129 473.0
39 TraesCS6B01G458400 chr6D 93.950 281 14 2 1729 2007 50532 50253 9.010000e-114 422.0
40 TraesCS6B01G458400 chr6D 93.929 280 16 1 1729 2007 12463770 12464049 9.010000e-114 422.0
41 TraesCS6B01G458400 chr6D 82.825 361 47 8 2338 2692 467909598 467909949 7.320000e-80 309.0
42 TraesCS6B01G458400 chr6D 95.420 131 6 0 3881 4011 467911132 467911262 7.640000e-50 209.0
43 TraesCS6B01G458400 chr6D 75.294 340 71 10 3526 3862 467841827 467842156 4.690000e-32 150.0
44 TraesCS6B01G458400 chr1B 96.403 278 10 0 1729 2006 626492354 626492631 6.870000e-125 459.0
45 TraesCS6B01G458400 chr4B 96.043 278 11 0 1728 2005 598390767 598391044 3.200000e-123 453.0
46 TraesCS6B01G458400 chr5B 95.035 282 14 0 1729 2010 14688396 14688115 1.920000e-120 444.0
47 TraesCS6B01G458400 chr5B 93.594 281 12 3 1729 2009 467021037 467020763 1.510000e-111 414.0
48 TraesCS6B01G458400 chr5B 91.756 279 13 1 1731 1999 119420606 119420884 5.500000e-101 379.0
49 TraesCS6B01G458400 chrUn 93.772 289 8 1 1729 2007 38969577 38969289 6.970000e-115 425.0
50 TraesCS6B01G458400 chr7B 91.724 290 14 3 1729 2008 725691524 725691813 1.960000e-105 394.0
51 TraesCS6B01G458400 chr7D 92.941 255 17 1 1752 2005 37109760 37110014 3.310000e-98 370.0
52 TraesCS6B01G458400 chr3D 90.385 52 5 0 6279 6330 446091989 446092040 1.350000e-07 69.4


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 TraesCS6B01G458400 chr6B 713506284 713513794 7510 False 6599.500000 8227 100.000000 1 7511 2 chr6B.!!$F10 7510
1 TraesCS6B01G458400 chr6B 713956697 713971775 15078 False 1290.244444 4628 90.181667 1 7509 9 chr6B.!!$F12 7508
2 TraesCS6B01G458400 chr6B 713487741 713488687 946 False 819.000000 819 82.297000 4635 5581 1 chr6B.!!$F4 946
3 TraesCS6B01G458400 chr6B 713701660 713702742 1082 False 741.000000 741 79.155000 4500 5581 1 chr6B.!!$F5 1081
4 TraesCS6B01G458400 chr6B 713381290 713382435 1145 False 710.000000 710 78.015000 456 1619 1 chr6B.!!$F3 1163
5 TraesCS6B01G458400 chr6B 713829890 713831032 1142 False 568.000000 568 76.093000 462 1606 1 chr6B.!!$F6 1144
6 TraesCS6B01G458400 chr6B 713391209 713392940 1731 False 508.500000 756 77.733000 4635 6338 2 chr6B.!!$F9 1703
7 TraesCS6B01G458400 chr6B 713743075 713744646 1571 False 453.000000 737 77.494500 4637 6109 2 chr6B.!!$F11 1472
8 TraesCS6B01G458400 chr6B 713779639 713788592 8953 True 387.250000 787 79.739250 461 6109 4 chr6B.!!$R1 5648
9 TraesCS6B01G458400 chr6B 713923531 713924054 523 False 298.000000 298 77.323000 1111 1641 1 chr6B.!!$F8 530
10 TraesCS6B01G458400 chr6B 713164565 713165214 649 False 248.000000 248 73.867000 5681 6336 1 chr6B.!!$F1 655
11 TraesCS6B01G458400 chr6A 613982455 613988891 6436 False 1660.400000 5361 90.807000 60 7509 5 chr6A.!!$F2 7449
12 TraesCS6B01G458400 chr6A 613958985 613963418 4433 False 489.000000 822 80.880500 3540 5584 2 chr6A.!!$F1 2044
13 TraesCS6B01G458400 chr6D 467907474 467914796 7322 False 1410.000000 4735 92.956714 1 7509 7 chr6D.!!$F3 7508

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
255 8179 1.282157 CCAAGCAGCTTAACTAGGGGT 59.718 52.381 7.52 0.0 0.00 4.95 F
1410 9365 0.035630 AGAGGTGCCTCATTGTGCTC 60.036 55.000 19.22 0.0 44.99 4.26 F
2016 10159 0.036164 AAACCATGGTCACGCTAGCA 59.964 50.000 20.07 0.0 0.00 3.49 F
2017 10160 0.253044 AACCATGGTCACGCTAGCAT 59.747 50.000 20.07 0.0 38.07 3.79 F
2211 10531 1.004277 TGGACAAGGTTAGCCATGGTC 59.996 52.381 14.67 5.8 37.76 4.02 F
3393 12198 1.480545 GTGGTGTTGGGAAAAGCACTT 59.519 47.619 2.27 0.0 38.84 3.16 F
4194 13397 1.810031 CGTGCTCTCCAAACAGGTTGA 60.810 52.381 0.00 0.0 39.87 3.18 F
4879 16829 2.178912 TCCAAAGTTTGAGGGCGTAG 57.821 50.000 17.33 0.0 0.00 3.51 F
5949 18013 0.177604 GCATGTCCTCACCTCCAGAG 59.822 60.000 0.00 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 10056 0.035176 TGCATTTCAGCCAAAAGGCC 59.965 50.000 13.40 0.00 43.34 5.19 R
2412 11185 0.887933 AGCAACGGGTATGCCAAAAG 59.112 50.000 1.04 0.00 44.91 2.27 R
4014 13180 1.551019 GCCTAACTCGGGACTGGGTT 61.551 60.000 1.55 1.55 0.00 4.11 R
4017 13183 1.961180 CTGGCCTAACTCGGGACTGG 61.961 65.000 3.32 0.00 31.96 4.00 R
4018 13184 1.517832 CTGGCCTAACTCGGGACTG 59.482 63.158 3.32 0.00 31.96 3.51 R
5270 17222 0.890683 CTTCATGGTGGCCTCAAACC 59.109 55.000 3.32 3.11 36.96 3.27 R
5400 17352 0.036732 TGTGCTCAAGGTGATGACCC 59.963 55.000 0.00 0.00 44.40 4.46 R
6435 18538 0.108472 CGAGCTGCTTCCTCATGTCA 60.108 55.000 2.53 0.00 0.00 3.58 R
7364 20676 0.935898 GCTCTGTTGGAGATGATGCG 59.064 55.000 0.00 0.00 44.45 4.73 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
88 8003 2.577644 GCATGCACGTTCGCCATG 60.578 61.111 14.21 16.34 0.00 3.66
132 8054 3.407424 TGTGCTGGCATATACTCCATC 57.593 47.619 0.00 0.00 0.00 3.51
255 8179 1.282157 CCAAGCAGCTTAACTAGGGGT 59.718 52.381 7.52 0.00 0.00 4.95
266 8190 6.550481 AGCTTAACTAGGGGTCATAGTAGAAC 59.450 42.308 0.00 0.00 33.15 3.01
412 8338 6.671190 TGGATATACGAATACAACGGTACAG 58.329 40.000 0.00 0.00 34.93 2.74
432 8358 4.188462 CAGCAAAAGGGATATACGTGACA 58.812 43.478 0.00 0.00 0.00 3.58
433 8359 4.271049 CAGCAAAAGGGATATACGTGACAG 59.729 45.833 0.00 0.00 0.00 3.51
434 8360 4.081087 AGCAAAAGGGATATACGTGACAGT 60.081 41.667 0.00 0.00 0.00 3.55
435 8361 4.034048 GCAAAAGGGATATACGTGACAGTG 59.966 45.833 0.00 0.00 0.00 3.66
436 8362 3.454371 AAGGGATATACGTGACAGTGC 57.546 47.619 0.00 0.00 0.00 4.40
486 8412 2.670414 GACCTGCGTTTTCAGATCTCAG 59.330 50.000 0.00 0.00 36.19 3.35
684 8611 2.766400 CGGACGAGCTGGAGAGGAC 61.766 68.421 1.44 0.00 0.00 3.85
1031 8959 4.555313 CGTTGATGAAGCAACAAGACATGT 60.555 41.667 11.55 0.00 46.45 3.21
1254 9205 2.335712 GCAGCCTTTCCAACCCGAG 61.336 63.158 0.00 0.00 0.00 4.63
1257 9208 1.674651 GCCTTTCCAACCCGAGGAC 60.675 63.158 0.00 0.00 34.19 3.85
1410 9365 0.035630 AGAGGTGCCTCATTGTGCTC 60.036 55.000 19.22 0.00 44.99 4.26
1448 9404 1.211457 GGAAGAGTGGCACCAGATCAT 59.789 52.381 15.27 0.00 0.00 2.45
1628 9738 9.740710 ACTAGCTAGTTCAATTTTGGAAATAGT 57.259 29.630 20.95 0.00 42.09 2.12
1709 9852 8.747538 ATGTCACCTTTAATACCCTCATTTAC 57.252 34.615 0.00 0.00 0.00 2.01
1728 9871 3.131240 ACTTGTTTTGTTGTCACGCTC 57.869 42.857 0.00 0.00 0.00 5.03
1729 9872 2.486203 ACTTGTTTTGTTGTCACGCTCA 59.514 40.909 0.00 0.00 0.00 4.26
1730 9873 3.128589 ACTTGTTTTGTTGTCACGCTCAT 59.871 39.130 0.00 0.00 0.00 2.90
1731 9874 3.063670 TGTTTTGTTGTCACGCTCATG 57.936 42.857 0.00 0.00 0.00 3.07
1732 9875 2.223456 TGTTTTGTTGTCACGCTCATGG 60.223 45.455 0.00 0.00 0.00 3.66
1734 9877 1.674359 TTGTTGTCACGCTCATGGTT 58.326 45.000 0.00 0.00 0.00 3.67
1735 9878 1.674359 TGTTGTCACGCTCATGGTTT 58.326 45.000 0.00 0.00 0.00 3.27
1736 9879 2.020720 TGTTGTCACGCTCATGGTTTT 58.979 42.857 0.00 0.00 0.00 2.43
1737 9880 2.032799 TGTTGTCACGCTCATGGTTTTC 59.967 45.455 0.00 0.00 0.00 2.29
1738 9881 1.960417 TGTCACGCTCATGGTTTTCA 58.040 45.000 0.00 0.00 0.00 2.69
1739 9882 1.601903 TGTCACGCTCATGGTTTTCAC 59.398 47.619 0.00 0.00 0.00 3.18
1740 9883 1.873591 GTCACGCTCATGGTTTTCACT 59.126 47.619 0.00 0.00 0.00 3.41
1741 9884 2.290641 GTCACGCTCATGGTTTTCACTT 59.709 45.455 0.00 0.00 0.00 3.16
1742 9885 2.948979 TCACGCTCATGGTTTTCACTTT 59.051 40.909 0.00 0.00 0.00 2.66
1743 9886 3.003275 TCACGCTCATGGTTTTCACTTTC 59.997 43.478 0.00 0.00 0.00 2.62
1744 9887 2.948979 ACGCTCATGGTTTTCACTTTCA 59.051 40.909 0.00 0.00 0.00 2.69
1745 9888 3.003689 ACGCTCATGGTTTTCACTTTCAG 59.996 43.478 0.00 0.00 0.00 3.02
1746 9889 3.003689 CGCTCATGGTTTTCACTTTCAGT 59.996 43.478 0.00 0.00 0.00 3.41
1770 9913 7.806409 TGAGATTTCACTGAAATTCACTGAA 57.194 32.000 16.48 12.02 41.56 3.02
1771 9914 8.400184 TGAGATTTCACTGAAATTCACTGAAT 57.600 30.769 16.48 0.00 41.56 2.57
1772 9915 8.853126 TGAGATTTCACTGAAATTCACTGAATT 58.147 29.630 16.48 10.71 41.56 2.17
1792 9935 9.294030 CTGAATTTCATTAATTTCAGTAGGCAC 57.706 33.333 15.18 0.00 42.63 5.01
1793 9936 9.023962 TGAATTTCATTAATTTCAGTAGGCACT 57.976 29.630 0.00 0.00 38.46 4.40
1794 9937 9.294030 GAATTTCATTAATTTCAGTAGGCACTG 57.706 33.333 9.81 9.81 43.42 3.66
1828 9971 8.939201 TGTTTCAGTCAAAATATTTCAGCAAA 57.061 26.923 0.10 0.00 0.00 3.68
1829 9972 9.545105 TGTTTCAGTCAAAATATTTCAGCAAAT 57.455 25.926 0.10 0.00 36.18 2.32
1832 9975 9.761504 TTCAGTCAAAATATTTCAGCAAATTCA 57.238 25.926 0.10 0.00 33.95 2.57
1833 9976 9.414295 TCAGTCAAAATATTTCAGCAAATTCAG 57.586 29.630 0.10 0.00 33.95 3.02
1834 9977 9.199982 CAGTCAAAATATTTCAGCAAATTCAGT 57.800 29.630 0.10 0.00 33.95 3.41
1842 9985 7.744087 ATTTCAGCAAATTCAGTAGTACACA 57.256 32.000 2.52 0.00 0.00 3.72
1843 9986 6.785488 TTCAGCAAATTCAGTAGTACACAG 57.215 37.500 2.52 0.00 0.00 3.66
1844 9987 5.237815 TCAGCAAATTCAGTAGTACACAGG 58.762 41.667 2.52 0.00 0.00 4.00
1845 9988 5.011635 TCAGCAAATTCAGTAGTACACAGGA 59.988 40.000 2.52 0.00 0.00 3.86
1846 9989 5.700832 CAGCAAATTCAGTAGTACACAGGAA 59.299 40.000 2.52 1.65 0.00 3.36
1847 9990 6.204688 CAGCAAATTCAGTAGTACACAGGAAA 59.795 38.462 2.52 0.00 0.00 3.13
1848 9991 6.770785 AGCAAATTCAGTAGTACACAGGAAAA 59.229 34.615 2.52 0.00 0.00 2.29
1849 9992 6.856426 GCAAATTCAGTAGTACACAGGAAAAC 59.144 38.462 2.52 0.00 0.00 2.43
1850 9993 7.468084 GCAAATTCAGTAGTACACAGGAAAACA 60.468 37.037 2.52 0.00 0.00 2.83
1851 9994 8.402472 CAAATTCAGTAGTACACAGGAAAACAA 58.598 33.333 2.52 0.00 0.00 2.83
1852 9995 8.514330 AATTCAGTAGTACACAGGAAAACAAA 57.486 30.769 2.52 0.00 0.00 2.83
1853 9996 8.691661 ATTCAGTAGTACACAGGAAAACAAAT 57.308 30.769 2.52 0.00 0.00 2.32
1854 9997 9.787435 ATTCAGTAGTACACAGGAAAACAAATA 57.213 29.630 2.52 0.00 0.00 1.40
1855 9998 9.787435 TTCAGTAGTACACAGGAAAACAAATAT 57.213 29.630 2.52 0.00 0.00 1.28
1856 9999 9.787435 TCAGTAGTACACAGGAAAACAAATATT 57.213 29.630 2.52 0.00 0.00 1.28
1918 10061 9.883142 TTAAATTCAAATGAATATTTCGGCCTT 57.117 25.926 8.94 0.41 43.41 4.35
1919 10062 8.791327 AAATTCAAATGAATATTTCGGCCTTT 57.209 26.923 8.94 0.00 43.41 3.11
1920 10063 8.791327 AATTCAAATGAATATTTCGGCCTTTT 57.209 26.923 8.94 0.00 43.41 2.27
1921 10064 7.593875 TTCAAATGAATATTTCGGCCTTTTG 57.406 32.000 0.00 0.00 34.34 2.44
1922 10065 6.105333 TCAAATGAATATTTCGGCCTTTTGG 58.895 36.000 0.00 0.00 37.22 3.28
1935 10078 3.883631 CCTTTTGGCTGAAATGCAAAC 57.116 42.857 0.00 0.00 34.04 2.93
1936 10079 3.469739 CCTTTTGGCTGAAATGCAAACT 58.530 40.909 0.00 0.00 34.04 2.66
1937 10080 3.249080 CCTTTTGGCTGAAATGCAAACTG 59.751 43.478 0.00 0.00 34.04 3.16
1938 10081 3.815856 TTTGGCTGAAATGCAAACTGA 57.184 38.095 0.00 0.00 34.04 3.41
1939 10082 3.815856 TTGGCTGAAATGCAAACTGAA 57.184 38.095 0.00 0.00 34.04 3.02
1940 10083 3.374220 TGGCTGAAATGCAAACTGAAG 57.626 42.857 0.00 0.00 34.04 3.02
1941 10084 2.694628 TGGCTGAAATGCAAACTGAAGT 59.305 40.909 0.00 0.00 34.04 3.01
1942 10085 3.888323 TGGCTGAAATGCAAACTGAAGTA 59.112 39.130 0.00 0.00 34.04 2.24
1943 10086 4.340666 TGGCTGAAATGCAAACTGAAGTAA 59.659 37.500 0.00 0.00 34.04 2.24
1944 10087 4.681483 GGCTGAAATGCAAACTGAAGTAAC 59.319 41.667 0.00 0.00 34.04 2.50
1945 10088 5.507985 GGCTGAAATGCAAACTGAAGTAACT 60.508 40.000 0.00 0.00 34.04 2.24
1946 10089 5.400485 GCTGAAATGCAAACTGAAGTAACTG 59.600 40.000 0.00 0.00 0.00 3.16
1947 10090 6.691754 TGAAATGCAAACTGAAGTAACTGA 57.308 33.333 0.00 0.00 0.00 3.41
1948 10091 7.094508 TGAAATGCAAACTGAAGTAACTGAA 57.905 32.000 0.00 0.00 0.00 3.02
1949 10092 7.715657 TGAAATGCAAACTGAAGTAACTGAAT 58.284 30.769 0.00 0.00 0.00 2.57
1950 10093 8.196771 TGAAATGCAAACTGAAGTAACTGAATT 58.803 29.630 0.00 0.00 0.00 2.17
1951 10094 8.947055 AAATGCAAACTGAAGTAACTGAATTT 57.053 26.923 0.00 2.43 0.00 1.82
1952 10095 8.579682 AATGCAAACTGAAGTAACTGAATTTC 57.420 30.769 0.00 0.00 0.00 2.17
1953 10096 7.094508 TGCAAACTGAAGTAACTGAATTTCA 57.905 32.000 0.00 0.00 0.00 2.69
1968 10111 6.713762 TGAATTTCAGTGATTTCAGTTGGT 57.286 33.333 12.59 0.00 0.00 3.67
1969 10112 6.506147 TGAATTTCAGTGATTTCAGTTGGTG 58.494 36.000 12.59 0.00 0.00 4.17
1970 10113 3.988379 TTCAGTGATTTCAGTTGGTGC 57.012 42.857 0.00 0.00 0.00 5.01
1971 10114 3.213206 TCAGTGATTTCAGTTGGTGCT 57.787 42.857 0.00 0.00 0.00 4.40
1972 10115 2.880268 TCAGTGATTTCAGTTGGTGCTG 59.120 45.455 0.00 0.00 37.81 4.41
1973 10116 2.880268 CAGTGATTTCAGTTGGTGCTGA 59.120 45.455 0.00 0.00 43.03 4.26
1981 10124 4.734398 TCAGTTGGTGCTGAAATTTTGT 57.266 36.364 0.00 0.00 41.93 2.83
1982 10125 5.083533 TCAGTTGGTGCTGAAATTTTGTT 57.916 34.783 0.00 0.00 41.93 2.83
1983 10126 4.869297 TCAGTTGGTGCTGAAATTTTGTTG 59.131 37.500 0.00 0.00 41.93 3.33
1984 10127 4.869297 CAGTTGGTGCTGAAATTTTGTTGA 59.131 37.500 0.00 0.00 38.70 3.18
1985 10128 5.350914 CAGTTGGTGCTGAAATTTTGTTGAA 59.649 36.000 0.00 0.00 38.70 2.69
1986 10129 5.936956 AGTTGGTGCTGAAATTTTGTTGAAA 59.063 32.000 0.00 0.00 0.00 2.69
1987 10130 5.793026 TGGTGCTGAAATTTTGTTGAAAC 57.207 34.783 0.00 0.00 0.00 2.78
1988 10131 5.486526 TGGTGCTGAAATTTTGTTGAAACT 58.513 33.333 0.00 0.00 0.00 2.66
1989 10132 5.350914 TGGTGCTGAAATTTTGTTGAAACTG 59.649 36.000 0.00 0.00 0.00 3.16
1990 10133 5.580297 GGTGCTGAAATTTTGTTGAAACTGA 59.420 36.000 0.00 0.00 0.00 3.41
1991 10134 6.091986 GGTGCTGAAATTTTGTTGAAACTGAA 59.908 34.615 0.00 0.00 0.00 3.02
1992 10135 7.360776 GGTGCTGAAATTTTGTTGAAACTGAAA 60.361 33.333 0.00 0.00 0.00 2.69
1993 10136 8.177013 GTGCTGAAATTTTGTTGAAACTGAAAT 58.823 29.630 0.00 0.00 31.55 2.17
1994 10137 8.728833 TGCTGAAATTTTGTTGAAACTGAAATT 58.271 25.926 11.56 11.56 37.16 1.82
1995 10138 9.002080 GCTGAAATTTTGTTGAAACTGAAATTG 57.998 29.630 15.20 8.85 36.47 2.32
2001 10144 9.838975 ATTTTGTTGAAACTGAAATTGAAAACC 57.161 25.926 0.00 0.00 0.00 3.27
2002 10145 7.969536 TTGTTGAAACTGAAATTGAAAACCA 57.030 28.000 0.00 0.00 0.00 3.67
2003 10146 8.558973 TTGTTGAAACTGAAATTGAAAACCAT 57.441 26.923 0.00 0.00 0.00 3.55
2004 10147 7.972527 TGTTGAAACTGAAATTGAAAACCATG 58.027 30.769 0.00 0.00 0.00 3.66
2005 10148 7.065563 TGTTGAAACTGAAATTGAAAACCATGG 59.934 33.333 11.19 11.19 0.00 3.66
2006 10149 6.648192 TGAAACTGAAATTGAAAACCATGGT 58.352 32.000 13.00 13.00 0.00 3.55
2007 10150 6.760770 TGAAACTGAAATTGAAAACCATGGTC 59.239 34.615 20.07 6.47 0.00 4.02
2008 10151 5.867903 ACTGAAATTGAAAACCATGGTCA 57.132 34.783 20.07 9.48 0.00 4.02
2009 10152 5.600696 ACTGAAATTGAAAACCATGGTCAC 58.399 37.500 20.07 12.91 0.00 3.67
2010 10153 4.615949 TGAAATTGAAAACCATGGTCACG 58.384 39.130 20.07 0.00 0.00 4.35
2011 10154 2.723124 ATTGAAAACCATGGTCACGC 57.277 45.000 20.07 8.86 0.00 5.34
2012 10155 1.686355 TTGAAAACCATGGTCACGCT 58.314 45.000 20.07 0.00 0.00 5.07
2013 10156 2.552599 TGAAAACCATGGTCACGCTA 57.447 45.000 20.07 0.00 0.00 4.26
2014 10157 2.422597 TGAAAACCATGGTCACGCTAG 58.577 47.619 20.07 0.00 0.00 3.42
2015 10158 1.130561 GAAAACCATGGTCACGCTAGC 59.869 52.381 20.07 4.06 0.00 3.42
2016 10159 0.036164 AAACCATGGTCACGCTAGCA 59.964 50.000 20.07 0.00 0.00 3.49
2017 10160 0.253044 AACCATGGTCACGCTAGCAT 59.747 50.000 20.07 0.00 38.07 3.79
2018 10161 0.253044 ACCATGGTCACGCTAGCATT 59.747 50.000 13.00 0.00 35.46 3.56
2019 10162 1.484653 ACCATGGTCACGCTAGCATTA 59.515 47.619 13.00 0.00 35.46 1.90
2020 10163 2.093181 ACCATGGTCACGCTAGCATTAA 60.093 45.455 13.00 0.00 35.46 1.40
2021 10164 3.141398 CCATGGTCACGCTAGCATTAAT 58.859 45.455 16.45 0.00 35.46 1.40
2022 10165 4.202315 ACCATGGTCACGCTAGCATTAATA 60.202 41.667 13.00 0.00 35.46 0.98
2068 10211 5.356751 AGATGCGTCTCTAGATATTAGCTGG 59.643 44.000 1.48 0.00 0.00 4.85
2069 10212 3.759086 TGCGTCTCTAGATATTAGCTGGG 59.241 47.826 0.00 0.00 0.00 4.45
2070 10213 4.011023 GCGTCTCTAGATATTAGCTGGGA 58.989 47.826 0.00 0.00 0.00 4.37
2150 10295 6.141369 GCAAAGCTTAATTATCTTGACGCATC 59.859 38.462 0.00 0.00 0.00 3.91
2211 10531 1.004277 TGGACAAGGTTAGCCATGGTC 59.996 52.381 14.67 5.80 37.76 4.02
2389 11001 3.761218 TGGATAATGTTGCGATGGTTTGT 59.239 39.130 0.00 0.00 0.00 2.83
2425 11198 3.320826 ACAAGAACACTTTTGGCATACCC 59.679 43.478 0.00 0.00 33.59 3.69
2443 11217 2.491693 ACCCGTTGCTAATGTGAAATGG 59.508 45.455 0.00 0.00 0.00 3.16
2642 11429 6.785488 TGTGAGCAAAACTGACTTGTATAG 57.215 37.500 0.00 0.00 33.01 1.31
2655 11442 7.776969 ACTGACTTGTATAGATGCCATTTGATT 59.223 33.333 0.00 0.00 0.00 2.57
3285 12087 3.202151 AGAGGAATTTCGGCTTATTGGGA 59.798 43.478 0.00 0.00 0.00 4.37
3393 12198 1.480545 GTGGTGTTGGGAAAAGCACTT 59.519 47.619 2.27 0.00 38.84 3.16
3667 12508 4.475028 TGTTTGCTTGCAATGAATAGTCG 58.525 39.130 8.93 0.00 0.00 4.18
3800 12641 5.836898 TGACCTCTTCACAGAAAAGGTACTA 59.163 40.000 4.83 0.00 38.49 1.82
3898 13055 8.317679 AGGGTCATATTTCAGATTAGCATACTC 58.682 37.037 0.00 0.00 0.00 2.59
3983 13149 2.673258 TCGGCTATCATGTTGTAGGGA 58.327 47.619 0.00 0.00 0.00 4.20
3989 13155 7.179516 TCGGCTATCATGTTGTAGGGAAATATA 59.820 37.037 0.00 0.00 0.00 0.86
4016 13182 8.539770 AGGAATCATATACATTCGACATGAAC 57.460 34.615 0.00 0.00 40.00 3.18
4017 13183 7.604164 AGGAATCATATACATTCGACATGAACC 59.396 37.037 0.00 9.42 40.00 3.62
4018 13184 7.148407 GGAATCATATACATTCGACATGAACCC 60.148 40.741 0.00 5.31 40.00 4.11
4019 13185 6.168270 TCATATACATTCGACATGAACCCA 57.832 37.500 0.00 0.00 40.00 4.51
4020 13186 6.223120 TCATATACATTCGACATGAACCCAG 58.777 40.000 0.00 0.00 40.00 4.45
4194 13397 1.810031 CGTGCTCTCCAAACAGGTTGA 60.810 52.381 0.00 0.00 39.87 3.18
4198 13401 4.702131 GTGCTCTCCAAACAGGTTGATATT 59.298 41.667 0.00 0.00 39.87 1.28
4238 14777 6.775234 AGTACTTCTCCTTTTCCCCTTTTA 57.225 37.500 0.00 0.00 0.00 1.52
4444 15856 8.995220 GTTTTTGTACATACAGAACTATGTCCA 58.005 33.333 0.00 0.00 38.18 4.02
4448 15860 7.903145 TGTACATACAGAACTATGTCCAAGTT 58.097 34.615 0.00 0.00 38.18 2.66
4458 15870 8.822805 AGAACTATGTCCAAGTTACTCCAATTA 58.177 33.333 0.00 0.00 37.31 1.40
4524 16429 8.345565 CCTGATGTTTATTACCAAGTCAATAGC 58.654 37.037 0.00 0.00 0.00 2.97
4879 16829 2.178912 TCCAAAGTTTGAGGGCGTAG 57.821 50.000 17.33 0.00 0.00 3.51
5110 17062 3.076621 TCACTTTGCAGCATACAAGGAG 58.923 45.455 9.61 3.01 0.00 3.69
5316 17268 4.579753 TCATGTATACGGTCATTGACGGTA 59.420 41.667 28.49 28.49 46.60 4.02
5366 17318 8.859236 ATTTCTGACAAGATGAGATTTCTTCA 57.141 30.769 2.53 0.00 31.11 3.02
5400 17352 5.171147 TCGAAGGAACTAAAGATCTAGCG 57.829 43.478 0.00 0.00 38.49 4.26
5520 17476 1.524355 CTGCGACAACTTGAGACACTG 59.476 52.381 0.00 0.00 0.00 3.66
5594 17550 4.645535 AGCAAGCTATGTGAACTGAAAGA 58.354 39.130 0.00 0.00 37.43 2.52
5949 18013 0.177604 GCATGTCCTCACCTCCAGAG 59.822 60.000 0.00 0.00 0.00 3.35
6141 18205 4.070716 AGAAATCTTTCCAGAGTGCACTG 58.929 43.478 27.27 11.99 37.92 3.66
6435 18538 3.395941 ACAGGGAAGACAAAGTCAAGGAT 59.604 43.478 0.00 0.00 34.60 3.24
6486 18589 2.799126 ACTGCCCCATTATGAACGAA 57.201 45.000 0.00 0.00 0.00 3.85
6490 18593 4.196193 CTGCCCCATTATGAACGAACTAA 58.804 43.478 0.00 0.00 0.00 2.24
6497 18600 5.293569 CCATTATGAACGAACTAAGTCCACC 59.706 44.000 0.00 0.00 0.00 4.61
6570 19840 1.906824 TCAGCGAGGGGTTTCGACT 60.907 57.895 0.00 0.00 43.03 4.18
6571 19841 1.004918 CAGCGAGGGGTTTCGACTT 60.005 57.895 0.00 0.00 43.03 3.01
6572 19842 1.004918 AGCGAGGGGTTTCGACTTG 60.005 57.895 0.00 0.00 43.03 3.16
6573 19843 1.301479 GCGAGGGGTTTCGACTTGT 60.301 57.895 0.00 0.00 43.03 3.16
6574 19844 0.883370 GCGAGGGGTTTCGACTTGTT 60.883 55.000 0.00 0.00 43.03 2.83
6583 19853 2.187351 TTCGACTTGTTGCTTGTTGC 57.813 45.000 0.00 0.00 43.25 4.17
6722 19998 6.827586 CCTTGGGCAATAACTTTGTAACTA 57.172 37.500 0.00 0.00 0.00 2.24
6872 20184 2.439507 TGGTTCTGCCTAGATGATTCCC 59.560 50.000 0.00 0.00 38.35 3.97
6895 20207 4.560716 CGAACCTCATCAACTTGGTAGACA 60.561 45.833 0.00 0.00 31.82 3.41
6989 20301 4.281182 CACTCAGGTACTACTGAAACACCT 59.719 45.833 3.81 0.00 46.05 4.00
6993 20305 4.481072 AGGTACTACTGAAACACCTGAGT 58.519 43.478 0.00 0.00 38.20 3.41
6994 20306 4.900054 AGGTACTACTGAAACACCTGAGTT 59.100 41.667 0.00 0.00 38.20 3.01
6995 20307 5.010820 AGGTACTACTGAAACACCTGAGTTC 59.989 44.000 0.00 0.00 38.20 3.01
6996 20308 5.221382 GGTACTACTGAAACACCTGAGTTCA 60.221 44.000 0.00 0.00 0.00 3.18
6997 20309 4.950050 ACTACTGAAACACCTGAGTTCAG 58.050 43.478 15.77 15.77 43.40 3.02
6998 20310 3.914426 ACTGAAACACCTGAGTTCAGT 57.086 42.857 16.63 16.63 42.27 3.41
6999 20311 5.597182 ACTACTGAAACACCTGAGTTCAGTA 59.403 40.000 21.67 21.67 42.27 2.74
7000 20312 5.552870 ACTGAAACACCTGAGTTCAGTAT 57.447 39.130 19.00 5.01 42.27 2.12
7001 20313 5.300752 ACTGAAACACCTGAGTTCAGTATG 58.699 41.667 19.00 8.30 42.27 2.39
7082 20394 8.528917 AGATGTTCATTGTCAATCAACATTTG 57.471 30.769 23.52 1.43 38.97 2.32
7117 20429 3.211865 TGCATCTGGAATGATTCAGCTC 58.788 45.455 7.56 0.00 0.00 4.09
7143 20455 4.073293 ACCATACACAGATTTCCCGATC 57.927 45.455 0.00 0.00 0.00 3.69
7189 20501 2.747855 CCGAACTTGCTGCTCCCC 60.748 66.667 0.00 0.00 0.00 4.81
7256 20568 0.867753 CGTTCTCCCGCATCTTCTCG 60.868 60.000 0.00 0.00 0.00 4.04
7364 20676 2.202810 CTCCCGCTCTTCCGCTTC 60.203 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 7935 6.823689 TCAAGCTTAGTTTCTTGAGTTGACTT 59.176 34.615 0.00 0.00 42.43 3.01
39 7954 4.500375 GGTTGTTGAGCTGAAAATCAAGCT 60.500 41.667 8.85 0.00 36.16 3.74
132 8054 5.562307 GCTTTGATGCTAATAGCTGTCCATG 60.562 44.000 13.88 7.15 42.97 3.66
172 8096 9.840427 CACGTCATGGATTAAAGTTTAGAAAAT 57.160 29.630 0.00 0.00 0.00 1.82
292 8216 1.941377 AATCAAGATTTGCCAGGCCA 58.059 45.000 9.64 0.00 0.00 5.36
412 8338 4.034048 CACTGTCACGTATATCCCTTTTGC 59.966 45.833 0.00 0.00 0.00 3.68
432 8358 7.105588 TCTAAATGTTGAGATGTGTATGCACT 58.894 34.615 15.25 0.72 45.44 4.40
433 8359 7.307493 TCTAAATGTTGAGATGTGTATGCAC 57.693 36.000 7.03 7.03 45.44 4.57
434 8360 6.037500 GCTCTAAATGTTGAGATGTGTATGCA 59.962 38.462 0.00 0.00 32.44 3.96
435 8361 6.425504 GCTCTAAATGTTGAGATGTGTATGC 58.574 40.000 0.00 0.00 32.44 3.14
436 8362 6.017605 GGGCTCTAAATGTTGAGATGTGTATG 60.018 42.308 0.00 0.00 32.44 2.39
442 8368 4.774124 TCAGGGCTCTAAATGTTGAGATG 58.226 43.478 0.00 0.00 32.44 2.90
443 8369 4.718774 TCTCAGGGCTCTAAATGTTGAGAT 59.281 41.667 0.00 0.00 35.85 2.75
444 8370 4.081420 GTCTCAGGGCTCTAAATGTTGAGA 60.081 45.833 0.00 0.00 37.74 3.27
445 8371 4.187694 GTCTCAGGGCTCTAAATGTTGAG 58.812 47.826 0.00 0.00 33.63 3.02
446 8372 3.055094 GGTCTCAGGGCTCTAAATGTTGA 60.055 47.826 0.00 0.00 0.00 3.18
447 8373 3.054802 AGGTCTCAGGGCTCTAAATGTTG 60.055 47.826 0.00 0.00 0.00 3.33
448 8374 3.054802 CAGGTCTCAGGGCTCTAAATGTT 60.055 47.826 0.00 0.00 0.00 2.71
449 8375 2.503356 CAGGTCTCAGGGCTCTAAATGT 59.497 50.000 0.00 0.00 0.00 2.71
450 8376 2.744494 GCAGGTCTCAGGGCTCTAAATG 60.744 54.545 0.00 0.00 0.00 2.32
451 8377 1.488393 GCAGGTCTCAGGGCTCTAAAT 59.512 52.381 0.00 0.00 0.00 1.40
452 8378 0.905357 GCAGGTCTCAGGGCTCTAAA 59.095 55.000 0.00 0.00 0.00 1.85
486 8412 1.298339 GTGAGCGTTTGTGTGTGGC 60.298 57.895 0.00 0.00 0.00 5.01
591 8518 3.814268 CGGATTTGGCGCACCCAG 61.814 66.667 10.83 0.00 46.39 4.45
684 8611 1.402968 CCACCATCAGGAAAGATTGCG 59.597 52.381 0.00 0.00 38.69 4.85
1117 9057 1.139734 CCCACACTCCGATCACTCG 59.860 63.158 0.00 0.00 44.62 4.18
1238 9189 1.846124 TCCTCGGGTTGGAAAGGCT 60.846 57.895 0.00 0.00 0.00 4.58
1381 9336 1.876156 GAGGCACCTCTTGTTGTTGAG 59.124 52.381 9.54 0.00 39.80 3.02
1448 9404 1.152652 TTTTCGGGGAAGCAAGCCA 60.153 52.632 0.00 0.00 0.00 4.75
1502 9458 3.056607 ACACAAGCTTGCAACTTCAACTT 60.057 39.130 26.27 0.00 0.00 2.66
1664 9774 7.387948 GTGACATATCCTAACGGCTTTTGATAT 59.612 37.037 0.00 3.93 0.00 1.63
1674 9784 7.601508 GGTATTAAAGGTGACATATCCTAACGG 59.398 40.741 0.00 0.00 33.27 4.44
1709 9852 3.129852 TGAGCGTGACAACAAAACAAG 57.870 42.857 0.00 0.00 0.00 3.16
1719 9862 1.601903 GTGAAAACCATGAGCGTGACA 59.398 47.619 0.00 0.00 0.00 3.58
1764 9907 9.294030 GCCTACTGAAATTAATGAAATTCAGTG 57.706 33.333 26.81 18.83 41.20 3.66
1765 9908 9.023962 TGCCTACTGAAATTAATGAAATTCAGT 57.976 29.630 23.77 23.77 42.31 3.41
1766 9909 9.294030 GTGCCTACTGAAATTAATGAAATTCAG 57.706 33.333 16.28 16.28 36.76 3.02
1767 9910 9.023962 AGTGCCTACTGAAATTAATGAAATTCA 57.976 29.630 0.00 0.00 34.62 2.57
1802 9945 9.545105 TTTGCTGAAATATTTTGACTGAAACAT 57.455 25.926 1.43 0.00 0.00 2.71
1803 9946 8.939201 TTTGCTGAAATATTTTGACTGAAACA 57.061 26.923 1.43 0.00 0.00 2.83
1806 9949 9.761504 TGAATTTGCTGAAATATTTTGACTGAA 57.238 25.926 1.43 0.00 31.18 3.02
1807 9950 9.414295 CTGAATTTGCTGAAATATTTTGACTGA 57.586 29.630 1.43 0.00 31.18 3.41
1808 9951 9.199982 ACTGAATTTGCTGAAATATTTTGACTG 57.800 29.630 1.43 0.00 31.18 3.51
1816 9959 9.448438 TGTGTACTACTGAATTTGCTGAAATAT 57.552 29.630 0.00 0.00 31.18 1.28
1817 9960 8.840833 TGTGTACTACTGAATTTGCTGAAATA 57.159 30.769 0.00 0.00 31.18 1.40
1818 9961 7.094634 CCTGTGTACTACTGAATTTGCTGAAAT 60.095 37.037 0.00 0.00 32.87 2.17
1819 9962 6.204688 CCTGTGTACTACTGAATTTGCTGAAA 59.795 38.462 0.00 0.00 0.00 2.69
1820 9963 5.700832 CCTGTGTACTACTGAATTTGCTGAA 59.299 40.000 0.00 0.00 0.00 3.02
1821 9964 5.011635 TCCTGTGTACTACTGAATTTGCTGA 59.988 40.000 0.00 0.00 0.00 4.26
1822 9965 5.237815 TCCTGTGTACTACTGAATTTGCTG 58.762 41.667 0.00 0.00 0.00 4.41
1823 9966 5.483685 TCCTGTGTACTACTGAATTTGCT 57.516 39.130 0.00 0.00 0.00 3.91
1824 9967 6.554334 TTTCCTGTGTACTACTGAATTTGC 57.446 37.500 0.00 0.00 0.00 3.68
1825 9968 7.925993 TGTTTTCCTGTGTACTACTGAATTTG 58.074 34.615 0.00 0.00 0.00 2.32
1826 9969 8.514330 TTGTTTTCCTGTGTACTACTGAATTT 57.486 30.769 0.00 0.00 0.00 1.82
1827 9970 8.514330 TTTGTTTTCCTGTGTACTACTGAATT 57.486 30.769 0.00 0.00 0.00 2.17
1828 9971 8.691661 ATTTGTTTTCCTGTGTACTACTGAAT 57.308 30.769 0.00 0.00 0.00 2.57
1829 9972 9.787435 ATATTTGTTTTCCTGTGTACTACTGAA 57.213 29.630 0.00 0.00 0.00 3.02
1830 9973 9.787435 AATATTTGTTTTCCTGTGTACTACTGA 57.213 29.630 0.00 0.00 0.00 3.41
1892 10035 9.883142 AAGGCCGAAATATTCATTTGAATTTAA 57.117 25.926 10.81 0.00 41.64 1.52
1893 10036 9.883142 AAAGGCCGAAATATTCATTTGAATTTA 57.117 25.926 10.81 0.00 41.64 1.40
1894 10037 8.791327 AAAGGCCGAAATATTCATTTGAATTT 57.209 26.923 10.81 1.94 41.64 1.82
1895 10038 8.667463 CAAAAGGCCGAAATATTCATTTGAATT 58.333 29.630 10.81 0.00 41.64 2.17
1896 10039 7.280652 CCAAAAGGCCGAAATATTCATTTGAAT 59.719 33.333 10.42 10.42 45.77 2.57
1897 10040 6.593382 CCAAAAGGCCGAAATATTCATTTGAA 59.407 34.615 0.00 0.00 34.44 2.69
1898 10041 6.105333 CCAAAAGGCCGAAATATTCATTTGA 58.895 36.000 0.00 0.00 34.44 2.69
1899 10042 5.220643 GCCAAAAGGCCGAAATATTCATTTG 60.221 40.000 0.00 0.00 34.44 2.32
1900 10043 4.875536 GCCAAAAGGCCGAAATATTCATTT 59.124 37.500 0.00 0.00 37.06 2.32
1901 10044 4.162131 AGCCAAAAGGCCGAAATATTCATT 59.838 37.500 2.33 0.00 35.12 2.57
1902 10045 3.706086 AGCCAAAAGGCCGAAATATTCAT 59.294 39.130 2.33 0.00 35.12 2.57
1903 10046 3.096092 AGCCAAAAGGCCGAAATATTCA 58.904 40.909 2.33 0.00 35.12 2.57
1904 10047 3.130340 TCAGCCAAAAGGCCGAAATATTC 59.870 43.478 2.33 0.00 35.12 1.75
1905 10048 3.096092 TCAGCCAAAAGGCCGAAATATT 58.904 40.909 2.33 0.00 35.12 1.28
1906 10049 2.733956 TCAGCCAAAAGGCCGAAATAT 58.266 42.857 2.33 0.00 35.12 1.28
1907 10050 2.208132 TCAGCCAAAAGGCCGAAATA 57.792 45.000 2.33 0.00 35.12 1.40
1908 10051 1.337118 TTCAGCCAAAAGGCCGAAAT 58.663 45.000 2.33 0.00 29.74 2.17
1909 10052 1.115467 TTTCAGCCAAAAGGCCGAAA 58.885 45.000 12.48 12.48 38.45 3.46
1910 10053 1.000731 CATTTCAGCCAAAAGGCCGAA 59.999 47.619 2.33 1.74 35.12 4.30
1911 10054 0.602562 CATTTCAGCCAAAAGGCCGA 59.397 50.000 2.33 0.00 35.12 5.54
1912 10055 1.015607 GCATTTCAGCCAAAAGGCCG 61.016 55.000 2.33 0.00 39.37 6.13
1913 10056 0.035176 TGCATTTCAGCCAAAAGGCC 59.965 50.000 13.40 0.00 43.34 5.19
1914 10057 1.881591 TTGCATTTCAGCCAAAAGGC 58.118 45.000 10.18 10.18 44.03 4.35
1915 10058 3.249080 CAGTTTGCATTTCAGCCAAAAGG 59.751 43.478 0.00 0.00 0.00 3.11
1916 10059 4.121317 TCAGTTTGCATTTCAGCCAAAAG 58.879 39.130 0.00 0.00 0.00 2.27
1917 10060 4.134379 TCAGTTTGCATTTCAGCCAAAA 57.866 36.364 0.00 0.00 0.00 2.44
1918 10061 3.815856 TCAGTTTGCATTTCAGCCAAA 57.184 38.095 0.00 0.00 0.00 3.28
1919 10062 3.132646 ACTTCAGTTTGCATTTCAGCCAA 59.867 39.130 0.00 0.00 0.00 4.52
1920 10063 2.694628 ACTTCAGTTTGCATTTCAGCCA 59.305 40.909 0.00 0.00 0.00 4.75
1921 10064 3.375782 ACTTCAGTTTGCATTTCAGCC 57.624 42.857 0.00 0.00 0.00 4.85
1922 10065 5.400485 CAGTTACTTCAGTTTGCATTTCAGC 59.600 40.000 0.00 0.00 0.00 4.26
1923 10066 6.728200 TCAGTTACTTCAGTTTGCATTTCAG 58.272 36.000 0.00 0.00 0.00 3.02
1924 10067 6.691754 TCAGTTACTTCAGTTTGCATTTCA 57.308 33.333 0.00 0.00 0.00 2.69
1925 10068 8.579682 AATTCAGTTACTTCAGTTTGCATTTC 57.420 30.769 0.00 0.00 0.00 2.17
1926 10069 8.947055 AAATTCAGTTACTTCAGTTTGCATTT 57.053 26.923 0.00 0.00 0.00 2.32
1927 10070 8.196771 TGAAATTCAGTTACTTCAGTTTGCATT 58.803 29.630 0.00 0.00 0.00 3.56
1928 10071 7.715657 TGAAATTCAGTTACTTCAGTTTGCAT 58.284 30.769 0.00 0.00 0.00 3.96
1929 10072 7.094508 TGAAATTCAGTTACTTCAGTTTGCA 57.905 32.000 0.00 0.00 0.00 4.08
1930 10073 7.614674 CTGAAATTCAGTTACTTCAGTTTGC 57.385 36.000 14.47 0.00 39.58 3.68
1945 10088 6.506147 CACCAACTGAAATCACTGAAATTCA 58.494 36.000 0.00 0.00 0.00 2.57
1946 10089 5.403466 GCACCAACTGAAATCACTGAAATTC 59.597 40.000 0.00 0.00 0.00 2.17
1947 10090 5.069516 AGCACCAACTGAAATCACTGAAATT 59.930 36.000 0.00 0.00 0.00 1.82
1948 10091 4.586001 AGCACCAACTGAAATCACTGAAAT 59.414 37.500 0.00 0.00 0.00 2.17
1949 10092 3.953612 AGCACCAACTGAAATCACTGAAA 59.046 39.130 0.00 0.00 0.00 2.69
1950 10093 3.316029 CAGCACCAACTGAAATCACTGAA 59.684 43.478 0.00 0.00 40.25 3.02
1951 10094 2.880268 CAGCACCAACTGAAATCACTGA 59.120 45.455 0.00 0.00 40.25 3.41
1952 10095 2.880268 TCAGCACCAACTGAAATCACTG 59.120 45.455 0.00 0.00 43.59 3.66
1953 10096 3.213206 TCAGCACCAACTGAAATCACT 57.787 42.857 0.00 0.00 43.59 3.41
1960 10103 4.734398 ACAAAATTTCAGCACCAACTGA 57.266 36.364 0.00 0.00 44.84 3.41
1961 10104 4.869297 TCAACAAAATTTCAGCACCAACTG 59.131 37.500 0.00 0.00 39.12 3.16
1962 10105 5.083533 TCAACAAAATTTCAGCACCAACT 57.916 34.783 0.00 0.00 0.00 3.16
1963 10106 5.793026 TTCAACAAAATTTCAGCACCAAC 57.207 34.783 0.00 0.00 0.00 3.77
1964 10107 5.936956 AGTTTCAACAAAATTTCAGCACCAA 59.063 32.000 0.00 0.00 0.00 3.67
1965 10108 5.350914 CAGTTTCAACAAAATTTCAGCACCA 59.649 36.000 0.00 0.00 0.00 4.17
1966 10109 5.580297 TCAGTTTCAACAAAATTTCAGCACC 59.420 36.000 0.00 0.00 0.00 5.01
1967 10110 6.645700 TCAGTTTCAACAAAATTTCAGCAC 57.354 33.333 0.00 0.00 0.00 4.40
1968 10111 7.664082 TTTCAGTTTCAACAAAATTTCAGCA 57.336 28.000 0.00 0.00 0.00 4.41
1969 10112 9.002080 CAATTTCAGTTTCAACAAAATTTCAGC 57.998 29.630 10.66 0.00 35.86 4.26
1975 10118 9.838975 GGTTTTCAATTTCAGTTTCAACAAAAT 57.161 25.926 0.00 0.00 31.86 1.82
1976 10119 8.840321 TGGTTTTCAATTTCAGTTTCAACAAAA 58.160 25.926 0.00 0.00 0.00 2.44
1977 10120 8.383318 TGGTTTTCAATTTCAGTTTCAACAAA 57.617 26.923 0.00 0.00 0.00 2.83
1978 10121 7.969536 TGGTTTTCAATTTCAGTTTCAACAA 57.030 28.000 0.00 0.00 0.00 2.83
1979 10122 7.065563 CCATGGTTTTCAATTTCAGTTTCAACA 59.934 33.333 2.57 0.00 0.00 3.33
1980 10123 7.065683 ACCATGGTTTTCAATTTCAGTTTCAAC 59.934 33.333 13.00 0.00 0.00 3.18
1981 10124 7.108847 ACCATGGTTTTCAATTTCAGTTTCAA 58.891 30.769 13.00 0.00 0.00 2.69
1982 10125 6.648192 ACCATGGTTTTCAATTTCAGTTTCA 58.352 32.000 13.00 0.00 0.00 2.69
1983 10126 6.760770 TGACCATGGTTTTCAATTTCAGTTTC 59.239 34.615 20.85 0.00 0.00 2.78
1984 10127 6.538381 GTGACCATGGTTTTCAATTTCAGTTT 59.462 34.615 20.85 0.00 0.00 2.66
1985 10128 6.048509 GTGACCATGGTTTTCAATTTCAGTT 58.951 36.000 20.85 0.00 0.00 3.16
1986 10129 5.600696 GTGACCATGGTTTTCAATTTCAGT 58.399 37.500 20.85 0.00 0.00 3.41
1987 10130 4.681025 CGTGACCATGGTTTTCAATTTCAG 59.319 41.667 20.85 0.00 0.00 3.02
1988 10131 4.615949 CGTGACCATGGTTTTCAATTTCA 58.384 39.130 20.85 5.89 0.00 2.69
1989 10132 3.428534 GCGTGACCATGGTTTTCAATTTC 59.571 43.478 20.85 2.92 0.00 2.17
1990 10133 3.069443 AGCGTGACCATGGTTTTCAATTT 59.931 39.130 20.85 0.00 0.00 1.82
1991 10134 2.627699 AGCGTGACCATGGTTTTCAATT 59.372 40.909 20.85 0.00 0.00 2.32
1992 10135 2.238521 AGCGTGACCATGGTTTTCAAT 58.761 42.857 20.85 1.00 0.00 2.57
1993 10136 1.686355 AGCGTGACCATGGTTTTCAA 58.314 45.000 20.85 0.00 0.00 2.69
1994 10137 2.422597 CTAGCGTGACCATGGTTTTCA 58.577 47.619 20.85 9.98 0.00 2.69
1995 10138 1.130561 GCTAGCGTGACCATGGTTTTC 59.869 52.381 20.85 7.01 0.00 2.29
1996 10139 1.165270 GCTAGCGTGACCATGGTTTT 58.835 50.000 20.85 5.85 0.00 2.43
1997 10140 0.036164 TGCTAGCGTGACCATGGTTT 59.964 50.000 20.85 0.00 0.00 3.27
1998 10141 0.253044 ATGCTAGCGTGACCATGGTT 59.747 50.000 20.85 4.86 0.00 3.67
1999 10142 0.253044 AATGCTAGCGTGACCATGGT 59.747 50.000 19.89 19.89 0.00 3.55
2000 10143 2.238942 TAATGCTAGCGTGACCATGG 57.761 50.000 10.93 11.19 0.00 3.66
2001 10144 7.042456 GGATATATTAATGCTAGCGTGACCATG 60.042 40.741 10.93 0.00 0.00 3.66
2002 10145 6.986817 GGATATATTAATGCTAGCGTGACCAT 59.013 38.462 10.93 5.05 0.00 3.55
2003 10146 6.154534 AGGATATATTAATGCTAGCGTGACCA 59.845 38.462 10.93 0.00 0.00 4.02
2004 10147 6.574350 AGGATATATTAATGCTAGCGTGACC 58.426 40.000 10.93 0.00 0.00 4.02
2005 10148 8.407064 AGTAGGATATATTAATGCTAGCGTGAC 58.593 37.037 10.93 0.00 31.35 3.67
2006 10149 8.521170 AGTAGGATATATTAATGCTAGCGTGA 57.479 34.615 10.93 0.00 31.35 4.35
2109 10254 0.600557 TTGCGCAGGTGTTTAATGGG 59.399 50.000 11.31 0.00 0.00 4.00
2150 10295 1.156736 GGATGTTCCACAAGACCACG 58.843 55.000 0.00 0.00 36.28 4.94
2332 10773 3.893753 TGGAAACCTCTCCAATGGAAA 57.106 42.857 2.61 0.00 42.69 3.13
2408 11181 1.989706 ACGGGTATGCCAAAAGTGTT 58.010 45.000 1.04 0.00 36.17 3.32
2409 11182 1.611491 CAACGGGTATGCCAAAAGTGT 59.389 47.619 1.04 0.00 36.17 3.55
2410 11183 1.668628 GCAACGGGTATGCCAAAAGTG 60.669 52.381 1.04 0.00 37.85 3.16
2412 11185 0.887933 AGCAACGGGTATGCCAAAAG 59.112 50.000 1.04 0.00 44.91 2.27
2425 11198 6.559042 GAAATCCATTTCACATTAGCAACG 57.441 37.500 7.09 0.00 44.19 4.10
2443 11217 8.028354 TCACATGACCAAATACAACATGAAATC 58.972 33.333 0.00 0.00 40.13 2.17
2490 11265 7.620880 AGCAGTACCACAACAGAATATAAAGA 58.379 34.615 0.00 0.00 0.00 2.52
2507 11282 4.515191 TCATGTCAAAAGTTGAGCAGTACC 59.485 41.667 0.00 0.00 41.01 3.34
2546 11321 4.759516 AAAACATACACGACCATGAACC 57.240 40.909 0.00 0.00 0.00 3.62
2642 11429 6.534793 ACCGTAAATCAAAATCAAATGGCATC 59.465 34.615 0.00 0.00 0.00 3.91
2655 11442 6.378710 TGTCACAATGAACCGTAAATCAAA 57.621 33.333 0.00 0.00 0.00 2.69
3274 12076 2.509964 TCTTTCTCCCTCCCAATAAGCC 59.490 50.000 0.00 0.00 0.00 4.35
3393 12198 7.744733 TGGCTATGGTAAATATCACTGATCAA 58.255 34.615 0.00 0.00 0.00 2.57
3800 12641 9.975218 AGTGAATAATATGGGTAGTGTTCTTTT 57.025 29.630 0.00 0.00 30.46 2.27
3898 13055 2.228822 GGGATGGTTGTGTTGTGCTTAG 59.771 50.000 0.00 0.00 0.00 2.18
4014 13180 1.551019 GCCTAACTCGGGACTGGGTT 61.551 60.000 1.55 1.55 0.00 4.11
4015 13181 1.988406 GCCTAACTCGGGACTGGGT 60.988 63.158 0.00 0.00 0.00 4.51
4016 13182 2.732619 GGCCTAACTCGGGACTGGG 61.733 68.421 0.00 0.00 0.00 4.45
4017 13183 1.961180 CTGGCCTAACTCGGGACTGG 61.961 65.000 3.32 0.00 31.96 4.00
4018 13184 1.517832 CTGGCCTAACTCGGGACTG 59.482 63.158 3.32 0.00 31.96 3.51
4019 13185 1.686110 CCTGGCCTAACTCGGGACT 60.686 63.158 3.32 0.00 31.96 3.85
4020 13186 1.551019 AACCTGGCCTAACTCGGGAC 61.551 60.000 3.32 0.00 33.75 4.46
4198 13401 7.676947 AGAAGTACTTTTCTAGCACCATGTAA 58.323 34.615 10.02 0.00 35.70 2.41
4524 16429 5.107453 GCTAGTACGCAATAGGCTATGTTTG 60.107 44.000 7.99 4.90 41.67 2.93
5270 17222 0.890683 CTTCATGGTGGCCTCAAACC 59.109 55.000 3.32 3.11 36.96 3.27
5366 17318 0.904865 TCCTTCGAGGTCCAGCACAT 60.905 55.000 0.00 0.00 36.53 3.21
5400 17352 0.036732 TGTGCTCAAGGTGATGACCC 59.963 55.000 0.00 0.00 44.40 4.46
5584 17540 6.628185 AGAATTCATTGCCATCTTTCAGTTC 58.372 36.000 8.44 0.00 0.00 3.01
5594 17550 6.950842 TCTCCGATATAGAATTCATTGCCAT 58.049 36.000 8.44 0.00 0.00 4.40
5949 18013 1.952193 GCTTGAGGCTCTGGAGATTC 58.048 55.000 16.72 0.00 38.06 2.52
6435 18538 0.108472 CGAGCTGCTTCCTCATGTCA 60.108 55.000 2.53 0.00 0.00 3.58
6486 18589 6.126409 TCAGAAAACAATTGGTGGACTTAGT 58.874 36.000 10.83 0.00 0.00 2.24
6490 18593 4.099419 GGTTCAGAAAACAATTGGTGGACT 59.901 41.667 10.83 1.07 0.00 3.85
6497 18600 7.752239 CAGCATAGTAGGTTCAGAAAACAATTG 59.248 37.037 3.24 3.24 0.00 2.32
6583 19853 1.880027 GAAACACACTGGCAAGTAGGG 59.120 52.381 0.00 0.00 33.79 3.53
6722 19998 4.899352 AGCCAAAGTAGAAGTGATGTCT 57.101 40.909 0.00 0.00 0.00 3.41
6872 20184 3.927142 GTCTACCAAGTTGATGAGGTTCG 59.073 47.826 3.87 0.00 35.62 3.95
6895 20207 8.749354 TCAGTAGTACATGAGTGACATTACATT 58.251 33.333 0.00 0.00 37.07 2.71
6989 20301 8.902540 ACTTTTGTAATGTCATACTGAACTCA 57.097 30.769 0.00 0.00 0.00 3.41
6990 20302 9.813080 GAACTTTTGTAATGTCATACTGAACTC 57.187 33.333 0.00 0.00 0.00 3.01
6991 20303 9.337396 TGAACTTTTGTAATGTCATACTGAACT 57.663 29.630 0.00 0.00 0.00 3.01
6992 20304 9.599322 CTGAACTTTTGTAATGTCATACTGAAC 57.401 33.333 0.00 0.00 0.00 3.18
6993 20305 9.337396 ACTGAACTTTTGTAATGTCATACTGAA 57.663 29.630 0.00 0.00 0.00 3.02
6994 20306 8.902540 ACTGAACTTTTGTAATGTCATACTGA 57.097 30.769 0.00 0.00 0.00 3.41
6997 20309 9.543018 GCTTACTGAACTTTTGTAATGTCATAC 57.457 33.333 0.00 0.00 0.00 2.39
6998 20310 9.502091 AGCTTACTGAACTTTTGTAATGTCATA 57.498 29.630 0.00 0.00 0.00 2.15
6999 20311 8.396272 AGCTTACTGAACTTTTGTAATGTCAT 57.604 30.769 0.00 0.00 0.00 3.06
7000 20312 7.801716 AGCTTACTGAACTTTTGTAATGTCA 57.198 32.000 0.00 0.00 0.00 3.58
7001 20313 9.813080 CTTAGCTTACTGAACTTTTGTAATGTC 57.187 33.333 0.00 0.00 0.00 3.06
7002 20314 8.784043 CCTTAGCTTACTGAACTTTTGTAATGT 58.216 33.333 0.00 0.00 0.00 2.71
7003 20315 8.237267 CCCTTAGCTTACTGAACTTTTGTAATG 58.763 37.037 0.00 0.00 0.00 1.90
7004 20316 7.942894 ACCCTTAGCTTACTGAACTTTTGTAAT 59.057 33.333 0.00 0.00 0.00 1.89
7005 20317 7.284820 ACCCTTAGCTTACTGAACTTTTGTAA 58.715 34.615 0.00 0.00 0.00 2.41
7006 20318 6.834107 ACCCTTAGCTTACTGAACTTTTGTA 58.166 36.000 0.00 0.00 0.00 2.41
7007 20319 5.691896 ACCCTTAGCTTACTGAACTTTTGT 58.308 37.500 0.00 0.00 0.00 2.83
7008 20320 6.708949 TGTACCCTTAGCTTACTGAACTTTTG 59.291 38.462 0.00 0.00 0.00 2.44
7009 20321 6.709397 GTGTACCCTTAGCTTACTGAACTTTT 59.291 38.462 0.00 0.00 0.00 2.27
7010 20322 6.183361 TGTGTACCCTTAGCTTACTGAACTTT 60.183 38.462 0.00 0.00 0.00 2.66
7011 20323 5.306160 TGTGTACCCTTAGCTTACTGAACTT 59.694 40.000 0.00 0.00 0.00 2.66
7012 20324 4.836736 TGTGTACCCTTAGCTTACTGAACT 59.163 41.667 0.00 0.00 0.00 3.01
7013 20325 5.143376 TGTGTACCCTTAGCTTACTGAAC 57.857 43.478 0.00 0.00 0.00 3.18
7014 20326 6.170506 CAATGTGTACCCTTAGCTTACTGAA 58.829 40.000 0.00 0.00 0.00 3.02
7015 20327 5.247564 ACAATGTGTACCCTTAGCTTACTGA 59.752 40.000 0.00 0.00 0.00 3.41
7016 20328 5.488341 ACAATGTGTACCCTTAGCTTACTG 58.512 41.667 0.00 0.00 0.00 2.74
7017 20329 5.338137 GGACAATGTGTACCCTTAGCTTACT 60.338 44.000 0.00 0.00 0.00 2.24
7018 20330 4.874396 GGACAATGTGTACCCTTAGCTTAC 59.126 45.833 0.00 0.00 0.00 2.34
7117 20429 4.130118 GGGAAATCTGTGTATGGTAGCTG 58.870 47.826 0.00 0.00 0.00 4.24
7143 20455 3.060098 GTGCTCTGTCGATTCTCTTTTCG 59.940 47.826 0.00 0.00 36.72 3.46
7256 20568 4.778143 AAGGGCCGGCACATCGTC 62.778 66.667 34.08 10.14 0.00 4.20
7364 20676 0.935898 GCTCTGTTGGAGATGATGCG 59.064 55.000 0.00 0.00 44.45 4.73


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

AutoCloner maintained by Alex Coulton.