Multiple sequence alignment - TraesCS5A01G111900

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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 TraesCS5A01G111900 chr5A 100.000 6231 0 0 1 6231 216687918 216694148 0.000000e+00 11507.0
1 TraesCS5A01G111900 chr5D 97.151 4352 100 11 1885 6231 199082079 199086411 0.000000e+00 7328.0
2 TraesCS5A01G111900 chr5D 97.212 1112 26 1 644 1755 199080982 199082088 0.000000e+00 1877.0
3 TraesCS5A01G111900 chr5D 92.732 399 24 2 185 583 199080313 199080706 7.010000e-159 571.0
4 TraesCS5A01G111900 chr5D 88.961 154 17 0 2 155 199080065 199080218 2.290000e-44 191.0
5 TraesCS5A01G111900 chr5B 96.707 3432 86 19 2802 6231 209635157 209631751 0.000000e+00 5686.0
6 TraesCS5A01G111900 chr5B 95.179 1120 28 9 645 1755 209637250 209636148 0.000000e+00 1746.0
7 TraesCS5A01G111900 chr5B 96.718 914 27 3 1891 2803 209636151 209635240 0.000000e+00 1519.0
8 TraesCS5A01G111900 chr5B 89.116 147 16 0 9 155 209637710 209637564 3.840000e-42 183.0
9 TraesCS5A01G111900 chr2B 95.539 3385 129 12 2408 5790 539962180 539965544 0.000000e+00 5395.0
10 TraesCS5A01G111900 chr7D 96.766 1917 50 6 3874 5790 311618775 311620679 0.000000e+00 3186.0
11 TraesCS5A01G111900 chr7D 96.549 1449 36 7 2408 3850 311617339 311618779 0.000000e+00 2386.0
12 TraesCS5A01G111900 chr3B 96.082 1914 70 5 3877 5790 371039939 371038031 0.000000e+00 3114.0
13 TraesCS5A01G111900 chr3B 96.547 1448 46 4 2408 3854 371041378 371039934 0.000000e+00 2394.0
14 TraesCS5A01G111900 chr3B 96.995 366 11 0 3086 3451 363589381 363589016 3.190000e-172 616.0
15 TraesCS5A01G111900 chr3B 97.276 257 6 1 3597 3853 363589022 363588767 9.590000e-118 435.0
16 TraesCS5A01G111900 chr3B 100.000 59 0 0 3162 3220 279755754 279755812 6.600000e-20 110.0
17 TraesCS5A01G111900 chr3A 96.492 1682 54 5 4109 5790 361576865 361575189 0.000000e+00 2774.0
18 TraesCS5A01G111900 chr3A 90.625 128 7 4 1756 1881 69642916 69643040 1.390000e-36 165.0
19 TraesCS5A01G111900 chr3A 89.922 129 9 4 1754 1878 546416841 546416969 5.000000e-36 163.0
20 TraesCS5A01G111900 chr6A 96.078 1683 60 6 4109 5790 197861226 197859549 0.000000e+00 2737.0
21 TraesCS5A01G111900 chr6A 90.076 131 9 4 1758 1884 584949387 584949257 3.860000e-37 167.0
22 TraesCS5A01G111900 chr4B 95.616 1688 64 8 4104 5790 175308786 175307108 0.000000e+00 2699.0
23 TraesCS5A01G111900 chr4B 95.950 1037 37 5 2408 3442 175310728 175309695 0.000000e+00 1677.0
24 TraesCS5A01G111900 chr4B 95.853 1037 36 6 2408 3442 531338155 531339186 0.000000e+00 1670.0
25 TraesCS5A01G111900 chr4B 90.551 127 10 2 1756 1881 18701930 18701805 3.860000e-37 167.0
26 TraesCS5A01G111900 chr4B 95.161 62 1 2 2408 2469 609107551 609107492 5.140000e-16 97.1
27 TraesCS5A01G111900 chr4D 97.042 1589 44 3 4202 5790 366045591 366047176 0.000000e+00 2671.0
28 TraesCS5A01G111900 chr1D 91.667 132 7 4 1753 1881 471826162 471826292 4.960000e-41 180.0
29 TraesCS5A01G111900 chr6D 90.909 132 9 3 1756 1884 468870420 468870289 2.310000e-39 174.0
30 TraesCS5A01G111900 chr6B 89.844 128 11 2 1752 1878 672809832 672809958 5.000000e-36 163.0
31 TraesCS5A01G111900 chr6B 88.636 132 12 3 1756 1884 642914216 642914085 2.330000e-34 158.0
32 TraesCS5A01G111900 chr1A 89.051 137 8 7 1746 1878 5131522 5131655 5.000000e-36 163.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G111900 chr5A 216687918 216694148 6230 False 11507.00 11507 100.0000 1 6231 1 chr5A.!!$F1 6230
1 TraesCS5A01G111900 chr5D 199080065 199086411 6346 False 2491.75 7328 94.0140 2 6231 4 chr5D.!!$F1 6229
2 TraesCS5A01G111900 chr5B 209631751 209637710 5959 True 2283.50 5686 94.4300 9 6231 4 chr5B.!!$R1 6222
3 TraesCS5A01G111900 chr2B 539962180 539965544 3364 False 5395.00 5395 95.5390 2408 5790 1 chr2B.!!$F1 3382
4 TraesCS5A01G111900 chr7D 311617339 311620679 3340 False 2786.00 3186 96.6575 2408 5790 2 chr7D.!!$F1 3382
5 TraesCS5A01G111900 chr3B 371038031 371041378 3347 True 2754.00 3114 96.3145 2408 5790 2 chr3B.!!$R2 3382
6 TraesCS5A01G111900 chr3B 363588767 363589381 614 True 525.50 616 97.1355 3086 3853 2 chr3B.!!$R1 767
7 TraesCS5A01G111900 chr3A 361575189 361576865 1676 True 2774.00 2774 96.4920 4109 5790 1 chr3A.!!$R1 1681
8 TraesCS5A01G111900 chr6A 197859549 197861226 1677 True 2737.00 2737 96.0780 4109 5790 1 chr6A.!!$R1 1681
9 TraesCS5A01G111900 chr4B 175307108 175310728 3620 True 2188.00 2699 95.7830 2408 5790 2 chr4B.!!$R3 3382
10 TraesCS5A01G111900 chr4B 531338155 531339186 1031 False 1670.00 1670 95.8530 2408 3442 1 chr4B.!!$F1 1034
11 TraesCS5A01G111900 chr4D 366045591 366047176 1585 False 2671.00 2671 97.0420 4202 5790 1 chr4D.!!$F1 1588

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
473 539 0.036590 GCCACCCACTAAAACCCGTA 59.963 55.000 0.00 0.00 0.00 4.02 F
475 541 1.445871 CACCCACTAAAACCCGTAGC 58.554 55.000 0.00 0.00 0.00 3.58 F
1849 2139 1.488390 CCCCTGATTTTCATGGGGTG 58.512 55.000 16.71 1.74 45.29 4.61 F
1870 2160 0.325390 CCCCGTCTCCCTCTTAACCT 60.325 60.000 0.00 0.00 0.00 3.50 F
1871 2161 1.112950 CCCGTCTCCCTCTTAACCTC 58.887 60.000 0.00 0.00 0.00 3.85 F
1872 2162 1.112950 CCGTCTCCCTCTTAACCTCC 58.887 60.000 0.00 0.00 0.00 4.30 F
1873 2163 1.618888 CCGTCTCCCTCTTAACCTCCA 60.619 57.143 0.00 0.00 0.00 3.86 F
2022 2312 2.159599 GCAGTCAGTGTAAATGAGCTGC 60.160 50.000 12.71 12.71 44.02 5.25 F
4195 5013 2.645838 AGTTCAGTGCCATCAGTTGT 57.354 45.000 0.00 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2141 0.325390 AGGTTAAGAGGGAGACGGGG 60.325 60.000 0.00 0.0 0.00 5.73 R
1852 2142 1.112950 GAGGTTAAGAGGGAGACGGG 58.887 60.000 0.00 0.0 0.00 5.28 R
3155 3536 3.128589 GTCAAACAAACTGCTCCAGACAA 59.871 43.478 0.00 0.0 35.18 3.18 R
3572 4096 3.743521 CAATCTATTCGAGAATGGGGCA 58.256 45.455 8.46 0.0 37.85 5.36 R
3814 4539 6.489127 ACAGTGTGCGCAAATTTTAGTATA 57.511 33.333 14.00 0.0 0.00 1.47 R
4195 5013 6.993079 TGTTCTGAATGCTACTAAAGAGACA 58.007 36.000 0.00 0.0 0.00 3.41 R
4331 5151 0.245539 CGGAGGCAACGTAGAGGAAA 59.754 55.000 0.00 0.0 46.39 3.13 R
4389 5209 2.222227 AAAAGAGGGAACATCTGGCC 57.778 50.000 0.00 0.0 0.00 5.36 R
6069 6915 0.108992 CGAGGACCCGACGAAAATCA 60.109 55.000 0.00 0.0 0.00 2.57 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
40 41 1.079621 TCTGTGGGGTGTATCGGGT 59.920 57.895 0.00 0.00 0.00 5.28
107 108 9.823647 ATACATGATTTAACTTCTCTCGACAAT 57.176 29.630 0.00 0.00 0.00 2.71
113 114 3.859411 ACTTCTCTCGACAATGACCTC 57.141 47.619 0.00 0.00 0.00 3.85
119 120 1.374125 CGACAATGACCTCGCCACA 60.374 57.895 0.00 0.00 0.00 4.17
128 129 0.400213 ACCTCGCCACAAAATCAGGA 59.600 50.000 0.00 0.00 0.00 3.86
137 138 3.415212 CACAAAATCAGGAAGGAGCTGA 58.585 45.455 0.00 0.00 0.00 4.26
149 150 3.905705 GAGCTGAGCGTGCGACAGT 62.906 63.158 17.78 9.04 34.60 3.55
155 156 1.609840 GAGCGTGCGACAGTTGAGAC 61.610 60.000 0.00 0.00 0.00 3.36
156 157 1.949133 GCGTGCGACAGTTGAGACA 60.949 57.895 0.00 0.00 0.00 3.41
157 158 1.880601 GCGTGCGACAGTTGAGACAG 61.881 60.000 0.00 0.00 0.00 3.51
158 159 0.317854 CGTGCGACAGTTGAGACAGA 60.318 55.000 0.00 0.00 0.00 3.41
159 160 1.852942 GTGCGACAGTTGAGACAGAA 58.147 50.000 0.00 0.00 0.00 3.02
161 162 2.219674 GTGCGACAGTTGAGACAGAAAG 59.780 50.000 0.00 0.00 0.00 2.62
163 164 3.067601 TGCGACAGTTGAGACAGAAAGTA 59.932 43.478 0.00 0.00 0.00 2.24
164 165 3.670991 GCGACAGTTGAGACAGAAAGTAG 59.329 47.826 0.00 0.00 0.00 2.57
165 166 4.230657 CGACAGTTGAGACAGAAAGTAGG 58.769 47.826 0.00 0.00 0.00 3.18
166 167 4.561105 GACAGTTGAGACAGAAAGTAGGG 58.439 47.826 0.00 0.00 0.00 3.53
167 168 3.244249 ACAGTTGAGACAGAAAGTAGGGC 60.244 47.826 0.00 0.00 0.00 5.19
168 169 2.972713 AGTTGAGACAGAAAGTAGGGCA 59.027 45.455 0.00 0.00 0.00 5.36
170 171 2.889512 TGAGACAGAAAGTAGGGCAGA 58.110 47.619 0.00 0.00 0.00 4.26
171 172 3.239449 TGAGACAGAAAGTAGGGCAGAA 58.761 45.455 0.00 0.00 0.00 3.02
174 175 3.648545 AGACAGAAAGTAGGGCAGAAAGT 59.351 43.478 0.00 0.00 0.00 2.66
176 177 5.046950 AGACAGAAAGTAGGGCAGAAAGTAG 60.047 44.000 0.00 0.00 0.00 2.57
177 178 4.020128 ACAGAAAGTAGGGCAGAAAGTAGG 60.020 45.833 0.00 0.00 0.00 3.18
179 180 1.205055 AGTAGGGCAGAAAGTAGGGC 58.795 55.000 0.00 0.00 0.00 5.19
180 181 1.205055 GTAGGGCAGAAAGTAGGGCT 58.795 55.000 0.00 0.00 0.00 5.19
182 183 1.224870 GGGCAGAAAGTAGGGCTCC 59.775 63.158 0.00 0.00 0.00 4.70
183 184 1.275421 GGGCAGAAAGTAGGGCTCCT 61.275 60.000 0.00 0.00 37.71 3.69
291 357 1.522580 GTGAGGAAGGAGATGCGGC 60.523 63.158 0.00 0.00 0.00 6.53
292 358 1.989508 TGAGGAAGGAGATGCGGCA 60.990 57.895 4.58 4.58 0.00 5.69
333 399 6.055588 CGTGGACCAAATTAGGATAAGTCAT 58.944 40.000 0.00 0.00 0.00 3.06
342 408 3.760580 AGGATAAGTCATACTGCAGCC 57.239 47.619 15.27 2.29 0.00 4.85
362 428 2.041620 CCTCCCTCACCTGATTTCCAAA 59.958 50.000 0.00 0.00 0.00 3.28
364 430 2.986019 TCCCTCACCTGATTTCCAAAGA 59.014 45.455 0.00 0.00 0.00 2.52
366 432 3.507622 CCCTCACCTGATTTCCAAAGAAC 59.492 47.826 0.00 0.00 0.00 3.01
372 438 3.304659 CCTGATTTCCAAAGAACACGTGG 60.305 47.826 21.57 0.00 0.00 4.94
376 442 0.393132 TCCAAAGAACACGTGGTGCA 60.393 50.000 21.57 0.00 36.98 4.57
385 451 1.550524 ACACGTGGTGCATAGATGAGT 59.449 47.619 21.57 0.00 36.98 3.41
400 466 7.095691 GCATAGATGAGTGAGCTGATTTAGAAC 60.096 40.741 0.00 0.00 0.00 3.01
413 479 9.959749 AGCTGATTTAGAACGTTTTTCAATAAA 57.040 25.926 0.46 2.77 0.00 1.40
462 528 5.914898 ATAACTCAATAAAAGCCACCCAC 57.085 39.130 0.00 0.00 0.00 4.61
464 530 4.650972 ACTCAATAAAAGCCACCCACTA 57.349 40.909 0.00 0.00 0.00 2.74
472 538 1.228337 GCCACCCACTAAAACCCGT 60.228 57.895 0.00 0.00 0.00 5.28
473 539 0.036590 GCCACCCACTAAAACCCGTA 59.963 55.000 0.00 0.00 0.00 4.02
474 540 1.947212 GCCACCCACTAAAACCCGTAG 60.947 57.143 0.00 0.00 0.00 3.51
475 541 1.445871 CACCCACTAAAACCCGTAGC 58.554 55.000 0.00 0.00 0.00 3.58
492 558 2.706339 AGCTAGCAGGGAGAAATGTG 57.294 50.000 18.83 0.00 0.00 3.21
585 651 5.503194 GCCGCTTCTTGAATTTGATCTACTC 60.503 44.000 0.00 0.00 0.00 2.59
606 838 6.534634 ACTCTACATAGTTTGCAAACTCCTT 58.465 36.000 40.27 28.01 45.65 3.36
611 843 6.064717 ACATAGTTTGCAAACTCCTTCTTCT 58.935 36.000 40.27 20.81 45.65 2.85
616 848 6.377146 AGTTTGCAAACTCCTTCTTCTGTAAA 59.623 34.615 33.85 0.00 45.65 2.01
663 944 8.449251 AATGCTCTCTCATAGATTTTCCTTTC 57.551 34.615 0.00 0.00 32.41 2.62
669 950 7.549488 TCTCTCATAGATTTTCCTTTCGAAACC 59.451 37.037 6.47 0.00 40.23 3.27
682 963 6.146673 TCCTTTCGAAACCGAAGTAGAATTTC 59.853 38.462 6.47 0.00 45.33 2.17
687 968 7.373493 TCGAAACCGAAGTAGAATTTCTAAGT 58.627 34.615 7.70 0.00 29.61 2.24
789 1071 4.166523 ACAATCAAGACACATAGACGTCG 58.833 43.478 10.46 0.00 37.23 5.12
840 1122 3.711704 TCCACCAATAGGAGAAGACCATC 59.288 47.826 0.00 0.00 38.69 3.51
998 1288 4.244326 GCTACTGAGGGAGCGAGA 57.756 61.111 0.00 0.00 0.00 4.04
1646 1936 5.994887 TTGCGCAAAAAGTCTTAGTTCTA 57.005 34.783 22.78 0.00 0.00 2.10
1726 2016 2.362736 ACGGCTACACTCGTGATCTTA 58.637 47.619 3.74 0.00 38.25 2.10
1727 2017 2.950309 ACGGCTACACTCGTGATCTTAT 59.050 45.455 3.74 0.00 38.25 1.73
1728 2018 3.003482 ACGGCTACACTCGTGATCTTATC 59.997 47.826 3.74 0.00 38.25 1.75
1729 2019 3.251245 CGGCTACACTCGTGATCTTATCT 59.749 47.826 3.74 0.00 0.00 1.98
1730 2020 4.261238 CGGCTACACTCGTGATCTTATCTT 60.261 45.833 3.74 0.00 0.00 2.40
1755 2045 5.239087 GGATGTACTCCTGTGTACTACTAGC 59.761 48.000 9.97 0.00 42.22 3.42
1756 2046 5.169992 TGTACTCCTGTGTACTACTAGCA 57.830 43.478 9.97 0.00 42.22 3.49
1757 2047 5.563592 TGTACTCCTGTGTACTACTAGCAA 58.436 41.667 9.97 0.00 42.22 3.91
1758 2048 6.185511 TGTACTCCTGTGTACTACTAGCAAT 58.814 40.000 9.97 0.00 42.22 3.56
1759 2049 7.341030 TGTACTCCTGTGTACTACTAGCAATA 58.659 38.462 9.97 0.00 42.22 1.90
1760 2050 7.830697 TGTACTCCTGTGTACTACTAGCAATAA 59.169 37.037 9.97 0.00 42.22 1.40
1761 2051 7.899648 ACTCCTGTGTACTACTAGCAATAAT 57.100 36.000 0.00 0.00 0.00 1.28
1762 2052 7.717568 ACTCCTGTGTACTACTAGCAATAATG 58.282 38.462 0.00 0.00 0.00 1.90
1785 2075 7.112528 TGCTAAACATACAAAGAGTTACACG 57.887 36.000 0.00 0.00 0.00 4.49
1786 2076 6.013689 GCTAAACATACAAAGAGTTACACGC 58.986 40.000 0.00 0.00 0.00 5.34
1787 2077 5.994887 AAACATACAAAGAGTTACACGCA 57.005 34.783 0.00 0.00 0.00 5.24
1788 2078 5.994887 AACATACAAAGAGTTACACGCAA 57.005 34.783 0.00 0.00 0.00 4.85
1789 2079 6.554334 AACATACAAAGAGTTACACGCAAT 57.446 33.333 0.00 0.00 0.00 3.56
1790 2080 6.554334 ACATACAAAGAGTTACACGCAATT 57.446 33.333 0.00 0.00 0.00 2.32
1791 2081 7.661127 ACATACAAAGAGTTACACGCAATTA 57.339 32.000 0.00 0.00 0.00 1.40
1792 2082 7.515643 ACATACAAAGAGTTACACGCAATTAC 58.484 34.615 0.00 0.00 0.00 1.89
1793 2083 5.994887 ACAAAGAGTTACACGCAATTACA 57.005 34.783 0.00 0.00 0.00 2.41
1794 2084 6.554334 ACAAAGAGTTACACGCAATTACAT 57.446 33.333 0.00 0.00 0.00 2.29
1795 2085 6.370593 ACAAAGAGTTACACGCAATTACATG 58.629 36.000 0.00 0.00 0.00 3.21
1796 2086 4.600012 AGAGTTACACGCAATTACATGC 57.400 40.909 0.00 0.00 42.94 4.06
1797 2087 4.253685 AGAGTTACACGCAATTACATGCT 58.746 39.130 0.00 0.00 44.21 3.79
1798 2088 4.093408 AGAGTTACACGCAATTACATGCTG 59.907 41.667 0.00 0.00 44.21 4.41
1799 2089 4.000325 AGTTACACGCAATTACATGCTGA 59.000 39.130 0.00 0.00 44.21 4.26
1800 2090 2.900122 ACACGCAATTACATGCTGAC 57.100 45.000 0.00 0.00 44.21 3.51
1801 2091 2.426522 ACACGCAATTACATGCTGACT 58.573 42.857 0.00 0.00 44.21 3.41
1802 2092 3.595173 ACACGCAATTACATGCTGACTA 58.405 40.909 0.00 0.00 44.21 2.59
1803 2093 3.618594 ACACGCAATTACATGCTGACTAG 59.381 43.478 0.00 0.00 44.21 2.57
1818 2108 6.803154 GCTGACTAGCCTTTTTCTTTCTAA 57.197 37.500 0.00 0.00 44.33 2.10
1819 2109 6.604012 GCTGACTAGCCTTTTTCTTTCTAAC 58.396 40.000 0.00 0.00 44.33 2.34
1820 2110 6.428465 GCTGACTAGCCTTTTTCTTTCTAACT 59.572 38.462 0.00 0.00 44.33 2.24
1821 2111 7.603024 GCTGACTAGCCTTTTTCTTTCTAACTA 59.397 37.037 0.00 0.00 44.33 2.24
1822 2112 9.490379 CTGACTAGCCTTTTTCTTTCTAACTAA 57.510 33.333 0.00 0.00 0.00 2.24
1823 2113 9.269453 TGACTAGCCTTTTTCTTTCTAACTAAC 57.731 33.333 0.00 0.00 0.00 2.34
1824 2114 8.618702 ACTAGCCTTTTTCTTTCTAACTAACC 57.381 34.615 0.00 0.00 0.00 2.85
1825 2115 8.215736 ACTAGCCTTTTTCTTTCTAACTAACCA 58.784 33.333 0.00 0.00 0.00 3.67
1826 2116 7.273320 AGCCTTTTTCTTTCTAACTAACCAC 57.727 36.000 0.00 0.00 0.00 4.16
1827 2117 7.061054 AGCCTTTTTCTTTCTAACTAACCACT 58.939 34.615 0.00 0.00 0.00 4.00
1828 2118 7.228906 AGCCTTTTTCTTTCTAACTAACCACTC 59.771 37.037 0.00 0.00 0.00 3.51
1829 2119 7.521748 GCCTTTTTCTTTCTAACTAACCACTCC 60.522 40.741 0.00 0.00 0.00 3.85
1830 2120 7.040617 CCTTTTTCTTTCTAACTAACCACTCCC 60.041 40.741 0.00 0.00 0.00 4.30
1831 2121 5.494390 TTCTTTCTAACTAACCACTCCCC 57.506 43.478 0.00 0.00 0.00 4.81
1832 2122 3.842436 TCTTTCTAACTAACCACTCCCCC 59.158 47.826 0.00 0.00 0.00 5.40
1849 2139 1.488390 CCCCTGATTTTCATGGGGTG 58.512 55.000 16.71 1.74 45.29 4.61
1850 2140 1.488390 CCCTGATTTTCATGGGGTGG 58.512 55.000 0.00 0.00 33.76 4.61
1851 2141 0.826062 CCTGATTTTCATGGGGTGGC 59.174 55.000 0.00 0.00 0.00 5.01
1852 2142 0.826062 CTGATTTTCATGGGGTGGCC 59.174 55.000 0.00 0.00 0.00 5.36
1853 2143 0.617249 TGATTTTCATGGGGTGGCCC 60.617 55.000 0.00 0.00 44.51 5.80
1865 2155 4.332543 TGGCCCCGTCTCCCTCTT 62.333 66.667 0.00 0.00 0.00 2.85
1866 2156 2.042230 GGCCCCGTCTCCCTCTTA 60.042 66.667 0.00 0.00 0.00 2.10
1867 2157 1.688187 GGCCCCGTCTCCCTCTTAA 60.688 63.158 0.00 0.00 0.00 1.85
1868 2158 1.521141 GCCCCGTCTCCCTCTTAAC 59.479 63.158 0.00 0.00 0.00 2.01
1869 2159 1.969200 GCCCCGTCTCCCTCTTAACC 61.969 65.000 0.00 0.00 0.00 2.85
1870 2160 0.325390 CCCCGTCTCCCTCTTAACCT 60.325 60.000 0.00 0.00 0.00 3.50
1871 2161 1.112950 CCCGTCTCCCTCTTAACCTC 58.887 60.000 0.00 0.00 0.00 3.85
1872 2162 1.112950 CCGTCTCCCTCTTAACCTCC 58.887 60.000 0.00 0.00 0.00 4.30
1873 2163 1.618888 CCGTCTCCCTCTTAACCTCCA 60.619 57.143 0.00 0.00 0.00 3.86
1874 2164 2.176889 CGTCTCCCTCTTAACCTCCAA 58.823 52.381 0.00 0.00 0.00 3.53
1875 2165 2.766828 CGTCTCCCTCTTAACCTCCAAT 59.233 50.000 0.00 0.00 0.00 3.16
1876 2166 3.181474 CGTCTCCCTCTTAACCTCCAATC 60.181 52.174 0.00 0.00 0.00 2.67
1877 2167 3.775316 GTCTCCCTCTTAACCTCCAATCA 59.225 47.826 0.00 0.00 0.00 2.57
1878 2168 3.775316 TCTCCCTCTTAACCTCCAATCAC 59.225 47.826 0.00 0.00 0.00 3.06
1879 2169 3.519510 CTCCCTCTTAACCTCCAATCACA 59.480 47.826 0.00 0.00 0.00 3.58
1880 2170 3.913799 TCCCTCTTAACCTCCAATCACAA 59.086 43.478 0.00 0.00 0.00 3.33
1881 2171 4.540099 TCCCTCTTAACCTCCAATCACAAT 59.460 41.667 0.00 0.00 0.00 2.71
1882 2172 4.884164 CCCTCTTAACCTCCAATCACAATC 59.116 45.833 0.00 0.00 0.00 2.67
1883 2173 4.884164 CCTCTTAACCTCCAATCACAATCC 59.116 45.833 0.00 0.00 0.00 3.01
1884 2174 4.513442 TCTTAACCTCCAATCACAATCCG 58.487 43.478 0.00 0.00 0.00 4.18
1885 2175 2.879103 AACCTCCAATCACAATCCGT 57.121 45.000 0.00 0.00 0.00 4.69
1886 2176 3.992943 AACCTCCAATCACAATCCGTA 57.007 42.857 0.00 0.00 0.00 4.02
1887 2177 3.261981 ACCTCCAATCACAATCCGTAC 57.738 47.619 0.00 0.00 0.00 3.67
1888 2178 2.838202 ACCTCCAATCACAATCCGTACT 59.162 45.455 0.00 0.00 0.00 2.73
1889 2179 4.028131 ACCTCCAATCACAATCCGTACTA 58.972 43.478 0.00 0.00 0.00 1.82
1890 2180 4.142004 ACCTCCAATCACAATCCGTACTAC 60.142 45.833 0.00 0.00 0.00 2.73
1891 2181 4.099573 CCTCCAATCACAATCCGTACTACT 59.900 45.833 0.00 0.00 0.00 2.57
1892 2182 5.301045 CCTCCAATCACAATCCGTACTACTA 59.699 44.000 0.00 0.00 0.00 1.82
1893 2183 6.387041 TCCAATCACAATCCGTACTACTAG 57.613 41.667 0.00 0.00 0.00 2.57
2022 2312 2.159599 GCAGTCAGTGTAAATGAGCTGC 60.160 50.000 12.71 12.71 44.02 5.25
2026 2316 3.124297 GTCAGTGTAAATGAGCTGCTCAC 59.876 47.826 32.54 20.49 44.02 3.51
2076 2367 7.041372 TGCTCCAAAATACTCTGAACTTAACAC 60.041 37.037 0.00 0.00 0.00 3.32
2256 2547 8.594881 AACCTAACTGCTCTTATCAATAATCG 57.405 34.615 0.00 0.00 0.00 3.34
2747 3039 8.497745 AGGTGTATTATTCATCCAAAGATCACT 58.502 33.333 0.00 0.00 0.00 3.41
2783 3075 3.499338 TCTTTTTGGTCACATGCCATCT 58.501 40.909 0.00 0.00 35.71 2.90
2796 3088 2.995283 TGCCATCTGATCTTCTGTTGG 58.005 47.619 0.00 6.98 37.88 3.77
3149 3530 3.484407 AGCAGTTGTCTCTTGCTCATTT 58.516 40.909 0.00 0.00 0.00 2.32
4195 5013 2.645838 AGTTCAGTGCCATCAGTTGT 57.354 45.000 0.00 0.00 0.00 3.32
4237 5055 9.520204 TTCAGAACAAATTTAGAAGCTTTCAAG 57.480 29.630 0.00 0.00 0.00 3.02
4331 5151 3.258123 GCATGGGGTTTGACAATACAACT 59.742 43.478 0.00 0.00 0.00 3.16
4389 5209 2.159057 GCAAAATACATGGCTCCCCTTG 60.159 50.000 0.00 0.00 40.97 3.61
4807 5628 5.278169 GGTCAGTTTGAGCTGCCATTATATG 60.278 44.000 0.00 0.00 41.34 1.78
4938 5759 2.906389 TCACCATCCAAGACTGTAGCTT 59.094 45.455 0.00 0.00 0.00 3.74
5324 6146 2.289820 GCATCGTTGACTGCATGATCAT 59.710 45.455 1.18 1.18 38.28 2.45
5447 6269 5.241728 GGATATAATGGTCAAAAGGTGCCTC 59.758 44.000 0.00 0.00 0.00 4.70
5464 6286 3.697542 TGCCTCATGACAATGAATTCCAG 59.302 43.478 2.27 0.00 42.28 3.86
5471 6293 4.785301 TGACAATGAATTCCAGAGGATCC 58.215 43.478 2.48 2.48 33.66 3.36
5487 6309 2.810852 GGATCCGAAATTGAGAGGATGC 59.189 50.000 0.00 7.79 42.96 3.91
5509 6341 6.465948 TGCGAGGGATTTTGTAAAGTTAGTA 58.534 36.000 0.00 0.00 0.00 1.82
5608 6440 4.926238 CGAGATTGGGTTGTAGATATGAGC 59.074 45.833 0.00 0.00 0.00 4.26
5766 6606 4.390297 GCATGTTCTTACAGTTCAGACCTC 59.610 45.833 0.00 0.00 37.77 3.85
5876 6721 7.446001 AAAGTTTTTGTGCCTTGATTTTGAA 57.554 28.000 0.00 0.00 0.00 2.69
5877 6722 7.628769 AAGTTTTTGTGCCTTGATTTTGAAT 57.371 28.000 0.00 0.00 0.00 2.57
5878 6723 7.628769 AGTTTTTGTGCCTTGATTTTGAATT 57.371 28.000 0.00 0.00 0.00 2.17
5879 6724 8.054152 AGTTTTTGTGCCTTGATTTTGAATTT 57.946 26.923 0.00 0.00 0.00 1.82
5880 6725 7.969508 AGTTTTTGTGCCTTGATTTTGAATTTG 59.030 29.630 0.00 0.00 0.00 2.32
5881 6726 6.998968 TTTGTGCCTTGATTTTGAATTTGT 57.001 29.167 0.00 0.00 0.00 2.83
5882 6727 5.987777 TGTGCCTTGATTTTGAATTTGTG 57.012 34.783 0.00 0.00 0.00 3.33
5883 6728 4.815308 TGTGCCTTGATTTTGAATTTGTGG 59.185 37.500 0.00 0.00 0.00 4.17
5884 6729 3.814283 TGCCTTGATTTTGAATTTGTGGC 59.186 39.130 0.00 0.00 37.38 5.01
5885 6730 4.067192 GCCTTGATTTTGAATTTGTGGCT 58.933 39.130 0.00 0.00 34.42 4.75
5886 6731 4.516321 GCCTTGATTTTGAATTTGTGGCTT 59.484 37.500 0.00 0.00 34.42 4.35
5887 6732 5.561339 GCCTTGATTTTGAATTTGTGGCTTG 60.561 40.000 0.00 0.00 34.42 4.01
5888 6733 5.759273 CCTTGATTTTGAATTTGTGGCTTGA 59.241 36.000 0.00 0.00 0.00 3.02
5889 6734 6.428771 CCTTGATTTTGAATTTGTGGCTTGAT 59.571 34.615 0.00 0.00 0.00 2.57
5890 6735 6.788684 TGATTTTGAATTTGTGGCTTGATG 57.211 33.333 0.00 0.00 0.00 3.07
5891 6736 6.289834 TGATTTTGAATTTGTGGCTTGATGT 58.710 32.000 0.00 0.00 0.00 3.06
5892 6737 6.766944 TGATTTTGAATTTGTGGCTTGATGTT 59.233 30.769 0.00 0.00 0.00 2.71
5893 6738 5.987777 TTTGAATTTGTGGCTTGATGTTG 57.012 34.783 0.00 0.00 0.00 3.33
5894 6739 4.933505 TGAATTTGTGGCTTGATGTTGA 57.066 36.364 0.00 0.00 0.00 3.18
5920 6765 2.281761 CTTGCTTGACGGGCCTGT 60.282 61.111 19.82 19.82 0.00 4.00
5921 6766 1.898574 CTTGCTTGACGGGCCTGTT 60.899 57.895 20.79 1.91 0.00 3.16
5949 6794 4.086706 TCTGACGTCTAGGCTATGATGA 57.913 45.455 17.92 0.00 0.00 2.92
5969 6814 2.629017 ATGATTTTTGCTGGGACCCT 57.371 45.000 13.00 0.00 0.00 4.34
6045 6891 2.617274 GCGCGGCCTCTTGTTCTTT 61.617 57.895 8.83 0.00 0.00 2.52
6054 6900 2.695147 CCTCTTGTTCTTTGCCAAGGTT 59.305 45.455 0.00 0.00 38.83 3.50
6069 6915 0.182061 AGGTTGCCGCTGATGATCAT 59.818 50.000 8.25 8.25 0.00 2.45
6071 6917 1.302366 GTTGCCGCTGATGATCATGA 58.698 50.000 14.30 3.22 0.00 3.07
6140 6986 3.070576 GCTGGAAAGGCGGCCATT 61.071 61.111 23.09 16.52 32.89 3.16
6194 7040 6.466812 GTTGGGTCAATGGATTTCTTGATTT 58.533 36.000 0.00 0.00 34.18 2.17
6199 7046 6.153340 GGTCAATGGATTTCTTGATTTCCTCA 59.847 38.462 0.00 0.00 34.18 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.444553 GACACCAGAAGGCTCGTCG 60.445 63.158 0.00 0.00 39.06 5.12
7 8 1.115930 ACAGACACCAGAAGGCTCGT 61.116 55.000 0.00 0.00 39.06 4.18
54 55 3.565307 TGTCTTCCTTCACTGCCAAAAT 58.435 40.909 0.00 0.00 0.00 1.82
64 65 2.499693 TGTATCGGCATGTCTTCCTTCA 59.500 45.455 0.00 0.00 0.00 3.02
107 108 1.522668 CTGATTTTGTGGCGAGGTCA 58.477 50.000 0.00 0.00 0.00 4.02
113 114 1.470098 CTCCTTCCTGATTTTGTGGCG 59.530 52.381 0.00 0.00 0.00 5.69
119 120 2.720915 GCTCAGCTCCTTCCTGATTTT 58.279 47.619 0.00 0.00 38.54 1.82
128 129 3.684990 TCGCACGCTCAGCTCCTT 61.685 61.111 0.00 0.00 0.00 3.36
137 138 1.661821 GTCTCAACTGTCGCACGCT 60.662 57.895 0.00 0.00 0.00 5.07
149 150 3.239449 TCTGCCCTACTTTCTGTCTCAA 58.761 45.455 0.00 0.00 0.00 3.02
155 156 4.508662 CCTACTTTCTGCCCTACTTTCTG 58.491 47.826 0.00 0.00 0.00 3.02
156 157 3.519913 CCCTACTTTCTGCCCTACTTTCT 59.480 47.826 0.00 0.00 0.00 2.52
157 158 3.875125 CCCTACTTTCTGCCCTACTTTC 58.125 50.000 0.00 0.00 0.00 2.62
158 159 2.026169 GCCCTACTTTCTGCCCTACTTT 60.026 50.000 0.00 0.00 0.00 2.66
159 160 1.560146 GCCCTACTTTCTGCCCTACTT 59.440 52.381 0.00 0.00 0.00 2.24
161 162 1.139256 GAGCCCTACTTTCTGCCCTAC 59.861 57.143 0.00 0.00 0.00 3.18
163 164 1.275421 GGAGCCCTACTTTCTGCCCT 61.275 60.000 0.00 0.00 0.00 5.19
164 165 1.224870 GGAGCCCTACTTTCTGCCC 59.775 63.158 0.00 0.00 0.00 5.36
165 166 0.179234 GAGGAGCCCTACTTTCTGCC 59.821 60.000 0.00 0.00 31.76 4.85
166 167 0.179234 GGAGGAGCCCTACTTTCTGC 59.821 60.000 0.00 0.00 31.76 4.26
167 168 0.461961 CGGAGGAGCCCTACTTTCTG 59.538 60.000 2.42 0.00 30.74 3.02
168 169 2.903404 CGGAGGAGCCCTACTTTCT 58.097 57.895 2.42 0.00 30.74 2.52
182 183 3.080121 AGCTTCCCTCAGCCGGAG 61.080 66.667 5.05 0.00 41.12 4.63
183 184 3.077556 GAGCTTCCCTCAGCCGGA 61.078 66.667 5.05 0.00 41.12 5.14
244 310 6.542821 GGATCTTCTCTCTATCTCTCCTTCA 58.457 44.000 0.00 0.00 0.00 3.02
260 326 3.702045 CCTTCCTCACTAACGGATCTTCT 59.298 47.826 0.00 0.00 0.00 2.85
291 357 1.202203 CGCATTTTTCATGCCCGATG 58.798 50.000 1.28 0.00 41.71 3.84
292 358 0.817013 ACGCATTTTTCATGCCCGAT 59.183 45.000 1.28 0.00 41.71 4.18
333 399 1.990060 GGTGAGGGAGGCTGCAGTA 60.990 63.158 16.64 0.00 0.00 2.74
342 408 3.009473 TCTTTGGAAATCAGGTGAGGGAG 59.991 47.826 0.00 0.00 0.00 4.30
362 428 2.233676 TCATCTATGCACCACGTGTTCT 59.766 45.455 15.65 0.00 35.75 3.01
364 430 2.028112 ACTCATCTATGCACCACGTGTT 60.028 45.455 15.65 0.00 35.75 3.32
366 432 1.929169 CACTCATCTATGCACCACGTG 59.071 52.381 9.08 9.08 36.51 4.49
372 438 3.449528 TCAGCTCACTCATCTATGCAC 57.550 47.619 0.00 0.00 0.00 4.57
376 442 7.144661 CGTTCTAAATCAGCTCACTCATCTAT 58.855 38.462 0.00 0.00 0.00 1.98
385 451 6.612247 TGAAAAACGTTCTAAATCAGCTCA 57.388 33.333 0.00 0.00 0.00 4.26
413 479 8.654094 AGATTCATCTTTCTTTGGACCATTTTT 58.346 29.630 0.00 0.00 31.97 1.94
414 480 8.198807 AGATTCATCTTTCTTTGGACCATTTT 57.801 30.769 0.00 0.00 31.97 1.82
434 500 8.568794 GGGTGGCTTTTATTGAGTTATAGATTC 58.431 37.037 0.00 0.00 0.00 2.52
462 528 2.483188 CCCTGCTAGCTACGGGTTTTAG 60.483 54.545 21.85 6.74 31.89 1.85
464 530 0.252197 CCCTGCTAGCTACGGGTTTT 59.748 55.000 21.85 0.00 31.89 2.43
472 538 2.158900 GCACATTTCTCCCTGCTAGCTA 60.159 50.000 17.23 1.31 0.00 3.32
473 539 1.407989 GCACATTTCTCCCTGCTAGCT 60.408 52.381 17.23 0.00 0.00 3.32
474 540 1.020437 GCACATTTCTCCCTGCTAGC 58.980 55.000 8.10 8.10 0.00 3.42
475 541 2.706339 AGCACATTTCTCCCTGCTAG 57.294 50.000 0.00 0.00 38.22 3.42
663 944 7.578169 ACTTAGAAATTCTACTTCGGTTTCG 57.422 36.000 1.61 0.00 34.79 3.46
669 950 9.582223 GTCAACAAACTTAGAAATTCTACTTCG 57.418 33.333 1.61 0.00 0.00 3.79
682 963 9.817365 CATTCTATGTCTTGTCAACAAACTTAG 57.183 33.333 15.40 15.40 35.15 2.18
687 968 6.545666 ACACCATTCTATGTCTTGTCAACAAA 59.454 34.615 0.00 0.00 35.15 2.83
789 1071 2.186076 CTCGCCGACTTATTGACTGTC 58.814 52.381 0.00 0.00 0.00 3.51
1110 1400 2.833121 TATGCCAGCGCGAGGAGA 60.833 61.111 23.47 10.57 38.08 3.71
1564 1854 1.816679 GTATTGGGCGTCGTTCCCC 60.817 63.158 5.58 2.75 43.24 4.81
1646 1936 3.528078 GGGAAGGGGAAAACTAGGAATCT 59.472 47.826 0.00 0.00 0.00 2.40
1759 2049 8.227791 CGTGTAACTCTTTGTATGTTTAGCATT 58.772 33.333 0.00 0.00 35.02 3.56
1760 2050 7.623506 GCGTGTAACTCTTTGTATGTTTAGCAT 60.624 37.037 0.00 0.00 36.70 3.79
1761 2051 6.347079 GCGTGTAACTCTTTGTATGTTTAGCA 60.347 38.462 0.00 0.00 31.75 3.49
1762 2052 6.013689 GCGTGTAACTCTTTGTATGTTTAGC 58.986 40.000 0.00 0.00 31.75 3.09
1763 2053 7.112528 TGCGTGTAACTCTTTGTATGTTTAG 57.887 36.000 0.00 0.00 31.75 1.85
1764 2054 7.479897 TTGCGTGTAACTCTTTGTATGTTTA 57.520 32.000 0.00 0.00 31.75 2.01
1765 2055 5.994887 TGCGTGTAACTCTTTGTATGTTT 57.005 34.783 0.00 0.00 31.75 2.83
1766 2056 5.994887 TTGCGTGTAACTCTTTGTATGTT 57.005 34.783 0.00 0.00 31.75 2.71
1767 2057 6.554334 AATTGCGTGTAACTCTTTGTATGT 57.446 33.333 0.00 0.00 31.75 2.29
1768 2058 7.514805 TGTAATTGCGTGTAACTCTTTGTATG 58.485 34.615 0.00 0.00 31.75 2.39
1769 2059 7.661127 TGTAATTGCGTGTAACTCTTTGTAT 57.339 32.000 0.00 0.00 31.75 2.29
1770 2060 7.514805 CATGTAATTGCGTGTAACTCTTTGTA 58.485 34.615 7.52 0.00 31.75 2.41
1771 2061 5.994887 TGTAATTGCGTGTAACTCTTTGT 57.005 34.783 0.00 0.00 31.75 2.83
1772 2062 5.283717 GCATGTAATTGCGTGTAACTCTTTG 59.716 40.000 15.87 0.00 32.06 2.77
1773 2063 5.390613 GCATGTAATTGCGTGTAACTCTTT 58.609 37.500 15.87 0.00 32.06 2.52
1774 2064 4.969816 GCATGTAATTGCGTGTAACTCTT 58.030 39.130 15.87 0.00 32.06 2.85
1775 2065 4.600012 GCATGTAATTGCGTGTAACTCT 57.400 40.909 15.87 0.00 32.06 3.24
1796 2086 7.971183 AGTTAGAAAGAAAAAGGCTAGTCAG 57.029 36.000 0.00 0.00 0.00 3.51
1797 2087 9.269453 GTTAGTTAGAAAGAAAAAGGCTAGTCA 57.731 33.333 0.00 0.00 0.00 3.41
1798 2088 8.719648 GGTTAGTTAGAAAGAAAAAGGCTAGTC 58.280 37.037 0.00 0.00 0.00 2.59
1799 2089 8.215736 TGGTTAGTTAGAAAGAAAAAGGCTAGT 58.784 33.333 0.00 0.00 0.00 2.57
1800 2090 8.504815 GTGGTTAGTTAGAAAGAAAAAGGCTAG 58.495 37.037 0.00 0.00 0.00 3.42
1801 2091 8.215736 AGTGGTTAGTTAGAAAGAAAAAGGCTA 58.784 33.333 0.00 0.00 0.00 3.93
1802 2092 7.061054 AGTGGTTAGTTAGAAAGAAAAAGGCT 58.939 34.615 0.00 0.00 0.00 4.58
1803 2093 7.273320 AGTGGTTAGTTAGAAAGAAAAAGGC 57.727 36.000 0.00 0.00 0.00 4.35
1804 2094 7.040617 GGGAGTGGTTAGTTAGAAAGAAAAAGG 60.041 40.741 0.00 0.00 0.00 3.11
1805 2095 7.040617 GGGGAGTGGTTAGTTAGAAAGAAAAAG 60.041 40.741 0.00 0.00 0.00 2.27
1806 2096 6.774170 GGGGAGTGGTTAGTTAGAAAGAAAAA 59.226 38.462 0.00 0.00 0.00 1.94
1807 2097 6.301486 GGGGAGTGGTTAGTTAGAAAGAAAA 58.699 40.000 0.00 0.00 0.00 2.29
1808 2098 5.221986 GGGGGAGTGGTTAGTTAGAAAGAAA 60.222 44.000 0.00 0.00 0.00 2.52
1809 2099 4.287845 GGGGGAGTGGTTAGTTAGAAAGAA 59.712 45.833 0.00 0.00 0.00 2.52
1810 2100 3.842436 GGGGGAGTGGTTAGTTAGAAAGA 59.158 47.826 0.00 0.00 0.00 2.52
1811 2101 4.217836 GGGGGAGTGGTTAGTTAGAAAG 57.782 50.000 0.00 0.00 0.00 2.62
1832 2122 0.826062 GCCACCCCATGAAAATCAGG 59.174 55.000 0.00 0.00 0.00 3.86
1833 2123 0.826062 GGCCACCCCATGAAAATCAG 59.174 55.000 0.00 0.00 0.00 2.90
1834 2124 2.989480 GGCCACCCCATGAAAATCA 58.011 52.632 0.00 0.00 0.00 2.57
1848 2138 2.465010 TTAAGAGGGAGACGGGGCCA 62.465 60.000 4.39 0.00 0.00 5.36
1849 2139 1.688187 TTAAGAGGGAGACGGGGCC 60.688 63.158 0.00 0.00 0.00 5.80
1850 2140 1.521141 GTTAAGAGGGAGACGGGGC 59.479 63.158 0.00 0.00 0.00 5.80
1851 2141 0.325390 AGGTTAAGAGGGAGACGGGG 60.325 60.000 0.00 0.00 0.00 5.73
1852 2142 1.112950 GAGGTTAAGAGGGAGACGGG 58.887 60.000 0.00 0.00 0.00 5.28
1853 2143 1.112950 GGAGGTTAAGAGGGAGACGG 58.887 60.000 0.00 0.00 0.00 4.79
1854 2144 1.848652 TGGAGGTTAAGAGGGAGACG 58.151 55.000 0.00 0.00 0.00 4.18
1855 2145 3.775316 TGATTGGAGGTTAAGAGGGAGAC 59.225 47.826 0.00 0.00 0.00 3.36
1856 2146 3.775316 GTGATTGGAGGTTAAGAGGGAGA 59.225 47.826 0.00 0.00 0.00 3.71
1857 2147 3.519510 TGTGATTGGAGGTTAAGAGGGAG 59.480 47.826 0.00 0.00 0.00 4.30
1858 2148 3.526899 TGTGATTGGAGGTTAAGAGGGA 58.473 45.455 0.00 0.00 0.00 4.20
1859 2149 4.301072 TTGTGATTGGAGGTTAAGAGGG 57.699 45.455 0.00 0.00 0.00 4.30
1860 2150 4.884164 GGATTGTGATTGGAGGTTAAGAGG 59.116 45.833 0.00 0.00 0.00 3.69
1861 2151 4.572389 CGGATTGTGATTGGAGGTTAAGAG 59.428 45.833 0.00 0.00 0.00 2.85
1862 2152 4.019681 ACGGATTGTGATTGGAGGTTAAGA 60.020 41.667 0.00 0.00 0.00 2.10
1863 2153 4.261801 ACGGATTGTGATTGGAGGTTAAG 58.738 43.478 0.00 0.00 0.00 1.85
1864 2154 4.295141 ACGGATTGTGATTGGAGGTTAA 57.705 40.909 0.00 0.00 0.00 2.01
1865 2155 3.992943 ACGGATTGTGATTGGAGGTTA 57.007 42.857 0.00 0.00 0.00 2.85
1866 2156 2.879103 ACGGATTGTGATTGGAGGTT 57.121 45.000 0.00 0.00 0.00 3.50
1867 2157 2.838202 AGTACGGATTGTGATTGGAGGT 59.162 45.455 0.00 0.00 0.00 3.85
1868 2158 3.543680 AGTACGGATTGTGATTGGAGG 57.456 47.619 0.00 0.00 0.00 4.30
1869 2159 5.263968 AGTAGTACGGATTGTGATTGGAG 57.736 43.478 0.00 0.00 0.00 3.86
1870 2160 5.889853 ACTAGTAGTACGGATTGTGATTGGA 59.110 40.000 0.00 0.00 0.00 3.53
1871 2161 6.145338 ACTAGTAGTACGGATTGTGATTGG 57.855 41.667 0.00 0.00 0.00 3.16
1875 2165 9.650539 GAGATATACTAGTAGTACGGATTGTGA 57.349 37.037 12.25 0.00 32.84 3.58
1876 2166 9.656040 AGAGATATACTAGTAGTACGGATTGTG 57.344 37.037 12.25 0.00 32.84 3.33
1877 2167 9.656040 CAGAGATATACTAGTAGTACGGATTGT 57.344 37.037 12.25 0.00 32.84 2.71
1878 2168 8.605746 GCAGAGATATACTAGTAGTACGGATTG 58.394 40.741 12.25 8.22 32.84 2.67
1879 2169 8.542080 AGCAGAGATATACTAGTAGTACGGATT 58.458 37.037 12.25 0.00 32.84 3.01
1880 2170 8.081517 AGCAGAGATATACTAGTAGTACGGAT 57.918 38.462 12.25 6.55 32.84 4.18
1881 2171 7.479352 AGCAGAGATATACTAGTAGTACGGA 57.521 40.000 12.25 1.98 32.84 4.69
1882 2172 9.251792 CATAGCAGAGATATACTAGTAGTACGG 57.748 40.741 12.25 2.07 32.84 4.02
1883 2173 8.757789 GCATAGCAGAGATATACTAGTAGTACG 58.242 40.741 12.25 0.00 32.84 3.67
1884 2174 9.048446 GGCATAGCAGAGATATACTAGTAGTAC 57.952 40.741 12.25 0.59 32.84 2.73
1885 2175 8.769359 TGGCATAGCAGAGATATACTAGTAGTA 58.231 37.037 12.38 12.38 34.82 1.82
1886 2176 7.634718 TGGCATAGCAGAGATATACTAGTAGT 58.365 38.462 8.85 8.14 0.00 2.73
1887 2177 8.512966 TTGGCATAGCAGAGATATACTAGTAG 57.487 38.462 8.85 0.00 0.00 2.57
1888 2178 8.740906 GTTTGGCATAGCAGAGATATACTAGTA 58.259 37.037 4.77 4.77 0.00 1.82
1889 2179 7.233553 TGTTTGGCATAGCAGAGATATACTAGT 59.766 37.037 0.00 0.00 0.00 2.57
1890 2180 7.606349 TGTTTGGCATAGCAGAGATATACTAG 58.394 38.462 0.00 0.00 0.00 2.57
1891 2181 7.539034 TGTTTGGCATAGCAGAGATATACTA 57.461 36.000 0.00 0.00 0.00 1.82
1892 2182 6.425210 TGTTTGGCATAGCAGAGATATACT 57.575 37.500 0.00 0.00 0.00 2.12
1893 2183 6.148480 CCTTGTTTGGCATAGCAGAGATATAC 59.852 42.308 0.00 0.00 0.00 1.47
2747 3039 7.014134 TGACCAAAAAGATGAAAGCAAGTATCA 59.986 33.333 0.00 0.00 0.00 2.15
2752 3044 5.350633 TGTGACCAAAAAGATGAAAGCAAG 58.649 37.500 0.00 0.00 0.00 4.01
3149 3530 6.463995 ACAAACTGCTCCAGACAATAAAAA 57.536 33.333 0.00 0.00 35.18 1.94
3155 3536 3.128589 GTCAAACAAACTGCTCCAGACAA 59.871 43.478 0.00 0.00 35.18 3.18
3235 3617 9.614792 AGGAAGAACCAATACATATTAGAACAC 57.385 33.333 0.00 0.00 42.04 3.32
3572 4096 3.743521 CAATCTATTCGAGAATGGGGCA 58.256 45.455 8.46 0.00 37.85 5.36
3814 4539 6.489127 ACAGTGTGCGCAAATTTTAGTATA 57.511 33.333 14.00 0.00 0.00 1.47
4195 5013 6.993079 TGTTCTGAATGCTACTAAAGAGACA 58.007 36.000 0.00 0.00 0.00 3.41
4331 5151 0.245539 CGGAGGCAACGTAGAGGAAA 59.754 55.000 0.00 0.00 46.39 3.13
4389 5209 2.222227 AAAAGAGGGAACATCTGGCC 57.778 50.000 0.00 0.00 0.00 5.36
4807 5628 9.783256 GGTGTGATTTATAATACTTTGTTGACC 57.217 33.333 0.00 0.00 0.00 4.02
4823 5644 6.480524 CTGAAACTGATTCGGTGTGATTTA 57.519 37.500 0.00 0.00 41.18 1.40
4938 5759 2.946329 TGCGTTCTGAAAAGTAGGCAAA 59.054 40.909 0.00 0.00 29.68 3.68
5185 6007 2.949963 GCAATCAGGCATTGGGAAGGTA 60.950 50.000 0.45 0.00 42.18 3.08
5324 6146 7.317390 CAGTTTTCATCATGACCATCAAATCA 58.683 34.615 0.00 0.00 0.00 2.57
5447 6269 5.241064 GGATCCTCTGGAATTCATTGTCATG 59.759 44.000 3.84 0.00 34.34 3.07
5464 6286 4.314121 CATCCTCTCAATTTCGGATCCTC 58.686 47.826 10.75 0.00 34.15 3.71
5471 6293 1.863454 CCTCGCATCCTCTCAATTTCG 59.137 52.381 0.00 0.00 0.00 3.46
5487 6309 9.983804 GATTTACTAACTTTACAAAATCCCTCG 57.016 33.333 0.00 0.00 30.66 4.63
5876 6721 4.877378 ATGTCAACATCAAGCCACAAAT 57.123 36.364 0.00 0.00 28.78 2.32
5877 6722 4.669206 AATGTCAACATCAAGCCACAAA 57.331 36.364 0.00 0.00 35.10 2.83
5878 6723 4.218200 CCTAATGTCAACATCAAGCCACAA 59.782 41.667 0.00 0.00 35.10 3.33
5879 6724 3.758023 CCTAATGTCAACATCAAGCCACA 59.242 43.478 0.00 0.00 35.10 4.17
5880 6725 3.129287 CCCTAATGTCAACATCAAGCCAC 59.871 47.826 0.00 0.00 35.10 5.01
5881 6726 3.355378 CCCTAATGTCAACATCAAGCCA 58.645 45.455 0.00 0.00 35.10 4.75
5882 6727 2.099756 GCCCTAATGTCAACATCAAGCC 59.900 50.000 0.00 0.00 35.10 4.35
5883 6728 3.019564 AGCCCTAATGTCAACATCAAGC 58.980 45.455 0.00 0.00 35.10 4.01
5884 6729 4.676196 GCAAGCCCTAATGTCAACATCAAG 60.676 45.833 0.00 0.00 35.10 3.02
5885 6730 3.193267 GCAAGCCCTAATGTCAACATCAA 59.807 43.478 0.00 0.00 35.10 2.57
5886 6731 2.754552 GCAAGCCCTAATGTCAACATCA 59.245 45.455 0.00 0.00 35.10 3.07
5887 6732 3.019564 AGCAAGCCCTAATGTCAACATC 58.980 45.455 0.00 0.00 35.10 3.06
5888 6733 3.091633 AGCAAGCCCTAATGTCAACAT 57.908 42.857 0.00 0.00 38.41 2.71
5889 6734 2.557924 CAAGCAAGCCCTAATGTCAACA 59.442 45.455 0.00 0.00 0.00 3.33
5890 6735 2.819608 TCAAGCAAGCCCTAATGTCAAC 59.180 45.455 0.00 0.00 0.00 3.18
5891 6736 2.819608 GTCAAGCAAGCCCTAATGTCAA 59.180 45.455 0.00 0.00 0.00 3.18
5892 6737 2.436417 GTCAAGCAAGCCCTAATGTCA 58.564 47.619 0.00 0.00 0.00 3.58
5893 6738 1.398390 CGTCAAGCAAGCCCTAATGTC 59.602 52.381 0.00 0.00 0.00 3.06
5894 6739 1.453155 CGTCAAGCAAGCCCTAATGT 58.547 50.000 0.00 0.00 0.00 2.71
5920 6765 3.321111 AGCCTAGACGTCAGAAAAGACAA 59.679 43.478 19.50 0.00 38.43 3.18
5921 6766 2.891580 AGCCTAGACGTCAGAAAAGACA 59.108 45.455 19.50 0.00 38.43 3.41
5949 6794 2.568509 CAGGGTCCCAGCAAAAATCATT 59.431 45.455 11.55 0.00 0.00 2.57
5993 6839 3.242867 TCAGAGACAACTGGGACATCTT 58.757 45.455 0.00 0.00 38.20 2.40
6054 6900 2.265589 AATCATGATCATCAGCGGCA 57.734 45.000 9.06 0.00 0.00 5.69
6069 6915 0.108992 CGAGGACCCGACGAAAATCA 60.109 55.000 0.00 0.00 0.00 2.57
6071 6917 1.217244 CCGAGGACCCGACGAAAAT 59.783 57.895 0.00 0.00 0.00 1.82
6163 7009 1.580942 CATTGACCCAACCACTGCG 59.419 57.895 0.00 0.00 0.00 5.18
6194 7040 0.322975 GCTTCCACAGAGCTTGAGGA 59.677 55.000 9.72 9.72 43.69 3.71


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

AutoCloner maintained by Alex Coulton.