Multiple sequence alignment - TraesCS5B01G049500

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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 TraesCS5B01G049500 chr5B 100.000 6582 0 0 528 7109 55179032 55185613 0.000000e+00 12155.0
1 TraesCS5B01G049500 chr5B 100.000 177 0 0 1 177 55178505 55178681 1.910000e-85 327.0
2 TraesCS5B01G049500 chr5B 93.151 73 3 1 3755 3825 337830842 337830914 9.750000e-19 106.0
3 TraesCS5B01G049500 chr5D 93.931 2768 109 22 528 3273 52054106 52056836 0.000000e+00 4126.0
4 TraesCS5B01G049500 chr5D 94.411 2648 99 22 4490 7109 52057326 52059952 0.000000e+00 4024.0
5 TraesCS5B01G049500 chr5D 96.620 503 17 0 3826 4328 52056822 52057324 0.000000e+00 835.0
6 TraesCS5B01G049500 chr5D 91.765 170 11 2 5265 5432 6162092 6162260 4.290000e-57 233.0
7 TraesCS5B01G049500 chr5D 91.176 170 12 2 5265 5432 512405731 512405563 1.990000e-55 228.0
8 TraesCS5B01G049500 chr5D 97.674 129 3 0 1 129 52053961 52054089 9.280000e-54 222.0
9 TraesCS5B01G049500 chr5D 90.476 168 13 2 5265 5430 6260085 6260251 1.200000e-52 219.0
10 TraesCS5B01G049500 chr5A 93.614 2803 97 33 528 3273 41302306 41305083 0.000000e+00 4109.0
11 TraesCS5B01G049500 chr5A 92.980 1567 52 27 5572 7109 41306633 41308170 0.000000e+00 2231.0
12 TraesCS5B01G049500 chr5A 94.621 1041 40 5 4490 5514 41305573 41306613 0.000000e+00 1598.0
13 TraesCS5B01G049500 chr5A 94.681 564 18 2 3274 3825 602838627 602839190 0.000000e+00 865.0
14 TraesCS5B01G049500 chr5A 97.217 503 14 0 3826 4328 41305069 41305571 0.000000e+00 852.0
15 TraesCS5B01G049500 chr5A 98.413 126 2 0 1 126 41302172 41302297 9.280000e-54 222.0
16 TraesCS5B01G049500 chr5A 84.932 146 18 3 4330 4471 277726654 277726509 2.070000e-30 145.0
17 TraesCS5B01G049500 chr7D 94.894 568 17 2 3274 3829 465339997 465340564 0.000000e+00 878.0
18 TraesCS5B01G049500 chr7D 94.484 562 19 2 3274 3823 548867196 548866635 0.000000e+00 856.0
19 TraesCS5B01G049500 chr7D 91.176 170 12 2 5265 5432 231596079 231596247 1.990000e-55 228.0
20 TraesCS5B01G049500 chr2A 94.858 564 17 2 3274 3825 90420260 90419697 0.000000e+00 870.0
21 TraesCS5B01G049500 chr2A 87.255 510 44 12 3353 3849 310406658 310407159 4.820000e-156 562.0
22 TraesCS5B01G049500 chr2A 90.164 122 7 3 4348 4465 205493208 205493328 3.430000e-33 154.0
23 TraesCS5B01G049500 chr7A 94.681 564 18 2 3274 3825 319591426 319591989 0.000000e+00 865.0
24 TraesCS5B01G049500 chr7A 92.654 599 28 6 3274 3856 176249949 176249351 0.000000e+00 848.0
25 TraesCS5B01G049500 chr2D 94.681 564 18 2 3274 3825 351053205 351053768 0.000000e+00 865.0
26 TraesCS5B01G049500 chr2D 92.035 113 7 2 4353 4464 140307736 140307847 2.650000e-34 158.0
27 TraesCS5B01G049500 chr2D 89.706 68 1 2 3770 3831 361408482 361408415 1.640000e-11 82.4
28 TraesCS5B01G049500 chr4D 94.504 564 19 2 3274 3825 242938397 242938960 0.000000e+00 859.0
29 TraesCS5B01G049500 chr6B 94.614 557 25 2 3274 3825 713265129 713265685 0.000000e+00 857.0
30 TraesCS5B01G049500 chr6B 90.833 120 3 4 4333 4452 557418206 557418317 3.430000e-33 154.0
31 TraesCS5B01G049500 chr6B 90.769 65 6 0 963 1027 145900601 145900665 3.530000e-13 87.9
32 TraesCS5B01G049500 chr4A 93.015 587 27 4 3274 3846 692132774 692132188 0.000000e+00 845.0
33 TraesCS5B01G049500 chr4A 92.979 584 27 4 3274 3843 18854372 18853789 0.000000e+00 839.0
34 TraesCS5B01G049500 chr7B 92.650 585 27 6 3274 3845 397288402 397287821 0.000000e+00 828.0
35 TraesCS5B01G049500 chr7B 90.698 129 11 1 4333 4461 541688144 541688271 3.410000e-38 171.0
36 TraesCS5B01G049500 chr2B 93.537 557 31 2 3274 3825 481879109 481879665 0.000000e+00 824.0
37 TraesCS5B01G049500 chr1D 90.588 170 13 2 5265 5432 51838941 51839109 9.280000e-54 222.0
38 TraesCS5B01G049500 chr1D 90.588 170 13 2 5265 5432 254449835 254449667 9.280000e-54 222.0
39 TraesCS5B01G049500 chr1A 90.058 171 12 3 5265 5432 241517868 241517700 4.320000e-52 217.0
40 TraesCS5B01G049500 chr3B 95.763 118 4 1 4359 4476 640073076 640072960 9.410000e-44 189.0
41 TraesCS5B01G049500 chr3B 85.816 141 10 6 4347 4485 821850810 821850678 2.670000e-29 141.0
42 TraesCS5B01G049500 chr3A 93.694 111 6 1 4360 4470 30398824 30398715 1.590000e-36 165.0
43 TraesCS5B01G049500 chr6A 86.806 144 12 4 4333 4470 546479636 546479494 3.430000e-33 154.0
44 TraesCS5B01G049500 chr6A 89.916 119 9 2 4346 4464 514023236 514023351 4.440000e-32 150.0


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 TraesCS5B01G049500 chr5B 55178505 55185613 7108 False 6241.00 12155 100.000 1 7109 2 chr5B.!!$F2 7108
1 TraesCS5B01G049500 chr5D 52053961 52059952 5991 False 2301.75 4126 95.659 1 7109 4 chr5D.!!$F3 7108
2 TraesCS5B01G049500 chr5A 41302172 41308170 5998 False 1802.40 4109 95.369 1 7109 5 chr5A.!!$F2 7108
3 TraesCS5B01G049500 chr5A 602838627 602839190 563 False 865.00 865 94.681 3274 3825 1 chr5A.!!$F1 551
4 TraesCS5B01G049500 chr7D 465339997 465340564 567 False 878.00 878 94.894 3274 3829 1 chr7D.!!$F2 555
5 TraesCS5B01G049500 chr7D 548866635 548867196 561 True 856.00 856 94.484 3274 3823 1 chr7D.!!$R1 549
6 TraesCS5B01G049500 chr2A 90419697 90420260 563 True 870.00 870 94.858 3274 3825 1 chr2A.!!$R1 551
7 TraesCS5B01G049500 chr2A 310406658 310407159 501 False 562.00 562 87.255 3353 3849 1 chr2A.!!$F2 496
8 TraesCS5B01G049500 chr7A 319591426 319591989 563 False 865.00 865 94.681 3274 3825 1 chr7A.!!$F1 551
9 TraesCS5B01G049500 chr7A 176249351 176249949 598 True 848.00 848 92.654 3274 3856 1 chr7A.!!$R1 582
10 TraesCS5B01G049500 chr2D 351053205 351053768 563 False 865.00 865 94.681 3274 3825 1 chr2D.!!$F2 551
11 TraesCS5B01G049500 chr4D 242938397 242938960 563 False 859.00 859 94.504 3274 3825 1 chr4D.!!$F1 551
12 TraesCS5B01G049500 chr6B 713265129 713265685 556 False 857.00 857 94.614 3274 3825 1 chr6B.!!$F3 551
13 TraesCS5B01G049500 chr4A 692132188 692132774 586 True 845.00 845 93.015 3274 3846 1 chr4A.!!$R2 572
14 TraesCS5B01G049500 chr4A 18853789 18854372 583 True 839.00 839 92.979 3274 3843 1 chr4A.!!$R1 569
15 TraesCS5B01G049500 chr7B 397287821 397288402 581 True 828.00 828 92.650 3274 3845 1 chr7B.!!$R1 571
16 TraesCS5B01G049500 chr2B 481879109 481879665 556 False 824.00 824 93.537 3274 3825 1 chr2B.!!$F1 551

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
903 923 0.107831 TAGTTGGTTCTTGCGGTGCT 59.892 50.000 0.00 0.00 0.00 4.40 F
1499 1531 0.110192 GCTAGCACAAAGTGGAACGC 60.110 55.000 10.63 0.00 45.86 4.84 F
1501 1533 0.179043 TAGCACAAAGTGGAACGCCA 60.179 50.000 0.00 0.00 45.86 5.69 F
2126 2187 0.339859 ATGGAGGCTCCTCTGTGGTA 59.660 55.000 32.28 11.66 42.38 3.25 F
3723 3785 1.008449 ACTAGCTATGGACAGGGGTGT 59.992 52.381 0.00 0.00 0.00 4.16 F
4481 4555 0.029433 CATCGGCTCATCGACTCGAA 59.971 55.000 5.00 0.00 42.21 3.71 F
5401 5498 0.330604 TCTACCGAGTGTACAGCCCT 59.669 55.000 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2733 2794 0.107897 ACTCGCACGCCAATGGATTA 60.108 50.000 2.05 0.0 0.0 1.75 R
3396 3457 0.586319 AACTGTTGAACATGTCGCCG 59.414 50.000 0.00 0.0 0.0 6.46 R
3431 3492 3.557185 CCACACATCATCTCAACATACGG 59.443 47.826 0.00 0.0 0.0 4.02 R
3748 3810 0.798776 CGCAACCAACTCATGACTCC 59.201 55.000 0.00 0.0 0.0 3.85 R
5225 5320 0.462225 TGCCGACGTCAACAAGGAAA 60.462 50.000 17.16 0.0 0.0 3.13 R
5620 5719 1.067846 TCCACCTCACAAGATCGAACG 60.068 52.381 0.00 0.0 0.0 3.95 R
6377 6485 1.080772 CACGCCGAACAGCTACTCA 60.081 57.895 0.00 0.0 0.0 3.41 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
129 130 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
130 131 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
131 132 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
133 134 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
135 136 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
138 139 2.906897 CACCACCACCACCACTGC 60.907 66.667 0.00 0.00 0.00 4.40
142 143 3.807839 ACCACCACCACTGCAGCA 61.808 61.111 15.27 0.00 0.00 4.41
153 154 1.545136 CACTGCAGCAAGAGAGAGAGA 59.455 52.381 15.27 0.00 0.00 3.10
156 157 2.093890 TGCAGCAAGAGAGAGAGAGAG 58.906 52.381 0.00 0.00 0.00 3.20
157 158 2.290832 TGCAGCAAGAGAGAGAGAGAGA 60.291 50.000 0.00 0.00 0.00 3.10
158 159 2.357009 GCAGCAAGAGAGAGAGAGAGAG 59.643 54.545 0.00 0.00 0.00 3.20
159 160 3.877559 CAGCAAGAGAGAGAGAGAGAGA 58.122 50.000 0.00 0.00 0.00 3.10
160 161 3.875727 CAGCAAGAGAGAGAGAGAGAGAG 59.124 52.174 0.00 0.00 0.00 3.20
161 162 3.776969 AGCAAGAGAGAGAGAGAGAGAGA 59.223 47.826 0.00 0.00 0.00 3.10
162 163 4.125703 GCAAGAGAGAGAGAGAGAGAGAG 58.874 52.174 0.00 0.00 0.00 3.20
163 164 4.141846 GCAAGAGAGAGAGAGAGAGAGAGA 60.142 50.000 0.00 0.00 0.00 3.10
164 165 5.599732 CAAGAGAGAGAGAGAGAGAGAGAG 58.400 50.000 0.00 0.00 0.00 3.20
165 166 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
166 167 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
167 168 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
168 169 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
169 170 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
170 171 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
171 172 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
172 173 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
173 174 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
174 175 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
175 176 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
176 177 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
557 558 2.176792 CGAAAGCTCGGGCAAAGC 59.823 61.111 11.40 0.00 41.57 3.51
558 559 2.176792 GAAAGCTCGGGCAAAGCG 59.823 61.111 11.40 0.00 44.59 4.68
584 585 4.162690 AGCGTCGGCAGATTCCCC 62.163 66.667 0.00 0.00 43.41 4.81
585 586 4.162690 GCGTCGGCAGATTCCCCT 62.163 66.667 0.00 0.00 39.62 4.79
586 587 2.584608 CGTCGGCAGATTCCCCTT 59.415 61.111 0.00 0.00 0.00 3.95
587 588 1.815421 CGTCGGCAGATTCCCCTTG 60.815 63.158 0.00 0.00 0.00 3.61
588 589 1.452108 GTCGGCAGATTCCCCTTGG 60.452 63.158 0.00 0.00 0.00 3.61
589 590 2.124151 CGGCAGATTCCCCTTGGG 60.124 66.667 0.00 0.00 46.11 4.12
590 591 2.442830 GGCAGATTCCCCTTGGGC 60.443 66.667 0.00 0.00 43.94 5.36
613 614 0.299597 CGTCGCCGCTATTTTACCAC 59.700 55.000 0.00 0.00 0.00 4.16
654 655 4.123545 GATCCAACCCCCACCCCG 62.124 72.222 0.00 0.00 0.00 5.73
727 733 2.791396 TTCTCGTCGTTTCTCGGGCG 62.791 60.000 0.00 0.00 40.32 6.13
756 762 0.907230 GCCACTCTGGACCTCTTCCT 60.907 60.000 0.00 0.00 46.10 3.36
758 764 0.814457 CACTCTGGACCTCTTCCTCG 59.186 60.000 0.00 0.00 46.10 4.63
782 788 1.373121 GGCGTCTTATAGCTCCGGC 60.373 63.158 0.00 0.00 36.94 6.13
842 848 3.307339 GGTTCTGGATGACTTCTTGAGCT 60.307 47.826 0.00 0.00 0.00 4.09
845 851 2.235650 CTGGATGACTTCTTGAGCTGGA 59.764 50.000 0.00 0.00 0.00 3.86
853 873 2.015456 TCTTGAGCTGGACCTCTTCA 57.985 50.000 0.00 0.00 33.02 3.02
903 923 0.107831 TAGTTGGTTCTTGCGGTGCT 59.892 50.000 0.00 0.00 0.00 4.40
951 971 1.752694 CAATCGGGGGAAATGGCGT 60.753 57.895 0.00 0.00 0.00 5.68
952 972 1.000145 AATCGGGGGAAATGGCGTT 60.000 52.632 0.00 0.00 0.00 4.84
1287 1312 1.959899 GCTTCGTGTGCATGACCTCG 61.960 60.000 0.00 0.00 0.00 4.63
1314 1339 2.764547 GCCCTCTACGCCCTCCTT 60.765 66.667 0.00 0.00 0.00 3.36
1351 1380 1.753073 CAAATCATCCCTCACCTTGCC 59.247 52.381 0.00 0.00 0.00 4.52
1375 1407 3.924507 GCAAATCAGCCCGGATGT 58.075 55.556 0.73 0.00 0.00 3.06
1408 1440 2.490903 AGGATTTGTCATGTGCTGCTTC 59.509 45.455 0.00 0.00 0.00 3.86
1409 1441 2.490903 GGATTTGTCATGTGCTGCTTCT 59.509 45.455 0.00 0.00 0.00 2.85
1481 1513 7.920738 AGCATAGTTAAAGTAGTAATTGCTGC 58.079 34.615 6.28 4.82 35.56 5.25
1485 1517 7.541122 AGTTAAAGTAGTAATTGCTGCTAGC 57.459 36.000 14.05 8.10 42.82 3.42
1495 1527 2.932663 GCTGCTAGCACAAAGTGGA 58.067 52.632 14.93 0.00 41.89 4.02
1496 1528 1.238439 GCTGCTAGCACAAAGTGGAA 58.762 50.000 14.93 0.00 41.89 3.53
1497 1529 1.068954 GCTGCTAGCACAAAGTGGAAC 60.069 52.381 14.93 0.00 41.89 3.62
1498 1530 1.195448 CTGCTAGCACAAAGTGGAACG 59.805 52.381 14.93 0.00 45.86 3.95
1499 1531 0.110192 GCTAGCACAAAGTGGAACGC 60.110 55.000 10.63 0.00 45.86 4.84
1500 1532 0.517316 CTAGCACAAAGTGGAACGCC 59.483 55.000 0.00 0.00 45.86 5.68
1501 1533 0.179043 TAGCACAAAGTGGAACGCCA 60.179 50.000 0.00 0.00 45.86 5.69
1575 1610 6.530019 TCTGATGTCATGCTTTAGTACTCA 57.470 37.500 0.00 0.00 0.00 3.41
1579 1614 8.565896 TGATGTCATGCTTTAGTACTCATTTT 57.434 30.769 0.00 0.00 0.00 1.82
1583 1618 7.040478 TGTCATGCTTTAGTACTCATTTTTGCT 60.040 33.333 0.00 0.00 0.00 3.91
1655 1690 1.701847 CTTCCACTGGGGGATATCTGG 59.298 57.143 2.05 1.41 36.67 3.86
1726 1762 8.986929 ATAATAGAGAAAATATAGGGCCATGC 57.013 34.615 6.18 0.00 0.00 4.06
1743 1779 4.530875 CCATGCCTCCTGTTATTTTCTCT 58.469 43.478 0.00 0.00 0.00 3.10
1781 1817 2.745821 TGCAATGCAGACAATGTCTCTC 59.254 45.455 13.72 8.89 41.37 3.20
1798 1834 5.240403 TGTCTCTCGTTCCATCATCATCTAG 59.760 44.000 0.00 0.00 0.00 2.43
1804 1840 6.299922 TCGTTCCATCATCATCTAGTCTACT 58.700 40.000 0.00 0.00 0.00 2.57
1847 1906 8.809066 TCTGCTTACAAGTAAGGATACAAGTTA 58.191 33.333 18.60 0.00 41.52 2.24
2059 2120 4.984295 TGGAGGTTGTTCATCTGAATTGA 58.016 39.130 0.00 0.00 36.33 2.57
2126 2187 0.339859 ATGGAGGCTCCTCTGTGGTA 59.660 55.000 32.28 11.66 42.38 3.25
2176 2237 2.741517 TGCACGATTTGTCATACCTGTG 59.258 45.455 0.00 0.00 0.00 3.66
2200 2261 5.437289 TGGCTATGTATGCTGTTTATTGC 57.563 39.130 0.00 0.00 0.00 3.56
2304 2365 2.444388 TGCAAGGATATGAGGGAAGCAT 59.556 45.455 0.00 0.00 0.00 3.79
2567 2628 6.376248 ACCTATTATGATGTTTTGGGCATCT 58.624 36.000 6.80 0.00 42.21 2.90
2649 2710 6.699575 AGACAACAACACTTTAAGCTGAAT 57.300 33.333 0.00 0.00 0.00 2.57
2733 2794 4.956075 GTCCATCCTGATAAAAACATGGGT 59.044 41.667 0.00 0.00 0.00 4.51
2851 2912 7.484035 AGTTTTCTCAAATCTGACAGTGTAC 57.516 36.000 1.59 0.00 0.00 2.90
2881 2942 8.394971 TCTTGATCACAACTGTGTTATTTGAT 57.605 30.769 9.56 0.02 45.76 2.57
2981 3042 3.949132 ACAGCTGAGGAAAGAAGAATCC 58.051 45.455 23.35 0.00 35.88 3.01
3238 3299 6.038714 CCCCTCAACAGATACTTTTATTCTGC 59.961 42.308 0.00 0.00 32.16 4.26
3239 3300 6.038714 CCCTCAACAGATACTTTTATTCTGCC 59.961 42.308 0.00 0.00 32.16 4.85
3326 3387 2.355010 AGAGAGTGCCACAAAAGCTT 57.645 45.000 0.00 0.00 0.00 3.74
3366 3427 1.372872 GTGGTTCAACCCGCAATGC 60.373 57.895 3.42 0.00 37.50 3.56
3396 3457 1.798813 CTGAGTGTTGGCCGACTAAAC 59.201 52.381 23.87 13.75 0.00 2.01
3431 3492 2.234908 ACAGTTAGGTGTGGCAGAGATC 59.765 50.000 0.00 0.00 0.00 2.75
3541 3603 1.734465 GAGAAGCTTGTCCAACATCGG 59.266 52.381 12.50 0.00 0.00 4.18
3696 3758 5.222870 AGACCTGAAGGATTGGAGTATCAT 58.777 41.667 2.62 0.00 38.94 2.45
3723 3785 1.008449 ACTAGCTATGGACAGGGGTGT 59.992 52.381 0.00 0.00 0.00 4.16
3748 3810 0.816825 AGCTTGCTATCCATGTGCCG 60.817 55.000 0.00 0.00 0.00 5.69
3752 3814 1.337384 TGCTATCCATGTGCCGGAGT 61.337 55.000 5.05 0.00 35.56 3.85
3829 3903 6.902224 AGGCTTTGTTGTTGTTGTTTTATC 57.098 33.333 0.00 0.00 0.00 1.75
3832 3906 7.277760 AGGCTTTGTTGTTGTTGTTTTATCTTC 59.722 33.333 0.00 0.00 0.00 2.87
3834 3908 9.296400 GCTTTGTTGTTGTTGTTTTATCTTCTA 57.704 29.630 0.00 0.00 0.00 2.10
3859 3933 8.986477 ATTGTTTTGTTACTATGGAATTCAGC 57.014 30.769 7.93 0.00 0.00 4.26
3895 3969 8.650143 ATGTATGTAACCTGGTCAATTTCTTT 57.350 30.769 0.00 0.00 0.00 2.52
4140 4214 1.850289 TGCCAGGTTAGGAGCCCAA 60.850 57.895 0.00 0.00 0.00 4.12
4158 4232 3.192633 CCCAACATGTACTTTTAGGGCAC 59.807 47.826 0.00 0.00 0.00 5.01
4177 4251 5.479306 GGCACTTGTTAACTGAGAGTATCA 58.521 41.667 7.22 0.00 37.82 2.15
4191 4265 7.093112 ACTGAGAGTATCACTCCAGCTAATTTT 60.093 37.037 17.43 2.69 46.18 1.82
4195 4269 8.928448 AGAGTATCACTCCAGCTAATTTTCATA 58.072 33.333 2.74 0.00 46.18 2.15
4334 4408 9.683870 TGTAAACTTCATTATATTTTACGGGGT 57.316 29.630 0.00 0.00 36.05 4.95
4339 4413 9.863845 ACTTCATTATATTTTACGGGGTTTTTG 57.136 29.630 0.00 0.00 0.00 2.44
4342 4416 9.245481 TCATTATATTTTACGGGGTTTTTGAGT 57.755 29.630 0.00 0.00 0.00 3.41
4343 4417 9.511144 CATTATATTTTACGGGGTTTTTGAGTC 57.489 33.333 0.00 0.00 0.00 3.36
4344 4418 3.967203 TTTTACGGGGTTTTTGAGTCG 57.033 42.857 0.00 0.00 0.00 4.18
4345 4419 1.228533 TTACGGGGTTTTTGAGTCGC 58.771 50.000 0.00 0.00 0.00 5.19
4346 4420 0.945265 TACGGGGTTTTTGAGTCGCG 60.945 55.000 0.00 0.00 40.53 5.87
4347 4421 2.254350 GGGGTTTTTGAGTCGCGC 59.746 61.111 0.00 0.00 0.00 6.86
4348 4422 2.127383 GGGTTTTTGAGTCGCGCG 60.127 61.111 26.76 26.76 0.00 6.86
4349 4423 2.600475 GGGTTTTTGAGTCGCGCGA 61.600 57.895 31.40 31.40 0.00 5.87
4350 4424 1.438222 GGTTTTTGAGTCGCGCGAC 60.438 57.895 46.21 46.21 44.86 5.19
4401 4475 4.910746 AAAAATGTCGACTCATGACTCG 57.089 40.909 17.92 15.98 37.26 4.18
4402 4476 3.850122 AAATGTCGACTCATGACTCGA 57.150 42.857 19.46 19.46 37.26 4.04
4403 4477 3.412981 AATGTCGACTCATGACTCGAG 57.587 47.619 22.57 11.84 39.51 4.04
4404 4478 1.809684 TGTCGACTCATGACTCGAGT 58.190 50.000 22.57 20.18 46.32 4.18
4414 4488 2.371902 GACTCGAGTCGCGACTAGT 58.628 57.895 39.33 36.15 45.59 2.57
4415 4489 0.298411 GACTCGAGTCGCGACTAGTC 59.702 60.000 37.11 37.11 45.59 2.59
4416 4490 3.267322 GACTCGAGTCGCGACTAGTCG 62.267 61.905 37.11 34.47 45.59 4.18
4424 4498 4.552278 CGACTAGTCGCAACTGCA 57.448 55.556 30.44 0.00 46.50 4.41
4425 4499 2.353807 CGACTAGTCGCAACTGCAG 58.646 57.895 30.44 13.48 46.50 4.41
4426 4500 1.073216 CGACTAGTCGCAACTGCAGG 61.073 60.000 30.44 1.57 46.50 4.85
4427 4501 1.355066 GACTAGTCGCAACTGCAGGC 61.355 60.000 19.93 11.86 42.21 4.85
4428 4502 1.079543 CTAGTCGCAACTGCAGGCT 60.080 57.895 19.93 0.99 42.21 4.58
4429 4503 1.079819 TAGTCGCAACTGCAGGCTC 60.080 57.895 19.93 8.48 42.21 4.70
4430 4504 2.819117 TAGTCGCAACTGCAGGCTCG 62.819 60.000 19.93 16.84 42.21 5.03
4431 4505 3.989787 TCGCAACTGCAGGCTCGA 61.990 61.111 19.93 18.82 42.21 4.04
4432 4506 3.782244 CGCAACTGCAGGCTCGAC 61.782 66.667 19.93 0.00 42.21 4.20
4433 4507 2.358003 GCAACTGCAGGCTCGACT 60.358 61.111 19.93 0.00 41.59 4.18
4434 4508 1.963338 GCAACTGCAGGCTCGACTT 60.963 57.895 19.93 0.00 41.59 3.01
4435 4509 1.510480 GCAACTGCAGGCTCGACTTT 61.510 55.000 19.93 0.00 41.59 2.66
4436 4510 0.947244 CAACTGCAGGCTCGACTTTT 59.053 50.000 19.93 0.00 0.00 2.27
4437 4511 1.334869 CAACTGCAGGCTCGACTTTTT 59.665 47.619 19.93 0.00 0.00 1.94
4438 4512 1.230324 ACTGCAGGCTCGACTTTTTC 58.770 50.000 19.93 0.00 0.00 2.29
4439 4513 0.519077 CTGCAGGCTCGACTTTTTCC 59.481 55.000 5.57 0.00 0.00 3.13
4440 4514 0.179032 TGCAGGCTCGACTTTTTCCA 60.179 50.000 0.00 0.00 0.00 3.53
4441 4515 0.951558 GCAGGCTCGACTTTTTCCAA 59.048 50.000 0.00 0.00 0.00 3.53
4442 4516 1.068954 GCAGGCTCGACTTTTTCCAAG 60.069 52.381 0.00 0.00 0.00 3.61
4443 4517 2.222027 CAGGCTCGACTTTTTCCAAGT 58.778 47.619 0.00 0.00 0.00 3.16
4444 4518 2.224314 CAGGCTCGACTTTTTCCAAGTC 59.776 50.000 4.88 4.88 42.33 3.01
4450 4524 3.808116 GACTTTTTCCAAGTCGCTACC 57.192 47.619 0.00 0.00 37.51 3.18
4451 4525 2.483106 GACTTTTTCCAAGTCGCTACCC 59.517 50.000 0.00 0.00 37.51 3.69
4452 4526 1.810755 CTTTTTCCAAGTCGCTACCCC 59.189 52.381 0.00 0.00 0.00 4.95
4453 4527 0.766131 TTTTCCAAGTCGCTACCCCA 59.234 50.000 0.00 0.00 0.00 4.96
4454 4528 0.323629 TTTCCAAGTCGCTACCCCAG 59.676 55.000 0.00 0.00 0.00 4.45
4455 4529 0.543410 TTCCAAGTCGCTACCCCAGA 60.543 55.000 0.00 0.00 0.00 3.86
4456 4530 0.543410 TCCAAGTCGCTACCCCAGAA 60.543 55.000 0.00 0.00 0.00 3.02
4457 4531 0.391263 CCAAGTCGCTACCCCAGAAC 60.391 60.000 0.00 0.00 0.00 3.01
4458 4532 0.736325 CAAGTCGCTACCCCAGAACG 60.736 60.000 0.00 0.00 0.00 3.95
4459 4533 0.896940 AAGTCGCTACCCCAGAACGA 60.897 55.000 0.00 0.00 0.00 3.85
4460 4534 1.153881 GTCGCTACCCCAGAACGAC 60.154 63.158 0.00 0.00 45.10 4.34
4461 4535 1.303888 TCGCTACCCCAGAACGACT 60.304 57.895 0.00 0.00 0.00 4.18
4462 4536 1.139095 CGCTACCCCAGAACGACTC 59.861 63.158 0.00 0.00 0.00 3.36
4463 4537 1.592400 CGCTACCCCAGAACGACTCA 61.592 60.000 0.00 0.00 0.00 3.41
4464 4538 0.824759 GCTACCCCAGAACGACTCAT 59.175 55.000 0.00 0.00 0.00 2.90
4465 4539 1.202428 GCTACCCCAGAACGACTCATC 60.202 57.143 0.00 0.00 0.00 2.92
4474 4548 4.218597 CGACTCATCGGCTCATCG 57.781 61.111 0.00 0.00 44.99 3.84
4475 4549 1.649267 CGACTCATCGGCTCATCGA 59.351 57.895 0.00 0.00 44.99 3.59
4476 4550 0.658829 CGACTCATCGGCTCATCGAC 60.659 60.000 0.00 0.00 44.99 4.20
4477 4551 0.665835 GACTCATCGGCTCATCGACT 59.334 55.000 0.00 0.00 42.21 4.18
4478 4552 0.665835 ACTCATCGGCTCATCGACTC 59.334 55.000 0.00 0.00 42.21 3.36
4479 4553 0.385348 CTCATCGGCTCATCGACTCG 60.385 60.000 0.00 0.00 42.21 4.18
4480 4554 0.814010 TCATCGGCTCATCGACTCGA 60.814 55.000 3.06 3.06 42.21 4.04
4481 4555 0.029433 CATCGGCTCATCGACTCGAA 59.971 55.000 5.00 0.00 42.21 3.71
4482 4556 0.738975 ATCGGCTCATCGACTCGAAA 59.261 50.000 5.00 0.00 42.21 3.46
4483 4557 0.524414 TCGGCTCATCGACTCGAAAA 59.476 50.000 5.00 0.00 39.99 2.29
4484 4558 0.640768 CGGCTCATCGACTCGAAAAC 59.359 55.000 5.00 0.00 39.99 2.43
4485 4559 1.710013 GGCTCATCGACTCGAAAACA 58.290 50.000 5.00 0.00 39.99 2.83
4486 4560 2.066262 GGCTCATCGACTCGAAAACAA 58.934 47.619 5.00 0.00 39.99 2.83
4487 4561 2.159827 GGCTCATCGACTCGAAAACAAC 60.160 50.000 5.00 0.00 39.99 3.32
4488 4562 2.470781 GCTCATCGACTCGAAAACAACG 60.471 50.000 5.00 0.00 39.99 4.10
4545 4619 5.066505 CCTATTGCAGTCATCTTGGGTTTAC 59.933 44.000 0.00 0.00 0.00 2.01
4590 4664 5.304357 AGTGGTTTAAACAAAGGGAGAATGG 59.696 40.000 19.57 0.00 0.00 3.16
4671 4745 5.642063 CCTATTTGGTAGAAAACTCAGCGAA 59.358 40.000 0.00 0.00 31.71 4.70
4867 4941 3.503363 TGCTAAAGTGGATGCTCAAAGTG 59.497 43.478 0.00 0.00 0.00 3.16
5006 5086 5.220931 GCCTGCAGAAACTAATGTCCAATAG 60.221 44.000 17.39 0.00 0.00 1.73
5009 5089 7.284034 CCTGCAGAAACTAATGTCCAATAGAAT 59.716 37.037 17.39 0.00 0.00 2.40
5010 5090 8.213518 TGCAGAAACTAATGTCCAATAGAATC 57.786 34.615 0.00 0.00 0.00 2.52
5041 5121 6.260936 TCTGTTCTTTCTTGATTGTTCACTCC 59.739 38.462 0.00 0.00 0.00 3.85
5042 5122 5.885352 TGTTCTTTCTTGATTGTTCACTCCA 59.115 36.000 0.00 0.00 0.00 3.86
5043 5123 6.038603 TGTTCTTTCTTGATTGTTCACTCCAG 59.961 38.462 0.00 0.00 0.00 3.86
5044 5124 5.684704 TCTTTCTTGATTGTTCACTCCAGT 58.315 37.500 0.00 0.00 0.00 4.00
5224 5319 8.440059 CACGTGATATGCTTTAACTTTTAGTCA 58.560 33.333 10.90 0.00 0.00 3.41
5225 5320 9.162764 ACGTGATATGCTTTAACTTTTAGTCAT 57.837 29.630 0.00 0.00 0.00 3.06
5318 5413 9.745018 AGAAGGATCTGTTATCTTGAAAATTCA 57.255 29.630 0.00 0.00 33.59 2.57
5375 5472 5.563475 GCATACCATATCTCAACATTGGTGC 60.563 44.000 0.00 0.00 40.75 5.01
5401 5498 0.330604 TCTACCGAGTGTACAGCCCT 59.669 55.000 0.00 0.00 0.00 5.19
5422 5519 8.157476 AGCCCTATAATAATAGTGTTTGTCCAG 58.843 37.037 0.00 0.00 34.36 3.86
5570 5668 8.780249 TGGCTGAATTTAGTCTTTGTAGTTTAC 58.220 33.333 3.31 0.00 0.00 2.01
5571 5669 9.000486 GGCTGAATTTAGTCTTTGTAGTTTACT 58.000 33.333 0.00 0.00 0.00 2.24
5620 5719 7.506328 ACTTTGTAAATAGGTTCAGTTGGTC 57.494 36.000 0.00 0.00 0.00 4.02
5633 5732 2.155732 CAGTTGGTCGTTCGATCTTGTG 59.844 50.000 7.00 0.00 0.00 3.33
5652 5751 5.614324 TGTGAGGTGGATAGAATACCAAG 57.386 43.478 0.00 0.00 37.94 3.61
5707 5806 4.771054 TCTAGAAAGTAGGACCCAGAACAC 59.229 45.833 0.00 0.00 0.00 3.32
5708 5807 3.314693 AGAAAGTAGGACCCAGAACACA 58.685 45.455 0.00 0.00 0.00 3.72
5723 5822 6.017109 CCCAGAACACATATTGCAGGTAATAC 60.017 42.308 0.00 0.00 0.00 1.89
5724 5823 6.542005 CCAGAACACATATTGCAGGTAATACA 59.458 38.462 0.00 0.00 0.00 2.29
5741 5840 1.999648 ACAATGGCCACATCAACTGT 58.000 45.000 8.16 0.00 35.94 3.55
5749 5848 2.294233 GCCACATCAACTGTTGACATGT 59.706 45.455 24.17 21.25 43.48 3.21
5750 5849 3.610114 GCCACATCAACTGTTGACATGTC 60.610 47.826 24.17 19.27 43.48 3.06
5751 5850 3.565063 CCACATCAACTGTTGACATGTCA 59.435 43.478 24.56 24.56 43.48 3.58
5752 5851 4.216902 CCACATCAACTGTTGACATGTCAT 59.783 41.667 28.32 11.57 43.48 3.06
5753 5852 5.278610 CCACATCAACTGTTGACATGTCATT 60.279 40.000 28.32 16.89 43.48 2.57
5815 5914 7.716799 ATATCTGAAAAATGGGCAACACTTA 57.283 32.000 0.00 0.00 39.74 2.24
5833 5932 9.191995 CAACACTTATTTAACCCATTCTGTTTC 57.808 33.333 0.00 0.00 0.00 2.78
5928 6027 2.426738 GGATAGGATGCCTCAGAGATCG 59.573 54.545 0.00 0.00 34.61 3.69
5931 6030 0.319727 GGATGCCTCAGAGATCGCAG 60.320 60.000 0.00 0.00 34.15 5.18
6114 6213 2.240500 GCGATCGTCATGAGGGTGC 61.241 63.158 17.81 12.26 0.00 5.01
6188 6288 7.165485 GGAAAAAGGCAATAATACAAGGGTTT 58.835 34.615 0.00 0.00 0.00 3.27
6318 6424 7.012421 AGTGAACCTGACTGTTGAAATTAGTTC 59.988 37.037 0.00 0.00 36.70 3.01
6377 6485 0.680921 CAGGCATGGGGTCGAAACAT 60.681 55.000 0.00 0.00 0.00 2.71
6435 6543 2.792374 TCGACGACGAAAAGAGTGC 58.208 52.632 7.68 0.00 45.74 4.40
6488 6596 0.870393 TTGCGCTGCTCTTTCTGAAG 59.130 50.000 9.73 0.00 0.00 3.02
6493 6601 1.062294 GCTGCTCTTTCTGAAGCATCG 59.938 52.381 3.22 0.00 36.65 3.84
6501 6609 0.897621 TCTGAAGCATCGCTGAAGGA 59.102 50.000 0.00 0.00 39.62 3.36
6543 6651 1.194098 CAGCAAGTTCTGTGAAGCTCG 59.806 52.381 0.00 0.00 0.00 5.03
6559 6667 2.491693 AGCTCGTTCTGGAGAAGAGAAG 59.508 50.000 14.77 3.17 35.91 2.85
6560 6668 2.416701 GCTCGTTCTGGAGAAGAGAAGG 60.417 54.545 14.77 0.00 35.91 3.46
6753 6864 0.168128 GCCGCGCTCTGTAACATTTT 59.832 50.000 5.56 0.00 0.00 1.82
6754 6865 1.790481 GCCGCGCTCTGTAACATTTTC 60.790 52.381 5.56 0.00 0.00 2.29
6757 6868 1.790481 GCGCTCTGTAACATTTTCGGC 60.790 52.381 0.00 0.00 0.00 5.54
6762 6873 4.116961 CTCTGTAACATTTTCGGCGGATA 58.883 43.478 7.21 0.00 0.00 2.59
6835 6948 4.022329 GGTTAATCTGTTTTCCTGGGTGTG 60.022 45.833 0.00 0.00 0.00 3.82
6868 6981 0.105593 AGTGAGTGGCGGCTGATATG 59.894 55.000 11.43 0.00 0.00 1.78
6875 6988 0.601311 GGCGGCTGATATGGACAGAC 60.601 60.000 0.00 0.00 39.72 3.51
6931 7046 5.280011 GGTTATTTCTGTCTGAGAGGAACCA 60.280 44.000 16.45 1.47 37.89 3.67
7025 7147 3.043199 GGGTGGATCCTCCCCCTA 58.957 66.667 33.68 0.76 41.26 3.53
7028 7150 0.764752 GGTGGATCCTCCCCCTACTG 60.765 65.000 20.45 0.00 35.03 2.74
7065 7189 1.951209 TACCATCTTGAGCCCAGACA 58.049 50.000 0.00 0.00 0.00 3.41
7069 7193 1.067295 ATCTTGAGCCCAGACACCAA 58.933 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.996168 AAAAGGCACACGCTCGCTCT 62.996 55.000 0.00 0.00 38.60 4.09
48 49 2.605535 ATTGGGGCGAGGAGGAGCTA 62.606 60.000 0.00 0.00 0.00 3.32
129 130 0.954449 CTCTCTTGCTGCAGTGGTGG 60.954 60.000 16.64 3.81 0.00 4.61
130 131 0.034476 TCTCTCTTGCTGCAGTGGTG 59.966 55.000 16.64 6.96 0.00 4.17
131 132 0.321021 CTCTCTCTTGCTGCAGTGGT 59.679 55.000 16.64 0.00 0.00 4.16
133 134 1.545136 TCTCTCTCTCTTGCTGCAGTG 59.455 52.381 16.64 6.38 0.00 3.66
135 136 2.093890 TCTCTCTCTCTCTTGCTGCAG 58.906 52.381 10.11 10.11 0.00 4.41
138 139 3.875727 CTCTCTCTCTCTCTCTCTTGCTG 59.124 52.174 0.00 0.00 0.00 4.41
142 143 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
153 154 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
527 528 2.680352 TTTCGCCGCCCTCTCTCT 60.680 61.111 0.00 0.00 0.00 3.10
528 529 2.202810 CTTTCGCCGCCCTCTCTC 60.203 66.667 0.00 0.00 0.00 3.20
529 530 4.459089 GCTTTCGCCGCCCTCTCT 62.459 66.667 0.00 0.00 0.00 3.10
530 531 4.459089 AGCTTTCGCCGCCCTCTC 62.459 66.667 0.00 0.00 36.60 3.20
531 532 4.459089 GAGCTTTCGCCGCCCTCT 62.459 66.667 0.00 0.00 36.60 3.69
756 762 2.067091 CTATAAGACGCCACCGCCGA 62.067 60.000 0.00 0.00 38.22 5.54
758 764 1.954651 GCTATAAGACGCCACCGCC 60.955 63.158 0.00 0.00 38.22 6.13
782 788 2.025359 GAAAACCAGCGGATCGAGCG 62.025 60.000 0.00 0.00 40.04 5.03
842 848 1.205655 CAAGCTCGATGAAGAGGTCCA 59.794 52.381 0.00 0.00 46.85 4.02
880 900 2.223377 CACCGCAAGAACCAACTACTTC 59.777 50.000 0.00 0.00 43.02 3.01
883 903 0.237498 GCACCGCAAGAACCAACTAC 59.763 55.000 0.00 0.00 43.02 2.73
884 904 0.107831 AGCACCGCAAGAACCAACTA 59.892 50.000 0.00 0.00 43.02 2.24
966 986 0.321564 CTCGGCCAGATTGGTCAACA 60.322 55.000 2.24 0.00 43.88 3.33
1363 1392 1.339631 CCAGTAAAACATCCGGGCTGA 60.340 52.381 4.63 0.00 0.00 4.26
1375 1407 8.739039 CACATGACAAATCCTTATCCAGTAAAA 58.261 33.333 0.00 0.00 0.00 1.52
1408 1440 3.881089 TGCAATCCACAATCAGATAGCAG 59.119 43.478 0.00 0.00 0.00 4.24
1409 1441 3.888583 TGCAATCCACAATCAGATAGCA 58.111 40.909 0.00 0.00 0.00 3.49
1481 1513 0.517316 GGCGTTCCACTTTGTGCTAG 59.483 55.000 0.00 0.00 31.34 3.42
1484 1516 0.031994 ATTGGCGTTCCACTTTGTGC 59.968 50.000 0.00 0.00 43.33 4.57
1485 1517 2.507339 AATTGGCGTTCCACTTTGTG 57.493 45.000 0.00 0.00 43.33 3.33
1486 1518 4.098807 AGTTTAATTGGCGTTCCACTTTGT 59.901 37.500 0.00 0.00 43.33 2.83
1487 1519 4.616953 AGTTTAATTGGCGTTCCACTTTG 58.383 39.130 0.00 0.00 43.33 2.77
1489 1521 5.708230 TGATAGTTTAATTGGCGTTCCACTT 59.292 36.000 0.00 0.00 43.33 3.16
1491 1523 5.106475 TGTGATAGTTTAATTGGCGTTCCAC 60.106 40.000 0.00 0.00 43.33 4.02
1492 1524 5.004448 TGTGATAGTTTAATTGGCGTTCCA 58.996 37.500 0.00 0.00 41.55 3.53
1494 1526 5.353123 TCCTGTGATAGTTTAATTGGCGTTC 59.647 40.000 0.00 0.00 0.00 3.95
1495 1527 5.250200 TCCTGTGATAGTTTAATTGGCGTT 58.750 37.500 0.00 0.00 0.00 4.84
1496 1528 4.839121 TCCTGTGATAGTTTAATTGGCGT 58.161 39.130 0.00 0.00 0.00 5.68
1497 1529 6.377327 AATCCTGTGATAGTTTAATTGGCG 57.623 37.500 0.00 0.00 0.00 5.69
1579 1614 9.147732 TGGACAGATAGAATCTAGAAATAGCAA 57.852 33.333 0.00 0.00 37.58 3.91
1583 1618 9.647918 ACAGTGGACAGATAGAATCTAGAAATA 57.352 33.333 0.00 0.00 37.58 1.40
1640 1675 0.028642 AAGGCCAGATATCCCCCAGT 60.029 55.000 5.01 0.00 0.00 4.00
1655 1690 2.159324 GGTGCATTCTAGCTGAAAAGGC 60.159 50.000 0.00 1.65 38.29 4.35
1706 1742 4.039603 GGCATGGCCCTATATTTTCTCT 57.960 45.455 8.35 0.00 44.06 3.10
1721 1757 4.530875 AGAGAAAATAACAGGAGGCATGG 58.469 43.478 0.00 0.00 0.00 3.66
1725 1761 3.625313 GCAGAGAGAAAATAACAGGAGGC 59.375 47.826 0.00 0.00 0.00 4.70
1726 1762 4.195416 GGCAGAGAGAAAATAACAGGAGG 58.805 47.826 0.00 0.00 0.00 4.30
1735 1771 8.302438 CAATAAGAAAAGTGGCAGAGAGAAAAT 58.698 33.333 0.00 0.00 0.00 1.82
1743 1779 5.472148 CATTGCAATAAGAAAAGTGGCAGA 58.528 37.500 12.53 0.00 0.00 4.26
1781 1817 6.567687 AGTAGACTAGATGATGATGGAACG 57.432 41.667 0.00 0.00 0.00 3.95
1847 1906 6.846505 TCTTCTGATATCCTTCTTACATGGGT 59.153 38.462 0.00 0.00 0.00 4.51
1888 1949 2.704725 AACAGTGCGCCATTAAACAG 57.295 45.000 4.18 0.00 0.00 3.16
2059 2120 4.130118 GCCGAATGAGGTAACATCAGAAT 58.870 43.478 0.00 0.00 41.41 2.40
2126 2187 3.077484 AGAGCACATACAACCTGCATT 57.923 42.857 0.00 0.00 33.06 3.56
2176 2237 5.687285 GCAATAAACAGCATACATAGCCAAC 59.313 40.000 0.00 0.00 0.00 3.77
2200 2261 3.403057 CCGACACGAACAGCCACG 61.403 66.667 0.00 0.00 0.00 4.94
2304 2365 5.567037 TTCTTCAAATGGTCTCTCTTCCA 57.433 39.130 0.00 0.00 38.14 3.53
2618 2679 8.347035 GCTTAAAGTGTTGTTGTCTATTACCAA 58.653 33.333 0.00 0.00 0.00 3.67
2649 2710 9.685276 AATAAGTAACAGAAACATGGATGATCA 57.315 29.630 0.00 0.00 0.00 2.92
2733 2794 0.107897 ACTCGCACGCCAATGGATTA 60.108 50.000 2.05 0.00 0.00 1.75
2881 2942 5.750352 AGACCGGTTACCTTTATCAAGAA 57.250 39.130 9.42 0.00 30.57 2.52
2981 3042 2.208431 GATCTCTGAGTCATTTGCCGG 58.792 52.381 0.00 0.00 0.00 6.13
3238 3299 9.838339 AAGATAACTGACTAAATTCCATACTGG 57.162 33.333 0.00 0.00 39.43 4.00
3326 3387 3.306502 CCGTCCTGTAGAACTTGCCTTTA 60.307 47.826 0.00 0.00 0.00 1.85
3366 3427 0.723414 CAACACTCAGCGCCATACAG 59.277 55.000 2.29 0.00 0.00 2.74
3396 3457 0.586319 AACTGTTGAACATGTCGCCG 59.414 50.000 0.00 0.00 0.00 6.46
3431 3492 3.557185 CCACACATCATCTCAACATACGG 59.443 47.826 0.00 0.00 0.00 4.02
3503 3565 2.912956 TCTCTTCAATTGGTGCTACCCT 59.087 45.455 5.42 0.00 37.50 4.34
3541 3603 2.057137 TATGCCCAAACCATCTCAGC 57.943 50.000 0.00 0.00 0.00 4.26
3696 3758 4.162320 CCCTGTCCATAGCTAGTTCTTTGA 59.838 45.833 0.00 0.00 0.00 2.69
3723 3785 2.025981 ACATGGATAGCAAGCTTCCACA 60.026 45.455 20.41 8.68 42.09 4.17
3748 3810 0.798776 CGCAACCAACTCATGACTCC 59.201 55.000 0.00 0.00 0.00 3.85
3752 3814 2.234661 AGATCTCGCAACCAACTCATGA 59.765 45.455 0.00 0.00 0.00 3.07
3834 3908 8.806146 AGCTGAATTCCATAGTAACAAAACAAT 58.194 29.630 2.27 0.00 0.00 2.71
3870 3944 8.650143 AAAGAAATTGACCAGGTTACATACAT 57.350 30.769 0.00 0.00 0.00 2.29
3895 3969 5.359576 GGGTCATGCATAAATCACCTTGTTA 59.640 40.000 0.00 0.00 0.00 2.41
3914 3988 1.217916 TGTCCAAAACAGGAGGGTCA 58.782 50.000 0.00 0.00 38.64 4.02
4140 4214 4.725490 ACAAGTGCCCTAAAAGTACATGT 58.275 39.130 2.69 2.69 0.00 3.21
4158 4232 6.925211 TGGAGTGATACTCTCAGTTAACAAG 58.075 40.000 8.61 5.08 44.46 3.16
4177 4251 8.806146 ACACAATTTATGAAAATTAGCTGGAGT 58.194 29.630 0.00 0.00 42.18 3.85
4191 4265 3.825585 TCCTGCAAGCACACAATTTATGA 59.174 39.130 0.00 0.00 0.00 2.15
4195 4269 3.181463 ACAATCCTGCAAGCACACAATTT 60.181 39.130 0.00 0.00 0.00 1.82
4328 4402 2.248835 CGCGACTCAAAAACCCCGT 61.249 57.895 0.00 0.00 0.00 5.28
4329 4403 2.554272 CGCGACTCAAAAACCCCG 59.446 61.111 0.00 0.00 0.00 5.73
4330 4404 2.254350 GCGCGACTCAAAAACCCC 59.746 61.111 12.10 0.00 0.00 4.95
4331 4405 2.127383 CGCGCGACTCAAAAACCC 60.127 61.111 28.94 0.00 0.00 4.11
4332 4406 1.438222 GTCGCGCGACTCAAAAACC 60.438 57.895 45.56 23.44 41.57 3.27
4333 4407 4.095355 GTCGCGCGACTCAAAAAC 57.905 55.556 45.56 24.68 41.57 2.43
4391 4465 1.716172 TCGCGACTCGAGTCATGAG 59.284 57.895 37.14 25.74 44.99 2.90
4392 4466 3.884900 TCGCGACTCGAGTCATGA 58.115 55.556 37.14 30.71 44.99 3.07
4399 4473 3.381733 CGACTAGTCGCGACTCGA 58.618 61.111 42.28 26.42 46.50 4.04
4408 4482 1.355066 GCCTGCAGTTGCGACTAGTC 61.355 60.000 13.81 13.18 45.83 2.59
4409 4483 1.374758 GCCTGCAGTTGCGACTAGT 60.375 57.895 13.81 0.00 45.83 2.57
4410 4484 1.079543 AGCCTGCAGTTGCGACTAG 60.080 57.895 13.81 1.26 45.83 2.57
4411 4485 1.079819 GAGCCTGCAGTTGCGACTA 60.080 57.895 13.81 0.00 45.83 2.59
4412 4486 2.358003 GAGCCTGCAGTTGCGACT 60.358 61.111 13.81 0.00 45.83 4.18
4413 4487 3.782244 CGAGCCTGCAGTTGCGAC 61.782 66.667 13.81 8.67 45.83 5.19
4414 4488 3.989787 TCGAGCCTGCAGTTGCGA 61.990 61.111 13.81 14.63 45.83 5.10
4415 4489 3.782244 GTCGAGCCTGCAGTTGCG 61.782 66.667 13.81 12.51 45.83 4.85
4416 4490 1.510480 AAAGTCGAGCCTGCAGTTGC 61.510 55.000 13.81 10.03 42.50 4.17
4417 4491 0.947244 AAAAGTCGAGCCTGCAGTTG 59.053 50.000 13.81 0.00 0.00 3.16
4418 4492 1.604278 GAAAAAGTCGAGCCTGCAGTT 59.396 47.619 13.81 0.00 0.00 3.16
4419 4493 1.230324 GAAAAAGTCGAGCCTGCAGT 58.770 50.000 13.81 0.00 0.00 4.40
4420 4494 0.519077 GGAAAAAGTCGAGCCTGCAG 59.481 55.000 6.78 6.78 0.00 4.41
4421 4495 0.179032 TGGAAAAAGTCGAGCCTGCA 60.179 50.000 0.00 0.00 0.00 4.41
4422 4496 0.951558 TTGGAAAAAGTCGAGCCTGC 59.048 50.000 0.00 0.00 0.00 4.85
4423 4497 2.222027 ACTTGGAAAAAGTCGAGCCTG 58.778 47.619 0.00 0.00 0.00 4.85
4424 4498 2.495084 GACTTGGAAAAAGTCGAGCCT 58.505 47.619 2.72 0.00 37.51 4.58
4425 4499 2.971430 GACTTGGAAAAAGTCGAGCC 57.029 50.000 2.72 0.00 37.51 4.70
4430 4504 2.483106 GGGTAGCGACTTGGAAAAAGTC 59.517 50.000 7.94 7.94 42.33 3.01
4431 4505 2.501261 GGGTAGCGACTTGGAAAAAGT 58.499 47.619 0.00 0.00 0.00 2.66
4432 4506 1.810755 GGGGTAGCGACTTGGAAAAAG 59.189 52.381 0.00 0.00 0.00 2.27
4433 4507 1.143277 TGGGGTAGCGACTTGGAAAAA 59.857 47.619 0.00 0.00 0.00 1.94
4434 4508 0.766131 TGGGGTAGCGACTTGGAAAA 59.234 50.000 0.00 0.00 0.00 2.29
4435 4509 0.323629 CTGGGGTAGCGACTTGGAAA 59.676 55.000 0.00 0.00 0.00 3.13
4436 4510 0.543410 TCTGGGGTAGCGACTTGGAA 60.543 55.000 0.00 0.00 0.00 3.53
4437 4511 0.543410 TTCTGGGGTAGCGACTTGGA 60.543 55.000 0.00 0.00 0.00 3.53
4438 4512 0.391263 GTTCTGGGGTAGCGACTTGG 60.391 60.000 0.00 0.00 0.00 3.61
4439 4513 0.736325 CGTTCTGGGGTAGCGACTTG 60.736 60.000 0.00 0.00 0.00 3.16
4440 4514 0.896940 TCGTTCTGGGGTAGCGACTT 60.897 55.000 0.00 0.00 0.00 3.01
4441 4515 1.303888 TCGTTCTGGGGTAGCGACT 60.304 57.895 0.00 0.00 0.00 4.18
4442 4516 1.153881 GTCGTTCTGGGGTAGCGAC 60.154 63.158 0.00 0.00 43.53 5.19
4443 4517 1.303888 AGTCGTTCTGGGGTAGCGA 60.304 57.895 0.00 0.00 0.00 4.93
4444 4518 1.139095 GAGTCGTTCTGGGGTAGCG 59.861 63.158 0.00 0.00 0.00 4.26
4445 4519 0.824759 ATGAGTCGTTCTGGGGTAGC 59.175 55.000 0.00 0.00 0.00 3.58
4446 4520 1.065701 CGATGAGTCGTTCTGGGGTAG 59.934 57.143 0.00 0.00 42.78 3.18
4447 4521 1.100510 CGATGAGTCGTTCTGGGGTA 58.899 55.000 0.00 0.00 42.78 3.69
4448 4522 1.605058 CCGATGAGTCGTTCTGGGGT 61.605 60.000 0.00 0.00 46.25 4.95
4449 4523 1.141881 CCGATGAGTCGTTCTGGGG 59.858 63.158 0.00 0.00 46.25 4.96
4450 4524 1.519455 GCCGATGAGTCGTTCTGGG 60.519 63.158 0.00 0.00 46.25 4.45
4451 4525 0.526524 GAGCCGATGAGTCGTTCTGG 60.527 60.000 0.00 0.00 46.25 3.86
4452 4526 0.171231 TGAGCCGATGAGTCGTTCTG 59.829 55.000 0.00 0.00 46.25 3.02
4453 4527 1.066303 GATGAGCCGATGAGTCGTTCT 59.934 52.381 0.00 0.00 46.25 3.01
4454 4528 1.482278 GATGAGCCGATGAGTCGTTC 58.518 55.000 0.00 0.00 46.25 3.95
4455 4529 0.248661 CGATGAGCCGATGAGTCGTT 60.249 55.000 0.00 0.00 46.25 3.85
4456 4530 1.095807 TCGATGAGCCGATGAGTCGT 61.096 55.000 0.00 0.00 46.25 4.34
4458 4532 0.665835 AGTCGATGAGCCGATGAGTC 59.334 55.000 0.00 0.00 40.91 3.36
4459 4533 0.665835 GAGTCGATGAGCCGATGAGT 59.334 55.000 0.00 0.00 40.91 3.41
4460 4534 0.385348 CGAGTCGATGAGCCGATGAG 60.385 60.000 6.73 0.00 40.91 2.90
4461 4535 0.814010 TCGAGTCGATGAGCCGATGA 60.814 55.000 12.09 0.00 40.91 2.92
4462 4536 0.029433 TTCGAGTCGATGAGCCGATG 59.971 55.000 17.34 0.00 40.91 3.84
4463 4537 0.738975 TTTCGAGTCGATGAGCCGAT 59.261 50.000 17.34 0.00 40.91 4.18
4464 4538 0.524414 TTTTCGAGTCGATGAGCCGA 59.476 50.000 17.34 0.00 35.23 5.54
4465 4539 0.640768 GTTTTCGAGTCGATGAGCCG 59.359 55.000 17.34 0.00 35.23 5.52
4466 4540 1.710013 TGTTTTCGAGTCGATGAGCC 58.290 50.000 17.34 3.87 35.23 4.70
4467 4541 2.470781 CGTTGTTTTCGAGTCGATGAGC 60.471 50.000 17.34 10.73 35.23 4.26
4468 4542 2.977829 TCGTTGTTTTCGAGTCGATGAG 59.022 45.455 17.34 4.43 35.23 2.90
4469 4543 3.002708 TCGTTGTTTTCGAGTCGATGA 57.997 42.857 17.34 5.52 35.23 2.92
4470 4544 3.972706 ATCGTTGTTTTCGAGTCGATG 57.027 42.857 17.34 0.00 40.57 3.84
4471 4545 4.985044 AAATCGTTGTTTTCGAGTCGAT 57.015 36.364 17.34 0.00 40.57 3.59
4472 4546 4.782252 AAAATCGTTGTTTTCGAGTCGA 57.218 36.364 12.09 12.09 40.57 4.20
4473 4547 4.837050 GGTAAAATCGTTGTTTTCGAGTCG 59.163 41.667 6.09 6.09 40.57 4.18
4474 4548 5.982324 AGGTAAAATCGTTGTTTTCGAGTC 58.018 37.500 0.00 0.00 40.57 3.36
4475 4549 5.524646 TGAGGTAAAATCGTTGTTTTCGAGT 59.475 36.000 0.00 0.00 40.57 4.18
4476 4550 5.981174 TGAGGTAAAATCGTTGTTTTCGAG 58.019 37.500 0.00 0.00 40.57 4.04
4477 4551 5.559417 GCTGAGGTAAAATCGTTGTTTTCGA 60.559 40.000 0.00 0.00 41.45 3.71
4478 4552 4.611366 GCTGAGGTAAAATCGTTGTTTTCG 59.389 41.667 0.00 0.00 33.62 3.46
4479 4553 4.611366 CGCTGAGGTAAAATCGTTGTTTTC 59.389 41.667 0.00 0.00 33.62 2.29
4480 4554 4.035909 ACGCTGAGGTAAAATCGTTGTTTT 59.964 37.500 0.00 0.00 35.60 2.43
4481 4555 3.562557 ACGCTGAGGTAAAATCGTTGTTT 59.437 39.130 0.00 0.00 0.00 2.83
4482 4556 3.135994 ACGCTGAGGTAAAATCGTTGTT 58.864 40.909 0.00 0.00 0.00 2.83
4483 4557 2.762745 ACGCTGAGGTAAAATCGTTGT 58.237 42.857 0.00 0.00 0.00 3.32
4484 4558 3.806316 AACGCTGAGGTAAAATCGTTG 57.194 42.857 0.00 0.00 38.49 4.10
4485 4559 4.563061 ACTAACGCTGAGGTAAAATCGTT 58.437 39.130 0.00 0.00 41.91 3.85
4486 4560 4.184079 ACTAACGCTGAGGTAAAATCGT 57.816 40.909 0.00 0.00 0.00 3.73
4487 4561 5.526010 AAACTAACGCTGAGGTAAAATCG 57.474 39.130 0.00 0.00 0.00 3.34
4488 4562 7.823149 TCTAAACTAACGCTGAGGTAAAATC 57.177 36.000 0.00 0.00 0.00 2.17
4545 4619 2.027561 TGGTTCCCAGTAGTTCATTCCG 60.028 50.000 0.00 0.00 0.00 4.30
4624 4698 3.234349 ACTGTGCAGAGTGCCAGT 58.766 55.556 16.85 7.68 44.29 4.00
4693 4767 3.083122 AGCGAGTAGTAAGGGACTGAA 57.917 47.619 0.00 0.00 40.86 3.02
4704 4778 6.973474 CAGTTTAAGCAGTATAAGCGAGTAGT 59.027 38.462 0.00 0.00 37.01 2.73
4705 4779 6.418226 CCAGTTTAAGCAGTATAAGCGAGTAG 59.582 42.308 0.00 0.00 37.01 2.57
4753 4827 1.702182 TTTGCTCAAGCCCAACATCA 58.298 45.000 0.00 0.00 41.18 3.07
4867 4941 4.641989 TGAGATAAGCTGGAAATTCAAGGC 59.358 41.667 0.00 0.00 0.00 4.35
4944 5018 3.729163 GCTTTAAAGTGATTCCTCAGCGC 60.729 47.826 16.38 0.00 30.18 5.92
4946 5020 5.338365 CATGCTTTAAAGTGATTCCTCAGC 58.662 41.667 16.38 0.00 30.18 4.26
5041 5121 7.875971 ACAAAAGCTCTTGGTATTTCTAACTG 58.124 34.615 4.51 0.00 0.00 3.16
5042 5122 7.939588 AGACAAAAGCTCTTGGTATTTCTAACT 59.060 33.333 4.51 0.00 0.00 2.24
5043 5123 8.017946 CAGACAAAAGCTCTTGGTATTTCTAAC 58.982 37.037 4.51 0.00 0.00 2.34
5044 5124 7.719633 ACAGACAAAAGCTCTTGGTATTTCTAA 59.280 33.333 4.51 0.00 0.00 2.10
5200 5295 9.988350 AATGACTAAAAGTTAAAGCATATCACG 57.012 29.630 0.00 0.00 0.00 4.35
5224 5319 0.872388 GCCGACGTCAACAAGGAAAT 59.128 50.000 17.16 0.00 0.00 2.17
5225 5320 0.462225 TGCCGACGTCAACAAGGAAA 60.462 50.000 17.16 0.00 0.00 3.13
5344 5439 6.179756 TGTTGAGATATGGTATGCAACAAGT 58.820 36.000 0.00 0.00 41.53 3.16
5375 5472 5.390567 GGCTGTACACTCGGTAGAAAAATTG 60.391 44.000 0.00 0.00 31.13 2.32
5422 5519 6.650427 ACAACCCTCCAATAAGTTTTCTTC 57.350 37.500 0.00 0.00 40.91 2.87
5471 5569 8.792633 ACTATAAACAAATAAAACAGCAGAGCA 58.207 29.630 0.00 0.00 0.00 4.26
5527 5625 1.945819 GCCATGAGCAAAGGAGTCGAA 60.946 52.381 0.00 0.00 42.97 3.71
5620 5719 1.067846 TCCACCTCACAAGATCGAACG 60.068 52.381 0.00 0.00 0.00 3.95
5633 5732 5.367060 AGGAACTTGGTATTCTATCCACCTC 59.633 44.000 0.00 0.00 27.25 3.85
5652 5751 5.045797 ACATGGTCCCTACTCTAAAAGGAAC 60.046 44.000 0.00 0.00 34.58 3.62
5707 5806 5.243507 TGGCCATTGTATTACCTGCAATATG 59.756 40.000 0.00 0.00 38.00 1.78
5708 5807 5.243730 GTGGCCATTGTATTACCTGCAATAT 59.756 40.000 9.72 0.00 38.00 1.28
5723 5822 2.296752 TCAACAGTTGATGTGGCCATTG 59.703 45.455 9.72 6.11 43.00 2.82
5724 5823 2.297033 GTCAACAGTTGATGTGGCCATT 59.703 45.455 19.04 0.00 43.00 3.16
6114 6213 3.799963 TGTAGCCATGCTATTTAACGTCG 59.200 43.478 0.00 0.00 43.30 5.12
6220 6320 3.418684 AAATTAGTTGCTCGTCCAGGT 57.581 42.857 0.00 0.00 0.00 4.00
6367 6475 2.960819 ACAGCTACTCATGTTTCGACC 58.039 47.619 0.00 0.00 0.00 4.79
6377 6485 1.080772 CACGCCGAACAGCTACTCA 60.081 57.895 0.00 0.00 0.00 3.41
6488 6596 1.268437 GCATCTTTCCTTCAGCGATGC 60.268 52.381 0.00 6.77 46.61 3.91
6543 6651 1.557371 CCCCCTTCTCTTCTCCAGAAC 59.443 57.143 0.00 0.00 0.00 3.01
6559 6667 2.158370 TCAGGTTTCTTCCTTTTCCCCC 60.158 50.000 0.00 0.00 35.37 5.40
6560 6668 3.238788 TCAGGTTTCTTCCTTTTCCCC 57.761 47.619 0.00 0.00 35.37 4.81
6753 6864 4.038763 ACAAGATCACTATTTATCCGCCGA 59.961 41.667 0.00 0.00 0.00 5.54
6754 6865 4.307432 ACAAGATCACTATTTATCCGCCG 58.693 43.478 0.00 0.00 0.00 6.46
6757 6868 5.928839 CCAGGACAAGATCACTATTTATCCG 59.071 44.000 0.00 0.00 0.00 4.18
6762 6873 6.725364 ACAATCCAGGACAAGATCACTATTT 58.275 36.000 0.00 0.00 0.00 1.40
6835 6948 1.268899 ACTCACTTGCAGCAAATCAGC 59.731 47.619 9.65 0.00 0.00 4.26
6868 6981 2.108157 TGCACGTGTGGTCTGTCC 59.892 61.111 18.38 0.00 0.00 4.02
6875 6988 3.896648 AAAAATAGAGTGCACGTGTGG 57.103 42.857 18.38 0.00 0.00 4.17
6931 7046 3.525199 ACTGAAAACCATAGCCTGATCCT 59.475 43.478 0.00 0.00 0.00 3.24
7022 7144 4.081420 ACAGTGCTATTCCAGAACAGTAGG 60.081 45.833 0.00 0.00 34.84 3.18
7024 7146 5.483685 AACAGTGCTATTCCAGAACAGTA 57.516 39.130 0.00 0.00 31.43 2.74
7025 7147 4.357918 AACAGTGCTATTCCAGAACAGT 57.642 40.909 0.00 0.00 34.04 3.55
7028 7150 4.575885 TGGTAACAGTGCTATTCCAGAAC 58.424 43.478 0.00 0.00 46.17 3.01
7065 7189 4.927049 AGATGACACATTCTTCCATTGGT 58.073 39.130 1.86 0.00 0.00 3.67
7069 7193 7.997223 ACATTCATAGATGACACATTCTTCCAT 59.003 33.333 0.00 0.00 36.36 3.41


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

AutoCloner maintained by Alex Coulton.