Multiple sequence alignment - TraesCS1D01G163300

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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 TraesCS1D01G163300 chr1D 100.000 7014 0 0 1 7014 233900878 233907891 0.000000e+00 12953.0
1 TraesCS1D01G163300 chr1D 92.073 164 13 0 3146 3309 408915727 408915890 1.520000e-56 231.0
2 TraesCS1D01G163300 chr1A 93.569 2208 91 18 3412 5587 313741512 313739324 0.000000e+00 3243.0
3 TraesCS1D01G163300 chr1A 93.405 1865 73 17 1 1852 313745098 313743271 0.000000e+00 2717.0
4 TraesCS1D01G163300 chr1A 97.051 1458 40 3 1948 3404 313743095 313741640 0.000000e+00 2451.0
5 TraesCS1D01G163300 chr1A 90.940 596 37 3 5719 6297 313739290 313738695 0.000000e+00 785.0
6 TraesCS1D01G163300 chr1A 94.103 390 17 5 6629 7014 313738423 313738036 7.840000e-164 588.0
7 TraesCS1D01G163300 chr1A 88.889 207 9 4 6295 6500 313738614 313738421 7.030000e-60 243.0
8 TraesCS1D01G163300 chr1A 98.077 52 1 0 1896 1947 313743192 313743141 2.690000e-14 91.6
9 TraesCS1D01G163300 chr1B 94.547 2109 76 15 3503 5587 368553894 368555987 0.000000e+00 3221.0
10 TraesCS1D01G163300 chr1B 96.334 1555 45 6 1948 3500 368551858 368553402 0.000000e+00 2545.0
11 TraesCS1D01G163300 chr1B 95.248 1389 51 13 1 1385 368549862 368551239 0.000000e+00 2185.0
12 TraesCS1D01G163300 chr1B 91.299 747 34 16 6295 7014 368556834 368557576 0.000000e+00 990.0
13 TraesCS1D01G163300 chr1B 90.685 569 36 3 5719 6270 368556021 368556589 0.000000e+00 741.0
14 TraesCS1D01G163300 chr1B 90.566 371 16 6 1375 1732 368551264 368551628 2.290000e-129 473.0
15 TraesCS1D01G163300 chr1B 83.509 285 43 4 4845 5127 331137827 331137545 5.400000e-66 263.0
16 TraesCS1D01G163300 chr1B 81.301 123 7 6 1841 1947 368551690 368551812 1.250000e-12 86.1
17 TraesCS1D01G163300 chr1B 100.000 30 0 0 6268 6297 368556702 368556731 1.000000e-03 56.5
18 TraesCS1D01G163300 chr2D 92.073 164 13 0 3146 3309 650785741 650785904 1.520000e-56 231.0
19 TraesCS1D01G163300 chr2D 88.021 192 18 2 500 691 234337019 234337205 9.160000e-54 222.0
20 TraesCS1D01G163300 chr2D 93.478 46 2 1 1953 1998 22611607 22611563 4.540000e-07 67.6
21 TraesCS1D01G163300 chr2D 94.595 37 1 1 1849 1885 394780819 394780854 1.000000e-03 56.5
22 TraesCS1D01G163300 chr3B 88.950 181 15 2 500 680 5769879 5770054 1.180000e-52 219.0
23 TraesCS1D01G163300 chr3B 90.244 164 16 0 3146 3309 88150383 88150546 1.530000e-51 215.0
24 TraesCS1D01G163300 chr2A 88.950 181 15 2 500 680 573418819 573418644 1.180000e-52 219.0
25 TraesCS1D01G163300 chr2A 85.417 192 23 2 500 691 98887760 98887946 2.000000e-45 195.0
26 TraesCS1D01G163300 chr2A 86.614 127 16 1 565 691 98888646 98888771 9.490000e-29 139.0
27 TraesCS1D01G163300 chr2A 88.000 50 5 1 1836 1885 532848679 532848727 2.730000e-04 58.4
28 TraesCS1D01G163300 chr5D 87.500 192 19 2 500 691 58253370 58253556 4.260000e-52 217.0
29 TraesCS1D01G163300 chr5D 90.780 141 13 0 500 640 17818031 17818171 9.290000e-44 189.0
30 TraesCS1D01G163300 chr5D 94.595 37 2 0 1849 1885 111954784 111954820 2.730000e-04 58.4
31 TraesCS1D01G163300 chr6B 87.500 72 8 1 1948 2018 655254016 655254087 1.620000e-11 82.4
32 TraesCS1D01G163300 chr4B 97.143 35 1 0 1851 1885 96274748 96274782 7.600000e-05 60.2
33 TraesCS1D01G163300 chr4B 92.308 39 2 1 1841 1878 13392639 13392677 4.000000e-03 54.7
34 TraesCS1D01G163300 chr6D 94.595 37 2 0 1951 1987 174399627 174399591 2.730000e-04 58.4
35 TraesCS1D01G163300 chr4D 97.059 34 1 0 1852 1885 480860366 480860399 2.730000e-04 58.4
36 TraesCS1D01G163300 chr4D 97.059 34 1 0 1852 1885 480869157 480869190 2.730000e-04 58.4
37 TraesCS1D01G163300 chr4D 94.444 36 2 0 1849 1884 65580549 65580584 1.000000e-03 56.5
38 TraesCS1D01G163300 chr2B 84.746 59 8 1 1890 1947 176413058 176413116 2.730000e-04 58.4
39 TraesCS1D01G163300 chr5A 94.595 37 1 1 1851 1886 640728316 640728280 1.000000e-03 56.5


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 TraesCS1D01G163300 chr1D 233900878 233907891 7013 False 12953.000000 12953 100.000000 1 7014 1 chr1D.!!$F1 7013
1 TraesCS1D01G163300 chr1A 313738036 313745098 7062 True 1445.514286 3243 93.719143 1 7014 7 chr1A.!!$R1 7013
2 TraesCS1D01G163300 chr1B 368549862 368557576 7714 False 1287.200000 3221 92.497500 1 7014 8 chr1B.!!$F1 7013

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
71 72 0.105709 CCCTCTTCCTCCTCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30 F
903 906 0.685097 TCCTCACTATATTGGGCCGC 59.315 55.000 0.00 0.00 0.00 6.53 F
2587 2729 0.393402 TGGCTAACTGGCAGCAGATG 60.393 55.000 15.89 1.84 46.76 2.90 F
3381 3523 1.485895 GGAAAGAGCTCTGCCATCTCT 59.514 52.381 24.01 3.07 38.72 3.10 F
4400 5156 0.530288 GTGCCGGCCAAATGTACATT 59.470 50.000 26.77 15.47 0.00 2.71 F
5055 5811 0.392706 TCAGAGAAGGCAGCGTCAAA 59.607 50.000 0.00 0.00 0.00 2.69 F
5548 6323 0.320247 CTCGGGATGCATAGTGCTCC 60.320 60.000 0.00 0.00 45.31 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 1976 0.174162 AAGCAAATTGCCATCCTCGC 59.826 50.000 15.04 0.00 46.52 5.03 R
2779 2921 2.057137 TGGCAACTTGATATGGCCTC 57.943 50.000 3.32 0.00 44.85 4.70 R
3853 4604 0.178921 TTCTCTGTCAGTCCCTGGCT 60.179 55.000 0.00 0.00 36.97 4.75 R
4450 5206 1.760086 CTCGACTGGGCTCCCTGAT 60.760 63.158 17.30 3.34 38.26 2.90 R
5537 6312 0.249657 CGGAGAAGGGAGCACTATGC 60.250 60.000 0.00 0.00 45.46 3.14 R
6001 6778 0.798776 GTGATTGTCAAGGTGCTCCG 59.201 55.000 0.00 0.00 39.05 4.63 R
6467 7481 1.185315 CATGGGTGTGCTTTTAGGGG 58.815 55.000 0.00 0.00 0.00 4.79 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
23 24 1.397672 TTGCTGTAGTGGCAAGCAAA 58.602 45.000 19.04 5.95 43.50 3.68
71 72 0.105709 CCCTCTTCCTCCTCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
892 895 1.206371 GCCTACGGCTTTTCCTCACTA 59.794 52.381 0.00 0.00 46.69 2.74
894 897 3.069158 GCCTACGGCTTTTCCTCACTATA 59.931 47.826 0.00 0.00 46.69 1.31
902 905 3.485463 TTTCCTCACTATATTGGGCCG 57.515 47.619 0.00 0.00 0.00 6.13
903 906 0.685097 TCCTCACTATATTGGGCCGC 59.315 55.000 0.00 0.00 0.00 6.53
937 940 3.713826 TTCGAAATTCTAGGCCCAACT 57.286 42.857 0.00 0.00 0.00 3.16
958 970 2.843545 GTCCTGGGGTTCAAGGCA 59.156 61.111 0.00 0.00 0.00 4.75
1008 1021 1.269448 GCTTTTGTTTCCATGGAGCGA 59.731 47.619 15.53 9.23 0.00 4.93
1191 1204 2.367202 CCGGGGCACTAGTCACCAT 61.367 63.158 12.46 0.00 0.00 3.55
1199 1212 2.541999 GCACTAGTCACCATCGTAGCTC 60.542 54.545 0.00 0.00 0.00 4.09
1220 1233 3.288484 CGCTGGTCTCAGTGGCTA 58.712 61.111 0.00 0.00 45.14 3.93
1226 1239 1.291132 GGTCTCAGTGGCTATTTCGC 58.709 55.000 0.00 0.00 0.00 4.70
1254 1267 3.842923 AGGTCATCGGCGAGCTGG 61.843 66.667 17.22 5.00 42.01 4.85
1298 1311 2.121506 AAGGACAAGGGGAGGGCA 60.122 61.111 0.00 0.00 0.00 5.36
1460 1508 6.601332 AGAGAGAGTTTTGTTCCAAACCATA 58.399 36.000 0.00 0.00 0.00 2.74
1467 1515 5.389859 TTTGTTCCAAACCATATGCAGAG 57.610 39.130 0.00 0.00 0.00 3.35
1650 1711 2.868583 CGATTAGTTCTGATGGCACTGG 59.131 50.000 0.00 0.00 0.00 4.00
1714 1775 7.557358 TCCACTATGCATGTGAGTTTTTGATAT 59.443 33.333 22.76 0.00 37.60 1.63
1746 1807 2.821969 AGAATCTGGACATGTTTGGTGC 59.178 45.455 0.00 0.00 0.00 5.01
1761 1822 8.649841 CATGTTTGGTGCAGTTTTCTTATTATG 58.350 33.333 0.00 0.00 0.00 1.90
1795 1856 7.707624 TTTCCATCAAAAATAGTGAGCATCT 57.292 32.000 0.00 0.00 34.92 2.90
1796 1857 7.707624 TTCCATCAAAAATAGTGAGCATCTT 57.292 32.000 0.00 0.00 34.92 2.40
1797 1858 7.092137 TCCATCAAAAATAGTGAGCATCTTG 57.908 36.000 0.00 0.00 34.92 3.02
1798 1859 6.095860 TCCATCAAAAATAGTGAGCATCTTGG 59.904 38.462 0.00 0.00 34.92 3.61
1799 1860 5.902613 TCAAAAATAGTGAGCATCTTGGG 57.097 39.130 0.00 0.00 34.92 4.12
1800 1861 5.569355 TCAAAAATAGTGAGCATCTTGGGA 58.431 37.500 0.00 0.00 34.92 4.37
1801 1862 5.649395 TCAAAAATAGTGAGCATCTTGGGAG 59.351 40.000 0.00 0.00 34.92 4.30
1802 1863 3.853355 AATAGTGAGCATCTTGGGAGG 57.147 47.619 0.00 0.00 34.92 4.30
1815 1876 2.337359 TGGGAGGCAGGTACTAAACT 57.663 50.000 0.00 0.00 36.02 2.66
1821 1882 4.504340 GGAGGCAGGTACTAAACTTTGTCA 60.504 45.833 0.00 0.00 36.02 3.58
1828 1889 8.347035 GCAGGTACTAAACTTTGTCATGTTTAA 58.653 33.333 10.75 0.00 37.92 1.52
1874 1958 6.034898 CGTCAGATTTTTAACCATGGCAAATC 59.965 38.462 21.12 21.12 35.11 2.17
1878 1962 7.278424 CAGATTTTTAACCATGGCAAATCGAAT 59.722 33.333 21.79 15.03 38.39 3.34
2031 2172 6.686630 TGTAGCGAAATCCAAAATGATTTGT 58.313 32.000 3.91 0.00 43.23 2.83
2195 2336 6.094048 GGAGTGTGATAGTTGTAACAATGCAT 59.906 38.462 0.00 0.00 30.71 3.96
2450 2591 4.642437 TGTTAAAGCCTCAATGTGTGAACA 59.358 37.500 0.00 0.00 35.22 3.18
2586 2728 1.993653 TGGCTAACTGGCAGCAGAT 59.006 52.632 15.89 0.93 46.76 2.90
2587 2729 0.393402 TGGCTAACTGGCAGCAGATG 60.393 55.000 15.89 1.84 46.76 2.90
2650 2792 4.222336 AGGTAGAGGAATGACATCTCCAG 58.778 47.826 14.96 0.00 40.27 3.86
2710 2852 2.684881 CCTCTTGCTGCGGTATGATTTT 59.315 45.455 0.00 0.00 0.00 1.82
2779 2921 6.995511 TCCTGTTGTCCTATTTATTTTCGG 57.004 37.500 0.00 0.00 0.00 4.30
3081 3223 2.224606 CCTGCAGATGTTGTGTTCTGT 58.775 47.619 17.39 0.00 41.16 3.41
3227 3369 3.072476 AGCCTAACTTCTACAAGGTGCAA 59.928 43.478 0.00 0.00 33.37 4.08
3232 3374 2.637872 ACTTCTACAAGGTGCAAGGCTA 59.362 45.455 0.00 0.00 33.37 3.93
3235 3377 2.028112 TCTACAAGGTGCAAGGCTACAG 60.028 50.000 0.00 0.00 0.00 2.74
3246 3388 4.202315 TGCAAGGCTACAGACTCTAAACAA 60.202 41.667 0.00 0.00 29.30 2.83
3381 3523 1.485895 GGAAAGAGCTCTGCCATCTCT 59.514 52.381 24.01 3.07 38.72 3.10
3390 3532 1.704628 TCTGCCATCTCTGGTCCAAAA 59.295 47.619 0.00 0.00 45.10 2.44
3391 3533 2.108075 TCTGCCATCTCTGGTCCAAAAA 59.892 45.455 0.00 0.00 45.10 1.94
3436 3698 9.950680 ATATTTTCATACGAGCTTACCATTTTG 57.049 29.630 0.00 0.00 0.00 2.44
3522 4272 7.179694 ACAAGTATTCTAAGTACTGTTAGGCCA 59.820 37.037 5.01 0.00 32.94 5.36
3545 4295 3.960755 GGAACTAATGGGCTAAAATGGCT 59.039 43.478 0.00 0.00 0.00 4.75
3573 4323 5.795972 CAGGATCTCATTCAGCACTATGAT 58.204 41.667 0.00 0.00 30.91 2.45
3682 4432 6.613755 TTTCGTGGAAAGAGGAAACTTTAG 57.386 37.500 0.00 0.00 44.43 1.85
3684 4434 4.065789 CGTGGAAAGAGGAAACTTTAGCT 58.934 43.478 0.00 0.00 44.43 3.32
3701 4452 8.534954 ACTTTAGCTCAGGTATATGTGACTTA 57.465 34.615 0.00 0.00 0.00 2.24
3745 4496 6.426937 ACGTACATGGGTATTGCTTTGATATC 59.573 38.462 0.00 0.00 0.00 1.63
3784 4535 9.453572 AATAAGCATTCTTTGATCTTGTACAGA 57.546 29.630 0.00 0.00 32.98 3.41
3899 4650 2.812591 GGTATTCTGCAGCTGATGATGG 59.187 50.000 20.43 0.00 0.00 3.51
3935 4686 2.703536 TGGAGCAGGTTTGTCTTCTACA 59.296 45.455 0.00 0.00 35.88 2.74
4035 4786 8.547967 TGCGTCTTATTATTGATTTATCCTCC 57.452 34.615 0.00 0.00 0.00 4.30
4058 4809 9.499479 CTCCGACCTTTAGATATTAGTACACTA 57.501 37.037 0.00 0.00 0.00 2.74
4076 4827 3.059868 CACTACTTAAGCACACGGTGTTG 60.060 47.826 11.82 8.53 35.75 3.33
4116 4868 9.539194 AAACTTGATAAGATCCAGGAAAAAGAT 57.461 29.630 0.00 0.00 0.00 2.40
4166 4922 8.870160 TTGAGAAAATGTGTGGAATGTTTTAG 57.130 30.769 0.00 0.00 0.00 1.85
4168 4924 8.134895 TGAGAAAATGTGTGGAATGTTTTAGAC 58.865 33.333 0.00 0.00 0.00 2.59
4173 4929 5.197451 TGTGTGGAATGTTTTAGACCTTGT 58.803 37.500 0.00 0.00 0.00 3.16
4192 4948 6.106673 CCTTGTTATGTCAAGTAGGTACCTG 58.893 44.000 25.33 8.68 42.01 4.00
4199 4955 6.921486 TGTCAAGTAGGTACCTGTAAATCA 57.079 37.500 25.33 13.43 0.00 2.57
4216 4972 9.634163 CTGTAAATCACACTACATTACACTGTA 57.366 33.333 0.00 0.00 34.02 2.74
4239 4995 4.350816 AGGGTTAGTATAGAATGCATGGCA 59.649 41.667 0.00 0.00 44.86 4.92
4400 5156 0.530288 GTGCCGGCCAAATGTACATT 59.470 50.000 26.77 15.47 0.00 2.71
4514 5270 3.969976 TCCCATCCTTCCTCTCTTGTATG 59.030 47.826 0.00 0.00 0.00 2.39
4515 5271 3.713764 CCCATCCTTCCTCTCTTGTATGT 59.286 47.826 0.00 0.00 0.00 2.29
4516 5272 4.444022 CCCATCCTTCCTCTCTTGTATGTG 60.444 50.000 0.00 0.00 0.00 3.21
4517 5273 4.163078 CCATCCTTCCTCTCTTGTATGTGT 59.837 45.833 0.00 0.00 0.00 3.72
4518 5274 5.363868 CCATCCTTCCTCTCTTGTATGTGTA 59.636 44.000 0.00 0.00 0.00 2.90
4519 5275 6.042552 CCATCCTTCCTCTCTTGTATGTGTAT 59.957 42.308 0.00 0.00 0.00 2.29
4520 5276 6.716934 TCCTTCCTCTCTTGTATGTGTATC 57.283 41.667 0.00 0.00 0.00 2.24
4521 5277 6.194967 TCCTTCCTCTCTTGTATGTGTATCA 58.805 40.000 0.00 0.00 0.00 2.15
4522 5278 6.322456 TCCTTCCTCTCTTGTATGTGTATCAG 59.678 42.308 0.00 0.00 0.00 2.90
4525 5281 5.952347 TCCTCTCTTGTATGTGTATCAGTGT 59.048 40.000 0.00 0.00 0.00 3.55
4538 5294 7.607250 TGTGTATCAGTGTATGTGTGACATAA 58.393 34.615 0.00 0.00 42.15 1.90
4741 5497 1.005037 TAGCTGTCTTGGTGCCGTG 60.005 57.895 0.00 0.00 0.00 4.94
4783 5539 2.143122 TCCGAAGAGAATTGTGTGCAC 58.857 47.619 10.75 10.75 0.00 4.57
4790 5546 2.020720 AGAATTGTGTGCACGTTTCCA 58.979 42.857 13.13 0.61 0.00 3.53
4862 5618 5.374071 TCCCTCCCGAAATTTTCTAATAGC 58.626 41.667 7.50 0.00 0.00 2.97
4962 5718 8.782144 TGGGAAATTGTTTTTCAGAAATAATGC 58.218 29.630 0.00 0.00 0.00 3.56
5015 5771 6.985188 TGAGCTGTAGATCACAAATTAACC 57.015 37.500 0.00 0.00 35.30 2.85
5050 5806 1.850377 CTACATCAGAGAAGGCAGCG 58.150 55.000 0.00 0.00 0.00 5.18
5055 5811 0.392706 TCAGAGAAGGCAGCGTCAAA 59.607 50.000 0.00 0.00 0.00 2.69
5075 5831 8.223769 CGTCAAAGATCAATAGGTATGTTATGC 58.776 37.037 0.00 0.00 0.00 3.14
5096 5853 6.321848 TGCATTATTGAATGTGGCTATCTG 57.678 37.500 0.08 0.00 43.82 2.90
5191 5948 4.124851 AGGAACTTGCAGTTATAGACGG 57.875 45.455 2.17 0.00 38.80 4.79
5224 5981 3.929955 TCCCATCACAGATGCATTACA 57.070 42.857 0.00 0.00 0.00 2.41
5299 6056 2.570302 AGGTTAGGGCGTTCATGTTACT 59.430 45.455 0.00 0.00 0.00 2.24
5300 6057 2.934553 GGTTAGGGCGTTCATGTTACTC 59.065 50.000 0.00 0.00 0.00 2.59
5301 6058 3.592059 GTTAGGGCGTTCATGTTACTCA 58.408 45.455 0.00 0.00 0.00 3.41
5338 6095 1.615384 GCTCCAAATTCTCCTGGCACT 60.615 52.381 0.00 0.00 32.33 4.40
5339 6096 2.363683 CTCCAAATTCTCCTGGCACTC 58.636 52.381 0.00 0.00 32.33 3.51
5350 6107 2.023673 CCTGGCACTCACTGTTGAAAA 58.976 47.619 0.00 0.00 0.00 2.29
5357 6114 5.858581 GGCACTCACTGTTGAAAAATATGTC 59.141 40.000 0.00 0.00 0.00 3.06
5360 6117 7.520453 GCACTCACTGTTGAAAAATATGTCTCA 60.520 37.037 0.00 0.00 0.00 3.27
5470 6229 7.013655 GCATCAATTATGGTAGTCACCTCAATT 59.986 37.037 0.00 0.00 45.98 2.32
5483 6242 4.507756 TCACCTCAATTATCGCTCAAATCG 59.492 41.667 0.00 0.00 0.00 3.34
5493 6252 1.654105 CGCTCAAATCGCTAACTCGTT 59.346 47.619 0.00 0.00 0.00 3.85
5509 6268 8.870879 GCTAACTCGTTTACTGAGAAATACAAT 58.129 33.333 0.00 0.00 36.93 2.71
5537 6312 6.051717 AGAAATGTACTTTGATCTCGGGATG 58.948 40.000 0.20 0.00 31.46 3.51
5541 6316 4.343814 TGTACTTTGATCTCGGGATGCATA 59.656 41.667 0.20 0.00 31.46 3.14
5548 6323 0.320247 CTCGGGATGCATAGTGCTCC 60.320 60.000 0.00 0.00 45.31 4.70
5552 6327 1.889545 GGATGCATAGTGCTCCCTTC 58.110 55.000 0.00 0.00 45.31 3.46
5587 6362 6.989169 CAGTAGTCAAATTATCAGCTAGGCTT 59.011 38.462 0.00 0.00 36.40 4.35
5588 6363 7.497249 CAGTAGTCAAATTATCAGCTAGGCTTT 59.503 37.037 0.00 0.00 36.40 3.51
5589 6364 8.705594 AGTAGTCAAATTATCAGCTAGGCTTTA 58.294 33.333 0.00 0.00 36.40 1.85
5590 6365 7.793927 AGTCAAATTATCAGCTAGGCTTTAC 57.206 36.000 0.00 0.00 36.40 2.01
5591 6366 7.338710 AGTCAAATTATCAGCTAGGCTTTACA 58.661 34.615 0.00 0.00 36.40 2.41
5592 6367 7.829211 AGTCAAATTATCAGCTAGGCTTTACAA 59.171 33.333 0.00 0.00 36.40 2.41
5593 6368 8.458843 GTCAAATTATCAGCTAGGCTTTACAAA 58.541 33.333 0.00 0.00 36.40 2.83
5594 6369 8.677300 TCAAATTATCAGCTAGGCTTTACAAAG 58.323 33.333 0.00 0.00 36.40 2.77
5595 6370 8.677300 CAAATTATCAGCTAGGCTTTACAAAGA 58.323 33.333 5.89 0.00 36.40 2.52
5596 6371 8.986929 AATTATCAGCTAGGCTTTACAAAGAT 57.013 30.769 5.89 0.00 36.40 2.40
5598 6373 9.717942 ATTATCAGCTAGGCTTTACAAAGATAG 57.282 33.333 5.89 7.65 36.40 2.08
5599 6374 5.918608 TCAGCTAGGCTTTACAAAGATAGG 58.081 41.667 5.89 0.00 36.40 2.57
5636 6411 6.906157 ATCACAATTTTGGACTTCATCACT 57.094 33.333 0.00 0.00 0.00 3.41
5637 6412 6.713762 TCACAATTTTGGACTTCATCACTT 57.286 33.333 0.00 0.00 0.00 3.16
5638 6413 7.815840 TCACAATTTTGGACTTCATCACTTA 57.184 32.000 0.00 0.00 0.00 2.24
5639 6414 8.231692 TCACAATTTTGGACTTCATCACTTAA 57.768 30.769 0.00 0.00 0.00 1.85
5640 6415 8.134895 TCACAATTTTGGACTTCATCACTTAAC 58.865 33.333 0.00 0.00 0.00 2.01
5641 6416 8.137437 CACAATTTTGGACTTCATCACTTAACT 58.863 33.333 0.00 0.00 0.00 2.24
5642 6417 8.695456 ACAATTTTGGACTTCATCACTTAACTT 58.305 29.630 0.00 0.00 0.00 2.66
5643 6418 8.971321 CAATTTTGGACTTCATCACTTAACTTG 58.029 33.333 0.00 0.00 0.00 3.16
5644 6419 7.639113 TTTTGGACTTCATCACTTAACTTGT 57.361 32.000 0.00 0.00 0.00 3.16
5645 6420 6.861065 TTGGACTTCATCACTTAACTTGTC 57.139 37.500 0.00 0.00 0.00 3.18
5646 6421 5.924356 TGGACTTCATCACTTAACTTGTCA 58.076 37.500 0.00 0.00 0.00 3.58
5647 6422 6.533730 TGGACTTCATCACTTAACTTGTCAT 58.466 36.000 0.00 0.00 0.00 3.06
5648 6423 6.427853 TGGACTTCATCACTTAACTTGTCATG 59.572 38.462 0.00 0.00 0.00 3.07
5649 6424 6.650807 GGACTTCATCACTTAACTTGTCATGA 59.349 38.462 0.00 0.00 0.00 3.07
5650 6425 7.148507 GGACTTCATCACTTAACTTGTCATGAG 60.149 40.741 0.00 0.00 0.00 2.90
5651 6426 7.445121 ACTTCATCACTTAACTTGTCATGAGA 58.555 34.615 0.00 0.00 0.00 3.27
5652 6427 7.601886 ACTTCATCACTTAACTTGTCATGAGAG 59.398 37.037 0.00 0.00 0.00 3.20
5653 6428 6.401394 TCATCACTTAACTTGTCATGAGAGG 58.599 40.000 0.00 0.00 0.00 3.69
5654 6429 6.211384 TCATCACTTAACTTGTCATGAGAGGA 59.789 38.462 9.08 0.00 0.00 3.71
5655 6430 6.419484 TCACTTAACTTGTCATGAGAGGAA 57.581 37.500 9.08 3.08 0.00 3.36
5656 6431 6.459066 TCACTTAACTTGTCATGAGAGGAAG 58.541 40.000 9.08 12.82 0.00 3.46
5657 6432 5.121454 CACTTAACTTGTCATGAGAGGAAGC 59.879 44.000 9.08 0.00 0.00 3.86
5658 6433 2.777832 ACTTGTCATGAGAGGAAGCC 57.222 50.000 9.08 0.00 0.00 4.35
5659 6434 2.264455 ACTTGTCATGAGAGGAAGCCT 58.736 47.619 9.08 0.00 36.03 4.58
5669 6444 2.869101 GAGGAAGCCTCTGGAAACTT 57.131 50.000 6.23 0.00 46.41 2.66
5670 6445 2.431454 GAGGAAGCCTCTGGAAACTTG 58.569 52.381 6.23 0.00 46.41 3.16
5671 6446 1.777272 AGGAAGCCTCTGGAAACTTGT 59.223 47.619 0.00 0.00 0.00 3.16
5672 6447 2.175715 AGGAAGCCTCTGGAAACTTGTT 59.824 45.455 0.00 0.00 0.00 2.83
5673 6448 2.959030 GGAAGCCTCTGGAAACTTGTTT 59.041 45.455 0.00 0.00 0.00 2.83
5674 6449 3.243535 GGAAGCCTCTGGAAACTTGTTTG 60.244 47.826 3.27 0.00 0.00 2.93
5675 6450 1.683385 AGCCTCTGGAAACTTGTTTGC 59.317 47.619 10.15 10.15 0.00 3.68
5676 6451 1.683385 GCCTCTGGAAACTTGTTTGCT 59.317 47.619 16.31 0.00 0.00 3.91
5677 6452 2.287849 GCCTCTGGAAACTTGTTTGCTC 60.288 50.000 16.31 0.00 0.00 4.26
5678 6453 2.294512 CCTCTGGAAACTTGTTTGCTCC 59.705 50.000 16.31 7.34 0.00 4.70
5679 6454 2.294512 CTCTGGAAACTTGTTTGCTCCC 59.705 50.000 16.31 6.93 0.00 4.30
5680 6455 2.091885 TCTGGAAACTTGTTTGCTCCCT 60.092 45.455 16.31 0.00 0.00 4.20
5681 6456 3.137544 TCTGGAAACTTGTTTGCTCCCTA 59.862 43.478 16.31 0.00 0.00 3.53
5682 6457 3.486383 TGGAAACTTGTTTGCTCCCTAG 58.514 45.455 16.31 0.00 0.00 3.02
5683 6458 3.137544 TGGAAACTTGTTTGCTCCCTAGA 59.862 43.478 16.31 0.00 0.00 2.43
5684 6459 4.202567 TGGAAACTTGTTTGCTCCCTAGAT 60.203 41.667 16.31 0.00 0.00 1.98
5685 6460 5.013704 TGGAAACTTGTTTGCTCCCTAGATA 59.986 40.000 16.31 0.00 0.00 1.98
5686 6461 5.944007 GGAAACTTGTTTGCTCCCTAGATAA 59.056 40.000 9.87 0.00 0.00 1.75
5687 6462 6.433093 GGAAACTTGTTTGCTCCCTAGATAAA 59.567 38.462 9.87 0.00 0.00 1.40
5688 6463 6.819397 AACTTGTTTGCTCCCTAGATAAAC 57.181 37.500 0.00 0.00 34.50 2.01
5689 6464 4.935808 ACTTGTTTGCTCCCTAGATAAACG 59.064 41.667 0.00 0.00 35.64 3.60
5690 6465 3.869065 TGTTTGCTCCCTAGATAAACGG 58.131 45.455 0.00 0.00 35.64 4.44
5691 6466 2.612672 GTTTGCTCCCTAGATAAACGGC 59.387 50.000 0.00 0.00 0.00 5.68
5692 6467 1.789523 TGCTCCCTAGATAAACGGCT 58.210 50.000 0.00 0.00 0.00 5.52
5693 6468 2.953453 TGCTCCCTAGATAAACGGCTA 58.047 47.619 0.00 0.00 0.00 3.93
5694 6469 3.302161 TGCTCCCTAGATAAACGGCTAA 58.698 45.455 0.00 0.00 0.00 3.09
5695 6470 3.707611 TGCTCCCTAGATAAACGGCTAAA 59.292 43.478 0.00 0.00 0.00 1.85
5696 6471 4.347000 TGCTCCCTAGATAAACGGCTAAAT 59.653 41.667 0.00 0.00 0.00 1.40
5697 6472 5.163237 TGCTCCCTAGATAAACGGCTAAATT 60.163 40.000 0.00 0.00 0.00 1.82
5698 6473 5.408909 GCTCCCTAGATAAACGGCTAAATTC 59.591 44.000 0.00 0.00 0.00 2.17
5699 6474 6.488769 TCCCTAGATAAACGGCTAAATTCA 57.511 37.500 0.00 0.00 0.00 2.57
5700 6475 7.074653 TCCCTAGATAAACGGCTAAATTCAT 57.925 36.000 0.00 0.00 0.00 2.57
5701 6476 6.934645 TCCCTAGATAAACGGCTAAATTCATG 59.065 38.462 0.00 0.00 0.00 3.07
5702 6477 6.348540 CCCTAGATAAACGGCTAAATTCATGC 60.349 42.308 0.00 0.00 0.00 4.06
5703 6478 6.428159 CCTAGATAAACGGCTAAATTCATGCT 59.572 38.462 0.00 0.00 0.00 3.79
5704 6479 7.602644 CCTAGATAAACGGCTAAATTCATGCTA 59.397 37.037 0.00 0.00 0.00 3.49
5705 6480 7.801716 AGATAAACGGCTAAATTCATGCTAA 57.198 32.000 0.00 0.00 0.00 3.09
5706 6481 7.865707 AGATAAACGGCTAAATTCATGCTAAG 58.134 34.615 0.00 0.00 0.00 2.18
5707 6482 7.715249 AGATAAACGGCTAAATTCATGCTAAGA 59.285 33.333 0.00 0.00 0.00 2.10
5708 6483 6.509418 AAACGGCTAAATTCATGCTAAGAA 57.491 33.333 0.00 0.00 0.00 2.52
5709 6484 5.741388 ACGGCTAAATTCATGCTAAGAAG 57.259 39.130 0.00 0.00 0.00 2.85
5710 6485 5.186198 ACGGCTAAATTCATGCTAAGAAGT 58.814 37.500 0.00 0.00 0.00 3.01
5711 6486 5.065218 ACGGCTAAATTCATGCTAAGAAGTG 59.935 40.000 0.00 0.00 0.00 3.16
5712 6487 5.065218 CGGCTAAATTCATGCTAAGAAGTGT 59.935 40.000 0.00 0.00 0.00 3.55
5713 6488 6.261118 GGCTAAATTCATGCTAAGAAGTGTG 58.739 40.000 0.00 0.00 0.00 3.82
5714 6489 6.127897 GGCTAAATTCATGCTAAGAAGTGTGT 60.128 38.462 0.00 0.00 0.00 3.72
5715 6490 7.308435 GCTAAATTCATGCTAAGAAGTGTGTT 58.692 34.615 0.00 0.00 0.00 3.32
5716 6491 7.809806 GCTAAATTCATGCTAAGAAGTGTGTTT 59.190 33.333 0.00 0.00 0.00 2.83
5717 6492 7.935338 AAATTCATGCTAAGAAGTGTGTTTG 57.065 32.000 0.00 0.00 0.00 2.93
5735 6510 4.572795 TGTTTGTCGATTACAGCTTCACAA 59.427 37.500 0.00 0.00 39.87 3.33
5738 6513 5.940192 TGTCGATTACAGCTTCACAAAAT 57.060 34.783 0.00 0.00 33.01 1.82
5795 6572 7.879070 GCATCTTTTAATAATGCAGATCCTCA 58.121 34.615 10.62 0.00 44.07 3.86
5830 6607 1.549620 CCCAAACACATAGCCATTGCA 59.450 47.619 0.00 0.00 41.13 4.08
5837 6614 1.679680 ACATAGCCATTGCACATGAGC 59.320 47.619 8.32 8.32 41.13 4.26
5900 6677 1.081892 AAGTGCAGCAGCTACATTCG 58.918 50.000 1.76 0.00 42.74 3.34
5909 6686 1.748879 GCTACATTCGCCCAGGCAA 60.749 57.895 9.78 2.90 42.06 4.52
5920 6697 0.954452 CCCAGGCAAAGGCGATATTC 59.046 55.000 0.00 0.00 42.47 1.75
5945 6722 5.527214 TCGCTTTATTATGGACCTGATGTTG 59.473 40.000 0.00 0.00 0.00 3.33
5959 6736 4.884164 CCTGATGTTGAGAGGATTTTACCC 59.116 45.833 0.00 0.00 0.00 3.69
6001 6778 3.983044 ACTGTTAGTGGAGGGTTCATC 57.017 47.619 0.00 0.00 0.00 2.92
6007 6784 1.612146 TGGAGGGTTCATCGGAGCA 60.612 57.895 0.00 0.00 0.00 4.26
6015 6792 0.684535 TTCATCGGAGCACCTTGACA 59.315 50.000 0.00 0.00 0.00 3.58
6043 6821 1.680735 GAGCAGACGATCCTCACAGAT 59.319 52.381 0.00 0.00 0.00 2.90
6046 6824 3.894427 AGCAGACGATCCTCACAGATATT 59.106 43.478 0.00 0.00 0.00 1.28
6140 6932 0.322008 ACAAAGCTAGGACAGGCAGC 60.322 55.000 0.00 0.00 35.49 5.25
6334 7346 3.944422 TGCGTGAAGAGAAAACAGTTC 57.056 42.857 0.00 0.00 0.00 3.01
6467 7481 7.781548 ATTTTGAAAATGCATAAGATGAGGC 57.218 32.000 0.00 0.00 0.00 4.70
6566 7583 0.040958 GAGCCTTCACAACGCAACTG 60.041 55.000 0.00 0.00 0.00 3.16
6570 7587 0.592247 CTTCACAACGCAACTGTGGC 60.592 55.000 0.00 0.00 43.60 5.01
6571 7588 1.308783 TTCACAACGCAACTGTGGCA 61.309 50.000 8.09 0.00 43.60 4.92
6572 7589 1.138459 CACAACGCAACTGTGGCAA 59.862 52.632 8.09 0.00 40.44 4.52
6573 7590 1.138671 ACAACGCAACTGTGGCAAC 59.861 52.632 8.09 0.00 0.00 4.17
6582 7613 2.555325 CAACTGTGGCAACTGTGATGAT 59.445 45.455 4.30 0.00 38.37 2.45
6691 7724 0.762842 AGTGACTGTACAGGGTGCCA 60.763 55.000 26.12 12.61 0.00 4.92
6905 7938 4.579753 TGATGCACTCATTTTCTGTGACAA 59.420 37.500 0.00 0.00 33.95 3.18
6909 7942 4.515191 GCACTCATTTTCTGTGACAAGGTA 59.485 41.667 0.00 0.00 33.95 3.08
6937 7970 1.275856 GCCTGCATTGGTGATGGAAAA 59.724 47.619 0.00 0.00 35.52 2.29
6954 7987 3.373130 GGAAAACGGAGCATGTTACTACC 59.627 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 4.394729 AGAAGAGTATCGAGGAGCTTAGG 58.605 47.826 0.00 0.00 42.67 2.69
158 159 3.074412 CTGGTACATGTCGAAGCCTTTT 58.926 45.455 0.00 0.00 38.20 2.27
892 895 1.069049 GCAGAAAATGCGGCCCAATAT 59.931 47.619 0.00 0.00 46.99 1.28
894 897 1.218854 GCAGAAAATGCGGCCCAAT 59.781 52.632 0.00 0.00 46.99 3.16
903 906 6.327934 AGAATTTCGAATCTGGCAGAAAATG 58.672 36.000 22.84 11.74 36.39 2.32
937 940 3.172106 TTGAACCCCAGGACGGCA 61.172 61.111 0.00 0.00 0.00 5.69
1008 1021 2.746277 GGCACCGCCGATTTCAGT 60.746 61.111 0.00 0.00 39.62 3.41
1155 1168 1.673168 GGCCAGGAGCACAGAATAAG 58.327 55.000 0.00 0.00 46.50 1.73
1185 1198 1.712018 CGACCGAGCTACGATGGTGA 61.712 60.000 7.07 0.00 45.77 4.02
1199 1212 2.126307 CACTGAGACCAGCGACCG 60.126 66.667 0.00 0.00 44.16 4.79
1220 1233 1.517257 CTGAGAGACGGCGCGAAAT 60.517 57.895 12.10 0.00 0.00 2.17
1226 1239 1.064946 GATGACCTGAGAGACGGCG 59.935 63.158 4.80 4.80 0.00 6.46
1401 1449 1.968017 CACAGGTGCAATGAGCCGT 60.968 57.895 7.15 0.00 44.83 5.68
1460 1508 2.304180 ACTTCACTGCTTACCTCTGCAT 59.696 45.455 0.00 0.00 38.59 3.96
1467 1515 2.417719 CCACAGACTTCACTGCTTACC 58.582 52.381 0.00 0.00 41.06 2.85
1575 1636 6.679327 ACGAAAGAAAAGCCTATTATCACC 57.321 37.500 0.00 0.00 0.00 4.02
1627 1688 2.501723 AGTGCCATCAGAACTAATCGGT 59.498 45.455 0.00 0.00 0.00 4.69
1650 1711 9.102757 CATATAATGCAGGTACCAAGATATCAC 57.897 37.037 15.94 0.00 0.00 3.06
1772 1833 7.363181 CCAAGATGCTCACTATTTTTGATGGAA 60.363 37.037 0.00 0.00 0.00 3.53
1773 1834 6.095860 CCAAGATGCTCACTATTTTTGATGGA 59.904 38.462 0.00 0.00 0.00 3.41
1775 1836 6.095860 TCCCAAGATGCTCACTATTTTTGATG 59.904 38.462 0.00 0.00 0.00 3.07
1776 1837 6.189859 TCCCAAGATGCTCACTATTTTTGAT 58.810 36.000 0.00 0.00 0.00 2.57
1777 1838 5.569355 TCCCAAGATGCTCACTATTTTTGA 58.431 37.500 0.00 0.00 0.00 2.69
1778 1839 5.163581 CCTCCCAAGATGCTCACTATTTTTG 60.164 44.000 0.00 0.00 0.00 2.44
1795 1856 2.627933 AGTTTAGTACCTGCCTCCCAA 58.372 47.619 0.00 0.00 0.00 4.12
1796 1857 2.337359 AGTTTAGTACCTGCCTCCCA 57.663 50.000 0.00 0.00 0.00 4.37
1797 1858 3.244805 ACAAAGTTTAGTACCTGCCTCCC 60.245 47.826 0.00 0.00 0.00 4.30
1798 1859 4.001652 GACAAAGTTTAGTACCTGCCTCC 58.998 47.826 0.00 0.00 0.00 4.30
1799 1860 4.638304 TGACAAAGTTTAGTACCTGCCTC 58.362 43.478 0.00 0.00 0.00 4.70
1800 1861 4.699925 TGACAAAGTTTAGTACCTGCCT 57.300 40.909 0.00 0.00 0.00 4.75
1801 1862 4.760204 ACATGACAAAGTTTAGTACCTGCC 59.240 41.667 0.00 0.00 0.00 4.85
1802 1863 5.941948 ACATGACAAAGTTTAGTACCTGC 57.058 39.130 0.00 0.00 0.00 4.85
1815 1876 8.429493 TTCACAATGCAATTAAACATGACAAA 57.571 26.923 0.00 0.00 32.46 2.83
1846 1907 5.221342 TGCCATGGTTAAAAATCTGACGTTT 60.221 36.000 14.67 0.00 0.00 3.60
1852 1913 6.098679 TCGATTTGCCATGGTTAAAAATCTG 58.901 36.000 25.14 21.05 35.87 2.90
1854 1915 6.959671 TTCGATTTGCCATGGTTAAAAATC 57.040 33.333 21.77 21.77 35.08 2.17
1855 1916 6.878389 ACATTCGATTTGCCATGGTTAAAAAT 59.122 30.769 14.67 13.80 0.00 1.82
1887 1971 4.812476 TTGCCATCCTCGCGACCG 62.812 66.667 3.71 0.00 0.00 4.79
1890 1974 1.992233 GCAAATTGCCATCCTCGCGA 61.992 55.000 9.26 9.26 37.42 5.87
1891 1975 1.587088 GCAAATTGCCATCCTCGCG 60.587 57.895 6.72 0.00 37.42 5.87
1892 1976 0.174162 AAGCAAATTGCCATCCTCGC 59.826 50.000 15.04 0.00 46.52 5.03
1893 1977 2.660189 AAAGCAAATTGCCATCCTCG 57.340 45.000 15.04 0.00 46.52 4.63
1894 1978 3.451526 GCTAAAGCAAATTGCCATCCTC 58.548 45.455 15.04 0.00 46.52 3.71
1924 2020 3.118592 TGTTCAGTTTTTGCCCGGATTTT 60.119 39.130 0.73 0.00 0.00 1.82
1969 2110 5.365403 TTTTAGCATGGAAAATCGAACGT 57.635 34.783 0.00 0.00 0.00 3.99
2003 2144 5.568482 TCATTTTGGATTTCGCTACAATCG 58.432 37.500 0.00 0.00 32.22 3.34
2031 2172 3.287222 CACCTCAGGAAACAGGACAAAA 58.713 45.455 0.00 0.00 33.52 2.44
2195 2336 5.693104 AGAGAAACAAACATTACGCGTAAGA 59.307 36.000 32.39 15.11 43.02 2.10
2259 2400 7.093945 ACACAGAAACAGGTCAAACTAAAACAT 60.094 33.333 0.00 0.00 0.00 2.71
2380 2521 3.117888 TGTTGCTCTTCCCAGAAGAAGTT 60.118 43.478 8.30 0.00 43.17 2.66
2450 2591 4.464008 TCACTGCTTGATCTTCCAACTTT 58.536 39.130 0.00 0.00 0.00 2.66
2650 2792 3.436243 AGGAGGTCGGAGGAATATCATC 58.564 50.000 0.00 0.00 0.00 2.92
2779 2921 2.057137 TGGCAACTTGATATGGCCTC 57.943 50.000 3.32 0.00 44.85 4.70
2941 3083 9.552114 CAGTTTAAAACAATTGACAATTTTGCA 57.448 25.926 13.59 0.00 0.00 4.08
2964 3106 9.046296 CAAGTAAGAGACATACAAAACTTCAGT 57.954 33.333 0.00 0.00 0.00 3.41
3081 3223 4.986054 AACTGGTATTGTACACAAGGGA 57.014 40.909 0.00 0.00 39.47 4.20
3227 3369 5.412904 GCAATTTGTTTAGAGTCTGTAGCCT 59.587 40.000 1.86 0.00 0.00 4.58
3232 3374 6.318648 TGTTCAGCAATTTGTTTAGAGTCTGT 59.681 34.615 1.86 0.00 0.00 3.41
3235 3377 7.965107 CCTATGTTCAGCAATTTGTTTAGAGTC 59.035 37.037 0.00 0.00 0.00 3.36
3246 3388 2.710377 TCGTGCCTATGTTCAGCAATT 58.290 42.857 0.00 0.00 38.45 2.32
3405 3547 9.826574 TGGTAAGCTCGTATGAAAATATAAGTT 57.173 29.630 0.00 0.00 0.00 2.66
3406 3548 9.998106 ATGGTAAGCTCGTATGAAAATATAAGT 57.002 29.630 0.00 0.00 0.00 2.24
3410 3552 9.950680 CAAAATGGTAAGCTCGTATGAAAATAT 57.049 29.630 0.00 0.00 0.00 1.28
3510 4260 4.163458 CCATTAGTTCCTGGCCTAACAGTA 59.837 45.833 3.32 0.00 36.75 2.74
3516 4266 0.843984 GCCCATTAGTTCCTGGCCTA 59.156 55.000 3.32 0.00 36.07 3.93
3522 4272 3.960755 GCCATTTTAGCCCATTAGTTCCT 59.039 43.478 0.00 0.00 0.00 3.36
3545 4295 4.132336 GTGCTGAATGAGATCCTGCAATA 58.868 43.478 0.00 0.00 32.40 1.90
3573 4323 6.096987 CCAACTTGCTAGTAGGAGAATCTACA 59.903 42.308 0.00 0.00 41.39 2.74
3629 4379 7.211573 TGATTTATAATGCTTTTGGAGGCATG 58.788 34.615 1.16 0.00 46.70 4.06
3704 4455 5.033589 TGTACGTAAGGGGAAACTCAAAA 57.966 39.130 0.00 0.00 46.39 2.44
3720 4471 3.945346 TCAAAGCAATACCCATGTACGT 58.055 40.909 0.00 0.00 0.00 3.57
3745 4496 3.281727 TGCTTATTAACCCCTGCTGAG 57.718 47.619 0.00 0.00 0.00 3.35
3853 4604 0.178921 TTCTCTGTCAGTCCCTGGCT 60.179 55.000 0.00 0.00 36.97 4.75
3872 4623 4.778213 TCAGCTGCAGAATACCCTTTAT 57.222 40.909 20.43 0.00 0.00 1.40
3899 4650 4.177026 CTGCTCCACACTACACATAACTC 58.823 47.826 0.00 0.00 0.00 3.01
3935 4686 4.469469 TGATCCCAGAAAAGAAAAGGGT 57.531 40.909 0.00 0.00 40.48 4.34
4007 4758 9.725019 AGGATAAATCAATAATAAGACGCATCA 57.275 29.630 0.00 0.00 0.00 3.07
4058 4809 1.937899 GACAACACCGTGTGCTTAAGT 59.062 47.619 4.57 0.00 36.98 2.24
4068 4819 3.547054 TTACTTTCAGGACAACACCGT 57.453 42.857 0.00 0.00 34.73 4.83
4173 4929 9.038072 TGATTTACAGGTACCTACTTGACATAA 57.962 33.333 15.80 1.18 36.84 1.90
4216 4972 4.350816 TGCCATGCATTCTATACTAACCCT 59.649 41.667 0.00 0.00 31.71 4.34
4239 4995 6.758254 AGCCACATAAAGCAAAGTAAACAAT 58.242 32.000 0.00 0.00 0.00 2.71
4244 5000 5.564651 GCAGAAGCCACATAAAGCAAAGTAA 60.565 40.000 0.00 0.00 33.58 2.24
4400 5156 3.871006 AGAGTGCGCGAATGAAAATATGA 59.129 39.130 12.10 0.00 0.00 2.15
4450 5206 1.760086 CTCGACTGGGCTCCCTGAT 60.760 63.158 17.30 3.34 38.26 2.90
4514 5270 8.648557 ATTATGTCACACATACACTGATACAC 57.351 34.615 0.00 0.00 40.47 2.90
4550 5306 6.715344 AACAGTGCAAAGCATAAATTCATG 57.285 33.333 0.00 0.00 41.91 3.07
4650 5406 2.939460 ACAACTTGAACACTGGCAAC 57.061 45.000 0.00 0.00 0.00 4.17
4741 5497 6.317857 GGATTTGTAGCAAGTTGATTCTGAC 58.682 40.000 7.16 0.00 0.00 3.51
4783 5539 9.085250 CAGATATCAGATTCATCTATGGAAACG 57.915 37.037 5.32 0.00 34.85 3.60
4862 5618 3.005554 CAGACTGATGCCACCAAACTAG 58.994 50.000 0.00 0.00 0.00 2.57
4962 5718 8.865420 ATATCCAGGATCAATCTTCAAATCAG 57.135 34.615 4.75 0.00 0.00 2.90
4975 5731 3.329814 AGCTCATGCAATATCCAGGATCA 59.670 43.478 4.75 0.00 42.74 2.92
5015 5771 2.759191 TGTAGCAACAGCAGAAGACAG 58.241 47.619 0.00 0.00 0.00 3.51
5050 5806 9.056005 TGCATAACATACCTATTGATCTTTGAC 57.944 33.333 0.00 0.00 0.00 3.18
5075 5831 9.976511 AAATTCAGATAGCCACATTCAATAATG 57.023 29.630 0.00 0.00 46.66 1.90
5080 5836 5.716228 ACCAAATTCAGATAGCCACATTCAA 59.284 36.000 0.00 0.00 0.00 2.69
5096 5853 5.075858 TGATGGAAGATGCAACCAAATTC 57.924 39.130 8.80 4.43 37.24 2.17
5133 5890 7.441890 TTGAATTGTTATCCGACTTTGCTAA 57.558 32.000 0.00 0.00 0.00 3.09
5191 5948 4.199310 TGTGATGGGAATTTCGGAGATTC 58.801 43.478 11.68 11.68 35.04 2.52
5224 5981 8.383175 TCAACTTCTTTATCTGTTGTAGGGATT 58.617 33.333 0.00 0.00 40.20 3.01
5287 6044 6.330278 TCTATCAAGGTGAGTAACATGAACG 58.670 40.000 0.00 0.00 32.08 3.95
5289 6046 9.739276 AATTTCTATCAAGGTGAGTAACATGAA 57.261 29.630 0.00 0.00 32.08 2.57
5299 6056 4.949856 GGAGCCAAATTTCTATCAAGGTGA 59.050 41.667 0.00 0.00 0.00 4.02
5300 6057 4.706476 TGGAGCCAAATTTCTATCAAGGTG 59.294 41.667 0.00 0.00 0.00 4.00
5301 6058 4.934356 TGGAGCCAAATTTCTATCAAGGT 58.066 39.130 0.00 0.00 0.00 3.50
5350 6107 7.707893 GCCTGCATGTAAATTTTGAGACATATT 59.292 33.333 0.00 0.00 31.41 1.28
5357 6114 5.063180 TCTGCCTGCATGTAAATTTTGAG 57.937 39.130 0.00 0.00 0.00 3.02
5360 6117 5.726980 TCTTCTGCCTGCATGTAAATTTT 57.273 34.783 0.00 0.00 0.00 1.82
5470 6229 3.242969 ACGAGTTAGCGATTTGAGCGATA 60.243 43.478 0.00 0.00 40.04 2.92
5483 6242 7.807687 TGTATTTCTCAGTAAACGAGTTAGC 57.192 36.000 0.00 0.00 0.00 3.09
5493 6252 9.177608 CATTTCTCCCATTGTATTTCTCAGTAA 57.822 33.333 0.00 0.00 0.00 2.24
5509 6268 5.419542 CGAGATCAAAGTACATTTCTCCCA 58.580 41.667 6.86 0.00 0.00 4.37
5537 6312 0.249657 CGGAGAAGGGAGCACTATGC 60.250 60.000 0.00 0.00 45.46 3.14
5541 6316 0.832135 TTGTCGGAGAAGGGAGCACT 60.832 55.000 0.00 0.00 39.69 4.40
5548 6323 1.546476 ACTACTGCTTGTCGGAGAAGG 59.454 52.381 15.67 3.77 39.69 3.46
5552 6327 2.724977 TTGACTACTGCTTGTCGGAG 57.275 50.000 0.00 0.00 36.10 4.63
5612 6387 8.408043 AAGTGATGAAGTCCAAAATTGTGATA 57.592 30.769 0.00 0.00 0.00 2.15
5614 6389 6.713762 AAGTGATGAAGTCCAAAATTGTGA 57.286 33.333 0.00 0.00 0.00 3.58
5619 6394 8.237811 ACAAGTTAAGTGATGAAGTCCAAAAT 57.762 30.769 0.00 0.00 0.00 1.82
5629 6404 6.211384 TCCTCTCATGACAAGTTAAGTGATGA 59.789 38.462 0.00 0.00 37.29 2.92
5630 6405 6.401394 TCCTCTCATGACAAGTTAAGTGATG 58.599 40.000 0.00 0.00 32.81 3.07
5631 6406 6.611613 TCCTCTCATGACAAGTTAAGTGAT 57.388 37.500 0.00 0.00 0.00 3.06
5632 6407 6.419484 TTCCTCTCATGACAAGTTAAGTGA 57.581 37.500 0.00 0.00 0.00 3.41
5633 6408 5.121454 GCTTCCTCTCATGACAAGTTAAGTG 59.879 44.000 0.00 0.00 0.00 3.16
5634 6409 5.241662 GCTTCCTCTCATGACAAGTTAAGT 58.758 41.667 0.00 0.00 0.00 2.24
5635 6410 4.633565 GGCTTCCTCTCATGACAAGTTAAG 59.366 45.833 0.00 0.76 0.00 1.85
5636 6411 4.287067 AGGCTTCCTCTCATGACAAGTTAA 59.713 41.667 0.00 0.00 0.00 2.01
5637 6412 3.840666 AGGCTTCCTCTCATGACAAGTTA 59.159 43.478 0.00 0.00 0.00 2.24
5638 6413 2.641815 AGGCTTCCTCTCATGACAAGTT 59.358 45.455 0.00 0.00 0.00 2.66
5639 6414 2.235898 GAGGCTTCCTCTCATGACAAGT 59.764 50.000 5.65 0.00 46.41 3.16
5640 6415 2.903798 GAGGCTTCCTCTCATGACAAG 58.096 52.381 5.65 0.00 46.41 3.16
5651 6426 1.777272 ACAAGTTTCCAGAGGCTTCCT 59.223 47.619 0.00 0.00 36.03 3.36
5652 6427 2.278332 ACAAGTTTCCAGAGGCTTCC 57.722 50.000 0.00 0.00 0.00 3.46
5653 6428 3.796844 GCAAACAAGTTTCCAGAGGCTTC 60.797 47.826 0.00 0.00 0.00 3.86
5654 6429 2.101415 GCAAACAAGTTTCCAGAGGCTT 59.899 45.455 0.00 0.00 0.00 4.35
5655 6430 1.683385 GCAAACAAGTTTCCAGAGGCT 59.317 47.619 0.00 0.00 0.00 4.58
5656 6431 1.683385 AGCAAACAAGTTTCCAGAGGC 59.317 47.619 0.00 0.00 0.00 4.70
5657 6432 2.294512 GGAGCAAACAAGTTTCCAGAGG 59.705 50.000 0.00 0.00 0.00 3.69
5658 6433 2.294512 GGGAGCAAACAAGTTTCCAGAG 59.705 50.000 0.00 0.00 0.00 3.35
5659 6434 2.091885 AGGGAGCAAACAAGTTTCCAGA 60.092 45.455 0.00 0.00 0.00 3.86
5660 6435 2.310538 AGGGAGCAAACAAGTTTCCAG 58.689 47.619 0.00 0.00 0.00 3.86
5661 6436 2.452600 AGGGAGCAAACAAGTTTCCA 57.547 45.000 0.00 0.00 0.00 3.53
5662 6437 3.751518 TCTAGGGAGCAAACAAGTTTCC 58.248 45.455 0.00 0.00 0.00 3.13
5663 6438 7.306213 GTTTATCTAGGGAGCAAACAAGTTTC 58.694 38.462 0.00 0.00 33.86 2.78
5664 6439 6.072673 CGTTTATCTAGGGAGCAAACAAGTTT 60.073 38.462 0.00 0.00 33.55 2.66
5665 6440 5.411669 CGTTTATCTAGGGAGCAAACAAGTT 59.588 40.000 0.00 0.00 33.55 2.66
5666 6441 4.935808 CGTTTATCTAGGGAGCAAACAAGT 59.064 41.667 0.00 0.00 33.55 3.16
5667 6442 4.332819 CCGTTTATCTAGGGAGCAAACAAG 59.667 45.833 0.00 0.00 33.55 3.16
5668 6443 4.258543 CCGTTTATCTAGGGAGCAAACAA 58.741 43.478 0.00 0.00 33.55 2.83
5669 6444 3.869065 CCGTTTATCTAGGGAGCAAACA 58.131 45.455 0.00 0.00 33.55 2.83
5670 6445 2.612672 GCCGTTTATCTAGGGAGCAAAC 59.387 50.000 0.00 0.00 32.05 2.93
5671 6446 2.504175 AGCCGTTTATCTAGGGAGCAAA 59.496 45.455 0.00 0.00 0.00 3.68
5672 6447 2.116238 AGCCGTTTATCTAGGGAGCAA 58.884 47.619 0.00 0.00 0.00 3.91
5673 6448 1.789523 AGCCGTTTATCTAGGGAGCA 58.210 50.000 0.00 0.00 0.00 4.26
5674 6449 4.332428 TTTAGCCGTTTATCTAGGGAGC 57.668 45.455 0.00 0.00 0.00 4.70
5675 6450 6.522054 TGAATTTAGCCGTTTATCTAGGGAG 58.478 40.000 0.00 0.00 0.00 4.30
5676 6451 6.488769 TGAATTTAGCCGTTTATCTAGGGA 57.511 37.500 0.00 0.00 0.00 4.20
5677 6452 6.348540 GCATGAATTTAGCCGTTTATCTAGGG 60.349 42.308 0.00 0.00 0.00 3.53
5678 6453 6.428159 AGCATGAATTTAGCCGTTTATCTAGG 59.572 38.462 0.00 0.00 0.00 3.02
5679 6454 7.426929 AGCATGAATTTAGCCGTTTATCTAG 57.573 36.000 0.00 0.00 0.00 2.43
5680 6455 8.896320 TTAGCATGAATTTAGCCGTTTATCTA 57.104 30.769 0.00 0.00 0.00 1.98
5681 6456 7.715249 TCTTAGCATGAATTTAGCCGTTTATCT 59.285 33.333 0.00 0.00 0.00 1.98
5682 6457 7.861630 TCTTAGCATGAATTTAGCCGTTTATC 58.138 34.615 0.00 0.00 0.00 1.75
5683 6458 7.801716 TCTTAGCATGAATTTAGCCGTTTAT 57.198 32.000 0.00 0.00 0.00 1.40
5684 6459 7.335924 ACTTCTTAGCATGAATTTAGCCGTTTA 59.664 33.333 0.00 0.00 0.00 2.01
5685 6460 6.151144 ACTTCTTAGCATGAATTTAGCCGTTT 59.849 34.615 0.00 0.00 0.00 3.60
5686 6461 5.648092 ACTTCTTAGCATGAATTTAGCCGTT 59.352 36.000 0.00 0.00 0.00 4.44
5687 6462 5.065218 CACTTCTTAGCATGAATTTAGCCGT 59.935 40.000 0.00 0.00 0.00 5.68
5688 6463 5.065218 ACACTTCTTAGCATGAATTTAGCCG 59.935 40.000 0.00 0.00 0.00 5.52
5689 6464 6.127897 ACACACTTCTTAGCATGAATTTAGCC 60.128 38.462 0.00 0.00 0.00 3.93
5690 6465 6.846350 ACACACTTCTTAGCATGAATTTAGC 58.154 36.000 0.00 0.00 0.00 3.09
5691 6466 9.121517 CAAACACACTTCTTAGCATGAATTTAG 57.878 33.333 0.00 0.00 0.00 1.85
5692 6467 8.629158 ACAAACACACTTCTTAGCATGAATTTA 58.371 29.630 0.00 0.00 0.00 1.40
5693 6468 7.491682 ACAAACACACTTCTTAGCATGAATTT 58.508 30.769 0.00 0.00 0.00 1.82
5694 6469 7.042797 ACAAACACACTTCTTAGCATGAATT 57.957 32.000 0.00 0.00 0.00 2.17
5695 6470 6.566564 CGACAAACACACTTCTTAGCATGAAT 60.567 38.462 0.00 0.00 0.00 2.57
5696 6471 5.277297 CGACAAACACACTTCTTAGCATGAA 60.277 40.000 0.00 0.00 0.00 2.57
5697 6472 4.211164 CGACAAACACACTTCTTAGCATGA 59.789 41.667 0.00 0.00 0.00 3.07
5698 6473 4.211164 TCGACAAACACACTTCTTAGCATG 59.789 41.667 0.00 0.00 0.00 4.06
5699 6474 4.377021 TCGACAAACACACTTCTTAGCAT 58.623 39.130 0.00 0.00 0.00 3.79
5700 6475 3.787785 TCGACAAACACACTTCTTAGCA 58.212 40.909 0.00 0.00 0.00 3.49
5701 6476 4.992381 ATCGACAAACACACTTCTTAGC 57.008 40.909 0.00 0.00 0.00 3.09
5702 6477 7.402811 TGTAATCGACAAACACACTTCTTAG 57.597 36.000 0.00 0.00 34.15 2.18
5703 6478 6.073980 GCTGTAATCGACAAACACACTTCTTA 60.074 38.462 0.00 0.00 37.70 2.10
5704 6479 5.277345 GCTGTAATCGACAAACACACTTCTT 60.277 40.000 0.00 0.00 37.70 2.52
5705 6480 4.211374 GCTGTAATCGACAAACACACTTCT 59.789 41.667 0.00 0.00 37.70 2.85
5706 6481 4.211374 AGCTGTAATCGACAAACACACTTC 59.789 41.667 0.00 0.00 37.70 3.01
5707 6482 4.127171 AGCTGTAATCGACAAACACACTT 58.873 39.130 0.00 0.00 37.70 3.16
5708 6483 3.728845 AGCTGTAATCGACAAACACACT 58.271 40.909 0.00 0.00 37.70 3.55
5709 6484 4.025229 TGAAGCTGTAATCGACAAACACAC 60.025 41.667 0.00 0.00 37.70 3.82
5710 6485 4.025229 GTGAAGCTGTAATCGACAAACACA 60.025 41.667 0.00 0.00 37.70 3.72
5711 6486 4.025229 TGTGAAGCTGTAATCGACAAACAC 60.025 41.667 0.00 0.00 37.70 3.32
5712 6487 4.123506 TGTGAAGCTGTAATCGACAAACA 58.876 39.130 0.00 0.00 37.70 2.83
5713 6488 4.725556 TGTGAAGCTGTAATCGACAAAC 57.274 40.909 0.00 0.00 37.70 2.93
5714 6489 5.743026 TTTGTGAAGCTGTAATCGACAAA 57.257 34.783 0.00 0.00 37.70 2.83
5715 6490 5.743026 TTTTGTGAAGCTGTAATCGACAA 57.257 34.783 0.00 0.00 37.70 3.18
5716 6491 5.106712 GGATTTTGTGAAGCTGTAATCGACA 60.107 40.000 0.00 0.00 36.35 4.35
5717 6492 5.106712 TGGATTTTGTGAAGCTGTAATCGAC 60.107 40.000 0.00 0.00 0.00 4.20
5738 6513 9.500785 AGAAAAAGTGAAAATTTCAAAAGTGGA 57.499 25.926 10.27 0.00 42.15 4.02
5777 6554 7.228108 CAGCTTCTTGAGGATCTGCATTATTAA 59.772 37.037 0.00 0.00 34.92 1.40
5779 6556 5.531659 CAGCTTCTTGAGGATCTGCATTATT 59.468 40.000 0.00 0.00 34.92 1.40
5900 6677 1.109323 AATATCGCCTTTGCCTGGGC 61.109 55.000 4.43 4.43 44.43 5.36
5920 6697 5.300752 ACATCAGGTCCATAATAAAGCGAG 58.699 41.667 0.00 0.00 0.00 5.03
5923 6700 6.767902 TCTCAACATCAGGTCCATAATAAAGC 59.232 38.462 0.00 0.00 0.00 3.51
5945 6722 6.205658 GCATCAACATAGGGTAAAATCCTCTC 59.794 42.308 0.00 0.00 35.92 3.20
5959 6736 5.416952 AGTTCTTTTCAGGGCATCAACATAG 59.583 40.000 0.00 0.00 0.00 2.23
6001 6778 0.798776 GTGATTGTCAAGGTGCTCCG 59.201 55.000 0.00 0.00 39.05 4.63
6007 6784 1.421268 TGCTCCTGTGATTGTCAAGGT 59.579 47.619 0.00 0.00 31.26 3.50
6015 6792 1.137872 GGATCGTCTGCTCCTGTGATT 59.862 52.381 0.00 0.00 0.00 2.57
6038 6816 2.939103 GCGAAGAGGTGCAAATATCTGT 59.061 45.455 0.00 0.00 0.00 3.41
6140 6932 4.133820 TGTAACACAATGGGTCAAGTCAG 58.866 43.478 0.00 0.00 0.00 3.51
6334 7346 7.383029 TGAGAGAATTTGTGCTTTGCAAAATAG 59.617 33.333 13.84 2.55 41.47 1.73
6437 7451 9.485591 CATCTTATGCATTTTCAAAATTTCAGC 57.514 29.630 3.54 0.00 0.00 4.26
6467 7481 1.185315 CATGGGTGTGCTTTTAGGGG 58.815 55.000 0.00 0.00 0.00 4.79
6566 7583 3.011818 TCATCATCATCACAGTTGCCAC 58.988 45.455 0.00 0.00 0.00 5.01
6570 7587 5.998363 AGATGGATCATCATCATCACAGTTG 59.002 40.000 12.67 0.00 44.30 3.16
6571 7588 6.189036 AGATGGATCATCATCATCACAGTT 57.811 37.500 12.67 0.00 44.30 3.16
6572 7589 5.827326 AGATGGATCATCATCATCACAGT 57.173 39.130 12.67 0.00 44.30 3.55
6573 7590 7.036829 GTCTAGATGGATCATCATCATCACAG 58.963 42.308 12.67 8.52 44.30 3.66
6582 7613 5.278660 CGTGACATGTCTAGATGGATCATCA 60.279 44.000 25.55 0.00 42.72 3.07
6691 7724 3.234353 TGCATCTAGATGGACGATCCTT 58.766 45.455 29.43 0.00 39.16 3.36
6905 7938 4.084287 CCAATGCAGGCAATATGATACCT 58.916 43.478 0.00 0.00 0.00 3.08
6909 7942 3.568443 TCACCAATGCAGGCAATATGAT 58.432 40.909 0.00 0.00 0.00 2.45
6937 7970 3.259876 TCTTTGGTAGTAACATGCTCCGT 59.740 43.478 0.00 0.00 0.00 4.69
6954 7987 8.934973 ACTTCGATTCGTTTTCTTTATCTTTG 57.065 30.769 5.89 0.00 0.00 2.77
6974 8011 7.755582 ATTGGTCTTTTCTTTTTGAACTTCG 57.244 32.000 0.00 0.00 33.88 3.79


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

AutoCloner maintained by Alex Coulton.