Multiple sequence alignment - TraesCS1D01G064500

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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 TraesCS1D01G064500 chr1D 100.000 7056 0 0 1 7056 45484815 45491870 0.000000e+00 13031.0
1 TraesCS1D01G064500 chr1D 87.288 118 6 5 6779 6887 45498021 45498138 7.430000e-25 126.0
2 TraesCS1D01G064500 chr1B 92.752 6678 279 88 314 6884 65347551 65354130 0.000000e+00 9461.0
3 TraesCS1D01G064500 chr1B 87.079 178 11 2 22 187 65347072 65347249 2.600000e-44 191.0
4 TraesCS1D01G064500 chr1B 100.000 30 0 0 9 38 65347024 65347053 1.000000e-03 56.5
5 TraesCS1D01G064500 chr1A 94.243 3109 102 29 3875 6944 45545929 45548999 0.000000e+00 4678.0
6 TraesCS1D01G064500 chr1A 92.449 2887 135 36 967 3816 45543088 45545928 0.000000e+00 4047.0
7 TraesCS1D01G064500 chr1A 92.017 238 15 2 1 237 45541652 45541886 1.470000e-86 331.0
8 TraesCS1D01G064500 chr1A 82.486 354 14 16 305 647 45542240 45542556 4.200000e-67 267.0
9 TraesCS1D01G064500 chr3D 86.735 196 26 0 1415 1610 31443183 31443378 1.190000e-52 219.0
10 TraesCS1D01G064500 chr3A 85.714 196 28 0 1415 1610 51756482 51756287 2.580000e-49 207.0


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 TraesCS1D01G064500 chr1D 45484815 45491870 7055 False 13031.000000 13031 100.00000 1 7056 1 chr1D.!!$F1 7055
1 TraesCS1D01G064500 chr1B 65347024 65354130 7106 False 3236.166667 9461 93.27700 9 6884 3 chr1B.!!$F1 6875
2 TraesCS1D01G064500 chr1A 45541652 45548999 7347 False 2330.750000 4678 90.29875 1 6944 4 chr1A.!!$F1 6943

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
426 925 0.036952 ACTGAACCATCGAGGCACAG 60.037 55.0 17.38 17.38 44.26 3.66 F
987 1736 0.107654 GAGGGGTCGGAGGATTTGTG 60.108 60.0 0.00 0.00 0.00 3.33 F
1338 2087 1.188219 GCCCGAGGAGGATGCTGATA 61.188 60.0 0.00 0.00 45.00 2.15 F
2252 3017 0.323087 TCATGCCTCTGTTGCTGCAT 60.323 50.0 1.84 0.00 44.79 3.96 F
3594 4379 0.881118 CATCGGTTTTGACCAGGGTG 59.119 55.0 0.00 0.00 0.00 4.61 F
3696 4483 1.173043 CTGTTTGCCTAATTGCCCGA 58.827 50.0 0.00 0.00 0.00 5.14 F
5552 6361 0.459899 ACTTAGCGCGTCATCATCCA 59.540 50.0 8.43 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2769 0.104120 ACGGCTGCCAAAACCTTTTC 59.896 50.000 20.29 0.00 0.00 2.29 R
2015 2770 0.179086 CACGGCTGCCAAAACCTTTT 60.179 50.000 20.29 0.00 0.00 2.27 R
2720 3495 0.240145 GCTCCAAAACGGTAGGCAAC 59.760 55.000 0.00 0.00 35.57 4.17 R
4181 4980 0.466372 GCCCAGAATTAGGCTCCACC 60.466 60.000 0.00 0.00 46.14 4.61 R
5552 6361 0.838122 ACTAGTGGGGTGCAGCTCTT 60.838 55.000 18.13 7.93 0.00 2.85 R
5605 6414 2.169789 CAGCGATCAGTGCTTCGGG 61.170 63.158 14.50 0.00 41.72 5.14 R
6826 7688 0.038744 ATCAGAAAGCCCACCCACAG 59.961 55.000 0.00 0.00 0.00 3.66 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
130 174 2.348362 GTGTTTGCTTGTGAAAACCAGC 59.652 45.455 0.00 0.00 40.22 4.85
131 175 1.933181 GTTTGCTTGTGAAAACCAGCC 59.067 47.619 0.15 0.00 36.05 4.85
166 215 1.209747 GGTAAAGGCACCCTAGTCCAG 59.790 57.143 0.00 0.00 31.13 3.86
181 230 2.820787 AGTCCAGTCCAACGAGTCTAAG 59.179 50.000 0.00 0.00 0.00 2.18
187 236 4.058817 AGTCCAACGAGTCTAAGCTTTTG 58.941 43.478 3.20 0.53 0.00 2.44
308 705 5.738619 TGCACAGAAGTAATCAGGAACTA 57.261 39.130 0.00 0.00 36.02 2.24
312 789 5.187967 CACAGAAGTAATCAGGAACTAGGGT 59.812 44.000 0.00 0.00 36.02 4.34
409 908 2.146342 CAAGCATGTCTCAACCGAACT 58.854 47.619 0.00 0.00 0.00 3.01
410 909 1.800805 AGCATGTCTCAACCGAACTG 58.199 50.000 0.00 0.00 0.00 3.16
411 910 1.344438 AGCATGTCTCAACCGAACTGA 59.656 47.619 0.00 0.00 0.00 3.41
412 911 2.143122 GCATGTCTCAACCGAACTGAA 58.857 47.619 0.00 0.00 0.00 3.02
413 912 2.096218 GCATGTCTCAACCGAACTGAAC 60.096 50.000 0.00 0.00 0.00 3.18
414 913 2.234300 TGTCTCAACCGAACTGAACC 57.766 50.000 0.00 0.00 0.00 3.62
415 914 1.483004 TGTCTCAACCGAACTGAACCA 59.517 47.619 0.00 0.00 0.00 3.67
416 915 2.104111 TGTCTCAACCGAACTGAACCAT 59.896 45.455 0.00 0.00 0.00 3.55
417 916 2.737252 GTCTCAACCGAACTGAACCATC 59.263 50.000 0.00 0.00 0.00 3.51
418 917 1.726791 CTCAACCGAACTGAACCATCG 59.273 52.381 0.00 0.00 36.39 3.84
419 918 1.341852 TCAACCGAACTGAACCATCGA 59.658 47.619 0.00 0.00 38.82 3.59
420 919 1.726791 CAACCGAACTGAACCATCGAG 59.273 52.381 0.00 0.00 38.82 4.04
421 920 0.246635 ACCGAACTGAACCATCGAGG 59.753 55.000 0.00 0.00 45.67 4.63
422 921 1.084370 CCGAACTGAACCATCGAGGC 61.084 60.000 0.00 0.00 43.14 4.70
423 922 0.389817 CGAACTGAACCATCGAGGCA 60.390 55.000 0.00 0.00 43.14 4.75
424 923 1.079503 GAACTGAACCATCGAGGCAC 58.920 55.000 0.00 0.00 43.14 5.01
425 924 0.396435 AACTGAACCATCGAGGCACA 59.604 50.000 0.00 0.00 43.14 4.57
426 925 0.036952 ACTGAACCATCGAGGCACAG 60.037 55.000 17.38 17.38 44.26 3.66
427 926 1.364626 CTGAACCATCGAGGCACAGC 61.365 60.000 0.00 0.00 43.14 4.40
428 927 1.375908 GAACCATCGAGGCACAGCA 60.376 57.895 0.00 0.00 43.14 4.41
429 928 1.639298 GAACCATCGAGGCACAGCAC 61.639 60.000 0.00 0.00 43.14 4.40
436 935 2.593725 AGGCACAGCACAGCACAG 60.594 61.111 0.00 0.00 0.00 3.66
438 937 3.588906 GCACAGCACAGCACAGCA 61.589 61.111 0.00 0.00 0.00 4.41
453 952 0.249447 CAGCACAACCTCGACAGTGA 60.249 55.000 0.00 0.00 33.99 3.41
498 997 0.609406 GAAAACCCAGACCCAGGAGC 60.609 60.000 0.00 0.00 0.00 4.70
499 998 1.360393 AAAACCCAGACCCAGGAGCA 61.360 55.000 0.00 0.00 0.00 4.26
506 1005 4.341783 ACCCAGGAGCAGCAGCAC 62.342 66.667 3.17 0.00 45.49 4.40
642 1152 2.287194 CACCATCCCCCTCCCCTT 60.287 66.667 0.00 0.00 0.00 3.95
645 1155 2.778717 CATCCCCCTCCCCTTCCC 60.779 72.222 0.00 0.00 0.00 3.97
646 1156 4.138815 ATCCCCCTCCCCTTCCCC 62.139 72.222 0.00 0.00 0.00 4.81
695 1220 4.787534 ACCTTCCATCCTGATCTTCTTCTT 59.212 41.667 0.00 0.00 0.00 2.52
700 1225 3.205519 TCCTGATCTTCTTCTTCCCCA 57.794 47.619 0.00 0.00 0.00 4.96
730 1255 4.115199 GGCGGGCACATTCCTCCT 62.115 66.667 0.00 0.00 0.00 3.69
790 1315 3.565449 CCACATTAATTGTCCTTCCCCCA 60.565 47.826 0.00 0.00 36.00 4.96
815 1340 1.002033 GCTCCATCCGCATTGATTCAC 60.002 52.381 0.00 0.00 0.00 3.18
840 1365 3.019003 GCAGACAGGGCGGCTTCTA 62.019 63.158 9.56 0.00 0.00 2.10
841 1366 1.142748 CAGACAGGGCGGCTTCTAG 59.857 63.158 9.56 0.00 0.00 2.43
842 1367 2.202946 GACAGGGCGGCTTCTAGC 60.203 66.667 9.56 0.00 41.46 3.42
843 1368 2.685380 ACAGGGCGGCTTCTAGCT 60.685 61.111 9.56 0.00 41.99 3.32
872 1397 0.462759 CCCGCAGAGTCCAATCCTTC 60.463 60.000 0.00 0.00 0.00 3.46
894 1419 0.536460 TCTTTGGGCCTCGTTGGTTC 60.536 55.000 4.53 0.00 38.35 3.62
895 1420 0.537371 CTTTGGGCCTCGTTGGTTCT 60.537 55.000 4.53 0.00 38.35 3.01
897 1422 0.821711 TTGGGCCTCGTTGGTTCTTG 60.822 55.000 4.53 0.00 38.35 3.02
898 1423 1.072505 GGGCCTCGTTGGTTCTTGA 59.927 57.895 0.84 0.00 38.35 3.02
900 1425 1.087501 GGCCTCGTTGGTTCTTGATC 58.912 55.000 0.00 0.00 38.35 2.92
901 1426 1.339151 GGCCTCGTTGGTTCTTGATCT 60.339 52.381 0.00 0.00 38.35 2.75
902 1427 1.734465 GCCTCGTTGGTTCTTGATCTG 59.266 52.381 0.00 0.00 38.35 2.90
913 1450 1.694169 TTGATCTGGGAGGGGAGGC 60.694 63.158 0.00 0.00 0.00 4.70
932 1469 4.101448 AGGTGATCTGTGGCGGGC 62.101 66.667 0.00 0.00 0.00 6.13
987 1736 0.107654 GAGGGGTCGGAGGATTTGTG 60.108 60.000 0.00 0.00 0.00 3.33
991 1740 1.439679 GGTCGGAGGATTTGTGTGTC 58.560 55.000 0.00 0.00 0.00 3.67
1338 2087 1.188219 GCCCGAGGAGGATGCTGATA 61.188 60.000 0.00 0.00 45.00 2.15
1344 2093 2.703007 GAGGAGGATGCTGATAGTGGTT 59.297 50.000 0.00 0.00 36.27 3.67
1611 2360 2.050351 CACGTCGAGAAGCACCGT 60.050 61.111 0.00 0.00 0.00 4.83
1707 2456 7.221067 CAGATCGAGTGAGTACCAAATCTTAAC 59.779 40.741 0.00 0.00 0.00 2.01
1800 2552 4.183101 CAATGTGCCAAACTGACTGTTTT 58.817 39.130 7.65 0.00 45.69 2.43
1802 2554 5.590530 ATGTGCCAAACTGACTGTTTTTA 57.409 34.783 7.65 0.00 45.69 1.52
1808 2560 5.650543 CCAAACTGACTGTTTTTACTTGCT 58.349 37.500 7.65 0.00 45.69 3.91
1817 2569 6.199393 ACTGTTTTTACTTGCTGATTTCGAC 58.801 36.000 0.00 0.00 0.00 4.20
1818 2570 6.125327 TGTTTTTACTTGCTGATTTCGACA 57.875 33.333 0.00 0.00 0.00 4.35
1866 2618 1.602377 CACCGTTCTTTCAGGGTGTTC 59.398 52.381 4.70 0.00 44.44 3.18
1873 2625 5.107065 CGTTCTTTCAGGGTGTTCAATCTAC 60.107 44.000 0.00 0.00 0.00 2.59
1876 2629 6.361433 TCTTTCAGGGTGTTCAATCTACAAA 58.639 36.000 0.00 0.00 0.00 2.83
1879 2632 7.595819 TTCAGGGTGTTCAATCTACAAATTT 57.404 32.000 0.00 0.00 0.00 1.82
2012 2767 9.471702 ACACTAGTACTACTAATTTTCTAGCCA 57.528 33.333 0.00 0.00 29.00 4.75
2045 2800 1.574428 CAGCCGTGTAGTTTGGTGC 59.426 57.895 0.00 0.00 0.00 5.01
2124 2885 5.220710 AGAATAAGATGATTGACCCCTCG 57.779 43.478 0.00 0.00 0.00 4.63
2234 2999 2.807676 TCCCTTTTCCTCCAGCAAATC 58.192 47.619 0.00 0.00 0.00 2.17
2252 3017 0.323087 TCATGCCTCTGTTGCTGCAT 60.323 50.000 1.84 0.00 44.79 3.96
2544 3317 4.569162 CCTAAAGCATGCATTGAATGTTGG 59.431 41.667 21.98 0.00 0.00 3.77
2568 3341 5.357878 GGATGTTGATGCTCCTAACATTTGA 59.642 40.000 0.00 0.00 43.03 2.69
2592 3365 8.505625 TGATTGGAAGAAATTTGCTAAAAATGC 58.494 29.630 0.00 0.00 0.00 3.56
2595 3368 6.073112 TGGAAGAAATTTGCTAAAAATGCTGC 60.073 34.615 0.00 0.00 0.00 5.25
2664 3439 5.047092 ACTCCATTAAAAGAAATGCCCACAG 60.047 40.000 0.00 0.00 35.85 3.66
2720 3495 2.420628 TTTGAAATGCACAGCCGAAG 57.579 45.000 0.00 0.00 0.00 3.79
2740 3515 1.231958 TTGCCTACCGTTTTGGAGCG 61.232 55.000 0.00 0.00 42.00 5.03
2809 3584 4.095410 TGCGAAATTAGTGCCTGAATTG 57.905 40.909 0.00 0.00 0.00 2.32
3016 3792 7.094933 GGTCAAACATACCGTCTTTGTTCTATT 60.095 37.037 0.00 0.00 32.66 1.73
3017 3793 7.744715 GTCAAACATACCGTCTTTGTTCTATTG 59.255 37.037 0.00 0.00 32.66 1.90
3109 3885 2.514458 TCAAATCCTTCCAAGGCTCC 57.486 50.000 0.00 0.00 46.06 4.70
3126 3902 8.027189 CCAAGGCTCCTACTTTTTAAATTGTAC 58.973 37.037 0.00 0.00 0.00 2.90
3127 3903 8.793592 CAAGGCTCCTACTTTTTAAATTGTACT 58.206 33.333 0.00 0.00 0.00 2.73
3143 3919 6.893958 ATTGTACTAGCATTCTGACTTTCG 57.106 37.500 0.00 0.00 0.00 3.46
3146 3922 3.589988 ACTAGCATTCTGACTTTCGTGG 58.410 45.455 0.00 0.00 0.00 4.94
3594 4379 0.881118 CATCGGTTTTGACCAGGGTG 59.119 55.000 0.00 0.00 0.00 4.61
3694 4481 2.823154 TGTACTGTTTGCCTAATTGCCC 59.177 45.455 0.00 0.00 0.00 5.36
3696 4483 1.173043 CTGTTTGCCTAATTGCCCGA 58.827 50.000 0.00 0.00 0.00 5.14
3716 4503 4.684703 CCGAACAAGTGTACTTAACCTGAG 59.315 45.833 0.00 0.00 34.28 3.35
3738 4525 6.018262 TGAGTTGAGTACATTGTTTGCAGTAC 60.018 38.462 0.00 4.05 37.65 2.73
3752 4544 4.617253 TGCAGTACTGTTTGACCATACT 57.383 40.909 23.44 0.00 0.00 2.12
3794 4586 3.493503 GCACAGTAAGTAAAGTCTTGCGT 59.506 43.478 0.00 0.00 35.71 5.24
3929 4728 7.639062 AGTGGATGATTTAGTCTATTCCCAT 57.361 36.000 0.00 0.00 0.00 4.00
4010 4809 3.284793 AGTGTCTAGTAGCGTGGAGAT 57.715 47.619 0.00 0.00 0.00 2.75
4254 5054 3.177228 AGCCTTAATCACTGACCAGTCT 58.823 45.455 0.00 0.00 40.20 3.24
4356 5156 8.970020 TGCATGTTTCTGATGTTCCTTATAATT 58.030 29.630 0.00 0.00 0.00 1.40
4380 5180 1.184970 AAATGGACAGGGCGTTTGGG 61.185 55.000 0.00 0.00 0.00 4.12
4389 5189 2.988684 GCGTTTGGGACATGGCCA 60.989 61.111 22.13 8.56 39.30 5.36
4676 5476 4.021368 ACAGGTTAGTTCACTCGCAGTAAT 60.021 41.667 0.00 0.00 0.00 1.89
4870 5673 8.349568 TCGCAACTACTTATCTATACCATGAT 57.650 34.615 0.00 0.00 0.00 2.45
4872 5675 9.504710 CGCAACTACTTATCTATACCATGATAC 57.495 37.037 0.00 0.00 0.00 2.24
5003 5806 7.066525 CCAAATAATAAACCTCCGAAACTAGCA 59.933 37.037 0.00 0.00 0.00 3.49
5157 5962 4.235079 TCTTATCCTGTCAATTGGTGGG 57.765 45.455 5.42 5.49 0.00 4.61
5352 6161 2.103094 CCTATCTGAATTCACTGCCCGA 59.897 50.000 3.38 0.00 0.00 5.14
5370 6179 4.393680 GCCCGACTTACACAATTATCAACA 59.606 41.667 0.00 0.00 0.00 3.33
5552 6361 0.459899 ACTTAGCGCGTCATCATCCA 59.540 50.000 8.43 0.00 0.00 3.41
5562 6371 1.669779 GTCATCATCCAAGAGCTGCAC 59.330 52.381 1.02 0.00 0.00 4.57
5605 6414 0.109781 CATGCGCCACTACAACCAAC 60.110 55.000 4.18 0.00 0.00 3.77
5661 6471 0.904865 ATCACTTCGGTCCCTCTGCA 60.905 55.000 0.00 0.00 0.00 4.41
5684 6494 1.077828 TCCCTCACTCCATCTGTGTCT 59.922 52.381 0.00 0.00 36.83 3.41
5685 6495 1.905215 CCCTCACTCCATCTGTGTCTT 59.095 52.381 0.00 0.00 36.83 3.01
5686 6496 2.093764 CCCTCACTCCATCTGTGTCTTC 60.094 54.545 0.00 0.00 36.83 2.87
5687 6497 2.830923 CCTCACTCCATCTGTGTCTTCT 59.169 50.000 0.00 0.00 36.83 2.85
5688 6498 3.368220 CCTCACTCCATCTGTGTCTTCTG 60.368 52.174 0.00 0.00 36.83 3.02
5689 6499 3.234353 TCACTCCATCTGTGTCTTCTGT 58.766 45.455 0.00 0.00 36.83 3.41
5710 6525 0.846693 AGTTGCACCAGAAAGACCCT 59.153 50.000 0.00 0.00 0.00 4.34
5767 6583 8.451908 TCCAAGAAGCTAATAATTTCCTTAGC 57.548 34.615 14.50 14.50 46.53 3.09
6108 6925 3.814577 CTTCCGCGGAGAAGAAGAA 57.185 52.632 29.20 10.04 45.08 2.52
6109 6926 1.351153 CTTCCGCGGAGAAGAAGAAC 58.649 55.000 29.20 0.00 45.08 3.01
6110 6927 0.677288 TTCCGCGGAGAAGAAGAACA 59.323 50.000 29.20 6.31 0.00 3.18
6111 6928 0.243907 TCCGCGGAGAAGAAGAACAG 59.756 55.000 27.28 0.00 0.00 3.16
6114 6931 1.603172 CGCGGAGAAGAAGAACAGTGT 60.603 52.381 0.00 0.00 0.00 3.55
6115 6932 2.484889 GCGGAGAAGAAGAACAGTGTT 58.515 47.619 8.61 8.61 0.00 3.32
6116 6933 2.221981 GCGGAGAAGAAGAACAGTGTTG 59.778 50.000 14.57 0.00 0.00 3.33
6148 6965 5.121768 AGTTGATGTAAGTAAATGTGGCGAC 59.878 40.000 0.00 0.00 0.00 5.19
6193 7010 2.618709 GGTTGCTGCTTACACTGAGTTT 59.381 45.455 0.00 0.00 0.00 2.66
6194 7011 3.066760 GGTTGCTGCTTACACTGAGTTTT 59.933 43.478 0.00 0.00 0.00 2.43
6195 7012 4.440112 GGTTGCTGCTTACACTGAGTTTTT 60.440 41.667 0.00 0.00 0.00 1.94
6196 7013 4.552166 TGCTGCTTACACTGAGTTTTTC 57.448 40.909 0.00 0.00 0.00 2.29
6197 7014 4.199310 TGCTGCTTACACTGAGTTTTTCT 58.801 39.130 0.00 0.00 0.00 2.52
6198 7015 4.640201 TGCTGCTTACACTGAGTTTTTCTT 59.360 37.500 0.00 0.00 0.00 2.52
6199 7016 5.125417 TGCTGCTTACACTGAGTTTTTCTTT 59.875 36.000 0.00 0.00 0.00 2.52
6200 7017 6.036470 GCTGCTTACACTGAGTTTTTCTTTT 58.964 36.000 0.00 0.00 0.00 2.27
6201 7018 6.531594 GCTGCTTACACTGAGTTTTTCTTTTT 59.468 34.615 0.00 0.00 0.00 1.94
6202 7019 7.253783 GCTGCTTACACTGAGTTTTTCTTTTTC 60.254 37.037 0.00 0.00 0.00 2.29
6235 7052 9.586435 TTCTTTCTCTCAATTTTGTCCTTTTTC 57.414 29.630 0.00 0.00 0.00 2.29
6358 7179 1.076339 CCTCCTTCCTCGCTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
6415 7246 6.901887 CGCAATAATAAGCTGTGTAGAAAGTG 59.098 38.462 0.00 0.00 0.00 3.16
6418 7249 7.849804 ATAATAAGCTGTGTAGAAAGTGTGG 57.150 36.000 0.00 0.00 0.00 4.17
6421 7252 2.037772 AGCTGTGTAGAAAGTGTGGGAG 59.962 50.000 0.00 0.00 0.00 4.30
6426 7257 4.021104 TGTGTAGAAAGTGTGGGAGATCTG 60.021 45.833 0.00 0.00 0.00 2.90
6436 7267 2.092753 GTGGGAGATCTGGCAGATGAAA 60.093 50.000 33.30 12.01 34.53 2.69
6437 7268 2.781757 TGGGAGATCTGGCAGATGAAAT 59.218 45.455 33.30 16.36 34.53 2.17
6438 7269 3.147629 GGGAGATCTGGCAGATGAAATG 58.852 50.000 33.30 0.00 34.53 2.32
6459 7290 4.274978 TGATGATGAATTCACAGCATGGT 58.725 39.130 19.21 0.00 44.96 3.55
6494 7326 9.545105 AAATTTCAGCATAAATGAACTGTTTCA 57.455 25.926 0.00 0.00 45.93 2.69
6496 7328 5.688823 TCAGCATAAATGAACTGTTTCACG 58.311 37.500 0.00 0.00 44.66 4.35
6501 7333 6.198216 GCATAAATGAACTGTTTCACGTGTTT 59.802 34.615 16.51 7.03 44.66 2.83
6549 7381 7.541162 TCAGAATTGCTGTAAAATCCAGAATG 58.459 34.615 0.00 0.00 45.14 2.67
6793 7637 0.608640 ATTCCTGACTGACACCGACC 59.391 55.000 0.00 0.00 0.00 4.79
6871 7736 0.253327 GGAACGGAAGAAGCCATCCT 59.747 55.000 0.00 0.00 33.16 3.24
6882 7747 4.410099 AGAAGCCATCCTTGTGAAATGAA 58.590 39.130 0.00 0.00 32.78 2.57
6883 7748 4.834496 AGAAGCCATCCTTGTGAAATGAAA 59.166 37.500 0.00 0.00 32.78 2.69
6884 7749 5.482878 AGAAGCCATCCTTGTGAAATGAAAT 59.517 36.000 0.00 0.00 32.78 2.17
6885 7750 5.080969 AGCCATCCTTGTGAAATGAAATG 57.919 39.130 0.00 0.00 0.00 2.32
6886 7751 4.773674 AGCCATCCTTGTGAAATGAAATGA 59.226 37.500 0.00 0.00 0.00 2.57
6899 7764 3.425577 TGAAATGAAATGATGCCGCTC 57.574 42.857 0.00 0.00 0.00 5.03
6925 7790 1.860078 CTCGAACGCACAGGTTTCC 59.140 57.895 0.00 0.00 0.00 3.13
6929 7794 1.202200 CGAACGCACAGGTTTCCAAAA 60.202 47.619 0.00 0.00 0.00 2.44
6930 7795 2.732597 CGAACGCACAGGTTTCCAAAAA 60.733 45.455 0.00 0.00 0.00 1.94
6955 7821 5.022282 CCTTTGGTTCACAATGGTTTTCT 57.978 39.130 0.00 0.00 44.95 2.52
6956 7822 5.427378 CCTTTGGTTCACAATGGTTTTCTT 58.573 37.500 0.00 0.00 44.95 2.52
6957 7823 6.578023 CCTTTGGTTCACAATGGTTTTCTTA 58.422 36.000 0.00 0.00 44.95 2.10
6958 7824 6.701400 CCTTTGGTTCACAATGGTTTTCTTAG 59.299 38.462 0.00 0.00 44.95 2.18
6959 7825 6.783708 TTGGTTCACAATGGTTTTCTTAGT 57.216 33.333 0.00 0.00 33.18 2.24
6960 7826 7.883391 TTGGTTCACAATGGTTTTCTTAGTA 57.117 32.000 0.00 0.00 33.18 1.82
6961 7827 7.266922 TGGTTCACAATGGTTTTCTTAGTAC 57.733 36.000 0.00 0.00 0.00 2.73
6962 7828 6.017770 TGGTTCACAATGGTTTTCTTAGTACG 60.018 38.462 0.00 0.00 0.00 3.67
6963 7829 6.203338 GGTTCACAATGGTTTTCTTAGTACGA 59.797 38.462 0.00 0.00 0.00 3.43
6964 7830 7.254863 GGTTCACAATGGTTTTCTTAGTACGAA 60.255 37.037 0.00 0.00 0.00 3.85
6965 7831 7.972832 TCACAATGGTTTTCTTAGTACGAAT 57.027 32.000 0.00 0.00 0.00 3.34
6966 7832 8.385898 TCACAATGGTTTTCTTAGTACGAATT 57.614 30.769 0.00 0.00 0.00 2.17
6967 7833 9.491675 TCACAATGGTTTTCTTAGTACGAATTA 57.508 29.630 0.00 0.00 0.00 1.40
7001 7867 6.515043 AAAAATGTTCTGCGTGAGAAAATG 57.485 33.333 3.55 0.00 42.56 2.32
7002 7868 4.836125 AATGTTCTGCGTGAGAAAATGT 57.164 36.364 3.55 0.00 42.56 2.71
7003 7869 3.607422 TGTTCTGCGTGAGAAAATGTG 57.393 42.857 1.17 0.00 42.56 3.21
7004 7870 2.942376 TGTTCTGCGTGAGAAAATGTGT 59.058 40.909 1.17 0.00 42.56 3.72
7005 7871 3.002246 TGTTCTGCGTGAGAAAATGTGTC 59.998 43.478 1.17 0.00 42.56 3.67
7006 7872 2.143122 TCTGCGTGAGAAAATGTGTCC 58.857 47.619 0.00 0.00 0.00 4.02
7007 7873 1.872952 CTGCGTGAGAAAATGTGTCCA 59.127 47.619 0.00 0.00 0.00 4.02
7008 7874 2.485426 CTGCGTGAGAAAATGTGTCCAT 59.515 45.455 0.00 0.00 0.00 3.41
7009 7875 2.483877 TGCGTGAGAAAATGTGTCCATC 59.516 45.455 0.00 0.00 0.00 3.51
7010 7876 2.744202 GCGTGAGAAAATGTGTCCATCT 59.256 45.455 0.00 0.00 0.00 2.90
7011 7877 3.189287 GCGTGAGAAAATGTGTCCATCTT 59.811 43.478 0.00 0.00 0.00 2.40
7012 7878 4.670221 GCGTGAGAAAATGTGTCCATCTTC 60.670 45.833 0.00 0.00 29.68 2.87
7013 7879 4.142816 CGTGAGAAAATGTGTCCATCTTCC 60.143 45.833 0.00 0.00 29.79 3.46
7014 7880 4.761739 GTGAGAAAATGTGTCCATCTTCCA 59.238 41.667 0.00 0.00 29.79 3.53
7015 7881 5.416952 GTGAGAAAATGTGTCCATCTTCCAT 59.583 40.000 0.00 0.00 29.79 3.41
7016 7882 5.416639 TGAGAAAATGTGTCCATCTTCCATG 59.583 40.000 0.00 0.00 29.79 3.66
7017 7883 5.573219 AGAAAATGTGTCCATCTTCCATGA 58.427 37.500 0.00 0.00 29.79 3.07
7018 7884 5.651139 AGAAAATGTGTCCATCTTCCATGAG 59.349 40.000 0.00 0.00 29.79 2.90
7019 7885 3.572632 ATGTGTCCATCTTCCATGAGG 57.427 47.619 0.00 0.00 0.00 3.86
7020 7886 2.550175 TGTGTCCATCTTCCATGAGGA 58.450 47.619 0.00 0.00 43.93 3.71
7032 7898 4.789012 TCCATGAGGAAAAAGTTCATGC 57.211 40.909 7.91 0.00 44.21 4.06
7033 7899 3.191162 TCCATGAGGAAAAAGTTCATGCG 59.809 43.478 7.91 3.18 44.21 4.73
7034 7900 3.057315 CCATGAGGAAAAAGTTCATGCGT 60.057 43.478 7.91 0.00 44.21 5.24
7035 7901 3.624326 TGAGGAAAAAGTTCATGCGTG 57.376 42.857 0.00 0.00 35.25 5.34
7036 7902 2.948979 TGAGGAAAAAGTTCATGCGTGT 59.051 40.909 5.68 0.00 35.25 4.49
7037 7903 3.243035 TGAGGAAAAAGTTCATGCGTGTG 60.243 43.478 5.68 0.00 35.25 3.82
7038 7904 2.948979 AGGAAAAAGTTCATGCGTGTGA 59.051 40.909 5.68 0.00 35.25 3.58
7039 7905 3.380004 AGGAAAAAGTTCATGCGTGTGAA 59.620 39.130 5.68 0.18 35.25 3.18
7040 7906 4.109050 GGAAAAAGTTCATGCGTGTGAAA 58.891 39.130 5.68 0.00 39.61 2.69
7041 7907 4.564769 GGAAAAAGTTCATGCGTGTGAAAA 59.435 37.500 5.68 0.00 39.61 2.29
7042 7908 5.234116 GGAAAAAGTTCATGCGTGTGAAAAT 59.766 36.000 5.68 0.00 39.61 1.82
7043 7909 6.419413 GGAAAAAGTTCATGCGTGTGAAAATA 59.581 34.615 5.68 0.00 39.61 1.40
7044 7910 7.043059 GGAAAAAGTTCATGCGTGTGAAAATAA 60.043 33.333 5.68 0.00 39.61 1.40
7045 7911 7.945033 AAAAGTTCATGCGTGTGAAAATAAT 57.055 28.000 5.68 0.00 39.61 1.28
7046 7912 6.932901 AAGTTCATGCGTGTGAAAATAATG 57.067 33.333 5.68 0.00 39.61 1.90
7047 7913 6.012658 AGTTCATGCGTGTGAAAATAATGT 57.987 33.333 5.68 0.00 39.61 2.71
7048 7914 6.086222 AGTTCATGCGTGTGAAAATAATGTC 58.914 36.000 5.68 0.00 39.61 3.06
7049 7915 4.980590 TCATGCGTGTGAAAATAATGTCC 58.019 39.130 5.68 0.00 0.00 4.02
7050 7916 4.457257 TCATGCGTGTGAAAATAATGTCCA 59.543 37.500 5.68 0.00 0.00 4.02
7051 7917 5.125257 TCATGCGTGTGAAAATAATGTCCAT 59.875 36.000 5.68 0.00 0.00 3.41
7052 7918 4.731720 TGCGTGTGAAAATAATGTCCATG 58.268 39.130 0.00 0.00 0.00 3.66
7053 7919 4.217334 TGCGTGTGAAAATAATGTCCATGT 59.783 37.500 0.00 0.00 0.00 3.21
7054 7920 4.558470 GCGTGTGAAAATAATGTCCATGTG 59.442 41.667 0.00 0.00 0.00 3.21
7055 7921 5.698832 CGTGTGAAAATAATGTCCATGTGT 58.301 37.500 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 174 3.644966 TTACCTGGCAGTTTCCTATGG 57.355 47.619 14.43 0.00 0.00 2.74
131 175 3.947834 CCTTTACCTGGCAGTTTCCTATG 59.052 47.826 14.43 0.00 0.00 2.23
166 215 3.808174 ACAAAAGCTTAGACTCGTTGGAC 59.192 43.478 0.00 0.00 0.00 4.02
263 452 8.772705 TGCAAAATTAAGCATTTCTTAAACCTG 58.227 29.630 0.97 1.82 46.77 4.00
312 789 2.961559 AAATTGGGGCACACCTGGCA 62.962 55.000 0.00 0.00 44.99 4.92
400 883 1.726791 CTCGATGGTTCAGTTCGGTTG 59.273 52.381 0.00 0.00 33.82 3.77
409 908 1.375908 GCTGTGCCTCGATGGTTCA 60.376 57.895 0.00 0.00 38.35 3.18
410 909 1.375908 TGCTGTGCCTCGATGGTTC 60.376 57.895 0.00 0.00 38.35 3.62
411 910 1.672356 GTGCTGTGCCTCGATGGTT 60.672 57.895 0.00 0.00 38.35 3.67
412 911 2.046892 GTGCTGTGCCTCGATGGT 60.047 61.111 0.00 0.00 38.35 3.55
413 912 2.046988 TGTGCTGTGCCTCGATGG 60.047 61.111 0.00 0.00 39.35 3.51
414 913 2.747822 GCTGTGCTGTGCCTCGATG 61.748 63.158 0.00 0.00 0.00 3.84
415 914 2.435586 GCTGTGCTGTGCCTCGAT 60.436 61.111 0.00 0.00 0.00 3.59
416 915 3.927548 TGCTGTGCTGTGCCTCGA 61.928 61.111 0.00 0.00 0.00 4.04
417 916 3.720193 GTGCTGTGCTGTGCCTCG 61.720 66.667 0.00 0.00 0.00 4.63
418 917 2.592574 TGTGCTGTGCTGTGCCTC 60.593 61.111 0.00 0.00 0.00 4.70
419 918 2.593725 CTGTGCTGTGCTGTGCCT 60.594 61.111 0.00 0.00 0.00 4.75
420 919 4.338539 GCTGTGCTGTGCTGTGCC 62.339 66.667 0.00 0.00 0.00 5.01
421 920 3.588906 TGCTGTGCTGTGCTGTGC 61.589 61.111 0.00 0.00 0.00 4.57
422 921 1.995646 TTGTGCTGTGCTGTGCTGTG 61.996 55.000 0.00 0.00 0.00 3.66
423 922 1.750018 TTGTGCTGTGCTGTGCTGT 60.750 52.632 0.00 0.00 0.00 4.40
424 923 1.298863 GTTGTGCTGTGCTGTGCTG 60.299 57.895 0.00 0.00 0.00 4.41
425 924 2.484062 GGTTGTGCTGTGCTGTGCT 61.484 57.895 0.00 0.00 0.00 4.40
426 925 2.026590 GGTTGTGCTGTGCTGTGC 59.973 61.111 0.00 0.00 0.00 4.57
427 926 1.650912 GAGGTTGTGCTGTGCTGTG 59.349 57.895 0.00 0.00 0.00 3.66
428 927 1.889105 CGAGGTTGTGCTGTGCTGT 60.889 57.895 0.00 0.00 0.00 4.40
429 928 1.595109 TCGAGGTTGTGCTGTGCTG 60.595 57.895 0.00 0.00 0.00 4.41
436 935 1.295792 TTTCACTGTCGAGGTTGTGC 58.704 50.000 0.00 0.00 0.00 4.57
438 937 3.132289 TCTCTTTTCACTGTCGAGGTTGT 59.868 43.478 0.00 0.00 0.00 3.32
453 952 4.272489 TCCGCCATTGATTCATCTCTTTT 58.728 39.130 0.00 0.00 0.00 2.27
506 1005 1.134280 CCTGTCCCTCAACAGCTATGG 60.134 57.143 0.00 0.00 44.34 2.74
655 1165 2.525877 TAGTAGGCGGGATGGGGC 60.526 66.667 0.00 0.00 0.00 5.80
665 1175 2.679082 TCAGGATGGAAGGTAGTAGGC 58.321 52.381 0.00 0.00 36.16 3.93
671 1181 5.533112 AGAAGAAGATCAGGATGGAAGGTA 58.467 41.667 0.00 0.00 36.16 3.08
718 1243 1.863155 TTGGGGGAGGAGGAATGTGC 61.863 60.000 0.00 0.00 0.00 4.57
780 1305 1.281925 GGAGCAAGATGGGGGAAGGA 61.282 60.000 0.00 0.00 0.00 3.36
842 1367 4.135153 CTGCGGGGGTGACGAGAG 62.135 72.222 0.00 0.00 0.00 3.20
843 1368 4.671590 TCTGCGGGGGTGACGAGA 62.672 66.667 0.00 0.00 0.00 4.04
872 1397 2.032071 AACGAGGCCCAAAGACCG 59.968 61.111 0.00 0.00 0.00 4.79
894 1419 1.704007 GCCTCCCCTCCCAGATCAAG 61.704 65.000 0.00 0.00 0.00 3.02
895 1420 1.694169 GCCTCCCCTCCCAGATCAA 60.694 63.158 0.00 0.00 0.00 2.57
897 1422 3.237741 CGCCTCCCCTCCCAGATC 61.238 72.222 0.00 0.00 0.00 2.75
898 1423 3.765257 CTCGCCTCCCCTCCCAGAT 62.765 68.421 0.00 0.00 0.00 2.90
913 1450 2.202797 CCGCCACAGATCACCTCG 60.203 66.667 0.00 0.00 0.00 4.63
932 1469 5.049474 TCACAACTTTCAGATCAAATCACGG 60.049 40.000 0.00 0.00 0.00 4.94
1293 2042 3.364249 CTCGTCGTCGTCCAGGTCG 62.364 68.421 0.00 0.00 38.33 4.79
1324 2073 2.485966 ACCACTATCAGCATCCTCCT 57.514 50.000 0.00 0.00 0.00 3.69
1326 2075 3.388024 TGGTAACCACTATCAGCATCCTC 59.612 47.826 0.00 0.00 0.00 3.71
1327 2076 3.384168 TGGTAACCACTATCAGCATCCT 58.616 45.455 0.00 0.00 0.00 3.24
1344 2093 2.677524 CCGGACCTGGTCGTGGTA 60.678 66.667 22.07 0.00 38.03 3.25
1593 2342 3.470567 CGGTGCTTCTCGACGTGC 61.471 66.667 0.00 0.00 0.00 5.34
1611 2360 4.710167 TGGACGACGCCGGAGAGA 62.710 66.667 13.83 0.00 40.78 3.10
1707 2456 2.305009 GAAGCAGAGGGAATGAATGGG 58.695 52.381 0.00 0.00 0.00 4.00
1774 2526 5.312895 ACAGTCAGTTTGGCACATTGTATA 58.687 37.500 0.00 0.00 39.30 1.47
1775 2527 4.144297 ACAGTCAGTTTGGCACATTGTAT 58.856 39.130 0.00 0.00 39.30 2.29
1800 2552 4.123506 TGTGTGTCGAAATCAGCAAGTAA 58.876 39.130 0.00 0.00 0.00 2.24
1802 2554 2.560504 TGTGTGTCGAAATCAGCAAGT 58.439 42.857 0.00 0.00 0.00 3.16
1808 2560 3.304592 CCAGCATTTGTGTGTCGAAATCA 60.305 43.478 0.00 0.00 0.00 2.57
1817 2569 3.567164 AGAGAAGTTCCAGCATTTGTGTG 59.433 43.478 0.00 0.00 0.00 3.82
1818 2570 3.825328 AGAGAAGTTCCAGCATTTGTGT 58.175 40.909 0.00 0.00 0.00 3.72
1879 2632 8.872845 GCTGTTCAAAATTGAAGAAGAAGAAAA 58.127 29.630 16.81 0.00 46.80 2.29
2004 2759 5.529581 CCAAAACCTTTTCTTGGCTAGAA 57.470 39.130 7.31 7.31 41.11 2.10
2010 2765 2.212652 GCTGCCAAAACCTTTTCTTGG 58.787 47.619 0.00 0.00 42.17 3.61
2011 2766 2.212652 GGCTGCCAAAACCTTTTCTTG 58.787 47.619 15.17 0.00 0.00 3.02
2012 2767 1.202521 CGGCTGCCAAAACCTTTTCTT 60.203 47.619 20.29 0.00 0.00 2.52
2013 2768 0.389025 CGGCTGCCAAAACCTTTTCT 59.611 50.000 20.29 0.00 0.00 2.52
2014 2769 0.104120 ACGGCTGCCAAAACCTTTTC 59.896 50.000 20.29 0.00 0.00 2.29
2015 2770 0.179086 CACGGCTGCCAAAACCTTTT 60.179 50.000 20.29 0.00 0.00 2.27
2045 2800 4.274459 GTGCTGCCTTCAATTATACTCTGG 59.726 45.833 0.00 0.00 0.00 3.86
2124 2885 2.658373 TGCAATGTTCATGGTGATGC 57.342 45.000 0.00 0.00 31.37 3.91
2234 2999 1.385528 TATGCAGCAACAGAGGCATG 58.614 50.000 0.00 0.00 45.74 4.06
2484 3257 1.058284 TTGTTAGGTTAGTGCCGGGT 58.942 50.000 2.18 0.00 0.00 5.28
2544 3317 5.357878 TCAAATGTTAGGAGCATCAACATCC 59.642 40.000 6.49 0.00 40.94 3.51
2568 3341 8.508875 CAGCATTTTTAGCAAATTTCTTCCAAT 58.491 29.630 0.00 0.00 0.00 3.16
2592 3365 2.952978 ACTATCTTCTACCACCTCGCAG 59.047 50.000 0.00 0.00 0.00 5.18
2595 3368 6.204495 GGTTACTACTATCTTCTACCACCTCG 59.796 46.154 0.00 0.00 0.00 4.63
2664 3439 2.222911 GTCAGTCAGAGAAAGCAACAGC 59.777 50.000 0.00 0.00 0.00 4.40
2720 3495 0.240145 GCTCCAAAACGGTAGGCAAC 59.760 55.000 0.00 0.00 35.57 4.17
2763 3538 1.277273 CAGTCTCCATGAACAGCTGGA 59.723 52.381 19.93 4.12 39.23 3.86
2809 3584 1.067915 TCGCCCTTGCTTATTTGCAAC 60.068 47.619 0.00 0.00 46.43 4.17
3016 3792 3.161866 GGTCAAATGTTAGGCCTTTCCA 58.838 45.455 12.58 5.77 37.29 3.53
3017 3793 3.431415 AGGTCAAATGTTAGGCCTTTCC 58.569 45.455 12.58 0.00 0.00 3.13
3274 4056 7.499563 AGGATTCTTCTTCATCTTCATGTCATG 59.500 37.037 6.47 6.47 0.00 3.07
3275 4057 7.575505 AGGATTCTTCTTCATCTTCATGTCAT 58.424 34.615 0.00 0.00 0.00 3.06
3276 4058 6.955364 AGGATTCTTCTTCATCTTCATGTCA 58.045 36.000 0.00 0.00 0.00 3.58
3277 4059 7.862512 AAGGATTCTTCTTCATCTTCATGTC 57.137 36.000 0.00 0.00 0.00 3.06
3278 4060 8.521176 CAAAAGGATTCTTCTTCATCTTCATGT 58.479 33.333 0.00 0.00 31.82 3.21
3594 4379 1.977056 AAACACGGGGGAGACTTTTC 58.023 50.000 0.00 0.00 0.00 2.29
3694 4481 5.287226 ACTCAGGTTAAGTACACTTGTTCG 58.713 41.667 4.86 0.00 37.40 3.95
3696 4483 6.646267 TCAACTCAGGTTAAGTACACTTGTT 58.354 36.000 4.86 0.00 37.40 2.83
3716 4503 6.136071 CAGTACTGCAAACAATGTACTCAAC 58.864 40.000 10.54 0.00 42.23 3.18
3738 4525 5.403166 CACAATGCAAAGTATGGTCAAACAG 59.597 40.000 0.00 0.00 0.00 3.16
3752 4544 3.999001 TGCACAAACTTTCACAATGCAAA 59.001 34.783 0.00 0.00 38.56 3.68
3929 4728 5.208463 TGCAACTGTCTCACAATACTACA 57.792 39.130 0.00 0.00 0.00 2.74
4010 4809 2.708759 TCTAAAACTTCCTCCCACCCA 58.291 47.619 0.00 0.00 0.00 4.51
4181 4980 0.466372 GCCCAGAATTAGGCTCCACC 60.466 60.000 0.00 0.00 46.14 4.61
4254 5054 8.023021 AGCTGTGATTATATCAACCTCAACTA 57.977 34.615 0.00 0.00 41.69 2.24
4293 5093 4.695396 TCCACTAGTCGTTTGCAAACTTA 58.305 39.130 33.03 21.42 36.77 2.24
4356 5156 0.400213 ACGCCCTGTCCATTTCAAGA 59.600 50.000 0.00 0.00 0.00 3.02
4389 5189 2.616330 CGCGGACATTGTTGCCACT 61.616 57.895 0.00 0.00 0.00 4.00
4398 5198 4.077184 TTCTCGCCCGCGGACATT 62.077 61.111 30.73 0.00 40.25 2.71
4765 5565 7.254727 GCCAATCAGAGATCATTACTTGACTTC 60.255 40.741 0.00 0.00 37.11 3.01
5003 5806 1.292242 TCTGAGGATCCTAGTGGGCTT 59.708 52.381 16.16 0.00 34.39 4.35
5352 6161 8.650143 AAAGGGATGTTGATAATTGTGTAAGT 57.350 30.769 0.00 0.00 0.00 2.24
5370 6179 3.557264 GGTCAGTCAACTTCGAAAGGGAT 60.557 47.826 0.00 0.00 0.00 3.85
5552 6361 0.838122 ACTAGTGGGGTGCAGCTCTT 60.838 55.000 18.13 7.93 0.00 2.85
5605 6414 2.169789 CAGCGATCAGTGCTTCGGG 61.170 63.158 14.50 0.00 41.72 5.14
5661 6471 2.915604 ACACAGATGGAGTGAGGGATTT 59.084 45.455 0.00 0.00 40.16 2.17
5684 6494 4.574828 GTCTTTCTGGTGCAACTAACAGAA 59.425 41.667 2.04 8.89 45.24 3.02
5685 6495 4.127171 GTCTTTCTGGTGCAACTAACAGA 58.873 43.478 2.04 2.79 38.12 3.41
5686 6496 3.251004 GGTCTTTCTGGTGCAACTAACAG 59.749 47.826 2.04 0.20 36.74 3.16
5687 6497 3.211045 GGTCTTTCTGGTGCAACTAACA 58.789 45.455 2.04 0.00 36.74 2.41
5688 6498 2.552743 GGGTCTTTCTGGTGCAACTAAC 59.447 50.000 2.04 0.00 36.74 2.34
5689 6499 2.441750 AGGGTCTTTCTGGTGCAACTAA 59.558 45.455 2.04 0.00 36.74 2.24
5710 6525 3.234353 TGCATTGTGGTGGTTGGAAATA 58.766 40.909 0.00 0.00 0.00 1.40
5767 6583 3.837213 CCATTTGGTAGCAGTTCAGTG 57.163 47.619 0.00 0.00 0.00 3.66
6106 6923 1.141053 ACTCCACTCCCAACACTGTTC 59.859 52.381 0.00 0.00 0.00 3.18
6108 6925 1.134098 CAACTCCACTCCCAACACTGT 60.134 52.381 0.00 0.00 0.00 3.55
6109 6926 1.140852 TCAACTCCACTCCCAACACTG 59.859 52.381 0.00 0.00 0.00 3.66
6110 6927 1.507140 TCAACTCCACTCCCAACACT 58.493 50.000 0.00 0.00 0.00 3.55
6111 6928 2.154462 CATCAACTCCACTCCCAACAC 58.846 52.381 0.00 0.00 0.00 3.32
6114 6931 3.650942 ACTTACATCAACTCCACTCCCAA 59.349 43.478 0.00 0.00 0.00 4.12
6115 6932 3.248024 ACTTACATCAACTCCACTCCCA 58.752 45.455 0.00 0.00 0.00 4.37
6116 6933 3.983044 ACTTACATCAACTCCACTCCC 57.017 47.619 0.00 0.00 0.00 4.30
6168 6985 2.104792 TCAGTGTAAGCAGCAACCTTCT 59.895 45.455 0.00 0.00 0.00 2.85
6346 7167 2.230189 ATCACCCAGAGGAGCGAGGA 62.230 60.000 0.00 0.00 36.73 3.71
6347 7168 1.743321 GATCACCCAGAGGAGCGAGG 61.743 65.000 0.00 0.00 36.73 4.63
6348 7169 0.754957 AGATCACCCAGAGGAGCGAG 60.755 60.000 0.00 0.00 36.73 5.03
6349 7170 0.753479 GAGATCACCCAGAGGAGCGA 60.753 60.000 0.00 0.00 36.73 4.93
6358 7179 1.043116 AGAATCCGCGAGATCACCCA 61.043 55.000 8.23 0.00 32.47 4.51
6382 7205 3.065233 CAGCTTATTATTGCGCTCCACAA 59.935 43.478 9.73 0.00 0.00 3.33
6415 7246 1.126488 TCATCTGCCAGATCTCCCAC 58.874 55.000 3.68 0.00 31.32 4.61
6418 7249 4.082665 TCATTTCATCTGCCAGATCTCC 57.917 45.455 3.68 0.00 31.32 3.71
6421 7252 5.705905 TCATCATCATTTCATCTGCCAGATC 59.294 40.000 3.68 0.00 31.32 2.75
6426 7257 6.641314 GTGAATTCATCATCATTTCATCTGCC 59.359 38.462 12.12 0.00 40.97 4.85
6436 7267 4.893524 ACCATGCTGTGAATTCATCATCAT 59.106 37.500 12.12 14.32 40.97 2.45
6437 7268 4.274978 ACCATGCTGTGAATTCATCATCA 58.725 39.130 12.12 12.84 40.97 3.07
6438 7269 4.913335 ACCATGCTGTGAATTCATCATC 57.087 40.909 12.12 7.93 40.97 2.92
6459 7290 7.660617 TCATTTATGCTGAAATTTGCTGGAAAA 59.339 29.630 0.00 0.00 0.00 2.29
6507 7339 5.384063 TTCTGAACAACAGCAAAGAAACA 57.616 34.783 0.00 0.00 45.38 2.83
6508 7340 6.699063 CAATTCTGAACAACAGCAAAGAAAC 58.301 36.000 0.00 0.00 45.38 2.78
6549 7381 4.828829 TCTCCCGAACAGGAAACTAAATC 58.171 43.478 0.00 0.00 45.00 2.17
6793 7637 1.597302 AGCACAGCACAGTCAGCAG 60.597 57.895 0.00 0.00 0.00 4.24
6826 7688 0.038744 ATCAGAAAGCCCACCCACAG 59.961 55.000 0.00 0.00 0.00 3.66
6871 7736 6.091034 CGGCATCATTTCATTTCATTTCACAA 59.909 34.615 0.00 0.00 0.00 3.33
6882 7747 1.406539 GGTGAGCGGCATCATTTCATT 59.593 47.619 1.45 0.00 0.00 2.57
6883 7748 1.027357 GGTGAGCGGCATCATTTCAT 58.973 50.000 1.45 0.00 0.00 2.57
6884 7749 1.031571 GGGTGAGCGGCATCATTTCA 61.032 55.000 1.45 0.00 0.00 2.69
6885 7750 1.031571 TGGGTGAGCGGCATCATTTC 61.032 55.000 1.45 0.00 0.00 2.17
6886 7751 1.001020 TGGGTGAGCGGCATCATTT 60.001 52.632 1.45 0.00 0.00 2.32
6978 7844 6.019640 CACATTTTCTCACGCAGAACATTTTT 60.020 34.615 0.00 0.00 41.13 1.94
6979 7845 5.459762 CACATTTTCTCACGCAGAACATTTT 59.540 36.000 0.00 0.00 41.13 1.82
6980 7846 4.977963 CACATTTTCTCACGCAGAACATTT 59.022 37.500 0.00 0.00 41.13 2.32
6981 7847 4.036734 ACACATTTTCTCACGCAGAACATT 59.963 37.500 0.00 0.00 41.13 2.71
6982 7848 3.565482 ACACATTTTCTCACGCAGAACAT 59.435 39.130 0.00 0.00 41.13 2.71
6983 7849 2.942376 ACACATTTTCTCACGCAGAACA 59.058 40.909 0.00 0.00 41.13 3.18
6984 7850 3.545633 GACACATTTTCTCACGCAGAAC 58.454 45.455 0.00 0.00 41.13 3.01
6985 7851 2.548057 GGACACATTTTCTCACGCAGAA 59.452 45.455 0.00 0.00 39.56 3.02
6986 7852 2.143122 GGACACATTTTCTCACGCAGA 58.857 47.619 0.00 0.00 0.00 4.26
6987 7853 1.872952 TGGACACATTTTCTCACGCAG 59.127 47.619 0.00 0.00 0.00 5.18
6988 7854 1.960417 TGGACACATTTTCTCACGCA 58.040 45.000 0.00 0.00 0.00 5.24
6989 7855 2.744202 AGATGGACACATTTTCTCACGC 59.256 45.455 0.00 0.00 37.47 5.34
6990 7856 4.142816 GGAAGATGGACACATTTTCTCACG 60.143 45.833 9.77 0.00 43.81 4.35
6991 7857 4.761739 TGGAAGATGGACACATTTTCTCAC 59.238 41.667 9.77 0.00 43.81 3.51
6992 7858 4.984295 TGGAAGATGGACACATTTTCTCA 58.016 39.130 9.77 5.18 43.81 3.27
6993 7859 5.649395 TCATGGAAGATGGACACATTTTCTC 59.351 40.000 9.77 3.26 43.81 2.87
6994 7860 5.573219 TCATGGAAGATGGACACATTTTCT 58.427 37.500 9.77 0.00 43.81 2.52
6995 7861 5.163581 CCTCATGGAAGATGGACACATTTTC 60.164 44.000 0.00 3.25 43.68 2.29
6996 7862 4.708421 CCTCATGGAAGATGGACACATTTT 59.292 41.667 0.00 0.00 34.35 1.82
6997 7863 4.018141 TCCTCATGGAAGATGGACACATTT 60.018 41.667 0.00 0.00 39.87 2.32
6998 7864 3.524789 TCCTCATGGAAGATGGACACATT 59.475 43.478 0.00 0.00 39.87 2.71
6999 7865 3.117745 TCCTCATGGAAGATGGACACAT 58.882 45.455 0.00 0.00 39.87 3.21
7000 7866 2.550175 TCCTCATGGAAGATGGACACA 58.450 47.619 0.00 0.00 39.87 3.72
7001 7867 3.634397 TTCCTCATGGAAGATGGACAC 57.366 47.619 0.00 0.00 46.57 3.67
7011 7877 3.191162 CGCATGAACTTTTTCCTCATGGA 59.809 43.478 11.94 0.00 44.32 3.41
7012 7878 3.057315 ACGCATGAACTTTTTCCTCATGG 60.057 43.478 11.94 6.03 44.32 3.66
7013 7879 3.916172 CACGCATGAACTTTTTCCTCATG 59.084 43.478 0.00 6.87 46.04 3.07
7014 7880 3.569701 ACACGCATGAACTTTTTCCTCAT 59.430 39.130 0.00 0.00 0.00 2.90
7015 7881 2.948979 ACACGCATGAACTTTTTCCTCA 59.051 40.909 0.00 0.00 0.00 3.86
7016 7882 3.003275 TCACACGCATGAACTTTTTCCTC 59.997 43.478 0.00 0.00 0.00 3.71
7017 7883 2.948979 TCACACGCATGAACTTTTTCCT 59.051 40.909 0.00 0.00 0.00 3.36
7018 7884 3.347958 TCACACGCATGAACTTTTTCC 57.652 42.857 0.00 0.00 0.00 3.13
7019 7885 5.694674 TTTTCACACGCATGAACTTTTTC 57.305 34.783 0.00 0.00 38.31 2.29
7020 7886 7.763172 TTATTTTCACACGCATGAACTTTTT 57.237 28.000 0.00 0.00 38.31 1.94
7021 7887 7.437862 ACATTATTTTCACACGCATGAACTTTT 59.562 29.630 0.00 0.00 38.31 2.27
7022 7888 6.922957 ACATTATTTTCACACGCATGAACTTT 59.077 30.769 0.00 0.00 38.31 2.66
7023 7889 6.446318 ACATTATTTTCACACGCATGAACTT 58.554 32.000 0.00 0.00 38.31 2.66
7024 7890 6.012658 ACATTATTTTCACACGCATGAACT 57.987 33.333 0.00 0.00 38.31 3.01
7025 7891 5.286082 GGACATTATTTTCACACGCATGAAC 59.714 40.000 0.00 0.00 38.31 3.18
7026 7892 5.048434 TGGACATTATTTTCACACGCATGAA 60.048 36.000 0.00 0.00 36.80 2.57
7027 7893 4.457257 TGGACATTATTTTCACACGCATGA 59.543 37.500 0.00 0.00 0.00 3.07
7028 7894 4.731720 TGGACATTATTTTCACACGCATG 58.268 39.130 0.00 0.00 0.00 4.06
7029 7895 5.105797 ACATGGACATTATTTTCACACGCAT 60.106 36.000 0.00 0.00 0.00 4.73
7030 7896 4.217334 ACATGGACATTATTTTCACACGCA 59.783 37.500 0.00 0.00 0.00 5.24
7031 7897 4.558470 CACATGGACATTATTTTCACACGC 59.442 41.667 0.00 0.00 0.00 5.34
7032 7898 5.698832 ACACATGGACATTATTTTCACACG 58.301 37.500 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.