Multiple sequence alignment - TraesCS5A01G256700

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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 TraesCS5A01G256700 chr5A 100.000 5451 0 0 1 5451 472273579 472279029 0.000000e+00 10067.0
1 TraesCS5A01G256700 chr5B 91.893 4564 250 56 1 4533 439055542 439060016 0.000000e+00 6268.0
2 TraesCS5A01G256700 chr5B 89.189 666 49 13 4531 5184 439060062 439060716 0.000000e+00 809.0
3 TraesCS5A01G256700 chr5B 88.550 131 12 3 5313 5443 439060879 439061006 7.310000e-34 156.0
4 TraesCS5A01G256700 chr5B 88.333 60 3 3 5195 5251 705988901 705988843 9.800000e-08 69.4
5 TraesCS5A01G256700 chr5B 96.970 33 1 0 978 1010 126239503 126239471 7.630000e-04 56.5
6 TraesCS5A01G256700 chr5D 94.288 1243 56 9 3213 4453 369719493 369720722 0.000000e+00 1888.0
7 TraesCS5A01G256700 chr5D 95.545 1055 37 5 802 1853 369715613 369716660 0.000000e+00 1679.0
8 TraesCS5A01G256700 chr5D 97.636 719 13 2 2368 3085 369717397 369718112 0.000000e+00 1230.0
9 TraesCS5A01G256700 chr5D 88.473 668 56 9 4531 5191 369720829 369721482 0.000000e+00 787.0
10 TraesCS5A01G256700 chr5D 84.029 814 93 22 1 795 369714775 369715570 0.000000e+00 749.0
11 TraesCS5A01G256700 chr5D 91.525 413 31 3 1852 2264 369716876 369717284 2.850000e-157 566.0
12 TraesCS5A01G256700 chr5D 94.631 149 6 2 3077 3224 369718765 369718912 4.250000e-56 230.0
13 TraesCS5A01G256700 chr5D 96.694 121 3 1 2219 2339 369717282 369717401 3.330000e-47 200.0
14 TraesCS5A01G256700 chr5D 96.970 33 1 0 978 1010 114889192 114889160 7.630000e-04 56.5
15 TraesCS5A01G256700 chr7A 94.286 35 2 0 971 1005 567587335 567587369 3.000000e-03 54.7
16 TraesCS5A01G256700 chr7A 100.000 28 0 0 976 1003 451521221 451521194 1.000000e-02 52.8
17 TraesCS5A01G256700 chr1B 96.970 33 0 1 971 1003 655104379 655104348 3.000000e-03 54.7
18 TraesCS5A01G256700 chr7B 100.000 28 0 0 978 1005 530383448 530383475 1.000000e-02 52.8


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 TraesCS5A01G256700 chr5A 472273579 472279029 5450 False 10067.000 10067 100.000000 1 5451 1 chr5A.!!$F1 5450
1 TraesCS5A01G256700 chr5B 439055542 439061006 5464 False 2411.000 6268 89.877333 1 5443 3 chr5B.!!$F1 5442
2 TraesCS5A01G256700 chr5D 369714775 369721482 6707 False 916.125 1888 92.852625 1 5191 8 chr5D.!!$F1 5190

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
706 717 0.037697 TCGTTGGTGCAATCGTAGCT 60.038 50.000 0.0 0.00 0.00 3.32 F
979 1037 0.473886 AACCACAGCACCTACCTCCT 60.474 55.000 0.0 0.00 0.00 3.69 F
2407 2728 0.108945 GGACCAATTGCAGCTTGCTC 60.109 55.000 0.0 2.79 45.31 4.26 F
3392 4966 1.206849 TGCGTGGATCATAGAAGTGCA 59.793 47.619 0.0 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2280 0.963225 GGGGTACGGTTGCAACAAAT 59.037 50.0 29.55 16.69 0.00 2.32 R
2581 2902 2.770802 CAGATTCATCCACCTCCTCAGT 59.229 50.0 0.00 0.00 0.00 3.41 R
3451 5030 1.032014 AACAAGCATGAAAGCACCGT 58.968 45.0 0.00 0.00 36.85 4.83 R
5146 6785 0.475044 AACGCCCAACCTAAGGACAA 59.525 50.0 0.00 0.00 0.00 3.18 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
122 125 2.635444 CGAACACAAACTAAACTGGCG 58.365 47.619 0.00 0.00 0.00 5.69
126 129 3.275999 ACACAAACTAAACTGGCGACTT 58.724 40.909 0.00 0.00 0.00 3.01
203 206 3.438087 CACTCGAGCAATTCTCACCATTT 59.562 43.478 13.61 0.00 41.98 2.32
314 320 2.038387 ATTGTAGGCCCACGATTCAC 57.962 50.000 0.00 0.00 0.00 3.18
322 329 1.406069 GCCCACGATTCACTGAGATGT 60.406 52.381 0.00 0.00 0.00 3.06
335 342 5.426509 TCACTGAGATGTATGTCCCTCAATT 59.573 40.000 0.00 0.00 35.52 2.32
337 344 4.454678 TGAGATGTATGTCCCTCAATTGC 58.545 43.478 0.00 0.00 33.26 3.56
339 346 2.435372 TGTATGTCCCTCAATTGCCC 57.565 50.000 0.00 0.00 0.00 5.36
349 356 3.447229 CCCTCAATTGCCCGATAAAACTT 59.553 43.478 0.00 0.00 0.00 2.66
381 388 4.039852 TGTCGCAAGCATATCTACCCATTA 59.960 41.667 0.00 0.00 37.18 1.90
424 433 8.739039 CACTTCCAAAACACAATAGATATTGGA 58.261 33.333 15.17 0.00 45.54 3.53
430 439 6.382869 AACACAATAGATATTGGAAGCAGC 57.617 37.500 15.17 0.00 45.54 5.25
437 446 0.530744 TATTGGAAGCAGCGACGAGT 59.469 50.000 0.00 0.00 0.00 4.18
454 463 6.306356 GCGACGAGTGATAAAGTTACAAACTA 59.694 38.462 0.00 0.00 41.91 2.24
493 502 9.575783 TTTAAGTTTGAAATTGTCCACTAACAC 57.424 29.630 0.00 0.00 0.00 3.32
553 563 7.681441 TCCCCCTATTCCATCTATATAACCAT 58.319 38.462 0.00 0.00 0.00 3.55
590 600 1.482954 CTCACATGGGCTCTCTCAGA 58.517 55.000 0.00 0.00 0.00 3.27
643 654 5.456186 GCTAATATAGGAAAGGAAGGCACCA 60.456 44.000 3.78 0.00 0.00 4.17
682 693 1.134699 CGCTCTCCCATACACACACAT 60.135 52.381 0.00 0.00 0.00 3.21
684 695 3.243873 CGCTCTCCCATACACACACATAT 60.244 47.826 0.00 0.00 0.00 1.78
693 704 2.076100 ACACACACATATGCTCGTTGG 58.924 47.619 1.58 0.00 0.00 3.77
706 717 0.037697 TCGTTGGTGCAATCGTAGCT 60.038 50.000 0.00 0.00 0.00 3.32
718 729 2.060326 TCGTAGCTTGTTTGTCTCGG 57.940 50.000 0.00 0.00 0.00 4.63
734 754 5.651530 TGTCTCGGTCTAGATTCATCAAAC 58.348 41.667 0.00 0.00 0.00 2.93
748 768 8.446273 AGATTCATCAAACTCGTTCAACTTATG 58.554 33.333 0.00 0.00 0.00 1.90
749 769 7.490962 TTCATCAAACTCGTTCAACTTATGT 57.509 32.000 0.00 0.00 0.00 2.29
753 773 7.310072 TCAAACTCGTTCAACTTATGTTTCA 57.690 32.000 0.00 0.00 33.52 2.69
771 791 2.392662 TCAAGCCCACACAAATTTGGA 58.607 42.857 21.74 3.79 34.46 3.53
795 815 4.653806 TTTGTTTTGTTTTTGCCACTCG 57.346 36.364 0.00 0.00 0.00 4.18
798 818 3.675698 TGTTTTGTTTTTGCCACTCGAAC 59.324 39.130 0.00 0.00 0.00 3.95
845 902 5.170748 GTCAAATTTGAAGTGGCATAAGGG 58.829 41.667 22.07 0.00 39.21 3.95
851 908 4.314522 TGAAGTGGCATAAGGGAAATGA 57.685 40.909 0.00 0.00 0.00 2.57
893 950 5.436175 ACAACAAAATTTCTCCCCCAAAAG 58.564 37.500 0.00 0.00 0.00 2.27
936 994 1.587054 CACGGTCTCACTCTCACCC 59.413 63.158 0.00 0.00 0.00 4.61
977 1035 1.207329 CCTAACCACAGCACCTACCTC 59.793 57.143 0.00 0.00 0.00 3.85
978 1036 1.207329 CTAACCACAGCACCTACCTCC 59.793 57.143 0.00 0.00 0.00 4.30
979 1037 0.473886 AACCACAGCACCTACCTCCT 60.474 55.000 0.00 0.00 0.00 3.69
980 1038 0.905337 ACCACAGCACCTACCTCCTC 60.905 60.000 0.00 0.00 0.00 3.71
981 1039 1.617947 CCACAGCACCTACCTCCTCC 61.618 65.000 0.00 0.00 0.00 4.30
982 1040 0.616111 CACAGCACCTACCTCCTCCT 60.616 60.000 0.00 0.00 0.00 3.69
1131 1189 1.198759 ACAACGCCTACACCATCCCT 61.199 55.000 0.00 0.00 0.00 4.20
1205 1263 1.201429 TTCCCTTCCTCCACCTCTGC 61.201 60.000 0.00 0.00 0.00 4.26
1323 1381 2.266055 GTGGCCTCCTCCTTCGTG 59.734 66.667 3.32 0.00 0.00 4.35
1365 1423 1.671379 GCAACTTCCCCTGGACGTC 60.671 63.158 7.13 7.13 32.93 4.34
1678 1736 2.573915 GGATGAAAGTGAGGAAGAGGGT 59.426 50.000 0.00 0.00 0.00 4.34
1720 1778 4.093556 GTGGAAAATGATGAGGAGTTCGAC 59.906 45.833 0.00 0.00 0.00 4.20
1721 1779 4.253685 GGAAAATGATGAGGAGTTCGACA 58.746 43.478 0.00 0.00 0.00 4.35
1731 1789 3.165875 AGGAGTTCGACAATGAAGAGGA 58.834 45.455 0.00 0.00 0.00 3.71
1778 1836 5.808540 CGATTGCTGGATGAACAATTTGATT 59.191 36.000 2.79 0.00 34.28 2.57
1803 1861 6.913170 TGGTGAGCTTCTTTCATTTGATAAC 58.087 36.000 0.00 0.00 0.00 1.89
1807 1865 6.375455 TGAGCTTCTTTCATTTGATAACCCTC 59.625 38.462 0.00 0.00 0.00 4.30
1831 1889 2.029743 TTGCTTTGCAAGACGGTCC 58.970 52.632 4.14 0.00 43.99 4.46
1895 2170 6.005583 TGATTGCTAGCTTGTTTCTGAAAG 57.994 37.500 17.23 0.00 0.00 2.62
1954 2229 8.029642 ACTATAACTTGCTAACACACAATGAC 57.970 34.615 0.00 0.00 0.00 3.06
1997 2272 6.627243 TGTTACTGTCAGCGTTGAATACTAT 58.373 36.000 2.60 0.00 34.49 2.12
1998 2273 7.764331 TGTTACTGTCAGCGTTGAATACTATA 58.236 34.615 2.60 0.00 34.49 1.31
1999 2274 7.699391 TGTTACTGTCAGCGTTGAATACTATAC 59.301 37.037 2.60 0.00 34.49 1.47
2000 2275 6.452494 ACTGTCAGCGTTGAATACTATACT 57.548 37.500 2.60 0.00 34.49 2.12
2005 2280 5.361571 TCAGCGTTGAATACTATACTTCCCA 59.638 40.000 0.00 0.00 0.00 4.37
2017 2292 2.908688 ACTTCCCATTTGTTGCAACC 57.091 45.000 26.14 9.39 0.00 3.77
2026 2301 0.763652 TTGTTGCAACCGTACCCCTA 59.236 50.000 26.14 1.54 0.00 3.53
2037 2314 3.236896 CCGTACCCCTACTGTTATGGAT 58.763 50.000 0.00 0.00 0.00 3.41
2147 2424 3.190744 TCAGTAGATTCAACGCGTTCTCT 59.809 43.478 23.92 23.71 0.00 3.10
2150 2427 5.172232 CAGTAGATTCAACGCGTTCTCTATG 59.828 44.000 23.92 19.62 0.00 2.23
2195 2472 3.127425 AGGCACTTTCCTGTTGTAGAC 57.873 47.619 0.00 0.00 34.56 2.59
2207 2484 6.120905 TCCTGTTGTAGACTAGGACTATGTC 58.879 44.000 0.00 0.00 33.46 3.06
2221 2498 9.582431 CTAGGACTATGTCGAAAGTTAAATTGA 57.418 33.333 0.00 0.00 32.65 2.57
2270 2589 7.805083 ATAGGATGGAGTATCTTGTATTGCT 57.195 36.000 0.00 0.00 36.03 3.91
2303 2622 2.288395 CCGCCTGCTGTTTCTGAAATTT 60.288 45.455 6.06 0.00 0.00 1.82
2340 2659 5.129634 TGTTCTATGCTTTGAACCTTCACA 58.870 37.500 19.10 3.21 41.10 3.58
2344 2663 7.994425 TCTATGCTTTGAACCTTCACATTTA 57.006 32.000 0.00 0.00 36.83 1.40
2346 2665 9.023962 TCTATGCTTTGAACCTTCACATTTATT 57.976 29.630 0.00 0.00 36.83 1.40
2349 2668 9.995003 ATGCTTTGAACCTTCACATTTATTTTA 57.005 25.926 0.00 0.00 36.83 1.52
2388 2708 4.804108 ACTTCAGATCTTGACTTCTCGTG 58.196 43.478 0.00 0.00 34.94 4.35
2407 2728 0.108945 GGACCAATTGCAGCTTGCTC 60.109 55.000 0.00 2.79 45.31 4.26
2520 2841 7.725251 AGTTGTTCCACAATCAAAATGTATGT 58.275 30.769 0.00 0.00 40.59 2.29
2581 2902 3.020984 GGAAAACTTGACTCAACCACCA 58.979 45.455 0.00 0.00 0.00 4.17
2685 3006 3.884895 TGAAGAGGTCTTGCTTGTTTCA 58.115 40.909 0.00 0.00 36.11 2.69
2757 3078 6.100004 CACGTACTCTAACTTGGACAATCAT 58.900 40.000 0.00 0.00 0.00 2.45
3155 4138 8.253113 CCATTCTTAAAAATTGACCAGCTACAT 58.747 33.333 0.00 0.00 0.00 2.29
3164 4147 7.886629 AATTGACCAGCTACATGTGATAAAT 57.113 32.000 9.11 0.00 0.00 1.40
3171 4154 7.340232 ACCAGCTACATGTGATAAATTGATGTT 59.660 33.333 9.11 0.00 0.00 2.71
3183 4166 3.756082 ATTGATGTTGGCTTAGGGGAA 57.244 42.857 0.00 0.00 0.00 3.97
3237 4811 4.925054 TGGACCGTTAATTCTCTTACAACG 59.075 41.667 0.00 0.00 41.10 4.10
3324 4898 7.848223 TCTGTCATCACAAAACCTATACATG 57.152 36.000 0.00 0.00 29.82 3.21
3325 4899 7.619965 TCTGTCATCACAAAACCTATACATGA 58.380 34.615 0.00 0.00 29.82 3.07
3349 4923 7.865385 TGAATGGACTAATTGTTTGTTAAGCAC 59.135 33.333 0.00 0.00 0.00 4.40
3386 4960 4.129380 CCTGAAAATGCGTGGATCATAGA 58.871 43.478 0.00 0.00 0.00 1.98
3392 4966 1.206849 TGCGTGGATCATAGAAGTGCA 59.793 47.619 0.00 0.00 0.00 4.57
3406 4980 3.567164 AGAAGTGCAGTCATGTTTCTTGG 59.433 43.478 0.00 0.00 0.00 3.61
3492 5072 7.653647 TGTTGTTAATGGATCTGTAAAACCAC 58.346 34.615 0.00 0.00 35.19 4.16
3576 5156 4.966168 TGACAACCTTATCCTATGTGCCTA 59.034 41.667 0.00 0.00 0.00 3.93
3577 5157 5.427157 TGACAACCTTATCCTATGTGCCTAA 59.573 40.000 0.00 0.00 0.00 2.69
3637 5217 2.351157 CCGGAAAGCAAAGAAAGAGCTG 60.351 50.000 0.00 0.00 38.86 4.24
3682 5262 1.538950 CAGAAGGCTCAGAAAGTTGCC 59.461 52.381 0.00 0.00 45.21 4.52
3734 5314 6.293626 GCTAATGTAAGTGGCCATACTGATTG 60.294 42.308 9.72 1.94 0.00 2.67
3795 5375 7.165812 GGTAATTGTCACAATTCATTACATCGC 59.834 37.037 19.22 0.00 0.00 4.58
3911 5491 9.636879 CTCTATCCATATGACTTAAGTGACATG 57.363 37.037 14.14 9.74 0.00 3.21
4078 5658 6.153924 AGTAACCTGGATATCCATCTTCCTT 58.846 40.000 24.73 11.55 46.46 3.36
4165 5745 7.999679 AGCTTGCATAATCTTTTAGCATGTTA 58.000 30.769 4.25 0.00 34.87 2.41
4307 5888 4.768583 ACTTGAAGCTTTTTGCATGGAAA 58.231 34.783 8.47 8.47 45.94 3.13
4317 5898 7.444792 AGCTTTTTGCATGGAAATATTTGAACA 59.555 29.630 13.51 2.56 45.94 3.18
4399 5980 4.038642 GCACTTGATTTTCCCACCACTAAA 59.961 41.667 0.00 0.00 0.00 1.85
4470 6051 9.201127 CAGATAATTGTCCTGTGTCATATGTAG 57.799 37.037 1.90 0.00 0.00 2.74
4472 6053 4.817318 TTGTCCTGTGTCATATGTAGCA 57.183 40.909 1.90 0.00 0.00 3.49
4494 6075 3.325870 TGTTTCCTACATCTGCTGAACG 58.674 45.455 0.00 0.00 0.00 3.95
4515 6099 2.291741 GGTTGAAGCCTTGAAGACAGTG 59.708 50.000 0.00 0.00 0.00 3.66
4578 6213 2.664568 CAGTGAATGATTTTGCTTGGCG 59.335 45.455 0.00 0.00 0.00 5.69
4661 6296 4.804108 TCAAATGGGCGAATAGTTTTGTG 58.196 39.130 0.00 0.00 0.00 3.33
4662 6297 4.520874 TCAAATGGGCGAATAGTTTTGTGA 59.479 37.500 0.00 0.00 0.00 3.58
4689 6324 3.508793 ACACAGAAATTTGCAGGATCCAG 59.491 43.478 15.82 7.25 0.00 3.86
4847 6482 7.807977 ATATGAGATTGTTTATGAAAGCGGT 57.192 32.000 0.00 0.00 0.00 5.68
4849 6484 6.662414 TGAGATTGTTTATGAAAGCGGTAG 57.338 37.500 0.00 0.00 0.00 3.18
4863 6498 2.950309 AGCGGTAGTATGACAATCGAGT 59.050 45.455 0.00 0.00 0.00 4.18
4887 6522 2.370849 ACGTGGTCCTGGTATCTTTGTT 59.629 45.455 0.00 0.00 0.00 2.83
4907 6542 1.142667 TGTTTGGGATCTGTGACTGCA 59.857 47.619 0.00 0.00 0.00 4.41
4911 6546 1.421268 TGGGATCTGTGACTGCAGTTT 59.579 47.619 22.65 0.00 37.70 2.66
4941 6576 0.401738 ATACCGGGCTGCAGCAATAT 59.598 50.000 37.63 24.36 44.36 1.28
4951 6586 4.157289 GGCTGCAGCAATATTAGCATACAT 59.843 41.667 37.63 0.00 44.36 2.29
4957 6592 9.012161 TGCAGCAATATTAGCATACATTCATAA 57.988 29.630 0.00 0.00 31.05 1.90
4996 6631 2.064434 TGTGGCCTTGTGACATTTCA 57.936 45.000 3.32 0.00 0.00 2.69
4997 6632 2.382882 TGTGGCCTTGTGACATTTCAA 58.617 42.857 3.32 0.00 31.90 2.69
5002 6637 3.305335 GGCCTTGTGACATTTCAAATCGT 60.305 43.478 0.00 0.00 31.90 3.73
5011 6646 6.684555 GTGACATTTCAAATCGTTAGAGCATC 59.315 38.462 0.00 0.00 31.90 3.91
5012 6647 7.413438 GTGACATTTCAAATCGTTAGAGCATCT 60.413 37.037 0.00 0.00 41.03 2.90
5034 6669 2.074729 ACCCTCTACCAGATTCCTCG 57.925 55.000 0.00 0.00 0.00 4.63
5061 6696 9.841295 AAAGTAAAAGTTATATCCGAGGCAATA 57.159 29.630 0.00 0.00 0.00 1.90
5066 6701 9.965824 AAAAGTTATATCCGAGGCAATATTTTG 57.034 29.630 0.00 0.00 35.85 2.44
5110 6749 3.246301 CCATCCACCTGATCCTCTATGT 58.754 50.000 0.00 0.00 0.00 2.29
5184 6830 4.201980 GCGTTCAGGTTTACCAGAAAACTT 60.202 41.667 8.14 0.00 42.09 2.66
5191 6837 4.865925 GGTTTACCAGAAAACTTGCGTTTT 59.134 37.500 2.57 2.57 44.18 2.43
5219 6865 8.990163 TTTAATTTTTGAACAGAGTAGGGTCT 57.010 30.769 0.00 0.00 0.00 3.85
5220 6866 8.617290 TTAATTTTTGAACAGAGTAGGGTCTC 57.383 34.615 0.00 0.00 34.96 3.36
5221 6867 3.936372 TTTGAACAGAGTAGGGTCTCG 57.064 47.619 0.00 0.00 39.21 4.04
5223 6869 3.150458 TGAACAGAGTAGGGTCTCGAA 57.850 47.619 0.00 0.00 39.21 3.71
5224 6870 3.082548 TGAACAGAGTAGGGTCTCGAAG 58.917 50.000 0.00 0.00 39.21 3.79
5225 6871 2.131776 ACAGAGTAGGGTCTCGAAGG 57.868 55.000 0.00 0.00 39.21 3.46
5226 6872 1.634459 ACAGAGTAGGGTCTCGAAGGA 59.366 52.381 0.00 0.00 39.21 3.36
5227 6873 2.018515 CAGAGTAGGGTCTCGAAGGAC 58.981 57.143 0.00 0.00 39.21 3.85
5237 6883 1.893801 TCTCGAAGGACCCAGACTTTC 59.106 52.381 0.00 0.00 0.00 2.62
5238 6884 1.618837 CTCGAAGGACCCAGACTTTCA 59.381 52.381 0.00 0.00 0.00 2.69
5239 6885 2.234908 CTCGAAGGACCCAGACTTTCAT 59.765 50.000 0.00 0.00 0.00 2.57
5242 6888 4.081642 TCGAAGGACCCAGACTTTCATTAG 60.082 45.833 0.00 0.00 0.00 1.73
5243 6889 4.081642 CGAAGGACCCAGACTTTCATTAGA 60.082 45.833 0.00 0.00 0.00 2.10
5244 6890 5.395768 CGAAGGACCCAGACTTTCATTAGAT 60.396 44.000 0.00 0.00 0.00 1.98
5245 6891 6.183360 CGAAGGACCCAGACTTTCATTAGATA 60.183 42.308 0.00 0.00 0.00 1.98
5246 6892 6.487299 AGGACCCAGACTTTCATTAGATAC 57.513 41.667 0.00 0.00 0.00 2.24
5247 6893 6.206042 AGGACCCAGACTTTCATTAGATACT 58.794 40.000 0.00 0.00 0.00 2.12
5248 6894 6.325286 AGGACCCAGACTTTCATTAGATACTC 59.675 42.308 0.00 0.00 0.00 2.59
5249 6895 6.463190 GGACCCAGACTTTCATTAGATACTCC 60.463 46.154 0.00 0.00 0.00 3.85
5251 6897 6.098982 ACCCAGACTTTCATTAGATACTCCAG 59.901 42.308 0.00 0.00 0.00 3.86
5252 6898 6.098982 CCCAGACTTTCATTAGATACTCCAGT 59.901 42.308 0.00 0.00 0.00 4.00
5253 6899 6.983307 CCAGACTTTCATTAGATACTCCAGTG 59.017 42.308 0.00 0.00 0.00 3.66
5255 6901 6.897966 AGACTTTCATTAGATACTCCAGTGGA 59.102 38.462 12.40 12.40 0.00 4.02
5256 6902 7.400339 AGACTTTCATTAGATACTCCAGTGGAA 59.600 37.037 14.17 0.00 0.00 3.53
5258 6904 8.043710 ACTTTCATTAGATACTCCAGTGGAAAG 58.956 37.037 14.17 11.23 41.75 2.62
5260 6906 2.969628 AGATACTCCAGTGGAAAGCG 57.030 50.000 14.17 3.81 0.00 4.68
5261 6907 2.180276 AGATACTCCAGTGGAAAGCGT 58.820 47.619 14.17 10.08 0.00 5.07
5262 6908 2.567615 AGATACTCCAGTGGAAAGCGTT 59.432 45.455 14.17 0.00 0.00 4.84
5263 6909 2.163818 TACTCCAGTGGAAAGCGTTG 57.836 50.000 14.17 1.83 0.00 4.10
5264 6910 0.535102 ACTCCAGTGGAAAGCGTTGG 60.535 55.000 14.17 1.04 0.00 3.77
5265 6911 1.856265 CTCCAGTGGAAAGCGTTGGC 61.856 60.000 14.17 0.00 40.37 4.52
5266 6912 2.644992 CAGTGGAAAGCGTTGGCC 59.355 61.111 0.00 0.00 41.24 5.36
5267 6913 2.978010 AGTGGAAAGCGTTGGCCG 60.978 61.111 0.00 0.00 41.24 6.13
5276 6922 3.118454 CGTTGGCCGCCTACAGTG 61.118 66.667 21.57 4.23 0.00 3.66
5285 6931 2.604046 CGCCTACAGTGGAAAGCTAT 57.396 50.000 0.00 0.00 0.00 2.97
5286 6932 2.906354 CGCCTACAGTGGAAAGCTATT 58.094 47.619 0.00 0.00 0.00 1.73
5287 6933 3.270877 CGCCTACAGTGGAAAGCTATTT 58.729 45.455 0.00 0.00 0.00 1.40
5289 6935 4.010349 GCCTACAGTGGAAAGCTATTTGT 58.990 43.478 0.00 0.00 0.00 2.83
5290 6936 5.183228 GCCTACAGTGGAAAGCTATTTGTA 58.817 41.667 0.00 0.00 0.00 2.41
5291 6937 5.823045 GCCTACAGTGGAAAGCTATTTGTAT 59.177 40.000 0.00 0.00 0.00 2.29
5294 6940 8.204836 CCTACAGTGGAAAGCTATTTGTATACT 58.795 37.037 4.17 0.00 0.00 2.12
5295 6941 9.601217 CTACAGTGGAAAGCTATTTGTATACTT 57.399 33.333 4.17 0.00 0.00 2.24
5307 6953 8.656849 GCTATTTGTATACTTATTCATGGACGG 58.343 37.037 4.17 0.00 0.00 4.79
5308 6954 9.706691 CTATTTGTATACTTATTCATGGACGGT 57.293 33.333 4.17 0.00 0.00 4.83
5310 6956 6.718522 TGTATACTTATTCATGGACGGTCA 57.281 37.500 10.76 0.00 0.00 4.02
5311 6957 7.114866 TGTATACTTATTCATGGACGGTCAA 57.885 36.000 10.76 0.00 0.00 3.18
5318 6998 2.925724 TCATGGACGGTCAAAGTTTGT 58.074 42.857 15.08 0.00 0.00 2.83
5322 7002 2.011222 GGACGGTCAAAGTTTGTGACA 58.989 47.619 15.08 0.00 45.94 3.58
5339 7019 2.038952 TGACATGACTTTCCACCTCCAG 59.961 50.000 0.00 0.00 0.00 3.86
5348 7028 3.972227 CACCTCCAGTGGAAAGCG 58.028 61.111 14.17 0.83 43.26 4.68
5349 7029 1.672356 CACCTCCAGTGGAAAGCGG 60.672 63.158 14.17 13.25 43.26 5.52
5352 7032 0.323629 CCTCCAGTGGAAAGCGGTTA 59.676 55.000 14.17 0.00 0.00 2.85
5364 7044 1.221021 GCGGTTAGCTGCCTACCTT 59.779 57.895 15.91 0.00 44.04 3.50
5371 7051 2.674796 AGCTGCCTACCTTCGTAAAG 57.325 50.000 0.00 0.00 0.00 1.85
5380 7060 1.339727 ACCTTCGTAAAGCATGACCCC 60.340 52.381 0.00 0.00 0.00 4.95
5381 7061 1.065418 CCTTCGTAAAGCATGACCCCT 60.065 52.381 0.00 0.00 0.00 4.79
5382 7062 2.618045 CCTTCGTAAAGCATGACCCCTT 60.618 50.000 0.00 0.00 0.00 3.95
5385 7065 2.039216 TCGTAAAGCATGACCCCTTTGA 59.961 45.455 0.00 0.00 33.64 2.69
5393 7073 5.388654 AGCATGACCCCTTTGAATATTAGG 58.611 41.667 0.00 0.00 0.00 2.69
5399 7079 6.160483 ACCCCTTTGAATATTAGGGTTCAA 57.840 37.500 17.18 2.62 45.61 2.69
5402 7082 8.298926 ACCCCTTTGAATATTAGGGTTCAATGG 61.299 40.741 17.18 18.39 45.61 3.16
5445 7125 7.528996 AAGATCAATCTTGGACACATTTCAA 57.471 32.000 4.47 0.00 44.91 2.69
5446 7126 7.713734 AGATCAATCTTGGACACATTTCAAT 57.286 32.000 0.00 0.00 31.97 2.57
5447 7127 7.544622 AGATCAATCTTGGACACATTTCAATG 58.455 34.615 0.00 0.00 36.77 2.82
5448 7128 7.177921 AGATCAATCTTGGACACATTTCAATGT 59.822 33.333 0.00 0.00 41.33 2.71
5449 7129 7.053316 TCAATCTTGGACACATTTCAATGTT 57.947 32.000 2.25 0.00 46.95 2.71
5450 7130 7.499292 TCAATCTTGGACACATTTCAATGTTT 58.501 30.769 2.25 0.00 46.95 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.264172 ACCCCATTCACCAACTGCTTTATA 60.264 41.667 0.00 0.00 0.00 0.98
75 76 9.485206 CTTGTTTTCATCTCCATCAATTCTTTT 57.515 29.630 0.00 0.00 0.00 2.27
122 125 6.850752 TGAATTTGGAGGGGATTTTAAGTC 57.149 37.500 0.00 0.00 0.00 3.01
126 129 5.028802 TGCATGAATTTGGAGGGGATTTTA 58.971 37.500 0.00 0.00 0.00 1.52
224 227 3.274586 CATCAGCGACATGGGCCG 61.275 66.667 0.00 4.05 0.00 6.13
279 282 5.009631 CCTACAATTGGTGGTCTTCAATGA 58.990 41.667 10.83 0.00 34.28 2.57
314 320 4.514441 GCAATTGAGGGACATACATCTCAG 59.486 45.833 10.34 0.00 37.52 3.35
322 329 1.208706 TCGGGCAATTGAGGGACATA 58.791 50.000 10.34 0.00 0.00 2.29
335 342 8.514330 ACAAGATAATAAAGTTTTATCGGGCA 57.486 30.769 0.00 0.00 39.80 5.36
337 344 7.797123 GCGACAAGATAATAAAGTTTTATCGGG 59.203 37.037 0.00 0.00 39.80 5.14
339 346 9.697250 TTGCGACAAGATAATAAAGTTTTATCG 57.303 29.630 0.00 0.00 39.80 2.92
349 356 9.140286 GTAGATATGCTTGCGACAAGATAATAA 57.860 33.333 19.38 3.28 0.00 1.40
381 388 9.606631 TTTGGAAGTGCTTTTGTACATATTTTT 57.393 25.926 0.00 0.00 37.51 1.94
392 399 5.799681 ATTGTGTTTTGGAAGTGCTTTTG 57.200 34.783 0.00 0.00 0.00 2.44
397 404 7.489113 CCAATATCTATTGTGTTTTGGAAGTGC 59.511 37.037 8.66 0.00 41.04 4.40
424 433 2.263077 CTTTATCACTCGTCGCTGCTT 58.737 47.619 0.00 0.00 0.00 3.91
430 439 6.686130 AGTTTGTAACTTTATCACTCGTCG 57.314 37.500 0.00 0.00 39.04 5.12
460 469 8.314751 TGGACAATTTCAAACTTAAACCTTTCA 58.685 29.630 0.00 0.00 0.00 2.69
493 502 2.877043 AGGTGAAGCTGCAGTTTTTG 57.123 45.000 17.41 0.00 0.00 2.44
557 567 5.285651 CCCATGTGAGCGTCTTTTTAAAAA 58.714 37.500 12.62 12.62 0.00 1.94
558 568 4.794655 GCCCATGTGAGCGTCTTTTTAAAA 60.795 41.667 0.00 0.00 0.00 1.52
559 569 3.305064 GCCCATGTGAGCGTCTTTTTAAA 60.305 43.478 0.00 0.00 0.00 1.52
560 570 2.227865 GCCCATGTGAGCGTCTTTTTAA 59.772 45.455 0.00 0.00 0.00 1.52
561 571 1.810151 GCCCATGTGAGCGTCTTTTTA 59.190 47.619 0.00 0.00 0.00 1.52
562 572 0.598065 GCCCATGTGAGCGTCTTTTT 59.402 50.000 0.00 0.00 0.00 1.94
565 575 1.078848 GAGCCCATGTGAGCGTCTT 60.079 57.895 0.00 0.00 0.00 3.01
567 577 1.520342 GAGAGCCCATGTGAGCGTC 60.520 63.158 0.00 0.00 0.00 5.19
568 578 1.954362 GAGAGAGCCCATGTGAGCGT 61.954 60.000 0.00 0.00 0.00 5.07
577 587 3.443925 CGCGTCTGAGAGAGCCCA 61.444 66.667 0.00 0.00 0.00 5.36
618 628 5.456186 GGTGCCTTCCTTTCCTATATTAGCA 60.456 44.000 0.00 0.00 0.00 3.49
659 670 2.109181 GTGTATGGGAGAGCGGGC 59.891 66.667 0.00 0.00 0.00 6.13
660 671 1.144057 GTGTGTATGGGAGAGCGGG 59.856 63.158 0.00 0.00 0.00 6.13
682 693 1.006086 CGATTGCACCAACGAGCATA 58.994 50.000 0.00 0.00 40.94 3.14
684 695 0.319986 TACGATTGCACCAACGAGCA 60.320 50.000 7.74 0.00 39.32 4.26
693 704 3.058914 AGACAAACAAGCTACGATTGCAC 60.059 43.478 6.11 2.58 0.00 4.57
706 717 5.462530 TGAATCTAGACCGAGACAAACAA 57.537 39.130 0.00 0.00 0.00 2.83
718 729 7.329717 AGTTGAACGAGTTTGATGAATCTAGAC 59.670 37.037 0.00 0.00 0.00 2.59
734 754 5.147162 GGCTTGAAACATAAGTTGAACGAG 58.853 41.667 0.00 0.00 38.17 4.18
748 768 3.312146 CCAAATTTGTGTGGGCTTGAAAC 59.688 43.478 16.73 0.00 0.00 2.78
749 769 3.198635 TCCAAATTTGTGTGGGCTTGAAA 59.801 39.130 16.73 0.00 35.46 2.69
753 773 4.436113 AAATCCAAATTTGTGTGGGCTT 57.564 36.364 16.73 0.00 33.78 4.35
771 791 6.073003 TCGAGTGGCAAAAACAAAACAAAAAT 60.073 30.769 0.00 0.00 0.00 1.82
828 884 5.083122 TCATTTCCCTTATGCCACTTCAAA 58.917 37.500 0.00 0.00 0.00 2.69
831 887 3.067320 GCTCATTTCCCTTATGCCACTTC 59.933 47.826 0.00 0.00 0.00 3.01
845 902 3.696548 CCCCTCTAGGTTTTGCTCATTTC 59.303 47.826 0.00 0.00 0.00 2.17
851 908 1.351350 GTCACCCCTCTAGGTTTTGCT 59.649 52.381 0.00 0.00 38.39 3.91
936 994 1.073125 GTTTGGGGATTTGGGTTTGGG 59.927 52.381 0.00 0.00 0.00 4.12
1365 1423 5.696270 GGCTTTTGAGAAATAACCAACCTTG 59.304 40.000 0.00 0.00 0.00 3.61
1651 1709 3.920231 TCCTCACTTTCATCCTCCATG 57.080 47.619 0.00 0.00 0.00 3.66
1678 1736 1.211703 ACATCACTGAACACACCACCA 59.788 47.619 0.00 0.00 0.00 4.17
1720 1778 2.723322 TGGGCTCATCCTCTTCATTG 57.277 50.000 0.00 0.00 34.39 2.82
1721 1779 2.686118 GCTTGGGCTCATCCTCTTCATT 60.686 50.000 0.00 0.00 35.22 2.57
1731 1789 3.801997 CCCTCGGCTTGGGCTCAT 61.802 66.667 0.00 0.00 37.99 2.90
1756 1814 6.373216 CCAAATCAAATTGTTCATCCAGCAAT 59.627 34.615 0.00 0.00 34.69 3.56
1778 1836 7.370383 GTTATCAAATGAAAGAAGCTCACCAA 58.630 34.615 0.00 0.00 0.00 3.67
1803 1861 1.321474 TGCAAAGCAAACTGAGAGGG 58.679 50.000 0.00 0.00 34.76 4.30
1954 2229 3.775202 ACATACTAAAGCTGCAGACTCG 58.225 45.455 20.43 8.77 0.00 4.18
1997 2272 2.294791 CGGTTGCAACAAATGGGAAGTA 59.705 45.455 29.55 0.00 0.00 2.24
1998 2273 1.068434 CGGTTGCAACAAATGGGAAGT 59.932 47.619 29.55 0.00 0.00 3.01
1999 2274 1.068434 ACGGTTGCAACAAATGGGAAG 59.932 47.619 29.55 11.50 0.00 3.46
2000 2275 1.115467 ACGGTTGCAACAAATGGGAA 58.885 45.000 29.55 0.00 0.00 3.97
2005 2280 0.963225 GGGGTACGGTTGCAACAAAT 59.037 50.000 29.55 16.69 0.00 2.32
2017 2292 6.600882 ATTATCCATAACAGTAGGGGTACG 57.399 41.667 0.00 0.00 31.72 3.67
2147 2424 7.124298 ACACAGTCCTGCTAAATCTTCTACATA 59.876 37.037 0.00 0.00 0.00 2.29
2150 2427 5.725362 ACACAGTCCTGCTAAATCTTCTAC 58.275 41.667 0.00 0.00 0.00 2.59
2182 2459 6.491383 ACATAGTCCTAGTCTACAACAGGAA 58.509 40.000 0.00 0.00 37.11 3.36
2195 2472 9.582431 TCAATTTAACTTTCGACATAGTCCTAG 57.418 33.333 0.00 0.00 0.00 3.02
2221 2498 9.959721 ATATGTTCACTTGAATAGTTACAAGGT 57.040 29.630 0.00 0.00 45.03 3.50
2270 2589 2.942376 CAGCAGGCGGTTAATGATACAA 59.058 45.455 0.00 0.00 0.00 2.41
2303 2622 5.104360 AGCATAGAACAAGATTTCCAGCCTA 60.104 40.000 0.00 0.00 0.00 3.93
2388 2708 4.584688 GCAAGCTGCAATTGGTCC 57.415 55.556 7.72 0.00 44.26 4.46
2407 2728 4.211125 TCACTAGCTCCATACTCTTCCAG 58.789 47.826 0.00 0.00 0.00 3.86
2415 2736 6.278172 TCATCATCATCACTAGCTCCATAC 57.722 41.667 0.00 0.00 0.00 2.39
2475 2796 9.965902 AACAACTTCAATTCATCTATAACCTCT 57.034 29.630 0.00 0.00 0.00 3.69
2520 2841 7.280876 GCTGGTGTTCTATATTCTTCATCAACA 59.719 37.037 0.00 0.00 0.00 3.33
2581 2902 2.770802 CAGATTCATCCACCTCCTCAGT 59.229 50.000 0.00 0.00 0.00 3.41
2685 3006 5.558818 ACTTCAGATTCATCACTGCTTTCT 58.441 37.500 0.00 0.00 34.57 2.52
2757 3078 3.303938 TGGAGTTTGAATTTTGCCAGGA 58.696 40.909 0.00 0.00 0.00 3.86
3155 4138 6.096705 CCCTAAGCCAACATCAATTTATCACA 59.903 38.462 0.00 0.00 0.00 3.58
3164 4147 3.534357 TTTCCCCTAAGCCAACATCAA 57.466 42.857 0.00 0.00 0.00 2.57
3171 4154 5.399113 ACAAAGTAAATTTCCCCTAAGCCA 58.601 37.500 0.00 0.00 0.00 4.75
3209 4192 4.203654 AGAGAATTAACGGTCCAGGTTC 57.796 45.455 0.00 0.00 0.00 3.62
3323 4897 7.865385 GTGCTTAACAAACAATTAGTCCATTCA 59.135 33.333 0.00 0.00 0.00 2.57
3324 4898 8.082242 AGTGCTTAACAAACAATTAGTCCATTC 58.918 33.333 0.00 0.00 0.00 2.67
3325 4899 7.951591 AGTGCTTAACAAACAATTAGTCCATT 58.048 30.769 0.00 0.00 0.00 3.16
3343 4917 5.652014 CAGGATTGGAATTTGGTAGTGCTTA 59.348 40.000 0.00 0.00 0.00 3.09
3349 4923 6.536224 GCATTTTCAGGATTGGAATTTGGTAG 59.464 38.462 0.00 0.00 0.00 3.18
3386 4960 3.290710 ACCAAGAAACATGACTGCACTT 58.709 40.909 0.00 0.00 0.00 3.16
3451 5030 1.032014 AACAAGCATGAAAGCACCGT 58.968 45.000 0.00 0.00 36.85 4.83
3519 5099 5.948162 AGCAAATGTTATCTCAATCAGGTGT 59.052 36.000 0.00 0.00 0.00 4.16
3567 5147 5.526111 GCGGACTAGAAAAATTAGGCACATA 59.474 40.000 0.00 0.00 0.00 2.29
3576 5156 5.702209 TCTTTTACCGCGGACTAGAAAAATT 59.298 36.000 35.90 6.98 0.00 1.82
3577 5157 5.240121 TCTTTTACCGCGGACTAGAAAAAT 58.760 37.500 35.90 7.61 0.00 1.82
3682 5262 2.271800 GAAGATGGTCCTGTAACAGCG 58.728 52.381 0.00 0.00 0.00 5.18
3911 5491 7.170998 CCGGTTAATATGAAGGTATCAACAGAC 59.829 40.741 0.00 0.00 42.54 3.51
3961 5541 9.784531 TCAAAGATGAAAATCAAAGAGTACTCT 57.215 29.630 20.00 20.00 35.30 3.24
4104 5684 7.138736 TCAACTCATTTGTTTCGGAAGAATTC 58.861 34.615 0.00 0.00 41.09 2.17
4274 5854 9.000018 GCAAAAAGCTTCAAGTTAATACGATAG 58.000 33.333 0.00 0.00 41.15 2.08
4276 5856 7.367285 TGCAAAAAGCTTCAAGTTAATACGAT 58.633 30.769 0.00 0.00 45.94 3.73
4294 5875 9.947669 CTTTGTTCAAATATTTCCATGCAAAAA 57.052 25.926 0.00 0.00 0.00 1.94
4295 5876 9.334947 TCTTTGTTCAAATATTTCCATGCAAAA 57.665 25.926 0.00 0.00 0.00 2.44
4317 5898 6.825610 TGGGTCAAGCAACAAATATTTCTTT 58.174 32.000 0.00 0.00 0.00 2.52
4399 5980 7.050970 AGCATGCACAGAATATTTGATCAAT 57.949 32.000 21.98 2.50 0.00 2.57
4494 6075 2.291741 CACTGTCTTCAAGGCTTCAACC 59.708 50.000 0.00 0.00 0.00 3.77
4515 6099 2.237392 ACAACCTATCTTGCTCTGGACC 59.763 50.000 0.00 0.00 0.00 4.46
4578 6213 5.366829 ACATTCGGCAGTAAAAAGGTAAC 57.633 39.130 0.00 0.00 0.00 2.50
4661 6296 4.216257 TCCTGCAAATTTCTGTGTAAGCTC 59.784 41.667 0.00 0.00 0.00 4.09
4662 6297 4.144297 TCCTGCAAATTTCTGTGTAAGCT 58.856 39.130 0.00 0.00 0.00 3.74
4678 6313 1.722034 GGAGGTATCTGGATCCTGCA 58.278 55.000 14.23 3.42 39.07 4.41
4722 6357 8.197439 CCCCTGGAATTGATAAATCTTTGTAAC 58.803 37.037 0.00 0.00 0.00 2.50
4826 6461 6.170506 ACTACCGCTTTCATAAACAATCTCA 58.829 36.000 0.00 0.00 0.00 3.27
4847 6482 3.943381 ACGTCCACTCGATTGTCATACTA 59.057 43.478 1.83 0.00 34.70 1.82
4849 6484 2.852413 CACGTCCACTCGATTGTCATAC 59.148 50.000 1.83 0.00 34.70 2.39
4887 6522 1.142667 TGCAGTCACAGATCCCAAACA 59.857 47.619 0.00 0.00 0.00 2.83
4907 6542 3.827876 CCCGGTATTTTACCCAACAAACT 59.172 43.478 0.00 0.00 46.27 2.66
4911 6546 1.355043 AGCCCGGTATTTTACCCAACA 59.645 47.619 0.00 0.00 46.27 3.33
4951 6586 6.372937 TGGCAATCTGACAAATACGTTATGAA 59.627 34.615 0.00 0.00 28.38 2.57
4957 6592 4.009675 ACATGGCAATCTGACAAATACGT 58.990 39.130 0.00 0.00 39.86 3.57
4985 6620 5.468409 TGCTCTAACGATTTGAAATGTCACA 59.532 36.000 0.00 0.00 31.90 3.58
5002 6637 4.415846 TGGTAGAGGGTAGAGATGCTCTAA 59.584 45.833 5.79 0.00 43.53 2.10
5011 6646 4.403734 GAGGAATCTGGTAGAGGGTAGAG 58.596 52.174 0.00 0.00 0.00 2.43
5012 6647 3.181442 CGAGGAATCTGGTAGAGGGTAGA 60.181 52.174 0.00 0.00 0.00 2.59
5013 6648 3.150767 CGAGGAATCTGGTAGAGGGTAG 58.849 54.545 0.00 0.00 0.00 3.18
5014 6649 2.781757 TCGAGGAATCTGGTAGAGGGTA 59.218 50.000 0.00 0.00 0.00 3.69
5015 6650 1.569548 TCGAGGAATCTGGTAGAGGGT 59.430 52.381 0.00 0.00 0.00 4.34
5016 6651 2.366640 TCGAGGAATCTGGTAGAGGG 57.633 55.000 0.00 0.00 0.00 4.30
5017 6652 3.702045 ACTTTCGAGGAATCTGGTAGAGG 59.298 47.826 0.00 0.00 0.00 3.69
5034 6669 7.781548 TGCCTCGGATATAACTTTTACTTTC 57.218 36.000 0.00 0.00 0.00 2.62
5050 6685 3.829601 ACCAAACAAAATATTGCCTCGGA 59.170 39.130 0.00 0.00 40.34 4.55
5061 6696 9.772973 GTCTAATCCCTTAAAACCAAACAAAAT 57.227 29.630 0.00 0.00 0.00 1.82
5066 6701 5.186409 GGGGTCTAATCCCTTAAAACCAAAC 59.814 44.000 1.72 0.00 46.27 2.93
5094 6733 6.723298 ACTAAAGACATAGAGGATCAGGTG 57.277 41.667 0.00 0.00 37.82 4.00
5146 6785 0.475044 AACGCCCAACCTAAGGACAA 59.525 50.000 0.00 0.00 0.00 3.18
5153 6799 0.475044 AAACCTGAACGCCCAACCTA 59.525 50.000 0.00 0.00 0.00 3.08
5193 6839 9.416284 AGACCCTACTCTGTTCAAAAATTAAAA 57.584 29.630 0.00 0.00 0.00 1.52
5194 6840 8.990163 AGACCCTACTCTGTTCAAAAATTAAA 57.010 30.769 0.00 0.00 0.00 1.52
5197 6843 5.701290 CGAGACCCTACTCTGTTCAAAAATT 59.299 40.000 0.00 0.00 35.06 1.82
5198 6844 5.011738 TCGAGACCCTACTCTGTTCAAAAAT 59.988 40.000 0.00 0.00 35.06 1.82
5199 6845 4.342951 TCGAGACCCTACTCTGTTCAAAAA 59.657 41.667 0.00 0.00 35.06 1.94
5200 6846 3.893200 TCGAGACCCTACTCTGTTCAAAA 59.107 43.478 0.00 0.00 35.06 2.44
5203 6849 2.873094 TCGAGACCCTACTCTGTTCA 57.127 50.000 0.00 0.00 35.06 3.18
5204 6850 2.424246 CCTTCGAGACCCTACTCTGTTC 59.576 54.545 0.00 0.00 35.06 3.18
5207 6853 2.018515 GTCCTTCGAGACCCTACTCTG 58.981 57.143 0.00 0.00 35.06 3.35
5216 6862 1.258676 AAGTCTGGGTCCTTCGAGAC 58.741 55.000 0.00 0.00 35.97 3.36
5218 6864 1.618837 TGAAAGTCTGGGTCCTTCGAG 59.381 52.381 0.00 0.00 0.00 4.04
5219 6865 1.712056 TGAAAGTCTGGGTCCTTCGA 58.288 50.000 0.00 0.00 0.00 3.71
5220 6866 2.770164 ATGAAAGTCTGGGTCCTTCG 57.230 50.000 0.00 0.00 0.00 3.79
5221 6867 5.422214 TCTAATGAAAGTCTGGGTCCTTC 57.578 43.478 0.00 0.00 0.00 3.46
5223 6869 6.206042 AGTATCTAATGAAAGTCTGGGTCCT 58.794 40.000 0.00 0.00 0.00 3.85
5224 6870 6.463190 GGAGTATCTAATGAAAGTCTGGGTCC 60.463 46.154 0.00 0.00 33.73 4.46
5225 6871 6.098409 TGGAGTATCTAATGAAAGTCTGGGTC 59.902 42.308 0.00 0.00 33.73 4.46
5226 6872 5.964477 TGGAGTATCTAATGAAAGTCTGGGT 59.036 40.000 0.00 0.00 33.73 4.51
5227 6873 6.098982 ACTGGAGTATCTAATGAAAGTCTGGG 59.901 42.308 0.00 0.00 33.73 4.45
5231 6877 7.113658 TCCACTGGAGTATCTAATGAAAGTC 57.886 40.000 0.00 0.00 33.73 3.01
5233 6879 7.011857 GCTTTCCACTGGAGTATCTAATGAAAG 59.988 40.741 0.00 0.00 36.63 2.62
5237 6883 4.747108 CGCTTTCCACTGGAGTATCTAATG 59.253 45.833 0.00 0.00 31.21 1.90
5238 6884 4.406003 ACGCTTTCCACTGGAGTATCTAAT 59.594 41.667 0.00 0.00 31.21 1.73
5239 6885 3.767673 ACGCTTTCCACTGGAGTATCTAA 59.232 43.478 0.00 0.00 31.21 2.10
5242 6888 2.673368 CAACGCTTTCCACTGGAGTATC 59.327 50.000 0.00 0.00 31.21 2.24
5243 6889 2.615493 CCAACGCTTTCCACTGGAGTAT 60.615 50.000 0.00 0.00 31.21 2.12
5244 6890 1.270625 CCAACGCTTTCCACTGGAGTA 60.271 52.381 0.00 0.00 31.21 2.59
5245 6891 0.535102 CCAACGCTTTCCACTGGAGT 60.535 55.000 0.00 0.00 31.21 3.85
5246 6892 1.856265 GCCAACGCTTTCCACTGGAG 61.856 60.000 0.00 0.00 31.21 3.86
5247 6893 1.896660 GCCAACGCTTTCCACTGGA 60.897 57.895 0.00 0.00 0.00 3.86
5248 6894 2.644992 GCCAACGCTTTCCACTGG 59.355 61.111 0.00 0.00 0.00 4.00
5249 6895 2.644992 GGCCAACGCTTTCCACTG 59.355 61.111 0.00 0.00 34.44 3.66
5260 6906 2.741486 TTCCACTGTAGGCGGCCAAC 62.741 60.000 23.09 5.09 0.00 3.77
5261 6907 2.058125 TTTCCACTGTAGGCGGCCAA 62.058 55.000 23.09 5.30 0.00 4.52
5262 6908 2.463589 CTTTCCACTGTAGGCGGCCA 62.464 60.000 23.09 4.27 0.00 5.36
5263 6909 1.745489 CTTTCCACTGTAGGCGGCC 60.745 63.158 12.11 12.11 0.00 6.13
5264 6910 2.399356 GCTTTCCACTGTAGGCGGC 61.399 63.158 0.00 0.00 0.00 6.53
5265 6911 0.535335 TAGCTTTCCACTGTAGGCGG 59.465 55.000 0.00 0.00 0.00 6.13
5266 6912 2.604046 ATAGCTTTCCACTGTAGGCG 57.396 50.000 0.00 0.00 0.00 5.52
5267 6913 4.010349 ACAAATAGCTTTCCACTGTAGGC 58.990 43.478 0.00 0.00 0.00 3.93
5269 6915 9.601217 AAGTATACAAATAGCTTTCCACTGTAG 57.399 33.333 5.50 0.00 0.00 2.74
5282 6928 9.706691 ACCGTCCATGAATAAGTATACAAATAG 57.293 33.333 5.50 0.00 0.00 1.73
5283 6929 9.701098 GACCGTCCATGAATAAGTATACAAATA 57.299 33.333 5.50 0.00 0.00 1.40
5284 6930 8.208224 TGACCGTCCATGAATAAGTATACAAAT 58.792 33.333 5.50 0.00 0.00 2.32
5285 6931 7.557724 TGACCGTCCATGAATAAGTATACAAA 58.442 34.615 5.50 0.00 0.00 2.83
5286 6932 7.114866 TGACCGTCCATGAATAAGTATACAA 57.885 36.000 5.50 0.00 0.00 2.41
5287 6933 6.718522 TGACCGTCCATGAATAAGTATACA 57.281 37.500 5.50 0.00 0.00 2.29
5289 6935 7.788026 ACTTTGACCGTCCATGAATAAGTATA 58.212 34.615 0.00 0.00 0.00 1.47
5290 6936 6.650120 ACTTTGACCGTCCATGAATAAGTAT 58.350 36.000 0.00 0.00 0.00 2.12
5291 6937 6.045072 ACTTTGACCGTCCATGAATAAGTA 57.955 37.500 0.00 0.00 0.00 2.24
5294 6940 5.533154 ACAAACTTTGACCGTCCATGAATAA 59.467 36.000 8.55 0.00 0.00 1.40
5295 6941 5.049060 CACAAACTTTGACCGTCCATGAATA 60.049 40.000 8.55 0.00 0.00 1.75
5296 6942 3.888930 ACAAACTTTGACCGTCCATGAAT 59.111 39.130 8.55 0.00 0.00 2.57
5297 6943 3.066064 CACAAACTTTGACCGTCCATGAA 59.934 43.478 8.55 0.00 0.00 2.57
5300 6946 2.616842 GTCACAAACTTTGACCGTCCAT 59.383 45.455 8.55 0.00 37.93 3.41
5301 6947 2.011222 GTCACAAACTTTGACCGTCCA 58.989 47.619 8.55 0.00 37.93 4.02
5303 6949 3.311322 TCATGTCACAAACTTTGACCGTC 59.689 43.478 8.55 0.00 42.40 4.79
5304 6950 3.064820 GTCATGTCACAAACTTTGACCGT 59.935 43.478 8.55 0.00 42.40 4.83
5305 6951 3.312421 AGTCATGTCACAAACTTTGACCG 59.688 43.478 8.55 0.00 42.40 4.79
5307 6953 5.743872 GGAAAGTCATGTCACAAACTTTGAC 59.256 40.000 20.61 12.03 40.89 3.18
5308 6954 5.417266 TGGAAAGTCATGTCACAAACTTTGA 59.583 36.000 20.61 8.85 40.89 2.69
5310 6956 5.394115 GGTGGAAAGTCATGTCACAAACTTT 60.394 40.000 17.29 17.29 42.86 2.66
5311 6957 4.097892 GGTGGAAAGTCATGTCACAAACTT 59.902 41.667 3.64 3.64 33.53 2.66
5318 6998 2.038952 CTGGAGGTGGAAAGTCATGTCA 59.961 50.000 0.00 0.00 0.00 3.58
5322 7002 2.867109 CACTGGAGGTGGAAAGTCAT 57.133 50.000 0.00 0.00 41.90 3.06
5348 7028 0.535797 ACGAAGGTAGGCAGCTAACC 59.464 55.000 8.27 8.27 0.00 2.85
5349 7029 3.515330 TTACGAAGGTAGGCAGCTAAC 57.485 47.619 0.00 0.00 0.00 2.34
5352 7032 1.405661 GCTTTACGAAGGTAGGCAGCT 60.406 52.381 0.00 0.00 33.34 4.24
5355 7035 2.235155 TCATGCTTTACGAAGGTAGGCA 59.765 45.455 0.00 0.00 40.61 4.75
5364 7044 2.039216 TCAAAGGGGTCATGCTTTACGA 59.961 45.455 0.00 0.00 0.00 3.43
5371 7051 4.524328 CCCTAATATTCAAAGGGGTCATGC 59.476 45.833 12.47 0.00 45.43 4.06
5380 7060 8.066612 ACACCATTGAACCCTAATATTCAAAG 57.933 34.615 3.73 0.15 45.34 2.77
5381 7061 8.310382 CAACACCATTGAACCCTAATATTCAAA 58.690 33.333 3.73 0.00 45.34 2.69
5382 7062 7.671819 TCAACACCATTGAACCCTAATATTCAA 59.328 33.333 2.19 2.19 46.03 2.69
5385 7065 8.429237 TTTCAACACCATTGAACCCTAATATT 57.571 30.769 1.65 0.00 38.05 1.28
5393 7073 8.655651 TTTAAAGATTTCAACACCATTGAACC 57.344 30.769 1.65 0.00 38.05 3.62
5399 7079 7.725251 TCTTGCTTTAAAGATTTCAACACCAT 58.275 30.769 19.48 0.00 31.19 3.55
5402 7082 8.801715 TGATCTTGCTTTAAAGATTTCAACAC 57.198 30.769 19.48 6.19 44.96 3.32


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

AutoCloner maintained by Alex Coulton.