Multiple sequence alignment - TraesCS5B01G392800

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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 TraesCS5B01G392800 chr5B 100.000 8923 0 0 1 8923 571469044 571460122 0.000000e+00 16478.0
1 TraesCS5B01G392800 chr5B 92.606 541 33 4 8043 8578 3902119 3901581 0.000000e+00 771.0
2 TraesCS5B01G392800 chr5D 94.462 7349 271 71 778 8045 464283697 464276404 0.000000e+00 11191.0
3 TraesCS5B01G392800 chr5D 88.042 853 75 11 2 833 464284538 464283692 0.000000e+00 985.0
4 TraesCS5B01G392800 chr5D 88.462 78 6 1 271 345 280774036 280773959 3.430000e-14 91.6
5 TraesCS5B01G392800 chr5A 95.417 4211 125 28 1071 5255 584679599 584675431 0.000000e+00 6645.0
6 TraesCS5B01G392800 chr5A 96.054 2534 86 8 5241 7769 584675219 584672695 0.000000e+00 4113.0
7 TraesCS5B01G392800 chr5A 85.668 935 82 22 180 1070 584680563 584679637 0.000000e+00 937.0
8 TraesCS5B01G392800 chr5A 96.436 477 13 4 8450 8923 678282638 678283113 0.000000e+00 784.0
9 TraesCS5B01G392800 chr5A 86.957 253 14 8 7801 8045 584672696 584672455 5.310000e-67 267.0
10 TraesCS5B01G392800 chr5A 100.000 41 0 0 7338 7378 584672318 584672278 9.610000e-10 76.8
11 TraesCS5B01G392800 chr1B 93.187 910 30 12 8043 8923 36516441 36517347 0.000000e+00 1308.0
12 TraesCS5B01G392800 chr1B 96.855 477 11 4 8450 8923 54870206 54869731 0.000000e+00 795.0
13 TraesCS5B01G392800 chr7B 92.849 909 19 10 8042 8923 725145323 725144434 0.000000e+00 1277.0
14 TraesCS5B01G392800 chr7B 94.142 734 39 3 8043 8773 710080295 710079563 0.000000e+00 1114.0
15 TraesCS5B01G392800 chr7B 95.807 477 16 4 8450 8923 734761603 734762078 0.000000e+00 767.0
16 TraesCS5B01G392800 chr7B 100.000 139 0 0 8773 8911 710079476 710079338 3.200000e-64 257.0
17 TraesCS5B01G392800 chr2B 96.751 554 13 5 8373 8923 335390423 335390974 0.000000e+00 918.0
18 TraesCS5B01G392800 chr2B 92.532 549 26 11 8043 8583 91069228 91069769 0.000000e+00 773.0
19 TraesCS5B01G392800 chrUn 97.269 476 11 2 8450 8923 12545680 12545205 0.000000e+00 806.0
20 TraesCS5B01G392800 chrUn 92.674 546 27 11 8041 8580 12546123 12545585 0.000000e+00 774.0
21 TraesCS5B01G392800 chr7A 92.463 544 25 12 8046 8583 286991110 286990577 0.000000e+00 763.0
22 TraesCS5B01G392800 chr6B 91.786 560 24 12 8039 8583 533998123 533998675 0.000000e+00 760.0
23 TraesCS5B01G392800 chr2A 92.139 547 29 10 8043 8583 172557142 172556604 0.000000e+00 760.0
24 TraesCS5B01G392800 chr4B 94.979 478 19 5 8450 8923 339464246 339463770 0.000000e+00 745.0
25 TraesCS5B01G392800 chr4A 91.336 554 29 13 8040 8583 627587556 627588100 0.000000e+00 739.0
26 TraesCS5B01G392800 chr3D 81.818 132 23 1 14 145 477899607 477899477 9.470000e-20 110.0
27 TraesCS5B01G392800 chr2D 83.544 79 10 1 270 345 522511610 522511532 4.470000e-08 71.3
28 TraesCS5B01G392800 chr3A 84.932 73 6 3 270 338 489053705 489053776 1.610000e-07 69.4


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 TraesCS5B01G392800 chr5B 571460122 571469044 8922 True 16478.00 16478 100.0000 1 8923 1 chr5B.!!$R2 8922
1 TraesCS5B01G392800 chr5B 3901581 3902119 538 True 771.00 771 92.6060 8043 8578 1 chr5B.!!$R1 535
2 TraesCS5B01G392800 chr5D 464276404 464284538 8134 True 6088.00 11191 91.2520 2 8045 2 chr5D.!!$R2 8043
3 TraesCS5B01G392800 chr5A 584672278 584680563 8285 True 2407.76 6645 92.8192 180 8045 5 chr5A.!!$R1 7865
4 TraesCS5B01G392800 chr1B 36516441 36517347 906 False 1308.00 1308 93.1870 8043 8923 1 chr1B.!!$F1 880
5 TraesCS5B01G392800 chr7B 725144434 725145323 889 True 1277.00 1277 92.8490 8042 8923 1 chr7B.!!$R1 881
6 TraesCS5B01G392800 chr7B 710079338 710080295 957 True 685.50 1114 97.0710 8043 8911 2 chr7B.!!$R2 868
7 TraesCS5B01G392800 chr2B 335390423 335390974 551 False 918.00 918 96.7510 8373 8923 1 chr2B.!!$F2 550
8 TraesCS5B01G392800 chr2B 91069228 91069769 541 False 773.00 773 92.5320 8043 8583 1 chr2B.!!$F1 540
9 TraesCS5B01G392800 chrUn 12545205 12546123 918 True 790.00 806 94.9715 8041 8923 2 chrUn.!!$R1 882
10 TraesCS5B01G392800 chr7A 286990577 286991110 533 True 763.00 763 92.4630 8046 8583 1 chr7A.!!$R1 537
11 TraesCS5B01G392800 chr6B 533998123 533998675 552 False 760.00 760 91.7860 8039 8583 1 chr6B.!!$F1 544
12 TraesCS5B01G392800 chr2A 172556604 172557142 538 True 760.00 760 92.1390 8043 8583 1 chr2A.!!$R1 540
13 TraesCS5B01G392800 chr4A 627587556 627588100 544 False 739.00 739 91.3360 8040 8583 1 chr4A.!!$F1 543

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
628 648 0.026285 GTTCCGAAATCCGACATGCG 59.974 55.000 0.00 0.0 41.76 4.73 F
1420 1550 0.321298 TTCCCCTTTTCTTCGGCTCG 60.321 55.000 0.00 0.0 0.00 5.03 F
1537 1667 1.916506 CGGAGGAGCAGGAGATCATA 58.083 55.000 0.00 0.0 0.00 2.15 F
3308 3458 1.654105 GTGTAAGTGATCTTGCGTCCG 59.346 52.381 0.00 0.0 38.74 4.79 F
4579 4738 2.489073 GGGTTCTGGTCATTTGTGGTCT 60.489 50.000 0.00 0.0 0.00 3.85 F
5618 6011 0.111061 TGGTTGCTGGATTGAGTGCT 59.889 50.000 0.00 0.0 0.00 4.40 F
6764 7164 0.108424 CAGCCTGTCAGAGTGCTACC 60.108 60.000 0.00 0.0 31.69 3.18 F
7727 8129 1.542915 CACTGTGCCCCAGAAAGAATG 59.457 52.381 7.43 0.0 44.49 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2622 2772 0.250989 TGTTACAAAAGGCCCCTCGG 60.251 55.000 0.0 0.0 0.00 4.63 R
3304 3454 0.322546 AGGGGAAGAATGCAACGGAC 60.323 55.000 0.0 0.0 0.00 4.79 R
3424 3574 3.073798 TCTTCCACACTTTATCTTGGCCA 59.926 43.478 0.0 0.0 0.00 5.36 R
4678 4842 0.593128 ATTGACGTGCTTGTTGAGGC 59.407 50.000 0.0 0.0 0.00 4.70 R
6466 6866 1.068741 GGGATGGTCTGGTACTTAGCG 59.931 57.143 0.0 0.0 0.00 4.26 R
7255 7656 1.142778 GCCTAGCTCTGCTCGTTTCG 61.143 60.000 0.0 0.0 40.44 3.46 R
7765 8168 0.242825 TCGTCCTGTCGTTAGCAAGG 59.757 55.000 0.0 0.0 0.00 3.61 R
8616 9143 0.389025 GTTGTGGTTTGCTTCCCTGG 59.611 55.000 0.0 0.0 0.00 4.45 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
31 32 2.423185 CGACCATGCCATAGAAAAGCAA 59.577 45.455 0.00 0.00 40.46 3.91
52 53 2.037251 ACCTCATAACAGTCGTGCACTT 59.963 45.455 16.19 4.31 30.26 3.16
53 54 2.413112 CCTCATAACAGTCGTGCACTTG 59.587 50.000 16.19 12.67 30.26 3.16
54 55 2.412870 TCATAACAGTCGTGCACTTGG 58.587 47.619 16.19 4.24 30.26 3.61
78 81 4.217767 GGTAACCAGAGAACCCAATGTTTC 59.782 45.833 0.00 0.00 37.29 2.78
130 133 1.898863 ATCATAGGCCCTGACACCTT 58.101 50.000 7.73 0.00 37.50 3.50
137 140 0.912486 GCCCTGACACCTTGGTAGAT 59.088 55.000 0.00 0.00 0.00 1.98
159 162 4.843147 TGCGTTTGAAAGTAGTTGTCATG 58.157 39.130 0.00 0.00 0.00 3.07
177 180 1.965935 TGCAACATCATATGTCCCGG 58.034 50.000 1.90 0.00 44.07 5.73
178 181 1.211703 TGCAACATCATATGTCCCGGT 59.788 47.619 0.00 0.00 44.07 5.28
179 182 1.603802 GCAACATCATATGTCCCGGTG 59.396 52.381 0.00 0.42 44.07 4.94
180 183 1.603802 CAACATCATATGTCCCGGTGC 59.396 52.381 0.00 0.00 44.07 5.01
181 184 0.108585 ACATCATATGTCCCGGTGCC 59.891 55.000 0.00 0.00 39.92 5.01
195 198 1.235281 GGTGCCGAACCCTTGAAGTC 61.235 60.000 0.00 0.00 44.02 3.01
210 213 2.897641 AAGTCGAGAGCATGCTCCGC 62.898 60.000 37.79 30.42 43.70 5.54
267 270 1.522676 CGTCGTTTGATCATCATCCGG 59.477 52.381 0.00 0.00 0.00 5.14
297 303 6.380274 TCCATGAACTCGTAGAAGTAATCCTT 59.620 38.462 0.00 0.00 34.09 3.36
300 306 6.989659 TGAACTCGTAGAAGTAATCCTTGTT 58.010 36.000 0.00 0.00 34.09 2.83
302 308 6.585695 ACTCGTAGAAGTAATCCTTGTTCA 57.414 37.500 0.00 0.00 34.09 3.18
306 312 8.475331 TCGTAGAAGTAATCCTTGTTCAAATC 57.525 34.615 0.00 0.00 32.03 2.17
309 315 7.693969 AGAAGTAATCCTTGTTCAAATCCAG 57.306 36.000 0.00 0.00 32.03 3.86
343 349 5.053811 TCAAAGTAAACAATGAGAGCGTCA 58.946 37.500 0.00 0.00 40.38 4.35
486 505 3.637273 GGGTGGAGCCGACAAGGT 61.637 66.667 0.00 0.00 43.70 3.50
520 539 2.412325 CGGAGTGGTAAAACAACGATGC 60.412 50.000 0.00 0.00 0.00 3.91
528 547 0.034896 AAACAACGATGCCGGAGTCT 59.965 50.000 5.05 0.00 40.78 3.24
556 576 3.882888 CGTGAATATAAAGCACATGGGGT 59.117 43.478 0.00 0.00 32.96 4.95
563 583 0.409092 AAGCACATGGGGTTGGATGA 59.591 50.000 12.49 0.00 0.00 2.92
591 611 7.989741 GTGAAAGAATGAGATCTTTGGATAGGA 59.010 37.037 6.99 0.00 46.77 2.94
611 631 3.698263 TTTTGGGTTGGCCGGGGTT 62.698 57.895 2.18 0.00 34.97 4.11
612 632 4.607025 TTGGGTTGGCCGGGGTTC 62.607 66.667 2.18 0.00 34.97 3.62
627 647 0.377203 GGTTCCGAAATCCGACATGC 59.623 55.000 0.00 0.00 41.76 4.06
628 648 0.026285 GTTCCGAAATCCGACATGCG 59.974 55.000 0.00 0.00 41.76 4.73
637 657 3.541831 CGACATGCGGACGTTCGG 61.542 66.667 19.64 3.65 36.03 4.30
638 658 3.849953 GACATGCGGACGTTCGGC 61.850 66.667 19.64 10.98 42.22 5.54
656 677 1.674057 CCTGTCGCAAACCTCCTCT 59.326 57.895 0.00 0.00 0.00 3.69
683 704 2.566724 GGTGCTGATTTTGGGGATTTCA 59.433 45.455 0.00 0.00 0.00 2.69
688 709 4.442472 GCTGATTTTGGGGATTTCAGATGG 60.442 45.833 2.60 0.00 36.72 3.51
729 751 1.005394 GGTGACCGTCGTTGGATGT 60.005 57.895 2.72 0.00 0.00 3.06
807 829 4.644685 TGAGGAAAAGAGAGGTTTGGTTTG 59.355 41.667 0.00 0.00 0.00 2.93
855 932 3.492102 TTGAGTCCAAGAGAGGTTTGG 57.508 47.619 0.00 0.00 45.17 3.28
858 935 2.368875 GAGTCCAAGAGAGGTTTGGTGA 59.631 50.000 4.14 0.00 44.35 4.02
860 937 3.008485 AGTCCAAGAGAGGTTTGGTGATC 59.992 47.826 4.14 0.00 44.35 2.92
861 938 2.305927 TCCAAGAGAGGTTTGGTGATCC 59.694 50.000 4.14 0.00 44.35 3.36
862 939 2.350522 CAAGAGAGGTTTGGTGATCCG 58.649 52.381 0.00 0.00 36.30 4.18
868 953 1.749258 GTTTGGTGATCCGGGAGCC 60.749 63.158 10.23 8.80 36.30 4.70
928 1013 0.609151 TGATGCACAGGCCCATTTTG 59.391 50.000 0.00 0.00 40.13 2.44
934 1019 1.688197 CACAGGCCCATTTTGACAGTT 59.312 47.619 0.00 0.00 0.00 3.16
1115 1239 3.305516 CCAGCCAACCAGCCAACC 61.306 66.667 0.00 0.00 0.00 3.77
1116 1240 2.203538 CAGCCAACCAGCCAACCT 60.204 61.111 0.00 0.00 0.00 3.50
1172 1296 1.613610 CTCCTCGTCCCACTCCCTA 59.386 63.158 0.00 0.00 0.00 3.53
1383 1507 2.746362 GGCACATCTTATCTATGCTGCC 59.254 50.000 0.00 11.25 40.69 4.85
1386 1510 2.634940 ACATCTTATCTATGCTGCCCGT 59.365 45.455 0.00 0.00 0.00 5.28
1416 1546 6.775594 AATAATTCTTCCCCTTTTCTTCGG 57.224 37.500 0.00 0.00 0.00 4.30
1420 1550 0.321298 TTCCCCTTTTCTTCGGCTCG 60.321 55.000 0.00 0.00 0.00 5.03
1462 1592 4.424566 TAACCGCAGCCGTCGTCC 62.425 66.667 0.00 0.00 0.00 4.79
1537 1667 1.916506 CGGAGGAGCAGGAGATCATA 58.083 55.000 0.00 0.00 0.00 2.15
1633 1763 5.483685 TCTGTACTGTAATTTCACCTGCT 57.516 39.130 0.00 0.00 0.00 4.24
1634 1764 5.479306 TCTGTACTGTAATTTCACCTGCTC 58.521 41.667 0.00 0.00 0.00 4.26
1635 1765 5.246203 TCTGTACTGTAATTTCACCTGCTCT 59.754 40.000 0.00 0.00 0.00 4.09
1686 1816 7.041167 TCACAGAAATGTTGATGAATCTTTCGT 60.041 33.333 0.00 0.00 0.00 3.85
1847 1995 6.020916 CACATCTTTCTCTTATTGCAAATGCG 60.021 38.462 1.71 0.00 45.83 4.73
1891 2039 2.738000 TGTTTGCTGTGCATGGAAACAC 60.738 45.455 26.02 12.22 45.75 3.32
1983 2131 4.142622 CGCTCTTGCCATTTGATAAAGACA 60.143 41.667 0.00 0.00 35.36 3.41
2066 2214 2.179517 CTGCTGGACGAGTCGGTC 59.820 66.667 18.30 11.51 36.18 4.79
2142 2290 5.594317 AGTTGGCAGGTATGATAAAATCCAC 59.406 40.000 0.00 0.00 0.00 4.02
2158 2306 4.767578 ATCCACACAGTATCTGAATGCT 57.232 40.909 3.70 0.00 35.18 3.79
2450 2600 2.158370 TCAGGTACACTTGTCTGGGAGA 60.158 50.000 0.00 0.00 0.00 3.71
2521 2671 7.213678 CCTTCTGTCCTTCTATTTATCTGACC 58.786 42.308 0.00 0.00 0.00 4.02
2655 2805 8.293867 GCCTTTTGTAACATAATCTGTACACAA 58.706 33.333 0.00 0.00 39.38 3.33
2864 3014 8.214364 AGGGAATTAGAGGAAAAGATACACATC 58.786 37.037 0.00 0.00 0.00 3.06
2896 3046 5.250200 TGCACCAGTGGTATTTTACTAAGG 58.750 41.667 16.22 0.00 32.11 2.69
2926 3076 3.139077 GAGTGACCGAAACTTGAATGGT 58.861 45.455 0.00 0.00 35.14 3.55
2985 3135 3.441572 GGGATGAATGAAGGTTGTGTCTG 59.558 47.826 0.00 0.00 0.00 3.51
3304 3454 6.019801 GGTATAACTGTGTAAGTGATCTTGCG 60.020 42.308 0.00 0.00 39.81 4.85
3308 3458 1.654105 GTGTAAGTGATCTTGCGTCCG 59.346 52.381 0.00 0.00 38.74 4.79
3472 3622 5.127845 TCAGAGACAGCTATTACCCAGAAAG 59.872 44.000 0.00 0.00 0.00 2.62
3487 3637 6.997655 ACCCAGAAAGAGGAAAAATCAAATC 58.002 36.000 0.00 0.00 0.00 2.17
3548 3698 8.579850 TTAATGACTGCAATTATTCCTCAACT 57.420 30.769 0.00 0.00 0.00 3.16
3821 3971 4.142600 CCAAATAGAGTGTTACTGCTTGCC 60.143 45.833 0.00 0.00 0.00 4.52
4044 4197 5.563751 GTGTGCATCGTATAATTATTTGCCG 59.436 40.000 2.68 2.33 0.00 5.69
4355 4513 4.958509 TGGTAAATGTCACGTACTTGGAA 58.041 39.130 0.00 0.00 0.00 3.53
4356 4514 5.366460 TGGTAAATGTCACGTACTTGGAAA 58.634 37.500 0.00 0.00 0.00 3.13
4357 4515 5.998981 TGGTAAATGTCACGTACTTGGAAAT 59.001 36.000 0.00 0.00 0.00 2.17
4358 4516 6.148150 TGGTAAATGTCACGTACTTGGAAATC 59.852 38.462 0.00 0.00 0.00 2.17
4359 4517 6.370718 GGTAAATGTCACGTACTTGGAAATCT 59.629 38.462 0.00 0.00 0.00 2.40
4360 4518 6.877611 AAATGTCACGTACTTGGAAATCTT 57.122 33.333 0.00 0.00 0.00 2.40
4362 4520 5.666969 TGTCACGTACTTGGAAATCTTTG 57.333 39.130 0.00 0.00 0.00 2.77
4363 4521 4.513692 TGTCACGTACTTGGAAATCTTTGG 59.486 41.667 0.00 0.00 0.00 3.28
4364 4522 4.514066 GTCACGTACTTGGAAATCTTTGGT 59.486 41.667 0.00 0.00 0.00 3.67
4365 4523 5.697633 GTCACGTACTTGGAAATCTTTGGTA 59.302 40.000 0.00 0.00 0.00 3.25
4366 4524 6.203338 GTCACGTACTTGGAAATCTTTGGTAA 59.797 38.462 0.00 0.00 0.00 2.85
4367 4525 6.938030 TCACGTACTTGGAAATCTTTGGTAAT 59.062 34.615 0.00 0.00 0.00 1.89
4368 4526 7.118680 TCACGTACTTGGAAATCTTTGGTAATC 59.881 37.037 0.00 0.00 0.00 1.75
4369 4527 7.119262 CACGTACTTGGAAATCTTTGGTAATCT 59.881 37.037 0.00 0.00 0.00 2.40
4370 4528 7.664318 ACGTACTTGGAAATCTTTGGTAATCTT 59.336 33.333 0.00 0.00 0.00 2.40
4371 4529 8.512138 CGTACTTGGAAATCTTTGGTAATCTTT 58.488 33.333 0.00 0.00 0.00 2.52
4405 4563 5.012239 TCTTTCCATAGCTCAAAGCAATGT 58.988 37.500 0.00 0.00 45.56 2.71
4495 4653 4.742438 TTATGTTTGACCGTCTCTTTGC 57.258 40.909 0.00 0.00 0.00 3.68
4532 4690 6.612247 TGTTTATATGATTTGCCTGTACGG 57.388 37.500 0.00 0.00 0.00 4.02
4579 4738 2.489073 GGGTTCTGGTCATTTGTGGTCT 60.489 50.000 0.00 0.00 0.00 3.85
4609 4768 4.565022 ACGAAATTTAGCCCATTGGTTTG 58.435 39.130 1.20 0.00 0.00 2.93
4658 4822 5.823861 AGCACCCCATTATTTTCTTTTGT 57.176 34.783 0.00 0.00 0.00 2.83
4710 4874 1.202722 ACGTCAATGTTCCCGTTCCTT 60.203 47.619 0.00 0.00 0.00 3.36
4771 4937 8.372459 TGCTTCGGTGGTCAATATATACTTATT 58.628 33.333 0.00 0.00 0.00 1.40
4852 5018 4.866508 ATCTTGACCGTAACAGTCTTGA 57.133 40.909 0.00 0.00 35.21 3.02
5193 5360 8.537728 TCATAATTAAGCATTTGGACATTCCT 57.462 30.769 0.00 0.00 37.46 3.36
5267 5660 4.406456 TGACATTTGTTGGGCTCTTACAT 58.594 39.130 0.00 0.00 0.00 2.29
5284 5677 7.064016 GCTCTTACATGGCTTATAACTCTATGC 59.936 40.741 0.00 0.00 0.00 3.14
5355 5748 4.852134 TTTGTTTCCTGACCACATGATG 57.148 40.909 0.00 0.00 0.00 3.07
5388 5781 4.462483 GTCCAAAATGCAGTGGAATTCCTA 59.538 41.667 24.73 9.10 45.42 2.94
5444 5837 5.305644 ACCTTACTGATCTAGGTATGCCTTG 59.694 44.000 7.98 6.27 44.18 3.61
5468 5861 8.327941 TGTATTCTGATTTCTTCCAAACTCTG 57.672 34.615 0.00 0.00 0.00 3.35
5471 5864 5.132502 TCTGATTTCTTCCAAACTCTGCAA 58.867 37.500 0.00 0.00 0.00 4.08
5618 6011 0.111061 TGGTTGCTGGATTGAGTGCT 59.889 50.000 0.00 0.00 0.00 4.40
5676 6069 7.989826 AGATGTATGACTTTAATTTCCACTGC 58.010 34.615 0.00 0.00 0.00 4.40
5679 6072 5.904362 ATGACTTTAATTTCCACTGCCTC 57.096 39.130 0.00 0.00 0.00 4.70
5804 6197 0.902531 ACACGGTGGCTGTTAGCTAT 59.097 50.000 13.48 0.00 41.99 2.97
5805 6198 1.290203 CACGGTGGCTGTTAGCTATG 58.710 55.000 0.00 0.00 41.99 2.23
5806 6199 0.462047 ACGGTGGCTGTTAGCTATGC 60.462 55.000 0.00 0.00 41.99 3.14
5807 6200 1.160329 CGGTGGCTGTTAGCTATGCC 61.160 60.000 19.74 19.74 41.99 4.40
5808 6201 0.819666 GGTGGCTGTTAGCTATGCCC 60.820 60.000 22.12 15.81 44.32 5.36
5809 6202 0.181350 GTGGCTGTTAGCTATGCCCT 59.819 55.000 22.12 0.00 44.32 5.19
5810 6203 1.416401 GTGGCTGTTAGCTATGCCCTA 59.584 52.381 22.12 8.75 44.32 3.53
5837 6230 5.478233 TTGATTATGTTCCGTTCATTCCG 57.522 39.130 0.00 0.00 0.00 4.30
5890 6284 7.989826 AGGCTTAGCTTATAGTTTTGTCATTG 58.010 34.615 3.59 0.00 0.00 2.82
6128 6522 8.201554 TGATAGACTCTGATGCAAATACAAAC 57.798 34.615 0.00 0.00 0.00 2.93
6179 6573 3.142951 TCGTGGTGTAATTTGTTCTGGG 58.857 45.455 0.00 0.00 0.00 4.45
6247 6641 8.934825 ACAATTTCCATTGCATTTGTATTACAC 58.065 29.630 0.00 0.00 43.39 2.90
6394 6788 0.673644 CTCATGTCCAACACCCCGTC 60.674 60.000 0.00 0.00 0.00 4.79
6403 6797 3.520317 TCCAACACCCCGTCTAATACATT 59.480 43.478 0.00 0.00 0.00 2.71
6440 6840 7.089770 TGTTGATATCTGAGTACTCTGACAC 57.910 40.000 28.42 22.02 39.73 3.67
6571 6971 6.909550 ACTGGAGTATCAGATTCCATACTC 57.090 41.667 17.60 17.60 42.69 2.59
6586 6986 5.376625 TCCATACTCATCTTATTTGGTGGC 58.623 41.667 0.00 0.00 0.00 5.01
6604 7004 1.607148 GGCGCTGTTACAAAAGGAAGT 59.393 47.619 7.64 0.00 0.00 3.01
6688 7088 6.257411 CACTGATCTATGCCTTCTAACTTGTG 59.743 42.308 0.00 0.00 0.00 3.33
6764 7164 0.108424 CAGCCTGTCAGAGTGCTACC 60.108 60.000 0.00 0.00 31.69 3.18
6926 7326 8.428186 TTCGGTGATACTTTATGTACCAAATC 57.572 34.615 0.00 0.00 33.45 2.17
7053 7453 8.626526 ACGTGTCACCAGTAAGAAATTAAAAAT 58.373 29.630 0.00 0.00 0.00 1.82
7255 7656 2.726850 GAAGGTTTGTGTTCGGCCGC 62.727 60.000 23.51 8.29 0.00 6.53
7327 7728 5.319043 TCATAAAGGATGGTATGAACCCC 57.681 43.478 0.00 0.00 46.16 4.95
7444 7845 2.893489 GGAGTTCAAAGGGATGCAGTTT 59.107 45.455 0.00 0.00 0.00 2.66
7474 7875 1.543429 CCGAAGAGGAACAAGCAGGTT 60.543 52.381 0.00 0.00 45.00 3.50
7585 7986 2.474816 GACCTGACCGATAACATGCTC 58.525 52.381 0.00 0.00 0.00 4.26
7662 8063 2.695359 GCAAGGTTAGGTTCATCGACA 58.305 47.619 0.00 0.00 0.00 4.35
7683 8084 2.223971 ACCTGACAGTTAACTGACACCG 60.224 50.000 36.14 26.54 46.59 4.94
7727 8129 1.542915 CACTGTGCCCCAGAAAGAATG 59.457 52.381 7.43 0.00 44.49 2.67
7761 8164 2.352503 GCAAGTGCGTGGAATTTCAT 57.647 45.000 0.00 0.00 0.00 2.57
7765 8168 0.523335 GTGCGTGGAATTTCATCCGC 60.523 55.000 13.35 13.35 44.78 5.54
7769 8172 1.202177 CGTGGAATTTCATCCGCCTTG 60.202 52.381 0.00 0.00 45.32 3.61
7772 8175 2.297701 GGAATTTCATCCGCCTTGCTA 58.702 47.619 0.00 0.00 0.00 3.49
7783 8186 1.352156 GCCTTGCTAACGACAGGACG 61.352 60.000 0.00 0.00 39.31 4.79
7821 8224 0.620556 ATCATCCGCCTTCTGGTTGT 59.379 50.000 0.00 0.00 35.27 3.32
7844 8247 1.896220 TGGTTCTGAGCCATGTGTTC 58.104 50.000 9.35 0.00 0.00 3.18
7862 8265 8.869897 CATGTGTTCGATACTGTGTTATTTACT 58.130 33.333 0.00 0.00 0.00 2.24
7864 8267 9.563898 TGTGTTCGATACTGTGTTATTTACTAG 57.436 33.333 0.00 0.00 0.00 2.57
7865 8268 9.565213 GTGTTCGATACTGTGTTATTTACTAGT 57.435 33.333 0.00 0.00 0.00 2.57
7888 8292 1.827681 TCATCGGGGCGAATTGAAAA 58.172 45.000 0.00 0.00 39.99 2.29
7889 8293 1.470890 TCATCGGGGCGAATTGAAAAC 59.529 47.619 0.00 0.00 39.99 2.43
7890 8294 1.472480 CATCGGGGCGAATTGAAAACT 59.528 47.619 0.00 0.00 39.99 2.66
7936 8340 9.939802 GAATAAGGTTTCGTATAGGGTATCAAT 57.060 33.333 0.00 0.00 0.00 2.57
7941 8350 8.311836 AGGTTTCGTATAGGGTATCAATGTATG 58.688 37.037 0.00 0.00 0.00 2.39
7979 8394 4.753610 CACTGAAGCTGAGATTTGTTCAGA 59.246 41.667 15.39 0.00 44.56 3.27
8020 8435 0.741915 TTTTGTTCCACTCCGTTGGC 59.258 50.000 0.00 0.00 36.48 4.52
8026 8441 4.003788 CACTCCGTTGGCCCTCGT 62.004 66.667 13.98 0.00 0.00 4.18
8217 8641 3.309954 GCATCCGCTCTATCTTTCGTTTT 59.690 43.478 0.00 0.00 34.30 2.43
8316 8774 1.768684 TTCTCCGGCCATCTATGCCC 61.769 60.000 2.24 0.00 46.48 5.36
8602 9129 7.417116 GGTGAATTTGAATCTGGTAGCATTCAT 60.417 37.037 10.79 0.00 38.51 2.57
8606 9133 7.649533 TTTGAATCTGGTAGCATTCATCAAT 57.350 32.000 10.79 0.00 38.51 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.069823 TGGCATGGTCGCAAATTTGTT 59.930 42.857 19.03 0.00 0.00 2.83
13 14 2.762327 AGGTTGCTTTTCTATGGCATGG 59.238 45.455 10.98 7.51 35.84 3.66
14 15 3.444742 TGAGGTTGCTTTTCTATGGCATG 59.555 43.478 10.98 0.16 35.84 4.06
15 16 3.700538 TGAGGTTGCTTTTCTATGGCAT 58.299 40.909 4.88 4.88 35.84 4.40
31 32 1.618837 AGTGCACGACTGTTATGAGGT 59.381 47.619 12.01 0.00 31.75 3.85
52 53 2.781631 GGGTTCTCTGGTTACCCCA 58.218 57.895 0.00 0.00 44.75 4.96
63 64 4.753107 TGTCGTTAGAAACATTGGGTTCTC 59.247 41.667 7.82 0.00 39.29 2.87
110 113 2.705658 CAAGGTGTCAGGGCCTATGATA 59.294 50.000 5.28 8.76 34.15 2.15
113 116 0.107017 CCAAGGTGTCAGGGCCTATG 60.107 60.000 5.28 1.80 34.15 2.23
114 117 0.550147 ACCAAGGTGTCAGGGCCTAT 60.550 55.000 5.28 0.00 34.15 2.57
130 133 4.890088 ACTACTTTCAAACGCATCTACCA 58.110 39.130 0.00 0.00 0.00 3.25
137 140 4.788201 GCATGACAACTACTTTCAAACGCA 60.788 41.667 0.00 0.00 0.00 5.24
159 162 1.603802 CACCGGGACATATGATGTTGC 59.396 52.381 10.38 0.00 45.03 4.17
177 180 1.566018 CGACTTCAAGGGTTCGGCAC 61.566 60.000 0.00 0.00 0.00 5.01
178 181 1.301401 CGACTTCAAGGGTTCGGCA 60.301 57.895 0.00 0.00 0.00 5.69
179 182 1.005394 TCGACTTCAAGGGTTCGGC 60.005 57.895 0.00 0.00 0.00 5.54
180 183 0.601558 TCTCGACTTCAAGGGTTCGG 59.398 55.000 0.00 0.00 0.00 4.30
181 184 1.983972 CTCTCGACTTCAAGGGTTCG 58.016 55.000 0.00 0.00 0.00 3.95
210 213 3.871006 TCTTAAAGACACATAGCATGCGG 59.129 43.478 13.01 8.77 0.00 5.69
267 270 3.079960 TCTACGAGTTCATGGATTCGC 57.920 47.619 18.01 0.00 36.58 4.70
297 303 2.797792 GCAAACACGCTGGATTTGAACA 60.798 45.455 0.30 0.00 35.73 3.18
300 306 1.317613 AGCAAACACGCTGGATTTGA 58.682 45.000 0.30 0.00 41.85 2.69
302 308 1.680735 TGAAGCAAACACGCTGGATTT 59.319 42.857 0.00 0.00 42.89 2.17
306 312 1.202290 ACTTTGAAGCAAACACGCTGG 60.202 47.619 0.00 0.00 42.89 4.85
309 315 3.854809 TGTTTACTTTGAAGCAAACACGC 59.145 39.130 14.98 0.00 43.61 5.34
366 374 0.320073 CACACCCGGCGAGTCTTAAA 60.320 55.000 9.30 0.00 0.00 1.52
367 375 1.290955 CACACCCGGCGAGTCTTAA 59.709 57.895 9.30 0.00 0.00 1.85
368 376 2.642254 CCACACCCGGCGAGTCTTA 61.642 63.158 9.30 0.00 0.00 2.10
413 421 0.609131 CCCACGATCCAGTTGCCTTT 60.609 55.000 0.00 0.00 0.00 3.11
465 474 2.397413 CTTGTCGGCTCCACCCAAGT 62.397 60.000 0.00 0.00 34.62 3.16
486 505 0.878523 CACTCCGAACGTTGCCAAGA 60.879 55.000 5.00 0.00 0.00 3.02
520 539 4.135153 CACGCTCCCAGACTCCGG 62.135 72.222 0.00 0.00 0.00 5.14
528 547 3.202906 GTGCTTTATATTCACGCTCCCA 58.797 45.455 0.00 0.00 0.00 4.37
556 576 7.400439 AGATCTCATTCTTTCACTTCATCCAA 58.600 34.615 0.00 0.00 0.00 3.53
563 583 9.393512 CTATCCAAAGATCTCATTCTTTCACTT 57.606 33.333 0.00 0.00 42.58 3.16
591 611 2.220586 CCCCGGCCAACCCAAAAAT 61.221 57.895 2.24 0.00 0.00 1.82
611 631 4.102561 CGCATGTCGGATTTCGGA 57.897 55.556 0.00 0.00 39.77 4.55
630 650 4.595538 TTGCGACAGGCCGAACGT 62.596 61.111 16.64 5.31 42.61 3.99
631 651 3.342627 TTTGCGACAGGCCGAACG 61.343 61.111 12.58 12.58 42.61 3.95
632 652 2.251371 GTTTGCGACAGGCCGAAC 59.749 61.111 0.00 0.00 42.61 3.95
633 653 2.975799 GGTTTGCGACAGGCCGAA 60.976 61.111 0.00 0.00 42.61 4.30
636 656 3.056328 GGAGGTTTGCGACAGGCC 61.056 66.667 0.00 0.00 42.61 5.19
637 657 2.032681 AGGAGGTTTGCGACAGGC 59.967 61.111 0.00 0.00 43.96 4.85
638 658 0.895530 TAGAGGAGGTTTGCGACAGG 59.104 55.000 0.00 0.00 0.00 4.00
656 677 2.896685 CCCCAAAATCAGCACCAAACTA 59.103 45.455 0.00 0.00 0.00 2.24
683 704 1.153369 CGAACCGGTCATGCCATCT 60.153 57.895 8.04 0.00 36.97 2.90
729 751 4.124238 CCAAACTGTCCGACACTTTTAGA 58.876 43.478 0.00 0.00 0.00 2.10
755 777 4.546674 ACAAAAACCTCTCCCAAATGTCT 58.453 39.130 0.00 0.00 0.00 3.41
788 810 8.194769 TCATAAACAAACCAAACCTCTCTTTTC 58.805 33.333 0.00 0.00 0.00 2.29
791 813 7.060421 TCTCATAAACAAACCAAACCTCTCTT 58.940 34.615 0.00 0.00 0.00 2.85
850 927 1.749258 GGCTCCCGGATCACCAAAC 60.749 63.158 0.73 0.00 35.59 2.93
851 928 2.674754 GGCTCCCGGATCACCAAA 59.325 61.111 0.73 0.00 35.59 3.28
852 929 3.781307 CGGCTCCCGGATCACCAA 61.781 66.667 0.73 0.00 44.15 3.67
928 1013 2.479275 GGTTCTTTACGGCTCAACTGTC 59.521 50.000 0.00 0.00 39.22 3.51
934 1019 1.337447 CCTTCGGTTCTTTACGGCTCA 60.337 52.381 0.00 0.00 0.00 4.26
960 1046 4.823989 CCTTACTGGGCCATAAGAAGAATG 59.176 45.833 24.91 8.41 31.20 2.67
961 1047 4.689983 GCCTTACTGGGCCATAAGAAGAAT 60.690 45.833 24.91 3.25 45.92 2.40
962 1048 3.371595 GCCTTACTGGGCCATAAGAAGAA 60.372 47.826 24.91 7.57 45.92 2.52
963 1049 2.172717 GCCTTACTGGGCCATAAGAAGA 59.827 50.000 24.91 4.33 45.92 2.87
964 1050 2.576615 GCCTTACTGGGCCATAAGAAG 58.423 52.381 24.91 17.63 45.92 2.85
1115 1239 4.285149 GACGCGGCGCATGCTAAG 62.285 66.667 32.61 15.83 42.25 2.18
1116 1240 4.812476 AGACGCGGCGCATGCTAA 62.812 61.111 32.61 0.00 42.25 3.09
1395 1519 4.014406 GCCGAAGAAAAGGGGAAGAATTA 58.986 43.478 0.00 0.00 0.00 1.40
1399 1528 1.003233 GAGCCGAAGAAAAGGGGAAGA 59.997 52.381 0.00 0.00 0.00 2.87
1400 1529 1.454201 GAGCCGAAGAAAAGGGGAAG 58.546 55.000 0.00 0.00 0.00 3.46
1402 1531 1.295423 CGAGCCGAAGAAAAGGGGA 59.705 57.895 0.00 0.00 0.00 4.81
1416 1546 2.883253 GAGAGGCAGCGAACGAGC 60.883 66.667 0.00 1.11 37.41 5.03
1420 1550 2.029844 GGTGTGAGAGGCAGCGAAC 61.030 63.158 0.00 0.00 0.00 3.95
1462 1592 2.158959 GTCGATGTTCGCCACCGAG 61.159 63.158 0.00 0.00 45.35 4.63
1537 1667 3.364964 TCCCTCCGGTCCCTGGAT 61.365 66.667 0.00 0.00 34.32 3.41
1633 1763 7.345691 TGCATATGAAATTAAGAACTGGGAGA 58.654 34.615 6.97 0.00 0.00 3.71
1634 1764 7.284034 ACTGCATATGAAATTAAGAACTGGGAG 59.716 37.037 6.97 0.00 0.00 4.30
1635 1765 7.118723 ACTGCATATGAAATTAAGAACTGGGA 58.881 34.615 6.97 0.00 0.00 4.37
1686 1816 4.994471 CACAGAGGCAGCACCGCA 62.994 66.667 0.00 0.00 46.52 5.69
1847 1995 6.922957 ACACATACACACCATTCAAATGAAAC 59.077 34.615 4.30 0.00 38.70 2.78
1891 2039 1.613317 TAGCGGGATCACCACCTGTG 61.613 60.000 0.00 0.00 46.88 3.66
1983 2131 1.212935 ACCACTTTCTGTCTTGCCACT 59.787 47.619 0.00 0.00 0.00 4.00
2054 2202 1.030488 TCTCCATGACCGACTCGTCC 61.030 60.000 0.00 0.00 31.35 4.79
2142 2290 5.593183 CTATGCAGCATTCAGATACTGTG 57.407 43.478 14.58 0.00 30.63 3.66
2196 2346 9.678941 CCTTTGTTTCTTTCCTCTAACATAAAC 57.321 33.333 0.00 0.00 31.30 2.01
2260 2410 6.089551 GCTCGCGTACAGACATATAAATGAAT 59.910 38.462 5.77 0.00 36.54 2.57
2450 2600 6.488006 ACTGAGTGCACAAATCTCATAAGTTT 59.512 34.615 21.04 0.00 37.54 2.66
2622 2772 0.250989 TGTTACAAAAGGCCCCTCGG 60.251 55.000 0.00 0.00 0.00 4.63
2655 2805 3.879295 CCATTGCAGATATTCTTCGTGGT 59.121 43.478 0.00 0.00 0.00 4.16
2864 3014 2.851195 ACCACTGGTGCAGAAAAGTAG 58.149 47.619 0.00 0.00 32.98 2.57
2896 3046 1.014044 TTCGGTCACTCAGCAATCGC 61.014 55.000 0.00 0.00 38.99 4.58
2926 3076 7.742556 TTCATCAACAAATACATGAGACACA 57.257 32.000 0.00 0.00 0.00 3.72
2985 3135 8.691661 TCATAAGGGCAAATAATAAGGTCTTC 57.308 34.615 0.00 0.00 0.00 2.87
3304 3454 0.322546 AGGGGAAGAATGCAACGGAC 60.323 55.000 0.00 0.00 0.00 4.79
3308 3458 3.511146 TGAATTCAGGGGAAGAATGCAAC 59.489 43.478 3.38 0.00 37.93 4.17
3424 3574 3.073798 TCTTCCACACTTTATCTTGGCCA 59.926 43.478 0.00 0.00 0.00 5.36
3472 3622 8.352942 ACAAGTGTAGTGATTTGATTTTTCCTC 58.647 33.333 0.00 0.00 0.00 3.71
3487 3637 5.357257 ACAAGTACCTCAACAAGTGTAGTG 58.643 41.667 0.00 0.00 0.00 2.74
3596 3746 5.011023 CCTTGAGCCATAGGTTTCAAAGTTT 59.989 40.000 0.00 0.00 31.78 2.66
3791 3941 3.434940 AACACTCTATTTGGGTCACCC 57.565 47.619 5.63 5.63 45.71 4.61
4355 4513 6.127619 GCTGGTGCTAAAGATTACCAAAGATT 60.128 38.462 0.00 0.00 42.19 2.40
4356 4514 5.358160 GCTGGTGCTAAAGATTACCAAAGAT 59.642 40.000 0.00 0.00 42.19 2.40
4357 4515 4.700213 GCTGGTGCTAAAGATTACCAAAGA 59.300 41.667 0.00 0.00 42.19 2.52
4358 4516 4.986622 GCTGGTGCTAAAGATTACCAAAG 58.013 43.478 0.00 0.00 42.19 2.77
4373 4531 1.403323 GCTATGGAAAGAAGCTGGTGC 59.597 52.381 0.00 0.00 40.05 5.01
4405 4563 9.391006 GTCAACATATAACATACAGAAGGGAAA 57.609 33.333 0.00 0.00 0.00 3.13
4579 4738 6.827586 ATGGGCTAAATTTCGTCAAGTTAA 57.172 33.333 0.00 0.00 0.00 2.01
4609 4768 7.051000 AGAAGATAGGCCTTTTGACTTGATAC 58.949 38.462 12.58 0.00 0.00 2.24
4678 4842 0.593128 ATTGACGTGCTTGTTGAGGC 59.407 50.000 0.00 0.00 0.00 4.70
4710 4874 7.542890 TGCTTTGACTAAAACAACTTCATGAA 58.457 30.769 8.12 8.12 0.00 2.57
4852 5018 3.071457 TGAGTGTGATCATATCGCCCAAT 59.929 43.478 0.00 0.00 38.99 3.16
4890 5057 6.170506 AGCAAAGAACGATGACCTATAAACA 58.829 36.000 0.00 0.00 0.00 2.83
4896 5063 4.794278 TGTAGCAAAGAACGATGACCTA 57.206 40.909 0.00 0.00 0.00 3.08
4898 5065 4.946784 ATTGTAGCAAAGAACGATGACC 57.053 40.909 0.00 0.00 0.00 4.02
4899 5066 6.128553 TGAGAATTGTAGCAAAGAACGATGAC 60.129 38.462 0.00 0.00 0.00 3.06
5052 5219 6.176183 ACATAGTGAATTCAAAGGAGTCCTG 58.824 40.000 13.89 1.64 32.13 3.86
5187 5354 5.718724 AAGGCAAAGAGAGAAAAGGAATG 57.281 39.130 0.00 0.00 0.00 2.67
5193 5360 2.687935 ACGCAAAGGCAAAGAGAGAAAA 59.312 40.909 0.00 0.00 41.24 2.29
5239 5406 4.162131 AGAGCCCAACAAATGTCAAAAGTT 59.838 37.500 0.00 0.00 0.00 2.66
5267 5660 7.214381 ACAATAACGCATAGAGTTATAAGCCA 58.786 34.615 6.58 0.00 42.10 4.75
5284 5677 9.537848 CTTTACTGCCTACTTAAAACAATAACG 57.462 33.333 0.00 0.00 0.00 3.18
5339 5732 6.005066 ACATATTCATCATGTGGTCAGGAA 57.995 37.500 0.00 0.00 37.89 3.36
5341 5734 5.936372 CCTACATATTCATCATGTGGTCAGG 59.064 44.000 0.00 0.00 37.22 3.86
5355 5748 6.460123 CCACTGCATTTTGGACCTACATATTC 60.460 42.308 3.53 0.00 34.46 1.75
5444 5837 7.094634 TGCAGAGTTTGGAAGAAATCAGAATAC 60.095 37.037 0.00 0.00 0.00 1.89
5468 5861 3.373439 TGTTTCAGTGCCAACATTTTTGC 59.627 39.130 4.14 0.00 0.00 3.68
5471 5864 7.215789 TGAATATGTTTCAGTGCCAACATTTT 58.784 30.769 19.66 17.93 40.05 1.82
5753 6146 8.480501 ACTGTACGTATTGGTGGTATTTAGATT 58.519 33.333 0.00 0.00 0.00 2.40
5805 6198 4.379813 CGGAACATAATCAATGCATAGGGC 60.380 45.833 0.00 0.00 39.39 5.19
5806 6199 4.761739 ACGGAACATAATCAATGCATAGGG 59.238 41.667 0.00 0.00 39.39 3.53
5807 6200 5.947228 ACGGAACATAATCAATGCATAGG 57.053 39.130 0.00 0.00 39.39 2.57
5808 6201 6.958255 TGAACGGAACATAATCAATGCATAG 58.042 36.000 0.00 0.00 39.39 2.23
5809 6202 6.934048 TGAACGGAACATAATCAATGCATA 57.066 33.333 0.00 0.00 39.39 3.14
5810 6203 5.833406 TGAACGGAACATAATCAATGCAT 57.167 34.783 0.00 0.00 39.39 3.96
5819 6212 3.372822 GCTTCGGAATGAACGGAACATAA 59.627 43.478 0.00 0.00 31.87 1.90
6128 6522 9.976511 AATGATTGATTATGGCTCAAACTATTG 57.023 29.630 0.00 0.00 36.30 1.90
6179 6573 5.136105 ACAGATGATATCCCAGGAAAAAGC 58.864 41.667 0.00 0.00 0.00 3.51
6247 6641 8.850452 GCTAAAAATTAATTGAACTGTCTTCCG 58.150 33.333 0.39 0.00 0.00 4.30
6440 6840 7.496529 TCACAGAATTCTGAACAAACCTTAG 57.503 36.000 36.15 10.26 46.59 2.18
6466 6866 1.068741 GGGATGGTCTGGTACTTAGCG 59.931 57.143 0.00 0.00 0.00 4.26
6571 6971 1.745087 ACAGCGCCACCAAATAAGATG 59.255 47.619 2.29 0.00 0.00 2.90
6586 6986 2.650608 GCACTTCCTTTTGTAACAGCG 58.349 47.619 0.00 0.00 0.00 5.18
6604 7004 4.081917 TGACAGAATACTCAACATACCGCA 60.082 41.667 0.00 0.00 0.00 5.69
6688 7088 4.207165 TCTTCAAATGCCCAGCCTATTAC 58.793 43.478 0.00 0.00 0.00 1.89
6764 7164 9.950680 TTTATCAAGTTCTTCTTTAAGTTGCAG 57.049 29.630 0.00 0.00 37.24 4.41
6901 7301 8.041919 TGATTTGGTACATAAAGTATCACCGAA 58.958 33.333 0.00 0.00 43.33 4.30
6926 7326 4.521146 ACTAGAAATGGCAGAGGATTGTG 58.479 43.478 0.00 0.00 0.00 3.33
7255 7656 1.142778 GCCTAGCTCTGCTCGTTTCG 61.143 60.000 0.00 0.00 40.44 3.46
7292 7693 6.103997 CATCCTTTATGATGTTGCTTTTGCT 58.896 36.000 0.00 0.00 41.36 3.91
7327 7728 2.039405 GGTCTGCAGCAGGCTCTTG 61.039 63.158 25.98 0.00 45.15 3.02
7585 7986 2.746362 CCTTGGTCTAGAAAGCAGCTTG 59.254 50.000 8.88 0.00 0.00 4.01
7662 8063 2.223971 CGGTGTCAGTTAACTGTCAGGT 60.224 50.000 28.28 0.00 41.30 4.00
7683 8084 5.617751 GCATCCAATACTGTCAACAGACAAC 60.618 44.000 16.71 0.00 46.59 3.32
7752 8154 1.106285 AGCAAGGCGGATGAAATTCC 58.894 50.000 0.00 0.00 0.00 3.01
7755 8158 1.670811 CGTTAGCAAGGCGGATGAAAT 59.329 47.619 0.00 0.00 0.00 2.17
7761 8164 1.080093 CTGTCGTTAGCAAGGCGGA 60.080 57.895 0.00 0.00 0.00 5.54
7765 8168 0.242825 TCGTCCTGTCGTTAGCAAGG 59.757 55.000 0.00 0.00 0.00 3.61
7769 8172 0.454600 TCCATCGTCCTGTCGTTAGC 59.545 55.000 0.00 0.00 0.00 3.09
7772 8175 1.182667 TCATCCATCGTCCTGTCGTT 58.817 50.000 0.00 0.00 0.00 3.85
7808 8211 2.159382 ACCAAATACAACCAGAAGGCG 58.841 47.619 0.00 0.00 39.06 5.52
7821 8224 4.032960 ACACATGGCTCAGAACCAAATA 57.967 40.909 0.00 0.00 41.49 1.40
7862 8265 4.707934 TCAATTCGCCCCGATGATATACTA 59.292 41.667 0.00 0.00 35.23 1.82
7863 8266 3.513912 TCAATTCGCCCCGATGATATACT 59.486 43.478 0.00 0.00 35.23 2.12
7864 8267 3.857052 TCAATTCGCCCCGATGATATAC 58.143 45.455 0.00 0.00 35.23 1.47
7865 8268 4.545208 TTCAATTCGCCCCGATGATATA 57.455 40.909 0.00 0.00 35.23 0.86
7866 8269 3.417069 TTCAATTCGCCCCGATGATAT 57.583 42.857 0.00 0.00 35.23 1.63
7936 8340 8.068892 TCAGTGGTGTTGTATACATACATACA 57.931 34.615 22.15 19.14 42.32 2.29
7941 8350 6.036083 CAGCTTCAGTGGTGTTGTATACATAC 59.964 42.308 6.36 9.04 39.39 2.39
8020 8435 1.079127 CAGGTAAGTGCCACGAGGG 60.079 63.158 0.00 0.00 40.85 4.30
8026 8441 0.847373 TCCCAAACAGGTAAGTGCCA 59.153 50.000 0.00 0.00 34.66 4.92
8616 9143 0.389025 GTTGTGGTTTGCTTCCCTGG 59.611 55.000 0.00 0.00 0.00 4.45
8759 9287 0.541392 CCGACTCAACATCCCCATCA 59.459 55.000 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.