Multiple sequence alignment - TraesCS4A01G352400

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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 TraesCS4A01G352400 chr4A 100.000 3995 0 0 1 3995 627824406 627820412 0.000000e+00 7378.0
1 TraesCS4A01G352400 chr4A 88.000 575 54 5 947 1516 627917822 627917258 0.000000e+00 665.0
2 TraesCS4A01G352400 chr4A 86.095 525 57 8 2135 2644 627905920 627905397 5.840000e-153 551.0
3 TraesCS4A01G352400 chr4A 77.086 899 115 34 2756 3623 627905361 627904523 6.130000e-118 435.0
4 TraesCS4A01G352400 chr4A 86.473 207 25 3 3696 3899 614577027 614577233 1.440000e-54 224.0
5 TraesCS4A01G352400 chr4A 83.243 185 29 2 2738 2921 602893186 602893003 6.870000e-38 169.0
6 TraesCS4A01G352400 chr4A 87.324 142 16 2 3716 3857 627904271 627904132 1.150000e-35 161.0
7 TraesCS4A01G352400 chr4A 83.908 174 14 9 247 419 627918794 627918634 1.920000e-33 154.0
8 TraesCS4A01G352400 chr4A 79.310 203 33 8 3141 3339 614576550 614576747 2.500000e-27 134.0
9 TraesCS4A01G352400 chr4A 88.406 69 8 0 38 106 627919014 627918946 2.560000e-12 84.2
10 TraesCS4A01G352400 chr4A 97.368 38 1 0 192 229 540532627 540532664 9.270000e-07 65.8
11 TraesCS4A01G352400 chr4A 87.273 55 6 1 803 857 627918410 627918357 1.200000e-05 62.1
12 TraesCS4A01G352400 chr5D 84.232 2949 346 62 648 3517 539977629 539974721 0.000000e+00 2760.0
13 TraesCS4A01G352400 chr5D 82.028 1213 160 32 1746 2914 539983955 539982757 0.000000e+00 979.0
14 TraesCS4A01G352400 chr5D 88.184 804 83 8 892 1684 539984789 539983987 0.000000e+00 948.0
15 TraesCS4A01G352400 chr5D 94.764 191 10 0 3805 3995 539981803 539981613 8.390000e-77 298.0
16 TraesCS4A01G352400 chr5D 94.241 191 11 0 3805 3995 539974117 539973927 3.910000e-75 292.0
17 TraesCS4A01G352400 chr5D 93.478 184 12 0 1 184 539978815 539978632 1.410000e-69 274.0
18 TraesCS4A01G352400 chr5D 92.105 114 9 0 3710 3823 539981964 539981851 1.150000e-35 161.0
19 TraesCS4A01G352400 chr5D 83.529 170 25 2 3389 3555 539982345 539982176 5.350000e-34 156.0
20 TraesCS4A01G352400 chr5D 86.957 115 14 1 19 133 539991223 539991110 1.170000e-25 128.0
21 TraesCS4A01G352400 chr5D 96.078 51 1 1 243 292 539978638 539978588 9.200000e-12 82.4
22 TraesCS4A01G352400 chr5D 90.566 53 2 1 367 419 539978563 539978514 2.580000e-07 67.6
23 TraesCS4A01G352400 chr5B 85.305 2232 264 45 765 2940 682187057 682184834 0.000000e+00 2246.0
24 TraesCS4A01G352400 chr5B 82.601 2368 323 48 814 3133 682954929 682952603 0.000000e+00 2008.0
25 TraesCS4A01G352400 chr5B 83.690 2054 282 33 887 2914 682196921 682194895 0.000000e+00 1888.0
26 TraesCS4A01G352400 chr5B 83.932 529 56 11 3469 3995 682184346 682183845 2.790000e-131 479.0
27 TraesCS4A01G352400 chr5B 80.962 499 77 14 3503 3990 682952292 682951801 2.910000e-101 379.0
28 TraesCS4A01G352400 chr5B 78.571 490 65 14 3144 3631 682194685 682194234 1.820000e-73 287.0
29 TraesCS4A01G352400 chr5B 76.894 528 62 30 3146 3671 682184612 682184143 1.110000e-60 244.0
30 TraesCS4A01G352400 chr5B 87.629 194 20 2 3710 3899 696703845 696704038 5.200000e-54 222.0
31 TraesCS4A01G352400 chr5B 84.659 176 8 10 249 413 682187378 682187211 1.490000e-34 158.0
32 TraesCS4A01G352400 chr3B 81.343 268 47 2 1240 1504 2991948 2991681 8.700000e-52 215.0
33 TraesCS4A01G352400 chr4B 84.211 171 25 2 2737 2906 3637730 3637899 8.880000e-37 165.0
34 TraesCS4A01G352400 chr4B 84.211 171 25 2 2737 2906 3638420 3638589 8.880000e-37 165.0
35 TraesCS4A01G352400 chr7A 82.653 98 13 4 603 698 642187935 642188030 2.560000e-12 84.2
36 TraesCS4A01G352400 chr6A 87.671 73 8 1 630 701 455995540 455995468 2.560000e-12 84.2
37 TraesCS4A01G352400 chr7D 82.653 98 12 5 603 698 556468912 556469006 9.200000e-12 82.4
38 TraesCS4A01G352400 chr1A 82.418 91 15 1 611 701 9697485 9697396 1.190000e-10 78.7
39 TraesCS4A01G352400 chr1B 100.000 37 0 0 193 229 48992279 48992315 7.160000e-08 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 TraesCS4A01G352400 chr4A 627820412 627824406 3994 True 7378.000000 7378 100.000000 1 3995 1 chr4A.!!$R2 3994
1 TraesCS4A01G352400 chr4A 627904132 627905920 1788 True 382.333333 551 83.501667 2135 3857 3 chr4A.!!$R3 1722
2 TraesCS4A01G352400 chr4A 627917258 627919014 1756 True 241.325000 665 86.896750 38 1516 4 chr4A.!!$R4 1478
3 TraesCS4A01G352400 chr5D 539973927 539984789 10862 True 601.800000 2760 89.920500 1 3995 10 chr5D.!!$R2 3994
4 TraesCS4A01G352400 chr5B 682951801 682954929 3128 True 1193.500000 2008 81.781500 814 3990 2 chr5B.!!$R3 3176
5 TraesCS4A01G352400 chr5B 682194234 682196921 2687 True 1087.500000 1888 81.130500 887 3631 2 chr5B.!!$R2 2744
6 TraesCS4A01G352400 chr5B 682183845 682187378 3533 True 781.750000 2246 82.697500 249 3995 4 chr5B.!!$R1 3746

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
173 6232 0.179124 GCCTCAAGCTACGTCCTGAG 60.179 60.0 0.00 4.19 38.99 3.35 F
1416 8818 0.036875 CCGGCCAGAAGAAACTCCTT 59.963 55.0 2.24 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 9136 0.094730 GTAGTTCATTGCACGGCGTC 59.905 55.0 10.85 6.01 0.0 5.19 R
3127 10609 0.039074 ACTCAACTCGCGGTCTCTTG 60.039 55.0 6.13 1.05 0.0 3.02 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
90 6065 2.039480 AGAGGCATCTGAGCTTTGTTCA 59.961 45.455 0.00 0.00 33.30 3.18
92 6067 2.555757 AGGCATCTGAGCTTTGTTCAAC 59.444 45.455 0.00 0.00 34.17 3.18
133 6108 2.034066 ACAAGCCGTGGATGTGGG 59.966 61.111 0.00 0.00 0.00 4.61
168 6227 1.797025 AGTTTGCCTCAAGCTACGTC 58.203 50.000 0.00 0.00 44.23 4.34
170 6229 0.685097 TTTGCCTCAAGCTACGTCCT 59.315 50.000 0.00 0.00 44.23 3.85
173 6232 0.179124 GCCTCAAGCTACGTCCTGAG 60.179 60.000 0.00 4.19 38.99 3.35
184 6243 3.103447 ACGTCCTGAGATGTATGCATG 57.897 47.619 10.16 0.00 40.57 4.06
185 6244 2.432146 ACGTCCTGAGATGTATGCATGT 59.568 45.455 10.16 0.00 40.57 3.21
186 6245 3.118629 ACGTCCTGAGATGTATGCATGTT 60.119 43.478 10.16 0.00 40.57 2.71
187 6246 3.873361 CGTCCTGAGATGTATGCATGTTT 59.127 43.478 10.16 0.00 35.07 2.83
188 6247 4.333649 CGTCCTGAGATGTATGCATGTTTT 59.666 41.667 10.16 0.00 35.07 2.43
189 6248 5.163723 CGTCCTGAGATGTATGCATGTTTTT 60.164 40.000 10.16 0.00 35.07 1.94
217 6276 4.586306 TTTGAAAAGGAGGATAGACCCC 57.414 45.455 0.00 0.00 40.05 4.95
218 6277 2.488836 TGAAAAGGAGGATAGACCCCC 58.511 52.381 0.00 0.00 40.05 5.40
219 6278 1.416772 GAAAAGGAGGATAGACCCCCG 59.583 57.143 0.00 0.00 40.05 5.73
220 6279 0.400093 AAAGGAGGATAGACCCCCGG 60.400 60.000 0.00 0.00 40.05 5.73
221 6280 2.923568 GGAGGATAGACCCCCGGC 60.924 72.222 0.00 0.00 40.05 6.13
222 6281 2.923568 GAGGATAGACCCCCGGCC 60.924 72.222 0.00 0.00 40.05 6.13
223 6282 3.449126 AGGATAGACCCCCGGCCT 61.449 66.667 0.00 0.00 40.05 5.19
224 6283 2.923568 GGATAGACCCCCGGCCTC 60.924 72.222 0.00 0.00 0.00 4.70
225 6284 2.201771 GATAGACCCCCGGCCTCT 59.798 66.667 0.00 0.00 0.00 3.69
226 6285 1.463824 GATAGACCCCCGGCCTCTA 59.536 63.158 0.00 0.38 0.00 2.43
227 6286 0.899253 GATAGACCCCCGGCCTCTAC 60.899 65.000 0.00 0.00 0.00 2.59
228 6287 1.661990 ATAGACCCCCGGCCTCTACA 61.662 60.000 0.00 0.00 0.00 2.74
229 6288 2.578586 TAGACCCCCGGCCTCTACAC 62.579 65.000 0.00 0.00 0.00 2.90
235 6294 2.509336 CGGCCTCTACACCGCAAG 60.509 66.667 0.00 0.00 43.44 4.01
236 6295 2.820037 GGCCTCTACACCGCAAGC 60.820 66.667 0.00 0.00 0.00 4.01
237 6296 2.047274 GCCTCTACACCGCAAGCA 60.047 61.111 0.00 0.00 0.00 3.91
238 6297 2.391389 GCCTCTACACCGCAAGCAC 61.391 63.158 0.00 0.00 0.00 4.40
239 6298 1.005037 CCTCTACACCGCAAGCACA 60.005 57.895 0.00 0.00 0.00 4.57
240 6299 0.391661 CCTCTACACCGCAAGCACAT 60.392 55.000 0.00 0.00 0.00 3.21
241 6300 1.442769 CTCTACACCGCAAGCACATT 58.557 50.000 0.00 0.00 0.00 2.71
242 6301 1.806542 CTCTACACCGCAAGCACATTT 59.193 47.619 0.00 0.00 0.00 2.32
243 6302 3.000041 CTCTACACCGCAAGCACATTTA 59.000 45.455 0.00 0.00 0.00 1.40
244 6303 3.605634 TCTACACCGCAAGCACATTTAT 58.394 40.909 0.00 0.00 0.00 1.40
245 6304 2.634982 ACACCGCAAGCACATTTATG 57.365 45.000 0.00 0.00 0.00 1.90
292 6351 3.628032 TCTGATTCTGAGCTACTACACCG 59.372 47.826 0.00 0.00 0.00 4.94
293 6352 2.099263 TGATTCTGAGCTACTACACCGC 59.901 50.000 0.00 0.00 0.00 5.68
294 6353 1.541379 TTCTGAGCTACTACACCGCA 58.459 50.000 0.00 0.00 0.00 5.69
295 6354 1.541379 TCTGAGCTACTACACCGCAA 58.459 50.000 0.00 0.00 0.00 4.85
349 6408 3.258123 TCCAAAACAAAGCAAGGGATAGC 59.742 43.478 0.00 0.00 0.00 2.97
360 6435 3.448660 GCAAGGGATAGCAACCAGAAAAT 59.551 43.478 0.00 0.00 0.00 1.82
361 6436 4.678840 GCAAGGGATAGCAACCAGAAAATG 60.679 45.833 0.00 0.00 0.00 2.32
362 6437 4.591321 AGGGATAGCAACCAGAAAATGA 57.409 40.909 0.00 0.00 0.00 2.57
363 6438 4.934356 AGGGATAGCAACCAGAAAATGAA 58.066 39.130 0.00 0.00 0.00 2.57
364 6439 5.332743 AGGGATAGCAACCAGAAAATGAAA 58.667 37.500 0.00 0.00 0.00 2.69
365 6440 5.960202 AGGGATAGCAACCAGAAAATGAAAT 59.040 36.000 0.00 0.00 0.00 2.17
366 6441 6.044682 GGGATAGCAACCAGAAAATGAAATG 58.955 40.000 0.00 0.00 0.00 2.32
367 6442 6.127366 GGGATAGCAACCAGAAAATGAAATGA 60.127 38.462 0.00 0.00 0.00 2.57
368 6443 7.322664 GGATAGCAACCAGAAAATGAAATGAA 58.677 34.615 0.00 0.00 0.00 2.57
418 6625 0.613260 ATGCTCACACGTGGGTATGT 59.387 50.000 19.06 0.00 35.04 2.29
445 6652 2.124695 CCTACCGGCCCTTTGAGC 60.125 66.667 0.00 0.00 0.00 4.26
467 6674 0.328258 ATGTGTGCACCCTTACCCTC 59.672 55.000 15.69 0.00 0.00 4.30
475 6682 1.137086 CACCCTTACCCTCAGATCACG 59.863 57.143 0.00 0.00 0.00 4.35
481 6688 2.415010 CCTCAGATCACGGCGAGG 59.585 66.667 16.62 3.54 39.20 4.63
535 6742 5.825151 GGCTAAGGTGAAGAAGCAGAATATT 59.175 40.000 0.00 0.00 36.68 1.28
536 6743 6.319911 GGCTAAGGTGAAGAAGCAGAATATTT 59.680 38.462 0.00 0.00 36.68 1.40
544 6751 7.533222 GTGAAGAAGCAGAATATTTATGCATCG 59.467 37.037 21.66 0.00 41.27 3.84
552 6759 7.535258 GCAGAATATTTATGCATCGTTTCGATT 59.465 33.333 17.20 0.00 44.59 3.34
553 6760 8.834212 CAGAATATTTATGCATCGTTTCGATTG 58.166 33.333 0.19 0.82 44.59 2.67
555 6762 8.939586 AATATTTATGCATCGTTTCGATTGAG 57.060 30.769 0.19 0.00 44.59 3.02
557 6764 5.641777 TTATGCATCGTTTCGATTGAGAG 57.358 39.130 0.19 0.00 44.59 3.20
559 6766 3.182182 TGCATCGTTTCGATTGAGAGAG 58.818 45.455 1.82 0.00 44.59 3.20
560 6767 2.034170 GCATCGTTTCGATTGAGAGAGC 60.034 50.000 1.82 0.00 44.59 4.09
561 6768 3.182182 CATCGTTTCGATTGAGAGAGCA 58.818 45.455 1.82 0.00 44.59 4.26
562 6769 2.596452 TCGTTTCGATTGAGAGAGCAC 58.404 47.619 0.00 0.00 0.00 4.40
564 6771 2.329379 GTTTCGATTGAGAGAGCACGT 58.671 47.619 0.00 0.00 0.00 4.49
567 6774 2.081462 TCGATTGAGAGAGCACGTGTA 58.919 47.619 18.38 0.00 0.00 2.90
570 6777 3.859961 CGATTGAGAGAGCACGTGTAATT 59.140 43.478 18.38 0.28 0.00 1.40
571 6778 4.327357 CGATTGAGAGAGCACGTGTAATTT 59.673 41.667 18.38 0.29 0.00 1.82
572 6779 5.163953 CGATTGAGAGAGCACGTGTAATTTT 60.164 40.000 18.38 0.00 0.00 1.82
573 6780 6.034577 CGATTGAGAGAGCACGTGTAATTTTA 59.965 38.462 18.38 0.00 0.00 1.52
574 6781 6.462073 TTGAGAGAGCACGTGTAATTTTAC 57.538 37.500 18.38 0.00 0.00 2.01
575 6782 5.779922 TGAGAGAGCACGTGTAATTTTACT 58.220 37.500 18.38 2.28 34.77 2.24
577 6784 5.169295 AGAGAGCACGTGTAATTTTACTCC 58.831 41.667 18.38 6.66 34.77 3.85
578 6785 4.251268 AGAGCACGTGTAATTTTACTCCC 58.749 43.478 18.38 0.00 34.77 4.30
581 6788 4.020485 AGCACGTGTAATTTTACTCCCTCT 60.020 41.667 18.38 0.00 34.77 3.69
582 6789 4.092968 GCACGTGTAATTTTACTCCCTCTG 59.907 45.833 18.38 0.00 34.77 3.35
583 6790 5.235516 CACGTGTAATTTTACTCCCTCTGT 58.764 41.667 7.58 0.00 34.77 3.41
584 6791 5.699458 CACGTGTAATTTTACTCCCTCTGTT 59.301 40.000 7.58 0.00 34.77 3.16
585 6792 6.204108 CACGTGTAATTTTACTCCCTCTGTTT 59.796 38.462 7.58 0.00 34.77 2.83
586 6793 6.769341 ACGTGTAATTTTACTCCCTCTGTTTT 59.231 34.615 0.00 0.00 34.77 2.43
587 6794 7.283807 ACGTGTAATTTTACTCCCTCTGTTTTT 59.716 33.333 0.00 0.00 34.77 1.94
609 6816 2.247311 CAACTTCGCATAGTTGTGCC 57.753 50.000 16.05 0.00 46.27 5.01
611 6818 2.185004 ACTTCGCATAGTTGTGCCTT 57.815 45.000 0.00 0.00 42.06 4.35
612 6819 3.328382 ACTTCGCATAGTTGTGCCTTA 57.672 42.857 0.00 0.00 42.06 2.69
614 6821 3.684788 ACTTCGCATAGTTGTGCCTTAAG 59.315 43.478 0.00 0.00 42.06 1.85
615 6822 3.328382 TCGCATAGTTGTGCCTTAAGT 57.672 42.857 0.97 0.00 42.06 2.24
616 6823 3.259064 TCGCATAGTTGTGCCTTAAGTC 58.741 45.455 0.97 0.00 42.06 3.01
617 6824 3.000041 CGCATAGTTGTGCCTTAAGTCA 59.000 45.455 0.97 0.00 42.06 3.41
618 6825 3.435327 CGCATAGTTGTGCCTTAAGTCAA 59.565 43.478 0.97 1.82 42.06 3.18
619 6826 4.083537 CGCATAGTTGTGCCTTAAGTCAAA 60.084 41.667 0.97 0.00 42.06 2.69
620 6827 5.391950 CGCATAGTTGTGCCTTAAGTCAAAT 60.392 40.000 0.97 6.19 42.06 2.32
622 6829 6.868339 GCATAGTTGTGCCTTAAGTCAAATTT 59.132 34.615 0.97 0.00 39.18 1.82
623 6830 7.384932 GCATAGTTGTGCCTTAAGTCAAATTTT 59.615 33.333 0.97 0.00 39.18 1.82
624 6831 8.915654 CATAGTTGTGCCTTAAGTCAAATTTTC 58.084 33.333 0.97 0.00 0.00 2.29
625 6832 7.112452 AGTTGTGCCTTAAGTCAAATTTTCT 57.888 32.000 0.97 0.00 0.00 2.52
626 6833 6.980397 AGTTGTGCCTTAAGTCAAATTTTCTG 59.020 34.615 0.97 0.00 0.00 3.02
627 6834 5.841810 TGTGCCTTAAGTCAAATTTTCTGG 58.158 37.500 0.97 0.00 0.00 3.86
628 6835 5.596361 TGTGCCTTAAGTCAAATTTTCTGGA 59.404 36.000 0.97 0.00 0.00 3.86
629 6836 6.152379 GTGCCTTAAGTCAAATTTTCTGGAG 58.848 40.000 0.97 0.00 0.00 3.86
630 6837 5.833131 TGCCTTAAGTCAAATTTTCTGGAGT 59.167 36.000 0.97 0.00 0.00 3.85
631 6838 6.323739 TGCCTTAAGTCAAATTTTCTGGAGTT 59.676 34.615 0.97 0.00 0.00 3.01
632 6839 7.147742 TGCCTTAAGTCAAATTTTCTGGAGTTT 60.148 33.333 0.97 0.00 0.00 2.66
638 6845 6.537453 TCAAATTTTCTGGAGTTTGACCAA 57.463 33.333 0.00 0.00 36.11 3.67
639 6846 6.940739 TCAAATTTTCTGGAGTTTGACCAAA 58.059 32.000 0.00 0.00 36.11 3.28
640 6847 7.563906 TCAAATTTTCTGGAGTTTGACCAAAT 58.436 30.769 0.00 0.00 36.11 2.32
641 6848 8.046107 TCAAATTTTCTGGAGTTTGACCAAATT 58.954 29.630 0.00 0.00 36.11 1.82
642 6849 8.676401 CAAATTTTCTGGAGTTTGACCAAATTT 58.324 29.630 0.00 0.00 36.57 1.82
643 6850 9.898152 AAATTTTCTGGAGTTTGACCAAATTTA 57.102 25.926 0.00 0.00 35.47 1.40
734 7621 2.813908 GCGACCGAAAGTGGCGAT 60.814 61.111 0.00 0.00 40.58 4.58
809 7711 7.961325 TTTAGCTTTGATGTTTCATTTTCCC 57.039 32.000 0.00 0.00 0.00 3.97
882 8177 1.604593 ATCACAAGGCAGCACCACC 60.605 57.895 0.00 0.00 43.14 4.61
907 8215 6.813649 CCTTTCATGTATGTATAGGGTCATCG 59.186 42.308 0.00 0.00 0.00 3.84
1102 8495 5.832221 TCTTCCTCTACTTCTCTGATTGGA 58.168 41.667 0.00 0.00 0.00 3.53
1284 8677 0.335019 TCCTCCTCATTCACCTCGGA 59.665 55.000 0.00 0.00 0.00 4.55
1291 8684 1.306141 ATTCACCTCGGAGGCCAGA 60.306 57.895 23.84 15.88 39.63 3.86
1326 8728 0.107945 GCCTCGAGGACAATGAGCTT 60.108 55.000 35.69 0.00 37.39 3.74
1340 8742 2.964978 GCTTTGGAAGCGGCATGT 59.035 55.556 1.45 0.00 45.74 3.21
1356 8758 3.599343 GCATGTCATAACTCTGGTGTCA 58.401 45.455 0.00 0.00 0.00 3.58
1410 8812 3.569849 TGGTCCGGCCAGAAGAAA 58.430 55.556 12.86 0.00 43.61 2.52
1416 8818 0.036875 CCGGCCAGAAGAAACTCCTT 59.963 55.000 2.24 0.00 0.00 3.36
1460 8862 1.197721 CGTTGGCATCCTCAAGTTCAC 59.802 52.381 0.00 0.00 0.00 3.18
1526 8928 1.112916 TCCAGAAGTCTGTCCGTGCA 61.113 55.000 7.51 0.00 42.27 4.57
1541 8943 4.454504 GTCCGTGCAAAGAGAAAAAGGATA 59.545 41.667 0.00 0.00 0.00 2.59
1570 8972 1.250328 ATGTTGGACATGGTGCACTG 58.750 50.000 17.98 10.79 37.45 3.66
1579 8981 0.241749 ATGGTGCACTGTGAATTGCG 59.758 50.000 17.98 0.00 41.96 4.85
1595 8997 0.539438 TGCGGGGATTTTGCTTCAGT 60.539 50.000 0.00 0.00 0.00 3.41
1596 8998 0.109132 GCGGGGATTTTGCTTCAGTG 60.109 55.000 0.00 0.00 0.00 3.66
1597 8999 0.527565 CGGGGATTTTGCTTCAGTGG 59.472 55.000 0.00 0.00 0.00 4.00
1598 9000 0.897621 GGGGATTTTGCTTCAGTGGG 59.102 55.000 0.00 0.00 0.00 4.61
1601 9003 0.109132 GATTTTGCTTCAGTGGGGCG 60.109 55.000 0.00 0.00 0.00 6.13
1621 9024 1.645710 GGAAGGAGAGGAAGGACACA 58.354 55.000 0.00 0.00 0.00 3.72
1629 9032 1.880027 GAGGAAGGACACAAACGCAAT 59.120 47.619 0.00 0.00 0.00 3.56
1649 9052 6.195983 CGCAATCTTTCACTTGAAGAATATGC 59.804 38.462 0.00 10.18 35.21 3.14
1684 9093 2.689646 AGCTTGTAAAAGAGACGGAGC 58.310 47.619 0.00 0.00 0.00 4.70
1686 9095 2.413453 GCTTGTAAAAGAGACGGAGCTG 59.587 50.000 0.00 0.00 0.00 4.24
1694 9103 4.803426 GACGGAGCTGGCGAGTGG 62.803 72.222 0.00 0.00 0.00 4.00
1697 9106 2.347490 GGAGCTGGCGAGTGGAAA 59.653 61.111 0.00 0.00 0.00 3.13
1713 9122 3.068024 GTGGAAATGACCAAAGAACAGCA 59.932 43.478 0.00 0.00 41.87 4.41
1714 9123 3.896888 TGGAAATGACCAAAGAACAGCAT 59.103 39.130 0.00 0.00 36.96 3.79
1717 9126 6.127647 TGGAAATGACCAAAGAACAGCATATC 60.128 38.462 0.00 0.00 36.96 1.63
1727 9136 7.148918 CCAAAGAACAGCATATCAAAAGTTTCG 60.149 37.037 0.00 0.00 0.00 3.46
1767 9180 4.554960 CATCTCTATGATGCTGGTGGAT 57.445 45.455 0.00 0.00 44.96 3.41
1858 9271 6.127591 TGGACACAAAATTTTACGGATATGGG 60.128 38.462 2.44 0.00 0.00 4.00
1859 9272 5.656480 ACACAAAATTTTACGGATATGGGC 58.344 37.500 2.44 0.00 0.00 5.36
1864 9277 4.569719 ATTTTACGGATATGGGCTAGGG 57.430 45.455 0.00 0.00 0.00 3.53
1879 9292 2.840651 GCTAGGGATACATATGGTGCCT 59.159 50.000 21.29 21.29 39.74 4.75
1907 9320 5.163622 ACACCAAAACAAGATCACTCAACAG 60.164 40.000 0.00 0.00 0.00 3.16
1912 9325 5.490139 AACAAGATCACTCAACAGTTGTG 57.510 39.130 13.14 12.97 0.00 3.33
1932 9345 1.200948 GTTGGCTTCTGCTCATGGTTC 59.799 52.381 0.00 0.00 39.59 3.62
1941 9354 0.449388 GCTCATGGTTCTTGCTTCCG 59.551 55.000 0.00 0.00 0.00 4.30
1973 9386 1.674057 CTTCCCTGGTGCTCTTCGT 59.326 57.895 0.00 0.00 0.00 3.85
1999 9412 8.598916 TCAAGAGTAACAAGGATGGTTACAATA 58.401 33.333 15.33 0.00 36.38 1.90
2004 9417 9.227777 AGTAACAAGGATGGTTACAATAAGAAC 57.772 33.333 15.33 0.00 36.38 3.01
2008 9421 5.107133 AGGATGGTTACAATAAGAACGACG 58.893 41.667 0.00 0.00 0.00 5.12
2010 9423 5.220340 GGATGGTTACAATAAGAACGACGTG 60.220 44.000 0.00 0.00 0.00 4.49
2031 9444 7.952671 ACGTGATAGTATCATACATCCTGTTT 58.047 34.615 15.77 0.00 42.04 2.83
2033 9446 7.148738 CGTGATAGTATCATACATCCTGTTTGC 60.149 40.741 15.77 0.00 42.04 3.68
2058 9471 5.224135 TGCACAGTCATGATTCAATTGTTG 58.776 37.500 5.13 0.00 0.00 3.33
2065 9478 5.121142 GTCATGATTCAATTGTTGCCCTTTG 59.879 40.000 5.13 0.00 0.00 2.77
2071 9484 1.412079 ATTGTTGCCCTTTGTGCTCA 58.588 45.000 0.00 0.00 0.00 4.26
2075 9488 2.282745 GCCCTTTGTGCTCAGGCT 60.283 61.111 9.57 0.00 40.57 4.58
2076 9489 2.338785 GCCCTTTGTGCTCAGGCTC 61.339 63.158 9.57 0.00 40.57 4.70
2077 9490 2.037136 CCCTTTGTGCTCAGGCTCG 61.037 63.158 0.00 0.00 39.59 5.03
2079 9492 1.004560 CTTTGTGCTCAGGCTCGGA 60.005 57.895 0.00 0.00 39.59 4.55
2081 9494 0.603707 TTTGTGCTCAGGCTCGGAAG 60.604 55.000 0.00 0.00 39.59 3.46
2099 9527 0.961753 AGCAAAACTGCTACTTGGCC 59.038 50.000 0.00 0.00 44.28 5.36
2188 9616 2.338381 CTTGCTGCCTTCAAGTGCT 58.662 52.632 0.00 0.00 36.93 4.40
2201 9629 2.037251 TCAAGTGCTTCAGGGAGTACAC 59.963 50.000 0.00 0.00 35.08 2.90
2264 9692 1.064060 GATTGAAGGGTTGATTCGCCG 59.936 52.381 0.00 0.00 0.00 6.46
2288 9722 3.968265 ACATAAAAGATGGGTGGGAGTG 58.032 45.455 0.00 0.00 0.00 3.51
2299 9739 2.224606 GGTGGGAGTGCATACATGATG 58.775 52.381 0.00 0.00 38.73 3.07
2322 9762 4.437930 GCTGCCACATACAGAAGATTCAAC 60.438 45.833 0.00 0.00 37.32 3.18
2341 9781 1.352352 ACAATCTCAGGGGACAACAGG 59.648 52.381 0.00 0.00 0.00 4.00
2351 9791 0.033504 GGACAACAGGCTCTGTCGAA 59.966 55.000 16.22 0.00 44.62 3.71
2376 9816 1.517242 CTCAGCTGGGACAACAACTC 58.483 55.000 8.28 0.00 38.70 3.01
2454 9894 0.910088 ACCTCTGCTTCTACCACCCC 60.910 60.000 0.00 0.00 0.00 4.95
2474 9926 1.352352 CAACACATCCTCCCAAGGTCT 59.648 52.381 0.00 0.00 43.82 3.85
2576 10028 2.009042 GCCAGGGACGAGACAAGATTG 61.009 57.143 0.00 0.00 0.00 2.67
2593 10045 1.180907 TTGGTTCACAGTTGCTTGCA 58.819 45.000 0.00 0.00 0.00 4.08
2688 10146 5.940470 ACATGGTGAACTTAAAGGAGATGTC 59.060 40.000 0.00 0.00 0.00 3.06
2802 10260 3.118629 TGCTCTGTTATTCTGCCAGTAGG 60.119 47.826 0.00 0.00 38.23 3.18
2838 10296 1.578215 ATGCCAAGAGCCTGGGTGAT 61.578 55.000 1.59 0.00 42.71 3.06
2853 10311 2.367202 TGATGGCGGGGAGTTCCTC 61.367 63.158 0.00 0.00 35.95 3.71
2959 10417 6.593382 AGAAGAGATCTGCATAACAAGTCAAC 59.407 38.462 0.00 0.00 36.88 3.18
2969 10427 6.265196 TGCATAACAAGTCAACCTCTTGAAAT 59.735 34.615 11.72 3.28 43.17 2.17
3026 10488 3.058224 GGTCAGTGTGTGCTGGTAATTTC 60.058 47.826 0.00 0.00 37.12 2.17
3041 10519 2.977772 ATTTCCAGCTCTCCTCTTCG 57.022 50.000 0.00 0.00 0.00 3.79
3042 10520 0.898320 TTTCCAGCTCTCCTCTTCGG 59.102 55.000 0.00 0.00 0.00 4.30
3052 10530 2.328099 CCTCTTCGGGTTGTGCTGC 61.328 63.158 0.00 0.00 0.00 5.25
3095 10575 2.849880 TTTTGAGTTGAGTGTGCTGC 57.150 45.000 0.00 0.00 0.00 5.25
3127 10609 3.253230 ACTTGTGTGCTTTGCTTTCAAC 58.747 40.909 0.00 0.00 30.75 3.18
3134 10616 3.793492 GTGCTTTGCTTTCAACAAGAGAC 59.207 43.478 0.00 0.00 30.75 3.36
3142 10651 0.387929 TCAACAAGAGACCGCGAGTT 59.612 50.000 8.23 0.00 0.00 3.01
3179 10690 2.360350 AGCATGTTCGCACTGGGG 60.360 61.111 0.00 0.00 0.00 4.96
3180 10691 2.359850 GCATGTTCGCACTGGGGA 60.360 61.111 0.00 0.00 0.00 4.81
3191 10704 2.116238 GCACTGGGGAATGTCCTAGTA 58.884 52.381 3.81 0.00 45.14 1.82
3192 10705 2.504175 GCACTGGGGAATGTCCTAGTAA 59.496 50.000 3.81 0.00 45.14 2.24
3201 10714 1.191535 TGTCCTAGTAATGCAGCCGT 58.808 50.000 0.00 0.00 0.00 5.68
3202 10715 1.553248 TGTCCTAGTAATGCAGCCGTT 59.447 47.619 0.00 0.00 0.00 4.44
3203 10716 2.202566 GTCCTAGTAATGCAGCCGTTC 58.797 52.381 0.00 0.00 0.00 3.95
3235 10748 0.107456 ATTCTAGCTGTGGGATGGCG 59.893 55.000 0.00 0.00 0.00 5.69
3283 10796 1.221414 GAGCGGATTGTCATAGCACC 58.779 55.000 0.00 0.00 0.00 5.01
3284 10797 0.179045 AGCGGATTGTCATAGCACCC 60.179 55.000 0.00 0.00 0.00 4.61
3285 10798 0.463654 GCGGATTGTCATAGCACCCA 60.464 55.000 0.00 0.00 0.00 4.51
3286 10799 1.815408 GCGGATTGTCATAGCACCCAT 60.815 52.381 0.00 0.00 0.00 4.00
3287 10800 1.875514 CGGATTGTCATAGCACCCATG 59.124 52.381 0.00 0.00 0.00 3.66
3288 10801 2.485302 CGGATTGTCATAGCACCCATGA 60.485 50.000 0.00 0.00 0.00 3.07
3289 10802 3.144506 GGATTGTCATAGCACCCATGAG 58.855 50.000 0.00 0.00 33.18 2.90
3290 10803 2.715749 TTGTCATAGCACCCATGAGG 57.284 50.000 0.00 0.00 43.78 3.86
3348 10888 0.109132 GCTATTTGTGTGCCCTGTGC 60.109 55.000 0.00 0.00 41.77 4.57
3349 10889 1.538047 CTATTTGTGTGCCCTGTGCT 58.462 50.000 0.00 0.00 42.00 4.40
3350 10890 1.200716 CTATTTGTGTGCCCTGTGCTG 59.799 52.381 0.00 0.00 42.00 4.41
3351 10891 0.756442 ATTTGTGTGCCCTGTGCTGT 60.756 50.000 0.00 0.00 42.00 4.40
3352 10892 1.665264 TTTGTGTGCCCTGTGCTGTG 61.665 55.000 0.00 0.00 42.00 3.66
3353 10893 3.969802 GTGTGCCCTGTGCTGTGC 61.970 66.667 0.00 0.00 42.00 4.57
3358 10898 4.601794 CCCTGTGCTGTGCCCCAA 62.602 66.667 0.00 0.00 0.00 4.12
3359 10899 3.297620 CCTGTGCTGTGCCCCAAC 61.298 66.667 0.00 0.00 0.00 3.77
3360 10900 2.203394 CTGTGCTGTGCCCCAACT 60.203 61.111 0.00 0.00 0.00 3.16
3361 10901 1.829533 CTGTGCTGTGCCCCAACTT 60.830 57.895 0.00 0.00 0.00 2.66
3362 10902 2.079020 CTGTGCTGTGCCCCAACTTG 62.079 60.000 0.00 0.00 0.00 3.16
3363 10903 2.127232 GTGCTGTGCCCCAACTTGT 61.127 57.895 0.00 0.00 0.00 3.16
3364 10904 1.827789 TGCTGTGCCCCAACTTGTC 60.828 57.895 0.00 0.00 0.00 3.18
3365 10905 1.529244 GCTGTGCCCCAACTTGTCT 60.529 57.895 0.00 0.00 0.00 3.41
3366 10906 1.799258 GCTGTGCCCCAACTTGTCTG 61.799 60.000 0.00 0.00 0.00 3.51
3367 10907 1.799258 CTGTGCCCCAACTTGTCTGC 61.799 60.000 0.00 0.00 0.00 4.26
3368 10908 2.594303 TGCCCCAACTTGTCTGCG 60.594 61.111 0.00 0.00 0.00 5.18
3369 10909 4.043200 GCCCCAACTTGTCTGCGC 62.043 66.667 0.00 0.00 0.00 6.09
3370 10910 3.726517 CCCCAACTTGTCTGCGCG 61.727 66.667 0.00 0.00 0.00 6.86
3371 10911 4.389576 CCCAACTTGTCTGCGCGC 62.390 66.667 27.26 27.26 0.00 6.86
3424 10964 9.148104 GGTTATGGTTATACGATTTCATCTACC 57.852 37.037 0.00 0.00 0.00 3.18
3426 10966 9.923143 TTATGGTTATACGATTTCATCTACCTG 57.077 33.333 0.00 0.00 0.00 4.00
3547 11383 8.438676 ACCGAGTTTATCCAGAAAAATATCAG 57.561 34.615 0.00 0.00 0.00 2.90
3574 11410 2.262572 GGCACGAAACCAACATCATC 57.737 50.000 0.00 0.00 0.00 2.92
3593 11429 7.873505 ACATCATCAGATCTGTCATGAAGTATG 59.126 37.037 23.31 19.81 33.24 2.39
3598 11434 8.853077 TCAGATCTGTCATGAAGTATGTTTTT 57.147 30.769 21.92 0.00 38.01 1.94
3661 11686 4.471904 TGATAAACTCGGTCAATGAGCT 57.528 40.909 10.85 0.00 36.94 4.09
3664 11689 6.403049 TGATAAACTCGGTCAATGAGCTTTA 58.597 36.000 10.85 8.90 36.94 1.85
3675 11700 9.436957 CGGTCAATGAGCTTTATATATAAACCT 57.563 33.333 12.90 12.04 0.00 3.50
3745 11779 6.582636 TCTATACAAATCTGCTCGGTTTGAT 58.417 36.000 15.89 9.33 36.58 2.57
3749 11813 6.515272 ACAAATCTGCTCGGTTTGATTAAT 57.485 33.333 15.89 0.00 36.58 1.40
3891 11970 3.306019 CCACATTGTAGCCCAAAACCTTC 60.306 47.826 0.00 0.00 36.44 3.46
3933 12012 2.954318 CCGGAGAGTCTTCCCGTTTATA 59.046 50.000 16.61 0.00 41.53 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 6065 5.047802 CCAGAATGCTCAAATACCAGTTGTT 60.048 40.000 0.00 0.00 31.97 2.83
92 6067 4.142315 CCCAGAATGCTCAAATACCAGTTG 60.142 45.833 0.00 0.00 31.97 3.16
133 6108 5.355350 AGGCAAACTTCATAAGAGTATGCAC 59.645 40.000 0.00 0.00 37.59 4.57
194 6253 5.330233 GGGGTCTATCCTCCTTTTCAAAAA 58.670 41.667 0.00 0.00 36.25 1.94
195 6254 4.930696 GGGGTCTATCCTCCTTTTCAAAA 58.069 43.478 0.00 0.00 36.25 2.44
196 6255 4.586306 GGGGTCTATCCTCCTTTTCAAA 57.414 45.455 0.00 0.00 36.25 2.69
205 6264 2.923568 GGCCGGGGGTCTATCCTC 60.924 72.222 2.18 0.00 36.25 3.71
206 6265 3.449126 AGGCCGGGGGTCTATCCT 61.449 66.667 2.18 0.00 34.99 3.24
207 6266 2.090377 TAGAGGCCGGGGGTCTATCC 62.090 65.000 2.18 0.00 38.01 2.59
208 6267 0.899253 GTAGAGGCCGGGGGTCTATC 60.899 65.000 2.18 0.00 38.01 2.08
209 6268 1.155624 GTAGAGGCCGGGGGTCTAT 59.844 63.158 2.18 0.00 38.01 1.98
210 6269 2.318966 TGTAGAGGCCGGGGGTCTA 61.319 63.158 2.18 0.00 38.01 2.59
211 6270 3.680196 TGTAGAGGCCGGGGGTCT 61.680 66.667 2.18 0.00 42.15 3.85
212 6271 3.468140 GTGTAGAGGCCGGGGGTC 61.468 72.222 2.18 0.00 0.00 4.46
219 6278 2.820037 GCTTGCGGTGTAGAGGCC 60.820 66.667 0.00 0.00 0.00 5.19
220 6279 2.047274 TGCTTGCGGTGTAGAGGC 60.047 61.111 0.00 0.00 0.00 4.70
221 6280 0.391661 ATGTGCTTGCGGTGTAGAGG 60.392 55.000 0.00 0.00 0.00 3.69
222 6281 1.442769 AATGTGCTTGCGGTGTAGAG 58.557 50.000 0.00 0.00 0.00 2.43
223 6282 1.890876 AAATGTGCTTGCGGTGTAGA 58.109 45.000 0.00 0.00 0.00 2.59
224 6283 3.126858 ACATAAATGTGCTTGCGGTGTAG 59.873 43.478 0.00 0.00 40.03 2.74
225 6284 3.078097 ACATAAATGTGCTTGCGGTGTA 58.922 40.909 0.00 0.00 40.03 2.90
226 6285 1.885887 ACATAAATGTGCTTGCGGTGT 59.114 42.857 0.00 0.00 40.03 4.16
227 6286 2.634982 ACATAAATGTGCTTGCGGTG 57.365 45.000 0.00 0.00 40.03 4.94
228 6287 3.489059 GCATACATAAATGTGCTTGCGGT 60.489 43.478 5.85 0.00 41.89 5.68
229 6288 3.044986 GCATACATAAATGTGCTTGCGG 58.955 45.455 5.85 0.00 41.89 5.69
230 6289 3.693654 TGCATACATAAATGTGCTTGCG 58.306 40.909 5.85 0.00 41.34 4.85
231 6290 4.084745 GCATGCATACATAAATGTGCTTGC 60.085 41.667 20.45 20.45 44.86 4.01
232 6291 5.044558 TGCATGCATACATAAATGTGCTTG 58.955 37.500 18.46 10.29 41.89 4.01
233 6292 5.045215 GTGCATGCATACATAAATGTGCTT 58.955 37.500 25.64 0.00 41.89 3.91
234 6293 4.098196 TGTGCATGCATACATAAATGTGCT 59.902 37.500 25.64 0.00 41.89 4.40
235 6294 4.361420 TGTGCATGCATACATAAATGTGC 58.639 39.130 25.64 6.40 41.89 4.57
236 6295 6.446659 CATGTGCATGCATACATAAATGTG 57.553 37.500 25.64 9.75 35.86 3.21
418 6625 0.688749 GGCCGGTAGGGTTCCTCTAA 60.689 60.000 1.90 0.00 38.44 2.10
431 6638 0.394352 CATAAGCTCAAAGGGCCGGT 60.394 55.000 1.90 0.00 0.00 5.28
445 6652 2.026262 AGGGTAAGGGTGCACACATAAG 60.026 50.000 23.57 0.00 0.00 1.73
467 6674 0.803768 CTGTTCCTCGCCGTGATCTG 60.804 60.000 0.00 0.00 0.00 2.90
475 6682 0.678048 ATTCTTGCCTGTTCCTCGCC 60.678 55.000 0.00 0.00 0.00 5.54
520 6727 7.579726 ACGATGCATAAATATTCTGCTTCTTC 58.420 34.615 22.59 14.41 37.71 2.87
535 6742 5.348164 TCTCTCAATCGAAACGATGCATAA 58.652 37.500 0.00 0.00 46.30 1.90
536 6743 4.932146 TCTCTCAATCGAAACGATGCATA 58.068 39.130 0.00 0.00 46.30 3.14
544 6751 2.091277 CACGTGCTCTCTCAATCGAAAC 59.909 50.000 0.82 0.00 0.00 2.78
551 6758 6.220930 AGTAAAATTACACGTGCTCTCTCAA 58.779 36.000 17.22 0.00 36.12 3.02
552 6759 5.779922 AGTAAAATTACACGTGCTCTCTCA 58.220 37.500 17.22 0.00 36.12 3.27
553 6760 5.288952 GGAGTAAAATTACACGTGCTCTCTC 59.711 44.000 17.22 11.95 36.12 3.20
555 6762 4.329256 GGGAGTAAAATTACACGTGCTCTC 59.671 45.833 17.22 7.57 36.12 3.20
557 6764 4.251268 AGGGAGTAAAATTACACGTGCTC 58.749 43.478 17.22 11.00 36.12 4.26
559 6766 4.092968 CAGAGGGAGTAAAATTACACGTGC 59.907 45.833 17.22 0.00 36.12 5.34
560 6767 5.235516 ACAGAGGGAGTAAAATTACACGTG 58.764 41.667 15.48 15.48 36.12 4.49
561 6768 5.479124 ACAGAGGGAGTAAAATTACACGT 57.521 39.130 6.13 0.00 36.12 4.49
562 6769 6.796705 AAACAGAGGGAGTAAAATTACACG 57.203 37.500 6.13 0.00 36.12 4.49
598 6805 8.816640 AAAATTTGACTTAAGGCACAACTATG 57.183 30.769 11.56 0.00 0.00 2.23
599 6806 8.860088 AGAAAATTTGACTTAAGGCACAACTAT 58.140 29.630 11.56 0.00 0.00 2.12
600 6807 8.134895 CAGAAAATTTGACTTAAGGCACAACTA 58.865 33.333 11.56 0.00 0.00 2.24
601 6808 6.980397 CAGAAAATTTGACTTAAGGCACAACT 59.020 34.615 11.56 2.41 0.00 3.16
602 6809 6.200854 CCAGAAAATTTGACTTAAGGCACAAC 59.799 38.462 11.56 0.01 0.00 3.32
603 6810 6.097554 TCCAGAAAATTTGACTTAAGGCACAA 59.902 34.615 11.56 9.29 0.00 3.33
604 6811 5.596361 TCCAGAAAATTTGACTTAAGGCACA 59.404 36.000 11.56 4.72 0.00 4.57
605 6812 6.084326 TCCAGAAAATTTGACTTAAGGCAC 57.916 37.500 11.56 0.00 0.00 5.01
607 6814 6.332735 ACTCCAGAAAATTTGACTTAAGGC 57.667 37.500 7.53 3.92 0.00 4.35
608 6815 8.413229 TCAAACTCCAGAAAATTTGACTTAAGG 58.587 33.333 7.53 0.00 36.42 2.69
615 6822 6.537453 TTGGTCAAACTCCAGAAAATTTGA 57.463 33.333 0.00 0.00 38.42 2.69
616 6823 7.790823 ATTTGGTCAAACTCCAGAAAATTTG 57.209 32.000 0.00 0.00 36.28 2.32
617 6824 8.806429 AAATTTGGTCAAACTCCAGAAAATTT 57.194 26.923 0.00 0.00 36.28 1.82
622 6829 9.581289 TTCTATAAATTTGGTCAAACTCCAGAA 57.419 29.630 0.00 2.90 36.28 3.02
623 6830 9.581289 TTTCTATAAATTTGGTCAAACTCCAGA 57.419 29.630 0.00 0.00 36.28 3.86
697 7527 3.181526 CGCTGTGTGCTAGATCTGTTTTC 60.182 47.826 5.18 0.00 40.11 2.29
762 7649 4.002797 GCTGTAGGCAACCCCTTG 57.997 61.111 0.00 0.00 43.06 3.61
772 7664 1.726853 AGCTAAAACGCTGCTGTAGG 58.273 50.000 0.00 0.00 39.16 3.18
882 8177 6.813649 CGATGACCCTATACATACATGAAAGG 59.186 42.308 0.00 0.26 0.00 3.11
907 8215 2.636830 CTCTGGTGACCCAATGTGATC 58.363 52.381 0.00 0.00 41.27 2.92
951 8325 5.941555 TGTTCACTTGGGTATTTTGGTTT 57.058 34.783 0.00 0.00 0.00 3.27
1054 8447 3.857217 CAGAGAGGCTGCACAAGAT 57.143 52.632 0.50 0.00 37.90 2.40
1224 8617 2.181777 GCGTCGCTCTCCACATCA 59.818 61.111 10.68 0.00 0.00 3.07
1284 8677 0.995024 AGGCACTTATGTTCTGGCCT 59.005 50.000 3.32 0.00 46.33 5.19
1291 8684 2.418746 CGAGGCTGTAGGCACTTATGTT 60.419 50.000 8.22 0.00 44.01 2.71
1326 8728 1.742831 GTTATGACATGCCGCTTCCAA 59.257 47.619 0.00 0.00 0.00 3.53
1340 8742 4.558697 CGACTTGTGACACCAGAGTTATGA 60.559 45.833 13.31 0.00 0.00 2.15
1410 8812 2.925170 ACTGCCGCCTGAAGGAGT 60.925 61.111 0.00 0.00 37.39 3.85
1480 8882 0.533755 CTATTGAAGCTGGCCCTCCG 60.534 60.000 0.00 0.00 34.14 4.63
1570 8972 1.066929 AGCAAAATCCCCGCAATTCAC 60.067 47.619 0.00 0.00 0.00 3.18
1579 8981 0.897621 CCCACTGAAGCAAAATCCCC 59.102 55.000 0.00 0.00 0.00 4.81
1596 8998 4.798682 TCCTCTCCTTCCCGCCCC 62.799 72.222 0.00 0.00 0.00 5.80
1597 8999 2.687566 TTCCTCTCCTTCCCGCCC 60.688 66.667 0.00 0.00 0.00 6.13
1598 9000 2.736826 CCTTCCTCTCCTTCCCGCC 61.737 68.421 0.00 0.00 0.00 6.13
1601 9003 0.906066 GTGTCCTTCCTCTCCTTCCC 59.094 60.000 0.00 0.00 0.00 3.97
1621 9024 5.499139 TCTTCAAGTGAAAGATTGCGTTT 57.501 34.783 0.00 0.00 33.07 3.60
1629 9032 8.849168 TCTTTTGCATATTCTTCAAGTGAAAGA 58.151 29.630 0.00 0.00 33.07 2.52
1649 9052 7.467557 TTTACAAGCTTCTTTGCATCTTTTG 57.532 32.000 0.00 0.00 34.99 2.44
1672 9075 2.219325 CTCGCCAGCTCCGTCTCTTT 62.219 60.000 3.53 0.00 0.00 2.52
1684 9093 0.321564 TGGTCATTTCCACTCGCCAG 60.322 55.000 0.00 0.00 31.96 4.85
1686 9095 1.200020 CTTTGGTCATTTCCACTCGCC 59.800 52.381 0.00 0.00 37.20 5.54
1694 9103 6.855836 TGATATGCTGTTCTTTGGTCATTTC 58.144 36.000 0.00 0.00 0.00 2.17
1697 9106 6.839124 TTTGATATGCTGTTCTTTGGTCAT 57.161 33.333 0.00 0.00 0.00 3.06
1713 9122 2.997986 ACGGCGTCGAAACTTTTGATAT 59.002 40.909 20.03 0.00 40.11 1.63
1714 9123 2.156117 CACGGCGTCGAAACTTTTGATA 59.844 45.455 20.03 0.00 40.11 2.15
1717 9126 1.259544 GCACGGCGTCGAAACTTTTG 61.260 55.000 20.03 2.23 40.11 2.44
1727 9136 0.094730 GTAGTTCATTGCACGGCGTC 59.905 55.000 10.85 6.01 0.00 5.19
1761 9174 4.909001 AGTACCGAGTAGATAGATCCACC 58.091 47.826 0.00 0.00 0.00 4.61
1767 9180 5.163468 ACGAACAGAGTACCGAGTAGATAGA 60.163 44.000 0.00 0.00 0.00 1.98
1858 9271 2.840651 AGGCACCATATGTATCCCTAGC 59.159 50.000 1.24 0.00 0.00 3.42
1859 9272 4.287067 ACAAGGCACCATATGTATCCCTAG 59.713 45.833 1.24 0.00 0.00 3.02
1864 9277 5.924475 GTGTACAAGGCACCATATGTATC 57.076 43.478 0.00 0.00 31.57 2.24
1879 9292 5.883115 TGAGTGATCTTGTTTTGGTGTACAA 59.117 36.000 0.00 0.00 37.28 2.41
1892 9305 5.490139 AACACAACTGTTGAGTGATCTTG 57.510 39.130 26.00 13.46 39.28 3.02
1907 9320 1.024271 TGAGCAGAAGCCAACACAAC 58.976 50.000 0.00 0.00 43.56 3.32
1912 9325 1.200948 GAACCATGAGCAGAAGCCAAC 59.799 52.381 0.00 0.00 43.56 3.77
1932 9345 1.813513 ATGTCAGGAACGGAAGCAAG 58.186 50.000 0.00 0.00 32.22 4.01
1941 9354 3.274288 CAGGGAAGCTAATGTCAGGAAC 58.726 50.000 0.00 0.00 0.00 3.62
1973 9386 6.428083 TGTAACCATCCTTGTTACTCTTGA 57.572 37.500 12.78 0.00 45.24 3.02
1981 9394 6.938030 TCGTTCTTATTGTAACCATCCTTGTT 59.062 34.615 0.00 0.00 0.00 2.83
1999 9412 7.255491 TGTATGATACTATCACGTCGTTCTT 57.745 36.000 4.03 0.00 43.01 2.52
2004 9417 6.251549 CAGGATGTATGATACTATCACGTCG 58.748 44.000 4.03 0.00 43.01 5.12
2031 9444 2.506444 TGAATCATGACTGTGCAAGCA 58.494 42.857 0.00 0.00 0.00 3.91
2033 9446 5.466819 ACAATTGAATCATGACTGTGCAAG 58.533 37.500 13.59 0.00 0.00 4.01
2058 9471 2.282745 AGCCTGAGCACAAAGGGC 60.283 61.111 4.96 4.96 43.56 5.19
2065 9478 2.817396 GCTTCCGAGCCTGAGCAC 60.817 66.667 0.00 0.00 43.29 4.40
2084 9497 1.142870 TGTCTGGCCAAGTAGCAGTTT 59.857 47.619 7.01 0.00 0.00 2.66
2085 9498 0.764890 TGTCTGGCCAAGTAGCAGTT 59.235 50.000 7.01 0.00 0.00 3.16
2086 9499 0.987294 ATGTCTGGCCAAGTAGCAGT 59.013 50.000 7.01 0.00 0.00 4.40
2087 9500 1.376543 CATGTCTGGCCAAGTAGCAG 58.623 55.000 7.01 0.00 0.00 4.24
2099 9527 1.948834 TGTGCTGTGAAACCATGTCTG 59.051 47.619 0.00 0.00 34.36 3.51
2129 9557 0.165511 CTTCTTGCGAGCACAGAAGC 59.834 55.000 23.26 0.00 36.02 3.86
2133 9561 1.496393 CTGCTTCTTGCGAGCACAG 59.504 57.895 0.00 0.00 44.63 3.66
2188 9616 3.644265 TGCTTGTTAGTGTACTCCCTGAA 59.356 43.478 0.00 0.00 0.00 3.02
2201 9629 4.864247 GCCAATTGTACCAATGCTTGTTAG 59.136 41.667 4.43 0.00 0.00 2.34
2241 9669 3.009723 GCGAATCAACCCTTCAATCTCA 58.990 45.455 0.00 0.00 0.00 3.27
2242 9670 2.356069 GGCGAATCAACCCTTCAATCTC 59.644 50.000 0.00 0.00 0.00 2.75
2264 9692 4.079958 ACTCCCACCCATCTTTTATGTACC 60.080 45.833 0.00 0.00 0.00 3.34
2299 9739 3.273434 TGAATCTTCTGTATGTGGCAGC 58.727 45.455 0.00 0.00 34.21 5.25
2302 9742 5.627499 TTGTTGAATCTTCTGTATGTGGC 57.373 39.130 0.00 0.00 0.00 5.01
2322 9762 1.952367 GCCTGTTGTCCCCTGAGATTG 60.952 57.143 0.00 0.00 0.00 2.67
2341 9781 1.446966 GAGGGTGCTTCGACAGAGC 60.447 63.158 0.49 0.49 0.00 4.09
2436 9876 0.909610 TGGGGTGGTAGAAGCAGAGG 60.910 60.000 0.00 0.00 0.00 3.69
2454 9894 1.352352 AGACCTTGGGAGGATGTGTTG 59.648 52.381 0.00 0.00 46.74 3.33
2576 10028 2.129607 CATTGCAAGCAACTGTGAACC 58.870 47.619 9.97 0.00 38.88 3.62
2593 10045 5.237996 CCGTGAGAATGTGCTTGATATCATT 59.762 40.000 6.17 0.00 33.95 2.57
2633 10085 3.015327 AGAATCCTCTGTGCAATGCTTC 58.985 45.455 6.82 0.00 0.00 3.86
2688 10146 1.007964 TTTGTGCGCATTGGGAACG 60.008 52.632 15.91 0.00 0.00 3.95
2712 10170 2.519013 GGGTGTTCCATGAGCTTCTTT 58.481 47.619 0.00 0.00 35.00 2.52
2716 10174 0.482446 TTGGGGTGTTCCATGAGCTT 59.518 50.000 0.00 0.00 36.58 3.74
2853 10311 5.390885 CGACCATAAGAACCAGACATTTGTG 60.391 44.000 0.00 0.00 0.00 3.33
2944 10402 4.713553 TCAAGAGGTTGACTTGTTATGCA 58.286 39.130 0.00 0.00 43.30 3.96
2947 10405 9.793259 TTCTATTTCAAGAGGTTGACTTGTTAT 57.207 29.630 0.00 0.00 42.60 1.89
2959 10417 7.230913 AGCATCCATGATTTCTATTTCAAGAGG 59.769 37.037 0.00 0.00 0.00 3.69
3026 10488 1.261238 AACCCGAAGAGGAGAGCTGG 61.261 60.000 0.00 0.00 45.00 4.85
3041 10519 2.531522 AATGAAAAGCAGCACAACCC 57.468 45.000 0.00 0.00 0.00 4.11
3042 10520 3.456280 TGAAATGAAAAGCAGCACAACC 58.544 40.909 0.00 0.00 0.00 3.77
3095 10575 4.900635 AGCACACAAGTTTAGAAACCAG 57.099 40.909 1.52 0.00 39.71 4.00
3127 10609 0.039074 ACTCAACTCGCGGTCTCTTG 60.039 55.000 6.13 1.05 0.00 3.02
3151 10660 2.781595 GAACATGCTCGACACCGGGT 62.782 60.000 6.32 0.00 38.83 5.28
3179 10690 2.802816 CGGCTGCATTACTAGGACATTC 59.197 50.000 0.50 0.00 0.00 2.67
3180 10691 2.170607 ACGGCTGCATTACTAGGACATT 59.829 45.455 0.50 0.00 0.00 2.71
3191 10704 3.788766 GACGCGAACGGCTGCATT 61.789 61.111 15.93 0.00 46.72 3.56
3235 10748 2.286654 GCCATGATTCTTTCGTAGCTGC 60.287 50.000 0.00 0.00 0.00 5.25
3243 10756 1.064654 GCTCCGTGCCATGATTCTTTC 59.935 52.381 0.00 0.00 35.15 2.62
3348 10888 1.799258 GCAGACAAGTTGGGGCACAG 61.799 60.000 7.96 0.00 0.00 3.66
3349 10889 1.827789 GCAGACAAGTTGGGGCACA 60.828 57.895 7.96 0.00 0.00 4.57
3350 10890 2.908073 CGCAGACAAGTTGGGGCAC 61.908 63.158 7.96 0.00 0.00 5.01
3351 10891 2.594303 CGCAGACAAGTTGGGGCA 60.594 61.111 7.96 0.00 0.00 5.36
3352 10892 4.043200 GCGCAGACAAGTTGGGGC 62.043 66.667 0.30 5.90 0.00 5.80
3353 10893 3.726517 CGCGCAGACAAGTTGGGG 61.727 66.667 8.75 0.00 0.00 4.96
3354 10894 4.389576 GCGCGCAGACAAGTTGGG 62.390 66.667 29.10 0.00 0.00 4.12
3355 10895 3.349006 AGCGCGCAGACAAGTTGG 61.349 61.111 35.10 0.00 0.00 3.77
3356 10896 2.127496 CAGCGCGCAGACAAGTTG 60.127 61.111 35.10 16.38 0.00 3.16
3357 10897 2.588877 ACAGCGCGCAGACAAGTT 60.589 55.556 35.10 6.63 0.00 2.66
3358 10898 3.341043 CACAGCGCGCAGACAAGT 61.341 61.111 35.10 17.69 0.00 3.16
3359 10899 4.731503 GCACAGCGCGCAGACAAG 62.732 66.667 35.10 18.01 0.00 3.16
3368 10908 4.347453 CAAGTTGGGGCACAGCGC 62.347 66.667 0.00 0.00 40.84 5.92
3369 10909 2.906897 ACAAGTTGGGGCACAGCG 60.907 61.111 7.96 0.00 35.19 5.18
3370 10910 1.529244 AGACAAGTTGGGGCACAGC 60.529 57.895 7.96 0.00 0.00 4.40
3371 10911 1.799258 GCAGACAAGTTGGGGCACAG 61.799 60.000 7.96 0.00 0.00 3.66
3519 11065 6.743575 ATTTTTCTGGATAAACTCGGTCAG 57.256 37.500 0.00 0.00 0.00 3.51
3547 11383 1.017177 TGGTTTCGTGCCGTAGATGC 61.017 55.000 0.00 0.00 0.00 3.91
3564 11400 5.365619 TCATGACAGATCTGATGATGTTGG 58.634 41.667 29.27 8.24 32.19 3.77
3568 11404 7.873505 ACATACTTCATGACAGATCTGATGATG 59.126 37.037 29.27 26.10 38.10 3.07
3573 11409 8.853077 AAAAACATACTTCATGACAGATCTGA 57.147 30.769 29.27 8.23 38.10 3.27
3685 11710 3.252458 CCGGGCAGGTTTATATGTAAAGC 59.748 47.826 14.25 14.25 44.61 3.51
3686 11711 4.710324 TCCGGGCAGGTTTATATGTAAAG 58.290 43.478 0.00 0.00 41.99 1.85
3687 11712 4.445162 CCTCCGGGCAGGTTTATATGTAAA 60.445 45.833 0.00 0.00 41.99 2.01
3691 11716 1.697432 TCCTCCGGGCAGGTTTATATG 59.303 52.381 8.95 0.00 41.99 1.78
3692 11717 1.978580 CTCCTCCGGGCAGGTTTATAT 59.021 52.381 8.95 0.00 41.99 0.86
3694 11719 0.620700 ACTCCTCCGGGCAGGTTTAT 60.621 55.000 8.95 0.00 41.99 1.40
3701 11728 1.760875 GGATGTACTCCTCCGGGCA 60.761 63.158 0.00 0.00 41.29 5.36
3702 11729 1.122019 ATGGATGTACTCCTCCGGGC 61.122 60.000 0.00 0.00 45.21 6.13
3745 11779 7.398746 CGATACTCTGTTTTTGCATCGATTAA 58.601 34.615 0.00 0.00 36.75 1.40
3749 11813 3.616821 CCGATACTCTGTTTTTGCATCGA 59.383 43.478 0.00 0.00 36.75 3.59
3933 12012 3.314331 CTGGACAGCGACTGGGGT 61.314 66.667 10.80 0.00 35.51 4.95


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

AutoCloner maintained by Alex Coulton.