Multiple sequence alignment - TraesCS5D01G515300

Loading Multiple Alignment...

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 TraesCS5D01G515300 chr5D 100.000 2483 0 0 1 2483 538661355 538658873 0.000000e+00 4586
1 TraesCS5D01G515300 chr5B 87.128 1849 77 70 730 2483 679678389 679676607 0.000000e+00 1947
2 TraesCS5D01G515300 chr5B 80.060 336 41 11 1 326 679679169 679678850 2.480000e-55 226
3 TraesCS5D01G515300 chr5B 81.081 185 32 3 407 590 9342909 9343091 7.160000e-31 145
4 TraesCS5D01G515300 chr4A 87.938 1484 80 54 683 2127 630863353 630864776 0.000000e+00 1657
5 TraesCS5D01G515300 chr4A 90.780 141 5 5 2327 2467 630864900 630865032 5.460000e-42 182
6 TraesCS5D01G515300 chr2D 82.682 179 26 5 408 584 200780961 200781136 1.190000e-33 154
7 TraesCS5D01G515300 chr2D 79.114 158 30 3 435 590 255615782 255615938 3.380000e-19 106
8 TraesCS5D01G515300 chr2B 84.459 148 20 3 439 584 374253867 374254013 2.570000e-30 143
9 TraesCS5D01G515300 chr5A 81.383 188 21 10 407 590 649374347 649374170 9.260000e-30 141
10 TraesCS5D01G515300 chr3A 82.667 150 21 5 447 595 382257418 382257273 7.210000e-26 128
11 TraesCS5D01G515300 chr7B 79.429 175 31 5 411 582 702846579 702846407 4.340000e-23 119
12 TraesCS5D01G515300 chr3D 79.070 172 33 2 414 584 87483643 87483812 5.610000e-22 115
13 TraesCS5D01G515300 chr6A 79.355 155 27 5 439 590 18356667 18356819 1.210000e-18 104


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 TraesCS5D01G515300 chr5D 538658873 538661355 2482 True 4586.0 4586 100.000 1 2483 1 chr5D.!!$R1 2482
1 TraesCS5D01G515300 chr5B 679676607 679679169 2562 True 1086.5 1947 83.594 1 2483 2 chr5B.!!$R1 2482
2 TraesCS5D01G515300 chr4A 630863353 630865032 1679 False 919.5 1657 89.359 683 2467 2 chr4A.!!$F1 1784

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
143 154 0.3199 TGCTTCTCGGCAACTCAGTC 60.32 55.0 0.0 0.0 39.43 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1733 0.034186 AATTGCAGATCCGGCCAAGA 60.034 50.0 2.24 0.0 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
49 50 5.428184 AATTACCACAGAGAGGGAAAGAG 57.572 43.478 0.00 0.00 31.42 2.85
60 61 5.066913 AGAGGGAAAGAGACCACAAAAAT 57.933 39.130 0.00 0.00 0.00 1.82
64 75 5.536538 AGGGAAAGAGACCACAAAAATCTTC 59.463 40.000 0.00 0.00 30.16 2.87
68 79 5.053978 AGAGACCACAAAAATCTTCACCT 57.946 39.130 0.00 0.00 0.00 4.00
126 137 8.239314 TCATCTTATTCTTTCATTTGTGTCTGC 58.761 33.333 0.00 0.00 0.00 4.26
127 138 7.750229 TCTTATTCTTTCATTTGTGTCTGCT 57.250 32.000 0.00 0.00 0.00 4.24
128 139 8.169977 TCTTATTCTTTCATTTGTGTCTGCTT 57.830 30.769 0.00 0.00 0.00 3.91
143 154 0.319900 TGCTTCTCGGCAACTCAGTC 60.320 55.000 0.00 0.00 39.43 3.51
150 161 1.592400 CGGCAACTCAGTCGGAGGTA 61.592 60.000 4.95 0.00 43.39 3.08
170 181 7.639113 AGGTACTCACAACAAGAAATTGAAA 57.361 32.000 0.00 0.00 0.00 2.69
171 182 8.062065 AGGTACTCACAACAAGAAATTGAAAA 57.938 30.769 0.00 0.00 0.00 2.29
172 183 8.190784 AGGTACTCACAACAAGAAATTGAAAAG 58.809 33.333 0.00 0.00 0.00 2.27
193 204 2.325583 AGAAGCTTTGTGACGGACAA 57.674 45.000 0.00 0.00 43.11 3.18
197 208 2.851195 AGCTTTGTGACGGACAAGAAT 58.149 42.857 2.96 0.00 45.43 2.40
198 209 4.002906 AGCTTTGTGACGGACAAGAATA 57.997 40.909 2.96 0.00 45.43 1.75
213 224 9.250624 CGGACAAGAATAGGACTTTAAGATTAG 57.749 37.037 0.00 0.00 0.00 1.73
292 459 6.734137 ACATGTTTTATGTTCATGTCGTTGT 58.266 32.000 0.00 0.00 45.67 3.32
301 468 2.469826 TCATGTCGTTGTGTCTGTGTC 58.530 47.619 0.00 0.00 0.00 3.67
302 469 2.159170 TCATGTCGTTGTGTCTGTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
313 480 3.251004 GTGTCTGTGTCAATGGAACTTCC 59.749 47.826 0.20 0.20 36.96 3.46
322 489 1.923356 ATGGAACTTCCCGCAATTGT 58.077 45.000 7.40 0.00 35.03 2.71
326 493 2.151202 GAACTTCCCGCAATTGTGAGA 58.849 47.619 20.47 10.01 0.00 3.27
327 494 1.813513 ACTTCCCGCAATTGTGAGAG 58.186 50.000 20.47 15.33 0.00 3.20
331 498 1.651240 CCCGCAATTGTGAGAGCCAG 61.651 60.000 20.47 1.60 0.00 4.85
332 499 0.674581 CCGCAATTGTGAGAGCCAGA 60.675 55.000 20.47 0.00 0.00 3.86
334 501 1.741706 CGCAATTGTGAGAGCCAGATT 59.258 47.619 13.88 0.00 0.00 2.40
335 502 2.163010 CGCAATTGTGAGAGCCAGATTT 59.837 45.455 13.88 0.00 0.00 2.17
336 503 3.374988 CGCAATTGTGAGAGCCAGATTTA 59.625 43.478 13.88 0.00 0.00 1.40
337 504 4.036027 CGCAATTGTGAGAGCCAGATTTAT 59.964 41.667 13.88 0.00 0.00 1.40
338 505 5.517904 GCAATTGTGAGAGCCAGATTTATC 58.482 41.667 7.40 0.00 0.00 1.75
340 507 6.513066 GCAATTGTGAGAGCCAGATTTATCTC 60.513 42.308 7.40 0.00 38.91 2.75
342 509 5.946942 TGTGAGAGCCAGATTTATCTCTT 57.053 39.130 3.06 0.00 39.15 2.85
343 510 5.911752 TGTGAGAGCCAGATTTATCTCTTC 58.088 41.667 3.06 0.00 39.15 2.87
344 511 5.660417 TGTGAGAGCCAGATTTATCTCTTCT 59.340 40.000 3.06 0.00 39.15 2.85
347 514 6.610830 TGAGAGCCAGATTTATCTCTTCTTCT 59.389 38.462 3.06 0.00 39.15 2.85
348 515 7.125507 TGAGAGCCAGATTTATCTCTTCTTCTT 59.874 37.037 3.06 0.00 39.15 2.52
349 516 8.546083 AGAGCCAGATTTATCTCTTCTTCTTA 57.454 34.615 0.00 0.00 34.22 2.10
350 517 9.158097 AGAGCCAGATTTATCTCTTCTTCTTAT 57.842 33.333 0.00 0.00 34.22 1.73
351 518 9.423061 GAGCCAGATTTATCTCTTCTTCTTATC 57.577 37.037 0.00 0.00 34.22 1.75
352 519 8.932610 AGCCAGATTTATCTCTTCTTCTTATCA 58.067 33.333 0.00 0.00 34.22 2.15
353 520 9.553064 GCCAGATTTATCTCTTCTTCTTATCAA 57.447 33.333 0.00 0.00 34.22 2.57
379 546 8.848474 TTCAAAAAGAATTACTCCGAGATCTT 57.152 30.769 1.33 3.97 0.00 2.40
380 547 8.480643 TCAAAAAGAATTACTCCGAGATCTTC 57.519 34.615 1.33 2.03 0.00 2.87
381 548 8.314751 TCAAAAAGAATTACTCCGAGATCTTCT 58.685 33.333 1.33 4.20 0.00 2.85
382 549 8.940952 CAAAAAGAATTACTCCGAGATCTTCTT 58.059 33.333 1.33 9.50 34.03 2.52
384 551 9.810545 AAAAGAATTACTCCGAGATCTTCTTAG 57.189 33.333 16.71 0.00 32.73 2.18
385 552 8.528044 AAGAATTACTCCGAGATCTTCTTAGT 57.472 34.615 15.69 1.63 31.63 2.24
386 553 9.629878 AAGAATTACTCCGAGATCTTCTTAGTA 57.370 33.333 15.69 0.66 31.63 1.82
387 554 9.059260 AGAATTACTCCGAGATCTTCTTAGTAC 57.941 37.037 1.33 0.00 0.00 2.73
388 555 8.749026 AATTACTCCGAGATCTTCTTAGTACA 57.251 34.615 1.33 0.00 0.00 2.90
389 556 7.551035 TTACTCCGAGATCTTCTTAGTACAC 57.449 40.000 1.33 0.00 0.00 2.90
390 557 5.498393 ACTCCGAGATCTTCTTAGTACACA 58.502 41.667 1.33 0.00 0.00 3.72
391 558 5.944599 ACTCCGAGATCTTCTTAGTACACAA 59.055 40.000 1.33 0.00 0.00 3.33
392 559 6.094325 ACTCCGAGATCTTCTTAGTACACAAG 59.906 42.308 1.33 0.00 0.00 3.16
393 560 5.944599 TCCGAGATCTTCTTAGTACACAAGT 59.055 40.000 0.00 0.00 0.00 3.16
394 561 6.093771 TCCGAGATCTTCTTAGTACACAAGTC 59.906 42.308 0.00 0.00 0.00 3.01
395 562 6.094325 CCGAGATCTTCTTAGTACACAAGTCT 59.906 42.308 0.00 0.00 0.00 3.24
396 563 7.362229 CCGAGATCTTCTTAGTACACAAGTCTT 60.362 40.741 0.00 0.00 0.00 3.01
397 564 7.694784 CGAGATCTTCTTAGTACACAAGTCTTC 59.305 40.741 0.00 0.00 0.00 2.87
398 565 8.410673 AGATCTTCTTAGTACACAAGTCTTCA 57.589 34.615 0.00 0.00 0.00 3.02
399 566 9.030452 AGATCTTCTTAGTACACAAGTCTTCAT 57.970 33.333 0.00 0.00 0.00 2.57
400 567 9.646427 GATCTTCTTAGTACACAAGTCTTCATT 57.354 33.333 0.00 0.00 0.00 2.57
403 570 9.360093 CTTCTTAGTACACAAGTCTTCATTAGG 57.640 37.037 0.00 0.00 0.00 2.69
404 571 7.837863 TCTTAGTACACAAGTCTTCATTAGGG 58.162 38.462 0.00 0.00 0.00 3.53
405 572 5.422214 AGTACACAAGTCTTCATTAGGGG 57.578 43.478 0.00 0.00 0.00 4.79
406 573 5.091552 AGTACACAAGTCTTCATTAGGGGA 58.908 41.667 0.00 0.00 0.00 4.81
407 574 4.287766 ACACAAGTCTTCATTAGGGGAC 57.712 45.455 0.00 0.00 0.00 4.46
427 594 5.669164 GACCAAGAGTTCAGGTCTTAGAT 57.331 43.478 13.36 0.00 46.45 1.98
434 601 8.713271 CAAGAGTTCAGGTCTTAGATTTAACAC 58.287 37.037 0.00 0.00 32.81 3.32
451 618 2.430465 ACACTGATGCTCGCATTTTCT 58.570 42.857 5.79 0.00 36.70 2.52
462 629 5.638657 TGCTCGCATTTTCTTGCATTTATTT 59.361 32.000 0.00 0.00 42.91 1.40
463 630 6.180567 GCTCGCATTTTCTTGCATTTATTTC 58.819 36.000 0.00 0.00 42.91 2.17
468 635 6.676213 GCATTTTCTTGCATTTATTTCAGGCC 60.676 38.462 0.00 0.00 42.31 5.19
472 639 4.771577 TCTTGCATTTATTTCAGGCCTTCA 59.228 37.500 0.00 0.00 0.00 3.02
499 666 2.027192 TGTGCATTAAGTGGGAGGAGAC 60.027 50.000 0.00 0.00 0.00 3.36
503 670 3.868754 GCATTAAGTGGGAGGAGACGTTT 60.869 47.826 0.00 0.00 0.00 3.60
506 673 1.420430 AGTGGGAGGAGACGTTTTCA 58.580 50.000 0.00 0.00 0.00 2.69
508 675 2.028020 AGTGGGAGGAGACGTTTTCATC 60.028 50.000 7.01 7.01 0.00 2.92
510 677 1.067071 GGGAGGAGACGTTTTCATCGT 60.067 52.381 8.80 0.00 44.27 3.73
531 698 4.383602 CGAAGGCGTTTGTGGCGG 62.384 66.667 0.00 0.00 39.82 6.13
541 708 2.324860 GTTTGTGGCGGCTTTGTAATC 58.675 47.619 11.43 0.00 0.00 1.75
551 718 4.494855 GCGGCTTTGTAATCTCAAGATGAC 60.495 45.833 1.07 1.07 36.61 3.06
556 723 4.456280 TGTAATCTCAAGATGACGTGCT 57.544 40.909 0.00 0.00 38.49 4.40
557 724 4.176271 TGTAATCTCAAGATGACGTGCTG 58.824 43.478 0.00 0.00 38.49 4.41
559 726 0.390340 TCTCAAGATGACGTGCTGGC 60.390 55.000 0.00 0.00 0.00 4.85
567 734 1.445238 GACGTGCTGGCTCAGTCTC 60.445 63.158 0.00 0.00 33.43 3.36
569 736 1.291588 CGTGCTGGCTCAGTCTCTT 59.708 57.895 4.45 0.00 33.43 2.85
574 741 1.274728 GCTGGCTCAGTCTCTTGAAGA 59.725 52.381 0.00 0.00 33.43 2.87
578 745 2.093553 GGCTCAGTCTCTTGAAGATGCT 60.094 50.000 0.00 0.00 36.11 3.79
584 751 5.890419 TCAGTCTCTTGAAGATGCTCATAGA 59.110 40.000 0.00 0.00 36.11 1.98
586 753 6.039605 CAGTCTCTTGAAGATGCTCATAGAGA 59.960 42.308 0.00 0.00 37.32 3.10
590 757 8.162746 TCTCTTGAAGATGCTCATAGAGATAGA 58.837 37.037 0.00 0.00 36.17 1.98
591 758 8.703378 TCTTGAAGATGCTCATAGAGATAGAA 57.297 34.615 0.00 0.00 0.00 2.10
592 759 8.795513 TCTTGAAGATGCTCATAGAGATAGAAG 58.204 37.037 0.00 0.00 0.00 2.85
593 760 7.465353 TGAAGATGCTCATAGAGATAGAAGG 57.535 40.000 0.00 0.00 0.00 3.46
594 761 7.237255 TGAAGATGCTCATAGAGATAGAAGGA 58.763 38.462 0.00 0.00 0.00 3.36
611 785 5.860941 GAAGGATTCATAGAGGTGAGTGA 57.139 43.478 0.00 0.00 46.62 3.41
615 789 4.754114 GGATTCATAGAGGTGAGTGAATGC 59.246 45.833 4.38 3.85 40.35 3.56
616 790 5.454471 GGATTCATAGAGGTGAGTGAATGCT 60.454 44.000 10.03 0.00 42.47 3.79
617 791 4.662468 TCATAGAGGTGAGTGAATGCTC 57.338 45.455 0.00 0.00 36.12 4.26
618 792 4.026052 TCATAGAGGTGAGTGAATGCTCA 58.974 43.478 0.00 0.00 42.56 4.26
619 793 4.652881 TCATAGAGGTGAGTGAATGCTCAT 59.347 41.667 0.00 0.00 45.81 2.90
621 795 2.570752 AGAGGTGAGTGAATGCTCATGT 59.429 45.455 0.00 0.00 45.81 3.21
622 796 3.771479 AGAGGTGAGTGAATGCTCATGTA 59.229 43.478 0.00 0.00 45.81 2.29
624 798 4.449131 AGGTGAGTGAATGCTCATGTATG 58.551 43.478 0.00 0.00 45.81 2.39
625 799 3.003068 GGTGAGTGAATGCTCATGTATGC 59.997 47.826 0.00 0.00 45.81 3.14
628 802 3.129109 AGTGAATGCTCATGTATGCGAG 58.871 45.455 0.00 0.00 33.05 5.03
636 810 1.926510 TCATGTATGCGAGCAACTTCG 59.073 47.619 0.57 0.00 43.23 3.79
637 811 1.926510 CATGTATGCGAGCAACTTCGA 59.073 47.619 0.57 0.00 43.03 3.71
640 814 2.348362 TGTATGCGAGCAACTTCGATTG 59.652 45.455 0.57 0.00 43.03 2.67
642 816 2.073117 TGCGAGCAACTTCGATTGTA 57.927 45.000 0.00 0.00 43.03 2.41
643 817 1.724623 TGCGAGCAACTTCGATTGTAC 59.275 47.619 0.00 0.00 43.03 2.90
644 818 1.060698 GCGAGCAACTTCGATTGTACC 59.939 52.381 0.00 0.00 43.03 3.34
645 819 1.320555 CGAGCAACTTCGATTGTACCG 59.679 52.381 1.06 0.00 43.03 4.02
646 820 2.334838 GAGCAACTTCGATTGTACCGT 58.665 47.619 1.06 0.00 31.83 4.83
647 821 2.066262 AGCAACTTCGATTGTACCGTG 58.934 47.619 1.06 0.00 31.83 4.94
648 822 1.796459 GCAACTTCGATTGTACCGTGT 59.204 47.619 1.06 0.00 31.83 4.49
649 823 2.222445 GCAACTTCGATTGTACCGTGTT 59.778 45.455 1.06 0.00 31.83 3.32
650 824 3.429543 GCAACTTCGATTGTACCGTGTTA 59.570 43.478 1.06 0.00 31.83 2.41
651 825 4.084433 GCAACTTCGATTGTACCGTGTTAA 60.084 41.667 1.06 0.00 31.83 2.01
652 826 5.558653 GCAACTTCGATTGTACCGTGTTAAA 60.559 40.000 1.06 0.00 31.83 1.52
653 827 6.595794 CAACTTCGATTGTACCGTGTTAAAT 58.404 36.000 0.00 0.00 0.00 1.40
669 843 9.590451 CCGTGTTAAATAAAACTAGGACTATCA 57.410 33.333 0.00 0.00 32.24 2.15
677 851 8.719645 ATAAAACTAGGACTATCATGCTCTCT 57.280 34.615 0.00 0.00 0.00 3.10
680 854 4.832266 ACTAGGACTATCATGCTCTCTTGG 59.168 45.833 0.00 0.00 0.00 3.61
753 929 8.436200 GCAATATCAAAATCACGGAGACTATAC 58.564 37.037 0.00 0.00 0.00 1.47
767 943 6.249951 GGAGACTATACATAGTGGGAGACAT 58.750 44.000 6.62 0.00 43.27 3.06
770 946 4.528596 ACTATACATAGTGGGAGACATGGC 59.471 45.833 0.00 0.00 41.77 4.40
777 956 4.530857 GGAGACATGGCGGGACCG 62.531 72.222 6.35 6.35 43.94 4.79
835 1021 4.725790 AAGAAAATATCCACTTGCCAGC 57.274 40.909 0.00 0.00 0.00 4.85
837 1023 4.088634 AGAAAATATCCACTTGCCAGCAA 58.911 39.130 4.78 4.78 0.00 3.91
865 1055 5.393068 AATATCCATTTCTCAAGAGGCCA 57.607 39.130 5.01 0.00 0.00 5.36
906 1096 5.707495 ACCACCTTCACCTTGGTTAATTAA 58.293 37.500 0.00 0.00 40.98 1.40
907 1097 6.319715 ACCACCTTCACCTTGGTTAATTAAT 58.680 36.000 0.31 0.00 40.98 1.40
908 1098 6.785466 ACCACCTTCACCTTGGTTAATTAATT 59.215 34.615 5.89 5.89 40.98 1.40
909 1099 7.951245 ACCACCTTCACCTTGGTTAATTAATTA 59.049 33.333 3.71 3.71 40.98 1.40
987 1178 4.381932 CCAAATCAAAGCTTCCCATACACC 60.382 45.833 0.00 0.00 0.00 4.16
988 1179 2.507407 TCAAAGCTTCCCATACACCC 57.493 50.000 0.00 0.00 0.00 4.61
989 1180 1.992557 TCAAAGCTTCCCATACACCCT 59.007 47.619 0.00 0.00 0.00 4.34
990 1181 2.094675 CAAAGCTTCCCATACACCCTG 58.905 52.381 0.00 0.00 0.00 4.45
1001 1194 8.694171 TTCCCATACACCCTGAATATACATAT 57.306 34.615 0.00 0.00 0.00 1.78
1002 1195 8.089625 TCCCATACACCCTGAATATACATATG 57.910 38.462 0.00 0.00 0.00 1.78
1093 1291 5.455612 CCTCCCACTTTTCCGCCTATAAATA 60.456 44.000 0.00 0.00 0.00 1.40
1148 1346 4.824515 ACCGCTCTCCCTCTCCCG 62.825 72.222 0.00 0.00 0.00 5.14
1152 1350 4.150454 CTCTCCCTCTCCCGGCCT 62.150 72.222 0.00 0.00 0.00 5.19
1230 1441 0.768221 TGAAGCCCCCTCACTTCACT 60.768 55.000 1.49 0.00 45.48 3.41
1236 1447 2.463441 CCCTCACTTCACTGGGGAA 58.537 57.895 0.00 0.00 39.42 3.97
1239 1450 0.671781 CTCACTTCACTGGGGAAGCG 60.672 60.000 11.96 3.63 46.48 4.68
1242 1453 3.551496 CTTCACTGGGGAAGCGGCA 62.551 63.158 1.45 0.00 38.01 5.69
1486 1697 0.322098 CTGGGGCCACACATAAACGA 60.322 55.000 1.54 0.00 0.00 3.85
1566 1785 7.548075 ACCTCAACAAAAATATGGACTAGTACG 59.452 37.037 0.00 0.00 0.00 3.67
1593 1812 0.108585 ATGTGGCCGTATGGACCATC 59.891 55.000 11.17 12.23 46.01 3.51
1670 1903 2.486472 AGAAGATGTGGTGCTTGAGG 57.514 50.000 0.00 0.00 0.00 3.86
1729 1975 2.725008 GGGAGATCTCGCCTGACG 59.275 66.667 25.34 0.00 45.62 4.35
1732 1978 2.043852 AGATCTCGCCTGACGGGT 60.044 61.111 1.33 0.00 44.96 5.28
1735 1981 1.079127 ATCTCGCCTGACGGGTTTG 60.079 57.895 1.33 0.00 44.96 2.93
1766 2012 2.418083 GGCCTATGGGTGTTGCTGC 61.418 63.158 0.00 0.00 34.45 5.25
1768 2014 1.304282 CCTATGGGTGTTGCTGCCT 59.696 57.895 0.00 0.00 0.00 4.75
1769 2015 1.033746 CCTATGGGTGTTGCTGCCTG 61.034 60.000 0.00 0.00 0.00 4.85
1770 2016 1.001020 TATGGGTGTTGCTGCCTGG 60.001 57.895 0.00 0.00 0.00 4.45
1873 2133 6.591448 TGTGAAAAGCTATGTGTGTATGAGAG 59.409 38.462 0.00 0.00 0.00 3.20
1874 2134 6.813649 GTGAAAAGCTATGTGTGTATGAGAGA 59.186 38.462 0.00 0.00 0.00 3.10
1886 2146 5.471797 TGTGTATGAGAGACTATGAGCTAGC 59.528 44.000 6.62 6.62 0.00 3.42
1892 2155 6.336566 TGAGAGACTATGAGCTAGCAAAAAG 58.663 40.000 18.83 11.18 0.00 2.27
1893 2156 6.071108 TGAGAGACTATGAGCTAGCAAAAAGT 60.071 38.462 18.83 14.34 0.00 2.66
1905 2168 5.335269 GCTAGCAAAAAGTTCTTCCTCCTTC 60.335 44.000 10.63 0.00 0.00 3.46
1911 2174 1.283321 AGTTCTTCCTCCTTCCCATGC 59.717 52.381 0.00 0.00 0.00 4.06
1917 2185 0.032813 CCTCCTTCCCATGCCATGTT 60.033 55.000 3.63 0.00 0.00 2.71
1919 2187 2.358090 CCTCCTTCCCATGCCATGTTTA 60.358 50.000 3.63 0.00 0.00 2.01
1937 2205 0.988832 TATCCGGTTGTTCCTTGCCT 59.011 50.000 0.00 0.00 0.00 4.75
1949 2217 2.306847 TCCTTGCCTTGTTGGTTTCTC 58.693 47.619 0.00 0.00 38.35 2.87
1962 2230 2.238521 GGTTTCTCCTGTGCATCCAAA 58.761 47.619 0.00 0.00 0.00 3.28
1963 2231 2.627699 GGTTTCTCCTGTGCATCCAAAA 59.372 45.455 0.00 0.00 0.00 2.44
1964 2232 3.259123 GGTTTCTCCTGTGCATCCAAAAT 59.741 43.478 0.00 0.00 0.00 1.82
1969 2237 2.752354 TCCTGTGCATCCAAAATAACCG 59.248 45.455 0.00 0.00 0.00 4.44
1990 2258 4.438200 CCGTGGTGTTAATTCCTGCAATAC 60.438 45.833 0.00 0.00 0.00 1.89
2038 2328 5.007724 GCTTAATTCTAGTATGTGGTGGTGC 59.992 44.000 0.00 0.00 0.00 5.01
2039 2329 4.844349 AATTCTAGTATGTGGTGGTGCT 57.156 40.909 0.00 0.00 0.00 4.40
2040 2330 5.950544 AATTCTAGTATGTGGTGGTGCTA 57.049 39.130 0.00 0.00 0.00 3.49
2041 2331 5.950544 ATTCTAGTATGTGGTGGTGCTAA 57.049 39.130 0.00 0.00 0.00 3.09
2042 2332 5.950544 TTCTAGTATGTGGTGGTGCTAAT 57.049 39.130 0.00 0.00 0.00 1.73
2043 2333 5.950544 TCTAGTATGTGGTGGTGCTAATT 57.049 39.130 0.00 0.00 0.00 1.40
2044 2334 6.308015 TCTAGTATGTGGTGGTGCTAATTT 57.692 37.500 0.00 0.00 0.00 1.82
2045 2335 7.426606 TCTAGTATGTGGTGGTGCTAATTTA 57.573 36.000 0.00 0.00 0.00 1.40
2046 2336 7.853299 TCTAGTATGTGGTGGTGCTAATTTAA 58.147 34.615 0.00 0.00 0.00 1.52
2047 2337 7.985184 TCTAGTATGTGGTGGTGCTAATTTAAG 59.015 37.037 0.00 0.00 0.00 1.85
2048 2338 6.481643 AGTATGTGGTGGTGCTAATTTAAGT 58.518 36.000 0.00 0.00 0.00 2.24
2049 2339 6.946009 AGTATGTGGTGGTGCTAATTTAAGTT 59.054 34.615 0.00 0.00 0.00 2.66
2050 2340 5.446143 TGTGGTGGTGCTAATTTAAGTTG 57.554 39.130 0.00 0.00 0.00 3.16
2051 2341 4.234574 GTGGTGGTGCTAATTTAAGTTGC 58.765 43.478 0.00 0.00 0.00 4.17
2052 2342 4.022329 GTGGTGGTGCTAATTTAAGTTGCT 60.022 41.667 0.63 0.00 0.00 3.91
2053 2343 4.022416 TGGTGGTGCTAATTTAAGTTGCTG 60.022 41.667 0.63 0.00 0.00 4.41
2054 2344 4.485163 GTGGTGCTAATTTAAGTTGCTGG 58.515 43.478 0.63 0.00 0.00 4.85
2055 2345 4.022329 GTGGTGCTAATTTAAGTTGCTGGT 60.022 41.667 0.63 0.00 0.00 4.00
2056 2346 4.022416 TGGTGCTAATTTAAGTTGCTGGTG 60.022 41.667 0.63 0.00 0.00 4.17
2057 2347 4.022329 GGTGCTAATTTAAGTTGCTGGTGT 60.022 41.667 0.63 0.00 0.00 4.16
2067 2357 2.573462 AGTTGCTGGTGTGACTATGGAT 59.427 45.455 0.00 0.00 0.00 3.41
2070 2360 2.292267 GCTGGTGTGACTATGGATTGG 58.708 52.381 0.00 0.00 0.00 3.16
2074 2364 3.197766 TGGTGTGACTATGGATTGGTCTC 59.802 47.826 0.00 0.00 0.00 3.36
2075 2365 3.432326 GGTGTGACTATGGATTGGTCTCC 60.432 52.174 0.00 0.00 35.74 3.71
2139 2435 4.166539 CCTGGATCCTAGTCATGGAAGAT 58.833 47.826 14.23 0.00 37.13 2.40
2141 2437 5.186797 CCTGGATCCTAGTCATGGAAGATAC 59.813 48.000 14.23 0.00 37.13 2.24
2143 2439 6.326161 TGGATCCTAGTCATGGAAGATACAT 58.674 40.000 14.23 0.00 37.13 2.29
2144 2440 6.212187 TGGATCCTAGTCATGGAAGATACATG 59.788 42.308 14.23 0.00 45.39 3.21
2145 2441 6.212388 GGATCCTAGTCATGGAAGATACATGT 59.788 42.308 3.84 2.69 44.57 3.21
2146 2442 7.256475 GGATCCTAGTCATGGAAGATACATGTT 60.256 40.741 2.30 0.00 44.57 2.71
2147 2443 6.820335 TCCTAGTCATGGAAGATACATGTTG 58.180 40.000 2.30 0.00 44.57 3.33
2148 2444 6.611236 TCCTAGTCATGGAAGATACATGTTGA 59.389 38.462 2.30 0.00 44.57 3.18
2149 2445 7.290948 TCCTAGTCATGGAAGATACATGTTGAT 59.709 37.037 2.30 0.00 44.57 2.57
2150 2446 7.387122 CCTAGTCATGGAAGATACATGTTGATG 59.613 40.741 2.30 0.00 44.57 3.07
2151 2447 6.892485 AGTCATGGAAGATACATGTTGATGA 58.108 36.000 2.30 0.00 44.57 2.92
2152 2448 7.515586 AGTCATGGAAGATACATGTTGATGAT 58.484 34.615 2.30 0.00 44.57 2.45
2153 2449 7.660617 AGTCATGGAAGATACATGTTGATGATC 59.339 37.037 2.30 0.00 44.57 2.92
2154 2450 6.938596 TCATGGAAGATACATGTTGATGATCC 59.061 38.462 2.30 5.94 44.57 3.36
2155 2451 6.251255 TGGAAGATACATGTTGATGATCCA 57.749 37.500 2.30 8.53 33.36 3.41
2156 2452 6.844829 TGGAAGATACATGTTGATGATCCAT 58.155 36.000 2.30 0.00 33.36 3.41
2157 2453 6.713450 TGGAAGATACATGTTGATGATCCATG 59.287 38.462 2.30 9.26 41.31 3.66
2158 2454 6.150641 GGAAGATACATGTTGATGATCCATGG 59.849 42.308 4.97 4.97 40.16 3.66
2159 2455 6.443995 AGATACATGTTGATGATCCATGGA 57.556 37.500 18.88 18.88 40.16 3.41
2160 2456 7.029053 AGATACATGTTGATGATCCATGGAT 57.971 36.000 27.66 27.66 41.67 3.41
2161 2457 6.884836 AGATACATGTTGATGATCCATGGATG 59.115 38.462 32.05 17.38 39.63 3.51
2165 2461 3.181437 TGTTGATGATCCATGGATGAGGG 60.181 47.826 32.05 0.00 34.60 4.30
2182 2478 2.948315 GAGGGAGTTCATCATGCTTTCC 59.052 50.000 0.00 0.00 0.00 3.13
2183 2479 2.579860 AGGGAGTTCATCATGCTTTCCT 59.420 45.455 0.00 0.00 0.00 3.36
2184 2480 2.686915 GGGAGTTCATCATGCTTTCCTG 59.313 50.000 0.00 0.00 0.00 3.86
2205 2501 2.507484 CTGCAAGGTCCAGATCACAAA 58.493 47.619 0.00 0.00 32.03 2.83
2232 2528 7.308782 GAGGGTACTCTTTGTCATATGTTTG 57.691 40.000 0.00 0.00 40.68 2.93
2233 2529 6.779860 AGGGTACTCTTTGTCATATGTTTGT 58.220 36.000 1.90 0.00 0.00 2.83
2234 2530 7.231467 AGGGTACTCTTTGTCATATGTTTGTT 58.769 34.615 1.90 0.00 0.00 2.83
2235 2531 7.724061 AGGGTACTCTTTGTCATATGTTTGTTT 59.276 33.333 1.90 0.00 0.00 2.83
2236 2532 7.807907 GGGTACTCTTTGTCATATGTTTGTTTG 59.192 37.037 1.90 0.00 0.00 2.93
2237 2533 8.349983 GGTACTCTTTGTCATATGTTTGTTTGT 58.650 33.333 1.90 0.00 0.00 2.83
2238 2534 9.730420 GTACTCTTTGTCATATGTTTGTTTGTT 57.270 29.630 1.90 0.00 0.00 2.83
2240 2536 9.086336 ACTCTTTGTCATATGTTTGTTTGTTTG 57.914 29.630 1.90 0.00 0.00 2.93
2241 2537 8.994429 TCTTTGTCATATGTTTGTTTGTTTGT 57.006 26.923 1.90 0.00 0.00 2.83
2242 2538 9.429359 TCTTTGTCATATGTTTGTTTGTTTGTT 57.571 25.926 1.90 0.00 0.00 2.83
2244 2540 9.817365 TTTGTCATATGTTTGTTTGTTTGTTTG 57.183 25.926 1.90 0.00 0.00 2.93
2320 2621 1.073284 GGTTGTTGGAGACCAGCCTTA 59.927 52.381 0.00 0.00 33.72 2.69
2426 2735 9.260002 AGGCAATAATTCACAAGTAAACAAAAG 57.740 29.630 0.00 0.00 0.00 2.27
2434 2743 7.931578 TCACAAGTAAACAAAAGAGAAGGAA 57.068 32.000 0.00 0.00 0.00 3.36
2471 2783 5.872070 AGACTTTGAATTCGATTCCTCTGTC 59.128 40.000 0.04 0.00 38.50 3.51
2472 2784 4.938226 ACTTTGAATTCGATTCCTCTGTCC 59.062 41.667 0.04 0.00 38.50 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.468153 GTCTCTTTCCCTCTCTGTGGTAAT 59.532 45.833 0.00 0.00 0.00 1.89
36 37 2.704190 TGTGGTCTCTTTCCCTCTCT 57.296 50.000 0.00 0.00 0.00 3.10
37 38 3.771577 TTTGTGGTCTCTTTCCCTCTC 57.228 47.619 0.00 0.00 0.00 3.20
105 116 8.169977 AGAAGCAGACACAAATGAAAGAATAA 57.830 30.769 0.00 0.00 0.00 1.40
107 118 6.567321 CGAGAAGCAGACACAAATGAAAGAAT 60.567 38.462 0.00 0.00 0.00 2.40
122 133 0.037882 CTGAGTTGCCGAGAAGCAGA 60.038 55.000 0.00 0.00 45.13 4.26
123 134 0.320247 ACTGAGTTGCCGAGAAGCAG 60.320 55.000 0.00 0.00 45.13 4.24
126 137 0.734253 CCGACTGAGTTGCCGAGAAG 60.734 60.000 0.00 0.00 0.00 2.85
127 138 1.176619 TCCGACTGAGTTGCCGAGAA 61.177 55.000 0.00 0.00 0.00 2.87
128 139 1.587043 CTCCGACTGAGTTGCCGAGA 61.587 60.000 0.00 0.00 36.27 4.04
143 154 3.380479 TTCTTGTTGTGAGTACCTCCG 57.620 47.619 0.00 0.00 0.00 4.63
150 161 8.522830 TCTTCTTTTCAATTTCTTGTTGTGAGT 58.477 29.630 0.00 0.00 33.87 3.41
158 169 8.876790 ACAAAGCTTCTTCTTTTCAATTTCTTG 58.123 29.630 0.00 0.00 34.31 3.02
163 174 6.473455 CGTCACAAAGCTTCTTCTTTTCAATT 59.527 34.615 0.00 0.00 34.31 2.32
164 175 5.973565 CGTCACAAAGCTTCTTCTTTTCAAT 59.026 36.000 0.00 0.00 34.31 2.57
170 181 2.872858 GTCCGTCACAAAGCTTCTTCTT 59.127 45.455 0.00 0.00 0.00 2.52
171 182 2.158957 TGTCCGTCACAAAGCTTCTTCT 60.159 45.455 0.00 0.00 29.30 2.85
172 183 2.210116 TGTCCGTCACAAAGCTTCTTC 58.790 47.619 0.00 0.00 29.30 2.87
288 299 3.627577 AGTTCCATTGACACAGACACAAC 59.372 43.478 0.00 0.00 0.00 3.32
292 459 3.476552 GGAAGTTCCATTGACACAGACA 58.523 45.455 17.44 0.00 36.28 3.41
301 468 2.029110 ACAATTGCGGGAAGTTCCATTG 60.029 45.455 23.33 22.66 38.64 2.82
302 469 2.029110 CACAATTGCGGGAAGTTCCATT 60.029 45.455 23.33 11.28 38.64 3.16
313 480 0.674581 TCTGGCTCTCACAATTGCGG 60.675 55.000 5.05 0.00 0.00 5.69
322 489 6.610830 AGAAGAAGAGATAAATCTGGCTCTCA 59.389 38.462 0.00 0.00 36.76 3.27
326 493 8.932610 TGATAAGAAGAAGAGATAAATCTGGCT 58.067 33.333 0.00 0.00 37.25 4.75
327 494 9.553064 TTGATAAGAAGAAGAGATAAATCTGGC 57.447 33.333 0.00 0.00 37.25 4.85
353 520 9.454859 AAGATCTCGGAGTAATTCTTTTTGAAT 57.545 29.630 4.69 0.00 46.49 2.57
354 521 8.848474 AAGATCTCGGAGTAATTCTTTTTGAA 57.152 30.769 4.69 0.00 39.24 2.69
355 522 8.314751 AGAAGATCTCGGAGTAATTCTTTTTGA 58.685 33.333 4.69 0.00 0.00 2.69
356 523 8.485976 AGAAGATCTCGGAGTAATTCTTTTTG 57.514 34.615 4.69 0.00 0.00 2.44
358 525 9.810545 CTAAGAAGATCTCGGAGTAATTCTTTT 57.189 33.333 24.53 14.20 36.96 2.27
359 526 8.973182 ACTAAGAAGATCTCGGAGTAATTCTTT 58.027 33.333 24.53 13.98 36.96 2.52
360 527 8.528044 ACTAAGAAGATCTCGGAGTAATTCTT 57.472 34.615 23.67 23.67 38.61 2.52
361 528 9.059260 GTACTAAGAAGATCTCGGAGTAATTCT 57.941 37.037 4.69 9.56 31.69 2.40
362 529 8.838365 TGTACTAAGAAGATCTCGGAGTAATTC 58.162 37.037 4.69 7.61 31.69 2.17
363 530 8.623030 GTGTACTAAGAAGATCTCGGAGTAATT 58.377 37.037 4.69 0.00 31.69 1.40
364 531 7.774157 TGTGTACTAAGAAGATCTCGGAGTAAT 59.226 37.037 4.69 0.00 31.69 1.89
365 532 7.108194 TGTGTACTAAGAAGATCTCGGAGTAA 58.892 38.462 4.69 0.00 31.69 2.24
366 533 6.647229 TGTGTACTAAGAAGATCTCGGAGTA 58.353 40.000 4.69 0.00 0.00 2.59
367 534 5.498393 TGTGTACTAAGAAGATCTCGGAGT 58.502 41.667 4.69 0.28 0.00 3.85
368 535 6.094325 ACTTGTGTACTAAGAAGATCTCGGAG 59.906 42.308 14.61 0.00 0.00 4.63
369 536 5.944599 ACTTGTGTACTAAGAAGATCTCGGA 59.055 40.000 14.61 0.00 0.00 4.55
370 537 6.094325 AGACTTGTGTACTAAGAAGATCTCGG 59.906 42.308 14.61 0.00 0.00 4.63
371 538 7.079182 AGACTTGTGTACTAAGAAGATCTCG 57.921 40.000 14.61 0.00 0.00 4.04
372 539 8.516234 TGAAGACTTGTGTACTAAGAAGATCTC 58.484 37.037 14.61 0.00 0.00 2.75
373 540 8.410673 TGAAGACTTGTGTACTAAGAAGATCT 57.589 34.615 14.61 0.00 0.00 2.75
374 541 9.646427 AATGAAGACTTGTGTACTAAGAAGATC 57.354 33.333 14.61 8.95 0.00 2.75
377 544 9.360093 CCTAATGAAGACTTGTGTACTAAGAAG 57.640 37.037 14.61 3.63 0.00 2.85
378 545 8.311836 CCCTAATGAAGACTTGTGTACTAAGAA 58.688 37.037 14.61 0.00 0.00 2.52
379 546 7.093465 CCCCTAATGAAGACTTGTGTACTAAGA 60.093 40.741 14.61 0.00 0.00 2.10
380 547 7.042335 CCCCTAATGAAGACTTGTGTACTAAG 58.958 42.308 0.00 8.34 0.00 2.18
381 548 6.727231 TCCCCTAATGAAGACTTGTGTACTAA 59.273 38.462 0.00 0.00 0.00 2.24
382 549 6.154021 GTCCCCTAATGAAGACTTGTGTACTA 59.846 42.308 0.00 0.00 0.00 1.82
383 550 5.046520 GTCCCCTAATGAAGACTTGTGTACT 60.047 44.000 0.00 0.00 0.00 2.73
384 551 5.176592 GTCCCCTAATGAAGACTTGTGTAC 58.823 45.833 0.00 0.00 0.00 2.90
385 552 4.224370 GGTCCCCTAATGAAGACTTGTGTA 59.776 45.833 0.00 0.00 0.00 2.90
386 553 3.009143 GGTCCCCTAATGAAGACTTGTGT 59.991 47.826 0.00 0.00 0.00 3.72
387 554 3.009033 TGGTCCCCTAATGAAGACTTGTG 59.991 47.826 0.00 0.00 0.00 3.33
388 555 3.256704 TGGTCCCCTAATGAAGACTTGT 58.743 45.455 0.00 0.00 0.00 3.16
389 556 4.019321 TCTTGGTCCCCTAATGAAGACTTG 60.019 45.833 0.00 0.00 0.00 3.16
390 557 4.175962 TCTTGGTCCCCTAATGAAGACTT 58.824 43.478 0.00 0.00 0.00 3.01
391 558 3.777522 CTCTTGGTCCCCTAATGAAGACT 59.222 47.826 0.00 0.00 0.00 3.24
392 559 3.519913 ACTCTTGGTCCCCTAATGAAGAC 59.480 47.826 0.00 0.00 0.00 3.01
393 560 3.803340 ACTCTTGGTCCCCTAATGAAGA 58.197 45.455 0.00 0.00 0.00 2.87
394 561 4.019321 TGAACTCTTGGTCCCCTAATGAAG 60.019 45.833 0.00 0.00 0.00 3.02
395 562 3.913799 TGAACTCTTGGTCCCCTAATGAA 59.086 43.478 0.00 0.00 0.00 2.57
396 563 3.519510 CTGAACTCTTGGTCCCCTAATGA 59.480 47.826 0.00 0.00 0.00 2.57
397 564 3.370953 CCTGAACTCTTGGTCCCCTAATG 60.371 52.174 0.00 0.00 0.00 1.90
398 565 2.846827 CCTGAACTCTTGGTCCCCTAAT 59.153 50.000 0.00 0.00 0.00 1.73
399 566 2.266279 CCTGAACTCTTGGTCCCCTAA 58.734 52.381 0.00 0.00 0.00 2.69
400 567 1.151413 ACCTGAACTCTTGGTCCCCTA 59.849 52.381 0.00 0.00 0.00 3.53
401 568 0.104409 ACCTGAACTCTTGGTCCCCT 60.104 55.000 0.00 0.00 0.00 4.79
402 569 0.325272 GACCTGAACTCTTGGTCCCC 59.675 60.000 0.00 0.00 43.10 4.81
403 570 3.938109 GACCTGAACTCTTGGTCCC 57.062 57.895 0.00 0.00 43.10 4.46
406 573 6.441088 AAATCTAAGACCTGAACTCTTGGT 57.559 37.500 0.00 0.00 36.70 3.67
407 574 7.878127 TGTTAAATCTAAGACCTGAACTCTTGG 59.122 37.037 0.00 0.00 0.00 3.61
408 575 8.713271 GTGTTAAATCTAAGACCTGAACTCTTG 58.287 37.037 0.00 0.00 0.00 3.02
409 576 8.652290 AGTGTTAAATCTAAGACCTGAACTCTT 58.348 33.333 0.00 0.00 32.88 2.85
410 577 8.091449 CAGTGTTAAATCTAAGACCTGAACTCT 58.909 37.037 0.00 0.00 32.88 3.24
411 578 8.088981 TCAGTGTTAAATCTAAGACCTGAACTC 58.911 37.037 0.00 0.00 32.88 3.01
412 579 7.963532 TCAGTGTTAAATCTAAGACCTGAACT 58.036 34.615 0.00 0.00 32.88 3.01
413 580 8.660373 CATCAGTGTTAAATCTAAGACCTGAAC 58.340 37.037 0.00 0.00 32.88 3.18
414 581 7.334421 GCATCAGTGTTAAATCTAAGACCTGAA 59.666 37.037 0.00 0.00 32.88 3.02
415 582 6.818644 GCATCAGTGTTAAATCTAAGACCTGA 59.181 38.462 0.00 0.00 32.88 3.86
416 583 6.820656 AGCATCAGTGTTAAATCTAAGACCTG 59.179 38.462 0.00 0.00 32.88 4.00
417 584 6.951971 AGCATCAGTGTTAAATCTAAGACCT 58.048 36.000 0.00 0.00 32.88 3.85
418 585 6.019479 CGAGCATCAGTGTTAAATCTAAGACC 60.019 42.308 0.00 0.00 32.88 3.85
419 586 6.508721 GCGAGCATCAGTGTTAAATCTAAGAC 60.509 42.308 0.00 0.00 32.67 3.01
420 587 5.520288 GCGAGCATCAGTGTTAAATCTAAGA 59.480 40.000 0.00 0.00 33.17 2.10
421 588 5.291858 TGCGAGCATCAGTGTTAAATCTAAG 59.708 40.000 0.00 0.00 33.17 2.18
422 589 5.175127 TGCGAGCATCAGTGTTAAATCTAA 58.825 37.500 0.00 0.00 33.17 2.10
427 594 4.764679 AAATGCGAGCATCAGTGTTAAA 57.235 36.364 11.26 0.00 35.31 1.52
434 601 2.182825 GCAAGAAAATGCGAGCATCAG 58.817 47.619 11.26 0.00 36.45 2.90
451 618 4.081531 CCTGAAGGCCTGAAATAAATGCAA 60.082 41.667 5.69 0.00 0.00 4.08
468 635 2.679837 ACTTAATGCACATCGCCTGAAG 59.320 45.455 0.00 0.00 41.33 3.02
472 639 1.382522 CCACTTAATGCACATCGCCT 58.617 50.000 0.00 0.00 41.33 5.52
482 649 3.611766 AACGTCTCCTCCCACTTAATG 57.388 47.619 0.00 0.00 0.00 1.90
483 650 4.041198 TGAAAACGTCTCCTCCCACTTAAT 59.959 41.667 0.00 0.00 0.00 1.40
486 653 1.766496 TGAAAACGTCTCCTCCCACTT 59.234 47.619 0.00 0.00 0.00 3.16
515 682 4.700365 GCCGCCACAAACGCCTTC 62.700 66.667 0.00 0.00 0.00 3.46
519 686 2.395367 TACAAAGCCGCCACAAACGC 62.395 55.000 0.00 0.00 0.00 4.84
520 687 0.029567 TTACAAAGCCGCCACAAACG 59.970 50.000 0.00 0.00 0.00 3.60
523 690 1.810151 GAGATTACAAAGCCGCCACAA 59.190 47.619 0.00 0.00 0.00 3.33
528 695 3.623060 TCATCTTGAGATTACAAAGCCGC 59.377 43.478 0.00 0.00 31.21 6.53
531 698 5.554636 CACGTCATCTTGAGATTACAAAGC 58.445 41.667 6.24 0.00 30.24 3.51
541 708 0.390866 AGCCAGCACGTCATCTTGAG 60.391 55.000 0.00 0.00 0.00 3.02
551 718 1.013005 CAAGAGACTGAGCCAGCACG 61.013 60.000 2.50 0.00 34.37 5.34
556 723 2.354503 GCATCTTCAAGAGACTGAGCCA 60.355 50.000 0.00 0.00 37.17 4.75
557 724 2.093553 AGCATCTTCAAGAGACTGAGCC 60.094 50.000 0.00 0.00 37.17 4.70
559 726 4.453177 TGAGCATCTTCAAGAGACTGAG 57.547 45.455 0.00 0.00 37.17 3.35
567 734 8.030692 CCTTCTATCTCTATGAGCATCTTCAAG 58.969 40.741 0.00 0.00 34.92 3.02
569 736 7.237255 TCCTTCTATCTCTATGAGCATCTTCA 58.763 38.462 0.00 0.00 34.92 3.02
574 741 8.612486 ATGAATCCTTCTATCTCTATGAGCAT 57.388 34.615 0.00 0.00 0.00 3.79
578 745 9.919416 CCTCTATGAATCCTTCTATCTCTATGA 57.081 37.037 0.00 0.00 0.00 2.15
584 751 7.451255 CACTCACCTCTATGAATCCTTCTATCT 59.549 40.741 0.00 0.00 0.00 1.98
586 753 7.301420 TCACTCACCTCTATGAATCCTTCTAT 58.699 38.462 0.00 0.00 0.00 1.98
590 757 6.590068 CATTCACTCACCTCTATGAATCCTT 58.410 40.000 0.00 0.00 39.25 3.36
591 758 5.454471 GCATTCACTCACCTCTATGAATCCT 60.454 44.000 0.00 0.00 39.25 3.24
592 759 4.754114 GCATTCACTCACCTCTATGAATCC 59.246 45.833 0.00 0.00 39.25 3.01
593 760 5.609423 AGCATTCACTCACCTCTATGAATC 58.391 41.667 0.00 0.00 39.25 2.52
594 761 5.129980 TGAGCATTCACTCACCTCTATGAAT 59.870 40.000 0.00 0.00 41.72 2.57
615 789 2.034254 CGAAGTTGCTCGCATACATGAG 60.034 50.000 0.00 0.00 35.30 2.90
616 790 1.926510 CGAAGTTGCTCGCATACATGA 59.073 47.619 0.00 0.00 31.04 3.07
617 791 1.926510 TCGAAGTTGCTCGCATACATG 59.073 47.619 0.00 0.00 38.73 3.21
618 792 2.293677 TCGAAGTTGCTCGCATACAT 57.706 45.000 0.00 0.00 38.73 2.29
619 793 2.293677 ATCGAAGTTGCTCGCATACA 57.706 45.000 0.00 0.00 38.73 2.29
621 795 2.616960 ACAATCGAAGTTGCTCGCATA 58.383 42.857 0.00 0.00 38.73 3.14
622 796 1.442769 ACAATCGAAGTTGCTCGCAT 58.557 45.000 0.00 0.00 38.73 4.73
624 798 1.060698 GGTACAATCGAAGTTGCTCGC 59.939 52.381 0.00 0.00 38.73 5.03
625 799 1.320555 CGGTACAATCGAAGTTGCTCG 59.679 52.381 0.00 0.00 40.25 5.03
628 802 1.796459 ACACGGTACAATCGAAGTTGC 59.204 47.619 0.00 0.00 32.32 4.17
629 803 5.579384 TTAACACGGTACAATCGAAGTTG 57.421 39.130 0.00 0.00 34.01 3.16
631 805 7.887996 TTATTTAACACGGTACAATCGAAGT 57.112 32.000 0.00 0.00 0.00 3.01
632 806 9.043678 GTTTTATTTAACACGGTACAATCGAAG 57.956 33.333 0.00 0.00 0.00 3.79
633 807 8.772705 AGTTTTATTTAACACGGTACAATCGAA 58.227 29.630 0.00 0.00 0.00 3.71
636 810 9.977762 CCTAGTTTTATTTAACACGGTACAATC 57.022 33.333 0.00 0.00 0.00 2.67
637 811 9.723601 TCCTAGTTTTATTTAACACGGTACAAT 57.276 29.630 0.00 0.00 0.00 2.71
640 814 8.763049 AGTCCTAGTTTTATTTAACACGGTAC 57.237 34.615 0.00 0.00 0.00 3.34
642 816 9.591792 GATAGTCCTAGTTTTATTTAACACGGT 57.408 33.333 0.00 0.00 0.00 4.83
643 817 9.590451 TGATAGTCCTAGTTTTATTTAACACGG 57.410 33.333 0.00 0.00 0.00 4.94
650 824 9.771534 GAGAGCATGATAGTCCTAGTTTTATTT 57.228 33.333 0.00 0.00 0.00 1.40
651 825 9.153479 AGAGAGCATGATAGTCCTAGTTTTATT 57.847 33.333 0.00 0.00 0.00 1.40
652 826 8.719645 AGAGAGCATGATAGTCCTAGTTTTAT 57.280 34.615 0.00 0.00 0.00 1.40
653 827 8.417106 CAAGAGAGCATGATAGTCCTAGTTTTA 58.583 37.037 0.00 0.00 0.00 1.52
667 841 0.401356 TTGCACCCAAGAGAGCATGA 59.599 50.000 0.00 0.00 36.80 3.07
669 843 0.403271 AGTTGCACCCAAGAGAGCAT 59.597 50.000 0.00 0.00 36.80 3.79
670 844 0.183492 AAGTTGCACCCAAGAGAGCA 59.817 50.000 0.00 0.00 34.79 4.26
677 851 2.630580 GGTAATCCAAAGTTGCACCCAA 59.369 45.455 0.00 0.00 0.00 4.12
680 854 1.201414 CCGGTAATCCAAAGTTGCACC 59.799 52.381 0.00 0.00 0.00 5.01
708 884 1.743394 GCCATGTCCTTTTAGTTCGGG 59.257 52.381 0.00 0.00 0.00 5.14
709 885 2.432444 TGCCATGTCCTTTTAGTTCGG 58.568 47.619 0.00 0.00 0.00 4.30
710 886 4.701956 ATTGCCATGTCCTTTTAGTTCG 57.298 40.909 0.00 0.00 0.00 3.95
753 929 0.250038 CCGCCATGTCTCCCACTATG 60.250 60.000 0.00 0.00 0.00 2.23
770 946 2.029369 TTGTTCGTTCCGGTCCCG 59.971 61.111 0.00 2.24 39.44 5.14
777 956 4.365899 AAAGGAAAGTGTTGTTCGTTCC 57.634 40.909 0.00 0.00 41.38 3.62
854 1044 0.676151 GCTCTTGGTGGCCTCTTGAG 60.676 60.000 3.32 10.53 0.00 3.02
865 1055 1.074775 TTGCCCGATTGCTCTTGGT 59.925 52.632 0.00 0.00 0.00 3.67
906 1096 2.043980 CAGCGGGGGCGTTGTTAAT 61.044 57.895 0.00 0.00 0.00 1.40
907 1097 2.670251 CAGCGGGGGCGTTGTTAA 60.670 61.111 0.00 0.00 0.00 2.01
908 1098 3.627952 TCAGCGGGGGCGTTGTTA 61.628 61.111 0.00 0.00 0.00 2.41
987 1178 5.237815 ACACGCACCATATGTATATTCAGG 58.762 41.667 1.24 0.00 0.00 3.86
988 1179 6.035005 GCTACACGCACCATATGTATATTCAG 59.965 42.308 1.24 0.00 38.92 3.02
989 1180 5.867174 GCTACACGCACCATATGTATATTCA 59.133 40.000 1.24 0.00 38.92 2.57
990 1181 6.100004 AGCTACACGCACCATATGTATATTC 58.900 40.000 1.24 0.00 42.61 1.75
1001 1194 1.411246 CCCTAATAGCTACACGCACCA 59.589 52.381 0.00 0.00 42.61 4.17
1002 1195 1.411612 ACCCTAATAGCTACACGCACC 59.588 52.381 0.00 0.00 42.61 5.01
1070 1264 3.553828 TTATAGGCGGAAAAGTGGGAG 57.446 47.619 0.00 0.00 0.00 4.30
1071 1265 4.513406 ATTTATAGGCGGAAAAGTGGGA 57.487 40.909 0.00 0.00 0.00 4.37
1072 1266 4.517832 GGTATTTATAGGCGGAAAAGTGGG 59.482 45.833 0.00 0.00 0.00 4.61
1075 1273 5.128205 GGTGGTATTTATAGGCGGAAAAGT 58.872 41.667 0.00 0.00 0.00 2.66
1148 1346 2.595463 TGCTTGTGAGTGCAGGCC 60.595 61.111 0.00 0.00 40.20 5.19
1152 1350 2.974148 CCGCTGCTTGTGAGTGCA 60.974 61.111 0.00 0.00 37.63 4.57
1157 1361 3.043713 CTTCGCCGCTGCTTGTGA 61.044 61.111 0.00 0.00 34.43 3.58
1486 1697 0.248621 GTGCGTGCACTTGCTTTTCT 60.249 50.000 17.32 0.00 43.12 2.52
1516 1731 2.123248 TTGCAGATCCGGCCAAGACA 62.123 55.000 2.24 0.00 0.00 3.41
1517 1732 0.749454 ATTGCAGATCCGGCCAAGAC 60.749 55.000 2.24 0.00 0.00 3.01
1518 1733 0.034186 AATTGCAGATCCGGCCAAGA 60.034 50.000 2.24 0.00 0.00 3.02
1519 1734 0.101759 CAATTGCAGATCCGGCCAAG 59.898 55.000 2.24 0.00 0.00 3.61
1520 1735 1.947597 GCAATTGCAGATCCGGCCAA 61.948 55.000 25.36 0.00 41.59 4.52
1566 1785 6.041182 TGGTCCATACGGCCACATATATATAC 59.959 42.308 2.24 0.00 34.66 1.47
1670 1903 8.099364 TCTCCAAGAGAAACATGAACAAATAC 57.901 34.615 0.00 0.00 35.59 1.89
1725 1967 3.569194 ATATATGCACCAAACCCGTCA 57.431 42.857 0.00 0.00 0.00 4.35
1726 1968 4.394920 CCATATATATGCACCAAACCCGTC 59.605 45.833 16.08 0.00 32.40 4.79
1727 1969 4.331968 CCATATATATGCACCAAACCCGT 58.668 43.478 16.08 0.00 32.40 5.28
1728 1970 3.128589 GCCATATATATGCACCAAACCCG 59.871 47.826 16.08 1.51 32.40 5.28
1729 1975 3.447229 GGCCATATATATGCACCAAACCC 59.553 47.826 20.26 7.59 32.08 4.11
1732 1978 6.128486 CCATAGGCCATATATATGCACCAAA 58.872 40.000 24.17 16.49 33.38 3.28
1735 1981 4.104738 ACCCATAGGCCATATATATGCACC 59.895 45.833 16.08 17.55 36.11 5.01
1768 2014 4.577677 TGCAGCTTCAACCGGCCA 62.578 61.111 0.00 0.00 0.00 5.36
1769 2015 3.741476 CTGCAGCTTCAACCGGCC 61.741 66.667 0.00 0.00 0.00 6.13
1770 2016 4.410743 GCTGCAGCTTCAACCGGC 62.411 66.667 31.33 0.78 38.21 6.13
1832 2092 2.540383 TCACAGGCTCTTGGTACAGAT 58.460 47.619 0.00 0.00 42.39 2.90
1873 2133 6.976636 AGAACTTTTTGCTAGCTCATAGTC 57.023 37.500 17.23 5.57 33.65 2.59
1874 2134 6.372937 GGAAGAACTTTTTGCTAGCTCATAGT 59.627 38.462 17.23 11.21 33.65 2.12
1886 2146 4.215109 TGGGAAGGAGGAAGAACTTTTTG 58.785 43.478 0.00 0.00 0.00 2.44
1892 2155 1.683319 GGCATGGGAAGGAGGAAGAAC 60.683 57.143 0.00 0.00 0.00 3.01
1893 2156 0.625849 GGCATGGGAAGGAGGAAGAA 59.374 55.000 0.00 0.00 0.00 2.52
1905 2168 0.961019 CCGGATAAACATGGCATGGG 59.039 55.000 29.49 15.96 33.60 4.00
1911 2174 3.352648 AGGAACAACCGGATAAACATGG 58.647 45.455 9.46 0.00 44.74 3.66
1917 2185 1.353022 AGGCAAGGAACAACCGGATAA 59.647 47.619 9.46 0.00 44.74 1.75
1919 2187 0.112412 AAGGCAAGGAACAACCGGAT 59.888 50.000 9.46 0.00 44.74 4.18
1937 2205 2.136298 TGCACAGGAGAAACCAACAA 57.864 45.000 0.00 0.00 42.04 2.83
1949 2217 2.491693 ACGGTTATTTTGGATGCACAGG 59.508 45.455 0.00 0.00 0.00 4.00
1962 2230 4.157105 GCAGGAATTAACACCACGGTTATT 59.843 41.667 3.18 0.00 33.56 1.40
1963 2231 3.692593 GCAGGAATTAACACCACGGTTAT 59.307 43.478 3.18 0.00 33.56 1.89
1964 2232 3.075884 GCAGGAATTAACACCACGGTTA 58.924 45.455 3.18 0.00 32.29 2.85
1969 2237 4.658071 CGTATTGCAGGAATTAACACCAC 58.342 43.478 0.00 0.00 0.00 4.16
1990 2258 1.743252 GGCTGGTTCTTCCTCTGCG 60.743 63.158 0.00 0.00 37.07 5.18
2038 2328 6.560253 AGTCACACCAGCAACTTAAATTAG 57.440 37.500 0.00 0.00 0.00 1.73
2039 2329 7.120579 CCATAGTCACACCAGCAACTTAAATTA 59.879 37.037 0.00 0.00 0.00 1.40
2040 2330 6.071952 CCATAGTCACACCAGCAACTTAAATT 60.072 38.462 0.00 0.00 0.00 1.82
2041 2331 5.415701 CCATAGTCACACCAGCAACTTAAAT 59.584 40.000 0.00 0.00 0.00 1.40
2042 2332 4.759693 CCATAGTCACACCAGCAACTTAAA 59.240 41.667 0.00 0.00 0.00 1.52
2043 2333 4.041075 TCCATAGTCACACCAGCAACTTAA 59.959 41.667 0.00 0.00 0.00 1.85
2044 2334 3.580895 TCCATAGTCACACCAGCAACTTA 59.419 43.478 0.00 0.00 0.00 2.24
2045 2335 2.371841 TCCATAGTCACACCAGCAACTT 59.628 45.455 0.00 0.00 0.00 2.66
2046 2336 1.977854 TCCATAGTCACACCAGCAACT 59.022 47.619 0.00 0.00 0.00 3.16
2047 2337 2.472695 TCCATAGTCACACCAGCAAC 57.527 50.000 0.00 0.00 0.00 4.17
2048 2338 3.346315 CAATCCATAGTCACACCAGCAA 58.654 45.455 0.00 0.00 0.00 3.91
2049 2339 2.356022 CCAATCCATAGTCACACCAGCA 60.356 50.000 0.00 0.00 0.00 4.41
2050 2340 2.292267 CCAATCCATAGTCACACCAGC 58.708 52.381 0.00 0.00 0.00 4.85
2051 2341 3.198635 AGACCAATCCATAGTCACACCAG 59.801 47.826 0.00 0.00 32.82 4.00
2052 2342 3.181329 AGACCAATCCATAGTCACACCA 58.819 45.455 0.00 0.00 32.82 4.17
2053 2343 3.432326 GGAGACCAATCCATAGTCACACC 60.432 52.174 0.00 0.00 39.34 4.16
2054 2344 3.798202 GGAGACCAATCCATAGTCACAC 58.202 50.000 0.00 0.00 39.34 3.82
2070 2360 6.317391 CAGATCAAAAGGACATAAAGGGAGAC 59.683 42.308 0.00 0.00 0.00 3.36
2074 2364 5.509498 TCCAGATCAAAAGGACATAAAGGG 58.491 41.667 0.00 0.00 0.00 3.95
2075 2365 7.466746 TTTCCAGATCAAAAGGACATAAAGG 57.533 36.000 0.00 0.00 0.00 3.11
2127 2423 6.892485 TCATCAACATGTATCTTCCATGACT 58.108 36.000 0.00 0.00 41.78 3.41
2139 2435 6.190346 TCATCCATGGATCATCAACATGTA 57.810 37.500 24.93 0.04 40.16 2.29
2141 2437 4.459337 CCTCATCCATGGATCATCAACATG 59.541 45.833 24.93 11.84 41.15 3.21
2143 2439 3.181437 CCCTCATCCATGGATCATCAACA 60.181 47.826 24.93 0.00 31.62 3.33
2144 2440 3.073503 TCCCTCATCCATGGATCATCAAC 59.926 47.826 24.93 0.00 31.62 3.18
2145 2441 3.329277 TCCCTCATCCATGGATCATCAA 58.671 45.455 24.93 7.83 31.62 2.57
2146 2442 2.910977 CTCCCTCATCCATGGATCATCA 59.089 50.000 24.93 8.02 31.62 3.07
2147 2443 2.911636 ACTCCCTCATCCATGGATCATC 59.088 50.000 24.93 0.00 31.62 2.92
2148 2444 3.001325 ACTCCCTCATCCATGGATCAT 57.999 47.619 24.93 1.68 31.62 2.45
2149 2445 2.502068 ACTCCCTCATCCATGGATCA 57.498 50.000 24.93 11.85 31.62 2.92
2150 2446 2.707791 TGAACTCCCTCATCCATGGATC 59.292 50.000 24.93 11.50 31.62 3.36
2151 2447 2.780414 TGAACTCCCTCATCCATGGAT 58.220 47.619 22.15 22.15 34.81 3.41
2152 2448 2.268796 TGAACTCCCTCATCCATGGA 57.731 50.000 18.88 18.88 0.00 3.41
2153 2449 3.137446 GATGAACTCCCTCATCCATGG 57.863 52.381 4.97 4.97 44.01 3.66
2159 2455 3.947612 AAGCATGATGAACTCCCTCAT 57.052 42.857 0.00 0.00 38.79 2.90
2160 2456 3.614092 GAAAGCATGATGAACTCCCTCA 58.386 45.455 0.00 0.00 0.00 3.86
2161 2457 2.948315 GGAAAGCATGATGAACTCCCTC 59.052 50.000 0.00 0.00 0.00 4.30
2165 2461 3.015327 AGCAGGAAAGCATGATGAACTC 58.985 45.455 0.00 0.00 36.85 3.01
2182 2478 0.035725 TGATCTGGACCTTGCAGCAG 60.036 55.000 0.00 0.00 35.65 4.24
2183 2479 0.321919 GTGATCTGGACCTTGCAGCA 60.322 55.000 0.00 0.00 35.65 4.41
2184 2480 0.321919 TGTGATCTGGACCTTGCAGC 60.322 55.000 0.00 0.00 35.65 5.25
2229 2525 6.852664 ACAACCAAACAAACAAACAAACAAA 58.147 28.000 0.00 0.00 0.00 2.83
2230 2526 6.436843 ACAACCAAACAAACAAACAAACAA 57.563 29.167 0.00 0.00 0.00 2.83
2231 2527 6.128007 ACAACAACCAAACAAACAAACAAACA 60.128 30.769 0.00 0.00 0.00 2.83
2232 2528 6.195428 CACAACAACCAAACAAACAAACAAAC 59.805 34.615 0.00 0.00 0.00 2.93
2233 2529 6.128007 ACACAACAACCAAACAAACAAACAAA 60.128 30.769 0.00 0.00 0.00 2.83
2234 2530 5.354234 ACACAACAACCAAACAAACAAACAA 59.646 32.000 0.00 0.00 0.00 2.83
2235 2531 4.876107 ACACAACAACCAAACAAACAAACA 59.124 33.333 0.00 0.00 0.00 2.83
2236 2532 5.006746 TCACACAACAACCAAACAAACAAAC 59.993 36.000 0.00 0.00 0.00 2.93
2237 2533 5.116180 TCACACAACAACCAAACAAACAAA 58.884 33.333 0.00 0.00 0.00 2.83
2238 2534 4.693283 TCACACAACAACCAAACAAACAA 58.307 34.783 0.00 0.00 0.00 2.83
2239 2535 4.038042 TCTCACACAACAACCAAACAAACA 59.962 37.500 0.00 0.00 0.00 2.83
2240 2536 4.551388 TCTCACACAACAACCAAACAAAC 58.449 39.130 0.00 0.00 0.00 2.93
2241 2537 4.804108 CTCTCACACAACAACCAAACAAA 58.196 39.130 0.00 0.00 0.00 2.83
2242 2538 3.366883 GCTCTCACACAACAACCAAACAA 60.367 43.478 0.00 0.00 0.00 2.83
2243 2539 2.163412 GCTCTCACACAACAACCAAACA 59.837 45.455 0.00 0.00 0.00 2.83
2244 2540 2.163412 TGCTCTCACACAACAACCAAAC 59.837 45.455 0.00 0.00 0.00 2.93
2320 2621 5.518848 TTGATGAGCATGTTTCACAGTTT 57.481 34.783 4.50 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.