Multiple sequence alignment - TraesCS1A01G096000

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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 TraesCS1A01G096000 chr1A 100.000 5157 0 0 1 5157 91498073 91503229 0.000000e+00 9524.0
1 TraesCS1A01G096000 chr1A 79.433 282 45 7 827 1107 91470011 91470280 2.450000e-43 187.0
2 TraesCS1A01G096000 chr1A 97.674 43 1 0 2234 2276 276972126 276972168 1.990000e-09 75.0
3 TraesCS1A01G096000 chr1B 89.667 2342 140 45 912 3212 156598936 156596656 0.000000e+00 2891.0
4 TraesCS1A01G096000 chr1B 86.855 1377 92 39 626 1964 156599214 156597889 0.000000e+00 1458.0
5 TraesCS1A01G096000 chr1B 92.282 907 29 8 3601 4468 156595918 156595014 0.000000e+00 1249.0
6 TraesCS1A01G096000 chr1B 92.530 656 33 7 3204 3845 156596572 156595919 0.000000e+00 926.0
7 TraesCS1A01G096000 chr1B 89.884 692 42 7 4488 5155 156594618 156593931 0.000000e+00 865.0
8 TraesCS1A01G096000 chr1B 82.414 290 39 7 819 1107 156602457 156602179 5.160000e-60 243.0
9 TraesCS1A01G096000 chr1D 92.590 1201 55 9 786 1964 96915248 96916436 0.000000e+00 1694.0
10 TraesCS1A01G096000 chr1D 90.925 1146 45 17 2092 3212 96916661 96917772 0.000000e+00 1485.0
11 TraesCS1A01G096000 chr1D 92.453 848 34 4 3651 4468 96920030 96920877 0.000000e+00 1184.0
12 TraesCS1A01G096000 chr1D 91.038 703 33 11 4478 5156 96923792 96923096 0.000000e+00 922.0
13 TraesCS1A01G096000 chr1D 93.860 456 22 3 3204 3654 96917871 96918325 0.000000e+00 682.0
14 TraesCS1A01G096000 chr1D 82.095 296 42 4 813 1107 96908295 96908580 5.160000e-60 243.0
15 TraesCS1A01G096000 chr1D 91.228 171 10 3 1927 2093 96916368 96916537 1.440000e-55 228.0
16 TraesCS1A01G096000 chr1D 97.674 43 1 0 2234 2276 216332773 216332815 1.990000e-09 75.0
17 TraesCS1A01G096000 chrUn 92.022 539 37 6 4 537 260712583 260712046 0.000000e+00 752.0
18 TraesCS1A01G096000 chrUn 90.858 536 42 7 4 536 362187384 362186853 0.000000e+00 712.0
19 TraesCS1A01G096000 chr5A 91.651 539 39 5 5 539 296306514 296307050 0.000000e+00 741.0
20 TraesCS1A01G096000 chr7A 91.215 535 43 4 5 536 7144506 7145039 0.000000e+00 725.0
21 TraesCS1A01G096000 chr7A 91.111 540 40 6 4 538 712206995 712206459 0.000000e+00 725.0
22 TraesCS1A01G096000 chr3D 91.078 538 43 5 3 538 566071520 566070986 0.000000e+00 723.0
23 TraesCS1A01G096000 chr3D 85.057 87 8 4 2193 2275 250931572 250931487 3.310000e-12 84.2
24 TraesCS1A01G096000 chr5D 90.875 537 43 5 5 538 170318403 170318936 0.000000e+00 715.0
25 TraesCS1A01G096000 chr5D 90.476 546 46 6 5 544 443784176 443783631 0.000000e+00 715.0
26 TraesCS1A01G096000 chr2D 90.758 541 41 9 1 539 590061680 590062213 0.000000e+00 713.0
27 TraesCS1A01G096000 chr6B 85.714 77 6 4 2193 2269 255522278 255522207 5.540000e-10 76.8
28 TraesCS1A01G096000 chr6A 84.615 78 10 2 2193 2269 301951289 301951365 5.540000e-10 76.8
29 TraesCS1A01G096000 chr4D 81.522 92 8 6 2193 2276 365838504 365838414 3.330000e-07 67.6
30 TraesCS1A01G096000 chr7D 82.895 76 7 5 2193 2268 263524184 263524253 4.310000e-06 63.9


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 TraesCS1A01G096000 chr1A 91498073 91503229 5156 False 9524.0 9524 100.000000 1 5157 1 chr1A.!!$F2 5156
1 TraesCS1A01G096000 chr1B 156593931 156602457 8526 True 1272.0 2891 88.938667 626 5155 6 chr1B.!!$R1 4529
2 TraesCS1A01G096000 chr1D 96915248 96920877 5629 False 1054.6 1694 92.211200 786 4468 5 chr1D.!!$F3 3682
3 TraesCS1A01G096000 chr1D 96923096 96923792 696 True 922.0 922 91.038000 4478 5156 1 chr1D.!!$R1 678
4 TraesCS1A01G096000 chrUn 260712046 260712583 537 True 752.0 752 92.022000 4 537 1 chrUn.!!$R1 533
5 TraesCS1A01G096000 chrUn 362186853 362187384 531 True 712.0 712 90.858000 4 536 1 chrUn.!!$R2 532
6 TraesCS1A01G096000 chr5A 296306514 296307050 536 False 741.0 741 91.651000 5 539 1 chr5A.!!$F1 534
7 TraesCS1A01G096000 chr7A 7144506 7145039 533 False 725.0 725 91.215000 5 536 1 chr7A.!!$F1 531
8 TraesCS1A01G096000 chr7A 712206459 712206995 536 True 725.0 725 91.111000 4 538 1 chr7A.!!$R1 534
9 TraesCS1A01G096000 chr3D 566070986 566071520 534 True 723.0 723 91.078000 3 538 1 chr3D.!!$R2 535
10 TraesCS1A01G096000 chr5D 170318403 170318936 533 False 715.0 715 90.875000 5 538 1 chr5D.!!$F1 533
11 TraesCS1A01G096000 chr5D 443783631 443784176 545 True 715.0 715 90.476000 5 544 1 chr5D.!!$R1 539
12 TraesCS1A01G096000 chr2D 590061680 590062213 533 False 713.0 713 90.758000 1 539 1 chr2D.!!$F1 538

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
617 631 0.037882 TTCAGAGCAGCGACTTCAGG 60.038 55.0 0.0 0.0 0.00 3.86 F
1440 4103 0.249489 CGGTCTGCTTAATCCGAGGG 60.249 60.0 0.0 0.0 44.86 4.30 F
2233 5028 0.250295 AGCTTGTTGTGCTTAGCGGA 60.250 50.0 0.0 0.0 37.52 5.54 F
3596 6538 0.746063 TCCTGCCTGCTGTTTTGTTG 59.254 50.0 0.0 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2563 5358 1.314730 GGGTATGCACATTAACCGGG 58.685 55.0 6.32 0.0 32.53 5.73 R
3313 6249 0.441921 GCTCACGCTTCTGCTTCTTC 59.558 55.0 0.00 0.0 36.97 2.87 R
3792 8708 0.321564 CGTGGAAAGATGCCCAGTCA 60.322 55.0 0.00 0.0 32.28 3.41 R
4697 10025 2.737252 GCAGCGAGGCATATAACTTACC 59.263 50.0 0.00 0.0 0.00 2.85 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
277 286 2.078392 GCCCTGTTATTTTCGTCCGAA 58.922 47.619 0.00 0.00 0.00 4.30
539 553 8.302515 AGTACTCCTTAATTAGTGATTTCGGA 57.697 34.615 0.00 0.00 0.00 4.55
540 554 8.414778 AGTACTCCTTAATTAGTGATTTCGGAG 58.585 37.037 16.68 16.68 42.61 4.63
541 555 7.184067 ACTCCTTAATTAGTGATTTCGGAGT 57.816 36.000 17.55 17.55 43.71 3.85
543 557 7.764901 ACTCCTTAATTAGTGATTTCGGAGTTC 59.235 37.037 17.55 0.00 44.81 3.01
544 558 7.848128 TCCTTAATTAGTGATTTCGGAGTTCT 58.152 34.615 0.00 0.00 0.00 3.01
545 559 7.764443 TCCTTAATTAGTGATTTCGGAGTTCTG 59.236 37.037 0.00 0.00 0.00 3.02
546 560 7.011482 CCTTAATTAGTGATTTCGGAGTTCTGG 59.989 40.741 0.00 0.00 0.00 3.86
548 562 3.320673 AGTGATTTCGGAGTTCTGGTC 57.679 47.619 0.00 0.00 0.00 4.02
551 565 3.433615 GTGATTTCGGAGTTCTGGTCTTG 59.566 47.826 0.00 0.00 0.00 3.02
552 566 1.878953 TTTCGGAGTTCTGGTCTTGC 58.121 50.000 0.00 0.00 0.00 4.01
554 568 1.919240 TCGGAGTTCTGGTCTTGCTA 58.081 50.000 0.00 0.00 0.00 3.49
555 569 1.544691 TCGGAGTTCTGGTCTTGCTAC 59.455 52.381 0.00 0.00 0.00 3.58
557 571 2.288825 CGGAGTTCTGGTCTTGCTACAA 60.289 50.000 0.00 0.00 0.00 2.41
558 572 3.617531 CGGAGTTCTGGTCTTGCTACAAT 60.618 47.826 0.00 0.00 0.00 2.71
559 573 3.686726 GGAGTTCTGGTCTTGCTACAATG 59.313 47.826 0.00 0.00 0.00 2.82
560 574 3.077359 AGTTCTGGTCTTGCTACAATGC 58.923 45.455 0.00 0.00 0.00 3.56
561 575 2.113860 TCTGGTCTTGCTACAATGCC 57.886 50.000 0.00 0.00 0.00 4.40
563 577 0.323360 TGGTCTTGCTACAATGCCCC 60.323 55.000 0.00 0.00 0.00 5.80
564 578 0.323360 GGTCTTGCTACAATGCCCCA 60.323 55.000 0.00 0.00 0.00 4.96
565 579 1.098050 GTCTTGCTACAATGCCCCAG 58.902 55.000 0.00 0.00 0.00 4.45
566 580 0.991146 TCTTGCTACAATGCCCCAGA 59.009 50.000 0.00 0.00 0.00 3.86
567 581 1.565759 TCTTGCTACAATGCCCCAGAT 59.434 47.619 0.00 0.00 0.00 2.90
568 582 1.679680 CTTGCTACAATGCCCCAGATG 59.320 52.381 0.00 0.00 0.00 2.90
570 584 1.005805 TGCTACAATGCCCCAGATGTT 59.994 47.619 0.00 0.00 0.00 2.71
571 585 2.102578 GCTACAATGCCCCAGATGTTT 58.897 47.619 0.00 0.00 0.00 2.83
572 586 2.099756 GCTACAATGCCCCAGATGTTTC 59.900 50.000 0.00 0.00 0.00 2.78
573 587 2.307496 ACAATGCCCCAGATGTTTCA 57.693 45.000 0.00 0.00 0.00 2.69
574 588 2.173519 ACAATGCCCCAGATGTTTCAG 58.826 47.619 0.00 0.00 0.00 3.02
575 589 2.225091 ACAATGCCCCAGATGTTTCAGA 60.225 45.455 0.00 0.00 0.00 3.27
576 590 2.426024 CAATGCCCCAGATGTTTCAGAG 59.574 50.000 0.00 0.00 0.00 3.35
577 591 0.322816 TGCCCCAGATGTTTCAGAGC 60.323 55.000 0.00 0.00 0.00 4.09
578 592 0.322816 GCCCCAGATGTTTCAGAGCA 60.323 55.000 0.00 0.00 0.00 4.26
579 593 1.887956 GCCCCAGATGTTTCAGAGCAA 60.888 52.381 0.00 0.00 0.00 3.91
580 594 1.815003 CCCCAGATGTTTCAGAGCAAC 59.185 52.381 0.00 0.00 0.00 4.17
581 595 2.507484 CCCAGATGTTTCAGAGCAACA 58.493 47.619 0.00 0.00 38.49 3.33
582 596 2.227388 CCCAGATGTTTCAGAGCAACAC 59.773 50.000 0.00 0.00 36.97 3.32
585 599 4.318332 CAGATGTTTCAGAGCAACACCTA 58.682 43.478 0.00 0.00 36.97 3.08
586 600 4.756642 CAGATGTTTCAGAGCAACACCTAA 59.243 41.667 0.00 0.00 36.97 2.69
587 601 5.239306 CAGATGTTTCAGAGCAACACCTAAA 59.761 40.000 0.00 0.00 36.97 1.85
588 602 5.827797 AGATGTTTCAGAGCAACACCTAAAA 59.172 36.000 0.00 0.00 36.97 1.52
589 603 5.906113 TGTTTCAGAGCAACACCTAAAAA 57.094 34.783 0.00 0.00 0.00 1.94
609 623 3.549299 AAAAGATGTTTCAGAGCAGCG 57.451 42.857 0.00 0.00 0.00 5.18
610 624 2.462456 AAGATGTTTCAGAGCAGCGA 57.538 45.000 0.00 0.00 0.00 4.93
611 625 1.719600 AGATGTTTCAGAGCAGCGAC 58.280 50.000 0.00 0.00 0.00 5.19
614 628 1.502231 TGTTTCAGAGCAGCGACTTC 58.498 50.000 0.00 0.00 0.00 3.01
615 629 1.202521 TGTTTCAGAGCAGCGACTTCA 60.203 47.619 0.00 0.00 0.00 3.02
616 630 1.458827 GTTTCAGAGCAGCGACTTCAG 59.541 52.381 0.00 0.00 0.00 3.02
617 631 0.037882 TTCAGAGCAGCGACTTCAGG 60.038 55.000 0.00 0.00 0.00 3.86
618 632 1.447489 CAGAGCAGCGACTTCAGGG 60.447 63.158 0.00 0.00 0.00 4.45
619 633 1.607756 AGAGCAGCGACTTCAGGGA 60.608 57.895 0.00 0.00 0.00 4.20
620 634 1.188219 AGAGCAGCGACTTCAGGGAA 61.188 55.000 0.00 0.00 0.00 3.97
621 635 0.739112 GAGCAGCGACTTCAGGGAAG 60.739 60.000 4.51 4.51 44.37 3.46
633 647 4.884247 CTTCAGGGAAGTTACTTTCGAGT 58.116 43.478 0.00 0.00 35.21 4.18
636 650 5.054477 TCAGGGAAGTTACTTTCGAGTTTG 58.946 41.667 0.00 0.00 0.00 2.93
637 651 5.054477 CAGGGAAGTTACTTTCGAGTTTGA 58.946 41.667 0.00 0.00 0.00 2.69
638 652 5.177696 CAGGGAAGTTACTTTCGAGTTTGAG 59.822 44.000 0.00 0.00 0.00 3.02
639 653 4.083961 GGGAAGTTACTTTCGAGTTTGAGC 60.084 45.833 0.00 0.00 0.00 4.26
641 655 5.924825 GGAAGTTACTTTCGAGTTTGAGCTA 59.075 40.000 0.00 0.00 0.00 3.32
642 656 6.089685 GGAAGTTACTTTCGAGTTTGAGCTAG 59.910 42.308 0.00 0.00 0.00 3.42
643 657 6.328641 AGTTACTTTCGAGTTTGAGCTAGA 57.671 37.500 0.00 0.00 0.00 2.43
644 658 6.383415 AGTTACTTTCGAGTTTGAGCTAGAG 58.617 40.000 0.00 0.00 0.00 2.43
645 659 6.207025 AGTTACTTTCGAGTTTGAGCTAGAGA 59.793 38.462 0.00 0.00 0.00 3.10
646 660 5.455056 ACTTTCGAGTTTGAGCTAGAGAA 57.545 39.130 0.00 0.00 0.00 2.87
660 3280 7.978982 TGAGCTAGAGAATGTAATTTTGAAGC 58.021 34.615 0.00 0.00 36.07 3.86
677 3297 7.956420 TTTGAAGCTCGTGATTTAGTTAAGA 57.044 32.000 0.00 0.00 0.00 2.10
699 3319 1.486310 AGCTGTTTCACTGTCAGTGGA 59.514 47.619 28.47 20.50 45.94 4.02
703 3323 1.461127 GTTTCACTGTCAGTGGATCGC 59.539 52.381 28.47 12.64 45.94 4.58
724 3344 2.093500 CCACATGTGGCTAGAGTGCTTA 60.093 50.000 31.13 0.00 44.73 3.09
733 3353 4.406972 TGGCTAGAGTGCTTATCAGACATT 59.593 41.667 0.00 0.00 0.00 2.71
745 3365 9.851686 TGCTTATCAGACATTATTTGTATTCCT 57.148 29.630 0.00 0.00 39.18 3.36
836 3481 3.047877 CCGAACCAACGAGCCCAC 61.048 66.667 0.00 0.00 35.09 4.61
902 3547 6.398918 CAACCCGAGAAAATAGAAGAGAAGA 58.601 40.000 0.00 0.00 0.00 2.87
1216 3863 2.821991 ATGTATTCGCTACCTCTGGC 57.178 50.000 0.00 0.00 0.00 4.85
1219 3866 0.952280 TATTCGCTACCTCTGGCTCG 59.048 55.000 0.00 0.00 0.00 5.03
1226 3873 4.379243 CCTCTGGCTCGCCGTTGT 62.379 66.667 3.14 0.00 39.42 3.32
1236 3883 4.090057 GCCGTTGTTCCTCTGCGC 62.090 66.667 0.00 0.00 0.00 6.09
1271 3918 4.069232 CGGCGCTTCTCCAGGACA 62.069 66.667 7.64 0.00 0.00 4.02
1279 3942 1.264288 CTTCTCCAGGACACGTTTTGC 59.736 52.381 0.00 0.00 0.00 3.68
1316 3979 2.440501 CGCTAATGAAATTCCGTGTGC 58.559 47.619 0.00 0.00 37.87 4.57
1319 3982 3.366883 GCTAATGAAATTCCGTGTGCCAA 60.367 43.478 0.00 0.00 37.87 4.52
1362 4025 1.802960 GTAGTCGTTGTCTCGTGGAGA 59.197 52.381 0.00 0.00 36.22 3.71
1365 4028 1.001597 GTCGTTGTCTCGTGGAGAAGT 60.002 52.381 0.00 0.00 40.59 3.01
1440 4103 0.249489 CGGTCTGCTTAATCCGAGGG 60.249 60.000 0.00 0.00 44.86 4.30
1441 4104 0.533085 GGTCTGCTTAATCCGAGGGC 60.533 60.000 0.00 0.00 0.00 5.19
1475 4138 6.869695 TGTTTGATGTACCGAGCTAATAGAA 58.130 36.000 0.00 0.00 0.00 2.10
1511 4174 8.831550 GGTCATGAAAGTAAGATTACATTCTCC 58.168 37.037 16.95 11.90 40.25 3.71
1512 4175 9.383519 GTCATGAAAGTAAGATTACATTCTCCA 57.616 33.333 16.95 3.80 40.25 3.86
1523 4186 7.042335 AGATTACATTCTCCAGTTTACCGAAG 58.958 38.462 0.00 0.00 0.00 3.79
1559 4222 3.801638 GCATACCCTGTACTGCATCTCTG 60.802 52.174 0.00 0.00 34.77 3.35
1577 4240 7.571244 GCATCTCTGAATTTTGAAGTCGTTACA 60.571 37.037 0.00 0.00 0.00 2.41
1578 4241 7.408132 TCTCTGAATTTTGAAGTCGTTACAG 57.592 36.000 0.00 0.00 0.00 2.74
1579 4242 6.984474 TCTCTGAATTTTGAAGTCGTTACAGT 59.016 34.615 0.00 0.00 0.00 3.55
1580 4243 7.169308 TCTCTGAATTTTGAAGTCGTTACAGTC 59.831 37.037 0.00 0.00 0.00 3.51
1581 4244 5.969741 TGAATTTTGAAGTCGTTACAGTCG 58.030 37.500 0.00 0.00 0.00 4.18
1582 4245 5.521010 TGAATTTTGAAGTCGTTACAGTCGT 59.479 36.000 0.00 0.00 0.00 4.34
1583 4246 5.978934 ATTTTGAAGTCGTTACAGTCGTT 57.021 34.783 0.00 0.00 0.00 3.85
1584 4247 7.222417 TGAATTTTGAAGTCGTTACAGTCGTTA 59.778 33.333 0.00 0.00 0.00 3.18
1585 4248 5.871531 TTTGAAGTCGTTACAGTCGTTAC 57.128 39.130 0.00 0.00 0.00 2.50
1616 4279 7.394816 TCTGCTGAGCCTTATTTAGTTTTACT 58.605 34.615 0.23 0.00 0.00 2.24
1730 4393 3.863142 ATCATTGAGGTGCTTGCTTTC 57.137 42.857 0.00 0.00 0.00 2.62
1848 4511 3.886505 TGACAAACCCATGGTGAGTTTAC 59.113 43.478 11.73 11.29 35.34 2.01
1873 4537 3.976169 TGAATTGGTGTTACAGCTTTGC 58.024 40.909 15.65 2.67 32.61 3.68
1881 4545 1.953686 GTTACAGCTTTGCTTGTCCCA 59.046 47.619 0.00 0.00 36.40 4.37
1901 4565 8.222637 TGTCCCATAATTTGATCTGATCTGATT 58.777 33.333 17.82 17.36 0.00 2.57
1902 4566 9.075678 GTCCCATAATTTGATCTGATCTGATTT 57.924 33.333 17.82 8.92 0.00 2.17
1903 4567 9.650714 TCCCATAATTTGATCTGATCTGATTTT 57.349 29.630 17.82 10.12 0.00 1.82
2068 4736 8.562052 TCTACTGCTTGCAATTATGTCATAATG 58.438 33.333 17.00 12.44 35.71 1.90
2139 4934 6.721571 TCTATTGAAGCGGTTTGTTCTAAG 57.278 37.500 0.00 0.00 0.00 2.18
2171 4966 6.806217 ACTGCCTAGGTGGTCTATAATCTAT 58.194 40.000 11.31 0.00 38.35 1.98
2191 4986 7.834068 TCTATCTTGTTTGTGCTTAGATGAC 57.166 36.000 0.00 0.00 0.00 3.06
2232 5027 2.247790 AGCTTGTTGTGCTTAGCGG 58.752 52.632 0.00 0.00 37.52 5.52
2233 5028 0.250295 AGCTTGTTGTGCTTAGCGGA 60.250 50.000 0.00 0.00 37.52 5.54
2323 5118 6.821665 GGCATGTCTAGTCAATACCAAACTAA 59.178 38.462 0.00 0.00 0.00 2.24
2358 5153 9.405587 TGTTCAAATTGCTTAACTAACTATTGC 57.594 29.630 0.00 0.00 0.00 3.56
2421 5216 5.049198 TGCATTTTGACTTCTGAAGCTGTAG 60.049 40.000 17.00 3.46 0.00 2.74
2438 5233 7.369803 AGCTGTAGTATTTTTGTCACTCATG 57.630 36.000 0.00 0.00 0.00 3.07
2495 5290 2.227388 GCCAAGACCAAGTCAGATGTTG 59.773 50.000 0.00 0.00 34.60 3.33
2515 5310 1.815003 GTAGCAAAAGCTGATGGCACT 59.185 47.619 0.00 0.00 44.79 4.40
2563 5358 7.206687 AGAGGAATGATGAGAAACGTAAGATC 58.793 38.462 0.00 0.00 43.62 2.75
2595 5390 3.194542 GTGCATACCCCTTTACATTTGCA 59.805 43.478 0.00 0.00 36.58 4.08
2620 5415 1.074951 CTTTGGCCCCTCGGAACTT 59.925 57.895 0.00 0.00 0.00 2.66
2628 5423 2.919228 CCCCTCGGAACTTTATCTTGG 58.081 52.381 0.00 0.00 0.00 3.61
2654 5449 7.532682 TTGCACTTCTTTATTTTGTTTGGAC 57.467 32.000 0.00 0.00 0.00 4.02
2659 5454 7.911205 CACTTCTTTATTTTGTTTGGACACGTA 59.089 33.333 0.00 0.00 34.98 3.57
2665 5460 0.941542 TGTTTGGACACGTAGCTTGC 59.058 50.000 0.00 0.00 0.00 4.01
2677 5472 2.161410 CGTAGCTTGCCATTTGTTAGCA 59.839 45.455 0.00 0.00 34.37 3.49
2678 5473 2.730550 AGCTTGCCATTTGTTAGCAC 57.269 45.000 0.00 0.00 35.96 4.40
2679 5474 1.068333 AGCTTGCCATTTGTTAGCACG 60.068 47.619 0.00 0.00 35.96 5.34
2680 5475 1.981254 CTTGCCATTTGTTAGCACGG 58.019 50.000 0.00 0.00 35.96 4.94
2681 5476 1.269448 CTTGCCATTTGTTAGCACGGT 59.731 47.619 0.00 0.00 35.96 4.83
2682 5477 2.186532 TGCCATTTGTTAGCACGGTA 57.813 45.000 0.00 0.00 0.00 4.02
2683 5478 2.717390 TGCCATTTGTTAGCACGGTAT 58.283 42.857 0.00 0.00 0.00 2.73
2684 5479 2.421775 TGCCATTTGTTAGCACGGTATG 59.578 45.455 0.00 0.00 0.00 2.39
2685 5480 2.422127 GCCATTTGTTAGCACGGTATGT 59.578 45.455 0.00 0.00 0.00 2.29
2686 5481 3.119637 GCCATTTGTTAGCACGGTATGTT 60.120 43.478 0.00 0.00 0.00 2.71
2687 5482 4.658071 CCATTTGTTAGCACGGTATGTTC 58.342 43.478 0.00 0.00 0.00 3.18
2688 5483 4.155099 CCATTTGTTAGCACGGTATGTTCA 59.845 41.667 0.00 0.00 0.00 3.18
2736 5531 0.900421 TGTGCTGGAGATGGACTCTG 59.100 55.000 0.00 0.00 44.37 3.35
2763 5558 4.155099 CACGTAGCCATGGATTGTTGTTTA 59.845 41.667 18.40 0.00 0.00 2.01
2903 5698 3.005155 ACAGCAAGAATCAGACCTTTTGC 59.995 43.478 0.00 0.00 40.74 3.68
3005 5800 3.609853 AGATGCACTCATTCGCCTAAAA 58.390 40.909 0.00 0.00 31.96 1.52
3196 6023 6.138761 CACACTTTGTTGATAGAGTTGCTTC 58.861 40.000 0.00 0.00 0.00 3.86
3216 6150 5.431765 CTTCGTACTGGGAGGTACTACTTA 58.568 45.833 0.00 0.00 40.83 2.24
3230 6164 8.473358 AGGTACTACTTATTTTGCTGGTTTTT 57.527 30.769 0.00 0.00 36.02 1.94
3285 6221 8.776680 TTTAAATTCACGAGCAAAACTTAGTC 57.223 30.769 0.00 0.00 0.00 2.59
3292 6228 3.364366 CGAGCAAAACTTAGTCTGCCTTG 60.364 47.826 13.53 3.45 35.33 3.61
3313 6249 5.556355 TGTTCTTTGATAATGCAGCTGAG 57.444 39.130 20.43 2.00 0.00 3.35
3483 6419 5.460419 GGTTTTTGTTGTTGCATATGAACGA 59.540 36.000 6.97 5.51 0.00 3.85
3495 6431 7.132694 TGCATATGAACGATGGAATATGTTC 57.867 36.000 6.97 0.00 40.34 3.18
3497 6433 7.445096 TGCATATGAACGATGGAATATGTTCTT 59.555 33.333 6.97 2.43 40.48 2.52
3571 6513 7.068716 ACACAATCTCCTTTTAACTTCTTTGCT 59.931 33.333 0.00 0.00 0.00 3.91
3595 6537 1.342174 CATCCTGCCTGCTGTTTTGTT 59.658 47.619 0.00 0.00 0.00 2.83
3596 6538 0.746063 TCCTGCCTGCTGTTTTGTTG 59.254 50.000 0.00 0.00 0.00 3.33
3609 6551 6.045955 GCTGTTTTGTTGTTCTATTTTGGGA 58.954 36.000 0.00 0.00 0.00 4.37
3657 8565 6.015688 CCAGTGATTCCTGCTTGCATAATTAT 60.016 38.462 0.00 0.00 0.00 1.28
3753 8669 6.212955 GGAATAGTCATGACTCAGACTTAGC 58.787 44.000 31.09 11.32 42.12 3.09
3762 8678 3.467803 ACTCAGACTTAGCGCAAAGTTT 58.532 40.909 11.47 0.00 39.78 2.66
3807 8723 5.053145 CAGTACTATGACTGGGCATCTTTC 58.947 45.833 0.00 0.00 42.68 2.62
3824 8740 7.415206 GGCATCTTTCCACGTTTATTCTGTAAT 60.415 37.037 0.00 0.00 0.00 1.89
3967 8883 3.103911 GAACTCCCACACGACGCG 61.104 66.667 3.53 3.53 0.00 6.01
4006 8922 0.690762 TGTTCTTCTGCCAGTACCCC 59.309 55.000 0.00 0.00 0.00 4.95
4036 8952 1.148157 AAGTGCGGATGATCGAAGCG 61.148 55.000 0.00 0.00 0.00 4.68
4198 9114 6.010219 ACTTGAATTAATGTTGTAGGCCTGT 58.990 36.000 17.99 0.00 0.00 4.00
4210 9126 0.681175 AGGCCTGTTTTTGCACCATC 59.319 50.000 3.11 0.00 0.00 3.51
4245 9161 7.956328 TCTTCACATGTAAGGTAGACTACAT 57.044 36.000 14.48 4.32 33.87 2.29
4249 9165 7.941919 TCACATGTAAGGTAGACTACATCATC 58.058 38.462 14.48 2.92 31.51 2.92
4250 9166 7.014326 TCACATGTAAGGTAGACTACATCATCC 59.986 40.741 14.48 0.00 31.51 3.51
4252 9168 6.961360 TGTAAGGTAGACTACATCATCCAG 57.039 41.667 14.48 0.00 0.00 3.86
4253 9169 6.432581 TGTAAGGTAGACTACATCATCCAGT 58.567 40.000 14.48 0.00 0.00 4.00
4255 9171 8.057011 TGTAAGGTAGACTACATCATCCAGTAA 58.943 37.037 14.48 0.00 0.00 2.24
4259 9203 9.656323 AGGTAGACTACATCATCCAGTAAATTA 57.344 33.333 14.48 0.00 0.00 1.40
4349 9293 7.830940 TTGTCAAATCATATGTTGCCAATTC 57.169 32.000 1.90 0.00 0.00 2.17
4458 9404 7.435784 TGATGTTTGTGATGACAATTGTTTCTG 59.564 33.333 13.36 0.00 41.77 3.02
4468 9414 7.800155 TGACAATTGTTTCTGTAGAACATGA 57.200 32.000 13.36 0.00 33.13 3.07
4469 9415 7.639039 TGACAATTGTTTCTGTAGAACATGAC 58.361 34.615 13.36 0.00 33.13 3.06
4472 9418 7.915397 ACAATTGTTTCTGTAGAACATGACAAC 59.085 33.333 4.92 0.00 31.66 3.32
4473 9419 6.371809 TTGTTTCTGTAGAACATGACAACC 57.628 37.500 0.00 0.00 33.13 3.77
4474 9420 5.432645 TGTTTCTGTAGAACATGACAACCA 58.567 37.500 0.00 0.00 33.13 3.67
4476 9422 7.220740 TGTTTCTGTAGAACATGACAACCATA 58.779 34.615 0.00 0.00 33.31 2.74
4477 9423 7.717436 TGTTTCTGTAGAACATGACAACCATAA 59.283 33.333 0.00 0.00 33.31 1.90
4478 9424 8.730680 GTTTCTGTAGAACATGACAACCATAAT 58.269 33.333 0.00 0.00 33.31 1.28
4512 9834 8.375506 TCCTTGTCATACTGTTAACTCAAATCT 58.624 33.333 7.22 0.00 0.00 2.40
4513 9835 8.660373 CCTTGTCATACTGTTAACTCAAATCTC 58.340 37.037 7.22 0.00 0.00 2.75
4538 9865 8.865090 TCAACAAAACCATGTCCTACATTAAAT 58.135 29.630 0.00 0.00 36.53 1.40
4595 9923 1.613437 CAAAACTTTCCGTGCCATCCT 59.387 47.619 0.00 0.00 0.00 3.24
4741 10069 5.755375 GCAATGCAGAGACAATTAGCTAGTA 59.245 40.000 0.00 0.00 0.00 1.82
4850 10195 3.120130 TGTTCCACAACGAAACAAGACAC 60.120 43.478 0.00 0.00 34.95 3.67
4897 10242 7.806180 AGATCCTAAACATTAGTTATGCTGGT 58.194 34.615 0.00 0.00 36.84 4.00
4915 10260 1.876156 GGTTTGTCTCTTGGCTGACAG 59.124 52.381 0.00 0.00 42.98 3.51
4962 10309 2.000429 GCCACACAGAATTTCATGGC 58.000 50.000 14.33 14.33 45.26 4.40
5016 10363 3.997021 GGAATCAAACTCTTTCGAGCTCA 59.003 43.478 15.40 0.00 41.09 4.26
5098 10445 1.093159 CTTGGCAATGAGCTCAGACC 58.907 55.000 22.96 21.38 44.79 3.85
5100 10447 1.571955 TGGCAATGAGCTCAGACCTA 58.428 50.000 22.96 7.35 44.79 3.08
5156 10503 4.475028 TGCAGCTCAAACATGAAAATACG 58.525 39.130 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 214 0.250727 CCCTTTCCGAAAGAGGCACA 60.251 55.000 20.43 0.00 41.02 4.57
233 242 2.035237 AAACCGAACCAGGAGCACGA 62.035 55.000 0.00 0.00 34.73 4.35
369 381 3.712091 AAACCGTGCGTCCAAATTTTA 57.288 38.095 0.00 0.00 0.00 1.52
460 474 1.468520 GACAAATGGCGTACATGCAGT 59.531 47.619 0.00 0.00 40.44 4.40
539 553 3.077359 GCATTGTAGCAAGACCAGAACT 58.923 45.455 0.00 0.00 0.00 3.01
540 554 2.162408 GGCATTGTAGCAAGACCAGAAC 59.838 50.000 0.00 0.00 35.83 3.01
541 555 2.436417 GGCATTGTAGCAAGACCAGAA 58.564 47.619 0.00 0.00 35.83 3.02
543 557 1.098050 GGGCATTGTAGCAAGACCAG 58.902 55.000 0.00 0.00 35.83 4.00
544 558 0.323360 GGGGCATTGTAGCAAGACCA 60.323 55.000 0.00 0.00 35.83 4.02
545 559 0.323360 TGGGGCATTGTAGCAAGACC 60.323 55.000 0.00 0.00 35.83 3.85
546 560 1.098050 CTGGGGCATTGTAGCAAGAC 58.902 55.000 0.00 0.00 35.83 3.01
548 562 1.679680 CATCTGGGGCATTGTAGCAAG 59.320 52.381 0.00 0.00 35.83 4.01
551 565 1.767759 AACATCTGGGGCATTGTAGC 58.232 50.000 0.00 0.00 0.00 3.58
552 566 3.355378 TGAAACATCTGGGGCATTGTAG 58.645 45.455 0.00 0.00 0.00 2.74
554 568 2.173519 CTGAAACATCTGGGGCATTGT 58.826 47.619 0.00 0.00 0.00 2.71
555 569 2.426024 CTCTGAAACATCTGGGGCATTG 59.574 50.000 0.00 0.00 0.00 2.82
557 571 1.684248 GCTCTGAAACATCTGGGGCAT 60.684 52.381 0.00 0.00 0.00 4.40
558 572 0.322816 GCTCTGAAACATCTGGGGCA 60.323 55.000 0.00 0.00 0.00 5.36
559 573 0.322816 TGCTCTGAAACATCTGGGGC 60.323 55.000 0.00 0.00 0.00 5.80
560 574 1.815003 GTTGCTCTGAAACATCTGGGG 59.185 52.381 0.00 0.00 0.00 4.96
561 575 2.227388 GTGTTGCTCTGAAACATCTGGG 59.773 50.000 0.00 0.00 39.57 4.45
563 577 3.144506 AGGTGTTGCTCTGAAACATCTG 58.855 45.455 7.10 0.00 45.13 2.90
564 578 3.498774 AGGTGTTGCTCTGAAACATCT 57.501 42.857 2.84 2.84 42.74 2.90
565 579 5.689383 TTTAGGTGTTGCTCTGAAACATC 57.311 39.130 0.00 0.00 39.57 3.06
566 580 6.463995 TTTTTAGGTGTTGCTCTGAAACAT 57.536 33.333 0.00 0.00 39.57 2.71
567 581 5.906113 TTTTTAGGTGTTGCTCTGAAACA 57.094 34.783 0.00 0.00 35.22 2.83
588 602 3.565482 TCGCTGCTCTGAAACATCTTTTT 59.435 39.130 0.00 0.00 0.00 1.94
589 603 3.058639 GTCGCTGCTCTGAAACATCTTTT 60.059 43.478 0.00 0.00 0.00 2.27
590 604 2.481952 GTCGCTGCTCTGAAACATCTTT 59.518 45.455 0.00 0.00 0.00 2.52
592 606 1.274728 AGTCGCTGCTCTGAAACATCT 59.725 47.619 0.00 0.00 0.00 2.90
593 607 1.719600 AGTCGCTGCTCTGAAACATC 58.280 50.000 0.00 0.00 0.00 3.06
594 608 2.072298 GAAGTCGCTGCTCTGAAACAT 58.928 47.619 0.00 0.00 0.00 2.71
595 609 1.202521 TGAAGTCGCTGCTCTGAAACA 60.203 47.619 0.00 0.00 0.00 2.83
596 610 1.458827 CTGAAGTCGCTGCTCTGAAAC 59.541 52.381 0.00 0.00 0.00 2.78
600 614 1.447489 CCCTGAAGTCGCTGCTCTG 60.447 63.158 0.00 0.00 0.00 3.35
601 615 1.188219 TTCCCTGAAGTCGCTGCTCT 61.188 55.000 0.00 0.00 0.00 4.09
602 616 0.739112 CTTCCCTGAAGTCGCTGCTC 60.739 60.000 0.00 0.00 35.21 4.26
603 617 1.294780 CTTCCCTGAAGTCGCTGCT 59.705 57.895 0.00 0.00 35.21 4.24
604 618 3.882025 CTTCCCTGAAGTCGCTGC 58.118 61.111 0.00 0.00 35.21 5.25
609 623 6.959456 AACTCGAAAGTAACTTCCCTGAAGTC 60.959 42.308 9.71 0.00 42.45 3.01
610 624 5.163332 AACTCGAAAGTAACTTCCCTGAAGT 60.163 40.000 3.71 3.71 43.89 3.01
611 625 4.884247 ACTCGAAAGTAACTTCCCTGAAG 58.116 43.478 2.40 2.40 38.60 3.02
614 628 5.054477 TCAAACTCGAAAGTAACTTCCCTG 58.946 41.667 0.00 0.00 33.48 4.45
615 629 5.286267 TCAAACTCGAAAGTAACTTCCCT 57.714 39.130 0.00 0.00 33.48 4.20
616 630 4.083961 GCTCAAACTCGAAAGTAACTTCCC 60.084 45.833 0.00 0.00 33.48 3.97
617 631 4.750598 AGCTCAAACTCGAAAGTAACTTCC 59.249 41.667 0.00 0.00 33.48 3.46
618 632 5.908916 AGCTCAAACTCGAAAGTAACTTC 57.091 39.130 0.00 0.00 33.48 3.01
619 633 6.746120 TCTAGCTCAAACTCGAAAGTAACTT 58.254 36.000 0.00 0.00 33.48 2.66
620 634 6.207025 TCTCTAGCTCAAACTCGAAAGTAACT 59.793 38.462 0.00 0.00 33.48 2.24
621 635 6.380190 TCTCTAGCTCAAACTCGAAAGTAAC 58.620 40.000 0.00 0.00 33.48 2.50
622 636 6.570672 TCTCTAGCTCAAACTCGAAAGTAA 57.429 37.500 0.00 0.00 33.48 2.24
623 637 6.570672 TTCTCTAGCTCAAACTCGAAAGTA 57.429 37.500 0.00 0.00 33.48 2.24
625 639 5.866633 ACATTCTCTAGCTCAAACTCGAAAG 59.133 40.000 0.00 0.00 0.00 2.62
630 644 9.766277 CAAAATTACATTCTCTAGCTCAAACTC 57.234 33.333 0.00 0.00 0.00 3.01
631 645 9.507329 TCAAAATTACATTCTCTAGCTCAAACT 57.493 29.630 0.00 0.00 0.00 2.66
636 650 8.207521 AGCTTCAAAATTACATTCTCTAGCTC 57.792 34.615 0.00 0.00 28.73 4.09
637 651 7.010923 CGAGCTTCAAAATTACATTCTCTAGCT 59.989 37.037 0.00 0.00 36.84 3.32
638 652 7.122550 CGAGCTTCAAAATTACATTCTCTAGC 58.877 38.462 0.00 0.00 0.00 3.42
639 653 8.113062 CACGAGCTTCAAAATTACATTCTCTAG 58.887 37.037 0.00 0.00 0.00 2.43
641 655 6.650807 TCACGAGCTTCAAAATTACATTCTCT 59.349 34.615 0.00 0.00 0.00 3.10
642 656 6.831769 TCACGAGCTTCAAAATTACATTCTC 58.168 36.000 0.00 0.00 0.00 2.87
643 657 6.801539 TCACGAGCTTCAAAATTACATTCT 57.198 33.333 0.00 0.00 0.00 2.40
644 658 8.452989 AAATCACGAGCTTCAAAATTACATTC 57.547 30.769 0.00 0.00 0.00 2.67
645 659 9.559958 CTAAATCACGAGCTTCAAAATTACATT 57.440 29.630 0.00 0.00 0.00 2.71
646 660 8.730680 ACTAAATCACGAGCTTCAAAATTACAT 58.269 29.630 0.00 0.00 0.00 2.29
660 3280 5.864474 ACAGCTGTCTTAACTAAATCACGAG 59.136 40.000 15.25 0.00 0.00 4.18
710 3330 3.365472 TGTCTGATAAGCACTCTAGCCA 58.635 45.455 0.00 0.00 34.23 4.75
711 3331 4.599047 ATGTCTGATAAGCACTCTAGCC 57.401 45.455 0.00 0.00 34.23 3.93
712 3332 8.494347 CAAATAATGTCTGATAAGCACTCTAGC 58.506 37.037 0.00 0.00 0.00 3.42
713 3333 9.539825 ACAAATAATGTCTGATAAGCACTCTAG 57.460 33.333 0.00 0.00 37.96 2.43
748 3368 9.533831 AGGGACTTTATTAAAACTCAATGACAT 57.466 29.630 0.00 0.00 27.25 3.06
749 3369 8.934023 AGGGACTTTATTAAAACTCAATGACA 57.066 30.769 0.00 0.00 27.25 3.58
799 3444 1.064463 GCAAACATCAGATCTGGGGGA 60.064 52.381 22.42 3.45 0.00 4.81
836 3481 0.667993 TTCAAAAGAGGCTTGCCGTG 59.332 50.000 5.95 1.74 0.00 4.94
921 3568 1.309499 CCGTGTCCTCTCTCGCTCTT 61.309 60.000 0.00 0.00 0.00 2.85
1216 3863 2.383527 GCAGAGGAACAACGGCGAG 61.384 63.158 16.62 8.41 0.00 5.03
1219 3866 4.090057 GCGCAGAGGAACAACGGC 62.090 66.667 0.30 0.00 0.00 5.68
1236 3883 1.452108 GAGATTTCCACCGGGCCAG 60.452 63.158 6.32 0.00 0.00 4.85
1271 3918 4.211986 ACGTGTCTGGCAAAACGT 57.788 50.000 13.98 13.98 43.87 3.99
1316 3979 2.650778 GAAAACAGCCGGGCTTGG 59.349 61.111 21.26 12.13 36.40 3.61
1329 3992 1.593265 GACTACCTCCGCCGGAAAA 59.407 57.895 7.50 0.00 0.00 2.29
1362 4025 0.598680 GCGAGATATCTGCGGCACTT 60.599 55.000 10.74 0.00 0.00 3.16
1440 4103 4.083271 GGTACATCAAACAAAGAGGACTGC 60.083 45.833 0.00 0.00 0.00 4.40
1441 4104 4.152402 CGGTACATCAAACAAAGAGGACTG 59.848 45.833 0.00 0.00 0.00 3.51
1475 4138 4.494091 ACTTTCATGACCCAGATTCGAT 57.506 40.909 0.00 0.00 0.00 3.59
1511 4174 4.915704 TGCTGTTTTTCTTCGGTAAACTG 58.084 39.130 0.00 0.00 35.27 3.16
1512 4175 5.570234 TTGCTGTTTTTCTTCGGTAAACT 57.430 34.783 0.00 0.00 33.92 2.66
1523 4186 4.389687 CAGGGTATGCAATTGCTGTTTTTC 59.610 41.667 29.37 13.55 42.66 2.29
1559 4222 5.970879 ACGACTGTAACGACTTCAAAATTC 58.029 37.500 0.00 0.00 34.70 2.17
1577 4240 4.489810 CTCAGCAGAAATCTGTAACGACT 58.510 43.478 11.77 0.00 45.45 4.18
1578 4241 3.061429 GCTCAGCAGAAATCTGTAACGAC 59.939 47.826 11.77 0.00 45.45 4.34
1579 4242 3.254060 GCTCAGCAGAAATCTGTAACGA 58.746 45.455 11.77 3.51 45.45 3.85
1580 4243 2.349886 GGCTCAGCAGAAATCTGTAACG 59.650 50.000 11.77 1.16 45.45 3.18
1581 4244 3.604582 AGGCTCAGCAGAAATCTGTAAC 58.395 45.455 11.77 0.00 45.45 2.50
1582 4245 3.988976 AGGCTCAGCAGAAATCTGTAA 57.011 42.857 11.77 0.00 45.45 2.41
1583 4246 3.988976 AAGGCTCAGCAGAAATCTGTA 57.011 42.857 11.77 0.00 45.45 2.74
1584 4247 2.875094 AAGGCTCAGCAGAAATCTGT 57.125 45.000 11.77 0.00 45.45 3.41
1585 4248 5.831702 AAATAAGGCTCAGCAGAAATCTG 57.168 39.130 0.00 6.05 46.40 2.90
1667 4330 3.619979 CGGCATTGAGGGACTTCTTAAGT 60.620 47.826 1.63 0.00 46.38 2.24
1730 4393 4.022068 TGCCCTTTATGCTTCAAAGTCTTG 60.022 41.667 0.00 0.00 32.23 3.02
1848 4511 3.207474 GCTGTAACACCAATTCAGCTG 57.793 47.619 7.63 7.63 45.14 4.24
1979 4647 1.753956 GCTTGGCTAACAACACAACG 58.246 50.000 0.00 0.00 34.76 4.10
1982 4650 2.242047 TACGCTTGGCTAACAACACA 57.758 45.000 0.00 0.00 34.76 3.72
2043 4711 8.347771 ACATTATGACATAATTGCAAGCAGTAG 58.652 33.333 16.48 5.41 33.34 2.57
2139 4934 2.017049 CCACCTAGGCAGTAATGTTGC 58.983 52.381 9.30 0.00 40.80 4.17
2171 4966 5.368145 AGTGTCATCTAAGCACAAACAAGA 58.632 37.500 0.00 0.00 35.75 3.02
2191 4986 2.781681 ATTTTGGTACGGAGGGAGTG 57.218 50.000 0.00 0.00 0.00 3.51
2290 5085 2.766263 TGACTAGACATGCCCAGTAAGG 59.234 50.000 0.00 0.00 37.03 2.69
2323 5118 8.034804 AGTTAAGCAATTTGAACAACTCAAGTT 58.965 29.630 0.00 0.00 44.84 2.66
2374 5169 3.079578 TGCAAAGGAGCAGATGAAAGAG 58.920 45.455 0.00 0.00 40.11 2.85
2421 5216 9.683069 ACAAGATTTCATGAGTGACAAAAATAC 57.317 29.630 0.00 0.00 33.11 1.89
2563 5358 1.314730 GGGTATGCACATTAACCGGG 58.685 55.000 6.32 0.00 32.53 5.73
2595 5390 1.546998 CCGAGGGGCCAAAGTAAAACT 60.547 52.381 4.39 0.00 0.00 2.66
2628 5423 7.902917 GTCCAAACAAAATAAAGAAGTGCAAAC 59.097 33.333 0.00 0.00 0.00 2.93
2654 5449 2.704725 AACAAATGGCAAGCTACGTG 57.295 45.000 0.00 0.00 0.00 4.49
2665 5460 4.155099 TGAACATACCGTGCTAACAAATGG 59.845 41.667 0.00 0.00 0.00 3.16
2736 5531 1.094785 AATCCATGGCTACGTGCAAC 58.905 50.000 6.96 0.00 45.15 4.17
2903 5698 2.028112 TGAAGACTGGAATCAAGGACCG 60.028 50.000 0.00 0.00 0.00 4.79
3040 5859 6.346096 AGTAACAGTAAGTGCAAGAACAGAA 58.654 36.000 0.00 0.00 0.00 3.02
3196 6023 6.705863 AAATAAGTAGTACCTCCCAGTACG 57.294 41.667 0.00 0.00 45.91 3.67
3230 6164 4.814234 CCAAGTTGCCATAAGCTCGTATAA 59.186 41.667 0.00 0.00 44.23 0.98
3285 6221 5.063180 TGCATTATCAAAGAACAAGGCAG 57.937 39.130 0.00 0.00 33.29 4.85
3292 6228 5.808042 TCTCAGCTGCATTATCAAAGAAC 57.192 39.130 9.47 0.00 0.00 3.01
3313 6249 0.441921 GCTCACGCTTCTGCTTCTTC 59.558 55.000 0.00 0.00 36.97 2.87
3340 6276 0.676466 CGCCAGCCTGGTTAACATCA 60.676 55.000 13.35 0.00 40.46 3.07
3495 6431 3.068590 AGCTTGGAAAACATGGTCACAAG 59.931 43.478 14.31 14.31 37.48 3.16
3497 6433 2.622942 GAGCTTGGAAAACATGGTCACA 59.377 45.455 0.00 0.00 45.68 3.58
3552 6488 7.730364 TGTCTAGCAAAGAAGTTAAAAGGAG 57.270 36.000 0.00 0.00 35.47 3.69
3595 6537 6.553100 ACAAACTCCATTCCCAAAATAGAACA 59.447 34.615 0.00 0.00 0.00 3.18
3596 6538 6.993079 ACAAACTCCATTCCCAAAATAGAAC 58.007 36.000 0.00 0.00 0.00 3.01
3609 6551 4.082571 GCTTGCAGACATACAAACTCCATT 60.083 41.667 0.00 0.00 0.00 3.16
3762 8678 6.605995 ACTGGGCGTATATATGATAGTAAGCA 59.394 38.462 6.12 0.00 0.00 3.91
3792 8708 0.321564 CGTGGAAAGATGCCCAGTCA 60.322 55.000 0.00 0.00 32.28 3.41
3824 8740 7.665559 AGCCAGTAATGATGTGAAGAAAACTAA 59.334 33.333 0.00 0.00 0.00 2.24
3967 8883 1.136147 CTGCAGCATCAAAGCGGTC 59.864 57.895 0.00 0.00 40.15 4.79
3970 8886 0.450583 ACATCTGCAGCATCAAAGCG 59.549 50.000 9.47 0.00 40.15 4.68
4006 8922 2.325082 CCGCACTTCCTTGAACCCG 61.325 63.158 0.00 0.00 0.00 5.28
4081 8997 1.228552 AAGGTTCATGGCTGCGGTT 60.229 52.632 0.00 0.00 0.00 4.44
4193 9109 1.606224 CCAGATGGTGCAAAAACAGGC 60.606 52.381 0.00 0.00 0.00 4.85
4210 9126 7.607991 ACCTTACATGTGAAGAAAATCTACCAG 59.392 37.037 9.11 0.00 0.00 4.00
4245 9161 5.432645 TGGACGCATTAATTTACTGGATGA 58.567 37.500 0.00 0.00 0.00 2.92
4249 9165 4.036734 AGCATGGACGCATTAATTTACTGG 59.963 41.667 0.00 0.00 0.00 4.00
4250 9166 5.173774 AGCATGGACGCATTAATTTACTG 57.826 39.130 0.00 0.00 0.00 2.74
4252 9168 5.871531 CAAGCATGGACGCATTAATTTAC 57.128 39.130 0.00 0.00 0.00 2.01
4349 9293 8.395633 CAAAAGTAGGAAATGGTTATTAGACGG 58.604 37.037 0.00 0.00 0.00 4.79
4458 9404 8.739972 AGGAAAATTATGGTTGTCATGTTCTAC 58.260 33.333 0.00 0.00 37.30 2.59
4468 9414 7.070571 TGACAAGGAAAGGAAAATTATGGTTGT 59.929 33.333 0.00 0.00 0.00 3.32
4469 9415 7.441017 TGACAAGGAAAGGAAAATTATGGTTG 58.559 34.615 0.00 0.00 0.00 3.77
4472 9418 8.971073 AGTATGACAAGGAAAGGAAAATTATGG 58.029 33.333 0.00 0.00 0.00 2.74
4473 9419 9.793252 CAGTATGACAAGGAAAGGAAAATTATG 57.207 33.333 0.00 0.00 39.69 1.90
4474 9420 9.533831 ACAGTATGACAAGGAAAGGAAAATTAT 57.466 29.630 0.00 0.00 39.69 1.28
4476 9422 7.839680 ACAGTATGACAAGGAAAGGAAAATT 57.160 32.000 0.00 0.00 39.69 1.82
4477 9423 7.839680 AACAGTATGACAAGGAAAGGAAAAT 57.160 32.000 0.00 0.00 39.69 1.82
4478 9424 8.626526 GTTAACAGTATGACAAGGAAAGGAAAA 58.373 33.333 0.00 0.00 39.69 2.29
4512 9834 7.825331 TTAATGTAGGACATGGTTTTGTTGA 57.175 32.000 0.00 0.00 37.97 3.18
4513 9835 9.487790 AATTTAATGTAGGACATGGTTTTGTTG 57.512 29.630 0.00 0.00 37.97 3.33
4586 9914 3.384789 TGAGTATGTGTAGAGGATGGCAC 59.615 47.826 0.00 0.00 0.00 5.01
4697 10025 2.737252 GCAGCGAGGCATATAACTTACC 59.263 50.000 0.00 0.00 0.00 2.85
4751 10079 8.469125 GCAAAACATGTACTCGAAAGTTAAAAG 58.531 33.333 0.00 0.00 36.92 2.27
4755 10083 6.606234 TGCAAAACATGTACTCGAAAGTTA 57.394 33.333 0.00 0.00 36.92 2.24
4850 10195 4.503741 AACCAGTCAAATTGTTCATCGG 57.496 40.909 0.00 0.00 0.00 4.18
4897 10242 3.558931 TTCTGTCAGCCAAGAGACAAA 57.441 42.857 0.00 0.00 43.48 2.83
4915 10260 4.758165 TGTTAGTCGTCCCTGGAAAAATTC 59.242 41.667 0.00 0.00 0.00 2.17
5016 10363 3.846180 CTGGGCAAGCACAACACT 58.154 55.556 0.00 0.00 0.00 3.55
5098 10445 5.930837 ATGGAGGAAGAACTGAAGACTAG 57.069 43.478 0.00 0.00 0.00 2.57
5100 10447 4.349342 ACAATGGAGGAAGAACTGAAGACT 59.651 41.667 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.