Multiple sequence alignment - TraesCS3B01G307100

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 TraesCS3B01G307100 chr3B 100.000 5942 0 0 1 5942 493162000 493167941 0.000000e+00 10973.0
1 TraesCS3B01G307100 chr3B 85.741 533 41 13 5301 5824 493274204 493274710 1.130000e-146 531.0
2 TraesCS3B01G307100 chr3B 97.479 238 6 0 4977 5214 493273961 493274198 1.990000e-109 407.0
3 TraesCS3B01G307100 chr3B 97.802 91 1 1 5208 5298 118309416 118309505 7.970000e-34 156.0
4 TraesCS3B01G307100 chr3B 84.615 117 8 3 5194 5301 747332954 747333069 2.260000e-19 108.0
5 TraesCS3B01G307100 chr3B 91.429 70 6 0 2166 2235 493164100 493164169 4.900000e-16 97.1
6 TraesCS3B01G307100 chr3B 91.429 70 6 0 2101 2170 493164165 493164234 4.900000e-16 97.1
7 TraesCS3B01G307100 chr3B 83.036 112 6 8 5199 5298 817183872 817183982 8.200000e-14 89.8
8 TraesCS3B01G307100 chr3A 94.037 4511 182 32 757 5216 502398578 502403052 0.000000e+00 6759.0
9 TraesCS3B01G307100 chr3A 83.051 649 53 22 5297 5927 502403052 502403661 2.440000e-148 536.0
10 TraesCS3B01G307100 chr3A 95.385 65 3 0 2166 2230 502399930 502399994 2.930000e-18 104.0
11 TraesCS3B01G307100 chr3D 93.823 4549 173 38 725 5216 378239039 378243536 0.000000e+00 6745.0
12 TraesCS3B01G307100 chr3D 91.190 647 27 10 5297 5927 378243536 378244168 0.000000e+00 852.0
13 TraesCS3B01G307100 chr3D 91.589 107 8 1 5210 5316 491624177 491624282 4.800000e-31 147.0
14 TraesCS3B01G307100 chr7A 95.733 703 30 0 1 703 42527907 42527205 0.000000e+00 1133.0
15 TraesCS3B01G307100 chr2D 95.611 319 14 0 1 319 551425380 551425698 4.110000e-141 512.0
16 TraesCS3B01G307100 chr4A 78.000 700 149 5 1 697 462869416 462870113 9.150000e-118 435.0
17 TraesCS3B01G307100 chr2A 97.826 92 2 0 5209 5300 303731289 303731198 6.160000e-35 159.0
18 TraesCS3B01G307100 chr2A 94.898 98 5 0 5213 5310 442579527 442579624 2.870000e-33 154.0
19 TraesCS3B01G307100 chr2A 87.156 109 12 2 5198 5305 61863114 61863007 8.090000e-24 122.0
20 TraesCS3B01G307100 chr1A 94.118 102 4 2 5205 5304 504269078 504269179 2.870000e-33 154.0
21 TraesCS3B01G307100 chr1D 90.991 111 8 2 5209 5318 107173589 107173698 1.330000e-31 148.0
22 TraesCS3B01G307100 chr1D 91.589 107 8 1 5213 5318 12153641 12153535 4.800000e-31 147.0
23 TraesCS3B01G307100 chr1D 95.652 92 3 1 5213 5303 13295737 13295828 4.800000e-31 147.0
24 TraesCS3B01G307100 chr7D 91.589 107 8 1 5213 5318 21884116 21884010 4.800000e-31 147.0


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 TraesCS3B01G307100 chr3B 493162000 493167941 5941 False 3722.400000 10973 94.286000 1 5942 3 chr3B.!!$F4 5941
1 TraesCS3B01G307100 chr3B 493273961 493274710 749 False 469.000000 531 91.610000 4977 5824 2 chr3B.!!$F5 847
2 TraesCS3B01G307100 chr3A 502398578 502403661 5083 False 2466.333333 6759 90.824333 757 5927 3 chr3A.!!$F1 5170
3 TraesCS3B01G307100 chr3D 378239039 378244168 5129 False 3798.500000 6745 92.506500 725 5927 2 chr3D.!!$F2 5202
4 TraesCS3B01G307100 chr7A 42527205 42527907 702 True 1133.000000 1133 95.733000 1 703 1 chr7A.!!$R1 702
5 TraesCS3B01G307100 chr4A 462869416 462870113 697 False 435.000000 435 78.000000 1 697 1 chr4A.!!$F1 696

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
913 930 0.099613 CTCTCGCATCGCACTACAGT 59.900 55.000 0.00 0.0 0.00 3.55 F
1420 1448 1.141881 CGTTCCCCTCACAGATCGG 59.858 63.158 0.00 0.0 0.00 4.18 F
1503 1531 1.152839 GAGGAGGACTCGGAGGAGG 60.153 68.421 10.23 0.0 44.93 4.30 F
2554 2583 1.550072 TGCAGTGATGTCTCGATGGAA 59.450 47.619 0.00 0.0 0.00 3.53 F
3096 3133 1.565390 CCCATGCTGGAAGAGGTGGA 61.565 60.000 4.00 0.0 40.96 4.02 F
4243 4288 0.392863 TTGGTGGCGATGATCTGGTG 60.393 55.000 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2367 0.107410 ATATTTGCCGCCGGAACTCA 60.107 50.000 7.68 0.0 0.00 3.41 R
3096 3133 0.617413 CCTCAGTCATCCCACTGCTT 59.383 55.000 0.00 0.0 43.18 3.91 R
3150 3187 1.977854 TCAGTAAGAGGAGCAAGCCAA 59.022 47.619 0.00 0.0 0.00 4.52 R
3614 3658 0.995803 TGCCCCTAGTTGTATGCCAA 59.004 50.000 0.00 0.0 0.00 4.52 R
4733 4789 2.285977 TGCATTGCATCAGTAGAGCAG 58.714 47.619 7.38 0.0 39.72 4.24 R
5776 5877 1.263217 ACAACGGCAGAAAACATCGTC 59.737 47.619 0.00 0.0 33.34 4.20 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
22 23 3.005554 CTCTGTCGACATGGATTGCTTT 58.994 45.455 20.40 0.00 0.00 3.51
40 41 7.765695 TTGCTTTGAAAGTCTCCATAAGAAT 57.234 32.000 6.81 0.00 35.21 2.40
324 326 2.672996 CCTGTTCCAAGTGGCCGG 60.673 66.667 0.00 0.00 34.44 6.13
374 376 2.550830 CGGAGGGTTTGCAGCTATAT 57.449 50.000 0.00 0.00 0.00 0.86
386 388 3.074412 GCAGCTATATTGCCGTATGGTT 58.926 45.455 5.48 0.00 37.67 3.67
406 408 3.581024 TGCAACATTTCATCTCTTGGC 57.419 42.857 0.00 0.00 0.00 4.52
524 526 0.475906 GATCTGGCTTGGGTGGCTAT 59.524 55.000 0.00 0.00 0.00 2.97
537 539 2.035066 GGTGGCTATCAATGGTTGCATC 59.965 50.000 2.03 0.00 0.00 3.91
538 540 2.954318 GTGGCTATCAATGGTTGCATCT 59.046 45.455 2.03 0.00 0.00 2.90
581 583 6.726490 AGTATATACTTTTCAGAAGGCGGA 57.274 37.500 9.71 0.00 31.13 5.54
691 693 2.695147 GCCTCCCAATGATTTAGGTTGG 59.305 50.000 0.00 0.00 41.57 3.77
700 702 4.137116 TGATTTAGGTTGGGTCATCTCG 57.863 45.455 0.00 0.00 0.00 4.04
703 705 5.188163 TGATTTAGGTTGGGTCATCTCGTTA 59.812 40.000 0.00 0.00 0.00 3.18
704 706 5.486735 TTTAGGTTGGGTCATCTCGTTAA 57.513 39.130 0.00 0.00 0.00 2.01
705 707 5.687166 TTAGGTTGGGTCATCTCGTTAAT 57.313 39.130 0.00 0.00 0.00 1.40
706 708 4.569719 AGGTTGGGTCATCTCGTTAATT 57.430 40.909 0.00 0.00 0.00 1.40
707 709 5.687166 AGGTTGGGTCATCTCGTTAATTA 57.313 39.130 0.00 0.00 0.00 1.40
708 710 5.671493 AGGTTGGGTCATCTCGTTAATTAG 58.329 41.667 0.00 0.00 0.00 1.73
709 711 5.189145 AGGTTGGGTCATCTCGTTAATTAGT 59.811 40.000 0.00 0.00 0.00 2.24
710 712 5.878669 GGTTGGGTCATCTCGTTAATTAGTT 59.121 40.000 0.00 0.00 0.00 2.24
711 713 6.183360 GGTTGGGTCATCTCGTTAATTAGTTG 60.183 42.308 0.00 0.00 0.00 3.16
712 714 4.873827 TGGGTCATCTCGTTAATTAGTTGC 59.126 41.667 0.00 0.00 0.00 4.17
713 715 5.116882 GGGTCATCTCGTTAATTAGTTGCT 58.883 41.667 0.00 0.00 0.00 3.91
714 716 5.234543 GGGTCATCTCGTTAATTAGTTGCTC 59.765 44.000 0.00 0.00 0.00 4.26
715 717 5.234543 GGTCATCTCGTTAATTAGTTGCTCC 59.765 44.000 0.00 0.00 0.00 4.70
716 718 5.234543 GTCATCTCGTTAATTAGTTGCTCCC 59.765 44.000 0.00 0.00 0.00 4.30
717 719 3.777478 TCTCGTTAATTAGTTGCTCCCG 58.223 45.455 0.00 0.00 0.00 5.14
718 720 2.864343 CTCGTTAATTAGTTGCTCCCGG 59.136 50.000 0.00 0.00 0.00 5.73
719 721 2.496871 TCGTTAATTAGTTGCTCCCGGA 59.503 45.455 0.73 0.00 0.00 5.14
720 722 2.606272 CGTTAATTAGTTGCTCCCGGAC 59.394 50.000 0.73 0.00 0.00 4.79
721 723 2.941064 GTTAATTAGTTGCTCCCGGACC 59.059 50.000 0.73 0.00 0.00 4.46
722 724 0.988832 AATTAGTTGCTCCCGGACCA 59.011 50.000 0.73 0.00 0.00 4.02
723 725 0.988832 ATTAGTTGCTCCCGGACCAA 59.011 50.000 0.73 0.00 0.00 3.67
724 726 0.323629 TTAGTTGCTCCCGGACCAAG 59.676 55.000 0.73 0.00 0.00 3.61
725 727 1.550130 TAGTTGCTCCCGGACCAAGG 61.550 60.000 0.73 0.00 0.00 3.61
726 728 2.528127 TTGCTCCCGGACCAAGGA 60.528 61.111 0.73 0.44 0.00 3.36
729 731 2.982130 CTCCCGGACCAAGGAGTG 59.018 66.667 16.43 0.00 44.01 3.51
730 732 1.913762 CTCCCGGACCAAGGAGTGT 60.914 63.158 16.43 0.00 44.01 3.55
731 733 0.613853 CTCCCGGACCAAGGAGTGTA 60.614 60.000 16.43 0.00 44.01 2.90
773 775 2.418368 TGTGCCTTGAGAACACAAGT 57.582 45.000 10.07 0.00 43.72 3.16
819 822 4.492160 GCGTGACCTCGATGCGGA 62.492 66.667 0.00 0.00 0.00 5.54
820 823 2.413351 CGTGACCTCGATGCGGAT 59.587 61.111 0.00 0.00 0.00 4.18
823 826 1.455773 TGACCTCGATGCGGATCCT 60.456 57.895 11.64 0.00 0.00 3.24
913 930 0.099613 CTCTCGCATCGCACTACAGT 59.900 55.000 0.00 0.00 0.00 3.55
932 949 2.300437 AGTCTGTACTCTGCAACCCTTC 59.700 50.000 0.00 0.00 0.00 3.46
976 998 3.110178 CAAACCCCGTCGTCTCGC 61.110 66.667 0.00 0.00 0.00 5.03
1389 1417 2.480416 CGCTTCGCTTCACCTCTTCTAT 60.480 50.000 0.00 0.00 0.00 1.98
1420 1448 1.141881 CGTTCCCCTCACAGATCGG 59.858 63.158 0.00 0.00 0.00 4.18
1503 1531 1.152839 GAGGAGGACTCGGAGGAGG 60.153 68.421 10.23 0.00 44.93 4.30
1685 1713 3.515330 TTCGTGCTTAAGGTAGGTAGC 57.485 47.619 4.29 0.00 0.00 3.58
1687 1715 1.568606 GTGCTTAAGGTAGGTAGCGC 58.431 55.000 0.00 0.00 36.43 5.92
1888 1917 2.094700 GTCGATGGTGAAGACACTAGCA 60.095 50.000 0.00 0.00 42.45 3.49
2039 2068 1.623811 ACAACCGACTCAAGGTATGCT 59.376 47.619 0.00 0.00 41.95 3.79
2095 2124 6.769512 AGGTTCAATAGCTTCTTCACTGTAA 58.230 36.000 0.00 0.00 0.00 2.41
2184 2213 9.801873 AATTTACTGAAATGAAATTGGTATCGG 57.198 29.630 0.00 0.00 36.10 4.18
2338 2367 3.200825 ACCGAGGAACAATCTCCAATGAT 59.799 43.478 0.00 0.00 38.02 2.45
2554 2583 1.550072 TGCAGTGATGTCTCGATGGAA 59.450 47.619 0.00 0.00 0.00 3.53
2810 2840 3.118000 CAGAGGTATGGGGGAAAACTACC 60.118 52.174 0.00 0.00 33.52 3.18
2864 2894 2.046023 CCTGGCATCAGCGTTCCA 60.046 61.111 0.00 0.00 43.41 3.53
2930 2960 4.201666 GCTTTTGAGAGAGTAATGCACGAG 60.202 45.833 0.00 0.00 0.00 4.18
2975 3005 1.898574 GTGCCCACAGGTGTCAAGG 60.899 63.158 0.00 0.00 34.57 3.61
3000 3030 7.148069 GGGAGAAGGTACAATTTACATTGGAAG 60.148 40.741 6.56 0.00 43.82 3.46
3001 3031 7.393515 GGAGAAGGTACAATTTACATTGGAAGT 59.606 37.037 6.56 0.00 43.82 3.01
3030 3067 9.452287 GTAGGTACATCATTTTGGGTAAGTTAA 57.548 33.333 0.00 0.00 0.00 2.01
3040 3077 8.987890 CATTTTGGGTAAGTTAACTGAAATTGG 58.012 33.333 9.34 0.00 0.00 3.16
3096 3133 1.565390 CCCATGCTGGAAGAGGTGGA 61.565 60.000 4.00 0.00 40.96 4.02
3290 3329 6.647334 TTTTTATTGTGCTGGTTCATCTGA 57.353 33.333 0.00 0.00 0.00 3.27
3332 3371 8.624776 AGTAGTCCAATTATTACCGTGTAGTAC 58.375 37.037 0.00 0.00 0.00 2.73
3347 3386 7.088905 CCGTGTAGTACTTTTTCTAGTGACAT 58.911 38.462 0.00 0.00 0.00 3.06
3387 3426 4.574013 GCATTTTCCAAACCAAATGTGTGA 59.426 37.500 6.51 0.00 40.89 3.58
3413 3457 5.701224 TCAAGTGTTTGGATCCCTTAACTT 58.299 37.500 9.90 11.23 34.97 2.66
3420 3464 6.834451 TGTTTGGATCCCTTAACTTTACACAA 59.166 34.615 9.90 0.00 0.00 3.33
3494 3538 8.632679 CAGTCAATAATTAGTGTGGGCATTTAT 58.367 33.333 12.28 0.00 0.00 1.40
3497 3541 8.420222 TCAATAATTAGTGTGGGCATTTATTGG 58.580 33.333 12.28 0.00 36.73 3.16
3511 3555 6.017852 GGCATTTATTGGTGAGCTACTCTTAC 60.018 42.308 0.00 0.00 0.00 2.34
3524 3568 9.409918 TGAGCTACTCTTACATTGATACTACTT 57.590 33.333 0.00 0.00 0.00 2.24
3614 3658 9.956640 GTTCTCTTATTATCTCCATCATTCCAT 57.043 33.333 0.00 0.00 0.00 3.41
3618 3662 7.613022 TCTTATTATCTCCATCATTCCATTGGC 59.387 37.037 0.00 0.00 0.00 4.52
3652 3696 5.450550 GGGGCATTGCATACTTTTAGAAGTC 60.451 44.000 11.39 0.00 44.75 3.01
3690 3734 5.476945 AGGATCAATTTGCTAAACGGTTCTT 59.523 36.000 0.00 0.00 0.00 2.52
3874 3919 6.693045 GCCCCTACTCCCATATTTGTTATGAA 60.693 42.308 0.00 0.00 40.22 2.57
4018 4063 2.040813 ACCACCAAGAGATCAGCAACAT 59.959 45.455 0.00 0.00 0.00 2.71
4075 4120 2.105477 TCTGAAAGAAAGCCAGCTGACT 59.895 45.455 17.39 5.81 42.31 3.41
4108 4153 2.657102 CTTCTCCTGATCTGCCGGCC 62.657 65.000 26.77 9.02 0.00 6.13
4138 4183 3.135994 TGGCGGTAAGAAGAAAGACAAC 58.864 45.455 0.00 0.00 0.00 3.32
4243 4288 0.392863 TTGGTGGCGATGATCTGGTG 60.393 55.000 0.00 0.00 0.00 4.17
4249 4294 1.134699 GGCGATGATCTGGTGTCAAGA 60.135 52.381 0.00 0.00 0.00 3.02
4261 4306 2.237143 GGTGTCAAGATCAGGGTCATCA 59.763 50.000 0.00 0.00 0.00 3.07
4372 4417 5.741011 TCTGGATTCTTAACACCATGGTAC 58.259 41.667 19.28 0.00 0.00 3.34
4377 4422 4.603989 TCTTAACACCATGGTACGTTCA 57.396 40.909 19.28 9.27 0.00 3.18
4443 4497 5.935945 TGGAAGTGAACTGTGGAATCTAAA 58.064 37.500 0.00 0.00 0.00 1.85
4483 4537 5.659463 AGTTAGCTCATCTGCTTAGAAGTG 58.341 41.667 0.00 0.00 43.74 3.16
4492 4546 6.434340 TCATCTGCTTAGAAGTGACAGACTAA 59.566 38.462 0.00 0.00 39.97 2.24
4540 4594 6.785488 TTGTAACTAGATGAGCACAAACTG 57.215 37.500 0.00 0.00 32.96 3.16
4567 4621 6.422100 ACGAGCAATCTAAGTTAGCACATATG 59.578 38.462 4.93 0.00 0.00 1.78
4624 4678 8.954950 AGTTCAGTATCAAGAATAACCATCTG 57.045 34.615 0.00 0.00 0.00 2.90
4625 4679 8.762645 AGTTCAGTATCAAGAATAACCATCTGA 58.237 33.333 0.00 0.00 0.00 3.27
4626 4680 9.383519 GTTCAGTATCAAGAATAACCATCTGAA 57.616 33.333 0.00 0.00 36.37 3.02
4628 4682 9.770097 TCAGTATCAAGAATAACCATCTGAATC 57.230 33.333 0.00 0.00 0.00 2.52
4629 4683 9.551734 CAGTATCAAGAATAACCATCTGAATCA 57.448 33.333 0.00 0.00 0.00 2.57
4630 4684 9.553064 AGTATCAAGAATAACCATCTGAATCAC 57.447 33.333 0.00 0.00 0.00 3.06
4631 4685 9.553064 GTATCAAGAATAACCATCTGAATCACT 57.447 33.333 0.00 0.00 0.00 3.41
4669 4723 8.743085 ATAGATATGAACTGAATGTGCTTTGT 57.257 30.769 0.00 0.00 0.00 2.83
4672 4726 8.025445 AGATATGAACTGAATGTGCTTTGTTTC 58.975 33.333 0.00 0.00 0.00 2.78
4676 4730 6.265196 TGAACTGAATGTGCTTTGTTTCCTAT 59.735 34.615 0.00 0.00 0.00 2.57
4681 4735 6.208402 TGAATGTGCTTTGTTTCCTATTGCTA 59.792 34.615 0.00 0.00 0.00 3.49
4692 4746 7.630082 TGTTTCCTATTGCTAGTTGAATAGGT 58.370 34.615 23.14 0.00 46.27 3.08
4758 4814 1.717791 TACTGATGCAATGCAGCCGC 61.718 55.000 21.20 7.08 44.94 6.53
4875 4931 1.406898 CAGAATGAGCGCCAGTCTCTA 59.593 52.381 20.73 0.00 46.10 2.43
4958 5014 4.532126 TCTGTAAGGAAGATCTTTCTGGCA 59.468 41.667 17.30 16.28 30.72 4.92
4973 5029 2.328099 GGCACTTCTTCCACTGGCG 61.328 63.158 0.00 0.00 0.00 5.69
5073 5138 2.432510 CCTCTGAGGGCTGTACCTTAAG 59.567 54.545 16.19 0.00 42.10 1.85
5082 5147 0.035439 TGTACCTTAAGGCAGGCTGC 60.035 55.000 30.93 30.93 44.08 5.25
5221 5289 2.861147 AGTTGCAACTTACTCCCTCC 57.139 50.000 26.36 0.00 35.21 4.30
5222 5290 1.002087 AGTTGCAACTTACTCCCTCCG 59.998 52.381 26.36 0.00 35.21 4.63
5223 5291 1.053424 TTGCAACTTACTCCCTCCGT 58.947 50.000 0.00 0.00 0.00 4.69
5224 5292 1.053424 TGCAACTTACTCCCTCCGTT 58.947 50.000 0.00 0.00 0.00 4.44
5225 5293 1.001633 TGCAACTTACTCCCTCCGTTC 59.998 52.381 0.00 0.00 0.00 3.95
5226 5294 1.675116 GCAACTTACTCCCTCCGTTCC 60.675 57.143 0.00 0.00 0.00 3.62
5227 5295 1.621814 CAACTTACTCCCTCCGTTCCA 59.378 52.381 0.00 0.00 0.00 3.53
5228 5296 2.019807 ACTTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
5229 5297 2.332117 ACTTACTCCCTCCGTTCCAAA 58.668 47.619 0.00 0.00 0.00 3.28
5230 5298 2.707257 ACTTACTCCCTCCGTTCCAAAA 59.293 45.455 0.00 0.00 0.00 2.44
5231 5299 3.329814 ACTTACTCCCTCCGTTCCAAAAT 59.670 43.478 0.00 0.00 0.00 1.82
5232 5300 4.533311 ACTTACTCCCTCCGTTCCAAAATA 59.467 41.667 0.00 0.00 0.00 1.40
5233 5301 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5234 5302 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5235 5303 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5236 5304 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5237 5305 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5238 5306 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
5239 5307 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
5240 5308 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
5241 5309 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
5242 5310 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
5243 5311 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
5244 5312 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
5245 5313 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
5246 5314 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
5247 5315 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
5248 5316 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
5249 5317 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
5250 5318 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
5251 5319 8.531146 CCAAAATAGATGACCCAACTTTGTATT 58.469 33.333 0.00 0.00 0.00 1.89
5256 5324 9.975218 ATAGATGACCCAACTTTGTATTAAAGT 57.025 29.630 0.00 0.00 41.82 2.66
5258 5326 9.802039 AGATGACCCAACTTTGTATTAAAGTTA 57.198 29.630 15.03 3.25 45.57 2.24
5260 5328 8.983702 TGACCCAACTTTGTATTAAAGTTAGT 57.016 30.769 15.03 14.80 45.57 2.24
5288 5356 8.463930 AAAGTTGAGTCATCTATTTTGGAACA 57.536 30.769 4.14 0.00 0.00 3.18
5289 5357 7.678947 AGTTGAGTCATCTATTTTGGAACAG 57.321 36.000 1.70 0.00 42.39 3.16
5290 5358 7.453393 AGTTGAGTCATCTATTTTGGAACAGA 58.547 34.615 1.70 0.00 42.39 3.41
5291 5359 7.605691 AGTTGAGTCATCTATTTTGGAACAGAG 59.394 37.037 1.70 0.00 42.39 3.35
5292 5360 6.409704 TGAGTCATCTATTTTGGAACAGAGG 58.590 40.000 0.00 0.00 42.39 3.69
5293 5361 5.749462 AGTCATCTATTTTGGAACAGAGGG 58.251 41.667 0.00 0.00 42.39 4.30
5294 5362 5.488919 AGTCATCTATTTTGGAACAGAGGGA 59.511 40.000 0.00 0.00 42.39 4.20
5295 5363 5.819901 GTCATCTATTTTGGAACAGAGGGAG 59.180 44.000 0.00 0.00 42.39 4.30
5344 5412 2.238942 TGTGCACAACTCCTGTACAG 57.761 50.000 19.28 16.34 36.10 2.74
5359 5429 8.880244 ACTCCTGTACAGCATATATCCATTTTA 58.120 33.333 17.86 0.00 0.00 1.52
5431 5507 0.538057 CAGCATGTGGTCTGGTTGGT 60.538 55.000 0.00 0.00 0.00 3.67
5508 5584 1.202177 CCGATTCAACAGATTTGGCCG 60.202 52.381 0.00 0.00 0.00 6.13
5513 5589 1.003839 AACAGATTTGGCCGCGAGA 60.004 52.632 8.23 0.00 0.00 4.04
5522 5598 2.127232 GCCGCGAGACAAAAGTGC 60.127 61.111 8.23 0.00 0.00 4.40
5575 5651 4.019858 TGTTGTTGGTTGGAGTTTGATGA 58.980 39.130 0.00 0.00 0.00 2.92
5579 5655 3.855255 TGGTTGGAGTTTGATGACTCA 57.145 42.857 7.27 0.00 46.21 3.41
5583 5659 4.503991 GGTTGGAGTTTGATGACTCACTCT 60.504 45.833 7.27 0.00 46.21 3.24
5599 5675 4.348486 TCACTCTCTGTATCTTTCTGGCT 58.652 43.478 0.00 0.00 0.00 4.75
5642 5718 1.931841 CTGTCACCTGCATGAGAATCG 59.068 52.381 0.00 0.00 38.61 3.34
5645 5721 0.935898 CACCTGCATGAGAATCGAGC 59.064 55.000 0.00 0.00 38.61 5.03
5672 5758 3.334691 TCTTCTACCATGTTTTCTGCCG 58.665 45.455 0.00 0.00 0.00 5.69
5759 5855 1.133025 CTAAGCCATGTTTTCTGCCCG 59.867 52.381 0.00 0.00 0.00 6.13
5767 5863 1.407258 TGTTTTCTGCCCGGTCAAAAG 59.593 47.619 0.00 0.00 0.00 2.27
5776 5877 2.350522 CCCGGTCAAAAGAGTGATGAG 58.649 52.381 0.00 0.00 0.00 2.90
5827 5929 1.068588 TGTCGAGGAATTGGGCGATAG 59.931 52.381 0.00 0.00 35.08 2.08
5844 5946 4.178540 CGATAGGTGGTTTCGCTTTCTAA 58.821 43.478 0.00 0.00 0.00 2.10
5869 5971 9.829507 AATTCATTTTGGACAGACATGTAAAAA 57.170 25.926 0.00 0.38 40.68 1.94
5880 5982 9.774742 GACAGACATGTAAAAATATTCTGGTTC 57.225 33.333 0.00 0.00 40.68 3.62
5923 6025 1.472480 TCCTTGGCTCGCTAAAATTGC 59.528 47.619 0.00 0.00 0.00 3.56
5926 6028 3.578688 CTTGGCTCGCTAAAATTGCTTT 58.421 40.909 0.00 0.00 0.00 3.51
5927 6029 3.216147 TGGCTCGCTAAAATTGCTTTC 57.784 42.857 0.00 0.00 0.00 2.62
5928 6030 2.819608 TGGCTCGCTAAAATTGCTTTCT 59.180 40.909 0.00 0.00 0.00 2.52
5929 6031 4.006989 TGGCTCGCTAAAATTGCTTTCTA 58.993 39.130 0.00 0.00 0.00 2.10
5930 6032 4.094887 TGGCTCGCTAAAATTGCTTTCTAG 59.905 41.667 0.00 0.00 0.00 2.43
5931 6033 4.095036 GGCTCGCTAAAATTGCTTTCTAGT 59.905 41.667 0.00 0.00 0.00 2.57
5932 6034 5.392057 GGCTCGCTAAAATTGCTTTCTAGTT 60.392 40.000 0.00 0.00 0.00 2.24
5933 6035 5.734963 GCTCGCTAAAATTGCTTTCTAGTTC 59.265 40.000 0.00 0.00 0.00 3.01
5934 6036 6.620733 GCTCGCTAAAATTGCTTTCTAGTTCA 60.621 38.462 0.00 0.00 0.00 3.18
5935 6037 7.197071 TCGCTAAAATTGCTTTCTAGTTCAA 57.803 32.000 0.00 0.00 0.00 2.69
5936 6038 7.644490 TCGCTAAAATTGCTTTCTAGTTCAAA 58.356 30.769 0.00 0.00 0.00 2.69
5937 6039 7.589954 TCGCTAAAATTGCTTTCTAGTTCAAAC 59.410 33.333 0.00 0.00 0.00 2.93
5938 6040 7.591426 CGCTAAAATTGCTTTCTAGTTCAAACT 59.409 33.333 0.46 0.46 42.91 2.66
5939 6041 8.906693 GCTAAAATTGCTTTCTAGTTCAAACTC 58.093 33.333 0.00 0.00 40.37 3.01
5940 6042 9.950680 CTAAAATTGCTTTCTAGTTCAAACTCA 57.049 29.630 0.00 0.00 40.37 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.553085 TCAGGATATTCTTATGGAGACTTTCA 57.447 34.615 0.00 0.00 33.02 2.69
40 41 2.326428 GTTCCGGGGAAGATCAGGATA 58.674 52.381 0.00 0.00 34.49 2.59
324 326 1.819905 GAGCTGCTGGACTCTACCC 59.180 63.158 7.01 0.00 0.00 3.69
374 376 1.252175 ATGTTGCAACCATACGGCAA 58.748 45.000 26.14 5.01 44.50 4.52
386 388 2.892215 TGCCAAGAGATGAAATGTTGCA 59.108 40.909 0.00 0.00 0.00 4.08
406 408 6.949352 AATATTTGGTCAGATAACTGGCTG 57.051 37.500 4.49 0.00 46.60 4.85
517 519 2.954318 AGATGCAACCATTGATAGCCAC 59.046 45.455 0.00 0.00 0.00 5.01
524 526 6.380560 TCATCCATTTTAGATGCAACCATTGA 59.619 34.615 0.00 0.00 40.79 2.57
537 539 5.133221 ACTTCCCGGAATCATCCATTTTAG 58.867 41.667 0.73 0.00 46.97 1.85
538 540 5.124036 ACTTCCCGGAATCATCCATTTTA 57.876 39.130 0.73 0.00 46.97 1.52
581 583 7.836685 TCTTCAATATCCAGAGTCTCTTAGTGT 59.163 37.037 0.00 0.00 0.00 3.55
691 693 5.234543 GGAGCAACTAATTAACGAGATGACC 59.765 44.000 0.00 0.00 0.00 4.02
700 702 2.941064 GGTCCGGGAGCAACTAATTAAC 59.059 50.000 20.82 0.00 0.00 2.01
703 705 0.988832 TGGTCCGGGAGCAACTAATT 59.011 50.000 25.57 0.00 37.11 1.40
704 706 0.988832 TTGGTCCGGGAGCAACTAAT 59.011 50.000 31.75 0.00 43.62 1.73
705 707 0.323629 CTTGGTCCGGGAGCAACTAA 59.676 55.000 31.75 16.17 43.62 2.24
706 708 1.550130 CCTTGGTCCGGGAGCAACTA 61.550 60.000 31.75 16.50 43.62 2.24
707 709 2.750350 CTTGGTCCGGGAGCAACT 59.250 61.111 31.75 0.00 43.62 3.16
708 710 2.359975 CCTTGGTCCGGGAGCAAC 60.360 66.667 31.75 6.31 43.62 4.17
709 711 2.528127 TCCTTGGTCCGGGAGCAA 60.528 61.111 32.61 32.61 45.75 3.91
710 712 3.003173 CTCCTTGGTCCGGGAGCA 61.003 66.667 24.17 24.17 41.92 4.26
713 715 0.613853 CTACACTCCTTGGTCCGGGA 60.614 60.000 0.00 0.00 0.00 5.14
714 716 0.903454 ACTACACTCCTTGGTCCGGG 60.903 60.000 0.00 0.00 0.00 5.73
715 717 0.246635 CACTACACTCCTTGGTCCGG 59.753 60.000 0.00 0.00 0.00 5.14
716 718 0.389948 GCACTACACTCCTTGGTCCG 60.390 60.000 0.00 0.00 0.00 4.79
717 719 0.977395 AGCACTACACTCCTTGGTCC 59.023 55.000 0.00 0.00 0.00 4.46
718 720 2.808543 CAAAGCACTACACTCCTTGGTC 59.191 50.000 0.00 0.00 0.00 4.02
719 721 2.172717 ACAAAGCACTACACTCCTTGGT 59.827 45.455 0.00 0.00 0.00 3.67
720 722 2.549754 CACAAAGCACTACACTCCTTGG 59.450 50.000 0.00 0.00 0.00 3.61
721 723 2.549754 CCACAAAGCACTACACTCCTTG 59.450 50.000 0.00 0.00 0.00 3.61
722 724 2.487265 CCCACAAAGCACTACACTCCTT 60.487 50.000 0.00 0.00 0.00 3.36
723 725 1.072331 CCCACAAAGCACTACACTCCT 59.928 52.381 0.00 0.00 0.00 3.69
724 726 1.523758 CCCACAAAGCACTACACTCC 58.476 55.000 0.00 0.00 0.00 3.85
725 727 0.875059 GCCCACAAAGCACTACACTC 59.125 55.000 0.00 0.00 0.00 3.51
726 728 0.474184 AGCCCACAAAGCACTACACT 59.526 50.000 0.00 0.00 0.00 3.55
727 729 1.804748 GTAGCCCACAAAGCACTACAC 59.195 52.381 0.00 0.00 34.65 2.90
728 730 1.697432 AGTAGCCCACAAAGCACTACA 59.303 47.619 0.00 0.00 36.51 2.74
729 731 2.076863 CAGTAGCCCACAAAGCACTAC 58.923 52.381 0.00 0.00 34.71 2.73
730 732 1.003118 CCAGTAGCCCACAAAGCACTA 59.997 52.381 0.00 0.00 0.00 2.74
731 733 0.250901 CCAGTAGCCCACAAAGCACT 60.251 55.000 0.00 0.00 0.00 4.40
772 774 0.038892 TCCAGCCGTCGTTAGTGAAC 60.039 55.000 0.00 0.00 0.00 3.18
773 775 0.892755 ATCCAGCCGTCGTTAGTGAA 59.107 50.000 0.00 0.00 0.00 3.18
818 821 2.317149 CTTCCACGCCTCCCAGGATC 62.317 65.000 0.00 0.00 37.67 3.36
819 822 2.285368 TTCCACGCCTCCCAGGAT 60.285 61.111 0.00 0.00 37.67 3.24
820 823 3.003173 CTTCCACGCCTCCCAGGA 61.003 66.667 0.00 0.00 37.67 3.86
823 826 2.525629 TGTCTTCCACGCCTCCCA 60.526 61.111 0.00 0.00 0.00 4.37
913 930 1.623811 GGAAGGGTTGCAGAGTACAGA 59.376 52.381 0.00 0.00 0.00 3.41
1372 1400 2.457598 ACCATAGAAGAGGTGAAGCGA 58.542 47.619 0.00 0.00 36.60 4.93
1420 1448 2.152016 GTTTACCAGAAGCACCAGACC 58.848 52.381 0.00 0.00 0.00 3.85
1596 1624 1.442526 CTCATGACGATGGGCTTGGC 61.443 60.000 0.00 0.00 0.00 4.52
1685 1713 1.800805 ATCACTGAACTGAAGTGGCG 58.199 50.000 3.91 0.00 44.26 5.69
1687 1715 5.505173 AAACAATCACTGAACTGAAGTGG 57.495 39.130 3.91 0.00 44.26 4.00
2039 2068 0.828762 ATTGTTCTGCAGGCTGGCAA 60.829 50.000 17.64 11.92 44.40 4.52
2095 2124 7.147915 ACACAGTACCAACTTCATTTCACAATT 60.148 33.333 0.00 0.00 31.97 2.32
2109 2138 8.718102 ACAATATCATAAGACACAGTACCAAC 57.282 34.615 0.00 0.00 0.00 3.77
2184 2213 3.126831 CAGGCGACAATATCAGAAGACC 58.873 50.000 0.00 0.00 0.00 3.85
2338 2367 0.107410 ATATTTGCCGCCGGAACTCA 60.107 50.000 7.68 0.00 0.00 3.41
2564 2593 3.228188 TGCTTGAAGTTTGGAGTCCAT 57.772 42.857 14.00 0.00 31.53 3.41
2578 2607 2.902486 AGAGACATCAGAGGTTGCTTGA 59.098 45.455 0.00 0.00 0.00 3.02
2810 2840 1.129998 CTGTGCATTTGCTCCTCTTCG 59.870 52.381 3.94 0.00 42.66 3.79
2864 2894 3.263681 GGCTAGAGTTGGGAGGTTTTACT 59.736 47.826 0.00 0.00 0.00 2.24
2975 3005 7.393515 ACTTCCAATGTAAATTGTACCTTCTCC 59.606 37.037 4.91 0.00 0.00 3.71
3000 3030 6.584185 ACCCAAAATGATGTACCTACAAAC 57.416 37.500 0.00 0.00 39.99 2.93
3001 3031 7.945664 ACTTACCCAAAATGATGTACCTACAAA 59.054 33.333 0.00 0.00 39.99 2.83
3030 3067 5.078949 TGACATCAACATCCCAATTTCAGT 58.921 37.500 0.00 0.00 0.00 3.41
3040 3077 3.181493 GCAACCTGATGACATCAACATCC 60.181 47.826 18.49 4.80 42.11 3.51
3096 3133 0.617413 CCTCAGTCATCCCACTGCTT 59.383 55.000 0.00 0.00 43.18 3.91
3138 3175 2.042831 AAGCCAAGATCGTGCAGCC 61.043 57.895 2.75 0.00 0.00 4.85
3150 3187 1.977854 TCAGTAAGAGGAGCAAGCCAA 59.022 47.619 0.00 0.00 0.00 4.52
3208 3245 3.119531 CGCTCCATTGCAAGGTCAAATAA 60.120 43.478 10.60 0.00 0.00 1.40
3290 3329 8.605325 TTGGACTACTAAATAAGGCTAGAAGT 57.395 34.615 0.00 0.00 0.00 3.01
3319 3358 8.076178 GTCACTAGAAAAAGTACTACACGGTAA 58.924 37.037 0.00 0.00 0.00 2.85
3322 3361 6.441274 TGTCACTAGAAAAAGTACTACACGG 58.559 40.000 0.00 0.00 0.00 4.94
3323 3362 9.616634 TTATGTCACTAGAAAAAGTACTACACG 57.383 33.333 0.00 0.00 0.00 4.49
3332 3371 7.361286 GCAGTTCCCTTATGTCACTAGAAAAAG 60.361 40.741 0.00 0.00 0.00 2.27
3372 3411 5.232626 CACTTGATGTCACACATTTGGTTTG 59.767 40.000 0.00 0.00 39.27 2.93
3387 3426 3.814504 AGGGATCCAAACACTTGATGT 57.185 42.857 15.23 0.00 46.42 3.06
3428 3472 6.096987 GGAGACAGTGATCAACAGTAATAGGA 59.903 42.308 0.00 0.00 0.00 2.94
3494 3538 5.738619 TCAATGTAAGAGTAGCTCACCAA 57.261 39.130 0.00 0.00 32.06 3.67
3497 3541 8.842280 AGTAGTATCAATGTAAGAGTAGCTCAC 58.158 37.037 0.00 0.00 32.06 3.51
3603 3647 4.342951 AGTTGTATGCCAATGGAATGATGG 59.657 41.667 2.05 0.00 35.02 3.51
3614 3658 0.995803 TGCCCCTAGTTGTATGCCAA 59.004 50.000 0.00 0.00 0.00 4.52
3618 3662 2.653726 TGCAATGCCCCTAGTTGTATG 58.346 47.619 1.53 0.00 0.00 2.39
3652 3696 4.760530 TTGATCCTGATGTACTCCAAGG 57.239 45.455 0.00 0.00 0.00 3.61
3713 3758 9.826574 ATCCATATTTTCAACATTTTGATCTGG 57.173 29.630 0.00 0.01 41.50 3.86
3874 3919 1.507141 CGCCACCAAGAAAGTCGCTT 61.507 55.000 0.00 0.00 0.00 4.68
4018 4063 3.543680 GCTTTAGCAGGTGGAGTCATA 57.456 47.619 0.00 0.00 41.59 2.15
4075 4120 2.746697 AGAAGGCGTCTCAGGAACA 58.253 52.632 0.00 0.00 0.00 3.18
4108 4153 5.055642 TCTTCTTACCGCCATGTATATCG 57.944 43.478 0.00 0.00 0.00 2.92
4120 4165 3.645884 TCCGTTGTCTTTCTTCTTACCG 58.354 45.455 0.00 0.00 0.00 4.02
4138 4183 3.507233 CCCCACCATCATTCATATTTCCG 59.493 47.826 0.00 0.00 0.00 4.30
4243 4288 5.510520 GGAGTATGATGACCCTGATCTTGAC 60.511 48.000 0.00 0.00 0.00 3.18
4249 4294 2.636893 GCTGGAGTATGATGACCCTGAT 59.363 50.000 0.00 0.00 0.00 2.90
4372 4417 5.057149 AGCTATAGCCCATAAGTTTGAACG 58.943 41.667 21.17 0.00 43.38 3.95
4377 4422 9.722317 AGAGATATAGCTATAGCCCATAAGTTT 57.278 33.333 22.27 3.73 43.38 2.66
4443 4497 7.775093 TGAGCTAACTTAGGCATGAATTACAAT 59.225 33.333 0.00 0.00 0.00 2.71
4540 4594 4.625742 TGTGCTAACTTAGATTGCTCGTTC 59.374 41.667 0.00 0.00 0.00 3.95
4567 4621 3.067833 GCCTAGTGGAAGTGTCTTCAAC 58.932 50.000 8.48 8.48 34.57 3.18
4676 4730 6.553953 TGGATACACCTATTCAACTAGCAA 57.446 37.500 0.00 0.00 46.17 3.91
4721 4775 7.923344 GCATCAGTAGAGCAGAAGTATTAGAAA 59.077 37.037 0.00 0.00 0.00 2.52
4733 4789 2.285977 TGCATTGCATCAGTAGAGCAG 58.714 47.619 7.38 0.00 39.72 4.24
4758 4814 4.502645 CCAAGTGCTAAAAACAACCTTTCG 59.497 41.667 0.00 0.00 0.00 3.46
4806 4862 4.214119 ACAAACATGTCCATGAACTTCTCG 59.786 41.667 13.93 0.00 41.20 4.04
4875 4931 4.576463 AGCAGAATCTTTTGACGTTTCAGT 59.424 37.500 0.00 0.00 31.71 3.41
4958 5014 4.779475 CACGCCAGTGGAAGAAGT 57.221 55.556 15.20 0.92 44.34 3.01
4973 5029 4.265073 ACCCTGAAGCTCATGAAATACAC 58.735 43.478 0.00 0.00 0.00 2.90
5082 5147 7.921786 TTGACATACAGAGAATACAAAAGGG 57.078 36.000 0.00 0.00 0.00 3.95
5215 5283 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
5216 5284 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
5217 5285 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
5218 5286 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
5219 5287 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
5220 5288 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
5221 5289 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
5222 5290 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
5223 5291 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
5224 5292 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
5225 5293 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
5230 5298 9.975218 ACTTTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 37.18 1.98
5231 5299 9.802039 AACTTTAATACAAAGTTGGGTCATCTA 57.198 29.630 12.88 0.00 45.58 1.98
5232 5300 8.706322 AACTTTAATACAAAGTTGGGTCATCT 57.294 30.769 12.88 0.00 45.58 2.90
5234 5302 9.582648 ACTAACTTTAATACAAAGTTGGGTCAT 57.417 29.630 21.95 6.17 46.38 3.06
5235 5303 8.983702 ACTAACTTTAATACAAAGTTGGGTCA 57.016 30.769 21.95 6.46 46.38 4.02
5262 5330 9.567776 TGTTCCAAAATAGATGACTCAACTTTA 57.432 29.630 0.00 0.00 0.00 1.85
5263 5331 8.463930 TGTTCCAAAATAGATGACTCAACTTT 57.536 30.769 0.00 0.00 0.00 2.66
5264 5332 7.939039 TCTGTTCCAAAATAGATGACTCAACTT 59.061 33.333 0.00 0.00 28.72 2.66
5265 5333 7.453393 TCTGTTCCAAAATAGATGACTCAACT 58.547 34.615 0.00 0.00 28.72 3.16
5266 5334 7.148340 CCTCTGTTCCAAAATAGATGACTCAAC 60.148 40.741 0.00 0.00 32.88 3.18
5267 5335 6.881065 CCTCTGTTCCAAAATAGATGACTCAA 59.119 38.462 0.00 0.00 32.88 3.02
5268 5336 6.409704 CCTCTGTTCCAAAATAGATGACTCA 58.590 40.000 0.00 0.00 32.88 3.41
5269 5337 5.819901 CCCTCTGTTCCAAAATAGATGACTC 59.180 44.000 0.00 0.00 32.88 3.36
5270 5338 5.488919 TCCCTCTGTTCCAAAATAGATGACT 59.511 40.000 0.00 0.00 32.88 3.41
5271 5339 5.745227 TCCCTCTGTTCCAAAATAGATGAC 58.255 41.667 0.00 0.00 32.88 3.06
5272 5340 5.488919 ACTCCCTCTGTTCCAAAATAGATGA 59.511 40.000 0.00 0.00 32.88 2.92
5273 5341 5.749462 ACTCCCTCTGTTCCAAAATAGATG 58.251 41.667 0.00 0.00 32.88 2.90
5274 5342 6.903534 TCTACTCCCTCTGTTCCAAAATAGAT 59.096 38.462 0.00 0.00 32.88 1.98
5275 5343 6.261435 TCTACTCCCTCTGTTCCAAAATAGA 58.739 40.000 0.00 0.00 32.42 1.98
5276 5344 6.546428 TCTACTCCCTCTGTTCCAAAATAG 57.454 41.667 0.00 0.00 0.00 1.73
5277 5345 7.510675 AATCTACTCCCTCTGTTCCAAAATA 57.489 36.000 0.00 0.00 0.00 1.40
5278 5346 6.394345 AATCTACTCCCTCTGTTCCAAAAT 57.606 37.500 0.00 0.00 0.00 1.82
5279 5347 5.843019 AATCTACTCCCTCTGTTCCAAAA 57.157 39.130 0.00 0.00 0.00 2.44
5280 5348 5.843019 AAATCTACTCCCTCTGTTCCAAA 57.157 39.130 0.00 0.00 0.00 3.28
5281 5349 5.843019 AAAATCTACTCCCTCTGTTCCAA 57.157 39.130 0.00 0.00 0.00 3.53
5282 5350 6.672218 TCATAAAATCTACTCCCTCTGTTCCA 59.328 38.462 0.00 0.00 0.00 3.53
5283 5351 7.125792 TCATAAAATCTACTCCCTCTGTTCC 57.874 40.000 0.00 0.00 0.00 3.62
5284 5352 8.646900 AGATCATAAAATCTACTCCCTCTGTTC 58.353 37.037 0.00 0.00 34.21 3.18
5285 5353 8.560124 AGATCATAAAATCTACTCCCTCTGTT 57.440 34.615 0.00 0.00 34.21 3.16
5286 5354 7.040062 CGAGATCATAAAATCTACTCCCTCTGT 60.040 40.741 0.00 0.00 36.13 3.41
5287 5355 7.175816 TCGAGATCATAAAATCTACTCCCTCTG 59.824 40.741 0.00 0.00 36.13 3.35
5288 5356 7.235079 TCGAGATCATAAAATCTACTCCCTCT 58.765 38.462 0.00 0.00 36.13 3.69
5289 5357 7.455641 TCGAGATCATAAAATCTACTCCCTC 57.544 40.000 0.00 0.00 36.13 4.30
5290 5358 7.841282 TTCGAGATCATAAAATCTACTCCCT 57.159 36.000 0.00 0.00 36.13 4.20
5291 5359 8.527810 AGATTCGAGATCATAAAATCTACTCCC 58.472 37.037 9.55 0.00 36.13 4.30
5292 5360 9.567848 GAGATTCGAGATCATAAAATCTACTCC 57.432 37.037 10.68 0.05 36.94 3.85
5294 5362 9.906660 GTGAGATTCGAGATCATAAAATCTACT 57.093 33.333 10.68 0.00 36.94 2.57
5295 5363 9.134734 GGTGAGATTCGAGATCATAAAATCTAC 57.865 37.037 10.68 9.59 36.94 2.59
5359 5429 4.394920 ACGAATTGTGCGGTATCTTGAAAT 59.605 37.500 0.00 0.00 0.00 2.17
5371 5441 2.286184 GCCCTAACATACGAATTGTGCG 60.286 50.000 0.00 0.00 0.00 5.34
5431 5507 6.746745 ACTAAAACCAAAACGAGAAACAGA 57.253 33.333 0.00 0.00 0.00 3.41
5508 5584 3.433615 ACATCTAAGCACTTTTGTCTCGC 59.566 43.478 0.00 0.00 0.00 5.03
5575 5651 4.159506 GCCAGAAAGATACAGAGAGTGAGT 59.840 45.833 0.00 0.00 0.00 3.41
5579 5655 4.093011 ACAGCCAGAAAGATACAGAGAGT 58.907 43.478 0.00 0.00 0.00 3.24
5583 5659 7.394016 TGAAAATACAGCCAGAAAGATACAGA 58.606 34.615 0.00 0.00 0.00 3.41
5599 5675 4.764823 GGGTGATGGACAGTTGAAAATACA 59.235 41.667 0.00 0.00 0.00 2.29
5642 5718 6.749923 AAACATGGTAGAAGAAATCAGCTC 57.250 37.500 0.00 0.00 0.00 4.09
5645 5721 7.025963 GCAGAAAACATGGTAGAAGAAATCAG 58.974 38.462 0.00 0.00 0.00 2.90
5759 5855 3.914312 TCGTCTCATCACTCTTTTGACC 58.086 45.455 0.00 0.00 0.00 4.02
5767 5863 4.201666 GCAGAAAACATCGTCTCATCACTC 60.202 45.833 0.00 0.00 0.00 3.51
5776 5877 1.263217 ACAACGGCAGAAAACATCGTC 59.737 47.619 0.00 0.00 33.34 4.20
5827 5929 4.759516 TGAATTAGAAAGCGAAACCACC 57.240 40.909 0.00 0.00 0.00 4.61
5869 5971 7.124147 CATTGTTACCAAAGGGAACCAGAATAT 59.876 37.037 8.59 0.00 41.80 1.28
5880 5982 3.368323 GGCATGTCATTGTTACCAAAGGG 60.368 47.826 0.00 0.00 41.29 3.95
5904 6006 1.474077 AGCAATTTTAGCGAGCCAAGG 59.526 47.619 0.00 0.00 37.01 3.61


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

AutoCloner maintained by Alex Coulton.