Multiple sequence alignment - TraesCS4B01G097900

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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 TraesCS4B01G097900 chr4B 100.000 3652 0 0 1 3652 102489851 102486200 0.000000e+00 6745.0
1 TraesCS4B01G097900 chr4B 90.252 636 55 5 3023 3652 176841577 176840943 0.000000e+00 824.0
2 TraesCS4B01G097900 chr4D 93.959 2119 92 16 734 2822 69544084 69541972 0.000000e+00 3171.0
3 TraesCS4B01G097900 chr4D 79.513 698 77 33 1 665 69544858 69544194 1.560000e-118 436.0
4 TraesCS4B01G097900 chr4A 91.853 2148 115 29 709 2822 521626233 521624112 0.000000e+00 2942.0
5 TraesCS4B01G097900 chr4A 84.353 556 43 20 134 665 521627848 521627313 4.210000e-139 505.0
6 TraesCS4B01G097900 chr4A 90.604 149 12 2 1 148 521629361 521629214 2.880000e-46 196.0
7 TraesCS4B01G097900 chr1B 91.837 637 43 6 3023 3652 615013193 615012559 0.000000e+00 880.0
8 TraesCS4B01G097900 chr1B 90.016 641 59 4 3014 3649 6429377 6430017 0.000000e+00 824.0
9 TraesCS4B01G097900 chr1B 90.348 632 54 6 3023 3649 260325982 260326611 0.000000e+00 822.0
10 TraesCS4B01G097900 chr6B 91.009 634 51 6 3022 3649 181099256 181099889 0.000000e+00 850.0
11 TraesCS4B01G097900 chr6B 90.669 643 53 4 3017 3652 526740642 526740000 0.000000e+00 848.0
12 TraesCS4B01G097900 chr5B 90.358 643 55 6 3013 3649 100773990 100774631 0.000000e+00 837.0
13 TraesCS4B01G097900 chr7A 90.236 635 57 5 3021 3652 310984412 310983780 0.000000e+00 824.0
14 TraesCS4B01G097900 chr3D 89.704 641 60 6 3016 3652 549355332 549354694 0.000000e+00 813.0
15 TraesCS4B01G097900 chr5A 83.459 266 25 12 39 295 637998337 637998592 2.840000e-56 230.0
16 TraesCS4B01G097900 chr5A 88.172 93 9 2 40 130 565672793 565672885 3.860000e-20 110.0
17 TraesCS4B01G097900 chr2A 87.209 172 19 1 41 209 5698663 5698834 3.720000e-45 193.0
18 TraesCS4B01G097900 chr7D 78.209 335 40 17 2 319 557376864 557377182 2.240000e-42 183.0
19 TraesCS4B01G097900 chr7D 87.037 54 6 1 667 719 633924326 633924273 3.940000e-05 60.2
20 TraesCS4B01G097900 chr2D 80.952 84 8 3 219 295 87444955 87444873 3.940000e-05 60.2


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 TraesCS4B01G097900 chr4B 102486200 102489851 3651 True 6745.000000 6745 100.000000 1 3652 1 chr4B.!!$R1 3651
1 TraesCS4B01G097900 chr4B 176840943 176841577 634 True 824.000000 824 90.252000 3023 3652 1 chr4B.!!$R2 629
2 TraesCS4B01G097900 chr4D 69541972 69544858 2886 True 1803.500000 3171 86.736000 1 2822 2 chr4D.!!$R1 2821
3 TraesCS4B01G097900 chr4A 521624112 521629361 5249 True 1214.333333 2942 88.936667 1 2822 3 chr4A.!!$R1 2821
4 TraesCS4B01G097900 chr1B 615012559 615013193 634 True 880.000000 880 91.837000 3023 3652 1 chr1B.!!$R1 629
5 TraesCS4B01G097900 chr1B 6429377 6430017 640 False 824.000000 824 90.016000 3014 3649 1 chr1B.!!$F1 635
6 TraesCS4B01G097900 chr1B 260325982 260326611 629 False 822.000000 822 90.348000 3023 3649 1 chr1B.!!$F2 626
7 TraesCS4B01G097900 chr6B 181099256 181099889 633 False 850.000000 850 91.009000 3022 3649 1 chr6B.!!$F1 627
8 TraesCS4B01G097900 chr6B 526740000 526740642 642 True 848.000000 848 90.669000 3017 3652 1 chr6B.!!$R1 635
9 TraesCS4B01G097900 chr5B 100773990 100774631 641 False 837.000000 837 90.358000 3013 3649 1 chr5B.!!$F1 636
10 TraesCS4B01G097900 chr7A 310983780 310984412 632 True 824.000000 824 90.236000 3021 3652 1 chr7A.!!$R1 631
11 TraesCS4B01G097900 chr3D 549354694 549355332 638 True 813.000000 813 89.704000 3016 3652 1 chr3D.!!$R1 636

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
297 1683 0.112412 AACGGAGGCCCAAGACATTT 59.888 50.0 0.00 0.0 0.00 2.32 F
1492 3989 0.317103 GATCGTGGATCACTCGACCG 60.317 60.0 9.48 0.0 38.77 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 4621 0.238289 CCGTGCACTTGTGGATGAAC 59.762 55.0 16.19 0.0 0.0 3.18 R
2892 5417 0.034059 GGGCTCCATGATGTCGGTAG 59.966 60.0 0.00 0.0 0.0 3.18 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 8.750515 AAAATTCAAATCCATGGTGAACTTTT 57.249 26.923 16.21 17.56 29.22 2.27
190 1572 1.595382 GGATGAGCCATCGAACGGG 60.595 63.158 6.40 1.91 41.35 5.28
245 1629 2.293170 GGGAAGGAATGAAGCTAGCAC 58.707 52.381 18.83 11.11 0.00 4.40
264 1650 3.368236 GCACCTAAACTGAACGAAGCTAG 59.632 47.826 0.00 0.00 0.00 3.42
265 1651 3.927142 CACCTAAACTGAACGAAGCTAGG 59.073 47.826 0.00 1.12 34.43 3.02
297 1683 0.112412 AACGGAGGCCCAAGACATTT 59.888 50.000 0.00 0.00 0.00 2.32
330 1719 0.825010 CTGCAAGCCCTGAACAACCT 60.825 55.000 0.00 0.00 0.00 3.50
333 1722 1.242076 CAAGCCCTGAACAACCTGAG 58.758 55.000 0.00 0.00 0.00 3.35
338 1727 2.693074 GCCCTGAACAACCTGAGAAAAA 59.307 45.455 0.00 0.00 0.00 1.94
390 1783 6.761714 AGATGTAATTTATGTCACCTCCGAAC 59.238 38.462 0.00 0.00 0.00 3.95
426 1822 7.220740 TGTCACATTTTGGATGTGTCTTAGTA 58.779 34.615 16.15 0.00 46.82 1.82
431 1827 6.428083 TTTTGGATGTGTCTTAGTAGGACA 57.572 37.500 10.84 10.84 40.78 4.02
432 1828 6.428083 TTTGGATGTGTCTTAGTAGGACAA 57.572 37.500 15.95 7.90 43.90 3.18
433 1829 5.401531 TGGATGTGTCTTAGTAGGACAAC 57.598 43.478 15.95 11.04 43.90 3.32
463 1860 2.823154 TGTGTCTCGGTCACATCATACA 59.177 45.455 4.66 0.00 40.26 2.29
509 1906 0.963962 AGCCTGCCATGAACAACAAG 59.036 50.000 0.00 0.00 0.00 3.16
511 1908 1.068055 GCCTGCCATGAACAACAAGAG 60.068 52.381 0.00 0.00 0.00 2.85
514 1933 3.144506 CTGCCATGAACAACAAGAGTCT 58.855 45.455 0.00 0.00 0.00 3.24
526 1945 7.907214 ACAACAAGAGTCTTATAGCGAATTT 57.093 32.000 4.74 0.00 0.00 1.82
537 1956 9.472361 GTCTTATAGCGAATTTATCTGTGGTTA 57.528 33.333 0.00 0.00 0.00 2.85
561 1980 5.667626 AGATGGTTAGATGGACACTGGTATT 59.332 40.000 0.00 0.00 0.00 1.89
563 1982 4.163458 TGGTTAGATGGACACTGGTATTCC 59.837 45.833 0.00 0.00 0.00 3.01
564 1983 4.163458 GGTTAGATGGACACTGGTATTCCA 59.837 45.833 5.93 5.93 43.60 3.53
566 1985 4.494091 AGATGGACACTGGTATTCCAAG 57.506 45.455 7.16 0.00 42.71 3.61
568 1987 3.695830 TGGACACTGGTATTCCAAGTC 57.304 47.619 12.51 12.51 43.81 3.01
580 1999 3.343941 TTCCAAGTCCATTAGGGTTCG 57.656 47.619 0.00 0.00 38.11 3.95
582 2001 2.500098 TCCAAGTCCATTAGGGTTCGAG 59.500 50.000 0.00 0.00 38.11 4.04
586 2005 4.203654 AGTCCATTAGGGTTCGAGTTTC 57.796 45.455 0.00 0.00 38.11 2.78
647 2066 2.224042 ACAATGCGTGTTCAGTGAGAGA 60.224 45.455 0.00 0.00 37.01 3.10
648 2067 2.071688 ATGCGTGTTCAGTGAGAGAC 57.928 50.000 0.00 0.00 0.00 3.36
650 2069 0.317938 GCGTGTTCAGTGAGAGACGT 60.318 55.000 18.72 0.00 36.70 4.34
655 2077 2.052157 GTTCAGTGAGAGACGTTTCCG 58.948 52.381 1.88 0.00 40.83 4.30
690 3161 7.096023 GCTGTCGTTTATAGGAATGAGTGTATG 60.096 40.741 0.00 0.00 0.00 2.39
696 3167 5.784578 ATAGGAATGAGTGTATGCGTGTA 57.215 39.130 0.00 0.00 0.00 2.90
700 3171 5.068591 AGGAATGAGTGTATGCGTGTATACA 59.931 40.000 0.08 0.08 40.28 2.29
701 3172 5.926542 GGAATGAGTGTATGCGTGTATACAT 59.073 40.000 9.18 0.00 43.27 2.29
702 3173 7.039993 AGGAATGAGTGTATGCGTGTATACATA 60.040 37.037 9.18 0.00 43.27 2.29
703 3174 7.597369 GGAATGAGTGTATGCGTGTATACATAA 59.403 37.037 9.18 0.00 43.27 1.90
704 3175 8.880878 AATGAGTGTATGCGTGTATACATAAA 57.119 30.769 9.18 0.00 43.27 1.40
705 3176 7.688478 TGAGTGTATGCGTGTATACATAAAC 57.312 36.000 9.18 2.86 43.27 2.01
706 3177 6.415573 TGAGTGTATGCGTGTATACATAAACG 59.584 38.462 9.18 8.92 43.27 3.60
707 3178 5.688621 AGTGTATGCGTGTATACATAAACGG 59.311 40.000 9.18 0.00 43.27 4.44
708 3179 5.459762 GTGTATGCGTGTATACATAAACGGT 59.540 40.000 9.18 0.00 43.27 4.83
709 3180 6.019640 GTGTATGCGTGTATACATAAACGGTT 60.020 38.462 9.18 0.00 43.27 4.44
710 3181 4.843879 TGCGTGTATACATAAACGGTTG 57.156 40.909 9.18 0.00 42.66 3.77
711 3182 3.062369 TGCGTGTATACATAAACGGTTGC 59.938 43.478 9.18 3.57 42.66 4.17
724 3195 7.492020 ACATAAACGGTTGCGTCTGTATTATAA 59.508 33.333 0.00 0.00 0.00 0.98
728 3199 5.813672 ACGGTTGCGTCTGTATTATAATGTT 59.186 36.000 8.28 0.00 0.00 2.71
729 3200 6.979817 ACGGTTGCGTCTGTATTATAATGTTA 59.020 34.615 8.28 0.00 0.00 2.41
730 3201 7.492020 ACGGTTGCGTCTGTATTATAATGTTAA 59.508 33.333 8.28 0.00 0.00 2.01
731 3202 8.329583 CGGTTGCGTCTGTATTATAATGTTAAA 58.670 33.333 8.28 0.00 0.00 1.52
1047 3525 5.347093 CCATTCTCAGATCGATCAATTACGG 59.653 44.000 26.47 14.14 0.00 4.02
1066 3552 2.805353 CGAGGAACCGAGCACACG 60.805 66.667 0.00 0.00 0.00 4.49
1083 3569 1.400494 CACGCTATGGCCAAGGTAAAC 59.600 52.381 10.96 0.00 34.44 2.01
1089 3575 1.344065 TGGCCAAGGTAAACGAGAGA 58.656 50.000 0.61 0.00 0.00 3.10
1091 3577 2.074576 GGCCAAGGTAAACGAGAGAAC 58.925 52.381 0.00 0.00 0.00 3.01
1092 3578 1.725164 GCCAAGGTAAACGAGAGAACG 59.275 52.381 0.00 0.00 39.31 3.95
1094 3580 2.609737 CCAAGGTAAACGAGAGAACGCT 60.610 50.000 0.00 0.00 36.70 5.07
1185 3678 2.434185 TTCCGATGTGGCAGACGC 60.434 61.111 0.00 0.00 37.80 5.19
1301 3797 2.281208 GTGGTGGTAAGCGTGCCA 60.281 61.111 5.16 5.16 37.14 4.92
1492 3989 0.317103 GATCGTGGATCACTCGACCG 60.317 60.000 9.48 0.00 38.77 4.79
1608 4105 2.587194 CCATCGCCGGAGAAGCTG 60.587 66.667 13.28 6.11 0.00 4.24
1650 4150 1.467342 GATACCAAGAAACACGGTGCC 59.533 52.381 8.30 0.00 34.12 5.01
1705 4205 5.109903 AGTTCGACATGGTATTTACTGAGC 58.890 41.667 0.00 0.00 0.00 4.26
1711 4211 6.183360 CGACATGGTATTTACTGAGCCAATTT 60.183 38.462 0.00 0.00 32.54 1.82
1739 4239 6.183360 TGCTGCTAGTTGCTGTTAATATCCTA 60.183 38.462 0.00 0.00 43.37 2.94
1768 4268 8.288689 AGTTCACTACTACCATTTTGTTTTGT 57.711 30.769 0.00 0.00 34.56 2.83
1854 4354 2.749621 CCAGGAAATGGTTGTAGTGCTC 59.250 50.000 0.00 0.00 44.91 4.26
1860 4360 5.880332 GGAAATGGTTGTAGTGCTCAAGATA 59.120 40.000 0.00 0.00 0.00 1.98
1906 4406 6.016024 CAGTGAGGAGATGAAGAAGAGGATAG 60.016 46.154 0.00 0.00 0.00 2.08
1986 4492 4.418392 GAATACGTCGACTTCCTTGCTTA 58.582 43.478 14.70 0.00 0.00 3.09
2007 4517 4.136517 AGTTTGTTGCGGTATTTACACG 57.863 40.909 0.00 0.00 0.00 4.49
2226 4736 3.142162 CAGCGGATGCCAATGCCA 61.142 61.111 0.00 0.00 44.31 4.92
2292 4802 3.841255 AGGGGTAGAAGAAGAGACCAAAG 59.159 47.826 0.00 0.00 33.33 2.77
2345 4858 1.000866 GAAGCCAGGCAAAGGGGAT 59.999 57.895 15.80 0.00 0.00 3.85
2351 4864 0.554792 CAGGCAAAGGGGATGGAGAT 59.445 55.000 0.00 0.00 0.00 2.75
2383 4896 3.236896 AGGAGACGGTTGTAGAGGAAAA 58.763 45.455 0.00 0.00 0.00 2.29
2387 4900 3.064931 GACGGTTGTAGAGGAAAACCAG 58.935 50.000 4.82 0.75 42.93 4.00
2388 4901 2.701951 ACGGTTGTAGAGGAAAACCAGA 59.298 45.455 4.82 0.00 42.93 3.86
2389 4902 3.064931 CGGTTGTAGAGGAAAACCAGAC 58.935 50.000 4.82 0.00 42.93 3.51
2396 4909 2.037381 AGAGGAAAACCAGACGAAGGAC 59.963 50.000 0.00 0.00 0.00 3.85
2416 4929 1.474077 CCACCTATTCAAACTGCCTGC 59.526 52.381 0.00 0.00 0.00 4.85
2510 5026 1.521681 CCCAGCAGCCTACGCTTAC 60.522 63.158 0.00 0.00 45.55 2.34
2513 5029 2.508439 GCAGCCTACGCTTACGCA 60.508 61.111 0.00 0.00 45.55 5.24
2558 5074 5.324409 CAATACCACCAATACCCATATGCT 58.676 41.667 0.00 0.00 0.00 3.79
2560 5076 2.158475 ACCACCAATACCCATATGCTGG 60.158 50.000 0.00 0.00 45.51 4.85
2561 5077 2.158475 CCACCAATACCCATATGCTGGT 60.158 50.000 8.49 8.49 44.30 4.00
2567 5083 5.516415 CCAATACCCATATGCTGGTAATCCA 60.516 44.000 13.01 0.00 44.30 3.41
2587 5103 1.413445 AGCAACGTATTATGGGCCGTA 59.587 47.619 0.00 0.00 32.49 4.02
2650 5166 2.882137 CAGATGCATGCACCATCATGTA 59.118 45.455 25.37 0.00 44.20 2.29
2655 5171 3.447944 TGCATGCACCATCATGTAATGTT 59.552 39.130 18.46 0.00 46.80 2.71
2659 5175 6.515365 GCATGCACCATCATGTAATGTTATGA 60.515 38.462 14.21 0.00 46.80 2.15
2671 5191 7.119605 TGTAATGTTATGAACCGTGTGTAAC 57.880 36.000 0.00 0.00 37.35 2.50
2675 5195 5.472148 TGTTATGAACCGTGTGTAACTAGG 58.528 41.667 0.00 0.00 39.37 3.02
2685 5205 4.082081 CGTGTGTAACTAGGTTCCATGGTA 60.082 45.833 12.58 0.00 38.04 3.25
2697 5217 3.290948 TCCATGGTAACCATAAGCCAC 57.709 47.619 12.58 0.00 43.15 5.01
2715 5235 3.560068 GCCACCGTACATGGAATAAAGAG 59.440 47.826 15.76 0.00 39.87 2.85
2716 5236 4.682320 GCCACCGTACATGGAATAAAGAGA 60.682 45.833 15.76 0.00 39.87 3.10
2752 5272 0.877071 CTGTGTGCACCTTCCATGTC 59.123 55.000 15.69 0.00 0.00 3.06
2761 5286 3.480470 CACCTTCCATGTCACAAGTCTT 58.520 45.455 0.00 0.00 0.00 3.01
2762 5287 3.499918 CACCTTCCATGTCACAAGTCTTC 59.500 47.826 0.00 0.00 0.00 2.87
2763 5288 3.136443 ACCTTCCATGTCACAAGTCTTCA 59.864 43.478 0.00 0.00 0.00 3.02
2764 5289 4.202503 ACCTTCCATGTCACAAGTCTTCAT 60.203 41.667 0.00 0.00 0.00 2.57
2771 5296 9.933723 TCCATGTCACAAGTCTTCATATATATG 57.066 33.333 15.47 15.47 35.04 1.78
2806 5331 7.503566 AGCATCTGGTTACTGCAATGTATAAAT 59.496 33.333 0.00 0.00 38.37 1.40
2829 5354 4.795970 AAATAACGGCTTTCTAGATGCG 57.204 40.909 10.75 9.11 0.00 4.73
2830 5355 2.953466 TAACGGCTTTCTAGATGCGT 57.047 45.000 10.75 9.58 0.00 5.24
2831 5356 1.641577 AACGGCTTTCTAGATGCGTC 58.358 50.000 0.00 0.00 0.00 5.19
2832 5357 0.179108 ACGGCTTTCTAGATGCGTCC 60.179 55.000 1.23 1.15 0.00 4.79
2833 5358 0.103208 CGGCTTTCTAGATGCGTCCT 59.897 55.000 1.23 0.00 0.00 3.85
2834 5359 1.337071 CGGCTTTCTAGATGCGTCCTA 59.663 52.381 1.23 0.00 0.00 2.94
2835 5360 2.223735 CGGCTTTCTAGATGCGTCCTAA 60.224 50.000 1.23 0.00 0.00 2.69
2836 5361 3.737047 CGGCTTTCTAGATGCGTCCTAAA 60.737 47.826 1.23 0.40 0.00 1.85
2837 5362 4.381411 GGCTTTCTAGATGCGTCCTAAAT 58.619 43.478 1.23 0.00 0.00 1.40
2838 5363 4.212214 GGCTTTCTAGATGCGTCCTAAATG 59.788 45.833 1.23 0.00 0.00 2.32
2839 5364 4.811557 GCTTTCTAGATGCGTCCTAAATGT 59.188 41.667 1.23 0.00 0.00 2.71
2840 5365 5.050702 GCTTTCTAGATGCGTCCTAAATGTC 60.051 44.000 1.23 0.00 0.00 3.06
2841 5366 4.585955 TCTAGATGCGTCCTAAATGTCC 57.414 45.455 1.23 0.00 0.00 4.02
2842 5367 4.215908 TCTAGATGCGTCCTAAATGTCCT 58.784 43.478 1.23 0.00 0.00 3.85
2843 5368 5.382616 TCTAGATGCGTCCTAAATGTCCTA 58.617 41.667 1.23 0.00 0.00 2.94
2844 5369 6.010850 TCTAGATGCGTCCTAAATGTCCTAT 58.989 40.000 1.23 0.00 0.00 2.57
2845 5370 4.887748 AGATGCGTCCTAAATGTCCTATG 58.112 43.478 1.23 0.00 0.00 2.23
2846 5371 2.833794 TGCGTCCTAAATGTCCTATGC 58.166 47.619 0.00 0.00 0.00 3.14
2847 5372 2.143925 GCGTCCTAAATGTCCTATGCC 58.856 52.381 0.00 0.00 0.00 4.40
2848 5373 2.484770 GCGTCCTAAATGTCCTATGCCA 60.485 50.000 0.00 0.00 0.00 4.92
2849 5374 3.807209 GCGTCCTAAATGTCCTATGCCAT 60.807 47.826 0.00 0.00 0.00 4.40
2850 5375 4.389374 CGTCCTAAATGTCCTATGCCATT 58.611 43.478 0.00 0.00 32.83 3.16
2851 5376 4.214119 CGTCCTAAATGTCCTATGCCATTG 59.786 45.833 0.00 0.00 31.89 2.82
2852 5377 5.376625 GTCCTAAATGTCCTATGCCATTGA 58.623 41.667 0.00 0.00 31.89 2.57
2853 5378 6.006449 GTCCTAAATGTCCTATGCCATTGAT 58.994 40.000 0.00 0.00 31.89 2.57
2854 5379 7.168219 GTCCTAAATGTCCTATGCCATTGATA 58.832 38.462 0.00 0.00 31.89 2.15
2855 5380 7.831193 GTCCTAAATGTCCTATGCCATTGATAT 59.169 37.037 0.00 0.00 31.89 1.63
2856 5381 8.049117 TCCTAAATGTCCTATGCCATTGATATC 58.951 37.037 0.00 0.00 31.89 1.63
2857 5382 7.284034 CCTAAATGTCCTATGCCATTGATATCC 59.716 40.741 0.00 0.00 31.89 2.59
2858 5383 6.398655 AATGTCCTATGCCATTGATATCCT 57.601 37.500 0.00 0.00 30.39 3.24
2859 5384 5.848286 TGTCCTATGCCATTGATATCCTT 57.152 39.130 0.00 0.00 0.00 3.36
2860 5385 6.204852 TGTCCTATGCCATTGATATCCTTT 57.795 37.500 0.00 0.00 0.00 3.11
2861 5386 6.613699 TGTCCTATGCCATTGATATCCTTTT 58.386 36.000 0.00 0.00 0.00 2.27
2862 5387 6.491062 TGTCCTATGCCATTGATATCCTTTTG 59.509 38.462 0.00 0.00 0.00 2.44
2863 5388 6.716628 GTCCTATGCCATTGATATCCTTTTGA 59.283 38.462 0.00 0.00 0.00 2.69
2864 5389 7.231317 GTCCTATGCCATTGATATCCTTTTGAA 59.769 37.037 0.00 0.00 0.00 2.69
2865 5390 7.449395 TCCTATGCCATTGATATCCTTTTGAAG 59.551 37.037 0.00 0.00 0.00 3.02
2866 5391 7.449395 CCTATGCCATTGATATCCTTTTGAAGA 59.551 37.037 0.00 0.00 0.00 2.87
2867 5392 7.664552 ATGCCATTGATATCCTTTTGAAGAA 57.335 32.000 0.00 0.00 0.00 2.52
2868 5393 7.479352 TGCCATTGATATCCTTTTGAAGAAA 57.521 32.000 0.00 0.00 0.00 2.52
2869 5394 7.549839 TGCCATTGATATCCTTTTGAAGAAAG 58.450 34.615 0.00 0.00 0.00 2.62
2870 5395 7.396907 TGCCATTGATATCCTTTTGAAGAAAGA 59.603 33.333 0.00 0.00 0.00 2.52
2871 5396 8.419442 GCCATTGATATCCTTTTGAAGAAAGAT 58.581 33.333 0.00 0.00 0.00 2.40
2881 5406 9.989296 TCCTTTTGAAGAAAGATATAATGGGAA 57.011 29.630 0.34 0.00 0.00 3.97
2897 5422 6.651975 AATGGGAATTACTCTACTCTACCG 57.348 41.667 0.00 0.00 0.00 4.02
2898 5423 5.378230 TGGGAATTACTCTACTCTACCGA 57.622 43.478 0.00 0.00 0.00 4.69
2899 5424 5.128919 TGGGAATTACTCTACTCTACCGAC 58.871 45.833 0.00 0.00 0.00 4.79
2900 5425 5.128919 GGGAATTACTCTACTCTACCGACA 58.871 45.833 0.00 0.00 0.00 4.35
2901 5426 5.769162 GGGAATTACTCTACTCTACCGACAT 59.231 44.000 0.00 0.00 0.00 3.06
2902 5427 6.072563 GGGAATTACTCTACTCTACCGACATC 60.073 46.154 0.00 0.00 0.00 3.06
2903 5428 6.485984 GGAATTACTCTACTCTACCGACATCA 59.514 42.308 0.00 0.00 0.00 3.07
2904 5429 7.175293 GGAATTACTCTACTCTACCGACATCAT 59.825 40.741 0.00 0.00 0.00 2.45
2905 5430 6.862711 TTACTCTACTCTACCGACATCATG 57.137 41.667 0.00 0.00 0.00 3.07
2906 5431 4.138290 ACTCTACTCTACCGACATCATGG 58.862 47.826 0.00 0.00 0.00 3.66
2907 5432 4.141459 ACTCTACTCTACCGACATCATGGA 60.141 45.833 0.00 0.00 0.00 3.41
2908 5433 4.390264 TCTACTCTACCGACATCATGGAG 58.610 47.826 0.00 0.00 0.00 3.86
2909 5434 1.683917 ACTCTACCGACATCATGGAGC 59.316 52.381 0.00 0.00 0.00 4.70
2910 5435 1.000283 CTCTACCGACATCATGGAGCC 60.000 57.143 0.00 0.00 0.00 4.70
2911 5436 0.034059 CTACCGACATCATGGAGCCC 59.966 60.000 0.00 0.00 0.00 5.19
2912 5437 0.689412 TACCGACATCATGGAGCCCA 60.689 55.000 0.00 0.00 38.19 5.36
2913 5438 1.227764 CCGACATCATGGAGCCCAG 60.228 63.158 0.00 0.00 36.75 4.45
2914 5439 1.227764 CGACATCATGGAGCCCAGG 60.228 63.158 0.00 0.04 36.75 4.45
2915 5440 1.918253 GACATCATGGAGCCCAGGT 59.082 57.895 5.90 0.00 36.75 4.00
2916 5441 0.465097 GACATCATGGAGCCCAGGTG 60.465 60.000 5.90 6.42 36.75 4.00
2917 5442 0.915872 ACATCATGGAGCCCAGGTGA 60.916 55.000 5.90 3.61 36.75 4.02
2918 5443 0.477204 CATCATGGAGCCCAGGTGAT 59.523 55.000 5.90 5.48 36.75 3.06
2919 5444 1.133575 CATCATGGAGCCCAGGTGATT 60.134 52.381 5.90 0.00 36.75 2.57
2920 5445 0.256752 TCATGGAGCCCAGGTGATTG 59.743 55.000 5.90 0.00 36.75 2.67
2921 5446 0.754217 CATGGAGCCCAGGTGATTGG 60.754 60.000 0.41 0.00 36.75 3.16
2922 5447 2.440980 GGAGCCCAGGTGATTGGC 60.441 66.667 0.00 0.00 45.70 4.52
2939 5464 3.376078 CGCCAGCCTTTGCCACAT 61.376 61.111 0.00 0.00 38.69 3.21
2940 5465 2.045708 CGCCAGCCTTTGCCACATA 61.046 57.895 0.00 0.00 38.69 2.29
2941 5466 1.512694 GCCAGCCTTTGCCACATAC 59.487 57.895 0.00 0.00 38.69 2.39
2942 5467 1.802636 CCAGCCTTTGCCACATACG 59.197 57.895 0.00 0.00 38.69 3.06
2943 5468 0.960364 CCAGCCTTTGCCACATACGT 60.960 55.000 0.00 0.00 38.69 3.57
2944 5469 0.168788 CAGCCTTTGCCACATACGTG 59.831 55.000 0.00 0.00 43.21 4.49
2969 5494 3.780925 GCATTTCGCTTTGCTGAGT 57.219 47.368 0.00 0.00 37.77 3.41
2970 5495 1.334054 GCATTTCGCTTTGCTGAGTG 58.666 50.000 0.00 0.00 37.77 3.51
2971 5496 1.334054 CATTTCGCTTTGCTGAGTGC 58.666 50.000 0.00 0.00 43.25 4.40
2972 5497 0.242017 ATTTCGCTTTGCTGAGTGCC 59.758 50.000 0.00 0.00 42.00 5.01
2973 5498 2.116736 TTTCGCTTTGCTGAGTGCCG 62.117 55.000 0.00 0.00 42.00 5.69
2974 5499 4.093952 CGCTTTGCTGAGTGCCGG 62.094 66.667 0.00 0.00 42.00 6.13
2975 5500 2.980233 GCTTTGCTGAGTGCCGGT 60.980 61.111 1.90 0.00 42.00 5.28
2976 5501 2.555547 GCTTTGCTGAGTGCCGGTT 61.556 57.895 1.90 0.00 42.00 4.44
2977 5502 2.032981 CTTTGCTGAGTGCCGGTTT 58.967 52.632 1.90 0.00 42.00 3.27
2978 5503 0.318107 CTTTGCTGAGTGCCGGTTTG 60.318 55.000 1.90 0.00 42.00 2.93
2979 5504 1.034838 TTTGCTGAGTGCCGGTTTGT 61.035 50.000 1.90 0.00 42.00 2.83
2980 5505 1.034838 TTGCTGAGTGCCGGTTTGTT 61.035 50.000 1.90 0.00 42.00 2.83
2981 5506 1.034838 TGCTGAGTGCCGGTTTGTTT 61.035 50.000 1.90 0.00 42.00 2.83
2982 5507 0.594796 GCTGAGTGCCGGTTTGTTTG 60.595 55.000 1.90 0.00 35.15 2.93
2983 5508 0.594796 CTGAGTGCCGGTTTGTTTGC 60.595 55.000 1.90 0.00 0.00 3.68
2984 5509 1.299850 GAGTGCCGGTTTGTTTGCC 60.300 57.895 1.90 0.00 0.00 4.52
2985 5510 2.656973 GTGCCGGTTTGTTTGCCG 60.657 61.111 1.90 0.00 46.80 5.69
2990 5515 4.319249 GGTTTGTTTGCCGAGTGC 57.681 55.556 0.00 0.00 41.77 4.40
3001 5526 1.621107 GCCGAGTGCAAAATGTCATG 58.379 50.000 0.00 0.00 40.77 3.07
3002 5527 1.068333 GCCGAGTGCAAAATGTCATGT 60.068 47.619 0.00 0.00 40.77 3.21
3003 5528 2.161410 GCCGAGTGCAAAATGTCATGTA 59.839 45.455 0.00 0.00 40.77 2.29
3004 5529 3.365868 GCCGAGTGCAAAATGTCATGTAA 60.366 43.478 0.00 0.00 40.77 2.41
3005 5530 4.158384 CCGAGTGCAAAATGTCATGTAAC 58.842 43.478 0.00 0.00 0.00 2.50
3006 5531 4.158384 CGAGTGCAAAATGTCATGTAACC 58.842 43.478 0.00 0.00 0.00 2.85
3007 5532 4.158384 GAGTGCAAAATGTCATGTAACCG 58.842 43.478 0.00 0.00 0.00 4.44
3008 5533 3.818210 AGTGCAAAATGTCATGTAACCGA 59.182 39.130 0.00 0.00 0.00 4.69
3009 5534 4.083324 AGTGCAAAATGTCATGTAACCGAG 60.083 41.667 0.00 0.00 0.00 4.63
3010 5535 3.818210 TGCAAAATGTCATGTAACCGAGT 59.182 39.130 0.00 0.00 0.00 4.18
3011 5536 4.158384 GCAAAATGTCATGTAACCGAGTG 58.842 43.478 0.00 0.00 0.00 3.51
3014 5539 6.566942 GCAAAATGTCATGTAACCGAGTGTAA 60.567 38.462 0.00 0.00 0.00 2.41
3018 5543 7.681939 ATGTCATGTAACCGAGTGTAAAAAT 57.318 32.000 0.00 0.00 0.00 1.82
3025 5550 8.851541 TGTAACCGAGTGTAAAAATAAAGGAT 57.148 30.769 0.00 0.00 0.00 3.24
3029 5554 6.938030 ACCGAGTGTAAAAATAAAGGATGTCA 59.062 34.615 0.00 0.00 0.00 3.58
3102 5627 4.880886 CAAATAGATTGCCACGTCATCA 57.119 40.909 0.00 0.00 31.00 3.07
3128 5653 4.353737 GCATGCATGCGAGAATCTTTTTA 58.646 39.130 33.99 0.00 44.67 1.52
3129 5654 4.799949 GCATGCATGCGAGAATCTTTTTAA 59.200 37.500 33.99 0.00 44.67 1.52
3232 5757 9.582431 TCGACGAGATGTTTAAAATTAGATCTT 57.418 29.630 0.00 0.00 0.00 2.40
3288 5818 3.765511 AGTTGCCATGTCTATTGCACATT 59.234 39.130 0.00 0.00 34.99 2.71
3410 5941 4.338879 AGAAATTAGACTTGCCATGCACT 58.661 39.130 0.00 0.00 38.71 4.40
3539 6074 9.807649 AATTGCCATGATCTACAAACTAAAATC 57.192 29.630 0.00 0.00 0.00 2.17
3636 6175 6.902224 ATTCGTCGAAACATATCAACATGA 57.098 33.333 12.40 0.00 0.00 3.07
3649 6188 8.103305 ACATATCAACATGAGGTCTAGTTTTGT 58.897 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.750515 AAAGTTCACCATGGATTTGAATTTTT 57.249 26.923 21.47 17.42 36.39 1.94
25 26 8.750515 AAAAAGTTCACCATGGATTTGAATTT 57.249 26.923 21.47 17.16 32.41 1.82
49 50 6.783708 AGAAAAGTGTCCACATGGTTTAAA 57.216 33.333 0.00 0.00 36.34 1.52
204 1588 1.887198 CGTAGGCTATCCTCCGTTCAT 59.113 52.381 0.00 0.00 43.06 2.57
227 1611 3.274095 AGGTGCTAGCTTCATTCCTTC 57.726 47.619 17.23 0.00 0.00 3.46
245 1629 4.189639 ACCTAGCTTCGTTCAGTTTAGG 57.810 45.455 0.00 0.00 33.13 2.69
264 1650 3.434641 GCCTCCGTTCAGTTTAGTTTACC 59.565 47.826 0.00 0.00 0.00 2.85
265 1651 3.434641 GGCCTCCGTTCAGTTTAGTTTAC 59.565 47.826 0.00 0.00 0.00 2.01
412 1808 5.401531 TGTTGTCCTACTAAGACACATCC 57.598 43.478 0.00 0.00 43.70 3.51
497 1894 6.531594 TCGCTATAAGACTCTTGTTGTTCATG 59.468 38.462 1.17 0.00 0.00 3.07
500 1897 6.946229 TTCGCTATAAGACTCTTGTTGTTC 57.054 37.500 1.17 0.00 0.00 3.18
509 1906 7.868415 ACCACAGATAAATTCGCTATAAGACTC 59.132 37.037 0.00 0.00 0.00 3.36
511 1908 7.948278 ACCACAGATAAATTCGCTATAAGAC 57.052 36.000 0.00 0.00 0.00 3.01
526 1945 7.015292 GTCCATCTAACCATCTAACCACAGATA 59.985 40.741 0.00 0.00 33.41 1.98
537 1956 3.454858 ACCAGTGTCCATCTAACCATCT 58.545 45.455 0.00 0.00 0.00 2.90
561 1980 2.500098 CTCGAACCCTAATGGACTTGGA 59.500 50.000 0.00 0.00 38.00 3.53
563 1982 3.611766 ACTCGAACCCTAATGGACTTG 57.388 47.619 0.00 0.00 38.00 3.16
564 1983 4.576879 GAAACTCGAACCCTAATGGACTT 58.423 43.478 0.00 0.00 38.00 3.01
566 1985 2.928116 CGAAACTCGAACCCTAATGGAC 59.072 50.000 0.00 0.00 43.74 4.02
568 1987 3.241067 TCGAAACTCGAACCCTAATGG 57.759 47.619 0.00 0.00 46.90 3.16
623 2042 2.481568 CTCACTGAACACGCATTGTCAT 59.518 45.455 0.00 0.00 37.51 3.06
628 2047 2.408050 GTCTCTCACTGAACACGCATT 58.592 47.619 0.00 0.00 0.00 3.56
665 2087 7.096023 GCATACACTCATTCCTATAAACGACAG 60.096 40.741 0.00 0.00 0.00 3.51
666 2088 6.700081 GCATACACTCATTCCTATAAACGACA 59.300 38.462 0.00 0.00 0.00 4.35
667 2089 6.129168 CGCATACACTCATTCCTATAAACGAC 60.129 42.308 0.00 0.00 0.00 4.34
670 2092 6.479001 ACACGCATACACTCATTCCTATAAAC 59.521 38.462 0.00 0.00 0.00 2.01
672 2094 6.156748 ACACGCATACACTCATTCCTATAA 57.843 37.500 0.00 0.00 0.00 0.98
673 2095 5.784578 ACACGCATACACTCATTCCTATA 57.215 39.130 0.00 0.00 0.00 1.31
674 2096 4.672587 ACACGCATACACTCATTCCTAT 57.327 40.909 0.00 0.00 0.00 2.57
675 2097 5.784578 ATACACGCATACACTCATTCCTA 57.215 39.130 0.00 0.00 0.00 2.94
676 2098 4.672587 ATACACGCATACACTCATTCCT 57.327 40.909 0.00 0.00 0.00 3.36
677 2099 5.286438 TGTATACACGCATACACTCATTCC 58.714 41.667 0.08 0.00 36.66 3.01
678 2100 8.515473 TTATGTATACACGCATACACTCATTC 57.485 34.615 7.96 0.00 42.58 2.67
679 2101 8.761497 GTTTATGTATACACGCATACACTCATT 58.239 33.333 7.96 0.00 42.58 2.57
680 2102 7.114388 CGTTTATGTATACACGCATACACTCAT 59.886 37.037 7.96 0.00 42.58 2.90
681 2103 6.415573 CGTTTATGTATACACGCATACACTCA 59.584 38.462 7.96 0.00 42.58 3.41
682 2104 6.129273 CCGTTTATGTATACACGCATACACTC 60.129 42.308 7.96 0.00 42.58 3.51
690 3161 3.600346 GCAACCGTTTATGTATACACGC 58.400 45.455 7.96 0.00 35.70 5.34
705 3176 5.900339 ACATTATAATACAGACGCAACCG 57.100 39.130 0.00 0.00 41.14 4.44
706 3177 9.991388 TTTTAACATTATAATACAGACGCAACC 57.009 29.630 0.00 0.00 0.00 3.77
762 3233 1.684869 GGCTGGAAATGGGGATCGAAA 60.685 52.381 0.00 0.00 0.00 3.46
1047 3525 1.733399 GTGTGCTCGGTTCCTCGAC 60.733 63.158 0.00 0.00 35.18 4.20
1066 3552 1.940613 CTCGTTTACCTTGGCCATAGC 59.059 52.381 6.09 0.00 38.76 2.97
1089 3575 1.227853 AGAAGGTTTGGCGAGCGTT 60.228 52.632 0.00 0.00 0.00 4.84
1091 3577 1.355066 GAGAGAAGGTTTGGCGAGCG 61.355 60.000 0.00 0.00 0.00 5.03
1092 3578 1.021920 GGAGAGAAGGTTTGGCGAGC 61.022 60.000 0.00 0.00 0.00 5.03
1094 3580 1.677552 GGGAGAGAAGGTTTGGCGA 59.322 57.895 0.00 0.00 0.00 5.54
1096 3582 0.673956 GACGGGAGAGAAGGTTTGGC 60.674 60.000 0.00 0.00 0.00 4.52
1252 3748 2.586245 CATCGCTGCCTCCCTTCA 59.414 61.111 0.00 0.00 0.00 3.02
1301 3797 2.267006 CAGCCATCGCAGTGGACT 59.733 61.111 8.47 2.74 42.02 3.85
1492 3989 0.601841 CCAGTTACCACCACCGTGTC 60.602 60.000 0.00 0.00 38.41 3.67
1522 4019 1.141657 CACCATGATCGGGTTCTCCAT 59.858 52.381 6.16 0.00 36.19 3.41
1650 4150 4.776322 TTCATGTCTGGCGCCCCG 62.776 66.667 26.77 15.72 0.00 5.73
1705 4205 3.248266 GCAACTAGCAGCAAGAAATTGG 58.752 45.455 0.00 0.00 44.79 3.16
1739 4239 9.623000 AAACAAAATGGTAGTAGTGAACTAAGT 57.377 29.630 0.00 0.00 42.37 2.24
1854 4354 6.732531 TCTTCACAGTGCAATTCTATCTTG 57.267 37.500 0.00 0.00 0.00 3.02
1860 4360 3.570975 TGCAATCTTCACAGTGCAATTCT 59.429 39.130 0.00 0.00 43.65 2.40
1906 4406 6.480320 AGTGCATCGATACCTTTTATCTTGAC 59.520 38.462 0.00 0.00 0.00 3.18
1923 4425 5.220381 ACTATTAACATACGGAGTGCATCG 58.780 41.667 0.00 0.00 45.73 3.84
1986 4492 3.058777 CCGTGTAAATACCGCAACAAACT 60.059 43.478 0.00 0.00 0.00 2.66
2007 4517 4.022416 TGATCAACAGTTTGCAACCATACC 60.022 41.667 0.00 0.00 32.17 2.73
2111 4621 0.238289 CCGTGCACTTGTGGATGAAC 59.762 55.000 16.19 0.00 0.00 3.18
2226 4736 7.282675 CAGATTATCAGATGGTTCTTGCTTCTT 59.717 37.037 0.00 0.00 0.00 2.52
2292 4802 2.440539 TCTTCTCTGTTCACGGCTTC 57.559 50.000 0.00 0.00 0.00 3.86
2345 4858 1.203428 TCCTTCTCAACCCCATCTCCA 60.203 52.381 0.00 0.00 0.00 3.86
2351 4864 1.192146 CCGTCTCCTTCTCAACCCCA 61.192 60.000 0.00 0.00 0.00 4.96
2383 4896 0.113776 TAGGTGGTCCTTCGTCTGGT 59.886 55.000 0.00 0.00 42.12 4.00
2387 4900 3.604875 TTGAATAGGTGGTCCTTCGTC 57.395 47.619 0.00 0.00 42.12 4.20
2388 4901 3.326880 AGTTTGAATAGGTGGTCCTTCGT 59.673 43.478 0.00 0.00 42.12 3.85
2389 4902 3.684788 CAGTTTGAATAGGTGGTCCTTCG 59.315 47.826 0.00 0.00 42.12 3.79
2396 4909 1.474077 GCAGGCAGTTTGAATAGGTGG 59.526 52.381 0.00 0.00 0.00 4.61
2416 4929 2.252260 CAACAAGTGAAGCCGGCG 59.748 61.111 23.20 7.32 0.00 6.46
2463 4979 0.604578 TACTGGTAGTGGCCGTTCAC 59.395 55.000 0.00 0.00 37.89 3.18
2473 4989 3.168292 GGGTGGTAGTTGTACTGGTAGT 58.832 50.000 0.00 0.00 0.00 2.73
2510 5026 3.244105 GCATAGTGCGGGTATGCG 58.756 61.111 8.49 0.00 42.44 4.73
2558 5074 5.060506 CCATAATACGTTGCTGGATTACCA 58.939 41.667 0.00 0.00 44.76 3.25
2560 5076 4.083484 GCCCATAATACGTTGCTGGATTAC 60.083 45.833 0.00 0.00 0.00 1.89
2561 5077 4.069304 GCCCATAATACGTTGCTGGATTA 58.931 43.478 0.00 0.00 0.00 1.75
2567 5083 0.179468 ACGGCCCATAATACGTTGCT 59.821 50.000 0.00 0.00 35.90 3.91
2587 5103 2.029666 GCGGATAGTGCTGCGGAT 59.970 61.111 0.00 0.00 0.00 4.18
2650 5166 6.592607 CCTAGTTACACACGGTTCATAACATT 59.407 38.462 7.52 0.00 0.00 2.71
2655 5171 5.336690 GGAACCTAGTTACACACGGTTCATA 60.337 44.000 17.95 0.00 44.40 2.15
2659 5175 2.699846 TGGAACCTAGTTACACACGGTT 59.300 45.455 0.00 0.00 36.21 4.44
2671 5191 5.063880 GCTTATGGTTACCATGGAACCTAG 58.936 45.833 30.07 25.48 44.84 3.02
2675 5195 3.380320 GTGGCTTATGGTTACCATGGAAC 59.620 47.826 25.61 17.34 44.84 3.62
2685 5205 2.639065 CATGTACGGTGGCTTATGGTT 58.361 47.619 0.00 0.00 0.00 3.67
2697 5217 4.141801 TGGGTCTCTTTATTCCATGTACGG 60.142 45.833 0.00 0.00 0.00 4.02
2715 5235 3.935203 CACAGTTCACTACATGATGGGTC 59.065 47.826 0.00 0.00 37.11 4.46
2716 5236 3.327757 ACACAGTTCACTACATGATGGGT 59.672 43.478 0.00 0.00 37.11 4.51
2771 5296 6.030228 GCAGTAACCAGATGCTTTATTCAAC 58.970 40.000 0.00 0.00 37.00 3.18
2773 5298 5.252547 TGCAGTAACCAGATGCTTTATTCA 58.747 37.500 0.00 0.00 40.62 2.57
2806 5331 5.813672 ACGCATCTAGAAAGCCGTTATTTTA 59.186 36.000 13.12 0.00 0.00 1.52
2822 5347 5.566826 GCATAGGACATTTAGGACGCATCTA 60.567 44.000 0.00 0.00 0.00 1.98
2823 5348 4.800914 GCATAGGACATTTAGGACGCATCT 60.801 45.833 0.00 0.00 0.00 2.90
2824 5349 3.433615 GCATAGGACATTTAGGACGCATC 59.566 47.826 0.00 0.00 0.00 3.91
2825 5350 3.403038 GCATAGGACATTTAGGACGCAT 58.597 45.455 0.00 0.00 0.00 4.73
2826 5351 2.484770 GGCATAGGACATTTAGGACGCA 60.485 50.000 0.00 0.00 0.00 5.24
2827 5352 2.143925 GGCATAGGACATTTAGGACGC 58.856 52.381 0.00 0.00 0.00 5.19
2828 5353 3.469008 TGGCATAGGACATTTAGGACG 57.531 47.619 0.00 0.00 0.00 4.79
2837 5362 5.848286 AAGGATATCAATGGCATAGGACA 57.152 39.130 0.00 0.00 35.65 4.02
2838 5363 6.716628 TCAAAAGGATATCAATGGCATAGGAC 59.283 38.462 0.00 0.00 0.00 3.85
2839 5364 6.851318 TCAAAAGGATATCAATGGCATAGGA 58.149 36.000 0.00 1.87 0.00 2.94
2840 5365 7.449395 TCTTCAAAAGGATATCAATGGCATAGG 59.551 37.037 0.00 0.00 0.00 2.57
2841 5366 8.400184 TCTTCAAAAGGATATCAATGGCATAG 57.600 34.615 0.00 0.00 0.00 2.23
2842 5367 8.765488 TTCTTCAAAAGGATATCAATGGCATA 57.235 30.769 0.00 0.00 0.00 3.14
2843 5368 7.664552 TTCTTCAAAAGGATATCAATGGCAT 57.335 32.000 4.83 0.00 0.00 4.40
2844 5369 7.396907 TCTTTCTTCAAAAGGATATCAATGGCA 59.603 33.333 4.83 0.00 0.00 4.92
2845 5370 7.775120 TCTTTCTTCAAAAGGATATCAATGGC 58.225 34.615 4.83 0.00 0.00 4.40
2855 5380 9.989296 TTCCCATTATATCTTTCTTCAAAAGGA 57.011 29.630 0.00 0.00 0.00 3.36
2871 5396 9.458727 CGGTAGAGTAGAGTAATTCCCATTATA 57.541 37.037 0.00 0.00 0.00 0.98
2872 5397 8.168725 TCGGTAGAGTAGAGTAATTCCCATTAT 58.831 37.037 0.00 0.00 0.00 1.28
2873 5398 7.446625 GTCGGTAGAGTAGAGTAATTCCCATTA 59.553 40.741 0.00 0.00 0.00 1.90
2874 5399 6.264970 GTCGGTAGAGTAGAGTAATTCCCATT 59.735 42.308 0.00 0.00 0.00 3.16
2875 5400 5.769162 GTCGGTAGAGTAGAGTAATTCCCAT 59.231 44.000 0.00 0.00 0.00 4.00
2876 5401 5.128919 GTCGGTAGAGTAGAGTAATTCCCA 58.871 45.833 0.00 0.00 0.00 4.37
2877 5402 5.128919 TGTCGGTAGAGTAGAGTAATTCCC 58.871 45.833 0.00 0.00 0.00 3.97
2878 5403 6.485984 TGATGTCGGTAGAGTAGAGTAATTCC 59.514 42.308 0.00 0.00 0.00 3.01
2879 5404 7.493743 TGATGTCGGTAGAGTAGAGTAATTC 57.506 40.000 0.00 0.00 0.00 2.17
2880 5405 7.040340 CCATGATGTCGGTAGAGTAGAGTAATT 60.040 40.741 0.00 0.00 0.00 1.40
2881 5406 6.431543 CCATGATGTCGGTAGAGTAGAGTAAT 59.568 42.308 0.00 0.00 0.00 1.89
2882 5407 5.763698 CCATGATGTCGGTAGAGTAGAGTAA 59.236 44.000 0.00 0.00 0.00 2.24
2883 5408 5.071384 TCCATGATGTCGGTAGAGTAGAGTA 59.929 44.000 0.00 0.00 0.00 2.59
2884 5409 4.138290 CCATGATGTCGGTAGAGTAGAGT 58.862 47.826 0.00 0.00 0.00 3.24
2885 5410 4.390264 TCCATGATGTCGGTAGAGTAGAG 58.610 47.826 0.00 0.00 0.00 2.43
2886 5411 4.390264 CTCCATGATGTCGGTAGAGTAGA 58.610 47.826 0.00 0.00 0.00 2.59
2887 5412 3.057876 GCTCCATGATGTCGGTAGAGTAG 60.058 52.174 0.00 0.00 0.00 2.57
2888 5413 2.885266 GCTCCATGATGTCGGTAGAGTA 59.115 50.000 0.00 0.00 0.00 2.59
2889 5414 1.683917 GCTCCATGATGTCGGTAGAGT 59.316 52.381 0.00 0.00 0.00 3.24
2890 5415 1.000283 GGCTCCATGATGTCGGTAGAG 60.000 57.143 0.00 0.00 0.00 2.43
2891 5416 1.040646 GGCTCCATGATGTCGGTAGA 58.959 55.000 0.00 0.00 0.00 2.59
2892 5417 0.034059 GGGCTCCATGATGTCGGTAG 59.966 60.000 0.00 0.00 0.00 3.18
2893 5418 0.689412 TGGGCTCCATGATGTCGGTA 60.689 55.000 0.00 0.00 0.00 4.02
2894 5419 1.976132 CTGGGCTCCATGATGTCGGT 61.976 60.000 0.00 0.00 30.82 4.69
2895 5420 1.227764 CTGGGCTCCATGATGTCGG 60.228 63.158 0.00 0.00 30.82 4.79
2896 5421 1.227764 CCTGGGCTCCATGATGTCG 60.228 63.158 0.00 0.00 30.82 4.35
2897 5422 0.465097 CACCTGGGCTCCATGATGTC 60.465 60.000 0.00 0.00 30.82 3.06
2898 5423 0.915872 TCACCTGGGCTCCATGATGT 60.916 55.000 0.00 0.00 30.82 3.06
2899 5424 0.477204 ATCACCTGGGCTCCATGATG 59.523 55.000 0.00 0.00 33.55 3.07
2900 5425 1.133575 CAATCACCTGGGCTCCATGAT 60.134 52.381 0.00 4.63 35.51 2.45
2901 5426 0.256752 CAATCACCTGGGCTCCATGA 59.743 55.000 0.00 2.75 30.82 3.07
2902 5427 0.754217 CCAATCACCTGGGCTCCATG 60.754 60.000 0.00 0.00 30.82 3.66
2903 5428 1.616921 CCAATCACCTGGGCTCCAT 59.383 57.895 0.00 0.00 30.82 3.41
2904 5429 3.089838 CCAATCACCTGGGCTCCA 58.910 61.111 0.00 0.00 32.32 3.86
2905 5430 2.440980 GCCAATCACCTGGGCTCC 60.441 66.667 0.00 0.00 44.32 4.70
2906 5431 2.825836 CGCCAATCACCTGGGCTC 60.826 66.667 0.00 0.00 45.53 4.70
2909 5434 4.738998 TGGCGCCAATCACCTGGG 62.739 66.667 30.74 0.00 36.92 4.45
2910 5435 3.136123 CTGGCGCCAATCACCTGG 61.136 66.667 32.09 12.49 39.71 4.45
2911 5436 3.818787 GCTGGCGCCAATCACCTG 61.819 66.667 32.09 17.97 0.00 4.00
2924 5449 0.960364 ACGTATGTGGCAAAGGCTGG 60.960 55.000 0.00 0.00 40.87 4.85
2925 5450 0.168788 CACGTATGTGGCAAAGGCTG 59.831 55.000 7.22 0.00 42.59 4.85
2926 5451 2.555123 CACGTATGTGGCAAAGGCT 58.445 52.632 7.22 0.00 42.59 4.58
2935 5460 4.318050 CGAAATGCTGTATCCACGTATGTG 60.318 45.833 8.18 8.18 46.00 3.21
2936 5461 3.802139 CGAAATGCTGTATCCACGTATGT 59.198 43.478 0.00 0.00 0.00 2.29
2937 5462 3.362986 GCGAAATGCTGTATCCACGTATG 60.363 47.826 0.00 0.00 41.73 2.39
2938 5463 2.800544 GCGAAATGCTGTATCCACGTAT 59.199 45.455 0.00 0.00 41.73 3.06
2939 5464 2.198406 GCGAAATGCTGTATCCACGTA 58.802 47.619 0.00 0.00 41.73 3.57
2940 5465 1.006832 GCGAAATGCTGTATCCACGT 58.993 50.000 0.00 0.00 41.73 4.49
2941 5466 3.806257 GCGAAATGCTGTATCCACG 57.194 52.632 0.00 0.00 41.73 4.94
2951 5476 1.334054 CACTCAGCAAAGCGAAATGC 58.666 50.000 0.00 0.00 46.98 3.56
2952 5477 1.334054 GCACTCAGCAAAGCGAAATG 58.666 50.000 0.00 0.00 44.79 2.32
2953 5478 3.780925 GCACTCAGCAAAGCGAAAT 57.219 47.368 0.00 0.00 44.79 2.17
2963 5488 0.594796 CAAACAAACCGGCACTCAGC 60.595 55.000 0.00 0.00 44.65 4.26
2964 5489 0.594796 GCAAACAAACCGGCACTCAG 60.595 55.000 0.00 0.00 0.00 3.35
2965 5490 1.435515 GCAAACAAACCGGCACTCA 59.564 52.632 0.00 0.00 0.00 3.41
2966 5491 1.299850 GGCAAACAAACCGGCACTC 60.300 57.895 0.00 0.00 0.00 3.51
2967 5492 2.811799 GGCAAACAAACCGGCACT 59.188 55.556 0.00 0.00 0.00 4.40
2968 5493 2.656973 CGGCAAACAAACCGGCAC 60.657 61.111 0.00 0.00 45.74 5.01
2973 5498 4.319249 GCACTCGGCAAACAAACC 57.681 55.556 0.00 0.00 43.97 3.27
2982 5507 1.068333 ACATGACATTTTGCACTCGGC 60.068 47.619 0.00 0.00 45.13 5.54
2983 5508 2.995466 ACATGACATTTTGCACTCGG 57.005 45.000 0.00 0.00 0.00 4.63
2984 5509 4.158384 GGTTACATGACATTTTGCACTCG 58.842 43.478 0.00 0.00 0.00 4.18
2985 5510 4.083537 TCGGTTACATGACATTTTGCACTC 60.084 41.667 0.00 0.00 0.00 3.51
2986 5511 3.818210 TCGGTTACATGACATTTTGCACT 59.182 39.130 0.00 0.00 0.00 4.40
2987 5512 4.153958 TCGGTTACATGACATTTTGCAC 57.846 40.909 0.00 0.00 0.00 4.57
2988 5513 3.818210 ACTCGGTTACATGACATTTTGCA 59.182 39.130 0.00 0.00 0.00 4.08
2989 5514 4.158384 CACTCGGTTACATGACATTTTGC 58.842 43.478 0.00 0.00 0.00 3.68
2990 5515 5.356882 ACACTCGGTTACATGACATTTTG 57.643 39.130 0.00 0.00 0.00 2.44
2991 5516 7.499321 TTTACACTCGGTTACATGACATTTT 57.501 32.000 0.00 0.00 0.00 1.82
2992 5517 7.499321 TTTTACACTCGGTTACATGACATTT 57.501 32.000 0.00 0.00 0.00 2.32
2993 5518 7.499321 TTTTTACACTCGGTTACATGACATT 57.501 32.000 0.00 0.00 0.00 2.71
2994 5519 7.681939 ATTTTTACACTCGGTTACATGACAT 57.318 32.000 0.00 0.00 0.00 3.06
2995 5520 8.604640 TTATTTTTACACTCGGTTACATGACA 57.395 30.769 0.00 0.00 0.00 3.58
2996 5521 9.537848 CTTTATTTTTACACTCGGTTACATGAC 57.462 33.333 0.00 0.00 0.00 3.06
2997 5522 8.723311 CCTTTATTTTTACACTCGGTTACATGA 58.277 33.333 0.00 0.00 0.00 3.07
2998 5523 8.723311 TCCTTTATTTTTACACTCGGTTACATG 58.277 33.333 0.00 0.00 0.00 3.21
2999 5524 8.851541 TCCTTTATTTTTACACTCGGTTACAT 57.148 30.769 0.00 0.00 0.00 2.29
3000 5525 8.723311 CATCCTTTATTTTTACACTCGGTTACA 58.277 33.333 0.00 0.00 0.00 2.41
3001 5526 8.724229 ACATCCTTTATTTTTACACTCGGTTAC 58.276 33.333 0.00 0.00 0.00 2.50
3002 5527 8.851541 ACATCCTTTATTTTTACACTCGGTTA 57.148 30.769 0.00 0.00 0.00 2.85
3003 5528 7.446013 TGACATCCTTTATTTTTACACTCGGTT 59.554 33.333 0.00 0.00 0.00 4.44
3004 5529 6.938030 TGACATCCTTTATTTTTACACTCGGT 59.062 34.615 0.00 0.00 0.00 4.69
3005 5530 7.372451 TGACATCCTTTATTTTTACACTCGG 57.628 36.000 0.00 0.00 0.00 4.63
3018 5543 7.882791 ACATGTGACAGTTATTGACATCCTTTA 59.117 33.333 0.00 0.00 34.15 1.85
3029 5554 3.503363 CTGCCACACATGTGACAGTTATT 59.497 43.478 31.94 4.03 46.80 1.40
3065 5590 5.961272 TCTATTTGCATTAGAGACGTGTGA 58.039 37.500 0.00 0.00 0.00 3.58
3171 5696 6.720012 TGATGAAAACGAATCTTCAATCGA 57.280 33.333 1.84 0.00 41.43 3.59
3206 5731 9.582431 AAGATCTAATTTTAAACATCTCGTCGA 57.418 29.630 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.