Multiple sequence alignment - TraesCS5A01G423600

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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 TraesCS5A01G423600 chr5A 100.000 2963 0 0 1 2963 609260578 609257616 0.000000e+00 5472.0
1 TraesCS5A01G423600 chr5D 90.488 2786 152 47 1 2732 488427154 488424428 0.000000e+00 3572.0
2 TraesCS5A01G423600 chr5B 92.219 1902 81 28 662 2525 601407336 601405464 0.000000e+00 2630.0
3 TraesCS5A01G423600 chr5B 92.941 680 30 8 1 665 601410282 601409606 0.000000e+00 974.0
4 TraesCS5A01G423600 chr4B 95.758 165 6 1 1503 1667 10704411 10704248 6.300000e-67 265.0
5 TraesCS5A01G423600 chr4B 100.000 37 0 0 1891 1927 10704174 10704138 5.300000e-08 69.4
6 TraesCS5A01G423600 chr4D 93.333 165 10 1 1503 1667 6078207 6078044 2.950000e-60 243.0
7 TraesCS5A01G423600 chr4D 100.000 32 0 0 1603 1634 6078042 6078011 3.190000e-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 TraesCS5A01G423600 chr5A 609257616 609260578 2962 True 5472 5472 100.000 1 2963 1 chr5A.!!$R1 2962
1 TraesCS5A01G423600 chr5D 488424428 488427154 2726 True 3572 3572 90.488 1 2732 1 chr5D.!!$R1 2731
2 TraesCS5A01G423600 chr5B 601405464 601410282 4818 True 1802 2630 92.580 1 2525 2 chr5B.!!$R1 2524

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
293 304 0.394216 TGCATAGCATTCGGCCAAGT 60.394 50.0 2.24 0.0 46.5 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 4553 0.034198 TGGCACGTCCGAGAAATTCA 59.966 50.0 0.0 0.0 37.8 2.57 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
98 99 6.591834 AGTTGAACTGCTCACATAGTATGTTC 59.408 38.462 13.25 7.38 42.70 3.18
99 100 5.419542 TGAACTGCTCACATAGTATGTTCC 58.580 41.667 13.25 5.52 42.70 3.62
105 109 5.186198 GCTCACATAGTATGTTCCCTTGTT 58.814 41.667 13.25 0.00 42.70 2.83
142 153 3.037431 CAGAACTCTGGTCTTCCTGTG 57.963 52.381 0.00 0.00 40.20 3.66
143 154 1.974236 AGAACTCTGGTCTTCCTGTGG 59.026 52.381 0.00 0.00 34.80 4.17
144 155 0.398318 AACTCTGGTCTTCCTGTGGC 59.602 55.000 0.00 0.00 34.80 5.01
145 156 0.764369 ACTCTGGTCTTCCTGTGGCA 60.764 55.000 0.00 0.00 34.80 4.92
166 177 1.948145 CAGGATGATCAAGCAGCTTCC 59.052 52.381 4.07 2.14 39.69 3.46
248 259 0.547712 TCTTCCTACCCAGCCAGCTT 60.548 55.000 0.00 0.00 0.00 3.74
293 304 0.394216 TGCATAGCATTCGGCCAAGT 60.394 50.000 2.24 0.00 46.50 3.16
353 364 1.303643 GCTGCCTGCTGTACCCTTT 60.304 57.895 0.00 0.00 38.95 3.11
496 522 6.454705 TCGGAAGAGTCGATTCAAATCGCT 62.455 45.833 17.93 17.07 45.60 4.93
596 622 7.827236 TGTAAGACACTGTTTATATTCTTGGGG 59.173 37.037 0.00 0.00 0.00 4.96
917 3224 1.696832 GAGATTCCACTTCGCCGCAC 61.697 60.000 0.00 0.00 0.00 5.34
918 3225 2.746277 ATTCCACTTCGCCGCACC 60.746 61.111 0.00 0.00 0.00 5.01
970 3278 3.937706 CGAACCATCAGATCAAGAAGCTT 59.062 43.478 0.00 0.00 0.00 3.74
991 3299 4.882396 GAGAGAAGCTCCGGCCGC 62.882 72.222 22.85 6.25 37.69 6.53
1057 3365 2.852075 TGCCGAAACCCCACTCCT 60.852 61.111 0.00 0.00 0.00 3.69
1175 3504 0.248825 GAGAGCACAGCGTCGATGAT 60.249 55.000 18.74 0.00 0.00 2.45
1341 3670 2.047179 GCGGTGGTGACCTTCCTC 60.047 66.667 2.11 0.00 40.58 3.71
1751 4080 2.557056 TCAACGTGGAGAGGAACTACAG 59.443 50.000 0.00 0.00 40.52 2.74
1775 4104 0.974383 AAGTTCGAGTACCTGGTGGG 59.026 55.000 10.23 0.00 41.89 4.61
2052 4392 1.897398 GCGGGTGCTTCGTACACTTG 61.897 60.000 0.00 1.15 38.14 3.16
2077 4417 2.585247 GCTATGGCGACCACGGTC 60.585 66.667 6.12 6.12 35.80 4.79
2103 4443 8.887036 TGTACTGTACATAATGATCAATGGTC 57.113 34.615 16.26 5.24 32.89 4.02
2140 4487 2.926200 GACTCACATCGTGAAGTGATGG 59.074 50.000 8.21 1.64 45.90 3.51
2195 4545 7.876936 AAGTATACCAATGAAGTAGTCGAGA 57.123 36.000 0.00 0.00 0.00 4.04
2196 4546 7.499321 AGTATACCAATGAAGTAGTCGAGAG 57.501 40.000 0.00 0.00 0.00 3.20
2197 4547 3.512033 ACCAATGAAGTAGTCGAGAGC 57.488 47.619 0.00 0.00 0.00 4.09
2198 4548 2.166664 ACCAATGAAGTAGTCGAGAGCC 59.833 50.000 0.00 0.00 0.00 4.70
2199 4549 2.166459 CCAATGAAGTAGTCGAGAGCCA 59.834 50.000 0.00 0.00 0.00 4.75
2200 4550 3.368427 CCAATGAAGTAGTCGAGAGCCAA 60.368 47.826 0.00 0.00 0.00 4.52
2201 4551 4.245660 CAATGAAGTAGTCGAGAGCCAAA 58.754 43.478 0.00 0.00 0.00 3.28
2202 4552 3.577649 TGAAGTAGTCGAGAGCCAAAG 57.422 47.619 0.00 0.00 0.00 2.77
2203 4553 2.891580 TGAAGTAGTCGAGAGCCAAAGT 59.108 45.455 0.00 0.00 0.00 2.66
2204 4554 3.246619 GAAGTAGTCGAGAGCCAAAGTG 58.753 50.000 0.00 0.00 0.00 3.16
2205 4555 2.515854 AGTAGTCGAGAGCCAAAGTGA 58.484 47.619 0.00 0.00 0.00 3.41
2206 4556 2.891580 AGTAGTCGAGAGCCAAAGTGAA 59.108 45.455 0.00 0.00 0.00 3.18
2207 4557 3.511934 AGTAGTCGAGAGCCAAAGTGAAT 59.488 43.478 0.00 0.00 0.00 2.57
2208 4558 3.409026 AGTCGAGAGCCAAAGTGAATT 57.591 42.857 0.00 0.00 0.00 2.17
2209 4559 3.744660 AGTCGAGAGCCAAAGTGAATTT 58.255 40.909 0.00 0.00 0.00 1.82
2210 4560 3.748568 AGTCGAGAGCCAAAGTGAATTTC 59.251 43.478 0.00 0.00 0.00 2.17
2211 4561 3.748568 GTCGAGAGCCAAAGTGAATTTCT 59.251 43.478 0.00 0.00 0.00 2.52
2212 4562 3.997021 TCGAGAGCCAAAGTGAATTTCTC 59.003 43.478 0.00 0.00 0.00 2.87
2216 4566 2.814336 AGCCAAAGTGAATTTCTCGGAC 59.186 45.455 0.00 0.00 0.00 4.79
2237 4587 3.258228 CGTGCCATGTGTATAGTGTTCA 58.742 45.455 0.00 0.00 0.00 3.18
2253 4604 2.560542 TGTTCATAACACATGTTGGGGC 59.439 45.455 7.53 0.00 38.90 5.80
2254 4605 2.560542 GTTCATAACACATGTTGGGGCA 59.439 45.455 7.53 0.00 38.90 5.36
2342 4693 3.354397 CAGAGTGAACGTGAAACTTTGC 58.646 45.455 0.00 0.00 31.75 3.68
2344 4695 2.004017 AGTGAACGTGAAACTTTGCGA 58.996 42.857 0.00 0.00 31.75 5.10
2362 4713 3.559655 TGCGACCATCCGATCTATTTTTG 59.440 43.478 0.00 0.00 0.00 2.44
2408 4764 6.156748 TCTCTAGTGTAAGTTTGCAACTGA 57.843 37.500 0.00 0.00 41.91 3.41
2410 4766 7.045416 TCTCTAGTGTAAGTTTGCAACTGAAA 58.955 34.615 0.00 0.00 41.91 2.69
2411 4767 7.011109 TCTCTAGTGTAAGTTTGCAACTGAAAC 59.989 37.037 0.00 0.00 41.91 2.78
2412 4768 5.637006 AGTGTAAGTTTGCAACTGAAACA 57.363 34.783 0.00 0.00 41.91 2.83
2413 4769 6.019779 AGTGTAAGTTTGCAACTGAAACAA 57.980 33.333 0.00 0.00 41.91 2.83
2415 4771 6.072175 AGTGTAAGTTTGCAACTGAAACAAGA 60.072 34.615 0.00 0.00 41.91 3.02
2416 4772 6.584563 GTGTAAGTTTGCAACTGAAACAAGAA 59.415 34.615 0.00 0.00 41.91 2.52
2417 4773 7.115663 GTGTAAGTTTGCAACTGAAACAAGAAA 59.884 33.333 0.00 0.00 41.91 2.52
2433 4789 6.254281 ACAAGAAATGTAATCCTTTCCACG 57.746 37.500 0.00 0.00 41.63 4.94
2482 4838 5.209659 ACCGGTTCTAGTAGAGGAATCAAT 58.790 41.667 0.00 0.00 0.00 2.57
2512 4868 2.941025 TGGAAGGCAGGAAGGGGG 60.941 66.667 0.00 0.00 0.00 5.40
2539 4895 4.394712 GTGGCCTCCCCGTCTGTG 62.395 72.222 3.32 0.00 35.87 3.66
2540 4896 4.631740 TGGCCTCCCCGTCTGTGA 62.632 66.667 3.32 0.00 35.87 3.58
2541 4897 4.083862 GGCCTCCCCGTCTGTGAC 62.084 72.222 0.00 0.00 0.00 3.67
2557 4916 4.702081 ACTGCACGCCTCGACGTC 62.702 66.667 5.18 5.18 46.34 4.34
2571 4930 4.765611 CGTCATCGTCTTCTCGCA 57.234 55.556 0.00 0.00 0.00 5.10
2586 4945 4.683334 GCAACCGCGTGCCTCAAC 62.683 66.667 10.36 0.00 38.66 3.18
2587 4946 4.368808 CAACCGCGTGCCTCAACG 62.369 66.667 4.92 0.00 46.30 4.10
2588 4947 4.595538 AACCGCGTGCCTCAACGA 62.596 61.111 4.92 0.00 46.49 3.85
2596 4955 0.252197 GTGCCTCAACGACCCCTATT 59.748 55.000 0.00 0.00 0.00 1.73
2598 4957 0.179054 GCCTCAACGACCCCTATTCC 60.179 60.000 0.00 0.00 0.00 3.01
2599 4958 1.200519 CCTCAACGACCCCTATTCCA 58.799 55.000 0.00 0.00 0.00 3.53
2610 4969 0.466189 CCTATTCCAATGGCCGCACT 60.466 55.000 0.00 0.00 0.00 4.40
2622 4981 4.180946 CGCACTCCTCCTCCGACG 62.181 72.222 0.00 0.00 0.00 5.12
2636 4995 2.433664 GACGGCTACGGGTTGTGG 60.434 66.667 0.00 0.00 46.48 4.17
2664 5026 1.528542 CCCGATGGTAGGAGCTCGA 60.529 63.158 7.83 0.00 33.07 4.04
2691 5053 2.726912 CGTACAACGGTCGCGTGT 60.727 61.111 5.77 5.11 38.08 4.49
2693 5055 1.658102 GTACAACGGTCGCGTGTCA 60.658 57.895 5.77 0.00 0.00 3.58
2695 5057 4.042060 CAACGGTCGCGTGTCACG 62.042 66.667 21.02 21.02 45.88 4.35
2736 5098 3.851128 GGCTCGCCTCCCCTGTAC 61.851 72.222 0.00 0.00 0.00 2.90
2737 5099 3.075005 GCTCGCCTCCCCTGTACA 61.075 66.667 0.00 0.00 0.00 2.90
2738 5100 2.435693 GCTCGCCTCCCCTGTACAT 61.436 63.158 0.00 0.00 0.00 2.29
2739 5101 1.443407 CTCGCCTCCCCTGTACATG 59.557 63.158 0.00 0.00 0.00 3.21
2740 5102 2.032860 CTCGCCTCCCCTGTACATGG 62.033 65.000 10.06 10.06 0.00 3.66
2741 5103 2.193248 GCCTCCCCTGTACATGGC 59.807 66.667 11.46 9.33 0.00 4.40
2742 5104 2.679342 GCCTCCCCTGTACATGGCA 61.679 63.158 11.46 0.00 40.04 4.92
2743 5105 1.224592 CCTCCCCTGTACATGGCAC 59.775 63.158 11.46 0.00 0.00 5.01
2757 5119 4.643387 GCACACTTGCCTCCCCGT 62.643 66.667 0.00 0.00 43.66 5.28
2758 5120 2.113139 CACACTTGCCTCCCCGTT 59.887 61.111 0.00 0.00 0.00 4.44
2759 5121 2.113139 ACACTTGCCTCCCCGTTG 59.887 61.111 0.00 0.00 0.00 4.10
2760 5122 2.429930 CACTTGCCTCCCCGTTGA 59.570 61.111 0.00 0.00 0.00 3.18
2761 5123 1.002134 CACTTGCCTCCCCGTTGAT 60.002 57.895 0.00 0.00 0.00 2.57
2762 5124 1.002134 ACTTGCCTCCCCGTTGATG 60.002 57.895 0.00 0.00 0.00 3.07
2763 5125 1.750399 CTTGCCTCCCCGTTGATGG 60.750 63.158 0.00 0.00 0.00 3.51
2764 5126 2.484287 CTTGCCTCCCCGTTGATGGT 62.484 60.000 0.00 0.00 0.00 3.55
2765 5127 2.124695 GCCTCCCCGTTGATGGTC 60.125 66.667 0.00 0.00 0.00 4.02
2766 5128 2.966732 GCCTCCCCGTTGATGGTCA 61.967 63.158 0.00 0.00 0.00 4.02
2767 5129 1.915228 CCTCCCCGTTGATGGTCAT 59.085 57.895 0.00 0.00 0.00 3.06
2768 5130 0.179045 CCTCCCCGTTGATGGTCATC 60.179 60.000 4.13 4.13 38.29 2.92
2769 5131 0.833287 CTCCCCGTTGATGGTCATCT 59.167 55.000 11.62 0.00 38.60 2.90
2770 5132 0.830648 TCCCCGTTGATGGTCATCTC 59.169 55.000 11.62 5.07 38.60 2.75
2771 5133 0.833287 CCCCGTTGATGGTCATCTCT 59.167 55.000 11.62 0.00 38.60 3.10
2772 5134 1.202580 CCCCGTTGATGGTCATCTCTC 60.203 57.143 11.62 2.78 38.60 3.20
2773 5135 1.202580 CCCGTTGATGGTCATCTCTCC 60.203 57.143 11.62 0.00 38.60 3.71
2774 5136 1.759445 CCGTTGATGGTCATCTCTCCT 59.241 52.381 11.62 0.00 38.60 3.69
2775 5137 2.169352 CCGTTGATGGTCATCTCTCCTT 59.831 50.000 11.62 0.00 38.60 3.36
2776 5138 3.452474 CGTTGATGGTCATCTCTCCTTC 58.548 50.000 11.62 0.00 38.60 3.46
2777 5139 3.739519 CGTTGATGGTCATCTCTCCTTCC 60.740 52.174 11.62 0.00 38.60 3.46
2778 5140 2.402564 TGATGGTCATCTCTCCTTCCC 58.597 52.381 11.62 0.00 38.60 3.97
2779 5141 1.342819 GATGGTCATCTCTCCTTCCCG 59.657 57.143 3.87 0.00 35.04 5.14
2780 5142 1.330655 TGGTCATCTCTCCTTCCCGC 61.331 60.000 0.00 0.00 0.00 6.13
2781 5143 1.443828 GTCATCTCTCCTTCCCGCC 59.556 63.158 0.00 0.00 0.00 6.13
2782 5144 1.762460 TCATCTCTCCTTCCCGCCC 60.762 63.158 0.00 0.00 0.00 6.13
2783 5145 2.840102 ATCTCTCCTTCCCGCCCG 60.840 66.667 0.00 0.00 0.00 6.13
2786 5148 4.064768 TCTCCTTCCCGCCCGGTA 62.065 66.667 0.00 0.00 0.00 4.02
2787 5149 3.537874 CTCCTTCCCGCCCGGTAG 61.538 72.222 0.00 2.92 0.00 3.18
2813 5175 2.366972 CCCCCTCCCCTAGGTGTG 60.367 72.222 8.29 0.00 44.90 3.82
2814 5176 2.784984 CCCCTCCCCTAGGTGTGA 59.215 66.667 8.29 0.29 44.90 3.58
2815 5177 1.082206 CCCCTCCCCTAGGTGTGAA 59.918 63.158 8.29 0.00 44.90 3.18
2816 5178 0.549169 CCCCTCCCCTAGGTGTGAAA 60.549 60.000 8.29 0.00 44.90 2.69
2817 5179 1.368374 CCCTCCCCTAGGTGTGAAAA 58.632 55.000 8.29 0.00 44.90 2.29
2818 5180 1.004394 CCCTCCCCTAGGTGTGAAAAC 59.996 57.143 8.29 0.00 44.90 2.43
2819 5181 1.702957 CCTCCCCTAGGTGTGAAAACA 59.297 52.381 8.29 0.00 40.94 2.83
2820 5182 2.107552 CCTCCCCTAGGTGTGAAAACAA 59.892 50.000 8.29 0.00 40.94 2.83
2821 5183 3.435890 CCTCCCCTAGGTGTGAAAACAAA 60.436 47.826 8.29 0.00 40.94 2.83
2822 5184 3.558033 TCCCCTAGGTGTGAAAACAAAC 58.442 45.455 8.29 0.00 0.00 2.93
2823 5185 3.203487 TCCCCTAGGTGTGAAAACAAACT 59.797 43.478 8.29 0.00 0.00 2.66
2824 5186 4.412858 TCCCCTAGGTGTGAAAACAAACTA 59.587 41.667 8.29 0.00 0.00 2.24
2825 5187 4.760204 CCCCTAGGTGTGAAAACAAACTAG 59.240 45.833 8.29 9.93 33.21 2.57
2826 5188 4.215613 CCCTAGGTGTGAAAACAAACTAGC 59.784 45.833 8.29 0.00 32.63 3.42
2827 5189 5.063880 CCTAGGTGTGAAAACAAACTAGCT 58.936 41.667 0.00 0.00 32.63 3.32
2828 5190 5.179555 CCTAGGTGTGAAAACAAACTAGCTC 59.820 44.000 0.00 0.00 32.63 4.09
2829 5191 4.781934 AGGTGTGAAAACAAACTAGCTCT 58.218 39.130 0.00 0.00 0.00 4.09
2830 5192 4.576463 AGGTGTGAAAACAAACTAGCTCTG 59.424 41.667 0.00 0.00 0.00 3.35
2831 5193 4.261197 GGTGTGAAAACAAACTAGCTCTGG 60.261 45.833 0.00 0.00 0.00 3.86
2832 5194 3.882888 TGTGAAAACAAACTAGCTCTGGG 59.117 43.478 0.00 0.00 0.00 4.45
2833 5195 4.134563 GTGAAAACAAACTAGCTCTGGGA 58.865 43.478 0.00 0.00 0.00 4.37
2834 5196 4.578928 GTGAAAACAAACTAGCTCTGGGAA 59.421 41.667 0.00 0.00 0.00 3.97
2835 5197 4.578928 TGAAAACAAACTAGCTCTGGGAAC 59.421 41.667 0.00 0.00 0.00 3.62
2855 5217 7.754851 GGAACCAACTTAGGTATGAAAGAAA 57.245 36.000 0.00 0.00 42.25 2.52
2856 5218 8.173542 GGAACCAACTTAGGTATGAAAGAAAA 57.826 34.615 0.00 0.00 42.25 2.29
2857 5219 8.080417 GGAACCAACTTAGGTATGAAAGAAAAC 58.920 37.037 0.00 0.00 42.25 2.43
2858 5220 7.520451 ACCAACTTAGGTATGAAAGAAAACC 57.480 36.000 0.00 0.00 40.98 3.27
2859 5221 7.064229 ACCAACTTAGGTATGAAAGAAAACCA 58.936 34.615 0.00 0.00 40.98 3.67
2860 5222 7.562088 ACCAACTTAGGTATGAAAGAAAACCAA 59.438 33.333 0.00 0.00 40.98 3.67
2861 5223 7.865889 CCAACTTAGGTATGAAAGAAAACCAAC 59.134 37.037 0.00 0.00 34.29 3.77
2862 5224 8.630037 CAACTTAGGTATGAAAGAAAACCAACT 58.370 33.333 0.00 0.00 34.29 3.16
2863 5225 8.762481 ACTTAGGTATGAAAGAAAACCAACTT 57.238 30.769 0.00 0.00 34.29 2.66
2864 5226 9.197306 ACTTAGGTATGAAAGAAAACCAACTTT 57.803 29.630 0.00 0.00 38.74 2.66
2867 5229 8.178313 AGGTATGAAAGAAAACCAACTTTAGG 57.822 34.615 0.00 0.00 36.63 2.69
2868 5230 8.002459 AGGTATGAAAGAAAACCAACTTTAGGA 58.998 33.333 0.00 0.00 36.63 2.94
2869 5231 8.635328 GGTATGAAAGAAAACCAACTTTAGGAA 58.365 33.333 0.00 0.00 36.63 3.36
2878 5240 9.639601 GAAAACCAACTTTAGGAATTAATGAGG 57.360 33.333 0.00 0.00 0.00 3.86
2879 5241 8.721133 AAACCAACTTTAGGAATTAATGAGGT 57.279 30.769 0.00 0.00 33.87 3.85
2880 5242 9.816787 AAACCAACTTTAGGAATTAATGAGGTA 57.183 29.630 0.00 0.00 33.07 3.08
2881 5243 9.462606 AACCAACTTTAGGAATTAATGAGGTAG 57.537 33.333 0.00 0.00 33.07 3.18
2882 5244 8.053355 ACCAACTTTAGGAATTAATGAGGTAGG 58.947 37.037 0.00 0.00 32.40 3.18
2883 5245 8.053355 CCAACTTTAGGAATTAATGAGGTAGGT 58.947 37.037 0.00 0.00 0.00 3.08
2884 5246 9.462606 CAACTTTAGGAATTAATGAGGTAGGTT 57.537 33.333 0.00 0.00 0.00 3.50
2895 5257 6.715347 AATGAGGTAGGTTATGAAATTGCC 57.285 37.500 0.00 0.00 0.00 4.52
2896 5258 5.186256 TGAGGTAGGTTATGAAATTGCCA 57.814 39.130 0.00 0.00 0.00 4.92
2897 5259 5.192927 TGAGGTAGGTTATGAAATTGCCAG 58.807 41.667 0.00 0.00 0.00 4.85
2898 5260 4.536765 AGGTAGGTTATGAAATTGCCAGG 58.463 43.478 0.00 0.00 0.00 4.45
2899 5261 4.017499 AGGTAGGTTATGAAATTGCCAGGT 60.017 41.667 0.00 0.00 0.00 4.00
2900 5262 5.192923 AGGTAGGTTATGAAATTGCCAGGTA 59.807 40.000 0.00 0.00 0.00 3.08
2901 5263 5.889289 GGTAGGTTATGAAATTGCCAGGTAA 59.111 40.000 0.00 0.00 0.00 2.85
2902 5264 6.549736 GGTAGGTTATGAAATTGCCAGGTAAT 59.450 38.462 0.00 0.00 0.00 1.89
2903 5265 6.469782 AGGTTATGAAATTGCCAGGTAATG 57.530 37.500 3.11 0.00 0.00 1.90
2904 5266 5.957774 AGGTTATGAAATTGCCAGGTAATGT 59.042 36.000 3.11 0.00 0.00 2.71
2905 5267 6.440328 AGGTTATGAAATTGCCAGGTAATGTT 59.560 34.615 3.11 1.06 0.00 2.71
2906 5268 7.038373 AGGTTATGAAATTGCCAGGTAATGTTT 60.038 33.333 3.11 0.00 0.00 2.83
2907 5269 7.064490 GGTTATGAAATTGCCAGGTAATGTTTG 59.936 37.037 3.11 0.00 0.00 2.93
2908 5270 4.892433 TGAAATTGCCAGGTAATGTTTGG 58.108 39.130 3.11 0.00 35.06 3.28
2909 5271 3.979101 AATTGCCAGGTAATGTTTGGG 57.021 42.857 3.11 0.00 32.53 4.12
2910 5272 2.390225 TTGCCAGGTAATGTTTGGGT 57.610 45.000 0.00 0.00 32.53 4.51
2911 5273 3.527507 TTGCCAGGTAATGTTTGGGTA 57.472 42.857 0.00 0.00 32.53 3.69
2912 5274 3.080300 TGCCAGGTAATGTTTGGGTAG 57.920 47.619 0.00 0.00 32.53 3.18
2913 5275 1.749063 GCCAGGTAATGTTTGGGTAGC 59.251 52.381 0.00 0.00 32.53 3.58
2914 5276 2.620627 GCCAGGTAATGTTTGGGTAGCT 60.621 50.000 0.00 0.00 32.53 3.32
2915 5277 3.016736 CCAGGTAATGTTTGGGTAGCTG 58.983 50.000 0.00 0.00 41.07 4.24
2916 5278 3.016736 CAGGTAATGTTTGGGTAGCTGG 58.983 50.000 0.00 0.00 38.89 4.85
2917 5279 2.647802 AGGTAATGTTTGGGTAGCTGGT 59.352 45.455 0.00 0.00 0.00 4.00
2918 5280 3.014623 GGTAATGTTTGGGTAGCTGGTC 58.985 50.000 0.00 0.00 0.00 4.02
2919 5281 2.215942 AATGTTTGGGTAGCTGGTCC 57.784 50.000 0.00 0.00 0.00 4.46
2920 5282 1.372501 ATGTTTGGGTAGCTGGTCCT 58.627 50.000 0.00 0.00 0.00 3.85
2921 5283 0.400213 TGTTTGGGTAGCTGGTCCTG 59.600 55.000 0.00 0.00 0.00 3.86
2922 5284 0.690762 GTTTGGGTAGCTGGTCCTGA 59.309 55.000 0.00 0.00 0.00 3.86
2923 5285 1.282157 GTTTGGGTAGCTGGTCCTGAT 59.718 52.381 0.00 0.00 0.00 2.90
2924 5286 1.204146 TTGGGTAGCTGGTCCTGATC 58.796 55.000 0.00 0.00 0.00 2.92
2925 5287 0.042581 TGGGTAGCTGGTCCTGATCA 59.957 55.000 0.00 0.00 0.00 2.92
2926 5288 1.204146 GGGTAGCTGGTCCTGATCAA 58.796 55.000 0.00 0.00 0.00 2.57
2927 5289 1.559682 GGGTAGCTGGTCCTGATCAAA 59.440 52.381 0.00 0.00 0.00 2.69
2928 5290 2.633488 GGTAGCTGGTCCTGATCAAAC 58.367 52.381 0.00 0.00 0.00 2.93
2929 5291 2.027192 GGTAGCTGGTCCTGATCAAACA 60.027 50.000 0.00 0.00 0.00 2.83
2930 5292 3.370953 GGTAGCTGGTCCTGATCAAACAT 60.371 47.826 0.00 0.00 0.00 2.71
2931 5293 3.446442 AGCTGGTCCTGATCAAACATT 57.554 42.857 0.00 0.00 0.00 2.71
2932 5294 3.087031 AGCTGGTCCTGATCAAACATTG 58.913 45.455 0.00 0.00 0.00 2.82
2933 5295 2.821969 GCTGGTCCTGATCAAACATTGT 59.178 45.455 0.00 0.00 0.00 2.71
2934 5296 3.256631 GCTGGTCCTGATCAAACATTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2935 5297 4.262164 GCTGGTCCTGATCAAACATTGTTT 60.262 41.667 8.97 8.97 0.00 2.83
2936 5298 5.739935 GCTGGTCCTGATCAAACATTGTTTT 60.740 40.000 12.02 0.00 0.00 2.43
2937 5299 5.599732 TGGTCCTGATCAAACATTGTTTTG 58.400 37.500 12.02 8.32 37.75 2.44
2938 5300 4.448732 GGTCCTGATCAAACATTGTTTTGC 59.551 41.667 12.02 5.63 36.56 3.68
2939 5301 4.448732 GTCCTGATCAAACATTGTTTTGCC 59.551 41.667 12.02 5.13 36.56 4.52
2940 5302 4.100653 TCCTGATCAAACATTGTTTTGCCA 59.899 37.500 12.02 8.91 36.56 4.92
2941 5303 4.449743 CCTGATCAAACATTGTTTTGCCAG 59.550 41.667 12.02 16.04 36.56 4.85
2942 5304 5.273674 TGATCAAACATTGTTTTGCCAGA 57.726 34.783 12.02 6.84 36.56 3.86
2943 5305 5.668471 TGATCAAACATTGTTTTGCCAGAA 58.332 33.333 12.02 0.00 36.56 3.02
2944 5306 6.289834 TGATCAAACATTGTTTTGCCAGAAT 58.710 32.000 12.02 0.00 36.56 2.40
2945 5307 7.440198 TGATCAAACATTGTTTTGCCAGAATA 58.560 30.769 12.02 0.00 36.56 1.75
2946 5308 8.095792 TGATCAAACATTGTTTTGCCAGAATAT 58.904 29.630 12.02 0.00 36.56 1.28
2947 5309 7.655236 TCAAACATTGTTTTGCCAGAATATG 57.345 32.000 12.02 0.00 36.56 1.78
2948 5310 7.440198 TCAAACATTGTTTTGCCAGAATATGA 58.560 30.769 12.02 0.65 36.56 2.15
2949 5311 7.930325 TCAAACATTGTTTTGCCAGAATATGAA 59.070 29.630 12.02 0.00 36.56 2.57
2950 5312 7.656707 AACATTGTTTTGCCAGAATATGAAC 57.343 32.000 0.00 0.00 0.00 3.18
2951 5313 6.757237 ACATTGTTTTGCCAGAATATGAACA 58.243 32.000 0.00 0.00 0.00 3.18
2952 5314 7.388437 ACATTGTTTTGCCAGAATATGAACAT 58.612 30.769 0.00 0.00 0.00 2.71
2953 5315 8.530311 ACATTGTTTTGCCAGAATATGAACATA 58.470 29.630 0.00 0.00 0.00 2.29
2954 5316 9.027129 CATTGTTTTGCCAGAATATGAACATAG 57.973 33.333 1.20 0.00 0.00 2.23
2955 5317 7.701539 TGTTTTGCCAGAATATGAACATAGT 57.298 32.000 1.20 0.00 0.00 2.12
2956 5318 8.121305 TGTTTTGCCAGAATATGAACATAGTT 57.879 30.769 1.20 0.00 0.00 2.24
2957 5319 8.584157 TGTTTTGCCAGAATATGAACATAGTTT 58.416 29.630 1.20 0.00 0.00 2.66
2958 5320 9.076596 GTTTTGCCAGAATATGAACATAGTTTC 57.923 33.333 1.20 1.65 0.00 2.78
2959 5321 8.579850 TTTGCCAGAATATGAACATAGTTTCT 57.420 30.769 5.41 5.41 0.00 2.52
2960 5322 8.579850 TTGCCAGAATATGAACATAGTTTCTT 57.420 30.769 7.51 0.00 0.00 2.52
2961 5323 8.213518 TGCCAGAATATGAACATAGTTTCTTC 57.786 34.615 7.51 3.76 0.00 2.87
2962 5324 7.828717 TGCCAGAATATGAACATAGTTTCTTCA 59.171 33.333 7.51 6.76 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.450531 AACTCTGCAAGGCACACTGC 61.451 55.000 0.00 0.00 44.08 4.40
63 64 1.311859 CAGTTCAACTCTGCAAGGCA 58.688 50.000 0.00 0.00 36.92 4.75
105 109 2.820178 TCTGTGAGGATAGCTTGGTGA 58.180 47.619 0.00 0.00 0.00 4.02
138 149 2.014857 CTTGATCATCCTGTGCCACAG 58.985 52.381 18.02 18.02 45.53 3.66
139 150 1.951895 GCTTGATCATCCTGTGCCACA 60.952 52.381 0.00 0.00 0.00 4.17
140 151 0.737219 GCTTGATCATCCTGTGCCAC 59.263 55.000 0.00 0.00 0.00 5.01
141 152 0.328926 TGCTTGATCATCCTGTGCCA 59.671 50.000 0.00 0.00 0.00 4.92
142 153 1.022735 CTGCTTGATCATCCTGTGCC 58.977 55.000 0.00 0.00 0.00 5.01
143 154 0.381089 GCTGCTTGATCATCCTGTGC 59.619 55.000 0.00 0.00 0.00 4.57
144 155 2.039818 AGCTGCTTGATCATCCTGTG 57.960 50.000 0.00 0.00 0.00 3.66
145 156 2.641305 GAAGCTGCTTGATCATCCTGT 58.359 47.619 21.25 0.00 0.00 4.00
248 259 0.468226 AGAAGCAGGTGGACGAAACA 59.532 50.000 0.00 0.00 0.00 2.83
293 304 1.819208 CGGATGCGCCAATCTGGAA 60.819 57.895 4.18 0.00 40.96 3.53
353 364 3.054728 TCCGATGCCAGACCTAATTTTGA 60.055 43.478 0.00 0.00 0.00 2.69
596 622 1.404315 CGAACTAGGTGTCAGGCCTTC 60.404 57.143 0.00 0.00 37.54 3.46
755 3062 6.264292 AGAGACAACAAGCGATAGACATATCT 59.736 38.462 0.00 0.00 36.42 1.98
756 3063 6.442952 AGAGACAACAAGCGATAGACATATC 58.557 40.000 0.00 0.00 35.40 1.63
918 3225 2.520536 GGGGAGACGATGATGGGGG 61.521 68.421 0.00 0.00 0.00 5.40
939 3246 1.123077 CTGATGGTTCGGAGATGGGA 58.877 55.000 0.00 0.00 35.04 4.37
940 3247 1.123077 TCTGATGGTTCGGAGATGGG 58.877 55.000 0.00 0.00 35.04 4.00
944 3251 3.365472 TCTTGATCTGATGGTTCGGAGA 58.635 45.455 0.00 0.00 40.57 3.71
945 3252 3.808466 TCTTGATCTGATGGTTCGGAG 57.192 47.619 0.00 0.00 40.57 4.63
946 3253 3.679917 GCTTCTTGATCTGATGGTTCGGA 60.680 47.826 0.00 0.00 41.47 4.55
947 3254 2.611292 GCTTCTTGATCTGATGGTTCGG 59.389 50.000 0.00 0.00 0.00 4.30
949 3256 5.392811 CCAAAGCTTCTTGATCTGATGGTTC 60.393 44.000 0.00 0.00 31.86 3.62
1042 3350 1.971695 GCAAGGAGTGGGGTTTCGG 60.972 63.158 0.00 0.00 0.00 4.30
1044 3352 1.606601 GGGCAAGGAGTGGGGTTTC 60.607 63.158 0.00 0.00 0.00 2.78
1047 3355 2.936032 GAGGGCAAGGAGTGGGGT 60.936 66.667 0.00 0.00 0.00 4.95
1093 3422 4.445545 CGGCGGCGACTTCTTTGC 62.446 66.667 29.19 0.00 0.00 3.68
1160 3489 2.322422 GCATCATCGACGCTGTGC 59.678 61.111 9.34 9.34 0.00 4.57
1332 3661 2.182030 CGCGACTGGAGGAAGGTC 59.818 66.667 0.00 0.00 0.00 3.85
1751 4080 0.391263 CAGGTACTCGAACTTGGGCC 60.391 60.000 0.00 0.00 34.60 5.80
2001 4337 4.899687 CATGAGCATGGCGCACGC 62.900 66.667 10.83 6.46 41.64 5.34
2043 4383 2.380410 GCTCGGTGGCAAGTGTACG 61.380 63.158 0.00 0.00 0.00 3.67
2077 4417 8.893219 ACCATTGATCATTATGTACAGTACAG 57.107 34.615 18.30 5.57 42.77 2.74
2118 4465 2.331809 TCACTTCACGATGTGAGTCG 57.668 50.000 10.71 0.00 43.69 4.18
2140 4487 6.205658 ACATCCTCTACAAAAGAAAGAAGCAC 59.794 38.462 0.00 0.00 32.46 4.40
2170 4517 8.969260 TCTCGACTACTTCATTGGTATACTTA 57.031 34.615 2.25 0.00 0.00 2.24
2171 4518 7.468906 GCTCTCGACTACTTCATTGGTATACTT 60.469 40.741 2.25 0.00 0.00 2.24
2173 4520 6.144175 GCTCTCGACTACTTCATTGGTATAC 58.856 44.000 0.00 0.00 0.00 1.47
2174 4521 5.241064 GGCTCTCGACTACTTCATTGGTATA 59.759 44.000 0.00 0.00 0.00 1.47
2192 4542 3.126000 CCGAGAAATTCACTTTGGCTCTC 59.874 47.826 0.00 0.00 0.00 3.20
2193 4543 3.077359 CCGAGAAATTCACTTTGGCTCT 58.923 45.455 0.00 0.00 0.00 4.09
2194 4544 3.074412 TCCGAGAAATTCACTTTGGCTC 58.926 45.455 0.00 0.00 0.00 4.70
2195 4545 2.814336 GTCCGAGAAATTCACTTTGGCT 59.186 45.455 0.00 0.00 0.00 4.75
2196 4546 2.412847 CGTCCGAGAAATTCACTTTGGC 60.413 50.000 0.00 0.00 0.00 4.52
2197 4547 2.806244 ACGTCCGAGAAATTCACTTTGG 59.194 45.455 0.00 0.00 0.00 3.28
2198 4548 3.799035 CACGTCCGAGAAATTCACTTTG 58.201 45.455 0.00 0.00 0.00 2.77
2199 4549 2.223377 GCACGTCCGAGAAATTCACTTT 59.777 45.455 0.00 0.00 0.00 2.66
2200 4550 1.798813 GCACGTCCGAGAAATTCACTT 59.201 47.619 0.00 0.00 0.00 3.16
2201 4551 1.429463 GCACGTCCGAGAAATTCACT 58.571 50.000 0.00 0.00 0.00 3.41
2202 4552 0.442699 GGCACGTCCGAGAAATTCAC 59.557 55.000 0.00 0.00 0.00 3.18
2203 4553 0.034198 TGGCACGTCCGAGAAATTCA 59.966 50.000 0.00 0.00 37.80 2.57
2204 4554 1.062587 CATGGCACGTCCGAGAAATTC 59.937 52.381 0.00 0.00 37.80 2.17
2205 4555 1.086696 CATGGCACGTCCGAGAAATT 58.913 50.000 0.00 0.00 37.80 1.82
2206 4556 0.036388 ACATGGCACGTCCGAGAAAT 60.036 50.000 0.00 0.00 37.80 2.17
2207 4557 0.948623 CACATGGCACGTCCGAGAAA 60.949 55.000 0.00 0.00 37.80 2.52
2208 4558 1.374125 CACATGGCACGTCCGAGAA 60.374 57.895 0.00 0.00 37.80 2.87
2209 4559 1.245376 TACACATGGCACGTCCGAGA 61.245 55.000 0.00 0.00 37.80 4.04
2210 4560 0.179111 ATACACATGGCACGTCCGAG 60.179 55.000 0.00 0.00 37.80 4.63
2211 4561 1.066454 CTATACACATGGCACGTCCGA 59.934 52.381 0.00 0.00 37.80 4.55
2212 4562 1.202371 ACTATACACATGGCACGTCCG 60.202 52.381 0.00 0.00 37.80 4.79
2216 4566 3.258228 TGAACACTATACACATGGCACG 58.742 45.455 0.00 0.00 0.00 5.34
2237 4587 2.603075 ACTGCCCCAACATGTGTTAT 57.397 45.000 0.00 0.00 36.32 1.89
2252 4603 7.121315 ACTTTCCTCCATGACTTTATTTACTGC 59.879 37.037 0.00 0.00 0.00 4.40
2253 4604 8.567285 ACTTTCCTCCATGACTTTATTTACTG 57.433 34.615 0.00 0.00 0.00 2.74
2254 4605 9.232473 GAACTTTCCTCCATGACTTTATTTACT 57.768 33.333 0.00 0.00 0.00 2.24
2342 4693 5.984233 TTCAAAAATAGATCGGATGGTCG 57.016 39.130 0.00 0.00 0.00 4.79
2344 4695 6.545504 CGATTCAAAAATAGATCGGATGGT 57.454 37.500 0.00 0.00 0.00 3.55
2362 4713 1.224965 GCTCTTGAGCCATCCGATTC 58.775 55.000 11.24 0.00 0.00 2.52
2408 4764 7.145323 CGTGGAAAGGATTACATTTCTTGTTT 58.855 34.615 0.00 0.00 43.45 2.83
2410 4766 5.183140 CCGTGGAAAGGATTACATTTCTTGT 59.817 40.000 0.00 0.00 43.45 3.16
2411 4767 5.640732 CCGTGGAAAGGATTACATTTCTTG 58.359 41.667 0.00 0.00 43.45 3.02
2412 4768 4.157840 GCCGTGGAAAGGATTACATTTCTT 59.842 41.667 0.00 0.00 43.45 2.52
2413 4769 3.694566 GCCGTGGAAAGGATTACATTTCT 59.305 43.478 0.00 0.00 43.45 2.52
2415 4771 3.426615 TGCCGTGGAAAGGATTACATTT 58.573 40.909 0.00 0.00 37.88 2.32
2416 4772 3.080300 TGCCGTGGAAAGGATTACATT 57.920 42.857 0.00 0.00 37.88 2.71
2417 4773 2.752903 GTTGCCGTGGAAAGGATTACAT 59.247 45.455 0.00 0.00 37.88 2.29
2454 4810 3.009916 TCCTCTACTAGAACCGGTTGACT 59.990 47.826 27.87 19.02 0.00 3.41
2456 4812 3.726557 TCCTCTACTAGAACCGGTTGA 57.273 47.619 27.87 13.62 0.00 3.18
2482 4838 1.455849 CTTCCACTGCTTCCACCCA 59.544 57.895 0.00 0.00 0.00 4.51
2531 4887 3.406361 GCGTGCAGTCACAGACGG 61.406 66.667 0.00 0.00 43.28 4.79
2535 4891 3.108289 CGAGGCGTGCAGTCACAG 61.108 66.667 0.00 0.00 43.28 3.66
2536 4892 3.601685 TCGAGGCGTGCAGTCACA 61.602 61.111 0.00 0.00 43.28 3.58
2537 4893 3.106407 GTCGAGGCGTGCAGTCAC 61.106 66.667 0.00 0.00 39.78 3.67
2538 4894 4.700365 CGTCGAGGCGTGCAGTCA 62.700 66.667 0.00 0.00 0.00 3.41
2539 4895 4.702081 ACGTCGAGGCGTGCAGTC 62.702 66.667 0.67 0.00 43.99 3.51
2540 4896 4.702081 GACGTCGAGGCGTGCAGT 62.702 66.667 7.69 0.00 45.79 4.40
2541 4897 3.971453 ATGACGTCGAGGCGTGCAG 62.971 63.158 7.69 0.00 45.79 4.41
2556 4915 0.456142 CGGTTGCGAGAAGACGATGA 60.456 55.000 0.00 0.00 35.09 2.92
2557 4916 1.991430 CGGTTGCGAGAAGACGATG 59.009 57.895 0.00 0.00 35.09 3.84
2571 4930 4.595538 TCGTTGAGGCACGCGGTT 62.596 61.111 12.47 0.00 40.14 4.44
2582 4941 2.092646 CCATTGGAATAGGGGTCGTTGA 60.093 50.000 0.00 0.00 0.00 3.18
2583 4942 2.297701 CCATTGGAATAGGGGTCGTTG 58.702 52.381 0.00 0.00 0.00 4.10
2584 4943 1.409661 GCCATTGGAATAGGGGTCGTT 60.410 52.381 6.95 0.00 0.00 3.85
2585 4944 0.182775 GCCATTGGAATAGGGGTCGT 59.817 55.000 6.95 0.00 0.00 4.34
2586 4945 0.537371 GGCCATTGGAATAGGGGTCG 60.537 60.000 6.95 0.00 0.00 4.79
2587 4946 0.537371 CGGCCATTGGAATAGGGGTC 60.537 60.000 6.95 0.00 0.00 4.46
2588 4947 1.536676 CGGCCATTGGAATAGGGGT 59.463 57.895 6.95 0.00 0.00 4.95
2589 4948 1.903404 GCGGCCATTGGAATAGGGG 60.903 63.158 6.95 0.00 0.00 4.79
2596 4955 3.329542 GAGGAGTGCGGCCATTGGA 62.330 63.158 6.95 0.00 0.00 3.53
2598 4957 2.825836 GGAGGAGTGCGGCCATTG 60.826 66.667 2.24 0.00 0.00 2.82
2599 4958 3.011517 AGGAGGAGTGCGGCCATT 61.012 61.111 2.24 0.00 0.00 3.16
2610 4969 2.124403 GTAGCCGTCGGAGGAGGA 60.124 66.667 17.49 0.00 0.00 3.71
2620 4979 4.011517 CCCACAACCCGTAGCCGT 62.012 66.667 0.00 0.00 0.00 5.68
2622 4981 3.971109 GAGCCCACAACCCGTAGCC 62.971 68.421 0.00 0.00 0.00 3.93
2628 4987 3.324108 TACGGGAGCCCACAACCC 61.324 66.667 6.34 0.00 40.17 4.11
2629 4988 2.046604 GTACGGGAGCCCACAACC 60.047 66.667 6.34 0.00 35.37 3.77
2631 4990 3.324108 GGGTACGGGAGCCCACAA 61.324 66.667 6.34 0.00 44.23 3.33
2636 4995 3.925090 CCATCGGGTACGGGAGCC 61.925 72.222 0.00 0.00 42.83 4.70
2650 5012 1.102222 GGTCGTCGAGCTCCTACCAT 61.102 60.000 16.89 0.00 0.00 3.55
2664 5026 2.629656 CGTTGTACGGGGAGGTCGT 61.630 63.158 0.00 0.00 43.64 4.34
2712 5074 4.021925 GGAGGCGAGCCCAACTGT 62.022 66.667 10.95 0.00 36.58 3.55
2741 5103 2.113139 AACGGGGAGGCAAGTGTG 59.887 61.111 0.00 0.00 0.00 3.82
2742 5104 1.779061 ATCAACGGGGAGGCAAGTGT 61.779 55.000 0.00 0.00 0.00 3.55
2743 5105 1.002134 ATCAACGGGGAGGCAAGTG 60.002 57.895 0.00 0.00 0.00 3.16
2744 5106 1.002134 CATCAACGGGGAGGCAAGT 60.002 57.895 0.00 0.00 0.00 3.16
2745 5107 1.750399 CCATCAACGGGGAGGCAAG 60.750 63.158 0.00 0.00 0.00 4.01
2746 5108 2.354729 CCATCAACGGGGAGGCAA 59.645 61.111 0.00 0.00 0.00 4.52
2747 5109 2.933287 ACCATCAACGGGGAGGCA 60.933 61.111 0.00 0.00 0.00 4.75
2748 5110 2.124695 GACCATCAACGGGGAGGC 60.125 66.667 0.00 0.00 0.00 4.70
2749 5111 0.179045 GATGACCATCAACGGGGAGG 60.179 60.000 5.21 0.00 37.74 4.30
2750 5112 0.833287 AGATGACCATCAACGGGGAG 59.167 55.000 12.01 0.00 40.22 4.30
2751 5113 0.830648 GAGATGACCATCAACGGGGA 59.169 55.000 12.01 0.00 40.22 4.81
2752 5114 0.833287 AGAGATGACCATCAACGGGG 59.167 55.000 12.01 0.00 40.22 5.73
2753 5115 1.202580 GGAGAGATGACCATCAACGGG 60.203 57.143 12.01 0.00 40.22 5.28
2754 5116 1.759445 AGGAGAGATGACCATCAACGG 59.241 52.381 12.01 0.00 40.22 4.44
2755 5117 3.452474 GAAGGAGAGATGACCATCAACG 58.548 50.000 12.01 0.00 40.22 4.10
2756 5118 3.432890 GGGAAGGAGAGATGACCATCAAC 60.433 52.174 12.01 6.08 40.22 3.18
2757 5119 2.774234 GGGAAGGAGAGATGACCATCAA 59.226 50.000 12.01 0.00 40.22 2.57
2758 5120 2.402564 GGGAAGGAGAGATGACCATCA 58.597 52.381 12.01 0.00 40.22 3.07
2759 5121 1.342819 CGGGAAGGAGAGATGACCATC 59.657 57.143 1.90 1.90 38.09 3.51
2760 5122 1.418334 CGGGAAGGAGAGATGACCAT 58.582 55.000 0.00 0.00 0.00 3.55
2761 5123 1.330655 GCGGGAAGGAGAGATGACCA 61.331 60.000 0.00 0.00 0.00 4.02
2762 5124 1.443828 GCGGGAAGGAGAGATGACC 59.556 63.158 0.00 0.00 0.00 4.02
2763 5125 1.443828 GGCGGGAAGGAGAGATGAC 59.556 63.158 0.00 0.00 0.00 3.06
2764 5126 1.762460 GGGCGGGAAGGAGAGATGA 60.762 63.158 0.00 0.00 0.00 2.92
2765 5127 2.825264 GGGCGGGAAGGAGAGATG 59.175 66.667 0.00 0.00 0.00 2.90
2766 5128 2.840102 CGGGCGGGAAGGAGAGAT 60.840 66.667 0.00 0.00 0.00 2.75
2769 5131 4.064768 TACCGGGCGGGAAGGAGA 62.065 66.667 18.95 0.00 39.97 3.71
2770 5132 3.537874 CTACCGGGCGGGAAGGAG 61.538 72.222 18.95 5.52 39.97 3.69
2800 5162 3.502123 TTGTTTTCACACCTAGGGGAG 57.498 47.619 20.81 10.82 36.25 4.30
2801 5163 3.203487 AGTTTGTTTTCACACCTAGGGGA 59.797 43.478 20.81 7.02 36.25 4.81
2802 5164 3.562182 AGTTTGTTTTCACACCTAGGGG 58.438 45.455 10.33 10.33 31.54 4.79
2803 5165 4.215613 GCTAGTTTGTTTTCACACCTAGGG 59.784 45.833 14.81 4.64 36.27 3.53
2804 5166 5.063880 AGCTAGTTTGTTTTCACACCTAGG 58.936 41.667 7.41 7.41 36.27 3.02
2805 5167 5.992217 AGAGCTAGTTTGTTTTCACACCTAG 59.008 40.000 0.00 0.00 37.57 3.02
2806 5168 5.758296 CAGAGCTAGTTTGTTTTCACACCTA 59.242 40.000 0.00 0.00 31.54 3.08
2807 5169 4.576463 CAGAGCTAGTTTGTTTTCACACCT 59.424 41.667 0.00 0.00 31.54 4.00
2808 5170 4.261197 CCAGAGCTAGTTTGTTTTCACACC 60.261 45.833 0.00 0.00 31.54 4.16
2809 5171 4.261197 CCCAGAGCTAGTTTGTTTTCACAC 60.261 45.833 0.00 0.00 30.32 3.82
2810 5172 3.882888 CCCAGAGCTAGTTTGTTTTCACA 59.117 43.478 0.00 0.00 0.00 3.58
2811 5173 4.134563 TCCCAGAGCTAGTTTGTTTTCAC 58.865 43.478 0.00 0.00 0.00 3.18
2812 5174 4.431416 TCCCAGAGCTAGTTTGTTTTCA 57.569 40.909 0.00 0.00 0.00 2.69
2813 5175 4.023107 GGTTCCCAGAGCTAGTTTGTTTTC 60.023 45.833 0.00 0.00 0.00 2.29
2814 5176 3.889538 GGTTCCCAGAGCTAGTTTGTTTT 59.110 43.478 0.00 0.00 0.00 2.43
2815 5177 3.117663 TGGTTCCCAGAGCTAGTTTGTTT 60.118 43.478 0.00 0.00 0.00 2.83
2816 5178 2.441750 TGGTTCCCAGAGCTAGTTTGTT 59.558 45.455 0.00 0.00 0.00 2.83
2817 5179 2.054799 TGGTTCCCAGAGCTAGTTTGT 58.945 47.619 0.00 0.00 0.00 2.83
2818 5180 2.814336 GTTGGTTCCCAGAGCTAGTTTG 59.186 50.000 0.00 0.00 33.81 2.93
2819 5181 2.711547 AGTTGGTTCCCAGAGCTAGTTT 59.288 45.455 0.00 0.00 33.81 2.66
2820 5182 2.339769 AGTTGGTTCCCAGAGCTAGTT 58.660 47.619 0.00 0.00 33.81 2.24
2821 5183 2.031495 AGTTGGTTCCCAGAGCTAGT 57.969 50.000 0.00 0.00 33.81 2.57
2822 5184 3.118592 CCTAAGTTGGTTCCCAGAGCTAG 60.119 52.174 0.00 0.00 33.81 3.42
2823 5185 2.838202 CCTAAGTTGGTTCCCAGAGCTA 59.162 50.000 0.00 0.00 33.81 3.32
2824 5186 1.630878 CCTAAGTTGGTTCCCAGAGCT 59.369 52.381 0.00 0.00 33.81 4.09
2825 5187 1.351350 ACCTAAGTTGGTTCCCAGAGC 59.649 52.381 0.00 0.00 36.89 4.09
2826 5188 4.469945 TCATACCTAAGTTGGTTCCCAGAG 59.530 45.833 2.88 0.00 41.22 3.35
2827 5189 4.431378 TCATACCTAAGTTGGTTCCCAGA 58.569 43.478 2.88 0.00 41.22 3.86
2828 5190 4.837093 TCATACCTAAGTTGGTTCCCAG 57.163 45.455 2.88 0.00 41.22 4.45
2829 5191 5.311121 TCTTTCATACCTAAGTTGGTTCCCA 59.689 40.000 2.88 0.00 41.22 4.37
2830 5192 5.812286 TCTTTCATACCTAAGTTGGTTCCC 58.188 41.667 2.88 0.00 41.22 3.97
2831 5193 7.754851 TTTCTTTCATACCTAAGTTGGTTCC 57.245 36.000 2.88 0.00 41.22 3.62
2832 5194 8.080417 GGTTTTCTTTCATACCTAAGTTGGTTC 58.920 37.037 2.88 0.00 41.22 3.62
2833 5195 7.562088 TGGTTTTCTTTCATACCTAAGTTGGTT 59.438 33.333 2.88 0.00 41.22 3.67
2834 5196 7.064229 TGGTTTTCTTTCATACCTAAGTTGGT 58.936 34.615 0.00 3.08 43.66 3.67
2835 5197 7.519032 TGGTTTTCTTTCATACCTAAGTTGG 57.481 36.000 0.00 0.00 0.00 3.77
2836 5198 8.630037 AGTTGGTTTTCTTTCATACCTAAGTTG 58.370 33.333 0.00 0.00 0.00 3.16
2837 5199 8.762481 AGTTGGTTTTCTTTCATACCTAAGTT 57.238 30.769 0.00 0.00 0.00 2.66
2838 5200 8.762481 AAGTTGGTTTTCTTTCATACCTAAGT 57.238 30.769 0.00 0.00 0.00 2.24
2841 5203 9.292195 CCTAAAGTTGGTTTTCTTTCATACCTA 57.708 33.333 0.00 0.00 35.79 3.08
2842 5204 8.002459 TCCTAAAGTTGGTTTTCTTTCATACCT 58.998 33.333 0.00 0.00 35.79 3.08
2843 5205 8.173542 TCCTAAAGTTGGTTTTCTTTCATACC 57.826 34.615 0.00 0.00 35.79 2.73
2852 5214 9.639601 CCTCATTAATTCCTAAAGTTGGTTTTC 57.360 33.333 0.00 0.00 0.00 2.29
2853 5215 9.154632 ACCTCATTAATTCCTAAAGTTGGTTTT 57.845 29.630 0.00 0.00 0.00 2.43
2854 5216 8.721133 ACCTCATTAATTCCTAAAGTTGGTTT 57.279 30.769 0.00 0.00 0.00 3.27
2855 5217 9.462606 CTACCTCATTAATTCCTAAAGTTGGTT 57.537 33.333 0.00 0.00 0.00 3.67
2856 5218 8.053355 CCTACCTCATTAATTCCTAAAGTTGGT 58.947 37.037 0.00 0.00 0.00 3.67
2857 5219 8.053355 ACCTACCTCATTAATTCCTAAAGTTGG 58.947 37.037 0.00 0.00 0.00 3.77
2858 5220 9.462606 AACCTACCTCATTAATTCCTAAAGTTG 57.537 33.333 0.00 0.00 0.00 3.16
2869 5231 8.860088 GGCAATTTCATAACCTACCTCATTAAT 58.140 33.333 0.00 0.00 0.00 1.40
2870 5232 7.836685 TGGCAATTTCATAACCTACCTCATTAA 59.163 33.333 0.00 0.00 0.00 1.40
2871 5233 7.350382 TGGCAATTTCATAACCTACCTCATTA 58.650 34.615 0.00 0.00 0.00 1.90
2872 5234 6.194235 TGGCAATTTCATAACCTACCTCATT 58.806 36.000 0.00 0.00 0.00 2.57
2873 5235 5.765510 TGGCAATTTCATAACCTACCTCAT 58.234 37.500 0.00 0.00 0.00 2.90
2874 5236 5.186256 TGGCAATTTCATAACCTACCTCA 57.814 39.130 0.00 0.00 0.00 3.86
2875 5237 4.580580 CCTGGCAATTTCATAACCTACCTC 59.419 45.833 0.00 0.00 0.00 3.85
2876 5238 4.017499 ACCTGGCAATTTCATAACCTACCT 60.017 41.667 0.00 0.00 0.00 3.08
2877 5239 4.278310 ACCTGGCAATTTCATAACCTACC 58.722 43.478 0.00 0.00 0.00 3.18
2878 5240 7.068226 ACATTACCTGGCAATTTCATAACCTAC 59.932 37.037 0.00 0.00 0.00 3.18
2879 5241 7.122715 ACATTACCTGGCAATTTCATAACCTA 58.877 34.615 0.00 0.00 0.00 3.08
2880 5242 5.957774 ACATTACCTGGCAATTTCATAACCT 59.042 36.000 0.00 0.00 0.00 3.50
2881 5243 6.220726 ACATTACCTGGCAATTTCATAACC 57.779 37.500 0.00 0.00 0.00 2.85
2882 5244 7.064490 CCAAACATTACCTGGCAATTTCATAAC 59.936 37.037 0.00 0.00 0.00 1.89
2883 5245 7.102346 CCAAACATTACCTGGCAATTTCATAA 58.898 34.615 0.00 0.00 0.00 1.90
2884 5246 6.351711 CCCAAACATTACCTGGCAATTTCATA 60.352 38.462 0.00 0.00 0.00 2.15
2885 5247 5.490159 CCAAACATTACCTGGCAATTTCAT 58.510 37.500 0.00 0.00 0.00 2.57
2886 5248 4.262808 CCCAAACATTACCTGGCAATTTCA 60.263 41.667 0.00 0.00 0.00 2.69
2887 5249 4.252878 CCCAAACATTACCTGGCAATTTC 58.747 43.478 0.00 0.00 0.00 2.17
2888 5250 3.650461 ACCCAAACATTACCTGGCAATTT 59.350 39.130 0.00 0.00 0.00 1.82
2889 5251 3.247162 ACCCAAACATTACCTGGCAATT 58.753 40.909 0.00 0.00 0.00 2.32
2890 5252 2.901291 ACCCAAACATTACCTGGCAAT 58.099 42.857 0.00 0.00 0.00 3.56
2891 5253 2.390225 ACCCAAACATTACCTGGCAA 57.610 45.000 0.00 0.00 0.00 4.52
2892 5254 2.882229 GCTACCCAAACATTACCTGGCA 60.882 50.000 0.00 0.00 0.00 4.92
2893 5255 1.749063 GCTACCCAAACATTACCTGGC 59.251 52.381 0.00 0.00 0.00 4.85
2894 5256 3.016736 CAGCTACCCAAACATTACCTGG 58.983 50.000 0.00 0.00 0.00 4.45
2895 5257 3.016736 CCAGCTACCCAAACATTACCTG 58.983 50.000 0.00 0.00 0.00 4.00
2896 5258 2.647802 ACCAGCTACCCAAACATTACCT 59.352 45.455 0.00 0.00 0.00 3.08
2897 5259 3.014623 GACCAGCTACCCAAACATTACC 58.985 50.000 0.00 0.00 0.00 2.85
2898 5260 3.014623 GGACCAGCTACCCAAACATTAC 58.985 50.000 0.00 0.00 0.00 1.89
2899 5261 2.916934 AGGACCAGCTACCCAAACATTA 59.083 45.455 0.00 0.00 0.00 1.90
2900 5262 1.710809 AGGACCAGCTACCCAAACATT 59.289 47.619 0.00 0.00 0.00 2.71
2901 5263 1.004745 CAGGACCAGCTACCCAAACAT 59.995 52.381 0.00 0.00 0.00 2.71
2902 5264 0.400213 CAGGACCAGCTACCCAAACA 59.600 55.000 0.00 0.00 0.00 2.83
2903 5265 0.690762 TCAGGACCAGCTACCCAAAC 59.309 55.000 0.00 0.00 0.00 2.93
2904 5266 1.559682 GATCAGGACCAGCTACCCAAA 59.440 52.381 0.00 0.00 0.00 3.28
2905 5267 1.204146 GATCAGGACCAGCTACCCAA 58.796 55.000 0.00 0.00 0.00 4.12
2906 5268 0.042581 TGATCAGGACCAGCTACCCA 59.957 55.000 0.00 0.00 0.00 4.51
2907 5269 1.204146 TTGATCAGGACCAGCTACCC 58.796 55.000 0.00 0.00 0.00 3.69
2908 5270 2.027192 TGTTTGATCAGGACCAGCTACC 60.027 50.000 0.00 0.00 0.00 3.18
2909 5271 3.334583 TGTTTGATCAGGACCAGCTAC 57.665 47.619 0.00 0.00 0.00 3.58
2910 5272 4.263462 ACAATGTTTGATCAGGACCAGCTA 60.263 41.667 0.00 0.00 0.00 3.32
2911 5273 3.087031 CAATGTTTGATCAGGACCAGCT 58.913 45.455 0.00 0.00 0.00 4.24
2912 5274 2.821969 ACAATGTTTGATCAGGACCAGC 59.178 45.455 0.00 0.00 0.00 4.85
2913 5275 5.458041 AAACAATGTTTGATCAGGACCAG 57.542 39.130 10.91 0.00 0.00 4.00
2914 5276 5.599732 CAAAACAATGTTTGATCAGGACCA 58.400 37.500 12.50 0.00 40.29 4.02
2915 5277 4.448732 GCAAAACAATGTTTGATCAGGACC 59.551 41.667 12.50 0.00 40.29 4.46
2916 5278 4.448732 GGCAAAACAATGTTTGATCAGGAC 59.551 41.667 12.50 0.00 40.29 3.85
2917 5279 4.100653 TGGCAAAACAATGTTTGATCAGGA 59.899 37.500 12.50 0.00 40.29 3.86
2918 5280 4.378774 TGGCAAAACAATGTTTGATCAGG 58.621 39.130 12.50 0.29 40.29 3.86
2919 5281 5.291178 TCTGGCAAAACAATGTTTGATCAG 58.709 37.500 12.50 17.17 40.29 2.90
2920 5282 5.273674 TCTGGCAAAACAATGTTTGATCA 57.726 34.783 12.50 9.48 40.29 2.92
2921 5283 6.790285 ATTCTGGCAAAACAATGTTTGATC 57.210 33.333 12.50 5.55 40.29 2.92
2922 5284 8.095792 TCATATTCTGGCAAAACAATGTTTGAT 58.904 29.630 12.50 0.00 40.29 2.57
2923 5285 7.440198 TCATATTCTGGCAAAACAATGTTTGA 58.560 30.769 12.50 2.06 40.29 2.69
2924 5286 7.655236 TCATATTCTGGCAAAACAATGTTTG 57.345 32.000 12.50 7.84 40.72 2.93
2925 5287 7.714377 TGTTCATATTCTGGCAAAACAATGTTT 59.286 29.630 5.41 5.41 0.00 2.83
2926 5288 7.215789 TGTTCATATTCTGGCAAAACAATGTT 58.784 30.769 0.00 0.00 0.00 2.71
2927 5289 6.757237 TGTTCATATTCTGGCAAAACAATGT 58.243 32.000 0.00 0.00 0.00 2.71
2928 5290 7.837202 ATGTTCATATTCTGGCAAAACAATG 57.163 32.000 0.00 0.00 0.00 2.82
2929 5291 8.752187 ACTATGTTCATATTCTGGCAAAACAAT 58.248 29.630 0.00 0.00 0.00 2.71
2930 5292 8.121305 ACTATGTTCATATTCTGGCAAAACAA 57.879 30.769 0.00 0.00 0.00 2.83
2931 5293 7.701539 ACTATGTTCATATTCTGGCAAAACA 57.298 32.000 0.00 0.00 0.00 2.83
2932 5294 8.986477 AAACTATGTTCATATTCTGGCAAAAC 57.014 30.769 0.00 0.00 0.00 2.43
2933 5295 9.023962 AGAAACTATGTTCATATTCTGGCAAAA 57.976 29.630 7.46 0.00 0.00 2.44
2934 5296 8.579850 AGAAACTATGTTCATATTCTGGCAAA 57.420 30.769 7.46 0.00 0.00 3.68
2935 5297 8.579850 AAGAAACTATGTTCATATTCTGGCAA 57.420 30.769 8.49 0.00 0.00 4.52
2936 5298 7.828717 TGAAGAAACTATGTTCATATTCTGGCA 59.171 33.333 8.49 0.00 36.47 4.92
2937 5299 8.213518 TGAAGAAACTATGTTCATATTCTGGC 57.786 34.615 8.49 6.18 36.47 4.85


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

AutoCloner maintained by Alex Coulton.