Multiple sequence alignment - TraesCS5A01G231200

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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 TraesCS5A01G231200 chr5A 100.000 2948 0 0 1 2948 446638746 446635799 0.000000e+00 5445.0
1 TraesCS5A01G231200 chr5A 92.000 200 15 1 260 458 446652876 446652677 2.240000e-71 279.0
2 TraesCS5A01G231200 chr5D 93.477 1579 59 14 684 2252 345082658 345084202 0.000000e+00 2305.0
3 TraesCS5A01G231200 chr5D 89.130 322 20 3 2513 2831 345084205 345084514 1.280000e-103 387.0
4 TraesCS5A01G231200 chr5D 93.798 129 8 0 465 593 345082534 345082662 8.340000e-46 195.0
5 TraesCS5A01G231200 chr5B 92.663 1581 78 18 684 2254 406528757 406527205 0.000000e+00 2242.0
6 TraesCS5A01G231200 chr5B 91.000 100 9 0 494 593 406528852 406528753 5.130000e-28 135.0
7 TraesCS5A01G231200 chr5B 86.905 84 7 2 2774 2857 406526987 406526908 1.130000e-14 91.6
8 TraesCS5A01G231200 chr4D 92.748 262 19 0 2250 2511 3381354 3381093 2.140000e-101 379.0
9 TraesCS5A01G231200 chr4D 90.037 271 26 1 2241 2511 334180305 334180036 1.680000e-92 350.0
10 TraesCS5A01G231200 chr4D 90.291 103 8 2 590 691 499455049 499454948 1.840000e-27 134.0
11 TraesCS5A01G231200 chr4D 86.441 59 8 0 2561 2619 295116168 295116226 6.820000e-07 65.8
12 TraesCS5A01G231200 chr7A 93.023 258 17 1 202 458 271038099 271037842 2.770000e-100 375.0
13 TraesCS5A01G231200 chr7A 91.538 260 20 2 2253 2511 265204178 265203920 1.000000e-94 357.0
14 TraesCS5A01G231200 chr7A 91.255 263 20 3 2249 2511 584381834 584381575 3.610000e-94 355.0
15 TraesCS5A01G231200 chr7A 92.195 205 16 0 1 205 271038860 271038656 1.030000e-74 291.0
16 TraesCS5A01G231200 chr7A 92.079 202 15 1 258 458 271042796 271042595 1.730000e-72 283.0
17 TraesCS5A01G231200 chr7A 79.255 188 33 6 21 205 115095992 115095808 3.080000e-25 126.0
18 TraesCS5A01G231200 chr7A 81.034 116 19 3 2653 2766 725594639 725594525 4.050000e-14 89.8
19 TraesCS5A01G231200 chr6B 91.954 261 19 2 2252 2511 4952981 4953240 6.000000e-97 364.0
20 TraesCS5A01G231200 chr6B 91.954 261 19 2 2252 2511 4975363 4975622 6.000000e-97 364.0
21 TraesCS5A01G231200 chr6B 91.571 261 20 2 2252 2511 5032758 5033017 2.790000e-95 359.0
22 TraesCS5A01G231200 chr6B 88.889 108 11 1 585 691 622020081 622019974 6.630000e-27 132.0
23 TraesCS5A01G231200 chr6B 75.449 167 27 10 2559 2714 112899299 112899462 5.270000e-08 69.4
24 TraesCS5A01G231200 chr4B 91.085 258 21 2 202 458 618028383 618028127 6.050000e-92 348.0
25 TraesCS5A01G231200 chr4B 92.683 205 15 0 1 205 618029163 618028959 2.220000e-76 296.0
26 TraesCS5A01G231200 chr4B 90.955 199 17 1 261 458 618060438 618060240 1.740000e-67 267.0
27 TraesCS5A01G231200 chr4B 89.320 103 10 1 591 693 107776969 107776868 8.580000e-26 128.0
28 TraesCS5A01G231200 chr7D 89.925 268 27 0 2244 2511 98664352 98664619 2.170000e-91 346.0
29 TraesCS5A01G231200 chr7D 76.190 189 39 2 2560 2742 93615861 93616049 8.700000e-16 95.3
30 TraesCS5A01G231200 chr7D 82.407 108 16 3 2618 2724 26790399 26790504 1.130000e-14 91.6
31 TraesCS5A01G231200 chr2A 90.530 264 21 3 2248 2511 779509016 779509275 2.170000e-91 346.0
32 TraesCS5A01G231200 chr1A 79.079 239 43 2 2564 2795 449691752 449691514 1.090000e-34 158.0
33 TraesCS5A01G231200 chr6A 91.089 101 9 0 591 691 507082098 507081998 1.420000e-28 137.0
34 TraesCS5A01G231200 chr6D 90.909 99 9 0 591 689 428262137 428262039 1.840000e-27 134.0
35 TraesCS5A01G231200 chr6D 86.047 86 10 2 2635 2718 5477829 5477914 1.130000e-14 91.6
36 TraesCS5A01G231200 chr3B 90.816 98 9 0 591 688 114602241 114602338 6.630000e-27 132.0
37 TraesCS5A01G231200 chr3B 90.816 98 8 1 591 687 52883244 52883147 2.380000e-26 130.0
38 TraesCS5A01G231200 chr3B 76.048 167 31 7 2561 2718 773564920 773565086 8.760000e-11 78.7
39 TraesCS5A01G231200 chr3B 73.653 167 35 5 2559 2716 729380510 729380344 4.100000e-04 56.5
40 TraesCS5A01G231200 chr3B 92.308 39 2 1 2553 2591 823979484 823979521 1.000000e-03 54.7
41 TraesCS5A01G231200 chr4A 89.899 99 10 0 590 688 650040979 650040881 8.580000e-26 128.0
42 TraesCS5A01G231200 chr4A 94.595 74 4 0 261 334 743286766 743286839 6.680000e-22 115.0
43 TraesCS5A01G231200 chr1B 87.387 111 11 3 577 687 322747406 322747513 1.110000e-24 124.0
44 TraesCS5A01G231200 chr1B 78.689 183 33 5 2614 2794 474461430 474461252 1.860000e-22 117.0
45 TraesCS5A01G231200 chr2D 86.316 95 12 1 2653 2746 367224760 367224854 5.200000e-18 102.0
46 TraesCS5A01G231200 chr3D 78.986 138 25 2 2663 2800 591541825 591541958 1.130000e-14 91.6
47 TraesCS5A01G231200 chr3D 91.525 59 5 0 2732 2790 153143502 153143560 6.770000e-12 82.4
48 TraesCS5A01G231200 chr3D 76.048 167 31 6 2561 2718 579298147 579298313 8.760000e-11 78.7
49 TraesCS5A01G231200 chr3D 90.741 54 5 0 2728 2781 379605020 379605073 4.080000e-09 73.1
50 TraesCS5A01G231200 chr3A 76.647 167 31 6 2560 2718 57269837 57269671 5.240000e-13 86.1
51 TraesCS5A01G231200 chr3A 92.000 50 4 0 2745 2794 177046145 177046096 1.470000e-08 71.3
52 TraesCS5A01G231200 chr7B 75.904 166 32 6 2559 2716 528255662 528255827 8.760000e-11 78.7


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 TraesCS5A01G231200 chr5A 446635799 446638746 2947 True 5445.000000 5445 100.000000 1 2948 1 chr5A.!!$R1 2947
1 TraesCS5A01G231200 chr5D 345082534 345084514 1980 False 962.333333 2305 92.135000 465 2831 3 chr5D.!!$F1 2366
2 TraesCS5A01G231200 chr5B 406526908 406528852 1944 True 822.866667 2242 90.189333 494 2857 3 chr5B.!!$R1 2363
3 TraesCS5A01G231200 chr7A 271037842 271042796 4954 True 316.333333 375 92.432333 1 458 3 chr7A.!!$R5 457
4 TraesCS5A01G231200 chr4B 618028127 618029163 1036 True 322.000000 348 91.884000 1 458 2 chr4B.!!$R3 457

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
988 5517 0.034198 TGCAGCTACGTTGCAGGTAA 59.966 50.0 23.41 6.05 44.16 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 7134 0.396435 TCTCAAGATGTGGCGTTGGT 59.604 50.0 0.0 0.0 0.0 3.67 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
60 3997 4.379243 AAGGCACGACAGCGGAGG 62.379 66.667 0.00 0.00 43.17 4.30
72 4009 2.652530 CGGAGGAACGTCGGGAAA 59.347 61.111 0.00 0.00 0.00 3.13
78 4015 1.375140 GAACGTCGGGAAAGGGGTC 60.375 63.158 0.00 0.00 0.00 4.46
89 4026 0.400213 AAAGGGGTCTGCATCGTCAA 59.600 50.000 0.00 0.00 0.00 3.18
155 4092 1.003233 GTTCAGAACCTGGTCCCGATT 59.997 52.381 0.00 0.00 31.51 3.34
168 4105 1.215382 CCGATTGGTGACGAGCTCA 59.785 57.895 15.40 0.00 0.00 4.26
190 4127 1.305297 AGGTCTGTCAGGCGATCCA 60.305 57.895 0.00 0.00 33.74 3.41
213 4729 2.163211 GCATTCTTTGAGGAAGAGTGGC 59.837 50.000 11.53 4.02 46.51 5.01
220 4736 2.125350 GGAAGAGTGGCAGCGGAG 60.125 66.667 0.00 0.00 0.00 4.63
221 4737 2.650116 GGAAGAGTGGCAGCGGAGA 61.650 63.158 0.00 0.00 0.00 3.71
234 4750 1.935327 GCGGAGAGAGTTACAGGCGT 61.935 60.000 0.00 0.00 0.00 5.68
344 4861 1.373812 GGAGTTACAACAGGGGCGT 59.626 57.895 0.00 0.00 0.00 5.68
370 4887 2.125512 GCTGTACAGGGGCACGAG 60.126 66.667 23.95 0.00 0.00 4.18
400 4917 0.532573 GAGTGGAGATCGTGCAGGAA 59.467 55.000 13.87 0.00 0.00 3.36
458 4975 3.424703 ACTACGGGTAGACTGCTAACAA 58.575 45.455 12.54 0.00 35.96 2.83
459 4976 4.021916 ACTACGGGTAGACTGCTAACAAT 58.978 43.478 12.54 0.00 35.96 2.71
460 4977 5.195940 ACTACGGGTAGACTGCTAACAATA 58.804 41.667 12.54 0.00 35.96 1.90
461 4978 4.650754 ACGGGTAGACTGCTAACAATAG 57.349 45.455 0.00 0.00 35.96 1.73
462 4979 4.275810 ACGGGTAGACTGCTAACAATAGA 58.724 43.478 0.00 0.00 35.96 1.98
463 4980 4.338682 ACGGGTAGACTGCTAACAATAGAG 59.661 45.833 0.00 0.00 35.96 2.43
472 4989 7.289782 AGACTGCTAACAATAGAGATTCTCCAT 59.710 37.037 10.09 0.00 0.00 3.41
505 5022 7.396339 AGTGTGTTCTACCATAGTCTCAACATA 59.604 37.037 0.00 0.00 0.00 2.29
526 5043 7.203910 ACATATTCACGTGGAAATCTACTCTC 58.796 38.462 17.00 0.00 39.39 3.20
532 5049 3.304559 CGTGGAAATCTACTCTCAAAGCG 59.695 47.826 0.00 0.00 0.00 4.68
538 5055 1.618837 TCTACTCTCAAAGCGTTGCCT 59.381 47.619 7.57 0.00 34.50 4.75
583 5100 4.217550 GCTATGTTAGGTCTGGTGCAAAAA 59.782 41.667 0.00 0.00 0.00 1.94
585 5102 6.094881 GCTATGTTAGGTCTGGTGCAAAAATA 59.905 38.462 0.00 0.00 0.00 1.40
588 5105 7.113658 TGTTAGGTCTGGTGCAAAAATAAAA 57.886 32.000 0.00 0.00 0.00 1.52
589 5106 7.206687 TGTTAGGTCTGGTGCAAAAATAAAAG 58.793 34.615 0.00 0.00 0.00 2.27
590 5107 5.869649 AGGTCTGGTGCAAAAATAAAAGT 57.130 34.783 0.00 0.00 0.00 2.66
591 5108 6.969993 AGGTCTGGTGCAAAAATAAAAGTA 57.030 33.333 0.00 0.00 0.00 2.24
592 5109 6.745116 AGGTCTGGTGCAAAAATAAAAGTAC 58.255 36.000 0.00 0.00 0.00 2.73
593 5110 6.549736 AGGTCTGGTGCAAAAATAAAAGTACT 59.450 34.615 0.00 0.00 0.00 2.73
594 5111 6.861572 GGTCTGGTGCAAAAATAAAAGTACTC 59.138 38.462 0.00 0.00 0.00 2.59
595 5112 7.255486 GGTCTGGTGCAAAAATAAAAGTACTCT 60.255 37.037 0.00 0.00 0.00 3.24
596 5113 7.803659 GTCTGGTGCAAAAATAAAAGTACTCTC 59.196 37.037 0.00 0.00 0.00 3.20
597 5114 7.719633 TCTGGTGCAAAAATAAAAGTACTCTCT 59.280 33.333 0.00 0.00 0.00 3.10
598 5115 7.871853 TGGTGCAAAAATAAAAGTACTCTCTC 58.128 34.615 0.00 0.00 0.00 3.20
599 5116 7.719633 TGGTGCAAAAATAAAAGTACTCTCTCT 59.280 33.333 0.00 0.00 0.00 3.10
600 5117 8.017946 GGTGCAAAAATAAAAGTACTCTCTCTG 58.982 37.037 0.00 0.00 0.00 3.35
601 5118 8.560374 GTGCAAAAATAAAAGTACTCTCTCTGT 58.440 33.333 0.00 0.00 0.00 3.41
602 5119 9.120538 TGCAAAAATAAAAGTACTCTCTCTGTT 57.879 29.630 0.00 0.00 0.00 3.16
603 5120 9.600646 GCAAAAATAAAAGTACTCTCTCTGTTC 57.399 33.333 0.00 0.00 0.00 3.18
605 5122 9.847224 AAAAATAAAAGTACTCTCTCTGTTCCA 57.153 29.630 0.00 0.00 0.00 3.53
606 5123 9.847224 AAAATAAAAGTACTCTCTCTGTTCCAA 57.153 29.630 0.00 0.00 0.00 3.53
607 5124 9.847224 AAATAAAAGTACTCTCTCTGTTCCAAA 57.153 29.630 0.00 0.00 0.00 3.28
608 5125 9.847224 AATAAAAGTACTCTCTCTGTTCCAAAA 57.153 29.630 0.00 0.00 0.00 2.44
611 5128 9.495572 AAAAGTACTCTCTCTGTTCCAAAATAG 57.504 33.333 0.00 0.00 0.00 1.73
612 5129 8.423906 AAGTACTCTCTCTGTTCCAAAATAGA 57.576 34.615 0.00 0.00 32.42 1.98
613 5130 8.602472 AGTACTCTCTCTGTTCCAAAATAGAT 57.398 34.615 0.00 0.00 32.88 1.98
614 5131 8.474025 AGTACTCTCTCTGTTCCAAAATAGATG 58.526 37.037 0.00 0.00 32.88 2.90
615 5132 7.487822 ACTCTCTCTGTTCCAAAATAGATGA 57.512 36.000 0.00 0.00 32.88 2.92
616 5133 7.327214 ACTCTCTCTGTTCCAAAATAGATGAC 58.673 38.462 0.00 0.00 32.88 3.06
617 5134 7.180051 ACTCTCTCTGTTCCAAAATAGATGACT 59.820 37.037 0.00 0.00 32.88 3.41
618 5135 7.551585 TCTCTCTGTTCCAAAATAGATGACTC 58.448 38.462 0.00 0.00 32.88 3.36
619 5136 7.179160 TCTCTCTGTTCCAAAATAGATGACTCA 59.821 37.037 0.00 0.00 32.88 3.41
620 5137 7.679783 TCTCTGTTCCAAAATAGATGACTCAA 58.320 34.615 0.00 0.00 32.88 3.02
621 5138 7.604164 TCTCTGTTCCAAAATAGATGACTCAAC 59.396 37.037 0.00 0.00 32.88 3.18
622 5139 7.453393 TCTGTTCCAAAATAGATGACTCAACT 58.547 34.615 0.00 0.00 28.72 3.16
623 5140 7.939039 TCTGTTCCAAAATAGATGACTCAACTT 59.061 33.333 0.00 0.00 28.72 2.66
624 5141 8.463930 TGTTCCAAAATAGATGACTCAACTTT 57.536 30.769 0.00 0.00 0.00 2.66
625 5142 8.352201 TGTTCCAAAATAGATGACTCAACTTTG 58.648 33.333 0.00 0.00 0.00 2.77
626 5143 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
627 5144 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
628 5145 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
629 5146 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
636 5153 9.046296 AGATGACTCAACTTTGTACTAACTTTG 57.954 33.333 0.00 0.00 0.00 2.77
637 5154 8.732746 ATGACTCAACTTTGTACTAACTTTGT 57.267 30.769 0.00 0.00 0.00 2.83
638 5155 9.826574 ATGACTCAACTTTGTACTAACTTTGTA 57.173 29.630 0.00 0.00 0.00 2.41
639 5156 9.826574 TGACTCAACTTTGTACTAACTTTGTAT 57.173 29.630 0.00 0.00 0.00 2.29
679 5196 9.713684 AAATTAGGTCATTTATTCTGGAATGGA 57.286 29.630 6.13 0.00 34.74 3.41
680 5197 8.930846 ATTAGGTCATTTATTCTGGAATGGAG 57.069 34.615 6.13 0.00 34.74 3.86
681 5198 5.699143 AGGTCATTTATTCTGGAATGGAGG 58.301 41.667 6.13 0.00 34.74 4.30
682 5199 4.829492 GGTCATTTATTCTGGAATGGAGGG 59.171 45.833 6.13 0.00 34.74 4.30
727 5244 7.362056 GCATGCAACCTTTTCTTAGAAGACATA 60.362 37.037 14.21 0.00 34.13 2.29
787 5304 1.901591 ACTTGCCACATGAACAGGAG 58.098 50.000 0.00 0.00 0.00 3.69
863 5384 2.756283 AAGGACGAGCTCCCTCCG 60.756 66.667 11.49 1.08 40.53 4.63
864 5385 4.824515 AGGACGAGCTCCCTCCGG 62.825 72.222 16.11 0.00 40.53 5.14
869 5390 3.934962 GAGCTCCCTCCGGCCATC 61.935 72.222 2.24 0.00 31.68 3.51
870 5391 4.804420 AGCTCCCTCCGGCCATCA 62.804 66.667 2.24 0.00 0.00 3.07
871 5392 3.797353 GCTCCCTCCGGCCATCAA 61.797 66.667 2.24 0.00 0.00 2.57
872 5393 2.190578 CTCCCTCCGGCCATCAAC 59.809 66.667 2.24 0.00 0.00 3.18
873 5394 2.609299 TCCCTCCGGCCATCAACA 60.609 61.111 2.24 0.00 0.00 3.33
874 5395 2.438434 CCCTCCGGCCATCAACAC 60.438 66.667 2.24 0.00 0.00 3.32
875 5396 2.819595 CCTCCGGCCATCAACACG 60.820 66.667 2.24 0.00 0.00 4.49
876 5397 2.264480 CTCCGGCCATCAACACGA 59.736 61.111 2.24 0.00 0.00 4.35
889 5410 1.978455 AACACGACCAACCCTGCTGA 61.978 55.000 0.00 0.00 0.00 4.26
890 5411 1.961277 CACGACCAACCCTGCTGAC 60.961 63.158 0.00 0.00 0.00 3.51
892 5413 1.961277 CGACCAACCCTGCTGACAC 60.961 63.158 0.00 0.00 0.00 3.67
896 5417 0.179020 CCAACCCTGCTGACACTTCA 60.179 55.000 0.00 0.00 0.00 3.02
920 5443 9.337396 TCATACAAACTGCCACCTTTTATATAG 57.663 33.333 0.00 0.00 0.00 1.31
932 5456 7.285401 CCACCTTTTATATAGCTGACCAATGTT 59.715 37.037 0.00 0.00 0.00 2.71
937 5461 2.380084 TAGCTGACCAATGTTCCGAC 57.620 50.000 0.00 0.00 0.00 4.79
943 5467 1.671054 CCAATGTTCCGACCGCACT 60.671 57.895 0.00 0.00 0.00 4.40
952 5476 0.319211 CCGACCGCACTACTCAAACA 60.319 55.000 0.00 0.00 0.00 2.83
955 5484 2.480845 GACCGCACTACTCAAACAGTT 58.519 47.619 0.00 0.00 36.43 3.16
968 5497 4.710324 TCAAACAGTTAATCGGTCCAACT 58.290 39.130 0.00 0.00 32.82 3.16
980 5509 1.226746 GTCCAACTTGCAGCTACGTT 58.773 50.000 0.00 0.00 0.00 3.99
982 5511 0.385974 CCAACTTGCAGCTACGTTGC 60.386 55.000 14.34 14.34 40.12 4.17
986 5515 2.425592 TGCAGCTACGTTGCAGGT 59.574 55.556 23.41 3.56 44.16 4.00
987 5516 1.668867 TGCAGCTACGTTGCAGGTA 59.331 52.632 23.41 11.84 44.16 3.08
988 5517 0.034198 TGCAGCTACGTTGCAGGTAA 59.966 50.000 23.41 6.05 44.16 2.85
989 5518 0.721718 GCAGCTACGTTGCAGGTAAG 59.278 55.000 23.41 7.33 39.50 2.34
1312 5841 3.804153 ATCATCTGCCTGGCGCTCG 62.804 63.158 14.98 2.84 38.78 5.03
1752 6281 1.209747 GGGTGGTACCTGTCCTTCATC 59.790 57.143 14.36 0.00 38.64 2.92
1768 6297 0.038618 CATCACCGTGTTCGTCCTCA 60.039 55.000 0.00 0.00 35.01 3.86
1938 6467 1.135315 CTTCGCGCCACTGGAAATG 59.865 57.895 0.00 0.00 0.00 2.32
1943 6472 2.409870 CGCCACTGGAAATGGAGGC 61.410 63.158 0.00 0.00 39.87 4.70
1989 6518 0.975556 TAGAGTCCCCGCAGATGCAA 60.976 55.000 5.55 0.00 42.21 4.08
1998 6530 1.739466 CCGCAGATGCAATGTACAGTT 59.261 47.619 0.33 0.00 42.21 3.16
2015 6547 6.701841 TGTACAGTTCTTGTCTGAATCTGAAC 59.298 38.462 0.00 0.00 41.29 3.18
2060 6592 3.167945 CGACCGGTTCGTACGTGC 61.168 66.667 16.05 9.07 43.24 5.34
2061 6593 2.256461 GACCGGTTCGTACGTGCT 59.744 61.111 16.05 0.00 0.00 4.40
2062 6594 1.372128 GACCGGTTCGTACGTGCTT 60.372 57.895 16.05 0.00 0.00 3.91
2063 6595 1.339946 GACCGGTTCGTACGTGCTTC 61.340 60.000 16.05 2.21 0.00 3.86
2064 6596 2.090524 CCGGTTCGTACGTGCTTCC 61.091 63.158 16.05 10.29 0.00 3.46
2147 6681 0.099436 GCACGCATTGATTGGAGACC 59.901 55.000 0.00 0.00 0.00 3.85
2193 6727 1.679153 TGCCAGCGTATGATCGAGTTA 59.321 47.619 0.00 0.00 0.00 2.24
2211 6745 3.136626 AGTTAGGTGAAACAAGCAGACCT 59.863 43.478 0.00 0.00 39.98 3.85
2217 6751 4.338400 GGTGAAACAAGCAGACCTTTACTT 59.662 41.667 0.00 0.00 39.98 2.24
2260 6795 9.503399 TTTTCCAAGAAAATAAGGTACTCTCTC 57.497 33.333 0.00 0.00 38.49 3.20
2261 6796 7.184067 TCCAAGAAAATAAGGTACTCTCTCC 57.816 40.000 0.00 0.00 38.49 3.71
2262 6797 6.043411 CCAAGAAAATAAGGTACTCTCTCCG 58.957 44.000 0.00 0.00 38.49 4.63
2263 6798 6.351117 CCAAGAAAATAAGGTACTCTCTCCGT 60.351 42.308 0.00 0.00 38.49 4.69
2264 6799 6.854091 AGAAAATAAGGTACTCTCTCCGTT 57.146 37.500 0.00 0.00 38.49 4.44
2265 6800 7.242322 AGAAAATAAGGTACTCTCTCCGTTT 57.758 36.000 0.00 0.00 38.49 3.60
2266 6801 7.321908 AGAAAATAAGGTACTCTCTCCGTTTC 58.678 38.462 0.00 0.00 38.49 2.78
2267 6802 6.600882 AAATAAGGTACTCTCTCCGTTTCA 57.399 37.500 0.00 0.00 38.49 2.69
2268 6803 6.793505 AATAAGGTACTCTCTCCGTTTCAT 57.206 37.500 0.00 0.00 38.49 2.57
2269 6804 6.793505 ATAAGGTACTCTCTCCGTTTCATT 57.206 37.500 0.00 0.00 38.49 2.57
2270 6805 5.485209 AAGGTACTCTCTCCGTTTCATTT 57.515 39.130 0.00 0.00 38.49 2.32
2271 6806 5.485209 AGGTACTCTCTCCGTTTCATTTT 57.515 39.130 0.00 0.00 0.00 1.82
2272 6807 6.600882 AGGTACTCTCTCCGTTTCATTTTA 57.399 37.500 0.00 0.00 0.00 1.52
2273 6808 6.631962 AGGTACTCTCTCCGTTTCATTTTAG 58.368 40.000 0.00 0.00 0.00 1.85
2274 6809 6.210984 AGGTACTCTCTCCGTTTCATTTTAGT 59.789 38.462 0.00 0.00 0.00 2.24
2275 6810 6.530887 GGTACTCTCTCCGTTTCATTTTAGTC 59.469 42.308 0.00 0.00 0.00 2.59
2276 6811 6.347859 ACTCTCTCCGTTTCATTTTAGTCT 57.652 37.500 0.00 0.00 0.00 3.24
2277 6812 6.159988 ACTCTCTCCGTTTCATTTTAGTCTG 58.840 40.000 0.00 0.00 0.00 3.51
2278 6813 4.929808 TCTCTCCGTTTCATTTTAGTCTGC 59.070 41.667 0.00 0.00 0.00 4.26
2279 6814 4.637276 TCTCCGTTTCATTTTAGTCTGCA 58.363 39.130 0.00 0.00 0.00 4.41
2280 6815 5.245531 TCTCCGTTTCATTTTAGTCTGCAT 58.754 37.500 0.00 0.00 0.00 3.96
2281 6816 6.403049 TCTCCGTTTCATTTTAGTCTGCATA 58.597 36.000 0.00 0.00 0.00 3.14
2282 6817 7.047891 TCTCCGTTTCATTTTAGTCTGCATAT 58.952 34.615 0.00 0.00 0.00 1.78
2283 6818 8.201464 TCTCCGTTTCATTTTAGTCTGCATATA 58.799 33.333 0.00 0.00 0.00 0.86
2284 6819 8.725405 TCCGTTTCATTTTAGTCTGCATATAA 57.275 30.769 0.00 0.00 0.00 0.98
2285 6820 8.826710 TCCGTTTCATTTTAGTCTGCATATAAG 58.173 33.333 0.00 0.00 0.00 1.73
2286 6821 8.826710 CCGTTTCATTTTAGTCTGCATATAAGA 58.173 33.333 0.00 0.00 0.00 2.10
2298 6833 9.050601 AGTCTGCATATAAGATTTAGTCAAAGC 57.949 33.333 0.00 0.00 0.00 3.51
2299 6834 8.286097 GTCTGCATATAAGATTTAGTCAAAGCC 58.714 37.037 0.00 0.00 30.10 4.35
2300 6835 7.992608 TCTGCATATAAGATTTAGTCAAAGCCA 59.007 33.333 0.00 0.00 30.10 4.75
2301 6836 8.518430 TGCATATAAGATTTAGTCAAAGCCAA 57.482 30.769 0.00 0.00 30.10 4.52
2302 6837 8.965819 TGCATATAAGATTTAGTCAAAGCCAAA 58.034 29.630 0.00 0.00 30.10 3.28
2303 6838 9.237846 GCATATAAGATTTAGTCAAAGCCAAAC 57.762 33.333 0.00 0.00 30.10 2.93
2307 6842 6.959639 AGATTTAGTCAAAGCCAAACTTCA 57.040 33.333 0.00 0.00 37.75 3.02
2308 6843 7.530426 AGATTTAGTCAAAGCCAAACTTCAT 57.470 32.000 0.00 0.00 37.75 2.57
2309 6844 8.635765 AGATTTAGTCAAAGCCAAACTTCATA 57.364 30.769 0.00 0.00 37.75 2.15
2310 6845 9.077885 AGATTTAGTCAAAGCCAAACTTCATAA 57.922 29.630 0.00 0.00 37.75 1.90
2311 6846 9.691362 GATTTAGTCAAAGCCAAACTTCATAAA 57.309 29.630 0.00 0.00 37.75 1.40
2312 6847 9.696917 ATTTAGTCAAAGCCAAACTTCATAAAG 57.303 29.630 0.00 0.00 37.75 1.85
2398 6933 9.941325 AAAATTAATTTCATGGTGCATCTAACA 57.059 25.926 13.68 0.00 0.00 2.41
2399 6934 9.941325 AAATTAATTTCATGGTGCATCTAACAA 57.059 25.926 7.64 0.00 0.00 2.83
2404 6939 9.537192 AATTTCATGGTGCATCTAACAATATTG 57.463 29.630 14.01 14.01 0.00 1.90
2405 6940 7.878547 TTCATGGTGCATCTAACAATATTGA 57.121 32.000 22.16 0.00 0.00 2.57
2406 6941 8.467963 TTCATGGTGCATCTAACAATATTGAT 57.532 30.769 22.16 12.82 0.00 2.57
2407 6942 8.467963 TCATGGTGCATCTAACAATATTGATT 57.532 30.769 22.16 13.80 0.00 2.57
2408 6943 8.916062 TCATGGTGCATCTAACAATATTGATTT 58.084 29.630 22.16 9.25 0.00 2.17
2409 6944 9.188588 CATGGTGCATCTAACAATATTGATTTC 57.811 33.333 22.16 5.00 0.00 2.17
2410 6945 8.291191 TGGTGCATCTAACAATATTGATTTCA 57.709 30.769 22.16 7.26 0.00 2.69
2411 6946 8.916062 TGGTGCATCTAACAATATTGATTTCAT 58.084 29.630 22.16 4.50 0.00 2.57
2490 7025 9.617523 TGACTTTGATCAAATCTTATATGCAGA 57.382 29.630 20.76 0.00 0.00 4.26
2491 7026 9.875675 GACTTTGATCAAATCTTATATGCAGAC 57.124 33.333 20.76 2.27 0.00 3.51
2492 7027 9.624373 ACTTTGATCAAATCTTATATGCAGACT 57.376 29.630 20.76 0.00 0.00 3.24
2540 7075 3.159472 TGTGATGCTTTTTCATGGAGCT 58.841 40.909 10.88 0.00 37.32 4.09
2557 7092 2.666508 GAGCTAGACAATTCGTGCGAAA 59.333 45.455 11.09 0.00 37.69 3.46
2558 7093 3.064207 AGCTAGACAATTCGTGCGAAAA 58.936 40.909 11.09 0.00 37.69 2.29
2599 7134 1.729586 AGCACCTCTGGGTTACTGAA 58.270 50.000 0.00 0.00 44.73 3.02
2616 7152 1.234821 GAACCAACGCCACATCTTGA 58.765 50.000 0.00 0.00 0.00 3.02
2629 7172 5.067413 GCCACATCTTGAGAAATCATCACAT 59.933 40.000 0.00 0.00 0.00 3.21
2651 7194 2.912967 GCGTCTCGTAGTCGATGAAAAA 59.087 45.455 0.00 0.00 45.21 1.94
2653 7196 4.156915 CGTCTCGTAGTCGATGAAAAAGT 58.843 43.478 0.00 0.00 45.21 2.66
2701 7244 8.600625 CGTCGGAAATTCTGAAATAAATACAGA 58.399 33.333 6.03 0.00 38.61 3.41
2716 7259 1.217882 ACAGAAAAACTCGAGCACCG 58.782 50.000 13.61 0.00 40.25 4.94
2760 7303 1.040339 TTGTGGGCTGGTTTCACCAC 61.040 55.000 5.78 5.78 44.79 4.16
2764 7307 0.467290 GGGCTGGTTTCACCACAAGA 60.467 55.000 0.00 0.00 44.79 3.02
2831 7376 2.149973 AAAATGGCAAGCCTCCTAGG 57.850 50.000 12.96 0.82 38.80 3.02
2832 7377 0.259938 AAATGGCAAGCCTCCTAGGG 59.740 55.000 9.46 0.00 35.37 3.53
2833 7378 0.624500 AATGGCAAGCCTCCTAGGGA 60.625 55.000 9.46 0.00 35.37 4.20
2834 7379 0.402566 ATGGCAAGCCTCCTAGGGAT 60.403 55.000 9.46 0.00 35.37 3.85
2836 7381 0.553333 GGCAAGCCTCCTAGGGATTT 59.447 55.000 9.46 0.00 35.37 2.17
2837 7382 1.063642 GGCAAGCCTCCTAGGGATTTT 60.064 52.381 9.46 0.00 35.37 1.82
2838 7383 2.302260 GCAAGCCTCCTAGGGATTTTC 58.698 52.381 9.46 0.00 35.37 2.29
2839 7384 2.937519 CAAGCCTCCTAGGGATTTTCC 58.062 52.381 9.46 0.00 35.37 3.13
2840 7385 2.511637 CAAGCCTCCTAGGGATTTTCCT 59.488 50.000 9.46 0.00 40.79 3.36
2841 7386 2.131023 AGCCTCCTAGGGATTTTCCTG 58.869 52.381 9.46 0.00 37.75 3.86
2852 7397 7.834181 CCTAGGGATTTTCCTGACTATCAAAAA 59.166 37.037 0.00 0.00 37.75 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 3997 1.375140 GACCCCTTTCCCGACGTTC 60.375 63.158 0.00 0.00 0.00 3.95
72 4009 1.496060 TATTGACGATGCAGACCCCT 58.504 50.000 0.00 0.00 0.00 4.79
78 4015 4.568359 GCCATACCTATATTGACGATGCAG 59.432 45.833 0.00 0.00 0.00 4.41
89 4026 4.096081 GTCTTCGCTACGCCATACCTATAT 59.904 45.833 0.00 0.00 0.00 0.86
114 4051 2.361104 TTTCGTGGCCTGCATCCC 60.361 61.111 3.32 0.00 0.00 3.85
168 4105 3.374402 CGCCTGACAGACCTCGGT 61.374 66.667 3.32 0.00 0.00 4.69
190 4127 3.070018 CACTCTTCCTCAAAGAATGCGT 58.930 45.455 0.00 0.00 43.39 5.24
213 4729 0.179124 GCCTGTAACTCTCTCCGCTG 60.179 60.000 0.00 0.00 0.00 5.18
220 4736 1.063764 CGTCCTACGCCTGTAACTCTC 59.936 57.143 0.00 0.00 33.65 3.20
221 4737 1.093159 CGTCCTACGCCTGTAACTCT 58.907 55.000 0.00 0.00 33.65 3.24
305 4821 7.445121 ACTCCATATATTGATGATCAACACGT 58.555 34.615 10.45 0.00 39.45 4.49
344 4861 4.476410 CTGTACAGCGCGCTCCGA 62.476 66.667 34.28 16.84 40.02 4.55
366 4883 2.259818 CTCTCTTGCGCACCTCGT 59.740 61.111 11.12 0.00 41.07 4.18
370 4887 1.739562 CTCCACTCTCTTGCGCACC 60.740 63.158 11.12 0.00 0.00 5.01
378 4895 1.102154 CTGCACGATCTCCACTCTCT 58.898 55.000 0.00 0.00 0.00 3.10
400 4917 1.595382 GCTGACCGAGTTGTGCACT 60.595 57.895 19.41 0.00 39.07 4.40
407 4924 0.679505 TAACTGCAGCTGACCGAGTT 59.320 50.000 20.43 19.32 0.00 3.01
434 4951 2.041251 AGCAGTCTACCCGTAGTCTC 57.959 55.000 1.96 0.00 34.84 3.36
458 4975 8.954350 CACACTTGAAAAATGGAGAATCTCTAT 58.046 33.333 10.38 6.77 33.14 1.98
459 4976 7.939039 ACACACTTGAAAAATGGAGAATCTCTA 59.061 33.333 10.38 4.25 33.73 2.43
460 4977 6.774656 ACACACTTGAAAAATGGAGAATCTCT 59.225 34.615 10.38 0.00 33.73 3.10
461 4978 6.974965 ACACACTTGAAAAATGGAGAATCTC 58.025 36.000 0.71 0.71 33.73 2.75
462 4979 6.966534 ACACACTTGAAAAATGGAGAATCT 57.033 33.333 0.00 0.00 33.73 2.40
463 4980 7.428826 AGAACACACTTGAAAAATGGAGAATC 58.571 34.615 0.00 0.00 0.00 2.52
472 4989 7.990886 AGACTATGGTAGAACACACTTGAAAAA 59.009 33.333 0.00 0.00 0.00 1.94
505 5022 5.661056 TGAGAGTAGATTTCCACGTGAAT 57.339 39.130 19.30 9.86 31.67 2.57
526 5043 3.059665 GGAAATTTTGAGGCAACGCTTTG 60.060 43.478 0.00 0.00 46.39 2.77
532 5049 3.679502 CGATTGGGAAATTTTGAGGCAAC 59.320 43.478 0.00 0.00 0.00 4.17
538 5055 3.057876 CCACGTCGATTGGGAAATTTTGA 60.058 43.478 0.00 0.00 0.00 2.69
585 5102 9.495572 CTATTTTGGAACAGAGAGAGTACTTTT 57.504 33.333 0.00 0.00 42.39 2.27
588 5105 8.474025 CATCTATTTTGGAACAGAGAGAGTACT 58.526 37.037 0.00 0.00 42.39 2.73
589 5106 8.470805 TCATCTATTTTGGAACAGAGAGAGTAC 58.529 37.037 0.00 0.00 42.39 2.73
590 5107 8.470805 GTCATCTATTTTGGAACAGAGAGAGTA 58.529 37.037 0.00 0.00 42.39 2.59
591 5108 7.180051 AGTCATCTATTTTGGAACAGAGAGAGT 59.820 37.037 0.00 0.00 42.39 3.24
592 5109 7.555087 AGTCATCTATTTTGGAACAGAGAGAG 58.445 38.462 0.00 0.00 42.39 3.20
593 5110 7.179160 TGAGTCATCTATTTTGGAACAGAGAGA 59.821 37.037 0.00 0.00 42.39 3.10
594 5111 7.326454 TGAGTCATCTATTTTGGAACAGAGAG 58.674 38.462 0.00 0.00 42.39 3.20
595 5112 7.244886 TGAGTCATCTATTTTGGAACAGAGA 57.755 36.000 0.00 0.00 42.39 3.10
596 5113 7.605691 AGTTGAGTCATCTATTTTGGAACAGAG 59.394 37.037 1.70 0.00 42.39 3.35
597 5114 7.453393 AGTTGAGTCATCTATTTTGGAACAGA 58.547 34.615 1.70 0.00 42.39 3.41
598 5115 7.678947 AGTTGAGTCATCTATTTTGGAACAG 57.321 36.000 1.70 0.00 42.39 3.16
599 5116 8.352201 CAAAGTTGAGTCATCTATTTTGGAACA 58.648 33.333 4.14 0.00 35.65 3.18
600 5117 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
601 5118 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
602 5119 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
603 5120 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
610 5127 9.046296 CAAAGTTAGTACAAAGTTGAGTCATCT 57.954 33.333 0.00 0.00 0.00 2.90
611 5128 8.827677 ACAAAGTTAGTACAAAGTTGAGTCATC 58.172 33.333 0.00 0.00 0.00 2.92
612 5129 8.732746 ACAAAGTTAGTACAAAGTTGAGTCAT 57.267 30.769 0.00 0.00 0.00 3.06
613 5130 9.826574 ATACAAAGTTAGTACAAAGTTGAGTCA 57.173 29.630 0.00 0.00 0.00 3.41
653 5170 9.713684 TCCATTCCAGAATAAATGACCTAATTT 57.286 29.630 0.00 0.00 35.35 1.82
654 5171 9.359653 CTCCATTCCAGAATAAATGACCTAATT 57.640 33.333 0.00 0.00 35.35 1.40
655 5172 7.946776 CCTCCATTCCAGAATAAATGACCTAAT 59.053 37.037 0.00 0.00 35.35 1.73
656 5173 7.290061 CCTCCATTCCAGAATAAATGACCTAA 58.710 38.462 0.00 0.00 35.35 2.69
657 5174 6.183361 CCCTCCATTCCAGAATAAATGACCTA 60.183 42.308 0.00 0.00 35.35 3.08
658 5175 5.399497 CCCTCCATTCCAGAATAAATGACCT 60.399 44.000 0.00 0.00 35.35 3.85
659 5176 4.829492 CCCTCCATTCCAGAATAAATGACC 59.171 45.833 0.00 0.00 35.35 4.02
660 5177 5.694995 TCCCTCCATTCCAGAATAAATGAC 58.305 41.667 0.00 0.00 35.35 3.06
661 5178 5.433051 ACTCCCTCCATTCCAGAATAAATGA 59.567 40.000 0.00 0.00 35.35 2.57
662 5179 5.699143 ACTCCCTCCATTCCAGAATAAATG 58.301 41.667 0.00 0.00 33.57 2.32
663 5180 6.389869 TGTACTCCCTCCATTCCAGAATAAAT 59.610 38.462 0.00 0.00 0.00 1.40
664 5181 5.729229 TGTACTCCCTCCATTCCAGAATAAA 59.271 40.000 0.00 0.00 0.00 1.40
665 5182 5.285401 TGTACTCCCTCCATTCCAGAATAA 58.715 41.667 0.00 0.00 0.00 1.40
666 5183 4.890988 TGTACTCCCTCCATTCCAGAATA 58.109 43.478 0.00 0.00 0.00 1.75
667 5184 3.736094 TGTACTCCCTCCATTCCAGAAT 58.264 45.455 0.00 0.00 0.00 2.40
668 5185 3.199442 TGTACTCCCTCCATTCCAGAA 57.801 47.619 0.00 0.00 0.00 3.02
669 5186 2.940514 TGTACTCCCTCCATTCCAGA 57.059 50.000 0.00 0.00 0.00 3.86
670 5187 5.832539 ATATTGTACTCCCTCCATTCCAG 57.167 43.478 0.00 0.00 0.00 3.86
671 5188 5.690097 GCAATATTGTACTCCCTCCATTCCA 60.690 44.000 16.61 0.00 0.00 3.53
672 5189 4.762251 GCAATATTGTACTCCCTCCATTCC 59.238 45.833 16.61 0.00 0.00 3.01
673 5190 5.376625 TGCAATATTGTACTCCCTCCATTC 58.623 41.667 16.61 0.00 0.00 2.67
674 5191 5.387113 TGCAATATTGTACTCCCTCCATT 57.613 39.130 16.61 0.00 0.00 3.16
675 5192 5.387113 TTGCAATATTGTACTCCCTCCAT 57.613 39.130 16.61 0.00 0.00 3.41
676 5193 4.853468 TTGCAATATTGTACTCCCTCCA 57.147 40.909 16.61 0.43 0.00 3.86
677 5194 5.010012 CCAATTGCAATATTGTACTCCCTCC 59.990 44.000 13.39 0.00 34.42 4.30
678 5195 5.507985 GCCAATTGCAATATTGTACTCCCTC 60.508 44.000 13.39 0.00 40.77 4.30
679 5196 4.342092 GCCAATTGCAATATTGTACTCCCT 59.658 41.667 13.39 0.00 40.77 4.20
680 5197 4.620982 GCCAATTGCAATATTGTACTCCC 58.379 43.478 13.39 0.00 40.77 4.30
863 5384 1.579429 GTTGGTCGTGTTGATGGCC 59.421 57.895 0.00 0.00 32.87 5.36
864 5385 1.579429 GGTTGGTCGTGTTGATGGC 59.421 57.895 0.00 0.00 0.00 4.40
865 5386 0.250727 AGGGTTGGTCGTGTTGATGG 60.251 55.000 0.00 0.00 0.00 3.51
866 5387 0.874390 CAGGGTTGGTCGTGTTGATG 59.126 55.000 0.00 0.00 0.00 3.07
867 5388 0.889186 GCAGGGTTGGTCGTGTTGAT 60.889 55.000 0.00 0.00 0.00 2.57
868 5389 1.525077 GCAGGGTTGGTCGTGTTGA 60.525 57.895 0.00 0.00 0.00 3.18
869 5390 1.525995 AGCAGGGTTGGTCGTGTTG 60.526 57.895 0.00 0.00 0.00 3.33
870 5391 1.525995 CAGCAGGGTTGGTCGTGTT 60.526 57.895 0.00 0.00 31.36 3.32
871 5392 2.111043 CAGCAGGGTTGGTCGTGT 59.889 61.111 0.00 0.00 31.36 4.49
872 5393 1.961277 GTCAGCAGGGTTGGTCGTG 60.961 63.158 0.00 0.00 31.36 4.35
873 5394 2.426023 GTCAGCAGGGTTGGTCGT 59.574 61.111 0.00 0.00 31.36 4.34
874 5395 1.961277 GTGTCAGCAGGGTTGGTCG 60.961 63.158 0.00 0.00 31.36 4.79
875 5396 0.179018 AAGTGTCAGCAGGGTTGGTC 60.179 55.000 0.00 0.00 31.36 4.02
876 5397 0.179018 GAAGTGTCAGCAGGGTTGGT 60.179 55.000 0.00 0.00 34.83 3.67
889 5410 2.884639 GGTGGCAGTTTGTATGAAGTGT 59.115 45.455 0.00 0.00 33.48 3.55
890 5411 3.149196 AGGTGGCAGTTTGTATGAAGTG 58.851 45.455 0.00 0.00 33.95 3.16
892 5413 4.853924 AAAGGTGGCAGTTTGTATGAAG 57.146 40.909 0.00 0.00 0.00 3.02
896 5417 7.998964 AGCTATATAAAAGGTGGCAGTTTGTAT 59.001 33.333 10.34 10.34 0.00 2.29
920 5443 1.635663 CGGTCGGAACATTGGTCAGC 61.636 60.000 3.73 0.00 0.00 4.26
932 5456 0.038892 GTTTGAGTAGTGCGGTCGGA 60.039 55.000 0.00 0.00 0.00 4.55
937 5461 4.201589 CGATTAACTGTTTGAGTAGTGCGG 60.202 45.833 0.00 0.00 33.09 5.69
943 5467 5.471556 TGGACCGATTAACTGTTTGAGTA 57.528 39.130 0.00 0.00 33.09 2.59
952 5476 3.074412 CTGCAAGTTGGACCGATTAACT 58.926 45.455 4.75 0.00 36.29 2.24
955 5484 1.003118 AGCTGCAAGTTGGACCGATTA 59.997 47.619 4.75 0.00 35.30 1.75
980 5509 4.077184 CCGGCGGTCTTACCTGCA 62.077 66.667 19.97 0.00 38.76 4.41
982 5511 4.832608 GGCCGGCGGTCTTACCTG 62.833 72.222 28.82 0.00 35.66 4.00
985 5514 2.895372 CATGGCCGGCGGTCTTAC 60.895 66.667 32.34 12.29 0.00 2.34
986 5515 4.169696 CCATGGCCGGCGGTCTTA 62.170 66.667 32.34 13.33 0.00 2.10
1752 6281 3.932289 GTGAGGACGAACACGGTG 58.068 61.111 6.58 6.58 0.00 4.94
1768 6297 1.446907 CACACGTAGAGGTAGACCGT 58.553 55.000 0.00 0.00 42.08 4.83
1851 6380 1.365633 CGCCTCTAGGTCATGCTCC 59.634 63.158 0.00 0.00 37.57 4.70
1935 6464 3.066291 TGACACATTTACGCCTCCATT 57.934 42.857 0.00 0.00 0.00 3.16
1938 6467 1.130561 GCTTGACACATTTACGCCTCC 59.869 52.381 0.00 0.00 0.00 4.30
1943 6472 3.991069 GCTACAGCTTGACACATTTACG 58.009 45.455 0.00 0.00 38.21 3.18
1969 6498 0.760567 TGCATCTGCGGGGACTCTAT 60.761 55.000 0.00 0.00 45.83 1.98
1989 6518 6.997655 TCAGATTCAGACAAGAACTGTACAT 58.002 36.000 0.00 0.00 38.84 2.29
1998 6530 6.925211 AGATAACGTTCAGATTCAGACAAGA 58.075 36.000 2.82 0.00 0.00 3.02
2015 6547 8.837389 TCCATGGATATTCGTAGATAGATAACG 58.163 37.037 11.44 0.00 35.04 3.18
2089 6622 3.306225 GCATGTTTTCCTCTTCAATGCCA 60.306 43.478 0.00 0.00 0.00 4.92
2147 6681 4.701651 TGGCTATCCAACTCATTTGTCTTG 59.298 41.667 0.00 0.00 39.99 3.02
2193 6727 2.736670 AAGGTCTGCTTGTTTCACCT 57.263 45.000 0.00 0.00 39.26 4.00
2217 6751 9.635404 TCTTGGAAAATAGAAACTTACCTTTGA 57.365 29.630 0.00 0.00 0.00 2.69
2237 6771 6.127423 CGGAGAGAGTACCTTATTTTCTTGGA 60.127 42.308 0.00 0.00 0.00 3.53
2247 6781 6.600882 AAATGAAACGGAGAGAGTACCTTA 57.399 37.500 0.00 0.00 0.00 2.69
2252 6787 7.313646 CAGACTAAAATGAAACGGAGAGAGTA 58.686 38.462 0.00 0.00 0.00 2.59
2253 6788 6.159988 CAGACTAAAATGAAACGGAGAGAGT 58.840 40.000 0.00 0.00 0.00 3.24
2254 6789 5.062809 GCAGACTAAAATGAAACGGAGAGAG 59.937 44.000 0.00 0.00 0.00 3.20
2255 6790 4.929808 GCAGACTAAAATGAAACGGAGAGA 59.070 41.667 0.00 0.00 0.00 3.10
2256 6791 4.690748 TGCAGACTAAAATGAAACGGAGAG 59.309 41.667 0.00 0.00 0.00 3.20
2257 6792 4.637276 TGCAGACTAAAATGAAACGGAGA 58.363 39.130 0.00 0.00 0.00 3.71
2258 6793 5.551760 ATGCAGACTAAAATGAAACGGAG 57.448 39.130 0.00 0.00 0.00 4.63
2259 6794 8.725405 TTATATGCAGACTAAAATGAAACGGA 57.275 30.769 0.00 0.00 0.00 4.69
2260 6795 8.826710 TCTTATATGCAGACTAAAATGAAACGG 58.173 33.333 0.00 0.00 0.00 4.44
2272 6807 9.050601 GCTTTGACTAAATCTTATATGCAGACT 57.949 33.333 0.00 0.00 0.00 3.24
2273 6808 8.286097 GGCTTTGACTAAATCTTATATGCAGAC 58.714 37.037 0.00 0.00 0.00 3.51
2274 6809 7.992608 TGGCTTTGACTAAATCTTATATGCAGA 59.007 33.333 0.00 0.00 0.00 4.26
2275 6810 8.158169 TGGCTTTGACTAAATCTTATATGCAG 57.842 34.615 0.00 0.00 0.00 4.41
2276 6811 8.518430 TTGGCTTTGACTAAATCTTATATGCA 57.482 30.769 0.00 0.00 0.00 3.96
2277 6812 9.237846 GTTTGGCTTTGACTAAATCTTATATGC 57.762 33.333 0.00 0.00 0.00 3.14
2281 6816 9.077885 TGAAGTTTGGCTTTGACTAAATCTTAT 57.922 29.630 0.00 0.00 37.59 1.73
2282 6817 8.458573 TGAAGTTTGGCTTTGACTAAATCTTA 57.541 30.769 0.00 0.00 37.59 2.10
2283 6818 7.346751 TGAAGTTTGGCTTTGACTAAATCTT 57.653 32.000 0.00 0.00 37.59 2.40
2284 6819 6.959639 TGAAGTTTGGCTTTGACTAAATCT 57.040 33.333 0.00 0.00 37.59 2.40
2285 6820 9.691362 TTTATGAAGTTTGGCTTTGACTAAATC 57.309 29.630 0.00 0.00 37.59 2.17
2286 6821 9.696917 CTTTATGAAGTTTGGCTTTGACTAAAT 57.303 29.630 0.00 0.00 37.59 1.40
2287 6822 8.691797 ACTTTATGAAGTTTGGCTTTGACTAAA 58.308 29.630 0.00 0.00 43.48 1.85
2288 6823 8.232913 ACTTTATGAAGTTTGGCTTTGACTAA 57.767 30.769 0.00 0.00 43.48 2.24
2289 6824 7.817418 ACTTTATGAAGTTTGGCTTTGACTA 57.183 32.000 0.00 0.00 43.48 2.59
2290 6825 6.715347 ACTTTATGAAGTTTGGCTTTGACT 57.285 33.333 0.00 0.00 43.48 3.41
2372 6907 9.941325 TGTTAGATGCACCATGAAATTAATTTT 57.059 25.926 14.45 0.00 0.00 1.82
2373 6908 9.941325 TTGTTAGATGCACCATGAAATTAATTT 57.059 25.926 13.24 13.24 0.00 1.82
2378 6913 9.537192 CAATATTGTTAGATGCACCATGAAATT 57.463 29.630 7.32 0.00 0.00 1.82
2379 6914 8.916062 TCAATATTGTTAGATGCACCATGAAAT 58.084 29.630 14.97 0.00 0.00 2.17
2380 6915 8.291191 TCAATATTGTTAGATGCACCATGAAA 57.709 30.769 14.97 0.00 0.00 2.69
2381 6916 7.878547 TCAATATTGTTAGATGCACCATGAA 57.121 32.000 14.97 0.00 0.00 2.57
2382 6917 8.467963 AATCAATATTGTTAGATGCACCATGA 57.532 30.769 14.97 0.00 0.00 3.07
2383 6918 9.188588 GAAATCAATATTGTTAGATGCACCATG 57.811 33.333 14.97 0.00 0.00 3.66
2384 6919 8.916062 TGAAATCAATATTGTTAGATGCACCAT 58.084 29.630 14.97 0.00 0.00 3.55
2385 6920 8.291191 TGAAATCAATATTGTTAGATGCACCA 57.709 30.769 14.97 0.00 0.00 4.17
2464 6999 9.617523 TCTGCATATAAGATTTGATCAAAGTCA 57.382 29.630 24.17 11.02 33.32 3.41
2465 7000 9.875675 GTCTGCATATAAGATTTGATCAAAGTC 57.124 33.333 24.17 19.70 33.32 3.01
2466 7001 9.624373 AGTCTGCATATAAGATTTGATCAAAGT 57.376 29.630 24.17 14.86 33.32 2.66
2497 7032 2.067365 AACTTGCTCCCTCCGTTTTT 57.933 45.000 0.00 0.00 0.00 1.94
2498 7033 2.067365 AAACTTGCTCCCTCCGTTTT 57.933 45.000 0.00 0.00 0.00 2.43
2499 7034 2.067365 AAAACTTGCTCCCTCCGTTT 57.933 45.000 0.00 0.00 0.00 3.60
2500 7035 1.681264 CAAAAACTTGCTCCCTCCGTT 59.319 47.619 0.00 0.00 0.00 4.44
2501 7036 1.318576 CAAAAACTTGCTCCCTCCGT 58.681 50.000 0.00 0.00 0.00 4.69
2502 7037 1.001378 CACAAAAACTTGCTCCCTCCG 60.001 52.381 0.00 0.00 0.00 4.63
2503 7038 2.306847 TCACAAAAACTTGCTCCCTCC 58.693 47.619 0.00 0.00 0.00 4.30
2504 7039 3.858503 GCATCACAAAAACTTGCTCCCTC 60.859 47.826 0.00 0.00 0.00 4.30
2505 7040 2.036346 GCATCACAAAAACTTGCTCCCT 59.964 45.455 0.00 0.00 0.00 4.20
2506 7041 2.036346 AGCATCACAAAAACTTGCTCCC 59.964 45.455 0.00 0.00 0.00 4.30
2507 7042 3.375782 AGCATCACAAAAACTTGCTCC 57.624 42.857 0.00 0.00 0.00 4.70
2508 7043 5.723492 AAAAGCATCACAAAAACTTGCTC 57.277 34.783 0.00 0.00 0.00 4.26
2509 7044 5.642919 TGAAAAAGCATCACAAAAACTTGCT 59.357 32.000 0.00 0.00 0.00 3.91
2510 7045 5.867166 TGAAAAAGCATCACAAAAACTTGC 58.133 33.333 0.00 0.00 0.00 4.01
2511 7046 6.908284 CCATGAAAAAGCATCACAAAAACTTG 59.092 34.615 0.00 0.00 0.00 3.16
2540 7075 4.123276 GTGTTTTCGCACGAATTGTCTA 57.877 40.909 6.28 0.00 33.79 2.59
2557 7092 2.428622 GGGTAGGGTGTGCGTGTT 59.571 61.111 0.00 0.00 0.00 3.32
2558 7093 2.735151 TAGGGGTAGGGTGTGCGTGT 62.735 60.000 0.00 0.00 0.00 4.49
2592 7127 2.147958 GATGTGGCGTTGGTTCAGTAA 58.852 47.619 0.00 0.00 0.00 2.24
2599 7134 0.396435 TCTCAAGATGTGGCGTTGGT 59.604 50.000 0.00 0.00 0.00 3.67
2602 7137 3.411446 TGATTTCTCAAGATGTGGCGTT 58.589 40.909 0.00 0.00 0.00 4.84
2605 7140 4.397103 TGTGATGATTTCTCAAGATGTGGC 59.603 41.667 0.00 0.00 34.37 5.01
2606 7141 6.495706 CATGTGATGATTTCTCAAGATGTGG 58.504 40.000 0.00 0.00 34.37 4.17
2616 7152 2.862536 CGAGACGCATGTGATGATTTCT 59.137 45.455 14.43 3.75 0.00 2.52
2651 7194 1.996798 TCGTTCAGTGGGAGAAGACT 58.003 50.000 0.00 0.00 0.00 3.24
2653 7196 2.036387 TGTTCGTTCAGTGGGAGAAGA 58.964 47.619 0.00 0.00 0.00 2.87
2701 7244 0.463116 ACACCGGTGCTCGAGTTTTT 60.463 50.000 34.26 7.93 42.43 1.94
2707 7250 2.023414 AACTTGACACCGGTGCTCGA 62.023 55.000 34.26 25.36 42.43 4.04
2751 7294 6.385649 TGGTTAGATTTCTTGTGGTGAAAC 57.614 37.500 0.00 0.00 36.43 2.78
2754 7297 5.939883 CAGATGGTTAGATTTCTTGTGGTGA 59.060 40.000 0.00 0.00 0.00 4.02
2760 7303 8.341173 GCATAACTCAGATGGTTAGATTTCTTG 58.659 37.037 0.00 0.00 33.50 3.02
2795 7338 6.320164 TGCCATTTTACACAACTAAACAGAGT 59.680 34.615 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.