Multiple sequence alignment - TraesCS4B01G232300

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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 TraesCS4B01G232300 chr4B 100.000 5438 0 0 1 5438 483770935 483765498 0.000000e+00 10043.0
1 TraesCS4B01G232300 chr4B 93.333 315 18 2 2750 3064 660500954 660500643 3.840000e-126 462.0
2 TraesCS4B01G232300 chr4B 89.610 77 6 2 4909 4983 517170767 517170843 4.480000e-16 97.1
3 TraesCS4B01G232300 chr4B 82.203 118 10 5 4940 5049 337742359 337742473 2.090000e-14 91.6
4 TraesCS4B01G232300 chr4B 100.000 47 0 0 2704 2750 660501042 660500996 2.700000e-13 87.9
5 TraesCS4B01G232300 chr4D 94.008 1185 34 19 866 2022 394151863 394150688 0.000000e+00 1760.0
6 TraesCS4B01G232300 chr4D 92.675 628 45 1 3563 4190 394150215 394149589 0.000000e+00 904.0
7 TraesCS4B01G232300 chr4D 91.993 537 26 9 4261 4787 394148316 394147787 0.000000e+00 737.0
8 TraesCS4B01G232300 chr4D 90.336 476 36 3 3062 3530 394150690 394150218 2.780000e-172 616.0
9 TraesCS4B01G232300 chr4D 94.792 384 20 0 5055 5438 394147077 394146694 2.800000e-167 599.0
10 TraesCS4B01G232300 chr4D 90.833 120 11 0 4769 4888 394147749 394147630 1.570000e-35 161.0
11 TraesCS4B01G232300 chr4A 92.111 938 34 23 871 1785 75436216 75435296 0.000000e+00 1286.0
12 TraesCS4B01G232300 chr4A 91.888 752 54 2 3195 3939 75431915 75431164 0.000000e+00 1044.0
13 TraesCS4B01G232300 chr4A 91.452 737 49 9 3938 4666 75430774 75430044 0.000000e+00 1000.0
14 TraesCS4B01G232300 chr4A 93.750 384 17 2 5055 5438 75429274 75428898 2.200000e-158 569.0
15 TraesCS4B01G232300 chr4A 94.422 251 12 2 1757 2006 75432598 75432349 8.540000e-103 385.0
16 TraesCS4B01G232300 chr4A 91.892 222 16 1 4669 4888 75429799 75429578 5.290000e-80 309.0
17 TraesCS4B01G232300 chr4A 80.153 131 13 6 4915 5033 522959147 522959018 9.700000e-13 86.1
18 TraesCS4B01G232300 chr7A 98.057 669 13 0 2021 2689 27223797 27223129 0.000000e+00 1164.0
19 TraesCS4B01G232300 chr7A 97.015 670 20 0 2020 2689 486232926 486233595 0.000000e+00 1127.0
20 TraesCS4B01G232300 chr7A 93.370 362 15 3 2704 3060 486235362 486235719 1.340000e-145 527.0
21 TraesCS4B01G232300 chr7A 92.663 368 18 2 2704 3064 27220159 27219794 6.240000e-144 521.0
22 TraesCS4B01G232300 chr7A 89.347 291 14 5 2019 2309 166079548 166079821 3.120000e-92 350.0
23 TraesCS4B01G232300 chr6B 97.305 668 18 0 2022 2689 387165926 387165259 0.000000e+00 1134.0
24 TraesCS4B01G232300 chr6B 91.599 369 17 5 2704 3060 387162623 387162257 1.050000e-136 497.0
25 TraesCS4B01G232300 chr6B 79.730 148 23 5 4892 5033 66778677 66778823 3.470000e-17 100.0
26 TraesCS4B01G232300 chr3D 96.861 669 21 0 2021 2689 357440678 357441346 0.000000e+00 1120.0
27 TraesCS4B01G232300 chr3D 90.774 672 45 7 143 810 61929486 61928828 0.000000e+00 881.0
28 TraesCS4B01G232300 chr3D 83.654 416 43 19 1045 1440 7433115 7433525 8.610000e-98 368.0
29 TraesCS4B01G232300 chr3D 89.180 305 20 5 2693 2997 357634584 357634875 8.610000e-98 368.0
30 TraesCS4B01G232300 chr3D 90.566 159 15 0 3301 3459 7434311 7434469 1.530000e-50 211.0
31 TraesCS4B01G232300 chr3D 89.189 74 6 2 4911 4983 153507057 153507129 2.090000e-14 91.6
32 TraesCS4B01G232300 chr1A 91.688 770 32 14 68 832 565153056 565152314 0.000000e+00 1038.0
33 TraesCS4B01G232300 chr1A 93.467 597 32 6 239 832 8731600 8731008 0.000000e+00 880.0
34 TraesCS4B01G232300 chr1A 94.828 58 0 2 68 123 8731888 8731832 2.700000e-13 87.9
35 TraesCS4B01G232300 chr3B 90.546 751 53 12 95 832 766097920 766097175 0.000000e+00 977.0
36 TraesCS4B01G232300 chr3B 82.082 413 47 23 1045 1432 9439359 9439769 1.460000e-85 327.0
37 TraesCS4B01G232300 chr3B 91.549 142 12 0 3318 3459 9440630 9440771 4.300000e-46 196.0
38 TraesCS4B01G232300 chr3B 80.000 145 27 2 3316 3459 780553279 780553136 7.450000e-19 106.0
39 TraesCS4B01G232300 chr3B 89.189 74 6 2 4911 4983 225173231 225173303 2.090000e-14 91.6
40 TraesCS4B01G232300 chr2A 92.708 672 36 10 175 842 674578070 674578732 0.000000e+00 957.0
41 TraesCS4B01G232300 chr2A 92.560 672 37 10 175 842 674693068 674693730 0.000000e+00 952.0
42 TraesCS4B01G232300 chr2A 91.716 676 40 11 175 845 674786761 674787425 0.000000e+00 924.0
43 TraesCS4B01G232300 chr2A 90.659 182 15 2 2017 2197 73550213 73550393 1.960000e-59 241.0
44 TraesCS4B01G232300 chr2A 83.750 160 24 2 2019 2177 655678463 655678621 3.390000e-32 150.0
45 TraesCS4B01G232300 chr2B 90.603 713 47 15 143 841 77331756 77331050 0.000000e+00 928.0
46 TraesCS4B01G232300 chr2B 95.584 385 14 2 2015 2396 521639952 521640336 1.000000e-171 614.0
47 TraesCS4B01G232300 chr2B 89.922 387 29 1 2685 3061 521642448 521642834 1.760000e-134 490.0
48 TraesCS4B01G232300 chr2B 79.901 607 95 22 2088 2688 369503870 369504455 2.340000e-113 420.0
49 TraesCS4B01G232300 chr2B 74.825 286 50 12 3186 3459 432934949 432935224 5.760000e-20 110.0
50 TraesCS4B01G232300 chr6D 86.312 884 57 37 1 839 15117286 15116422 0.000000e+00 904.0
51 TraesCS4B01G232300 chr6D 96.970 66 1 1 866 930 14353634 14353569 5.760000e-20 110.0
52 TraesCS4B01G232300 chr6A 89.769 694 60 10 142 832 162277248 162277933 0.000000e+00 878.0
53 TraesCS4B01G232300 chr5A 98.204 501 9 0 2189 2689 17270127 17270627 0.000000e+00 876.0
54 TraesCS4B01G232300 chr5A 92.954 369 15 4 2704 3065 17273376 17273740 1.340000e-145 527.0
55 TraesCS4B01G232300 chr7D 93.671 474 19 2 2014 2476 565216777 565217250 0.000000e+00 699.0
56 TraesCS4B01G232300 chr7D 81.607 473 54 17 3328 3775 93781559 93781095 1.440000e-95 361.0
57 TraesCS4B01G232300 chr7D 94.149 188 8 3 2694 2881 565218286 565218470 3.210000e-72 283.0
58 TraesCS4B01G232300 chr7D 74.468 282 57 11 3186 3459 466669827 466669553 2.070000e-19 108.0
59 TraesCS4B01G232300 chr5B 96.809 376 12 0 2688 3063 3924668 3924293 3.580000e-176 628.0
60 TraesCS4B01G232300 chr7B 92.330 352 19 4 2688 3031 750179609 750179960 1.360000e-135 494.0
61 TraesCS4B01G232300 chr7B 87.941 340 40 1 2340 2679 158311244 158310906 3.050000e-107 399.0
62 TraesCS4B01G232300 chrUn 91.159 328 15 5 2704 3019 387503505 387503830 3.010000e-117 433.0
63 TraesCS4B01G232300 chrUn 79.720 143 14 9 4918 5049 88784847 88784709 7.500000e-14 89.8
64 TraesCS4B01G232300 chr2D 79.470 604 105 14 2089 2688 293714710 293715298 1.410000e-110 411.0
65 TraesCS4B01G232300 chr2D 81.319 455 47 16 2019 2473 261738861 261738445 8.730000e-88 335.0
66 TraesCS4B01G232300 chr2D 90.055 181 18 0 2017 2197 74156652 74156832 9.110000e-58 235.0
67 TraesCS4B01G232300 chr2D 81.538 130 11 6 4929 5049 246704683 246704558 1.610000e-15 95.3
68 TraesCS4B01G232300 chr5D 88.589 333 38 0 2351 2683 522481259 522481591 6.560000e-109 405.0
69 TraesCS4B01G232300 chr3A 82.944 428 45 20 1045 1447 12855655 12855231 1.440000e-95 361.0
70 TraesCS4B01G232300 chr3A 91.195 159 14 0 3301 3459 12854374 12854216 3.300000e-52 217.0
71 TraesCS4B01G232300 chr3A 86.667 90 8 4 4911 4999 176148176 176148090 4.480000e-16 97.1
72 TraesCS4B01G232300 chr1B 82.877 146 11 7 4915 5050 26268793 26268934 9.570000e-23 119.0
73 TraesCS4B01G232300 chr1D 80.952 147 12 8 4915 5049 397047719 397047577 9.640000e-18 102.0
74 TraesCS4B01G232300 chr1D 89.231 65 3 2 4986 5049 494305024 494305085 1.620000e-10 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 TraesCS4B01G232300 chr4B 483765498 483770935 5437 True 10043.000000 10043 100.000000 1 5438 1 chr4B.!!$R1 5437
1 TraesCS4B01G232300 chr4D 394146694 394151863 5169 True 796.166667 1760 92.439500 866 5438 6 chr4D.!!$R1 4572
2 TraesCS4B01G232300 chr4A 75428898 75436216 7318 True 765.500000 1286 92.585833 871 5438 6 chr4A.!!$R2 4567
3 TraesCS4B01G232300 chr7A 27219794 27223797 4003 True 842.500000 1164 95.360000 2021 3064 2 chr7A.!!$R1 1043
4 TraesCS4B01G232300 chr7A 486232926 486235719 2793 False 827.000000 1127 95.192500 2020 3060 2 chr7A.!!$F2 1040
5 TraesCS4B01G232300 chr6B 387162257 387165926 3669 True 815.500000 1134 94.452000 2022 3060 2 chr6B.!!$R1 1038
6 TraesCS4B01G232300 chr3D 357440678 357441346 668 False 1120.000000 1120 96.861000 2021 2689 1 chr3D.!!$F2 668
7 TraesCS4B01G232300 chr3D 61928828 61929486 658 True 881.000000 881 90.774000 143 810 1 chr3D.!!$R1 667
8 TraesCS4B01G232300 chr3D 7433115 7434469 1354 False 289.500000 368 87.110000 1045 3459 2 chr3D.!!$F4 2414
9 TraesCS4B01G232300 chr1A 565152314 565153056 742 True 1038.000000 1038 91.688000 68 832 1 chr1A.!!$R1 764
10 TraesCS4B01G232300 chr1A 8731008 8731888 880 True 483.950000 880 94.147500 68 832 2 chr1A.!!$R2 764
11 TraesCS4B01G232300 chr3B 766097175 766097920 745 True 977.000000 977 90.546000 95 832 1 chr3B.!!$R1 737
12 TraesCS4B01G232300 chr3B 9439359 9440771 1412 False 261.500000 327 86.815500 1045 3459 2 chr3B.!!$F2 2414
13 TraesCS4B01G232300 chr2A 674578070 674578732 662 False 957.000000 957 92.708000 175 842 1 chr2A.!!$F3 667
14 TraesCS4B01G232300 chr2A 674693068 674693730 662 False 952.000000 952 92.560000 175 842 1 chr2A.!!$F4 667
15 TraesCS4B01G232300 chr2A 674786761 674787425 664 False 924.000000 924 91.716000 175 845 1 chr2A.!!$F5 670
16 TraesCS4B01G232300 chr2B 77331050 77331756 706 True 928.000000 928 90.603000 143 841 1 chr2B.!!$R1 698
17 TraesCS4B01G232300 chr2B 521639952 521642834 2882 False 552.000000 614 92.753000 2015 3061 2 chr2B.!!$F3 1046
18 TraesCS4B01G232300 chr2B 369503870 369504455 585 False 420.000000 420 79.901000 2088 2688 1 chr2B.!!$F1 600
19 TraesCS4B01G232300 chr6D 15116422 15117286 864 True 904.000000 904 86.312000 1 839 1 chr6D.!!$R2 838
20 TraesCS4B01G232300 chr6A 162277248 162277933 685 False 878.000000 878 89.769000 142 832 1 chr6A.!!$F1 690
21 TraesCS4B01G232300 chr5A 17270127 17273740 3613 False 701.500000 876 95.579000 2189 3065 2 chr5A.!!$F1 876
22 TraesCS4B01G232300 chr7D 565216777 565218470 1693 False 491.000000 699 93.910000 2014 2881 2 chr7D.!!$F1 867
23 TraesCS4B01G232300 chr2D 293714710 293715298 588 False 411.000000 411 79.470000 2089 2688 1 chr2D.!!$F2 599
24 TraesCS4B01G232300 chr3A 12854216 12855655 1439 True 289.000000 361 87.069500 1045 3459 2 chr3A.!!$R2 2414

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
19 20 0.255890 GGTGCAGCTGATTTAGGGGA 59.744 55.0 20.43 0.00 0.00 4.81 F
864 1029 0.320374 ATTCGCGTCACCCTCAAGAA 59.680 50.0 5.77 0.00 0.00 2.52 F
2104 5489 0.254178 GCTTCTCCCAGAATCAGCCA 59.746 55.0 0.00 0.00 33.13 4.75 F
2942 10123 1.208259 GACCCAAAACGCTGCTTTTG 58.792 50.0 20.52 20.52 39.76 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 5384 0.405585 ACTGGGCCTAAGTTGCATGT 59.594 50.0 4.53 0.0 0.00 3.21 R
2757 9938 0.173481 CTGTCCTCGCTCGATTTCCA 59.827 55.0 0.00 0.0 0.00 3.53 R
3597 11100 0.247576 CTCGAGAAATGCTTGCTGCG 60.248 55.0 6.58 0.0 46.63 5.18 R
4924 14428 0.323629 TAAAGTTGCCGTCCTCAGGG 59.676 55.0 0.00 0.0 0.00 4.45 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
19 20 0.255890 GGTGCAGCTGATTTAGGGGA 59.744 55.000 20.43 0.00 0.00 4.81
52 53 5.819825 AAAAGACAGTTGAAGGTTCAGAC 57.180 39.130 0.00 0.00 38.61 3.51
53 54 4.762289 AAGACAGTTGAAGGTTCAGACT 57.238 40.909 0.00 0.00 38.61 3.24
54 55 5.871396 AAGACAGTTGAAGGTTCAGACTA 57.129 39.130 7.02 0.00 38.61 2.59
55 56 5.203060 AGACAGTTGAAGGTTCAGACTAC 57.797 43.478 7.02 0.00 38.61 2.73
56 57 4.649674 AGACAGTTGAAGGTTCAGACTACA 59.350 41.667 7.02 0.00 38.61 2.74
57 58 4.950050 ACAGTTGAAGGTTCAGACTACAG 58.050 43.478 7.02 0.00 38.61 2.74
58 59 4.649674 ACAGTTGAAGGTTCAGACTACAGA 59.350 41.667 7.02 0.00 38.61 3.41
59 60 5.221342 ACAGTTGAAGGTTCAGACTACAGAG 60.221 44.000 7.02 0.00 38.61 3.35
60 61 5.010112 CAGTTGAAGGTTCAGACTACAGAGA 59.990 44.000 7.02 0.00 38.61 3.10
62 63 5.455056 TGAAGGTTCAGACTACAGAGAAC 57.545 43.478 0.00 0.00 39.59 3.01
64 65 5.362717 TGAAGGTTCAGACTACAGAGAACAA 59.637 40.000 0.00 0.00 41.49 2.83
66 67 6.426646 AGGTTCAGACTACAGAGAACAAAT 57.573 37.500 0.00 0.00 41.49 2.32
67 68 7.540474 AGGTTCAGACTACAGAGAACAAATA 57.460 36.000 0.00 0.00 41.49 1.40
69 70 6.814146 GGTTCAGACTACAGAGAACAAATAGG 59.186 42.308 0.00 0.00 41.49 2.57
70 71 5.967088 TCAGACTACAGAGAACAAATAGGC 58.033 41.667 0.00 0.00 0.00 3.93
72 73 4.463186 AGACTACAGAGAACAAATAGGCGT 59.537 41.667 0.00 0.00 0.00 5.68
124 141 2.573462 AGATTTAGAACAGAGGGCAGCA 59.427 45.455 0.00 0.00 0.00 4.41
125 142 2.479566 TTTAGAACAGAGGGCAGCAG 57.520 50.000 0.00 0.00 0.00 4.24
126 143 0.615331 TTAGAACAGAGGGCAGCAGG 59.385 55.000 0.00 0.00 0.00 4.85
127 144 1.267574 TAGAACAGAGGGCAGCAGGG 61.268 60.000 0.00 0.00 0.00 4.45
263 396 3.726631 GAGGACGAGTCGCAGCGAG 62.727 68.421 20.23 9.59 36.23 5.03
381 515 1.075151 GACCTAGGGGGAGGACCTG 60.075 68.421 14.81 0.00 39.15 4.00
388 522 3.075641 GGGAGGACCTGACCGGAC 61.076 72.222 9.46 1.07 36.31 4.79
389 523 3.450115 GGAGGACCTGACCGGACG 61.450 72.222 9.46 0.00 36.31 4.79
390 524 3.450115 GAGGACCTGACCGGACGG 61.450 72.222 9.46 7.25 42.03 4.79
437 573 4.148825 GAGGATGGTGGCGCGACT 62.149 66.667 22.08 2.92 0.00 4.18
440 576 2.171725 GGATGGTGGCGCGACTTAC 61.172 63.158 22.08 2.90 0.00 2.34
509 645 3.916438 TTGCCGCAGTAGGAGGGGA 62.916 63.158 0.00 0.00 41.25 4.81
578 737 1.316706 CGCCCTCTCGTTCCTCTCTT 61.317 60.000 0.00 0.00 0.00 2.85
624 789 0.466124 GGAAGAGGCTGAAGCGGTAT 59.534 55.000 0.00 0.00 43.26 2.73
842 1007 3.685836 AACGCAGTGTGAAAGTAAACC 57.314 42.857 11.43 0.00 45.00 3.27
843 1008 1.595794 ACGCAGTGTGAAAGTAAACCG 59.404 47.619 11.43 0.00 42.51 4.44
844 1009 1.595794 CGCAGTGTGAAAGTAAACCGT 59.404 47.619 0.00 0.00 0.00 4.83
845 1010 2.796031 CGCAGTGTGAAAGTAAACCGTA 59.204 45.455 0.00 0.00 0.00 4.02
846 1011 3.430895 CGCAGTGTGAAAGTAAACCGTAT 59.569 43.478 0.00 0.00 0.00 3.06
847 1012 4.084223 CGCAGTGTGAAAGTAAACCGTATT 60.084 41.667 0.00 0.00 0.00 1.89
848 1013 5.379827 GCAGTGTGAAAGTAAACCGTATTC 58.620 41.667 0.00 0.00 0.00 1.75
849 1014 5.605327 CAGTGTGAAAGTAAACCGTATTCG 58.395 41.667 0.00 0.00 0.00 3.34
850 1015 4.151157 AGTGTGAAAGTAAACCGTATTCGC 59.849 41.667 0.00 0.00 35.54 4.70
851 1016 3.121611 TGTGAAAGTAAACCGTATTCGCG 59.878 43.478 0.00 0.00 34.21 5.87
852 1017 3.121778 GTGAAAGTAAACCGTATTCGCGT 59.878 43.478 5.77 0.00 35.54 6.01
853 1018 3.364621 TGAAAGTAAACCGTATTCGCGTC 59.635 43.478 5.77 0.00 35.54 5.19
854 1019 2.634982 AGTAAACCGTATTCGCGTCA 57.365 45.000 5.77 0.00 35.54 4.35
855 1020 2.253603 AGTAAACCGTATTCGCGTCAC 58.746 47.619 5.77 1.43 35.54 3.67
856 1021 1.321445 GTAAACCGTATTCGCGTCACC 59.679 52.381 5.77 0.00 35.54 4.02
857 1022 1.015607 AAACCGTATTCGCGTCACCC 61.016 55.000 5.77 0.00 35.54 4.61
858 1023 1.880819 AACCGTATTCGCGTCACCCT 61.881 55.000 5.77 0.00 35.54 4.34
859 1024 1.588139 CCGTATTCGCGTCACCCTC 60.588 63.158 5.77 0.00 35.54 4.30
860 1025 1.138036 CGTATTCGCGTCACCCTCA 59.862 57.895 5.77 0.00 0.00 3.86
861 1026 0.457166 CGTATTCGCGTCACCCTCAA 60.457 55.000 5.77 0.00 0.00 3.02
862 1027 1.278238 GTATTCGCGTCACCCTCAAG 58.722 55.000 5.77 0.00 0.00 3.02
863 1028 1.135199 GTATTCGCGTCACCCTCAAGA 60.135 52.381 5.77 0.00 0.00 3.02
864 1029 0.320374 ATTCGCGTCACCCTCAAGAA 59.680 50.000 5.77 0.00 0.00 2.52
869 1034 0.868406 CGTCACCCTCAAGAACAAGC 59.132 55.000 0.00 0.00 0.00 4.01
1298 1473 1.537202 GGTCTGTGGACACTGAATTGC 59.463 52.381 12.61 2.38 43.77 3.56
1362 1555 1.107538 TCACGGATCGGATGGAGGTC 61.108 60.000 7.35 0.00 0.00 3.85
1509 1729 3.467776 GGATGGTCCTGCTGTTCTC 57.532 57.895 0.00 0.00 32.53 2.87
1512 1732 2.286872 GATGGTCCTGCTGTTCTCATG 58.713 52.381 0.00 0.00 0.00 3.07
1527 1751 5.764686 TGTTCTCATGTTTTGCTGTATGAGT 59.235 36.000 11.48 0.00 44.21 3.41
1558 1782 1.470098 AGCTGACAATGCGAACAATCC 59.530 47.619 0.00 0.00 35.28 3.01
1721 1955 8.169977 ACGGATTGCACAATTTTCTCATATAT 57.830 30.769 0.00 0.00 0.00 0.86
1722 1956 9.283768 ACGGATTGCACAATTTTCTCATATATA 57.716 29.630 0.00 0.00 0.00 0.86
1727 1961 8.995027 TGCACAATTTTCTCATATATAACCCT 57.005 30.769 0.00 0.00 0.00 4.34
1765 4725 4.028993 TCATGGTTGGAACTTAGAACCC 57.971 45.455 0.00 0.00 38.75 4.11
1794 4754 6.985645 ACTTTAAGCAGAACAATTGCAATCAA 59.014 30.769 13.38 0.00 43.92 2.57
1855 4815 2.030628 GGTTCACCATTGTGTTAACCCG 60.031 50.000 2.48 0.00 40.74 5.28
1875 4835 1.607628 GATGCTGGTGATTGATGAGGC 59.392 52.381 0.00 0.00 0.00 4.70
1942 4916 4.192317 GGAGCAGAGTGTTAACCCAATAG 58.808 47.826 2.48 0.00 0.00 1.73
1970 5344 6.931281 TGTGAGTTATGAGGTTTCTCTTTGAG 59.069 38.462 0.00 0.00 40.58 3.02
1971 5345 6.931840 GTGAGTTATGAGGTTTCTCTTTGAGT 59.068 38.462 0.00 0.00 40.58 3.41
2018 5393 6.712547 AGTTAGCTCTTTTTCTACATGCAACT 59.287 34.615 0.00 0.00 0.00 3.16
2104 5489 0.254178 GCTTCTCCCAGAATCAGCCA 59.746 55.000 0.00 0.00 33.13 4.75
2276 5665 9.884465 ACGATTTATGAATATTTTAGCTTGCTC 57.116 29.630 0.00 0.00 0.00 4.26
2396 5785 3.001330 GGTAGCAATAGCATCACGTGTTC 59.999 47.826 16.51 5.92 45.49 3.18
2760 9941 3.071206 GCTGGAGAGCGAGGTGGA 61.071 66.667 0.00 0.00 34.87 4.02
2873 10054 3.618997 CGTGCTGAAATAGGGGTACAGTT 60.619 47.826 0.00 0.00 0.00 3.16
2942 10123 1.208259 GACCCAAAACGCTGCTTTTG 58.792 50.000 20.52 20.52 39.76 2.44
3014 10195 6.532365 AACGAGTTCTTTCTAGCTTTTGAG 57.468 37.500 0.00 0.00 0.00 3.02
3066 10247 4.156739 GTCAAAAGAACTGGGCCTTAGATG 59.843 45.833 4.53 0.00 0.00 2.90
3100 10281 7.235399 ACCAGAAATTGAATCTTTGGTTGGTAT 59.765 33.333 0.00 0.00 0.00 2.73
3126 10307 2.262423 AACCACTCCTGCTCTGTTTC 57.738 50.000 0.00 0.00 0.00 2.78
3131 10312 4.042187 ACCACTCCTGCTCTGTTTCTTTAT 59.958 41.667 0.00 0.00 0.00 1.40
3134 10315 4.287067 ACTCCTGCTCTGTTTCTTTATCCA 59.713 41.667 0.00 0.00 0.00 3.41
3137 10318 6.957631 TCCTGCTCTGTTTCTTTATCCAATA 58.042 36.000 0.00 0.00 0.00 1.90
3198 10379 7.180322 TCTGTGTGGTAATATAAAACCGGTA 57.820 36.000 8.00 0.00 38.70 4.02
3269 10765 7.436080 CCATGTGCATATTTTGAAGTGATTACC 59.564 37.037 0.00 0.00 0.00 2.85
3279 10775 7.875327 TTTGAAGTGATTACCCTATAAAGCC 57.125 36.000 0.00 0.00 0.00 4.35
3282 10778 6.157994 TGAAGTGATTACCCTATAAAGCCTGT 59.842 38.462 0.00 0.00 0.00 4.00
3283 10779 6.576778 AGTGATTACCCTATAAAGCCTGTT 57.423 37.500 0.00 0.00 0.00 3.16
3308 10804 8.650143 TTTAATTAGATTTTGACTCCTGGCTT 57.350 30.769 0.00 0.00 0.00 4.35
3391 10893 9.431887 AGCAAAAGTTAATAGAGTTGATTCGTA 57.568 29.630 0.00 0.00 0.00 3.43
3405 10907 7.768240 AGTTGATTCGTATGGGGAAAATAAAC 58.232 34.615 0.00 0.00 0.00 2.01
3478 10980 9.561069 AAAATGTGAGTTGTAGTGTCTCTATTT 57.439 29.630 0.00 0.00 32.79 1.40
3482 10984 8.082852 TGTGAGTTGTAGTGTCTCTATTTCTTC 58.917 37.037 0.00 0.00 0.00 2.87
3494 10996 7.148222 TGTCTCTATTTCTTCAGTTAGGACTCG 60.148 40.741 0.00 0.00 32.54 4.18
3498 11000 6.591750 ATTTCTTCAGTTAGGACTCGAGAA 57.408 37.500 21.68 0.00 34.53 2.87
3509 11011 4.065789 AGGACTCGAGAATTCAAACCAAC 58.934 43.478 21.68 0.00 0.00 3.77
3542 11045 5.730550 TCAGAACGCACTATATTTCTTGGT 58.269 37.500 0.00 0.00 0.00 3.67
3548 11051 8.951787 AACGCACTATATTTCTTGGTAATACA 57.048 30.769 0.00 0.00 0.00 2.29
3574 11077 5.049828 TGATATTAAGACCATGCTGTGACG 58.950 41.667 0.00 0.00 0.00 4.35
3582 11085 4.083324 AGACCATGCTGTGACGTTATTTTG 60.083 41.667 0.00 0.00 0.00 2.44
3597 11100 7.934594 ACGTTATTTTGCGTTATTGAAATGTC 58.065 30.769 0.00 0.00 38.21 3.06
3607 11110 0.667453 TTGAAATGTCGCAGCAAGCA 59.333 45.000 0.00 0.00 46.13 3.91
3613 11116 0.518636 TGTCGCAGCAAGCATTTCTC 59.481 50.000 0.00 0.00 46.13 2.87
3634 11137 6.390721 TCTCGAGGAAATAGAGAAAACTGTG 58.609 40.000 13.56 0.00 36.81 3.66
3770 11273 2.029828 CACGAGAAAGGTCAGTAGCACT 60.030 50.000 0.00 0.00 0.00 4.40
3788 11291 4.002982 GCACTAGGATGTGAATGTTGTGA 58.997 43.478 0.00 0.00 40.12 3.58
3789 11292 4.142816 GCACTAGGATGTGAATGTTGTGAC 60.143 45.833 0.00 0.00 40.12 3.67
3803 11306 3.244875 TGTTGTGACCTTGTGATGCCTAT 60.245 43.478 0.00 0.00 0.00 2.57
3819 11322 8.995220 GTGATGCCTATTATTTATCCGTTTGTA 58.005 33.333 0.00 0.00 0.00 2.41
3837 11340 6.951530 CGTTTGTATATTTCGTGATTTCGTGT 59.048 34.615 0.00 0.00 0.00 4.49
3845 11348 2.034179 TCGTGATTTCGTGTGACTGAGT 59.966 45.455 0.00 0.00 0.00 3.41
3850 11353 5.405571 GTGATTTCGTGTGACTGAGTTGTAT 59.594 40.000 0.00 0.00 0.00 2.29
3857 11360 4.692625 GTGTGACTGAGTTGTATCTGCATT 59.307 41.667 0.00 0.00 0.00 3.56
3915 11418 9.019656 TCTTATTTTAGAACATGCTGCCTTTTA 57.980 29.630 0.00 0.00 0.00 1.52
3916 11419 8.980143 TTATTTTAGAACATGCTGCCTTTTAC 57.020 30.769 0.00 0.00 0.00 2.01
3963 11857 9.802039 AAGTGTAAACCCTATCTAAAACAATGA 57.198 29.630 0.00 0.00 0.00 2.57
4026 11920 8.981647 CAAAGCAAAGCTAATACTGAATTTTGT 58.018 29.630 0.00 0.00 38.25 2.83
4027 11921 8.524870 AAGCAAAGCTAATACTGAATTTTGTG 57.475 30.769 0.00 0.00 38.25 3.33
4081 11975 2.092267 AGACATGGCCATGCTCAATACA 60.092 45.455 39.74 0.00 42.39 2.29
4082 11976 2.889045 GACATGGCCATGCTCAATACAT 59.111 45.455 39.74 20.91 42.39 2.29
4149 12043 9.388506 AGGAAATACTGATAAACATGAGTCAAG 57.611 33.333 0.00 0.00 0.00 3.02
4175 12069 1.033746 GCATAGGGCTGCTGCTTGAA 61.034 55.000 15.64 0.00 39.12 2.69
4190 12084 6.201425 TGCTGCTTGAAAATCATTTTGAGAAC 59.799 34.615 0.00 0.00 31.94 3.01
4205 13348 3.963665 TGAGAACGTGCCATTGAAAAAG 58.036 40.909 0.00 0.00 0.00 2.27
4207 13350 4.222114 GAGAACGTGCCATTGAAAAAGAG 58.778 43.478 0.00 0.00 0.00 2.85
4210 13353 4.853924 ACGTGCCATTGAAAAAGAGATT 57.146 36.364 0.00 0.00 0.00 2.40
4243 13386 3.751479 AACAGGATGAAAGTTTTGCCC 57.249 42.857 0.00 0.00 39.69 5.36
4249 13392 4.898861 AGGATGAAAGTTTTGCCCTTTGTA 59.101 37.500 0.00 0.00 32.47 2.41
4253 13396 5.841810 TGAAAGTTTTGCCCTTTGTATCTG 58.158 37.500 0.00 0.00 32.47 2.90
4254 13397 4.871933 AAGTTTTGCCCTTTGTATCTGG 57.128 40.909 0.00 0.00 0.00 3.86
4255 13398 3.165071 AGTTTTGCCCTTTGTATCTGGG 58.835 45.455 0.00 0.00 43.62 4.45
4277 13420 3.798878 GGCTCTTTCAAACTTGCTTTCAC 59.201 43.478 0.00 0.00 0.00 3.18
4279 13422 4.677779 GCTCTTTCAAACTTGCTTTCACCA 60.678 41.667 0.00 0.00 0.00 4.17
4286 13429 3.018423 ACTTGCTTTCACCAAAGGTCT 57.982 42.857 0.00 0.00 39.69 3.85
4304 13447 7.454260 AAGGTCTTTGATCCTTATGTTTGTC 57.546 36.000 0.00 0.00 41.55 3.18
4402 13545 4.396166 CAGCATATCCCCGAATCAATAACC 59.604 45.833 0.00 0.00 0.00 2.85
4468 13611 2.287915 CCCAAAGTGTTCGAGTGTTGAG 59.712 50.000 0.00 0.00 0.00 3.02
4529 13677 3.383825 ACTCTGTCGTAGGTCTGTTGTTT 59.616 43.478 0.00 0.00 0.00 2.83
4614 13763 6.597562 TCCTGTTGTATAGGTTGTTCTTGTT 58.402 36.000 0.00 0.00 36.67 2.83
4615 13764 7.057894 TCCTGTTGTATAGGTTGTTCTTGTTT 58.942 34.615 0.00 0.00 36.67 2.83
4805 14259 6.671614 TTTTACTGGTTTCATAGGCATACG 57.328 37.500 0.00 0.00 0.00 3.06
4824 14278 8.015658 GGCATACGATAAGTGAAAAATCATACC 58.984 37.037 0.00 0.00 0.00 2.73
4863 14317 5.912892 ACCAAAAACCGTTGAAAATCAGAT 58.087 33.333 0.00 0.00 0.00 2.90
4866 14320 6.257630 CCAAAAACCGTTGAAAATCAGATGTT 59.742 34.615 0.00 0.00 0.00 2.71
4868 14322 5.514274 AACCGTTGAAAATCAGATGTTGT 57.486 34.783 0.00 0.00 0.00 3.32
4884 14338 8.681806 TCAGATGTTGTACATTTTCAAACTGAA 58.318 29.630 0.00 0.00 39.27 3.02
4888 14342 7.254852 TGTTGTACATTTTCAAACTGAAGGAC 58.745 34.615 0.00 0.00 37.70 3.85
4889 14343 6.385649 TGTACATTTTCAAACTGAAGGACC 57.614 37.500 0.00 0.00 37.70 4.46
4890 14344 4.937201 ACATTTTCAAACTGAAGGACCC 57.063 40.909 0.00 0.00 37.70 4.46
4891 14345 4.285863 ACATTTTCAAACTGAAGGACCCA 58.714 39.130 0.00 0.00 37.70 4.51
4892 14346 4.342092 ACATTTTCAAACTGAAGGACCCAG 59.658 41.667 0.00 0.00 37.70 4.45
4893 14347 1.981256 TTCAAACTGAAGGACCCAGC 58.019 50.000 0.00 0.00 35.14 4.85
4894 14348 0.843309 TCAAACTGAAGGACCCAGCA 59.157 50.000 0.00 0.00 35.14 4.41
4899 14353 2.962859 ACTGAAGGACCCAGCAATTTT 58.037 42.857 0.00 0.00 35.14 1.82
4900 14354 2.629617 ACTGAAGGACCCAGCAATTTTG 59.370 45.455 0.00 0.00 35.14 2.44
4923 14427 8.911918 TTGCCTTATGTTTGAGAAGTTTAGTA 57.088 30.769 0.00 0.00 0.00 1.82
4924 14428 8.319143 TGCCTTATGTTTGAGAAGTTTAGTAC 57.681 34.615 0.00 0.00 0.00 2.73
4933 14437 4.771054 TGAGAAGTTTAGTACCCTGAGGAC 59.229 45.833 0.00 0.00 36.73 3.85
4935 14439 2.454538 AGTTTAGTACCCTGAGGACGG 58.545 52.381 0.00 0.00 36.73 4.79
4966 14470 3.540314 TGTGAAGCATGGCAACTTTTT 57.460 38.095 7.47 0.00 37.61 1.94
4972 14476 3.871485 AGCATGGCAACTTTTTGTTTGA 58.129 36.364 0.00 0.00 36.63 2.69
4974 14478 4.883006 AGCATGGCAACTTTTTGTTTGAAT 59.117 33.333 0.00 0.00 36.63 2.57
4975 14479 4.971220 GCATGGCAACTTTTTGTTTGAATG 59.029 37.500 0.00 0.00 36.63 2.67
4976 14480 5.220815 GCATGGCAACTTTTTGTTTGAATGA 60.221 36.000 0.00 0.00 36.63 2.57
4977 14481 5.793026 TGGCAACTTTTTGTTTGAATGAC 57.207 34.783 0.00 0.00 36.63 3.06
4978 14482 5.240891 TGGCAACTTTTTGTTTGAATGACA 58.759 33.333 0.00 0.00 36.63 3.58
4979 14483 5.702670 TGGCAACTTTTTGTTTGAATGACAA 59.297 32.000 0.00 0.00 36.63 3.18
4980 14484 6.128336 TGGCAACTTTTTGTTTGAATGACAAG 60.128 34.615 0.00 0.00 36.63 3.16
4984 14504 7.595311 ACTTTTTGTTTGAATGACAAGTTCC 57.405 32.000 0.00 0.00 39.77 3.62
5013 14533 8.804688 TTTGTTTCGGATGGTAATTTTAGTTG 57.195 30.769 0.00 0.00 0.00 3.16
5025 14545 9.719279 TGGTAATTTTAGTTGTAAAAACGTCAG 57.281 29.630 0.00 0.00 40.65 3.51
5029 14549 7.935804 TTTTAGTTGTAAAAACGTCAGAACG 57.064 32.000 0.00 0.00 42.09 3.95
5038 14558 3.573569 CGTCAGAACGGTGGTGTTA 57.426 52.632 0.00 0.00 45.21 2.41
5039 14559 1.134226 CGTCAGAACGGTGGTGTTAC 58.866 55.000 0.00 0.00 45.21 2.50
5041 14561 2.800629 CGTCAGAACGGTGGTGTTACTT 60.801 50.000 0.00 0.00 45.21 2.24
5042 14562 2.798847 GTCAGAACGGTGGTGTTACTTC 59.201 50.000 0.00 0.00 30.75 3.01
5043 14563 2.431419 TCAGAACGGTGGTGTTACTTCA 59.569 45.455 0.00 0.00 30.75 3.02
5045 14565 3.186409 CAGAACGGTGGTGTTACTTCATG 59.814 47.826 0.00 0.00 30.75 3.07
5047 14567 0.802494 CGGTGGTGTTACTTCATGCC 59.198 55.000 0.00 0.00 0.00 4.40
5051 14571 3.367292 GGTGGTGTTACTTCATGCCATTG 60.367 47.826 0.00 0.00 0.00 2.82
5053 14573 3.505680 TGGTGTTACTTCATGCCATTGTC 59.494 43.478 0.00 0.00 0.00 3.18
5109 15024 1.142748 GATCCTCACTGCCGTCCTG 59.857 63.158 0.00 0.00 0.00 3.86
5188 15103 1.523711 CCGACGCCATTGCCACTAT 60.524 57.895 0.00 0.00 0.00 2.12
5189 15104 1.498865 CCGACGCCATTGCCACTATC 61.499 60.000 0.00 0.00 0.00 2.08
5353 15268 4.711949 CAGCCCTCCACGCTGCTT 62.712 66.667 0.00 0.00 46.54 3.91
5384 15299 1.075600 CTCCACCTCCTCTCCTCCC 60.076 68.421 0.00 0.00 0.00 4.30
5387 15302 1.687493 CACCTCCTCTCCTCCCACC 60.687 68.421 0.00 0.00 0.00 4.61
5389 15304 2.443016 CTCCTCTCCTCCCACCCG 60.443 72.222 0.00 0.00 0.00 5.28
5411 15326 4.824515 CTCTCCCCGACGCCCTCT 62.825 72.222 0.00 0.00 0.00 3.69
5417 15332 4.824515 CCGACGCCCTCTCCCTCT 62.825 72.222 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.621286 TCTGAACCTTCAACTGTCTTTTTAATC 58.379 33.333 0.00 0.00 36.64 1.75
26 27 8.406297 GTCTGAACCTTCAACTGTCTTTTTAAT 58.594 33.333 0.00 0.00 36.64 1.40
27 28 7.610305 AGTCTGAACCTTCAACTGTCTTTTTAA 59.390 33.333 3.53 0.00 36.64 1.52
32 33 4.762289 AGTCTGAACCTTCAACTGTCTT 57.238 40.909 3.53 0.00 36.64 3.01
41 42 5.455056 TGTTCTCTGTAGTCTGAACCTTC 57.545 43.478 0.00 0.00 38.29 3.46
43 44 5.871396 TTTGTTCTCTGTAGTCTGAACCT 57.129 39.130 0.00 0.00 38.29 3.50
45 46 6.311690 GCCTATTTGTTCTCTGTAGTCTGAAC 59.688 42.308 0.00 0.00 39.18 3.18
52 53 5.168569 TGAACGCCTATTTGTTCTCTGTAG 58.831 41.667 6.65 0.00 43.73 2.74
53 54 5.047590 TCTGAACGCCTATTTGTTCTCTGTA 60.048 40.000 6.65 0.00 43.73 2.74
54 55 3.997021 CTGAACGCCTATTTGTTCTCTGT 59.003 43.478 6.65 0.00 43.73 3.41
55 56 4.092091 GTCTGAACGCCTATTTGTTCTCTG 59.908 45.833 6.65 0.00 43.73 3.35
56 57 4.021016 AGTCTGAACGCCTATTTGTTCTCT 60.021 41.667 6.65 1.18 43.73 3.10
57 58 4.246458 AGTCTGAACGCCTATTTGTTCTC 58.754 43.478 6.65 0.00 43.73 2.87
58 59 4.273148 AGTCTGAACGCCTATTTGTTCT 57.727 40.909 6.65 0.00 43.73 3.01
59 60 4.927425 TGTAGTCTGAACGCCTATTTGTTC 59.073 41.667 0.00 0.00 43.67 3.18
60 61 4.890088 TGTAGTCTGAACGCCTATTTGTT 58.110 39.130 0.00 0.00 0.00 2.83
62 63 4.744570 TCTGTAGTCTGAACGCCTATTTG 58.255 43.478 0.00 0.00 0.00 2.32
64 65 4.270834 TCTCTGTAGTCTGAACGCCTATT 58.729 43.478 0.00 0.00 0.00 1.73
66 67 3.345508 TCTCTGTAGTCTGAACGCCTA 57.654 47.619 0.00 0.00 0.00 3.93
67 68 2.201921 TCTCTGTAGTCTGAACGCCT 57.798 50.000 0.00 0.00 0.00 5.52
69 70 3.284323 TGTTCTCTGTAGTCTGAACGC 57.716 47.619 0.00 0.00 40.93 4.84
70 71 5.041287 TGTTTGTTCTCTGTAGTCTGAACG 58.959 41.667 0.00 0.00 40.93 3.95
72 73 5.128827 ACCTGTTTGTTCTCTGTAGTCTGAA 59.871 40.000 0.00 0.00 0.00 3.02
150 167 0.894835 TACATCCACGAGAGCAGCAA 59.105 50.000 0.00 0.00 0.00 3.91
183 200 3.066190 CCCCGTCTACTGCGTCCA 61.066 66.667 0.00 0.00 0.00 4.02
331 464 2.504244 GTCTCCGGTCGACTTGCG 60.504 66.667 16.46 10.57 42.69 4.85
372 506 3.450115 CGTCCGGTCAGGTCCTCC 61.450 72.222 0.00 0.00 41.99 4.30
393 527 2.823147 CCTAGGTCGCGGACTCGT 60.823 66.667 6.13 0.00 38.89 4.18
394 528 2.513204 TCCTAGGTCGCGGACTCG 60.513 66.667 9.08 0.60 39.81 4.18
395 529 2.188161 CCTCCTAGGTCGCGGACTC 61.188 68.421 9.08 0.00 32.47 3.36
396 530 2.124236 CCTCCTAGGTCGCGGACT 60.124 66.667 9.08 7.56 32.47 3.85
398 532 2.192443 CTCCTCCTAGGTCGCGGA 59.808 66.667 9.08 9.73 36.53 5.54
437 573 2.103538 GTCCGCCGCATCTCGTAA 59.896 61.111 0.00 0.00 36.19 3.18
509 645 2.679287 GTCCGTTCCCTCTCCGGT 60.679 66.667 0.00 0.00 42.30 5.28
720 885 2.752903 GGCACTCCGTAATGAAACCAAT 59.247 45.455 0.00 0.00 0.00 3.16
835 1000 2.253603 GTGACGCGAATACGGTTTACT 58.746 47.619 15.93 0.00 40.15 2.24
839 1004 1.446618 GGGTGACGCGAATACGGTT 60.447 57.895 15.93 0.00 40.15 4.44
840 1005 2.182537 GGGTGACGCGAATACGGT 59.817 61.111 15.93 0.00 40.15 4.83
841 1006 1.588139 GAGGGTGACGCGAATACGG 60.588 63.158 15.93 0.00 40.15 4.02
842 1007 0.457166 TTGAGGGTGACGCGAATACG 60.457 55.000 15.93 0.00 42.93 3.06
843 1008 1.135199 TCTTGAGGGTGACGCGAATAC 60.135 52.381 15.93 8.44 0.00 1.89
844 1009 1.179152 TCTTGAGGGTGACGCGAATA 58.821 50.000 15.93 0.00 0.00 1.75
845 1010 0.320374 TTCTTGAGGGTGACGCGAAT 59.680 50.000 15.93 0.00 0.00 3.34
846 1011 0.599204 GTTCTTGAGGGTGACGCGAA 60.599 55.000 15.93 0.00 0.00 4.70
847 1012 1.006571 GTTCTTGAGGGTGACGCGA 60.007 57.895 15.93 0.00 0.00 5.87
848 1013 0.878523 TTGTTCTTGAGGGTGACGCG 60.879 55.000 3.53 3.53 0.00 6.01
849 1014 0.868406 CTTGTTCTTGAGGGTGACGC 59.132 55.000 0.00 0.00 0.00 5.19
850 1015 0.868406 GCTTGTTCTTGAGGGTGACG 59.132 55.000 0.00 0.00 0.00 4.35
851 1016 1.202818 AGGCTTGTTCTTGAGGGTGAC 60.203 52.381 0.00 0.00 0.00 3.67
852 1017 1.140312 AGGCTTGTTCTTGAGGGTGA 58.860 50.000 0.00 0.00 0.00 4.02
853 1018 1.882623 GAAGGCTTGTTCTTGAGGGTG 59.117 52.381 3.46 0.00 0.00 4.61
854 1019 1.202940 GGAAGGCTTGTTCTTGAGGGT 60.203 52.381 3.46 0.00 0.00 4.34
855 1020 1.202927 TGGAAGGCTTGTTCTTGAGGG 60.203 52.381 3.46 0.00 0.00 4.30
856 1021 2.276732 TGGAAGGCTTGTTCTTGAGG 57.723 50.000 3.46 0.00 0.00 3.86
857 1022 3.192212 GGATTGGAAGGCTTGTTCTTGAG 59.808 47.826 3.46 0.00 0.00 3.02
858 1023 3.157087 GGATTGGAAGGCTTGTTCTTGA 58.843 45.455 3.46 0.00 0.00 3.02
859 1024 2.892852 TGGATTGGAAGGCTTGTTCTTG 59.107 45.455 3.46 0.00 0.00 3.02
860 1025 2.893489 GTGGATTGGAAGGCTTGTTCTT 59.107 45.455 3.46 0.00 0.00 2.52
861 1026 2.519013 GTGGATTGGAAGGCTTGTTCT 58.481 47.619 3.46 0.00 0.00 3.01
862 1027 1.546029 GGTGGATTGGAAGGCTTGTTC 59.454 52.381 3.46 0.00 0.00 3.18
863 1028 1.133199 TGGTGGATTGGAAGGCTTGTT 60.133 47.619 3.46 0.00 0.00 2.83
864 1029 0.482446 TGGTGGATTGGAAGGCTTGT 59.518 50.000 3.46 0.00 0.00 3.16
869 1034 0.394899 GAGGCTGGTGGATTGGAAGG 60.395 60.000 0.00 0.00 0.00 3.46
1116 1284 1.860641 TGTCCTCCTTGCGGATCTTA 58.139 50.000 0.00 0.00 39.01 2.10
1245 1413 5.296283 CACAAGAGATGGATGATTCTTGACC 59.704 44.000 17.12 0.00 45.82 4.02
1434 1627 0.798776 AAATTGCGAGGCGACAGAAG 59.201 50.000 0.00 0.00 0.00 2.85
1506 1726 5.874810 GGTACTCATACAGCAAAACATGAGA 59.125 40.000 15.32 0.00 44.65 3.27
1509 1729 6.072508 ACAAGGTACTCATACAGCAAAACATG 60.073 38.462 0.00 0.00 38.49 3.21
1512 1732 5.334879 CCACAAGGTACTCATACAGCAAAAC 60.335 44.000 0.00 0.00 38.49 2.43
1558 1782 3.125316 CAAATTGCCTGGCATATTTCCG 58.875 45.455 24.03 14.51 38.76 4.30
1611 1835 7.600752 ACAAAGACTAGTAATCTGAAGAGCAAC 59.399 37.037 0.00 0.00 0.00 4.17
1661 1885 9.732130 AAGCTCTATTCTCTTCTTTGTACAATT 57.268 29.630 9.56 0.00 0.00 2.32
1662 1886 9.377312 GAAGCTCTATTCTCTTCTTTGTACAAT 57.623 33.333 9.56 0.00 34.83 2.71
1663 1887 7.819900 GGAAGCTCTATTCTCTTCTTTGTACAA 59.180 37.037 3.59 3.59 37.11 2.41
1680 1904 2.244695 TCCGTTCAGTTGGAAGCTCTA 58.755 47.619 0.00 0.00 35.82 2.43
1681 1905 1.048601 TCCGTTCAGTTGGAAGCTCT 58.951 50.000 0.00 0.00 35.82 4.09
1765 4725 4.851558 GCAATTGTTCTGCTTAAAGTACCG 59.148 41.667 7.40 0.00 36.84 4.02
1794 4754 2.662535 TGCCATGCCATATGCTAGTT 57.337 45.000 0.00 0.00 42.00 2.24
1855 4815 1.607628 GCCTCATCAATCACCAGCATC 59.392 52.381 0.00 0.00 0.00 3.91
1942 4916 5.542779 AGAGAAACCTCATAACTCACACAC 58.457 41.667 0.00 0.00 33.16 3.82
2009 5384 0.405585 ACTGGGCCTAAGTTGCATGT 59.594 50.000 4.53 0.00 0.00 3.21
2018 5393 4.382386 AGCTAAAAAGAACTGGGCCTAA 57.618 40.909 4.53 0.00 0.00 2.69
2104 5489 6.712547 ACCAAAATCTCAGAAAAGAACTCGAT 59.287 34.615 0.00 0.00 0.00 3.59
2287 5676 5.854010 AGGAAACTTGGAAACCTTCTTTC 57.146 39.130 0.00 0.00 37.44 2.62
2343 5732 8.397575 TGTACCATGAGATTAGTCAGTCTATC 57.602 38.462 0.00 0.00 0.00 2.08
2396 5785 0.606401 GATGATGGTACCATGGCCGG 60.606 60.000 32.07 0.00 36.70 6.13
2757 9938 0.173481 CTGTCCTCGCTCGATTTCCA 59.827 55.000 0.00 0.00 0.00 3.53
2760 9941 1.517832 CCCTGTCCTCGCTCGATTT 59.482 57.895 0.00 0.00 0.00 2.17
2788 9969 2.040544 CCAGAAAACGCATCGGCCT 61.041 57.895 0.00 0.00 36.38 5.19
2825 10006 1.345415 ACAAGCAAAATGCCCTTCCAG 59.655 47.619 0.00 0.00 46.52 3.86
2962 10143 7.818493 TTCTGTAGAATCGTCAAAATCAGAG 57.182 36.000 0.00 0.00 32.42 3.35
3014 10195 4.021102 TGGAGATTCTGGGTCTGAAAAC 57.979 45.455 0.00 0.00 0.00 2.43
3066 10247 6.560253 AGATTCAATTTCTGGTACACACAC 57.440 37.500 0.00 0.00 0.00 3.82
3100 10281 1.072331 GAGCAGGAGTGGTTTTCTGGA 59.928 52.381 0.00 0.00 33.41 3.86
3131 10312 8.574251 ACACAAAATAGCAACATACTATTGGA 57.426 30.769 0.00 0.00 39.63 3.53
3160 10341 1.070289 ACACAGAACTTCCCTCGGAAC 59.930 52.381 0.00 0.00 36.71 3.62
3198 10379 8.998377 GTGAAAAATGCACAATAAAAACCCTAT 58.002 29.630 0.00 0.00 36.31 2.57
3279 10775 9.846248 CCAGGAGTCAAAATCTAATTAAAACAG 57.154 33.333 0.00 0.00 0.00 3.16
3282 10778 8.650143 AGCCAGGAGTCAAAATCTAATTAAAA 57.350 30.769 0.00 0.00 0.00 1.52
3283 10779 8.522830 CAAGCCAGGAGTCAAAATCTAATTAAA 58.477 33.333 0.00 0.00 0.00 1.52
3308 10804 7.885009 TCCAGAATCTGCATATCAAAATTCA 57.115 32.000 4.40 0.00 0.00 2.57
3360 10862 6.486657 TCAACTCTATTAACTTTTGCTGCTGT 59.513 34.615 0.00 0.00 0.00 4.40
3391 10893 5.478407 CAAAGCTTCGTTTATTTTCCCCAT 58.522 37.500 0.00 0.00 0.00 4.00
3405 10907 1.603802 TGAGCAAACTCCAAAGCTTCG 59.396 47.619 0.00 0.00 42.74 3.79
3478 10980 5.710567 TGAATTCTCGAGTCCTAACTGAAGA 59.289 40.000 13.13 0.00 35.28 2.87
3482 10984 5.348997 GGTTTGAATTCTCGAGTCCTAACTG 59.651 44.000 13.13 0.00 35.28 3.16
3522 11024 9.037737 TGTATTACCAAGAAATATAGTGCGTTC 57.962 33.333 0.00 0.00 0.00 3.95
3523 11025 8.951787 TGTATTACCAAGAAATATAGTGCGTT 57.048 30.769 0.00 0.00 0.00 4.84
3548 11051 6.540189 GTCACAGCATGGTCTTAATATCAGTT 59.460 38.462 0.00 0.00 43.62 3.16
3567 11070 6.074642 TCAATAACGCAAAATAACGTCACAG 58.925 36.000 0.00 0.00 42.68 3.66
3574 11077 6.887247 GCGACATTTCAATAACGCAAAATAAC 59.113 34.615 0.00 0.00 39.79 1.89
3582 11085 1.840141 GCTGCGACATTTCAATAACGC 59.160 47.619 0.00 0.00 40.13 4.84
3597 11100 0.247576 CTCGAGAAATGCTTGCTGCG 60.248 55.000 6.58 0.00 46.63 5.18
3613 11116 4.093556 GCCACAGTTTTCTCTATTTCCTCG 59.906 45.833 0.00 0.00 0.00 4.63
3634 11137 3.518634 TCTTCAAAAACCAACAGTGCC 57.481 42.857 0.00 0.00 0.00 5.01
3664 11167 2.424601 CAACAGTTCACCATATGGGCAG 59.575 50.000 25.55 14.61 42.05 4.85
3770 11273 4.908601 AGGTCACAACATTCACATCCTA 57.091 40.909 0.00 0.00 0.00 2.94
3788 11291 6.655003 CGGATAAATAATAGGCATCACAAGGT 59.345 38.462 0.00 0.00 0.00 3.50
3789 11292 6.655003 ACGGATAAATAATAGGCATCACAAGG 59.345 38.462 0.00 0.00 0.00 3.61
3819 11322 5.867174 TCAGTCACACGAAATCACGAAATAT 59.133 36.000 0.00 0.00 37.03 1.28
3826 11329 3.555956 ACAACTCAGTCACACGAAATCAC 59.444 43.478 0.00 0.00 0.00 3.06
3833 11336 2.663602 GCAGATACAACTCAGTCACACG 59.336 50.000 0.00 0.00 0.00 4.49
3837 11340 5.151297 TGAATGCAGATACAACTCAGTCA 57.849 39.130 0.00 0.00 30.74 3.41
3845 11348 7.716123 TCATATGTCACATGAATGCAGATACAA 59.284 33.333 0.00 0.00 29.55 2.41
3850 11353 5.881443 TGTTCATATGTCACATGAATGCAGA 59.119 36.000 9.66 0.00 42.63 4.26
3857 11360 9.264719 GATATCAGTTGTTCATATGTCACATGA 57.735 33.333 0.00 8.94 0.00 3.07
3902 11405 7.487189 CAGATTCTTTTAGTAAAAGGCAGCATG 59.513 37.037 27.29 17.45 46.11 4.06
4124 12018 9.167311 ACTTGACTCATGTTTATCAGTATTTCC 57.833 33.333 0.00 0.00 0.00 3.13
4138 12032 6.319658 CCCTATGCAATTAACTTGACTCATGT 59.680 38.462 0.00 0.00 36.97 3.21
4175 12069 4.582701 TGGCACGTTCTCAAAATGATTT 57.417 36.364 0.00 0.00 0.00 2.17
4190 12084 7.816945 AATTAATCTCTTTTTCAATGGCACG 57.183 32.000 0.00 0.00 0.00 5.34
4219 13362 5.452636 GGGCAAAACTTTCATCCTGTTAACA 60.453 40.000 8.28 8.28 0.00 2.41
4228 13371 6.587608 CAGATACAAAGGGCAAAACTTTCATC 59.412 38.462 0.00 0.00 36.09 2.92
4243 13386 3.955471 TGAAAGAGCCCCAGATACAAAG 58.045 45.455 0.00 0.00 0.00 2.77
4249 13392 3.160269 CAAGTTTGAAAGAGCCCCAGAT 58.840 45.455 0.00 0.00 0.00 2.90
4253 13396 1.332195 AGCAAGTTTGAAAGAGCCCC 58.668 50.000 0.00 0.00 0.00 5.80
4254 13397 3.181476 TGAAAGCAAGTTTGAAAGAGCCC 60.181 43.478 0.00 0.00 0.00 5.19
4255 13398 3.798878 GTGAAAGCAAGTTTGAAAGAGCC 59.201 43.478 0.00 0.00 0.00 4.70
4279 13422 7.308589 CGACAAACATAAGGATCAAAGACCTTT 60.309 37.037 0.00 0.00 42.93 3.11
4286 13429 5.895636 ATGCGACAAACATAAGGATCAAA 57.104 34.783 0.00 0.00 0.00 2.69
4304 13447 4.153117 GGAGCTTTGGATCTGTTATATGCG 59.847 45.833 0.00 0.00 0.00 4.73
4445 13588 1.157870 ACACTCGAACACTTTGGGCG 61.158 55.000 0.00 0.00 0.00 6.13
4468 13611 4.829588 GGTGCCTAAGCTCCGTAC 57.170 61.111 0.00 0.00 42.42 3.67
4493 13639 3.249091 GACAGAGTGTACATGCAGACAG 58.751 50.000 0.00 0.00 0.00 3.51
4529 13677 7.361201 GCATTAAGCTAGAACACTGATGAAACA 60.361 37.037 0.00 0.00 41.15 2.83
4623 13772 8.523523 TCAAATGCAACATTTATCTCTGTTTG 57.476 30.769 5.30 0.00 33.45 2.93
4666 13819 5.645929 ACATTATCGCCAATAGTTCAACACA 59.354 36.000 0.00 0.00 0.00 3.72
4667 13820 5.965334 CACATTATCGCCAATAGTTCAACAC 59.035 40.000 0.00 0.00 0.00 3.32
4702 14097 5.340803 CATCATTCCAGCAGAACAAATGAG 58.659 41.667 0.00 0.00 39.09 2.90
4707 14102 2.516906 TGCATCATTCCAGCAGAACAA 58.483 42.857 0.00 0.00 37.29 2.83
4824 14278 7.312899 GGTTTTTGGTACAGATTTGGATAGTG 58.687 38.462 0.00 0.00 42.39 2.74
4830 14284 4.577834 ACGGTTTTTGGTACAGATTTGG 57.422 40.909 0.00 0.00 42.39 3.28
4863 14317 7.254852 GTCCTTCAGTTTGAAAATGTACAACA 58.745 34.615 0.00 0.00 35.73 3.33
4866 14320 5.300792 GGGTCCTTCAGTTTGAAAATGTACA 59.699 40.000 5.23 0.00 35.73 2.90
4868 14322 5.450453 TGGGTCCTTCAGTTTGAAAATGTA 58.550 37.500 5.23 0.00 35.73 2.29
4893 14347 7.951530 ACTTCTCAAACATAAGGCAAAATTG 57.048 32.000 0.00 0.00 0.00 2.32
4894 14348 8.962884 AAACTTCTCAAACATAAGGCAAAATT 57.037 26.923 0.00 0.00 0.00 1.82
4899 14353 7.389607 GGTACTAAACTTCTCAAACATAAGGCA 59.610 37.037 0.00 0.00 0.00 4.75
4900 14354 7.148289 GGGTACTAAACTTCTCAAACATAAGGC 60.148 40.741 0.00 0.00 0.00 4.35
4901 14355 8.101419 AGGGTACTAAACTTCTCAAACATAAGG 58.899 37.037 0.00 0.00 0.00 2.69
4902 14356 8.936864 CAGGGTACTAAACTTCTCAAACATAAG 58.063 37.037 0.00 0.00 0.00 1.73
4905 14409 7.074653 TCAGGGTACTAAACTTCTCAAACAT 57.925 36.000 0.00 0.00 0.00 2.71
4907 14411 5.932883 CCTCAGGGTACTAAACTTCTCAAAC 59.067 44.000 0.00 0.00 0.00 2.93
4909 14413 5.245526 GTCCTCAGGGTACTAAACTTCTCAA 59.754 44.000 0.00 0.00 0.00 3.02
4913 14417 3.119209 CCGTCCTCAGGGTACTAAACTTC 60.119 52.174 0.00 0.00 0.00 3.01
4923 14427 1.705997 AAAGTTGCCGTCCTCAGGGT 61.706 55.000 0.00 0.00 0.00 4.34
4924 14428 0.323629 TAAAGTTGCCGTCCTCAGGG 59.676 55.000 0.00 0.00 0.00 4.45
5025 14545 2.095919 GCATGAAGTAACACCACCGTTC 60.096 50.000 0.00 0.00 0.00 3.95
5027 14547 1.519408 GCATGAAGTAACACCACCGT 58.481 50.000 0.00 0.00 0.00 4.83
5028 14548 0.802494 GGCATGAAGTAACACCACCG 59.198 55.000 0.00 0.00 0.00 4.94
5029 14549 1.904287 TGGCATGAAGTAACACCACC 58.096 50.000 0.00 0.00 0.00 4.61
5031 14551 3.495331 ACAATGGCATGAAGTAACACCA 58.505 40.909 0.00 0.00 0.00 4.17
5032 14552 3.505680 TGACAATGGCATGAAGTAACACC 59.494 43.478 0.00 0.00 0.00 4.16
5033 14553 4.764679 TGACAATGGCATGAAGTAACAC 57.235 40.909 0.00 0.00 0.00 3.32
5034 14554 5.981088 AATGACAATGGCATGAAGTAACA 57.019 34.783 0.67 0.00 0.00 2.41
5038 14558 5.471556 TTCAAATGACAATGGCATGAAGT 57.528 34.783 0.67 0.00 0.00 3.01
5039 14559 5.697178 TGTTTCAAATGACAATGGCATGAAG 59.303 36.000 0.67 0.00 0.00 3.02
5041 14561 5.211174 TGTTTCAAATGACAATGGCATGA 57.789 34.783 0.67 0.00 0.00 3.07
5042 14562 5.467399 ACTTGTTTCAAATGACAATGGCATG 59.533 36.000 0.67 0.00 35.44 4.06
5043 14563 5.613329 ACTTGTTTCAAATGACAATGGCAT 58.387 33.333 0.00 0.00 35.44 4.40
5045 14565 5.989551 AACTTGTTTCAAATGACAATGGC 57.010 34.783 0.00 0.00 35.44 4.40
5047 14567 7.904461 GTCCAAAACTTGTTTCAAATGACAATG 59.096 33.333 0.00 0.00 35.44 2.82
5051 14571 6.589907 ACTGTCCAAAACTTGTTTCAAATGAC 59.410 34.615 0.00 3.87 0.00 3.06
5053 14573 6.966435 ACTGTCCAAAACTTGTTTCAAATG 57.034 33.333 0.00 0.00 0.00 2.32
5188 15103 0.548031 GCTTGGTCCTCATGGATGGA 59.452 55.000 0.00 0.00 45.29 3.41
5189 15104 0.466922 GGCTTGGTCCTCATGGATGG 60.467 60.000 0.00 0.00 45.29 3.51
5337 15252 3.909086 GAAAGCAGCGTGGAGGGCT 62.909 63.158 0.00 0.00 42.61 5.19
5353 15268 2.528127 TGGAGGAGGCGGTTGGAA 60.528 61.111 0.00 0.00 0.00 3.53
5395 15310 4.816984 GAGAGGGCGTCGGGGAGA 62.817 72.222 0.96 0.00 0.00 3.71
5411 15326 0.266152 GGGATGGAGGAGAAGAGGGA 59.734 60.000 0.00 0.00 0.00 4.20
5417 15332 1.762460 GGCTCGGGATGGAGGAGAA 60.762 63.158 0.00 0.00 34.56 2.87


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

AutoCloner maintained by Alex Coulton.