Multiple sequence alignment - TraesCS7B01G468300

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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 TraesCS7B01G468300 chr7B 100.000 6389 0 0 1 6389 725521785 725528173 0.000000e+00 11799.0
1 TraesCS7B01G468300 chr7B 86.304 2687 304 40 2669 5320 725519965 725517308 0.000000e+00 2865.0
2 TraesCS7B01G468300 chr7B 97.826 138 3 0 2267 2404 725523118 725523255 8.280000e-59 239.0
3 TraesCS7B01G468300 chr7B 97.826 138 3 0 1334 1471 725524051 725524188 8.280000e-59 239.0
4 TraesCS7B01G468300 chr7B 92.857 42 3 0 595 636 725520818 725520777 1.920000e-05 62.1
5 TraesCS7B01G468300 chr7D 96.815 3140 82 7 2267 5404 625603455 625606578 0.000000e+00 5228.0
6 TraesCS7B01G468300 chr7D 87.081 2655 275 42 2686 5321 625599301 625596696 0.000000e+00 2940.0
7 TraesCS7B01G468300 chr7D 93.712 1463 66 17 25 1474 625602146 625603595 0.000000e+00 2169.0
8 TraesCS7B01G468300 chr7D 90.502 558 40 6 1718 2270 362360689 362361238 0.000000e+00 725.0
9 TraesCS7B01G468300 chr7D 82.428 552 57 17 5842 6389 625607079 625607594 4.540000e-121 446.0
10 TraesCS7B01G468300 chr7D 85.366 246 24 7 966 1200 625600130 625599886 1.780000e-60 244.0
11 TraesCS7B01G468300 chr7D 89.785 186 15 2 342 525 625600486 625600669 1.070000e-57 235.0
12 TraesCS7B01G468300 chr7D 92.453 53 4 0 595 647 625600298 625600246 6.870000e-10 76.8
13 TraesCS7B01G468300 chr7D 100.000 35 0 0 1 35 625601232 625601266 1.490000e-06 65.8
14 TraesCS7B01G468300 chr7A 94.668 3151 137 16 2267 5404 721172395 721175527 0.000000e+00 4859.0
15 TraesCS7B01G468300 chr7A 87.934 1525 162 13 2669 4177 721165432 721163914 0.000000e+00 1777.0
16 TraesCS7B01G468300 chr7A 83.877 1104 121 42 4226 5315 721163914 721162854 0.000000e+00 1000.0
17 TraesCS7B01G468300 chr7A 90.519 559 39 12 1718 2270 283157483 283158033 0.000000e+00 726.0
18 TraesCS7B01G468300 chr7A 89.261 568 41 9 274 838 721167662 721168212 0.000000e+00 693.0
19 TraesCS7B01G468300 chr7A 88.285 589 36 9 901 1474 721171965 721172535 0.000000e+00 675.0
20 TraesCS7B01G468300 chr7A 87.345 403 47 4 5985 6386 721175701 721176100 5.840000e-125 459.0
21 TraesCS7B01G468300 chr7A 78.535 587 95 19 1477 2050 230487665 230488233 2.190000e-94 357.0
22 TraesCS7B01G468300 chr7A 90.043 231 13 5 1 231 721171480 721171700 2.250000e-74 291.0
23 TraesCS7B01G468300 chr7A 88.839 224 20 4 304 525 721170971 721171191 2.940000e-68 270.0
24 TraesCS7B01G468300 chr7A 84.000 250 22 12 968 1200 721166167 721165919 2.320000e-54 224.0
25 TraesCS7B01G468300 chr7A 100.000 29 0 0 595 623 721166321 721166293 3.000000e-03 54.7
26 TraesCS7B01G468300 chr1B 86.255 2670 275 64 2668 5293 30544381 30547002 0.000000e+00 2813.0
27 TraesCS7B01G468300 chr1B 82.966 816 101 27 1477 2270 10838092 10837293 0.000000e+00 702.0
28 TraesCS7B01G468300 chr1B 72.259 757 155 44 4083 4819 626154405 626155126 3.930000e-42 183.0
29 TraesCS7B01G468300 chr1B 82.022 178 24 6 342 515 30524826 30524999 1.860000e-30 145.0
30 TraesCS7B01G468300 chr1D 86.799 2515 257 47 2684 5158 16610720 16613199 0.000000e+00 2736.0
31 TraesCS7B01G468300 chr1D 72.316 1416 313 65 3647 5041 112469736 112468379 2.810000e-98 370.0
32 TraesCS7B01G468300 chr1D 84.932 219 21 8 19 231 16609551 16609763 1.800000e-50 211.0
33 TraesCS7B01G468300 chr1D 82.308 260 23 12 964 1200 16610354 16610613 3.020000e-48 204.0
34 TraesCS7B01G468300 chr1D 89.381 113 8 3 527 639 16609472 16609580 8.640000e-29 139.0
35 TraesCS7B01G468300 chr1A 86.219 2235 252 32 2952 5158 17008893 17011099 0.000000e+00 2370.0
36 TraesCS7B01G468300 chr1A 71.335 1978 439 97 3118 5041 119711438 119709535 1.670000e-105 394.0
37 TraesCS7B01G468300 chr1A 90.496 242 19 2 2674 2911 17008649 17008890 3.720000e-82 316.0
38 TraesCS7B01G468300 chr1A 86.239 218 19 8 19 231 17007158 17007369 6.450000e-55 226.0
39 TraesCS7B01G468300 chr1A 73.614 523 108 24 4120 4630 549359065 549358561 2.370000e-39 174.0
40 TraesCS7B01G468300 chr1A 88.034 117 9 3 524 639 17007075 17007187 4.020000e-27 134.0
41 TraesCS7B01G468300 chr1A 87.156 109 9 4 418 522 17006732 17006839 1.130000e-22 119.0
42 TraesCS7B01G468300 chr1A 95.122 41 2 0 808 848 17007730 17007770 1.490000e-06 65.8
43 TraesCS7B01G468300 chr6D 86.374 844 62 21 1476 2271 359522069 359522907 0.000000e+00 872.0
44 TraesCS7B01G468300 chr2A 86.885 793 74 22 1497 2270 20959425 20960206 0.000000e+00 861.0
45 TraesCS7B01G468300 chr4D 86.403 809 82 19 1475 2270 389480159 389479366 0.000000e+00 859.0
46 TraesCS7B01G468300 chr6A 85.502 807 92 18 1480 2271 101543175 101542379 0.000000e+00 819.0
47 TraesCS7B01G468300 chr2B 84.458 830 84 21 1475 2271 522542231 522543048 0.000000e+00 776.0
48 TraesCS7B01G468300 chr3D 86.092 719 75 15 1477 2185 515970463 515969760 0.000000e+00 750.0
49 TraesCS7B01G468300 chr3D 84.703 438 43 12 1475 1897 601085993 601085565 3.560000e-112 416.0
50 TraesCS7B01G468300 chr5D 84.655 782 69 23 1476 2240 390365670 390366417 0.000000e+00 732.0
51 TraesCS7B01G468300 chr5D 89.331 478 23 5 3455 3932 299063633 299064082 5.560000e-160 575.0
52 TraesCS7B01G468300 chr5D 84.941 425 46 14 1522 1934 135524760 135525178 1.280000e-111 414.0
53 TraesCS7B01G468300 chr5D 83.333 114 13 5 5536 5647 486836108 486836217 4.080000e-17 100.0
54 TraesCS7B01G468300 chr2D 90.681 558 39 11 1718 2271 497918054 497917506 0.000000e+00 730.0
55 TraesCS7B01G468300 chrUn 72.500 1960 429 76 2730 4638 156674913 156676813 3.390000e-147 532.0
56 TraesCS7B01G468300 chr4B 72.231 1959 427 83 2730 4634 660353091 660354986 4.450000e-136 496.0
57 TraesCS7B01G468300 chr5B 80.409 587 82 19 1477 2050 552839496 552840062 3.560000e-112 416.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G468300 chr7B 725521785 725528173 6388 False 11799.000000 11799 100.000000 1 6389 1 chr7B.!!$F1 6388
1 TraesCS7B01G468300 chr7B 725517308 725520818 3510 True 1463.550000 2865 89.580500 595 5320 2 chr7B.!!$R1 4725
2 TraesCS7B01G468300 chr7B 725523118 725524188 1070 False 239.000000 239 97.826000 1334 2404 2 chr7B.!!$F2 1070
3 TraesCS7B01G468300 chr7D 625600486 625607594 7108 False 1628.760000 5228 92.548000 1 6389 5 chr7D.!!$F2 6388
4 TraesCS7B01G468300 chr7D 625596696 625600298 3602 True 1086.933333 2940 88.300000 595 5321 3 chr7D.!!$R1 4726
5 TraesCS7B01G468300 chr7D 362360689 362361238 549 False 725.000000 725 90.502000 1718 2270 1 chr7D.!!$F1 552
6 TraesCS7B01G468300 chr7A 721167662 721176100 8438 False 1207.833333 4859 89.740167 1 6386 6 chr7A.!!$F3 6385
7 TraesCS7B01G468300 chr7A 721162854 721166321 3467 True 763.925000 1777 88.952750 595 5315 4 chr7A.!!$R1 4720
8 TraesCS7B01G468300 chr7A 283157483 283158033 550 False 726.000000 726 90.519000 1718 2270 1 chr7A.!!$F2 552
9 TraesCS7B01G468300 chr7A 230487665 230488233 568 False 357.000000 357 78.535000 1477 2050 1 chr7A.!!$F1 573
10 TraesCS7B01G468300 chr1B 30544381 30547002 2621 False 2813.000000 2813 86.255000 2668 5293 1 chr1B.!!$F2 2625
11 TraesCS7B01G468300 chr1B 10837293 10838092 799 True 702.000000 702 82.966000 1477 2270 1 chr1B.!!$R1 793
12 TraesCS7B01G468300 chr1D 16609472 16613199 3727 False 822.500000 2736 85.855000 19 5158 4 chr1D.!!$F1 5139
13 TraesCS7B01G468300 chr1D 112468379 112469736 1357 True 370.000000 370 72.316000 3647 5041 1 chr1D.!!$R1 1394
14 TraesCS7B01G468300 chr1A 17006732 17011099 4367 False 538.466667 2370 88.877667 19 5158 6 chr1A.!!$F1 5139
15 TraesCS7B01G468300 chr1A 119709535 119711438 1903 True 394.000000 394 71.335000 3118 5041 1 chr1A.!!$R1 1923
16 TraesCS7B01G468300 chr6D 359522069 359522907 838 False 872.000000 872 86.374000 1476 2271 1 chr6D.!!$F1 795
17 TraesCS7B01G468300 chr2A 20959425 20960206 781 False 861.000000 861 86.885000 1497 2270 1 chr2A.!!$F1 773
18 TraesCS7B01G468300 chr4D 389479366 389480159 793 True 859.000000 859 86.403000 1475 2270 1 chr4D.!!$R1 795
19 TraesCS7B01G468300 chr6A 101542379 101543175 796 True 819.000000 819 85.502000 1480 2271 1 chr6A.!!$R1 791
20 TraesCS7B01G468300 chr2B 522542231 522543048 817 False 776.000000 776 84.458000 1475 2271 1 chr2B.!!$F1 796
21 TraesCS7B01G468300 chr3D 515969760 515970463 703 True 750.000000 750 86.092000 1477 2185 1 chr3D.!!$R1 708
22 TraesCS7B01G468300 chr5D 390365670 390366417 747 False 732.000000 732 84.655000 1476 2240 1 chr5D.!!$F3 764
23 TraesCS7B01G468300 chr2D 497917506 497918054 548 True 730.000000 730 90.681000 1718 2271 1 chr2D.!!$R1 553
24 TraesCS7B01G468300 chrUn 156674913 156676813 1900 False 532.000000 532 72.500000 2730 4638 1 chrUn.!!$F1 1908
25 TraesCS7B01G468300 chr4B 660353091 660354986 1895 False 496.000000 496 72.231000 2730 4634 1 chr4B.!!$F1 1904
26 TraesCS7B01G468300 chr5B 552839496 552840062 566 False 416.000000 416 80.409000 1477 2050 1 chr5B.!!$F1 573

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
271 4557 0.027716 CGCAGATCATTGCAGCAGAC 59.972 55.000 7.61 0.00 44.28 3.51 F
693 5590 0.319040 CAGCCCTCGATATCCACACG 60.319 60.000 0.00 0.00 0.00 4.49 F
697 5594 0.385751 CCTCGATATCCACACGCACT 59.614 55.000 0.00 0.00 0.00 4.40 F
1206 6634 1.369091 GGCAATGTACGTCAGCTGGG 61.369 60.000 15.13 9.04 0.00 4.45 F
2584 8448 2.698797 TGGGCTTAGCTTCGCTATAACT 59.301 45.455 3.59 0.00 41.01 2.24 F
2888 9182 0.521450 CCGACGTCGTCATCTCTGTG 60.521 60.000 33.49 12.62 37.74 3.66 F
4545 10911 0.652592 CGAATACCAGCCTGCGAAAG 59.347 55.000 0.00 0.00 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1259 6687 1.840635 GGGAGGGCTCTTTAGTGACAT 59.159 52.381 0.00 0.00 0.00 3.06 R
2590 8454 1.192534 CGACGGCTCTGTCAAAAACTC 59.807 52.381 9.27 0.00 38.84 3.01 R
2644 8508 5.009110 TCGATAATTCAGAGTGTAGGCAGAG 59.991 44.000 0.00 0.00 0.00 3.35 R
2888 9182 1.505477 GGCCAAGCTGCTCGATCATC 61.505 60.000 1.00 0.00 0.00 2.92 R
4028 10394 1.896183 CACGGTGGCCATGTTGTCA 60.896 57.895 9.72 0.00 0.00 3.58 R
4858 11278 0.109342 GACATCCGGAAGCCATGGAT 59.891 55.000 18.40 6.18 43.19 3.41 R
5944 12514 0.038166 TGAGCTTGATTCCCACCCAC 59.962 55.000 0.00 0.00 0.00 4.61 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
50 1788 9.173021 CACATGACTAACCTATAAACCAATTGA 57.827 33.333 7.12 0.00 0.00 2.57
68 1806 6.469782 AATTGAACAATTGGGTGCTATAGG 57.530 37.500 10.83 0.00 39.36 2.57
69 1807 4.584638 TGAACAATTGGGTGCTATAGGT 57.415 40.909 10.83 0.00 0.00 3.08
70 1808 5.702065 TGAACAATTGGGTGCTATAGGTA 57.298 39.130 10.83 0.00 0.00 3.08
231 4517 5.050490 GCAAGAATCGATGAACTTAGCCTA 58.950 41.667 0.00 0.00 0.00 3.93
237 4523 7.870445 AGAATCGATGAACTTAGCCTAAAGATC 59.130 37.037 0.00 0.00 0.00 2.75
251 4537 5.062308 GCCTAAAGATCGGATATGCTTTACG 59.938 44.000 6.37 5.12 33.16 3.18
253 4539 2.596452 AGATCGGATATGCTTTACGCG 58.404 47.619 3.53 3.53 43.27 6.01
271 4557 0.027716 CGCAGATCATTGCAGCAGAC 59.972 55.000 7.61 0.00 44.28 3.51
272 4558 1.092348 GCAGATCATTGCAGCAGACA 58.908 50.000 0.00 0.00 43.53 3.41
273 4559 1.471287 GCAGATCATTGCAGCAGACAA 59.529 47.619 0.00 0.00 43.53 3.18
326 4836 5.446143 TTAGCATATAAACCAATTGGCCG 57.554 39.130 24.79 6.22 39.32 6.13
430 4940 4.930592 GCCTCCAGCTCTCAGTTC 57.069 61.111 0.00 0.00 38.99 3.01
472 4982 5.515270 CAGAATATGTGCATGTGAAGCAAAG 59.485 40.000 0.00 0.00 44.64 2.77
479 4989 2.159462 GCATGTGAAGCAAAGCTAGGTC 60.159 50.000 0.00 0.00 38.25 3.85
480 4990 3.341823 CATGTGAAGCAAAGCTAGGTCT 58.658 45.455 0.00 0.00 38.25 3.85
481 4991 3.492102 TGTGAAGCAAAGCTAGGTCTT 57.508 42.857 0.00 0.00 38.25 3.01
482 4992 4.617253 TGTGAAGCAAAGCTAGGTCTTA 57.383 40.909 0.00 0.00 38.25 2.10
484 4994 5.560724 TGTGAAGCAAAGCTAGGTCTTAAT 58.439 37.500 0.00 0.00 38.25 1.40
487 4999 6.372937 GTGAAGCAAAGCTAGGTCTTAATTCT 59.627 38.462 0.00 0.00 38.25 2.40
564 5310 1.982073 GCGTCAAGATGGGGCTTTCG 61.982 60.000 0.00 0.00 0.00 3.46
568 5314 1.379044 AAGATGGGGCTTTCGGCAG 60.379 57.895 0.00 0.00 44.01 4.85
665 5561 7.592885 ATTGGCTAATGTTGAAGCATCTAAT 57.407 32.000 0.00 0.00 40.61 1.73
682 5579 2.938956 AATTTATCCTCCAGCCCTCG 57.061 50.000 0.00 0.00 0.00 4.63
693 5590 0.319040 CAGCCCTCGATATCCACACG 60.319 60.000 0.00 0.00 0.00 4.49
694 5591 1.664965 GCCCTCGATATCCACACGC 60.665 63.158 0.00 0.00 0.00 5.34
695 5592 1.739667 CCCTCGATATCCACACGCA 59.260 57.895 0.00 0.00 0.00 5.24
696 5593 0.597637 CCCTCGATATCCACACGCAC 60.598 60.000 0.00 0.00 0.00 5.34
697 5594 0.385751 CCTCGATATCCACACGCACT 59.614 55.000 0.00 0.00 0.00 4.40
777 5922 2.752354 CAACACCTCGAATTGGCCAATA 59.248 45.455 30.84 15.00 0.00 1.90
792 5937 4.821805 TGGCCAATAGCTAATTTCAGTAGC 59.178 41.667 0.61 0.00 43.61 3.58
803 5948 5.957771 AATTTCAGTAGCAGGATCCACTA 57.042 39.130 15.82 12.31 0.00 2.74
810 5955 1.693062 AGCAGGATCCACTAGATGCAG 59.307 52.381 19.99 0.00 45.38 4.41
926 6291 3.876320 GGTCTGATCTGAAGCAAGAATCC 59.124 47.826 3.59 0.00 0.00 3.01
954 6319 4.344679 ACTTAGCCTCCATCTCTCAATCTG 59.655 45.833 0.00 0.00 0.00 2.90
962 6327 2.941453 TCTCTCAATCTGCACGTACC 57.059 50.000 0.00 0.00 0.00 3.34
1069 6490 2.438021 TCATTCCCATTCTCCTTACCGG 59.562 50.000 0.00 0.00 0.00 5.28
1150 6578 2.388232 GGCCGACAACATCCACGAC 61.388 63.158 0.00 0.00 0.00 4.34
1206 6634 1.369091 GGCAATGTACGTCAGCTGGG 61.369 60.000 15.13 9.04 0.00 4.45
1233 6661 6.972901 GTCTCGTTGGTCTTTTCATTTTTCTT 59.027 34.615 0.00 0.00 0.00 2.52
1234 6662 7.488150 GTCTCGTTGGTCTTTTCATTTTTCTTT 59.512 33.333 0.00 0.00 0.00 2.52
1258 6686 5.671493 ACACCAAAGTTAGCTTCGCTATAT 58.329 37.500 0.00 0.00 41.01 0.86
1259 6687 6.812998 ACACCAAAGTTAGCTTCGCTATATA 58.187 36.000 0.00 0.00 41.01 0.86
1286 6717 5.253096 TCACTAAAGAGCCCTCCCTTTAAAT 59.747 40.000 0.00 0.00 35.29 1.40
2581 8445 4.351874 AAATGGGCTTAGCTTCGCTATA 57.648 40.909 3.59 0.00 41.01 1.31
2582 8446 4.351874 AATGGGCTTAGCTTCGCTATAA 57.648 40.909 3.59 0.00 41.01 0.98
2583 8447 3.107642 TGGGCTTAGCTTCGCTATAAC 57.892 47.619 3.59 0.00 41.01 1.89
2584 8448 2.698797 TGGGCTTAGCTTCGCTATAACT 59.301 45.455 3.59 0.00 41.01 2.24
2585 8449 3.134081 TGGGCTTAGCTTCGCTATAACTT 59.866 43.478 3.59 0.00 41.01 2.66
2586 8450 4.127907 GGGCTTAGCTTCGCTATAACTTT 58.872 43.478 3.59 0.00 41.01 2.66
2587 8451 4.575236 GGGCTTAGCTTCGCTATAACTTTT 59.425 41.667 3.59 0.00 41.01 2.27
2588 8452 5.277393 GGGCTTAGCTTCGCTATAACTTTTC 60.277 44.000 3.59 0.00 41.01 2.29
2589 8453 5.293569 GGCTTAGCTTCGCTATAACTTTTCA 59.706 40.000 3.59 0.00 41.01 2.69
2590 8454 6.414890 GCTTAGCTTCGCTATAACTTTTCAG 58.585 40.000 0.00 0.00 41.01 3.02
2644 8508 8.562892 ACATAGCATGCTATTCAAAACTATGAC 58.437 33.333 32.84 0.00 37.70 3.06
2888 9182 0.521450 CCGACGTCGTCATCTCTGTG 60.521 60.000 33.49 12.62 37.74 3.66
2903 9197 1.479730 TCTGTGATGATCGAGCAGCTT 59.520 47.619 20.50 0.00 0.00 3.74
2979 9279 0.858583 CAACAGCGACGACACAATCA 59.141 50.000 0.00 0.00 0.00 2.57
3179 9494 2.184322 CTGTACCAGGACGCGCAT 59.816 61.111 5.73 0.00 0.00 4.73
3611 9950 1.187567 GCCACCACCAGAAGGCAATT 61.188 55.000 0.00 0.00 46.26 2.32
3637 9994 2.179517 CCAGGAGCTGTCGTCGTC 59.820 66.667 0.00 0.00 0.00 4.20
3731 10088 1.127567 CCCACTCCCTGTTCAGGACA 61.128 60.000 19.12 5.54 36.65 4.02
3840 10197 1.377072 CCATGGCACGACATCCACA 60.377 57.895 0.00 0.00 34.81 4.17
4028 10394 1.675641 GCAGCTGTTCCGGTCCATT 60.676 57.895 16.64 0.00 0.00 3.16
4545 10911 0.652592 CGAATACCAGCCTGCGAAAG 59.347 55.000 0.00 0.00 0.00 2.62
4616 10982 5.400066 TCATGATCTACGTTCACTCCAAA 57.600 39.130 0.00 0.00 0.00 3.28
4965 11385 0.329596 GGAGGGTCAACAAGATGGCT 59.670 55.000 0.00 0.00 0.00 4.75
5207 11638 7.068348 TCCTAGCTAGTAGTGGTGTTTGATTAG 59.932 40.741 19.31 0.00 0.00 1.73
5241 11678 7.605691 ACGTCAGCTTTCTTAGTTACTAGTAGA 59.394 37.037 3.59 0.00 0.00 2.59
5336 11773 0.676782 GAGCCATGCCTTTGTACCGT 60.677 55.000 0.00 0.00 0.00 4.83
5361 11798 1.021968 GGCAGTTCACACGTTTTCCT 58.978 50.000 0.00 0.00 0.00 3.36
5404 11844 6.128688 GGAAGAAATGAGAAAACACTCTCTCG 60.129 42.308 2.57 0.00 42.11 4.04
5406 11846 6.696411 AGAAATGAGAAAACACTCTCTCGAT 58.304 36.000 2.57 0.00 42.11 3.59
5407 11847 7.831753 AGAAATGAGAAAACACTCTCTCGATA 58.168 34.615 2.57 0.00 42.11 2.92
5408 11848 8.307483 AGAAATGAGAAAACACTCTCTCGATAA 58.693 33.333 2.57 0.00 42.11 1.75
5409 11849 8.472683 AAATGAGAAAACACTCTCTCGATAAG 57.527 34.615 2.57 0.00 42.11 1.73
5411 11851 6.382608 TGAGAAAACACTCTCTCGATAAGTG 58.617 40.000 16.16 16.16 44.68 3.16
5416 11865 4.677584 ACACTCTCTCGATAAGTGATTGC 58.322 43.478 21.73 0.00 42.37 3.56
5418 11867 3.701542 ACTCTCTCGATAAGTGATTGCCA 59.298 43.478 0.00 0.00 0.00 4.92
5433 11882 2.764314 GCCATCGCCGCAGTTCATT 61.764 57.895 0.00 0.00 0.00 2.57
5434 11883 1.436195 GCCATCGCCGCAGTTCATTA 61.436 55.000 0.00 0.00 0.00 1.90
5436 11885 1.003545 CCATCGCCGCAGTTCATTAAG 60.004 52.381 0.00 0.00 0.00 1.85
5437 11886 0.657840 ATCGCCGCAGTTCATTAAGC 59.342 50.000 0.00 0.00 0.00 3.09
5438 11887 0.391130 TCGCCGCAGTTCATTAAGCT 60.391 50.000 0.00 0.00 0.00 3.74
5439 11888 1.134936 TCGCCGCAGTTCATTAAGCTA 60.135 47.619 0.00 0.00 0.00 3.32
5440 11889 1.258982 CGCCGCAGTTCATTAAGCTAG 59.741 52.381 0.00 0.00 0.00 3.42
5441 11890 2.550978 GCCGCAGTTCATTAAGCTAGA 58.449 47.619 0.00 0.00 0.00 2.43
5442 11891 3.134458 GCCGCAGTTCATTAAGCTAGAT 58.866 45.455 0.00 0.00 0.00 1.98
5443 11892 3.561725 GCCGCAGTTCATTAAGCTAGATT 59.438 43.478 0.00 0.00 0.00 2.40
5452 12005 9.331282 AGTTCATTAAGCTAGATTGTACCATTC 57.669 33.333 2.82 0.00 0.00 2.67
5460 12013 6.989169 AGCTAGATTGTACCATTCATCTTCAC 59.011 38.462 0.00 0.00 0.00 3.18
5470 12023 4.439700 CCATTCATCTTCACCTGTTGATGC 60.440 45.833 0.00 0.00 37.00 3.91
5471 12024 3.421919 TCATCTTCACCTGTTGATGCA 57.578 42.857 0.00 0.00 37.00 3.96
5472 12025 3.959293 TCATCTTCACCTGTTGATGCAT 58.041 40.909 0.00 0.00 37.00 3.96
5479 12032 5.781210 TCACCTGTTGATGCATTGTTTTA 57.219 34.783 0.00 0.00 0.00 1.52
5484 12037 8.192774 CACCTGTTGATGCATTGTTTTATCTAT 58.807 33.333 0.00 0.00 0.00 1.98
5511 12064 5.718649 AGAACGATATGTGATTGTTTCCG 57.281 39.130 0.00 0.00 0.00 4.30
5513 12066 6.049149 AGAACGATATGTGATTGTTTCCGAT 58.951 36.000 0.00 0.00 0.00 4.18
5531 12084 6.866010 TCCGATCAGGATATGTTTTTGATG 57.134 37.500 2.65 0.00 45.98 3.07
5533 12086 5.142265 CGATCAGGATATGTTTTTGATGCG 58.858 41.667 0.00 0.00 0.00 4.73
5534 12087 5.277490 CGATCAGGATATGTTTTTGATGCGT 60.277 40.000 0.00 0.00 0.00 5.24
5621 12191 5.646692 AGGCTTGCATTTACCCTATAAGA 57.353 39.130 0.00 0.00 0.00 2.10
5624 12194 6.491403 AGGCTTGCATTTACCCTATAAGATTG 59.509 38.462 0.00 0.00 0.00 2.67
5637 12207 6.929049 CCCTATAAGATTGTGCGAGTTGATAA 59.071 38.462 0.00 0.00 0.00 1.75
5656 12226 9.660180 GTTGATAATCTGGTCTTAACTTCTCTT 57.340 33.333 0.00 0.00 0.00 2.85
5657 12227 9.877178 TTGATAATCTGGTCTTAACTTCTCTTC 57.123 33.333 0.00 0.00 0.00 2.87
5667 12237 7.338462 GTCTTAACTTCTCTTCACTTCAAACG 58.662 38.462 0.00 0.00 0.00 3.60
5668 12238 7.222224 GTCTTAACTTCTCTTCACTTCAAACGA 59.778 37.037 0.00 0.00 0.00 3.85
5669 12239 5.975410 AACTTCTCTTCACTTCAAACGAG 57.025 39.130 0.00 0.00 0.00 4.18
5686 12256 6.602406 TCAAACGAGAGAGGTATAGCTAAACT 59.398 38.462 4.01 4.75 0.00 2.66
5687 12257 6.380095 AACGAGAGAGGTATAGCTAAACTG 57.620 41.667 4.01 0.00 0.00 3.16
5696 12266 8.763601 AGAGGTATAGCTAAACTGAAACAGAAT 58.236 33.333 4.01 0.00 35.18 2.40
5747 12317 8.753497 TCATCTGAGTACATGTAACTATCTGT 57.247 34.615 7.25 0.00 0.00 3.41
5813 12383 9.899661 AATAAAGGTAGTACATTAGTGCATCAA 57.100 29.630 0.00 0.00 32.20 2.57
5814 12384 9.899661 ATAAAGGTAGTACATTAGTGCATCAAA 57.100 29.630 0.00 0.00 32.20 2.69
5815 12385 7.611213 AAGGTAGTACATTAGTGCATCAAAC 57.389 36.000 0.00 0.00 32.20 2.93
5816 12386 6.707290 AGGTAGTACATTAGTGCATCAAACA 58.293 36.000 2.06 0.00 32.20 2.83
5817 12387 7.165485 AGGTAGTACATTAGTGCATCAAACAA 58.835 34.615 2.06 0.00 32.20 2.83
5818 12388 7.663905 AGGTAGTACATTAGTGCATCAAACAAA 59.336 33.333 2.06 0.00 32.20 2.83
5819 12389 8.293867 GGTAGTACATTAGTGCATCAAACAAAA 58.706 33.333 2.06 0.00 32.20 2.44
5820 12390 9.329913 GTAGTACATTAGTGCATCAAACAAAAG 57.670 33.333 0.00 0.00 32.20 2.27
5821 12391 6.863126 AGTACATTAGTGCATCAAACAAAAGC 59.137 34.615 0.00 0.00 32.20 3.51
5822 12392 5.599732 ACATTAGTGCATCAAACAAAAGCA 58.400 33.333 0.00 0.00 0.00 3.91
5823 12393 5.693104 ACATTAGTGCATCAAACAAAAGCAG 59.307 36.000 0.00 0.00 35.66 4.24
5824 12394 5.512753 TTAGTGCATCAAACAAAAGCAGA 57.487 34.783 0.00 0.00 35.66 4.26
5825 12395 4.595762 AGTGCATCAAACAAAAGCAGAT 57.404 36.364 0.00 0.00 35.66 2.90
5826 12396 4.304110 AGTGCATCAAACAAAAGCAGATG 58.696 39.130 0.00 0.00 39.17 2.90
5827 12397 4.038282 AGTGCATCAAACAAAAGCAGATGA 59.962 37.500 0.00 0.00 38.62 2.92
5828 12398 4.384846 GTGCATCAAACAAAAGCAGATGAG 59.615 41.667 0.00 0.00 38.62 2.90
5829 12399 4.278919 TGCATCAAACAAAAGCAGATGAGA 59.721 37.500 0.00 0.00 38.62 3.27
5830 12400 5.047590 TGCATCAAACAAAAGCAGATGAGAT 60.048 36.000 0.00 0.00 38.62 2.75
5831 12401 5.288712 GCATCAAACAAAAGCAGATGAGATG 59.711 40.000 0.00 0.00 38.62 2.90
5832 12402 6.387465 CATCAAACAAAAGCAGATGAGATGT 58.613 36.000 0.00 0.00 38.62 3.06
5833 12403 7.532571 CATCAAACAAAAGCAGATGAGATGTA 58.467 34.615 0.00 0.00 38.62 2.29
5834 12404 6.902341 TCAAACAAAAGCAGATGAGATGTAC 58.098 36.000 0.00 0.00 0.00 2.90
5835 12405 6.486320 TCAAACAAAAGCAGATGAGATGTACA 59.514 34.615 0.00 0.00 0.00 2.90
5836 12406 7.175467 TCAAACAAAAGCAGATGAGATGTACAT 59.825 33.333 8.43 8.43 0.00 2.29
5837 12407 8.453320 CAAACAAAAGCAGATGAGATGTACATA 58.547 33.333 8.71 0.00 0.00 2.29
5838 12408 8.743085 AACAAAAGCAGATGAGATGTACATAT 57.257 30.769 8.71 5.28 0.00 1.78
5839 12409 9.836864 AACAAAAGCAGATGAGATGTACATATA 57.163 29.630 8.71 0.00 0.00 0.86
5874 12444 5.568620 AAAGTTTTCTAGGCTTCTCCTGA 57.431 39.130 0.00 0.00 46.98 3.86
5878 12448 7.259088 AGTTTTCTAGGCTTCTCCTGATTTA 57.741 36.000 0.00 0.00 46.98 1.40
5881 12451 8.961634 GTTTTCTAGGCTTCTCCTGATTTATTT 58.038 33.333 0.00 0.00 46.98 1.40
5911 12481 1.339631 TGAAAGGGGATGCGTACAAGG 60.340 52.381 0.00 0.00 0.00 3.61
5912 12482 0.696501 AAAGGGGATGCGTACAAGGT 59.303 50.000 0.00 0.00 0.00 3.50
5919 12489 1.463444 GATGCGTACAAGGTGTGGTTC 59.537 52.381 0.00 0.00 0.00 3.62
5944 12514 4.531332 GCTAAATCAGCCAGAAATAAGCG 58.469 43.478 0.00 0.00 45.23 4.68
5945 12515 4.035675 GCTAAATCAGCCAGAAATAAGCGT 59.964 41.667 0.00 0.00 45.23 5.07
5946 12516 4.361451 AAATCAGCCAGAAATAAGCGTG 57.639 40.909 0.00 0.00 0.00 5.34
5947 12517 1.737838 TCAGCCAGAAATAAGCGTGG 58.262 50.000 0.00 0.00 0.00 4.94
5948 12518 0.734889 CAGCCAGAAATAAGCGTGGG 59.265 55.000 0.00 0.00 0.00 4.61
5949 12519 0.328258 AGCCAGAAATAAGCGTGGGT 59.672 50.000 0.00 0.00 35.95 4.51
5950 12520 0.451783 GCCAGAAATAAGCGTGGGTG 59.548 55.000 0.00 0.00 0.00 4.61
5951 12521 1.094785 CCAGAAATAAGCGTGGGTGG 58.905 55.000 0.00 0.00 0.00 4.61
5952 12522 1.094785 CAGAAATAAGCGTGGGTGGG 58.905 55.000 0.00 0.00 0.00 4.61
5953 12523 0.988832 AGAAATAAGCGTGGGTGGGA 59.011 50.000 0.00 0.00 0.00 4.37
5954 12524 1.353022 AGAAATAAGCGTGGGTGGGAA 59.647 47.619 0.00 0.00 0.00 3.97
5955 12525 2.025321 AGAAATAAGCGTGGGTGGGAAT 60.025 45.455 0.00 0.00 0.00 3.01
5956 12526 2.052782 AATAAGCGTGGGTGGGAATC 57.947 50.000 0.00 0.00 0.00 2.52
5957 12527 0.916086 ATAAGCGTGGGTGGGAATCA 59.084 50.000 0.00 0.00 0.00 2.57
5958 12528 0.693622 TAAGCGTGGGTGGGAATCAA 59.306 50.000 0.00 0.00 0.00 2.57
5959 12529 0.609131 AAGCGTGGGTGGGAATCAAG 60.609 55.000 0.00 0.00 0.00 3.02
5960 12530 2.700773 GCGTGGGTGGGAATCAAGC 61.701 63.158 0.00 0.00 0.00 4.01
5975 12545 3.124051 AAGCTCACCACTGCCAGCA 62.124 57.895 0.00 0.00 34.08 4.41
5979 12549 0.820891 CTCACCACTGCCAGCAAGTT 60.821 55.000 0.00 0.00 0.00 2.66
6003 12573 2.303022 TCAGCTAGGGTTTTGAGTCAGG 59.697 50.000 0.00 0.00 0.00 3.86
6004 12574 2.039084 CAGCTAGGGTTTTGAGTCAGGT 59.961 50.000 0.00 0.00 0.00 4.00
6006 12576 2.814336 GCTAGGGTTTTGAGTCAGGTTG 59.186 50.000 0.00 0.00 0.00 3.77
6007 12577 2.364972 AGGGTTTTGAGTCAGGTTGG 57.635 50.000 0.00 0.00 0.00 3.77
6008 12578 1.569072 AGGGTTTTGAGTCAGGTTGGT 59.431 47.619 0.00 0.00 0.00 3.67
6009 12579 1.954382 GGGTTTTGAGTCAGGTTGGTC 59.046 52.381 0.00 0.00 0.00 4.02
6014 12585 0.895530 TGAGTCAGGTTGGTCCGATC 59.104 55.000 0.00 0.00 41.99 3.69
6022 12593 0.736325 GTTGGTCCGATCGACACTGG 60.736 60.000 18.66 0.00 43.95 4.00
6033 12604 1.202722 TCGACACTGGTTCTTTTCCCC 60.203 52.381 0.00 0.00 0.00 4.81
6034 12605 1.235724 GACACTGGTTCTTTTCCCCG 58.764 55.000 0.00 0.00 0.00 5.73
6048 12619 2.498644 TCCCCGCAAATACAACATGA 57.501 45.000 0.00 0.00 0.00 3.07
6052 12623 3.500982 CCCGCAAATACAACATGACAAG 58.499 45.455 0.00 0.00 0.00 3.16
6056 12627 5.965334 CCGCAAATACAACATGACAAGATAC 59.035 40.000 0.00 0.00 0.00 2.24
6062 12633 9.601217 AAATACAACATGACAAGATACTACTCC 57.399 33.333 0.00 0.00 0.00 3.85
6063 12634 5.651530 ACAACATGACAAGATACTACTCCG 58.348 41.667 0.00 0.00 0.00 4.63
6064 12635 5.185249 ACAACATGACAAGATACTACTCCGT 59.815 40.000 0.00 0.00 0.00 4.69
6066 12637 5.892568 ACATGACAAGATACTACTCCGTTC 58.107 41.667 0.00 0.00 0.00 3.95
6067 12638 4.611310 TGACAAGATACTACTCCGTTCG 57.389 45.455 0.00 0.00 0.00 3.95
6068 12639 4.005650 TGACAAGATACTACTCCGTTCGT 58.994 43.478 0.00 0.00 0.00 3.85
6069 12640 4.093998 TGACAAGATACTACTCCGTTCGTC 59.906 45.833 0.00 0.00 0.00 4.20
6071 12642 2.570135 AGATACTACTCCGTTCGTCCC 58.430 52.381 0.00 0.00 0.00 4.46
6072 12643 2.092753 AGATACTACTCCGTTCGTCCCA 60.093 50.000 0.00 0.00 0.00 4.37
6073 12644 2.425143 TACTACTCCGTTCGTCCCAT 57.575 50.000 0.00 0.00 0.00 4.00
6074 12645 2.425143 ACTACTCCGTTCGTCCCATA 57.575 50.000 0.00 0.00 0.00 2.74
6076 12647 3.294214 ACTACTCCGTTCGTCCCATAAT 58.706 45.455 0.00 0.00 0.00 1.28
6077 12648 3.703052 ACTACTCCGTTCGTCCCATAATT 59.297 43.478 0.00 0.00 0.00 1.40
6090 12661 5.469760 CGTCCCATAATTGAAGCACATATCA 59.530 40.000 0.00 0.00 0.00 2.15
6182 12753 5.416013 CACCTTATTTCTCTGGAAAAGGGAC 59.584 44.000 11.48 0.00 43.51 4.46
6209 12780 2.175202 AGCGATGACCTTCTTCTCTGT 58.825 47.619 0.00 0.00 0.00 3.41
6221 12792 6.783482 ACCTTCTTCTCTGTAGAAAGGTTACT 59.217 38.462 9.03 0.00 44.99 2.24
6259 12830 7.331026 CAATGTTTCCTGTCCTCTCTGTTATA 58.669 38.462 0.00 0.00 0.00 0.98
6349 12920 5.065218 GGCATCCACTTATTGAGTTACAGTG 59.935 44.000 0.00 0.00 36.10 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.670546 CACTTCCCTCAATCGCACGT 60.671 55.000 0.00 0.00 0.00 4.49
4 5 1.361668 CCACTTCCCTCAATCGCACG 61.362 60.000 0.00 0.00 0.00 5.34
6 7 1.377202 GCCACTTCCCTCAATCGCA 60.377 57.895 0.00 0.00 0.00 5.10
8 9 0.321564 TGTGCCACTTCCCTCAATCG 60.322 55.000 0.00 0.00 0.00 3.34
9 10 1.747355 CATGTGCCACTTCCCTCAATC 59.253 52.381 0.00 0.00 0.00 2.67
11 12 0.770499 TCATGTGCCACTTCCCTCAA 59.230 50.000 0.00 0.00 0.00 3.02
12 13 0.036732 GTCATGTGCCACTTCCCTCA 59.963 55.000 0.00 0.00 0.00 3.86
13 14 0.326264 AGTCATGTGCCACTTCCCTC 59.674 55.000 0.00 0.00 0.00 4.30
14 15 1.656587 TAGTCATGTGCCACTTCCCT 58.343 50.000 0.00 0.00 0.00 4.20
16 17 2.084546 GGTTAGTCATGTGCCACTTCC 58.915 52.381 0.00 0.00 0.00 3.46
17 18 3.059352 AGGTTAGTCATGTGCCACTTC 57.941 47.619 0.00 0.00 0.00 3.01
50 1788 7.617723 TCAAATTACCTATAGCACCCAATTGTT 59.382 33.333 4.43 0.00 0.00 2.83
251 4537 1.298413 CTGCTGCAATGATCTGCGC 60.298 57.895 3.02 0.00 45.74 6.09
253 4539 1.092348 TGTCTGCTGCAATGATCTGC 58.908 50.000 3.02 0.09 42.95 4.26
326 4836 0.655733 CATACAACCGACGCCCAATC 59.344 55.000 0.00 0.00 0.00 2.67
340 4850 7.180766 TGCAGTCATATGGATCCTATTCATACA 59.819 37.037 14.23 0.00 0.00 2.29
430 4940 0.740149 TGCACCTTGCTTCAAGTGTG 59.260 50.000 16.58 16.58 45.31 3.82
472 4982 7.851387 AGTTTGCTAAGAATTAAGACCTAGC 57.149 36.000 0.00 0.00 0.00 3.42
564 5310 0.796927 GTGCTAAACCGAACTCTGCC 59.203 55.000 0.00 0.00 0.00 4.85
568 5314 0.163146 GCACGTGCTAAACCGAACTC 59.837 55.000 32.55 0.00 38.21 3.01
665 5561 2.103153 ATCGAGGGCTGGAGGATAAA 57.897 50.000 0.00 0.00 0.00 1.40
682 5579 0.652592 GTGCAGTGCGTGTGGATATC 59.347 55.000 11.20 0.00 0.00 1.63
693 5590 0.031043 TGCTTCAACATGTGCAGTGC 59.969 50.000 8.58 8.58 0.00 4.40
694 5591 2.228103 AGATGCTTCAACATGTGCAGTG 59.772 45.455 13.25 2.15 38.87 3.66
695 5592 2.511659 AGATGCTTCAACATGTGCAGT 58.488 42.857 13.25 2.19 38.87 4.40
696 5593 3.570926 AAGATGCTTCAACATGTGCAG 57.429 42.857 13.25 5.06 38.87 4.41
697 5594 3.570975 AGAAAGATGCTTCAACATGTGCA 59.429 39.130 10.60 10.60 39.83 4.57
777 5922 4.410228 TGGATCCTGCTACTGAAATTAGCT 59.590 41.667 14.23 0.00 42.21 3.32
789 5934 2.896044 CTGCATCTAGTGGATCCTGCTA 59.104 50.000 18.89 16.07 31.07 3.49
792 5937 2.806019 GCACTGCATCTAGTGGATCCTG 60.806 54.545 14.23 2.41 46.32 3.86
803 5948 2.034878 TCGATTCTAGGCACTGCATCT 58.965 47.619 2.82 0.00 41.52 2.90
857 6035 9.386010 CCAATTGGCCAAATGAATTATATATGG 57.614 33.333 31.09 10.72 0.00 2.74
926 6291 4.100653 TGAGAGATGGAGGCTAAGTTCATG 59.899 45.833 0.00 0.00 0.00 3.07
962 6327 0.884704 AGTGCATTTATAGCCGGCCG 60.885 55.000 26.15 21.04 0.00 6.13
1069 6490 0.529378 CCATTGCTTGCTCCTTGGAC 59.471 55.000 0.00 0.00 0.00 4.02
1171 6599 3.315949 CCGAGGAAACCGGGGACA 61.316 66.667 6.32 0.00 43.05 4.02
1206 6634 4.813296 AATGAAAAGACCAACGAGACAC 57.187 40.909 0.00 0.00 0.00 3.67
1258 6686 3.039011 GGGAGGGCTCTTTAGTGACATA 58.961 50.000 0.00 0.00 0.00 2.29
1259 6687 1.840635 GGGAGGGCTCTTTAGTGACAT 59.159 52.381 0.00 0.00 0.00 3.06
1286 6717 7.656412 TCAATTTAGCACTAACAATGCAAAGA 58.344 30.769 0.00 0.00 45.92 2.52
2404 8261 8.851541 ATTCATTAACCAAGTTTTGCATCAAT 57.148 26.923 0.00 0.00 0.00 2.57
2405 8262 8.674263 AATTCATTAACCAAGTTTTGCATCAA 57.326 26.923 0.00 0.00 0.00 2.57
2406 8263 9.421806 CTAATTCATTAACCAAGTTTTGCATCA 57.578 29.630 0.00 0.00 0.00 3.07
2407 8264 8.872845 CCTAATTCATTAACCAAGTTTTGCATC 58.127 33.333 0.00 0.00 0.00 3.91
2408 8265 8.592809 TCCTAATTCATTAACCAAGTTTTGCAT 58.407 29.630 0.00 0.00 0.00 3.96
2424 8281 5.709164 GCACTGATAAGGCATCCTAATTCAT 59.291 40.000 0.00 0.00 31.13 2.57
2581 8445 6.325596 GCTCTGTCAAAAACTCTGAAAAGTT 58.674 36.000 0.00 0.00 41.20 2.66
2582 8446 5.163612 GGCTCTGTCAAAAACTCTGAAAAGT 60.164 40.000 0.00 0.00 0.00 2.66
2583 8447 5.277047 GGCTCTGTCAAAAACTCTGAAAAG 58.723 41.667 0.00 0.00 0.00 2.27
2584 8448 4.201910 CGGCTCTGTCAAAAACTCTGAAAA 60.202 41.667 0.00 0.00 0.00 2.29
2585 8449 3.312421 CGGCTCTGTCAAAAACTCTGAAA 59.688 43.478 0.00 0.00 0.00 2.69
2586 8450 2.872245 CGGCTCTGTCAAAAACTCTGAA 59.128 45.455 0.00 0.00 0.00 3.02
2587 8451 2.158957 ACGGCTCTGTCAAAAACTCTGA 60.159 45.455 0.00 0.00 0.00 3.27
2588 8452 2.213499 ACGGCTCTGTCAAAAACTCTG 58.787 47.619 0.00 0.00 0.00 3.35
2589 8453 2.484889 GACGGCTCTGTCAAAAACTCT 58.515 47.619 4.09 0.00 38.75 3.24
2590 8454 1.192534 CGACGGCTCTGTCAAAAACTC 59.807 52.381 9.27 0.00 38.84 3.01
2644 8508 5.009110 TCGATAATTCAGAGTGTAGGCAGAG 59.991 44.000 0.00 0.00 0.00 3.35
2888 9182 1.505477 GGCCAAGCTGCTCGATCATC 61.505 60.000 1.00 0.00 0.00 2.92
3179 9494 1.579932 GTCGAACTCCTCAGACGCA 59.420 57.895 0.00 0.00 0.00 5.24
3335 9650 1.701031 TTTCCTGCTGGTTCCCGTCA 61.701 55.000 9.73 0.00 34.23 4.35
3611 9950 2.282251 AGCTCCTGGTCGACGACA 60.282 61.111 27.77 13.81 33.68 4.35
4028 10394 1.896183 CACGGTGGCCATGTTGTCA 60.896 57.895 9.72 0.00 0.00 3.58
4858 11278 0.109342 GACATCCGGAAGCCATGGAT 59.891 55.000 18.40 6.18 43.19 3.41
4965 11385 3.945921 CGTAGAGGTTCCAGTACTCATCA 59.054 47.826 0.00 0.00 33.76 3.07
5207 11638 0.235926 GAAAGCTGACGTGCCAGAAC 59.764 55.000 8.35 0.00 36.29 3.01
5336 11773 1.595109 CGTGTGAACTGCCTGCTCA 60.595 57.895 0.00 0.00 0.00 4.26
5404 11844 1.195448 CGGCGATGGCAATCACTTATC 59.805 52.381 0.00 0.00 42.47 1.75
5406 11846 1.436195 GCGGCGATGGCAATCACTTA 61.436 55.000 12.98 0.00 42.47 2.24
5407 11847 2.764314 GCGGCGATGGCAATCACTT 61.764 57.895 12.98 0.00 42.47 3.16
5408 11848 3.204827 GCGGCGATGGCAATCACT 61.205 61.111 12.98 0.00 42.47 3.41
5409 11849 3.459378 CTGCGGCGATGGCAATCAC 62.459 63.158 12.98 0.00 40.39 3.06
5411 11851 2.652893 GAACTGCGGCGATGGCAATC 62.653 60.000 12.98 0.00 40.39 2.67
5416 11865 1.003545 CTTAATGAACTGCGGCGATGG 60.004 52.381 12.98 1.25 0.00 3.51
5418 11867 0.657840 GCTTAATGAACTGCGGCGAT 59.342 50.000 12.98 0.00 0.00 4.58
5441 11890 7.963361 TCAACAGGTGAAGATGAATGGTACAAT 60.963 37.037 0.00 0.00 35.52 2.71
5442 11891 6.690203 TCAACAGGTGAAGATGAATGGTACAA 60.690 38.462 0.00 0.00 35.52 2.41
5443 11892 5.221823 TCAACAGGTGAAGATGAATGGTACA 60.222 40.000 0.00 0.00 36.26 2.90
5452 12005 4.082408 ACAATGCATCAACAGGTGAAGATG 60.082 41.667 0.00 10.19 40.50 2.90
5460 12013 9.888878 CTATAGATAAAACAATGCATCAACAGG 57.111 33.333 0.00 0.00 0.00 4.00
5484 12037 8.879759 GGAAACAATCACATATCGTTCTTTCTA 58.120 33.333 0.00 0.00 0.00 2.10
5494 12047 5.991606 TCCTGATCGGAAACAATCACATATC 59.008 40.000 2.08 0.00 39.40 1.63
5511 12064 6.064846 ACGCATCAAAAACATATCCTGATC 57.935 37.500 0.00 0.00 0.00 2.92
5513 12066 5.182950 ACAACGCATCAAAAACATATCCTGA 59.817 36.000 0.00 0.00 0.00 3.86
5524 12077 8.803201 TTGACAAATTATACAACGCATCAAAA 57.197 26.923 0.00 0.00 0.00 2.44
5525 12078 8.803201 TTTGACAAATTATACAACGCATCAAA 57.197 26.923 0.00 0.00 31.76 2.69
5526 12079 8.293157 TCTTTGACAAATTATACAACGCATCAA 58.707 29.630 0.05 0.00 0.00 2.57
5528 12081 8.841444 ATCTTTGACAAATTATACAACGCATC 57.159 30.769 0.05 0.00 0.00 3.91
5577 12140 6.709846 GCCTAAGCTTGATGAGACAGATTAAT 59.290 38.462 9.86 0.00 35.50 1.40
5595 12158 2.379005 AGGGTAAATGCAAGCCTAAGC 58.621 47.619 5.82 0.00 42.95 3.09
5596 12159 7.224297 TCTTATAGGGTAAATGCAAGCCTAAG 58.776 38.462 16.59 12.90 46.95 2.18
5605 12168 5.468746 TCGCACAATCTTATAGGGTAAATGC 59.531 40.000 0.00 0.00 0.00 3.56
5621 12191 4.517285 ACCAGATTATCAACTCGCACAAT 58.483 39.130 0.00 0.00 0.00 2.71
5624 12194 3.786635 AGACCAGATTATCAACTCGCAC 58.213 45.455 0.00 0.00 0.00 5.34
5637 12207 6.926630 AGTGAAGAGAAGTTAAGACCAGAT 57.073 37.500 0.00 0.00 0.00 2.90
5656 12226 5.163642 GCTATACCTCTCTCGTTTGAAGTGA 60.164 44.000 0.00 0.00 0.00 3.41
5657 12227 5.038033 GCTATACCTCTCTCGTTTGAAGTG 58.962 45.833 0.00 0.00 0.00 3.16
5667 12237 7.773149 TGTTTCAGTTTAGCTATACCTCTCTC 58.227 38.462 10.32 0.20 0.00 3.20
5668 12238 7.616150 TCTGTTTCAGTTTAGCTATACCTCTCT 59.384 37.037 10.32 0.00 32.61 3.10
5669 12239 7.773149 TCTGTTTCAGTTTAGCTATACCTCTC 58.227 38.462 10.32 0.62 32.61 3.20
5713 12283 9.942850 TTACATGTACTCAGATGAAAGATGAAA 57.057 29.630 4.68 0.00 0.00 2.69
5714 12284 9.371136 GTTACATGTACTCAGATGAAAGATGAA 57.629 33.333 4.68 0.00 0.00 2.57
5715 12285 8.753133 AGTTACATGTACTCAGATGAAAGATGA 58.247 33.333 4.68 0.00 0.00 2.92
5716 12286 8.939201 AGTTACATGTACTCAGATGAAAGATG 57.061 34.615 4.68 0.00 0.00 2.90
5787 12357 9.899661 TTGATGCACTAATGTACTACCTTTATT 57.100 29.630 0.00 0.00 0.00 1.40
5788 12358 9.899661 TTTGATGCACTAATGTACTACCTTTAT 57.100 29.630 0.00 0.00 0.00 1.40
5789 12359 9.158233 GTTTGATGCACTAATGTACTACCTTTA 57.842 33.333 0.00 0.00 0.00 1.85
5790 12360 7.663905 TGTTTGATGCACTAATGTACTACCTTT 59.336 33.333 0.00 0.00 0.00 3.11
5791 12361 7.165485 TGTTTGATGCACTAATGTACTACCTT 58.835 34.615 0.00 0.00 0.00 3.50
5792 12362 6.707290 TGTTTGATGCACTAATGTACTACCT 58.293 36.000 0.00 0.00 0.00 3.08
5793 12363 6.978343 TGTTTGATGCACTAATGTACTACC 57.022 37.500 0.00 0.00 0.00 3.18
5794 12364 9.329913 CTTTTGTTTGATGCACTAATGTACTAC 57.670 33.333 0.00 0.00 0.00 2.73
5795 12365 8.020819 GCTTTTGTTTGATGCACTAATGTACTA 58.979 33.333 0.00 0.00 0.00 1.82
5796 12366 6.863126 GCTTTTGTTTGATGCACTAATGTACT 59.137 34.615 0.00 0.00 0.00 2.73
5797 12367 6.640499 TGCTTTTGTTTGATGCACTAATGTAC 59.360 34.615 0.00 0.00 0.00 2.90
5798 12368 6.743110 TGCTTTTGTTTGATGCACTAATGTA 58.257 32.000 0.00 0.00 0.00 2.29
5799 12369 5.599732 TGCTTTTGTTTGATGCACTAATGT 58.400 33.333 0.00 0.00 0.00 2.71
5800 12370 5.921976 TCTGCTTTTGTTTGATGCACTAATG 59.078 36.000 0.00 0.00 0.00 1.90
5801 12371 6.088016 TCTGCTTTTGTTTGATGCACTAAT 57.912 33.333 0.00 0.00 0.00 1.73
5802 12372 5.512753 TCTGCTTTTGTTTGATGCACTAA 57.487 34.783 0.00 0.00 0.00 2.24
5803 12373 5.241285 TCATCTGCTTTTGTTTGATGCACTA 59.759 36.000 0.00 0.00 35.74 2.74
5804 12374 4.038282 TCATCTGCTTTTGTTTGATGCACT 59.962 37.500 0.00 0.00 35.74 4.40
5805 12375 4.300803 TCATCTGCTTTTGTTTGATGCAC 58.699 39.130 0.00 0.00 35.74 4.57
5806 12376 4.278919 TCTCATCTGCTTTTGTTTGATGCA 59.721 37.500 0.00 0.00 35.74 3.96
5807 12377 4.801891 TCTCATCTGCTTTTGTTTGATGC 58.198 39.130 0.00 0.00 35.74 3.91
5808 12378 6.387465 ACATCTCATCTGCTTTTGTTTGATG 58.613 36.000 0.00 0.00 36.73 3.07
5809 12379 6.585695 ACATCTCATCTGCTTTTGTTTGAT 57.414 33.333 0.00 0.00 0.00 2.57
5810 12380 6.486320 TGTACATCTCATCTGCTTTTGTTTGA 59.514 34.615 0.00 0.00 0.00 2.69
5811 12381 6.671190 TGTACATCTCATCTGCTTTTGTTTG 58.329 36.000 0.00 0.00 0.00 2.93
5812 12382 6.882610 TGTACATCTCATCTGCTTTTGTTT 57.117 33.333 0.00 0.00 0.00 2.83
5813 12383 8.743085 ATATGTACATCTCATCTGCTTTTGTT 57.257 30.769 12.68 0.00 0.00 2.83
5847 12417 5.221244 GGAGAAGCCTAGAAAACTTTTTGCA 60.221 40.000 0.00 0.00 0.00 4.08
5863 12433 9.521503 GTGAAAATAAATAAATCAGGAGAAGCC 57.478 33.333 0.00 0.00 0.00 4.35
5878 12448 7.105588 GCATCCCCTTTCAAGTGAAAATAAAT 58.894 34.615 7.80 0.00 42.72 1.40
5881 12451 4.157656 CGCATCCCCTTTCAAGTGAAAATA 59.842 41.667 7.80 0.00 42.72 1.40
5882 12452 3.056607 CGCATCCCCTTTCAAGTGAAAAT 60.057 43.478 7.80 0.00 42.72 1.82
5886 12456 0.400213 ACGCATCCCCTTTCAAGTGA 59.600 50.000 0.00 0.00 0.00 3.41
5897 12467 1.024579 CCACACCTTGTACGCATCCC 61.025 60.000 0.00 0.00 0.00 3.85
5899 12469 1.463444 GAACCACACCTTGTACGCATC 59.537 52.381 0.00 0.00 0.00 3.91
5944 12514 0.038166 TGAGCTTGATTCCCACCCAC 59.962 55.000 0.00 0.00 0.00 4.61
5945 12515 0.038166 GTGAGCTTGATTCCCACCCA 59.962 55.000 0.00 0.00 0.00 4.51
5946 12516 0.681243 GGTGAGCTTGATTCCCACCC 60.681 60.000 7.15 0.00 40.90 4.61
5947 12517 0.038166 TGGTGAGCTTGATTCCCACC 59.962 55.000 10.72 10.72 45.47 4.61
5948 12518 1.168714 GTGGTGAGCTTGATTCCCAC 58.831 55.000 0.00 0.00 35.99 4.61
5949 12519 1.067295 AGTGGTGAGCTTGATTCCCA 58.933 50.000 0.00 0.00 0.00 4.37
5950 12520 1.457346 CAGTGGTGAGCTTGATTCCC 58.543 55.000 0.00 0.00 0.00 3.97
5951 12521 0.807496 GCAGTGGTGAGCTTGATTCC 59.193 55.000 0.00 0.00 0.00 3.01
5952 12522 0.807496 GGCAGTGGTGAGCTTGATTC 59.193 55.000 0.00 0.00 0.00 2.52
5953 12523 0.111061 TGGCAGTGGTGAGCTTGATT 59.889 50.000 0.00 0.00 0.00 2.57
5954 12524 0.322277 CTGGCAGTGGTGAGCTTGAT 60.322 55.000 6.28 0.00 0.00 2.57
5955 12525 1.071987 CTGGCAGTGGTGAGCTTGA 59.928 57.895 6.28 0.00 0.00 3.02
5956 12526 2.623915 GCTGGCAGTGGTGAGCTTG 61.624 63.158 17.16 0.00 0.00 4.01
5957 12527 2.282040 GCTGGCAGTGGTGAGCTT 60.282 61.111 17.16 0.00 0.00 3.74
5958 12528 3.124051 TTGCTGGCAGTGGTGAGCT 62.124 57.895 17.16 0.00 32.41 4.09
5959 12529 2.595463 TTGCTGGCAGTGGTGAGC 60.595 61.111 17.16 0.46 0.00 4.26
5960 12530 0.820891 AACTTGCTGGCAGTGGTGAG 60.821 55.000 17.16 9.33 0.00 3.51
5975 12545 2.887152 CAAAACCCTAGCTGAGCAACTT 59.113 45.455 7.39 0.00 0.00 2.66
5979 12549 1.699634 ACTCAAAACCCTAGCTGAGCA 59.300 47.619 7.39 0.00 39.13 4.26
5982 12552 2.303022 CCTGACTCAAAACCCTAGCTGA 59.697 50.000 0.00 0.00 0.00 4.26
5983 12553 2.039084 ACCTGACTCAAAACCCTAGCTG 59.961 50.000 0.00 0.00 0.00 4.24
6003 12573 0.736325 CCAGTGTCGATCGGACCAAC 60.736 60.000 16.41 6.09 45.46 3.77
6004 12574 1.183030 ACCAGTGTCGATCGGACCAA 61.183 55.000 16.41 0.00 45.46 3.67
6006 12576 0.458025 GAACCAGTGTCGATCGGACC 60.458 60.000 16.41 4.36 45.46 4.46
6007 12577 0.526662 AGAACCAGTGTCGATCGGAC 59.473 55.000 16.41 12.34 46.27 4.79
6008 12578 1.254026 AAGAACCAGTGTCGATCGGA 58.746 50.000 16.41 0.00 0.00 4.55
6009 12579 2.080286 AAAGAACCAGTGTCGATCGG 57.920 50.000 16.41 0.00 0.00 4.18
6014 12585 1.235724 GGGGAAAAGAACCAGTGTCG 58.764 55.000 0.00 0.00 0.00 4.35
6022 12593 3.926821 TGTATTTGCGGGGAAAAGAAC 57.073 42.857 0.00 0.00 0.00 3.01
6033 12604 6.775088 AGTATCTTGTCATGTTGTATTTGCG 58.225 36.000 0.00 0.00 0.00 4.85
6034 12605 8.883731 AGTAGTATCTTGTCATGTTGTATTTGC 58.116 33.333 0.00 0.00 0.00 3.68
6048 12619 3.376546 GGACGAACGGAGTAGTATCTTGT 59.623 47.826 0.00 0.00 45.00 3.16
6052 12623 2.292267 TGGGACGAACGGAGTAGTATC 58.708 52.381 0.00 0.00 45.00 2.24
6056 12627 4.049186 CAATTATGGGACGAACGGAGTAG 58.951 47.826 0.00 0.00 45.00 2.57
6061 12632 2.031683 GCTTCAATTATGGGACGAACGG 59.968 50.000 0.00 0.00 0.00 4.44
6062 12633 2.675844 TGCTTCAATTATGGGACGAACG 59.324 45.455 0.00 0.00 0.00 3.95
6063 12634 3.438781 TGTGCTTCAATTATGGGACGAAC 59.561 43.478 0.00 0.00 0.00 3.95
6064 12635 3.680490 TGTGCTTCAATTATGGGACGAA 58.320 40.909 0.00 0.00 0.00 3.85
6066 12637 5.469760 TGATATGTGCTTCAATTATGGGACG 59.530 40.000 0.00 0.00 0.00 4.79
6067 12638 6.882610 TGATATGTGCTTCAATTATGGGAC 57.117 37.500 0.00 0.00 0.00 4.46
6068 12639 7.894753 TTTGATATGTGCTTCAATTATGGGA 57.105 32.000 0.00 0.00 32.27 4.37
6077 12648 9.836864 ACAGAGTAATATTTGATATGTGCTTCA 57.163 29.630 0.00 0.00 0.00 3.02
6182 12753 5.355596 AGAAGAAGGTCATCGCTATTTCAG 58.644 41.667 0.00 0.00 0.00 3.02
6209 12780 6.879458 GCATCTCTTTTCCAGTAACCTTTCTA 59.121 38.462 0.00 0.00 0.00 2.10
6221 12792 4.834496 AGGAAACATTGCATCTCTTTTCCA 59.166 37.500 19.66 0.00 42.95 3.53
6349 12920 4.735662 TTAGTTGTTCGGTTGTGCATAC 57.264 40.909 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.