Multiple sequence alignment - TraesCS4D01G357300

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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 TraesCS4D01G357300 chr4D 100.000 4134 0 0 1 4134 505513785 505517918 0.000000e+00 7635.0
1 TraesCS4D01G357300 chr4D 89.894 663 50 10 2643 3298 505499993 505500645 0.000000e+00 837.0
2 TraesCS4D01G357300 chr4D 84.861 753 71 25 772 1493 505497821 505498561 0.000000e+00 719.0
3 TraesCS4D01G357300 chr4D 89.610 462 36 7 1044 1493 505553344 505553805 9.970000e-161 577.0
4 TraesCS4D01G357300 chr4D 82.133 694 92 20 2660 3340 505554224 505554898 2.160000e-157 566.0
5 TraesCS4D01G357300 chr4D 89.573 422 40 2 2639 3060 505495088 505495505 2.190000e-147 532.0
6 TraesCS4D01G357300 chr4D 93.519 216 12 2 3425 3640 426843382 426843169 1.850000e-83 320.0
7 TraesCS4D01G357300 chr4D 85.019 267 29 9 3149 3411 505495836 505496095 1.140000e-65 261.0
8 TraesCS4D01G357300 chr4D 79.747 395 46 15 889 1271 505490727 505491099 5.300000e-64 255.0
9 TraesCS4D01G357300 chr4D 90.722 97 5 1 2113 2209 505499524 505499616 4.340000e-25 126.0
10 TraesCS4D01G357300 chr4D 94.000 50 3 0 772 821 505464218 505464267 4.430000e-10 76.8
11 TraesCS4D01G357300 chr4B 91.770 972 49 8 2450 3392 652399216 652400185 0.000000e+00 1323.0
12 TraesCS4D01G357300 chr4B 93.750 608 28 7 891 1493 652397968 652398570 0.000000e+00 904.0
13 TraesCS4D01G357300 chr4B 86.802 788 65 19 1 776 652394727 652395487 0.000000e+00 843.0
14 TraesCS4D01G357300 chr4B 89.303 617 51 9 2639 3248 652378105 652378713 0.000000e+00 760.0
15 TraesCS4D01G357300 chr4B 86.656 622 60 16 889 1497 652371066 652371677 0.000000e+00 667.0
16 TraesCS4D01G357300 chr4B 90.400 500 29 7 1013 1493 652376112 652376611 1.250000e-179 640.0
17 TraesCS4D01G357300 chr4B 82.107 693 89 24 2660 3340 652415898 652416567 1.000000e-155 560.0
18 TraesCS4D01G357300 chr4B 87.619 420 21 5 1991 2379 652398682 652399101 3.770000e-125 459.0
19 TraesCS4D01G357300 chr4B 97.826 46 1 0 772 817 652370915 652370960 3.430000e-11 80.5
20 TraesCS4D01G357300 chr5A 94.304 790 35 5 2639 3425 689957035 689957817 0.000000e+00 1201.0
21 TraesCS4D01G357300 chr5A 88.608 790 53 7 1783 2542 689956182 689956964 0.000000e+00 926.0
22 TraesCS4D01G357300 chr5A 90.760 671 33 7 889 1536 689955185 689955849 0.000000e+00 869.0
23 TraesCS4D01G357300 chr5A 89.055 667 56 11 2639 3298 689946906 689947562 0.000000e+00 811.0
24 TraesCS4D01G357300 chr5A 82.568 849 73 40 1 820 689954273 689955075 0.000000e+00 678.0
25 TraesCS4D01G357300 chr5A 89.580 547 34 10 968 1493 689944471 689945015 0.000000e+00 673.0
26 TraesCS4D01G357300 chr5A 89.338 544 40 6 968 1493 689933102 689933645 0.000000e+00 667.0
27 TraesCS4D01G357300 chr5A 80.743 888 110 38 2521 3369 689935061 689935926 1.620000e-178 636.0
28 TraesCS4D01G357300 chr5A 84.976 619 60 15 890 1493 689927687 689928287 7.650000e-167 597.0
29 TraesCS4D01G357300 chr5A 91.837 245 12 5 1529 1769 689955882 689956122 6.620000e-88 335.0
30 TraesCS4D01G357300 chr5A 98.148 54 1 0 772 825 689943901 689943954 1.220000e-15 95.3
31 TraesCS4D01G357300 chr5A 94.000 50 3 0 772 821 689932922 689932971 4.430000e-10 76.8
32 TraesCS4D01G357300 chr3D 97.988 497 8 2 3639 4134 14054258 14054753 0.000000e+00 861.0
33 TraesCS4D01G357300 chr3D 97.787 497 10 1 3639 4134 587028477 587027981 0.000000e+00 856.0
34 TraesCS4D01G357300 chr3D 97.177 496 13 1 3639 4133 568032480 568031985 0.000000e+00 837.0
35 TraesCS4D01G357300 chr3D 92.694 219 16 0 3422 3640 169309851 169310069 2.400000e-82 316.0
36 TraesCS4D01G357300 chr3D 89.944 179 14 4 1770 1945 532171917 532172094 1.160000e-55 228.0
37 TraesCS4D01G357300 chr7D 97.041 507 12 3 3629 4134 597483922 597484426 0.000000e+00 850.0
38 TraesCS4D01G357300 chr7D 97.379 496 13 0 3639 4134 596584230 596584725 0.000000e+00 845.0
39 TraesCS4D01G357300 chr7D 82.990 194 26 7 327 519 70836123 70836310 7.110000e-38 169.0
40 TraesCS4D01G357300 chr7D 83.146 178 23 7 349 522 524549074 524549248 5.530000e-34 156.0
41 TraesCS4D01G357300 chr5D 97.018 503 14 1 3633 4134 451155499 451154997 0.000000e+00 845.0
42 TraesCS4D01G357300 chr5D 93.119 218 15 0 3423 3640 148097860 148098077 1.850000e-83 320.0
43 TraesCS4D01G357300 chr5D 83.957 187 21 3 1770 1947 5812757 5812571 1.980000e-38 171.0
44 TraesCS4D01G357300 chr5D 100.000 28 0 0 1914 1941 1385543 1385516 7.000000e-03 52.8
45 TraesCS4D01G357300 chr2D 97.189 498 13 1 3638 4134 12808478 12808975 0.000000e+00 841.0
46 TraesCS4D01G357300 chr2D 97.183 497 13 1 3639 4134 651075446 651075942 0.000000e+00 839.0
47 TraesCS4D01G357300 chr2D 94.444 216 12 0 3425 3640 379969196 379968981 2.380000e-87 333.0
48 TraesCS4D01G357300 chr2D 93.981 216 13 0 3425 3640 420572388 420572173 1.110000e-85 327.0
49 TraesCS4D01G357300 chr1D 97.183 497 13 1 3639 4134 254774881 254774385 0.000000e+00 839.0
50 TraesCS4D01G357300 chr7B 93.151 219 15 0 3422 3640 74735970 74736188 5.160000e-84 322.0
51 TraesCS4D01G357300 chr7B 81.522 184 26 7 341 522 621455960 621456137 1.200000e-30 145.0
52 TraesCS4D01G357300 chr6D 93.519 216 14 0 3425 3640 358330131 358330346 5.160000e-84 322.0
53 TraesCS4D01G357300 chr6D 76.923 169 30 8 1783 1945 454824000 454823835 2.050000e-13 87.9
54 TraesCS4D01G357300 chrUn 92.727 220 16 0 3421 3640 126990410 126990629 6.670000e-83 318.0
55 TraesCS4D01G357300 chrUn 82.386 176 25 5 349 522 444395237 444395408 9.260000e-32 148.0
56 TraesCS4D01G357300 chr5B 93.056 216 15 0 3425 3640 230244776 230244561 2.400000e-82 316.0
57 TraesCS4D01G357300 chr5B 82.514 183 20 8 346 522 510385099 510384923 2.570000e-32 150.0
58 TraesCS4D01G357300 chr5B 100.000 29 0 0 747 775 510728682 510728710 2.000000e-03 54.7
59 TraesCS4D01G357300 chr1B 80.657 274 48 5 3615 3885 604387338 604387067 1.510000e-49 207.0
60 TraesCS4D01G357300 chr7A 82.386 176 25 5 349 522 706133925 706133754 9.260000e-32 148.0
61 TraesCS4D01G357300 chr7A 82.386 176 25 5 349 522 706135013 706134842 9.260000e-32 148.0
62 TraesCS4D01G357300 chr7A 88.889 99 9 2 1794 1890 460586057 460585959 2.020000e-23 121.0
63 TraesCS4D01G357300 chr7A 80.822 146 23 3 1781 1923 681817218 681817075 4.370000e-20 110.0
64 TraesCS4D01G357300 chr3B 82.222 180 24 7 346 523 694179324 694179497 9.260000e-32 148.0
65 TraesCS4D01G357300 chr6B 80.000 200 33 7 329 522 68385955 68386153 1.550000e-29 141.0
66 TraesCS4D01G357300 chr2A 81.319 182 18 14 1772 1945 221308481 221308654 2.590000e-27 134.0
67 TraesCS4D01G357300 chr2B 80.357 168 28 5 1779 1944 13310305 13310141 5.610000e-24 122.0
68 TraesCS4D01G357300 chr3A 77.640 161 30 4 1772 1928 650436390 650436232 4.400000e-15 93.5
69 TraesCS4D01G357300 chr6A 87.013 77 8 1 1781 1857 601146019 601145945 7.360000e-13 86.1
70 TraesCS4D01G357300 chr4A 92.982 57 3 1 2213 2269 554917969 554918024 9.520000e-12 82.4


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 TraesCS4D01G357300 chr4D 505513785 505517918 4133 False 7635.000000 7635 100.00000 1 4134 1 chr4D.!!$F2 4133
1 TraesCS4D01G357300 chr4D 505553344 505554898 1554 False 571.500000 577 85.87150 1044 3340 2 chr4D.!!$F4 2296
2 TraesCS4D01G357300 chr4D 505490727 505500645 9918 False 455.000000 837 86.63600 772 3411 6 chr4D.!!$F3 2639
3 TraesCS4D01G357300 chr4B 652394727 652400185 5458 False 882.250000 1323 89.98525 1 3392 4 chr4B.!!$F4 3391
4 TraesCS4D01G357300 chr4B 652376112 652378713 2601 False 700.000000 760 89.85150 1013 3248 2 chr4B.!!$F3 2235
5 TraesCS4D01G357300 chr4B 652415898 652416567 669 False 560.000000 560 82.10700 2660 3340 1 chr4B.!!$F1 680
6 TraesCS4D01G357300 chr4B 652370915 652371677 762 False 373.750000 667 92.24100 772 1497 2 chr4B.!!$F2 725
7 TraesCS4D01G357300 chr5A 689954273 689957817 3544 False 801.800000 1201 89.61540 1 3425 5 chr5A.!!$F4 3424
8 TraesCS4D01G357300 chr5A 689927687 689928287 600 False 597.000000 597 84.97600 890 1493 1 chr5A.!!$F1 603
9 TraesCS4D01G357300 chr5A 689943901 689947562 3661 False 526.433333 811 92.26100 772 3298 3 chr5A.!!$F3 2526
10 TraesCS4D01G357300 chr5A 689932922 689935926 3004 False 459.933333 667 88.02700 772 3369 3 chr5A.!!$F2 2597
11 TraesCS4D01G357300 chr7D 597483922 597484426 504 False 850.000000 850 97.04100 3629 4134 1 chr7D.!!$F4 505
12 TraesCS4D01G357300 chr5D 451154997 451155499 502 True 845.000000 845 97.01800 3633 4134 1 chr5D.!!$R3 501

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
878 7270 0.250467 GGCGACCCTATGCATGACAT 60.250 55.0 10.16 2.13 43.18 3.06 F
963 7695 0.384309 CGCGCACACCTTCCTATCTA 59.616 55.0 8.75 0.00 0.00 1.98 F
1041 7791 0.622665 CTCAGGAAGGGAAGCACCAT 59.377 55.0 2.58 0.00 41.20 3.55 F
2435 10616 0.965866 TGTCGGAGTTGGATCTCGCT 60.966 55.0 0.00 0.00 35.52 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 8977 0.401356 TACCCCCTCCGTTCCAAAAC 59.599 55.000 0.00 0.00 0.00 2.43 R
2462 10726 0.550914 TGAAGTTGGCCAAGTGGAGT 59.449 50.000 26.45 10.86 37.39 3.85 R
2675 11046 1.058748 CGCGTTGAATGGTGTAGCG 59.941 57.895 0.00 0.00 40.14 4.26 R
3409 11831 0.905357 GGCCTCAGTAGTGACACCAT 59.095 55.000 0.84 0.00 0.00 3.55 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
71 80 1.347707 TGGATTGATGGCCGGAGTATC 59.652 52.381 5.05 5.81 0.00 2.24
80 89 1.614413 GGCCGGAGTATCTAGAACCAG 59.386 57.143 5.05 0.00 33.73 4.00
228 246 9.838339 CTAAACTACACTCCTTCAATTCCATAT 57.162 33.333 0.00 0.00 0.00 1.78
373 400 2.742372 CCTGAAGTGAACGCCGGG 60.742 66.667 2.18 0.00 0.00 5.73
503 530 5.301045 CCATAGAGGGTGTAGATACAACGAA 59.699 44.000 2.12 0.00 44.67 3.85
547 575 5.398012 GCTACTCCCTCCTTTCCATAATGTT 60.398 44.000 0.00 0.00 0.00 2.71
552 580 3.763360 CCTCCTTTCCATAATGTTGTGCA 59.237 43.478 0.00 0.00 0.00 4.57
555 583 3.866910 CCTTTCCATAATGTTGTGCATGC 59.133 43.478 11.82 11.82 37.96 4.06
582 611 8.314021 AGATTTTCTGAAAAGTCAAACCAAACT 58.686 29.630 19.14 0.00 34.49 2.66
585 614 9.936759 TTTTCTGAAAAGTCAAACCAAACTAAT 57.063 25.926 11.33 0.00 31.88 1.73
681 710 9.729023 TCGACAATATGCATTTGGTATTTTAAG 57.271 29.630 3.54 0.00 0.00 1.85
701 730 7.624360 TTAAGTGTCCATGTTTTGCCTATAG 57.376 36.000 0.00 0.00 0.00 1.31
830 7177 1.482593 GGATCACATCGGTCCACTCTT 59.517 52.381 0.00 0.00 32.23 2.85
843 7190 2.050918 CCACTCTTTCCTCCTATCCCC 58.949 57.143 0.00 0.00 0.00 4.81
845 7192 3.115390 CACTCTTTCCTCCTATCCCCAA 58.885 50.000 0.00 0.00 0.00 4.12
852 7223 0.981277 CTCCTATCCCCAACCCACGT 60.981 60.000 0.00 0.00 0.00 4.49
859 7232 0.889186 CCCCAACCCACGTTCTGAAG 60.889 60.000 0.00 0.00 0.00 3.02
878 7270 0.250467 GGCGACCCTATGCATGACAT 60.250 55.000 10.16 2.13 43.18 3.06
879 7271 1.151668 GCGACCCTATGCATGACATC 58.848 55.000 10.16 1.15 40.38 3.06
880 7272 1.541015 GCGACCCTATGCATGACATCA 60.541 52.381 10.16 0.00 40.38 3.07
881 7273 2.837498 CGACCCTATGCATGACATCAA 58.163 47.619 10.16 0.00 40.38 2.57
882 7274 2.545526 CGACCCTATGCATGACATCAAC 59.454 50.000 10.16 0.00 40.38 3.18
883 7275 2.880890 GACCCTATGCATGACATCAACC 59.119 50.000 10.16 0.00 40.38 3.77
884 7276 2.233271 CCCTATGCATGACATCAACCC 58.767 52.381 10.16 0.00 40.38 4.11
887 7279 0.752743 ATGCATGACATCAACCCCCG 60.753 55.000 0.00 0.00 31.52 5.73
936 7668 6.650807 TCAGTTAATTTACCTCAAGCTCACAG 59.349 38.462 0.00 0.00 0.00 3.66
961 7693 2.526120 GCGCGCACACCTTCCTATC 61.526 63.158 29.10 0.00 0.00 2.08
962 7694 1.141881 CGCGCACACCTTCCTATCT 59.858 57.895 8.75 0.00 0.00 1.98
963 7695 0.384309 CGCGCACACCTTCCTATCTA 59.616 55.000 8.75 0.00 0.00 1.98
964 7696 1.202371 CGCGCACACCTTCCTATCTAA 60.202 52.381 8.75 0.00 0.00 2.10
965 7697 2.202566 GCGCACACCTTCCTATCTAAC 58.797 52.381 0.30 0.00 0.00 2.34
966 7698 2.418197 GCGCACACCTTCCTATCTAACA 60.418 50.000 0.30 0.00 0.00 2.41
1015 7761 5.112129 TCCCTTCCTATTTAACAAGCTCC 57.888 43.478 0.00 0.00 0.00 4.70
1027 7773 0.959372 CAAGCTCCTTGCACCTCAGG 60.959 60.000 0.00 0.00 45.94 3.86
1041 7791 0.622665 CTCAGGAAGGGAAGCACCAT 59.377 55.000 2.58 0.00 41.20 3.55
1060 7819 4.188462 CCATTACACACGCTAGAAATGGA 58.812 43.478 11.87 0.00 43.89 3.41
1401 8178 1.309499 CGTCGACTCCCTCAAGCTCT 61.309 60.000 14.70 0.00 0.00 4.09
1481 8258 1.509463 CTACTACGCCAAGCACGGA 59.491 57.895 0.00 0.00 34.00 4.69
1530 8364 5.262588 TCTATGCTACGTGTGTTCATCAT 57.737 39.130 0.00 0.00 0.00 2.45
1584 8421 5.145564 AGTAAAACTCTGACCACACCTCTA 58.854 41.667 0.00 0.00 0.00 2.43
1585 8422 5.601313 AGTAAAACTCTGACCACACCTCTAA 59.399 40.000 0.00 0.00 0.00 2.10
1588 8426 4.608948 ACTCTGACCACACCTCTAAAAG 57.391 45.455 0.00 0.00 0.00 2.27
1593 8431 6.601332 TCTGACCACACCTCTAAAAGAAAAT 58.399 36.000 0.00 0.00 0.00 1.82
1705 8666 6.506147 TGCATATTTTGGACATCATTACTGC 58.494 36.000 0.00 0.00 0.00 4.40
1769 8771 5.316167 ACAAGAGCAAAACATACTCCATCA 58.684 37.500 0.00 0.00 0.00 3.07
1770 8772 5.182001 ACAAGAGCAAAACATACTCCATCAC 59.818 40.000 0.00 0.00 0.00 3.06
1771 8773 4.910195 AGAGCAAAACATACTCCATCACA 58.090 39.130 0.00 0.00 0.00 3.58
1774 8776 6.435277 AGAGCAAAACATACTCCATCACATTT 59.565 34.615 0.00 0.00 0.00 2.32
1775 8777 6.392354 AGCAAAACATACTCCATCACATTTG 58.608 36.000 0.00 0.00 0.00 2.32
1776 8778 5.062558 GCAAAACATACTCCATCACATTTGC 59.937 40.000 0.00 0.00 41.93 3.68
1777 8779 4.989279 AACATACTCCATCACATTTGCC 57.011 40.909 0.00 0.00 0.00 4.52
1778 8780 4.240881 ACATACTCCATCACATTTGCCT 57.759 40.909 0.00 0.00 0.00 4.75
1779 8781 4.202441 ACATACTCCATCACATTTGCCTC 58.798 43.478 0.00 0.00 0.00 4.70
1780 8782 4.080129 ACATACTCCATCACATTTGCCTCT 60.080 41.667 0.00 0.00 0.00 3.69
1781 8783 5.130975 ACATACTCCATCACATTTGCCTCTA 59.869 40.000 0.00 0.00 0.00 2.43
1793 8841 2.877097 TGCCTCTAGAATGCCAAACA 57.123 45.000 10.51 0.00 0.00 2.83
1995 9088 3.054508 TGTGATGTGATGGGCATCTGTTA 60.055 43.478 6.80 0.00 42.21 2.41
2056 9156 9.261180 CAACCGTCATTATCAACTGATTACTAT 57.739 33.333 0.00 0.00 36.05 2.12
2135 10149 4.837093 ATCTAACAAATCGAGGGGTTCA 57.163 40.909 2.18 0.00 0.00 3.18
2162 10176 5.280654 ACTTTGCTTCACCACAATCATTT 57.719 34.783 0.00 0.00 0.00 2.32
2163 10177 5.051816 ACTTTGCTTCACCACAATCATTTG 58.948 37.500 0.00 0.00 38.86 2.32
2435 10616 0.965866 TGTCGGAGTTGGATCTCGCT 60.966 55.000 0.00 0.00 35.52 4.93
2440 10621 1.476891 GGAGTTGGATCTCGCTGTGTA 59.523 52.381 0.00 0.00 35.52 2.90
2530 10830 2.667473 ACTACGTACAGCATTGGGTC 57.333 50.000 0.00 0.00 0.00 4.46
2540 10840 2.501723 CAGCATTGGGTCTAGGTACTGT 59.498 50.000 0.00 0.00 41.52 3.55
2547 10847 2.361438 GGGTCTAGGTACTGTTCATCCG 59.639 54.545 0.00 0.00 41.52 4.18
2607 10949 9.386010 ACATACTTCGGTTTGCATAATTACTTA 57.614 29.630 0.00 0.00 31.59 2.24
2641 11012 9.749340 ACTGGTATGCATATAGTACTACACATA 57.251 33.333 19.21 8.05 0.00 2.29
3035 11406 2.263741 CCGCACTTTCAAGCTGCCT 61.264 57.895 0.00 0.00 32.88 4.75
3041 11412 1.580845 CTTTCAAGCTGCCTGACCCG 61.581 60.000 0.00 0.00 0.00 5.28
3111 11503 2.533266 TCTCGAATAAGCTCCATGCC 57.467 50.000 0.00 0.00 44.23 4.40
3194 11597 9.903682 CATTGTTGAGAACTTGAGATTAATTGT 57.096 29.630 0.00 0.00 0.00 2.71
3248 11656 7.720957 AGTTGCATGTTGCTTAATCTATGGATA 59.279 33.333 0.75 0.00 45.31 2.59
3425 11847 7.142021 GTCACATATATGGTGTCACTACTGAG 58.858 42.308 16.96 0.00 37.52 3.35
3426 11848 6.265422 TCACATATATGGTGTCACTACTGAGG 59.735 42.308 16.96 0.00 37.52 3.86
3427 11849 5.011125 ACATATATGGTGTCACTACTGAGGC 59.989 44.000 16.96 0.00 0.00 4.70
3428 11850 0.905357 ATGGTGTCACTACTGAGGCC 59.095 55.000 2.35 0.00 0.00 5.19
3429 11851 1.192146 TGGTGTCACTACTGAGGCCC 61.192 60.000 0.00 0.00 0.00 5.80
3430 11852 0.905337 GGTGTCACTACTGAGGCCCT 60.905 60.000 0.00 0.00 0.00 5.19
3431 11853 0.247736 GTGTCACTACTGAGGCCCTG 59.752 60.000 0.00 0.00 0.00 4.45
3432 11854 0.178932 TGTCACTACTGAGGCCCTGT 60.179 55.000 0.00 3.96 0.00 4.00
3433 11855 0.977395 GTCACTACTGAGGCCCTGTT 59.023 55.000 0.00 0.00 0.00 3.16
3434 11856 1.348036 GTCACTACTGAGGCCCTGTTT 59.652 52.381 0.00 0.00 0.00 2.83
3435 11857 1.347707 TCACTACTGAGGCCCTGTTTG 59.652 52.381 0.00 3.18 0.00 2.93
3436 11858 0.693049 ACTACTGAGGCCCTGTTTGG 59.307 55.000 0.00 0.00 0.00 3.28
3437 11859 0.693049 CTACTGAGGCCCTGTTTGGT 59.307 55.000 0.00 0.00 0.00 3.67
3438 11860 1.073923 CTACTGAGGCCCTGTTTGGTT 59.926 52.381 0.00 0.00 0.00 3.67
3439 11861 0.178990 ACTGAGGCCCTGTTTGGTTC 60.179 55.000 0.00 0.00 0.00 3.62
3440 11862 0.178992 CTGAGGCCCTGTTTGGTTCA 60.179 55.000 0.00 0.00 0.00 3.18
3441 11863 0.482446 TGAGGCCCTGTTTGGTTCAT 59.518 50.000 0.00 0.00 0.00 2.57
3442 11864 1.707989 TGAGGCCCTGTTTGGTTCATA 59.292 47.619 0.00 0.00 0.00 2.15
3443 11865 2.109128 TGAGGCCCTGTTTGGTTCATAA 59.891 45.455 0.00 0.00 0.00 1.90
3444 11866 2.755103 GAGGCCCTGTTTGGTTCATAAG 59.245 50.000 0.00 0.00 0.00 1.73
3445 11867 2.110011 AGGCCCTGTTTGGTTCATAAGT 59.890 45.455 0.00 0.00 0.00 2.24
3446 11868 2.492088 GGCCCTGTTTGGTTCATAAGTC 59.508 50.000 0.00 0.00 0.00 3.01
3447 11869 2.492088 GCCCTGTTTGGTTCATAAGTCC 59.508 50.000 0.00 0.00 0.00 3.85
3448 11870 3.814316 GCCCTGTTTGGTTCATAAGTCCT 60.814 47.826 0.00 0.00 0.00 3.85
3449 11871 4.566907 GCCCTGTTTGGTTCATAAGTCCTA 60.567 45.833 0.00 0.00 0.00 2.94
3450 11872 5.186198 CCCTGTTTGGTTCATAAGTCCTAG 58.814 45.833 0.00 0.00 0.00 3.02
3451 11873 5.186198 CCTGTTTGGTTCATAAGTCCTAGG 58.814 45.833 0.82 0.82 0.00 3.02
3452 11874 5.045869 CCTGTTTGGTTCATAAGTCCTAGGA 60.046 44.000 7.62 7.62 0.00 2.94
3453 11875 5.801380 TGTTTGGTTCATAAGTCCTAGGAC 58.199 41.667 31.29 31.29 44.86 3.85
3479 11901 6.413783 TTTTTAGTCCCACCTCAAAATTCC 57.586 37.500 0.00 0.00 0.00 3.01
3480 11902 4.733077 TTAGTCCCACCTCAAAATTCCA 57.267 40.909 0.00 0.00 0.00 3.53
3481 11903 3.833559 AGTCCCACCTCAAAATTCCAT 57.166 42.857 0.00 0.00 0.00 3.41
3482 11904 4.946160 AGTCCCACCTCAAAATTCCATA 57.054 40.909 0.00 0.00 0.00 2.74
3483 11905 4.860022 AGTCCCACCTCAAAATTCCATAG 58.140 43.478 0.00 0.00 0.00 2.23
3484 11906 4.292306 AGTCCCACCTCAAAATTCCATAGT 59.708 41.667 0.00 0.00 0.00 2.12
3485 11907 4.640647 GTCCCACCTCAAAATTCCATAGTC 59.359 45.833 0.00 0.00 0.00 2.59
3486 11908 3.954258 CCCACCTCAAAATTCCATAGTCC 59.046 47.826 0.00 0.00 0.00 3.85
3487 11909 3.954258 CCACCTCAAAATTCCATAGTCCC 59.046 47.826 0.00 0.00 0.00 4.46
3488 11910 4.325344 CCACCTCAAAATTCCATAGTCCCT 60.325 45.833 0.00 0.00 0.00 4.20
3489 11911 5.104109 CCACCTCAAAATTCCATAGTCCCTA 60.104 44.000 0.00 0.00 0.00 3.53
3490 11912 6.423182 CACCTCAAAATTCCATAGTCCCTAA 58.577 40.000 0.00 0.00 0.00 2.69
3491 11913 6.889722 CACCTCAAAATTCCATAGTCCCTAAA 59.110 38.462 0.00 0.00 0.00 1.85
3492 11914 7.396055 CACCTCAAAATTCCATAGTCCCTAAAA 59.604 37.037 0.00 0.00 0.00 1.52
3493 11915 7.953493 ACCTCAAAATTCCATAGTCCCTAAAAA 59.047 33.333 0.00 0.00 0.00 1.94
3494 11916 8.470002 CCTCAAAATTCCATAGTCCCTAAAAAG 58.530 37.037 0.00 0.00 0.00 2.27
3495 11917 8.950007 TCAAAATTCCATAGTCCCTAAAAAGT 57.050 30.769 0.00 0.00 0.00 2.66
3496 11918 9.374711 TCAAAATTCCATAGTCCCTAAAAAGTT 57.625 29.630 0.00 0.00 0.00 2.66
3497 11919 9.639601 CAAAATTCCATAGTCCCTAAAAAGTTC 57.360 33.333 0.00 0.00 0.00 3.01
3498 11920 7.956328 AATTCCATAGTCCCTAAAAAGTTCC 57.044 36.000 0.00 0.00 0.00 3.62
3499 11921 6.713731 TTCCATAGTCCCTAAAAAGTTCCT 57.286 37.500 0.00 0.00 0.00 3.36
3500 11922 6.309389 TCCATAGTCCCTAAAAAGTTCCTC 57.691 41.667 0.00 0.00 0.00 3.71
3501 11923 5.191124 TCCATAGTCCCTAAAAAGTTCCTCC 59.809 44.000 0.00 0.00 0.00 4.30
3502 11924 5.045140 CCATAGTCCCTAAAAAGTTCCTCCA 60.045 44.000 0.00 0.00 0.00 3.86
3503 11925 6.353951 CCATAGTCCCTAAAAAGTTCCTCCAT 60.354 42.308 0.00 0.00 0.00 3.41
3504 11926 4.923415 AGTCCCTAAAAAGTTCCTCCATG 58.077 43.478 0.00 0.00 0.00 3.66
3505 11927 4.354087 AGTCCCTAAAAAGTTCCTCCATGT 59.646 41.667 0.00 0.00 0.00 3.21
3506 11928 5.077564 GTCCCTAAAAAGTTCCTCCATGTT 58.922 41.667 0.00 0.00 0.00 2.71
3507 11929 5.538813 GTCCCTAAAAAGTTCCTCCATGTTT 59.461 40.000 0.00 0.00 0.00 2.83
3508 11930 5.538433 TCCCTAAAAAGTTCCTCCATGTTTG 59.462 40.000 0.00 0.00 0.00 2.93
3509 11931 5.304357 CCCTAAAAAGTTCCTCCATGTTTGT 59.696 40.000 0.00 0.00 0.00 2.83
3510 11932 6.183360 CCCTAAAAAGTTCCTCCATGTTTGTT 60.183 38.462 0.00 0.00 0.00 2.83
3511 11933 7.272244 CCTAAAAAGTTCCTCCATGTTTGTTT 58.728 34.615 0.00 0.00 0.00 2.83
3512 11934 7.768582 CCTAAAAAGTTCCTCCATGTTTGTTTT 59.231 33.333 0.00 0.00 0.00 2.43
3513 11935 7.609760 AAAAAGTTCCTCCATGTTTGTTTTC 57.390 32.000 0.00 0.00 0.00 2.29
3514 11936 5.930837 AAGTTCCTCCATGTTTGTTTTCA 57.069 34.783 0.00 0.00 0.00 2.69
3515 11937 5.520376 AGTTCCTCCATGTTTGTTTTCAG 57.480 39.130 0.00 0.00 0.00 3.02
3516 11938 4.342092 AGTTCCTCCATGTTTGTTTTCAGG 59.658 41.667 0.00 0.00 0.00 3.86
3517 11939 3.230134 TCCTCCATGTTTGTTTTCAGGG 58.770 45.455 0.00 0.00 36.93 4.45
3518 11940 3.117322 TCCTCCATGTTTGTTTTCAGGGA 60.117 43.478 0.00 0.00 41.24 4.20
3519 11941 3.005791 CCTCCATGTTTGTTTTCAGGGAC 59.994 47.826 0.00 0.00 39.15 4.46
3520 11942 3.891366 CTCCATGTTTGTTTTCAGGGACT 59.109 43.478 0.00 0.00 39.15 3.85
3521 11943 5.055265 TCCATGTTTGTTTTCAGGGACTA 57.945 39.130 0.00 0.00 39.15 2.59
3522 11944 5.450453 TCCATGTTTGTTTTCAGGGACTAA 58.550 37.500 0.00 0.00 39.15 2.24
3523 11945 5.894393 TCCATGTTTGTTTTCAGGGACTAAA 59.106 36.000 0.00 0.00 39.15 1.85
3524 11946 6.381420 TCCATGTTTGTTTTCAGGGACTAAAA 59.619 34.615 0.00 0.00 39.15 1.52
3525 11947 7.044798 CCATGTTTGTTTTCAGGGACTAAAAA 58.955 34.615 0.00 0.00 37.66 1.94
3526 11948 7.224557 CCATGTTTGTTTTCAGGGACTAAAAAG 59.775 37.037 0.00 0.00 37.66 2.27
3527 11949 7.234661 TGTTTGTTTTCAGGGACTAAAAAGT 57.765 32.000 0.00 0.00 36.02 2.66
3528 11950 7.317390 TGTTTGTTTTCAGGGACTAAAAAGTC 58.683 34.615 0.00 0.00 36.02 3.01
3540 11962 5.732633 GACTAAAAAGTCCCTAGTTCCTCC 58.267 45.833 0.00 0.00 32.97 4.30
3541 11963 4.535294 ACTAAAAAGTCCCTAGTTCCTCCC 59.465 45.833 0.00 0.00 0.00 4.30
3542 11964 3.293215 AAAAGTCCCTAGTTCCTCCCT 57.707 47.619 0.00 0.00 0.00 4.20
3543 11965 4.431158 AAAAGTCCCTAGTTCCTCCCTA 57.569 45.455 0.00 0.00 0.00 3.53
3544 11966 4.431158 AAAGTCCCTAGTTCCTCCCTAA 57.569 45.455 0.00 0.00 0.00 2.69
3545 11967 4.431158 AAGTCCCTAGTTCCTCCCTAAA 57.569 45.455 0.00 0.00 0.00 1.85
3546 11968 3.996957 AGTCCCTAGTTCCTCCCTAAAG 58.003 50.000 0.00 0.00 0.00 1.85
3547 11969 3.601537 AGTCCCTAGTTCCTCCCTAAAGA 59.398 47.826 0.00 0.00 0.00 2.52
3548 11970 4.235636 AGTCCCTAGTTCCTCCCTAAAGAT 59.764 45.833 0.00 0.00 0.00 2.40
3549 11971 4.969999 GTCCCTAGTTCCTCCCTAAAGATT 59.030 45.833 0.00 0.00 0.00 2.40
3550 11972 6.067781 AGTCCCTAGTTCCTCCCTAAAGATTA 60.068 42.308 0.00 0.00 0.00 1.75
3551 11973 6.788456 GTCCCTAGTTCCTCCCTAAAGATTAT 59.212 42.308 0.00 0.00 0.00 1.28
3552 11974 7.292827 GTCCCTAGTTCCTCCCTAAAGATTATT 59.707 40.741 0.00 0.00 0.00 1.40
3553 11975 8.525577 TCCCTAGTTCCTCCCTAAAGATTATTA 58.474 37.037 0.00 0.00 0.00 0.98
3554 11976 9.167387 CCCTAGTTCCTCCCTAAAGATTATTAA 57.833 37.037 0.00 0.00 0.00 1.40
3581 12003 5.576447 CATGTAAAAGACCATGTTACCCC 57.424 43.478 0.00 0.00 34.97 4.95
3582 12004 5.261216 CATGTAAAAGACCATGTTACCCCT 58.739 41.667 0.00 0.00 34.97 4.79
3583 12005 6.419791 CATGTAAAAGACCATGTTACCCCTA 58.580 40.000 0.00 0.00 34.97 3.53
3584 12006 6.057321 TGTAAAAGACCATGTTACCCCTAG 57.943 41.667 0.00 0.00 0.00 3.02
3585 12007 5.548836 TGTAAAAGACCATGTTACCCCTAGT 59.451 40.000 0.00 0.00 0.00 2.57
3586 12008 6.730038 TGTAAAAGACCATGTTACCCCTAGTA 59.270 38.462 0.00 0.00 0.00 1.82
3587 12009 6.903340 AAAAGACCATGTTACCCCTAGTAT 57.097 37.500 0.00 0.00 0.00 2.12
3588 12010 8.927411 GTAAAAGACCATGTTACCCCTAGTATA 58.073 37.037 0.00 0.00 0.00 1.47
3589 12011 6.990908 AAGACCATGTTACCCCTAGTATAC 57.009 41.667 0.00 0.00 0.00 1.47
3590 12012 6.034442 AGACCATGTTACCCCTAGTATACA 57.966 41.667 5.50 0.00 0.00 2.29
3591 12013 6.075984 AGACCATGTTACCCCTAGTATACAG 58.924 44.000 5.50 0.84 30.65 2.74
3592 12014 6.034442 ACCATGTTACCCCTAGTATACAGA 57.966 41.667 5.50 0.00 30.65 3.41
3593 12015 6.446451 ACCATGTTACCCCTAGTATACAGAA 58.554 40.000 5.50 0.00 30.65 3.02
3594 12016 6.904654 ACCATGTTACCCCTAGTATACAGAAA 59.095 38.462 5.50 0.00 30.65 2.52
3595 12017 7.403813 ACCATGTTACCCCTAGTATACAGAAAA 59.596 37.037 5.50 0.00 30.65 2.29
3596 12018 8.269317 CCATGTTACCCCTAGTATACAGAAAAA 58.731 37.037 5.50 0.00 30.65 1.94
3597 12019 9.847224 CATGTTACCCCTAGTATACAGAAAAAT 57.153 33.333 5.50 0.00 30.65 1.82
3603 12025 9.676861 ACCCCTAGTATACAGAAAAATAACAAC 57.323 33.333 5.50 0.00 0.00 3.32
3604 12026 9.117183 CCCCTAGTATACAGAAAAATAACAACC 57.883 37.037 5.50 0.00 0.00 3.77
3605 12027 9.675464 CCCTAGTATACAGAAAAATAACAACCA 57.325 33.333 5.50 0.00 0.00 3.67
3612 12034 9.877178 ATACAGAAAAATAACAACCAAACAACA 57.123 25.926 0.00 0.00 0.00 3.33
3613 12035 8.024146 ACAGAAAAATAACAACCAAACAACAC 57.976 30.769 0.00 0.00 0.00 3.32
3614 12036 7.118535 ACAGAAAAATAACAACCAAACAACACC 59.881 33.333 0.00 0.00 0.00 4.16
3615 12037 7.118390 CAGAAAAATAACAACCAAACAACACCA 59.882 33.333 0.00 0.00 0.00 4.17
3616 12038 7.826744 AGAAAAATAACAACCAAACAACACCAT 59.173 29.630 0.00 0.00 0.00 3.55
3617 12039 6.917217 AAATAACAACCAAACAACACCATG 57.083 33.333 0.00 0.00 0.00 3.66
3618 12040 2.977772 ACAACCAAACAACACCATGG 57.022 45.000 11.19 11.19 38.91 3.66
3619 12041 1.484240 ACAACCAAACAACACCATGGG 59.516 47.619 18.09 7.72 37.26 4.00
3620 12042 1.127343 AACCAAACAACACCATGGGG 58.873 50.000 14.08 14.08 37.26 4.96
3621 12043 1.370810 CCAAACAACACCATGGGGC 59.629 57.895 15.93 0.00 37.90 5.80
3622 12044 1.006337 CAAACAACACCATGGGGCG 60.006 57.895 15.93 8.39 37.90 6.13
3623 12045 2.206536 AAACAACACCATGGGGCGG 61.207 57.895 15.93 9.17 37.90 6.13
3713 12135 2.166254 TCTTATACGAACCGGGACCAAC 59.834 50.000 6.32 0.00 0.00 3.77
3840 12262 2.443394 CCAATGGGCCTCGCTCCTA 61.443 63.158 4.53 0.00 0.00 2.94
3861 12283 1.607071 CCACATCCATTGGTCCCGA 59.393 57.895 1.86 0.00 0.00 5.14
3871 12293 1.570857 TTGGTCCCGATTCCAGCCAT 61.571 55.000 0.00 0.00 35.05 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 3.238788 TCTAGATACTCCGGCCATCAA 57.761 47.619 2.24 0.00 0.00 2.57
355 382 2.030562 CCGGCGTTCACTTCAGGT 59.969 61.111 6.01 0.00 0.00 4.00
484 511 4.978083 TCTTCGTTGTATCTACACCCTC 57.022 45.455 0.00 0.00 35.64 4.30
547 575 4.587584 TTTCAGAAAATCTGCATGCACA 57.412 36.364 18.46 7.34 43.95 4.57
552 580 6.703165 GGTTTGACTTTTCAGAAAATCTGCAT 59.297 34.615 8.81 0.00 43.95 3.96
555 583 8.382875 GTTTGGTTTGACTTTTCAGAAAATCTG 58.617 33.333 8.81 0.88 45.59 2.90
681 710 4.941263 TGTCTATAGGCAAAACATGGACAC 59.059 41.667 4.08 0.00 35.88 3.67
685 714 8.394971 TGAATATGTCTATAGGCAAAACATGG 57.605 34.615 11.80 0.00 33.01 3.66
759 789 8.937634 TTCAGTTAATTATACTCCCTTCGTTC 57.062 34.615 0.00 0.00 0.00 3.95
830 7177 0.423956 TGGGTTGGGGATAGGAGGAA 59.576 55.000 0.00 0.00 0.00 3.36
843 7190 1.841663 CGCCTTCAGAACGTGGGTTG 61.842 60.000 0.00 0.00 36.24 3.77
845 7192 2.030562 CGCCTTCAGAACGTGGGT 59.969 61.111 0.00 0.00 0.00 4.51
852 7223 0.178068 GCATAGGGTCGCCTTCAGAA 59.822 55.000 0.00 0.00 0.00 3.02
859 7232 0.250467 ATGTCATGCATAGGGTCGCC 60.250 55.000 0.00 0.00 35.74 5.54
878 7270 4.603097 AGGGGGTTCGGGGGTTGA 62.603 66.667 0.00 0.00 0.00 3.18
879 7271 4.043100 GAGGGGGTTCGGGGGTTG 62.043 72.222 0.00 0.00 0.00 3.77
884 7276 3.945064 AAGAGGGAGGGGGTTCGGG 62.945 68.421 0.00 0.00 0.00 5.14
887 7279 0.778083 ACAAAAGAGGGAGGGGGTTC 59.222 55.000 0.00 0.00 0.00 3.62
945 7677 2.202566 GTTAGATAGGAAGGTGTGCGC 58.797 52.381 0.00 0.00 0.00 6.09
949 7681 6.515200 CGATCGATTGTTAGATAGGAAGGTGT 60.515 42.308 10.26 0.00 0.00 4.16
950 7682 5.859114 CGATCGATTGTTAGATAGGAAGGTG 59.141 44.000 10.26 0.00 0.00 4.00
951 7683 5.768662 TCGATCGATTGTTAGATAGGAAGGT 59.231 40.000 15.15 0.00 0.00 3.50
952 7684 6.255596 TCGATCGATTGTTAGATAGGAAGG 57.744 41.667 15.15 0.00 0.00 3.46
953 7685 6.252441 GCATCGATCGATTGTTAGATAGGAAG 59.748 42.308 27.45 12.13 31.62 3.46
954 7686 6.093404 GCATCGATCGATTGTTAGATAGGAA 58.907 40.000 27.45 0.00 31.62 3.36
957 7689 5.004251 GCTGCATCGATCGATTGTTAGATAG 59.996 44.000 27.45 16.70 31.62 2.08
961 7693 3.055591 AGCTGCATCGATCGATTGTTAG 58.944 45.455 27.45 21.03 31.62 2.34
962 7694 3.097877 AGCTGCATCGATCGATTGTTA 57.902 42.857 27.45 12.84 31.62 2.41
963 7695 1.945387 AGCTGCATCGATCGATTGTT 58.055 45.000 27.45 15.21 31.62 2.83
964 7696 1.863454 GAAGCTGCATCGATCGATTGT 59.137 47.619 27.45 5.81 31.62 2.71
965 7697 1.194098 GGAAGCTGCATCGATCGATTG 59.806 52.381 27.45 21.65 31.62 2.67
966 7698 1.506493 GGAAGCTGCATCGATCGATT 58.494 50.000 27.45 13.34 31.62 3.34
1015 7761 0.401738 TTCCCTTCCTGAGGTGCAAG 59.598 55.000 0.00 0.00 44.71 4.01
1027 7773 2.488153 GTGTGTAATGGTGCTTCCCTTC 59.512 50.000 0.00 0.00 34.77 3.46
1041 7791 4.794278 TCTCCATTTCTAGCGTGTGTAA 57.206 40.909 0.00 0.00 0.00 2.41
1060 7819 2.362503 TCGTCGTCCTGGCCATCT 60.363 61.111 5.51 0.00 0.00 2.90
1530 8364 3.819368 TGAAAAGATCAGTGCAAGTCCA 58.181 40.909 0.00 0.00 33.04 4.02
1584 8421 9.561069 TCTAGCTAGTGAGTTGAATTTTCTTTT 57.439 29.630 20.10 0.00 0.00 2.27
1585 8422 9.561069 TTCTAGCTAGTGAGTTGAATTTTCTTT 57.439 29.630 20.10 0.00 0.00 2.52
1588 8426 7.960195 GCTTTCTAGCTAGTGAGTTGAATTTTC 59.040 37.037 20.10 1.22 44.27 2.29
1691 8566 3.462021 GAGGTGAGCAGTAATGATGTCC 58.538 50.000 0.00 0.00 0.00 4.02
1705 8666 5.352569 GTGACTGTGATTAATTGGAGGTGAG 59.647 44.000 0.00 0.00 0.00 3.51
1769 8771 3.370840 TGGCATTCTAGAGGCAAATGT 57.629 42.857 17.14 0.00 37.37 2.71
1774 8776 2.877097 TGTTTGGCATTCTAGAGGCA 57.123 45.000 17.14 11.43 38.64 4.75
1775 8777 8.970859 ATATATATGTTTGGCATTCTAGAGGC 57.029 34.615 9.35 9.35 38.94 4.70
1925 8977 0.401356 TACCCCCTCCGTTCCAAAAC 59.599 55.000 0.00 0.00 0.00 2.43
1931 8983 0.979187 TGATGGTACCCCCTCCGTTC 60.979 60.000 10.07 0.00 0.00 3.95
1937 8989 2.588720 TGTAGTAGTGATGGTACCCCCT 59.411 50.000 10.07 2.27 0.00 4.79
1941 8993 6.600822 TCACTAACTGTAGTAGTGATGGTACC 59.399 42.308 15.07 4.43 43.44 3.34
1964 9016 4.823442 GCCCATCACATCACATCTTTATCA 59.177 41.667 0.00 0.00 0.00 2.15
1995 9088 5.236478 CGTTCGATAAAATAGCCAAGTGGAT 59.764 40.000 0.18 0.00 37.39 3.41
2135 10149 5.359576 TGATTGTGGTGAAGCAAAGTTACTT 59.640 36.000 0.00 0.00 0.00 2.24
2462 10726 0.550914 TGAAGTTGGCCAAGTGGAGT 59.449 50.000 26.45 10.86 37.39 3.85
2530 10830 3.802948 AAGCGGATGAACAGTACCTAG 57.197 47.619 0.00 0.00 0.00 3.02
2540 10840 1.067000 CAAATGGCCAAAGCGGATGAA 60.067 47.619 10.96 0.00 41.24 2.57
2675 11046 1.058748 CGCGTTGAATGGTGTAGCG 59.941 57.895 0.00 0.00 40.14 4.26
2861 11232 1.379916 CAGCAGGTTCATCCACCCA 59.620 57.895 0.00 0.00 37.58 4.51
3194 11597 9.476202 CTCCACGAACACATCTAATTATAATGA 57.524 33.333 12.53 0.00 0.00 2.57
3278 11693 7.560991 ACATCAAACAAGAATAGCCCATGAATA 59.439 33.333 0.00 0.00 0.00 1.75
3409 11831 0.905357 GGCCTCAGTAGTGACACCAT 59.095 55.000 0.84 0.00 0.00 3.55
3425 11847 2.492088 GACTTATGAACCAAACAGGGCC 59.508 50.000 0.00 0.00 43.89 5.80
3426 11848 2.492088 GGACTTATGAACCAAACAGGGC 59.508 50.000 0.00 0.00 43.89 5.19
3427 11849 4.034285 AGGACTTATGAACCAAACAGGG 57.966 45.455 0.00 0.00 43.89 4.45
3428 11850 5.045869 TCCTAGGACTTATGAACCAAACAGG 60.046 44.000 7.62 0.00 45.67 4.00
3429 11851 5.875359 GTCCTAGGACTTATGAACCAAACAG 59.125 44.000 31.12 0.00 41.57 3.16
3430 11852 5.801380 GTCCTAGGACTTATGAACCAAACA 58.199 41.667 31.12 0.00 41.57 2.83
3456 11878 5.900123 TGGAATTTTGAGGTGGGACTAAAAA 59.100 36.000 0.00 0.00 35.76 1.94
3457 11879 5.459505 TGGAATTTTGAGGTGGGACTAAAA 58.540 37.500 0.00 0.00 0.00 1.52
3458 11880 5.068215 TGGAATTTTGAGGTGGGACTAAA 57.932 39.130 0.00 0.00 0.00 1.85
3459 11881 4.733077 TGGAATTTTGAGGTGGGACTAA 57.267 40.909 0.00 0.00 0.00 2.24
3460 11882 4.946160 ATGGAATTTTGAGGTGGGACTA 57.054 40.909 0.00 0.00 0.00 2.59
3461 11883 3.833559 ATGGAATTTTGAGGTGGGACT 57.166 42.857 0.00 0.00 0.00 3.85
3462 11884 4.600062 ACTATGGAATTTTGAGGTGGGAC 58.400 43.478 0.00 0.00 0.00 4.46
3463 11885 4.325030 GGACTATGGAATTTTGAGGTGGGA 60.325 45.833 0.00 0.00 0.00 4.37
3464 11886 3.954258 GGACTATGGAATTTTGAGGTGGG 59.046 47.826 0.00 0.00 0.00 4.61
3465 11887 3.954258 GGGACTATGGAATTTTGAGGTGG 59.046 47.826 0.00 0.00 0.00 4.61
3466 11888 4.860022 AGGGACTATGGAATTTTGAGGTG 58.140 43.478 0.00 0.00 36.02 4.00
3467 11889 6.652205 TTAGGGACTATGGAATTTTGAGGT 57.348 37.500 0.00 0.00 42.38 3.85
3468 11890 7.954666 TTTTAGGGACTATGGAATTTTGAGG 57.045 36.000 0.00 0.00 42.38 3.86
3469 11891 9.025041 ACTTTTTAGGGACTATGGAATTTTGAG 57.975 33.333 0.00 0.00 42.38 3.02
3470 11892 8.950007 ACTTTTTAGGGACTATGGAATTTTGA 57.050 30.769 0.00 0.00 42.38 2.69
3471 11893 9.639601 GAACTTTTTAGGGACTATGGAATTTTG 57.360 33.333 0.00 0.00 42.38 2.44
3472 11894 8.812972 GGAACTTTTTAGGGACTATGGAATTTT 58.187 33.333 0.00 0.00 42.38 1.82
3473 11895 8.177456 AGGAACTTTTTAGGGACTATGGAATTT 58.823 33.333 0.00 0.00 36.07 1.82
3474 11896 7.709601 AGGAACTTTTTAGGGACTATGGAATT 58.290 34.615 0.00 0.00 36.07 2.17
3475 11897 7.285340 AGGAACTTTTTAGGGACTATGGAAT 57.715 36.000 0.00 0.00 36.07 3.01
3476 11898 6.296836 GGAGGAACTTTTTAGGGACTATGGAA 60.297 42.308 0.00 0.00 39.57 3.53
3477 11899 5.191124 GGAGGAACTTTTTAGGGACTATGGA 59.809 44.000 0.00 0.00 39.57 3.41
3478 11900 5.045140 TGGAGGAACTTTTTAGGGACTATGG 60.045 44.000 0.00 0.00 39.57 2.74
3479 11901 6.062258 TGGAGGAACTTTTTAGGGACTATG 57.938 41.667 0.00 0.00 39.57 2.23
3480 11902 6.217693 ACATGGAGGAACTTTTTAGGGACTAT 59.782 38.462 0.00 0.00 39.57 2.12
3481 11903 5.550403 ACATGGAGGAACTTTTTAGGGACTA 59.450 40.000 0.00 0.00 41.55 2.59
3482 11904 4.354087 ACATGGAGGAACTTTTTAGGGACT 59.646 41.667 0.00 0.00 41.55 3.85
3483 11905 4.663334 ACATGGAGGAACTTTTTAGGGAC 58.337 43.478 0.00 0.00 41.55 4.46
3484 11906 5.333566 AACATGGAGGAACTTTTTAGGGA 57.666 39.130 0.00 0.00 41.55 4.20
3485 11907 5.304357 ACAAACATGGAGGAACTTTTTAGGG 59.696 40.000 0.00 0.00 41.55 3.53
3486 11908 6.405278 ACAAACATGGAGGAACTTTTTAGG 57.595 37.500 0.00 0.00 41.55 2.69
3487 11909 8.716646 AAAACAAACATGGAGGAACTTTTTAG 57.283 30.769 0.00 0.00 41.55 1.85
3488 11910 8.314751 TGAAAACAAACATGGAGGAACTTTTTA 58.685 29.630 0.00 0.00 41.55 1.52
3489 11911 7.164803 TGAAAACAAACATGGAGGAACTTTTT 58.835 30.769 0.00 0.00 41.55 1.94
3490 11912 6.706295 TGAAAACAAACATGGAGGAACTTTT 58.294 32.000 0.00 0.00 41.55 2.27
3491 11913 6.293004 TGAAAACAAACATGGAGGAACTTT 57.707 33.333 0.00 0.00 41.55 2.66
3492 11914 5.163416 CCTGAAAACAAACATGGAGGAACTT 60.163 40.000 0.00 0.00 41.55 2.66
3494 11916 4.501400 CCCTGAAAACAAACATGGAGGAAC 60.501 45.833 0.00 0.00 0.00 3.62
3495 11917 3.640967 CCCTGAAAACAAACATGGAGGAA 59.359 43.478 0.00 0.00 0.00 3.36
3496 11918 3.117322 TCCCTGAAAACAAACATGGAGGA 60.117 43.478 0.00 0.00 0.00 3.71
3497 11919 3.005791 GTCCCTGAAAACAAACATGGAGG 59.994 47.826 0.00 0.00 33.08 4.30
3498 11920 3.891366 AGTCCCTGAAAACAAACATGGAG 59.109 43.478 0.00 0.00 33.08 3.86
3499 11921 3.909732 AGTCCCTGAAAACAAACATGGA 58.090 40.909 0.00 0.00 0.00 3.41
3500 11922 5.782893 TTAGTCCCTGAAAACAAACATGG 57.217 39.130 0.00 0.00 0.00 3.66
3501 11923 7.763985 ACTTTTTAGTCCCTGAAAACAAACATG 59.236 33.333 0.00 0.00 28.65 3.21
3502 11924 7.847096 ACTTTTTAGTCCCTGAAAACAAACAT 58.153 30.769 0.00 0.00 28.65 2.71
3503 11925 7.234661 ACTTTTTAGTCCCTGAAAACAAACA 57.765 32.000 0.00 0.00 28.65 2.83
3504 11926 7.751047 GACTTTTTAGTCCCTGAAAACAAAC 57.249 36.000 0.00 0.00 32.97 2.93
3517 11939 5.338219 GGGAGGAACTAGGGACTTTTTAGTC 60.338 48.000 0.00 0.00 41.55 2.59
3518 11940 4.535294 GGGAGGAACTAGGGACTTTTTAGT 59.465 45.833 0.00 0.00 41.55 2.24
3519 11941 4.783763 AGGGAGGAACTAGGGACTTTTTAG 59.216 45.833 0.00 0.00 41.55 1.85
3520 11942 4.771338 AGGGAGGAACTAGGGACTTTTTA 58.229 43.478 0.00 0.00 41.55 1.52
3521 11943 3.610260 AGGGAGGAACTAGGGACTTTTT 58.390 45.455 0.00 0.00 41.55 1.94
3522 11944 3.293215 AGGGAGGAACTAGGGACTTTT 57.707 47.619 0.00 0.00 41.55 2.27
3523 11945 4.431158 TTAGGGAGGAACTAGGGACTTT 57.569 45.455 0.00 0.00 41.55 2.66
3524 11946 4.046876 TCTTTAGGGAGGAACTAGGGACTT 59.953 45.833 0.00 0.00 41.55 3.01
3525 11947 3.601537 TCTTTAGGGAGGAACTAGGGACT 59.398 47.826 0.00 0.00 41.55 3.85
3526 11948 3.991683 TCTTTAGGGAGGAACTAGGGAC 58.008 50.000 0.00 0.00 41.55 4.46
3527 11949 4.920781 ATCTTTAGGGAGGAACTAGGGA 57.079 45.455 0.00 0.00 41.55 4.20
3528 11950 7.634526 AATAATCTTTAGGGAGGAACTAGGG 57.365 40.000 0.00 0.00 41.55 3.53
3560 11982 5.530176 AGGGGTAACATGGTCTTTTACAT 57.470 39.130 0.00 0.00 39.74 2.29
3561 11983 5.548836 ACTAGGGGTAACATGGTCTTTTACA 59.451 40.000 0.00 0.00 39.74 2.41
3562 11984 6.058553 ACTAGGGGTAACATGGTCTTTTAC 57.941 41.667 0.00 0.00 39.74 2.01
3563 11985 8.927411 GTATACTAGGGGTAACATGGTCTTTTA 58.073 37.037 0.00 0.00 39.74 1.52
3564 11986 6.903340 ATACTAGGGGTAACATGGTCTTTT 57.097 37.500 0.00 0.00 39.74 2.27
3565 11987 6.904654 TGTATACTAGGGGTAACATGGTCTTT 59.095 38.462 4.17 0.00 39.74 2.52
3566 11988 6.446451 TGTATACTAGGGGTAACATGGTCTT 58.554 40.000 4.17 0.00 39.74 3.01
3567 11989 6.034442 TGTATACTAGGGGTAACATGGTCT 57.966 41.667 4.17 0.00 39.74 3.85
3568 11990 6.073314 TCTGTATACTAGGGGTAACATGGTC 58.927 44.000 4.17 0.00 39.74 4.02
3569 11991 6.034442 TCTGTATACTAGGGGTAACATGGT 57.966 41.667 4.17 0.00 39.74 3.55
3570 11992 6.989155 TTCTGTATACTAGGGGTAACATGG 57.011 41.667 4.17 0.00 39.74 3.66
3571 11993 9.847224 ATTTTTCTGTATACTAGGGGTAACATG 57.153 33.333 4.17 0.00 39.74 3.21
3577 11999 9.676861 GTTGTTATTTTTCTGTATACTAGGGGT 57.323 33.333 4.17 0.00 0.00 4.95
3578 12000 9.117183 GGTTGTTATTTTTCTGTATACTAGGGG 57.883 37.037 4.17 0.00 0.00 4.79
3579 12001 9.675464 TGGTTGTTATTTTTCTGTATACTAGGG 57.325 33.333 4.17 0.00 0.00 3.53
3586 12008 9.877178 TGTTGTTTGGTTGTTATTTTTCTGTAT 57.123 25.926 0.00 0.00 0.00 2.29
3587 12009 9.141400 GTGTTGTTTGGTTGTTATTTTTCTGTA 57.859 29.630 0.00 0.00 0.00 2.74
3588 12010 7.118535 GGTGTTGTTTGGTTGTTATTTTTCTGT 59.881 33.333 0.00 0.00 0.00 3.41
3589 12011 7.118390 TGGTGTTGTTTGGTTGTTATTTTTCTG 59.882 33.333 0.00 0.00 0.00 3.02
3590 12012 7.162082 TGGTGTTGTTTGGTTGTTATTTTTCT 58.838 30.769 0.00 0.00 0.00 2.52
3591 12013 7.365840 TGGTGTTGTTTGGTTGTTATTTTTC 57.634 32.000 0.00 0.00 0.00 2.29
3592 12014 7.148171 CCATGGTGTTGTTTGGTTGTTATTTTT 60.148 33.333 2.57 0.00 0.00 1.94
3593 12015 6.317391 CCATGGTGTTGTTTGGTTGTTATTTT 59.683 34.615 2.57 0.00 0.00 1.82
3594 12016 5.819901 CCATGGTGTTGTTTGGTTGTTATTT 59.180 36.000 2.57 0.00 0.00 1.40
3595 12017 5.363939 CCATGGTGTTGTTTGGTTGTTATT 58.636 37.500 2.57 0.00 0.00 1.40
3596 12018 4.202305 CCCATGGTGTTGTTTGGTTGTTAT 60.202 41.667 11.73 0.00 0.00 1.89
3597 12019 3.133003 CCCATGGTGTTGTTTGGTTGTTA 59.867 43.478 11.73 0.00 0.00 2.41
3598 12020 2.093235 CCCATGGTGTTGTTTGGTTGTT 60.093 45.455 11.73 0.00 0.00 2.83
3599 12021 1.484240 CCCATGGTGTTGTTTGGTTGT 59.516 47.619 11.73 0.00 0.00 3.32
3600 12022 1.202627 CCCCATGGTGTTGTTTGGTTG 60.203 52.381 11.73 0.00 0.00 3.77
3601 12023 1.127343 CCCCATGGTGTTGTTTGGTT 58.873 50.000 11.73 0.00 0.00 3.67
3602 12024 1.406860 GCCCCATGGTGTTGTTTGGT 61.407 55.000 11.73 0.00 0.00 3.67
3603 12025 1.370810 GCCCCATGGTGTTGTTTGG 59.629 57.895 11.73 2.83 0.00 3.28
3604 12026 1.006337 CGCCCCATGGTGTTGTTTG 60.006 57.895 11.73 0.00 37.37 2.93
3605 12027 2.206536 CCGCCCCATGGTGTTGTTT 61.207 57.895 11.73 0.00 40.77 2.83
3606 12028 2.600173 CCGCCCCATGGTGTTGTT 60.600 61.111 11.73 0.00 40.77 2.83
3629 12051 5.106157 CCTTTTTCTACTAGTGCACCCATTG 60.106 44.000 14.63 1.64 0.00 2.82
3630 12052 5.010282 CCTTTTTCTACTAGTGCACCCATT 58.990 41.667 14.63 0.00 0.00 3.16
3631 12053 4.567747 CCCTTTTTCTACTAGTGCACCCAT 60.568 45.833 14.63 0.88 0.00 4.00
3637 12059 3.351794 AGCCCCTTTTTCTACTAGTGC 57.648 47.619 5.39 0.00 0.00 4.40
3840 12262 1.307647 GGACCAATGGATGTGGGCT 59.692 57.895 6.16 0.00 44.42 5.19
3861 12283 1.076777 CCCGGTTCATGGCTGGAAT 60.077 57.895 14.94 0.00 34.35 3.01
3871 12293 2.029470 GCAAATCATTTGTCCCGGTTCA 60.029 45.455 11.80 0.00 42.56 3.18
4007 12430 1.003003 TGTGGCTCGGACATTTCATCA 59.997 47.619 0.00 0.00 0.00 3.07
4068 12491 5.885912 CCTAGAAAAATCTCGGGGAAAATGA 59.114 40.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.