Multiple sequence alignment - TraesCS6A01G343100

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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 TraesCS6A01G343100 chr6A 100.000 5615 0 0 1 5615 576910102 576915716 0.000000e+00 10370.0
1 TraesCS6A01G343100 chr6A 94.571 1271 60 4 2455 3717 17909226 17910495 0.000000e+00 1956.0
2 TraesCS6A01G343100 chr6A 78.210 514 95 9 1021 1533 553913268 553912771 4.220000e-81 313.0
3 TraesCS6A01G343100 chr7A 98.547 1790 26 0 1926 3715 37925516 37923727 0.000000e+00 3162.0
4 TraesCS6A01G343100 chr7A 82.100 419 56 11 1952 2369 3058705 3059105 1.940000e-89 340.0
5 TraesCS6A01G343100 chr5A 97.910 1770 34 1 1951 3717 663844930 663846699 0.000000e+00 3061.0
6 TraesCS6A01G343100 chr5A 94.450 937 49 3 4680 5615 40703920 40704854 0.000000e+00 1439.0
7 TraesCS6A01G343100 chr5A 97.712 437 10 0 1932 2368 15044532 15044096 0.000000e+00 752.0
8 TraesCS6A01G343100 chr7B 97.364 1252 30 2 2467 3716 80068997 80067747 0.000000e+00 2126.0
9 TraesCS6A01G343100 chr6D 95.112 1289 61 2 638 1924 430401291 430402579 0.000000e+00 2030.0
10 TraesCS6A01G343100 chr6D 92.308 1092 71 4 834 1924 430321276 430322355 0.000000e+00 1539.0
11 TraesCS6A01G343100 chr6D 94.813 964 47 2 3717 4678 430402576 430403538 0.000000e+00 1500.0
12 TraesCS6A01G343100 chr6D 92.124 965 43 11 3717 4678 430322352 430323286 0.000000e+00 1330.0
13 TraesCS6A01G343100 chr6D 86.072 998 105 17 837 1820 430318114 430319091 0.000000e+00 1042.0
14 TraesCS6A01G343100 chr6D 96.646 477 14 2 1 475 430400829 430401305 0.000000e+00 791.0
15 TraesCS6A01G343100 chr6D 79.527 845 150 14 3749 4575 420568417 420567578 1.050000e-161 580.0
16 TraesCS6A01G343100 chr6D 77.953 889 171 16 3746 4615 408156366 408155484 2.980000e-147 532.0
17 TraesCS6A01G343100 chr6D 87.528 441 31 9 1 438 430320289 430320708 6.540000e-134 488.0
18 TraesCS6A01G343100 chr6D 78.947 513 93 8 1021 1533 408157055 408156558 9.010000e-88 335.0
19 TraesCS6A01G343100 chr6D 78.295 516 91 13 1021 1533 59089058 59088561 4.220000e-81 313.0
20 TraesCS6A01G343100 chr6D 85.000 180 14 6 476 643 307532534 307532356 2.690000e-38 171.0
21 TraesCS6A01G343100 chr6D 86.228 167 11 4 642 798 430321104 430321268 2.690000e-38 171.0
22 TraesCS6A01G343100 chrUn 95.854 1230 42 4 2494 3715 257168007 257169235 0.000000e+00 1980.0
23 TraesCS6A01G343100 chrUn 93.490 937 56 3 4680 5615 65692655 65693587 0.000000e+00 1387.0
24 TraesCS6A01G343100 chrUn 86.364 176 18 6 467 640 424990817 424990988 2.670000e-43 187.0
25 TraesCS6A01G343100 chrUn 85.393 178 18 7 467 640 262008411 262008238 1.610000e-40 178.0
26 TraesCS6A01G343100 chrUn 85.393 178 18 7 467 640 286376883 286376710 1.610000e-40 178.0
27 TraesCS6A01G343100 chrUn 85.393 178 18 8 467 640 416580910 416581083 1.610000e-40 178.0
28 TraesCS6A01G343100 chrUn 85.165 182 14 6 474 643 297964005 297963825 2.080000e-39 174.0
29 TraesCS6A01G343100 chrUn 85.143 175 11 10 481 643 75273571 75273400 1.250000e-36 165.0
30 TraesCS6A01G343100 chrUn 82.609 184 13 12 480 649 369332973 369332795 1.630000e-30 145.0
31 TraesCS6A01G343100 chrUn 82.162 185 13 12 480 649 281281783 281281962 2.110000e-29 141.0
32 TraesCS6A01G343100 chrUn 89.286 112 9 3 542 652 287443312 287443203 2.730000e-28 137.0
33 TraesCS6A01G343100 chrUn 81.522 184 15 12 480 649 308142776 308142954 3.530000e-27 134.0
34 TraesCS6A01G343100 chrUn 82.407 108 10 5 543 645 290147109 290147212 1.000000e-12 86.1
35 TraesCS6A01G343100 chrUn 94.595 37 2 0 476 512 41303705 41303741 2.180000e-04 58.4
36 TraesCS6A01G343100 chr7D 95.854 1230 42 4 2494 3715 629977731 629978959 0.000000e+00 1980.0
37 TraesCS6A01G343100 chr5D 95.854 1230 42 4 2494 3715 559648460 559649688 0.000000e+00 1980.0
38 TraesCS6A01G343100 chr5D 86.061 165 14 6 485 644 482925741 482925901 9.670000e-38 169.0
39 TraesCS6A01G343100 chr5D 80.519 231 32 12 1019 1244 416259145 416258923 1.250000e-36 165.0
40 TraesCS6A01G343100 chr3A 94.957 1269 53 5 2455 3716 712382111 712383375 0.000000e+00 1978.0
41 TraesCS6A01G343100 chr3A 94.569 939 45 5 4680 5615 701672806 701673741 0.000000e+00 1447.0
42 TraesCS6A01G343100 chr3A 93.917 937 53 3 4679 5615 693650982 693651914 0.000000e+00 1411.0
43 TraesCS6A01G343100 chr3A 81.818 891 137 14 3743 4610 65467327 65468215 0.000000e+00 725.0
44 TraesCS6A01G343100 chr3A 81.092 513 84 5 1023 1533 65466660 65467161 1.130000e-106 398.0
45 TraesCS6A01G343100 chr3A 86.364 176 18 5 467 640 735519868 735519697 2.670000e-43 187.0
46 TraesCS6A01G343100 chr3A 88.889 99 5 1 2368 2460 433425539 433425637 3.550000e-22 117.0
47 TraesCS6A01G343100 chr1A 95.068 1257 54 3 2467 3716 61004801 61003546 0.000000e+00 1971.0
48 TraesCS6A01G343100 chr6B 91.358 1296 73 20 642 1924 648694758 648696027 0.000000e+00 1736.0
49 TraesCS6A01G343100 chr6B 94.704 963 50 1 3717 4678 648696024 648696986 0.000000e+00 1495.0
50 TraesCS6A01G343100 chr6B 78.824 850 159 13 3743 4575 633731405 633732250 2.290000e-153 553.0
51 TraesCS6A01G343100 chr6B 90.761 368 26 5 76 438 648694000 648694364 8.460000e-133 484.0
52 TraesCS6A01G343100 chr6B 78.752 513 94 7 1021 1533 612271419 612270922 4.190000e-86 329.0
53 TraesCS6A01G343100 chr6B 89.848 197 10 6 1625 1820 648691682 648691869 1.560000e-60 244.0
54 TraesCS6A01G343100 chr6B 86.364 176 18 6 467 640 22770260 22770431 2.670000e-43 187.0
55 TraesCS6A01G343100 chr1B 93.917 937 54 3 4680 5615 12817679 12818613 0.000000e+00 1411.0
56 TraesCS6A01G343100 chr1B 93.723 940 50 4 4680 5615 6835115 6836049 0.000000e+00 1400.0
57 TraesCS6A01G343100 chr1B 85.876 177 18 6 467 640 124869829 124869657 1.240000e-41 182.0
58 TraesCS6A01G343100 chr1B 87.879 99 6 1 2368 2460 532721338 532721436 1.650000e-20 111.0
59 TraesCS6A01G343100 chr5B 93.597 937 57 3 4680 5615 473623762 473622828 0.000000e+00 1395.0
60 TraesCS6A01G343100 chr5B 88.701 177 18 1 2193 2369 12655991 12656165 1.230000e-51 215.0
61 TraesCS6A01G343100 chr5B 86.364 176 17 7 467 640 287102341 287102511 9.610000e-43 185.0
62 TraesCS6A01G343100 chr3B 93.497 938 59 2 4679 5615 44006497 44007433 0.000000e+00 1393.0
63 TraesCS6A01G343100 chr3B 82.195 893 132 19 3743 4611 85093213 85092324 0.000000e+00 743.0
64 TraesCS6A01G343100 chr3B 81.395 516 81 8 1028 1539 85093855 85093351 1.880000e-109 407.0
65 TraesCS6A01G343100 chr2B 93.490 937 59 2 4680 5615 174347301 174348236 0.000000e+00 1391.0
66 TraesCS6A01G343100 chr2B 86.364 176 18 5 467 640 482041956 482041785 2.670000e-43 187.0
67 TraesCS6A01G343100 chr2A 96.154 442 14 1 1928 2369 778838763 778839201 0.000000e+00 719.0
68 TraesCS6A01G343100 chr2A 94.624 93 5 0 2368 2460 778839240 778839332 1.630000e-30 145.0
69 TraesCS6A01G343100 chr3D 81.777 878 139 9 3743 4599 54985241 54984364 0.000000e+00 715.0
70 TraesCS6A01G343100 chr3D 82.147 857 126 13 3743 4575 54830760 54829907 0.000000e+00 710.0
71 TraesCS6A01G343100 chr3D 88.482 382 38 3 1990 2369 97566031 97566408 1.840000e-124 457.0
72 TraesCS6A01G343100 chr3D 81.323 514 81 7 1023 1533 54831421 54830920 2.440000e-108 403.0
73 TraesCS6A01G343100 chr3D 80.606 495 87 2 1028 1522 54985889 54985404 1.910000e-99 374.0
74 TraesCS6A01G343100 chr3D 85.965 171 20 4 496 663 70738276 70738445 4.470000e-41 180.0
75 TraesCS6A01G343100 chr3D 86.538 156 17 4 511 663 556157327 556157173 9.670000e-38 169.0
76 TraesCS6A01G343100 chr3D 88.764 89 4 1 2370 2452 500537053 500536965 2.770000e-18 104.0
77 TraesCS6A01G343100 chr3D 95.000 60 3 0 1944 2003 97549373 97549432 1.670000e-15 95.3
78 TraesCS6A01G343100 chr4A 93.878 441 22 4 1930 2369 668360076 668360512 0.000000e+00 660.0
79 TraesCS6A01G343100 chr4A 94.422 251 13 1 2119 2369 668364704 668364953 8.820000e-103 385.0
80 TraesCS6A01G343100 chr4B 76.553 499 90 9 1019 1517 604139337 604139808 1.210000e-61 248.0
81 TraesCS6A01G343100 chr4B 85.795 176 19 6 467 640 500972093 500972264 1.240000e-41 182.0
82 TraesCS6A01G343100 chr4B 85.876 177 18 7 467 640 526399404 526399576 1.240000e-41 182.0
83 TraesCS6A01G343100 chr4B 85.876 177 18 7 467 640 616394351 616394523 1.240000e-41 182.0
84 TraesCS6A01G343100 chr4B 85.876 177 18 6 467 640 631643673 631643501 1.240000e-41 182.0
85 TraesCS6A01G343100 chr4B 81.818 99 12 1 2368 2460 235341012 235341110 1.680000e-10 78.7
86 TraesCS6A01G343100 chr2D 87.368 190 18 6 468 654 623515038 623514852 4.410000e-51 213.0
87 TraesCS6A01G343100 chr4D 83.902 205 18 11 473 663 493943693 493943896 1.240000e-41 182.0
88 TraesCS6A01G343100 chr4D 90.551 127 9 2 518 643 547100 546976 1.250000e-36 165.0
89 TraesCS6A01G343100 chr4D 84.181 177 11 10 480 640 418740448 418740273 7.530000e-34 156.0
90 TraesCS6A01G343100 chr4D 83.516 182 13 9 475 640 29656653 29656473 2.710000e-33 154.0
91 TraesCS6A01G343100 chr4D 82.840 169 13 7 476 639 419156311 419156154 2.730000e-28 137.0
92 TraesCS6A01G343100 chr1D 85.876 177 18 7 467 640 439366888 439367060 1.240000e-41 182.0


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 TraesCS6A01G343100 chr6A 576910102 576915716 5614 False 10370.000000 10370 100.000000 1 5615 1 chr6A.!!$F2 5614
1 TraesCS6A01G343100 chr6A 17909226 17910495 1269 False 1956.000000 1956 94.571000 2455 3717 1 chr6A.!!$F1 1262
2 TraesCS6A01G343100 chr7A 37923727 37925516 1789 True 3162.000000 3162 98.547000 1926 3715 1 chr7A.!!$R1 1789
3 TraesCS6A01G343100 chr5A 663844930 663846699 1769 False 3061.000000 3061 97.910000 1951 3717 1 chr5A.!!$F2 1766
4 TraesCS6A01G343100 chr5A 40703920 40704854 934 False 1439.000000 1439 94.450000 4680 5615 1 chr5A.!!$F1 935
5 TraesCS6A01G343100 chr7B 80067747 80068997 1250 True 2126.000000 2126 97.364000 2467 3716 1 chr7B.!!$R1 1249
6 TraesCS6A01G343100 chr6D 430400829 430403538 2709 False 1440.333333 2030 95.523667 1 4678 3 chr6D.!!$F2 4677
7 TraesCS6A01G343100 chr6D 430318114 430323286 5172 False 914.000000 1539 88.852000 1 4678 5 chr6D.!!$F1 4677
8 TraesCS6A01G343100 chr6D 420567578 420568417 839 True 580.000000 580 79.527000 3749 4575 1 chr6D.!!$R3 826
9 TraesCS6A01G343100 chr6D 408155484 408157055 1571 True 433.500000 532 78.450000 1021 4615 2 chr6D.!!$R4 3594
10 TraesCS6A01G343100 chrUn 257168007 257169235 1228 False 1980.000000 1980 95.854000 2494 3715 1 chrUn.!!$F3 1221
11 TraesCS6A01G343100 chrUn 65692655 65693587 932 False 1387.000000 1387 93.490000 4680 5615 1 chrUn.!!$F2 935
12 TraesCS6A01G343100 chr7D 629977731 629978959 1228 False 1980.000000 1980 95.854000 2494 3715 1 chr7D.!!$F1 1221
13 TraesCS6A01G343100 chr5D 559648460 559649688 1228 False 1980.000000 1980 95.854000 2494 3715 1 chr5D.!!$F2 1221
14 TraesCS6A01G343100 chr3A 712382111 712383375 1264 False 1978.000000 1978 94.957000 2455 3716 1 chr3A.!!$F4 1261
15 TraesCS6A01G343100 chr3A 701672806 701673741 935 False 1447.000000 1447 94.569000 4680 5615 1 chr3A.!!$F3 935
16 TraesCS6A01G343100 chr3A 693650982 693651914 932 False 1411.000000 1411 93.917000 4679 5615 1 chr3A.!!$F2 936
17 TraesCS6A01G343100 chr3A 65466660 65468215 1555 False 561.500000 725 81.455000 1023 4610 2 chr3A.!!$F5 3587
18 TraesCS6A01G343100 chr1A 61003546 61004801 1255 True 1971.000000 1971 95.068000 2467 3716 1 chr1A.!!$R1 1249
19 TraesCS6A01G343100 chr6B 648691682 648696986 5304 False 989.750000 1736 91.667750 76 4678 4 chr6B.!!$F3 4602
20 TraesCS6A01G343100 chr6B 633731405 633732250 845 False 553.000000 553 78.824000 3743 4575 1 chr6B.!!$F2 832
21 TraesCS6A01G343100 chr1B 12817679 12818613 934 False 1411.000000 1411 93.917000 4680 5615 1 chr1B.!!$F2 935
22 TraesCS6A01G343100 chr1B 6835115 6836049 934 False 1400.000000 1400 93.723000 4680 5615 1 chr1B.!!$F1 935
23 TraesCS6A01G343100 chr5B 473622828 473623762 934 True 1395.000000 1395 93.597000 4680 5615 1 chr5B.!!$R1 935
24 TraesCS6A01G343100 chr3B 44006497 44007433 936 False 1393.000000 1393 93.497000 4679 5615 1 chr3B.!!$F1 936
25 TraesCS6A01G343100 chr3B 85092324 85093855 1531 True 575.000000 743 81.795000 1028 4611 2 chr3B.!!$R1 3583
26 TraesCS6A01G343100 chr2B 174347301 174348236 935 False 1391.000000 1391 93.490000 4680 5615 1 chr2B.!!$F1 935
27 TraesCS6A01G343100 chr2A 778838763 778839332 569 False 432.000000 719 95.389000 1928 2460 2 chr2A.!!$F1 532
28 TraesCS6A01G343100 chr3D 54829907 54831421 1514 True 556.500000 710 81.735000 1023 4575 2 chr3D.!!$R3 3552
29 TraesCS6A01G343100 chr3D 54984364 54985889 1525 True 544.500000 715 81.191500 1028 4599 2 chr3D.!!$R4 3571

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
673 4165 0.253894 ATGGCAGCAGAGCACACATA 59.746 50.000 0.0 0.0 35.83 2.29 F
1935 5453 0.399233 GGATACCTCTGTCTGGCCCT 60.399 60.000 0.0 0.0 0.00 5.19 F
2736 6305 1.270826 CAGAGACGGTGATGAGTGTGT 59.729 52.381 0.0 0.0 0.00 3.72 F
3787 7362 0.179070 GGACTTCCCGAGCTTCATCC 60.179 60.000 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 5738 2.027605 CGACGTAGCGGATGCCAT 59.972 61.111 0.00 0.00 44.31 4.40 R
2883 6452 0.548031 CAAAGCCCCAGATCTAGCCA 59.452 55.000 0.00 0.00 0.00 4.75 R
3971 7576 0.523072 GCTACCGACGGTACTTGTCA 59.477 55.000 22.70 2.76 37.09 3.58 R
4941 8552 0.319211 CTGTCGGCGTAGGTTCAACA 60.319 55.000 6.85 0.00 0.00 3.33 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
21 22 4.249181 CAAAATAATTTTGCTGAGCGGC 57.751 40.909 0.00 0.00 42.91 6.53
22 23 2.193306 AATAATTTTGCTGAGCGGCG 57.807 45.000 0.51 0.51 34.52 6.46
23 24 0.381801 ATAATTTTGCTGAGCGGCGG 59.618 50.000 9.78 0.00 34.52 6.13
45 46 3.648009 CGTGAGCAAGAGAGAGAACTTT 58.352 45.455 0.00 0.00 0.00 2.66
48 49 4.447389 GTGAGCAAGAGAGAGAACTTTGAC 59.553 45.833 0.00 0.00 0.00 3.18
49 50 4.100035 TGAGCAAGAGAGAGAACTTTGACA 59.900 41.667 0.00 0.00 0.00 3.58
52 53 5.526846 AGCAAGAGAGAGAACTTTGACAAAG 59.473 40.000 23.41 23.41 44.10 2.77
53 54 5.525378 GCAAGAGAGAGAACTTTGACAAAGA 59.475 40.000 30.01 0.00 41.02 2.52
54 55 6.292811 GCAAGAGAGAGAACTTTGACAAAGAG 60.293 42.308 30.01 9.87 41.02 2.85
56 57 5.070313 AGAGAGAGAACTTTGACAAAGAGCT 59.930 40.000 30.01 24.20 41.02 4.09
57 58 5.679601 AGAGAGAACTTTGACAAAGAGCTT 58.320 37.500 30.01 16.39 41.02 3.74
58 59 6.821388 AGAGAGAACTTTGACAAAGAGCTTA 58.179 36.000 30.01 0.00 41.02 3.09
59 60 7.275920 AGAGAGAACTTTGACAAAGAGCTTAA 58.724 34.615 30.01 0.00 41.02 1.85
61 62 6.823689 AGAGAACTTTGACAAAGAGCTTAACA 59.176 34.615 30.01 0.00 41.02 2.41
62 63 7.336931 AGAGAACTTTGACAAAGAGCTTAACAA 59.663 33.333 30.01 0.00 41.02 2.83
63 64 8.000780 AGAACTTTGACAAAGAGCTTAACAAT 57.999 30.769 30.01 4.94 41.02 2.71
64 65 7.917505 AGAACTTTGACAAAGAGCTTAACAATG 59.082 33.333 30.01 4.47 41.02 2.82
65 66 7.100458 ACTTTGACAAAGAGCTTAACAATGT 57.900 32.000 30.01 5.07 41.02 2.71
67 68 6.691754 TTGACAAAGAGCTTAACAATGTGA 57.308 33.333 0.00 0.00 0.00 3.58
68 69 6.691754 TGACAAAGAGCTTAACAATGTGAA 57.308 33.333 0.00 0.00 0.00 3.18
69 70 7.275888 TGACAAAGAGCTTAACAATGTGAAT 57.724 32.000 0.00 0.00 0.00 2.57
70 71 7.362662 TGACAAAGAGCTTAACAATGTGAATC 58.637 34.615 0.00 0.00 0.00 2.52
71 72 7.013178 TGACAAAGAGCTTAACAATGTGAATCA 59.987 33.333 0.00 0.00 0.00 2.57
72 73 7.365741 ACAAAGAGCTTAACAATGTGAATCAG 58.634 34.615 0.00 0.00 0.00 2.90
74 75 6.734104 AGAGCTTAACAATGTGAATCAGAC 57.266 37.500 0.00 0.00 0.00 3.51
75 76 6.471146 AGAGCTTAACAATGTGAATCAGACT 58.529 36.000 0.00 0.00 0.00 3.24
76 77 6.370994 AGAGCTTAACAATGTGAATCAGACTG 59.629 38.462 0.00 0.00 0.00 3.51
77 78 6.233434 AGCTTAACAATGTGAATCAGACTGA 58.767 36.000 7.80 7.80 0.00 3.41
79 80 6.621596 GCTTAACAATGTGAATCAGACTGACC 60.622 42.308 7.47 3.55 0.00 4.02
80 81 4.356405 ACAATGTGAATCAGACTGACCA 57.644 40.909 7.47 6.30 0.00 4.02
450 3939 7.552458 ACAATTTGGATTTGTCAAAGTTTCC 57.448 32.000 8.83 8.83 37.50 3.13
469 3958 1.804151 CCGAGTTGGCGAAATTGAAGA 59.196 47.619 0.00 0.00 0.00 2.87
470 3959 2.420022 CCGAGTTGGCGAAATTGAAGAT 59.580 45.455 0.00 0.00 0.00 2.40
471 3960 3.621268 CCGAGTTGGCGAAATTGAAGATA 59.379 43.478 0.00 0.00 0.00 1.98
472 3961 4.094294 CCGAGTTGGCGAAATTGAAGATAA 59.906 41.667 0.00 0.00 0.00 1.75
473 3962 5.391523 CCGAGTTGGCGAAATTGAAGATAAA 60.392 40.000 0.00 0.00 0.00 1.40
474 3963 6.083630 CGAGTTGGCGAAATTGAAGATAAAA 58.916 36.000 0.00 0.00 0.00 1.52
475 3964 6.249260 CGAGTTGGCGAAATTGAAGATAAAAG 59.751 38.462 0.00 0.00 0.00 2.27
476 3965 6.389906 AGTTGGCGAAATTGAAGATAAAAGG 58.610 36.000 0.00 0.00 0.00 3.11
477 3966 5.323371 TGGCGAAATTGAAGATAAAAGGG 57.677 39.130 0.00 0.00 0.00 3.95
478 3967 4.112634 GGCGAAATTGAAGATAAAAGGGC 58.887 43.478 0.00 0.00 0.00 5.19
479 3968 4.112634 GCGAAATTGAAGATAAAAGGGCC 58.887 43.478 0.00 0.00 0.00 5.80
480 3969 4.142160 GCGAAATTGAAGATAAAAGGGCCT 60.142 41.667 0.00 0.00 0.00 5.19
481 3970 5.343249 CGAAATTGAAGATAAAAGGGCCTG 58.657 41.667 6.92 0.00 0.00 4.85
482 3971 5.105756 CGAAATTGAAGATAAAAGGGCCTGT 60.106 40.000 6.92 0.00 0.00 4.00
483 3972 6.572314 CGAAATTGAAGATAAAAGGGCCTGTT 60.572 38.462 14.69 14.69 0.00 3.16
484 3973 6.686484 AATTGAAGATAAAAGGGCCTGTTT 57.314 33.333 15.62 15.21 0.00 2.83
485 3974 7.790782 AATTGAAGATAAAAGGGCCTGTTTA 57.209 32.000 15.62 16.77 0.00 2.01
486 3975 6.834168 TTGAAGATAAAAGGGCCTGTTTAG 57.166 37.500 15.62 0.00 0.00 1.85
537 4026 8.773404 ACTTAATGTCTACTATGTTTGTGGTC 57.227 34.615 0.00 0.00 0.00 4.02
538 4027 8.594550 ACTTAATGTCTACTATGTTTGTGGTCT 58.405 33.333 0.00 0.00 0.00 3.85
542 4031 9.959721 AATGTCTACTATGTTTGTGGTCTATTT 57.040 29.630 0.00 0.00 0.00 1.40
543 4032 9.959721 ATGTCTACTATGTTTGTGGTCTATTTT 57.040 29.630 0.00 0.00 0.00 1.82
544 4033 9.787435 TGTCTACTATGTTTGTGGTCTATTTTT 57.213 29.630 0.00 0.00 0.00 1.94
580 4069 3.325293 TTTTTGTTCCTTGTTGCTGCA 57.675 38.095 0.00 0.00 0.00 4.41
581 4070 3.540314 TTTTGTTCCTTGTTGCTGCAT 57.460 38.095 1.84 0.00 0.00 3.96
582 4071 3.540314 TTTGTTCCTTGTTGCTGCATT 57.460 38.095 1.84 0.00 0.00 3.56
583 4072 4.662468 TTTGTTCCTTGTTGCTGCATTA 57.338 36.364 1.84 0.00 0.00 1.90
584 4073 4.870123 TTGTTCCTTGTTGCTGCATTAT 57.130 36.364 1.84 0.00 0.00 1.28
585 4074 4.870123 TGTTCCTTGTTGCTGCATTATT 57.130 36.364 1.84 0.00 0.00 1.40
586 4075 5.212532 TGTTCCTTGTTGCTGCATTATTT 57.787 34.783 1.84 0.00 0.00 1.40
587 4076 4.989797 TGTTCCTTGTTGCTGCATTATTTG 59.010 37.500 1.84 0.00 0.00 2.32
588 4077 4.870123 TCCTTGTTGCTGCATTATTTGT 57.130 36.364 1.84 0.00 0.00 2.83
589 4078 4.558178 TCCTTGTTGCTGCATTATTTGTG 58.442 39.130 1.84 0.00 0.00 3.33
590 4079 3.680937 CCTTGTTGCTGCATTATTTGTGG 59.319 43.478 1.84 0.00 0.00 4.17
591 4080 3.316071 TGTTGCTGCATTATTTGTGGG 57.684 42.857 1.84 0.00 0.00 4.61
592 4081 2.896044 TGTTGCTGCATTATTTGTGGGA 59.104 40.909 1.84 0.00 0.00 4.37
593 4082 3.056678 TGTTGCTGCATTATTTGTGGGAG 60.057 43.478 1.84 0.00 0.00 4.30
594 4083 1.477700 TGCTGCATTATTTGTGGGAGC 59.522 47.619 0.00 0.00 0.00 4.70
595 4084 1.753073 GCTGCATTATTTGTGGGAGCT 59.247 47.619 0.00 0.00 0.00 4.09
596 4085 2.167075 GCTGCATTATTTGTGGGAGCTT 59.833 45.455 0.00 0.00 0.00 3.74
597 4086 3.381272 GCTGCATTATTTGTGGGAGCTTA 59.619 43.478 0.00 0.00 0.00 3.09
598 4087 4.498682 GCTGCATTATTTGTGGGAGCTTAG 60.499 45.833 0.00 0.00 0.00 2.18
599 4088 4.854173 TGCATTATTTGTGGGAGCTTAGA 58.146 39.130 0.00 0.00 0.00 2.10
600 4089 5.448654 TGCATTATTTGTGGGAGCTTAGAT 58.551 37.500 0.00 0.00 0.00 1.98
601 4090 5.300034 TGCATTATTTGTGGGAGCTTAGATG 59.700 40.000 0.00 0.00 0.00 2.90
602 4091 5.300286 GCATTATTTGTGGGAGCTTAGATGT 59.700 40.000 0.00 0.00 0.00 3.06
603 4092 6.732154 CATTATTTGTGGGAGCTTAGATGTG 58.268 40.000 0.00 0.00 0.00 3.21
604 4093 4.574674 ATTTGTGGGAGCTTAGATGTGA 57.425 40.909 0.00 0.00 0.00 3.58
605 4094 3.334583 TTGTGGGAGCTTAGATGTGAC 57.665 47.619 0.00 0.00 0.00 3.67
606 4095 2.256306 TGTGGGAGCTTAGATGTGACA 58.744 47.619 0.00 0.00 0.00 3.58
607 4096 2.840038 TGTGGGAGCTTAGATGTGACAT 59.160 45.455 0.00 0.00 0.00 3.06
608 4097 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
609 4098 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
610 4099 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
611 4100 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
612 4101 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
613 4102 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
614 4103 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
615 4104 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
616 4105 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
617 4106 8.814038 AGCTTAGATGTGACATCCTTAAAAAT 57.186 30.769 21.05 3.65 0.00 1.82
618 4107 9.905713 AGCTTAGATGTGACATCCTTAAAAATA 57.094 29.630 21.05 2.69 0.00 1.40
643 4132 8.812513 ATCTAGATGTGAATTGGACAAATTGA 57.187 30.769 3.89 0.00 38.64 2.57
644 4133 8.634335 TCTAGATGTGAATTGGACAAATTGAA 57.366 30.769 0.00 0.00 38.64 2.69
645 4134 8.733458 TCTAGATGTGAATTGGACAAATTGAAG 58.267 33.333 0.00 0.00 38.64 3.02
669 4161 2.133281 AAATATGGCAGCAGAGCACA 57.867 45.000 0.00 0.00 35.83 4.57
673 4165 0.253894 ATGGCAGCAGAGCACACATA 59.746 50.000 0.00 0.00 35.83 2.29
984 4484 2.202756 GCGCGGAGTAGGAACCAG 60.203 66.667 8.83 0.00 0.00 4.00
998 4498 1.264288 GAACCAGACCTGCAGAAAACG 59.736 52.381 17.39 0.00 0.00 3.60
1201 4701 4.344865 GCTCCCCGGGCTTTCACA 62.345 66.667 17.73 0.00 0.00 3.58
1203 4703 1.000896 CTCCCCGGGCTTTCACATT 60.001 57.895 17.73 0.00 0.00 2.71
1215 4715 0.409092 TTCACATTGCCACCATCCCT 59.591 50.000 0.00 0.00 0.00 4.20
1333 4833 4.070552 GCCGCCTTCTCACCGAGT 62.071 66.667 0.00 0.00 0.00 4.18
1352 4852 2.440796 CAATGGTGCGGCCTCCAT 60.441 61.111 17.15 17.15 44.88 3.41
1355 4855 1.344953 AATGGTGCGGCCTCCATAGA 61.345 55.000 21.16 0.82 42.82 1.98
1543 5043 5.049405 CCACTTCAAGGTACACATGTCTTTC 60.049 44.000 0.00 0.00 0.00 2.62
1584 5084 7.530426 ACAATTTCTTGCTTATCACTTCCTT 57.470 32.000 0.00 0.00 35.69 3.36
1596 5096 7.704047 GCTTATCACTTCCTTTGAAATTCATCC 59.296 37.037 0.00 0.00 0.00 3.51
1598 5098 6.975196 TCACTTCCTTTGAAATTCATCCAA 57.025 33.333 0.00 0.00 0.00 3.53
1660 5160 0.452987 TCAGCCATCACCGTACGTAC 59.547 55.000 15.90 15.90 0.00 3.67
1875 5389 7.051000 GCTGTATTCTCCTCCCCATTTATATC 58.949 42.308 0.00 0.00 0.00 1.63
1876 5390 7.092668 GCTGTATTCTCCTCCCCATTTATATCT 60.093 40.741 0.00 0.00 0.00 1.98
1881 5395 5.372363 TCTCCTCCCCATTTATATCTTTGCA 59.628 40.000 0.00 0.00 0.00 4.08
1924 5442 2.628657 ACAGCTTACGGATGGATACCTC 59.371 50.000 0.00 0.00 35.35 3.85
1935 5453 0.399233 GGATACCTCTGTCTGGCCCT 60.399 60.000 0.00 0.00 0.00 5.19
1986 5504 1.453928 GCCATCAACCCTAGCCCAC 60.454 63.158 0.00 0.00 0.00 4.61
2100 5621 3.288308 CTCGTGACGGCCTCTTGCT 62.288 63.158 4.70 0.00 40.92 3.91
2280 5801 2.418368 TTGCTAGATTTGGGCACGAT 57.582 45.000 0.00 0.00 35.62 3.73
2736 6305 1.270826 CAGAGACGGTGATGAGTGTGT 59.729 52.381 0.00 0.00 0.00 3.72
2883 6452 1.380785 TTGGTCGCCGGATCTAGGT 60.381 57.895 5.05 0.00 0.00 3.08
3011 6580 2.120232 CGGTGATGACGATGCTCTTAC 58.880 52.381 0.00 0.00 0.00 2.34
3378 6947 3.657398 ACATGCTTTGAGGATGGATCA 57.343 42.857 12.92 0.00 46.66 2.92
3516 7085 0.451783 GATGTTAGGCCTTTGTGCGG 59.548 55.000 12.58 0.00 0.00 5.69
3699 7268 1.697754 AGGCCGGGGATGATTCCTT 60.698 57.895 2.18 0.00 42.20 3.36
3736 7305 3.778622 ACCTTGATACCCCACTAGAGT 57.221 47.619 0.00 0.00 0.00 3.24
3787 7362 0.179070 GGACTTCCCGAGCTTCATCC 60.179 60.000 0.00 0.00 0.00 3.51
3841 7416 0.438830 CAAAGTAACCGAGAGTGCGC 59.561 55.000 0.00 0.00 0.00 6.09
3876 7451 3.370978 CCGTAATCGTCAACAGCTTTGAT 59.629 43.478 12.42 2.74 35.01 2.57
3982 7590 2.726691 CCGCGCTTGACAAGTACCG 61.727 63.158 16.39 14.74 0.00 4.02
4073 7681 3.329567 CGTCGTCTACGTAAACTTTGC 57.670 47.619 2.02 0.00 46.72 3.68
4182 7790 2.556459 CGATCTCGTCAGGGGCGAT 61.556 63.158 0.00 0.00 37.74 4.58
4217 7825 2.435069 CTCCTGAGTTCATGGCAGAGAT 59.565 50.000 0.00 0.00 0.00 2.75
4385 7993 1.822990 CTCGGACCAGCTTACCAACTA 59.177 52.381 0.00 0.00 0.00 2.24
4427 8035 2.355126 CGTCGGCATGGAGATCGG 60.355 66.667 0.00 0.00 0.00 4.18
4632 8240 8.324191 AGAAATAGGACAGATCTTTCCATGTA 57.676 34.615 26.11 12.80 33.92 2.29
4662 8272 2.777832 AGACTTCCTTGGATGACTGC 57.222 50.000 9.17 0.00 0.00 4.40
4663 8273 1.980765 AGACTTCCTTGGATGACTGCA 59.019 47.619 9.17 0.00 0.00 4.41
4665 8275 3.149196 GACTTCCTTGGATGACTGCAAA 58.851 45.455 9.17 0.00 31.82 3.68
4839 8450 2.353607 GTCGGCATAGACGAGGCG 60.354 66.667 0.00 0.00 46.55 5.52
4941 8552 2.325082 GCGCTGACCATTTGACGGT 61.325 57.895 0.00 0.00 40.30 4.83
4947 8558 2.616376 CTGACCATTTGACGGTGTTGAA 59.384 45.455 0.00 0.00 36.69 2.69
4959 8570 0.598158 GTGTTGAACCTACGCCGACA 60.598 55.000 0.00 0.00 0.00 4.35
5043 8654 4.329545 GCCCCTCTGCCACGTCAA 62.330 66.667 0.00 0.00 0.00 3.18
5087 8698 1.189524 TCGATCCGTGGGACAACCTT 61.190 55.000 0.00 0.00 44.16 3.50
5100 8711 0.662619 CAACCTTCGTGTGTGCACAT 59.337 50.000 24.69 0.22 45.50 3.21
5107 8718 3.177997 TCGTGTGTGCACATATATGCT 57.822 42.857 24.69 0.00 46.28 3.79
5109 8720 2.032636 CGTGTGTGCACATATATGCTGG 60.033 50.000 24.69 4.17 46.28 4.85
5136 8747 4.805231 CGTCGGCATACGTGGGCA 62.805 66.667 14.04 1.01 44.69 5.36
5137 8748 2.203015 GTCGGCATACGTGGGCAT 60.203 61.111 14.04 0.00 44.69 4.40
5138 8749 1.817941 GTCGGCATACGTGGGCATT 60.818 57.895 14.04 0.00 44.69 3.56
5139 8750 0.531090 GTCGGCATACGTGGGCATTA 60.531 55.000 14.04 0.00 44.69 1.90
5140 8751 0.531090 TCGGCATACGTGGGCATTAC 60.531 55.000 14.04 0.00 44.69 1.89
5410 9030 1.372582 AGTGTTCATGCATGCGTAGG 58.627 50.000 22.25 0.97 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.742201 TCTCTTGCTCACGCCGCC 62.742 66.667 0.00 0.00 34.43 6.13
20 21 3.184683 CTCTCTTGCTCACGCCGC 61.185 66.667 0.00 0.00 34.43 6.53
21 22 1.515952 CTCTCTCTTGCTCACGCCG 60.516 63.158 0.00 0.00 34.43 6.46
22 23 0.244994 TTCTCTCTCTTGCTCACGCC 59.755 55.000 0.00 0.00 34.43 5.68
23 24 1.067915 AGTTCTCTCTCTTGCTCACGC 60.068 52.381 0.00 0.00 0.00 5.34
24 25 3.296322 AAGTTCTCTCTCTTGCTCACG 57.704 47.619 0.00 0.00 0.00 4.35
25 26 4.447389 GTCAAAGTTCTCTCTCTTGCTCAC 59.553 45.833 0.00 0.00 0.00 3.51
27 28 4.626042 TGTCAAAGTTCTCTCTCTTGCTC 58.374 43.478 0.00 0.00 0.00 4.26
28 29 4.679373 TGTCAAAGTTCTCTCTCTTGCT 57.321 40.909 0.00 0.00 0.00 3.91
31 32 5.757808 GCTCTTTGTCAAAGTTCTCTCTCTT 59.242 40.000 21.81 0.00 39.52 2.85
34 35 5.289083 AGCTCTTTGTCAAAGTTCTCTCT 57.711 39.130 21.81 10.11 39.52 3.10
36 37 6.823689 TGTTAAGCTCTTTGTCAAAGTTCTCT 59.176 34.615 21.81 12.87 39.52 3.10
37 38 7.016361 TGTTAAGCTCTTTGTCAAAGTTCTC 57.984 36.000 21.81 11.22 39.52 2.87
38 39 7.391148 TTGTTAAGCTCTTTGTCAAAGTTCT 57.609 32.000 21.81 16.82 39.52 3.01
39 40 7.702348 ACATTGTTAAGCTCTTTGTCAAAGTTC 59.298 33.333 21.81 15.21 39.52 3.01
40 41 7.489113 CACATTGTTAAGCTCTTTGTCAAAGTT 59.511 33.333 21.81 13.15 39.52 2.66
41 42 6.974622 CACATTGTTAAGCTCTTTGTCAAAGT 59.025 34.615 21.81 8.03 39.52 2.66
43 44 7.094508 TCACATTGTTAAGCTCTTTGTCAAA 57.905 32.000 0.00 0.00 0.00 2.69
45 46 6.691754 TTCACATTGTTAAGCTCTTTGTCA 57.308 33.333 0.00 0.00 0.00 3.58
48 49 7.536622 GTCTGATTCACATTGTTAAGCTCTTTG 59.463 37.037 1.23 0.00 0.00 2.77
49 50 7.446625 AGTCTGATTCACATTGTTAAGCTCTTT 59.553 33.333 1.23 0.00 0.00 2.52
52 53 6.369890 TCAGTCTGATTCACATTGTTAAGCTC 59.630 38.462 0.00 0.00 0.00 4.09
53 54 6.148480 GTCAGTCTGATTCACATTGTTAAGCT 59.852 38.462 5.68 0.00 0.00 3.74
54 55 6.310197 GTCAGTCTGATTCACATTGTTAAGC 58.690 40.000 5.68 0.00 0.00 3.09
56 57 6.295249 TGGTCAGTCTGATTCACATTGTTAA 58.705 36.000 5.68 0.00 0.00 2.01
57 58 5.863965 TGGTCAGTCTGATTCACATTGTTA 58.136 37.500 5.68 0.00 0.00 2.41
58 59 4.717877 TGGTCAGTCTGATTCACATTGTT 58.282 39.130 5.68 0.00 0.00 2.83
59 60 4.321718 CTGGTCAGTCTGATTCACATTGT 58.678 43.478 5.68 0.00 0.00 2.71
61 62 3.871463 GCCTGGTCAGTCTGATTCACATT 60.871 47.826 5.68 0.00 0.00 2.71
62 63 2.355513 GCCTGGTCAGTCTGATTCACAT 60.356 50.000 5.68 0.00 0.00 3.21
63 64 1.002430 GCCTGGTCAGTCTGATTCACA 59.998 52.381 5.68 3.00 0.00 3.58
64 65 1.731720 GCCTGGTCAGTCTGATTCAC 58.268 55.000 5.68 0.00 0.00 3.18
65 66 0.247460 CGCCTGGTCAGTCTGATTCA 59.753 55.000 5.68 7.18 0.00 2.57
67 68 1.599047 CCGCCTGGTCAGTCTGATT 59.401 57.895 5.68 0.00 0.00 2.57
68 69 3.303189 CCGCCTGGTCAGTCTGAT 58.697 61.111 5.68 0.00 0.00 2.90
79 80 3.848272 ACACAATTTGATTACCGCCTG 57.152 42.857 2.79 0.00 0.00 4.85
80 81 4.839121 TCTACACAATTTGATTACCGCCT 58.161 39.130 2.79 0.00 0.00 5.52
400 3513 0.605319 TTGCACCTTACTTCCCGCAG 60.605 55.000 0.00 0.00 0.00 5.18
450 3939 3.747099 ATCTTCAATTTCGCCAACTCG 57.253 42.857 0.00 0.00 0.00 4.18
469 3958 4.202631 TGTGTCCTAAACAGGCCCTTTTAT 60.203 41.667 0.00 0.00 38.97 1.40
470 3959 3.138653 TGTGTCCTAAACAGGCCCTTTTA 59.861 43.478 0.00 2.37 38.97 1.52
471 3960 2.091555 TGTGTCCTAAACAGGCCCTTTT 60.092 45.455 0.00 1.02 38.97 2.27
472 3961 1.497286 TGTGTCCTAAACAGGCCCTTT 59.503 47.619 0.00 0.00 38.97 3.11
473 3962 1.145571 TGTGTCCTAAACAGGCCCTT 58.854 50.000 0.00 0.00 38.97 3.95
474 3963 1.282157 GATGTGTCCTAAACAGGCCCT 59.718 52.381 0.00 0.00 38.97 5.19
475 3964 1.282157 AGATGTGTCCTAAACAGGCCC 59.718 52.381 0.00 0.00 38.97 5.80
476 3965 2.789409 AGATGTGTCCTAAACAGGCC 57.211 50.000 0.00 0.00 38.97 5.19
477 3966 4.737855 TCTAGATGTGTCCTAAACAGGC 57.262 45.455 0.00 0.00 38.97 4.85
511 4000 9.216117 GACCACAAACATAGTAGACATTAAGTT 57.784 33.333 0.00 0.00 0.00 2.66
512 4001 8.594550 AGACCACAAACATAGTAGACATTAAGT 58.405 33.333 0.00 0.00 0.00 2.24
516 4005 9.959721 AAATAGACCACAAACATAGTAGACATT 57.040 29.630 0.00 0.00 0.00 2.71
517 4006 9.959721 AAAATAGACCACAAACATAGTAGACAT 57.040 29.630 0.00 0.00 0.00 3.06
518 4007 9.787435 AAAAATAGACCACAAACATAGTAGACA 57.213 29.630 0.00 0.00 0.00 3.41
560 4049 3.325293 TGCAGCAACAAGGAACAAAAA 57.675 38.095 0.00 0.00 0.00 1.94
561 4050 3.540314 ATGCAGCAACAAGGAACAAAA 57.460 38.095 0.00 0.00 0.00 2.44
562 4051 3.540314 AATGCAGCAACAAGGAACAAA 57.460 38.095 0.00 0.00 0.00 2.83
563 4052 4.870123 ATAATGCAGCAACAAGGAACAA 57.130 36.364 0.00 0.00 0.00 2.83
564 4053 4.870123 AATAATGCAGCAACAAGGAACA 57.130 36.364 0.00 0.00 0.00 3.18
565 4054 4.990426 ACAAATAATGCAGCAACAAGGAAC 59.010 37.500 0.00 0.00 0.00 3.62
566 4055 4.989797 CACAAATAATGCAGCAACAAGGAA 59.010 37.500 0.00 0.00 0.00 3.36
567 4056 4.558178 CACAAATAATGCAGCAACAAGGA 58.442 39.130 0.00 0.00 0.00 3.36
568 4057 3.680937 CCACAAATAATGCAGCAACAAGG 59.319 43.478 0.00 0.00 0.00 3.61
569 4058 3.680937 CCCACAAATAATGCAGCAACAAG 59.319 43.478 0.00 0.00 0.00 3.16
570 4059 3.323115 TCCCACAAATAATGCAGCAACAA 59.677 39.130 0.00 0.00 0.00 2.83
571 4060 2.896044 TCCCACAAATAATGCAGCAACA 59.104 40.909 0.00 0.00 0.00 3.33
572 4061 3.514645 CTCCCACAAATAATGCAGCAAC 58.485 45.455 0.00 0.00 0.00 4.17
573 4062 2.094078 GCTCCCACAAATAATGCAGCAA 60.094 45.455 0.00 0.00 0.00 3.91
574 4063 1.477700 GCTCCCACAAATAATGCAGCA 59.522 47.619 0.00 0.00 0.00 4.41
575 4064 1.753073 AGCTCCCACAAATAATGCAGC 59.247 47.619 0.00 0.00 0.00 5.25
576 4065 4.883585 TCTAAGCTCCCACAAATAATGCAG 59.116 41.667 0.00 0.00 0.00 4.41
577 4066 4.854173 TCTAAGCTCCCACAAATAATGCA 58.146 39.130 0.00 0.00 0.00 3.96
578 4067 5.300286 ACATCTAAGCTCCCACAAATAATGC 59.700 40.000 0.00 0.00 0.00 3.56
579 4068 6.543465 TCACATCTAAGCTCCCACAAATAATG 59.457 38.462 0.00 0.00 0.00 1.90
580 4069 6.543831 GTCACATCTAAGCTCCCACAAATAAT 59.456 38.462 0.00 0.00 0.00 1.28
581 4070 5.880332 GTCACATCTAAGCTCCCACAAATAA 59.120 40.000 0.00 0.00 0.00 1.40
582 4071 5.045942 TGTCACATCTAAGCTCCCACAAATA 60.046 40.000 0.00 0.00 0.00 1.40
583 4072 4.263462 TGTCACATCTAAGCTCCCACAAAT 60.263 41.667 0.00 0.00 0.00 2.32
584 4073 3.072330 TGTCACATCTAAGCTCCCACAAA 59.928 43.478 0.00 0.00 0.00 2.83
585 4074 2.637382 TGTCACATCTAAGCTCCCACAA 59.363 45.455 0.00 0.00 0.00 3.33
586 4075 2.256306 TGTCACATCTAAGCTCCCACA 58.744 47.619 0.00 0.00 0.00 4.17
587 4076 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
588 4077 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
589 4078 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
590 4079 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
591 4080 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
592 4081 8.814038 ATTTTTAAGGATGTCACATCTAAGCT 57.186 30.769 17.46 3.19 0.00 3.74
617 4106 9.904198 TCAATTTGTCCAATTCACATCTAGATA 57.096 29.630 4.54 0.00 32.24 1.98
618 4107 8.812513 TCAATTTGTCCAATTCACATCTAGAT 57.187 30.769 0.00 0.00 32.24 1.98
619 4108 8.634335 TTCAATTTGTCCAATTCACATCTAGA 57.366 30.769 0.00 0.00 32.24 2.43
620 4109 8.733458 TCTTCAATTTGTCCAATTCACATCTAG 58.267 33.333 0.00 0.00 32.24 2.43
621 4110 8.634335 TCTTCAATTTGTCCAATTCACATCTA 57.366 30.769 0.00 0.00 32.24 1.98
622 4111 7.528996 TCTTCAATTTGTCCAATTCACATCT 57.471 32.000 0.00 0.00 32.24 2.90
623 4112 9.859427 TTATCTTCAATTTGTCCAATTCACATC 57.141 29.630 0.00 0.00 32.24 3.06
632 4121 9.598517 GCCATATTTTTATCTTCAATTTGTCCA 57.401 29.630 0.00 0.00 0.00 4.02
633 4122 9.598517 TGCCATATTTTTATCTTCAATTTGTCC 57.401 29.630 0.00 0.00 0.00 4.02
635 4124 9.101655 GCTGCCATATTTTTATCTTCAATTTGT 57.898 29.630 0.00 0.00 0.00 2.83
636 4125 9.100554 TGCTGCCATATTTTTATCTTCAATTTG 57.899 29.630 0.00 0.00 0.00 2.32
637 4126 9.321562 CTGCTGCCATATTTTTATCTTCAATTT 57.678 29.630 0.00 0.00 0.00 1.82
638 4127 8.698210 TCTGCTGCCATATTTTTATCTTCAATT 58.302 29.630 0.00 0.00 0.00 2.32
639 4128 8.241497 TCTGCTGCCATATTTTTATCTTCAAT 57.759 30.769 0.00 0.00 0.00 2.57
640 4129 7.643569 TCTGCTGCCATATTTTTATCTTCAA 57.356 32.000 0.00 0.00 0.00 2.69
641 4130 6.238842 GCTCTGCTGCCATATTTTTATCTTCA 60.239 38.462 0.00 0.00 0.00 3.02
642 4131 6.148264 GCTCTGCTGCCATATTTTTATCTTC 58.852 40.000 0.00 0.00 0.00 2.87
643 4132 5.595542 TGCTCTGCTGCCATATTTTTATCTT 59.404 36.000 0.00 0.00 0.00 2.40
644 4133 5.009410 GTGCTCTGCTGCCATATTTTTATCT 59.991 40.000 0.00 0.00 0.00 1.98
645 4134 5.218139 GTGCTCTGCTGCCATATTTTTATC 58.782 41.667 0.00 0.00 0.00 1.75
669 4161 7.558604 AGCATCATGGCAAAAATTTAGTATGT 58.441 30.769 0.00 0.00 35.83 2.29
673 4165 6.576185 CCTAGCATCATGGCAAAAATTTAGT 58.424 36.000 0.00 0.00 35.83 2.24
846 4345 2.030274 AGCAAAATTGTTACCAGCGGTC 60.030 45.455 3.45 0.00 37.09 4.79
861 4360 1.800586 CGAGCAAGAGCACTAGCAAAA 59.199 47.619 0.00 0.00 45.49 2.44
975 4475 2.024176 TTCTGCAGGTCTGGTTCCTA 57.976 50.000 15.13 0.00 33.54 2.94
984 4484 2.151202 TCCATTCGTTTTCTGCAGGTC 58.849 47.619 15.13 1.28 0.00 3.85
998 4498 0.813210 CTCGCCTGCTCCTTCCATTC 60.813 60.000 0.00 0.00 0.00 2.67
1101 4601 3.712881 GTGACGTGGAAGCCGTGC 61.713 66.667 0.00 0.00 38.92 5.34
1199 4699 0.632835 ATCAGGGATGGTGGCAATGT 59.367 50.000 0.00 0.00 0.00 2.71
1201 4701 3.526211 CATCAGGGATGGTGGCAAT 57.474 52.632 0.00 0.00 36.51 3.56
1241 4741 1.211743 CGTGACATCATCATCCACGG 58.788 55.000 0.00 0.00 44.51 4.94
1333 4833 2.361104 GGAGGCCGCACCATTGAA 60.361 61.111 9.31 0.00 43.14 2.69
1352 4852 0.611062 CACGACTGGGTGGTCCTCTA 60.611 60.000 0.00 0.00 34.27 2.43
1355 4855 2.200370 TCACGACTGGGTGGTCCT 59.800 61.111 0.00 0.00 38.46 3.85
1543 5043 7.186804 AGAAATTGTACAGTGTTCAAACTTCG 58.813 34.615 17.74 0.00 31.19 3.79
1604 5104 7.872993 CCGAAACAGTATCTACCAATATGACAT 59.127 37.037 0.00 0.00 0.00 3.06
1611 5111 5.670792 TGACCGAAACAGTATCTACCAAT 57.329 39.130 0.00 0.00 0.00 3.16
1810 5310 5.122082 CACAATGTATGTAGTGTGCACATCA 59.878 40.000 24.69 21.21 41.46 3.07
1881 5395 5.121811 GTTTCTCATCTGCAGTCCATGTAT 58.878 41.667 14.67 0.00 0.00 2.29
1986 5504 3.157949 GGAGGAGGAAGGCCCGAG 61.158 72.222 0.00 0.00 40.87 4.63
2217 5738 2.027605 CGACGTAGCGGATGCCAT 59.972 61.111 0.00 0.00 44.31 4.40
2883 6452 0.548031 CAAAGCCCCAGATCTAGCCA 59.452 55.000 0.00 0.00 0.00 4.75
3378 6947 1.533469 CGTCACCTCCGTCTTCCCTT 61.533 60.000 0.00 0.00 0.00 3.95
3516 7085 2.029380 GGGCCAAATACCAAACAGACAC 60.029 50.000 4.39 0.00 0.00 3.67
3717 7286 5.646215 AGATACTCTAGTGGGGTATCAAGG 58.354 45.833 23.90 0.00 42.21 3.61
3718 7287 6.660094 GGTAGATACTCTAGTGGGGTATCAAG 59.340 46.154 23.90 0.00 42.21 3.02
3719 7288 6.550163 GGTAGATACTCTAGTGGGGTATCAA 58.450 44.000 23.90 0.00 42.21 2.57
3732 7301 0.851469 TCAGCCCCGGTAGATACTCT 59.149 55.000 0.00 0.00 0.00 3.24
3736 7305 0.559205 TTCCTCAGCCCCGGTAGATA 59.441 55.000 0.00 0.00 0.00 1.98
3787 7362 3.198635 ACCATGTAGTCATCTGGGTTCAG 59.801 47.826 0.00 0.00 42.21 3.02
3971 7576 0.523072 GCTACCGACGGTACTTGTCA 59.477 55.000 22.70 2.76 37.09 3.58
3982 7590 2.352032 ACAGGCTGAGGCTACCGAC 61.352 63.158 23.66 0.00 36.44 4.79
4073 7681 0.729116 GGTCATGACCGTGATGCTTG 59.271 55.000 28.52 0.00 42.29 4.01
4336 7944 0.952497 CAACTGATGACTGGCACGCT 60.952 55.000 0.00 0.00 0.00 5.07
4385 7993 1.066430 ACTCGTTGCATTGGTACCGAT 60.066 47.619 9.03 9.03 0.00 4.18
4427 8035 3.462333 TTGCGCTGGACGTTGTTGC 62.462 57.895 9.73 0.00 46.11 4.17
4560 8168 4.702131 AGCTCTTTTAAATTGCGGTGAGAT 59.298 37.500 0.00 0.00 0.00 2.75
4575 8183 4.530161 AGTACATCACAGAGGAGCTCTTTT 59.470 41.667 14.64 0.00 38.99 2.27
4641 8250 3.582647 TGCAGTCATCCAAGGAAGTCTTA 59.417 43.478 0.00 0.00 33.68 2.10
4656 8266 3.006537 GGAGGTACAGTACTTTGCAGTCA 59.993 47.826 10.62 0.00 34.06 3.41
4662 8272 4.081807 GGTAGTGGGAGGTACAGTACTTTG 60.082 50.000 10.62 0.00 41.95 2.77
4663 8273 4.092279 GGTAGTGGGAGGTACAGTACTTT 58.908 47.826 10.62 0.00 41.95 2.66
4665 8275 2.651334 TGGTAGTGGGAGGTACAGTACT 59.349 50.000 10.62 0.00 41.95 2.73
4742 8352 2.355837 CCGTCGGCATATGTCCGG 60.356 66.667 27.12 19.84 46.43 5.14
4891 8502 4.626081 GGCCCGTGCTATGCCGAT 62.626 66.667 0.00 0.00 35.08 4.18
4941 8552 0.319211 CTGTCGGCGTAGGTTCAACA 60.319 55.000 6.85 0.00 0.00 3.33
5100 8711 1.600636 GCAAGGCCGCCAGCATATA 60.601 57.895 18.79 0.00 46.50 0.86
5336 8955 2.537401 GTGACATAGCTACACCCGAAC 58.463 52.381 0.00 0.00 0.00 3.95
5483 9104 4.487412 GTAGACCCCACGCGTCCG 62.487 72.222 9.86 1.40 41.14 4.79
5532 9154 3.299503 AGGAACACTTTGGAGCAACATT 58.700 40.909 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.