Multiple sequence alignment - TraesCS7D01G372500

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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 TraesCS7D01G372500 chr7D 100.000 6159 0 0 1 6159 481849069 481842911 0.000000e+00 11374.0
1 TraesCS7D01G372500 chr7D 86.950 636 55 12 925 1533 481844991 481844357 0.000000e+00 689.0
2 TraesCS7D01G372500 chr7D 86.950 636 55 12 4079 4713 481848145 481847537 0.000000e+00 689.0
3 TraesCS7D01G372500 chr7D 98.750 80 1 0 5183 5262 41837676 41837755 6.440000e-30 143.0
4 TraesCS7D01G372500 chr7D 98.734 79 1 0 5184 5262 485090876 485090954 2.310000e-29 141.0
5 TraesCS7D01G372500 chr7D 96.471 85 2 1 5178 5262 79628435 79628352 8.320000e-29 139.0
6 TraesCS7D01G372500 chr7A 93.397 1257 47 13 3937 5189 549011960 549010736 0.000000e+00 1829.0
7 TraesCS7D01G372500 chr7A 93.068 1082 48 11 2062 3118 693127188 693126109 0.000000e+00 1557.0
8 TraesCS7D01G372500 chr7A 88.581 1191 86 17 368 1533 549019440 549018275 0.000000e+00 1400.0
9 TraesCS7D01G372500 chr7A 91.834 894 48 11 5263 6147 549010737 549009860 0.000000e+00 1223.0
10 TraesCS7D01G372500 chr7A 89.910 892 76 8 4079 4969 549018897 549018019 0.000000e+00 1136.0
11 TraesCS7D01G372500 chr7A 88.394 629 58 9 917 1533 549011824 549011199 0.000000e+00 743.0
12 TraesCS7D01G372500 chr7A 90.926 551 30 7 5263 5809 549009480 549008946 0.000000e+00 723.0
13 TraesCS7D01G372500 chr7A 92.903 465 24 6 3209 3666 693126128 693125666 0.000000e+00 667.0
14 TraesCS7D01G372500 chr7A 88.947 380 33 3 1 371 549100270 549099891 1.560000e-125 460.0
15 TraesCS7D01G372500 chr7A 90.104 192 18 1 4999 5189 549009670 549009479 1.330000e-61 248.0
16 TraesCS7D01G372500 chr7A 82.609 276 25 13 3668 3932 549013489 549013226 8.040000e-54 222.0
17 TraesCS7D01G372500 chr7A 97.260 73 2 0 4923 4995 549009723 549009651 2.330000e-24 124.0
18 TraesCS7D01G372500 chr7A 89.362 94 10 0 3113 3206 33720245 33720152 1.080000e-22 119.0
19 TraesCS7D01G372500 chr7A 96.774 31 1 0 6117 6147 549008947 549008917 1.100000e-02 52.8
20 TraesCS7D01G372500 chr7B 93.960 1192 45 10 4003 5189 507850535 507849366 0.000000e+00 1777.0
21 TraesCS7D01G372500 chr7B 92.484 785 46 9 759 1533 507946101 507945320 0.000000e+00 1110.0
22 TraesCS7D01G372500 chr7B 88.354 893 80 14 4079 4969 507945934 507945064 0.000000e+00 1051.0
23 TraesCS7D01G372500 chr7B 90.710 549 29 8 5263 5804 507849367 507848834 0.000000e+00 712.0
24 TraesCS7D01G372500 chr7B 87.025 632 58 13 925 1533 507850458 507849828 0.000000e+00 691.0
25 TraesCS7D01G372500 chr7B 84.957 698 74 10 1 689 507947141 507946466 0.000000e+00 678.0
26 TraesCS7D01G372500 chr7B 94.377 409 22 1 5736 6144 507848826 507848419 1.460000e-175 627.0
27 TraesCS7D01G372500 chr7B 82.847 274 27 13 3670 3936 507944945 507944685 1.730000e-55 228.0
28 TraesCS7D01G372500 chr7B 97.500 80 2 0 5183 5262 626240352 626240273 2.990000e-28 137.0
29 TraesCS7D01G372500 chr2B 93.579 1059 50 8 2063 3118 523437889 523436846 0.000000e+00 1563.0
30 TraesCS7D01G372500 chr2B 90.554 487 35 8 3209 3687 523436865 523436382 8.710000e-178 634.0
31 TraesCS7D01G372500 chr2B 88.776 98 11 0 3115 3212 198149239 198149336 3.020000e-23 121.0
32 TraesCS7D01G372500 chr2B 87.097 93 10 2 3768 3858 584481898 584481990 3.040000e-18 104.0
33 TraesCS7D01G372500 chr2B 75.258 194 34 13 1879 2065 772578809 772578995 5.120000e-11 80.5
34 TraesCS7D01G372500 chr2B 92.500 40 3 0 2036 2075 772575797 772575836 2.400000e-04 58.4
35 TraesCS7D01G372500 chr4A 95.794 951 40 0 2062 3012 670674291 670675241 0.000000e+00 1535.0
36 TraesCS7D01G372500 chr4A 91.048 458 31 7 3217 3666 670676090 670676545 1.470000e-170 610.0
37 TraesCS7D01G372500 chr4A 87.768 466 44 11 1549 2011 63707815 63708270 3.270000e-147 532.0
38 TraesCS7D01G372500 chr4A 98.611 72 0 1 3012 3083 670676021 670676091 6.480000e-25 126.0
39 TraesCS7D01G372500 chr3D 89.225 529 42 9 1549 2063 609861739 609862266 0.000000e+00 647.0
40 TraesCS7D01G372500 chr3D 89.057 530 37 10 1549 2063 253524832 253525355 6.730000e-179 638.0
41 TraesCS7D01G372500 chr3D 89.245 530 28 9 1549 2063 253523388 253523903 2.420000e-178 636.0
42 TraesCS7D01G372500 chr3D 84.688 529 56 16 1549 2055 11336656 11336131 7.120000e-139 505.0
43 TraesCS7D01G372500 chr3D 100.000 77 0 0 5186 5262 303788541 303788465 6.440000e-30 143.0
44 TraesCS7D01G372500 chr3D 96.512 86 2 1 5177 5262 26654119 26654203 2.310000e-29 141.0
45 TraesCS7D01G372500 chr3D 92.453 53 4 0 3160 3212 380448638 380448690 6.620000e-10 76.8
46 TraesCS7D01G372500 chr1D 83.514 552 62 19 1549 2075 312478034 312478581 7.180000e-134 488.0
47 TraesCS7D01G372500 chr1D 87.065 402 34 16 1549 1936 312479509 312479906 7.330000e-119 438.0
48 TraesCS7D01G372500 chr1D 98.734 79 1 0 5184 5262 440050356 440050434 2.310000e-29 141.0
49 TraesCS7D01G372500 chr3A 84.368 467 52 16 1549 2009 518720264 518720715 7.330000e-119 438.0
50 TraesCS7D01G372500 chr2D 81.339 493 52 22 1549 2013 124209858 124210338 1.260000e-96 364.0
51 TraesCS7D01G372500 chr2D 76.587 252 38 15 3694 3933 99729781 99729539 1.080000e-22 119.0
52 TraesCS7D01G372500 chr2D 88.095 84 6 2 694 777 166856746 166856825 5.080000e-16 97.1
53 TraesCS7D01G372500 chrUn 77.712 507 76 23 1582 2070 146408627 146409114 6.080000e-70 276.0
54 TraesCS7D01G372500 chrUn 76.550 516 85 24 1578 2075 146421108 146421605 3.690000e-62 250.0
55 TraesCS7D01G372500 chrUn 75.581 516 92 23 1578 2075 146416808 146417307 2.230000e-54 224.0
56 TraesCS7D01G372500 chrUn 96.552 87 1 2 5178 5262 84435474 84435388 6.440000e-30 143.0
57 TraesCS7D01G372500 chrUn 90.244 82 8 0 1699 1780 146412449 146412530 2.350000e-19 108.0
58 TraesCS7D01G372500 chr4B 79.358 218 31 11 573 783 89459620 89459410 2.310000e-29 141.0
59 TraesCS7D01G372500 chr4B 92.000 100 8 0 3113 3212 517559144 517559045 2.310000e-29 141.0
60 TraesCS7D01G372500 chr6B 95.402 87 3 1 5175 5260 618334936 618335022 2.990000e-28 137.0
61 TraesCS7D01G372500 chr1B 85.821 134 12 7 1549 1679 24688050 24687921 1.080000e-27 135.0
62 TraesCS7D01G372500 chr1B 79.532 171 23 10 3772 3933 582937652 582937819 1.810000e-20 111.0
63 TraesCS7D01G372500 chr5D 78.022 182 23 8 3772 3937 427590714 427590534 1.410000e-16 99.0
64 TraesCS7D01G372500 chr5D 79.195 149 24 5 3790 3932 559459973 559459826 5.080000e-16 97.1
65 TraesCS7D01G372500 chr5B 86.022 93 11 2 3773 3864 326908849 326908758 1.410000e-16 99.0
66 TraesCS7D01G372500 chr5B 83.838 99 12 4 3768 3864 90957337 90957241 2.360000e-14 91.6
67 TraesCS7D01G372500 chr6A 79.195 149 21 6 3523 3668 35552613 35552754 1.830000e-15 95.3
68 TraesCS7D01G372500 chr3B 76.111 180 25 14 1909 2075 819986058 819986232 1.840000e-10 78.7
69 TraesCS7D01G372500 chr6D 89.583 48 5 0 3163 3210 284488855 284488808 1.850000e-05 62.1
70 TraesCS7D01G372500 chr4D 100.000 31 0 0 624 654 495614880 495614910 2.400000e-04 58.4


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 TraesCS7D01G372500 chr7D 481842911 481849069 6158 True 11374.00 11374 100.00000 1 6159 1 chr7D.!!$R2 6158
1 TraesCS7D01G372500 chr7D 481844357 481848145 3788 True 689.00 689 86.95000 925 4713 2 chr7D.!!$R3 3788
2 TraesCS7D01G372500 chr7A 549018019 549019440 1421 True 1268.00 1400 89.24550 368 4969 2 chr7A.!!$R4 4601
3 TraesCS7D01G372500 chr7A 693125666 693127188 1522 True 1112.00 1557 92.98550 2062 3666 2 chr7A.!!$R5 1604
4 TraesCS7D01G372500 chr7A 549008917 549013489 4572 True 645.60 1829 91.41225 917 6147 8 chr7A.!!$R3 5230
5 TraesCS7D01G372500 chr7B 507848419 507850535 2116 True 951.75 1777 91.51800 925 6144 4 chr7B.!!$R2 5219
6 TraesCS7D01G372500 chr7B 507944685 507947141 2456 True 766.75 1110 87.16050 1 4969 4 chr7B.!!$R3 4968
7 TraesCS7D01G372500 chr2B 523436382 523437889 1507 True 1098.50 1563 92.06650 2063 3687 2 chr2B.!!$R1 1624
8 TraesCS7D01G372500 chr4A 670674291 670676545 2254 False 757.00 1535 95.15100 2062 3666 3 chr4A.!!$F2 1604
9 TraesCS7D01G372500 chr3D 609861739 609862266 527 False 647.00 647 89.22500 1549 2063 1 chr3D.!!$F3 514
10 TraesCS7D01G372500 chr3D 253523388 253525355 1967 False 637.00 638 89.15100 1549 2063 2 chr3D.!!$F4 514
11 TraesCS7D01G372500 chr3D 11336131 11336656 525 True 505.00 505 84.68800 1549 2055 1 chr3D.!!$R1 506
12 TraesCS7D01G372500 chr1D 312478034 312479906 1872 False 463.00 488 85.28950 1549 2075 2 chr1D.!!$F2 526
13 TraesCS7D01G372500 chrUn 146416808 146421605 4797 False 237.00 250 76.06550 1578 2075 2 chrUn.!!$F2 497

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
611 621 0.403271 AAGAACACATGGCAGCTCCT 59.597 50.000 0.00 0.0 35.26 3.69 F
752 765 0.620556 AGGACCGGATTGCTTCATGT 59.379 50.000 9.46 0.0 0.00 3.21 F
907 1219 1.300233 CACGCGGCCTCTTCTATCC 60.300 63.158 12.47 0.0 0.00 2.59 F
4818 7389 1.307343 AGCTGGGAGGGTGTGCTAT 60.307 57.895 0.00 0.0 31.71 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4803 7374 2.063979 CCGATAGCACACCCTCCCA 61.064 63.158 0.00 0.00 0.0 4.37 R
4887 10558 2.202797 CCATCCGGTGAGCACTCG 60.203 66.667 0.00 3.05 0.0 4.18 R
4982 10656 0.034186 TCACCATTCCATCCCAGCAC 60.034 55.000 0.00 0.00 0.0 4.40 R
5675 11420 0.110486 CAGTACTGCCCCCACAAAGT 59.890 55.000 10.54 0.00 0.0 2.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.465705 ATAGACACCATGCTCCGTGG 59.534 55.000 2.02 2.02 45.34 4.94
22 23 4.720902 CACCATGCTCCGTGGGCA 62.721 66.667 8.23 0.80 44.23 5.36
54 55 1.276622 TCTAGACTTTGTGAGGGCCC 58.723 55.000 16.46 16.46 0.00 5.80
56 57 1.351017 CTAGACTTTGTGAGGGCCCAA 59.649 52.381 27.56 9.26 0.00 4.12
70 71 1.337167 GGCCCAAAGAGCATTGTGTTC 60.337 52.381 0.00 0.00 0.00 3.18
71 72 1.337167 GCCCAAAGAGCATTGTGTTCC 60.337 52.381 0.00 0.00 0.00 3.62
72 73 1.962807 CCCAAAGAGCATTGTGTTCCA 59.037 47.619 0.00 0.00 0.00 3.53
78 79 0.957395 AGCATTGTGTTCCAGAGGCG 60.957 55.000 0.00 0.00 0.00 5.52
104 105 2.171003 CCTCCCTTTGTTGACCCATTC 58.829 52.381 0.00 0.00 0.00 2.67
113 114 3.370104 TGTTGACCCATTCCTTGTGTTT 58.630 40.909 0.00 0.00 0.00 2.83
114 115 3.131933 TGTTGACCCATTCCTTGTGTTTG 59.868 43.478 0.00 0.00 0.00 2.93
128 129 4.882671 TGTGTTTGTCTCTCTTTGCTTC 57.117 40.909 0.00 0.00 0.00 3.86
140 141 5.564550 TCTCTTTGCTTCAAGGCTATCTTT 58.435 37.500 0.00 0.00 32.41 2.52
180 182 7.389053 AGAAACTTATGAGTTGTTAAGAGGCTG 59.611 37.037 3.30 0.00 45.18 4.85
216 218 4.489810 TGCAAACAAAATCTGAACAACGT 58.510 34.783 0.00 0.00 0.00 3.99
219 221 5.231991 GCAAACAAAATCTGAACAACGTCAT 59.768 36.000 0.00 0.00 0.00 3.06
224 226 9.528018 AACAAAATCTGAACAACGTCATTAAAT 57.472 25.926 0.00 0.00 0.00 1.40
315 317 7.326968 TGATGTTTTGATTAGAACACACACA 57.673 32.000 0.00 0.00 38.46 3.72
316 318 7.766283 TGATGTTTTGATTAGAACACACACAA 58.234 30.769 0.00 0.00 38.46 3.33
318 320 9.891828 GATGTTTTGATTAGAACACACACAATA 57.108 29.630 0.00 0.00 38.46 1.90
330 339 6.839124 ACACACACAATATGACATCCAAAT 57.161 33.333 0.00 0.00 0.00 2.32
335 344 7.118101 ACACACAATATGACATCCAAATTTTGC 59.882 33.333 3.50 0.00 0.00 3.68
336 345 7.117956 CACACAATATGACATCCAAATTTTGCA 59.882 33.333 3.50 0.00 0.00 4.08
340 349 8.723311 CAATATGACATCCAAATTTTGCAAAGT 58.277 29.630 12.41 6.68 0.00 2.66
343 352 7.475771 TGACATCCAAATTTTGCAAAGTAAC 57.524 32.000 12.41 0.00 0.00 2.50
372 382 2.159184 TCAAAATTGGCAAGTGAACGCA 60.159 40.909 5.96 0.00 0.00 5.24
379 389 2.161410 TGGCAAGTGAACGCATCAATAC 59.839 45.455 0.00 0.00 40.50 1.89
410 420 5.538053 TCCAAATGCATCCACAAACTTAGAA 59.462 36.000 0.00 0.00 0.00 2.10
454 464 8.657729 GGTGATTAAAAGTTAAGAGCACTACTC 58.342 37.037 0.00 0.00 46.66 2.59
467 477 6.466885 GAGCACTACTCTTTTATGGTCCTA 57.533 41.667 0.00 0.00 42.62 2.94
487 497 8.639761 GGTCCTATTATGTTTTAGCTCACTAGA 58.360 37.037 0.00 0.00 0.00 2.43
502 512 3.572255 TCACTAGAATTTTGGCAACCCAC 59.428 43.478 0.00 0.00 41.97 4.61
606 616 2.343506 TGGCAAGAACACATGGCAG 58.656 52.632 0.00 0.00 45.76 4.85
610 620 0.524862 CAAGAACACATGGCAGCTCC 59.475 55.000 0.00 0.00 0.00 4.70
611 621 0.403271 AAGAACACATGGCAGCTCCT 59.597 50.000 0.00 0.00 35.26 3.69
615 625 0.692476 ACACATGGCAGCTCCTAACA 59.308 50.000 0.00 0.00 35.26 2.41
650 661 2.004808 TAGTGACGCGAGGATGGCAG 62.005 60.000 15.93 0.00 41.24 4.85
654 665 3.267860 CGCGAGGATGGCAGCTTC 61.268 66.667 0.00 4.61 41.24 3.86
674 685 5.523438 TTCCTTTTCGTATGGCAAGTTTT 57.477 34.783 0.00 0.00 0.00 2.43
711 724 9.203421 GGTTTATTTTTCTTTTCGGATGACAAT 57.797 29.630 0.00 0.00 0.00 2.71
717 730 9.810545 TTTTTCTTTTCGGATGACAATTTTAGT 57.189 25.926 0.00 0.00 0.00 2.24
747 760 3.864789 AATATCAGGACCGGATTGCTT 57.135 42.857 9.46 2.34 0.00 3.91
749 762 0.911769 ATCAGGACCGGATTGCTTCA 59.088 50.000 9.46 0.00 0.00 3.02
752 765 0.620556 AGGACCGGATTGCTTCATGT 59.379 50.000 9.46 0.00 0.00 3.21
755 768 1.398390 GACCGGATTGCTTCATGTCAC 59.602 52.381 9.46 0.00 0.00 3.67
848 1160 6.687081 TCTTTCGGAAGCTCAAAAACTTTA 57.313 33.333 0.00 0.00 32.75 1.85
876 1188 3.039134 CGGCCCGCAAGTTTTCTT 58.961 55.556 0.00 0.00 41.31 2.52
907 1219 1.300233 CACGCGGCCTCTTCTATCC 60.300 63.158 12.47 0.00 0.00 2.59
922 1234 3.713288 TCTATCCTAAAACATGACGGCG 58.287 45.455 4.80 4.80 0.00 6.46
4818 7389 1.307343 AGCTGGGAGGGTGTGCTAT 60.307 57.895 0.00 0.00 31.71 2.97
4887 10558 3.154589 GGTTTGTCCCAGGATCGAC 57.845 57.895 0.00 0.00 0.00 4.20
4896 10567 1.657751 CCAGGATCGACGAGTGCTCA 61.658 60.000 3.01 0.00 0.00 4.26
4920 10591 1.918293 TGGGGTCATCTCGCCAACT 60.918 57.895 0.16 0.00 45.16 3.16
4980 10654 2.437359 GCAGCGAGCCCTGTGAAT 60.437 61.111 0.00 0.00 37.23 2.57
4981 10655 2.042831 GCAGCGAGCCCTGTGAATT 61.043 57.895 0.00 0.00 37.23 2.17
4982 10656 1.798735 CAGCGAGCCCTGTGAATTG 59.201 57.895 0.00 0.00 0.00 2.32
4984 10658 0.957395 AGCGAGCCCTGTGAATTGTG 60.957 55.000 0.00 0.00 0.00 3.33
4985 10659 1.503542 CGAGCCCTGTGAATTGTGC 59.496 57.895 0.00 0.00 0.00 4.57
4986 10660 0.957395 CGAGCCCTGTGAATTGTGCT 60.957 55.000 0.00 0.00 0.00 4.40
4987 10661 0.524862 GAGCCCTGTGAATTGTGCTG 59.475 55.000 0.00 0.00 0.00 4.41
4988 10662 0.896940 AGCCCTGTGAATTGTGCTGG 60.897 55.000 0.00 0.00 0.00 4.85
4989 10663 1.880819 GCCCTGTGAATTGTGCTGGG 61.881 60.000 9.63 9.63 42.20 4.45
4990 10664 0.251297 CCCTGTGAATTGTGCTGGGA 60.251 55.000 8.75 0.00 41.97 4.37
4991 10665 1.617804 CCCTGTGAATTGTGCTGGGAT 60.618 52.381 8.75 0.00 41.97 3.85
4992 10666 1.475280 CCTGTGAATTGTGCTGGGATG 59.525 52.381 0.00 0.00 0.00 3.51
4993 10667 1.475280 CTGTGAATTGTGCTGGGATGG 59.525 52.381 0.00 0.00 0.00 3.51
4994 10668 1.075212 TGTGAATTGTGCTGGGATGGA 59.925 47.619 0.00 0.00 0.00 3.41
4995 10669 2.170166 GTGAATTGTGCTGGGATGGAA 58.830 47.619 0.00 0.00 0.00 3.53
4996 10670 2.762327 GTGAATTGTGCTGGGATGGAAT 59.238 45.455 0.00 0.00 0.00 3.01
4997 10671 2.761767 TGAATTGTGCTGGGATGGAATG 59.238 45.455 0.00 0.00 0.00 2.67
5027 10701 2.292389 TGCTGGGATGGATTGGTGAATT 60.292 45.455 0.00 0.00 0.00 2.17
5033 10707 3.065371 GGATGGATTGGTGAATTGTCGTC 59.935 47.826 0.00 0.00 0.00 4.20
5039 10713 5.220662 GGATTGGTGAATTGTCGTCAGTATG 60.221 44.000 0.00 0.00 37.54 2.39
5055 10730 1.093972 TATGCACTTGTGGGATTGCG 58.906 50.000 2.81 0.00 37.82 4.85
5056 10731 2.126346 GCACTTGTGGGATTGCGC 60.126 61.111 0.00 0.00 0.00 6.09
5057 10732 2.176546 CACTTGTGGGATTGCGCG 59.823 61.111 0.00 0.00 0.00 6.86
5079 10755 3.002656 GCTTCCGATCATATGGTGTTGTG 59.997 47.826 2.13 0.00 0.00 3.33
5102 10778 5.105473 TGTTTGTAGTCTAGGATGTGGTAGC 60.105 44.000 0.00 0.00 0.00 3.58
5109 10785 1.529244 GGATGTGGTAGCCATGCCC 60.529 63.158 1.34 0.00 35.28 5.36
5138 10880 8.894731 TGCTTACCGCATTTGAGTATTTTTATA 58.105 29.630 0.00 0.00 45.47 0.98
5139 10881 9.166126 GCTTACCGCATTTGAGTATTTTTATAC 57.834 33.333 0.00 0.00 38.92 1.47
5192 10934 1.897560 GCACTTTGCAGTTACTCCCT 58.102 50.000 0.00 0.00 44.26 4.20
5194 10936 2.427506 CACTTTGCAGTTACTCCCTCC 58.572 52.381 0.00 0.00 0.00 4.30
5196 10938 1.002087 CTTTGCAGTTACTCCCTCCGT 59.998 52.381 0.00 0.00 0.00 4.69
5197 10939 0.606604 TTGCAGTTACTCCCTCCGTC 59.393 55.000 0.00 0.00 0.00 4.79
5198 10940 1.255667 TGCAGTTACTCCCTCCGTCC 61.256 60.000 0.00 0.00 0.00 4.79
5199 10941 1.957765 GCAGTTACTCCCTCCGTCCC 61.958 65.000 0.00 0.00 0.00 4.46
5200 10942 0.613853 CAGTTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
5202 10944 1.572415 AGTTACTCCCTCCGTCCCATA 59.428 52.381 0.00 0.00 0.00 2.74
5203 10945 2.023695 AGTTACTCCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 0.00 1.90
5204 10946 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
5205 10947 4.140853 AGTTACTCCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
5206 10948 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5207 10949 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5208 10950 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5209 10951 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5210 10952 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5211 10953 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5212 10954 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
5213 10955 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5214 10956 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
5215 10957 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
5216 10958 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
5217 10959 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
5218 10960 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5219 10961 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
5221 10963 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
5222 10964 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
5223 10965 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
5224 10966 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
5227 10969 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
5228 10970 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
5229 10971 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
5230 10972 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
5231 10973 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
5232 10974 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
5245 10987 4.743644 ACTACACTAGTGTGAAAAACGCTC 59.256 41.667 33.77 0.00 46.98 5.03
5246 10988 3.793559 ACACTAGTGTGAAAAACGCTCT 58.206 40.909 27.41 0.00 46.98 4.09
5247 10989 4.189231 ACACTAGTGTGAAAAACGCTCTT 58.811 39.130 27.41 0.00 46.98 2.85
5248 10990 5.353938 ACACTAGTGTGAAAAACGCTCTTA 58.646 37.500 27.41 0.00 46.98 2.10
5249 10991 5.989777 ACACTAGTGTGAAAAACGCTCTTAT 59.010 36.000 27.41 0.00 46.98 1.73
5250 10992 7.149973 ACACTAGTGTGAAAAACGCTCTTATA 58.850 34.615 27.41 0.00 46.98 0.98
5251 10993 7.817962 ACACTAGTGTGAAAAACGCTCTTATAT 59.182 33.333 27.41 0.00 46.98 0.86
5252 10994 8.656849 CACTAGTGTGAAAAACGCTCTTATATT 58.343 33.333 15.06 0.00 46.98 1.28
5253 10995 9.865321 ACTAGTGTGAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 46.98 0.98
5256 10998 8.612619 AGTGTGAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 46.98 2.74
5257 10999 7.855904 GTGTGAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 36.31 4.00
5258 11000 7.771361 TGTGAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
5259 11001 8.068380 GTGAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
5260 11002 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
5261 11003 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
5281 11023 4.452455 ACGGCTTTAGAAGTCTGTTCAATG 59.548 41.667 0.00 0.00 0.00 2.82
5297 11039 7.014134 TCTGTTCAATGACAACATACCAAATGT 59.986 33.333 0.00 0.00 35.50 2.71
5403 11145 5.432060 AGCTGAAACCCCCTATAACAGTAAT 59.568 40.000 0.00 0.00 0.00 1.89
5431 11173 1.978455 TACGCCATGTCCCATGGTCC 61.978 60.000 21.01 7.68 41.17 4.46
5450 11192 6.711277 TGGTCCAATCCTATATTATCTGCAC 58.289 40.000 0.00 0.00 0.00 4.57
5483 11225 1.270550 TCGGGACTGTAAACTTCGACC 59.729 52.381 0.00 0.00 0.00 4.79
5565 11310 2.271944 AGGTGTTTGTCCTAGTTGCC 57.728 50.000 0.00 0.00 33.04 4.52
5585 11330 4.202315 TGCCCACATATGATGTACAGGTAC 60.202 45.833 10.38 2.66 42.70 3.34
5615 11360 5.934625 TCCTCTTTCAGAACTCTATTGTTGC 59.065 40.000 0.00 0.00 0.00 4.17
5663 11408 4.932799 CCAGATTTACGACACCACACATTA 59.067 41.667 0.00 0.00 0.00 1.90
5675 11420 3.587061 ACCACACATTAGTTCTGGATGGA 59.413 43.478 0.00 0.00 30.56 3.41
5676 11421 3.941483 CCACACATTAGTTCTGGATGGAC 59.059 47.826 0.00 0.00 0.00 4.02
5685 11430 0.698238 TCTGGATGGACTTTGTGGGG 59.302 55.000 0.00 0.00 0.00 4.96
5686 11431 0.323725 CTGGATGGACTTTGTGGGGG 60.324 60.000 0.00 0.00 0.00 5.40
5687 11432 1.682344 GGATGGACTTTGTGGGGGC 60.682 63.158 0.00 0.00 0.00 5.80
5688 11433 1.076549 GATGGACTTTGTGGGGGCA 59.923 57.895 0.00 0.00 0.00 5.36
5689 11434 0.967380 GATGGACTTTGTGGGGGCAG 60.967 60.000 0.00 0.00 0.00 4.85
5690 11435 1.729267 ATGGACTTTGTGGGGGCAGT 61.729 55.000 0.00 0.00 0.00 4.40
5691 11436 1.063070 TGGACTTTGTGGGGGCAGTA 61.063 55.000 0.00 0.00 0.00 2.74
5692 11437 0.608308 GGACTTTGTGGGGGCAGTAC 60.608 60.000 0.00 0.00 0.00 2.73
5693 11438 0.400594 GACTTTGTGGGGGCAGTACT 59.599 55.000 0.00 0.00 0.00 2.73
5694 11439 0.110486 ACTTTGTGGGGGCAGTACTG 59.890 55.000 18.93 18.93 0.00 2.74
5695 11440 0.110486 CTTTGTGGGGGCAGTACTGT 59.890 55.000 23.44 0.00 0.00 3.55
5696 11441 0.553819 TTTGTGGGGGCAGTACTGTT 59.446 50.000 23.44 0.00 0.00 3.16
5697 11442 0.179004 TTGTGGGGGCAGTACTGTTG 60.179 55.000 23.44 0.13 0.00 3.33
5698 11443 1.971695 GTGGGGGCAGTACTGTTGC 60.972 63.158 23.44 10.73 40.80 4.17
5707 11452 0.250467 AGTACTGTTGCTGGCACTGG 60.250 55.000 0.00 0.00 0.00 4.00
5727 11473 4.638304 TGGTAACTGGTTTAGCTTCTGTC 58.362 43.478 0.00 0.00 38.73 3.51
5729 11475 1.797025 ACTGGTTTAGCTTCTGTCGC 58.203 50.000 0.00 0.00 0.00 5.19
5766 11515 4.481930 TGTTGGACTGTAAAGCAATTCG 57.518 40.909 0.00 0.00 0.00 3.34
5795 11618 8.581578 TGTTTTATGGATGATATGTAGCGAGTA 58.418 33.333 0.00 0.00 0.00 2.59
5903 11727 4.380128 GGATTGTTAATTGGTGGTCGGTTC 60.380 45.833 0.00 0.00 0.00 3.62
6020 11845 6.653320 TGGTTTACAGAACACTGGTATGAATC 59.347 38.462 0.00 0.00 36.12 2.52
6115 11940 4.825085 TGGTTTATCTGGTGTTTCTTCCAC 59.175 41.667 0.00 0.00 0.00 4.02
6144 11969 9.712305 GGTTAGCTACTTATGATGTATGTGATT 57.288 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.279173 AGTCTAGAAAATGGCCCACCT 58.721 47.619 0.00 0.00 36.63 4.00
27 28 4.156739 CCTCACAAAGTCTAGAAAATGGCC 59.843 45.833 0.00 0.00 0.00 5.36
35 36 1.276622 GGGCCCTCACAAAGTCTAGA 58.723 55.000 17.04 0.00 0.00 2.43
54 55 3.057736 CCTCTGGAACACAATGCTCTTTG 60.058 47.826 0.00 0.00 0.00 2.77
56 57 2.787994 CCTCTGGAACACAATGCTCTT 58.212 47.619 0.00 0.00 0.00 2.85
70 71 2.498726 GAGGAGCTTCGCCTCTGG 59.501 66.667 11.78 0.00 44.99 3.86
78 79 2.155279 GTCAACAAAGGGAGGAGCTTC 58.845 52.381 0.00 0.00 0.00 3.86
104 105 3.629398 AGCAAAGAGAGACAAACACAAGG 59.371 43.478 0.00 0.00 0.00 3.61
113 114 2.105477 AGCCTTGAAGCAAAGAGAGACA 59.895 45.455 0.00 0.00 34.23 3.41
114 115 2.777094 AGCCTTGAAGCAAAGAGAGAC 58.223 47.619 0.00 0.00 34.23 3.36
128 129 6.808008 TTTTCACTCTCAAAGATAGCCTTG 57.192 37.500 0.00 0.00 34.79 3.61
140 141 9.265901 CTCATAAGTTTCTCTTTTTCACTCTCA 57.734 33.333 0.00 0.00 37.56 3.27
180 182 8.593492 ATTTTGTTTGCAACTAAAATCTCCTC 57.407 30.769 19.48 0.00 39.01 3.71
224 226 8.841300 TGTGTTGTAACTGCAACTTATTGAATA 58.159 29.630 11.22 0.00 46.33 1.75
308 310 8.436970 CAAAATTTGGATGTCATATTGTGTGTG 58.563 33.333 0.00 0.00 31.53 3.82
315 317 8.851541 ACTTTGCAAAATTTGGATGTCATATT 57.148 26.923 13.84 0.00 0.00 1.28
316 318 9.941325 TTACTTTGCAAAATTTGGATGTCATAT 57.059 25.926 13.84 0.00 0.00 1.78
318 320 7.173047 GGTTACTTTGCAAAATTTGGATGTCAT 59.827 33.333 13.84 0.00 0.00 3.06
330 339 4.712337 TGAAGAAGGGGTTACTTTGCAAAA 59.288 37.500 13.84 0.00 0.00 2.44
335 344 6.705825 CCAATTTTGAAGAAGGGGTTACTTTG 59.294 38.462 0.00 0.00 0.00 2.77
336 345 6.687901 GCCAATTTTGAAGAAGGGGTTACTTT 60.688 38.462 0.00 0.00 0.00 2.66
340 349 4.227197 TGCCAATTTTGAAGAAGGGGTTA 58.773 39.130 0.00 0.00 0.00 2.85
343 352 3.071457 ACTTGCCAATTTTGAAGAAGGGG 59.929 43.478 0.00 0.00 0.00 4.79
372 382 6.751514 TGCATTTGGAACTAACGTATTGAT 57.248 33.333 0.00 0.00 0.00 2.57
379 389 3.190327 TGTGGATGCATTTGGAACTAACG 59.810 43.478 0.00 0.00 0.00 3.18
487 497 2.894126 TCATACGTGGGTTGCCAAAATT 59.106 40.909 0.00 0.00 0.00 1.82
488 498 2.520069 TCATACGTGGGTTGCCAAAAT 58.480 42.857 0.00 0.00 0.00 1.82
521 531 2.812358 AGAAAAATGGTTTCACCCGC 57.188 45.000 2.00 0.00 37.50 6.13
522 532 4.688021 TGAAAGAAAAATGGTTTCACCCG 58.312 39.130 2.00 0.00 37.50 5.28
523 533 7.095229 GCTTATGAAAGAAAAATGGTTTCACCC 60.095 37.037 0.00 0.00 41.65 4.61
524 534 7.657354 AGCTTATGAAAGAAAAATGGTTTCACC 59.343 33.333 0.00 0.00 41.65 4.02
526 536 9.044150 CAAGCTTATGAAAGAAAAATGGTTTCA 57.956 29.630 0.00 0.00 42.70 2.69
527 537 8.011673 GCAAGCTTATGAAAGAAAAATGGTTTC 58.988 33.333 0.00 0.00 34.37 2.78
528 538 7.498570 TGCAAGCTTATGAAAGAAAAATGGTTT 59.501 29.630 0.00 0.00 34.37 3.27
529 539 6.991531 TGCAAGCTTATGAAAGAAAAATGGTT 59.008 30.769 0.00 0.00 34.37 3.67
530 540 6.523840 TGCAAGCTTATGAAAGAAAAATGGT 58.476 32.000 0.00 0.00 34.37 3.55
531 541 7.424227 TTGCAAGCTTATGAAAGAAAAATGG 57.576 32.000 0.00 0.00 34.37 3.16
565 575 4.506654 ACACGTGTGACACTTATCAAAGTC 59.493 41.667 22.71 0.00 44.28 3.01
591 601 0.524862 GGAGCTGCCATGTGTTCTTG 59.475 55.000 0.00 0.00 36.34 3.02
592 602 0.403271 AGGAGCTGCCATGTGTTCTT 59.597 50.000 0.00 0.00 40.02 2.52
593 603 1.279496 TAGGAGCTGCCATGTGTTCT 58.721 50.000 0.00 0.00 40.02 3.01
623 633 2.095059 TCCTCGCGTCACTAAACTTACC 60.095 50.000 5.77 0.00 0.00 2.85
625 635 3.428452 CCATCCTCGCGTCACTAAACTTA 60.428 47.826 5.77 0.00 0.00 2.24
626 636 2.607187 CATCCTCGCGTCACTAAACTT 58.393 47.619 5.77 0.00 0.00 2.66
628 638 1.278238 CCATCCTCGCGTCACTAAAC 58.722 55.000 5.77 0.00 0.00 2.01
629 639 0.459585 GCCATCCTCGCGTCACTAAA 60.460 55.000 5.77 0.00 0.00 1.85
634 645 4.819761 GCTGCCATCCTCGCGTCA 62.820 66.667 5.77 0.00 0.00 4.35
650 661 2.488153 ACTTGCCATACGAAAAGGAAGC 59.512 45.455 0.00 0.00 0.00 3.86
654 665 6.009115 ACTAAAACTTGCCATACGAAAAGG 57.991 37.500 0.00 0.00 0.00 3.11
728 741 2.705658 TGAAGCAATCCGGTCCTGATAT 59.294 45.455 0.00 0.00 0.00 1.63
729 742 2.115427 TGAAGCAATCCGGTCCTGATA 58.885 47.619 0.00 0.00 0.00 2.15
730 743 0.911769 TGAAGCAATCCGGTCCTGAT 59.088 50.000 0.00 0.00 0.00 2.90
735 748 1.398390 GTGACATGAAGCAATCCGGTC 59.602 52.381 0.00 0.00 33.21 4.79
737 750 1.452110 TGTGACATGAAGCAATCCGG 58.548 50.000 0.00 0.00 0.00 5.14
739 752 3.192001 ACACATGTGACATGAAGCAATCC 59.808 43.478 31.94 0.00 0.00 3.01
755 768 7.087409 TCTCAAATAATAAGTGCCACACATG 57.913 36.000 0.00 0.00 36.74 3.21
876 1188 1.933500 GCCGCGTGAAAAGACTAGTCA 60.934 52.381 24.44 1.09 0.00 3.41
907 1219 1.659098 GGTCTCGCCGTCATGTTTTAG 59.341 52.381 0.00 0.00 0.00 1.85
922 1234 2.035783 GGGGTTTGGCTGGGTCTC 59.964 66.667 0.00 0.00 0.00 3.36
4803 7374 2.063979 CCGATAGCACACCCTCCCA 61.064 63.158 0.00 0.00 0.00 4.37
4842 10513 3.055328 TGGAATCCCTTCTATCATGCCA 58.945 45.455 0.00 0.00 0.00 4.92
4887 10558 2.202797 CCATCCGGTGAGCACTCG 60.203 66.667 0.00 3.05 0.00 4.18
4975 10649 1.838112 TCCATCCCAGCACAATTCAC 58.162 50.000 0.00 0.00 0.00 3.18
4977 10651 2.101917 CCATTCCATCCCAGCACAATTC 59.898 50.000 0.00 0.00 0.00 2.17
4978 10652 2.112998 CCATTCCATCCCAGCACAATT 58.887 47.619 0.00 0.00 0.00 2.32
4980 10654 0.409092 ACCATTCCATCCCAGCACAA 59.591 50.000 0.00 0.00 0.00 3.33
4981 10655 0.323633 CACCATTCCATCCCAGCACA 60.324 55.000 0.00 0.00 0.00 4.57
4982 10656 0.034186 TCACCATTCCATCCCAGCAC 60.034 55.000 0.00 0.00 0.00 4.40
4984 10658 2.077687 ATTCACCATTCCATCCCAGC 57.922 50.000 0.00 0.00 0.00 4.85
4985 10659 3.131577 CACAATTCACCATTCCATCCCAG 59.868 47.826 0.00 0.00 0.00 4.45
4986 10660 3.098377 CACAATTCACCATTCCATCCCA 58.902 45.455 0.00 0.00 0.00 4.37
4987 10661 2.159057 GCACAATTCACCATTCCATCCC 60.159 50.000 0.00 0.00 0.00 3.85
4988 10662 2.762327 AGCACAATTCACCATTCCATCC 59.238 45.455 0.00 0.00 0.00 3.51
4989 10663 3.429822 CCAGCACAATTCACCATTCCATC 60.430 47.826 0.00 0.00 0.00 3.51
4990 10664 2.498481 CCAGCACAATTCACCATTCCAT 59.502 45.455 0.00 0.00 0.00 3.41
4991 10665 1.894466 CCAGCACAATTCACCATTCCA 59.106 47.619 0.00 0.00 0.00 3.53
4992 10666 1.205417 CCCAGCACAATTCACCATTCC 59.795 52.381 0.00 0.00 0.00 3.01
4993 10667 2.170166 TCCCAGCACAATTCACCATTC 58.830 47.619 0.00 0.00 0.00 2.67
4994 10668 2.307496 TCCCAGCACAATTCACCATT 57.693 45.000 0.00 0.00 0.00 3.16
4995 10669 2.104967 CATCCCAGCACAATTCACCAT 58.895 47.619 0.00 0.00 0.00 3.55
4996 10670 1.548081 CATCCCAGCACAATTCACCA 58.452 50.000 0.00 0.00 0.00 4.17
4997 10671 0.819582 CCATCCCAGCACAATTCACC 59.180 55.000 0.00 0.00 0.00 4.02
5027 10701 2.403259 CACAAGTGCATACTGACGACA 58.597 47.619 0.00 0.00 37.19 4.35
5033 10707 2.159338 GCAATCCCACAAGTGCATACTG 60.159 50.000 0.00 0.00 39.88 2.74
5039 10713 2.126346 GCGCAATCCCACAAGTGC 60.126 61.111 0.30 0.00 36.91 4.40
5055 10730 0.792640 CACCATATGATCGGAAGCGC 59.207 55.000 3.65 0.00 0.00 5.92
5056 10731 2.154854 ACACCATATGATCGGAAGCG 57.845 50.000 3.65 0.00 0.00 4.68
5057 10732 3.002656 CACAACACCATATGATCGGAAGC 59.997 47.826 3.65 0.00 0.00 3.86
5079 10755 5.349809 GCTACCACATCCTAGACTACAAAC 58.650 45.833 0.00 0.00 0.00 2.93
5138 10880 6.426328 GCAATAGCTCTGCAACTGATATTAGT 59.574 38.462 14.26 0.00 39.69 2.24
5139 10881 6.400834 CGCAATAGCTCTGCAACTGATATTAG 60.401 42.308 18.02 0.00 39.91 1.73
5140 10882 5.406477 CGCAATAGCTCTGCAACTGATATTA 59.594 40.000 18.02 0.00 39.91 0.98
5151 10893 3.951979 AACAATACGCAATAGCTCTGC 57.048 42.857 10.07 10.07 39.10 4.26
5187 10929 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
5188 10930 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
5189 10931 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
5190 10932 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
5191 10933 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
5192 10934 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
5194 10936 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
5196 10938 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
5197 10939 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
5198 10940 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
5202 10944 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
5203 10945 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
5204 10946 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
5205 10947 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
5206 10948 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
5207 10949 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
5208 10950 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
5209 10951 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
5222 10964 4.690122 AGCGTTTTTCACACTAGTGTAGT 58.310 39.130 27.48 3.18 46.01 2.73
5223 10965 4.982916 AGAGCGTTTTTCACACTAGTGTAG 59.017 41.667 27.48 20.38 46.01 2.74
5224 10966 4.940463 AGAGCGTTTTTCACACTAGTGTA 58.060 39.130 27.48 11.32 46.01 2.90
5227 10969 8.773404 AATATAAGAGCGTTTTTCACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
5230 10972 8.612619 CCATAATATAAGAGCGTTTTTCACACT 58.387 33.333 0.00 0.00 0.00 3.55
5231 10973 7.855904 CCCATAATATAAGAGCGTTTTTCACAC 59.144 37.037 0.00 0.00 0.00 3.82
5232 10974 7.771361 TCCCATAATATAAGAGCGTTTTTCACA 59.229 33.333 0.00 0.00 0.00 3.58
5233 10975 8.068380 GTCCCATAATATAAGAGCGTTTTTCAC 58.932 37.037 0.00 0.00 0.00 3.18
5234 10976 7.042321 CGTCCCATAATATAAGAGCGTTTTTCA 60.042 37.037 0.00 0.00 0.00 2.69
5235 10977 7.288672 CGTCCCATAATATAAGAGCGTTTTTC 58.711 38.462 0.00 0.00 0.00 2.29
5236 10978 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5237 10979 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
5238 10980 5.235516 CCGTCCCATAATATAAGAGCGTTT 58.764 41.667 0.00 0.00 0.00 3.60
5239 10981 4.817517 CCGTCCCATAATATAAGAGCGTT 58.182 43.478 0.00 0.00 0.00 4.84
5240 10982 3.368116 GCCGTCCCATAATATAAGAGCGT 60.368 47.826 0.00 0.00 0.00 5.07
5241 10983 3.119101 AGCCGTCCCATAATATAAGAGCG 60.119 47.826 0.00 0.00 0.00 5.03
5242 10984 4.473477 AGCCGTCCCATAATATAAGAGC 57.527 45.455 0.00 0.00 0.00 4.09
5243 10985 7.837863 TCTAAAGCCGTCCCATAATATAAGAG 58.162 38.462 0.00 0.00 0.00 2.85
5244 10986 7.786046 TCTAAAGCCGTCCCATAATATAAGA 57.214 36.000 0.00 0.00 0.00 2.10
5245 10987 8.095169 ACTTCTAAAGCCGTCCCATAATATAAG 58.905 37.037 0.00 0.00 0.00 1.73
5246 10988 7.970102 ACTTCTAAAGCCGTCCCATAATATAA 58.030 34.615 0.00 0.00 0.00 0.98
5247 10989 7.453752 AGACTTCTAAAGCCGTCCCATAATATA 59.546 37.037 0.00 0.00 0.00 0.86
5248 10990 6.270231 AGACTTCTAAAGCCGTCCCATAATAT 59.730 38.462 0.00 0.00 0.00 1.28
5249 10991 5.601313 AGACTTCTAAAGCCGTCCCATAATA 59.399 40.000 0.00 0.00 0.00 0.98
5250 10992 4.409247 AGACTTCTAAAGCCGTCCCATAAT 59.591 41.667 0.00 0.00 0.00 1.28
5251 10993 3.773119 AGACTTCTAAAGCCGTCCCATAA 59.227 43.478 0.00 0.00 0.00 1.90
5252 10994 3.132289 CAGACTTCTAAAGCCGTCCCATA 59.868 47.826 0.00 0.00 0.00 2.74
5253 10995 2.093447 CAGACTTCTAAAGCCGTCCCAT 60.093 50.000 0.00 0.00 0.00 4.00
5254 10996 1.275291 CAGACTTCTAAAGCCGTCCCA 59.725 52.381 0.00 0.00 0.00 4.37
5255 10997 1.275573 ACAGACTTCTAAAGCCGTCCC 59.724 52.381 0.00 0.00 0.00 4.46
5256 10998 2.745515 ACAGACTTCTAAAGCCGTCC 57.254 50.000 0.00 0.00 0.00 4.79
5257 10999 3.650139 TGAACAGACTTCTAAAGCCGTC 58.350 45.455 0.00 0.00 0.00 4.79
5258 11000 3.746045 TGAACAGACTTCTAAAGCCGT 57.254 42.857 0.00 0.00 0.00 5.68
5259 11001 4.690748 TCATTGAACAGACTTCTAAAGCCG 59.309 41.667 0.00 0.00 0.00 5.52
5260 11002 5.470098 TGTCATTGAACAGACTTCTAAAGCC 59.530 40.000 0.00 0.00 35.81 4.35
5261 11003 6.545504 TGTCATTGAACAGACTTCTAAAGC 57.454 37.500 0.00 0.00 35.81 3.51
5281 11023 7.391148 ACCATTAGACATTTGGTATGTTGTC 57.609 36.000 0.00 0.00 41.88 3.18
5403 11145 5.491323 TGGGACATGGCGTATAATGATTA 57.509 39.130 0.00 0.00 0.00 1.75
5431 11173 7.101700 TGAGCAGTGCAGATAATATAGGATTG 58.898 38.462 19.20 0.00 0.00 2.67
5450 11192 2.932614 CAGTCCCGACTAAATTGAGCAG 59.067 50.000 0.00 0.00 40.20 4.24
5483 11225 4.685924 AGTTGTGAGCTGACCAAATTTTG 58.314 39.130 0.00 1.99 0.00 2.44
5565 11310 5.985530 CACAGTACCTGTACATCATATGTGG 59.014 44.000 16.75 7.18 43.43 4.17
5615 11360 4.161333 CAGAAAAGGCTTCACTAAATGCG 58.839 43.478 0.00 0.00 0.00 4.73
5663 11408 2.224867 CCCACAAAGTCCATCCAGAACT 60.225 50.000 0.00 0.00 0.00 3.01
5675 11420 0.110486 CAGTACTGCCCCCACAAAGT 59.890 55.000 10.54 0.00 0.00 2.66
5676 11421 0.110486 ACAGTACTGCCCCCACAAAG 59.890 55.000 22.90 0.00 0.00 2.77
5685 11430 1.600636 TGCCAGCAACAGTACTGCC 60.601 57.895 22.90 11.27 40.86 4.85
5686 11431 0.886490 AGTGCCAGCAACAGTACTGC 60.886 55.000 22.90 10.15 40.24 4.40
5687 11432 0.870393 CAGTGCCAGCAACAGTACTG 59.130 55.000 21.44 21.44 39.73 2.74
5688 11433 0.250467 CCAGTGCCAGCAACAGTACT 60.250 55.000 0.00 0.00 0.00 2.73
5689 11434 0.535102 ACCAGTGCCAGCAACAGTAC 60.535 55.000 0.00 0.00 0.00 2.73
5690 11435 1.052617 TACCAGTGCCAGCAACAGTA 58.947 50.000 0.00 0.00 0.00 2.74
5691 11436 0.182537 TTACCAGTGCCAGCAACAGT 59.817 50.000 0.00 0.00 0.00 3.55
5692 11437 0.593128 GTTACCAGTGCCAGCAACAG 59.407 55.000 0.00 0.00 0.00 3.16
5693 11438 0.182537 AGTTACCAGTGCCAGCAACA 59.817 50.000 0.00 0.00 0.00 3.33
5694 11439 0.593128 CAGTTACCAGTGCCAGCAAC 59.407 55.000 0.00 0.00 0.00 4.17
5695 11440 0.537143 CCAGTTACCAGTGCCAGCAA 60.537 55.000 0.00 0.00 0.00 3.91
5696 11441 1.073025 CCAGTTACCAGTGCCAGCA 59.927 57.895 0.00 0.00 0.00 4.41
5697 11442 0.537371 AACCAGTTACCAGTGCCAGC 60.537 55.000 0.00 0.00 0.00 4.85
5698 11443 1.981256 AAACCAGTTACCAGTGCCAG 58.019 50.000 0.00 0.00 0.00 4.85
5707 11452 3.123116 GCGACAGAAGCTAAACCAGTTAC 59.877 47.826 0.00 0.00 0.00 2.50
5729 11475 5.049680 AGTCCAACAATTACACAAGCGTAAG 60.050 40.000 0.00 0.00 34.95 2.34
5766 11515 7.598869 TCGCTACATATCATCCATAAAACACTC 59.401 37.037 0.00 0.00 0.00 3.51
5868 11691 7.069331 ACCAATTAACAATCCAACACAGAAAGA 59.931 33.333 0.00 0.00 0.00 2.52
5930 11754 9.620259 AGACTTCTGAACCCTTTCATTATAATC 57.380 33.333 0.00 0.00 41.05 1.75
5979 11804 1.448893 CCACCAATTGGCATGCAGC 60.449 57.895 24.79 3.15 39.07 5.25
6020 11845 6.810911 ACTGTCATTGTATGCTAGTAAGAGG 58.189 40.000 0.00 0.00 0.00 3.69
6088 11913 6.434340 GGAAGAAACACCAGATAAACCATTCT 59.566 38.462 0.00 0.00 0.00 2.40
6115 11940 7.114953 CACATACATCATAAGTAGCTAACCACG 59.885 40.741 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.