Multiple sequence alignment - TraesCS6A01G387600

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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 TraesCS6A01G387600 chr6A 100.000 9922 0 0 1 9922 604116408 604106487 0.000000e+00 18323.0
1 TraesCS6A01G387600 chr6A 93.939 462 25 3 9464 9922 346587090 346586629 0.000000e+00 695.0
2 TraesCS6A01G387600 chr6A 85.230 413 45 12 9213 9617 556914528 556914124 2.580000e-110 411.0
3 TraesCS6A01G387600 chr6A 100.000 30 0 0 7263 7292 604109058 604109029 1.000000e-03 56.5
4 TraesCS6A01G387600 chr6A 100.000 30 0 0 7351 7380 604109146 604109117 1.000000e-03 56.5
5 TraesCS6A01G387600 chr5B 99.014 5069 41 1 1774 6833 570982176 570977108 0.000000e+00 9075.0
6 TraesCS6A01G387600 chr5B 98.658 5068 59 1 1774 6832 588764379 588769446 0.000000e+00 8973.0
7 TraesCS6A01G387600 chr5B 83.598 378 30 15 451 806 396326779 396326412 9.610000e-85 326.0
8 TraesCS6A01G387600 chr5B 92.683 82 6 0 7784 7865 538915627 538915708 1.750000e-22 119.0
9 TraesCS6A01G387600 chr3A 99.014 5069 40 2 1773 6832 158181518 158176451 0.000000e+00 9075.0
10 TraesCS6A01G387600 chr3A 98.720 5077 54 3 1769 6835 468533953 468539028 0.000000e+00 9005.0
11 TraesCS6A01G387600 chr3A 84.300 414 50 11 9212 9617 697227438 697227032 3.360000e-104 390.0
12 TraesCS6A01G387600 chr3A 84.119 403 53 9 9217 9617 212134198 212133805 7.270000e-101 379.0
13 TraesCS6A01G387600 chr3A 88.421 95 10 1 7783 7876 412799413 412799319 8.140000e-21 113.0
14 TraesCS6A01G387600 chr3B 99.013 5068 40 2 1774 6832 56086036 56080970 0.000000e+00 9073.0
15 TraesCS6A01G387600 chr3B 94.332 247 14 0 9217 9463 767298155 767297909 7.270000e-101 379.0
16 TraesCS6A01G387600 chr3B 90.722 97 8 1 7774 7870 623657657 623657562 2.910000e-25 128.0
17 TraesCS6A01G387600 chr1A 98.800 5083 51 2 1762 6835 39355538 39350457 0.000000e+00 9040.0
18 TraesCS6A01G387600 chr7A 98.836 5069 50 1 1773 6832 292821127 292826195 0.000000e+00 9025.0
19 TraesCS6A01G387600 chr7A 93.976 249 15 0 9215 9463 43323596 43323844 2.620000e-100 377.0
20 TraesCS6A01G387600 chr5A 98.720 5080 51 5 1764 6832 656865787 656870863 0.000000e+00 9009.0
21 TraesCS6A01G387600 chr5A 93.557 1071 45 5 7867 8916 531467776 531468843 0.000000e+00 1574.0
22 TraesCS6A01G387600 chr5A 97.900 762 13 1 1 762 531465177 531465935 0.000000e+00 1315.0
23 TraesCS6A01G387600 chr5A 91.701 976 35 6 822 1773 531465940 531466893 0.000000e+00 1312.0
24 TraesCS6A01G387600 chr5A 99.259 675 5 0 6158 6832 451711445 451710771 0.000000e+00 1219.0
25 TraesCS6A01G387600 chr5A 95.630 389 14 2 7398 7785 531467391 531467777 1.090000e-173 621.0
26 TraesCS6A01G387600 chr5A 89.315 365 24 7 7014 7372 531467037 531467392 2.540000e-120 444.0
27 TraesCS6A01G387600 chr5A 93.839 211 9 2 8877 9086 531468843 531469050 2.080000e-81 315.0
28 TraesCS6A01G387600 chr5A 91.603 131 4 2 6832 6962 531466888 531467011 3.680000e-39 174.0
29 TraesCS6A01G387600 chr5A 86.207 58 2 1 7351 7408 531467288 531467339 3.870000e-04 58.4
30 TraesCS6A01G387600 chr5A 100.000 29 0 0 921 949 531467038 531467010 5.000000e-03 54.7
31 TraesCS6A01G387600 chr4A 98.737 5068 51 3 1774 6832 662635020 662629957 0.000000e+00 8992.0
32 TraesCS6A01G387600 chr4A 90.909 88 8 0 7786 7873 596682370 596682283 1.750000e-22 119.0
33 TraesCS6A01G387600 chr7B 98.304 5072 76 2 1774 6836 740666179 740661109 0.000000e+00 8881.0
34 TraesCS6A01G387600 chr7B 98.303 5068 77 1 1774 6832 660656462 660661529 0.000000e+00 8874.0
35 TraesCS6A01G387600 chr7B 92.045 88 7 0 7781 7868 540297443 540297356 3.760000e-24 124.0
36 TraesCS6A01G387600 chr7B 90.361 83 8 0 7783 7865 686855327 686855409 1.050000e-19 110.0
37 TraesCS6A01G387600 chr6B 94.444 1350 62 5 7870 9214 695795505 695794164 0.000000e+00 2065.0
38 TraesCS6A01G387600 chr6B 91.485 963 60 13 6832 7785 695796463 695795514 0.000000e+00 1304.0
39 TraesCS6A01G387600 chr6B 93.074 823 39 10 1 815 695798911 695798099 0.000000e+00 1188.0
40 TraesCS6A01G387600 chr6B 95.623 594 19 2 822 1411 695797789 695797199 0.000000e+00 946.0
41 TraesCS6A01G387600 chr6B 81.699 306 19 12 1490 1773 695796748 695796458 4.670000e-53 220.0
42 TraesCS6A01G387600 chr6B 89.583 96 9 1 7784 7878 47140701 47140796 4.870000e-23 121.0
43 TraesCS6A01G387600 chr6D 94.430 1185 54 6 7867 9049 457140097 457138923 0.000000e+00 1812.0
44 TraesCS6A01G387600 chr6D 94.634 969 35 6 822 1773 457142001 457141033 0.000000e+00 1485.0
45 TraesCS6A01G387600 chr6D 93.229 960 42 12 6832 7785 457141038 457140096 0.000000e+00 1391.0
46 TraesCS6A01G387600 chr6D 95.741 587 23 2 1 587 457143271 457142687 0.000000e+00 944.0
47 TraesCS6A01G387600 chr6D 95.041 363 11 6 8758 9117 457130039 457129681 1.870000e-156 564.0
48 TraesCS6A01G387600 chr6D 93.478 184 7 1 632 815 457142550 457142372 1.640000e-67 268.0
49 TraesCS6A01G387600 chr6D 93.617 94 3 2 8595 8687 457133911 457133820 4.830000e-28 137.0
50 TraesCS6A01G387600 chr6D 93.023 86 6 0 7780 7865 426893127 426893212 1.050000e-24 126.0
51 TraesCS6A01G387600 chr6D 94.872 78 3 1 8686 8762 457133293 457133216 4.870000e-23 121.0
52 TraesCS6A01G387600 chr6D 88.764 89 10 0 7784 7872 284108446 284108358 1.050000e-19 110.0
53 TraesCS6A01G387600 chr6D 88.764 89 6 4 7782 7868 366623713 366623627 1.360000e-18 106.0
54 TraesCS6A01G387600 chr6D 91.045 67 6 0 7786 7852 449284041 449284107 3.820000e-14 91.6
55 TraesCS6A01G387600 chr6D 95.833 48 0 1 9046 9091 457138811 457138764 1.070000e-09 76.8
56 TraesCS6A01G387600 chr6D 100.000 29 0 0 7782 7810 13600152 13600180 5.000000e-03 54.7
57 TraesCS6A01G387600 chr2B 94.156 462 24 3 9464 9922 17154597 17154136 0.000000e+00 701.0
58 TraesCS6A01G387600 chr2B 86.517 178 16 3 129 305 606750443 606750613 1.320000e-43 189.0
59 TraesCS6A01G387600 chr5D 93.952 463 24 4 9464 9922 128586096 128586558 0.000000e+00 697.0
60 TraesCS6A01G387600 chr5D 93.737 463 23 4 9464 9922 488166354 488165894 0.000000e+00 689.0
61 TraesCS6A01G387600 chr5D 84.879 496 49 12 315 806 337531864 337531391 2.510000e-130 477.0
62 TraesCS6A01G387600 chr5D 92.941 255 16 2 9210 9463 128585704 128585957 4.380000e-98 370.0
63 TraesCS6A01G387600 chr7D 93.939 462 25 3 9464 9922 583081979 583081518 0.000000e+00 695.0
64 TraesCS6A01G387600 chr7D 93.873 457 26 2 9467 9921 509531555 509531099 0.000000e+00 688.0
65 TraesCS6A01G387600 chr7D 87.113 582 65 7 9345 9922 59871354 59870779 0.000000e+00 651.0
66 TraesCS6A01G387600 chr7D 88.235 85 10 0 7784 7868 575730646 575730562 1.760000e-17 102.0
67 TraesCS6A01G387600 chr3D 82.380 857 92 19 1 814 94651914 94651074 0.000000e+00 691.0
68 TraesCS6A01G387600 chr3D 93.737 463 24 5 9464 9922 583586095 583585634 0.000000e+00 689.0
69 TraesCS6A01G387600 chr1D 93.709 461 27 2 9464 9922 365751759 365751299 0.000000e+00 689.0
70 TraesCS6A01G387600 chr1D 83.777 413 52 10 9214 9617 365752080 365751674 2.620000e-100 377.0
71 TraesCS6A01G387600 chr1D 95.402 87 4 0 7783 7869 127266899 127266813 1.340000e-28 139.0
72 TraesCS6A01G387600 chr1D 91.837 49 4 0 7822 7870 412076983 412077031 1.790000e-07 69.4
73 TraesCS6A01G387600 chr2D 93.625 251 16 0 9214 9464 458302607 458302357 9.410000e-100 375.0
74 TraesCS6A01G387600 chr2D 80.984 447 56 11 390 814 514999794 515000233 2.670000e-85 327.0
75 TraesCS6A01G387600 chr2D 80.761 447 57 11 390 814 515013141 515013580 1.240000e-83 322.0
76 TraesCS6A01G387600 chr2D 88.764 178 18 2 128 305 514999561 514999736 6.030000e-52 217.0
77 TraesCS6A01G387600 chr2D 88.764 178 18 2 128 305 515012908 515013083 6.030000e-52 217.0
78 TraesCS6A01G387600 chr4D 92.308 260 17 3 9207 9463 464130868 464131127 5.660000e-97 366.0
79 TraesCS6A01G387600 chrUn 80.984 447 56 11 390 814 269147941 269148380 2.670000e-85 327.0
80 TraesCS6A01G387600 chrUn 88.764 178 18 2 128 305 269147708 269147883 6.030000e-52 217.0
81 TraesCS6A01G387600 chrUn 89.796 98 5 5 7781 7875 320620066 320620161 4.870000e-23 121.0
82 TraesCS6A01G387600 chrUn 89.773 88 5 4 7780 7865 58070905 58070990 1.050000e-19 110.0
83 TraesCS6A01G387600 chrUn 89.535 86 5 4 7782 7865 55437149 55437232 1.360000e-18 106.0
84 TraesCS6A01G387600 chr1B 92.432 185 14 0 629 813 4949342 4949526 2.120000e-66 265.0
85 TraesCS6A01G387600 chr1B 91.566 83 7 0 7783 7865 402275174 402275256 2.260000e-21 115.0
86 TraesCS6A01G387600 chr4B 88.764 89 6 4 7782 7868 292186619 292186533 1.360000e-18 106.0
87 TraesCS6A01G387600 chr4B 87.059 85 9 2 7782 7865 131980578 131980661 2.950000e-15 95.3


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 TraesCS6A01G387600 chr6A 604106487 604116408 9921 True 18323.000000 18323 100.0000 1 9922 1 chr6A.!!$R3 9921
1 TraesCS6A01G387600 chr5B 570977108 570982176 5068 True 9075.000000 9075 99.0140 1774 6833 1 chr5B.!!$R2 5059
2 TraesCS6A01G387600 chr5B 588764379 588769446 5067 False 8973.000000 8973 98.6580 1774 6832 1 chr5B.!!$F2 5058
3 TraesCS6A01G387600 chr3A 158176451 158181518 5067 True 9075.000000 9075 99.0140 1773 6832 1 chr3A.!!$R1 5059
4 TraesCS6A01G387600 chr3A 468533953 468539028 5075 False 9005.000000 9005 98.7200 1769 6835 1 chr3A.!!$F1 5066
5 TraesCS6A01G387600 chr3B 56080970 56086036 5066 True 9073.000000 9073 99.0130 1774 6832 1 chr3B.!!$R1 5058
6 TraesCS6A01G387600 chr1A 39350457 39355538 5081 True 9040.000000 9040 98.8000 1762 6835 1 chr1A.!!$R1 5073
7 TraesCS6A01G387600 chr7A 292821127 292826195 5068 False 9025.000000 9025 98.8360 1773 6832 1 chr7A.!!$F2 5059
8 TraesCS6A01G387600 chr5A 656865787 656870863 5076 False 9009.000000 9009 98.7200 1764 6832 1 chr5A.!!$F1 5068
9 TraesCS6A01G387600 chr5A 451710771 451711445 674 True 1219.000000 1219 99.2590 6158 6832 1 chr5A.!!$R1 674
10 TraesCS6A01G387600 chr5A 531465177 531469050 3873 False 726.675000 1574 92.4690 1 9086 8 chr5A.!!$F2 9085
11 TraesCS6A01G387600 chr4A 662629957 662635020 5063 True 8992.000000 8992 98.7370 1774 6832 1 chr4A.!!$R2 5058
12 TraesCS6A01G387600 chr7B 740661109 740666179 5070 True 8881.000000 8881 98.3040 1774 6836 1 chr7B.!!$R2 5062
13 TraesCS6A01G387600 chr7B 660656462 660661529 5067 False 8874.000000 8874 98.3030 1774 6832 1 chr7B.!!$F1 5058
14 TraesCS6A01G387600 chr6B 695794164 695798911 4747 True 1144.600000 2065 91.2650 1 9214 5 chr6B.!!$R1 9213
15 TraesCS6A01G387600 chr6D 457138764 457143271 4507 True 996.133333 1812 94.5575 1 9091 6 chr6D.!!$R4 9090
16 TraesCS6A01G387600 chr6D 457129681 457133911 4230 True 274.000000 564 94.5100 8595 9117 3 chr6D.!!$R3 522
17 TraesCS6A01G387600 chr5D 128585704 128586558 854 False 533.500000 697 93.4465 9210 9922 2 chr5D.!!$F1 712
18 TraesCS6A01G387600 chr7D 59870779 59871354 575 True 651.000000 651 87.1130 9345 9922 1 chr7D.!!$R1 577
19 TraesCS6A01G387600 chr3D 94651074 94651914 840 True 691.000000 691 82.3800 1 814 1 chr3D.!!$R1 813
20 TraesCS6A01G387600 chr1D 365751299 365752080 781 True 533.000000 689 88.7430 9214 9922 2 chr1D.!!$R2 708
21 TraesCS6A01G387600 chr2D 514999561 515000233 672 False 272.000000 327 84.8740 128 814 2 chr2D.!!$F1 686
22 TraesCS6A01G387600 chr2D 515012908 515013580 672 False 269.500000 322 84.7625 128 814 2 chr2D.!!$F2 686
23 TraesCS6A01G387600 chrUn 269147708 269148380 672 False 272.000000 327 84.8740 128 814 2 chrUn.!!$F4 686

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
896 1386 0.108520 TCCATGCCGGAAGACGTAAC 60.109 55.000 5.05 0.00 42.52 2.50 F
1563 2449 0.842635 AGGCAGATCAGGTGGGATTC 59.157 55.000 0.00 0.00 0.00 2.52 F
2450 3358 0.878523 CAAGTTCGACGGCAAGTCCA 60.879 55.000 6.06 0.00 46.92 4.02 F
3871 4784 0.888619 TCATCCGAGCGAGTTGTTCT 59.111 50.000 0.00 0.00 0.00 3.01 F
4259 5172 3.005554 CTCATTTTCAGCGAGACATGGT 58.994 45.455 0.00 0.00 0.00 3.55 F
5211 6124 3.155167 GTCCCCGCTACTCCAGGG 61.155 72.222 0.00 0.00 44.67 4.45 F
5287 6200 4.514577 CTCCGCCGCGACTTCCAT 62.515 66.667 15.93 0.00 0.00 3.41 F
6378 7309 1.404391 GAAGGGTGAAGCAGCATCATG 59.596 52.381 3.15 0.00 33.07 3.07 F
6891 7823 3.685139 TCGGATGATAGGAAGAATGCC 57.315 47.619 0.00 0.00 0.00 4.40 F
7606 8558 0.680921 ATCACCCGCAATGTGAAGGG 60.681 55.000 0.00 7.44 45.15 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 2676 0.036164 GTGCCCCACATGACAGTACA 59.964 55.000 0.00 0.0 34.08 2.90 R
3558 4471 0.179000 GAATGTCATGGAGAGGGCGT 59.821 55.000 0.00 0.0 0.00 5.68 R
4259 5172 1.478105 CACATGTCGGAGATGGTCAGA 59.522 52.381 18.07 0.0 40.67 3.27 R
5287 6200 0.394938 TCTTGCGAAGGTTAGGTGCA 59.605 50.000 0.00 0.0 0.00 4.57 R
6020 6933 2.189257 CCGAATGTCCCGATGGCA 59.811 61.111 0.00 0.0 0.00 4.92 R
6378 7309 2.968574 TCAAGATCCTCCCATGTAGCTC 59.031 50.000 0.00 0.0 0.00 4.09 R
7228 8167 3.172339 AGAGTGCTTCTTCCTGATCACT 58.828 45.455 0.00 0.0 39.70 3.41 R
7606 8558 1.786579 GGTGAAACAAATCAACTGCGC 59.213 47.619 0.00 0.0 39.98 6.09 R
8741 10251 0.317160 TCCAGCACCGACAGTACTTG 59.683 55.000 0.00 0.0 0.00 3.16 R
8968 13705 0.108585 GGCCATAATTCCTCGGAGCA 59.891 55.000 0.00 0.0 0.00 4.26 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
298 299 3.658757 TGCAATTGTTACTCTTTGGGC 57.341 42.857 7.40 0.00 0.00 5.36
355 379 5.779771 ACCCATTCTGATATTGTTTGTTGGT 59.220 36.000 0.00 0.00 0.00 3.67
369 396 1.202952 TGTTGGTGTAATGGTGGACCC 60.203 52.381 0.00 0.00 34.29 4.46
482 513 1.781025 TTCAGGTGCAACGGCTTTCG 61.781 55.000 0.00 0.00 45.88 3.46
498 529 3.262420 CTTTCGAGAACACATTCCCGAT 58.738 45.455 0.00 0.00 43.52 4.18
773 896 6.876257 CAGAACCAGTCTTACAAGCTTAAGAT 59.124 38.462 13.44 0.00 39.67 2.40
815 938 8.391106 GGTTTCCATTAGCGAATGATGATATAC 58.609 37.037 19.74 8.17 44.59 1.47
816 939 8.391106 GTTTCCATTAGCGAATGATGATATACC 58.609 37.037 19.74 0.00 44.59 2.73
817 940 7.423844 TCCATTAGCGAATGATGATATACCT 57.576 36.000 19.74 0.00 44.59 3.08
820 943 7.010830 CCATTAGCGAATGATGATATACCTGTG 59.989 40.741 19.74 0.00 44.59 3.66
856 1346 5.168569 TGGAAGACGTAAAGCAGTTAGATG 58.831 41.667 0.00 0.00 0.00 2.90
882 1372 1.875009 ATAGCTGTGCGTGATCCATG 58.125 50.000 0.00 0.00 0.00 3.66
896 1386 0.108520 TCCATGCCGGAAGACGTAAC 60.109 55.000 5.05 0.00 42.52 2.50
899 1389 1.262640 ATGCCGGAAGACGTAACCCT 61.263 55.000 5.05 0.00 42.24 4.34
1563 2449 0.842635 AGGCAGATCAGGTGGGATTC 59.157 55.000 0.00 0.00 0.00 2.52
1568 2454 2.686915 CAGATCAGGTGGGATTCTTTGC 59.313 50.000 0.00 0.00 0.00 3.68
1711 2619 5.022282 ACCATGCAGTTGCTTAAAAGTTT 57.978 34.783 5.62 0.00 42.66 2.66
1712 2620 4.810491 ACCATGCAGTTGCTTAAAAGTTTG 59.190 37.500 5.62 0.00 42.66 2.93
1720 2628 6.256321 CAGTTGCTTAAAAGTTTGTTCATGCT 59.744 34.615 0.00 0.00 0.00 3.79
1731 2639 5.716228 AGTTTGTTCATGCTATGATTTGGGA 59.284 36.000 0.00 0.00 39.39 4.37
1743 2651 6.183360 GCTATGATTTGGGACTTTGCTGTATT 60.183 38.462 0.00 0.00 0.00 1.89
1768 2676 4.527509 AGTGAACTGTCTGTCGATTGAT 57.472 40.909 0.00 0.00 0.00 2.57
1769 2677 4.240888 AGTGAACTGTCTGTCGATTGATG 58.759 43.478 0.00 0.00 0.00 3.07
1770 2678 3.990469 GTGAACTGTCTGTCGATTGATGT 59.010 43.478 0.00 0.00 0.00 3.06
1771 2679 5.048013 AGTGAACTGTCTGTCGATTGATGTA 60.048 40.000 0.00 0.00 0.00 2.29
1852 2760 3.120105 CATCAGGCGAGGCGTAGA 58.880 61.111 0.00 0.00 0.00 2.59
1958 2866 4.879295 CCCATGGGGCCTTTATATATCA 57.121 45.455 24.53 0.00 35.35 2.15
2155 3063 4.698201 TGACAACTTGGTATCAGGTTCA 57.302 40.909 0.00 0.00 40.54 3.18
2450 3358 0.878523 CAAGTTCGACGGCAAGTCCA 60.879 55.000 6.06 0.00 46.92 4.02
3871 4784 0.888619 TCATCCGAGCGAGTTGTTCT 59.111 50.000 0.00 0.00 0.00 3.01
4259 5172 3.005554 CTCATTTTCAGCGAGACATGGT 58.994 45.455 0.00 0.00 0.00 3.55
4535 5448 4.666397 TTGCCGCGCCACTAACGA 62.666 61.111 0.00 0.00 0.00 3.85
4788 5701 3.717707 CATATGAACGGGAACTCATCGT 58.282 45.455 0.00 0.00 38.89 3.73
5211 6124 3.155167 GTCCCCGCTACTCCAGGG 61.155 72.222 0.00 0.00 44.67 4.45
5287 6200 4.514577 CTCCGCCGCGACTTCCAT 62.515 66.667 15.93 0.00 0.00 3.41
6020 6933 5.816777 GTCTACAAGTCCTACTACGACAGAT 59.183 44.000 0.00 0.00 32.41 2.90
6378 7309 1.404391 GAAGGGTGAAGCAGCATCATG 59.596 52.381 3.15 0.00 33.07 3.07
6887 7819 5.646360 GGTTGTTTTCGGATGATAGGAAGAA 59.354 40.000 0.00 0.00 0.00 2.52
6891 7823 3.685139 TCGGATGATAGGAAGAATGCC 57.315 47.619 0.00 0.00 0.00 4.40
6916 7848 5.910931 TGTAGGCTATATAGGTTGGATGGA 58.089 41.667 11.72 0.00 0.00 3.41
6917 7849 6.512120 TGTAGGCTATATAGGTTGGATGGAT 58.488 40.000 11.72 0.00 0.00 3.41
6918 7850 6.611642 TGTAGGCTATATAGGTTGGATGGATC 59.388 42.308 11.72 0.00 0.00 3.36
6919 7851 4.651503 AGGCTATATAGGTTGGATGGATCG 59.348 45.833 11.72 0.00 0.00 3.69
6920 7852 4.649674 GGCTATATAGGTTGGATGGATCGA 59.350 45.833 11.72 0.00 0.00 3.59
6921 7853 5.128827 GGCTATATAGGTTGGATGGATCGAA 59.871 44.000 11.72 0.00 0.00 3.71
6922 7854 6.351881 GGCTATATAGGTTGGATGGATCGAAA 60.352 42.308 11.72 0.00 0.00 3.46
6923 7855 7.103641 GCTATATAGGTTGGATGGATCGAAAA 58.896 38.462 11.72 0.00 0.00 2.29
7094 8030 4.453480 TCCAAGGAATTCCCATACATCC 57.547 45.455 21.22 0.00 37.41 3.51
7097 8033 4.386761 CCAAGGAATTCCCATACATCCTGT 60.387 45.833 21.22 0.00 40.33 4.00
7109 8045 5.365605 CCATACATCCTGTAGTGGGAACTTA 59.634 44.000 0.00 0.00 36.14 2.24
7110 8046 6.126883 CCATACATCCTGTAGTGGGAACTTAA 60.127 42.308 0.00 0.00 36.14 1.85
7130 8066 7.406104 ACTTAAACTCTCTGGAGCCATAAATT 58.594 34.615 0.00 0.00 42.98 1.82
7140 8076 5.056480 TGGAGCCATAAATTATCGTGTCAG 58.944 41.667 0.00 0.00 0.00 3.51
7220 8159 4.724399 TCCAACTGACTTCTTAATGCCAA 58.276 39.130 0.00 0.00 0.00 4.52
7228 8167 5.012664 TGACTTCTTAATGCCAACAGTCCTA 59.987 40.000 0.00 0.00 0.00 2.94
7444 8394 5.409520 TGAGTTCATGTGTAGCATCTGTTTC 59.590 40.000 0.00 0.00 35.19 2.78
7453 8404 8.479313 TGTGTAGCATCTGTTTCTTATTGTAG 57.521 34.615 0.00 0.00 0.00 2.74
7606 8558 0.680921 ATCACCCGCAATGTGAAGGG 60.681 55.000 0.00 7.44 45.15 3.95
7686 8639 7.033791 TCTGTTCATCTCGTGGTTATACTTTC 58.966 38.462 0.00 0.00 0.00 2.62
7773 8726 9.150348 CCCAAATCTGTGTTTATTTTGGTAATC 57.850 33.333 10.76 0.00 42.99 1.75
7786 8739 9.515226 TTATTTTGGTAATCTTCTGCAACTACT 57.485 29.630 0.00 0.00 0.00 2.57
7787 8740 7.435068 TTTTGGTAATCTTCTGCAACTACTC 57.565 36.000 0.00 0.00 0.00 2.59
7788 8741 5.086104 TGGTAATCTTCTGCAACTACTCC 57.914 43.478 0.00 0.00 0.00 3.85
7789 8742 4.081087 TGGTAATCTTCTGCAACTACTCCC 60.081 45.833 0.00 0.00 0.00 4.30
7790 8743 4.162509 GGTAATCTTCTGCAACTACTCCCT 59.837 45.833 0.00 0.00 0.00 4.20
7791 8744 4.479786 AATCTTCTGCAACTACTCCCTC 57.520 45.455 0.00 0.00 0.00 4.30
7792 8745 3.176924 TCTTCTGCAACTACTCCCTCT 57.823 47.619 0.00 0.00 0.00 3.69
7793 8746 4.317530 TCTTCTGCAACTACTCCCTCTA 57.682 45.455 0.00 0.00 0.00 2.43
7794 8747 4.873010 TCTTCTGCAACTACTCCCTCTAT 58.127 43.478 0.00 0.00 0.00 1.98
7795 8748 4.890581 TCTTCTGCAACTACTCCCTCTATC 59.109 45.833 0.00 0.00 0.00 2.08
7796 8749 3.567397 TCTGCAACTACTCCCTCTATCC 58.433 50.000 0.00 0.00 0.00 2.59
7797 8750 2.630580 CTGCAACTACTCCCTCTATCCC 59.369 54.545 0.00 0.00 0.00 3.85
7798 8751 2.023404 TGCAACTACTCCCTCTATCCCA 60.023 50.000 0.00 0.00 0.00 4.37
7799 8752 3.243724 GCAACTACTCCCTCTATCCCAT 58.756 50.000 0.00 0.00 0.00 4.00
7800 8753 4.140782 TGCAACTACTCCCTCTATCCCATA 60.141 45.833 0.00 0.00 0.00 2.74
7801 8754 4.838986 GCAACTACTCCCTCTATCCCATAA 59.161 45.833 0.00 0.00 0.00 1.90
7802 8755 5.485708 GCAACTACTCCCTCTATCCCATAAT 59.514 44.000 0.00 0.00 0.00 1.28
7803 8756 6.668283 GCAACTACTCCCTCTATCCCATAATA 59.332 42.308 0.00 0.00 0.00 0.98
7804 8757 7.345914 GCAACTACTCCCTCTATCCCATAATAT 59.654 40.741 0.00 0.00 0.00 1.28
7805 8758 9.937876 CAACTACTCCCTCTATCCCATAATATA 57.062 37.037 0.00 0.00 0.00 0.86
7810 8763 7.780745 ACTCCCTCTATCCCATAATATAAGACG 59.219 40.741 0.00 0.00 0.00 4.18
7811 8764 7.649715 TCCCTCTATCCCATAATATAAGACGT 58.350 38.462 0.00 0.00 0.00 4.34
7812 8765 8.784880 TCCCTCTATCCCATAATATAAGACGTA 58.215 37.037 0.00 0.00 0.00 3.57
7813 8766 9.589461 CCCTCTATCCCATAATATAAGACGTAT 57.411 37.037 0.00 0.00 0.00 3.06
7829 8782 9.784680 ATAAGACGTATTTTGACACTAGTGTAG 57.215 33.333 27.98 13.57 45.05 2.74
7830 8783 7.211966 AGACGTATTTTGACACTAGTGTAGT 57.788 36.000 27.98 16.22 45.05 2.73
7844 8797 7.291411 ACTAGTGTAGTGTCAAAAGACATCT 57.709 36.000 0.00 4.31 37.69 2.90
7845 8798 7.727181 ACTAGTGTAGTGTCAAAAGACATCTT 58.273 34.615 0.00 0.00 37.69 2.40
7846 8799 8.857098 ACTAGTGTAGTGTCAAAAGACATCTTA 58.143 33.333 0.00 0.00 37.69 2.10
7847 8800 7.948278 AGTGTAGTGTCAAAAGACATCTTAC 57.052 36.000 1.30 6.35 37.42 2.34
7848 8801 7.497595 AGTGTAGTGTCAAAAGACATCTTACA 58.502 34.615 1.30 8.44 37.42 2.41
7849 8802 8.150945 AGTGTAGTGTCAAAAGACATCTTACAT 58.849 33.333 16.21 8.62 37.42 2.29
7850 8803 8.774586 GTGTAGTGTCAAAAGACATCTTACATT 58.225 33.333 16.21 0.00 37.42 2.71
7851 8804 9.990360 TGTAGTGTCAAAAGACATCTTACATTA 57.010 29.630 1.30 0.00 37.42 1.90
7854 8807 8.950210 AGTGTCAAAAGACATCTTACATTATGG 58.050 33.333 1.30 0.00 37.42 2.74
7855 8808 8.184192 GTGTCAAAAGACATCTTACATTATGGG 58.816 37.037 1.30 0.00 37.42 4.00
7856 8809 8.106462 TGTCAAAAGACATCTTACATTATGGGA 58.894 33.333 0.00 0.00 34.61 4.37
7857 8810 8.398665 GTCAAAAGACATCTTACATTATGGGAC 58.601 37.037 0.00 0.00 34.61 4.46
7858 8811 7.279981 TCAAAAGACATCTTACATTATGGGACG 59.720 37.037 0.00 0.00 34.61 4.79
7859 8812 5.215252 AGACATCTTACATTATGGGACGG 57.785 43.478 0.00 0.00 0.00 4.79
7860 8813 4.899457 AGACATCTTACATTATGGGACGGA 59.101 41.667 0.00 0.00 0.00 4.69
7861 8814 5.011125 AGACATCTTACATTATGGGACGGAG 59.989 44.000 0.00 0.00 0.00 4.63
7862 8815 4.040461 ACATCTTACATTATGGGACGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
7863 8816 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
7864 8817 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
7865 8818 1.887797 ACATTATGGGACGGAGGGAA 58.112 50.000 0.00 0.00 0.00 3.97
7866 8819 2.418669 ACATTATGGGACGGAGGGAAT 58.581 47.619 0.00 0.00 0.00 3.01
7867 8820 3.593942 ACATTATGGGACGGAGGGAATA 58.406 45.455 0.00 0.00 0.00 1.75
7922 8882 2.356125 CGATCTCCCCAATCCTTGTGTT 60.356 50.000 0.00 0.00 0.00 3.32
7944 8904 6.714810 TGTTATGTAGAAAGGCTGAATGTTGT 59.285 34.615 0.00 0.00 0.00 3.32
7948 8908 7.377766 TGTAGAAAGGCTGAATGTTGTTATC 57.622 36.000 0.00 0.00 0.00 1.75
7952 8912 6.825721 AGAAAGGCTGAATGTTGTTATCTAGG 59.174 38.462 0.00 0.00 0.00 3.02
8027 8987 5.123186 TCATGGTTTACTTTATGCTCAACCG 59.877 40.000 0.00 0.00 37.14 4.44
8089 9049 6.656693 AGTGAAATAACTTTCCAGGATCTGTG 59.343 38.462 0.00 0.00 40.09 3.66
8306 9266 6.865205 GCATTTTTCATCCCATTATGTAGCTC 59.135 38.462 0.00 0.00 0.00 4.09
8310 9270 2.820059 TCCCATTATGTAGCTCAGCG 57.180 50.000 0.00 0.00 0.00 5.18
8350 9315 2.362077 AGTTCACTTTGTGCCATGGTTC 59.638 45.455 14.67 7.46 32.98 3.62
8478 9448 4.632688 CCATGAATCAAAAGGAATTGTGCC 59.367 41.667 0.00 0.00 0.00 5.01
8741 10251 0.035056 CATGGTGTCTTCACTCCCCC 60.035 60.000 0.00 0.00 43.41 5.40
8926 13662 9.358872 GAAAGAAATTTGTTTTCAGTTCTGACT 57.641 29.630 13.88 0.00 45.19 3.41
8952 13689 1.241165 CAGCTTCAAGCATGGTGTCA 58.759 50.000 13.10 0.00 45.56 3.58
8968 13705 3.565482 GGTGTCAATTACGGATGCATCAT 59.435 43.478 27.25 17.09 0.00 2.45
9137 13990 3.143728 CAGGTACGCCTTTAAACCTTGT 58.856 45.455 0.00 0.00 44.18 3.16
9140 13993 2.243602 ACGCCTTTAAACCTTGTCGA 57.756 45.000 0.00 0.00 0.00 4.20
9142 13995 1.196127 CGCCTTTAAACCTTGTCGACC 59.804 52.381 14.12 0.00 0.00 4.79
9147 14000 0.320073 TAAACCTTGTCGACCGCTGG 60.320 55.000 14.12 11.82 0.00 4.85
9152 14005 0.242825 CTTGTCGACCGCTGGTAAGA 59.757 55.000 14.12 1.70 35.25 2.10
9159 14012 3.434299 TCGACCGCTGGTAAGAATTTTTC 59.566 43.478 0.09 0.00 35.25 2.29
9171 14024 5.745312 AAGAATTTTTCCATCCACCCTTC 57.255 39.130 0.00 0.00 0.00 3.46
9190 14043 5.336213 CCCTTCCACATGTTTTCAGATTCTG 60.336 44.000 7.38 7.38 0.00 3.02
9191 14044 5.242393 CCTTCCACATGTTTTCAGATTCTGT 59.758 40.000 13.23 0.00 32.61 3.41
9192 14045 5.947228 TCCACATGTTTTCAGATTCTGTC 57.053 39.130 13.23 4.35 32.61 3.51
9264 14117 4.988598 CCAACTCGCCCACACGCT 62.989 66.667 0.00 0.00 0.00 5.07
9273 14126 1.671054 CCCACACGCTTGGATCGTT 60.671 57.895 4.43 0.00 39.24 3.85
9334 14187 2.851263 TTTTCTGTGCCACGTAGGAT 57.149 45.000 8.04 0.00 41.22 3.24
9438 14292 3.873679 CTGCCCACACAGCCACCAT 62.874 63.158 0.00 0.00 0.00 3.55
9443 14297 0.615331 CCACACAGCCACCATCTAGT 59.385 55.000 0.00 0.00 0.00 2.57
9485 14410 1.404748 CACACACATGGCAACTGTGAA 59.595 47.619 26.05 0.00 45.44 3.18
9487 14412 2.694628 ACACACATGGCAACTGTGAATT 59.305 40.909 26.05 10.13 45.44 2.17
9537 14530 2.151202 ACGTGGCAACCAGATAAACAG 58.849 47.619 0.00 0.00 32.34 3.16
9562 14555 8.939929 AGACATGACAACTGTGATTAACAATAG 58.060 33.333 0.00 0.00 38.67 1.73
9606 14599 1.802365 CGTGGCAACTAGGTAAACACC 59.198 52.381 0.00 0.00 37.61 4.16
9635 14629 6.530120 ACAACTACTGTTTGACCATATGTGA 58.470 36.000 1.24 0.00 32.99 3.58
9645 14639 7.500892 TGTTTGACCATATGTGACAAGTAGTTT 59.499 33.333 1.24 0.00 0.00 2.66
9649 14643 8.758829 TGACCATATGTGACAAGTAGTTTATCT 58.241 33.333 1.24 0.00 0.00 1.98
9677 14671 3.499157 GGCAACTACGGTTTGATTACACA 59.501 43.478 0.00 0.00 32.73 3.72
9739 14733 5.815581 ACCAAAACAGATAGAGTTGCCATA 58.184 37.500 0.00 0.00 0.00 2.74
9765 14759 1.423541 ACAACTACACTTGCCATCCCA 59.576 47.619 0.00 0.00 0.00 4.37
9815 14809 0.031585 CTAAATCGTCATCCCGCGGA 59.968 55.000 30.73 13.82 35.55 5.54
9840 14834 1.672854 TAACGTAGCTGCGCCAGGAT 61.673 55.000 24.60 0.00 34.88 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
298 299 2.485426 ACCAGTCATGCACAAAATCTCG 59.515 45.455 0.00 0.00 0.00 4.04
355 379 1.275856 GTGTACGGGTCCACCATTACA 59.724 52.381 0.00 1.75 40.22 2.41
369 396 7.428282 TGGCCAATATTTATACATGTGTACG 57.572 36.000 0.61 0.00 32.72 3.67
482 513 2.083774 TGCAATCGGGAATGTGTTCTC 58.916 47.619 0.00 0.00 34.68 2.87
688 811 6.127758 TGTGCATACCAATGAAAGTAACATCC 60.128 38.462 0.00 0.00 34.84 3.51
773 896 4.202556 TGGAAACCACCTCAATGATCTTGA 60.203 41.667 0.00 1.11 0.00 3.02
815 938 0.740868 CAGTATGGGTCACGCACAGG 60.741 60.000 0.00 0.00 31.73 4.00
816 939 2.754648 CAGTATGGGTCACGCACAG 58.245 57.895 0.00 0.00 31.73 3.66
856 1346 2.401766 ACGCACAGCTATTGCAGGC 61.402 57.895 17.27 1.03 40.20 4.85
882 1372 1.447314 CAGGGTTACGTCTTCCGGC 60.447 63.158 0.00 0.00 42.24 6.13
896 1386 1.067635 CCGCATTTTTCTCCAACAGGG 60.068 52.381 0.00 0.00 38.37 4.45
899 1389 0.039617 CGCCGCATTTTTCTCCAACA 60.040 50.000 0.00 0.00 0.00 3.33
1414 1927 2.921435 GGGCATGATCTGGAGGCA 59.079 61.111 0.00 0.00 0.00 4.75
1459 1972 1.215655 GGGAATCAGAATCCGACGCG 61.216 60.000 3.53 3.53 37.87 6.01
1465 1978 3.339141 GCCGATAAGGGAATCAGAATCC 58.661 50.000 0.00 0.00 41.48 3.01
1563 2449 2.562298 TGAGCTACATTTTGGGGCAAAG 59.438 45.455 0.00 0.00 34.72 2.77
1568 2454 4.463891 ACTGAATTGAGCTACATTTTGGGG 59.536 41.667 0.00 0.00 0.00 4.96
1684 2592 2.566833 AAGCAACTGCATGGTAGTGA 57.433 45.000 4.22 0.00 45.16 3.41
1711 2619 4.858850 AGTCCCAAATCATAGCATGAACA 58.141 39.130 0.00 0.00 43.50 3.18
1712 2620 5.841957 AAGTCCCAAATCATAGCATGAAC 57.158 39.130 0.00 0.00 43.50 3.18
1720 2628 8.815565 TTAATACAGCAAAGTCCCAAATCATA 57.184 30.769 0.00 0.00 0.00 2.15
1731 2639 8.848474 ACAGTTCACTATTAATACAGCAAAGT 57.152 30.769 0.00 0.00 0.00 2.66
1743 2651 7.153217 TCAATCGACAGACAGTTCACTATTA 57.847 36.000 0.00 0.00 0.00 0.98
1768 2676 0.036164 GTGCCCCACATGACAGTACA 59.964 55.000 0.00 0.00 34.08 2.90
1769 2677 1.019278 CGTGCCCCACATGACAGTAC 61.019 60.000 0.00 0.00 37.49 2.73
1770 2678 1.295101 CGTGCCCCACATGACAGTA 59.705 57.895 0.00 0.00 37.49 2.74
1771 2679 2.032528 CGTGCCCCACATGACAGT 59.967 61.111 0.00 0.00 37.49 3.55
2450 3358 2.047179 GAGGAAAGCGAGCGGGTT 60.047 61.111 0.00 0.00 38.16 4.11
2763 3671 1.998315 CTGCGGTGAAGATCTGAACTG 59.002 52.381 11.03 11.03 0.00 3.16
3059 3969 1.862049 TTGAAGCATAGGCCCAGGCA 61.862 55.000 11.12 0.00 44.11 4.75
3558 4471 0.179000 GAATGTCATGGAGAGGGCGT 59.821 55.000 0.00 0.00 0.00 5.68
4259 5172 1.478105 CACATGTCGGAGATGGTCAGA 59.522 52.381 18.07 0.00 40.67 3.27
4452 5365 4.994471 GAAACCCCCGAACCGCGT 62.994 66.667 4.92 0.00 38.67 6.01
4788 5701 2.184322 GAATCGCGAGCACCAGGA 59.816 61.111 16.66 0.00 0.00 3.86
5211 6124 1.375908 TGCACGGCACTGAGAATCC 60.376 57.895 0.00 0.00 31.71 3.01
5287 6200 0.394938 TCTTGCGAAGGTTAGGTGCA 59.605 50.000 0.00 0.00 0.00 4.57
6020 6933 2.189257 CCGAATGTCCCGATGGCA 59.811 61.111 0.00 0.00 0.00 4.92
6378 7309 2.968574 TCAAGATCCTCCCATGTAGCTC 59.031 50.000 0.00 0.00 0.00 4.09
6891 7823 6.440647 TCCATCCAACCTATATAGCCTACAAG 59.559 42.308 4.04 0.00 0.00 3.16
6916 7848 9.299963 TTTGCATATCAAATTTCGATTTTCGAT 57.700 25.926 0.00 0.00 42.81 3.59
6917 7849 8.582930 GTTTGCATATCAAATTTCGATTTTCGA 58.417 29.630 7.96 0.00 45.41 3.71
6918 7850 7.840797 GGTTTGCATATCAAATTTCGATTTTCG 59.159 33.333 7.96 0.00 45.43 3.46
6919 7851 8.116136 GGGTTTGCATATCAAATTTCGATTTTC 58.884 33.333 7.96 0.00 45.43 2.29
6920 7852 7.605691 TGGGTTTGCATATCAAATTTCGATTTT 59.394 29.630 7.96 0.00 45.43 1.82
6921 7853 7.102346 TGGGTTTGCATATCAAATTTCGATTT 58.898 30.769 7.96 0.00 45.43 2.17
6922 7854 6.638610 TGGGTTTGCATATCAAATTTCGATT 58.361 32.000 7.96 0.00 45.43 3.34
6923 7855 6.219417 TGGGTTTGCATATCAAATTTCGAT 57.781 33.333 0.00 7.82 45.43 3.59
6982 7915 5.182487 TGAGGTATAATGTTGTGCGAACAT 58.818 37.500 0.00 7.85 42.19 2.71
7024 7959 4.041049 CAGAGCAAGACGTACTGATCATC 58.959 47.826 14.78 0.00 0.00 2.92
7066 8002 7.361438 TGTATGGGAATTCCTTGGAATAACAT 58.639 34.615 23.63 16.10 36.20 2.71
7094 8030 6.159988 CAGAGAGTTTAAGTTCCCACTACAG 58.840 44.000 0.00 0.00 30.68 2.74
7097 8033 5.399991 TCCAGAGAGTTTAAGTTCCCACTA 58.600 41.667 0.00 0.00 30.68 2.74
7109 8045 6.708054 CGATAATTTATGGCTCCAGAGAGTTT 59.292 38.462 0.00 0.00 42.59 2.66
7110 8046 6.183361 ACGATAATTTATGGCTCCAGAGAGTT 60.183 38.462 0.00 0.00 42.59 3.01
7130 8066 6.682423 AATGCATGATTTTCTGACACGATA 57.318 33.333 0.00 0.00 0.00 2.92
7220 8159 4.323569 TCTTCCTGATCACTAGGACTGT 57.676 45.455 1.74 0.00 43.75 3.55
7228 8167 3.172339 AGAGTGCTTCTTCCTGATCACT 58.828 45.455 0.00 0.00 39.70 3.41
7330 8280 3.093814 AGCAACATCCAAATCTGATGCA 58.906 40.909 7.39 0.00 41.87 3.96
7444 8394 8.948631 TTAGTCTGGCAGATTTCTACAATAAG 57.051 34.615 21.84 0.00 0.00 1.73
7453 8404 5.428253 TGTACCATTAGTCTGGCAGATTTC 58.572 41.667 21.84 8.05 40.15 2.17
7555 8507 7.060421 CCTCCTGTGTAATACCAATGGTAATT 58.940 38.462 16.90 12.89 41.85 1.40
7556 8508 6.410388 CCCTCCTGTGTAATACCAATGGTAAT 60.410 42.308 16.90 10.86 41.85 1.89
7557 8509 5.104277 CCCTCCTGTGTAATACCAATGGTAA 60.104 44.000 16.90 0.00 41.85 2.85
7606 8558 1.786579 GGTGAAACAAATCAACTGCGC 59.213 47.619 0.00 0.00 39.98 6.09
7737 8690 2.224079 CACAGATTTGGGTTGAGTGTCG 59.776 50.000 0.00 0.00 0.00 4.35
7773 8726 4.038642 GGATAGAGGGAGTAGTTGCAGAAG 59.961 50.000 0.00 0.00 0.00 2.85
7785 8738 7.780745 ACGTCTTATATTATGGGATAGAGGGAG 59.219 40.741 0.00 0.00 0.00 4.30
7786 8739 7.649715 ACGTCTTATATTATGGGATAGAGGGA 58.350 38.462 0.00 0.00 0.00 4.20
7787 8740 7.899648 ACGTCTTATATTATGGGATAGAGGG 57.100 40.000 0.00 0.00 0.00 4.30
7803 8756 9.784680 CTACACTAGTGTCAAAATACGTCTTAT 57.215 33.333 31.11 3.94 43.74 1.73
7804 8757 8.786898 ACTACACTAGTGTCAAAATACGTCTTA 58.213 33.333 31.11 8.36 43.74 2.10
7805 8758 7.655490 ACTACACTAGTGTCAAAATACGTCTT 58.345 34.615 31.11 4.99 43.74 3.01
7806 8759 7.211966 ACTACACTAGTGTCAAAATACGTCT 57.788 36.000 31.11 5.44 43.74 4.18
7832 8785 7.279981 CGTCCCATAATGTAAGATGTCTTTTGA 59.720 37.037 0.00 0.00 37.40 2.69
7833 8786 7.409697 CGTCCCATAATGTAAGATGTCTTTTG 58.590 38.462 0.00 0.00 37.40 2.44
7834 8787 6.542370 CCGTCCCATAATGTAAGATGTCTTTT 59.458 38.462 0.00 0.00 37.40 2.27
7835 8788 6.055588 CCGTCCCATAATGTAAGATGTCTTT 58.944 40.000 0.00 0.00 37.40 2.52
7836 8789 5.365605 TCCGTCCCATAATGTAAGATGTCTT 59.634 40.000 0.45 0.45 39.85 3.01
7837 8790 4.899457 TCCGTCCCATAATGTAAGATGTCT 59.101 41.667 0.00 0.00 0.00 3.41
7838 8791 5.209818 TCCGTCCCATAATGTAAGATGTC 57.790 43.478 0.00 0.00 0.00 3.06
7839 8792 4.040461 CCTCCGTCCCATAATGTAAGATGT 59.960 45.833 0.00 0.00 0.00 3.06
7840 8793 4.563580 CCCTCCGTCCCATAATGTAAGATG 60.564 50.000 0.00 0.00 0.00 2.90
7841 8794 3.583086 CCCTCCGTCCCATAATGTAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
7842 8795 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
7843 8796 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
7844 8797 3.049108 TCCCTCCGTCCCATAATGTAA 57.951 47.619 0.00 0.00 0.00 2.41
7845 8798 2.779429 TCCCTCCGTCCCATAATGTA 57.221 50.000 0.00 0.00 0.00 2.29
7846 8799 1.887797 TTCCCTCCGTCCCATAATGT 58.112 50.000 0.00 0.00 0.00 2.71
7847 8800 3.583086 ACTATTCCCTCCGTCCCATAATG 59.417 47.826 0.00 0.00 0.00 1.90
7848 8801 3.870559 ACTATTCCCTCCGTCCCATAAT 58.129 45.455 0.00 0.00 0.00 1.28
7849 8802 3.339713 ACTATTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
7850 8803 3.339713 AACTATTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
7851 8804 2.191981 AACTATTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
7852 8805 1.835531 GAAACTATTCCCTCCGTCCCA 59.164 52.381 0.00 0.00 0.00 4.37
7853 8806 2.117051 AGAAACTATTCCCTCCGTCCC 58.883 52.381 0.00 0.00 36.12 4.46
7854 8807 3.532542 CAAGAAACTATTCCCTCCGTCC 58.467 50.000 0.00 0.00 36.12 4.79
7855 8808 2.937149 GCAAGAAACTATTCCCTCCGTC 59.063 50.000 0.00 0.00 36.12 4.79
7856 8809 2.304761 TGCAAGAAACTATTCCCTCCGT 59.695 45.455 0.00 0.00 36.12 4.69
7857 8810 2.678336 GTGCAAGAAACTATTCCCTCCG 59.322 50.000 0.00 0.00 36.12 4.63
7858 8811 3.017442 GGTGCAAGAAACTATTCCCTCC 58.983 50.000 0.00 0.00 36.12 4.30
7859 8812 3.956744 AGGTGCAAGAAACTATTCCCTC 58.043 45.455 0.00 0.00 36.12 4.30
7860 8813 4.388577 AAGGTGCAAGAAACTATTCCCT 57.611 40.909 0.00 0.00 36.12 4.20
7861 8814 4.767409 AGAAAGGTGCAAGAAACTATTCCC 59.233 41.667 0.00 0.00 36.12 3.97
7862 8815 5.473504 TCAGAAAGGTGCAAGAAACTATTCC 59.526 40.000 0.00 0.00 36.12 3.01
7863 8816 6.560253 TCAGAAAGGTGCAAGAAACTATTC 57.440 37.500 0.00 0.00 35.70 1.75
7864 8817 6.321181 TGTTCAGAAAGGTGCAAGAAACTATT 59.679 34.615 0.00 0.00 0.00 1.73
7865 8818 5.827797 TGTTCAGAAAGGTGCAAGAAACTAT 59.172 36.000 0.00 0.00 0.00 2.12
7866 8819 5.189928 TGTTCAGAAAGGTGCAAGAAACTA 58.810 37.500 0.00 0.00 0.00 2.24
7867 8820 4.016444 TGTTCAGAAAGGTGCAAGAAACT 58.984 39.130 0.00 0.00 0.00 2.66
7922 8882 9.109393 GATAACAACATTCAGCCTTTCTACATA 57.891 33.333 0.00 0.00 0.00 2.29
7948 8908 8.225603 ACAACATAACCTCATAATTTGCCTAG 57.774 34.615 0.00 0.00 0.00 3.02
7952 8912 9.503427 GAGTTACAACATAACCTCATAATTTGC 57.497 33.333 0.00 0.00 0.00 3.68
8008 8968 5.857822 AGTCGGTTGAGCATAAAGTAAAC 57.142 39.130 0.00 0.00 0.00 2.01
8009 8969 5.992829 TCAAGTCGGTTGAGCATAAAGTAAA 59.007 36.000 0.00 0.00 40.45 2.01
8177 9137 2.158097 AGCTGGATCTGGCTTATAGGGA 60.158 50.000 7.05 0.00 34.96 4.20
8279 9239 7.070322 AGCTACATAATGGGATGAAAAATGCTT 59.930 33.333 0.00 0.00 0.00 3.91
8306 9266 7.093354 ACTGTATAGGAATCATTCATACGCTG 58.907 38.462 0.00 0.93 0.00 5.18
8310 9270 9.988815 AGTGAACTGTATAGGAATCATTCATAC 57.011 33.333 0.00 0.76 0.00 2.39
8350 9315 6.071896 TCCTGATAGTATGCCTTGATAACTCG 60.072 42.308 0.00 0.00 0.00 4.18
8741 10251 0.317160 TCCAGCACCGACAGTACTTG 59.683 55.000 0.00 0.00 0.00 3.16
8926 13662 1.201414 CATGCTTGAAGCTGCATCACA 59.799 47.619 18.94 3.95 46.65 3.58
8968 13705 0.108585 GGCCATAATTCCTCGGAGCA 59.891 55.000 0.00 0.00 0.00 4.26
9030 13768 6.095160 ACTCTACTACTAAATTCCAGTCACCG 59.905 42.308 0.00 0.00 0.00 4.94
9137 13990 2.754946 AAATTCTTACCAGCGGTCGA 57.245 45.000 3.45 0.61 37.09 4.20
9140 13993 3.492337 TGGAAAAATTCTTACCAGCGGT 58.508 40.909 5.58 5.58 40.16 5.68
9142 13995 4.157656 TGGATGGAAAAATTCTTACCAGCG 59.842 41.667 0.00 0.00 37.82 5.18
9147 14000 6.351033 GGAAGGGTGGATGGAAAAATTCTTAC 60.351 42.308 0.00 0.00 0.00 2.34
9152 14005 3.582647 GTGGAAGGGTGGATGGAAAAATT 59.417 43.478 0.00 0.00 0.00 1.82
9159 14012 0.332632 ACATGTGGAAGGGTGGATGG 59.667 55.000 0.00 0.00 0.00 3.51
9171 14024 5.954296 AGACAGAATCTGAAAACATGTGG 57.046 39.130 18.20 0.00 35.81 4.17
9273 14126 1.013596 CGTGCAAAAGACACTGGACA 58.986 50.000 0.00 0.00 33.87 4.02
9282 14135 1.952990 TGCCAAGATTCGTGCAAAAGA 59.047 42.857 0.00 0.00 0.00 2.52
9438 14292 0.735978 CCACACGCGCATGAACTAGA 60.736 55.000 11.87 0.00 0.00 2.43
9537 14530 8.935844 TCTATTGTTAATCACAGTTGTCATGTC 58.064 33.333 0.00 0.00 36.48 3.06
9606 14599 4.133820 TGGTCAAACAGTAGTTGTCATGG 58.866 43.478 0.00 0.00 39.73 3.66
9635 14629 4.243270 GCCGTGTGAGATAAACTACTTGT 58.757 43.478 0.00 0.00 0.00 3.16
9645 14639 1.133598 CCGTAGTTGCCGTGTGAGATA 59.866 52.381 0.00 0.00 0.00 1.98
9649 14643 0.179078 AAACCGTAGTTGCCGTGTGA 60.179 50.000 0.00 0.00 35.97 3.58
9677 14671 5.736813 TGTCTAATTTATGGTAGTTGCCGT 58.263 37.500 0.00 0.00 0.00 5.68
9739 14733 5.240844 GGATGGCAAGTGTAGTTGTAAAAGT 59.759 40.000 0.00 0.00 0.00 2.66
9765 14759 4.099573 CCCGGTTGACAGATGTAGTTATCT 59.900 45.833 0.00 0.00 37.90 1.98
9780 14774 0.693622 TTAGTTGCCATCCCGGTTGA 59.306 50.000 0.00 0.00 36.97 3.18
9786 14780 2.639065 TGACGATTTAGTTGCCATCCC 58.361 47.619 0.00 0.00 0.00 3.85
9840 14834 1.537776 CGAAGCAAAAATGCCCACACA 60.538 47.619 0.00 0.00 34.90 3.72


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

AutoCloner maintained by Alex Coulton.