Multiple sequence alignment - TraesCS1B01G040600

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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 TraesCS1B01G040600 chr1B 100.000 3245 0 0 1 3245 20062082 20058838 0.000000e+00 5993.0
1 TraesCS1B01G040600 chr1B 94.409 1860 76 14 631 2469 20292602 20294454 0.000000e+00 2833.0
2 TraesCS1B01G040600 chr1B 88.769 926 90 8 907 1828 20127543 20126628 0.000000e+00 1122.0
3 TraesCS1B01G040600 chr1B 93.111 479 22 5 2774 3245 20294445 20294919 0.000000e+00 691.0
4 TraesCS1B01G040600 chr1B 89.593 442 30 12 1836 2271 20102667 20102236 6.120000e-152 547.0
5 TraesCS1B01G040600 chr1B 94.915 59 3 0 2541 2599 20059501 20059443 3.450000e-15 93.5
6 TraesCS1B01G040600 chr1B 94.915 59 3 0 2582 2640 20059542 20059484 3.450000e-15 93.5
7 TraesCS1B01G040600 chr1D 94.348 1840 89 7 631 2463 13853596 13851765 0.000000e+00 2808.0
8 TraesCS1B01G040600 chr1D 89.927 1370 105 16 907 2268 14188339 14186995 0.000000e+00 1735.0
9 TraesCS1B01G040600 chr1D 91.400 593 28 11 1873 2463 13970056 13969485 0.000000e+00 791.0
10 TraesCS1B01G040600 chr1D 90.725 593 23 6 1873 2463 14001355 14000793 0.000000e+00 761.0
11 TraesCS1B01G040600 chr1D 90.693 462 31 8 2792 3245 13851765 13851308 3.580000e-169 604.0
12 TraesCS1B01G040600 chr1D 92.363 419 28 3 631 1047 14001768 14001352 7.750000e-166 593.0
13 TraesCS1B01G040600 chr1D 91.647 419 31 3 631 1047 13970469 13970053 7.810000e-161 577.0
14 TraesCS1B01G040600 chr1D 92.920 339 21 2 163 500 13857050 13856714 1.050000e-134 490.0
15 TraesCS1B01G040600 chr1D 92.920 339 20 3 163 500 13973954 13973619 1.050000e-134 490.0
16 TraesCS1B01G040600 chr1D 93.051 331 20 2 171 500 13890317 13889989 6.300000e-132 481.0
17 TraesCS1B01G040600 chr1D 92.749 331 21 2 171 500 14005240 14004912 2.930000e-130 475.0
18 TraesCS1B01G040600 chr1D 93.443 122 8 0 507 628 13854312 13854191 7.150000e-42 182.0
19 TraesCS1B01G040600 chr1D 92.623 122 9 0 507 628 13971207 13971086 3.330000e-40 176.0
20 TraesCS1B01G040600 chr1D 80.631 222 26 6 2470 2690 431964197 431964402 4.330000e-34 156.0
21 TraesCS1B01G040600 chr1D 94.253 87 4 1 3 89 14006680 14006765 7.310000e-27 132.0
22 TraesCS1B01G040600 chr1D 93.902 82 3 1 8 89 13891692 13891771 4.400000e-24 122.0
23 TraesCS1B01G040600 chr1D 97.561 41 0 1 94 133 13857741 13857781 5.810000e-08 69.4
24 TraesCS1B01G040600 chr1D 95.349 43 2 0 94 136 13974887 13974845 5.810000e-08 69.4
25 TraesCS1B01G040600 chr1D 97.561 41 0 1 94 133 13975025 13975065 5.810000e-08 69.4
26 TraesCS1B01G040600 chr1D 97.561 41 0 1 94 133 14006841 14006881 5.810000e-08 69.4
27 TraesCS1B01G040600 chr1D 95.122 41 1 1 94 133 13891846 13891886 2.700000e-06 63.9
28 TraesCS1B01G040600 chr1D 100.000 32 0 0 2309 2340 14186963 14186932 3.500000e-05 60.2
29 TraesCS1B01G040600 chr1A 90.703 1850 128 25 644 2468 14800860 14799030 0.000000e+00 2423.0
30 TraesCS1B01G040600 chr1A 85.780 1751 167 48 631 2340 14858650 14856941 0.000000e+00 1779.0
31 TraesCS1B01G040600 chr1A 89.770 479 38 7 2774 3245 14799038 14798564 1.290000e-168 603.0
32 TraesCS1B01G040600 chr1A 90.182 275 23 3 227 500 14851757 14851486 3.980000e-94 355.0
33 TraesCS1B01G040600 chr1A 92.174 115 8 1 130 244 14851884 14851771 9.320000e-36 161.0
34 TraesCS1B01G040600 chr1A 84.672 137 16 1 2470 2601 19088972 19089108 7.310000e-27 132.0
35 TraesCS1B01G040600 chr1A 94.186 86 4 1 2691 2775 96362976 96362891 2.630000e-26 130.0
36 TraesCS1B01G040600 chr2A 78.287 327 45 17 2469 2775 755768299 755767979 1.540000e-43 187.0
37 TraesCS1B01G040600 chr3B 78.154 325 39 21 2470 2775 160350740 160351051 9.250000e-41 178.0
38 TraesCS1B01G040600 chr3B 82.353 85 12 3 176 259 253736239 253736157 1.620000e-08 71.3
39 TraesCS1B01G040600 chr3D 78.659 328 21 20 2470 2775 581570630 581570930 4.300000e-39 172.0
40 TraesCS1B01G040600 chr3D 87.970 133 9 3 2470 2601 297372593 297372467 2.020000e-32 150.0
41 TraesCS1B01G040600 chr4A 89.130 138 13 1 2466 2601 101610378 101610515 1.550000e-38 171.0
42 TraesCS1B01G040600 chr7A 76.923 325 50 16 2470 2775 657713544 657713226 9.320000e-36 161.0
43 TraesCS1B01G040600 chr7A 94.186 86 4 1 2691 2775 48919188 48919103 2.630000e-26 130.0
44 TraesCS1B01G040600 chr7A 77.005 187 26 9 2505 2690 730733860 730734030 1.240000e-14 91.6
45 TraesCS1B01G040600 chr5D 88.406 138 10 4 2470 2601 457748744 457748881 9.320000e-36 161.0
46 TraesCS1B01G040600 chr4B 82.323 198 20 7 2469 2652 119564268 119564464 1.210000e-34 158.0
47 TraesCS1B01G040600 chr4B 80.645 186 30 5 161 344 563229432 563229613 4.370000e-29 139.0
48 TraesCS1B01G040600 chr6D 88.148 135 11 2 2470 2604 173409251 173409122 4.330000e-34 156.0
49 TraesCS1B01G040600 chr6D 76.981 265 43 11 2505 2756 411556363 411556622 5.650000e-28 135.0
50 TraesCS1B01G040600 chr5B 87.970 133 11 2 2469 2601 58062540 58062413 5.610000e-33 152.0
51 TraesCS1B01G040600 chr5B 75.698 358 48 25 2454 2785 423625882 423626226 3.370000e-30 143.0
52 TraesCS1B01G040600 chr7B 80.269 223 24 6 2469 2689 597112019 597111815 2.020000e-32 150.0
53 TraesCS1B01G040600 chr7B 81.765 170 24 6 2469 2637 552681034 552680871 5.650000e-28 135.0
54 TraesCS1B01G040600 chr7B 77.021 235 30 12 2505 2736 697808745 697808532 2.650000e-21 113.0
55 TraesCS1B01G040600 chr2D 78.516 256 33 13 2505 2758 80472113 80471878 7.250000e-32 148.0
56 TraesCS1B01G040600 chr2D 92.233 103 8 0 2458 2560 125458903 125459005 2.610000e-31 147.0
57 TraesCS1B01G040600 chr3A 95.506 89 3 1 2691 2778 52197246 52197334 1.210000e-29 141.0


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 TraesCS1B01G040600 chr1B 20058838 20062082 3244 True 2060.000000 5993 96.610000 1 3245 3 chr1B.!!$R3 3244
1 TraesCS1B01G040600 chr1B 20292602 20294919 2317 False 1762.000000 2833 93.760000 631 3245 2 chr1B.!!$F1 2614
2 TraesCS1B01G040600 chr1B 20126628 20127543 915 True 1122.000000 1122 88.769000 907 1828 1 chr1B.!!$R2 921
3 TraesCS1B01G040600 chr1D 13851308 13857050 5742 True 1021.000000 2808 92.851000 163 3245 4 chr1D.!!$R2 3082
4 TraesCS1B01G040600 chr1D 14186932 14188339 1407 True 897.600000 1735 94.963500 907 2340 2 chr1D.!!$R5 1433
5 TraesCS1B01G040600 chr1D 14000793 14005240 4447 True 609.666667 761 91.945667 171 2463 3 chr1D.!!$R4 2292
6 TraesCS1B01G040600 chr1D 13969485 13974887 5402 True 420.680000 791 92.787800 94 2463 5 chr1D.!!$R3 2369
7 TraesCS1B01G040600 chr1A 14856941 14858650 1709 True 1779.000000 1779 85.780000 631 2340 1 chr1A.!!$R1 1709
8 TraesCS1B01G040600 chr1A 14798564 14800860 2296 True 1513.000000 2423 90.236500 644 3245 2 chr1A.!!$R3 2601

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
504 1370 0.033920 TGCACGCATCTGTCTTCACT 59.966 50.0 0.0 0.0 0.0 3.41 F
538 3818 0.339859 TCTCACTGCTCTACCCCCAT 59.660 55.0 0.0 0.0 0.0 4.00 F
1527 5470 0.179119 GCTTGTATGGCGTCGGTAGT 60.179 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 5272 0.034059 CCACCAGCAGACGAGAAACT 59.966 55.0 0.0 0.0 0.00 2.66 R
1590 5533 0.392461 GTTCACGGATAGCAAGGGCA 60.392 55.0 0.0 0.0 44.61 5.36 R
3121 7139 0.037232 AACCTCTCCCTTTTCTCGCG 60.037 55.0 0.0 0.0 0.00 5.87 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 4.957759 GCAAGGCGAACTATTTAAAGGA 57.042 40.909 0.00 0.00 0.00 3.36
22 23 5.500645 GCAAGGCGAACTATTTAAAGGAT 57.499 39.130 0.00 0.00 0.00 3.24
23 24 5.891451 GCAAGGCGAACTATTTAAAGGATT 58.109 37.500 0.00 0.00 0.00 3.01
24 25 6.330278 GCAAGGCGAACTATTTAAAGGATTT 58.670 36.000 0.00 0.00 43.42 2.17
25 26 6.811665 GCAAGGCGAACTATTTAAAGGATTTT 59.188 34.615 0.00 0.00 40.09 1.82
26 27 7.330946 GCAAGGCGAACTATTTAAAGGATTTTT 59.669 33.333 0.00 0.00 40.09 1.94
64 65 8.862325 TCTGGAAATGATTATGTTTGTAGTGT 57.138 30.769 0.00 0.00 0.00 3.55
65 66 8.729756 TCTGGAAATGATTATGTTTGTAGTGTG 58.270 33.333 0.00 0.00 0.00 3.82
66 67 8.402798 TGGAAATGATTATGTTTGTAGTGTGT 57.597 30.769 0.00 0.00 0.00 3.72
67 68 8.855110 TGGAAATGATTATGTTTGTAGTGTGTT 58.145 29.630 0.00 0.00 0.00 3.32
68 69 9.341899 GGAAATGATTATGTTTGTAGTGTGTTC 57.658 33.333 0.00 0.00 0.00 3.18
69 70 8.948853 AAATGATTATGTTTGTAGTGTGTTCG 57.051 30.769 0.00 0.00 0.00 3.95
70 71 7.667043 ATGATTATGTTTGTAGTGTGTTCGT 57.333 32.000 0.00 0.00 0.00 3.85
71 72 8.766000 ATGATTATGTTTGTAGTGTGTTCGTA 57.234 30.769 0.00 0.00 0.00 3.43
72 73 8.766000 TGATTATGTTTGTAGTGTGTTCGTAT 57.234 30.769 0.00 0.00 0.00 3.06
73 74 9.210329 TGATTATGTTTGTAGTGTGTTCGTATT 57.790 29.630 0.00 0.00 0.00 1.89
75 76 9.820229 ATTATGTTTGTAGTGTGTTCGTATTTG 57.180 29.630 0.00 0.00 0.00 2.32
76 77 6.665474 TGTTTGTAGTGTGTTCGTATTTGT 57.335 33.333 0.00 0.00 0.00 2.83
77 78 6.707711 TGTTTGTAGTGTGTTCGTATTTGTC 58.292 36.000 0.00 0.00 0.00 3.18
78 79 6.535865 TGTTTGTAGTGTGTTCGTATTTGTCT 59.464 34.615 0.00 0.00 0.00 3.41
79 80 7.064847 TGTTTGTAGTGTGTTCGTATTTGTCTT 59.935 33.333 0.00 0.00 0.00 3.01
80 81 6.519353 TGTAGTGTGTTCGTATTTGTCTTG 57.481 37.500 0.00 0.00 0.00 3.02
81 82 6.044046 TGTAGTGTGTTCGTATTTGTCTTGT 58.956 36.000 0.00 0.00 0.00 3.16
82 83 7.201835 TGTAGTGTGTTCGTATTTGTCTTGTA 58.798 34.615 0.00 0.00 0.00 2.41
83 84 7.868922 TGTAGTGTGTTCGTATTTGTCTTGTAT 59.131 33.333 0.00 0.00 0.00 2.29
84 85 7.724305 AGTGTGTTCGTATTTGTCTTGTATT 57.276 32.000 0.00 0.00 0.00 1.89
85 86 8.149973 AGTGTGTTCGTATTTGTCTTGTATTT 57.850 30.769 0.00 0.00 0.00 1.40
86 87 8.617809 AGTGTGTTCGTATTTGTCTTGTATTTT 58.382 29.630 0.00 0.00 0.00 1.82
87 88 9.228636 GTGTGTTCGTATTTGTCTTGTATTTTT 57.771 29.630 0.00 0.00 0.00 1.94
136 148 8.947115 ACCTTACTTCTTAGTTGCATTGTATTC 58.053 33.333 0.00 0.00 35.78 1.75
140 152 8.621532 ACTTCTTAGTTGCATTGTATTCAGAA 57.378 30.769 0.00 0.00 0.00 3.02
189 1054 5.826737 CAGCTGGTGAATGGATTCTAAGATT 59.173 40.000 5.57 0.00 37.67 2.40
193 1058 8.686334 GCTGGTGAATGGATTCTAAGATTTTTA 58.314 33.333 1.26 0.00 37.67 1.52
271 1137 4.814771 GGGATTGTTACTGCATACTACACC 59.185 45.833 0.00 0.00 0.00 4.16
276 1142 9.326413 GATTGTTACTGCATACTACACCTTTAT 57.674 33.333 0.00 0.00 0.00 1.40
352 1218 2.257409 ATTCCGGGTGCAGATCGCTT 62.257 55.000 0.00 0.00 43.06 4.68
388 1254 3.385577 GAACAAACAAATAGCCGCCAAA 58.614 40.909 0.00 0.00 0.00 3.28
426 1292 2.238646 ACAGCCGGGTTGATAGAAATCA 59.761 45.455 18.32 0.00 40.43 2.57
441 1307 1.125093 AATCAGGACGACACACCCCA 61.125 55.000 0.00 0.00 0.00 4.96
476 1342 1.946984 ACCATTAGAACCGGTCCTGA 58.053 50.000 8.04 0.00 0.00 3.86
478 1344 2.027469 ACCATTAGAACCGGTCCTGAAC 60.027 50.000 8.04 0.00 0.00 3.18
500 1366 0.952497 CACCTGCACGCATCTGTCTT 60.952 55.000 0.00 0.00 0.00 3.01
501 1367 0.671781 ACCTGCACGCATCTGTCTTC 60.672 55.000 0.00 0.00 0.00 2.87
502 1368 0.671472 CCTGCACGCATCTGTCTTCA 60.671 55.000 0.00 0.00 0.00 3.02
503 1369 0.441533 CTGCACGCATCTGTCTTCAC 59.558 55.000 0.00 0.00 0.00 3.18
504 1370 0.033920 TGCACGCATCTGTCTTCACT 59.966 50.000 0.00 0.00 0.00 3.41
505 1371 0.441533 GCACGCATCTGTCTTCACTG 59.558 55.000 0.00 0.00 0.00 3.66
525 3805 1.152030 TCCCAGCAACCCTCTCACT 60.152 57.895 0.00 0.00 0.00 3.41
538 3818 0.339859 TCTCACTGCTCTACCCCCAT 59.660 55.000 0.00 0.00 0.00 4.00
540 3820 1.689273 CTCACTGCTCTACCCCCATAC 59.311 57.143 0.00 0.00 0.00 2.39
628 3908 4.702831 TGATCAGGCGCTCATTAATACAA 58.297 39.130 7.64 0.00 0.00 2.41
629 3909 5.308014 TGATCAGGCGCTCATTAATACAAT 58.692 37.500 7.64 0.00 0.00 2.71
654 4548 7.889469 TGAGATTGCTTCTGCTTAAGATTTTT 58.111 30.769 6.67 0.00 40.48 1.94
656 4550 8.120140 AGATTGCTTCTGCTTAAGATTTTTCT 57.880 30.769 6.67 0.00 40.48 2.52
673 4567 6.494893 TTTTTCTTGTGCATTATAGTCGCT 57.505 33.333 0.00 0.00 0.00 4.93
674 4568 6.494893 TTTTCTTGTGCATTATAGTCGCTT 57.505 33.333 0.00 0.00 0.00 4.68
692 4586 4.156190 TCGCTTTTTATACAAATTCCCGCA 59.844 37.500 0.00 0.00 0.00 5.69
694 4588 5.407502 GCTTTTTATACAAATTCCCGCAGT 58.592 37.500 0.00 0.00 0.00 4.40
714 4608 1.536943 AAGGCGTGGAGTGTCCTCTC 61.537 60.000 0.00 0.00 37.46 3.20
765 4661 7.812191 GCATTCTGACATCTAGTAGGTGAATAG 59.188 40.741 17.49 11.11 0.00 1.73
797 4693 3.546271 GGTTGTTGCTTCGAAAAGAACAC 59.454 43.478 18.65 12.35 34.85 3.32
798 4694 4.162812 GTTGTTGCTTCGAAAAGAACACA 58.837 39.130 14.39 3.85 34.85 3.72
905 4820 1.723608 CGCCGCCTCATAATTTGCCA 61.724 55.000 0.00 0.00 0.00 4.92
991 4910 8.493547 GTCCATTCGTAATACCTATAGCAAAAC 58.506 37.037 0.00 0.00 0.00 2.43
1003 4922 6.053005 CCTATAGCAAAACTACGGGAAATGA 58.947 40.000 0.00 0.00 32.32 2.57
1344 5272 3.275143 CACAGTTTACCACCTCAACACA 58.725 45.455 0.00 0.00 0.00 3.72
1356 5284 2.797156 CCTCAACACAGTTTCTCGTCTG 59.203 50.000 0.00 0.00 37.65 3.51
1503 5446 2.046411 TTCACGATGGCGCATGGT 60.046 55.556 10.83 5.69 42.48 3.55
1527 5470 0.179119 GCTTGTATGGCGTCGGTAGT 60.179 55.000 0.00 0.00 0.00 2.73
1547 5490 1.067425 TCGTGATCCCGAATTCAACGT 60.067 47.619 6.22 0.00 33.15 3.99
1590 5533 0.957395 CCACCAGCAAGTTCATCGCT 60.957 55.000 0.00 0.00 36.10 4.93
1609 5552 0.392461 TGCCCTTGCTATCCGTGAAC 60.392 55.000 0.00 0.00 38.71 3.18
1746 5689 4.111577 TCCCACAGGTGATAGAAGGAATT 58.888 43.478 0.00 0.00 0.00 2.17
1747 5690 4.164221 TCCCACAGGTGATAGAAGGAATTC 59.836 45.833 0.00 0.00 0.00 2.17
1818 5761 1.207089 CCTCCCGCTGATGTTGTTCTA 59.793 52.381 0.00 0.00 0.00 2.10
2068 6025 3.596310 TTGATACCGTCGTTGGATCAA 57.404 42.857 5.36 5.36 35.29 2.57
2403 6399 4.770010 GCATGCTTCTCTATACCCTCTACT 59.230 45.833 11.37 0.00 0.00 2.57
2463 6459 8.894768 AACTGAATACCTTGCTCATATTACTC 57.105 34.615 0.00 0.00 0.00 2.59
2464 6460 8.256356 ACTGAATACCTTGCTCATATTACTCT 57.744 34.615 0.00 0.00 0.00 3.24
2465 6461 9.368416 ACTGAATACCTTGCTCATATTACTCTA 57.632 33.333 0.00 0.00 0.00 2.43
2466 6462 9.853555 CTGAATACCTTGCTCATATTACTCTAG 57.146 37.037 0.00 0.00 0.00 2.43
2467 6463 8.807118 TGAATACCTTGCTCATATTACTCTAGG 58.193 37.037 0.00 0.00 0.00 3.02
2468 6464 5.476091 ACCTTGCTCATATTACTCTAGGC 57.524 43.478 0.00 0.00 0.00 3.93
2469 6465 5.151454 ACCTTGCTCATATTACTCTAGGCT 58.849 41.667 0.00 0.00 0.00 4.58
2470 6466 6.315714 ACCTTGCTCATATTACTCTAGGCTA 58.684 40.000 0.00 0.00 0.00 3.93
2471 6467 6.957020 ACCTTGCTCATATTACTCTAGGCTAT 59.043 38.462 0.00 0.00 0.00 2.97
2472 6468 8.116669 ACCTTGCTCATATTACTCTAGGCTATA 58.883 37.037 0.00 0.00 0.00 1.31
2473 6469 8.410141 CCTTGCTCATATTACTCTAGGCTATAC 58.590 40.741 0.00 0.00 0.00 1.47
2474 6470 9.184523 CTTGCTCATATTACTCTAGGCTATACT 57.815 37.037 0.00 0.00 0.00 2.12
2475 6471 9.535170 TTGCTCATATTACTCTAGGCTATACTT 57.465 33.333 0.00 0.00 0.00 2.24
2476 6472 8.961634 TGCTCATATTACTCTAGGCTATACTTG 58.038 37.037 0.00 0.00 0.00 3.16
2477 6473 8.410141 GCTCATATTACTCTAGGCTATACTTGG 58.590 40.741 0.00 0.00 0.00 3.61
2478 6474 8.294954 TCATATTACTCTAGGCTATACTTGGC 57.705 38.462 0.00 0.00 0.00 4.52
2487 6483 2.960819 GCTATACTTGGCCATACCTCG 58.039 52.381 6.09 0.00 40.22 4.63
2488 6484 2.353803 GCTATACTTGGCCATACCTCGG 60.354 54.545 6.09 0.00 40.22 4.63
2489 6485 1.056660 ATACTTGGCCATACCTCGGG 58.943 55.000 6.09 0.00 40.22 5.14
2528 6524 2.592861 GCCTAGCCAAGCCCGATG 60.593 66.667 0.00 0.00 0.00 3.84
2529 6525 2.592861 CCTAGCCAAGCCCGATGC 60.593 66.667 0.00 0.00 41.71 3.91
2530 6526 2.190313 CTAGCCAAGCCCGATGCA 59.810 61.111 0.00 0.00 44.83 3.96
2531 6527 1.451927 CTAGCCAAGCCCGATGCAA 60.452 57.895 0.00 0.00 44.83 4.08
2532 6528 1.001517 TAGCCAAGCCCGATGCAAA 60.002 52.632 0.00 0.00 44.83 3.68
2533 6529 0.610509 TAGCCAAGCCCGATGCAAAA 60.611 50.000 0.00 0.00 44.83 2.44
2534 6530 1.005156 GCCAAGCCCGATGCAAAAA 60.005 52.632 0.00 0.00 44.83 1.94
2568 6564 4.740822 GGCCCGGCCTGAACATGT 62.741 66.667 22.31 0.00 46.69 3.21
2569 6565 2.270850 GCCCGGCCTGAACATGTA 59.729 61.111 0.00 0.00 0.00 2.29
2570 6566 1.377987 GCCCGGCCTGAACATGTAA 60.378 57.895 0.00 0.00 0.00 2.41
2571 6567 0.963355 GCCCGGCCTGAACATGTAAA 60.963 55.000 0.00 0.00 0.00 2.01
2572 6568 1.540267 CCCGGCCTGAACATGTAAAA 58.460 50.000 0.00 0.00 0.00 1.52
2573 6569 1.472480 CCCGGCCTGAACATGTAAAAG 59.528 52.381 0.00 0.00 0.00 2.27
2574 6570 1.135402 CCGGCCTGAACATGTAAAAGC 60.135 52.381 0.00 0.08 0.00 3.51
2575 6571 1.135402 CGGCCTGAACATGTAAAAGCC 60.135 52.381 16.12 16.12 35.78 4.35
2576 6572 1.204704 GGCCTGAACATGTAAAAGCCC 59.795 52.381 15.50 3.34 32.93 5.19
2577 6573 1.135402 GCCTGAACATGTAAAAGCCCG 60.135 52.381 0.00 0.00 0.00 6.13
2578 6574 2.159382 CCTGAACATGTAAAAGCCCGT 58.841 47.619 0.00 0.00 0.00 5.28
2579 6575 2.161609 CCTGAACATGTAAAAGCCCGTC 59.838 50.000 0.00 0.00 0.00 4.79
2580 6576 1.801771 TGAACATGTAAAAGCCCGTCG 59.198 47.619 0.00 0.00 0.00 5.12
2581 6577 1.129811 GAACATGTAAAAGCCCGTCGG 59.870 52.381 3.60 3.60 0.00 4.79
2609 6605 4.740822 GGCCCGGCCTGAACATGT 62.741 66.667 22.31 0.00 46.69 3.21
2610 6606 2.270850 GCCCGGCCTGAACATGTA 59.729 61.111 0.00 0.00 0.00 2.29
2611 6607 1.377987 GCCCGGCCTGAACATGTAA 60.378 57.895 0.00 0.00 0.00 2.41
2612 6608 0.963355 GCCCGGCCTGAACATGTAAA 60.963 55.000 0.00 0.00 0.00 2.01
2613 6609 1.540267 CCCGGCCTGAACATGTAAAA 58.460 50.000 0.00 0.00 0.00 1.52
2614 6610 1.472480 CCCGGCCTGAACATGTAAAAG 59.528 52.381 0.00 0.00 0.00 2.27
2615 6611 1.135402 CCGGCCTGAACATGTAAAAGC 60.135 52.381 0.00 0.08 0.00 3.51
2616 6612 1.135402 CGGCCTGAACATGTAAAAGCC 60.135 52.381 16.12 16.12 35.78 4.35
2617 6613 1.204704 GGCCTGAACATGTAAAAGCCC 59.795 52.381 15.50 3.34 32.93 5.19
2618 6614 1.135402 GCCTGAACATGTAAAAGCCCG 60.135 52.381 0.00 0.00 0.00 6.13
2619 6615 2.159382 CCTGAACATGTAAAAGCCCGT 58.841 47.619 0.00 0.00 0.00 5.28
2620 6616 2.161609 CCTGAACATGTAAAAGCCCGTC 59.838 50.000 0.00 0.00 0.00 4.79
2621 6617 2.811431 CTGAACATGTAAAAGCCCGTCA 59.189 45.455 0.00 0.00 0.00 4.35
2622 6618 2.811431 TGAACATGTAAAAGCCCGTCAG 59.189 45.455 0.00 0.00 0.00 3.51
2623 6619 1.821216 ACATGTAAAAGCCCGTCAGG 58.179 50.000 0.00 0.00 39.47 3.86
2662 6658 4.338710 CCCGGCCCGACCTTCAAA 62.339 66.667 3.71 0.00 35.61 2.69
2663 6659 2.281900 CCGGCCCGACCTTCAAAA 60.282 61.111 3.71 0.00 35.61 2.44
2664 6660 1.899534 CCGGCCCGACCTTCAAAAA 60.900 57.895 3.71 0.00 35.61 1.94
2696 6692 4.626081 CGGGCCCGGGCAATCTAG 62.626 72.222 44.46 24.34 44.11 2.43
2697 6693 4.271016 GGGCCCGGGCAATCTAGG 62.271 72.222 44.46 5.93 44.11 3.02
2698 6694 4.956932 GGCCCGGGCAATCTAGGC 62.957 72.222 44.46 22.62 44.11 3.93
2704 6700 2.281139 GGCAATCTAGGCCCGAGC 60.281 66.667 0.00 0.00 45.87 5.03
2771 6767 4.066139 GGCTTCCCATGGCCAGGT 62.066 66.667 17.55 0.00 46.84 4.00
2772 6768 2.689691 GGCTTCCCATGGCCAGGTA 61.690 63.158 17.55 3.27 46.84 3.08
2773 6769 1.538666 GCTTCCCATGGCCAGGTAT 59.461 57.895 17.55 0.00 0.00 2.73
2774 6770 0.771127 GCTTCCCATGGCCAGGTATA 59.229 55.000 17.55 0.00 0.00 1.47
2775 6771 1.545651 GCTTCCCATGGCCAGGTATAC 60.546 57.143 17.55 0.00 0.00 1.47
2776 6772 2.057922 CTTCCCATGGCCAGGTATACT 58.942 52.381 17.55 0.00 0.00 2.12
2777 6773 1.729586 TCCCATGGCCAGGTATACTC 58.270 55.000 17.55 0.00 0.00 2.59
2778 6774 1.223077 TCCCATGGCCAGGTATACTCT 59.777 52.381 17.55 0.00 0.00 3.24
2779 6775 2.453212 TCCCATGGCCAGGTATACTCTA 59.547 50.000 17.55 0.00 0.00 2.43
2780 6776 2.834549 CCCATGGCCAGGTATACTCTAG 59.165 54.545 17.55 0.00 0.00 2.43
2781 6777 2.834549 CCATGGCCAGGTATACTCTAGG 59.165 54.545 17.55 1.46 0.00 3.02
2782 6778 2.011122 TGGCCAGGTATACTCTAGGC 57.989 55.000 0.00 15.34 41.29 3.93
2783 6779 0.889306 GGCCAGGTATACTCTAGGCG 59.111 60.000 16.40 0.00 42.89 5.52
2784 6780 1.618487 GCCAGGTATACTCTAGGCGT 58.382 55.000 2.25 0.00 31.88 5.68
2785 6781 1.540707 GCCAGGTATACTCTAGGCGTC 59.459 57.143 2.25 0.00 31.88 5.19
2786 6782 2.161030 CCAGGTATACTCTAGGCGTCC 58.839 57.143 2.25 0.00 0.00 4.79
2787 6783 2.161030 CAGGTATACTCTAGGCGTCCC 58.839 57.143 2.25 0.00 0.00 4.46
2788 6784 1.779092 AGGTATACTCTAGGCGTCCCA 59.221 52.381 2.25 0.00 0.00 4.37
2789 6785 2.379226 AGGTATACTCTAGGCGTCCCAT 59.621 50.000 2.25 0.00 0.00 4.00
2790 6786 3.163467 GGTATACTCTAGGCGTCCCATT 58.837 50.000 2.25 0.00 0.00 3.16
2810 6821 6.266103 CCCATTTACCTAGTGCATTGATTGAT 59.734 38.462 0.00 0.00 0.00 2.57
2965 6983 3.680786 TGTCGCAGCGCTGGTAGT 61.681 61.111 36.47 0.00 0.00 2.73
2991 7009 8.815565 AATACATGGTTGTATGTGTGGATTAA 57.184 30.769 0.00 0.00 46.10 1.40
2993 7011 7.716799 ACATGGTTGTATGTGTGGATTAATT 57.283 32.000 0.00 0.00 39.68 1.40
3069 7087 3.285215 GCCATCCCAGCGCATGAG 61.285 66.667 11.47 0.00 0.00 2.90
3121 7139 7.029563 CCTATTAGTGTTTTGATTTGGCAGAC 58.970 38.462 0.00 0.00 0.00 3.51
3157 7175 7.119992 GGGAGAGGTTCAGATTAGAAAGAAAAC 59.880 40.741 0.00 0.00 0.00 2.43
3183 7201 0.751643 GTGCACACACCTTCAACCCT 60.752 55.000 13.17 0.00 41.21 4.34
3200 7218 8.561738 TTCAACCCTTTTGTGAAGAGATATAC 57.438 34.615 0.00 0.00 0.00 1.47
3236 7254 4.142315 CCCCTGAGCATAATCAACAACTTG 60.142 45.833 0.00 0.00 0.00 3.16
3237 7255 4.460382 CCCTGAGCATAATCAACAACTTGT 59.540 41.667 0.00 0.00 0.00 3.16
3238 7256 5.647658 CCCTGAGCATAATCAACAACTTGTA 59.352 40.000 0.00 0.00 0.00 2.41
3239 7257 6.319658 CCCTGAGCATAATCAACAACTTGTAT 59.680 38.462 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.957759 TCCTTTAAATAGTTCGCCTTGC 57.042 40.909 0.00 0.00 0.00 4.01
1 2 8.757164 AAAAATCCTTTAAATAGTTCGCCTTG 57.243 30.769 0.00 0.00 0.00 3.61
38 39 9.466497 ACACTACAAACATAATCATTTCCAGAT 57.534 29.630 0.00 0.00 0.00 2.90
39 40 8.729756 CACACTACAAACATAATCATTTCCAGA 58.270 33.333 0.00 0.00 0.00 3.86
40 41 8.514594 ACACACTACAAACATAATCATTTCCAG 58.485 33.333 0.00 0.00 0.00 3.86
41 42 8.402798 ACACACTACAAACATAATCATTTCCA 57.597 30.769 0.00 0.00 0.00 3.53
42 43 9.341899 GAACACACTACAAACATAATCATTTCC 57.658 33.333 0.00 0.00 0.00 3.13
43 44 9.051027 CGAACACACTACAAACATAATCATTTC 57.949 33.333 0.00 0.00 0.00 2.17
44 45 8.564574 ACGAACACACTACAAACATAATCATTT 58.435 29.630 0.00 0.00 0.00 2.32
45 46 8.094798 ACGAACACACTACAAACATAATCATT 57.905 30.769 0.00 0.00 0.00 2.57
46 47 7.667043 ACGAACACACTACAAACATAATCAT 57.333 32.000 0.00 0.00 0.00 2.45
47 48 8.766000 ATACGAACACACTACAAACATAATCA 57.234 30.769 0.00 0.00 0.00 2.57
49 50 9.820229 CAAATACGAACACACTACAAACATAAT 57.180 29.630 0.00 0.00 0.00 1.28
50 51 8.828644 ACAAATACGAACACACTACAAACATAA 58.171 29.630 0.00 0.00 0.00 1.90
51 52 8.367943 ACAAATACGAACACACTACAAACATA 57.632 30.769 0.00 0.00 0.00 2.29
52 53 7.225931 AGACAAATACGAACACACTACAAACAT 59.774 33.333 0.00 0.00 0.00 2.71
53 54 6.535865 AGACAAATACGAACACACTACAAACA 59.464 34.615 0.00 0.00 0.00 2.83
54 55 6.940714 AGACAAATACGAACACACTACAAAC 58.059 36.000 0.00 0.00 0.00 2.93
55 56 7.064847 ACAAGACAAATACGAACACACTACAAA 59.935 33.333 0.00 0.00 0.00 2.83
56 57 6.535865 ACAAGACAAATACGAACACACTACAA 59.464 34.615 0.00 0.00 0.00 2.41
57 58 6.044046 ACAAGACAAATACGAACACACTACA 58.956 36.000 0.00 0.00 0.00 2.74
58 59 6.520792 ACAAGACAAATACGAACACACTAC 57.479 37.500 0.00 0.00 0.00 2.73
59 60 8.821147 AATACAAGACAAATACGAACACACTA 57.179 30.769 0.00 0.00 0.00 2.74
60 61 7.724305 AATACAAGACAAATACGAACACACT 57.276 32.000 0.00 0.00 0.00 3.55
61 62 8.776680 AAAATACAAGACAAATACGAACACAC 57.223 30.769 0.00 0.00 0.00 3.82
86 87 9.974980 GGTGAACTATTTAAAGGATTCAACAAA 57.025 29.630 15.83 0.00 34.59 2.83
87 88 9.362151 AGGTGAACTATTTAAAGGATTCAACAA 57.638 29.630 19.94 0.00 36.45 2.83
88 89 8.934023 AGGTGAACTATTTAAAGGATTCAACA 57.066 30.769 19.94 2.69 36.45 3.33
146 158 8.571336 ACCAGCTGAAGCATGTTAATAATTATC 58.429 33.333 17.39 0.00 45.16 1.75
165 1030 4.774124 TCTTAGAATCCATTCACCAGCTG 58.226 43.478 6.78 6.78 39.23 4.24
189 1054 3.976015 AGAAAGCCGGGGAATGATAAAA 58.024 40.909 2.18 0.00 0.00 1.52
193 1058 1.284785 TGAAGAAAGCCGGGGAATGAT 59.715 47.619 2.18 0.00 0.00 2.45
198 1064 1.892474 CAAAATGAAGAAAGCCGGGGA 59.108 47.619 2.18 0.00 0.00 4.81
317 1183 7.470841 GCACCCGGAATTGTAATAATATTGGTT 60.471 37.037 0.73 0.00 0.00 3.67
319 1185 6.015856 TGCACCCGGAATTGTAATAATATTGG 60.016 38.462 0.73 0.00 0.00 3.16
320 1186 6.976088 TGCACCCGGAATTGTAATAATATTG 58.024 36.000 0.73 0.00 0.00 1.90
321 1187 7.001674 TCTGCACCCGGAATTGTAATAATATT 58.998 34.615 0.73 0.00 0.00 1.28
388 1254 0.537143 TGTTGCACTGCCCGATTCTT 60.537 50.000 0.00 0.00 0.00 2.52
426 1292 1.908793 CTCTGGGGTGTGTCGTCCT 60.909 63.158 0.00 0.00 0.00 3.85
441 1307 0.112995 TGGTTGAGGCCATTTGCTCT 59.887 50.000 5.01 0.00 40.92 4.09
476 1342 2.203337 ATGCGTGCAGGTGTGGTT 60.203 55.556 8.40 0.00 0.00 3.67
478 1344 2.359107 AGATGCGTGCAGGTGTGG 60.359 61.111 8.40 0.00 0.00 4.17
505 1371 2.270527 GAGAGGGTTGCTGGGAGC 59.729 66.667 0.00 0.00 42.82 4.70
525 3805 0.693092 GTGGGTATGGGGGTAGAGCA 60.693 60.000 0.00 0.00 0.00 4.26
540 3820 2.437716 ATTGCCTTACCGCGTGGG 60.438 61.111 21.14 6.53 40.75 4.61
599 3879 2.829914 GCGCCTGATCAATGCCCA 60.830 61.111 10.40 0.00 0.00 5.36
606 3886 4.335400 TGTATTAATGAGCGCCTGATCA 57.665 40.909 2.29 0.40 45.95 2.92
607 3887 5.409520 TCATTGTATTAATGAGCGCCTGATC 59.590 40.000 2.29 0.00 33.20 2.92
628 3908 7.642082 AAATCTTAAGCAGAAGCAATCTCAT 57.358 32.000 0.00 0.00 45.49 2.90
629 3909 7.458409 AAAATCTTAAGCAGAAGCAATCTCA 57.542 32.000 0.00 0.00 45.49 3.27
654 4548 6.494893 AAAAAGCGACTATAATGCACAAGA 57.505 33.333 0.00 0.00 0.00 3.02
656 4550 8.884726 TGTATAAAAAGCGACTATAATGCACAA 58.115 29.630 0.00 0.00 0.00 3.33
673 4567 7.540299 CCTTACTGCGGGAATTTGTATAAAAA 58.460 34.615 0.00 0.00 0.00 1.94
674 4568 6.404954 GCCTTACTGCGGGAATTTGTATAAAA 60.405 38.462 0.00 0.00 0.00 1.52
692 4586 0.542232 AGGACACTCCACGCCTTACT 60.542 55.000 0.00 0.00 39.61 2.24
694 4588 0.251653 AGAGGACACTCCACGCCTTA 60.252 55.000 0.00 0.00 45.11 2.69
736 4632 7.007116 TCACCTACTAGATGTCAGAATGCTAT 58.993 38.462 0.00 0.00 34.76 2.97
765 4661 1.730547 GCAACAACCTGCGCACATC 60.731 57.895 5.66 0.00 31.50 3.06
797 4693 1.200716 GACAAGTGGCCATGACACATG 59.799 52.381 9.72 18.26 45.35 3.21
798 4694 1.538047 GACAAGTGGCCATGACACAT 58.462 50.000 9.72 7.58 45.35 3.21
883 4784 2.542907 AAATTATGAGGCGGCGCGG 61.543 57.895 26.95 11.08 0.00 6.46
905 4820 2.497675 AGCACCACACGATCATAAGAGT 59.502 45.455 0.00 0.00 0.00 3.24
991 4910 3.871594 GTGGTCTGATTCATTTCCCGTAG 59.128 47.826 0.00 0.00 0.00 3.51
994 4913 2.679837 CTGTGGTCTGATTCATTTCCCG 59.320 50.000 0.00 0.00 0.00 5.14
1003 4922 0.682209 GGCATGGCTGTGGTCTGATT 60.682 55.000 12.86 0.00 0.00 2.57
1326 5254 3.926058 ACTGTGTTGAGGTGGTAAACT 57.074 42.857 0.00 0.00 0.00 2.66
1344 5272 0.034059 CCACCAGCAGACGAGAAACT 59.966 55.000 0.00 0.00 0.00 2.66
1503 5446 1.220749 GACGCCATACAAGCTCCCA 59.779 57.895 0.00 0.00 0.00 4.37
1527 5470 1.067425 ACGTTGAATTCGGGATCACGA 60.067 47.619 17.88 17.88 41.76 4.35
1547 5490 1.228003 ATCGCCCCGTTGAACAACA 60.228 52.632 16.13 0.00 41.20 3.33
1590 5533 0.392461 GTTCACGGATAGCAAGGGCA 60.392 55.000 0.00 0.00 44.61 5.36
2068 6025 2.254546 TCAAGCATTTCGTGTGAGGT 57.745 45.000 0.00 0.00 0.00 3.85
2403 6399 0.453793 CCGCAACCAATAATGCCGAA 59.546 50.000 0.00 0.00 39.39 4.30
2467 6463 2.353803 CCGAGGTATGGCCAAGTATAGC 60.354 54.545 10.96 7.44 40.61 2.97
2468 6464 2.233922 CCCGAGGTATGGCCAAGTATAG 59.766 54.545 10.96 0.00 40.61 1.31
2469 6465 2.253610 CCCGAGGTATGGCCAAGTATA 58.746 52.381 10.96 0.00 40.61 1.47
2470 6466 1.056660 CCCGAGGTATGGCCAAGTAT 58.943 55.000 10.96 0.00 40.61 2.12
2471 6467 1.692173 GCCCGAGGTATGGCCAAGTA 61.692 60.000 10.96 0.00 41.97 2.24
2472 6468 3.043999 GCCCGAGGTATGGCCAAGT 62.044 63.158 10.96 0.00 41.97 3.16
2473 6469 2.203209 GCCCGAGGTATGGCCAAG 60.203 66.667 10.96 0.00 41.97 3.61
2512 6508 2.592861 GCATCGGGCTTGGCTAGG 60.593 66.667 0.00 0.00 40.25 3.02
2513 6509 1.031571 TTTGCATCGGGCTTGGCTAG 61.032 55.000 0.00 0.00 45.15 3.42
2514 6510 0.610509 TTTTGCATCGGGCTTGGCTA 60.611 50.000 0.00 0.00 45.15 3.93
2515 6511 1.470996 TTTTTGCATCGGGCTTGGCT 61.471 50.000 0.00 0.00 45.15 4.75
2516 6512 1.005156 TTTTTGCATCGGGCTTGGC 60.005 52.632 0.00 0.00 45.15 4.52
2552 6548 0.963355 TTTACATGTTCAGGCCGGGC 60.963 55.000 22.67 22.67 0.00 6.13
2553 6549 1.472480 CTTTTACATGTTCAGGCCGGG 59.528 52.381 2.30 0.00 0.00 5.73
2554 6550 1.135402 GCTTTTACATGTTCAGGCCGG 60.135 52.381 2.30 0.00 0.00 6.13
2555 6551 1.135402 GGCTTTTACATGTTCAGGCCG 60.135 52.381 2.30 0.00 0.00 6.13
2556 6552 1.204704 GGGCTTTTACATGTTCAGGCC 59.795 52.381 21.18 21.18 42.39 5.19
2557 6553 1.135402 CGGGCTTTTACATGTTCAGGC 60.135 52.381 2.30 9.98 0.00 4.85
2558 6554 2.159382 ACGGGCTTTTACATGTTCAGG 58.841 47.619 2.30 0.00 0.00 3.86
2559 6555 2.159707 CGACGGGCTTTTACATGTTCAG 60.160 50.000 2.30 0.00 0.00 3.02
2560 6556 1.801771 CGACGGGCTTTTACATGTTCA 59.198 47.619 2.30 0.00 0.00 3.18
2561 6557 1.129811 CCGACGGGCTTTTACATGTTC 59.870 52.381 2.30 0.00 0.00 3.18
2562 6558 1.161843 CCGACGGGCTTTTACATGTT 58.838 50.000 2.30 0.00 0.00 2.71
2563 6559 0.675522 CCCGACGGGCTTTTACATGT 60.676 55.000 22.37 2.69 35.35 3.21
2564 6560 2.094904 CCCGACGGGCTTTTACATG 58.905 57.895 22.37 0.00 35.35 3.21
2565 6561 4.629779 CCCGACGGGCTTTTACAT 57.370 55.556 22.37 0.00 35.35 2.29
2593 6589 0.963355 TTTACATGTTCAGGCCGGGC 60.963 55.000 22.67 22.67 0.00 6.13
2594 6590 1.472480 CTTTTACATGTTCAGGCCGGG 59.528 52.381 2.30 0.00 0.00 5.73
2595 6591 1.135402 GCTTTTACATGTTCAGGCCGG 60.135 52.381 2.30 0.00 0.00 6.13
2596 6592 1.135402 GGCTTTTACATGTTCAGGCCG 60.135 52.381 2.30 0.00 0.00 6.13
2597 6593 1.204704 GGGCTTTTACATGTTCAGGCC 59.795 52.381 21.18 21.18 42.39 5.19
2598 6594 1.135402 CGGGCTTTTACATGTTCAGGC 60.135 52.381 2.30 9.98 0.00 4.85
2599 6595 2.159382 ACGGGCTTTTACATGTTCAGG 58.841 47.619 2.30 0.00 0.00 3.86
2600 6596 2.811431 TGACGGGCTTTTACATGTTCAG 59.189 45.455 2.30 0.00 0.00 3.02
2601 6597 2.811431 CTGACGGGCTTTTACATGTTCA 59.189 45.455 2.30 0.00 0.00 3.18
2602 6598 2.161609 CCTGACGGGCTTTTACATGTTC 59.838 50.000 2.30 0.00 0.00 3.18
2603 6599 2.159382 CCTGACGGGCTTTTACATGTT 58.841 47.619 2.30 0.00 0.00 2.71
2604 6600 1.821216 CCTGACGGGCTTTTACATGT 58.179 50.000 2.69 2.69 0.00 3.21
2645 6641 3.853698 TTTTGAAGGTCGGGCCGGG 62.854 63.158 27.98 0.00 43.70 5.73
2646 6642 1.899534 TTTTTGAAGGTCGGGCCGG 60.900 57.895 27.98 7.65 43.70 6.13
2647 6643 3.752704 TTTTTGAAGGTCGGGCCG 58.247 55.556 22.51 22.51 43.70 6.13
2679 6675 4.626081 CTAGATTGCCCGGGCCCG 62.626 72.222 41.75 37.99 41.09 6.13
2680 6676 4.271016 CCTAGATTGCCCGGGCCC 62.271 72.222 41.75 29.09 41.09 5.80
2681 6677 4.956932 GCCTAGATTGCCCGGGCC 62.957 72.222 41.75 26.88 41.09 5.80
2682 6678 4.956932 GGCCTAGATTGCCCGGGC 62.957 72.222 39.40 39.40 43.33 6.13
2755 6751 0.771127 TATACCTGGCCATGGGAAGC 59.229 55.000 17.65 0.00 0.00 3.86
2756 6752 2.039084 GAGTATACCTGGCCATGGGAAG 59.961 54.545 17.65 0.00 0.00 3.46
2757 6753 2.054799 GAGTATACCTGGCCATGGGAA 58.945 52.381 17.65 9.02 0.00 3.97
2758 6754 1.223077 AGAGTATACCTGGCCATGGGA 59.777 52.381 17.65 12.89 0.00 4.37
2759 6755 1.734655 AGAGTATACCTGGCCATGGG 58.265 55.000 20.97 16.10 0.00 4.00
2760 6756 2.834549 CCTAGAGTATACCTGGCCATGG 59.165 54.545 5.51 13.05 0.00 3.66
2761 6757 2.234908 GCCTAGAGTATACCTGGCCATG 59.765 54.545 5.51 6.06 34.81 3.66
2762 6758 2.541466 GCCTAGAGTATACCTGGCCAT 58.459 52.381 5.51 0.00 34.81 4.40
2763 6759 1.822062 CGCCTAGAGTATACCTGGCCA 60.822 57.143 4.71 4.71 37.29 5.36
2764 6760 0.889306 CGCCTAGAGTATACCTGGCC 59.111 60.000 15.63 0.00 37.29 5.36
2765 6761 1.540707 GACGCCTAGAGTATACCTGGC 59.459 57.143 12.96 12.96 37.24 4.85
2766 6762 2.161030 GGACGCCTAGAGTATACCTGG 58.839 57.143 0.00 0.00 0.00 4.45
2767 6763 2.161030 GGGACGCCTAGAGTATACCTG 58.839 57.143 0.00 0.00 0.00 4.00
2768 6764 1.779092 TGGGACGCCTAGAGTATACCT 59.221 52.381 0.00 0.00 0.00 3.08
2769 6765 2.283145 TGGGACGCCTAGAGTATACC 57.717 55.000 0.00 0.00 0.00 2.73
2770 6766 4.868314 AAATGGGACGCCTAGAGTATAC 57.132 45.455 0.00 0.00 0.00 1.47
2771 6767 4.768968 GGTAAATGGGACGCCTAGAGTATA 59.231 45.833 0.00 0.00 0.00 1.47
2772 6768 3.577415 GGTAAATGGGACGCCTAGAGTAT 59.423 47.826 0.00 0.00 0.00 2.12
2773 6769 2.961062 GGTAAATGGGACGCCTAGAGTA 59.039 50.000 0.00 0.00 0.00 2.59
2774 6770 1.761198 GGTAAATGGGACGCCTAGAGT 59.239 52.381 0.00 0.00 0.00 3.24
2775 6771 2.040178 AGGTAAATGGGACGCCTAGAG 58.960 52.381 0.00 0.00 0.00 2.43
2776 6772 2.170012 AGGTAAATGGGACGCCTAGA 57.830 50.000 0.00 0.00 0.00 2.43
2777 6773 3.662247 CTAGGTAAATGGGACGCCTAG 57.338 52.381 0.00 0.00 41.64 3.02
2778 6774 2.696707 CACTAGGTAAATGGGACGCCTA 59.303 50.000 0.00 0.00 0.00 3.93
2779 6775 1.485066 CACTAGGTAAATGGGACGCCT 59.515 52.381 0.00 0.00 0.00 5.52
2780 6776 1.949465 CACTAGGTAAATGGGACGCC 58.051 55.000 0.00 0.00 0.00 5.68
2781 6777 1.296727 GCACTAGGTAAATGGGACGC 58.703 55.000 0.00 0.00 0.00 5.19
2782 6778 2.684001 TGCACTAGGTAAATGGGACG 57.316 50.000 0.00 0.00 0.00 4.79
2783 6779 4.523083 TCAATGCACTAGGTAAATGGGAC 58.477 43.478 0.00 0.00 0.00 4.46
2784 6780 4.853468 TCAATGCACTAGGTAAATGGGA 57.147 40.909 0.00 0.00 0.00 4.37
2785 6781 5.593909 TCAATCAATGCACTAGGTAAATGGG 59.406 40.000 0.00 0.00 0.00 4.00
2786 6782 6.698008 TCAATCAATGCACTAGGTAAATGG 57.302 37.500 0.00 0.00 0.00 3.16
2787 6783 9.836076 CATATCAATCAATGCACTAGGTAAATG 57.164 33.333 0.00 0.00 0.00 2.32
2788 6784 9.797642 TCATATCAATCAATGCACTAGGTAAAT 57.202 29.630 0.00 0.00 0.00 1.40
2789 6785 9.797642 ATCATATCAATCAATGCACTAGGTAAA 57.202 29.630 0.00 0.00 0.00 2.01
2790 6786 9.797642 AATCATATCAATCAATGCACTAGGTAA 57.202 29.630 0.00 0.00 0.00 2.85
2837 6853 7.152645 CGGTCTATGCTAGTGGTAATTTACAT 58.847 38.462 8.73 0.00 0.00 2.29
2938 6954 1.483316 CGCTGCGACACGGATTAATA 58.517 50.000 18.66 0.00 0.00 0.98
2991 7009 6.748132 AGCAGCTGTTAACAACAAACATAAT 58.252 32.000 16.64 0.00 41.61 1.28
2993 7011 5.766150 AGCAGCTGTTAACAACAAACATA 57.234 34.783 16.64 0.00 41.61 2.29
3095 7113 6.719370 TCTGCCAAATCAAAACACTAATAGGT 59.281 34.615 0.00 0.00 0.00 3.08
3109 7127 0.320334 TTCTCGCGTCTGCCAAATCA 60.320 50.000 5.77 0.00 38.08 2.57
3121 7139 0.037232 AACCTCTCCCTTTTCTCGCG 60.037 55.000 0.00 0.00 0.00 5.87
3200 7218 2.360165 GCTCAGGGGCAAATTGATACTG 59.640 50.000 0.00 1.19 0.00 2.74


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

AutoCloner maintained by Alex Coulton.