Multiple sequence alignment - TraesCS3A01G437000

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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 TraesCS3A01G437000 chr3A 100.000 2564 0 0 1 2564 680971927 680969364 0.000000e+00 4735.0
1 TraesCS3A01G437000 chr3A 88.868 1051 63 30 646 1691 681050913 681049912 0.000000e+00 1243.0
2 TraesCS3A01G437000 chr3A 89.752 888 53 18 975 1835 680765119 680764243 0.000000e+00 1101.0
3 TraesCS3A01G437000 chr3A 89.189 259 16 7 374 631 681051232 681050985 1.920000e-81 313.0
4 TraesCS3A01G437000 chr3A 87.831 189 15 6 717 903 681068218 681068036 5.560000e-52 215.0
5 TraesCS3A01G437000 chr3A 91.503 153 12 1 117 269 681106348 681106197 2.590000e-50 209.0
6 TraesCS3A01G437000 chr3A 86.243 189 18 6 717 903 681085390 681085208 5.600000e-47 198.0
7 TraesCS3A01G437000 chr3A 87.135 171 15 5 120 284 681051444 681051275 1.210000e-43 187.0
8 TraesCS3A01G437000 chr3A 93.617 94 5 1 412 504 681104349 681104256 3.440000e-29 139.0
9 TraesCS3A01G437000 chr3A 92.308 91 4 3 279 366 201038073 201038163 2.680000e-25 126.0
10 TraesCS3A01G437000 chr3A 94.805 77 4 0 519 595 680765690 680765614 1.250000e-23 121.0
11 TraesCS3A01G437000 chr3A 91.781 73 5 1 1719 1790 681049910 681049838 1.620000e-17 100.0
12 TraesCS3A01G437000 chr3A 86.420 81 8 3 20 100 681106479 681106402 4.550000e-13 86.1
13 TraesCS3A01G437000 chr3B 88.393 1904 116 59 374 2219 719828874 719827018 0.000000e+00 2194.0
14 TraesCS3A01G437000 chr3B 89.988 809 53 13 775 1579 719880215 719879431 0.000000e+00 1020.0
15 TraesCS3A01G437000 chr3B 87.879 528 34 14 1257 1782 719879415 719878916 6.110000e-166 593.0
16 TraesCS3A01G437000 chr3B 91.150 339 26 3 2217 2555 719826972 719826638 8.360000e-125 457.0
17 TraesCS3A01G437000 chr3B 87.348 411 25 13 1151 1561 790491935 790491552 1.810000e-121 446.0
18 TraesCS3A01G437000 chr3B 89.820 167 14 3 120 284 719829082 719828917 7.190000e-51 211.0
19 TraesCS3A01G437000 chr3B 92.308 130 9 1 142 270 719880968 719880839 1.570000e-42 183.0
20 TraesCS3A01G437000 chr3B 84.158 202 9 11 380 566 719880588 719880395 9.430000e-40 174.0
21 TraesCS3A01G437000 chr3D 87.767 1406 94 48 412 1794 543935948 543934598 0.000000e+00 1572.0
22 TraesCS3A01G437000 chr3D 86.569 1087 80 36 706 1790 543970775 543969753 0.000000e+00 1138.0
23 TraesCS3A01G437000 chr3D 86.207 348 37 7 2218 2564 543933483 543933146 1.450000e-97 366.0
24 TraesCS3A01G437000 chr3D 86.047 301 29 11 1850 2148 543933986 543933697 6.890000e-81 311.0
25 TraesCS3A01G437000 chr3D 88.760 258 14 9 379 631 543971358 543971111 4.150000e-78 302.0
26 TraesCS3A01G437000 chr7B 85.339 457 37 15 1148 1603 646488068 646488495 1.810000e-121 446.0
27 TraesCS3A01G437000 chr5A 91.209 91 5 3 279 366 392304203 392304293 1.250000e-23 121.0
28 TraesCS3A01G437000 chr5A 77.841 176 24 10 1959 2122 355465413 355465585 7.550000e-16 95.3
29 TraesCS3A01G437000 chr2D 91.111 90 5 3 275 361 446270223 446270312 4.480000e-23 119.0
30 TraesCS3A01G437000 chr2D 91.765 85 5 2 279 361 211559158 211559242 1.610000e-22 117.0
31 TraesCS3A01G437000 chr2D 91.765 85 5 2 279 361 532305998 532305914 1.610000e-22 117.0
32 TraesCS3A01G437000 chr1D 91.860 86 5 2 278 361 240128164 240128249 4.480000e-23 119.0
33 TraesCS3A01G437000 chr7D 90.909 88 6 2 276 361 617181661 617181748 1.610000e-22 117.0
34 TraesCS3A01G437000 chr6D 91.765 85 5 2 279 361 51507424 51507508 1.610000e-22 117.0
35 TraesCS3A01G437000 chr6A 90.909 88 6 2 276 361 557906758 557906845 1.610000e-22 117.0
36 TraesCS3A01G437000 chr5D 77.835 194 26 11 1941 2121 268280911 268281100 1.250000e-18 104.0


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 TraesCS3A01G437000 chr3A 680969364 680971927 2563 True 4735.000000 4735 100.000000 1 2564 1 chr3A.!!$R1 2563
1 TraesCS3A01G437000 chr3A 680764243 680765690 1447 True 611.000000 1101 92.278500 519 1835 2 chr3A.!!$R4 1316
2 TraesCS3A01G437000 chr3A 681049838 681051444 1606 True 460.750000 1243 89.243250 120 1790 4 chr3A.!!$R5 1670
3 TraesCS3A01G437000 chr3B 719826638 719829082 2444 True 954.000000 2194 89.787667 120 2555 3 chr3B.!!$R2 2435
4 TraesCS3A01G437000 chr3B 719878916 719880968 2052 True 492.500000 1020 88.583250 142 1782 4 chr3B.!!$R3 1640
5 TraesCS3A01G437000 chr3D 543933146 543935948 2802 True 749.666667 1572 86.673667 412 2564 3 chr3D.!!$R1 2152
6 TraesCS3A01G437000 chr3D 543969753 543971358 1605 True 720.000000 1138 87.664500 379 1790 2 chr3D.!!$R2 1411

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
404 597 0.308993 GCCATAGCAAAAGCCTAGCG 59.691 55.0 0.0 0.0 39.53 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 3687 0.173255 GGGGATGGCAATTGTGAACG 59.827 55.0 7.4 0.0 0.0 3.95 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
54 55 8.856490 AAATATGTCACAAAGTCAAAACTCAC 57.144 30.769 0.00 0.00 33.48 3.51
55 56 5.895636 ATGTCACAAAGTCAAAACTCACA 57.104 34.783 0.00 0.00 33.48 3.58
56 57 5.295431 TGTCACAAAGTCAAAACTCACAG 57.705 39.130 0.00 0.00 33.48 3.66
57 58 4.098416 GTCACAAAGTCAAAACTCACAGC 58.902 43.478 0.00 0.00 33.48 4.40
58 59 3.755905 TCACAAAGTCAAAACTCACAGCA 59.244 39.130 0.00 0.00 33.48 4.41
59 60 3.853671 CACAAAGTCAAAACTCACAGCAC 59.146 43.478 0.00 0.00 33.48 4.40
60 61 3.100817 CAAAGTCAAAACTCACAGCACG 58.899 45.455 0.00 0.00 33.48 5.34
61 62 2.309528 AGTCAAAACTCACAGCACGA 57.690 45.000 0.00 0.00 0.00 4.35
62 63 2.205074 AGTCAAAACTCACAGCACGAG 58.795 47.619 0.00 0.00 36.53 4.18
63 64 2.159099 AGTCAAAACTCACAGCACGAGA 60.159 45.455 4.29 0.00 34.47 4.04
64 65 2.219674 GTCAAAACTCACAGCACGAGAG 59.780 50.000 4.29 2.16 38.23 3.20
65 66 2.159099 TCAAAACTCACAGCACGAGAGT 60.159 45.455 4.29 2.75 46.18 3.24
66 67 3.067601 TCAAAACTCACAGCACGAGAGTA 59.932 43.478 6.66 0.00 43.80 2.59
67 68 2.999507 AACTCACAGCACGAGAGTAG 57.000 50.000 6.66 0.00 43.80 2.57
68 69 2.505405 AACTCACAGCACGAGAGTAGA 58.495 47.619 6.66 0.00 43.80 2.59
69 70 2.885266 AACTCACAGCACGAGAGTAGAA 59.115 45.455 6.66 0.00 43.80 2.10
70 71 3.318275 AACTCACAGCACGAGAGTAGAAA 59.682 43.478 6.66 0.00 43.80 2.52
71 72 4.557695 AACTCACAGCACGAGAGTAGAAAG 60.558 45.833 6.66 0.00 43.80 2.62
72 73 6.950308 AACTCACAGCACGAGAGTAGAAAGT 61.950 44.000 6.66 0.00 43.80 2.66
73 74 7.682611 AACTCACAGCACGAGAGTAGAAAGTA 61.683 42.308 6.66 0.00 43.80 2.24
74 75 9.374787 AACTCACAGCACGAGAGTAGAAAGTAG 62.375 44.444 6.66 0.00 43.80 2.57
87 88 9.328845 AGAGTAGAAAGTAGAAGATACTAACCG 57.671 37.037 0.00 0.00 0.00 4.44
88 89 9.108284 GAGTAGAAAGTAGAAGATACTAACCGT 57.892 37.037 0.00 0.00 0.00 4.83
89 90 9.108284 AGTAGAAAGTAGAAGATACTAACCGTC 57.892 37.037 0.00 0.00 0.00 4.79
90 91 7.934855 AGAAAGTAGAAGATACTAACCGTCA 57.065 36.000 0.00 0.00 0.00 4.35
91 92 7.760437 AGAAAGTAGAAGATACTAACCGTCAC 58.240 38.462 0.00 0.00 0.00 3.67
92 93 7.611079 AGAAAGTAGAAGATACTAACCGTCACT 59.389 37.037 0.00 0.00 0.00 3.41
93 94 6.680874 AGTAGAAGATACTAACCGTCACTG 57.319 41.667 0.00 0.00 0.00 3.66
94 95 6.413052 AGTAGAAGATACTAACCGTCACTGA 58.587 40.000 0.00 0.00 0.00 3.41
95 96 6.883217 AGTAGAAGATACTAACCGTCACTGAA 59.117 38.462 0.00 0.00 0.00 3.02
96 97 6.585695 AGAAGATACTAACCGTCACTGAAA 57.414 37.500 0.00 0.00 0.00 2.69
97 98 7.171630 AGAAGATACTAACCGTCACTGAAAT 57.828 36.000 0.00 0.00 0.00 2.17
98 99 8.289939 AGAAGATACTAACCGTCACTGAAATA 57.710 34.615 0.00 0.00 0.00 1.40
99 100 8.915036 AGAAGATACTAACCGTCACTGAAATAT 58.085 33.333 0.00 0.00 0.00 1.28
100 101 8.873215 AAGATACTAACCGTCACTGAAATATG 57.127 34.615 0.00 0.00 0.00 1.78
101 102 7.434492 AGATACTAACCGTCACTGAAATATGG 58.566 38.462 0.00 0.00 0.00 2.74
102 103 5.416271 ACTAACCGTCACTGAAATATGGT 57.584 39.130 0.00 0.00 33.90 3.55
103 104 6.534475 ACTAACCGTCACTGAAATATGGTA 57.466 37.500 0.00 0.00 32.19 3.25
104 105 6.938507 ACTAACCGTCACTGAAATATGGTAA 58.061 36.000 0.00 0.00 32.19 2.85
105 106 7.388437 ACTAACCGTCACTGAAATATGGTAAA 58.612 34.615 0.00 0.00 32.19 2.01
106 107 7.879160 ACTAACCGTCACTGAAATATGGTAAAA 59.121 33.333 0.00 0.00 32.19 1.52
107 108 7.513371 AACCGTCACTGAAATATGGTAAAAA 57.487 32.000 0.00 0.00 32.19 1.94
108 109 6.905578 ACCGTCACTGAAATATGGTAAAAAC 58.094 36.000 0.00 0.00 30.66 2.43
109 110 6.487331 ACCGTCACTGAAATATGGTAAAAACA 59.513 34.615 0.00 0.00 30.66 2.83
110 111 7.013464 ACCGTCACTGAAATATGGTAAAAACAA 59.987 33.333 0.00 0.00 30.66 2.83
111 112 7.537306 CCGTCACTGAAATATGGTAAAAACAAG 59.463 37.037 0.00 0.00 0.00 3.16
112 113 8.073768 CGTCACTGAAATATGGTAAAAACAAGT 58.926 33.333 0.00 0.00 0.00 3.16
113 114 9.180678 GTCACTGAAATATGGTAAAAACAAGTG 57.819 33.333 0.00 0.00 0.00 3.16
114 115 8.356657 TCACTGAAATATGGTAAAAACAAGTGG 58.643 33.333 0.00 0.00 0.00 4.00
115 116 8.356657 CACTGAAATATGGTAAAAACAAGTGGA 58.643 33.333 0.00 0.00 0.00 4.02
116 117 9.088987 ACTGAAATATGGTAAAAACAAGTGGAT 57.911 29.630 0.00 0.00 0.00 3.41
117 118 9.357652 CTGAAATATGGTAAAAACAAGTGGATG 57.642 33.333 0.00 0.00 0.00 3.51
118 119 8.310382 TGAAATATGGTAAAAACAAGTGGATGG 58.690 33.333 0.00 0.00 0.00 3.51
132 133 5.184892 AGTGGATGGATTCAGCTTTAACT 57.815 39.130 0.00 0.00 0.00 2.24
138 139 3.258123 TGGATTCAGCTTTAACTTTGGGC 59.742 43.478 0.00 0.00 0.00 5.36
147 149 6.536941 CAGCTTTAACTTTGGGCTAAAAACAA 59.463 34.615 0.00 0.00 0.00 2.83
153 155 9.939802 TTAACTTTGGGCTAAAAACAAAAGTAA 57.060 25.926 0.00 0.00 34.13 2.24
179 181 7.117812 AGTGAAAATACATGTTACAAGAGGACG 59.882 37.037 2.30 0.00 0.00 4.79
184 186 5.916661 ACATGTTACAAGAGGACGACTAT 57.083 39.130 0.00 0.00 0.00 2.12
270 277 7.122948 ACGAGAGTTGAAAGTGGAATATACTCT 59.877 37.037 0.00 0.00 46.40 3.24
271 278 7.646130 CGAGAGTTGAAAGTGGAATATACTCTC 59.354 40.741 15.39 15.39 46.95 3.20
292 299 9.620259 ACTCTCAATAATTACTCCTTTCATTCC 57.380 33.333 0.00 0.00 0.00 3.01
303 310 9.973661 TTACTCCTTTCATTCCAAAATAGATGA 57.026 29.630 0.00 0.00 0.00 2.92
347 354 9.850198 TTAGTACAAAGTAATACAAAGTTGGGT 57.150 29.630 0.00 0.00 0.00 4.51
348 355 8.387190 AGTACAAAGTAATACAAAGTTGGGTC 57.613 34.615 0.00 0.00 0.00 4.46
349 356 7.994334 AGTACAAAGTAATACAAAGTTGGGTCA 59.006 33.333 0.00 0.00 0.00 4.02
350 357 7.833285 ACAAAGTAATACAAAGTTGGGTCAT 57.167 32.000 0.00 0.00 0.00 3.06
351 358 7.882179 ACAAAGTAATACAAAGTTGGGTCATC 58.118 34.615 0.00 0.00 0.00 2.92
352 359 7.724061 ACAAAGTAATACAAAGTTGGGTCATCT 59.276 33.333 0.00 0.00 0.00 2.90
353 360 9.226606 CAAAGTAATACAAAGTTGGGTCATCTA 57.773 33.333 0.00 0.00 0.00 1.98
354 361 9.975218 AAAGTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
355 362 9.975218 AAGTAATACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
356 363 9.975218 AGTAATACAAAGTTGGGTCATCTATTT 57.025 29.630 0.00 0.00 0.00 1.40
359 366 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
360 367 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
361 368 6.725834 ACAAAGTTGGGTCATCTATTTTGGAT 59.274 34.615 0.00 0.00 0.00 3.41
362 369 6.780457 AAGTTGGGTCATCTATTTTGGATG 57.220 37.500 0.00 0.00 41.14 3.51
363 370 5.203528 AGTTGGGTCATCTATTTTGGATGG 58.796 41.667 0.00 0.00 40.44 3.51
364 371 5.044179 AGTTGGGTCATCTATTTTGGATGGA 60.044 40.000 0.00 0.00 40.44 3.41
365 372 5.052693 TGGGTCATCTATTTTGGATGGAG 57.947 43.478 0.00 0.00 40.44 3.86
366 373 4.726317 TGGGTCATCTATTTTGGATGGAGA 59.274 41.667 0.00 0.00 40.44 3.71
367 374 5.193527 TGGGTCATCTATTTTGGATGGAGAA 59.806 40.000 0.00 0.00 40.44 2.87
368 375 6.129179 GGGTCATCTATTTTGGATGGAGAAA 58.871 40.000 0.00 0.00 40.44 2.52
369 376 6.607198 GGGTCATCTATTTTGGATGGAGAAAA 59.393 38.462 0.00 0.00 40.44 2.29
370 377 7.288621 GGGTCATCTATTTTGGATGGAGAAAAT 59.711 37.037 0.00 0.00 40.44 1.82
371 378 9.354673 GGTCATCTATTTTGGATGGAGAAAATA 57.645 33.333 0.00 0.00 40.44 1.40
396 589 3.087781 TGCATGTGTAGCCATAGCAAAA 58.912 40.909 0.00 0.00 43.56 2.44
397 590 3.129113 TGCATGTGTAGCCATAGCAAAAG 59.871 43.478 0.00 0.00 43.56 2.27
399 592 2.091541 TGTGTAGCCATAGCAAAAGCC 58.908 47.619 0.00 0.00 43.56 4.35
400 593 2.290896 TGTGTAGCCATAGCAAAAGCCT 60.291 45.455 0.00 0.00 43.56 4.58
401 594 3.054728 TGTGTAGCCATAGCAAAAGCCTA 60.055 43.478 0.00 0.00 43.56 3.93
402 595 3.561725 GTGTAGCCATAGCAAAAGCCTAG 59.438 47.826 0.00 0.00 43.56 3.02
403 596 1.685148 AGCCATAGCAAAAGCCTAGC 58.315 50.000 0.00 0.00 43.56 3.42
404 597 0.308993 GCCATAGCAAAAGCCTAGCG 59.691 55.000 0.00 0.00 39.53 4.26
405 598 1.953559 CCATAGCAAAAGCCTAGCGA 58.046 50.000 0.00 0.00 0.00 4.93
406 599 1.869767 CCATAGCAAAAGCCTAGCGAG 59.130 52.381 0.00 0.00 0.00 5.03
407 600 1.869767 CATAGCAAAAGCCTAGCGAGG 59.130 52.381 8.78 8.78 46.93 4.63
587 803 3.430895 GCTGCAATCACAAAATCCACTTG 59.569 43.478 0.00 0.00 0.00 3.16
588 804 3.391965 TGCAATCACAAAATCCACTTGC 58.608 40.909 0.00 0.00 38.33 4.01
589 805 2.409378 GCAATCACAAAATCCACTTGCG 59.591 45.455 0.00 0.00 0.00 4.85
595 811 1.000385 CAAAATCCACTTGCGGCTTCA 60.000 47.619 0.00 0.00 0.00 3.02
596 812 0.883833 AAATCCACTTGCGGCTTCAG 59.116 50.000 0.00 0.00 0.00 3.02
606 822 1.228657 GCGGCTTCAGTTTCTCCGTT 61.229 55.000 0.00 0.00 41.89 4.44
627 843 4.118480 GCACATGCATGGCCATTG 57.882 55.556 29.41 18.86 41.59 2.82
633 849 3.006003 CACATGCATGGCCATTGCTAATA 59.994 43.478 29.41 16.25 37.74 0.98
635 851 1.962807 TGCATGGCCATTGCTAATACC 59.037 47.619 28.58 9.39 37.74 2.73
636 852 1.273327 GCATGGCCATTGCTAATACCC 59.727 52.381 17.92 0.00 37.74 3.69
639 855 4.406456 CATGGCCATTGCTAATACCCTAA 58.594 43.478 17.92 0.00 37.74 2.69
684 985 7.679638 GCCCAGCAATAAGTCAGTAGTTAATTG 60.680 40.741 0.00 0.00 0.00 2.32
694 1241 9.969001 AAGTCAGTAGTTAATTGCCCTAATTAA 57.031 29.630 0.00 0.00 44.73 1.40
708 1372 8.876275 TGCCCTAATTAAGTACGTACTTATTG 57.124 34.615 36.21 25.78 45.23 1.90
709 1373 7.439056 TGCCCTAATTAAGTACGTACTTATTGC 59.561 37.037 36.21 29.78 45.23 3.56
710 1374 7.654923 GCCCTAATTAAGTACGTACTTATTGCT 59.345 37.037 36.21 25.35 45.23 3.91
711 1375 9.538508 CCCTAATTAAGTACGTACTTATTGCTT 57.461 33.333 36.21 28.28 45.23 3.91
716 1380 8.847444 TTAAGTACGTACTTATTGCTTAGAGC 57.153 34.615 36.21 5.01 45.23 4.09
717 1381 6.696441 AGTACGTACTTATTGCTTAGAGCT 57.304 37.500 22.45 0.00 36.09 4.09
720 1384 5.521544 ACGTACTTATTGCTTAGAGCTAGC 58.478 41.667 6.62 6.62 42.97 3.42
798 1467 2.108976 ACCATATGACCCTGCGCG 59.891 61.111 0.00 0.00 0.00 6.86
799 1468 3.349006 CCATATGACCCTGCGCGC 61.349 66.667 27.26 27.26 0.00 6.86
836 1512 2.689471 GTCATAAGTCAATGCATGCCCA 59.311 45.455 16.68 0.00 0.00 5.36
874 1550 2.196776 GGCTAGCCCACCATGCAT 59.803 61.111 24.19 0.00 0.00 3.96
875 1551 2.198287 GGCTAGCCCACCATGCATG 61.198 63.158 24.19 20.19 0.00 4.06
907 1583 3.103911 GTGTCGCCGTCCGTCTTG 61.104 66.667 0.00 0.00 38.35 3.02
916 1592 1.015109 CGTCCGTCTTGAGCTAGCTA 58.985 55.000 19.38 1.34 0.00 3.32
917 1593 1.003331 CGTCCGTCTTGAGCTAGCTAG 60.003 57.143 19.38 16.84 0.00 3.42
938 1614 2.224818 GCTAGCTAGCTACCTAGACCCA 60.225 54.545 33.71 0.00 45.62 4.51
940 1616 3.163616 AGCTAGCTACCTAGACCCATC 57.836 52.381 17.69 0.00 43.07 3.51
941 1617 2.719705 AGCTAGCTACCTAGACCCATCT 59.280 50.000 17.69 0.00 43.07 2.90
949 1632 1.341531 CCTAGACCCATCTACCTTGCG 59.658 57.143 0.00 0.00 36.29 4.85
1025 1716 3.949586 TGCCATCATCCTTACAATCCA 57.050 42.857 0.00 0.00 0.00 3.41
1046 1746 2.045926 GGCGCATCCACTCTTGGT 60.046 61.111 10.83 0.00 44.35 3.67
1067 1767 3.827898 CAGCCCCGTCTCGAGTCC 61.828 72.222 13.13 3.55 0.00 3.85
1131 1835 3.343788 GAGCCTGGTGTCGAGGACG 62.344 68.421 2.15 0.00 34.95 4.79
1402 2106 2.281002 TCCAGGACGACGACGACA 60.281 61.111 15.32 0.00 42.66 4.35
1410 2114 4.400109 GACGACGACAGCGAGGCA 62.400 66.667 0.00 0.00 41.64 4.75
1411 2115 3.891586 GACGACGACAGCGAGGCAA 62.892 63.158 0.00 0.00 41.64 4.52
1567 2271 1.455217 GGCGGTAGGAGGTGAGCTA 60.455 63.158 0.00 0.00 0.00 3.32
1717 2760 8.616076 CCTAGCTGATTTAGATTGTAAAAGTGG 58.384 37.037 0.00 0.00 0.00 4.00
1903 3504 8.352942 GGGTGATCATTTTGTTTGATCTATACC 58.647 37.037 13.15 11.85 46.28 2.73
1936 3537 8.041323 ACTTGTGTTTCTTTATGGAGTATCGAT 58.959 33.333 2.16 2.16 37.34 3.59
1951 3552 6.312426 GGAGTATCGATCATTTTCTATGGCAG 59.688 42.308 0.00 0.00 34.37 4.85
2003 3604 1.290009 GCAAGCACGGCAAATCCTT 59.710 52.632 0.00 0.00 0.00 3.36
2045 3646 1.815003 GAGTTGCCATGCTTGCTAACT 59.185 47.619 15.02 15.02 34.82 2.24
2053 3654 6.229733 TGCCATGCTTGCTAACTAAAATTTT 58.770 32.000 8.75 8.75 0.00 1.82
2058 3659 8.598075 CATGCTTGCTAACTAAAATTTTCATCC 58.402 33.333 6.72 0.00 0.00 3.51
2062 3663 7.915293 TGCTAACTAAAATTTTCATCCTCGA 57.085 32.000 6.72 0.00 0.00 4.04
2064 3665 6.900299 GCTAACTAAAATTTTCATCCTCGACG 59.100 38.462 6.72 0.00 0.00 5.12
2084 3685 5.113975 CGACGAACACAAATTGTCATCAAAG 59.886 40.000 0.00 0.00 37.51 2.77
2086 3687 5.971202 ACGAACACAAATTGTCATCAAAGTC 59.029 36.000 0.00 0.00 37.51 3.01
2091 3692 5.970612 CACAAATTGTCATCAAAGTCGTTCA 59.029 36.000 0.00 0.00 37.11 3.18
2113 3716 4.776322 TGCCATCCCCAGCGAACG 62.776 66.667 0.00 0.00 0.00 3.95
2148 3751 5.074804 AGCCGGTCCAAAATTAACTAGTTT 58.925 37.500 14.49 0.00 0.00 2.66
2183 3794 9.254133 GGTAACTAATTAGTTAATTCGGGTCTC 57.746 37.037 30.48 17.87 46.73 3.36
2260 4085 6.869315 TGGTCAATTCTTGTCGTTTATTCA 57.131 33.333 0.00 0.00 0.00 2.57
2267 4092 4.710324 TCTTGTCGTTTATTCAACCAGGT 58.290 39.130 0.00 0.00 30.65 4.00
2303 4128 6.560003 TGTACTGGGTATTGACAGAATGAT 57.440 37.500 0.00 0.00 39.69 2.45
2346 4171 9.027202 TGAGTTACCTGAAACTTTTTAAAACCT 57.973 29.630 0.00 0.00 39.78 3.50
2365 4190 5.886960 ACCTGAATCACATTTCTAAGCAC 57.113 39.130 0.00 0.00 0.00 4.40
2377 4202 8.982685 CACATTTCTAAGCACTCGTATGAATAT 58.017 33.333 0.00 0.00 0.00 1.28
2380 4205 5.939457 TCTAAGCACTCGTATGAATATCCG 58.061 41.667 0.00 0.00 0.00 4.18
2467 4292 6.766944 TCAAAAAGTTCGGTTTCACCATAGTA 59.233 34.615 0.00 0.00 38.47 1.82
2483 4308 9.845740 TCACCATAGTAGTGTGCAATTATTAAT 57.154 29.630 0.00 0.00 36.58 1.40
2512 4337 6.696411 TGTGAATTGGGCAATTTAAGGTAAG 58.304 36.000 0.00 0.00 40.77 2.34
2520 4345 8.616799 TGGGCAATTTAAGGTAAGGAATATTT 57.383 30.769 0.00 0.00 0.00 1.40
2521 4346 9.052365 TGGGCAATTTAAGGTAAGGAATATTTT 57.948 29.630 0.00 0.00 0.00 1.82
2561 4386 8.728088 ACTACAAATTAGCAAAAGTGATTTCG 57.272 30.769 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 9.301153 GTGAGTTTTGACTTTGTGACATATTTT 57.699 29.630 0.00 0.00 0.00 1.82
29 30 8.465999 TGTGAGTTTTGACTTTGTGACATATTT 58.534 29.630 0.00 0.00 0.00 1.40
30 31 7.995289 TGTGAGTTTTGACTTTGTGACATATT 58.005 30.769 0.00 0.00 0.00 1.28
31 32 7.566760 TGTGAGTTTTGACTTTGTGACATAT 57.433 32.000 0.00 0.00 0.00 1.78
32 33 6.458206 GCTGTGAGTTTTGACTTTGTGACATA 60.458 38.462 0.00 0.00 0.00 2.29
33 34 5.677091 GCTGTGAGTTTTGACTTTGTGACAT 60.677 40.000 0.00 0.00 0.00 3.06
34 35 4.379394 GCTGTGAGTTTTGACTTTGTGACA 60.379 41.667 0.00 0.00 0.00 3.58
35 36 4.098416 GCTGTGAGTTTTGACTTTGTGAC 58.902 43.478 0.00 0.00 0.00 3.67
36 37 3.755905 TGCTGTGAGTTTTGACTTTGTGA 59.244 39.130 0.00 0.00 0.00 3.58
37 38 3.853671 GTGCTGTGAGTTTTGACTTTGTG 59.146 43.478 0.00 0.00 0.00 3.33
38 39 3.426159 CGTGCTGTGAGTTTTGACTTTGT 60.426 43.478 0.00 0.00 0.00 2.83
39 40 3.100817 CGTGCTGTGAGTTTTGACTTTG 58.899 45.455 0.00 0.00 0.00 2.77
40 41 3.006940 TCGTGCTGTGAGTTTTGACTTT 58.993 40.909 0.00 0.00 0.00 2.66
41 42 2.609459 CTCGTGCTGTGAGTTTTGACTT 59.391 45.455 0.00 0.00 0.00 3.01
42 43 2.159099 TCTCGTGCTGTGAGTTTTGACT 60.159 45.455 0.00 0.00 34.99 3.41
43 44 2.201732 TCTCGTGCTGTGAGTTTTGAC 58.798 47.619 0.00 0.00 34.99 3.18
44 45 2.159099 ACTCTCGTGCTGTGAGTTTTGA 60.159 45.455 7.98 0.00 46.46 2.69
45 46 2.205074 ACTCTCGTGCTGTGAGTTTTG 58.795 47.619 7.98 0.00 46.46 2.44
46 47 2.604046 ACTCTCGTGCTGTGAGTTTT 57.396 45.000 7.98 0.00 46.46 2.43
47 48 2.885266 TCTACTCTCGTGCTGTGAGTTT 59.115 45.455 15.79 2.40 46.46 2.66
48 49 2.505405 TCTACTCTCGTGCTGTGAGTT 58.495 47.619 15.79 5.04 46.46 3.01
50 51 3.057876 ACTTTCTACTCTCGTGCTGTGAG 60.058 47.826 6.94 6.94 42.58 3.51
51 52 2.885266 ACTTTCTACTCTCGTGCTGTGA 59.115 45.455 0.00 0.00 0.00 3.58
52 53 3.290308 ACTTTCTACTCTCGTGCTGTG 57.710 47.619 0.00 0.00 0.00 3.66
53 54 4.325119 TCTACTTTCTACTCTCGTGCTGT 58.675 43.478 0.00 0.00 0.00 4.40
54 55 4.948608 TCTACTTTCTACTCTCGTGCTG 57.051 45.455 0.00 0.00 0.00 4.41
55 56 5.247084 TCTTCTACTTTCTACTCTCGTGCT 58.753 41.667 0.00 0.00 0.00 4.40
56 57 5.548706 TCTTCTACTTTCTACTCTCGTGC 57.451 43.478 0.00 0.00 0.00 5.34
57 58 8.428186 AGTATCTTCTACTTTCTACTCTCGTG 57.572 38.462 0.00 0.00 0.00 4.35
61 62 9.328845 CGGTTAGTATCTTCTACTTTCTACTCT 57.671 37.037 0.00 0.00 0.00 3.24
62 63 9.108284 ACGGTTAGTATCTTCTACTTTCTACTC 57.892 37.037 0.00 0.00 0.00 2.59
63 64 9.108284 GACGGTTAGTATCTTCTACTTTCTACT 57.892 37.037 0.00 0.00 0.00 2.57
64 65 8.887717 TGACGGTTAGTATCTTCTACTTTCTAC 58.112 37.037 0.00 0.00 0.00 2.59
65 66 8.887717 GTGACGGTTAGTATCTTCTACTTTCTA 58.112 37.037 0.00 0.00 0.00 2.10
66 67 7.611079 AGTGACGGTTAGTATCTTCTACTTTCT 59.389 37.037 0.00 0.00 0.00 2.52
67 68 7.697291 CAGTGACGGTTAGTATCTTCTACTTTC 59.303 40.741 0.00 0.00 0.00 2.62
68 69 7.392673 TCAGTGACGGTTAGTATCTTCTACTTT 59.607 37.037 0.00 0.00 0.00 2.66
69 70 6.883217 TCAGTGACGGTTAGTATCTTCTACTT 59.117 38.462 0.00 0.00 0.00 2.24
70 71 6.413052 TCAGTGACGGTTAGTATCTTCTACT 58.587 40.000 0.00 0.00 0.00 2.57
71 72 6.674694 TCAGTGACGGTTAGTATCTTCTAC 57.325 41.667 0.00 0.00 0.00 2.59
72 73 7.692460 TTTCAGTGACGGTTAGTATCTTCTA 57.308 36.000 0.00 0.00 0.00 2.10
73 74 6.585695 TTTCAGTGACGGTTAGTATCTTCT 57.414 37.500 0.00 0.00 0.00 2.85
74 75 8.969267 CATATTTCAGTGACGGTTAGTATCTTC 58.031 37.037 0.00 0.00 0.00 2.87
75 76 7.926555 CCATATTTCAGTGACGGTTAGTATCTT 59.073 37.037 0.00 0.00 0.00 2.40
76 77 7.069578 ACCATATTTCAGTGACGGTTAGTATCT 59.930 37.037 0.00 0.00 0.00 1.98
77 78 7.208080 ACCATATTTCAGTGACGGTTAGTATC 58.792 38.462 0.00 0.00 0.00 2.24
78 79 7.120923 ACCATATTTCAGTGACGGTTAGTAT 57.879 36.000 0.00 0.00 0.00 2.12
79 80 6.534475 ACCATATTTCAGTGACGGTTAGTA 57.466 37.500 0.00 0.00 0.00 1.82
80 81 5.416271 ACCATATTTCAGTGACGGTTAGT 57.584 39.130 0.00 0.00 0.00 2.24
81 82 7.837202 TTTACCATATTTCAGTGACGGTTAG 57.163 36.000 0.00 0.00 0.00 2.34
82 83 8.505625 GTTTTTACCATATTTCAGTGACGGTTA 58.494 33.333 0.00 0.00 0.00 2.85
83 84 7.013464 TGTTTTTACCATATTTCAGTGACGGTT 59.987 33.333 0.00 0.00 0.00 4.44
84 85 6.487331 TGTTTTTACCATATTTCAGTGACGGT 59.513 34.615 0.00 0.00 0.00 4.83
85 86 6.904498 TGTTTTTACCATATTTCAGTGACGG 58.096 36.000 0.00 0.00 0.00 4.79
86 87 8.073768 ACTTGTTTTTACCATATTTCAGTGACG 58.926 33.333 0.00 0.00 0.00 4.35
87 88 9.180678 CACTTGTTTTTACCATATTTCAGTGAC 57.819 33.333 0.00 0.00 0.00 3.67
88 89 8.356657 CCACTTGTTTTTACCATATTTCAGTGA 58.643 33.333 0.00 0.00 0.00 3.41
89 90 8.356657 TCCACTTGTTTTTACCATATTTCAGTG 58.643 33.333 0.00 0.00 0.00 3.66
90 91 8.472007 TCCACTTGTTTTTACCATATTTCAGT 57.528 30.769 0.00 0.00 0.00 3.41
91 92 9.357652 CATCCACTTGTTTTTACCATATTTCAG 57.642 33.333 0.00 0.00 0.00 3.02
92 93 8.310382 CCATCCACTTGTTTTTACCATATTTCA 58.690 33.333 0.00 0.00 0.00 2.69
93 94 8.527810 TCCATCCACTTGTTTTTACCATATTTC 58.472 33.333 0.00 0.00 0.00 2.17
94 95 8.429237 TCCATCCACTTGTTTTTACCATATTT 57.571 30.769 0.00 0.00 0.00 1.40
95 96 8.608185 ATCCATCCACTTGTTTTTACCATATT 57.392 30.769 0.00 0.00 0.00 1.28
96 97 8.608185 AATCCATCCACTTGTTTTTACCATAT 57.392 30.769 0.00 0.00 0.00 1.78
97 98 7.671819 TGAATCCATCCACTTGTTTTTACCATA 59.328 33.333 0.00 0.00 0.00 2.74
98 99 6.496565 TGAATCCATCCACTTGTTTTTACCAT 59.503 34.615 0.00 0.00 0.00 3.55
99 100 5.835819 TGAATCCATCCACTTGTTTTTACCA 59.164 36.000 0.00 0.00 0.00 3.25
100 101 6.339587 TGAATCCATCCACTTGTTTTTACC 57.660 37.500 0.00 0.00 0.00 2.85
101 102 5.863935 GCTGAATCCATCCACTTGTTTTTAC 59.136 40.000 0.00 0.00 0.00 2.01
102 103 5.774690 AGCTGAATCCATCCACTTGTTTTTA 59.225 36.000 0.00 0.00 0.00 1.52
103 104 4.590222 AGCTGAATCCATCCACTTGTTTTT 59.410 37.500 0.00 0.00 0.00 1.94
104 105 4.154942 AGCTGAATCCATCCACTTGTTTT 58.845 39.130 0.00 0.00 0.00 2.43
105 106 3.771216 AGCTGAATCCATCCACTTGTTT 58.229 40.909 0.00 0.00 0.00 2.83
106 107 3.446442 AGCTGAATCCATCCACTTGTT 57.554 42.857 0.00 0.00 0.00 2.83
107 108 3.446442 AAGCTGAATCCATCCACTTGT 57.554 42.857 0.00 0.00 0.00 3.16
108 109 5.416952 AGTTAAAGCTGAATCCATCCACTTG 59.583 40.000 0.00 0.00 0.00 3.16
109 110 5.574188 AGTTAAAGCTGAATCCATCCACTT 58.426 37.500 0.00 0.00 0.00 3.16
110 111 5.184892 AGTTAAAGCTGAATCCATCCACT 57.815 39.130 0.00 0.00 0.00 4.00
111 112 5.904362 AAGTTAAAGCTGAATCCATCCAC 57.096 39.130 0.00 0.00 0.00 4.02
112 113 5.185635 CCAAAGTTAAAGCTGAATCCATCCA 59.814 40.000 0.00 0.00 0.00 3.41
113 114 5.394553 CCCAAAGTTAAAGCTGAATCCATCC 60.395 44.000 0.00 0.00 0.00 3.51
114 115 5.654497 CCCAAAGTTAAAGCTGAATCCATC 58.346 41.667 0.00 0.00 0.00 3.51
115 116 4.081476 GCCCAAAGTTAAAGCTGAATCCAT 60.081 41.667 0.00 0.00 0.00 3.41
116 117 3.258123 GCCCAAAGTTAAAGCTGAATCCA 59.742 43.478 0.00 0.00 0.00 3.41
117 118 3.511540 AGCCCAAAGTTAAAGCTGAATCC 59.488 43.478 0.00 0.00 31.23 3.01
118 119 4.790765 AGCCCAAAGTTAAAGCTGAATC 57.209 40.909 0.00 0.00 31.23 2.52
132 133 7.612677 TCACTTACTTTTGTTTTTAGCCCAAA 58.387 30.769 0.00 0.00 0.00 3.28
153 155 7.117812 CGTCCTCTTGTAACATGTATTTTCACT 59.882 37.037 0.00 0.00 0.00 3.41
176 178 4.391830 TCAGATTTTTGCACCATAGTCGTC 59.608 41.667 0.00 0.00 0.00 4.20
179 181 5.627499 TGTCAGATTTTTGCACCATAGTC 57.373 39.130 0.00 0.00 0.00 2.59
184 186 5.534207 AATCTTGTCAGATTTTTGCACCA 57.466 34.783 0.00 0.00 46.07 4.17
225 227 2.462889 GTGTTGTGGCTTTGTGACATG 58.537 47.619 0.00 0.00 35.31 3.21
279 286 9.484806 AATCATCTATTTTGGAATGAAAGGAGT 57.515 29.630 0.00 0.00 0.00 3.85
324 331 8.156994 TGACCCAACTTTGTATTACTTTGTAC 57.843 34.615 0.00 0.00 0.00 2.90
325 332 8.927675 ATGACCCAACTTTGTATTACTTTGTA 57.072 30.769 0.00 0.00 0.00 2.41
327 334 8.110860 AGATGACCCAACTTTGTATTACTTTG 57.889 34.615 0.00 0.00 0.00 2.77
328 335 9.975218 ATAGATGACCCAACTTTGTATTACTTT 57.025 29.630 0.00 0.00 0.00 2.66
329 336 9.975218 AATAGATGACCCAACTTTGTATTACTT 57.025 29.630 0.00 0.00 0.00 2.24
330 337 9.975218 AAATAGATGACCCAACTTTGTATTACT 57.025 29.630 0.00 0.00 0.00 2.24
333 340 8.531146 CCAAAATAGATGACCCAACTTTGTATT 58.469 33.333 0.00 0.00 0.00 1.89
334 341 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
335 342 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
336 343 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
337 344 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
338 345 6.155049 CCATCCAAAATAGATGACCCAACTTT 59.845 38.462 2.39 0.00 43.15 2.66
339 346 5.658190 CCATCCAAAATAGATGACCCAACTT 59.342 40.000 2.39 0.00 43.15 2.66
340 347 5.044179 TCCATCCAAAATAGATGACCCAACT 60.044 40.000 2.39 0.00 43.15 3.16
341 348 5.200483 TCCATCCAAAATAGATGACCCAAC 58.800 41.667 2.39 0.00 43.15 3.77
342 349 5.193527 TCTCCATCCAAAATAGATGACCCAA 59.806 40.000 2.39 0.00 43.15 4.12
343 350 4.726317 TCTCCATCCAAAATAGATGACCCA 59.274 41.667 2.39 0.00 43.15 4.51
344 351 5.310409 TCTCCATCCAAAATAGATGACCC 57.690 43.478 2.39 0.00 43.15 4.46
345 352 7.645058 TTTTCTCCATCCAAAATAGATGACC 57.355 36.000 2.39 0.00 43.15 4.02
347 354 9.056005 CGTATTTTCTCCATCCAAAATAGATGA 57.944 33.333 2.39 0.00 43.15 2.92
348 355 8.292448 CCGTATTTTCTCCATCCAAAATAGATG 58.708 37.037 0.00 0.00 40.71 2.90
349 356 7.998964 ACCGTATTTTCTCCATCCAAAATAGAT 59.001 33.333 0.00 0.00 35.90 1.98
350 357 7.282224 CACCGTATTTTCTCCATCCAAAATAGA 59.718 37.037 0.00 0.00 35.90 1.98
351 358 7.417612 CACCGTATTTTCTCCATCCAAAATAG 58.582 38.462 0.00 0.00 35.90 1.73
352 359 6.183360 GCACCGTATTTTCTCCATCCAAAATA 60.183 38.462 0.00 0.00 34.68 1.40
353 360 5.394115 GCACCGTATTTTCTCCATCCAAAAT 60.394 40.000 0.00 0.00 36.43 1.82
354 361 4.082463 GCACCGTATTTTCTCCATCCAAAA 60.082 41.667 0.00 0.00 0.00 2.44
355 362 3.442273 GCACCGTATTTTCTCCATCCAAA 59.558 43.478 0.00 0.00 0.00 3.28
356 363 3.013921 GCACCGTATTTTCTCCATCCAA 58.986 45.455 0.00 0.00 0.00 3.53
357 364 2.026729 TGCACCGTATTTTCTCCATCCA 60.027 45.455 0.00 0.00 0.00 3.41
358 365 2.639065 TGCACCGTATTTTCTCCATCC 58.361 47.619 0.00 0.00 0.00 3.51
359 366 3.627577 ACATGCACCGTATTTTCTCCATC 59.372 43.478 0.00 0.00 0.00 3.51
360 367 3.378112 CACATGCACCGTATTTTCTCCAT 59.622 43.478 0.00 0.00 0.00 3.41
361 368 2.746904 CACATGCACCGTATTTTCTCCA 59.253 45.455 0.00 0.00 0.00 3.86
362 369 2.747446 ACACATGCACCGTATTTTCTCC 59.253 45.455 0.00 0.00 0.00 3.71
363 370 4.494199 GCTACACATGCACCGTATTTTCTC 60.494 45.833 0.00 0.00 0.00 2.87
364 371 3.374058 GCTACACATGCACCGTATTTTCT 59.626 43.478 0.00 0.00 0.00 2.52
365 372 3.486875 GGCTACACATGCACCGTATTTTC 60.487 47.826 0.00 0.00 0.00 2.29
366 373 2.422127 GGCTACACATGCACCGTATTTT 59.578 45.455 0.00 0.00 0.00 1.82
367 374 2.014128 GGCTACACATGCACCGTATTT 58.986 47.619 0.00 0.00 0.00 1.40
368 375 1.065782 TGGCTACACATGCACCGTATT 60.066 47.619 0.00 0.00 0.00 1.89
369 376 0.539518 TGGCTACACATGCACCGTAT 59.460 50.000 0.00 0.00 0.00 3.06
370 377 0.539518 ATGGCTACACATGCACCGTA 59.460 50.000 0.00 0.00 0.00 4.02
371 378 0.539518 TATGGCTACACATGCACCGT 59.460 50.000 0.00 0.00 32.39 4.83
372 379 1.220529 CTATGGCTACACATGCACCG 58.779 55.000 0.00 0.00 32.39 4.94
399 592 0.249784 ATCTGCATGTGCCTCGCTAG 60.250 55.000 2.07 0.00 41.18 3.42
400 593 0.531311 CATCTGCATGTGCCTCGCTA 60.531 55.000 2.07 0.00 41.18 4.26
401 594 1.818363 CATCTGCATGTGCCTCGCT 60.818 57.895 2.07 0.00 41.18 4.93
402 595 2.713770 CATCTGCATGTGCCTCGC 59.286 61.111 2.07 0.00 41.18 5.03
403 596 2.713770 GCATCTGCATGTGCCTCG 59.286 61.111 11.29 0.00 41.18 4.63
428 621 2.420022 CCTTCCGAATGTGATGTGGAAC 59.580 50.000 0.00 0.00 35.06 3.62
587 803 1.228657 AACGGAGAAACTGAAGCCGC 61.229 55.000 0.00 0.00 45.45 6.53
588 804 0.512952 CAACGGAGAAACTGAAGCCG 59.487 55.000 0.00 0.00 46.83 5.52
589 805 1.878953 TCAACGGAGAAACTGAAGCC 58.121 50.000 0.00 0.00 0.00 4.35
595 811 2.254546 TGTGCATCAACGGAGAAACT 57.745 45.000 0.00 0.00 0.00 2.66
596 812 2.855180 CATGTGCATCAACGGAGAAAC 58.145 47.619 0.00 0.00 0.00 2.78
633 849 7.674120 CCGGCTACTTAACTAATAATTAGGGT 58.326 38.462 0.00 0.00 37.57 4.34
635 851 6.592994 GGCCGGCTACTTAACTAATAATTAGG 59.407 42.308 28.56 0.00 37.57 2.69
636 852 6.592994 GGGCCGGCTACTTAACTAATAATTAG 59.407 42.308 28.56 0.00 39.18 1.73
639 855 4.348754 TGGGCCGGCTACTTAACTAATAAT 59.651 41.667 28.56 0.00 0.00 1.28
651 952 1.153046 TTATTGCTGGGCCGGCTAC 60.153 57.895 35.51 20.18 36.58 3.58
694 1241 6.696441 AGCTCTAAGCAATAAGTACGTACT 57.304 37.500 22.45 22.45 45.56 2.73
698 1362 4.613448 CGCTAGCTCTAAGCAATAAGTACG 59.387 45.833 13.93 0.00 45.56 3.67
706 1370 2.619177 CTCCTACGCTAGCTCTAAGCAA 59.381 50.000 13.93 0.00 45.56 3.91
707 1371 2.222886 CTCCTACGCTAGCTCTAAGCA 58.777 52.381 13.93 0.00 45.56 3.91
708 1372 1.068816 GCTCCTACGCTAGCTCTAAGC 60.069 57.143 13.93 11.12 42.84 3.09
709 1373 2.031508 GTGCTCCTACGCTAGCTCTAAG 60.032 54.545 13.93 5.02 39.53 2.18
710 1374 1.948145 GTGCTCCTACGCTAGCTCTAA 59.052 52.381 13.93 0.00 39.53 2.10
711 1375 1.134189 TGTGCTCCTACGCTAGCTCTA 60.134 52.381 13.93 0.97 39.53 2.43
712 1376 0.394488 TGTGCTCCTACGCTAGCTCT 60.394 55.000 13.93 0.00 39.53 4.09
713 1377 0.671251 ATGTGCTCCTACGCTAGCTC 59.329 55.000 13.93 0.00 39.53 4.09
714 1378 0.671251 GATGTGCTCCTACGCTAGCT 59.329 55.000 13.93 2.46 39.53 3.32
715 1379 0.671251 AGATGTGCTCCTACGCTAGC 59.329 55.000 4.06 4.06 39.25 3.42
716 1380 2.697431 GAGATGTGCTCCTACGCTAG 57.303 55.000 0.00 0.00 37.69 3.42
836 1512 1.671850 CCATTAGTTGACCTGACGCGT 60.672 52.381 13.85 13.85 0.00 6.01
872 1548 4.088762 GGCGTGCGGTGTGACATG 62.089 66.667 0.00 0.00 0.00 3.21
898 1574 1.268845 GCTAGCTAGCTCAAGACGGAC 60.269 57.143 33.71 4.79 45.62 4.79
919 1595 3.917629 AGATGGGTCTAGGTAGCTAGCTA 59.082 47.826 26.60 26.60 35.39 3.32
920 1596 2.719705 AGATGGGTCTAGGTAGCTAGCT 59.280 50.000 27.23 27.23 37.80 3.32
933 1609 5.305399 AAGCTACGCAAGGTAGATGGGTC 62.305 52.174 5.13 0.00 46.69 4.46
936 1612 2.205074 CAAGCTACGCAAGGTAGATGG 58.795 52.381 5.13 0.00 46.69 3.51
941 1617 0.527113 TACGCAAGCTACGCAAGGTA 59.473 50.000 8.84 0.66 43.11 3.08
957 1640 9.442033 CGGGTTGTGTGTATATATATATGTACG 57.558 37.037 19.05 5.88 34.29 3.67
963 1652 5.163530 CGGCCGGGTTGTGTGTATATATATA 60.164 44.000 20.10 0.00 0.00 0.86
1046 1746 4.671590 TCGAGACGGGGCTGGTGA 62.672 66.667 0.00 0.00 0.00 4.02
1149 1853 4.641645 CCACCGCTGTTCAGCCCA 62.642 66.667 17.42 0.00 0.00 5.36
1458 2162 1.682849 CCGGACCTTGATGTTCCCA 59.317 57.895 0.00 0.00 0.00 4.37
1596 2300 1.364626 CCTCTCGGTTCTGCATGCAC 61.365 60.000 18.46 7.33 0.00 4.57
1717 2760 9.723601 ATGCATAGAATAGATCTTCTTTCCTTC 57.276 33.333 0.00 0.00 39.71 3.46
1805 2849 5.648092 TGTTTCTAATTTAGGAGCTCAAGCC 59.352 40.000 17.19 0.00 43.38 4.35
1835 2879 0.329931 TCCCACACATAAACCCGCAT 59.670 50.000 0.00 0.00 0.00 4.73
1836 2880 0.329931 ATCCCACACATAAACCCGCA 59.670 50.000 0.00 0.00 0.00 5.69
1837 2881 1.944709 GTATCCCACACATAAACCCGC 59.055 52.381 0.00 0.00 0.00 6.13
1838 2882 3.269538 TGTATCCCACACATAAACCCG 57.730 47.619 0.00 0.00 30.04 5.28
1864 3465 7.410120 AAATGATCACCCAAAGTTAATCTCC 57.590 36.000 0.00 0.00 0.00 3.71
1903 3504 6.039270 TCCATAAAGAAACACAAGTTCCACTG 59.961 38.462 0.00 0.00 36.84 3.66
1912 3513 8.038351 TGATCGATACTCCATAAAGAAACACAA 58.962 33.333 0.00 0.00 0.00 3.33
1943 3544 6.146184 CCTCACGACAATATAAACTGCCATAG 59.854 42.308 0.00 0.00 0.00 2.23
1951 3552 7.534085 TTGTCATCCTCACGACAATATAAAC 57.466 36.000 1.03 0.00 44.88 2.01
2003 3604 2.538737 CGCTTCAGTTCTGTTTTTCGCA 60.539 45.455 0.00 0.00 0.00 5.10
2045 3646 6.203145 TGTGTTCGTCGAGGATGAAAATTTTA 59.797 34.615 8.88 0.00 38.96 1.52
2053 3654 2.804697 TTTGTGTTCGTCGAGGATGA 57.195 45.000 8.88 0.00 0.00 2.92
2058 3659 3.852471 TGACAATTTGTGTTCGTCGAG 57.148 42.857 6.80 0.00 41.96 4.04
2062 3663 5.890334 ACTTTGATGACAATTTGTGTTCGT 58.110 33.333 6.80 0.00 41.96 3.85
2064 3665 5.971202 ACGACTTTGATGACAATTTGTGTTC 59.029 36.000 6.80 4.29 41.96 3.18
2084 3685 1.135402 GGGATGGCAATTGTGAACGAC 60.135 52.381 7.40 0.00 0.00 4.34
2086 3687 0.173255 GGGGATGGCAATTGTGAACG 59.827 55.000 7.40 0.00 0.00 3.95
2091 3692 2.053865 CGCTGGGGATGGCAATTGT 61.054 57.895 7.40 0.00 0.00 2.71
2154 3765 8.320617 ACCCGAATTAACTAATTAGTTACCACA 58.679 33.333 29.36 19.09 45.49 4.17
2162 3773 5.924825 CCCGAGACCCGAATTAACTAATTAG 59.075 44.000 11.05 11.05 41.76 1.73
2163 3774 5.739935 GCCCGAGACCCGAATTAACTAATTA 60.740 44.000 0.00 0.00 41.76 1.40
2166 3777 2.159057 GCCCGAGACCCGAATTAACTAA 60.159 50.000 0.00 0.00 41.76 2.24
2174 3785 1.107538 CATCTAGCCCGAGACCCGAA 61.108 60.000 0.00 0.00 41.76 4.30
2177 3788 1.686325 TTGCATCTAGCCCGAGACCC 61.686 60.000 0.00 0.00 44.83 4.46
2183 3794 2.550830 ATAGGTTTGCATCTAGCCCG 57.449 50.000 0.00 0.00 44.83 6.13
2283 4108 5.667626 ACCTATCATTCTGTCAATACCCAGT 59.332 40.000 0.00 0.00 0.00 4.00
2303 4128 7.553334 GGTAACTCATGAATAGACAACACCTA 58.447 38.462 0.00 0.00 0.00 3.08
2346 4171 5.237815 ACGAGTGCTTAGAAATGTGATTCA 58.762 37.500 0.00 0.00 0.00 2.57
2377 4202 3.533720 GATCCATGACGGGTCGGA 58.466 61.111 0.00 0.00 34.35 4.55
2380 4205 0.830648 TTGGAGATCCATGACGGGTC 59.169 55.000 1.61 0.00 46.97 4.46
2436 4261 2.863401 ACCGAACTTTTTGAAGGTGC 57.137 45.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.