Multiple sequence alignment - TraesCS5B01G383900

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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 TraesCS5B01G383900 chr5B 100.000 5447 0 0 1 5447 562951250 562956696 0.000000e+00 10059.0
1 TraesCS5B01G383900 chr5B 87.527 465 54 4 3501 3964 562492188 562492649 8.030000e-148 534.0
2 TraesCS5B01G383900 chr5B 80.696 316 46 11 2779 3086 562490534 562490842 1.180000e-56 231.0
3 TraesCS5B01G383900 chr5B 95.349 43 0 2 4151 4191 562955353 562955395 3.520000e-07 67.6
4 TraesCS5B01G383900 chr5B 95.349 43 0 2 4104 4146 562955400 562955440 3.520000e-07 67.6
5 TraesCS5B01G383900 chr5A 91.791 3228 163 40 900 4075 577932143 577935320 0.000000e+00 4399.0
6 TraesCS5B01G383900 chr5A 84.425 687 69 21 4278 4952 577935337 577935997 4.600000e-180 641.0
7 TraesCS5B01G383900 chr5A 86.296 467 57 6 3501 3964 577901813 577902275 8.150000e-138 501.0
8 TraesCS5B01G383900 chr5A 89.591 269 20 5 5120 5387 577936444 577936705 8.740000e-88 335.0
9 TraesCS5B01G383900 chr5A 85.062 241 27 3 998 1235 577887173 577887407 2.540000e-58 237.0
10 TraesCS5B01G383900 chr5A 79.114 316 50 13 2779 3087 577889744 577890050 2.570000e-48 204.0
11 TraesCS5B01G383900 chr5A 88.095 84 7 3 5045 5126 577936344 577936426 4.490000e-16 97.1
12 TraesCS5B01G383900 chr5D 93.341 1832 74 27 754 2545 458897291 458899114 0.000000e+00 2663.0
13 TraesCS5B01G383900 chr5D 94.672 1539 64 14 2624 4159 458899143 458900666 0.000000e+00 2372.0
14 TraesCS5B01G383900 chr5D 92.228 772 35 4 2 772 458896528 458897275 0.000000e+00 1070.0
15 TraesCS5B01G383900 chr5D 83.024 807 85 24 4157 4952 458900619 458901384 0.000000e+00 684.0
16 TraesCS5B01G383900 chr5D 85.792 549 37 13 950 1483 458866851 458867373 1.330000e-150 544.0
17 TraesCS5B01G383900 chr5D 86.842 456 57 3 3510 3964 458839720 458840173 1.750000e-139 507.0
18 TraesCS5B01G383900 chr5D 86.239 327 37 6 5120 5445 458901837 458902156 1.120000e-91 348.0
19 TraesCS5B01G383900 chr5D 84.462 251 31 3 996 1245 458818129 458818372 1.960000e-59 241.0
20 TraesCS5B01G383900 chr5D 83.665 251 31 4 998 1245 458836045 458836288 1.530000e-55 228.0
21 TraesCS5B01G383900 chr5D 87.349 166 21 0 1607 1772 458818472 458818637 2.000000e-44 191.0
22 TraesCS5B01G383900 chr5D 78.000 300 53 10 2792 3085 458838013 458838305 5.610000e-40 176.0
23 TraesCS5B01G383900 chr5D 88.095 84 7 3 5045 5126 458901737 458901819 4.490000e-16 97.1
24 TraesCS5B01G383900 chr3D 92.629 1533 95 13 2630 4159 16164946 16166463 0.000000e+00 2189.0
25 TraesCS5B01G383900 chr3D 89.805 1540 86 25 1047 2556 16163449 16164947 0.000000e+00 1908.0
26 TraesCS5B01G383900 chr3D 81.592 804 103 26 4157 4952 16166416 16167182 1.670000e-174 623.0
27 TraesCS5B01G383900 chr3D 84.008 494 51 15 4962 5442 16162292 16162770 2.990000e-122 449.0
28 TraesCS5B01G383900 chr3D 81.087 460 37 12 4962 5387 16167897 16168340 6.810000e-84 322.0
29 TraesCS5B01G383900 chr3B 92.638 1535 89 15 2628 4159 23705103 23706616 0.000000e+00 2187.0
30 TraesCS5B01G383900 chr3B 91.304 989 56 8 1598 2559 23704117 23705102 0.000000e+00 1323.0
31 TraesCS5B01G383900 chr3B 86.515 482 57 6 4157 4632 23706569 23707048 1.740000e-144 523.0
32 TraesCS5B01G383900 chr3B 85.434 357 15 14 1047 1397 23703791 23704116 2.430000e-88 337.0
33 TraesCS5B01G383900 chr3A 91.209 910 52 14 2462 3365 20231564 20230677 0.000000e+00 1212.0
34 TraesCS5B01G383900 chr3A 92.637 842 48 11 3260 4099 20218838 20218009 0.000000e+00 1199.0
35 TraesCS5B01G383900 chr3A 90.617 810 58 10 3360 4159 20229781 20228980 0.000000e+00 1059.0
36 TraesCS5B01G383900 chr3A 87.973 873 45 15 1047 1892 20226879 20226040 0.000000e+00 976.0
37 TraesCS5B01G383900 chr3A 95.525 581 26 0 1979 2559 20225992 20225412 0.000000e+00 929.0
38 TraesCS5B01G383900 chr3A 92.504 627 39 4 2628 3253 20225411 20224792 0.000000e+00 891.0
39 TraesCS5B01G383900 chr3A 83.045 808 101 21 4157 4952 20217833 20217050 0.000000e+00 701.0
40 TraesCS5B01G383900 chr3A 86.014 429 48 8 4157 4579 20229027 20228605 2.990000e-122 449.0
41 TraesCS5B01G383900 chr3A 82.787 488 57 11 4962 5444 20228000 20227535 1.410000e-110 411.0
42 TraesCS5B01G383900 chr3A 79.271 521 49 26 4962 5444 20216382 20215883 5.300000e-80 309.0
43 TraesCS5B01G383900 chr3A 80.337 356 32 15 4606 4952 20228611 20228285 9.120000e-58 235.0
44 TraesCS5B01G383900 chr2D 84.906 424 47 12 430 851 431525919 431526327 3.930000e-111 412.0
45 TraesCS5B01G383900 chr2D 84.434 424 49 12 430 851 52015699 52016107 8.500000e-108 401.0
46 TraesCS5B01G383900 chr2D 83.023 430 40 21 450 857 473094861 473095279 5.190000e-95 359.0
47 TraesCS5B01G383900 chr4D 82.512 406 44 18 449 851 490979850 490979469 1.130000e-86 331.0


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 TraesCS5B01G383900 chr5B 562951250 562956696 5446 False 3398.066667 10059 96.899333 1 5447 3 chr5B.!!$F2 5446
1 TraesCS5B01G383900 chr5B 562490534 562492649 2115 False 382.500000 534 84.111500 2779 3964 2 chr5B.!!$F1 1185
2 TraesCS5B01G383900 chr5A 577932143 577936705 4562 False 1368.025000 4399 88.475500 900 5387 4 chr5A.!!$F3 4487
3 TraesCS5B01G383900 chr5A 577887173 577890050 2877 False 220.500000 237 82.088000 998 3087 2 chr5A.!!$F2 2089
4 TraesCS5B01G383900 chr5D 458896528 458902156 5628 False 1205.683333 2663 89.599833 2 5445 6 chr5D.!!$F4 5443
5 TraesCS5B01G383900 chr5D 458866851 458867373 522 False 544.000000 544 85.792000 950 1483 1 chr5D.!!$F1 533
6 TraesCS5B01G383900 chr5D 458836045 458840173 4128 False 303.666667 507 82.835667 998 3964 3 chr5D.!!$F3 2966
7 TraesCS5B01G383900 chr5D 458818129 458818637 508 False 216.000000 241 85.905500 996 1772 2 chr5D.!!$F2 776
8 TraesCS5B01G383900 chr3D 16162292 16168340 6048 False 1098.200000 2189 85.824200 1047 5442 5 chr3D.!!$F1 4395
9 TraesCS5B01G383900 chr3B 23703791 23707048 3257 False 1092.500000 2187 88.972750 1047 4632 4 chr3B.!!$F1 3585
10 TraesCS5B01G383900 chr3A 20224792 20231564 6772 True 770.250000 1212 88.370750 1047 5444 8 chr3A.!!$R2 4397
11 TraesCS5B01G383900 chr3A 20215883 20218838 2955 True 736.333333 1199 84.984333 3260 5444 3 chr3A.!!$R1 2184

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
73 74 0.104855 TGGCATCTACGATCTGTGGC 59.895 55.000 0.0 0.0 36.09 5.01 F
325 327 1.348696 TGTTTTTAGTCTCCCCCGGTC 59.651 52.381 0.0 0.0 0.00 4.79 F
1421 5150 0.395311 ATGCCAGGGTGAAGCTGATG 60.395 55.000 0.0 0.0 0.00 3.07 F
3138 8286 0.956633 AGTCTGCAGGCATGTGTTTG 59.043 50.000 22.5 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 5040 2.133553 CATGCTGGAGTATCTGCTTCG 58.866 52.381 0.0 0.0 36.05 3.79 R
2269 7374 0.818296 CTAGGGACACAAGGGACGAG 59.182 60.000 0.0 0.0 0.00 4.18 R
3337 9596 2.024414 ACCAGCCACTTCAGACAAAAC 58.976 47.619 0.0 0.0 0.00 2.43 R
4660 11107 0.107800 TGGAACAACCGTCCGTTTCA 60.108 50.000 0.0 0.0 42.61 2.69 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
55 56 1.469917 CTTGTTGCTTCTTGTGCGTG 58.530 50.000 0.00 0.00 0.00 5.34
63 64 1.394917 CTTCTTGTGCGTGGCATCTAC 59.605 52.381 0.00 0.00 41.91 2.59
69 70 0.249031 TGCGTGGCATCTACGATCTG 60.249 55.000 6.90 0.00 43.82 2.90
73 74 0.104855 TGGCATCTACGATCTGTGGC 59.895 55.000 0.00 0.00 36.09 5.01
75 76 1.604185 GGCATCTACGATCTGTGGCTC 60.604 57.143 0.00 0.00 33.18 4.70
118 119 2.874701 GCCATAGCTGTATGTTCACCTG 59.125 50.000 0.00 0.00 35.15 4.00
200 202 4.283678 CGAGTGCCGTTAAAATTTGTTGA 58.716 39.130 0.00 0.00 0.00 3.18
201 203 4.915085 CGAGTGCCGTTAAAATTTGTTGAT 59.085 37.500 0.00 0.00 0.00 2.57
210 212 6.582295 CGTTAAAATTTGTTGATGAGGGTCAG 59.418 38.462 0.00 0.00 0.00 3.51
239 241 9.294030 CATTGAAAAATAGCCTTTTAGCAGTAG 57.706 33.333 0.00 0.00 34.23 2.57
270 272 9.331689 TCATGAATTATGCATTGGTCATCACCG 62.332 40.741 3.54 0.55 40.07 4.94
285 287 6.460123 GGTCATCACCGATTGAGCATAAAAAT 60.460 38.462 0.00 0.00 37.77 1.82
325 327 1.348696 TGTTTTTAGTCTCCCCCGGTC 59.651 52.381 0.00 0.00 0.00 4.79
338 340 3.723681 TCCCCCGGTCTCTCTAATACTTA 59.276 47.826 0.00 0.00 0.00 2.24
339 341 3.825585 CCCCCGGTCTCTCTAATACTTAC 59.174 52.174 0.00 0.00 0.00 2.34
437 439 8.499162 GCTCGAAGCAACATATTTATATTCTGT 58.501 33.333 2.53 0.00 41.89 3.41
606 608 8.169977 ACAATTGAGAAACAACATGTAGACAT 57.830 30.769 13.59 0.00 41.52 3.06
862 898 3.450904 ACTACTGCTTCCCTGGACAATA 58.549 45.455 0.00 0.00 0.00 1.90
863 899 3.452627 ACTACTGCTTCCCTGGACAATAG 59.547 47.826 0.00 0.00 0.00 1.73
1263 4978 2.602676 CCGCTTTCCCCTTCCTCCA 61.603 63.158 0.00 0.00 0.00 3.86
1315 5040 2.644676 GATTAGTTCCCAGAACCAGGC 58.355 52.381 3.91 0.00 0.00 4.85
1383 5108 2.128771 TTTGGAGCACTTGGATAGCC 57.871 50.000 0.00 0.00 0.00 3.93
1421 5150 0.395311 ATGCCAGGGTGAAGCTGATG 60.395 55.000 0.00 0.00 0.00 3.07
1432 5165 4.540824 GTGAAGCTGATGAGTGTTTTTCC 58.459 43.478 0.00 0.00 0.00 3.13
1447 5183 5.989168 GTGTTTTTCCCCCAAAGTAAATCTG 59.011 40.000 0.00 0.00 0.00 2.90
1455 5191 5.067805 CCCCCAAAGTAAATCTGTTAGATGC 59.932 44.000 0.00 0.00 34.65 3.91
1492 5235 1.866601 TGAATGTGTGTGCGTCTCTTG 59.133 47.619 0.00 0.00 0.00 3.02
1512 5255 3.637432 TGTTTAATCCAAGTGCTTTGCG 58.363 40.909 0.00 0.00 35.37 4.85
1521 5264 6.019779 TCCAAGTGCTTTGCGTTAAATTAT 57.980 33.333 0.00 0.00 35.37 1.28
1535 5278 6.073548 GCGTTAAATTATCTGGAGGTGATCTG 60.074 42.308 0.00 0.00 0.00 2.90
1757 5530 6.546395 CAAGATATTCCTTGGTTTCACTTCG 58.454 40.000 0.00 0.00 39.74 3.79
2215 7320 5.525378 CCAGATGCTACAAGAACAATCTACC 59.475 44.000 0.00 0.00 33.77 3.18
2224 7329 6.106673 ACAAGAACAATCTACCGAGGTAATG 58.893 40.000 3.37 5.83 33.77 1.90
2264 7369 6.743575 ACACAGCTGGTAATAATCTGTTTC 57.256 37.500 19.93 0.00 36.01 2.78
2269 7374 8.462016 ACAGCTGGTAATAATCTGTTTCAATTC 58.538 33.333 19.93 0.00 34.69 2.17
2275 7381 8.336080 GGTAATAATCTGTTTCAATTCTCGTCC 58.664 37.037 0.00 0.00 0.00 4.79
2276 7382 6.927294 ATAATCTGTTTCAATTCTCGTCCC 57.073 37.500 0.00 0.00 0.00 4.46
2279 7385 4.065088 TCTGTTTCAATTCTCGTCCCTTG 58.935 43.478 0.00 0.00 0.00 3.61
2305 7411 2.709397 CCTAGTTACCGAAATCCCCCAT 59.291 50.000 0.00 0.00 0.00 4.00
2345 7457 3.330701 ACCCTTCCTTGTATGTGTCATGT 59.669 43.478 0.00 0.00 0.00 3.21
2366 7478 2.091939 TGCCCATTATAGTGCACATGGT 60.092 45.455 24.56 7.27 35.31 3.55
2564 7676 4.488879 GAACAGCAAATAAGCAGGAAAGG 58.511 43.478 0.00 0.00 36.85 3.11
2569 7681 6.168389 CAGCAAATAAGCAGGAAAGGAAAAT 58.832 36.000 0.00 0.00 36.85 1.82
2571 7683 7.818930 CAGCAAATAAGCAGGAAAGGAAAATAA 59.181 33.333 0.00 0.00 36.85 1.40
2616 7728 7.440523 AAATCTGGCTCAAAGTACTTACAAG 57.559 36.000 8.92 7.86 0.00 3.16
2617 7729 5.546621 TCTGGCTCAAAGTACTTACAAGT 57.453 39.130 8.92 0.00 42.91 3.16
2618 7730 5.925509 TCTGGCTCAAAGTACTTACAAGTT 58.074 37.500 8.92 0.00 40.37 2.66
2619 7731 7.058023 TCTGGCTCAAAGTACTTACAAGTTA 57.942 36.000 8.92 0.69 40.37 2.24
2620 7732 6.927381 TCTGGCTCAAAGTACTTACAAGTTAC 59.073 38.462 8.92 3.37 40.37 2.50
2621 7733 6.584488 TGGCTCAAAGTACTTACAAGTTACA 58.416 36.000 8.92 5.54 40.37 2.41
2622 7734 6.704493 TGGCTCAAAGTACTTACAAGTTACAG 59.296 38.462 8.92 0.00 40.37 2.74
2623 7735 6.704937 GGCTCAAAGTACTTACAAGTTACAGT 59.295 38.462 8.92 0.00 40.37 3.55
2624 7736 7.869429 GGCTCAAAGTACTTACAAGTTACAGTA 59.131 37.037 8.92 0.00 40.37 2.74
2625 7737 8.697960 GCTCAAAGTACTTACAAGTTACAGTAC 58.302 37.037 8.92 9.11 41.29 2.73
2626 7738 9.740239 CTCAAAGTACTTACAAGTTACAGTACA 57.260 33.333 8.92 1.46 42.75 2.90
2698 7811 4.087510 TCTACGTAACATGAAGTCACGG 57.912 45.455 0.00 0.00 36.95 4.94
2713 7826 5.479124 AGTCACGGACTTTATTGTAACCT 57.521 39.130 1.23 0.00 40.28 3.50
2808 7950 4.702131 AGGATCTTGTCAAACCTAATGTGC 59.298 41.667 0.00 0.00 0.00 4.57
2835 7977 7.347508 AGTACACTTTATAAGTTTCTGCACG 57.652 36.000 0.00 0.00 40.46 5.34
2879 8021 4.519540 ATTGTTGCACCTTGGTTGATAC 57.480 40.909 0.00 0.00 0.00 2.24
3075 8223 5.198207 ACCTTTATTGGGCATACAAGGTAC 58.802 41.667 0.00 0.00 37.23 3.34
3098 8246 5.359576 ACCATGCTTTTGACAGTTCTTTGTA 59.640 36.000 0.00 0.00 0.00 2.41
3136 8284 1.610522 GAAAGTCTGCAGGCATGTGTT 59.389 47.619 22.50 1.98 0.00 3.32
3137 8285 1.696063 AAGTCTGCAGGCATGTGTTT 58.304 45.000 22.50 1.14 0.00 2.83
3138 8286 0.956633 AGTCTGCAGGCATGTGTTTG 59.043 50.000 22.50 0.00 0.00 2.93
3210 8497 6.027482 TGGTAAACAGGGAGATAAAGTAGGT 58.973 40.000 0.00 0.00 0.00 3.08
3337 9596 8.143835 AGTAATCATTCCTGAACCAAACTTTTG 58.856 33.333 0.00 0.00 34.37 2.44
3353 9612 4.494484 ACTTTTGTTTTGTCTGAAGTGGC 58.506 39.130 0.00 0.00 0.00 5.01
3428 9691 4.216257 CACTTATTGGGTTGTCCTTCACTG 59.784 45.833 0.00 0.00 36.20 3.66
3433 9696 3.750371 TGGGTTGTCCTTCACTGTATTG 58.250 45.455 0.00 0.00 36.20 1.90
3901 10170 0.389166 GGAAGTGACTCAGGAGCACG 60.389 60.000 13.97 0.00 39.07 5.34
3960 10229 5.506815 GGTTCAGCAAAACCTGTAAAGGTAC 60.507 44.000 4.58 0.00 44.45 3.34
3966 10235 9.120538 CAGCAAAACCTGTAAAGGTACATATAT 57.879 33.333 4.58 0.00 42.20 0.86
4001 10270 6.892310 AGTTCAGAGATGTTTTTGTTTTGC 57.108 33.333 0.00 0.00 0.00 3.68
4019 10288 2.825086 GCGTTTTGCATACTAGTGGG 57.175 50.000 5.39 0.00 45.45 4.61
4020 10289 1.202143 GCGTTTTGCATACTAGTGGGC 60.202 52.381 5.39 9.58 45.45 5.36
4021 10290 2.356135 CGTTTTGCATACTAGTGGGCT 58.644 47.619 17.87 0.00 0.00 5.19
4022 10291 2.351726 CGTTTTGCATACTAGTGGGCTC 59.648 50.000 17.87 8.07 0.00 4.70
4024 10293 2.988010 TTGCATACTAGTGGGCTCTG 57.012 50.000 17.87 3.58 0.00 3.35
4025 10294 1.866015 TGCATACTAGTGGGCTCTGT 58.134 50.000 17.87 0.00 0.00 3.41
4027 10296 2.093500 TGCATACTAGTGGGCTCTGTTG 60.093 50.000 17.87 0.37 0.00 3.33
4028 10297 2.743183 GCATACTAGTGGGCTCTGTTGG 60.743 54.545 5.39 0.00 0.00 3.77
4029 10298 2.320681 TACTAGTGGGCTCTGTTGGT 57.679 50.000 5.39 0.00 0.00 3.67
4030 10299 0.687354 ACTAGTGGGCTCTGTTGGTG 59.313 55.000 0.00 0.00 0.00 4.17
4031 10300 0.976641 CTAGTGGGCTCTGTTGGTGA 59.023 55.000 0.00 0.00 0.00 4.02
4032 10301 1.347707 CTAGTGGGCTCTGTTGGTGAA 59.652 52.381 0.00 0.00 0.00 3.18
4033 10302 0.550914 AGTGGGCTCTGTTGGTGAAA 59.449 50.000 0.00 0.00 0.00 2.69
4034 10303 1.064017 AGTGGGCTCTGTTGGTGAAAA 60.064 47.619 0.00 0.00 0.00 2.29
4049 10319 8.219178 TGTTGGTGAAAAGTTCCTTAGGTATAA 58.781 33.333 0.00 0.00 0.00 0.98
4070 10340 9.618890 GTATAAGGTATAATGACCATGATGCAT 57.381 33.333 0.00 0.00 42.47 3.96
4081 10351 3.181448 ACCATGATGCATCTGCTCATGTA 60.181 43.478 26.32 4.16 44.97 2.29
4084 10354 4.618920 TGATGCATCTGCTCATGTATCT 57.381 40.909 26.32 0.00 42.99 1.98
4122 10556 7.966339 AGAAAATTTCATCCATGATCCTGAA 57.034 32.000 8.55 0.00 36.56 3.02
4127 10561 2.440627 TCATCCATGATCCTGAACTGGG 59.559 50.000 0.00 0.00 0.00 4.45
4164 10598 7.986704 AGACCATCTTGATTTATCATGATCCT 58.013 34.615 12.53 0.00 44.77 3.24
4165 10599 7.883833 AGACCATCTTGATTTATCATGATCCTG 59.116 37.037 12.53 8.48 44.77 3.86
4166 10600 7.752638 ACCATCTTGATTTATCATGATCCTGA 58.247 34.615 12.53 2.98 44.77 3.86
4167 10601 8.222637 ACCATCTTGATTTATCATGATCCTGAA 58.777 33.333 12.53 4.00 44.77 3.02
4168 10602 8.512956 CCATCTTGATTTATCATGATCCTGAAC 58.487 37.037 12.53 1.48 44.77 3.18
4169 10603 9.286170 CATCTTGATTTATCATGATCCTGAACT 57.714 33.333 12.53 0.00 44.77 3.01
4170 10604 8.672823 TCTTGATTTATCATGATCCTGAACTG 57.327 34.615 12.53 0.00 36.45 3.16
4171 10605 7.718314 TCTTGATTTATCATGATCCTGAACTGG 59.282 37.037 12.53 0.00 36.45 4.00
4172 10606 6.301486 TGATTTATCATGATCCTGAACTGGG 58.699 40.000 12.53 0.00 0.00 4.45
4173 10607 5.715439 TTTATCATGATCCTGAACTGGGT 57.285 39.130 12.53 0.00 0.00 4.51
4174 10608 5.715439 TTATCATGATCCTGAACTGGGTT 57.285 39.130 12.53 0.00 0.00 4.11
4175 10609 6.823286 TTATCATGATCCTGAACTGGGTTA 57.177 37.500 12.53 0.00 0.00 2.85
4176 10610 5.919348 ATCATGATCCTGAACTGGGTTAT 57.081 39.130 1.18 0.00 0.00 1.89
4177 10611 8.504811 TTATCATGATCCTGAACTGGGTTATA 57.495 34.615 12.53 0.00 0.00 0.98
4178 10612 6.823286 TCATGATCCTGAACTGGGTTATAA 57.177 37.500 0.00 0.00 0.00 0.98
4179 10613 7.392766 TCATGATCCTGAACTGGGTTATAAT 57.607 36.000 0.00 0.00 0.00 1.28
4180 10614 8.504811 TCATGATCCTGAACTGGGTTATAATA 57.495 34.615 0.00 0.00 0.00 0.98
4181 10615 9.116080 TCATGATCCTGAACTGGGTTATAATAT 57.884 33.333 0.00 0.00 0.00 1.28
4182 10616 9.745018 CATGATCCTGAACTGGGTTATAATATT 57.255 33.333 0.00 0.00 0.00 1.28
4188 10622 9.503399 CCTGAACTGGGTTATAATATTTAGACC 57.497 37.037 0.00 0.00 0.00 3.85
4205 10639 7.880160 TTTAGACCATAATCACTTTCCCATG 57.120 36.000 0.00 0.00 0.00 3.66
4206 10640 5.456921 AGACCATAATCACTTTCCCATGT 57.543 39.130 0.00 0.00 0.00 3.21
4207 10641 6.575244 AGACCATAATCACTTTCCCATGTA 57.425 37.500 0.00 0.00 0.00 2.29
4208 10642 6.357367 AGACCATAATCACTTTCCCATGTAC 58.643 40.000 0.00 0.00 0.00 2.90
4209 10643 6.069673 AGACCATAATCACTTTCCCATGTACA 60.070 38.462 0.00 0.00 0.00 2.90
4210 10644 6.489603 ACCATAATCACTTTCCCATGTACAA 58.510 36.000 0.00 0.00 0.00 2.41
4211 10645 6.377146 ACCATAATCACTTTCCCATGTACAAC 59.623 38.462 0.00 0.00 0.00 3.32
4212 10646 6.603201 CCATAATCACTTTCCCATGTACAACT 59.397 38.462 0.00 0.00 0.00 3.16
4213 10647 7.122650 CCATAATCACTTTCCCATGTACAACTT 59.877 37.037 0.00 0.00 0.00 2.66
4214 10648 6.976934 AATCACTTTCCCATGTACAACTTT 57.023 33.333 0.00 0.00 0.00 2.66
4252 10686 6.595682 AGTATTGCAGCCTATGAGTTTATGT 58.404 36.000 0.00 0.00 0.00 2.29
4255 10689 4.191544 TGCAGCCTATGAGTTTATGTCAC 58.808 43.478 0.00 0.00 0.00 3.67
4258 10692 6.183361 TGCAGCCTATGAGTTTATGTCACTAT 60.183 38.462 0.00 0.00 0.00 2.12
4348 10784 6.558009 TCATTGCAATCTAACATTTCAGCTC 58.442 36.000 9.53 0.00 0.00 4.09
4362 10800 1.556911 TCAGCTCTTGGAATCCAGGTC 59.443 52.381 11.29 5.02 33.81 3.85
4374 10812 1.126948 TCCAGGTCCACTGTGATGCA 61.127 55.000 9.86 0.00 46.06 3.96
4456 10897 3.295093 TCAACCAACTGAATTTCTGGCA 58.705 40.909 8.00 0.00 31.74 4.92
4478 10919 2.159379 GCGAACTAAGGGCCTCAAATTG 60.159 50.000 6.46 0.00 0.00 2.32
4510 10951 4.984295 TGATCTCCAATTGTTTGTCTGGA 58.016 39.130 4.43 0.00 36.53 3.86
4529 10974 5.102953 TGGACTCTTTGGAGGATAACATG 57.897 43.478 0.00 0.00 43.46 3.21
4558 11005 0.320683 TTGTCAGATGCCGACCACAG 60.321 55.000 0.00 0.00 32.15 3.66
4575 11022 5.445964 ACCACAGTTACTGATTCCTTTTGT 58.554 37.500 20.07 0.00 35.18 2.83
4577 11024 6.379988 ACCACAGTTACTGATTCCTTTTGTTT 59.620 34.615 20.07 0.00 35.18 2.83
4635 11082 9.797642 ATGCTTTGTAATGAGATTATGTATGGA 57.202 29.630 0.00 0.00 0.00 3.41
4637 11084 9.277783 GCTTTGTAATGAGATTATGTATGGAGT 57.722 33.333 0.00 0.00 0.00 3.85
4639 11086 8.607441 TTGTAATGAGATTATGTATGGAGTGC 57.393 34.615 0.00 0.00 0.00 4.40
4640 11087 7.161404 TGTAATGAGATTATGTATGGAGTGCC 58.839 38.462 0.00 0.00 0.00 5.01
4653 11100 4.853468 TGGAGTGCCAACATATTAGGAA 57.147 40.909 0.00 0.00 42.49 3.36
4654 11101 5.186256 TGGAGTGCCAACATATTAGGAAA 57.814 39.130 0.00 0.00 42.49 3.13
4655 11102 5.765510 TGGAGTGCCAACATATTAGGAAAT 58.234 37.500 0.00 0.00 42.49 2.17
4656 11103 6.905736 TGGAGTGCCAACATATTAGGAAATA 58.094 36.000 0.00 0.00 42.49 1.40
4657 11104 7.526041 TGGAGTGCCAACATATTAGGAAATAT 58.474 34.615 0.00 0.00 42.49 1.28
4658 11105 8.004215 TGGAGTGCCAACATATTAGGAAATATT 58.996 33.333 0.00 0.00 42.49 1.28
4659 11106 9.515226 GGAGTGCCAACATATTAGGAAATATTA 57.485 33.333 0.00 0.00 36.36 0.98
4673 11120 6.117488 AGGAAATATTATGAAACGGACGGTT 58.883 36.000 0.00 0.00 41.76 4.44
4679 11126 0.107800 TGAAACGGACGGTTGTTCCA 60.108 50.000 0.00 0.00 39.30 3.53
4680 11127 1.015868 GAAACGGACGGTTGTTCCAA 58.984 50.000 0.00 0.00 39.30 3.53
4682 11129 2.547299 AACGGACGGTTGTTCCAATA 57.453 45.000 0.00 0.00 37.50 1.90
4705 11154 9.965902 AATATTTATCTGACTCTGGAAAACTGT 57.034 29.630 0.00 0.00 0.00 3.55
4713 11162 6.591935 TGACTCTGGAAAACTGTGACTTTAT 58.408 36.000 0.00 0.00 0.00 1.40
4716 11165 8.974060 ACTCTGGAAAACTGTGACTTTATAAA 57.026 30.769 0.00 0.00 0.00 1.40
4717 11166 9.057089 ACTCTGGAAAACTGTGACTTTATAAAG 57.943 33.333 21.21 21.21 41.73 1.85
4744 11193 4.703379 ATCTGGTGAGGATCCTTTGATC 57.297 45.455 17.42 3.05 45.61 2.92
4748 11197 4.848357 TGGTGAGGATCCTTTGATCTTTC 58.152 43.478 17.42 0.00 45.62 2.62
4783 11240 0.681175 AAAAGGTGGACATGCTTGGC 59.319 50.000 4.44 0.00 0.00 4.52
4797 11254 6.054295 ACATGCTTGGCTCAACAAAATAAAA 58.946 32.000 4.44 0.00 0.00 1.52
4803 11260 7.587392 GCTTGGCTCAACAAAATAAAATTGTTC 59.413 33.333 1.92 0.00 45.27 3.18
4809 11266 7.910304 TCAACAAAATAAAATTGTTCGGTTGG 58.090 30.769 13.82 0.00 45.27 3.77
4835 11292 3.753272 AGTTTGTTGATTGATCCCTCGTG 59.247 43.478 0.00 0.00 0.00 4.35
4847 11306 3.353836 CTCGTGCAAACGGGTGGG 61.354 66.667 0.00 0.00 0.00 4.61
4850 11309 2.482333 CGTGCAAACGGGTGGGAAA 61.482 57.895 0.00 0.00 0.00 3.13
4853 11312 1.614413 GTGCAAACGGGTGGGAAATTA 59.386 47.619 0.00 0.00 0.00 1.40
4863 11322 5.105513 ACGGGTGGGAAATTATTGCTAAAAG 60.106 40.000 0.00 0.00 0.00 2.27
4868 11327 7.758076 GGTGGGAAATTATTGCTAAAAGTGTAC 59.242 37.037 0.00 0.00 0.00 2.90
4871 11330 9.301153 GGGAAATTATTGCTAAAAGTGTACATG 57.699 33.333 0.00 0.00 0.00 3.21
4878 11337 6.048732 TGCTAAAAGTGTACATGGAGATCA 57.951 37.500 0.00 0.00 0.00 2.92
4902 11361 9.399797 TCATGATACAGTATTCTGAAAAATGCT 57.600 29.630 6.32 0.00 43.76 3.79
4919 11378 2.962125 TGCTTTGCAAATGCTATGGTG 58.038 42.857 24.26 9.19 46.10 4.17
4925 11384 2.886523 TGCAAATGCTATGGTGCCTATC 59.113 45.455 6.97 0.00 42.66 2.08
4927 11386 3.508793 GCAAATGCTATGGTGCCTATCAT 59.491 43.478 0.00 0.00 38.21 2.45
4931 11390 6.572182 AATGCTATGGTGCCTATCATATCT 57.428 37.500 0.00 0.00 29.84 1.98
4952 11411 0.032540 AGTTCGTTAACCGGCGTCTT 59.967 50.000 6.01 0.00 36.15 3.01
4953 11412 0.861185 GTTCGTTAACCGGCGTCTTT 59.139 50.000 6.01 0.00 37.11 2.52
4954 11413 2.058057 GTTCGTTAACCGGCGTCTTTA 58.942 47.619 6.01 0.00 37.11 1.85
4955 11414 1.981254 TCGTTAACCGGCGTCTTTAG 58.019 50.000 6.01 0.00 37.11 1.85
4956 11415 0.367887 CGTTAACCGGCGTCTTTAGC 59.632 55.000 6.01 1.79 0.00 3.09
4986 12163 3.010420 GGTGAAGAGATGTAAGCAACCC 58.990 50.000 0.00 0.00 0.00 4.11
4988 12165 2.301870 TGAAGAGATGTAAGCAACCCGT 59.698 45.455 0.00 0.00 0.00 5.28
5014 12191 3.431856 GACTTGTTCGGTTTGTGGTTTC 58.568 45.455 0.00 0.00 0.00 2.78
5021 12198 2.640826 TCGGTTTGTGGTTTCCCTAGAT 59.359 45.455 0.00 0.00 0.00 1.98
5044 12221 8.834465 AGATGATTCTTACAAGATTTTGATCCG 58.166 33.333 2.48 0.00 37.73 4.18
5045 12222 7.320443 TGATTCTTACAAGATTTTGATCCGG 57.680 36.000 2.48 0.00 37.73 5.14
5047 12224 7.609918 TGATTCTTACAAGATTTTGATCCGGAA 59.390 33.333 9.01 0.00 37.73 4.30
5048 12225 7.938140 TTCTTACAAGATTTTGATCCGGAAT 57.062 32.000 9.01 0.00 37.73 3.01
5049 12226 7.938140 TCTTACAAGATTTTGATCCGGAATT 57.062 32.000 9.01 0.00 37.73 2.17
5050 12227 8.348285 TCTTACAAGATTTTGATCCGGAATTT 57.652 30.769 9.01 0.00 37.73 1.82
5052 12229 8.980143 TTACAAGATTTTGATCCGGAATTTTC 57.020 30.769 9.01 1.00 37.73 2.29
5053 12230 6.398095 ACAAGATTTTGATCCGGAATTTTCC 58.602 36.000 9.01 0.00 39.54 3.13
5054 12231 5.598416 AGATTTTGATCCGGAATTTTCCC 57.402 39.130 9.01 0.00 44.67 3.97
5055 12232 4.405680 AGATTTTGATCCGGAATTTTCCCC 59.594 41.667 9.01 0.00 44.67 4.81
5070 12252 5.441709 TTTTCCCCGTGTAGAATTTGTTC 57.558 39.130 0.00 0.00 0.00 3.18
5075 12257 3.756434 CCCGTGTAGAATTTGTTCCACAT 59.244 43.478 0.00 0.00 0.00 3.21
5234 12472 3.089284 CCTACCCCTGTGATTTGGAAAC 58.911 50.000 0.00 0.00 0.00 2.78
5236 12474 1.219213 ACCCCTGTGATTTGGAAACCA 59.781 47.619 0.00 0.00 0.00 3.67
5299 12542 3.069729 ACGCTCCCCACAAGATAGATTAC 59.930 47.826 0.00 0.00 0.00 1.89
5309 12552 7.713507 CCCACAAGATAGATTACCAAATCGTTA 59.286 37.037 0.00 0.00 45.24 3.18
5320 12563 7.598189 TTACCAAATCGTTATTTCATCGTCA 57.402 32.000 0.00 0.00 32.87 4.35
5328 12571 5.236695 TCGTTATTTCATCGTCAAACAACCA 59.763 36.000 0.00 0.00 0.00 3.67
5332 12575 4.811555 TTCATCGTCAAACAACCAGAAG 57.188 40.909 0.00 0.00 0.00 2.85
5336 12579 3.611970 TCGTCAAACAACCAGAAGGAAA 58.388 40.909 0.00 0.00 38.69 3.13
5337 12580 4.011023 TCGTCAAACAACCAGAAGGAAAA 58.989 39.130 0.00 0.00 38.69 2.29
5387 12630 8.098220 ACAAGTTTGGGAATTTCATAAAATGC 57.902 30.769 0.00 0.00 35.27 3.56
5389 12632 8.445493 CAAGTTTGGGAATTTCATAAAATGCTC 58.555 33.333 0.00 0.00 35.27 4.26
5391 12634 4.681744 TGGGAATTTCATAAAATGCTCGC 58.318 39.130 0.00 0.00 33.98 5.03
5397 12640 7.008810 GGAATTTCATAAAATGCTCGCGTTTTA 59.991 33.333 23.43 23.43 45.51 1.52
5399 12642 7.804614 TTTCATAAAATGCTCGCGTTTTAAT 57.195 28.000 24.42 14.56 44.98 1.40
5400 12643 7.804614 TTCATAAAATGCTCGCGTTTTAATT 57.195 28.000 24.42 12.37 44.98 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.390860 AGCCACAGATCGTAGATGCC 59.609 55.000 0.00 0.00 45.12 4.40
73 74 2.110967 CCAAGTGATGCGGGCAGAG 61.111 63.158 0.00 0.00 0.00 3.35
75 76 3.136123 CCCAAGTGATGCGGGCAG 61.136 66.667 0.00 0.00 31.89 4.85
118 119 5.303078 TCCTTTATGAGCACCTATGAGAGAC 59.697 44.000 0.00 0.00 0.00 3.36
200 202 1.002069 TTCAATGGCCTGACCCTCAT 58.998 50.000 3.32 0.00 37.83 2.90
201 203 0.776810 TTTCAATGGCCTGACCCTCA 59.223 50.000 3.32 0.00 37.83 3.86
247 249 4.036616 CGGTGATGACCAATGCATAATTCA 59.963 41.667 0.00 2.89 43.33 2.57
261 263 5.484173 TTTTATGCTCAATCGGTGATGAC 57.516 39.130 0.00 0.00 35.07 3.06
633 635 7.925043 TGTGGCTAAATTTCGGTCTATTTAA 57.075 32.000 0.00 0.00 0.00 1.52
647 649 1.476488 GCGTTTGGGATGTGGCTAAAT 59.524 47.619 0.00 0.00 0.00 1.40
726 728 7.363431 CCAAACAAATTAGTCCTCTCAGAAAC 58.637 38.462 0.00 0.00 0.00 2.78
746 748 7.606456 TGACTAACATCATTAGTCTTCCCAAAC 59.394 37.037 21.36 0.88 46.69 2.93
862 898 1.985116 GTGGAACCGGCTCCTCTCT 60.985 63.158 24.04 0.00 36.35 3.10
863 899 2.579738 GTGGAACCGGCTCCTCTC 59.420 66.667 24.04 11.18 36.35 3.20
1158 4854 4.821589 GAGGCGAGCGACCCAAGG 62.822 72.222 0.00 0.00 0.00 3.61
1315 5040 2.133553 CATGCTGGAGTATCTGCTTCG 58.866 52.381 0.00 0.00 36.05 3.79
1345 5070 4.267452 CCAAATGGCGAAATAAACGGAATG 59.733 41.667 0.00 0.00 0.00 2.67
1383 5108 5.519927 TGGCATCGAAACGATATATATGCAG 59.480 40.000 13.61 0.00 45.19 4.41
1421 5150 5.601583 TTTACTTTGGGGGAAAAACACTC 57.398 39.130 0.00 0.00 0.00 3.51
1432 5165 5.652014 TGCATCTAACAGATTTACTTTGGGG 59.348 40.000 0.00 0.00 31.32 4.96
1447 5183 5.461737 GCTAGACTGTTCAGATGCATCTAAC 59.538 44.000 28.27 26.76 34.85 2.34
1492 5235 3.638484 ACGCAAAGCACTTGGATTAAAC 58.362 40.909 1.30 0.00 35.38 2.01
1521 5264 3.963374 CCTTCATACAGATCACCTCCAGA 59.037 47.826 0.00 0.00 0.00 3.86
1535 5278 6.148480 GTGATATGACAGGCATTCCTTCATAC 59.852 42.308 13.95 10.54 41.93 2.39
1757 5530 4.328169 CGTATACCGGAAGAAACAAGGTTC 59.672 45.833 9.46 0.00 36.49 3.62
2224 7329 4.379918 GCTGTGTTTAAGCCAAGAGGAATC 60.380 45.833 0.00 0.00 36.89 2.52
2264 7369 2.076863 GGACACAAGGGACGAGAATTG 58.923 52.381 0.00 0.00 0.00 2.32
2269 7374 0.818296 CTAGGGACACAAGGGACGAG 59.182 60.000 0.00 0.00 0.00 4.18
2275 7381 2.173519 TCGGTAACTAGGGACACAAGG 58.826 52.381 0.00 0.00 0.00 3.61
2276 7382 3.947910 TTCGGTAACTAGGGACACAAG 57.052 47.619 0.00 0.00 0.00 3.16
2279 7385 3.431346 GGGATTTCGGTAACTAGGGACAC 60.431 52.174 0.00 0.00 0.00 3.67
2305 7411 5.922960 AGGGTAGCCATAATCCACATTAA 57.077 39.130 14.62 0.00 0.00 1.40
2345 7457 2.091939 ACCATGTGCACTATAATGGGCA 60.092 45.455 28.09 4.14 43.26 5.36
2366 7478 6.072838 GCAGCTAATTTATGCATCAGAAGCTA 60.073 38.462 17.75 3.88 39.75 3.32
2575 7687 8.864087 AGCCAGATTTAAGTTCTCTTCATTTTT 58.136 29.630 0.00 0.00 35.36 1.94
2698 7811 4.585879 TGGAGCCAGGTTACAATAAAGTC 58.414 43.478 0.00 0.00 0.00 3.01
2713 7826 2.376518 AGAAAGGAAACTCATGGAGCCA 59.623 45.455 0.00 0.00 42.68 4.75
2808 7950 7.950496 GTGCAGAAACTTATAAAGTGTACTTCG 59.050 37.037 0.00 0.00 41.91 3.79
2835 7977 3.254060 TCTGCGTAGACTTCAGCAATTC 58.746 45.455 0.00 0.00 39.26 2.17
3075 8223 4.685924 ACAAAGAACTGTCAAAAGCATGG 58.314 39.130 0.00 0.00 0.00 3.66
3285 8972 7.843490 TTTCTGGGTAAAATCATAAGACTCG 57.157 36.000 0.00 0.00 0.00 4.18
3337 9596 2.024414 ACCAGCCACTTCAGACAAAAC 58.976 47.619 0.00 0.00 0.00 2.43
3353 9612 3.668447 ACATCTGCTAAACTGTGACCAG 58.332 45.455 0.00 0.00 44.68 4.00
3433 9696 5.123502 CCAGTATGAAGCATATTCTCCATGC 59.876 44.000 0.00 0.00 43.89 4.06
3504 9772 4.675146 GCACTTTGCAACTTCAGTCTTTGA 60.675 41.667 0.00 0.00 44.26 2.69
3901 10170 1.538047 TGAAACTGCTTCATCTGGCC 58.462 50.000 0.00 0.00 39.20 5.36
3966 10235 7.473735 ACATCTCTGAACTTGTGAAGATCTA 57.526 36.000 0.00 0.00 32.14 1.98
3967 10236 6.357579 ACATCTCTGAACTTGTGAAGATCT 57.642 37.500 0.00 0.00 32.14 2.75
3971 10240 7.253422 ACAAAAACATCTCTGAACTTGTGAAG 58.747 34.615 0.00 0.00 0.00 3.02
3982 10251 5.701029 AACGCAAAACAAAAACATCTCTG 57.299 34.783 0.00 0.00 0.00 3.35
3983 10252 6.533185 CAAAACGCAAAACAAAAACATCTCT 58.467 32.000 0.00 0.00 0.00 3.10
4001 10270 2.351726 GAGCCCACTAGTATGCAAAACG 59.648 50.000 15.75 0.00 0.00 3.60
4017 10286 1.692411 ACTTTTCACCAACAGAGCCC 58.308 50.000 0.00 0.00 0.00 5.19
4018 10287 2.034685 GGAACTTTTCACCAACAGAGCC 59.965 50.000 0.00 0.00 0.00 4.70
4019 10288 2.952310 AGGAACTTTTCACCAACAGAGC 59.048 45.455 0.00 0.00 27.25 4.09
4049 10319 6.178324 CAGATGCATCATGGTCATTATACCT 58.822 40.000 27.81 0.00 40.44 3.08
4060 10330 2.997485 CATGAGCAGATGCATCATGG 57.003 50.000 27.81 17.24 44.01 3.66
4070 10340 3.881089 CCATTGCAAGATACATGAGCAGA 59.119 43.478 4.94 0.00 36.47 4.26
4106 10540 2.440627 CCCAGTTCAGGATCATGGATGA 59.559 50.000 7.64 0.00 41.70 2.92
4110 10544 2.814805 AACCCAGTTCAGGATCATGG 57.185 50.000 7.64 0.00 0.00 3.66
4179 10613 9.573166 CATGGGAAAGTGATTATGGTCTAAATA 57.427 33.333 0.00 0.00 0.00 1.40
4180 10614 8.061304 ACATGGGAAAGTGATTATGGTCTAAAT 58.939 33.333 0.00 0.00 0.00 1.40
4181 10615 7.410174 ACATGGGAAAGTGATTATGGTCTAAA 58.590 34.615 0.00 0.00 0.00 1.85
4182 10616 6.969043 ACATGGGAAAGTGATTATGGTCTAA 58.031 36.000 0.00 0.00 0.00 2.10
4183 10617 6.575244 ACATGGGAAAGTGATTATGGTCTA 57.425 37.500 0.00 0.00 0.00 2.59
4184 10618 5.456921 ACATGGGAAAGTGATTATGGTCT 57.543 39.130 0.00 0.00 0.00 3.85
4185 10619 6.119536 TGTACATGGGAAAGTGATTATGGTC 58.880 40.000 0.00 0.00 0.00 4.02
4186 10620 6.073447 TGTACATGGGAAAGTGATTATGGT 57.927 37.500 0.00 0.00 0.00 3.55
4187 10621 6.603201 AGTTGTACATGGGAAAGTGATTATGG 59.397 38.462 0.00 0.00 0.00 2.74
4188 10622 7.630242 AGTTGTACATGGGAAAGTGATTATG 57.370 36.000 0.00 0.00 0.00 1.90
4189 10623 8.650143 AAAGTTGTACATGGGAAAGTGATTAT 57.350 30.769 0.00 0.00 0.00 1.28
4190 10624 8.472007 AAAAGTTGTACATGGGAAAGTGATTA 57.528 30.769 0.00 0.00 0.00 1.75
4191 10625 6.976934 AAAGTTGTACATGGGAAAGTGATT 57.023 33.333 0.00 0.00 0.00 2.57
4192 10626 6.976934 AAAAGTTGTACATGGGAAAGTGAT 57.023 33.333 0.00 0.00 0.00 3.06
4193 10627 6.829298 TGTAAAAGTTGTACATGGGAAAGTGA 59.171 34.615 1.49 0.00 0.00 3.41
4194 10628 6.915843 GTGTAAAAGTTGTACATGGGAAAGTG 59.084 38.462 9.13 0.00 34.15 3.16
4195 10629 6.831868 AGTGTAAAAGTTGTACATGGGAAAGT 59.168 34.615 9.13 0.00 34.15 2.66
4196 10630 7.138736 CAGTGTAAAAGTTGTACATGGGAAAG 58.861 38.462 9.13 0.00 34.15 2.62
4197 10631 6.603997 ACAGTGTAAAAGTTGTACATGGGAAA 59.396 34.615 9.13 0.00 34.15 3.13
4198 10632 6.123651 ACAGTGTAAAAGTTGTACATGGGAA 58.876 36.000 9.13 0.00 34.15 3.97
4199 10633 5.686753 ACAGTGTAAAAGTTGTACATGGGA 58.313 37.500 9.13 0.00 34.15 4.37
4200 10634 6.932400 TCTACAGTGTAAAAGTTGTACATGGG 59.068 38.462 9.13 5.03 34.15 4.00
4201 10635 7.956420 TCTACAGTGTAAAAGTTGTACATGG 57.044 36.000 9.13 7.22 34.15 3.66
4210 10644 9.938280 TGCAATACTATTCTACAGTGTAAAAGT 57.062 29.630 4.21 7.81 0.00 2.66
4212 10646 8.879759 GCTGCAATACTATTCTACAGTGTAAAA 58.120 33.333 4.21 0.00 0.00 1.52
4213 10647 7.494625 GGCTGCAATACTATTCTACAGTGTAAA 59.505 37.037 4.21 2.86 0.00 2.01
4214 10648 6.984474 GGCTGCAATACTATTCTACAGTGTAA 59.016 38.462 4.21 0.00 0.00 2.41
4229 10663 6.483307 TGACATAAACTCATAGGCTGCAATAC 59.517 38.462 0.50 0.00 0.00 1.89
4319 10755 9.791820 CTGAAATGTTAGATTGCAATGATAACA 57.208 29.630 30.23 30.23 39.78 2.41
4320 10756 8.749499 GCTGAAATGTTAGATTGCAATGATAAC 58.251 33.333 24.39 24.39 0.00 1.89
4322 10758 8.229253 AGCTGAAATGTTAGATTGCAATGATA 57.771 30.769 18.59 6.76 0.00 2.15
4325 10761 6.561614 AGAGCTGAAATGTTAGATTGCAATG 58.438 36.000 18.59 0.00 0.00 2.82
4330 10766 6.748333 TCCAAGAGCTGAAATGTTAGATTG 57.252 37.500 0.00 0.00 0.00 2.67
4348 10784 1.352352 ACAGTGGACCTGGATTCCAAG 59.648 52.381 6.88 3.04 44.94 3.61
4362 10800 1.328680 GCGATAGTTGCATCACAGTGG 59.671 52.381 0.00 0.00 39.35 4.00
4374 10812 3.881937 AGTAACGGGAAAGCGATAGTT 57.118 42.857 0.00 0.00 39.35 2.24
4416 10854 4.299586 TGAATTTGCACCATGAGACCTA 57.700 40.909 0.00 0.00 0.00 3.08
4456 10897 0.690762 TTTGAGGCCCTTAGTTCGCT 59.309 50.000 0.00 0.00 0.00 4.93
4499 10940 3.433598 CCTCCAAAGAGTCCAGACAAACA 60.434 47.826 0.00 0.00 38.58 2.83
4510 10951 5.339530 CCTTCCATGTTATCCTCCAAAGAGT 60.340 44.000 0.00 0.00 38.58 3.24
4552 10997 5.445964 ACAAAAGGAATCAGTAACTGTGGT 58.554 37.500 0.00 0.00 32.61 4.16
4558 11005 9.394477 GTACATCAAACAAAAGGAATCAGTAAC 57.606 33.333 0.00 0.00 0.00 2.50
4575 11022 4.431416 ACAACCTCAGGTGTACATCAAA 57.569 40.909 9.22 0.00 35.34 2.69
4577 11024 5.755409 ATTACAACCTCAGGTGTACATCA 57.245 39.130 9.22 0.00 35.34 3.07
4632 11079 4.853468 TTCCTAATATGTTGGCACTCCA 57.147 40.909 0.00 0.00 41.55 3.86
4649 11096 5.677567 ACCGTCCGTTTCATAATATTTCCT 58.322 37.500 0.00 0.00 0.00 3.36
4650 11097 5.996669 ACCGTCCGTTTCATAATATTTCC 57.003 39.130 0.00 0.00 0.00 3.13
4651 11098 6.778108 ACAACCGTCCGTTTCATAATATTTC 58.222 36.000 0.00 0.00 29.93 2.17
4652 11099 6.746745 ACAACCGTCCGTTTCATAATATTT 57.253 33.333 0.00 0.00 29.93 1.40
4653 11100 6.183360 GGAACAACCGTCCGTTTCATAATATT 60.183 38.462 0.00 0.00 29.93 1.28
4654 11101 5.295045 GGAACAACCGTCCGTTTCATAATAT 59.705 40.000 0.00 0.00 29.93 1.28
4655 11102 4.630940 GGAACAACCGTCCGTTTCATAATA 59.369 41.667 0.00 0.00 29.93 0.98
4656 11103 3.437741 GGAACAACCGTCCGTTTCATAAT 59.562 43.478 0.00 0.00 29.93 1.28
4657 11104 2.807392 GGAACAACCGTCCGTTTCATAA 59.193 45.455 0.00 0.00 29.93 1.90
4658 11105 2.224233 TGGAACAACCGTCCGTTTCATA 60.224 45.455 0.00 0.00 42.61 2.15
4659 11106 1.232119 GGAACAACCGTCCGTTTCAT 58.768 50.000 0.00 0.00 29.93 2.57
4660 11107 0.107800 TGGAACAACCGTCCGTTTCA 60.108 50.000 0.00 0.00 42.61 2.69
4661 11108 2.692817 TGGAACAACCGTCCGTTTC 58.307 52.632 0.00 0.00 42.61 2.78
4662 11109 4.959399 TGGAACAACCGTCCGTTT 57.041 50.000 0.00 0.00 42.61 3.60
4673 11120 8.089625 TCCAGAGTCAGATAAATATTGGAACA 57.910 34.615 0.00 0.00 29.86 3.18
4679 11126 9.965902 ACAGTTTTCCAGAGTCAGATAAATATT 57.034 29.630 0.00 0.00 0.00 1.28
4680 11127 9.388506 CACAGTTTTCCAGAGTCAGATAAATAT 57.611 33.333 0.00 0.00 0.00 1.28
4682 11129 7.389053 GTCACAGTTTTCCAGAGTCAGATAAAT 59.611 37.037 0.00 0.00 0.00 1.40
4713 11162 8.337118 AGGATCCTCACCAGATAATTTCTTTA 57.663 34.615 9.02 0.00 29.93 1.85
4716 11165 6.838401 AAGGATCCTCACCAGATAATTTCT 57.162 37.500 16.52 0.00 33.90 2.52
4717 11166 7.056635 TCAAAGGATCCTCACCAGATAATTTC 58.943 38.462 16.52 0.00 0.00 2.17
4721 11170 6.179906 GATCAAAGGATCCTCACCAGATAA 57.820 41.667 16.52 0.00 43.44 1.75
4737 11186 2.749621 CCCCCGTCTTGAAAGATCAAAG 59.250 50.000 0.00 0.00 44.64 2.77
4744 11193 1.071699 TCAAGTCCCCCGTCTTGAAAG 59.928 52.381 5.34 0.00 44.29 2.62
4748 11197 1.880027 CTTTTCAAGTCCCCCGTCTTG 59.120 52.381 0.00 0.00 41.36 3.02
4768 11217 0.895100 TTGAGCCAAGCATGTCCACC 60.895 55.000 0.00 0.00 0.00 4.61
4777 11234 6.958255 ACAATTTTATTTTGTTGAGCCAAGC 58.042 32.000 0.00 0.00 33.64 4.01
4778 11235 7.793427 CGAACAATTTTATTTTGTTGAGCCAAG 59.207 33.333 6.53 0.00 44.90 3.61
4783 11240 8.061268 CCAACCGAACAATTTTATTTTGTTGAG 58.939 33.333 6.53 1.35 44.90 3.02
4797 11254 3.888930 ACAAACTGATCCAACCGAACAAT 59.111 39.130 0.00 0.00 0.00 2.71
4803 11260 4.023279 TCAATCAACAAACTGATCCAACCG 60.023 41.667 0.00 0.00 34.90 4.44
4809 11266 5.220739 CGAGGGATCAATCAACAAACTGATC 60.221 44.000 0.00 2.92 42.21 2.92
4835 11292 3.258228 CAATAATTTCCCACCCGTTTGC 58.742 45.455 0.00 0.00 0.00 3.68
4850 11309 9.632638 ATCTCCATGTACACTTTTAGCAATAAT 57.367 29.630 0.00 0.00 0.00 1.28
4853 11312 7.112122 TGATCTCCATGTACACTTTTAGCAAT 58.888 34.615 0.00 0.00 0.00 3.56
4868 11327 8.529476 TCAGAATACTGTATCATGATCTCCATG 58.471 37.037 12.53 2.76 46.32 3.66
4871 11330 9.770097 TTTTCAGAATACTGTATCATGATCTCC 57.230 33.333 12.53 2.27 43.81 3.71
4891 11350 5.103290 AGCATTTGCAAAGCATTTTTCAG 57.897 34.783 25.24 6.87 45.16 3.02
4898 11357 3.527533 CACCATAGCATTTGCAAAGCAT 58.472 40.909 25.24 17.17 45.16 3.79
4900 11359 1.662122 GCACCATAGCATTTGCAAAGC 59.338 47.619 18.19 19.01 45.16 3.51
4901 11360 2.093869 AGGCACCATAGCATTTGCAAAG 60.094 45.455 18.19 10.61 45.16 2.77
4902 11361 1.901159 AGGCACCATAGCATTTGCAAA 59.099 42.857 15.44 15.44 45.16 3.68
4919 11378 6.586844 GGTTAACGAACTGAGATATGATAGGC 59.413 42.308 0.00 0.00 35.74 3.93
4952 11411 3.964688 TCTCTTCACCGGATAATGGCTAA 59.035 43.478 9.46 0.00 0.00 3.09
4953 11412 3.572642 TCTCTTCACCGGATAATGGCTA 58.427 45.455 9.46 0.00 0.00 3.93
4954 11413 2.398588 TCTCTTCACCGGATAATGGCT 58.601 47.619 9.46 0.00 0.00 4.75
4955 11414 2.910688 TCTCTTCACCGGATAATGGC 57.089 50.000 9.46 0.00 0.00 4.40
4956 11415 4.342862 ACATCTCTTCACCGGATAATGG 57.657 45.455 9.46 0.00 0.00 3.16
4957 11416 5.406780 GCTTACATCTCTTCACCGGATAATG 59.593 44.000 9.46 0.00 0.00 1.90
4958 11417 5.070446 TGCTTACATCTCTTCACCGGATAAT 59.930 40.000 9.46 0.00 0.00 1.28
4959 11418 4.404394 TGCTTACATCTCTTCACCGGATAA 59.596 41.667 9.46 0.00 0.00 1.75
4960 11419 3.958147 TGCTTACATCTCTTCACCGGATA 59.042 43.478 9.46 0.00 0.00 2.59
4986 12163 1.578583 AACCGAACAAGTCCTCAACG 58.421 50.000 0.00 0.00 0.00 4.10
4988 12165 2.680841 CACAAACCGAACAAGTCCTCAA 59.319 45.455 0.00 0.00 0.00 3.02
5014 12191 9.618890 TCAAAATCTTGTAAGAATCATCTAGGG 57.381 33.333 0.00 0.00 38.77 3.53
5021 12198 7.109501 TCCGGATCAAAATCTTGTAAGAATCA 58.890 34.615 0.00 0.00 38.77 2.57
5044 12221 5.047590 ACAAATTCTACACGGGGAAAATTCC 60.048 40.000 3.49 3.49 46.82 3.01
5045 12222 6.020971 ACAAATTCTACACGGGGAAAATTC 57.979 37.500 0.00 0.00 0.00 2.17
5047 12224 5.047590 GGAACAAATTCTACACGGGGAAAAT 60.048 40.000 0.00 0.00 34.98 1.82
5048 12225 4.278919 GGAACAAATTCTACACGGGGAAAA 59.721 41.667 0.00 0.00 34.98 2.29
5049 12226 3.822167 GGAACAAATTCTACACGGGGAAA 59.178 43.478 0.00 0.00 34.98 3.13
5050 12227 3.181442 TGGAACAAATTCTACACGGGGAA 60.181 43.478 0.00 0.00 34.98 3.97
5052 12229 2.486592 GTGGAACAAATTCTACACGGGG 59.513 50.000 0.00 0.00 43.80 5.73
5053 12230 3.824414 GTGGAACAAATTCTACACGGG 57.176 47.619 0.00 0.00 43.80 5.28
5070 12252 2.039746 TCTTGTACCCCTGTTCATGTGG 59.960 50.000 0.00 0.00 0.00 4.17
5075 12257 2.983192 TGGAATCTTGTACCCCTGTTCA 59.017 45.455 0.00 0.00 0.00 3.18
5082 12264 4.080299 ACAATCCTCTGGAATCTTGTACCC 60.080 45.833 3.18 0.00 32.70 3.69
5136 12366 3.130516 TGAGGTCTCACGTAATGCTAAGG 59.869 47.826 0.00 0.00 34.14 2.69
5166 12399 6.723298 TGCCAACTCAAATCCTTAGAAAAA 57.277 33.333 0.00 0.00 0.00 1.94
5234 12472 1.737793 GGCCTCGTTCAGTTTACATGG 59.262 52.381 0.00 0.00 0.00 3.66
5236 12474 2.301870 TGAGGCCTCGTTCAGTTTACAT 59.698 45.455 27.43 0.00 0.00 2.29
5299 12542 6.799441 TGTTTGACGATGAAATAACGATTTGG 59.201 34.615 0.00 0.00 35.33 3.28
5309 12552 5.278463 CCTTCTGGTTGTTTGACGATGAAAT 60.278 40.000 0.00 0.00 0.00 2.17
5336 12579 6.347696 TGGTTTCATTTCATGCTCTTGTTTT 58.652 32.000 0.00 0.00 0.00 2.43
5337 12580 5.916318 TGGTTTCATTTCATGCTCTTGTTT 58.084 33.333 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.