Multiple sequence alignment - TraesCS5B01G296900

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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 TraesCS5B01G296900 chr5B 100.000 4809 0 0 1 4809 479825573 479830381 0.000000e+00 8881.0
1 TraesCS5B01G296900 chr5D 91.423 4477 200 59 1 4364 399945251 399949656 0.000000e+00 5971.0
2 TraesCS5B01G296900 chr5D 86.000 100 14 0 3655 3754 546906678 546906579 1.830000e-19 108.0
3 TraesCS5B01G296900 chr5D 100.000 31 0 0 4779 4809 399949687 399949717 1.870000e-04 58.4
4 TraesCS5B01G296900 chr5A 93.182 2772 108 34 1 2711 505502009 505504760 0.000000e+00 3997.0
5 TraesCS5B01G296900 chr5A 92.748 979 54 9 3405 4375 505505915 505506884 0.000000e+00 1399.0
6 TraesCS5B01G296900 chr5A 91.748 618 27 6 2817 3410 505504921 505505538 0.000000e+00 837.0
7 TraesCS5B01G296900 chr5A 95.181 83 4 0 2709 2791 505504841 505504923 1.090000e-26 132.0
8 TraesCS5B01G296900 chr5A 82.927 123 17 4 4581 4700 607690344 607690465 1.830000e-19 108.0
9 TraesCS5B01G296900 chr7D 85.714 287 41 0 2351 2637 250670893 250671179 2.170000e-78 303.0
10 TraesCS5B01G296900 chr7B 85.366 287 42 0 2351 2637 227282175 227282461 1.010000e-76 298.0
11 TraesCS5B01G296900 chr7B 77.535 503 83 19 1739 2231 227281562 227282044 4.740000e-70 276.0
12 TraesCS5B01G296900 chr7A 85.366 287 42 0 2351 2637 270763544 270763258 1.010000e-76 298.0
13 TraesCS5B01G296900 chr7A 97.059 34 1 0 4617 4650 164810319 164810352 1.870000e-04 58.4
14 TraesCS5B01G296900 chr3B 77.941 204 31 12 4474 4672 394944259 394944065 1.090000e-21 115.0
15 TraesCS5B01G296900 chr2B 83.193 119 14 6 4627 4743 84974889 84974775 2.370000e-18 104.0
16 TraesCS5B01G296900 chr2B 75.536 233 35 16 4484 4711 754992845 754993060 1.420000e-15 95.3
17 TraesCS5B01G296900 chr2D 80.952 105 18 1 4595 4699 180882379 180882277 1.110000e-11 82.4
18 TraesCS5B01G296900 chr1D 91.525 59 5 0 4596 4654 16506531 16506589 1.110000e-11 82.4
19 TraesCS5B01G296900 chr2A 80.583 103 16 3 4597 4699 195314131 195314033 5.160000e-10 76.8
20 TraesCS5B01G296900 chr6B 92.105 38 3 0 4627 4664 682565726 682565689 2.000000e-03 54.7


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 TraesCS5B01G296900 chr5B 479825573 479830381 4808 False 8881.00 8881 100.00000 1 4809 1 chr5B.!!$F1 4808
1 TraesCS5B01G296900 chr5D 399945251 399949717 4466 False 3014.70 5971 95.71150 1 4809 2 chr5D.!!$F1 4808
2 TraesCS5B01G296900 chr5A 505502009 505506884 4875 False 1591.25 3997 93.21475 1 4375 4 chr5A.!!$F2 4374
3 TraesCS5B01G296900 chr7B 227281562 227282461 899 False 287.00 298 81.45050 1739 2637 2 chr7B.!!$F1 898

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
126 133 0.104671 CTTTGGTGCCCAACTTGGTG 59.895 55.0 7.06 0.1 43.82 4.17 F
137 144 0.180406 AACTTGGTGTCACTTCGCCT 59.820 50.0 2.35 0.0 38.63 5.52 F
222 242 0.321671 ACCACTGGTTCATCTCACGG 59.678 55.0 0.00 0.0 27.29 4.94 F
291 311 0.323360 TTGGCCACCAGCATAAGGTC 60.323 55.0 3.88 0.0 46.50 3.85 F
2162 2240 0.035317 TGCTTGGCTACTGTGTGGAG 59.965 55.0 0.00 0.0 0.00 3.86 F
3560 4164 0.251832 TGCCTCTCTTCTTCCCTCGT 60.252 55.0 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1436 0.740737 GTCAATACATGCTGGGTGGC 59.259 55.000 0.0 0.0 0.00 5.01 R
1442 1487 5.779529 ATATCCATTTTGGTGCTCATGTC 57.220 39.130 0.0 0.0 39.03 3.06 R
2162 2240 1.165270 CCACCAGACGTTGATTTCCC 58.835 55.000 0.0 0.0 0.00 3.97 R
2341 2432 9.463443 CACCTTTTCTTCCTTTTGTATGTAAAG 57.537 33.333 0.0 0.0 33.42 1.85 R
3802 4406 0.178903 TGAACTGGGTAGGTCAGGCT 60.179 55.000 0.0 0.0 45.47 4.58 R
4403 5031 0.321564 TGTTCATCCCGTGAGCTTGG 60.322 55.000 0.0 0.0 38.70 3.61 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
105 112 1.390123 CGTCGTCATTTGCATCTCGTT 59.610 47.619 0.00 0.00 0.00 3.85
126 133 0.104671 CTTTGGTGCCCAACTTGGTG 59.895 55.000 7.06 0.10 43.82 4.17
129 136 1.454847 GGTGCCCAACTTGGTGTCA 60.455 57.895 7.06 0.00 35.17 3.58
130 137 1.733526 GTGCCCAACTTGGTGTCAC 59.266 57.895 7.06 7.89 35.17 3.67
133 140 0.668535 GCCCAACTTGGTGTCACTTC 59.331 55.000 7.06 0.00 35.17 3.01
135 142 0.307760 CCAACTTGGTGTCACTTCGC 59.692 55.000 2.35 0.00 31.35 4.70
136 143 0.307760 CAACTTGGTGTCACTTCGCC 59.692 55.000 2.35 0.00 38.35 5.54
137 144 0.180406 AACTTGGTGTCACTTCGCCT 59.820 50.000 2.35 0.00 38.63 5.52
139 146 0.951040 CTTGGTGTCACTTCGCCTCC 60.951 60.000 2.35 0.00 38.63 4.30
140 147 1.691195 TTGGTGTCACTTCGCCTCCA 61.691 55.000 2.35 0.00 38.63 3.86
141 148 1.296715 GGTGTCACTTCGCCTCCAT 59.703 57.895 2.35 0.00 35.37 3.41
143 150 1.523758 GTGTCACTTCGCCTCCATTT 58.476 50.000 0.00 0.00 0.00 2.32
144 151 1.880027 GTGTCACTTCGCCTCCATTTT 59.120 47.619 0.00 0.00 0.00 1.82
217 237 2.363306 TTTGCACCACTGGTTCATCT 57.637 45.000 1.01 0.00 31.02 2.90
218 238 1.896220 TTGCACCACTGGTTCATCTC 58.104 50.000 1.01 0.00 31.02 2.75
219 239 0.764271 TGCACCACTGGTTCATCTCA 59.236 50.000 0.00 0.00 31.02 3.27
220 240 1.160137 GCACCACTGGTTCATCTCAC 58.840 55.000 0.00 0.00 31.02 3.51
221 241 1.432514 CACCACTGGTTCATCTCACG 58.567 55.000 0.00 0.00 31.02 4.35
222 242 0.321671 ACCACTGGTTCATCTCACGG 59.678 55.000 0.00 0.00 27.29 4.94
271 291 3.544834 CGCAGACAATGTGCACTTATAGC 60.545 47.826 19.41 11.97 41.26 2.97
279 299 1.401905 GTGCACTTATAGCTTGGCCAC 59.598 52.381 3.88 0.00 0.00 5.01
291 311 0.323360 TTGGCCACCAGCATAAGGTC 60.323 55.000 3.88 0.00 46.50 3.85
384 413 4.206477 TGCTCTGCTTTGTTCTAGCATA 57.794 40.909 0.00 0.00 46.63 3.14
392 421 6.649155 TGCTTTGTTCTAGCATATCCAACTA 58.351 36.000 0.00 0.00 43.30 2.24
405 434 0.620556 CCAACTAGGTGCCATCTGGT 59.379 55.000 0.87 0.00 37.57 4.00
419 448 3.610911 CATCTGGTTACCCTGTTTCTCC 58.389 50.000 0.00 0.00 0.00 3.71
422 451 2.637872 CTGGTTACCCTGTTTCTCCTCA 59.362 50.000 0.00 0.00 0.00 3.86
462 491 5.734550 CAGTTCAGACTTCCAGAGCTGGG 62.735 56.522 16.06 4.18 41.86 4.45
483 512 2.922740 AGTAACCGAGGTTTCTGCAA 57.077 45.000 13.18 0.00 39.31 4.08
567 596 3.334691 TGTGCACTCATAGTTTGGCTAC 58.665 45.455 19.41 0.00 31.59 3.58
568 597 2.348666 GTGCACTCATAGTTTGGCTACG 59.651 50.000 10.32 0.00 31.59 3.51
597 626 3.937706 AGATTGCACATAGAGTCAACAGC 59.062 43.478 0.00 0.00 0.00 4.40
598 627 2.837532 TGCACATAGAGTCAACAGCA 57.162 45.000 0.00 0.00 0.00 4.41
635 664 5.065218 GCATGGTCCAAGTTATTAGTGAGTG 59.935 44.000 0.00 0.00 0.00 3.51
677 706 1.338973 CTTGCAGCTCACCATGTGTTT 59.661 47.619 0.00 0.00 34.79 2.83
682 711 3.671433 GCAGCTCACCATGTGTTTGTATG 60.671 47.826 0.00 0.00 34.79 2.39
698 727 5.637006 TTGTATGGAAAATCGTGGAAAGG 57.363 39.130 0.00 0.00 0.00 3.11
790 824 2.042686 TTCCCAGTCAGTGCATATGC 57.957 50.000 21.09 21.09 42.50 3.14
819 854 2.609459 GACCTGTCATGAATTGCCTACG 59.391 50.000 0.00 0.00 0.00 3.51
863 899 7.174946 AGTTTTGTCACTCGGATATTTTCATGT 59.825 33.333 0.00 0.00 0.00 3.21
865 901 7.447374 TTGTCACTCGGATATTTTCATGTTT 57.553 32.000 0.00 0.00 0.00 2.83
891 927 4.212143 TGAGTGTCCTGATTGAGATTGG 57.788 45.455 0.00 0.00 0.00 3.16
1276 1312 4.195416 GGGTTCTCCAGAATCATCTTGTC 58.805 47.826 2.06 0.00 36.90 3.18
1278 1314 4.323792 GGTTCTCCAGAATCATCTTGTCCA 60.324 45.833 0.00 0.00 35.32 4.02
1280 1316 3.840078 TCTCCAGAATCATCTTGTCCACA 59.160 43.478 0.00 0.00 32.03 4.17
1335 1380 5.630121 TGGAACATCACATAGTGTTTCCTT 58.370 37.500 19.02 1.47 38.57 3.36
1442 1487 7.189693 TGCTATTGAGTAACAGAACAAGTTG 57.810 36.000 0.00 0.00 0.00 3.16
1443 1488 6.989759 TGCTATTGAGTAACAGAACAAGTTGA 59.010 34.615 10.54 0.00 0.00 3.18
1466 1511 7.005902 TGACATGAGCACCAAAATGGATATAT 58.994 34.615 0.00 0.00 40.96 0.86
1566 1611 5.308014 TCAGCATAGTCATTTGTCAACACT 58.692 37.500 0.00 0.00 0.00 3.55
1630 1679 7.658575 TGTACGGGCTAGGTATTTATTTCATTC 59.341 37.037 0.00 0.00 0.00 2.67
2095 2173 8.413229 TCTTGAACTTATTTTCCTCTTTTGGTG 58.587 33.333 0.00 0.00 0.00 4.17
2162 2240 0.035317 TGCTTGGCTACTGTGTGGAG 59.965 55.000 0.00 0.00 0.00 3.86
2341 2432 5.156804 TCTGACGTCTTTTCTGCTTTTTC 57.843 39.130 17.92 0.00 0.00 2.29
2582 2676 0.964700 CTCCTGATATGGCTGCTCGA 59.035 55.000 0.00 0.00 0.00 4.04
2757 2954 4.023707 GCACCAATGATAGGATTGTAGCAC 60.024 45.833 0.00 0.00 34.16 4.40
3088 3285 3.134804 GCAGAGTCTGGTTACATGGGTAT 59.865 47.826 21.54 0.00 31.21 2.73
3096 3293 5.825679 TCTGGTTACATGGGTATGTATTTGC 59.174 40.000 0.00 0.00 46.22 3.68
3097 3294 4.890581 TGGTTACATGGGTATGTATTTGCC 59.109 41.667 0.00 3.63 46.22 4.52
3106 3303 5.133660 TGGGTATGTATTTGCCTCCTAACAT 59.866 40.000 0.00 0.00 0.00 2.71
3131 3328 9.632638 ATTCTGACAGTACTATATTTTGCCAAT 57.367 29.630 1.59 0.00 0.00 3.16
3209 3425 4.910458 ACAAGAGTAGGGCATTAACACT 57.090 40.909 0.00 0.00 0.00 3.55
3212 3428 5.221843 ACAAGAGTAGGGCATTAACACTGAA 60.222 40.000 0.00 0.00 0.00 3.02
3214 3430 3.610911 AGTAGGGCATTAACACTGAAGC 58.389 45.455 0.00 0.00 0.00 3.86
3250 3466 7.857734 TGAACTTCAGAGAGTCTCATACTAG 57.142 40.000 22.05 12.89 39.07 2.57
3303 3522 5.180868 TGGGCGGAATTTGAATCAAAATTTG 59.819 36.000 12.75 0.00 39.31 2.32
3315 3534 8.665643 TGAATCAAAATTTGCTGTTCTTGATT 57.334 26.923 13.05 13.05 42.93 2.57
3333 3552 3.118408 TGATTTATGTCCTCCGGTTCAGG 60.118 47.826 0.00 0.13 0.00 3.86
3349 3568 5.465724 CGGTTCAGGGTGCTTACTATATTTC 59.534 44.000 0.00 0.00 0.00 2.17
3361 3580 4.278678 ACTATATTTCGTGCTGCTTTGC 57.721 40.909 0.00 0.00 0.00 3.68
3559 4163 0.459489 CTGCCTCTCTTCTTCCCTCG 59.541 60.000 0.00 0.00 0.00 4.63
3560 4164 0.251832 TGCCTCTCTTCTTCCCTCGT 60.252 55.000 0.00 0.00 0.00 4.18
3561 4165 1.005569 TGCCTCTCTTCTTCCCTCGTA 59.994 52.381 0.00 0.00 0.00 3.43
3631 4235 7.319646 ACAGCTTGAAACAAATTTGAACACTA 58.680 30.769 24.64 8.66 0.00 2.74
3802 4406 4.617959 CTCCTAACACAACGACTTCAGAA 58.382 43.478 0.00 0.00 0.00 3.02
4091 4709 3.495193 CCATTGTGATTTTGAGCTGACG 58.505 45.455 0.00 0.00 0.00 4.35
4112 4730 6.204688 TGACGCCCATTGATTTGTATAATCTC 59.795 38.462 0.00 0.00 0.00 2.75
4136 4754 3.069586 TGAACTCGAAGTTGGTGTGAGAT 59.930 43.478 5.20 0.00 38.80 2.75
4142 4760 2.847327 AGTTGGTGTGAGATGTGAGG 57.153 50.000 0.00 0.00 0.00 3.86
4209 4834 7.681939 TCAAAATTATGTGAGACTTGGTACC 57.318 36.000 4.43 4.43 0.00 3.34
4324 4949 0.177836 TATCCGTGCACCTGTGATGG 59.822 55.000 12.15 4.70 0.00 3.51
4365 4993 5.988287 TGGTGAGATGATAGTGCAATACAA 58.012 37.500 0.00 0.00 0.00 2.41
4366 4994 5.817296 TGGTGAGATGATAGTGCAATACAAC 59.183 40.000 0.00 0.00 0.00 3.32
4367 4995 5.050769 GGTGAGATGATAGTGCAATACAACG 60.051 44.000 0.00 0.00 0.00 4.10
4368 4996 5.520288 GTGAGATGATAGTGCAATACAACGT 59.480 40.000 0.00 0.00 0.00 3.99
4369 4997 6.695713 GTGAGATGATAGTGCAATACAACGTA 59.304 38.462 0.00 0.00 0.00 3.57
4392 5020 9.298113 CGTAAGTTGTACGAATTTAAGTGAAAG 57.702 33.333 0.34 0.00 42.94 2.62
4396 5024 9.538508 AGTTGTACGAATTTAAGTGAAAGTACT 57.461 29.630 0.00 0.00 35.56 2.73
4397 5025 9.789029 GTTGTACGAATTTAAGTGAAAGTACTC 57.211 33.333 0.00 0.00 35.56 2.59
4398 5026 9.754382 TTGTACGAATTTAAGTGAAAGTACTCT 57.246 29.630 0.00 0.00 35.56 3.24
4399 5027 9.754382 TGTACGAATTTAAGTGAAAGTACTCTT 57.246 29.630 0.00 0.00 35.56 2.85
4403 5031 9.595357 CGAATTTAAGTGAAAGTACTCTTTTCC 57.405 33.333 0.00 0.00 42.99 3.13
4404 5032 9.894783 GAATTTAAGTGAAAGTACTCTTTTCCC 57.105 33.333 0.00 0.00 42.99 3.97
4405 5033 8.990163 ATTTAAGTGAAAGTACTCTTTTCCCA 57.010 30.769 0.00 0.00 42.99 4.37
4406 5034 8.810990 TTTAAGTGAAAGTACTCTTTTCCCAA 57.189 30.769 0.00 0.00 42.99 4.12
4407 5035 6.944234 AAGTGAAAGTACTCTTTTCCCAAG 57.056 37.500 0.00 0.00 42.99 3.61
4408 5036 4.822350 AGTGAAAGTACTCTTTTCCCAAGC 59.178 41.667 0.00 0.00 42.99 4.01
4409 5037 4.822350 GTGAAAGTACTCTTTTCCCAAGCT 59.178 41.667 0.00 0.00 42.99 3.74
4410 5038 5.049336 GTGAAAGTACTCTTTTCCCAAGCTC 60.049 44.000 0.00 0.00 42.99 4.09
4411 5039 4.706842 AAGTACTCTTTTCCCAAGCTCA 57.293 40.909 0.00 0.00 0.00 4.26
4412 5040 4.009370 AGTACTCTTTTCCCAAGCTCAC 57.991 45.455 0.00 0.00 0.00 3.51
4413 5041 1.884235 ACTCTTTTCCCAAGCTCACG 58.116 50.000 0.00 0.00 0.00 4.35
4414 5042 1.160137 CTCTTTTCCCAAGCTCACGG 58.840 55.000 0.00 0.00 0.00 4.94
4415 5043 0.250727 TCTTTTCCCAAGCTCACGGG 60.251 55.000 9.14 9.14 44.60 5.28
4418 5046 2.989639 TCCCAAGCTCACGGGATG 59.010 61.111 13.23 0.00 46.93 3.51
4419 5047 1.612146 TCCCAAGCTCACGGGATGA 60.612 57.895 13.23 0.00 46.93 2.92
4420 5048 1.198094 TCCCAAGCTCACGGGATGAA 61.198 55.000 13.23 0.00 46.93 2.57
4421 5049 1.026718 CCCAAGCTCACGGGATGAAC 61.027 60.000 9.73 0.00 46.34 3.18
4422 5050 0.321564 CCAAGCTCACGGGATGAACA 60.322 55.000 0.00 0.00 36.69 3.18
4423 5051 1.522668 CAAGCTCACGGGATGAACAA 58.477 50.000 0.00 0.00 36.69 2.83
4424 5052 2.086869 CAAGCTCACGGGATGAACAAT 58.913 47.619 0.00 0.00 36.69 2.71
4425 5053 3.270027 CAAGCTCACGGGATGAACAATA 58.730 45.455 0.00 0.00 36.69 1.90
4426 5054 3.627395 AGCTCACGGGATGAACAATAA 57.373 42.857 0.00 0.00 36.69 1.40
4427 5055 3.950397 AGCTCACGGGATGAACAATAAA 58.050 40.909 0.00 0.00 36.69 1.40
4428 5056 4.331968 AGCTCACGGGATGAACAATAAAA 58.668 39.130 0.00 0.00 36.69 1.52
4429 5057 4.949856 AGCTCACGGGATGAACAATAAAAT 59.050 37.500 0.00 0.00 36.69 1.82
4430 5058 5.066505 AGCTCACGGGATGAACAATAAAATC 59.933 40.000 0.00 0.00 36.69 2.17
4431 5059 5.163663 GCTCACGGGATGAACAATAAAATCA 60.164 40.000 0.00 0.00 36.69 2.57
4432 5060 6.435430 TCACGGGATGAACAATAAAATCAG 57.565 37.500 0.00 0.00 33.02 2.90
4433 5061 5.356751 TCACGGGATGAACAATAAAATCAGG 59.643 40.000 0.00 0.00 33.02 3.86
4434 5062 5.356751 CACGGGATGAACAATAAAATCAGGA 59.643 40.000 0.00 0.00 0.00 3.86
4435 5063 5.949354 ACGGGATGAACAATAAAATCAGGAA 59.051 36.000 0.00 0.00 0.00 3.36
4436 5064 6.435904 ACGGGATGAACAATAAAATCAGGAAA 59.564 34.615 0.00 0.00 0.00 3.13
4437 5065 7.039363 ACGGGATGAACAATAAAATCAGGAAAA 60.039 33.333 0.00 0.00 0.00 2.29
4438 5066 7.816995 CGGGATGAACAATAAAATCAGGAAAAA 59.183 33.333 0.00 0.00 0.00 1.94
4507 5135 7.692908 TTTTGAGTGCTTGTAAAATTACAGC 57.307 32.000 15.00 15.00 43.77 4.40
4508 5136 5.029650 TGAGTGCTTGTAAAATTACAGCG 57.970 39.130 15.97 9.82 43.77 5.18
4509 5137 4.513692 TGAGTGCTTGTAAAATTACAGCGT 59.486 37.500 15.97 10.08 43.77 5.07
4510 5138 5.008217 TGAGTGCTTGTAAAATTACAGCGTT 59.992 36.000 15.97 10.42 43.77 4.84
4511 5139 6.203145 TGAGTGCTTGTAAAATTACAGCGTTA 59.797 34.615 15.97 6.70 43.77 3.18
4512 5140 6.961576 AGTGCTTGTAAAATTACAGCGTTAA 58.038 32.000 15.97 0.71 43.77 2.01
4513 5141 7.419204 AGTGCTTGTAAAATTACAGCGTTAAA 58.581 30.769 15.97 0.20 43.77 1.52
4514 5142 8.079809 AGTGCTTGTAAAATTACAGCGTTAAAT 58.920 29.630 15.97 3.64 43.77 1.40
4515 5143 8.153411 GTGCTTGTAAAATTACAGCGTTAAATG 58.847 33.333 15.97 0.00 43.77 2.32
4516 5144 8.076781 TGCTTGTAAAATTACAGCGTTAAATGA 58.923 29.630 15.97 0.00 43.77 2.57
4517 5145 8.363029 GCTTGTAAAATTACAGCGTTAAATGAC 58.637 33.333 6.16 0.00 43.77 3.06
4518 5146 9.388346 CTTGTAAAATTACAGCGTTAAATGACA 57.612 29.630 6.16 0.00 43.77 3.58
4519 5147 9.900710 TTGTAAAATTACAGCGTTAAATGACAT 57.099 25.926 6.16 0.00 43.77 3.06
4520 5148 9.900710 TGTAAAATTACAGCGTTAAATGACATT 57.099 25.926 1.96 0.00 38.64 2.71
4523 5151 8.810652 AAATTACAGCGTTAAATGACATTTGT 57.189 26.923 21.21 13.28 33.82 2.83
4524 5152 9.900710 AAATTACAGCGTTAAATGACATTTGTA 57.099 25.926 21.21 12.39 33.82 2.41
4525 5153 9.554724 AATTACAGCGTTAAATGACATTTGTAG 57.445 29.630 21.21 13.16 33.82 2.74
4526 5154 6.795098 ACAGCGTTAAATGACATTTGTAGA 57.205 33.333 21.21 0.68 33.82 2.59
4527 5155 7.197071 ACAGCGTTAAATGACATTTGTAGAA 57.803 32.000 21.21 6.69 33.82 2.10
4528 5156 7.298122 ACAGCGTTAAATGACATTTGTAGAAG 58.702 34.615 21.21 10.77 33.82 2.85
4529 5157 7.041372 ACAGCGTTAAATGACATTTGTAGAAGT 60.041 33.333 21.21 11.30 33.82 3.01
4530 5158 7.478667 CAGCGTTAAATGACATTTGTAGAAGTC 59.521 37.037 21.21 4.72 33.82 3.01
4531 5159 6.461698 GCGTTAAATGACATTTGTAGAAGTCG 59.538 38.462 21.21 13.91 33.83 4.18
4532 5160 7.507304 CGTTAAATGACATTTGTAGAAGTCGT 58.493 34.615 21.21 0.00 33.83 4.34
4533 5161 7.474332 CGTTAAATGACATTTGTAGAAGTCGTG 59.526 37.037 21.21 0.00 33.83 4.35
4534 5162 5.862924 AATGACATTTGTAGAAGTCGTGG 57.137 39.130 0.00 0.00 33.83 4.94
4535 5163 4.594123 TGACATTTGTAGAAGTCGTGGA 57.406 40.909 0.00 0.00 33.83 4.02
4536 5164 4.951254 TGACATTTGTAGAAGTCGTGGAA 58.049 39.130 0.00 0.00 33.83 3.53
4537 5165 5.361427 TGACATTTGTAGAAGTCGTGGAAA 58.639 37.500 0.00 0.00 33.83 3.13
4538 5166 5.818336 TGACATTTGTAGAAGTCGTGGAAAA 59.182 36.000 0.00 0.00 33.83 2.29
4539 5167 6.316640 TGACATTTGTAGAAGTCGTGGAAAAA 59.683 34.615 0.00 0.00 33.83 1.94
4565 5193 7.647907 AGACAAAATCATCACTCAAAAATGC 57.352 32.000 0.00 0.00 0.00 3.56
4566 5194 7.439381 AGACAAAATCATCACTCAAAAATGCT 58.561 30.769 0.00 0.00 0.00 3.79
4567 5195 7.929785 AGACAAAATCATCACTCAAAAATGCTT 59.070 29.630 0.00 0.00 0.00 3.91
4568 5196 8.441312 ACAAAATCATCACTCAAAAATGCTTT 57.559 26.923 0.00 0.00 0.00 3.51
4569 5197 8.895737 ACAAAATCATCACTCAAAAATGCTTTT 58.104 25.926 0.00 0.00 35.02 2.27
4586 5214 7.775397 ATGCTTTTGGAAATGATATTTTCGG 57.225 32.000 0.00 0.00 36.63 4.30
4587 5215 6.696411 TGCTTTTGGAAATGATATTTTCGGT 58.304 32.000 0.00 0.00 36.63 4.69
4588 5216 6.589523 TGCTTTTGGAAATGATATTTTCGGTG 59.410 34.615 0.00 0.00 36.63 4.94
4589 5217 6.455513 GCTTTTGGAAATGATATTTTCGGTGC 60.456 38.462 0.00 0.00 36.63 5.01
4590 5218 5.651387 TTGGAAATGATATTTTCGGTGCA 57.349 34.783 0.00 0.00 36.63 4.57
4591 5219 5.850557 TGGAAATGATATTTTCGGTGCAT 57.149 34.783 0.00 0.00 36.63 3.96
4592 5220 5.830912 TGGAAATGATATTTTCGGTGCATC 58.169 37.500 0.00 0.00 36.63 3.91
4593 5221 5.359292 TGGAAATGATATTTTCGGTGCATCA 59.641 36.000 0.00 0.00 36.63 3.07
4594 5222 6.040729 TGGAAATGATATTTTCGGTGCATCAT 59.959 34.615 0.00 0.00 37.82 2.45
4595 5223 6.925165 GGAAATGATATTTTCGGTGCATCATT 59.075 34.615 0.00 0.00 44.26 2.57
4597 5225 8.721019 AAATGATATTTTCGGTGCATCATTTT 57.279 26.923 11.45 0.63 46.45 1.82
4598 5226 8.721019 AATGATATTTTCGGTGCATCATTTTT 57.279 26.923 0.00 0.00 41.31 1.94
4622 5250 5.518848 TTTTGCCATGGCTTCTACATATG 57.481 39.130 35.53 0.00 42.51 1.78
4623 5251 3.862877 TGCCATGGCTTCTACATATGT 57.137 42.857 35.53 13.93 42.51 2.29
4624 5252 3.743521 TGCCATGGCTTCTACATATGTC 58.256 45.455 35.53 3.76 42.51 3.06
4625 5253 3.136260 TGCCATGGCTTCTACATATGTCA 59.864 43.478 35.53 8.95 42.51 3.58
4626 5254 4.202493 TGCCATGGCTTCTACATATGTCAT 60.202 41.667 35.53 5.65 42.51 3.06
4627 5255 4.763793 GCCATGGCTTCTACATATGTCATT 59.236 41.667 29.98 0.00 38.26 2.57
4628 5256 5.242393 GCCATGGCTTCTACATATGTCATTT 59.758 40.000 29.98 0.00 38.26 2.32
4629 5257 6.569226 GCCATGGCTTCTACATATGTCATTTC 60.569 42.308 29.98 0.42 38.26 2.17
4630 5258 6.487668 CCATGGCTTCTACATATGTCATTTCA 59.512 38.462 12.68 5.97 0.00 2.69
4631 5259 7.176165 CCATGGCTTCTACATATGTCATTTCAT 59.824 37.037 12.68 7.94 0.00 2.57
4632 5260 7.500720 TGGCTTCTACATATGTCATTTCATG 57.499 36.000 12.68 0.00 0.00 3.07
4633 5261 7.281841 TGGCTTCTACATATGTCATTTCATGA 58.718 34.615 12.68 0.00 36.84 3.07
4634 5262 7.940688 TGGCTTCTACATATGTCATTTCATGAT 59.059 33.333 12.68 0.00 42.04 2.45
4635 5263 8.235226 GGCTTCTACATATGTCATTTCATGATG 58.765 37.037 12.68 0.00 42.04 3.07
4636 5264 8.996271 GCTTCTACATATGTCATTTCATGATGA 58.004 33.333 12.68 0.00 42.04 2.92
4648 5276 5.910637 TTTCATGATGAAACTTTGCAAGC 57.089 34.783 16.04 0.00 41.02 4.01
4649 5277 4.587584 TCATGATGAAACTTTGCAAGCA 57.412 36.364 0.00 0.00 0.00 3.91
4650 5278 5.142061 TCATGATGAAACTTTGCAAGCAT 57.858 34.783 0.00 0.10 0.00 3.79
4651 5279 5.543714 TCATGATGAAACTTTGCAAGCATT 58.456 33.333 0.00 0.00 0.00 3.56
4652 5280 6.073494 TTCATGATGAAACTTTGCAAGCATTG 60.073 34.615 5.21 0.00 40.56 2.82
4653 5281 8.165185 TTCATGATGAAACTTTGCAAGCATTGA 61.165 33.333 5.21 0.23 40.23 2.57
4675 5303 5.850557 ACACCATTTGTCAATCTTTGTCA 57.149 34.783 0.00 0.00 29.79 3.58
4676 5304 5.591099 ACACCATTTGTCAATCTTTGTCAC 58.409 37.500 0.00 0.00 29.79 3.67
4677 5305 5.126869 ACACCATTTGTCAATCTTTGTCACA 59.873 36.000 0.00 0.00 29.79 3.58
4678 5306 6.041511 CACCATTTGTCAATCTTTGTCACAA 58.958 36.000 0.00 0.00 0.00 3.33
4679 5307 6.019640 CACCATTTGTCAATCTTTGTCACAAC 60.020 38.462 0.00 0.00 0.00 3.32
4680 5308 6.041511 CCATTTGTCAATCTTTGTCACAACA 58.958 36.000 0.00 0.00 0.00 3.33
4681 5309 6.534436 CCATTTGTCAATCTTTGTCACAACAA 59.466 34.615 0.00 0.00 43.58 2.83
4744 5372 8.635765 TTTTGATTTTACTATTCACCAGAGCT 57.364 30.769 0.00 0.00 0.00 4.09
4745 5373 8.635765 TTTGATTTTACTATTCACCAGAGCTT 57.364 30.769 0.00 0.00 0.00 3.74
4746 5374 7.615582 TGATTTTACTATTCACCAGAGCTTG 57.384 36.000 0.00 0.00 0.00 4.01
4747 5375 7.168219 TGATTTTACTATTCACCAGAGCTTGT 58.832 34.615 0.00 0.00 0.00 3.16
4748 5376 8.318412 TGATTTTACTATTCACCAGAGCTTGTA 58.682 33.333 0.00 0.00 0.00 2.41
4749 5377 8.723942 ATTTTACTATTCACCAGAGCTTGTAG 57.276 34.615 0.00 0.00 0.00 2.74
4750 5378 6.852420 TTACTATTCACCAGAGCTTGTAGT 57.148 37.500 0.00 0.00 0.00 2.73
4751 5379 7.949690 TTACTATTCACCAGAGCTTGTAGTA 57.050 36.000 0.00 0.00 0.00 1.82
4752 5380 8.534954 TTACTATTCACCAGAGCTTGTAGTAT 57.465 34.615 0.00 0.00 0.00 2.12
4753 5381 6.810911 ACTATTCACCAGAGCTTGTAGTATG 58.189 40.000 0.00 0.00 0.00 2.39
4754 5382 4.471904 TTCACCAGAGCTTGTAGTATGG 57.528 45.455 0.00 0.00 0.00 2.74
4755 5383 2.168521 TCACCAGAGCTTGTAGTATGGC 59.831 50.000 0.00 0.00 0.00 4.40
4756 5384 2.093500 CACCAGAGCTTGTAGTATGGCA 60.093 50.000 0.00 0.00 0.00 4.92
4757 5385 2.571653 ACCAGAGCTTGTAGTATGGCAA 59.428 45.455 0.00 0.00 0.00 4.52
4758 5386 3.201290 CCAGAGCTTGTAGTATGGCAAG 58.799 50.000 0.00 0.00 43.42 4.01
4759 5387 3.118629 CCAGAGCTTGTAGTATGGCAAGA 60.119 47.826 8.27 0.00 43.29 3.02
4760 5388 4.507710 CAGAGCTTGTAGTATGGCAAGAA 58.492 43.478 8.27 0.00 43.29 2.52
4761 5389 4.569966 CAGAGCTTGTAGTATGGCAAGAAG 59.430 45.833 8.27 0.00 43.29 2.85
4762 5390 4.467795 AGAGCTTGTAGTATGGCAAGAAGA 59.532 41.667 8.27 0.00 43.29 2.87
4763 5391 5.046304 AGAGCTTGTAGTATGGCAAGAAGAA 60.046 40.000 8.27 0.00 43.29 2.52
4764 5392 4.938226 AGCTTGTAGTATGGCAAGAAGAAC 59.062 41.667 8.27 0.00 43.29 3.01
4765 5393 4.695455 GCTTGTAGTATGGCAAGAAGAACA 59.305 41.667 8.27 0.00 43.29 3.18
4766 5394 5.355350 GCTTGTAGTATGGCAAGAAGAACAT 59.645 40.000 8.27 0.00 43.29 2.71
4767 5395 6.457528 GCTTGTAGTATGGCAAGAAGAACATC 60.458 42.308 8.27 0.00 43.29 3.06
4768 5396 6.299805 TGTAGTATGGCAAGAAGAACATCT 57.700 37.500 0.00 0.00 0.00 2.90
4769 5397 6.341316 TGTAGTATGGCAAGAAGAACATCTC 58.659 40.000 0.00 0.00 0.00 2.75
4770 5398 5.690464 AGTATGGCAAGAAGAACATCTCT 57.310 39.130 0.00 0.00 35.13 3.10
4771 5399 6.798427 AGTATGGCAAGAAGAACATCTCTA 57.202 37.500 0.00 0.00 32.46 2.43
4772 5400 7.372260 AGTATGGCAAGAAGAACATCTCTAT 57.628 36.000 0.00 0.00 32.46 1.98
4773 5401 7.215789 AGTATGGCAAGAAGAACATCTCTATG 58.784 38.462 0.00 0.00 39.17 2.23
4775 5403 6.544928 TGGCAAGAAGAACATCTCTATGTA 57.455 37.500 0.00 0.00 45.79 2.29
4776 5404 6.341316 TGGCAAGAAGAACATCTCTATGTAC 58.659 40.000 0.00 0.00 45.79 2.90
4777 5405 6.070824 TGGCAAGAAGAACATCTCTATGTACA 60.071 38.462 0.00 0.00 45.79 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 150 5.184864 TGGAAGTCTGAACTGAAAGCAAAAA 59.815 36.000 0.00 0.00 37.60 1.94
144 151 4.704540 TGGAAGTCTGAACTGAAAGCAAAA 59.295 37.500 0.00 0.00 37.60 2.44
146 153 3.879295 CTGGAAGTCTGAACTGAAAGCAA 59.121 43.478 0.00 0.00 37.60 3.91
147 154 3.470709 CTGGAAGTCTGAACTGAAAGCA 58.529 45.455 0.00 0.00 37.60 3.91
181 200 7.655732 GTGGTGCAAAAACCTCAATTACTAATT 59.344 33.333 0.00 0.00 41.16 1.40
183 202 6.322712 AGTGGTGCAAAAACCTCAATTACTAA 59.677 34.615 0.00 0.00 41.16 2.24
199 218 1.142667 TGAGATGAACCAGTGGTGCAA 59.857 47.619 27.21 7.74 45.47 4.08
217 237 2.093341 GGTTTCTACCATAAGCCCGTGA 60.093 50.000 0.00 0.00 44.36 4.35
218 238 2.285977 GGTTTCTACCATAAGCCCGTG 58.714 52.381 0.00 0.00 44.36 4.94
219 239 1.134610 CGGTTTCTACCATAAGCCCGT 60.135 52.381 0.00 0.00 45.31 5.28
220 240 1.137479 TCGGTTTCTACCATAAGCCCG 59.863 52.381 0.00 0.00 45.31 6.13
221 241 2.994186 TCGGTTTCTACCATAAGCCC 57.006 50.000 0.00 0.00 45.31 5.19
222 242 4.879545 TCATTTCGGTTTCTACCATAAGCC 59.120 41.667 0.00 0.00 45.31 4.35
246 266 1.877637 AGTGCACATTGTCTGCGTTA 58.122 45.000 21.04 0.00 37.46 3.18
271 291 0.323725 ACCTTATGCTGGTGGCCAAG 60.324 55.000 7.24 2.68 40.92 3.61
279 299 0.599991 TATGCGCGACCTTATGCTGG 60.600 55.000 12.10 0.00 0.00 4.85
291 311 3.039405 TGTTTGTTTCAGTTTATGCGCG 58.961 40.909 0.00 0.00 0.00 6.86
346 374 3.787001 AAGCCAGCCTAGACCGCC 61.787 66.667 0.00 0.00 0.00 6.13
347 375 2.512515 CAAGCCAGCCTAGACCGC 60.513 66.667 0.00 0.00 0.00 5.68
348 376 2.512515 GCAAGCCAGCCTAGACCG 60.513 66.667 0.00 0.00 0.00 4.79
349 377 1.153269 GAGCAAGCCAGCCTAGACC 60.153 63.158 0.00 0.00 34.23 3.85
384 413 1.492176 CCAGATGGCACCTAGTTGGAT 59.508 52.381 0.00 0.00 39.71 3.41
405 434 2.904434 GAGGTGAGGAGAAACAGGGTAA 59.096 50.000 0.00 0.00 0.00 2.85
419 448 3.822735 TGAAAGCAGAAAATGGAGGTGAG 59.177 43.478 0.00 0.00 0.00 3.51
422 451 3.837355 ACTGAAAGCAGAAAATGGAGGT 58.163 40.909 0.00 0.00 45.17 3.85
462 491 3.308438 TGCAGAAACCTCGGTTACTAC 57.692 47.619 1.08 0.00 37.35 2.73
465 494 2.215196 TGTTGCAGAAACCTCGGTTAC 58.785 47.619 1.08 0.00 38.06 2.50
470 499 3.461843 GCTTGTTGCAGAAACCTCG 57.538 52.632 0.00 0.00 42.31 4.63
483 512 2.620115 CTGATGGTGAAACAGTGCTTGT 59.380 45.455 0.00 0.00 43.45 3.16
513 542 7.463913 GCGTTGTCATTTTCAGTTTCAATTTCA 60.464 33.333 0.00 0.00 0.00 2.69
518 547 4.738124 TGCGTTGTCATTTTCAGTTTCAA 58.262 34.783 0.00 0.00 0.00 2.69
557 586 0.392998 CTCATGCCCGTAGCCAAACT 60.393 55.000 0.00 0.00 42.71 2.66
567 596 1.534163 CTATGTGCAATCTCATGCCCG 59.466 52.381 0.00 0.00 45.83 6.13
568 597 2.812591 CTCTATGTGCAATCTCATGCCC 59.187 50.000 0.00 0.00 45.83 5.36
609 638 5.185454 TCACTAATAACTTGGACCATGCTG 58.815 41.667 7.28 0.00 0.00 4.41
617 646 6.722590 TGTCCTACACTCACTAATAACTTGGA 59.277 38.462 0.00 0.00 0.00 3.53
621 650 6.895756 TCCATGTCCTACACTCACTAATAACT 59.104 38.462 0.00 0.00 0.00 2.24
635 664 8.669243 GCAAGCTTTTATATATCCATGTCCTAC 58.331 37.037 0.00 0.00 0.00 3.18
671 700 4.822350 TCCACGATTTTCCATACAAACACA 59.178 37.500 0.00 0.00 0.00 3.72
677 706 4.698304 GTCCTTTCCACGATTTTCCATACA 59.302 41.667 0.00 0.00 0.00 2.29
682 711 2.510613 TGGTCCTTTCCACGATTTTCC 58.489 47.619 0.00 0.00 31.96 3.13
698 727 0.248866 CCGTGTTGTGCCTTTTGGTC 60.249 55.000 0.00 0.00 42.99 4.02
790 824 5.575606 GCAATTCATGACAGGTCAAAGATTG 59.424 40.000 19.52 19.52 43.58 2.67
803 838 6.959361 ACATAAATCGTAGGCAATTCATGAC 58.041 36.000 0.00 0.00 37.30 3.06
863 899 5.046376 TCTCAATCAGGACACTCATAGCAAA 60.046 40.000 0.00 0.00 0.00 3.68
865 901 4.026052 TCTCAATCAGGACACTCATAGCA 58.974 43.478 0.00 0.00 0.00 3.49
891 927 9.708222 CATCAATACAAATGCTTACAAGAGTAC 57.292 33.333 0.00 0.00 0.00 2.73
1380 1425 1.406341 GCTGGGTGGCGATACTACAAA 60.406 52.381 0.00 0.00 0.00 2.83
1391 1436 0.740737 GTCAATACATGCTGGGTGGC 59.259 55.000 0.00 0.00 0.00 5.01
1442 1487 5.779529 ATATCCATTTTGGTGCTCATGTC 57.220 39.130 0.00 0.00 39.03 3.06
1443 1488 7.005902 TCATATATCCATTTTGGTGCTCATGT 58.994 34.615 0.00 0.00 39.03 3.21
1466 1511 6.289834 TCCCTCACTTGTAACGTTAAAATCA 58.710 36.000 11.28 1.97 0.00 2.57
1538 1583 8.143193 TGTTGACAAATGACTATGCTGAAAATT 58.857 29.630 0.00 0.00 0.00 1.82
1566 1611 8.928448 AGCTGATAGGTAAGATAATCTGAAACA 58.072 33.333 0.00 0.00 0.00 2.83
2162 2240 1.165270 CCACCAGACGTTGATTTCCC 58.835 55.000 0.00 0.00 0.00 3.97
2341 2432 9.463443 CACCTTTTCTTCCTTTTGTATGTAAAG 57.537 33.333 0.00 0.00 33.42 1.85
2582 2676 0.965363 GGACACGGGTGGAATGCAAT 60.965 55.000 0.00 0.00 34.19 3.56
2703 2817 9.994432 CATGAAGTGAAATAAACAGGTATCTTC 57.006 33.333 0.00 0.00 0.00 2.87
2720 2917 3.500448 TTGGTGCCTAACATGAAGTGA 57.500 42.857 0.00 0.00 0.00 3.41
2723 2920 5.240183 CCTATCATTGGTGCCTAACATGAAG 59.760 44.000 0.00 0.00 0.00 3.02
2757 2954 6.205853 AGCTATAATGAAGGTCGTCTGACTAG 59.794 42.308 6.21 0.00 44.83 2.57
2824 3021 4.910458 ACTGGTGGAACTACAGCTATTT 57.090 40.909 0.00 0.00 39.48 1.40
3088 3285 5.880332 GTCAGAATGTTAGGAGGCAAATACA 59.120 40.000 0.00 0.00 37.40 2.29
3096 3293 5.923733 AGTACTGTCAGAATGTTAGGAGG 57.076 43.478 6.91 0.00 37.40 4.30
3106 3303 9.461312 AATTGGCAAAATATAGTACTGTCAGAA 57.539 29.630 6.91 0.00 0.00 3.02
3209 3425 2.031258 TCAAACCGTTGACTGCTTCA 57.969 45.000 0.00 0.00 38.88 3.02
3212 3428 2.038387 AGTTCAAACCGTTGACTGCT 57.962 45.000 0.00 0.00 43.52 4.24
3214 3430 3.621268 TCTGAAGTTCAAACCGTTGACTG 59.379 43.478 7.06 0.00 43.52 3.51
3250 3466 4.797471 TGCTTGTTTACATGATTGCAGTC 58.203 39.130 0.00 1.56 0.00 3.51
3303 3522 4.034510 CGGAGGACATAAATCAAGAACAGC 59.965 45.833 0.00 0.00 0.00 4.40
3333 3552 4.318831 GCAGCACGAAATATAGTAAGCACC 60.319 45.833 0.00 0.00 0.00 5.01
3349 3568 2.427410 GGAACGCAAAGCAGCACG 60.427 61.111 0.00 0.00 0.00 5.34
3403 3624 6.401047 ACCAATCAGAATATGCAAATCAGG 57.599 37.500 0.00 0.00 0.00 3.86
3559 4163 1.130561 GGGAGTGCGCAACAAAGATAC 59.869 52.381 14.00 0.00 0.00 2.24
3560 4164 1.003118 AGGGAGTGCGCAACAAAGATA 59.997 47.619 14.00 0.00 0.00 1.98
3561 4165 0.250901 AGGGAGTGCGCAACAAAGAT 60.251 50.000 14.00 0.00 0.00 2.40
3639 4243 2.694628 AGCTGCATTCAACACAAGGAAA 59.305 40.909 1.02 0.00 0.00 3.13
3640 4244 2.309613 AGCTGCATTCAACACAAGGAA 58.690 42.857 1.02 0.00 0.00 3.36
3643 4247 1.790623 GCAAGCTGCATTCAACACAAG 59.209 47.619 1.02 0.00 44.26 3.16
3645 4249 3.573569 GCAAGCTGCATTCAACACA 57.426 47.368 1.02 0.00 44.26 3.72
3694 4298 1.079750 GCTGGGTCTGAACTCCGAC 60.080 63.158 0.00 0.00 0.00 4.79
3802 4406 0.178903 TGAACTGGGTAGGTCAGGCT 60.179 55.000 0.00 0.00 45.47 4.58
3812 4416 4.202567 ACATACATCCTTGTTGAACTGGGT 60.203 41.667 0.00 0.00 37.28 4.51
3813 4417 4.335416 ACATACATCCTTGTTGAACTGGG 58.665 43.478 0.00 0.00 37.28 4.45
4091 4709 6.716628 TCAGGAGATTATACAAATCAATGGGC 59.283 38.462 1.01 0.00 0.00 5.36
4112 4730 1.867233 CACACCAACTTCGAGTTCAGG 59.133 52.381 0.00 0.00 36.03 3.86
4136 4754 6.601613 GGACAATAATGTTACCATTCCTCACA 59.398 38.462 0.00 0.00 41.50 3.58
4168 4793 3.370840 TTGATCAGGCAAGCAGGTAAT 57.629 42.857 0.00 0.00 0.00 1.89
4209 4834 1.160137 GAGGCCAACAAGCAGTAGTG 58.840 55.000 5.01 0.00 0.00 2.74
4324 4949 0.802494 CAGACACCGGCATTACAACC 59.198 55.000 0.00 0.00 0.00 3.77
4365 4993 7.928908 TCACTTAAATTCGTACAACTTACGT 57.071 32.000 0.00 0.00 41.25 3.57
4366 4994 9.298113 CTTTCACTTAAATTCGTACAACTTACG 57.702 33.333 0.00 0.00 41.79 3.18
4371 4999 9.789029 GAGTACTTTCACTTAAATTCGTACAAC 57.211 33.333 0.00 0.00 32.58 3.32
4372 5000 9.754382 AGAGTACTTTCACTTAAATTCGTACAA 57.246 29.630 0.00 0.00 32.58 2.41
4377 5005 9.595357 GGAAAAGAGTACTTTCACTTAAATTCG 57.405 33.333 0.00 0.00 44.32 3.34
4378 5006 9.894783 GGGAAAAGAGTACTTTCACTTAAATTC 57.105 33.333 0.00 0.00 44.32 2.17
4379 5007 9.416284 TGGGAAAAGAGTACTTTCACTTAAATT 57.584 29.630 8.99 0.00 44.32 1.82
4380 5008 8.990163 TGGGAAAAGAGTACTTTCACTTAAAT 57.010 30.769 8.99 0.00 44.32 1.40
4381 5009 8.810990 TTGGGAAAAGAGTACTTTCACTTAAA 57.189 30.769 8.99 0.00 44.32 1.52
4382 5010 7.012989 GCTTGGGAAAAGAGTACTTTCACTTAA 59.987 37.037 8.99 0.00 44.32 1.85
4383 5011 6.485648 GCTTGGGAAAAGAGTACTTTCACTTA 59.514 38.462 8.99 0.00 44.32 2.24
4385 5013 4.822350 GCTTGGGAAAAGAGTACTTTCACT 59.178 41.667 8.99 0.00 44.32 3.41
4386 5014 4.822350 AGCTTGGGAAAAGAGTACTTTCAC 59.178 41.667 0.00 0.00 44.32 3.18
4388 5016 5.049336 GTGAGCTTGGGAAAAGAGTACTTTC 60.049 44.000 0.00 0.00 44.32 2.62
4389 5017 4.822350 GTGAGCTTGGGAAAAGAGTACTTT 59.178 41.667 0.00 0.00 46.64 2.66
4390 5018 4.390264 GTGAGCTTGGGAAAAGAGTACTT 58.610 43.478 0.00 0.00 38.05 2.24
4391 5019 3.555168 CGTGAGCTTGGGAAAAGAGTACT 60.555 47.826 0.00 0.00 0.00 2.73
4392 5020 2.737252 CGTGAGCTTGGGAAAAGAGTAC 59.263 50.000 0.00 0.00 0.00 2.73
4393 5021 2.289444 CCGTGAGCTTGGGAAAAGAGTA 60.289 50.000 0.00 0.00 0.00 2.59
4394 5022 1.543429 CCGTGAGCTTGGGAAAAGAGT 60.543 52.381 0.00 0.00 0.00 3.24
4395 5023 1.160137 CCGTGAGCTTGGGAAAAGAG 58.840 55.000 0.00 0.00 0.00 2.85
4396 5024 3.322514 CCGTGAGCTTGGGAAAAGA 57.677 52.632 0.00 0.00 0.00 2.52
4403 5031 0.321564 TGTTCATCCCGTGAGCTTGG 60.322 55.000 0.00 0.00 38.70 3.61
4404 5032 1.522668 TTGTTCATCCCGTGAGCTTG 58.477 50.000 0.00 0.00 38.70 4.01
4405 5033 2.496899 ATTGTTCATCCCGTGAGCTT 57.503 45.000 0.00 0.00 38.70 3.74
4406 5034 3.627395 TTATTGTTCATCCCGTGAGCT 57.373 42.857 0.00 0.00 38.70 4.09
4407 5035 4.695217 TTTTATTGTTCATCCCGTGAGC 57.305 40.909 0.00 0.00 38.29 4.26
4408 5036 6.435430 TGATTTTATTGTTCATCCCGTGAG 57.565 37.500 0.00 0.00 38.29 3.51
4409 5037 5.356751 CCTGATTTTATTGTTCATCCCGTGA 59.643 40.000 0.00 0.00 34.25 4.35
4410 5038 5.356751 TCCTGATTTTATTGTTCATCCCGTG 59.643 40.000 0.00 0.00 0.00 4.94
4411 5039 5.505780 TCCTGATTTTATTGTTCATCCCGT 58.494 37.500 0.00 0.00 0.00 5.28
4412 5040 6.449635 TTCCTGATTTTATTGTTCATCCCG 57.550 37.500 0.00 0.00 0.00 5.14
4481 5109 9.405587 GCTGTAATTTTACAAGCACTCAAAATA 57.594 29.630 14.49 0.00 42.55 1.40
4482 5110 7.114811 CGCTGTAATTTTACAAGCACTCAAAAT 59.885 33.333 17.20 0.00 42.55 1.82
4483 5111 6.416455 CGCTGTAATTTTACAAGCACTCAAAA 59.584 34.615 17.20 0.00 42.55 2.44
4484 5112 5.912396 CGCTGTAATTTTACAAGCACTCAAA 59.088 36.000 17.20 0.00 42.55 2.69
4485 5113 5.008217 ACGCTGTAATTTTACAAGCACTCAA 59.992 36.000 17.20 0.00 42.55 3.02
4486 5114 4.513692 ACGCTGTAATTTTACAAGCACTCA 59.486 37.500 17.20 0.00 42.55 3.41
4487 5115 5.030874 ACGCTGTAATTTTACAAGCACTC 57.969 39.130 17.20 2.01 42.55 3.51
4488 5116 5.432885 AACGCTGTAATTTTACAAGCACT 57.567 34.783 17.20 7.29 42.55 4.40
4489 5117 7.611821 TTTAACGCTGTAATTTTACAAGCAC 57.388 32.000 17.20 5.00 42.55 4.40
4490 5118 8.076781 TCATTTAACGCTGTAATTTTACAAGCA 58.923 29.630 17.20 5.68 42.55 3.91
4491 5119 8.363029 GTCATTTAACGCTGTAATTTTACAAGC 58.637 33.333 4.82 8.85 42.55 4.01
4492 5120 9.388346 TGTCATTTAACGCTGTAATTTTACAAG 57.612 29.630 4.82 4.85 42.55 3.16
4493 5121 9.900710 ATGTCATTTAACGCTGTAATTTTACAA 57.099 25.926 4.82 0.00 42.55 2.41
4494 5122 9.900710 AATGTCATTTAACGCTGTAATTTTACA 57.099 25.926 3.34 3.34 41.06 2.41
4497 5125 9.255304 ACAAATGTCATTTAACGCTGTAATTTT 57.745 25.926 10.46 0.00 0.00 1.82
4498 5126 8.810652 ACAAATGTCATTTAACGCTGTAATTT 57.189 26.923 10.46 0.00 0.00 1.82
4499 5127 9.554724 CTACAAATGTCATTTAACGCTGTAATT 57.445 29.630 10.46 0.00 0.00 1.40
4500 5128 8.941977 TCTACAAATGTCATTTAACGCTGTAAT 58.058 29.630 10.46 0.00 0.00 1.89
4501 5129 8.312896 TCTACAAATGTCATTTAACGCTGTAA 57.687 30.769 10.46 0.00 0.00 2.41
4502 5130 7.892778 TCTACAAATGTCATTTAACGCTGTA 57.107 32.000 10.46 7.68 0.00 2.74
4503 5131 6.795098 TCTACAAATGTCATTTAACGCTGT 57.205 33.333 10.46 6.96 0.00 4.40
4504 5132 7.298122 ACTTCTACAAATGTCATTTAACGCTG 58.702 34.615 10.46 1.22 0.00 5.18
4505 5133 7.435068 ACTTCTACAAATGTCATTTAACGCT 57.565 32.000 10.46 0.00 0.00 5.07
4506 5134 6.461698 CGACTTCTACAAATGTCATTTAACGC 59.538 38.462 10.46 0.00 0.00 4.84
4507 5135 7.474332 CACGACTTCTACAAATGTCATTTAACG 59.526 37.037 10.46 9.55 0.00 3.18
4508 5136 7.744715 CCACGACTTCTACAAATGTCATTTAAC 59.255 37.037 10.46 0.00 0.00 2.01
4509 5137 7.658167 TCCACGACTTCTACAAATGTCATTTAA 59.342 33.333 10.46 1.40 0.00 1.52
4510 5138 7.156000 TCCACGACTTCTACAAATGTCATTTA 58.844 34.615 10.46 0.00 0.00 1.40
4511 5139 5.995282 TCCACGACTTCTACAAATGTCATTT 59.005 36.000 4.91 4.91 0.00 2.32
4512 5140 5.547465 TCCACGACTTCTACAAATGTCATT 58.453 37.500 0.00 0.00 0.00 2.57
4513 5141 5.147330 TCCACGACTTCTACAAATGTCAT 57.853 39.130 0.00 0.00 0.00 3.06
4514 5142 4.594123 TCCACGACTTCTACAAATGTCA 57.406 40.909 0.00 0.00 0.00 3.58
4515 5143 5.917541 TTTCCACGACTTCTACAAATGTC 57.082 39.130 0.00 0.00 0.00 3.06
4516 5144 6.687081 TTTTTCCACGACTTCTACAAATGT 57.313 33.333 0.00 0.00 0.00 2.71
4539 5167 8.553696 GCATTTTTGAGTGATGATTTTGTCTTT 58.446 29.630 0.00 0.00 0.00 2.52
4540 5168 7.929785 AGCATTTTTGAGTGATGATTTTGTCTT 59.070 29.630 0.00 0.00 0.00 3.01
4541 5169 7.439381 AGCATTTTTGAGTGATGATTTTGTCT 58.561 30.769 0.00 0.00 0.00 3.41
4542 5170 7.647907 AGCATTTTTGAGTGATGATTTTGTC 57.352 32.000 0.00 0.00 0.00 3.18
4543 5171 8.441312 AAAGCATTTTTGAGTGATGATTTTGT 57.559 26.923 0.00 0.00 36.36 2.83
4560 5188 8.667463 CCGAAAATATCATTTCCAAAAGCATTT 58.333 29.630 0.00 0.00 36.54 2.32
4561 5189 7.823799 ACCGAAAATATCATTTCCAAAAGCATT 59.176 29.630 0.00 0.00 36.21 3.56
4562 5190 7.278424 CACCGAAAATATCATTTCCAAAAGCAT 59.722 33.333 0.00 0.00 36.21 3.79
4563 5191 6.589523 CACCGAAAATATCATTTCCAAAAGCA 59.410 34.615 0.00 0.00 36.21 3.91
4564 5192 6.455513 GCACCGAAAATATCATTTCCAAAAGC 60.456 38.462 0.00 0.00 36.21 3.51
4565 5193 6.589523 TGCACCGAAAATATCATTTCCAAAAG 59.410 34.615 0.00 0.00 36.21 2.27
4566 5194 6.459066 TGCACCGAAAATATCATTTCCAAAA 58.541 32.000 0.00 0.00 36.21 2.44
4567 5195 6.030548 TGCACCGAAAATATCATTTCCAAA 57.969 33.333 0.00 0.00 36.21 3.28
4568 5196 5.651387 TGCACCGAAAATATCATTTCCAA 57.349 34.783 0.00 0.00 36.21 3.53
4569 5197 5.359292 TGATGCACCGAAAATATCATTTCCA 59.641 36.000 0.00 0.00 36.21 3.53
4570 5198 5.830912 TGATGCACCGAAAATATCATTTCC 58.169 37.500 0.00 0.00 36.21 3.13
4571 5199 7.935338 AATGATGCACCGAAAATATCATTTC 57.065 32.000 0.00 0.00 42.59 2.17
4573 5201 8.721019 AAAAATGATGCACCGAAAATATCATT 57.279 26.923 0.00 0.00 45.36 2.57
4599 5227 5.421693 ACATATGTAGAAGCCATGGCAAAAA 59.578 36.000 37.18 17.79 44.88 1.94
4600 5228 4.955450 ACATATGTAGAAGCCATGGCAAAA 59.045 37.500 37.18 17.42 44.88 2.44
4601 5229 4.535781 ACATATGTAGAAGCCATGGCAAA 58.464 39.130 37.18 17.06 44.88 3.68
4602 5230 4.136796 GACATATGTAGAAGCCATGGCAA 58.863 43.478 37.18 17.42 44.88 4.52
4603 5231 3.136260 TGACATATGTAGAAGCCATGGCA 59.864 43.478 37.18 17.20 44.88 4.92
4604 5232 3.743521 TGACATATGTAGAAGCCATGGC 58.256 45.455 30.12 30.12 42.33 4.40
4605 5233 6.487668 TGAAATGACATATGTAGAAGCCATGG 59.512 38.462 8.71 7.63 0.00 3.66
4606 5234 7.500720 TGAAATGACATATGTAGAAGCCATG 57.499 36.000 8.71 0.00 0.00 3.66
4624 5252 6.073494 TGCTTGCAAAGTTTCATCATGAAATG 60.073 34.615 15.91 11.25 46.55 2.32
4625 5253 5.992829 TGCTTGCAAAGTTTCATCATGAAAT 59.007 32.000 15.91 0.00 46.55 2.17
4639 5267 6.705287 ACAAATGGTGTCAATGCTTGCAAAG 61.705 40.000 0.00 0.00 41.72 2.77
4640 5268 3.472283 AATGGTGTCAATGCTTGCAAA 57.528 38.095 0.00 0.00 0.00 3.68
4641 5269 3.132160 CAAATGGTGTCAATGCTTGCAA 58.868 40.909 0.00 0.00 0.00 4.08
4642 5270 2.102757 ACAAATGGTGTCAATGCTTGCA 59.897 40.909 0.00 0.00 34.38 4.08
4643 5271 2.758009 ACAAATGGTGTCAATGCTTGC 58.242 42.857 0.00 0.00 34.38 4.01
4653 5281 5.126869 TGTGACAAAGATTGACAAATGGTGT 59.873 36.000 0.00 0.00 45.74 4.16
4654 5282 5.590145 TGTGACAAAGATTGACAAATGGTG 58.410 37.500 0.00 0.00 37.10 4.17
4655 5283 5.850557 TGTGACAAAGATTGACAAATGGT 57.149 34.783 0.00 0.00 37.10 3.55
4656 5284 6.041511 TGTTGTGACAAAGATTGACAAATGG 58.958 36.000 0.00 0.00 37.10 3.16
4657 5285 7.522901 TTGTTGTGACAAAGATTGACAAATG 57.477 32.000 0.00 0.00 42.54 2.32
4718 5346 9.077885 AGCTCTGGTGAATAGTAAAATCAAAAA 57.922 29.630 0.00 0.00 0.00 1.94
4719 5347 8.635765 AGCTCTGGTGAATAGTAAAATCAAAA 57.364 30.769 0.00 0.00 0.00 2.44
4720 5348 8.514594 CAAGCTCTGGTGAATAGTAAAATCAAA 58.485 33.333 0.00 0.00 0.00 2.69
4721 5349 7.665559 ACAAGCTCTGGTGAATAGTAAAATCAA 59.334 33.333 0.00 0.00 0.00 2.57
4722 5350 7.168219 ACAAGCTCTGGTGAATAGTAAAATCA 58.832 34.615 0.00 0.00 0.00 2.57
4723 5351 7.617041 ACAAGCTCTGGTGAATAGTAAAATC 57.383 36.000 0.00 0.00 0.00 2.17
4724 5352 8.322091 ACTACAAGCTCTGGTGAATAGTAAAAT 58.678 33.333 0.00 0.00 0.00 1.82
4725 5353 7.676947 ACTACAAGCTCTGGTGAATAGTAAAA 58.323 34.615 0.00 0.00 0.00 1.52
4726 5354 7.241042 ACTACAAGCTCTGGTGAATAGTAAA 57.759 36.000 0.00 0.00 0.00 2.01
4727 5355 6.852420 ACTACAAGCTCTGGTGAATAGTAA 57.148 37.500 0.00 0.00 0.00 2.24
4728 5356 7.014326 CCATACTACAAGCTCTGGTGAATAGTA 59.986 40.741 0.00 0.00 0.00 1.82
4729 5357 6.183360 CCATACTACAAGCTCTGGTGAATAGT 60.183 42.308 0.00 0.00 0.00 2.12
4730 5358 6.219473 CCATACTACAAGCTCTGGTGAATAG 58.781 44.000 0.00 0.00 0.00 1.73
4731 5359 5.453339 GCCATACTACAAGCTCTGGTGAATA 60.453 44.000 0.00 0.00 0.00 1.75
4732 5360 4.684485 GCCATACTACAAGCTCTGGTGAAT 60.684 45.833 0.00 0.00 0.00 2.57
4733 5361 3.369471 GCCATACTACAAGCTCTGGTGAA 60.369 47.826 0.00 0.00 0.00 3.18
4734 5362 2.168521 GCCATACTACAAGCTCTGGTGA 59.831 50.000 0.00 0.00 0.00 4.02
4735 5363 2.093500 TGCCATACTACAAGCTCTGGTG 60.093 50.000 0.00 0.00 0.00 4.17
4736 5364 2.187958 TGCCATACTACAAGCTCTGGT 58.812 47.619 0.00 0.00 0.00 4.00
4737 5365 2.988010 TGCCATACTACAAGCTCTGG 57.012 50.000 0.00 0.00 0.00 3.86
4738 5366 4.128925 TCTTGCCATACTACAAGCTCTG 57.871 45.455 0.00 0.00 42.41 3.35
4739 5367 4.467795 TCTTCTTGCCATACTACAAGCTCT 59.532 41.667 0.00 0.00 42.41 4.09
4740 5368 4.759782 TCTTCTTGCCATACTACAAGCTC 58.240 43.478 0.00 0.00 42.41 4.09
4741 5369 4.826274 TCTTCTTGCCATACTACAAGCT 57.174 40.909 0.00 0.00 42.41 3.74
4742 5370 4.695455 TGTTCTTCTTGCCATACTACAAGC 59.305 41.667 0.00 0.00 42.41 4.01
4743 5371 6.820656 AGATGTTCTTCTTGCCATACTACAAG 59.179 38.462 0.00 0.00 43.73 3.16
4744 5372 6.711277 AGATGTTCTTCTTGCCATACTACAA 58.289 36.000 0.00 0.00 0.00 2.41
4745 5373 6.155221 AGAGATGTTCTTCTTGCCATACTACA 59.845 38.462 0.00 0.00 29.61 2.74
4746 5374 6.578023 AGAGATGTTCTTCTTGCCATACTAC 58.422 40.000 0.00 0.00 29.61 2.73
4747 5375 6.798427 AGAGATGTTCTTCTTGCCATACTA 57.202 37.500 0.00 0.00 29.61 1.82
4748 5376 5.690464 AGAGATGTTCTTCTTGCCATACT 57.310 39.130 0.00 0.00 29.61 2.12
4749 5377 6.989169 ACATAGAGATGTTCTTCTTGCCATAC 59.011 38.462 0.00 0.00 44.18 2.39
4750 5378 7.129457 ACATAGAGATGTTCTTCTTGCCATA 57.871 36.000 0.00 0.00 44.18 2.74
4751 5379 5.999044 ACATAGAGATGTTCTTCTTGCCAT 58.001 37.500 0.00 0.00 44.18 4.40
4752 5380 5.426689 ACATAGAGATGTTCTTCTTGCCA 57.573 39.130 0.00 0.00 44.18 4.92
4753 5381 6.341316 TGTACATAGAGATGTTCTTCTTGCC 58.659 40.000 0.00 0.00 44.18 4.52
4754 5382 7.547370 AGTTGTACATAGAGATGTTCTTCTTGC 59.453 37.037 0.00 0.00 44.18 4.01
4755 5383 8.994429 AGTTGTACATAGAGATGTTCTTCTTG 57.006 34.615 0.00 0.00 44.18 3.02
4756 5384 7.971168 CGAGTTGTACATAGAGATGTTCTTCTT 59.029 37.037 0.00 0.00 44.18 2.52
4757 5385 7.476667 CGAGTTGTACATAGAGATGTTCTTCT 58.523 38.462 0.00 0.00 44.18 2.85
4758 5386 6.197468 GCGAGTTGTACATAGAGATGTTCTTC 59.803 42.308 0.00 0.00 44.18 2.87
4759 5387 6.037098 GCGAGTTGTACATAGAGATGTTCTT 58.963 40.000 0.00 0.00 44.18 2.52
4760 5388 5.450688 GGCGAGTTGTACATAGAGATGTTCT 60.451 44.000 0.00 0.00 44.18 3.01
4761 5389 4.740695 GGCGAGTTGTACATAGAGATGTTC 59.259 45.833 0.00 0.00 44.18 3.18
4762 5390 4.159693 TGGCGAGTTGTACATAGAGATGTT 59.840 41.667 0.00 0.00 44.18 2.71
4764 5392 4.307443 TGGCGAGTTGTACATAGAGATG 57.693 45.455 0.00 0.00 39.16 2.90
4765 5393 5.339008 TTTGGCGAGTTGTACATAGAGAT 57.661 39.130 0.00 0.00 0.00 2.75
4766 5394 4.794278 TTTGGCGAGTTGTACATAGAGA 57.206 40.909 0.00 0.00 0.00 3.10
4767 5395 7.491372 TCTTATTTTGGCGAGTTGTACATAGAG 59.509 37.037 0.00 0.00 0.00 2.43
4768 5396 7.324935 TCTTATTTTGGCGAGTTGTACATAGA 58.675 34.615 0.00 0.00 0.00 1.98
4769 5397 7.534085 TCTTATTTTGGCGAGTTGTACATAG 57.466 36.000 0.00 0.00 0.00 2.23
4770 5398 7.604927 ACTTCTTATTTTGGCGAGTTGTACATA 59.395 33.333 0.00 0.00 0.00 2.29
4771 5399 6.430000 ACTTCTTATTTTGGCGAGTTGTACAT 59.570 34.615 0.00 0.00 0.00 2.29
4772 5400 5.761234 ACTTCTTATTTTGGCGAGTTGTACA 59.239 36.000 0.00 0.00 0.00 2.90
4773 5401 6.237313 ACTTCTTATTTTGGCGAGTTGTAC 57.763 37.500 0.00 0.00 0.00 2.90
4774 5402 6.347079 CGAACTTCTTATTTTGGCGAGTTGTA 60.347 38.462 0.00 0.00 0.00 2.41
4775 5403 5.560183 CGAACTTCTTATTTTGGCGAGTTGT 60.560 40.000 0.00 0.00 0.00 3.32
4776 5404 4.846137 CGAACTTCTTATTTTGGCGAGTTG 59.154 41.667 0.00 0.00 0.00 3.16
4777 5405 4.514066 ACGAACTTCTTATTTTGGCGAGTT 59.486 37.500 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.