Multiple sequence alignment - TraesCS5B01G294100

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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 TraesCS5B01G294100 chr5B 100.000 5456 0 0 1 5456 478487453 478492908 0.000000e+00 10076.0
1 TraesCS5B01G294100 chr5D 95.351 4689 183 16 261 4933 398536294 398540963 0.000000e+00 7419.0
2 TraesCS5B01G294100 chr5D 97.701 261 5 1 1 260 398536003 398536263 1.080000e-121 448.0
3 TraesCS5B01G294100 chr5A 95.853 4341 148 13 261 4583 503529175 503533501 0.000000e+00 6990.0
4 TraesCS5B01G294100 chr5A 97.692 260 6 0 1 260 503528878 503529137 1.080000e-121 448.0
5 TraesCS5B01G294100 chr5A 93.865 163 7 2 4962 5124 503533723 503533882 5.460000e-60 243.0
6 TraesCS5B01G294100 chr5A 91.597 119 6 3 5073 5191 503533881 503533995 1.570000e-35 161.0
7 TraesCS5B01G294100 chr5A 91.667 108 9 0 4581 4688 503533560 503533667 3.400000e-32 150.0
8 TraesCS5B01G294100 chr5A 100.000 38 0 0 4716 4753 503533674 503533711 2.730000e-08 71.3
9 TraesCS5B01G294100 chr6B 83.828 1045 142 23 3728 4757 642964145 642963113 0.000000e+00 968.0
10 TraesCS5B01G294100 chr6B 84.951 206 27 3 1217 1422 642972512 642972311 7.160000e-49 206.0
11 TraesCS5B01G294100 chr6D 83.174 1046 148 24 3728 4757 427123685 427122652 0.000000e+00 931.0
12 TraesCS5B01G294100 chr6D 80.420 286 40 11 1217 1491 427126878 427126598 2.580000e-48 204.0
13 TraesCS5B01G294100 chr6A 84.665 926 126 15 3728 4642 571845714 571844794 0.000000e+00 909.0
14 TraesCS5B01G294100 chr6A 84.541 207 26 5 1217 1422 571848755 571848554 3.330000e-47 200.0
15 TraesCS5B01G294100 chrUn 84.884 258 36 3 4212 4467 30182680 30182936 1.950000e-64 257.0
16 TraesCS5B01G294100 chr4B 81.724 290 44 6 4187 4468 666802089 666801801 3.290000e-57 233.0
17 TraesCS5B01G294100 chr4B 93.443 61 3 1 5317 5376 44658516 44658456 7.530000e-14 89.8
18 TraesCS5B01G294100 chr2A 85.635 181 20 3 3591 3766 18301984 18301805 9.330000e-43 185.0
19 TraesCS5B01G294100 chr1B 90.000 50 4 1 4414 4463 323637196 323637244 4.560000e-06 63.9


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 TraesCS5B01G294100 chr5B 478487453 478492908 5455 False 10076.000000 10076 100.000000 1 5456 1 chr5B.!!$F1 5455
1 TraesCS5B01G294100 chr5D 398536003 398540963 4960 False 3933.500000 7419 96.526000 1 4933 2 chr5D.!!$F1 4932
2 TraesCS5B01G294100 chr5A 503528878 503533995 5117 False 1343.883333 6990 95.112333 1 5191 6 chr5A.!!$F1 5190
3 TraesCS5B01G294100 chr6B 642963113 642964145 1032 True 968.000000 968 83.828000 3728 4757 1 chr6B.!!$R1 1029
4 TraesCS5B01G294100 chr6D 427122652 427126878 4226 True 567.500000 931 81.797000 1217 4757 2 chr6D.!!$R1 3540
5 TraesCS5B01G294100 chr6A 571844794 571848755 3961 True 554.500000 909 84.603000 1217 4642 2 chr6A.!!$R1 3425

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
426 465 0.314935 CTCCACGCCAGCAAACATTT 59.685 50.000 0.00 0.0 0.00 2.32 F
772 824 0.974383 ACACTACCTGGGAAAGACCG 59.026 55.000 0.00 0.0 40.11 4.79 F
774 826 1.621814 CACTACCTGGGAAAGACCGAA 59.378 52.381 0.00 0.0 40.11 4.30 F
1681 1861 2.149383 AGGCCTGTGTCCTTGCAGA 61.149 57.895 3.11 0.0 34.87 4.26 F
1874 2500 0.323360 TGGACATTGCCTTAGCCCAC 60.323 55.000 0.00 0.0 38.69 4.61 F
3297 4161 0.605589 GAAAACTAGGTGGCGTGCCT 60.606 55.000 12.84 0.0 40.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1283 1339 0.751277 TTCCACCCACTGCAGTTGTG 60.751 55.000 27.84 27.84 35.39 3.33 R
1663 1843 1.495579 ATCTGCAAGGACACAGGCCT 61.496 55.000 0.00 0.00 37.35 5.19 R
1757 1937 2.819608 CACCTTGACCCGATGACAATTT 59.180 45.455 0.00 0.00 0.00 1.82 R
3641 4527 0.798776 CAAGCTTGTTACTCTGCCCG 59.201 55.000 18.65 0.00 0.00 6.13 R
3723 4609 3.891366 GGGGAATTCCAAACATGATCGAT 59.109 43.478 25.67 0.00 37.91 3.59 R
5251 6274 0.391927 TACCAACATACGGGTGCAGC 60.392 55.000 7.55 7.55 38.06 5.25 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
263 302 6.952935 AGTAGAAACTTCGCAGAAATACTG 57.047 37.500 0.00 0.00 45.90 2.74
353 392 8.503573 TCCCTGACTAGAGAAGATAATAAGACA 58.496 37.037 0.00 0.00 0.00 3.41
426 465 0.314935 CTCCACGCCAGCAAACATTT 59.685 50.000 0.00 0.00 0.00 2.32
436 475 4.869297 GCCAGCAAACATTTATGCAACATA 59.131 37.500 0.00 0.00 44.95 2.29
465 504 5.407407 TTGCTTTTTAACCAACCAGTTGA 57.593 34.783 12.06 0.00 42.93 3.18
468 507 5.127845 TGCTTTTTAACCAACCAGTTGATCA 59.872 36.000 12.06 0.00 42.93 2.92
474 513 4.051661 ACCAACCAGTTGATCAATCCAT 57.948 40.909 12.12 0.00 42.93 3.41
772 824 0.974383 ACACTACCTGGGAAAGACCG 59.026 55.000 0.00 0.00 40.11 4.79
774 826 1.621814 CACTACCTGGGAAAGACCGAA 59.378 52.381 0.00 0.00 40.11 4.30
797 849 3.680196 GCAGAACAAGGACTAGGATGACC 60.680 52.174 0.00 0.00 0.00 4.02
949 1003 7.290061 AGCCAGATAGCAAAACCAGAATATAA 58.710 34.615 0.00 0.00 34.23 0.98
1428 1484 7.448777 GTGATGATACAAGAGAGGTATCCTACA 59.551 40.741 9.36 5.29 44.08 2.74
1486 1553 4.058817 GGTGCTTATTAGAGTTCATCCGG 58.941 47.826 0.00 0.00 0.00 5.14
1514 1581 9.836864 AAGCATTCTAGTCATGTGATATTTGTA 57.163 29.630 0.00 0.00 0.00 2.41
1681 1861 2.149383 AGGCCTGTGTCCTTGCAGA 61.149 57.895 3.11 0.00 34.87 4.26
1757 1937 7.255590 CCTGGTAAAGAAGCTCAAAATCAAGAA 60.256 37.037 0.00 0.00 0.00 2.52
1798 1978 6.520272 AGGTGAGATCATAGCATGAACTAAC 58.480 40.000 0.00 11.93 41.69 2.34
1874 2500 0.323360 TGGACATTGCCTTAGCCCAC 60.323 55.000 0.00 0.00 38.69 4.61
1888 2514 1.618343 AGCCCACAAAACAGCATAACC 59.382 47.619 0.00 0.00 0.00 2.85
2067 2693 8.511604 AAATTAGTTGATGGATGAGATCGTTT 57.488 30.769 0.00 0.00 0.00 3.60
2290 2951 6.151648 CCATGGTTCAGAGTTTTGATACATGT 59.848 38.462 2.57 2.69 38.51 3.21
2343 3006 3.181471 GGAAGACGATGTCATGGATGAGT 60.181 47.826 1.37 0.00 37.51 3.41
2376 3039 2.428171 CCAATGGATGGTGATGGACAAC 59.572 50.000 0.00 0.00 44.85 3.32
2477 3154 2.899976 TGACGACACACACAGAAACAT 58.100 42.857 0.00 0.00 0.00 2.71
2732 3560 2.979814 TTCTGGTGATGACATACGGG 57.020 50.000 0.00 0.00 0.00 5.28
2974 3832 1.069358 TGTGTCACACAGCATCGGTAA 59.931 47.619 6.50 0.00 39.62 2.85
3192 4056 5.372343 TCCCAGAACATATTGTGCAGTAT 57.628 39.130 0.00 0.00 0.00 2.12
3201 4065 6.121590 ACATATTGTGCAGTATTCCATGTCA 58.878 36.000 0.00 0.00 0.00 3.58
3203 4067 3.415457 TGTGCAGTATTCCATGTCACA 57.585 42.857 0.00 0.00 33.87 3.58
3297 4161 0.605589 GAAAACTAGGTGGCGTGCCT 60.606 55.000 12.84 0.00 40.00 4.75
3546 4432 5.011023 ACCCTTATTTTCCTGCAGTTCTTTG 59.989 40.000 13.81 0.00 0.00 2.77
3641 4527 8.305317 ACAACTCCACAAAGTAGATAAGTAGAC 58.695 37.037 0.00 0.00 0.00 2.59
3693 4579 7.546250 ACTACTTGGAGAAGAATCTTCTGAA 57.454 36.000 28.10 18.47 37.65 3.02
3705 4591 7.317842 AGAATCTTCTGAACTGCATTACATG 57.682 36.000 0.00 0.00 35.89 3.21
3708 4594 6.968131 TCTTCTGAACTGCATTACATGTAC 57.032 37.500 4.68 0.00 0.00 2.90
3713 4599 7.611770 TCTGAACTGCATTACATGTACTAACT 58.388 34.615 4.68 0.00 0.00 2.24
3771 4657 2.031769 CGTTGTGCTGAGCAGAATCAAA 60.032 45.455 20.10 0.00 43.30 2.69
3981 4867 0.396435 ATGCGGACCTGAAGTTGACA 59.604 50.000 0.00 0.00 0.00 3.58
4032 4918 0.396001 GGCTAGGAGACTTCGGGACT 60.396 60.000 0.00 0.00 43.67 3.85
4035 4921 0.039180 TAGGAGACTTCGGGACTGCA 59.961 55.000 0.00 0.00 43.67 4.41
4377 5263 3.790437 CCAGCTGCCACCTCCGAT 61.790 66.667 8.66 0.00 0.00 4.18
4380 5266 4.479993 GCTGCCACCTCCGATGCT 62.480 66.667 0.00 0.00 0.00 3.79
4511 5416 5.639757 CGAAATGCCAACTGAACATAATGA 58.360 37.500 0.00 0.00 0.00 2.57
4579 5488 5.047164 TGCCATAGCATTTCTGTTGTGAATT 60.047 36.000 0.00 0.00 46.52 2.17
4691 5662 9.391006 TGGAGTGGTAAACAATAGATAAATGTC 57.609 33.333 0.00 0.00 0.00 3.06
4714 5685 0.242555 GGAAATTTCGGGAAGCGCAA 59.757 50.000 11.47 0.00 0.00 4.85
4763 5738 5.275494 CGCATGAAGCAATATGTTGATCAA 58.725 37.500 3.38 3.38 46.13 2.57
4770 5745 9.524106 TGAAGCAATATGTTGATCAATTCATTC 57.476 29.630 12.12 8.35 37.53 2.67
4771 5746 9.524106 GAAGCAATATGTTGATCAATTCATTCA 57.476 29.630 12.12 3.99 37.53 2.57
4772 5747 9.529325 AAGCAATATGTTGATCAATTCATTCAG 57.471 29.630 12.12 5.88 37.53 3.02
4773 5748 8.692710 AGCAATATGTTGATCAATTCATTCAGT 58.307 29.630 12.12 0.00 37.53 3.41
4774 5749 8.752254 GCAATATGTTGATCAATTCATTCAGTG 58.248 33.333 12.12 7.87 37.53 3.66
4775 5750 9.244799 CAATATGTTGATCAATTCATTCAGTGG 57.755 33.333 12.12 0.00 37.53 4.00
4776 5751 5.648178 TGTTGATCAATTCATTCAGTGGG 57.352 39.130 12.12 0.00 33.34 4.61
4777 5752 5.078949 TGTTGATCAATTCATTCAGTGGGT 58.921 37.500 12.12 0.00 33.34 4.51
4778 5753 5.539574 TGTTGATCAATTCATTCAGTGGGTT 59.460 36.000 12.12 0.00 33.34 4.11
4779 5754 5.648178 TGATCAATTCATTCAGTGGGTTG 57.352 39.130 0.00 0.00 0.00 3.77
4780 5755 5.323581 TGATCAATTCATTCAGTGGGTTGA 58.676 37.500 0.00 0.00 36.64 3.18
4781 5756 5.774184 TGATCAATTCATTCAGTGGGTTGAA 59.226 36.000 0.00 5.99 41.00 2.69
4782 5757 6.267242 TGATCAATTCATTCAGTGGGTTGAAA 59.733 34.615 0.00 0.00 40.21 2.69
4793 5768 1.407258 TGGGTTGAAACTTGAAAGGCG 59.593 47.619 0.00 0.00 0.00 5.52
4821 5796 1.179152 CCCCGGTTCCCATGTAAAAC 58.821 55.000 0.00 0.00 0.00 2.43
4849 5824 1.680522 GCTGCGGGAGATGGAAGAGA 61.681 60.000 0.00 0.00 0.00 3.10
4879 5854 2.457080 GGTGCAGCTAAACCGAGAC 58.543 57.895 9.07 0.00 0.00 3.36
4921 5897 4.569023 CACGGCGCGGCTCTCATA 62.569 66.667 30.60 0.00 0.00 2.15
4928 5904 0.179137 CGCGGCTCTCATAGAACACA 60.179 55.000 0.00 0.00 0.00 3.72
4933 5909 3.182967 GGCTCTCATAGAACACAGTTCG 58.817 50.000 4.43 0.00 0.00 3.95
4934 5910 3.182967 GCTCTCATAGAACACAGTTCGG 58.817 50.000 4.43 0.00 0.00 4.30
4935 5911 3.367498 GCTCTCATAGAACACAGTTCGGT 60.367 47.826 4.43 0.00 0.00 4.69
4936 5912 4.810790 CTCTCATAGAACACAGTTCGGTT 58.189 43.478 4.43 0.00 0.00 4.44
4937 5913 4.556233 TCTCATAGAACACAGTTCGGTTG 58.444 43.478 4.43 4.47 0.00 3.77
4938 5914 4.279922 TCTCATAGAACACAGTTCGGTTGA 59.720 41.667 4.43 7.81 0.00 3.18
4956 5932 3.036959 GAGAGAGGGGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
4957 5933 3.039526 AGAGAGGGGGAGGGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
4958 5934 4.179599 GAGAGGGGGAGGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
4998 5974 1.456145 GGGACGGGTTGGTTGGTTT 60.456 57.895 0.00 0.00 0.00 3.27
5126 6102 2.651361 CGACAACCGGACAGAGCT 59.349 61.111 9.46 0.00 33.91 4.09
5127 6103 1.734477 CGACAACCGGACAGAGCTG 60.734 63.158 9.46 0.00 33.91 4.24
5140 6163 1.204467 CAGAGCTGGGTCTTGACTCTC 59.796 57.143 0.00 4.23 35.57 3.20
5151 6174 2.235650 TCTTGACTCTCAGATGGGCTTG 59.764 50.000 0.00 0.00 0.00 4.01
5153 6176 0.463474 GACTCTCAGATGGGCTTGGC 60.463 60.000 0.00 0.00 0.00 4.52
5168 6191 2.748647 GGCCCGCCGTGTGTATTT 60.749 61.111 0.00 0.00 0.00 1.40
5181 6204 4.142902 CGTGTGTATTTTGGGCTTCTAGTG 60.143 45.833 0.00 0.00 0.00 2.74
5191 6214 1.749033 CTTCTAGTGGCCGGGGATC 59.251 63.158 2.18 0.00 0.00 3.36
5192 6215 0.760945 CTTCTAGTGGCCGGGGATCT 60.761 60.000 2.18 0.00 0.00 2.75
5193 6216 1.048724 TTCTAGTGGCCGGGGATCTG 61.049 60.000 2.18 0.00 0.00 2.90
5194 6217 3.161450 TAGTGGCCGGGGATCTGC 61.161 66.667 2.18 0.00 0.00 4.26
5195 6218 3.696518 TAGTGGCCGGGGATCTGCT 62.697 63.158 2.18 0.00 0.00 4.24
5196 6219 4.864334 GTGGCCGGGGATCTGCTG 62.864 72.222 2.18 0.00 0.00 4.41
5200 6223 4.864334 CCGGGGATCTGCTGCACC 62.864 72.222 0.00 0.00 0.00 5.01
5202 6225 4.864334 GGGGATCTGCTGCACCGG 62.864 72.222 0.00 0.00 0.00 5.28
5203 6226 4.101448 GGGATCTGCTGCACCGGT 62.101 66.667 0.00 0.00 0.00 5.28
5204 6227 2.821366 GGATCTGCTGCACCGGTG 60.821 66.667 30.66 30.66 0.00 4.94
5215 6238 2.701587 CACCGGTGCTTTTCACTCA 58.298 52.632 24.02 0.00 44.98 3.41
5216 6239 1.021202 CACCGGTGCTTTTCACTCAA 58.979 50.000 24.02 0.00 44.98 3.02
5217 6240 1.403679 CACCGGTGCTTTTCACTCAAA 59.596 47.619 24.02 0.00 44.98 2.69
5218 6241 2.096248 ACCGGTGCTTTTCACTCAAAA 58.904 42.857 6.12 0.00 44.98 2.44
5219 6242 2.494073 ACCGGTGCTTTTCACTCAAAAA 59.506 40.909 6.12 0.00 44.98 1.94
5241 6264 4.619437 AAAAACGGTGCTTTCGACTAAA 57.381 36.364 0.00 0.00 0.00 1.85
5242 6265 4.619437 AAAACGGTGCTTTCGACTAAAA 57.381 36.364 0.00 0.00 0.00 1.52
5243 6266 4.619437 AAACGGTGCTTTCGACTAAAAA 57.381 36.364 0.00 0.00 0.00 1.94
5244 6267 4.823790 AACGGTGCTTTCGACTAAAAAT 57.176 36.364 0.00 0.00 0.00 1.82
5245 6268 4.823790 ACGGTGCTTTCGACTAAAAATT 57.176 36.364 0.00 0.00 0.00 1.82
5246 6269 5.177725 ACGGTGCTTTCGACTAAAAATTT 57.822 34.783 0.00 0.00 0.00 1.82
5247 6270 5.584442 ACGGTGCTTTCGACTAAAAATTTT 58.416 33.333 0.00 0.00 0.00 1.82
5248 6271 6.037726 ACGGTGCTTTCGACTAAAAATTTTT 58.962 32.000 19.44 19.44 0.00 1.94
5265 6288 1.323412 TTTTTGCTGCACCCGTATGT 58.677 45.000 0.00 0.00 0.00 2.29
5266 6289 1.323412 TTTTGCTGCACCCGTATGTT 58.677 45.000 0.00 0.00 0.00 2.71
5267 6290 0.595588 TTTGCTGCACCCGTATGTTG 59.404 50.000 0.00 0.00 0.00 3.33
5268 6291 1.240641 TTGCTGCACCCGTATGTTGG 61.241 55.000 0.00 0.00 0.00 3.77
5269 6292 1.674322 GCTGCACCCGTATGTTGGT 60.674 57.895 0.00 0.00 34.40 3.67
5270 6293 0.391927 GCTGCACCCGTATGTTGGTA 60.392 55.000 0.00 0.00 32.32 3.25
5271 6294 1.651987 CTGCACCCGTATGTTGGTAG 58.348 55.000 0.00 0.00 32.32 3.18
5272 6295 0.978151 TGCACCCGTATGTTGGTAGT 59.022 50.000 0.00 0.00 32.32 2.73
5273 6296 2.166870 CTGCACCCGTATGTTGGTAGTA 59.833 50.000 0.00 0.00 32.32 1.82
5274 6297 2.094078 TGCACCCGTATGTTGGTAGTAC 60.094 50.000 0.00 0.00 32.32 2.73
5275 6298 2.167075 GCACCCGTATGTTGGTAGTACT 59.833 50.000 0.00 0.00 32.32 2.73
5276 6299 3.381272 GCACCCGTATGTTGGTAGTACTA 59.619 47.826 0.00 0.00 32.32 1.82
5277 6300 4.734695 GCACCCGTATGTTGGTAGTACTAC 60.735 50.000 22.53 22.53 32.32 2.73
5278 6301 4.641989 CACCCGTATGTTGGTAGTACTACT 59.358 45.833 27.71 13.50 36.36 2.57
5279 6302 5.822519 CACCCGTATGTTGGTAGTACTACTA 59.177 44.000 27.71 21.66 36.36 1.82
5288 6311 3.779573 GTAGTACTACTACCGTAGCGC 57.220 52.381 23.17 0.00 43.96 5.92
5289 6312 2.315925 AGTACTACTACCGTAGCGCA 57.684 50.000 11.47 0.00 45.63 6.09
5290 6313 2.843701 AGTACTACTACCGTAGCGCAT 58.156 47.619 11.47 0.00 45.63 4.73
5291 6314 3.209410 AGTACTACTACCGTAGCGCATT 58.791 45.455 11.47 0.00 45.63 3.56
5292 6315 3.629398 AGTACTACTACCGTAGCGCATTT 59.371 43.478 11.47 0.00 45.63 2.32
5293 6316 4.816385 AGTACTACTACCGTAGCGCATTTA 59.184 41.667 11.47 0.00 45.63 1.40
5294 6317 3.957468 ACTACTACCGTAGCGCATTTAC 58.043 45.455 11.47 2.15 45.63 2.01
5295 6318 2.214387 ACTACCGTAGCGCATTTACC 57.786 50.000 11.47 0.00 0.00 2.85
5296 6319 1.477700 ACTACCGTAGCGCATTTACCA 59.522 47.619 11.47 0.00 0.00 3.25
5297 6320 2.094078 ACTACCGTAGCGCATTTACCAA 60.094 45.455 11.47 0.00 0.00 3.67
5298 6321 2.032680 ACCGTAGCGCATTTACCAAT 57.967 45.000 11.47 0.00 0.00 3.16
5299 6322 1.668751 ACCGTAGCGCATTTACCAATG 59.331 47.619 11.47 0.00 42.60 2.82
5313 6336 8.984891 CATTTACCAATGCTTGATGTTAGAAA 57.015 30.769 0.00 0.00 33.57 2.52
5314 6337 9.421806 CATTTACCAATGCTTGATGTTAGAAAA 57.578 29.630 0.00 0.00 33.57 2.29
5315 6338 9.643693 ATTTACCAATGCTTGATGTTAGAAAAG 57.356 29.630 0.00 0.00 0.00 2.27
5316 6339 6.899393 ACCAATGCTTGATGTTAGAAAAGA 57.101 33.333 0.00 0.00 0.00 2.52
5317 6340 7.288810 ACCAATGCTTGATGTTAGAAAAGAA 57.711 32.000 0.00 0.00 0.00 2.52
5318 6341 7.725251 ACCAATGCTTGATGTTAGAAAAGAAA 58.275 30.769 0.00 0.00 0.00 2.52
5319 6342 8.203485 ACCAATGCTTGATGTTAGAAAAGAAAA 58.797 29.630 0.00 0.00 0.00 2.29
5320 6343 9.044150 CCAATGCTTGATGTTAGAAAAGAAAAA 57.956 29.630 0.00 0.00 0.00 1.94
5335 6358 9.325198 AGAAAAGAAAAATTAACACATTCACCC 57.675 29.630 0.00 0.00 0.00 4.61
5336 6359 9.103861 GAAAAGAAAAATTAACACATTCACCCA 57.896 29.630 0.00 0.00 0.00 4.51
5337 6360 9.454859 AAAAGAAAAATTAACACATTCACCCAA 57.545 25.926 0.00 0.00 0.00 4.12
5338 6361 8.432110 AAGAAAAATTAACACATTCACCCAAC 57.568 30.769 0.00 0.00 0.00 3.77
5339 6362 7.560368 AGAAAAATTAACACATTCACCCAACA 58.440 30.769 0.00 0.00 0.00 3.33
5340 6363 8.210265 AGAAAAATTAACACATTCACCCAACAT 58.790 29.630 0.00 0.00 0.00 2.71
5341 6364 8.744568 AAAAATTAACACATTCACCCAACATT 57.255 26.923 0.00 0.00 0.00 2.71
5342 6365 7.727331 AAATTAACACATTCACCCAACATTG 57.273 32.000 0.00 0.00 0.00 2.82
5351 6374 4.380843 TCACCCAACATTGGTCTATGTT 57.619 40.909 9.76 5.26 46.73 2.71
5360 6383 7.499321 AACATTGGTCTATGTTGTCGTAAAA 57.501 32.000 9.30 0.00 44.71 1.52
5361 6384 7.681939 ACATTGGTCTATGTTGTCGTAAAAT 57.318 32.000 0.00 0.00 35.24 1.82
5362 6385 8.106247 ACATTGGTCTATGTTGTCGTAAAATT 57.894 30.769 0.00 0.00 35.24 1.82
5363 6386 8.573035 ACATTGGTCTATGTTGTCGTAAAATTT 58.427 29.630 0.00 0.00 35.24 1.82
5364 6387 9.405587 CATTGGTCTATGTTGTCGTAAAATTTT 57.594 29.630 8.75 8.75 0.00 1.82
5390 6413 5.914085 TCAAAATTTTACAACATTGCCCG 57.086 34.783 2.44 0.00 0.00 6.13
5391 6414 5.360591 TCAAAATTTTACAACATTGCCCGT 58.639 33.333 2.44 0.00 0.00 5.28
5392 6415 5.235186 TCAAAATTTTACAACATTGCCCGTG 59.765 36.000 2.44 0.00 0.00 4.94
5393 6416 4.592485 AATTTTACAACATTGCCCGTGA 57.408 36.364 0.00 0.00 0.00 4.35
5394 6417 4.799564 ATTTTACAACATTGCCCGTGAT 57.200 36.364 0.00 0.00 0.00 3.06
5395 6418 5.906113 ATTTTACAACATTGCCCGTGATA 57.094 34.783 0.00 0.00 0.00 2.15
5396 6419 5.906113 TTTTACAACATTGCCCGTGATAT 57.094 34.783 0.00 0.00 0.00 1.63
5397 6420 4.891627 TTACAACATTGCCCGTGATATG 57.108 40.909 0.00 0.00 0.00 1.78
5398 6421 2.997980 ACAACATTGCCCGTGATATGA 58.002 42.857 0.00 0.00 0.00 2.15
5399 6422 3.351740 ACAACATTGCCCGTGATATGAA 58.648 40.909 0.00 0.00 0.00 2.57
5400 6423 3.761218 ACAACATTGCCCGTGATATGAAA 59.239 39.130 0.00 0.00 0.00 2.69
5401 6424 4.402155 ACAACATTGCCCGTGATATGAAAT 59.598 37.500 0.00 0.00 0.00 2.17
5402 6425 5.105392 ACAACATTGCCCGTGATATGAAATT 60.105 36.000 0.00 0.00 0.00 1.82
5403 6426 5.596836 ACATTGCCCGTGATATGAAATTT 57.403 34.783 0.00 0.00 0.00 1.82
5404 6427 5.976458 ACATTGCCCGTGATATGAAATTTT 58.024 33.333 0.00 0.00 0.00 1.82
5405 6428 5.811613 ACATTGCCCGTGATATGAAATTTTG 59.188 36.000 0.00 0.00 0.00 2.44
5406 6429 5.398603 TTGCCCGTGATATGAAATTTTGT 57.601 34.783 0.00 0.00 0.00 2.83
5407 6430 4.742417 TGCCCGTGATATGAAATTTTGTG 58.258 39.130 0.00 0.00 0.00 3.33
5408 6431 4.460731 TGCCCGTGATATGAAATTTTGTGA 59.539 37.500 0.00 0.00 0.00 3.58
5409 6432 5.126869 TGCCCGTGATATGAAATTTTGTGAT 59.873 36.000 0.00 0.00 0.00 3.06
5410 6433 5.459762 GCCCGTGATATGAAATTTTGTGATG 59.540 40.000 0.00 0.00 0.00 3.07
5411 6434 5.978919 CCCGTGATATGAAATTTTGTGATGG 59.021 40.000 0.00 0.00 0.00 3.51
5412 6435 5.459762 CCGTGATATGAAATTTTGTGATGGC 59.540 40.000 0.00 0.00 0.00 4.40
5413 6436 6.035217 CGTGATATGAAATTTTGTGATGGCA 58.965 36.000 0.00 0.00 0.00 4.92
5414 6437 6.698329 CGTGATATGAAATTTTGTGATGGCAT 59.302 34.615 0.00 0.00 0.00 4.40
5415 6438 7.861872 CGTGATATGAAATTTTGTGATGGCATA 59.138 33.333 0.00 0.00 0.00 3.14
5416 6439 8.971321 GTGATATGAAATTTTGTGATGGCATAC 58.029 33.333 0.00 0.00 0.00 2.39
5417 6440 8.143193 TGATATGAAATTTTGTGATGGCATACC 58.857 33.333 0.00 0.00 0.00 2.73
5418 6441 5.999205 TGAAATTTTGTGATGGCATACCT 57.001 34.783 0.00 0.00 36.63 3.08
5419 6442 6.357579 TGAAATTTTGTGATGGCATACCTT 57.642 33.333 0.00 0.00 36.63 3.50
5420 6443 6.397272 TGAAATTTTGTGATGGCATACCTTC 58.603 36.000 0.00 0.00 39.93 3.46
5421 6444 5.999205 AATTTTGTGATGGCATACCTTCA 57.001 34.783 0.00 0.00 45.32 3.02
5427 6450 4.233632 TGATGGCATACCTTCATGTTGA 57.766 40.909 0.00 0.00 43.31 3.18
5428 6451 4.201657 TGATGGCATACCTTCATGTTGAG 58.798 43.478 0.00 0.00 43.31 3.02
5429 6452 3.719268 TGGCATACCTTCATGTTGAGT 57.281 42.857 0.00 0.00 36.63 3.41
5430 6453 3.609853 TGGCATACCTTCATGTTGAGTC 58.390 45.455 0.00 0.00 36.63 3.36
5431 6454 3.008923 TGGCATACCTTCATGTTGAGTCA 59.991 43.478 0.00 0.00 36.63 3.41
5432 6455 4.009675 GGCATACCTTCATGTTGAGTCAA 58.990 43.478 0.08 0.08 0.00 3.18
5433 6456 4.641989 GGCATACCTTCATGTTGAGTCAAT 59.358 41.667 9.18 0.00 0.00 2.57
5434 6457 5.220931 GGCATACCTTCATGTTGAGTCAATC 60.221 44.000 9.18 3.86 0.00 2.67
5435 6458 5.587844 GCATACCTTCATGTTGAGTCAATCT 59.412 40.000 9.18 0.00 0.00 2.40
5436 6459 6.763135 GCATACCTTCATGTTGAGTCAATCTA 59.237 38.462 9.18 0.00 0.00 1.98
5437 6460 7.254590 GCATACCTTCATGTTGAGTCAATCTAC 60.255 40.741 9.18 0.00 34.64 2.59
5438 6461 6.365970 ACCTTCATGTTGAGTCAATCTACT 57.634 37.500 9.18 0.00 35.06 2.57
5439 6462 6.402222 ACCTTCATGTTGAGTCAATCTACTC 58.598 40.000 9.18 0.00 45.10 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
326 365 8.789762 GTCTTATTATCTTCTCTAGTCAGGGAC 58.210 40.741 0.00 0.00 28.07 4.46
465 504 6.684613 GCATACTTCAAAAGGCATGGATTGAT 60.685 38.462 0.00 0.00 32.35 2.57
468 507 4.467082 TGCATACTTCAAAAGGCATGGATT 59.533 37.500 0.00 0.00 0.00 3.01
474 513 2.819608 GTCCTGCATACTTCAAAAGGCA 59.180 45.455 0.00 0.00 0.00 4.75
549 588 9.914834 TTGTAGTAGCCATTCCAGTTTATAAAT 57.085 29.630 0.31 0.00 0.00 1.40
638 690 5.583457 CAGTGAGTGCATCATCAAGTCAATA 59.417 40.000 0.00 0.00 40.92 1.90
772 824 3.963428 TCCTAGTCCTTGTTCTGCTTC 57.037 47.619 0.00 0.00 0.00 3.86
774 826 3.196685 GTCATCCTAGTCCTTGTTCTGCT 59.803 47.826 0.00 0.00 0.00 4.24
810 862 3.181440 ACCACTTTTCTTCAGCTCCATGA 60.181 43.478 0.00 0.00 0.00 3.07
813 865 2.487265 GGACCACTTTTCTTCAGCTCCA 60.487 50.000 0.00 0.00 0.00 3.86
949 1003 8.866093 TGAGAAATCATGAATTGGCATCATATT 58.134 29.630 0.00 0.84 35.80 1.28
1283 1339 0.751277 TTCCACCCACTGCAGTTGTG 60.751 55.000 27.84 27.84 35.39 3.33
1486 1553 9.661187 CAAATATCACATGACTAGAATGCTTTC 57.339 33.333 0.00 4.20 0.00 2.62
1514 1581 6.441093 ACACTTAATTCATCATGATTGCGT 57.559 33.333 5.16 0.00 0.00 5.24
1579 1740 3.489047 CCACATGGTTTGTTTGCTTAACG 59.511 43.478 0.00 0.00 39.72 3.18
1663 1843 1.495579 ATCTGCAAGGACACAGGCCT 61.496 55.000 0.00 0.00 37.35 5.19
1681 1861 5.444744 TGTGTAAGGTAATGTGCCCTAAT 57.555 39.130 0.00 0.00 0.00 1.73
1757 1937 2.819608 CACCTTGACCCGATGACAATTT 59.180 45.455 0.00 0.00 0.00 1.82
1798 1978 3.129287 AGGCAATTGCTTCCTTATTCGTG 59.871 43.478 28.42 0.00 41.70 4.35
1888 2514 9.494271 ACATGTTCCTGCATAACTTACTATATG 57.506 33.333 11.92 8.35 33.58 1.78
2048 2674 7.693951 CACTTAAAAACGATCTCATCCATCAAC 59.306 37.037 0.00 0.00 0.00 3.18
2067 2693 5.163591 CCAGATGATCATTGCTGCACTTAAA 60.164 40.000 10.14 0.00 0.00 1.52
2290 2951 3.101437 ACATACTGGAATACACCACGGA 58.899 45.455 0.00 0.00 35.91 4.69
2343 3006 4.116782 CATCCATTGGAATCACCCCATA 57.883 45.455 9.98 0.00 34.34 2.74
2371 3034 6.379386 GCAAGTTATACCTTTTCCAGTTGTC 58.621 40.000 0.00 0.00 0.00 3.18
2417 3086 6.073657 GCAGACATTTTAATGCACATGTTGTT 60.074 34.615 0.00 0.00 40.04 2.83
2477 3154 9.513906 TGGAGTGAACTCAATCAAATGTAATTA 57.486 29.630 12.32 0.00 44.60 1.40
2517 3318 9.337091 CAACGGTGGTAAATCTAAAATTGTTAG 57.663 33.333 0.00 0.00 0.00 2.34
2519 3320 6.643360 GCAACGGTGGTAAATCTAAAATTGTT 59.357 34.615 0.90 0.00 0.00 2.83
2647 3457 3.632643 TCAGCTTCCTGCACATCATAA 57.367 42.857 0.00 0.00 45.94 1.90
2732 3560 6.410540 ACTCTTCACTCATATTTCTGGAACC 58.589 40.000 0.00 0.00 0.00 3.62
2820 3677 4.327680 AGTTGAAACCTTCATCTAGCCAC 58.672 43.478 0.00 0.00 39.84 5.01
2965 3823 2.538939 GGATTCAACGCTTTACCGATGC 60.539 50.000 0.00 0.00 32.05 3.91
2974 3832 5.161943 AGTAGTTAAGGGATTCAACGCTT 57.838 39.130 0.00 0.00 43.48 4.68
3192 4056 4.402155 GCTTTCCCAATATGTGACATGGAA 59.598 41.667 8.61 9.49 34.82 3.53
3201 4065 2.799126 TGGTCGCTTTCCCAATATGT 57.201 45.000 0.00 0.00 0.00 2.29
3258 4122 5.968676 TTCCTTTGTACACTAGGCCATAT 57.031 39.130 15.45 0.00 0.00 1.78
3595 4481 5.241403 TGTTTGAGATAAGCAAGGAGGAA 57.759 39.130 0.00 0.00 0.00 3.36
3641 4527 0.798776 CAAGCTTGTTACTCTGCCCG 59.201 55.000 18.65 0.00 0.00 6.13
3705 4591 7.883217 TGATCGATATTTCCTCCAGTTAGTAC 58.117 38.462 0.00 0.00 0.00 2.73
3708 4594 7.382110 ACATGATCGATATTTCCTCCAGTTAG 58.618 38.462 0.00 0.00 0.00 2.34
3713 4599 5.764686 CCAAACATGATCGATATTTCCTCCA 59.235 40.000 0.00 0.00 0.00 3.86
3723 4609 3.891366 GGGGAATTCCAAACATGATCGAT 59.109 43.478 25.67 0.00 37.91 3.59
3927 4813 2.283529 CCGGCTGGAGTGTAGGTGT 61.284 63.158 5.28 0.00 37.49 4.16
3981 4867 1.218316 GGCGTCGAGGAGGATGTTT 59.782 57.895 9.75 0.00 0.00 2.83
4035 4921 1.683790 GCTTTATCTGCACGACGCGT 61.684 55.000 13.85 13.85 46.97 6.01
4050 4936 2.607750 TCCTCCTCCAGCGGCTTT 60.608 61.111 0.00 0.00 0.00 3.51
4326 5212 1.071987 CAGGTTGCAGCACCTCAGA 59.928 57.895 7.14 0.00 44.63 3.27
4377 5263 3.763356 AGCGATCGCCAGTCAGCA 61.763 61.111 34.89 0.00 43.17 4.41
4380 5266 3.068064 TCCAGCGATCGCCAGTCA 61.068 61.111 34.89 13.20 43.17 3.41
4500 5404 7.703058 TCACAGACTAGACTCATTATGTTCA 57.297 36.000 0.00 0.00 0.00 3.18
4511 5416 6.209589 TGCAGTTTAGATTCACAGACTAGACT 59.790 38.462 0.00 0.00 33.80 3.24
4649 5619 7.722949 ACCACTCCATTGACATGATAAAATT 57.277 32.000 0.00 0.00 31.07 1.82
4650 5620 8.821686 TTACCACTCCATTGACATGATAAAAT 57.178 30.769 0.00 0.00 31.07 1.82
4691 5662 2.287009 GCGCTTCCCGAAATTTCCATAG 60.287 50.000 12.54 6.31 40.02 2.23
4714 5685 4.868172 TTGGATCCTGAGATGTTTGGAT 57.132 40.909 14.23 0.00 41.49 3.41
4763 5738 5.598005 TCAAGTTTCAACCCACTGAATGAAT 59.402 36.000 0.00 0.00 35.31 2.57
4770 5745 3.737972 GCCTTTCAAGTTTCAACCCACTG 60.738 47.826 0.00 0.00 0.00 3.66
4771 5746 2.430694 GCCTTTCAAGTTTCAACCCACT 59.569 45.455 0.00 0.00 0.00 4.00
4772 5747 2.798145 CGCCTTTCAAGTTTCAACCCAC 60.798 50.000 0.00 0.00 0.00 4.61
4773 5748 1.407258 CGCCTTTCAAGTTTCAACCCA 59.593 47.619 0.00 0.00 0.00 4.51
4774 5749 1.868109 GCGCCTTTCAAGTTTCAACCC 60.868 52.381 0.00 0.00 0.00 4.11
4775 5750 1.067060 AGCGCCTTTCAAGTTTCAACC 59.933 47.619 2.29 0.00 0.00 3.77
4776 5751 2.492019 AGCGCCTTTCAAGTTTCAAC 57.508 45.000 2.29 0.00 0.00 3.18
4777 5752 3.443976 GAAAGCGCCTTTCAAGTTTCAA 58.556 40.909 20.31 0.00 46.23 2.69
4778 5753 3.078594 GAAAGCGCCTTTCAAGTTTCA 57.921 42.857 20.31 0.00 46.23 2.69
4807 5782 1.201414 CGGCTGGTTTTACATGGGAAC 59.799 52.381 0.00 0.00 0.00 3.62
4872 5847 4.406173 CTCGTGCTGCGTCTCGGT 62.406 66.667 0.00 0.00 42.13 4.69
4873 5848 3.402691 ATCTCGTGCTGCGTCTCGG 62.403 63.158 0.00 0.00 42.13 4.63
4879 5854 2.298629 CCATCGATCTCGTGCTGCG 61.299 63.158 0.00 0.00 40.80 5.18
4888 5863 1.586422 CGTGCAAATCCCATCGATCT 58.414 50.000 0.00 0.00 0.00 2.75
4892 5867 2.408835 GCCGTGCAAATCCCATCG 59.591 61.111 0.00 0.00 0.00 3.84
4912 5888 3.182967 CGAACTGTGTTCTATGAGAGCC 58.817 50.000 8.51 0.00 0.00 4.70
4921 5897 2.693591 TCTCTCAACCGAACTGTGTTCT 59.306 45.455 8.51 0.00 0.00 3.01
4928 5904 1.551452 CCCTCTCTCTCAACCGAACT 58.449 55.000 0.00 0.00 0.00 3.01
4933 5909 0.689412 CCTCCCCCTCTCTCTCAACC 60.689 65.000 0.00 0.00 0.00 3.77
4934 5910 0.689412 CCCTCCCCCTCTCTCTCAAC 60.689 65.000 0.00 0.00 0.00 3.18
4935 5911 1.706575 CCCTCCCCCTCTCTCTCAA 59.293 63.158 0.00 0.00 0.00 3.02
4936 5912 2.328589 CCCCTCCCCCTCTCTCTCA 61.329 68.421 0.00 0.00 0.00 3.27
4937 5913 2.612251 CCCCTCCCCCTCTCTCTC 59.388 72.222 0.00 0.00 0.00 3.20
4938 5914 3.039526 CCCCCTCCCCCTCTCTCT 61.040 72.222 0.00 0.00 0.00 3.10
4972 5948 3.254617 AACCCGTCCCTCCAACCC 61.255 66.667 0.00 0.00 0.00 4.11
4973 5949 2.033602 CAACCCGTCCCTCCAACC 59.966 66.667 0.00 0.00 0.00 3.77
4974 5950 2.033602 CCAACCCGTCCCTCCAAC 59.966 66.667 0.00 0.00 0.00 3.77
4975 5951 2.079911 AACCAACCCGTCCCTCCAA 61.080 57.895 0.00 0.00 0.00 3.53
4976 5952 2.448931 AACCAACCCGTCCCTCCA 60.449 61.111 0.00 0.00 0.00 3.86
5070 6046 1.571919 CCTTTCTCTTATGGCGTCGG 58.428 55.000 0.00 0.00 0.00 4.79
5081 6057 2.663196 CGGCGTTCCCCTTTCTCT 59.337 61.111 0.00 0.00 0.00 3.10
5124 6100 1.261480 TCTGAGAGTCAAGACCCAGC 58.739 55.000 0.00 0.00 0.00 4.85
5125 6101 2.168106 CCATCTGAGAGTCAAGACCCAG 59.832 54.545 0.00 3.13 0.00 4.45
5126 6102 2.182827 CCATCTGAGAGTCAAGACCCA 58.817 52.381 0.00 0.00 0.00 4.51
5127 6103 1.484240 CCCATCTGAGAGTCAAGACCC 59.516 57.143 0.00 0.00 0.00 4.46
5151 6174 2.337246 AAAATACACACGGCGGGCC 61.337 57.895 10.14 0.00 0.00 5.80
5153 6176 1.504446 CCAAAATACACACGGCGGG 59.496 57.895 8.04 8.04 0.00 6.13
5220 6243 4.619437 TTTAGTCGAAAGCACCGTTTTT 57.381 36.364 0.00 0.00 0.00 1.94
5221 6244 4.619437 TTTTAGTCGAAAGCACCGTTTT 57.381 36.364 0.00 0.00 0.00 2.43
5222 6245 4.619437 TTTTTAGTCGAAAGCACCGTTT 57.381 36.364 0.00 0.00 0.00 3.60
5223 6246 4.823790 ATTTTTAGTCGAAAGCACCGTT 57.176 36.364 0.00 0.00 0.00 4.44
5224 6247 4.823790 AATTTTTAGTCGAAAGCACCGT 57.176 36.364 0.00 0.00 0.00 4.83
5225 6248 6.505039 AAAAATTTTTAGTCGAAAGCACCG 57.495 33.333 14.46 0.00 0.00 4.94
5246 6269 1.323412 ACATACGGGTGCAGCAAAAA 58.677 45.000 19.06 0.00 0.00 1.94
5247 6270 1.000827 CAACATACGGGTGCAGCAAAA 60.001 47.619 19.06 1.76 0.00 2.44
5248 6271 0.595588 CAACATACGGGTGCAGCAAA 59.404 50.000 19.06 2.16 0.00 3.68
5249 6272 1.240641 CCAACATACGGGTGCAGCAA 61.241 55.000 19.06 2.55 0.00 3.91
5250 6273 1.673993 CCAACATACGGGTGCAGCA 60.674 57.895 19.06 0.00 0.00 4.41
5251 6274 0.391927 TACCAACATACGGGTGCAGC 60.392 55.000 7.55 7.55 38.06 5.25
5252 6275 1.066430 ACTACCAACATACGGGTGCAG 60.066 52.381 0.00 0.00 38.06 4.41
5253 6276 0.978151 ACTACCAACATACGGGTGCA 59.022 50.000 0.00 0.00 38.06 4.57
5254 6277 2.167075 AGTACTACCAACATACGGGTGC 59.833 50.000 0.00 0.00 38.06 5.01
5255 6278 4.641989 AGTAGTACTACCAACATACGGGTG 59.358 45.833 25.97 0.00 38.06 4.61
5256 6279 4.860022 AGTAGTACTACCAACATACGGGT 58.140 43.478 25.97 3.63 41.21 5.28
5257 6280 6.305693 GTAGTAGTACTACCAACATACGGG 57.694 45.833 25.97 0.00 43.96 5.28
5274 6297 7.972850 CATTGGTAAATGCGCTACGGTAGTAG 61.973 46.154 16.05 11.57 43.07 2.57
5275 6298 2.687425 TGGTAAATGCGCTACGGTAGTA 59.313 45.455 16.05 4.55 0.00 1.82
5276 6299 1.477700 TGGTAAATGCGCTACGGTAGT 59.522 47.619 16.05 0.00 0.00 2.73
5277 6300 2.212869 TGGTAAATGCGCTACGGTAG 57.787 50.000 9.73 10.83 0.00 3.18
5278 6301 2.669300 TTGGTAAATGCGCTACGGTA 57.331 45.000 9.73 0.00 0.00 4.02
5279 6302 1.668751 CATTGGTAAATGCGCTACGGT 59.331 47.619 9.73 0.00 36.99 4.83
5280 6303 2.383298 CATTGGTAAATGCGCTACGG 57.617 50.000 9.73 0.00 36.99 4.02
5309 6332 9.325198 GGGTGAATGTGTTAATTTTTCTTTTCT 57.675 29.630 0.00 0.00 0.00 2.52
5310 6333 9.103861 TGGGTGAATGTGTTAATTTTTCTTTTC 57.896 29.630 0.00 0.00 0.00 2.29
5311 6334 9.454859 TTGGGTGAATGTGTTAATTTTTCTTTT 57.545 25.926 0.00 0.00 0.00 2.27
5312 6335 8.888716 GTTGGGTGAATGTGTTAATTTTTCTTT 58.111 29.630 0.00 0.00 0.00 2.52
5313 6336 8.043710 TGTTGGGTGAATGTGTTAATTTTTCTT 58.956 29.630 0.00 0.00 0.00 2.52
5314 6337 7.560368 TGTTGGGTGAATGTGTTAATTTTTCT 58.440 30.769 0.00 0.00 0.00 2.52
5315 6338 7.778470 TGTTGGGTGAATGTGTTAATTTTTC 57.222 32.000 0.00 0.00 0.00 2.29
5316 6339 8.619546 CAATGTTGGGTGAATGTGTTAATTTTT 58.380 29.630 0.00 0.00 0.00 1.94
5317 6340 7.228308 CCAATGTTGGGTGAATGTGTTAATTTT 59.772 33.333 3.80 0.00 44.70 1.82
5318 6341 6.709846 CCAATGTTGGGTGAATGTGTTAATTT 59.290 34.615 3.80 0.00 44.70 1.82
5319 6342 6.229733 CCAATGTTGGGTGAATGTGTTAATT 58.770 36.000 3.80 0.00 44.70 1.40
5320 6343 5.792741 CCAATGTTGGGTGAATGTGTTAAT 58.207 37.500 3.80 0.00 44.70 1.40
5321 6344 5.207110 CCAATGTTGGGTGAATGTGTTAA 57.793 39.130 3.80 0.00 44.70 2.01
5322 6345 4.862902 CCAATGTTGGGTGAATGTGTTA 57.137 40.909 3.80 0.00 44.70 2.41
5323 6346 3.749665 CCAATGTTGGGTGAATGTGTT 57.250 42.857 3.80 0.00 44.70 3.32
5337 6360 7.681939 ATTTTACGACAACATAGACCAATGT 57.318 32.000 0.00 0.00 41.87 2.71
5338 6361 8.964420 AAATTTTACGACAACATAGACCAATG 57.036 30.769 0.00 0.00 0.00 2.82
5364 6387 8.499162 CGGGCAATGTTGTAAAATTTTGATTTA 58.501 29.630 13.76 0.00 0.00 1.40
5365 6388 7.012799 ACGGGCAATGTTGTAAAATTTTGATTT 59.987 29.630 13.76 0.00 0.00 2.17
5366 6389 6.484977 ACGGGCAATGTTGTAAAATTTTGATT 59.515 30.769 13.76 1.90 0.00 2.57
5367 6390 5.994668 ACGGGCAATGTTGTAAAATTTTGAT 59.005 32.000 13.76 0.00 0.00 2.57
5368 6391 5.235186 CACGGGCAATGTTGTAAAATTTTGA 59.765 36.000 13.76 0.00 0.00 2.69
5369 6392 5.235186 TCACGGGCAATGTTGTAAAATTTTG 59.765 36.000 13.76 0.00 0.00 2.44
5370 6393 5.360591 TCACGGGCAATGTTGTAAAATTTT 58.639 33.333 8.75 8.75 0.00 1.82
5371 6394 4.950050 TCACGGGCAATGTTGTAAAATTT 58.050 34.783 0.00 0.00 0.00 1.82
5372 6395 4.592485 TCACGGGCAATGTTGTAAAATT 57.408 36.364 0.00 0.00 0.00 1.82
5373 6396 4.799564 ATCACGGGCAATGTTGTAAAAT 57.200 36.364 0.00 0.00 0.00 1.82
5374 6397 5.416013 TCATATCACGGGCAATGTTGTAAAA 59.584 36.000 0.00 0.00 0.00 1.52
5375 6398 4.944317 TCATATCACGGGCAATGTTGTAAA 59.056 37.500 0.00 0.00 0.00 2.01
5376 6399 4.518249 TCATATCACGGGCAATGTTGTAA 58.482 39.130 0.00 0.00 0.00 2.41
5377 6400 4.143986 TCATATCACGGGCAATGTTGTA 57.856 40.909 0.00 0.00 0.00 2.41
5378 6401 2.997980 TCATATCACGGGCAATGTTGT 58.002 42.857 0.00 0.00 0.00 3.32
5379 6402 4.368874 TTTCATATCACGGGCAATGTTG 57.631 40.909 0.00 0.00 0.00 3.33
5380 6403 5.596836 AATTTCATATCACGGGCAATGTT 57.403 34.783 0.00 0.00 0.00 2.71
5381 6404 5.596836 AAATTTCATATCACGGGCAATGT 57.403 34.783 0.00 0.00 0.00 2.71
5382 6405 5.811613 ACAAAATTTCATATCACGGGCAATG 59.188 36.000 0.00 0.00 0.00 2.82
5383 6406 5.811613 CACAAAATTTCATATCACGGGCAAT 59.188 36.000 0.00 0.00 0.00 3.56
5384 6407 5.047731 TCACAAAATTTCATATCACGGGCAA 60.048 36.000 0.00 0.00 0.00 4.52
5385 6408 4.460731 TCACAAAATTTCATATCACGGGCA 59.539 37.500 0.00 0.00 0.00 5.36
5386 6409 4.992688 TCACAAAATTTCATATCACGGGC 58.007 39.130 0.00 0.00 0.00 6.13
5387 6410 5.978919 CCATCACAAAATTTCATATCACGGG 59.021 40.000 0.00 0.00 0.00 5.28
5388 6411 5.459762 GCCATCACAAAATTTCATATCACGG 59.540 40.000 0.00 0.00 0.00 4.94
5389 6412 6.035217 TGCCATCACAAAATTTCATATCACG 58.965 36.000 0.00 0.00 0.00 4.35
5390 6413 8.971321 GTATGCCATCACAAAATTTCATATCAC 58.029 33.333 0.00 0.00 0.00 3.06
5391 6414 8.143193 GGTATGCCATCACAAAATTTCATATCA 58.857 33.333 0.00 0.00 34.09 2.15
5392 6415 8.362639 AGGTATGCCATCACAAAATTTCATATC 58.637 33.333 1.54 0.00 37.19 1.63
5393 6416 8.253867 AGGTATGCCATCACAAAATTTCATAT 57.746 30.769 1.54 0.00 37.19 1.78
5394 6417 7.658525 AGGTATGCCATCACAAAATTTCATA 57.341 32.000 1.54 0.00 37.19 2.15
5395 6418 6.549433 AGGTATGCCATCACAAAATTTCAT 57.451 33.333 1.54 0.00 37.19 2.57
5396 6419 5.999205 AGGTATGCCATCACAAAATTTCA 57.001 34.783 1.54 0.00 37.19 2.69
5397 6420 6.397272 TGAAGGTATGCCATCACAAAATTTC 58.603 36.000 3.43 0.00 37.54 2.17
5398 6421 6.357579 TGAAGGTATGCCATCACAAAATTT 57.642 33.333 3.43 0.00 37.54 1.82
5399 6422 5.999205 TGAAGGTATGCCATCACAAAATT 57.001 34.783 3.43 0.00 37.54 1.82
5400 6423 5.422970 ACATGAAGGTATGCCATCACAAAAT 59.577 36.000 10.06 0.00 44.12 1.82
5401 6424 4.771577 ACATGAAGGTATGCCATCACAAAA 59.228 37.500 10.06 0.00 44.12 2.44
5402 6425 4.343231 ACATGAAGGTATGCCATCACAAA 58.657 39.130 10.06 0.00 44.12 2.83
5403 6426 3.966979 ACATGAAGGTATGCCATCACAA 58.033 40.909 10.06 0.00 44.12 3.33
5404 6427 3.650281 ACATGAAGGTATGCCATCACA 57.350 42.857 10.06 0.76 44.12 3.58
5405 6428 3.947196 TCAACATGAAGGTATGCCATCAC 59.053 43.478 10.06 0.00 44.12 3.06
5406 6429 4.201657 CTCAACATGAAGGTATGCCATCA 58.798 43.478 10.26 10.26 45.20 3.07
5407 6430 4.202441 ACTCAACATGAAGGTATGCCATC 58.798 43.478 1.54 0.00 37.19 3.51
5408 6431 4.202441 GACTCAACATGAAGGTATGCCAT 58.798 43.478 1.54 0.00 37.19 4.40
5409 6432 3.008923 TGACTCAACATGAAGGTATGCCA 59.991 43.478 1.54 0.00 37.19 4.92
5410 6433 3.609853 TGACTCAACATGAAGGTATGCC 58.390 45.455 0.00 0.00 0.00 4.40
5411 6434 5.587844 AGATTGACTCAACATGAAGGTATGC 59.412 40.000 0.00 0.00 0.00 3.14
5412 6435 7.984050 AGTAGATTGACTCAACATGAAGGTATG 59.016 37.037 0.00 0.00 0.00 2.39
5413 6436 8.083828 AGTAGATTGACTCAACATGAAGGTAT 57.916 34.615 0.00 0.00 0.00 2.73
5414 6437 7.482169 AGTAGATTGACTCAACATGAAGGTA 57.518 36.000 0.00 0.00 0.00 3.08
5415 6438 6.365970 AGTAGATTGACTCAACATGAAGGT 57.634 37.500 0.00 0.00 0.00 3.50
5416 6439 5.518128 CGAGTAGATTGACTCAACATGAAGG 59.482 44.000 0.00 0.00 45.23 3.46
5417 6440 5.518128 CCGAGTAGATTGACTCAACATGAAG 59.482 44.000 0.00 0.00 45.23 3.02
5418 6441 5.047306 ACCGAGTAGATTGACTCAACATGAA 60.047 40.000 0.00 0.00 45.23 2.57
5419 6442 4.462834 ACCGAGTAGATTGACTCAACATGA 59.537 41.667 0.00 0.00 45.23 3.07
5420 6443 4.748892 ACCGAGTAGATTGACTCAACATG 58.251 43.478 4.58 0.00 45.23 3.21
5421 6444 5.407407 AACCGAGTAGATTGACTCAACAT 57.593 39.130 4.58 0.00 45.23 2.71
5422 6445 4.866508 AACCGAGTAGATTGACTCAACA 57.133 40.909 4.58 0.00 45.23 3.33
5423 6446 6.541111 AAAAACCGAGTAGATTGACTCAAC 57.459 37.500 4.58 0.00 45.23 3.18


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

AutoCloner maintained by Alex Coulton.