Multiple sequence alignment - TraesCS7D01G449500

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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 TraesCS7D01G449500 chr7D 100.000 5249 0 0 1 5249 568632878 568627630 0.000000e+00 9694.0
1 TraesCS7D01G449500 chr7D 83.650 263 15 6 320 557 194467388 194467129 6.840000e-54 222.0
2 TraesCS7D01G449500 chr7A 96.196 4916 138 21 1 4902 657421448 657416568 0.000000e+00 7997.0
3 TraesCS7D01G449500 chr7A 80.025 3139 603 18 1110 4234 625913088 625909960 0.000000e+00 2302.0
4 TraesCS7D01G449500 chr7B 96.441 4440 128 14 1 4421 624710947 624706519 0.000000e+00 7297.0
5 TraesCS7D01G449500 chr7B 92.308 273 18 1 4420 4689 624706357 624706085 8.250000e-103 385.0
6 TraesCS7D01G449500 chr7B 88.424 311 22 7 4588 4892 570672831 570672529 3.860000e-96 363.0
7 TraesCS7D01G449500 chr7B 91.018 167 7 3 4737 4902 624705894 624705735 8.850000e-53 219.0
8 TraesCS7D01G449500 chr7B 91.791 134 10 1 320 453 549936207 549936339 8.980000e-43 185.0
9 TraesCS7D01G449500 chr7B 93.651 63 3 1 4737 4798 624705995 624705933 5.600000e-15 93.5
10 TraesCS7D01G449500 chr2B 83.699 3147 479 27 1106 4234 734396035 734399165 0.000000e+00 2939.0
11 TraesCS7D01G449500 chr2B 88.274 307 23 9 4592 4892 558684132 558683833 6.470000e-94 355.0
12 TraesCS7D01G449500 chr2B 87.419 310 25 7 4588 4891 311967147 311966846 1.400000e-90 344.0
13 TraesCS7D01G449500 chr2B 83.525 261 16 9 320 555 355392562 355392820 8.850000e-53 219.0
14 TraesCS7D01G449500 chr3D 82.934 3211 510 29 1050 4241 26587053 26583862 0.000000e+00 2859.0
15 TraesCS7D01G449500 chr3A 82.563 3223 532 25 1063 4270 36662569 36659362 0.000000e+00 2811.0
16 TraesCS7D01G449500 chr3A 83.178 321 51 2 3924 4241 14770740 14770420 1.850000e-74 291.0
17 TraesCS7D01G449500 chr6B 81.523 3480 583 44 793 4234 65091125 65087668 0.000000e+00 2809.0
18 TraesCS7D01G449500 chr6B 82.368 3227 529 30 1027 4234 64689710 64686505 0.000000e+00 2771.0
19 TraesCS7D01G449500 chr6B 78.988 652 135 2 1081 1731 15277569 15276919 1.340000e-120 444.0
20 TraesCS7D01G449500 chr3B 82.539 3190 523 29 1063 4234 44787491 44784318 0.000000e+00 2774.0
21 TraesCS7D01G449500 chr3B 78.512 968 194 10 1663 2623 44761078 44762038 1.610000e-174 623.0
22 TraesCS7D01G449500 chr5B 81.332 3348 562 48 1020 4343 35549006 35545698 0.000000e+00 2662.0
23 TraesCS7D01G449500 chr5B 89.389 311 19 7 4588 4892 302655895 302655593 3.840000e-101 379.0
24 TraesCS7D01G449500 chr5B 87.781 311 24 8 4588 4892 611085806 611085504 8.360000e-93 351.0
25 TraesCS7D01G449500 chr4A 81.242 3204 560 31 1054 4233 657097087 657100273 0.000000e+00 2549.0
26 TraesCS7D01G449500 chr4A 81.220 3147 557 27 1106 4234 657201029 657204159 0.000000e+00 2507.0
27 TraesCS7D01G449500 chr6A 79.945 3276 591 41 1081 4341 1757644 1754420 0.000000e+00 2350.0
28 TraesCS7D01G449500 chr6A 79.908 652 129 2 1081 1731 9015593 9014943 1.320000e-130 477.0
29 TraesCS7D01G449500 chr6A 88.312 308 21 8 4592 4892 542012411 542012112 6.470000e-94 355.0
30 TraesCS7D01G449500 chrUn 81.469 2860 476 33 1508 4340 94836791 94839623 0.000000e+00 2296.0
31 TraesCS7D01G449500 chr6D 79.479 2534 469 34 1081 3602 2750548 2748054 0.000000e+00 1751.0
32 TraesCS7D01G449500 chr6D 78.931 655 133 4 1081 1731 24751461 24750808 1.740000e-119 440.0
33 TraesCS7D01G449500 chr2D 88.131 337 26 7 4592 4921 99507653 99507982 6.370000e-104 388.0
34 TraesCS7D01G449500 chr4B 88.746 311 21 7 4588 4892 139868384 139868686 8.300000e-98 368.0
35 TraesCS7D01G449500 chr1D 78.733 442 90 4 1614 2053 17672557 17672996 5.140000e-75 292.0
36 TraesCS7D01G449500 chr1A 90.625 64 4 2 5166 5228 552275570 552275508 3.370000e-12 84.2


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 TraesCS7D01G449500 chr7D 568627630 568632878 5248 True 9694.000 9694 100.0000 1 5249 1 chr7D.!!$R2 5248
1 TraesCS7D01G449500 chr7A 657416568 657421448 4880 True 7997.000 7997 96.1960 1 4902 1 chr7A.!!$R2 4901
2 TraesCS7D01G449500 chr7A 625909960 625913088 3128 True 2302.000 2302 80.0250 1110 4234 1 chr7A.!!$R1 3124
3 TraesCS7D01G449500 chr7B 624705735 624710947 5212 True 1998.625 7297 93.3545 1 4902 4 chr7B.!!$R2 4901
4 TraesCS7D01G449500 chr2B 734396035 734399165 3130 False 2939.000 2939 83.6990 1106 4234 1 chr2B.!!$F2 3128
5 TraesCS7D01G449500 chr3D 26583862 26587053 3191 True 2859.000 2859 82.9340 1050 4241 1 chr3D.!!$R1 3191
6 TraesCS7D01G449500 chr3A 36659362 36662569 3207 True 2811.000 2811 82.5630 1063 4270 1 chr3A.!!$R2 3207
7 TraesCS7D01G449500 chr6B 65087668 65091125 3457 True 2809.000 2809 81.5230 793 4234 1 chr6B.!!$R3 3441
8 TraesCS7D01G449500 chr6B 64686505 64689710 3205 True 2771.000 2771 82.3680 1027 4234 1 chr6B.!!$R2 3207
9 TraesCS7D01G449500 chr6B 15276919 15277569 650 True 444.000 444 78.9880 1081 1731 1 chr6B.!!$R1 650
10 TraesCS7D01G449500 chr3B 44784318 44787491 3173 True 2774.000 2774 82.5390 1063 4234 1 chr3B.!!$R1 3171
11 TraesCS7D01G449500 chr3B 44761078 44762038 960 False 623.000 623 78.5120 1663 2623 1 chr3B.!!$F1 960
12 TraesCS7D01G449500 chr5B 35545698 35549006 3308 True 2662.000 2662 81.3320 1020 4343 1 chr5B.!!$R1 3323
13 TraesCS7D01G449500 chr4A 657097087 657100273 3186 False 2549.000 2549 81.2420 1054 4233 1 chr4A.!!$F1 3179
14 TraesCS7D01G449500 chr4A 657201029 657204159 3130 False 2507.000 2507 81.2200 1106 4234 1 chr4A.!!$F2 3128
15 TraesCS7D01G449500 chr6A 1754420 1757644 3224 True 2350.000 2350 79.9450 1081 4341 1 chr6A.!!$R1 3260
16 TraesCS7D01G449500 chr6A 9014943 9015593 650 True 477.000 477 79.9080 1081 1731 1 chr6A.!!$R2 650
17 TraesCS7D01G449500 chrUn 94836791 94839623 2832 False 2296.000 2296 81.4690 1508 4340 1 chrUn.!!$F1 2832
18 TraesCS7D01G449500 chr6D 2748054 2750548 2494 True 1751.000 1751 79.4790 1081 3602 1 chr6D.!!$R1 2521
19 TraesCS7D01G449500 chr6D 24750808 24751461 653 True 440.000 440 78.9310 1081 1731 1 chr6D.!!$R2 650


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
780 793 0.330604 ATCTCACCAACTGCCATGCT 59.669 50.000 0.00 0.00 0.00 3.79 F
1777 1830 0.934496 CAACTTGTCGTCGCTGGAAA 59.066 50.000 0.00 0.00 0.00 3.13 F
3302 3367 2.482721 ACGGTGCAGTTTATAAGTGTGC 59.517 45.455 8.21 8.21 34.28 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2568 2630 0.245539 CCAAGCTGCCAACCTCATTG 59.754 55.000 0.00 0.0 38.12 2.82 R
3463 3528 2.887152 ACACCAATGCCTTGAACTCTTC 59.113 45.455 2.97 0.0 34.04 2.87 R
5007 5413 0.031515 TCCCCGGAGATTGCCTTCTA 60.032 55.000 0.73 0.0 0.00 2.10 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
71 72 6.405538 AGCAAAGGTTCTGAAACATGAAAAA 58.594 32.000 8.34 0.00 37.10 1.94
130 131 8.344831 CGCATCCATCTATTGAGAAATTTAACA 58.655 33.333 0.00 0.00 34.61 2.41
223 224 6.116806 TCCTAAAAAGTCGCTAAATATGGCA 58.883 36.000 0.00 0.00 31.43 4.92
540 545 2.936202 TCAAAGCAGAAACCTTGAGCT 58.064 42.857 0.00 0.00 37.08 4.09
687 692 6.109359 AGTAGCCAAACTCAGATACAATCAC 58.891 40.000 0.00 0.00 0.00 3.06
688 693 4.910195 AGCCAAACTCAGATACAATCACA 58.090 39.130 0.00 0.00 0.00 3.58
780 793 0.330604 ATCTCACCAACTGCCATGCT 59.669 50.000 0.00 0.00 0.00 3.79
786 799 1.179152 CCAACTGCCATGCTGATTGA 58.821 50.000 0.00 0.00 0.00 2.57
869 883 6.633500 TGTTGGACAGTTTTGAGATTTAGG 57.367 37.500 0.00 0.00 0.00 2.69
917 932 7.093945 GGACAAAAGGTCTAAATTATTGCTGGA 60.094 37.037 0.00 0.00 46.16 3.86
976 995 4.394920 AGTTGTTGGAATATTAGCACACCG 59.605 41.667 0.00 0.00 0.00 4.94
1539 1590 2.364842 ATCCCAGCTGAGCTCGGT 60.365 61.111 23.36 13.62 38.11 4.69
1777 1830 0.934496 CAACTTGTCGTCGCTGGAAA 59.066 50.000 0.00 0.00 0.00 3.13
1845 1898 5.242838 TGATATTGACAACAAGTTCCCCAAC 59.757 40.000 0.00 0.00 39.46 3.77
1912 1965 9.051259 CCATCCCTTCCTCAATATCTAATCTAA 57.949 37.037 0.00 0.00 0.00 2.10
2660 2722 5.300752 ACCGGATAGTATTCAGAATTGCAG 58.699 41.667 9.46 0.00 0.00 4.41
2668 2730 6.705302 AGTATTCAGAATTGCAGAGTCTTGA 58.295 36.000 0.00 0.00 28.33 3.02
3163 3228 2.610479 CGTAGGAAGCTCAGACAAAGCA 60.610 50.000 0.00 0.00 42.35 3.91
3302 3367 2.482721 ACGGTGCAGTTTATAAGTGTGC 59.517 45.455 8.21 8.21 34.28 4.57
3553 3618 2.069273 CTCAAGAGCCCACTACAAACG 58.931 52.381 0.00 0.00 0.00 3.60
3971 4047 3.745799 TGCTTGAGATGTTTACCGGAAA 58.254 40.909 9.46 1.01 0.00 3.13
4243 4322 2.081725 TGCATACCTCGCGTTTGTTA 57.918 45.000 5.77 0.00 0.00 2.41
4358 4437 3.751175 TCCTGCAATTTATATGTAGCGCC 59.249 43.478 2.29 0.00 0.00 6.53
4524 4776 1.471287 CACACATGCTGGGAACATCAG 59.529 52.381 0.00 0.00 40.26 2.90
4544 4796 8.708378 ACATCAGTTCATGATTAAGATAGACCA 58.292 33.333 0.00 0.00 46.97 4.02
4556 4808 9.303537 GATTAAGATAGACCAGTAGACAACAAC 57.696 37.037 0.00 0.00 0.00 3.32
4568 4820 2.169352 AGACAACAACTGAGACTGCACT 59.831 45.455 0.00 0.00 0.00 4.40
4598 4850 6.072286 AGCATGGTTCATCTGTAGAAAAACAG 60.072 38.462 0.00 0.00 46.78 3.16
4604 4856 7.148787 GGTTCATCTGTAGAAAAACAGTAGACG 60.149 40.741 4.11 0.00 45.78 4.18
4685 4947 5.181811 CAGCATAGATTCAGACACCACAAAA 59.818 40.000 0.00 0.00 0.00 2.44
4707 4969 7.977789 AAAAAGCTGTCCAAAAGAAAGAAAA 57.022 28.000 0.00 0.00 30.30 2.29
4708 4970 7.977789 AAAAGCTGTCCAAAAGAAAGAAAAA 57.022 28.000 0.00 0.00 30.30 1.94
4709 4971 6.968131 AAGCTGTCCAAAAGAAAGAAAAAC 57.032 33.333 0.00 0.00 30.30 2.43
4710 4972 5.102313 AGCTGTCCAAAAGAAAGAAAAACG 58.898 37.500 0.00 0.00 30.30 3.60
4764 5068 6.186957 TCAGACATACACCAGGCAATAATTT 58.813 36.000 0.00 0.00 0.00 1.82
4767 5071 6.835488 AGACATACACCAGGCAATAATTTCAT 59.165 34.615 0.00 0.00 0.00 2.57
4786 5192 5.996669 TCATAAGTAGCAGCACATCAATG 57.003 39.130 0.00 0.00 0.00 2.82
4827 5233 2.846039 ACGATACTACAAGGCTCACG 57.154 50.000 0.00 0.00 0.00 4.35
4828 5234 2.362736 ACGATACTACAAGGCTCACGA 58.637 47.619 0.00 0.00 0.00 4.35
4829 5235 2.355132 ACGATACTACAAGGCTCACGAG 59.645 50.000 0.00 0.00 0.00 4.18
4830 5236 2.355132 CGATACTACAAGGCTCACGAGT 59.645 50.000 0.00 0.00 0.00 4.18
4831 5237 3.546417 CGATACTACAAGGCTCACGAGTC 60.546 52.174 0.00 0.00 0.00 3.36
4832 5238 1.617322 ACTACAAGGCTCACGAGTCA 58.383 50.000 0.87 0.00 34.98 3.41
4833 5239 1.269998 ACTACAAGGCTCACGAGTCAC 59.730 52.381 0.87 0.00 34.98 3.67
4838 5244 2.872001 GCTCACGAGTCACGAGCG 60.872 66.667 13.36 0.00 45.77 5.03
4902 5308 1.003355 AGGGTGTGATCTTGGTGCG 60.003 57.895 0.00 0.00 0.00 5.34
4903 5309 2.040544 GGGTGTGATCTTGGTGCGG 61.041 63.158 0.00 0.00 0.00 5.69
4904 5310 2.690778 GGTGTGATCTTGGTGCGGC 61.691 63.158 0.00 0.00 0.00 6.53
4905 5311 2.741985 TGTGATCTTGGTGCGGCG 60.742 61.111 0.51 0.51 0.00 6.46
4906 5312 2.742372 GTGATCTTGGTGCGGCGT 60.742 61.111 9.37 0.00 0.00 5.68
4907 5313 2.741985 TGATCTTGGTGCGGCGTG 60.742 61.111 9.37 0.00 0.00 5.34
4908 5314 4.166011 GATCTTGGTGCGGCGTGC 62.166 66.667 9.37 0.96 46.70 5.34
4909 5315 4.704833 ATCTTGGTGCGGCGTGCT 62.705 61.111 9.37 0.00 46.63 4.40
4910 5316 4.927782 TCTTGGTGCGGCGTGCTT 62.928 61.111 9.37 0.00 46.63 3.91
4911 5317 4.688419 CTTGGTGCGGCGTGCTTG 62.688 66.667 9.37 0.00 46.63 4.01
4939 5345 3.528370 CGGGTAGGGTGAGGCGAG 61.528 72.222 0.00 0.00 0.00 5.03
4940 5346 3.851128 GGGTAGGGTGAGGCGAGC 61.851 72.222 0.00 0.00 0.00 5.03
4941 5347 4.208686 GGTAGGGTGAGGCGAGCG 62.209 72.222 0.00 0.00 0.00 5.03
4942 5348 4.208686 GTAGGGTGAGGCGAGCGG 62.209 72.222 0.00 0.00 0.00 5.52
4943 5349 4.435970 TAGGGTGAGGCGAGCGGA 62.436 66.667 0.00 0.00 0.00 5.54
4958 5364 2.107141 GGAGGTCCGGATCTTGCG 59.893 66.667 20.66 0.00 0.00 4.85
4959 5365 2.423898 GGAGGTCCGGATCTTGCGA 61.424 63.158 20.66 0.00 30.86 5.10
4960 5366 1.066587 GAGGTCCGGATCTTGCGAG 59.933 63.158 20.66 0.00 30.86 5.03
4961 5367 1.379977 AGGTCCGGATCTTGCGAGA 60.380 57.895 12.79 6.01 30.86 4.04
4962 5368 1.066587 GGTCCGGATCTTGCGAGAG 59.933 63.158 7.81 0.00 34.85 3.20
4963 5369 1.384989 GGTCCGGATCTTGCGAGAGA 61.385 60.000 7.81 0.00 34.85 3.10
4964 5370 0.030101 GTCCGGATCTTGCGAGAGAG 59.970 60.000 7.81 3.22 34.85 3.20
4965 5371 0.107165 TCCGGATCTTGCGAGAGAGA 60.107 55.000 10.06 0.70 34.85 3.10
4966 5372 0.958091 CCGGATCTTGCGAGAGAGAT 59.042 55.000 10.06 0.00 34.85 2.75
4967 5373 1.335780 CCGGATCTTGCGAGAGAGATG 60.336 57.143 10.06 0.00 34.85 2.90
4968 5374 1.782044 GGATCTTGCGAGAGAGATGC 58.218 55.000 10.06 0.31 34.85 3.91
4969 5375 1.407434 GATCTTGCGAGAGAGATGCG 58.593 55.000 10.06 0.00 34.85 4.73
4970 5376 0.031857 ATCTTGCGAGAGAGATGCGG 59.968 55.000 10.06 0.00 34.85 5.69
4971 5377 1.032114 TCTTGCGAGAGAGATGCGGA 61.032 55.000 0.00 0.00 0.00 5.54
4972 5378 0.594540 CTTGCGAGAGAGATGCGGAG 60.595 60.000 0.00 0.00 0.00 4.63
4973 5379 2.009424 TTGCGAGAGAGATGCGGAGG 62.009 60.000 0.00 0.00 0.00 4.30
4974 5380 2.190170 GCGAGAGAGATGCGGAGGA 61.190 63.158 0.00 0.00 0.00 3.71
4975 5381 1.652012 CGAGAGAGATGCGGAGGAC 59.348 63.158 0.00 0.00 0.00 3.85
4976 5382 0.817634 CGAGAGAGATGCGGAGGACT 60.818 60.000 0.00 0.00 0.00 3.85
4977 5383 0.667993 GAGAGAGATGCGGAGGACTG 59.332 60.000 0.00 0.00 0.00 3.51
4978 5384 0.754957 AGAGAGATGCGGAGGACTGG 60.755 60.000 0.00 0.00 0.00 4.00
4979 5385 1.000993 AGAGATGCGGAGGACTGGT 59.999 57.895 0.00 0.00 0.00 4.00
4980 5386 1.142748 GAGATGCGGAGGACTGGTG 59.857 63.158 0.00 0.00 0.00 4.17
4981 5387 2.187946 GATGCGGAGGACTGGTGG 59.812 66.667 0.00 0.00 0.00 4.61
4982 5388 2.284625 ATGCGGAGGACTGGTGGA 60.285 61.111 0.00 0.00 0.00 4.02
4983 5389 2.303549 GATGCGGAGGACTGGTGGAG 62.304 65.000 0.00 0.00 0.00 3.86
4984 5390 3.775654 GCGGAGGACTGGTGGAGG 61.776 72.222 0.00 0.00 0.00 4.30
4985 5391 3.077556 CGGAGGACTGGTGGAGGG 61.078 72.222 0.00 0.00 0.00 4.30
4986 5392 2.450243 GGAGGACTGGTGGAGGGA 59.550 66.667 0.00 0.00 0.00 4.20
4987 5393 1.003573 GGAGGACTGGTGGAGGGAT 59.996 63.158 0.00 0.00 0.00 3.85
4988 5394 0.621862 GGAGGACTGGTGGAGGGATT 60.622 60.000 0.00 0.00 0.00 3.01
4989 5395 0.833949 GAGGACTGGTGGAGGGATTC 59.166 60.000 0.00 0.00 0.00 2.52
4990 5396 0.119155 AGGACTGGTGGAGGGATTCA 59.881 55.000 0.00 0.00 0.00 2.57
4991 5397 0.253327 GGACTGGTGGAGGGATTCAC 59.747 60.000 0.00 0.00 0.00 3.18
4992 5398 1.280457 GACTGGTGGAGGGATTCACT 58.720 55.000 0.00 0.00 34.57 3.41
4993 5399 0.987294 ACTGGTGGAGGGATTCACTG 59.013 55.000 0.00 0.00 34.57 3.66
4994 5400 0.254178 CTGGTGGAGGGATTCACTGG 59.746 60.000 0.00 0.00 34.57 4.00
4995 5401 1.077429 GGTGGAGGGATTCACTGGC 60.077 63.158 0.00 0.00 34.57 4.85
4996 5402 1.450312 GTGGAGGGATTCACTGGCG 60.450 63.158 0.00 0.00 0.00 5.69
4997 5403 2.190578 GGAGGGATTCACTGGCGG 59.809 66.667 0.00 0.00 0.00 6.13
4998 5404 2.367202 GGAGGGATTCACTGGCGGA 61.367 63.158 0.00 0.00 0.00 5.54
4999 5405 1.144936 GAGGGATTCACTGGCGGAG 59.855 63.158 0.00 0.00 0.00 4.63
5000 5406 2.190578 GGGATTCACTGGCGGAGG 59.809 66.667 0.00 0.00 0.00 4.30
5001 5407 2.190578 GGATTCACTGGCGGAGGG 59.809 66.667 0.00 0.00 0.00 4.30
5002 5408 2.190578 GATTCACTGGCGGAGGGG 59.809 66.667 0.00 0.00 0.00 4.79
5003 5409 3.406595 GATTCACTGGCGGAGGGGG 62.407 68.421 0.00 0.00 0.00 5.40
5012 5418 3.917760 CGGAGGGGGCGCTAGAAG 61.918 72.222 7.64 0.00 0.00 2.85
5013 5419 3.551407 GGAGGGGGCGCTAGAAGG 61.551 72.222 7.64 0.00 0.00 3.46
5014 5420 4.243008 GAGGGGGCGCTAGAAGGC 62.243 72.222 7.64 0.00 0.00 4.35
5016 5422 4.109675 GGGGGCGCTAGAAGGCAA 62.110 66.667 7.64 0.00 35.71 4.52
5017 5423 2.193248 GGGGCGCTAGAAGGCAAT 59.807 61.111 7.64 0.00 35.71 3.56
5018 5424 1.894282 GGGGCGCTAGAAGGCAATC 60.894 63.158 7.64 0.00 35.71 2.67
5019 5425 1.147153 GGGCGCTAGAAGGCAATCT 59.853 57.895 7.64 0.00 35.71 2.40
5020 5426 0.882484 GGGCGCTAGAAGGCAATCTC 60.882 60.000 7.64 0.00 35.71 2.75
5021 5427 0.882484 GGCGCTAGAAGGCAATCTCC 60.882 60.000 7.64 0.00 0.00 3.71
5022 5428 1.218230 GCGCTAGAAGGCAATCTCCG 61.218 60.000 0.00 3.31 0.00 4.63
5023 5429 0.598680 CGCTAGAAGGCAATCTCCGG 60.599 60.000 0.00 0.00 0.00 5.14
5024 5430 0.250081 GCTAGAAGGCAATCTCCGGG 60.250 60.000 0.00 0.00 0.00 5.73
5025 5431 0.394565 CTAGAAGGCAATCTCCGGGG 59.605 60.000 0.00 0.00 0.00 5.73
5026 5432 0.031515 TAGAAGGCAATCTCCGGGGA 60.032 55.000 6.42 6.42 0.00 4.81
5027 5433 0.695803 AGAAGGCAATCTCCGGGGAT 60.696 55.000 12.32 12.32 0.00 3.85
5028 5434 0.250510 GAAGGCAATCTCCGGGGATC 60.251 60.000 19.50 5.78 0.00 3.36
5029 5435 2.031163 GGCAATCTCCGGGGATCG 59.969 66.667 19.50 7.85 38.88 3.69
5030 5436 2.507854 GGCAATCTCCGGGGATCGA 61.508 63.158 19.50 0.00 42.43 3.59
5031 5437 1.445942 GCAATCTCCGGGGATCGAA 59.554 57.895 19.50 0.00 42.43 3.71
5032 5438 0.880718 GCAATCTCCGGGGATCGAAC 60.881 60.000 19.50 3.56 42.43 3.95
5033 5439 0.753262 CAATCTCCGGGGATCGAACT 59.247 55.000 19.50 0.00 42.43 3.01
5034 5440 1.961394 CAATCTCCGGGGATCGAACTA 59.039 52.381 19.50 0.00 42.43 2.24
5035 5441 2.364324 CAATCTCCGGGGATCGAACTAA 59.636 50.000 19.50 0.00 42.43 2.24
5036 5442 2.148446 TCTCCGGGGATCGAACTAAA 57.852 50.000 0.00 0.00 42.43 1.85
5037 5443 2.459644 TCTCCGGGGATCGAACTAAAA 58.540 47.619 0.00 0.00 42.43 1.52
5038 5444 3.036091 TCTCCGGGGATCGAACTAAAAT 58.964 45.455 0.00 0.00 42.43 1.82
5039 5445 4.217510 TCTCCGGGGATCGAACTAAAATA 58.782 43.478 0.00 0.00 42.43 1.40
5040 5446 4.836736 TCTCCGGGGATCGAACTAAAATAT 59.163 41.667 0.00 0.00 42.43 1.28
5041 5447 4.890088 TCCGGGGATCGAACTAAAATATG 58.110 43.478 0.00 0.00 42.43 1.78
5042 5448 3.435671 CCGGGGATCGAACTAAAATATGC 59.564 47.826 0.00 0.00 42.43 3.14
5043 5449 4.062293 CGGGGATCGAACTAAAATATGCA 58.938 43.478 0.00 0.00 42.43 3.96
5044 5450 4.084013 CGGGGATCGAACTAAAATATGCAC 60.084 45.833 0.00 0.00 42.43 4.57
5045 5451 4.819630 GGGGATCGAACTAAAATATGCACA 59.180 41.667 0.00 0.00 0.00 4.57
5046 5452 5.473504 GGGGATCGAACTAAAATATGCACAT 59.526 40.000 0.00 0.00 0.00 3.21
5047 5453 6.348540 GGGGATCGAACTAAAATATGCACATC 60.349 42.308 0.00 0.00 0.00 3.06
5048 5454 6.428159 GGGATCGAACTAAAATATGCACATCT 59.572 38.462 0.00 0.00 0.00 2.90
5049 5455 7.293745 GGATCGAACTAAAATATGCACATCTG 58.706 38.462 0.00 0.00 0.00 2.90
5050 5456 6.603237 TCGAACTAAAATATGCACATCTGG 57.397 37.500 0.00 0.00 0.00 3.86
5051 5457 5.527214 TCGAACTAAAATATGCACATCTGGG 59.473 40.000 0.00 0.00 0.00 4.45
5052 5458 5.277974 CGAACTAAAATATGCACATCTGGGG 60.278 44.000 0.00 0.00 0.00 4.96
5053 5459 3.891366 ACTAAAATATGCACATCTGGGGC 59.109 43.478 0.00 0.00 0.00 5.80
5054 5460 1.321474 AAATATGCACATCTGGGGCG 58.679 50.000 0.00 0.00 0.00 6.13
5055 5461 0.538057 AATATGCACATCTGGGGCGG 60.538 55.000 0.00 0.00 0.00 6.13
5056 5462 1.708993 ATATGCACATCTGGGGCGGT 61.709 55.000 0.00 0.00 0.00 5.68
5057 5463 1.920734 TATGCACATCTGGGGCGGTT 61.921 55.000 0.00 0.00 0.00 4.44
5058 5464 3.134127 GCACATCTGGGGCGGTTC 61.134 66.667 0.00 0.00 0.00 3.62
5059 5465 2.671070 CACATCTGGGGCGGTTCT 59.329 61.111 0.00 0.00 0.00 3.01
5060 5466 1.450312 CACATCTGGGGCGGTTCTC 60.450 63.158 0.00 0.00 0.00 2.87
5061 5467 2.190578 CATCTGGGGCGGTTCTCC 59.809 66.667 0.00 0.00 0.00 3.71
5062 5468 2.285368 ATCTGGGGCGGTTCTCCA 60.285 61.111 0.00 0.00 0.00 3.86
5063 5469 1.694169 ATCTGGGGCGGTTCTCCAT 60.694 57.895 0.00 0.00 0.00 3.41
5064 5470 1.281925 ATCTGGGGCGGTTCTCCATT 61.282 55.000 0.00 0.00 0.00 3.16
5065 5471 1.750399 CTGGGGCGGTTCTCCATTG 60.750 63.158 0.00 0.00 0.00 2.82
5066 5472 2.440247 GGGGCGGTTCTCCATTGG 60.440 66.667 0.00 0.00 0.00 3.16
5067 5473 2.440247 GGGCGGTTCTCCATTGGG 60.440 66.667 2.09 0.00 0.00 4.12
5068 5474 2.440247 GGCGGTTCTCCATTGGGG 60.440 66.667 2.09 0.00 38.37 4.96
5069 5475 2.440247 GCGGTTCTCCATTGGGGG 60.440 66.667 1.86 0.00 37.22 5.40
5070 5476 2.440247 CGGTTCTCCATTGGGGGC 60.440 66.667 1.86 0.00 33.18 5.80
5071 5477 2.042944 GGTTCTCCATTGGGGGCC 60.043 66.667 1.86 0.00 33.18 5.80
5072 5478 2.770130 GTTCTCCATTGGGGGCCA 59.230 61.111 4.39 0.00 33.18 5.36
5081 5487 3.567902 TTGGGGGCCAAAGAACATT 57.432 47.368 4.39 0.00 40.92 2.71
5082 5488 1.813102 TTGGGGGCCAAAGAACATTT 58.187 45.000 4.39 0.00 40.92 2.32
5083 5489 1.813102 TGGGGGCCAAAGAACATTTT 58.187 45.000 4.39 0.00 0.00 1.82
5084 5490 2.131023 TGGGGGCCAAAGAACATTTTT 58.869 42.857 4.39 0.00 0.00 1.94
5107 5513 5.773239 TTTTTAACGATAACAGGAGAGCG 57.227 39.130 0.00 0.00 0.00 5.03
5108 5514 4.707030 TTTAACGATAACAGGAGAGCGA 57.293 40.909 0.00 0.00 0.00 4.93
5109 5515 4.707030 TTAACGATAACAGGAGAGCGAA 57.293 40.909 0.00 0.00 0.00 4.70
5110 5516 3.587797 AACGATAACAGGAGAGCGAAA 57.412 42.857 0.00 0.00 0.00 3.46
5111 5517 3.587797 ACGATAACAGGAGAGCGAAAA 57.412 42.857 0.00 0.00 0.00 2.29
5112 5518 4.124851 ACGATAACAGGAGAGCGAAAAT 57.875 40.909 0.00 0.00 0.00 1.82
5113 5519 4.504858 ACGATAACAGGAGAGCGAAAATT 58.495 39.130 0.00 0.00 0.00 1.82
5114 5520 4.567159 ACGATAACAGGAGAGCGAAAATTC 59.433 41.667 0.00 0.00 0.00 2.17
5115 5521 4.025647 CGATAACAGGAGAGCGAAAATTCC 60.026 45.833 0.00 0.00 0.00 3.01
5116 5522 3.425162 AACAGGAGAGCGAAAATTCCT 57.575 42.857 0.00 0.00 40.63 3.36
5117 5523 3.425162 ACAGGAGAGCGAAAATTCCTT 57.575 42.857 0.00 0.00 37.97 3.36
5118 5524 3.756117 ACAGGAGAGCGAAAATTCCTTT 58.244 40.909 0.00 0.00 37.97 3.11
5119 5525 3.753797 ACAGGAGAGCGAAAATTCCTTTC 59.246 43.478 0.00 0.00 37.97 2.62
5126 5532 2.941453 GAAAATTCCTTTCGGAGGCC 57.059 50.000 0.00 0.00 45.87 5.19
5137 5543 2.203126 GGAGGCCGAGCTCCAATG 60.203 66.667 8.47 0.00 39.45 2.82
5138 5544 2.735772 GGAGGCCGAGCTCCAATGA 61.736 63.158 8.47 0.00 39.45 2.57
5139 5545 1.227497 GAGGCCGAGCTCCAATGAG 60.227 63.158 8.47 0.00 41.84 2.90
5140 5546 2.203126 GGCCGAGCTCCAATGAGG 60.203 66.667 8.47 3.22 39.14 3.86
5141 5547 2.899339 GCCGAGCTCCAATGAGGC 60.899 66.667 8.47 10.27 39.14 4.70
5142 5548 2.906458 CCGAGCTCCAATGAGGCT 59.094 61.111 8.47 0.00 39.14 4.58
5143 5549 1.523258 CCGAGCTCCAATGAGGCTG 60.523 63.158 8.47 0.00 39.14 4.85
5144 5550 1.523258 CGAGCTCCAATGAGGCTGG 60.523 63.158 8.47 0.00 39.14 4.85
5145 5551 1.606531 GAGCTCCAATGAGGCTGGT 59.393 57.895 0.87 0.00 39.14 4.00
5146 5552 0.034670 GAGCTCCAATGAGGCTGGTT 60.035 55.000 0.87 0.00 39.14 3.67
5147 5553 0.407139 AGCTCCAATGAGGCTGGTTT 59.593 50.000 0.00 0.00 39.14 3.27
5148 5554 1.203100 AGCTCCAATGAGGCTGGTTTT 60.203 47.619 0.00 0.00 39.14 2.43
5149 5555 1.620323 GCTCCAATGAGGCTGGTTTTT 59.380 47.619 0.00 0.00 39.14 1.94
5150 5556 2.611224 GCTCCAATGAGGCTGGTTTTTG 60.611 50.000 0.00 0.00 39.14 2.44
5151 5557 2.892852 CTCCAATGAGGCTGGTTTTTGA 59.107 45.455 0.00 0.00 37.29 2.69
5152 5558 3.303938 TCCAATGAGGCTGGTTTTTGAA 58.696 40.909 0.00 0.00 37.29 2.69
5153 5559 3.708631 TCCAATGAGGCTGGTTTTTGAAA 59.291 39.130 0.00 0.00 37.29 2.69
5154 5560 4.163078 TCCAATGAGGCTGGTTTTTGAAAA 59.837 37.500 0.00 0.00 37.29 2.29
5155 5561 4.880696 CCAATGAGGCTGGTTTTTGAAAAA 59.119 37.500 0.00 0.00 0.00 1.94
5156 5562 5.532032 CCAATGAGGCTGGTTTTTGAAAAAT 59.468 36.000 6.35 0.00 0.00 1.82
5157 5563 6.039605 CCAATGAGGCTGGTTTTTGAAAAATT 59.960 34.615 6.35 0.00 0.00 1.82
5158 5564 6.866010 ATGAGGCTGGTTTTTGAAAAATTC 57.134 33.333 6.35 3.53 0.00 2.17
5159 5565 5.738909 TGAGGCTGGTTTTTGAAAAATTCA 58.261 33.333 6.35 7.58 38.04 2.57
5222 5628 9.775854 ACATAGATATAGATGAAGGCATAATGC 57.224 33.333 3.84 0.00 44.08 3.56
5236 5642 5.673337 GCATAATGCATAAGAGGACGAAA 57.327 39.130 0.00 0.00 44.26 3.46
5237 5643 6.246420 GCATAATGCATAAGAGGACGAAAT 57.754 37.500 0.00 0.00 44.26 2.17
5238 5644 7.364522 GCATAATGCATAAGAGGACGAAATA 57.635 36.000 0.00 0.00 44.26 1.40
5239 5645 7.237173 GCATAATGCATAAGAGGACGAAATAC 58.763 38.462 0.00 0.00 44.26 1.89
5240 5646 7.095229 GCATAATGCATAAGAGGACGAAATACA 60.095 37.037 0.00 0.00 44.26 2.29
5241 5647 8.939929 CATAATGCATAAGAGGACGAAATACAT 58.060 33.333 0.00 0.00 0.00 2.29
5242 5648 7.807977 AATGCATAAGAGGACGAAATACATT 57.192 32.000 0.00 0.00 0.00 2.71
5243 5649 6.603237 TGCATAAGAGGACGAAATACATTG 57.397 37.500 0.00 0.00 0.00 2.82
5244 5650 6.345298 TGCATAAGAGGACGAAATACATTGA 58.655 36.000 0.00 0.00 0.00 2.57
5245 5651 6.821160 TGCATAAGAGGACGAAATACATTGAA 59.179 34.615 0.00 0.00 0.00 2.69
5246 5652 7.335673 TGCATAAGAGGACGAAATACATTGAAA 59.664 33.333 0.00 0.00 0.00 2.69
5247 5653 8.345565 GCATAAGAGGACGAAATACATTGAAAT 58.654 33.333 0.00 0.00 0.00 2.17
5248 5654 9.655769 CATAAGAGGACGAAATACATTGAAATG 57.344 33.333 1.45 1.45 42.10 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 3.391506 TCTCAATAGATGGATGCGTGG 57.608 47.619 0.00 0.00 0.00 4.94
130 131 4.160252 AGGAGAGCATGTGTTTTTGTTTGT 59.840 37.500 0.00 0.00 0.00 2.83
180 181 4.526970 AGGATGTTTTATTGGCATCTCGT 58.473 39.130 0.00 0.00 39.04 4.18
233 234 1.002087 CTGCTAACAGTTCGGGAGGTT 59.998 52.381 0.00 0.00 39.22 3.50
255 256 8.974060 ACTAAATTGATATATCGGGTTGTTGT 57.026 30.769 8.19 0.00 0.00 3.32
318 319 8.402326 TGTCGATGTTGTTATGTATACAGTTC 57.598 34.615 11.91 4.64 0.00 3.01
453 458 2.875672 GCAGTAACCTCATGCCTTGACA 60.876 50.000 0.00 0.00 33.81 3.58
533 538 7.872113 ATACTATGAAGGGAAAAAGCTCAAG 57.128 36.000 0.00 0.00 0.00 3.02
780 793 9.066892 GGTTGCTAAATAGGATAATGTCAATCA 57.933 33.333 0.00 0.00 0.00 2.57
786 799 8.766994 ACAATGGTTGCTAAATAGGATAATGT 57.233 30.769 0.00 0.00 0.00 2.71
869 883 5.354234 TCCTCTTTTGACAACTTGACAGTTC 59.646 40.000 0.00 0.00 41.69 3.01
896 911 9.657419 CATTTTCCAGCAATAATTTAGACCTTT 57.343 29.630 0.00 0.00 0.00 3.11
917 932 6.039941 TGTTTATGTCCCGTCACTTTCATTTT 59.960 34.615 0.00 0.00 0.00 1.82
1539 1590 4.263905 ACTGCCAGGGATATGAACTTTTCA 60.264 41.667 0.00 0.00 45.01 2.69
1912 1965 4.081420 CAGGCTGAGTTGTATGAGGTTAGT 60.081 45.833 9.42 0.00 0.00 2.24
2568 2630 0.245539 CCAAGCTGCCAACCTCATTG 59.754 55.000 0.00 0.00 38.12 2.82
2660 2722 9.871238 TGTCTAATAATAACCAGTTCAAGACTC 57.129 33.333 0.00 0.00 36.10 3.36
3163 3228 4.827835 TGAGTACTGCACTAGTGTCTTCTT 59.172 41.667 23.44 6.72 40.65 2.52
3302 3367 5.772825 TGTTCTGTCCTCATTTTCCAAAG 57.227 39.130 0.00 0.00 0.00 2.77
3463 3528 2.887152 ACACCAATGCCTTGAACTCTTC 59.113 45.455 2.97 0.00 34.04 2.87
3553 3618 3.426568 GGCAAGGCTGAGCGTGTC 61.427 66.667 0.00 0.00 0.00 3.67
3971 4047 1.376424 CTGTCATCTGTTGGGCGCT 60.376 57.895 7.64 0.00 0.00 5.92
4243 4322 1.581223 GGTTCCCCTGTAACCTAGCT 58.419 55.000 0.00 0.00 42.63 3.32
4262 4341 1.172175 GGCTTCTTTCCCTGCTTCAG 58.828 55.000 0.00 0.00 0.00 3.02
4272 4351 8.253113 TGAATTTATTGATTCAGGGCTTCTTTC 58.747 33.333 0.00 0.00 40.20 2.62
4449 4698 7.974675 TGACTAGAACTTGCTATTATTGCAAC 58.025 34.615 9.75 1.90 44.24 4.17
4522 4774 9.689976 CTACTGGTCTATCTTAATCATGAACTG 57.310 37.037 0.00 0.00 0.00 3.16
4524 4776 9.685828 GTCTACTGGTCTATCTTAATCATGAAC 57.314 37.037 0.00 0.00 0.00 3.18
4540 4792 4.038162 AGTCTCAGTTGTTGTCTACTGGTC 59.962 45.833 9.12 2.78 43.71 4.02
4544 4796 3.384789 TGCAGTCTCAGTTGTTGTCTACT 59.615 43.478 0.00 0.00 0.00 2.57
4556 4808 1.543358 TGCTCTGTAGTGCAGTCTCAG 59.457 52.381 16.02 16.02 45.23 3.35
4568 4820 4.956075 TCTACAGATGAACCATGCTCTGTA 59.044 41.667 10.00 10.00 44.80 2.74
4572 4824 6.072508 TGTTTTTCTACAGATGAACCATGCTC 60.073 38.462 0.00 0.00 0.00 4.26
4598 4850 4.421948 CTGTTACTGGATTCCACGTCTAC 58.578 47.826 0.00 7.21 0.00 2.59
4604 4856 4.380867 CCATTTGCTGTTACTGGATTCCAC 60.381 45.833 0.00 0.00 0.00 4.02
4631 4888 9.788960 TGCTTGCTTATCGTATAATCTAGTATG 57.211 33.333 0.00 0.00 0.00 2.39
4640 4897 4.944048 TGCTCTGCTTGCTTATCGTATAA 58.056 39.130 0.00 0.00 0.00 0.98
4641 4898 4.550422 CTGCTCTGCTTGCTTATCGTATA 58.450 43.478 0.00 0.00 0.00 1.47
4685 4947 6.090763 CGTTTTTCTTTCTTTTGGACAGCTTT 59.909 34.615 0.00 0.00 0.00 3.51
4689 4951 5.102313 AGCGTTTTTCTTTCTTTTGGACAG 58.898 37.500 0.00 0.00 0.00 3.51
4691 4953 5.004440 GTGAGCGTTTTTCTTTCTTTTGGAC 59.996 40.000 0.00 0.00 0.00 4.02
4692 4954 5.099575 GTGAGCGTTTTTCTTTCTTTTGGA 58.900 37.500 0.00 0.00 0.00 3.53
4693 4955 4.027702 CGTGAGCGTTTTTCTTTCTTTTGG 60.028 41.667 0.00 0.00 0.00 3.28
4694 4956 5.041467 CGTGAGCGTTTTTCTTTCTTTTG 57.959 39.130 0.00 0.00 0.00 2.44
4764 5068 4.274214 GCATTGATGTGCTGCTACTTATGA 59.726 41.667 0.00 0.00 41.82 2.15
4767 5071 3.608796 TGCATTGATGTGCTGCTACTTA 58.391 40.909 0.00 0.00 45.27 2.24
4786 5192 6.260050 TCGTTAGTGATTCTGGGAATTTATGC 59.740 38.462 0.00 0.00 0.00 3.14
4827 5233 0.179134 ATTACTGCCGCTCGTGACTC 60.179 55.000 0.00 0.00 0.00 3.36
4828 5234 0.246635 AATTACTGCCGCTCGTGACT 59.753 50.000 0.00 0.00 0.00 3.41
4829 5235 1.917273 TAATTACTGCCGCTCGTGAC 58.083 50.000 0.00 0.00 0.00 3.67
4830 5236 2.264813 GTTAATTACTGCCGCTCGTGA 58.735 47.619 0.00 0.00 0.00 4.35
4831 5237 1.996898 TGTTAATTACTGCCGCTCGTG 59.003 47.619 0.00 0.00 0.00 4.35
4832 5238 1.997606 GTGTTAATTACTGCCGCTCGT 59.002 47.619 0.00 0.00 0.00 4.18
4833 5239 1.326548 GGTGTTAATTACTGCCGCTCG 59.673 52.381 0.00 0.00 0.00 5.03
4838 5244 1.662122 CCGTCGGTGTTAATTACTGCC 59.338 52.381 2.08 0.00 0.00 4.85
4917 5323 3.528370 CTCACCCTACCCGGCGAG 61.528 72.222 9.30 0.00 0.00 5.03
4922 5328 3.528370 CTCGCCTCACCCTACCCG 61.528 72.222 0.00 0.00 0.00 5.28
4923 5329 3.851128 GCTCGCCTCACCCTACCC 61.851 72.222 0.00 0.00 0.00 3.69
4924 5330 4.208686 CGCTCGCCTCACCCTACC 62.209 72.222 0.00 0.00 0.00 3.18
4925 5331 4.208686 CCGCTCGCCTCACCCTAC 62.209 72.222 0.00 0.00 0.00 3.18
4926 5332 4.435970 TCCGCTCGCCTCACCCTA 62.436 66.667 0.00 0.00 0.00 3.53
4930 5336 4.500116 GACCTCCGCTCGCCTCAC 62.500 72.222 0.00 0.00 0.00 3.51
4941 5347 2.107141 CGCAAGATCCGGACCTCC 59.893 66.667 6.12 0.00 43.02 4.30
4942 5348 3.207354 TCGCAAGATCCGGACCTC 58.793 61.111 6.12 0.17 45.01 3.85
4953 5359 0.594540 CTCCGCATCTCTCTCGCAAG 60.595 60.000 0.00 0.00 0.00 4.01
4954 5360 1.435105 CTCCGCATCTCTCTCGCAA 59.565 57.895 0.00 0.00 0.00 4.85
4955 5361 2.484928 CCTCCGCATCTCTCTCGCA 61.485 63.158 0.00 0.00 0.00 5.10
4956 5362 2.190170 TCCTCCGCATCTCTCTCGC 61.190 63.158 0.00 0.00 0.00 5.03
4957 5363 0.817634 AGTCCTCCGCATCTCTCTCG 60.818 60.000 0.00 0.00 0.00 4.04
4958 5364 0.667993 CAGTCCTCCGCATCTCTCTC 59.332 60.000 0.00 0.00 0.00 3.20
4959 5365 0.754957 CCAGTCCTCCGCATCTCTCT 60.755 60.000 0.00 0.00 0.00 3.10
4960 5366 1.040339 ACCAGTCCTCCGCATCTCTC 61.040 60.000 0.00 0.00 0.00 3.20
4961 5367 1.000993 ACCAGTCCTCCGCATCTCT 59.999 57.895 0.00 0.00 0.00 3.10
4962 5368 1.142748 CACCAGTCCTCCGCATCTC 59.857 63.158 0.00 0.00 0.00 2.75
4963 5369 2.362369 CCACCAGTCCTCCGCATCT 61.362 63.158 0.00 0.00 0.00 2.90
4964 5370 2.187946 CCACCAGTCCTCCGCATC 59.812 66.667 0.00 0.00 0.00 3.91
4965 5371 2.284625 TCCACCAGTCCTCCGCAT 60.285 61.111 0.00 0.00 0.00 4.73
4966 5372 2.997315 CTCCACCAGTCCTCCGCA 60.997 66.667 0.00 0.00 0.00 5.69
4967 5373 3.775654 CCTCCACCAGTCCTCCGC 61.776 72.222 0.00 0.00 0.00 5.54
4968 5374 2.880629 ATCCCTCCACCAGTCCTCCG 62.881 65.000 0.00 0.00 0.00 4.63
4969 5375 0.621862 AATCCCTCCACCAGTCCTCC 60.622 60.000 0.00 0.00 0.00 4.30
4970 5376 0.833949 GAATCCCTCCACCAGTCCTC 59.166 60.000 0.00 0.00 0.00 3.71
4971 5377 0.119155 TGAATCCCTCCACCAGTCCT 59.881 55.000 0.00 0.00 0.00 3.85
4972 5378 0.253327 GTGAATCCCTCCACCAGTCC 59.747 60.000 0.00 0.00 0.00 3.85
4973 5379 1.065854 CAGTGAATCCCTCCACCAGTC 60.066 57.143 0.00 0.00 34.00 3.51
4974 5380 0.987294 CAGTGAATCCCTCCACCAGT 59.013 55.000 0.00 0.00 34.00 4.00
4975 5381 0.254178 CCAGTGAATCCCTCCACCAG 59.746 60.000 0.00 0.00 34.00 4.00
4976 5382 1.852157 GCCAGTGAATCCCTCCACCA 61.852 60.000 0.00 0.00 34.00 4.17
4977 5383 1.077429 GCCAGTGAATCCCTCCACC 60.077 63.158 0.00 0.00 34.00 4.61
4978 5384 1.450312 CGCCAGTGAATCCCTCCAC 60.450 63.158 0.00 0.00 0.00 4.02
4979 5385 2.669133 CCGCCAGTGAATCCCTCCA 61.669 63.158 0.00 0.00 0.00 3.86
4980 5386 2.190578 CCGCCAGTGAATCCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
4981 5387 1.144936 CTCCGCCAGTGAATCCCTC 59.855 63.158 0.00 0.00 0.00 4.30
4982 5388 2.370445 CCTCCGCCAGTGAATCCCT 61.370 63.158 0.00 0.00 0.00 4.20
4983 5389 2.190578 CCTCCGCCAGTGAATCCC 59.809 66.667 0.00 0.00 0.00 3.85
4984 5390 2.190578 CCCTCCGCCAGTGAATCC 59.809 66.667 0.00 0.00 0.00 3.01
4985 5391 2.190578 CCCCTCCGCCAGTGAATC 59.809 66.667 0.00 0.00 0.00 2.52
4986 5392 3.411517 CCCCCTCCGCCAGTGAAT 61.412 66.667 0.00 0.00 0.00 2.57
4995 5401 3.917760 CTTCTAGCGCCCCCTCCG 61.918 72.222 2.29 0.00 0.00 4.63
4996 5402 3.551407 CCTTCTAGCGCCCCCTCC 61.551 72.222 2.29 0.00 0.00 4.30
4997 5403 4.243008 GCCTTCTAGCGCCCCCTC 62.243 72.222 2.29 0.00 0.00 4.30
4999 5405 3.421728 ATTGCCTTCTAGCGCCCCC 62.422 63.158 2.29 0.00 34.65 5.40
5000 5406 1.894282 GATTGCCTTCTAGCGCCCC 60.894 63.158 2.29 0.00 34.65 5.80
5001 5407 0.882484 GAGATTGCCTTCTAGCGCCC 60.882 60.000 2.29 0.00 34.65 6.13
5002 5408 0.882484 GGAGATTGCCTTCTAGCGCC 60.882 60.000 2.29 0.00 34.65 6.53
5003 5409 1.218230 CGGAGATTGCCTTCTAGCGC 61.218 60.000 0.00 0.00 34.65 5.92
5004 5410 0.598680 CCGGAGATTGCCTTCTAGCG 60.599 60.000 0.00 0.00 34.65 4.26
5005 5411 0.250081 CCCGGAGATTGCCTTCTAGC 60.250 60.000 0.73 0.00 0.00 3.42
5006 5412 0.394565 CCCCGGAGATTGCCTTCTAG 59.605 60.000 0.73 0.00 0.00 2.43
5007 5413 0.031515 TCCCCGGAGATTGCCTTCTA 60.032 55.000 0.73 0.00 0.00 2.10
5008 5414 0.695803 ATCCCCGGAGATTGCCTTCT 60.696 55.000 0.73 0.00 0.00 2.85
5009 5415 0.250510 GATCCCCGGAGATTGCCTTC 60.251 60.000 0.73 0.00 0.00 3.46
5010 5416 1.839894 GATCCCCGGAGATTGCCTT 59.160 57.895 0.73 0.00 0.00 4.35
5011 5417 2.511452 CGATCCCCGGAGATTGCCT 61.511 63.158 0.73 0.00 33.91 4.75
5012 5418 2.031163 CGATCCCCGGAGATTGCC 59.969 66.667 0.73 0.00 33.91 4.52
5013 5419 0.880718 GTTCGATCCCCGGAGATTGC 60.881 60.000 8.33 0.00 39.14 3.56
5014 5420 0.753262 AGTTCGATCCCCGGAGATTG 59.247 55.000 0.73 4.51 39.14 2.67
5015 5421 2.376695 TAGTTCGATCCCCGGAGATT 57.623 50.000 0.73 0.00 39.14 2.40
5016 5422 2.376695 TTAGTTCGATCCCCGGAGAT 57.623 50.000 0.73 0.00 39.14 2.75
5017 5423 2.148446 TTTAGTTCGATCCCCGGAGA 57.852 50.000 0.73 0.00 39.14 3.71
5018 5424 2.973694 TTTTAGTTCGATCCCCGGAG 57.026 50.000 0.73 0.00 39.14 4.63
5019 5425 4.801581 GCATATTTTAGTTCGATCCCCGGA 60.802 45.833 0.73 0.00 39.14 5.14
5020 5426 3.435671 GCATATTTTAGTTCGATCCCCGG 59.564 47.826 0.00 0.00 39.14 5.73
5021 5427 4.062293 TGCATATTTTAGTTCGATCCCCG 58.938 43.478 0.00 0.00 40.25 5.73
5022 5428 4.819630 TGTGCATATTTTAGTTCGATCCCC 59.180 41.667 0.00 0.00 0.00 4.81
5023 5429 6.428159 AGATGTGCATATTTTAGTTCGATCCC 59.572 38.462 0.00 0.00 0.00 3.85
5024 5430 7.293745 CAGATGTGCATATTTTAGTTCGATCC 58.706 38.462 0.00 0.00 0.00 3.36
5025 5431 7.293745 CCAGATGTGCATATTTTAGTTCGATC 58.706 38.462 0.00 0.00 0.00 3.69
5026 5432 6.205464 CCCAGATGTGCATATTTTAGTTCGAT 59.795 38.462 0.00 0.00 0.00 3.59
5027 5433 5.527214 CCCAGATGTGCATATTTTAGTTCGA 59.473 40.000 0.00 0.00 0.00 3.71
5028 5434 5.277974 CCCCAGATGTGCATATTTTAGTTCG 60.278 44.000 0.00 0.00 0.00 3.95
5029 5435 5.507985 GCCCCAGATGTGCATATTTTAGTTC 60.508 44.000 0.00 0.00 0.00 3.01
5030 5436 4.342092 GCCCCAGATGTGCATATTTTAGTT 59.658 41.667 0.00 0.00 0.00 2.24
5031 5437 3.891366 GCCCCAGATGTGCATATTTTAGT 59.109 43.478 0.00 0.00 0.00 2.24
5032 5438 3.058016 CGCCCCAGATGTGCATATTTTAG 60.058 47.826 0.00 0.00 0.00 1.85
5033 5439 2.884012 CGCCCCAGATGTGCATATTTTA 59.116 45.455 0.00 0.00 0.00 1.52
5034 5440 1.682854 CGCCCCAGATGTGCATATTTT 59.317 47.619 0.00 0.00 0.00 1.82
5035 5441 1.321474 CGCCCCAGATGTGCATATTT 58.679 50.000 0.00 0.00 0.00 1.40
5036 5442 0.538057 CCGCCCCAGATGTGCATATT 60.538 55.000 0.00 0.00 0.00 1.28
5037 5443 1.073722 CCGCCCCAGATGTGCATAT 59.926 57.895 0.00 0.00 0.00 1.78
5038 5444 1.920734 AACCGCCCCAGATGTGCATA 61.921 55.000 0.00 0.00 0.00 3.14
5039 5445 3.286694 AACCGCCCCAGATGTGCAT 62.287 57.895 0.00 0.00 0.00 3.96
5040 5446 3.918253 GAACCGCCCCAGATGTGCA 62.918 63.158 0.00 0.00 0.00 4.57
5041 5447 3.134127 GAACCGCCCCAGATGTGC 61.134 66.667 0.00 0.00 0.00 4.57
5042 5448 1.450312 GAGAACCGCCCCAGATGTG 60.450 63.158 0.00 0.00 0.00 3.21
5043 5449 2.670148 GGAGAACCGCCCCAGATGT 61.670 63.158 0.00 0.00 0.00 3.06
5044 5450 1.987807 ATGGAGAACCGCCCCAGATG 61.988 60.000 0.00 0.00 39.42 2.90
5045 5451 1.281925 AATGGAGAACCGCCCCAGAT 61.282 55.000 0.00 0.00 39.42 2.90
5046 5452 1.923395 AATGGAGAACCGCCCCAGA 60.923 57.895 0.00 0.00 39.42 3.86
5047 5453 1.750399 CAATGGAGAACCGCCCCAG 60.750 63.158 0.00 0.00 39.42 4.45
5048 5454 2.354729 CAATGGAGAACCGCCCCA 59.645 61.111 0.00 0.00 39.42 4.96
5049 5455 2.440247 CCAATGGAGAACCGCCCC 60.440 66.667 0.00 0.00 39.42 5.80
5050 5456 2.440247 CCCAATGGAGAACCGCCC 60.440 66.667 0.00 0.00 39.42 6.13
5051 5457 2.440247 CCCCAATGGAGAACCGCC 60.440 66.667 0.00 0.00 39.42 6.13
5052 5458 2.440247 CCCCCAATGGAGAACCGC 60.440 66.667 0.00 0.00 39.42 5.68
5053 5459 2.440247 GCCCCCAATGGAGAACCG 60.440 66.667 0.00 0.00 39.42 4.44
5054 5460 2.042944 GGCCCCCAATGGAGAACC 60.043 66.667 0.00 0.00 35.39 3.62
5055 5461 0.544120 TTTGGCCCCCAATGGAGAAC 60.544 55.000 0.00 0.00 43.55 3.01
5056 5462 0.252193 CTTTGGCCCCCAATGGAGAA 60.252 55.000 0.00 0.00 43.55 2.87
5057 5463 1.145900 TCTTTGGCCCCCAATGGAGA 61.146 55.000 0.00 0.00 43.55 3.71
5058 5464 0.252193 TTCTTTGGCCCCCAATGGAG 60.252 55.000 0.00 0.00 43.55 3.86
5059 5465 0.544120 GTTCTTTGGCCCCCAATGGA 60.544 55.000 0.00 0.00 43.55 3.41
5060 5466 0.835543 TGTTCTTTGGCCCCCAATGG 60.836 55.000 0.00 0.00 43.55 3.16
5061 5467 1.278537 ATGTTCTTTGGCCCCCAATG 58.721 50.000 0.00 0.85 43.55 2.82
5062 5468 2.043307 AATGTTCTTTGGCCCCCAAT 57.957 45.000 0.00 0.00 43.55 3.16
5063 5469 1.813102 AAATGTTCTTTGGCCCCCAA 58.187 45.000 0.00 0.00 42.29 4.12
5064 5470 1.813102 AAAATGTTCTTTGGCCCCCA 58.187 45.000 0.00 0.00 0.00 4.96
5065 5471 2.949177 AAAAATGTTCTTTGGCCCCC 57.051 45.000 0.00 0.00 0.00 5.40
5085 5491 5.472148 TCGCTCTCCTGTTATCGTTAAAAA 58.528 37.500 0.00 0.00 0.00 1.94
5086 5492 5.063180 TCGCTCTCCTGTTATCGTTAAAA 57.937 39.130 0.00 0.00 0.00 1.52
5087 5493 4.707030 TCGCTCTCCTGTTATCGTTAAA 57.293 40.909 0.00 0.00 0.00 1.52
5088 5494 4.707030 TTCGCTCTCCTGTTATCGTTAA 57.293 40.909 0.00 0.00 0.00 2.01
5089 5495 4.707030 TTTCGCTCTCCTGTTATCGTTA 57.293 40.909 0.00 0.00 0.00 3.18
5090 5496 3.587797 TTTCGCTCTCCTGTTATCGTT 57.412 42.857 0.00 0.00 0.00 3.85
5091 5497 3.587797 TTTTCGCTCTCCTGTTATCGT 57.412 42.857 0.00 0.00 0.00 3.73
5092 5498 4.025647 GGAATTTTCGCTCTCCTGTTATCG 60.026 45.833 0.00 0.00 0.00 2.92
5093 5499 5.119694 AGGAATTTTCGCTCTCCTGTTATC 58.880 41.667 0.00 0.00 36.92 1.75
5094 5500 5.104259 AGGAATTTTCGCTCTCCTGTTAT 57.896 39.130 0.00 0.00 36.92 1.89
5095 5501 4.553330 AGGAATTTTCGCTCTCCTGTTA 57.447 40.909 0.00 0.00 36.92 2.41
5096 5502 3.425162 AGGAATTTTCGCTCTCCTGTT 57.575 42.857 0.00 0.00 36.92 3.16
5097 5503 3.425162 AAGGAATTTTCGCTCTCCTGT 57.575 42.857 0.00 0.00 38.34 4.00
5098 5504 4.348198 GAAAGGAATTTTCGCTCTCCTG 57.652 45.455 0.00 0.00 38.34 3.86
5121 5527 1.227497 CTCATTGGAGCTCGGCCTC 60.227 63.158 7.83 0.00 33.67 4.70
5122 5528 2.739996 CCTCATTGGAGCTCGGCCT 61.740 63.158 7.83 0.00 39.96 5.19
5123 5529 2.203126 CCTCATTGGAGCTCGGCC 60.203 66.667 7.83 0.00 39.96 6.13
5124 5530 2.899339 GCCTCATTGGAGCTCGGC 60.899 66.667 11.57 11.57 39.96 5.54
5125 5531 1.523258 CAGCCTCATTGGAGCTCGG 60.523 63.158 7.83 2.99 39.96 4.63
5126 5532 1.523258 CCAGCCTCATTGGAGCTCG 60.523 63.158 7.83 0.00 39.96 5.03
5127 5533 0.034670 AACCAGCCTCATTGGAGCTC 60.035 55.000 4.71 4.71 39.96 4.09
5128 5534 0.407139 AAACCAGCCTCATTGGAGCT 59.593 50.000 0.00 0.00 39.96 4.09
5129 5535 1.260544 AAAACCAGCCTCATTGGAGC 58.739 50.000 0.00 0.00 39.96 4.70
5130 5536 2.892852 TCAAAAACCAGCCTCATTGGAG 59.107 45.455 0.00 0.00 39.08 3.86
5131 5537 2.956132 TCAAAAACCAGCCTCATTGGA 58.044 42.857 0.00 0.00 39.08 3.53
5132 5538 3.749665 TTCAAAAACCAGCCTCATTGG 57.250 42.857 0.00 0.00 41.60 3.16
5133 5539 6.622833 ATTTTTCAAAAACCAGCCTCATTG 57.377 33.333 0.00 0.00 0.00 2.82
5134 5540 6.827762 TGAATTTTTCAAAAACCAGCCTCATT 59.172 30.769 0.00 0.00 36.59 2.57
5135 5541 6.355747 TGAATTTTTCAAAAACCAGCCTCAT 58.644 32.000 0.00 0.00 36.59 2.90
5136 5542 5.738909 TGAATTTTTCAAAAACCAGCCTCA 58.261 33.333 0.00 0.00 36.59 3.86
5137 5543 6.676237 TTGAATTTTTCAAAAACCAGCCTC 57.324 33.333 0.00 0.00 45.94 4.70
5196 5602 9.775854 GCATTATGCCTTCATCTATATCTATGT 57.224 33.333 5.80 0.00 37.42 2.29
5197 5603 9.774413 TGCATTATGCCTTCATCTATATCTATG 57.226 33.333 15.06 0.00 44.23 2.23
5203 5609 9.828039 CTCTTATGCATTATGCCTTCATCTATA 57.172 33.333 15.06 0.43 44.23 1.31
5204 5610 7.774157 CCTCTTATGCATTATGCCTTCATCTAT 59.226 37.037 15.06 1.40 44.23 1.98
5205 5611 7.038088 TCCTCTTATGCATTATGCCTTCATCTA 60.038 37.037 15.06 0.00 44.23 1.98
5206 5612 5.944599 CCTCTTATGCATTATGCCTTCATCT 59.055 40.000 15.06 0.00 44.23 2.90
5207 5613 5.942236 TCCTCTTATGCATTATGCCTTCATC 59.058 40.000 15.06 0.00 44.23 2.92
5208 5614 5.709164 GTCCTCTTATGCATTATGCCTTCAT 59.291 40.000 15.06 3.94 44.23 2.57
5209 5615 5.065914 GTCCTCTTATGCATTATGCCTTCA 58.934 41.667 15.06 0.00 44.23 3.02
5210 5616 4.153117 CGTCCTCTTATGCATTATGCCTTC 59.847 45.833 15.06 0.00 44.23 3.46
5211 5617 4.067896 CGTCCTCTTATGCATTATGCCTT 58.932 43.478 15.06 4.92 44.23 4.35
5212 5618 3.324846 TCGTCCTCTTATGCATTATGCCT 59.675 43.478 15.06 7.49 44.23 4.75
5213 5619 3.664107 TCGTCCTCTTATGCATTATGCC 58.336 45.455 15.06 0.00 44.23 4.40
5214 5620 5.673337 TTTCGTCCTCTTATGCATTATGC 57.327 39.130 10.65 10.65 45.29 3.14
5215 5621 8.310406 TGTATTTCGTCCTCTTATGCATTATG 57.690 34.615 3.54 0.00 0.00 1.90
5216 5622 9.507329 AATGTATTTCGTCCTCTTATGCATTAT 57.493 29.630 3.54 0.00 32.34 1.28
5217 5623 8.773645 CAATGTATTTCGTCCTCTTATGCATTA 58.226 33.333 3.54 0.00 32.34 1.90
5218 5624 7.498900 TCAATGTATTTCGTCCTCTTATGCATT 59.501 33.333 3.54 0.00 33.68 3.56
5219 5625 6.992123 TCAATGTATTTCGTCCTCTTATGCAT 59.008 34.615 3.79 3.79 0.00 3.96
5220 5626 6.345298 TCAATGTATTTCGTCCTCTTATGCA 58.655 36.000 0.00 0.00 0.00 3.96
5221 5627 6.844696 TCAATGTATTTCGTCCTCTTATGC 57.155 37.500 0.00 0.00 0.00 3.14
5222 5628 9.655769 CATTTCAATGTATTTCGTCCTCTTATG 57.344 33.333 0.00 0.00 0.00 1.90



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

AutoCloner maintained by Alex Coulton.