Multiple sequence alignment - TraesCS4D01G307500

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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 TraesCS4D01G307500 chr4D 100.000 5105 0 0 1 5105 475180105 475175001 0.000000e+00 9428.0
1 TraesCS4D01G307500 chr4D 94.152 171 3 1 4942 5105 99642514 99642344 2.360000e-63 254.0
2 TraesCS4D01G307500 chr4D 83.471 242 12 14 4198 4417 475175543 475175308 3.120000e-47 200.0
3 TraesCS4D01G307500 chr4D 83.471 242 12 14 4563 4798 475175908 475175689 3.120000e-47 200.0
4 TraesCS4D01G307500 chr4D 81.739 115 20 1 3503 3617 88142352 88142239 1.510000e-15 95.3
5 TraesCS4D01G307500 chr4A 95.632 4693 157 25 270 4940 681921377 681916711 0.000000e+00 7487.0
6 TraesCS4D01G307500 chr4A 86.216 769 92 8 1040 1795 629294194 629293427 0.000000e+00 821.0
7 TraesCS4D01G307500 chr4A 79.884 691 105 23 2479 3161 629293438 629292774 4.630000e-130 475.0
8 TraesCS4D01G307500 chr4A 90.511 274 10 2 1 273 681921747 681921489 1.050000e-91 348.0
9 TraesCS4D01G307500 chr4A 85.124 242 10 12 4198 4417 681917090 681916853 1.850000e-54 224.0
10 TraesCS4D01G307500 chr4A 81.405 242 17 16 4563 4798 681917437 681917218 6.800000e-39 172.0
11 TraesCS4D01G307500 chr4A 81.739 115 20 1 3503 3617 501124396 501124283 1.510000e-15 95.3
12 TraesCS4D01G307500 chr4B 95.252 4486 135 30 1 4444 599888161 599883712 0.000000e+00 7033.0
13 TraesCS4D01G307500 chr4B 92.208 231 14 3 4572 4799 599883968 599883739 1.770000e-84 324.0
14 TraesCS4D01G307500 chr4B 90.698 129 11 1 4813 4941 599883753 599883626 2.440000e-38 171.0
15 TraesCS4D01G307500 chr5B 84.920 2175 290 26 1006 3161 680993543 680995698 0.000000e+00 2165.0
16 TraesCS4D01G307500 chr5D 84.782 2129 275 23 1057 3159 539453810 539455915 0.000000e+00 2091.0
17 TraesCS4D01G307500 chr6B 78.026 983 168 38 3072 4036 25924608 25923656 4.430000e-160 575.0
18 TraesCS4D01G307500 chr6A 77.961 971 166 37 3072 4024 15438442 15439382 9.600000e-157 564.0
19 TraesCS4D01G307500 chr6A 72.563 1713 424 40 1182 2871 15436567 15438256 7.580000e-143 518.0
20 TraesCS4D01G307500 chr6D 94.737 171 2 1 4942 5105 52593654 52593484 5.070000e-65 259.0
21 TraesCS4D01G307500 chrUn 94.152 171 3 1 4942 5105 100724803 100724633 2.360000e-63 254.0
22 TraesCS4D01G307500 chr3D 92.778 180 4 3 4934 5105 473293443 473293621 8.480000e-63 252.0
23 TraesCS4D01G307500 chr3D 93.605 172 4 1 4941 5105 122957286 122957457 3.050000e-62 250.0
24 TraesCS4D01G307500 chr3D 77.778 108 21 2 3515 3619 395059520 395059627 4.270000e-06 63.9
25 TraesCS4D01G307500 chr1D 94.118 170 3 1 4943 5105 68991807 68991638 8.480000e-63 252.0
26 TraesCS4D01G307500 chr1D 93.567 171 4 1 4942 5105 46256726 46256556 1.100000e-61 248.0
27 TraesCS4D01G307500 chr7D 93.567 171 4 1 4942 5105 343877245 343877415 1.100000e-61 248.0
28 TraesCS4D01G307500 chr2D 93.567 171 4 1 4942 5105 255342169 255342339 1.100000e-61 248.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G307500 chr4D 475175001 475180105 5104 True 9428 9428 100.000 1 5105 1 chr4D.!!$R3 5104
1 TraesCS4D01G307500 chr4A 681916711 681921377 4666 True 7487 7487 95.632 270 4940 1 chr4A.!!$R2 4670
2 TraesCS4D01G307500 chr4A 629292774 629294194 1420 True 648 821 83.050 1040 3161 2 chr4A.!!$R4 2121
3 TraesCS4D01G307500 chr4B 599883626 599888161 4535 True 3602 7033 92.975 1 4941 2 chr4B.!!$R2 4940
4 TraesCS4D01G307500 chr5B 680993543 680995698 2155 False 2165 2165 84.920 1006 3161 1 chr5B.!!$F1 2155
5 TraesCS4D01G307500 chr5D 539453810 539455915 2105 False 2091 2091 84.782 1057 3159 1 chr5D.!!$F1 2102
6 TraesCS4D01G307500 chr6B 25923656 25924608 952 True 575 575 78.026 3072 4036 1 chr6B.!!$R1 964
7 TraesCS4D01G307500 chr6A 15436567 15439382 2815 False 541 564 75.262 1182 4024 2 chr6A.!!$F1 2842

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
909 932 0.099968 CAATCAATGGAGGCACGCAG 59.900 55.0 0.0 0.0 0.00 5.18 F
1903 1950 1.863662 GCTCGACCTCTCCGACAACA 61.864 60.0 0.0 0.0 32.18 3.33 F
3003 3062 1.032014 GTGCTGTCTTCCTTGGCAAA 58.968 50.0 0.0 0.0 34.65 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2423 0.456221 GGTCGATGAAGGAGAGCGAA 59.544 55.0 0.00 0.00 32.39 4.70 R
3711 3788 1.550327 AGATGTCGCTCTTCTGGTCA 58.450 50.0 0.00 0.00 0.00 4.02 R
4836 4919 0.458543 ATGTCCATGTCGACGACAGC 60.459 55.0 31.72 21.72 46.04 4.40 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
92 94 7.280428 CAGATTGTTCAGAATAGCACTCAAGAT 59.720 37.037 0.00 0.00 0.00 2.40
94 96 6.041423 TGTTCAGAATAGCACTCAAGATGA 57.959 37.500 0.00 0.00 0.00 2.92
103 105 3.084039 GCACTCAAGATGACAATCCCAA 58.916 45.455 0.00 0.00 32.77 4.12
105 107 4.616835 GCACTCAAGATGACAATCCCAAAC 60.617 45.833 0.00 0.00 32.77 2.93
111 113 5.505181 AGATGACAATCCCAAACTGTACT 57.495 39.130 0.00 0.00 32.77 2.73
147 149 6.657966 TGAGCTCAAGATTGTTCATGATTTCT 59.342 34.615 15.67 0.00 29.84 2.52
154 157 8.433126 CAAGATTGTTCATGATTTCTTTTCAGC 58.567 33.333 0.00 0.00 0.00 4.26
169 172 6.569780 TCTTTTCAGCTTGTAAAACCCTTTC 58.430 36.000 0.00 0.00 0.00 2.62
175 178 6.379988 TCAGCTTGTAAAACCCTTTCTCTTTT 59.620 34.615 0.00 0.00 0.00 2.27
193 196 9.744468 TTCTCTTTTAAGAACAAACTTTATGGC 57.256 29.630 0.00 0.00 34.03 4.40
194 197 8.908903 TCTCTTTTAAGAACAAACTTTATGGCA 58.091 29.630 0.00 0.00 34.03 4.92
199 202 8.655651 TTAAGAACAAACTTTATGGCAAAAGG 57.344 30.769 19.22 9.46 40.16 3.11
200 203 6.478512 AGAACAAACTTTATGGCAAAAGGA 57.521 33.333 19.22 0.00 40.16 3.36
202 205 6.323739 AGAACAAACTTTATGGCAAAAGGAGA 59.676 34.615 19.22 0.00 40.16 3.71
207 210 6.705863 ACTTTATGGCAAAAGGAGATCATC 57.294 37.500 19.22 0.00 40.16 2.92
209 212 6.320672 ACTTTATGGCAAAAGGAGATCATCTG 59.679 38.462 19.22 0.00 40.16 2.90
210 213 3.726557 TGGCAAAAGGAGATCATCTGT 57.273 42.857 0.00 0.00 0.00 3.41
211 214 4.038271 TGGCAAAAGGAGATCATCTGTT 57.962 40.909 0.00 0.00 0.00 3.16
212 215 5.178096 TGGCAAAAGGAGATCATCTGTTA 57.822 39.130 0.00 0.00 0.00 2.41
215 218 5.591877 GGCAAAAGGAGATCATCTGTTATGT 59.408 40.000 0.00 0.00 0.00 2.29
217 220 7.363268 GGCAAAAGGAGATCATCTGTTATGTTT 60.363 37.037 0.00 0.00 0.00 2.83
218 221 8.677300 GCAAAAGGAGATCATCTGTTATGTTTA 58.323 33.333 0.00 0.00 0.00 2.01
221 224 9.739276 AAAGGAGATCATCTGTTATGTTTAACA 57.261 29.630 0.00 0.00 44.16 2.41
222 225 8.723942 AGGAGATCATCTGTTATGTTTAACAC 57.276 34.615 0.00 0.00 42.10 3.32
223 226 8.543774 AGGAGATCATCTGTTATGTTTAACACT 58.456 33.333 0.00 0.00 42.10 3.55
224 227 9.817809 GGAGATCATCTGTTATGTTTAACACTA 57.182 33.333 0.00 0.00 42.10 2.74
244 247 9.807649 AACACTAATCATATTTGCTGGAAATTC 57.192 29.630 12.38 0.00 35.74 2.17
259 262 6.459298 GCTGGAAATTCAGTATGTTCATCCAG 60.459 42.308 12.43 12.43 46.87 3.86
265 268 3.261643 TCAGTATGTTCATCCAGTGCAGT 59.738 43.478 0.00 0.00 37.40 4.40
327 344 6.947464 TCCTCCTTCAGTAGAATAACCTTTG 58.053 40.000 0.00 0.00 32.31 2.77
356 373 3.555547 GCAAAATCAAGTTTGTCCACACC 59.444 43.478 5.02 0.00 40.06 4.16
411 428 3.245052 CCCATCAATCTTAGGGCTTAGGG 60.245 52.174 0.00 0.00 33.91 3.53
496 513 4.844349 TCCTCTCTCCAATAACCAAAGG 57.156 45.455 0.00 0.00 0.00 3.11
546 564 1.649271 GGGCCATGTCTCCCCAATCT 61.649 60.000 4.39 0.00 38.70 2.40
642 660 6.683110 GCTGTTCTTGTGCTAGCTACCTAATA 60.683 42.308 17.23 3.06 0.00 0.98
717 739 0.102481 AACGCACCCTAGTAGCATCG 59.898 55.000 0.00 0.00 0.00 3.84
812 835 9.660544 ATGGACCTTAAAATAATGGCTTAATCT 57.339 29.630 0.00 0.00 0.00 2.40
901 924 3.258872 TCAAACCAAGGCAATCAATGGAG 59.741 43.478 0.00 0.00 36.75 3.86
904 927 1.187974 CAAGGCAATCAATGGAGGCA 58.812 50.000 0.00 0.00 0.00 4.75
909 932 0.099968 CAATCAATGGAGGCACGCAG 59.900 55.000 0.00 0.00 0.00 5.18
972 996 2.125350 GCGGCAAGGAGTGGAGAG 60.125 66.667 0.00 0.00 0.00 3.20
1903 1950 1.863662 GCTCGACCTCTCCGACAACA 61.864 60.000 0.00 0.00 32.18 3.33
1959 2006 2.596631 ACCAACCTGCAGCTGCTG 60.597 61.111 36.61 34.20 42.66 4.41
2376 2423 3.444805 GACCTGGCGCTCTCGACT 61.445 66.667 7.64 0.00 45.91 4.18
2457 2504 3.664025 CTCCATCCCGACGCTGCAA 62.664 63.158 0.00 0.00 0.00 4.08
2496 2543 3.950232 GAGCTGATCGGGGGTGTA 58.050 61.111 3.14 0.00 0.00 2.90
2580 2627 2.549198 CGCGATACCGACCAGCCTA 61.549 63.158 0.00 0.00 38.22 3.93
2652 2699 2.678580 CAAATTCCCGGGGCGGTT 60.679 61.111 23.50 7.25 46.80 4.44
2694 2741 3.070734 CCATCCTCGATCTCTCCAACAAT 59.929 47.826 0.00 0.00 0.00 2.71
2903 2953 2.257676 GGCTTCGTCGTCGGAAGT 59.742 61.111 11.34 0.00 37.69 3.01
3003 3062 1.032014 GTGCTGTCTTCCTTGGCAAA 58.968 50.000 0.00 0.00 34.65 3.68
3585 3662 2.847234 AACGTGCTCCTGGACCCA 60.847 61.111 0.00 0.00 0.00 4.51
3612 3689 1.745489 GGCCAAGATCGCCGACTTT 60.745 57.895 0.00 0.00 36.47 2.66
3711 3788 1.713297 ACGGGTACACTCTGAAGGTT 58.287 50.000 0.00 0.00 0.00 3.50
4163 4240 3.311106 GTGACCAAGATTCAACGACGTA 58.689 45.455 0.00 0.00 0.00 3.57
4437 4518 1.748493 GGTGTTGCCACTGTCTTTGAA 59.252 47.619 0.00 0.00 41.53 2.69
4474 4555 2.024941 AGTTGTTTCCTCCCATGATCCC 60.025 50.000 0.00 0.00 0.00 3.85
4475 4556 0.546122 TGTTTCCTCCCATGATCCCG 59.454 55.000 0.00 0.00 0.00 5.14
4476 4557 0.837272 GTTTCCTCCCATGATCCCGA 59.163 55.000 0.00 0.00 0.00 5.14
4477 4558 0.837272 TTTCCTCCCATGATCCCGAC 59.163 55.000 0.00 0.00 0.00 4.79
4478 4559 0.326143 TTCCTCCCATGATCCCGACA 60.326 55.000 0.00 0.00 0.00 4.35
4479 4560 0.326143 TCCTCCCATGATCCCGACAA 60.326 55.000 0.00 0.00 0.00 3.18
4480 4561 0.179045 CCTCCCATGATCCCGACAAC 60.179 60.000 0.00 0.00 0.00 3.32
4481 4562 0.179045 CTCCCATGATCCCGACAACC 60.179 60.000 0.00 0.00 0.00 3.77
4482 4563 0.912006 TCCCATGATCCCGACAACCA 60.912 55.000 0.00 0.00 0.00 3.67
4483 4564 0.464373 CCCATGATCCCGACAACCAG 60.464 60.000 0.00 0.00 0.00 4.00
4484 4565 0.464373 CCATGATCCCGACAACCAGG 60.464 60.000 0.00 0.00 0.00 4.45
4508 4589 7.400339 AGGGAGAGATAGTTGTTCATTGTTAGA 59.600 37.037 0.00 0.00 0.00 2.10
4524 4605 7.990886 TCATTGTTAGAGTTAGAGTTGTTTGGT 59.009 33.333 0.00 0.00 0.00 3.67
4543 4624 2.225041 GGTCCCTCTTTGCTTTACCCTT 60.225 50.000 0.00 0.00 0.00 3.95
4544 4625 3.497332 GTCCCTCTTTGCTTTACCCTTT 58.503 45.455 0.00 0.00 0.00 3.11
4545 4626 3.506455 GTCCCTCTTTGCTTTACCCTTTC 59.494 47.826 0.00 0.00 0.00 2.62
4553 4634 1.718396 CTTTACCCTTTCCGTCGTCC 58.282 55.000 0.00 0.00 0.00 4.79
4559 4640 2.049802 TTTCCGTCGTCCGCACTC 60.050 61.111 0.00 0.00 34.38 3.51
4560 4641 3.884581 TTTCCGTCGTCCGCACTCG 62.885 63.158 0.00 0.00 34.38 4.18
4605 4686 8.443953 TTTTTCACATAGTTTTGAATTTGGGG 57.556 30.769 0.00 0.00 31.87 4.96
4621 4704 7.455008 TGAATTTGGGGTTATTTGGTTTAGCTA 59.545 33.333 0.00 0.00 0.00 3.32
4760 4843 3.557595 GGAATGGATGTAGCAAACTCTCG 59.442 47.826 0.00 0.00 0.00 4.04
4765 4848 4.645136 TGGATGTAGCAAACTCTCGTCTAT 59.355 41.667 0.00 0.00 0.00 1.98
4821 4904 6.576551 TTTTTCCGCAAAAACACATCTAAC 57.423 33.333 0.00 0.00 36.70 2.34
4836 4919 0.179134 CTAACTCCTTGGTCTCGCCG 60.179 60.000 0.00 0.00 41.21 6.46
4877 4960 3.515502 TGGACCAAGGAGAGATAGTTGTG 59.484 47.826 0.00 0.00 0.00 3.33
4882 4965 4.946157 CCAAGGAGAGATAGTTGTGCATTT 59.054 41.667 0.00 0.00 0.00 2.32
4887 4970 7.398024 AGGAGAGATAGTTGTGCATTTTTAGT 58.602 34.615 0.00 0.00 0.00 2.24
4896 4979 6.870965 AGTTGTGCATTTTTAGTGTTGTTTGA 59.129 30.769 0.00 0.00 0.00 2.69
4898 4981 6.393990 TGTGCATTTTTAGTGTTGTTTGAGT 58.606 32.000 0.00 0.00 0.00 3.41
4907 4990 4.843728 AGTGTTGTTTGAGTCCTCTTTGA 58.156 39.130 0.00 0.00 0.00 2.69
4932 5015 1.143305 CCTCGTCTGCACTTGACTTG 58.857 55.000 3.43 0.00 32.70 3.16
4940 5023 3.118261 TCTGCACTTGACTTGAAACCTCT 60.118 43.478 0.00 0.00 0.00 3.69
4941 5024 3.206150 TGCACTTGACTTGAAACCTCTC 58.794 45.455 0.00 0.00 0.00 3.20
4942 5025 3.206150 GCACTTGACTTGAAACCTCTCA 58.794 45.455 0.00 0.00 0.00 3.27
4943 5026 3.002759 GCACTTGACTTGAAACCTCTCAC 59.997 47.826 0.00 0.00 0.00 3.51
4944 5027 4.446371 CACTTGACTTGAAACCTCTCACT 58.554 43.478 0.00 0.00 0.00 3.41
4945 5028 5.601662 CACTTGACTTGAAACCTCTCACTA 58.398 41.667 0.00 0.00 0.00 2.74
4946 5029 5.463724 CACTTGACTTGAAACCTCTCACTAC 59.536 44.000 0.00 0.00 0.00 2.73
4947 5030 5.364157 ACTTGACTTGAAACCTCTCACTACT 59.636 40.000 0.00 0.00 0.00 2.57
4948 5031 5.201713 TGACTTGAAACCTCTCACTACTG 57.798 43.478 0.00 0.00 0.00 2.74
4949 5032 4.039245 TGACTTGAAACCTCTCACTACTGG 59.961 45.833 0.00 0.00 0.00 4.00
4950 5033 4.223953 ACTTGAAACCTCTCACTACTGGA 58.776 43.478 0.00 0.00 0.00 3.86
4951 5034 4.654262 ACTTGAAACCTCTCACTACTGGAA 59.346 41.667 0.00 0.00 0.00 3.53
4952 5035 5.130477 ACTTGAAACCTCTCACTACTGGAAA 59.870 40.000 0.00 0.00 0.00 3.13
4953 5036 4.957296 TGAAACCTCTCACTACTGGAAAC 58.043 43.478 0.00 0.00 0.00 2.78
4954 5037 4.407621 TGAAACCTCTCACTACTGGAAACA 59.592 41.667 0.00 0.00 39.59 2.83
4968 5051 4.454728 TGGAAACAGCTAATTTGCCATC 57.545 40.909 8.30 2.47 35.01 3.51
4969 5052 4.088634 TGGAAACAGCTAATTTGCCATCT 58.911 39.130 8.30 0.00 35.01 2.90
4970 5053 4.082081 TGGAAACAGCTAATTTGCCATCTG 60.082 41.667 8.30 3.09 35.01 2.90
4971 5054 3.515330 AACAGCTAATTTGCCATCTGC 57.485 42.857 8.30 0.00 41.77 4.26
4972 5055 1.753073 ACAGCTAATTTGCCATCTGCC 59.247 47.619 8.30 0.00 40.16 4.85
4973 5056 1.752498 CAGCTAATTTGCCATCTGCCA 59.248 47.619 8.30 0.00 40.16 4.92
4974 5057 2.029623 AGCTAATTTGCCATCTGCCAG 58.970 47.619 8.30 0.00 40.16 4.85
4975 5058 1.537562 GCTAATTTGCCATCTGCCAGC 60.538 52.381 0.00 0.00 40.16 4.85
4976 5059 2.029623 CTAATTTGCCATCTGCCAGCT 58.970 47.619 0.00 0.00 40.16 4.24
4977 5060 0.822164 AATTTGCCATCTGCCAGCTC 59.178 50.000 0.00 0.00 40.16 4.09
4978 5061 0.033405 ATTTGCCATCTGCCAGCTCT 60.033 50.000 0.00 0.00 40.16 4.09
4979 5062 0.251474 TTTGCCATCTGCCAGCTCTT 60.251 50.000 0.00 0.00 40.16 2.85
4980 5063 0.251474 TTGCCATCTGCCAGCTCTTT 60.251 50.000 0.00 0.00 40.16 2.52
4981 5064 0.963856 TGCCATCTGCCAGCTCTTTG 60.964 55.000 0.00 0.00 40.16 2.77
4982 5065 1.807886 CCATCTGCCAGCTCTTTGC 59.192 57.895 0.00 0.00 43.29 3.68
4983 5066 1.664321 CCATCTGCCAGCTCTTTGCC 61.664 60.000 0.00 0.00 44.23 4.52
4984 5067 1.748122 ATCTGCCAGCTCTTTGCCG 60.748 57.895 0.00 0.00 44.23 5.69
4985 5068 2.475371 ATCTGCCAGCTCTTTGCCGT 62.475 55.000 0.00 0.00 44.23 5.68
4986 5069 2.669569 TGCCAGCTCTTTGCCGTC 60.670 61.111 0.00 0.00 44.23 4.79
4987 5070 2.359230 GCCAGCTCTTTGCCGTCT 60.359 61.111 0.00 0.00 44.23 4.18
4988 5071 2.684843 GCCAGCTCTTTGCCGTCTG 61.685 63.158 0.00 0.00 44.23 3.51
4989 5072 2.684843 CCAGCTCTTTGCCGTCTGC 61.685 63.158 0.00 0.00 44.23 4.26
4990 5073 1.670406 CAGCTCTTTGCCGTCTGCT 60.670 57.895 0.00 0.00 44.23 4.24
4991 5074 0.390340 CAGCTCTTTGCCGTCTGCTA 60.390 55.000 0.00 0.00 44.23 3.49
4992 5075 0.108424 AGCTCTTTGCCGTCTGCTAG 60.108 55.000 0.00 0.00 44.23 3.42
4993 5076 1.700600 GCTCTTTGCCGTCTGCTAGC 61.701 60.000 8.10 8.10 42.00 3.42
4994 5077 0.390340 CTCTTTGCCGTCTGCTAGCA 60.390 55.000 18.22 18.22 42.00 3.49
4995 5078 0.034756 TCTTTGCCGTCTGCTAGCAA 59.965 50.000 19.86 7.18 44.32 3.91
4996 5079 4.789977 TTGCCGTCTGCTAGCAAA 57.210 50.000 19.86 1.56 43.14 3.68
4997 5080 2.543578 TTGCCGTCTGCTAGCAAAG 58.456 52.632 19.86 12.29 43.14 2.77
4998 5081 0.034756 TTGCCGTCTGCTAGCAAAGA 59.965 50.000 19.86 10.82 43.14 2.52
4999 5082 0.034756 TGCCGTCTGCTAGCAAAGAA 59.965 50.000 19.86 1.68 42.00 2.52
5000 5083 0.723981 GCCGTCTGCTAGCAAAGAAG 59.276 55.000 19.86 14.85 36.87 2.85
5001 5084 0.723981 CCGTCTGCTAGCAAAGAAGC 59.276 55.000 19.86 2.01 39.25 3.86
5003 5086 1.658095 CGTCTGCTAGCAAAGAAGCTC 59.342 52.381 19.86 0.96 45.26 4.09
5004 5087 2.673610 CGTCTGCTAGCAAAGAAGCTCT 60.674 50.000 19.86 0.00 45.26 4.09
5005 5088 3.333804 GTCTGCTAGCAAAGAAGCTCTT 58.666 45.455 19.86 0.00 45.26 2.85
5006 5089 3.750652 GTCTGCTAGCAAAGAAGCTCTTT 59.249 43.478 19.86 5.61 46.75 2.52
5015 5098 1.461559 AGAAGCTCTTTGCCATCAGC 58.538 50.000 0.00 0.00 44.23 4.26
5016 5099 1.004511 AGAAGCTCTTTGCCATCAGCT 59.995 47.619 0.00 0.00 44.28 4.24
5017 5100 1.132643 GAAGCTCTTTGCCATCAGCTG 59.867 52.381 7.63 7.63 41.48 4.24
5018 5101 1.139095 GCTCTTTGCCATCAGCTGC 59.861 57.895 9.47 0.00 44.23 5.25
5019 5102 1.807886 CTCTTTGCCATCAGCTGCC 59.192 57.895 9.47 0.00 44.23 4.85
5020 5103 1.664321 CTCTTTGCCATCAGCTGCCC 61.664 60.000 9.47 0.00 44.23 5.36
5021 5104 1.980232 CTTTGCCATCAGCTGCCCA 60.980 57.895 9.47 0.00 44.23 5.36
5022 5105 1.533513 TTTGCCATCAGCTGCCCAA 60.534 52.632 9.47 6.46 44.23 4.12
5023 5106 1.120184 TTTGCCATCAGCTGCCCAAA 61.120 50.000 9.47 11.97 44.23 3.28
5024 5107 1.120184 TTGCCATCAGCTGCCCAAAA 61.120 50.000 9.47 0.00 44.23 2.44
5025 5108 1.217244 GCCATCAGCTGCCCAAAAG 59.783 57.895 9.47 0.00 38.99 2.27
5026 5109 1.217244 CCATCAGCTGCCCAAAAGC 59.783 57.895 9.47 0.00 41.15 3.51
5027 5110 1.537814 CCATCAGCTGCCCAAAAGCA 61.538 55.000 9.47 0.00 43.37 3.91
5033 5116 3.294493 TGCCCAAAAGCAGACGGC 61.294 61.111 0.00 0.00 45.30 5.68
5043 5126 3.406682 GCAGACGGCAAAGAAATGG 57.593 52.632 0.00 0.00 43.97 3.16
5044 5127 0.733909 GCAGACGGCAAAGAAATGGC 60.734 55.000 0.00 0.00 43.97 4.40
5048 5131 4.889427 GGCAAAGAAATGGCGGAC 57.111 55.556 0.00 0.00 36.07 4.79
5049 5132 1.154035 GGCAAAGAAATGGCGGACG 60.154 57.895 0.00 0.00 36.07 4.79
5050 5133 1.154035 GCAAAGAAATGGCGGACGG 60.154 57.895 0.00 0.00 0.00 4.79
5051 5134 1.154035 CAAAGAAATGGCGGACGGC 60.154 57.895 11.56 11.56 42.51 5.68
5059 5142 4.103103 GGCGGACGGCAAAGAAGC 62.103 66.667 13.57 0.00 46.16 3.86
5060 5143 3.050275 GCGGACGGCAAAGAAGCT 61.050 61.111 0.00 0.00 42.87 3.74
5061 5144 3.028366 GCGGACGGCAAAGAAGCTC 62.028 63.158 0.00 0.00 42.87 4.09
5062 5145 1.374758 CGGACGGCAAAGAAGCTCT 60.375 57.895 0.00 0.00 34.17 4.09
5063 5146 0.951040 CGGACGGCAAAGAAGCTCTT 60.951 55.000 0.00 0.00 38.59 2.85
5064 5147 1.239347 GGACGGCAAAGAAGCTCTTT 58.761 50.000 0.00 5.61 46.75 2.52
5072 5155 1.457346 AAGAAGCTCTTTGCCATCCG 58.543 50.000 0.00 0.00 44.23 4.18
5073 5156 1.028868 AGAAGCTCTTTGCCATCCGC 61.029 55.000 0.00 0.00 44.23 5.54
5074 5157 2.315038 GAAGCTCTTTGCCATCCGCG 62.315 60.000 0.00 0.00 44.23 6.46
5075 5158 2.803155 AAGCTCTTTGCCATCCGCGA 62.803 55.000 8.23 0.00 44.23 5.87
5076 5159 2.817423 GCTCTTTGCCATCCGCGAG 61.817 63.158 8.23 0.00 42.08 5.03
5077 5160 2.817423 CTCTTTGCCATCCGCGAGC 61.817 63.158 8.23 5.45 42.08 5.03
5078 5161 2.821366 CTTTGCCATCCGCGAGCT 60.821 61.111 8.23 0.00 42.08 4.09
5079 5162 2.817423 CTTTGCCATCCGCGAGCTC 61.817 63.158 8.23 2.73 42.08 4.09
5080 5163 3.315142 TTTGCCATCCGCGAGCTCT 62.315 57.895 8.23 0.00 42.08 4.09
5081 5164 2.803155 TTTGCCATCCGCGAGCTCTT 62.803 55.000 8.23 0.00 42.08 2.85
5082 5165 2.512515 GCCATCCGCGAGCTCTTT 60.513 61.111 8.23 0.00 0.00 2.52
5083 5166 2.817423 GCCATCCGCGAGCTCTTTG 61.817 63.158 8.23 0.79 0.00 2.77
5084 5167 2.705826 CATCCGCGAGCTCTTTGC 59.294 61.111 8.23 7.10 43.29 3.68
5085 5168 2.512515 ATCCGCGAGCTCTTTGCC 60.513 61.111 8.23 0.00 44.23 4.52
5088 5171 3.843240 CGCGAGCTCTTTGCCGTC 61.843 66.667 12.85 0.00 44.23 4.79
5089 5172 3.491652 GCGAGCTCTTTGCCGTCC 61.492 66.667 12.85 0.00 44.23 4.79
5090 5173 3.181967 CGAGCTCTTTGCCGTCCG 61.182 66.667 12.85 0.00 44.23 4.79
5091 5174 3.491652 GAGCTCTTTGCCGTCCGC 61.492 66.667 6.43 0.00 44.23 5.54
5092 5175 3.941657 GAGCTCTTTGCCGTCCGCT 62.942 63.158 6.43 0.00 44.23 5.52
5093 5176 3.793144 GCTCTTTGCCGTCCGCTG 61.793 66.667 0.00 0.00 38.78 5.18
5094 5177 3.121030 CTCTTTGCCGTCCGCTGG 61.121 66.667 0.00 0.00 38.78 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.679638 GCATGGTTAGCAACAGGATTACTTTAG 60.680 40.741 0.00 0.00 0.00 1.85
80 82 3.519107 TGGGATTGTCATCTTGAGTGCTA 59.481 43.478 0.00 0.00 0.00 3.49
81 83 2.306805 TGGGATTGTCATCTTGAGTGCT 59.693 45.455 0.00 0.00 0.00 4.40
92 94 4.698201 TCAGTACAGTTTGGGATTGTCA 57.302 40.909 0.00 0.00 0.00 3.58
94 96 5.630121 TGATTCAGTACAGTTTGGGATTGT 58.370 37.500 0.00 0.00 0.00 2.71
103 105 8.043113 TGAGCTCATTAATGATTCAGTACAGTT 58.957 33.333 18.26 2.02 36.02 3.16
105 107 8.429493 TTGAGCTCATTAATGATTCAGTACAG 57.571 34.615 19.04 5.08 36.02 2.74
111 113 8.515695 ACAATCTTGAGCTCATTAATGATTCA 57.484 30.769 19.04 19.59 36.02 2.57
147 149 6.379988 AGAGAAAGGGTTTTACAAGCTGAAAA 59.620 34.615 0.00 0.00 0.00 2.29
169 172 9.528018 TTGCCATAAAGTTTGTTCTTAAAAGAG 57.472 29.630 0.00 0.00 36.22 2.85
175 178 8.012957 TCCTTTTGCCATAAAGTTTGTTCTTA 57.987 30.769 0.00 0.00 34.11 2.10
192 195 6.690194 ACATAACAGATGATCTCCTTTTGC 57.310 37.500 0.00 0.00 0.00 3.68
197 200 8.543774 AGTGTTAAACATAACAGATGATCTCCT 58.456 33.333 0.00 0.00 40.21 3.69
198 201 8.723942 AGTGTTAAACATAACAGATGATCTCC 57.276 34.615 0.00 0.00 40.21 3.71
218 221 9.807649 GAATTTCCAGCAAATATGATTAGTGTT 57.192 29.630 0.00 0.00 33.16 3.32
219 222 8.970020 TGAATTTCCAGCAAATATGATTAGTGT 58.030 29.630 0.00 0.00 33.16 3.55
220 223 9.459640 CTGAATTTCCAGCAAATATGATTAGTG 57.540 33.333 0.00 0.00 33.16 2.74
221 224 9.193806 ACTGAATTTCCAGCAAATATGATTAGT 57.806 29.630 0.00 0.00 37.68 2.24
224 227 9.976511 CATACTGAATTTCCAGCAAATATGATT 57.023 29.630 0.00 0.00 37.68 2.57
225 228 9.139734 ACATACTGAATTTCCAGCAAATATGAT 57.860 29.630 0.00 0.00 37.68 2.45
226 229 8.523915 ACATACTGAATTTCCAGCAAATATGA 57.476 30.769 0.00 0.00 37.68 2.15
227 230 9.241317 GAACATACTGAATTTCCAGCAAATATG 57.759 33.333 0.00 0.00 37.68 1.78
228 231 8.970020 TGAACATACTGAATTTCCAGCAAATAT 58.030 29.630 0.00 0.00 37.68 1.28
229 232 8.347004 TGAACATACTGAATTTCCAGCAAATA 57.653 30.769 0.00 0.00 37.68 1.40
230 233 7.230849 TGAACATACTGAATTTCCAGCAAAT 57.769 32.000 0.00 0.00 37.68 2.32
244 247 3.603532 ACTGCACTGGATGAACATACTG 58.396 45.455 3.03 3.03 0.00 2.74
259 262 3.497262 GGAAACACCTACTTGTACTGCAC 59.503 47.826 0.00 0.00 35.41 4.57
295 307 9.892444 TTATTCTACTGAAGGAGGATTATGGTA 57.108 33.333 0.00 0.00 35.44 3.25
327 344 6.533367 TGGACAAACTTGATTTTGCAGTTAAC 59.467 34.615 0.00 0.00 39.67 2.01
340 357 5.419155 TGTTAATTGGTGTGGACAAACTTGA 59.581 36.000 0.00 0.00 0.00 3.02
395 412 0.108774 GCGCCCTAAGCCCTAAGATT 59.891 55.000 0.00 0.00 38.78 2.40
411 428 1.207593 GACACACAGAACATGGCGC 59.792 57.895 0.00 0.00 0.00 6.53
496 513 1.550524 GGGAATGTGGGGAAAAGAAGC 59.449 52.381 0.00 0.00 0.00 3.86
546 564 6.127083 GGAAAATGCTCTTGGAATTATTGGGA 60.127 38.462 0.00 0.00 0.00 4.37
642 660 4.163078 ACATGGCTAGTGATTAGTGAGCTT 59.837 41.667 0.00 0.00 33.57 3.74
812 835 5.278512 GCGAGTGTGTCTATGATTAGGATGA 60.279 44.000 0.00 0.00 0.00 2.92
901 924 0.591741 CTACGTACTAGCTGCGTGCC 60.592 60.000 14.92 0.66 41.77 5.01
958 982 1.201429 TTCCCCTCTCCACTCCTTGC 61.201 60.000 0.00 0.00 0.00 4.01
972 996 3.093172 CCTCTGCTCCCCTTCCCC 61.093 72.222 0.00 0.00 0.00 4.81
1713 1760 2.560105 GAGGTTCTTGAGCTTGCCAATT 59.440 45.455 0.00 0.00 35.91 2.32
1959 2006 1.875963 CCGGTTGCACATGAGGTTC 59.124 57.895 0.00 0.00 0.00 3.62
2169 2216 7.533426 AGACATTGTTGAACAATATCAGCTTC 58.467 34.615 25.61 12.95 46.22 3.86
2376 2423 0.456221 GGTCGATGAAGGAGAGCGAA 59.544 55.000 0.00 0.00 32.39 4.70
2430 2477 2.418746 CGTCGGGATGGAGAGAATGTTT 60.419 50.000 0.00 0.00 0.00 2.83
2496 2543 1.680522 AATCGCCGAGCTCATCAGGT 61.681 55.000 15.40 0.00 0.00 4.00
2652 2699 0.680601 ACAATGTCGGCATCATGGCA 60.681 50.000 12.41 0.00 43.94 4.92
3585 3662 1.755179 CGATCTTGGCCTCCATGTTT 58.245 50.000 3.32 0.00 31.53 2.83
3702 3779 2.037772 GCTCTTCTGGTCAACCTTCAGA 59.962 50.000 0.10 0.00 35.95 3.27
3711 3788 1.550327 AGATGTCGCTCTTCTGGTCA 58.450 50.000 0.00 0.00 0.00 4.02
3936 4013 3.357079 GACTTGGCCGTGCACAGG 61.357 66.667 18.64 19.06 0.00 4.00
4163 4240 9.552114 GAGCTACGATACGTATACAAAACATAT 57.448 33.333 8.34 0.00 41.53 1.78
4295 4376 9.586435 GACCAATTCCTTTACATCCTAAAATTG 57.414 33.333 0.00 0.00 0.00 2.32
4296 4377 9.547279 AGACCAATTCCTTTACATCCTAAAATT 57.453 29.630 0.00 0.00 0.00 1.82
4404 4485 4.361451 GGCAACACCAATGAGTTAGATG 57.639 45.455 0.00 0.00 38.86 2.90
4464 4545 0.464373 CTGGTTGTCGGGATCATGGG 60.464 60.000 0.00 0.00 0.00 4.00
4474 4555 2.379972 ACTATCTCTCCCTGGTTGTCG 58.620 52.381 0.00 0.00 0.00 4.35
4475 4556 3.515901 ACAACTATCTCTCCCTGGTTGTC 59.484 47.826 0.00 0.00 41.89 3.18
4476 4557 3.521727 ACAACTATCTCTCCCTGGTTGT 58.478 45.455 0.00 0.00 41.19 3.32
4477 4558 4.020218 TGAACAACTATCTCTCCCTGGTTG 60.020 45.833 0.00 0.00 39.58 3.77
4478 4559 4.168101 TGAACAACTATCTCTCCCTGGTT 58.832 43.478 0.00 0.00 0.00 3.67
4479 4560 3.791320 TGAACAACTATCTCTCCCTGGT 58.209 45.455 0.00 0.00 0.00 4.00
4480 4561 5.121811 CAATGAACAACTATCTCTCCCTGG 58.878 45.833 0.00 0.00 0.00 4.45
4481 4562 5.738909 ACAATGAACAACTATCTCTCCCTG 58.261 41.667 0.00 0.00 0.00 4.45
4482 4563 6.380079 AACAATGAACAACTATCTCTCCCT 57.620 37.500 0.00 0.00 0.00 4.20
4483 4564 7.556844 TCTAACAATGAACAACTATCTCTCCC 58.443 38.462 0.00 0.00 0.00 4.30
4484 4565 8.254508 ACTCTAACAATGAACAACTATCTCTCC 58.745 37.037 0.00 0.00 0.00 3.71
4485 4566 9.646427 AACTCTAACAATGAACAACTATCTCTC 57.354 33.333 0.00 0.00 0.00 3.20
4508 4589 3.974642 AGAGGGACCAAACAACTCTAACT 59.025 43.478 0.00 0.00 36.80 2.24
4512 4593 3.555966 CAAAGAGGGACCAAACAACTCT 58.444 45.455 0.00 0.00 40.02 3.24
4513 4594 2.034685 GCAAAGAGGGACCAAACAACTC 59.965 50.000 0.00 0.00 0.00 3.01
4514 4595 2.031870 GCAAAGAGGGACCAAACAACT 58.968 47.619 0.00 0.00 0.00 3.16
4515 4596 2.031870 AGCAAAGAGGGACCAAACAAC 58.968 47.619 0.00 0.00 0.00 3.32
4516 4597 2.452600 AGCAAAGAGGGACCAAACAA 57.547 45.000 0.00 0.00 0.00 2.83
4517 4598 2.452600 AAGCAAAGAGGGACCAAACA 57.547 45.000 0.00 0.00 0.00 2.83
4524 4605 3.499745 GGAAAGGGTAAAGCAAAGAGGGA 60.500 47.826 0.00 0.00 0.00 4.20
4553 4634 1.085091 AGGTGTAGTAGTCGAGTGCG 58.915 55.000 2.10 0.00 39.35 5.34
4559 4640 6.734104 AAAGTAGTGTAGGTGTAGTAGTCG 57.266 41.667 0.00 0.00 0.00 4.18
4560 4641 8.571336 TGAAAAAGTAGTGTAGGTGTAGTAGTC 58.429 37.037 0.00 0.00 0.00 2.59
4627 4710 4.511082 ACATTGTTTACATTGGTTGCTTGC 59.489 37.500 8.95 0.00 33.04 4.01
4629 4712 8.900983 ATAAACATTGTTTACATTGGTTGCTT 57.099 26.923 21.07 1.91 37.60 3.91
4630 4713 9.418045 GTATAAACATTGTTTACATTGGTTGCT 57.582 29.630 21.07 6.95 37.60 3.91
4803 4886 3.502211 AGGAGTTAGATGTGTTTTTGCGG 59.498 43.478 0.00 0.00 0.00 5.69
4807 4890 6.365520 AGACCAAGGAGTTAGATGTGTTTTT 58.634 36.000 0.00 0.00 0.00 1.94
4821 4904 3.764466 AGCGGCGAGACCAAGGAG 61.764 66.667 12.98 0.00 39.03 3.69
4836 4919 0.458543 ATGTCCATGTCGACGACAGC 60.459 55.000 31.72 21.72 46.04 4.40
4877 4960 6.273071 AGGACTCAAACAACACTAAAAATGC 58.727 36.000 0.00 0.00 0.00 3.56
4882 4965 6.882140 TCAAAGAGGACTCAAACAACACTAAA 59.118 34.615 1.75 0.00 0.00 1.85
4887 4970 6.773976 AAATCAAAGAGGACTCAAACAACA 57.226 33.333 1.75 0.00 0.00 3.33
4896 4979 3.838903 ACGAGGGTAAATCAAAGAGGACT 59.161 43.478 0.00 0.00 0.00 3.85
4898 4981 4.081642 CAGACGAGGGTAAATCAAAGAGGA 60.082 45.833 0.00 0.00 0.00 3.71
4907 4990 2.301870 TCAAGTGCAGACGAGGGTAAAT 59.698 45.455 0.00 0.00 0.00 1.40
4932 5015 4.957296 TGTTTCCAGTAGTGAGAGGTTTC 58.043 43.478 0.00 0.00 0.00 2.78
4940 5023 5.181245 GCAAATTAGCTGTTTCCAGTAGTGA 59.819 40.000 0.00 0.00 41.02 3.41
4941 5024 5.393962 GCAAATTAGCTGTTTCCAGTAGTG 58.606 41.667 0.00 0.00 41.02 2.74
4942 5025 4.459337 GGCAAATTAGCTGTTTCCAGTAGT 59.541 41.667 0.00 0.00 41.02 2.73
4943 5026 4.458989 TGGCAAATTAGCTGTTTCCAGTAG 59.541 41.667 0.00 0.00 41.02 2.57
4944 5027 4.402829 TGGCAAATTAGCTGTTTCCAGTA 58.597 39.130 0.00 0.00 41.02 2.74
4945 5028 3.230134 TGGCAAATTAGCTGTTTCCAGT 58.770 40.909 0.00 0.00 41.02 4.00
4946 5029 3.940209 TGGCAAATTAGCTGTTTCCAG 57.060 42.857 0.00 0.00 41.91 3.86
4947 5030 4.082081 CAGATGGCAAATTAGCTGTTTCCA 60.082 41.667 0.00 7.98 34.17 3.53
4948 5031 4.427312 CAGATGGCAAATTAGCTGTTTCC 58.573 43.478 0.00 2.83 34.17 3.13
4949 5032 3.861689 GCAGATGGCAAATTAGCTGTTTC 59.138 43.478 0.00 0.00 43.97 2.78
4950 5033 3.853475 GCAGATGGCAAATTAGCTGTTT 58.147 40.909 0.00 0.00 43.97 2.83
4951 5034 3.515330 GCAGATGGCAAATTAGCTGTT 57.485 42.857 0.00 0.00 43.97 3.16
4963 5046 1.807886 CAAAGAGCTGGCAGATGGC 59.192 57.895 20.86 2.95 43.74 4.40
4964 5047 1.664321 GGCAAAGAGCTGGCAGATGG 61.664 60.000 20.86 2.18 44.79 3.51
4965 5048 1.807886 GGCAAAGAGCTGGCAGATG 59.192 57.895 20.86 9.26 44.79 2.90
4966 5049 1.748122 CGGCAAAGAGCTGGCAGAT 60.748 57.895 20.86 13.42 46.20 2.90
4967 5050 2.359107 CGGCAAAGAGCTGGCAGA 60.359 61.111 20.86 0.00 46.20 4.26
4975 5058 3.443552 TTTGCTAGCAGACGGCAAAGAG 61.444 50.000 18.45 0.00 46.45 2.85
4976 5059 1.542328 TTTGCTAGCAGACGGCAAAGA 60.542 47.619 18.45 0.00 46.45 2.52
4977 5060 0.874390 TTTGCTAGCAGACGGCAAAG 59.126 50.000 18.45 0.00 46.45 2.77
4981 5064 0.723981 CTTCTTTGCTAGCAGACGGC 59.276 55.000 18.45 0.00 45.30 5.68
4982 5065 0.723981 GCTTCTTTGCTAGCAGACGG 59.276 55.000 18.45 9.39 37.35 4.79
4983 5066 1.658095 GAGCTTCTTTGCTAGCAGACG 59.342 52.381 18.45 11.38 44.17 4.18
4984 5067 2.971307 AGAGCTTCTTTGCTAGCAGAC 58.029 47.619 18.45 1.36 44.17 3.51
4985 5068 3.692257 AAGAGCTTCTTTGCTAGCAGA 57.308 42.857 18.45 13.03 44.17 4.26
4994 5077 2.230750 GCTGATGGCAAAGAGCTTCTTT 59.769 45.455 4.85 5.61 46.75 2.52
4995 5078 1.817447 GCTGATGGCAAAGAGCTTCTT 59.183 47.619 4.85 0.00 44.79 2.52
4996 5079 1.004511 AGCTGATGGCAAAGAGCTTCT 59.995 47.619 11.30 0.00 44.79 2.85
4997 5080 1.132643 CAGCTGATGGCAAAGAGCTTC 59.867 52.381 8.42 0.00 39.82 3.86
4998 5081 1.174783 CAGCTGATGGCAAAGAGCTT 58.825 50.000 8.42 0.56 39.82 3.74
4999 5082 1.313812 GCAGCTGATGGCAAAGAGCT 61.314 55.000 20.43 11.30 42.59 4.09
5000 5083 1.139095 GCAGCTGATGGCAAAGAGC 59.861 57.895 20.43 7.47 44.79 4.09
5008 5091 1.217244 GCTTTTGGGCAGCTGATGG 59.783 57.895 20.43 0.47 34.15 3.51
5009 5092 1.969085 TGCTTTTGGGCAGCTGATG 59.031 52.632 20.43 0.00 38.19 3.07
5010 5093 4.525467 TGCTTTTGGGCAGCTGAT 57.475 50.000 20.43 0.00 38.19 2.90
5016 5099 3.294493 GCCGTCTGCTTTTGGGCA 61.294 61.111 0.00 0.00 43.23 5.36
5017 5100 2.362329 TTTGCCGTCTGCTTTTGGGC 62.362 55.000 0.00 0.00 44.00 5.36
5018 5101 0.318955 CTTTGCCGTCTGCTTTTGGG 60.319 55.000 0.00 0.00 42.00 4.12
5019 5102 0.667993 TCTTTGCCGTCTGCTTTTGG 59.332 50.000 0.00 0.00 42.00 3.28
5020 5103 2.490328 TTCTTTGCCGTCTGCTTTTG 57.510 45.000 0.00 0.00 42.00 2.44
5021 5104 3.383761 CATTTCTTTGCCGTCTGCTTTT 58.616 40.909 0.00 0.00 42.00 2.27
5022 5105 2.288395 CCATTTCTTTGCCGTCTGCTTT 60.288 45.455 0.00 0.00 42.00 3.51
5023 5106 1.270550 CCATTTCTTTGCCGTCTGCTT 59.729 47.619 0.00 0.00 42.00 3.91
5024 5107 0.883833 CCATTTCTTTGCCGTCTGCT 59.116 50.000 0.00 0.00 42.00 4.24
5025 5108 0.733909 GCCATTTCTTTGCCGTCTGC 60.734 55.000 0.00 0.00 41.77 4.26
5026 5109 0.454957 CGCCATTTCTTTGCCGTCTG 60.455 55.000 0.00 0.00 0.00 3.51
5027 5110 1.586154 CCGCCATTTCTTTGCCGTCT 61.586 55.000 0.00 0.00 0.00 4.18
5028 5111 1.154035 CCGCCATTTCTTTGCCGTC 60.154 57.895 0.00 0.00 0.00 4.79
5029 5112 1.602323 TCCGCCATTTCTTTGCCGT 60.602 52.632 0.00 0.00 0.00 5.68
5030 5113 1.154035 GTCCGCCATTTCTTTGCCG 60.154 57.895 0.00 0.00 0.00 5.69
5031 5114 1.154035 CGTCCGCCATTTCTTTGCC 60.154 57.895 0.00 0.00 0.00 4.52
5032 5115 1.154035 CCGTCCGCCATTTCTTTGC 60.154 57.895 0.00 0.00 0.00 3.68
5033 5116 1.154035 GCCGTCCGCCATTTCTTTG 60.154 57.895 0.00 0.00 0.00 2.77
5034 5117 1.175983 TTGCCGTCCGCCATTTCTTT 61.176 50.000 0.00 0.00 36.24 2.52
5035 5118 1.175983 TTTGCCGTCCGCCATTTCTT 61.176 50.000 0.00 0.00 36.24 2.52
5036 5119 1.586154 CTTTGCCGTCCGCCATTTCT 61.586 55.000 0.00 0.00 36.24 2.52
5037 5120 1.154035 CTTTGCCGTCCGCCATTTC 60.154 57.895 0.00 0.00 36.24 2.17
5038 5121 1.175983 TTCTTTGCCGTCCGCCATTT 61.176 50.000 0.00 0.00 36.24 2.32
5039 5122 1.586154 CTTCTTTGCCGTCCGCCATT 61.586 55.000 0.00 0.00 36.24 3.16
5040 5123 2.033448 TTCTTTGCCGTCCGCCAT 59.967 55.556 0.00 0.00 36.24 4.40
5041 5124 2.668212 CTTCTTTGCCGTCCGCCA 60.668 61.111 0.00 0.00 36.24 5.69
5042 5125 4.103103 GCTTCTTTGCCGTCCGCC 62.103 66.667 0.00 0.00 36.24 6.13
5043 5126 3.028366 GAGCTTCTTTGCCGTCCGC 62.028 63.158 0.00 0.00 38.31 5.54
5044 5127 0.951040 AAGAGCTTCTTTGCCGTCCG 60.951 55.000 0.00 0.00 31.57 4.79
5045 5128 1.239347 AAAGAGCTTCTTTGCCGTCC 58.761 50.000 9.46 0.00 44.34 4.79
5052 5135 1.815003 CGGATGGCAAAGAGCTTCTTT 59.185 47.619 0.00 5.61 46.75 2.52
5053 5136 1.457346 CGGATGGCAAAGAGCTTCTT 58.543 50.000 0.00 0.00 44.79 2.52
5054 5137 1.028868 GCGGATGGCAAAGAGCTTCT 61.029 55.000 0.00 0.00 44.79 2.85
5055 5138 1.431036 GCGGATGGCAAAGAGCTTC 59.569 57.895 0.00 0.00 44.79 3.86
5056 5139 2.401766 CGCGGATGGCAAAGAGCTT 61.402 57.895 0.00 0.00 44.79 3.74
5057 5140 2.821366 CGCGGATGGCAAAGAGCT 60.821 61.111 0.00 0.00 44.79 4.09
5058 5141 2.817423 CTCGCGGATGGCAAAGAGC 61.817 63.158 6.13 0.00 43.84 4.09
5059 5142 2.817423 GCTCGCGGATGGCAAAGAG 61.817 63.158 6.13 0.00 43.84 2.85
5060 5143 2.819595 GCTCGCGGATGGCAAAGA 60.820 61.111 6.13 0.00 43.84 2.52
5061 5144 2.817423 GAGCTCGCGGATGGCAAAG 61.817 63.158 6.13 0.00 43.84 2.77
5062 5145 2.803155 AAGAGCTCGCGGATGGCAAA 62.803 55.000 6.13 0.00 43.84 3.68
5063 5146 2.803155 AAAGAGCTCGCGGATGGCAA 62.803 55.000 6.13 0.00 43.84 4.52
5064 5147 3.315142 AAAGAGCTCGCGGATGGCA 62.315 57.895 6.13 0.00 43.84 4.92
5065 5148 2.512515 AAAGAGCTCGCGGATGGC 60.513 61.111 6.13 6.21 38.69 4.40
5066 5149 2.817423 GCAAAGAGCTCGCGGATGG 61.817 63.158 6.13 0.00 41.15 3.51
5067 5150 2.705826 GCAAAGAGCTCGCGGATG 59.294 61.111 6.13 5.57 41.15 3.51
5068 5151 2.512515 GGCAAAGAGCTCGCGGAT 60.513 61.111 6.13 0.00 44.79 4.18
5071 5154 3.843240 GACGGCAAAGAGCTCGCG 61.843 66.667 8.37 0.00 44.79 5.87
5072 5155 3.491652 GGACGGCAAAGAGCTCGC 61.492 66.667 8.37 5.76 44.79 5.03
5073 5156 3.181967 CGGACGGCAAAGAGCTCG 61.182 66.667 8.37 0.00 44.79 5.03
5074 5157 3.491652 GCGGACGGCAAAGAGCTC 61.492 66.667 5.27 5.27 44.79 4.09


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

AutoCloner maintained by Alex Coulton.