Multiple sequence alignment - TraesCS7D01G239600

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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 TraesCS7D01G239600 chr7D 100.000 5015 0 0 1 5015 204107970 204112984 0.000000e+00 9262.0
1 TraesCS7D01G239600 chr7D 90.426 658 38 13 4378 5013 565204615 565205269 0.000000e+00 843.0
2 TraesCS7D01G239600 chr7D 88.191 669 50 11 4371 5015 527730615 527731278 0.000000e+00 771.0
3 TraesCS7D01G239600 chr7A 95.504 3603 130 17 661 4243 215934013 215937603 0.000000e+00 5727.0
4 TraesCS7D01G239600 chr7A 91.071 336 13 3 342 661 215933650 215933984 5.960000e-119 438.0
5 TraesCS7D01G239600 chr7A 95.973 149 4 2 3 150 215933297 215933444 1.800000e-59 241.0
6 TraesCS7D01G239600 chr7A 85.065 154 21 2 4378 4530 89628655 89628503 6.720000e-34 156.0
7 TraesCS7D01G239600 chr7A 84.416 154 21 3 4378 4530 256890013 256889862 1.120000e-31 148.0
8 TraesCS7D01G239600 chr7A 86.076 79 4 1 270 341 215933502 215933580 1.500000e-10 78.7
9 TraesCS7D01G239600 chr7A 93.478 46 3 0 4267 4312 6778429 6778474 9.010000e-08 69.4
10 TraesCS7D01G239600 chr7B 93.445 3631 166 33 662 4243 168073926 168077533 0.000000e+00 5321.0
11 TraesCS7D01G239600 chr7B 91.629 669 20 12 1 665 168073266 168073902 0.000000e+00 893.0
12 TraesCS7D01G239600 chr7B 89.855 69 6 1 4240 4308 707968155 707968088 2.490000e-13 87.9
13 TraesCS7D01G239600 chr7B 85.526 76 7 1 4240 4311 621626908 621626833 5.380000e-10 76.8
14 TraesCS7D01G239600 chr5A 77.034 2704 554 45 1343 4008 473010119 473012793 0.000000e+00 1491.0
15 TraesCS7D01G239600 chr5A 83.056 661 48 23 4378 5015 546332173 546331554 4.420000e-150 542.0
16 TraesCS7D01G239600 chr5D 76.377 2887 601 58 1158 4008 370463018 370465859 0.000000e+00 1478.0
17 TraesCS7D01G239600 chr5D 88.839 663 46 8 4376 5015 375278926 375278269 0.000000e+00 789.0
18 TraesCS7D01G239600 chr5D 85.075 67 8 2 4240 4304 529772027 529771961 3.240000e-07 67.6
19 TraesCS7D01G239600 chr5D 89.130 46 3 2 4224 4267 2624260 2624305 7.010000e-04 56.5
20 TraesCS7D01G239600 chr5B 75.932 2896 627 49 1158 4021 439716058 439718915 0.000000e+00 1423.0
21 TraesCS7D01G239600 chr5B 89.855 69 6 1 4240 4308 621396102 621396169 2.490000e-13 87.9
22 TraesCS7D01G239600 chr2D 89.426 662 41 8 4376 5015 573910388 573909734 0.000000e+00 808.0
23 TraesCS7D01G239600 chr2D 88.956 661 49 5 4378 5015 472144546 472145205 0.000000e+00 795.0
24 TraesCS7D01G239600 chr2D 88.404 664 53 9 4369 5009 70288957 70289619 0.000000e+00 778.0
25 TraesCS7D01G239600 chr2D 88.688 663 41 17 4375 5015 480539228 480539878 0.000000e+00 778.0
26 TraesCS7D01G239600 chr2D 92.276 492 29 6 4530 5015 249984114 249984602 0.000000e+00 689.0
27 TraesCS7D01G239600 chr2D 87.500 72 4 1 4237 4308 367592301 367592367 1.500000e-10 78.7
28 TraesCS7D01G239600 chrUn 88.190 652 60 12 4376 5015 31230454 31231100 0.000000e+00 761.0
29 TraesCS7D01G239600 chr1A 87.444 669 48 19 4371 5015 531512782 531512126 0.000000e+00 737.0
30 TraesCS7D01G239600 chr4D 82.175 662 76 30 4376 5015 37498965 37498324 9.560000e-147 531.0
31 TraesCS7D01G239600 chr4D 82.500 160 24 4 4373 4530 22228121 22228278 2.430000e-28 137.0
32 TraesCS7D01G239600 chr3B 82.282 666 53 34 4376 5015 95463007 95463633 2.680000e-142 516.0
33 TraesCS7D01G239600 chr3B 97.297 37 0 1 4232 4267 497700769 497700805 1.510000e-05 62.1
34 TraesCS7D01G239600 chr3B 87.755 49 3 3 4220 4267 6944586 6944540 3.000000e-03 54.7
35 TraesCS7D01G239600 chr3D 82.353 170 26 4 4376 4544 427230252 427230086 1.460000e-30 145.0
36 TraesCS7D01G239600 chr1B 92.453 53 1 3 4270 4320 20038466 20038415 6.960000e-09 73.1
37 TraesCS7D01G239600 chr1D 97.500 40 1 0 4270 4309 128533771 128533732 9.010000e-08 69.4
38 TraesCS7D01G239600 chr2A 100.000 36 0 0 4274 4309 77935851 77935816 3.240000e-07 67.6
39 TraesCS7D01G239600 chr6D 92.683 41 1 2 4228 4267 350223050 350223089 1.950000e-04 58.4


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 TraesCS7D01G239600 chr7D 204107970 204112984 5014 False 9262.000 9262 100.000 1 5015 1 chr7D.!!$F1 5014
1 TraesCS7D01G239600 chr7D 565204615 565205269 654 False 843.000 843 90.426 4378 5013 1 chr7D.!!$F3 635
2 TraesCS7D01G239600 chr7D 527730615 527731278 663 False 771.000 771 88.191 4371 5015 1 chr7D.!!$F2 644
3 TraesCS7D01G239600 chr7A 215933297 215937603 4306 False 1621.175 5727 92.156 3 4243 4 chr7A.!!$F2 4240
4 TraesCS7D01G239600 chr7B 168073266 168077533 4267 False 3107.000 5321 92.537 1 4243 2 chr7B.!!$F1 4242
5 TraesCS7D01G239600 chr5A 473010119 473012793 2674 False 1491.000 1491 77.034 1343 4008 1 chr5A.!!$F1 2665
6 TraesCS7D01G239600 chr5A 546331554 546332173 619 True 542.000 542 83.056 4378 5015 1 chr5A.!!$R1 637
7 TraesCS7D01G239600 chr5D 370463018 370465859 2841 False 1478.000 1478 76.377 1158 4008 1 chr5D.!!$F2 2850
8 TraesCS7D01G239600 chr5D 375278269 375278926 657 True 789.000 789 88.839 4376 5015 1 chr5D.!!$R1 639
9 TraesCS7D01G239600 chr5B 439716058 439718915 2857 False 1423.000 1423 75.932 1158 4021 1 chr5B.!!$F1 2863
10 TraesCS7D01G239600 chr2D 573909734 573910388 654 True 808.000 808 89.426 4376 5015 1 chr2D.!!$R1 639
11 TraesCS7D01G239600 chr2D 472144546 472145205 659 False 795.000 795 88.956 4378 5015 1 chr2D.!!$F4 637
12 TraesCS7D01G239600 chr2D 70288957 70289619 662 False 778.000 778 88.404 4369 5009 1 chr2D.!!$F1 640
13 TraesCS7D01G239600 chr2D 480539228 480539878 650 False 778.000 778 88.688 4375 5015 1 chr2D.!!$F5 640
14 TraesCS7D01G239600 chrUn 31230454 31231100 646 False 761.000 761 88.190 4376 5015 1 chrUn.!!$F1 639
15 TraesCS7D01G239600 chr1A 531512126 531512782 656 True 737.000 737 87.444 4371 5015 1 chr1A.!!$R1 644
16 TraesCS7D01G239600 chr4D 37498324 37498965 641 True 531.000 531 82.175 4376 5015 1 chr4D.!!$R1 639
17 TraesCS7D01G239600 chr3B 95463007 95463633 626 False 516.000 516 82.282 4376 5015 1 chr3B.!!$F1 639

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
565 655 0.320374 ATGGTGCTCGAGTCGGAAAA 59.680 50.0 15.13 0.00 0.00 2.29 F
1440 1597 0.035056 ACCCGGCCAAGATTTCAGAG 60.035 55.0 2.24 0.00 0.00 3.35 F
1731 1900 0.036765 TTATCTGCTCCGTGGCGTTT 60.037 50.0 0.00 0.00 34.52 3.60 F
1791 1960 0.548510 TCAGCCTCGAGGAGATCAGA 59.451 55.0 35.69 16.02 37.39 3.27 F
2814 2989 0.602638 TGCCACGTGTGATGAACCTC 60.603 55.0 15.65 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1729 0.604243 GGTGGCCAATGTACACGTCA 60.604 55.000 7.24 0.00 36.02 4.35 R
2829 3004 0.452184 CGATGTACGAGAGCTGTGGT 59.548 55.000 3.55 3.55 45.77 4.16 R
3474 3652 1.676968 CCTCATCACCCCGTTCACA 59.323 57.895 0.00 0.00 0.00 3.58 R
3561 3739 4.329545 TGAACGGCAGGTGGCTCC 62.330 66.667 0.00 0.00 44.01 4.70 R
4105 4301 0.107312 GGCTGGCATCACATCAGAGT 60.107 55.000 0.00 0.00 0.00 3.24 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
156 158 3.849002 CATCCAGTGCTGCAGTACT 57.151 52.632 29.16 29.16 41.69 2.73
157 159 2.967599 CATCCAGTGCTGCAGTACTA 57.032 50.000 32.93 21.29 38.95 1.82
158 160 2.544685 CATCCAGTGCTGCAGTACTAC 58.455 52.381 32.93 18.09 38.95 2.73
181 183 5.307196 ACTGTACATGGTCAAAACTCCTAGT 59.693 40.000 0.00 0.00 0.00 2.57
196 198 2.442502 TCCTAGTAGGAGGAGTACCAGC 59.557 54.545 15.33 0.00 40.06 4.85
197 199 2.175069 CCTAGTAGGAGGAGTACCAGCA 59.825 54.545 11.09 0.00 37.67 4.41
198 200 2.445682 AGTAGGAGGAGTACCAGCAG 57.554 55.000 0.00 0.00 38.94 4.24
199 201 1.641714 AGTAGGAGGAGTACCAGCAGT 59.358 52.381 0.00 0.00 38.94 4.40
200 202 2.043252 AGTAGGAGGAGTACCAGCAGTT 59.957 50.000 0.00 0.00 38.94 3.16
242 244 2.356278 GACAGGATGGCTTGGGCA 59.644 61.111 0.00 0.00 44.72 5.36
248 250 3.305314 ATGGCTTGGGCATTGCTG 58.695 55.556 8.82 0.00 46.61 4.41
249 251 3.026431 ATGGCTTGGGCATTGCTGC 62.026 57.895 8.82 8.03 46.61 5.25
258 260 3.203442 CATTGCTGCATTCGGGCT 58.797 55.556 1.84 0.00 34.04 5.19
259 261 1.065273 CATTGCTGCATTCGGGCTC 59.935 57.895 1.84 0.00 34.04 4.70
260 262 1.077212 ATTGCTGCATTCGGGCTCT 60.077 52.632 1.84 0.00 34.04 4.09
261 263 1.381928 ATTGCTGCATTCGGGCTCTG 61.382 55.000 1.84 0.00 34.04 3.35
262 264 3.885521 GCTGCATTCGGGCTCTGC 61.886 66.667 0.00 0.00 36.45 4.26
275 277 2.525629 TCTGCCCACCGTTCCTCA 60.526 61.111 0.00 0.00 0.00 3.86
326 335 2.747855 GGCAGTGGCACTGGTAGC 60.748 66.667 39.74 28.59 46.01 3.58
565 655 0.320374 ATGGTGCTCGAGTCGGAAAA 59.680 50.000 15.13 0.00 0.00 2.29
594 684 0.887933 TTTTCAAATCCGGCTCCAGC 59.112 50.000 0.00 0.00 41.14 4.85
652 746 1.001860 GCAAGTGGCTCTGAAGAGAGT 59.998 52.381 11.56 0.00 46.76 3.24
656 750 1.220477 GGCTCTGAAGAGAGTGGGC 59.780 63.158 11.56 0.00 46.76 5.36
698 827 8.308207 GGATTCTTGAAGGATACCTCAGTATAC 58.692 40.741 0.00 0.00 39.36 1.47
735 867 5.398603 TTTGCTTGACCTGTTTCTTCAAA 57.601 34.783 0.00 0.00 0.00 2.69
758 890 3.054878 TCTCGCTTCCTTTACACGTTTC 58.945 45.455 0.00 0.00 0.00 2.78
791 923 0.379669 GTGCGGAATCTGCAGATTGG 59.620 55.000 39.54 30.49 44.14 3.16
793 925 1.098050 GCGGAATCTGCAGATTGGTT 58.902 50.000 39.54 21.81 44.14 3.67
801 933 2.158623 TCTGCAGATTGGTTCAGGTTGT 60.159 45.455 13.74 0.00 0.00 3.32
803 935 2.361757 TGCAGATTGGTTCAGGTTGTTG 59.638 45.455 0.00 0.00 0.00 3.33
804 936 2.622942 GCAGATTGGTTCAGGTTGTTGA 59.377 45.455 0.00 0.00 0.00 3.18
811 943 4.590918 TGGTTCAGGTTGTTGAAACAGTA 58.409 39.130 2.58 0.00 46.72 2.74
865 1000 5.596836 TGTGACCAAATGCTTTCTCTTTT 57.403 34.783 0.00 0.00 0.00 2.27
866 1001 5.350633 TGTGACCAAATGCTTTCTCTTTTG 58.649 37.500 0.00 0.00 33.49 2.44
867 1002 5.105392 TGTGACCAAATGCTTTCTCTTTTGT 60.105 36.000 0.00 0.00 32.47 2.83
868 1003 5.232838 GTGACCAAATGCTTTCTCTTTTGTG 59.767 40.000 0.00 0.00 32.47 3.33
869 1004 5.105392 TGACCAAATGCTTTCTCTTTTGTGT 60.105 36.000 0.00 0.00 32.47 3.72
870 1005 5.733676 ACCAAATGCTTTCTCTTTTGTGTT 58.266 33.333 0.00 0.00 32.47 3.32
876 1011 6.751514 TGCTTTCTCTTTTGTGTTGTTCTA 57.248 33.333 0.00 0.00 0.00 2.10
879 1014 8.898761 TGCTTTCTCTTTTGTGTTGTTCTAATA 58.101 29.630 0.00 0.00 0.00 0.98
1362 1507 2.851801 TCCCAGTCCGAGGACACT 59.148 61.111 22.66 1.72 46.76 3.55
1440 1597 0.035056 ACCCGGCCAAGATTTCAGAG 60.035 55.000 2.24 0.00 0.00 3.35
1579 1745 0.796312 CTGTGACGTGTACATTGGCC 59.204 55.000 0.00 0.00 0.00 5.36
1704 1873 0.302890 CGCAGATTCACGAGATTGCC 59.697 55.000 0.00 0.00 0.00 4.52
1731 1900 0.036765 TTATCTGCTCCGTGGCGTTT 60.037 50.000 0.00 0.00 34.52 3.60
1791 1960 0.548510 TCAGCCTCGAGGAGATCAGA 59.451 55.000 35.69 16.02 37.39 3.27
1815 1984 5.808366 TCTTTGCTCAGAAGAAGAACCTA 57.192 39.130 0.00 0.00 30.60 3.08
2196 2368 3.665675 AAGATCCAGCGGCGTGTCC 62.666 63.158 9.37 0.00 0.00 4.02
2337 2512 1.252904 TGTCGTCGGGGAAAGGTAGG 61.253 60.000 0.00 0.00 0.00 3.18
2484 2659 2.257034 GAGTTTGCTTACCGGTACTCG 58.743 52.381 15.53 7.09 38.88 4.18
2634 2809 1.914798 AGCTTTGAGGAGCAGGAGATT 59.085 47.619 0.00 0.00 45.12 2.40
2727 2902 2.055042 CGAGAGGGACTGGTGGGAG 61.055 68.421 0.00 0.00 41.55 4.30
2766 2941 1.378514 CATCCCAAGGAACACCGGG 60.379 63.158 6.32 0.00 40.32 5.73
2814 2989 0.602638 TGCCACGTGTGATGAACCTC 60.603 55.000 15.65 0.00 0.00 3.85
2829 3004 2.724377 CTCGAGCCGATGCAGCTA 59.276 61.111 0.00 0.00 41.75 3.32
2979 3154 0.937699 TCGTCGGTTCACTGCTTTCG 60.938 55.000 0.00 0.00 0.00 3.46
3561 3739 2.541588 CCTTGTGTTTGGCTTCAAGTCG 60.542 50.000 0.00 0.00 36.53 4.18
3891 4069 4.681978 GGCGGGCTGTTCGACACT 62.682 66.667 0.00 0.00 35.41 3.55
4016 4194 5.770663 TCAGATACAGGAGTAAGGTATGAGC 59.229 44.000 0.00 0.00 33.13 4.26
4070 4266 3.343941 TTGCAGCCGTTATTAGAAGGT 57.656 42.857 0.00 0.00 0.00 3.50
4105 4301 2.903784 TCATTTCTCCCGGTTTCTGAGA 59.096 45.455 0.00 1.37 33.50 3.27
4109 4305 1.075698 TCTCCCGGTTTCTGAGACTCT 59.924 52.381 0.00 0.00 30.48 3.24
4112 4308 1.827969 CCCGGTTTCTGAGACTCTGAT 59.172 52.381 12.29 0.00 0.00 2.90
4151 4347 4.492791 TTTGTCAGTGATCTGTGCAATG 57.507 40.909 0.00 0.00 41.91 2.82
4166 4365 2.229543 TGCAATGTCCAAGCTTCATGAC 59.770 45.455 0.00 4.65 0.00 3.06
4208 4410 7.866393 AGTTGTTATGTACAGTACAGTTCAGTC 59.134 37.037 18.30 12.21 42.77 3.51
4250 4463 9.543231 TTATTATCTTCATATTACTCCCTCCGT 57.457 33.333 0.00 0.00 0.00 4.69
4251 4464 7.850935 TTATCTTCATATTACTCCCTCCGTT 57.149 36.000 0.00 0.00 0.00 4.44
4252 4465 6.749036 ATCTTCATATTACTCCCTCCGTTT 57.251 37.500 0.00 0.00 0.00 3.60
4253 4466 6.158023 TCTTCATATTACTCCCTCCGTTTC 57.842 41.667 0.00 0.00 0.00 2.78
4254 4467 5.659525 TCTTCATATTACTCCCTCCGTTTCA 59.340 40.000 0.00 0.00 0.00 2.69
4255 4468 5.943349 TCATATTACTCCCTCCGTTTCAA 57.057 39.130 0.00 0.00 0.00 2.69
4256 4469 6.302535 TCATATTACTCCCTCCGTTTCAAA 57.697 37.500 0.00 0.00 0.00 2.69
4257 4470 6.713276 TCATATTACTCCCTCCGTTTCAAAA 58.287 36.000 0.00 0.00 0.00 2.44
4258 4471 7.343357 TCATATTACTCCCTCCGTTTCAAAAT 58.657 34.615 0.00 0.00 0.00 1.82
4259 4472 8.487848 TCATATTACTCCCTCCGTTTCAAAATA 58.512 33.333 0.00 0.00 0.00 1.40
4260 4473 8.774586 CATATTACTCCCTCCGTTTCAAAATAG 58.225 37.037 0.00 0.00 0.00 1.73
4261 4474 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
4262 4475 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
4263 4476 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
4264 4477 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
4265 4478 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
4266 4479 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
4267 4480 5.648092 CCCTCCGTTTCAAAATAGATGACTT 59.352 40.000 0.00 0.00 0.00 3.01
4268 4481 6.403636 CCCTCCGTTTCAAAATAGATGACTTG 60.404 42.308 0.00 0.00 0.00 3.16
4269 4482 6.403636 CCTCCGTTTCAAAATAGATGACTTGG 60.404 42.308 0.00 0.00 0.00 3.61
4270 4483 6.001460 TCCGTTTCAAAATAGATGACTTGGT 58.999 36.000 0.00 0.00 0.00 3.67
4271 4484 7.162761 TCCGTTTCAAAATAGATGACTTGGTA 58.837 34.615 0.00 0.00 0.00 3.25
4272 4485 7.118680 TCCGTTTCAAAATAGATGACTTGGTAC 59.881 37.037 0.00 0.00 0.00 3.34
4273 4486 7.094975 CCGTTTCAAAATAGATGACTTGGTACA 60.095 37.037 0.00 0.00 0.00 2.90
4291 4504 7.604657 TGGTACAAAGTTGGGTCATTTATTT 57.395 32.000 0.00 0.00 31.92 1.40
4292 4505 8.024145 TGGTACAAAGTTGGGTCATTTATTTT 57.976 30.769 0.00 0.00 31.92 1.82
4293 4506 9.144298 TGGTACAAAGTTGGGTCATTTATTTTA 57.856 29.630 0.00 0.00 31.92 1.52
4294 4507 9.984190 GGTACAAAGTTGGGTCATTTATTTTAA 57.016 29.630 0.00 0.00 0.00 1.52
4298 4511 9.856803 CAAAGTTGGGTCATTTATTTTAAAACG 57.143 29.630 1.97 0.00 0.00 3.60
4299 4512 8.596271 AAGTTGGGTCATTTATTTTAAAACGG 57.404 30.769 1.97 0.00 0.00 4.44
4300 4513 7.953752 AGTTGGGTCATTTATTTTAAAACGGA 58.046 30.769 1.97 0.00 0.00 4.69
4301 4514 8.085909 AGTTGGGTCATTTATTTTAAAACGGAG 58.914 33.333 1.97 0.00 0.00 4.63
4302 4515 6.926313 TGGGTCATTTATTTTAAAACGGAGG 58.074 36.000 1.97 0.00 0.00 4.30
4303 4516 6.071278 TGGGTCATTTATTTTAAAACGGAGGG 60.071 38.462 1.97 0.00 0.00 4.30
4304 4517 6.153170 GGGTCATTTATTTTAAAACGGAGGGA 59.847 38.462 1.97 0.00 0.00 4.20
4305 4518 7.255569 GGTCATTTATTTTAAAACGGAGGGAG 58.744 38.462 1.97 0.00 0.00 4.30
4306 4519 7.094075 GGTCATTTATTTTAAAACGGAGGGAGT 60.094 37.037 1.97 0.00 0.00 3.85
4307 4520 8.949177 GTCATTTATTTTAAAACGGAGGGAGTA 58.051 33.333 1.97 0.00 0.00 2.59
4308 4521 8.949177 TCATTTATTTTAAAACGGAGGGAGTAC 58.051 33.333 1.97 0.00 0.00 2.73
4309 4522 8.953313 CATTTATTTTAAAACGGAGGGAGTACT 58.047 33.333 1.97 0.00 0.00 2.73
4310 4523 8.922931 TTTATTTTAAAACGGAGGGAGTACTT 57.077 30.769 1.97 0.00 0.00 2.24
4311 4524 8.922931 TTATTTTAAAACGGAGGGAGTACTTT 57.077 30.769 1.97 0.00 0.00 2.66
4312 4525 6.866010 TTTTAAAACGGAGGGAGTACTTTC 57.134 37.500 0.00 0.00 0.00 2.62
4313 4526 2.738013 AAACGGAGGGAGTACTTTCG 57.262 50.000 0.00 0.00 0.00 3.46
4314 4527 1.625511 AACGGAGGGAGTACTTTCGT 58.374 50.000 0.00 0.00 34.08 3.85
4315 4528 0.886563 ACGGAGGGAGTACTTTCGTG 59.113 55.000 0.00 0.00 32.42 4.35
4316 4529 0.458025 CGGAGGGAGTACTTTCGTGC 60.458 60.000 0.00 0.00 0.00 5.34
4317 4530 0.896226 GGAGGGAGTACTTTCGTGCT 59.104 55.000 0.00 0.00 38.89 4.40
4318 4531 1.275573 GGAGGGAGTACTTTCGTGCTT 59.724 52.381 0.00 0.00 36.15 3.91
4319 4532 2.289506 GGAGGGAGTACTTTCGTGCTTT 60.290 50.000 0.00 0.00 36.15 3.51
4320 4533 2.994578 GAGGGAGTACTTTCGTGCTTTC 59.005 50.000 0.00 0.00 36.15 2.62
4321 4534 2.074576 GGGAGTACTTTCGTGCTTTCC 58.925 52.381 0.00 0.00 36.15 3.13
4322 4535 1.725164 GGAGTACTTTCGTGCTTTCCG 59.275 52.381 0.00 0.00 36.15 4.30
4323 4536 2.608752 GGAGTACTTTCGTGCTTTCCGA 60.609 50.000 0.00 0.00 36.15 4.55
4324 4537 2.662156 GAGTACTTTCGTGCTTTCCGAG 59.338 50.000 0.00 0.00 36.15 4.63
4325 4538 2.295349 AGTACTTTCGTGCTTTCCGAGA 59.705 45.455 0.00 0.00 31.65 4.04
4326 4539 2.457366 ACTTTCGTGCTTTCCGAGAT 57.543 45.000 0.00 0.00 35.49 2.75
4327 4540 2.767505 ACTTTCGTGCTTTCCGAGATT 58.232 42.857 0.00 0.00 35.49 2.40
4328 4541 2.480419 ACTTTCGTGCTTTCCGAGATTG 59.520 45.455 0.00 0.00 35.49 2.67
4329 4542 2.448926 TTCGTGCTTTCCGAGATTGA 57.551 45.000 0.00 0.00 35.49 2.57
4330 4543 2.448926 TCGTGCTTTCCGAGATTGAA 57.551 45.000 0.00 0.00 0.00 2.69
4331 4544 2.066262 TCGTGCTTTCCGAGATTGAAC 58.934 47.619 0.00 0.00 0.00 3.18
4332 4545 2.069273 CGTGCTTTCCGAGATTGAACT 58.931 47.619 0.00 0.00 0.00 3.01
4333 4546 2.480419 CGTGCTTTCCGAGATTGAACTT 59.520 45.455 0.00 0.00 0.00 2.66
4334 4547 3.423645 CGTGCTTTCCGAGATTGAACTTC 60.424 47.826 0.00 0.00 0.00 3.01
4335 4548 3.074412 TGCTTTCCGAGATTGAACTTCC 58.926 45.455 0.00 0.00 0.00 3.46
4336 4549 3.074412 GCTTTCCGAGATTGAACTTCCA 58.926 45.455 0.00 0.00 0.00 3.53
4337 4550 3.120165 GCTTTCCGAGATTGAACTTCCAC 60.120 47.826 0.00 0.00 0.00 4.02
4338 4551 4.319177 CTTTCCGAGATTGAACTTCCACT 58.681 43.478 0.00 0.00 0.00 4.00
4339 4552 4.351874 TTCCGAGATTGAACTTCCACTT 57.648 40.909 0.00 0.00 0.00 3.16
4340 4553 4.351874 TCCGAGATTGAACTTCCACTTT 57.648 40.909 0.00 0.00 0.00 2.66
4341 4554 5.477607 TCCGAGATTGAACTTCCACTTTA 57.522 39.130 0.00 0.00 0.00 1.85
4342 4555 5.479306 TCCGAGATTGAACTTCCACTTTAG 58.521 41.667 0.00 0.00 0.00 1.85
4343 4556 5.245301 TCCGAGATTGAACTTCCACTTTAGA 59.755 40.000 0.00 0.00 0.00 2.10
4344 4557 6.070767 TCCGAGATTGAACTTCCACTTTAGAT 60.071 38.462 0.00 0.00 0.00 1.98
4345 4558 7.123697 TCCGAGATTGAACTTCCACTTTAGATA 59.876 37.037 0.00 0.00 0.00 1.98
4346 4559 7.928706 CCGAGATTGAACTTCCACTTTAGATAT 59.071 37.037 0.00 0.00 0.00 1.63
4347 4560 8.973378 CGAGATTGAACTTCCACTTTAGATATC 58.027 37.037 0.00 0.00 0.00 1.63
4348 4561 9.823647 GAGATTGAACTTCCACTTTAGATATCA 57.176 33.333 5.32 0.00 0.00 2.15
4354 4567 9.508567 GAACTTCCACTTTAGATATCAAAATGC 57.491 33.333 5.32 0.00 0.00 3.56
4355 4568 7.697691 ACTTCCACTTTAGATATCAAAATGCG 58.302 34.615 5.32 0.00 0.00 4.73
4356 4569 6.618287 TCCACTTTAGATATCAAAATGCGG 57.382 37.500 5.32 5.26 0.00 5.69
4357 4570 6.119536 TCCACTTTAGATATCAAAATGCGGT 58.880 36.000 5.32 0.00 0.00 5.68
4358 4571 6.260050 TCCACTTTAGATATCAAAATGCGGTC 59.740 38.462 5.32 0.00 0.00 4.79
4359 4572 6.260936 CCACTTTAGATATCAAAATGCGGTCT 59.739 38.462 5.32 0.00 0.00 3.85
4360 4573 7.201732 CCACTTTAGATATCAAAATGCGGTCTT 60.202 37.037 5.32 0.00 0.00 3.01
4361 4574 7.852945 CACTTTAGATATCAAAATGCGGTCTTC 59.147 37.037 5.32 0.00 0.00 2.87
4362 4575 7.770897 ACTTTAGATATCAAAATGCGGTCTTCT 59.229 33.333 5.32 0.00 0.00 2.85
4363 4576 8.506168 TTTAGATATCAAAATGCGGTCTTCTT 57.494 30.769 5.32 0.00 0.00 2.52
4364 4577 8.506168 TTAGATATCAAAATGCGGTCTTCTTT 57.494 30.769 5.32 0.00 0.00 2.52
4365 4578 7.396540 AGATATCAAAATGCGGTCTTCTTTT 57.603 32.000 5.32 0.00 0.00 2.27
4366 4579 7.830739 AGATATCAAAATGCGGTCTTCTTTTT 58.169 30.769 5.32 0.00 0.00 1.94
4411 4624 1.445582 GGCGACTCATTTCGTCCGT 60.446 57.895 0.00 0.00 41.26 4.69
4418 4631 2.031465 ATTTCGTCCGTGGCCGTT 59.969 55.556 0.00 0.00 0.00 4.44
4451 4664 2.034221 GGACAGAAAAGGCGGCCT 59.966 61.111 17.69 17.69 33.87 5.19
4479 4692 1.545136 TGACCCAAATAGACGCGTGTA 59.455 47.619 20.70 19.74 0.00 2.90
4530 4743 2.624636 GCCCATTTTTGAGCCTGATTG 58.375 47.619 0.00 0.00 0.00 2.67
4531 4744 2.234414 GCCCATTTTTGAGCCTGATTGA 59.766 45.455 0.00 0.00 0.00 2.57
4599 4833 3.023735 ACATTGGCCTCCCCTCCC 61.024 66.667 3.32 0.00 0.00 4.30
4601 4835 4.058505 ATTGGCCTCCCCTCCCCT 62.059 66.667 3.32 0.00 0.00 4.79
4715 4963 2.672651 CACATCCGCCCAGCAACA 60.673 61.111 0.00 0.00 0.00 3.33
4779 5029 1.072505 GAGCAAACTGGTTCCCCGA 59.927 57.895 0.00 0.00 0.00 5.14
4884 5136 1.205064 CGTTACACTCGTCGGACGT 59.795 57.895 27.53 12.84 43.14 4.34
4890 5142 4.175489 CTCGTCGGACGTCGGCAT 62.175 66.667 27.53 0.00 44.96 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.679638 GCCTAATCCCTTGTTTTATGTGCTG 60.680 44.000 0.00 0.00 0.00 4.41
153 155 6.495872 AGGAGTTTTGACCATGTACAGTAGTA 59.504 38.462 0.33 0.00 0.00 1.82
154 156 5.307196 AGGAGTTTTGACCATGTACAGTAGT 59.693 40.000 0.33 0.00 0.00 2.73
155 157 5.794894 AGGAGTTTTGACCATGTACAGTAG 58.205 41.667 0.33 0.00 0.00 2.57
156 158 5.818678 AGGAGTTTTGACCATGTACAGTA 57.181 39.130 0.33 0.00 0.00 2.74
157 159 4.706842 AGGAGTTTTGACCATGTACAGT 57.293 40.909 0.33 0.00 0.00 3.55
158 160 5.794894 ACTAGGAGTTTTGACCATGTACAG 58.205 41.667 0.33 0.00 0.00 2.74
181 183 2.832129 CAAACTGCTGGTACTCCTCCTA 59.168 50.000 0.00 0.00 34.23 2.94
187 189 3.633361 AGCCAAACTGCTGGTACTC 57.367 52.632 0.00 0.00 40.90 2.59
197 199 5.510179 CCAATTTCAAGATCACAGCCAAACT 60.510 40.000 0.00 0.00 0.00 2.66
198 200 4.687483 CCAATTTCAAGATCACAGCCAAAC 59.313 41.667 0.00 0.00 0.00 2.93
199 201 4.588106 TCCAATTTCAAGATCACAGCCAAA 59.412 37.500 0.00 0.00 0.00 3.28
200 202 4.022068 GTCCAATTTCAAGATCACAGCCAA 60.022 41.667 0.00 0.00 0.00 4.52
241 243 1.065273 GAGCCCGAATGCAGCAATG 59.935 57.895 0.00 0.00 0.00 2.82
242 244 1.077212 AGAGCCCGAATGCAGCAAT 60.077 52.632 0.00 0.00 0.00 3.56
244 246 2.437180 CAGAGCCCGAATGCAGCA 60.437 61.111 0.00 0.00 0.00 4.41
245 247 3.885521 GCAGAGCCCGAATGCAGC 61.886 66.667 0.00 0.00 39.75 5.25
246 248 3.207669 GGCAGAGCCCGAATGCAG 61.208 66.667 0.00 0.00 44.06 4.41
256 258 3.959991 GAGGAACGGTGGGCAGAGC 62.960 68.421 0.00 0.00 0.00 4.09
257 259 2.266055 GAGGAACGGTGGGCAGAG 59.734 66.667 0.00 0.00 0.00 3.35
258 260 2.525629 TGAGGAACGGTGGGCAGA 60.526 61.111 0.00 0.00 0.00 4.26
259 261 2.358737 GTGAGGAACGGTGGGCAG 60.359 66.667 0.00 0.00 0.00 4.85
260 262 3.948719 GGTGAGGAACGGTGGGCA 61.949 66.667 0.00 0.00 0.00 5.36
261 263 3.268103 ATGGTGAGGAACGGTGGGC 62.268 63.158 0.00 0.00 0.00 5.36
262 264 1.377202 CATGGTGAGGAACGGTGGG 60.377 63.158 0.00 0.00 0.00 4.61
263 265 1.377202 CCATGGTGAGGAACGGTGG 60.377 63.158 2.57 0.00 0.00 4.61
264 266 1.377202 CCCATGGTGAGGAACGGTG 60.377 63.158 11.73 0.00 0.00 4.94
265 267 1.131303 TTCCCATGGTGAGGAACGGT 61.131 55.000 11.73 0.00 37.23 4.83
266 268 0.037590 TTTCCCATGGTGAGGAACGG 59.962 55.000 11.73 0.00 41.83 4.44
267 269 1.745087 CATTTCCCATGGTGAGGAACG 59.255 52.381 11.73 0.00 41.83 3.95
268 270 2.102578 CCATTTCCCATGGTGAGGAAC 58.897 52.381 11.73 0.00 41.83 3.62
269 271 1.619432 GCCATTTCCCATGGTGAGGAA 60.619 52.381 11.73 3.92 41.17 3.36
270 272 0.033208 GCCATTTCCCATGGTGAGGA 60.033 55.000 11.73 0.00 41.17 3.71
271 273 2.508361 GCCATTTCCCATGGTGAGG 58.492 57.895 11.73 6.30 41.17 3.86
275 277 2.053865 CAGCGCCATTTCCCATGGT 61.054 57.895 11.73 0.00 41.17 3.55
326 335 3.628487 GTCTCCTAGTAGTAGCACCAGTG 59.372 52.174 0.00 0.00 0.00 3.66
437 515 1.987855 TACAGCCTCAGTTCGGGGG 60.988 63.158 0.00 0.00 0.00 5.40
652 746 2.101783 CAATGCCAATACTCTTGCCCA 58.898 47.619 0.00 0.00 0.00 5.36
656 750 6.095860 TCAAGAATCCAATGCCAATACTCTTG 59.904 38.462 0.00 0.00 38.92 3.02
718 850 4.570772 CGAGAGTTTGAAGAAACAGGTCAA 59.429 41.667 0.00 0.00 43.51 3.18
722 854 3.134458 AGCGAGAGTTTGAAGAAACAGG 58.866 45.455 0.00 0.00 43.51 4.00
726 858 4.073293 AGGAAGCGAGAGTTTGAAGAAA 57.927 40.909 0.00 0.00 33.53 2.52
735 867 1.612463 ACGTGTAAAGGAAGCGAGAGT 59.388 47.619 0.00 0.00 0.00 3.24
758 890 1.019673 CCGCACTTGATTCCATCCAG 58.980 55.000 0.00 0.00 0.00 3.86
791 923 8.474006 AAAAATACTGTTTCAACAACCTGAAC 57.526 30.769 0.00 0.00 38.66 3.18
818 953 5.048153 TCATTCGAAAAACAACACACACA 57.952 34.783 0.00 0.00 0.00 3.72
819 954 5.328691 TCTCATTCGAAAAACAACACACAC 58.671 37.500 0.00 0.00 0.00 3.82
820 955 5.553290 TCTCATTCGAAAAACAACACACA 57.447 34.783 0.00 0.00 0.00 3.72
821 956 5.971202 ACATCTCATTCGAAAAACAACACAC 59.029 36.000 0.00 0.00 0.00 3.82
825 960 5.625311 GGTCACATCTCATTCGAAAAACAAC 59.375 40.000 0.00 0.00 0.00 3.32
826 961 5.298026 TGGTCACATCTCATTCGAAAAACAA 59.702 36.000 0.00 0.00 0.00 2.83
827 962 4.819088 TGGTCACATCTCATTCGAAAAACA 59.181 37.500 0.00 0.00 0.00 2.83
828 963 5.356882 TGGTCACATCTCATTCGAAAAAC 57.643 39.130 0.00 0.00 0.00 2.43
865 1000 9.219603 CAGATTCTTCCTTATTAGAACAACACA 57.780 33.333 0.00 0.00 33.55 3.72
866 1001 9.220767 ACAGATTCTTCCTTATTAGAACAACAC 57.779 33.333 0.00 0.00 33.55 3.32
867 1002 9.793259 AACAGATTCTTCCTTATTAGAACAACA 57.207 29.630 0.00 0.00 33.55 3.33
971 1107 0.593128 ATCACAACAAAGCTCGGTGC 59.407 50.000 1.16 0.00 43.29 5.01
1119 1255 2.190578 GGCGAGATGGGGTTGGAG 59.809 66.667 0.00 0.00 0.00 3.86
1392 1540 2.708255 GAGTCGTACCGCTCCGAG 59.292 66.667 0.00 0.00 33.10 4.63
1563 1729 0.604243 GGTGGCCAATGTACACGTCA 60.604 55.000 7.24 0.00 36.02 4.35
1579 1745 1.226831 GGTTGCCGTTGTTGTGGTG 60.227 57.895 0.00 0.00 0.00 4.17
1671 1840 0.956633 TCTGCGTGTCGGAGTACTTT 59.043 50.000 10.04 0.00 45.16 2.66
1704 1873 3.498676 GGAGCAGATAATCCGGTCG 57.501 57.895 0.00 0.00 0.00 4.79
1731 1900 4.595538 GTGACCACCACGACGCCA 62.596 66.667 0.00 0.00 35.86 5.69
1791 1960 5.629125 AGGTTCTTCTTCTGAGCAAAGAAT 58.371 37.500 11.68 0.00 40.82 2.40
1815 1984 3.067742 CGGTGTCGAACAGTATAGGGATT 59.932 47.826 0.00 0.00 39.00 3.01
2337 2512 2.168106 TGATCTCTGCTTCTGAAGGCTC 59.832 50.000 18.38 3.36 0.00 4.70
2484 2659 1.982073 GCACCATCTTGTACCGCTGC 61.982 60.000 0.00 0.00 0.00 5.25
2530 2705 5.182001 ACAAATTGAGTATGTTCTGCCTCAC 59.818 40.000 0.00 0.00 33.90 3.51
2589 2764 1.002792 CCTGCCCCTCTCCTTCTCT 59.997 63.158 0.00 0.00 0.00 3.10
2634 2809 3.889815 CTTTACCCTCTGGAATGCATCA 58.110 45.455 0.00 0.00 34.81 3.07
2727 2902 1.077429 GTCATGGAGGTCCTTGCCC 60.077 63.158 6.97 0.00 40.03 5.36
2766 2941 2.221055 GGTGATAATGACATTCGTCGCC 59.779 50.000 21.03 21.03 45.80 5.54
2814 2989 2.659897 GGTAGCTGCATCGGCTCG 60.660 66.667 3.61 0.00 43.23 5.03
2829 3004 0.452184 CGATGTACGAGAGCTGTGGT 59.548 55.000 3.55 3.55 45.77 4.16
3105 3280 2.951642 CAAGGCAAAACAGAAGACCAGA 59.048 45.455 0.00 0.00 0.00 3.86
3462 3640 4.555709 TTCACAGCCGCGGTGGTT 62.556 61.111 28.70 7.43 41.21 3.67
3474 3652 1.676968 CCTCATCACCCCGTTCACA 59.323 57.895 0.00 0.00 0.00 3.58
3561 3739 4.329545 TGAACGGCAGGTGGCTCC 62.330 66.667 0.00 0.00 44.01 4.70
4016 4194 2.607771 CGCAAGGGTTTTTGGATGTCAG 60.608 50.000 0.00 0.00 0.00 3.51
4070 4266 6.518200 CGGGAGAAATGAAAATTCCTGGAAAA 60.518 38.462 14.03 0.00 31.94 2.29
4105 4301 0.107312 GGCTGGCATCACATCAGAGT 60.107 55.000 0.00 0.00 0.00 3.24
4109 4305 0.678684 CTGTGGCTGGCATCACATCA 60.679 55.000 19.33 0.00 42.14 3.07
4112 4308 0.467844 AAACTGTGGCTGGCATCACA 60.468 50.000 18.40 18.40 41.01 3.58
4151 4347 0.955428 TGGCGTCATGAAGCTTGGAC 60.955 55.000 28.59 14.88 36.09 4.02
4166 4365 0.599204 AACTCAGGTTACACGTGGCG 60.599 55.000 21.57 0.00 34.95 5.69
4235 4448 8.711170 TCTATTTTGAAACGGAGGGAGTAATAT 58.289 33.333 0.00 0.00 0.00 1.28
4243 4456 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
4244 4457 6.403636 CCAAGTCATCTATTTTGAAACGGAGG 60.404 42.308 0.00 0.00 0.00 4.30
4245 4458 6.149474 ACCAAGTCATCTATTTTGAAACGGAG 59.851 38.462 0.00 0.00 0.00 4.63
4246 4459 6.001460 ACCAAGTCATCTATTTTGAAACGGA 58.999 36.000 0.00 0.00 0.00 4.69
4247 4460 6.254281 ACCAAGTCATCTATTTTGAAACGG 57.746 37.500 0.00 0.00 0.00 4.44
4248 4461 7.802738 TGTACCAAGTCATCTATTTTGAAACG 58.197 34.615 0.00 0.00 0.00 3.60
4249 4462 9.959749 TTTGTACCAAGTCATCTATTTTGAAAC 57.040 29.630 0.00 0.00 0.00 2.78
4251 4464 9.349713 ACTTTGTACCAAGTCATCTATTTTGAA 57.650 29.630 6.52 0.00 0.00 2.69
4252 4465 8.918202 ACTTTGTACCAAGTCATCTATTTTGA 57.082 30.769 6.52 0.00 0.00 2.69
4253 4466 9.398170 CAACTTTGTACCAAGTCATCTATTTTG 57.602 33.333 12.36 1.32 0.00 2.44
4254 4467 8.576442 CCAACTTTGTACCAAGTCATCTATTTT 58.424 33.333 12.36 0.00 0.00 1.82
4255 4468 7.176690 CCCAACTTTGTACCAAGTCATCTATTT 59.823 37.037 12.36 0.00 0.00 1.40
4256 4469 6.659242 CCCAACTTTGTACCAAGTCATCTATT 59.341 38.462 12.36 0.00 0.00 1.73
4257 4470 6.180472 CCCAACTTTGTACCAAGTCATCTAT 58.820 40.000 12.36 0.00 0.00 1.98
4258 4471 5.072600 ACCCAACTTTGTACCAAGTCATCTA 59.927 40.000 12.36 0.00 0.00 1.98
4259 4472 4.141251 ACCCAACTTTGTACCAAGTCATCT 60.141 41.667 12.36 0.00 0.00 2.90
4260 4473 4.142038 ACCCAACTTTGTACCAAGTCATC 58.858 43.478 12.36 0.00 0.00 2.92
4261 4474 4.142038 GACCCAACTTTGTACCAAGTCAT 58.858 43.478 12.36 0.00 0.00 3.06
4262 4475 3.054287 TGACCCAACTTTGTACCAAGTCA 60.054 43.478 12.36 4.13 0.00 3.41
4263 4476 3.547746 TGACCCAACTTTGTACCAAGTC 58.452 45.455 12.36 1.71 0.00 3.01
4264 4477 3.655615 TGACCCAACTTTGTACCAAGT 57.344 42.857 6.52 6.52 0.00 3.16
4265 4478 5.529581 AAATGACCCAACTTTGTACCAAG 57.470 39.130 5.19 5.19 0.00 3.61
4266 4479 7.604657 AATAAATGACCCAACTTTGTACCAA 57.395 32.000 0.00 0.00 0.00 3.67
4267 4480 7.604657 AAATAAATGACCCAACTTTGTACCA 57.395 32.000 0.00 0.00 0.00 3.25
4268 4481 9.984190 TTAAAATAAATGACCCAACTTTGTACC 57.016 29.630 0.00 0.00 0.00 3.34
4272 4485 9.856803 CGTTTTAAAATAAATGACCCAACTTTG 57.143 29.630 3.52 0.00 0.00 2.77
4273 4486 9.047371 CCGTTTTAAAATAAATGACCCAACTTT 57.953 29.630 3.52 0.00 0.00 2.66
4274 4487 8.422566 TCCGTTTTAAAATAAATGACCCAACTT 58.577 29.630 3.52 0.00 0.00 2.66
4275 4488 7.953752 TCCGTTTTAAAATAAATGACCCAACT 58.046 30.769 3.52 0.00 0.00 3.16
4276 4489 7.329962 CCTCCGTTTTAAAATAAATGACCCAAC 59.670 37.037 3.52 0.00 0.00 3.77
4277 4490 7.379750 CCTCCGTTTTAAAATAAATGACCCAA 58.620 34.615 3.52 0.00 0.00 4.12
4278 4491 6.071278 CCCTCCGTTTTAAAATAAATGACCCA 60.071 38.462 3.52 0.00 0.00 4.51
4279 4492 6.153170 TCCCTCCGTTTTAAAATAAATGACCC 59.847 38.462 3.52 0.00 0.00 4.46
4280 4493 7.094075 ACTCCCTCCGTTTTAAAATAAATGACC 60.094 37.037 3.52 0.00 0.00 4.02
4281 4494 7.823665 ACTCCCTCCGTTTTAAAATAAATGAC 58.176 34.615 3.52 0.00 0.00 3.06
4282 4495 8.949177 GTACTCCCTCCGTTTTAAAATAAATGA 58.051 33.333 3.52 0.00 0.00 2.57
4283 4496 8.953313 AGTACTCCCTCCGTTTTAAAATAAATG 58.047 33.333 3.52 0.00 0.00 2.32
4284 4497 9.524496 AAGTACTCCCTCCGTTTTAAAATAAAT 57.476 29.630 3.52 0.00 0.00 1.40
4285 4498 8.922931 AAGTACTCCCTCCGTTTTAAAATAAA 57.077 30.769 3.52 0.00 0.00 1.40
4286 4499 8.922931 AAAGTACTCCCTCCGTTTTAAAATAA 57.077 30.769 3.52 0.00 0.00 1.40
4287 4500 7.331687 CGAAAGTACTCCCTCCGTTTTAAAATA 59.668 37.037 3.52 0.00 0.00 1.40
4288 4501 6.148315 CGAAAGTACTCCCTCCGTTTTAAAAT 59.852 38.462 3.52 0.00 0.00 1.82
4289 4502 5.466393 CGAAAGTACTCCCTCCGTTTTAAAA 59.534 40.000 0.00 0.00 0.00 1.52
4290 4503 4.990426 CGAAAGTACTCCCTCCGTTTTAAA 59.010 41.667 0.00 0.00 0.00 1.52
4291 4504 4.039124 ACGAAAGTACTCCCTCCGTTTTAA 59.961 41.667 0.00 0.00 46.88 1.52
4292 4505 3.573967 ACGAAAGTACTCCCTCCGTTTTA 59.426 43.478 0.00 0.00 46.88 1.52
4293 4506 2.366590 ACGAAAGTACTCCCTCCGTTTT 59.633 45.455 0.00 0.00 46.88 2.43
4294 4507 1.966354 ACGAAAGTACTCCCTCCGTTT 59.034 47.619 0.00 0.00 46.88 3.60
4295 4508 1.625511 ACGAAAGTACTCCCTCCGTT 58.374 50.000 0.00 0.00 46.88 4.44
4296 4509 3.353342 ACGAAAGTACTCCCTCCGT 57.647 52.632 0.00 0.00 46.88 4.69
4308 4521 2.736721 TCAATCTCGGAAAGCACGAAAG 59.263 45.455 0.00 0.00 40.16 2.62
4309 4522 2.761559 TCAATCTCGGAAAGCACGAAA 58.238 42.857 0.00 0.00 40.16 3.46
4310 4523 2.448926 TCAATCTCGGAAAGCACGAA 57.551 45.000 0.00 0.00 40.16 3.85
4311 4524 2.066262 GTTCAATCTCGGAAAGCACGA 58.934 47.619 0.00 0.00 38.79 4.35
4312 4525 2.069273 AGTTCAATCTCGGAAAGCACG 58.931 47.619 0.00 0.00 0.00 5.34
4313 4526 3.120165 GGAAGTTCAATCTCGGAAAGCAC 60.120 47.826 5.01 0.00 0.00 4.40
4314 4527 3.074412 GGAAGTTCAATCTCGGAAAGCA 58.926 45.455 5.01 0.00 0.00 3.91
4315 4528 3.074412 TGGAAGTTCAATCTCGGAAAGC 58.926 45.455 5.01 0.00 0.00 3.51
4316 4529 4.319177 AGTGGAAGTTCAATCTCGGAAAG 58.681 43.478 5.01 0.00 0.00 2.62
4317 4530 4.351874 AGTGGAAGTTCAATCTCGGAAA 57.648 40.909 5.01 0.00 0.00 3.13
4318 4531 4.351874 AAGTGGAAGTTCAATCTCGGAA 57.648 40.909 5.01 0.00 0.00 4.30
4319 4532 4.351874 AAAGTGGAAGTTCAATCTCGGA 57.648 40.909 5.01 0.00 0.00 4.55
4320 4533 5.479306 TCTAAAGTGGAAGTTCAATCTCGG 58.521 41.667 5.01 0.00 0.00 4.63
4321 4534 8.879342 ATATCTAAAGTGGAAGTTCAATCTCG 57.121 34.615 5.01 0.00 0.00 4.04
4322 4535 9.823647 TGATATCTAAAGTGGAAGTTCAATCTC 57.176 33.333 5.01 0.00 0.00 2.75
4328 4541 9.508567 GCATTTTGATATCTAAAGTGGAAGTTC 57.491 33.333 15.75 0.00 0.00 3.01
4329 4542 8.184192 CGCATTTTGATATCTAAAGTGGAAGTT 58.816 33.333 15.75 0.00 0.00 2.66
4330 4543 7.201732 CCGCATTTTGATATCTAAAGTGGAAGT 60.202 37.037 22.06 5.43 30.12 3.01
4331 4544 7.134815 CCGCATTTTGATATCTAAAGTGGAAG 58.865 38.462 22.06 11.14 30.12 3.46
4332 4545 6.601613 ACCGCATTTTGATATCTAAAGTGGAA 59.398 34.615 27.27 8.15 31.46 3.53
4333 4546 6.119536 ACCGCATTTTGATATCTAAAGTGGA 58.880 36.000 27.27 8.65 31.46 4.02
4334 4547 6.260936 AGACCGCATTTTGATATCTAAAGTGG 59.739 38.462 23.34 23.34 32.25 4.00
4335 4548 7.251704 AGACCGCATTTTGATATCTAAAGTG 57.748 36.000 15.75 14.56 0.00 3.16
4336 4549 7.770897 AGAAGACCGCATTTTGATATCTAAAGT 59.229 33.333 15.75 9.32 0.00 2.66
4337 4550 8.147642 AGAAGACCGCATTTTGATATCTAAAG 57.852 34.615 15.75 10.06 0.00 1.85
4338 4551 8.506168 AAGAAGACCGCATTTTGATATCTAAA 57.494 30.769 13.50 13.50 0.00 1.85
4339 4552 8.506168 AAAGAAGACCGCATTTTGATATCTAA 57.494 30.769 3.98 0.00 0.00 2.10
4340 4553 8.506168 AAAAGAAGACCGCATTTTGATATCTA 57.494 30.769 3.98 0.00 0.00 1.98
4341 4554 7.396540 AAAAGAAGACCGCATTTTGATATCT 57.603 32.000 3.98 0.00 0.00 1.98
4365 4578 9.897744 CATTGAAGTTGCTCTAACATCTTAAAA 57.102 29.630 0.00 0.00 41.88 1.52
4366 4579 8.514594 CCATTGAAGTTGCTCTAACATCTTAAA 58.485 33.333 0.00 0.00 41.88 1.52
4367 4580 7.121168 CCCATTGAAGTTGCTCTAACATCTTAA 59.879 37.037 0.00 0.00 41.88 1.85
4368 4581 6.599244 CCCATTGAAGTTGCTCTAACATCTTA 59.401 38.462 0.00 0.00 41.88 2.10
4369 4582 5.416952 CCCATTGAAGTTGCTCTAACATCTT 59.583 40.000 0.00 0.00 41.88 2.40
4411 4624 1.440938 CCGACTCAAACAAACGGCCA 61.441 55.000 2.24 0.00 37.32 5.36
4418 4631 1.144276 TCCGTGCCGACTCAAACAA 59.856 52.632 0.00 0.00 0.00 2.83
4451 4664 1.205179 TCTATTTGGGTCAGCGCGTTA 59.795 47.619 8.43 0.00 0.00 3.18
4487 4700 2.622903 GAATGGATCGTCCGCGGACA 62.623 60.000 46.26 35.56 44.77 4.02
4500 4713 1.824230 CAAAAATGGGCCGAGAATGGA 59.176 47.619 0.00 0.00 0.00 3.41
4546 4780 2.363795 CGGGGACAGGAGTAGGCA 60.364 66.667 0.00 0.00 0.00 4.75
4757 5005 1.152830 GGAACCAGTTTGCTCCCCA 59.847 57.895 0.00 0.00 0.00 4.96
4869 5121 2.382746 CCGACGTCCGACGAGTGTA 61.383 63.158 27.03 0.00 46.05 2.90
4884 5136 1.816679 CAGCTAGCTTGCATGCCGA 60.817 57.895 22.05 8.55 34.99 5.54
4890 5142 0.321034 CACAGACCAGCTAGCTTGCA 60.321 55.000 22.05 0.00 34.99 4.08
4892 5144 0.392193 CCCACAGACCAGCTAGCTTG 60.392 60.000 16.46 15.09 0.00 4.01
4893 5145 1.986413 CCCACAGACCAGCTAGCTT 59.014 57.895 16.46 0.21 0.00 3.74


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

AutoCloner maintained by Alex Coulton.