Multiple sequence alignment - TraesCS1D01G276100

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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 TraesCS1D01G276100 chr1D 100.000 7226 0 0 1 7226 372149045 372156270 0.000000e+00 13345
1 TraesCS1D01G276100 chr1B 94.367 5645 188 55 1447 7033 497126306 497131878 0.000000e+00 8543
2 TraesCS1D01G276100 chr1B 94.920 1063 39 7 367 1416 497124901 497125961 0.000000e+00 1650
3 TraesCS1D01G276100 chr1B 95.135 370 18 0 1 370 497124497 497124866 1.040000e-162 584
4 TraesCS1D01G276100 chr1A 95.870 3390 99 23 1458 4824 471695805 471699176 0.000000e+00 5446
5 TraesCS1D01G276100 chr1A 90.805 2175 117 42 4837 6972 471699265 471701395 0.000000e+00 2832
6 TraesCS1D01G276100 chr1A 93.321 1078 34 13 367 1422 471694438 471695499 0.000000e+00 1557
7 TraesCS1D01G276100 chr1A 98.108 370 7 0 1 370 471694034 471694403 0.000000e+00 645


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 TraesCS1D01G276100 chr1D 372149045 372156270 7225 False 13345.000000 13345 100.000000 1 7226 1 chr1D.!!$F1 7225
1 TraesCS1D01G276100 chr1B 497124497 497131878 7381 False 3592.333333 8543 94.807333 1 7033 3 chr1B.!!$F1 7032
2 TraesCS1D01G276100 chr1A 471694034 471701395 7361 False 2620.000000 5446 94.526000 1 6972 4 chr1A.!!$F1 6971

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
492 531 0.735978 CGCGTGACAAGGCAGTGATA 60.736 55.000 0.00 0.0 37.01 2.15 F
1427 1493 0.783850 ATAGGCCTCCTCTCCTCTCC 59.216 60.000 9.68 0.0 34.61 3.71 F
2119 2500 1.024579 AAATGGTGTGATCCCGCGAC 61.025 55.000 8.23 0.0 0.00 5.19 F
3453 3848 1.153509 GCATGGCCCTGCATTTCAC 60.154 57.895 26.10 0.0 41.87 3.18 F
4063 4471 0.321919 AAGACTGCATGCGACACCAT 60.322 50.000 14.09 0.0 0.00 3.55 F
5286 5791 0.460987 CGAGGGTTCAGTCCATGAGC 60.461 60.000 0.00 0.0 39.68 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 2769 0.178964 CCAAGAGCAACTTTCCCCCA 60.179 55.000 0.00 0.0 36.61 4.96 R
2909 3297 1.002659 CCCAACGACCACCATGAACTA 59.997 52.381 0.00 0.0 0.00 2.24 R
3784 4184 0.033504 GAGCAGACCCTGAAACGACA 59.966 55.000 0.00 0.0 32.44 4.35 R
5147 5634 0.779997 AGACTTGGCCAGAAATGGGT 59.220 50.000 5.11 0.0 0.00 4.51 R
5846 6376 0.885596 TGAAACGGGTTAACTGGCGG 60.886 55.000 5.42 0.0 0.00 6.13 R
7062 7621 0.098200 CATGCTTGTCTGATGCCACG 59.902 55.000 0.00 0.0 0.00 4.94 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
42 43 9.383519 ACATATTGTGGAAGTGAACAGTATAAG 57.616 33.333 0.00 0.00 30.67 1.73
121 122 5.470098 TCAAGCATTCTGTTCCTAACTTGAC 59.530 40.000 0.00 0.00 37.83 3.18
370 371 9.930158 TTTATCCAAAGGGTTAAGCACTAATAT 57.070 29.630 7.03 0.00 31.64 1.28
424 463 1.480205 CAAACAGAGCAAAACGGCAG 58.520 50.000 0.00 0.00 35.83 4.85
427 466 4.030452 AGAGCAAAACGGCAGCGC 62.030 61.111 0.00 0.00 35.83 5.92
450 489 7.901377 GCGCTAAAACTAAATTTCTATTCGACA 59.099 33.333 0.00 0.00 0.00 4.35
459 498 6.944234 AATTTCTATTCGACAGGGAAATCC 57.056 37.500 12.17 0.00 36.15 3.01
492 531 0.735978 CGCGTGACAAGGCAGTGATA 60.736 55.000 0.00 0.00 37.01 2.15
605 645 2.896685 CTCAAACCCCCTATTTTGCACA 59.103 45.455 0.00 0.00 33.50 4.57
613 653 5.963865 ACCCCCTATTTTGCACATAGAAAAT 59.036 36.000 12.06 5.57 36.14 1.82
650 690 3.139397 TCCCTCCTCTTATCTCTCTGTCC 59.861 52.174 0.00 0.00 0.00 4.02
733 774 2.514824 GGGCGCCCAATGAGAGAC 60.515 66.667 40.73 8.62 35.81 3.36
835 876 1.834822 CCCCTCCCCTCTCATCGTC 60.835 68.421 0.00 0.00 0.00 4.20
1055 1096 9.900710 ATCTATAGTTTCGCTGTATACTTGAAG 57.099 33.333 4.17 0.00 0.00 3.02
1056 1097 8.900781 TCTATAGTTTCGCTGTATACTTGAAGT 58.099 33.333 2.37 2.37 0.00 3.01
1058 1099 6.026947 AGTTTCGCTGTATACTTGAAGTCT 57.973 37.500 0.00 0.00 0.00 3.24
1060 1101 6.366332 AGTTTCGCTGTATACTTGAAGTCTTG 59.634 38.462 0.00 0.00 0.00 3.02
1061 1102 5.638596 TCGCTGTATACTTGAAGTCTTGA 57.361 39.130 0.00 0.00 0.00 3.02
1062 1103 6.020971 TCGCTGTATACTTGAAGTCTTGAA 57.979 37.500 0.00 0.00 0.00 2.69
1066 1107 7.488150 CGCTGTATACTTGAAGTCTTGAATACA 59.512 37.037 13.96 13.96 0.00 2.29
1222 1270 1.705337 CTGTACCATTCGGCCAAGCG 61.705 60.000 2.24 0.00 34.57 4.68
1246 1294 2.158475 TGGATATGGAATCCAAGGCCAC 60.158 50.000 5.89 0.00 44.54 5.01
1255 1303 3.710722 CAAGGCCACGCTCCTCCT 61.711 66.667 5.01 0.00 32.45 3.69
1305 1368 6.096423 TCCGCTCTCTAGTCTATATCTCTCTC 59.904 46.154 0.00 0.00 0.00 3.20
1306 1369 6.096987 CCGCTCTCTAGTCTATATCTCTCTCT 59.903 46.154 0.00 0.00 0.00 3.10
1307 1370 6.975197 CGCTCTCTAGTCTATATCTCTCTCTG 59.025 46.154 0.00 0.00 0.00 3.35
1308 1371 6.758886 GCTCTCTAGTCTATATCTCTCTCTGC 59.241 46.154 0.00 0.00 0.00 4.26
1310 1373 9.190317 CTCTCTAGTCTATATCTCTCTCTGCTA 57.810 40.741 0.00 0.00 0.00 3.49
1422 1488 6.384305 TGCTATAAAATATAGGCCTCCTCTCC 59.616 42.308 9.68 0.00 34.61 3.71
1423 1489 6.613679 GCTATAAAATATAGGCCTCCTCTCCT 59.386 42.308 9.68 0.00 34.61 3.69
1424 1490 7.201965 GCTATAAAATATAGGCCTCCTCTCCTC 60.202 44.444 9.68 0.00 34.61 3.71
1425 1491 4.776059 AAATATAGGCCTCCTCTCCTCT 57.224 45.455 9.68 0.00 34.61 3.69
1426 1492 4.331159 AATATAGGCCTCCTCTCCTCTC 57.669 50.000 9.68 0.00 34.61 3.20
1427 1493 0.783850 ATAGGCCTCCTCTCCTCTCC 59.216 60.000 9.68 0.00 34.61 3.71
1428 1494 1.365105 TAGGCCTCCTCTCCTCTCCC 61.365 65.000 9.68 0.00 34.61 4.30
1429 1495 2.123033 GCCTCCTCTCCTCTCCCC 60.123 72.222 0.00 0.00 0.00 4.81
1430 1496 2.710826 GCCTCCTCTCCTCTCCCCT 61.711 68.421 0.00 0.00 0.00 4.79
1431 1497 1.541672 CCTCCTCTCCTCTCCCCTC 59.458 68.421 0.00 0.00 0.00 4.30
1432 1498 1.541672 CTCCTCTCCTCTCCCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1433 1499 2.015726 TCCTCTCCTCTCCCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
1434 1500 2.018086 CCTCTCCTCTCCCCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
1435 1501 1.541672 CTCTCCTCTCCCCTCCCTC 59.458 68.421 0.00 0.00 0.00 4.30
1436 1502 2.015726 TCTCCTCTCCCCTCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
1437 1503 3.036959 TCCTCTCCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
1438 1504 3.039526 CCTCTCCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1439 1505 2.612251 CTCTCCCCTCCCTCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
1440 1506 3.036959 TCTCCCCTCCCTCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
1441 1507 4.179599 CTCCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1443 1509 3.795924 CCCCTCCCTCCCTCCCAT 61.796 72.222 0.00 0.00 0.00 4.00
1444 1510 2.122189 CCCTCCCTCCCTCCCATC 60.122 72.222 0.00 0.00 0.00 3.51
1445 1511 2.705410 CCTCCCTCCCTCCCATCA 59.295 66.667 0.00 0.00 0.00 3.07
1599 1980 3.696548 CCTCTTACCCTCCATCTTTTTGC 59.303 47.826 0.00 0.00 0.00 3.68
1638 2019 5.028549 TCCACCTCTCTAATCTTTCATGC 57.971 43.478 0.00 0.00 0.00 4.06
1654 2035 4.970662 TCATGCTGCCTTTACATTCTTC 57.029 40.909 0.00 0.00 0.00 2.87
2119 2500 1.024579 AAATGGTGTGATCCCGCGAC 61.025 55.000 8.23 0.00 0.00 5.19
2313 2696 3.106827 TGGCCAATGAGTCATCTACAGA 58.893 45.455 0.61 0.00 0.00 3.41
2386 2769 1.670406 CTTTCTGACCGCAGCAGCT 60.670 57.895 0.00 0.00 42.01 4.24
2882 3269 1.604278 GCTTGAGCGTCCTTTCAGTTT 59.396 47.619 0.00 0.00 0.00 2.66
2909 3297 8.829373 AGATATGCCTTTGAATAGAAAAACCT 57.171 30.769 0.00 0.00 0.00 3.50
2930 3318 1.602323 TTCATGGTGGTCGTTGGGC 60.602 57.895 0.00 0.00 0.00 5.36
3223 3616 1.871039 GACGTGCAGGTAAAAAGCTCA 59.129 47.619 12.81 0.00 0.00 4.26
3453 3848 1.153509 GCATGGCCCTGCATTTCAC 60.154 57.895 26.10 0.00 41.87 3.18
3483 3881 4.509600 GCCATACTCTTACTTGCACATCTC 59.490 45.833 0.00 0.00 0.00 2.75
3536 3934 3.521995 CAGAGAAGCTGCGAGGAAA 57.478 52.632 0.00 0.00 37.90 3.13
3670 4070 2.280628 CAGTTAGAAACAGGCCGGATC 58.719 52.381 10.86 7.61 0.00 3.36
3784 4184 6.429692 TGCCATATGCTGTAACGCTTTAATAT 59.570 34.615 0.00 0.00 42.00 1.28
3785 4185 6.742718 GCCATATGCTGTAACGCTTTAATATG 59.257 38.462 0.00 5.82 36.87 1.78
3824 4225 3.917760 GGAGGATGTAGCGCGCCT 61.918 66.667 30.33 17.01 0.00 5.52
3860 4261 2.808202 CGGTAAGCATCTCATCCCTTGG 60.808 54.545 0.00 0.00 0.00 3.61
3871 4279 4.018506 TCTCATCCCTTGGAGCATTACAAA 60.019 41.667 0.00 0.00 34.05 2.83
4031 4439 2.670592 TCCTCGACGCGAACCTCA 60.671 61.111 15.93 0.00 34.74 3.86
4039 4447 2.456119 CGCGAACCTCAGCACCATC 61.456 63.158 0.00 0.00 0.00 3.51
4063 4471 0.321919 AAGACTGCATGCGACACCAT 60.322 50.000 14.09 0.00 0.00 3.55
4102 4510 3.827898 GCCGTGCTCGCTAGGTCT 61.828 66.667 1.89 0.00 35.54 3.85
4117 4525 1.075050 AGGTCTGACGTCTTCCACCTA 59.925 52.381 17.92 0.00 35.55 3.08
4198 4606 3.054361 GGCCTTCAGAAATCCTCAAGGTA 60.054 47.826 0.00 0.00 36.71 3.08
4202 4610 6.529220 CCTTCAGAAATCCTCAAGGTATAGG 58.471 44.000 0.00 0.00 36.34 2.57
4227 4635 2.094675 AGTTGCTACATGAATGCACCC 58.905 47.619 0.00 0.62 36.37 4.61
4266 4674 6.475504 TGTCTGACCTTTGTGTGATGATTAT 58.524 36.000 5.17 0.00 0.00 1.28
4338 4746 1.847328 TACCTCAGCTTGATCCGTCA 58.153 50.000 0.00 0.00 0.00 4.35
4437 4845 1.895707 GCAGCTGCACCAGTCACTT 60.896 57.895 33.36 0.00 41.59 3.16
4549 4957 3.152261 ACCTCGAGAGCTTTTATCGTG 57.848 47.619 15.71 8.33 41.16 4.35
4592 5001 2.936928 CAGTTCATGCACTCTGCCA 58.063 52.632 0.00 0.00 44.23 4.92
4627 5036 7.334921 CCATGTTCTTGCATGATTAACCATTTT 59.665 33.333 2.75 0.00 46.65 1.82
4658 5067 9.628500 ACTTACAAAGAGAAATACACTCCTTTT 57.372 29.630 0.00 0.00 35.27 2.27
4716 5125 6.566197 AAATAGTTGGAGCTGAAAACTGAG 57.434 37.500 13.09 0.00 35.77 3.35
4736 5145 8.792830 ACTGAGTATGGGAAGTATATTTACCA 57.207 34.615 13.91 13.91 44.97 3.25
4976 5461 3.507162 TGACTGATGTTTGTGGACCAT 57.493 42.857 0.00 0.00 0.00 3.55
5071 5558 7.125811 AGAGGCATAAACACCTATCACTTTCTA 59.874 37.037 0.00 0.00 0.00 2.10
5110 5597 9.862371 GTAGGAATATCAGAATATGACGTTCAT 57.138 33.333 0.00 0.00 41.91 2.57
5147 5634 8.476447 TGTATAAATTATTCCGTGTGTCCTACA 58.524 33.333 0.00 0.00 36.82 2.74
5162 5649 1.272425 CCTACACCCATTTCTGGCCAA 60.272 52.381 7.01 0.00 41.64 4.52
5181 5668 3.007940 CCAAGTCTTGTGTATCCACTCCA 59.992 47.826 11.61 0.00 42.34 3.86
5187 5674 1.692749 TGTATCCACTCCAGCCCCC 60.693 63.158 0.00 0.00 0.00 5.40
5188 5675 1.692749 GTATCCACTCCAGCCCCCA 60.693 63.158 0.00 0.00 0.00 4.96
5192 5679 2.285368 CACTCCAGCCCCCACCTA 60.285 66.667 0.00 0.00 0.00 3.08
5194 5681 3.470888 CTCCAGCCCCCACCTACG 61.471 72.222 0.00 0.00 0.00 3.51
5197 5684 2.768344 CAGCCCCCACCTACGGAT 60.768 66.667 0.00 0.00 0.00 4.18
5198 5685 2.768344 AGCCCCCACCTACGGATG 60.768 66.667 0.00 0.00 0.00 3.51
5199 5686 4.564110 GCCCCCACCTACGGATGC 62.564 72.222 0.00 0.00 0.00 3.91
5200 5687 3.087253 CCCCCACCTACGGATGCA 61.087 66.667 0.00 0.00 0.00 3.96
5201 5688 2.189521 CCCCACCTACGGATGCAC 59.810 66.667 0.00 0.00 0.00 4.57
5202 5689 2.665089 CCCCACCTACGGATGCACA 61.665 63.158 0.00 0.00 0.00 4.57
5203 5690 1.298340 CCCACCTACGGATGCACAA 59.702 57.895 0.00 0.00 0.00 3.33
5234 5738 2.430248 ACAGCTTGGATCATGCATGA 57.570 45.000 30.47 30.47 41.70 3.07
5254 5759 6.415867 GCATGACATATATGTTGTTGCACTTC 59.584 38.462 26.83 12.34 41.95 3.01
5286 5791 0.460987 CGAGGGTTCAGTCCATGAGC 60.461 60.000 0.00 0.00 39.68 4.26
5301 5813 4.160439 TCCATGAGCTGTAATCGAGAAAGT 59.840 41.667 0.00 0.00 0.00 2.66
5304 5816 5.330455 TGAGCTGTAATCGAGAAAGTGAT 57.670 39.130 0.00 0.00 0.00 3.06
5319 5831 7.506328 AGAAAGTGATACAACAACCTAAACC 57.494 36.000 0.00 0.00 0.00 3.27
5328 5840 2.851195 ACAACCTAAACCTGAGCACTG 58.149 47.619 0.00 0.00 0.00 3.66
5424 5936 4.393371 GCATTGTCTTTCTGTAGGTTCTCC 59.607 45.833 0.00 0.00 0.00 3.71
5546 6061 7.800092 AGATATTTGGAGCAGTTTAGACATCT 58.200 34.615 0.00 0.00 0.00 2.90
5646 6171 9.761504 CATAGCATAGATTGTAGATTATGGAGG 57.238 37.037 0.00 0.00 0.00 4.30
5648 6173 8.441311 AGCATAGATTGTAGATTATGGAGGAA 57.559 34.615 0.00 0.00 0.00 3.36
5655 6180 9.354673 GATTGTAGATTATGGAGGAAAAATGGA 57.645 33.333 0.00 0.00 0.00 3.41
5664 6189 4.898265 TGGAGGAAAAATGGAATCACACAA 59.102 37.500 0.00 0.00 0.00 3.33
5665 6190 5.365025 TGGAGGAAAAATGGAATCACACAAA 59.635 36.000 0.00 0.00 0.00 2.83
5669 6194 8.017418 AGGAAAAATGGAATCACACAAACTAA 57.983 30.769 0.00 0.00 0.00 2.24
5670 6195 8.143835 AGGAAAAATGGAATCACACAAACTAAG 58.856 33.333 0.00 0.00 0.00 2.18
5671 6196 8.141268 GGAAAAATGGAATCACACAAACTAAGA 58.859 33.333 0.00 0.00 0.00 2.10
5676 6203 7.667043 TGGAATCACACAAACTAAGATGTAC 57.333 36.000 0.00 0.00 0.00 2.90
5711 6238 0.744771 GGAAGCTTCCAACTAGCCCG 60.745 60.000 35.71 0.00 46.76 6.13
5718 6245 1.153823 CCAACTAGCCCGTGTCTCG 60.154 63.158 0.00 0.00 39.52 4.04
5749 6279 4.022416 ACATTGGCTTTGCATCTTTCGTTA 60.022 37.500 0.00 0.00 0.00 3.18
5755 6285 4.972440 GCTTTGCATCTTTCGTTATCATCC 59.028 41.667 0.00 0.00 0.00 3.51
5799 6329 9.791820 TCATTAATTGCATTCTGAAGTGTATTG 57.208 29.630 0.00 0.00 0.00 1.90
5843 6373 6.506538 ACATTAGATATTTCCTGTCAGCCT 57.493 37.500 0.00 0.00 0.00 4.58
5844 6374 7.618019 ACATTAGATATTTCCTGTCAGCCTA 57.382 36.000 0.00 0.00 0.00 3.93
5846 6376 4.615588 AGATATTTCCTGTCAGCCTAGC 57.384 45.455 0.00 0.00 0.00 3.42
5876 6406 3.782656 ACCCGTTTCACTGACCTAATT 57.217 42.857 0.00 0.00 0.00 1.40
6030 6560 2.509916 CTCAGCTCCATCTGGGCC 59.490 66.667 0.00 0.00 36.21 5.80
6082 6612 5.586339 ACGATCTCACTCATCAACAGTATG 58.414 41.667 0.00 0.00 46.00 2.39
6118 6648 0.820891 TCTCACCCTCGGCGTATACC 60.821 60.000 6.85 0.00 0.00 2.73
6252 6785 1.526464 GCACAAATTCCGCCAACAAAG 59.474 47.619 0.00 0.00 0.00 2.77
6254 6787 2.794350 CACAAATTCCGCCAACAAAGAC 59.206 45.455 0.00 0.00 0.00 3.01
6283 6816 0.524816 GCTGCAGCATTGTTCCATCG 60.525 55.000 33.36 0.00 41.59 3.84
6285 6818 1.200716 CTGCAGCATTGTTCCATCGTT 59.799 47.619 0.00 0.00 0.00 3.85
6287 6820 1.621107 CAGCATTGTTCCATCGTTGC 58.379 50.000 0.00 0.00 0.00 4.17
6477 7010 1.745489 GGTGCAAAGCGTAGAGGGG 60.745 63.158 0.00 0.00 0.00 4.79
6478 7011 1.745489 GTGCAAAGCGTAGAGGGGG 60.745 63.158 0.00 0.00 0.00 5.40
6659 7194 4.729881 AGCCATTACCTAATTTGTCCCCTA 59.270 41.667 0.00 0.00 0.00 3.53
6730 7269 0.380378 GCAACTTGCGTGAAGGACAA 59.620 50.000 0.00 0.00 35.78 3.18
6800 7345 3.254657 CCTTTTCGGTGCTGGAAAACATA 59.745 43.478 6.18 0.00 38.18 2.29
6917 7470 1.269778 TGATGGATGTAGCTAGCGTGC 60.270 52.381 9.55 4.19 0.00 5.34
6976 7535 1.966845 ACAAAGCTTAGGGGCCTAGA 58.033 50.000 0.84 0.00 0.00 2.43
7013 7572 0.250295 CAACAAAGCTCACTCCCGGA 60.250 55.000 0.73 0.00 0.00 5.14
7027 7586 0.546122 CCCGGAATGGTCTTGATCCA 59.454 55.000 0.73 0.00 39.41 3.41
7028 7587 1.475751 CCCGGAATGGTCTTGATCCAG 60.476 57.143 0.73 0.00 38.42 3.86
7032 7591 0.259938 AATGGTCTTGATCCAGGGGC 59.740 55.000 0.00 0.00 38.42 5.80
7033 7592 0.625683 ATGGTCTTGATCCAGGGGCT 60.626 55.000 0.00 0.00 38.42 5.19
7034 7593 0.044092 TGGTCTTGATCCAGGGGCTA 59.956 55.000 0.00 0.00 0.00 3.93
7035 7594 0.470341 GGTCTTGATCCAGGGGCTAC 59.530 60.000 0.00 0.00 0.00 3.58
7036 7595 0.105039 GTCTTGATCCAGGGGCTACG 59.895 60.000 0.00 0.00 0.00 3.51
7037 7596 1.227674 CTTGATCCAGGGGCTACGC 60.228 63.158 0.00 0.00 0.00 4.42
7038 7597 1.689233 TTGATCCAGGGGCTACGCT 60.689 57.895 0.00 0.00 41.05 5.07
7039 7598 1.686325 TTGATCCAGGGGCTACGCTC 61.686 60.000 0.00 0.00 37.87 5.03
7040 7599 3.214250 GATCCAGGGGCTACGCTCG 62.214 68.421 0.00 0.00 37.87 5.03
7041 7600 3.733507 ATCCAGGGGCTACGCTCGA 62.734 63.158 0.00 0.00 37.87 4.04
7042 7601 3.227276 CCAGGGGCTACGCTCGAT 61.227 66.667 0.00 0.00 37.87 3.59
7043 7602 2.028190 CAGGGGCTACGCTCGATG 59.972 66.667 0.00 0.00 37.87 3.84
7044 7603 3.917760 AGGGGCTACGCTCGATGC 61.918 66.667 0.00 0.00 34.34 3.91
7053 7612 3.918220 GCTCGATGCGAACCTGCG 61.918 66.667 0.00 0.00 34.74 5.18
7054 7613 3.257561 CTCGATGCGAACCTGCGG 61.258 66.667 0.00 0.00 34.74 5.69
7055 7614 4.812476 TCGATGCGAACCTGCGGG 62.812 66.667 11.02 11.02 37.81 6.13
7057 7616 4.467084 GATGCGAACCTGCGGGGA 62.467 66.667 18.00 0.00 38.76 4.81
7058 7617 3.969250 GATGCGAACCTGCGGGGAA 62.969 63.158 18.00 0.00 38.76 3.97
7059 7618 3.561120 ATGCGAACCTGCGGGGAAA 62.561 57.895 18.00 0.00 38.76 3.13
7060 7619 3.431725 GCGAACCTGCGGGGAAAG 61.432 66.667 18.00 5.37 38.76 2.62
7061 7620 2.746277 CGAACCTGCGGGGAAAGG 60.746 66.667 18.00 0.00 39.65 3.11
7062 7621 3.062466 GAACCTGCGGGGAAAGGC 61.062 66.667 18.00 0.00 37.03 4.35
7070 7629 3.140814 GGGGAAAGGCGTGGCATC 61.141 66.667 0.00 0.00 0.00 3.91
7071 7630 2.361104 GGGAAAGGCGTGGCATCA 60.361 61.111 0.00 0.00 0.00 3.07
7072 7631 2.409870 GGGAAAGGCGTGGCATCAG 61.410 63.158 0.00 0.00 0.00 2.90
7073 7632 1.377202 GGAAAGGCGTGGCATCAGA 60.377 57.895 0.00 0.00 0.00 3.27
7074 7633 1.648467 GGAAAGGCGTGGCATCAGAC 61.648 60.000 0.00 0.00 0.00 3.51
7075 7634 0.955428 GAAAGGCGTGGCATCAGACA 60.955 55.000 0.00 0.00 0.00 3.41
7076 7635 0.537143 AAAGGCGTGGCATCAGACAA 60.537 50.000 0.00 0.00 31.85 3.18
7077 7636 0.957395 AAGGCGTGGCATCAGACAAG 60.957 55.000 0.00 0.00 31.85 3.16
7079 7638 3.970721 CGTGGCATCAGACAAGCA 58.029 55.556 0.00 0.00 31.85 3.91
7080 7639 2.474561 CGTGGCATCAGACAAGCAT 58.525 52.632 0.00 0.00 31.85 3.79
7081 7640 0.098200 CGTGGCATCAGACAAGCATG 59.902 55.000 0.00 0.00 31.85 4.06
7082 7641 0.179145 GTGGCATCAGACAAGCATGC 60.179 55.000 10.51 10.51 41.93 4.06
7084 7643 1.063649 GCATCAGACAAGCATGCCG 59.936 57.895 15.66 8.79 37.54 5.69
7085 7644 1.371337 GCATCAGACAAGCATGCCGA 61.371 55.000 15.66 1.97 37.54 5.54
7086 7645 1.089112 CATCAGACAAGCATGCCGAA 58.911 50.000 15.66 0.00 0.00 4.30
7087 7646 1.469703 CATCAGACAAGCATGCCGAAA 59.530 47.619 15.66 0.00 0.00 3.46
7088 7647 0.874390 TCAGACAAGCATGCCGAAAC 59.126 50.000 15.66 2.68 0.00 2.78
7089 7648 0.877071 CAGACAAGCATGCCGAAACT 59.123 50.000 15.66 5.14 0.00 2.66
7090 7649 1.135859 CAGACAAGCATGCCGAAACTC 60.136 52.381 15.66 0.68 0.00 3.01
7091 7650 0.179215 GACAAGCATGCCGAAACTCG 60.179 55.000 15.66 0.00 40.07 4.18
7092 7651 1.512734 CAAGCATGCCGAAACTCGC 60.513 57.895 15.66 0.00 38.82 5.03
7093 7652 3.027170 AAGCATGCCGAAACTCGCG 62.027 57.895 15.66 0.00 38.82 5.87
7094 7653 3.788766 GCATGCCGAAACTCGCGT 61.789 61.111 6.36 0.00 38.82 6.01
7095 7654 2.395690 CATGCCGAAACTCGCGTC 59.604 61.111 5.77 0.00 38.82 5.19
7096 7655 2.048597 ATGCCGAAACTCGCGTCA 60.049 55.556 5.77 0.00 38.82 4.35
7097 7656 1.666553 ATGCCGAAACTCGCGTCAA 60.667 52.632 5.77 0.00 38.82 3.18
7098 7657 1.626654 ATGCCGAAACTCGCGTCAAG 61.627 55.000 5.77 0.00 38.82 3.02
7099 7658 2.308039 GCCGAAACTCGCGTCAAGT 61.308 57.895 5.77 0.00 38.82 3.16
7100 7659 1.828331 GCCGAAACTCGCGTCAAGTT 61.828 55.000 5.77 5.85 38.82 2.66
7101 7660 0.161024 CCGAAACTCGCGTCAAGTTC 59.839 55.000 11.53 6.46 38.82 3.01
7102 7661 0.850217 CGAAACTCGCGTCAAGTTCA 59.150 50.000 11.53 0.00 35.96 3.18
7103 7662 1.136884 CGAAACTCGCGTCAAGTTCAG 60.137 52.381 11.53 5.97 35.96 3.02
7104 7663 2.124903 GAAACTCGCGTCAAGTTCAGA 58.875 47.619 11.53 0.00 35.96 3.27
7105 7664 2.440539 AACTCGCGTCAAGTTCAGAT 57.559 45.000 5.77 0.00 31.36 2.90
7106 7665 1.983972 ACTCGCGTCAAGTTCAGATC 58.016 50.000 5.77 0.00 0.00 2.75
7107 7666 1.272781 CTCGCGTCAAGTTCAGATCC 58.727 55.000 5.77 0.00 0.00 3.36
7108 7667 0.601057 TCGCGTCAAGTTCAGATCCA 59.399 50.000 5.77 0.00 0.00 3.41
7109 7668 0.994995 CGCGTCAAGTTCAGATCCAG 59.005 55.000 0.00 0.00 0.00 3.86
7110 7669 1.402852 CGCGTCAAGTTCAGATCCAGA 60.403 52.381 0.00 0.00 0.00 3.86
7111 7670 2.266554 GCGTCAAGTTCAGATCCAGAG 58.733 52.381 0.00 0.00 0.00 3.35
7112 7671 2.094494 GCGTCAAGTTCAGATCCAGAGA 60.094 50.000 0.00 0.00 0.00 3.10
7113 7672 3.615110 GCGTCAAGTTCAGATCCAGAGAA 60.615 47.826 0.00 0.00 0.00 2.87
7114 7673 3.923461 CGTCAAGTTCAGATCCAGAGAAC 59.077 47.826 8.90 8.90 41.37 3.01
7115 7674 4.559502 CGTCAAGTTCAGATCCAGAGAACA 60.560 45.833 15.72 0.00 43.00 3.18
7116 7675 4.928615 GTCAAGTTCAGATCCAGAGAACAG 59.071 45.833 15.72 10.17 43.00 3.16
7117 7676 4.835056 TCAAGTTCAGATCCAGAGAACAGA 59.165 41.667 15.72 11.63 43.00 3.41
7118 7677 4.799564 AGTTCAGATCCAGAGAACAGAC 57.200 45.455 15.72 0.12 43.00 3.51
7119 7678 3.513515 AGTTCAGATCCAGAGAACAGACC 59.486 47.826 15.72 0.00 43.00 3.85
7120 7679 2.461695 TCAGATCCAGAGAACAGACCC 58.538 52.381 0.00 0.00 0.00 4.46
7121 7680 1.484240 CAGATCCAGAGAACAGACCCC 59.516 57.143 0.00 0.00 0.00 4.95
7122 7681 0.461961 GATCCAGAGAACAGACCCCG 59.538 60.000 0.00 0.00 0.00 5.73
7123 7682 1.617947 ATCCAGAGAACAGACCCCGC 61.618 60.000 0.00 0.00 0.00 6.13
7124 7683 2.286523 CCAGAGAACAGACCCCGCT 61.287 63.158 0.00 0.00 0.00 5.52
7125 7684 0.970937 CCAGAGAACAGACCCCGCTA 60.971 60.000 0.00 0.00 0.00 4.26
7126 7685 0.895530 CAGAGAACAGACCCCGCTAA 59.104 55.000 0.00 0.00 0.00 3.09
7127 7686 1.275291 CAGAGAACAGACCCCGCTAAA 59.725 52.381 0.00 0.00 0.00 1.85
7128 7687 1.975680 AGAGAACAGACCCCGCTAAAA 59.024 47.619 0.00 0.00 0.00 1.52
7129 7688 2.370849 AGAGAACAGACCCCGCTAAAAA 59.629 45.455 0.00 0.00 0.00 1.94
7130 7689 2.742589 GAGAACAGACCCCGCTAAAAAG 59.257 50.000 0.00 0.00 0.00 2.27
7131 7690 2.370849 AGAACAGACCCCGCTAAAAAGA 59.629 45.455 0.00 0.00 0.00 2.52
7132 7691 2.180432 ACAGACCCCGCTAAAAAGAC 57.820 50.000 0.00 0.00 0.00 3.01
7133 7692 1.418637 ACAGACCCCGCTAAAAAGACA 59.581 47.619 0.00 0.00 0.00 3.41
7134 7693 2.076863 CAGACCCCGCTAAAAAGACAG 58.923 52.381 0.00 0.00 0.00 3.51
7135 7694 1.975680 AGACCCCGCTAAAAAGACAGA 59.024 47.619 0.00 0.00 0.00 3.41
7136 7695 2.028020 AGACCCCGCTAAAAAGACAGAG 60.028 50.000 0.00 0.00 0.00 3.35
7137 7696 1.975680 ACCCCGCTAAAAAGACAGAGA 59.024 47.619 0.00 0.00 0.00 3.10
7138 7697 2.370849 ACCCCGCTAAAAAGACAGAGAA 59.629 45.455 0.00 0.00 0.00 2.87
7139 7698 3.181448 ACCCCGCTAAAAAGACAGAGAAA 60.181 43.478 0.00 0.00 0.00 2.52
7140 7699 3.818773 CCCCGCTAAAAAGACAGAGAAAA 59.181 43.478 0.00 0.00 0.00 2.29
7141 7700 4.083271 CCCCGCTAAAAAGACAGAGAAAAG 60.083 45.833 0.00 0.00 0.00 2.27
7142 7701 4.467735 CCGCTAAAAAGACAGAGAAAAGC 58.532 43.478 0.00 0.00 0.00 3.51
7143 7702 4.467735 CGCTAAAAAGACAGAGAAAAGCC 58.532 43.478 0.00 0.00 0.00 4.35
7144 7703 4.214332 CGCTAAAAAGACAGAGAAAAGCCT 59.786 41.667 0.00 0.00 0.00 4.58
7145 7704 5.278022 CGCTAAAAAGACAGAGAAAAGCCTT 60.278 40.000 0.00 0.00 0.00 4.35
7146 7705 6.507900 GCTAAAAAGACAGAGAAAAGCCTTT 58.492 36.000 0.00 0.00 0.00 3.11
7147 7706 6.980978 GCTAAAAAGACAGAGAAAAGCCTTTT 59.019 34.615 1.18 1.18 35.96 2.27
7148 7707 7.492669 GCTAAAAAGACAGAGAAAAGCCTTTTT 59.507 33.333 3.56 0.00 42.64 1.94
7160 7719 6.966534 AAAAGCCTTTTTCAGATCAGAGAA 57.033 33.333 0.00 0.00 30.85 2.87
7161 7720 6.966534 AAAGCCTTTTTCAGATCAGAGAAA 57.033 33.333 4.17 4.17 32.34 2.52
7162 7721 6.966534 AAGCCTTTTTCAGATCAGAGAAAA 57.033 33.333 13.40 13.40 40.74 2.29
7163 7722 6.966534 AGCCTTTTTCAGATCAGAGAAAAA 57.033 33.333 21.59 21.59 45.91 1.94
7207 7766 3.942130 AAACAGATAAAAGTGGCAGCC 57.058 42.857 3.66 3.66 0.00 4.85
7208 7767 1.453155 ACAGATAAAAGTGGCAGCCG 58.547 50.000 7.03 0.00 0.00 5.52
7209 7768 0.734889 CAGATAAAAGTGGCAGCCGG 59.265 55.000 7.03 0.00 0.00 6.13
7210 7769 0.328258 AGATAAAAGTGGCAGCCGGT 59.672 50.000 7.03 0.00 0.00 5.28
7211 7770 1.173913 GATAAAAGTGGCAGCCGGTT 58.826 50.000 7.03 0.00 0.00 4.44
7212 7771 1.132453 GATAAAAGTGGCAGCCGGTTC 59.868 52.381 7.03 0.00 0.00 3.62
7213 7772 0.109723 TAAAAGTGGCAGCCGGTTCT 59.890 50.000 7.03 0.00 0.00 3.01
7214 7773 0.109723 AAAAGTGGCAGCCGGTTCTA 59.890 50.000 7.03 0.00 0.00 2.10
7215 7774 0.321653 AAAGTGGCAGCCGGTTCTAG 60.322 55.000 7.03 0.00 0.00 2.43
7216 7775 2.804828 AAGTGGCAGCCGGTTCTAGC 62.805 60.000 7.03 0.00 0.00 3.42
7217 7776 3.003173 TGGCAGCCGGTTCTAGCT 61.003 61.111 7.03 0.00 40.89 3.32
7218 7777 1.684391 TGGCAGCCGGTTCTAGCTA 60.684 57.895 7.03 0.00 37.18 3.32
7219 7778 1.068250 GGCAGCCGGTTCTAGCTAG 59.932 63.158 15.01 15.01 37.18 3.42
7220 7779 1.068250 GCAGCCGGTTCTAGCTAGG 59.932 63.158 20.58 6.26 37.18 3.02
7222 7781 3.539842 GCCGGTTCTAGCTAGGCT 58.460 61.111 20.58 0.00 44.06 4.58
7223 7782 1.823976 GCCGGTTCTAGCTAGGCTT 59.176 57.895 20.58 0.00 44.06 4.35
7224 7783 0.249531 GCCGGTTCTAGCTAGGCTTC 60.250 60.000 20.58 8.49 44.06 3.86
7225 7784 1.404843 CCGGTTCTAGCTAGGCTTCT 58.595 55.000 20.58 0.00 40.44 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.119137 GGCACAATCCTTGACCATTAACC 60.119 47.826 0.00 0.00 32.92 2.85
121 122 7.378995 CAGAAGAGAGAAATTTGCAAAGAACAG 59.621 37.037 18.19 0.00 0.00 3.16
205 206 0.918983 AGGCCGGGAAGATCATTTCA 59.081 50.000 2.18 0.00 0.00 2.69
424 463 7.901377 TGTCGAATAGAAATTTAGTTTTAGCGC 59.099 33.333 0.00 0.00 0.00 5.92
459 498 3.120477 TGTCACGCGCCAAATACTAAAAG 60.120 43.478 5.73 0.00 0.00 2.27
492 531 0.608640 CTTCCGGCTAACAGGTCAGT 59.391 55.000 0.00 0.00 0.00 3.41
506 545 7.095439 GCTCATTTGAGATTATCCTTACTTCCG 60.095 40.741 11.70 0.00 44.74 4.30
569 609 4.278419 GGGTTTGAGCAGTTCTACAAATGT 59.722 41.667 0.00 0.00 35.31 2.71
605 645 7.824779 GGGAGTACACAAGACTTCATTTTCTAT 59.175 37.037 0.00 0.00 0.00 1.98
613 653 2.897969 GGAGGGAGTACACAAGACTTCA 59.102 50.000 0.00 0.00 0.00 3.02
650 690 4.022603 TCATTGAGGAGAGAGAACAGAGG 58.977 47.826 0.00 0.00 0.00 3.69
733 774 1.990563 CGTAACTGTAACAGCCCTTCG 59.009 52.381 0.00 0.00 34.37 3.79
835 876 4.889409 AGATTTCACAGGCTAGAGAGAGAG 59.111 45.833 0.00 0.00 0.00 3.20
1055 1096 7.911362 GTAGGAAGTACGATGTATTCAAGAC 57.089 40.000 0.00 0.00 0.00 3.01
1246 1294 3.393970 TTGGCAGGAGGAGGAGCG 61.394 66.667 0.00 0.00 0.00 5.03
1255 1303 1.347707 CAGTACAGGAAGTTGGCAGGA 59.652 52.381 0.00 0.00 0.00 3.86
1305 1368 4.035792 ACGTACTAGCAGTTGAGATAGCAG 59.964 45.833 0.00 0.00 0.00 4.24
1306 1369 3.945921 ACGTACTAGCAGTTGAGATAGCA 59.054 43.478 0.00 0.00 0.00 3.49
1307 1370 4.283678 CACGTACTAGCAGTTGAGATAGC 58.716 47.826 0.00 0.00 0.00 2.97
1308 1371 4.283678 GCACGTACTAGCAGTTGAGATAG 58.716 47.826 0.00 0.00 0.00 2.08
1310 1373 2.478031 CGCACGTACTAGCAGTTGAGAT 60.478 50.000 7.11 0.00 0.00 2.75
1422 1488 2.612251 GAGGGAGGGAGGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
1423 1489 3.036959 GGAGGGAGGGAGGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
1424 1490 4.179599 GGGAGGGAGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1426 1492 3.795924 ATGGGAGGGAGGGAGGGG 61.796 72.222 0.00 0.00 0.00 4.79
1427 1493 2.122189 GATGGGAGGGAGGGAGGG 60.122 72.222 0.00 0.00 0.00 4.30
1428 1494 1.768077 GTGATGGGAGGGAGGGAGG 60.768 68.421 0.00 0.00 0.00 4.30
1429 1495 1.768077 GGTGATGGGAGGGAGGGAG 60.768 68.421 0.00 0.00 0.00 4.30
1430 1496 2.257541 GAGGTGATGGGAGGGAGGGA 62.258 65.000 0.00 0.00 0.00 4.20
1431 1497 1.768077 GAGGTGATGGGAGGGAGGG 60.768 68.421 0.00 0.00 0.00 4.30
1432 1498 0.327000 AAGAGGTGATGGGAGGGAGG 60.327 60.000 0.00 0.00 0.00 4.30
1433 1499 1.589414 AAAGAGGTGATGGGAGGGAG 58.411 55.000 0.00 0.00 0.00 4.30
1434 1500 2.059756 AAAAGAGGTGATGGGAGGGA 57.940 50.000 0.00 0.00 0.00 4.20
1435 1501 2.907458 AAAAAGAGGTGATGGGAGGG 57.093 50.000 0.00 0.00 0.00 4.30
1436 1502 4.017126 GGTTAAAAAGAGGTGATGGGAGG 58.983 47.826 0.00 0.00 0.00 4.30
1437 1503 4.459337 GTGGTTAAAAAGAGGTGATGGGAG 59.541 45.833 0.00 0.00 0.00 4.30
1438 1504 4.403734 GTGGTTAAAAAGAGGTGATGGGA 58.596 43.478 0.00 0.00 0.00 4.37
1439 1505 3.509967 GGTGGTTAAAAAGAGGTGATGGG 59.490 47.826 0.00 0.00 0.00 4.00
1440 1506 4.407365 AGGTGGTTAAAAAGAGGTGATGG 58.593 43.478 0.00 0.00 0.00 3.51
1441 1507 6.405278 AAAGGTGGTTAAAAAGAGGTGATG 57.595 37.500 0.00 0.00 0.00 3.07
1442 1508 9.816787 TTATAAAGGTGGTTAAAAAGAGGTGAT 57.183 29.630 0.00 0.00 0.00 3.06
1443 1509 9.070179 GTTATAAAGGTGGTTAAAAAGAGGTGA 57.930 33.333 0.00 0.00 0.00 4.02
1444 1510 8.301720 GGTTATAAAGGTGGTTAAAAAGAGGTG 58.698 37.037 0.00 0.00 0.00 4.00
1445 1511 8.005976 TGGTTATAAAGGTGGTTAAAAAGAGGT 58.994 33.333 0.00 0.00 0.00 3.85
1599 1980 5.588845 AGGTGGATAGATAAGGATGAGAGG 58.411 45.833 0.00 0.00 0.00 3.69
1638 2019 6.218746 AGCTTTTTGAAGAATGTAAAGGCAG 58.781 36.000 0.00 0.00 35.72 4.85
1654 2035 8.694394 GCAGATAAAAACTAGTGAAGCTTTTTG 58.306 33.333 0.00 2.89 35.58 2.44
2175 2558 2.107141 GTCAATCGCCCTCTCCCG 59.893 66.667 0.00 0.00 0.00 5.14
2246 2629 0.391793 GCCTAGCCGCAAGATATCCC 60.392 60.000 0.00 0.00 43.02 3.85
2386 2769 0.178964 CCAAGAGCAACTTTCCCCCA 60.179 55.000 0.00 0.00 36.61 4.96
2909 3297 1.002659 CCCAACGACCACCATGAACTA 59.997 52.381 0.00 0.00 0.00 2.24
2930 3318 3.451894 GCCATTTCCCAGTGCCCG 61.452 66.667 0.00 0.00 0.00 6.13
3483 3881 7.778470 ATCGCCTTTCAGTCTAAGAAATAAG 57.222 36.000 0.00 0.00 34.75 1.73
3670 4070 1.152989 GCTCGATCTGCTGAAGCCTG 61.153 60.000 0.00 0.00 41.18 4.85
3784 4184 0.033504 GAGCAGACCCTGAAACGACA 59.966 55.000 0.00 0.00 32.44 4.35
3785 4185 0.033504 TGAGCAGACCCTGAAACGAC 59.966 55.000 0.00 0.00 32.44 4.34
3824 4225 2.820728 TACCGGAACTCATCTCTCCA 57.179 50.000 9.46 0.00 0.00 3.86
3860 4261 4.844267 ACGTTGTGAAGTTTGTAATGCTC 58.156 39.130 0.00 0.00 0.00 4.26
4031 4439 0.109086 CAGTCTTCGACGATGGTGCT 60.109 55.000 10.47 4.75 37.67 4.40
4039 4447 1.801512 TCGCATGCAGTCTTCGACG 60.802 57.895 19.57 0.00 37.67 5.12
4057 4465 0.320771 GGAACAGCTCGTCATGGTGT 60.321 55.000 0.00 0.00 46.30 4.16
4096 4504 1.075050 AGGTGGAAGACGTCAGACCTA 59.925 52.381 19.50 6.13 38.36 3.08
4102 4510 2.232941 GGTCATTAGGTGGAAGACGTCA 59.767 50.000 19.50 0.00 0.00 4.35
4117 4525 2.755469 GCCCACATGCCGGTCATT 60.755 61.111 1.90 0.00 31.79 2.57
4198 4606 2.434336 TCATGTAGCAACTTCGCCCTAT 59.566 45.455 0.00 0.00 0.00 2.57
4202 4610 2.792542 GCATTCATGTAGCAACTTCGCC 60.793 50.000 0.00 0.00 0.00 5.54
4227 4635 5.934625 AGGTCAGACAAATTACAAGCACTAG 59.065 40.000 2.17 0.00 0.00 2.57
4236 4644 6.371809 TCACACAAAGGTCAGACAAATTAC 57.628 37.500 2.17 0.00 0.00 1.89
4266 4674 1.066215 ACTCAGCATGTAACATCGCCA 60.066 47.619 0.00 0.00 37.40 5.69
4549 4957 6.618805 GCAACGAAGAGAAAAATACTGACCTC 60.619 42.308 0.00 0.00 0.00 3.85
4592 5001 5.188163 TCATGCAAGAACATGGGATTTTGAT 59.812 36.000 0.00 0.00 46.08 2.57
4627 5036 9.477484 GAGTGTATTTCTCTTTGTAAGTTCAGA 57.523 33.333 0.00 0.00 0.00 3.27
4833 5242 9.489084 GCTACACAACCACATCTTATATATGAA 57.511 33.333 2.71 0.00 0.00 2.57
4834 5243 8.646900 TGCTACACAACCACATCTTATATATGA 58.353 33.333 0.00 1.15 0.00 2.15
4835 5244 8.831715 TGCTACACAACCACATCTTATATATG 57.168 34.615 0.00 0.00 0.00 1.78
4884 5369 6.527423 TGATGTTTATCTGCATGATCTAGCA 58.473 36.000 11.26 11.26 39.25 3.49
4976 5461 6.267471 AGGACTCAACCAATTGCTCAAAATAA 59.733 34.615 0.00 0.00 35.63 1.40
5035 5522 6.948309 AGGTGTTTATGCCTCTTAAGACATTT 59.052 34.615 12.36 0.00 0.00 2.32
5049 5536 7.843490 TGTAGAAAGTGATAGGTGTTTATGC 57.157 36.000 0.00 0.00 0.00 3.14
5071 5558 7.072454 TCTGATATTCCTACTTGGGCTTTATGT 59.928 37.037 0.00 0.00 36.20 2.29
5110 5597 8.836413 CGGAATAATTTATACAAGGCAAGAAGA 58.164 33.333 0.00 0.00 0.00 2.87
5147 5634 0.779997 AGACTTGGCCAGAAATGGGT 59.220 50.000 5.11 0.00 0.00 4.51
5190 5677 6.398095 TCCAGATATATTTGTGCATCCGTAG 58.602 40.000 2.84 0.00 0.00 3.51
5191 5678 6.353404 TCCAGATATATTTGTGCATCCGTA 57.647 37.500 2.84 0.00 0.00 4.02
5192 5679 5.227569 TCCAGATATATTTGTGCATCCGT 57.772 39.130 2.84 0.00 0.00 4.69
5194 5681 6.569226 GCTGTTCCAGATATATTTGTGCATCC 60.569 42.308 2.84 0.00 32.44 3.51
5195 5682 6.206243 AGCTGTTCCAGATATATTTGTGCATC 59.794 38.462 2.84 0.00 32.44 3.91
5196 5683 6.066690 AGCTGTTCCAGATATATTTGTGCAT 58.933 36.000 2.84 0.00 32.44 3.96
5197 5684 5.439721 AGCTGTTCCAGATATATTTGTGCA 58.560 37.500 2.84 0.00 32.44 4.57
5198 5685 6.204359 CAAGCTGTTCCAGATATATTTGTGC 58.796 40.000 2.84 0.37 32.44 4.57
5199 5686 6.543465 TCCAAGCTGTTCCAGATATATTTGTG 59.457 38.462 2.84 0.00 32.44 3.33
5200 5687 6.662755 TCCAAGCTGTTCCAGATATATTTGT 58.337 36.000 2.84 0.00 32.44 2.83
5201 5688 7.446319 TGATCCAAGCTGTTCCAGATATATTTG 59.554 37.037 0.00 0.00 32.44 2.32
5202 5689 7.520798 TGATCCAAGCTGTTCCAGATATATTT 58.479 34.615 0.00 0.00 32.44 1.40
5203 5690 7.083062 TGATCCAAGCTGTTCCAGATATATT 57.917 36.000 0.00 0.00 32.44 1.28
5234 5738 7.452880 ACAAGAAGTGCAACAACATATATGT 57.547 32.000 12.75 12.75 44.20 2.29
5254 5759 4.865776 TGAACCCTCGCAATTTTTACAAG 58.134 39.130 0.00 0.00 0.00 3.16
5286 5791 7.812309 TGTTGTATCACTTTCTCGATTACAG 57.188 36.000 0.00 0.00 0.00 2.74
5301 5813 5.001232 GCTCAGGTTTAGGTTGTTGTATCA 58.999 41.667 0.00 0.00 0.00 2.15
5304 5816 4.131596 GTGCTCAGGTTTAGGTTGTTGTA 58.868 43.478 0.00 0.00 0.00 2.41
5319 5831 2.094130 TGCTTCATCTCTCAGTGCTCAG 60.094 50.000 0.00 0.00 0.00 3.35
5328 5840 1.069049 GGCTCCTCTGCTTCATCTCTC 59.931 57.143 0.00 0.00 0.00 3.20
5546 6061 8.410912 GTTTCCTGTTTCTTTCTAAAGCCTTTA 58.589 33.333 0.00 0.00 35.99 1.85
5600 6122 9.143155 TGCTATGTAGGATCTTAACACAGATTA 57.857 33.333 5.48 0.00 33.36 1.75
5601 6123 8.023021 TGCTATGTAGGATCTTAACACAGATT 57.977 34.615 5.48 0.00 33.36 2.40
5639 6164 6.252233 TGTGTGATTCCATTTTTCCTCCATA 58.748 36.000 0.00 0.00 0.00 2.74
5646 6171 9.696917 ATCTTAGTTTGTGTGATTCCATTTTTC 57.303 29.630 0.00 0.00 0.00 2.29
5648 6173 8.641541 ACATCTTAGTTTGTGTGATTCCATTTT 58.358 29.630 0.00 0.00 0.00 1.82
5664 6189 6.260050 CCGGTTGCATATTGTACATCTTAGTT 59.740 38.462 0.00 0.00 0.00 2.24
5665 6190 5.758296 CCGGTTGCATATTGTACATCTTAGT 59.242 40.000 0.00 0.00 0.00 2.24
5669 6194 2.878406 GCCGGTTGCATATTGTACATCT 59.122 45.455 1.90 0.00 40.77 2.90
5670 6195 3.268013 GCCGGTTGCATATTGTACATC 57.732 47.619 1.90 0.00 40.77 3.06
5711 6238 1.728971 CAATGTTCCTGCTCGAGACAC 59.271 52.381 18.75 4.84 0.00 3.67
5718 6245 1.670967 GCAAAGCCAATGTTCCTGCTC 60.671 52.381 0.00 0.00 32.62 4.26
5749 6279 2.667536 GCGGCAGCATCGGATGAT 60.668 61.111 21.69 12.90 44.35 2.45
5799 6329 6.480524 TGTTTGTTGCACTATCTACATGAC 57.519 37.500 0.00 0.00 0.00 3.06
5843 6373 1.829523 AACGGGTTAACTGGCGGCTA 61.830 55.000 11.43 0.00 0.00 3.93
5844 6374 2.685804 AAACGGGTTAACTGGCGGCT 62.686 55.000 11.43 0.00 0.00 5.52
5846 6376 0.885596 TGAAACGGGTTAACTGGCGG 60.886 55.000 5.42 0.00 0.00 6.13
5876 6406 2.629137 ACTTGCAATGCCATGTTGAGAA 59.371 40.909 1.53 0.00 0.00 2.87
6082 6612 5.988561 GGGTGAGATGTGATTCTGAGTATTC 59.011 44.000 0.00 0.00 0.00 1.75
6118 6648 2.813754 TGAAGTTCCTGCAATCGAAAGG 59.186 45.455 0.00 0.00 0.00 3.11
6283 6816 6.405842 CCCTTTCCCAATATCTTAACAGCAAC 60.406 42.308 0.00 0.00 0.00 4.17
6285 6818 5.200483 CCCTTTCCCAATATCTTAACAGCA 58.800 41.667 0.00 0.00 0.00 4.41
6287 6820 6.013554 TCCCCTTTCCCAATATCTTAACAG 57.986 41.667 0.00 0.00 0.00 3.16
6477 7010 1.757118 GCCCTTGCCTTTTCCTAATCC 59.243 52.381 0.00 0.00 0.00 3.01
6672 7211 0.109179 TGCAACATCGCAAATCAGGC 60.109 50.000 0.00 0.00 39.45 4.85
6722 7261 5.163652 CCCGGATAATTTTGTCTTGTCCTTC 60.164 44.000 0.73 0.00 33.17 3.46
6723 7262 4.705023 CCCGGATAATTTTGTCTTGTCCTT 59.295 41.667 0.73 0.00 33.17 3.36
6727 7266 4.310022 TCCCCGGATAATTTTGTCTTGT 57.690 40.909 0.73 0.00 0.00 3.16
6730 7269 6.010219 CCATAATCCCCGGATAATTTTGTCT 58.990 40.000 0.73 0.00 33.97 3.41
6791 7336 8.521170 AGGGTTCTTATTAAGCTATGTTTTCC 57.479 34.615 0.00 0.00 0.00 3.13
6800 7345 3.632333 GGCCAAGGGTTCTTATTAAGCT 58.368 45.455 0.00 0.00 0.00 3.74
6917 7470 2.048222 ACCATCCGTCGTGTGCAG 60.048 61.111 0.00 0.00 0.00 4.41
6923 7476 2.654877 GTGGTCACCATCCGTCGT 59.345 61.111 0.00 0.00 35.28 4.34
6944 7503 1.143684 AGCTTTGTTCTGCCCTTCTGA 59.856 47.619 0.00 0.00 0.00 3.27
6945 7504 1.613836 AGCTTTGTTCTGCCCTTCTG 58.386 50.000 0.00 0.00 0.00 3.02
6946 7505 2.371658 AAGCTTTGTTCTGCCCTTCT 57.628 45.000 0.00 0.00 0.00 2.85
6947 7506 2.489722 CCTAAGCTTTGTTCTGCCCTTC 59.510 50.000 3.20 0.00 0.00 3.46
6976 7535 4.523083 TGTTGTTGTTCTGTTCTAGCCTT 58.477 39.130 0.00 0.00 0.00 4.35
6983 7542 4.558860 GTGAGCTTTGTTGTTGTTCTGTTC 59.441 41.667 0.00 0.00 0.00 3.18
6984 7543 4.218417 AGTGAGCTTTGTTGTTGTTCTGTT 59.782 37.500 0.00 0.00 0.00 3.16
6986 7545 4.346129 GAGTGAGCTTTGTTGTTGTTCTG 58.654 43.478 0.00 0.00 0.00 3.02
6987 7546 3.378427 GGAGTGAGCTTTGTTGTTGTTCT 59.622 43.478 0.00 0.00 0.00 3.01
6988 7547 3.489229 GGGAGTGAGCTTTGTTGTTGTTC 60.489 47.826 0.00 0.00 0.00 3.18
6989 7548 2.427095 GGGAGTGAGCTTTGTTGTTGTT 59.573 45.455 0.00 0.00 0.00 2.83
6990 7549 2.024414 GGGAGTGAGCTTTGTTGTTGT 58.976 47.619 0.00 0.00 0.00 3.32
6991 7550 1.002468 CGGGAGTGAGCTTTGTTGTTG 60.002 52.381 0.00 0.00 0.00 3.33
7013 7572 0.259938 GCCCCTGGATCAAGACCATT 59.740 55.000 0.00 0.00 36.79 3.16
7036 7595 3.918220 CGCAGGTTCGCATCGAGC 61.918 66.667 0.00 0.00 37.14 5.03
7053 7612 3.140814 GATGCCACGCCTTTCCCC 61.141 66.667 0.00 0.00 0.00 4.81
7054 7613 2.361104 TGATGCCACGCCTTTCCC 60.361 61.111 0.00 0.00 0.00 3.97
7055 7614 1.377202 TCTGATGCCACGCCTTTCC 60.377 57.895 0.00 0.00 0.00 3.13
7056 7615 0.955428 TGTCTGATGCCACGCCTTTC 60.955 55.000 0.00 0.00 0.00 2.62
7057 7616 0.537143 TTGTCTGATGCCACGCCTTT 60.537 50.000 0.00 0.00 0.00 3.11
7058 7617 0.957395 CTTGTCTGATGCCACGCCTT 60.957 55.000 0.00 0.00 0.00 4.35
7059 7618 1.376424 CTTGTCTGATGCCACGCCT 60.376 57.895 0.00 0.00 0.00 5.52
7060 7619 3.044059 GCTTGTCTGATGCCACGCC 62.044 63.158 0.00 0.00 0.00 5.68
7061 7620 1.651240 ATGCTTGTCTGATGCCACGC 61.651 55.000 0.00 0.00 0.00 5.34
7062 7621 0.098200 CATGCTTGTCTGATGCCACG 59.902 55.000 0.00 0.00 0.00 4.94
7063 7622 0.179145 GCATGCTTGTCTGATGCCAC 60.179 55.000 11.37 0.00 37.17 5.01
7064 7623 2.186155 GCATGCTTGTCTGATGCCA 58.814 52.632 11.37 0.00 37.17 4.92
7066 7625 1.063649 CGGCATGCTTGTCTGATGC 59.936 57.895 18.92 0.00 41.51 3.91
7067 7626 1.089112 TTCGGCATGCTTGTCTGATG 58.911 50.000 18.92 0.00 0.00 3.07
7068 7627 1.470098 GTTTCGGCATGCTTGTCTGAT 59.530 47.619 18.92 0.00 0.00 2.90
7069 7628 0.874390 GTTTCGGCATGCTTGTCTGA 59.126 50.000 18.92 3.60 0.00 3.27
7070 7629 0.877071 AGTTTCGGCATGCTTGTCTG 59.123 50.000 18.92 1.15 0.00 3.51
7071 7630 1.160137 GAGTTTCGGCATGCTTGTCT 58.840 50.000 18.92 9.83 0.00 3.41
7072 7631 0.179215 CGAGTTTCGGCATGCTTGTC 60.179 55.000 18.92 0.00 36.00 3.18
7073 7632 1.868997 CGAGTTTCGGCATGCTTGT 59.131 52.632 18.92 0.00 36.00 3.16
7074 7633 1.512734 GCGAGTTTCGGCATGCTTG 60.513 57.895 18.92 10.89 40.84 4.01
7075 7634 2.870372 GCGAGTTTCGGCATGCTT 59.130 55.556 18.92 0.00 40.84 3.91
7076 7635 3.490759 CGCGAGTTTCGGCATGCT 61.491 61.111 18.92 0.00 40.84 3.79
7077 7636 3.788766 ACGCGAGTTTCGGCATGC 61.789 61.111 15.93 9.90 46.40 4.06
7088 7647 1.272781 GGATCTGAACTTGACGCGAG 58.727 55.000 15.93 1.31 0.00 5.03
7089 7648 0.601057 TGGATCTGAACTTGACGCGA 59.399 50.000 15.93 0.00 0.00 5.87
7090 7649 0.994995 CTGGATCTGAACTTGACGCG 59.005 55.000 3.53 3.53 0.00 6.01
7091 7650 2.094494 TCTCTGGATCTGAACTTGACGC 60.094 50.000 0.00 0.00 0.00 5.19
7092 7651 3.857549 TCTCTGGATCTGAACTTGACG 57.142 47.619 0.00 0.00 0.00 4.35
7093 7652 4.887748 TGTTCTCTGGATCTGAACTTGAC 58.112 43.478 16.09 0.93 40.27 3.18
7094 7653 4.835056 TCTGTTCTCTGGATCTGAACTTGA 59.165 41.667 16.09 12.87 40.27 3.02
7095 7654 4.928615 GTCTGTTCTCTGGATCTGAACTTG 59.071 45.833 16.09 11.61 40.27 3.16
7096 7655 4.020662 GGTCTGTTCTCTGGATCTGAACTT 60.021 45.833 16.09 0.00 40.27 2.66
7097 7656 3.513515 GGTCTGTTCTCTGGATCTGAACT 59.486 47.826 16.09 0.00 40.27 3.01
7098 7657 3.368948 GGGTCTGTTCTCTGGATCTGAAC 60.369 52.174 11.53 11.53 40.09 3.18
7099 7658 2.834549 GGGTCTGTTCTCTGGATCTGAA 59.165 50.000 0.00 0.00 0.00 3.02
7100 7659 2.461695 GGGTCTGTTCTCTGGATCTGA 58.538 52.381 0.00 0.00 0.00 3.27
7101 7660 1.484240 GGGGTCTGTTCTCTGGATCTG 59.516 57.143 0.00 0.00 0.00 2.90
7102 7661 1.872773 GGGGTCTGTTCTCTGGATCT 58.127 55.000 0.00 0.00 0.00 2.75
7103 7662 0.461961 CGGGGTCTGTTCTCTGGATC 59.538 60.000 0.00 0.00 0.00 3.36
7104 7663 1.617947 GCGGGGTCTGTTCTCTGGAT 61.618 60.000 0.00 0.00 0.00 3.41
7105 7664 2.283529 GCGGGGTCTGTTCTCTGGA 61.284 63.158 0.00 0.00 0.00 3.86
7106 7665 0.970937 TAGCGGGGTCTGTTCTCTGG 60.971 60.000 0.00 0.00 0.00 3.86
7107 7666 0.895530 TTAGCGGGGTCTGTTCTCTG 59.104 55.000 0.00 0.00 0.00 3.35
7108 7667 1.640917 TTTAGCGGGGTCTGTTCTCT 58.359 50.000 0.00 0.00 0.00 3.10
7109 7668 2.467566 TTTTAGCGGGGTCTGTTCTC 57.532 50.000 0.00 0.00 0.00 2.87
7110 7669 2.370849 TCTTTTTAGCGGGGTCTGTTCT 59.629 45.455 0.00 0.00 0.00 3.01
7111 7670 2.483106 GTCTTTTTAGCGGGGTCTGTTC 59.517 50.000 0.00 0.00 0.00 3.18
7112 7671 2.158726 TGTCTTTTTAGCGGGGTCTGTT 60.159 45.455 0.00 0.00 0.00 3.16
7113 7672 1.418637 TGTCTTTTTAGCGGGGTCTGT 59.581 47.619 0.00 0.00 0.00 3.41
7114 7673 2.076863 CTGTCTTTTTAGCGGGGTCTG 58.923 52.381 0.00 0.00 0.00 3.51
7115 7674 1.975680 TCTGTCTTTTTAGCGGGGTCT 59.024 47.619 0.00 0.00 0.00 3.85
7116 7675 2.028385 TCTCTGTCTTTTTAGCGGGGTC 60.028 50.000 0.00 0.00 0.00 4.46
7117 7676 1.975680 TCTCTGTCTTTTTAGCGGGGT 59.024 47.619 0.00 0.00 0.00 4.95
7118 7677 2.762535 TCTCTGTCTTTTTAGCGGGG 57.237 50.000 0.00 0.00 0.00 5.73
7119 7678 4.613850 GCTTTTCTCTGTCTTTTTAGCGGG 60.614 45.833 0.00 0.00 0.00 6.13
7120 7679 4.467735 GCTTTTCTCTGTCTTTTTAGCGG 58.532 43.478 0.00 0.00 0.00 5.52
7121 7680 4.214332 AGGCTTTTCTCTGTCTTTTTAGCG 59.786 41.667 0.00 0.00 0.00 4.26
7122 7681 5.697473 AGGCTTTTCTCTGTCTTTTTAGC 57.303 39.130 0.00 0.00 0.00 3.09
7137 7696 6.966534 TTCTCTGATCTGAAAAAGGCTTTT 57.033 33.333 19.14 19.14 37.46 2.27
7138 7697 6.966534 TTTCTCTGATCTGAAAAAGGCTTT 57.033 33.333 6.68 6.68 30.41 3.51
7139 7698 6.966534 TTTTCTCTGATCTGAAAAAGGCTT 57.033 33.333 14.63 0.00 38.65 4.35
7140 7699 6.966534 TTTTTCTCTGATCTGAAAAAGGCT 57.033 33.333 20.04 0.00 43.09 4.58
7185 7744 4.631131 GGCTGCCACTTTTATCTGTTTTT 58.369 39.130 15.17 0.00 0.00 1.94
7186 7745 3.305335 CGGCTGCCACTTTTATCTGTTTT 60.305 43.478 20.29 0.00 0.00 2.43
7187 7746 2.228822 CGGCTGCCACTTTTATCTGTTT 59.771 45.455 20.29 0.00 0.00 2.83
7188 7747 1.812571 CGGCTGCCACTTTTATCTGTT 59.187 47.619 20.29 0.00 0.00 3.16
7189 7748 1.453155 CGGCTGCCACTTTTATCTGT 58.547 50.000 20.29 0.00 0.00 3.41
7190 7749 0.734889 CCGGCTGCCACTTTTATCTG 59.265 55.000 20.29 0.00 0.00 2.90
7191 7750 0.328258 ACCGGCTGCCACTTTTATCT 59.672 50.000 20.29 0.00 0.00 1.98
7192 7751 1.132453 GAACCGGCTGCCACTTTTATC 59.868 52.381 20.29 2.90 0.00 1.75
7193 7752 1.173913 GAACCGGCTGCCACTTTTAT 58.826 50.000 20.29 0.00 0.00 1.40
7194 7753 0.109723 AGAACCGGCTGCCACTTTTA 59.890 50.000 20.29 0.00 0.00 1.52
7195 7754 0.109723 TAGAACCGGCTGCCACTTTT 59.890 50.000 20.29 6.55 0.00 2.27
7196 7755 0.321653 CTAGAACCGGCTGCCACTTT 60.322 55.000 20.29 7.82 0.00 2.66
7197 7756 1.296715 CTAGAACCGGCTGCCACTT 59.703 57.895 20.29 8.56 0.00 3.16
7198 7757 2.982130 CTAGAACCGGCTGCCACT 59.018 61.111 20.29 13.60 0.00 4.00
7199 7758 1.956629 TAGCTAGAACCGGCTGCCAC 61.957 60.000 20.29 6.76 39.31 5.01
7200 7759 1.676678 CTAGCTAGAACCGGCTGCCA 61.677 60.000 20.29 0.00 39.31 4.92
7201 7760 1.068250 CTAGCTAGAACCGGCTGCC 59.932 63.158 16.15 9.11 39.31 4.85
7202 7761 1.068250 CCTAGCTAGAACCGGCTGC 59.932 63.158 22.70 0.00 39.31 5.25
7203 7762 1.068250 GCCTAGCTAGAACCGGCTG 59.932 63.158 22.70 3.73 39.31 4.85
7204 7763 1.075896 AGCCTAGCTAGAACCGGCT 60.076 57.895 22.70 18.89 45.70 5.52
7205 7764 0.249531 GAAGCCTAGCTAGAACCGGC 60.250 60.000 22.70 16.87 38.25 6.13
7206 7765 1.404843 AGAAGCCTAGCTAGAACCGG 58.595 55.000 22.70 6.97 38.25 5.28


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

AutoCloner maintained by Alex Coulton.