Multiple sequence alignment - TraesCS4B01G244400

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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 TraesCS4B01G244400 chr4B 100.000 5931 0 0 1 5931 506138247 506144177 0.000000e+00 10953.0
1 TraesCS4B01G244400 chr4B 88.095 84 10 0 5508 5591 34491316 34491233 3.780000e-17 100.0
2 TraesCS4B01G244400 chr4B 100.000 40 0 0 5824 5863 506144032 506144071 2.290000e-09 75.0
3 TraesCS4B01G244400 chr4B 100.000 40 0 0 5786 5825 506144070 506144109 2.290000e-09 75.0
4 TraesCS4B01G244400 chr4D 93.495 5427 209 50 1 5388 409645882 409640561 0.000000e+00 7934.0
5 TraesCS4B01G244400 chr4D 98.421 190 3 0 5636 5825 409640440 409640251 9.520000e-88 335.0
6 TraesCS4B01G244400 chr4D 94.595 111 3 1 5824 5931 409640290 409640180 1.020000e-37 169.0
7 TraesCS4B01G244400 chr4A 94.079 4003 169 45 1428 5388 64143104 64147080 0.000000e+00 6017.0
8 TraesCS4B01G244400 chr4A 90.916 1299 76 19 155 1430 64141605 64142884 0.000000e+00 1707.0
9 TraesCS4B01G244400 chr4A 92.893 197 11 1 5632 5825 64147109 64147305 3.500000e-72 283.0
10 TraesCS4B01G244400 chr4A 100.000 43 0 0 5824 5866 64147266 64147308 4.930000e-11 80.5
11 TraesCS4B01G244400 chr1D 94.508 437 19 5 2186 2619 340641524 340641090 0.000000e+00 669.0
12 TraesCS4B01G244400 chr1D 89.583 96 10 0 5397 5492 7770780 7770685 8.070000e-24 122.0
13 TraesCS4B01G244400 chr1D 87.500 96 11 1 5397 5492 446708542 446708448 6.280000e-20 110.0
14 TraesCS4B01G244400 chr2D 97.368 76 2 0 5505 5580 5385930 5386005 4.820000e-26 130.0
15 TraesCS4B01G244400 chr3A 88.571 105 12 0 5385 5489 734523118 734523222 1.730000e-25 128.0
16 TraesCS4B01G244400 chr3A 89.247 93 10 0 5397 5489 641321476 641321568 3.760000e-22 117.0
17 TraesCS4B01G244400 chr5D 90.426 94 9 0 5397 5490 538171546 538171639 2.240000e-24 124.0
18 TraesCS4B01G244400 chr5D 90.361 83 8 0 5502 5584 342594346 342594428 6.280000e-20 110.0
19 TraesCS4B01G244400 chr5D 84.466 103 12 4 5502 5602 92148740 92148840 1.360000e-16 99.0
20 TraesCS4B01G244400 chr3D 92.045 88 7 0 5402 5489 604609796 604609883 2.240000e-24 124.0
21 TraesCS4B01G244400 chr7D 86.792 106 14 0 5387 5492 603581024 603581129 1.040000e-22 119.0
22 TraesCS4B01G244400 chr5B 86.239 109 11 4 5502 5608 97493887 97493993 1.350000e-21 115.0
23 TraesCS4B01G244400 chr5B 90.361 83 8 0 5505 5587 712007051 712006969 6.280000e-20 110.0
24 TraesCS4B01G244400 chr5B 90.361 83 8 0 5505 5587 712024503 712024421 6.280000e-20 110.0
25 TraesCS4B01G244400 chr7B 88.298 94 11 0 5397 5490 218816987 218817080 4.860000e-21 113.0
26 TraesCS4B01G244400 chr1A 88.298 94 11 0 5397 5490 22251272 22251365 4.860000e-21 113.0
27 TraesCS4B01G244400 chr6D 90.361 83 8 0 5502 5584 464733797 464733879 6.280000e-20 110.0
28 TraesCS4B01G244400 chr2A 89.655 87 7 2 5505 5590 692710442 692710357 6.280000e-20 110.0


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 TraesCS4B01G244400 chr4B 506138247 506144177 5930 False 3701.000000 10953 100.000000 1 5931 3 chr4B.!!$F1 5930
1 TraesCS4B01G244400 chr4D 409640180 409645882 5702 True 2812.666667 7934 95.503667 1 5931 3 chr4D.!!$R1 5930
2 TraesCS4B01G244400 chr4A 64141605 64147308 5703 False 2021.875000 6017 94.472000 155 5866 4 chr4A.!!$F1 5711

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
981 1018 0.663688 ATCGGTTGATCGACCTCTCG 59.336 55.000 26.44 15.02 42.21 4.04 F
1537 1808 0.108615 CACTTGTAGCACCTCCCTCG 60.109 60.000 0.00 0.00 0.00 4.63 F
2184 2456 0.033601 ACCGCAGCCCCATTTTGATA 60.034 50.000 0.00 0.00 0.00 2.15 F
2828 3109 0.392193 CCCACAGAGTGTGCTGATCC 60.392 60.000 1.31 0.00 46.51 3.36 F
3480 3766 1.152419 TCCGTCCTCACAACTCCCA 60.152 57.895 0.00 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2129 0.253327 AGAAGAAGGTGGGCGGAATC 59.747 55.0 0.0 0.0 0.00 2.52 R
3521 3807 0.249489 GCTGGACGAGCCGACATATT 60.249 55.0 0.0 0.0 42.54 1.28 R
3994 4293 0.109597 GCGGCAATCACCTTCTTGTG 60.110 55.0 0.0 0.0 37.59 3.33 R
4126 4428 0.396435 TGCAAGGTGAAGGACATCGT 59.604 50.0 0.0 0.0 34.34 3.73 R
5143 5454 0.883833 GGCACAGAACAAGGACATGG 59.116 55.0 0.0 0.0 0.00 3.66 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
21 22 1.584175 CCAGCAAACAAAAGCATGCA 58.416 45.000 21.98 0.00 41.18 3.96
115 116 1.661341 GATGATCGATAGCCCATGCC 58.339 55.000 0.00 0.00 38.69 4.40
190 191 2.167075 GGTGGTACGTATGGTAGTTGCT 59.833 50.000 0.00 0.00 0.00 3.91
191 192 3.368739 GGTGGTACGTATGGTAGTTGCTT 60.369 47.826 0.00 0.00 0.00 3.91
192 193 3.615496 GTGGTACGTATGGTAGTTGCTTG 59.385 47.826 0.00 0.00 0.00 4.01
193 194 2.606272 GGTACGTATGGTAGTTGCTTGC 59.394 50.000 0.00 0.00 0.00 4.01
199 200 1.302993 GGTAGTTGCTTGCCGGGAA 60.303 57.895 8.57 8.57 0.00 3.97
277 282 1.339235 CGATCACGCAACGTAACGGT 61.339 55.000 13.77 0.95 38.32 4.83
388 402 4.742649 TCGGTCCCTCAGCTCGCT 62.743 66.667 0.00 0.00 0.00 4.93
470 484 3.381983 TCGTCGGCAGGAGCATGT 61.382 61.111 0.00 0.00 44.61 3.21
590 604 1.499502 GTCGCTTTCCTGCTCTTGC 59.500 57.895 0.00 0.00 40.20 4.01
670 690 1.202592 TGACCACACGCACACATAACT 60.203 47.619 0.00 0.00 0.00 2.24
720 741 6.932356 TTTCCATGTCAGCTGATTTATCTC 57.068 37.500 21.47 5.43 0.00 2.75
762 787 9.553418 GAAAAGCTGATTTATTTCTTGAGAGAC 57.447 33.333 0.00 0.00 0.00 3.36
862 887 1.078143 AGCTGCTGATCGGTTTCCC 60.078 57.895 0.00 0.00 0.00 3.97
915 940 1.039856 GCTCTCATCCCTCCTCTCAC 58.960 60.000 0.00 0.00 0.00 3.51
916 941 1.317613 CTCTCATCCCTCCTCTCACG 58.682 60.000 0.00 0.00 0.00 4.35
917 942 0.753479 TCTCATCCCTCCTCTCACGC 60.753 60.000 0.00 0.00 0.00 5.34
918 943 1.000359 TCATCCCTCCTCTCACGCA 60.000 57.895 0.00 0.00 0.00 5.24
959 988 3.058708 CGTATATACCCTGAACGAGCGAA 60.059 47.826 7.30 0.00 35.66 4.70
981 1018 0.663688 ATCGGTTGATCGACCTCTCG 59.336 55.000 26.44 15.02 42.21 4.04
1062 1103 4.353437 GTGGCCGTCGACGTTCCT 62.353 66.667 33.49 0.00 37.74 3.36
1067 1108 2.805353 CGTCGACGTTCCTGCAGG 60.805 66.667 29.08 27.87 34.11 4.85
1170 1211 1.414158 CCAGGACGACAGGGATGTAT 58.586 55.000 0.00 0.00 0.00 2.29
1224 1268 2.972625 TGCATCTCGTCGATTTCCTTT 58.027 42.857 0.00 0.00 0.00 3.11
1252 1297 1.200716 CGCCCAAGTACGTCTGTCTTA 59.799 52.381 0.00 0.00 0.00 2.10
1445 1712 4.967084 AGGTAAATACATACGGCCATCA 57.033 40.909 2.24 0.00 0.00 3.07
1454 1721 2.498644 TACGGCCATCAAATCAACCA 57.501 45.000 2.24 0.00 0.00 3.67
1465 1732 7.417116 GCCATCAAATCAACCAATCTATCTGTT 60.417 37.037 0.00 0.00 0.00 3.16
1537 1808 0.108615 CACTTGTAGCACCTCCCTCG 60.109 60.000 0.00 0.00 0.00 4.63
1538 1809 1.153549 CTTGTAGCACCTCCCTCGC 60.154 63.158 0.00 0.00 0.00 5.03
1539 1810 2.890847 CTTGTAGCACCTCCCTCGCG 62.891 65.000 0.00 0.00 0.00 5.87
1589 1860 4.262808 CGGGATAGATGGAGCTTCTCAATT 60.263 45.833 0.00 0.00 31.08 2.32
1601 1872 7.178983 TGGAGCTTCTCAATTAATTTTCACCAT 59.821 33.333 0.00 0.00 31.08 3.55
1639 1910 2.871096 AATTTTCACCGGCAGTCCTA 57.129 45.000 0.00 0.00 0.00 2.94
1641 1912 1.886886 TTTTCACCGGCAGTCCTAAC 58.113 50.000 0.00 0.00 0.00 2.34
1748 2019 5.652994 TTTGTCAGTTTGGCAAAGTAACT 57.347 34.783 19.26 8.18 45.74 2.24
1858 2129 2.415697 ATTTTTCACCTTTGCCGACG 57.584 45.000 0.00 0.00 0.00 5.12
1862 2133 1.153353 TTCACCTTTGCCGACGATTC 58.847 50.000 0.00 0.00 0.00 2.52
2083 2355 5.339008 TCTCGTCATACAATTGGTTAGCT 57.661 39.130 10.83 0.00 0.00 3.32
2138 2410 7.513371 TGTTACCTTGAAATAACCATTCGTT 57.487 32.000 0.00 0.00 38.57 3.85
2151 2423 5.091910 ACCATTCGTTCGTTTCTTTTCTC 57.908 39.130 0.00 0.00 0.00 2.87
2153 2425 2.916735 TCGTTCGTTTCTTTTCTCGC 57.083 45.000 0.00 0.00 0.00 5.03
2184 2456 0.033601 ACCGCAGCCCCATTTTGATA 60.034 50.000 0.00 0.00 0.00 2.15
2218 2494 5.496556 TGAGTATGTTCCCCATTTACACAG 58.503 41.667 0.00 0.00 34.86 3.66
2220 2496 6.134535 AGTATGTTCCCCATTTACACAGAA 57.865 37.500 0.00 0.00 34.86 3.02
2322 2602 3.545633 CTTGTCTAAGCAAGTCGCAAAC 58.454 45.455 0.00 0.00 46.13 2.93
2519 2799 3.821421 AACCAAGTCTCGAAAGTCTGT 57.179 42.857 0.00 0.00 0.00 3.41
2586 2866 6.774170 AGAAGATGCCATCATTAGCAAATACA 59.226 34.615 7.56 0.00 43.36 2.29
2678 2958 1.134367 TCTGGTACCGATTTCTCGCAG 59.866 52.381 7.57 0.00 43.66 5.18
2699 2980 8.372459 TCGCAGTATACCTGGTTTCATATATTT 58.628 33.333 3.84 0.00 41.81 1.40
2700 2981 8.999431 CGCAGTATACCTGGTTTCATATATTTT 58.001 33.333 3.84 0.00 41.81 1.82
2735 3016 2.550830 TTTGACCTCAGGACTGAAGC 57.449 50.000 0.00 0.00 39.39 3.86
2764 3045 4.103153 TCATGAATCCCTATGTGGAACTCC 59.897 45.833 0.00 0.00 38.10 3.85
2784 3065 3.579586 TCCGTTTTACAGGTGGTGATACT 59.420 43.478 0.00 0.00 0.00 2.12
2828 3109 0.392193 CCCACAGAGTGTGCTGATCC 60.392 60.000 1.31 0.00 46.51 3.36
2883 3164 3.717400 TCTGTGACATCGGCTCTAATC 57.283 47.619 0.00 0.00 0.00 1.75
2983 3264 7.225011 TGTGAAACATGTAGGTGTTATTACCA 58.775 34.615 0.00 0.00 45.67 3.25
3048 3329 8.672823 TGCTATCCATGATGCTAATTCATATC 57.327 34.615 0.00 0.00 32.63 1.63
3265 3546 7.164122 TCAGCTGGAATATGGATATCTGTTTC 58.836 38.462 15.13 1.96 0.00 2.78
3470 3756 2.457366 ATGTGTTTCAGTCCGTCCTC 57.543 50.000 0.00 0.00 0.00 3.71
3480 3766 1.152419 TCCGTCCTCACAACTCCCA 60.152 57.895 0.00 0.00 0.00 4.37
3521 3807 7.073208 TCAGGTACCTGATAACCATGATCTTA 58.927 38.462 35.91 12.06 46.80 2.10
3715 4007 3.449227 CTCGCGAGGGTGGTAGCA 61.449 66.667 28.40 0.00 0.00 3.49
3721 4013 1.251527 CGAGGGTGGTAGCAGTGACT 61.252 60.000 0.00 0.00 0.00 3.41
3817 4109 4.103103 CTCTGGCTCGCGACGTCA 62.103 66.667 17.16 8.77 0.00 4.35
3925 4224 6.155565 AGCTTCAGTAGAGACTAGAGAGTGTA 59.844 42.308 0.00 0.00 35.45 2.90
4097 4396 1.375551 AGAACACGCAAAAGGTTCGT 58.624 45.000 0.00 0.00 44.20 3.85
4109 4408 5.051307 GCAAAAGGTTCGTATTTTGGTTCAC 60.051 40.000 11.16 0.00 43.42 3.18
4126 4428 4.081420 GGTTCACTGAGAAGAGGCTAATGA 60.081 45.833 0.00 0.00 36.78 2.57
4134 4436 3.068873 AGAAGAGGCTAATGACGATGTCC 59.931 47.826 0.00 0.00 0.00 4.02
4155 4458 0.675837 TCACCTTGCAGCTGAGCATC 60.676 55.000 20.43 0.00 45.19 3.91
4231 4534 0.378962 CGTTTTCACAAAGGACGCCA 59.621 50.000 0.00 0.00 30.58 5.69
4325 4629 4.261825 CGAGAGATGACTATTTCCCAGGAC 60.262 50.000 0.00 0.00 0.00 3.85
4328 4632 4.624913 AGATGACTATTTCCCAGGACTCA 58.375 43.478 0.00 0.00 0.00 3.41
4345 4649 5.534654 AGGACTCAGACACTGAATATAGCTC 59.465 44.000 0.00 0.00 40.18 4.09
4476 4782 1.683943 TGGTACCGTAGATCCTTCCG 58.316 55.000 7.57 0.00 0.00 4.30
4477 4783 1.064463 TGGTACCGTAGATCCTTCCGT 60.064 52.381 7.57 0.00 0.00 4.69
4776 5082 2.522185 TCTAGTGCCGTTTACAGGAGT 58.478 47.619 0.00 0.00 0.00 3.85
4812 5119 4.889409 TCCTGCTGAAATTGAACTGTTCTT 59.111 37.500 20.18 7.55 0.00 2.52
4813 5120 5.009010 TCCTGCTGAAATTGAACTGTTCTTC 59.991 40.000 20.18 15.52 0.00 2.87
4814 5121 5.009410 CCTGCTGAAATTGAACTGTTCTTCT 59.991 40.000 20.18 3.83 0.00 2.85
4867 5176 4.228210 TCTTCAATTAGGGCTCATCAAGGT 59.772 41.667 0.00 0.00 0.00 3.50
4906 5215 4.804420 ATGGGGGCAGCGAGAGGA 62.804 66.667 0.00 0.00 0.00 3.71
4992 5301 4.160439 TGCATAGCTGGTAGATAGCCATAC 59.840 45.833 0.00 0.00 42.07 2.39
4993 5302 4.160439 GCATAGCTGGTAGATAGCCATACA 59.840 45.833 0.00 0.00 42.07 2.29
4998 5307 5.960811 AGCTGGTAGATAGCCATACACATAT 59.039 40.000 0.00 0.00 42.07 1.78
5071 5380 4.718961 CTTGGGGTATTGGAGTTAGATGG 58.281 47.826 0.00 0.00 0.00 3.51
5072 5381 3.053077 TGGGGTATTGGAGTTAGATGGG 58.947 50.000 0.00 0.00 0.00 4.00
5074 5383 2.224793 GGGTATTGGAGTTAGATGGGGC 60.225 54.545 0.00 0.00 0.00 5.80
5075 5384 2.711547 GGTATTGGAGTTAGATGGGGCT 59.288 50.000 0.00 0.00 0.00 5.19
5143 5454 4.870363 GAGGCTACTCTGATCTTGTGATC 58.130 47.826 0.00 0.00 40.51 2.92
5246 5563 8.429641 TGGTCTATCCCTAGTTATGTCATTTTC 58.570 37.037 0.00 0.00 34.77 2.29
5264 5581 8.047310 GTCATTTTCCCTCTCTTAATCCTTGTA 58.953 37.037 0.00 0.00 0.00 2.41
5265 5582 8.781951 TCATTTTCCCTCTCTTAATCCTTGTAT 58.218 33.333 0.00 0.00 0.00 2.29
5283 5600 5.618056 TGTATATCGAATGTACCCGAGAC 57.382 43.478 0.00 6.60 38.25 3.36
5296 5613 1.339055 CCCGAGACCATTCTTCTTGCA 60.339 52.381 0.00 0.00 29.47 4.08
5315 5632 5.186996 TGCAGAAGATGAGGTTTTGTTTC 57.813 39.130 0.00 0.00 0.00 2.78
5340 5657 7.822334 TCCGAGCTGAGAAATAAAATTGTCTTA 59.178 33.333 0.00 0.00 0.00 2.10
5388 5705 5.184892 ACCTCCAAGCTGAAAATGAGTAT 57.815 39.130 0.00 0.00 0.00 2.12
5390 5707 6.721318 ACCTCCAAGCTGAAAATGAGTATTA 58.279 36.000 0.00 0.00 0.00 0.98
5391 5708 7.349598 ACCTCCAAGCTGAAAATGAGTATTAT 58.650 34.615 0.00 0.00 0.00 1.28
5394 5711 9.770097 CTCCAAGCTGAAAATGAGTATTATCTA 57.230 33.333 0.00 0.00 0.00 1.98
5414 5731 2.891191 TGTCCAGGTTTATTGGTCCC 57.109 50.000 0.00 0.00 37.02 4.46
5415 5732 1.356398 TGTCCAGGTTTATTGGTCCCC 59.644 52.381 0.00 0.00 37.02 4.81
5417 5734 2.042569 GTCCAGGTTTATTGGTCCCCTT 59.957 50.000 0.00 0.00 37.02 3.95
5418 5735 2.310647 TCCAGGTTTATTGGTCCCCTTC 59.689 50.000 0.00 0.00 37.02 3.46
5420 5737 1.990327 AGGTTTATTGGTCCCCTTCGT 59.010 47.619 0.00 0.00 0.00 3.85
5421 5738 3.054948 CAGGTTTATTGGTCCCCTTCGTA 60.055 47.826 0.00 0.00 0.00 3.43
5422 5739 3.784202 AGGTTTATTGGTCCCCTTCGTAT 59.216 43.478 0.00 0.00 0.00 3.06
5426 5743 6.327154 GTTTATTGGTCCCCTTCGTATTTTG 58.673 40.000 0.00 0.00 0.00 2.44
5427 5744 3.512219 TTGGTCCCCTTCGTATTTTGT 57.488 42.857 0.00 0.00 0.00 2.83
5429 5746 2.106857 TGGTCCCCTTCGTATTTTGTGT 59.893 45.455 0.00 0.00 0.00 3.72
5433 5750 4.276431 GTCCCCTTCGTATTTTGTGTCAAA 59.724 41.667 0.00 0.00 0.00 2.69
5434 5751 5.048294 GTCCCCTTCGTATTTTGTGTCAAAT 60.048 40.000 0.00 0.00 0.00 2.32
5436 5753 6.041069 TCCCCTTCGTATTTTGTGTCAAATTT 59.959 34.615 0.00 0.00 0.00 1.82
5437 5754 6.704050 CCCCTTCGTATTTTGTGTCAAATTTT 59.296 34.615 0.00 0.00 0.00 1.82
5438 5755 7.307101 CCCCTTCGTATTTTGTGTCAAATTTTG 60.307 37.037 2.59 2.59 0.00 2.44
5440 5757 8.977505 CCTTCGTATTTTGTGTCAAATTTTGAT 58.022 29.630 14.54 0.44 42.47 2.57
5551 5868 9.522804 AAAGTCAAAATTTAGCACAAAATACGA 57.477 25.926 0.00 0.00 0.00 3.43
5552 5869 9.522804 AAGTCAAAATTTAGCACAAAATACGAA 57.477 25.926 0.00 0.00 0.00 3.85
5553 5870 9.180678 AGTCAAAATTTAGCACAAAATACGAAG 57.819 29.630 0.00 0.00 0.00 3.79
5554 5871 8.424731 GTCAAAATTTAGCACAAAATACGAAGG 58.575 33.333 0.00 0.00 0.00 3.46
5555 5872 7.596995 TCAAAATTTAGCACAAAATACGAAGGG 59.403 33.333 0.00 0.00 0.00 3.95
5556 5873 5.576447 ATTTAGCACAAAATACGAAGGGG 57.424 39.130 0.00 0.00 0.00 4.79
5557 5874 1.834188 AGCACAAAATACGAAGGGGG 58.166 50.000 0.00 0.00 0.00 5.40
5558 5875 0.172578 GCACAAAATACGAAGGGGGC 59.827 55.000 0.00 0.00 0.00 5.80
5559 5876 1.834188 CACAAAATACGAAGGGGGCT 58.166 50.000 0.00 0.00 0.00 5.19
5560 5877 2.942306 GCACAAAATACGAAGGGGGCTA 60.942 50.000 0.00 0.00 0.00 3.93
5561 5878 3.349022 CACAAAATACGAAGGGGGCTAA 58.651 45.455 0.00 0.00 0.00 3.09
5562 5879 3.951680 CACAAAATACGAAGGGGGCTAAT 59.048 43.478 0.00 0.00 0.00 1.73
5563 5880 5.127491 CACAAAATACGAAGGGGGCTAATA 58.873 41.667 0.00 0.00 0.00 0.98
5564 5881 5.591067 CACAAAATACGAAGGGGGCTAATAA 59.409 40.000 0.00 0.00 0.00 1.40
5565 5882 6.095720 CACAAAATACGAAGGGGGCTAATAAA 59.904 38.462 0.00 0.00 0.00 1.40
5566 5883 6.095860 ACAAAATACGAAGGGGGCTAATAAAC 59.904 38.462 0.00 0.00 0.00 2.01
5567 5884 2.723322 ACGAAGGGGGCTAATAAACC 57.277 50.000 0.00 0.00 0.00 3.27
5568 5885 1.917568 ACGAAGGGGGCTAATAAACCA 59.082 47.619 0.00 0.00 0.00 3.67
5569 5886 2.092592 ACGAAGGGGGCTAATAAACCAG 60.093 50.000 0.00 0.00 0.00 4.00
5570 5887 2.748465 CGAAGGGGGCTAATAAACCAGG 60.748 54.545 0.00 0.00 0.00 4.45
5571 5888 2.296943 AGGGGGCTAATAAACCAGGA 57.703 50.000 0.00 0.00 0.00 3.86
5572 5889 1.850998 AGGGGGCTAATAAACCAGGAC 59.149 52.381 0.00 0.00 0.00 3.85
5573 5890 1.476291 GGGGGCTAATAAACCAGGACG 60.476 57.143 0.00 0.00 0.00 4.79
5574 5891 1.476291 GGGGCTAATAAACCAGGACGG 60.476 57.143 0.00 0.00 42.50 4.79
5575 5892 1.487558 GGGCTAATAAACCAGGACGGA 59.512 52.381 0.00 0.00 38.63 4.69
5576 5893 2.484947 GGGCTAATAAACCAGGACGGAG 60.485 54.545 0.00 0.00 38.63 4.63
5577 5894 2.484947 GGCTAATAAACCAGGACGGAGG 60.485 54.545 0.00 0.00 38.63 4.30
5578 5895 2.169978 GCTAATAAACCAGGACGGAGGT 59.830 50.000 0.00 0.00 40.61 3.85
5579 5896 3.385755 GCTAATAAACCAGGACGGAGGTA 59.614 47.826 0.00 0.00 37.07 3.08
5580 5897 3.900966 AATAAACCAGGACGGAGGTAC 57.099 47.619 0.00 0.00 37.07 3.34
5582 5899 2.610438 AAACCAGGACGGAGGTACTA 57.390 50.000 0.00 0.00 41.55 1.82
5583 5900 1.844687 AACCAGGACGGAGGTACTAC 58.155 55.000 0.00 0.00 41.55 2.73
5602 5919 3.557228 ACTACAGTAGTACTCCCTCCG 57.443 52.381 11.84 0.00 37.23 4.63
5603 5920 2.843113 ACTACAGTAGTACTCCCTCCGT 59.157 50.000 11.84 0.00 37.23 4.69
5604 5921 2.125773 ACAGTAGTACTCCCTCCGTG 57.874 55.000 0.00 0.00 0.00 4.94
5605 5922 0.739561 CAGTAGTACTCCCTCCGTGC 59.260 60.000 0.00 0.00 0.00 5.34
5606 5923 0.395448 AGTAGTACTCCCTCCGTGCC 60.395 60.000 0.00 0.00 0.00 5.01
5607 5924 0.682209 GTAGTACTCCCTCCGTGCCA 60.682 60.000 0.00 0.00 0.00 4.92
5608 5925 0.040058 TAGTACTCCCTCCGTGCCAA 59.960 55.000 0.00 0.00 0.00 4.52
5609 5926 0.834687 AGTACTCCCTCCGTGCCAAA 60.835 55.000 0.00 0.00 0.00 3.28
5610 5927 0.035739 GTACTCCCTCCGTGCCAAAA 59.964 55.000 0.00 0.00 0.00 2.44
5611 5928 0.988832 TACTCCCTCCGTGCCAAAAT 59.011 50.000 0.00 0.00 0.00 1.82
5612 5929 0.988832 ACTCCCTCCGTGCCAAAATA 59.011 50.000 0.00 0.00 0.00 1.40
5613 5930 1.353022 ACTCCCTCCGTGCCAAAATAA 59.647 47.619 0.00 0.00 0.00 1.40
5614 5931 2.017049 CTCCCTCCGTGCCAAAATAAG 58.983 52.381 0.00 0.00 0.00 1.73
5615 5932 0.455815 CCCTCCGTGCCAAAATAAGC 59.544 55.000 0.00 0.00 0.00 3.09
5616 5933 0.098728 CCTCCGTGCCAAAATAAGCG 59.901 55.000 0.00 0.00 0.00 4.68
5617 5934 0.802494 CTCCGTGCCAAAATAAGCGT 59.198 50.000 0.00 0.00 0.00 5.07
5618 5935 0.800012 TCCGTGCCAAAATAAGCGTC 59.200 50.000 0.00 0.00 0.00 5.19
5619 5936 0.179174 CCGTGCCAAAATAAGCGTCC 60.179 55.000 0.00 0.00 0.00 4.79
5620 5937 0.179174 CGTGCCAAAATAAGCGTCCC 60.179 55.000 0.00 0.00 0.00 4.46
5621 5938 0.885196 GTGCCAAAATAAGCGTCCCA 59.115 50.000 0.00 0.00 0.00 4.37
5622 5939 1.271102 GTGCCAAAATAAGCGTCCCAA 59.729 47.619 0.00 0.00 0.00 4.12
5623 5940 1.271102 TGCCAAAATAAGCGTCCCAAC 59.729 47.619 0.00 0.00 0.00 3.77
5624 5941 1.544246 GCCAAAATAAGCGTCCCAACT 59.456 47.619 0.00 0.00 0.00 3.16
5625 5942 2.029380 GCCAAAATAAGCGTCCCAACTT 60.029 45.455 0.00 0.00 0.00 2.66
5626 5943 3.554129 GCCAAAATAAGCGTCCCAACTTT 60.554 43.478 0.00 0.00 0.00 2.66
5627 5944 3.987220 CCAAAATAAGCGTCCCAACTTTG 59.013 43.478 0.00 0.00 0.00 2.77
5628 5945 4.500716 CCAAAATAAGCGTCCCAACTTTGT 60.501 41.667 0.00 0.00 0.00 2.83
5629 5946 5.278561 CCAAAATAAGCGTCCCAACTTTGTA 60.279 40.000 0.00 0.00 0.00 2.41
5630 5947 5.366829 AAATAAGCGTCCCAACTTTGTAC 57.633 39.130 0.00 0.00 0.00 2.90
5634 5951 1.877443 GCGTCCCAACTTTGTACATGT 59.123 47.619 2.69 2.69 0.00 3.21
5682 5999 2.119611 TCGGAACAGAGGCTGGGA 59.880 61.111 0.00 0.00 35.51 4.37
5753 6073 9.965824 TGTAAACGTTATAATACTAACTAGCCC 57.034 33.333 0.00 0.00 30.88 5.19
5794 6114 9.310716 GTTATAACTGGATACTACACTTTGGTC 57.689 37.037 8.41 0.00 37.61 4.02
5795 6115 7.735326 ATAACTGGATACTACACTTTGGTCT 57.265 36.000 0.00 0.00 37.61 3.85
5796 6116 5.407407 ACTGGATACTACACTTTGGTCTG 57.593 43.478 0.00 0.00 37.61 3.51
5797 6117 4.184629 CTGGATACTACACTTTGGTCTGC 58.815 47.826 0.00 0.00 37.61 4.26
5798 6118 3.055385 TGGATACTACACTTTGGTCTGCC 60.055 47.826 0.00 0.00 37.61 4.85
5799 6119 3.197983 GGATACTACACTTTGGTCTGCCT 59.802 47.826 0.00 0.00 35.27 4.75
5800 6120 2.550830 ACTACACTTTGGTCTGCCTG 57.449 50.000 0.00 0.00 35.27 4.85
5801 6121 1.160137 CTACACTTTGGTCTGCCTGC 58.840 55.000 0.00 0.00 35.27 4.85
5802 6122 0.250727 TACACTTTGGTCTGCCTGCC 60.251 55.000 0.00 0.00 35.27 4.85
5803 6123 1.529010 CACTTTGGTCTGCCTGCCA 60.529 57.895 0.00 0.00 35.27 4.92
5804 6124 1.529244 ACTTTGGTCTGCCTGCCAC 60.529 57.895 0.00 0.00 34.02 5.01
5805 6125 1.529010 CTTTGGTCTGCCTGCCACA 60.529 57.895 0.00 0.00 34.02 4.17
5806 6126 1.076412 TTTGGTCTGCCTGCCACAA 60.076 52.632 0.00 0.00 34.02 3.33
5807 6127 1.391157 TTTGGTCTGCCTGCCACAAC 61.391 55.000 0.00 0.00 34.02 3.32
5808 6128 2.113986 GGTCTGCCTGCCACAACT 59.886 61.111 0.00 0.00 0.00 3.16
5809 6129 1.968540 GGTCTGCCTGCCACAACTC 60.969 63.158 0.00 0.00 0.00 3.01
5810 6130 1.227943 GTCTGCCTGCCACAACTCA 60.228 57.895 0.00 0.00 0.00 3.41
5811 6131 1.227943 TCTGCCTGCCACAACTCAC 60.228 57.895 0.00 0.00 0.00 3.51
5812 6132 1.526686 CTGCCTGCCACAACTCACA 60.527 57.895 0.00 0.00 0.00 3.58
5813 6133 1.077140 TGCCTGCCACAACTCACAA 60.077 52.632 0.00 0.00 0.00 3.33
5814 6134 1.360192 GCCTGCCACAACTCACAAC 59.640 57.895 0.00 0.00 0.00 3.32
5815 6135 1.103398 GCCTGCCACAACTCACAACT 61.103 55.000 0.00 0.00 0.00 3.16
5816 6136 0.664761 CCTGCCACAACTCACAACTG 59.335 55.000 0.00 0.00 0.00 3.16
5817 6137 0.029834 CTGCCACAACTCACAACTGC 59.970 55.000 0.00 0.00 0.00 4.40
5818 6138 0.679321 TGCCACAACTCACAACTGCA 60.679 50.000 0.00 0.00 0.00 4.41
5819 6139 0.029834 GCCACAACTCACAACTGCAG 59.970 55.000 13.48 13.48 0.00 4.41
5820 6140 1.382522 CCACAACTCACAACTGCAGT 58.617 50.000 15.25 15.25 0.00 4.40
5821 6141 1.745087 CCACAACTCACAACTGCAGTT 59.255 47.619 26.36 26.36 39.12 3.16
5906 6229 8.660373 CCATAACTAACTCAAGCTCTTAAAGTG 58.340 37.037 0.00 0.00 0.00 3.16
5923 6246 3.198409 AGTGTGTGCATTCTGTCTGAA 57.802 42.857 0.00 0.00 39.24 3.02
5925 6248 4.139786 AGTGTGTGCATTCTGTCTGAAAT 58.860 39.130 0.00 0.00 38.29 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.149987 ACGGCAAATGCATGCTTTTG 58.850 45.000 36.43 36.43 45.68 2.44
11 12 2.336667 GTACGGCAAATGCATGCTTTT 58.663 42.857 22.07 22.07 45.68 2.27
17 18 1.134818 TCTCTCGTACGGCAAATGCAT 60.135 47.619 16.52 0.00 44.36 3.96
21 22 2.223829 CCTCATCTCTCGTACGGCAAAT 60.224 50.000 16.52 1.96 0.00 2.32
52 53 3.344515 GGCCGGAAAGAGTTTCTGTTAT 58.655 45.455 5.05 0.00 43.06 1.89
193 194 4.760047 CCGTCAGTGCCTTCCCGG 62.760 72.222 0.00 0.00 0.00 5.73
199 200 2.885861 GTCGATCCGTCAGTGCCT 59.114 61.111 0.00 0.00 0.00 4.75
277 282 1.608696 GGCGGGGTATTGGTTGGTA 59.391 57.895 0.00 0.00 0.00 3.25
365 374 4.899239 CTGAGGGACCGATGCGCC 62.899 72.222 4.18 0.00 0.00 6.53
367 376 3.781770 GAGCTGAGGGACCGATGCG 62.782 68.421 0.00 0.00 0.00 4.73
388 402 3.822192 CCGATCGTCGAGTGCCCA 61.822 66.667 15.09 0.00 43.74 5.36
426 440 4.629523 GGAACGCCCGTGGTCCAA 62.630 66.667 7.47 0.00 0.00 3.53
452 466 2.279502 TACATGCTCCTGCCGACGAC 62.280 60.000 0.00 0.00 38.71 4.34
728 749 7.671398 AGAAATAAATCAGCTTTTCCCTCTGAA 59.329 33.333 3.29 0.00 39.88 3.02
730 751 7.401955 AGAAATAAATCAGCTTTTCCCTCTG 57.598 36.000 3.29 0.00 0.00 3.35
731 752 7.671398 TCAAGAAATAAATCAGCTTTTCCCTCT 59.329 33.333 3.29 0.00 0.00 3.69
732 753 7.830739 TCAAGAAATAAATCAGCTTTTCCCTC 58.169 34.615 3.29 0.00 0.00 4.30
733 754 7.671398 TCTCAAGAAATAAATCAGCTTTTCCCT 59.329 33.333 3.29 0.00 0.00 4.20
735 756 8.734386 TCTCTCAAGAAATAAATCAGCTTTTCC 58.266 33.333 3.29 0.00 0.00 3.13
825 850 2.086869 CTGTCACATGGAAAGGCGAAT 58.913 47.619 0.00 0.00 0.00 3.34
862 887 1.067495 GCAGCTCGCCCCTACTTATAG 60.067 57.143 0.00 0.00 32.94 1.31
916 941 3.343788 CTCGGACGGAGGACTGTGC 62.344 68.421 2.13 0.00 39.22 4.57
917 942 2.878429 CTCGGACGGAGGACTGTG 59.122 66.667 2.13 0.00 39.22 3.66
918 943 3.063084 GCTCGGACGGAGGACTGT 61.063 66.667 11.57 0.00 43.36 3.55
981 1018 0.322456 TACACAGTGGATGCTTGCCC 60.322 55.000 5.31 0.00 0.00 5.36
1089 1130 2.203788 TTCTCCTCTGGGCCGTGT 60.204 61.111 0.00 0.00 0.00 4.49
1098 1139 4.761058 TCCGCCGCCTTCTCCTCT 62.761 66.667 0.00 0.00 0.00 3.69
1170 1211 3.511540 ACCTGATGTTCATGACGAAGAGA 59.488 43.478 0.00 0.00 33.09 3.10
1224 1268 1.302192 GTACTTGGGCGCAAGGTGA 60.302 57.895 37.21 23.75 36.55 4.02
1252 1297 0.827925 TGAGGAACACGAGCACTCCT 60.828 55.000 0.00 0.00 41.11 3.69
1465 1732 8.579850 AGGTTTCTTCTTCATTGCATACATAA 57.420 30.769 0.00 0.00 0.00 1.90
1589 1860 7.577303 AGAAGCTCTATCCATGGTGAAAATTA 58.423 34.615 12.58 0.00 0.00 1.40
1601 1872 9.685276 TGAAAATTAATTGAGAAGCTCTATCCA 57.315 29.630 0.39 0.00 0.00 3.41
1639 1910 5.079643 TCCCTTGTACGACTACCTAAAGTT 58.920 41.667 0.00 0.00 0.00 2.66
1641 1912 5.649782 TTCCCTTGTACGACTACCTAAAG 57.350 43.478 0.00 0.00 0.00 1.85
1648 1919 3.119029 CCGGAAATTCCCTTGTACGACTA 60.119 47.826 6.42 0.00 31.13 2.59
1748 2019 3.865446 TCGATACTGTAGACCGAAGTCA 58.135 45.455 7.10 0.00 46.15 3.41
1858 2129 0.253327 AGAAGAAGGTGGGCGGAATC 59.747 55.000 0.00 0.00 0.00 2.52
1862 2133 0.674895 CAGAAGAAGAAGGTGGGCGG 60.675 60.000 0.00 0.00 0.00 6.13
1986 2258 8.017946 TGCACAAAAGAACAAATAAAAACCAAC 58.982 29.630 0.00 0.00 0.00 3.77
1988 2260 7.672983 TGCACAAAAGAACAAATAAAAACCA 57.327 28.000 0.00 0.00 0.00 3.67
2067 2339 4.881273 TGTGCCTAGCTAACCAATTGTATG 59.119 41.667 4.43 0.00 0.00 2.39
2083 2355 3.054875 AGAATGAACTCAGCATGTGCCTA 60.055 43.478 0.57 0.00 43.38 3.93
2138 2410 1.855513 TTCGGCGAGAAAAGAAACGA 58.144 45.000 10.46 0.00 35.61 3.85
2184 2456 5.047590 GGGGAACATACTCAAAACGGAAAAT 60.048 40.000 0.00 0.00 0.00 1.82
2434 2714 6.128200 CGAACCTGATCATTGAGAAATTGTGA 60.128 38.462 0.00 0.00 0.00 3.58
2443 2723 2.093500 TCCACCGAACCTGATCATTGAG 60.093 50.000 0.00 0.00 0.00 3.02
2586 2866 8.870075 AGGTCTTTGCTGTTATTTTCTTCTAT 57.130 30.769 0.00 0.00 0.00 1.98
2735 3016 6.301486 TCCACATAGGGATTCATGAAGAATG 58.699 40.000 14.54 13.45 40.84 2.67
2764 3045 3.930848 GGAGTATCACCACCTGTAAAACG 59.069 47.826 0.00 0.00 36.25 3.60
2784 3065 2.076100 CAAGAATTAGCGCACACTGGA 58.924 47.619 11.47 0.00 0.00 3.86
2828 3109 1.180029 CTTGCACCCTTGATTGGAGG 58.820 55.000 0.00 0.00 0.00 4.30
2883 3164 1.982073 GCCCGAGAAATGAGCCAACG 61.982 60.000 0.00 0.00 0.00 4.10
3048 3329 6.927936 CCTGGAATAGTGTGATGTAGATGAAG 59.072 42.308 0.00 0.00 0.00 3.02
3265 3546 7.812669 AGTAACGCTTCAAATATTTTTCCTTGG 59.187 33.333 0.00 0.00 0.00 3.61
3470 3756 5.473066 AAAAGATGGAATTGGGAGTTGTG 57.527 39.130 0.00 0.00 0.00 3.33
3480 3766 7.177392 CAGGTACCTGAAGAAAAAGATGGAATT 59.823 37.037 34.54 0.00 46.30 2.17
3521 3807 0.249489 GCTGGACGAGCCGACATATT 60.249 55.000 0.00 0.00 42.54 1.28
3721 4013 1.664649 CGCCAGAGTGACGCAGAAA 60.665 57.895 0.00 0.00 0.00 2.52
3817 4109 0.179073 CCAATCCATCGGCGAGAAGT 60.179 55.000 17.22 0.00 0.00 3.01
3898 4193 5.045869 ACTCTCTAGTCTCTACTGAAGCTGT 60.046 44.000 0.00 0.00 36.36 4.40
3925 4224 1.525995 CAACACGCCCCAGTTCAGT 60.526 57.895 0.00 0.00 0.00 3.41
3994 4293 0.109597 GCGGCAATCACCTTCTTGTG 60.110 55.000 0.00 0.00 37.59 3.33
3995 4294 1.577328 CGCGGCAATCACCTTCTTGT 61.577 55.000 0.00 0.00 0.00 3.16
4042 4341 2.160417 GGAGAAGTGGCAAGAATCAACG 59.840 50.000 0.00 0.00 0.00 4.10
4071 4370 0.475044 TTTTGCGTGTTCTAGGGGGT 59.525 50.000 0.00 0.00 0.00 4.95
4097 4396 5.003804 GCCTCTTCTCAGTGAACCAAAATA 58.996 41.667 0.00 0.00 0.00 1.40
4109 4408 4.202101 ACATCGTCATTAGCCTCTTCTCAG 60.202 45.833 0.00 0.00 0.00 3.35
4126 4428 0.396435 TGCAAGGTGAAGGACATCGT 59.604 50.000 0.00 0.00 34.34 3.73
4155 4458 1.264749 TGAGACCCATCCCCAGAACG 61.265 60.000 0.00 0.00 0.00 3.95
4231 4534 1.135373 GTGGATGACGTCGATCACAGT 60.135 52.381 21.72 0.00 0.00 3.55
4325 4629 6.389830 ACAGAGCTATATTCAGTGTCTGAG 57.610 41.667 9.38 0.00 41.75 3.35
4328 4632 6.344500 CCAAACAGAGCTATATTCAGTGTCT 58.656 40.000 0.00 0.00 0.00 3.41
4345 4649 2.226437 CGAACTGAACATCCCCAAACAG 59.774 50.000 0.00 0.00 0.00 3.16
4476 4782 7.802251 CAGAGCTAAAATATTTGATGCTGCTAC 59.198 37.037 20.28 10.67 0.00 3.58
4477 4783 7.716560 TCAGAGCTAAAATATTTGATGCTGCTA 59.283 33.333 20.28 8.27 0.00 3.49
4703 5009 1.693062 CTGATGAGGTGATGAGGAGGG 59.307 57.143 0.00 0.00 0.00 4.30
4708 5014 3.320541 GGAGGTACTGATGAGGTGATGAG 59.679 52.174 0.00 0.00 41.55 2.90
4712 5018 2.919772 TGGAGGTACTGATGAGGTGA 57.080 50.000 0.00 0.00 41.55 4.02
4713 5019 4.163078 AGAAATGGAGGTACTGATGAGGTG 59.837 45.833 0.00 0.00 41.55 4.00
4714 5020 4.366267 AGAAATGGAGGTACTGATGAGGT 58.634 43.478 0.00 0.00 41.55 3.85
4715 5021 5.363939 GAAGAAATGGAGGTACTGATGAGG 58.636 45.833 0.00 0.00 41.55 3.86
4716 5022 5.046529 CGAAGAAATGGAGGTACTGATGAG 58.953 45.833 0.00 0.00 41.55 2.90
4749 5055 2.651382 AAACGGCACTAGAAAAGGGT 57.349 45.000 0.00 0.00 0.00 4.34
4776 5082 8.991026 CAATTTCAGCAGGATTTGAAAACATTA 58.009 29.630 4.06 0.00 43.95 1.90
4812 5119 7.669427 ACACATATTTTGCAAGGATTTCAAGA 58.331 30.769 0.00 0.00 0.00 3.02
4813 5120 7.894376 ACACATATTTTGCAAGGATTTCAAG 57.106 32.000 0.00 0.00 0.00 3.02
4814 5121 7.930325 TGAACACATATTTTGCAAGGATTTCAA 59.070 29.630 0.00 0.00 0.00 2.69
4854 5163 2.029918 GTCACAAAACCTTGATGAGCCC 60.030 50.000 0.00 0.00 36.33 5.19
4906 5215 2.677228 CGGAGGAAAGCCCATGGT 59.323 61.111 11.73 0.00 37.41 3.55
4992 5301 5.929697 ATTACATGGAACGAGCATATGTG 57.070 39.130 4.29 0.00 34.22 3.21
4993 5302 7.441836 TCTAATTACATGGAACGAGCATATGT 58.558 34.615 4.29 0.00 36.15 2.29
4998 5307 7.985184 ACTTATTCTAATTACATGGAACGAGCA 59.015 33.333 0.00 0.00 0.00 4.26
5071 5380 2.262211 CGAAGCAAAGCAATAAAGCCC 58.738 47.619 0.00 0.00 34.23 5.19
5143 5454 0.883833 GGCACAGAACAAGGACATGG 59.116 55.000 0.00 0.00 0.00 3.66
5172 5489 5.240713 CAGAGCACTGGTCCAATTAAATC 57.759 43.478 2.82 0.00 40.14 2.17
5218 5535 6.726490 TGACATAACTAGGGATAGACCAAC 57.274 41.667 0.00 0.00 41.20 3.77
5246 5563 7.704578 TCGATATACAAGGATTAAGAGAGGG 57.295 40.000 0.00 0.00 0.00 4.30
5264 5581 3.493334 TGGTCTCGGGTACATTCGATAT 58.507 45.455 0.00 0.00 34.77 1.63
5265 5582 2.934887 TGGTCTCGGGTACATTCGATA 58.065 47.619 0.00 0.00 34.77 2.92
5296 5613 4.714632 TCGGAAACAAAACCTCATCTTCT 58.285 39.130 0.00 0.00 0.00 2.85
5315 5632 6.428385 AGACAATTTTATTTCTCAGCTCGG 57.572 37.500 0.00 0.00 0.00 4.63
5353 5670 4.162131 AGCTTGGAGGTTTGTTTGACAATT 59.838 37.500 0.00 0.00 38.00 2.32
5388 5705 7.420913 GGGACCAATAAACCTGGACATAGATAA 60.421 40.741 0.00 0.00 37.40 1.75
5390 5707 5.163088 GGGACCAATAAACCTGGACATAGAT 60.163 44.000 0.00 0.00 37.40 1.98
5391 5708 4.165372 GGGACCAATAAACCTGGACATAGA 59.835 45.833 0.00 0.00 37.40 1.98
5394 5711 3.382083 GGGACCAATAAACCTGGACAT 57.618 47.619 0.00 0.00 37.40 3.06
5411 5728 3.773418 TGACACAAAATACGAAGGGGA 57.227 42.857 0.00 0.00 0.00 4.81
5414 5731 8.346476 TCAAAATTTGACACAAAATACGAAGG 57.654 30.769 4.03 0.00 34.08 3.46
5525 5842 9.522804 TCGTATTTTGTGCTAAATTTTGACTTT 57.477 25.926 3.69 0.00 0.00 2.66
5526 5843 9.522804 TTCGTATTTTGTGCTAAATTTTGACTT 57.477 25.926 3.69 0.00 0.00 3.01
5527 5844 9.180678 CTTCGTATTTTGTGCTAAATTTTGACT 57.819 29.630 3.69 0.00 0.00 3.41
5528 5845 8.424731 CCTTCGTATTTTGTGCTAAATTTTGAC 58.575 33.333 3.69 0.67 0.00 3.18
5529 5846 7.596995 CCCTTCGTATTTTGTGCTAAATTTTGA 59.403 33.333 3.69 0.00 0.00 2.69
5530 5847 7.148656 CCCCTTCGTATTTTGTGCTAAATTTTG 60.149 37.037 0.00 0.00 0.00 2.44
5531 5848 6.871492 CCCCTTCGTATTTTGTGCTAAATTTT 59.129 34.615 0.00 0.00 0.00 1.82
5532 5849 6.394809 CCCCTTCGTATTTTGTGCTAAATTT 58.605 36.000 0.00 0.00 0.00 1.82
5533 5850 5.105513 CCCCCTTCGTATTTTGTGCTAAATT 60.106 40.000 0.00 0.00 0.00 1.82
5534 5851 4.401202 CCCCCTTCGTATTTTGTGCTAAAT 59.599 41.667 0.00 0.00 0.00 1.40
5535 5852 3.759618 CCCCCTTCGTATTTTGTGCTAAA 59.240 43.478 0.00 0.00 0.00 1.85
5536 5853 3.349022 CCCCCTTCGTATTTTGTGCTAA 58.651 45.455 0.00 0.00 0.00 3.09
5537 5854 2.942306 GCCCCCTTCGTATTTTGTGCTA 60.942 50.000 0.00 0.00 0.00 3.49
5538 5855 1.834188 CCCCCTTCGTATTTTGTGCT 58.166 50.000 0.00 0.00 0.00 4.40
5539 5856 0.172578 GCCCCCTTCGTATTTTGTGC 59.827 55.000 0.00 0.00 0.00 4.57
5540 5857 1.834188 AGCCCCCTTCGTATTTTGTG 58.166 50.000 0.00 0.00 0.00 3.33
5541 5858 3.724732 TTAGCCCCCTTCGTATTTTGT 57.275 42.857 0.00 0.00 0.00 2.83
5542 5859 6.460537 GGTTTATTAGCCCCCTTCGTATTTTG 60.461 42.308 0.00 0.00 0.00 2.44
5543 5860 5.595542 GGTTTATTAGCCCCCTTCGTATTTT 59.404 40.000 0.00 0.00 0.00 1.82
5544 5861 5.135383 GGTTTATTAGCCCCCTTCGTATTT 58.865 41.667 0.00 0.00 0.00 1.40
5545 5862 4.166531 TGGTTTATTAGCCCCCTTCGTATT 59.833 41.667 0.00 0.00 0.00 1.89
5546 5863 3.717913 TGGTTTATTAGCCCCCTTCGTAT 59.282 43.478 0.00 0.00 0.00 3.06
5547 5864 3.113824 TGGTTTATTAGCCCCCTTCGTA 58.886 45.455 0.00 0.00 0.00 3.43
5548 5865 1.917568 TGGTTTATTAGCCCCCTTCGT 59.082 47.619 0.00 0.00 0.00 3.85
5549 5866 2.572290 CTGGTTTATTAGCCCCCTTCG 58.428 52.381 0.00 0.00 0.00 3.79
5550 5867 2.512476 TCCTGGTTTATTAGCCCCCTTC 59.488 50.000 0.00 0.00 0.00 3.46
5551 5868 2.243994 GTCCTGGTTTATTAGCCCCCTT 59.756 50.000 0.00 0.00 0.00 3.95
5552 5869 1.850998 GTCCTGGTTTATTAGCCCCCT 59.149 52.381 0.00 0.00 0.00 4.79
5553 5870 1.476291 CGTCCTGGTTTATTAGCCCCC 60.476 57.143 0.00 0.00 0.00 5.40
5554 5871 1.476291 CCGTCCTGGTTTATTAGCCCC 60.476 57.143 0.00 0.00 0.00 5.80
5555 5872 1.487558 TCCGTCCTGGTTTATTAGCCC 59.512 52.381 0.00 0.00 39.52 5.19
5556 5873 2.484947 CCTCCGTCCTGGTTTATTAGCC 60.485 54.545 0.00 0.00 39.52 3.93
5557 5874 2.169978 ACCTCCGTCCTGGTTTATTAGC 59.830 50.000 0.00 0.00 39.52 3.09
5558 5875 4.648307 AGTACCTCCGTCCTGGTTTATTAG 59.352 45.833 0.00 0.00 39.52 1.73
5559 5876 4.613437 AGTACCTCCGTCCTGGTTTATTA 58.387 43.478 0.00 0.00 39.52 0.98
5560 5877 3.447950 AGTACCTCCGTCCTGGTTTATT 58.552 45.455 0.00 0.00 39.52 1.40
5561 5878 3.111741 AGTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
5562 5879 2.610438 AGTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
5563 5880 2.174360 GTAGTACCTCCGTCCTGGTTT 58.826 52.381 0.00 0.00 39.52 3.27
5564 5881 1.357079 AGTAGTACCTCCGTCCTGGTT 59.643 52.381 0.00 0.00 39.52 3.67
5565 5882 0.998145 AGTAGTACCTCCGTCCTGGT 59.002 55.000 0.00 0.00 39.52 4.00
5566 5883 2.092753 TGTAGTAGTACCTCCGTCCTGG 60.093 54.545 5.26 0.00 40.09 4.45
5567 5884 3.204526 CTGTAGTAGTACCTCCGTCCTG 58.795 54.545 5.26 0.00 0.00 3.86
5568 5885 2.843113 ACTGTAGTAGTACCTCCGTCCT 59.157 50.000 5.26 0.00 38.04 3.85
5569 5886 3.274095 ACTGTAGTAGTACCTCCGTCC 57.726 52.381 5.26 0.00 38.04 4.79
5581 5898 4.033709 ACGGAGGGAGTACTACTGTAGTA 58.966 47.826 20.74 20.74 40.14 1.82
5582 5899 2.843113 ACGGAGGGAGTACTACTGTAGT 59.157 50.000 22.72 22.72 42.68 2.73
5583 5900 3.204526 CACGGAGGGAGTACTACTGTAG 58.795 54.545 13.13 13.13 0.00 2.74
5598 5915 0.802494 ACGCTTATTTTGGCACGGAG 59.198 50.000 0.00 0.00 0.00 4.63
5599 5916 0.800012 GACGCTTATTTTGGCACGGA 59.200 50.000 0.00 0.00 0.00 4.69
5601 5918 0.179174 GGGACGCTTATTTTGGCACG 60.179 55.000 0.00 0.00 0.00 5.34
5602 5919 0.885196 TGGGACGCTTATTTTGGCAC 59.115 50.000 0.00 0.00 0.00 5.01
5603 5920 1.271102 GTTGGGACGCTTATTTTGGCA 59.729 47.619 0.00 0.00 0.00 4.92
5604 5921 1.544246 AGTTGGGACGCTTATTTTGGC 59.456 47.619 0.00 0.00 0.00 4.52
5605 5922 3.934457 AAGTTGGGACGCTTATTTTGG 57.066 42.857 0.00 0.00 0.00 3.28
5606 5923 4.616953 ACAAAGTTGGGACGCTTATTTTG 58.383 39.130 0.00 9.65 0.00 2.44
5607 5924 4.929819 ACAAAGTTGGGACGCTTATTTT 57.070 36.364 0.00 0.00 0.00 1.82
5608 5925 4.822896 TGTACAAAGTTGGGACGCTTATTT 59.177 37.500 0.00 0.00 0.00 1.40
5609 5926 4.391155 TGTACAAAGTTGGGACGCTTATT 58.609 39.130 0.00 0.00 0.00 1.40
5610 5927 4.010667 TGTACAAAGTTGGGACGCTTAT 57.989 40.909 0.00 0.00 0.00 1.73
5611 5928 3.472283 TGTACAAAGTTGGGACGCTTA 57.528 42.857 0.00 0.00 0.00 3.09
5612 5929 2.335316 TGTACAAAGTTGGGACGCTT 57.665 45.000 0.00 0.00 0.00 4.68
5613 5930 2.151202 CATGTACAAAGTTGGGACGCT 58.849 47.619 0.00 0.00 0.00 5.07
5614 5931 1.877443 ACATGTACAAAGTTGGGACGC 59.123 47.619 0.00 0.00 0.00 5.19
5615 5932 2.350388 GCACATGTACAAAGTTGGGACG 60.350 50.000 0.00 0.00 0.00 4.79
5616 5933 2.030274 GGCACATGTACAAAGTTGGGAC 60.030 50.000 0.00 0.00 0.00 4.46
5617 5934 2.235016 GGCACATGTACAAAGTTGGGA 58.765 47.619 0.00 0.00 0.00 4.37
5618 5935 1.959985 TGGCACATGTACAAAGTTGGG 59.040 47.619 0.00 0.00 0.00 4.12
5619 5936 2.622942 AGTGGCACATGTACAAAGTTGG 59.377 45.455 21.41 0.00 44.52 3.77
5620 5937 3.988379 AGTGGCACATGTACAAAGTTG 57.012 42.857 21.41 0.00 44.52 3.16
5621 5938 4.400884 TGAAAGTGGCACATGTACAAAGTT 59.599 37.500 21.41 0.00 44.52 2.66
5622 5939 3.951037 TGAAAGTGGCACATGTACAAAGT 59.049 39.130 21.41 0.00 44.52 2.66
5623 5940 4.566545 TGAAAGTGGCACATGTACAAAG 57.433 40.909 21.41 0.00 44.52 2.77
5624 5941 4.202101 CCTTGAAAGTGGCACATGTACAAA 60.202 41.667 21.41 3.92 44.52 2.83
5625 5942 3.317711 CCTTGAAAGTGGCACATGTACAA 59.682 43.478 21.41 15.65 44.52 2.41
5626 5943 2.884012 CCTTGAAAGTGGCACATGTACA 59.116 45.455 21.41 9.36 44.52 2.90
5627 5944 3.559238 CCTTGAAAGTGGCACATGTAC 57.441 47.619 21.41 6.86 44.52 2.90
5682 5999 0.466922 GGTAGGCAATGCATCCAGCT 60.467 55.000 7.79 0.00 45.94 4.24
5794 6114 1.102809 TTGTGAGTTGTGGCAGGCAG 61.103 55.000 0.00 0.00 0.00 4.85
5795 6115 1.077140 TTGTGAGTTGTGGCAGGCA 60.077 52.632 0.00 0.00 0.00 4.75
5796 6116 1.103398 AGTTGTGAGTTGTGGCAGGC 61.103 55.000 0.00 0.00 0.00 4.85
5797 6117 0.664761 CAGTTGTGAGTTGTGGCAGG 59.335 55.000 0.00 0.00 0.00 4.85
5798 6118 0.029834 GCAGTTGTGAGTTGTGGCAG 59.970 55.000 0.00 0.00 0.00 4.85
5799 6119 0.679321 TGCAGTTGTGAGTTGTGGCA 60.679 50.000 0.00 0.00 0.00 4.92
5800 6120 0.029834 CTGCAGTTGTGAGTTGTGGC 59.970 55.000 5.25 0.00 0.00 5.01
5801 6121 1.382522 ACTGCAGTTGTGAGTTGTGG 58.617 50.000 15.25 0.00 0.00 4.17
5816 6136 3.865825 GGCAGACCAAAGTGCAACTGC 62.866 57.143 0.00 0.00 41.36 4.40
5817 6137 0.031178 GGCAGACCAAAGTGCAACTG 59.969 55.000 0.00 0.00 41.36 3.16
5818 6138 0.106519 AGGCAGACCAAAGTGCAACT 60.107 50.000 0.00 0.00 46.20 3.16
5819 6139 0.031178 CAGGCAGACCAAAGTGCAAC 59.969 55.000 0.00 0.00 41.75 4.17
5820 6140 1.737355 GCAGGCAGACCAAAGTGCAA 61.737 55.000 0.00 0.00 41.75 4.08
5821 6141 2.195567 GCAGGCAGACCAAAGTGCA 61.196 57.895 0.00 0.00 41.75 4.57
5822 6142 2.647297 GCAGGCAGACCAAAGTGC 59.353 61.111 0.00 0.00 39.06 4.40
5823 6143 1.529010 TGGCAGGCAGACCAAAGTG 60.529 57.895 0.00 0.00 39.06 3.16
5824 6144 1.529244 GTGGCAGGCAGACCAAAGT 60.529 57.895 0.00 0.00 37.79 2.66
5825 6145 1.108727 TTGTGGCAGGCAGACCAAAG 61.109 55.000 0.00 0.00 37.79 2.77
5826 6146 1.076412 TTGTGGCAGGCAGACCAAA 60.076 52.632 0.00 0.00 37.79 3.28
5827 6147 1.827789 GTTGTGGCAGGCAGACCAA 60.828 57.895 0.00 0.00 37.79 3.67
5828 6148 2.203337 GTTGTGGCAGGCAGACCA 60.203 61.111 0.00 0.00 39.06 4.02
5829 6149 1.968540 GAGTTGTGGCAGGCAGACC 60.969 63.158 0.00 0.00 0.00 3.85
5830 6150 1.227943 TGAGTTGTGGCAGGCAGAC 60.228 57.895 0.00 0.00 0.00 3.51
5831 6151 1.227943 GTGAGTTGTGGCAGGCAGA 60.228 57.895 0.00 0.00 0.00 4.26
5906 6229 3.254166 ACCATTTCAGACAGAATGCACAC 59.746 43.478 0.00 0.00 42.53 3.82


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

AutoCloner maintained by Alex Coulton.