Multiple sequence alignment - TraesCS6B01G054700

Loading Multiple Alignment...

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 TraesCS6B01G054700 chr6B 100.000 4170 0 0 1 4170 35411616 35415785 0.000000e+00 7701.0
1 TraesCS6B01G054700 chr6B 84.694 98 13 1 218 315 32820745 32820650 3.430000e-16 97.1
2 TraesCS6B01G054700 chr6B 94.118 51 3 0 2788 2838 123913543 123913593 1.240000e-10 78.7
3 TraesCS6B01G054700 chr6D 92.475 2485 149 22 319 2770 20550031 20552510 0.000000e+00 3518.0
4 TraesCS6B01G054700 chr6D 91.049 1497 110 11 951 2426 20548521 20550014 0.000000e+00 2001.0
5 TraesCS6B01G054700 chr6D 81.976 1842 229 40 674 2475 5254459 5252681 0.000000e+00 1467.0
6 TraesCS6B01G054700 chr6D 93.360 738 31 6 2766 3495 20552668 20553395 0.000000e+00 1075.0
7 TraesCS6B01G054700 chr6D 92.664 259 16 2 3551 3806 20553393 20553651 1.830000e-98 370.0
8 TraesCS6B01G054700 chr6D 85.714 329 28 10 1 314 20547798 20548122 3.110000e-86 329.0
9 TraesCS6B01G054700 chr6D 88.060 268 24 5 3839 4101 20553750 20554014 1.130000e-80 311.0
10 TraesCS6B01G054700 chr6D 92.308 52 4 0 2788 2839 47636045 47635994 1.610000e-09 75.0
11 TraesCS6B01G054700 chr6D 97.297 37 1 0 862 898 20548455 20548491 3.480000e-06 63.9
12 TraesCS6B01G054700 chr6D 100.000 32 0 0 3815 3846 68580742 68580773 4.500000e-05 60.2
13 TraesCS6B01G054700 chr6A 90.958 2035 137 28 775 2770 20505998 20508024 0.000000e+00 2695.0
14 TraesCS6B01G054700 chr6A 80.851 376 30 20 356 702 20505482 20505844 1.490000e-64 257.0
15 TraesCS6B01G054700 chr7D 84.667 300 27 10 2 300 64379911 64380192 8.830000e-72 281.0
16 TraesCS6B01G054700 chr2B 93.151 73 5 0 4098 4170 494753015 494752943 1.590000e-19 108.0
17 TraesCS6B01G054700 chr2B 89.041 73 8 0 4098 4170 543302157 543302085 1.600000e-14 91.6
18 TraesCS6B01G054700 chr3B 93.750 64 4 0 4107 4170 636446404 636446341 3.430000e-16 97.1
19 TraesCS6B01G054700 chr7B 75.926 216 21 19 99 289 736087303 736087512 9.610000e-12 82.4
20 TraesCS6B01G054700 chr5A 95.455 44 0 2 4098 4140 184070597 184070555 7.480000e-08 69.4
21 TraesCS6B01G054700 chr5A 97.143 35 1 0 3815 3849 291097666 291097700 4.500000e-05 60.2
22 TraesCS6B01G054700 chr5A 97.143 35 1 0 3815 3849 317912930 317912896 4.500000e-05 60.2
23 TraesCS6B01G054700 chr2A 97.297 37 1 0 3813 3849 724365799 724365835 3.480000e-06 63.9
24 TraesCS6B01G054700 chr2A 97.297 37 0 1 3815 3850 68506358 68506322 1.250000e-05 62.1
25 TraesCS6B01G054700 chr2A 97.143 35 1 0 3815 3849 125039557 125039591 4.500000e-05 60.2
26 TraesCS6B01G054700 chr1A 95.000 40 2 0 4097 4136 6018547 6018586 3.480000e-06 63.9
27 TraesCS6B01G054700 chr1A 100.000 32 0 0 3815 3846 493101972 493101941 4.500000e-05 60.2
28 TraesCS6B01G054700 chr2D 97.297 37 0 1 3814 3849 649876934 649876898 1.250000e-05 62.1
29 TraesCS6B01G054700 chr7A 97.222 36 0 1 3815 3849 93625158 93625123 4.500000e-05 60.2
30 TraesCS6B01G054700 chr3A 100.000 29 0 0 3149 3177 702520003 702520031 2.000000e-03 54.7


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 TraesCS6B01G054700 chr6B 35411616 35415785 4169 False 7701.000000 7701 100.0000 1 4170 1 chr6B.!!$F1 4169
1 TraesCS6B01G054700 chr6D 5252681 5254459 1778 True 1467.000000 1467 81.9760 674 2475 1 chr6D.!!$R1 1801
2 TraesCS6B01G054700 chr6D 20547798 20554014 6216 False 1095.414286 3518 91.5170 1 4101 7 chr6D.!!$F2 4100
3 TraesCS6B01G054700 chr6A 20505482 20508024 2542 False 1476.000000 2695 85.9045 356 2770 2 chr6A.!!$F1 2414

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
20 21 0.107214 CCTCCGCAGTCTCTCTCTCT 60.107 60.0 0.00 0.0 0.00 3.10 F
179 180 0.247736 TCTCTTCTTTCCCAGCTCGC 59.752 55.0 0.00 0.0 0.00 5.03 F
1450 3589 0.951040 GTTGCCGGAGAACCTGTCTG 60.951 60.0 5.05 0.0 36.41 3.51 F
2157 4296 0.106819 ATGTCATCCTCTTGGCAGGC 60.107 55.0 0.00 0.0 34.15 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 3474 0.036010 CGAGGAGCTTCCAATGGTGT 60.036 55.0 0.00 0.0 39.61 4.16 R
1602 3741 0.038251 CTGCGCTCACAACAGAGGTA 60.038 55.0 9.73 0.0 36.15 3.08 R
3139 5444 0.615331 TGATCCAAGACTGAGGTGGC 59.385 55.0 0.00 0.0 32.10 5.01 R
3790 6104 0.816421 ACACGCGCCAAGTTAACCTT 60.816 50.0 5.73 0.0 0.00 3.50 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
18 19 1.077068 CCCTCCGCAGTCTCTCTCT 60.077 63.158 0.00 0.00 0.00 3.10
19 20 1.101049 CCCTCCGCAGTCTCTCTCTC 61.101 65.000 0.00 0.00 0.00 3.20
20 21 0.107214 CCTCCGCAGTCTCTCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
21 22 1.299541 CTCCGCAGTCTCTCTCTCTC 58.700 60.000 0.00 0.00 0.00 3.20
42 43 1.722034 ACTGCAGTGAGAGGAAGGAA 58.278 50.000 20.97 0.00 0.00 3.36
109 110 0.811915 CCACGAATCGAGGTCAGTCT 59.188 55.000 10.55 0.00 33.22 3.24
124 125 2.112190 CAGTCTACCCCTTCTCCTTCC 58.888 57.143 0.00 0.00 0.00 3.46
132 133 2.556766 CCCTTCTCCTTCCTCTCCTTT 58.443 52.381 0.00 0.00 0.00 3.11
133 134 2.503765 CCCTTCTCCTTCCTCTCCTTTC 59.496 54.545 0.00 0.00 0.00 2.62
141 142 2.948889 TCCTCTCCTTTCCCATCTCA 57.051 50.000 0.00 0.00 0.00 3.27
145 146 3.969976 CCTCTCCTTTCCCATCTCATACA 59.030 47.826 0.00 0.00 0.00 2.29
167 168 7.315066 ACAGATTTCTTCTCCTTTCTCTTCT 57.685 36.000 0.00 0.00 29.93 2.85
172 173 5.491323 TCTTCTCCTTTCTCTTCTTTCCC 57.509 43.478 0.00 0.00 0.00 3.97
178 179 2.751166 TTCTCTTCTTTCCCAGCTCG 57.249 50.000 0.00 0.00 0.00 5.03
179 180 0.247736 TCTCTTCTTTCCCAGCTCGC 59.752 55.000 0.00 0.00 0.00 5.03
242 256 2.692368 GAGGTGGGGCCATCTCCA 60.692 66.667 4.39 0.00 45.69 3.86
247 261 1.308128 TGGGGCCATCTCCATCTGT 60.308 57.895 4.39 0.00 0.00 3.41
258 272 0.974010 TCCATCTGTACCGGGTCACC 60.974 60.000 6.32 0.00 0.00 4.02
285 303 2.252012 TAATGGTCGCCCTCCTCCCT 62.252 60.000 0.00 0.00 0.00 4.20
387 2309 7.873739 AGTTTGTTGCAGTTTGATTATAAGC 57.126 32.000 0.00 0.00 0.00 3.09
388 2310 7.432869 AGTTTGTTGCAGTTTGATTATAAGCA 58.567 30.769 0.00 0.00 0.00 3.91
471 2399 3.005554 CTCTCGGTCAACAATTGATGCT 58.994 45.455 13.59 0.00 42.47 3.79
520 2452 2.766313 CAGAACCGTGAGTTTGATCCA 58.234 47.619 0.00 0.00 39.40 3.41
546 2478 5.809001 TGCTAAGGATCAAACAGAGACAAT 58.191 37.500 0.00 0.00 0.00 2.71
582 2536 9.047947 AGGAATTAAGTTATAGGTATAGGCCTG 57.952 37.037 17.99 0.00 39.60 4.85
593 2547 2.409948 ATAGGCCTGTTCTCTTGTGC 57.590 50.000 17.99 0.00 0.00 4.57
617 2575 7.717436 TGCGTGTAATATGAGGGAAATTATCAA 59.283 33.333 0.00 0.00 0.00 2.57
707 2673 5.930837 TGTGGAAATTGATTAATGGGGTC 57.069 39.130 0.00 0.00 0.00 4.46
711 2677 1.995376 ATTGATTAATGGGGTCGGGC 58.005 50.000 0.00 0.00 0.00 6.13
716 2682 1.055551 TTAATGGGGTCGGGCGGTAT 61.056 55.000 0.00 0.00 0.00 2.73
733 2704 4.034048 GCGGTATTATAGGGCAAATGATCG 59.966 45.833 0.00 0.00 0.00 3.69
917 3033 5.762279 TCTTTTGTCCTAGTGGAAAACCTT 58.238 37.500 0.00 0.00 45.18 3.50
940 3056 3.444034 GCTTGATTCCCACTCTTAAACCC 59.556 47.826 0.00 0.00 0.00 4.11
942 3058 4.301072 TGATTCCCACTCTTAAACCCTG 57.699 45.455 0.00 0.00 0.00 4.45
948 3065 3.056607 CCCACTCTTAAACCCTGCATTTG 60.057 47.826 0.00 0.00 0.00 2.32
949 3066 3.573967 CCACTCTTAAACCCTGCATTTGT 59.426 43.478 0.00 0.00 0.00 2.83
953 3070 5.362430 ACTCTTAAACCCTGCATTTGTTTGA 59.638 36.000 14.90 8.55 34.33 2.69
974 3091 3.576078 TTTGACAGCTGAGGGAAAGAA 57.424 42.857 23.35 0.62 0.00 2.52
977 3094 2.705658 TGACAGCTGAGGGAAAGAAAGA 59.294 45.455 23.35 0.00 0.00 2.52
1059 3176 5.774498 AATTTCTCCCTTCACTTTGTGTC 57.226 39.130 0.00 0.00 34.79 3.67
1087 3204 2.180204 GGTCCGCCGGATGAATGTG 61.180 63.158 10.04 0.00 32.73 3.21
1158 3296 2.943265 AGGGTTGATGCCAGGCCT 60.943 61.111 9.64 0.00 0.00 5.19
1383 3522 8.402798 TCTTCTACCAACAATTTAATGAAGCA 57.597 30.769 0.00 0.00 0.00 3.91
1448 3587 2.027625 CGTTGCCGGAGAACCTGTC 61.028 63.158 5.05 0.00 0.00 3.51
1450 3589 0.951040 GTTGCCGGAGAACCTGTCTG 60.951 60.000 5.05 0.00 36.41 3.51
1451 3590 2.111999 TTGCCGGAGAACCTGTCTGG 62.112 60.000 5.05 0.00 42.68 3.86
1467 3606 5.205056 CTGTCTGGTCCTTATTCTCTAGGT 58.795 45.833 0.00 0.00 33.15 3.08
1566 3705 2.202899 ACCGGGGGCAAAAACCAT 59.797 55.556 6.32 0.00 0.00 3.55
1570 3709 1.467678 CGGGGGCAAAAACCATGTGA 61.468 55.000 0.00 0.00 0.00 3.58
1584 3723 1.955778 CATGTGACTTTTCCACCAGCA 59.044 47.619 0.00 0.00 33.80 4.41
1591 3730 1.876156 CTTTTCCACCAGCAGTCAGTC 59.124 52.381 0.00 0.00 0.00 3.51
1602 3741 1.741732 GCAGTCAGTCATGGCTTCGAT 60.742 52.381 0.00 0.00 38.58 3.59
1620 3759 0.608130 ATACCTCTGTTGTGAGCGCA 59.392 50.000 11.47 0.00 33.02 6.09
1679 3818 1.330521 GCACAACGAGAACTGCTTGAA 59.669 47.619 0.00 0.00 0.00 2.69
1734 3873 3.701532 TTCGCTAACCAAACAAAGGTG 57.298 42.857 0.00 0.00 39.86 4.00
1793 3932 6.557253 TGGGGAGATATTATATCCATAACGGG 59.443 42.308 17.01 0.00 42.43 5.28
1833 3972 2.124736 GCAAGGCCCAGCGTCATA 60.125 61.111 0.00 0.00 0.00 2.15
1987 4126 3.935818 TCCAGATCTTACGAGGAGAGT 57.064 47.619 0.00 0.00 0.00 3.24
2058 4197 3.858638 AGTTATGGGGGAGGAAGTCAAAT 59.141 43.478 0.00 0.00 0.00 2.32
2127 4266 0.108585 AGCTCTTTTCAAGACCCGCA 59.891 50.000 0.00 0.00 33.12 5.69
2148 4287 2.749621 ACGCAGGAAAAATGTCATCCTC 59.250 45.455 0.00 0.00 41.63 3.71
2154 4293 3.511146 GGAAAAATGTCATCCTCTTGGCA 59.489 43.478 0.00 0.00 35.34 4.92
2157 4296 0.106819 ATGTCATCCTCTTGGCAGGC 60.107 55.000 0.00 0.00 34.15 4.85
2269 4408 2.079925 GGAGAGAATGCACACACTTCC 58.920 52.381 0.00 0.00 0.00 3.46
2314 4453 7.582667 AATTTCTACATTGCAGGTAATACCC 57.417 36.000 5.71 0.00 39.75 3.69
2414 4553 3.270877 AGGTCGGCAAGATATTTGTGAC 58.729 45.455 0.00 11.76 0.00 3.67
2510 4649 3.375647 TTCCTTGGCCAATACCCTTAC 57.624 47.619 20.85 0.00 0.00 2.34
2623 4764 4.671880 TGTGCGTAAACGAAATGCTATT 57.328 36.364 6.71 0.00 43.02 1.73
2679 4820 6.017523 CGATGCATACTCTACCGAGATATCAT 60.018 42.308 0.00 0.00 39.74 2.45
2702 4843 1.600413 GCAAGGTGCTGTGTAAAGTGC 60.600 52.381 0.00 0.00 40.96 4.40
2727 4868 2.158623 AGTTGACAGGAAATGAGCCACA 60.159 45.455 0.00 0.00 0.00 4.17
2798 5103 5.551760 GAACCAACTTCCATGTCTGTATG 57.448 43.478 0.00 0.00 0.00 2.39
2948 5253 6.957631 TCTTGCCTTCTTCTATGACCAATTA 58.042 36.000 0.00 0.00 0.00 1.40
3069 5374 6.649155 TGTACAGCTGATTGGCTTCTAAATA 58.351 36.000 23.35 0.00 41.00 1.40
3073 5378 6.054295 CAGCTGATTGGCTTCTAAATAGTCT 58.946 40.000 8.42 0.00 41.00 3.24
3083 5388 8.982723 TGGCTTCTAAATAGTCTAGATCTTGTT 58.017 33.333 0.00 0.00 0.00 2.83
3139 5444 3.480470 TGTTTTTCTTGGAGCAGAGAGG 58.520 45.455 0.00 0.00 0.00 3.69
3157 5462 0.107459 GGCCACCTCAGTCTTGGATC 60.107 60.000 0.00 0.00 31.39 3.36
3187 5498 1.580845 GAGCTGCATCGTGGCAACTT 61.581 55.000 1.02 0.00 44.40 2.66
3197 5508 3.047877 GGCAACTTGGTCCGTCGG 61.048 66.667 4.39 4.39 0.00 4.79
3225 5536 7.432350 AAAATCTGTCTTAGAGAAGCAAGTG 57.568 36.000 0.00 0.00 39.20 3.16
3230 5541 6.940867 TCTGTCTTAGAGAAGCAAGTGTAGTA 59.059 38.462 0.00 0.00 32.21 1.82
3243 5554 5.109903 CAAGTGTAGTAGTATCCACAAGCC 58.890 45.833 0.00 0.00 0.00 4.35
3281 5592 7.412129 CGGTTGTTTATTGCGTACTGAATTAGA 60.412 37.037 0.00 0.00 0.00 2.10
3285 5596 7.908082 TGTTTATTGCGTACTGAATTAGAATGC 59.092 33.333 0.00 0.00 0.00 3.56
3299 5610 9.905713 TGAATTAGAATGCTCTATTTAACTGGT 57.094 29.630 0.00 0.00 34.06 4.00
3322 5633 5.215252 TCAGGTGCTCCTATATTTGCTAC 57.785 43.478 7.08 0.00 43.07 3.58
3343 5654 6.145696 GCTACGAAATCCTAACTATTTGCGAT 59.854 38.462 0.00 0.00 0.00 4.58
3355 5666 9.779237 CTAACTATTTGCGATAATCTTTGTACG 57.221 33.333 0.00 0.00 0.00 3.67
3358 5669 5.866335 TTTGCGATAATCTTTGTACGGTT 57.134 34.783 0.00 0.00 0.00 4.44
3366 5677 7.849026 CGATAATCTTTGTACGGTTATGTTTGG 59.151 37.037 0.00 0.00 0.00 3.28
3367 5678 8.795842 ATAATCTTTGTACGGTTATGTTTGGA 57.204 30.769 0.00 0.00 0.00 3.53
3368 5679 7.513371 AATCTTTGTACGGTTATGTTTGGAA 57.487 32.000 0.00 0.00 0.00 3.53
3369 5680 6.939132 TCTTTGTACGGTTATGTTTGGAAA 57.061 33.333 0.00 0.00 0.00 3.13
3406 5717 2.228582 TGTATTGCATGCCAACACAGTC 59.771 45.455 16.68 0.00 36.01 3.51
3407 5718 1.624336 ATTGCATGCCAACACAGTCT 58.376 45.000 16.68 0.00 35.99 3.24
3409 5720 1.522668 TGCATGCCAACACAGTCTAC 58.477 50.000 16.68 0.00 0.00 2.59
3410 5721 1.202746 TGCATGCCAACACAGTCTACA 60.203 47.619 16.68 0.00 0.00 2.74
3411 5722 1.466167 GCATGCCAACACAGTCTACAG 59.534 52.381 6.36 0.00 0.00 2.74
3426 5737 5.470098 CAGTCTACAGTGTGCCTATTTGTTT 59.530 40.000 5.88 0.00 0.00 2.83
3428 5739 7.172532 CAGTCTACAGTGTGCCTATTTGTTTTA 59.827 37.037 5.88 0.00 0.00 1.52
3492 5803 8.999431 TGTAGTCTAGCAAGTTTAATTTTGAGG 58.001 33.333 4.22 0.00 0.00 3.86
3493 5804 9.216117 GTAGTCTAGCAAGTTTAATTTTGAGGA 57.784 33.333 4.22 0.00 0.00 3.71
3494 5805 8.100508 AGTCTAGCAAGTTTAATTTTGAGGAC 57.899 34.615 4.22 7.30 0.00 3.85
3495 5806 7.719633 AGTCTAGCAAGTTTAATTTTGAGGACA 59.280 33.333 4.22 0.00 0.00 4.02
3496 5807 7.803659 GTCTAGCAAGTTTAATTTTGAGGACAC 59.196 37.037 4.22 0.00 0.00 3.67
3497 5808 6.715347 AGCAAGTTTAATTTTGAGGACACT 57.285 33.333 4.22 0.00 0.00 3.55
3498 5809 6.507023 AGCAAGTTTAATTTTGAGGACACTG 58.493 36.000 4.22 0.00 0.00 3.66
3499 5810 6.321181 AGCAAGTTTAATTTTGAGGACACTGA 59.679 34.615 4.22 0.00 0.00 3.41
3500 5811 6.417930 GCAAGTTTAATTTTGAGGACACTGAC 59.582 38.462 4.22 0.00 0.00 3.51
3501 5812 7.682021 GCAAGTTTAATTTTGAGGACACTGACT 60.682 37.037 4.22 0.00 0.00 3.41
3502 5813 8.836413 CAAGTTTAATTTTGAGGACACTGACTA 58.164 33.333 0.00 0.00 0.00 2.59
3503 5814 8.379457 AGTTTAATTTTGAGGACACTGACTAC 57.621 34.615 0.00 0.00 0.00 2.73
3504 5815 7.990886 AGTTTAATTTTGAGGACACTGACTACA 59.009 33.333 0.00 0.00 0.00 2.74
3505 5816 8.784043 GTTTAATTTTGAGGACACTGACTACAT 58.216 33.333 0.00 0.00 0.00 2.29
3507 5818 7.907214 AATTTTGAGGACACTGACTACATAC 57.093 36.000 0.00 0.00 0.00 2.39
3508 5819 6.413783 TTTTGAGGACACTGACTACATACA 57.586 37.500 0.00 0.00 0.00 2.29
3509 5820 6.605471 TTTGAGGACACTGACTACATACAT 57.395 37.500 0.00 0.00 0.00 2.29
3510 5821 5.836821 TGAGGACACTGACTACATACATC 57.163 43.478 0.00 0.00 0.00 3.06
3511 5822 4.645136 TGAGGACACTGACTACATACATCC 59.355 45.833 0.00 0.00 0.00 3.51
3512 5823 4.610333 AGGACACTGACTACATACATCCA 58.390 43.478 0.00 0.00 0.00 3.41
3513 5824 5.023452 AGGACACTGACTACATACATCCAA 58.977 41.667 0.00 0.00 0.00 3.53
3514 5825 5.127845 AGGACACTGACTACATACATCCAAG 59.872 44.000 0.00 0.00 0.00 3.61
3515 5826 5.344743 ACACTGACTACATACATCCAAGG 57.655 43.478 0.00 0.00 0.00 3.61
3516 5827 4.777896 ACACTGACTACATACATCCAAGGT 59.222 41.667 0.00 0.00 0.00 3.50
3517 5828 5.111989 CACTGACTACATACATCCAAGGTG 58.888 45.833 0.00 0.00 0.00 4.00
3518 5829 5.023452 ACTGACTACATACATCCAAGGTGA 58.977 41.667 0.00 0.00 0.00 4.02
3519 5830 5.127845 ACTGACTACATACATCCAAGGTGAG 59.872 44.000 0.00 0.00 0.00 3.51
3520 5831 5.269189 TGACTACATACATCCAAGGTGAGA 58.731 41.667 0.00 0.00 0.00 3.27
3521 5832 5.899547 TGACTACATACATCCAAGGTGAGAT 59.100 40.000 0.00 0.00 0.00 2.75
3522 5833 6.384015 TGACTACATACATCCAAGGTGAGATT 59.616 38.462 0.00 0.00 0.00 2.40
3523 5834 6.821388 ACTACATACATCCAAGGTGAGATTC 58.179 40.000 0.00 0.00 0.00 2.52
3524 5835 5.041191 ACATACATCCAAGGTGAGATTCC 57.959 43.478 0.00 0.00 0.00 3.01
3525 5836 4.723789 ACATACATCCAAGGTGAGATTCCT 59.276 41.667 0.00 0.00 36.81 3.36
3526 5837 3.922171 ACATCCAAGGTGAGATTCCTC 57.078 47.619 0.00 0.00 39.86 3.71
3527 5838 3.184628 ACATCCAAGGTGAGATTCCTCA 58.815 45.455 0.00 0.00 46.48 3.86
3539 5850 4.520874 TGAGATTCCTCATCTAGTTAGCCG 59.479 45.833 0.00 0.00 42.92 5.52
3540 5851 3.257127 AGATTCCTCATCTAGTTAGCCGC 59.743 47.826 0.00 0.00 40.85 6.53
3541 5852 2.366640 TCCTCATCTAGTTAGCCGCT 57.633 50.000 0.00 0.00 0.00 5.52
3542 5853 3.503800 TCCTCATCTAGTTAGCCGCTA 57.496 47.619 0.00 0.00 0.00 4.26
3543 5854 4.035612 TCCTCATCTAGTTAGCCGCTAT 57.964 45.455 0.00 0.00 0.00 2.97
3544 5855 4.408276 TCCTCATCTAGTTAGCCGCTATT 58.592 43.478 0.00 0.00 0.00 1.73
3545 5856 4.218635 TCCTCATCTAGTTAGCCGCTATTG 59.781 45.833 0.00 0.00 0.00 1.90
3546 5857 3.914312 TCATCTAGTTAGCCGCTATTGC 58.086 45.455 0.00 0.00 0.00 3.56
3547 5858 3.574396 TCATCTAGTTAGCCGCTATTGCT 59.426 43.478 0.00 3.32 42.81 3.91
3548 5859 4.765339 TCATCTAGTTAGCCGCTATTGCTA 59.235 41.667 0.00 4.26 40.23 3.49
3549 5860 5.419155 TCATCTAGTTAGCCGCTATTGCTAT 59.581 40.000 0.00 0.00 40.75 2.97
3556 5867 2.028930 AGCCGCTATTGCTATGACCTAC 60.029 50.000 0.00 0.00 37.28 3.18
3561 5872 3.325135 GCTATTGCTATGACCTACCAGGT 59.675 47.826 0.00 0.00 43.54 4.00
3583 5895 6.825721 AGGTGGTAGATAAGAGCTTTGAATTG 59.174 38.462 0.00 0.00 0.00 2.32
3614 5926 6.150140 ACTGCTATTGAGTCTTGAATTTGGAC 59.850 38.462 0.00 0.00 0.00 4.02
3616 5928 5.415701 GCTATTGAGTCTTGAATTTGGACCA 59.584 40.000 0.00 0.00 0.00 4.02
3618 5930 3.149196 TGAGTCTTGAATTTGGACCAGC 58.851 45.455 0.00 0.00 0.00 4.85
3637 5949 4.780021 CCAGCCAGGTTATGAGTATCCTAT 59.220 45.833 0.00 0.00 30.49 2.57
3640 5952 5.719085 AGCCAGGTTATGAGTATCCTATCAG 59.281 44.000 0.00 0.00 30.49 2.90
3659 5971 7.752686 CCTATCAGTGTATAGATTGTCATCGTG 59.247 40.741 9.75 0.00 34.17 4.35
3660 5972 5.831997 TCAGTGTATAGATTGTCATCGTGG 58.168 41.667 0.00 0.00 34.17 4.94
3790 6104 1.405105 GCTGTGTTTTGAGCTGGTCAA 59.595 47.619 17.52 17.52 43.82 3.18
3806 6120 0.589223 TCAAAGGTTAACTTGGCGCG 59.411 50.000 0.00 0.00 39.96 6.86
3807 6121 0.309612 CAAAGGTTAACTTGGCGCGT 59.690 50.000 8.43 0.00 39.96 6.01
3809 6123 0.816421 AAGGTTAACTTGGCGCGTGT 60.816 50.000 8.43 0.00 38.21 4.49
3811 6125 0.659123 GGTTAACTTGGCGCGTGTTG 60.659 55.000 8.43 0.00 0.00 3.33
3813 6127 1.261089 GTTAACTTGGCGCGTGTTGTA 59.739 47.619 8.43 6.49 0.00 2.41
3814 6128 1.798283 TAACTTGGCGCGTGTTGTAT 58.202 45.000 8.43 0.00 0.00 2.29
3815 6129 0.948678 AACTTGGCGCGTGTTGTATT 59.051 45.000 8.43 0.00 0.00 1.89
3816 6130 0.237235 ACTTGGCGCGTGTTGTATTG 59.763 50.000 8.43 0.00 0.00 1.90
3817 6131 1.065031 CTTGGCGCGTGTTGTATTGC 61.065 55.000 8.43 0.00 0.00 3.56
3818 6132 1.786049 TTGGCGCGTGTTGTATTGCA 61.786 50.000 8.43 0.00 0.00 4.08
3819 6133 1.081774 GGCGCGTGTTGTATTGCAA 60.082 52.632 8.43 0.00 34.16 4.08
3826 6140 2.707192 GTTGTATTGCAACGCACGG 58.293 52.632 0.00 0.00 46.52 4.94
3827 6141 0.727793 GTTGTATTGCAACGCACGGG 60.728 55.000 0.00 0.00 46.52 5.28
3833 6147 4.279043 GCAACGCACGGGCCTTTT 62.279 61.111 2.82 0.00 36.38 2.27
3835 6149 1.948635 CAACGCACGGGCCTTTTTG 60.949 57.895 2.82 0.00 36.38 2.44
3836 6150 3.783478 AACGCACGGGCCTTTTTGC 62.783 57.895 2.82 5.50 36.38 3.68
3837 6151 3.977244 CGCACGGGCCTTTTTGCT 61.977 61.111 2.82 0.00 36.38 3.91
3845 6225 3.453353 ACGGGCCTTTTTGCTAGTATCTA 59.547 43.478 0.84 0.00 0.00 1.98
3912 6296 8.868522 TCTAGAAAATATGGATATGCCCTTTG 57.131 34.615 0.00 0.00 34.97 2.77
3913 6297 6.923199 AGAAAATATGGATATGCCCTTTGG 57.077 37.500 0.00 0.00 34.97 3.28
3927 6311 2.677337 CCCTTTGGTGCTGTTGTTTTTG 59.323 45.455 0.00 0.00 0.00 2.44
3928 6312 3.333804 CCTTTGGTGCTGTTGTTTTTGT 58.666 40.909 0.00 0.00 0.00 2.83
3929 6313 4.499183 CCTTTGGTGCTGTTGTTTTTGTA 58.501 39.130 0.00 0.00 0.00 2.41
3930 6314 4.328712 CCTTTGGTGCTGTTGTTTTTGTAC 59.671 41.667 0.00 0.00 0.00 2.90
3931 6315 4.792521 TTGGTGCTGTTGTTTTTGTACT 57.207 36.364 0.00 0.00 0.00 2.73
3932 6316 4.792521 TGGTGCTGTTGTTTTTGTACTT 57.207 36.364 0.00 0.00 0.00 2.24
3933 6317 4.489810 TGGTGCTGTTGTTTTTGTACTTG 58.510 39.130 0.00 0.00 0.00 3.16
3934 6318 4.021894 TGGTGCTGTTGTTTTTGTACTTGT 60.022 37.500 0.00 0.00 0.00 3.16
3936 6320 5.164002 GGTGCTGTTGTTTTTGTACTTGTTG 60.164 40.000 0.00 0.00 0.00 3.33
3937 6321 5.404066 GTGCTGTTGTTTTTGTACTTGTTGT 59.596 36.000 0.00 0.00 0.00 3.32
3938 6322 5.631512 TGCTGTTGTTTTTGTACTTGTTGTC 59.368 36.000 0.00 0.00 0.00 3.18
3939 6323 5.061684 GCTGTTGTTTTTGTACTTGTTGTCC 59.938 40.000 0.00 0.00 0.00 4.02
3940 6324 5.471257 TGTTGTTTTTGTACTTGTTGTCCC 58.529 37.500 0.00 0.00 0.00 4.46
3941 6325 5.010719 TGTTGTTTTTGTACTTGTTGTCCCA 59.989 36.000 0.00 0.00 0.00 4.37
3944 6328 4.974368 TTTTGTACTTGTTGTCCCAGTG 57.026 40.909 0.00 0.00 0.00 3.66
3945 6329 3.637911 TTGTACTTGTTGTCCCAGTGT 57.362 42.857 0.00 0.00 0.00 3.55
3946 6330 3.637911 TGTACTTGTTGTCCCAGTGTT 57.362 42.857 0.00 0.00 0.00 3.32
3948 6332 5.100344 TGTACTTGTTGTCCCAGTGTTAA 57.900 39.130 0.00 0.00 0.00 2.01
3949 6333 5.498393 TGTACTTGTTGTCCCAGTGTTAAA 58.502 37.500 0.00 0.00 0.00 1.52
3950 6334 4.976224 ACTTGTTGTCCCAGTGTTAAAC 57.024 40.909 0.00 0.00 0.00 2.01
3985 6369 4.504858 ACTTTCCAGTGATAAAGGTAGCG 58.495 43.478 17.17 0.00 37.09 4.26
3998 6382 2.294074 AGGTAGCGAGTGATCTGACTC 58.706 52.381 3.61 3.61 39.28 3.36
4027 6411 5.551233 CAAGGACTACAAGAACCTGATGAA 58.449 41.667 0.00 0.00 32.73 2.57
4028 6412 5.825593 AGGACTACAAGAACCTGATGAAA 57.174 39.130 0.00 0.00 0.00 2.69
4041 6425 1.202915 TGATGAAACTGCAGGCTGGAA 60.203 47.619 19.93 0.00 0.00 3.53
4058 6442 5.229423 GCTGGAACAATTGTAGCATTTGAA 58.771 37.500 21.54 0.00 38.70 2.69
4094 6478 5.006261 CGTAATATTTGACCTTCATCACGCA 59.994 40.000 0.00 0.00 0.00 5.24
4101 6485 2.924290 GACCTTCATCACGCAACTACTC 59.076 50.000 0.00 0.00 0.00 2.59
4102 6486 2.271800 CCTTCATCACGCAACTACTCC 58.728 52.381 0.00 0.00 0.00 3.85
4103 6487 2.093973 CCTTCATCACGCAACTACTCCT 60.094 50.000 0.00 0.00 0.00 3.69
4104 6488 3.589988 CTTCATCACGCAACTACTCCTT 58.410 45.455 0.00 0.00 0.00 3.36
4105 6489 3.232213 TCATCACGCAACTACTCCTTC 57.768 47.619 0.00 0.00 0.00 3.46
4106 6490 2.094182 TCATCACGCAACTACTCCTTCC 60.094 50.000 0.00 0.00 0.00 3.46
4107 6491 0.242825 TCACGCAACTACTCCTTCCG 59.757 55.000 0.00 0.00 0.00 4.30
4108 6492 0.038526 CACGCAACTACTCCTTCCGT 60.039 55.000 0.00 0.00 0.00 4.69
4109 6493 0.677842 ACGCAACTACTCCTTCCGTT 59.322 50.000 0.00 0.00 0.00 4.44
4110 6494 1.336609 ACGCAACTACTCCTTCCGTTC 60.337 52.381 0.00 0.00 0.00 3.95
4111 6495 1.723220 GCAACTACTCCTTCCGTTCC 58.277 55.000 0.00 0.00 0.00 3.62
4112 6496 1.275573 GCAACTACTCCTTCCGTTCCT 59.724 52.381 0.00 0.00 0.00 3.36
4113 6497 2.494870 GCAACTACTCCTTCCGTTCCTA 59.505 50.000 0.00 0.00 0.00 2.94
4114 6498 3.056322 GCAACTACTCCTTCCGTTCCTAA 60.056 47.826 0.00 0.00 0.00 2.69
4115 6499 4.562143 GCAACTACTCCTTCCGTTCCTAAA 60.562 45.833 0.00 0.00 0.00 1.85
4116 6500 5.731591 CAACTACTCCTTCCGTTCCTAAAT 58.268 41.667 0.00 0.00 0.00 1.40
4117 6501 6.628844 GCAACTACTCCTTCCGTTCCTAAATA 60.629 42.308 0.00 0.00 0.00 1.40
4118 6502 7.498443 CAACTACTCCTTCCGTTCCTAAATAT 58.502 38.462 0.00 0.00 0.00 1.28
4119 6503 8.636213 CAACTACTCCTTCCGTTCCTAAATATA 58.364 37.037 0.00 0.00 0.00 0.86
4120 6504 8.773033 ACTACTCCTTCCGTTCCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
4121 6505 9.205513 ACTACTCCTTCCGTTCCTAAATATAAA 57.794 33.333 0.00 0.00 0.00 1.40
4124 6508 8.935741 ACTCCTTCCGTTCCTAAATATAAATCT 58.064 33.333 0.00 0.00 0.00 2.40
4125 6509 9.780186 CTCCTTCCGTTCCTAAATATAAATCTT 57.220 33.333 0.00 0.00 0.00 2.40
4143 6527 9.853177 ATAAATCTTTGTAGGGATTTCACTAGG 57.147 33.333 4.52 0.00 40.91 3.02
4144 6528 6.893020 ATCTTTGTAGGGATTTCACTAGGT 57.107 37.500 0.00 0.00 31.50 3.08
4145 6529 6.049955 TCTTTGTAGGGATTTCACTAGGTG 57.950 41.667 0.00 0.00 31.50 4.00
4146 6530 4.837093 TTGTAGGGATTTCACTAGGTGG 57.163 45.455 0.00 0.00 31.50 4.61
4147 6531 4.069312 TGTAGGGATTTCACTAGGTGGA 57.931 45.455 0.00 0.00 31.50 4.02
4148 6532 4.631234 TGTAGGGATTTCACTAGGTGGAT 58.369 43.478 0.00 0.00 31.50 3.41
4149 6533 5.036916 TGTAGGGATTTCACTAGGTGGATT 58.963 41.667 0.00 0.00 31.50 3.01
4150 6534 6.206787 TGTAGGGATTTCACTAGGTGGATTA 58.793 40.000 0.00 0.00 31.50 1.75
4151 6535 5.632034 AGGGATTTCACTAGGTGGATTAC 57.368 43.478 0.00 0.00 33.87 1.89
4152 6536 5.036916 AGGGATTTCACTAGGTGGATTACA 58.963 41.667 0.00 0.00 33.87 2.41
4153 6537 5.672194 AGGGATTTCACTAGGTGGATTACAT 59.328 40.000 0.00 0.00 33.87 2.29
4154 6538 6.849697 AGGGATTTCACTAGGTGGATTACATA 59.150 38.462 0.00 0.00 33.87 2.29
4155 6539 7.517604 AGGGATTTCACTAGGTGGATTACATAT 59.482 37.037 0.00 0.00 33.87 1.78
4156 6540 8.822805 GGGATTTCACTAGGTGGATTACATATA 58.177 37.037 0.00 0.00 33.87 0.86
4157 6541 9.877178 GGATTTCACTAGGTGGATTACATATAG 57.123 37.037 0.00 0.00 33.87 1.31
4160 6544 7.704578 TCACTAGGTGGATTACATATAGAGC 57.295 40.000 0.00 0.00 33.87 4.09
4161 6545 7.238710 TCACTAGGTGGATTACATATAGAGCA 58.761 38.462 0.00 0.00 33.87 4.26
4162 6546 7.728532 TCACTAGGTGGATTACATATAGAGCAA 59.271 37.037 0.00 0.00 33.87 3.91
4163 6547 8.367911 CACTAGGTGGATTACATATAGAGCAAA 58.632 37.037 0.00 0.00 0.00 3.68
4164 6548 8.934697 ACTAGGTGGATTACATATAGAGCAAAA 58.065 33.333 0.00 0.00 0.00 2.44
4165 6549 9.950496 CTAGGTGGATTACATATAGAGCAAAAT 57.050 33.333 0.00 0.00 0.00 1.82
4166 6550 8.627208 AGGTGGATTACATATAGAGCAAAATG 57.373 34.615 0.00 0.00 0.00 2.32
4167 6551 8.439971 AGGTGGATTACATATAGAGCAAAATGA 58.560 33.333 0.00 0.00 0.00 2.57
4168 6552 9.066892 GGTGGATTACATATAGAGCAAAATGAA 57.933 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.113190 TCCTCTCACTGCAGTGGAGA 59.887 55.000 39.05 34.70 45.65 3.71
19 20 0.972134 TTCCTCTCACTGCAGTGGAG 59.028 55.000 39.04 36.61 45.65 3.86
20 21 0.972134 CTTCCTCTCACTGCAGTGGA 59.028 55.000 39.04 31.90 45.65 4.02
21 22 0.036577 CCTTCCTCTCACTGCAGTGG 60.037 60.000 39.04 30.03 45.65 4.00
32 33 1.517832 CGCCGATGTTCCTTCCTCT 59.482 57.895 0.00 0.00 0.00 3.69
61 62 4.891727 CGACGGGGCCGATTGAGG 62.892 72.222 0.00 0.00 42.83 3.86
87 88 0.246635 CTGACCTCGATTCGTGGGTT 59.753 55.000 25.84 10.32 43.59 4.11
109 110 1.291335 GGAGAGGAAGGAGAAGGGGTA 59.709 57.143 0.00 0.00 0.00 3.69
124 125 4.898265 TCTGTATGAGATGGGAAAGGAGAG 59.102 45.833 0.00 0.00 0.00 3.20
132 133 6.042552 GGAGAAGAAATCTGTATGAGATGGGA 59.957 42.308 0.00 0.00 40.89 4.37
133 134 6.043012 AGGAGAAGAAATCTGTATGAGATGGG 59.957 42.308 0.00 0.00 40.89 4.00
141 142 9.045745 AGAAGAGAAAGGAGAAGAAATCTGTAT 57.954 33.333 0.00 0.00 38.96 2.29
145 146 7.882791 GGAAAGAAGAGAAAGGAGAAGAAATCT 59.117 37.037 0.00 0.00 42.61 2.40
208 209 4.379243 CCTCGCACGGCTGTTCCT 62.379 66.667 0.00 0.00 0.00 3.36
232 246 0.034059 CGGTACAGATGGAGATGGCC 59.966 60.000 0.00 0.00 0.00 5.36
233 247 0.034059 CCGGTACAGATGGAGATGGC 59.966 60.000 0.00 0.00 0.00 4.40
308 326 2.897762 TTGGTAACCCGGTGGAGGC 61.898 63.158 0.00 0.00 34.81 4.70
314 332 0.184211 AGCAAAGTTGGTAACCCGGT 59.816 50.000 0.00 0.00 37.09 5.28
315 333 1.324383 AAGCAAAGTTGGTAACCCGG 58.676 50.000 0.00 0.00 38.04 5.73
316 334 3.315749 TGTAAAGCAAAGTTGGTAACCCG 59.684 43.478 0.00 0.00 38.04 5.28
387 2309 8.500773 CAATTTCAAATCCAAATCTGGTCTTTG 58.499 33.333 8.63 8.63 43.97 2.77
388 2310 7.662669 CCAATTTCAAATCCAAATCTGGTCTTT 59.337 33.333 0.00 0.00 43.97 2.52
423 2345 5.932303 AGTGTAGTGCTACAACAAGGTTATG 59.068 40.000 12.94 0.00 46.33 1.90
425 2347 5.540400 AGTGTAGTGCTACAACAAGGTTA 57.460 39.130 12.94 0.00 46.33 2.85
427 2349 4.377897 GAAGTGTAGTGCTACAACAAGGT 58.622 43.478 12.94 0.00 46.33 3.50
520 2452 6.240894 TGTCTCTGTTTGATCCTTAGCAAAT 58.759 36.000 0.00 0.00 42.49 2.32
556 2488 9.047947 CAGGCCTATACCTATAACTTAATTCCT 57.952 37.037 3.98 0.00 38.26 3.36
581 2535 5.474825 TCATATTACACGCACAAGAGAACA 58.525 37.500 0.00 0.00 0.00 3.18
582 2536 5.005779 CCTCATATTACACGCACAAGAGAAC 59.994 44.000 0.00 0.00 0.00 3.01
617 2575 2.326428 CCCCGTATTAGACTGGTCCAT 58.674 52.381 0.00 0.00 30.55 3.41
633 2591 2.383855 TGCCTTTAATCATTTCCCCCG 58.616 47.619 0.00 0.00 0.00 5.73
707 2673 0.322322 TTGCCCTATAATACCGCCCG 59.678 55.000 0.00 0.00 0.00 6.13
711 2677 5.416083 TCGATCATTTGCCCTATAATACCG 58.584 41.667 0.00 0.00 0.00 4.02
716 2682 6.212589 TGGTCTATCGATCATTTGCCCTATAA 59.787 38.462 0.00 0.00 0.00 0.98
733 2704 6.719370 TGCCCCAATATTACATTTGGTCTATC 59.281 38.462 0.00 0.00 40.68 2.08
797 2883 9.734984 ATATATAACCCTTATTACTTGCACACC 57.265 33.333 0.00 0.00 0.00 4.16
830 2916 4.453478 TGACATCAAATCTTCAGTGTCTGC 59.547 41.667 0.00 0.00 37.46 4.26
917 3033 4.079253 GGTTTAAGAGTGGGAATCAAGCA 58.921 43.478 0.00 0.00 0.00 3.91
940 3056 4.748102 AGCTGTCAAATCAAACAAATGCAG 59.252 37.500 0.00 0.00 0.00 4.41
942 3058 4.746115 TCAGCTGTCAAATCAAACAAATGC 59.254 37.500 14.67 0.00 0.00 3.56
948 3065 3.149196 TCCCTCAGCTGTCAAATCAAAC 58.851 45.455 14.67 0.00 0.00 2.93
949 3066 3.507162 TCCCTCAGCTGTCAAATCAAA 57.493 42.857 14.67 0.00 0.00 2.69
953 3070 3.795688 TCTTTCCCTCAGCTGTCAAAT 57.204 42.857 14.67 0.00 0.00 2.32
974 3091 1.004440 GTCGCAGCACCCTCTTCTT 60.004 57.895 0.00 0.00 0.00 2.52
977 3094 1.548357 ATCTGTCGCAGCACCCTCTT 61.548 55.000 0.00 0.00 0.00 2.85
1110 3227 3.059461 GCAACAGCCACAACAAATCAATG 60.059 43.478 0.00 0.00 0.00 2.82
1335 3474 0.036010 CGAGGAGCTTCCAATGGTGT 60.036 55.000 0.00 0.00 39.61 4.16
1383 3522 3.347216 CGAAATTGGAGTGAAGATGGGT 58.653 45.455 0.00 0.00 0.00 4.51
1448 3587 3.070302 GCCACCTAGAGAATAAGGACCAG 59.930 52.174 0.00 0.00 36.66 4.00
1450 3589 2.036089 CGCCACCTAGAGAATAAGGACC 59.964 54.545 0.00 0.00 36.66 4.46
1451 3590 2.694109 ACGCCACCTAGAGAATAAGGAC 59.306 50.000 0.00 0.00 36.66 3.85
1463 3602 1.980052 CCAAGGAAGACGCCACCTA 59.020 57.895 0.00 0.00 33.34 3.08
1467 3606 2.032528 CAGCCAAGGAAGACGCCA 59.967 61.111 0.00 0.00 0.00 5.69
1566 3705 1.064758 ACTGCTGGTGGAAAAGTCACA 60.065 47.619 0.00 0.00 36.90 3.58
1570 3709 1.212935 ACTGACTGCTGGTGGAAAAGT 59.787 47.619 0.00 0.00 0.00 2.66
1584 3723 2.101582 GGTATCGAAGCCATGACTGACT 59.898 50.000 0.00 0.00 0.00 3.41
1591 3730 2.868583 CAACAGAGGTATCGAAGCCATG 59.131 50.000 10.62 10.42 0.00 3.66
1602 3741 0.038251 CTGCGCTCACAACAGAGGTA 60.038 55.000 9.73 0.00 36.15 3.08
1620 3759 1.672356 GGCAGAACACATCACCGCT 60.672 57.895 0.00 0.00 0.00 5.52
1647 3786 1.000233 CGTTGTGCAAGTGCTGATGC 61.000 55.000 4.69 1.91 42.66 3.91
1679 3818 3.882888 CACCAGTACCAGTTTGAATGTGT 59.117 43.478 0.00 0.00 0.00 3.72
1734 3873 2.597520 GAGTCGTAGAGGCAAACAGAC 58.402 52.381 0.00 0.00 36.95 3.51
1833 3972 3.157087 CCAGTAAAGTGCATTCCCAACT 58.843 45.455 0.00 0.00 0.00 3.16
1889 4028 1.338020 CAACAAGGGTCTGCCTTTCAC 59.662 52.381 0.00 0.00 31.05 3.18
1911 4050 4.201950 GCATATGTTGTCGGCTTCTCAATT 60.202 41.667 4.29 0.00 0.00 2.32
1987 4126 1.680735 CGCAAGGCCAAGGCAATTATA 59.319 47.619 13.87 0.00 44.11 0.98
2058 4197 3.117926 CCCATGAGACAATACCATCACCA 60.118 47.826 0.00 0.00 0.00 4.17
2127 4266 2.749621 GAGGATGACATTTTTCCTGCGT 59.250 45.455 0.00 0.00 39.98 5.24
2148 4287 1.419012 TCCTCATCATAGCCTGCCAAG 59.581 52.381 0.00 0.00 0.00 3.61
2154 4293 4.458397 CATTTGTGTCCTCATCATAGCCT 58.542 43.478 0.00 0.00 0.00 4.58
2157 4296 4.122046 TCGCATTTGTGTCCTCATCATAG 58.878 43.478 0.00 0.00 0.00 2.23
2314 4453 5.065914 TCAACAGAAGAAATCACTCAAGGG 58.934 41.667 0.00 0.00 0.00 3.95
2349 4488 6.889177 TCACATCAAGCATTTACCATAAGGAA 59.111 34.615 0.00 0.00 38.69 3.36
2351 4490 6.698008 TCACATCAAGCATTTACCATAAGG 57.302 37.500 0.00 0.00 42.21 2.69
2365 4504 5.298527 AGCACACCAATGATATCACATCAAG 59.701 40.000 7.78 0.00 0.00 3.02
2702 4843 3.128242 GGCTCATTTCCTGTCAACTCATG 59.872 47.826 0.00 0.00 0.00 3.07
2779 5084 5.003160 TCAACATACAGACATGGAAGTTGG 58.997 41.667 8.28 0.00 36.64 3.77
2798 5103 6.128445 CCATGTGAGAGACAACATACTTCAAC 60.128 42.308 0.00 0.00 38.36 3.18
2948 5253 5.937111 ACAGTTCACCCACTAAAACATACT 58.063 37.500 0.00 0.00 0.00 2.12
3000 5305 8.889717 CCGGTACTAAGTCAAAATGATACAAAT 58.110 33.333 0.00 0.00 0.00 2.32
3001 5306 7.148373 GCCGGTACTAAGTCAAAATGATACAAA 60.148 37.037 1.90 0.00 0.00 2.83
3002 5307 6.314400 GCCGGTACTAAGTCAAAATGATACAA 59.686 38.462 1.90 0.00 0.00 2.41
3003 5308 5.813672 GCCGGTACTAAGTCAAAATGATACA 59.186 40.000 1.90 0.00 0.00 2.29
3009 5314 9.623000 AAATATTAGCCGGTACTAAGTCAAAAT 57.377 29.630 1.90 0.00 35.67 1.82
3105 5410 8.690203 TCCAAGAAAAACAGAACATAGATCAA 57.310 30.769 0.00 0.00 0.00 2.57
3139 5444 0.615331 TGATCCAAGACTGAGGTGGC 59.385 55.000 0.00 0.00 32.10 5.01
3157 5462 2.093941 CGATGCAGCTCACTCTTCTTTG 59.906 50.000 0.00 0.00 0.00 2.77
3187 5498 1.208535 AGATTTTATGCCGACGGACCA 59.791 47.619 20.50 7.46 0.00 4.02
3197 5508 7.545362 TGCTTCTCTAAGACAGATTTTATGC 57.455 36.000 0.00 0.00 34.37 3.14
3225 5536 3.703420 CACGGCTTGTGGATACTACTAC 58.297 50.000 2.21 0.00 45.21 2.73
3243 5554 2.817538 AACAACCGACTGAAAACACG 57.182 45.000 0.00 0.00 0.00 4.49
3281 5592 6.375455 CACCTGAACCAGTTAAATAGAGCATT 59.625 38.462 0.00 0.00 0.00 3.56
3285 5596 5.491982 AGCACCTGAACCAGTTAAATAGAG 58.508 41.667 0.00 0.00 0.00 2.43
3322 5633 8.926710 AGATTATCGCAAATAGTTAGGATTTCG 58.073 33.333 0.00 0.00 0.00 3.46
3335 5646 6.431198 AACCGTACAAAGATTATCGCAAAT 57.569 33.333 0.00 0.00 0.00 2.32
3339 5650 6.520792 ACATAACCGTACAAAGATTATCGC 57.479 37.500 0.00 0.00 0.00 4.58
3343 5654 8.618702 TTCCAAACATAACCGTACAAAGATTA 57.381 30.769 0.00 0.00 0.00 1.75
3355 5666 5.914898 AGCAGGTATTTCCAAACATAACC 57.085 39.130 0.00 0.00 39.02 2.85
3358 5669 6.068461 TGGTAGCAGGTATTTCCAAACATA 57.932 37.500 0.00 0.00 39.02 2.29
3366 5677 3.951663 ACAGGTTGGTAGCAGGTATTTC 58.048 45.455 0.00 0.00 0.00 2.17
3367 5678 5.710409 ATACAGGTTGGTAGCAGGTATTT 57.290 39.130 0.00 0.00 0.00 1.40
3368 5679 5.437060 CAATACAGGTTGGTAGCAGGTATT 58.563 41.667 13.12 13.12 36.14 1.89
3369 5680 4.686122 GCAATACAGGTTGGTAGCAGGTAT 60.686 45.833 0.00 0.46 0.00 2.73
3406 5717 8.296713 ACAATAAAACAAATAGGCACACTGTAG 58.703 33.333 0.00 0.00 0.00 2.74
3407 5718 8.172352 ACAATAAAACAAATAGGCACACTGTA 57.828 30.769 0.00 0.00 0.00 2.74
3409 5720 7.945033 AACAATAAAACAAATAGGCACACTG 57.055 32.000 0.00 0.00 0.00 3.66
3410 5721 7.984617 ACAAACAATAAAACAAATAGGCACACT 59.015 29.630 0.00 0.00 0.00 3.55
3411 5722 8.137210 ACAAACAATAAAACAAATAGGCACAC 57.863 30.769 0.00 0.00 0.00 3.82
3448 5759 7.667557 AGACTACACACTGCTAATTAGAACAA 58.332 34.615 16.85 0.00 0.00 2.83
3492 5803 5.105310 ACCTTGGATGTATGTAGTCAGTGTC 60.105 44.000 0.00 0.00 0.00 3.67
3493 5804 4.777896 ACCTTGGATGTATGTAGTCAGTGT 59.222 41.667 0.00 0.00 0.00 3.55
3494 5805 5.105351 TCACCTTGGATGTATGTAGTCAGTG 60.105 44.000 0.00 0.00 0.00 3.66
3495 5806 5.023452 TCACCTTGGATGTATGTAGTCAGT 58.977 41.667 0.00 0.00 0.00 3.41
3496 5807 5.360999 TCTCACCTTGGATGTATGTAGTCAG 59.639 44.000 0.00 0.00 0.00 3.51
3497 5808 5.269189 TCTCACCTTGGATGTATGTAGTCA 58.731 41.667 0.00 0.00 0.00 3.41
3498 5809 5.854010 TCTCACCTTGGATGTATGTAGTC 57.146 43.478 0.00 0.00 0.00 2.59
3499 5810 6.183361 GGAATCTCACCTTGGATGTATGTAGT 60.183 42.308 0.00 0.00 0.00 2.73
3500 5811 6.042552 AGGAATCTCACCTTGGATGTATGTAG 59.957 42.308 0.00 0.00 33.55 2.74
3501 5812 5.905331 AGGAATCTCACCTTGGATGTATGTA 59.095 40.000 0.00 0.00 33.55 2.29
3502 5813 4.723789 AGGAATCTCACCTTGGATGTATGT 59.276 41.667 0.00 0.00 33.55 2.29
3503 5814 5.163269 TGAGGAATCTCACCTTGGATGTATG 60.163 44.000 0.00 0.00 44.39 2.39
3504 5815 4.971282 TGAGGAATCTCACCTTGGATGTAT 59.029 41.667 0.00 0.00 44.39 2.29
3505 5816 4.361783 TGAGGAATCTCACCTTGGATGTA 58.638 43.478 0.00 0.00 44.39 2.29
3506 5817 3.184628 TGAGGAATCTCACCTTGGATGT 58.815 45.455 0.00 0.00 44.39 3.06
3507 5818 3.920231 TGAGGAATCTCACCTTGGATG 57.080 47.619 0.00 0.00 44.39 3.51
3517 5828 4.617298 GCGGCTAACTAGATGAGGAATCTC 60.617 50.000 0.00 0.00 42.27 2.75
3519 5830 3.257127 AGCGGCTAACTAGATGAGGAATC 59.743 47.826 0.00 0.00 35.29 2.52
3520 5831 3.235200 AGCGGCTAACTAGATGAGGAAT 58.765 45.455 0.00 0.00 0.00 3.01
3521 5832 2.667470 AGCGGCTAACTAGATGAGGAA 58.333 47.619 0.00 0.00 0.00 3.36
3522 5833 2.366640 AGCGGCTAACTAGATGAGGA 57.633 50.000 0.00 0.00 0.00 3.71
3523 5834 4.489810 CAATAGCGGCTAACTAGATGAGG 58.510 47.826 14.54 0.00 0.00 3.86
3524 5835 3.923461 GCAATAGCGGCTAACTAGATGAG 59.077 47.826 14.54 0.00 0.00 2.90
3525 5836 3.914312 GCAATAGCGGCTAACTAGATGA 58.086 45.455 14.54 0.00 0.00 2.92
3526 5837 5.518128 CATAGCAATAGCGGCTAACTAGATG 59.482 44.000 14.54 11.06 46.03 2.90
3527 5838 5.419155 TCATAGCAATAGCGGCTAACTAGAT 59.581 40.000 14.54 5.69 46.03 1.98
3528 5839 4.765339 TCATAGCAATAGCGGCTAACTAGA 59.235 41.667 14.54 11.44 46.03 2.43
3529 5840 4.859798 GTCATAGCAATAGCGGCTAACTAG 59.140 45.833 14.54 5.52 46.03 2.57
3530 5841 4.321750 GGTCATAGCAATAGCGGCTAACTA 60.322 45.833 14.54 15.21 46.03 2.24
3531 5842 3.555168 GGTCATAGCAATAGCGGCTAACT 60.555 47.826 14.54 13.61 46.03 2.24
3532 5843 2.737252 GGTCATAGCAATAGCGGCTAAC 59.263 50.000 14.54 6.86 46.03 2.34
3533 5844 2.632996 AGGTCATAGCAATAGCGGCTAA 59.367 45.455 14.54 0.00 46.03 3.09
3539 5850 3.931578 CCTGGTAGGTCATAGCAATAGC 58.068 50.000 0.00 0.00 41.20 2.97
3556 5867 4.162320 TCAAAGCTCTTATCTACCACCTGG 59.838 45.833 0.00 0.00 42.17 4.45
3561 5872 6.317140 CAGCAATTCAAAGCTCTTATCTACCA 59.683 38.462 0.00 0.00 39.50 3.25
3583 5895 3.451141 AGACTCAATAGCAGTAGCAGC 57.549 47.619 0.00 0.00 45.49 5.25
3614 5926 3.409026 GGATACTCATAACCTGGCTGG 57.591 52.381 9.11 9.11 42.93 4.85
3637 5949 5.359860 ACCACGATGACAATCTATACACTGA 59.640 40.000 0.00 0.00 0.00 3.41
3640 5952 5.276868 GCAACCACGATGACAATCTATACAC 60.277 44.000 0.00 0.00 0.00 2.90
3653 5965 4.937696 TGTTAGTTATGCAACCACGATG 57.062 40.909 0.00 0.00 35.05 3.84
3659 5971 7.360946 CCTCAAGTACTTGTTAGTTATGCAACC 60.361 40.741 29.83 0.00 41.16 3.77
3660 5972 7.519002 CCTCAAGTACTTGTTAGTTATGCAAC 58.481 38.462 29.83 0.00 41.16 4.17
3790 6104 0.816421 ACACGCGCCAAGTTAACCTT 60.816 50.000 5.73 0.00 0.00 3.50
3809 6123 1.576920 CCCGTGCGTTGCAATACAA 59.423 52.632 0.59 0.00 41.47 2.41
3811 6125 2.202427 GCCCGTGCGTTGCAATAC 60.202 61.111 0.59 1.79 41.47 1.89
3816 6130 3.783478 AAAAAGGCCCGTGCGTTGC 62.783 57.895 0.00 0.00 44.30 4.17
3817 6131 1.948635 CAAAAAGGCCCGTGCGTTG 60.949 57.895 0.00 0.00 44.30 4.10
3818 6132 2.415426 CAAAAAGGCCCGTGCGTT 59.585 55.556 0.00 0.00 46.85 4.84
3819 6133 4.279043 GCAAAAAGGCCCGTGCGT 62.279 61.111 0.00 0.00 38.85 5.24
3820 6134 2.527547 CTAGCAAAAAGGCCCGTGCG 62.528 60.000 0.00 0.00 41.90 5.34
3821 6135 1.212751 CTAGCAAAAAGGCCCGTGC 59.787 57.895 0.00 4.01 37.26 5.34
3822 6136 1.816074 TACTAGCAAAAAGGCCCGTG 58.184 50.000 0.00 0.00 0.00 4.94
3823 6137 2.238898 AGATACTAGCAAAAAGGCCCGT 59.761 45.455 0.00 0.00 0.00 5.28
3824 6138 2.919228 AGATACTAGCAAAAAGGCCCG 58.081 47.619 0.00 0.00 0.00 6.13
3825 6139 7.173390 CAGTTATAGATACTAGCAAAAAGGCCC 59.827 40.741 0.00 0.00 0.00 5.80
3826 6140 7.173390 CCAGTTATAGATACTAGCAAAAAGGCC 59.827 40.741 0.00 0.00 0.00 5.19
3827 6141 7.931948 TCCAGTTATAGATACTAGCAAAAAGGC 59.068 37.037 0.00 0.00 0.00 4.35
3832 6146 8.807118 CCTGATCCAGTTATAGATACTAGCAAA 58.193 37.037 0.00 0.00 0.00 3.68
3833 6147 7.950684 ACCTGATCCAGTTATAGATACTAGCAA 59.049 37.037 0.00 0.00 0.00 3.91
3835 6149 7.629652 GCACCTGATCCAGTTATAGATACTAGC 60.630 44.444 0.00 0.00 0.00 3.42
3836 6150 7.613801 AGCACCTGATCCAGTTATAGATACTAG 59.386 40.741 0.00 0.00 0.00 2.57
3837 6151 7.471041 AGCACCTGATCCAGTTATAGATACTA 58.529 38.462 0.00 0.00 0.00 1.82
3845 6225 4.785346 AATGAGCACCTGATCCAGTTAT 57.215 40.909 0.00 0.00 0.00 1.89
3895 6275 3.076484 AGCACCAAAGGGCATATCCATAT 59.924 43.478 0.00 0.00 37.90 1.78
3896 6276 2.446666 AGCACCAAAGGGCATATCCATA 59.553 45.455 0.00 0.00 37.90 2.74
3897 6277 1.218704 AGCACCAAAGGGCATATCCAT 59.781 47.619 0.00 0.00 37.90 3.41
3899 6279 1.035139 CAGCACCAAAGGGCATATCC 58.965 55.000 0.00 0.00 37.90 2.59
3912 6296 4.490743 ACAAGTACAAAAACAACAGCACC 58.509 39.130 0.00 0.00 0.00 5.01
3913 6297 5.404066 ACAACAAGTACAAAAACAACAGCAC 59.596 36.000 0.00 0.00 0.00 4.40
3927 6311 5.587443 AGTTTAACACTGGGACAACAAGTAC 59.413 40.000 0.00 0.00 38.70 2.73
3928 6312 5.747342 AGTTTAACACTGGGACAACAAGTA 58.253 37.500 0.00 0.00 38.70 2.24
3929 6313 4.595986 AGTTTAACACTGGGACAACAAGT 58.404 39.130 0.00 0.00 38.70 3.16
3941 6325 8.446599 AAGTGCAGTATTAACAGTTTAACACT 57.553 30.769 0.00 0.00 35.68 3.55
3944 6328 8.347035 TGGAAAGTGCAGTATTAACAGTTTAAC 58.653 33.333 0.00 0.00 37.14 2.01
3945 6329 8.453238 TGGAAAGTGCAGTATTAACAGTTTAA 57.547 30.769 0.00 0.00 37.14 1.52
3946 6330 8.094798 CTGGAAAGTGCAGTATTAACAGTTTA 57.905 34.615 0.00 0.00 37.14 2.01
3948 6332 6.560253 CTGGAAAGTGCAGTATTAACAGTT 57.440 37.500 0.00 0.00 30.66 3.16
3962 6346 4.330074 CGCTACCTTTATCACTGGAAAGTG 59.670 45.833 0.00 0.00 40.90 3.16
3964 6348 4.755411 TCGCTACCTTTATCACTGGAAAG 58.245 43.478 0.00 0.00 33.31 2.62
3985 6369 1.547820 TGCACTGGAGTCAGATCACTC 59.452 52.381 4.91 4.91 43.49 3.51
3998 6382 2.808543 GTTCTTGTAGTCCTTGCACTGG 59.191 50.000 0.00 0.00 0.00 4.00
4027 6411 1.342174 CAATTGTTCCAGCCTGCAGTT 59.658 47.619 13.81 0.00 0.00 3.16
4028 6412 0.963962 CAATTGTTCCAGCCTGCAGT 59.036 50.000 13.81 0.00 0.00 4.40
4041 6425 7.095523 GCACTCAAATTCAAATGCTACAATTGT 60.096 33.333 16.68 16.68 0.00 2.71
4058 6442 4.334203 TCAAATATTACGCGGCACTCAAAT 59.666 37.500 12.47 1.05 0.00 2.32
4094 6478 7.672122 ATATTTAGGAACGGAAGGAGTAGTT 57.328 36.000 0.00 0.00 0.00 2.24
4117 6501 9.853177 CCTAGTGAAATCCCTACAAAGATTTAT 57.147 33.333 0.00 0.00 41.56 1.40
4118 6502 8.832735 ACCTAGTGAAATCCCTACAAAGATTTA 58.167 33.333 0.00 0.00 41.56 1.40
4119 6503 7.611855 CACCTAGTGAAATCCCTACAAAGATTT 59.388 37.037 0.00 0.00 43.58 2.17
4120 6504 7.112779 CACCTAGTGAAATCCCTACAAAGATT 58.887 38.462 0.00 0.00 35.23 2.40
4121 6505 6.353082 CCACCTAGTGAAATCCCTACAAAGAT 60.353 42.308 0.00 0.00 35.23 2.40
4122 6506 5.045869 CCACCTAGTGAAATCCCTACAAAGA 60.046 44.000 0.00 0.00 35.23 2.52
4123 6507 5.045869 TCCACCTAGTGAAATCCCTACAAAG 60.046 44.000 0.00 0.00 35.23 2.77
4124 6508 4.847512 TCCACCTAGTGAAATCCCTACAAA 59.152 41.667 0.00 0.00 35.23 2.83
4125 6509 4.431378 TCCACCTAGTGAAATCCCTACAA 58.569 43.478 0.00 0.00 35.23 2.41
4126 6510 4.069312 TCCACCTAGTGAAATCCCTACA 57.931 45.455 0.00 0.00 35.23 2.74
4127 6511 5.632034 AATCCACCTAGTGAAATCCCTAC 57.368 43.478 0.00 0.00 35.23 3.18
4128 6512 6.206787 TGTAATCCACCTAGTGAAATCCCTA 58.793 40.000 0.00 0.00 35.23 3.53
4129 6513 5.036916 TGTAATCCACCTAGTGAAATCCCT 58.963 41.667 0.00 0.00 35.23 4.20
4130 6514 5.367945 TGTAATCCACCTAGTGAAATCCC 57.632 43.478 0.00 0.00 35.23 3.85
4131 6515 9.877178 CTATATGTAATCCACCTAGTGAAATCC 57.123 37.037 0.00 0.00 35.23 3.01
4134 6518 8.585881 GCTCTATATGTAATCCACCTAGTGAAA 58.414 37.037 0.00 0.00 35.23 2.69
4135 6519 7.728532 TGCTCTATATGTAATCCACCTAGTGAA 59.271 37.037 0.00 0.00 35.23 3.18
4136 6520 7.238710 TGCTCTATATGTAATCCACCTAGTGA 58.761 38.462 0.00 0.00 35.23 3.41
4137 6521 7.468141 TGCTCTATATGTAATCCACCTAGTG 57.532 40.000 0.00 0.00 0.00 2.74
4138 6522 8.492415 TTTGCTCTATATGTAATCCACCTAGT 57.508 34.615 0.00 0.00 0.00 2.57
4139 6523 9.950496 ATTTTGCTCTATATGTAATCCACCTAG 57.050 33.333 0.00 0.00 0.00 3.02
4140 6524 9.725019 CATTTTGCTCTATATGTAATCCACCTA 57.275 33.333 0.00 0.00 0.00 3.08
4141 6525 8.439971 TCATTTTGCTCTATATGTAATCCACCT 58.560 33.333 0.00 0.00 0.00 4.00
4142 6526 8.621532 TCATTTTGCTCTATATGTAATCCACC 57.378 34.615 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.