Multiple sequence alignment - TraesCS3B01G293300

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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 TraesCS3B01G293300 chr3B 100.000 4005 0 0 1 4005 472325446 472321442 0.000000e+00 7396
1 TraesCS3B01G293300 chr3D 95.917 3747 80 16 1 3707 362433785 362430072 0.000000e+00 6004
2 TraesCS3B01G293300 chr3A 93.652 2678 108 26 1 2625 482978471 482975803 0.000000e+00 3947
3 TraesCS3B01G293300 chr3A 89.453 1024 57 18 2687 3707 482974294 482973319 0.000000e+00 1245
4 TraesCS3B01G293300 chr3A 92.208 154 11 1 3811 3964 746623934 746623782 2.420000e-52 217
5 TraesCS3B01G293300 chr3A 94.231 104 6 0 3708 3811 76558894 76558791 4.140000e-35 159
6 TraesCS3B01G293300 chr3A 93.269 104 7 0 3708 3811 76558481 76558584 1.930000e-33 154
7 TraesCS3B01G293300 chr6D 86.517 267 22 4 3708 3961 316566932 316567197 8.470000e-72 281
8 TraesCS3B01G293300 chr4A 94.737 152 8 0 3811 3962 617237212 617237061 1.860000e-58 237
9 TraesCS3B01G293300 chr6B 94.156 154 9 0 3811 3964 225313712 225313559 6.690000e-58 235
10 TraesCS3B01G293300 chr6B 89.571 163 9 3 1437 1592 542943513 542943674 2.440000e-47 200
11 TraesCS3B01G293300 chr6B 94.595 111 5 1 3702 3811 225313862 225313752 1.910000e-38 171
12 TraesCS3B01G293300 chr6B 94.231 104 6 0 3708 3811 676472283 676472386 4.140000e-35 159
13 TraesCS3B01G293300 chr6A 94.000 150 9 0 3811 3960 98219554 98219703 1.120000e-55 228
14 TraesCS3B01G293300 chr6A 87.435 191 17 2 1437 1621 265783484 265783295 3.140000e-51 213
15 TraesCS3B01G293300 chr2B 93.333 150 10 0 3811 3960 322557042 322557191 5.210000e-54 222
16 TraesCS3B01G293300 chr2B 92.035 113 8 1 3700 3811 322556891 322557003 1.490000e-34 158
17 TraesCS3B01G293300 chr5B 93.836 146 9 0 3815 3960 244122371 244122226 1.870000e-53 220
18 TraesCS3B01G293300 chr5B 93.836 146 9 0 3811 3956 658381501 658381646 1.870000e-53 220
19 TraesCS3B01G293300 chr5B 95.146 103 5 0 3708 3810 658381358 658381460 3.200000e-36 163
20 TraesCS3B01G293300 chr5B 94.231 104 6 0 3708 3811 244122511 244122408 4.140000e-35 159
21 TraesCS3B01G293300 chr5A 93.333 150 9 1 3811 3960 572354008 572353860 1.870000e-53 220
22 TraesCS3B01G293300 chr5A 86.387 191 19 2 1437 1621 162033605 162033416 6.790000e-48 202
23 TraesCS3B01G293300 chr1A 94.891 137 7 0 3811 3947 278370916 278371052 8.720000e-52 215
24 TraesCS3B01G293300 chr2A 92.920 113 7 1 3700 3811 592747049 592746937 3.200000e-36 163


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 TraesCS3B01G293300 chr3B 472321442 472325446 4004 True 7396 7396 100.0000 1 4005 1 chr3B.!!$R1 4004
1 TraesCS3B01G293300 chr3D 362430072 362433785 3713 True 6004 6004 95.9170 1 3707 1 chr3D.!!$R1 3706
2 TraesCS3B01G293300 chr3A 482973319 482978471 5152 True 2596 3947 91.5525 1 3707 2 chr3A.!!$R3 3706

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
72 73 0.686789 CCCGGGATCTGATGTGCATA 59.313 55.000 18.48 0.0 0.00 3.14 F
82 83 1.135333 TGATGTGCATACGCGTTCCTA 59.865 47.619 20.78 0.0 42.97 2.94 F
216 217 1.216175 ACCATGCCCTGATTGCACTAT 59.784 47.619 0.00 0.0 42.38 2.12 F
263 264 1.593196 TGCTGTTCCTCCTTTGTTCG 58.407 50.000 0.00 0.0 0.00 3.95 F
292 293 2.002586 CCACTTGATACTGAACCTGCG 58.997 52.381 0.00 0.0 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2020 0.314935 AGTTTTGCAACATGGCCTCG 59.685 50.000 3.32 0.00 35.05 4.63 R
2563 2619 7.565680 AGGGATATCGTTCAAGAGTTTGTTAT 58.434 34.615 0.00 0.00 35.73 1.89 R
2576 2632 2.872858 GGCACTTCAAGGGATATCGTTC 59.127 50.000 0.00 0.00 0.00 3.95 R
2617 2673 4.889995 TGGTGACAAAACATAATGGTGACA 59.110 37.500 0.00 0.00 41.82 3.58 R
3876 5400 0.032515 TCTCCTGGCCGTTGGATCTA 60.033 55.000 11.60 0.27 0.00 1.98 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
24 25 1.160137 CGGTGCTTCTTTTCTGAGGG 58.840 55.000 0.00 0.00 0.00 4.30
72 73 0.686789 CCCGGGATCTGATGTGCATA 59.313 55.000 18.48 0.00 0.00 3.14
82 83 1.135333 TGATGTGCATACGCGTTCCTA 59.865 47.619 20.78 0.00 42.97 2.94
85 86 1.135333 TGTGCATACGCGTTCCTATCA 59.865 47.619 20.78 7.84 42.97 2.15
94 95 3.186909 CGCGTTCCTATCATGAACTTGA 58.813 45.455 0.00 0.00 39.92 3.02
216 217 1.216175 ACCATGCCCTGATTGCACTAT 59.784 47.619 0.00 0.00 42.38 2.12
263 264 1.593196 TGCTGTTCCTCCTTTGTTCG 58.407 50.000 0.00 0.00 0.00 3.95
292 293 2.002586 CCACTTGATACTGAACCTGCG 58.997 52.381 0.00 0.00 0.00 5.18
296 297 2.654749 TGATACTGAACCTGCGACAG 57.345 50.000 0.00 0.00 37.62 3.51
558 563 2.737252 GTTCTAGTTTTGCCTCGTCCTG 59.263 50.000 0.00 0.00 0.00 3.86
899 920 6.239008 GGTTCTTGAATGTGGTGATTGAAAGA 60.239 38.462 0.00 0.00 0.00 2.52
1003 1024 3.126001 TCAAAACTCAGGAAGCGATGT 57.874 42.857 0.00 0.00 0.00 3.06
1636 1686 2.002586 CCTTCGCACGATTTCATCTGT 58.997 47.619 0.00 0.00 0.00 3.41
1970 2020 8.568732 TGGTAAAATCAAAGTTTTTGATCGAC 57.431 30.769 15.17 12.88 38.11 4.20
2563 2619 9.642327 CAATTTCCAGTTCATCACATAATTTGA 57.358 29.630 0.00 0.00 0.00 2.69
2597 2653 2.622064 ACGATATCCCTTGAAGTGCC 57.378 50.000 0.00 0.00 0.00 5.01
2613 2669 7.156876 TGAAGTGCCCAAACTAATCTTTATG 57.843 36.000 0.00 0.00 0.00 1.90
2614 2670 6.719370 TGAAGTGCCCAAACTAATCTTTATGT 59.281 34.615 0.00 0.00 0.00 2.29
2615 2671 7.232534 TGAAGTGCCCAAACTAATCTTTATGTT 59.767 33.333 0.00 0.00 0.00 2.71
2616 2672 7.539034 AGTGCCCAAACTAATCTTTATGTTT 57.461 32.000 0.00 0.00 33.56 2.83
2617 2673 7.962441 AGTGCCCAAACTAATCTTTATGTTTT 58.038 30.769 0.00 0.00 31.30 2.43
2618 2674 7.872483 AGTGCCCAAACTAATCTTTATGTTTTG 59.128 33.333 0.00 0.00 31.30 2.44
2619 2675 7.655732 GTGCCCAAACTAATCTTTATGTTTTGT 59.344 33.333 0.00 0.00 31.30 2.83
2620 2676 7.870445 TGCCCAAACTAATCTTTATGTTTTGTC 59.130 33.333 0.00 0.00 31.30 3.18
2621 2677 7.870445 GCCCAAACTAATCTTTATGTTTTGTCA 59.130 33.333 0.00 0.00 31.30 3.58
2622 2678 9.191995 CCCAAACTAATCTTTATGTTTTGTCAC 57.808 33.333 0.00 0.00 31.30 3.67
2623 2679 9.191995 CCAAACTAATCTTTATGTTTTGTCACC 57.808 33.333 0.00 0.00 31.30 4.02
2624 2680 9.743057 CAAACTAATCTTTATGTTTTGTCACCA 57.257 29.630 0.00 0.00 31.30 4.17
2911 4431 2.279517 GGTCTATGGCCTCACGCG 60.280 66.667 3.53 3.53 38.94 6.01
3357 4877 4.359105 TGGAGGTTGTAGCAAGTAGGTAT 58.641 43.478 0.00 0.00 31.99 2.73
3360 4880 5.105064 GGAGGTTGTAGCAAGTAGGTATGAA 60.105 44.000 0.00 0.00 31.99 2.57
3371 4891 8.680903 AGCAAGTAGGTATGAATGATTTTGAAG 58.319 33.333 0.00 0.00 0.00 3.02
3527 5051 8.515414 TGTCACTATATTCATCTAACTGATCCG 58.485 37.037 0.00 0.00 32.05 4.18
3623 5147 1.154225 CCCACGAGCGTCAAAATGC 60.154 57.895 0.00 0.00 37.71 3.56
3629 5153 0.881118 GAGCGTCAAAATGCCTCCAA 59.119 50.000 0.00 0.00 38.23 3.53
3644 5168 3.549794 CCTCCAAGTTCCATGATTCCTC 58.450 50.000 0.00 0.00 0.00 3.71
3648 5172 3.599343 CAAGTTCCATGATTCCTCGTGA 58.401 45.455 0.00 0.00 40.28 4.35
3680 5204 3.732849 GCCCTAGCACCTGCCCTT 61.733 66.667 0.00 0.00 43.38 3.95
3711 5235 3.933722 CCATGCTCCGGCCGAGAT 61.934 66.667 30.73 9.63 41.63 2.75
3712 5236 2.356793 CATGCTCCGGCCGAGATC 60.357 66.667 30.73 17.86 41.63 2.75
3713 5237 3.620785 ATGCTCCGGCCGAGATCC 61.621 66.667 30.73 15.48 41.63 3.36
3723 5247 2.202932 CGAGATCCGGTGCCTTGG 60.203 66.667 0.00 0.00 33.91 3.61
3724 5248 2.514824 GAGATCCGGTGCCTTGGC 60.515 66.667 0.00 4.43 0.00 4.52
3725 5249 3.329542 GAGATCCGGTGCCTTGGCA 62.330 63.158 10.65 10.65 0.00 4.92
3726 5250 3.134127 GATCCGGTGCCTTGGCAC 61.134 66.667 30.40 30.40 39.72 5.01
3727 5251 3.918253 GATCCGGTGCCTTGGCACA 62.918 63.158 35.86 22.00 41.97 4.57
3728 5252 4.947147 TCCGGTGCCTTGGCACAC 62.947 66.667 35.86 26.15 41.97 3.82
3730 5254 3.964875 CGGTGCCTTGGCACACAC 61.965 66.667 35.86 22.49 41.97 3.82
3731 5255 2.832661 GGTGCCTTGGCACACACA 60.833 61.111 35.86 5.15 41.97 3.72
3732 5256 2.422231 GGTGCCTTGGCACACACAA 61.422 57.895 35.86 4.44 41.97 3.33
3733 5257 1.066257 GTGCCTTGGCACACACAAG 59.934 57.895 32.37 0.00 43.73 3.16
3736 5260 3.524014 CTTGGCACACACAAGGCA 58.476 55.556 0.00 0.00 41.16 4.75
3737 5261 1.066257 CTTGGCACACACAAGGCAC 59.934 57.895 0.00 0.00 41.16 5.01
3738 5262 1.665264 CTTGGCACACACAAGGCACA 61.665 55.000 0.00 0.00 41.16 4.57
3739 5263 1.042003 TTGGCACACACAAGGCACAT 61.042 50.000 0.00 0.00 39.29 3.21
3740 5264 1.007038 GGCACACACAAGGCACATG 60.007 57.895 0.00 0.00 0.00 3.21
3741 5265 1.735360 GCACACACAAGGCACATGT 59.265 52.632 0.00 0.00 42.78 3.21
3756 5280 3.441163 CACATGTGAATAGTGCAATGCC 58.559 45.455 21.64 0.00 0.00 4.40
3757 5281 3.129813 CACATGTGAATAGTGCAATGCCT 59.870 43.478 21.64 1.90 0.00 4.75
3758 5282 3.765511 ACATGTGAATAGTGCAATGCCTT 59.234 39.130 1.53 0.00 0.00 4.35
3759 5283 3.853831 TGTGAATAGTGCAATGCCTTG 57.146 42.857 1.53 0.00 35.36 3.61
3760 5284 3.419943 TGTGAATAGTGCAATGCCTTGA 58.580 40.909 1.53 0.00 34.04 3.02
3761 5285 3.441222 TGTGAATAGTGCAATGCCTTGAG 59.559 43.478 1.53 0.00 34.04 3.02
3762 5286 2.424601 TGAATAGTGCAATGCCTTGAGC 59.575 45.455 1.53 0.00 44.14 4.26
3763 5287 2.431954 ATAGTGCAATGCCTTGAGCT 57.568 45.000 1.53 5.06 44.23 4.09
3764 5288 2.205022 TAGTGCAATGCCTTGAGCTT 57.795 45.000 1.53 0.00 44.23 3.74
3765 5289 1.335145 AGTGCAATGCCTTGAGCTTT 58.665 45.000 1.53 0.00 44.23 3.51
3766 5290 1.271656 AGTGCAATGCCTTGAGCTTTC 59.728 47.619 1.53 0.00 44.23 2.62
3767 5291 1.000060 GTGCAATGCCTTGAGCTTTCA 60.000 47.619 1.53 0.00 44.23 2.69
3768 5292 1.271379 TGCAATGCCTTGAGCTTTCAG 59.729 47.619 1.53 0.00 44.23 3.02
3769 5293 1.992170 CAATGCCTTGAGCTTTCAGC 58.008 50.000 0.00 0.00 44.23 4.26
3770 5294 0.893447 AATGCCTTGAGCTTTCAGCC 59.107 50.000 0.00 0.00 43.77 4.85
3771 5295 1.310933 ATGCCTTGAGCTTTCAGCCG 61.311 55.000 0.00 0.00 43.77 5.52
3772 5296 1.968540 GCCTTGAGCTTTCAGCCGT 60.969 57.895 0.00 0.00 43.77 5.68
3773 5297 1.518903 GCCTTGAGCTTTCAGCCGTT 61.519 55.000 0.00 0.00 43.77 4.44
3774 5298 1.808411 CCTTGAGCTTTCAGCCGTTA 58.192 50.000 0.00 0.00 43.77 3.18
3775 5299 1.734465 CCTTGAGCTTTCAGCCGTTAG 59.266 52.381 0.00 0.00 43.77 2.34
3776 5300 2.612972 CCTTGAGCTTTCAGCCGTTAGA 60.613 50.000 0.00 0.00 43.77 2.10
3777 5301 3.265791 CTTGAGCTTTCAGCCGTTAGAT 58.734 45.455 0.00 0.00 43.77 1.98
3778 5302 2.893637 TGAGCTTTCAGCCGTTAGATC 58.106 47.619 0.00 0.00 43.77 2.75
3779 5303 1.855360 GAGCTTTCAGCCGTTAGATCG 59.145 52.381 0.00 0.00 43.77 3.69
3792 5316 5.796350 CGTTAGATCGGAAATCAAGGTTT 57.204 39.130 0.00 0.00 0.00 3.27
3793 5317 5.796813 CGTTAGATCGGAAATCAAGGTTTC 58.203 41.667 0.00 0.00 37.37 2.78
3794 5318 5.350365 CGTTAGATCGGAAATCAAGGTTTCA 59.650 40.000 7.97 0.00 39.33 2.69
3795 5319 6.455646 CGTTAGATCGGAAATCAAGGTTTCAG 60.456 42.308 7.97 4.17 39.33 3.02
3796 5320 5.165961 AGATCGGAAATCAAGGTTTCAGA 57.834 39.130 10.28 10.28 43.12 3.27
3798 5322 6.183347 AGATCGGAAATCAAGGTTTCAGATT 58.817 36.000 18.05 9.05 46.03 2.40
3799 5323 6.660949 AGATCGGAAATCAAGGTTTCAGATTT 59.339 34.615 18.05 12.25 46.03 2.17
3800 5324 6.648879 TCGGAAATCAAGGTTTCAGATTTT 57.351 33.333 7.97 0.00 40.83 1.82
3801 5325 7.753309 TCGGAAATCAAGGTTTCAGATTTTA 57.247 32.000 7.97 0.00 40.83 1.52
3802 5326 7.816640 TCGGAAATCAAGGTTTCAGATTTTAG 58.183 34.615 7.97 0.00 40.83 1.85
3803 5327 7.447238 TCGGAAATCAAGGTTTCAGATTTTAGT 59.553 33.333 7.97 0.00 40.83 2.24
3804 5328 7.538678 CGGAAATCAAGGTTTCAGATTTTAGTG 59.461 37.037 7.97 0.00 40.83 2.74
3805 5329 7.814587 GGAAATCAAGGTTTCAGATTTTAGTGG 59.185 37.037 7.97 0.00 40.83 4.00
3806 5330 8.477419 AAATCAAGGTTTCAGATTTTAGTGGA 57.523 30.769 0.00 0.00 38.44 4.02
3807 5331 6.877611 TCAAGGTTTCAGATTTTAGTGGAC 57.122 37.500 0.00 0.00 0.00 4.02
3808 5332 6.361433 TCAAGGTTTCAGATTTTAGTGGACA 58.639 36.000 0.00 0.00 0.00 4.02
3809 5333 6.486657 TCAAGGTTTCAGATTTTAGTGGACAG 59.513 38.462 0.00 0.00 0.00 3.51
3810 5334 5.941788 AGGTTTCAGATTTTAGTGGACAGT 58.058 37.500 0.00 0.00 0.00 3.55
3811 5335 5.765182 AGGTTTCAGATTTTAGTGGACAGTG 59.235 40.000 0.00 0.00 0.00 3.66
3812 5336 5.531287 GGTTTCAGATTTTAGTGGACAGTGT 59.469 40.000 0.00 0.00 0.00 3.55
3813 5337 6.708949 GGTTTCAGATTTTAGTGGACAGTGTA 59.291 38.462 0.00 0.00 0.00 2.90
3814 5338 7.095187 GGTTTCAGATTTTAGTGGACAGTGTAG 60.095 40.741 0.00 0.00 0.00 2.74
3815 5339 5.479306 TCAGATTTTAGTGGACAGTGTAGC 58.521 41.667 0.00 0.00 0.00 3.58
3816 5340 5.011635 TCAGATTTTAGTGGACAGTGTAGCA 59.988 40.000 0.00 0.00 0.00 3.49
3817 5341 5.349817 CAGATTTTAGTGGACAGTGTAGCAG 59.650 44.000 0.00 0.00 0.00 4.24
3818 5342 4.948341 TTTTAGTGGACAGTGTAGCAGA 57.052 40.909 0.00 0.00 0.00 4.26
3819 5343 3.936372 TTAGTGGACAGTGTAGCAGAC 57.064 47.619 0.00 0.00 0.00 3.51
3820 5344 2.002505 AGTGGACAGTGTAGCAGACT 57.997 50.000 0.00 0.00 0.00 3.24
3821 5345 2.320781 AGTGGACAGTGTAGCAGACTT 58.679 47.619 0.00 0.00 0.00 3.01
3822 5346 2.297597 AGTGGACAGTGTAGCAGACTTC 59.702 50.000 0.00 0.00 0.00 3.01
3823 5347 1.618837 TGGACAGTGTAGCAGACTTCC 59.381 52.381 0.00 0.00 0.00 3.46
3824 5348 1.896465 GGACAGTGTAGCAGACTTCCT 59.104 52.381 0.00 0.00 0.00 3.36
3825 5349 2.353208 GGACAGTGTAGCAGACTTCCTG 60.353 54.545 0.00 0.00 45.67 3.86
3826 5350 2.297597 GACAGTGTAGCAGACTTCCTGT 59.702 50.000 0.00 0.00 44.71 4.00
3827 5351 3.497332 ACAGTGTAGCAGACTTCCTGTA 58.503 45.455 0.00 0.00 44.71 2.74
3828 5352 3.508012 ACAGTGTAGCAGACTTCCTGTAG 59.492 47.826 0.00 0.00 44.71 2.74
3829 5353 2.494073 AGTGTAGCAGACTTCCTGTAGC 59.506 50.000 0.00 0.00 44.71 3.58
3830 5354 1.472878 TGTAGCAGACTTCCTGTAGCG 59.527 52.381 0.00 0.00 44.71 4.26
3831 5355 1.103803 TAGCAGACTTCCTGTAGCGG 58.896 55.000 0.00 0.00 44.71 5.52
3832 5356 0.900647 AGCAGACTTCCTGTAGCGGT 60.901 55.000 0.00 0.00 44.71 5.68
3833 5357 0.737715 GCAGACTTCCTGTAGCGGTG 60.738 60.000 0.00 0.00 44.71 4.94
3834 5358 0.603569 CAGACTTCCTGTAGCGGTGT 59.396 55.000 0.00 0.00 38.10 4.16
3835 5359 1.816835 CAGACTTCCTGTAGCGGTGTA 59.183 52.381 0.00 0.00 38.10 2.90
3836 5360 1.817447 AGACTTCCTGTAGCGGTGTAC 59.183 52.381 0.00 0.00 0.00 2.90
3837 5361 1.817447 GACTTCCTGTAGCGGTGTACT 59.183 52.381 0.00 0.00 0.00 2.73
3838 5362 1.544691 ACTTCCTGTAGCGGTGTACTG 59.455 52.381 0.00 0.00 0.00 2.74
3839 5363 1.544691 CTTCCTGTAGCGGTGTACTGT 59.455 52.381 0.00 0.00 0.00 3.55
3840 5364 2.495155 TCCTGTAGCGGTGTACTGTA 57.505 50.000 0.00 0.00 0.00 2.74
3841 5365 2.362736 TCCTGTAGCGGTGTACTGTAG 58.637 52.381 0.00 0.00 0.00 2.74
3842 5366 2.089980 CCTGTAGCGGTGTACTGTAGT 58.910 52.381 0.00 0.00 0.00 2.73
3843 5367 2.159421 CCTGTAGCGGTGTACTGTAGTG 60.159 54.545 0.00 0.00 0.00 2.74
3844 5368 1.814394 TGTAGCGGTGTACTGTAGTGG 59.186 52.381 0.00 0.00 0.00 4.00
3845 5369 1.815003 GTAGCGGTGTACTGTAGTGGT 59.185 52.381 0.00 0.00 0.00 4.16
3846 5370 0.601558 AGCGGTGTACTGTAGTGGTG 59.398 55.000 0.00 0.00 0.00 4.17
3847 5371 0.599558 GCGGTGTACTGTAGTGGTGA 59.400 55.000 0.00 0.00 0.00 4.02
3848 5372 1.668047 GCGGTGTACTGTAGTGGTGAC 60.668 57.143 0.00 0.00 0.00 3.67
3849 5373 1.884579 CGGTGTACTGTAGTGGTGACT 59.115 52.381 0.00 0.00 36.07 3.41
3850 5374 2.095364 CGGTGTACTGTAGTGGTGACTC 60.095 54.545 0.00 0.00 33.21 3.36
3851 5375 3.155501 GGTGTACTGTAGTGGTGACTCT 58.844 50.000 0.00 0.00 37.95 3.24
3852 5376 3.573110 GGTGTACTGTAGTGGTGACTCTT 59.427 47.826 0.00 0.00 35.43 2.85
3853 5377 4.547532 GTGTACTGTAGTGGTGACTCTTG 58.452 47.826 0.00 0.00 35.43 3.02
3854 5378 4.277672 GTGTACTGTAGTGGTGACTCTTGA 59.722 45.833 0.00 0.00 35.43 3.02
3855 5379 5.047943 GTGTACTGTAGTGGTGACTCTTGAT 60.048 44.000 0.00 0.00 35.43 2.57
3856 5380 4.527509 ACTGTAGTGGTGACTCTTGATG 57.472 45.455 0.00 0.00 35.43 3.07
3857 5381 3.898123 ACTGTAGTGGTGACTCTTGATGT 59.102 43.478 0.00 0.00 35.43 3.06
3858 5382 4.345257 ACTGTAGTGGTGACTCTTGATGTT 59.655 41.667 0.00 0.00 35.43 2.71
3859 5383 4.883083 TGTAGTGGTGACTCTTGATGTTC 58.117 43.478 0.00 0.00 35.43 3.18
3860 5384 4.343814 TGTAGTGGTGACTCTTGATGTTCA 59.656 41.667 0.00 0.00 35.43 3.18
3861 5385 4.630644 AGTGGTGACTCTTGATGTTCAT 57.369 40.909 0.00 0.00 0.00 2.57
3862 5386 4.573900 AGTGGTGACTCTTGATGTTCATC 58.426 43.478 5.91 5.91 0.00 2.92
3863 5387 4.040829 AGTGGTGACTCTTGATGTTCATCA 59.959 41.667 10.88 10.88 0.00 3.07
3864 5388 4.391216 GTGGTGACTCTTGATGTTCATCAG 59.609 45.833 13.89 9.57 31.46 2.90
3865 5389 4.284234 TGGTGACTCTTGATGTTCATCAGA 59.716 41.667 13.89 12.42 31.46 3.27
3866 5390 4.629200 GGTGACTCTTGATGTTCATCAGAC 59.371 45.833 13.89 6.03 31.46 3.51
3867 5391 4.629200 GTGACTCTTGATGTTCATCAGACC 59.371 45.833 13.89 5.97 31.46 3.85
3868 5392 3.854666 ACTCTTGATGTTCATCAGACCG 58.145 45.455 13.89 8.11 31.46 4.79
3869 5393 3.259374 ACTCTTGATGTTCATCAGACCGT 59.741 43.478 13.89 8.59 31.46 4.83
3870 5394 3.849911 TCTTGATGTTCATCAGACCGTC 58.150 45.455 13.89 0.00 31.46 4.79
3871 5395 2.278026 TGATGTTCATCAGACCGTCG 57.722 50.000 10.88 0.00 0.00 5.12
3872 5396 0.924090 GATGTTCATCAGACCGTCGC 59.076 55.000 7.78 0.00 0.00 5.19
3873 5397 0.532573 ATGTTCATCAGACCGTCGCT 59.467 50.000 0.00 0.00 0.00 4.93
3874 5398 0.317160 TGTTCATCAGACCGTCGCTT 59.683 50.000 0.00 0.00 0.00 4.68
3875 5399 0.716108 GTTCATCAGACCGTCGCTTG 59.284 55.000 0.00 0.00 0.00 4.01
3876 5400 0.317160 TTCATCAGACCGTCGCTTGT 59.683 50.000 0.00 0.00 0.00 3.16
3877 5401 1.170442 TCATCAGACCGTCGCTTGTA 58.830 50.000 0.00 0.00 0.00 2.41
3878 5402 1.132453 TCATCAGACCGTCGCTTGTAG 59.868 52.381 0.00 0.00 0.00 2.74
3879 5403 1.132453 CATCAGACCGTCGCTTGTAGA 59.868 52.381 0.00 0.00 0.00 2.59
3880 5404 1.460504 TCAGACCGTCGCTTGTAGAT 58.539 50.000 0.00 0.00 0.00 1.98
3881 5405 1.400846 TCAGACCGTCGCTTGTAGATC 59.599 52.381 0.00 0.00 0.00 2.75
3882 5406 0.739561 AGACCGTCGCTTGTAGATCC 59.260 55.000 0.00 0.00 0.00 3.36
3883 5407 0.454600 GACCGTCGCTTGTAGATCCA 59.545 55.000 0.00 0.00 0.00 3.41
3884 5408 0.892755 ACCGTCGCTTGTAGATCCAA 59.107 50.000 0.00 0.00 0.00 3.53
3885 5409 1.278238 CCGTCGCTTGTAGATCCAAC 58.722 55.000 0.00 0.00 0.00 3.77
3886 5410 0.914551 CGTCGCTTGTAGATCCAACG 59.085 55.000 0.00 0.00 0.00 4.10
3887 5411 1.278238 GTCGCTTGTAGATCCAACGG 58.722 55.000 0.00 0.00 0.00 4.44
3888 5412 0.459585 TCGCTTGTAGATCCAACGGC 60.460 55.000 0.00 0.00 0.00 5.68
3889 5413 1.429148 CGCTTGTAGATCCAACGGCC 61.429 60.000 0.00 0.00 0.00 6.13
3890 5414 0.392461 GCTTGTAGATCCAACGGCCA 60.392 55.000 2.24 0.00 0.00 5.36
3891 5415 1.656652 CTTGTAGATCCAACGGCCAG 58.343 55.000 2.24 0.00 0.00 4.85
3892 5416 0.251916 TTGTAGATCCAACGGCCAGG 59.748 55.000 2.24 0.60 0.00 4.45
3893 5417 0.616395 TGTAGATCCAACGGCCAGGA 60.616 55.000 10.66 10.66 38.50 3.86
3894 5418 0.105039 GTAGATCCAACGGCCAGGAG 59.895 60.000 13.35 0.00 37.34 3.69
3895 5419 0.032515 TAGATCCAACGGCCAGGAGA 60.033 55.000 13.35 0.17 37.34 3.71
3896 5420 0.692419 AGATCCAACGGCCAGGAGAT 60.692 55.000 13.35 5.05 37.34 2.75
3897 5421 0.533755 GATCCAACGGCCAGGAGATG 60.534 60.000 13.35 0.00 37.34 2.90
3898 5422 2.615227 ATCCAACGGCCAGGAGATGC 62.615 60.000 13.35 0.00 37.34 3.91
3899 5423 2.825836 CAACGGCCAGGAGATGCC 60.826 66.667 2.24 0.00 44.41 4.40
3900 5424 4.115199 AACGGCCAGGAGATGCCC 62.115 66.667 2.24 0.00 45.07 5.36
3902 5426 4.247380 CGGCCAGGAGATGCCCTC 62.247 72.222 2.24 0.00 45.07 4.30
3903 5427 3.092511 GGCCAGGAGATGCCCTCA 61.093 66.667 0.00 0.00 43.76 3.86
3904 5428 2.683465 GGCCAGGAGATGCCCTCAA 61.683 63.158 0.00 0.00 43.76 3.02
3905 5429 1.153005 GCCAGGAGATGCCCTCAAG 60.153 63.158 0.00 0.00 43.76 3.02
3906 5430 1.530771 CCAGGAGATGCCCTCAAGG 59.469 63.158 5.71 3.16 43.76 3.61
3916 5440 3.369381 CCCTCAAGGCACGATACTG 57.631 57.895 0.00 0.00 0.00 2.74
3917 5441 0.537188 CCCTCAAGGCACGATACTGT 59.463 55.000 0.00 0.00 0.00 3.55
3918 5442 1.066143 CCCTCAAGGCACGATACTGTT 60.066 52.381 0.00 0.00 0.00 3.16
3919 5443 2.271800 CCTCAAGGCACGATACTGTTC 58.728 52.381 0.00 0.00 0.00 3.18
3920 5444 2.353704 CCTCAAGGCACGATACTGTTCA 60.354 50.000 0.00 0.00 0.00 3.18
3921 5445 3.525537 CTCAAGGCACGATACTGTTCAT 58.474 45.455 0.00 0.00 0.00 2.57
3922 5446 3.521560 TCAAGGCACGATACTGTTCATC 58.478 45.455 0.00 0.00 0.00 2.92
3923 5447 2.604046 AGGCACGATACTGTTCATCC 57.396 50.000 0.00 0.00 0.00 3.51
3924 5448 1.202417 AGGCACGATACTGTTCATCCG 60.202 52.381 0.00 0.00 0.00 4.18
3925 5449 1.470979 GGCACGATACTGTTCATCCGT 60.471 52.381 0.00 0.00 0.00 4.69
3926 5450 1.588404 GCACGATACTGTTCATCCGTG 59.412 52.381 0.00 0.00 33.76 4.94
3927 5451 1.588404 CACGATACTGTTCATCCGTGC 59.412 52.381 0.00 0.00 0.00 5.34
3928 5452 1.209128 CGATACTGTTCATCCGTGCC 58.791 55.000 0.00 0.00 0.00 5.01
3929 5453 1.202417 CGATACTGTTCATCCGTGCCT 60.202 52.381 0.00 0.00 0.00 4.75
3930 5454 2.738643 CGATACTGTTCATCCGTGCCTT 60.739 50.000 0.00 0.00 0.00 4.35
3931 5455 2.093306 TACTGTTCATCCGTGCCTTG 57.907 50.000 0.00 0.00 0.00 3.61
3932 5456 0.108585 ACTGTTCATCCGTGCCTTGT 59.891 50.000 0.00 0.00 0.00 3.16
3933 5457 0.518636 CTGTTCATCCGTGCCTTGTG 59.481 55.000 0.00 0.00 0.00 3.33
3934 5458 0.179032 TGTTCATCCGTGCCTTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
3935 5459 0.238289 GTTCATCCGTGCCTTGTGTG 59.762 55.000 0.00 0.00 0.00 3.82
3936 5460 0.179032 TTCATCCGTGCCTTGTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
3937 5461 0.884259 TCATCCGTGCCTTGTGTGTG 60.884 55.000 0.00 0.00 0.00 3.82
3938 5462 1.148273 ATCCGTGCCTTGTGTGTGT 59.852 52.632 0.00 0.00 0.00 3.72
3939 5463 0.884704 ATCCGTGCCTTGTGTGTGTC 60.885 55.000 0.00 0.00 0.00 3.67
3940 5464 1.817520 CCGTGCCTTGTGTGTGTCA 60.818 57.895 0.00 0.00 0.00 3.58
3941 5465 1.372838 CCGTGCCTTGTGTGTGTCAA 61.373 55.000 0.00 0.00 0.00 3.18
3942 5466 0.027979 CGTGCCTTGTGTGTGTCAAG 59.972 55.000 0.00 0.00 41.06 3.02
3943 5467 1.094785 GTGCCTTGTGTGTGTCAAGT 58.905 50.000 0.00 0.00 40.15 3.16
3944 5468 1.064060 GTGCCTTGTGTGTGTCAAGTC 59.936 52.381 0.00 0.00 40.15 3.01
3945 5469 1.339535 TGCCTTGTGTGTGTCAAGTCA 60.340 47.619 0.00 0.00 40.15 3.41
3946 5470 1.064060 GCCTTGTGTGTGTCAAGTCAC 59.936 52.381 0.00 0.00 40.15 3.67
3947 5471 2.632377 CCTTGTGTGTGTCAAGTCACT 58.368 47.619 0.00 0.00 40.15 3.41
3948 5472 2.352651 CCTTGTGTGTGTCAAGTCACTG 59.647 50.000 0.00 0.00 40.15 3.66
3949 5473 2.022764 TGTGTGTGTCAAGTCACTGG 57.977 50.000 0.00 0.00 38.90 4.00
3950 5474 1.552792 TGTGTGTGTCAAGTCACTGGA 59.447 47.619 0.00 0.00 38.90 3.86
3951 5475 2.170397 TGTGTGTGTCAAGTCACTGGAT 59.830 45.455 0.00 0.00 38.90 3.41
3952 5476 2.802816 GTGTGTGTCAAGTCACTGGATC 59.197 50.000 0.00 0.00 38.90 3.36
3953 5477 2.700371 TGTGTGTCAAGTCACTGGATCT 59.300 45.455 0.00 0.00 38.90 2.75
3954 5478 3.243873 TGTGTGTCAAGTCACTGGATCTC 60.244 47.826 0.00 0.00 38.90 2.75
3955 5479 2.965147 TGTGTCAAGTCACTGGATCTCA 59.035 45.455 0.00 0.00 38.90 3.27
3956 5480 3.387699 TGTGTCAAGTCACTGGATCTCAA 59.612 43.478 0.00 0.00 38.90 3.02
3957 5481 4.040829 TGTGTCAAGTCACTGGATCTCAAT 59.959 41.667 0.00 0.00 38.90 2.57
3958 5482 4.629200 GTGTCAAGTCACTGGATCTCAATC 59.371 45.833 0.00 0.00 35.68 2.67
3959 5483 8.689626 TGTGTCAAGTCACTGGATCTCAATCC 62.690 46.154 0.00 0.00 42.20 3.01
3965 5489 4.663444 GGATCTCAATCCGCTCCG 57.337 61.111 0.00 0.00 42.16 4.63
3977 5501 4.175337 GCTCCGGCCACCATGCTA 62.175 66.667 2.24 0.00 0.00 3.49
3978 5502 2.203070 CTCCGGCCACCATGCTAC 60.203 66.667 2.24 0.00 0.00 3.58
3979 5503 3.757248 CTCCGGCCACCATGCTACC 62.757 68.421 2.24 0.00 0.00 3.18
3981 5505 4.155733 CGGCCACCATGCTACCGA 62.156 66.667 2.24 0.00 46.71 4.69
3982 5506 2.203070 GGCCACCATGCTACCGAG 60.203 66.667 0.00 0.00 0.00 4.63
3983 5507 2.731571 GGCCACCATGCTACCGAGA 61.732 63.158 0.00 0.00 0.00 4.04
3984 5508 1.220749 GCCACCATGCTACCGAGAA 59.779 57.895 0.00 0.00 0.00 2.87
3985 5509 0.179045 GCCACCATGCTACCGAGAAT 60.179 55.000 0.00 0.00 0.00 2.40
3986 5510 1.871080 CCACCATGCTACCGAGAATC 58.129 55.000 0.00 0.00 0.00 2.52
4000 5524 3.078594 GAGAATCGAGTCTGAAGCCTC 57.921 52.381 21.67 0.00 0.00 4.70
4001 5525 1.754226 AGAATCGAGTCTGAAGCCTCC 59.246 52.381 15.64 0.00 0.00 4.30
4002 5526 1.478510 GAATCGAGTCTGAAGCCTCCA 59.521 52.381 5.45 0.00 0.00 3.86
4003 5527 1.561643 ATCGAGTCTGAAGCCTCCAA 58.438 50.000 0.00 0.00 0.00 3.53
4004 5528 0.603569 TCGAGTCTGAAGCCTCCAAC 59.396 55.000 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.115343 AACCTGTAGCAAAGCTAGCC 57.885 50.000 12.13 0.00 42.11 3.93
82 83 7.065085 CGAAATTAGTCACCTCAAGTTCATGAT 59.935 37.037 0.00 0.00 0.00 2.45
85 86 5.122396 GCGAAATTAGTCACCTCAAGTTCAT 59.878 40.000 0.00 0.00 0.00 2.57
94 95 2.851263 TGGTGCGAAATTAGTCACCT 57.149 45.000 18.02 0.00 46.74 4.00
141 142 1.876714 GCGCTCGACTATTTGCCGA 60.877 57.895 0.00 0.00 0.00 5.54
222 223 1.670811 CTCCTTCGCGTTATTGGCAAT 59.329 47.619 18.01 18.01 0.00 3.56
227 228 1.732259 AGCAACTCCTTCGCGTTATTG 59.268 47.619 5.77 5.06 0.00 1.90
263 264 4.065088 TCAGTATCAAGTGGAAGTTGCAC 58.935 43.478 18.89 18.89 46.75 4.57
345 346 3.060003 GCTGCAGTAAAGATATGCGTGAG 60.060 47.826 16.64 0.00 42.92 3.51
463 468 9.991388 GTCCTCGATTAAACTATATAGCACTAG 57.009 37.037 9.78 0.00 0.00 2.57
604 609 6.093404 ACAGTCACGTGATTGTAAGTGATAG 58.907 40.000 36.24 13.89 42.13 2.08
1003 1024 3.006217 CGAATAGGTGCTGATGGAGATGA 59.994 47.826 0.00 0.00 0.00 2.92
1636 1686 5.116084 AGCCATAAGTTGCATAGAAAGGA 57.884 39.130 0.00 0.00 0.00 3.36
1842 1892 4.697352 CAGGTAGCATGTAAAAGCTCTTGT 59.303 41.667 0.00 0.00 42.05 3.16
1970 2020 0.314935 AGTTTTGCAACATGGCCTCG 59.685 50.000 3.32 0.00 35.05 4.63
2563 2619 7.565680 AGGGATATCGTTCAAGAGTTTGTTAT 58.434 34.615 0.00 0.00 35.73 1.89
2576 2632 2.872858 GGCACTTCAAGGGATATCGTTC 59.127 50.000 0.00 0.00 0.00 3.95
2597 2653 9.191995 GGTGACAAAACATAAAGATTAGTTTGG 57.808 33.333 0.00 0.00 34.70 3.28
2614 2670 7.579531 TGGTGACAAAACATAATGGTGACAAAA 60.580 33.333 0.00 0.00 41.00 2.44
2615 2671 6.127338 TGGTGACAAAACATAATGGTGACAAA 60.127 34.615 0.00 0.00 41.00 2.83
2616 2672 5.360999 TGGTGACAAAACATAATGGTGACAA 59.639 36.000 0.00 0.00 41.00 3.18
2617 2673 4.889995 TGGTGACAAAACATAATGGTGACA 59.110 37.500 0.00 0.00 41.82 3.58
2618 2674 5.219633 GTGGTGACAAAACATAATGGTGAC 58.780 41.667 0.00 0.00 46.06 3.67
2619 2675 4.889995 TGTGGTGACAAAACATAATGGTGA 59.110 37.500 0.00 0.00 46.06 4.02
2620 2676 5.193663 TGTGGTGACAAAACATAATGGTG 57.806 39.130 0.00 0.00 46.06 4.17
2621 2677 5.860941 TTGTGGTGACAAAACATAATGGT 57.139 34.783 0.00 0.00 46.06 3.55
2622 2678 6.927936 TCAATTGTGGTGACAAAACATAATGG 59.072 34.615 5.13 0.00 45.23 3.16
2623 2679 7.786114 GTCAATTGTGGTGACAAAACATAATG 58.214 34.615 5.13 0.00 45.23 1.90
2624 2680 7.945033 GTCAATTGTGGTGACAAAACATAAT 57.055 32.000 5.13 0.00 45.23 1.28
2911 4431 3.250040 GGTTATCAATGTGCCGGATGTAC 59.750 47.826 5.05 0.00 0.00 2.90
2971 4491 2.251371 GCACCGAGTTTTGGCGAC 59.749 61.111 0.00 0.00 0.00 5.19
3206 4726 7.236225 TCATCCTGAGAATTATCTTCATAGCCA 59.764 37.037 1.19 0.00 35.54 4.75
3213 4733 9.334947 TGAACAATCATCCTGAGAATTATCTTC 57.665 33.333 1.19 0.00 35.54 2.87
3298 4818 4.141251 AGTTACAAAGAACAGGGGTCACAT 60.141 41.667 0.00 0.00 0.00 3.21
3371 4891 7.331791 ACTTCAAGGGTAAGACTACAATGATC 58.668 38.462 0.00 0.00 0.00 2.92
3512 5036 4.220821 GCCTATTCCGGATCAGTTAGATGA 59.779 45.833 4.15 0.00 37.00 2.92
3518 5042 3.199946 TGAAAGCCTATTCCGGATCAGTT 59.800 43.478 4.15 0.00 0.00 3.16
3527 5051 5.675684 TTTGGGATTTGAAAGCCTATTCC 57.324 39.130 12.37 0.00 37.07 3.01
3623 5147 3.549794 GAGGAATCATGGAACTTGGAGG 58.450 50.000 0.00 0.00 0.00 4.30
3629 5153 3.099905 TCTCACGAGGAATCATGGAACT 58.900 45.455 0.00 0.00 0.00 3.01
3648 5172 1.183549 AGGGCGTGAATACTCGTTCT 58.816 50.000 0.00 0.00 35.78 3.01
3707 5231 2.514824 GCCAAGGCACCGGATCTC 60.515 66.667 9.46 0.00 41.49 2.75
3719 5243 1.066257 GTGCCTTGTGTGTGCCAAG 59.934 57.895 0.00 0.00 39.19 3.61
3720 5244 1.042003 ATGTGCCTTGTGTGTGCCAA 61.042 50.000 0.00 0.00 0.00 4.52
3721 5245 1.455402 ATGTGCCTTGTGTGTGCCA 60.455 52.632 0.00 0.00 0.00 4.92
3722 5246 1.007038 CATGTGCCTTGTGTGTGCC 60.007 57.895 0.00 0.00 0.00 5.01
3723 5247 0.595567 CACATGTGCCTTGTGTGTGC 60.596 55.000 13.94 0.00 39.66 4.57
3724 5248 1.023502 TCACATGTGCCTTGTGTGTG 58.976 50.000 21.38 0.00 43.86 3.82
3725 5249 1.761449 TTCACATGTGCCTTGTGTGT 58.239 45.000 21.38 0.00 43.86 3.72
3726 5250 3.503363 ACTATTCACATGTGCCTTGTGTG 59.497 43.478 21.38 7.73 43.86 3.82
3727 5251 3.503363 CACTATTCACATGTGCCTTGTGT 59.497 43.478 21.38 11.21 43.86 3.72
3728 5252 4.087510 CACTATTCACATGTGCCTTGTG 57.912 45.455 21.38 19.98 44.62 3.33
3735 5259 3.129813 AGGCATTGCACTATTCACATGTG 59.870 43.478 20.18 20.18 35.08 3.21
3736 5260 3.359033 AGGCATTGCACTATTCACATGT 58.641 40.909 11.39 0.00 0.00 3.21
3737 5261 4.109766 CAAGGCATTGCACTATTCACATG 58.890 43.478 11.39 0.00 0.00 3.21
3738 5262 4.018490 TCAAGGCATTGCACTATTCACAT 58.982 39.130 11.39 0.00 36.30 3.21
3739 5263 3.419943 TCAAGGCATTGCACTATTCACA 58.580 40.909 11.39 0.00 36.30 3.58
3740 5264 3.733077 GCTCAAGGCATTGCACTATTCAC 60.733 47.826 11.39 0.00 41.35 3.18
3741 5265 2.424601 GCTCAAGGCATTGCACTATTCA 59.575 45.455 11.39 0.00 41.35 2.57
3742 5266 2.686915 AGCTCAAGGCATTGCACTATTC 59.313 45.455 11.39 0.00 44.79 1.75
3743 5267 2.731572 AGCTCAAGGCATTGCACTATT 58.268 42.857 11.39 0.00 44.79 1.73
3744 5268 2.431954 AGCTCAAGGCATTGCACTAT 57.568 45.000 11.39 0.00 44.79 2.12
3745 5269 2.205022 AAGCTCAAGGCATTGCACTA 57.795 45.000 11.39 0.00 44.79 2.74
3746 5270 1.271656 GAAAGCTCAAGGCATTGCACT 59.728 47.619 11.39 2.98 44.79 4.40
3747 5271 1.000060 TGAAAGCTCAAGGCATTGCAC 60.000 47.619 11.39 0.40 44.79 4.57
3748 5272 1.271379 CTGAAAGCTCAAGGCATTGCA 59.729 47.619 11.39 0.00 44.79 4.08
3749 5273 1.992170 CTGAAAGCTCAAGGCATTGC 58.008 50.000 6.15 0.00 44.79 3.56
3770 5294 5.350365 TGAAACCTTGATTTCCGATCTAACG 59.650 40.000 0.00 0.00 37.72 3.18
3771 5295 6.594159 TCTGAAACCTTGATTTCCGATCTAAC 59.406 38.462 0.00 0.00 37.72 2.34
3772 5296 6.707290 TCTGAAACCTTGATTTCCGATCTAA 58.293 36.000 0.00 0.00 37.72 2.10
3773 5297 6.294361 TCTGAAACCTTGATTTCCGATCTA 57.706 37.500 0.00 0.00 37.72 1.98
3774 5298 5.165961 TCTGAAACCTTGATTTCCGATCT 57.834 39.130 0.00 0.00 37.72 2.75
3775 5299 6.442513 AATCTGAAACCTTGATTTCCGATC 57.557 37.500 5.87 0.00 39.91 3.69
3776 5300 6.840780 AAATCTGAAACCTTGATTTCCGAT 57.159 33.333 0.00 0.00 41.51 4.18
3777 5301 6.648879 AAAATCTGAAACCTTGATTTCCGA 57.351 33.333 0.00 0.00 38.84 4.55
3778 5302 7.538678 CACTAAAATCTGAAACCTTGATTTCCG 59.461 37.037 0.00 0.00 38.84 4.30
3779 5303 7.814587 CCACTAAAATCTGAAACCTTGATTTCC 59.185 37.037 0.00 0.00 38.84 3.13
3780 5304 8.576442 TCCACTAAAATCTGAAACCTTGATTTC 58.424 33.333 0.00 0.00 38.84 2.17
3781 5305 8.360390 GTCCACTAAAATCTGAAACCTTGATTT 58.640 33.333 0.00 0.00 40.71 2.17
3782 5306 7.505585 TGTCCACTAAAATCTGAAACCTTGATT 59.494 33.333 0.00 0.00 32.52 2.57
3783 5307 7.004086 TGTCCACTAAAATCTGAAACCTTGAT 58.996 34.615 0.00 0.00 0.00 2.57
3784 5308 6.361433 TGTCCACTAAAATCTGAAACCTTGA 58.639 36.000 0.00 0.00 0.00 3.02
3785 5309 6.263168 ACTGTCCACTAAAATCTGAAACCTTG 59.737 38.462 0.00 0.00 0.00 3.61
3786 5310 6.263168 CACTGTCCACTAAAATCTGAAACCTT 59.737 38.462 0.00 0.00 0.00 3.50
3787 5311 5.765182 CACTGTCCACTAAAATCTGAAACCT 59.235 40.000 0.00 0.00 0.00 3.50
3788 5312 5.531287 ACACTGTCCACTAAAATCTGAAACC 59.469 40.000 0.00 0.00 0.00 3.27
3789 5313 6.619801 ACACTGTCCACTAAAATCTGAAAC 57.380 37.500 0.00 0.00 0.00 2.78
3790 5314 6.426937 GCTACACTGTCCACTAAAATCTGAAA 59.573 38.462 0.00 0.00 0.00 2.69
3791 5315 5.932303 GCTACACTGTCCACTAAAATCTGAA 59.068 40.000 0.00 0.00 0.00 3.02
3792 5316 5.011635 TGCTACACTGTCCACTAAAATCTGA 59.988 40.000 0.00 0.00 0.00 3.27
3793 5317 5.237815 TGCTACACTGTCCACTAAAATCTG 58.762 41.667 0.00 0.00 0.00 2.90
3794 5318 5.246203 TCTGCTACACTGTCCACTAAAATCT 59.754 40.000 0.00 0.00 0.00 2.40
3795 5319 5.348997 GTCTGCTACACTGTCCACTAAAATC 59.651 44.000 0.00 0.00 0.00 2.17
3796 5320 5.012148 AGTCTGCTACACTGTCCACTAAAAT 59.988 40.000 0.00 0.00 0.00 1.82
3797 5321 4.344102 AGTCTGCTACACTGTCCACTAAAA 59.656 41.667 0.00 0.00 0.00 1.52
3798 5322 3.895656 AGTCTGCTACACTGTCCACTAAA 59.104 43.478 0.00 0.00 0.00 1.85
3799 5323 3.497332 AGTCTGCTACACTGTCCACTAA 58.503 45.455 0.00 0.00 0.00 2.24
3800 5324 3.156288 AGTCTGCTACACTGTCCACTA 57.844 47.619 0.00 0.00 0.00 2.74
3801 5325 2.002505 AGTCTGCTACACTGTCCACT 57.997 50.000 0.00 0.00 0.00 4.00
3802 5326 2.610727 GGAAGTCTGCTACACTGTCCAC 60.611 54.545 0.00 0.00 0.00 4.02
3803 5327 1.618837 GGAAGTCTGCTACACTGTCCA 59.381 52.381 0.00 0.00 0.00 4.02
3804 5328 1.896465 AGGAAGTCTGCTACACTGTCC 59.104 52.381 0.00 0.00 0.00 4.02
3805 5329 2.953020 CAGGAAGTCTGCTACACTGTC 58.047 52.381 0.00 0.00 36.60 3.51
3816 5340 1.817447 GTACACCGCTACAGGAAGTCT 59.183 52.381 0.00 0.00 34.73 3.24
3817 5341 1.817447 AGTACACCGCTACAGGAAGTC 59.183 52.381 0.00 0.00 34.73 3.01
3818 5342 1.544691 CAGTACACCGCTACAGGAAGT 59.455 52.381 0.00 0.00 34.73 3.01
3819 5343 1.544691 ACAGTACACCGCTACAGGAAG 59.455 52.381 0.00 0.00 34.73 3.46
3820 5344 1.624336 ACAGTACACCGCTACAGGAA 58.376 50.000 0.00 0.00 34.73 3.36
3821 5345 2.290514 ACTACAGTACACCGCTACAGGA 60.291 50.000 0.00 0.00 34.73 3.86
3822 5346 2.089980 ACTACAGTACACCGCTACAGG 58.910 52.381 0.00 0.00 37.30 4.00
3823 5347 2.159421 CCACTACAGTACACCGCTACAG 60.159 54.545 0.00 0.00 0.00 2.74
3824 5348 1.814394 CCACTACAGTACACCGCTACA 59.186 52.381 0.00 0.00 0.00 2.74
3825 5349 1.815003 ACCACTACAGTACACCGCTAC 59.185 52.381 0.00 0.00 0.00 3.58
3826 5350 1.814394 CACCACTACAGTACACCGCTA 59.186 52.381 0.00 0.00 0.00 4.26
3827 5351 0.601558 CACCACTACAGTACACCGCT 59.398 55.000 0.00 0.00 0.00 5.52
3828 5352 0.599558 TCACCACTACAGTACACCGC 59.400 55.000 0.00 0.00 0.00 5.68
3829 5353 1.884579 AGTCACCACTACAGTACACCG 59.115 52.381 0.00 0.00 0.00 4.94
3830 5354 3.155501 AGAGTCACCACTACAGTACACC 58.844 50.000 0.00 0.00 30.63 4.16
3831 5355 4.277672 TCAAGAGTCACCACTACAGTACAC 59.722 45.833 0.00 0.00 30.63 2.90
3832 5356 4.466827 TCAAGAGTCACCACTACAGTACA 58.533 43.478 0.00 0.00 30.63 2.90
3833 5357 5.047943 ACATCAAGAGTCACCACTACAGTAC 60.048 44.000 0.00 0.00 30.63 2.73
3834 5358 5.077564 ACATCAAGAGTCACCACTACAGTA 58.922 41.667 0.00 0.00 30.63 2.74
3835 5359 3.898123 ACATCAAGAGTCACCACTACAGT 59.102 43.478 0.00 0.00 30.63 3.55
3836 5360 4.527509 ACATCAAGAGTCACCACTACAG 57.472 45.455 0.00 0.00 30.63 2.74
3837 5361 4.343814 TGAACATCAAGAGTCACCACTACA 59.656 41.667 0.00 0.00 30.63 2.74
3838 5362 4.883083 TGAACATCAAGAGTCACCACTAC 58.117 43.478 0.00 0.00 30.63 2.73
3839 5363 5.245977 TGATGAACATCAAGAGTCACCACTA 59.754 40.000 14.00 0.00 44.14 2.74
3840 5364 4.040829 TGATGAACATCAAGAGTCACCACT 59.959 41.667 14.00 0.00 44.14 4.00
3841 5365 4.318332 TGATGAACATCAAGAGTCACCAC 58.682 43.478 14.00 0.00 44.14 4.16
3842 5366 4.284234 TCTGATGAACATCAAGAGTCACCA 59.716 41.667 16.49 0.00 46.10 4.17
3843 5367 4.629200 GTCTGATGAACATCAAGAGTCACC 59.371 45.833 16.49 3.83 46.10 4.02
3844 5368 4.629200 GGTCTGATGAACATCAAGAGTCAC 59.371 45.833 16.49 7.91 46.10 3.67
3845 5369 4.619160 CGGTCTGATGAACATCAAGAGTCA 60.619 45.833 16.49 0.00 46.10 3.41
3846 5370 3.862267 CGGTCTGATGAACATCAAGAGTC 59.138 47.826 16.49 10.63 46.10 3.36
3847 5371 3.259374 ACGGTCTGATGAACATCAAGAGT 59.741 43.478 16.49 11.74 46.10 3.24
3848 5372 3.854666 ACGGTCTGATGAACATCAAGAG 58.145 45.455 16.49 11.25 46.10 2.85
3849 5373 3.673323 CGACGGTCTGATGAACATCAAGA 60.673 47.826 16.49 13.09 46.10 3.02
3850 5374 2.600420 CGACGGTCTGATGAACATCAAG 59.400 50.000 16.49 11.44 46.10 3.02
3851 5375 2.606108 CGACGGTCTGATGAACATCAA 58.394 47.619 16.49 7.10 46.10 2.57
3852 5376 1.735700 GCGACGGTCTGATGAACATCA 60.736 52.381 15.25 15.25 44.83 3.07
3853 5377 0.924090 GCGACGGTCTGATGAACATC 59.076 55.000 6.57 7.73 38.29 3.06
3854 5378 0.532573 AGCGACGGTCTGATGAACAT 59.467 50.000 6.57 0.00 0.00 2.71
3855 5379 0.317160 AAGCGACGGTCTGATGAACA 59.683 50.000 6.57 0.00 0.00 3.18
3856 5380 0.716108 CAAGCGACGGTCTGATGAAC 59.284 55.000 6.57 0.00 0.00 3.18
3857 5381 0.317160 ACAAGCGACGGTCTGATGAA 59.683 50.000 6.57 0.00 0.00 2.57
3858 5382 1.132453 CTACAAGCGACGGTCTGATGA 59.868 52.381 6.57 0.00 0.00 2.92
3859 5383 1.132453 TCTACAAGCGACGGTCTGATG 59.868 52.381 6.57 0.00 0.00 3.07
3860 5384 1.460504 TCTACAAGCGACGGTCTGAT 58.539 50.000 6.57 0.00 0.00 2.90
3861 5385 1.400846 GATCTACAAGCGACGGTCTGA 59.599 52.381 6.57 0.00 0.00 3.27
3862 5386 1.534175 GGATCTACAAGCGACGGTCTG 60.534 57.143 6.57 3.96 0.00 3.51
3863 5387 0.739561 GGATCTACAAGCGACGGTCT 59.260 55.000 6.57 0.00 0.00 3.85
3864 5388 0.454600 TGGATCTACAAGCGACGGTC 59.545 55.000 0.00 0.00 0.00 4.79
3865 5389 0.892755 TTGGATCTACAAGCGACGGT 59.107 50.000 0.00 0.00 0.00 4.83
3866 5390 1.278238 GTTGGATCTACAAGCGACGG 58.722 55.000 0.00 0.00 0.00 4.79
3867 5391 0.914551 CGTTGGATCTACAAGCGACG 59.085 55.000 0.00 0.00 31.39 5.12
3868 5392 1.278238 CCGTTGGATCTACAAGCGAC 58.722 55.000 0.00 0.00 31.39 5.19
3869 5393 0.459585 GCCGTTGGATCTACAAGCGA 60.460 55.000 0.00 0.00 31.39 4.93
3870 5394 1.429148 GGCCGTTGGATCTACAAGCG 61.429 60.000 0.00 0.00 0.00 4.68
3871 5395 0.392461 TGGCCGTTGGATCTACAAGC 60.392 55.000 0.00 0.00 0.00 4.01
3872 5396 1.656652 CTGGCCGTTGGATCTACAAG 58.343 55.000 0.00 0.00 0.00 3.16
3873 5397 0.251916 CCTGGCCGTTGGATCTACAA 59.748 55.000 0.00 0.00 0.00 2.41
3874 5398 0.616395 TCCTGGCCGTTGGATCTACA 60.616 55.000 7.73 0.00 0.00 2.74
3875 5399 0.105039 CTCCTGGCCGTTGGATCTAC 59.895 60.000 11.60 0.00 0.00 2.59
3876 5400 0.032515 TCTCCTGGCCGTTGGATCTA 60.033 55.000 11.60 0.27 0.00 1.98
3877 5401 0.692419 ATCTCCTGGCCGTTGGATCT 60.692 55.000 11.60 1.39 0.00 2.75
3878 5402 0.533755 CATCTCCTGGCCGTTGGATC 60.534 60.000 11.60 0.00 0.00 3.36
3879 5403 1.528824 CATCTCCTGGCCGTTGGAT 59.471 57.895 11.60 4.20 0.00 3.41
3880 5404 2.989639 CATCTCCTGGCCGTTGGA 59.010 61.111 10.85 10.85 0.00 3.53
3881 5405 2.825836 GCATCTCCTGGCCGTTGG 60.826 66.667 0.00 0.00 0.00 3.77
3882 5406 2.825836 GGCATCTCCTGGCCGTTG 60.826 66.667 0.00 0.00 44.46 4.10
3888 5412 1.530771 CCTTGAGGGCATCTCCTGG 59.469 63.158 0.00 0.00 41.76 4.45
3898 5422 0.537188 ACAGTATCGTGCCTTGAGGG 59.463 55.000 0.00 0.00 35.18 4.30
3899 5423 2.271800 GAACAGTATCGTGCCTTGAGG 58.728 52.381 0.00 0.00 38.53 3.86
3900 5424 2.959516 TGAACAGTATCGTGCCTTGAG 58.040 47.619 0.00 0.00 0.00 3.02
3901 5425 3.521560 GATGAACAGTATCGTGCCTTGA 58.478 45.455 0.00 0.00 0.00 3.02
3902 5426 2.609459 GGATGAACAGTATCGTGCCTTG 59.391 50.000 0.00 0.00 0.00 3.61
3903 5427 2.738643 CGGATGAACAGTATCGTGCCTT 60.739 50.000 0.00 0.00 0.00 4.35
3904 5428 1.202417 CGGATGAACAGTATCGTGCCT 60.202 52.381 0.00 0.00 0.00 4.75
3905 5429 1.209128 CGGATGAACAGTATCGTGCC 58.791 55.000 0.00 0.00 0.00 5.01
3906 5430 1.588404 CACGGATGAACAGTATCGTGC 59.412 52.381 0.00 0.00 0.00 5.34
3907 5431 1.588404 GCACGGATGAACAGTATCGTG 59.412 52.381 8.95 8.95 34.88 4.35
3908 5432 1.470979 GGCACGGATGAACAGTATCGT 60.471 52.381 0.00 0.00 0.00 3.73
3909 5433 1.202417 AGGCACGGATGAACAGTATCG 60.202 52.381 0.00 0.00 0.00 2.92
3910 5434 2.604046 AGGCACGGATGAACAGTATC 57.396 50.000 0.00 0.00 0.00 2.24
3911 5435 2.027192 ACAAGGCACGGATGAACAGTAT 60.027 45.455 0.00 0.00 0.00 2.12
3912 5436 1.346395 ACAAGGCACGGATGAACAGTA 59.654 47.619 0.00 0.00 0.00 2.74
3913 5437 0.108585 ACAAGGCACGGATGAACAGT 59.891 50.000 0.00 0.00 0.00 3.55
3914 5438 0.518636 CACAAGGCACGGATGAACAG 59.481 55.000 0.00 0.00 0.00 3.16
3915 5439 0.179032 ACACAAGGCACGGATGAACA 60.179 50.000 0.00 0.00 0.00 3.18
3916 5440 0.238289 CACACAAGGCACGGATGAAC 59.762 55.000 0.00 0.00 0.00 3.18
3917 5441 0.179032 ACACACAAGGCACGGATGAA 60.179 50.000 0.00 0.00 0.00 2.57
3918 5442 0.884259 CACACACAAGGCACGGATGA 60.884 55.000 0.00 0.00 0.00 2.92
3919 5443 1.165907 ACACACACAAGGCACGGATG 61.166 55.000 0.00 0.00 0.00 3.51
3920 5444 0.884704 GACACACACAAGGCACGGAT 60.885 55.000 0.00 0.00 0.00 4.18
3921 5445 1.522806 GACACACACAAGGCACGGA 60.523 57.895 0.00 0.00 0.00 4.69
3922 5446 1.372838 TTGACACACACAAGGCACGG 61.373 55.000 0.00 0.00 0.00 4.94
3923 5447 0.027979 CTTGACACACACAAGGCACG 59.972 55.000 0.00 0.00 40.39 5.34
3924 5448 1.094785 ACTTGACACACACAAGGCAC 58.905 50.000 0.00 0.00 45.92 5.01
3925 5449 3.568000 ACTTGACACACACAAGGCA 57.432 47.368 0.00 0.00 45.92 4.75
3927 5451 2.352651 CAGTGACTTGACACACACAAGG 59.647 50.000 0.00 0.00 45.92 3.61
3928 5452 2.352651 CCAGTGACTTGACACACACAAG 59.647 50.000 0.00 0.00 46.69 3.16
3929 5453 2.027653 TCCAGTGACTTGACACACACAA 60.028 45.455 0.00 0.00 42.45 3.33
3930 5454 1.552792 TCCAGTGACTTGACACACACA 59.447 47.619 0.00 0.00 42.45 3.72
3931 5455 2.309528 TCCAGTGACTTGACACACAC 57.690 50.000 0.00 0.00 42.45 3.82
3932 5456 2.700371 AGATCCAGTGACTTGACACACA 59.300 45.455 0.00 0.00 42.45 3.72
3933 5457 3.243873 TGAGATCCAGTGACTTGACACAC 60.244 47.826 0.00 0.00 42.45 3.82
3934 5458 2.965147 TGAGATCCAGTGACTTGACACA 59.035 45.455 0.00 0.00 42.45 3.72
3935 5459 3.667497 TGAGATCCAGTGACTTGACAC 57.333 47.619 0.00 0.00 40.60 3.67
3936 5460 4.825422 GATTGAGATCCAGTGACTTGACA 58.175 43.478 0.00 0.00 0.00 3.58
3960 5484 4.175337 TAGCATGGTGGCCGGAGC 62.175 66.667 5.05 0.00 38.76 4.70
3961 5485 2.203070 GTAGCATGGTGGCCGGAG 60.203 66.667 5.05 0.00 0.00 4.63
3962 5486 3.792736 GGTAGCATGGTGGCCGGA 61.793 66.667 5.05 0.00 0.00 5.14
3964 5488 4.155733 TCGGTAGCATGGTGGCCG 62.156 66.667 26.29 26.29 43.32 6.13
3965 5489 2.203070 CTCGGTAGCATGGTGGCC 60.203 66.667 7.89 8.84 0.00 5.36
3966 5490 0.179045 ATTCTCGGTAGCATGGTGGC 60.179 55.000 7.89 0.00 0.00 5.01
3967 5491 1.869754 CGATTCTCGGTAGCATGGTGG 60.870 57.143 7.89 0.00 36.00 4.61
3968 5492 1.067060 TCGATTCTCGGTAGCATGGTG 59.933 52.381 7.89 0.00 40.88 4.17
3969 5493 1.338337 CTCGATTCTCGGTAGCATGGT 59.662 52.381 1.62 1.62 40.88 3.55
3970 5494 1.338337 ACTCGATTCTCGGTAGCATGG 59.662 52.381 0.00 0.00 40.88 3.66
3971 5495 2.292016 AGACTCGATTCTCGGTAGCATG 59.708 50.000 0.00 0.00 40.88 4.06
3972 5496 2.292016 CAGACTCGATTCTCGGTAGCAT 59.708 50.000 1.71 0.00 40.88 3.79
3973 5497 1.671328 CAGACTCGATTCTCGGTAGCA 59.329 52.381 1.71 0.00 40.88 3.49
3974 5498 1.941294 TCAGACTCGATTCTCGGTAGC 59.059 52.381 1.71 0.00 40.88 3.58
3975 5499 3.547214 GCTTCAGACTCGATTCTCGGTAG 60.547 52.174 1.71 0.00 40.88 3.18
3976 5500 2.355132 GCTTCAGACTCGATTCTCGGTA 59.645 50.000 1.71 0.00 40.88 4.02
3977 5501 1.133407 GCTTCAGACTCGATTCTCGGT 59.867 52.381 1.71 0.00 40.88 4.69
3978 5502 1.535015 GGCTTCAGACTCGATTCTCGG 60.535 57.143 1.71 0.00 40.88 4.63
3979 5503 1.403679 AGGCTTCAGACTCGATTCTCG 59.596 52.381 1.71 0.00 42.10 4.04
3980 5504 3.078594 GAGGCTTCAGACTCGATTCTC 57.921 52.381 1.71 0.00 40.87 2.87


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

AutoCloner maintained by Alex Coulton.