Multiple sequence alignment - TraesCS2D01G023900

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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 TraesCS2D01G023900 chr2D 100.000 4815 0 0 1 4815 10726335 10721521 0.000000e+00 8892.0
1 TraesCS2D01G023900 chr2D 77.064 218 40 10 80 291 470155556 470155343 3.040000e-22 117.0
2 TraesCS2D01G023900 chr2D 82.292 96 11 6 3103 3194 481141194 481141101 1.440000e-10 78.7
3 TraesCS2D01G023900 chr2B 91.099 3550 222 51 1099 4607 14836407 14832911 0.000000e+00 4719.0
4 TraesCS2D01G023900 chr2B 90.824 752 46 14 2 735 14839049 14838303 0.000000e+00 985.0
5 TraesCS2D01G023900 chr2B 95.029 342 14 2 765 1103 14836803 14836462 7.090000e-148 534.0
6 TraesCS2D01G023900 chr2B 92.982 114 7 1 4592 4704 14817285 14817172 1.070000e-36 165.0
7 TraesCS2D01G023900 chr2B 78.395 162 28 6 117 274 464456539 464456697 1.100000e-16 99.0
8 TraesCS2D01G023900 chr2A 91.948 2012 122 22 1106 3096 10995746 10993754 0.000000e+00 2782.0
9 TraesCS2D01G023900 chr2A 93.146 1211 69 11 3053 4260 10993755 10992556 0.000000e+00 1764.0
10 TraesCS2D01G023900 chr2A 86.916 321 18 19 801 1103 10996106 10995792 5.970000e-89 339.0
11 TraesCS2D01G023900 chr2A 88.793 116 9 2 4592 4705 10992205 10992092 6.500000e-29 139.0
12 TraesCS2D01G023900 chr2A 97.436 39 1 0 1651 1689 709260793 709260831 3.110000e-07 67.6
13 TraesCS2D01G023900 chr4D 88.442 199 20 3 1499 1694 459020492 459020294 2.240000e-58 237.0
14 TraesCS2D01G023900 chr4D 76.355 203 39 9 77 274 469834 470032 3.070000e-17 100.0
15 TraesCS2D01G023900 chr7B 77.711 332 62 10 3935 4260 206332217 206332542 4.920000e-45 193.0
16 TraesCS2D01G023900 chr7B 81.481 216 29 8 1397 1601 699915767 699915552 2.980000e-37 167.0
17 TraesCS2D01G023900 chr4B 89.130 138 12 2 1556 1691 551741535 551741671 8.290000e-38 169.0
18 TraesCS2D01G023900 chr4B 95.000 40 0 2 3102 3140 665219302 665219264 1.450000e-05 62.1
19 TraesCS2D01G023900 chr7D 93.103 87 4 2 3102 3187 463263158 463263073 5.060000e-25 126.0
20 TraesCS2D01G023900 chr6D 90.698 86 8 0 3102 3187 325727796 325727711 1.100000e-21 115.0
21 TraesCS2D01G023900 chr6A 90.698 86 8 0 3102 3187 464514514 464514429 1.100000e-21 115.0
22 TraesCS2D01G023900 chr3A 93.421 76 5 0 3112 3187 86601828 86601753 3.940000e-21 113.0
23 TraesCS2D01G023900 chr1D 89.773 88 7 2 3103 3190 365743741 365743656 1.420000e-20 111.0
24 TraesCS2D01G023900 chrUn 77.000 200 34 11 80 274 35907241 35907049 2.370000e-18 104.0
25 TraesCS2D01G023900 chr3B 77.000 200 34 11 80 274 6168300 6168108 2.370000e-18 104.0
26 TraesCS2D01G023900 chr1A 81.395 86 16 0 3103 3188 481292206 481292121 2.400000e-08 71.3


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 TraesCS2D01G023900 chr2D 10721521 10726335 4814 True 8892.000000 8892 100.000000 1 4815 1 chr2D.!!$R1 4814
1 TraesCS2D01G023900 chr2B 14832911 14839049 6138 True 2079.333333 4719 92.317333 2 4607 3 chr2B.!!$R2 4605
2 TraesCS2D01G023900 chr2A 10992092 10996106 4014 True 1256.000000 2782 90.200750 801 4705 4 chr2A.!!$R1 3904

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
758 2260 2.347452 CGAAAAACGGATGCGACATACT 59.653 45.455 15.49 0.0 38.46 2.12 F
1726 3327 0.906775 TTGGTACCCGTCCAATCTCC 59.093 55.000 10.07 0.0 39.62 3.71 F
2203 3810 0.594602 CGAAAAAGACGGTTTCCCCC 59.405 55.000 0.00 0.0 32.40 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 3645 2.025981 AGCTGCTGTGATTACAATGGGA 60.026 45.455 0.0 0.0 36.14 4.37 R
2821 4436 2.221169 TCTGGCACTAAAACAGCACTG 58.779 47.619 0.0 0.0 32.42 3.66 R
4154 5820 0.973632 AACAGTACGCATGACCTGGA 59.026 50.000 0.0 0.0 0.00 3.86 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
431 435 9.725019 TTTGATGTCTACTCTTTTCATACACAT 57.275 29.630 0.00 0.00 0.00 3.21
435 439 8.310406 TGTCTACTCTTTTCATACACATTGTG 57.690 34.615 15.18 15.18 39.75 3.33
627 631 8.522003 ACACATGTCTAACAAATTTGATATGCA 58.478 29.630 24.64 16.66 40.38 3.96
628 632 8.800972 CACATGTCTAACAAATTTGATATGCAC 58.199 33.333 24.64 13.19 40.38 4.57
720 734 8.702163 AGTTCCAAACATAAACAAAAGTGAAG 57.298 30.769 0.00 0.00 0.00 3.02
721 735 8.527810 AGTTCCAAACATAAACAAAAGTGAAGA 58.472 29.630 0.00 0.00 0.00 2.87
724 738 9.712305 TCCAAACATAAACAAAAGTGAAGAAAA 57.288 25.926 0.00 0.00 0.00 2.29
755 2257 3.967734 CGAAAAACGGATGCGACAT 57.032 47.368 15.49 0.00 38.46 3.06
757 2259 2.689635 CGAAAAACGGATGCGACATAC 58.310 47.619 15.49 0.78 38.46 2.39
758 2260 2.347452 CGAAAAACGGATGCGACATACT 59.653 45.455 15.49 0.00 38.46 2.12
759 2261 3.548668 CGAAAAACGGATGCGACATACTA 59.451 43.478 15.49 0.00 38.46 1.82
760 2262 4.208460 CGAAAAACGGATGCGACATACTAT 59.792 41.667 15.49 0.00 38.46 2.12
761 2263 5.400188 CGAAAAACGGATGCGACATACTATA 59.600 40.000 15.49 0.00 38.46 1.31
762 2264 6.089016 CGAAAAACGGATGCGACATACTATAT 59.911 38.462 15.49 0.00 38.46 0.86
763 2265 7.271868 CGAAAAACGGATGCGACATACTATATA 59.728 37.037 15.49 0.00 38.46 0.86
864 2366 3.745797 GCATTATCTCCTCCCTCCAACAC 60.746 52.174 0.00 0.00 0.00 3.32
1131 2716 3.105283 AGACTTGGCGGATAAGGTTAGT 58.895 45.455 0.00 0.00 0.00 2.24
1132 2717 4.098960 CAGACTTGGCGGATAAGGTTAGTA 59.901 45.833 0.00 0.00 0.00 1.82
1133 2718 4.341520 AGACTTGGCGGATAAGGTTAGTAG 59.658 45.833 0.00 0.00 0.00 2.57
1134 2719 4.028825 ACTTGGCGGATAAGGTTAGTAGT 58.971 43.478 0.00 0.00 0.00 2.73
1135 2720 5.203528 ACTTGGCGGATAAGGTTAGTAGTA 58.796 41.667 0.00 0.00 0.00 1.82
1136 2721 5.658190 ACTTGGCGGATAAGGTTAGTAGTAA 59.342 40.000 0.00 0.00 0.00 2.24
1142 2727 8.026026 GGCGGATAAGGTTAGTAGTAAGTAATC 58.974 40.741 0.00 0.00 0.00 1.75
1149 2734 6.322456 AGGTTAGTAGTAAGTAATCGGGGTTC 59.678 42.308 0.00 0.00 28.49 3.62
1152 2737 6.018433 AGTAGTAAGTAATCGGGGTTCCTA 57.982 41.667 0.00 0.00 0.00 2.94
1174 2759 4.760530 TTGTAGAGCAGCAGGTGAATAT 57.239 40.909 3.02 0.00 0.00 1.28
1257 2842 2.409752 CCGTTATCGATTTTCGGCATCG 60.410 50.000 17.63 5.70 44.09 3.84
1258 2843 2.217847 CGTTATCGATTTTCGGCATCGT 59.782 45.455 1.71 3.43 43.36 3.73
1268 2853 4.497473 TTTCGGCATCGTTTTTCTTGAT 57.503 36.364 0.00 0.00 37.69 2.57
1278 2863 4.153296 TCGTTTTTCTTGATAATCGCTGCA 59.847 37.500 0.00 0.00 0.00 4.41
1400 2989 1.602311 CAGCTTGCTTCAGTTGAGGT 58.398 50.000 0.00 0.00 0.00 3.85
1505 3095 7.730084 TCCTGAATACTCCACTGATTGATTAG 58.270 38.462 0.00 0.00 0.00 1.73
1514 3104 9.606631 ACTCCACTGATTGATTAGTTTCTTATC 57.393 33.333 0.00 0.00 0.00 1.75
1518 3108 7.848051 CACTGATTGATTAGTTTCTTATCACGC 59.152 37.037 0.00 0.00 30.78 5.34
1527 3121 8.997621 TTAGTTTCTTATCACGCACTCTATTT 57.002 30.769 0.00 0.00 0.00 1.40
1557 3151 3.173240 GAGCCAGCGAACGTCGAC 61.173 66.667 5.18 5.18 43.74 4.20
1574 3168 1.305201 GACGTTTGCCCAAGTCTTCA 58.695 50.000 0.00 0.00 0.00 3.02
1603 3199 7.848128 ACCTCTTTCCGATGAAGTATCTTTTA 58.152 34.615 0.00 0.00 33.44 1.52
1654 3250 4.341235 TCGGTATCTTATTGGTGAGACTGG 59.659 45.833 0.00 0.00 33.21 4.00
1688 3284 5.576447 TCAACAGAACCCTTGTTTTCTTC 57.424 39.130 0.00 0.00 33.97 2.87
1701 3302 9.720769 CCCTTGTTTTCTTCTTCTTATGTACTA 57.279 33.333 0.00 0.00 0.00 1.82
1721 3322 4.470664 ACTATATGTTTGGTACCCGTCCAA 59.529 41.667 10.07 0.00 42.29 3.53
1726 3327 0.906775 TTGGTACCCGTCCAATCTCC 59.093 55.000 10.07 0.00 39.62 3.71
1733 3334 1.555075 CCCGTCCAATCTCCTTCAAGA 59.445 52.381 0.00 0.00 0.00 3.02
1738 3339 4.390297 CGTCCAATCTCCTTCAAGAACTTC 59.610 45.833 0.00 0.00 0.00 3.01
1739 3340 5.308825 GTCCAATCTCCTTCAAGAACTTCA 58.691 41.667 0.00 0.00 0.00 3.02
1746 3349 8.647256 ATCTCCTTCAAGAACTTCAAATCAAT 57.353 30.769 0.00 0.00 0.00 2.57
1754 3357 7.502226 TCAAGAACTTCAAATCAATACAGTGGT 59.498 33.333 0.00 0.00 0.00 4.16
1777 3380 5.643379 TTTCATCCTTTCAACTGTATGGC 57.357 39.130 0.00 0.00 0.00 4.40
2037 3644 7.288810 TCTTTCTACAGACAAATTTTGCCAT 57.711 32.000 9.04 0.00 0.00 4.40
2038 3645 7.725251 TCTTTCTACAGACAAATTTTGCCATT 58.275 30.769 9.04 0.00 0.00 3.16
2203 3810 0.594602 CGAAAAAGACGGTTTCCCCC 59.405 55.000 0.00 0.00 32.40 5.40
2210 3817 4.740822 CGGTTTCCCCCTGGCCTG 62.741 72.222 3.32 2.54 0.00 4.85
2231 3843 7.984617 GGCCTGTGCATAAATATTTTTCCTTTA 59.015 33.333 5.91 0.00 40.13 1.85
2271 3883 6.464222 AGAACTGGATATGTCTTTTGTTCGA 58.536 36.000 0.00 0.00 37.98 3.71
2392 4004 9.485206 GGAAACTGAAAACTACAATCTACTACA 57.515 33.333 0.00 0.00 0.00 2.74
2419 4031 7.395772 TCAGGTGATGCCAAACAAATAAGAATA 59.604 33.333 0.00 0.00 40.61 1.75
2457 4069 2.615447 TGTGAGCTGCTTCACTTGAAAG 59.385 45.455 23.08 0.00 46.00 2.62
2459 4071 2.158769 TGAGCTGCTTCACTTGAAAGGA 60.159 45.455 2.53 0.00 33.07 3.36
2463 4075 2.551459 CTGCTTCACTTGAAAGGACCAG 59.449 50.000 0.00 0.00 33.07 4.00
2471 4083 6.522054 TCACTTGAAAGGACCAGTACTTAAG 58.478 40.000 0.00 0.00 31.17 1.85
2487 4099 7.766278 CAGTACTTAAGCACTCCATAGTCATTT 59.234 37.037 5.32 0.00 31.97 2.32
2490 4102 7.820648 ACTTAAGCACTCCATAGTCATTTTTG 58.179 34.615 1.29 0.00 31.97 2.44
2496 4108 7.119846 AGCACTCCATAGTCATTTTTGTTACTC 59.880 37.037 0.00 0.00 31.97 2.59
2503 4115 5.941788 AGTCATTTTTGTTACTCCCAGAGT 58.058 37.500 2.38 2.38 45.54 3.24
2660 4272 8.500753 TGTACTTGTCAAGTTATGTCAACTTT 57.499 30.769 22.81 0.00 42.81 2.66
2821 4436 1.159285 GGGTGGGTTGTACGTTTAGC 58.841 55.000 0.00 0.00 0.00 3.09
2886 4501 6.546484 ACCAGATATAGGCATGTAAGCATTT 58.454 36.000 0.00 0.00 35.83 2.32
2922 4537 9.768662 AAAGAAAAATCTGCACATTTCAGTTAT 57.231 25.926 0.09 0.00 34.91 1.89
2993 4608 3.945921 ACAATGACAGATCAATGAGCCTG 59.054 43.478 11.99 11.99 37.88 4.85
3000 4615 1.948145 GATCAATGAGCCTGGCTTGAG 59.052 52.381 24.26 13.19 39.88 3.02
3006 4621 1.133823 TGAGCCTGGCTTGAGTTTTCA 60.134 47.619 24.26 10.78 39.88 2.69
3049 4664 4.041444 AGGCATGAGGAGGATTATCTTGTC 59.959 45.833 0.00 0.00 0.00 3.18
3126 4785 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
3131 4790 6.823689 CCCTCCGTCCCATAATATAAAATCAG 59.176 42.308 0.00 0.00 0.00 2.90
3151 4810 5.339990 TCAGTTTGCAAGTTGTTTTAGCTC 58.660 37.500 4.48 0.00 0.00 4.09
3181 4840 7.698506 ACGATCTTATATTATTGGACGGAGA 57.301 36.000 0.00 0.00 0.00 3.71
3203 4862 8.147058 GGAGAGAGTACATCATATGATTGTTGT 58.853 37.037 15.74 14.10 34.70 3.32
3347 5006 6.147492 GCATAAGATCTGAGAATAAGCCACAG 59.853 42.308 0.00 0.00 0.00 3.66
3367 5026 7.161404 CCACAGGCTTGAGCTAACATAATATA 58.839 38.462 1.40 0.00 41.70 0.86
3421 5080 6.341316 TGACAGATCTTCAGTATTAACAGGC 58.659 40.000 0.00 0.00 0.00 4.85
3497 5156 6.070829 GTGAAATTTTTGGCGCATTTACTTC 58.929 36.000 10.83 4.05 0.00 3.01
3498 5157 5.755375 TGAAATTTTTGGCGCATTTACTTCA 59.245 32.000 10.83 6.79 0.00 3.02
3499 5158 5.844301 AATTTTTGGCGCATTTACTTCAG 57.156 34.783 10.83 0.00 0.00 3.02
3616 5276 3.317711 ACAATGACAATGAAAACAGGCGA 59.682 39.130 0.00 0.00 0.00 5.54
3879 5540 0.833287 ACATCCAGATACAGGCGCTT 59.167 50.000 7.64 0.00 0.00 4.68
3915 5576 2.736670 ATGGTTACCTCCATGCTTCC 57.263 50.000 2.07 0.00 45.26 3.46
3921 5582 2.905415 ACCTCCATGCTTCCAAATCA 57.095 45.000 0.00 0.00 0.00 2.57
3955 5616 4.495565 ACCGATATATCAGTTTGGGGGTA 58.504 43.478 13.11 0.00 0.00 3.69
3956 5617 4.285260 ACCGATATATCAGTTTGGGGGTAC 59.715 45.833 13.11 0.00 0.00 3.34
3981 5647 9.186837 ACCTACCAACATAGATATAACCTATCG 57.813 37.037 0.00 0.00 0.00 2.92
4027 5693 7.345653 ACACATATCATCCCATATAGACCGAAT 59.654 37.037 0.00 0.00 0.00 3.34
4104 5770 8.543774 CGATACCTAGATGTCAACATTTCTTTC 58.456 37.037 0.00 0.00 36.57 2.62
4105 5771 9.606631 GATACCTAGATGTCAACATTTCTTTCT 57.393 33.333 0.00 0.00 36.57 2.52
4156 5822 8.892723 TGTGTTCACAACTTCATCATATTATCC 58.107 33.333 2.99 0.00 0.00 2.59
4157 5823 8.892723 GTGTTCACAACTTCATCATATTATCCA 58.107 33.333 0.00 0.00 0.00 3.41
4158 5824 9.112725 TGTTCACAACTTCATCATATTATCCAG 57.887 33.333 0.00 0.00 0.00 3.86
4166 5832 5.422145 TCATCATATTATCCAGGTCATGCG 58.578 41.667 0.00 0.00 0.00 4.73
4172 5838 1.195115 ATCCAGGTCATGCGTACTGT 58.805 50.000 0.00 0.00 0.00 3.55
4179 5845 4.391830 CAGGTCATGCGTACTGTTTTGTAT 59.608 41.667 0.00 0.00 0.00 2.29
4218 5890 9.804758 AATGTATTGCTTGTAGTCTTAGAGTAC 57.195 33.333 17.67 17.67 38.52 2.73
4236 5908 7.133891 AGAGTACGGATTTTGTGAATCTTTG 57.866 36.000 0.00 0.00 0.00 2.77
4278 5950 8.854614 AACAGTTTTGCTAATTCTCATCTACT 57.145 30.769 0.00 0.00 0.00 2.57
4279 5951 8.485976 ACAGTTTTGCTAATTCTCATCTACTC 57.514 34.615 0.00 0.00 0.00 2.59
4280 5952 8.097038 ACAGTTTTGCTAATTCTCATCTACTCA 58.903 33.333 0.00 0.00 0.00 3.41
4281 5953 9.107177 CAGTTTTGCTAATTCTCATCTACTCAT 57.893 33.333 0.00 0.00 0.00 2.90
4282 5954 9.323985 AGTTTTGCTAATTCTCATCTACTCATC 57.676 33.333 0.00 0.00 0.00 2.92
4283 5955 9.323985 GTTTTGCTAATTCTCATCTACTCATCT 57.676 33.333 0.00 0.00 0.00 2.90
4339 6011 7.273188 TCTTCACAGTTCGATTTATAACGTG 57.727 36.000 0.00 0.00 34.47 4.49
4356 6035 4.434713 ACGTGAAGCTTTTTCTTTGTGT 57.565 36.364 0.00 0.00 0.00 3.72
4358 6037 5.227152 ACGTGAAGCTTTTTCTTTGTGTTT 58.773 33.333 0.00 0.00 0.00 2.83
4359 6038 5.118510 ACGTGAAGCTTTTTCTTTGTGTTTG 59.881 36.000 0.00 0.00 0.00 2.93
4360 6039 5.118510 CGTGAAGCTTTTTCTTTGTGTTTGT 59.881 36.000 0.00 0.00 0.00 2.83
4361 6040 6.346518 CGTGAAGCTTTTTCTTTGTGTTTGTT 60.347 34.615 0.00 0.00 0.00 2.83
4362 6041 6.791775 GTGAAGCTTTTTCTTTGTGTTTGTTG 59.208 34.615 0.00 0.00 0.00 3.33
4363 6042 6.703607 TGAAGCTTTTTCTTTGTGTTTGTTGA 59.296 30.769 0.00 0.00 0.00 3.18
4364 6043 6.466308 AGCTTTTTCTTTGTGTTTGTTGAC 57.534 33.333 0.00 0.00 0.00 3.18
4365 6044 6.223120 AGCTTTTTCTTTGTGTTTGTTGACT 58.777 32.000 0.00 0.00 0.00 3.41
4368 6047 4.448537 TTCTTTGTGTTTGTTGACTGGG 57.551 40.909 0.00 0.00 0.00 4.45
4369 6048 2.757868 TCTTTGTGTTTGTTGACTGGGG 59.242 45.455 0.00 0.00 0.00 4.96
4370 6049 1.479709 TTGTGTTTGTTGACTGGGGG 58.520 50.000 0.00 0.00 0.00 5.40
4371 6050 0.333312 TGTGTTTGTTGACTGGGGGT 59.667 50.000 0.00 0.00 0.00 4.95
4373 6052 1.040339 TGTTTGTTGACTGGGGGTGC 61.040 55.000 0.00 0.00 0.00 5.01
4375 6054 3.783362 TTGTTGACTGGGGGTGCGG 62.783 63.158 0.00 0.00 0.00 5.69
4404 6083 0.796312 CGCTATGTTCCGTTGTGCTT 59.204 50.000 0.00 0.00 0.00 3.91
4425 6104 2.199236 GTATCGTTTTACCTCGGCTGG 58.801 52.381 0.00 0.00 0.00 4.85
4449 6128 4.215965 CCGTTTCCACGTTTGTATTTCTG 58.784 43.478 0.00 0.00 45.62 3.02
4458 6137 5.851177 CACGTTTGTATTTCTGTTTAGCTGG 59.149 40.000 0.00 0.00 0.00 4.85
4477 6160 2.202046 CACGCACGCATTGTCGAC 60.202 61.111 9.11 9.11 0.00 4.20
4483 6166 1.959226 ACGCATTGTCGACGCCTTT 60.959 52.632 11.62 0.00 0.00 3.11
4484 6167 1.509787 CGCATTGTCGACGCCTTTG 60.510 57.895 11.62 5.00 0.00 2.77
4485 6168 1.574428 GCATTGTCGACGCCTTTGT 59.426 52.632 11.62 0.00 0.00 2.83
4505 6188 8.624776 CCTTTGTGAAATTAAGAGAACAGAGTT 58.375 33.333 0.00 0.00 0.00 3.01
4529 6212 2.544721 AGGAGATGAGAAAGCCTGACA 58.455 47.619 0.00 0.00 0.00 3.58
4530 6213 3.113824 AGGAGATGAGAAAGCCTGACAT 58.886 45.455 0.00 0.00 0.00 3.06
4537 6224 2.485814 GAGAAAGCCTGACATGTTGTCC 59.514 50.000 0.00 0.00 46.40 4.02
4541 6228 2.440409 AGCCTGACATGTTGTCCATTC 58.560 47.619 0.00 0.00 46.40 2.67
4564 6251 4.261405 CGTGCCATTACTTTTTCTCCAACA 60.261 41.667 0.00 0.00 0.00 3.33
4579 6266 4.648762 TCTCCAACACCATTTTTGTGATGT 59.351 37.500 0.00 0.00 35.46 3.06
4581 6268 3.248125 CCAACACCATTTTTGTGATGTGC 59.752 43.478 0.00 0.00 35.46 4.57
4604 6365 1.608055 TCAACCATTCTGTGCACTGG 58.392 50.000 21.80 20.12 34.84 4.00
4611 6372 0.181114 TTCTGTGCACTGGAGCTGTT 59.819 50.000 21.80 0.00 34.99 3.16
4649 6412 6.706270 CACATAAACTTGTCTGGTCTAGTTGT 59.294 38.462 0.00 0.00 34.73 3.32
4660 6423 8.467598 TGTCTGGTCTAGTTGTATGTCTATTTC 58.532 37.037 0.00 0.00 0.00 2.17
4661 6424 8.688151 GTCTGGTCTAGTTGTATGTCTATTTCT 58.312 37.037 0.00 0.00 0.00 2.52
4663 6426 8.589701 TGGTCTAGTTGTATGTCTATTTCTGA 57.410 34.615 0.00 0.00 0.00 3.27
4664 6427 8.467598 TGGTCTAGTTGTATGTCTATTTCTGAC 58.532 37.037 0.00 0.00 35.21 3.51
4692 6455 8.686418 CACAGATTTATCTCGTCTCGAATTTAG 58.314 37.037 0.00 0.00 34.74 1.85
4705 6468 8.808529 CGTCTCGAATTTAGTTTCATGTCTATT 58.191 33.333 0.00 0.00 0.00 1.73
4719 6482 4.718940 TGTCTATTTCTGACATGCGAGA 57.281 40.909 0.00 0.00 39.23 4.04
4720 6483 4.676546 TGTCTATTTCTGACATGCGAGAG 58.323 43.478 0.00 0.00 39.23 3.20
4721 6484 4.399303 TGTCTATTTCTGACATGCGAGAGA 59.601 41.667 0.00 0.00 39.23 3.10
4722 6485 4.737765 GTCTATTTCTGACATGCGAGAGAC 59.262 45.833 0.00 0.00 34.80 3.36
4723 6486 3.883830 ATTTCTGACATGCGAGAGACT 57.116 42.857 0.00 0.00 0.00 3.24
4724 6487 3.667497 TTTCTGACATGCGAGAGACTT 57.333 42.857 0.00 0.00 0.00 3.01
4725 6488 2.929531 TCTGACATGCGAGAGACTTC 57.070 50.000 0.00 0.00 0.00 3.01
4726 6489 1.474478 TCTGACATGCGAGAGACTTCC 59.526 52.381 0.00 0.00 0.00 3.46
4727 6490 1.203287 CTGACATGCGAGAGACTTCCA 59.797 52.381 0.00 0.00 0.00 3.53
4728 6491 1.827344 TGACATGCGAGAGACTTCCAT 59.173 47.619 0.00 0.00 0.00 3.41
4729 6492 2.234661 TGACATGCGAGAGACTTCCATT 59.765 45.455 0.00 0.00 0.00 3.16
4730 6493 3.265791 GACATGCGAGAGACTTCCATTT 58.734 45.455 0.00 0.00 0.00 2.32
4731 6494 3.679389 ACATGCGAGAGACTTCCATTTT 58.321 40.909 0.00 0.00 0.00 1.82
4732 6495 4.074970 ACATGCGAGAGACTTCCATTTTT 58.925 39.130 0.00 0.00 0.00 1.94
4733 6496 4.154918 ACATGCGAGAGACTTCCATTTTTC 59.845 41.667 0.00 0.00 0.00 2.29
4734 6497 3.738982 TGCGAGAGACTTCCATTTTTCA 58.261 40.909 0.00 0.00 0.00 2.69
4735 6498 4.326826 TGCGAGAGACTTCCATTTTTCAT 58.673 39.130 0.00 0.00 0.00 2.57
4736 6499 4.761739 TGCGAGAGACTTCCATTTTTCATT 59.238 37.500 0.00 0.00 0.00 2.57
4737 6500 5.241506 TGCGAGAGACTTCCATTTTTCATTT 59.758 36.000 0.00 0.00 0.00 2.32
4738 6501 6.152379 GCGAGAGACTTCCATTTTTCATTTT 58.848 36.000 0.00 0.00 0.00 1.82
4739 6502 6.306596 GCGAGAGACTTCCATTTTTCATTTTC 59.693 38.462 0.00 0.00 0.00 2.29
4740 6503 7.362662 CGAGAGACTTCCATTTTTCATTTTCA 58.637 34.615 0.00 0.00 0.00 2.69
4741 6504 8.025445 CGAGAGACTTCCATTTTTCATTTTCAT 58.975 33.333 0.00 0.00 0.00 2.57
4742 6505 9.136952 GAGAGACTTCCATTTTTCATTTTCATG 57.863 33.333 0.00 0.00 0.00 3.07
4743 6506 8.863086 AGAGACTTCCATTTTTCATTTTCATGA 58.137 29.630 0.00 0.00 37.67 3.07
4744 6507 9.480053 GAGACTTCCATTTTTCATTTTCATGAA 57.520 29.630 3.38 3.38 45.96 2.57
4759 6522 8.949953 CATTTTCATGAAAAAGAACAAATGTGC 58.050 29.630 31.39 0.00 42.71 4.57
4760 6523 6.601741 TTCATGAAAAAGAACAAATGTGCC 57.398 33.333 5.45 0.00 0.00 5.01
4761 6524 5.668471 TCATGAAAAAGAACAAATGTGCCA 58.332 33.333 0.00 0.00 0.00 4.92
4762 6525 6.111382 TCATGAAAAAGAACAAATGTGCCAA 58.889 32.000 0.00 0.00 0.00 4.52
4763 6526 5.793026 TGAAAAAGAACAAATGTGCCAAC 57.207 34.783 0.00 0.00 0.00 3.77
4764 6527 5.240891 TGAAAAAGAACAAATGTGCCAACA 58.759 33.333 0.00 0.00 41.58 3.33
4779 6542 8.851541 ATGTGCCAACATTTCATATTTCTTTT 57.148 26.923 0.00 0.00 44.94 2.27
4780 6543 8.309163 TGTGCCAACATTTCATATTTCTTTTC 57.691 30.769 0.00 0.00 0.00 2.29
4781 6544 8.149647 TGTGCCAACATTTCATATTTCTTTTCT 58.850 29.630 0.00 0.00 0.00 2.52
4782 6545 8.650714 GTGCCAACATTTCATATTTCTTTTCTC 58.349 33.333 0.00 0.00 0.00 2.87
4783 6546 7.818930 TGCCAACATTTCATATTTCTTTTCTCC 59.181 33.333 0.00 0.00 0.00 3.71
4784 6547 8.037166 GCCAACATTTCATATTTCTTTTCTCCT 58.963 33.333 0.00 0.00 0.00 3.69
4788 6551 9.413734 ACATTTCATATTTCTTTTCTCCTAGGG 57.586 33.333 9.46 0.00 0.00 3.53
4789 6552 8.854117 CATTTCATATTTCTTTTCTCCTAGGGG 58.146 37.037 9.46 5.31 0.00 4.79
4790 6553 7.765149 TTCATATTTCTTTTCTCCTAGGGGA 57.235 36.000 7.47 7.47 39.70 4.81
4798 6561 2.442272 TCCTAGGGGAGCGCTCAC 60.442 66.667 36.27 34.15 36.57 3.51
4799 6562 2.759973 CCTAGGGGAGCGCTCACA 60.760 66.667 38.34 20.24 33.84 3.58
4800 6563 2.136878 CCTAGGGGAGCGCTCACAT 61.137 63.158 38.34 34.85 33.84 3.21
4801 6564 1.068753 CTAGGGGAGCGCTCACATG 59.931 63.158 38.34 23.73 33.84 3.21
4802 6565 2.985512 CTAGGGGAGCGCTCACATGC 62.986 65.000 38.34 22.75 33.84 4.06
4803 6566 4.783621 GGGGAGCGCTCACATGCA 62.784 66.667 38.34 0.00 33.84 3.96
4804 6567 2.515523 GGGAGCGCTCACATGCAT 60.516 61.111 36.27 0.00 32.06 3.96
4805 6568 1.227645 GGGAGCGCTCACATGCATA 60.228 57.895 36.27 0.00 32.06 3.14
4806 6569 1.226686 GGGAGCGCTCACATGCATAG 61.227 60.000 36.27 0.00 32.06 2.23
4807 6570 0.531532 GGAGCGCTCACATGCATAGT 60.532 55.000 36.27 0.00 0.00 2.12
4808 6571 0.857935 GAGCGCTCACATGCATAGTC 59.142 55.000 31.91 0.00 0.00 2.59
4809 6572 0.531532 AGCGCTCACATGCATAGTCC 60.532 55.000 2.64 0.00 0.00 3.85
4810 6573 0.531532 GCGCTCACATGCATAGTCCT 60.532 55.000 0.00 0.00 0.00 3.85
4811 6574 1.215244 CGCTCACATGCATAGTCCTG 58.785 55.000 0.00 0.00 0.00 3.86
4812 6575 0.942962 GCTCACATGCATAGTCCTGC 59.057 55.000 0.00 0.00 42.62 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 435 9.344772 AGTACAAGGTGTATGTAAAATTCACAA 57.655 29.630 0.00 0.00 35.05 3.33
446 450 7.608761 TGTTGTAGAAAAGAAAGTACAAGGTGT 59.391 33.333 0.00 0.00 36.35 4.16
456 460 9.586435 AAAATGTTCCTGTTGTAGAAAAGAAAG 57.414 29.630 0.00 0.00 0.00 2.62
514 518 8.938047 ACCTAAACACGTAAAAATGTTAATCG 57.062 30.769 0.00 0.00 38.08 3.34
601 605 8.522003 TGCATATCAAATTTGTTAGACATGTGT 58.478 29.630 17.47 0.22 0.00 3.72
736 2238 1.153353 ATGTCGCATCCGTTTTTCGT 58.847 45.000 0.00 0.00 37.94 3.85
738 2240 5.652744 ATAGTATGTCGCATCCGTTTTTC 57.347 39.130 0.00 0.00 35.54 2.29
744 2246 8.066000 TCGTTATTATATAGTATGTCGCATCCG 58.934 37.037 0.00 0.00 0.00 4.18
745 2247 9.726232 TTCGTTATTATATAGTATGTCGCATCC 57.274 33.333 0.00 0.00 0.00 3.51
1101 2686 4.785453 GCCAAGTCTGAGGGCCGG 62.785 72.222 0.00 0.00 41.90 6.13
1111 2696 3.538634 ACTAACCTTATCCGCCAAGTC 57.461 47.619 0.00 0.00 0.00 3.01
1131 2716 6.840705 ACAATAGGAACCCCGATTACTTACTA 59.159 38.462 0.00 0.00 35.90 1.82
1132 2717 5.664457 ACAATAGGAACCCCGATTACTTACT 59.336 40.000 0.00 0.00 35.90 2.24
1133 2718 5.922053 ACAATAGGAACCCCGATTACTTAC 58.078 41.667 0.00 0.00 35.90 2.34
1134 2719 7.068702 TCTACAATAGGAACCCCGATTACTTA 58.931 38.462 0.00 0.00 35.90 2.24
1135 2720 5.901276 TCTACAATAGGAACCCCGATTACTT 59.099 40.000 0.00 0.00 35.90 2.24
1136 2721 5.461327 TCTACAATAGGAACCCCGATTACT 58.539 41.667 0.00 0.00 35.90 2.24
1142 2727 1.760613 TGCTCTACAATAGGAACCCCG 59.239 52.381 0.00 0.00 37.58 5.73
1149 2734 2.432146 TCACCTGCTGCTCTACAATAGG 59.568 50.000 0.00 0.00 37.43 2.57
1152 2737 3.641434 ATTCACCTGCTGCTCTACAAT 57.359 42.857 0.00 0.00 0.00 2.71
1174 2759 9.225682 ACTAAACTGGAATCAGGGAATCTAATA 57.774 33.333 0.00 0.00 44.99 0.98
1227 2812 2.694829 ATCGATAACGGCAGCGGTCC 62.695 60.000 6.00 0.00 40.21 4.46
1228 2813 0.874607 AATCGATAACGGCAGCGGTC 60.875 55.000 6.00 0.00 40.21 4.79
1257 2842 6.086222 TCTTGCAGCGATTATCAAGAAAAAC 58.914 36.000 7.15 0.00 41.08 2.43
1258 2843 6.252967 TCTTGCAGCGATTATCAAGAAAAA 57.747 33.333 7.15 0.00 41.08 1.94
1268 2853 1.405105 GGCCAAATCTTGCAGCGATTA 59.595 47.619 12.07 0.00 31.27 1.75
1278 2863 9.333724 GAAATTGATGAATTATGGCCAAATCTT 57.666 29.630 10.96 0.40 31.18 2.40
1329 2917 2.769095 ACCCTCTCTTCCTATTGACAGC 59.231 50.000 0.00 0.00 0.00 4.40
1462 3052 6.534475 TCAGGAGCAGCAATTTAATCATTT 57.466 33.333 0.00 0.00 0.00 2.32
1505 3095 7.965045 AGAAAATAGAGTGCGTGATAAGAAAC 58.035 34.615 0.00 0.00 0.00 2.78
1514 3104 3.058293 TGGCAAAGAAAATAGAGTGCGTG 60.058 43.478 0.00 0.00 32.77 5.34
1518 3108 6.309737 GCTCATTTGGCAAAGAAAATAGAGTG 59.690 38.462 18.61 7.57 31.20 3.51
1527 3121 1.001181 GCTGGCTCATTTGGCAAAGAA 59.999 47.619 18.61 7.75 41.92 2.52
1557 3151 3.334691 TCTATGAAGACTTGGGCAAACG 58.665 45.455 0.00 0.00 0.00 3.60
1574 3168 7.007723 AGATACTTCATCGGAAAGAGGTCTAT 58.992 38.462 2.65 0.00 38.81 1.98
1603 3199 4.221041 TGCATCACATTTGGAATGACACAT 59.779 37.500 7.59 0.00 0.00 3.21
1654 3250 7.454260 AGGGTTCTGTTGAATTTCAAGTATC 57.546 36.000 12.02 1.81 37.00 2.24
1721 3322 8.647256 ATTGATTTGAAGTTCTTGAAGGAGAT 57.353 30.769 4.17 0.00 0.00 2.75
1726 3327 9.390795 CACTGTATTGATTTGAAGTTCTTGAAG 57.609 33.333 4.17 0.00 0.00 3.02
1733 3334 8.474025 TGAAAACCACTGTATTGATTTGAAGTT 58.526 29.630 0.00 0.00 0.00 2.66
1738 3339 7.605449 AGGATGAAAACCACTGTATTGATTTG 58.395 34.615 0.00 0.00 0.00 2.32
1739 3340 7.781324 AGGATGAAAACCACTGTATTGATTT 57.219 32.000 0.00 0.00 0.00 2.17
1746 3349 6.039270 CAGTTGAAAGGATGAAAACCACTGTA 59.961 38.462 0.00 0.00 0.00 2.74
1754 3357 5.335583 CGCCATACAGTTGAAAGGATGAAAA 60.336 40.000 0.00 0.00 0.00 2.29
1777 3380 6.798482 ACTAAAAACTAAAGGGGTTTCAACG 58.202 36.000 0.00 0.00 36.09 4.10
1848 3451 6.465439 AAAGTTCTTGAAGGGGTTTGTAAG 57.535 37.500 0.00 0.00 0.00 2.34
1909 3513 8.924691 GCATAACAAACAAATCTTTCAGCAATA 58.075 29.630 0.00 0.00 0.00 1.90
1914 3518 7.864379 AGACTGCATAACAAACAAATCTTTCAG 59.136 33.333 0.00 0.00 0.00 3.02
2030 3637 4.529769 TGTGATTACAATGGGAATGGCAAA 59.470 37.500 0.00 0.00 32.88 3.68
2037 3644 2.754552 GCTGCTGTGATTACAATGGGAA 59.245 45.455 0.00 0.00 36.14 3.97
2038 3645 2.025981 AGCTGCTGTGATTACAATGGGA 60.026 45.455 0.00 0.00 36.14 4.37
2203 3810 5.754890 GGAAAAATATTTATGCACAGGCCAG 59.245 40.000 5.01 0.00 40.13 4.85
2289 3901 8.786826 TGAGATTTGAACCGATACTGTAAAAT 57.213 30.769 0.00 0.00 0.00 1.82
2308 3920 9.844257 CAGGGTTTAGAATCTATTTCTGAGATT 57.156 33.333 0.00 0.00 44.54 2.40
2392 4004 5.716228 TCTTATTTGTTTGGCATCACCTGAT 59.284 36.000 0.00 0.00 40.22 2.90
2419 4031 7.220030 CAGCTCACACCACTAGGATTAATAAT 58.780 38.462 0.00 0.00 38.69 1.28
2457 4069 2.565834 TGGAGTGCTTAAGTACTGGTCC 59.434 50.000 28.02 22.35 41.05 4.46
2459 4071 5.024118 ACTATGGAGTGCTTAAGTACTGGT 58.976 41.667 28.02 16.16 41.05 4.00
2463 4075 8.494016 AAAATGACTATGGAGTGCTTAAGTAC 57.506 34.615 15.15 15.15 35.45 2.73
2471 4083 7.145932 AGTAACAAAAATGACTATGGAGTGC 57.854 36.000 0.00 0.00 35.45 4.40
2487 4099 5.061179 GCTTTGTACTCTGGGAGTAACAAA 58.939 41.667 20.27 20.27 45.12 2.83
2490 4102 3.007614 TGGCTTTGTACTCTGGGAGTAAC 59.992 47.826 8.69 5.17 45.12 2.50
2496 4108 2.568623 AACTGGCTTTGTACTCTGGG 57.431 50.000 0.00 0.00 0.00 4.45
2503 4115 7.575414 TGTGAAGAAATAAACTGGCTTTGTA 57.425 32.000 0.00 0.00 0.00 2.41
2598 4210 9.549509 GATGAAAACAAAAACATATACGTAGCA 57.450 29.630 0.08 0.00 0.00 3.49
2660 4272 8.468399 TGCAATGCAGATTATTAACTTCATGAA 58.532 29.630 2.72 8.12 33.32 2.57
2821 4436 2.221169 TCTGGCACTAAAACAGCACTG 58.779 47.619 0.00 0.00 32.42 3.66
2886 4501 6.915843 GTGCAGATTTTTCTTTAAAACGAGGA 59.084 34.615 0.00 0.00 38.48 3.71
2921 4536 9.985730 CATTAAATGTGAATATTGCAACCCTAT 57.014 29.630 0.00 0.00 0.00 2.57
2922 4537 8.976353 ACATTAAATGTGAATATTGCAACCCTA 58.024 29.630 0.00 0.00 43.01 3.53
2993 4608 3.737774 GCTGTTTCATGAAAACTCAAGCC 59.262 43.478 22.07 8.15 46.19 4.35
3000 4615 3.187022 GGCCATTGCTGTTTCATGAAAAC 59.813 43.478 22.07 15.86 46.22 2.43
3006 4621 3.133362 CCTAATGGCCATTGCTGTTTCAT 59.867 43.478 36.21 12.49 37.74 2.57
3049 4664 6.697019 AGCTATAATGCCTTGCAAAATAAACG 59.303 34.615 0.00 0.00 43.62 3.60
3089 4746 4.383118 CGGAGGGAGTAAGATTGAACACAT 60.383 45.833 0.00 0.00 0.00 3.21
3090 4747 3.056107 CGGAGGGAGTAAGATTGAACACA 60.056 47.826 0.00 0.00 0.00 3.72
3126 4785 6.340522 AGCTAAAACAACTTGCAAACTGATT 58.659 32.000 13.01 5.93 0.00 2.57
3131 4790 3.061205 GCGAGCTAAAACAACTTGCAAAC 60.061 43.478 0.00 0.00 40.03 2.93
3151 4810 7.474332 CGTCCAATAATATAAGATCGTTTTGCG 59.526 37.037 0.00 0.00 43.01 4.85
3172 4831 2.801077 TGATGTACTCTCTCCGTCCA 57.199 50.000 0.00 0.00 0.00 4.02
3247 4906 7.681939 TTATAATCCAACGAATAAGATGGCC 57.318 36.000 0.00 0.00 34.50 5.36
3347 5006 6.655003 TGCCTTATATTATGTTAGCTCAAGCC 59.345 38.462 0.00 0.00 43.38 4.35
3497 5156 8.786826 TGGTGTTCTAAGATTATAACCAACTG 57.213 34.615 0.00 0.00 33.67 3.16
3498 5157 9.449719 CTTGGTGTTCTAAGATTATAACCAACT 57.550 33.333 0.00 0.00 40.53 3.16
3499 5158 9.444600 TCTTGGTGTTCTAAGATTATAACCAAC 57.555 33.333 0.00 0.00 40.53 3.77
3616 5276 4.160329 TCAGGACTTGGACAACATACTCT 58.840 43.478 0.00 0.00 0.00 3.24
3861 5521 1.224075 CAAGCGCCTGTATCTGGATG 58.776 55.000 2.29 0.00 0.00 3.51
3879 5540 3.505386 ACCATGCCCATCTTTAACAACA 58.495 40.909 0.00 0.00 0.00 3.33
3915 5576 1.994779 GGTTGCATCGGCTTTGATTTG 59.005 47.619 0.00 0.00 41.91 2.32
3921 5582 1.967319 ATATCGGTTGCATCGGCTTT 58.033 45.000 9.55 0.00 41.91 3.51
3955 5616 9.186837 CGATAGGTTATATCTATGTTGGTAGGT 57.813 37.037 2.10 0.00 0.00 3.08
3956 5617 9.186837 ACGATAGGTTATATCTATGTTGGTAGG 57.813 37.037 0.00 0.00 43.77 3.18
4133 5799 8.562892 CCTGGATAATATGATGAAGTTGTGAAC 58.437 37.037 0.00 0.00 0.00 3.18
4146 5812 4.890158 ACGCATGACCTGGATAATATGA 57.110 40.909 0.00 0.00 0.00 2.15
4151 5817 2.764010 ACAGTACGCATGACCTGGATAA 59.236 45.455 0.00 0.00 0.00 1.75
4152 5818 2.384828 ACAGTACGCATGACCTGGATA 58.615 47.619 0.00 0.00 0.00 2.59
4153 5819 1.195115 ACAGTACGCATGACCTGGAT 58.805 50.000 0.00 0.00 0.00 3.41
4154 5820 0.973632 AACAGTACGCATGACCTGGA 59.026 50.000 0.00 0.00 0.00 3.86
4155 5821 1.808411 AAACAGTACGCATGACCTGG 58.192 50.000 0.00 0.00 0.00 4.45
4156 5822 2.548057 ACAAAACAGTACGCATGACCTG 59.452 45.455 0.00 0.00 0.00 4.00
4157 5823 2.846193 ACAAAACAGTACGCATGACCT 58.154 42.857 0.00 0.00 0.00 3.85
4158 5824 4.939509 ATACAAAACAGTACGCATGACC 57.060 40.909 0.00 0.00 0.00 4.02
4199 5865 4.582869 TCCGTACTCTAAGACTACAAGCA 58.417 43.478 0.00 0.00 0.00 3.91
4204 5876 7.533426 TCACAAAATCCGTACTCTAAGACTAC 58.467 38.462 0.00 0.00 0.00 2.73
4209 5881 8.480643 AAGATTCACAAAATCCGTACTCTAAG 57.519 34.615 0.00 0.00 0.00 2.18
4213 5885 6.899114 ACAAAGATTCACAAAATCCGTACTC 58.101 36.000 0.00 0.00 0.00 2.59
4255 5927 8.484641 TGAGTAGATGAGAATTAGCAAAACTG 57.515 34.615 0.00 0.00 0.00 3.16
4281 5953 9.907229 TGAGATAACAAACTCTCATCTACTAGA 57.093 33.333 0.00 0.00 42.17 2.43
4322 5994 6.963049 AAGCTTCACGTTATAAATCGAACT 57.037 33.333 0.00 0.00 0.00 3.01
4339 6011 7.009440 GTCAACAAACACAAAGAAAAAGCTTC 58.991 34.615 0.00 0.00 0.00 3.86
4356 6035 1.826054 CGCACCCCCAGTCAACAAA 60.826 57.895 0.00 0.00 0.00 2.83
4358 6037 4.263572 CCGCACCCCCAGTCAACA 62.264 66.667 0.00 0.00 0.00 3.33
4376 6055 4.856801 AACATAGCGCTGGGCCGG 62.857 66.667 22.90 8.39 45.17 6.13
4377 6056 3.272334 GAACATAGCGCTGGGCCG 61.272 66.667 22.90 5.98 45.17 6.13
4378 6057 2.902343 GGAACATAGCGCTGGGCC 60.902 66.667 22.90 13.80 45.17 5.80
4379 6058 3.272334 CGGAACATAGCGCTGGGC 61.272 66.667 22.90 8.86 44.05 5.36
4380 6059 1.449601 AACGGAACATAGCGCTGGG 60.450 57.895 22.90 14.61 0.00 4.45
4381 6060 1.019278 ACAACGGAACATAGCGCTGG 61.019 55.000 22.90 15.02 0.00 4.85
4382 6061 0.095245 CACAACGGAACATAGCGCTG 59.905 55.000 22.90 7.81 0.00 5.18
4383 6062 1.635663 GCACAACGGAACATAGCGCT 61.636 55.000 17.26 17.26 0.00 5.92
4384 6063 1.226018 GCACAACGGAACATAGCGC 60.226 57.895 0.00 0.00 0.00 5.92
4385 6064 0.796312 AAGCACAACGGAACATAGCG 59.204 50.000 0.00 0.00 0.00 4.26
4386 6065 1.535462 ACAAGCACAACGGAACATAGC 59.465 47.619 0.00 0.00 0.00 2.97
4387 6066 4.259810 CGATACAAGCACAACGGAACATAG 60.260 45.833 0.00 0.00 0.00 2.23
4404 6083 2.417651 CCAGCCGAGGTAAAACGATACA 60.418 50.000 0.00 0.00 0.00 2.29
4425 6104 0.876399 ATACAAACGTGGAAACGGCC 59.124 50.000 0.00 0.00 37.45 6.13
4432 6111 5.761234 AGCTAAACAGAAATACAAACGTGGA 59.239 36.000 0.00 0.00 0.00 4.02
4449 6128 2.561373 GTGCGTGGCCAGCTAAAC 59.439 61.111 22.36 12.30 35.28 2.01
4468 6147 0.865111 TCACAAAGGCGTCGACAATG 59.135 50.000 17.16 8.70 0.00 2.82
4477 6160 5.757886 TGTTCTCTTAATTTCACAAAGGCG 58.242 37.500 0.00 0.00 0.00 5.52
4505 6188 5.013079 TGTCAGGCTTTCTCATCTCCTTTTA 59.987 40.000 0.00 0.00 0.00 1.52
4529 6212 1.838112 ATGGCACGAATGGACAACAT 58.162 45.000 0.00 0.00 43.07 2.71
4530 6213 1.614996 AATGGCACGAATGGACAACA 58.385 45.000 0.00 0.00 0.00 3.33
4537 6224 5.095490 GGAGAAAAAGTAATGGCACGAATG 58.905 41.667 0.00 0.00 0.00 2.67
4541 6228 4.226761 GTTGGAGAAAAAGTAATGGCACG 58.773 43.478 0.00 0.00 0.00 5.34
4564 6251 1.340889 AGCGCACATCACAAAAATGGT 59.659 42.857 11.47 0.00 0.00 3.55
4579 6266 0.592637 CACAGAATGGTTGAAGCGCA 59.407 50.000 11.47 0.00 43.62 6.09
4581 6268 0.592637 TGCACAGAATGGTTGAAGCG 59.407 50.000 0.00 0.00 43.62 4.68
4604 6365 3.060473 GTGTCAAGTTACACGAACAGCTC 60.060 47.826 0.00 0.00 40.31 4.09
4660 6423 5.645624 AGACGAGATAAATCTGTGTGTCAG 58.354 41.667 0.00 0.00 44.85 3.51
4661 6424 5.641709 GAGACGAGATAAATCTGTGTGTCA 58.358 41.667 0.00 0.00 37.25 3.58
4663 6426 4.395231 TCGAGACGAGATAAATCTGTGTGT 59.605 41.667 0.00 0.00 37.25 3.72
4664 6427 4.909894 TCGAGACGAGATAAATCTGTGTG 58.090 43.478 0.00 0.00 37.25 3.82
4676 6439 6.387465 ACATGAAACTAAATTCGAGACGAGA 58.613 36.000 0.00 0.00 37.14 4.04
4678 6441 6.387465 AGACATGAAACTAAATTCGAGACGA 58.613 36.000 0.00 0.00 31.80 4.20
4679 6442 6.633668 AGACATGAAACTAAATTCGAGACG 57.366 37.500 0.00 0.00 31.80 4.18
4705 6468 2.094494 GGAAGTCTCTCGCATGTCAGAA 60.094 50.000 0.00 0.00 0.00 3.02
4706 6469 1.474478 GGAAGTCTCTCGCATGTCAGA 59.526 52.381 0.00 0.00 0.00 3.27
4707 6470 1.203287 TGGAAGTCTCTCGCATGTCAG 59.797 52.381 0.00 0.00 0.00 3.51
4708 6471 1.256812 TGGAAGTCTCTCGCATGTCA 58.743 50.000 0.00 0.00 0.00 3.58
4709 6472 2.593346 ATGGAAGTCTCTCGCATGTC 57.407 50.000 0.00 0.00 0.00 3.06
4710 6473 3.340814 AAATGGAAGTCTCTCGCATGT 57.659 42.857 0.00 0.00 0.00 3.21
4711 6474 4.154737 TGAAAAATGGAAGTCTCTCGCATG 59.845 41.667 0.00 0.00 0.00 4.06
4712 6475 4.326826 TGAAAAATGGAAGTCTCTCGCAT 58.673 39.130 0.00 0.00 0.00 4.73
4713 6476 3.738982 TGAAAAATGGAAGTCTCTCGCA 58.261 40.909 0.00 0.00 0.00 5.10
4714 6477 4.954092 ATGAAAAATGGAAGTCTCTCGC 57.046 40.909 0.00 0.00 0.00 5.03
4715 6478 7.362662 TGAAAATGAAAAATGGAAGTCTCTCG 58.637 34.615 0.00 0.00 0.00 4.04
4716 6479 9.136952 CATGAAAATGAAAAATGGAAGTCTCTC 57.863 33.333 0.00 0.00 0.00 3.20
4717 6480 8.863086 TCATGAAAATGAAAAATGGAAGTCTCT 58.137 29.630 0.00 0.00 0.00 3.10
4718 6481 9.480053 TTCATGAAAATGAAAAATGGAAGTCTC 57.520 29.630 5.45 0.00 37.59 3.36
4719 6482 9.835389 TTTCATGAAAATGAAAAATGGAAGTCT 57.165 25.926 18.45 0.00 44.64 3.24
4733 6496 8.949953 GCACATTTGTTCTTTTTCATGAAAATG 58.050 29.630 29.13 28.65 39.69 2.32
4734 6497 8.130469 GGCACATTTGTTCTTTTTCATGAAAAT 58.870 29.630 29.13 12.74 39.69 1.82
4735 6498 7.120285 TGGCACATTTGTTCTTTTTCATGAAAA 59.880 29.630 26.01 26.01 38.40 2.29
4736 6499 6.596888 TGGCACATTTGTTCTTTTTCATGAAA 59.403 30.769 16.91 16.91 0.00 2.69
4737 6500 6.111382 TGGCACATTTGTTCTTTTTCATGAA 58.889 32.000 3.38 3.38 0.00 2.57
4738 6501 5.668471 TGGCACATTTGTTCTTTTTCATGA 58.332 33.333 0.00 0.00 0.00 3.07
4739 6502 5.987777 TGGCACATTTGTTCTTTTTCATG 57.012 34.783 0.00 0.00 0.00 3.07
4740 6503 5.879223 TGTTGGCACATTTGTTCTTTTTCAT 59.121 32.000 0.00 0.00 39.30 2.57
4741 6504 5.240891 TGTTGGCACATTTGTTCTTTTTCA 58.759 33.333 0.00 0.00 39.30 2.69
4742 6505 5.793026 TGTTGGCACATTTGTTCTTTTTC 57.207 34.783 0.00 0.00 39.30 2.29
4754 6517 8.851541 AAAAGAAATATGAAATGTTGGCACAT 57.148 26.923 0.00 0.00 46.34 3.21
4755 6518 8.149647 AGAAAAGAAATATGAAATGTTGGCACA 58.850 29.630 0.00 0.00 37.31 4.57
4756 6519 8.538409 AGAAAAGAAATATGAAATGTTGGCAC 57.462 30.769 0.00 0.00 0.00 5.01
4757 6520 7.818930 GGAGAAAAGAAATATGAAATGTTGGCA 59.181 33.333 0.00 0.00 0.00 4.92
4758 6521 8.037166 AGGAGAAAAGAAATATGAAATGTTGGC 58.963 33.333 0.00 0.00 0.00 4.52
4762 6525 9.413734 CCCTAGGAGAAAAGAAATATGAAATGT 57.586 33.333 11.48 0.00 0.00 2.71
4763 6526 8.854117 CCCCTAGGAGAAAAGAAATATGAAATG 58.146 37.037 11.48 0.00 33.47 2.32
4764 6527 8.791749 TCCCCTAGGAGAAAAGAAATATGAAAT 58.208 33.333 11.48 0.00 37.19 2.17
4765 6528 8.170121 TCCCCTAGGAGAAAAGAAATATGAAA 57.830 34.615 11.48 0.00 37.19 2.69
4766 6529 7.765149 TCCCCTAGGAGAAAAGAAATATGAA 57.235 36.000 11.48 0.00 37.19 2.57
4781 6544 2.442272 GTGAGCGCTCCCCTAGGA 60.442 66.667 33.23 11.24 41.08 2.94
4782 6545 2.136878 ATGTGAGCGCTCCCCTAGG 61.137 63.158 33.23 0.06 0.00 3.02
4783 6546 1.068753 CATGTGAGCGCTCCCCTAG 59.931 63.158 33.23 16.06 0.00 3.02
4784 6547 3.094062 GCATGTGAGCGCTCCCCTA 62.094 63.158 33.23 17.34 0.00 3.53
4785 6548 4.479993 GCATGTGAGCGCTCCCCT 62.480 66.667 33.23 13.70 0.00 4.79
4786 6549 2.665008 TATGCATGTGAGCGCTCCCC 62.665 60.000 33.23 23.54 37.31 4.81
4787 6550 1.226686 CTATGCATGTGAGCGCTCCC 61.227 60.000 33.23 23.98 37.31 4.30
4788 6551 0.531532 ACTATGCATGTGAGCGCTCC 60.532 55.000 33.23 23.92 37.31 4.70
4789 6552 0.857935 GACTATGCATGTGAGCGCTC 59.142 55.000 30.42 30.42 37.31 5.03
4790 6553 0.531532 GGACTATGCATGTGAGCGCT 60.532 55.000 11.27 11.27 37.31 5.92
4791 6554 0.531532 AGGACTATGCATGTGAGCGC 60.532 55.000 10.16 0.00 37.31 5.92
4792 6555 1.215244 CAGGACTATGCATGTGAGCG 58.785 55.000 10.16 0.00 37.31 5.03
4793 6556 0.942962 GCAGGACTATGCATGTGAGC 59.057 55.000 10.16 2.21 45.77 4.26


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

AutoCloner maintained by Alex Coulton.