Multiple sequence alignment - TraesCS5D01G338100

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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 TraesCS5D01G338100 chr5D 100.000 5370 0 0 1 5370 426468953 426463584 0.000000e+00 9917.0
1 TraesCS5D01G338100 chr5B 92.551 2309 98 35 631 2923 516473151 516470901 0.000000e+00 3243.0
2 TraesCS5D01G338100 chr5B 94.059 1212 57 8 3811 5018 516469997 516468797 0.000000e+00 1825.0
3 TraesCS5D01G338100 chr5B 93.541 867 28 9 2922 3761 516470859 516469994 0.000000e+00 1266.0
4 TraesCS5D01G338100 chr5B 85.452 653 49 24 1 635 516474064 516473440 5.870000e-179 638.0
5 TraesCS5D01G338100 chr5A 90.476 2352 115 40 2924 5219 540611867 540609569 0.000000e+00 3001.0
6 TraesCS5D01G338100 chr5A 93.120 2035 100 15 884 2907 540614158 540612153 0.000000e+00 2946.0
7 TraesCS5D01G338100 chr5A 82.885 520 21 33 1 478 540615575 540615082 6.480000e-109 405.0
8 TraesCS5D01G338100 chr5A 91.057 123 6 3 480 601 540615023 540614905 1.550000e-35 161.0
9 TraesCS5D01G338100 chr5A 91.549 71 4 2 601 670 540614746 540614677 4.430000e-16 97.1


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 TraesCS5D01G338100 chr5D 426463584 426468953 5369 True 9917.00 9917 100.00000 1 5370 1 chr5D.!!$R1 5369
1 TraesCS5D01G338100 chr5B 516468797 516474064 5267 True 1743.00 3243 91.40075 1 5018 4 chr5B.!!$R1 5017
2 TraesCS5D01G338100 chr5A 540609569 540615575 6006 True 1322.02 3001 89.81740 1 5219 5 chr5A.!!$R1 5218

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
848 1414 0.334676 TCCGGCTCCATCCCATTTTT 59.665 50.000 0.00 0.0 0.00 1.94 F
1594 2471 0.260230 CTCTCCTCCTCCTAGTGCCA 59.740 60.000 0.00 0.0 0.00 4.92 F
1595 2472 0.260230 TCTCCTCCTCCTAGTGCCAG 59.740 60.000 0.00 0.0 0.00 4.85 F
1728 2605 0.813210 GCACTCATAGCCAGAGCACC 60.813 60.000 0.00 0.0 43.56 5.01 F
2950 4107 1.402968 GCATGGCCACTACAGATGTTG 59.597 52.381 8.16 0.0 0.00 3.33 F
3358 4521 5.358725 TGGTTACCTTCTTTCCAAGTTGAAC 59.641 40.000 3.87 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2966 1.235724 GGCAATGTACGGGAATAGCC 58.764 55.000 0.00 0.0 0.00 3.93 R
3358 4521 2.517650 TTTGCAAAACGGCCCTAAAG 57.482 45.000 10.02 0.0 0.00 1.85 R
3551 4744 2.906389 ACCAGCTTCAGTTCCATACTCA 59.094 45.455 0.00 0.0 33.85 3.41 R
3705 4900 7.728847 AAATGCATCTTACAAAGGAAAAACC 57.271 32.000 0.00 0.0 39.35 3.27 R
3766 4961 0.322546 CCTTGGTGGACCTAAGTGCC 60.323 60.000 0.00 0.0 38.35 5.01 R
5249 6466 1.113788 CGGTATCGGGTGTCCCTTAA 58.886 55.000 3.25 0.0 42.67 1.85 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 2.666190 CTGGCCAGTCACCACACG 60.666 66.667 25.53 0.00 32.49 4.49
83 99 9.857957 TTTACAGACCGTTTTCTTTACATTTTT 57.142 25.926 0.00 0.00 0.00 1.94
131 147 1.305219 GCTTCTGCCGCCATAACACA 61.305 55.000 0.00 0.00 0.00 3.72
270 294 3.423154 GGACGAAACGGCAGCTGG 61.423 66.667 17.12 1.57 36.10 4.85
280 304 4.664677 GCAGCTGGTCCACGTCGT 62.665 66.667 17.12 0.00 0.00 4.34
281 305 2.734723 CAGCTGGTCCACGTCGTG 60.735 66.667 18.54 18.54 0.00 4.35
392 435 4.452733 GGTCTGAAGCCGGGACCG 62.453 72.222 10.57 3.25 39.80 4.79
421 464 3.449737 TGTTAGCCAGTCCACATACTACC 59.550 47.826 0.00 0.00 0.00 3.18
422 465 2.247699 AGCCAGTCCACATACTACCA 57.752 50.000 0.00 0.00 0.00 3.25
423 466 1.831736 AGCCAGTCCACATACTACCAC 59.168 52.381 0.00 0.00 0.00 4.16
424 467 1.831736 GCCAGTCCACATACTACCACT 59.168 52.381 0.00 0.00 0.00 4.00
425 468 2.418746 GCCAGTCCACATACTACCACTG 60.419 54.545 0.00 0.00 0.00 3.66
426 469 2.832129 CCAGTCCACATACTACCACTGT 59.168 50.000 0.00 0.00 31.19 3.55
427 470 4.021229 CCAGTCCACATACTACCACTGTA 58.979 47.826 0.00 0.00 31.19 2.74
428 471 4.142227 CCAGTCCACATACTACCACTGTAC 60.142 50.000 0.00 0.00 31.19 2.90
429 472 4.705507 CAGTCCACATACTACCACTGTACT 59.294 45.833 0.00 0.00 0.00 2.73
430 473 5.884232 CAGTCCACATACTACCACTGTACTA 59.116 44.000 0.00 0.00 0.00 1.82
431 474 6.038382 CAGTCCACATACTACCACTGTACTAG 59.962 46.154 0.00 0.00 0.00 2.57
432 475 5.884792 GTCCACATACTACCACTGTACTAGT 59.115 44.000 0.00 0.00 41.36 2.57
498 598 0.382272 CGCTGCTGATAAATCGCACG 60.382 55.000 0.00 9.50 34.47 5.34
543 650 5.073965 CACTCCTCCTCCTCCTAATAGTAGT 59.926 48.000 0.00 0.00 0.00 2.73
545 652 6.273026 ACTCCTCCTCCTCCTAATAGTAGTAC 59.727 46.154 0.00 0.00 0.00 2.73
681 1242 1.210155 GCACGGCCATTGTCTGTTC 59.790 57.895 2.24 0.00 0.00 3.18
684 1245 0.606401 ACGGCCATTGTCTGTTCAGG 60.606 55.000 2.24 0.00 0.00 3.86
736 1300 5.224888 CACAACAAAATCATTCTGTCCTGG 58.775 41.667 0.00 0.00 0.00 4.45
737 1301 4.281688 ACAACAAAATCATTCTGTCCTGGG 59.718 41.667 0.00 0.00 0.00 4.45
738 1302 3.434309 ACAAAATCATTCTGTCCTGGGG 58.566 45.455 0.00 0.00 0.00 4.96
739 1303 3.075882 ACAAAATCATTCTGTCCTGGGGA 59.924 43.478 0.00 0.00 0.00 4.81
740 1304 3.659183 AAATCATTCTGTCCTGGGGAG 57.341 47.619 0.00 0.00 29.39 4.30
741 1305 1.516110 ATCATTCTGTCCTGGGGAGG 58.484 55.000 0.00 0.00 29.39 4.30
744 1308 1.837533 ATTCTGTCCTGGGGAGGGGA 61.838 60.000 0.00 0.00 29.39 4.81
757 1321 4.678743 GGGGAGGGCGTGCCTTTT 62.679 66.667 17.35 0.00 36.69 2.27
788 1352 2.818274 CGCGGGTTGCCCTAGAAC 60.818 66.667 0.00 0.00 42.67 3.01
799 1363 1.485480 GCCCTAGAACTTCCCACCTAC 59.515 57.143 0.00 0.00 0.00 3.18
836 1402 2.683933 TCAACTCCCCTCCGGCTC 60.684 66.667 0.00 0.00 0.00 4.70
838 1404 4.332543 AACTCCCCTCCGGCTCCA 62.333 66.667 0.00 0.00 0.00 3.86
840 1406 3.237741 CTCCCCTCCGGCTCCATC 61.238 72.222 0.00 0.00 0.00 3.51
848 1414 0.334676 TCCGGCTCCATCCCATTTTT 59.665 50.000 0.00 0.00 0.00 1.94
849 1415 0.746659 CCGGCTCCATCCCATTTTTC 59.253 55.000 0.00 0.00 0.00 2.29
850 1416 0.746659 CGGCTCCATCCCATTTTTCC 59.253 55.000 0.00 0.00 0.00 3.13
851 1417 1.864669 GGCTCCATCCCATTTTTCCA 58.135 50.000 0.00 0.00 0.00 3.53
852 1418 1.482182 GGCTCCATCCCATTTTTCCAC 59.518 52.381 0.00 0.00 0.00 4.02
855 1421 1.203237 CCATCCCATTTTTCCACCCC 58.797 55.000 0.00 0.00 0.00 4.95
913 1779 4.486503 CCTGCCTGCAGCCTCCTC 62.487 72.222 13.63 0.00 42.35 3.71
914 1780 4.486503 CTGCCTGCAGCCTCCTCC 62.487 72.222 8.66 0.00 42.71 4.30
957 1824 4.502645 CGATTAAATCGCAATCCAAAACCC 59.497 41.667 0.00 0.00 46.55 4.11
1281 2155 3.003173 TGGCCCAAGTCCTCCTCG 61.003 66.667 0.00 0.00 0.00 4.63
1284 2158 2.885861 CCCAAGTCCTCCTCGTCG 59.114 66.667 0.00 0.00 0.00 5.12
1345 2219 1.152383 GCCGGTAACTGAATCTCGCC 61.152 60.000 1.90 0.00 0.00 5.54
1354 2228 3.265791 ACTGAATCTCGCCATCAACTTC 58.734 45.455 0.00 0.00 0.00 3.01
1362 2236 0.944386 GCCATCAACTTCACACGTGT 59.056 50.000 17.22 17.22 0.00 4.49
1363 2237 1.333619 GCCATCAACTTCACACGTGTT 59.666 47.619 20.79 0.52 0.00 3.32
1366 2240 3.312421 CCATCAACTTCACACGTGTTCTT 59.688 43.478 20.79 4.78 0.00 2.52
1371 2245 2.747446 ACTTCACACGTGTTCTTTGCTT 59.253 40.909 20.79 0.00 0.00 3.91
1428 2305 4.963276 TTTTTCAGCAATACCCGATGAG 57.037 40.909 0.00 0.00 29.21 2.90
1506 2383 1.902918 GATTGTGCCACTGGTGCCA 60.903 57.895 0.00 0.00 0.00 4.92
1507 2384 2.146073 GATTGTGCCACTGGTGCCAC 62.146 60.000 7.72 7.72 39.16 5.01
1508 2385 4.892965 TGTGCCACTGGTGCCACC 62.893 66.667 7.01 7.01 38.06 4.61
1542 2419 5.163581 GCTACAACCAGTTTCTACTCCGATA 60.164 44.000 0.00 0.00 30.26 2.92
1546 2423 3.568853 ACCAGTTTCTACTCCGATATCCG 59.431 47.826 0.00 0.00 32.83 4.18
1589 2466 2.642807 CCTCTACCTCTCCTCCTCCTAG 59.357 59.091 0.00 0.00 0.00 3.02
1590 2467 3.323775 CTCTACCTCTCCTCCTCCTAGT 58.676 54.545 0.00 0.00 0.00 2.57
1591 2468 3.050089 TCTACCTCTCCTCCTCCTAGTG 58.950 54.545 0.00 0.00 0.00 2.74
1592 2469 0.260523 ACCTCTCCTCCTCCTAGTGC 59.739 60.000 0.00 0.00 0.00 4.40
1593 2470 0.469144 CCTCTCCTCCTCCTAGTGCC 60.469 65.000 0.00 0.00 0.00 5.01
1594 2471 0.260230 CTCTCCTCCTCCTAGTGCCA 59.740 60.000 0.00 0.00 0.00 4.92
1595 2472 0.260230 TCTCCTCCTCCTAGTGCCAG 59.740 60.000 0.00 0.00 0.00 4.85
1665 2542 2.279935 TTTTAGTTCGGCATGGTGGT 57.720 45.000 0.00 0.00 0.00 4.16
1666 2543 1.529226 TTTAGTTCGGCATGGTGGTG 58.471 50.000 0.00 0.00 0.00 4.17
1728 2605 0.813210 GCACTCATAGCCAGAGCACC 60.813 60.000 0.00 0.00 43.56 5.01
1796 2673 2.780010 ACTGGAATGATGGGGGTCTTAG 59.220 50.000 0.00 0.00 0.00 2.18
1805 2682 1.765074 GGGGTCTTAGTGGTGGCAA 59.235 57.895 0.00 0.00 0.00 4.52
1878 2755 4.342359 ACAATAGTAGGAGAGTGTTCGGT 58.658 43.478 0.00 0.00 0.00 4.69
2089 2966 3.267031 AGGGAGTAATTTCTCACCAAGGG 59.733 47.826 10.44 0.00 38.51 3.95
2090 2967 3.621558 GGAGTAATTTCTCACCAAGGGG 58.378 50.000 13.34 0.00 41.29 4.79
2514 3392 9.965824 TTTGAAAATTCTTGAGGAGTTATTGTC 57.034 29.630 0.00 0.00 0.00 3.18
2711 3589 7.540400 GTCAAATCGAGATGTATCCTATCTGTG 59.460 40.741 0.00 0.00 35.14 3.66
2725 3603 7.589958 TCCTATCTGTGGTTCTAAATCTCTC 57.410 40.000 0.00 0.00 0.00 3.20
2852 3732 9.302345 CACTATATTCTACGAACAACATGAGTT 57.698 33.333 0.00 3.61 38.88 3.01
2853 3733 9.871238 ACTATATTCTACGAACAACATGAGTTT 57.129 29.630 0.00 0.00 35.28 2.66
2855 3735 6.861065 ATTCTACGAACAACATGAGTTTGT 57.139 33.333 22.74 22.74 43.87 2.83
2856 3736 5.651172 TCTACGAACAACATGAGTTTGTG 57.349 39.130 25.37 18.76 42.13 3.33
2857 3737 5.353111 TCTACGAACAACATGAGTTTGTGA 58.647 37.500 25.37 19.94 42.13 3.58
2858 3738 4.536364 ACGAACAACATGAGTTTGTGAG 57.464 40.909 20.30 11.75 40.97 3.51
2859 3739 3.938963 ACGAACAACATGAGTTTGTGAGT 59.061 39.130 20.30 12.21 40.97 3.41
2904 3792 6.538945 TGTATCTGCATTTACCTGTCTACA 57.461 37.500 0.00 0.00 0.00 2.74
2935 4092 2.033801 CGGCTCTTTATTCAAGGCATGG 59.966 50.000 0.00 0.00 35.46 3.66
2950 4107 1.402968 GCATGGCCACTACAGATGTTG 59.597 52.381 8.16 0.00 0.00 3.33
3358 4521 5.358725 TGGTTACCTTCTTTCCAAGTTGAAC 59.641 40.000 3.87 0.00 0.00 3.18
3398 4581 9.877137 TGCAAAATATTATTACTAGCACATTCG 57.123 29.630 0.00 0.00 0.00 3.34
3671 4865 8.826710 CATTGTTCTCTTAGTGTTTCACAACTA 58.173 33.333 2.80 0.00 36.74 2.24
3672 4866 8.958119 TTGTTCTCTTAGTGTTTCACAACTAT 57.042 30.769 2.80 0.00 36.74 2.12
3762 4957 9.562583 GGAGAATATAAGATTGCTTAGAGTACG 57.437 37.037 0.00 0.00 39.79 3.67
3766 4961 8.951954 ATATAAGATTGCTTAGAGTACGTTCG 57.048 34.615 0.00 0.00 39.79 3.95
3804 4999 5.163426 CCAAGGTTGCCATATTGCATCTAAA 60.163 40.000 1.79 0.00 41.70 1.85
3805 5000 5.520376 AGGTTGCCATATTGCATCTAAAC 57.480 39.130 1.79 0.00 41.70 2.01
3837 5032 5.753921 AGTAATTTCTGCGGCACTAGTATTC 59.246 40.000 0.00 0.00 0.00 1.75
4181 5377 1.197910 GCAGGTTCGTCGCTATACAC 58.802 55.000 0.00 0.00 0.00 2.90
4196 5392 0.105401 TACACACCTGGGACACTGGA 60.105 55.000 7.76 0.00 40.42 3.86
4203 5399 2.305927 ACCTGGGACACTGGATTTACAG 59.694 50.000 7.76 0.00 44.03 2.74
4230 5426 5.825593 TCCTTCCATTCTAGTGACTGTTT 57.174 39.130 0.00 0.00 0.00 2.83
4278 5475 4.217767 ACATGTCATATGCCTGCATGATTC 59.782 41.667 23.25 4.11 39.21 2.52
4374 5571 4.148838 CCACCACCTTCAAATTAGGTTGA 58.851 43.478 4.42 0.00 43.45 3.18
4435 5632 1.686052 TGAGCTTTTTGGTTGCCGATT 59.314 42.857 0.00 0.00 0.00 3.34
4483 5680 4.327680 AGTATTTTCTTCAGGTCCAGTGC 58.672 43.478 0.00 0.00 0.00 4.40
4515 5712 2.684881 CTGCTTGTTATTGCCGGAGAAT 59.315 45.455 5.05 4.82 0.00 2.40
4521 5718 3.559655 TGTTATTGCCGGAGAATCGATTG 59.440 43.478 16.96 1.36 34.37 2.67
4530 5727 3.495100 CGGAGAATCGATTGGAAGGGATT 60.495 47.826 16.96 0.00 34.37 3.01
4541 5738 3.486383 TGGAAGGGATTGTCTGTTTGAC 58.514 45.455 0.00 0.00 45.54 3.18
4610 5807 3.056035 GGTTACATTTCCAGAGTCGGACT 60.056 47.826 11.09 11.09 33.75 3.85
4800 5999 0.531532 GGATGATGCGTCCTGTGGAG 60.532 60.000 2.83 0.00 36.66 3.86
5025 6227 3.588955 GGAAACAGGAAATGTGAATGCC 58.411 45.455 0.00 0.00 43.00 4.40
5030 6232 2.988493 CAGGAAATGTGAATGCCGTTTG 59.012 45.455 0.00 0.00 0.00 2.93
5057 6259 1.079127 CAACCTCTACGGGCCTGTG 60.079 63.158 28.18 16.67 36.97 3.66
5058 6260 1.535687 AACCTCTACGGGCCTGTGT 60.536 57.895 28.18 13.66 36.97 3.72
5061 6263 3.000819 TCTACGGGCCTGTGTGGG 61.001 66.667 28.18 13.97 36.00 4.61
5077 6293 1.329599 GTGGGTCGAGTGAAACAACAC 59.670 52.381 0.00 0.00 41.43 3.32
5099 6315 7.745015 ACACTACGTACAATTTATTGCGATTT 58.255 30.769 2.46 0.00 41.38 2.17
5112 6328 9.850628 ATTTATTGCGATTTCTTATGATCCATG 57.149 29.630 0.00 0.00 0.00 3.66
5113 6329 4.754372 TGCGATTTCTTATGATCCATGC 57.246 40.909 0.00 0.00 0.00 4.06
5114 6330 4.136051 TGCGATTTCTTATGATCCATGCA 58.864 39.130 0.00 0.00 0.00 3.96
5115 6331 4.579753 TGCGATTTCTTATGATCCATGCAA 59.420 37.500 0.00 0.00 0.00 4.08
5116 6332 5.067544 TGCGATTTCTTATGATCCATGCAAA 59.932 36.000 0.00 0.00 0.00 3.68
5117 6333 5.628193 GCGATTTCTTATGATCCATGCAAAG 59.372 40.000 0.00 0.00 0.00 2.77
5118 6334 5.628193 CGATTTCTTATGATCCATGCAAAGC 59.372 40.000 0.00 0.00 0.00 3.51
5119 6335 4.924305 TTCTTATGATCCATGCAAAGCC 57.076 40.909 0.00 0.00 0.00 4.35
5120 6336 3.225104 TCTTATGATCCATGCAAAGCCC 58.775 45.455 0.00 0.00 0.00 5.19
5165 6381 2.191128 AGCAATGGACTCTGTTGGAC 57.809 50.000 0.00 0.00 0.00 4.02
5166 6382 0.798776 GCAATGGACTCTGTTGGACG 59.201 55.000 0.00 0.00 0.00 4.79
5167 6383 0.798776 CAATGGACTCTGTTGGACGC 59.201 55.000 0.00 0.00 0.00 5.19
5178 6394 1.138859 TGTTGGACGCCATATGAGAGG 59.861 52.381 3.65 0.00 31.53 3.69
5183 6399 3.901222 TGGACGCCATATGAGAGGAATTA 59.099 43.478 3.65 0.00 0.00 1.40
5190 6406 7.119846 ACGCCATATGAGAGGAATTAATTAAGC 59.880 37.037 3.65 0.00 0.00 3.09
5192 6408 7.334421 GCCATATGAGAGGAATTAATTAAGCGA 59.666 37.037 3.65 0.00 0.00 4.93
5193 6409 9.388506 CCATATGAGAGGAATTAATTAAGCGAT 57.611 33.333 3.65 0.00 0.00 4.58
5210 6427 6.927294 AAGCGATACTCAAAAGATTAAGGG 57.073 37.500 0.00 0.00 0.00 3.95
5214 6431 5.007724 CGATACTCAAAAGATTAAGGGGCAC 59.992 44.000 0.00 0.00 0.00 5.01
5227 6444 2.440247 GGCACCCCTAGCGCAATT 60.440 61.111 11.47 0.00 0.00 2.32
5228 6445 1.153046 GGCACCCCTAGCGCAATTA 60.153 57.895 11.47 0.00 0.00 1.40
5229 6446 0.750182 GGCACCCCTAGCGCAATTAA 60.750 55.000 11.47 0.00 0.00 1.40
5230 6447 1.318576 GCACCCCTAGCGCAATTAAT 58.681 50.000 11.47 0.00 0.00 1.40
5231 6448 1.681264 GCACCCCTAGCGCAATTAATT 59.319 47.619 11.47 0.00 0.00 1.40
5232 6449 2.882137 GCACCCCTAGCGCAATTAATTA 59.118 45.455 11.47 0.00 0.00 1.40
5233 6450 3.316868 GCACCCCTAGCGCAATTAATTAA 59.683 43.478 11.47 0.00 0.00 1.40
5234 6451 4.556699 GCACCCCTAGCGCAATTAATTAAG 60.557 45.833 11.47 0.00 0.00 1.85
5235 6452 4.023193 CACCCCTAGCGCAATTAATTAAGG 60.023 45.833 11.47 1.62 0.00 2.69
5236 6453 3.506067 CCCCTAGCGCAATTAATTAAGGG 59.494 47.826 11.47 17.06 41.81 3.95
5237 6454 3.506067 CCCTAGCGCAATTAATTAAGGGG 59.494 47.826 11.47 7.93 39.04 4.79
5238 6455 4.142038 CCTAGCGCAATTAATTAAGGGGT 58.858 43.478 11.47 6.47 0.00 4.95
5239 6456 5.310451 CCTAGCGCAATTAATTAAGGGGTA 58.690 41.667 11.47 7.22 0.00 3.69
5240 6457 5.180680 CCTAGCGCAATTAATTAAGGGGTAC 59.819 44.000 11.47 0.00 0.00 3.34
5241 6458 4.788679 AGCGCAATTAATTAAGGGGTACT 58.211 39.130 11.47 0.00 0.00 2.73
5242 6459 4.820173 AGCGCAATTAATTAAGGGGTACTC 59.180 41.667 11.47 0.00 0.00 2.59
5243 6460 4.577283 GCGCAATTAATTAAGGGGTACTCA 59.423 41.667 0.30 0.00 0.00 3.41
5244 6461 5.066764 GCGCAATTAATTAAGGGGTACTCAA 59.933 40.000 0.30 0.00 0.00 3.02
5245 6462 6.404954 GCGCAATTAATTAAGGGGTACTCAAA 60.405 38.462 0.30 0.00 0.00 2.69
5246 6463 7.540299 CGCAATTAATTAAGGGGTACTCAAAA 58.460 34.615 0.00 0.00 0.00 2.44
5247 6464 7.700656 CGCAATTAATTAAGGGGTACTCAAAAG 59.299 37.037 0.00 0.00 0.00 2.27
5248 6465 8.745590 GCAATTAATTAAGGGGTACTCAAAAGA 58.254 33.333 0.00 0.00 0.00 2.52
5254 6471 9.475620 AATTAAGGGGTACTCAAAAGATTAAGG 57.524 33.333 0.00 0.00 0.00 2.69
5255 6472 5.452341 AGGGGTACTCAAAAGATTAAGGG 57.548 43.478 0.00 0.00 0.00 3.95
5256 6473 5.105853 AGGGGTACTCAAAAGATTAAGGGA 58.894 41.667 0.00 0.00 0.00 4.20
5257 6474 5.045066 AGGGGTACTCAAAAGATTAAGGGAC 60.045 44.000 0.00 0.00 0.00 4.46
5258 6475 5.280830 GGGGTACTCAAAAGATTAAGGGACA 60.281 44.000 0.00 0.00 0.00 4.02
5259 6476 5.646793 GGGTACTCAAAAGATTAAGGGACAC 59.353 44.000 0.00 0.00 0.00 3.67
5260 6477 5.646793 GGTACTCAAAAGATTAAGGGACACC 59.353 44.000 0.00 0.00 0.00 4.16
5261 6478 4.663334 ACTCAAAAGATTAAGGGACACCC 58.337 43.478 0.00 0.00 45.90 4.61
5270 6487 3.463585 GGGACACCCGATACCGCA 61.464 66.667 0.00 0.00 32.13 5.69
5271 6488 2.580276 GGACACCCGATACCGCAA 59.420 61.111 0.00 0.00 0.00 4.85
5272 6489 1.520787 GGACACCCGATACCGCAAG 60.521 63.158 0.00 0.00 0.00 4.01
5273 6490 2.125269 ACACCCGATACCGCAAGC 60.125 61.111 0.00 0.00 0.00 4.01
5274 6491 2.186903 CACCCGATACCGCAAGCT 59.813 61.111 0.00 0.00 0.00 3.74
5275 6492 2.173669 CACCCGATACCGCAAGCTG 61.174 63.158 0.00 0.00 0.00 4.24
5276 6493 3.272334 CCCGATACCGCAAGCTGC 61.272 66.667 0.00 0.00 40.69 5.25
5277 6494 2.511373 CCGATACCGCAAGCTGCA 60.511 61.111 1.02 0.00 45.36 4.41
5278 6495 2.528743 CCGATACCGCAAGCTGCAG 61.529 63.158 10.11 10.11 45.36 4.41
5279 6496 2.711924 GATACCGCAAGCTGCAGC 59.288 61.111 31.53 31.53 45.36 5.25
5280 6497 2.825836 ATACCGCAAGCTGCAGCC 60.826 61.111 34.39 18.66 45.36 4.85
5281 6498 3.626996 ATACCGCAAGCTGCAGCCA 62.627 57.895 34.39 11.72 45.36 4.75
5282 6499 2.898920 ATACCGCAAGCTGCAGCCAT 62.899 55.000 34.39 21.47 45.36 4.40
5283 6500 4.492160 CCGCAAGCTGCAGCCATG 62.492 66.667 34.39 31.06 45.36 3.66
5284 6501 3.744719 CGCAAGCTGCAGCCATGT 61.745 61.111 34.39 14.18 45.36 3.21
5285 6502 2.126071 GCAAGCTGCAGCCATGTG 60.126 61.111 34.39 25.73 44.26 3.21
5286 6503 2.126071 CAAGCTGCAGCCATGTGC 60.126 61.111 34.39 9.63 44.27 4.57
5287 6504 3.379445 AAGCTGCAGCCATGTGCC 61.379 61.111 34.39 5.26 43.28 5.01
5296 6513 3.353029 CCATGTGCCGCGTGTTGA 61.353 61.111 4.92 0.00 32.30 3.18
5297 6514 2.174107 CATGTGCCGCGTGTTGAG 59.826 61.111 4.92 0.00 0.00 3.02
5298 6515 2.280797 ATGTGCCGCGTGTTGAGT 60.281 55.556 4.92 0.00 0.00 3.41
5299 6516 2.606961 ATGTGCCGCGTGTTGAGTG 61.607 57.895 4.92 0.00 0.00 3.51
5300 6517 3.269347 GTGCCGCGTGTTGAGTGT 61.269 61.111 4.92 0.00 0.00 3.55
5301 6518 3.268603 TGCCGCGTGTTGAGTGTG 61.269 61.111 4.92 0.00 0.00 3.82
5302 6519 3.269347 GCCGCGTGTTGAGTGTGT 61.269 61.111 4.92 0.00 0.00 3.72
5303 6520 1.952133 GCCGCGTGTTGAGTGTGTA 60.952 57.895 4.92 0.00 0.00 2.90
5304 6521 1.289109 GCCGCGTGTTGAGTGTGTAT 61.289 55.000 4.92 0.00 0.00 2.29
5305 6522 1.144969 CCGCGTGTTGAGTGTGTATT 58.855 50.000 4.92 0.00 0.00 1.89
5306 6523 1.529438 CCGCGTGTTGAGTGTGTATTT 59.471 47.619 4.92 0.00 0.00 1.40
5307 6524 2.032377 CCGCGTGTTGAGTGTGTATTTT 60.032 45.455 4.92 0.00 0.00 1.82
5308 6525 3.547214 CCGCGTGTTGAGTGTGTATTTTT 60.547 43.478 4.92 0.00 0.00 1.94
5309 6526 3.657625 CGCGTGTTGAGTGTGTATTTTTC 59.342 43.478 0.00 0.00 0.00 2.29
5310 6527 4.551990 CGCGTGTTGAGTGTGTATTTTTCT 60.552 41.667 0.00 0.00 0.00 2.52
5311 6528 4.904154 GCGTGTTGAGTGTGTATTTTTCTC 59.096 41.667 0.00 0.00 0.00 2.87
5312 6529 5.277345 GCGTGTTGAGTGTGTATTTTTCTCT 60.277 40.000 0.00 0.00 0.00 3.10
5313 6530 6.129393 CGTGTTGAGTGTGTATTTTTCTCTG 58.871 40.000 0.00 0.00 0.00 3.35
5314 6531 6.238103 CGTGTTGAGTGTGTATTTTTCTCTGT 60.238 38.462 0.00 0.00 0.00 3.41
5315 6532 7.042992 CGTGTTGAGTGTGTATTTTTCTCTGTA 60.043 37.037 0.00 0.00 0.00 2.74
5316 6533 8.062448 GTGTTGAGTGTGTATTTTTCTCTGTAC 58.938 37.037 0.00 0.00 0.00 2.90
5317 6534 7.042992 TGTTGAGTGTGTATTTTTCTCTGTACG 60.043 37.037 0.00 0.00 0.00 3.67
5318 6535 6.509656 TGAGTGTGTATTTTTCTCTGTACGT 58.490 36.000 0.00 0.00 0.00 3.57
5319 6536 6.419710 TGAGTGTGTATTTTTCTCTGTACGTG 59.580 38.462 0.00 0.00 0.00 4.49
5320 6537 6.278363 AGTGTGTATTTTTCTCTGTACGTGT 58.722 36.000 0.00 0.00 0.00 4.49
5321 6538 6.759827 AGTGTGTATTTTTCTCTGTACGTGTT 59.240 34.615 0.00 0.00 0.00 3.32
5322 6539 7.279313 AGTGTGTATTTTTCTCTGTACGTGTTT 59.721 33.333 0.00 0.00 0.00 2.83
5323 6540 7.906527 GTGTGTATTTTTCTCTGTACGTGTTTT 59.093 33.333 0.00 0.00 0.00 2.43
5324 6541 8.452534 TGTGTATTTTTCTCTGTACGTGTTTTT 58.547 29.630 0.00 0.00 0.00 1.94
5325 6542 8.730427 GTGTATTTTTCTCTGTACGTGTTTTTG 58.270 33.333 0.00 0.00 0.00 2.44
5326 6543 7.911205 TGTATTTTTCTCTGTACGTGTTTTTGG 59.089 33.333 0.00 0.00 0.00 3.28
5327 6544 4.886247 TTTCTCTGTACGTGTTTTTGGG 57.114 40.909 0.00 0.00 0.00 4.12
5328 6545 2.841215 TCTCTGTACGTGTTTTTGGGG 58.159 47.619 0.00 0.00 0.00 4.96
5329 6546 2.171027 TCTCTGTACGTGTTTTTGGGGT 59.829 45.455 0.00 0.00 0.00 4.95
5330 6547 2.946990 CTCTGTACGTGTTTTTGGGGTT 59.053 45.455 0.00 0.00 0.00 4.11
5331 6548 3.354467 TCTGTACGTGTTTTTGGGGTTT 58.646 40.909 0.00 0.00 0.00 3.27
5332 6549 4.521146 TCTGTACGTGTTTTTGGGGTTTA 58.479 39.130 0.00 0.00 0.00 2.01
5333 6550 4.946157 TCTGTACGTGTTTTTGGGGTTTAA 59.054 37.500 0.00 0.00 0.00 1.52
5334 6551 5.416952 TCTGTACGTGTTTTTGGGGTTTAAA 59.583 36.000 0.00 0.00 0.00 1.52
5335 6552 6.096564 TCTGTACGTGTTTTTGGGGTTTAAAT 59.903 34.615 0.00 0.00 0.00 1.40
5336 6553 6.637657 TGTACGTGTTTTTGGGGTTTAAATT 58.362 32.000 0.00 0.00 0.00 1.82
5337 6554 7.101700 TGTACGTGTTTTTGGGGTTTAAATTT 58.898 30.769 0.00 0.00 0.00 1.82
5338 6555 7.605309 TGTACGTGTTTTTGGGGTTTAAATTTT 59.395 29.630 0.00 0.00 0.00 1.82
5339 6556 7.450124 ACGTGTTTTTGGGGTTTAAATTTTT 57.550 28.000 0.00 0.00 0.00 1.94
5366 6583 8.620116 TTTTGGCTTTACGGTTTTATACTAGT 57.380 30.769 0.00 0.00 0.00 2.57
5367 6584 8.620116 TTTGGCTTTACGGTTTTATACTAGTT 57.380 30.769 0.00 0.00 0.00 2.24
5368 6585 7.832503 TGGCTTTACGGTTTTATACTAGTTC 57.167 36.000 0.00 0.00 0.00 3.01
5369 6586 6.818142 TGGCTTTACGGTTTTATACTAGTTCC 59.182 38.462 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.465632 AACCAAAAGGAAAACTGTCACC 57.534 40.909 0.00 0.00 0.00 4.02
26 27 5.476091 ACAAACCAAAAGGAAAACTGTCA 57.524 34.783 0.00 0.00 0.00 3.58
27 28 5.350365 GGAACAAACCAAAAGGAAAACTGTC 59.650 40.000 0.00 0.00 0.00 3.51
28 29 5.221742 TGGAACAAACCAAAAGGAAAACTGT 60.222 36.000 0.00 0.00 36.96 3.55
29 30 5.121611 GTGGAACAAACCAAAAGGAAAACTG 59.878 40.000 0.00 0.00 44.16 3.16
30 31 5.242434 GTGGAACAAACCAAAAGGAAAACT 58.758 37.500 0.00 0.00 44.16 2.66
31 32 4.092237 CGTGGAACAAACCAAAAGGAAAAC 59.908 41.667 0.00 0.00 44.16 2.43
32 33 4.246458 CGTGGAACAAACCAAAAGGAAAA 58.754 39.130 0.00 0.00 44.16 2.29
189 209 1.234615 TAACCAGCAACTGAAGGCGC 61.235 55.000 0.00 0.00 32.44 6.53
190 210 1.234821 TTAACCAGCAACTGAAGGCG 58.765 50.000 0.00 0.00 32.44 5.52
191 211 2.094545 CCATTAACCAGCAACTGAAGGC 60.095 50.000 0.00 0.00 32.44 4.35
192 212 2.094545 GCCATTAACCAGCAACTGAAGG 60.095 50.000 0.00 0.00 32.44 3.46
194 214 1.539388 CGCCATTAACCAGCAACTGAA 59.461 47.619 0.00 0.00 32.44 3.02
196 216 0.881118 ACGCCATTAACCAGCAACTG 59.119 50.000 0.00 0.00 0.00 3.16
197 217 0.881118 CACGCCATTAACCAGCAACT 59.119 50.000 0.00 0.00 0.00 3.16
199 219 1.175347 TGCACGCCATTAACCAGCAA 61.175 50.000 0.00 0.00 0.00 3.91
429 472 6.041511 CGACTCTTCACTAGTAGTAGCACTA 58.958 44.000 1.57 0.00 0.00 2.74
430 473 4.871557 CGACTCTTCACTAGTAGTAGCACT 59.128 45.833 1.57 0.00 0.00 4.40
431 474 4.494526 GCGACTCTTCACTAGTAGTAGCAC 60.495 50.000 18.28 0.00 39.47 4.40
432 475 3.622163 GCGACTCTTCACTAGTAGTAGCA 59.378 47.826 18.28 0.00 39.47 3.49
433 476 3.872771 AGCGACTCTTCACTAGTAGTAGC 59.127 47.826 16.45 16.45 39.83 3.58
434 477 4.271533 CCAGCGACTCTTCACTAGTAGTAG 59.728 50.000 1.57 2.87 0.00 2.57
435 478 4.190001 CCAGCGACTCTTCACTAGTAGTA 58.810 47.826 1.57 0.00 0.00 1.82
436 479 3.011119 CCAGCGACTCTTCACTAGTAGT 58.989 50.000 0.00 0.00 0.00 2.73
437 480 2.356382 CCCAGCGACTCTTCACTAGTAG 59.644 54.545 0.00 0.00 0.00 2.57
441 484 0.888619 CACCCAGCGACTCTTCACTA 59.111 55.000 0.00 0.00 0.00 2.74
485 585 3.925379 AGGATATGCGTGCGATTTATCA 58.075 40.909 0.00 0.00 0.00 2.15
498 598 2.259618 CCGTACGTGCATAGGATATGC 58.740 52.381 15.21 13.55 44.76 3.14
543 650 1.135603 GCACGTCACCTCATGTACGTA 60.136 52.381 0.00 0.00 40.63 3.57
545 652 0.109272 AGCACGTCACCTCATGTACG 60.109 55.000 0.00 0.00 37.65 3.67
740 1304 4.678743 AAAAGGCACGCCCTCCCC 62.679 66.667 3.95 0.00 45.62 4.81
741 1305 3.062466 GAAAAGGCACGCCCTCCC 61.062 66.667 3.95 0.00 45.62 4.30
788 1352 1.272554 GGTGGAGGGTAGGTGGGAAG 61.273 65.000 0.00 0.00 0.00 3.46
836 1402 1.203237 GGGGTGGAAAAATGGGATGG 58.797 55.000 0.00 0.00 0.00 3.51
838 1404 3.730116 GGGGGTGGAAAAATGGGAT 57.270 52.632 0.00 0.00 0.00 3.85
855 1421 0.688087 GGGACTAGAGAGGTGGTGGG 60.688 65.000 0.00 0.00 0.00 4.61
858 1424 0.632294 GGAGGGACTAGAGAGGTGGT 59.368 60.000 0.00 0.00 41.55 4.16
915 1781 4.493747 GAACGGAGGCGACGAGGG 62.494 72.222 10.63 0.00 34.93 4.30
1324 2198 0.870307 CGAGATTCAGTTACCGGCGG 60.870 60.000 27.06 27.06 0.00 6.13
1345 2219 4.536364 AAGAACACGTGTGAAGTTGATG 57.464 40.909 24.16 0.00 0.00 3.07
1354 2228 2.973224 GCATAAGCAAAGAACACGTGTG 59.027 45.455 24.16 10.51 41.58 3.82
1382 2256 4.073293 ACTAAATACGGGAGATGGCTTG 57.927 45.455 0.00 0.00 0.00 4.01
1445 2322 7.567458 TCCACAGATTCATTCATCAGATACAA 58.433 34.615 0.00 0.00 0.00 2.41
1446 2323 7.128234 TCCACAGATTCATTCATCAGATACA 57.872 36.000 0.00 0.00 0.00 2.29
1449 2326 6.838382 TCATCCACAGATTCATTCATCAGAT 58.162 36.000 0.00 0.00 0.00 2.90
1520 2397 6.040166 GGATATCGGAGTAGAAACTGGTTGTA 59.960 42.308 0.00 0.00 35.56 2.41
1542 2419 2.249413 CTGGACTTGAGGCAGCGGAT 62.249 60.000 0.00 0.00 0.00 4.18
1575 2452 0.260230 TGGCACTAGGAGGAGGAGAG 59.740 60.000 0.00 0.00 0.00 3.20
1590 2467 4.892965 GTGGTGGTGGCACTGGCA 62.893 66.667 18.45 0.07 43.71 4.92
1665 2542 2.371179 TCCATTGTTACCACCGTTACCA 59.629 45.455 0.00 0.00 0.00 3.25
1666 2543 3.004862 CTCCATTGTTACCACCGTTACC 58.995 50.000 0.00 0.00 0.00 2.85
1697 2574 2.139323 ATGAGTGCTCACATTGCCAT 57.861 45.000 3.80 0.00 43.11 4.40
1728 2605 3.005050 TCCCGTCACTGCTATAATTACCG 59.995 47.826 0.00 0.00 0.00 4.02
1796 2673 2.888834 ATTCAAGTTGTTGCCACCAC 57.111 45.000 2.11 0.00 33.23 4.16
1805 2682 7.148573 CGCTATGAACACTAGAATTCAAGTTGT 60.149 37.037 8.44 2.44 38.29 3.32
1815 2692 1.801395 GCGCCGCTATGAACACTAGAA 60.801 52.381 0.00 0.00 0.00 2.10
1848 2725 7.126733 ACACTCTCCTACTATTGTCAATACCT 58.873 38.462 0.89 0.00 0.00 3.08
1878 2755 4.156922 CCGTTGCCATTCCAATTGTTACTA 59.843 41.667 4.43 0.00 0.00 1.82
1938 2815 2.556840 ATCTGTTGCCCCCATCACCG 62.557 60.000 0.00 0.00 0.00 4.94
2033 2910 2.884207 GATTCCGACCGCCACGAC 60.884 66.667 0.00 0.00 0.00 4.34
2089 2966 1.235724 GGCAATGTACGGGAATAGCC 58.764 55.000 0.00 0.00 0.00 3.93
2090 2967 1.873591 CTGGCAATGTACGGGAATAGC 59.126 52.381 0.00 0.00 0.00 2.97
2145 3022 1.600023 GTGGTGGTCGTTGAAATGGA 58.400 50.000 0.00 0.00 0.00 3.41
2320 3198 5.975988 AAGGATAGGAGGCTTGTAAATCA 57.024 39.130 0.00 0.00 0.00 2.57
2693 3571 6.909550 AGAACCACAGATAGGATACATCTC 57.090 41.667 0.00 0.00 41.41 2.75
2711 3589 6.127196 ACCTGTCATCAGAGAGATTTAGAACC 60.127 42.308 0.00 0.00 43.76 3.62
2725 3603 4.331992 CACTAGCATTCAACCTGTCATCAG 59.668 45.833 0.00 0.00 41.01 2.90
2852 3732 5.527511 TCGTTTACGAAACAAACTCACAA 57.472 34.783 1.95 0.00 46.30 3.33
2904 3792 6.942532 TGAATAAAGAGCCGCAAGAAATAT 57.057 33.333 0.00 0.00 43.02 1.28
2909 3797 3.009723 CCTTGAATAAAGAGCCGCAAGA 58.990 45.455 0.00 0.00 38.24 3.02
2935 4092 3.888934 CACAAACAACATCTGTAGTGGC 58.111 45.455 0.00 0.00 39.08 5.01
2950 4107 4.625311 GCCACATTTATAGCAACCACAAAC 59.375 41.667 0.00 0.00 0.00 2.93
3130 4288 6.435428 CGTAGAAGCACTACCAAACAAATTT 58.565 36.000 12.99 0.00 46.09 1.82
3133 4291 3.810941 CCGTAGAAGCACTACCAAACAAA 59.189 43.478 12.99 0.00 46.09 2.83
3185 4346 3.389329 TCAGGAAGAGAACAACTGAGCTT 59.611 43.478 0.00 0.00 33.62 3.74
3261 4422 9.725019 ATCAAACTCACATTCATAGTCTGTAAA 57.275 29.630 0.00 0.00 0.00 2.01
3326 4489 4.767409 GGAAAGAAGGTAACCAGCAAGAAT 59.233 41.667 0.00 0.00 37.17 2.40
3358 4521 2.517650 TTTGCAAAACGGCCCTAAAG 57.482 45.000 10.02 0.00 0.00 1.85
3394 4577 7.442969 TCATTTCACCTGTTAACTACAACGAAT 59.557 33.333 7.22 0.00 36.02 3.34
3398 4581 6.261381 TGGTCATTTCACCTGTTAACTACAAC 59.739 38.462 7.22 0.00 37.34 3.32
3551 4744 2.906389 ACCAGCTTCAGTTCCATACTCA 59.094 45.455 0.00 0.00 33.85 3.41
3705 4900 7.728847 AAATGCATCTTACAAAGGAAAAACC 57.271 32.000 0.00 0.00 39.35 3.27
3746 4941 3.734293 GCCGAACGTACTCTAAGCAATCT 60.734 47.826 0.00 0.00 0.00 2.40
3762 4957 0.672711 GGTGGACCTAAGTGCCGAAC 60.673 60.000 0.00 0.00 32.35 3.95
3766 4961 0.322546 CCTTGGTGGACCTAAGTGCC 60.323 60.000 0.00 0.00 38.35 5.01
3804 4999 5.163447 TGCCGCAGAAATTACTACTAGATGT 60.163 40.000 0.00 0.00 0.00 3.06
3805 5000 5.175856 GTGCCGCAGAAATTACTACTAGATG 59.824 44.000 0.00 0.00 0.00 2.90
3856 5051 3.826157 TGGGAGGCTTAAGTGTTCATTTG 59.174 43.478 4.02 0.00 0.00 2.32
3921 5116 9.606631 GTGTTCATTTCTCAGAATAATAGAGGT 57.393 33.333 0.00 0.00 0.00 3.85
4181 5377 2.039746 TGTAAATCCAGTGTCCCAGGTG 59.960 50.000 0.00 0.00 0.00 4.00
4203 5399 7.331791 ACAGTCACTAGAATGGAAGGATAAAC 58.668 38.462 0.00 0.00 43.78 2.01
4230 5426 5.938125 CAGATGTGCCAGATATGATCATCAA 59.062 40.000 12.53 0.00 34.55 2.57
4374 5571 4.958581 GTGGAGGAATTGGAAATCTGGAAT 59.041 41.667 0.00 0.00 0.00 3.01
4483 5680 5.556194 GCAATAACAAGCAGTTTTGTTTCGG 60.556 40.000 9.12 2.04 46.18 4.30
4515 5712 2.571653 ACAGACAATCCCTTCCAATCGA 59.428 45.455 0.00 0.00 0.00 3.59
4541 5738 2.750350 GGGATATCCTGCCCGTGG 59.250 66.667 21.18 0.00 34.00 4.94
4610 5807 5.856156 TGTCCGACCTAGACAAACAAAATA 58.144 37.500 0.00 0.00 41.17 1.40
4662 5859 1.691976 GTTTGCCCCCTTACTGCTTTT 59.308 47.619 0.00 0.00 0.00 2.27
4800 5999 4.985538 ACCCCATATATCATCCACAACAC 58.014 43.478 0.00 0.00 0.00 3.32
4875 6074 7.232534 ACTGTAAGCCCAATGATACAAAAGAAA 59.767 33.333 0.00 0.00 37.60 2.52
4925 6125 6.811665 TCAACACTACAGAATAAGGACAATCG 59.188 38.462 0.00 0.00 0.00 3.34
4980 6182 1.739466 TGCACGCTGGAGATGAAAATC 59.261 47.619 0.00 0.00 0.00 2.17
5057 6259 1.329599 GTGTTGTTTCACTCGACCCAC 59.670 52.381 0.00 0.00 35.68 4.61
5058 6260 1.208535 AGTGTTGTTTCACTCGACCCA 59.791 47.619 0.00 0.00 44.07 4.51
5061 6263 3.111098 ACGTAGTGTTGTTTCACTCGAC 58.889 45.455 17.67 7.33 45.79 4.20
5099 6315 3.225104 GGGCTTTGCATGGATCATAAGA 58.775 45.455 1.00 0.00 0.00 2.10
5111 6327 3.609853 CTGAGTTATACTGGGCTTTGCA 58.390 45.455 0.00 0.00 0.00 4.08
5112 6328 2.945668 CCTGAGTTATACTGGGCTTTGC 59.054 50.000 0.00 0.00 0.00 3.68
5113 6329 4.487714 TCCTGAGTTATACTGGGCTTTG 57.512 45.455 0.00 0.00 0.00 2.77
5114 6330 5.308237 CCTATCCTGAGTTATACTGGGCTTT 59.692 44.000 0.00 0.00 0.00 3.51
5115 6331 4.841246 CCTATCCTGAGTTATACTGGGCTT 59.159 45.833 0.00 0.00 0.00 4.35
5116 6332 4.421131 CCTATCCTGAGTTATACTGGGCT 58.579 47.826 0.00 0.00 0.00 5.19
5117 6333 3.055747 GCCTATCCTGAGTTATACTGGGC 60.056 52.174 0.00 0.00 0.00 5.36
5118 6334 3.515901 GGCCTATCCTGAGTTATACTGGG 59.484 52.174 0.00 0.00 0.00 4.45
5119 6335 3.515901 GGGCCTATCCTGAGTTATACTGG 59.484 52.174 0.84 0.00 34.39 4.00
5120 6336 4.160329 TGGGCCTATCCTGAGTTATACTG 58.840 47.826 4.53 0.00 34.39 2.74
5165 6381 7.467623 GCTTAATTAATTCCTCTCATATGGCG 58.532 38.462 3.39 0.00 0.00 5.69
5166 6382 7.334421 TCGCTTAATTAATTCCTCTCATATGGC 59.666 37.037 3.39 0.00 0.00 4.40
5167 6383 8.777865 TCGCTTAATTAATTCCTCTCATATGG 57.222 34.615 3.39 0.00 0.00 2.74
5190 6406 5.007724 GTGCCCCTTAATCTTTTGAGTATCG 59.992 44.000 0.00 0.00 38.61 2.92
5192 6408 5.201243 GGTGCCCCTTAATCTTTTGAGTAT 58.799 41.667 0.00 0.00 0.00 2.12
5193 6409 4.569015 GGGTGCCCCTTAATCTTTTGAGTA 60.569 45.833 3.16 0.00 41.34 2.59
5214 6431 3.506067 CCCTTAATTAATTGCGCTAGGGG 59.494 47.826 9.73 6.15 37.91 4.79
5218 6435 5.932455 AGTACCCCTTAATTAATTGCGCTA 58.068 37.500 9.73 0.00 0.00 4.26
5219 6436 4.788679 AGTACCCCTTAATTAATTGCGCT 58.211 39.130 9.73 0.00 0.00 5.92
5220 6437 4.577283 TGAGTACCCCTTAATTAATTGCGC 59.423 41.667 11.05 0.00 0.00 6.09
5221 6438 6.687081 TTGAGTACCCCTTAATTAATTGCG 57.313 37.500 11.05 1.76 0.00 4.85
5222 6439 8.745590 TCTTTTGAGTACCCCTTAATTAATTGC 58.254 33.333 11.05 0.00 0.00 3.56
5228 6445 9.475620 CCTTAATCTTTTGAGTACCCCTTAATT 57.524 33.333 0.00 0.00 0.00 1.40
5229 6446 8.059461 CCCTTAATCTTTTGAGTACCCCTTAAT 58.941 37.037 0.00 0.00 0.00 1.40
5230 6447 7.240194 TCCCTTAATCTTTTGAGTACCCCTTAA 59.760 37.037 0.00 0.00 0.00 1.85
5231 6448 6.736655 TCCCTTAATCTTTTGAGTACCCCTTA 59.263 38.462 0.00 0.00 0.00 2.69
5232 6449 5.554350 TCCCTTAATCTTTTGAGTACCCCTT 59.446 40.000 0.00 0.00 0.00 3.95
5233 6450 5.045066 GTCCCTTAATCTTTTGAGTACCCCT 60.045 44.000 0.00 0.00 0.00 4.79
5234 6451 5.191426 GTCCCTTAATCTTTTGAGTACCCC 58.809 45.833 0.00 0.00 0.00 4.95
5235 6452 5.646793 GTGTCCCTTAATCTTTTGAGTACCC 59.353 44.000 0.00 0.00 0.00 3.69
5236 6453 5.646793 GGTGTCCCTTAATCTTTTGAGTACC 59.353 44.000 0.00 0.00 0.00 3.34
5237 6454 5.646793 GGGTGTCCCTTAATCTTTTGAGTAC 59.353 44.000 0.00 0.00 41.34 2.73
5238 6455 5.570034 CGGGTGTCCCTTAATCTTTTGAGTA 60.570 44.000 3.25 0.00 42.67 2.59
5239 6456 4.663334 GGGTGTCCCTTAATCTTTTGAGT 58.337 43.478 0.00 0.00 41.34 3.41
5240 6457 3.689649 CGGGTGTCCCTTAATCTTTTGAG 59.310 47.826 3.25 0.00 42.67 3.02
5241 6458 3.328343 TCGGGTGTCCCTTAATCTTTTGA 59.672 43.478 3.25 0.00 42.67 2.69
5242 6459 3.681593 TCGGGTGTCCCTTAATCTTTTG 58.318 45.455 3.25 0.00 42.67 2.44
5243 6460 4.586306 ATCGGGTGTCCCTTAATCTTTT 57.414 40.909 3.25 0.00 42.67 2.27
5244 6461 4.141551 GGTATCGGGTGTCCCTTAATCTTT 60.142 45.833 3.25 0.00 42.67 2.52
5245 6462 3.390311 GGTATCGGGTGTCCCTTAATCTT 59.610 47.826 3.25 0.00 42.67 2.40
5246 6463 2.970640 GGTATCGGGTGTCCCTTAATCT 59.029 50.000 3.25 0.00 42.67 2.40
5247 6464 2.288640 CGGTATCGGGTGTCCCTTAATC 60.289 54.545 3.25 0.00 42.67 1.75
5248 6465 1.690352 CGGTATCGGGTGTCCCTTAAT 59.310 52.381 3.25 0.00 42.67 1.40
5249 6466 1.113788 CGGTATCGGGTGTCCCTTAA 58.886 55.000 3.25 0.00 42.67 1.85
5250 6467 1.394266 GCGGTATCGGGTGTCCCTTA 61.394 60.000 0.00 0.00 42.67 2.69
5251 6468 2.728435 GCGGTATCGGGTGTCCCTT 61.728 63.158 0.00 0.00 42.67 3.95
5252 6469 3.152400 GCGGTATCGGGTGTCCCT 61.152 66.667 0.00 0.00 42.67 4.20
5253 6470 2.918230 CTTGCGGTATCGGGTGTCCC 62.918 65.000 0.00 0.00 41.09 4.46
5254 6471 1.520787 CTTGCGGTATCGGGTGTCC 60.521 63.158 0.00 0.00 36.79 4.02
5255 6472 2.171725 GCTTGCGGTATCGGGTGTC 61.172 63.158 0.00 0.00 36.79 3.67
5256 6473 2.125269 GCTTGCGGTATCGGGTGT 60.125 61.111 0.00 0.00 36.79 4.16
5257 6474 2.173669 CAGCTTGCGGTATCGGGTG 61.174 63.158 0.00 0.00 36.79 4.61
5258 6475 2.186903 CAGCTTGCGGTATCGGGT 59.813 61.111 0.00 0.00 36.79 5.28
5259 6476 3.272334 GCAGCTTGCGGTATCGGG 61.272 66.667 0.00 0.00 36.79 5.14
5268 6485 2.126071 CACATGGCTGCAGCTTGC 60.126 61.111 35.82 21.24 45.29 4.01
5269 6486 2.126071 GCACATGGCTGCAGCTTG 60.126 61.111 35.82 31.71 41.70 4.01
5270 6487 3.379445 GGCACATGGCTGCAGCTT 61.379 61.111 35.82 21.99 44.01 3.74
5279 6496 3.313007 CTCAACACGCGGCACATGG 62.313 63.158 12.47 0.00 0.00 3.66
5280 6497 2.174107 CTCAACACGCGGCACATG 59.826 61.111 12.47 0.56 0.00 3.21
5281 6498 2.280797 ACTCAACACGCGGCACAT 60.281 55.556 12.47 0.00 0.00 3.21
5282 6499 3.268603 CACTCAACACGCGGCACA 61.269 61.111 12.47 0.00 0.00 4.57
5283 6500 3.269347 ACACTCAACACGCGGCAC 61.269 61.111 12.47 0.00 0.00 5.01
5284 6501 2.630592 TACACACTCAACACGCGGCA 62.631 55.000 12.47 0.00 0.00 5.69
5285 6502 1.289109 ATACACACTCAACACGCGGC 61.289 55.000 12.47 0.00 0.00 6.53
5286 6503 1.144969 AATACACACTCAACACGCGG 58.855 50.000 12.47 1.27 0.00 6.46
5287 6504 2.941891 AAATACACACTCAACACGCG 57.058 45.000 3.53 3.53 0.00 6.01
5288 6505 4.844267 AGAAAAATACACACTCAACACGC 58.156 39.130 0.00 0.00 0.00 5.34
5289 6506 6.129393 CAGAGAAAAATACACACTCAACACG 58.871 40.000 0.00 0.00 0.00 4.49
5290 6507 7.016361 ACAGAGAAAAATACACACTCAACAC 57.984 36.000 0.00 0.00 0.00 3.32
5291 6508 7.042992 CGTACAGAGAAAAATACACACTCAACA 60.043 37.037 0.00 0.00 0.00 3.33
5292 6509 7.042925 ACGTACAGAGAAAAATACACACTCAAC 60.043 37.037 0.00 0.00 0.00 3.18
5293 6510 6.982141 ACGTACAGAGAAAAATACACACTCAA 59.018 34.615 0.00 0.00 0.00 3.02
5294 6511 6.419710 CACGTACAGAGAAAAATACACACTCA 59.580 38.462 0.00 0.00 0.00 3.41
5295 6512 6.420008 ACACGTACAGAGAAAAATACACACTC 59.580 38.462 0.00 0.00 0.00 3.51
5296 6513 6.278363 ACACGTACAGAGAAAAATACACACT 58.722 36.000 0.00 0.00 0.00 3.55
5297 6514 6.520792 ACACGTACAGAGAAAAATACACAC 57.479 37.500 0.00 0.00 0.00 3.82
5298 6515 7.542534 AAACACGTACAGAGAAAAATACACA 57.457 32.000 0.00 0.00 0.00 3.72
5299 6516 8.730427 CAAAAACACGTACAGAGAAAAATACAC 58.270 33.333 0.00 0.00 0.00 2.90
5300 6517 7.911205 CCAAAAACACGTACAGAGAAAAATACA 59.089 33.333 0.00 0.00 0.00 2.29
5301 6518 7.377662 CCCAAAAACACGTACAGAGAAAAATAC 59.622 37.037 0.00 0.00 0.00 1.89
5302 6519 7.419204 CCCAAAAACACGTACAGAGAAAAATA 58.581 34.615 0.00 0.00 0.00 1.40
5303 6520 6.270064 CCCAAAAACACGTACAGAGAAAAAT 58.730 36.000 0.00 0.00 0.00 1.82
5304 6521 5.393243 CCCCAAAAACACGTACAGAGAAAAA 60.393 40.000 0.00 0.00 0.00 1.94
5305 6522 4.096682 CCCCAAAAACACGTACAGAGAAAA 59.903 41.667 0.00 0.00 0.00 2.29
5306 6523 3.628487 CCCCAAAAACACGTACAGAGAAA 59.372 43.478 0.00 0.00 0.00 2.52
5307 6524 3.207778 CCCCAAAAACACGTACAGAGAA 58.792 45.455 0.00 0.00 0.00 2.87
5308 6525 2.171027 ACCCCAAAAACACGTACAGAGA 59.829 45.455 0.00 0.00 0.00 3.10
5309 6526 2.567985 ACCCCAAAAACACGTACAGAG 58.432 47.619 0.00 0.00 0.00 3.35
5310 6527 2.713863 ACCCCAAAAACACGTACAGA 57.286 45.000 0.00 0.00 0.00 3.41
5311 6528 3.786516 AAACCCCAAAAACACGTACAG 57.213 42.857 0.00 0.00 0.00 2.74
5312 6529 5.649782 TTTAAACCCCAAAAACACGTACA 57.350 34.783 0.00 0.00 0.00 2.90
5313 6530 7.536895 AAATTTAAACCCCAAAAACACGTAC 57.463 32.000 0.00 0.00 0.00 3.67
5314 6531 8.557592 AAAAATTTAAACCCCAAAAACACGTA 57.442 26.923 0.00 0.00 0.00 3.57
5315 6532 7.450124 AAAAATTTAAACCCCAAAAACACGT 57.550 28.000 0.00 0.00 0.00 4.49
5340 6557 9.065798 ACTAGTATAAAACCGTAAAGCCAAAAA 57.934 29.630 0.00 0.00 0.00 1.94
5341 6558 8.620116 ACTAGTATAAAACCGTAAAGCCAAAA 57.380 30.769 0.00 0.00 0.00 2.44
5342 6559 8.620116 AACTAGTATAAAACCGTAAAGCCAAA 57.380 30.769 0.00 0.00 0.00 3.28
5343 6560 7.334171 GGAACTAGTATAAAACCGTAAAGCCAA 59.666 37.037 0.00 0.00 0.00 4.52
5344 6561 6.818142 GGAACTAGTATAAAACCGTAAAGCCA 59.182 38.462 0.00 0.00 0.00 4.75
5345 6562 7.239166 GGAACTAGTATAAAACCGTAAAGCC 57.761 40.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.