Multiple sequence alignment - TraesCS1B01G229300

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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 TraesCS1B01G229300 chr1B 100.000 5675 0 0 1 5675 411826126 411820452 0.000000e+00 10480.0
1 TraesCS1B01G229300 chr1A 93.962 3362 153 20 1675 5010 381317861 381314524 0.000000e+00 5038.0
2 TraesCS1B01G229300 chr1A 90.480 1229 41 22 503 1683 381319212 381318012 0.000000e+00 1552.0
3 TraesCS1B01G229300 chr1A 85.714 196 23 4 5470 5664 139567475 139567284 9.640000e-48 202.0
4 TraesCS1B01G229300 chrUn 93.709 2448 107 20 786 3199 268926708 268924274 0.000000e+00 3624.0
5 TraesCS1B01G229300 chrUn 94.524 1333 58 5 3626 4949 268921673 268920347 0.000000e+00 2043.0
6 TraesCS1B01G229300 chrUn 81.537 807 81 38 5 789 315121819 315121059 2.260000e-168 603.0
7 TraesCS1B01G229300 chrUn 95.342 365 13 3 3234 3595 268922037 268921674 1.370000e-160 577.0
8 TraesCS1B01G229300 chrUn 77.007 274 42 13 2787 3053 110513662 110513921 2.760000e-28 137.0
9 TraesCS1B01G229300 chrUn 85.507 69 7 2 2628 2696 110513500 110513565 1.020000e-07 69.4
10 TraesCS1B01G229300 chr3B 86.141 469 63 2 3 469 161150931 161150463 6.560000e-139 505.0
11 TraesCS1B01G229300 chr3B 84.829 468 69 2 3 469 641800416 641800882 2.390000e-128 470.0
12 TraesCS1B01G229300 chr3B 87.838 74 6 3 5593 5664 512412017 512411945 3.640000e-12 84.2
13 TraesCS1B01G229300 chr7D 86.517 445 54 5 3 443 515397009 515397451 8.550000e-133 484.0
14 TraesCS1B01G229300 chr7D 77.008 635 77 34 5051 5643 39133660 39133053 3.320000e-77 300.0
15 TraesCS1B01G229300 chr5B 86.323 446 60 1 4 448 504520706 504520261 8.550000e-133 484.0
16 TraesCS1B01G229300 chr5B 76.289 388 52 16 5061 5410 221909612 221909997 2.720000e-38 171.0
17 TraesCS1B01G229300 chr4D 86.222 450 52 8 5 448 481620348 481619903 3.980000e-131 479.0
18 TraesCS1B01G229300 chr4D 85.385 130 17 2 5042 5170 121480263 121480391 3.570000e-27 134.0
19 TraesCS1B01G229300 chr4D 83.846 130 19 2 5042 5170 8892017 8892145 7.720000e-24 122.0
20 TraesCS1B01G229300 chr5A 85.106 470 66 3 1 466 397141666 397141197 1.430000e-130 477.0
21 TraesCS1B01G229300 chr5A 76.493 268 42 13 2787 3047 700437094 700437347 5.970000e-25 126.0
22 TraesCS1B01G229300 chr5A 85.507 69 7 2 2628 2696 700436932 700436997 1.020000e-07 69.4
23 TraesCS1B01G229300 chr2D 83.629 507 78 5 3 505 632298934 632299439 6.660000e-129 472.0
24 TraesCS1B01G229300 chr2D 77.849 623 103 19 5066 5664 476344224 476343613 2.520000e-93 353.0
25 TraesCS1B01G229300 chr5D 85.097 463 65 4 11 469 529762833 529763295 2.390000e-128 470.0
26 TraesCS1B01G229300 chr5D 78.801 684 87 21 5037 5674 512213899 512213228 1.900000e-109 407.0
27 TraesCS1B01G229300 chr2B 85.249 461 62 6 12 469 770298996 770298539 2.390000e-128 470.0
28 TraesCS1B01G229300 chr3D 79.920 503 66 16 5178 5675 597476616 597476144 2.530000e-88 337.0
29 TraesCS1B01G229300 chr3D 88.024 167 14 2 5462 5627 443445149 443445310 5.800000e-45 193.0
30 TraesCS1B01G229300 chr3D 83.969 131 20 1 5035 5164 523636184 523636314 2.150000e-24 124.0
31 TraesCS1B01G229300 chr6D 80.361 499 49 14 5166 5650 367532839 367532376 3.280000e-87 333.0
32 TraesCS1B01G229300 chr6D 86.038 265 34 3 5035 5298 242990222 242989960 1.200000e-71 281.0
33 TraesCS1B01G229300 chr6D 79.429 350 48 14 5316 5663 446641743 446642070 5.720000e-55 226.0
34 TraesCS1B01G229300 chr4A 79.317 527 70 19 5169 5675 211475404 211475911 3.280000e-87 333.0
35 TraesCS1B01G229300 chr4A 75.477 367 48 22 5036 5380 433732033 433731687 2.130000e-29 141.0
36 TraesCS1B01G229300 chr4A 85.246 122 18 0 5036 5157 463842456 463842577 5.970000e-25 126.0
37 TraesCS1B01G229300 chr4A 84.375 128 19 1 5051 5177 441932058 441932185 2.150000e-24 124.0
38 TraesCS1B01G229300 chr1D 75.948 686 104 30 5035 5675 52738494 52739163 4.300000e-76 296.0
39 TraesCS1B01G229300 chr6A 76.163 516 85 25 5178 5671 602599214 602599713 2.640000e-58 237.0
40 TraesCS1B01G229300 chr6A 81.362 279 25 13 5180 5439 335774206 335774476 9.640000e-48 202.0
41 TraesCS1B01G229300 chr6A 83.459 133 20 2 5042 5173 457369434 457369303 7.720000e-24 122.0
42 TraesCS1B01G229300 chr7A 76.152 499 84 24 5163 5643 491970950 491970469 4.420000e-56 230.0
43 TraesCS1B01G229300 chr7A 84.677 124 17 2 5051 5173 43175339 43175217 7.720000e-24 122.0
44 TraesCS1B01G229300 chr2A 79.003 381 44 16 5061 5410 162424773 162425148 1.590000e-55 228.0
45 TraesCS1B01G229300 chr6B 82.239 259 35 5 5035 5282 177277261 177277519 4.450000e-51 213.0
46 TraesCS1B01G229300 chr6B 73.022 493 84 37 5181 5664 553048698 553049150 1.660000e-25 128.0
47 TraesCS1B01G229300 chr7B 78.369 282 38 13 5061 5322 632837569 632837291 1.640000e-35 161.0
48 TraesCS1B01G229300 chr4B 83.240 179 26 3 5164 5340 188590293 188590117 1.640000e-35 161.0
49 TraesCS1B01G229300 chr4B 75.735 272 53 8 2787 3054 660580398 660580660 2.150000e-24 124.0
50 TraesCS1B01G229300 chr4B 85.507 69 7 2 2628 2696 660580229 660580294 1.020000e-07 69.4


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 TraesCS1B01G229300 chr1B 411820452 411826126 5674 True 10480.000000 10480 100.000 1 5675 1 chr1B.!!$R1 5674
1 TraesCS1B01G229300 chr1A 381314524 381319212 4688 True 3295.000000 5038 92.221 503 5010 2 chr1A.!!$R2 4507
2 TraesCS1B01G229300 chrUn 268920347 268926708 6361 True 2081.333333 3624 94.525 786 4949 3 chrUn.!!$R2 4163
3 TraesCS1B01G229300 chrUn 315121059 315121819 760 True 603.000000 603 81.537 5 789 1 chrUn.!!$R1 784
4 TraesCS1B01G229300 chr7D 39133053 39133660 607 True 300.000000 300 77.008 5051 5643 1 chr7D.!!$R1 592
5 TraesCS1B01G229300 chr2D 632298934 632299439 505 False 472.000000 472 83.629 3 505 1 chr2D.!!$F1 502
6 TraesCS1B01G229300 chr2D 476343613 476344224 611 True 353.000000 353 77.849 5066 5664 1 chr2D.!!$R1 598
7 TraesCS1B01G229300 chr5D 512213228 512213899 671 True 407.000000 407 78.801 5037 5674 1 chr5D.!!$R1 637
8 TraesCS1B01G229300 chr4A 211475404 211475911 507 False 333.000000 333 79.317 5169 5675 1 chr4A.!!$F1 506
9 TraesCS1B01G229300 chr1D 52738494 52739163 669 False 296.000000 296 75.948 5035 5675 1 chr1D.!!$F1 640

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
531 537 0.177373 GGGTTGATCTACCACGGGAC 59.823 60.000 24.77 5.61 40.09 4.46 F
1281 1345 0.249489 GGCCGTGTAGACTGCTATGG 60.249 60.000 6.39 0.00 33.12 2.74 F
1936 2176 1.623811 ACTATGACACGGTGAAGCCTT 59.376 47.619 16.29 0.00 34.25 4.35 F
2857 3105 1.827315 TTGGCGACTTTGTTCGAGCG 61.827 55.000 0.00 0.00 41.78 5.03 F
3459 5920 0.038166 CCTAAAACCAGGCAGCTCCA 59.962 55.000 5.21 0.00 37.29 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2326 2571 0.321298 GTAAGCCAGGAAACGAGCCA 60.321 55.000 0.00 0.00 34.24 4.75 R
2809 3057 1.202879 ACGCCCCTTTTCTTGACATCA 60.203 47.619 0.00 0.00 0.00 3.07 R
3222 3470 1.205893 GAATGGAAGCTGAGACGAGGT 59.794 52.381 0.00 0.00 0.00 3.85 R
4487 6965 0.323360 GGGTACAAGAAGCCATGGCA 60.323 55.000 37.18 13.31 44.88 4.92 R
5047 7530 0.318699 TTCTGTCTGCAACGACCGAG 60.319 55.000 3.85 0.00 30.59 4.63 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
20 21 3.517140 GCGCCGCCATTTCCATCA 61.517 61.111 0.00 0.00 0.00 3.07
76 77 2.423088 GGACTCCTCCGAGGATGAGTAA 60.423 54.545 23.61 0.00 44.81 2.24
147 148 2.455032 CATGTTCTACTCTTCCTCGCG 58.545 52.381 0.00 0.00 0.00 5.87
149 150 1.093159 GTTCTACTCTTCCTCGCGGA 58.907 55.000 6.13 0.00 37.60 5.54
170 171 0.798776 GACCGCACCTTCACTTCATG 59.201 55.000 0.00 0.00 0.00 3.07
197 198 2.507944 GCCGGTGCTCATGGAGAT 59.492 61.111 1.90 0.00 33.53 2.75
210 211 2.746359 GAGATGGCGGATGGAGGG 59.254 66.667 0.00 0.00 0.00 4.30
226 227 4.778143 GGCGACACGGGCTTGGAT 62.778 66.667 0.00 0.00 0.00 3.41
261 262 2.298446 GTCGTAGGATAGGTTTAGGGGC 59.702 54.545 0.00 0.00 0.00 5.80
307 308 6.869315 TTCGAAATATAATGAAATCCGCCA 57.131 33.333 0.00 0.00 0.00 5.69
313 314 8.592105 AAATATAATGAAATCCGCCATGTTTG 57.408 30.769 0.00 0.00 0.00 2.93
324 325 4.950475 TCCGCCATGTTTGTATAAAATCCA 59.050 37.500 0.00 0.00 0.00 3.41
370 371 3.613737 GTGTTTGCATGAATTTCATCCGG 59.386 43.478 8.95 0.00 34.28 5.14
374 375 5.651387 TTGCATGAATTTCATCCGGTTTA 57.349 34.783 8.95 0.00 34.28 2.01
428 431 1.736586 GATGTCGTCCTCCGCATCT 59.263 57.895 9.98 0.00 42.05 2.90
433 436 0.678684 TCGTCCTCCGCATCTGTGTA 60.679 55.000 0.00 0.00 36.19 2.90
436 439 0.963856 TCCTCCGCATCTGTGTACGT 60.964 55.000 0.00 0.00 0.00 3.57
437 440 0.736636 CCTCCGCATCTGTGTACGTA 59.263 55.000 0.00 0.00 0.00 3.57
448 451 1.202915 TGTGTACGTAGACTGGTCCCA 60.203 52.381 21.80 0.00 0.00 4.37
450 453 1.202915 TGTACGTAGACTGGTCCCACA 60.203 52.381 0.00 0.00 0.00 4.17
451 454 1.471684 GTACGTAGACTGGTCCCACAG 59.528 57.143 0.00 0.00 44.03 3.66
459 462 1.866015 CTGGTCCCACAGTCCATAGA 58.134 55.000 0.00 0.00 33.81 1.98
460 463 1.482593 CTGGTCCCACAGTCCATAGAC 59.517 57.143 0.00 0.00 43.89 2.59
469 474 2.038690 GTCCATAGACGGATGCGGA 58.961 57.895 12.44 0.00 37.41 5.54
471 476 1.116308 TCCATAGACGGATGCGGAAA 58.884 50.000 12.44 0.00 0.00 3.13
472 477 1.202486 TCCATAGACGGATGCGGAAAC 60.202 52.381 12.44 0.00 0.00 2.78
479 484 3.754323 AGACGGATGCGGAAACAAATTTA 59.246 39.130 12.44 0.00 0.00 1.40
483 489 4.378978 CGGATGCGGAAACAAATTTACAGA 60.379 41.667 0.00 0.00 0.00 3.41
489 495 5.150683 CGGAAACAAATTTACAGATTGCGA 58.849 37.500 5.45 0.00 32.96 5.10
491 497 6.964370 CGGAAACAAATTTACAGATTGCGATA 59.036 34.615 5.45 0.00 32.96 2.92
496 502 6.260936 ACAAATTTACAGATTGCGATAGGAGG 59.739 38.462 0.00 0.00 38.10 4.30
507 513 2.166664 GCGATAGGAGGTGCCCTAATAG 59.833 54.545 0.00 0.00 41.71 1.73
508 514 2.761208 CGATAGGAGGTGCCCTAATAGG 59.239 54.545 0.00 0.00 41.71 2.57
524 530 0.761702 TAGGGCGGGGTTGATCTACC 60.762 60.000 17.01 17.01 37.47 3.18
529 535 1.525442 GGGGTTGATCTACCACGGG 59.475 63.158 24.77 0.00 40.09 5.28
530 536 0.979187 GGGGTTGATCTACCACGGGA 60.979 60.000 24.77 0.00 40.09 5.14
531 537 0.177373 GGGTTGATCTACCACGGGAC 59.823 60.000 24.77 5.61 40.09 4.46
532 538 0.177373 GGTTGATCTACCACGGGACC 59.823 60.000 19.84 0.00 38.12 4.46
569 575 2.701006 CGTATGCGTTCCAAGCGG 59.299 61.111 0.00 0.00 37.44 5.52
570 576 2.098233 CGTATGCGTTCCAAGCGGT 61.098 57.895 0.00 0.00 37.44 5.68
571 577 1.423845 GTATGCGTTCCAAGCGGTG 59.576 57.895 0.00 0.00 37.44 4.94
664 684 2.185608 GAAGCAGACTCGCTCCCC 59.814 66.667 0.75 0.00 42.89 4.81
702 723 1.484232 GACCGTCACGTGCGTAAAC 59.516 57.895 23.70 11.70 0.00 2.01
804 828 1.064017 TCCATATCCCACCAGCCAAAC 60.064 52.381 0.00 0.00 0.00 2.93
806 830 1.006813 ATATCCCACCAGCCAAACCA 58.993 50.000 0.00 0.00 0.00 3.67
807 831 0.331278 TATCCCACCAGCCAAACCAG 59.669 55.000 0.00 0.00 0.00 4.00
808 832 1.434513 ATCCCACCAGCCAAACCAGA 61.435 55.000 0.00 0.00 0.00 3.86
809 833 1.903404 CCCACCAGCCAAACCAGAC 60.903 63.158 0.00 0.00 0.00 3.51
811 835 2.113139 ACCAGCCAAACCAGACCG 59.887 61.111 0.00 0.00 0.00 4.79
931 982 1.278985 CACTTCTATGCAGTGGGTGGA 59.721 52.381 0.00 0.00 38.43 4.02
1148 1199 1.683011 CCCATTCCGTGAATCCAGCTT 60.683 52.381 0.00 0.00 28.87 3.74
1182 1233 5.811190 TCTCGAAAAAGGGTAAATGGATCA 58.189 37.500 0.00 0.00 0.00 2.92
1274 1338 3.760035 CTGCCGGCCGTGTAGACT 61.760 66.667 26.77 0.00 0.00 3.24
1275 1339 3.989698 CTGCCGGCCGTGTAGACTG 62.990 68.421 26.77 6.93 0.00 3.51
1277 1341 3.760035 CCGGCCGTGTAGACTGCT 61.760 66.667 26.12 0.00 33.12 4.24
1278 1342 2.412323 CCGGCCGTGTAGACTGCTA 61.412 63.158 26.12 0.00 33.12 3.49
1279 1343 1.734137 CGGCCGTGTAGACTGCTAT 59.266 57.895 19.50 0.00 33.12 2.97
1280 1344 0.595053 CGGCCGTGTAGACTGCTATG 60.595 60.000 19.50 0.00 33.12 2.23
1281 1345 0.249489 GGCCGTGTAGACTGCTATGG 60.249 60.000 6.39 0.00 33.12 2.74
1301 1365 2.421670 GGATCCTGTAGACAGTCGAGGA 60.422 54.545 16.96 16.96 42.27 3.71
1321 1385 8.076714 CGAGGAAAATCGAATAATCTGATCAA 57.923 34.615 0.00 0.00 45.56 2.57
1477 1557 2.658285 CACTTGCTGTTCTGTTCATGC 58.342 47.619 0.00 0.00 0.00 4.06
1595 1675 5.156355 TCTTACGAACGTGTGATTCCTTAC 58.844 41.667 10.14 0.00 0.00 2.34
1608 1688 6.069673 TGTGATTCCTTACCAGGTTGACATAT 60.070 38.462 0.00 0.00 41.69 1.78
1611 1691 6.877668 TTCCTTACCAGGTTGACATATACA 57.122 37.500 0.00 0.00 41.69 2.29
1678 1758 4.628333 TCGGTACCATTGAAACGAAATCTC 59.372 41.667 13.54 0.00 0.00 2.75
1852 2091 3.997681 TGTCGCCAATCGTTTATTCTTGA 59.002 39.130 0.00 0.00 39.67 3.02
1870 2110 2.715046 TGATGTCAACTCAATGAGCCC 58.285 47.619 10.62 0.00 32.04 5.19
1890 2130 5.883673 AGCCCGTTTGATAAATAGCTACAAA 59.116 36.000 0.00 0.00 0.00 2.83
1905 2145 6.604735 AGCTACAAATTAGAGCCGTTATTG 57.395 37.500 0.00 0.00 36.87 1.90
1936 2176 1.623811 ACTATGACACGGTGAAGCCTT 59.376 47.619 16.29 0.00 34.25 4.35
1979 2219 6.102897 TGCTCCTGGCTCTAAATAAGTATC 57.897 41.667 0.00 0.00 42.39 2.24
2067 2307 8.593492 AGTTTTATGCAAAGTTTTCCATTCTC 57.407 30.769 0.00 0.00 0.00 2.87
2172 2417 7.481642 ACTATAAGTAACACATCTTCTCACGG 58.518 38.462 0.00 0.00 0.00 4.94
2325 2570 7.404985 CGTTATCGTAGTCTAGCTAAACTTCA 58.595 38.462 4.76 0.00 0.00 3.02
2326 2571 8.068977 CGTTATCGTAGTCTAGCTAAACTTCAT 58.931 37.037 4.76 0.00 0.00 2.57
2337 2583 3.426292 GCTAAACTTCATGGCTCGTTTCC 60.426 47.826 0.00 0.00 32.46 3.13
2359 2605 5.425539 TCCTGGCTTACTTCTTACATAAGCT 59.574 40.000 13.27 0.00 46.54 3.74
2417 2663 6.872628 TGATTTGATCATTCATGGTAGAGC 57.127 37.500 0.00 0.00 33.59 4.09
2424 2670 6.952938 TGATCATTCATGGTAGAGCTCTAGAT 59.047 38.462 23.87 18.29 0.00 1.98
2538 2786 4.523083 ACCGGTACATGTCTGCAATTATT 58.477 39.130 4.49 0.00 0.00 1.40
2562 2810 6.605471 TGTACCACAGTGAACTATCATCTT 57.395 37.500 0.62 0.00 38.01 2.40
2612 2860 7.592938 TGGCAACTGAAACTATGAGTAATTTG 58.407 34.615 0.00 0.00 37.61 2.32
2725 2973 5.327091 CCTTGTCAACTATTCTCATTTGCG 58.673 41.667 0.00 0.00 0.00 4.85
2809 3057 7.391620 TGACCTTGTAGATATTCGACCTTTTT 58.608 34.615 0.00 0.00 0.00 1.94
2827 3075 4.335400 TTTTGATGTCAAGAAAAGGGGC 57.665 40.909 0.00 0.00 37.15 5.80
2857 3105 1.827315 TTGGCGACTTTGTTCGAGCG 61.827 55.000 0.00 0.00 41.78 5.03
2943 3191 9.477484 TTTCTGTCTTGTCTTCAGTTTATAGAC 57.523 33.333 0.00 0.00 38.96 2.59
3132 3380 8.766000 TTAGTCGTAGATACAAAAGAAATGCA 57.234 30.769 0.00 0.00 40.67 3.96
3138 3386 7.485913 CGTAGATACAAAAGAAATGCATTGCTT 59.514 33.333 24.61 24.61 37.24 3.91
3254 5713 7.766278 TCTCAGCTTCCATTCTAGAAACATAAC 59.234 37.037 9.71 0.00 0.00 1.89
3456 5917 0.038310 GACCCTAAAACCAGGCAGCT 59.962 55.000 0.00 0.00 34.02 4.24
3459 5920 0.038166 CCTAAAACCAGGCAGCTCCA 59.962 55.000 5.21 0.00 37.29 3.86
3621 6083 5.309638 TCACCAAGAACCAAATGATAACGA 58.690 37.500 0.00 0.00 0.00 3.85
3624 6086 7.279981 TCACCAAGAACCAAATGATAACGATAG 59.720 37.037 0.00 0.00 46.19 2.08
3719 6183 6.334102 AGTATAGGAGCCTTCGTTTATCAG 57.666 41.667 0.00 0.00 0.00 2.90
3902 6366 6.413783 TGTGTCCAGTATTGAAGTGTAGAA 57.586 37.500 0.00 0.00 0.00 2.10
4062 6526 7.379797 CCTCAAGTGAGTATGACGTAACATATG 59.620 40.741 7.51 0.00 40.48 1.78
4297 6775 4.148128 TGCACATGTGGGATTTGTTTTT 57.852 36.364 26.55 0.00 0.00 1.94
4407 6885 5.412594 ACAAGCACATTCTAGTTACATGTGG 59.587 40.000 9.11 11.20 45.36 4.17
4408 6886 5.420725 AGCACATTCTAGTTACATGTGGA 57.579 39.130 9.11 0.00 45.36 4.02
4409 6887 5.994250 AGCACATTCTAGTTACATGTGGAT 58.006 37.500 9.11 0.00 45.36 3.41
4410 6888 5.819379 AGCACATTCTAGTTACATGTGGATG 59.181 40.000 9.11 4.21 45.36 3.51
4411 6889 5.586243 GCACATTCTAGTTACATGTGGATGT 59.414 40.000 9.11 4.89 45.36 3.06
4412 6890 6.457392 GCACATTCTAGTTACATGTGGATGTG 60.457 42.308 21.82 21.82 45.36 3.21
4515 6993 4.229582 TGGCTTCTTGTACCCTTTCCATAT 59.770 41.667 0.00 0.00 0.00 1.78
4539 7017 1.001378 GTTTGATGACAGTGTGGTGCC 60.001 52.381 0.00 0.00 0.00 5.01
4576 7054 3.740044 ACATTTGATACGAAGCAACGG 57.260 42.857 7.39 0.00 37.61 4.44
4602 7080 7.894376 AATTCTTGCTAATCATTTGTGTTGG 57.106 32.000 0.00 0.00 0.00 3.77
4603 7081 4.808558 TCTTGCTAATCATTTGTGTTGGC 58.191 39.130 0.00 0.00 0.00 4.52
4604 7082 4.280425 TCTTGCTAATCATTTGTGTTGGCA 59.720 37.500 0.00 0.00 37.52 4.92
4665 7143 5.614324 TTCACTCGGAGGTTGATGATATT 57.386 39.130 10.23 0.00 0.00 1.28
4700 7178 4.872691 GTGATCCTCACAAAGATGTACAGG 59.127 45.833 0.33 0.00 46.22 4.00
4709 7187 6.929049 TCACAAAGATGTACAGGTAACAGAAG 59.071 38.462 0.33 0.00 37.82 2.85
4781 7259 2.417379 GGCTAATGTTGCTCGAGAGTCA 60.417 50.000 18.75 11.24 0.00 3.41
4841 7321 9.939802 ACCGAGAGTTAGTCTTGTTAAATATTT 57.060 29.630 5.89 5.89 34.71 1.40
4911 7391 2.988010 TGTCGAGAATATGGCTGCTT 57.012 45.000 0.00 0.00 0.00 3.91
4974 7454 5.521735 GTGCTTCATGAATCTACTACCACTG 59.478 44.000 8.96 0.00 0.00 3.66
4975 7455 4.509600 GCTTCATGAATCTACTACCACTGC 59.490 45.833 8.96 0.10 0.00 4.40
4977 7457 4.030216 TCATGAATCTACTACCACTGCCA 58.970 43.478 0.00 0.00 0.00 4.92
5010 7493 2.233431 AGCAAAACAGCACCACAAAGAA 59.767 40.909 0.00 0.00 36.85 2.52
5011 7494 2.999355 GCAAAACAGCACCACAAAGAAA 59.001 40.909 0.00 0.00 0.00 2.52
5012 7495 3.622612 GCAAAACAGCACCACAAAGAAAT 59.377 39.130 0.00 0.00 0.00 2.17
5013 7496 4.494526 GCAAAACAGCACCACAAAGAAATG 60.495 41.667 0.00 0.00 0.00 2.32
5014 7497 4.470334 AAACAGCACCACAAAGAAATGT 57.530 36.364 0.00 0.00 0.00 2.71
5015 7498 5.590530 AAACAGCACCACAAAGAAATGTA 57.409 34.783 0.00 0.00 30.84 2.29
5016 7499 5.789643 AACAGCACCACAAAGAAATGTAT 57.210 34.783 0.00 0.00 30.84 2.29
5017 7500 5.376854 ACAGCACCACAAAGAAATGTATC 57.623 39.130 0.00 0.00 30.84 2.24
5018 7501 4.218417 ACAGCACCACAAAGAAATGTATCC 59.782 41.667 0.00 0.00 30.84 2.59
5019 7502 4.460382 CAGCACCACAAAGAAATGTATCCT 59.540 41.667 0.00 0.00 30.84 3.24
5020 7503 5.047802 CAGCACCACAAAGAAATGTATCCTT 60.048 40.000 0.00 0.00 30.84 3.36
5021 7504 6.150976 CAGCACCACAAAGAAATGTATCCTTA 59.849 38.462 0.00 0.00 30.84 2.69
5022 7505 6.375455 AGCACCACAAAGAAATGTATCCTTAG 59.625 38.462 0.00 0.00 30.84 2.18
5023 7506 6.374333 GCACCACAAAGAAATGTATCCTTAGA 59.626 38.462 0.00 0.00 30.84 2.10
5024 7507 7.094377 GCACCACAAAGAAATGTATCCTTAGAA 60.094 37.037 0.00 0.00 30.84 2.10
5025 7508 8.792633 CACCACAAAGAAATGTATCCTTAGAAA 58.207 33.333 0.00 0.00 30.84 2.52
5026 7509 8.793592 ACCACAAAGAAATGTATCCTTAGAAAC 58.206 33.333 0.00 0.00 30.84 2.78
5027 7510 9.014297 CCACAAAGAAATGTATCCTTAGAAACT 57.986 33.333 0.00 0.00 30.84 2.66
5029 7512 9.232473 ACAAAGAAATGTATCCTTAGAAACTCC 57.768 33.333 0.00 0.00 0.00 3.85
5030 7513 9.231297 CAAAGAAATGTATCCTTAGAAACTCCA 57.769 33.333 0.00 0.00 0.00 3.86
5031 7514 9.807921 AAAGAAATGTATCCTTAGAAACTCCAA 57.192 29.630 0.00 0.00 0.00 3.53
5032 7515 8.794335 AGAAATGTATCCTTAGAAACTCCAAC 57.206 34.615 0.00 0.00 0.00 3.77
5033 7516 8.606830 AGAAATGTATCCTTAGAAACTCCAACT 58.393 33.333 0.00 0.00 0.00 3.16
5040 7523 0.387929 AGAAACTCCAACTCGCACGA 59.612 50.000 0.00 0.00 0.00 4.35
5049 7532 4.755546 CTCGCACGAGTCTGTCTC 57.244 61.111 11.82 0.00 37.47 3.36
5059 7542 1.007734 GTCTGTCTCGGTCGTTGCA 60.008 57.895 0.00 0.00 0.00 4.08
5101 7585 2.728383 CGACTCAAACGGACGCGT 60.728 61.111 13.85 13.85 0.00 6.01
5118 7602 0.041312 CGTGTCCGCTTTTTGTCTGG 60.041 55.000 0.00 0.00 0.00 3.86
5158 7643 1.003349 CCAATTTGGGCCTCATTTGCA 59.997 47.619 4.53 0.00 32.67 4.08
5189 7695 2.682494 GTGCGTACTCCTCCCCCA 60.682 66.667 0.00 0.00 0.00 4.96
5232 7741 1.076705 GCCATTCTCTTCCACCCCC 60.077 63.158 0.00 0.00 0.00 5.40
5236 7745 1.849039 CATTCTCTTCCACCCCCATCT 59.151 52.381 0.00 0.00 0.00 2.90
5322 7851 2.772191 TGCACCCACACACCTCCT 60.772 61.111 0.00 0.00 0.00 3.69
5410 7967 2.594592 GCACAAAGTCGCACCCCT 60.595 61.111 0.00 0.00 0.00 4.79
5411 7968 1.302192 GCACAAAGTCGCACCCCTA 60.302 57.895 0.00 0.00 0.00 3.53
5412 7969 0.887387 GCACAAAGTCGCACCCCTAA 60.887 55.000 0.00 0.00 0.00 2.69
5413 7970 0.872388 CACAAAGTCGCACCCCTAAC 59.128 55.000 0.00 0.00 0.00 2.34
5414 7971 0.250597 ACAAAGTCGCACCCCTAACC 60.251 55.000 0.00 0.00 0.00 2.85
5415 7972 0.958876 CAAAGTCGCACCCCTAACCC 60.959 60.000 0.00 0.00 0.00 4.11
5416 7973 2.133359 AAAGTCGCACCCCTAACCCC 62.133 60.000 0.00 0.00 0.00 4.95
5442 7999 2.415608 CGGCCAGCTCCTTCGTCTA 61.416 63.158 2.24 0.00 0.00 2.59
5443 8000 1.739338 CGGCCAGCTCCTTCGTCTAT 61.739 60.000 2.24 0.00 0.00 1.98
5445 8002 0.318275 GCCAGCTCCTTCGTCTATCG 60.318 60.000 0.00 0.00 41.41 2.92
5463 8020 4.166888 ACGCCATGCTCGCCTGAT 62.167 61.111 5.65 0.00 0.00 2.90
5483 8040 2.809174 CGCCATGCTCGTCGAACA 60.809 61.111 0.03 0.03 0.00 3.18
5528 8089 4.919653 GAGGCATGCGTCTCTTCA 57.080 55.556 28.47 0.00 40.94 3.02
5565 8126 1.484227 CGACGTCCGCAAGTTGTTCA 61.484 55.000 10.58 0.00 0.00 3.18
5590 8152 3.742433 TTTGCACCAAGGTACAAATGG 57.258 42.857 12.45 8.73 36.71 3.16
5591 8153 2.666272 TGCACCAAGGTACAAATGGA 57.334 45.000 15.32 0.00 37.66 3.41
5647 8209 1.003759 CTACGACTCCGACGATTCCTG 60.004 57.143 0.00 0.00 39.50 3.86
5665 8227 2.892852 CCTGATCTGATGAGGAGGAGAC 59.107 54.545 17.08 0.00 30.13 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.848858 ATGATGGAAATGGCGGCGC 61.849 57.895 26.17 26.17 0.00 6.53
128 129 2.853731 CGCGAGGAAGAGTAGAACAT 57.146 50.000 0.00 0.00 0.00 2.71
147 148 0.250338 AAGTGAAGGTGCGGTCTTCC 60.250 55.000 9.85 3.77 39.72 3.46
149 150 0.468226 TGAAGTGAAGGTGCGGTCTT 59.532 50.000 0.00 0.00 0.00 3.01
170 171 2.588034 GCACCGGCGATAAGACCC 60.588 66.667 9.30 0.00 0.00 4.46
210 211 3.499737 CATCCAAGCCCGTGTCGC 61.500 66.667 0.00 0.00 0.00 5.19
233 234 1.452953 CCTATCCTACGACAGCGGCA 61.453 60.000 1.45 0.00 43.17 5.69
282 283 7.304735 TGGCGGATTTCATTATATTTCGAATG 58.695 34.615 0.00 0.00 34.89 2.67
283 284 7.447374 TGGCGGATTTCATTATATTTCGAAT 57.553 32.000 0.00 0.00 0.00 3.34
292 293 5.596836 ACAAACATGGCGGATTTCATTAT 57.403 34.783 0.00 0.00 0.00 1.28
295 296 6.707440 TTATACAAACATGGCGGATTTCAT 57.293 33.333 0.00 0.00 0.00 2.57
297 298 7.169140 GGATTTTATACAAACATGGCGGATTTC 59.831 37.037 0.00 0.00 0.00 2.17
307 308 9.820725 CCAACATGATGGATTTTATACAAACAT 57.179 29.630 16.73 0.00 43.54 2.71
313 314 8.373048 TCGTACCAACATGATGGATTTTATAC 57.627 34.615 27.18 16.08 43.54 1.47
324 325 3.202906 CCGGATTTCGTACCAACATGAT 58.797 45.455 0.00 0.00 37.11 2.45
332 333 1.799544 ACACAACCGGATTTCGTACC 58.200 50.000 9.46 0.00 37.11 3.34
336 337 1.268794 TGCAAACACAACCGGATTTCG 60.269 47.619 9.46 0.00 38.88 3.46
388 390 5.063204 TCCAACGCTAGCTGCATATATTTT 58.937 37.500 13.93 0.00 43.06 1.82
428 431 1.202915 TGGGACCAGTCTACGTACACA 60.203 52.381 3.76 0.00 0.00 3.72
433 436 0.178970 ACTGTGGGACCAGTCTACGT 60.179 55.000 0.00 0.00 41.84 3.57
448 451 0.385751 CGCATCCGTCTATGGACTGT 59.614 55.000 7.68 0.00 41.85 3.55
450 453 0.467474 TCCGCATCCGTCTATGGACT 60.467 55.000 7.68 0.00 41.85 3.85
451 454 0.387929 TTCCGCATCCGTCTATGGAC 59.612 55.000 0.00 0.00 41.85 4.02
455 458 2.684001 TTGTTTCCGCATCCGTCTAT 57.316 45.000 0.00 0.00 0.00 1.98
456 459 2.459060 TTTGTTTCCGCATCCGTCTA 57.541 45.000 0.00 0.00 0.00 2.59
457 460 1.821216 ATTTGTTTCCGCATCCGTCT 58.179 45.000 0.00 0.00 0.00 4.18
459 462 3.253677 TGTAAATTTGTTTCCGCATCCGT 59.746 39.130 0.00 0.00 0.00 4.69
460 463 3.827625 TGTAAATTTGTTTCCGCATCCG 58.172 40.909 0.00 0.00 0.00 4.18
469 474 8.050778 TCCTATCGCAATCTGTAAATTTGTTT 57.949 30.769 0.00 0.00 0.00 2.83
471 476 6.260936 CCTCCTATCGCAATCTGTAAATTTGT 59.739 38.462 0.00 0.00 0.00 2.83
472 477 6.260936 ACCTCCTATCGCAATCTGTAAATTTG 59.739 38.462 0.00 0.00 0.00 2.32
479 484 1.202580 GCACCTCCTATCGCAATCTGT 60.203 52.381 0.00 0.00 0.00 3.41
507 513 2.372074 TGGTAGATCAACCCCGCCC 61.372 63.158 0.00 0.00 38.90 6.13
508 514 1.153229 GTGGTAGATCAACCCCGCC 60.153 63.158 0.00 0.00 38.90 6.13
524 530 3.450115 GTCTCCCTCGGTCCCGTG 61.450 72.222 5.52 3.10 40.74 4.94
529 535 1.592223 CCACTTGTCTCCCTCGGTC 59.408 63.158 0.00 0.00 0.00 4.79
530 536 2.584391 GCCACTTGTCTCCCTCGGT 61.584 63.158 0.00 0.00 0.00 4.69
531 537 1.903877 ATGCCACTTGTCTCCCTCGG 61.904 60.000 0.00 0.00 0.00 4.63
532 538 0.742281 CATGCCACTTGTCTCCCTCG 60.742 60.000 0.00 0.00 0.00 4.63
538 544 1.372582 CATACGCATGCCACTTGTCT 58.627 50.000 13.15 0.00 0.00 3.41
569 575 4.681978 AAGAGGACGCGTGCCCAC 62.682 66.667 27.74 16.26 0.00 4.61
570 576 2.102109 TAAAAGAGGACGCGTGCCCA 62.102 55.000 27.74 3.31 0.00 5.36
571 577 0.743345 ATAAAAGAGGACGCGTGCCC 60.743 55.000 27.74 16.82 0.00 5.36
573 579 0.247695 GCATAAAAGAGGACGCGTGC 60.248 55.000 24.26 24.26 0.00 5.34
574 580 0.025001 CGCATAAAAGAGGACGCGTG 59.975 55.000 20.70 0.00 38.03 5.34
575 581 1.693083 GCGCATAAAAGAGGACGCGT 61.693 55.000 13.85 13.85 44.25 6.01
578 584 0.742990 TGGGCGCATAAAAGAGGACG 60.743 55.000 10.83 0.00 0.00 4.79
580 586 0.326595 TGTGGGCGCATAAAAGAGGA 59.673 50.000 10.83 0.00 0.00 3.71
581 587 0.451783 GTGTGGGCGCATAAAAGAGG 59.548 55.000 10.83 0.00 0.00 3.69
664 684 1.808390 GTCGAAATCCACCCGGACG 60.808 63.158 0.73 0.00 46.79 4.79
669 690 1.449070 GGTCGGTCGAAATCCACCC 60.449 63.158 0.00 0.00 0.00 4.61
992 1043 3.369410 ATGCACCCCATGGCCTGAG 62.369 63.158 6.09 0.00 31.48 3.35
993 1044 3.349304 ATGCACCCCATGGCCTGA 61.349 61.111 6.09 0.00 31.48 3.86
994 1045 2.836360 GATGCACCCCATGGCCTG 60.836 66.667 6.09 4.25 33.29 4.85
1044 1095 4.371417 ACGGGGTCCTCGTAGCCA 62.371 66.667 17.23 0.00 39.22 4.75
1091 1142 1.977293 AAAGGGATGGGAGCGAGCTC 61.977 60.000 16.14 16.14 42.04 4.09
1092 1143 1.566298 AAAAGGGATGGGAGCGAGCT 61.566 55.000 0.00 0.00 0.00 4.09
1101 1152 3.190383 AGAAAAGGGGAAAAGGGATGG 57.810 47.619 0.00 0.00 0.00 3.51
1148 1199 3.188460 CCTTTTTCGAGAAATGAAGCGGA 59.812 43.478 1.11 0.00 0.00 5.54
1269 1333 5.163088 TGTCTACAGGATCCATAGCAGTCTA 60.163 44.000 15.82 0.00 0.00 2.59
1270 1334 4.148838 GTCTACAGGATCCATAGCAGTCT 58.851 47.826 15.82 0.00 0.00 3.24
1271 1335 3.891977 TGTCTACAGGATCCATAGCAGTC 59.108 47.826 15.82 2.41 0.00 3.51
1272 1336 3.894427 CTGTCTACAGGATCCATAGCAGT 59.106 47.826 15.82 4.99 40.20 4.40
1273 1337 4.517952 CTGTCTACAGGATCCATAGCAG 57.482 50.000 15.82 18.94 40.20 4.24
1359 1423 1.006639 ACATAGGTTCCCCCGCAAAAT 59.993 47.619 0.00 0.00 38.74 1.82
1401 1472 2.050144 GGCAGGAGGTGGATCAATAGA 58.950 52.381 0.00 0.00 0.00 1.98
1477 1557 0.941463 AACTTCGCTGACGCTGACTG 60.941 55.000 0.00 0.00 39.84 3.51
1595 1675 5.917462 TGATGTCTGTATATGTCAACCTGG 58.083 41.667 0.00 0.00 0.00 4.45
1608 1688 4.081365 TCGGGTGCTTATTTGATGTCTGTA 60.081 41.667 0.00 0.00 0.00 2.74
1611 1691 3.197766 TCTCGGGTGCTTATTTGATGTCT 59.802 43.478 0.00 0.00 0.00 3.41
1678 1758 7.168637 GGAATGTAATTTCAGCATAGCAATGTG 59.831 37.037 0.00 0.00 36.07 3.21
1757 1996 7.998383 ACTATTGATGGCTAAATGTAATCACCA 59.002 33.333 0.00 0.00 0.00 4.17
1852 2091 1.003580 ACGGGCTCATTGAGTTGACAT 59.996 47.619 14.90 0.00 31.39 3.06
1890 2130 9.938280 TTATTATGCTACAATAACGGCTCTAAT 57.062 29.630 0.00 0.00 0.00 1.73
1905 2145 7.143340 TCACCGTGTCATAGTTATTATGCTAC 58.857 38.462 0.00 0.00 39.23 3.58
2055 2295 1.200020 CAGGCCACGAGAATGGAAAAC 59.800 52.381 5.01 0.00 43.02 2.43
2067 2307 2.942376 TCTATATTTTGCACAGGCCACG 59.058 45.455 5.01 0.00 40.13 4.94
2146 2391 7.644551 CCGTGAGAAGATGTGTTACTTATAGTC 59.355 40.741 0.00 0.00 0.00 2.59
2148 2393 7.704271 TCCGTGAGAAGATGTGTTACTTATAG 58.296 38.462 0.00 0.00 0.00 1.31
2149 2394 7.555195 TCTCCGTGAGAAGATGTGTTACTTATA 59.445 37.037 1.64 0.00 35.59 0.98
2150 2395 6.377429 TCTCCGTGAGAAGATGTGTTACTTAT 59.623 38.462 1.64 0.00 35.59 1.73
2151 2396 5.708697 TCTCCGTGAGAAGATGTGTTACTTA 59.291 40.000 1.64 0.00 35.59 2.24
2152 2397 4.523173 TCTCCGTGAGAAGATGTGTTACTT 59.477 41.667 1.64 0.00 35.59 2.24
2153 2398 4.079970 TCTCCGTGAGAAGATGTGTTACT 58.920 43.478 1.64 0.00 35.59 2.24
2154 2399 4.436242 TCTCCGTGAGAAGATGTGTTAC 57.564 45.455 1.64 0.00 35.59 2.50
2172 2417 6.685527 AGGAACAAGTTCTTTCAAGTTCTC 57.314 37.500 12.22 0.00 39.45 2.87
2325 2570 0.618458 TAAGCCAGGAAACGAGCCAT 59.382 50.000 0.00 0.00 34.24 4.40
2326 2571 0.321298 GTAAGCCAGGAAACGAGCCA 60.321 55.000 0.00 0.00 34.24 4.75
2417 2663 4.020662 GGCATTCTCCCAAGGTATCTAGAG 60.021 50.000 0.00 0.00 0.00 2.43
2424 2670 1.564348 GGAAGGCATTCTCCCAAGGTA 59.436 52.381 11.37 0.00 35.63 3.08
2501 2747 4.880120 TGTACCGGTTAACATGACAACAAA 59.120 37.500 15.04 0.00 0.00 2.83
2538 2786 6.605471 AGATGATAGTTCACTGTGGTACAA 57.395 37.500 8.11 0.00 35.21 2.41
2562 2810 8.150296 CAGTGAATATAGTACCCAATGACATCA 58.850 37.037 0.00 0.00 0.00 3.07
2725 2973 9.442047 GAGCCCCAGCATATTATATGTAATATC 57.558 37.037 13.03 7.33 40.06 1.63
2737 2985 2.761786 ACATTGAGCCCCAGCATATT 57.238 45.000 0.00 0.00 43.56 1.28
2809 3057 1.202879 ACGCCCCTTTTCTTGACATCA 60.203 47.619 0.00 0.00 0.00 3.07
2827 3075 2.900122 AGTCGCCAAAATCAATGACG 57.100 45.000 0.00 0.00 0.00 4.35
2943 3191 5.177326 CCTTCAGAAAGAGAGAGAATGGTG 58.823 45.833 0.00 0.00 34.14 4.17
3116 3364 7.742963 CACAAAGCAATGCATTTCTTTTGTATC 59.257 33.333 27.44 0.08 0.00 2.24
3132 3380 5.916318 TGGATTTTTCAGTCACAAAGCAAT 58.084 33.333 0.00 0.00 0.00 3.56
3138 3386 4.213270 CGCTACTGGATTTTTCAGTCACAA 59.787 41.667 0.00 0.00 43.55 3.33
3200 3448 8.712228 AGGTCATCTCCTTGTCTTTTTAATTT 57.288 30.769 0.00 0.00 33.52 1.82
3208 3456 2.530701 ACGAGGTCATCTCCTTGTCTT 58.469 47.619 0.00 0.00 46.00 3.01
3222 3470 1.205893 GAATGGAAGCTGAGACGAGGT 59.794 52.381 0.00 0.00 0.00 3.85
3223 3471 1.480137 AGAATGGAAGCTGAGACGAGG 59.520 52.381 0.00 0.00 0.00 4.63
3254 5713 3.185188 CCGCAATCGTTGGAAGATATGAG 59.815 47.826 0.00 0.00 0.00 2.90
3340 5799 2.327325 AGGTCAGTCCTGCTTCCTTA 57.673 50.000 0.00 0.00 46.19 2.69
3470 5931 1.383523 GCTTGGCTTCCAGATGGTAC 58.616 55.000 0.00 0.00 33.81 3.34
3562 6024 6.545666 TCTCACTTTGAGCCAATAAAAACTCA 59.454 34.615 0.00 0.00 43.95 3.41
3594 6056 3.499338 TCATTTGGTTCTTGGTGAGCAT 58.501 40.909 0.00 0.00 0.00 3.79
3621 6083 7.607991 GGGATGATAATTGGTTCGATTGTCTAT 59.392 37.037 0.00 0.78 30.15 1.98
3624 6086 5.530915 TGGGATGATAATTGGTTCGATTGTC 59.469 40.000 0.00 0.00 0.00 3.18
3693 6155 8.241497 TGATAAACGAAGGCTCCTATACTTTA 57.759 34.615 0.00 0.00 0.00 1.85
3694 6156 7.120923 TGATAAACGAAGGCTCCTATACTTT 57.879 36.000 0.00 0.00 0.00 2.66
3695 6157 6.324254 ACTGATAAACGAAGGCTCCTATACTT 59.676 38.462 0.00 0.00 0.00 2.24
3697 6159 6.086785 ACTGATAAACGAAGGCTCCTATAC 57.913 41.667 0.00 0.00 0.00 1.47
3700 6162 6.534475 TTAACTGATAAACGAAGGCTCCTA 57.466 37.500 0.00 0.00 0.00 2.94
3701 6163 3.983044 AACTGATAAACGAAGGCTCCT 57.017 42.857 0.00 0.00 0.00 3.69
3702 6164 6.490566 TTTTAACTGATAAACGAAGGCTCC 57.509 37.500 0.00 0.00 33.26 4.70
3703 6165 8.965986 AAATTTTAACTGATAAACGAAGGCTC 57.034 30.769 0.00 0.00 33.26 4.70
3865 6329 8.862325 ATACTGGACACAAGAATTATCAACAA 57.138 30.769 0.00 0.00 0.00 2.83
3902 6366 5.815740 GTCACCATTAACCAGTCATTATCGT 59.184 40.000 0.00 0.00 0.00 3.73
4062 6526 1.857602 GCGGCGAATGCTTCTGAATTC 60.858 52.381 12.98 0.00 42.25 2.17
4200 6670 2.546368 TGCTTGAAAGTCGTAAATGCGT 59.454 40.909 0.00 0.00 0.00 5.24
4201 6671 3.181826 TGCTTGAAAGTCGTAAATGCG 57.818 42.857 0.00 0.00 0.00 4.73
4218 6688 6.825610 TGTGGGATTGTTTTAAAGATTTGCT 58.174 32.000 0.00 0.00 0.00 3.91
4297 6775 8.635765 AGTGCATTTCTAGGTTTCAGAAAATA 57.364 30.769 0.00 0.00 43.30 1.40
4312 6790 7.281040 TGAAATTCTTGAGAAGTGCATTTCT 57.719 32.000 22.93 22.93 40.02 2.52
4313 6791 7.935338 TTGAAATTCTTGAGAAGTGCATTTC 57.065 32.000 13.69 13.69 37.49 2.17
4407 6885 8.395633 GGTCACATAAACAATTACTACCACATC 58.604 37.037 0.00 0.00 0.00 3.06
4408 6886 8.107095 AGGTCACATAAACAATTACTACCACAT 58.893 33.333 0.00 0.00 0.00 3.21
4409 6887 7.455058 AGGTCACATAAACAATTACTACCACA 58.545 34.615 0.00 0.00 0.00 4.17
4410 6888 7.065443 GGAGGTCACATAAACAATTACTACCAC 59.935 40.741 0.00 0.00 0.00 4.16
4411 6889 7.107542 GGAGGTCACATAAACAATTACTACCA 58.892 38.462 0.00 0.00 0.00 3.25
4412 6890 7.065443 GTGGAGGTCACATAAACAATTACTACC 59.935 40.741 0.00 0.00 45.39 3.18
4468 6946 7.415206 CCATGGCATTTAAGGTGAACTACTTAC 60.415 40.741 0.00 0.00 0.00 2.34
4469 6947 6.601613 CCATGGCATTTAAGGTGAACTACTTA 59.398 38.462 0.00 0.00 0.00 2.24
4478 6956 2.762327 AGAAGCCATGGCATTTAAGGTG 59.238 45.455 37.18 0.00 44.88 4.00
4482 6960 4.159506 GGTACAAGAAGCCATGGCATTTAA 59.840 41.667 37.18 15.67 44.88 1.52
4487 6965 0.323360 GGGTACAAGAAGCCATGGCA 60.323 55.000 37.18 13.31 44.88 4.92
4515 6993 3.565063 CACCACACTGTCATCAAACATCA 59.435 43.478 0.00 0.00 0.00 3.07
4539 7017 5.010922 TCAAATGTTCATGGAAAGAACCCAG 59.989 40.000 0.00 0.00 43.57 4.45
4576 7054 8.437742 CCAACACAAATGATTAGCAAGAATTTC 58.562 33.333 0.00 0.00 0.00 2.17
4602 7080 2.354821 GGTCGTTATGTCCCTGAAATGC 59.645 50.000 0.00 0.00 0.00 3.56
4603 7081 3.374058 GTGGTCGTTATGTCCCTGAAATG 59.626 47.826 0.00 0.00 0.00 2.32
4604 7082 3.606687 GTGGTCGTTATGTCCCTGAAAT 58.393 45.455 0.00 0.00 0.00 2.17
4665 7143 2.829120 TGAGGATCACCGTCATGTAACA 59.171 45.455 0.00 0.00 42.56 2.41
4700 7178 8.041323 TGATGATAGGTTCTTTCCTTCTGTTAC 58.959 37.037 0.00 0.00 38.86 2.50
4760 7238 2.197577 GACTCTCGAGCAACATTAGCC 58.802 52.381 7.81 0.00 0.00 3.93
4841 7321 7.541783 GCAAATTGAAGCTCACAAACATACATA 59.458 33.333 9.69 0.00 0.00 2.29
4890 7370 2.831333 AGCAGCCATATTCTCGACAAG 58.169 47.619 0.00 0.00 0.00 3.16
4911 7391 9.616156 TTAGTCAGGTTGAACAACAGTTTATTA 57.384 29.630 17.43 1.51 42.85 0.98
4987 7470 2.758736 TTGTGGTGCTGTTTTGCTTT 57.241 40.000 0.00 0.00 0.00 3.51
5004 7487 9.231297 TGGAGTTTCTAAGGATACATTTCTTTG 57.769 33.333 0.00 0.00 41.41 2.77
5010 7493 7.042335 CGAGTTGGAGTTTCTAAGGATACATT 58.958 38.462 0.00 0.00 41.41 2.71
5011 7494 6.574350 CGAGTTGGAGTTTCTAAGGATACAT 58.426 40.000 0.00 0.00 41.41 2.29
5012 7495 5.623824 GCGAGTTGGAGTTTCTAAGGATACA 60.624 44.000 0.00 0.00 41.41 2.29
5013 7496 4.804665 GCGAGTTGGAGTTTCTAAGGATAC 59.195 45.833 0.00 0.00 0.00 2.24
5014 7497 4.464951 TGCGAGTTGGAGTTTCTAAGGATA 59.535 41.667 0.00 0.00 0.00 2.59
5015 7498 3.260884 TGCGAGTTGGAGTTTCTAAGGAT 59.739 43.478 0.00 0.00 0.00 3.24
5016 7499 2.631062 TGCGAGTTGGAGTTTCTAAGGA 59.369 45.455 0.00 0.00 0.00 3.36
5017 7500 2.737252 GTGCGAGTTGGAGTTTCTAAGG 59.263 50.000 0.00 0.00 0.00 2.69
5018 7501 2.408704 CGTGCGAGTTGGAGTTTCTAAG 59.591 50.000 0.00 0.00 0.00 2.18
5019 7502 2.034939 TCGTGCGAGTTGGAGTTTCTAA 59.965 45.455 0.00 0.00 0.00 2.10
5020 7503 1.610038 TCGTGCGAGTTGGAGTTTCTA 59.390 47.619 0.00 0.00 0.00 2.10
5021 7504 0.387929 TCGTGCGAGTTGGAGTTTCT 59.612 50.000 0.00 0.00 0.00 2.52
5022 7505 0.784778 CTCGTGCGAGTTGGAGTTTC 59.215 55.000 12.87 0.00 37.47 2.78
5023 7506 2.900528 CTCGTGCGAGTTGGAGTTT 58.099 52.632 12.87 0.00 37.47 2.66
5024 7507 4.655527 CTCGTGCGAGTTGGAGTT 57.344 55.556 12.87 0.00 37.47 3.01
5032 7515 4.755546 GAGACAGACTCGTGCGAG 57.244 61.111 18.57 18.57 46.91 5.03
5040 7523 1.286260 GCAACGACCGAGACAGACT 59.714 57.895 0.00 0.00 0.00 3.24
5044 7527 1.007734 GTCTGCAACGACCGAGACA 60.008 57.895 0.00 0.00 35.82 3.41
5047 7530 0.318699 TTCTGTCTGCAACGACCGAG 60.319 55.000 3.85 0.00 30.59 4.63
5049 7532 0.934496 TTTTCTGTCTGCAACGACCG 59.066 50.000 3.85 0.00 32.97 4.79
5055 7538 0.944386 GCCGACTTTTCTGTCTGCAA 59.056 50.000 6.26 0.00 43.45 4.08
5056 7539 0.884704 GGCCGACTTTTCTGTCTGCA 60.885 55.000 11.73 0.00 44.97 4.41
5059 7542 0.472471 TTGGGCCGACTTTTCTGTCT 59.528 50.000 0.00 0.00 35.00 3.41
5101 7585 0.465460 AGCCAGACAAAAAGCGGACA 60.465 50.000 0.00 0.00 0.00 4.02
5118 7602 2.825836 CAGGAATGGGTCGCCAGC 60.826 66.667 0.00 0.00 0.00 4.85
5173 7678 2.363795 CTGGGGGAGGAGTACGCA 60.364 66.667 0.00 0.00 0.00 5.24
5232 7741 1.009829 GCGAGGGCTTGTTGTAGATG 58.990 55.000 0.00 0.00 35.83 2.90
5236 7745 2.349755 GGGCGAGGGCTTGTTGTA 59.650 61.111 0.00 0.00 39.81 2.41
5322 7851 2.360600 GGTGGTGGCGGCAATGTA 60.361 61.111 15.50 0.00 0.00 2.29
5397 7954 1.377612 GGGTTAGGGGTGCGACTTT 59.622 57.895 0.00 0.00 0.00 2.66
5423 7980 2.831894 TAGACGAAGGAGCTGGCCGA 62.832 60.000 0.00 0.00 0.00 5.54
5445 8002 4.819761 TCAGGCGAGCATGGCGTC 62.820 66.667 9.88 0.00 42.57 5.19
5510 8071 0.108424 GTGAAGAGACGCATGCCTCT 60.108 55.000 17.66 17.66 41.17 3.69
5516 8077 2.125512 GCCGGTGAAGAGACGCAT 60.126 61.111 1.90 0.00 0.00 4.73
5528 8089 3.311110 TCGAAGAAGCTGGCCGGT 61.311 61.111 14.55 3.15 0.00 5.28
5565 8126 4.744795 TTGTACCTTGGTGCAAATTGTT 57.255 36.364 18.39 0.00 0.00 2.83
5575 8136 3.009143 GGAGTCTCCATTTGTACCTTGGT 59.991 47.826 14.46 0.00 36.28 3.67
5590 8152 2.580720 GAACTCGTCGGCGGAGTCTC 62.581 65.000 17.09 13.06 38.89 3.36
5591 8153 2.672307 AACTCGTCGGCGGAGTCT 60.672 61.111 17.09 7.07 38.89 3.24
5629 8191 0.675837 TCAGGAATCGTCGGAGTCGT 60.676 55.000 0.00 0.00 38.13 4.34
5647 8209 1.885887 CCGTCTCCTCCTCATCAGATC 59.114 57.143 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.