Multiple sequence alignment - TraesCS2B01G070800

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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 TraesCS2B01G070800 chr2B 100.000 2364 0 0 1 2364 37431270 37433633 0.000000e+00 4366.0
1 TraesCS2B01G070800 chr2B 96.089 179 6 1 1857 2034 302047449 302047271 8.270000e-75 291.0
2 TraesCS2B01G070800 chr2B 96.471 170 6 0 1858 2027 139801803 139801972 4.970000e-72 281.0
3 TraesCS2B01G070800 chr2B 94.413 179 8 2 1850 2027 54784878 54784701 8.320000e-70 274.0
4 TraesCS2B01G070800 chr2B 91.146 192 16 1 1837 2027 556659007 556659198 2.330000e-65 259.0
5 TraesCS2B01G070800 chr2B 81.625 283 40 7 1593 1865 38136376 38136656 8.500000e-55 224.0
6 TraesCS2B01G070800 chr2B 81.625 283 40 7 1593 1865 38193146 38193426 8.500000e-55 224.0
7 TraesCS2B01G070800 chr2B 81.272 283 41 7 1593 1865 38183654 38183934 3.960000e-53 219.0
8 TraesCS2B01G070800 chr2B 84.444 180 20 6 1280 1453 617124451 617124274 1.120000e-38 171.0
9 TraesCS2B01G070800 chr2B 80.500 200 37 2 2152 2351 73073826 73073629 4.070000e-33 152.0
10 TraesCS2B01G070800 chr2B 83.942 137 16 5 2026 2156 73073997 73073861 2.470000e-25 126.0
11 TraesCS2B01G070800 chr2B 90.667 75 7 0 2029 2103 38136660 38136734 1.500000e-17 100.0
12 TraesCS2B01G070800 chr2B 90.667 75 7 0 2029 2103 38183938 38184012 1.500000e-17 100.0
13 TraesCS2B01G070800 chr2B 88.750 80 7 2 2026 2103 38193425 38193504 1.930000e-16 97.1
14 TraesCS2B01G070800 chr2D 85.522 1409 94 44 1 1368 22963099 22961760 0.000000e+00 1371.0
15 TraesCS2B01G070800 chr2D 79.302 430 60 17 1458 1865 22959228 22958806 8.320000e-70 274.0
16 TraesCS2B01G070800 chr2D 93.048 187 12 1 2177 2363 22957740 22957555 2.990000e-69 272.0
17 TraesCS2B01G070800 chr2D 83.456 272 24 11 1118 1368 22927209 22926938 1.410000e-57 233.0
18 TraesCS2B01G070800 chr2D 95.455 132 6 0 2026 2157 22958807 22958676 6.620000e-51 211.0
19 TraesCS2B01G070800 chr2D 100.000 34 0 0 2151 2184 22958642 22958609 1.960000e-06 63.9
20 TraesCS2B01G070800 chr2A 84.286 1400 108 50 1 1368 24531006 24529687 0.000000e+00 1264.0
21 TraesCS2B01G070800 chr2A 87.526 481 50 8 103 575 269268817 269269295 4.440000e-152 547.0
22 TraesCS2B01G070800 chr2A 87.318 481 51 8 103 575 269306591 269307069 2.070000e-150 542.0
23 TraesCS2B01G070800 chr2A 79.099 799 95 32 1102 1865 64043553 64042792 3.530000e-133 484.0
24 TraesCS2B01G070800 chr2A 78.537 615 70 25 24 611 579890870 579890291 4.840000e-92 348.0
25 TraesCS2B01G070800 chr2A 93.953 215 11 2 2151 2364 24528007 24527794 8.150000e-85 324.0
26 TraesCS2B01G070800 chr2A 86.111 216 27 3 2151 2364 24529023 24528809 1.830000e-56 230.0
27 TraesCS2B01G070800 chr2A 91.241 137 7 2 2026 2157 24528177 24528041 5.190000e-42 182.0
28 TraesCS2B01G070800 chrUn 88.150 481 46 9 103 575 295944470 295944947 1.590000e-156 562.0
29 TraesCS2B01G070800 chrUn 87.164 483 49 10 106 578 265948440 265947961 9.620000e-149 536.0
30 TraesCS2B01G070800 chrUn 86.749 483 51 9 103 575 324062164 324062643 2.080000e-145 525.0
31 TraesCS2B01G070800 chr4A 88.150 481 46 9 106 578 611288985 611288508 1.590000e-156 562.0
32 TraesCS2B01G070800 chr7A 87.318 481 51 8 103 575 199440084 199440562 2.070000e-150 542.0
33 TraesCS2B01G070800 chr3A 87.110 481 52 8 103 575 689755022 689755500 9.620000e-149 536.0
34 TraesCS2B01G070800 chr5A 78.758 612 71 24 24 611 163399626 163399050 2.890000e-94 355.0
35 TraesCS2B01G070800 chr4B 78.431 612 73 24 24 611 50449067 50449643 6.260000e-91 344.0
36 TraesCS2B01G070800 chr4B 91.163 215 18 1 478 691 597430631 597430845 8.270000e-75 291.0
37 TraesCS2B01G070800 chr4B 93.820 178 10 1 1851 2027 102467678 102467855 1.390000e-67 267.0
38 TraesCS2B01G070800 chr4B 83.000 200 32 2 2152 2351 327139416 327139219 1.870000e-41 180.0
39 TraesCS2B01G070800 chr4B 85.401 137 14 2 2026 2156 327139587 327139451 1.140000e-28 137.0
40 TraesCS2B01G070800 chr6B 97.059 170 5 0 1859 2028 222683534 222683703 1.070000e-73 287.0
41 TraesCS2B01G070800 chr6B 96.970 165 5 0 1864 2028 95349575 95349411 6.430000e-71 278.0
42 TraesCS2B01G070800 chr3B 97.041 169 5 0 1860 2028 545070434 545070602 3.850000e-73 285.0
43 TraesCS2B01G070800 chr5D 96.471 170 6 0 1862 2031 198477386 198477555 4.970000e-72 281.0
44 TraesCS2B01G070800 chr5B 80.451 266 48 3 232 496 41800175 41800437 1.430000e-47 200.0


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 TraesCS2B01G070800 chr2B 37431270 37433633 2363 False 4366.00 4366 100.00000 1 2364 1 chr2B.!!$F1 2363
1 TraesCS2B01G070800 chr2D 22957555 22963099 5544 True 438.38 1371 90.66540 1 2363 5 chr2D.!!$R2 2362
2 TraesCS2B01G070800 chr2A 24527794 24531006 3212 True 500.00 1264 88.89775 1 2364 4 chr2A.!!$R3 2363
3 TraesCS2B01G070800 chr2A 64042792 64043553 761 True 484.00 484 79.09900 1102 1865 1 chr2A.!!$R1 763
4 TraesCS2B01G070800 chr2A 579890291 579890870 579 True 348.00 348 78.53700 24 611 1 chr2A.!!$R2 587
5 TraesCS2B01G070800 chr5A 163399050 163399626 576 True 355.00 355 78.75800 24 611 1 chr5A.!!$R1 587
6 TraesCS2B01G070800 chr4B 50449067 50449643 576 False 344.00 344 78.43100 24 611 1 chr4B.!!$F1 587

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
962 1012 0.107017 CACCCATCCACCCATCACTC 60.107 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 4419 0.650512 CAATACACTTAGCACGGCCG 59.349 55.0 26.86 26.86 0.0 6.13 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
26 27 5.103558 ACCATTTGGGGATCATACATCTGAA 60.104 40.000 0.96 0.00 42.91 3.02
136 139 3.636153 AGAACCTGAATGGGCTAGAAC 57.364 47.619 0.00 0.00 41.11 3.01
202 211 5.233689 GTCTACTACCACGCCAAATATGAAC 59.766 44.000 0.00 0.00 0.00 3.18
216 225 2.440539 ATGAACGACAGTGTCTCCAC 57.559 50.000 20.64 9.92 42.17 4.02
218 227 0.319641 GAACGACAGTGTCTCCACCC 60.320 60.000 20.64 1.24 42.88 4.61
219 228 2.083835 AACGACAGTGTCTCCACCCG 62.084 60.000 20.64 9.02 42.88 5.28
237 246 2.285977 CCGTTGCCTTATCCACCTTAC 58.714 52.381 0.00 0.00 0.00 2.34
277 292 5.475220 TGGTTGAAACAGAGACAACTCAAAA 59.525 36.000 0.00 0.00 44.79 2.44
279 294 6.528072 GGTTGAAACAGAGACAACTCAAAAAG 59.472 38.462 0.00 0.00 44.79 2.27
368 384 1.807142 GGGTTTAGAGCAGCAACTGAC 59.193 52.381 0.00 0.00 32.44 3.51
392 408 1.396996 AGTTCGCACTGAAACACACAC 59.603 47.619 0.00 0.00 38.60 3.82
404 424 6.365789 ACTGAAACACACACAAGAAAACATTG 59.634 34.615 0.00 0.00 0.00 2.82
415 435 5.009010 ACAAGAAAACATTGTCAGCACCTAG 59.991 40.000 0.00 0.00 36.10 3.02
453 482 5.913534 TCTCTCCAAGAAAATCATATCCCCT 59.086 40.000 0.00 0.00 0.00 4.79
454 483 7.016661 GTCTCTCCAAGAAAATCATATCCCCTA 59.983 40.741 0.00 0.00 35.21 3.53
463 503 6.460103 AAATCATATCCCCTACTCAAGCAT 57.540 37.500 0.00 0.00 0.00 3.79
468 508 1.559682 TCCCCTACTCAAGCATCCAAC 59.440 52.381 0.00 0.00 0.00 3.77
469 509 1.281867 CCCCTACTCAAGCATCCAACA 59.718 52.381 0.00 0.00 0.00 3.33
474 514 3.996150 ACTCAAGCATCCAACAAACAG 57.004 42.857 0.00 0.00 0.00 3.16
475 515 2.035066 ACTCAAGCATCCAACAAACAGC 59.965 45.455 0.00 0.00 0.00 4.40
479 519 1.888512 AGCATCCAACAAACAGCGAAT 59.111 42.857 0.00 0.00 0.00 3.34
488 529 4.764679 ACAAACAGCGAATAATTCTGCA 57.235 36.364 0.00 0.00 33.67 4.41
496 537 6.146837 ACAGCGAATAATTCTGCATATCTGAC 59.853 38.462 0.00 0.00 33.67 3.51
500 541 7.412346 GCGAATAATTCTGCATATCTGACGAAT 60.412 37.037 0.00 0.00 32.28 3.34
508 549 3.798889 GCATATCTGACGAATGGAACCGA 60.799 47.826 0.00 0.00 0.00 4.69
538 579 0.181350 ACATCGGAGCCTCCCAATTC 59.819 55.000 4.85 0.00 31.13 2.17
542 583 1.152881 GGAGCCTCCCAATTCGCAT 60.153 57.895 0.00 0.00 0.00 4.73
546 587 1.893808 CCTCCCAATTCGCATCCCG 60.894 63.158 0.00 0.00 38.61 5.14
547 588 1.146041 CTCCCAATTCGCATCCCGA 59.854 57.895 0.00 0.00 45.77 5.14
554 595 4.609995 TCGCATCCCGAAAAGGAC 57.390 55.556 0.00 0.00 44.21 3.85
556 597 2.112815 CGCATCCCGAAAAGGACCC 61.113 63.158 0.00 0.00 45.00 4.46
557 598 1.001393 GCATCCCGAAAAGGACCCA 60.001 57.895 0.00 0.00 45.00 4.51
558 599 0.610785 GCATCCCGAAAAGGACCCAA 60.611 55.000 0.00 0.00 45.00 4.12
559 600 1.463674 CATCCCGAAAAGGACCCAAG 58.536 55.000 0.00 0.00 45.00 3.61
561 602 1.074951 CCCGAAAAGGACCCAAGCT 59.925 57.895 0.00 0.00 45.00 3.74
562 603 0.326927 CCCGAAAAGGACCCAAGCTA 59.673 55.000 0.00 0.00 45.00 3.32
564 605 2.017049 CCGAAAAGGACCCAAGCTATG 58.983 52.381 0.00 0.00 45.00 2.23
566 607 2.728007 GAAAAGGACCCAAGCTATGCT 58.272 47.619 0.00 0.00 42.56 3.79
567 608 2.426842 AAAGGACCCAAGCTATGCTC 57.573 50.000 0.00 0.00 38.25 4.26
568 609 1.589414 AAGGACCCAAGCTATGCTCT 58.411 50.000 0.00 0.00 38.25 4.09
570 611 2.764269 AGGACCCAAGCTATGCTCTTA 58.236 47.619 0.00 0.00 38.25 2.10
571 612 2.703007 AGGACCCAAGCTATGCTCTTAG 59.297 50.000 0.00 0.00 38.25 2.18
572 613 2.488952 GACCCAAGCTATGCTCTTAGC 58.511 52.381 6.66 6.66 44.03 3.09
687 736 2.683933 GGCGAGGGGAGGAAGTGA 60.684 66.667 0.00 0.00 0.00 3.41
734 783 2.202810 CCCTTCCGCTCGCTTCTC 60.203 66.667 0.00 0.00 0.00 2.87
735 784 2.202810 CCTTCCGCTCGCTTCTCC 60.203 66.667 0.00 0.00 0.00 3.71
736 785 2.202810 CTTCCGCTCGCTTCTCCC 60.203 66.667 0.00 0.00 0.00 4.30
737 786 3.724914 CTTCCGCTCGCTTCTCCCC 62.725 68.421 0.00 0.00 0.00 4.81
739 788 4.821589 CCGCTCGCTTCTCCCCAC 62.822 72.222 0.00 0.00 0.00 4.61
740 789 4.821589 CGCTCGCTTCTCCCCACC 62.822 72.222 0.00 0.00 0.00 4.61
741 790 4.475135 GCTCGCTTCTCCCCACCC 62.475 72.222 0.00 0.00 0.00 4.61
742 791 3.787001 CTCGCTTCTCCCCACCCC 61.787 72.222 0.00 0.00 0.00 4.95
792 841 2.125350 GGCTCAGCCGTCTTGGAG 60.125 66.667 0.00 0.00 39.62 3.86
846 895 3.068881 CTCCTTCTGTTCGGGCCA 58.931 61.111 4.39 0.00 0.00 5.36
848 897 2.747855 CCTTCTGTTCGGGCCAGC 60.748 66.667 4.39 0.00 0.00 4.85
896 945 3.104512 CTCGGCCCAACCCTATGATATA 58.895 50.000 0.00 0.00 33.26 0.86
941 991 2.493273 AAAACCATCCCGGCGTCCAT 62.493 55.000 6.01 0.00 39.03 3.41
953 1003 1.153168 CGTCCATCCACCCATCCAC 60.153 63.158 0.00 0.00 0.00 4.02
954 1004 1.227383 GTCCATCCACCCATCCACC 59.773 63.158 0.00 0.00 0.00 4.61
955 1005 2.006415 TCCATCCACCCATCCACCC 61.006 63.158 0.00 0.00 0.00 4.61
956 1006 2.315794 CCATCCACCCATCCACCCA 61.316 63.158 0.00 0.00 0.00 4.51
959 1009 0.627170 ATCCACCCATCCACCCATCA 60.627 55.000 0.00 0.00 0.00 3.07
960 1010 1.076777 CCACCCATCCACCCATCAC 60.077 63.158 0.00 0.00 0.00 3.06
961 1011 1.574526 CCACCCATCCACCCATCACT 61.575 60.000 0.00 0.00 0.00 3.41
962 1012 0.107017 CACCCATCCACCCATCACTC 60.107 60.000 0.00 0.00 0.00 3.51
963 1013 1.146930 CCCATCCACCCATCACTCG 59.853 63.158 0.00 0.00 0.00 4.18
964 1014 1.524621 CCATCCACCCATCACTCGC 60.525 63.158 0.00 0.00 0.00 5.03
965 1015 1.884464 CATCCACCCATCACTCGCG 60.884 63.158 0.00 0.00 0.00 5.87
966 1016 3.094062 ATCCACCCATCACTCGCGG 62.094 63.158 6.13 0.00 0.00 6.46
1254 1321 1.424493 CTCGCTGAATCGTTCCTGGC 61.424 60.000 0.00 0.00 0.00 4.85
1274 1341 4.617520 TGGCGGCGCTCAACTGAA 62.618 61.111 32.30 4.50 0.00 3.02
1369 1442 2.941025 CCCTTCCCCTGAAGCCCA 60.941 66.667 0.00 0.00 45.53 5.36
1371 1444 2.044551 CTTCCCCTGAAGCCCAGC 60.045 66.667 0.00 0.00 41.45 4.85
1418 1506 0.984230 CCTCTGCCCCTCTGTTAACA 59.016 55.000 8.28 8.28 0.00 2.41
1419 1514 1.339151 CCTCTGCCCCTCTGTTAACAC 60.339 57.143 3.59 0.00 0.00 3.32
1420 1515 1.625818 CTCTGCCCCTCTGTTAACACT 59.374 52.381 3.59 0.00 0.00 3.55
1486 4056 2.507407 TTTGGGAATCCAGTGGTAGC 57.493 50.000 9.54 0.00 45.04 3.58
1487 4057 0.623723 TTGGGAATCCAGTGGTAGCC 59.376 55.000 9.54 8.59 45.04 3.93
1493 4063 3.136626 GGAATCCAGTGGTAGCCAACTAT 59.863 47.826 9.54 0.00 34.18 2.12
1495 4065 3.627395 TCCAGTGGTAGCCAACTATTG 57.373 47.619 9.54 0.00 34.18 1.90
1514 4090 1.147153 GGCTACTGACCCCATGAGC 59.853 63.158 0.00 0.00 32.27 4.26
1526 4102 1.442526 CCATGAGCGATCAGGGTTGC 61.443 60.000 25.26 0.00 36.86 4.17
1528 4104 1.960040 ATGAGCGATCAGGGTTGCGA 61.960 55.000 10.08 0.00 33.60 5.10
1577 4167 4.572985 TCAGATTTTTGGTCAACAGCTG 57.427 40.909 13.48 13.48 0.00 4.24
1588 4178 6.109156 TGGTCAACAGCTGAGAAATAAGTA 57.891 37.500 23.35 0.00 33.60 2.24
1589 4179 6.166279 TGGTCAACAGCTGAGAAATAAGTAG 58.834 40.000 23.35 0.00 33.60 2.57
1632 4222 3.814842 TCTGATTTTGTACACACTGCAGG 59.185 43.478 19.93 9.66 0.00 4.85
1649 4239 2.202479 GCCGCTGAAATGTTCGCC 60.202 61.111 0.00 0.00 0.00 5.54
1651 4241 2.331893 CCGCTGAAATGTTCGCCCA 61.332 57.895 0.00 0.00 0.00 5.36
1653 4243 0.039617 CGCTGAAATGTTCGCCCAAA 60.040 50.000 0.00 0.00 0.00 3.28
1656 4246 2.609350 CTGAAATGTTCGCCCAAATGG 58.391 47.619 0.00 0.00 37.09 3.16
1669 4259 2.259266 CAAATGGCTTGGCTTTTGGT 57.741 45.000 20.12 0.00 32.47 3.67
1670 4260 1.874872 CAAATGGCTTGGCTTTTGGTG 59.125 47.619 20.12 4.11 32.47 4.17
1671 4261 0.250424 AATGGCTTGGCTTTTGGTGC 60.250 50.000 0.00 0.00 0.00 5.01
1672 4262 1.409251 ATGGCTTGGCTTTTGGTGCA 61.409 50.000 0.00 0.00 0.00 4.57
1717 4307 4.621068 ACGAACAATAGCATCATTGTGG 57.379 40.909 10.84 9.12 46.00 4.17
1721 4311 4.724074 ACAATAGCATCATTGTGGTTGG 57.276 40.909 9.68 0.00 45.22 3.77
1729 4319 4.300803 CATCATTGTGGTTGGAAGTTGTG 58.699 43.478 0.00 0.00 0.00 3.33
1730 4320 3.360867 TCATTGTGGTTGGAAGTTGTGT 58.639 40.909 0.00 0.00 0.00 3.72
1731 4321 3.130164 TCATTGTGGTTGGAAGTTGTGTG 59.870 43.478 0.00 0.00 0.00 3.82
1733 4323 3.351794 TGTGGTTGGAAGTTGTGTGTA 57.648 42.857 0.00 0.00 0.00 2.90
1734 4324 3.275143 TGTGGTTGGAAGTTGTGTGTAG 58.725 45.455 0.00 0.00 0.00 2.74
1735 4325 3.275999 GTGGTTGGAAGTTGTGTGTAGT 58.724 45.455 0.00 0.00 0.00 2.73
1738 4328 4.406326 TGGTTGGAAGTTGTGTGTAGTCTA 59.594 41.667 0.00 0.00 0.00 2.59
1739 4329 4.989168 GGTTGGAAGTTGTGTGTAGTCTAG 59.011 45.833 0.00 0.00 0.00 2.43
1741 4331 3.006537 TGGAAGTTGTGTGTAGTCTAGGC 59.993 47.826 0.00 0.00 0.00 3.93
1765 4364 1.072806 TCTTGCTGATCAGTGTTGGCT 59.927 47.619 23.38 0.00 0.00 4.75
1780 4379 0.981183 TGGCTTACCGTGACCATCTT 59.019 50.000 0.00 0.00 39.70 2.40
1833 4435 1.518572 CTACCGGCCGTGCTAAGTG 60.519 63.158 26.12 8.44 0.00 3.16
1865 4467 7.986085 AGGGAATCAACATACTTGCATATAC 57.014 36.000 0.00 0.00 0.00 1.47
1866 4468 7.749666 AGGGAATCAACATACTTGCATATACT 58.250 34.615 0.00 0.00 0.00 2.12
1867 4469 7.880195 AGGGAATCAACATACTTGCATATACTC 59.120 37.037 0.00 0.00 0.00 2.59
1868 4470 7.119846 GGGAATCAACATACTTGCATATACTCC 59.880 40.741 0.00 0.00 0.00 3.85
1869 4471 7.119846 GGAATCAACATACTTGCATATACTCCC 59.880 40.741 0.00 0.00 0.00 4.30
1870 4472 6.747414 TCAACATACTTGCATATACTCCCT 57.253 37.500 0.00 0.00 0.00 4.20
1871 4473 6.759272 TCAACATACTTGCATATACTCCCTC 58.241 40.000 0.00 0.00 0.00 4.30
1872 4474 5.746990 ACATACTTGCATATACTCCCTCC 57.253 43.478 0.00 0.00 0.00 4.30
1873 4475 4.220821 ACATACTTGCATATACTCCCTCCG 59.779 45.833 0.00 0.00 0.00 4.63
1874 4476 2.679082 ACTTGCATATACTCCCTCCGT 58.321 47.619 0.00 0.00 0.00 4.69
1875 4477 3.039011 ACTTGCATATACTCCCTCCGTT 58.961 45.455 0.00 0.00 0.00 4.44
1876 4478 3.454812 ACTTGCATATACTCCCTCCGTTT 59.545 43.478 0.00 0.00 0.00 3.60
1877 4479 3.746045 TGCATATACTCCCTCCGTTTC 57.254 47.619 0.00 0.00 0.00 2.78
1878 4480 2.367567 TGCATATACTCCCTCCGTTTCC 59.632 50.000 0.00 0.00 0.00 3.13
1879 4481 2.367567 GCATATACTCCCTCCGTTTCCA 59.632 50.000 0.00 0.00 0.00 3.53
1880 4482 3.181458 GCATATACTCCCTCCGTTTCCAA 60.181 47.826 0.00 0.00 0.00 3.53
1881 4483 4.685030 GCATATACTCCCTCCGTTTCCAAA 60.685 45.833 0.00 0.00 0.00 3.28
1882 4484 5.621193 CATATACTCCCTCCGTTTCCAAAT 58.379 41.667 0.00 0.00 0.00 2.32
1883 4485 6.743208 GCATATACTCCCTCCGTTTCCAAATA 60.743 42.308 0.00 0.00 0.00 1.40
1884 4486 5.906772 ATACTCCCTCCGTTTCCAAATAT 57.093 39.130 0.00 0.00 0.00 1.28
1885 4487 4.586306 ACTCCCTCCGTTTCCAAATATT 57.414 40.909 0.00 0.00 0.00 1.28
1886 4488 4.930696 ACTCCCTCCGTTTCCAAATATTT 58.069 39.130 0.00 0.00 0.00 1.40
1887 4489 4.705023 ACTCCCTCCGTTTCCAAATATTTG 59.295 41.667 19.40 19.40 37.90 2.32
1888 4490 4.668636 TCCCTCCGTTTCCAAATATTTGT 58.331 39.130 23.24 0.00 36.45 2.83
1889 4491 4.703093 TCCCTCCGTTTCCAAATATTTGTC 59.297 41.667 23.24 11.68 36.45 3.18
1890 4492 4.705023 CCCTCCGTTTCCAAATATTTGTCT 59.295 41.667 23.24 0.00 36.45 3.41
1891 4493 5.185056 CCCTCCGTTTCCAAATATTTGTCTT 59.815 40.000 23.24 0.00 36.45 3.01
1892 4494 6.295067 CCCTCCGTTTCCAAATATTTGTCTTT 60.295 38.462 23.24 0.00 36.45 2.52
1893 4495 6.806739 CCTCCGTTTCCAAATATTTGTCTTTC 59.193 38.462 23.24 10.84 36.45 2.62
1894 4496 7.309194 CCTCCGTTTCCAAATATTTGTCTTTCT 60.309 37.037 23.24 0.00 36.45 2.52
1895 4497 8.624367 TCCGTTTCCAAATATTTGTCTTTCTA 57.376 30.769 23.24 5.03 36.45 2.10
1896 4498 8.726988 TCCGTTTCCAAATATTTGTCTTTCTAG 58.273 33.333 23.24 8.49 36.45 2.43
1897 4499 7.968405 CCGTTTCCAAATATTTGTCTTTCTAGG 59.032 37.037 23.24 13.30 36.45 3.02
1898 4500 7.484959 CGTTTCCAAATATTTGTCTTTCTAGGC 59.515 37.037 23.24 5.12 36.45 3.93
1899 4501 8.303876 GTTTCCAAATATTTGTCTTTCTAGGCA 58.696 33.333 23.24 0.00 36.45 4.75
1900 4502 8.593945 TTCCAAATATTTGTCTTTCTAGGCAT 57.406 30.769 23.24 0.00 35.56 4.40
1901 4503 8.593945 TCCAAATATTTGTCTTTCTAGGCATT 57.406 30.769 23.24 0.00 35.56 3.56
1902 4504 9.034800 TCCAAATATTTGTCTTTCTAGGCATTT 57.965 29.630 23.24 0.00 35.56 2.32
1903 4505 9.305925 CCAAATATTTGTCTTTCTAGGCATTTC 57.694 33.333 23.24 0.00 35.56 2.17
1904 4506 9.859427 CAAATATTTGTCTTTCTAGGCATTTCA 57.141 29.630 18.32 0.00 35.56 2.69
1908 4510 8.767478 ATTTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
1909 4511 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
1910 4512 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
1911 4513 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
1912 4514 6.009589 TCTTTCTAGGCATTTCAAATGGACA 58.990 36.000 12.14 0.00 0.00 4.02
1913 4515 5.643379 TTCTAGGCATTTCAAATGGACAC 57.357 39.130 12.14 0.00 0.00 3.67
1914 4516 4.661222 TCTAGGCATTTCAAATGGACACA 58.339 39.130 12.14 0.00 0.00 3.72
1915 4517 5.076182 TCTAGGCATTTCAAATGGACACAA 58.924 37.500 12.14 0.00 0.00 3.33
1916 4518 3.993920 AGGCATTTCAAATGGACACAAC 58.006 40.909 12.14 0.00 0.00 3.32
1917 4519 3.387374 AGGCATTTCAAATGGACACAACA 59.613 39.130 12.14 0.00 0.00 3.33
1918 4520 4.040706 AGGCATTTCAAATGGACACAACAT 59.959 37.500 12.14 0.00 0.00 2.71
1919 4521 5.245751 AGGCATTTCAAATGGACACAACATA 59.754 36.000 12.14 0.00 0.00 2.29
1920 4522 5.348451 GGCATTTCAAATGGACACAACATAC 59.652 40.000 12.14 0.00 0.00 2.39
1921 4523 5.060816 GCATTTCAAATGGACACAACATACG 59.939 40.000 12.14 0.00 0.00 3.06
1922 4524 4.757799 TTCAAATGGACACAACATACGG 57.242 40.909 0.00 0.00 0.00 4.02
1923 4525 4.009370 TCAAATGGACACAACATACGGA 57.991 40.909 0.00 0.00 0.00 4.69
1924 4526 4.584874 TCAAATGGACACAACATACGGAT 58.415 39.130 0.00 0.00 0.00 4.18
1925 4527 4.394610 TCAAATGGACACAACATACGGATG 59.605 41.667 5.94 5.94 39.16 3.51
1927 4529 4.746535 ATGGACACAACATACGGATGTA 57.253 40.909 15.10 0.00 45.93 2.29
1928 4530 4.746535 TGGACACAACATACGGATGTAT 57.253 40.909 15.10 2.23 45.93 2.29
1967 4569 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1968 4570 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1969 4571 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1970 4572 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1971 4573 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1972 4574 4.631813 AGATTCACTCATTTTGCTCCGTAC 59.368 41.667 0.00 0.00 0.00 3.67
1973 4575 2.333926 TCACTCATTTTGCTCCGTACG 58.666 47.619 8.69 8.69 0.00 3.67
1974 4576 2.066262 CACTCATTTTGCTCCGTACGT 58.934 47.619 15.21 0.00 0.00 3.57
1975 4577 3.057386 TCACTCATTTTGCTCCGTACGTA 60.057 43.478 15.21 0.00 0.00 3.57
1976 4578 3.303495 CACTCATTTTGCTCCGTACGTAG 59.697 47.826 15.21 9.26 0.00 3.51
1978 4580 3.504863 TCATTTTGCTCCGTACGTAGTC 58.495 45.455 15.21 5.03 43.93 2.59
1979 4581 3.057386 TCATTTTGCTCCGTACGTAGTCA 60.057 43.478 15.21 7.62 43.93 3.41
1980 4582 2.336554 TTTGCTCCGTACGTAGTCAC 57.663 50.000 15.21 0.00 43.93 3.67
1981 4583 1.527034 TTGCTCCGTACGTAGTCACT 58.473 50.000 15.21 0.00 43.93 3.41
1982 4584 1.527034 TGCTCCGTACGTAGTCACTT 58.473 50.000 15.21 0.00 43.93 3.16
1983 4585 1.198408 TGCTCCGTACGTAGTCACTTG 59.802 52.381 15.21 0.00 43.93 3.16
1984 4586 1.198637 GCTCCGTACGTAGTCACTTGT 59.801 52.381 15.21 0.00 43.93 3.16
1985 4587 2.351157 GCTCCGTACGTAGTCACTTGTT 60.351 50.000 15.21 0.00 43.93 2.83
1986 4588 3.231965 CTCCGTACGTAGTCACTTGTTG 58.768 50.000 15.21 0.00 43.93 3.33
1987 4589 2.877786 TCCGTACGTAGTCACTTGTTGA 59.122 45.455 15.21 0.00 43.93 3.18
1988 4590 3.503363 TCCGTACGTAGTCACTTGTTGAT 59.497 43.478 15.21 0.00 43.93 2.57
1989 4591 4.694982 TCCGTACGTAGTCACTTGTTGATA 59.305 41.667 15.21 0.00 43.93 2.15
1990 4592 5.355071 TCCGTACGTAGTCACTTGTTGATAT 59.645 40.000 15.21 0.00 43.93 1.63
1991 4593 5.680229 CCGTACGTAGTCACTTGTTGATATC 59.320 44.000 15.21 0.00 43.93 1.63
1992 4594 6.457934 CCGTACGTAGTCACTTGTTGATATCT 60.458 42.308 15.21 0.00 43.93 1.98
1993 4595 6.628065 CGTACGTAGTCACTTGTTGATATCTC 59.372 42.308 7.22 0.00 43.93 2.75
1994 4596 6.761099 ACGTAGTCACTTGTTGATATCTCT 57.239 37.500 3.98 0.00 29.74 3.10
1995 4597 7.860918 ACGTAGTCACTTGTTGATATCTCTA 57.139 36.000 3.98 0.00 29.74 2.43
1996 4598 7.921787 ACGTAGTCACTTGTTGATATCTCTAG 58.078 38.462 3.98 6.38 29.74 2.43
1997 4599 7.769507 ACGTAGTCACTTGTTGATATCTCTAGA 59.230 37.037 3.98 0.00 29.74 2.43
1998 4600 8.613482 CGTAGTCACTTGTTGATATCTCTAGAA 58.387 37.037 3.98 0.00 36.32 2.10
2001 4603 9.249053 AGTCACTTGTTGATATCTCTAGAAAGA 57.751 33.333 3.98 0.00 36.32 2.52
2002 4604 9.296400 GTCACTTGTTGATATCTCTAGAAAGAC 57.704 37.037 3.98 9.93 36.32 3.01
2003 4605 9.025041 TCACTTGTTGATATCTCTAGAAAGACA 57.975 33.333 3.98 0.00 0.00 3.41
2004 4606 9.645059 CACTTGTTGATATCTCTAGAAAGACAA 57.355 33.333 3.98 0.00 0.00 3.18
2016 4618 9.367444 TCTCTAGAAAGACAAATATTTCGGAAC 57.633 33.333 0.00 0.00 40.33 3.62
2191 5720 6.365970 ACAAGTTCATCACTAGTCCAAGAT 57.634 37.500 0.00 0.00 32.94 2.40
2196 5725 7.122715 AGTTCATCACTAGTCCAAGATAGTCT 58.877 38.462 0.00 0.00 31.97 3.24
2241 5770 1.068610 GCTCGACTAGGCAGCTCATAG 60.069 57.143 11.46 0.00 35.33 2.23
2273 5802 1.032014 TTGGAACCTCTTTGCTGTGC 58.968 50.000 0.00 0.00 0.00 4.57
2275 5804 1.419762 TGGAACCTCTTTGCTGTGCTA 59.580 47.619 0.00 0.00 0.00 3.49
2300 5829 4.744631 CGAATGTGACGATCATGTGGATAA 59.255 41.667 0.00 0.00 36.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.678837 TCCTTGAGAAATGTTTATGGCAAATT 58.321 30.769 0.00 0.00 0.00 1.82
136 139 4.873817 TGCAACATCTTCAGAAACCAATG 58.126 39.130 0.00 0.00 0.00 2.82
216 225 0.034477 AAGGTGGATAAGGCAACGGG 60.034 55.000 0.00 0.00 46.39 5.28
218 227 1.931172 CGTAAGGTGGATAAGGCAACG 59.069 52.381 0.00 0.00 46.39 4.10
219 228 1.669265 GCGTAAGGTGGATAAGGCAAC 59.331 52.381 0.00 0.00 38.28 4.17
237 246 4.631131 TCAACCATACAATCCATCTAGCG 58.369 43.478 0.00 0.00 0.00 4.26
277 292 1.677820 GGTGGCCGTGTATTACTGCTT 60.678 52.381 0.00 0.00 39.23 3.91
279 294 0.107848 AGGTGGCCGTGTATTACTGC 60.108 55.000 0.00 0.00 38.62 4.40
308 324 3.137459 CGAGCAGCGAGTCTCCCT 61.137 66.667 0.00 0.00 44.57 4.20
368 384 0.878523 TGTTTCAGTGCGAACTCGGG 60.879 55.000 0.00 0.00 40.23 5.14
392 408 4.311816 AGGTGCTGACAATGTTTTCTTG 57.688 40.909 0.00 0.00 0.00 3.02
404 424 4.011023 TCTCTACTGAACTAGGTGCTGAC 58.989 47.826 0.00 0.00 0.00 3.51
453 482 3.253188 GCTGTTTGTTGGATGCTTGAGTA 59.747 43.478 0.00 0.00 0.00 2.59
454 483 2.035066 GCTGTTTGTTGGATGCTTGAGT 59.965 45.455 0.00 0.00 0.00 3.41
463 503 5.698832 CAGAATTATTCGCTGTTTGTTGGA 58.301 37.500 0.00 0.00 34.02 3.53
468 508 7.322938 CAGATATGCAGAATTATTCGCTGTTTG 59.677 37.037 17.32 4.88 32.88 2.93
469 509 7.227314 TCAGATATGCAGAATTATTCGCTGTTT 59.773 33.333 17.32 6.77 32.88 2.83
474 514 5.346011 TCGTCAGATATGCAGAATTATTCGC 59.654 40.000 12.34 12.34 34.02 4.70
475 515 6.934561 TCGTCAGATATGCAGAATTATTCG 57.065 37.500 0.00 0.00 34.02 3.34
479 519 6.758254 TCCATTCGTCAGATATGCAGAATTA 58.242 36.000 7.17 0.00 0.00 1.40
488 529 3.889538 TCTCGGTTCCATTCGTCAGATAT 59.110 43.478 0.00 0.00 0.00 1.63
508 549 2.037772 GGCTCCGATGTTATCACCATCT 59.962 50.000 0.00 0.00 37.22 2.90
538 579 2.112815 GGGTCCTTTTCGGGATGCG 61.113 63.158 0.00 0.00 37.73 4.73
542 583 1.074248 GCTTGGGTCCTTTTCGGGA 59.926 57.895 0.00 0.00 0.00 5.14
546 587 2.685388 GAGCATAGCTTGGGTCCTTTTC 59.315 50.000 0.00 0.00 39.88 2.29
547 588 2.310052 AGAGCATAGCTTGGGTCCTTTT 59.690 45.455 11.48 0.00 39.88 2.27
551 592 2.808567 GCTAAGAGCATAGCTTGGGTCC 60.809 54.545 11.48 0.00 43.94 4.46
559 600 5.584251 AGTTCTTTTCAGCTAAGAGCATAGC 59.416 40.000 12.39 7.81 45.56 2.97
561 602 6.591834 GTGAGTTCTTTTCAGCTAAGAGCATA 59.408 38.462 12.39 0.93 45.56 3.14
562 603 5.411053 GTGAGTTCTTTTCAGCTAAGAGCAT 59.589 40.000 12.39 0.82 45.56 3.79
564 605 4.153296 GGTGAGTTCTTTTCAGCTAAGAGC 59.847 45.833 3.98 3.98 42.84 4.09
571 612 2.810852 CCAGAGGTGAGTTCTTTTCAGC 59.189 50.000 0.00 0.00 41.97 4.26
572 613 2.810852 GCCAGAGGTGAGTTCTTTTCAG 59.189 50.000 0.00 0.00 0.00 3.02
573 614 2.487265 GGCCAGAGGTGAGTTCTTTTCA 60.487 50.000 0.00 0.00 0.00 2.69
574 615 2.155279 GGCCAGAGGTGAGTTCTTTTC 58.845 52.381 0.00 0.00 0.00 2.29
707 756 4.148825 CGGAAGGGAGAGCCACGG 62.149 72.222 0.00 0.00 35.15 4.94
741 790 4.308458 TCCTCACAACGCCACCGG 62.308 66.667 0.00 0.00 39.22 5.28
742 791 3.041940 GTCCTCACAACGCCACCG 61.042 66.667 0.00 0.00 41.14 4.94
786 835 1.228510 GCCCCAATCTCCCTCCAAG 59.771 63.158 0.00 0.00 0.00 3.61
789 838 3.878667 CGGCCCCAATCTCCCTCC 61.879 72.222 0.00 0.00 0.00 4.30
790 839 4.570874 GCGGCCCCAATCTCCCTC 62.571 72.222 0.00 0.00 0.00 4.30
829 878 1.078848 CTGGCCCGAACAGAAGGAG 60.079 63.158 0.00 0.00 38.20 3.69
830 879 3.068881 CTGGCCCGAACAGAAGGA 58.931 61.111 0.00 0.00 38.20 3.36
831 880 2.747855 GCTGGCCCGAACAGAAGG 60.748 66.667 0.00 0.00 38.20 3.46
832 881 2.747855 GGCTGGCCCGAACAGAAG 60.748 66.667 0.00 0.00 38.20 2.85
896 945 1.403780 GCGGTCGAGGCGGATATTATT 60.404 52.381 0.00 0.00 0.00 1.40
941 991 1.230116 TGATGGGTGGATGGGTGGA 60.230 57.895 0.00 0.00 0.00 4.02
996 1046 2.124983 CTCCCTGCCGACATGGTG 60.125 66.667 0.00 0.00 41.21 4.17
1263 1330 0.957395 AGCACCCATTCAGTTGAGCG 60.957 55.000 0.00 0.00 0.00 5.03
1274 1341 1.303888 CACCAAGAGCAGCACCCAT 60.304 57.895 0.00 0.00 0.00 4.00
1369 1442 3.838271 ATCCATGACGACGCGGCT 61.838 61.111 11.76 0.00 35.04 5.52
1371 1444 2.344521 TACCATCCATGACGACGCGG 62.345 60.000 12.47 0.00 0.00 6.46
1378 1451 1.141053 GAGGGGTGTACCATCCATGAC 59.859 57.143 3.11 0.00 44.24 3.06
1395 1483 2.767496 CAGAGGGGCAGAGGGAGG 60.767 72.222 0.00 0.00 0.00 4.30
1396 1484 0.325671 TAACAGAGGGGCAGAGGGAG 60.326 60.000 0.00 0.00 0.00 4.30
1397 1485 0.118346 TTAACAGAGGGGCAGAGGGA 59.882 55.000 0.00 0.00 0.00 4.20
1398 1486 0.253327 GTTAACAGAGGGGCAGAGGG 59.747 60.000 0.00 0.00 0.00 4.30
1399 1487 0.984230 TGTTAACAGAGGGGCAGAGG 59.016 55.000 3.59 0.00 0.00 3.69
1401 1489 1.729586 AGTGTTAACAGAGGGGCAGA 58.270 50.000 8.98 0.00 0.00 4.26
1418 1506 7.335422 CAGCACAGAGGAAAATTACAAGATAGT 59.665 37.037 0.00 0.00 0.00 2.12
1419 1514 7.678218 GCAGCACAGAGGAAAATTACAAGATAG 60.678 40.741 0.00 0.00 0.00 2.08
1420 1515 6.094048 GCAGCACAGAGGAAAATTACAAGATA 59.906 38.462 0.00 0.00 0.00 1.98
1454 1549 7.290596 TGGATTCCCAAAATACAGAGCCTGT 62.291 44.000 11.76 11.76 42.87 4.00
1455 1550 3.633986 GGATTCCCAAAATACAGAGCCTG 59.366 47.826 0.00 1.16 37.52 4.85
1456 1551 3.269381 TGGATTCCCAAAATACAGAGCCT 59.731 43.478 0.00 0.00 40.09 4.58
1487 4057 2.919228 GGGTCAGTAGCCCAATAGTTG 58.081 52.381 0.00 0.00 45.40 3.16
1507 4083 1.442526 GCAACCCTGATCGCTCATGG 61.443 60.000 8.78 8.78 41.53 3.66
1514 4090 2.032860 ATCCCTCGCAACCCTGATCG 62.033 60.000 0.00 0.00 0.00 3.69
1526 4102 4.512944 CCTAATCATTTGACACATCCCTCG 59.487 45.833 0.00 0.00 0.00 4.63
1528 4104 4.210331 GCCTAATCATTTGACACATCCCT 58.790 43.478 0.00 0.00 0.00 4.20
1577 4167 6.595772 CACCACATGCTCTACTTATTTCTC 57.404 41.667 0.00 0.00 0.00 2.87
1632 4222 2.202479 GGCGAACATTTCAGCGGC 60.202 61.111 0.00 0.00 41.85 6.53
1651 4241 1.815021 GCACCAAAAGCCAAGCCATTT 60.815 47.619 0.00 0.00 0.00 2.32
1653 4243 1.372307 GCACCAAAAGCCAAGCCAT 59.628 52.632 0.00 0.00 0.00 4.40
1656 4246 1.596603 AATTGCACCAAAAGCCAAGC 58.403 45.000 0.00 0.00 0.00 4.01
1660 4250 4.149910 CAATCAAATTGCACCAAAAGCC 57.850 40.909 0.00 0.00 32.92 4.35
1698 4288 5.104374 CCAACCACAATGATGCTATTGTTC 58.896 41.667 10.46 0.00 46.18 3.18
1704 4294 4.032960 ACTTCCAACCACAATGATGCTA 57.967 40.909 0.00 0.00 0.00 3.49
1717 4307 4.989168 CCTAGACTACACACAACTTCCAAC 59.011 45.833 0.00 0.00 0.00 3.77
1721 4311 4.238514 CTGCCTAGACTACACACAACTTC 58.761 47.826 0.00 0.00 0.00 3.01
1729 4319 2.417515 GCAAGACCTGCCTAGACTACAC 60.418 54.545 0.00 0.00 46.13 2.90
1730 4320 1.825474 GCAAGACCTGCCTAGACTACA 59.175 52.381 0.00 0.00 46.13 2.74
1731 4321 2.588027 GCAAGACCTGCCTAGACTAC 57.412 55.000 0.00 0.00 46.13 2.73
1741 4331 2.469274 ACACTGATCAGCAAGACCTG 57.531 50.000 22.83 13.41 0.00 4.00
1765 4364 7.513371 AAAAATTGTAAGATGGTCACGGTAA 57.487 32.000 0.00 0.00 0.00 2.85
1809 4409 1.590792 GCACGGCCGGTAGTATGTC 60.591 63.158 31.76 9.68 0.00 3.06
1816 4416 0.964860 TACACTTAGCACGGCCGGTA 60.965 55.000 31.76 16.02 0.00 4.02
1819 4419 0.650512 CAATACACTTAGCACGGCCG 59.349 55.000 26.86 26.86 0.00 6.13
1833 4435 8.129211 GCAAGTATGTTGATTCCCTAACAATAC 58.871 37.037 0.00 0.00 39.89 1.89
1865 4467 4.705023 ACAAATATTTGGAAACGGAGGGAG 59.295 41.667 27.43 2.64 42.34 4.30
1866 4468 4.668636 ACAAATATTTGGAAACGGAGGGA 58.331 39.130 27.43 0.00 42.34 4.20
1867 4469 4.705023 AGACAAATATTTGGAAACGGAGGG 59.295 41.667 27.43 3.22 42.34 4.30
1868 4470 5.897377 AGACAAATATTTGGAAACGGAGG 57.103 39.130 27.43 3.68 42.34 4.30
1869 4471 7.593825 AGAAAGACAAATATTTGGAAACGGAG 58.406 34.615 27.43 4.34 42.34 4.63
1870 4472 7.519032 AGAAAGACAAATATTTGGAAACGGA 57.481 32.000 27.43 0.00 42.34 4.69
1871 4473 7.968405 CCTAGAAAGACAAATATTTGGAAACGG 59.032 37.037 27.43 14.87 42.34 4.44
1872 4474 7.484959 GCCTAGAAAGACAAATATTTGGAAACG 59.515 37.037 27.43 6.31 42.34 3.60
1873 4475 8.303876 TGCCTAGAAAGACAAATATTTGGAAAC 58.696 33.333 27.43 16.80 42.34 2.78
1874 4476 8.415950 TGCCTAGAAAGACAAATATTTGGAAA 57.584 30.769 27.43 8.61 42.34 3.13
1875 4477 8.593945 ATGCCTAGAAAGACAAATATTTGGAA 57.406 30.769 27.43 5.94 42.34 3.53
1876 4478 8.593945 AATGCCTAGAAAGACAAATATTTGGA 57.406 30.769 27.43 2.86 42.34 3.53
1877 4479 9.305925 GAAATGCCTAGAAAGACAAATATTTGG 57.694 33.333 27.43 12.85 42.34 3.28
1878 4480 9.859427 TGAAATGCCTAGAAAGACAAATATTTG 57.141 29.630 23.60 23.60 43.62 2.32
1882 4484 9.859427 CATTTGAAATGCCTAGAAAGACAAATA 57.141 29.630 4.82 0.00 34.96 1.40
1883 4485 7.820872 CCATTTGAAATGCCTAGAAAGACAAAT 59.179 33.333 12.26 0.00 36.38 2.32
1884 4486 7.015098 TCCATTTGAAATGCCTAGAAAGACAAA 59.985 33.333 12.26 0.00 0.00 2.83
1885 4487 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
1886 4488 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
1887 4489 6.071952 TGTCCATTTGAAATGCCTAGAAAGAC 60.072 38.462 12.26 11.27 0.00 3.01
1888 4490 6.009589 TGTCCATTTGAAATGCCTAGAAAGA 58.990 36.000 12.26 0.00 0.00 2.52
1889 4491 6.095377 GTGTCCATTTGAAATGCCTAGAAAG 58.905 40.000 12.26 0.00 0.00 2.62
1890 4492 5.538053 TGTGTCCATTTGAAATGCCTAGAAA 59.462 36.000 12.26 0.00 0.00 2.52
1891 4493 5.076182 TGTGTCCATTTGAAATGCCTAGAA 58.924 37.500 12.26 0.00 0.00 2.10
1892 4494 4.661222 TGTGTCCATTTGAAATGCCTAGA 58.339 39.130 12.26 1.83 0.00 2.43
1893 4495 5.163513 GTTGTGTCCATTTGAAATGCCTAG 58.836 41.667 12.26 0.00 0.00 3.02
1894 4496 4.586421 TGTTGTGTCCATTTGAAATGCCTA 59.414 37.500 12.26 0.00 0.00 3.93
1895 4497 3.387374 TGTTGTGTCCATTTGAAATGCCT 59.613 39.130 12.26 0.00 0.00 4.75
1896 4498 3.726607 TGTTGTGTCCATTTGAAATGCC 58.273 40.909 12.26 5.75 0.00 4.40
1897 4499 5.060816 CGTATGTTGTGTCCATTTGAAATGC 59.939 40.000 12.26 0.87 0.00 3.56
1898 4500 5.572511 CCGTATGTTGTGTCCATTTGAAATG 59.427 40.000 10.84 10.84 0.00 2.32
1899 4501 5.475220 TCCGTATGTTGTGTCCATTTGAAAT 59.525 36.000 0.00 0.00 0.00 2.17
1900 4502 4.822350 TCCGTATGTTGTGTCCATTTGAAA 59.178 37.500 0.00 0.00 0.00 2.69
1901 4503 4.390264 TCCGTATGTTGTGTCCATTTGAA 58.610 39.130 0.00 0.00 0.00 2.69
1902 4504 4.009370 TCCGTATGTTGTGTCCATTTGA 57.991 40.909 0.00 0.00 0.00 2.69
1903 4505 4.155826 ACATCCGTATGTTGTGTCCATTTG 59.844 41.667 0.00 0.00 44.07 2.32
1904 4506 4.331968 ACATCCGTATGTTGTGTCCATTT 58.668 39.130 0.00 0.00 44.07 2.32
1905 4507 3.950397 ACATCCGTATGTTGTGTCCATT 58.050 40.909 0.00 0.00 44.07 3.16
1906 4508 3.627395 ACATCCGTATGTTGTGTCCAT 57.373 42.857 0.00 0.00 44.07 3.41
1907 4509 4.438148 CATACATCCGTATGTTGTGTCCA 58.562 43.478 0.00 0.00 46.70 4.02
1945 4547 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1946 4548 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1947 4549 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1948 4550 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1949 4551 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1950 4552 4.492570 CGTACGGAGCAAAATGAGTGAATC 60.493 45.833 7.57 0.00 0.00 2.52
1951 4553 3.370978 CGTACGGAGCAAAATGAGTGAAT 59.629 43.478 7.57 0.00 0.00 2.57
1952 4554 2.734606 CGTACGGAGCAAAATGAGTGAA 59.265 45.455 7.57 0.00 0.00 3.18
1953 4555 2.288579 ACGTACGGAGCAAAATGAGTGA 60.289 45.455 21.06 0.00 0.00 3.41
1954 4556 2.066262 ACGTACGGAGCAAAATGAGTG 58.934 47.619 21.06 0.00 0.00 3.51
1955 4557 2.450609 ACGTACGGAGCAAAATGAGT 57.549 45.000 21.06 0.00 0.00 3.41
1956 4558 3.508762 ACTACGTACGGAGCAAAATGAG 58.491 45.455 27.33 1.42 0.00 2.90
1957 4559 3.057386 TGACTACGTACGGAGCAAAATGA 60.057 43.478 27.33 0.00 0.00 2.57
1958 4560 3.060363 GTGACTACGTACGGAGCAAAATG 59.940 47.826 27.33 3.03 0.00 2.32
1959 4561 3.057033 AGTGACTACGTACGGAGCAAAAT 60.057 43.478 27.33 7.40 0.00 1.82
1960 4562 2.294233 AGTGACTACGTACGGAGCAAAA 59.706 45.455 27.33 7.64 0.00 2.44
1961 4563 1.881973 AGTGACTACGTACGGAGCAAA 59.118 47.619 27.33 10.27 0.00 3.68
1962 4564 1.527034 AGTGACTACGTACGGAGCAA 58.473 50.000 27.33 12.96 0.00 3.91
1963 4565 1.198408 CAAGTGACTACGTACGGAGCA 59.802 52.381 27.33 21.55 0.00 4.26
1964 4566 1.198637 ACAAGTGACTACGTACGGAGC 59.801 52.381 27.33 19.29 0.00 4.70
1965 4567 3.058708 TCAACAAGTGACTACGTACGGAG 60.059 47.826 25.90 25.90 0.00 4.63
1966 4568 2.877786 TCAACAAGTGACTACGTACGGA 59.122 45.455 21.06 10.81 0.00 4.69
1967 4569 3.272439 TCAACAAGTGACTACGTACGG 57.728 47.619 21.06 5.00 0.00 4.02
1968 4570 6.484540 AGATATCAACAAGTGACTACGTACG 58.515 40.000 15.01 15.01 39.72 3.67
1969 4571 7.695820 AGAGATATCAACAAGTGACTACGTAC 58.304 38.462 5.32 0.00 39.72 3.67
1970 4572 7.860918 AGAGATATCAACAAGTGACTACGTA 57.139 36.000 5.32 0.00 39.72 3.57
1971 4573 6.761099 AGAGATATCAACAAGTGACTACGT 57.239 37.500 5.32 0.00 39.72 3.57
1972 4574 8.144155 TCTAGAGATATCAACAAGTGACTACG 57.856 38.462 5.32 0.00 39.72 3.51
1975 4577 9.249053 TCTTTCTAGAGATATCAACAAGTGACT 57.751 33.333 5.32 0.00 39.72 3.41
1976 4578 9.296400 GTCTTTCTAGAGATATCAACAAGTGAC 57.704 37.037 5.32 1.29 39.72 3.67
1977 4579 9.025041 TGTCTTTCTAGAGATATCAACAAGTGA 57.975 33.333 5.32 0.00 41.67 3.41
1978 4580 9.645059 TTGTCTTTCTAGAGATATCAACAAGTG 57.355 33.333 5.32 0.00 0.00 3.16
1990 4592 9.367444 GTTCCGAAATATTTGTCTTTCTAGAGA 57.633 33.333 5.17 0.00 30.80 3.10
1991 4593 8.321716 CGTTCCGAAATATTTGTCTTTCTAGAG 58.678 37.037 5.17 0.00 30.80 2.43
1992 4594 7.277098 CCGTTCCGAAATATTTGTCTTTCTAGA 59.723 37.037 5.17 0.00 30.80 2.43
1993 4595 7.277098 TCCGTTCCGAAATATTTGTCTTTCTAG 59.723 37.037 5.17 0.00 30.80 2.43
1994 4596 7.098477 TCCGTTCCGAAATATTTGTCTTTCTA 58.902 34.615 5.17 0.00 30.80 2.10
1995 4597 5.935789 TCCGTTCCGAAATATTTGTCTTTCT 59.064 36.000 5.17 0.00 30.80 2.52
1996 4598 6.173191 TCCGTTCCGAAATATTTGTCTTTC 57.827 37.500 5.17 0.00 0.00 2.62
1997 4599 5.123344 CCTCCGTTCCGAAATATTTGTCTTT 59.877 40.000 5.17 0.00 0.00 2.52
1998 4600 4.634443 CCTCCGTTCCGAAATATTTGTCTT 59.366 41.667 5.17 0.00 0.00 3.01
1999 4601 4.189231 CCTCCGTTCCGAAATATTTGTCT 58.811 43.478 5.17 0.00 0.00 3.41
2000 4602 3.311596 CCCTCCGTTCCGAAATATTTGTC 59.688 47.826 5.17 0.00 0.00 3.18
2001 4603 3.054948 TCCCTCCGTTCCGAAATATTTGT 60.055 43.478 5.17 0.00 0.00 2.83
2002 4604 3.537580 TCCCTCCGTTCCGAAATATTTG 58.462 45.455 5.17 0.00 0.00 2.32
2003 4605 3.199289 ACTCCCTCCGTTCCGAAATATTT 59.801 43.478 0.00 0.00 0.00 1.40
2004 4606 2.770232 ACTCCCTCCGTTCCGAAATATT 59.230 45.455 0.00 0.00 0.00 1.28
2005 4607 2.395619 ACTCCCTCCGTTCCGAAATAT 58.604 47.619 0.00 0.00 0.00 1.28
2006 4608 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2007 4609 1.856629 TACTCCCTCCGTTCCGAAAT 58.143 50.000 0.00 0.00 0.00 2.17
2008 4610 1.856629 ATACTCCCTCCGTTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
2009 4611 1.856629 AATACTCCCTCCGTTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
2010 4612 2.734755 TAATACTCCCTCCGTTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
2011 4613 3.806625 TTTAATACTCCCTCCGTTCCG 57.193 47.619 0.00 0.00 0.00 4.30
2012 4614 7.001099 TCATATTTAATACTCCCTCCGTTCC 57.999 40.000 0.00 0.00 0.00 3.62
2013 4615 7.549488 CCATCATATTTAATACTCCCTCCGTTC 59.451 40.741 0.00 0.00 0.00 3.95
2014 4616 7.236847 TCCATCATATTTAATACTCCCTCCGTT 59.763 37.037 0.00 0.00 0.00 4.44
2015 4617 6.729100 TCCATCATATTTAATACTCCCTCCGT 59.271 38.462 0.00 0.00 0.00 4.69
2016 4618 7.182817 TCCATCATATTTAATACTCCCTCCG 57.817 40.000 0.00 0.00 0.00 4.63
2017 4619 8.826765 TCTTCCATCATATTTAATACTCCCTCC 58.173 37.037 0.00 0.00 0.00 4.30
2044 4653 7.227910 GCATATGCCAATCAATTTTCTTTCCAT 59.772 33.333 17.26 0.00 34.31 3.41
2097 4706 1.002087 CCATATCAGACCCCGTTAGCC 59.998 57.143 0.00 0.00 0.00 3.93
2145 4758 2.549134 CGACAACTTGATGTACCCACCA 60.549 50.000 0.00 0.00 32.57 4.17
2191 5720 3.753272 GCAAATTCTGCCTGAACAGACTA 59.247 43.478 3.19 0.00 46.13 2.59
2218 5747 1.949847 GAGCTGCCTAGTCGAGCCAA 61.950 60.000 0.00 0.00 32.86 4.52
2227 5756 0.972883 GACCCCTATGAGCTGCCTAG 59.027 60.000 0.00 0.00 0.00 3.02
2241 5770 3.762288 GAGGTTCCAAAACATTAGACCCC 59.238 47.826 0.00 0.00 37.10 4.95
2273 5802 4.383948 CCACATGATCGTCACATTCGATAG 59.616 45.833 0.00 0.00 45.90 2.08
2300 5829 5.410355 AAGCACAATGCCAAAAGACATAT 57.590 34.783 0.00 0.00 46.52 1.78


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

AutoCloner maintained by Alex Coulton.