Multiple sequence alignment - TraesCS5B01G446600

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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 TraesCS5B01G446600 chr5B 100.000 6133 0 0 1 6133 618119481 618125613 0.000000e+00 11326.0
1 TraesCS5B01G446600 chr5A 94.605 3800 143 23 1363 5131 622986730 622990498 0.000000e+00 5825.0
2 TraesCS5B01G446600 chr5A 84.867 489 46 13 5649 6133 622991444 622991908 9.310000e-128 468.0
3 TraesCS5B01G446600 chr5A 83.725 510 41 23 861 1342 622986149 622986644 1.570000e-120 444.0
4 TraesCS5B01G446600 chr5A 90.826 109 9 1 545 653 622985872 622985979 1.780000e-30 145.0
5 TraesCS5B01G446600 chr5D 96.804 2628 64 11 2513 5131 498623511 498626127 0.000000e+00 4370.0
6 TraesCS5B01G446600 chr5D 93.808 1292 54 11 1213 2489 498621893 498623173 0.000000e+00 1919.0
7 TraesCS5B01G446600 chr5D 89.515 515 53 1 25 538 399788446 399788960 0.000000e+00 651.0
8 TraesCS5B01G446600 chr5D 89.189 518 53 3 25 541 458647749 458647234 1.440000e-180 643.0
9 TraesCS5B01G446600 chr5D 87.640 534 26 15 5134 5638 498626158 498626680 8.860000e-163 584.0
10 TraesCS5B01G446600 chr5D 88.728 346 26 4 793 1125 498621445 498621790 1.590000e-110 411.0
11 TraesCS5B01G446600 chr5D 91.901 284 10 8 5851 6133 498627391 498627662 9.640000e-103 385.0
12 TraesCS5B01G446600 chr4D 86.134 3808 377 77 1529 5259 55068110 55064377 0.000000e+00 3967.0
13 TraesCS5B01G446600 chr4D 89.903 515 50 2 25 538 469762188 469762701 0.000000e+00 662.0
14 TraesCS5B01G446600 chr4A 87.530 2943 272 53 1577 4469 542020514 542023411 0.000000e+00 3314.0
15 TraesCS5B01G446600 chr4A 82.818 809 98 23 4542 5317 542023547 542024347 0.000000e+00 686.0
16 TraesCS5B01G446600 chr4B 87.737 2797 267 44 1576 4323 82022014 82019245 0.000000e+00 3195.0
17 TraesCS5B01G446600 chr4B 84.367 774 87 19 4397 5162 82019061 82018314 0.000000e+00 728.0
18 TraesCS5B01G446600 chr4B 93.431 137 8 1 997 1133 82022213 82022078 1.040000e-47 202.0
19 TraesCS5B01G446600 chr6B 89.057 2440 210 37 2753 5162 551033292 551030880 0.000000e+00 2974.0
20 TraesCS5B01G446600 chr6B 89.320 515 49 4 25 538 491885404 491885913 5.180000e-180 641.0
21 TraesCS5B01G446600 chr6B 85.441 522 65 10 2213 2732 551033857 551033345 3.250000e-147 532.0
22 TraesCS5B01G446600 chr6B 84.694 490 55 10 1630 2113 551034694 551034219 7.200000e-129 472.0
23 TraesCS5B01G446600 chr6B 93.431 137 8 1 997 1133 551034940 551034805 1.040000e-47 202.0
24 TraesCS5B01G446600 chr7B 90.157 508 44 4 25 530 375211132 375210629 0.000000e+00 656.0
25 TraesCS5B01G446600 chr7B 100.000 28 0 0 1 28 132037178 132037205 1.100000e-02 52.8
26 TraesCS5B01G446600 chr2B 89.744 507 51 1 25 530 663177164 663177670 0.000000e+00 647.0
27 TraesCS5B01G446600 chr2B 89.147 516 54 2 25 538 227502822 227503337 5.180000e-180 641.0
28 TraesCS5B01G446600 chr3B 89.210 519 53 3 25 541 585675212 585674695 0.000000e+00 645.0
29 TraesCS5B01G446600 chr2D 89.189 518 49 4 25 541 51912265 51911754 1.860000e-179 640.0
30 TraesCS5B01G446600 chr1B 100.000 28 0 0 1 28 570800794 570800821 1.100000e-02 52.8


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 TraesCS5B01G446600 chr5B 618119481 618125613 6132 False 11326.0 11326 100.000000 1 6133 1 chr5B.!!$F1 6132
1 TraesCS5B01G446600 chr5A 622985872 622991908 6036 False 1720.5 5825 88.505750 545 6133 4 chr5A.!!$F1 5588
2 TraesCS5B01G446600 chr5D 498621445 498627662 6217 False 1533.8 4370 91.776200 793 6133 5 chr5D.!!$F2 5340
3 TraesCS5B01G446600 chr5D 399788446 399788960 514 False 651.0 651 89.515000 25 538 1 chr5D.!!$F1 513
4 TraesCS5B01G446600 chr5D 458647234 458647749 515 True 643.0 643 89.189000 25 541 1 chr5D.!!$R1 516
5 TraesCS5B01G446600 chr4D 55064377 55068110 3733 True 3967.0 3967 86.134000 1529 5259 1 chr4D.!!$R1 3730
6 TraesCS5B01G446600 chr4D 469762188 469762701 513 False 662.0 662 89.903000 25 538 1 chr4D.!!$F1 513
7 TraesCS5B01G446600 chr4A 542020514 542024347 3833 False 2000.0 3314 85.174000 1577 5317 2 chr4A.!!$F1 3740
8 TraesCS5B01G446600 chr4B 82018314 82022213 3899 True 1375.0 3195 88.511667 997 5162 3 chr4B.!!$R1 4165
9 TraesCS5B01G446600 chr6B 551030880 551034940 4060 True 1045.0 2974 88.155750 997 5162 4 chr6B.!!$R1 4165
10 TraesCS5B01G446600 chr6B 491885404 491885913 509 False 641.0 641 89.320000 25 538 1 chr6B.!!$F1 513
11 TraesCS5B01G446600 chr7B 375210629 375211132 503 True 656.0 656 90.157000 25 530 1 chr7B.!!$R1 505
12 TraesCS5B01G446600 chr2B 663177164 663177670 506 False 647.0 647 89.744000 25 530 1 chr2B.!!$F2 505
13 TraesCS5B01G446600 chr2B 227502822 227503337 515 False 641.0 641 89.147000 25 538 1 chr2B.!!$F1 513
14 TraesCS5B01G446600 chr3B 585674695 585675212 517 True 645.0 645 89.210000 25 541 1 chr3B.!!$R1 516
15 TraesCS5B01G446600 chr2D 51911754 51912265 511 True 640.0 640 89.189000 25 541 1 chr2D.!!$R1 516

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
636 641 0.034756 GGACGGCCCAAATGCTTTTT 59.965 50.0 0.00 0.00 34.14 1.94 F
930 976 0.669619 GAACCCTAGCTAGACGAGGC 59.330 60.0 22.70 2.78 39.73 4.70 F
1136 1194 0.681733 CTCAGGTATCCATCCACCCG 59.318 60.0 0.00 0.00 35.25 5.28 F
2509 3031 0.492730 TGTACTCTACCCCCAACCCA 59.507 55.0 0.00 0.00 0.00 4.51 F
2511 3033 0.252835 TACTCTACCCCCAACCCACC 60.253 60.0 0.00 0.00 0.00 4.61 F
4382 5422 0.322975 GGAACAGAGGCTCAGCTGAA 59.677 55.0 18.85 1.63 36.07 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1768 0.771127 ACACCAAGCCAGGAAAGCTA 59.229 50.000 0.00 0.0 40.49 3.32 R
2336 2856 0.979665 TAGCAAGCTCAGCTTCCTGT 59.020 50.000 13.58 0.0 46.77 4.00 R
2511 3033 1.007502 CAACATTGTGCGTGGGTGG 60.008 57.895 0.00 0.0 0.00 4.61 R
4139 5038 0.514691 CGTTGAAGAACTCCAGCTGC 59.485 55.000 8.66 0.0 0.00 5.25 R
4423 5466 3.378427 GTCCATACAATTTGAGGGTGAGC 59.622 47.826 2.79 0.0 0.00 4.26 R
5557 6792 1.064017 TGCCAAAACCTGACCTGAGTT 60.064 47.619 0.00 0.0 0.00 3.01 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
47 48 6.810676 CACATATCATCTACACATAGACCTGC 59.189 42.308 0.00 0.00 40.32 4.85
86 87 6.334102 TGGGAAACGTAGCATGTAATTTTT 57.666 33.333 0.00 0.00 0.00 1.94
239 242 0.806102 CGTTCCGACCGATCAAGCAT 60.806 55.000 0.00 0.00 0.00 3.79
296 299 1.671850 GCTCAATGACGTCCCTCGAAA 60.672 52.381 14.12 0.00 42.86 3.46
347 350 3.858868 GAGTTCCGCCAGCACGACA 62.859 63.158 0.00 0.00 34.06 4.35
376 380 3.324556 TGACTGTGATGGTGAAGTGATCA 59.675 43.478 0.00 0.00 35.05 2.92
404 408 2.493713 CTTCGCCTAAGCACTACGAT 57.506 50.000 0.00 0.00 39.83 3.73
531 536 1.929088 GGGGAACAACCTAGGGGCT 60.929 63.158 14.81 0.00 38.98 5.19
532 537 1.506907 GGGGAACAACCTAGGGGCTT 61.507 60.000 14.81 0.00 38.98 4.35
549 554 4.542697 GGGCTTCCCAAATATTTAGGTCA 58.457 43.478 11.74 1.09 44.65 4.02
550 555 4.341235 GGGCTTCCCAAATATTTAGGTCAC 59.659 45.833 11.74 3.63 44.65 3.67
551 556 4.953579 GGCTTCCCAAATATTTAGGTCACA 59.046 41.667 11.74 0.00 0.00 3.58
552 557 5.598417 GGCTTCCCAAATATTTAGGTCACAT 59.402 40.000 11.74 0.00 0.00 3.21
569 574 4.454504 GTCACATGGGATTTTTCACTACGT 59.545 41.667 0.00 0.00 0.00 3.57
573 578 3.071479 TGGGATTTTTCACTACGTGAGC 58.929 45.455 0.00 0.00 43.69 4.26
591 596 0.319900 GCAGAGCACAAGAAGGACGA 60.320 55.000 0.00 0.00 0.00 4.20
594 599 1.689273 AGAGCACAAGAAGGACGACTT 59.311 47.619 0.00 0.00 43.65 3.01
635 640 1.671166 GGACGGCCCAAATGCTTTT 59.329 52.632 0.00 0.00 34.14 2.27
636 641 0.034756 GGACGGCCCAAATGCTTTTT 59.965 50.000 0.00 0.00 34.14 1.94
733 738 8.950403 AGACAAATTTTGAGAATTAGTTACGC 57.050 30.769 15.81 0.00 0.00 4.42
734 739 8.564574 AGACAAATTTTGAGAATTAGTTACGCA 58.435 29.630 15.81 0.00 0.00 5.24
735 740 9.176181 GACAAATTTTGAGAATTAGTTACGCAA 57.824 29.630 15.81 0.00 0.00 4.85
736 741 9.522804 ACAAATTTTGAGAATTAGTTACGCAAA 57.477 25.926 15.81 0.00 33.27 3.68
760 765 8.556213 AATTTTGAGAATTAGTTACGCTGGTA 57.444 30.769 0.00 0.00 0.00 3.25
766 771 9.656040 TGAGAATTAGTTACGCTGGTATTTTTA 57.344 29.630 0.00 0.00 0.00 1.52
768 773 9.880157 AGAATTAGTTACGCTGGTATTTTTAGA 57.120 29.630 0.00 0.00 0.00 2.10
769 774 9.911980 GAATTAGTTACGCTGGTATTTTTAGAC 57.088 33.333 0.00 0.00 0.00 2.59
771 776 8.830201 TTAGTTACGCTGGTATTTTTAGACAA 57.170 30.769 0.00 0.00 0.00 3.18
772 777 7.733402 AGTTACGCTGGTATTTTTAGACAAA 57.267 32.000 0.00 0.00 0.00 2.83
773 778 8.331730 AGTTACGCTGGTATTTTTAGACAAAT 57.668 30.769 0.00 0.00 0.00 2.32
778 783 9.826574 ACGCTGGTATTTTTAGACAAATATAGA 57.173 29.630 0.00 0.00 32.49 1.98
791 796 8.579850 AGACAAATATAGAGAGAGCCATAGAG 57.420 38.462 0.00 0.00 0.00 2.43
826 859 1.815003 CTCTGTCAGCCCATTTGTTCC 59.185 52.381 0.00 0.00 0.00 3.62
838 871 0.884704 TTTGTTCCAGCGGCAGACTC 60.885 55.000 1.45 0.00 0.00 3.36
839 872 2.038814 TTGTTCCAGCGGCAGACTCA 62.039 55.000 1.45 0.00 0.00 3.41
840 873 1.301716 GTTCCAGCGGCAGACTCAA 60.302 57.895 1.45 0.00 0.00 3.02
925 971 3.070302 CCATTCCAGAACCCTAGCTAGAC 59.930 52.174 22.70 10.11 0.00 2.59
926 972 2.054232 TCCAGAACCCTAGCTAGACG 57.946 55.000 22.70 13.53 0.00 4.18
927 973 1.562942 TCCAGAACCCTAGCTAGACGA 59.437 52.381 22.70 3.70 0.00 4.20
928 974 1.950909 CCAGAACCCTAGCTAGACGAG 59.049 57.143 22.70 9.97 0.00 4.18
930 976 0.669619 GAACCCTAGCTAGACGAGGC 59.330 60.000 22.70 2.78 39.73 4.70
987 1045 4.636435 AAACCCACCCACTCGCGG 62.636 66.667 6.13 0.00 0.00 6.46
1017 1075 3.770589 ATGGCGCTAGCGATCTCT 58.229 55.556 39.52 18.02 46.35 3.10
1129 1187 3.244887 TCGACATCCTCAGGTATCCAT 57.755 47.619 0.00 0.00 0.00 3.41
1134 1192 2.103153 TCCTCAGGTATCCATCCACC 57.897 55.000 0.00 0.00 34.86 4.61
1136 1194 0.681733 CTCAGGTATCCATCCACCCG 59.318 60.000 0.00 0.00 35.25 5.28
1158 1238 1.081174 ACCTCCTTCCTTCCAGATCCA 59.919 52.381 0.00 0.00 0.00 3.41
1187 1267 2.831526 GTTGGTTGATGGCCCTATTTGT 59.168 45.455 0.00 0.00 0.00 2.83
1197 1277 6.998074 TGATGGCCCTATTTGTTTAGAGTATG 59.002 38.462 0.00 0.00 0.00 2.39
1229 1338 3.134458 CGGGAGGATTGTTAGAATCTGC 58.866 50.000 2.20 0.00 0.00 4.26
1251 1360 9.950680 TCTGCGAAATAATAATGATTTTCCTTC 57.049 29.630 0.00 0.00 0.00 3.46
1272 1385 1.645034 CCGCAGATTCTAGTGGTGTG 58.355 55.000 7.25 0.00 0.00 3.82
1273 1386 1.066858 CCGCAGATTCTAGTGGTGTGT 60.067 52.381 7.25 0.00 0.00 3.72
1274 1387 2.165641 CCGCAGATTCTAGTGGTGTGTA 59.834 50.000 7.25 0.00 0.00 2.90
1275 1388 3.179830 CGCAGATTCTAGTGGTGTGTAC 58.820 50.000 0.00 0.00 0.00 2.90
1345 1458 6.216936 AGTATGCTACTGACCCACTCTATGG 61.217 48.000 0.00 0.00 42.35 2.74
1367 1480 5.105716 TGGCTCTCTGTATGTTCAAGTAGAC 60.106 44.000 0.00 0.00 0.00 2.59
1369 1482 6.406400 GGCTCTCTGTATGTTCAAGTAGACAT 60.406 42.308 0.00 0.00 0.00 3.06
1388 1576 4.429108 ACATGTGTTGCTGTTTTGGTTAC 58.571 39.130 0.00 0.00 0.00 2.50
1427 1629 3.181477 TGCTTTTATTGTTGTGCTGCTGT 60.181 39.130 0.00 0.00 0.00 4.40
1440 1642 4.219033 GTGCTGCTGTTACATTGTTACAC 58.781 43.478 4.60 3.81 0.00 2.90
1487 1689 5.869888 GGGTAGCTATATCAAAGATCCAACG 59.130 44.000 0.00 0.00 0.00 4.10
1492 1694 6.480320 AGCTATATCAAAGATCCAACGTGTTC 59.520 38.462 0.00 0.00 0.00 3.18
1513 1724 8.041323 GTGTTCAAGAAGAATACCTCAATCCTA 58.959 37.037 0.00 0.00 41.08 2.94
1554 1765 9.643693 GGGGCATCTTCACATTATTTATTTATG 57.356 33.333 0.00 0.00 0.00 1.90
1574 1785 2.576191 TGTATAGCTTTCCTGGCTTGGT 59.424 45.455 0.00 0.00 40.74 3.67
1608 1819 4.817464 ACTTTGTTACCTGTGTTGCGATTA 59.183 37.500 0.00 0.00 0.00 1.75
1609 1820 5.472137 ACTTTGTTACCTGTGTTGCGATTAT 59.528 36.000 0.00 0.00 0.00 1.28
1790 2003 1.541588 GGTGTCATCAAAGAAGGTGGC 59.458 52.381 0.00 0.00 0.00 5.01
1962 2185 3.419943 TGCAAGTCATGTGCATTCCTTA 58.580 40.909 5.43 0.00 46.76 2.69
2003 2226 9.320295 TCCCAGTTTCATTTGAATTATTTACCT 57.680 29.630 0.00 0.00 33.54 3.08
2170 2394 7.435068 TCAAAGCAAGAGTATTTGTACTTCC 57.565 36.000 0.00 0.00 35.80 3.46
2507 3029 3.640498 GAGTATGTACTCTACCCCCAACC 59.360 52.174 11.90 0.00 46.99 3.77
2508 3030 1.889174 ATGTACTCTACCCCCAACCC 58.111 55.000 0.00 0.00 0.00 4.11
2509 3031 0.492730 TGTACTCTACCCCCAACCCA 59.507 55.000 0.00 0.00 0.00 4.51
2510 3032 0.907486 GTACTCTACCCCCAACCCAC 59.093 60.000 0.00 0.00 0.00 4.61
2511 3033 0.252835 TACTCTACCCCCAACCCACC 60.253 60.000 0.00 0.00 0.00 4.61
2530 3377 1.661197 CACCCACGCACAATGTTGC 60.661 57.895 0.00 0.00 39.28 4.17
2582 3431 6.116711 ACTTGGGTGTTATATGTGTGTGTA 57.883 37.500 0.00 0.00 0.00 2.90
2639 3488 3.515602 AAGGCCAGAGATCAGTTTGTT 57.484 42.857 5.01 0.00 0.00 2.83
2756 3638 8.755696 TGTGGATTTAGATTGCATTACAAAAC 57.244 30.769 0.00 0.00 42.86 2.43
2797 3686 5.129650 GGAGGCCTATTCTATATGGAGAACC 59.870 48.000 4.42 0.00 38.25 3.62
3300 4190 3.634397 AATATGGGTGTCTCTGGTGTG 57.366 47.619 0.00 0.00 0.00 3.82
3381 4271 7.582719 ACTTATTAGGTTGCCCTGAATTGATA 58.417 34.615 0.00 0.00 42.67 2.15
3559 4457 2.753247 AGTTGGTCTCCTACTGATCCC 58.247 52.381 2.49 0.00 38.11 3.85
3626 4525 2.165641 GCCAGGGTAAGTACAAATTGCC 59.834 50.000 0.00 0.00 0.00 4.52
3651 4550 6.528423 CACAGTTACCTCTTCTAAGATGTTCG 59.472 42.308 6.05 0.00 35.81 3.95
4022 4921 4.910195 TCTACACCATGAAAGCAGTCAAT 58.090 39.130 0.00 0.00 0.00 2.57
4139 5038 0.897621 GGCTGAAGGGTTTCAATGGG 59.102 55.000 0.00 0.00 42.48 4.00
4240 5139 3.468071 TCCTACTGGAAGGTGAGCTTA 57.532 47.619 0.00 0.00 39.87 3.09
4338 5372 9.838339 AAACATCTACTGAATTGGTTATAGGAG 57.162 33.333 0.00 0.00 0.00 3.69
4382 5422 0.322975 GGAACAGAGGCTCAGCTGAA 59.677 55.000 18.85 1.63 36.07 3.02
4385 5425 2.875094 ACAGAGGCTCAGCTGAAATT 57.125 45.000 18.85 5.53 36.07 1.82
4388 5428 3.280295 CAGAGGCTCAGCTGAAATTGAT 58.720 45.455 18.85 0.50 34.06 2.57
4390 5430 2.358267 GAGGCTCAGCTGAAATTGATGG 59.642 50.000 18.85 4.37 0.00 3.51
4391 5431 2.025605 AGGCTCAGCTGAAATTGATGGA 60.026 45.455 18.85 0.00 0.00 3.41
4392 5432 2.756760 GGCTCAGCTGAAATTGATGGAA 59.243 45.455 18.85 0.00 0.00 3.53
4393 5433 3.383825 GGCTCAGCTGAAATTGATGGAAT 59.616 43.478 18.85 0.00 0.00 3.01
4394 5434 4.142004 GGCTCAGCTGAAATTGATGGAATT 60.142 41.667 18.85 0.00 35.65 2.17
4395 5435 5.416947 GCTCAGCTGAAATTGATGGAATTT 58.583 37.500 18.85 0.00 45.29 1.82
4396 5436 5.873164 GCTCAGCTGAAATTGATGGAATTTT 59.127 36.000 18.85 0.00 43.12 1.82
4397 5437 6.370718 GCTCAGCTGAAATTGATGGAATTTTT 59.629 34.615 18.85 0.00 43.12 1.94
4450 5493 7.054124 TCACCCTCAAATTGTATGGACTTATC 58.946 38.462 5.50 0.00 0.00 1.75
4580 5689 3.837355 AGATGGTTCTGGAACTTGCTTT 58.163 40.909 12.34 0.00 40.94 3.51
4679 5788 9.705290 GGGAAGCTAATTTACAAGATTTCAAAA 57.295 29.630 0.00 0.00 0.00 2.44
4702 5811 6.168270 AGATCACTTCTATCAGGTAAAGCC 57.832 41.667 0.00 0.00 30.96 4.35
5015 6168 1.337071 GAGCGATCGTACAGGATGGAA 59.663 52.381 17.81 0.00 43.62 3.53
5137 6290 0.820871 CTGGACCAGGAGTAGTCTGC 59.179 60.000 14.26 0.00 33.39 4.26
5138 6291 0.409876 TGGACCAGGAGTAGTCTGCT 59.590 55.000 0.00 0.00 43.00 4.24
5202 6397 0.588252 ATGCGTGCAAGCGGATAATC 59.412 50.000 19.67 0.00 40.95 1.75
5242 6445 7.309194 GCCAGTACACTTTTCCTAAATTCACAT 60.309 37.037 0.00 0.00 0.00 3.21
5301 6504 9.438291 GAATGTTAACCATCATAATCTGTTTCG 57.562 33.333 2.48 0.00 31.75 3.46
5344 6552 9.921637 TTTATTTTCTTTAGTATTTGCCTGTGG 57.078 29.630 0.00 0.00 0.00 4.17
5368 6576 6.518736 GGTATCGAAATTGTCTGAAAAACGAC 59.481 38.462 8.97 0.00 0.00 4.34
5389 6597 1.815408 GCTCTTCCTGGTGTTTGAGCA 60.815 52.381 17.02 0.00 44.19 4.26
5398 6611 2.423185 TGGTGTTTGAGCAGTTCTGTTG 59.577 45.455 1.78 0.00 0.00 3.33
5399 6612 2.423538 GGTGTTTGAGCAGTTCTGTTGT 59.576 45.455 1.78 0.00 0.00 3.32
5400 6613 3.487544 GGTGTTTGAGCAGTTCTGTTGTC 60.488 47.826 1.78 0.00 0.00 3.18
5403 6616 2.708216 TGAGCAGTTCTGTTGTCCAA 57.292 45.000 1.78 0.00 0.00 3.53
5442 6670 6.972328 ACTGTTTGATCAACATTGTGTTACAC 59.028 34.615 7.89 8.76 44.72 2.90
5451 6679 3.181469 ACATTGTGTTACACGTCAGGAGT 60.181 43.478 11.07 0.15 37.14 3.85
5453 6681 2.304092 TGTGTTACACGTCAGGAGTCT 58.696 47.619 11.07 0.00 37.14 3.24
5454 6682 2.034179 TGTGTTACACGTCAGGAGTCTG 59.966 50.000 11.07 0.00 38.55 3.51
5459 6687 1.609555 ACACGTCAGGAGTCTGTCTTC 59.390 52.381 0.00 0.00 41.59 2.87
5481 6709 4.870426 TCAGAAAATACTCGCCTTGCTTAG 59.130 41.667 0.00 0.00 0.00 2.18
5511 6746 0.592637 TGGCGTCATGTTTTCAGCAG 59.407 50.000 0.00 0.00 0.00 4.24
5530 6765 1.152546 AACCTCCCACCCAACTTGC 60.153 57.895 0.00 0.00 0.00 4.01
5531 6766 2.283173 CCTCCCACCCAACTTGCC 60.283 66.667 0.00 0.00 0.00 4.52
5550 6785 2.065512 CCGCATTTTGGCAAGGTAAAC 58.934 47.619 0.00 0.00 0.00 2.01
5552 6787 3.324993 CGCATTTTGGCAAGGTAAACAT 58.675 40.909 0.00 0.00 0.00 2.71
5553 6788 3.123284 CGCATTTTGGCAAGGTAAACATG 59.877 43.478 0.00 0.00 0.00 3.21
5556 6791 5.334028 GCATTTTGGCAAGGTAAACATGTTC 60.334 40.000 12.39 0.00 0.00 3.18
5557 6792 5.344743 TTTTGGCAAGGTAAACATGTTCA 57.655 34.783 12.39 0.00 0.00 3.18
5559 6794 4.314740 TGGCAAGGTAAACATGTTCAAC 57.685 40.909 12.39 12.86 0.00 3.18
5560 6795 3.957497 TGGCAAGGTAAACATGTTCAACT 59.043 39.130 12.39 1.48 0.00 3.16
5563 6798 5.215160 GCAAGGTAAACATGTTCAACTCAG 58.785 41.667 12.39 3.23 0.00 3.35
5564 6799 5.762045 CAAGGTAAACATGTTCAACTCAGG 58.238 41.667 12.39 0.00 0.00 3.86
5620 6863 0.110056 GTCAACATCAAGTGGCAGCG 60.110 55.000 0.00 0.00 0.00 5.18
5642 7440 2.018542 TACAGCCAAACGCAGATACC 57.981 50.000 0.00 0.00 41.38 2.73
5699 7511 0.039798 TTCGCTGCGACGAACTTACT 60.040 50.000 25.94 0.00 46.39 2.24
5702 7514 1.774085 CGCTGCGACGAACTTACTATC 59.226 52.381 18.66 0.00 34.06 2.08
5710 7522 5.507974 CGACGAACTTACTATCACATGCTA 58.492 41.667 0.00 0.00 0.00 3.49
5729 7541 9.539825 ACATGCTATATCACTTTCTTCTTACAG 57.460 33.333 0.00 0.00 0.00 2.74
5785 7597 4.214119 ACACATCAAACACATTTCTCCTCG 59.786 41.667 0.00 0.00 0.00 4.63
5796 7608 2.579207 TTCTCCTCGCACTATTTCCG 57.421 50.000 0.00 0.00 0.00 4.30
5799 7611 0.464036 TCCTCGCACTATTTCCGCAT 59.536 50.000 0.00 0.00 0.00 4.73
5839 7651 5.381174 TGATCAAAGATGAAGTTTGCTGG 57.619 39.130 0.00 0.00 39.49 4.85
5841 7653 2.957680 TCAAAGATGAAGTTTGCTGGCA 59.042 40.909 0.00 0.00 35.29 4.92
5849 7661 5.664294 TGAAGTTTGCTGGCAATATCAAT 57.336 34.783 8.86 0.00 35.70 2.57
5852 7664 5.002464 AGTTTGCTGGCAATATCAATCAC 57.998 39.130 8.86 2.18 35.70 3.06
5885 7697 5.829924 ACCAAAGCCGATAAATGATCTGAAT 59.170 36.000 0.00 0.00 31.70 2.57
5888 7700 8.517878 CCAAAGCCGATAAATGATCTGAATTAT 58.482 33.333 0.00 0.00 31.70 1.28
6092 7908 0.689412 CCTTCCTCCTCTCCCTCACC 60.689 65.000 0.00 0.00 0.00 4.02
6093 7909 1.000486 TTCCTCCTCTCCCTCACCG 60.000 63.158 0.00 0.00 0.00 4.94
6094 7910 1.506907 TTCCTCCTCTCCCTCACCGA 61.507 60.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.505044 TGTGAAAGTGCTAGTATTCGACTA 57.495 37.500 0.00 0.00 39.81 2.59
4 5 7.648112 TGATATGTGAAAGTGCTAGTATTCGAC 59.352 37.037 0.00 0.00 0.00 4.20
5 6 7.712797 TGATATGTGAAAGTGCTAGTATTCGA 58.287 34.615 0.00 0.00 0.00 3.71
7 8 9.703892 AGATGATATGTGAAAGTGCTAGTATTC 57.296 33.333 0.00 0.00 0.00 1.75
10 11 9.131791 TGTAGATGATATGTGAAAGTGCTAGTA 57.868 33.333 0.00 0.00 0.00 1.82
11 12 7.923344 GTGTAGATGATATGTGAAAGTGCTAGT 59.077 37.037 0.00 0.00 0.00 2.57
12 13 7.922811 TGTGTAGATGATATGTGAAAGTGCTAG 59.077 37.037 0.00 0.00 0.00 3.42
13 14 7.781056 TGTGTAGATGATATGTGAAAGTGCTA 58.219 34.615 0.00 0.00 0.00 3.49
14 15 6.643388 TGTGTAGATGATATGTGAAAGTGCT 58.357 36.000 0.00 0.00 0.00 4.40
15 16 6.908870 TGTGTAGATGATATGTGAAAGTGC 57.091 37.500 0.00 0.00 0.00 4.40
16 17 9.971922 TCTATGTGTAGATGATATGTGAAAGTG 57.028 33.333 0.00 0.00 32.04 3.16
17 18 9.973450 GTCTATGTGTAGATGATATGTGAAAGT 57.027 33.333 0.00 0.00 39.08 2.66
18 19 9.416794 GGTCTATGTGTAGATGATATGTGAAAG 57.583 37.037 0.00 0.00 39.08 2.62
19 20 9.147732 AGGTCTATGTGTAGATGATATGTGAAA 57.852 33.333 0.00 0.00 39.08 2.69
20 21 8.579863 CAGGTCTATGTGTAGATGATATGTGAA 58.420 37.037 0.00 0.00 39.08 3.18
21 22 7.309438 GCAGGTCTATGTGTAGATGATATGTGA 60.309 40.741 0.00 0.00 39.08 3.58
22 23 6.810676 GCAGGTCTATGTGTAGATGATATGTG 59.189 42.308 0.00 0.00 39.08 3.21
23 24 6.071108 GGCAGGTCTATGTGTAGATGATATGT 60.071 42.308 0.00 0.00 39.08 2.29
47 48 1.308069 CCCAACAGTGGCATTCGAGG 61.308 60.000 0.00 0.00 44.46 4.63
239 242 2.567497 GGAGGTGTCGTGGGTTCGA 61.567 63.158 0.00 0.00 37.51 3.71
245 248 0.393077 AGAACTTGGAGGTGTCGTGG 59.607 55.000 0.00 0.00 0.00 4.94
246 249 1.502231 CAGAACTTGGAGGTGTCGTG 58.498 55.000 0.00 0.00 0.00 4.35
296 299 4.203226 TCGACACTCTGCTAGATCAAGAT 58.797 43.478 0.00 0.00 0.00 2.40
337 340 2.108976 ACCACACTGTCGTGCTGG 59.891 61.111 10.43 10.43 45.10 4.85
347 350 1.131638 ACCATCACAGTCACCACACT 58.868 50.000 0.00 0.00 0.00 3.55
358 362 2.703416 GCTGATCACTTCACCATCACA 58.297 47.619 0.00 0.00 0.00 3.58
404 408 3.638160 AGTTTACGCCTCCGGTCATATTA 59.362 43.478 0.00 0.00 39.22 0.98
456 460 3.612860 CGCCTAGAACACACATCAACTAC 59.387 47.826 0.00 0.00 0.00 2.73
491 496 5.380206 CCCTCCCTCTCCCACCTATATATAT 59.620 48.000 0.00 0.00 0.00 0.86
508 513 0.253207 CCTAGGTTGTTCCCCTCCCT 60.253 60.000 0.00 0.00 36.75 4.20
531 536 5.896678 CCCATGTGACCTAAATATTTGGGAA 59.103 40.000 30.88 18.28 43.21 3.97
532 537 5.194740 TCCCATGTGACCTAAATATTTGGGA 59.805 40.000 30.88 21.61 46.06 4.37
538 543 8.695456 GTGAAAAATCCCATGTGACCTAAATAT 58.305 33.333 0.00 0.00 0.00 1.28
541 546 6.074648 AGTGAAAAATCCCATGTGACCTAAA 58.925 36.000 0.00 0.00 0.00 1.85
542 547 5.640147 AGTGAAAAATCCCATGTGACCTAA 58.360 37.500 0.00 0.00 0.00 2.69
543 548 5.255397 AGTGAAAAATCCCATGTGACCTA 57.745 39.130 0.00 0.00 0.00 3.08
544 549 4.118168 AGTGAAAAATCCCATGTGACCT 57.882 40.909 0.00 0.00 0.00 3.85
545 550 4.142687 CGTAGTGAAAAATCCCATGTGACC 60.143 45.833 0.00 0.00 0.00 4.02
546 551 4.454504 ACGTAGTGAAAAATCCCATGTGAC 59.545 41.667 0.00 0.00 42.51 3.67
547 552 4.647611 ACGTAGTGAAAAATCCCATGTGA 58.352 39.130 0.00 0.00 42.51 3.58
569 574 1.051008 TCCTTCTTGTGCTCTGCTCA 58.949 50.000 0.00 0.00 0.00 4.26
573 578 1.000283 AGTCGTCCTTCTTGTGCTCTG 60.000 52.381 0.00 0.00 0.00 3.35
591 596 3.367646 TGTCTGTCCCTCGATCTAAGT 57.632 47.619 0.00 0.00 0.00 2.24
594 599 3.646736 TCTTGTCTGTCCCTCGATCTA 57.353 47.619 0.00 0.00 0.00 1.98
708 713 8.564574 TGCGTAACTAATTCTCAAAATTTGTCT 58.435 29.630 5.56 0.00 0.00 3.41
709 714 8.722342 TGCGTAACTAATTCTCAAAATTTGTC 57.278 30.769 5.56 0.00 0.00 3.18
710 715 9.522804 TTTGCGTAACTAATTCTCAAAATTTGT 57.477 25.926 5.56 0.00 0.00 2.83
716 721 9.737427 TCAAAATTTGCGTAACTAATTCTCAAA 57.263 25.926 0.00 0.00 33.38 2.69
717 722 9.393249 CTCAAAATTTGCGTAACTAATTCTCAA 57.607 29.630 0.00 0.00 33.38 3.02
718 723 8.779303 TCTCAAAATTTGCGTAACTAATTCTCA 58.221 29.630 0.00 0.00 33.38 3.27
719 724 9.607285 TTCTCAAAATTTGCGTAACTAATTCTC 57.393 29.630 0.00 0.00 33.38 2.87
728 733 9.320406 CGTAACTAATTCTCAAAATTTGCGTAA 57.680 29.630 0.00 0.00 0.00 3.18
729 734 7.479291 GCGTAACTAATTCTCAAAATTTGCGTA 59.521 33.333 0.00 0.00 0.00 4.42
730 735 6.304683 GCGTAACTAATTCTCAAAATTTGCGT 59.695 34.615 0.00 0.00 0.00 5.24
731 736 6.523201 AGCGTAACTAATTCTCAAAATTTGCG 59.477 34.615 0.00 0.00 0.00 4.85
732 737 7.201350 CCAGCGTAACTAATTCTCAAAATTTGC 60.201 37.037 0.00 0.00 0.00 3.68
733 738 7.807907 ACCAGCGTAACTAATTCTCAAAATTTG 59.192 33.333 0.00 0.00 0.00 2.32
734 739 7.882179 ACCAGCGTAACTAATTCTCAAAATTT 58.118 30.769 0.00 0.00 0.00 1.82
735 740 7.448748 ACCAGCGTAACTAATTCTCAAAATT 57.551 32.000 0.00 0.00 0.00 1.82
736 741 8.732746 ATACCAGCGTAACTAATTCTCAAAAT 57.267 30.769 0.00 0.00 0.00 1.82
766 771 7.122650 GCTCTATGGCTCTCTCTATATTTGTCT 59.877 40.741 0.00 0.00 0.00 3.41
767 772 7.093988 TGCTCTATGGCTCTCTCTATATTTGTC 60.094 40.741 0.00 0.00 0.00 3.18
768 773 6.723515 TGCTCTATGGCTCTCTCTATATTTGT 59.276 38.462 0.00 0.00 0.00 2.83
769 774 7.167924 TGCTCTATGGCTCTCTCTATATTTG 57.832 40.000 0.00 0.00 0.00 2.32
771 776 6.183360 GCATGCTCTATGGCTCTCTCTATATT 60.183 42.308 11.37 0.00 37.26 1.28
772 777 5.302568 GCATGCTCTATGGCTCTCTCTATAT 59.697 44.000 11.37 0.00 37.26 0.86
773 778 4.644234 GCATGCTCTATGGCTCTCTCTATA 59.356 45.833 11.37 0.00 37.26 1.31
775 780 2.824936 GCATGCTCTATGGCTCTCTCTA 59.175 50.000 11.37 0.00 37.26 2.43
777 782 1.343789 TGCATGCTCTATGGCTCTCTC 59.656 52.381 20.33 0.00 37.26 3.20
778 783 1.421480 TGCATGCTCTATGGCTCTCT 58.579 50.000 20.33 0.00 37.26 3.10
779 784 2.476126 ATGCATGCTCTATGGCTCTC 57.524 50.000 20.33 0.00 37.26 3.20
780 785 2.885266 CAAATGCATGCTCTATGGCTCT 59.115 45.455 20.33 0.00 37.26 4.09
781 786 2.882761 TCAAATGCATGCTCTATGGCTC 59.117 45.455 20.33 0.00 37.26 4.70
782 787 2.621998 GTCAAATGCATGCTCTATGGCT 59.378 45.455 20.33 0.00 37.26 4.75
783 788 2.621998 AGTCAAATGCATGCTCTATGGC 59.378 45.455 20.33 13.66 37.26 4.40
784 789 3.550233 GCAGTCAAATGCATGCTCTATGG 60.550 47.826 20.33 3.88 45.77 2.74
785 790 3.315470 AGCAGTCAAATGCATGCTCTATG 59.685 43.478 20.33 12.44 45.57 2.23
786 791 3.552875 AGCAGTCAAATGCATGCTCTAT 58.447 40.909 20.33 0.44 45.57 1.98
826 859 1.633852 GCTTCTTGAGTCTGCCGCTG 61.634 60.000 0.00 0.00 0.00 5.18
838 871 2.677875 GTGGGCCTGGGCTTCTTG 60.678 66.667 20.47 0.00 41.60 3.02
839 872 4.351054 CGTGGGCCTGGGCTTCTT 62.351 66.667 20.47 0.00 41.60 2.52
926 972 4.828925 GGAGACGCTGCTGGCCTC 62.829 72.222 3.32 0.00 37.74 4.70
980 1038 2.473664 CTTCGTTCCTCACCGCGAGT 62.474 60.000 8.23 0.00 40.48 4.18
987 1045 1.696832 GCGCCATCTTCGTTCCTCAC 61.697 60.000 0.00 0.00 0.00 3.51
1017 1075 1.672737 CGCGCATCTATGGCTTCCATA 60.673 52.381 8.75 5.54 43.19 2.74
1044 1102 1.583986 GAGATCGATCCCCAGCTCG 59.416 63.158 21.66 0.00 36.25 5.03
1079 1137 4.554036 GCGGGAGGGTGATGGAGC 62.554 72.222 0.00 0.00 0.00 4.70
1129 1187 3.319198 GAAGGAGGTGCGGGTGGA 61.319 66.667 0.00 0.00 0.00 4.02
1134 1192 2.269241 GGAAGGAAGGAGGTGCGG 59.731 66.667 0.00 0.00 0.00 5.69
1136 1194 0.915364 ATCTGGAAGGAAGGAGGTGC 59.085 55.000 0.00 0.00 0.00 5.01
1158 1238 1.533625 CCATCAACCAACCACGTGAT 58.466 50.000 19.30 0.00 0.00 3.06
1187 1267 5.299531 CCCGATGAGACAGACATACTCTAAA 59.700 44.000 0.00 0.00 0.00 1.85
1197 1277 1.698506 ATCCTCCCGATGAGACAGAC 58.301 55.000 3.77 0.00 44.42 3.51
1229 1338 7.059488 CGGCGAAGGAAAATCATTATTATTTCG 59.941 37.037 0.00 0.00 33.62 3.46
1251 1360 1.141881 ACCACTAGAATCTGCGGCG 59.858 57.895 0.51 0.51 0.00 6.46
1345 1458 5.955488 TGTCTACTTGAACATACAGAGAGC 58.045 41.667 0.00 0.00 0.00 4.09
1346 1459 7.487509 CACATGTCTACTTGAACATACAGAGAG 59.512 40.741 0.00 0.00 0.00 3.20
1347 1460 7.039714 ACACATGTCTACTTGAACATACAGAGA 60.040 37.037 0.00 0.00 0.00 3.10
1367 1480 3.485378 CGTAACCAAAACAGCAACACATG 59.515 43.478 0.00 0.00 0.00 3.21
1369 1482 2.732597 GCGTAACCAAAACAGCAACACA 60.733 45.455 0.00 0.00 0.00 3.72
1388 1576 2.743938 AGCAGTAATAGACCGATTGCG 58.256 47.619 0.00 0.00 32.26 4.85
1427 1629 7.148705 GCTGATTAGTGTCGTGTAACAATGTAA 60.149 37.037 0.00 0.00 35.74 2.41
1440 1642 8.088981 ACCCTAATAATTAGCTGATTAGTGTCG 58.911 37.037 18.24 9.24 33.23 4.35
1472 1674 6.227522 TCTTGAACACGTTGGATCTTTGATA 58.772 36.000 0.00 0.00 0.00 2.15
1487 1689 6.881602 AGGATTGAGGTATTCTTCTTGAACAC 59.118 38.462 0.00 0.00 37.52 3.32
1554 1765 2.945668 CACCAAGCCAGGAAAGCTATAC 59.054 50.000 0.00 0.00 40.49 1.47
1557 1768 0.771127 ACACCAAGCCAGGAAAGCTA 59.229 50.000 0.00 0.00 40.49 3.32
1574 1785 7.554835 ACACAGGTAACAAAGTCAAGAAATACA 59.445 33.333 0.00 0.00 41.41 2.29
1790 2003 1.463674 GGTGTGTAGGCATCCAAAGG 58.536 55.000 0.00 0.00 0.00 3.11
1902 2121 4.401022 GGCATTACCTCATTCCATCATGA 58.599 43.478 0.00 0.00 34.51 3.07
1962 2185 6.953520 TGAAACTGGGATGACCTTTTTCATAT 59.046 34.615 8.12 0.00 41.61 1.78
2003 2226 9.593134 TTAACTACTAGTAAAAACGTGAACCAA 57.407 29.630 3.76 0.00 0.00 3.67
2218 2444 6.814146 TGGACGGACATTTAAATAAATTTGGC 59.186 34.615 0.00 0.00 33.88 4.52
2336 2856 0.979665 TAGCAAGCTCAGCTTCCTGT 59.020 50.000 13.58 0.00 46.77 4.00
2507 3029 4.885270 TTGTGCGTGGGTGGGTGG 62.885 66.667 0.00 0.00 0.00 4.61
2508 3030 2.597217 ATTGTGCGTGGGTGGGTG 60.597 61.111 0.00 0.00 0.00 4.61
2509 3031 2.597217 CATTGTGCGTGGGTGGGT 60.597 61.111 0.00 0.00 0.00 4.51
2510 3032 2.199652 AACATTGTGCGTGGGTGGG 61.200 57.895 0.00 0.00 0.00 4.61
2511 3033 1.007502 CAACATTGTGCGTGGGTGG 60.008 57.895 0.00 0.00 0.00 4.61
2530 3377 9.778993 CATGAAACCTGTCATAATGTAAAGAAG 57.221 33.333 0.00 0.00 36.04 2.85
2582 3431 5.047519 CCACTTCAGAAGATTTTCCTGCAAT 60.048 40.000 17.56 0.00 33.64 3.56
2639 3488 1.252215 TGAACGTCCCAGCACGGATA 61.252 55.000 0.00 0.00 44.41 2.59
2756 3638 3.066760 GCCTCCCATGAACTTTATTTCCG 59.933 47.826 0.00 0.00 0.00 4.30
2874 3763 1.566018 GCACGGTAGCCAAGTGTGTC 61.566 60.000 0.00 0.00 38.10 3.67
3147 4036 4.867047 CAGATAGGACACAAGACATGACAC 59.133 45.833 0.00 0.00 0.00 3.67
3300 4190 2.435805 TCACCTGAAGATAGGCCATGAC 59.564 50.000 5.01 0.00 41.75 3.06
4022 4921 6.311935 GCTTGGACACACGACTAACATTATTA 59.688 38.462 0.00 0.00 0.00 0.98
4139 5038 0.514691 CGTTGAAGAACTCCAGCTGC 59.485 55.000 8.66 0.00 0.00 5.25
4338 5372 7.709613 CCCAGTGTTCAGGTTATGTATAGTAAC 59.290 40.741 0.00 1.15 0.00 2.50
4342 5376 6.479972 TCCCAGTGTTCAGGTTATGTATAG 57.520 41.667 0.00 0.00 0.00 1.31
4423 5466 3.378427 GTCCATACAATTTGAGGGTGAGC 59.622 47.826 2.79 0.00 0.00 4.26
4580 5689 2.877786 TGCAGTTGCGAGAAATCTGAAA 59.122 40.909 0.00 0.00 45.83 2.69
4679 5788 6.168270 GGCTTTACCTGATAGAAGTGATCT 57.832 41.667 0.00 0.00 37.57 2.75
4698 5807 0.962356 CAAAGGATGGACGCAGGCTT 60.962 55.000 0.00 0.00 0.00 4.35
4702 5811 1.238439 ACAACAAAGGATGGACGCAG 58.762 50.000 0.00 0.00 0.00 5.18
4756 5905 8.188799 CCATCATGCAGCAAAGGATATATAAAG 58.811 37.037 0.00 0.00 0.00 1.85
4760 5912 5.577100 ACCATCATGCAGCAAAGGATATAT 58.423 37.500 0.00 0.00 0.00 0.86
4761 5913 4.989277 ACCATCATGCAGCAAAGGATATA 58.011 39.130 0.00 0.00 0.00 0.86
4762 5914 3.840991 ACCATCATGCAGCAAAGGATAT 58.159 40.909 0.00 0.00 0.00 1.63
4895 6048 2.923035 CCCACCTGGTTGGACACA 59.077 61.111 11.45 0.00 39.24 3.72
5015 6168 3.670629 CTCCTCCCCGCCTCTCAGT 62.671 68.421 0.00 0.00 0.00 3.41
5131 6284 0.598680 GAACACTCGTGCAGCAGACT 60.599 55.000 0.00 0.00 0.00 3.24
5132 6285 0.875908 TGAACACTCGTGCAGCAGAC 60.876 55.000 0.00 0.00 0.00 3.51
5133 6286 0.033920 ATGAACACTCGTGCAGCAGA 59.966 50.000 0.00 0.00 32.77 4.26
5134 6287 0.870393 AATGAACACTCGTGCAGCAG 59.130 50.000 0.00 0.00 32.77 4.24
5135 6288 1.308047 AAATGAACACTCGTGCAGCA 58.692 45.000 0.00 0.00 32.77 4.41
5136 6289 2.031682 AGAAAATGAACACTCGTGCAGC 60.032 45.455 0.00 0.00 32.77 5.25
5137 6290 3.548587 CAGAAAATGAACACTCGTGCAG 58.451 45.455 0.00 0.00 32.77 4.41
5138 6291 2.286950 GCAGAAAATGAACACTCGTGCA 60.287 45.455 0.00 0.00 34.22 4.57
5139 6292 2.310577 GCAGAAAATGAACACTCGTGC 58.689 47.619 0.00 0.00 0.00 5.34
5202 6397 4.153117 GTGTACTGGCAGAAAGATCAACAG 59.847 45.833 23.66 0.00 0.00 3.16
5242 6445 7.537596 AAATTTGGTCTCCATAAACATGACA 57.462 32.000 0.00 0.00 31.53 3.58
5301 6504 8.931775 AGAAAATAAAATAACCGGATTTGCAAC 58.068 29.630 9.46 0.00 0.00 4.17
5344 6552 6.243649 CGTCGTTTTTCAGACAATTTCGATAC 59.756 38.462 0.00 0.00 37.23 2.24
5368 6576 1.151668 CTCAAACACCAGGAAGAGCG 58.848 55.000 0.00 0.00 0.00 5.03
5389 6597 7.246171 AGATACTGTATTGGACAACAGAACT 57.754 36.000 9.30 3.22 44.79 3.01
5390 6598 9.601217 AATAGATACTGTATTGGACAACAGAAC 57.399 33.333 9.30 1.28 44.79 3.01
5442 6670 2.155279 TCTGAAGACAGACTCCTGACG 58.845 52.381 0.00 0.00 46.55 4.35
5453 6681 4.537135 AGGCGAGTATTTTCTGAAGACA 57.463 40.909 0.00 0.00 0.00 3.41
5454 6682 4.436183 GCAAGGCGAGTATTTTCTGAAGAC 60.436 45.833 0.00 0.00 0.00 3.01
5459 6687 4.631813 ACTAAGCAAGGCGAGTATTTTCTG 59.368 41.667 0.00 0.00 30.25 3.02
5481 6709 2.202650 GACGCCATGCATGCCAAC 60.203 61.111 21.69 8.92 0.00 3.77
5495 6723 2.549754 AGGTTCTGCTGAAAACATGACG 59.450 45.455 7.68 0.00 33.52 4.35
5511 6746 1.179174 GCAAGTTGGGTGGGAGGTTC 61.179 60.000 4.75 0.00 0.00 3.62
5530 6765 2.065512 GTTTACCTTGCCAAAATGCGG 58.934 47.619 0.00 0.00 0.00 5.69
5531 6766 2.748605 TGTTTACCTTGCCAAAATGCG 58.251 42.857 0.00 0.00 0.00 4.73
5550 6785 3.131709 ACCTGACCTGAGTTGAACATG 57.868 47.619 0.00 0.00 0.00 3.21
5552 6787 3.644966 AAACCTGACCTGAGTTGAACA 57.355 42.857 0.00 0.00 0.00 3.18
5553 6788 3.066760 CCAAAACCTGACCTGAGTTGAAC 59.933 47.826 0.00 0.00 0.00 3.18
5556 6791 1.338020 GCCAAAACCTGACCTGAGTTG 59.662 52.381 0.00 0.00 0.00 3.16
5557 6792 1.064017 TGCCAAAACCTGACCTGAGTT 60.064 47.619 0.00 0.00 0.00 3.01
5559 6794 1.691196 TTGCCAAAACCTGACCTGAG 58.309 50.000 0.00 0.00 0.00 3.35
5560 6795 2.364970 CAATTGCCAAAACCTGACCTGA 59.635 45.455 0.00 0.00 0.00 3.86
5563 6798 1.202627 TGCAATTGCCAAAACCTGACC 60.203 47.619 26.94 0.00 41.18 4.02
5564 6799 1.866601 GTGCAATTGCCAAAACCTGAC 59.133 47.619 26.94 11.55 41.18 3.51
5620 6863 3.002348 GGTATCTGCGTTTGGCTGTAATC 59.998 47.826 0.00 0.00 44.05 1.75
5642 7440 6.835914 AGATCAGCACAAGAGTTTTTAATCG 58.164 36.000 0.00 0.00 0.00 3.34
5702 7514 9.317936 TGTAAGAAGAAAGTGATATAGCATGTG 57.682 33.333 0.00 0.00 0.00 3.21
5729 7541 2.359967 CGAACCTGAGGGGGAGGTC 61.360 68.421 2.38 0.00 43.42 3.85
5818 7630 4.171754 GCCAGCAAACTTCATCTTTGATC 58.828 43.478 0.00 0.00 31.32 2.92
5822 7634 4.612264 ATTGCCAGCAAACTTCATCTTT 57.388 36.364 9.44 0.00 39.55 2.52
5860 7672 5.192927 TCAGATCATTTATCGGCTTTGGTT 58.807 37.500 0.00 0.00 39.79 3.67
5885 7697 7.063308 GTCCGTACATAAACCGTCTTCAAATAA 59.937 37.037 0.00 0.00 0.00 1.40
5888 7700 4.685628 GTCCGTACATAAACCGTCTTCAAA 59.314 41.667 0.00 0.00 0.00 2.69
6092 7908 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
6093 7909 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
6094 7910 4.064491 GGTCGTCGTCGTCGTCGT 62.064 66.667 18.44 0.00 45.27 4.34


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

AutoCloner maintained by Alex Coulton.