Multiple sequence alignment - TraesCS6A01G281000

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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 TraesCS6A01G281000 chr6A 100.000 4699 0 0 1 4699 510860902 510865600 0.000000e+00 8678.0
1 TraesCS6A01G281000 chr6D 92.483 4031 220 36 726 4699 369657782 369661786 0.000000e+00 5688.0
2 TraesCS6A01G281000 chr6B 91.113 2138 107 30 726 2823 555289688 555291782 0.000000e+00 2819.0
3 TraesCS6A01G281000 chr6B 95.561 1622 63 5 3082 4699 555292310 555293926 0.000000e+00 2588.0
4 TraesCS6A01G281000 chr6B 92.105 228 17 1 2846 3072 555291771 555291998 2.110000e-83 320.0
5 TraesCS6A01G281000 chr6B 76.000 650 108 32 84 706 584904535 584905163 4.600000e-75 292.0
6 TraesCS6A01G281000 chr6B 81.849 292 35 13 102 386 668893890 668893610 3.660000e-56 230.0
7 TraesCS6A01G281000 chr6B 93.939 66 1 1 4634 4699 432264147 432264085 3.870000e-16 97.1
8 TraesCS6A01G281000 chr5B 77.966 590 96 22 95 663 535398208 535398784 5.820000e-89 339.0
9 TraesCS6A01G281000 chr2B 76.444 675 107 34 57 706 76071720 76071073 7.590000e-83 318.0
10 TraesCS6A01G281000 chr2B 79.888 358 52 17 126 472 773387222 773386874 1.310000e-60 244.0
11 TraesCS6A01G281000 chr1D 77.817 568 87 25 161 706 100902528 100901978 9.820000e-82 315.0
12 TraesCS6A01G281000 chr7B 76.800 625 100 30 94 696 200717775 200717174 4.570000e-80 309.0
13 TraesCS6A01G281000 chr7D 77.827 451 69 22 181 607 23544667 23545110 2.810000e-62 250.0
14 TraesCS6A01G281000 chr2D 76.550 516 79 29 173 662 39832969 39832470 1.310000e-60 244.0


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 TraesCS6A01G281000 chr6A 510860902 510865600 4698 False 8678 8678 100.000000 1 4699 1 chr6A.!!$F1 4698
1 TraesCS6A01G281000 chr6D 369657782 369661786 4004 False 5688 5688 92.483000 726 4699 1 chr6D.!!$F1 3973
2 TraesCS6A01G281000 chr6B 555289688 555293926 4238 False 1909 2819 92.926333 726 4699 3 chr6B.!!$F2 3973
3 TraesCS6A01G281000 chr6B 584904535 584905163 628 False 292 292 76.000000 84 706 1 chr6B.!!$F1 622
4 TraesCS6A01G281000 chr5B 535398208 535398784 576 False 339 339 77.966000 95 663 1 chr5B.!!$F1 568
5 TraesCS6A01G281000 chr2B 76071073 76071720 647 True 318 318 76.444000 57 706 1 chr2B.!!$R1 649
6 TraesCS6A01G281000 chr1D 100901978 100902528 550 True 315 315 77.817000 161 706 1 chr1D.!!$R1 545
7 TraesCS6A01G281000 chr7B 200717174 200717775 601 True 309 309 76.800000 94 696 1 chr7B.!!$R1 602

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
118 120 0.112412 ACTTTTGGTCCCCTCGCATT 59.888 50.0 0.00 0.0 0.00 3.56 F
1635 1687 0.242017 GCTGAATGTGTGGTGCCTTC 59.758 55.0 0.00 0.0 0.00 3.46 F
2051 2103 0.631212 GACCATGGATTCCTGGGGTT 59.369 55.0 21.47 0.0 36.82 4.11 F
2840 2915 0.039035 TGGTTGCAGGGGTGAATACC 59.961 55.0 0.00 0.0 46.76 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1872 0.107654 GGCCCACTCTCCACATGTAC 60.108 60.000 0.00 0.00 0.00 2.90 R
2821 2896 0.039035 GGTATTCACCCCTGCAACCA 59.961 55.000 0.00 0.00 39.11 3.67 R
3037 3146 1.074248 CTACCACACCCAACACCCC 59.926 63.158 0.00 0.00 0.00 4.95 R
4155 4578 0.666577 CCTTCTCGTGGGTCGACAAC 60.667 60.000 18.91 13.76 44.01 3.32 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
25 26 8.746922 CAAATGCATGTATTACTTTCAACAGT 57.253 30.769 9.58 0.00 0.00 3.55
26 27 8.853345 CAAATGCATGTATTACTTTCAACAGTC 58.147 33.333 9.58 0.00 0.00 3.51
27 28 6.164408 TGCATGTATTACTTTCAACAGTCG 57.836 37.500 0.00 0.00 0.00 4.18
28 29 5.022021 GCATGTATTACTTTCAACAGTCGC 58.978 41.667 0.00 0.00 0.00 5.19
29 30 5.163854 GCATGTATTACTTTCAACAGTCGCT 60.164 40.000 0.00 0.00 0.00 4.93
30 31 5.839262 TGTATTACTTTCAACAGTCGCTG 57.161 39.130 5.47 5.47 37.52 5.18
31 32 4.688879 TGTATTACTTTCAACAGTCGCTGG 59.311 41.667 10.80 0.00 35.51 4.85
32 33 2.163818 TACTTTCAACAGTCGCTGGG 57.836 50.000 10.80 3.94 35.51 4.45
33 34 1.166531 ACTTTCAACAGTCGCTGGGC 61.167 55.000 10.80 0.00 35.51 5.36
34 35 0.886490 CTTTCAACAGTCGCTGGGCT 60.886 55.000 10.80 0.00 35.51 5.19
35 36 0.394938 TTTCAACAGTCGCTGGGCTA 59.605 50.000 10.80 0.00 35.51 3.93
36 37 0.320421 TTCAACAGTCGCTGGGCTAC 60.320 55.000 10.80 0.00 35.51 3.58
37 38 1.741770 CAACAGTCGCTGGGCTACC 60.742 63.158 10.80 0.00 35.51 3.18
38 39 2.955881 AACAGTCGCTGGGCTACCC 61.956 63.158 10.80 0.00 45.71 3.69
47 48 4.545929 GGGCTACCCGCGTTTTAT 57.454 55.556 4.92 0.00 40.44 1.40
48 49 2.784547 GGGCTACCCGCGTTTTATT 58.215 52.632 4.92 0.00 40.44 1.40
49 50 1.952193 GGGCTACCCGCGTTTTATTA 58.048 50.000 4.92 0.00 40.44 0.98
50 51 2.497138 GGGCTACCCGCGTTTTATTAT 58.503 47.619 4.92 0.00 40.44 1.28
51 52 3.663025 GGGCTACCCGCGTTTTATTATA 58.337 45.455 4.92 0.00 40.44 0.98
52 53 3.433274 GGGCTACCCGCGTTTTATTATAC 59.567 47.826 4.92 0.00 40.44 1.47
53 54 4.309933 GGCTACCCGCGTTTTATTATACT 58.690 43.478 4.92 0.00 40.44 2.12
54 55 4.751600 GGCTACCCGCGTTTTATTATACTT 59.248 41.667 4.92 0.00 40.44 2.24
55 56 5.237127 GGCTACCCGCGTTTTATTATACTTT 59.763 40.000 4.92 0.00 40.44 2.66
56 57 6.423604 GGCTACCCGCGTTTTATTATACTTTA 59.576 38.462 4.92 0.00 40.44 1.85
57 58 7.283633 GCTACCCGCGTTTTATTATACTTTAC 58.716 38.462 4.92 0.00 0.00 2.01
58 59 6.272698 ACCCGCGTTTTATTATACTTTACG 57.727 37.500 4.92 0.00 0.00 3.18
59 60 6.039616 ACCCGCGTTTTATTATACTTTACGA 58.960 36.000 4.92 0.00 0.00 3.43
60 61 6.533367 ACCCGCGTTTTATTATACTTTACGAA 59.467 34.615 4.92 0.00 0.00 3.85
61 62 7.059212 CCCGCGTTTTATTATACTTTACGAAG 58.941 38.462 4.92 0.00 38.87 3.79
71 72 2.410939 ACTTTACGAAGCGAGGGTTTC 58.589 47.619 0.00 0.00 36.29 2.78
80 81 1.141234 CGAGGGTTTCGTCTAGGGC 59.859 63.158 0.00 0.00 44.27 5.19
81 82 1.601419 CGAGGGTTTCGTCTAGGGCA 61.601 60.000 0.00 0.00 44.27 5.36
116 118 0.536460 GAACTTTTGGTCCCCTCGCA 60.536 55.000 0.00 0.00 0.00 5.10
118 120 0.112412 ACTTTTGGTCCCCTCGCATT 59.888 50.000 0.00 0.00 0.00 3.56
190 192 7.310664 AGAGTTCTATGTTTTTCGTCATCGTA 58.689 34.615 0.00 0.00 38.33 3.43
198 200 7.821595 TGTTTTTCGTCATCGTATAGTGATT 57.178 32.000 0.00 0.00 38.33 2.57
237 243 4.703899 TTTACTCTCGTTCTTTTGACGC 57.296 40.909 0.00 0.00 0.00 5.19
241 247 0.861837 CTCGTTCTTTTGACGCTGCT 59.138 50.000 0.00 0.00 0.00 4.24
242 248 2.058798 CTCGTTCTTTTGACGCTGCTA 58.941 47.619 0.00 0.00 0.00 3.49
243 249 2.668457 CTCGTTCTTTTGACGCTGCTAT 59.332 45.455 0.00 0.00 0.00 2.97
252 258 5.912360 TTTGACGCTGCTATATGAGATTG 57.088 39.130 0.00 0.00 0.00 2.67
253 259 4.853924 TGACGCTGCTATATGAGATTGA 57.146 40.909 0.00 0.00 0.00 2.57
263 269 8.357796 TGCTATATGAGATTGAAGAGTTTTCG 57.642 34.615 0.00 0.00 0.00 3.46
271 277 3.553828 TGAAGAGTTTTCGGTCCTTGT 57.446 42.857 0.00 0.00 0.00 3.16
275 281 4.254402 AGAGTTTTCGGTCCTTGTAGAC 57.746 45.455 0.00 0.00 35.95 2.59
408 416 0.889306 GACGTCCTGCACTTCTAGGT 59.111 55.000 3.51 0.00 35.54 3.08
420 429 2.320781 CTTCTAGGTGATCATCCCGGT 58.679 52.381 1.24 0.00 0.00 5.28
428 437 2.368875 GTGATCATCCCGGTCCAAGTAT 59.631 50.000 0.00 0.00 0.00 2.12
433 442 0.533491 TCCCGGTCCAAGTATGTTCG 59.467 55.000 0.00 0.00 0.00 3.95
449 458 2.224523 TGTTCGTCAATCAAGGCTTCCT 60.225 45.455 0.00 0.00 33.87 3.36
452 461 3.797039 TCGTCAATCAAGGCTTCCTATG 58.203 45.455 0.00 0.00 31.13 2.23
453 462 2.289002 CGTCAATCAAGGCTTCCTATGC 59.711 50.000 0.00 0.00 31.13 3.14
458 467 5.126061 TCAATCAAGGCTTCCTATGCTTTTC 59.874 40.000 0.00 0.00 31.13 2.29
459 468 4.032960 TCAAGGCTTCCTATGCTTTTCA 57.967 40.909 0.00 0.00 31.13 2.69
464 473 3.451526 GCTTCCTATGCTTTTCAATGGC 58.548 45.455 0.00 0.00 0.00 4.40
465 474 3.119029 GCTTCCTATGCTTTTCAATGGCA 60.119 43.478 0.00 0.00 40.32 4.92
466 475 4.621274 GCTTCCTATGCTTTTCAATGGCAA 60.621 41.667 0.00 0.00 39.46 4.52
467 476 4.454728 TCCTATGCTTTTCAATGGCAAC 57.545 40.909 0.00 0.00 39.46 4.17
468 477 4.088634 TCCTATGCTTTTCAATGGCAACT 58.911 39.130 0.00 0.00 39.46 3.16
469 478 4.158394 TCCTATGCTTTTCAATGGCAACTC 59.842 41.667 0.00 0.00 39.46 3.01
470 479 4.082081 CCTATGCTTTTCAATGGCAACTCA 60.082 41.667 0.00 0.00 39.46 3.41
478 490 4.734398 TCAATGGCAACTCAACACTTTT 57.266 36.364 0.00 0.00 37.61 2.27
508 520 9.577110 AAAAATCATTATTACGAGTACGACAGA 57.423 29.630 0.00 0.00 42.66 3.41
509 521 8.783999 AAATCATTATTACGAGTACGACAGAG 57.216 34.615 0.00 0.00 42.66 3.35
510 522 7.725818 ATCATTATTACGAGTACGACAGAGA 57.274 36.000 0.00 0.00 42.66 3.10
511 523 6.941802 TCATTATTACGAGTACGACAGAGAC 58.058 40.000 0.00 0.00 42.66 3.36
512 524 6.760298 TCATTATTACGAGTACGACAGAGACT 59.240 38.462 0.00 0.00 42.66 3.24
513 525 4.861389 ATTACGAGTACGACAGAGACTG 57.139 45.455 0.00 0.00 42.66 3.51
514 526 2.452295 ACGAGTACGACAGAGACTGA 57.548 50.000 5.76 0.00 42.66 3.41
515 527 2.975266 ACGAGTACGACAGAGACTGAT 58.025 47.619 5.76 0.00 42.66 2.90
516 528 4.120792 ACGAGTACGACAGAGACTGATA 57.879 45.455 5.76 0.00 42.66 2.15
518 530 5.117584 ACGAGTACGACAGAGACTGATATT 58.882 41.667 5.76 0.00 42.66 1.28
519 531 5.585445 ACGAGTACGACAGAGACTGATATTT 59.415 40.000 5.76 0.00 42.66 1.40
520 532 6.093771 ACGAGTACGACAGAGACTGATATTTT 59.906 38.462 5.76 0.00 42.66 1.82
540 562 1.651240 CTCCAGTCCAATTGCAGCCG 61.651 60.000 0.00 0.00 0.00 5.52
556 578 0.442699 GCCGCTTTACCGAAGTCTTG 59.557 55.000 0.00 0.00 37.69 3.02
578 604 5.569630 TTGGGACATTTTCTCTAGCAGAGAC 60.570 44.000 13.34 4.03 45.15 3.36
592 618 2.185841 CAGAGACTGATAGCGCGAAGC 61.186 57.143 12.10 0.00 42.18 3.86
696 723 7.861629 AGATCCAAATCAGTGACCTGTAATTA 58.138 34.615 0.00 0.00 39.82 1.40
700 727 9.391006 TCCAAATCAGTGACCTGTAATTATTAC 57.609 33.333 8.07 8.07 39.82 1.89
706 733 8.400947 TCAGTGACCTGTAATTATTACGAGTAC 58.599 37.037 10.09 6.10 39.82 2.73
707 734 7.375280 CAGTGACCTGTAATTATTACGAGTACG 59.625 40.741 10.09 0.00 38.98 3.67
708 735 6.634436 GTGACCTGTAATTATTACGAGTACGG 59.366 42.308 10.09 6.33 44.46 4.02
709 736 5.523369 ACCTGTAATTATTACGAGTACGGC 58.477 41.667 10.09 0.00 44.46 5.68
710 737 5.067674 ACCTGTAATTATTACGAGTACGGCA 59.932 40.000 10.09 0.00 44.46 5.69
711 738 5.628193 CCTGTAATTATTACGAGTACGGCAG 59.372 44.000 10.09 0.02 44.46 4.85
712 739 6.375945 TGTAATTATTACGAGTACGGCAGA 57.624 37.500 10.09 0.00 44.46 4.26
713 740 6.973843 TGTAATTATTACGAGTACGGCAGAT 58.026 36.000 10.09 0.00 44.46 2.90
714 741 7.428020 TGTAATTATTACGAGTACGGCAGATT 58.572 34.615 10.09 0.00 44.46 2.40
715 742 7.922278 TGTAATTATTACGAGTACGGCAGATTT 59.078 33.333 10.09 0.00 44.46 2.17
716 743 7.404139 AATTATTACGAGTACGGCAGATTTC 57.596 36.000 0.00 0.00 44.46 2.17
717 744 3.853831 TTACGAGTACGGCAGATTTCA 57.146 42.857 0.00 0.00 44.46 2.69
718 745 2.961526 ACGAGTACGGCAGATTTCAT 57.038 45.000 0.00 0.00 44.46 2.57
719 746 5.503662 TTACGAGTACGGCAGATTTCATA 57.496 39.130 0.00 0.00 44.46 2.15
720 747 4.380841 ACGAGTACGGCAGATTTCATAA 57.619 40.909 0.00 0.00 44.46 1.90
721 748 4.751060 ACGAGTACGGCAGATTTCATAAA 58.249 39.130 0.00 0.00 44.46 1.40
722 749 5.172934 ACGAGTACGGCAGATTTCATAAAA 58.827 37.500 0.00 0.00 44.46 1.52
723 750 5.640357 ACGAGTACGGCAGATTTCATAAAAA 59.360 36.000 0.00 0.00 44.46 1.94
775 802 3.269347 ACAAGTGGACGCGCACAC 61.269 61.111 21.75 21.75 37.86 3.82
794 821 0.951040 CGAAACAGGAGCCGCTTCTT 60.951 55.000 0.00 0.00 0.00 2.52
854 881 2.268920 CCAGCAGTGCCACCGTAT 59.731 61.111 12.58 0.00 0.00 3.06
997 1034 4.341520 GTCCCATCCACCAGTTACTACTAG 59.658 50.000 0.00 0.00 31.96 2.57
999 1036 4.341520 CCCATCCACCAGTTACTACTAGTC 59.658 50.000 0.00 0.00 31.96 2.59
1028 1065 4.025401 CAGCGCGGGTTCCACAAC 62.025 66.667 8.83 0.00 0.00 3.32
1071 1116 1.369625 CGGCAGCGGAATTTAACTCT 58.630 50.000 0.00 0.00 0.00 3.24
1072 1117 1.327764 CGGCAGCGGAATTTAACTCTC 59.672 52.381 0.00 0.00 0.00 3.20
1391 1439 7.224167 CCAGGTACTACTAAATGATTCCGTTTC 59.776 40.741 0.00 0.00 36.02 2.78
1414 1462 3.909285 GCCGTACCGTAGCCTCCC 61.909 72.222 0.00 0.00 0.00 4.30
1496 1545 6.327154 GGTCCGTCAAAATTATTAAGTTGGG 58.673 40.000 0.00 0.00 0.00 4.12
1514 1563 3.928754 TGGGCATTCTAGGATCAGTAGT 58.071 45.455 0.00 0.00 0.00 2.73
1515 1564 5.074746 TGGGCATTCTAGGATCAGTAGTA 57.925 43.478 0.00 0.00 0.00 1.82
1532 1583 6.491062 TCAGTAGTAAGTAGTACTTGTTGCCA 59.509 38.462 23.14 1.59 40.33 4.92
1542 1593 5.433526 AGTACTTGTTGCCAGTTCAAGTTA 58.566 37.500 13.49 0.72 45.97 2.24
1594 1645 4.380867 CGCCTTGAAAATTCAGGCACTTAT 60.381 41.667 23.72 0.00 44.49 1.73
1635 1687 0.242017 GCTGAATGTGTGGTGCCTTC 59.758 55.000 0.00 0.00 0.00 3.46
1756 1808 1.728971 CGACAAGGAGATGCAAGACAC 59.271 52.381 0.00 0.00 0.00 3.67
1886 1938 8.506168 TTAAGGTTGTCATTTCTACATGATCC 57.494 34.615 0.00 0.00 35.60 3.36
1929 1981 2.487762 TGAATGAATTCCACGCTTCACC 59.512 45.455 2.27 0.00 34.43 4.02
2051 2103 0.631212 GACCATGGATTCCTGGGGTT 59.369 55.000 21.47 0.00 36.82 4.11
2093 2145 3.517500 TGAGGTACATATCCAGTGCACAA 59.482 43.478 21.04 4.16 0.00 3.33
2097 2149 6.658849 AGGTACATATCCAGTGCACAATTTA 58.341 36.000 21.04 5.85 0.00 1.40
2104 2157 9.276590 CATATCCAGTGCACAATTTATCTAAGA 57.723 33.333 21.04 0.00 0.00 2.10
2140 2193 7.650890 TGCAGTTTATACATGGCAAATCTATG 58.349 34.615 0.00 0.00 39.31 2.23
2263 2316 6.430925 TCTTTGATGAAGGAGGTAATGTTGTG 59.569 38.462 0.00 0.00 35.98 3.33
2269 2322 6.542821 TGAAGGAGGTAATGTTGTGATTCTT 58.457 36.000 0.00 0.00 0.00 2.52
2286 2339 1.498865 CTTGGCACGCTCACTCGTTT 61.499 55.000 0.00 0.00 41.21 3.60
2355 2410 5.823045 GTGCCAAGTTCCAGCTATTAGTAAT 59.177 40.000 0.17 0.17 0.00 1.89
2402 2457 4.848357 AGGTGTGGTATGAGATCTTTTGG 58.152 43.478 0.00 0.00 0.00 3.28
2423 2478 4.109050 GGTTTTTCAGTCGTGCAATTCAA 58.891 39.130 0.00 0.00 0.00 2.69
2500 2573 6.834876 TCATGTTGAAGTTCTTTGATCATCG 58.165 36.000 4.17 0.00 0.00 3.84
2502 2575 5.989249 TGTTGAAGTTCTTTGATCATCGTG 58.011 37.500 4.17 0.00 0.00 4.35
2503 2576 4.668576 TGAAGTTCTTTGATCATCGTGC 57.331 40.909 4.17 0.00 0.00 5.34
2525 2598 4.874966 GCTGACACTGCTCAATTATTCTCT 59.125 41.667 0.00 0.00 0.00 3.10
2586 2659 4.517285 AGTAATCTGATGCGTCATGGTTT 58.483 39.130 9.53 3.22 32.98 3.27
2757 2830 3.219281 GGAAACAGGTTAGTTCTGCCAA 58.781 45.455 0.00 0.00 35.78 4.52
2827 2902 9.132521 GAAATGATACTTATGCATATTGGTTGC 57.867 33.333 7.36 4.25 40.55 4.17
2832 2907 2.899122 TGCATATTGGTTGCAGGGG 58.101 52.632 0.00 0.00 44.73 4.79
2833 2908 0.040942 TGCATATTGGTTGCAGGGGT 59.959 50.000 0.00 0.00 44.73 4.95
2834 2909 0.461135 GCATATTGGTTGCAGGGGTG 59.539 55.000 0.00 0.00 39.90 4.61
2835 2910 1.959508 GCATATTGGTTGCAGGGGTGA 60.960 52.381 0.00 0.00 39.90 4.02
2836 2911 2.455557 CATATTGGTTGCAGGGGTGAA 58.544 47.619 0.00 0.00 0.00 3.18
2837 2912 2.917713 TATTGGTTGCAGGGGTGAAT 57.082 45.000 0.00 0.00 0.00 2.57
2838 2913 2.917713 ATTGGTTGCAGGGGTGAATA 57.082 45.000 0.00 0.00 0.00 1.75
2839 2914 1.917872 TTGGTTGCAGGGGTGAATAC 58.082 50.000 0.00 0.00 0.00 1.89
2840 2915 0.039035 TGGTTGCAGGGGTGAATACC 59.961 55.000 0.00 0.00 46.76 2.73
3004 3113 9.614792 AAGGATCTGTAAATACTTGTATGGAAC 57.385 33.333 0.00 0.00 28.30 3.62
3028 3137 2.768492 GGCAAATGAGAGCTGGGCG 61.768 63.158 0.00 0.00 0.00 6.13
3037 3146 0.462047 AGAGCTGGGCGTTATTTCCG 60.462 55.000 0.00 0.00 0.00 4.30
3053 3162 4.198224 CGGGGTGTTGGGTGTGGT 62.198 66.667 0.00 0.00 0.00 4.16
3094 3507 9.066892 ACACACTAAACTGTCAATATTTGATGT 57.933 29.630 0.00 0.00 42.47 3.06
3125 3538 1.885887 GTGCAGTTGGAATGGCTTACA 59.114 47.619 0.00 0.00 0.00 2.41
3236 3649 4.042062 AGTTTGTGGAGGATCTCATCAACA 59.958 41.667 0.00 0.00 38.65 3.33
3279 3694 1.324383 TGTCTGCTAACCTCGTGACA 58.676 50.000 0.00 0.00 32.91 3.58
3294 3709 4.253685 TCGTGACAATTTCCAGAATCCTC 58.746 43.478 0.00 0.00 0.00 3.71
3308 3723 1.047596 ATCCTCTGTGCTCTGCCGAT 61.048 55.000 0.00 0.00 0.00 4.18
3425 3840 4.717877 CACCCAATGCTCATAGTTATCCA 58.282 43.478 0.00 0.00 0.00 3.41
3434 3849 6.878317 TGCTCATAGTTATCCACCTATATGC 58.122 40.000 0.00 0.00 0.00 3.14
3467 3882 1.051008 TGGAACAAGAGCTCTCAGCA 58.949 50.000 18.55 3.99 38.93 4.41
3470 3885 3.080319 GGAACAAGAGCTCTCAGCAATT 58.920 45.455 18.55 5.31 45.56 2.32
3681 4104 7.661437 TCCATGCTAAGTATATGTCCATTTGAC 59.339 37.037 0.00 0.00 44.72 3.18
3808 4231 5.207563 ACTGAACTGATATCAGCGTTGCTC 61.208 45.833 28.86 16.71 46.56 4.26
3818 4241 1.651138 CAGCGTTGCTCTCTACGAAAG 59.349 52.381 0.00 0.00 42.50 2.62
3910 4333 9.379791 CTAGTAACACTATTTTAGGGGTCAAAG 57.620 37.037 0.00 0.00 32.03 2.77
3931 4354 4.282496 AGTTATAGTCCACTCCACTCTGG 58.718 47.826 0.00 0.00 39.43 3.86
4018 4441 2.668212 GTACAGCACAGCGGCCAA 60.668 61.111 2.24 0.00 0.00 4.52
4029 4452 3.179265 CGGCCAAGCACGTAGTCG 61.179 66.667 2.24 0.00 41.61 4.18
4043 4466 2.602878 GTAGTCGAGGCGTTTCATCAA 58.397 47.619 0.00 0.00 0.00 2.57
4278 4701 2.109126 GCCGAAGTCCCACATGAGC 61.109 63.158 0.00 0.00 0.00 4.26
4509 4932 0.802607 GGTCGCTGTCGTCTTCCATC 60.803 60.000 0.00 0.00 36.96 3.51
4545 4968 2.284112 AAGCCCTGCACCCCATTG 60.284 61.111 0.00 0.00 0.00 2.82
4551 4974 0.687098 CCTGCACCCCATTGCCATTA 60.687 55.000 0.00 0.00 42.25 1.90
4571 4994 2.693069 ACCAAGAGCGAATCAGTTCAG 58.307 47.619 0.00 0.00 33.86 3.02
4599 5022 5.120399 GCACTAGAGCTAGAACTAGAGACA 58.880 45.833 21.88 0.00 39.25 3.41
4600 5023 5.763204 GCACTAGAGCTAGAACTAGAGACAT 59.237 44.000 21.88 5.02 39.25 3.06
4637 5060 1.146263 CTCCGGCATTGGTACCTCC 59.854 63.158 14.36 8.09 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.750458 CGACTGTTGAAAGTAATACATGCATTT 59.250 33.333 0.00 0.00 0.00 2.32
2 3 7.243487 CGACTGTTGAAAGTAATACATGCATT 58.757 34.615 0.00 0.00 0.00 3.56
4 5 5.390461 GCGACTGTTGAAAGTAATACATGCA 60.390 40.000 0.00 0.00 0.00 3.96
5 6 5.022021 GCGACTGTTGAAAGTAATACATGC 58.978 41.667 0.00 0.00 0.00 4.06
6 7 6.243551 CAGCGACTGTTGAAAGTAATACATG 58.756 40.000 0.00 0.00 0.00 3.21
7 8 5.351465 CCAGCGACTGTTGAAAGTAATACAT 59.649 40.000 0.00 0.00 0.00 2.29
8 9 4.688879 CCAGCGACTGTTGAAAGTAATACA 59.311 41.667 0.00 0.00 0.00 2.29
9 10 4.092968 CCCAGCGACTGTTGAAAGTAATAC 59.907 45.833 0.00 0.00 0.00 1.89
10 11 4.250464 CCCAGCGACTGTTGAAAGTAATA 58.750 43.478 0.00 0.00 0.00 0.98
11 12 3.074412 CCCAGCGACTGTTGAAAGTAAT 58.926 45.455 0.00 0.00 0.00 1.89
12 13 2.489971 CCCAGCGACTGTTGAAAGTAA 58.510 47.619 0.00 0.00 0.00 2.24
13 14 1.876416 GCCCAGCGACTGTTGAAAGTA 60.876 52.381 0.00 0.00 0.00 2.24
14 15 1.166531 GCCCAGCGACTGTTGAAAGT 61.167 55.000 0.00 0.00 0.00 2.66
15 16 0.886490 AGCCCAGCGACTGTTGAAAG 60.886 55.000 0.00 0.00 0.00 2.62
16 17 0.394938 TAGCCCAGCGACTGTTGAAA 59.605 50.000 0.00 0.00 0.00 2.69
17 18 0.320421 GTAGCCCAGCGACTGTTGAA 60.320 55.000 0.00 0.00 31.72 2.69
18 19 1.292223 GTAGCCCAGCGACTGTTGA 59.708 57.895 0.00 0.00 31.72 3.18
19 20 1.741770 GGTAGCCCAGCGACTGTTG 60.742 63.158 6.19 0.00 34.70 3.33
20 21 2.663196 GGTAGCCCAGCGACTGTT 59.337 61.111 6.19 0.00 34.70 3.16
21 22 3.391382 GGGTAGCCCAGCGACTGT 61.391 66.667 0.00 0.00 44.65 3.55
22 23 4.514577 CGGGTAGCCCAGCGACTG 62.515 72.222 5.12 0.00 45.83 3.51
28 29 0.463116 ATAAAACGCGGGTAGCCCAG 60.463 55.000 12.47 1.88 45.83 4.45
29 30 0.035247 AATAAAACGCGGGTAGCCCA 60.035 50.000 12.47 0.00 45.83 5.36
30 31 1.952193 TAATAAAACGCGGGTAGCCC 58.048 50.000 12.47 0.00 44.76 5.19
31 32 4.309933 AGTATAATAAAACGCGGGTAGCC 58.690 43.478 12.47 0.00 44.76 3.93
32 33 5.912360 AAGTATAATAAAACGCGGGTAGC 57.088 39.130 12.47 0.00 43.95 3.58
33 34 7.378461 TCGTAAAGTATAATAAAACGCGGGTAG 59.622 37.037 12.47 0.00 0.00 3.18
34 35 7.197017 TCGTAAAGTATAATAAAACGCGGGTA 58.803 34.615 12.47 0.00 0.00 3.69
35 36 6.039616 TCGTAAAGTATAATAAAACGCGGGT 58.960 36.000 12.47 0.00 0.00 5.28
36 37 6.509317 TCGTAAAGTATAATAAAACGCGGG 57.491 37.500 12.47 0.00 0.00 6.13
37 38 6.567512 GCTTCGTAAAGTATAATAAAACGCGG 59.432 38.462 12.47 0.00 34.79 6.46
38 39 6.293740 CGCTTCGTAAAGTATAATAAAACGCG 59.706 38.462 3.53 3.53 34.79 6.01
39 40 7.329582 TCGCTTCGTAAAGTATAATAAAACGC 58.670 34.615 0.00 0.00 34.79 4.84
40 41 7.994894 CCTCGCTTCGTAAAGTATAATAAAACG 59.005 37.037 0.00 0.00 34.79 3.60
41 42 8.271487 CCCTCGCTTCGTAAAGTATAATAAAAC 58.729 37.037 0.00 0.00 34.79 2.43
42 43 7.981225 ACCCTCGCTTCGTAAAGTATAATAAAA 59.019 33.333 0.00 0.00 34.79 1.52
43 44 7.491682 ACCCTCGCTTCGTAAAGTATAATAAA 58.508 34.615 0.00 0.00 34.79 1.40
44 45 7.042797 ACCCTCGCTTCGTAAAGTATAATAA 57.957 36.000 0.00 0.00 34.79 1.40
45 46 6.639632 ACCCTCGCTTCGTAAAGTATAATA 57.360 37.500 0.00 0.00 34.79 0.98
46 47 5.526506 ACCCTCGCTTCGTAAAGTATAAT 57.473 39.130 0.00 0.00 34.79 1.28
47 48 4.989279 ACCCTCGCTTCGTAAAGTATAA 57.011 40.909 0.00 0.00 34.79 0.98
48 49 4.989279 AACCCTCGCTTCGTAAAGTATA 57.011 40.909 0.00 0.00 34.79 1.47
49 50 3.881937 AACCCTCGCTTCGTAAAGTAT 57.118 42.857 0.00 0.00 34.79 2.12
50 51 3.578688 GAAACCCTCGCTTCGTAAAGTA 58.421 45.455 0.00 0.00 34.79 2.24
51 52 2.410939 GAAACCCTCGCTTCGTAAAGT 58.589 47.619 0.00 0.00 34.79 2.66
52 53 1.389106 CGAAACCCTCGCTTCGTAAAG 59.611 52.381 0.00 0.00 41.49 1.85
53 54 1.421382 CGAAACCCTCGCTTCGTAAA 58.579 50.000 0.00 0.00 41.49 2.01
54 55 3.111536 CGAAACCCTCGCTTCGTAA 57.888 52.632 0.00 0.00 41.49 3.18
55 56 4.874534 CGAAACCCTCGCTTCGTA 57.125 55.556 0.00 0.00 41.49 3.43
72 73 4.874977 GTCGCGGCTGCCCTAGAC 62.875 72.222 14.12 15.47 38.08 2.59
154 156 9.628500 AAAAACATAGAACTCTTGAAGGTAAGT 57.372 29.630 0.00 0.00 0.00 2.24
156 158 8.770828 CGAAAAACATAGAACTCTTGAAGGTAA 58.229 33.333 0.00 0.00 0.00 2.85
157 159 7.929785 ACGAAAAACATAGAACTCTTGAAGGTA 59.070 33.333 0.00 0.00 0.00 3.08
159 161 7.042051 TGACGAAAAACATAGAACTCTTGAAGG 60.042 37.037 0.00 0.00 0.00 3.46
237 243 8.486383 CGAAAACTCTTCAATCTCATATAGCAG 58.514 37.037 0.00 0.00 0.00 4.24
241 247 7.926555 GGACCGAAAACTCTTCAATCTCATATA 59.073 37.037 0.00 0.00 0.00 0.86
242 248 6.763610 GGACCGAAAACTCTTCAATCTCATAT 59.236 38.462 0.00 0.00 0.00 1.78
243 249 6.070767 AGGACCGAAAACTCTTCAATCTCATA 60.071 38.462 0.00 0.00 0.00 2.15
252 258 4.685165 GTCTACAAGGACCGAAAACTCTTC 59.315 45.833 0.00 0.00 0.00 2.87
253 259 4.502777 GGTCTACAAGGACCGAAAACTCTT 60.503 45.833 0.00 0.00 44.94 2.85
290 296 7.809546 TGACACACCAACATAAACTCATAAA 57.190 32.000 0.00 0.00 0.00 1.40
292 298 7.283354 TGTTTGACACACCAACATAAACTCATA 59.717 33.333 0.00 0.00 0.00 2.15
337 345 8.249638 TCGATGCAAGATTTCAATTCCATAAAA 58.750 29.630 0.00 0.00 0.00 1.52
338 346 7.701924 GTCGATGCAAGATTTCAATTCCATAAA 59.298 33.333 0.00 0.00 0.00 1.40
341 349 5.125900 TGTCGATGCAAGATTTCAATTCCAT 59.874 36.000 0.00 0.00 0.00 3.41
346 354 5.823209 TGATGTCGATGCAAGATTTCAAT 57.177 34.783 0.00 0.00 0.00 2.57
357 365 3.763097 TTTTCACCATGATGTCGATGC 57.237 42.857 0.00 0.00 0.00 3.91
408 416 2.168458 TACTTGGACCGGGATGATCA 57.832 50.000 6.32 0.00 0.00 2.92
420 429 4.935205 CCTTGATTGACGAACATACTTGGA 59.065 41.667 0.00 0.00 0.00 3.53
428 437 2.151202 GGAAGCCTTGATTGACGAACA 58.849 47.619 0.00 0.00 0.00 3.18
433 442 3.549794 AGCATAGGAAGCCTTGATTGAC 58.450 45.455 0.00 0.00 34.61 3.18
449 458 5.221402 TGTTGAGTTGCCATTGAAAAGCATA 60.221 36.000 0.00 0.00 36.20 3.14
452 461 3.245990 GTGTTGAGTTGCCATTGAAAAGC 59.754 43.478 0.00 0.00 0.00 3.51
453 462 4.685924 AGTGTTGAGTTGCCATTGAAAAG 58.314 39.130 0.00 0.00 0.00 2.27
458 467 6.900568 TTTAAAAGTGTTGAGTTGCCATTG 57.099 33.333 0.00 0.00 0.00 2.82
459 468 7.913674 TTTTTAAAAGTGTTGAGTTGCCATT 57.086 28.000 0.14 0.00 0.00 3.16
484 496 8.618677 TCTCTGTCGTACTCGTAATAATGATTT 58.381 33.333 0.00 0.00 38.33 2.17
485 497 8.068977 GTCTCTGTCGTACTCGTAATAATGATT 58.931 37.037 0.00 0.00 38.33 2.57
488 500 6.846786 CAGTCTCTGTCGTACTCGTAATAATG 59.153 42.308 0.00 0.00 38.33 1.90
492 504 4.502016 TCAGTCTCTGTCGTACTCGTAAT 58.498 43.478 0.00 0.00 38.33 1.89
493 505 3.917988 TCAGTCTCTGTCGTACTCGTAA 58.082 45.455 0.00 0.00 38.33 3.18
496 508 5.660629 AATATCAGTCTCTGTCGTACTCG 57.339 43.478 0.00 0.00 38.55 4.18
497 509 7.699566 AGAAAATATCAGTCTCTGTCGTACTC 58.300 38.462 0.00 0.00 32.61 2.59
498 510 7.201750 GGAGAAAATATCAGTCTCTGTCGTACT 60.202 40.741 9.08 0.00 38.29 2.73
499 511 6.913673 GGAGAAAATATCAGTCTCTGTCGTAC 59.086 42.308 9.08 0.00 38.29 3.67
501 513 5.419155 TGGAGAAAATATCAGTCTCTGTCGT 59.581 40.000 9.08 0.00 38.29 4.34
502 514 5.895928 TGGAGAAAATATCAGTCTCTGTCG 58.104 41.667 9.08 0.00 38.29 4.35
503 515 6.872920 ACTGGAGAAAATATCAGTCTCTGTC 58.127 40.000 9.08 0.00 38.29 3.51
504 516 6.865834 ACTGGAGAAAATATCAGTCTCTGT 57.134 37.500 9.08 6.80 38.29 3.41
510 522 6.096001 GCAATTGGACTGGAGAAAATATCAGT 59.904 38.462 7.72 0.00 42.37 3.41
511 523 6.095860 TGCAATTGGACTGGAGAAAATATCAG 59.904 38.462 7.72 0.00 0.00 2.90
512 524 5.951148 TGCAATTGGACTGGAGAAAATATCA 59.049 36.000 7.72 0.00 0.00 2.15
513 525 6.455360 TGCAATTGGACTGGAGAAAATATC 57.545 37.500 7.72 0.00 0.00 1.63
514 526 5.163478 GCTGCAATTGGACTGGAGAAAATAT 60.163 40.000 7.72 0.00 34.40 1.28
515 527 4.158394 GCTGCAATTGGACTGGAGAAAATA 59.842 41.667 7.72 0.00 34.40 1.40
516 528 3.056322 GCTGCAATTGGACTGGAGAAAAT 60.056 43.478 7.72 0.00 34.40 1.82
518 530 1.888512 GCTGCAATTGGACTGGAGAAA 59.111 47.619 7.72 0.00 34.40 2.52
519 531 1.538047 GCTGCAATTGGACTGGAGAA 58.462 50.000 7.72 0.00 34.40 2.87
520 532 0.322816 GGCTGCAATTGGACTGGAGA 60.323 55.000 7.72 0.00 34.40 3.71
540 562 2.074576 GTCCCAAGACTTCGGTAAAGC 58.925 52.381 0.00 0.00 40.10 3.51
578 604 1.227089 ACCTGCTTCGCGCTATCAG 60.227 57.895 5.56 7.31 40.11 2.90
584 610 1.725973 GAAAACACCTGCTTCGCGC 60.726 57.895 0.00 0.00 39.77 6.86
663 689 7.031975 GGTCACTGATTTGGATCTTCAAATTC 58.968 38.462 10.19 5.99 44.48 2.17
664 690 6.723052 AGGTCACTGATTTGGATCTTCAAATT 59.277 34.615 10.19 0.00 44.48 1.82
665 691 6.251471 AGGTCACTGATTTGGATCTTCAAAT 58.749 36.000 9.01 9.01 46.36 2.32
666 692 5.634118 AGGTCACTGATTTGGATCTTCAAA 58.366 37.500 0.44 0.44 40.37 2.69
667 693 5.246981 AGGTCACTGATTTGGATCTTCAA 57.753 39.130 0.00 0.00 33.28 2.69
668 694 4.916041 AGGTCACTGATTTGGATCTTCA 57.084 40.909 0.00 0.00 33.28 3.02
696 723 4.380841 TGAAATCTGCCGTACTCGTAAT 57.619 40.909 0.00 0.00 35.01 1.89
700 727 5.712217 TTTTATGAAATCTGCCGTACTCG 57.288 39.130 0.00 0.00 0.00 4.18
721 748 2.261361 GCCCGGCGATTGCTTTTT 59.739 55.556 9.30 0.00 42.25 1.94
722 749 2.676471 AGCCCGGCGATTGCTTTT 60.676 55.556 9.30 0.00 42.25 2.27
723 750 3.443045 CAGCCCGGCGATTGCTTT 61.443 61.111 9.30 0.00 42.25 3.51
775 802 0.951040 AAGAAGCGGCTCCTGTTTCG 60.951 55.000 1.45 0.00 0.00 3.46
843 870 2.106332 CTCCCGATACGGTGGCAC 59.894 66.667 9.70 9.70 46.80 5.01
844 871 3.151710 CCTCCCGATACGGTGGCA 61.152 66.667 9.28 0.00 46.80 4.92
848 875 1.803366 GATTCGCCTCCCGATACGGT 61.803 60.000 9.28 0.00 46.80 4.83
854 881 1.535833 GATAGAGATTCGCCTCCCGA 58.464 55.000 0.00 0.00 45.77 5.14
862 890 0.244994 CCGGCCTGGATAGAGATTCG 59.755 60.000 7.77 0.00 42.00 3.34
911 940 4.467107 AGGGAGGGAGAGTCGGGC 62.467 72.222 0.00 0.00 0.00 6.13
916 945 4.467107 GGCCGAGGGAGGGAGAGT 62.467 72.222 0.00 0.00 0.00 3.24
926 955 3.798511 GAAGGAAGGGGGCCGAGG 61.799 72.222 0.00 0.00 0.00 4.63
976 1013 4.287552 ACTAGTAGTAACTGGTGGATGGG 58.712 47.826 0.00 0.00 44.89 4.00
977 1014 4.954202 TGACTAGTAGTAACTGGTGGATGG 59.046 45.833 1.88 0.00 46.39 3.51
978 1015 5.417894 TGTGACTAGTAGTAACTGGTGGATG 59.582 44.000 17.21 0.00 46.39 3.51
979 1016 5.577100 TGTGACTAGTAGTAACTGGTGGAT 58.423 41.667 17.21 0.00 46.39 3.41
997 1034 3.418068 GCTGGCTGCGTCTGTGAC 61.418 66.667 0.00 0.00 0.00 3.67
1028 1065 3.924576 AAAAATGAGGGGGATCGGG 57.075 52.632 0.00 0.00 0.00 5.14
1475 1523 5.715070 TGCCCAACTTAATAATTTTGACGG 58.285 37.500 0.00 0.00 0.00 4.79
1496 1545 8.398878 ACTACTTACTACTGATCCTAGAATGC 57.601 38.462 0.00 0.00 0.00 3.56
1532 1583 6.870965 GCGGATCATATCAGATAACTTGAACT 59.129 38.462 0.00 0.00 0.00 3.01
1542 1593 3.908643 ATGCAGCGGATCATATCAGAT 57.091 42.857 0.00 0.00 0.00 2.90
1594 1645 9.990360 TCAGCGTAACTTTTGGATATATCAATA 57.010 29.630 14.60 0.00 0.00 1.90
1756 1808 2.625314 TCCTCTGGCATACTCTTGATCG 59.375 50.000 0.00 0.00 0.00 3.69
1820 1872 0.107654 GGCCCACTCTCCACATGTAC 60.108 60.000 0.00 0.00 0.00 2.90
1886 1938 4.212847 CAGACTTCCACATCACAGTGAAAG 59.787 45.833 7.50 8.73 42.05 2.62
1929 1981 2.290641 GACGCACAAATAATGGCTAGGG 59.709 50.000 0.00 0.00 0.00 3.53
2051 2103 7.218614 ACCTCAATTGCAGAAATCATTTTTGA 58.781 30.769 4.83 0.00 0.00 2.69
2097 2149 7.934855 AACTGCAGAAAACATCATCTTAGAT 57.065 32.000 23.35 0.00 0.00 1.98
2104 2157 8.192774 CCATGTATAAACTGCAGAAAACATCAT 58.807 33.333 23.35 12.82 0.00 2.45
2146 2199 6.206634 TGTGTCCAACCAACTTCTGAATATTC 59.793 38.462 8.60 8.60 0.00 1.75
2263 2316 0.723981 GAGTGAGCGTGCCAAGAATC 59.276 55.000 0.00 0.00 0.00 2.52
2269 2322 1.522806 AAAACGAGTGAGCGTGCCA 60.523 52.632 0.00 0.00 44.86 4.92
2321 2376 3.383185 TGGAACTTGGCACTGTTTTAAGG 59.617 43.478 6.53 0.00 0.00 2.69
2355 2410 8.423906 TTTAAACCCACTAAGGCATTGAAATA 57.576 30.769 0.00 0.00 35.39 1.40
2402 2457 4.560819 TGTTGAATTGCACGACTGAAAAAC 59.439 37.500 0.00 0.00 0.00 2.43
2471 2544 9.897744 TGATCAAAGAACTTCAACATGAATAAC 57.102 29.630 0.00 0.00 35.59 1.89
2500 2573 4.394300 AGAATAATTGAGCAGTGTCAGCAC 59.606 41.667 0.00 0.00 45.57 4.40
2502 2575 4.874966 AGAGAATAATTGAGCAGTGTCAGC 59.125 41.667 0.00 0.00 0.00 4.26
2503 2576 6.370994 ACAAGAGAATAATTGAGCAGTGTCAG 59.629 38.462 0.00 0.00 0.00 3.51
2525 2598 2.156098 GTGCGGTCCCTATTGAAACAA 58.844 47.619 0.00 0.00 0.00 2.83
2586 2659 0.395586 AGCAAACACAGTGCCCTCAA 60.396 50.000 0.00 0.00 43.27 3.02
2638 2711 2.104111 TGGAAATCTACTACGGCCATGG 59.896 50.000 7.63 7.63 0.00 3.66
2817 2892 2.917713 TTCACCCCTGCAACCAATAT 57.082 45.000 0.00 0.00 0.00 1.28
2818 2893 2.917713 ATTCACCCCTGCAACCAATA 57.082 45.000 0.00 0.00 0.00 1.90
2819 2894 2.456577 GTATTCACCCCTGCAACCAAT 58.543 47.619 0.00 0.00 0.00 3.16
2820 2895 1.549037 GGTATTCACCCCTGCAACCAA 60.549 52.381 0.00 0.00 39.11 3.67
2821 2896 0.039035 GGTATTCACCCCTGCAACCA 59.961 55.000 0.00 0.00 39.11 3.67
2822 2897 0.039035 TGGTATTCACCCCTGCAACC 59.961 55.000 0.00 0.00 45.11 3.77
2823 2898 1.271926 ACTGGTATTCACCCCTGCAAC 60.272 52.381 0.00 0.00 45.11 4.17
2824 2899 1.072266 ACTGGTATTCACCCCTGCAA 58.928 50.000 0.00 0.00 45.11 4.08
2825 2900 1.072266 AACTGGTATTCACCCCTGCA 58.928 50.000 0.00 0.00 45.11 4.41
2826 2901 2.215942 AAACTGGTATTCACCCCTGC 57.784 50.000 0.00 0.00 45.11 4.85
2827 2902 5.505780 TCATAAAACTGGTATTCACCCCTG 58.494 41.667 0.00 0.00 45.11 4.45
2828 2903 5.789574 TCATAAAACTGGTATTCACCCCT 57.210 39.130 0.00 0.00 45.11 4.79
2829 2904 8.706322 AATATCATAAAACTGGTATTCACCCC 57.294 34.615 0.00 0.00 45.11 4.95
2880 2988 9.774742 CAACTATTGCAGGAAAAATAGTACTTC 57.225 33.333 0.00 0.00 44.80 3.01
2888 2996 7.444299 ACAACATCAACTATTGCAGGAAAAAT 58.556 30.769 0.00 0.00 0.00 1.82
2986 3095 8.610035 GCCTAACAGTTCCATACAAGTATTTAC 58.390 37.037 0.00 0.00 0.00 2.01
3004 3113 2.681848 CCAGCTCTCATTTGCCTAACAG 59.318 50.000 0.00 0.00 0.00 3.16
3028 3137 1.179152 CCCAACACCCCGGAAATAAC 58.821 55.000 0.73 0.00 0.00 1.89
3037 3146 1.074248 CTACCACACCCAACACCCC 59.926 63.158 0.00 0.00 0.00 4.95
3053 3162 1.872952 GTGTGTGCACATGCTTCACTA 59.127 47.619 24.69 12.92 43.97 2.74
3075 3184 8.181904 AGGAACACATCAAATATTGACAGTTT 57.818 30.769 0.00 0.00 43.48 2.66
3076 3185 7.765695 AGGAACACATCAAATATTGACAGTT 57.234 32.000 0.00 1.52 43.48 3.16
3077 3186 7.765695 AAGGAACACATCAAATATTGACAGT 57.234 32.000 0.00 0.00 43.48 3.55
3081 3494 8.298854 CACAGAAAGGAACACATCAAATATTGA 58.701 33.333 0.00 0.00 45.01 2.57
3094 3507 2.023673 CCAACTGCACAGAAAGGAACA 58.976 47.619 4.31 0.00 0.00 3.18
3125 3538 2.375174 TCCAGCTAAACATTCACCACCT 59.625 45.455 0.00 0.00 0.00 4.00
3215 3628 4.042062 ACTGTTGATGAGATCCTCCACAAA 59.958 41.667 0.00 0.00 31.12 2.83
3236 3649 3.757493 CGTGGGAACTGAGAGTACTTACT 59.243 47.826 0.00 0.00 39.71 2.24
3294 3709 2.133553 CAATAGATCGGCAGAGCACAG 58.866 52.381 4.63 0.00 34.73 3.66
3425 3840 2.203728 TCCCCGGCGCATATAGGT 60.204 61.111 10.83 0.00 0.00 3.08
3434 3849 2.727392 TTCCACATACTCCCCGGCG 61.727 63.158 0.00 0.00 0.00 6.46
3464 3879 5.583932 ACCTTCCCTTTCAGATTAATTGCT 58.416 37.500 0.00 0.00 0.00 3.91
3467 3882 5.779771 TGCAACCTTCCCTTTCAGATTAATT 59.220 36.000 0.00 0.00 0.00 1.40
3470 3885 4.079253 GTGCAACCTTCCCTTTCAGATTA 58.921 43.478 0.00 0.00 0.00 1.75
3808 4231 3.849911 TGCAAGGATGACTTTCGTAGAG 58.150 45.455 0.00 0.00 37.29 2.43
3818 4241 3.244976 CAAAACGGATTGCAAGGATGAC 58.755 45.455 4.94 0.00 0.00 3.06
3910 4333 3.385111 CCCAGAGTGGAGTGGACTATAAC 59.615 52.174 0.00 0.00 40.96 1.89
4018 4441 2.138656 AAACGCCTCGACTACGTGCT 62.139 55.000 0.00 0.00 40.44 4.40
4029 4452 3.498397 TCTGAAGTTTGATGAAACGCCTC 59.502 43.478 1.98 2.17 45.34 4.70
4043 4466 2.654863 CCAACAACTGGGTCTGAAGTT 58.345 47.619 0.00 0.00 42.17 2.66
4155 4578 0.666577 CCTTCTCGTGGGTCGACAAC 60.667 60.000 18.91 13.76 44.01 3.32
4156 4579 0.824595 TCCTTCTCGTGGGTCGACAA 60.825 55.000 18.91 1.40 44.01 3.18
4157 4580 1.228337 TCCTTCTCGTGGGTCGACA 60.228 57.895 18.91 0.00 44.01 4.35
4278 4701 2.124983 CCCATCCTGCTCCACGTG 60.125 66.667 9.08 9.08 0.00 4.49
4335 4758 1.299926 GTGCTTCGACACCGTGTCT 60.300 57.895 25.37 0.00 44.85 3.41
4496 4919 2.648593 TCGGTGATGGAAGACGACA 58.351 52.632 0.00 0.00 0.00 4.35
4509 4932 1.664873 TCCTCTACATCTCGTCGGTG 58.335 55.000 0.00 0.00 0.00 4.94
4545 4968 2.288666 TGATTCGCTCTTGGTAATGGC 58.711 47.619 0.00 0.00 0.00 4.40
4551 4974 2.300152 TCTGAACTGATTCGCTCTTGGT 59.700 45.455 0.00 0.00 37.69 3.67
4571 4994 2.420722 AGTTCTAGCTCTAGTGCACGTC 59.579 50.000 18.36 0.01 34.84 4.34
4599 5022 4.841246 GGAGGAATGTCTGTCCCTGTATAT 59.159 45.833 0.00 0.00 35.59 0.86
4600 5023 4.223953 GGAGGAATGTCTGTCCCTGTATA 58.776 47.826 0.00 0.00 35.59 1.47


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

AutoCloner maintained by Alex Coulton.