Multiple sequence alignment - TraesCS4D01G308100

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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 TraesCS4D01G308100 chr4D 100.000 2902 0 0 501 3402 476230197 476227296 0.000000e+00 5360.0
1 TraesCS4D01G308100 chr4D 95.604 637 27 1 2767 3402 476222464 476221828 0.000000e+00 1020.0
2 TraesCS4D01G308100 chr4D 91.379 638 44 9 2767 3402 15324066 15324694 0.000000e+00 863.0
3 TraesCS4D01G308100 chr4D 100.000 173 0 0 1 173 476230697 476230525 1.520000e-83 320.0
4 TraesCS4D01G308100 chr4B 94.255 1793 52 16 872 2641 600606278 600604514 0.000000e+00 2693.0
5 TraesCS4D01G308100 chr4B 93.938 1798 61 14 872 2641 600517888 600516111 0.000000e+00 2673.0
6 TraesCS4D01G308100 chr4B 95.184 789 24 4 1654 2433 600599336 600598553 0.000000e+00 1234.0
7 TraesCS4D01G308100 chr4B 92.587 634 41 3 2767 3399 191195863 191196491 0.000000e+00 905.0
8 TraesCS4D01G308100 chr4B 91.057 246 16 1 596 841 600518125 600517886 9.100000e-86 327.0
9 TraesCS4D01G308100 chr4B 94.340 106 3 3 738 841 600606380 600606276 3.510000e-35 159.0
10 TraesCS4D01G308100 chr4B 95.122 41 2 0 1072 1112 600606058 600606018 7.880000e-07 65.8
11 TraesCS4D01G308100 chr4A 91.406 1536 62 31 912 2434 683443320 683441842 0.000000e+00 2041.0
12 TraesCS4D01G308100 chr4A 92.344 209 12 3 2436 2641 683441798 683441591 9.230000e-76 294.0
13 TraesCS4D01G308100 chr4A 96.063 127 5 0 2641 2767 683440688 683440562 1.240000e-49 207.0
14 TraesCS4D01G308100 chr2B 81.415 1329 193 40 1110 2413 24905696 24906995 0.000000e+00 1037.0
15 TraesCS4D01G308100 chr2B 80.669 1345 187 46 1110 2410 24889254 24890569 0.000000e+00 976.0
16 TraesCS4D01G308100 chr2B 80.522 1340 196 43 1110 2408 24882778 24884093 0.000000e+00 968.0
17 TraesCS4D01G308100 chr2A 80.422 1328 196 41 1120 2406 15906134 15904830 0.000000e+00 953.0
18 TraesCS4D01G308100 chr2A 80.964 851 121 23 1596 2409 15642268 15643114 1.330000e-178 636.0
19 TraesCS4D01G308100 chr2A 88.860 386 37 5 1116 1501 15641779 15642158 1.430000e-128 470.0
20 TraesCS4D01G308100 chr2A 82.759 406 64 4 1110 1515 14892708 14892309 1.160000e-94 357.0
21 TraesCS4D01G308100 chr5D 93.398 621 35 5 2768 3386 552628752 552628136 0.000000e+00 915.0
22 TraesCS4D01G308100 chr5D 100.000 36 0 0 79 114 315628661 315628626 2.190000e-07 67.6
23 TraesCS4D01G308100 chr6D 92.163 638 44 4 2767 3402 38487210 38486577 0.000000e+00 896.0
24 TraesCS4D01G308100 chr1D 91.993 612 42 3 2767 3377 339369530 339370135 0.000000e+00 852.0
25 TraesCS4D01G308100 chr1D 90.779 629 48 7 2767 3392 477413943 477414564 0.000000e+00 832.0
26 TraesCS4D01G308100 chr3D 90.654 642 45 9 2767 3402 589773177 589772545 0.000000e+00 839.0
27 TraesCS4D01G308100 chr3D 90.267 637 53 4 2767 3402 45022865 45023493 0.000000e+00 824.0
28 TraesCS4D01G308100 chr2D 80.471 850 127 22 1596 2409 13632964 13633810 6.240000e-172 614.0
29 TraesCS4D01G308100 chrUn 84.404 327 48 2 1110 1436 18084747 18085070 5.480000e-83 318.0
30 TraesCS4D01G308100 chr7D 100.000 34 0 0 501 534 535900919 535900952 2.830000e-06 63.9


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 TraesCS4D01G308100 chr4D 476227296 476230697 3401 True 2840.000000 5360 100.000000 1 3402 2 chr4D.!!$R2 3401
1 TraesCS4D01G308100 chr4D 476221828 476222464 636 True 1020.000000 1020 95.604000 2767 3402 1 chr4D.!!$R1 635
2 TraesCS4D01G308100 chr4D 15324066 15324694 628 False 863.000000 863 91.379000 2767 3402 1 chr4D.!!$F1 635
3 TraesCS4D01G308100 chr4B 600516111 600518125 2014 True 1500.000000 2673 92.497500 596 2641 2 chr4B.!!$R2 2045
4 TraesCS4D01G308100 chr4B 600598553 600599336 783 True 1234.000000 1234 95.184000 1654 2433 1 chr4B.!!$R1 779
5 TraesCS4D01G308100 chr4B 600604514 600606380 1866 True 972.600000 2693 94.572333 738 2641 3 chr4B.!!$R3 1903
6 TraesCS4D01G308100 chr4B 191195863 191196491 628 False 905.000000 905 92.587000 2767 3399 1 chr4B.!!$F1 632
7 TraesCS4D01G308100 chr4A 683440562 683443320 2758 True 847.333333 2041 93.271000 912 2767 3 chr4A.!!$R1 1855
8 TraesCS4D01G308100 chr2B 24905696 24906995 1299 False 1037.000000 1037 81.415000 1110 2413 1 chr2B.!!$F3 1303
9 TraesCS4D01G308100 chr2B 24889254 24890569 1315 False 976.000000 976 80.669000 1110 2410 1 chr2B.!!$F2 1300
10 TraesCS4D01G308100 chr2B 24882778 24884093 1315 False 968.000000 968 80.522000 1110 2408 1 chr2B.!!$F1 1298
11 TraesCS4D01G308100 chr2A 15904830 15906134 1304 True 953.000000 953 80.422000 1120 2406 1 chr2A.!!$R2 1286
12 TraesCS4D01G308100 chr2A 15641779 15643114 1335 False 553.000000 636 84.912000 1116 2409 2 chr2A.!!$F1 1293
13 TraesCS4D01G308100 chr5D 552628136 552628752 616 True 915.000000 915 93.398000 2768 3386 1 chr5D.!!$R2 618
14 TraesCS4D01G308100 chr6D 38486577 38487210 633 True 896.000000 896 92.163000 2767 3402 1 chr6D.!!$R1 635
15 TraesCS4D01G308100 chr1D 339369530 339370135 605 False 852.000000 852 91.993000 2767 3377 1 chr1D.!!$F1 610
16 TraesCS4D01G308100 chr1D 477413943 477414564 621 False 832.000000 832 90.779000 2767 3392 1 chr1D.!!$F2 625
17 TraesCS4D01G308100 chr3D 589772545 589773177 632 True 839.000000 839 90.654000 2767 3402 1 chr3D.!!$R1 635
18 TraesCS4D01G308100 chr3D 45022865 45023493 628 False 824.000000 824 90.267000 2767 3402 1 chr3D.!!$F1 635
19 TraesCS4D01G308100 chr2D 13632964 13633810 846 False 614.000000 614 80.471000 1596 2409 1 chr2D.!!$F1 813

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
650 651 0.178068 AGGAGCGATGGCGTTAACAT 59.822 50.0 6.39 0.0 46.35 2.71 F
854 857 0.249955 CCAATTGGATGTTGGGCACC 59.750 55.0 20.50 0.0 44.83 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2161 0.252148 TGCCCTCCATTTTCATGCCA 60.252 50.0 0.00 0.00 0.00 4.92 R
2662 3707 0.747283 CCAAAGCTAGCTGGGCTCAG 60.747 60.0 20.16 10.01 40.44 3.35 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
17 18 2.493973 CTCCTCTCTGTCGCCTGC 59.506 66.667 0.00 0.00 0.00 4.85
18 19 2.036414 TCCTCTCTGTCGCCTGCT 59.964 61.111 0.00 0.00 0.00 4.24
19 20 2.003658 CTCCTCTCTGTCGCCTGCTC 62.004 65.000 0.00 0.00 0.00 4.26
20 21 2.493973 CTCTCTGTCGCCTGCTCC 59.506 66.667 0.00 0.00 0.00 4.70
21 22 3.408501 CTCTCTGTCGCCTGCTCCG 62.409 68.421 0.00 0.00 0.00 4.63
22 23 3.753434 CTCTGTCGCCTGCTCCGT 61.753 66.667 0.00 0.00 0.00 4.69
23 24 3.691744 CTCTGTCGCCTGCTCCGTC 62.692 68.421 0.00 0.00 0.00 4.79
44 45 4.498520 CGCCATGAGCTCCGTCGT 62.499 66.667 12.15 0.00 40.39 4.34
45 46 2.887568 GCCATGAGCTCCGTCGTG 60.888 66.667 12.15 0.00 38.99 4.35
46 47 2.887568 CCATGAGCTCCGTCGTGC 60.888 66.667 12.15 0.00 32.84 5.34
47 48 3.250323 CATGAGCTCCGTCGTGCG 61.250 66.667 12.15 0.00 40.95 5.34
53 54 4.794439 CTCCGTCGTGCGCCATCA 62.794 66.667 4.18 0.00 39.71 3.07
54 55 4.794439 TCCGTCGTGCGCCATCAG 62.794 66.667 4.18 0.00 39.71 2.90
55 56 4.794439 CCGTCGTGCGCCATCAGA 62.794 66.667 4.18 0.00 39.71 3.27
56 57 2.583319 CGTCGTGCGCCATCAGAT 60.583 61.111 4.18 0.00 0.00 2.90
57 58 2.580470 CGTCGTGCGCCATCAGATC 61.580 63.158 4.18 0.00 0.00 2.75
58 59 2.106938 TCGTGCGCCATCAGATCC 59.893 61.111 4.18 0.00 0.00 3.36
59 60 3.333189 CGTGCGCCATCAGATCCG 61.333 66.667 4.18 0.00 0.00 4.18
60 61 3.643978 GTGCGCCATCAGATCCGC 61.644 66.667 4.18 15.03 45.99 5.54
61 62 4.916293 TGCGCCATCAGATCCGCC 62.916 66.667 17.82 5.49 45.28 6.13
63 64 3.933722 CGCCATCAGATCCGCCCT 61.934 66.667 0.00 0.00 0.00 5.19
64 65 2.574018 CGCCATCAGATCCGCCCTA 61.574 63.158 0.00 0.00 0.00 3.53
65 66 1.004440 GCCATCAGATCCGCCCTAC 60.004 63.158 0.00 0.00 0.00 3.18
66 67 1.290324 CCATCAGATCCGCCCTACG 59.710 63.158 0.00 0.00 43.15 3.51
67 68 1.373497 CATCAGATCCGCCCTACGC 60.373 63.158 0.00 0.00 41.76 4.42
68 69 1.531840 ATCAGATCCGCCCTACGCT 60.532 57.895 0.00 0.00 41.76 5.07
69 70 1.810606 ATCAGATCCGCCCTACGCTG 61.811 60.000 0.00 0.00 41.76 5.18
70 71 3.917760 AGATCCGCCCTACGCTGC 61.918 66.667 0.00 0.00 41.76 5.25
71 72 4.971125 GATCCGCCCTACGCTGCC 62.971 72.222 0.00 0.00 41.76 4.85
76 77 2.440247 GCCCTACGCTGCCCAAAT 60.440 61.111 0.00 0.00 0.00 2.32
77 78 2.774799 GCCCTACGCTGCCCAAATG 61.775 63.158 0.00 0.00 0.00 2.32
78 79 1.077787 CCCTACGCTGCCCAAATGA 60.078 57.895 0.00 0.00 0.00 2.57
79 80 1.376609 CCCTACGCTGCCCAAATGAC 61.377 60.000 0.00 0.00 0.00 3.06
80 81 1.705337 CCTACGCTGCCCAAATGACG 61.705 60.000 0.00 0.00 0.00 4.35
81 82 2.309764 CTACGCTGCCCAAATGACGC 62.310 60.000 0.00 0.00 0.00 5.19
82 83 4.481112 CGCTGCCCAAATGACGCC 62.481 66.667 0.00 0.00 0.00 5.68
83 84 4.481112 GCTGCCCAAATGACGCCG 62.481 66.667 0.00 0.00 0.00 6.46
84 85 4.481112 CTGCCCAAATGACGCCGC 62.481 66.667 0.00 0.00 0.00 6.53
86 87 4.179579 GCCCAAATGACGCCGCTC 62.180 66.667 0.00 0.00 0.00 5.03
87 88 3.508840 CCCAAATGACGCCGCTCC 61.509 66.667 0.00 0.00 0.00 4.70
88 89 3.508840 CCAAATGACGCCGCTCCC 61.509 66.667 0.00 0.00 0.00 4.30
89 90 3.508840 CAAATGACGCCGCTCCCC 61.509 66.667 0.00 0.00 0.00 4.81
90 91 4.796495 AAATGACGCCGCTCCCCC 62.796 66.667 0.00 0.00 0.00 5.40
147 148 3.966543 CCACCTTTGGGGGCGACT 61.967 66.667 0.00 0.00 39.57 4.18
148 149 2.598787 CCACCTTTGGGGGCGACTA 61.599 63.158 0.00 0.00 39.57 2.59
149 150 1.078426 CACCTTTGGGGGCGACTAG 60.078 63.158 0.00 0.00 40.03 2.57
150 151 2.298661 ACCTTTGGGGGCGACTAGG 61.299 63.158 0.00 0.00 40.03 3.02
151 152 2.590092 CTTTGGGGGCGACTAGGG 59.410 66.667 0.00 0.00 0.00 3.53
152 153 3.012722 TTTGGGGGCGACTAGGGG 61.013 66.667 0.00 0.00 0.00 4.79
153 154 3.566016 TTTGGGGGCGACTAGGGGA 62.566 63.158 0.00 0.00 0.00 4.81
154 155 3.995809 TTGGGGGCGACTAGGGGAG 62.996 68.421 0.00 0.00 0.00 4.30
156 157 4.862823 GGGGCGACTAGGGGAGCT 62.863 72.222 0.00 0.00 0.00 4.09
157 158 3.228017 GGGCGACTAGGGGAGCTC 61.228 72.222 4.71 4.71 0.00 4.09
158 159 3.597728 GGCGACTAGGGGAGCTCG 61.598 72.222 7.83 0.00 34.09 5.03
159 160 3.597728 GCGACTAGGGGAGCTCGG 61.598 72.222 7.83 0.00 32.60 4.63
160 161 2.192443 CGACTAGGGGAGCTCGGA 59.808 66.667 7.83 0.00 0.00 4.55
161 162 1.894756 CGACTAGGGGAGCTCGGAG 60.895 68.421 7.83 0.00 0.00 4.63
162 163 1.227946 GACTAGGGGAGCTCGGAGT 59.772 63.158 7.83 7.83 0.00 3.85
163 164 1.076632 ACTAGGGGAGCTCGGAGTG 60.077 63.158 7.83 0.41 0.00 3.51
164 165 1.830408 CTAGGGGAGCTCGGAGTGG 60.830 68.421 7.83 0.00 0.00 4.00
165 166 3.375443 TAGGGGAGCTCGGAGTGGG 62.375 68.421 7.83 0.00 0.00 4.61
167 168 3.775654 GGGAGCTCGGAGTGGGTG 61.776 72.222 7.83 0.00 0.00 4.61
168 169 3.775654 GGAGCTCGGAGTGGGTGG 61.776 72.222 7.83 0.00 0.00 4.61
169 170 3.775654 GAGCTCGGAGTGGGTGGG 61.776 72.222 6.90 0.00 0.00 4.61
170 171 4.316823 AGCTCGGAGTGGGTGGGA 62.317 66.667 6.90 0.00 0.00 4.37
171 172 3.319198 GCTCGGAGTGGGTGGGAA 61.319 66.667 6.90 0.00 0.00 3.97
172 173 2.982130 CTCGGAGTGGGTGGGAAG 59.018 66.667 0.00 0.00 0.00 3.46
533 534 3.090532 CGGGAGGGGAGGGGAAAG 61.091 72.222 0.00 0.00 0.00 2.62
534 535 2.127528 GGGAGGGGAGGGGAAAGT 59.872 66.667 0.00 0.00 0.00 2.66
535 536 2.001838 GGGAGGGGAGGGGAAAGTC 61.002 68.421 0.00 0.00 0.00 3.01
536 537 2.368011 GGAGGGGAGGGGAAAGTCG 61.368 68.421 0.00 0.00 0.00 4.18
537 538 1.305887 GAGGGGAGGGGAAAGTCGA 60.306 63.158 0.00 0.00 0.00 4.20
538 539 1.612739 AGGGGAGGGGAAAGTCGAC 60.613 63.158 7.70 7.70 0.00 4.20
539 540 2.667108 GGGGAGGGGAAAGTCGACC 61.667 68.421 13.01 0.00 0.00 4.79
540 541 2.667108 GGGAGGGGAAAGTCGACCC 61.667 68.421 13.01 6.05 45.06 4.46
544 545 4.466898 GGGAAAGTCGACCCCCTA 57.533 61.111 23.47 0.00 40.19 3.53
545 546 1.903294 GGGAAAGTCGACCCCCTAC 59.097 63.158 23.47 7.33 40.19 3.18
546 547 0.906282 GGGAAAGTCGACCCCCTACA 60.906 60.000 23.47 0.00 40.19 2.74
547 548 0.978907 GGAAAGTCGACCCCCTACAA 59.021 55.000 13.01 0.00 0.00 2.41
548 549 1.558294 GGAAAGTCGACCCCCTACAAT 59.442 52.381 13.01 0.00 0.00 2.71
549 550 2.629051 GAAAGTCGACCCCCTACAATG 58.371 52.381 13.01 0.00 0.00 2.82
550 551 1.652947 AAGTCGACCCCCTACAATGT 58.347 50.000 13.01 0.00 0.00 2.71
551 552 1.652947 AGTCGACCCCCTACAATGTT 58.347 50.000 13.01 0.00 0.00 2.71
552 553 1.982958 AGTCGACCCCCTACAATGTTT 59.017 47.619 13.01 0.00 0.00 2.83
553 554 2.027469 AGTCGACCCCCTACAATGTTTC 60.027 50.000 13.01 0.00 0.00 2.78
554 555 1.066716 TCGACCCCCTACAATGTTTCG 60.067 52.381 0.00 0.00 0.00 3.46
555 556 1.746470 GACCCCCTACAATGTTTCGG 58.254 55.000 0.00 0.00 0.00 4.30
556 557 1.003928 GACCCCCTACAATGTTTCGGT 59.996 52.381 0.00 0.00 0.00 4.69
557 558 1.003928 ACCCCCTACAATGTTTCGGTC 59.996 52.381 0.00 0.00 0.00 4.79
558 559 1.003812 CCCCCTACAATGTTTCGGTCA 59.996 52.381 0.00 0.00 0.00 4.02
559 560 2.356741 CCCCCTACAATGTTTCGGTCAT 60.357 50.000 0.00 0.00 0.00 3.06
560 561 3.118186 CCCCCTACAATGTTTCGGTCATA 60.118 47.826 0.00 0.00 0.00 2.15
561 562 4.519213 CCCCTACAATGTTTCGGTCATAA 58.481 43.478 0.00 0.00 0.00 1.90
562 563 4.334481 CCCCTACAATGTTTCGGTCATAAC 59.666 45.833 0.00 0.00 0.00 1.89
563 564 5.183228 CCCTACAATGTTTCGGTCATAACT 58.817 41.667 0.00 0.00 0.00 2.24
564 565 5.293569 CCCTACAATGTTTCGGTCATAACTC 59.706 44.000 0.00 0.00 0.00 3.01
565 566 4.921470 ACAATGTTTCGGTCATAACTCG 57.079 40.909 0.00 0.00 0.00 4.18
566 567 3.124636 ACAATGTTTCGGTCATAACTCGC 59.875 43.478 0.00 0.00 0.00 5.03
567 568 2.736144 TGTTTCGGTCATAACTCGCT 57.264 45.000 0.00 0.00 0.00 4.93
568 569 3.034721 TGTTTCGGTCATAACTCGCTT 57.965 42.857 0.00 0.00 0.00 4.68
569 570 2.734606 TGTTTCGGTCATAACTCGCTTG 59.265 45.455 0.00 0.00 0.00 4.01
570 571 2.735134 GTTTCGGTCATAACTCGCTTGT 59.265 45.455 0.00 0.00 0.00 3.16
571 572 2.736144 TCGGTCATAACTCGCTTGTT 57.264 45.000 0.00 0.00 0.00 2.83
572 573 2.602878 TCGGTCATAACTCGCTTGTTC 58.397 47.619 0.00 0.00 0.00 3.18
573 574 2.029739 TCGGTCATAACTCGCTTGTTCA 60.030 45.455 0.00 0.00 0.00 3.18
574 575 2.734606 CGGTCATAACTCGCTTGTTCAA 59.265 45.455 0.00 0.00 0.00 2.69
575 576 3.370978 CGGTCATAACTCGCTTGTTCAAT 59.629 43.478 0.00 0.00 0.00 2.57
576 577 4.565166 CGGTCATAACTCGCTTGTTCAATA 59.435 41.667 0.00 0.00 0.00 1.90
577 578 5.276395 CGGTCATAACTCGCTTGTTCAATAG 60.276 44.000 0.00 0.00 0.00 1.73
578 579 5.581085 GGTCATAACTCGCTTGTTCAATAGT 59.419 40.000 0.00 0.00 0.00 2.12
579 580 6.755141 GGTCATAACTCGCTTGTTCAATAGTA 59.245 38.462 0.00 0.00 0.00 1.82
580 581 7.043325 GGTCATAACTCGCTTGTTCAATAGTAG 60.043 40.741 0.00 0.00 0.00 2.57
581 582 7.701078 GTCATAACTCGCTTGTTCAATAGTAGA 59.299 37.037 0.00 0.00 0.00 2.59
582 583 7.915923 TCATAACTCGCTTGTTCAATAGTAGAG 59.084 37.037 0.00 0.00 0.00 2.43
583 584 5.646577 ACTCGCTTGTTCAATAGTAGAGT 57.353 39.130 0.00 0.00 31.58 3.24
584 585 5.403246 ACTCGCTTGTTCAATAGTAGAGTG 58.597 41.667 0.00 0.00 33.55 3.51
585 586 4.744570 TCGCTTGTTCAATAGTAGAGTGG 58.255 43.478 0.00 0.00 0.00 4.00
586 587 4.461431 TCGCTTGTTCAATAGTAGAGTGGA 59.539 41.667 0.00 0.00 0.00 4.02
587 588 4.800993 CGCTTGTTCAATAGTAGAGTGGAG 59.199 45.833 0.00 0.00 0.00 3.86
588 589 5.393135 CGCTTGTTCAATAGTAGAGTGGAGA 60.393 44.000 0.00 0.00 0.00 3.71
589 590 5.808030 GCTTGTTCAATAGTAGAGTGGAGAC 59.192 44.000 0.00 0.00 0.00 3.36
590 591 5.562506 TGTTCAATAGTAGAGTGGAGACG 57.437 43.478 0.00 0.00 0.00 4.18
591 592 4.398358 TGTTCAATAGTAGAGTGGAGACGG 59.602 45.833 0.00 0.00 0.00 4.79
592 593 4.498894 TCAATAGTAGAGTGGAGACGGA 57.501 45.455 0.00 0.00 0.00 4.69
593 594 4.197750 TCAATAGTAGAGTGGAGACGGAC 58.802 47.826 0.00 0.00 0.00 4.79
594 595 3.928005 ATAGTAGAGTGGAGACGGACA 57.072 47.619 0.00 0.00 0.00 4.02
615 616 2.421725 TGGAGATACATGGGGAAGCAT 58.578 47.619 0.00 0.00 0.00 3.79
633 634 6.253512 GGAAGCATTTTTATAAGCGTTGAAGG 59.746 38.462 0.00 0.00 0.00 3.46
648 649 0.651031 GAAGGAGCGATGGCGTTAAC 59.349 55.000 0.00 0.00 46.35 2.01
650 651 0.178068 AGGAGCGATGGCGTTAACAT 59.822 50.000 6.39 0.00 46.35 2.71
651 652 1.014352 GGAGCGATGGCGTTAACATT 58.986 50.000 6.39 0.00 46.35 2.71
652 653 1.268032 GGAGCGATGGCGTTAACATTG 60.268 52.381 6.39 0.00 46.35 2.82
653 654 1.396996 GAGCGATGGCGTTAACATTGT 59.603 47.619 6.39 0.00 46.35 2.71
654 655 1.810151 AGCGATGGCGTTAACATTGTT 59.190 42.857 7.30 7.30 46.35 2.83
655 656 2.159572 AGCGATGGCGTTAACATTGTTC 60.160 45.455 5.07 0.00 46.35 3.18
705 706 1.153086 CACCCCACAGGCATCTAGC 60.153 63.158 0.00 0.00 40.58 3.42
776 777 0.595095 GCCAGCACTTCTTCACCTTG 59.405 55.000 0.00 0.00 0.00 3.61
782 783 3.996150 CACTTCTTCACCTTGTGCAAT 57.004 42.857 0.00 0.00 32.98 3.56
796 799 2.101082 TGTGCAATTTCTCAGCTGCAAA 59.899 40.909 9.47 10.85 45.71 3.68
830 833 1.386533 ATGCTGCTGTTGTCTATGCC 58.613 50.000 0.00 0.00 0.00 4.40
838 841 1.702401 TGTTGTCTATGCCTGGACCAA 59.298 47.619 0.00 0.00 32.19 3.67
839 842 2.308570 TGTTGTCTATGCCTGGACCAAT 59.691 45.455 0.00 0.00 32.19 3.16
840 843 3.245229 TGTTGTCTATGCCTGGACCAATT 60.245 43.478 0.00 0.00 32.19 2.32
841 844 3.003394 TGTCTATGCCTGGACCAATTG 57.997 47.619 0.00 0.00 32.19 2.32
842 845 2.301346 GTCTATGCCTGGACCAATTGG 58.699 52.381 23.31 23.31 42.17 3.16
843 846 2.092429 GTCTATGCCTGGACCAATTGGA 60.092 50.000 31.22 7.88 38.94 3.53
844 847 2.785269 TCTATGCCTGGACCAATTGGAT 59.215 45.455 31.22 14.95 38.94 3.41
845 848 1.784358 ATGCCTGGACCAATTGGATG 58.216 50.000 31.22 15.71 38.94 3.51
846 849 0.409092 TGCCTGGACCAATTGGATGT 59.591 50.000 31.22 8.82 38.94 3.06
847 850 1.203162 TGCCTGGACCAATTGGATGTT 60.203 47.619 31.22 8.41 38.94 2.71
848 851 1.205417 GCCTGGACCAATTGGATGTTG 59.795 52.381 31.22 15.92 38.94 3.33
853 856 3.838795 CCAATTGGATGTTGGGCAC 57.161 52.632 20.50 0.00 41.90 5.01
854 857 0.249955 CCAATTGGATGTTGGGCACC 59.750 55.000 20.50 0.00 44.83 5.01
855 858 2.173230 CCAATTGGATGTTGGGCACCT 61.173 52.381 20.50 0.00 44.85 4.00
856 859 4.310642 CCAATTGGATGTTGGGCACCTG 62.311 54.545 20.50 0.00 44.85 4.00
867 870 2.747460 GCACCTGCCGAATCAGCA 60.747 61.111 0.00 0.00 38.82 4.41
907 910 1.977544 ACGAACAGAGGAGACGGGG 60.978 63.158 0.00 0.00 0.00 5.73
908 911 2.579738 GAACAGAGGAGACGGGGC 59.420 66.667 0.00 0.00 0.00 5.80
910 913 1.827399 GAACAGAGGAGACGGGGCAA 61.827 60.000 0.00 0.00 0.00 4.52
950 953 4.138487 AGTAGTTTTCTTCGGGCCATAG 57.862 45.455 4.39 0.00 0.00 2.23
1484 1497 2.357517 CTGCGCCGTCAACTTCCT 60.358 61.111 4.18 0.00 0.00 3.36
2074 2161 5.509670 GCTGCCTAAATTCAAGGTCAACTTT 60.510 40.000 8.24 0.00 37.29 2.66
2082 2169 3.295093 TCAAGGTCAACTTTGGCATGAA 58.705 40.909 0.00 0.00 37.29 2.57
2540 2678 6.747659 AACTTTTGCTATGTTTTAGTTGCG 57.252 33.333 0.00 0.00 0.00 4.85
2551 2689 4.143305 TGTTTTAGTTGCGTTGCACAAAAC 60.143 37.500 18.80 18.80 38.71 2.43
2599 2739 2.972713 TGGAACTAGATGATACCCCTGC 59.027 50.000 0.00 0.00 0.00 4.85
2641 2783 4.685628 GCGGGAATTGGTTGCAATATATTG 59.314 41.667 19.29 19.29 40.66 1.90
2642 2784 5.508825 GCGGGAATTGGTTGCAATATATTGA 60.509 40.000 26.22 10.67 40.14 2.57
2643 2785 5.920273 CGGGAATTGGTTGCAATATATTGAC 59.080 40.000 26.22 16.63 40.14 3.18
2644 2786 5.920273 GGGAATTGGTTGCAATATATTGACG 59.080 40.000 26.22 3.51 40.14 4.35
2645 2787 5.402270 GGAATTGGTTGCAATATATTGACGC 59.598 40.000 26.22 13.27 40.14 5.19
2652 3697 0.672401 AATATATTGACGCGCCCCCG 60.672 55.000 5.73 0.00 37.57 5.73
2694 3739 4.143009 GCTAGCTTTGGAAAGAAGTTCTCG 60.143 45.833 7.70 0.00 38.28 4.04
2784 3829 6.485984 AGATTCATGCTGAGTAAATAGGCAAG 59.514 38.462 0.00 0.00 36.49 4.01
2839 3884 5.653769 ACTAGCATGGCATTGACTAAATTGT 59.346 36.000 0.00 0.00 0.00 2.71
2931 3977 7.201496 GCTAGCACTGCTAATACGAAAGTAAAA 60.201 37.037 10.63 0.00 44.52 1.52
2977 4023 0.840288 TCCAGTAGGCCAGGCAGAAA 60.840 55.000 15.19 0.00 33.74 2.52
3106 4155 0.525882 GAAGCGGACGTAGAGGAAGC 60.526 60.000 0.00 0.00 0.00 3.86
3166 4219 2.088674 CTATTCGCCCCTCTCCCGTG 62.089 65.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.036414 AGCAGGCGACAGAGAGGA 59.964 61.111 0.00 0.00 0.00 3.71
6 7 3.749064 GACGGAGCAGGCGACAGA 61.749 66.667 0.00 0.00 0.00 3.41
28 29 2.887568 CACGACGGAGCTCATGGC 60.888 66.667 17.19 8.62 42.19 4.40
29 30 2.887568 GCACGACGGAGCTCATGG 60.888 66.667 17.19 6.87 0.00 3.66
30 31 3.250323 CGCACGACGGAGCTCATG 61.250 66.667 17.19 9.93 38.44 3.07
36 37 4.794439 TGATGGCGCACGACGGAG 62.794 66.667 10.83 0.00 43.93 4.63
37 38 4.794439 CTGATGGCGCACGACGGA 62.794 66.667 10.83 0.00 43.93 4.69
38 39 4.794439 TCTGATGGCGCACGACGG 62.794 66.667 10.83 2.51 43.93 4.79
40 41 2.240500 GGATCTGATGGCGCACGAC 61.241 63.158 10.83 0.00 0.00 4.34
41 42 2.106938 GGATCTGATGGCGCACGA 59.893 61.111 10.83 0.00 0.00 4.35
42 43 3.333189 CGGATCTGATGGCGCACG 61.333 66.667 10.83 0.00 0.00 5.34
43 44 3.643978 GCGGATCTGATGGCGCAC 61.644 66.667 10.83 0.00 0.00 5.34
44 45 4.916293 GGCGGATCTGATGGCGCA 62.916 66.667 10.83 0.00 0.00 6.09
46 47 2.574018 TAGGGCGGATCTGATGGCG 61.574 63.158 5.48 0.00 0.00 5.69
47 48 1.004440 GTAGGGCGGATCTGATGGC 60.004 63.158 5.48 0.00 0.00 4.40
48 49 1.290324 CGTAGGGCGGATCTGATGG 59.710 63.158 5.48 0.00 36.85 3.51
49 50 1.373497 GCGTAGGGCGGATCTGATG 60.373 63.158 5.48 0.00 41.69 3.07
50 51 3.052081 GCGTAGGGCGGATCTGAT 58.948 61.111 5.48 0.00 41.69 2.90
59 60 2.440247 ATTTGGGCAGCGTAGGGC 60.440 61.111 0.00 0.00 44.05 5.19
60 61 1.077787 TCATTTGGGCAGCGTAGGG 60.078 57.895 0.00 0.00 0.00 3.53
61 62 1.705337 CGTCATTTGGGCAGCGTAGG 61.705 60.000 0.00 0.00 0.00 3.18
62 63 1.715585 CGTCATTTGGGCAGCGTAG 59.284 57.895 0.00 0.00 0.00 3.51
63 64 2.395360 GCGTCATTTGGGCAGCGTA 61.395 57.895 0.00 0.00 0.00 4.42
64 65 3.737172 GCGTCATTTGGGCAGCGT 61.737 61.111 0.00 0.00 0.00 5.07
65 66 4.481112 GGCGTCATTTGGGCAGCG 62.481 66.667 0.00 0.00 0.00 5.18
66 67 4.481112 CGGCGTCATTTGGGCAGC 62.481 66.667 0.00 0.00 0.00 5.25
67 68 4.481112 GCGGCGTCATTTGGGCAG 62.481 66.667 9.37 0.00 0.00 4.85
69 70 4.179579 GAGCGGCGTCATTTGGGC 62.180 66.667 9.37 0.00 0.00 5.36
70 71 3.508840 GGAGCGGCGTCATTTGGG 61.509 66.667 9.37 0.00 0.00 4.12
71 72 3.508840 GGGAGCGGCGTCATTTGG 61.509 66.667 9.37 0.00 0.00 3.28
72 73 3.508840 GGGGAGCGGCGTCATTTG 61.509 66.667 9.37 0.00 0.00 2.32
73 74 4.796495 GGGGGAGCGGCGTCATTT 62.796 66.667 9.37 0.00 0.00 2.32
130 131 2.536997 CTAGTCGCCCCCAAAGGTGG 62.537 65.000 0.00 0.00 45.53 4.61
131 132 1.078426 CTAGTCGCCCCCAAAGGTG 60.078 63.158 0.00 0.00 38.86 4.00
132 133 2.298661 CCTAGTCGCCCCCAAAGGT 61.299 63.158 0.00 0.00 0.00 3.50
133 134 2.590092 CCTAGTCGCCCCCAAAGG 59.410 66.667 0.00 0.00 0.00 3.11
134 135 2.590092 CCCTAGTCGCCCCCAAAG 59.410 66.667 0.00 0.00 0.00 2.77
135 136 3.012722 CCCCTAGTCGCCCCCAAA 61.013 66.667 0.00 0.00 0.00 3.28
136 137 3.995809 CTCCCCTAGTCGCCCCCAA 62.996 68.421 0.00 0.00 0.00 4.12
137 138 4.475444 CTCCCCTAGTCGCCCCCA 62.475 72.222 0.00 0.00 0.00 4.96
139 140 4.862823 AGCTCCCCTAGTCGCCCC 62.863 72.222 0.00 0.00 0.00 5.80
140 141 3.228017 GAGCTCCCCTAGTCGCCC 61.228 72.222 0.87 0.00 0.00 6.13
141 142 3.597728 CGAGCTCCCCTAGTCGCC 61.598 72.222 8.47 0.00 0.00 5.54
142 143 3.597728 CCGAGCTCCCCTAGTCGC 61.598 72.222 8.47 0.00 31.50 5.19
143 144 1.894756 CTCCGAGCTCCCCTAGTCG 60.895 68.421 8.47 0.00 0.00 4.18
144 145 1.104577 CACTCCGAGCTCCCCTAGTC 61.105 65.000 8.47 0.00 0.00 2.59
145 146 1.076632 CACTCCGAGCTCCCCTAGT 60.077 63.158 8.47 3.68 0.00 2.57
146 147 1.830408 CCACTCCGAGCTCCCCTAG 60.830 68.421 8.47 3.03 0.00 3.02
147 148 2.279073 CCACTCCGAGCTCCCCTA 59.721 66.667 8.47 0.00 0.00 3.53
148 149 4.787280 CCCACTCCGAGCTCCCCT 62.787 72.222 8.47 0.00 0.00 4.79
150 151 3.775654 CACCCACTCCGAGCTCCC 61.776 72.222 8.47 0.00 0.00 4.30
151 152 3.775654 CCACCCACTCCGAGCTCC 61.776 72.222 8.47 0.00 0.00 4.70
152 153 3.775654 CCCACCCACTCCGAGCTC 61.776 72.222 2.73 2.73 0.00 4.09
153 154 3.846405 TTCCCACCCACTCCGAGCT 62.846 63.158 0.00 0.00 0.00 4.09
154 155 3.316573 CTTCCCACCCACTCCGAGC 62.317 68.421 0.00 0.00 0.00 5.03
155 156 2.982130 CTTCCCACCCACTCCGAG 59.018 66.667 0.00 0.00 0.00 4.63
515 516 4.752594 TTTCCCCTCCCCTCCCGG 62.753 72.222 0.00 0.00 0.00 5.73
516 517 3.090532 CTTTCCCCTCCCCTCCCG 61.091 72.222 0.00 0.00 0.00 5.14
517 518 2.001838 GACTTTCCCCTCCCCTCCC 61.002 68.421 0.00 0.00 0.00 4.30
518 519 2.368011 CGACTTTCCCCTCCCCTCC 61.368 68.421 0.00 0.00 0.00 4.30
519 520 1.305887 TCGACTTTCCCCTCCCCTC 60.306 63.158 0.00 0.00 0.00 4.30
520 521 1.612739 GTCGACTTTCCCCTCCCCT 60.613 63.158 8.70 0.00 0.00 4.79
521 522 2.667108 GGTCGACTTTCCCCTCCCC 61.667 68.421 16.46 0.00 0.00 4.81
522 523 2.667108 GGGTCGACTTTCCCCTCCC 61.667 68.421 16.46 0.22 37.89 4.30
523 524 2.987962 GGGTCGACTTTCCCCTCC 59.012 66.667 16.46 1.15 37.89 4.30
527 528 0.906282 TGTAGGGGGTCGACTTTCCC 60.906 60.000 24.54 24.54 42.73 3.97
528 529 0.978907 TTGTAGGGGGTCGACTTTCC 59.021 55.000 16.46 14.05 0.00 3.13
529 530 2.027469 ACATTGTAGGGGGTCGACTTTC 60.027 50.000 16.46 5.58 0.00 2.62
530 531 1.982958 ACATTGTAGGGGGTCGACTTT 59.017 47.619 16.46 1.39 0.00 2.66
531 532 1.652947 ACATTGTAGGGGGTCGACTT 58.347 50.000 16.46 1.76 0.00 3.01
532 533 1.652947 AACATTGTAGGGGGTCGACT 58.347 50.000 16.46 0.00 0.00 4.18
533 534 2.353323 GAAACATTGTAGGGGGTCGAC 58.647 52.381 7.13 7.13 0.00 4.20
534 535 1.066716 CGAAACATTGTAGGGGGTCGA 60.067 52.381 0.00 0.00 0.00 4.20
535 536 1.365699 CGAAACATTGTAGGGGGTCG 58.634 55.000 0.00 0.00 0.00 4.79
536 537 1.003928 ACCGAAACATTGTAGGGGGTC 59.996 52.381 9.66 0.00 0.00 4.46
537 538 1.003928 GACCGAAACATTGTAGGGGGT 59.996 52.381 9.66 6.25 0.00 4.95
538 539 1.003812 TGACCGAAACATTGTAGGGGG 59.996 52.381 9.66 3.64 0.00 5.40
539 540 2.483014 TGACCGAAACATTGTAGGGG 57.517 50.000 9.66 5.09 0.00 4.79
540 541 5.183228 AGTTATGACCGAAACATTGTAGGG 58.817 41.667 9.66 5.38 0.00 3.53
541 542 5.005394 CGAGTTATGACCGAAACATTGTAGG 59.995 44.000 0.00 0.00 0.00 3.18
542 543 5.500290 GCGAGTTATGACCGAAACATTGTAG 60.500 44.000 3.34 0.00 0.00 2.74
543 544 4.327898 GCGAGTTATGACCGAAACATTGTA 59.672 41.667 3.34 0.00 0.00 2.41
544 545 3.124636 GCGAGTTATGACCGAAACATTGT 59.875 43.478 3.34 0.00 0.00 2.71
545 546 3.370978 AGCGAGTTATGACCGAAACATTG 59.629 43.478 3.34 0.00 0.00 2.82
546 547 3.596214 AGCGAGTTATGACCGAAACATT 58.404 40.909 3.34 0.00 0.00 2.71
547 548 3.247006 AGCGAGTTATGACCGAAACAT 57.753 42.857 3.34 0.00 0.00 2.71
548 549 2.734606 CAAGCGAGTTATGACCGAAACA 59.265 45.455 3.34 0.00 0.00 2.83
549 550 2.735134 ACAAGCGAGTTATGACCGAAAC 59.265 45.455 3.34 0.00 0.00 2.78
550 551 3.034721 ACAAGCGAGTTATGACCGAAA 57.965 42.857 3.34 0.00 0.00 3.46
551 552 2.736144 ACAAGCGAGTTATGACCGAA 57.264 45.000 3.34 0.00 0.00 4.30
552 553 2.029739 TGAACAAGCGAGTTATGACCGA 60.030 45.455 3.34 0.00 0.00 4.69
553 554 2.333926 TGAACAAGCGAGTTATGACCG 58.666 47.619 0.00 0.00 0.00 4.79
554 555 4.946784 ATTGAACAAGCGAGTTATGACC 57.053 40.909 0.00 0.00 0.00 4.02
555 556 6.648725 ACTATTGAACAAGCGAGTTATGAC 57.351 37.500 0.00 0.00 0.00 3.06
556 557 7.768240 TCTACTATTGAACAAGCGAGTTATGA 58.232 34.615 0.00 0.00 0.00 2.15
557 558 7.702772 ACTCTACTATTGAACAAGCGAGTTATG 59.297 37.037 0.00 0.00 0.00 1.90
558 559 7.702772 CACTCTACTATTGAACAAGCGAGTTAT 59.297 37.037 0.00 0.00 29.49 1.89
559 560 7.027760 CACTCTACTATTGAACAAGCGAGTTA 58.972 38.462 0.00 0.00 29.49 2.24
560 561 5.864474 CACTCTACTATTGAACAAGCGAGTT 59.136 40.000 0.00 0.00 29.49 3.01
561 562 5.403246 CACTCTACTATTGAACAAGCGAGT 58.597 41.667 0.00 0.00 31.06 4.18
562 563 4.800993 CCACTCTACTATTGAACAAGCGAG 59.199 45.833 0.00 0.00 0.00 5.03
563 564 4.461431 TCCACTCTACTATTGAACAAGCGA 59.539 41.667 0.00 0.00 0.00 4.93
564 565 4.744570 TCCACTCTACTATTGAACAAGCG 58.255 43.478 0.00 0.00 0.00 4.68
565 566 5.808030 GTCTCCACTCTACTATTGAACAAGC 59.192 44.000 0.00 0.00 0.00 4.01
566 567 6.030849 CGTCTCCACTCTACTATTGAACAAG 58.969 44.000 0.00 0.00 0.00 3.16
567 568 5.105877 CCGTCTCCACTCTACTATTGAACAA 60.106 44.000 0.00 0.00 0.00 2.83
568 569 4.398358 CCGTCTCCACTCTACTATTGAACA 59.602 45.833 0.00 0.00 0.00 3.18
569 570 4.639310 TCCGTCTCCACTCTACTATTGAAC 59.361 45.833 0.00 0.00 0.00 3.18
570 571 4.639310 GTCCGTCTCCACTCTACTATTGAA 59.361 45.833 0.00 0.00 0.00 2.69
571 572 4.197750 GTCCGTCTCCACTCTACTATTGA 58.802 47.826 0.00 0.00 0.00 2.57
572 573 3.945921 TGTCCGTCTCCACTCTACTATTG 59.054 47.826 0.00 0.00 0.00 1.90
573 574 4.232188 TGTCCGTCTCCACTCTACTATT 57.768 45.455 0.00 0.00 0.00 1.73
574 575 3.928005 TGTCCGTCTCCACTCTACTAT 57.072 47.619 0.00 0.00 0.00 2.12
575 576 3.542648 CATGTCCGTCTCCACTCTACTA 58.457 50.000 0.00 0.00 0.00 1.82
576 577 2.370349 CATGTCCGTCTCCACTCTACT 58.630 52.381 0.00 0.00 0.00 2.57
577 578 1.405821 CCATGTCCGTCTCCACTCTAC 59.594 57.143 0.00 0.00 0.00 2.59
578 579 1.283905 TCCATGTCCGTCTCCACTCTA 59.716 52.381 0.00 0.00 0.00 2.43
579 580 0.039764 TCCATGTCCGTCTCCACTCT 59.960 55.000 0.00 0.00 0.00 3.24
580 581 0.457851 CTCCATGTCCGTCTCCACTC 59.542 60.000 0.00 0.00 0.00 3.51
581 582 0.039764 TCTCCATGTCCGTCTCCACT 59.960 55.000 0.00 0.00 0.00 4.00
582 583 1.115467 ATCTCCATGTCCGTCTCCAC 58.885 55.000 0.00 0.00 0.00 4.02
583 584 2.307768 GTATCTCCATGTCCGTCTCCA 58.692 52.381 0.00 0.00 0.00 3.86
584 585 2.307768 TGTATCTCCATGTCCGTCTCC 58.692 52.381 0.00 0.00 0.00 3.71
585 586 3.305676 CCATGTATCTCCATGTCCGTCTC 60.306 52.174 0.00 0.00 40.50 3.36
586 587 2.630098 CCATGTATCTCCATGTCCGTCT 59.370 50.000 0.00 0.00 40.50 4.18
587 588 2.289072 CCCATGTATCTCCATGTCCGTC 60.289 54.545 0.00 0.00 40.50 4.79
588 589 1.694150 CCCATGTATCTCCATGTCCGT 59.306 52.381 0.00 0.00 40.50 4.69
589 590 1.002430 CCCCATGTATCTCCATGTCCG 59.998 57.143 0.00 0.00 40.50 4.79
590 591 2.338809 TCCCCATGTATCTCCATGTCC 58.661 52.381 0.00 0.00 40.50 4.02
591 592 3.808618 GCTTCCCCATGTATCTCCATGTC 60.809 52.174 0.00 0.00 40.50 3.06
592 593 2.107204 GCTTCCCCATGTATCTCCATGT 59.893 50.000 0.00 0.00 40.50 3.21
593 594 2.107031 TGCTTCCCCATGTATCTCCATG 59.893 50.000 0.00 0.00 41.52 3.66
594 595 2.421725 TGCTTCCCCATGTATCTCCAT 58.578 47.619 0.00 0.00 0.00 3.41
608 609 6.253512 CCTTCAACGCTTATAAAAATGCTTCC 59.746 38.462 0.00 0.00 0.00 3.46
615 616 4.691685 TCGCTCCTTCAACGCTTATAAAAA 59.308 37.500 0.00 0.00 0.00 1.94
633 634 1.396996 ACAATGTTAACGCCATCGCTC 59.603 47.619 0.26 0.00 39.84 5.03
648 649 3.837213 ATGCGAGGAACAAGAACAATG 57.163 42.857 0.00 0.00 0.00 2.82
650 651 2.552315 GGAATGCGAGGAACAAGAACAA 59.448 45.455 0.00 0.00 0.00 2.83
651 652 2.151202 GGAATGCGAGGAACAAGAACA 58.849 47.619 0.00 0.00 0.00 3.18
652 653 2.095718 GTGGAATGCGAGGAACAAGAAC 60.096 50.000 0.00 0.00 0.00 3.01
653 654 2.151202 GTGGAATGCGAGGAACAAGAA 58.849 47.619 0.00 0.00 0.00 2.52
654 655 1.071542 TGTGGAATGCGAGGAACAAGA 59.928 47.619 0.00 0.00 0.00 3.02
655 656 1.522668 TGTGGAATGCGAGGAACAAG 58.477 50.000 0.00 0.00 0.00 3.16
713 714 4.395583 GTGCAGCTCGCTGGTTGC 62.396 66.667 19.42 7.39 43.77 4.17
727 728 2.162408 GGTATGGAAGACTTGCAAGTGC 59.838 50.000 35.67 24.55 39.88 4.40
730 731 2.009774 CGGGTATGGAAGACTTGCAAG 58.990 52.381 24.84 24.84 33.68 4.01
731 732 1.349688 ACGGGTATGGAAGACTTGCAA 59.650 47.619 13.75 0.00 33.68 4.08
736 737 0.815734 CACGACGGGTATGGAAGACT 59.184 55.000 0.00 0.00 0.00 3.24
766 767 4.206375 TGAGAAATTGCACAAGGTGAAGA 58.794 39.130 0.00 0.00 35.23 2.87
776 777 2.427232 TTGCAGCTGAGAAATTGCAC 57.573 45.000 20.43 0.00 45.29 4.57
782 783 6.576185 AGAAGAAAAATTTGCAGCTGAGAAA 58.424 32.000 20.43 15.44 0.00 2.52
830 833 1.826720 CCCAACATCCAATTGGTCCAG 59.173 52.381 23.76 13.96 44.46 3.86
838 841 1.259840 GCAGGTGCCCAACATCCAAT 61.260 55.000 0.00 0.00 34.31 3.16
839 842 1.907807 GCAGGTGCCCAACATCCAA 60.908 57.895 0.00 0.00 34.31 3.53
840 843 2.283101 GCAGGTGCCCAACATCCA 60.283 61.111 0.00 0.00 34.31 3.41
850 853 2.747460 TGCTGATTCGGCAGGTGC 60.747 61.111 16.17 0.00 41.16 5.01
855 858 0.966875 AAATGGCTGCTGATTCGGCA 60.967 50.000 18.78 18.78 44.04 5.69
856 859 0.248784 GAAATGGCTGCTGATTCGGC 60.249 55.000 10.66 10.66 37.61 5.54
857 860 1.332997 GAGAAATGGCTGCTGATTCGG 59.667 52.381 0.00 0.00 0.00 4.30
858 861 1.004185 CGAGAAATGGCTGCTGATTCG 60.004 52.381 0.00 0.00 0.00 3.34
859 862 1.332997 CCGAGAAATGGCTGCTGATTC 59.667 52.381 0.00 1.89 0.00 2.52
860 863 1.386533 CCGAGAAATGGCTGCTGATT 58.613 50.000 0.00 0.00 0.00 2.57
861 864 3.091318 CCGAGAAATGGCTGCTGAT 57.909 52.632 0.00 0.00 0.00 2.90
862 865 4.623814 CCGAGAAATGGCTGCTGA 57.376 55.556 0.00 0.00 0.00 4.26
869 872 0.240945 GTGTGGTTGCCGAGAAATGG 59.759 55.000 0.00 0.00 0.00 3.16
870 873 0.950836 TGTGTGGTTGCCGAGAAATG 59.049 50.000 0.00 0.00 0.00 2.32
908 911 0.611618 TAGCTGGCAATGGTGGGTTG 60.612 55.000 0.00 0.00 0.00 3.77
910 913 1.143684 CTATAGCTGGCAATGGTGGGT 59.856 52.381 0.00 0.00 0.00 4.51
913 916 4.342862 ACTACTATAGCTGGCAATGGTG 57.657 45.455 0.00 0.00 0.00 4.17
914 917 5.373812 AAACTACTATAGCTGGCAATGGT 57.626 39.130 0.00 0.00 0.00 3.55
915 918 6.058183 AGAAAACTACTATAGCTGGCAATGG 58.942 40.000 0.00 0.00 0.00 3.16
916 919 7.517417 CGAAGAAAACTACTATAGCTGGCAATG 60.517 40.741 0.00 0.00 0.00 2.82
920 923 4.745620 CCGAAGAAAACTACTATAGCTGGC 59.254 45.833 0.00 0.00 0.00 4.85
922 925 4.745620 GCCCGAAGAAAACTACTATAGCTG 59.254 45.833 0.00 0.00 0.00 4.24
950 953 0.737367 GCCTGGCGATTTTCTTTGCC 60.737 55.000 1.35 0.00 45.15 4.52
957 960 3.443045 CTGCGGCCTGGCGATTTT 61.443 61.111 17.76 0.00 35.06 1.82
1484 1497 2.811431 CGATGTGCACTAACCTTTTGGA 59.189 45.455 19.41 0.00 44.07 3.53
1554 1596 9.817365 GTACATAATGACAATCGTATACGTACT 57.183 33.333 23.67 8.32 40.80 2.73
1555 1597 8.770395 CGTACATAATGACAATCGTATACGTAC 58.230 37.037 23.67 12.83 40.80 3.67
1556 1598 8.495148 ACGTACATAATGACAATCGTATACGTA 58.505 33.333 23.67 11.79 42.00 3.57
1557 1599 7.355017 ACGTACATAATGACAATCGTATACGT 58.645 34.615 23.67 9.53 39.82 3.57
1558 1600 7.252447 CGACGTACATAATGACAATCGTATACG 60.252 40.741 19.23 19.23 38.07 3.06
2074 2161 0.252148 TGCCCTCCATTTTCATGCCA 60.252 50.000 0.00 0.00 0.00 4.92
2540 2678 6.416455 TCGTATGAATCTTTGTTTTGTGCAAC 59.584 34.615 0.00 0.00 37.35 4.17
2551 2689 4.437239 AGGCAGAGTCGTATGAATCTTTG 58.563 43.478 12.10 4.92 46.78 2.77
2599 2739 2.659757 CGCATGTTCTCAATGCAACAAG 59.340 45.455 8.90 0.34 41.05 3.16
2608 2750 1.818060 CCAATTCCCGCATGTTCTCAA 59.182 47.619 0.00 0.00 0.00 3.02
2662 3707 0.747283 CCAAAGCTAGCTGGGCTCAG 60.747 60.000 20.16 10.01 40.44 3.35
2839 3884 8.058667 TGTTTAGATTAGAACCAGTATGTCGA 57.941 34.615 0.00 0.00 0.00 4.20
2931 3977 0.611714 ACACGTTTATCCCGCTCCTT 59.388 50.000 0.00 0.00 0.00 3.36
3106 4155 1.340657 GACTGCTCGCTGTTCGTCTG 61.341 60.000 2.97 0.00 39.67 3.51
3223 4277 1.987855 GGTGACTCCATCCCGTCCA 60.988 63.158 0.00 0.00 35.97 4.02
3325 4385 4.299155 CCTATATAAGTGTGCGGTGTCTG 58.701 47.826 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.