Multiple sequence alignment - TraesCS2A01G263100

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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 TraesCS2A01G263100 chr2A 100.000 5326 0 0 1 5326 416014901 416009576 0.000000e+00 9836.0
1 TraesCS2A01G263100 chr2A 83.893 149 22 2 3948 4096 111429987 111429841 2.000000e-29 141.0
2 TraesCS2A01G263100 chr2A 100.000 28 0 0 707 734 71695551 71695578 1.000000e-02 52.8
3 TraesCS2A01G263100 chr2D 96.589 2375 55 8 873 3232 317863465 317865828 0.000000e+00 3914.0
4 TraesCS2A01G263100 chr2D 95.663 1199 34 5 3228 4426 317868066 317869246 0.000000e+00 1910.0
5 TraesCS2A01G263100 chr2D 86.044 910 58 15 4421 5326 317869287 317870131 0.000000e+00 913.0
6 TraesCS2A01G263100 chr2D 86.908 718 55 18 1 688 317861423 317862131 0.000000e+00 769.0
7 TraesCS2A01G263100 chr2D 89.552 134 12 2 741 873 579962478 579962346 9.170000e-38 169.0
8 TraesCS2A01G263100 chr2D 85.926 135 16 3 741 873 602182019 602181886 2.000000e-29 141.0
9 TraesCS2A01G263100 chr2D 85.185 135 17 3 741 873 602111632 602111499 9.300000e-28 135.0
10 TraesCS2A01G263100 chr2D 97.561 41 1 0 2746 2786 165479205 165479165 2.660000e-08 71.3
11 TraesCS2A01G263100 chr4A 91.391 151 13 0 3948 4098 472961654 472961804 1.940000e-49 207.0
12 TraesCS2A01G263100 chr7B 86.667 135 15 3 741 873 508191484 508191351 4.300000e-31 147.0
13 TraesCS2A01G263100 chr7B 94.286 35 2 0 698 732 641141802 641141768 3.000000e-03 54.7
14 TraesCS2A01G263100 chr6B 86.923 130 15 2 745 873 288414115 288414243 1.550000e-30 145.0
15 TraesCS2A01G263100 chr6B 92.157 51 4 0 2738 2788 7821332 7821382 7.400000e-09 73.1
16 TraesCS2A01G263100 chr6B 93.750 48 3 0 2739 2786 48674230 48674277 7.400000e-09 73.1
17 TraesCS2A01G263100 chr6B 93.750 48 3 0 2739 2786 48981425 48981472 7.400000e-09 73.1
18 TraesCS2A01G263100 chr3A 86.260 131 17 1 741 870 63193007 63192877 2.000000e-29 141.0
19 TraesCS2A01G263100 chr3A 87.500 48 6 0 441 488 515827620 515827573 7.450000e-04 56.5
20 TraesCS2A01G263100 chr3B 86.260 131 15 3 745 873 532644000 532643871 7.190000e-29 139.0
21 TraesCS2A01G263100 chr3B 90.698 43 4 0 691 733 173387960 173387918 2.070000e-04 58.4
22 TraesCS2A01G263100 chr2B 86.719 128 14 3 745 870 732348463 732348337 7.190000e-29 139.0
23 TraesCS2A01G263100 chr2B 100.000 28 0 0 706 733 789962935 789962908 1.000000e-02 52.8
24 TraesCS2A01G263100 chr3D 84.892 139 16 5 741 876 546705004 546704868 9.300000e-28 135.0
25 TraesCS2A01G263100 chr3D 97.619 42 1 0 2745 2786 611532904 611532945 7.400000e-09 73.1
26 TraesCS2A01G263100 chr4D 91.379 58 3 2 531 586 35173199 35173256 1.590000e-10 78.7
27 TraesCS2A01G263100 chr4D 95.349 43 0 2 691 732 400935197 400935156 3.440000e-07 67.6
28 TraesCS2A01G263100 chr7D 97.778 45 0 1 2744 2787 500925747 500925703 5.720000e-10 76.8
29 TraesCS2A01G263100 chrUn 93.750 48 3 0 2739 2786 205782104 205782151 7.400000e-09 73.1
30 TraesCS2A01G263100 chr5A 97.619 42 1 0 2745 2786 410510035 410509994 7.400000e-09 73.1
31 TraesCS2A01G263100 chr7A 91.489 47 4 0 687 733 105209832 105209878 1.240000e-06 65.8
32 TraesCS2A01G263100 chr6A 93.023 43 3 0 691 733 57899068 57899026 4.450000e-06 63.9
33 TraesCS2A01G263100 chr1D 97.222 36 1 0 692 727 7756946 7756981 1.600000e-05 62.1


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 TraesCS2A01G263100 chr2A 416009576 416014901 5325 True 9836.0 9836 100.000 1 5326 1 chr2A.!!$R2 5325
1 TraesCS2A01G263100 chr2D 317861423 317870131 8708 False 1876.5 3914 91.301 1 5326 4 chr2D.!!$F1 5325

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
858 910 0.036388 GAATTCACGGAGCAGGTGGA 60.036 55.0 0.00 0.0 36.09 4.02 F
1930 3119 0.587768 TCGCTGCCATTTATGCATCG 59.412 50.0 0.19 0.0 46.38 3.84 F
2677 3870 0.524862 GCTGAGCAAATGTCCTGGTG 59.475 55.0 0.00 0.0 0.00 4.17 F
3343 6779 0.823460 TGATGGTGTCTATGCGAGCA 59.177 50.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 3176 0.390340 GCTGGAGATTCTGCACGTCA 60.390 55.000 3.46 0.00 0.00 4.35 R
3891 7327 0.110486 TCTTTGGGAACAGGCTGTCC 59.890 55.000 22.31 21.47 44.54 4.02 R
3943 7379 1.334960 CGTGTGTGGAGCAATTTCACC 60.335 52.381 0.00 0.00 0.00 4.02 R
4882 8368 0.401356 TGCATGAGTGGGAAAGCTGA 59.599 50.000 0.00 0.00 0.00 4.26 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
23 24 1.226859 CGATTAGAGGCGCGGTGAA 60.227 57.895 8.83 0.00 0.00 3.18
25 26 0.102481 GATTAGAGGCGCGGTGAAGA 59.898 55.000 8.83 0.00 0.00 2.87
27 28 1.945354 TTAGAGGCGCGGTGAAGAGG 61.945 60.000 8.83 0.00 0.00 3.69
32 33 3.744719 CGCGGTGAAGAGGGACGA 61.745 66.667 0.00 0.00 0.00 4.20
50 51 3.528370 CGCGGGTCCGGAGAGATT 61.528 66.667 3.06 0.00 40.19 2.40
53 54 1.736586 CGGGTCCGGAGAGATTGAG 59.263 63.158 3.06 0.00 35.56 3.02
60 61 1.069823 CCGGAGAGATTGAGGGTGATG 59.930 57.143 0.00 0.00 0.00 3.07
62 63 2.122768 GGAGAGATTGAGGGTGATGGT 58.877 52.381 0.00 0.00 0.00 3.55
65 66 1.561542 GAGATTGAGGGTGATGGTGGT 59.438 52.381 0.00 0.00 0.00 4.16
69 70 1.002134 GAGGGTGATGGTGGTGTGG 60.002 63.158 0.00 0.00 0.00 4.17
73 74 1.002134 GTGATGGTGGTGTGGAGGG 60.002 63.158 0.00 0.00 0.00 4.30
93 94 1.758592 CGGAAGTTTCCCTCCCACA 59.241 57.895 5.36 0.00 44.67 4.17
98 99 2.658807 AGTTTCCCTCCCACAAAGTC 57.341 50.000 0.00 0.00 0.00 3.01
119 120 1.475169 CGCATGGGATAGAGGGAGCA 61.475 60.000 3.11 0.00 0.00 4.26
134 135 0.315251 GAGCAGCAAAACAGGGGAAC 59.685 55.000 0.00 0.00 0.00 3.62
148 149 3.256631 CAGGGGAACAACTGAAGATTTGG 59.743 47.826 0.00 0.00 37.09 3.28
171 172 4.299155 CGAGTGTAGGTCGAAATATGCAT 58.701 43.478 3.79 3.79 39.92 3.96
211 212 2.747446 CAAGACTGACCGTTTTATGGGG 59.253 50.000 0.00 0.00 0.00 4.96
220 221 1.066716 CGTTTTATGGGGTCTGGTCGA 60.067 52.381 0.00 0.00 0.00 4.20
263 264 7.920682 GGTTCTGTGAAATGGCGATTATTTTAT 59.079 33.333 0.00 0.00 0.00 1.40
308 310 5.948992 ACTAGAGTTGCTTTAAGCCTTTG 57.051 39.130 14.80 3.94 41.51 2.77
317 319 8.462016 AGTTGCTTTAAGCCTTTGTATGAATAG 58.538 33.333 14.80 0.00 41.51 1.73
339 341 5.454062 AGCATGCCACCCTAAATTAATACA 58.546 37.500 15.66 0.00 0.00 2.29
372 374 0.326927 TCCTTTACCCCCGCAAGAAG 59.673 55.000 0.00 0.00 43.02 2.85
377 379 2.194201 TACCCCCGCAAGAAGAAAAG 57.806 50.000 0.00 0.00 43.02 2.27
379 381 1.075536 ACCCCCGCAAGAAGAAAAGAT 59.924 47.619 0.00 0.00 43.02 2.40
384 386 3.440173 CCCGCAAGAAGAAAAGATTAGCA 59.560 43.478 0.00 0.00 43.02 3.49
390 392 6.618811 CAAGAAGAAAAGATTAGCATGCAGT 58.381 36.000 21.98 4.66 0.00 4.40
391 393 7.627088 GCAAGAAGAAAAGATTAGCATGCAGTA 60.627 37.037 21.98 4.54 0.00 2.74
414 416 3.756963 GCTCCTAGTAACACCCAAAAAGG 59.243 47.826 0.00 0.00 37.03 3.11
443 445 6.926630 AAAACCAATAAGTATTGAAGGCCA 57.073 33.333 5.01 0.00 44.40 5.36
444 446 6.530019 AAACCAATAAGTATTGAAGGCCAG 57.470 37.500 5.01 0.00 44.40 4.85
445 447 3.954258 ACCAATAAGTATTGAAGGCCAGC 59.046 43.478 5.01 0.00 44.40 4.85
446 448 4.210331 CCAATAAGTATTGAAGGCCAGCT 58.790 43.478 5.01 0.00 44.40 4.24
447 449 5.104109 ACCAATAAGTATTGAAGGCCAGCTA 60.104 40.000 5.01 0.00 44.40 3.32
470 472 0.310543 GCACATGGCAACTTCGAACA 59.689 50.000 0.00 0.00 43.97 3.18
481 483 3.643159 ACTTCGAACATTTTCAAGGGC 57.357 42.857 0.00 0.00 30.37 5.19
525 528 2.039216 TCCGAGGGCAAATTTAGTGACA 59.961 45.455 0.00 0.00 0.00 3.58
552 555 2.279582 AGTTTAGTGACGCGAGGATG 57.720 50.000 15.93 0.00 0.00 3.51
561 564 3.243177 GTGACGCGAGGATGATAACTTTC 59.757 47.826 15.93 0.00 0.00 2.62
564 567 2.216488 CGCGAGGATGATAACTTTCGTG 59.784 50.000 0.00 0.00 33.22 4.35
565 568 2.033662 GCGAGGATGATAACTTTCGTGC 60.034 50.000 0.00 0.00 0.00 5.34
566 569 3.448686 CGAGGATGATAACTTTCGTGCT 58.551 45.455 0.00 0.00 36.18 4.40
567 570 3.865745 CGAGGATGATAACTTTCGTGCTT 59.134 43.478 0.00 0.00 33.95 3.91
568 571 4.026475 CGAGGATGATAACTTTCGTGCTTC 60.026 45.833 0.00 0.00 33.95 3.86
611 641 4.399618 TGTTGTGCTTGCCAACTAACTTTA 59.600 37.500 19.50 4.10 42.09 1.85
618 648 5.048013 GCTTGCCAACTAACTTTACATCCTT 60.048 40.000 0.00 0.00 0.00 3.36
636 666 0.741326 TTGCGTTGCTAAACTTGCCA 59.259 45.000 0.00 0.00 33.87 4.92
637 667 0.958091 TGCGTTGCTAAACTTGCCAT 59.042 45.000 0.00 0.00 33.87 4.40
638 668 2.155279 TGCGTTGCTAAACTTGCCATA 58.845 42.857 0.00 0.00 33.87 2.74
639 669 2.752354 TGCGTTGCTAAACTTGCCATAT 59.248 40.909 0.00 0.00 33.87 1.78
701 752 5.860182 TCGGTAAGAAAACATACTCACTTCG 59.140 40.000 0.00 0.00 0.00 3.79
719 770 8.882415 TCACTTCGTCTTAAAATAAGTGTCTT 57.118 30.769 11.88 0.00 44.60 3.01
755 806 9.226606 CTAAATAAATACCTATTCGGCATTCCA 57.773 33.333 0.00 0.00 35.61 3.53
763 814 4.776322 CGGCATTCCACCGCTCCA 62.776 66.667 0.00 0.00 44.90 3.86
765 816 2.359850 GCATTCCACCGCTCCACA 60.360 61.111 0.00 0.00 0.00 4.17
766 817 2.690778 GCATTCCACCGCTCCACAC 61.691 63.158 0.00 0.00 0.00 3.82
767 818 1.003355 CATTCCACCGCTCCACACT 60.003 57.895 0.00 0.00 0.00 3.55
768 819 1.021390 CATTCCACCGCTCCACACTC 61.021 60.000 0.00 0.00 0.00 3.51
769 820 1.194781 ATTCCACCGCTCCACACTCT 61.195 55.000 0.00 0.00 0.00 3.24
771 822 2.279069 CCACCGCTCCACACTCTCT 61.279 63.158 0.00 0.00 0.00 3.10
776 827 1.662438 CGCTCCACACTCTCTCTCCC 61.662 65.000 0.00 0.00 0.00 4.30
777 828 0.613292 GCTCCACACTCTCTCTCCCA 60.613 60.000 0.00 0.00 0.00 4.37
792 843 2.435586 CCAGAGCTGGCGGAGTTG 60.436 66.667 3.18 0.00 44.73 3.16
793 844 2.659016 CAGAGCTGGCGGAGTTGA 59.341 61.111 0.00 0.00 0.00 3.18
803 854 4.558697 GCTGGCGGAGTTGAAGTTAAAAAT 60.559 41.667 0.00 0.00 0.00 1.82
804 855 5.523438 TGGCGGAGTTGAAGTTAAAAATT 57.477 34.783 0.00 0.00 0.00 1.82
807 858 5.566395 GGCGGAGTTGAAGTTAAAAATTACG 59.434 40.000 0.00 0.00 0.00 3.18
812 863 6.368213 AGTTGAAGTTAAAAATTACGGAGCG 58.632 36.000 0.00 0.00 0.00 5.03
813 864 6.203338 AGTTGAAGTTAAAAATTACGGAGCGA 59.797 34.615 0.00 0.00 0.00 4.93
814 865 6.160664 TGAAGTTAAAAATTACGGAGCGAG 57.839 37.500 0.00 0.00 0.00 5.03
815 866 5.121142 TGAAGTTAAAAATTACGGAGCGAGG 59.879 40.000 0.00 0.00 0.00 4.63
817 868 2.773993 AAAAATTACGGAGCGAGGGA 57.226 45.000 0.00 0.00 0.00 4.20
818 869 2.773993 AAAATTACGGAGCGAGGGAA 57.226 45.000 0.00 0.00 0.00 3.97
820 871 0.899720 AATTACGGAGCGAGGGAACA 59.100 50.000 0.00 0.00 0.00 3.18
821 872 0.460311 ATTACGGAGCGAGGGAACAG 59.540 55.000 0.00 0.00 0.00 3.16
822 873 1.601419 TTACGGAGCGAGGGAACAGG 61.601 60.000 0.00 0.00 0.00 4.00
823 874 2.776370 TACGGAGCGAGGGAACAGGT 62.776 60.000 0.00 0.00 0.00 4.00
824 875 2.266055 GGAGCGAGGGAACAGGTG 59.734 66.667 0.00 0.00 0.00 4.00
828 879 2.948720 GCGAGGGAACAGGTGCTCT 61.949 63.158 0.00 0.00 0.00 4.09
838 889 0.252479 CAGGTGCTCTGCAGATCCTT 59.748 55.000 23.63 8.71 40.08 3.36
839 890 0.252479 AGGTGCTCTGCAGATCCTTG 59.748 55.000 18.63 6.18 40.08 3.61
840 891 0.251354 GGTGCTCTGCAGATCCTTGA 59.749 55.000 18.63 0.00 40.08 3.02
845 897 3.276857 GCTCTGCAGATCCTTGAATTCA 58.723 45.455 18.63 3.38 0.00 2.57
846 898 3.065095 GCTCTGCAGATCCTTGAATTCAC 59.935 47.826 18.63 0.00 0.00 3.18
852 904 2.632377 GATCCTTGAATTCACGGAGCA 58.368 47.619 32.66 16.13 46.14 4.26
855 907 1.611673 CCTTGAATTCACGGAGCAGGT 60.612 52.381 23.22 0.00 37.45 4.00
858 910 0.036388 GAATTCACGGAGCAGGTGGA 60.036 55.000 0.00 0.00 36.09 4.02
862 914 2.045926 ACGGAGCAGGTGGATTGC 60.046 61.111 0.00 0.00 41.83 3.56
863 915 2.825836 CGGAGCAGGTGGATTGCC 60.826 66.667 0.00 0.00 42.48 4.52
870 922 1.002134 AGGTGGATTGCCGAACAGG 60.002 57.895 0.00 0.00 44.97 4.00
909 2089 1.486726 GGACAGAGGGGTACATGGAAG 59.513 57.143 0.00 0.00 0.00 3.46
977 2157 5.741011 CCAGTAGCTACCACATAAAAAGGA 58.259 41.667 20.31 0.00 0.00 3.36
1020 2200 3.259902 GAGGCTTTACGTCCCAGTTAAG 58.740 50.000 0.00 0.00 34.85 1.85
1021 2201 2.901839 AGGCTTTACGTCCCAGTTAAGA 59.098 45.455 0.00 0.00 33.94 2.10
1022 2202 2.998670 GGCTTTACGTCCCAGTTAAGAC 59.001 50.000 0.00 0.00 33.94 3.01
1023 2203 2.998670 GCTTTACGTCCCAGTTAAGACC 59.001 50.000 0.00 0.00 33.94 3.85
1024 2204 3.306571 GCTTTACGTCCCAGTTAAGACCT 60.307 47.826 0.00 0.00 33.94 3.85
1025 2205 4.082026 GCTTTACGTCCCAGTTAAGACCTA 60.082 45.833 0.00 0.00 33.94 3.08
1026 2206 5.391312 TTTACGTCCCAGTTAAGACCTAC 57.609 43.478 0.00 0.00 0.00 3.18
1027 2207 2.174360 ACGTCCCAGTTAAGACCTACC 58.826 52.381 0.00 0.00 0.00 3.18
1253 2433 4.029520 CGATATCCTCCATTCCATCCTCT 58.970 47.826 0.00 0.00 0.00 3.69
1259 2439 1.645455 CATTCCATCCTCTTGCGCG 59.355 57.895 0.00 0.00 0.00 6.86
1354 2534 0.768609 AGATCCGATTCCCCTTCCCC 60.769 60.000 0.00 0.00 0.00 4.81
1358 2538 2.808206 CGATTCCCCTTCCCCTCCG 61.808 68.421 0.00 0.00 0.00 4.63
1504 2693 3.613299 GCGGAGAGCTTTACTTCTACAAC 59.387 47.826 0.00 0.00 44.04 3.32
1626 2815 1.664321 CTAGGGTTCGTCGACCTGGG 61.664 65.000 10.58 0.00 39.71 4.45
1649 2838 4.657824 CACCGACCGGCGTGTTCT 62.658 66.667 15.38 0.00 39.32 3.01
1650 2839 3.920196 ACCGACCGGCGTGTTCTT 61.920 61.111 15.38 0.00 39.32 2.52
1691 2880 2.925724 TGGAACACGTGAATTTGGAGT 58.074 42.857 25.01 0.00 0.00 3.85
1720 2909 2.278206 CTCGGCGACATGGTCTCG 60.278 66.667 4.99 0.00 0.00 4.04
1759 2948 2.437180 CGGGAGCTCTGCATTGCA 60.437 61.111 14.64 11.50 36.92 4.08
1766 2955 2.681064 TCTGCATTGCAAGGGCCC 60.681 61.111 16.46 16.46 38.41 5.80
1930 3119 0.587768 TCGCTGCCATTTATGCATCG 59.412 50.000 0.19 0.00 46.38 3.84
1978 3167 2.201732 GCATTTGATCCGAGCTTCGTA 58.798 47.619 0.00 0.00 38.40 3.43
1985 3174 1.241165 TCCGAGCTTCGTACTGTTCA 58.759 50.000 0.00 0.00 38.40 3.18
1987 3176 1.068472 CCGAGCTTCGTACTGTTCAGT 60.068 52.381 10.33 10.33 38.40 3.41
1990 3179 2.981140 GAGCTTCGTACTGTTCAGTGAC 59.019 50.000 14.69 8.45 0.00 3.67
1994 3183 0.776451 CGTACTGTTCAGTGACGTGC 59.224 55.000 14.69 0.00 0.00 5.34
2068 3257 5.070446 TGATTACGCACTCCTTCAGGATTAT 59.930 40.000 0.00 0.00 44.46 1.28
2198 3387 9.239551 TGTACTTAGTAAGAAGCTACAATCTGA 57.760 33.333 16.89 0.00 0.00 3.27
2344 3537 5.527582 GTCAAACTTCAGAGTTGAGGCTAAA 59.472 40.000 0.00 0.00 45.18 1.85
2392 3585 9.656040 AATTAGCATTGCAATTGTTCATTCTTA 57.344 25.926 9.83 0.00 0.00 2.10
2495 3688 8.111224 GTCTTAATGAATAGACAGTTCGCTTTC 58.889 37.037 0.00 0.00 40.35 2.62
2670 3863 2.490903 GTTCCATCTGCTGAGCAAATGT 59.509 45.455 18.42 0.00 35.48 2.71
2677 3870 0.524862 GCTGAGCAAATGTCCTGGTG 59.475 55.000 0.00 0.00 0.00 4.17
2713 3906 9.371136 TGAAGCTGACATTACTTGATAACTTAG 57.629 33.333 0.00 0.00 0.00 2.18
2772 3965 6.407202 TCCCTCTGTAAAGAAATACAAGAGC 58.593 40.000 0.00 0.00 35.48 4.09
2849 4042 4.233789 TGATTGAAAAGCATTTACGCCAC 58.766 39.130 0.00 0.00 37.27 5.01
2851 4044 3.552604 TGAAAAGCATTTACGCCACTC 57.447 42.857 0.00 0.00 37.28 3.51
2991 4184 3.008266 TCAGTCATGCAGTCAATTCCTCA 59.992 43.478 0.00 0.00 0.00 3.86
3000 4193 3.066342 CAGTCAATTCCTCATGCATGTCC 59.934 47.826 25.43 5.19 0.00 4.02
3080 4273 6.382859 ACTTCAACCCACTTTGGTATTTTCTT 59.617 34.615 0.00 0.00 37.76 2.52
3162 4356 8.738645 AAACTATTGTGAAATGATCCTCTACC 57.261 34.615 0.00 0.00 0.00 3.18
3188 4382 9.965824 CATTTAGTTCCAGTGTTATGTTTTTCT 57.034 29.630 0.00 0.00 0.00 2.52
3271 6707 4.702131 AGGCCTCACACATTTGAAAGATAC 59.298 41.667 0.00 0.00 0.00 2.24
3285 6721 4.401519 TGAAAGATACTTCGAAGACCGGAT 59.598 41.667 31.08 14.80 39.14 4.18
3343 6779 0.823460 TGATGGTGTCTATGCGAGCA 59.177 50.000 0.00 0.00 0.00 4.26
3344 6780 1.202452 TGATGGTGTCTATGCGAGCAG 60.202 52.381 3.58 0.00 0.00 4.24
3463 6899 9.774413 ATATACTTAGGTTTGGTGCTATTGTAC 57.226 33.333 0.00 0.00 0.00 2.90
3469 6905 7.061566 AGGTTTGGTGCTATTGTACAAAAAT 57.938 32.000 13.23 0.00 34.37 1.82
3513 6949 5.324409 TGTTTGCACCAAGGATCTATTTCT 58.676 37.500 0.00 0.00 0.00 2.52
3718 7154 5.677319 AATCCGTAACTTCAGAGGATTGA 57.323 39.130 7.17 0.00 46.39 2.57
3735 7171 6.536447 AGGATTGAAACATGATTTTGCCTTT 58.464 32.000 0.00 0.00 0.00 3.11
3821 7257 1.067000 CAGTCCAAGTGAGGAGCTCTG 60.067 57.143 14.64 2.31 38.64 3.35
3880 7316 5.503662 TTATAATACGAGCAAGGTGTCGA 57.496 39.130 0.00 0.00 39.53 4.20
3891 7327 4.147322 GTGTCGAATGCACCGCCG 62.147 66.667 5.55 0.00 0.00 6.46
3927 7363 1.633774 AGACTCCGGATGACTGTTGT 58.366 50.000 3.57 0.00 0.00 3.32
3943 7379 5.927030 ACTGTTGTGAATAGTAATTGTGCG 58.073 37.500 0.00 0.00 30.51 5.34
3945 7381 4.757657 TGTTGTGAATAGTAATTGTGCGGT 59.242 37.500 0.00 0.00 0.00 5.68
4017 7453 2.742372 GAGCGGACATTGCACGGT 60.742 61.111 5.19 5.19 41.36 4.83
4050 7486 1.843851 TCCCTGGCTGGATTTTATCGT 59.156 47.619 12.58 0.00 38.35 3.73
4052 7488 2.421388 CCCTGGCTGGATTTTATCGTCA 60.421 50.000 12.58 0.00 38.35 4.35
4125 7561 2.589610 TAGTCTCGGGCCCTGATGCT 62.590 60.000 22.43 18.95 0.00 3.79
4148 7584 3.817709 TGATGCGGTATCTTGATGTGA 57.182 42.857 7.58 0.00 36.71 3.58
4259 7695 3.261580 GGATATTTGTTGCCAACTTGCC 58.738 45.455 9.30 0.00 0.00 4.52
4263 7699 1.103803 TTGTTGCCAACTTGCCGTTA 58.896 45.000 9.30 0.00 33.63 3.18
4289 7725 4.516321 TCATGTTTCATGTCAGGACACAAG 59.484 41.667 10.22 6.62 45.05 3.16
4290 7726 2.618241 TGTTTCATGTCAGGACACAAGC 59.382 45.455 4.08 3.98 45.05 4.01
4291 7727 2.880890 GTTTCATGTCAGGACACAAGCT 59.119 45.455 3.92 0.00 45.05 3.74
4292 7728 4.065088 GTTTCATGTCAGGACACAAGCTA 58.935 43.478 3.92 0.00 45.05 3.32
4293 7729 4.350368 TTCATGTCAGGACACAAGCTAA 57.650 40.909 3.92 0.00 45.05 3.09
4294 7730 4.558226 TCATGTCAGGACACAAGCTAAT 57.442 40.909 3.92 0.00 45.05 1.73
4295 7731 5.675684 TCATGTCAGGACACAAGCTAATA 57.324 39.130 3.92 0.00 45.05 0.98
4296 7732 6.239217 TCATGTCAGGACACAAGCTAATAT 57.761 37.500 3.92 0.00 45.05 1.28
4297 7733 6.283694 TCATGTCAGGACACAAGCTAATATC 58.716 40.000 3.92 0.00 45.05 1.63
4298 7734 5.939764 TGTCAGGACACAAGCTAATATCT 57.060 39.130 0.00 0.00 36.21 1.98
4299 7735 6.299805 TGTCAGGACACAAGCTAATATCTT 57.700 37.500 0.00 0.00 36.21 2.40
4300 7736 6.108687 TGTCAGGACACAAGCTAATATCTTG 58.891 40.000 2.65 2.65 44.71 3.02
4366 7802 7.012138 TGCAAATGTACAAGTTTCGTTAACCTA 59.988 33.333 0.00 0.00 37.46 3.08
4403 7839 0.243365 TGCCATGCCGTTGAAATGTC 59.757 50.000 0.00 0.00 0.00 3.06
4456 7938 3.459063 GTCCGGTCCTCTTCCCCG 61.459 72.222 0.00 0.00 41.37 5.73
4465 7947 1.203212 TCCTCTTCCCCGTTTCACCTA 60.203 52.381 0.00 0.00 0.00 3.08
4589 8071 1.353076 GCAAGCTGCAAAAGGTATGC 58.647 50.000 1.02 0.00 44.26 3.14
4621 8103 6.527722 ACATCACAAATACAAAATTGCTAGCG 59.472 34.615 10.77 0.00 0.00 4.26
4622 8104 6.247727 TCACAAATACAAAATTGCTAGCGA 57.752 33.333 7.23 7.23 0.00 4.93
4637 8119 2.781945 AGCGAGGAAACAGCAAAAAG 57.218 45.000 0.00 0.00 38.48 2.27
4697 8179 6.006449 ACTCATCAGCTTAATTGAAACCTGT 58.994 36.000 0.00 0.00 0.00 4.00
4703 8185 8.402798 TCAGCTTAATTGAAACCTGTCAAATA 57.597 30.769 0.00 0.00 40.76 1.40
4706 8188 8.806146 AGCTTAATTGAAACCTGTCAAATATGT 58.194 29.630 0.00 0.00 40.76 2.29
4759 8241 9.665719 TGCACTGAATATACTGTCAAGAAATAA 57.334 29.630 0.00 0.00 0.00 1.40
4768 8250 6.803154 ACTGTCAAGAAATAACTTAGCCAC 57.197 37.500 0.00 0.00 0.00 5.01
4770 8252 6.770785 ACTGTCAAGAAATAACTTAGCCACAA 59.229 34.615 0.00 0.00 0.00 3.33
4772 8254 7.422399 TGTCAAGAAATAACTTAGCCACAAAC 58.578 34.615 0.00 0.00 0.00 2.93
4774 8256 8.082242 GTCAAGAAATAACTTAGCCACAAACAT 58.918 33.333 0.00 0.00 0.00 2.71
4775 8257 9.290988 TCAAGAAATAACTTAGCCACAAACATA 57.709 29.630 0.00 0.00 0.00 2.29
4776 8258 9.906660 CAAGAAATAACTTAGCCACAAACATAA 57.093 29.630 0.00 0.00 0.00 1.90
4789 8271 9.590451 AGCCACAAACATAAAATCATAATTGAG 57.410 29.630 0.00 0.00 34.73 3.02
4790 8272 9.369904 GCCACAAACATAAAATCATAATTGAGT 57.630 29.630 0.00 0.00 34.73 3.41
4858 8340 6.374333 AGTTTTAAAAGCTGTGAACTGACAGA 59.626 34.615 10.08 0.00 45.39 3.41
4882 8368 8.370182 AGAAACTTGCTCCAATTTGTCATAAAT 58.630 29.630 0.00 0.00 0.00 1.40
4892 8378 6.536224 CCAATTTGTCATAAATCAGCTTTCCC 59.464 38.462 0.00 0.00 0.00 3.97
4917 8403 5.213891 TCATGCAGTTCACTGAAAGAGTA 57.786 39.130 11.29 0.00 46.59 2.59
4919 8405 6.233434 TCATGCAGTTCACTGAAAGAGTAAT 58.767 36.000 11.29 0.00 46.59 1.89
4926 8412 7.329717 CAGTTCACTGAAAGAGTAATCCAGTAC 59.670 40.741 0.14 0.00 46.59 2.73
5022 8508 5.610398 TCTAGAGTGCAATCACAGAAAACA 58.390 37.500 17.53 0.00 45.49 2.83
5026 8512 5.533903 AGAGTGCAATCACAGAAAACAAGAT 59.466 36.000 17.53 0.00 45.49 2.40
5028 8514 7.229306 AGAGTGCAATCACAGAAAACAAGATAA 59.771 33.333 17.53 0.00 45.49 1.75
5029 8515 7.141363 AGTGCAATCACAGAAAACAAGATAAC 58.859 34.615 0.00 0.00 45.49 1.89
5030 8516 7.013655 AGTGCAATCACAGAAAACAAGATAACT 59.986 33.333 0.00 0.00 45.49 2.24
5031 8517 7.649306 GTGCAATCACAGAAAACAAGATAACTT 59.351 33.333 0.00 0.00 42.66 2.66
5062 8548 6.644882 ACCAGAGAATTAGGGGAGGTATATT 58.355 40.000 0.00 0.00 0.00 1.28
5066 8552 9.289782 CAGAGAATTAGGGGAGGTATATTTTTG 57.710 37.037 0.00 0.00 0.00 2.44
5076 8562 7.272244 GGGAGGTATATTTTTGTTTTGATGGG 58.728 38.462 0.00 0.00 0.00 4.00
5077 8563 7.125053 GGGAGGTATATTTTTGTTTTGATGGGA 59.875 37.037 0.00 0.00 0.00 4.37
5090 8576 6.554605 TGTTTTGATGGGAAGGAAGAAAGAAT 59.445 34.615 0.00 0.00 0.00 2.40
5097 8583 7.616528 TGGGAAGGAAGAAAGAATTCAAATT 57.383 32.000 8.44 0.00 38.06 1.82
5127 8613 2.226315 ATGTCCCTGCAGAGCCACA 61.226 57.895 17.39 12.00 0.00 4.17
5140 8626 3.380004 CAGAGCCACAACCTAACACAAAA 59.620 43.478 0.00 0.00 0.00 2.44
5141 8627 3.380320 AGAGCCACAACCTAACACAAAAC 59.620 43.478 0.00 0.00 0.00 2.43
5142 8628 3.361786 AGCCACAACCTAACACAAAACT 58.638 40.909 0.00 0.00 0.00 2.66
5221 8707 6.842163 CAAGTGACATTTATACTTGTCCACC 58.158 40.000 10.32 1.89 43.75 4.61
5222 8708 6.121776 AGTGACATTTATACTTGTCCACCA 57.878 37.500 10.32 0.00 41.22 4.17
5223 8709 5.938125 AGTGACATTTATACTTGTCCACCAC 59.062 40.000 10.32 0.00 41.22 4.16
5224 8710 5.938125 GTGACATTTATACTTGTCCACCACT 59.062 40.000 10.32 0.00 41.22 4.00
5225 8711 6.430000 GTGACATTTATACTTGTCCACCACTT 59.570 38.462 10.32 0.00 41.22 3.16
5226 8712 7.001674 TGACATTTATACTTGTCCACCACTTT 58.998 34.615 10.32 0.00 41.22 2.66
5227 8713 8.158132 TGACATTTATACTTGTCCACCACTTTA 58.842 33.333 10.32 0.00 41.22 1.85
5228 8714 9.174166 GACATTTATACTTGTCCACCACTTTAT 57.826 33.333 3.76 0.00 36.98 1.40
5229 8715 8.956426 ACATTTATACTTGTCCACCACTTTATG 58.044 33.333 0.00 0.00 0.00 1.90
5282 8768 9.565213 GAATAGTGTGAAAGATGAAATTCTTGG 57.435 33.333 0.00 0.00 36.12 3.61
5313 8799 1.201998 CGCAGTTCACACATCAGCATC 60.202 52.381 0.00 0.00 0.00 3.91
5314 8800 1.808343 GCAGTTCACACATCAGCATCA 59.192 47.619 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.744719 TCGTCCCTCTTCACCGCG 61.745 66.667 0.00 0.00 0.00 6.46
17 18 2.178521 CGTCGTCCCTCTTCACCG 59.821 66.667 0.00 0.00 0.00 4.94
32 33 4.816984 ATCTCTCCGGACCCGCGT 62.817 66.667 0.00 0.00 38.24 6.01
50 51 1.760527 CACACCACCATCACCCTCA 59.239 57.895 0.00 0.00 0.00 3.86
53 54 1.002134 CTCCACACCACCATCACCC 60.002 63.158 0.00 0.00 0.00 4.61
65 66 2.406002 GAAACTTCCGCCCCTCCACA 62.406 60.000 0.00 0.00 0.00 4.17
69 70 2.603652 AGGGAAACTTCCGCCCCTC 61.604 63.158 2.43 0.00 45.69 4.30
93 94 0.464036 TCTATCCCATGCGCGACTTT 59.536 50.000 12.10 0.00 0.00 2.66
98 99 2.047844 CCCTCTATCCCATGCGCG 60.048 66.667 0.00 0.00 0.00 6.86
119 120 1.756538 CAGTTGTTCCCCTGTTTTGCT 59.243 47.619 0.00 0.00 0.00 3.91
134 135 2.549754 ACACTCGCCAAATCTTCAGTTG 59.450 45.455 0.00 0.00 0.00 3.16
148 149 2.471743 GCATATTTCGACCTACACTCGC 59.528 50.000 0.00 0.00 0.00 5.03
200 201 1.066716 TCGACCAGACCCCATAAAACG 60.067 52.381 0.00 0.00 0.00 3.60
236 237 2.198827 ATCGCCATTTCACAGAACCA 57.801 45.000 0.00 0.00 0.00 3.67
249 250 3.499563 CCCTCCCCATAAAATAATCGCCA 60.500 47.826 0.00 0.00 0.00 5.69
263 264 2.690881 CCGTGAATCCCCTCCCCA 60.691 66.667 0.00 0.00 0.00 4.96
308 310 3.146104 AGGGTGGCATGCTATTCATAC 57.854 47.619 18.92 4.46 33.19 2.39
317 319 5.782893 TGTATTAATTTAGGGTGGCATGC 57.217 39.130 9.90 9.90 0.00 4.06
339 341 5.103643 GGGGTAAAGGAGGTAAATGGAGATT 60.104 44.000 0.00 0.00 0.00 2.40
372 374 5.277731 GGAGCTACTGCATGCTAATCTTTTC 60.278 44.000 20.33 7.11 42.74 2.29
377 379 3.399440 AGGAGCTACTGCATGCTAATC 57.601 47.619 20.33 8.12 42.74 1.75
379 381 3.300388 ACTAGGAGCTACTGCATGCTAA 58.700 45.455 20.33 3.08 42.74 3.09
384 386 3.385111 GGTGTTACTAGGAGCTACTGCAT 59.615 47.826 9.36 0.00 42.74 3.96
390 392 5.280317 CCTTTTTGGGTGTTACTAGGAGCTA 60.280 44.000 0.00 0.00 0.00 3.32
391 393 4.506802 CCTTTTTGGGTGTTACTAGGAGCT 60.507 45.833 0.00 0.00 0.00 4.09
422 424 4.402474 GCTGGCCTTCAATACTTATTGGTT 59.598 41.667 3.32 0.00 42.46 3.67
423 425 3.954258 GCTGGCCTTCAATACTTATTGGT 59.046 43.478 3.32 0.00 42.46 3.67
424 426 4.210331 AGCTGGCCTTCAATACTTATTGG 58.790 43.478 3.32 0.00 42.46 3.16
425 427 5.050091 CGTAGCTGGCCTTCAATACTTATTG 60.050 44.000 3.32 2.98 43.32 1.90
428 430 3.702548 TCGTAGCTGGCCTTCAATACTTA 59.297 43.478 3.32 0.00 0.00 2.24
430 432 2.101582 CTCGTAGCTGGCCTTCAATACT 59.898 50.000 3.32 0.00 0.00 2.12
431 433 2.474816 CTCGTAGCTGGCCTTCAATAC 58.525 52.381 3.32 0.00 0.00 1.89
432 434 1.202533 GCTCGTAGCTGGCCTTCAATA 60.203 52.381 3.32 0.00 38.45 1.90
433 435 0.462759 GCTCGTAGCTGGCCTTCAAT 60.463 55.000 3.32 0.00 38.45 2.57
435 437 2.282783 TGCTCGTAGCTGGCCTTCA 61.283 57.895 3.32 0.00 42.97 3.02
436 438 1.811679 GTGCTCGTAGCTGGCCTTC 60.812 63.158 3.32 0.00 42.97 3.46
438 440 2.362369 ATGTGCTCGTAGCTGGCCT 61.362 57.895 3.32 0.00 42.97 5.19
440 442 2.176273 CCATGTGCTCGTAGCTGGC 61.176 63.158 0.00 0.00 42.97 4.85
441 443 2.176273 GCCATGTGCTCGTAGCTGG 61.176 63.158 0.00 8.23 42.97 4.85
442 444 1.020861 TTGCCATGTGCTCGTAGCTG 61.021 55.000 0.00 0.00 42.97 4.24
443 445 1.021390 GTTGCCATGTGCTCGTAGCT 61.021 55.000 7.54 0.00 42.97 3.32
444 446 1.021390 AGTTGCCATGTGCTCGTAGC 61.021 55.000 7.54 0.58 42.82 3.58
445 447 1.394917 GAAGTTGCCATGTGCTCGTAG 59.605 52.381 7.54 0.00 42.00 3.51
446 448 1.438651 GAAGTTGCCATGTGCTCGTA 58.561 50.000 7.54 0.00 42.00 3.43
447 449 1.568612 CGAAGTTGCCATGTGCTCGT 61.569 55.000 7.54 0.86 42.00 4.18
493 496 1.142060 TGCCCTCGGAAAACTCAGAAA 59.858 47.619 0.00 0.00 0.00 2.52
496 499 1.604604 TTTGCCCTCGGAAAACTCAG 58.395 50.000 0.00 0.00 0.00 3.35
525 528 1.779569 CGTCACTAAACTTGCCTCGT 58.220 50.000 0.00 0.00 0.00 4.18
591 621 3.948473 TGTAAAGTTAGTTGGCAAGCACA 59.052 39.130 0.00 0.00 0.00 4.57
593 623 4.217550 GGATGTAAAGTTAGTTGGCAAGCA 59.782 41.667 0.00 0.00 0.00 3.91
611 641 2.504367 AGTTTAGCAACGCAAGGATGT 58.496 42.857 0.00 0.00 46.39 3.06
618 648 0.958091 ATGGCAAGTTTAGCAACGCA 59.042 45.000 0.00 0.00 38.03 5.24
655 685 8.038944 ACCGAAAATGATAAGTACTACACACAT 58.961 33.333 0.00 0.00 0.00 3.21
656 686 7.380536 ACCGAAAATGATAAGTACTACACACA 58.619 34.615 0.00 0.00 0.00 3.72
738 789 2.922740 GGTGGAATGCCGAATAGGTA 57.077 50.000 0.00 0.00 43.70 3.08
739 790 3.800826 GGTGGAATGCCGAATAGGT 57.199 52.632 0.00 0.00 43.70 3.08
749 800 1.003355 AGTGTGGAGCGGTGGAATG 60.003 57.895 0.00 0.00 0.00 2.67
750 801 1.194781 AGAGTGTGGAGCGGTGGAAT 61.195 55.000 0.00 0.00 0.00 3.01
752 803 2.203640 AGAGTGTGGAGCGGTGGA 60.204 61.111 0.00 0.00 0.00 4.02
755 806 0.963355 GAGAGAGAGTGTGGAGCGGT 60.963 60.000 0.00 0.00 0.00 5.68
758 809 0.613292 TGGGAGAGAGAGTGTGGAGC 60.613 60.000 0.00 0.00 0.00 4.70
776 827 1.004560 TTCAACTCCGCCAGCTCTG 60.005 57.895 0.00 0.00 0.00 3.35
777 828 1.294780 CTTCAACTCCGCCAGCTCT 59.705 57.895 0.00 0.00 0.00 4.09
780 831 1.519408 TTAACTTCAACTCCGCCAGC 58.481 50.000 0.00 0.00 0.00 4.85
781 832 4.561735 TTTTTAACTTCAACTCCGCCAG 57.438 40.909 0.00 0.00 0.00 4.85
790 841 6.347888 CCTCGCTCCGTAATTTTTAACTTCAA 60.348 38.462 0.00 0.00 0.00 2.69
792 843 5.446875 CCCTCGCTCCGTAATTTTTAACTTC 60.447 44.000 0.00 0.00 0.00 3.01
793 844 4.393990 CCCTCGCTCCGTAATTTTTAACTT 59.606 41.667 0.00 0.00 0.00 2.66
803 854 1.601419 CCTGTTCCCTCGCTCCGTAA 61.601 60.000 0.00 0.00 0.00 3.18
804 855 2.050350 CCTGTTCCCTCGCTCCGTA 61.050 63.158 0.00 0.00 0.00 4.02
807 858 2.266055 CACCTGTTCCCTCGCTCC 59.734 66.667 0.00 0.00 0.00 4.70
812 863 1.376553 GCAGAGCACCTGTTCCCTC 60.377 63.158 7.76 0.00 44.71 4.30
813 864 2.121992 CTGCAGAGCACCTGTTCCCT 62.122 60.000 8.42 0.00 44.71 4.20
814 865 1.673665 CTGCAGAGCACCTGTTCCC 60.674 63.158 8.42 0.00 44.71 3.97
815 866 0.035630 ATCTGCAGAGCACCTGTTCC 60.036 55.000 22.96 0.00 44.71 3.62
817 868 0.035630 GGATCTGCAGAGCACCTGTT 60.036 55.000 31.24 8.15 44.71 3.16
818 869 0.908656 AGGATCTGCAGAGCACCTGT 60.909 55.000 31.24 8.96 44.71 4.00
820 871 0.252479 CAAGGATCTGCAGAGCACCT 59.748 55.000 31.24 27.47 33.79 4.00
821 872 0.251354 TCAAGGATCTGCAGAGCACC 59.749 55.000 31.24 25.95 33.79 5.01
822 873 2.105006 TTCAAGGATCTGCAGAGCAC 57.895 50.000 31.24 20.62 33.79 4.40
823 874 3.276857 GAATTCAAGGATCTGCAGAGCA 58.723 45.455 31.24 12.67 36.92 4.26
824 875 3.065095 GTGAATTCAAGGATCTGCAGAGC 59.935 47.826 23.68 23.68 0.00 4.09
828 879 2.027285 TCCGTGAATTCAAGGATCTGCA 60.027 45.455 31.57 14.35 46.83 4.41
838 889 0.321564 CCACCTGCTCCGTGAATTCA 60.322 55.000 3.38 3.38 32.77 2.57
839 890 0.036388 TCCACCTGCTCCGTGAATTC 60.036 55.000 0.00 0.00 32.77 2.17
840 891 0.620556 ATCCACCTGCTCCGTGAATT 59.379 50.000 0.70 0.00 32.77 2.17
845 897 2.045926 GCAATCCACCTGCTCCGT 60.046 61.111 0.00 0.00 36.84 4.69
846 898 2.825836 GGCAATCCACCTGCTCCG 60.826 66.667 0.00 0.00 39.82 4.63
852 904 1.002134 CCTGTTCGGCAATCCACCT 60.002 57.895 0.00 0.00 0.00 4.00
862 914 1.218316 GACACCTAGGCCTGTTCGG 59.782 63.158 17.99 12.90 0.00 4.30
863 915 0.608640 AAGACACCTAGGCCTGTTCG 59.391 55.000 17.99 3.80 0.00 3.95
870 922 3.945921 GTCCCAAAATAAGACACCTAGGC 59.054 47.826 9.30 0.00 0.00 3.93
871 923 5.045869 TCTGTCCCAAAATAAGACACCTAGG 60.046 44.000 7.41 7.41 35.67 3.02
875 2054 4.010349 CCTCTGTCCCAAAATAAGACACC 58.990 47.826 0.00 0.00 35.67 4.16
909 2089 3.623510 GGAAGATTCACCGATTCTTGGAC 59.376 47.826 6.00 0.00 34.00 4.02
920 2100 3.314635 CAGCTATTGCAGGAAGATTCACC 59.685 47.826 1.12 0.00 42.74 4.02
977 2157 0.557729 CATATTGGGCTTCCCTGGGT 59.442 55.000 13.56 0.00 45.70 4.51
1020 2200 1.064091 AGGAAGGTAGGTCGGTAGGTC 60.064 57.143 0.00 0.00 0.00 3.85
1021 2201 1.006020 AGGAAGGTAGGTCGGTAGGT 58.994 55.000 0.00 0.00 0.00 3.08
1022 2202 2.156102 AAGGAAGGTAGGTCGGTAGG 57.844 55.000 0.00 0.00 0.00 3.18
1023 2203 5.452917 CCAAATAAGGAAGGTAGGTCGGTAG 60.453 48.000 0.00 0.00 0.00 3.18
1024 2204 4.406649 CCAAATAAGGAAGGTAGGTCGGTA 59.593 45.833 0.00 0.00 0.00 4.02
1025 2205 3.199289 CCAAATAAGGAAGGTAGGTCGGT 59.801 47.826 0.00 0.00 0.00 4.69
1026 2206 3.805207 CCAAATAAGGAAGGTAGGTCGG 58.195 50.000 0.00 0.00 0.00 4.79
1027 2207 3.118371 AGCCAAATAAGGAAGGTAGGTCG 60.118 47.826 0.00 0.00 0.00 4.79
1471 2660 3.496875 CTCTCCGCCTGCGATGAGG 62.497 68.421 13.94 0.00 42.83 3.86
1560 2749 3.618780 AAGCAGGGCAGCTCGAAGG 62.619 63.158 4.11 0.00 45.89 3.46
1633 2822 3.853597 GAAGAACACGCCGGTCGGT 62.854 63.158 19.73 12.72 43.86 4.69
1691 2880 2.281484 GCCGAGCTGGAAACCACA 60.281 61.111 0.00 0.00 42.00 4.17
1776 2965 0.600518 CGAGATGATGCAGAGGCTGG 60.601 60.000 0.00 0.00 41.91 4.85
1930 3119 0.907230 ACCAGAGAACCTCCAGCCTC 60.907 60.000 0.00 0.00 0.00 4.70
1978 3167 0.459899 TCTGCACGTCACTGAACAGT 59.540 50.000 1.32 1.32 43.61 3.55
1985 3174 0.969149 TGGAGATTCTGCACGTCACT 59.031 50.000 3.46 0.00 0.00 3.41
1987 3176 0.390340 GCTGGAGATTCTGCACGTCA 60.390 55.000 3.46 0.00 0.00 4.35
1990 3179 1.703438 GCTGCTGGAGATTCTGCACG 61.703 60.000 3.46 2.56 36.83 5.34
1994 3183 1.654317 GTCAGCTGCTGGAGATTCTG 58.346 55.000 27.79 1.53 31.51 3.02
2198 3387 7.232534 TGAACTCTAAAGGTAATTTTGTGGCAT 59.767 33.333 0.00 0.00 32.01 4.40
2315 3508 5.704515 CCTCAACTCTGAAGTTTGACATGAT 59.295 40.000 0.00 0.00 43.28 2.45
2356 3549 9.745880 CAATTGCAATGCTAATTCTCTAGAAAT 57.254 29.630 13.82 0.00 37.61 2.17
2392 3585 3.873910 CCACTGAAGATTTCCACGGTAT 58.126 45.455 0.00 0.00 0.00 2.73
2467 3660 7.997482 AGCGAACTGTCTATTCATTAAGACTA 58.003 34.615 4.32 0.00 42.17 2.59
2474 3667 5.168569 TCGAAAGCGAACTGTCTATTCATT 58.831 37.500 0.00 0.00 44.78 2.57
2495 3688 5.685511 CCCAAAACTGAACAATGTAGTTTCG 59.314 40.000 12.89 4.31 42.11 3.46
2505 3698 2.733956 AGACAGCCCAAAACTGAACAA 58.266 42.857 0.00 0.00 38.55 2.83
2670 3863 2.604912 TCAGCTCTCTAACACCAGGA 57.395 50.000 0.00 0.00 0.00 3.86
2726 3919 7.776500 AGGGAGTACTACATAAGAGAAGTTCTC 59.224 40.741 22.97 22.97 43.70 2.87
2795 3988 4.156008 CACTCCAGCAATAACCAAAGTACC 59.844 45.833 0.00 0.00 0.00 3.34
2851 4044 2.619147 CAGATCAAGCCTCAGTGTGAG 58.381 52.381 0.00 0.00 43.91 3.51
2991 4184 1.210204 ACTGGGGTCTGGACATGCAT 61.210 55.000 0.00 0.00 0.00 3.96
3000 4193 3.490348 ACAAGATCAAAACTGGGGTCTG 58.510 45.455 0.00 0.00 0.00 3.51
3162 4356 9.965824 AGAAAAACATAACACTGGAACTAAATG 57.034 29.630 0.00 0.00 0.00 2.32
3271 6707 2.933495 TGTGTATCCGGTCTTCGAAG 57.067 50.000 19.35 19.35 42.43 3.79
3285 6721 4.023279 GCACCAATCTTTGTGACATGTGTA 60.023 41.667 1.15 0.00 0.00 2.90
3337 6773 2.666190 TTGGTGCTCACTGCTCGC 60.666 61.111 0.00 0.00 43.37 5.03
3343 6779 2.938354 GCATCTGTTGGTGCTCACT 58.062 52.632 0.00 0.00 38.30 3.41
3370 6806 1.772836 AATTGATCTGAGGCCAAGGC 58.227 50.000 5.01 1.52 41.06 4.35
3404 6840 5.360714 CACCAGTTGCCAGTTATCCATATTT 59.639 40.000 0.00 0.00 0.00 1.40
3718 7154 5.033589 TCCACAAAGGCAAAATCATGTTT 57.966 34.783 0.00 0.00 37.29 2.83
3735 7171 2.819019 CACACCAAACAGCATATCCACA 59.181 45.455 0.00 0.00 0.00 4.17
3891 7327 0.110486 TCTTTGGGAACAGGCTGTCC 59.890 55.000 22.31 21.47 44.54 4.02
3927 7363 6.751514 ATTTCACCGCACAATTACTATTCA 57.248 33.333 0.00 0.00 0.00 2.57
3943 7379 1.334960 CGTGTGTGGAGCAATTTCACC 60.335 52.381 0.00 0.00 0.00 4.02
3945 7381 1.601903 GTCGTGTGTGGAGCAATTTCA 59.398 47.619 0.00 0.00 0.00 2.69
4017 7453 1.547675 GCCAGGGAATCTTGTCCACAA 60.548 52.381 0.00 0.00 39.70 3.33
4050 7486 3.690280 TGGACGACCAGCGCATGA 61.690 61.111 11.47 0.00 46.04 3.07
4125 7561 4.122046 CACATCAAGATACCGCATCAAGA 58.878 43.478 0.00 0.00 35.96 3.02
4173 7609 8.416329 CAAGGATCTTCTTTCAGAAAGGAAAAA 58.584 33.333 20.70 8.43 39.01 1.94
4178 7614 4.763793 TGCAAGGATCTTCTTTCAGAAAGG 59.236 41.667 20.70 7.76 39.01 3.11
4180 7616 6.718454 AGAATGCAAGGATCTTCTTTCAGAAA 59.282 34.615 0.00 0.00 33.19 2.52
4248 7684 2.992593 TGATATAACGGCAAGTTGGCA 58.007 42.857 26.86 10.09 43.94 4.92
4259 7695 7.224557 TGTCCTGACATGAAACATGATATAACG 59.775 37.037 16.86 0.00 36.21 3.18
4263 7699 6.417258 TGTGTCCTGACATGAAACATGATAT 58.583 36.000 16.86 0.00 43.97 1.63
4289 7725 4.119862 TCTTCACGCCACAAGATATTAGC 58.880 43.478 0.00 0.00 0.00 3.09
4290 7726 7.412346 GCATATCTTCACGCCACAAGATATTAG 60.412 40.741 12.72 7.19 44.58 1.73
4291 7727 6.368791 GCATATCTTCACGCCACAAGATATTA 59.631 38.462 12.72 0.00 44.58 0.98
4292 7728 5.180117 GCATATCTTCACGCCACAAGATATT 59.820 40.000 12.72 1.87 44.58 1.28
4293 7729 4.692625 GCATATCTTCACGCCACAAGATAT 59.307 41.667 10.73 10.73 46.47 1.63
4294 7730 4.058124 GCATATCTTCACGCCACAAGATA 58.942 43.478 7.85 7.85 42.88 1.98
4295 7731 2.874701 GCATATCTTCACGCCACAAGAT 59.125 45.455 0.00 0.00 41.35 2.40
4296 7732 2.093500 AGCATATCTTCACGCCACAAGA 60.093 45.455 0.00 0.00 33.18 3.02
4297 7733 2.283298 AGCATATCTTCACGCCACAAG 58.717 47.619 0.00 0.00 0.00 3.16
4298 7734 2.401583 AGCATATCTTCACGCCACAA 57.598 45.000 0.00 0.00 0.00 3.33
4299 7735 2.401583 AAGCATATCTTCACGCCACA 57.598 45.000 0.00 0.00 0.00 4.17
4329 7765 6.039717 ACTTGTACATTTGCAGTTGAGAACAT 59.960 34.615 0.00 0.00 0.00 2.71
4335 7771 5.163703 ACGAAACTTGTACATTTGCAGTTGA 60.164 36.000 9.96 0.00 0.00 3.18
4366 7802 1.479323 GCATGCTCCAATTGGTGACAT 59.521 47.619 26.79 23.34 42.32 3.06
4456 7938 6.681777 ACAAAAGAATGCAGATAGGTGAAAC 58.318 36.000 0.00 0.00 0.00 2.78
4465 7947 9.985730 TCTTGATTTAAACAAAAGAATGCAGAT 57.014 25.926 0.00 0.00 0.00 2.90
4559 8041 3.455990 TGCAGCTTGCTGAATTTCAAA 57.544 38.095 24.67 0.00 45.31 2.69
4589 8071 8.489559 CAATTTTGTATTTGTGATGTTCCACAG 58.510 33.333 0.00 0.00 46.32 3.66
4606 8088 4.757657 TGTTTCCTCGCTAGCAATTTTGTA 59.242 37.500 16.45 0.00 0.00 2.41
4612 8094 1.339055 TGCTGTTTCCTCGCTAGCAAT 60.339 47.619 16.45 0.00 40.99 3.56
4637 8119 4.678287 CACATGCACACTGATTTGAGAAAC 59.322 41.667 0.00 0.00 0.00 2.78
4681 8163 8.986477 ACATATTTGACAGGTTTCAATTAAGC 57.014 30.769 0.00 0.00 35.42 3.09
4706 8188 3.066064 CCAACATTTTCCGTGTCACTTGA 59.934 43.478 0.65 0.00 0.00 3.02
4723 8205 2.949177 ATTCAGTGCAGTACCCAACA 57.051 45.000 0.00 0.00 0.00 3.33
4763 8245 9.590451 CTCAATTATGATTTTATGTTTGTGGCT 57.410 29.630 0.00 0.00 34.37 4.75
4795 8277 8.521176 GCAGATTATGAATTCAGCCAAGATTAT 58.479 33.333 14.54 0.00 0.00 1.28
4796 8278 7.308169 CGCAGATTATGAATTCAGCCAAGATTA 60.308 37.037 14.54 0.00 0.00 1.75
4802 8284 2.880268 CCGCAGATTATGAATTCAGCCA 59.120 45.455 14.54 0.41 0.00 4.75
4834 8316 6.551736 TCTGTCAGTTCACAGCTTTTAAAAC 58.448 36.000 0.00 0.00 43.18 2.43
4836 8318 6.751514 TTCTGTCAGTTCACAGCTTTTAAA 57.248 33.333 0.00 0.00 43.18 1.52
4837 8319 6.374333 AGTTTCTGTCAGTTCACAGCTTTTAA 59.626 34.615 0.00 0.00 43.18 1.52
4858 8340 8.149647 TGATTTATGACAAATTGGAGCAAGTTT 58.850 29.630 0.00 0.00 29.07 2.66
4882 8368 0.401356 TGCATGAGTGGGAAAGCTGA 59.599 50.000 0.00 0.00 0.00 4.26
4892 8378 3.811497 TCTTTCAGTGAACTGCATGAGTG 59.189 43.478 4.68 0.00 43.46 3.51
4926 8412 9.886132 ATTTCTTGTTACTGTTATACCTACAGG 57.114 33.333 7.73 0.00 45.67 4.00
4978 8464 5.316167 AGATTGTGAACTGATACTTTGCCA 58.684 37.500 0.00 0.00 0.00 4.92
4985 8471 6.333416 TGCACTCTAGATTGTGAACTGATAC 58.667 40.000 14.57 0.00 36.38 2.24
5026 8512 8.701895 CCCTAATTCTCTGGTACATACAAGTTA 58.298 37.037 0.00 0.00 38.20 2.24
5028 8514 6.099845 CCCCTAATTCTCTGGTACATACAAGT 59.900 42.308 0.00 0.00 38.20 3.16
5029 8515 6.326583 TCCCCTAATTCTCTGGTACATACAAG 59.673 42.308 0.00 0.00 38.20 3.16
5030 8516 6.206787 TCCCCTAATTCTCTGGTACATACAA 58.793 40.000 0.00 0.00 38.20 2.41
5031 8517 5.784023 TCCCCTAATTCTCTGGTACATACA 58.216 41.667 0.00 0.00 38.20 2.29
5032 8518 5.246429 CCTCCCCTAATTCTCTGGTACATAC 59.754 48.000 0.00 0.00 38.20 2.39
5033 8519 5.102783 ACCTCCCCTAATTCTCTGGTACATA 60.103 44.000 0.00 0.00 38.20 2.29
5034 8520 4.235372 CCTCCCCTAATTCTCTGGTACAT 58.765 47.826 0.00 0.00 38.20 2.29
5035 8521 3.013648 ACCTCCCCTAATTCTCTGGTACA 59.986 47.826 0.00 0.00 0.00 2.90
5036 8522 3.655384 ACCTCCCCTAATTCTCTGGTAC 58.345 50.000 0.00 0.00 0.00 3.34
5037 8523 5.698369 ATACCTCCCCTAATTCTCTGGTA 57.302 43.478 0.00 0.00 34.01 3.25
5038 8524 2.972153 ACCTCCCCTAATTCTCTGGT 57.028 50.000 0.00 0.00 0.00 4.00
5039 8525 7.575499 AAATATACCTCCCCTAATTCTCTGG 57.425 40.000 0.00 0.00 0.00 3.86
5040 8526 9.289782 CAAAAATATACCTCCCCTAATTCTCTG 57.710 37.037 0.00 0.00 0.00 3.35
5041 8527 9.015146 ACAAAAATATACCTCCCCTAATTCTCT 57.985 33.333 0.00 0.00 0.00 3.10
5042 8528 9.642343 AACAAAAATATACCTCCCCTAATTCTC 57.358 33.333 0.00 0.00 0.00 2.87
5050 8536 7.272244 CCATCAAAACAAAAATATACCTCCCC 58.728 38.462 0.00 0.00 0.00 4.81
5062 8548 6.552445 TTCTTCCTTCCCATCAAAACAAAA 57.448 33.333 0.00 0.00 0.00 2.44
5066 8552 6.405278 TTCTTTCTTCCTTCCCATCAAAAC 57.595 37.500 0.00 0.00 0.00 2.43
5104 8590 1.684248 GGCTCTGCAGGGACATGAAAT 60.684 52.381 20.53 0.00 0.00 2.17
5108 8594 1.748122 GTGGCTCTGCAGGGACATG 60.748 63.158 28.55 4.49 0.00 3.21
5127 8613 5.381757 TCAGCCATAGTTTTGTGTTAGGTT 58.618 37.500 0.00 0.00 0.00 3.50
5140 8626 7.789202 ATCTTGTCTGTATATCAGCCATAGT 57.211 36.000 0.00 0.00 43.32 2.12
5182 8668 6.899393 TGTCACTTGCAAAAATAGGAAGAT 57.101 33.333 0.00 0.00 37.78 2.40
5221 8707 8.612619 CCTTAATACACTGTTAGCCATAAAGTG 58.387 37.037 0.00 0.00 43.07 3.16
5222 8708 7.773690 CCCTTAATACACTGTTAGCCATAAAGT 59.226 37.037 0.00 0.00 0.00 2.66
5223 8709 7.773690 ACCCTTAATACACTGTTAGCCATAAAG 59.226 37.037 0.00 0.00 0.00 1.85
5224 8710 7.635648 ACCCTTAATACACTGTTAGCCATAAA 58.364 34.615 0.00 0.00 0.00 1.40
5225 8711 7.202972 ACCCTTAATACACTGTTAGCCATAA 57.797 36.000 0.00 0.00 0.00 1.90
5226 8712 6.818281 ACCCTTAATACACTGTTAGCCATA 57.182 37.500 0.00 0.00 0.00 2.74
5227 8713 5.710409 ACCCTTAATACACTGTTAGCCAT 57.290 39.130 0.00 0.00 0.00 4.40
5228 8714 6.623979 TTACCCTTAATACACTGTTAGCCA 57.376 37.500 0.00 0.00 0.00 4.75
5229 8715 8.515695 AATTTACCCTTAATACACTGTTAGCC 57.484 34.615 0.00 0.00 0.00 3.93
5230 8716 9.783256 CAAATTTACCCTTAATACACTGTTAGC 57.217 33.333 0.00 0.00 0.00 3.09
5259 8745 6.716628 AGCCAAGAATTTCATCTTTCACACTA 59.283 34.615 0.00 0.00 37.56 2.74
5269 8755 2.100418 GGGAGCAGCCAAGAATTTCATC 59.900 50.000 0.00 0.00 38.95 2.92


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

AutoCloner maintained by Alex Coulton.