Multiple sequence alignment - TraesCS3A01G336100

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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 TraesCS3A01G336100 chr3A 100.000 4238 0 0 1 4238 582940175 582944412 0.000000e+00 7827
1 TraesCS3A01G336100 chr3A 96.629 89 3 0 736 824 582940995 582940907 9.490000e-32 148
2 TraesCS3A01G336100 chr3A 84.071 113 18 0 19 131 434717498 434717610 4.480000e-20 110
3 TraesCS3A01G336100 chr3B 94.690 3465 123 16 818 4238 579284053 579287500 0.000000e+00 5323
4 TraesCS3A01G336100 chr3B 94.690 3465 123 16 818 4238 579300710 579304157 0.000000e+00 5323
5 TraesCS3A01G336100 chr3B 86.473 621 43 15 130 738 579283459 579284050 0.000000e+00 643
6 TraesCS3A01G336100 chr3B 86.473 621 43 15 130 738 579300116 579300707 0.000000e+00 643
7 TraesCS3A01G336100 chr3B 94.737 95 4 1 736 829 71403746 71403652 3.410000e-31 147
8 TraesCS3A01G336100 chr3D 94.836 3350 116 16 819 4121 442039273 442042612 0.000000e+00 5175
9 TraesCS3A01G336100 chr3D 89.233 613 38 10 129 737 442038689 442039277 0.000000e+00 741
10 TraesCS3A01G336100 chr3D 93.443 122 6 1 4117 4238 442042723 442042842 3.370000e-41 180
11 TraesCS3A01G336100 chr3D 87.037 108 13 1 24 131 487231685 487231579 2.070000e-23 121
12 TraesCS3A01G336100 chr1B 77.058 1482 314 22 1690 3161 543468256 543466791 0.000000e+00 830
13 TraesCS3A01G336100 chr1B 94.624 93 5 0 729 821 423857617 423857709 1.230000e-30 145
14 TraesCS3A01G336100 chr1D 96.703 91 3 0 736 826 110890419 110890509 7.340000e-33 152
15 TraesCS3A01G336100 chr6A 96.629 89 3 0 733 821 433968836 433968924 9.490000e-32 148
16 TraesCS3A01G336100 chr6A 89.691 97 10 0 35 131 479996500 479996404 1.600000e-24 124
17 TraesCS3A01G336100 chr2B 96.629 89 3 0 736 824 644847629 644847717 9.490000e-32 148
18 TraesCS3A01G336100 chr2B 87.037 108 14 0 24 131 209381453 209381346 5.750000e-24 122
19 TraesCS3A01G336100 chr1A 96.629 89 3 0 736 824 89574177 89574089 9.490000e-32 148
20 TraesCS3A01G336100 chrUn 95.652 92 3 1 736 826 17061956 17061865 3.410000e-31 147
21 TraesCS3A01G336100 chr4A 94.737 95 4 1 735 828 607427390 607427296 3.410000e-31 147
22 TraesCS3A01G336100 chr4A 84.071 113 18 0 19 131 674685256 674685368 4.480000e-20 110
23 TraesCS3A01G336100 chr7A 89.189 111 12 0 24 134 317908049 317908159 5.710000e-29 139
24 TraesCS3A01G336100 chr7A 84.071 113 18 0 19 131 575881878 575881990 4.480000e-20 110
25 TraesCS3A01G336100 chr5B 84.956 113 17 0 19 131 478035630 478035518 9.630000e-22 115
26 TraesCS3A01G336100 chr5D 87.629 97 12 0 35 131 46333085 46332989 3.460000e-21 113


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 TraesCS3A01G336100 chr3A 582940175 582944412 4237 False 7827 7827 100.0000 1 4238 1 chr3A.!!$F2 4237
1 TraesCS3A01G336100 chr3B 579283459 579287500 4041 False 2983 5323 90.5815 130 4238 2 chr3B.!!$F1 4108
2 TraesCS3A01G336100 chr3B 579300116 579304157 4041 False 2983 5323 90.5815 130 4238 2 chr3B.!!$F2 4108
3 TraesCS3A01G336100 chr3D 442038689 442042842 4153 False 2032 5175 92.5040 129 4238 3 chr3D.!!$F1 4109
4 TraesCS3A01G336100 chr1B 543466791 543468256 1465 True 830 830 77.0580 1690 3161 1 chr1B.!!$R1 1471

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
488 502 0.027716 GAGCTGCGAATCTGCACATG 59.972 55.0 0.00 0.00 40.62 3.21 F
666 681 0.036671 AGGGTTTCCGTCGACAATCC 60.037 55.0 17.16 12.11 38.33 3.01 F
1212 1238 0.517132 CTGCTTTCACGTCATTCGCG 60.517 55.0 0.00 0.00 44.19 5.87 F
1698 1724 0.259647 CATCCAGCAATCCCAGGGAA 59.740 55.0 13.94 0.00 34.34 3.97 F
1700 1726 0.846427 TCCAGCAATCCCAGGGAAGT 60.846 55.0 13.94 0.00 34.34 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1325 1351 0.034089 ATCAGCAAAGGTGGTAGCCC 60.034 55.000 0.0 0.0 33.05 5.19 R
1631 1657 1.228245 GCACCAGCCTTCCTGTGAA 60.228 57.895 0.0 0.0 40.06 3.18 R
3102 3131 0.255890 TGGGAGGGATGTGCTTTAGC 59.744 55.000 0.0 0.0 42.50 3.09 R
3105 3134 1.002069 TCATGGGAGGGATGTGCTTT 58.998 50.000 0.0 0.0 0.00 3.51 R
3391 3421 2.951457 TCGAATACGAACCAGATGCA 57.049 45.000 0.0 0.0 45.74 3.96 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
22 23 4.840401 TCACGAAATTGAGCGAGTATTG 57.160 40.909 0.00 0.00 0.00 1.90
23 24 4.242475 TCACGAAATTGAGCGAGTATTGT 58.758 39.130 0.00 0.00 0.00 2.71
24 25 5.404096 TCACGAAATTGAGCGAGTATTGTA 58.596 37.500 0.00 0.00 0.00 2.41
25 26 5.287752 TCACGAAATTGAGCGAGTATTGTAC 59.712 40.000 0.00 0.00 0.00 2.90
26 27 5.288712 CACGAAATTGAGCGAGTATTGTACT 59.711 40.000 0.00 0.00 42.86 2.73
27 28 5.867716 ACGAAATTGAGCGAGTATTGTACTT 59.132 36.000 0.00 0.00 39.59 2.24
28 29 6.034683 ACGAAATTGAGCGAGTATTGTACTTC 59.965 38.462 0.00 0.00 39.59 3.01
29 30 6.508088 CGAAATTGAGCGAGTATTGTACTTCC 60.508 42.308 0.00 0.00 39.59 3.46
30 31 5.599999 ATTGAGCGAGTATTGTACTTCCT 57.400 39.130 0.00 0.00 39.59 3.36
31 32 5.401531 TTGAGCGAGTATTGTACTTCCTT 57.598 39.130 0.00 0.00 39.59 3.36
32 33 5.401531 TGAGCGAGTATTGTACTTCCTTT 57.598 39.130 0.00 0.00 39.59 3.11
33 34 6.519679 TGAGCGAGTATTGTACTTCCTTTA 57.480 37.500 0.00 0.00 39.59 1.85
34 35 7.108841 TGAGCGAGTATTGTACTTCCTTTAT 57.891 36.000 0.00 0.00 39.59 1.40
35 36 7.553334 TGAGCGAGTATTGTACTTCCTTTATT 58.447 34.615 0.00 0.00 39.59 1.40
36 37 7.705325 TGAGCGAGTATTGTACTTCCTTTATTC 59.295 37.037 0.00 0.00 39.59 1.75
37 38 7.553334 AGCGAGTATTGTACTTCCTTTATTCA 58.447 34.615 0.00 0.00 39.59 2.57
38 39 8.204836 AGCGAGTATTGTACTTCCTTTATTCAT 58.795 33.333 0.00 0.00 39.59 2.57
39 40 8.827677 GCGAGTATTGTACTTCCTTTATTCATT 58.172 33.333 0.00 0.00 39.59 2.57
111 112 9.698309 TTTTTGAGTTGTTTGAAATGACTTACA 57.302 25.926 0.00 0.00 0.00 2.41
112 113 9.698309 TTTTGAGTTGTTTGAAATGACTTACAA 57.302 25.926 0.00 0.00 0.00 2.41
113 114 9.698309 TTTGAGTTGTTTGAAATGACTTACAAA 57.302 25.926 0.00 0.00 0.00 2.83
114 115 9.698309 TTGAGTTGTTTGAAATGACTTACAAAA 57.302 25.926 0.00 0.00 34.76 2.44
115 116 9.352784 TGAGTTGTTTGAAATGACTTACAAAAG 57.647 29.630 0.00 0.00 38.77 2.27
117 118 9.139174 AGTTGTTTGAAATGACTTACAAAAGTG 57.861 29.630 0.00 0.00 46.09 3.16
118 119 9.134734 GTTGTTTGAAATGACTTACAAAAGTGA 57.865 29.630 0.00 0.00 46.09 3.41
119 120 9.868277 TTGTTTGAAATGACTTACAAAAGTGAT 57.132 25.926 0.00 0.00 46.09 3.06
122 123 8.870160 TTGAAATGACTTACAAAAGTGATTGG 57.130 30.769 4.16 0.00 45.27 3.16
123 124 8.231692 TGAAATGACTTACAAAAGTGATTGGA 57.768 30.769 4.16 0.00 45.27 3.53
124 125 8.352201 TGAAATGACTTACAAAAGTGATTGGAG 58.648 33.333 4.16 0.00 45.27 3.86
125 126 6.824305 ATGACTTACAAAAGTGATTGGAGG 57.176 37.500 0.00 0.00 46.09 4.30
126 127 5.070001 TGACTTACAAAAGTGATTGGAGGG 58.930 41.667 0.00 0.00 46.09 4.30
127 128 5.163141 TGACTTACAAAAGTGATTGGAGGGA 60.163 40.000 0.00 0.00 46.09 4.20
144 145 3.805207 AGGGAGTACATAAATCCGTTGC 58.195 45.455 0.00 0.00 33.68 4.17
189 193 0.594796 AAAGCAAGCAAAGCCGTTCG 60.595 50.000 0.00 0.00 0.00 3.95
190 194 2.406452 AAGCAAGCAAAGCCGTTCGG 62.406 55.000 6.90 6.90 0.00 4.30
247 251 3.755628 CCGACGGGCGAGAGGAAA 61.756 66.667 3.94 0.00 44.57 3.13
250 254 2.920912 ACGGGCGAGAGGAAACCA 60.921 61.111 0.00 0.00 0.00 3.67
251 255 2.125512 CGGGCGAGAGGAAACCAG 60.126 66.667 0.00 0.00 0.00 4.00
284 288 1.740285 CGCGCCTCTTGGGTAGTAT 59.260 57.895 0.00 0.00 37.43 2.12
285 289 0.956633 CGCGCCTCTTGGGTAGTATA 59.043 55.000 0.00 0.00 37.43 1.47
286 290 1.068472 CGCGCCTCTTGGGTAGTATAG 60.068 57.143 0.00 0.00 37.43 1.31
288 292 1.961394 CGCCTCTTGGGTAGTATAGCA 59.039 52.381 0.00 0.00 41.82 3.49
289 293 2.288273 CGCCTCTTGGGTAGTATAGCAC 60.288 54.545 0.00 0.00 41.82 4.40
290 294 2.966516 GCCTCTTGGGTAGTATAGCACT 59.033 50.000 0.00 0.00 41.82 4.40
291 295 4.150359 GCCTCTTGGGTAGTATAGCACTA 58.850 47.826 0.00 0.00 41.82 2.74
315 319 4.106925 GGACAGGCCCAGAGCAGG 62.107 72.222 0.00 0.00 46.50 4.85
325 329 1.817099 CAGAGCAGGCGAACCATCC 60.817 63.158 0.00 0.00 39.06 3.51
326 330 1.992277 AGAGCAGGCGAACCATCCT 60.992 57.895 0.00 0.00 39.06 3.24
335 339 0.176680 CGAACCATCCTCTCCCACAG 59.823 60.000 0.00 0.00 0.00 3.66
344 348 0.319728 CTCTCCCACAGACCACACTG 59.680 60.000 0.00 0.00 42.78 3.66
366 370 0.617535 CCCACCAAATTTCCCCTCCC 60.618 60.000 0.00 0.00 0.00 4.30
391 395 0.514691 CCGAAGTTGAACAGAGCAGC 59.485 55.000 0.00 0.00 0.00 5.25
434 448 0.261991 TCCGTCCCCTAGAATCAGCT 59.738 55.000 0.00 0.00 0.00 4.24
472 486 0.100503 GAGCTCTTCTCCACTCGAGC 59.899 60.000 13.61 0.00 46.89 5.03
485 499 2.699809 CGAGCTGCGAATCTGCAC 59.300 61.111 0.00 0.00 44.57 4.57
486 500 2.096442 CGAGCTGCGAATCTGCACA 61.096 57.895 0.00 0.00 44.57 4.57
487 501 1.426816 CGAGCTGCGAATCTGCACAT 61.427 55.000 0.00 0.00 44.57 3.21
488 502 0.027716 GAGCTGCGAATCTGCACATG 59.972 55.000 0.00 0.00 40.62 3.21
489 503 1.063649 GCTGCGAATCTGCACATGG 59.936 57.895 0.00 0.00 40.62 3.66
490 504 1.651240 GCTGCGAATCTGCACATGGT 61.651 55.000 0.00 0.00 40.62 3.55
491 505 0.806868 CTGCGAATCTGCACATGGTT 59.193 50.000 0.00 0.00 40.62 3.67
500 514 1.987770 CTGCACATGGTTTGCGATTTC 59.012 47.619 0.00 0.00 43.34 2.17
580 595 1.028905 CACAAAACCCCAGCTTTCGA 58.971 50.000 0.00 0.00 0.00 3.71
656 671 2.202703 CGCGTCCTAGGGTTTCCG 60.203 66.667 9.46 5.25 38.33 4.30
658 673 1.153686 GCGTCCTAGGGTTTCCGTC 60.154 63.158 9.46 0.00 38.33 4.79
659 674 1.138247 CGTCCTAGGGTTTCCGTCG 59.862 63.158 9.46 0.00 38.33 5.12
661 676 0.172127 GTCCTAGGGTTTCCGTCGAC 59.828 60.000 9.46 5.18 38.33 4.20
666 681 0.036671 AGGGTTTCCGTCGACAATCC 60.037 55.000 17.16 12.11 38.33 3.01
740 765 6.424176 TCGATGTCGATTATCATCTACTCC 57.576 41.667 10.82 0.00 44.22 3.85
741 766 5.354513 TCGATGTCGATTATCATCTACTCCC 59.645 44.000 10.82 0.00 44.22 4.30
742 767 5.355630 CGATGTCGATTATCATCTACTCCCT 59.644 44.000 10.82 0.00 43.02 4.20
743 768 6.457663 CGATGTCGATTATCATCTACTCCCTC 60.458 46.154 10.82 0.00 43.02 4.30
744 769 5.010933 TGTCGATTATCATCTACTCCCTCC 58.989 45.833 0.00 0.00 0.00 4.30
745 770 4.095185 GTCGATTATCATCTACTCCCTCCG 59.905 50.000 0.00 0.00 0.00 4.63
746 771 4.011023 CGATTATCATCTACTCCCTCCGT 58.989 47.826 0.00 0.00 0.00 4.69
747 772 4.459685 CGATTATCATCTACTCCCTCCGTT 59.540 45.833 0.00 0.00 0.00 4.44
748 773 5.392165 CGATTATCATCTACTCCCTCCGTTC 60.392 48.000 0.00 0.00 0.00 3.95
749 774 2.068834 TCATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
750 775 1.286849 TCATCTACTCCCTCCGTTCCA 59.713 52.381 0.00 0.00 0.00 3.53
751 776 2.091278 TCATCTACTCCCTCCGTTCCAT 60.091 50.000 0.00 0.00 0.00 3.41
752 777 3.139584 TCATCTACTCCCTCCGTTCCATA 59.860 47.826 0.00 0.00 0.00 2.74
753 778 3.675348 TCTACTCCCTCCGTTCCATAA 57.325 47.619 0.00 0.00 0.00 1.90
754 779 4.194678 TCTACTCCCTCCGTTCCATAAT 57.805 45.455 0.00 0.00 0.00 1.28
755 780 5.329191 TCTACTCCCTCCGTTCCATAATA 57.671 43.478 0.00 0.00 0.00 0.98
756 781 5.322754 TCTACTCCCTCCGTTCCATAATAG 58.677 45.833 0.00 0.00 0.00 1.73
757 782 4.194678 ACTCCCTCCGTTCCATAATAGA 57.805 45.455 0.00 0.00 0.00 1.98
758 783 4.753186 ACTCCCTCCGTTCCATAATAGAT 58.247 43.478 0.00 0.00 0.00 1.98
759 784 4.528596 ACTCCCTCCGTTCCATAATAGATG 59.471 45.833 0.00 0.00 0.00 2.90
760 785 4.747583 TCCCTCCGTTCCATAATAGATGA 58.252 43.478 0.00 0.00 0.00 2.92
761 786 4.527038 TCCCTCCGTTCCATAATAGATGAC 59.473 45.833 0.00 0.00 0.00 3.06
762 787 4.322801 CCCTCCGTTCCATAATAGATGACC 60.323 50.000 0.00 0.00 0.00 4.02
763 788 4.322801 CCTCCGTTCCATAATAGATGACCC 60.323 50.000 0.00 0.00 0.00 4.46
764 789 4.228010 TCCGTTCCATAATAGATGACCCA 58.772 43.478 0.00 0.00 0.00 4.51
765 790 4.656575 TCCGTTCCATAATAGATGACCCAA 59.343 41.667 0.00 0.00 0.00 4.12
766 791 4.755123 CCGTTCCATAATAGATGACCCAAC 59.245 45.833 0.00 0.00 0.00 3.77
767 792 5.454755 CCGTTCCATAATAGATGACCCAACT 60.455 44.000 0.00 0.00 0.00 3.16
768 793 6.055588 CGTTCCATAATAGATGACCCAACTT 58.944 40.000 0.00 0.00 0.00 2.66
769 794 6.542370 CGTTCCATAATAGATGACCCAACTTT 59.458 38.462 0.00 0.00 0.00 2.66
770 795 7.467267 CGTTCCATAATAGATGACCCAACTTTG 60.467 40.741 0.00 0.00 0.00 2.77
771 796 6.969043 TCCATAATAGATGACCCAACTTTGT 58.031 36.000 0.00 0.00 0.00 2.83
772 797 8.096621 TCCATAATAGATGACCCAACTTTGTA 57.903 34.615 0.00 0.00 0.00 2.41
773 798 7.990886 TCCATAATAGATGACCCAACTTTGTAC 59.009 37.037 0.00 0.00 0.00 2.90
774 799 7.993183 CCATAATAGATGACCCAACTTTGTACT 59.007 37.037 0.00 0.00 0.00 2.73
777 802 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
778 803 5.557866 AGATGACCCAACTTTGTACTAACC 58.442 41.667 0.00 0.00 0.00 2.85
779 804 5.309806 AGATGACCCAACTTTGTACTAACCT 59.690 40.000 0.00 0.00 0.00 3.50
780 805 5.376756 TGACCCAACTTTGTACTAACCTT 57.623 39.130 0.00 0.00 0.00 3.50
781 806 6.497624 TGACCCAACTTTGTACTAACCTTA 57.502 37.500 0.00 0.00 0.00 2.69
782 807 6.527423 TGACCCAACTTTGTACTAACCTTAG 58.473 40.000 0.00 0.00 36.82 2.18
783 808 6.100134 TGACCCAACTTTGTACTAACCTTAGT 59.900 38.462 3.29 3.29 45.39 2.24
784 809 7.289782 TGACCCAACTTTGTACTAACCTTAGTA 59.710 37.037 1.45 1.45 43.36 1.82
795 820 6.505048 ACTAACCTTAGTACAAAGTTGGGT 57.495 37.500 0.00 0.00 41.92 4.51
796 821 6.528321 ACTAACCTTAGTACAAAGTTGGGTC 58.472 40.000 0.00 0.00 41.92 4.46
797 822 5.376756 AACCTTAGTACAAAGTTGGGTCA 57.623 39.130 0.00 0.00 0.00 4.02
798 823 5.578157 ACCTTAGTACAAAGTTGGGTCAT 57.422 39.130 0.00 0.00 0.00 3.06
799 824 5.557866 ACCTTAGTACAAAGTTGGGTCATC 58.442 41.667 0.00 0.00 0.00 2.92
800 825 5.309806 ACCTTAGTACAAAGTTGGGTCATCT 59.690 40.000 0.00 0.00 0.00 2.90
801 826 6.499350 ACCTTAGTACAAAGTTGGGTCATCTA 59.501 38.462 0.00 0.00 0.00 1.98
802 827 7.182206 ACCTTAGTACAAAGTTGGGTCATCTAT 59.818 37.037 0.00 0.00 0.00 1.98
803 828 8.047310 CCTTAGTACAAAGTTGGGTCATCTATT 58.953 37.037 0.00 0.00 0.00 1.73
806 831 8.964476 AGTACAAAGTTGGGTCATCTATTATG 57.036 34.615 0.00 0.00 0.00 1.90
807 832 7.993183 AGTACAAAGTTGGGTCATCTATTATGG 59.007 37.037 0.00 0.00 0.00 2.74
808 833 6.969043 ACAAAGTTGGGTCATCTATTATGGA 58.031 36.000 0.00 0.00 0.00 3.41
809 834 7.410174 ACAAAGTTGGGTCATCTATTATGGAA 58.590 34.615 0.00 0.00 0.00 3.53
810 835 7.339466 ACAAAGTTGGGTCATCTATTATGGAAC 59.661 37.037 0.00 0.00 0.00 3.62
811 836 5.611374 AGTTGGGTCATCTATTATGGAACG 58.389 41.667 0.00 0.00 0.00 3.95
812 837 4.617253 TGGGTCATCTATTATGGAACGG 57.383 45.455 0.00 0.00 0.00 4.44
813 838 4.228010 TGGGTCATCTATTATGGAACGGA 58.772 43.478 0.00 0.00 0.00 4.69
814 839 4.283467 TGGGTCATCTATTATGGAACGGAG 59.717 45.833 0.00 0.00 0.00 4.63
815 840 4.322801 GGGTCATCTATTATGGAACGGAGG 60.323 50.000 0.00 0.00 0.00 4.30
816 841 4.322801 GGTCATCTATTATGGAACGGAGGG 60.323 50.000 0.00 0.00 0.00 4.30
817 842 4.527038 GTCATCTATTATGGAACGGAGGGA 59.473 45.833 0.00 0.00 0.00 4.20
818 843 4.772624 TCATCTATTATGGAACGGAGGGAG 59.227 45.833 0.00 0.00 0.00 4.30
819 844 4.194678 TCTATTATGGAACGGAGGGAGT 57.805 45.455 0.00 0.00 0.00 3.85
820 845 5.329191 TCTATTATGGAACGGAGGGAGTA 57.671 43.478 0.00 0.00 0.00 2.59
821 846 5.900437 TCTATTATGGAACGGAGGGAGTAT 58.100 41.667 0.00 0.00 0.00 2.12
822 847 7.036154 TCTATTATGGAACGGAGGGAGTATA 57.964 40.000 0.00 0.00 0.00 1.47
866 891 3.920412 GGTTGGTTCGATTCTTGCATTTC 59.080 43.478 0.00 0.00 0.00 2.17
900 925 3.557686 GCCCGTCAGGAAACCTAAAGTTA 60.558 47.826 0.00 0.00 41.02 2.24
958 984 4.020662 TGTGCTATGTCATGGACACTAACA 60.021 41.667 17.77 2.31 45.65 2.41
959 985 4.935205 GTGCTATGTCATGGACACTAACAA 59.065 41.667 12.96 0.00 45.65 2.83
983 1009 3.741860 GCTTGATGCAGGGATCCG 58.258 61.111 5.45 0.00 42.31 4.18
1202 1228 2.409870 CCGGCCATCCTGCTTTCAC 61.410 63.158 2.24 0.00 0.00 3.18
1212 1238 0.517132 CTGCTTTCACGTCATTCGCG 60.517 55.000 0.00 0.00 44.19 5.87
1305 1331 0.687354 AACCTGCATCTTCTCGTGGT 59.313 50.000 0.00 0.00 0.00 4.16
1350 1376 5.368989 GCTACCACCTTTGCTGATAAGTAT 58.631 41.667 0.00 0.00 0.00 2.12
1476 1502 2.172717 GCCACCTGTTATACCACTGGAT 59.827 50.000 0.71 0.00 38.75 3.41
1626 1652 2.229062 TGTGAAGACCAAACGCAACAAA 59.771 40.909 0.00 0.00 0.00 2.83
1627 1653 3.119316 TGTGAAGACCAAACGCAACAAAT 60.119 39.130 0.00 0.00 0.00 2.32
1631 1657 2.693074 AGACCAAACGCAACAAATCCTT 59.307 40.909 0.00 0.00 0.00 3.36
1698 1724 0.259647 CATCCAGCAATCCCAGGGAA 59.740 55.000 13.94 0.00 34.34 3.97
1700 1726 0.846427 TCCAGCAATCCCAGGGAAGT 60.846 55.000 13.94 0.00 34.34 3.01
1759 1785 4.212214 GGCGTAGACATCTTCAATTGGATC 59.788 45.833 5.42 0.00 31.66 3.36
1805 1831 2.749621 CAGACCTTAAGATTGGTGCCAC 59.250 50.000 3.36 0.00 36.59 5.01
1839 1865 4.652421 TGTAATCTTAGGGCTAACATCGGT 59.348 41.667 0.00 0.00 0.00 4.69
1866 1892 3.696548 GGATTGGAGTTGTTCCTGGAATC 59.303 47.826 13.07 5.83 46.92 2.52
1869 1895 2.028112 TGGAGTTGTTCCTGGAATCGAG 60.028 50.000 13.07 0.00 46.92 4.04
2475 2501 5.070685 CCAGGCCTTTTCACCTATATTACC 58.929 45.833 0.00 0.00 33.38 2.85
2567 2593 1.134521 GCCCAGTGATACCGATTGTGA 60.135 52.381 0.00 0.00 0.00 3.58
2827 2853 5.815740 GGCGAGGTTATTGATGAGAGTAAAA 59.184 40.000 0.00 0.00 0.00 1.52
2828 2854 6.018669 GGCGAGGTTATTGATGAGAGTAAAAG 60.019 42.308 0.00 0.00 0.00 2.27
2841 2870 6.552008 TGAGAGTAAAAGGAATTTGGATGGT 58.448 36.000 0.00 0.00 32.27 3.55
2842 2871 6.434028 TGAGAGTAAAAGGAATTTGGATGGTG 59.566 38.462 0.00 0.00 32.27 4.17
2843 2872 6.552008 AGAGTAAAAGGAATTTGGATGGTGA 58.448 36.000 0.00 0.00 32.27 4.02
2844 2873 7.010160 AGAGTAAAAGGAATTTGGATGGTGAA 58.990 34.615 0.00 0.00 32.27 3.18
2845 2874 7.177392 AGAGTAAAAGGAATTTGGATGGTGAAG 59.823 37.037 0.00 0.00 32.27 3.02
2846 2875 7.010160 AGTAAAAGGAATTTGGATGGTGAAGA 58.990 34.615 0.00 0.00 32.27 2.87
2982 3011 1.952296 CCACTGCCCATCAAGATAAGC 59.048 52.381 0.00 0.00 0.00 3.09
3102 3131 3.378112 ACCCACATATCATGTTCTTTGCG 59.622 43.478 0.00 0.00 42.70 4.85
3105 3134 4.273235 CCACATATCATGTTCTTTGCGCTA 59.727 41.667 9.73 0.00 42.70 4.26
3166 3195 3.204526 GGTGAGATTGGAGCTGATTCTG 58.795 50.000 0.00 0.00 0.00 3.02
3371 3401 1.281867 CCTTGCTGTTGGACATCCCTA 59.718 52.381 0.00 0.00 35.38 3.53
3391 3421 7.517320 TCCCTACTTGTCATGCATATTTACAT 58.483 34.615 0.00 0.00 0.00 2.29
3439 3485 3.004734 AGCAACTAGTTGGATGTTTGTGC 59.995 43.478 31.42 17.11 40.74 4.57
3498 3544 6.422776 ACAGAAACTGTGTTAAGAGTGTTG 57.577 37.500 3.54 0.00 43.63 3.33
3609 3661 6.672266 TTCCTGTCTAGTGTCTTGAGAAAT 57.328 37.500 0.00 0.00 0.00 2.17
3650 3703 3.252974 ACTCGAGACATTTCATGGTCC 57.747 47.619 21.68 0.00 34.58 4.46
3721 3774 6.101650 TGTCGATGTATTTCATATCCTGCT 57.898 37.500 0.00 0.00 36.83 4.24
3815 3868 4.250464 TCTGATGTTTGTAAACTAGCCCG 58.750 43.478 8.74 0.00 39.59 6.13
3846 3899 4.948341 TCTGTGAACCTAACTTGTGCTA 57.052 40.909 0.00 0.00 0.00 3.49
3850 3903 3.995048 GTGAACCTAACTTGTGCTAGTCC 59.005 47.826 0.00 0.00 0.00 3.85
3906 3959 3.008485 CCTAGAAGAAGGGAAGTGTGCTT 59.992 47.826 0.00 0.00 37.71 3.91
4090 4168 3.054878 GTCGAACCAAAACTCTTAGCGA 58.945 45.455 0.00 0.00 0.00 4.93
4116 4194 1.009675 GCCTATTGCGCCATTGTCG 60.010 57.895 4.18 0.00 0.00 4.35
4166 4360 7.546778 TTTAAAAACTTGAATTTCCTGCCAC 57.453 32.000 0.00 0.00 0.00 5.01
4197 4391 8.352942 GTTCTATGTTGAGTTCTGTTTGGATTT 58.647 33.333 0.00 0.00 0.00 2.17
4198 4392 9.567776 TTCTATGTTGAGTTCTGTTTGGATTTA 57.432 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.870426 ACAATACTCGCTCAATTTCGTGAT 59.130 37.500 0.00 0.00 0.00 3.06
1 2 4.242475 ACAATACTCGCTCAATTTCGTGA 58.758 39.130 0.00 0.00 0.00 4.35
2 3 4.584029 ACAATACTCGCTCAATTTCGTG 57.416 40.909 0.00 0.00 0.00 4.35
3 4 5.408356 AGTACAATACTCGCTCAATTTCGT 58.592 37.500 0.00 0.00 32.47 3.85
4 5 5.950965 AGTACAATACTCGCTCAATTTCG 57.049 39.130 0.00 0.00 32.47 3.46
5 6 6.535508 AGGAAGTACAATACTCGCTCAATTTC 59.464 38.462 0.00 0.00 38.26 2.17
6 7 6.407202 AGGAAGTACAATACTCGCTCAATTT 58.593 36.000 0.00 0.00 38.26 1.82
7 8 5.978814 AGGAAGTACAATACTCGCTCAATT 58.021 37.500 0.00 0.00 38.26 2.32
8 9 5.599999 AGGAAGTACAATACTCGCTCAAT 57.400 39.130 0.00 0.00 38.26 2.57
9 10 5.401531 AAGGAAGTACAATACTCGCTCAA 57.598 39.130 0.00 0.00 38.26 3.02
10 11 5.401531 AAAGGAAGTACAATACTCGCTCA 57.598 39.130 0.00 0.00 38.26 4.26
11 12 7.705325 TGAATAAAGGAAGTACAATACTCGCTC 59.295 37.037 0.00 0.00 38.26 5.03
12 13 7.553334 TGAATAAAGGAAGTACAATACTCGCT 58.447 34.615 0.00 0.00 38.26 4.93
13 14 7.766219 TGAATAAAGGAAGTACAATACTCGC 57.234 36.000 0.00 0.00 38.26 5.03
85 86 9.698309 TGTAAGTCATTTCAAACAACTCAAAAA 57.302 25.926 0.00 0.00 0.00 1.94
86 87 9.698309 TTGTAAGTCATTTCAAACAACTCAAAA 57.302 25.926 0.00 0.00 0.00 2.44
87 88 9.698309 TTTGTAAGTCATTTCAAACAACTCAAA 57.302 25.926 0.00 0.00 0.00 2.69
88 89 9.698309 TTTTGTAAGTCATTTCAAACAACTCAA 57.302 25.926 0.00 0.00 31.07 3.02
89 90 9.352784 CTTTTGTAAGTCATTTCAAACAACTCA 57.647 29.630 0.00 0.00 31.07 3.41
90 91 9.353999 ACTTTTGTAAGTCATTTCAAACAACTC 57.646 29.630 0.00 0.00 40.60 3.01
91 92 9.139174 CACTTTTGTAAGTCATTTCAAACAACT 57.861 29.630 0.00 0.00 42.67 3.16
92 93 9.134734 TCACTTTTGTAAGTCATTTCAAACAAC 57.865 29.630 0.00 0.00 42.67 3.32
93 94 9.868277 ATCACTTTTGTAAGTCATTTCAAACAA 57.132 25.926 0.00 0.00 42.67 2.83
94 95 9.868277 AATCACTTTTGTAAGTCATTTCAAACA 57.132 25.926 0.00 0.00 42.67 2.83
96 97 9.311916 CCAATCACTTTTGTAAGTCATTTCAAA 57.688 29.630 0.00 0.00 42.67 2.69
97 98 8.690884 TCCAATCACTTTTGTAAGTCATTTCAA 58.309 29.630 0.00 0.00 42.67 2.69
98 99 8.231692 TCCAATCACTTTTGTAAGTCATTTCA 57.768 30.769 0.00 0.00 42.67 2.69
99 100 7.809806 CCTCCAATCACTTTTGTAAGTCATTTC 59.190 37.037 0.00 0.00 42.67 2.17
100 101 7.255942 CCCTCCAATCACTTTTGTAAGTCATTT 60.256 37.037 0.00 0.00 42.67 2.32
101 102 6.209391 CCCTCCAATCACTTTTGTAAGTCATT 59.791 38.462 0.00 0.00 42.67 2.57
102 103 5.711976 CCCTCCAATCACTTTTGTAAGTCAT 59.288 40.000 0.00 0.00 42.67 3.06
103 104 5.070001 CCCTCCAATCACTTTTGTAAGTCA 58.930 41.667 0.00 0.00 42.67 3.41
104 105 5.313712 TCCCTCCAATCACTTTTGTAAGTC 58.686 41.667 0.00 0.00 42.67 3.01
105 106 5.163088 ACTCCCTCCAATCACTTTTGTAAGT 60.163 40.000 0.00 0.00 45.40 2.24
106 107 5.316987 ACTCCCTCCAATCACTTTTGTAAG 58.683 41.667 0.00 0.00 37.40 2.34
107 108 5.319043 ACTCCCTCCAATCACTTTTGTAA 57.681 39.130 0.00 0.00 0.00 2.41
108 109 4.993705 ACTCCCTCCAATCACTTTTGTA 57.006 40.909 0.00 0.00 0.00 2.41
109 110 3.884037 ACTCCCTCCAATCACTTTTGT 57.116 42.857 0.00 0.00 0.00 2.83
110 111 4.651778 TGTACTCCCTCCAATCACTTTTG 58.348 43.478 0.00 0.00 0.00 2.44
111 112 4.993705 TGTACTCCCTCCAATCACTTTT 57.006 40.909 0.00 0.00 0.00 2.27
112 113 6.636454 TTATGTACTCCCTCCAATCACTTT 57.364 37.500 0.00 0.00 0.00 2.66
113 114 6.636454 TTTATGTACTCCCTCCAATCACTT 57.364 37.500 0.00 0.00 0.00 3.16
114 115 6.183361 GGATTTATGTACTCCCTCCAATCACT 60.183 42.308 0.00 0.00 0.00 3.41
115 116 5.998363 GGATTTATGTACTCCCTCCAATCAC 59.002 44.000 0.00 0.00 0.00 3.06
116 117 5.221641 CGGATTTATGTACTCCCTCCAATCA 60.222 44.000 0.00 0.00 0.00 2.57
117 118 5.221661 ACGGATTTATGTACTCCCTCCAATC 60.222 44.000 0.00 0.00 0.00 2.67
118 119 4.658901 ACGGATTTATGTACTCCCTCCAAT 59.341 41.667 0.00 0.00 0.00 3.16
119 120 4.035112 ACGGATTTATGTACTCCCTCCAA 58.965 43.478 0.00 0.00 0.00 3.53
120 121 3.649843 ACGGATTTATGTACTCCCTCCA 58.350 45.455 0.00 0.00 0.00 3.86
121 122 4.377897 CAACGGATTTATGTACTCCCTCC 58.622 47.826 0.00 0.00 0.00 4.30
122 123 3.808174 GCAACGGATTTATGTACTCCCTC 59.192 47.826 0.00 0.00 0.00 4.30
123 124 3.199071 TGCAACGGATTTATGTACTCCCT 59.801 43.478 0.00 0.00 0.00 4.20
124 125 3.537580 TGCAACGGATTTATGTACTCCC 58.462 45.455 0.00 0.00 0.00 4.30
125 126 4.439057 TCTGCAACGGATTTATGTACTCC 58.561 43.478 0.00 0.00 0.00 3.85
126 127 5.559035 GCATCTGCAACGGATTTATGTACTC 60.559 44.000 0.00 0.00 41.59 2.59
127 128 4.273480 GCATCTGCAACGGATTTATGTACT 59.727 41.667 0.00 0.00 41.59 2.73
279 283 6.465464 CCTGTCCCACTAGTAGTGCTATACTA 60.465 46.154 22.67 7.94 44.63 1.82
284 288 2.949054 GCCTGTCCCACTAGTAGTGCTA 60.949 54.545 22.67 11.00 44.63 3.49
285 289 1.853963 CCTGTCCCACTAGTAGTGCT 58.146 55.000 22.67 0.00 44.63 4.40
286 290 0.175989 GCCTGTCCCACTAGTAGTGC 59.824 60.000 22.67 11.27 44.63 4.40
288 292 3.301746 GGCCTGTCCCACTAGTAGT 57.698 57.895 0.00 0.00 0.00 2.73
315 319 1.153349 GTGGGAGAGGATGGTTCGC 60.153 63.158 0.00 0.00 0.00 4.70
325 329 0.319728 CAGTGTGGTCTGTGGGAGAG 59.680 60.000 0.00 0.00 0.00 3.20
326 330 1.758440 GCAGTGTGGTCTGTGGGAGA 61.758 60.000 0.00 0.00 37.70 3.71
335 339 4.660938 GGTGGGGGCAGTGTGGTC 62.661 72.222 0.00 0.00 0.00 4.02
344 348 2.297895 GGGGAAATTTGGTGGGGGC 61.298 63.158 0.00 0.00 0.00 5.80
366 370 1.228124 TGTTCAACTTCGGGCAGGG 60.228 57.895 0.00 0.00 0.00 4.45
434 448 1.380785 ACCTTGGCGAGTATCCGGA 60.381 57.895 6.61 6.61 0.00 5.14
472 486 0.806868 AACCATGTGCAGATTCGCAG 59.193 50.000 0.00 0.00 44.05 5.18
500 514 1.498865 AACCAGCGCAACACTCGAAG 61.499 55.000 11.47 0.00 0.00 3.79
656 671 1.463674 AAATGCCCAGGATTGTCGAC 58.536 50.000 9.11 9.11 0.00 4.20
658 673 3.443681 AGTAAAAATGCCCAGGATTGTCG 59.556 43.478 0.00 0.00 0.00 4.35
659 674 4.747810 CAGTAAAAATGCCCAGGATTGTC 58.252 43.478 0.00 0.00 0.00 3.18
661 676 3.196254 AGCAGTAAAAATGCCCAGGATTG 59.804 43.478 0.00 0.00 44.97 2.67
666 681 1.547372 AGCAGCAGTAAAAATGCCCAG 59.453 47.619 0.00 0.00 44.97 4.45
737 762 4.772624 TCATCTATTATGGAACGGAGGGAG 59.227 45.833 0.00 0.00 0.00 4.30
738 763 4.527038 GTCATCTATTATGGAACGGAGGGA 59.473 45.833 0.00 0.00 0.00 4.20
739 764 4.322801 GGTCATCTATTATGGAACGGAGGG 60.323 50.000 0.00 0.00 0.00 4.30
740 765 4.322801 GGGTCATCTATTATGGAACGGAGG 60.323 50.000 0.00 0.00 0.00 4.30
741 766 4.283467 TGGGTCATCTATTATGGAACGGAG 59.717 45.833 0.00 0.00 0.00 4.63
742 767 4.228010 TGGGTCATCTATTATGGAACGGA 58.772 43.478 0.00 0.00 0.00 4.69
743 768 4.617253 TGGGTCATCTATTATGGAACGG 57.383 45.455 0.00 0.00 0.00 4.44
744 769 5.611374 AGTTGGGTCATCTATTATGGAACG 58.389 41.667 0.00 0.00 0.00 3.95
745 770 7.339466 ACAAAGTTGGGTCATCTATTATGGAAC 59.661 37.037 0.00 0.00 0.00 3.62
746 771 7.410174 ACAAAGTTGGGTCATCTATTATGGAA 58.590 34.615 0.00 0.00 0.00 3.53
747 772 6.969043 ACAAAGTTGGGTCATCTATTATGGA 58.031 36.000 0.00 0.00 0.00 3.41
748 773 7.993183 AGTACAAAGTTGGGTCATCTATTATGG 59.007 37.037 0.00 0.00 0.00 2.74
749 774 8.964476 AGTACAAAGTTGGGTCATCTATTATG 57.036 34.615 0.00 0.00 0.00 1.90
751 776 9.880157 GTTAGTACAAAGTTGGGTCATCTATTA 57.120 33.333 0.00 0.00 0.00 0.98
752 777 7.827729 GGTTAGTACAAAGTTGGGTCATCTATT 59.172 37.037 0.00 0.00 0.00 1.73
753 778 7.182206 AGGTTAGTACAAAGTTGGGTCATCTAT 59.818 37.037 0.00 0.00 0.00 1.98
754 779 6.499350 AGGTTAGTACAAAGTTGGGTCATCTA 59.501 38.462 0.00 0.00 0.00 1.98
755 780 5.309806 AGGTTAGTACAAAGTTGGGTCATCT 59.690 40.000 0.00 0.00 0.00 2.90
756 781 5.557866 AGGTTAGTACAAAGTTGGGTCATC 58.442 41.667 0.00 0.00 0.00 2.92
757 782 5.578157 AGGTTAGTACAAAGTTGGGTCAT 57.422 39.130 0.00 0.00 0.00 3.06
758 783 5.376756 AAGGTTAGTACAAAGTTGGGTCA 57.623 39.130 0.00 0.00 0.00 4.02
759 784 6.528321 ACTAAGGTTAGTACAAAGTTGGGTC 58.472 40.000 0.32 0.00 41.92 4.46
760 785 6.505048 ACTAAGGTTAGTACAAAGTTGGGT 57.495 37.500 0.32 0.00 41.92 4.51
771 796 7.289782 TGACCCAACTTTGTACTAAGGTTAGTA 59.710 37.037 19.08 5.64 43.36 1.82
772 797 6.100134 TGACCCAACTTTGTACTAAGGTTAGT 59.900 38.462 19.08 12.61 45.39 2.24
773 798 6.527423 TGACCCAACTTTGTACTAAGGTTAG 58.473 40.000 19.08 9.91 36.82 2.34
774 799 6.497624 TGACCCAACTTTGTACTAAGGTTA 57.502 37.500 19.08 4.72 0.00 2.85
775 800 5.376756 TGACCCAACTTTGTACTAAGGTT 57.623 39.130 19.08 9.89 0.00 3.50
776 801 5.309806 AGATGACCCAACTTTGTACTAAGGT 59.690 40.000 19.08 11.48 0.00 3.50
777 802 5.805728 AGATGACCCAACTTTGTACTAAGG 58.194 41.667 19.08 6.74 0.00 2.69
781 806 7.993183 CCATAATAGATGACCCAACTTTGTACT 59.007 37.037 0.00 0.00 0.00 2.73
782 807 7.990886 TCCATAATAGATGACCCAACTTTGTAC 59.009 37.037 0.00 0.00 0.00 2.90
783 808 8.096621 TCCATAATAGATGACCCAACTTTGTA 57.903 34.615 0.00 0.00 0.00 2.41
784 809 6.969043 TCCATAATAGATGACCCAACTTTGT 58.031 36.000 0.00 0.00 0.00 2.83
785 810 7.467267 CGTTCCATAATAGATGACCCAACTTTG 60.467 40.741 0.00 0.00 0.00 2.77
786 811 6.542370 CGTTCCATAATAGATGACCCAACTTT 59.458 38.462 0.00 0.00 0.00 2.66
787 812 6.055588 CGTTCCATAATAGATGACCCAACTT 58.944 40.000 0.00 0.00 0.00 2.66
788 813 5.454755 CCGTTCCATAATAGATGACCCAACT 60.455 44.000 0.00 0.00 0.00 3.16
789 814 4.755123 CCGTTCCATAATAGATGACCCAAC 59.245 45.833 0.00 0.00 0.00 3.77
790 815 4.656575 TCCGTTCCATAATAGATGACCCAA 59.343 41.667 0.00 0.00 0.00 4.12
791 816 4.228010 TCCGTTCCATAATAGATGACCCA 58.772 43.478 0.00 0.00 0.00 4.51
792 817 4.322801 CCTCCGTTCCATAATAGATGACCC 60.323 50.000 0.00 0.00 0.00 4.46
793 818 4.322801 CCCTCCGTTCCATAATAGATGACC 60.323 50.000 0.00 0.00 0.00 4.02
794 819 4.527038 TCCCTCCGTTCCATAATAGATGAC 59.473 45.833 0.00 0.00 0.00 3.06
795 820 4.747583 TCCCTCCGTTCCATAATAGATGA 58.252 43.478 0.00 0.00 0.00 2.92
796 821 4.528596 ACTCCCTCCGTTCCATAATAGATG 59.471 45.833 0.00 0.00 0.00 2.90
797 822 4.753186 ACTCCCTCCGTTCCATAATAGAT 58.247 43.478 0.00 0.00 0.00 1.98
798 823 4.194678 ACTCCCTCCGTTCCATAATAGA 57.805 45.455 0.00 0.00 0.00 1.98
799 824 7.899648 ATATACTCCCTCCGTTCCATAATAG 57.100 40.000 0.00 0.00 0.00 1.73
800 825 8.674925 AAATATACTCCCTCCGTTCCATAATA 57.325 34.615 0.00 0.00 0.00 0.98
801 826 7.569599 AAATATACTCCCTCCGTTCCATAAT 57.430 36.000 0.00 0.00 0.00 1.28
802 827 7.147444 ACAAAATATACTCCCTCCGTTCCATAA 60.147 37.037 0.00 0.00 0.00 1.90
803 828 6.328148 ACAAAATATACTCCCTCCGTTCCATA 59.672 38.462 0.00 0.00 0.00 2.74
804 829 5.132144 ACAAAATATACTCCCTCCGTTCCAT 59.868 40.000 0.00 0.00 0.00 3.41
805 830 4.472108 ACAAAATATACTCCCTCCGTTCCA 59.528 41.667 0.00 0.00 0.00 3.53
806 831 5.032327 ACAAAATATACTCCCTCCGTTCC 57.968 43.478 0.00 0.00 0.00 3.62
807 832 6.997239 AAACAAAATATACTCCCTCCGTTC 57.003 37.500 0.00 0.00 0.00 3.95
808 833 6.152154 CCAAAACAAAATATACTCCCTCCGTT 59.848 38.462 0.00 0.00 0.00 4.44
809 834 5.650703 CCAAAACAAAATATACTCCCTCCGT 59.349 40.000 0.00 0.00 0.00 4.69
810 835 5.650703 ACCAAAACAAAATATACTCCCTCCG 59.349 40.000 0.00 0.00 0.00 4.63
811 836 7.476540 AACCAAAACAAAATATACTCCCTCC 57.523 36.000 0.00 0.00 0.00 4.30
812 837 9.203421 CAAAACCAAAACAAAATATACTCCCTC 57.797 33.333 0.00 0.00 0.00 4.30
813 838 7.659799 GCAAAACCAAAACAAAATATACTCCCT 59.340 33.333 0.00 0.00 0.00 4.20
814 839 7.659799 AGCAAAACCAAAACAAAATATACTCCC 59.340 33.333 0.00 0.00 0.00 4.30
815 840 8.601845 AGCAAAACCAAAACAAAATATACTCC 57.398 30.769 0.00 0.00 0.00 3.85
816 841 8.708742 GGAGCAAAACCAAAACAAAATATACTC 58.291 33.333 0.00 0.00 0.00 2.59
817 842 8.428852 AGGAGCAAAACCAAAACAAAATATACT 58.571 29.630 0.00 0.00 0.00 2.12
818 843 8.495148 CAGGAGCAAAACCAAAACAAAATATAC 58.505 33.333 0.00 0.00 0.00 1.47
819 844 7.659390 CCAGGAGCAAAACCAAAACAAAATATA 59.341 33.333 0.00 0.00 0.00 0.86
820 845 6.486320 CCAGGAGCAAAACCAAAACAAAATAT 59.514 34.615 0.00 0.00 0.00 1.28
821 846 5.819901 CCAGGAGCAAAACCAAAACAAAATA 59.180 36.000 0.00 0.00 0.00 1.40
822 847 4.639755 CCAGGAGCAAAACCAAAACAAAAT 59.360 37.500 0.00 0.00 0.00 1.82
866 891 1.445582 GACGGGCCACAGTAGTTCG 60.446 63.158 4.39 0.00 0.00 3.95
900 925 5.712917 TGCGGGGAAATGTAATAAAGTTTCT 59.287 36.000 0.00 0.00 32.61 2.52
907 932 3.290948 AGCTGCGGGGAAATGTAATAA 57.709 42.857 0.00 0.00 0.00 1.40
908 933 3.735591 GTAGCTGCGGGGAAATGTAATA 58.264 45.455 0.00 0.00 0.00 0.98
909 934 2.572290 GTAGCTGCGGGGAAATGTAAT 58.428 47.619 0.00 0.00 0.00 1.89
1047 1073 0.542938 TCCTCAGGGGCTGGATATCG 60.543 60.000 0.00 0.00 34.39 2.92
1119 1145 1.149986 TCAATGGTGGGGTGGTGTTA 58.850 50.000 0.00 0.00 0.00 2.41
1305 1331 3.083349 CCTCCACCGGCATCCTGA 61.083 66.667 0.00 0.00 0.00 3.86
1325 1351 0.034089 ATCAGCAAAGGTGGTAGCCC 60.034 55.000 0.00 0.00 33.05 5.19
1350 1376 1.225426 CTGGCCTCCATTAGCAGCA 59.775 57.895 3.32 0.00 30.82 4.41
1412 1438 6.275381 TGATATAGGGATGACATCAATTGGGT 59.725 38.462 17.08 4.46 0.00 4.51
1476 1502 3.438360 CTCATTGTCATCGTCATCGTCA 58.562 45.455 0.00 0.00 38.33 4.35
1631 1657 1.228245 GCACCAGCCTTCCTGTGAA 60.228 57.895 0.00 0.00 40.06 3.18
1698 1724 3.648067 TCATGAGAACCTCTTCCACAACT 59.352 43.478 0.00 0.00 0.00 3.16
1700 1726 4.389374 GTTCATGAGAACCTCTTCCACAA 58.611 43.478 0.00 0.00 46.68 3.33
1759 1785 2.808543 GTTTGGTACTCTCTTGTGCCTG 59.191 50.000 0.00 0.00 42.13 4.85
1805 1831 4.248859 CCTAAGATTACAGGCCATCATCG 58.751 47.826 5.01 0.00 0.00 3.84
1816 1842 4.652421 ACCGATGTTAGCCCTAAGATTACA 59.348 41.667 0.07 0.00 30.42 2.41
1866 1892 8.123639 TGAAGTAGAAAATATCCCCTATCTCG 57.876 38.462 0.00 0.00 0.00 4.04
1869 1895 8.437274 TCCTGAAGTAGAAAATATCCCCTATC 57.563 38.462 0.00 0.00 0.00 2.08
2567 2593 4.666512 ACCTCCATTAAACTCTGCACAAT 58.333 39.130 0.00 0.00 0.00 2.71
2827 2853 5.197224 TCATCTTCACCATCCAAATTCCT 57.803 39.130 0.00 0.00 0.00 3.36
2828 2854 5.653769 TCTTCATCTTCACCATCCAAATTCC 59.346 40.000 0.00 0.00 0.00 3.01
2841 2870 9.519191 TGAAAAAGGTAATCATCTTCATCTTCA 57.481 29.630 0.00 0.00 0.00 3.02
2843 2872 9.745018 TCTGAAAAAGGTAATCATCTTCATCTT 57.255 29.630 0.00 0.00 0.00 2.40
2844 2873 9.171877 GTCTGAAAAAGGTAATCATCTTCATCT 57.828 33.333 0.00 0.00 0.00 2.90
2845 2874 9.171877 AGTCTGAAAAAGGTAATCATCTTCATC 57.828 33.333 0.00 0.00 0.00 2.92
2846 2875 8.954350 CAGTCTGAAAAAGGTAATCATCTTCAT 58.046 33.333 0.00 0.00 0.00 2.57
2982 3011 4.559153 AGATGTTTCCCATTTTCTTTGCG 58.441 39.130 0.00 0.00 32.56 4.85
3018 3047 1.138266 GCGTTAGGGGAGCAACTATGA 59.862 52.381 0.00 0.00 0.00 2.15
3102 3131 0.255890 TGGGAGGGATGTGCTTTAGC 59.744 55.000 0.00 0.00 42.50 3.09
3105 3134 1.002069 TCATGGGAGGGATGTGCTTT 58.998 50.000 0.00 0.00 0.00 3.51
3166 3195 2.966516 CTCCAGGAGAACCTATACCACC 59.033 54.545 11.62 0.00 45.94 4.61
3391 3421 2.951457 TCGAATACGAACCAGATGCA 57.049 45.000 0.00 0.00 45.74 3.96
3815 3868 1.149148 GGTTCACAGAAAGTCGAGGC 58.851 55.000 0.00 0.00 0.00 4.70
3906 3959 2.090550 TCATGAGGGGAGCCATCTTAGA 60.091 50.000 0.00 0.00 35.13 2.10
3907 3960 2.038295 GTCATGAGGGGAGCCATCTTAG 59.962 54.545 0.00 0.00 35.13 2.18
3908 3961 2.050144 GTCATGAGGGGAGCCATCTTA 58.950 52.381 0.00 0.00 35.13 2.10
3909 3962 0.842635 GTCATGAGGGGAGCCATCTT 59.157 55.000 0.00 0.00 35.13 2.40
3910 3963 0.030297 AGTCATGAGGGGAGCCATCT 60.030 55.000 0.00 0.00 35.13 2.90
3911 3964 0.108207 CAGTCATGAGGGGAGCCATC 59.892 60.000 0.00 0.00 34.60 3.51
4090 4168 1.247567 GGCGCAATAGGCATATTGGT 58.752 50.000 27.13 0.00 45.67 3.67
4116 4194 2.678190 GCCCACTGGTCTGAACATACTC 60.678 54.545 0.00 0.00 0.00 2.59
4148 4342 3.299503 ACTGTGGCAGGAAATTCAAGTT 58.700 40.909 0.00 0.00 35.51 2.66
4149 4343 2.949447 ACTGTGGCAGGAAATTCAAGT 58.051 42.857 0.00 0.00 35.51 3.16
4166 4360 6.851222 ACAGAACTCAACATAGAACAACTG 57.149 37.500 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.