Multiple sequence alignment - TraesCS1A01G142500

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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 TraesCS1A01G142500 chr1A 100.000 6892 0 0 1 6892 243625532 243618641 0.000000e+00 12728.0
1 TraesCS1A01G142500 chr1A 92.810 153 6 3 3809 3961 243621571 243621424 4.190000e-52 217.0
2 TraesCS1A01G142500 chr1A 92.810 153 6 3 3962 4109 243621724 243621572 4.190000e-52 217.0
3 TraesCS1A01G142500 chr1D 95.851 2169 50 10 924 3068 195195624 195193472 0.000000e+00 3470.0
4 TraesCS1A01G142500 chr1D 95.415 1745 53 10 4615 6351 195191698 195189973 0.000000e+00 2754.0
5 TraesCS1A01G142500 chr1D 95.883 1093 21 3 3067 4159 195193348 195192280 0.000000e+00 1748.0
6 TraesCS1A01G142500 chr1D 89.480 789 78 4 1 785 202284562 202285349 0.000000e+00 992.0
7 TraesCS1A01G142500 chr1D 96.989 465 8 2 4157 4615 195192209 195191745 0.000000e+00 776.0
8 TraesCS1A01G142500 chr1D 95.570 158 5 1 6737 6892 54172994 54173151 1.150000e-62 252.0
9 TraesCS1A01G142500 chr1D 93.960 149 8 1 3962 4109 195192626 195192478 2.500000e-54 224.0
10 TraesCS1A01G142500 chr1D 93.464 153 5 3 3809 3961 195192477 195192330 9.000000e-54 222.0
11 TraesCS1A01G142500 chr1B 95.434 1555 48 9 4804 6351 270319992 270321530 0.000000e+00 2457.0
12 TraesCS1A01G142500 chr1B 95.238 924 29 4 1470 2381 270313842 270314762 0.000000e+00 1448.0
13 TraesCS1A01G142500 chr1B 97.798 772 16 1 3084 3855 270317670 270318440 0.000000e+00 1330.0
14 TraesCS1A01G142500 chr1B 97.784 722 15 1 2366 3086 270314776 270315497 0.000000e+00 1243.0
15 TraesCS1A01G142500 chr1B 94.384 552 15 5 924 1474 270312313 270312849 0.000000e+00 833.0
16 TraesCS1A01G142500 chr1B 94.839 465 18 2 4157 4615 270318932 270319396 0.000000e+00 721.0
17 TraesCS1A01G142500 chr1B 95.779 308 5 3 3852 4159 270318562 270318861 2.230000e-134 490.0
18 TraesCS1A01G142500 chr1B 94.118 170 7 2 4616 4785 270319447 270319613 8.870000e-64 255.0
19 TraesCS1A01G142500 chr1B 90.909 176 7 7 3786 3961 270318645 270318811 1.930000e-55 228.0
20 TraesCS1A01G142500 chr1B 91.837 98 6 2 4003 4100 270318563 270318658 1.210000e-27 135.0
21 TraesCS1A01G142500 chr7A 88.283 862 96 4 1 859 68339337 68340196 0.000000e+00 1027.0
22 TraesCS1A01G142500 chr7A 94.304 158 7 1 6737 6892 51366535 51366378 2.480000e-59 241.0
23 TraesCS1A01G142500 chr7A 100.000 28 0 0 2340 2367 50241795 50241822 1.200000e-02 52.8
24 TraesCS1A01G142500 chr4A 88.167 862 97 4 1 859 476335865 476336724 0.000000e+00 1022.0
25 TraesCS1A01G142500 chr7B 85.963 862 114 6 1 859 626060520 626059663 0.000000e+00 915.0
26 TraesCS1A01G142500 chr7B 93.038 158 9 1 6737 6892 14725618 14725775 5.380000e-56 230.0
27 TraesCS1A01G142500 chr3A 85.469 874 119 6 1 870 42452702 42453571 0.000000e+00 904.0
28 TraesCS1A01G142500 chr3A 92.500 40 2 1 6141 6179 26873306 26873345 1.000000e-03 56.5
29 TraesCS1A01G142500 chr3A 94.444 36 1 1 6141 6175 26827713 26827678 3.000000e-03 54.7
30 TraesCS1A01G142500 chr6D 85.698 853 111 9 11 859 139360608 139359763 0.000000e+00 889.0
31 TraesCS1A01G142500 chr3D 85.352 867 113 11 1 859 144255521 144254661 0.000000e+00 885.0
32 TraesCS1A01G142500 chr3D 92.405 158 10 1 6737 6892 582613034 582613191 2.500000e-54 224.0
33 TraesCS1A01G142500 chr7D 85.284 863 117 8 1 859 418680806 418679950 0.000000e+00 881.0
34 TraesCS1A01G142500 chr7D 89.000 300 27 5 6337 6632 633922889 633923186 3.930000e-97 366.0
35 TraesCS1A01G142500 chr7D 91.071 224 19 1 6669 6892 633923178 633923400 1.120000e-77 302.0
36 TraesCS1A01G142500 chr7D 90.654 214 14 2 6679 6892 372963147 372963354 5.260000e-71 279.0
37 TraesCS1A01G142500 chr7D 93.919 148 7 1 6737 6882 622500623 622500476 9.000000e-54 222.0
38 TraesCS1A01G142500 chr6A 84.977 872 120 8 1 867 496212736 496211871 0.000000e+00 874.0
39 TraesCS1A01G142500 chr2B 94.304 158 7 1 6737 6892 752942876 752942719 2.480000e-59 241.0
40 TraesCS1A01G142500 chr2B 80.114 176 23 10 6459 6628 18318885 18318716 3.380000e-23 121.0
41 TraesCS1A01G142500 chr3B 81.481 216 33 7 6680 6892 814629563 814629352 3.310000e-38 171.0
42 TraesCS1A01G142500 chr5A 88.525 61 5 1 6114 6172 41166214 41166274 9.590000e-09 73.1


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 TraesCS1A01G142500 chr1A 243618641 243625532 6891 True 12728.000000 12728 100.000000 1 6892 1 chr1A.!!$R1 6891
1 TraesCS1A01G142500 chr1D 195189973 195195624 5651 True 1532.333333 3470 95.260333 924 6351 6 chr1D.!!$R1 5427
2 TraesCS1A01G142500 chr1D 202284562 202285349 787 False 992.000000 992 89.480000 1 785 1 chr1D.!!$F2 784
3 TraesCS1A01G142500 chr1B 270312313 270321530 9217 False 914.000000 2457 94.812000 924 6351 10 chr1B.!!$F1 5427
4 TraesCS1A01G142500 chr7A 68339337 68340196 859 False 1027.000000 1027 88.283000 1 859 1 chr7A.!!$F2 858
5 TraesCS1A01G142500 chr4A 476335865 476336724 859 False 1022.000000 1022 88.167000 1 859 1 chr4A.!!$F1 858
6 TraesCS1A01G142500 chr7B 626059663 626060520 857 True 915.000000 915 85.963000 1 859 1 chr7B.!!$R1 858
7 TraesCS1A01G142500 chr3A 42452702 42453571 869 False 904.000000 904 85.469000 1 870 1 chr3A.!!$F2 869
8 TraesCS1A01G142500 chr6D 139359763 139360608 845 True 889.000000 889 85.698000 11 859 1 chr6D.!!$R1 848
9 TraesCS1A01G142500 chr3D 144254661 144255521 860 True 885.000000 885 85.352000 1 859 1 chr3D.!!$R1 858
10 TraesCS1A01G142500 chr7D 418679950 418680806 856 True 881.000000 881 85.284000 1 859 1 chr7D.!!$R1 858
11 TraesCS1A01G142500 chr7D 633922889 633923400 511 False 334.000000 366 90.035500 6337 6892 2 chr7D.!!$F2 555
12 TraesCS1A01G142500 chr6A 496211871 496212736 865 True 874.000000 874 84.977000 1 867 1 chr6A.!!$R1 866

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
825 837 0.106419 TGGGTTTTGTCTGGGTCCAC 60.106 55.000 0.00 0.0 0.00 4.02 F
908 920 0.109781 CGTGAAAAACGCATGGGAGG 60.110 55.000 17.76 0.0 46.99 4.30 F
909 921 0.243636 GTGAAAAACGCATGGGAGGG 59.756 55.000 17.76 0.0 0.00 4.30 F
910 922 1.215382 GAAAAACGCATGGGAGGGC 59.785 57.895 17.76 0.0 0.00 5.19 F
2211 3230 1.467374 GCGCGTTGCTATTGGAATTGT 60.467 47.619 8.43 0.0 41.73 2.71 F
3918 7408 0.041238 TGGGAAGAGGGACGATCTGT 59.959 55.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 3659 1.483595 CCCAGACTTCCTCAGGCACA 61.484 60.000 0.00 0.0 29.16 4.57 R
3062 4125 8.531982 AGCTGGCGAGTCAAAAAGATATATATA 58.468 33.333 0.00 0.0 0.00 0.86 R
3086 4274 2.891112 CTCTCAGTCAATGGTCAGAGC 58.109 52.381 0.00 0.0 0.00 4.09 R
3142 6507 7.319646 TCCCAATGTTATTTCAACTAATGCAC 58.680 34.615 0.00 0.0 0.00 4.57 R
4381 8020 0.397941 TGCATGCTAGGATAGGTGGC 59.602 55.000 20.33 0.0 39.70 5.01 R
6046 10116 1.172175 TTGCAACGCATAGGCAATCA 58.828 45.000 0.00 0.0 42.12 2.57 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
52 53 0.249120 TTGCCGATCTCGATGTGGTT 59.751 50.000 0.22 0.00 43.02 3.67
53 54 1.107945 TGCCGATCTCGATGTGGTTA 58.892 50.000 0.22 0.00 43.02 2.85
200 201 2.044555 CGTCCAGAGGGCGTGACTA 61.045 63.158 1.21 0.00 0.00 2.59
204 205 1.101635 CCAGAGGGCGTGACTATCGA 61.102 60.000 0.00 0.00 0.00 3.59
206 207 0.393944 AGAGGGCGTGACTATCGACA 60.394 55.000 0.00 0.00 38.15 4.35
341 342 3.374402 CTCCACGTCTCCGGCACT 61.374 66.667 0.00 0.00 38.78 4.40
351 352 4.758251 CCGGCACTCGCATGTCCA 62.758 66.667 0.00 0.00 41.24 4.02
388 389 1.006571 CCTCGTACAACAGCCGTGT 60.007 57.895 0.00 0.00 39.19 4.49
474 476 2.036733 TCGACCATCTTTTCTTGTCGGT 59.963 45.455 10.02 0.00 46.36 4.69
514 517 2.262915 CTTTCTGCGCCGGAGAGT 59.737 61.111 10.31 0.00 0.00 3.24
541 545 1.620739 ATGAGAGCTGTGGCGTCCAT 61.621 55.000 0.00 0.00 44.37 3.41
545 549 4.760047 GCTGTGGCGTCCATCGGT 62.760 66.667 1.90 0.00 40.26 4.69
710 715 1.607178 TCCCGCGGGAACTAAGACA 60.607 57.895 43.93 19.11 42.05 3.41
718 726 1.209747 GGGAACTAAGACAAGGGCGAT 59.790 52.381 0.00 0.00 0.00 4.58
764 772 1.080839 CCCATCCGTTTTTGTGCCG 60.081 57.895 0.00 0.00 0.00 5.69
776 784 2.506217 GTGCCGAATCGTCTCGCA 60.506 61.111 0.82 0.62 37.51 5.10
811 823 3.289834 CTTGCAGCGTGCTGGGTT 61.290 61.111 22.22 0.00 45.31 4.11
812 824 2.832661 TTGCAGCGTGCTGGGTTT 60.833 55.556 22.22 0.00 45.31 3.27
813 825 2.354074 CTTGCAGCGTGCTGGGTTTT 62.354 55.000 22.22 0.00 45.31 2.43
814 826 2.355009 GCAGCGTGCTGGGTTTTG 60.355 61.111 22.22 0.00 43.77 2.44
815 827 3.119193 CAGCGTGCTGGGTTTTGT 58.881 55.556 14.00 0.00 40.17 2.83
816 828 1.008538 CAGCGTGCTGGGTTTTGTC 60.009 57.895 14.00 0.00 40.17 3.18
817 829 1.152963 AGCGTGCTGGGTTTTGTCT 60.153 52.632 0.00 0.00 0.00 3.41
818 830 1.008538 GCGTGCTGGGTTTTGTCTG 60.009 57.895 0.00 0.00 0.00 3.51
819 831 1.654220 CGTGCTGGGTTTTGTCTGG 59.346 57.895 0.00 0.00 0.00 3.86
820 832 1.795170 CGTGCTGGGTTTTGTCTGGG 61.795 60.000 0.00 0.00 0.00 4.45
821 833 0.755327 GTGCTGGGTTTTGTCTGGGT 60.755 55.000 0.00 0.00 0.00 4.51
822 834 0.467290 TGCTGGGTTTTGTCTGGGTC 60.467 55.000 0.00 0.00 0.00 4.46
823 835 1.179174 GCTGGGTTTTGTCTGGGTCC 61.179 60.000 0.00 0.00 0.00 4.46
824 836 0.184933 CTGGGTTTTGTCTGGGTCCA 59.815 55.000 0.00 0.00 0.00 4.02
825 837 0.106419 TGGGTTTTGTCTGGGTCCAC 60.106 55.000 0.00 0.00 0.00 4.02
826 838 0.826256 GGGTTTTGTCTGGGTCCACC 60.826 60.000 0.00 0.00 40.81 4.61
827 839 1.170290 GGTTTTGTCTGGGTCCACCG 61.170 60.000 0.00 0.00 44.64 4.94
828 840 0.179040 GTTTTGTCTGGGTCCACCGA 60.179 55.000 0.00 0.00 44.64 4.69
829 841 0.179040 TTTTGTCTGGGTCCACCGAC 60.179 55.000 0.00 3.33 44.64 4.79
830 842 2.372040 TTTGTCTGGGTCCACCGACG 62.372 60.000 0.00 0.00 44.64 5.12
831 843 3.300765 GTCTGGGTCCACCGACGT 61.301 66.667 0.00 0.00 44.64 4.34
832 844 2.522436 TCTGGGTCCACCGACGTT 60.522 61.111 0.00 0.00 44.64 3.99
833 845 1.228521 TCTGGGTCCACCGACGTTA 60.229 57.895 0.00 0.00 44.64 3.18
834 846 0.827089 TCTGGGTCCACCGACGTTAA 60.827 55.000 0.00 0.00 44.64 2.01
835 847 0.248289 CTGGGTCCACCGACGTTAAT 59.752 55.000 0.00 0.00 44.64 1.40
836 848 0.686224 TGGGTCCACCGACGTTAATT 59.314 50.000 0.00 0.00 44.64 1.40
837 849 1.072015 TGGGTCCACCGACGTTAATTT 59.928 47.619 0.00 0.00 44.64 1.82
838 850 1.733912 GGGTCCACCGACGTTAATTTC 59.266 52.381 0.00 0.00 40.17 2.17
839 851 1.391144 GGTCCACCGACGTTAATTTCG 59.609 52.381 0.00 2.51 40.17 3.46
846 858 3.791993 CGACGTTAATTTCGGTCCAAA 57.208 42.857 0.00 0.00 0.00 3.28
847 859 3.472431 CGACGTTAATTTCGGTCCAAAC 58.528 45.455 0.00 0.00 0.00 2.93
848 860 3.184986 CGACGTTAATTTCGGTCCAAACT 59.815 43.478 0.00 0.00 0.00 2.66
849 861 4.460505 GACGTTAATTTCGGTCCAAACTG 58.539 43.478 0.00 0.00 0.00 3.16
850 862 4.128643 ACGTTAATTTCGGTCCAAACTGA 58.871 39.130 7.44 0.00 39.06 3.41
851 863 4.024641 ACGTTAATTTCGGTCCAAACTGAC 60.025 41.667 7.44 0.00 40.54 3.51
852 864 4.460505 GTTAATTTCGGTCCAAACTGACG 58.539 43.478 0.00 0.00 40.54 4.35
853 865 2.536761 ATTTCGGTCCAAACTGACGA 57.463 45.000 0.00 0.00 40.54 4.20
854 866 2.312722 TTTCGGTCCAAACTGACGAA 57.687 45.000 0.00 0.00 40.54 3.85
855 867 2.312722 TTCGGTCCAAACTGACGAAA 57.687 45.000 0.00 0.00 40.54 3.46
856 868 2.312722 TCGGTCCAAACTGACGAAAA 57.687 45.000 0.00 0.00 35.82 2.29
857 869 2.630158 TCGGTCCAAACTGACGAAAAA 58.370 42.857 0.00 0.00 35.82 1.94
858 870 2.352342 TCGGTCCAAACTGACGAAAAAC 59.648 45.455 0.00 0.00 35.82 2.43
859 871 2.096174 CGGTCCAAACTGACGAAAAACA 59.904 45.455 0.00 0.00 36.07 2.83
860 872 3.426426 CGGTCCAAACTGACGAAAAACAA 60.426 43.478 0.00 0.00 36.07 2.83
861 873 4.102649 GGTCCAAACTGACGAAAAACAAG 58.897 43.478 0.00 0.00 36.07 3.16
862 874 4.102649 GTCCAAACTGACGAAAAACAAGG 58.897 43.478 0.00 0.00 0.00 3.61
863 875 3.759618 TCCAAACTGACGAAAAACAAGGT 59.240 39.130 0.00 0.00 0.00 3.50
864 876 4.218852 TCCAAACTGACGAAAAACAAGGTT 59.781 37.500 0.00 0.00 0.00 3.50
865 877 4.561213 CCAAACTGACGAAAAACAAGGTTC 59.439 41.667 0.00 0.00 0.00 3.62
866 878 5.399013 CAAACTGACGAAAAACAAGGTTCT 58.601 37.500 0.00 0.00 0.00 3.01
867 879 4.616181 ACTGACGAAAAACAAGGTTCTG 57.384 40.909 0.00 0.00 0.00 3.02
868 880 4.258543 ACTGACGAAAAACAAGGTTCTGA 58.741 39.130 0.00 0.00 0.00 3.27
869 881 4.332819 ACTGACGAAAAACAAGGTTCTGAG 59.667 41.667 0.00 0.00 0.00 3.35
870 882 4.509616 TGACGAAAAACAAGGTTCTGAGA 58.490 39.130 0.00 0.00 0.00 3.27
871 883 5.123227 TGACGAAAAACAAGGTTCTGAGAT 58.877 37.500 0.00 0.00 0.00 2.75
872 884 6.285224 TGACGAAAAACAAGGTTCTGAGATA 58.715 36.000 0.00 0.00 0.00 1.98
873 885 6.934645 TGACGAAAAACAAGGTTCTGAGATAT 59.065 34.615 0.00 0.00 0.00 1.63
874 886 7.117812 TGACGAAAAACAAGGTTCTGAGATATC 59.882 37.037 0.00 0.00 0.00 1.63
875 887 6.934645 ACGAAAAACAAGGTTCTGAGATATCA 59.065 34.615 5.32 0.00 0.00 2.15
876 888 7.095187 ACGAAAAACAAGGTTCTGAGATATCAC 60.095 37.037 5.32 0.00 0.00 3.06
877 889 7.118390 CGAAAAACAAGGTTCTGAGATATCACT 59.882 37.037 5.32 0.00 0.00 3.41
878 890 8.697507 AAAAACAAGGTTCTGAGATATCACTT 57.302 30.769 5.32 0.00 0.00 3.16
879 891 8.697507 AAAACAAGGTTCTGAGATATCACTTT 57.302 30.769 5.32 0.00 0.00 2.66
880 892 7.678947 AACAAGGTTCTGAGATATCACTTTG 57.321 36.000 5.32 9.05 32.34 2.77
881 893 5.645497 ACAAGGTTCTGAGATATCACTTTGC 59.355 40.000 5.32 0.00 29.87 3.68
882 894 4.437239 AGGTTCTGAGATATCACTTTGCG 58.563 43.478 5.32 0.00 0.00 4.85
883 895 4.081420 AGGTTCTGAGATATCACTTTGCGT 60.081 41.667 5.32 0.00 0.00 5.24
884 896 4.268884 GGTTCTGAGATATCACTTTGCGTC 59.731 45.833 5.32 0.00 0.00 5.19
885 897 3.695816 TCTGAGATATCACTTTGCGTCG 58.304 45.455 5.32 0.00 0.00 5.12
886 898 2.791560 CTGAGATATCACTTTGCGTCGG 59.208 50.000 5.32 0.00 0.00 4.79
887 899 1.523095 GAGATATCACTTTGCGTCGGC 59.477 52.381 5.32 0.00 40.52 5.54
888 900 0.229753 GATATCACTTTGCGTCGGCG 59.770 55.000 4.29 4.29 44.10 6.46
898 910 2.789723 CGTCGGCGCGTGAAAAAC 60.790 61.111 8.43 0.00 0.00 2.43
907 919 3.383026 CGTGAAAAACGCATGGGAG 57.617 52.632 17.76 0.00 46.99 4.30
908 920 0.109781 CGTGAAAAACGCATGGGAGG 60.110 55.000 17.76 0.00 46.99 4.30
909 921 0.243636 GTGAAAAACGCATGGGAGGG 59.756 55.000 17.76 0.00 0.00 4.30
910 922 1.215382 GAAAAACGCATGGGAGGGC 59.785 57.895 17.76 0.00 0.00 5.19
1011 1026 3.423154 CGAGCAGCGGGGAAACAC 61.423 66.667 0.00 0.00 36.03 3.32
1173 1188 3.152341 CCAGAAACTCATCTGCAAAGGT 58.848 45.455 0.00 0.00 44.43 3.50
1222 1237 2.966516 ACGGGAATTTGCTTTGGGTTAA 59.033 40.909 0.00 0.00 0.00 2.01
1257 1272 6.932400 TGTTTCTCTTACTTTCCTTGCGATTA 59.068 34.615 0.00 0.00 0.00 1.75
1352 1367 1.945819 GCTTCGCAGGGTCTTCATCAA 60.946 52.381 0.00 0.00 0.00 2.57
1387 1402 9.035890 TCACCTTGATTTCTTCTCTAATCTGTA 57.964 33.333 0.00 0.00 33.08 2.74
1389 1404 7.976734 ACCTTGATTTCTTCTCTAATCTGTACG 59.023 37.037 0.00 0.00 33.08 3.67
1414 1429 1.490621 TTTCGTTCGTTCTCCCGTTC 58.509 50.000 0.00 0.00 0.00 3.95
1483 2494 5.648092 AGTCATGTGCTTTTATGGTTACTCC 59.352 40.000 0.00 0.00 0.00 3.85
1542 2553 4.024670 ACGTTAGTAGGATGAGGAGCTTT 58.975 43.478 0.00 0.00 0.00 3.51
1699 2710 8.239314 AGTCAATTGTAAAAGCATGTCATACAG 58.761 33.333 5.13 0.00 0.00 2.74
2046 3057 4.457949 GTGGAAGTTCCCGTGTCAATTAAT 59.542 41.667 19.42 0.00 35.03 1.40
2066 3077 4.552166 ATGGTGCGTTAATACAATCAGC 57.448 40.909 0.00 0.00 0.00 4.26
2074 3085 5.619607 GCGTTAATACAATCAGCGGTTAATG 59.380 40.000 0.00 0.00 0.00 1.90
2211 3230 1.467374 GCGCGTTGCTATTGGAATTGT 60.467 47.619 8.43 0.00 41.73 2.71
2532 3592 3.261897 TCCTTTACCTCTTGCCTTCTGAG 59.738 47.826 0.00 0.00 0.00 3.35
2599 3659 2.497273 GTTGTAATTTGGGATGCAGGCT 59.503 45.455 0.00 0.00 0.00 4.58
2692 3752 4.059511 CAATTCCACAGAAAATTGCTGCA 58.940 39.130 0.00 0.00 36.42 4.41
2693 3753 3.374220 TTCCACAGAAAATTGCTGCAG 57.626 42.857 10.11 10.11 36.86 4.41
3062 4125 7.433680 CCACTTGTAAAAGTTGCTCCTATTTT 58.566 34.615 0.00 0.00 0.00 1.82
3126 6491 4.081752 AGAGCAACCAATGTTTGACACAAA 60.082 37.500 0.00 0.00 39.50 2.83
3127 6492 4.573900 AGCAACCAATGTTTGACACAAAA 58.426 34.783 0.00 0.00 39.50 2.44
3132 6497 5.976458 ACCAATGTTTGACACAAAACTGAT 58.024 33.333 0.00 0.00 39.50 2.90
3142 6507 5.179929 TGACACAAAACTGATACATGCAGAG 59.820 40.000 5.90 0.00 36.86 3.35
3166 6531 7.322664 AGTGCATTAGTTGAAATAACATTGGG 58.677 34.615 0.00 0.00 0.00 4.12
3205 6570 2.484264 CCAGTAGCTTGGTTTTTCTCGG 59.516 50.000 0.00 0.00 33.38 4.63
3577 6942 8.809048 ATCACAAGATGCTTCGGTTTATAACCC 61.809 40.741 3.16 0.00 39.74 4.11
3917 7407 0.749649 CTGGGAAGAGGGACGATCTG 59.250 60.000 0.00 0.00 0.00 2.90
3918 7408 0.041238 TGGGAAGAGGGACGATCTGT 59.959 55.000 0.00 0.00 0.00 3.41
3919 7409 1.286849 TGGGAAGAGGGACGATCTGTA 59.713 52.381 0.00 0.00 0.00 2.74
3920 7410 2.091278 TGGGAAGAGGGACGATCTGTAT 60.091 50.000 0.00 0.00 0.00 2.29
4062 7552 1.205055 GAGGTTACTGGGAAGAGGGG 58.795 60.000 0.00 0.00 0.00 4.79
4340 7979 2.165437 AGGCGACTGTGAATCTCTCTTC 59.835 50.000 0.00 0.00 41.13 2.87
4381 8020 3.257873 TCTCTCTTTCTCCAGTGAAGCAG 59.742 47.826 0.00 0.00 0.00 4.24
4398 8037 1.610102 GCAGCCACCTATCCTAGCATG 60.610 57.143 0.00 0.00 0.00 4.06
4497 8139 4.590850 TCATCAGGTGGACTTATCATCG 57.409 45.455 0.00 0.00 0.00 3.84
4591 8233 2.810274 CCTACATGGGAAGATGCATTCG 59.190 50.000 0.00 0.00 0.00 3.34
4606 8248 4.395581 GCATTCGCAATCACTAGGTATG 57.604 45.455 0.00 0.00 38.36 2.39
4696 8388 3.441572 GCAGATGCTTAACCTGTGAATGT 59.558 43.478 0.00 0.00 38.21 2.71
4795 8860 2.130272 TGATCTCACGTAGGCTGAGT 57.870 50.000 0.00 0.00 37.12 3.41
4796 8861 2.447443 TGATCTCACGTAGGCTGAGTT 58.553 47.619 0.00 0.00 37.12 3.01
4797 8862 3.617284 TGATCTCACGTAGGCTGAGTTA 58.383 45.455 0.00 0.00 37.12 2.24
4798 8863 4.014406 TGATCTCACGTAGGCTGAGTTAA 58.986 43.478 0.00 0.00 37.12 2.01
4799 8864 3.844577 TCTCACGTAGGCTGAGTTAAC 57.155 47.619 0.00 0.00 37.12 2.01
4800 8865 3.418995 TCTCACGTAGGCTGAGTTAACT 58.581 45.455 8.13 8.13 37.12 2.24
4801 8866 3.439476 TCTCACGTAGGCTGAGTTAACTC 59.561 47.826 25.73 25.73 43.15 3.01
4802 8867 3.418995 TCACGTAGGCTGAGTTAACTCT 58.581 45.455 30.47 16.47 43.25 3.24
4803 8868 3.439476 TCACGTAGGCTGAGTTAACTCTC 59.561 47.826 30.47 22.45 43.25 3.20
4804 8869 3.440872 CACGTAGGCTGAGTTAACTCTCT 59.559 47.826 30.47 25.17 43.25 3.10
4805 8870 3.690628 ACGTAGGCTGAGTTAACTCTCTC 59.309 47.826 30.47 20.33 43.25 3.20
4806 8871 3.690139 CGTAGGCTGAGTTAACTCTCTCA 59.310 47.826 30.47 14.49 43.25 3.27
5147 9212 7.066525 TGTTTGTAAGAAGTTACTTCCAACAGG 59.933 37.037 20.05 0.00 40.98 4.00
5245 9310 2.242965 TGATCTCCATGGCACTGGAATT 59.757 45.455 6.96 8.96 44.59 2.17
5278 9343 7.556844 ACATTCTTCGACAGGTATAAGTTCAT 58.443 34.615 0.00 0.00 0.00 2.57
5329 9394 8.450964 AGGTAGTTTTGTTTGTTATCATCATCG 58.549 33.333 0.00 0.00 0.00 3.84
5355 9420 6.769512 TCCAGTGGAATTAAGATGGCTATAC 58.230 40.000 10.20 0.00 0.00 1.47
5360 9425 8.220559 AGTGGAATTAAGATGGCTATACACATT 58.779 33.333 0.00 0.00 0.00 2.71
5420 9489 9.533831 AGGAAATTATAGTTTCACCATTCAAGT 57.466 29.630 18.93 0.00 39.33 3.16
5623 9693 0.823356 GTTTGGCCTTGGCTCTGACA 60.823 55.000 11.71 0.00 0.00 3.58
5640 9710 7.148340 GGCTCTGACATAGATATTTTATGGTGC 60.148 40.741 10.93 7.00 34.21 5.01
5668 9738 9.931210 AATGTTATTTTACTTTATACGAGCAGC 57.069 29.630 0.00 0.00 0.00 5.25
5732 9802 4.877378 ATCAAAAGCAGCTGGATTTTCA 57.123 36.364 17.12 0.76 42.82 2.69
5791 9861 4.334552 TGATGATAACCGGCATGCATAAT 58.665 39.130 21.36 1.97 0.00 1.28
5900 9970 8.078596 GCTGATATTATTCCTCACATTTTGGTC 58.921 37.037 0.00 0.00 0.00 4.02
5919 9989 8.618702 TTTGGTCGTGTATTTGTTTATTCCTA 57.381 30.769 0.00 0.00 0.00 2.94
6023 10093 9.713740 CAGCATTCATAACTTATCAAGAACTTC 57.286 33.333 0.00 0.00 0.00 3.01
6074 10146 0.678366 ATGCGTTGCAACCGGGATTA 60.678 50.000 23.42 3.13 43.62 1.75
6091 10163 7.985752 ACCGGGATTAGAATTTTTCTAGTACTG 59.014 37.037 6.32 4.60 42.74 2.74
6179 10251 8.534496 AGCACTTATTGGCTTATGAAAGAAAAT 58.466 29.630 0.00 0.00 36.92 1.82
6373 10446 0.031449 AAATGTTTGGGAACGGTGCG 59.969 50.000 0.00 0.00 38.65 5.34
6375 10448 3.284449 GTTTGGGAACGGTGCGCT 61.284 61.111 9.73 0.00 0.00 5.92
6433 10507 0.756294 AACCACGACACAGATCCACA 59.244 50.000 0.00 0.00 0.00 4.17
6435 10509 0.670546 CCACGACACAGATCCACACC 60.671 60.000 0.00 0.00 0.00 4.16
6467 10541 2.893489 GGGAAGAAACACAAGAAGCCAT 59.107 45.455 0.00 0.00 0.00 4.40
6474 10548 2.880443 ACACAAGAAGCCATGTCCATT 58.120 42.857 0.00 0.00 0.00 3.16
6476 10550 2.559668 CACAAGAAGCCATGTCCATTGT 59.440 45.455 0.00 0.00 0.00 2.71
6478 10552 2.821378 CAAGAAGCCATGTCCATTGTGA 59.179 45.455 0.00 0.00 0.00 3.58
6502 10576 1.202533 CCACACACGATCTATCCCCAC 60.203 57.143 0.00 0.00 0.00 4.61
6518 10592 2.360854 CCCCACCTTATCTCTTCCTCCT 60.361 54.545 0.00 0.00 0.00 3.69
6520 10594 2.969262 CCACCTTATCTCTTCCTCCTCC 59.031 54.545 0.00 0.00 0.00 4.30
6521 10595 3.374762 CCACCTTATCTCTTCCTCCTCCT 60.375 52.174 0.00 0.00 0.00 3.69
6522 10596 3.895041 CACCTTATCTCTTCCTCCTCCTC 59.105 52.174 0.00 0.00 0.00 3.71
6523 10597 3.797269 ACCTTATCTCTTCCTCCTCCTCT 59.203 47.826 0.00 0.00 0.00 3.69
6525 10599 4.106341 CCTTATCTCTTCCTCCTCCTCTCT 59.894 50.000 0.00 0.00 0.00 3.10
6565 10639 4.301072 TTTTCTGTTTCATCCCGATCCT 57.699 40.909 0.00 0.00 0.00 3.24
6569 10643 3.455910 TCTGTTTCATCCCGATCCTGAAT 59.544 43.478 0.00 0.00 0.00 2.57
6581 10655 2.658593 CTGAATACCTCGCCGCCG 60.659 66.667 0.00 0.00 0.00 6.46
6584 10658 1.812507 GAATACCTCGCCGCCGTTT 60.813 57.895 0.00 0.00 35.54 3.60
6606 10680 2.445682 ACCTCCTGACGAGCTCTTAT 57.554 50.000 12.85 0.00 37.27 1.73
6612 10686 2.288702 CCTGACGAGCTCTTATCCATGG 60.289 54.545 12.85 4.97 0.00 3.66
6615 10689 0.315251 CGAGCTCTTATCCATGGCGA 59.685 55.000 12.85 0.00 0.00 5.54
6616 10690 1.668337 CGAGCTCTTATCCATGGCGAG 60.668 57.143 12.85 10.85 0.00 5.03
6617 10691 0.683973 AGCTCTTATCCATGGCGAGG 59.316 55.000 6.96 0.00 0.00 4.63
6620 10694 0.105194 TCTTATCCATGGCGAGGGGA 60.105 55.000 6.96 0.00 34.70 4.81
6636 10710 4.489771 GAGGGGGCGGGTGTGATG 62.490 72.222 0.00 0.00 0.00 3.07
6638 10712 4.360405 GGGGGCGGGTGTGATGTT 62.360 66.667 0.00 0.00 0.00 2.71
6639 10713 2.282887 GGGGCGGGTGTGATGTTT 60.283 61.111 0.00 0.00 0.00 2.83
6640 10714 1.906333 GGGGCGGGTGTGATGTTTT 60.906 57.895 0.00 0.00 0.00 2.43
6641 10715 1.288752 GGGCGGGTGTGATGTTTTG 59.711 57.895 0.00 0.00 0.00 2.44
6642 10716 1.460273 GGGCGGGTGTGATGTTTTGT 61.460 55.000 0.00 0.00 0.00 2.83
6643 10717 0.387565 GGCGGGTGTGATGTTTTGTT 59.612 50.000 0.00 0.00 0.00 2.83
6644 10718 1.486439 GCGGGTGTGATGTTTTGTTG 58.514 50.000 0.00 0.00 0.00 3.33
6645 10719 1.867698 GCGGGTGTGATGTTTTGTTGG 60.868 52.381 0.00 0.00 0.00 3.77
6646 10720 1.269517 CGGGTGTGATGTTTTGTTGGG 60.270 52.381 0.00 0.00 0.00 4.12
6647 10721 1.540146 GGGTGTGATGTTTTGTTGGGC 60.540 52.381 0.00 0.00 0.00 5.36
6648 10722 1.486439 GTGTGATGTTTTGTTGGGCG 58.514 50.000 0.00 0.00 0.00 6.13
6649 10723 1.066303 GTGTGATGTTTTGTTGGGCGA 59.934 47.619 0.00 0.00 0.00 5.54
6650 10724 1.066303 TGTGATGTTTTGTTGGGCGAC 59.934 47.619 0.00 0.00 0.00 5.19
6651 10725 0.309302 TGATGTTTTGTTGGGCGACG 59.691 50.000 0.00 0.00 0.00 5.12
6652 10726 0.386731 GATGTTTTGTTGGGCGACGG 60.387 55.000 0.00 0.00 0.00 4.79
6653 10727 1.104577 ATGTTTTGTTGGGCGACGGT 61.105 50.000 0.00 0.00 0.00 4.83
6654 10728 0.463295 TGTTTTGTTGGGCGACGGTA 60.463 50.000 0.00 0.00 0.00 4.02
6655 10729 0.236449 GTTTTGTTGGGCGACGGTAG 59.764 55.000 0.00 0.00 0.00 3.18
6656 10730 0.885596 TTTTGTTGGGCGACGGTAGG 60.886 55.000 0.00 0.00 0.00 3.18
6657 10731 2.734948 TTTGTTGGGCGACGGTAGGG 62.735 60.000 0.00 0.00 0.00 3.53
6710 10784 2.030562 AAAGGCACTGGACGACGG 59.969 61.111 0.00 0.00 40.86 4.79
6762 10836 0.171903 CAACTGCAAGCTATGTGGCC 59.828 55.000 0.00 0.00 37.60 5.36
6874 10948 1.741706 CTGCAAGGTTCCTACATGCTG 59.258 52.381 13.03 9.75 38.63 4.41
6876 10950 1.614317 GCAAGGTTCCTACATGCTGGT 60.614 52.381 6.72 0.00 36.36 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.441532 CCCTCGAGGCCGTCCTTA 60.442 66.667 26.87 0.00 44.46 2.69
53 54 4.698625 ACCCTCGAGGCCGTCCTT 62.699 66.667 26.87 0.23 44.46 3.36
102 103 4.953868 CCGCCACAACACCGACGA 62.954 66.667 0.00 0.00 0.00 4.20
176 177 0.755698 ACGCCCTCTGGACGATGTAT 60.756 55.000 0.00 0.00 35.82 2.29
200 201 2.102357 CCGCACTACGCTGTCGAT 59.898 61.111 0.00 0.00 41.76 3.59
204 205 4.778415 CGAGCCGCACTACGCTGT 62.778 66.667 0.00 0.00 41.76 4.40
206 207 3.966026 GAACGAGCCGCACTACGCT 62.966 63.158 0.00 0.00 41.76 5.07
367 368 2.260434 GGCTGTTGTACGAGGCGA 59.740 61.111 0.00 0.00 0.00 5.54
464 465 0.685097 CCTCTTCCCACCGACAAGAA 59.315 55.000 0.00 0.00 0.00 2.52
474 476 0.041833 CACTCTCTCCCCTCTTCCCA 59.958 60.000 0.00 0.00 0.00 4.37
514 517 1.272092 CCACAGCTCTCATTTTCCCCA 60.272 52.381 0.00 0.00 0.00 4.96
519 522 1.160137 GACGCCACAGCTCTCATTTT 58.840 50.000 0.00 0.00 36.60 1.82
545 549 1.766496 CTATAAAAGGCGACCTCCCCA 59.234 52.381 0.00 0.00 30.89 4.96
643 648 4.349048 TCAGCCTCTATTAATGCCTCATGT 59.651 41.667 0.00 0.00 0.00 3.21
654 659 2.038690 CGCCGGTCAGCCTCTATTA 58.961 57.895 1.90 0.00 0.00 0.98
704 709 1.739035 CGCTTCATCGCCCTTGTCTTA 60.739 52.381 0.00 0.00 0.00 2.10
705 710 1.021390 CGCTTCATCGCCCTTGTCTT 61.021 55.000 0.00 0.00 0.00 3.01
745 753 1.801309 CGGCACAAAAACGGATGGGT 61.801 55.000 0.00 0.00 0.00 4.51
754 762 1.193650 CGAGACGATTCGGCACAAAAA 59.806 47.619 15.45 0.00 37.34 1.94
760 768 2.506217 GTGCGAGACGATTCGGCA 60.506 61.111 15.45 9.08 37.34 5.69
764 772 3.255379 GCCGGTGCGAGACGATTC 61.255 66.667 1.90 0.00 0.00 2.52
797 809 2.355009 CAAAACCCAGCACGCTGC 60.355 61.111 13.65 0.00 45.46 5.25
798 810 1.008538 GACAAAACCCAGCACGCTG 60.009 57.895 12.17 12.17 43.26 5.18
799 811 1.152963 AGACAAAACCCAGCACGCT 60.153 52.632 0.00 0.00 0.00 5.07
800 812 1.008538 CAGACAAAACCCAGCACGC 60.009 57.895 0.00 0.00 0.00 5.34
801 813 1.654220 CCAGACAAAACCCAGCACG 59.346 57.895 0.00 0.00 0.00 5.34
802 814 0.755327 ACCCAGACAAAACCCAGCAC 60.755 55.000 0.00 0.00 0.00 4.40
803 815 0.467290 GACCCAGACAAAACCCAGCA 60.467 55.000 0.00 0.00 0.00 4.41
804 816 1.179174 GGACCCAGACAAAACCCAGC 61.179 60.000 0.00 0.00 0.00 4.85
805 817 0.184933 TGGACCCAGACAAAACCCAG 59.815 55.000 0.00 0.00 0.00 4.45
806 818 0.106419 GTGGACCCAGACAAAACCCA 60.106 55.000 0.00 0.00 0.00 4.51
807 819 0.826256 GGTGGACCCAGACAAAACCC 60.826 60.000 0.00 0.00 0.00 4.11
808 820 1.170290 CGGTGGACCCAGACAAAACC 61.170 60.000 0.00 0.00 0.00 3.27
809 821 0.179040 TCGGTGGACCCAGACAAAAC 60.179 55.000 0.00 0.00 0.00 2.43
810 822 0.179040 GTCGGTGGACCCAGACAAAA 60.179 55.000 7.88 0.00 36.99 2.44
811 823 1.448497 GTCGGTGGACCCAGACAAA 59.552 57.895 7.88 0.00 36.99 2.83
812 824 2.863346 CGTCGGTGGACCCAGACAA 61.863 63.158 11.62 0.00 40.17 3.18
813 825 3.299977 CGTCGGTGGACCCAGACA 61.300 66.667 11.62 0.00 40.17 3.41
814 826 1.526575 TAACGTCGGTGGACCCAGAC 61.527 60.000 0.00 0.00 40.17 3.51
815 827 0.827089 TTAACGTCGGTGGACCCAGA 60.827 55.000 0.00 0.00 40.17 3.86
816 828 0.248289 ATTAACGTCGGTGGACCCAG 59.752 55.000 0.00 0.00 40.17 4.45
817 829 0.686224 AATTAACGTCGGTGGACCCA 59.314 50.000 0.00 0.00 40.17 4.51
818 830 1.733912 GAAATTAACGTCGGTGGACCC 59.266 52.381 0.00 0.00 40.17 4.46
819 831 1.391144 CGAAATTAACGTCGGTGGACC 59.609 52.381 0.00 0.00 40.17 4.46
820 832 2.774864 CGAAATTAACGTCGGTGGAC 57.225 50.000 0.00 0.00 39.89 4.02
826 838 3.184986 AGTTTGGACCGAAATTAACGTCG 59.815 43.478 0.00 3.23 37.01 5.12
827 839 4.211794 TCAGTTTGGACCGAAATTAACGTC 59.788 41.667 0.00 0.00 0.00 4.34
828 840 4.024641 GTCAGTTTGGACCGAAATTAACGT 60.025 41.667 0.00 0.00 0.00 3.99
829 841 4.460505 GTCAGTTTGGACCGAAATTAACG 58.539 43.478 0.00 0.00 0.00 3.18
830 842 4.211794 TCGTCAGTTTGGACCGAAATTAAC 59.788 41.667 0.00 0.00 34.24 2.01
831 843 4.378774 TCGTCAGTTTGGACCGAAATTAA 58.621 39.130 0.00 0.00 34.24 1.40
832 844 3.992643 TCGTCAGTTTGGACCGAAATTA 58.007 40.909 0.00 0.00 34.24 1.40
833 845 2.841215 TCGTCAGTTTGGACCGAAATT 58.159 42.857 0.00 0.00 34.24 1.82
834 846 2.536761 TCGTCAGTTTGGACCGAAAT 57.463 45.000 0.00 0.00 34.24 2.17
835 847 2.312722 TTCGTCAGTTTGGACCGAAA 57.687 45.000 0.00 0.00 34.24 3.46
836 848 2.312722 TTTCGTCAGTTTGGACCGAA 57.687 45.000 0.00 0.00 34.24 4.30
837 849 2.312722 TTTTCGTCAGTTTGGACCGA 57.687 45.000 0.00 0.00 34.24 4.69
838 850 2.096174 TGTTTTTCGTCAGTTTGGACCG 59.904 45.455 0.00 0.00 34.24 4.79
839 851 3.768468 TGTTTTTCGTCAGTTTGGACC 57.232 42.857 0.00 0.00 34.24 4.46
840 852 4.102649 CCTTGTTTTTCGTCAGTTTGGAC 58.897 43.478 0.00 0.00 34.42 4.02
841 853 3.759618 ACCTTGTTTTTCGTCAGTTTGGA 59.240 39.130 0.00 0.00 0.00 3.53
842 854 4.104696 ACCTTGTTTTTCGTCAGTTTGG 57.895 40.909 0.00 0.00 0.00 3.28
843 855 5.286082 CAGAACCTTGTTTTTCGTCAGTTTG 59.714 40.000 0.00 0.00 0.00 2.93
844 856 5.182380 TCAGAACCTTGTTTTTCGTCAGTTT 59.818 36.000 0.00 0.00 0.00 2.66
845 857 4.698304 TCAGAACCTTGTTTTTCGTCAGTT 59.302 37.500 0.00 0.00 0.00 3.16
846 858 4.258543 TCAGAACCTTGTTTTTCGTCAGT 58.741 39.130 0.00 0.00 0.00 3.41
847 859 4.570772 TCTCAGAACCTTGTTTTTCGTCAG 59.429 41.667 0.00 0.00 0.00 3.51
848 860 4.509616 TCTCAGAACCTTGTTTTTCGTCA 58.490 39.130 0.00 0.00 0.00 4.35
849 861 5.674933 ATCTCAGAACCTTGTTTTTCGTC 57.325 39.130 0.00 0.00 0.00 4.20
850 862 6.934645 TGATATCTCAGAACCTTGTTTTTCGT 59.065 34.615 3.98 0.00 0.00 3.85
851 863 7.118390 AGTGATATCTCAGAACCTTGTTTTTCG 59.882 37.037 3.98 0.00 30.18 3.46
852 864 8.329203 AGTGATATCTCAGAACCTTGTTTTTC 57.671 34.615 3.98 0.00 30.18 2.29
853 865 8.697507 AAGTGATATCTCAGAACCTTGTTTTT 57.302 30.769 3.98 0.00 30.18 1.94
854 866 8.571336 CAAAGTGATATCTCAGAACCTTGTTTT 58.429 33.333 3.98 0.00 30.18 2.43
855 867 7.308830 GCAAAGTGATATCTCAGAACCTTGTTT 60.309 37.037 3.98 0.00 30.18 2.83
856 868 6.150140 GCAAAGTGATATCTCAGAACCTTGTT 59.850 38.462 3.98 0.00 30.18 2.83
857 869 5.645497 GCAAAGTGATATCTCAGAACCTTGT 59.355 40.000 3.98 0.00 30.18 3.16
858 870 5.220548 CGCAAAGTGATATCTCAGAACCTTG 60.221 44.000 3.98 1.34 30.18 3.61
859 871 4.872691 CGCAAAGTGATATCTCAGAACCTT 59.127 41.667 3.98 0.00 30.18 3.50
860 872 4.081420 ACGCAAAGTGATATCTCAGAACCT 60.081 41.667 3.98 0.00 30.18 3.50
861 873 4.184629 ACGCAAAGTGATATCTCAGAACC 58.815 43.478 3.98 0.00 30.18 3.62
862 874 4.027295 CGACGCAAAGTGATATCTCAGAAC 60.027 45.833 3.98 0.00 30.18 3.01
863 875 4.105486 CGACGCAAAGTGATATCTCAGAA 58.895 43.478 3.98 0.00 30.18 3.02
864 876 3.489229 CCGACGCAAAGTGATATCTCAGA 60.489 47.826 3.98 0.00 30.18 3.27
865 877 2.791560 CCGACGCAAAGTGATATCTCAG 59.208 50.000 3.98 0.00 30.18 3.35
866 878 2.809446 CCGACGCAAAGTGATATCTCA 58.191 47.619 3.98 0.00 0.00 3.27
867 879 1.523095 GCCGACGCAAAGTGATATCTC 59.477 52.381 3.98 0.00 34.03 2.75
868 880 1.571919 GCCGACGCAAAGTGATATCT 58.428 50.000 3.98 0.00 34.03 1.98
869 881 0.229753 CGCCGACGCAAAGTGATATC 59.770 55.000 0.00 0.00 34.03 1.63
870 882 2.297625 CGCCGACGCAAAGTGATAT 58.702 52.632 0.00 0.00 34.03 1.63
871 883 3.775314 CGCCGACGCAAAGTGATA 58.225 55.556 0.00 0.00 34.03 2.15
881 893 2.789723 GTTTTTCACGCGCCGACG 60.790 61.111 5.73 0.00 44.07 5.12
882 894 2.789723 CGTTTTTCACGCGCCGAC 60.790 61.111 5.73 0.00 43.37 4.79
890 902 0.243636 CCCTCCCATGCGTTTTTCAC 59.756 55.000 0.00 0.00 0.00 3.18
891 903 1.531739 GCCCTCCCATGCGTTTTTCA 61.532 55.000 0.00 0.00 0.00 2.69
892 904 1.215382 GCCCTCCCATGCGTTTTTC 59.785 57.895 0.00 0.00 0.00 2.29
893 905 2.635443 CGCCCTCCCATGCGTTTTT 61.635 57.895 0.00 0.00 45.43 1.94
894 906 3.061848 CGCCCTCCCATGCGTTTT 61.062 61.111 0.00 0.00 45.43 2.43
910 922 4.519437 TGCTCATCTCCAGCCGCG 62.519 66.667 0.00 0.00 35.89 6.46
911 923 2.588314 CTGCTCATCTCCAGCCGC 60.588 66.667 0.00 0.00 35.89 6.53
912 924 2.108566 CCTGCTCATCTCCAGCCG 59.891 66.667 0.00 0.00 35.89 5.52
913 925 2.203181 GCCTGCTCATCTCCAGCC 60.203 66.667 0.00 0.00 35.89 4.85
914 926 2.588314 CGCCTGCTCATCTCCAGC 60.588 66.667 0.00 0.00 37.40 4.85
915 927 1.964608 TTCCGCCTGCTCATCTCCAG 61.965 60.000 0.00 0.00 0.00 3.86
916 928 1.552799 TTTCCGCCTGCTCATCTCCA 61.553 55.000 0.00 0.00 0.00 3.86
917 929 0.813210 CTTTCCGCCTGCTCATCTCC 60.813 60.000 0.00 0.00 0.00 3.71
918 930 0.813210 CCTTTCCGCCTGCTCATCTC 60.813 60.000 0.00 0.00 0.00 2.75
919 931 1.222936 CCTTTCCGCCTGCTCATCT 59.777 57.895 0.00 0.00 0.00 2.90
920 932 1.821332 CCCTTTCCGCCTGCTCATC 60.821 63.158 0.00 0.00 0.00 2.92
921 933 2.273449 CCCTTTCCGCCTGCTCAT 59.727 61.111 0.00 0.00 0.00 2.90
922 934 4.033776 CCCCTTTCCGCCTGCTCA 62.034 66.667 0.00 0.00 0.00 4.26
1122 1137 1.226030 GAACGTTGGTTAGCGGCTGT 61.226 55.000 13.86 0.00 36.24 4.40
1173 1188 2.239402 GGTAAGGGTTTGGGATTCGGTA 59.761 50.000 0.00 0.00 0.00 4.02
1222 1237 4.793201 AGTAAGAGAAACAGCAAAAGGGT 58.207 39.130 0.00 0.00 0.00 4.34
1257 1272 1.947456 GTCGGCAAGAACTTTTCCTGT 59.053 47.619 0.00 0.00 0.00 4.00
1389 1404 4.328169 ACGGGAGAACGAACGAAAATAATC 59.672 41.667 0.14 0.00 37.61 1.75
1414 1429 9.339492 GTTCATTGCTAAAGATCTGAAGAAAAG 57.661 33.333 0.00 0.00 0.00 2.27
1483 2494 2.933495 TCCGGTCTGTATCGACTTTG 57.067 50.000 0.00 0.00 34.38 2.77
1651 2662 9.241919 TGACTCCTAATGAAATTTTAGCATTGA 57.758 29.630 11.79 3.73 37.87 2.57
1699 2710 7.553334 TGTGACAAACTACTCCATAGATAACC 58.447 38.462 0.00 0.00 34.65 2.85
2046 3057 2.350192 CGCTGATTGTATTAACGCACCA 59.650 45.455 0.00 0.00 0.00 4.17
2084 3103 1.618837 GTCTGGGCTCTACTCAACACA 59.381 52.381 0.00 0.00 0.00 3.72
2172 3191 3.639538 CGCGGTAACTAGCACAATAGAT 58.360 45.455 0.00 0.00 0.00 1.98
2330 3349 2.030893 TCTCAACATGCAAAAAGGCTCG 60.031 45.455 0.00 0.00 34.04 5.03
2380 3440 7.772757 TGACATTTGCACATATCCTACATAACA 59.227 33.333 0.00 0.00 0.00 2.41
2557 3617 7.590279 ACAACCAACGAGAAAAATTAGGTATG 58.410 34.615 0.00 0.00 0.00 2.39
2599 3659 1.483595 CCCAGACTTCCTCAGGCACA 61.484 60.000 0.00 0.00 29.16 4.57
3062 4125 8.531982 AGCTGGCGAGTCAAAAAGATATATATA 58.468 33.333 0.00 0.00 0.00 0.86
3086 4274 2.891112 CTCTCAGTCAATGGTCAGAGC 58.109 52.381 0.00 0.00 0.00 4.09
3142 6507 7.319646 TCCCAATGTTATTTCAACTAATGCAC 58.680 34.615 0.00 0.00 0.00 4.57
3205 6570 4.970711 ACAGGATTCCATCACAGATGATC 58.029 43.478 5.29 4.75 44.13 2.92
4340 7979 1.795286 GAAGAGAAAGCACACACCTCG 59.205 52.381 0.00 0.00 0.00 4.63
4381 8020 0.397941 TGCATGCTAGGATAGGTGGC 59.602 55.000 20.33 0.00 39.70 5.01
4398 8037 1.442769 TTGCTTCGAAGGATCACTGC 58.557 50.000 25.77 10.75 0.00 4.40
4445 8084 2.719531 TGGTGAACAACTGCCAACTA 57.280 45.000 0.00 0.00 0.00 2.24
4497 8139 6.403309 CCTTTGGTAGTTCGGCTAAAAGATTC 60.403 42.308 10.73 0.00 32.90 2.52
4591 8233 6.873605 TGCACATATACATACCTAGTGATTGC 59.126 38.462 0.00 0.00 0.00 3.56
4602 8244 7.439356 ACTCAGATGTTGTGCACATATACATAC 59.561 37.037 27.31 21.21 46.96 2.39
4606 8248 6.668541 AACTCAGATGTTGTGCACATATAC 57.331 37.500 22.39 16.62 46.96 1.47
4804 8869 5.474578 AAGAGAGTTAACTCACATGCTGA 57.525 39.130 31.80 0.00 45.21 4.26
4805 8870 5.468072 ACAAAGAGAGTTAACTCACATGCTG 59.532 40.000 31.80 22.38 45.21 4.41
4806 8871 5.615289 ACAAAGAGAGTTAACTCACATGCT 58.385 37.500 31.80 19.01 45.21 3.79
4807 8872 5.931441 ACAAAGAGAGTTAACTCACATGC 57.069 39.130 31.80 17.43 45.21 4.06
5019 9084 2.096174 GTGCAACACGGTTACACAAGAA 59.904 45.455 12.49 0.00 36.32 2.52
5147 9212 3.314635 CCATTGTTCCTTAGATGCAGAGC 59.685 47.826 0.00 0.00 0.00 4.09
5245 9310 5.547465 ACCTGTCGAAGAATGTCATTTGTA 58.453 37.500 0.00 0.00 39.69 2.41
5329 9394 2.620585 GCCATCTTAATTCCACTGGAGC 59.379 50.000 0.00 0.00 31.21 4.70
5370 9435 6.920569 ATTCCAAATGTAAGTATGTCGGTC 57.079 37.500 0.00 0.00 0.00 4.79
5371 9436 6.990349 CCTATTCCAAATGTAAGTATGTCGGT 59.010 38.462 0.00 0.00 0.00 4.69
5372 9437 7.214381 TCCTATTCCAAATGTAAGTATGTCGG 58.786 38.462 0.00 0.00 0.00 4.79
5400 9469 8.918202 ACAGAACTTGAATGGTGAAACTATAA 57.082 30.769 0.00 0.00 36.85 0.98
5402 9471 7.823745 AACAGAACTTGAATGGTGAAACTAT 57.176 32.000 0.00 0.00 41.06 2.12
5403 9472 7.122055 ACAAACAGAACTTGAATGGTGAAACTA 59.878 33.333 0.00 0.00 36.74 2.24
5415 9484 5.384063 TTGCAGAAACAAACAGAACTTGA 57.616 34.783 0.00 0.00 0.00 3.02
5420 9489 5.824624 AGAGAGATTGCAGAAACAAACAGAA 59.175 36.000 0.00 0.00 32.27 3.02
5668 9738 2.767496 CTCCTCCCAGCCCTCCAG 60.767 72.222 0.00 0.00 0.00 3.86
5732 9802 5.104941 TCGAAAACACCTGATGATCCTACAT 60.105 40.000 0.00 0.00 0.00 2.29
5791 9861 7.074653 ACCCTGTCTGTAATAAGAAAGACAA 57.925 36.000 5.91 0.00 46.10 3.18
6046 10116 1.172175 TTGCAACGCATAGGCAATCA 58.828 45.000 0.00 0.00 42.12 2.57
6074 10146 9.490379 CACAGGTTACAGTACTAGAAAAATTCT 57.510 33.333 0.00 0.00 43.72 2.40
6091 10163 3.681593 TGGGCAGATAAACACAGGTTAC 58.318 45.455 0.00 0.00 35.82 2.50
6357 10430 3.587933 GCGCACCGTTCCCAAACA 61.588 61.111 0.30 0.00 34.93 2.83
6366 10439 4.927782 TTTCAGCCAGCGCACCGT 62.928 61.111 11.47 0.00 37.52 4.83
6373 10446 2.653115 GGCCAAGTTTCAGCCAGC 59.347 61.111 0.00 0.00 46.34 4.85
6379 10452 2.975799 GCGACCGGCCAAGTTTCA 60.976 61.111 0.00 0.00 34.80 2.69
6411 10485 1.270625 TGGATCTGTGTCGTGGTTTCC 60.271 52.381 0.00 0.00 0.00 3.13
6426 10500 2.509336 CACGAGCGGGTGTGGATC 60.509 66.667 0.00 0.00 33.24 3.36
6446 10520 2.306847 TGGCTTCTTGTGTTTCTTCCC 58.693 47.619 0.00 0.00 0.00 3.97
6452 10526 2.665165 TGGACATGGCTTCTTGTGTTT 58.335 42.857 0.00 0.00 0.00 2.83
6476 10550 2.209690 TAGATCGTGTGTGGGTCTCA 57.790 50.000 0.00 0.00 0.00 3.27
6478 10552 2.032620 GGATAGATCGTGTGTGGGTCT 58.967 52.381 0.00 0.00 0.00 3.85
6490 10564 5.423931 GGAAGAGATAAGGTGGGGATAGATC 59.576 48.000 0.00 0.00 0.00 2.75
6502 10576 4.106341 AGAGAGGAGGAGGAAGAGATAAGG 59.894 50.000 0.00 0.00 0.00 2.69
6518 10592 3.373658 GGGATTGAGGAAGAGAGAGAGGA 60.374 52.174 0.00 0.00 0.00 3.71
6520 10594 2.965147 GGGGATTGAGGAAGAGAGAGAG 59.035 54.545 0.00 0.00 0.00 3.20
6521 10595 2.589664 AGGGGATTGAGGAAGAGAGAGA 59.410 50.000 0.00 0.00 0.00 3.10
6522 10596 3.044873 AGGGGATTGAGGAAGAGAGAG 57.955 52.381 0.00 0.00 0.00 3.20
6523 10597 3.498614 AAGGGGATTGAGGAAGAGAGA 57.501 47.619 0.00 0.00 0.00 3.10
6565 10639 2.510064 AAACGGCGGCGAGGTATTCA 62.510 55.000 38.93 0.00 0.00 2.57
6569 10643 2.634476 TACAAACGGCGGCGAGGTA 61.634 57.895 38.93 28.80 0.00 3.08
6581 10655 1.711206 GCTCGTCAGGAGGTACAAAC 58.289 55.000 0.00 0.00 43.36 2.93
6626 10700 1.269517 CCCAACAAAACATCACACCCG 60.270 52.381 0.00 0.00 0.00 5.28
6627 10701 1.540146 GCCCAACAAAACATCACACCC 60.540 52.381 0.00 0.00 0.00 4.61
6628 10702 1.864565 GCCCAACAAAACATCACACC 58.135 50.000 0.00 0.00 0.00 4.16
6629 10703 1.066303 TCGCCCAACAAAACATCACAC 59.934 47.619 0.00 0.00 0.00 3.82
6630 10704 1.066303 GTCGCCCAACAAAACATCACA 59.934 47.619 0.00 0.00 0.00 3.58
6631 10705 1.766069 GTCGCCCAACAAAACATCAC 58.234 50.000 0.00 0.00 0.00 3.06
6632 10706 0.309302 CGTCGCCCAACAAAACATCA 59.691 50.000 0.00 0.00 0.00 3.07
6633 10707 0.386731 CCGTCGCCCAACAAAACATC 60.387 55.000 0.00 0.00 0.00 3.06
6634 10708 1.104577 ACCGTCGCCCAACAAAACAT 61.105 50.000 0.00 0.00 0.00 2.71
6635 10709 0.463295 TACCGTCGCCCAACAAAACA 60.463 50.000 0.00 0.00 0.00 2.83
6636 10710 0.236449 CTACCGTCGCCCAACAAAAC 59.764 55.000 0.00 0.00 0.00 2.43
6637 10711 0.885596 CCTACCGTCGCCCAACAAAA 60.886 55.000 0.00 0.00 0.00 2.44
6638 10712 1.301874 CCTACCGTCGCCCAACAAA 60.302 57.895 0.00 0.00 0.00 2.83
6639 10713 2.344500 CCTACCGTCGCCCAACAA 59.656 61.111 0.00 0.00 0.00 2.83
6640 10714 3.697747 CCCTACCGTCGCCCAACA 61.698 66.667 0.00 0.00 0.00 3.33
6662 10736 3.561213 CGCCATCTGCTCGCAGTG 61.561 66.667 17.53 14.22 43.96 3.66
6663 10737 4.827087 CCGCCATCTGCTCGCAGT 62.827 66.667 17.53 3.87 43.96 4.40
6683 10757 1.152756 AGTGCCTTTGGACCACCAC 60.153 57.895 0.00 0.00 46.80 4.16
6691 10765 2.317609 CGTCGTCCAGTGCCTTTGG 61.318 63.158 0.00 0.00 37.04 3.28
6710 10784 3.906649 CTCGTGCTCGTGATGCGC 61.907 66.667 0.00 0.00 41.07 6.09
6795 10869 3.485431 CAGCTCTGCGGAACTGCG 61.485 66.667 12.82 0.00 37.81 5.18
6806 10880 2.031163 GACCACGGTTGCAGCTCT 59.969 61.111 0.00 0.00 0.00 4.09
6862 10936 0.911769 CCCTCACCAGCATGTAGGAA 59.088 55.000 11.80 0.50 0.00 3.36
6865 10939 1.274703 ACCCCCTCACCAGCATGTAG 61.275 60.000 0.00 0.00 0.00 2.74
6874 10948 3.490851 TTGTAGCACCCCCTCACC 58.509 61.111 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.