Multiple sequence alignment - TraesCS1B01G293500

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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 TraesCS1B01G293500 chr1B 100.000 5785 0 0 1 5785 511208684 511214468 0.000000e+00 10683.0
1 TraesCS1B01G293500 chr1B 95.665 692 28 2 1 692 136170608 136169919 0.000000e+00 1110.0
2 TraesCS1B01G293500 chr1B 83.871 496 42 11 1727 2221 646281003 646281461 6.880000e-119 438.0
3 TraesCS1B01G293500 chr1B 88.172 372 26 11 101 458 614937511 614937878 1.490000e-115 427.0
4 TraesCS1B01G293500 chr1B 96.818 220 7 0 1 220 614937363 614937582 9.160000e-98 368.0
5 TraesCS1B01G293500 chr1B 87.500 136 8 7 5194 5326 427472250 427472121 1.300000e-31 148.0
6 TraesCS1B01G293500 chr1D 92.444 4910 205 69 957 5785 381063642 381068466 0.000000e+00 6859.0
7 TraesCS1B01G293500 chr1A 93.493 2167 114 16 1144 3297 481880481 481882633 0.000000e+00 3195.0
8 TraesCS1B01G293500 chr1A 93.118 1177 57 10 3332 4492 481882629 481883797 0.000000e+00 1703.0
9 TraesCS1B01G293500 chr1A 85.119 672 74 17 5132 5785 481884888 481885551 0.000000e+00 664.0
10 TraesCS1B01G293500 chr1A 84.679 483 47 19 4489 4968 481883822 481884280 1.900000e-124 457.0
11 TraesCS1B01G293500 chr1A 91.216 148 11 1 959 1104 481880337 481880484 3.540000e-47 200.0
12 TraesCS1B01G293500 chr1A 88.820 161 9 6 5132 5287 481884479 481884635 7.650000e-44 189.0
13 TraesCS1B01G293500 chr1A 83.660 153 19 6 4945 5095 481884327 481884475 7.820000e-29 139.0
14 TraesCS1B01G293500 chr1A 83.660 153 19 6 4945 5095 481884736 481884884 7.820000e-29 139.0
15 TraesCS1B01G293500 chr2B 92.278 777 48 2 1 766 94426460 94427235 0.000000e+00 1092.0
16 TraesCS1B01G293500 chr2B 88.011 367 34 8 101 458 83924679 83925044 5.360000e-115 425.0
17 TraesCS1B01G293500 chr2B 95.021 241 12 0 222 462 68788419 68788659 4.230000e-101 379.0
18 TraesCS1B01G293500 chr2B 94.091 220 13 0 1 220 83855952 83856171 9.290000e-88 335.0
19 TraesCS1B01G293500 chr7B 89.260 689 44 13 101 766 186978474 186977793 0.000000e+00 835.0
20 TraesCS1B01G293500 chr7B 81.218 197 28 7 474 664 578444245 578444052 3.610000e-32 150.0
21 TraesCS1B01G293500 chr6B 89.373 367 29 7 101 458 98589885 98589520 2.460000e-123 453.0
22 TraesCS1B01G293500 chr6B 89.431 369 25 9 101 458 98645889 98645524 2.460000e-123 453.0
23 TraesCS1B01G293500 chr6B 88.618 369 28 9 101 458 98494419 98494054 2.480000e-118 436.0
24 TraesCS1B01G293500 chr6B 96.818 220 7 0 1 220 98590078 98589859 9.160000e-98 368.0
25 TraesCS1B01G293500 chr6B 96.818 220 7 0 1 220 98646082 98645863 9.160000e-98 368.0
26 TraesCS1B01G293500 chr6B 95.909 220 9 0 1 220 98494612 98494393 1.980000e-94 357.0
27 TraesCS1B01G293500 chr6B 89.947 189 13 5 2036 2221 686921786 686921971 7.490000e-59 239.0
28 TraesCS1B01G293500 chr3D 82.751 458 36 16 1733 2186 160282462 160282044 9.160000e-98 368.0
29 TraesCS1B01G293500 chr3D 90.860 186 11 5 2036 2218 231217632 231217814 1.610000e-60 244.0
30 TraesCS1B01G293500 chr3B 96.818 220 7 0 1 220 80101030 80100811 9.160000e-98 368.0
31 TraesCS1B01G293500 chr3B 91.743 109 7 2 5185 5291 659068006 659068114 3.610000e-32 150.0
32 TraesCS1B01G293500 chr3B 96.703 91 2 1 5197 5286 685059071 685059161 3.610000e-32 150.0
33 TraesCS1B01G293500 chr6A 95.000 220 11 0 1 220 102130703 102130484 4.290000e-91 346.0
34 TraesCS1B01G293500 chr2D 91.235 251 19 1 461 708 177801684 177801434 7.180000e-89 339.0
35 TraesCS1B01G293500 chr2D 83.505 291 27 9 1856 2143 38517731 38517459 9.620000e-63 252.0
36 TraesCS1B01G293500 chr2D 90.598 117 10 1 1695 1811 38519555 38519440 2.790000e-33 154.0
37 TraesCS1B01G293500 chr5B 87.582 306 19 6 461 766 49553204 49552918 2.580000e-88 337.0
38 TraesCS1B01G293500 chr5A 84.290 331 31 9 1856 2183 699178249 699178561 2.620000e-78 303.0
39 TraesCS1B01G293500 chr5D 91.327 196 12 3 461 652 439023595 439023789 4.450000e-66 263.0
40 TraesCS1B01G293500 chr5D 92.308 182 11 1 461 639 474551025 474550844 7.440000e-64 255.0
41 TraesCS1B01G293500 chr5D 96.552 58 2 0 708 765 474550797 474550740 4.770000e-16 97.1
42 TraesCS1B01G293500 chr5D 87.931 58 4 3 3844 3899 398905136 398905192 1.350000e-06 65.8
43 TraesCS1B01G293500 chr4D 90.323 186 12 4 2039 2221 73860478 73860296 7.490000e-59 239.0
44 TraesCS1B01G293500 chr4A 89.785 186 13 4 2039 2221 467940378 467940196 3.490000e-57 233.0
45 TraesCS1B01G293500 chr4A 89.418 189 14 5 2036 2221 566409805 566409990 3.490000e-57 233.0
46 TraesCS1B01G293500 chr2A 89.418 189 14 5 2036 2221 343549889 343550074 3.490000e-57 233.0
47 TraesCS1B01G293500 chr3A 95.789 95 0 3 5196 5286 703902686 703902592 3.610000e-32 150.0
48 TraesCS1B01G293500 chr3A 93.878 98 3 3 5195 5290 636159050 636158954 1.680000e-30 145.0
49 TraesCS1B01G293500 chr7D 93.939 99 3 3 5194 5290 590446686 590446783 4.670000e-31 147.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G293500 chr1B 511208684 511214468 5784 False 10683.00 10683 100.000000 1 5785 1 chr1B.!!$F1 5784
1 TraesCS1B01G293500 chr1B 136169919 136170608 689 True 1110.00 1110 95.665000 1 692 1 chr1B.!!$R1 691
2 TraesCS1B01G293500 chr1B 614937363 614937878 515 False 397.50 427 92.495000 1 458 2 chr1B.!!$F3 457
3 TraesCS1B01G293500 chr1D 381063642 381068466 4824 False 6859.00 6859 92.444000 957 5785 1 chr1D.!!$F1 4828
4 TraesCS1B01G293500 chr1A 481880337 481885551 5214 False 835.75 3195 87.970625 959 5785 8 chr1A.!!$F1 4826
5 TraesCS1B01G293500 chr2B 94426460 94427235 775 False 1092.00 1092 92.278000 1 766 1 chr2B.!!$F4 765
6 TraesCS1B01G293500 chr7B 186977793 186978474 681 True 835.00 835 89.260000 101 766 1 chr7B.!!$R1 665
7 TraesCS1B01G293500 chr6B 98589520 98590078 558 True 410.50 453 93.095500 1 458 2 chr6B.!!$R2 457
8 TraesCS1B01G293500 chr6B 98645524 98646082 558 True 410.50 453 93.124500 1 458 2 chr6B.!!$R3 457
9 TraesCS1B01G293500 chr6B 98494054 98494612 558 True 396.50 436 92.263500 1 458 2 chr6B.!!$R1 457
10 TraesCS1B01G293500 chr2D 38517459 38519555 2096 True 203.00 252 87.051500 1695 2143 2 chr2D.!!$R2 448

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
830 1004 0.103572 ACAAATATAGGTCGGCGCGT 59.896 50.000 8.43 1.54 0.00 6.01 F
1411 1598 0.037303 TACCCACCTCGAGTCGTTCT 59.963 55.000 13.12 0.00 0.00 3.01 F
1435 1622 0.872021 CTAATCGAGCAGTCACCGGC 60.872 60.000 0.00 0.00 0.00 6.13 F
1669 1857 0.905337 AGGAGGACAGGGTTTCCGAG 60.905 60.000 0.00 0.00 38.29 4.63 F
2866 4738 0.968405 TTGTGGCTGGAATCAAAGGC 59.032 50.000 2.48 2.48 39.33 4.35 F
3554 5435 1.339727 CCCCCTTCGTTAACTCCTTGG 60.340 57.143 3.71 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1827 0.606604 TGTCCTCCTTGCCGAAGTAC 59.393 55.000 0.0 0.0 0.0 2.73 R
2737 4609 1.135527 CAGCCATGCTTAATGTGTGGG 59.864 52.381 0.0 0.0 36.4 4.61 R
2863 4735 1.610886 GGGTGCTCTTAGTTTTCGCCT 60.611 52.381 0.0 0.0 0.0 5.52 R
3590 5471 3.138283 TGTTTGAAGGAATGGGAGACAGT 59.862 43.478 0.0 0.0 0.0 3.55 R
3914 5809 0.665835 TGCCTTGTGCGTTTAACAGG 59.334 50.000 0.0 0.0 45.6 4.00 R
5503 7928 0.251354 TGCCCATGTCTCAAGCTCTC 59.749 55.000 0.0 0.0 0.0 3.20 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
220 380 2.054687 CGAGTTAGTTACGCACCACA 57.945 50.000 0.00 0.00 0.00 4.17
424 585 0.179100 CAGAATCGTCCGTGCCTGAT 60.179 55.000 0.00 0.00 0.00 2.90
590 751 6.899393 AGAAGGATAAAATGTTCAGTTGCA 57.101 33.333 0.00 0.00 0.00 4.08
602 763 1.546923 TCAGTTGCATCAAATGGGCAG 59.453 47.619 7.08 0.00 39.46 4.85
603 764 0.899720 AGTTGCATCAAATGGGCAGG 59.100 50.000 0.00 0.00 38.97 4.85
628 789 6.054860 AGTGATGTTAGCTCAGTTGGTTAT 57.945 37.500 0.00 0.00 0.00 1.89
639 800 3.322541 TCAGTTGGTTATCCTCGTTGTGA 59.677 43.478 0.00 0.00 34.23 3.58
643 804 2.236146 TGGTTATCCTCGTTGTGATGCT 59.764 45.455 0.00 0.00 34.23 3.79
653 814 0.464036 TTGTGATGCTAGTAGGCGGG 59.536 55.000 0.00 0.00 34.52 6.13
661 822 0.824759 CTAGTAGGCGGGCAGAGTTT 59.175 55.000 3.78 0.00 0.00 2.66
683 844 0.610232 ATCCCCACTCAAGCAAGCAC 60.610 55.000 0.00 0.00 0.00 4.40
687 848 2.092968 CCCCACTCAAGCAAGCACTATA 60.093 50.000 0.00 0.00 0.00 1.31
766 940 3.181513 CGACTGGTCGTTAGATTTCTCGA 60.182 47.826 14.05 0.00 46.99 4.04
767 941 4.496010 CGACTGGTCGTTAGATTTCTCGAT 60.496 45.833 14.05 0.00 46.99 3.59
768 942 4.673441 ACTGGTCGTTAGATTTCTCGATG 58.327 43.478 0.00 0.00 34.93 3.84
769 943 4.158025 ACTGGTCGTTAGATTTCTCGATGT 59.842 41.667 0.00 0.00 34.93 3.06
770 944 5.356190 ACTGGTCGTTAGATTTCTCGATGTA 59.644 40.000 0.00 0.00 34.93 2.29
771 945 5.575957 TGGTCGTTAGATTTCTCGATGTAC 58.424 41.667 0.00 0.00 34.93 2.90
772 946 5.124297 TGGTCGTTAGATTTCTCGATGTACA 59.876 40.000 0.00 0.00 34.93 2.90
773 947 6.032094 GGTCGTTAGATTTCTCGATGTACAA 58.968 40.000 0.00 0.00 34.93 2.41
774 948 6.696148 GGTCGTTAGATTTCTCGATGTACAAT 59.304 38.462 0.00 0.00 34.93 2.71
775 949 7.859377 GGTCGTTAGATTTCTCGATGTACAATA 59.141 37.037 0.00 0.00 34.93 1.90
776 950 9.395707 GTCGTTAGATTTCTCGATGTACAATAT 57.604 33.333 0.00 0.00 34.93 1.28
777 951 9.394477 TCGTTAGATTTCTCGATGTACAATATG 57.606 33.333 0.00 0.00 0.00 1.78
778 952 9.181805 CGTTAGATTTCTCGATGTACAATATGT 57.818 33.333 0.00 0.00 0.00 2.29
780 954 7.413475 AGATTTCTCGATGTACAATATGTGC 57.587 36.000 0.00 0.00 33.42 4.57
781 955 6.986231 AGATTTCTCGATGTACAATATGTGCA 59.014 34.615 0.00 3.81 46.39 4.57
793 967 9.660180 TGTACAATATGTGCATACTTAGTTGAA 57.340 29.630 0.00 0.00 38.04 2.69
798 972 9.554724 AATATGTGCATACTTAGTTGAAAAACG 57.445 29.630 0.00 0.00 0.00 3.60
799 973 5.209240 TGTGCATACTTAGTTGAAAAACGC 58.791 37.500 0.00 0.00 0.00 4.84
800 974 4.615541 GTGCATACTTAGTTGAAAAACGCC 59.384 41.667 0.00 0.00 0.00 5.68
801 975 3.844099 GCATACTTAGTTGAAAAACGCCG 59.156 43.478 0.00 0.00 0.00 6.46
802 976 4.399978 CATACTTAGTTGAAAAACGCCGG 58.600 43.478 0.00 0.00 0.00 6.13
803 977 1.002142 ACTTAGTTGAAAAACGCCGGC 60.002 47.619 19.07 19.07 0.00 6.13
804 978 0.311477 TTAGTTGAAAAACGCCGGCC 59.689 50.000 23.46 5.93 0.00 6.13
805 979 0.818445 TAGTTGAAAAACGCCGGCCA 60.818 50.000 23.46 9.07 0.00 5.36
806 980 1.006688 GTTGAAAAACGCCGGCCAT 60.007 52.632 23.46 6.41 0.00 4.40
807 981 1.006805 TTGAAAAACGCCGGCCATG 60.007 52.632 23.46 9.96 0.00 3.66
808 982 2.809174 GAAAAACGCCGGCCATGC 60.809 61.111 23.46 3.36 0.00 4.06
809 983 4.371590 AAAAACGCCGGCCATGCC 62.372 61.111 23.46 0.00 46.75 4.40
821 995 1.812571 GGCCATGCCGACAAATATAGG 59.187 52.381 0.00 0.00 39.62 2.57
822 996 2.504367 GCCATGCCGACAAATATAGGT 58.496 47.619 0.00 0.00 0.00 3.08
823 997 2.484264 GCCATGCCGACAAATATAGGTC 59.516 50.000 0.00 0.00 0.00 3.85
829 1003 0.782384 GACAAATATAGGTCGGCGCG 59.218 55.000 0.00 0.00 0.00 6.86
830 1004 0.103572 ACAAATATAGGTCGGCGCGT 59.896 50.000 8.43 1.54 0.00 6.01
831 1005 0.506932 CAAATATAGGTCGGCGCGTG 59.493 55.000 8.43 0.00 0.00 5.34
832 1006 0.599204 AAATATAGGTCGGCGCGTGG 60.599 55.000 8.43 0.00 0.00 4.94
833 1007 3.569049 ATATAGGTCGGCGCGTGGC 62.569 63.158 13.27 13.27 42.51 5.01
847 1021 3.157949 TGGCACACTGACGACCCA 61.158 61.111 0.00 0.00 0.00 4.51
848 1022 2.110213 GGCACACTGACGACCCAA 59.890 61.111 0.00 0.00 0.00 4.12
849 1023 1.525077 GGCACACTGACGACCCAAA 60.525 57.895 0.00 0.00 0.00 3.28
850 1024 0.889186 GGCACACTGACGACCCAAAT 60.889 55.000 0.00 0.00 0.00 2.32
851 1025 0.517316 GCACACTGACGACCCAAATC 59.483 55.000 0.00 0.00 0.00 2.17
852 1026 1.877637 CACACTGACGACCCAAATCA 58.122 50.000 0.00 0.00 0.00 2.57
853 1027 2.217750 CACACTGACGACCCAAATCAA 58.782 47.619 0.00 0.00 0.00 2.57
854 1028 2.616376 CACACTGACGACCCAAATCAAA 59.384 45.455 0.00 0.00 0.00 2.69
855 1029 3.066064 CACACTGACGACCCAAATCAAAA 59.934 43.478 0.00 0.00 0.00 2.44
856 1030 3.697045 ACACTGACGACCCAAATCAAAAA 59.303 39.130 0.00 0.00 0.00 1.94
890 1064 2.422591 GGACGACCGACCCAAACA 59.577 61.111 0.00 0.00 0.00 2.83
891 1065 1.227615 GGACGACCGACCCAAACAA 60.228 57.895 0.00 0.00 0.00 2.83
892 1066 0.814812 GGACGACCGACCCAAACAAA 60.815 55.000 0.00 0.00 0.00 2.83
893 1067 1.232119 GACGACCGACCCAAACAAAT 58.768 50.000 0.00 0.00 0.00 2.32
894 1068 2.415776 GACGACCGACCCAAACAAATA 58.584 47.619 0.00 0.00 0.00 1.40
895 1069 2.807392 GACGACCGACCCAAACAAATAA 59.193 45.455 0.00 0.00 0.00 1.40
896 1070 3.212685 ACGACCGACCCAAACAAATAAA 58.787 40.909 0.00 0.00 0.00 1.40
897 1071 3.631227 ACGACCGACCCAAACAAATAAAA 59.369 39.130 0.00 0.00 0.00 1.52
898 1072 4.097589 ACGACCGACCCAAACAAATAAAAA 59.902 37.500 0.00 0.00 0.00 1.94
919 1093 6.899393 AAAACCAGACAAAATCATAGCTCA 57.101 33.333 0.00 0.00 0.00 4.26
920 1094 7.472334 AAAACCAGACAAAATCATAGCTCAT 57.528 32.000 0.00 0.00 0.00 2.90
921 1095 7.472334 AAACCAGACAAAATCATAGCTCATT 57.528 32.000 0.00 0.00 0.00 2.57
922 1096 7.472334 AACCAGACAAAATCATAGCTCATTT 57.528 32.000 0.00 0.00 0.00 2.32
923 1097 8.579850 AACCAGACAAAATCATAGCTCATTTA 57.420 30.769 0.00 0.00 0.00 1.40
924 1098 8.218338 ACCAGACAAAATCATAGCTCATTTAG 57.782 34.615 0.00 0.00 0.00 1.85
925 1099 8.049117 ACCAGACAAAATCATAGCTCATTTAGA 58.951 33.333 0.00 0.00 0.00 2.10
926 1100 9.064706 CCAGACAAAATCATAGCTCATTTAGAT 57.935 33.333 0.00 0.00 0.00 1.98
928 1102 8.986847 AGACAAAATCATAGCTCATTTAGATCG 58.013 33.333 0.00 0.00 0.00 3.69
929 1103 8.893219 ACAAAATCATAGCTCATTTAGATCGA 57.107 30.769 0.00 0.00 0.00 3.59
930 1104 8.768955 ACAAAATCATAGCTCATTTAGATCGAC 58.231 33.333 0.00 0.00 0.00 4.20
931 1105 7.573916 AAATCATAGCTCATTTAGATCGACG 57.426 36.000 0.00 0.00 0.00 5.12
932 1106 4.476862 TCATAGCTCATTTAGATCGACGC 58.523 43.478 0.00 0.00 0.00 5.19
933 1107 1.759994 AGCTCATTTAGATCGACGCG 58.240 50.000 3.53 3.53 0.00 6.01
934 1108 1.065701 AGCTCATTTAGATCGACGCGT 59.934 47.619 13.85 13.85 0.00 6.01
935 1109 1.852895 GCTCATTTAGATCGACGCGTT 59.147 47.619 15.53 0.00 0.00 4.84
936 1110 2.346741 GCTCATTTAGATCGACGCGTTG 60.347 50.000 20.76 20.76 0.00 4.10
937 1111 2.190161 TCATTTAGATCGACGCGTTGG 58.810 47.619 25.66 15.24 0.00 3.77
938 1112 2.159352 TCATTTAGATCGACGCGTTGGA 60.159 45.455 25.66 19.98 0.00 3.53
939 1113 1.904144 TTTAGATCGACGCGTTGGAG 58.096 50.000 25.66 12.06 0.00 3.86
940 1114 0.806868 TTAGATCGACGCGTTGGAGT 59.193 50.000 25.66 12.54 0.00 3.85
941 1115 0.806868 TAGATCGACGCGTTGGAGTT 59.193 50.000 25.66 14.00 0.00 3.01
942 1116 0.732880 AGATCGACGCGTTGGAGTTG 60.733 55.000 25.66 0.00 0.00 3.16
943 1117 2.279937 GATCGACGCGTTGGAGTTGC 62.280 60.000 25.66 3.32 0.00 4.17
944 1118 2.765250 ATCGACGCGTTGGAGTTGCT 62.765 55.000 25.66 2.84 0.00 3.91
945 1119 2.594962 CGACGCGTTGGAGTTGCTT 61.595 57.895 19.10 0.00 0.00 3.91
946 1120 1.279527 CGACGCGTTGGAGTTGCTTA 61.280 55.000 19.10 0.00 0.00 3.09
947 1121 0.863144 GACGCGTTGGAGTTGCTTAA 59.137 50.000 15.53 0.00 0.00 1.85
948 1122 1.463444 GACGCGTTGGAGTTGCTTAAT 59.537 47.619 15.53 0.00 0.00 1.40
949 1123 2.669434 GACGCGTTGGAGTTGCTTAATA 59.331 45.455 15.53 0.00 0.00 0.98
950 1124 3.068560 ACGCGTTGGAGTTGCTTAATAA 58.931 40.909 5.58 0.00 0.00 1.40
951 1125 3.499157 ACGCGTTGGAGTTGCTTAATAAA 59.501 39.130 5.58 0.00 0.00 1.40
952 1126 3.844099 CGCGTTGGAGTTGCTTAATAAAC 59.156 43.478 0.00 0.00 0.00 2.01
953 1127 4.611807 CGCGTTGGAGTTGCTTAATAAACA 60.612 41.667 0.00 0.00 0.00 2.83
954 1128 4.615541 GCGTTGGAGTTGCTTAATAAACAC 59.384 41.667 3.94 0.00 0.00 3.32
955 1129 5.151389 CGTTGGAGTTGCTTAATAAACACC 58.849 41.667 8.86 8.86 37.49 4.16
970 1144 2.943036 ACACCGTGGGTAGAATGTTT 57.057 45.000 3.03 0.00 32.11 2.83
973 1147 2.482721 CACCGTGGGTAGAATGTTTGAC 59.517 50.000 0.00 0.00 32.11 3.18
998 1174 1.077123 GCTCTCACGAGTCACGAGTA 58.923 55.000 0.00 0.00 45.77 2.59
1132 1308 1.597027 GGTCCACGACACCCAACTG 60.597 63.158 0.00 0.00 33.68 3.16
1166 1342 0.831288 CTCATCCCGATCTGCTCCCT 60.831 60.000 0.00 0.00 0.00 4.20
1209 1385 4.803426 CACCGCGTCAGCCTCTCC 62.803 72.222 4.92 0.00 41.18 3.71
1411 1598 0.037303 TACCCACCTCGAGTCGTTCT 59.963 55.000 13.12 0.00 0.00 3.01
1415 1602 1.409412 CACCTCGAGTCGTTCTTGTG 58.591 55.000 13.12 5.77 0.00 3.33
1421 1608 3.499048 TCGAGTCGTTCTTGTGCTAATC 58.501 45.455 13.12 0.00 0.00 1.75
1422 1609 2.276540 CGAGTCGTTCTTGTGCTAATCG 59.723 50.000 3.82 0.00 0.00 3.34
1423 1610 3.499048 GAGTCGTTCTTGTGCTAATCGA 58.501 45.455 0.00 0.00 0.00 3.59
1424 1611 3.502920 AGTCGTTCTTGTGCTAATCGAG 58.497 45.455 0.00 0.00 0.00 4.04
1434 1621 3.258225 CTAATCGAGCAGTCACCGG 57.742 57.895 0.00 0.00 0.00 5.28
1435 1622 0.872021 CTAATCGAGCAGTCACCGGC 60.872 60.000 0.00 0.00 0.00 6.13
1436 1623 1.600511 TAATCGAGCAGTCACCGGCA 61.601 55.000 0.00 0.00 33.84 5.69
1437 1624 2.449031 AATCGAGCAGTCACCGGCAA 62.449 55.000 0.00 0.00 33.84 4.52
1438 1625 2.244117 ATCGAGCAGTCACCGGCAAT 62.244 55.000 0.00 0.00 33.84 3.56
1456 1643 3.306973 GCAATTTCCTAAAATTCGCAGCC 59.693 43.478 10.41 0.00 41.96 4.85
1490 1678 4.069232 CAGCCGTCAGGGAAGCGA 62.069 66.667 0.00 0.00 38.47 4.93
1506 1694 5.393461 GGGAAGCGAAACATGATTTGAGATT 60.393 40.000 7.12 0.00 0.00 2.40
1602 1790 1.676006 GGTAATCCGATTTGTGCCTGG 59.324 52.381 0.00 0.00 0.00 4.45
1603 1791 2.639065 GTAATCCGATTTGTGCCTGGA 58.361 47.619 0.00 0.00 0.00 3.86
1604 1792 2.442236 AATCCGATTTGTGCCTGGAT 57.558 45.000 0.00 0.00 41.09 3.41
1639 1827 2.048597 TGCTACAAGGTGGACGCG 60.049 61.111 3.53 3.53 0.00 6.01
1663 1851 2.895424 CGGCAAGGAGGACAGGGTT 61.895 63.158 0.00 0.00 0.00 4.11
1669 1857 0.905337 AGGAGGACAGGGTTTCCGAG 60.905 60.000 0.00 0.00 38.29 4.63
1770 1958 2.103042 GCAGCGGCAAGACCTACAG 61.103 63.158 3.18 0.00 40.72 2.74
1792 1980 1.080569 GCAGGTGCCGTTTCCATTG 60.081 57.895 0.00 0.00 34.31 2.82
1851 3722 4.996434 GCCACACTGCGAGCCTGT 62.996 66.667 0.00 0.00 0.00 4.00
1883 3754 2.040544 CCTTGTTGCTACGCAGGGG 61.041 63.158 8.05 0.00 40.61 4.79
2009 3880 2.076863 GAACGGTGCTATGACTTGCTT 58.923 47.619 0.00 0.00 0.00 3.91
2087 3958 1.304891 AGGGCTTGGCTTGGGTAATA 58.695 50.000 0.00 0.00 0.00 0.98
2126 3997 4.806330 TCATCCTTGAGTCTACGTGTTTC 58.194 43.478 0.00 0.00 0.00 2.78
2493 4365 2.675348 CCGCCTTCAAGAAAGCTCTAAG 59.325 50.000 2.34 0.00 33.29 2.18
2586 4458 2.621055 CAGAGAGAGTAGATTGACCCGG 59.379 54.545 0.00 0.00 0.00 5.73
2737 4609 2.528134 TGGTATACCAGGAGGCAGC 58.472 57.895 21.05 0.00 42.01 5.25
2863 4735 2.367894 TGCAATTGTGGCTGGAATCAAA 59.632 40.909 7.40 0.00 0.00 2.69
2866 4738 0.968405 TTGTGGCTGGAATCAAAGGC 59.032 50.000 2.48 2.48 39.33 4.35
3096 4968 5.007528 GCTCTGAGCCATTTTATCTTCTGTC 59.992 44.000 18.80 0.00 34.48 3.51
3264 5145 4.580580 ACAAAGGTCAGTAAGCCAAGAAAG 59.419 41.667 0.00 0.00 0.00 2.62
3476 5357 7.492994 GGTTTGCTTGTTGTATAACTTTGGAAA 59.507 33.333 3.89 5.10 37.68 3.13
3554 5435 1.339727 CCCCCTTCGTTAACTCCTTGG 60.340 57.143 3.71 0.00 0.00 3.61
3590 5471 3.176411 TGAATCTCCTCTCAGGAAAGCA 58.824 45.455 0.00 0.00 45.28 3.91
3790 5684 2.286365 CCTGTTTTAGTTCAGGGCCA 57.714 50.000 6.18 0.00 45.11 5.36
3860 5754 8.390354 CAATATCTCGAGTTCTTAAATGTTGCA 58.610 33.333 13.13 0.00 0.00 4.08
3914 5809 7.843490 TGTAGTTCATTTATGTAGTTGGCTC 57.157 36.000 0.00 0.00 0.00 4.70
4014 5910 6.653740 ACAGCAACTAAAAGTATGGTCCTTAC 59.346 38.462 6.79 6.79 0.00 2.34
4275 6171 6.849697 ACTTGGGGAATATAGGTCTATCAACA 59.150 38.462 0.00 0.00 0.00 3.33
4402 6299 4.397103 GCATCAAACAGATCCAAGACATCA 59.603 41.667 0.00 0.00 33.72 3.07
4406 6303 6.710278 TCAAACAGATCCAAGACATCATACA 58.290 36.000 0.00 0.00 0.00 2.29
4450 6347 6.312141 TCAAATGATCACTGGAATGGACTA 57.688 37.500 0.00 0.00 0.00 2.59
4462 6359 5.271598 TGGAATGGACTATTGCCTGAAAAT 58.728 37.500 0.66 0.00 36.38 1.82
4485 6382 2.501723 ACAGAATGGACTGCCGTAATCT 59.498 45.455 0.00 0.00 43.62 2.40
4495 6420 1.414919 TGCCGTAATCTACCACCATCC 59.585 52.381 0.00 0.00 0.00 3.51
4504 6429 1.261938 TACCACCATCCGTGACCCAG 61.262 60.000 0.00 0.00 46.20 4.45
4565 6490 7.241663 TGTTGTTGACATAGTTGTAGTTGTC 57.758 36.000 0.00 0.00 39.11 3.18
4598 6523 0.592148 GCCTGCTGCTGATGCTATTC 59.408 55.000 8.20 0.00 40.48 1.75
4700 6661 1.068055 GCAGCTGAATGGTTGGTCTTG 60.068 52.381 20.43 0.00 0.00 3.02
4729 6690 7.465353 TGTGATGCAAATTTTCTCTGGAATA 57.535 32.000 0.00 0.00 0.00 1.75
4799 6760 5.045872 GCAACTGAAAATGAGTTCTGCTTT 58.954 37.500 0.00 0.00 31.05 3.51
4815 6776 4.560856 TTGGCAAACCGTGTGCGC 62.561 61.111 7.61 0.00 43.18 6.09
4865 6827 8.134261 TGATTTTCATGTTTCACGAAGATTTCA 58.866 29.630 0.00 0.00 0.00 2.69
4874 6836 4.832248 TCACGAAGATTTCAGGCATTAGT 58.168 39.130 0.00 0.00 0.00 2.24
4879 6841 8.020819 CACGAAGATTTCAGGCATTAGTTTTTA 58.979 33.333 0.00 0.00 0.00 1.52
4920 6886 4.317488 CATTAGTTTGCCTGGTTTGCATT 58.683 39.130 0.00 0.00 38.76 3.56
4935 6902 4.329462 TTGCATTTTTGTAGGAACCCAC 57.671 40.909 0.00 0.00 0.00 4.61
4958 6925 6.356977 CACGACATGATTGTGTACTTGTTTTC 59.643 38.462 0.00 0.00 37.86 2.29
4968 6935 8.902540 TTGTGTACTTGTTTTCACTCATATCT 57.097 30.769 0.00 0.00 0.00 1.98
4969 6936 8.902540 TGTGTACTTGTTTTCACTCATATCTT 57.097 30.769 0.00 0.00 0.00 2.40
4984 7022 8.610896 CACTCATATCTTTGGAAATCTTCTGAC 58.389 37.037 0.00 0.00 0.00 3.51
5044 7083 7.384932 AGCAAAGCCAATGTAATTTGTAAAGAC 59.615 33.333 0.00 0.00 31.22 3.01
5186 7605 5.591099 AGCCAATGTTGCCGAAAATAATAG 58.409 37.500 0.00 0.00 0.00 1.73
5192 7611 8.372521 CAATGTTGCCGAAAATAATAGAAACAC 58.627 33.333 0.00 0.00 0.00 3.32
5193 7612 6.971602 TGTTGCCGAAAATAATAGAAACACA 58.028 32.000 0.00 0.00 0.00 3.72
5292 7711 0.806492 GCTAGACGGGCTGCTTGTAC 60.806 60.000 0.00 0.00 0.00 2.90
5295 7714 0.320771 AGACGGGCTGCTTGTACAAG 60.321 55.000 27.85 27.85 41.24 3.16
5305 7724 5.983118 GGCTGCTTGTACAAGTTACAATTTT 59.017 36.000 30.90 0.00 40.45 1.82
5307 7726 6.918022 GCTGCTTGTACAAGTTACAATTTTCT 59.082 34.615 30.90 0.00 40.45 2.52
5308 7727 7.096477 GCTGCTTGTACAAGTTACAATTTTCTG 60.096 37.037 30.90 16.98 40.45 3.02
5309 7728 7.767261 TGCTTGTACAAGTTACAATTTTCTGT 58.233 30.769 30.90 0.00 40.45 3.41
5311 7730 9.724839 GCTTGTACAAGTTACAATTTTCTGTTA 57.275 29.630 30.90 0.00 40.45 2.41
5359 7784 7.645340 CAGCGATTTATCCAAGTATTCTTTTGG 59.355 37.037 0.00 0.00 44.15 3.28
5402 7827 6.519679 TGATGTCCTTGAAGATGAAAATGG 57.480 37.500 0.00 0.00 0.00 3.16
5407 7832 7.885297 TGTCCTTGAAGATGAAAATGGTTAAG 58.115 34.615 0.00 0.00 0.00 1.85
5412 7837 9.748708 CTTGAAGATGAAAATGGTTAAGTTGAA 57.251 29.630 0.00 0.00 0.00 2.69
5430 7855 7.194607 AGTTGAATATATTGTTGGCATCTCG 57.805 36.000 1.78 0.00 0.00 4.04
5446 7871 1.816835 TCTCGAAAGGAGTACGCACAT 59.183 47.619 0.00 0.00 43.60 3.21
5500 7925 4.755411 TGCAAGGAATTTCGTAGACTAGG 58.245 43.478 0.00 0.00 34.32 3.02
5503 7928 4.657436 AGGAATTTCGTAGACTAGGCAG 57.343 45.455 0.00 0.00 34.32 4.85
5505 7930 4.339814 AGGAATTTCGTAGACTAGGCAGAG 59.660 45.833 0.00 0.00 34.32 3.35
5588 8016 7.165460 TCTATTGTTCAAGTACATTCCTCGA 57.835 36.000 0.00 0.00 0.00 4.04
5590 8018 6.727824 ATTGTTCAAGTACATTCCTCGAAG 57.272 37.500 0.00 0.00 0.00 3.79
5605 8033 4.277423 TCCTCGAAGGGAAAAACAATTCAC 59.723 41.667 0.00 0.00 35.59 3.18
5721 8154 6.392354 ACATCATTCTCGCAACATTGAATTT 58.608 32.000 0.00 0.00 0.00 1.82
5723 8156 6.258230 TCATTCTCGCAACATTGAATTTCT 57.742 33.333 0.00 0.00 0.00 2.52
5747 8180 1.221466 TGCTTTGTTCCAGCGAGACG 61.221 55.000 0.00 0.00 40.45 4.18
5775 8208 7.175641 CACAAATTACACTCTTCTTTGATCCCT 59.824 37.037 0.00 0.00 32.54 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.044758 ACCACCTCACCTACGTTTCTT 58.955 47.619 0.00 0.00 0.00 2.52
12 13 1.202722 CCAACCACCTCACCTACGTTT 60.203 52.381 0.00 0.00 0.00 3.60
220 380 1.603802 CAACAAATCTGCACGACCTGT 59.396 47.619 0.00 0.00 0.00 4.00
231 391 5.163622 CCGAACCATAATCTGCAACAAATCT 60.164 40.000 0.00 0.00 0.00 2.40
424 585 2.254546 CAGTTGACTGGTGGTTAGCA 57.745 50.000 3.19 0.00 40.20 3.49
590 751 2.905415 TCACTTCCTGCCCATTTGAT 57.095 45.000 0.00 0.00 0.00 2.57
602 763 3.686726 CCAACTGAGCTAACATCACTTCC 59.313 47.826 0.00 0.00 0.00 3.46
603 764 4.319177 ACCAACTGAGCTAACATCACTTC 58.681 43.478 0.00 0.00 0.00 3.01
628 789 2.688446 CCTACTAGCATCACAACGAGGA 59.312 50.000 0.00 0.00 0.00 3.71
639 800 1.457643 TCTGCCCGCCTACTAGCAT 60.458 57.895 0.00 0.00 34.16 3.79
643 804 0.535335 CAAACTCTGCCCGCCTACTA 59.465 55.000 0.00 0.00 0.00 1.82
653 814 2.087646 GAGTGGGGATTCAAACTCTGC 58.912 52.381 0.00 0.00 36.85 4.26
661 822 1.887956 GCTTGCTTGAGTGGGGATTCA 60.888 52.381 0.00 0.00 0.00 2.57
766 940 9.830975 TCAACTAAGTATGCACATATTGTACAT 57.169 29.630 0.00 0.00 37.96 2.29
767 941 9.660180 TTCAACTAAGTATGCACATATTGTACA 57.340 29.630 0.00 0.00 0.00 2.90
772 946 9.554724 CGTTTTTCAACTAAGTATGCACATATT 57.445 29.630 0.00 0.00 0.00 1.28
773 947 7.696453 GCGTTTTTCAACTAAGTATGCACATAT 59.304 33.333 0.00 0.00 0.00 1.78
774 948 7.018826 GCGTTTTTCAACTAAGTATGCACATA 58.981 34.615 0.00 0.00 0.00 2.29
775 949 5.856455 GCGTTTTTCAACTAAGTATGCACAT 59.144 36.000 0.00 0.00 0.00 3.21
776 950 5.209240 GCGTTTTTCAACTAAGTATGCACA 58.791 37.500 0.00 0.00 0.00 4.57
777 951 4.615541 GGCGTTTTTCAACTAAGTATGCAC 59.384 41.667 0.00 0.00 0.00 4.57
778 952 4.611807 CGGCGTTTTTCAACTAAGTATGCA 60.612 41.667 0.00 0.00 0.00 3.96
779 953 3.844099 CGGCGTTTTTCAACTAAGTATGC 59.156 43.478 0.00 0.00 0.00 3.14
780 954 4.399978 CCGGCGTTTTTCAACTAAGTATG 58.600 43.478 6.01 0.00 0.00 2.39
781 955 3.120095 GCCGGCGTTTTTCAACTAAGTAT 60.120 43.478 12.58 0.00 0.00 2.12
782 956 2.223845 GCCGGCGTTTTTCAACTAAGTA 59.776 45.455 12.58 0.00 0.00 2.24
783 957 1.002142 GCCGGCGTTTTTCAACTAAGT 60.002 47.619 12.58 0.00 0.00 2.24
784 958 1.664874 GGCCGGCGTTTTTCAACTAAG 60.665 52.381 22.54 0.00 0.00 2.18
785 959 0.311477 GGCCGGCGTTTTTCAACTAA 59.689 50.000 22.54 0.00 0.00 2.24
786 960 0.818445 TGGCCGGCGTTTTTCAACTA 60.818 50.000 22.54 0.00 0.00 2.24
787 961 1.460273 ATGGCCGGCGTTTTTCAACT 61.460 50.000 22.54 0.00 0.00 3.16
788 962 1.006688 ATGGCCGGCGTTTTTCAAC 60.007 52.632 22.54 3.09 0.00 3.18
789 963 1.006805 CATGGCCGGCGTTTTTCAA 60.007 52.632 22.54 0.00 0.00 2.69
790 964 2.647875 CATGGCCGGCGTTTTTCA 59.352 55.556 22.54 12.23 0.00 2.69
791 965 2.809174 GCATGGCCGGCGTTTTTC 60.809 61.111 22.54 5.65 0.00 2.29
792 966 4.371590 GGCATGGCCGGCGTTTTT 62.372 61.111 22.54 0.00 39.62 1.94
801 975 1.812571 CCTATATTTGTCGGCATGGCC 59.187 52.381 14.46 0.00 46.75 5.36
802 976 2.484264 GACCTATATTTGTCGGCATGGC 59.516 50.000 9.69 9.69 0.00 4.40
810 984 0.782384 CGCGCCGACCTATATTTGTC 59.218 55.000 0.00 0.00 0.00 3.18
811 985 0.103572 ACGCGCCGACCTATATTTGT 59.896 50.000 5.73 0.00 0.00 2.83
812 986 0.506932 CACGCGCCGACCTATATTTG 59.493 55.000 5.73 0.00 0.00 2.32
813 987 0.599204 CCACGCGCCGACCTATATTT 60.599 55.000 5.73 0.00 0.00 1.40
814 988 1.006571 CCACGCGCCGACCTATATT 60.007 57.895 5.73 0.00 0.00 1.28
815 989 2.649034 CCACGCGCCGACCTATAT 59.351 61.111 5.73 0.00 0.00 0.86
816 990 4.274700 GCCACGCGCCGACCTATA 62.275 66.667 5.73 0.00 0.00 1.31
827 1001 3.702555 GTCGTCAGTGTGCCACGC 61.703 66.667 0.00 0.00 39.64 5.34
828 1002 3.036084 GGTCGTCAGTGTGCCACG 61.036 66.667 0.00 0.00 39.64 4.94
829 1003 2.665185 GGGTCGTCAGTGTGCCAC 60.665 66.667 0.00 0.00 34.10 5.01
830 1004 2.258748 TTTGGGTCGTCAGTGTGCCA 62.259 55.000 0.00 0.00 0.00 4.92
831 1005 0.889186 ATTTGGGTCGTCAGTGTGCC 60.889 55.000 0.00 0.00 0.00 5.01
832 1006 0.517316 GATTTGGGTCGTCAGTGTGC 59.483 55.000 0.00 0.00 0.00 4.57
833 1007 1.877637 TGATTTGGGTCGTCAGTGTG 58.122 50.000 0.00 0.00 0.00 3.82
834 1008 2.631160 TTGATTTGGGTCGTCAGTGT 57.369 45.000 0.00 0.00 0.00 3.55
835 1009 3.980646 TTTTGATTTGGGTCGTCAGTG 57.019 42.857 0.00 0.00 0.00 3.66
853 1027 2.538132 CCGTTCGACGTTTGCTCTTTTT 60.538 45.455 0.00 0.00 40.58 1.94
854 1028 1.004292 CCGTTCGACGTTTGCTCTTTT 60.004 47.619 0.00 0.00 40.58 2.27
855 1029 0.580104 CCGTTCGACGTTTGCTCTTT 59.420 50.000 0.00 0.00 40.58 2.52
856 1030 0.249155 TCCGTTCGACGTTTGCTCTT 60.249 50.000 0.00 0.00 40.58 2.85
857 1031 0.938168 GTCCGTTCGACGTTTGCTCT 60.938 55.000 0.00 0.00 40.58 4.09
858 1032 1.485943 GTCCGTTCGACGTTTGCTC 59.514 57.895 0.00 0.00 40.58 4.26
859 1033 3.621520 GTCCGTTCGACGTTTGCT 58.378 55.556 0.00 0.00 40.58 3.91
873 1047 0.814812 TTTGTTTGGGTCGGTCGTCC 60.815 55.000 0.00 0.00 0.00 4.79
874 1048 1.232119 ATTTGTTTGGGTCGGTCGTC 58.768 50.000 0.00 0.00 0.00 4.20
875 1049 2.547299 TATTTGTTTGGGTCGGTCGT 57.453 45.000 0.00 0.00 0.00 4.34
876 1050 3.900388 TTTATTTGTTTGGGTCGGTCG 57.100 42.857 0.00 0.00 0.00 4.79
895 1069 7.288810 TGAGCTATGATTTTGTCTGGTTTTT 57.711 32.000 0.00 0.00 0.00 1.94
896 1070 6.899393 TGAGCTATGATTTTGTCTGGTTTT 57.101 33.333 0.00 0.00 0.00 2.43
897 1071 7.472334 AATGAGCTATGATTTTGTCTGGTTT 57.528 32.000 0.00 0.00 0.00 3.27
898 1072 7.472334 AAATGAGCTATGATTTTGTCTGGTT 57.528 32.000 0.00 0.00 0.00 3.67
899 1073 8.049117 TCTAAATGAGCTATGATTTTGTCTGGT 58.951 33.333 0.00 0.00 0.00 4.00
900 1074 8.442632 TCTAAATGAGCTATGATTTTGTCTGG 57.557 34.615 0.00 0.00 0.00 3.86
902 1076 8.986847 CGATCTAAATGAGCTATGATTTTGTCT 58.013 33.333 0.00 0.00 0.00 3.41
903 1077 8.982685 TCGATCTAAATGAGCTATGATTTTGTC 58.017 33.333 0.00 0.00 0.00 3.18
904 1078 8.768955 GTCGATCTAAATGAGCTATGATTTTGT 58.231 33.333 0.00 0.00 0.00 2.83
905 1079 7.948895 CGTCGATCTAAATGAGCTATGATTTTG 59.051 37.037 0.00 0.00 0.00 2.44
906 1080 7.359598 GCGTCGATCTAAATGAGCTATGATTTT 60.360 37.037 0.00 0.00 0.00 1.82
907 1081 6.090088 GCGTCGATCTAAATGAGCTATGATTT 59.910 38.462 0.00 0.00 0.00 2.17
908 1082 5.574830 GCGTCGATCTAAATGAGCTATGATT 59.425 40.000 0.00 0.00 0.00 2.57
909 1083 5.098893 GCGTCGATCTAAATGAGCTATGAT 58.901 41.667 0.00 0.00 0.00 2.45
910 1084 4.476862 GCGTCGATCTAAATGAGCTATGA 58.523 43.478 0.00 0.00 0.00 2.15
911 1085 3.299281 CGCGTCGATCTAAATGAGCTATG 59.701 47.826 0.00 0.00 0.00 2.23
912 1086 3.058155 ACGCGTCGATCTAAATGAGCTAT 60.058 43.478 5.58 0.00 0.00 2.97
913 1087 2.289820 ACGCGTCGATCTAAATGAGCTA 59.710 45.455 5.58 0.00 0.00 3.32
914 1088 1.065701 ACGCGTCGATCTAAATGAGCT 59.934 47.619 5.58 0.00 0.00 4.09
915 1089 1.478137 ACGCGTCGATCTAAATGAGC 58.522 50.000 5.58 0.00 0.00 4.26
916 1090 2.216488 CCAACGCGTCGATCTAAATGAG 59.784 50.000 14.44 0.00 0.00 2.90
917 1091 2.159352 TCCAACGCGTCGATCTAAATGA 60.159 45.455 14.44 0.00 0.00 2.57
918 1092 2.190161 TCCAACGCGTCGATCTAAATG 58.810 47.619 14.44 3.04 0.00 2.32
919 1093 2.159282 ACTCCAACGCGTCGATCTAAAT 60.159 45.455 14.44 0.00 0.00 1.40
920 1094 1.200716 ACTCCAACGCGTCGATCTAAA 59.799 47.619 14.44 0.00 0.00 1.85
921 1095 0.806868 ACTCCAACGCGTCGATCTAA 59.193 50.000 14.44 0.00 0.00 2.10
922 1096 0.806868 AACTCCAACGCGTCGATCTA 59.193 50.000 14.44 0.00 0.00 1.98
923 1097 0.732880 CAACTCCAACGCGTCGATCT 60.733 55.000 14.44 0.00 0.00 2.75
924 1098 1.702299 CAACTCCAACGCGTCGATC 59.298 57.895 14.44 0.00 0.00 3.69
925 1099 2.380410 GCAACTCCAACGCGTCGAT 61.380 57.895 14.44 0.00 0.00 3.59
926 1100 2.964438 AAGCAACTCCAACGCGTCGA 62.964 55.000 14.44 10.76 0.00 4.20
927 1101 1.279527 TAAGCAACTCCAACGCGTCG 61.280 55.000 14.44 0.00 0.00 5.12
928 1102 0.863144 TTAAGCAACTCCAACGCGTC 59.137 50.000 14.44 0.00 0.00 5.19
929 1103 1.519408 ATTAAGCAACTCCAACGCGT 58.481 45.000 5.58 5.58 0.00 6.01
930 1104 3.733024 TTATTAAGCAACTCCAACGCG 57.267 42.857 3.53 3.53 0.00 6.01
931 1105 4.615541 GTGTTTATTAAGCAACTCCAACGC 59.384 41.667 0.00 0.00 0.00 4.84
932 1106 5.151389 GGTGTTTATTAAGCAACTCCAACG 58.849 41.667 12.55 0.00 36.80 4.10
933 1107 5.151389 CGGTGTTTATTAAGCAACTCCAAC 58.849 41.667 15.65 2.40 36.67 3.77
934 1108 4.822896 ACGGTGTTTATTAAGCAACTCCAA 59.177 37.500 15.65 0.00 36.67 3.53
935 1109 4.214545 CACGGTGTTTATTAAGCAACTCCA 59.785 41.667 15.65 0.00 36.67 3.86
936 1110 4.379082 CCACGGTGTTTATTAAGCAACTCC 60.379 45.833 7.45 9.25 34.52 3.85
937 1111 4.379082 CCCACGGTGTTTATTAAGCAACTC 60.379 45.833 7.45 0.00 0.00 3.01
938 1112 3.504520 CCCACGGTGTTTATTAAGCAACT 59.495 43.478 7.45 0.00 0.00 3.16
939 1113 3.253921 ACCCACGGTGTTTATTAAGCAAC 59.746 43.478 7.45 0.00 32.98 4.17
940 1114 3.488363 ACCCACGGTGTTTATTAAGCAA 58.512 40.909 7.45 0.00 32.98 3.91
941 1115 3.143211 ACCCACGGTGTTTATTAAGCA 57.857 42.857 7.45 0.00 32.98 3.91
942 1116 4.506758 TCTACCCACGGTGTTTATTAAGC 58.493 43.478 7.45 0.00 36.19 3.09
943 1117 6.596497 ACATTCTACCCACGGTGTTTATTAAG 59.404 38.462 7.45 0.00 36.19 1.85
944 1118 6.474630 ACATTCTACCCACGGTGTTTATTAA 58.525 36.000 7.45 0.00 36.19 1.40
945 1119 6.052405 ACATTCTACCCACGGTGTTTATTA 57.948 37.500 7.45 0.00 36.19 0.98
946 1120 4.913784 ACATTCTACCCACGGTGTTTATT 58.086 39.130 7.45 0.00 36.19 1.40
947 1121 4.563140 ACATTCTACCCACGGTGTTTAT 57.437 40.909 7.45 0.00 36.19 1.40
948 1122 4.354893 AACATTCTACCCACGGTGTTTA 57.645 40.909 7.45 0.00 36.19 2.01
949 1123 2.943036 ACATTCTACCCACGGTGTTT 57.057 45.000 7.45 0.00 36.19 2.83
950 1124 2.882137 CAAACATTCTACCCACGGTGTT 59.118 45.455 7.45 0.00 36.19 3.32
951 1125 2.105134 TCAAACATTCTACCCACGGTGT 59.895 45.455 7.45 0.00 36.19 4.16
952 1126 2.482721 GTCAAACATTCTACCCACGGTG 59.517 50.000 0.00 0.00 36.19 4.94
953 1127 2.774687 GTCAAACATTCTACCCACGGT 58.225 47.619 0.00 0.00 40.16 4.83
954 1128 1.730064 CGTCAAACATTCTACCCACGG 59.270 52.381 0.00 0.00 0.00 4.94
955 1129 2.666508 CTCGTCAAACATTCTACCCACG 59.333 50.000 0.00 0.00 0.00 4.94
1021 1197 2.504244 GGTCTGACGAAGGACGCG 60.504 66.667 3.53 3.53 46.94 6.01
1026 1202 3.358076 GAGGCGGGTCTGACGAAGG 62.358 68.421 1.07 0.00 0.00 3.46
1028 1204 3.379445 GGAGGCGGGTCTGACGAA 61.379 66.667 1.07 0.00 0.00 3.85
1128 1304 0.822121 GGCGAGGTTTTGGGTCAGTT 60.822 55.000 0.00 0.00 0.00 3.16
1132 1308 0.322546 ATGAGGCGAGGTTTTGGGTC 60.323 55.000 0.00 0.00 0.00 4.46
1421 1608 1.577328 AAATTGCCGGTGACTGCTCG 61.577 55.000 1.90 0.00 41.69 5.03
1422 1609 0.169009 GAAATTGCCGGTGACTGCTC 59.831 55.000 1.90 0.00 41.69 4.26
1423 1610 1.244019 GGAAATTGCCGGTGACTGCT 61.244 55.000 1.90 0.00 41.69 4.24
1424 1611 1.212751 GGAAATTGCCGGTGACTGC 59.787 57.895 1.90 0.00 41.49 4.40
1425 1612 2.107950 TAGGAAATTGCCGGTGACTG 57.892 50.000 1.90 0.00 0.00 3.51
1426 1613 2.871096 TTAGGAAATTGCCGGTGACT 57.129 45.000 1.90 0.00 0.00 3.41
1427 1614 3.926821 TTTTAGGAAATTGCCGGTGAC 57.073 42.857 1.90 0.00 0.00 3.67
1428 1615 4.380023 CGAATTTTAGGAAATTGCCGGTGA 60.380 41.667 1.90 0.00 43.61 4.02
1429 1616 3.857093 CGAATTTTAGGAAATTGCCGGTG 59.143 43.478 1.90 0.00 43.61 4.94
1430 1617 3.674955 GCGAATTTTAGGAAATTGCCGGT 60.675 43.478 1.90 0.00 43.61 5.28
1431 1618 2.857748 GCGAATTTTAGGAAATTGCCGG 59.142 45.455 0.00 0.00 43.61 6.13
1432 1619 3.506810 TGCGAATTTTAGGAAATTGCCG 58.493 40.909 0.00 2.66 43.61 5.69
1433 1620 3.306973 GCTGCGAATTTTAGGAAATTGCC 59.693 43.478 0.00 0.00 43.61 4.52
1434 1621 3.306973 GGCTGCGAATTTTAGGAAATTGC 59.693 43.478 2.17 6.86 43.61 3.56
1435 1622 3.865164 GGGCTGCGAATTTTAGGAAATTG 59.135 43.478 2.17 0.00 43.61 2.32
1436 1623 3.118775 GGGGCTGCGAATTTTAGGAAATT 60.119 43.478 0.00 0.00 45.62 1.82
1437 1624 2.430694 GGGGCTGCGAATTTTAGGAAAT 59.569 45.455 0.00 0.00 37.06 2.17
1438 1625 1.822371 GGGGCTGCGAATTTTAGGAAA 59.178 47.619 0.00 0.00 0.00 3.13
1456 1643 3.732849 GCACCAGGAGGGAAGGGG 61.733 72.222 0.00 0.00 41.15 4.79
1506 1694 6.590292 GCACAGCTACACTAAGAGTTAATCAA 59.410 38.462 0.00 0.00 0.00 2.57
1602 1790 3.344215 CGCTCCGGCTGCATGATC 61.344 66.667 17.12 0.00 36.09 2.92
1603 1791 3.804153 CTCGCTCCGGCTGCATGAT 62.804 63.158 17.12 0.00 36.09 2.45
1604 1792 4.519437 CTCGCTCCGGCTGCATGA 62.519 66.667 17.12 7.95 36.09 3.07
1639 1827 0.606604 TGTCCTCCTTGCCGAAGTAC 59.393 55.000 0.00 0.00 0.00 2.73
1770 1958 2.126346 GAAACGGCACCTGCATGC 60.126 61.111 11.82 11.82 45.34 4.06
1783 1971 0.898326 AAGGCCGGGACAATGGAAAC 60.898 55.000 0.92 0.00 0.00 2.78
1784 1972 0.897863 CAAGGCCGGGACAATGGAAA 60.898 55.000 0.92 0.00 0.00 3.13
1883 3754 1.227497 CCCTGGCAGATCTTCGCTC 60.227 63.158 17.94 0.00 0.00 5.03
2126 3997 2.505819 ACTGCCTAAGGTACATTCCAGG 59.494 50.000 15.32 10.97 0.00 4.45
2586 4458 4.233789 CTCCTAGCGAATCTTGCAGTATC 58.766 47.826 0.00 0.00 33.85 2.24
2737 4609 1.135527 CAGCCATGCTTAATGTGTGGG 59.864 52.381 0.00 0.00 36.40 4.61
2863 4735 1.610886 GGGTGCTCTTAGTTTTCGCCT 60.611 52.381 0.00 0.00 0.00 5.52
2866 4738 3.813166 TCTTTGGGTGCTCTTAGTTTTCG 59.187 43.478 0.00 0.00 0.00 3.46
3112 4984 3.261580 TGTTGTATGGACTGCTGAATCG 58.738 45.455 0.00 0.00 0.00 3.34
3219 5100 7.776618 TGTACGGTCAGAATCTATATCCAAT 57.223 36.000 0.00 0.00 0.00 3.16
3264 5145 9.020813 GTGTGTTCATTAGAGTTTTCCTTTTTC 57.979 33.333 0.00 0.00 0.00 2.29
3554 5435 6.413892 AGGAGATTCAGATTTGTCCTCTTTC 58.586 40.000 0.00 0.00 27.58 2.62
3590 5471 3.138283 TGTTTGAAGGAATGGGAGACAGT 59.862 43.478 0.00 0.00 0.00 3.55
3787 5681 8.900983 AACATAAGAGATCTTTAGAGATTGGC 57.099 34.615 0.00 0.00 42.66 4.52
3790 5684 9.685828 GCGTAACATAAGAGATCTTTAGAGATT 57.314 33.333 0.00 0.00 42.66 2.40
3914 5809 0.665835 TGCCTTGTGCGTTTAACAGG 59.334 50.000 0.00 0.00 45.60 4.00
4026 5922 5.222079 TGCCGCTATACCATTCATTAGAA 57.778 39.130 0.00 0.00 38.31 2.10
4034 5930 1.699634 AGGACATGCCGCTATACCATT 59.300 47.619 0.00 0.00 43.43 3.16
4275 6171 6.116126 AGTCAGCAGAAGAGTTACTTGTTTT 58.884 36.000 0.00 0.00 39.13 2.43
4323 6220 7.174772 TGTGCACATACATTGTACAAGAAAGAT 59.825 33.333 17.42 0.53 36.75 2.40
4339 6236 2.032030 AGAGCGTTGTTTGTGCACATAC 60.032 45.455 27.32 27.32 0.00 2.39
4354 6251 6.807230 CAGTATAGACAAGTGTTTAAGAGCGT 59.193 38.462 0.00 0.00 0.00 5.07
4402 6299 3.788227 TCCTGTGGCTGTTTTCTGTAT 57.212 42.857 0.00 0.00 0.00 2.29
4406 6303 3.515602 AGATTCCTGTGGCTGTTTTCT 57.484 42.857 0.00 0.00 0.00 2.52
4450 6347 4.773674 TCCATTCTGTGATTTTCAGGCAAT 59.226 37.500 0.00 0.00 34.15 3.56
4462 6359 1.262417 TACGGCAGTCCATTCTGTGA 58.738 50.000 0.00 0.00 37.70 3.58
4485 6382 1.229241 TGGGTCACGGATGGTGGTA 60.229 57.895 0.00 0.00 46.96 3.25
4504 6429 4.451096 CAGTACAGTTACAACACCATCCAC 59.549 45.833 0.00 0.00 0.00 4.02
4519 6444 2.224066 GGCTGACAGTTCACAGTACAGT 60.224 50.000 3.99 0.00 36.62 3.55
4598 6523 1.201429 ACAAGACCCACTGCCCTAGG 61.201 60.000 0.06 0.06 0.00 3.02
4642 6594 2.291411 GCTAGGCCATCCCATCATGAAT 60.291 50.000 5.01 0.00 35.39 2.57
4646 6598 1.075050 CAAGCTAGGCCATCCCATCAT 59.925 52.381 5.01 0.00 35.39 2.45
4683 6641 2.622942 TCAACAAGACCAACCATTCAGC 59.377 45.455 0.00 0.00 0.00 4.26
4694 6652 3.921119 TTGCATCACATCAACAAGACC 57.079 42.857 0.00 0.00 0.00 3.85
4700 6661 6.090358 CCAGAGAAAATTTGCATCACATCAAC 59.910 38.462 0.00 0.00 0.00 3.18
4815 6776 6.389622 TCTTGACATCGAAAATAGTTCACG 57.610 37.500 0.00 0.00 0.00 4.35
4816 6777 7.963981 TCATCTTGACATCGAAAATAGTTCAC 58.036 34.615 0.00 0.00 0.00 3.18
4845 6806 4.083324 GCCTGAAATCTTCGTGAAACATGA 60.083 41.667 0.00 0.00 35.74 3.07
4894 6857 2.584835 ACCAGGCAAACTAATGCTCA 57.415 45.000 0.00 0.00 45.68 4.26
4920 6886 3.142951 CATGTCGTGGGTTCCTACAAAA 58.857 45.455 6.20 0.00 0.00 2.44
4935 6902 6.356977 GTGAAAACAAGTACACAATCATGTCG 59.643 38.462 0.00 0.00 37.82 4.35
4958 6925 8.610896 GTCAGAAGATTTCCAAAGATATGAGTG 58.389 37.037 0.00 0.00 0.00 3.51
4968 6935 8.956426 GTATGTAATGGTCAGAAGATTTCCAAA 58.044 33.333 0.00 0.00 0.00 3.28
4969 6936 8.106462 TGTATGTAATGGTCAGAAGATTTCCAA 58.894 33.333 0.00 0.00 0.00 3.53
5044 7083 7.719483 ACAAATGCATCAAAACTAGGGATATG 58.281 34.615 0.00 0.00 0.00 1.78
5204 7623 3.601685 CACGGTGGGCGCCTTTTT 61.602 61.111 28.56 4.15 0.00 1.94
5311 7730 9.770503 CGCTGACGTATTATCTAAGTAATGTAT 57.229 33.333 0.00 0.00 33.53 2.29
5314 7733 8.897457 ATCGCTGACGTATTATCTAAGTAATG 57.103 34.615 0.00 0.00 41.18 1.90
5328 7747 4.380841 ACTTGGATAAATCGCTGACGTA 57.619 40.909 0.00 0.00 41.18 3.57
5343 7762 5.055265 TGGTGTCCAAAAGAATACTTGGA 57.945 39.130 0.00 0.00 46.99 3.53
5359 7784 7.748847 ACATCAAATTACGTTATCTTGGTGTC 58.251 34.615 15.88 0.00 36.82 3.67
5407 7832 7.189693 TCGAGATGCCAACAATATATTCAAC 57.810 36.000 0.00 0.00 0.00 3.18
5412 7837 6.533730 TCCTTTCGAGATGCCAACAATATAT 58.466 36.000 0.00 0.00 0.00 0.86
5413 7838 5.924356 TCCTTTCGAGATGCCAACAATATA 58.076 37.500 0.00 0.00 0.00 0.86
5430 7855 5.465390 TGCATATAATGTGCGTACTCCTTTC 59.535 40.000 4.97 0.00 45.37 2.62
5446 7871 1.946768 GCTGCTTCCGGTTGCATATAA 59.053 47.619 20.42 0.00 38.59 0.98
5500 7925 1.654317 CCATGTCTCAAGCTCTCTGC 58.346 55.000 0.00 0.00 43.29 4.26
5503 7928 0.251354 TGCCCATGTCTCAAGCTCTC 59.749 55.000 0.00 0.00 0.00 3.20
5505 7930 1.538047 TTTGCCCATGTCTCAAGCTC 58.462 50.000 0.00 0.00 0.00 4.09
5588 8016 6.484364 ACTGATGTGAATTGTTTTTCCCTT 57.516 33.333 0.00 0.00 0.00 3.95
5590 8018 6.981722 AGTACTGATGTGAATTGTTTTTCCC 58.018 36.000 0.00 0.00 0.00 3.97
5642 8070 7.601705 AAACCTTCTTCCTCAATGAAAATGA 57.398 32.000 0.00 0.00 0.00 2.57
5747 8180 6.072112 TCAAAGAAGAGTGTAATTTGTGGC 57.928 37.500 0.00 0.00 33.61 5.01


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

AutoCloner maintained by Alex Coulton.