Multiple sequence alignment - TraesCS6A01G136400

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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 TraesCS6A01G136400 chr6A 100.000 4635 0 0 1 4635 107680405 107685039 0.000000e+00 8560.0
1 TraesCS6A01G136400 chr6A 79.992 2664 486 38 993 3641 107214450 107217081 0.000000e+00 1923.0
2 TraesCS6A01G136400 chr6A 78.493 1632 312 24 2008 3624 107270618 107272225 0.000000e+00 1033.0
3 TraesCS6A01G136400 chr6B 90.574 3851 258 46 799 4591 171699851 171703654 0.000000e+00 5003.0
4 TraesCS6A01G136400 chr6B 80.370 2649 469 38 993 3624 171029192 171031806 0.000000e+00 1964.0
5 TraesCS6A01G136400 chr6B 78.829 1639 305 33 2008 3634 171206070 171207678 0.000000e+00 1066.0
6 TraesCS6A01G136400 chr6B 80.318 1133 214 6 1000 2125 171204913 171206043 0.000000e+00 848.0
7 TraesCS6A01G136400 chr6B 94.151 530 18 3 4102 4624 171707819 171708342 0.000000e+00 795.0
8 TraesCS6A01G136400 chr6B 81.818 693 60 37 3415 4064 171707141 171707810 5.310000e-144 521.0
9 TraesCS6A01G136400 chr6B 80.882 544 42 20 134 619 171699107 171699646 5.660000e-99 372.0
10 TraesCS6A01G136400 chr6B 85.149 101 12 3 1984 2082 171705586 171705685 2.950000e-17 100.0
11 TraesCS6A01G136400 chrUn 91.985 1859 141 8 1251 3104 325921126 325919271 0.000000e+00 2601.0
12 TraesCS6A01G136400 chrUn 90.210 1951 180 11 803 2747 335904424 335906369 0.000000e+00 2534.0
13 TraesCS6A01G136400 chrUn 90.159 1951 181 11 803 2747 335907106 335909051 0.000000e+00 2529.0
14 TraesCS6A01G136400 chrUn 92.210 1502 109 8 1251 2747 394420078 394421576 0.000000e+00 2119.0
15 TraesCS6A01G136400 chrUn 84.170 1156 123 40 3160 4270 325919287 325918147 0.000000e+00 1066.0
16 TraesCS6A01G136400 chrUn 86.731 309 38 3 803 1110 458178072 458178378 1.600000e-89 340.0
17 TraesCS6A01G136400 chrUn 95.699 93 4 0 4272 4364 335903788 335903880 2.890000e-32 150.0
18 TraesCS6A01G136400 chrUn 95.699 93 4 0 4272 4364 335906470 335906562 2.890000e-32 150.0
19 TraesCS6A01G136400 chrUn 95.699 93 4 0 4272 4364 458177436 458177528 2.890000e-32 150.0
20 TraesCS6A01G136400 chr6D 90.627 1579 145 3 1528 3104 89301360 89302937 0.000000e+00 2093.0
21 TraesCS6A01G136400 chr6D 79.262 2440 439 53 1220 3634 89166899 89169296 0.000000e+00 1640.0
22 TraesCS6A01G136400 chr6D 84.960 1250 128 40 3160 4364 89304501 89305735 0.000000e+00 1212.0
23 TraesCS6A01G136400 chr6D 85.515 1146 106 34 2955 4064 89305946 89307067 0.000000e+00 1142.0
24 TraesCS6A01G136400 chr6D 84.170 1156 123 40 3160 4270 89302921 89304061 0.000000e+00 1066.0
25 TraesCS6A01G136400 chr6D 87.035 779 41 25 134 874 89298822 89299578 0.000000e+00 824.0
26 TraesCS6A01G136400 chr6D 92.927 509 35 1 1040 1547 89299574 89300082 0.000000e+00 739.0
27 TraesCS6A01G136400 chr6D 97.430 428 11 0 4102 4529 89307076 89307503 0.000000e+00 730.0
28 TraesCS6A01G136400 chr6D 91.011 356 32 0 2749 3104 89304162 89304517 9.020000e-132 481.0
29 TraesCS6A01G136400 chr7A 80.100 1995 359 24 1667 3636 732158018 732156037 0.000000e+00 1450.0
30 TraesCS6A01G136400 chr7A 79.245 265 49 5 4104 4365 646483615 646483354 3.680000e-41 180.0
31 TraesCS6A01G136400 chr7D 79.554 269 49 5 4104 4369 561704946 561704681 2.200000e-43 187.0
32 TraesCS6A01G136400 chr3D 88.889 144 14 1 1 142 347486524 347486667 4.770000e-40 176.0
33 TraesCS6A01G136400 chr2A 89.437 142 12 2 1 140 15726055 15725915 4.770000e-40 176.0
34 TraesCS6A01G136400 chr2D 89.286 140 12 2 1 138 38059331 38059193 6.170000e-39 172.0
35 TraesCS6A01G136400 chr2D 97.059 34 1 0 4472 4505 324045937 324045904 1.800000e-04 58.4


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 TraesCS6A01G136400 chr6A 107680405 107685039 4634 False 8560.000 8560 100.000000 1 4635 1 chr6A.!!$F3 4634
1 TraesCS6A01G136400 chr6A 107214450 107217081 2631 False 1923.000 1923 79.992000 993 3641 1 chr6A.!!$F1 2648
2 TraesCS6A01G136400 chr6A 107270618 107272225 1607 False 1033.000 1033 78.493000 2008 3624 1 chr6A.!!$F2 1616
3 TraesCS6A01G136400 chr6B 171029192 171031806 2614 False 1964.000 1964 80.370000 993 3624 1 chr6B.!!$F1 2631
4 TraesCS6A01G136400 chr6B 171699107 171708342 9235 False 1358.200 5003 86.514800 134 4624 5 chr6B.!!$F3 4490
5 TraesCS6A01G136400 chr6B 171204913 171207678 2765 False 957.000 1066 79.573500 1000 3634 2 chr6B.!!$F2 2634
6 TraesCS6A01G136400 chrUn 394420078 394421576 1498 False 2119.000 2119 92.210000 1251 2747 1 chrUn.!!$F1 1496
7 TraesCS6A01G136400 chrUn 325918147 325921126 2979 True 1833.500 2601 88.077500 1251 4270 2 chrUn.!!$R1 3019
8 TraesCS6A01G136400 chrUn 335903788 335909051 5263 False 1340.750 2534 92.941750 803 4364 4 chrUn.!!$F2 3561
9 TraesCS6A01G136400 chrUn 458177436 458178378 942 False 245.000 340 91.215000 803 4364 2 chrUn.!!$F3 3561
10 TraesCS6A01G136400 chr6D 89166899 89169296 2397 False 1640.000 1640 79.262000 1220 3634 1 chr6D.!!$F1 2414
11 TraesCS6A01G136400 chr6D 89298822 89307503 8681 False 1035.875 2093 89.209375 134 4529 8 chr6D.!!$F2 4395
12 TraesCS6A01G136400 chr7A 732156037 732158018 1981 True 1450.000 1450 80.100000 1667 3636 1 chr7A.!!$R2 1969

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
769 855 0.031585 GCGTACACAGTCAGTCACCA 59.968 55.0 0.0 0.0 0.00 4.17 F
799 885 0.251209 TACTCACGACAGCAGAGGGT 60.251 55.0 0.0 0.0 33.76 4.34 F
1972 3440 0.109532 TCGGAACTTTGCCACCATCA 59.890 50.0 0.0 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 3281 0.467384 CGAGTGAGGCTGGGATTGAT 59.533 55.0 0.00 0.0 0.00 2.57 R
2192 3804 0.971386 AAGTTTGGCATGCTTCCCAG 59.029 50.0 18.92 0.0 31.73 4.45 R
3641 12597 0.324943 TAGGACAAAGCAGAGTGCCC 59.675 55.0 0.00 0.0 46.52 5.36 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 5.728351 CCTTGTTGTAAGAAAACGACTCA 57.272 39.130 0.00 0.00 35.20 3.41
23 24 6.300354 CCTTGTTGTAAGAAAACGACTCAT 57.700 37.500 0.00 0.00 35.20 2.90
34 35 4.194720 GACTCATCGCGCGGGACT 62.195 66.667 31.69 16.06 0.00 3.85
42 43 3.272334 GCGCGGGACTGCCTTATG 61.272 66.667 8.83 0.00 0.00 1.90
43 44 2.588877 CGCGGGACTGCCTTATGG 60.589 66.667 0.00 0.00 0.00 2.74
65 66 0.106819 AGCCTGGCTGCTTGATAAGG 60.107 55.000 22.71 0.00 38.85 2.69
66 67 0.107017 GCCTGGCTGCTTGATAAGGA 60.107 55.000 12.43 0.00 0.00 3.36
67 68 1.478288 GCCTGGCTGCTTGATAAGGAT 60.478 52.381 12.43 0.00 0.00 3.24
68 69 2.941480 CCTGGCTGCTTGATAAGGATT 58.059 47.619 0.00 0.00 0.00 3.01
71 72 4.142790 CTGGCTGCTTGATAAGGATTGAT 58.857 43.478 0.00 0.00 0.00 2.57
72 73 4.139786 TGGCTGCTTGATAAGGATTGATC 58.860 43.478 0.00 0.00 0.00 2.92
73 74 4.141321 TGGCTGCTTGATAAGGATTGATCT 60.141 41.667 0.00 0.00 0.00 2.75
74 75 4.215827 GGCTGCTTGATAAGGATTGATCTG 59.784 45.833 0.00 0.00 0.00 2.90
75 76 5.061853 GCTGCTTGATAAGGATTGATCTGA 58.938 41.667 0.00 0.00 0.00 3.27
77 78 5.052481 TGCTTGATAAGGATTGATCTGACG 58.948 41.667 0.00 0.00 0.00 4.35
79 80 3.995199 TGATAAGGATTGATCTGACGGC 58.005 45.455 0.00 0.00 0.00 5.68
80 81 3.643320 TGATAAGGATTGATCTGACGGCT 59.357 43.478 0.00 0.00 0.00 5.52
81 82 4.832823 TGATAAGGATTGATCTGACGGCTA 59.167 41.667 0.00 0.00 0.00 3.93
82 83 3.460857 AAGGATTGATCTGACGGCTAC 57.539 47.619 0.00 0.00 0.00 3.58
83 84 2.388735 AGGATTGATCTGACGGCTACA 58.611 47.619 0.00 0.00 0.00 2.74
86 87 3.521560 GATTGATCTGACGGCTACACAA 58.478 45.455 0.00 0.00 0.00 3.33
87 88 2.654749 TGATCTGACGGCTACACAAG 57.345 50.000 0.00 0.00 0.00 3.16
117 118 4.465512 GCGCACATCAGCCGGTTG 62.466 66.667 12.81 12.81 0.00 3.77
119 120 2.324330 CGCACATCAGCCGGTTGAA 61.324 57.895 25.48 8.93 0.00 2.69
121 122 1.926511 GCACATCAGCCGGTTGAAGG 61.927 60.000 25.48 21.01 0.00 3.46
123 124 0.981183 ACATCAGCCGGTTGAAGGTA 59.019 50.000 25.48 1.56 0.00 3.08
124 125 1.349688 ACATCAGCCGGTTGAAGGTAA 59.650 47.619 25.48 0.73 0.00 2.85
126 127 0.321298 TCAGCCGGTTGAAGGTAAGC 60.321 55.000 19.64 0.00 0.00 3.09
127 128 0.321653 CAGCCGGTTGAAGGTAAGCT 60.322 55.000 13.89 0.00 0.00 3.74
128 129 0.400594 AGCCGGTTGAAGGTAAGCTT 59.599 50.000 3.48 3.48 0.00 3.74
129 130 1.202891 AGCCGGTTGAAGGTAAGCTTT 60.203 47.619 3.20 0.00 0.00 3.51
130 131 1.611977 GCCGGTTGAAGGTAAGCTTTT 59.388 47.619 3.20 0.00 0.00 2.27
131 132 2.035449 GCCGGTTGAAGGTAAGCTTTTT 59.965 45.455 3.20 0.00 0.00 1.94
132 133 3.855895 GCCGGTTGAAGGTAAGCTTTTTC 60.856 47.826 3.20 7.63 0.00 2.29
168 169 8.112822 TGGAGTTTCATTGGATCTTTGGTATTA 58.887 33.333 0.00 0.00 0.00 0.98
175 176 5.438698 TGGATCTTTGGTATTAACGGGAA 57.561 39.130 0.00 0.00 0.00 3.97
181 182 7.385778 TCTTTGGTATTAACGGGAAATTCAG 57.614 36.000 0.00 0.00 0.00 3.02
192 193 2.416893 GGGAAATTCAGTCGAGTTGCTC 59.583 50.000 0.00 0.00 0.00 4.26
235 236 0.250513 AGGTTCCTGAATCGTGGCTC 59.749 55.000 0.00 0.00 0.00 4.70
254 255 0.953960 CGGTCCTCGTTTTCCCCTTG 60.954 60.000 0.00 0.00 0.00 3.61
307 308 3.822192 TGTCCTCCGATGACGCCG 61.822 66.667 0.14 0.00 38.29 6.46
399 433 1.777272 GGGCCATCTCCTTAACCAGAT 59.223 52.381 4.39 0.00 0.00 2.90
408 442 5.322754 TCTCCTTAACCAGATATACCCGAG 58.677 45.833 0.00 0.00 0.00 4.63
431 465 3.125573 CTCGCCTCGTCGTCCTCA 61.126 66.667 0.00 0.00 0.00 3.86
434 468 3.063084 GCCTCGTCGTCCTCACCT 61.063 66.667 0.00 0.00 0.00 4.00
572 645 5.815233 TTGCAAGTTGAAATCCCCAAATA 57.185 34.783 7.16 0.00 0.00 1.40
573 646 5.404466 TGCAAGTTGAAATCCCCAAATAG 57.596 39.130 7.16 0.00 0.00 1.73
681 754 4.393371 TGTTTGCGTAATCGGATGATTCAA 59.607 37.500 0.00 0.00 43.70 2.69
682 755 5.065859 TGTTTGCGTAATCGGATGATTCAAT 59.934 36.000 0.00 0.00 43.70 2.57
684 757 3.745975 TGCGTAATCGGATGATTCAATCC 59.254 43.478 0.00 0.00 43.70 3.01
685 758 3.997021 GCGTAATCGGATGATTCAATCCT 59.003 43.478 0.00 0.00 43.70 3.24
691 764 3.906218 TCGGATGATTCAATCCTGGAGAT 59.094 43.478 1.52 0.00 43.53 2.75
692 765 4.001652 CGGATGATTCAATCCTGGAGATG 58.998 47.826 1.52 4.23 43.53 2.90
693 766 4.333690 GGATGATTCAATCCTGGAGATGG 58.666 47.826 1.52 0.00 42.57 3.51
694 767 4.042560 GGATGATTCAATCCTGGAGATGGA 59.957 45.833 1.52 0.00 42.57 3.41
696 769 4.042884 TGATTCAATCCTGGAGATGGACT 58.957 43.478 1.52 0.00 34.43 3.85
697 770 3.920231 TTCAATCCTGGAGATGGACTG 57.080 47.619 1.52 0.00 34.43 3.51
698 771 3.120468 TCAATCCTGGAGATGGACTGA 57.880 47.619 1.52 0.00 37.48 3.41
700 773 2.770802 CAATCCTGGAGATGGACTGACT 59.229 50.000 1.52 0.00 33.14 3.41
701 774 1.857965 TCCTGGAGATGGACTGACTG 58.142 55.000 0.00 0.00 0.00 3.51
703 776 1.480137 CCTGGAGATGGACTGACTGAC 59.520 57.143 0.00 0.00 0.00 3.51
704 777 1.133982 CTGGAGATGGACTGACTGACG 59.866 57.143 0.00 0.00 0.00 4.35
705 778 0.179124 GGAGATGGACTGACTGACGC 60.179 60.000 0.00 0.00 0.00 5.19
711 784 0.459237 GGACTGACTGACGCATCTGG 60.459 60.000 0.00 0.00 0.00 3.86
712 785 0.528017 GACTGACTGACGCATCTGGA 59.472 55.000 0.00 0.00 0.00 3.86
713 786 0.244994 ACTGACTGACGCATCTGGAC 59.755 55.000 0.00 0.00 0.00 4.02
714 787 0.244721 CTGACTGACGCATCTGGACA 59.755 55.000 0.00 0.00 0.00 4.02
736 822 0.665835 TGGTTGGCTTTGTGTTAGCG 59.334 50.000 0.00 0.00 39.54 4.26
737 823 0.948678 GGTTGGCTTTGTGTTAGCGA 59.051 50.000 0.00 0.00 39.54 4.93
757 843 2.280321 AACCACACCCGCGTACAC 60.280 61.111 4.92 0.00 0.00 2.90
758 844 3.091499 AACCACACCCGCGTACACA 62.091 57.895 4.92 0.00 0.00 3.72
759 845 2.736995 CCACACCCGCGTACACAG 60.737 66.667 4.92 0.00 0.00 3.66
760 846 2.028484 CACACCCGCGTACACAGT 59.972 61.111 4.92 0.00 0.00 3.55
761 847 2.019951 CACACCCGCGTACACAGTC 61.020 63.158 4.92 0.00 0.00 3.51
763 849 1.733041 CACCCGCGTACACAGTCAG 60.733 63.158 4.92 0.00 0.00 3.51
765 851 1.443872 CCCGCGTACACAGTCAGTC 60.444 63.158 4.92 0.00 0.00 3.51
766 852 1.284715 CCGCGTACACAGTCAGTCA 59.715 57.895 4.92 0.00 0.00 3.41
767 853 1.002250 CCGCGTACACAGTCAGTCAC 61.002 60.000 4.92 0.00 0.00 3.67
768 854 1.002250 CGCGTACACAGTCAGTCACC 61.002 60.000 0.00 0.00 0.00 4.02
769 855 0.031585 GCGTACACAGTCAGTCACCA 59.968 55.000 0.00 0.00 0.00 4.17
770 856 1.930817 GCGTACACAGTCAGTCACCAG 60.931 57.143 0.00 0.00 0.00 4.00
771 857 1.337071 CGTACACAGTCAGTCACCAGT 59.663 52.381 0.00 0.00 0.00 4.00
772 858 2.604855 CGTACACAGTCAGTCACCAGTC 60.605 54.545 0.00 0.00 0.00 3.51
773 859 1.485124 ACACAGTCAGTCACCAGTCA 58.515 50.000 0.00 0.00 0.00 3.41
774 860 2.042464 ACACAGTCAGTCACCAGTCAT 58.958 47.619 0.00 0.00 0.00 3.06
775 861 2.036475 ACACAGTCAGTCACCAGTCATC 59.964 50.000 0.00 0.00 0.00 2.92
776 862 2.036346 CACAGTCAGTCACCAGTCATCA 59.964 50.000 0.00 0.00 0.00 3.07
778 864 1.620819 AGTCAGTCACCAGTCATCACC 59.379 52.381 0.00 0.00 0.00 4.02
779 865 1.620819 GTCAGTCACCAGTCATCACCT 59.379 52.381 0.00 0.00 0.00 4.00
780 866 2.037772 GTCAGTCACCAGTCATCACCTT 59.962 50.000 0.00 0.00 0.00 3.50
781 867 3.258372 GTCAGTCACCAGTCATCACCTTA 59.742 47.826 0.00 0.00 0.00 2.69
782 868 3.258372 TCAGTCACCAGTCATCACCTTAC 59.742 47.826 0.00 0.00 0.00 2.34
783 869 3.259374 CAGTCACCAGTCATCACCTTACT 59.741 47.826 0.00 0.00 0.00 2.24
784 870 3.511934 AGTCACCAGTCATCACCTTACTC 59.488 47.826 0.00 0.00 0.00 2.59
785 871 3.258372 GTCACCAGTCATCACCTTACTCA 59.742 47.826 0.00 0.00 0.00 3.41
787 873 2.231478 ACCAGTCATCACCTTACTCACG 59.769 50.000 0.00 0.00 0.00 4.35
791 877 3.191581 AGTCATCACCTTACTCACGACAG 59.808 47.826 0.00 0.00 0.00 3.51
792 878 2.094700 TCATCACCTTACTCACGACAGC 60.095 50.000 0.00 0.00 0.00 4.40
793 879 1.324383 TCACCTTACTCACGACAGCA 58.676 50.000 0.00 0.00 0.00 4.41
794 880 1.269723 TCACCTTACTCACGACAGCAG 59.730 52.381 0.00 0.00 0.00 4.24
795 881 1.269723 CACCTTACTCACGACAGCAGA 59.730 52.381 0.00 0.00 0.00 4.26
796 882 1.542030 ACCTTACTCACGACAGCAGAG 59.458 52.381 0.00 0.00 35.56 3.35
798 884 0.888619 TTACTCACGACAGCAGAGGG 59.111 55.000 0.00 0.00 33.76 4.30
799 885 0.251209 TACTCACGACAGCAGAGGGT 60.251 55.000 0.00 0.00 33.76 4.34
807 893 2.851102 AGCAGAGGGTGTGTGGCT 60.851 61.111 0.00 0.00 0.00 4.75
869 1025 5.059833 ACACAATTCCAAGTCTGAAGTCTC 58.940 41.667 0.00 0.00 0.00 3.36
876 1032 5.007034 TCCAAGTCTGAAGTCTCTAGTCAG 58.993 45.833 1.74 1.74 40.15 3.51
896 1052 2.549754 AGGTCTTCGTTTGCAATGACAG 59.450 45.455 0.00 3.13 0.00 3.51
912 1068 6.263344 CAATGACAGTGACATGATTTGATCC 58.737 40.000 8.86 0.00 0.00 3.36
929 1085 0.809385 TCCGTGTGCACTCTAGCTAC 59.191 55.000 19.41 4.72 34.99 3.58
930 1086 0.811915 CCGTGTGCACTCTAGCTACT 59.188 55.000 19.41 0.00 34.99 2.57
931 1087 1.202582 CCGTGTGCACTCTAGCTACTT 59.797 52.381 19.41 0.00 34.99 2.24
968 1126 5.091261 ACATAGAGCACCCTTCAACTTAG 57.909 43.478 0.00 0.00 0.00 2.18
994 1160 7.592938 CATTTTCTTATCAACACTGTAAGCCA 58.407 34.615 0.00 0.00 37.60 4.75
997 1163 6.599356 TCTTATCAACACTGTAAGCCACTA 57.401 37.500 0.00 0.00 37.60 2.74
1068 1234 0.394899 CAGCCAAGGAGATCAACCCC 60.395 60.000 0.00 0.00 0.00 4.95
1074 1240 1.521681 GGAGATCAACCCCGAAGCG 60.522 63.158 0.00 0.00 0.00 4.68
1146 1315 2.946329 CTCCTGGTCGATATCCTATCCG 59.054 54.545 0.00 0.00 0.00 4.18
1237 1406 1.404986 GCCTTCATGGTACGCTACACA 60.405 52.381 0.00 0.00 38.35 3.72
1326 1495 5.425217 TGTTGTCCCAGCAAATATCTCTCTA 59.575 40.000 0.00 0.00 0.00 2.43
1331 1500 7.147497 TGTCCCAGCAAATATCTCTCTATTTCA 60.147 37.037 0.00 0.00 30.68 2.69
1386 1555 1.006813 TTGTTGGTGCCATCCCCTAT 58.993 50.000 0.00 0.00 0.00 2.57
1419 1588 7.924412 AGCAAGCTACCAATGATTATCAAATTG 59.076 33.333 0.00 0.30 0.00 2.32
1470 1639 4.261322 CCAGAATATGCCAATTTCTCACCG 60.261 45.833 0.00 0.00 0.00 4.94
1535 1705 4.396357 TGGTACCTTCCCACAATTCATT 57.604 40.909 14.36 0.00 0.00 2.57
1757 3225 0.419459 AGGAGGAATCCCAGAGGTGT 59.581 55.000 0.00 0.00 33.88 4.16
1783 3251 1.481871 TGATACCTGGACTCCGAACC 58.518 55.000 0.00 0.00 0.00 3.62
1813 3281 6.753551 TACTATACAGTAACCCACTTGGTGGA 60.754 42.308 17.16 0.00 43.78 4.02
1972 3440 0.109532 TCGGAACTTTGCCACCATCA 59.890 50.000 0.00 0.00 0.00 3.07
2192 3804 2.107953 GCTCGATCCCAGTGGAGC 59.892 66.667 11.95 7.46 46.08 4.70
2449 4070 6.010219 AGTTGTCAAAGTGGCCAATAATAGT 58.990 36.000 7.24 0.00 0.00 2.12
2482 4103 1.952193 AACCATTGTGTGCCTTTTGC 58.048 45.000 0.00 0.00 41.77 3.68
2668 4289 3.056250 TGTTGCACTTGTCCAACAACAAT 60.056 39.130 7.68 0.00 45.74 2.71
2679 4300 4.803613 GTCCAACAACAATTTCACAGGTTC 59.196 41.667 0.00 0.00 0.00 3.62
2770 4391 0.106167 CACTCCCTCCGTGGATAGGA 60.106 60.000 7.40 7.40 38.35 2.94
2996 4629 4.265073 AGAATTGAGACCCTTCCGATTTG 58.735 43.478 0.00 0.00 0.00 2.32
3123 11079 4.141274 TGGTGAAATCCCTTCAGAGTTGAA 60.141 41.667 0.00 0.00 44.83 2.69
3205 11233 3.191162 CGAAGGACATTGGCAATCTCAAA 59.809 43.478 15.84 0.00 0.00 2.69
3206 11234 4.488879 GAAGGACATTGGCAATCTCAAAC 58.511 43.478 15.84 4.25 0.00 2.93
3383 11774 6.127338 CCCATCGATCTATAGCAATAACCTCA 60.127 42.308 0.00 0.00 0.00 3.86
3490 12446 6.038356 CCATGAACTTGAAACATTATGGCTC 58.962 40.000 0.00 0.00 0.00 4.70
3637 12593 0.035317 AGATGAAGCGCACCTGACAA 59.965 50.000 11.47 0.00 0.00 3.18
3641 12597 1.071605 GAAGCGCACCTGACAAGTAG 58.928 55.000 11.47 0.00 0.00 2.57
3667 12623 1.079127 TGCTTTGTCCTAGCGCCTC 60.079 57.895 2.29 0.00 41.54 4.70
3669 12625 0.462759 GCTTTGTCCTAGCGCCTCAT 60.463 55.000 2.29 0.00 0.00 2.90
3672 12628 0.613260 TTGTCCTAGCGCCTCATTGT 59.387 50.000 2.29 0.00 0.00 2.71
3673 12629 0.108186 TGTCCTAGCGCCTCATTGTG 60.108 55.000 2.29 0.00 0.00 3.33
3675 12631 0.613260 TCCTAGCGCCTCATTGTGTT 59.387 50.000 2.29 0.00 0.00 3.32
3677 12633 1.398390 CCTAGCGCCTCATTGTGTTTC 59.602 52.381 2.29 0.00 0.00 2.78
3678 12634 1.398390 CTAGCGCCTCATTGTGTTTCC 59.602 52.381 2.29 0.00 0.00 3.13
3692 12648 4.792068 TGTGTTTCCTGAAGTTTCCTCAT 58.208 39.130 0.00 0.00 0.00 2.90
3693 12649 4.580167 TGTGTTTCCTGAAGTTTCCTCATG 59.420 41.667 0.00 0.00 0.00 3.07
3704 12660 4.338879 AGTTTCCTCATGCTTGCAGTATT 58.661 39.130 0.87 0.00 0.00 1.89
3743 12704 6.976934 TGTATTGTCCATGACTCTGCTATA 57.023 37.500 0.00 0.00 33.15 1.31
3752 12713 7.497249 GTCCATGACTCTGCTATATGTTTCTTT 59.503 37.037 0.00 0.00 0.00 2.52
3753 12714 8.704668 TCCATGACTCTGCTATATGTTTCTTTA 58.295 33.333 0.00 0.00 0.00 1.85
3759 12720 9.726438 ACTCTGCTATATGTTTCTTTAAGTTGT 57.274 29.630 0.00 0.00 0.00 3.32
3786 12747 9.703892 AATAGTAATGATCAGTTGCTATCTGAC 57.296 33.333 18.93 4.66 43.32 3.51
3791 12752 4.099113 TGATCAGTTGCTATCTGACCAGAG 59.901 45.833 5.90 0.00 43.32 3.35
3808 12773 5.505173 CCAGAGGTGGCTTATATTTGTTG 57.495 43.478 0.00 0.00 36.89 3.33
3841 12810 9.500785 TGATGAGACAATTTCATACACTTGTAA 57.499 29.630 0.00 0.00 35.50 2.41
3879 12849 6.871492 TCTGAATTTTGTGAGTCGCAGTTATA 59.129 34.615 6.47 0.00 0.00 0.98
3893 12869 7.652105 AGTCGCAGTTATATATGTTTCGTCATT 59.348 33.333 0.00 0.00 0.00 2.57
3913 12889 8.182227 CGTCATTGCTACTTATATATCTTCCGA 58.818 37.037 0.00 0.00 0.00 4.55
3918 12903 9.511272 TTGCTACTTATATATCTTCCGAGTACA 57.489 33.333 0.00 0.00 0.00 2.90
3929 12914 9.688091 ATATCTTCCGAGTACATATGAGTACAT 57.312 33.333 10.38 0.00 45.25 2.29
3944 12932 9.988815 ATATGAGTACATCTTCAATCTTGTACC 57.011 33.333 8.09 2.52 43.37 3.34
3946 12934 7.548097 TGAGTACATCTTCAATCTTGTACCTC 58.452 38.462 8.09 6.54 43.37 3.85
3953 12941 3.937814 TCAATCTTGTACCTCGTGCATT 58.062 40.909 0.00 0.00 0.00 3.56
3954 12942 3.684305 TCAATCTTGTACCTCGTGCATTG 59.316 43.478 0.00 0.00 0.00 2.82
3955 12943 2.831685 TCTTGTACCTCGTGCATTGT 57.168 45.000 0.00 0.00 0.00 2.71
3956 12944 3.120321 TCTTGTACCTCGTGCATTGTT 57.880 42.857 0.00 0.00 0.00 2.83
3957 12945 3.064207 TCTTGTACCTCGTGCATTGTTC 58.936 45.455 0.00 0.00 0.00 3.18
3958 12946 2.535012 TGTACCTCGTGCATTGTTCA 57.465 45.000 0.00 0.00 0.00 3.18
3959 12947 2.139917 TGTACCTCGTGCATTGTTCAC 58.860 47.619 0.00 0.00 0.00 3.18
3960 12948 2.139917 GTACCTCGTGCATTGTTCACA 58.860 47.619 0.00 0.00 34.27 3.58
4054 13063 7.540055 CAGATGACCAAAGAATAAGAGCAAAAC 59.460 37.037 0.00 0.00 0.00 2.43
4076 13085 1.682854 ACAGCATCCACCAACAGTTTG 59.317 47.619 0.00 0.00 0.00 2.93
4077 13086 1.955778 CAGCATCCACCAACAGTTTGA 59.044 47.619 0.00 0.00 34.24 2.69
4087 13096 4.642885 CACCAACAGTTTGAAGGGAAAGTA 59.357 41.667 0.00 0.00 34.24 2.24
4097 13106 3.154589 GGGAAAGTAACCCTCGCTG 57.845 57.895 0.00 0.00 43.65 5.18
4098 13107 1.025113 GGGAAAGTAACCCTCGCTGC 61.025 60.000 0.00 0.00 43.65 5.25
4099 13108 1.359459 GGAAAGTAACCCTCGCTGCG 61.359 60.000 17.25 17.25 0.00 5.18
4552 13579 2.514824 GCACCTCAGGCCCGATTC 60.515 66.667 0.00 0.00 0.00 2.52
4561 13588 1.519455 GGCCCGATTCAGAGACACG 60.519 63.158 0.00 0.00 0.00 4.49
4570 13597 1.244816 TCAGAGACACGTTCGACCAT 58.755 50.000 0.00 0.00 0.00 3.55
4580 13607 2.159627 ACGTTCGACCATGCAAGAATTC 59.840 45.455 0.00 0.00 0.00 2.17
4584 13611 2.743664 TCGACCATGCAAGAATTCAGTG 59.256 45.455 8.44 6.51 0.00 3.66
4587 13614 2.895404 ACCATGCAAGAATTCAGTGCTT 59.105 40.909 25.52 19.65 39.09 3.91
4588 13615 3.250744 CCATGCAAGAATTCAGTGCTTG 58.749 45.455 26.52 26.52 40.95 4.01
4589 13616 3.305813 CCATGCAAGAATTCAGTGCTTGT 60.306 43.478 28.60 17.26 40.14 3.16
4591 13618 3.968649 TGCAAGAATTCAGTGCTTGTTC 58.031 40.909 25.52 5.73 40.73 3.18
4592 13619 3.243501 TGCAAGAATTCAGTGCTTGTTCC 60.244 43.478 25.52 5.20 40.73 3.62
4594 13621 4.791974 CAAGAATTCAGTGCTTGTTCCTC 58.208 43.478 8.44 0.00 35.49 3.71
4595 13622 4.363991 AGAATTCAGTGCTTGTTCCTCT 57.636 40.909 8.44 0.00 0.00 3.69
4596 13623 4.070716 AGAATTCAGTGCTTGTTCCTCTG 58.929 43.478 8.44 0.00 0.00 3.35
4598 13625 4.623932 ATTCAGTGCTTGTTCCTCTGTA 57.376 40.909 0.00 0.00 0.00 2.74
4601 13634 4.973168 TCAGTGCTTGTTCCTCTGTAAAT 58.027 39.130 0.00 0.00 0.00 1.40
4615 13648 9.762933 TTCCTCTGTAAATTTTTCCTTTTCATG 57.237 29.630 0.00 0.00 0.00 3.07
4624 13657 7.681939 ATTTTTCCTTTTCATGTACTCGCTA 57.318 32.000 0.00 0.00 0.00 4.26
4625 13658 7.499321 TTTTTCCTTTTCATGTACTCGCTAA 57.501 32.000 0.00 0.00 0.00 3.09
4626 13659 7.499321 TTTTCCTTTTCATGTACTCGCTAAA 57.501 32.000 0.00 0.00 0.00 1.85
4627 13660 6.476243 TTCCTTTTCATGTACTCGCTAAAC 57.524 37.500 0.00 0.00 0.00 2.01
4628 13661 5.790593 TCCTTTTCATGTACTCGCTAAACT 58.209 37.500 0.00 0.00 0.00 2.66
4629 13662 5.637810 TCCTTTTCATGTACTCGCTAAACTG 59.362 40.000 0.00 0.00 0.00 3.16
4630 13663 5.637810 CCTTTTCATGTACTCGCTAAACTGA 59.362 40.000 0.00 0.00 0.00 3.41
4631 13664 6.147164 CCTTTTCATGTACTCGCTAAACTGAA 59.853 38.462 0.00 0.00 0.00 3.02
4632 13665 6.462073 TTTCATGTACTCGCTAAACTGAAC 57.538 37.500 0.00 0.00 0.00 3.18
4633 13666 5.386958 TCATGTACTCGCTAAACTGAACT 57.613 39.130 0.00 0.00 0.00 3.01
4634 13667 5.779922 TCATGTACTCGCTAAACTGAACTT 58.220 37.500 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.065153 CGATGAGTCGTTTTCTTACAACAAG 58.935 40.000 0.00 0.00 42.78 3.16
17 18 4.194720 AGTCCCGCGCGATGAGTC 62.195 66.667 34.63 15.60 0.00 3.36
18 19 4.498520 CAGTCCCGCGCGATGAGT 62.499 66.667 34.63 25.55 0.00 3.41
25 26 3.272334 CATAAGGCAGTCCCGCGC 61.272 66.667 0.00 0.00 39.21 6.86
26 27 2.588877 CCATAAGGCAGTCCCGCG 60.589 66.667 0.00 0.00 39.21 6.46
47 48 0.107017 TCCTTATCAAGCAGCCAGGC 60.107 55.000 1.84 1.84 0.00 4.85
48 49 2.621998 CAATCCTTATCAAGCAGCCAGG 59.378 50.000 0.00 0.00 0.00 4.45
49 50 3.548770 TCAATCCTTATCAAGCAGCCAG 58.451 45.455 0.00 0.00 0.00 4.85
50 51 3.650281 TCAATCCTTATCAAGCAGCCA 57.350 42.857 0.00 0.00 0.00 4.75
52 53 5.049543 GTCAGATCAATCCTTATCAAGCAGC 60.050 44.000 0.00 0.00 0.00 5.25
54 55 5.052481 CGTCAGATCAATCCTTATCAAGCA 58.948 41.667 0.00 0.00 0.00 3.91
55 56 4.450419 CCGTCAGATCAATCCTTATCAAGC 59.550 45.833 0.00 0.00 0.00 4.01
56 57 4.450419 GCCGTCAGATCAATCCTTATCAAG 59.550 45.833 0.00 0.00 0.00 3.02
57 58 4.101585 AGCCGTCAGATCAATCCTTATCAA 59.898 41.667 0.00 0.00 0.00 2.57
59 60 4.264460 AGCCGTCAGATCAATCCTTATC 57.736 45.455 0.00 0.00 0.00 1.75
60 61 4.588951 TGTAGCCGTCAGATCAATCCTTAT 59.411 41.667 0.00 0.00 0.00 1.73
61 62 3.958147 TGTAGCCGTCAGATCAATCCTTA 59.042 43.478 0.00 0.00 0.00 2.69
63 64 2.101582 GTGTAGCCGTCAGATCAATCCT 59.898 50.000 0.00 0.00 0.00 3.24
65 66 3.165058 TGTGTAGCCGTCAGATCAATC 57.835 47.619 0.00 0.00 0.00 2.67
66 67 3.525537 CTTGTGTAGCCGTCAGATCAAT 58.474 45.455 0.00 0.00 0.00 2.57
67 68 2.930887 GCTTGTGTAGCCGTCAGATCAA 60.931 50.000 0.00 0.00 44.48 2.57
68 69 1.404181 GCTTGTGTAGCCGTCAGATCA 60.404 52.381 0.00 0.00 44.48 2.92
71 72 4.988065 GCTTGTGTAGCCGTCAGA 57.012 55.556 0.00 0.00 44.48 3.27
79 80 3.179265 CGTCCGCCGCTTGTGTAG 61.179 66.667 0.00 0.00 0.00 2.74
101 102 2.244436 CTTCAACCGGCTGATGTGCG 62.244 60.000 8.68 0.00 0.00 5.34
102 103 1.503542 CTTCAACCGGCTGATGTGC 59.496 57.895 8.68 0.00 0.00 4.57
103 104 0.606401 ACCTTCAACCGGCTGATGTG 60.606 55.000 8.68 7.80 0.00 3.21
104 105 0.981183 TACCTTCAACCGGCTGATGT 59.019 50.000 8.68 11.47 0.00 3.06
105 106 2.009774 CTTACCTTCAACCGGCTGATG 58.990 52.381 8.68 10.95 0.00 3.07
107 108 0.321298 GCTTACCTTCAACCGGCTGA 60.321 55.000 2.67 2.67 0.00 4.26
111 112 3.305131 GGAAAAAGCTTACCTTCAACCGG 60.305 47.826 0.00 0.00 31.99 5.28
112 113 3.316868 TGGAAAAAGCTTACCTTCAACCG 59.683 43.478 0.00 0.00 31.99 4.44
113 114 4.929819 TGGAAAAAGCTTACCTTCAACC 57.070 40.909 0.00 0.00 31.99 3.77
114 115 8.880878 TTAAATGGAAAAAGCTTACCTTCAAC 57.119 30.769 0.00 0.00 31.99 3.18
119 120 9.487442 TCCATATTAAATGGAAAAAGCTTACCT 57.513 29.630 0.00 0.00 44.54 3.08
124 125 9.875691 GAAACTCCATATTAAATGGAAAAAGCT 57.124 29.630 15.65 0.00 46.50 3.74
130 131 9.486123 TCCAATGAAACTCCATATTAAATGGAA 57.514 29.630 15.65 5.98 46.50 3.53
131 132 9.659135 ATCCAATGAAACTCCATATTAAATGGA 57.341 29.630 14.66 14.66 45.24 3.41
132 133 9.918630 GATCCAATGAAACTCCATATTAAATGG 57.081 33.333 9.25 9.25 40.48 3.16
155 156 7.992008 TGAATTTCCCGTTAATACCAAAGATC 58.008 34.615 0.00 0.00 0.00 2.75
168 169 2.806244 CAACTCGACTGAATTTCCCGTT 59.194 45.455 0.00 0.00 0.00 4.44
192 193 2.660064 CCCACTCCAAGGAGGACCG 61.660 68.421 19.62 5.76 45.88 4.79
222 223 1.519455 GGACCGAGCCACGATTCAG 60.519 63.158 2.48 0.00 45.77 3.02
235 236 0.953960 CAAGGGGAAAACGAGGACCG 60.954 60.000 0.00 0.00 45.44 4.79
254 255 2.303311 AGGAGAACTGTAGAAACTGGCC 59.697 50.000 0.00 0.00 0.00 5.36
399 433 2.599578 GAGGCGCCCTCGGGTATA 60.600 66.667 26.15 0.00 41.08 1.47
418 452 2.878429 CAGGTGAGGACGACGAGG 59.122 66.667 0.00 0.00 0.00 4.63
431 465 4.596585 CCCGTGGGGTTTGCAGGT 62.597 66.667 0.00 0.00 38.25 4.00
572 645 4.868734 GGGATTTTCTCGATCAAACGTACT 59.131 41.667 0.00 0.00 34.70 2.73
573 646 4.033702 GGGGATTTTCTCGATCAAACGTAC 59.966 45.833 0.00 0.00 34.70 3.67
647 720 4.481930 TTACGCAAACAATTCAGACCAG 57.518 40.909 0.00 0.00 0.00 4.00
681 754 2.023598 TCAGTCAGTCCATCTCCAGGAT 60.024 50.000 0.00 0.00 37.52 3.24
682 755 1.359130 TCAGTCAGTCCATCTCCAGGA 59.641 52.381 0.00 0.00 0.00 3.86
684 757 1.133982 CGTCAGTCAGTCCATCTCCAG 59.866 57.143 0.00 0.00 0.00 3.86
685 758 1.177401 CGTCAGTCAGTCCATCTCCA 58.823 55.000 0.00 0.00 0.00 3.86
691 764 0.244721 CAGATGCGTCAGTCAGTCCA 59.755 55.000 8.99 0.00 0.00 4.02
692 765 0.459237 CCAGATGCGTCAGTCAGTCC 60.459 60.000 8.99 0.00 0.00 3.85
693 766 0.528017 TCCAGATGCGTCAGTCAGTC 59.472 55.000 8.99 0.00 0.00 3.51
694 767 0.244994 GTCCAGATGCGTCAGTCAGT 59.755 55.000 8.99 0.00 0.00 3.41
696 769 0.244721 CTGTCCAGATGCGTCAGTCA 59.755 55.000 8.99 2.56 0.00 3.41
697 770 1.080995 GCTGTCCAGATGCGTCAGTC 61.081 60.000 8.99 0.00 0.00 3.51
698 771 1.079543 GCTGTCCAGATGCGTCAGT 60.080 57.895 8.99 0.00 0.00 3.41
700 773 1.079612 CAGCTGTCCAGATGCGTCA 60.080 57.895 8.99 0.00 38.05 4.35
701 774 1.812922 CCAGCTGTCCAGATGCGTC 60.813 63.158 13.81 0.00 43.03 5.19
703 776 1.376424 AACCAGCTGTCCAGATGCG 60.376 57.895 13.81 3.76 43.03 4.73
704 777 1.310933 CCAACCAGCTGTCCAGATGC 61.311 60.000 13.81 0.00 43.03 3.91
705 778 1.310933 GCCAACCAGCTGTCCAGATG 61.311 60.000 13.81 5.59 43.91 2.90
711 784 0.031178 CACAAAGCCAACCAGCTGTC 59.969 55.000 13.81 0.00 44.11 3.51
712 785 0.684153 ACACAAAGCCAACCAGCTGT 60.684 50.000 13.81 0.00 44.11 4.40
713 786 0.461135 AACACAAAGCCAACCAGCTG 59.539 50.000 6.78 6.78 44.11 4.24
736 822 3.869473 TACGCGGGTGTGGTTGCTC 62.869 63.158 16.34 0.00 0.00 4.26
737 823 3.931247 TACGCGGGTGTGGTTGCT 61.931 61.111 16.34 0.00 0.00 3.91
752 838 2.361119 TGACTGGTGACTGACTGTGTAC 59.639 50.000 0.00 0.00 0.00 2.90
757 843 2.611473 GGTGATGACTGGTGACTGACTG 60.611 54.545 0.00 0.00 0.00 3.51
758 844 1.620819 GGTGATGACTGGTGACTGACT 59.379 52.381 0.00 0.00 0.00 3.41
759 845 1.620819 AGGTGATGACTGGTGACTGAC 59.379 52.381 0.00 0.00 0.00 3.51
760 846 2.015456 AGGTGATGACTGGTGACTGA 57.985 50.000 0.00 0.00 0.00 3.41
761 847 2.847327 AAGGTGATGACTGGTGACTG 57.153 50.000 0.00 0.00 0.00 3.51
763 849 3.258372 TGAGTAAGGTGATGACTGGTGAC 59.742 47.826 0.00 0.00 0.00 3.67
765 851 3.589988 GTGAGTAAGGTGATGACTGGTG 58.410 50.000 0.00 0.00 0.00 4.17
766 852 2.231478 CGTGAGTAAGGTGATGACTGGT 59.769 50.000 0.00 0.00 0.00 4.00
767 853 2.492088 TCGTGAGTAAGGTGATGACTGG 59.508 50.000 0.00 0.00 0.00 4.00
768 854 3.057526 TGTCGTGAGTAAGGTGATGACTG 60.058 47.826 0.00 0.00 0.00 3.51
769 855 3.154710 TGTCGTGAGTAAGGTGATGACT 58.845 45.455 0.00 0.00 0.00 3.41
770 856 3.502920 CTGTCGTGAGTAAGGTGATGAC 58.497 50.000 0.00 0.00 0.00 3.06
771 857 2.094700 GCTGTCGTGAGTAAGGTGATGA 60.095 50.000 0.00 0.00 0.00 2.92
772 858 2.263077 GCTGTCGTGAGTAAGGTGATG 58.737 52.381 0.00 0.00 0.00 3.07
773 859 1.893137 TGCTGTCGTGAGTAAGGTGAT 59.107 47.619 0.00 0.00 0.00 3.06
774 860 1.269723 CTGCTGTCGTGAGTAAGGTGA 59.730 52.381 0.00 0.00 0.00 4.02
775 861 1.269723 TCTGCTGTCGTGAGTAAGGTG 59.730 52.381 0.00 0.00 0.00 4.00
776 862 1.542030 CTCTGCTGTCGTGAGTAAGGT 59.458 52.381 0.00 0.00 0.00 3.50
778 864 1.135257 CCCTCTGCTGTCGTGAGTAAG 60.135 57.143 0.00 0.00 0.00 2.34
779 865 0.888619 CCCTCTGCTGTCGTGAGTAA 59.111 55.000 0.00 0.00 0.00 2.24
780 866 0.251209 ACCCTCTGCTGTCGTGAGTA 60.251 55.000 0.00 0.00 0.00 2.59
781 867 1.531840 ACCCTCTGCTGTCGTGAGT 60.532 57.895 0.00 0.00 0.00 3.41
782 868 1.080230 CACCCTCTGCTGTCGTGAG 60.080 63.158 0.00 0.00 0.00 3.51
783 869 1.832608 ACACCCTCTGCTGTCGTGA 60.833 57.895 11.93 0.00 0.00 4.35
784 870 1.665916 CACACCCTCTGCTGTCGTG 60.666 63.158 0.00 0.00 0.00 4.35
785 871 2.134287 ACACACCCTCTGCTGTCGT 61.134 57.895 0.00 0.00 0.00 4.34
787 873 1.302033 CCACACACCCTCTGCTGTC 60.302 63.158 0.00 0.00 0.00 3.51
791 877 2.670934 CAGCCACACACCCTCTGC 60.671 66.667 0.00 0.00 0.00 4.26
792 878 2.670934 GCAGCCACACACCCTCTG 60.671 66.667 0.00 0.00 0.00 3.35
793 879 3.170672 TGCAGCCACACACCCTCT 61.171 61.111 0.00 0.00 0.00 3.69
794 880 2.670934 CTGCAGCCACACACCCTC 60.671 66.667 0.00 0.00 0.00 4.30
795 881 2.756042 TTCTGCAGCCACACACCCT 61.756 57.895 9.47 0.00 0.00 4.34
796 882 2.203337 TTCTGCAGCCACACACCC 60.203 61.111 9.47 0.00 0.00 4.61
798 884 1.097547 AGTGTTCTGCAGCCACACAC 61.098 55.000 33.11 27.40 42.81 3.82
799 885 0.467804 TAGTGTTCTGCAGCCACACA 59.532 50.000 33.11 22.81 42.81 3.72
800 886 0.868406 GTAGTGTTCTGCAGCCACAC 59.132 55.000 28.53 28.53 41.03 3.82
801 887 0.467804 TGTAGTGTTCTGCAGCCACA 59.532 50.000 27.39 21.08 32.82 4.17
802 888 0.868406 GTGTAGTGTTCTGCAGCCAC 59.132 55.000 21.79 21.79 37.00 5.01
803 889 0.467804 TGTGTAGTGTTCTGCAGCCA 59.532 50.000 9.47 5.23 37.00 4.75
804 890 1.593196 TTGTGTAGTGTTCTGCAGCC 58.407 50.000 9.47 2.21 37.00 4.85
805 891 3.904136 AATTGTGTAGTGTTCTGCAGC 57.096 42.857 9.47 0.00 37.00 5.25
807 893 7.686438 ATCATAAATTGTGTAGTGTTCTGCA 57.314 32.000 0.00 0.00 34.14 4.41
869 1025 3.026630 TGCAAACGAAGACCTGACTAG 57.973 47.619 0.00 0.00 0.00 2.57
876 1032 2.290641 ACTGTCATTGCAAACGAAGACC 59.709 45.455 1.71 0.00 0.00 3.85
896 1052 3.728864 GCACACGGATCAAATCATGTCAC 60.729 47.826 0.00 0.00 30.49 3.67
912 1068 2.162608 AGAAGTAGCTAGAGTGCACACG 59.837 50.000 21.04 4.99 36.20 4.49
929 1085 7.712639 TGCTCTATGTATTGGCTTTAGAAGAAG 59.287 37.037 0.00 0.00 0.00 2.85
930 1086 7.495934 GTGCTCTATGTATTGGCTTTAGAAGAA 59.504 37.037 0.00 0.00 0.00 2.52
931 1087 6.986817 GTGCTCTATGTATTGGCTTTAGAAGA 59.013 38.462 0.00 0.00 0.00 2.87
968 1126 6.528072 GGCTTACAGTGTTGATAAGAAAATGC 59.472 38.462 0.00 0.00 0.00 3.56
994 1160 0.321564 TTCTGCAGCGCCATTGTAGT 60.322 50.000 9.47 0.00 31.30 2.73
997 1163 1.174712 AGTTTCTGCAGCGCCATTGT 61.175 50.000 9.47 0.00 0.00 2.71
1068 1234 1.226717 GAGTAGTGCCTCCGCTTCG 60.227 63.158 0.00 0.00 35.36 3.79
1074 1240 0.755698 TCCATCGGAGTAGTGCCTCC 60.756 60.000 0.00 0.00 46.37 4.30
1146 1315 2.296190 GACCCCAAACCAAGAACATGTC 59.704 50.000 0.00 0.00 0.00 3.06
1237 1406 3.301274 GGAGCACTGGAGAGTATAAGGT 58.699 50.000 0.00 0.00 0.00 3.50
1326 1495 1.420138 AGAACGGTGAGGGTGTGAAAT 59.580 47.619 0.00 0.00 0.00 2.17
1331 1500 0.106149 GTTCAGAACGGTGAGGGTGT 59.894 55.000 0.00 0.00 0.00 4.16
1386 1555 2.928801 TTGGTAGCTTGCTGAGTTGA 57.071 45.000 5.26 0.00 0.00 3.18
1419 1588 5.337250 GGTCAGGTTGTTATTTCCCAAATCC 60.337 44.000 0.00 0.00 32.38 3.01
1470 1639 7.617041 AGATAACAGCTTTAAAGTGGACATC 57.383 36.000 16.38 12.92 0.00 3.06
1535 1705 1.191489 TCGGATGGGTGCAGTTGAGA 61.191 55.000 0.00 0.00 0.00 3.27
1592 3059 1.134098 AGTGAATCTGGTAATGGCCCG 60.134 52.381 0.00 0.00 0.00 6.13
1598 3065 6.157645 ACAATCTCTGGAGTGAATCTGGTAAT 59.842 38.462 0.57 0.00 39.58 1.89
1757 3225 2.408565 GAGTCCAGGTATCATCCCCAA 58.591 52.381 0.00 0.00 0.00 4.12
1783 3251 8.365647 CCAAGTGGGTTACTGTATAGTATAAGG 58.634 40.741 0.00 0.00 40.26 2.69
1813 3281 0.467384 CGAGTGAGGCTGGGATTGAT 59.533 55.000 0.00 0.00 0.00 2.57
1972 3440 2.169769 CAATTCCTGCATCCTGGCAAAT 59.830 45.455 0.00 0.00 44.40 2.32
2192 3804 0.971386 AAGTTTGGCATGCTTCCCAG 59.029 50.000 18.92 0.00 31.73 4.45
2443 4055 5.014202 GGTTTTCCCAAGAAGCCACTATTA 58.986 41.667 0.00 0.00 32.35 0.98
2449 4070 3.935371 TGGTTTTCCCAAGAAGCCA 57.065 47.368 0.00 0.00 41.50 4.75
2482 4103 3.997021 AGATTCGCAGAAGTGTTAGTTGG 59.003 43.478 0.00 0.00 45.90 3.77
2668 4289 2.306847 GCTGGAAAGGAACCTGTGAAA 58.693 47.619 0.00 0.00 0.00 2.69
2679 4300 2.575532 TCTTCAACACTGCTGGAAAGG 58.424 47.619 0.00 0.00 0.00 3.11
3123 11079 3.983044 ACTGGACGCCTCTAAGATTTT 57.017 42.857 0.00 0.00 0.00 1.82
3202 11230 5.316987 AGGTCAAGGGATTCTAACAGTTTG 58.683 41.667 0.00 0.00 0.00 2.93
3205 11233 4.430441 AGAGGTCAAGGGATTCTAACAGT 58.570 43.478 0.00 0.00 0.00 3.55
3206 11234 4.467795 TGAGAGGTCAAGGGATTCTAACAG 59.532 45.833 0.00 0.00 0.00 3.16
3490 12446 4.991153 TCCAGCAATCACTGAGTAGTAG 57.009 45.455 0.00 0.00 40.25 2.57
3637 12593 1.002544 GACAAAGCAGAGTGCCCTACT 59.997 52.381 0.00 0.00 46.52 2.57
3641 12597 0.324943 TAGGACAAAGCAGAGTGCCC 59.675 55.000 0.00 0.00 46.52 5.36
3667 12623 5.067674 TGAGGAAACTTCAGGAAACACAATG 59.932 40.000 0.00 0.00 44.43 2.82
3669 12625 4.594970 TGAGGAAACTTCAGGAAACACAA 58.405 39.130 0.00 0.00 44.43 3.33
3672 12628 3.569701 GCATGAGGAAACTTCAGGAAACA 59.430 43.478 0.00 0.00 44.43 2.83
3673 12629 3.823304 AGCATGAGGAAACTTCAGGAAAC 59.177 43.478 0.00 0.00 44.43 2.78
3675 12631 3.795688 AGCATGAGGAAACTTCAGGAA 57.204 42.857 0.00 0.00 44.43 3.36
3677 12633 2.094854 GCAAGCATGAGGAAACTTCAGG 60.095 50.000 0.00 0.00 44.43 3.86
3678 12634 2.555325 TGCAAGCATGAGGAAACTTCAG 59.445 45.455 0.00 0.00 44.43 3.02
3704 12660 6.203915 GGACAATACATATACGTCCATTGCAA 59.796 38.462 0.00 0.00 44.55 4.08
3753 12714 9.672673 AGCAACTGATCATTACTATTACAACTT 57.327 29.630 0.00 0.00 0.00 2.66
3760 12721 9.703892 GTCAGATAGCAACTGATCATTACTATT 57.296 33.333 0.00 0.00 44.41 1.73
3761 12722 8.310382 GGTCAGATAGCAACTGATCATTACTAT 58.690 37.037 11.35 2.24 44.41 2.12
3762 12723 7.287696 TGGTCAGATAGCAACTGATCATTACTA 59.712 37.037 13.84 0.00 46.26 1.82
3763 12724 6.098838 TGGTCAGATAGCAACTGATCATTACT 59.901 38.462 13.84 0.00 46.26 2.24
3773 12734 2.499289 CACCTCTGGTCAGATAGCAACT 59.501 50.000 0.75 0.00 36.76 3.16
3782 12743 4.696479 AATATAAGCCACCTCTGGTCAG 57.304 45.455 0.00 0.00 40.17 3.51
3786 12747 4.949856 ACAACAAATATAAGCCACCTCTGG 59.050 41.667 0.00 0.00 41.13 3.86
3791 12752 8.682710 TCAAATAGACAACAAATATAAGCCACC 58.317 33.333 0.00 0.00 0.00 4.61
3893 12869 9.682465 ATGTACTCGGAAGATATATAAGTAGCA 57.318 33.333 0.00 0.00 40.84 3.49
3907 12883 7.441890 AGATGTACTCATATGTACTCGGAAG 57.558 40.000 1.90 0.00 42.22 3.46
3910 12886 7.203255 TGAAGATGTACTCATATGTACTCGG 57.797 40.000 1.90 0.00 42.22 4.63
3918 12903 9.988815 GGTACAAGATTGAAGATGTACTCATAT 57.011 33.333 12.86 0.00 44.64 1.78
3924 12909 6.253727 CACGAGGTACAAGATTGAAGATGTAC 59.746 42.308 0.00 6.41 44.56 2.90
3929 12914 3.006430 TGCACGAGGTACAAGATTGAAGA 59.994 43.478 0.00 0.00 0.00 2.87
3943 12931 1.229428 AGTGTGAACAATGCACGAGG 58.771 50.000 0.00 0.00 39.07 4.63
3944 12932 3.363970 GGTTAGTGTGAACAATGCACGAG 60.364 47.826 0.00 0.00 39.07 4.18
3946 12934 2.548057 AGGTTAGTGTGAACAATGCACG 59.452 45.455 0.00 0.00 39.07 5.34
3953 12941 2.434336 AGTCTGCAGGTTAGTGTGAACA 59.566 45.455 15.13 0.00 0.00 3.18
3954 12942 3.060602 GAGTCTGCAGGTTAGTGTGAAC 58.939 50.000 15.13 0.00 0.00 3.18
3955 12943 2.698274 TGAGTCTGCAGGTTAGTGTGAA 59.302 45.455 15.13 0.00 0.00 3.18
3956 12944 2.297315 CTGAGTCTGCAGGTTAGTGTGA 59.703 50.000 15.13 0.00 32.26 3.58
3957 12945 2.036475 ACTGAGTCTGCAGGTTAGTGTG 59.964 50.000 15.13 0.00 40.20 3.82
3958 12946 2.320781 ACTGAGTCTGCAGGTTAGTGT 58.679 47.619 15.13 3.74 40.20 3.55
3959 12947 3.393089 AACTGAGTCTGCAGGTTAGTG 57.607 47.619 15.13 3.09 40.20 2.74
3960 12948 5.482175 AGAATAACTGAGTCTGCAGGTTAGT 59.518 40.000 15.13 12.61 40.20 2.24
4054 13063 0.538057 ACTGTTGGTGGATGCTGTGG 60.538 55.000 0.00 0.00 0.00 4.17
4099 13108 0.917259 CGTCGTCAACAGCTAGATGC 59.083 55.000 8.16 0.00 43.29 3.91
4461 13488 1.823976 GCCTCTACAGCTACCCCAC 59.176 63.158 0.00 0.00 0.00 4.61
4532 13559 3.628646 ATCGGGCCTGAGGTGCAAC 62.629 63.158 21.28 0.00 0.00 4.17
4546 13573 1.135774 TCGAACGTGTCTCTGAATCGG 60.136 52.381 0.00 0.00 0.00 4.18
4552 13579 1.340658 CATGGTCGAACGTGTCTCTG 58.659 55.000 14.74 0.00 0.00 3.35
4561 13588 3.189287 ACTGAATTCTTGCATGGTCGAAC 59.811 43.478 7.05 0.00 0.00 3.95
4570 13597 3.243501 GGAACAAGCACTGAATTCTTGCA 60.244 43.478 25.20 0.75 40.45 4.08
4580 13607 5.695851 AATTTACAGAGGAACAAGCACTG 57.304 39.130 0.00 0.00 35.14 3.66
4584 13611 6.749139 AGGAAAAATTTACAGAGGAACAAGC 58.251 36.000 0.00 0.00 0.00 4.01
4587 13614 8.754080 TGAAAAGGAAAAATTTACAGAGGAACA 58.246 29.630 0.00 0.00 0.00 3.18
4588 13615 9.764363 ATGAAAAGGAAAAATTTACAGAGGAAC 57.236 29.630 0.00 0.00 0.00 3.62
4589 13616 9.762933 CATGAAAAGGAAAAATTTACAGAGGAA 57.237 29.630 0.00 0.00 0.00 3.36
4595 13622 9.672086 CGAGTACATGAAAAGGAAAAATTTACA 57.328 29.630 0.00 0.00 0.00 2.41
4596 13623 8.635983 GCGAGTACATGAAAAGGAAAAATTTAC 58.364 33.333 0.00 0.00 0.00 2.01
4598 13625 7.433680 AGCGAGTACATGAAAAGGAAAAATTT 58.566 30.769 0.00 0.00 0.00 1.82
4601 13634 7.499321 TTAGCGAGTACATGAAAAGGAAAAA 57.501 32.000 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.