Multiple sequence alignment - TraesCS5A01G504600

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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 TraesCS5A01G504600 chr5A 100.000 2483 0 0 1 2483 670250004 670252486 0 4586
1 TraesCS5A01G504600 chr4B 90.529 1626 90 25 910 2483 625118679 625120292 0 2091
2 TraesCS5A01G504600 chr4B 92.593 513 29 1 164 667 624871181 624871693 0 728
3 TraesCS5A01G504600 chr4D 90.370 1620 69 39 903 2483 488496025 488497596 0 2047
4 TraesCS5A01G504600 chr4D 93.635 597 27 8 142 733 488495307 488495897 0 881


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 TraesCS5A01G504600 chr5A 670250004 670252486 2482 False 4586 4586 100.0000 1 2483 1 chr5A.!!$F1 2482
1 TraesCS5A01G504600 chr4B 625118679 625120292 1613 False 2091 2091 90.5290 910 2483 1 chr4B.!!$F2 1573
2 TraesCS5A01G504600 chr4B 624871181 624871693 512 False 728 728 92.5930 164 667 1 chr4B.!!$F1 503
3 TraesCS5A01G504600 chr4D 488495307 488497596 2289 False 1464 2047 92.0025 142 2483 2 chr4D.!!$F1 2341

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
847 909 0.103026 TCTGAATCATCGTGCTCCCG 59.897 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 2474 0.390472 CGAGGAGAACAACAGAGCCC 60.39 60.0 0.0 0.0 0.0 5.19 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
21 22 4.120646 GTGACGTCTGAATCTGTGTTTG 57.879 45.455 17.92 0.00 0.00 2.93
22 23 2.543848 TGACGTCTGAATCTGTGTTTGC 59.456 45.455 17.92 0.00 0.00 3.68
23 24 1.526887 ACGTCTGAATCTGTGTTTGCG 59.473 47.619 0.00 0.00 0.00 4.85
24 25 1.722751 CGTCTGAATCTGTGTTTGCGC 60.723 52.381 0.00 0.00 0.00 6.09
25 26 0.512518 TCTGAATCTGTGTTTGCGCG 59.487 50.000 0.00 0.00 0.00 6.86
26 27 0.235665 CTGAATCTGTGTTTGCGCGT 59.764 50.000 8.43 0.00 0.00 6.01
27 28 0.234625 TGAATCTGTGTTTGCGCGTC 59.765 50.000 8.43 0.00 0.00 5.19
28 29 0.452784 GAATCTGTGTTTGCGCGTCC 60.453 55.000 8.43 0.00 0.00 4.79
29 30 1.163420 AATCTGTGTTTGCGCGTCCA 61.163 50.000 8.43 0.00 0.00 4.02
30 31 1.841663 ATCTGTGTTTGCGCGTCCAC 61.842 55.000 8.43 14.06 0.00 4.02
31 32 3.838229 CTGTGTTTGCGCGTCCACG 62.838 63.158 8.43 0.00 43.27 4.94
32 33 3.932313 GTGTTTGCGCGTCCACGT 61.932 61.111 8.43 0.00 42.22 4.49
33 34 3.196394 TGTTTGCGCGTCCACGTT 61.196 55.556 8.43 0.00 42.22 3.99
34 35 2.720750 GTTTGCGCGTCCACGTTG 60.721 61.111 8.43 0.00 42.22 4.10
35 36 2.890961 TTTGCGCGTCCACGTTGA 60.891 55.556 8.43 0.00 42.22 3.18
36 37 3.158011 TTTGCGCGTCCACGTTGAC 62.158 57.895 8.43 9.65 42.22 3.18
37 38 4.578898 TGCGCGTCCACGTTGACT 62.579 61.111 16.73 0.00 42.22 3.41
38 39 3.335534 GCGCGTCCACGTTGACTT 61.336 61.111 16.73 0.00 42.22 3.01
39 40 2.877974 GCGCGTCCACGTTGACTTT 61.878 57.895 16.73 0.00 42.22 2.66
40 41 1.550659 GCGCGTCCACGTTGACTTTA 61.551 55.000 16.73 0.00 42.22 1.85
41 42 0.854062 CGCGTCCACGTTGACTTTAA 59.146 50.000 16.73 0.00 42.22 1.52
42 43 1.396316 CGCGTCCACGTTGACTTTAAC 60.396 52.381 16.73 1.97 42.22 2.01
43 44 1.070376 GCGTCCACGTTGACTTTAACC 60.070 52.381 16.73 0.00 42.22 2.85
44 45 2.203401 CGTCCACGTTGACTTTAACCA 58.797 47.619 16.73 0.00 32.97 3.67
45 46 2.220133 CGTCCACGTTGACTTTAACCAG 59.780 50.000 16.73 0.00 32.97 4.00
46 47 3.200483 GTCCACGTTGACTTTAACCAGT 58.800 45.455 12.27 0.00 32.39 4.00
47 48 3.246936 GTCCACGTTGACTTTAACCAGTC 59.753 47.826 12.27 1.04 43.23 3.51
48 49 2.220133 CCACGTTGACTTTAACCAGTCG 59.780 50.000 3.48 0.00 45.53 4.18
49 50 1.862827 ACGTTGACTTTAACCAGTCGC 59.137 47.619 3.48 0.00 45.53 5.19
50 51 1.193874 CGTTGACTTTAACCAGTCGCC 59.806 52.381 3.48 0.00 45.53 5.54
51 52 1.193874 GTTGACTTTAACCAGTCGCCG 59.806 52.381 3.48 0.00 45.53 6.46
52 53 0.675083 TGACTTTAACCAGTCGCCGA 59.325 50.000 3.48 0.00 45.53 5.54
53 54 1.068895 TGACTTTAACCAGTCGCCGAA 59.931 47.619 0.00 0.00 45.53 4.30
54 55 1.458445 GACTTTAACCAGTCGCCGAAC 59.542 52.381 0.00 0.00 34.12 3.95
55 56 1.202557 ACTTTAACCAGTCGCCGAACA 60.203 47.619 0.00 0.00 0.00 3.18
56 57 1.193874 CTTTAACCAGTCGCCGAACAC 59.806 52.381 0.00 0.00 0.00 3.32
57 58 0.104487 TTAACCAGTCGCCGAACACA 59.896 50.000 0.00 0.00 0.00 3.72
58 59 0.104487 TAACCAGTCGCCGAACACAA 59.896 50.000 0.00 0.00 0.00 3.33
59 60 1.157870 AACCAGTCGCCGAACACAAG 61.158 55.000 0.00 0.00 0.00 3.16
60 61 2.551270 CAGTCGCCGAACACAAGC 59.449 61.111 0.00 0.00 0.00 4.01
61 62 1.956170 CAGTCGCCGAACACAAGCT 60.956 57.895 0.00 0.00 0.00 3.74
62 63 1.227556 AGTCGCCGAACACAAGCTT 60.228 52.632 0.00 0.00 0.00 3.74
63 64 1.204312 GTCGCCGAACACAAGCTTC 59.796 57.895 0.00 0.00 0.00 3.86
64 65 1.069090 TCGCCGAACACAAGCTTCT 59.931 52.632 0.00 0.00 0.00 2.85
65 66 0.944311 TCGCCGAACACAAGCTTCTC 60.944 55.000 0.00 0.00 0.00 2.87
66 67 1.221466 CGCCGAACACAAGCTTCTCA 61.221 55.000 0.00 0.00 0.00 3.27
67 68 0.944386 GCCGAACACAAGCTTCTCAA 59.056 50.000 0.00 0.00 0.00 3.02
68 69 1.334149 GCCGAACACAAGCTTCTCAAC 60.334 52.381 0.00 0.00 0.00 3.18
69 70 1.070577 CCGAACACAAGCTTCTCAACG 60.071 52.381 0.00 0.31 0.00 4.10
70 71 1.657538 CGAACACAAGCTTCTCAACGC 60.658 52.381 0.00 0.00 0.00 4.84
71 72 0.663153 AACACAAGCTTCTCAACGCC 59.337 50.000 0.00 0.00 0.00 5.68
72 73 1.166531 ACACAAGCTTCTCAACGCCC 61.167 55.000 0.00 0.00 0.00 6.13
73 74 1.961277 ACAAGCTTCTCAACGCCCG 60.961 57.895 0.00 0.00 0.00 6.13
74 75 2.358737 AAGCTTCTCAACGCCCGG 60.359 61.111 0.00 0.00 0.00 5.73
75 76 3.178540 AAGCTTCTCAACGCCCGGT 62.179 57.895 0.00 0.00 0.00 5.28
76 77 3.119096 GCTTCTCAACGCCCGGTC 61.119 66.667 0.00 0.00 0.00 4.79
77 78 2.434359 CTTCTCAACGCCCGGTCC 60.434 66.667 0.00 0.00 0.00 4.46
78 79 3.234630 CTTCTCAACGCCCGGTCCA 62.235 63.158 0.00 0.00 0.00 4.02
79 80 2.725203 CTTCTCAACGCCCGGTCCAA 62.725 60.000 0.00 0.00 0.00 3.53
80 81 2.999739 TTCTCAACGCCCGGTCCAAC 63.000 60.000 0.00 0.00 0.00 3.77
81 82 4.973055 TCAACGCCCGGTCCAACG 62.973 66.667 0.00 0.00 0.00 4.10
88 89 3.283684 CCGGTCCAACGCAGCAAA 61.284 61.111 0.00 0.00 0.00 3.68
89 90 2.718731 CGGTCCAACGCAGCAAAA 59.281 55.556 0.00 0.00 0.00 2.44
90 91 1.657181 CGGTCCAACGCAGCAAAAC 60.657 57.895 0.00 0.00 0.00 2.43
91 92 1.299850 GGTCCAACGCAGCAAAACC 60.300 57.895 0.00 0.00 0.00 3.27
92 93 1.657181 GTCCAACGCAGCAAAACCG 60.657 57.895 0.00 0.00 0.00 4.44
93 94 2.115911 TCCAACGCAGCAAAACCGT 61.116 52.632 0.00 0.00 36.68 4.83
94 95 1.657181 CCAACGCAGCAAAACCGTC 60.657 57.895 0.00 0.00 33.59 4.79
95 96 1.657181 CAACGCAGCAAAACCGTCC 60.657 57.895 0.00 0.00 33.59 4.79
96 97 1.822186 AACGCAGCAAAACCGTCCT 60.822 52.632 0.00 0.00 33.59 3.85
97 98 1.381165 AACGCAGCAAAACCGTCCTT 61.381 50.000 0.00 0.00 33.59 3.36
98 99 1.082104 CGCAGCAAAACCGTCCTTC 60.082 57.895 0.00 0.00 0.00 3.46
99 100 1.781025 CGCAGCAAAACCGTCCTTCA 61.781 55.000 0.00 0.00 0.00 3.02
100 101 0.317854 GCAGCAAAACCGTCCTTCAC 60.318 55.000 0.00 0.00 0.00 3.18
101 102 0.310854 CAGCAAAACCGTCCTTCACC 59.689 55.000 0.00 0.00 0.00 4.02
102 103 0.822121 AGCAAAACCGTCCTTCACCC 60.822 55.000 0.00 0.00 0.00 4.61
103 104 1.946267 CAAAACCGTCCTTCACCCG 59.054 57.895 0.00 0.00 0.00 5.28
104 105 1.895231 AAAACCGTCCTTCACCCGC 60.895 57.895 0.00 0.00 0.00 6.13
105 106 2.612095 AAAACCGTCCTTCACCCGCA 62.612 55.000 0.00 0.00 0.00 5.69
106 107 2.612095 AAACCGTCCTTCACCCGCAA 62.612 55.000 0.00 0.00 0.00 4.85
107 108 2.742372 CCGTCCTTCACCCGCAAG 60.742 66.667 0.00 0.00 0.00 4.01
119 120 3.966543 CGCAAGGAACCACCCCCT 61.967 66.667 0.00 0.00 40.05 4.79
120 121 2.035783 GCAAGGAACCACCCCCTC 59.964 66.667 0.00 0.00 40.05 4.30
121 122 2.763902 CAAGGAACCACCCCCTCC 59.236 66.667 0.00 0.00 40.05 4.30
122 123 2.160171 CAAGGAACCACCCCCTCCA 61.160 63.158 0.00 0.00 40.05 3.86
123 124 1.388217 AAGGAACCACCCCCTCCAA 60.388 57.895 0.00 0.00 40.05 3.53
124 125 1.002242 AAGGAACCACCCCCTCCAAA 61.002 55.000 0.00 0.00 40.05 3.28
125 126 0.780090 AGGAACCACCCCCTCCAAAT 60.780 55.000 0.00 0.00 40.05 2.32
126 127 0.324368 GGAACCACCCCCTCCAAATC 60.324 60.000 0.00 0.00 0.00 2.17
127 128 0.324368 GAACCACCCCCTCCAAATCC 60.324 60.000 0.00 0.00 0.00 3.01
128 129 1.811025 AACCACCCCCTCCAAATCCC 61.811 60.000 0.00 0.00 0.00 3.85
129 130 2.689813 CACCCCCTCCAAATCCCC 59.310 66.667 0.00 0.00 0.00 4.81
130 131 2.620464 ACCCCCTCCAAATCCCCC 60.620 66.667 0.00 0.00 0.00 5.40
131 132 2.620137 CCCCCTCCAAATCCCCCA 60.620 66.667 0.00 0.00 0.00 4.96
132 133 2.689813 CCCCTCCAAATCCCCCAC 59.310 66.667 0.00 0.00 0.00 4.61
133 134 2.245379 CCCCTCCAAATCCCCCACA 61.245 63.158 0.00 0.00 0.00 4.17
134 135 1.307647 CCCTCCAAATCCCCCACAG 59.692 63.158 0.00 0.00 0.00 3.66
135 136 1.307647 CCTCCAAATCCCCCACAGG 59.692 63.158 0.00 0.00 0.00 4.00
136 137 1.380380 CTCCAAATCCCCCACAGGC 60.380 63.158 0.00 0.00 0.00 4.85
137 138 2.364186 CCAAATCCCCCACAGGCC 60.364 66.667 0.00 0.00 0.00 5.19
138 139 2.364186 CAAATCCCCCACAGGCCC 60.364 66.667 0.00 0.00 0.00 5.80
139 140 2.868566 AAATCCCCCACAGGCCCA 60.869 61.111 0.00 0.00 0.00 5.36
140 141 3.238197 AAATCCCCCACAGGCCCAC 62.238 63.158 0.00 0.00 0.00 4.61
155 156 1.231641 CCACACCACCCCTCCAAAA 59.768 57.895 0.00 0.00 0.00 2.44
156 157 0.397816 CCACACCACCCCTCCAAAAA 60.398 55.000 0.00 0.00 0.00 1.94
174 175 2.371910 AAACAAAACCCACACCAACG 57.628 45.000 0.00 0.00 0.00 4.10
320 324 2.117257 GAGGACCTACTTCGAGGCC 58.883 63.158 0.00 0.00 40.65 5.19
500 504 4.185059 GTCTACGACGACGGGCCC 62.185 72.222 13.57 13.57 44.46 5.80
651 665 3.181522 GCTGAGTTGAGAAGCTTGATTCG 60.182 47.826 2.10 0.00 34.27 3.34
672 686 2.106074 CCGTGGCGATGCTTGCTTA 61.106 57.895 0.00 0.00 0.00 3.09
674 688 1.634757 CGTGGCGATGCTTGCTTACA 61.635 55.000 0.00 0.00 0.00 2.41
703 717 3.569194 TGTGTTTCCTTCCTGCTGTAA 57.431 42.857 0.00 0.00 0.00 2.41
709 723 4.640771 TTCCTTCCTGCTGTAAATCAGT 57.359 40.909 0.00 0.00 45.23 3.41
710 724 5.755409 TTCCTTCCTGCTGTAAATCAGTA 57.245 39.130 0.00 0.00 45.23 2.74
711 725 5.086104 TCCTTCCTGCTGTAAATCAGTAC 57.914 43.478 0.00 0.00 45.23 2.73
712 726 4.777896 TCCTTCCTGCTGTAAATCAGTACT 59.222 41.667 0.00 0.00 45.23 2.73
759 799 5.009610 GTGGAATTTACTGTGGATTGTGTGT 59.990 40.000 0.00 0.00 0.00 3.72
760 800 5.009510 TGGAATTTACTGTGGATTGTGTGTG 59.990 40.000 0.00 0.00 0.00 3.82
761 801 5.240623 GGAATTTACTGTGGATTGTGTGTGA 59.759 40.000 0.00 0.00 0.00 3.58
762 802 6.238897 GGAATTTACTGTGGATTGTGTGTGAA 60.239 38.462 0.00 0.00 0.00 3.18
771 811 5.003160 TGGATTGTGTGTGAAATCGAAGAT 58.997 37.500 0.00 0.00 45.12 2.40
773 813 5.106555 GGATTGTGTGTGAAATCGAAGATGT 60.107 40.000 0.00 0.00 45.12 3.06
781 821 5.700373 TGTGAAATCGAAGATGTTGTGATCA 59.300 36.000 0.00 0.00 45.12 2.92
782 822 6.372381 TGTGAAATCGAAGATGTTGTGATCAT 59.628 34.615 0.00 0.00 45.12 2.45
783 823 6.904011 GTGAAATCGAAGATGTTGTGATCATC 59.096 38.462 0.00 0.00 45.12 2.92
784 824 6.594937 TGAAATCGAAGATGTTGTGATCATCA 59.405 34.615 0.00 0.00 45.12 3.07
786 826 6.600246 ATCGAAGATGTTGTGATCATCAAG 57.400 37.500 0.00 0.00 45.12 3.02
796 858 4.449131 TGTGATCATCAAGCTTCTGATCC 58.551 43.478 28.91 23.34 42.92 3.36
813 875 4.985413 TGATCCGATTTGCTGTGAAAATC 58.015 39.130 1.87 1.87 39.57 2.17
821 883 5.356882 TTTGCTGTGAAAATCGAAGTAGG 57.643 39.130 0.00 0.00 0.00 3.18
822 884 4.265904 TGCTGTGAAAATCGAAGTAGGA 57.734 40.909 0.00 0.00 0.00 2.94
823 885 4.245660 TGCTGTGAAAATCGAAGTAGGAG 58.754 43.478 0.00 0.00 0.00 3.69
824 886 4.246458 GCTGTGAAAATCGAAGTAGGAGT 58.754 43.478 0.00 0.00 0.00 3.85
825 887 5.047590 TGCTGTGAAAATCGAAGTAGGAGTA 60.048 40.000 0.00 0.00 0.00 2.59
826 888 5.517054 GCTGTGAAAATCGAAGTAGGAGTAG 59.483 44.000 0.00 0.00 0.00 2.57
827 889 6.585695 TGTGAAAATCGAAGTAGGAGTAGT 57.414 37.500 0.00 0.00 0.00 2.73
828 890 6.989659 TGTGAAAATCGAAGTAGGAGTAGTT 58.010 36.000 0.00 0.00 0.00 2.24
829 891 7.088905 TGTGAAAATCGAAGTAGGAGTAGTTC 58.911 38.462 0.00 0.00 35.84 3.01
830 892 7.039923 TGTGAAAATCGAAGTAGGAGTAGTTCT 60.040 37.037 0.00 0.00 36.70 3.01
831 893 7.273815 GTGAAAATCGAAGTAGGAGTAGTTCTG 59.726 40.741 0.00 0.00 36.70 3.02
832 894 7.176165 TGAAAATCGAAGTAGGAGTAGTTCTGA 59.824 37.037 0.00 0.00 36.70 3.27
833 895 7.463961 AAATCGAAGTAGGAGTAGTTCTGAA 57.536 36.000 0.00 0.00 36.70 3.02
834 896 7.648039 AATCGAAGTAGGAGTAGTTCTGAAT 57.352 36.000 0.00 0.00 36.70 2.57
835 897 6.680874 TCGAAGTAGGAGTAGTTCTGAATC 57.319 41.667 0.00 0.00 36.70 2.52
836 898 6.178324 TCGAAGTAGGAGTAGTTCTGAATCA 58.822 40.000 0.00 0.00 36.70 2.57
837 899 6.829298 TCGAAGTAGGAGTAGTTCTGAATCAT 59.171 38.462 0.00 0.00 36.70 2.45
838 900 7.012515 TCGAAGTAGGAGTAGTTCTGAATCATC 59.987 40.741 0.00 0.00 36.70 2.92
839 901 6.627395 AGTAGGAGTAGTTCTGAATCATCG 57.373 41.667 0.00 0.00 0.00 3.84
840 902 6.123651 AGTAGGAGTAGTTCTGAATCATCGT 58.876 40.000 0.00 0.00 0.00 3.73
841 903 5.255710 AGGAGTAGTTCTGAATCATCGTG 57.744 43.478 0.00 0.00 0.00 4.35
842 904 3.799420 GGAGTAGTTCTGAATCATCGTGC 59.201 47.826 0.00 0.00 0.00 5.34
843 905 4.440802 GGAGTAGTTCTGAATCATCGTGCT 60.441 45.833 0.00 0.00 0.00 4.40
844 906 4.677584 AGTAGTTCTGAATCATCGTGCTC 58.322 43.478 0.00 0.00 0.00 4.26
845 907 2.898705 AGTTCTGAATCATCGTGCTCC 58.101 47.619 0.00 0.00 0.00 4.70
846 908 1.936547 GTTCTGAATCATCGTGCTCCC 59.063 52.381 0.00 0.00 0.00 4.30
847 909 0.103026 TCTGAATCATCGTGCTCCCG 59.897 55.000 0.00 0.00 0.00 5.14
848 910 0.103026 CTGAATCATCGTGCTCCCGA 59.897 55.000 0.00 0.00 41.73 5.14
850 912 1.269778 TGAATCATCGTGCTCCCGATC 60.270 52.381 3.98 0.00 45.25 3.69
851 913 1.000283 GAATCATCGTGCTCCCGATCT 60.000 52.381 3.98 0.00 45.25 2.75
852 914 0.316522 ATCATCGTGCTCCCGATCTG 59.683 55.000 3.98 0.00 45.25 2.90
853 915 0.751643 TCATCGTGCTCCCGATCTGA 60.752 55.000 3.98 0.06 45.25 3.27
854 916 0.103026 CATCGTGCTCCCGATCTGAA 59.897 55.000 3.98 0.00 45.25 3.02
855 917 0.824109 ATCGTGCTCCCGATCTGAAA 59.176 50.000 1.51 0.00 43.74 2.69
856 918 0.824109 TCGTGCTCCCGATCTGAAAT 59.176 50.000 0.00 0.00 30.63 2.17
857 919 1.207089 TCGTGCTCCCGATCTGAAATT 59.793 47.619 0.00 0.00 30.63 1.82
858 920 1.594862 CGTGCTCCCGATCTGAAATTC 59.405 52.381 0.00 0.00 0.00 2.17
859 921 2.739932 CGTGCTCCCGATCTGAAATTCT 60.740 50.000 0.00 0.00 0.00 2.40
860 922 2.611292 GTGCTCCCGATCTGAAATTCTG 59.389 50.000 0.00 0.00 0.00 3.02
861 923 2.501316 TGCTCCCGATCTGAAATTCTGA 59.499 45.455 5.07 5.07 0.00 3.27
862 924 3.055167 TGCTCCCGATCTGAAATTCTGAA 60.055 43.478 6.66 0.00 0.00 3.02
863 925 3.311048 GCTCCCGATCTGAAATTCTGAAC 59.689 47.826 6.66 3.70 0.00 3.18
864 926 4.507710 CTCCCGATCTGAAATTCTGAACA 58.492 43.478 6.66 0.00 0.00 3.18
865 927 4.507710 TCCCGATCTGAAATTCTGAACAG 58.492 43.478 6.66 0.00 0.00 3.16
866 928 4.020218 TCCCGATCTGAAATTCTGAACAGT 60.020 41.667 6.66 0.00 0.00 3.55
867 929 4.697352 CCCGATCTGAAATTCTGAACAGTT 59.303 41.667 6.66 0.00 0.00 3.16
868 930 5.163814 CCCGATCTGAAATTCTGAACAGTTC 60.164 44.000 6.32 6.32 0.00 3.01
869 931 5.445142 CCGATCTGAAATTCTGAACAGTTCG 60.445 44.000 21.11 21.11 44.63 3.95
870 932 4.732285 TCTGAAATTCTGAACAGTTCGC 57.268 40.909 8.80 0.00 0.00 4.70
871 933 4.380531 TCTGAAATTCTGAACAGTTCGCT 58.619 39.130 8.80 0.00 0.00 4.93
881 943 2.621763 CAGTTCGCTGCTCTTTGGT 58.378 52.632 0.00 0.00 38.53 3.67
882 944 0.236711 CAGTTCGCTGCTCTTTGGTG 59.763 55.000 0.00 0.00 38.53 4.17
883 945 0.886490 AGTTCGCTGCTCTTTGGTGG 60.886 55.000 0.00 0.00 0.00 4.61
884 946 2.260869 TTCGCTGCTCTTTGGTGGC 61.261 57.895 0.00 0.00 0.00 5.01
885 947 3.741476 CGCTGCTCTTTGGTGGCC 61.741 66.667 0.00 0.00 0.00 5.36
886 948 2.282745 GCTGCTCTTTGGTGGCCT 60.283 61.111 3.32 0.00 0.00 5.19
887 949 2.633509 GCTGCTCTTTGGTGGCCTG 61.634 63.158 3.32 0.00 0.00 4.85
888 950 1.975407 CTGCTCTTTGGTGGCCTGG 60.975 63.158 3.32 0.00 0.00 4.45
889 951 2.116125 GCTCTTTGGTGGCCTGGT 59.884 61.111 3.32 0.00 0.00 4.00
890 952 2.270986 GCTCTTTGGTGGCCTGGTG 61.271 63.158 3.32 0.00 0.00 4.17
891 953 2.203480 TCTTTGGTGGCCTGGTGC 60.203 61.111 3.32 0.00 40.16 5.01
1119 1195 1.064946 CACCATCGACGAGCTCCTC 59.935 63.158 8.47 5.32 0.00 3.71
1141 1217 1.078848 CGCCACCTCTCCAAGAAGG 60.079 63.158 0.00 0.00 39.47 3.46
1142 1218 1.301293 GCCACCTCTCCAAGAAGGG 59.699 63.158 0.00 0.00 38.24 3.95
1143 1219 1.994463 CCACCTCTCCAAGAAGGGG 59.006 63.158 0.00 0.00 43.17 4.79
1251 1327 3.845259 TACCGGGACATCCTGCGC 61.845 66.667 6.32 0.00 41.13 6.09
1589 1677 6.405397 GGTTGTAAAATTCCCTATGTGCGAAT 60.405 38.462 0.00 0.00 0.00 3.34
1590 1678 7.201750 GGTTGTAAAATTCCCTATGTGCGAATA 60.202 37.037 0.00 0.00 0.00 1.75
1602 1690 7.119699 CCCTATGTGCGAATATTTATGTGATGT 59.880 37.037 0.00 0.00 0.00 3.06
1603 1691 7.959109 CCTATGTGCGAATATTTATGTGATGTG 59.041 37.037 0.00 0.00 0.00 3.21
1645 1734 5.988310 TGAAGCATTTCATCCTTGTCAAT 57.012 34.783 0.00 0.00 38.37 2.57
1646 1735 6.349243 TGAAGCATTTCATCCTTGTCAATT 57.651 33.333 0.00 0.00 38.37 2.32
1647 1736 6.160684 TGAAGCATTTCATCCTTGTCAATTG 58.839 36.000 0.00 0.00 38.37 2.32
1648 1737 5.733620 AGCATTTCATCCTTGTCAATTGT 57.266 34.783 5.13 0.00 0.00 2.71
1649 1738 5.717119 AGCATTTCATCCTTGTCAATTGTC 58.283 37.500 5.13 0.00 0.00 3.18
1650 1739 5.244402 AGCATTTCATCCTTGTCAATTGTCA 59.756 36.000 5.13 2.96 0.00 3.58
1656 1745 2.173519 CCTTGTCAATTGTCATGCCCT 58.826 47.619 6.21 0.00 0.00 5.19
1696 1785 6.974965 AGAAATGTGACAGGAAATCAACTTC 58.025 36.000 0.00 0.00 0.00 3.01
1704 1793 5.299949 ACAGGAAATCAACTTCCATTTTGC 58.700 37.500 5.24 0.00 46.38 3.68
1798 1905 9.630098 AAAATTGACTTTGTACATCACATCATC 57.370 29.630 0.00 0.00 36.90 2.92
1819 1926 7.753659 TCATCGTCAGTTACAAAAGTCAAAAA 58.246 30.769 0.00 0.00 0.00 1.94
1825 1932 5.977129 CAGTTACAAAAGTCAAAAAGGCGAT 59.023 36.000 0.00 0.00 0.00 4.58
1839 1955 0.665298 GGCGATGCTTCTTCCAATCC 59.335 55.000 0.00 0.00 0.00 3.01
1843 1959 2.632377 GATGCTTCTTCCAATCCGTGA 58.368 47.619 0.00 0.00 0.00 4.35
1877 1993 1.035139 CAGCAGCAAGACAAACCCTT 58.965 50.000 0.00 0.00 0.00 3.95
1896 2013 2.409243 CTCTTCGAGCCGATGCGA 59.591 61.111 0.00 0.00 44.33 5.10
1920 2043 4.098654 CGAGTACATGAGAGTTGATCCCTT 59.901 45.833 0.00 0.00 0.00 3.95
1956 2079 0.804989 GATTGTACTGGTGCTGGCAC 59.195 55.000 16.33 16.33 45.49 5.01
1976 2101 5.052481 GCACCAGAAATTCAGAAGCTTTTT 58.948 37.500 0.00 0.00 0.00 1.94
2016 2141 4.903054 TCAGAATTCAGAAGCTGTGTGAT 58.097 39.130 8.44 0.00 32.61 3.06
2147 2273 1.611977 TCTGTTCACCAGTAGTCACCG 59.388 52.381 0.00 0.00 42.19 4.94
2159 2285 2.666190 TCACCGCAGCAGCAAGAC 60.666 61.111 0.82 0.00 42.27 3.01
2165 2291 2.413142 GCAGCAGCAAGACCCATCC 61.413 63.158 0.00 0.00 41.58 3.51
2195 2321 3.428870 GGTGATAGATATTTGTGTCGCCG 59.571 47.826 0.00 0.00 29.44 6.46
2213 2339 0.739813 CGACAACAATCCTCCGTCCC 60.740 60.000 0.00 0.00 0.00 4.46
2348 2474 2.161012 CAGCCTCACACTATGCTTGTTG 59.839 50.000 0.00 0.00 30.08 3.33
2396 2522 6.120905 CAGAGAGGTTGGATCAGATTGATTT 58.879 40.000 0.00 0.00 37.20 2.17
2447 2573 3.541632 TGACAGAAAGTTGGACACTTCC 58.458 45.455 0.00 0.00 45.77 3.46
2475 2601 3.573772 TTGCTCTGAGGGTGCGTCG 62.574 63.158 6.83 0.00 37.26 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.604772 GCAAACACAGATTCAGACGTCAC 60.605 47.826 19.50 3.64 0.00 3.67
1 2 2.543848 GCAAACACAGATTCAGACGTCA 59.456 45.455 19.50 0.00 0.00 4.35
2 3 2.410262 CGCAAACACAGATTCAGACGTC 60.410 50.000 7.70 7.70 0.00 4.34
3 4 1.526887 CGCAAACACAGATTCAGACGT 59.473 47.619 0.00 0.00 0.00 4.34
4 5 1.722751 GCGCAAACACAGATTCAGACG 60.723 52.381 0.30 0.00 0.00 4.18
5 6 1.722751 CGCGCAAACACAGATTCAGAC 60.723 52.381 8.75 0.00 0.00 3.51
6 7 0.512518 CGCGCAAACACAGATTCAGA 59.487 50.000 8.75 0.00 0.00 3.27
8 9 0.234625 GACGCGCAAACACAGATTCA 59.765 50.000 5.73 0.00 0.00 2.57
10 11 1.163420 TGGACGCGCAAACACAGATT 61.163 50.000 5.73 0.00 0.00 2.40
11 12 1.596752 TGGACGCGCAAACACAGAT 60.597 52.632 5.73 0.00 0.00 2.90
12 13 2.202946 TGGACGCGCAAACACAGA 60.203 55.556 5.73 0.00 0.00 3.41
13 14 2.052237 GTGGACGCGCAAACACAG 60.052 61.111 17.16 0.00 34.16 3.66
14 15 3.931130 CGTGGACGCGCAAACACA 61.931 61.111 20.43 4.95 33.62 3.72
15 16 3.443261 AACGTGGACGCGCAAACAC 62.443 57.895 5.73 11.68 44.43 3.32
16 17 3.196394 AACGTGGACGCGCAAACA 61.196 55.556 5.73 0.00 44.43 2.83
17 18 2.720750 CAACGTGGACGCGCAAAC 60.721 61.111 5.73 0.00 44.43 2.93
18 19 2.890961 TCAACGTGGACGCGCAAA 60.891 55.556 5.73 0.00 44.43 3.68
19 20 3.632107 GTCAACGTGGACGCGCAA 61.632 61.111 7.46 0.00 44.43 4.85
20 21 4.578898 AGTCAACGTGGACGCGCA 62.579 61.111 17.27 0.00 44.43 6.09
21 22 1.550659 TAAAGTCAACGTGGACGCGC 61.551 55.000 17.27 0.00 44.43 6.86
22 23 0.854062 TTAAAGTCAACGTGGACGCG 59.146 50.000 17.27 3.53 44.43 6.01
23 24 1.070376 GGTTAAAGTCAACGTGGACGC 60.070 52.381 17.27 6.74 44.43 5.19
24 25 2.203401 TGGTTAAAGTCAACGTGGACG 58.797 47.619 17.27 0.00 42.62 4.79
25 26 3.200483 ACTGGTTAAAGTCAACGTGGAC 58.800 45.455 15.63 15.63 38.08 4.02
26 27 3.460103 GACTGGTTAAAGTCAACGTGGA 58.540 45.455 2.96 0.00 44.98 4.02
27 28 2.220133 CGACTGGTTAAAGTCAACGTGG 59.780 50.000 7.82 0.00 45.77 4.94
28 29 2.348218 GCGACTGGTTAAAGTCAACGTG 60.348 50.000 7.82 0.00 45.77 4.49
29 30 1.862827 GCGACTGGTTAAAGTCAACGT 59.137 47.619 7.82 0.00 45.77 3.99
30 31 1.193874 GGCGACTGGTTAAAGTCAACG 59.806 52.381 7.82 0.00 45.77 4.10
31 32 1.193874 CGGCGACTGGTTAAAGTCAAC 59.806 52.381 0.00 0.22 45.77 3.18
32 33 1.068895 TCGGCGACTGGTTAAAGTCAA 59.931 47.619 4.99 0.00 45.77 3.18
33 34 0.675083 TCGGCGACTGGTTAAAGTCA 59.325 50.000 4.99 0.00 45.77 3.41
34 35 1.458445 GTTCGGCGACTGGTTAAAGTC 59.542 52.381 10.16 0.00 42.68 3.01
35 36 1.202557 TGTTCGGCGACTGGTTAAAGT 60.203 47.619 10.16 0.00 0.00 2.66
36 37 1.193874 GTGTTCGGCGACTGGTTAAAG 59.806 52.381 10.16 0.00 0.00 1.85
37 38 1.219646 GTGTTCGGCGACTGGTTAAA 58.780 50.000 10.16 0.00 0.00 1.52
38 39 0.104487 TGTGTTCGGCGACTGGTTAA 59.896 50.000 10.16 0.00 0.00 2.01
39 40 0.104487 TTGTGTTCGGCGACTGGTTA 59.896 50.000 10.16 0.00 0.00 2.85
40 41 1.153329 TTGTGTTCGGCGACTGGTT 60.153 52.632 10.16 0.00 0.00 3.67
41 42 1.594293 CTTGTGTTCGGCGACTGGT 60.594 57.895 10.16 0.00 0.00 4.00
42 43 2.954753 GCTTGTGTTCGGCGACTGG 61.955 63.158 10.16 0.00 0.00 4.00
43 44 1.498865 AAGCTTGTGTTCGGCGACTG 61.499 55.000 10.16 0.00 0.00 3.51
44 45 1.222115 GAAGCTTGTGTTCGGCGACT 61.222 55.000 10.16 0.00 0.00 4.18
45 46 1.204312 GAAGCTTGTGTTCGGCGAC 59.796 57.895 10.16 5.76 0.00 5.19
46 47 0.944311 GAGAAGCTTGTGTTCGGCGA 60.944 55.000 4.99 4.99 0.00 5.54
47 48 1.221466 TGAGAAGCTTGTGTTCGGCG 61.221 55.000 2.10 0.00 0.00 6.46
48 49 0.944386 TTGAGAAGCTTGTGTTCGGC 59.056 50.000 2.10 0.00 0.00 5.54
49 50 1.070577 CGTTGAGAAGCTTGTGTTCGG 60.071 52.381 2.10 0.00 0.00 4.30
50 51 1.657538 GCGTTGAGAAGCTTGTGTTCG 60.658 52.381 2.10 5.15 0.00 3.95
51 52 1.334149 GGCGTTGAGAAGCTTGTGTTC 60.334 52.381 2.10 0.00 0.00 3.18
52 53 0.663153 GGCGTTGAGAAGCTTGTGTT 59.337 50.000 2.10 0.00 0.00 3.32
53 54 1.166531 GGGCGTTGAGAAGCTTGTGT 61.167 55.000 2.10 0.00 0.00 3.72
54 55 1.576421 GGGCGTTGAGAAGCTTGTG 59.424 57.895 2.10 0.00 0.00 3.33
55 56 1.961277 CGGGCGTTGAGAAGCTTGT 60.961 57.895 2.10 0.00 0.00 3.16
56 57 2.680913 CCGGGCGTTGAGAAGCTTG 61.681 63.158 2.10 0.00 0.00 4.01
57 58 2.358737 CCGGGCGTTGAGAAGCTT 60.359 61.111 0.00 0.00 0.00 3.74
58 59 3.591254 GACCGGGCGTTGAGAAGCT 62.591 63.158 6.32 0.00 0.00 3.74
59 60 3.119096 GACCGGGCGTTGAGAAGC 61.119 66.667 6.32 0.00 0.00 3.86
60 61 2.434359 GGACCGGGCGTTGAGAAG 60.434 66.667 6.32 0.00 0.00 2.85
61 62 2.809307 TTGGACCGGGCGTTGAGAA 61.809 57.895 6.32 0.00 0.00 2.87
62 63 3.235481 TTGGACCGGGCGTTGAGA 61.235 61.111 6.32 0.00 0.00 3.27
63 64 3.047877 GTTGGACCGGGCGTTGAG 61.048 66.667 6.32 0.00 0.00 3.02
64 65 4.973055 CGTTGGACCGGGCGTTGA 62.973 66.667 6.32 0.00 0.00 3.18
71 72 2.840066 TTTTGCTGCGTTGGACCGG 61.840 57.895 0.00 0.00 0.00 5.28
72 73 1.657181 GTTTTGCTGCGTTGGACCG 60.657 57.895 0.00 0.00 0.00 4.79
73 74 1.299850 GGTTTTGCTGCGTTGGACC 60.300 57.895 0.00 0.00 0.00 4.46
74 75 1.657181 CGGTTTTGCTGCGTTGGAC 60.657 57.895 0.00 0.00 0.00 4.02
75 76 2.054140 GACGGTTTTGCTGCGTTGGA 62.054 55.000 0.00 0.00 0.00 3.53
76 77 1.657181 GACGGTTTTGCTGCGTTGG 60.657 57.895 0.00 0.00 0.00 3.77
77 78 1.657181 GGACGGTTTTGCTGCGTTG 60.657 57.895 0.00 0.00 0.00 4.10
78 79 1.381165 AAGGACGGTTTTGCTGCGTT 61.381 50.000 0.00 0.00 0.00 4.84
79 80 1.782028 GAAGGACGGTTTTGCTGCGT 61.782 55.000 0.00 0.00 0.00 5.24
80 81 1.082104 GAAGGACGGTTTTGCTGCG 60.082 57.895 0.00 0.00 0.00 5.18
81 82 0.317854 GTGAAGGACGGTTTTGCTGC 60.318 55.000 0.00 0.00 0.00 5.25
82 83 0.310854 GGTGAAGGACGGTTTTGCTG 59.689 55.000 0.00 0.00 0.00 4.41
83 84 0.822121 GGGTGAAGGACGGTTTTGCT 60.822 55.000 0.00 0.00 0.00 3.91
84 85 1.658114 GGGTGAAGGACGGTTTTGC 59.342 57.895 0.00 0.00 0.00 3.68
85 86 1.946267 CGGGTGAAGGACGGTTTTG 59.054 57.895 0.00 0.00 0.00 2.44
86 87 1.895231 GCGGGTGAAGGACGGTTTT 60.895 57.895 0.00 0.00 0.00 2.43
87 88 2.281276 GCGGGTGAAGGACGGTTT 60.281 61.111 0.00 0.00 0.00 3.27
88 89 3.109592 TTGCGGGTGAAGGACGGTT 62.110 57.895 0.00 0.00 0.00 4.44
89 90 3.530910 CTTGCGGGTGAAGGACGGT 62.531 63.158 0.00 0.00 0.00 4.83
90 91 2.742372 CTTGCGGGTGAAGGACGG 60.742 66.667 0.00 0.00 0.00 4.79
91 92 2.742372 CCTTGCGGGTGAAGGACG 60.742 66.667 0.00 0.00 42.44 4.79
92 93 2.747686 TCCTTGCGGGTGAAGGAC 59.252 61.111 0.00 0.00 43.39 3.85
93 94 1.072505 GTTCCTTGCGGGTGAAGGA 59.927 57.895 0.00 0.00 45.99 3.36
94 95 1.971695 GGTTCCTTGCGGGTGAAGG 60.972 63.158 0.00 0.00 41.36 3.46
95 96 1.228124 TGGTTCCTTGCGGGTGAAG 60.228 57.895 0.00 0.00 36.25 3.02
96 97 1.527380 GTGGTTCCTTGCGGGTGAA 60.527 57.895 0.00 0.00 36.25 3.18
97 98 2.112297 GTGGTTCCTTGCGGGTGA 59.888 61.111 0.00 0.00 36.25 4.02
98 99 2.983592 GGTGGTTCCTTGCGGGTG 60.984 66.667 0.00 0.00 36.25 4.61
99 100 4.280019 GGGTGGTTCCTTGCGGGT 62.280 66.667 0.00 0.00 36.25 5.28
102 103 3.920093 GAGGGGGTGGTTCCTTGCG 62.920 68.421 0.00 0.00 36.25 4.85
103 104 2.035783 GAGGGGGTGGTTCCTTGC 59.964 66.667 0.00 0.00 36.25 4.01
104 105 1.725169 TTGGAGGGGGTGGTTCCTTG 61.725 60.000 0.00 0.00 36.25 3.61
105 106 1.002242 TTTGGAGGGGGTGGTTCCTT 61.002 55.000 0.00 0.00 36.25 3.36
106 107 0.780090 ATTTGGAGGGGGTGGTTCCT 60.780 55.000 0.00 0.00 36.25 3.36
107 108 0.324368 GATTTGGAGGGGGTGGTTCC 60.324 60.000 0.00 0.00 0.00 3.62
108 109 0.324368 GGATTTGGAGGGGGTGGTTC 60.324 60.000 0.00 0.00 0.00 3.62
109 110 1.781001 GGATTTGGAGGGGGTGGTT 59.219 57.895 0.00 0.00 0.00 3.67
110 111 2.246126 GGGATTTGGAGGGGGTGGT 61.246 63.158 0.00 0.00 0.00 4.16
111 112 2.689813 GGGATTTGGAGGGGGTGG 59.310 66.667 0.00 0.00 0.00 4.61
112 113 2.689813 GGGGATTTGGAGGGGGTG 59.310 66.667 0.00 0.00 0.00 4.61
113 114 2.620464 GGGGGATTTGGAGGGGGT 60.620 66.667 0.00 0.00 0.00 4.95
114 115 2.620137 TGGGGGATTTGGAGGGGG 60.620 66.667 0.00 0.00 0.00 5.40
115 116 2.228841 CTGTGGGGGATTTGGAGGGG 62.229 65.000 0.00 0.00 0.00 4.79
116 117 1.307647 CTGTGGGGGATTTGGAGGG 59.692 63.158 0.00 0.00 0.00 4.30
117 118 1.307647 CCTGTGGGGGATTTGGAGG 59.692 63.158 0.00 0.00 0.00 4.30
118 119 1.380380 GCCTGTGGGGGATTTGGAG 60.380 63.158 0.00 0.00 35.12 3.86
119 120 2.770130 GCCTGTGGGGGATTTGGA 59.230 61.111 0.00 0.00 35.12 3.53
120 121 2.364186 GGCCTGTGGGGGATTTGG 60.364 66.667 0.00 0.00 35.12 3.28
121 122 2.364186 GGGCCTGTGGGGGATTTG 60.364 66.667 0.84 0.00 35.12 2.32
122 123 2.868566 TGGGCCTGTGGGGGATTT 60.869 61.111 4.53 0.00 35.12 2.17
123 124 3.672503 GTGGGCCTGTGGGGGATT 61.673 66.667 4.53 0.00 35.12 3.01
128 129 4.974721 GTGGTGTGGGCCTGTGGG 62.975 72.222 4.53 0.00 0.00 4.61
129 130 4.974721 GGTGGTGTGGGCCTGTGG 62.975 72.222 4.53 0.00 0.00 4.17
130 131 4.974721 GGGTGGTGTGGGCCTGTG 62.975 72.222 4.53 0.00 0.00 3.66
136 137 2.305314 TTTTGGAGGGGTGGTGTGGG 62.305 60.000 0.00 0.00 0.00 4.61
137 138 0.397816 TTTTTGGAGGGGTGGTGTGG 60.398 55.000 0.00 0.00 0.00 4.17
138 139 3.215671 TTTTTGGAGGGGTGGTGTG 57.784 52.632 0.00 0.00 0.00 3.82
155 156 1.673329 GCGTTGGTGTGGGTTTTGTTT 60.673 47.619 0.00 0.00 0.00 2.83
156 157 0.108567 GCGTTGGTGTGGGTTTTGTT 60.109 50.000 0.00 0.00 0.00 2.83
157 158 1.251527 TGCGTTGGTGTGGGTTTTGT 61.252 50.000 0.00 0.00 0.00 2.83
158 159 0.103937 ATGCGTTGGTGTGGGTTTTG 59.896 50.000 0.00 0.00 0.00 2.44
159 160 0.387565 GATGCGTTGGTGTGGGTTTT 59.612 50.000 0.00 0.00 0.00 2.43
160 161 1.460273 GGATGCGTTGGTGTGGGTTT 61.460 55.000 0.00 0.00 0.00 3.27
161 162 1.901464 GGATGCGTTGGTGTGGGTT 60.901 57.895 0.00 0.00 0.00 4.11
162 163 2.282180 GGATGCGTTGGTGTGGGT 60.282 61.111 0.00 0.00 0.00 4.51
173 174 2.560861 CCGTGTGGTTTGGATGCG 59.439 61.111 0.00 0.00 0.00 4.73
174 175 2.258286 GCCGTGTGGTTTGGATGC 59.742 61.111 0.00 0.00 37.67 3.91
303 307 1.753463 CGGCCTCGAAGTAGGTCCT 60.753 63.158 0.00 0.00 38.05 3.85
651 665 3.499737 CAAGCATCGCCACGGGAC 61.500 66.667 0.00 0.00 0.00 4.46
672 686 5.063880 GGAAGGAAACACATCTGTAACTGT 58.936 41.667 0.00 0.00 0.00 3.55
674 688 5.308825 CAGGAAGGAAACACATCTGTAACT 58.691 41.667 0.00 0.00 0.00 2.24
733 747 5.774690 ACACAATCCACAGTAAATTCCACAT 59.225 36.000 0.00 0.00 0.00 3.21
734 748 5.009510 CACACAATCCACAGTAAATTCCACA 59.990 40.000 0.00 0.00 0.00 4.17
738 778 6.312399 TCACACACAATCCACAGTAAATTC 57.688 37.500 0.00 0.00 0.00 2.17
744 784 3.250762 CGATTTCACACACAATCCACAGT 59.749 43.478 0.00 0.00 0.00 3.55
749 789 5.106555 ACATCTTCGATTTCACACACAATCC 60.107 40.000 0.00 0.00 0.00 3.01
750 790 5.931532 ACATCTTCGATTTCACACACAATC 58.068 37.500 0.00 0.00 0.00 2.67
759 799 6.594937 TGATGATCACAACATCTTCGATTTCA 59.405 34.615 0.00 0.00 42.89 2.69
760 800 7.008440 TGATGATCACAACATCTTCGATTTC 57.992 36.000 0.00 0.00 42.89 2.17
761 801 6.990341 TGATGATCACAACATCTTCGATTT 57.010 33.333 0.00 0.00 42.89 2.17
762 802 6.457934 GCTTGATGATCACAACATCTTCGATT 60.458 38.462 0.00 0.00 42.89 3.34
771 811 4.644498 TCAGAAGCTTGATGATCACAACA 58.356 39.130 2.10 0.00 0.00 3.33
781 821 3.314635 GCAAATCGGATCAGAAGCTTGAT 59.685 43.478 2.10 1.06 40.40 2.57
782 822 2.679837 GCAAATCGGATCAGAAGCTTGA 59.320 45.455 2.10 0.00 0.00 3.02
783 823 2.681848 AGCAAATCGGATCAGAAGCTTG 59.318 45.455 2.10 11.09 0.00 4.01
784 824 2.681848 CAGCAAATCGGATCAGAAGCTT 59.318 45.455 14.71 0.00 0.00 3.74
786 826 2.012673 ACAGCAAATCGGATCAGAAGC 58.987 47.619 0.00 5.05 0.00 3.86
813 875 6.438259 TGATTCAGAACTACTCCTACTTCG 57.562 41.667 0.00 0.00 0.00 3.79
815 877 6.603997 ACGATGATTCAGAACTACTCCTACTT 59.396 38.462 0.00 0.00 0.00 2.24
816 878 6.038825 CACGATGATTCAGAACTACTCCTACT 59.961 42.308 0.00 0.00 0.00 2.57
817 879 6.202937 CACGATGATTCAGAACTACTCCTAC 58.797 44.000 0.00 0.00 0.00 3.18
818 880 5.221067 GCACGATGATTCAGAACTACTCCTA 60.221 44.000 0.00 0.00 0.00 2.94
819 881 4.440802 GCACGATGATTCAGAACTACTCCT 60.441 45.833 0.00 0.00 0.00 3.69
820 882 3.799420 GCACGATGATTCAGAACTACTCC 59.201 47.826 0.00 0.00 0.00 3.85
821 883 4.677584 AGCACGATGATTCAGAACTACTC 58.322 43.478 0.00 0.00 0.00 2.59
822 884 4.440802 GGAGCACGATGATTCAGAACTACT 60.441 45.833 0.00 0.00 0.00 2.57
823 885 3.799420 GGAGCACGATGATTCAGAACTAC 59.201 47.826 0.00 0.00 0.00 2.73
824 886 3.181475 GGGAGCACGATGATTCAGAACTA 60.181 47.826 0.00 0.00 0.00 2.24
825 887 2.419297 GGGAGCACGATGATTCAGAACT 60.419 50.000 0.00 0.00 0.00 3.01
826 888 1.936547 GGGAGCACGATGATTCAGAAC 59.063 52.381 0.00 0.00 0.00 3.01
827 889 1.471501 CGGGAGCACGATGATTCAGAA 60.472 52.381 0.00 0.00 35.47 3.02
828 890 0.103026 CGGGAGCACGATGATTCAGA 59.897 55.000 0.00 0.00 35.47 3.27
829 891 0.103026 TCGGGAGCACGATGATTCAG 59.897 55.000 0.00 0.00 38.06 3.02
830 892 2.198183 TCGGGAGCACGATGATTCA 58.802 52.632 0.00 0.00 38.06 2.57
838 900 1.594862 GAATTTCAGATCGGGAGCACG 59.405 52.381 0.00 0.00 0.00 5.34
839 901 2.611292 CAGAATTTCAGATCGGGAGCAC 59.389 50.000 0.00 0.00 0.00 4.40
840 902 2.501316 TCAGAATTTCAGATCGGGAGCA 59.499 45.455 0.00 0.00 0.00 4.26
841 903 3.185246 TCAGAATTTCAGATCGGGAGC 57.815 47.619 0.00 0.00 0.00 4.70
842 904 4.507710 TGTTCAGAATTTCAGATCGGGAG 58.492 43.478 0.00 0.00 0.00 4.30
843 905 4.020218 ACTGTTCAGAATTTCAGATCGGGA 60.020 41.667 6.83 0.00 0.00 5.14
844 906 4.256920 ACTGTTCAGAATTTCAGATCGGG 58.743 43.478 6.83 3.87 0.00 5.14
845 907 5.445142 CGAACTGTTCAGAATTTCAGATCGG 60.445 44.000 19.56 3.61 43.80 4.18
846 908 5.545527 CGAACTGTTCAGAATTTCAGATCG 58.454 41.667 19.56 13.79 42.81 3.69
847 909 5.121454 AGCGAACTGTTCAGAATTTCAGATC 59.879 40.000 19.56 3.70 0.00 2.75
848 910 4.999950 AGCGAACTGTTCAGAATTTCAGAT 59.000 37.500 19.56 0.00 0.00 2.90
849 911 4.212004 CAGCGAACTGTTCAGAATTTCAGA 59.788 41.667 19.56 0.00 39.22 3.27
850 912 4.461405 CAGCGAACTGTTCAGAATTTCAG 58.539 43.478 19.56 2.23 39.22 3.02
851 913 3.303990 GCAGCGAACTGTTCAGAATTTCA 60.304 43.478 19.56 0.00 46.30 2.69
852 914 3.058639 AGCAGCGAACTGTTCAGAATTTC 60.059 43.478 19.56 2.99 46.30 2.17
853 915 2.880890 AGCAGCGAACTGTTCAGAATTT 59.119 40.909 19.56 0.00 46.30 1.82
854 916 2.498167 AGCAGCGAACTGTTCAGAATT 58.502 42.857 19.56 0.43 46.30 2.17
855 917 2.175878 AGCAGCGAACTGTTCAGAAT 57.824 45.000 19.56 0.34 46.30 2.40
856 918 3.686622 AGCAGCGAACTGTTCAGAA 57.313 47.368 19.56 0.00 46.30 3.02
861 923 0.947244 CCAAAGAGCAGCGAACTGTT 59.053 50.000 0.00 0.00 46.30 3.16
862 924 0.179045 ACCAAAGAGCAGCGAACTGT 60.179 50.000 0.00 0.00 46.30 3.55
864 926 0.886490 CCACCAAAGAGCAGCGAACT 60.886 55.000 0.00 0.00 0.00 3.01
865 927 1.576421 CCACCAAAGAGCAGCGAAC 59.424 57.895 0.00 0.00 0.00 3.95
866 928 2.260869 GCCACCAAAGAGCAGCGAA 61.261 57.895 0.00 0.00 0.00 4.70
867 929 2.669569 GCCACCAAAGAGCAGCGA 60.670 61.111 0.00 0.00 0.00 4.93
868 930 3.741476 GGCCACCAAAGAGCAGCG 61.741 66.667 0.00 0.00 0.00 5.18
869 931 2.282745 AGGCCACCAAAGAGCAGC 60.283 61.111 5.01 0.00 0.00 5.25
870 932 1.975407 CCAGGCCACCAAAGAGCAG 60.975 63.158 5.01 0.00 0.00 4.24
871 933 2.115910 CCAGGCCACCAAAGAGCA 59.884 61.111 5.01 0.00 0.00 4.26
872 934 2.116125 ACCAGGCCACCAAAGAGC 59.884 61.111 5.01 0.00 0.00 4.09
873 935 2.270986 GCACCAGGCCACCAAAGAG 61.271 63.158 5.01 0.00 36.11 2.85
874 936 2.203480 GCACCAGGCCACCAAAGA 60.203 61.111 5.01 0.00 36.11 2.52
900 962 2.280524 TGGTTGGGTTGCGACTCG 60.281 61.111 3.59 0.00 0.00 4.18
901 963 1.966451 CCTGGTTGGGTTGCGACTC 60.966 63.158 3.59 0.00 0.00 3.36
902 964 2.113139 CCTGGTTGGGTTGCGACT 59.887 61.111 3.59 0.00 0.00 4.18
903 965 2.203294 ACCTGGTTGGGTTGCGAC 60.203 61.111 0.00 0.00 41.11 5.19
904 966 2.112297 GACCTGGTTGGGTTGCGA 59.888 61.111 0.00 0.00 40.06 5.10
1073 1149 3.860605 CGTGGATGGATCGGGCCA 61.861 66.667 4.39 0.00 43.23 5.36
1119 1195 3.649277 CTTGGAGAGGTGGCGGTCG 62.649 68.421 0.00 0.00 0.00 4.79
1156 1232 2.278013 GTCGTCGTCGAGGATGGC 60.278 66.667 23.17 19.53 46.96 4.40
1260 1336 3.691342 TCGGGCCACTCGAACAGG 61.691 66.667 4.39 0.00 33.42 4.00
1477 1553 2.440817 GGGGTGTGGGGATCTACGG 61.441 68.421 0.00 0.00 0.00 4.02
1577 1665 7.959109 CACATCACATAAATATTCGCACATAGG 59.041 37.037 0.00 0.00 0.00 2.57
1584 1672 6.714492 TGTGTCACATCACATAAATATTCGC 58.286 36.000 0.18 0.00 42.36 4.70
1590 1678 9.932207 ATTCATTTTGTGTCACATCACATAAAT 57.068 25.926 6.48 5.92 45.73 1.40
1594 1682 6.146510 GCAATTCATTTTGTGTCACATCACAT 59.853 34.615 6.48 0.00 45.73 3.21
1602 1690 8.523523 CTTCATAAGCAATTCATTTTGTGTCA 57.476 30.769 0.00 0.00 0.00 3.58
1634 1723 2.762327 GGGCATGACAATTGACAAGGAT 59.238 45.455 13.59 0.00 0.00 3.24
1644 1733 4.785346 AGATAGAACAGGGCATGACAAT 57.215 40.909 5.99 0.00 0.00 2.71
1645 1734 4.574674 AAGATAGAACAGGGCATGACAA 57.425 40.909 5.99 0.00 0.00 3.18
1646 1735 4.264253 CAAAGATAGAACAGGGCATGACA 58.736 43.478 5.99 0.00 0.00 3.58
1647 1736 3.065925 GCAAAGATAGAACAGGGCATGAC 59.934 47.826 5.99 0.00 0.00 3.06
1648 1737 3.282021 GCAAAGATAGAACAGGGCATGA 58.718 45.455 5.99 0.00 0.00 3.07
1649 1738 2.360165 GGCAAAGATAGAACAGGGCATG 59.640 50.000 0.00 0.00 0.00 4.06
1650 1739 2.025037 TGGCAAAGATAGAACAGGGCAT 60.025 45.455 0.00 0.00 0.00 4.40
1656 1745 6.489700 TCACATTTCTTGGCAAAGATAGAACA 59.510 34.615 3.86 0.00 42.04 3.18
1696 1785 6.987404 TCATACATGGATCAAATGCAAAATGG 59.013 34.615 0.00 0.00 33.18 3.16
1704 1793 9.620660 CACAATACATCATACATGGATCAAATG 57.379 33.333 0.00 6.17 0.00 2.32
1773 1880 7.964559 CGATGATGTGATGTACAAAGTCAATTT 59.035 33.333 0.00 0.00 43.77 1.82
1798 1905 5.229260 GCCTTTTTGACTTTTGTAACTGACG 59.771 40.000 0.00 0.00 0.00 4.35
1819 1926 1.673168 GATTGGAAGAAGCATCGCCT 58.327 50.000 5.68 0.00 0.00 5.52
1825 1932 1.347707 ACTCACGGATTGGAAGAAGCA 59.652 47.619 0.00 0.00 0.00 3.91
1839 1955 2.868583 CTGGCAATGGAGATTACTCACG 59.131 50.000 0.00 0.00 44.22 4.35
1843 1959 2.928334 CTGCTGGCAATGGAGATTACT 58.072 47.619 0.00 0.00 0.00 2.24
1896 2013 3.381908 GGGATCAACTCTCATGTACTCGT 59.618 47.826 0.00 0.00 0.00 4.18
1920 2043 8.204160 CAGTACAATCTTCAGGGAACATACATA 58.796 37.037 0.00 0.00 0.00 2.29
1976 2101 5.762179 TCTGATCCTCCTTTGCTCTAAAA 57.238 39.130 0.00 0.00 0.00 1.52
1992 2117 4.934001 TCACACAGCTTCTGAATTCTGATC 59.066 41.667 19.81 10.33 35.18 2.92
2016 2141 4.621510 GCTGGTATGTCACAGATTCAGACA 60.622 45.833 9.15 8.42 45.26 3.41
2147 2273 2.413142 GGATGGGTCTTGCTGCTGC 61.413 63.158 8.89 8.89 40.20 5.25
2159 2285 2.645838 ATCACCAATTCTCGGATGGG 57.354 50.000 0.84 0.00 38.58 4.00
2165 2291 8.370493 ACACAAATATCTATCACCAATTCTCG 57.630 34.615 0.00 0.00 0.00 4.04
2195 2321 3.154589 GGGACGGAGGATTGTTGTC 57.845 57.895 0.00 0.00 0.00 3.18
2348 2474 0.390472 CGAGGAGAACAACAGAGCCC 60.390 60.000 0.00 0.00 0.00 5.19
2447 2573 3.118334 ACCCTCAGAGCAAGATGATTCAG 60.118 47.826 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.