Multiple sequence alignment - TraesCS5D01G483400

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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 TraesCS5D01G483400 chr5D 100.000 3611 0 0 1 3611 520202085 520198475 0.000000e+00 6669
1 TraesCS5D01G483400 chr5D 82.540 315 33 18 249 551 270239143 270239447 1.290000e-64 257
2 TraesCS5D01G483400 chr5D 77.778 261 40 16 413 664 342964459 342964208 1.040000e-30 145
3 TraesCS5D01G483400 chr5D 75.134 374 54 30 317 664 457263179 457263539 4.860000e-29 139
4 TraesCS5D01G483400 chr5A 88.395 2697 243 38 945 3611 647487952 647485296 0.000000e+00 3182
5 TraesCS5D01G483400 chr5B 91.473 1935 89 23 900 2800 655210657 655208765 0.000000e+00 2590
6 TraesCS5D01G483400 chr5B 89.908 436 27 8 3185 3611 655208342 655207915 2.450000e-151 545
7 TraesCS5D01G483400 chr5B 91.943 211 16 1 2799 3009 655208735 655208526 9.800000e-76 294
8 TraesCS5D01G483400 chr5B 90.476 105 9 1 3077 3181 655208509 655208406 1.750000e-28 137
9 TraesCS5D01G483400 chr3A 91.462 1792 126 11 939 2714 170977274 170979054 0.000000e+00 2436
10 TraesCS5D01G483400 chr3A 93.152 920 44 5 2709 3611 170979902 170980819 0.000000e+00 1332
11 TraesCS5D01G483400 chr7B 77.818 550 81 29 126 660 684933015 684933538 5.860000e-78 302
12 TraesCS5D01G483400 chr7A 78.867 459 70 21 200 641 206587205 206586757 5.900000e-73 285
13 TraesCS5D01G483400 chr7A 82.011 189 23 9 376 554 691445755 691445942 2.250000e-32 150
14 TraesCS5D01G483400 chr1B 77.342 459 65 27 232 666 576512484 576512041 6.030000e-58 235
15 TraesCS5D01G483400 chr1A 77.199 307 55 12 370 664 128640389 128640086 8.020000e-37 165
16 TraesCS5D01G483400 chr1A 77.818 275 45 13 398 664 45553472 45553738 4.830000e-34 156
17 TraesCS5D01G483400 chr4D 77.580 281 47 14 394 663 3750893 3751168 4.830000e-34 156
18 TraesCS5D01G483400 chr2B 79.907 214 35 8 406 612 772345106 772345318 2.250000e-32 150


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 TraesCS5D01G483400 chr5D 520198475 520202085 3610 True 6669.0 6669 100.000 1 3611 1 chr5D.!!$R2 3610
1 TraesCS5D01G483400 chr5A 647485296 647487952 2656 True 3182.0 3182 88.395 945 3611 1 chr5A.!!$R1 2666
2 TraesCS5D01G483400 chr5B 655207915 655210657 2742 True 891.5 2590 90.950 900 3611 4 chr5B.!!$R1 2711
3 TraesCS5D01G483400 chr3A 170977274 170980819 3545 False 1884.0 2436 92.307 939 3611 2 chr3A.!!$F1 2672
4 TraesCS5D01G483400 chr7B 684933015 684933538 523 False 302.0 302 77.818 126 660 1 chr7B.!!$F1 534

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
61 62 0.039165 CGGCAAAAAGAGTGGAAGGC 60.039 55.0 0.00 0.0 0.00 4.35 F
704 732 0.104777 ATGGGATCTGGGCAGAGCTA 60.105 55.0 0.00 0.0 42.99 3.32 F
863 891 0.312416 CCCGAGCGGAGAGAATACAG 59.688 60.0 11.05 0.0 37.50 2.74 F
864 892 0.312416 CCGAGCGGAGAGAATACAGG 59.688 60.0 2.00 0.0 37.50 4.00 F
868 896 0.389757 GCGGAGAGAATACAGGACCC 59.610 60.0 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 1052 0.035725 TGAGGCTACGACGGAGAAGA 60.036 55.000 12.38 0.00 0.00 2.87 R
1931 1991 0.035820 GGCCATCGTAGTTGGACCAA 60.036 55.000 1.69 1.69 36.14 3.67 R
2190 2250 0.396695 CAGCATGAGGAGGCCCAAAT 60.397 55.000 0.00 0.00 39.69 2.32 R
2307 2367 2.692557 CCAAATGTTCAACACTGTCCCA 59.307 45.455 0.00 0.00 0.00 4.37 R
2633 2700 3.129287 GGAACTGACCAGCATACCAAATG 59.871 47.826 0.00 0.00 0.00 2.32 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
17 18 4.573162 GTCGTAGCACACTCACCC 57.427 61.111 0.00 0.00 0.00 4.61
18 19 1.443872 GTCGTAGCACACTCACCCG 60.444 63.158 0.00 0.00 0.00 5.28
19 20 2.809601 CGTAGCACACTCACCCGC 60.810 66.667 0.00 0.00 0.00 6.13
20 21 2.434359 GTAGCACACTCACCCGCC 60.434 66.667 0.00 0.00 0.00 6.13
21 22 3.702048 TAGCACACTCACCCGCCC 61.702 66.667 0.00 0.00 0.00 6.13
24 25 4.248842 CACACTCACCCGCCCACA 62.249 66.667 0.00 0.00 0.00 4.17
25 26 3.249189 ACACTCACCCGCCCACAT 61.249 61.111 0.00 0.00 0.00 3.21
26 27 2.436646 CACTCACCCGCCCACATC 60.437 66.667 0.00 0.00 0.00 3.06
27 28 2.927856 ACTCACCCGCCCACATCA 60.928 61.111 0.00 0.00 0.00 3.07
28 29 2.436646 CTCACCCGCCCACATCAC 60.437 66.667 0.00 0.00 0.00 3.06
29 30 4.386951 TCACCCGCCCACATCACG 62.387 66.667 0.00 0.00 0.00 4.35
36 37 3.055719 CCCACATCACGGTGCCAC 61.056 66.667 2.51 0.00 37.46 5.01
37 38 2.281414 CCACATCACGGTGCCACA 60.281 61.111 2.51 0.00 37.46 4.17
38 39 2.327343 CCACATCACGGTGCCACAG 61.327 63.158 2.51 0.00 37.46 3.66
39 40 2.669569 ACATCACGGTGCCACAGC 60.670 61.111 2.51 0.00 40.48 4.40
40 41 3.434319 CATCACGGTGCCACAGCC 61.434 66.667 2.51 0.00 38.69 4.85
41 42 3.952508 ATCACGGTGCCACAGCCA 61.953 61.111 2.51 0.00 38.69 4.75
42 43 4.927782 TCACGGTGCCACAGCCAC 62.928 66.667 2.51 0.00 38.69 5.01
50 51 2.811101 CCACAGCCACGGCAAAAA 59.189 55.556 11.35 0.00 44.88 1.94
51 52 1.300080 CCACAGCCACGGCAAAAAG 60.300 57.895 11.35 0.00 44.88 2.27
52 53 1.732917 CACAGCCACGGCAAAAAGA 59.267 52.632 11.35 0.00 44.88 2.52
53 54 0.318107 CACAGCCACGGCAAAAAGAG 60.318 55.000 11.35 0.00 44.88 2.85
54 55 0.751643 ACAGCCACGGCAAAAAGAGT 60.752 50.000 11.35 0.00 44.88 3.24
55 56 0.318107 CAGCCACGGCAAAAAGAGTG 60.318 55.000 11.35 0.00 44.88 3.51
59 60 2.405892 CACGGCAAAAAGAGTGGAAG 57.594 50.000 0.00 0.00 0.00 3.46
60 61 1.001378 CACGGCAAAAAGAGTGGAAGG 60.001 52.381 0.00 0.00 0.00 3.46
61 62 0.039165 CGGCAAAAAGAGTGGAAGGC 60.039 55.000 0.00 0.00 0.00 4.35
62 63 0.039165 GGCAAAAAGAGTGGAAGGCG 60.039 55.000 0.00 0.00 0.00 5.52
63 64 0.668535 GCAAAAAGAGTGGAAGGCGT 59.331 50.000 0.00 0.00 0.00 5.68
64 65 1.335051 GCAAAAAGAGTGGAAGGCGTC 60.335 52.381 0.00 0.00 0.00 5.19
75 76 3.069778 AGGCGTCCCCTTTGACTC 58.930 61.111 0.00 0.00 43.06 3.36
76 77 2.046217 GGCGTCCCCTTTGACTCC 60.046 66.667 0.00 0.00 33.37 3.85
77 78 2.593956 GGCGTCCCCTTTGACTCCT 61.594 63.158 0.00 0.00 37.20 3.69
78 79 1.262640 GGCGTCCCCTTTGACTCCTA 61.263 60.000 0.00 0.00 37.20 2.94
79 80 0.175989 GCGTCCCCTTTGACTCCTAG 59.824 60.000 0.00 0.00 32.97 3.02
80 81 0.175989 CGTCCCCTTTGACTCCTAGC 59.824 60.000 0.00 0.00 32.97 3.42
81 82 0.542333 GTCCCCTTTGACTCCTAGCC 59.458 60.000 0.00 0.00 32.39 3.93
82 83 0.620700 TCCCCTTTGACTCCTAGCCC 60.621 60.000 0.00 0.00 0.00 5.19
83 84 0.914417 CCCCTTTGACTCCTAGCCCA 60.914 60.000 0.00 0.00 0.00 5.36
84 85 0.991920 CCCTTTGACTCCTAGCCCAA 59.008 55.000 0.00 0.00 0.00 4.12
85 86 1.354368 CCCTTTGACTCCTAGCCCAAA 59.646 52.381 0.00 0.00 0.00 3.28
86 87 2.225017 CCCTTTGACTCCTAGCCCAAAA 60.225 50.000 0.00 0.00 0.00 2.44
87 88 3.564352 CCCTTTGACTCCTAGCCCAAAAT 60.564 47.826 0.00 0.00 0.00 1.82
88 89 3.696548 CCTTTGACTCCTAGCCCAAAATC 59.303 47.826 0.00 0.00 0.00 2.17
89 90 4.335416 CTTTGACTCCTAGCCCAAAATCA 58.665 43.478 0.00 0.00 0.00 2.57
90 91 3.634397 TGACTCCTAGCCCAAAATCAG 57.366 47.619 0.00 0.00 0.00 2.90
91 92 2.293170 GACTCCTAGCCCAAAATCAGC 58.707 52.381 0.00 0.00 0.00 4.26
92 93 1.064389 ACTCCTAGCCCAAAATCAGCC 60.064 52.381 0.00 0.00 0.00 4.85
93 94 0.998928 TCCTAGCCCAAAATCAGCCA 59.001 50.000 0.00 0.00 0.00 4.75
94 95 1.106285 CCTAGCCCAAAATCAGCCAC 58.894 55.000 0.00 0.00 0.00 5.01
95 96 0.734889 CTAGCCCAAAATCAGCCACG 59.265 55.000 0.00 0.00 0.00 4.94
96 97 0.679640 TAGCCCAAAATCAGCCACGG 60.680 55.000 0.00 0.00 0.00 4.94
97 98 3.005540 GCCCAAAATCAGCCACGGG 62.006 63.158 0.00 0.00 36.71 5.28
98 99 2.350458 CCCAAAATCAGCCACGGGG 61.350 63.158 0.00 0.00 37.18 5.73
99 100 1.606313 CCAAAATCAGCCACGGGGT 60.606 57.895 5.12 0.00 36.17 4.95
100 101 1.595093 CCAAAATCAGCCACGGGGTC 61.595 60.000 5.12 0.00 36.17 4.46
101 102 0.609131 CAAAATCAGCCACGGGGTCT 60.609 55.000 5.12 0.00 36.17 3.85
102 103 0.609131 AAAATCAGCCACGGGGTCTG 60.609 55.000 18.64 18.64 38.73 3.51
103 104 2.484287 AAATCAGCCACGGGGTCTGG 62.484 60.000 22.58 6.48 38.25 3.86
108 109 3.246112 CCACGGGGTCTGGGTTGA 61.246 66.667 0.00 0.00 0.00 3.18
109 110 2.602676 CCACGGGGTCTGGGTTGAT 61.603 63.158 0.00 0.00 0.00 2.57
110 111 1.377202 CACGGGGTCTGGGTTGATG 60.377 63.158 0.00 0.00 0.00 3.07
111 112 2.438434 CGGGGTCTGGGTTGATGC 60.438 66.667 0.00 0.00 0.00 3.91
112 113 2.043953 GGGGTCTGGGTTGATGCC 60.044 66.667 0.00 0.00 0.00 4.40
113 114 2.616458 GGGGTCTGGGTTGATGCCT 61.616 63.158 0.00 0.00 0.00 4.75
114 115 1.077429 GGGTCTGGGTTGATGCCTC 60.077 63.158 0.00 0.00 0.00 4.70
115 116 1.077429 GGTCTGGGTTGATGCCTCC 60.077 63.158 0.00 0.00 0.00 4.30
116 117 1.685224 GTCTGGGTTGATGCCTCCA 59.315 57.895 0.00 0.00 0.00 3.86
117 118 0.678048 GTCTGGGTTGATGCCTCCAC 60.678 60.000 0.00 0.00 0.00 4.02
118 119 1.379044 CTGGGTTGATGCCTCCACC 60.379 63.158 3.90 3.90 36.64 4.61
119 120 2.141011 CTGGGTTGATGCCTCCACCA 62.141 60.000 13.18 5.64 38.64 4.17
120 121 1.307647 GGGTTGATGCCTCCACCAT 59.692 57.895 13.18 0.00 38.64 3.55
121 122 0.550914 GGGTTGATGCCTCCACCATA 59.449 55.000 13.18 0.00 38.64 2.74
122 123 1.477558 GGGTTGATGCCTCCACCATAG 60.478 57.143 13.18 0.00 38.64 2.23
123 124 1.477558 GGTTGATGCCTCCACCATAGG 60.478 57.143 7.29 0.00 37.20 2.57
124 125 1.490490 GTTGATGCCTCCACCATAGGA 59.510 52.381 0.00 0.00 36.08 2.94
131 132 2.402564 CCTCCACCATAGGATGTGTCT 58.597 52.381 0.00 0.00 36.99 3.41
132 133 2.103771 CCTCCACCATAGGATGTGTCTG 59.896 54.545 0.00 0.00 36.99 3.51
137 138 2.168521 ACCATAGGATGTGTCTGGTTCG 59.831 50.000 0.00 0.00 36.86 3.95
139 140 3.190079 CATAGGATGTGTCTGGTTCGTG 58.810 50.000 0.00 0.00 0.00 4.35
145 146 3.401033 TGTGTCTGGTTCGTGATGAAT 57.599 42.857 0.00 0.00 39.21 2.57
148 149 3.498397 GTGTCTGGTTCGTGATGAATTGT 59.502 43.478 0.00 0.00 39.21 2.71
152 153 3.605634 TGGTTCGTGATGAATTGTAGGG 58.394 45.455 0.00 0.00 39.21 3.53
153 154 3.008594 TGGTTCGTGATGAATTGTAGGGT 59.991 43.478 0.00 0.00 39.21 4.34
154 155 3.374058 GGTTCGTGATGAATTGTAGGGTG 59.626 47.826 0.00 0.00 39.21 4.61
157 158 1.670811 GTGATGAATTGTAGGGTGCGG 59.329 52.381 0.00 0.00 0.00 5.69
161 162 1.077716 AATTGTAGGGTGCGGCCTC 60.078 57.895 0.00 0.00 37.43 4.70
163 164 4.715130 TGTAGGGTGCGGCCTCCT 62.715 66.667 14.19 14.19 37.43 3.69
168 169 1.749258 GGGTGCGGCCTCCTTTAAG 60.749 63.158 0.00 0.00 37.43 1.85
169 170 1.749258 GGTGCGGCCTCCTTTAAGG 60.749 63.158 4.29 4.29 39.62 2.69
176 177 3.871074 GCGGCCTCCTTTAAGGTAAAAGA 60.871 47.826 11.13 0.00 38.50 2.52
189 190 4.074466 GGTAAAAGACCGATTTTGTCCG 57.926 45.455 0.00 0.00 38.87 4.79
224 225 9.651913 TTTCTTTGTTTTATTCAGTTTGCTCTT 57.348 25.926 0.00 0.00 0.00 2.85
229 230 8.001881 TGTTTTATTCAGTTTGCTCTTGGTAA 57.998 30.769 0.00 0.00 0.00 2.85
235 236 7.769272 TTCAGTTTGCTCTTGGTAATTTTTG 57.231 32.000 0.00 0.00 0.00 2.44
236 237 6.872920 TCAGTTTGCTCTTGGTAATTTTTGT 58.127 32.000 0.00 0.00 0.00 2.83
237 238 7.327214 TCAGTTTGCTCTTGGTAATTTTTGTT 58.673 30.769 0.00 0.00 0.00 2.83
238 239 7.821846 TCAGTTTGCTCTTGGTAATTTTTGTTT 59.178 29.630 0.00 0.00 0.00 2.83
239 240 8.450180 CAGTTTGCTCTTGGTAATTTTTGTTTT 58.550 29.630 0.00 0.00 0.00 2.43
409 423 7.225523 TGTCAAGAACGTTTTTCTACTACAC 57.774 36.000 0.46 0.00 0.00 2.90
410 424 6.812656 TGTCAAGAACGTTTTTCTACTACACA 59.187 34.615 0.46 0.00 0.00 3.72
411 425 7.493320 TGTCAAGAACGTTTTTCTACTACACAT 59.507 33.333 0.46 0.00 0.00 3.21
561 586 8.612619 CATGGTCTACATTTTTCCTATACACAC 58.387 37.037 0.00 0.00 37.84 3.82
593 618 9.987272 AGCTTTTTCAAATTCTTTATTAGCAGT 57.013 25.926 0.00 0.00 0.00 4.40
639 667 7.840342 TTGCTAACACATGTTCAACATTTTT 57.160 28.000 0.00 0.00 36.53 1.94
679 707 9.488124 CATTTTTCAAAATTAATATTGGCACCG 57.512 29.630 0.00 0.00 36.52 4.94
680 708 8.833231 TTTTTCAAAATTAATATTGGCACCGA 57.167 26.923 0.00 0.00 0.00 4.69
681 709 8.833231 TTTTCAAAATTAATATTGGCACCGAA 57.167 26.923 0.00 0.00 0.00 4.30
682 710 8.833231 TTTCAAAATTAATATTGGCACCGAAA 57.167 26.923 0.00 0.00 0.00 3.46
683 711 8.833231 TTCAAAATTAATATTGGCACCGAAAA 57.167 26.923 0.00 0.00 0.00 2.29
684 712 8.833231 TCAAAATTAATATTGGCACCGAAAAA 57.167 26.923 0.00 0.00 0.00 1.94
700 728 2.925966 AAAAATGGGATCTGGGCAGA 57.074 45.000 0.00 0.00 42.37 4.26
701 729 2.449137 AAAATGGGATCTGGGCAGAG 57.551 50.000 0.00 0.00 41.33 3.35
702 730 0.106318 AAATGGGATCTGGGCAGAGC 60.106 55.000 0.00 0.00 42.72 4.09
703 731 0.992431 AATGGGATCTGGGCAGAGCT 60.992 55.000 0.00 0.00 42.99 4.09
704 732 0.104777 ATGGGATCTGGGCAGAGCTA 60.105 55.000 0.00 0.00 42.99 3.32
705 733 0.762082 TGGGATCTGGGCAGAGCTAG 60.762 60.000 0.00 0.00 42.99 3.42
706 734 1.370810 GGATCTGGGCAGAGCTAGC 59.629 63.158 6.62 6.62 42.99 3.42
712 740 4.906792 GGCAGAGCTAGCCGGCTG 62.907 72.222 38.98 27.28 43.15 4.85
714 742 4.906792 CAGAGCTAGCCGGCTGCC 62.907 72.222 38.98 27.17 43.20 4.85
732 760 3.134127 GCTGCCACCAACCGGATC 61.134 66.667 9.46 0.00 35.59 3.36
733 761 2.438434 CTGCCACCAACCGGATCC 60.438 66.667 9.46 0.00 35.59 3.36
734 762 2.933287 TGCCACCAACCGGATCCT 60.933 61.111 9.46 0.00 35.59 3.24
735 763 2.355115 GCCACCAACCGGATCCTT 59.645 61.111 9.46 0.00 35.59 3.36
736 764 1.749258 GCCACCAACCGGATCCTTC 60.749 63.158 9.46 0.00 35.59 3.46
737 765 1.682849 CCACCAACCGGATCCTTCA 59.317 57.895 9.46 0.00 35.59 3.02
738 766 0.392998 CCACCAACCGGATCCTTCAG 60.393 60.000 9.46 0.00 35.59 3.02
739 767 1.026718 CACCAACCGGATCCTTCAGC 61.027 60.000 9.46 0.00 35.59 4.26
740 768 1.452108 CCAACCGGATCCTTCAGCC 60.452 63.158 9.46 0.00 0.00 4.85
741 769 1.815421 CAACCGGATCCTTCAGCCG 60.815 63.158 9.46 0.00 44.42 5.52
742 770 3.682292 AACCGGATCCTTCAGCCGC 62.682 63.158 9.46 0.00 43.52 6.53
743 771 4.918201 CCGGATCCTTCAGCCGCC 62.918 72.222 10.75 0.00 43.52 6.13
744 772 4.161295 CGGATCCTTCAGCCGCCA 62.161 66.667 10.75 0.00 38.46 5.69
745 773 2.514824 GGATCCTTCAGCCGCCAC 60.515 66.667 3.84 0.00 0.00 5.01
746 774 2.514824 GATCCTTCAGCCGCCACC 60.515 66.667 0.00 0.00 0.00 4.61
747 775 4.473520 ATCCTTCAGCCGCCACCG 62.474 66.667 0.00 0.00 0.00 4.94
814 842 4.864334 GCCAGCCCATCGTCCCTG 62.864 72.222 0.00 0.00 0.00 4.45
815 843 4.864334 CCAGCCCATCGTCCCTGC 62.864 72.222 0.00 0.00 0.00 4.85
816 844 4.864334 CAGCCCATCGTCCCTGCC 62.864 72.222 0.00 0.00 0.00 4.85
820 848 4.227134 CCATCGTCCCTGCCCGAG 62.227 72.222 0.00 0.00 36.41 4.63
821 849 4.899239 CATCGTCCCTGCCCGAGC 62.899 72.222 0.00 0.00 36.41 5.03
859 887 3.541713 GCCCCGAGCGGAGAGAAT 61.542 66.667 11.05 0.00 37.50 2.40
860 888 2.201022 GCCCCGAGCGGAGAGAATA 61.201 63.158 11.05 0.00 37.50 1.75
861 889 1.660917 CCCCGAGCGGAGAGAATAC 59.339 63.158 11.05 0.00 37.50 1.89
862 890 1.107538 CCCCGAGCGGAGAGAATACA 61.108 60.000 11.05 0.00 37.50 2.29
863 891 0.312416 CCCGAGCGGAGAGAATACAG 59.688 60.000 11.05 0.00 37.50 2.74
864 892 0.312416 CCGAGCGGAGAGAATACAGG 59.688 60.000 2.00 0.00 37.50 4.00
865 893 1.309950 CGAGCGGAGAGAATACAGGA 58.690 55.000 0.00 0.00 0.00 3.86
866 894 1.002251 CGAGCGGAGAGAATACAGGAC 60.002 57.143 0.00 0.00 0.00 3.85
867 895 1.338655 GAGCGGAGAGAATACAGGACC 59.661 57.143 0.00 0.00 0.00 4.46
868 896 0.389757 GCGGAGAGAATACAGGACCC 59.610 60.000 0.00 0.00 0.00 4.46
869 897 1.041437 CGGAGAGAATACAGGACCCC 58.959 60.000 0.00 0.00 0.00 4.95
870 898 1.688311 CGGAGAGAATACAGGACCCCA 60.688 57.143 0.00 0.00 0.00 4.96
871 899 1.763545 GGAGAGAATACAGGACCCCAC 59.236 57.143 0.00 0.00 0.00 4.61
872 900 1.763545 GAGAGAATACAGGACCCCACC 59.236 57.143 0.00 0.00 0.00 4.61
873 901 0.464452 GAGAATACAGGACCCCACCG 59.536 60.000 0.00 0.00 34.73 4.94
874 902 1.153229 GAATACAGGACCCCACCGC 60.153 63.158 0.00 0.00 34.73 5.68
875 903 2.604299 GAATACAGGACCCCACCGCC 62.604 65.000 0.00 0.00 34.73 6.13
876 904 3.935456 ATACAGGACCCCACCGCCA 62.935 63.158 0.00 0.00 34.73 5.69
932 960 2.682155 GGATCACCCTCTGACTTGAC 57.318 55.000 0.00 0.00 0.00 3.18
995 1033 2.725203 TTCCAAACTCCGGTGAGCGG 62.725 60.000 18.22 18.22 42.74 5.52
1003 1041 2.480555 CGGTGAGCGGACAAATGC 59.519 61.111 0.00 0.00 0.00 3.56
1011 1049 2.679996 GGACAAATGCCCCGCCTT 60.680 61.111 0.00 0.00 0.00 4.35
1014 1052 1.228862 ACAAATGCCCCGCCTTCTT 60.229 52.632 0.00 0.00 0.00 2.52
1139 1177 1.196766 ACTCCCCTTCACCCCGTTAC 61.197 60.000 0.00 0.00 0.00 2.50
1181 1219 3.430497 TCCTCCCCCTCCTCCTCG 61.430 72.222 0.00 0.00 0.00 4.63
1183 1221 4.465446 CTCCCCCTCCTCCTCGCA 62.465 72.222 0.00 0.00 0.00 5.10
1293 1331 4.458829 TCCTCCACGGGCCTCGAT 62.459 66.667 18.74 2.53 42.43 3.59
1426 1464 3.241963 CGTACATACCTGCAACATTGTCG 60.242 47.826 0.00 0.00 0.00 4.35
1431 1469 1.202639 ACCTGCAACATTGTCGTCAGA 60.203 47.619 11.91 0.00 0.00 3.27
1457 1495 1.339535 GGGCAGGAGGAAGTTCTTCAG 60.340 57.143 16.01 9.24 0.00 3.02
1605 1643 1.133792 AGCGACCAATTTGGGATAGGG 60.134 52.381 19.39 3.43 43.37 3.53
1606 1644 1.981256 CGACCAATTTGGGATAGGGG 58.019 55.000 19.39 0.00 43.37 4.79
1615 1653 1.230212 GGGATAGGGGTTGGGCAAG 59.770 63.158 0.00 0.00 0.00 4.01
1642 1680 2.834549 CACAGAAAGGAGGCCTTCTCTA 59.165 50.000 16.01 0.00 43.92 2.43
1707 1767 1.213013 CTCGCTTGTACAGGTCGCT 59.787 57.895 13.98 0.00 0.00 4.93
1710 1770 2.445438 GCTTGTACAGGTCGCTCGC 61.445 63.158 6.86 0.00 0.00 5.03
1714 1774 3.506096 TACAGGTCGCTCGCGGAG 61.506 66.667 6.13 3.47 40.25 4.63
1875 1935 0.690744 TCATCGAGGCATTGGGGAGA 60.691 55.000 0.00 0.00 0.00 3.71
1931 1991 3.766051 GAGAAAATGGTGCAAGAGGGATT 59.234 43.478 0.00 0.00 0.00 3.01
1958 2018 3.531538 CAACTACGATGGCCTACAATGT 58.468 45.455 3.32 0.00 0.00 2.71
2190 2250 1.689984 TCATTGAGCCACTTTGCACA 58.310 45.000 0.00 0.00 0.00 4.57
2307 2367 3.625314 TGCCAGGTTTGGGAAAAGT 57.375 47.368 0.00 0.00 42.45 2.66
2473 2533 3.269906 AGGCTTCTGTCTAGGGAGAGTTA 59.730 47.826 0.00 0.00 34.84 2.24
2559 2619 5.402270 GTCAAAGAAAATCAAACATGGACGG 59.598 40.000 0.00 0.00 0.00 4.79
2624 2691 4.202010 GCACTTGTGAACATACTTGGTTGT 60.202 41.667 4.79 0.00 0.00 3.32
2625 2692 5.008217 GCACTTGTGAACATACTTGGTTGTA 59.992 40.000 4.79 0.00 0.00 2.41
2674 2746 7.334921 TCAGTTCCATATGGGTTTAAAAGTACG 59.665 37.037 21.78 0.71 38.11 3.67
2764 3700 5.815581 AGTATTCTTGACTGCCCATGTTTA 58.184 37.500 0.00 0.00 0.00 2.01
2923 3890 8.289939 ACGGATAGACATGTACTCTTTTCTTA 57.710 34.615 0.00 0.00 0.00 2.10
2951 3918 0.528017 TGCTGCTCTGGAGAACTACG 59.472 55.000 0.00 0.00 0.00 3.51
3063 4030 2.131854 TCAGAACTTGGGTCCCTTTGA 58.868 47.619 10.00 0.00 0.00 2.69
3064 4031 2.512056 TCAGAACTTGGGTCCCTTTGAA 59.488 45.455 10.00 0.00 0.00 2.69
3071 4038 1.574702 GGGTCCCTTTGAAAGTCGCG 61.575 60.000 0.00 0.00 0.00 5.87
3157 4124 2.920076 AAAGTTGAACCGGCAGGCCA 62.920 55.000 5.01 0.00 42.76 5.36
3196 4223 1.234821 ATATACGGCAAATGGGCACG 58.765 50.000 0.00 0.00 43.60 5.34
3199 4226 1.857318 TACGGCAAATGGGCACGTTG 61.857 55.000 0.00 0.00 43.60 4.10
3277 4305 4.487948 TGCTGACTGCTTTATTCAATTGC 58.512 39.130 0.00 0.00 43.37 3.56
3292 4320 6.857777 TTCAATTGCTGTGGGTTTTATTTG 57.142 33.333 0.00 0.00 0.00 2.32
3347 4384 9.979578 ATTAGTTGCAAATTGTTGTTCTCATTA 57.020 25.926 4.05 0.00 37.06 1.90
3385 4422 1.508632 TACTCTTTGTTCTGCACGGC 58.491 50.000 0.00 0.00 0.00 5.68
3386 4423 0.179045 ACTCTTTGTTCTGCACGGCT 60.179 50.000 0.00 0.00 0.00 5.52
3453 4491 5.601662 CCATTATCTTCACACGATGTAGGT 58.398 41.667 0.00 0.00 0.00 3.08
3461 4499 3.993736 TCACACGATGTAGGTTGTTGATG 59.006 43.478 0.00 0.00 0.00 3.07
3519 4557 1.740025 GCCCAGAACAGTTGCTATCAC 59.260 52.381 0.00 0.00 0.00 3.06
3530 4568 3.699538 AGTTGCTATCACGTATGAGGACA 59.300 43.478 0.00 0.00 38.57 4.02
3553 4591 6.321435 ACAGATATATCACGTGAGGTCAAAGA 59.679 38.462 24.41 3.51 0.00 2.52
3600 4639 8.186821 ACACAAGAAGAAAATGAAAAGACAGAG 58.813 33.333 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.443872 CGGGTGAGTGTGCTACGAC 60.444 63.158 0.00 0.00 0.00 4.34
1 2 2.959372 CGGGTGAGTGTGCTACGA 59.041 61.111 0.00 0.00 0.00 3.43
2 3 2.809601 GCGGGTGAGTGTGCTACG 60.810 66.667 0.00 0.00 0.00 3.51
3 4 2.434359 GGCGGGTGAGTGTGCTAC 60.434 66.667 0.00 0.00 0.00 3.58
4 5 3.702048 GGGCGGGTGAGTGTGCTA 61.702 66.667 0.00 0.00 0.00 3.49
7 8 3.551496 ATGTGGGCGGGTGAGTGTG 62.551 63.158 0.00 0.00 0.00 3.82
8 9 3.249189 ATGTGGGCGGGTGAGTGT 61.249 61.111 0.00 0.00 0.00 3.55
9 10 2.436646 GATGTGGGCGGGTGAGTG 60.437 66.667 0.00 0.00 0.00 3.51
10 11 2.927856 TGATGTGGGCGGGTGAGT 60.928 61.111 0.00 0.00 0.00 3.41
11 12 2.436646 GTGATGTGGGCGGGTGAG 60.437 66.667 0.00 0.00 0.00 3.51
12 13 4.386951 CGTGATGTGGGCGGGTGA 62.387 66.667 0.00 0.00 0.00 4.02
19 20 3.055719 GTGGCACCGTGATGTGGG 61.056 66.667 6.29 0.00 36.73 4.61
20 21 2.281414 TGTGGCACCGTGATGTGG 60.281 61.111 16.26 0.00 36.73 4.17
21 22 2.969806 GCTGTGGCACCGTGATGTG 61.970 63.158 16.26 0.00 39.29 3.21
22 23 2.669569 GCTGTGGCACCGTGATGT 60.670 61.111 16.26 0.00 38.54 3.06
23 24 3.434319 GGCTGTGGCACCGTGATG 61.434 66.667 16.26 0.00 40.87 3.07
24 25 3.952508 TGGCTGTGGCACCGTGAT 61.953 61.111 16.26 0.00 40.87 3.06
33 34 1.300080 CTTTTTGCCGTGGCTGTGG 60.300 57.895 12.84 0.00 42.51 4.17
34 35 0.318107 CTCTTTTTGCCGTGGCTGTG 60.318 55.000 12.84 0.00 42.51 3.66
35 36 0.751643 ACTCTTTTTGCCGTGGCTGT 60.752 50.000 12.84 0.00 42.51 4.40
36 37 0.318107 CACTCTTTTTGCCGTGGCTG 60.318 55.000 12.84 0.00 42.51 4.85
37 38 1.455383 CCACTCTTTTTGCCGTGGCT 61.455 55.000 12.84 0.00 40.27 4.75
38 39 1.007387 CCACTCTTTTTGCCGTGGC 60.007 57.895 3.30 3.30 40.27 5.01
39 40 1.001378 CTTCCACTCTTTTTGCCGTGG 60.001 52.381 0.00 0.00 46.35 4.94
40 41 1.001378 CCTTCCACTCTTTTTGCCGTG 60.001 52.381 0.00 0.00 0.00 4.94
41 42 1.318576 CCTTCCACTCTTTTTGCCGT 58.681 50.000 0.00 0.00 0.00 5.68
42 43 0.039165 GCCTTCCACTCTTTTTGCCG 60.039 55.000 0.00 0.00 0.00 5.69
43 44 0.039165 CGCCTTCCACTCTTTTTGCC 60.039 55.000 0.00 0.00 0.00 4.52
44 45 0.668535 ACGCCTTCCACTCTTTTTGC 59.331 50.000 0.00 0.00 0.00 3.68
45 46 1.266989 GGACGCCTTCCACTCTTTTTG 59.733 52.381 0.00 0.00 45.10 2.44
46 47 1.605753 GGACGCCTTCCACTCTTTTT 58.394 50.000 0.00 0.00 45.10 1.94
47 48 3.324207 GGACGCCTTCCACTCTTTT 57.676 52.632 0.00 0.00 45.10 2.27
48 49 2.125766 GGGGACGCCTTCCACTCTTT 62.126 60.000 0.24 0.00 45.83 2.52
49 50 2.593956 GGGGACGCCTTCCACTCTT 61.594 63.158 0.24 0.00 45.83 2.85
50 51 3.003763 GGGGACGCCTTCCACTCT 61.004 66.667 0.24 0.00 45.83 3.24
55 56 1.674651 GTCAAAGGGGACGCCTTCC 60.675 63.158 22.88 11.11 45.00 3.46
56 57 0.673956 GAGTCAAAGGGGACGCCTTC 60.674 60.000 22.88 11.60 42.62 3.46
57 58 1.375326 GAGTCAAAGGGGACGCCTT 59.625 57.895 17.70 17.70 42.62 4.35
58 59 3.069778 GAGTCAAAGGGGACGCCT 58.930 61.111 4.96 4.96 42.62 5.52
60 61 0.175989 CTAGGAGTCAAAGGGGACGC 59.824 60.000 0.00 0.00 42.62 5.19
61 62 0.175989 GCTAGGAGTCAAAGGGGACG 59.824 60.000 0.00 0.00 42.62 4.79
62 63 0.542333 GGCTAGGAGTCAAAGGGGAC 59.458 60.000 0.00 0.00 38.08 4.46
63 64 0.620700 GGGCTAGGAGTCAAAGGGGA 60.621 60.000 0.00 0.00 0.00 4.81
64 65 0.914417 TGGGCTAGGAGTCAAAGGGG 60.914 60.000 0.00 0.00 0.00 4.79
65 66 0.991920 TTGGGCTAGGAGTCAAAGGG 59.008 55.000 0.00 0.00 0.00 3.95
66 67 2.879103 TTTGGGCTAGGAGTCAAAGG 57.121 50.000 0.00 0.00 0.00 3.11
67 68 4.335416 TGATTTTGGGCTAGGAGTCAAAG 58.665 43.478 0.00 0.00 31.89 2.77
68 69 4.335416 CTGATTTTGGGCTAGGAGTCAAA 58.665 43.478 0.00 0.00 0.00 2.69
69 70 3.873801 GCTGATTTTGGGCTAGGAGTCAA 60.874 47.826 0.00 0.00 0.00 3.18
70 71 2.356125 GCTGATTTTGGGCTAGGAGTCA 60.356 50.000 0.00 0.00 0.00 3.41
71 72 2.293170 GCTGATTTTGGGCTAGGAGTC 58.707 52.381 0.00 0.00 0.00 3.36
72 73 1.064389 GGCTGATTTTGGGCTAGGAGT 60.064 52.381 0.00 0.00 0.00 3.85
73 74 1.064463 TGGCTGATTTTGGGCTAGGAG 60.064 52.381 0.00 0.00 0.00 3.69
74 75 0.998928 TGGCTGATTTTGGGCTAGGA 59.001 50.000 0.00 0.00 0.00 2.94
75 76 1.106285 GTGGCTGATTTTGGGCTAGG 58.894 55.000 0.00 0.00 0.00 3.02
76 77 0.734889 CGTGGCTGATTTTGGGCTAG 59.265 55.000 0.00 0.00 0.00 3.42
77 78 0.679640 CCGTGGCTGATTTTGGGCTA 60.680 55.000 0.00 0.00 0.00 3.93
78 79 1.978617 CCGTGGCTGATTTTGGGCT 60.979 57.895 0.00 0.00 0.00 5.19
79 80 2.573340 CCGTGGCTGATTTTGGGC 59.427 61.111 0.00 0.00 0.00 5.36
80 81 2.350458 CCCCGTGGCTGATTTTGGG 61.350 63.158 0.00 0.00 36.37 4.12
81 82 1.595093 GACCCCGTGGCTGATTTTGG 61.595 60.000 0.00 0.00 33.59 3.28
82 83 0.609131 AGACCCCGTGGCTGATTTTG 60.609 55.000 0.00 0.00 33.59 2.44
83 84 0.609131 CAGACCCCGTGGCTGATTTT 60.609 55.000 0.00 0.00 37.74 1.82
84 85 1.002134 CAGACCCCGTGGCTGATTT 60.002 57.895 0.00 0.00 37.74 2.17
85 86 2.671070 CAGACCCCGTGGCTGATT 59.329 61.111 0.00 0.00 37.74 2.57
86 87 3.402681 CCAGACCCCGTGGCTGAT 61.403 66.667 6.61 0.00 37.74 2.90
91 92 2.602676 ATCAACCCAGACCCCGTGG 61.603 63.158 0.00 0.00 37.80 4.94
92 93 1.377202 CATCAACCCAGACCCCGTG 60.377 63.158 0.00 0.00 0.00 4.94
93 94 3.077907 CATCAACCCAGACCCCGT 58.922 61.111 0.00 0.00 0.00 5.28
94 95 2.438434 GCATCAACCCAGACCCCG 60.438 66.667 0.00 0.00 0.00 5.73
95 96 2.043953 GGCATCAACCCAGACCCC 60.044 66.667 0.00 0.00 0.00 4.95
96 97 1.077429 GAGGCATCAACCCAGACCC 60.077 63.158 0.00 0.00 0.00 4.46
97 98 1.077429 GGAGGCATCAACCCAGACC 60.077 63.158 0.00 0.00 0.00 3.85
98 99 0.678048 GTGGAGGCATCAACCCAGAC 60.678 60.000 0.00 0.00 0.00 3.51
99 100 1.685224 GTGGAGGCATCAACCCAGA 59.315 57.895 0.00 0.00 0.00 3.86
100 101 1.379044 GGTGGAGGCATCAACCCAG 60.379 63.158 14.30 0.00 43.09 4.45
101 102 2.763215 GGTGGAGGCATCAACCCA 59.237 61.111 14.30 0.00 43.09 4.51
104 105 1.490490 TCCTATGGTGGAGGCATCAAC 59.510 52.381 0.00 0.00 33.73 3.18
105 106 1.891933 TCCTATGGTGGAGGCATCAA 58.108 50.000 0.00 0.00 33.73 2.57
106 107 1.701292 CATCCTATGGTGGAGGCATCA 59.299 52.381 0.00 0.00 39.78 3.07
107 108 1.701847 ACATCCTATGGTGGAGGCATC 59.298 52.381 0.00 0.00 41.15 3.91
108 109 1.422781 CACATCCTATGGTGGAGGCAT 59.577 52.381 0.00 0.00 41.15 4.40
109 110 0.839277 CACATCCTATGGTGGAGGCA 59.161 55.000 0.00 0.00 41.15 4.75
110 111 0.839946 ACACATCCTATGGTGGAGGC 59.160 55.000 0.00 0.00 41.15 4.70
111 112 2.103771 CAGACACATCCTATGGTGGAGG 59.896 54.545 0.00 0.00 42.90 4.30
112 113 2.103771 CCAGACACATCCTATGGTGGAG 59.896 54.545 0.00 0.00 39.78 3.86
113 114 2.118679 CCAGACACATCCTATGGTGGA 58.881 52.381 0.00 0.00 39.31 4.02
114 115 1.839994 ACCAGACACATCCTATGGTGG 59.160 52.381 0.00 0.00 42.56 4.61
115 116 3.535561 GAACCAGACACATCCTATGGTG 58.464 50.000 0.00 0.00 43.36 4.17
116 117 2.168521 CGAACCAGACACATCCTATGGT 59.831 50.000 0.00 0.00 46.05 3.55
117 118 2.168521 ACGAACCAGACACATCCTATGG 59.831 50.000 0.00 0.00 37.07 2.74
118 119 3.119137 TCACGAACCAGACACATCCTATG 60.119 47.826 0.00 0.00 0.00 2.23
119 120 3.096852 TCACGAACCAGACACATCCTAT 58.903 45.455 0.00 0.00 0.00 2.57
120 121 2.521126 TCACGAACCAGACACATCCTA 58.479 47.619 0.00 0.00 0.00 2.94
121 122 1.338107 TCACGAACCAGACACATCCT 58.662 50.000 0.00 0.00 0.00 3.24
122 123 2.002586 CATCACGAACCAGACACATCC 58.997 52.381 0.00 0.00 0.00 3.51
123 124 2.959516 TCATCACGAACCAGACACATC 58.040 47.619 0.00 0.00 0.00 3.06
124 125 3.401033 TTCATCACGAACCAGACACAT 57.599 42.857 0.00 0.00 0.00 3.21
131 132 3.008594 ACCCTACAATTCATCACGAACCA 59.991 43.478 0.00 0.00 36.12 3.67
132 133 3.374058 CACCCTACAATTCATCACGAACC 59.626 47.826 0.00 0.00 36.12 3.62
137 138 1.670811 CCGCACCCTACAATTCATCAC 59.329 52.381 0.00 0.00 0.00 3.06
139 140 0.663153 GCCGCACCCTACAATTCATC 59.337 55.000 0.00 0.00 0.00 2.92
145 146 3.712907 GGAGGCCGCACCCTACAA 61.713 66.667 9.31 0.00 40.58 2.41
148 149 0.910566 TTAAAGGAGGCCGCACCCTA 60.911 55.000 9.31 0.98 40.58 3.53
152 153 0.251073 TACCTTAAAGGAGGCCGCAC 59.749 55.000 9.31 0.00 40.65 5.34
153 154 0.985760 TTACCTTAAAGGAGGCCGCA 59.014 50.000 9.31 0.00 40.65 5.69
154 155 2.118313 TTTACCTTAAAGGAGGCCGC 57.882 50.000 0.00 0.00 40.65 6.53
168 169 3.668757 GCGGACAAAATCGGTCTTTTACC 60.669 47.826 0.00 0.00 45.77 2.85
169 170 3.485633 GCGGACAAAATCGGTCTTTTAC 58.514 45.455 0.00 0.00 35.61 2.01
176 177 1.253100 AAATGGCGGACAAAATCGGT 58.747 45.000 0.00 0.00 0.00 4.69
200 201 7.706179 CCAAGAGCAAACTGAATAAAACAAAGA 59.294 33.333 0.00 0.00 0.00 2.52
202 203 7.327214 ACCAAGAGCAAACTGAATAAAACAAA 58.673 30.769 0.00 0.00 0.00 2.83
203 204 6.872920 ACCAAGAGCAAACTGAATAAAACAA 58.127 32.000 0.00 0.00 0.00 2.83
204 205 6.463995 ACCAAGAGCAAACTGAATAAAACA 57.536 33.333 0.00 0.00 0.00 2.83
205 206 9.476202 AATTACCAAGAGCAAACTGAATAAAAC 57.524 29.630 0.00 0.00 0.00 2.43
267 268 8.489990 TGAAGAAACAAATGCAAAAAGAATGA 57.510 26.923 0.00 0.00 0.00 2.57
268 269 8.392612 ACTGAAGAAACAAATGCAAAAAGAATG 58.607 29.630 0.00 0.00 0.00 2.67
269 270 8.496707 ACTGAAGAAACAAATGCAAAAAGAAT 57.503 26.923 0.00 0.00 0.00 2.40
270 271 7.903995 ACTGAAGAAACAAATGCAAAAAGAA 57.096 28.000 0.00 0.00 0.00 2.52
334 335 9.513906 ACCAAAGAAAGGAAAATTTGAAAAGAA 57.486 25.926 0.00 0.00 35.19 2.52
339 340 9.289782 TGAAAACCAAAGAAAGGAAAATTTGAA 57.710 25.926 0.00 0.00 35.19 2.69
343 344 9.685276 AGAATGAAAACCAAAGAAAGGAAAATT 57.315 25.926 0.00 0.00 0.00 1.82
391 405 9.919348 TGTTAAATGTGTAGTAGAAAAACGTTC 57.081 29.630 0.00 0.00 0.00 3.95
551 576 9.959749 TTGAAAAAGCTTAAAAGTGTGTATAGG 57.040 29.630 0.00 0.00 0.00 2.57
612 637 9.539825 AAAATGTTGAACATGTGTTAGCAAATA 57.460 25.926 12.09 0.00 37.97 1.40
681 709 2.743553 CTCTGCCCAGATCCCATTTTT 58.256 47.619 0.00 0.00 36.76 1.94
682 710 1.687368 GCTCTGCCCAGATCCCATTTT 60.687 52.381 0.00 0.00 36.76 1.82
683 711 0.106318 GCTCTGCCCAGATCCCATTT 60.106 55.000 0.00 0.00 36.76 2.32
684 712 0.992431 AGCTCTGCCCAGATCCCATT 60.992 55.000 0.00 0.00 36.76 3.16
685 713 0.104777 TAGCTCTGCCCAGATCCCAT 60.105 55.000 0.00 0.00 36.76 4.00
686 714 0.762082 CTAGCTCTGCCCAGATCCCA 60.762 60.000 0.00 0.00 36.76 4.37
687 715 2.056985 CTAGCTCTGCCCAGATCCC 58.943 63.158 0.00 0.00 36.76 3.85
688 716 1.370810 GCTAGCTCTGCCCAGATCC 59.629 63.158 7.70 0.00 36.76 3.36
689 717 1.370810 GGCTAGCTCTGCCCAGATC 59.629 63.158 15.72 0.00 44.32 2.75
690 718 3.560989 GGCTAGCTCTGCCCAGAT 58.439 61.111 15.72 0.00 44.32 2.90
695 723 4.906792 CAGCCGGCTAGCTCTGCC 62.907 72.222 32.30 17.78 42.61 4.85
697 725 4.906792 GGCAGCCGGCTAGCTCTG 62.907 72.222 34.17 23.37 42.61 3.35
715 743 3.134127 GATCCGGTTGGTGGCAGC 61.134 66.667 10.30 10.30 36.30 5.25
716 744 2.438434 GGATCCGGTTGGTGGCAG 60.438 66.667 0.00 0.00 36.30 4.85
717 745 2.478335 GAAGGATCCGGTTGGTGGCA 62.478 60.000 5.98 0.00 36.30 4.92
718 746 1.749258 GAAGGATCCGGTTGGTGGC 60.749 63.158 5.98 0.00 36.30 5.01
719 747 0.392998 CTGAAGGATCCGGTTGGTGG 60.393 60.000 5.98 0.00 36.30 4.61
720 748 1.026718 GCTGAAGGATCCGGTTGGTG 61.027 60.000 5.98 0.00 36.30 4.17
721 749 1.299976 GCTGAAGGATCCGGTTGGT 59.700 57.895 5.98 0.00 36.30 3.67
722 750 1.452108 GGCTGAAGGATCCGGTTGG 60.452 63.158 5.98 0.00 0.00 3.77
723 751 1.815421 CGGCTGAAGGATCCGGTTG 60.815 63.158 5.98 0.00 39.52 3.77
724 752 2.584608 CGGCTGAAGGATCCGGTT 59.415 61.111 5.98 0.00 39.52 4.44
725 753 4.162690 GCGGCTGAAGGATCCGGT 62.163 66.667 5.98 0.00 43.11 5.28
726 754 4.918201 GGCGGCTGAAGGATCCGG 62.918 72.222 5.98 0.00 43.11 5.14
727 755 4.161295 TGGCGGCTGAAGGATCCG 62.161 66.667 11.43 0.00 45.46 4.18
728 756 2.514824 GTGGCGGCTGAAGGATCC 60.515 66.667 11.43 2.48 0.00 3.36
729 757 2.514824 GGTGGCGGCTGAAGGATC 60.515 66.667 11.43 0.00 0.00 3.36
730 758 4.473520 CGGTGGCGGCTGAAGGAT 62.474 66.667 11.43 0.00 0.00 3.24
797 825 4.864334 CAGGGACGATGGGCTGGC 62.864 72.222 0.00 0.00 0.00 4.85
798 826 4.864334 GCAGGGACGATGGGCTGG 62.864 72.222 0.00 0.00 0.00 4.85
799 827 4.864334 GGCAGGGACGATGGGCTG 62.864 72.222 0.00 0.00 0.00 4.85
803 831 4.227134 CTCGGGCAGGGACGATGG 62.227 72.222 0.00 0.00 38.56 3.51
804 832 4.899239 GCTCGGGCAGGGACGATG 62.899 72.222 0.00 0.00 38.56 3.84
842 870 2.201022 TATTCTCTCCGCTCGGGGC 61.201 63.158 8.59 0.00 35.22 5.80
843 871 1.107538 TGTATTCTCTCCGCTCGGGG 61.108 60.000 8.59 4.98 37.02 5.73
844 872 0.312416 CTGTATTCTCTCCGCTCGGG 59.688 60.000 8.59 0.00 35.59 5.14
845 873 0.312416 CCTGTATTCTCTCCGCTCGG 59.688 60.000 1.14 1.14 0.00 4.63
846 874 1.002251 GTCCTGTATTCTCTCCGCTCG 60.002 57.143 0.00 0.00 0.00 5.03
847 875 1.338655 GGTCCTGTATTCTCTCCGCTC 59.661 57.143 0.00 0.00 0.00 5.03
848 876 1.404843 GGTCCTGTATTCTCTCCGCT 58.595 55.000 0.00 0.00 0.00 5.52
849 877 0.389757 GGGTCCTGTATTCTCTCCGC 59.610 60.000 0.00 0.00 0.00 5.54
850 878 1.041437 GGGGTCCTGTATTCTCTCCG 58.959 60.000 0.00 0.00 0.00 4.63
851 879 1.763545 GTGGGGTCCTGTATTCTCTCC 59.236 57.143 0.00 0.00 0.00 3.71
852 880 1.763545 GGTGGGGTCCTGTATTCTCTC 59.236 57.143 0.00 0.00 0.00 3.20
853 881 1.880941 GGTGGGGTCCTGTATTCTCT 58.119 55.000 0.00 0.00 0.00 3.10
854 882 0.464452 CGGTGGGGTCCTGTATTCTC 59.536 60.000 0.00 0.00 0.00 2.87
855 883 1.623542 GCGGTGGGGTCCTGTATTCT 61.624 60.000 0.00 0.00 0.00 2.40
856 884 1.153229 GCGGTGGGGTCCTGTATTC 60.153 63.158 0.00 0.00 0.00 1.75
857 885 2.676265 GGCGGTGGGGTCCTGTATT 61.676 63.158 0.00 0.00 0.00 1.89
858 886 3.087906 GGCGGTGGGGTCCTGTAT 61.088 66.667 0.00 0.00 0.00 2.29
859 887 4.642488 TGGCGGTGGGGTCCTGTA 62.642 66.667 0.00 0.00 0.00 2.74
887 915 3.775654 CTCCTCCCAGCGGGTGAC 61.776 72.222 9.09 0.00 44.74 3.67
893 921 3.474570 CTTCCCCTCCTCCCAGCG 61.475 72.222 0.00 0.00 0.00 5.18
894 922 3.093172 CCTTCCCCTCCTCCCAGC 61.093 72.222 0.00 0.00 0.00 4.85
895 923 2.367512 CCCTTCCCCTCCTCCCAG 60.368 72.222 0.00 0.00 0.00 4.45
896 924 4.038804 CCCCTTCCCCTCCTCCCA 62.039 72.222 0.00 0.00 0.00 4.37
897 925 4.845307 CCCCCTTCCCCTCCTCCC 62.845 77.778 0.00 0.00 0.00 4.30
898 926 2.993038 GATCCCCCTTCCCCTCCTCC 62.993 70.000 0.00 0.00 0.00 4.30
930 958 1.437986 CGGAACCGGATGAGGAGTC 59.562 63.158 9.46 0.00 35.56 3.36
931 959 2.722201 GCGGAACCGGATGAGGAGT 61.722 63.158 9.46 0.00 40.19 3.85
932 960 2.107141 GCGGAACCGGATGAGGAG 59.893 66.667 9.46 0.00 40.19 3.69
961 993 3.462483 TTGGAAGACTCGCTGTTGTAA 57.538 42.857 0.00 0.00 0.00 2.41
962 994 3.128349 GTTTGGAAGACTCGCTGTTGTA 58.872 45.455 0.00 0.00 0.00 2.41
995 1033 1.250840 AAGAAGGCGGGGCATTTGTC 61.251 55.000 0.00 0.00 31.02 3.18
1003 1041 1.222113 GGAGAAGAAGAAGGCGGGG 59.778 63.158 0.00 0.00 0.00 5.73
1009 1047 2.478200 GGCTACGACGGAGAAGAAGAAG 60.478 54.545 12.38 0.00 0.00 2.85
1010 1048 1.471684 GGCTACGACGGAGAAGAAGAA 59.528 52.381 12.38 0.00 0.00 2.52
1011 1049 1.093159 GGCTACGACGGAGAAGAAGA 58.907 55.000 12.38 0.00 0.00 2.87
1014 1052 0.035725 TGAGGCTACGACGGAGAAGA 60.036 55.000 12.38 0.00 0.00 2.87
1093 1131 1.682344 GGGCTGATTTGGTGGGGTC 60.682 63.158 0.00 0.00 0.00 4.46
1139 1177 3.953775 CCGGATCGGGATTGGGGG 61.954 72.222 13.96 0.00 44.15 5.40
1181 1219 2.676471 GGATGGTGGTGGTGGTGC 60.676 66.667 0.00 0.00 0.00 5.01
1182 1220 1.002134 GAGGATGGTGGTGGTGGTG 60.002 63.158 0.00 0.00 0.00 4.17
1183 1221 2.231380 GGAGGATGGTGGTGGTGGT 61.231 63.158 0.00 0.00 0.00 4.16
1297 1335 1.000612 AGAGAACCTCCGGGGAGAC 59.999 63.158 16.29 7.24 44.53 3.36
1426 1464 1.958902 CTCCTGCCCAGAGCTCTGAC 61.959 65.000 39.34 30.22 46.59 3.51
1431 1469 1.994507 CTTCCTCCTGCCCAGAGCT 60.995 63.158 0.00 0.00 44.23 4.09
1615 1653 1.871126 GCCTCCTTTCTGTGGCAAGC 61.871 60.000 0.00 0.00 44.34 4.01
1642 1680 1.202510 GCAGAGGCATTCGATGAGAGT 60.203 52.381 0.00 0.00 40.72 3.24
1695 1733 4.111016 CCGCGAGCGACCTGTACA 62.111 66.667 19.72 0.00 42.83 2.90
1707 1767 0.460284 GATCAAAAGGCTCTCCGCGA 60.460 55.000 8.23 0.00 40.44 5.87
1710 1770 2.977914 TCAAGATCAAAAGGCTCTCCG 58.022 47.619 0.00 0.00 37.47 4.63
1931 1991 0.035820 GGCCATCGTAGTTGGACCAA 60.036 55.000 1.69 1.69 36.14 3.67
1981 2041 0.631212 GACCTGTCCAAATCCCCCAT 59.369 55.000 0.00 0.00 0.00 4.00
2190 2250 0.396695 CAGCATGAGGAGGCCCAAAT 60.397 55.000 0.00 0.00 39.69 2.32
2307 2367 2.692557 CCAAATGTTCAACACTGTCCCA 59.307 45.455 0.00 0.00 0.00 4.37
2473 2533 5.163754 GCCTGTCGTTCAGTTTGCTATAAAT 60.164 40.000 8.83 0.00 42.19 1.40
2531 2591 8.116136 GTCCATGTTTGATTTTCTTTGACAAAC 58.884 33.333 0.00 0.00 45.54 2.93
2559 2619 3.536158 TTGCGTGAATTAGCAAGTGTC 57.464 42.857 10.28 0.00 46.83 3.67
2633 2700 3.129287 GGAACTGACCAGCATACCAAATG 59.871 47.826 0.00 0.00 0.00 2.32
2707 3635 4.892934 TCACCAGCCAAACTTGAGTTTTAT 59.107 37.500 6.39 0.00 45.07 1.40
2764 3700 5.105269 TGCATGAAATAGCCAAACATGTCAT 60.105 36.000 0.00 0.00 39.95 3.06
2899 3866 9.186323 CATAAGAAAAGAGTACATGTCTATCCG 57.814 37.037 0.00 0.00 0.00 4.18
2923 3890 2.168106 CTCCAGAGCAGCAGAAGTACAT 59.832 50.000 0.00 0.00 0.00 2.29
3022 3989 4.753107 TGATACTTGAGACCCAACGTTTTC 59.247 41.667 0.00 0.00 0.00 2.29
3024 3991 4.039973 TCTGATACTTGAGACCCAACGTTT 59.960 41.667 0.00 0.00 0.00 3.60
3026 3993 3.162666 TCTGATACTTGAGACCCAACGT 58.837 45.455 0.00 0.00 0.00 3.99
3063 4030 1.672145 GGCTACTTTCTCCGCGACTTT 60.672 52.381 8.23 0.00 0.00 2.66
3064 4031 0.108756 GGCTACTTTCTCCGCGACTT 60.109 55.000 8.23 0.00 0.00 3.01
3071 4038 4.591072 AGGATACATCAGGCTACTTTCTCC 59.409 45.833 0.00 0.00 41.41 3.71
3182 4149 1.857318 TACAACGTGCCCATTTGCCG 61.857 55.000 0.00 0.00 0.00 5.69
3196 4223 4.156008 GTGATGTTCCATTCCAGGTACAAC 59.844 45.833 0.00 0.00 41.39 3.32
3199 4226 3.950397 TGTGATGTTCCATTCCAGGTAC 58.050 45.455 0.00 0.00 0.00 3.34
3224 4251 6.594788 AACTGGCATCACATAGAATTTTGT 57.405 33.333 0.00 0.00 0.00 2.83
3277 4305 5.423886 ACAAACCACAAATAAAACCCACAG 58.576 37.500 0.00 0.00 0.00 3.66
3453 4491 6.086785 TGCATCTTCATGAAACATCAACAA 57.913 33.333 9.88 0.00 30.57 2.83
3519 4557 6.092259 TCACGTGATATATCTGTCCTCATACG 59.908 42.308 15.76 12.92 0.00 3.06
3530 4568 6.961360 TCTTTGACCTCACGTGATATATCT 57.039 37.500 20.40 0.00 0.00 1.98
3553 4591 6.601613 TGTGTAATTGTTCAACCAGTTCTCTT 59.398 34.615 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.