Multiple sequence alignment - TraesCS6B01G170200

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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 TraesCS6B01G170200 chr6B 100.000 3577 0 0 1 3577 182587367 182583791 0.000000e+00 6606.0
1 TraesCS6B01G170200 chr6A 95.884 1409 52 2 1327 2733 116913196 116911792 0.000000e+00 2276.0
2 TraesCS6B01G170200 chr6A 96.522 575 16 2 3003 3577 116911589 116911019 0.000000e+00 948.0
3 TraesCS6B01G170200 chr6A 88.103 580 65 2 162 741 116941988 116941413 0.000000e+00 686.0
4 TraesCS6B01G170200 chr6A 83.761 585 87 8 162 741 590210951 590211532 6.750000e-152 547.0
5 TraesCS6B01G170200 chr6A 97.468 158 4 0 1068 1225 116920457 116920300 1.640000e-68 270.0
6 TraesCS6B01G170200 chr6D 92.071 1400 57 23 804 2159 97915235 97913846 0.000000e+00 1921.0
7 TraesCS6B01G170200 chr6D 96.273 805 21 3 2778 3577 97913100 97912300 0.000000e+00 1312.0
8 TraesCS6B01G170200 chr6D 88.272 162 14 2 2 160 97921693 97921534 4.710000e-44 189.0
9 TraesCS6B01G170200 chr2A 86.130 584 75 6 161 741 757811775 757812355 3.030000e-175 625.0
10 TraesCS6B01G170200 chr2D 85.935 583 73 7 162 741 627125228 627125804 6.560000e-172 614.0
11 TraesCS6B01G170200 chr2D 84.220 583 85 7 162 741 138372217 138371639 8.670000e-156 560.0
12 TraesCS6B01G170200 chr5D 85.299 585 77 9 162 741 411898182 411897602 2.380000e-166 595.0
13 TraesCS6B01G170200 chr5D 84.429 578 80 9 168 741 437602305 437601734 8.670000e-156 560.0
14 TraesCS6B01G170200 chr4B 84.391 583 83 6 162 741 192697383 192697960 1.860000e-157 566.0
15 TraesCS6B01G170200 chr4B 82.656 369 62 2 1385 1752 570138765 570139132 3.440000e-85 326.0
16 TraesCS6B01G170200 chr7D 84.111 579 83 9 168 741 74956542 74955968 5.220000e-153 551.0
17 TraesCS6B01G170200 chr4D 83.514 370 57 4 1385 1752 456047317 456047684 3.420000e-90 342.0
18 TraesCS6B01G170200 chr4D 83.529 85 14 0 1124 1208 455744256 455744340 2.960000e-11 80.5
19 TraesCS6B01G170200 chr4A 83.422 374 56 6 1385 1755 11678109 11677739 3.420000e-90 342.0
20 TraesCS6B01G170200 chr4A 81.935 155 26 2 1 154 4237550 4237703 2.900000e-26 130.0
21 TraesCS6B01G170200 chr4A 85.526 76 11 0 1133 1208 11813197 11813122 2.960000e-11 80.5
22 TraesCS6B01G170200 chr3B 83.146 178 30 0 1387 1564 17783914 17783737 2.860000e-36 163.0
23 TraesCS6B01G170200 chr3B 82.514 183 26 6 1385 1564 17988607 17988786 4.780000e-34 156.0
24 TraesCS6B01G170200 chr3B 81.356 177 33 0 1388 1564 17689079 17688903 1.040000e-30 145.0
25 TraesCS6B01G170200 chr3A 82.486 177 31 0 1388 1564 24781307 24781131 4.780000e-34 156.0
26 TraesCS6B01G170200 chr7A 85.333 150 19 2 2 151 57694267 57694413 6.190000e-33 152.0
27 TraesCS6B01G170200 chr1B 71.484 519 127 18 1886 2390 60108386 60107875 6.270000e-23 119.0
28 TraesCS6B01G170200 chr1D 80.667 150 29 0 1 150 332567628 332567777 2.260000e-22 117.0
29 TraesCS6B01G170200 chr1A 71.291 519 128 17 1886 2390 39871420 39870909 2.920000e-21 113.0
30 TraesCS6B01G170200 chr7B 100.000 29 0 0 61 89 563472072 563472100 2.000000e-03 54.7


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 TraesCS6B01G170200 chr6B 182583791 182587367 3576 True 6606.0 6606 100.000 1 3577 1 chr6B.!!$R1 3576
1 TraesCS6B01G170200 chr6A 116911019 116913196 2177 True 1612.0 2276 96.203 1327 3577 2 chr6A.!!$R3 2250
2 TraesCS6B01G170200 chr6A 116941413 116941988 575 True 686.0 686 88.103 162 741 1 chr6A.!!$R2 579
3 TraesCS6B01G170200 chr6A 590210951 590211532 581 False 547.0 547 83.761 162 741 1 chr6A.!!$F1 579
4 TraesCS6B01G170200 chr6D 97912300 97915235 2935 True 1616.5 1921 94.172 804 3577 2 chr6D.!!$R2 2773
5 TraesCS6B01G170200 chr2A 757811775 757812355 580 False 625.0 625 86.130 161 741 1 chr2A.!!$F1 580
6 TraesCS6B01G170200 chr2D 627125228 627125804 576 False 614.0 614 85.935 162 741 1 chr2D.!!$F1 579
7 TraesCS6B01G170200 chr2D 138371639 138372217 578 True 560.0 560 84.220 162 741 1 chr2D.!!$R1 579
8 TraesCS6B01G170200 chr5D 411897602 411898182 580 True 595.0 595 85.299 162 741 1 chr5D.!!$R1 579
9 TraesCS6B01G170200 chr5D 437601734 437602305 571 True 560.0 560 84.429 168 741 1 chr5D.!!$R2 573
10 TraesCS6B01G170200 chr4B 192697383 192697960 577 False 566.0 566 84.391 162 741 1 chr4B.!!$F1 579
11 TraesCS6B01G170200 chr7D 74955968 74956542 574 True 551.0 551 84.111 168 741 1 chr7D.!!$R1 573

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
466 472 0.259356 CCCGGTAGGAGAGAAGAGGT 59.741 60.0 0.0 0.0 41.02 3.85 F
1848 1902 0.179181 TCGCAGTAACGTCGATCACC 60.179 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2300 0.030638 GAGCGCTTGCCTGACAAAAA 59.969 50.0 13.26 0.0 37.96 1.94 R
2763 2823 0.413037 TGCCCTGATTTTCCCCATGT 59.587 50.0 0.00 0.0 0.00 3.21 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
31 32 3.307829 CGAGTACGTTCGCATGAGT 57.692 52.632 0.00 0.00 33.39 3.41
32 33 0.907837 CGAGTACGTTCGCATGAGTG 59.092 55.000 0.00 0.00 33.39 3.51
33 34 1.465187 CGAGTACGTTCGCATGAGTGA 60.465 52.381 0.00 0.00 33.39 3.41
34 35 2.177977 GAGTACGTTCGCATGAGTGAG 58.822 52.381 0.00 0.00 35.36 3.51
35 36 1.540267 AGTACGTTCGCATGAGTGAGT 59.460 47.619 0.00 0.00 35.36 3.41
36 37 1.912110 GTACGTTCGCATGAGTGAGTC 59.088 52.381 0.00 0.00 35.36 3.36
37 38 0.388649 ACGTTCGCATGAGTGAGTCC 60.389 55.000 0.00 0.00 35.36 3.85
38 39 0.388520 CGTTCGCATGAGTGAGTCCA 60.389 55.000 0.00 0.00 35.36 4.02
39 40 1.071605 GTTCGCATGAGTGAGTCCAC 58.928 55.000 0.00 0.00 43.50 4.02
53 54 5.784177 GTGAGTCCACTTGTCTAGATTTCA 58.216 41.667 0.00 0.00 40.10 2.69
54 55 6.402222 GTGAGTCCACTTGTCTAGATTTCAT 58.598 40.000 0.00 0.00 40.10 2.57
55 56 6.312426 GTGAGTCCACTTGTCTAGATTTCATG 59.688 42.308 0.00 0.00 40.10 3.07
56 57 6.014242 TGAGTCCACTTGTCTAGATTTCATGT 60.014 38.462 0.00 0.00 0.00 3.21
57 58 7.178451 TGAGTCCACTTGTCTAGATTTCATGTA 59.822 37.037 0.00 0.00 0.00 2.29
58 59 7.324178 AGTCCACTTGTCTAGATTTCATGTAC 58.676 38.462 0.00 0.00 0.00 2.90
59 60 7.039011 AGTCCACTTGTCTAGATTTCATGTACA 60.039 37.037 0.00 0.00 0.00 2.90
60 61 7.602644 GTCCACTTGTCTAGATTTCATGTACAA 59.397 37.037 0.00 0.00 0.00 2.41
61 62 7.819415 TCCACTTGTCTAGATTTCATGTACAAG 59.181 37.037 0.00 11.52 44.83 3.16
65 66 9.429359 CTTGTCTAGATTTCATGTACAAGTTCT 57.571 33.333 0.00 3.28 38.21 3.01
67 68 9.856488 TGTCTAGATTTCATGTACAAGTTCTAC 57.144 33.333 0.00 0.00 0.00 2.59
68 69 9.856488 GTCTAGATTTCATGTACAAGTTCTACA 57.144 33.333 0.00 0.00 0.00 2.74
71 72 8.553459 AGATTTCATGTACAAGTTCTACAAGG 57.447 34.615 0.00 0.00 0.00 3.61
72 73 6.554334 TTTCATGTACAAGTTCTACAAGGC 57.446 37.500 0.00 0.00 0.00 4.35
73 74 5.222079 TCATGTACAAGTTCTACAAGGCA 57.778 39.130 0.00 0.00 0.00 4.75
74 75 5.237815 TCATGTACAAGTTCTACAAGGCAG 58.762 41.667 0.00 0.00 0.00 4.85
75 76 4.682778 TGTACAAGTTCTACAAGGCAGT 57.317 40.909 0.00 0.00 0.00 4.40
76 77 4.377021 TGTACAAGTTCTACAAGGCAGTG 58.623 43.478 0.00 0.00 0.00 3.66
77 78 2.851195 ACAAGTTCTACAAGGCAGTGG 58.149 47.619 0.00 0.00 0.00 4.00
78 79 2.172717 ACAAGTTCTACAAGGCAGTGGT 59.827 45.455 0.00 0.00 0.00 4.16
79 80 2.549754 CAAGTTCTACAAGGCAGTGGTG 59.450 50.000 0.00 0.00 0.00 4.17
80 81 1.072331 AGTTCTACAAGGCAGTGGTGG 59.928 52.381 0.00 0.00 0.00 4.61
88 89 3.525221 GCAGTGGTGGCAGTGTTT 58.475 55.556 0.00 0.00 0.00 2.83
89 90 1.066257 GCAGTGGTGGCAGTGTTTG 59.934 57.895 0.00 0.00 0.00 2.93
98 99 4.907457 CAGTGTTTGCCCTGGAGT 57.093 55.556 0.00 0.00 0.00 3.85
100 101 1.523758 CAGTGTTTGCCCTGGAGTAC 58.476 55.000 0.00 0.00 0.00 2.73
101 102 1.072331 CAGTGTTTGCCCTGGAGTACT 59.928 52.381 0.00 0.00 0.00 2.73
102 103 1.774856 AGTGTTTGCCCTGGAGTACTT 59.225 47.619 0.00 0.00 0.00 2.24
103 104 1.880027 GTGTTTGCCCTGGAGTACTTG 59.120 52.381 0.00 0.00 0.00 3.16
104 105 1.771854 TGTTTGCCCTGGAGTACTTGA 59.228 47.619 0.00 0.00 0.00 3.02
105 106 2.224523 TGTTTGCCCTGGAGTACTTGAG 60.225 50.000 0.00 0.00 0.00 3.02
106 107 2.024176 TTGCCCTGGAGTACTTGAGA 57.976 50.000 0.00 0.00 0.00 3.27
107 108 1.561643 TGCCCTGGAGTACTTGAGAG 58.438 55.000 0.00 0.00 0.00 3.20
108 109 1.077169 TGCCCTGGAGTACTTGAGAGA 59.923 52.381 0.00 0.00 0.00 3.10
109 110 1.754226 GCCCTGGAGTACTTGAGAGAG 59.246 57.143 0.00 0.00 0.00 3.20
110 111 1.754226 CCCTGGAGTACTTGAGAGAGC 59.246 57.143 0.00 0.00 0.00 4.09
111 112 1.754226 CCTGGAGTACTTGAGAGAGCC 59.246 57.143 0.00 0.00 0.00 4.70
112 113 2.451490 CTGGAGTACTTGAGAGAGCCA 58.549 52.381 0.00 0.00 0.00 4.75
113 114 2.828520 CTGGAGTACTTGAGAGAGCCAA 59.171 50.000 0.00 0.00 0.00 4.52
114 115 2.563179 TGGAGTACTTGAGAGAGCCAAC 59.437 50.000 0.00 0.00 0.00 3.77
115 116 2.829120 GGAGTACTTGAGAGAGCCAACT 59.171 50.000 0.00 0.00 0.00 3.16
116 117 4.017808 GGAGTACTTGAGAGAGCCAACTA 58.982 47.826 0.00 0.00 0.00 2.24
117 118 4.142337 GGAGTACTTGAGAGAGCCAACTAC 60.142 50.000 0.00 0.00 0.00 2.73
118 119 4.668636 AGTACTTGAGAGAGCCAACTACT 58.331 43.478 0.00 0.00 0.00 2.57
119 120 3.951775 ACTTGAGAGAGCCAACTACTG 57.048 47.619 0.00 0.00 0.00 2.74
120 121 3.235200 ACTTGAGAGAGCCAACTACTGT 58.765 45.455 0.00 0.00 0.00 3.55
121 122 4.408276 ACTTGAGAGAGCCAACTACTGTA 58.592 43.478 0.00 0.00 0.00 2.74
122 123 4.461081 ACTTGAGAGAGCCAACTACTGTAG 59.539 45.833 13.13 13.13 0.00 2.74
123 124 4.302559 TGAGAGAGCCAACTACTGTAGA 57.697 45.455 21.01 0.00 0.00 2.59
124 125 4.861196 TGAGAGAGCCAACTACTGTAGAT 58.139 43.478 21.01 6.81 0.00 1.98
125 126 6.002653 TGAGAGAGCCAACTACTGTAGATA 57.997 41.667 21.01 0.00 0.00 1.98
126 127 5.823570 TGAGAGAGCCAACTACTGTAGATAC 59.176 44.000 21.01 5.66 0.00 2.24
127 128 5.756918 AGAGAGCCAACTACTGTAGATACA 58.243 41.667 21.01 0.00 34.56 2.29
128 129 6.188407 AGAGAGCCAACTACTGTAGATACAA 58.812 40.000 21.01 0.00 35.50 2.41
129 130 6.095720 AGAGAGCCAACTACTGTAGATACAAC 59.904 42.308 21.01 8.29 35.50 3.32
130 131 5.127356 AGAGCCAACTACTGTAGATACAACC 59.873 44.000 21.01 5.12 35.50 3.77
131 132 4.161754 AGCCAACTACTGTAGATACAACCC 59.838 45.833 21.01 2.01 35.50 4.11
132 133 4.679662 CCAACTACTGTAGATACAACCCG 58.320 47.826 21.01 0.00 35.50 5.28
133 134 4.400251 CCAACTACTGTAGATACAACCCGA 59.600 45.833 21.01 0.00 35.50 5.14
134 135 5.068723 CCAACTACTGTAGATACAACCCGAT 59.931 44.000 21.01 0.00 35.50 4.18
135 136 6.406624 CCAACTACTGTAGATACAACCCGATT 60.407 42.308 21.01 0.00 35.50 3.34
136 137 6.145338 ACTACTGTAGATACAACCCGATTG 57.855 41.667 21.01 0.00 44.60 2.67
146 147 2.710377 CAACCCGATTGTTGGAGATCA 58.290 47.619 0.00 0.00 41.49 2.92
147 148 3.081061 CAACCCGATTGTTGGAGATCAA 58.919 45.455 0.00 0.00 41.49 2.57
148 149 3.652057 ACCCGATTGTTGGAGATCAAT 57.348 42.857 0.00 0.00 37.73 2.57
149 150 3.282021 ACCCGATTGTTGGAGATCAATG 58.718 45.455 0.00 0.00 37.73 2.82
150 151 2.033801 CCCGATTGTTGGAGATCAATGC 59.966 50.000 0.00 0.00 37.73 3.56
151 152 2.684374 CCGATTGTTGGAGATCAATGCA 59.316 45.455 0.00 0.00 37.73 3.96
152 153 3.242969 CCGATTGTTGGAGATCAATGCAG 60.243 47.826 0.00 0.00 37.73 4.41
153 154 3.703420 GATTGTTGGAGATCAATGCAGC 58.297 45.455 0.00 0.00 37.73 5.25
154 155 2.502142 TGTTGGAGATCAATGCAGCT 57.498 45.000 0.00 0.00 37.73 4.24
155 156 3.632643 TGTTGGAGATCAATGCAGCTA 57.367 42.857 0.00 0.00 37.73 3.32
156 157 3.538591 TGTTGGAGATCAATGCAGCTAG 58.461 45.455 0.00 0.00 37.73 3.42
157 158 3.198417 TGTTGGAGATCAATGCAGCTAGA 59.802 43.478 0.00 0.00 37.73 2.43
158 159 3.747854 TGGAGATCAATGCAGCTAGAG 57.252 47.619 0.00 0.00 0.00 2.43
159 160 2.367894 TGGAGATCAATGCAGCTAGAGG 59.632 50.000 0.00 0.00 0.00 3.69
248 249 1.280133 TGGCTTCACAAGATCTCTGGG 59.720 52.381 0.00 0.00 0.00 4.45
265 270 1.407258 TGGGTTTGGCACTCTTTTTCG 59.593 47.619 0.00 0.00 0.00 3.46
266 271 1.269569 GGGTTTGGCACTCTTTTTCGG 60.270 52.381 0.00 0.00 0.00 4.30
267 272 1.407618 GGTTTGGCACTCTTTTTCGGT 59.592 47.619 0.00 0.00 0.00 4.69
282 288 1.226974 CGGTATGGCCACTCTCACG 60.227 63.158 8.16 3.34 36.97 4.35
299 305 0.850217 ACGACGACATCAACGTGTTG 59.150 50.000 0.00 6.39 43.97 3.33
304 310 0.588252 GACATCAACGTGTTGCAGCT 59.412 50.000 7.85 0.00 40.24 4.24
318 324 0.603975 GCAGCTTTCTCCGGTGTTCT 60.604 55.000 0.00 0.00 32.75 3.01
416 422 7.122715 ACCTAGCTAATGGTATCTATCCTCAG 58.877 42.308 2.88 0.00 34.36 3.35
466 472 0.259356 CCCGGTAGGAGAGAAGAGGT 59.741 60.000 0.00 0.00 41.02 3.85
480 486 5.833131 AGAGAAGAGGTAGAGATTTGCCTAG 59.167 44.000 0.00 0.00 0.00 3.02
495 501 1.406205 GCCTAGGCACAAGAGAGTTCC 60.406 57.143 29.33 0.00 41.49 3.62
524 531 1.678627 TGTGGATCGTGTTTTTGGTGG 59.321 47.619 0.00 0.00 0.00 4.61
538 545 2.743636 TGGTGGTCTTCAATCTCGAC 57.256 50.000 0.00 0.00 0.00 4.20
638 646 7.153985 TGCACAATATGATCATAGATGACGAA 58.846 34.615 26.22 14.86 40.03 3.85
669 678 6.381133 GGATGAAATCTATGACCAAGGGTTTT 59.619 38.462 0.00 0.00 44.71 2.43
741 750 7.095691 CGTTTGCACAGTTTATCCAATTTCATT 60.096 33.333 0.00 0.00 0.00 2.57
742 751 7.655236 TTGCACAGTTTATCCAATTTCATTG 57.345 32.000 0.00 0.00 39.94 2.82
758 767 8.757789 CAATTTCATTGGGATTAATGATTGACG 58.242 33.333 0.00 0.00 44.12 4.35
759 768 5.437289 TCATTGGGATTAATGATTGACGC 57.563 39.130 0.00 0.00 40.95 5.19
760 769 3.961477 TTGGGATTAATGATTGACGCG 57.039 42.857 3.53 3.53 0.00 6.01
761 770 2.912771 TGGGATTAATGATTGACGCGT 58.087 42.857 13.85 13.85 0.00 6.01
762 771 2.869801 TGGGATTAATGATTGACGCGTC 59.130 45.455 31.66 31.66 0.00 5.19
763 772 2.096909 GGGATTAATGATTGACGCGTCG 60.097 50.000 31.88 0.00 0.00 5.12
764 773 2.792674 GGATTAATGATTGACGCGTCGA 59.207 45.455 30.13 30.13 0.00 4.20
765 774 3.121328 GGATTAATGATTGACGCGTCGAG 60.121 47.826 31.05 0.00 0.00 4.04
766 775 1.197055 TAATGATTGACGCGTCGAGC 58.803 50.000 32.40 32.40 43.95 5.03
777 786 4.373116 GTCGAGCGTGGCAGGGAA 62.373 66.667 9.49 0.00 0.00 3.97
778 787 4.373116 TCGAGCGTGGCAGGGAAC 62.373 66.667 9.49 0.00 0.00 3.62
798 807 6.228258 GGAACCAAATTTTTCTTTCTACCCC 58.772 40.000 3.32 0.00 0.00 4.95
799 808 6.183361 GGAACCAAATTTTTCTTTCTACCCCA 60.183 38.462 3.32 0.00 0.00 4.96
800 809 6.816616 ACCAAATTTTTCTTTCTACCCCAA 57.183 33.333 0.00 0.00 0.00 4.12
801 810 7.201702 ACCAAATTTTTCTTTCTACCCCAAA 57.798 32.000 0.00 0.00 0.00 3.28
802 811 7.811282 ACCAAATTTTTCTTTCTACCCCAAAT 58.189 30.769 0.00 0.00 0.00 2.32
809 818 6.894339 TTCTTTCTACCCCAAATCAGTTTC 57.106 37.500 0.00 0.00 0.00 2.78
834 843 3.192922 GCCAAATAGACGCGCGGT 61.193 61.111 35.22 23.01 0.00 5.68
835 844 3.003478 CCAAATAGACGCGCGGTC 58.997 61.111 35.22 26.43 46.45 4.79
850 859 1.610624 GCGGTCTCCAGTCCAATTTCA 60.611 52.381 0.00 0.00 0.00 2.69
851 860 2.350522 CGGTCTCCAGTCCAATTTCAG 58.649 52.381 0.00 0.00 0.00 3.02
883 892 5.847111 TGCGCACCCTACCTTATATATAG 57.153 43.478 5.66 0.00 0.00 1.31
913 922 4.281435 ACATCACATCCAATTCACAAGCAA 59.719 37.500 0.00 0.00 0.00 3.91
926 935 3.831333 TCACAAGCAACATCTCTCTCTCT 59.169 43.478 0.00 0.00 0.00 3.10
931 940 4.603131 AGCAACATCTCTCTCTCTCTCTT 58.397 43.478 0.00 0.00 0.00 2.85
932 941 5.018809 AGCAACATCTCTCTCTCTCTCTTT 58.981 41.667 0.00 0.00 0.00 2.52
933 942 5.126061 AGCAACATCTCTCTCTCTCTCTTTC 59.874 44.000 0.00 0.00 0.00 2.62
934 943 5.126061 GCAACATCTCTCTCTCTCTCTTTCT 59.874 44.000 0.00 0.00 0.00 2.52
935 944 6.678900 GCAACATCTCTCTCTCTCTCTTTCTC 60.679 46.154 0.00 0.00 0.00 2.87
936 945 6.319048 ACATCTCTCTCTCTCTCTTTCTCT 57.681 41.667 0.00 0.00 0.00 3.10
949 958 2.963101 TCTTTCTCTGTTCCCGTTCTGA 59.037 45.455 0.00 0.00 0.00 3.27
963 972 2.694213 GTTCTGAAGTTCTGCTCTCCC 58.306 52.381 4.17 0.00 0.00 4.30
977 986 0.999712 TCTCCCCTGTTCCCCATTTC 59.000 55.000 0.00 0.00 0.00 2.17
983 994 1.616994 CCTGTTCCCCATTTCCACCTC 60.617 57.143 0.00 0.00 0.00 3.85
993 1004 1.741028 TTTCCACCTCCACTGATCCA 58.259 50.000 0.00 0.00 0.00 3.41
996 1007 1.361197 TCCACCTCCACTGATCCAGTA 59.639 52.381 0.00 0.00 43.43 2.74
999 1010 1.273267 ACCTCCACTGATCCAGTAGCA 60.273 52.381 0.00 0.00 43.43 3.49
1015 1026 2.268076 GCAATGCCGTGTCCCAAGT 61.268 57.895 0.00 0.00 0.00 3.16
1038 1049 3.319405 TGAAGAGTCTCAAGTCACTCACC 59.681 47.826 1.94 0.00 41.43 4.02
1122 1133 1.548973 CGCCGTCGTATGGAAGCATC 61.549 60.000 0.00 0.00 0.00 3.91
1129 1140 1.209128 GTATGGAAGCATCGTCACCG 58.791 55.000 0.00 0.00 0.00 4.94
1218 1229 1.831580 AGCTCCAGGTGAGAATTTGC 58.168 50.000 0.00 0.00 44.42 3.68
1235 1246 7.344913 AGAATTTGCTCAACTCTATGATTCCT 58.655 34.615 0.00 0.00 0.00 3.36
1236 1247 6.939132 ATTTGCTCAACTCTATGATTCCTG 57.061 37.500 0.00 0.00 0.00 3.86
1246 1284 0.749454 ATGATTCCTGGCGCTGGTTC 60.749 55.000 7.64 11.85 0.00 3.62
1247 1285 1.078143 GATTCCTGGCGCTGGTTCT 60.078 57.895 7.64 0.00 0.00 3.01
1257 1295 1.423395 CGCTGGTTCTGTTCTGACTC 58.577 55.000 0.00 0.00 0.00 3.36
1258 1296 1.000283 CGCTGGTTCTGTTCTGACTCT 60.000 52.381 0.00 0.00 0.00 3.24
1260 1298 2.805099 GCTGGTTCTGTTCTGACTCTTG 59.195 50.000 0.00 0.00 0.00 3.02
1262 1300 2.435805 TGGTTCTGTTCTGACTCTTGCT 59.564 45.455 0.00 0.00 0.00 3.91
1263 1301 2.805099 GGTTCTGTTCTGACTCTTGCTG 59.195 50.000 0.00 0.00 0.00 4.41
1264 1302 3.493350 GGTTCTGTTCTGACTCTTGCTGA 60.493 47.826 0.00 0.00 0.00 4.26
1265 1303 4.314121 GTTCTGTTCTGACTCTTGCTGAT 58.686 43.478 0.00 0.00 0.00 2.90
1266 1304 4.613925 TCTGTTCTGACTCTTGCTGATT 57.386 40.909 0.00 0.00 0.00 2.57
1275 1313 2.224719 ACTCTTGCTGATTCCTGCTTGT 60.225 45.455 0.00 0.00 37.99 3.16
1298 1336 1.006086 TGCTTCATCCATTACACGCG 58.994 50.000 3.53 3.53 0.00 6.01
1302 1340 0.529773 TCATCCATTACACGCGGCTC 60.530 55.000 12.47 0.00 0.00 4.70
1313 1353 1.154093 CGCGGCTCGTTCTGTTCTA 60.154 57.895 0.00 0.00 0.00 2.10
1316 1356 1.669211 GCGGCTCGTTCTGTTCTAACT 60.669 52.381 0.00 0.00 0.00 2.24
1323 1363 4.049186 TCGTTCTGTTCTAACTGTTGCTC 58.951 43.478 2.69 0.00 0.00 4.26
1347 1395 1.795162 GCGTTTGCTTCATCCATTCCG 60.795 52.381 0.00 0.00 38.39 4.30
1570 1618 0.457851 AAGATCTTCCCTCGCGTCAG 59.542 55.000 5.77 0.00 0.00 3.51
1765 1815 2.165845 ACGATGTAAGTTCTTCCCTCCG 59.834 50.000 0.00 0.00 0.00 4.63
1785 1835 2.224549 CGCTCCAAATAAACGTGTTCCA 59.775 45.455 0.00 0.00 0.00 3.53
1793 1843 5.873179 AATAAACGTGTTCCATCGTTCAT 57.127 34.783 3.60 0.00 46.95 2.57
1794 1844 5.873179 ATAAACGTGTTCCATCGTTCATT 57.127 34.783 3.60 0.00 46.95 2.57
1795 1845 4.561735 AAACGTGTTCCATCGTTCATTT 57.438 36.364 3.60 0.00 46.95 2.32
1796 1846 3.536158 ACGTGTTCCATCGTTCATTTG 57.464 42.857 0.00 0.00 36.93 2.32
1848 1902 0.179181 TCGCAGTAACGTCGATCACC 60.179 55.000 0.00 0.00 0.00 4.02
1881 1941 2.430921 AGGCTCAAAGCGACGTCG 60.431 61.111 32.57 32.57 43.62 5.12
1965 2025 1.362717 CACCACTTCGAGACCACGT 59.637 57.895 0.00 0.00 34.70 4.49
2162 2222 3.353836 GCCAAGCTCGCGGACAAA 61.354 61.111 6.13 0.00 0.00 2.83
2168 2228 1.058903 GCTCGCGGACAAATTCGAC 59.941 57.895 6.13 0.00 0.00 4.20
2225 2285 2.548480 GCTCTACAACAAAGGTGTGTCC 59.452 50.000 0.00 0.00 38.27 4.02
2240 2300 0.467474 TGTCCCCGCTCATCGATAGT 60.467 55.000 0.00 0.00 41.67 2.12
2330 2390 4.513519 CGCTACCTTCGCATCCAA 57.486 55.556 0.00 0.00 0.00 3.53
2354 2414 1.550976 GACGATCTCAAGGGGAACACT 59.449 52.381 0.00 0.00 0.00 3.55
2388 2448 2.742372 CCACGCCGGAGAACTTGG 60.742 66.667 13.83 5.00 36.56 3.61
2435 2495 4.442706 CACTACTGAAGAAACAGGTGTGT 58.557 43.478 0.00 0.00 41.59 3.72
2472 2532 2.548295 GGAAAAAGCGTGCCGGACA 61.548 57.895 5.05 0.00 0.00 4.02
2503 2563 0.318762 ACCAACGAGGAAGAGCTGAC 59.681 55.000 0.00 0.00 41.22 3.51
2520 2580 1.001393 ACCCATTTCGCCCGAATGT 60.001 52.632 3.77 0.00 33.79 2.71
2615 2675 4.097418 GGGATTTGAGGCTAGCTAGGATA 58.903 47.826 22.10 0.00 0.00 2.59
2626 2686 5.163364 GGCTAGCTAGGATATACATGCATGT 60.163 44.000 33.20 33.20 44.48 3.21
2629 2689 6.364568 AGCTAGGATATACATGCATGTCAA 57.635 37.500 34.54 23.45 41.97 3.18
2648 2708 8.676401 CATGTCAAATGATATGAACTGTTGGTA 58.324 33.333 13.09 0.00 43.58 3.25
2655 2715 9.866655 AATGATATGAACTGTTGGTATGGTATT 57.133 29.630 0.00 0.00 0.00 1.89
2663 2723 9.174166 GAACTGTTGGTATGGTATTTACTGATT 57.826 33.333 0.00 0.00 0.00 2.57
2753 2813 7.067496 TCATTAACTAGGATGAGTGATTCCC 57.933 40.000 0.00 0.00 32.05 3.97
2755 2815 7.293299 TCATTAACTAGGATGAGTGATTCCCAT 59.707 37.037 0.00 0.00 32.05 4.00
2757 2817 8.561536 TTAACTAGGATGAGTGATTCCCATTA 57.438 34.615 0.00 0.00 32.05 1.90
2759 2819 8.742125 AACTAGGATGAGTGATTCCCATTATA 57.258 34.615 0.00 0.00 32.05 0.98
2763 2823 8.685257 AGGATGAGTGATTCCCATTATATACA 57.315 34.615 0.00 0.00 32.05 2.29
2764 2824 8.543774 AGGATGAGTGATTCCCATTATATACAC 58.456 37.037 0.00 0.00 32.05 2.90
2766 2826 9.896645 GATGAGTGATTCCCATTATATACACAT 57.103 33.333 0.00 0.00 0.00 3.21
2767 2827 9.676861 ATGAGTGATTCCCATTATATACACATG 57.323 33.333 0.00 0.00 0.00 3.21
2768 2828 8.102676 TGAGTGATTCCCATTATATACACATGG 58.897 37.037 0.00 5.30 37.76 3.66
2800 3467 6.009589 CAGGGCATAATATATGTTTCCCACA 58.990 40.000 14.67 0.00 40.71 4.17
2930 3602 6.773976 TTTTAATGTTCATCCCTGGATCAC 57.226 37.500 0.00 0.00 31.62 3.06
3138 3810 7.250569 ACATTTATGTAATTGCAAACTCTCCG 58.749 34.615 1.71 0.00 39.68 4.63
3157 3829 7.562088 ACTCTCCGATTTCTTTCTAGGAGTAAT 59.438 37.037 8.86 0.00 44.02 1.89
3353 4025 0.773644 AACTGGGTGCTTGTCTCCAT 59.226 50.000 0.00 0.00 0.00 3.41
3382 4054 3.867984 GCTCCTTTCCAGAACTCTCCTTG 60.868 52.174 0.00 0.00 0.00 3.61
3552 4224 0.101939 GCAGGTACCACCGCTACTAC 59.898 60.000 15.94 0.00 44.90 2.73
3569 4241 1.407258 CTACCTGAAGAGAAGAGCCCG 59.593 57.143 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.907837 CACTCATGCGAACGTACTCG 59.092 55.000 5.29 5.29 41.84 4.18
14 15 2.177977 CTCACTCATGCGAACGTACTC 58.822 52.381 0.00 0.00 0.00 2.59
15 16 1.540267 ACTCACTCATGCGAACGTACT 59.460 47.619 0.00 0.00 0.00 2.73
16 17 1.912110 GACTCACTCATGCGAACGTAC 59.088 52.381 0.00 0.00 0.00 3.67
17 18 1.135489 GGACTCACTCATGCGAACGTA 60.135 52.381 0.00 0.00 0.00 3.57
18 19 0.388649 GGACTCACTCATGCGAACGT 60.389 55.000 0.00 0.00 0.00 3.99
19 20 0.388520 TGGACTCACTCATGCGAACG 60.389 55.000 0.00 0.00 0.00 3.95
20 21 1.071605 GTGGACTCACTCATGCGAAC 58.928 55.000 0.00 0.00 40.58 3.95
21 22 3.514777 GTGGACTCACTCATGCGAA 57.485 52.632 0.00 0.00 40.58 4.70
30 31 5.784177 TGAAATCTAGACAAGTGGACTCAC 58.216 41.667 0.00 0.00 43.93 3.51
31 32 6.014242 ACATGAAATCTAGACAAGTGGACTCA 60.014 38.462 0.00 0.00 0.00 3.41
32 33 6.402222 ACATGAAATCTAGACAAGTGGACTC 58.598 40.000 0.00 0.00 0.00 3.36
33 34 6.365970 ACATGAAATCTAGACAAGTGGACT 57.634 37.500 0.00 0.00 0.00 3.85
34 35 7.097192 TGTACATGAAATCTAGACAAGTGGAC 58.903 38.462 0.00 0.00 0.00 4.02
35 36 7.239763 TGTACATGAAATCTAGACAAGTGGA 57.760 36.000 0.00 0.00 0.00 4.02
36 37 7.905604 TTGTACATGAAATCTAGACAAGTGG 57.094 36.000 0.00 0.00 0.00 4.00
39 40 9.429359 AGAACTTGTACATGAAATCTAGACAAG 57.571 33.333 15.13 11.52 44.90 3.16
41 42 9.856488 GTAGAACTTGTACATGAAATCTAGACA 57.144 33.333 15.13 0.00 0.00 3.41
42 43 9.856488 TGTAGAACTTGTACATGAAATCTAGAC 57.144 33.333 15.13 10.76 0.00 2.59
45 46 9.653287 CCTTGTAGAACTTGTACATGAAATCTA 57.347 33.333 15.13 14.37 30.54 1.98
46 47 7.119846 GCCTTGTAGAACTTGTACATGAAATCT 59.880 37.037 15.13 15.17 30.54 2.40
47 48 7.094805 TGCCTTGTAGAACTTGTACATGAAATC 60.095 37.037 15.13 9.81 30.54 2.17
48 49 6.714810 TGCCTTGTAGAACTTGTACATGAAAT 59.285 34.615 15.13 1.70 30.54 2.17
49 50 6.058833 TGCCTTGTAGAACTTGTACATGAAA 58.941 36.000 15.13 0.00 30.54 2.69
50 51 5.616270 TGCCTTGTAGAACTTGTACATGAA 58.384 37.500 15.13 0.00 30.54 2.57
51 52 5.221641 ACTGCCTTGTAGAACTTGTACATGA 60.222 40.000 15.13 0.00 30.54 3.07
52 53 4.997395 ACTGCCTTGTAGAACTTGTACATG 59.003 41.667 7.18 7.18 30.54 3.21
53 54 4.997395 CACTGCCTTGTAGAACTTGTACAT 59.003 41.667 0.00 0.00 30.54 2.29
54 55 4.377021 CACTGCCTTGTAGAACTTGTACA 58.623 43.478 0.00 0.00 0.00 2.90
55 56 3.746492 CCACTGCCTTGTAGAACTTGTAC 59.254 47.826 0.00 0.00 0.00 2.90
56 57 3.389983 ACCACTGCCTTGTAGAACTTGTA 59.610 43.478 0.00 0.00 0.00 2.41
57 58 2.172717 ACCACTGCCTTGTAGAACTTGT 59.827 45.455 0.00 0.00 0.00 3.16
58 59 2.549754 CACCACTGCCTTGTAGAACTTG 59.450 50.000 0.00 0.00 0.00 3.16
59 60 2.487265 CCACCACTGCCTTGTAGAACTT 60.487 50.000 0.00 0.00 0.00 2.66
60 61 1.072331 CCACCACTGCCTTGTAGAACT 59.928 52.381 0.00 0.00 0.00 3.01
61 62 1.523758 CCACCACTGCCTTGTAGAAC 58.476 55.000 0.00 0.00 0.00 3.01
62 63 0.250727 GCCACCACTGCCTTGTAGAA 60.251 55.000 0.00 0.00 0.00 2.10
63 64 1.374947 GCCACCACTGCCTTGTAGA 59.625 57.895 0.00 0.00 0.00 2.59
64 65 0.957395 CTGCCACCACTGCCTTGTAG 60.957 60.000 0.00 0.00 0.00 2.74
65 66 1.073025 CTGCCACCACTGCCTTGTA 59.927 57.895 0.00 0.00 0.00 2.41
66 67 2.203394 CTGCCACCACTGCCTTGT 60.203 61.111 0.00 0.00 0.00 3.16
67 68 2.203394 ACTGCCACCACTGCCTTG 60.203 61.111 0.00 0.00 0.00 3.61
68 69 2.203394 CACTGCCACCACTGCCTT 60.203 61.111 0.00 0.00 0.00 4.35
69 70 2.572333 AAACACTGCCACCACTGCCT 62.572 55.000 0.00 0.00 0.00 4.75
70 71 2.127232 AAACACTGCCACCACTGCC 61.127 57.895 0.00 0.00 0.00 4.85
71 72 1.066257 CAAACACTGCCACCACTGC 59.934 57.895 0.00 0.00 0.00 4.40
72 73 1.066257 GCAAACACTGCCACCACTG 59.934 57.895 0.00 0.00 46.13 3.66
73 74 3.525221 GCAAACACTGCCACCACT 58.475 55.556 0.00 0.00 46.13 4.00
81 82 1.072331 AGTACTCCAGGGCAAACACTG 59.928 52.381 0.00 0.00 34.54 3.66
82 83 1.435256 AGTACTCCAGGGCAAACACT 58.565 50.000 0.00 0.00 0.00 3.55
83 84 1.880027 CAAGTACTCCAGGGCAAACAC 59.120 52.381 0.00 0.00 0.00 3.32
84 85 1.771854 TCAAGTACTCCAGGGCAAACA 59.228 47.619 0.00 0.00 0.00 2.83
85 86 2.038557 TCTCAAGTACTCCAGGGCAAAC 59.961 50.000 0.00 0.00 0.00 2.93
86 87 2.303022 CTCTCAAGTACTCCAGGGCAAA 59.697 50.000 0.00 0.00 0.00 3.68
87 88 1.902508 CTCTCAAGTACTCCAGGGCAA 59.097 52.381 0.00 0.00 0.00 4.52
88 89 1.077169 TCTCTCAAGTACTCCAGGGCA 59.923 52.381 0.00 0.00 0.00 5.36
89 90 1.754226 CTCTCTCAAGTACTCCAGGGC 59.246 57.143 0.00 0.00 0.00 5.19
90 91 1.754226 GCTCTCTCAAGTACTCCAGGG 59.246 57.143 0.00 0.00 0.00 4.45
91 92 1.754226 GGCTCTCTCAAGTACTCCAGG 59.246 57.143 0.00 0.00 0.00 4.45
92 93 2.451490 TGGCTCTCTCAAGTACTCCAG 58.549 52.381 0.00 0.00 0.00 3.86
93 94 2.563179 GTTGGCTCTCTCAAGTACTCCA 59.437 50.000 0.00 0.00 0.00 3.86
94 95 2.829120 AGTTGGCTCTCTCAAGTACTCC 59.171 50.000 0.00 0.00 0.00 3.85
95 96 4.989044 GTAGTTGGCTCTCTCAAGTACTC 58.011 47.826 0.00 0.00 42.87 2.59
97 98 4.218852 ACAGTAGTTGGCTCTCTCAAGTAC 59.781 45.833 11.63 11.63 44.81 2.73
98 99 4.408276 ACAGTAGTTGGCTCTCTCAAGTA 58.592 43.478 0.00 0.00 0.00 2.24
99 100 3.235200 ACAGTAGTTGGCTCTCTCAAGT 58.765 45.455 0.00 0.00 0.00 3.16
100 101 3.951775 ACAGTAGTTGGCTCTCTCAAG 57.048 47.619 0.00 0.00 0.00 3.02
101 102 4.663334 TCTACAGTAGTTGGCTCTCTCAA 58.337 43.478 7.50 0.00 0.00 3.02
102 103 4.302559 TCTACAGTAGTTGGCTCTCTCA 57.697 45.455 7.50 0.00 0.00 3.27
103 104 5.823570 TGTATCTACAGTAGTTGGCTCTCTC 59.176 44.000 7.50 0.00 0.00 3.20
104 105 5.756918 TGTATCTACAGTAGTTGGCTCTCT 58.243 41.667 7.50 0.00 0.00 3.10
105 106 6.267070 GTTGTATCTACAGTAGTTGGCTCTC 58.733 44.000 7.50 0.00 37.52 3.20
106 107 5.127356 GGTTGTATCTACAGTAGTTGGCTCT 59.873 44.000 7.50 0.00 37.52 4.09
107 108 5.349809 GGTTGTATCTACAGTAGTTGGCTC 58.650 45.833 7.50 0.00 37.52 4.70
108 109 4.161754 GGGTTGTATCTACAGTAGTTGGCT 59.838 45.833 7.50 0.00 37.52 4.75
109 110 4.439968 GGGTTGTATCTACAGTAGTTGGC 58.560 47.826 7.50 0.00 37.52 4.52
110 111 4.400251 TCGGGTTGTATCTACAGTAGTTGG 59.600 45.833 7.50 0.00 37.52 3.77
111 112 5.571784 TCGGGTTGTATCTACAGTAGTTG 57.428 43.478 7.50 0.00 37.52 3.16
112 113 6.570692 CAATCGGGTTGTATCTACAGTAGTT 58.429 40.000 7.50 2.04 37.52 2.24
113 114 6.145338 CAATCGGGTTGTATCTACAGTAGT 57.855 41.667 7.50 0.00 37.52 2.73
126 127 2.710377 TGATCTCCAACAATCGGGTTG 58.290 47.619 0.00 0.00 45.97 3.77
127 128 3.433306 TTGATCTCCAACAATCGGGTT 57.567 42.857 0.00 0.00 0.00 4.11
128 129 3.282021 CATTGATCTCCAACAATCGGGT 58.718 45.455 0.00 0.00 37.63 5.28
129 130 2.033801 GCATTGATCTCCAACAATCGGG 59.966 50.000 0.00 0.00 37.63 5.14
130 131 2.684374 TGCATTGATCTCCAACAATCGG 59.316 45.455 0.00 0.00 37.63 4.18
131 132 3.791122 GCTGCATTGATCTCCAACAATCG 60.791 47.826 0.00 0.00 37.63 3.34
132 133 3.380637 AGCTGCATTGATCTCCAACAATC 59.619 43.478 1.02 0.00 37.63 2.67
133 134 3.362706 AGCTGCATTGATCTCCAACAAT 58.637 40.909 1.02 0.00 37.63 2.71
134 135 2.799017 AGCTGCATTGATCTCCAACAA 58.201 42.857 1.02 0.00 37.63 2.83
135 136 2.502142 AGCTGCATTGATCTCCAACA 57.498 45.000 1.02 0.00 37.63 3.33
136 137 3.801698 TCTAGCTGCATTGATCTCCAAC 58.198 45.455 1.02 0.00 37.63 3.77
137 138 3.181457 CCTCTAGCTGCATTGATCTCCAA 60.181 47.826 1.02 0.00 39.41 3.53
138 139 2.367894 CCTCTAGCTGCATTGATCTCCA 59.632 50.000 1.02 0.00 0.00 3.86
139 140 2.632028 TCCTCTAGCTGCATTGATCTCC 59.368 50.000 1.02 0.00 0.00 3.71
140 141 4.247258 CATCCTCTAGCTGCATTGATCTC 58.753 47.826 1.02 0.00 0.00 2.75
141 142 3.647113 ACATCCTCTAGCTGCATTGATCT 59.353 43.478 1.02 0.00 0.00 2.75
142 143 3.995705 GACATCCTCTAGCTGCATTGATC 59.004 47.826 1.02 0.00 0.00 2.92
143 144 3.244491 GGACATCCTCTAGCTGCATTGAT 60.244 47.826 1.02 0.00 0.00 2.57
144 145 2.103771 GGACATCCTCTAGCTGCATTGA 59.896 50.000 1.02 0.00 0.00 2.57
145 146 2.158856 TGGACATCCTCTAGCTGCATTG 60.159 50.000 1.02 0.00 36.82 2.82
146 147 2.121948 TGGACATCCTCTAGCTGCATT 58.878 47.619 1.02 0.00 36.82 3.56
147 148 1.798626 TGGACATCCTCTAGCTGCAT 58.201 50.000 1.02 0.00 36.82 3.96
148 149 1.690893 GATGGACATCCTCTAGCTGCA 59.309 52.381 1.02 0.00 36.82 4.41
149 150 1.969923 AGATGGACATCCTCTAGCTGC 59.030 52.381 8.60 0.00 38.58 5.25
150 151 2.288948 GCAGATGGACATCCTCTAGCTG 60.289 54.545 8.60 0.00 44.56 4.24
151 152 1.969923 GCAGATGGACATCCTCTAGCT 59.030 52.381 8.60 0.00 38.58 3.32
152 153 1.969923 AGCAGATGGACATCCTCTAGC 59.030 52.381 8.60 6.07 38.58 3.42
153 154 3.244146 CCAAGCAGATGGACATCCTCTAG 60.244 52.174 8.60 0.00 43.54 2.43
154 155 2.702478 CCAAGCAGATGGACATCCTCTA 59.298 50.000 8.60 0.00 43.54 2.43
155 156 1.489649 CCAAGCAGATGGACATCCTCT 59.510 52.381 8.60 3.85 43.54 3.69
156 157 1.964552 CCAAGCAGATGGACATCCTC 58.035 55.000 8.60 1.71 43.54 3.71
157 158 0.106819 GCCAAGCAGATGGACATCCT 60.107 55.000 8.60 0.00 43.54 3.24
158 159 0.394762 TGCCAAGCAGATGGACATCC 60.395 55.000 8.60 0.00 43.54 3.51
159 160 3.179925 TGCCAAGCAGATGGACATC 57.820 52.632 7.33 4.15 43.54 3.06
248 249 2.863401 ACCGAAAAAGAGTGCCAAAC 57.137 45.000 0.00 0.00 0.00 2.93
265 270 0.179108 GTCGTGAGAGTGGCCATACC 60.179 60.000 9.72 0.49 43.49 2.73
266 271 0.525668 CGTCGTGAGAGTGGCCATAC 60.526 60.000 9.72 6.34 43.49 2.39
267 272 0.678684 TCGTCGTGAGAGTGGCCATA 60.679 55.000 9.72 0.00 43.49 2.74
282 288 0.579630 TGCAACACGTTGATGTCGTC 59.420 50.000 13.97 0.00 42.93 4.20
299 305 0.603975 AGAACACCGGAGAAAGCTGC 60.604 55.000 9.46 0.00 0.00 5.25
304 310 1.542547 GCCTTCAGAACACCGGAGAAA 60.543 52.381 9.46 0.00 0.00 2.52
318 324 1.949525 GTTGTCTTCTGCAAGCCTTCA 59.050 47.619 0.00 0.00 0.00 3.02
480 486 0.687354 TCCTGGAACTCTCTTGTGCC 59.313 55.000 0.00 0.00 36.17 5.01
495 501 2.977914 ACACGATCCACATTCTTCCTG 58.022 47.619 0.00 0.00 0.00 3.86
524 531 0.806492 GCCCCGTCGAGATTGAAGAC 60.806 60.000 0.00 0.00 0.00 3.01
538 545 0.748005 AGGATTTGAACGATGCCCCG 60.748 55.000 0.00 0.00 0.00 5.73
632 640 2.753055 TTTCATCCGGACATTCGTCA 57.247 45.000 6.12 0.00 44.54 4.35
638 646 4.347876 TGGTCATAGATTTCATCCGGACAT 59.652 41.667 6.12 0.00 0.00 3.06
669 678 6.922957 GGCACAACATTTTCACTCTGAAATTA 59.077 34.615 0.00 0.00 44.75 1.40
741 750 2.869801 GACGCGTCAATCATTAATCCCA 59.130 45.455 33.09 0.00 0.00 4.37
742 751 2.096909 CGACGCGTCAATCATTAATCCC 60.097 50.000 35.71 7.38 0.00 3.85
743 752 2.792674 TCGACGCGTCAATCATTAATCC 59.207 45.455 35.71 7.84 0.00 3.01
744 753 3.659364 GCTCGACGCGTCAATCATTAATC 60.659 47.826 35.71 8.05 0.00 1.75
745 754 2.218759 GCTCGACGCGTCAATCATTAAT 59.781 45.455 35.71 0.00 0.00 1.40
746 755 1.586578 GCTCGACGCGTCAATCATTAA 59.413 47.619 35.71 11.26 0.00 1.40
747 756 1.197055 GCTCGACGCGTCAATCATTA 58.803 50.000 35.71 12.55 0.00 1.90
748 757 1.999051 GCTCGACGCGTCAATCATT 59.001 52.632 35.71 0.00 0.00 2.57
749 758 3.693245 GCTCGACGCGTCAATCAT 58.307 55.556 35.71 0.44 0.00 2.45
760 769 4.373116 TTCCCTGCCACGCTCGAC 62.373 66.667 0.00 0.00 0.00 4.20
761 770 4.373116 GTTCCCTGCCACGCTCGA 62.373 66.667 0.00 0.00 0.00 4.04
763 772 3.842925 TTGGTTCCCTGCCACGCTC 62.843 63.158 0.00 0.00 35.46 5.03
764 773 2.713531 ATTTGGTTCCCTGCCACGCT 62.714 55.000 0.00 0.00 35.46 5.07
765 774 1.815817 AATTTGGTTCCCTGCCACGC 61.816 55.000 0.00 0.00 35.46 5.34
766 775 0.678950 AAATTTGGTTCCCTGCCACG 59.321 50.000 0.00 0.00 35.46 4.94
767 776 2.928801 AAAATTTGGTTCCCTGCCAC 57.071 45.000 0.00 0.00 35.46 5.01
768 777 3.044894 AGAAAAATTTGGTTCCCTGCCA 58.955 40.909 0.00 0.00 0.00 4.92
769 778 3.769739 AGAAAAATTTGGTTCCCTGCC 57.230 42.857 0.00 0.00 0.00 4.85
770 779 5.368145 AGAAAGAAAAATTTGGTTCCCTGC 58.632 37.500 0.00 0.00 0.00 4.85
771 780 6.929049 GGTAGAAAGAAAAATTTGGTTCCCTG 59.071 38.462 0.00 0.00 0.00 4.45
772 781 6.042781 GGGTAGAAAGAAAAATTTGGTTCCCT 59.957 38.462 0.00 0.00 0.00 4.20
773 782 6.228258 GGGTAGAAAGAAAAATTTGGTTCCC 58.772 40.000 0.00 0.00 0.00 3.97
774 783 6.183361 TGGGGTAGAAAGAAAAATTTGGTTCC 60.183 38.462 0.00 0.00 0.00 3.62
775 784 6.822442 TGGGGTAGAAAGAAAAATTTGGTTC 58.178 36.000 0.00 0.00 0.00 3.62
776 785 6.816616 TGGGGTAGAAAGAAAAATTTGGTT 57.183 33.333 0.00 0.00 0.00 3.67
777 786 6.816616 TTGGGGTAGAAAGAAAAATTTGGT 57.183 33.333 0.00 0.00 0.00 3.67
778 787 7.936301 TGATTTGGGGTAGAAAGAAAAATTTGG 59.064 33.333 0.00 0.00 0.00 3.28
779 788 8.900983 TGATTTGGGGTAGAAAGAAAAATTTG 57.099 30.769 0.00 0.00 0.00 2.32
780 789 8.713971 ACTGATTTGGGGTAGAAAGAAAAATTT 58.286 29.630 0.00 0.00 0.00 1.82
781 790 8.262601 ACTGATTTGGGGTAGAAAGAAAAATT 57.737 30.769 0.00 0.00 0.00 1.82
782 791 7.855784 ACTGATTTGGGGTAGAAAGAAAAAT 57.144 32.000 0.00 0.00 0.00 1.82
783 792 7.669089 AACTGATTTGGGGTAGAAAGAAAAA 57.331 32.000 0.00 0.00 0.00 1.94
784 793 7.201965 GGAAACTGATTTGGGGTAGAAAGAAAA 60.202 37.037 0.00 0.00 0.00 2.29
785 794 6.266786 GGAAACTGATTTGGGGTAGAAAGAAA 59.733 38.462 0.00 0.00 0.00 2.52
786 795 5.773176 GGAAACTGATTTGGGGTAGAAAGAA 59.227 40.000 0.00 0.00 0.00 2.52
787 796 5.163034 TGGAAACTGATTTGGGGTAGAAAGA 60.163 40.000 0.00 0.00 0.00 2.52
788 797 5.076873 TGGAAACTGATTTGGGGTAGAAAG 58.923 41.667 0.00 0.00 0.00 2.62
789 798 5.068215 TGGAAACTGATTTGGGGTAGAAA 57.932 39.130 0.00 0.00 0.00 2.52
790 799 4.662278 CTGGAAACTGATTTGGGGTAGAA 58.338 43.478 0.00 0.00 0.00 2.10
791 800 3.561313 GCTGGAAACTGATTTGGGGTAGA 60.561 47.826 0.00 0.00 0.00 2.59
792 801 2.755103 GCTGGAAACTGATTTGGGGTAG 59.245 50.000 0.00 0.00 0.00 3.18
793 802 2.556559 GGCTGGAAACTGATTTGGGGTA 60.557 50.000 0.00 0.00 0.00 3.69
794 803 1.632589 GCTGGAAACTGATTTGGGGT 58.367 50.000 0.00 0.00 0.00 4.95
795 804 0.897621 GGCTGGAAACTGATTTGGGG 59.102 55.000 0.00 0.00 0.00 4.96
796 805 1.928868 AGGCTGGAAACTGATTTGGG 58.071 50.000 0.00 0.00 0.00 4.12
797 806 2.611224 GCAAGGCTGGAAACTGATTTGG 60.611 50.000 0.00 0.00 0.00 3.28
798 807 2.611224 GGCAAGGCTGGAAACTGATTTG 60.611 50.000 0.00 0.00 0.00 2.32
799 808 1.620323 GGCAAGGCTGGAAACTGATTT 59.380 47.619 0.00 0.00 0.00 2.17
800 809 1.260544 GGCAAGGCTGGAAACTGATT 58.739 50.000 0.00 0.00 0.00 2.57
801 810 0.112995 TGGCAAGGCTGGAAACTGAT 59.887 50.000 0.00 0.00 0.00 2.90
802 811 0.106268 TTGGCAAGGCTGGAAACTGA 60.106 50.000 0.00 0.00 0.00 3.41
809 818 0.734889 CGTCTATTTGGCAAGGCTGG 59.265 55.000 0.00 0.00 0.00 4.85
834 843 1.004745 GGGCTGAAATTGGACTGGAGA 59.995 52.381 0.00 0.00 0.00 3.71
835 844 1.467920 GGGCTGAAATTGGACTGGAG 58.532 55.000 0.00 0.00 0.00 3.86
844 853 1.809207 CAATCGCCGGGCTGAAATT 59.191 52.632 18.34 8.50 0.00 1.82
883 892 1.585267 TTGGATGTGATGTGTGCGCC 61.585 55.000 4.18 0.00 0.00 6.53
913 922 6.118170 CAGAGAAAGAGAGAGAGAGAGATGT 58.882 44.000 0.00 0.00 0.00 3.06
926 935 3.005897 CAGAACGGGAACAGAGAAAGAGA 59.994 47.826 0.00 0.00 0.00 3.10
931 940 2.698797 ACTTCAGAACGGGAACAGAGAA 59.301 45.455 0.00 0.00 0.00 2.87
932 941 2.317040 ACTTCAGAACGGGAACAGAGA 58.683 47.619 0.00 0.00 0.00 3.10
933 942 2.821991 ACTTCAGAACGGGAACAGAG 57.178 50.000 0.00 0.00 0.00 3.35
934 943 2.698797 AGAACTTCAGAACGGGAACAGA 59.301 45.455 0.00 0.00 0.00 3.41
935 944 2.802816 CAGAACTTCAGAACGGGAACAG 59.197 50.000 0.00 0.00 0.00 3.16
936 945 2.833794 CAGAACTTCAGAACGGGAACA 58.166 47.619 0.00 0.00 0.00 3.18
949 958 1.349357 GAACAGGGGAGAGCAGAACTT 59.651 52.381 0.00 0.00 0.00 2.66
963 972 0.409484 AGGTGGAAATGGGGAACAGG 59.591 55.000 0.00 0.00 0.00 4.00
977 986 1.759445 CTACTGGATCAGTGGAGGTGG 59.241 57.143 10.46 0.00 44.01 4.61
983 994 1.945394 GCATTGCTACTGGATCAGTGG 59.055 52.381 10.46 8.68 45.01 4.00
993 1004 1.078426 GGGACACGGCATTGCTACT 60.078 57.895 8.82 0.00 0.00 2.57
996 1007 1.973281 CTTGGGACACGGCATTGCT 60.973 57.895 8.82 0.00 39.29 3.91
999 1010 0.179004 TCAACTTGGGACACGGCATT 60.179 50.000 0.00 0.00 39.29 3.56
1015 1026 4.202161 GGTGAGTGACTTGAGACTCTTCAA 60.202 45.833 3.68 0.00 39.54 2.69
1129 1140 2.583593 GCCGTCGATGCTCAGGAC 60.584 66.667 0.00 0.00 0.00 3.85
1218 1229 3.388308 CGCCAGGAATCATAGAGTTGAG 58.612 50.000 0.00 0.00 0.00 3.02
1235 1246 1.597854 CAGAACAGAACCAGCGCCA 60.598 57.895 2.29 0.00 0.00 5.69
1236 1247 1.301716 TCAGAACAGAACCAGCGCC 60.302 57.895 2.29 0.00 0.00 6.53
1246 1284 3.683822 GGAATCAGCAAGAGTCAGAACAG 59.316 47.826 8.52 0.00 42.95 3.16
1247 1285 3.326006 AGGAATCAGCAAGAGTCAGAACA 59.674 43.478 8.52 0.00 42.95 3.18
1257 1295 1.884579 ACACAAGCAGGAATCAGCAAG 59.115 47.619 0.14 0.00 0.00 4.01
1258 1296 1.985473 ACACAAGCAGGAATCAGCAA 58.015 45.000 0.14 0.00 0.00 3.91
1260 1298 2.669364 CAAACACAAGCAGGAATCAGC 58.331 47.619 0.00 0.00 0.00 4.26
1262 1300 2.309613 AGCAAACACAAGCAGGAATCA 58.690 42.857 0.00 0.00 0.00 2.57
1263 1301 3.243501 TGAAGCAAACACAAGCAGGAATC 60.244 43.478 0.00 0.00 0.00 2.52
1264 1302 2.694628 TGAAGCAAACACAAGCAGGAAT 59.305 40.909 0.00 0.00 0.00 3.01
1265 1303 2.098614 TGAAGCAAACACAAGCAGGAA 58.901 42.857 0.00 0.00 0.00 3.36
1266 1304 1.761449 TGAAGCAAACACAAGCAGGA 58.239 45.000 0.00 0.00 0.00 3.86
1275 1313 3.365868 GCGTGTAATGGATGAAGCAAACA 60.366 43.478 0.00 0.00 0.00 2.83
1298 1336 3.027974 ACAGTTAGAACAGAACGAGCC 57.972 47.619 0.00 0.00 31.85 4.70
1302 1340 3.184581 GGAGCAACAGTTAGAACAGAACG 59.815 47.826 0.00 0.00 31.85 3.95
1313 1353 1.102978 AAACGCAAGGAGCAACAGTT 58.897 45.000 0.00 0.00 46.13 3.16
1316 1356 1.065600 GCAAACGCAAGGAGCAACA 59.934 52.632 0.00 0.00 46.13 3.33
1323 1363 0.597568 TGGATGAAGCAAACGCAAGG 59.402 50.000 0.00 0.00 46.39 3.61
1347 1395 0.666577 ACAGTTAGAACCAGCGACGC 60.667 55.000 13.03 13.03 0.00 5.19
1430 1478 1.303561 GCTGGTCCCTGCAATCACA 60.304 57.895 10.00 0.00 40.03 3.58
1765 1815 3.907894 TGGAACACGTTTATTTGGAGC 57.092 42.857 0.00 0.00 0.00 4.70
1793 1843 9.995957 GCAACATACATACATGTAATACACAAA 57.004 29.630 10.14 0.00 45.40 2.83
1794 1844 8.616942 GGCAACATACATACATGTAATACACAA 58.383 33.333 10.14 0.00 45.40 3.33
1795 1845 7.990314 AGGCAACATACATACATGTAATACACA 59.010 33.333 10.14 0.00 45.40 3.72
1796 1846 8.282592 CAGGCAACATACATACATGTAATACAC 58.717 37.037 10.14 0.00 45.40 2.90
1881 1941 2.436824 GAGGAGGGCGTCTTTGGC 60.437 66.667 7.19 0.00 0.00 4.52
1965 2025 3.047280 CGGCTTGCCGTGCTTGTA 61.047 61.111 24.03 0.00 0.00 2.41
1982 2042 0.720500 CGATCAGATTGAATGCGCGC 60.720 55.000 27.26 27.26 0.00 6.86
2162 2222 2.434884 CACTGGGCTGCGTCGAAT 60.435 61.111 0.00 0.00 0.00 3.34
2225 2285 2.936498 ACAAAAACTATCGATGAGCGGG 59.064 45.455 8.54 0.00 41.33 6.13
2240 2300 0.030638 GAGCGCTTGCCTGACAAAAA 59.969 50.000 13.26 0.00 37.96 1.94
2330 2390 2.432510 GTTCCCCTTGAGATCGTCATCT 59.567 50.000 0.00 0.00 42.59 2.90
2378 2438 2.508526 ACAAGCATGTCCAAGTTCTCC 58.491 47.619 0.00 0.00 33.41 3.71
2435 2495 0.738762 CGGTCTCGACGTCCACTCTA 60.739 60.000 10.58 0.00 39.00 2.43
2472 2532 1.002134 CGTTGGTGCCCCTCTTCAT 60.002 57.895 0.00 0.00 0.00 2.57
2503 2563 0.179140 CAACATTCGGGCGAAATGGG 60.179 55.000 13.05 3.80 37.69 4.00
2520 2580 0.234625 GACTTGCGTTCATGCGACAA 59.765 50.000 0.00 1.02 37.81 3.18
2537 2597 0.884514 GCTTCTTTTGGAGCCTGGAC 59.115 55.000 0.00 0.00 0.00 4.02
2586 2646 0.551131 AGCCTCAAATCCCAGGTCCT 60.551 55.000 0.00 0.00 31.65 3.85
2593 2653 2.330216 TCCTAGCTAGCCTCAAATCCC 58.670 52.381 15.74 0.00 0.00 3.85
2615 2675 9.074576 AGTTCATATCATTTGACATGCATGTAT 57.925 29.630 31.45 21.36 41.95 2.29
2626 2686 7.833682 ACCATACCAACAGTTCATATCATTTGA 59.166 33.333 0.00 0.00 0.00 2.69
2629 2689 9.866655 AATACCATACCAACAGTTCATATCATT 57.133 29.630 0.00 0.00 0.00 2.57
2648 2708 7.132128 ACATGGGGAAAATCAGTAAATACCAT 58.868 34.615 0.00 0.00 35.52 3.55
2691 2751 1.202964 TCCCGACACACCTTCTCTGTA 60.203 52.381 0.00 0.00 0.00 2.74
2729 2789 6.615316 TGGGAATCACTCATCCTAGTTAATGA 59.385 38.462 0.00 0.00 35.95 2.57
2733 2793 8.742125 ATAATGGGAATCACTCATCCTAGTTA 57.258 34.615 0.00 0.00 38.99 2.24
2734 2794 5.983333 AATGGGAATCACTCATCCTAGTT 57.017 39.130 0.00 0.00 38.99 2.24
2735 2795 8.923838 ATATAATGGGAATCACTCATCCTAGT 57.076 34.615 0.00 0.00 38.99 2.57
2737 2797 9.782900 TGTATATAATGGGAATCACTCATCCTA 57.217 33.333 0.00 0.00 38.99 2.94
2739 2799 8.321353 TGTGTATATAATGGGAATCACTCATCC 58.679 37.037 0.00 0.00 38.99 3.51
2740 2800 9.896645 ATGTGTATATAATGGGAATCACTCATC 57.103 33.333 0.00 0.00 38.99 2.92
2741 2801 9.676861 CATGTGTATATAATGGGAATCACTCAT 57.323 33.333 0.00 0.00 42.14 2.90
2742 2802 8.102676 CCATGTGTATATAATGGGAATCACTCA 58.897 37.037 4.56 0.00 37.74 3.41
2743 2803 8.498054 CCATGTGTATATAATGGGAATCACTC 57.502 38.462 4.56 0.00 37.74 3.51
2752 2812 8.648698 TGATTTTCCCCATGTGTATATAATGG 57.351 34.615 5.30 5.30 40.53 3.16
2753 2813 8.742777 CCTGATTTTCCCCATGTGTATATAATG 58.257 37.037 0.00 0.00 0.00 1.90
2755 2815 7.237982 CCCTGATTTTCCCCATGTGTATATAA 58.762 38.462 0.00 0.00 0.00 0.98
2757 2817 5.644188 CCCTGATTTTCCCCATGTGTATAT 58.356 41.667 0.00 0.00 0.00 0.86
2759 2819 3.914771 CCCTGATTTTCCCCATGTGTAT 58.085 45.455 0.00 0.00 0.00 2.29
2761 2821 1.896755 GCCCTGATTTTCCCCATGTGT 60.897 52.381 0.00 0.00 0.00 3.72
2762 2822 0.826062 GCCCTGATTTTCCCCATGTG 59.174 55.000 0.00 0.00 0.00 3.21
2763 2823 0.413037 TGCCCTGATTTTCCCCATGT 59.587 50.000 0.00 0.00 0.00 3.21
2764 2824 1.797320 ATGCCCTGATTTTCCCCATG 58.203 50.000 0.00 0.00 0.00 3.66
2766 2826 3.704545 ATTATGCCCTGATTTTCCCCA 57.295 42.857 0.00 0.00 0.00 4.96
2767 2827 6.897413 ACATATATTATGCCCTGATTTTCCCC 59.103 38.462 0.00 0.00 0.00 4.81
2768 2828 7.961326 ACATATATTATGCCCTGATTTTCCC 57.039 36.000 0.00 0.00 0.00 3.97
2769 2829 9.860898 GAAACATATATTATGCCCTGATTTTCC 57.139 33.333 0.00 0.00 0.00 3.13
2772 2832 7.955185 TGGGAAACATATATTATGCCCTGATTT 59.045 33.333 10.67 0.00 35.36 2.17
2773 2833 7.397192 GTGGGAAACATATATTATGCCCTGATT 59.603 37.037 10.67 0.00 35.36 2.57
2775 2835 6.183361 TGTGGGAAACATATATTATGCCCTGA 60.183 38.462 10.67 0.00 35.36 3.86
2776 2836 6.009589 TGTGGGAAACATATATTATGCCCTG 58.990 40.000 10.67 0.00 35.36 4.45
2845 3517 3.554324 GTGTGTGTTCGTGTCTTGTATGT 59.446 43.478 0.00 0.00 0.00 2.29
2907 3579 6.252233 TGTGATCCAGGGATGAACATTAAAA 58.748 36.000 5.35 0.00 34.60 1.52
2930 3602 0.462789 GATTTTGCTCCCAGGGCATG 59.537 55.000 0.00 0.00 39.54 4.06
3090 3762 4.463050 TTAGTTTGTGGGGGAAATGACT 57.537 40.909 0.00 0.00 0.00 3.41
3138 3810 8.184848 GTGGCAAATTACTCCTAGAAAGAAATC 58.815 37.037 0.00 0.00 0.00 2.17
3278 3950 4.460382 CCTTGCTTATTCCTCTGCTGAAAA 59.540 41.667 0.00 0.00 0.00 2.29
3279 3951 4.012374 CCTTGCTTATTCCTCTGCTGAAA 58.988 43.478 0.00 0.00 0.00 2.69
3280 3952 3.264193 TCCTTGCTTATTCCTCTGCTGAA 59.736 43.478 0.00 0.00 0.00 3.02
3281 3953 2.840038 TCCTTGCTTATTCCTCTGCTGA 59.160 45.455 0.00 0.00 0.00 4.26
3353 4025 3.009473 AGTTCTGGAAAGGAGCAATAGCA 59.991 43.478 0.00 0.00 45.49 3.49
3552 4224 1.153469 GCGGGCTCTTCTCTTCAGG 60.153 63.158 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.