Multiple sequence alignment - TraesCS5A01G499500

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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 TraesCS5A01G499500 chr5A 100.000 2690 0 0 1 2690 666117670 666114981 0.000000e+00 4968.0
1 TraesCS5A01G499500 chr5A 89.001 791 69 5 953 1730 666073533 666072748 0.000000e+00 963.0
2 TraesCS5A01G499500 chr5A 80.093 643 88 20 469 1108 666072730 666072125 2.460000e-120 442.0
3 TraesCS5A01G499500 chr5A 97.826 46 1 0 390 435 666074088 666074043 2.220000e-11 80.5
4 TraesCS5A01G499500 chr4D 93.980 1578 67 8 438 1991 485065528 485063955 0.000000e+00 2362.0
5 TraesCS5A01G499500 chr4D 93.916 1578 68 12 438 1991 485043585 485042012 0.000000e+00 2357.0
6 TraesCS5A01G499500 chr4D 89.602 1433 111 16 437 1842 484952399 484950978 0.000000e+00 1786.0
7 TraesCS5A01G499500 chr4D 88.156 895 81 8 971 1851 484929896 484929013 0.000000e+00 1042.0
8 TraesCS5A01G499500 chr4D 79.854 1504 215 42 431 1905 484927930 484926486 0.000000e+00 1018.0
9 TraesCS5A01G499500 chr4D 88.342 386 29 11 437 811 484934475 484934095 1.470000e-122 449.0
10 TraesCS5A01G499500 chr4D 95.294 85 3 1 34 118 485087565 485087482 1.680000e-27 134.0
11 TraesCS5A01G499500 chr4D 78.947 190 16 16 270 435 484952637 484952448 1.020000e-19 108.0
12 TraesCS5A01G499500 chr4D 93.333 60 4 0 279 338 484936022 484935963 3.690000e-14 89.8
13 TraesCS5A01G499500 chr4D 92.982 57 3 1 380 435 484934580 484934524 6.170000e-12 82.4
14 TraesCS5A01G499500 chr4B 94.045 1058 43 4 952 1991 618251540 618250485 0.000000e+00 1587.0
15 TraesCS5A01G499500 chr4B 79.644 1459 215 34 504 1930 618227588 618226180 0.000000e+00 974.0
16 TraesCS5A01G499500 chr4B 92.715 453 27 6 431 879 618252266 618251816 0.000000e+00 649.0
17 TraesCS5A01G499500 chr4B 90.000 370 25 8 437 796 618241604 618241237 4.060000e-128 468.0
18 TraesCS5A01G499500 chr4B 95.238 168 8 0 271 438 618252460 618252293 1.590000e-67 267.0
19 TraesCS5A01G499500 chr4B 91.379 116 9 1 161 276 618257191 618257077 9.970000e-35 158.0
20 TraesCS5A01G499500 chr4B 77.419 186 18 16 274 435 618241840 618241655 3.690000e-14 89.8
21 TraesCS5A01G499500 chr7D 93.842 682 41 1 1989 2670 609688212 609687532 0.000000e+00 1026.0
22 TraesCS5A01G499500 chrUn 84.856 766 103 3 978 1730 46203795 46204560 0.000000e+00 760.0
23 TraesCS5A01G499500 chr7B 90.909 440 37 3 1988 2424 706134709 706134270 2.980000e-164 588.0
24 TraesCS5A01G499500 chr3A 80.946 740 125 11 968 1692 735976101 735975363 3.000000e-159 571.0
25 TraesCS5A01G499500 chr2B 92.260 323 24 1 1992 2314 168056754 168057075 8.780000e-125 457.0
26 TraesCS5A01G499500 chr2B 91.358 324 27 1 1991 2314 168486888 168487210 2.460000e-120 442.0
27 TraesCS5A01G499500 chr3D 78.511 712 136 8 979 1674 566080982 566081692 4.080000e-123 451.0
28 TraesCS5A01G499500 chr3D 82.873 181 25 6 584 762 605034392 605034568 9.970000e-35 158.0
29 TraesCS5A01G499500 chr3B 80.426 235 42 4 528 761 813902248 813902479 2.750000e-40 176.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G499500 chr5A 666114981 666117670 2689 True 4968.000000 4968 100.000000 1 2690 1 chr5A.!!$R1 2689
1 TraesCS5A01G499500 chr5A 666072125 666074088 1963 True 495.166667 963 88.973333 390 1730 3 chr5A.!!$R2 1340
2 TraesCS5A01G499500 chr4D 485063955 485065528 1573 True 2362.000000 2362 93.980000 438 1991 1 chr4D.!!$R2 1553
3 TraesCS5A01G499500 chr4D 485042012 485043585 1573 True 2357.000000 2357 93.916000 438 1991 1 chr4D.!!$R1 1553
4 TraesCS5A01G499500 chr4D 484926486 484929896 3410 True 1030.000000 1042 84.005000 431 1905 2 chr4D.!!$R4 1474
5 TraesCS5A01G499500 chr4D 484950978 484952637 1659 True 947.000000 1786 84.274500 270 1842 2 chr4D.!!$R6 1572
6 TraesCS5A01G499500 chr4D 484934095 484936022 1927 True 207.066667 449 91.552333 279 811 3 chr4D.!!$R5 532
7 TraesCS5A01G499500 chr4B 618226180 618227588 1408 True 974.000000 974 79.644000 504 1930 1 chr4B.!!$R1 1426
8 TraesCS5A01G499500 chr4B 618250485 618252460 1975 True 834.333333 1587 93.999333 271 1991 3 chr4B.!!$R4 1720
9 TraesCS5A01G499500 chr4B 618241237 618241840 603 True 278.900000 468 83.709500 274 796 2 chr4B.!!$R3 522
10 TraesCS5A01G499500 chr7D 609687532 609688212 680 True 1026.000000 1026 93.842000 1989 2670 1 chr7D.!!$R1 681
11 TraesCS5A01G499500 chrUn 46203795 46204560 765 False 760.000000 760 84.856000 978 1730 1 chrUn.!!$F1 752
12 TraesCS5A01G499500 chr3A 735975363 735976101 738 True 571.000000 571 80.946000 968 1692 1 chr3A.!!$R1 724
13 TraesCS5A01G499500 chr3D 566080982 566081692 710 False 451.000000 451 78.511000 979 1674 1 chr3D.!!$F1 695

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
950 2757 0.039437 TCAGCGACGACCTTTCTGAC 60.039 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 4165 0.470766 AGCGGTTTGTGTTACCCTCA 59.529 50.0 0.0 0.0 31.75 3.86 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
25 26 8.915057 CTGATTATCTTTAATGATGGAGGTGT 57.085 34.615 12.81 0.00 0.00 4.16
31 32 7.333528 TCTTTAATGATGGAGGTGTTATTGC 57.666 36.000 0.00 0.00 0.00 3.56
32 33 6.889177 TCTTTAATGATGGAGGTGTTATTGCA 59.111 34.615 0.00 0.00 0.00 4.08
33 34 4.989279 AATGATGGAGGTGTTATTGCAC 57.011 40.909 0.00 0.00 38.56 4.57
34 35 3.719268 TGATGGAGGTGTTATTGCACT 57.281 42.857 0.00 0.00 39.21 4.40
35 36 4.032960 TGATGGAGGTGTTATTGCACTT 57.967 40.909 0.00 0.00 39.21 3.16
38 39 2.890311 TGGAGGTGTTATTGCACTTTGG 59.110 45.455 0.00 0.00 39.21 3.28
40 41 1.618343 AGGTGTTATTGCACTTTGGGC 59.382 47.619 0.00 0.00 39.21 5.36
42 43 2.823154 GGTGTTATTGCACTTTGGGCTA 59.177 45.455 0.00 0.00 39.21 3.93
43 44 3.366985 GGTGTTATTGCACTTTGGGCTAC 60.367 47.826 0.00 0.00 39.21 3.58
45 46 3.089284 GTTATTGCACTTTGGGCTACCT 58.911 45.455 0.00 0.00 37.76 3.08
46 47 1.549203 ATTGCACTTTGGGCTACCTG 58.451 50.000 0.00 0.00 37.76 4.00
47 48 0.539438 TTGCACTTTGGGCTACCTGG 60.539 55.000 0.00 0.00 37.76 4.45
48 49 1.378762 GCACTTTGGGCTACCTGGA 59.621 57.895 0.00 0.00 37.76 3.86
49 50 0.960861 GCACTTTGGGCTACCTGGAC 60.961 60.000 0.00 0.00 37.76 4.02
50 51 0.673644 CACTTTGGGCTACCTGGACG 60.674 60.000 0.00 0.00 37.76 4.79
51 52 0.834687 ACTTTGGGCTACCTGGACGA 60.835 55.000 0.00 0.00 37.76 4.20
53 54 1.760613 CTTTGGGCTACCTGGACGATA 59.239 52.381 0.00 0.00 37.76 2.92
55 56 1.410004 TGGGCTACCTGGACGATAAG 58.590 55.000 0.00 0.00 37.76 1.73
56 57 0.680061 GGGCTACCTGGACGATAAGG 59.320 60.000 0.00 0.00 39.65 2.69
57 58 1.700955 GGCTACCTGGACGATAAGGA 58.299 55.000 0.00 0.00 37.01 3.36
59 60 1.614413 GCTACCTGGACGATAAGGAGG 59.386 57.143 0.00 0.00 37.01 4.30
60 61 2.752154 GCTACCTGGACGATAAGGAGGA 60.752 54.545 0.00 0.00 37.01 3.71
61 62 2.544844 ACCTGGACGATAAGGAGGAA 57.455 50.000 0.00 0.00 37.01 3.36
62 63 2.389715 ACCTGGACGATAAGGAGGAAG 58.610 52.381 0.00 0.00 37.01 3.46
63 64 1.069358 CCTGGACGATAAGGAGGAAGC 59.931 57.143 0.00 0.00 35.40 3.86
64 65 2.035632 CTGGACGATAAGGAGGAAGCT 58.964 52.381 0.00 0.00 0.00 3.74
66 67 3.637229 CTGGACGATAAGGAGGAAGCTTA 59.363 47.826 0.00 0.00 0.00 3.09
67 68 4.223953 TGGACGATAAGGAGGAAGCTTAT 58.776 43.478 0.00 0.00 0.00 1.73
68 69 4.654262 TGGACGATAAGGAGGAAGCTTATT 59.346 41.667 0.00 0.00 0.00 1.40
69 70 5.221461 TGGACGATAAGGAGGAAGCTTATTC 60.221 44.000 0.00 0.00 0.00 1.75
72 73 4.681942 CGATAAGGAGGAAGCTTATTCACG 59.318 45.833 0.00 0.00 0.00 4.35
75 76 2.159226 AGGAGGAAGCTTATTCACGACG 60.159 50.000 0.00 0.00 0.00 5.12
76 77 2.194271 GAGGAAGCTTATTCACGACGG 58.806 52.381 0.00 0.00 0.00 4.79
77 78 1.822990 AGGAAGCTTATTCACGACGGA 59.177 47.619 0.00 0.00 0.00 4.69
78 79 2.232941 AGGAAGCTTATTCACGACGGAA 59.767 45.455 0.00 0.25 0.00 4.30
79 80 3.118738 AGGAAGCTTATTCACGACGGAAT 60.119 43.478 0.00 13.59 40.45 3.01
80 81 3.621715 GGAAGCTTATTCACGACGGAATT 59.378 43.478 14.10 1.07 38.41 2.17
81 82 4.807304 GGAAGCTTATTCACGACGGAATTA 59.193 41.667 14.10 7.05 38.41 1.40
82 83 5.276726 GGAAGCTTATTCACGACGGAATTAC 60.277 44.000 14.10 7.00 38.41 1.89
83 84 5.007385 AGCTTATTCACGACGGAATTACT 57.993 39.130 14.10 8.55 38.41 2.24
86 87 5.290158 GCTTATTCACGACGGAATTACTCAA 59.710 40.000 14.10 4.81 38.41 3.02
87 88 6.183360 GCTTATTCACGACGGAATTACTCAAA 60.183 38.462 14.10 4.30 38.41 2.69
89 90 4.247267 TCACGACGGAATTACTCAAAGT 57.753 40.909 0.00 0.00 0.00 2.66
90 91 4.624015 TCACGACGGAATTACTCAAAGTT 58.376 39.130 0.00 0.00 0.00 2.66
91 92 5.051816 TCACGACGGAATTACTCAAAGTTT 58.948 37.500 0.00 0.00 0.00 2.66
93 94 4.812626 ACGACGGAATTACTCAAAGTTTGT 59.187 37.500 15.08 0.00 0.00 2.83
94 95 5.295045 ACGACGGAATTACTCAAAGTTTGTT 59.705 36.000 15.08 6.61 0.00 2.83
96 97 6.445357 ACGGAATTACTCAAAGTTTGTTGT 57.555 33.333 15.08 15.95 0.00 3.32
97 98 6.492254 ACGGAATTACTCAAAGTTTGTTGTC 58.508 36.000 15.08 5.91 0.00 3.18
98 99 6.094325 ACGGAATTACTCAAAGTTTGTTGTCA 59.906 34.615 15.08 7.85 0.00 3.58
99 100 6.970043 CGGAATTACTCAAAGTTTGTTGTCAA 59.030 34.615 15.08 10.31 0.00 3.18
100 101 7.044314 CGGAATTACTCAAAGTTTGTTGTCAAC 60.044 37.037 15.08 8.86 32.93 3.18
101 102 7.973944 GGAATTACTCAAAGTTTGTTGTCAACT 59.026 33.333 16.45 0.00 32.93 3.16
102 103 8.911247 AATTACTCAAAGTTTGTTGTCAACTC 57.089 30.769 16.45 7.45 32.93 3.01
103 104 4.969816 ACTCAAAGTTTGTTGTCAACTCG 58.030 39.130 16.45 0.00 32.93 4.18
104 105 4.454504 ACTCAAAGTTTGTTGTCAACTCGT 59.545 37.500 16.45 3.66 32.93 4.18
105 106 4.965062 TCAAAGTTTGTTGTCAACTCGTC 58.035 39.130 16.45 5.27 32.93 4.20
107 108 5.180492 TCAAAGTTTGTTGTCAACTCGTCTT 59.820 36.000 16.45 11.88 32.93 3.01
109 110 5.622770 AGTTTGTTGTCAACTCGTCTTTT 57.377 34.783 16.45 0.00 32.93 2.27
112 113 4.349663 TGTTGTCAACTCGTCTTTTTGG 57.650 40.909 16.45 0.00 0.00 3.28
113 114 3.754323 TGTTGTCAACTCGTCTTTTTGGT 59.246 39.130 16.45 0.00 0.00 3.67
114 115 4.936411 TGTTGTCAACTCGTCTTTTTGGTA 59.064 37.500 16.45 0.00 0.00 3.25
115 116 5.163834 TGTTGTCAACTCGTCTTTTTGGTAC 60.164 40.000 16.45 0.00 0.00 3.34
116 117 4.761975 TGTCAACTCGTCTTTTTGGTACT 58.238 39.130 0.00 0.00 0.00 2.73
117 118 5.904941 TGTCAACTCGTCTTTTTGGTACTA 58.095 37.500 0.00 0.00 0.00 1.82
118 119 6.339730 TGTCAACTCGTCTTTTTGGTACTAA 58.660 36.000 0.00 0.00 0.00 2.24
120 121 7.170320 TGTCAACTCGTCTTTTTGGTACTAATC 59.830 37.037 0.00 0.00 0.00 1.75
121 122 6.647895 TCAACTCGTCTTTTTGGTACTAATCC 59.352 38.462 0.00 0.00 0.00 3.01
122 123 5.166398 ACTCGTCTTTTTGGTACTAATCCG 58.834 41.667 0.00 0.00 0.00 4.18
123 124 5.138125 TCGTCTTTTTGGTACTAATCCGT 57.862 39.130 0.00 0.00 0.00 4.69
124 125 5.540911 TCGTCTTTTTGGTACTAATCCGTT 58.459 37.500 0.00 0.00 0.00 4.44
125 126 6.686630 TCGTCTTTTTGGTACTAATCCGTTA 58.313 36.000 0.00 0.00 0.00 3.18
126 127 7.322664 TCGTCTTTTTGGTACTAATCCGTTAT 58.677 34.615 0.00 0.00 0.00 1.89
128 129 9.086336 CGTCTTTTTGGTACTAATCCGTTATAA 57.914 33.333 0.00 0.00 0.00 0.98
134 135 7.754069 TGGTACTAATCCGTTATAAAACACG 57.246 36.000 0.00 0.00 35.16 4.49
135 136 7.319646 TGGTACTAATCCGTTATAAAACACGT 58.680 34.615 0.00 0.00 35.16 4.49
136 137 8.462811 TGGTACTAATCCGTTATAAAACACGTA 58.537 33.333 0.00 0.00 35.16 3.57
137 138 9.463443 GGTACTAATCCGTTATAAAACACGTAT 57.537 33.333 0.00 0.00 35.16 3.06
144 145 9.970395 ATCCGTTATAAAACACGTATCTAATCA 57.030 29.630 0.00 0.00 35.16 2.57
153 154 9.436957 AAAACACGTATCTAATCAAGATCAGTT 57.563 29.630 0.00 0.00 44.17 3.16
181 182 8.741603 AAACCTTGTACTTAATGTTGTACTGT 57.258 30.769 0.00 0.00 39.57 3.55
182 183 9.835389 AAACCTTGTACTTAATGTTGTACTGTA 57.165 29.630 0.00 0.00 39.57 2.74
183 184 9.835389 AACCTTGTACTTAATGTTGTACTGTAA 57.165 29.630 0.00 0.00 39.57 2.41
184 185 9.835389 ACCTTGTACTTAATGTTGTACTGTAAA 57.165 29.630 0.00 0.00 39.57 2.01
196 197 8.436046 TGTTGTACTGTAAAAACTAATCCGTT 57.564 30.769 12.93 0.00 0.00 4.44
197 198 8.891720 TGTTGTACTGTAAAAACTAATCCGTTT 58.108 29.630 12.93 0.00 38.66 3.60
198 199 9.720667 GTTGTACTGTAAAAACTAATCCGTTTT 57.279 29.630 0.00 0.00 45.98 2.43
199 200 9.719279 TTGTACTGTAAAAACTAATCCGTTTTG 57.281 29.630 2.83 0.00 43.97 2.44
200 201 8.891720 TGTACTGTAAAAACTAATCCGTTTTGT 58.108 29.630 2.83 0.49 43.97 2.83
211 212 9.804758 AACTAATCCGTTTTGTTTTTGTAATGA 57.195 25.926 0.00 0.00 30.54 2.57
212 213 9.804758 ACTAATCCGTTTTGTTTTTGTAATGAA 57.195 25.926 0.00 0.00 0.00 2.57
214 215 7.707774 ATCCGTTTTGTTTTTGTAATGAAGG 57.292 32.000 0.00 0.00 0.00 3.46
217 218 6.018343 CCGTTTTGTTTTTGTAATGAAGGCAT 60.018 34.615 0.00 0.00 35.92 4.40
218 219 6.845280 CGTTTTGTTTTTGTAATGAAGGCATG 59.155 34.615 0.00 0.00 34.26 4.06
219 220 5.921004 TTGTTTTTGTAATGAAGGCATGC 57.079 34.783 9.90 9.90 34.26 4.06
220 221 4.953667 TGTTTTTGTAATGAAGGCATGCA 58.046 34.783 21.36 0.00 34.26 3.96
221 222 5.549347 TGTTTTTGTAATGAAGGCATGCAT 58.451 33.333 21.36 10.32 34.26 3.96
222 223 5.638657 TGTTTTTGTAATGAAGGCATGCATC 59.361 36.000 21.36 17.14 34.26 3.91
223 224 5.664294 TTTTGTAATGAAGGCATGCATCT 57.336 34.783 21.36 5.19 34.26 2.90
224 225 4.642445 TTGTAATGAAGGCATGCATCTG 57.358 40.909 21.36 0.00 34.26 2.90
225 226 2.953648 TGTAATGAAGGCATGCATCTGG 59.046 45.455 21.36 0.00 34.26 3.86
226 227 2.154567 AATGAAGGCATGCATCTGGT 57.845 45.000 21.36 0.00 34.26 4.00
227 228 1.688772 ATGAAGGCATGCATCTGGTC 58.311 50.000 21.36 7.45 32.31 4.02
230 231 0.622136 AAGGCATGCATCTGGTCTGA 59.378 50.000 21.36 0.00 0.00 3.27
231 232 0.622136 AGGCATGCATCTGGTCTGAA 59.378 50.000 21.36 0.00 0.00 3.02
232 233 0.737219 GGCATGCATCTGGTCTGAAC 59.263 55.000 21.36 0.00 0.00 3.18
233 234 1.681166 GGCATGCATCTGGTCTGAACT 60.681 52.381 21.36 0.00 0.00 3.01
234 235 2.089980 GCATGCATCTGGTCTGAACTT 58.910 47.619 14.21 0.00 0.00 2.66
235 236 2.490903 GCATGCATCTGGTCTGAACTTT 59.509 45.455 14.21 0.00 0.00 2.66
236 237 3.672511 GCATGCATCTGGTCTGAACTTTG 60.673 47.826 14.21 0.00 0.00 2.77
237 238 2.507484 TGCATCTGGTCTGAACTTTGG 58.493 47.619 0.00 0.00 0.00 3.28
238 239 2.158623 TGCATCTGGTCTGAACTTTGGT 60.159 45.455 0.00 0.00 0.00 3.67
239 240 2.227388 GCATCTGGTCTGAACTTTGGTG 59.773 50.000 0.00 0.00 0.00 4.17
240 241 1.967319 TCTGGTCTGAACTTTGGTGC 58.033 50.000 0.00 0.00 0.00 5.01
243 244 1.202758 TGGTCTGAACTTTGGTGCGAT 60.203 47.619 0.00 0.00 0.00 4.58
244 245 1.880027 GGTCTGAACTTTGGTGCGATT 59.120 47.619 0.00 0.00 0.00 3.34
245 246 2.095718 GGTCTGAACTTTGGTGCGATTC 60.096 50.000 0.00 0.00 0.00 2.52
246 247 1.798223 TCTGAACTTTGGTGCGATTCG 59.202 47.619 0.62 0.62 0.00 3.34
247 248 1.798223 CTGAACTTTGGTGCGATTCGA 59.202 47.619 10.88 0.00 0.00 3.71
249 250 2.223144 TGAACTTTGGTGCGATTCGAAG 59.777 45.455 10.88 6.58 0.00 3.79
251 252 0.179189 CTTTGGTGCGATTCGAAGGC 60.179 55.000 10.88 14.99 0.00 4.35
253 254 2.813908 GGTGCGATTCGAAGGCGT 60.814 61.111 19.85 0.00 38.98 5.68
254 255 2.388232 GGTGCGATTCGAAGGCGTT 61.388 57.895 19.85 0.00 38.98 4.84
255 256 1.058903 GTGCGATTCGAAGGCGTTC 59.941 57.895 19.85 9.11 38.98 3.95
265 266 2.527442 GAAGGCGTTCGATTTTCTGG 57.473 50.000 2.98 0.00 0.00 3.86
266 267 1.804748 GAAGGCGTTCGATTTTCTGGT 59.195 47.619 2.98 0.00 0.00 4.00
267 268 1.892209 AGGCGTTCGATTTTCTGGTT 58.108 45.000 0.00 0.00 0.00 3.67
268 269 1.535462 AGGCGTTCGATTTTCTGGTTG 59.465 47.619 0.00 0.00 0.00 3.77
293 294 2.349532 CGATACTAAGCGATGCGAGTCA 60.350 50.000 3.23 0.00 36.35 3.41
341 342 2.623416 CTCCCAGACGTACAGATGCATA 59.377 50.000 0.00 0.00 0.00 3.14
429 1781 5.360714 CCTATAAATTCCCATGCAACACAGT 59.639 40.000 0.00 0.00 0.00 3.55
434 1786 2.710377 TCCCATGCAACACAGTCATAC 58.290 47.619 0.00 0.00 0.00 2.39
436 1788 3.084039 CCCATGCAACACAGTCATACTT 58.916 45.455 0.00 0.00 0.00 2.24
443 1993 6.052360 TGCAACACAGTCATACTTACTGAAA 58.948 36.000 10.02 0.00 45.89 2.69
476 2034 0.175760 TTAAGCTAGCACAGGCCTCG 59.824 55.000 18.83 0.52 42.56 4.63
617 2175 4.838152 CGCGTGATCCACCCAGGG 62.838 72.222 2.85 2.85 38.24 4.45
648 2206 1.442857 GAGGACGCAGACACTCACG 60.443 63.158 0.00 0.00 0.00 4.35
730 2288 3.691744 GAGTGCCTCGTCCTCTGCG 62.692 68.421 0.00 0.00 0.00 5.18
753 2311 0.098376 GCTGCAAGACATACTGCTGC 59.902 55.000 9.60 9.60 38.78 5.25
764 2329 4.186926 ACATACTGCTGCAAGACATACAG 58.813 43.478 3.02 0.00 38.00 2.74
769 2334 1.284657 CTGCAAGACATACAGCTCCG 58.715 55.000 0.00 0.00 34.07 4.63
803 2370 1.758280 TCAAGCCATGCATTCCATTCC 59.242 47.619 0.00 0.00 29.71 3.01
823 2395 9.189156 CCATTCCTTTTTAAGTGATGGAAGATA 57.811 33.333 10.43 0.00 39.51 1.98
950 2757 0.039437 TCAGCGACGACCTTTCTGAC 60.039 55.000 0.00 0.00 0.00 3.51
1148 2956 3.089838 CAACCCCTCCATGAGCCA 58.910 61.111 0.00 0.00 0.00 4.75
1196 3004 3.283684 CCGCTTCGCAAACCACCA 61.284 61.111 0.00 0.00 0.00 4.17
1351 3171 2.101783 GGACATCCATGACAAATGGCA 58.898 47.619 0.00 0.00 39.01 4.92
1454 3277 4.831674 ATGATGTGACAGAGGATGACAA 57.168 40.909 0.00 0.00 35.35 3.18
1491 3314 4.403734 ACATTGGGTTCAAATTCTACGGT 58.596 39.130 0.00 0.00 36.36 4.83
1873 4036 7.599245 CCCTATTTTTGCGGTTTTATGTTAACA 59.401 33.333 11.41 11.41 0.00 2.41
1918 4087 7.780271 ACTCTTTAATTTTGTCCTCCAACTCTT 59.220 33.333 0.00 0.00 31.20 2.85
1932 4101 4.345257 TCCAACTCTTGTTCTAGCACTCTT 59.655 41.667 0.00 0.00 33.52 2.85
1938 4107 6.661377 ACTCTTGTTCTAGCACTCTTCATAGA 59.339 38.462 0.00 0.00 0.00 1.98
1991 4160 8.217131 GGTACCCGTTATGAATTGTAGATTTT 57.783 34.615 0.00 0.00 0.00 1.82
1992 4161 8.680001 GGTACCCGTTATGAATTGTAGATTTTT 58.320 33.333 0.00 0.00 0.00 1.94
2067 4236 7.093354 TCAGAGATCACATCTAACACAAAGTC 58.907 38.462 0.00 0.00 40.38 3.01
2104 4273 3.628032 GCCCAAGCTTACATAACTCTTCC 59.372 47.826 0.00 0.00 35.50 3.46
2105 4274 4.626529 GCCCAAGCTTACATAACTCTTCCT 60.627 45.833 0.00 0.00 35.50 3.36
2143 4312 0.237235 ACTTGTGTGCGGCGTTATTG 59.763 50.000 9.37 0.00 0.00 1.90
2154 4323 1.017177 GCGTTATTGGCAGTCCGTCA 61.017 55.000 4.43 0.00 34.14 4.35
2159 4328 0.179084 ATTGGCAGTCCGTCATACCG 60.179 55.000 0.00 0.00 34.14 4.02
2278 4447 1.956170 CGCGACCACTTTGCTGTCT 60.956 57.895 0.00 0.00 31.40 3.41
2284 4453 1.202698 ACCACTTTGCTGTCTGTCTCC 60.203 52.381 0.00 0.00 0.00 3.71
2300 4469 4.089361 TGTCTCCAGATGTAGCTTCTCAA 58.911 43.478 0.00 0.00 0.00 3.02
2301 4470 4.081972 TGTCTCCAGATGTAGCTTCTCAAC 60.082 45.833 0.00 0.00 0.00 3.18
2311 4480 2.600731 AGCTTCTCAACGTTGATCTCG 58.399 47.619 29.79 18.55 36.46 4.04
2353 4555 1.165270 GGCACGCCATAAGTTCTGTT 58.835 50.000 2.36 0.00 35.81 3.16
2389 4591 1.065109 ACCGGCGAAAAAGTTGCAC 59.935 52.632 9.30 0.00 0.00 4.57
2416 4618 0.953471 CACGGAAATCGCCTTGGTCA 60.953 55.000 0.00 0.00 43.89 4.02
2428 4630 0.903454 CTTGGTCACCCCGGAGTACT 60.903 60.000 0.73 0.00 35.15 2.73
2430 4632 0.033796 TGGTCACCCCGGAGTACTAG 60.034 60.000 0.73 0.00 35.15 2.57
2438 4640 0.824182 CCGGAGTACTAGGCCTCCAG 60.824 65.000 22.58 4.25 46.31 3.86
2458 4660 3.361977 CCGTTGCCCCCGTTTCTG 61.362 66.667 0.00 0.00 0.00 3.02
2464 4666 2.264794 CCCCCGTTTCTGGAGACG 59.735 66.667 6.68 6.68 38.90 4.18
2496 4698 2.075355 TTGGCTTTGACCCATCCCGT 62.075 55.000 0.00 0.00 31.26 5.28
2527 4729 0.661552 CCCAGCGATGCATTTCTCTG 59.338 55.000 0.00 0.00 0.00 3.35
2544 4746 1.272490 TCTGGTGTTCGTAGCTGAAGG 59.728 52.381 0.00 0.00 0.00 3.46
2561 4763 4.641396 TGAAGGTTTCCTCACATGTACTG 58.359 43.478 0.00 0.00 30.89 2.74
2596 4798 1.279496 TGTAGGCCAGAACAGATGCT 58.721 50.000 5.01 0.00 0.00 3.79
2601 4803 1.679944 GGCCAGAACAGATGCTGCTAA 60.680 52.381 0.00 0.00 34.37 3.09
2602 4804 2.295885 GCCAGAACAGATGCTGCTAAT 58.704 47.619 0.00 0.00 34.37 1.73
2609 4811 2.105477 ACAGATGCTGCTAATACCTGGG 59.895 50.000 0.00 0.00 34.37 4.45
2613 4815 0.250510 GCTGCTAATACCTGGGGCTC 60.251 60.000 0.00 0.00 0.00 4.70
2621 4823 1.893315 TACCTGGGGCTCTGCTATTT 58.107 50.000 0.00 0.00 0.00 1.40
2635 4837 6.071672 GCTCTGCTATTTTCTTTCCTTCCTTT 60.072 38.462 0.00 0.00 0.00 3.11
2670 4872 1.054406 AGCCATAGCCCATACGTGGT 61.054 55.000 0.00 0.00 44.48 4.16
2671 4873 0.884704 GCCATAGCCCATACGTGGTG 60.885 60.000 0.00 0.00 44.48 4.17
2672 4874 0.250295 CCATAGCCCATACGTGGTGG 60.250 60.000 13.24 13.24 44.48 4.61
2673 4875 0.468226 CATAGCCCATACGTGGTGGT 59.532 55.000 17.31 5.85 44.48 4.16
2674 4876 1.134220 CATAGCCCATACGTGGTGGTT 60.134 52.381 17.31 7.20 44.48 3.67
2675 4877 0.985760 TAGCCCATACGTGGTGGTTT 59.014 50.000 17.31 9.56 44.48 3.27
2676 4878 0.322187 AGCCCATACGTGGTGGTTTC 60.322 55.000 17.31 8.59 44.48 2.78
2677 4879 1.310216 GCCCATACGTGGTGGTTTCC 61.310 60.000 17.31 3.40 44.48 3.13
2678 4880 0.326927 CCCATACGTGGTGGTTTCCT 59.673 55.000 17.31 0.00 44.48 3.36
2679 4881 1.271707 CCCATACGTGGTGGTTTCCTT 60.272 52.381 17.31 0.00 44.48 3.36
2680 4882 2.510613 CCATACGTGGTGGTTTCCTTT 58.489 47.619 12.26 0.00 40.83 3.11
2681 4883 2.486592 CCATACGTGGTGGTTTCCTTTC 59.513 50.000 12.26 0.00 40.83 2.62
2682 4884 3.142951 CATACGTGGTGGTTTCCTTTCA 58.857 45.455 0.00 0.00 0.00 2.69
2683 4885 2.358322 ACGTGGTGGTTTCCTTTCAT 57.642 45.000 0.00 0.00 0.00 2.57
2684 4886 1.953686 ACGTGGTGGTTTCCTTTCATG 59.046 47.619 0.00 0.00 0.00 3.07
2685 4887 1.335872 CGTGGTGGTTTCCTTTCATGC 60.336 52.381 0.00 0.00 0.00 4.06
2686 4888 1.686052 GTGGTGGTTTCCTTTCATGCA 59.314 47.619 0.00 0.00 0.00 3.96
2687 4889 2.102252 GTGGTGGTTTCCTTTCATGCAA 59.898 45.455 0.00 0.00 0.00 4.08
2688 4890 2.971330 TGGTGGTTTCCTTTCATGCAAT 59.029 40.909 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.974622 GTGCAATAACACCTCCATCATTAAAG 59.025 38.462 0.00 0.00 34.35 1.85
9 10 6.663093 AGTGCAATAACACCTCCATCATTAAA 59.337 34.615 0.00 0.00 41.67 1.52
11 12 5.754782 AGTGCAATAACACCTCCATCATTA 58.245 37.500 0.00 0.00 41.67 1.90
12 13 4.603131 AGTGCAATAACACCTCCATCATT 58.397 39.130 0.00 0.00 41.67 2.57
13 14 4.240881 AGTGCAATAACACCTCCATCAT 57.759 40.909 0.00 0.00 41.67 2.45
18 19 2.231235 CCCAAAGTGCAATAACACCTCC 59.769 50.000 0.00 0.00 41.67 4.30
19 20 2.352715 GCCCAAAGTGCAATAACACCTC 60.353 50.000 0.00 0.00 41.67 3.85
20 21 1.618343 GCCCAAAGTGCAATAACACCT 59.382 47.619 0.00 0.00 41.67 4.00
21 22 1.618343 AGCCCAAAGTGCAATAACACC 59.382 47.619 0.00 0.00 41.67 4.16
22 23 3.366985 GGTAGCCCAAAGTGCAATAACAC 60.367 47.826 0.00 0.00 41.02 3.32
23 24 2.823154 GGTAGCCCAAAGTGCAATAACA 59.177 45.455 0.00 0.00 0.00 2.41
24 25 3.089284 AGGTAGCCCAAAGTGCAATAAC 58.911 45.455 0.00 0.00 0.00 1.89
25 26 3.088532 CAGGTAGCCCAAAGTGCAATAA 58.911 45.455 0.00 0.00 0.00 1.40
27 28 1.549203 CAGGTAGCCCAAAGTGCAAT 58.451 50.000 0.00 0.00 0.00 3.56
28 29 0.539438 CCAGGTAGCCCAAAGTGCAA 60.539 55.000 0.00 0.00 0.00 4.08
29 30 1.074775 CCAGGTAGCCCAAAGTGCA 59.925 57.895 0.00 0.00 0.00 4.57
30 31 0.960861 GTCCAGGTAGCCCAAAGTGC 60.961 60.000 0.00 0.00 0.00 4.40
31 32 0.673644 CGTCCAGGTAGCCCAAAGTG 60.674 60.000 0.00 0.00 0.00 3.16
32 33 0.834687 TCGTCCAGGTAGCCCAAAGT 60.835 55.000 0.00 0.00 0.00 2.66
33 34 0.541863 ATCGTCCAGGTAGCCCAAAG 59.458 55.000 0.00 0.00 0.00 2.77
34 35 1.868713 TATCGTCCAGGTAGCCCAAA 58.131 50.000 0.00 0.00 0.00 3.28
35 36 1.760613 CTTATCGTCCAGGTAGCCCAA 59.239 52.381 0.00 0.00 0.00 4.12
38 39 1.614413 CTCCTTATCGTCCAGGTAGCC 59.386 57.143 0.00 0.00 0.00 3.93
40 41 3.225177 TCCTCCTTATCGTCCAGGTAG 57.775 52.381 0.00 0.00 0.00 3.18
42 43 2.389715 CTTCCTCCTTATCGTCCAGGT 58.610 52.381 0.00 0.00 0.00 4.00
43 44 1.069358 GCTTCCTCCTTATCGTCCAGG 59.931 57.143 0.00 0.00 0.00 4.45
45 46 2.160721 AGCTTCCTCCTTATCGTCCA 57.839 50.000 0.00 0.00 0.00 4.02
46 47 4.875561 ATAAGCTTCCTCCTTATCGTCC 57.124 45.455 0.00 0.00 31.62 4.79
47 48 5.692654 GTGAATAAGCTTCCTCCTTATCGTC 59.307 44.000 0.00 0.00 35.13 4.20
48 49 5.602628 GTGAATAAGCTTCCTCCTTATCGT 58.397 41.667 0.00 0.00 35.13 3.73
49 50 4.681942 CGTGAATAAGCTTCCTCCTTATCG 59.318 45.833 0.00 0.00 35.13 2.92
50 51 5.692654 GTCGTGAATAAGCTTCCTCCTTATC 59.307 44.000 0.00 0.00 35.13 1.75
51 52 5.602628 GTCGTGAATAAGCTTCCTCCTTAT 58.397 41.667 0.00 0.00 37.15 1.73
53 54 3.676324 CGTCGTGAATAAGCTTCCTCCTT 60.676 47.826 0.00 0.00 0.00 3.36
55 56 2.194271 CGTCGTGAATAAGCTTCCTCC 58.806 52.381 0.00 0.00 0.00 4.30
56 57 2.159282 TCCGTCGTGAATAAGCTTCCTC 60.159 50.000 0.00 0.96 0.00 3.71
57 58 1.822990 TCCGTCGTGAATAAGCTTCCT 59.177 47.619 0.00 0.00 0.00 3.36
59 60 4.859629 AATTCCGTCGTGAATAAGCTTC 57.140 40.909 0.00 0.00 33.91 3.86
60 61 5.416947 AGTAATTCCGTCGTGAATAAGCTT 58.583 37.500 3.48 3.48 33.91 3.74
61 62 5.007385 AGTAATTCCGTCGTGAATAAGCT 57.993 39.130 8.69 0.00 33.91 3.74
62 63 4.802039 TGAGTAATTCCGTCGTGAATAAGC 59.198 41.667 8.69 4.28 33.91 3.09
63 64 6.880822 TTGAGTAATTCCGTCGTGAATAAG 57.119 37.500 8.69 0.00 33.91 1.73
64 65 6.869913 ACTTTGAGTAATTCCGTCGTGAATAA 59.130 34.615 8.69 0.00 33.91 1.40
66 67 5.235516 ACTTTGAGTAATTCCGTCGTGAAT 58.764 37.500 3.89 3.89 36.53 2.57
67 68 4.624015 ACTTTGAGTAATTCCGTCGTGAA 58.376 39.130 0.00 0.00 0.00 3.18
68 69 4.247267 ACTTTGAGTAATTCCGTCGTGA 57.753 40.909 0.00 0.00 0.00 4.35
69 70 4.985044 AACTTTGAGTAATTCCGTCGTG 57.015 40.909 0.00 0.00 0.00 4.35
72 73 6.492254 ACAACAAACTTTGAGTAATTCCGTC 58.508 36.000 8.55 0.00 0.00 4.79
75 76 7.973944 AGTTGACAACAAACTTTGAGTAATTCC 59.026 33.333 20.08 0.00 37.77 3.01
76 77 8.911247 AGTTGACAACAAACTTTGAGTAATTC 57.089 30.769 20.08 0.00 37.77 2.17
77 78 7.696453 CGAGTTGACAACAAACTTTGAGTAATT 59.304 33.333 20.08 0.00 37.77 1.40
78 79 7.148306 ACGAGTTGACAACAAACTTTGAGTAAT 60.148 33.333 20.08 0.00 37.77 1.89
79 80 6.148150 ACGAGTTGACAACAAACTTTGAGTAA 59.852 34.615 20.08 0.00 37.77 2.24
80 81 5.640357 ACGAGTTGACAACAAACTTTGAGTA 59.360 36.000 20.08 0.00 37.77 2.59
81 82 4.454504 ACGAGTTGACAACAAACTTTGAGT 59.545 37.500 20.08 6.34 37.77 3.41
82 83 4.969816 ACGAGTTGACAACAAACTTTGAG 58.030 39.130 20.08 3.35 37.77 3.02
83 84 4.693566 AGACGAGTTGACAACAAACTTTGA 59.306 37.500 20.08 0.00 37.77 2.69
86 87 5.622770 AAAGACGAGTTGACAACAAACTT 57.377 34.783 20.08 14.91 37.77 2.66
87 88 5.622770 AAAAGACGAGTTGACAACAAACT 57.377 34.783 20.08 10.41 37.77 2.66
89 90 5.157781 CCAAAAAGACGAGTTGACAACAAA 58.842 37.500 20.08 0.00 37.77 2.83
90 91 4.216687 ACCAAAAAGACGAGTTGACAACAA 59.783 37.500 20.08 0.00 0.00 2.83
91 92 3.754323 ACCAAAAAGACGAGTTGACAACA 59.246 39.130 20.08 0.00 0.00 3.33
93 94 5.180271 AGTACCAAAAAGACGAGTTGACAA 58.820 37.500 0.00 0.00 0.00 3.18
94 95 4.761975 AGTACCAAAAAGACGAGTTGACA 58.238 39.130 0.00 0.00 0.00 3.58
96 97 6.647895 GGATTAGTACCAAAAAGACGAGTTGA 59.352 38.462 0.00 0.00 0.00 3.18
97 98 6.400727 CGGATTAGTACCAAAAAGACGAGTTG 60.401 42.308 0.00 0.00 0.00 3.16
98 99 5.636543 CGGATTAGTACCAAAAAGACGAGTT 59.363 40.000 0.00 0.00 0.00 3.01
99 100 5.166398 CGGATTAGTACCAAAAAGACGAGT 58.834 41.667 0.00 0.00 0.00 4.18
100 101 5.166398 ACGGATTAGTACCAAAAAGACGAG 58.834 41.667 0.00 0.00 0.00 4.18
101 102 5.138125 ACGGATTAGTACCAAAAAGACGA 57.862 39.130 0.00 0.00 0.00 4.20
102 103 5.851047 AACGGATTAGTACCAAAAAGACG 57.149 39.130 0.00 0.00 0.00 4.18
109 110 7.816995 ACGTGTTTTATAACGGATTAGTACCAA 59.183 33.333 0.00 0.00 43.96 3.67
118 119 9.970395 TGATTAGATACGTGTTTTATAACGGAT 57.030 29.630 0.00 0.00 45.80 4.18
155 156 9.835389 ACAGTACAACATTAAGTACAAGGTTTA 57.165 29.630 0.00 0.00 42.26 2.01
169 170 9.059260 ACGGATTAGTTTTTACAGTACAACATT 57.941 29.630 0.00 0.00 0.00 2.71
170 171 8.611654 ACGGATTAGTTTTTACAGTACAACAT 57.388 30.769 0.00 0.00 0.00 2.71
171 172 8.436046 AACGGATTAGTTTTTACAGTACAACA 57.564 30.769 0.00 0.00 0.00 3.33
186 187 9.804758 TTCATTACAAAAACAAAACGGATTAGT 57.195 25.926 0.00 0.00 0.00 2.24
188 189 9.250624 CCTTCATTACAAAAACAAAACGGATTA 57.749 29.630 0.00 0.00 0.00 1.75
190 191 6.201997 GCCTTCATTACAAAAACAAAACGGAT 59.798 34.615 0.00 0.00 0.00 4.18
191 192 5.520649 GCCTTCATTACAAAAACAAAACGGA 59.479 36.000 0.00 0.00 0.00 4.69
194 195 6.632434 GCATGCCTTCATTACAAAAACAAAAC 59.368 34.615 6.36 0.00 0.00 2.43
196 197 5.819379 TGCATGCCTTCATTACAAAAACAAA 59.181 32.000 16.68 0.00 0.00 2.83
197 198 5.363101 TGCATGCCTTCATTACAAAAACAA 58.637 33.333 16.68 0.00 0.00 2.83
198 199 4.953667 TGCATGCCTTCATTACAAAAACA 58.046 34.783 16.68 0.00 0.00 2.83
199 200 5.870978 AGATGCATGCCTTCATTACAAAAAC 59.129 36.000 16.68 0.00 0.00 2.43
200 201 5.870433 CAGATGCATGCCTTCATTACAAAAA 59.130 36.000 16.68 0.00 0.00 1.94
202 203 4.142116 CCAGATGCATGCCTTCATTACAAA 60.142 41.667 16.68 0.00 0.00 2.83
203 204 3.382227 CCAGATGCATGCCTTCATTACAA 59.618 43.478 16.68 0.00 0.00 2.41
204 205 2.953648 CCAGATGCATGCCTTCATTACA 59.046 45.455 16.68 0.00 0.00 2.41
205 206 2.954318 ACCAGATGCATGCCTTCATTAC 59.046 45.455 16.68 0.00 0.00 1.89
207 208 2.029623 GACCAGATGCATGCCTTCATT 58.970 47.619 16.68 0.74 0.00 2.57
208 209 1.214673 AGACCAGATGCATGCCTTCAT 59.785 47.619 16.68 0.71 0.00 2.57
209 210 0.622136 AGACCAGATGCATGCCTTCA 59.378 50.000 16.68 0.00 0.00 3.02
210 211 1.022735 CAGACCAGATGCATGCCTTC 58.977 55.000 16.68 12.33 0.00 3.46
211 212 0.622136 TCAGACCAGATGCATGCCTT 59.378 50.000 16.68 1.92 0.00 4.35
212 213 0.622136 TTCAGACCAGATGCATGCCT 59.378 50.000 16.68 4.84 0.00 4.75
213 214 0.737219 GTTCAGACCAGATGCATGCC 59.263 55.000 16.68 0.00 0.00 4.40
214 215 1.747709 AGTTCAGACCAGATGCATGC 58.252 50.000 11.82 11.82 0.00 4.06
217 218 2.158623 ACCAAAGTTCAGACCAGATGCA 60.159 45.455 0.00 0.00 0.00 3.96
218 219 2.227388 CACCAAAGTTCAGACCAGATGC 59.773 50.000 0.00 0.00 0.00 3.91
219 220 2.227388 GCACCAAAGTTCAGACCAGATG 59.773 50.000 0.00 0.00 0.00 2.90
220 221 2.508526 GCACCAAAGTTCAGACCAGAT 58.491 47.619 0.00 0.00 0.00 2.90
221 222 1.810031 CGCACCAAAGTTCAGACCAGA 60.810 52.381 0.00 0.00 0.00 3.86
222 223 0.588252 CGCACCAAAGTTCAGACCAG 59.412 55.000 0.00 0.00 0.00 4.00
223 224 0.179234 TCGCACCAAAGTTCAGACCA 59.821 50.000 0.00 0.00 0.00 4.02
224 225 1.523758 ATCGCACCAAAGTTCAGACC 58.476 50.000 0.00 0.00 0.00 3.85
225 226 2.411547 CGAATCGCACCAAAGTTCAGAC 60.412 50.000 0.00 0.00 0.00 3.51
226 227 1.798223 CGAATCGCACCAAAGTTCAGA 59.202 47.619 0.00 0.00 0.00 3.27
227 228 1.798223 TCGAATCGCACCAAAGTTCAG 59.202 47.619 0.00 0.00 0.00 3.02
230 231 1.535462 CCTTCGAATCGCACCAAAGTT 59.465 47.619 0.00 0.00 0.00 2.66
231 232 1.156736 CCTTCGAATCGCACCAAAGT 58.843 50.000 0.00 0.00 0.00 2.66
232 233 0.179189 GCCTTCGAATCGCACCAAAG 60.179 55.000 11.38 0.00 0.00 2.77
233 234 1.873165 GCCTTCGAATCGCACCAAA 59.127 52.632 11.38 0.00 0.00 3.28
234 235 2.387445 CGCCTTCGAATCGCACCAA 61.387 57.895 15.28 0.00 38.10 3.67
235 236 2.813474 CGCCTTCGAATCGCACCA 60.813 61.111 15.28 0.00 38.10 4.17
236 237 2.292802 GAACGCCTTCGAATCGCACC 62.293 60.000 16.55 5.80 39.41 5.01
237 238 1.058903 GAACGCCTTCGAATCGCAC 59.941 57.895 16.55 9.35 39.41 5.34
238 239 3.470267 GAACGCCTTCGAATCGCA 58.530 55.556 16.55 0.00 39.41 5.10
246 247 1.804748 ACCAGAAAATCGAACGCCTTC 59.195 47.619 0.00 0.00 0.00 3.46
247 248 1.892209 ACCAGAAAATCGAACGCCTT 58.108 45.000 0.00 0.00 0.00 4.35
249 250 1.401018 CCAACCAGAAAATCGAACGCC 60.401 52.381 0.00 0.00 0.00 5.68
251 252 2.916111 CACCAACCAGAAAATCGAACG 58.084 47.619 0.00 0.00 0.00 3.95
253 254 1.265635 CGCACCAACCAGAAAATCGAA 59.734 47.619 0.00 0.00 0.00 3.71
254 255 0.871722 CGCACCAACCAGAAAATCGA 59.128 50.000 0.00 0.00 0.00 3.59
255 256 0.871722 TCGCACCAACCAGAAAATCG 59.128 50.000 0.00 0.00 0.00 3.34
256 257 3.689649 AGTATCGCACCAACCAGAAAATC 59.310 43.478 0.00 0.00 0.00 2.17
258 259 3.134574 AGTATCGCACCAACCAGAAAA 57.865 42.857 0.00 0.00 0.00 2.29
260 261 3.857052 CTTAGTATCGCACCAACCAGAA 58.143 45.455 0.00 0.00 0.00 3.02
261 262 2.418197 GCTTAGTATCGCACCAACCAGA 60.418 50.000 0.00 0.00 0.00 3.86
263 264 1.737696 CGCTTAGTATCGCACCAACCA 60.738 52.381 0.00 0.00 0.00 3.67
264 265 0.928229 CGCTTAGTATCGCACCAACC 59.072 55.000 0.00 0.00 0.00 3.77
265 266 1.917273 TCGCTTAGTATCGCACCAAC 58.083 50.000 0.00 0.00 0.00 3.77
266 267 2.469826 CATCGCTTAGTATCGCACCAA 58.530 47.619 0.00 0.00 0.00 3.67
267 268 1.868109 GCATCGCTTAGTATCGCACCA 60.868 52.381 0.00 0.00 0.00 4.17
268 269 0.784778 GCATCGCTTAGTATCGCACC 59.215 55.000 0.00 0.00 0.00 5.01
341 342 2.983030 TTGCGCGCTTCCCACATT 60.983 55.556 33.29 0.00 0.00 2.71
429 1781 6.818644 GGCTGATCTGTTTTCAGTAAGTATGA 59.181 38.462 1.27 0.00 46.98 2.15
434 1786 5.947228 TTGGCTGATCTGTTTTCAGTAAG 57.053 39.130 1.27 0.00 46.98 2.34
436 1788 7.362056 GCTTAATTGGCTGATCTGTTTTCAGTA 60.362 37.037 1.27 0.00 46.98 2.74
443 1993 4.578105 GCTAGCTTAATTGGCTGATCTGTT 59.422 41.667 7.70 0.00 40.52 3.16
476 2034 1.525306 GGCCATTGCTACGTACCCC 60.525 63.158 0.00 0.00 37.74 4.95
614 2172 2.920912 TCTTGCCGAACCGTCCCT 60.921 61.111 0.00 0.00 0.00 4.20
617 2175 1.737008 GTCCTCTTGCCGAACCGTC 60.737 63.158 0.00 0.00 0.00 4.79
648 2206 1.803334 TGTCCTTGGTATTGTCGCAC 58.197 50.000 0.00 0.00 0.00 5.34
730 2288 0.731417 CAGTATGTCTTGCAGCTGGC 59.269 55.000 17.12 8.54 45.13 4.85
753 2311 3.724508 AGATCGGAGCTGTATGTCTTG 57.275 47.619 0.00 0.00 0.00 3.02
764 2329 0.827368 AGACTGGGAAAGATCGGAGC 59.173 55.000 0.00 0.00 0.00 4.70
769 2334 2.026822 TGGCTTGAGACTGGGAAAGATC 60.027 50.000 0.00 0.00 0.00 2.75
846 2418 4.878397 GTCCATCAAGATCGAATTGTCCTT 59.122 41.667 12.00 0.00 0.00 3.36
921 2728 1.015109 TCGTCGCTGATGGTCTAGAC 58.985 55.000 14.87 14.87 0.00 2.59
1148 2956 2.356535 GCCTGGATCCATGTGAAGTCTT 60.357 50.000 16.63 0.00 0.00 3.01
1196 3004 0.620556 CATGGCACCCAAGTAGAGGT 59.379 55.000 0.00 0.00 36.95 3.85
1351 3171 1.123928 CCCTTAAGCTCGACCCTCAT 58.876 55.000 0.00 0.00 0.00 2.90
1454 3277 1.541147 CAATGTCCAAATGTGCGAGGT 59.459 47.619 0.00 0.00 0.00 3.85
1491 3314 2.698803 CCATGAACATTGTCGGTGAGA 58.301 47.619 0.00 0.00 0.00 3.27
1818 3654 6.256321 CACCATTACAATTTGCTATGGAAAGC 59.744 38.462 25.46 0.00 43.08 3.51
1873 4036 4.220821 AGAGTACTTTCCACATGACATCGT 59.779 41.667 0.00 0.00 0.00 3.73
1932 4101 5.221621 TGTTCCACATATCCGCATTCTATGA 60.222 40.000 0.00 0.00 0.00 2.15
1938 4107 2.886523 CCATGTTCCACATATCCGCATT 59.113 45.455 0.00 0.00 36.53 3.56
1992 4161 3.429135 GCGGTTTGTGTTACCCTCAAAAA 60.429 43.478 0.00 0.00 38.03 1.94
1993 4162 2.099427 GCGGTTTGTGTTACCCTCAAAA 59.901 45.455 0.00 0.00 38.03 2.44
1994 4163 1.677052 GCGGTTTGTGTTACCCTCAAA 59.323 47.619 0.00 0.00 34.95 2.69
1995 4164 1.134037 AGCGGTTTGTGTTACCCTCAA 60.134 47.619 0.00 0.00 31.75 3.02
1996 4165 0.470766 AGCGGTTTGTGTTACCCTCA 59.529 50.000 0.00 0.00 31.75 3.86
1997 4166 1.601166 AAGCGGTTTGTGTTACCCTC 58.399 50.000 0.00 0.00 31.75 4.30
2049 4218 5.991606 CCTTCAGACTTTGTGTTAGATGTGA 59.008 40.000 0.00 0.00 0.00 3.58
2085 4254 6.981559 GGTAGAGGAAGAGTTATGTAAGCTTG 59.018 42.308 9.86 0.00 0.00 4.01
2104 4273 5.064314 AGTTAGCTAAGGTAGGGGTAGAG 57.936 47.826 6.38 0.00 0.00 2.43
2105 4274 5.206587 CAAGTTAGCTAAGGTAGGGGTAGA 58.793 45.833 6.38 0.00 0.00 2.59
2143 4312 0.597637 CATCGGTATGACGGACTGCC 60.598 60.000 0.00 0.00 34.84 4.85
2159 4328 4.990543 TCAACGATGTGAAAGTGTCATC 57.009 40.909 0.00 0.00 38.90 2.92
2200 4369 1.416772 GGGCCGCTAGTAGAGGAAATT 59.583 52.381 22.79 0.00 37.36 1.82
2203 4372 1.457079 GGGGCCGCTAGTAGAGGAA 60.457 63.158 22.79 0.00 37.36 3.36
2229 4398 2.483188 GGAGACACGAACAAGAACCTGT 60.483 50.000 0.00 0.00 0.00 4.00
2278 4447 3.701664 TGAGAAGCTACATCTGGAGACA 58.298 45.455 0.00 0.00 39.59 3.41
2284 4453 4.237724 TCAACGTTGAGAAGCTACATCTG 58.762 43.478 26.53 0.00 32.50 2.90
2300 4469 1.002251 GCTAGCTAGCGAGATCAACGT 60.002 52.381 28.89 0.00 39.82 3.99
2301 4470 1.680668 GCTAGCTAGCGAGATCAACG 58.319 55.000 28.89 1.48 39.82 4.10
2416 4618 2.281429 GGCCTAGTACTCCGGGGT 59.719 66.667 13.96 13.96 0.00 4.95
2428 4630 2.606519 AACGGTGCTGGAGGCCTA 60.607 61.111 4.42 0.00 40.92 3.93
2527 4729 2.165319 AACCTTCAGCTACGAACACC 57.835 50.000 0.00 0.00 0.00 4.16
2544 4746 3.433615 GTCAGCAGTACATGTGAGGAAAC 59.566 47.826 9.11 0.00 0.00 2.78
2596 4798 1.131638 CAGAGCCCCAGGTATTAGCA 58.868 55.000 0.00 0.00 0.00 3.49
2601 4803 2.124560 AATAGCAGAGCCCCAGGTAT 57.875 50.000 0.00 0.00 0.00 2.73
2602 4804 1.893315 AAATAGCAGAGCCCCAGGTA 58.107 50.000 0.00 0.00 0.00 3.08
2609 4811 4.097135 GGAAGGAAAGAAAATAGCAGAGCC 59.903 45.833 0.00 0.00 0.00 4.70
2613 4815 6.986250 ACAAAGGAAGGAAAGAAAATAGCAG 58.014 36.000 0.00 0.00 0.00 4.24
2621 4823 8.078060 AGAAATGAAACAAAGGAAGGAAAGAA 57.922 30.769 0.00 0.00 0.00 2.52
2635 4837 5.760253 GCTATGGCTAGCTAGAAATGAAACA 59.240 40.000 25.15 9.09 45.78 2.83


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

AutoCloner maintained by Alex Coulton.