Multiple sequence alignment - TraesCS6B01G190800

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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 TraesCS6B01G190800 chr6B 100.000 4369 0 0 1 4369 224213796 224209428 0.000000e+00 8069.0
1 TraesCS6B01G190800 chr6B 96.680 512 14 1 3858 4369 689252412 689251904 0.000000e+00 848.0
2 TraesCS6B01G190800 chr6B 87.407 135 9 8 3712 3842 224210040 224209910 9.790000e-32 148.0
3 TraesCS6B01G190800 chr7D 96.427 3638 69 19 758 4369 481161620 481158018 0.000000e+00 5941.0
4 TraesCS6B01G190800 chr7D 88.048 502 17 6 300 795 481162110 481161646 4.940000e-154 555.0
5 TraesCS6B01G190800 chr7D 90.741 54 4 1 3110 3162 481159416 481159363 2.180000e-08 71.3
6 TraesCS6B01G190800 chr3A 95.556 3735 95 17 313 4023 111889315 111885628 0.000000e+00 5912.0
7 TraesCS6B01G190800 chr3A 98.319 357 6 0 4013 4369 111885609 111885253 1.030000e-175 627.0
8 TraesCS6B01G190800 chr3A 86.525 141 12 7 3712 3848 111885893 111885756 9.790000e-32 148.0
9 TraesCS6B01G190800 chr6A 96.486 3358 61 8 1048 4367 420328053 420324715 0.000000e+00 5494.0
10 TraesCS6B01G190800 chr6A 94.212 501 24 3 311 810 420328545 420328049 0.000000e+00 760.0
11 TraesCS6B01G190800 chr6A 92.308 299 22 1 1 298 388057548 388057250 1.450000e-114 424.0
12 TraesCS6B01G190800 chr6A 74.143 321 57 19 1805 2112 435769932 435769625 4.620000e-20 110.0
13 TraesCS6B01G190800 chr1D 96.657 3261 63 16 557 3798 460253454 460256687 0.000000e+00 5376.0
14 TraesCS6B01G190800 chr1D 94.769 650 7 8 3736 4369 460256686 460257324 0.000000e+00 987.0
15 TraesCS6B01G190800 chr1D 95.783 166 7 0 300 465 460252880 460253045 7.200000e-68 268.0
16 TraesCS6B01G190800 chr2D 98.246 2908 34 2 892 3798 242962839 242959948 0.000000e+00 5072.0
17 TraesCS6B01G190800 chr2D 96.095 589 12 3 3781 4369 242959688 242959111 0.000000e+00 950.0
18 TraesCS6B01G190800 chr2D 95.661 484 16 2 313 796 242963425 242962947 0.000000e+00 773.0
19 TraesCS6B01G190800 chr4B 96.323 1822 26 5 2548 4369 667031788 667030008 0.000000e+00 2955.0
20 TraesCS6B01G190800 chr4B 92.173 626 13 15 560 1149 667032409 667031784 0.000000e+00 852.0
21 TraesCS6B01G190800 chr4B 92.617 298 21 1 1 298 414455262 414455558 1.120000e-115 427.0
22 TraesCS6B01G190800 chr4B 87.407 135 9 8 3712 3842 667030595 667030465 9.790000e-32 148.0
23 TraesCS6B01G190800 chr2A 95.326 1840 40 5 2187 4023 730083465 730085261 0.000000e+00 2880.0
24 TraesCS6B01G190800 chr2A 94.340 1749 61 10 446 2157 730081721 730083468 0.000000e+00 2647.0
25 TraesCS6B01G190800 chr2A 98.319 357 6 0 4013 4369 730085280 730085636 1.030000e-175 627.0
26 TraesCS6B01G190800 chr2A 93.377 151 10 0 300 450 730077768 730077918 1.580000e-54 224.0
27 TraesCS6B01G190800 chr2A 92.248 129 8 2 304 430 595023473 595023345 9.650000e-42 182.0
28 TraesCS6B01G190800 chr2A 86.567 134 12 6 3712 3842 730084996 730085126 4.550000e-30 143.0
29 TraesCS6B01G190800 chr1A 94.512 1148 62 1 1139 2285 303148763 303147616 0.000000e+00 1770.0
30 TraesCS6B01G190800 chr1A 81.229 602 56 26 300 877 181757665 181757097 2.410000e-117 433.0
31 TraesCS6B01G190800 chr6D 97.225 973 13 4 3400 4369 225152379 225151418 0.000000e+00 1635.0
32 TraesCS6B01G190800 chr6D 89.864 957 35 13 300 1204 225153321 225152375 0.000000e+00 1173.0
33 TraesCS6B01G190800 chrUn 99.485 388 2 0 2357 2744 480263364 480262977 0.000000e+00 706.0
34 TraesCS6B01G190800 chr5A 94.966 298 15 0 1 298 343764317 343764614 6.620000e-128 468.0
35 TraesCS6B01G190800 chr7A 93.960 298 18 0 1 298 264174688 264174391 6.660000e-123 451.0
36 TraesCS6B01G190800 chr7A 93.624 298 19 0 1 298 308453368 308453071 3.100000e-121 446.0
37 TraesCS6B01G190800 chr7A 73.521 355 66 21 1772 2112 15530763 15531103 4.620000e-20 110.0
38 TraesCS6B01G190800 chr3D 93.624 298 19 0 1 298 256147142 256147439 3.100000e-121 446.0
39 TraesCS6B01G190800 chr3D 92.282 298 23 0 1 298 250338455 250338158 1.450000e-114 424.0
40 TraesCS6B01G190800 chr5D 93.289 298 20 0 1 298 249157615 249157912 1.440000e-119 440.0
41 TraesCS6B01G190800 chr5B 92.617 298 22 0 1 298 139741667 139741370 3.120000e-116 429.0
42 TraesCS6B01G190800 chr4A 87.407 270 23 8 575 836 490598979 490599245 2.550000e-77 300.0


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 TraesCS6B01G190800 chr6B 224209428 224213796 4368 True 4108.500000 8069 93.703500 1 4369 2 chr6B.!!$R2 4368
1 TraesCS6B01G190800 chr6B 689251904 689252412 508 True 848.000000 848 96.680000 3858 4369 1 chr6B.!!$R1 511
2 TraesCS6B01G190800 chr7D 481158018 481162110 4092 True 2189.100000 5941 91.738667 300 4369 3 chr7D.!!$R1 4069
3 TraesCS6B01G190800 chr3A 111885253 111889315 4062 True 2229.000000 5912 93.466667 313 4369 3 chr3A.!!$R1 4056
4 TraesCS6B01G190800 chr6A 420324715 420328545 3830 True 3127.000000 5494 95.349000 311 4367 2 chr6A.!!$R3 4056
5 TraesCS6B01G190800 chr1D 460252880 460257324 4444 False 2210.333333 5376 95.736333 300 4369 3 chr1D.!!$F1 4069
6 TraesCS6B01G190800 chr2D 242959111 242963425 4314 True 2265.000000 5072 96.667333 313 4369 3 chr2D.!!$R1 4056
7 TraesCS6B01G190800 chr4B 667030008 667032409 2401 True 1318.333333 2955 91.967667 560 4369 3 chr4B.!!$R1 3809
8 TraesCS6B01G190800 chr2A 730077768 730085636 7868 False 1304.200000 2880 93.585800 300 4369 5 chr2A.!!$F1 4069
9 TraesCS6B01G190800 chr1A 303147616 303148763 1147 True 1770.000000 1770 94.512000 1139 2285 1 chr1A.!!$R2 1146
10 TraesCS6B01G190800 chr1A 181757097 181757665 568 True 433.000000 433 81.229000 300 877 1 chr1A.!!$R1 577
11 TraesCS6B01G190800 chr6D 225151418 225153321 1903 True 1404.000000 1635 93.544500 300 4369 2 chr6D.!!$R1 4069

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
184 185 0.105964 TGGGTCGGTGTGTTCAGAAG 59.894 55.000 0.00 0.0 0.00 2.85 F
229 230 0.249120 AATTGTCAGGATGCCGACGA 59.751 50.000 0.00 0.0 34.76 4.20 F
233 234 0.384309 GTCAGGATGCCGACGACATA 59.616 55.000 0.00 0.0 34.76 2.29 F
234 235 0.668535 TCAGGATGCCGACGACATAG 59.331 55.000 0.00 0.0 34.76 2.23 F
1426 5740 1.138661 CAACAGCAAAAAGGAAGGCCA 59.861 47.619 5.01 0.0 36.29 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 5717 1.138661 TGGCCTTCCTTTTTGCTGTTG 59.861 47.619 3.32 0.00 0.00 3.33 R
2222 6571 1.270839 CCCTCACAAGATCACGGTTGT 60.271 52.381 0.00 0.00 37.37 3.32 R
2348 6698 1.202651 CCGGTGAGGTTGACAACTTCT 60.203 52.381 25.36 13.03 38.24 2.85 R
2349 6699 1.226746 CCGGTGAGGTTGACAACTTC 58.773 55.000 20.37 20.37 37.94 3.01 R
3530 7883 2.373169 TCATCTTCTCCAACTTGGTGCT 59.627 45.455 7.72 0.00 39.03 4.40 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
20 21 2.112380 TGTGTGTGCCATATCCACTG 57.888 50.000 5.04 0.00 34.38 3.66
21 22 1.339920 TGTGTGTGCCATATCCACTGG 60.340 52.381 5.04 0.00 36.81 4.00
22 23 0.255604 TGTGTGCCATATCCACTGGG 59.744 55.000 0.00 0.00 34.16 4.45
34 35 3.874383 TCCACTGGGAAATGAACTGAA 57.126 42.857 0.00 0.00 41.32 3.02
35 36 3.754965 TCCACTGGGAAATGAACTGAAG 58.245 45.455 0.00 0.00 41.32 3.02
36 37 3.138283 TCCACTGGGAAATGAACTGAAGT 59.862 43.478 0.00 0.00 41.32 3.01
37 38 4.349636 TCCACTGGGAAATGAACTGAAGTA 59.650 41.667 0.00 0.00 41.32 2.24
38 39 4.455877 CCACTGGGAAATGAACTGAAGTAC 59.544 45.833 0.00 0.00 35.59 2.73
39 40 5.308825 CACTGGGAAATGAACTGAAGTACT 58.691 41.667 0.00 0.00 0.00 2.73
40 41 5.409826 CACTGGGAAATGAACTGAAGTACTC 59.590 44.000 0.00 0.00 0.00 2.59
41 42 4.566004 TGGGAAATGAACTGAAGTACTCG 58.434 43.478 0.00 0.00 0.00 4.18
42 43 3.933332 GGGAAATGAACTGAAGTACTCGG 59.067 47.826 0.00 0.00 36.38 4.63
43 44 3.371285 GGAAATGAACTGAAGTACTCGGC 59.629 47.826 0.00 0.00 33.14 5.54
44 45 2.674796 ATGAACTGAAGTACTCGGCC 57.325 50.000 0.00 0.00 33.14 6.13
45 46 0.606604 TGAACTGAAGTACTCGGCCC 59.393 55.000 0.00 0.00 33.14 5.80
46 47 0.108281 GAACTGAAGTACTCGGCCCC 60.108 60.000 0.00 0.00 33.14 5.80
47 48 1.551019 AACTGAAGTACTCGGCCCCC 61.551 60.000 0.00 0.00 33.14 5.40
48 49 1.987855 CTGAAGTACTCGGCCCCCA 60.988 63.158 0.00 0.00 0.00 4.96
49 50 1.536907 TGAAGTACTCGGCCCCCAA 60.537 57.895 0.00 0.00 0.00 4.12
50 51 0.912487 TGAAGTACTCGGCCCCCAAT 60.912 55.000 0.00 0.00 0.00 3.16
51 52 1.125633 GAAGTACTCGGCCCCCAATA 58.874 55.000 0.00 0.00 0.00 1.90
52 53 1.697982 GAAGTACTCGGCCCCCAATAT 59.302 52.381 0.00 0.00 0.00 1.28
53 54 1.815757 AGTACTCGGCCCCCAATATT 58.184 50.000 0.00 0.00 0.00 1.28
54 55 2.132686 AGTACTCGGCCCCCAATATTT 58.867 47.619 0.00 0.00 0.00 1.40
55 56 2.105993 AGTACTCGGCCCCCAATATTTC 59.894 50.000 0.00 0.00 0.00 2.17
56 57 0.923358 ACTCGGCCCCCAATATTTCA 59.077 50.000 0.00 0.00 0.00 2.69
57 58 1.499007 ACTCGGCCCCCAATATTTCAT 59.501 47.619 0.00 0.00 0.00 2.57
58 59 2.714250 ACTCGGCCCCCAATATTTCATA 59.286 45.455 0.00 0.00 0.00 2.15
59 60 3.081804 CTCGGCCCCCAATATTTCATAC 58.918 50.000 0.00 0.00 0.00 2.39
60 61 2.714250 TCGGCCCCCAATATTTCATACT 59.286 45.455 0.00 0.00 0.00 2.12
61 62 2.819608 CGGCCCCCAATATTTCATACTG 59.180 50.000 0.00 0.00 0.00 2.74
62 63 3.497763 CGGCCCCCAATATTTCATACTGA 60.498 47.826 0.00 0.00 0.00 3.41
63 64 4.479158 GGCCCCCAATATTTCATACTGAA 58.521 43.478 0.00 0.00 34.03 3.02
122 123 9.575868 TTAGTTTGGGTAGAAACATATTTCACA 57.424 29.630 0.00 0.00 45.78 3.58
123 124 8.650143 AGTTTGGGTAGAAACATATTTCACAT 57.350 30.769 0.00 0.00 45.78 3.21
124 125 9.088987 AGTTTGGGTAGAAACATATTTCACATT 57.911 29.630 0.00 0.00 45.78 2.71
143 144 8.850454 TCACATTAATTTTAATTAAGCGGAGC 57.150 30.769 11.87 0.00 43.61 4.70
144 145 8.462811 TCACATTAATTTTAATTAAGCGGAGCA 58.537 29.630 11.87 0.00 46.37 4.26
145 146 8.745837 CACATTAATTTTAATTAAGCGGAGCAG 58.254 33.333 11.87 0.00 46.37 4.24
146 147 8.682710 ACATTAATTTTAATTAAGCGGAGCAGA 58.317 29.630 11.87 0.00 46.37 4.26
147 148 9.173939 CATTAATTTTAATTAAGCGGAGCAGAG 57.826 33.333 11.87 0.00 46.37 3.35
148 149 8.352942 ATTAATTTTAATTAAGCGGAGCAGAGG 58.647 33.333 11.87 0.00 46.37 3.69
168 169 4.801164 AGGAATTTCCTCAATGAGATGGG 58.199 43.478 12.53 0.00 45.66 4.00
169 170 4.231426 AGGAATTTCCTCAATGAGATGGGT 59.769 41.667 12.53 0.00 45.66 4.51
170 171 4.582240 GGAATTTCCTCAATGAGATGGGTC 59.418 45.833 12.53 3.56 32.53 4.46
171 172 2.988010 TTCCTCAATGAGATGGGTCG 57.012 50.000 12.53 0.00 0.00 4.79
172 173 1.123077 TCCTCAATGAGATGGGTCGG 58.877 55.000 12.53 0.00 0.00 4.79
173 174 0.833287 CCTCAATGAGATGGGTCGGT 59.167 55.000 12.53 0.00 0.00 4.69
174 175 1.473965 CCTCAATGAGATGGGTCGGTG 60.474 57.143 12.53 0.00 0.00 4.94
175 176 1.208052 CTCAATGAGATGGGTCGGTGT 59.792 52.381 3.77 0.00 0.00 4.16
176 177 1.066215 TCAATGAGATGGGTCGGTGTG 60.066 52.381 0.00 0.00 0.00 3.82
177 178 0.984230 AATGAGATGGGTCGGTGTGT 59.016 50.000 0.00 0.00 0.00 3.72
178 179 0.984230 ATGAGATGGGTCGGTGTGTT 59.016 50.000 0.00 0.00 0.00 3.32
179 180 0.320374 TGAGATGGGTCGGTGTGTTC 59.680 55.000 0.00 0.00 0.00 3.18
180 181 0.320374 GAGATGGGTCGGTGTGTTCA 59.680 55.000 0.00 0.00 0.00 3.18
181 182 0.321671 AGATGGGTCGGTGTGTTCAG 59.678 55.000 0.00 0.00 0.00 3.02
182 183 0.320374 GATGGGTCGGTGTGTTCAGA 59.680 55.000 0.00 0.00 0.00 3.27
183 184 0.762418 ATGGGTCGGTGTGTTCAGAA 59.238 50.000 0.00 0.00 0.00 3.02
184 185 0.105964 TGGGTCGGTGTGTTCAGAAG 59.894 55.000 0.00 0.00 0.00 2.85
185 186 1.228657 GGGTCGGTGTGTTCAGAAGC 61.229 60.000 0.00 0.00 0.00 3.86
186 187 0.531974 GGTCGGTGTGTTCAGAAGCA 60.532 55.000 0.00 0.00 0.00 3.91
187 188 1.295792 GTCGGTGTGTTCAGAAGCAA 58.704 50.000 0.00 0.00 0.00 3.91
188 189 1.873591 GTCGGTGTGTTCAGAAGCAAT 59.126 47.619 0.00 0.00 0.00 3.56
189 190 2.290641 GTCGGTGTGTTCAGAAGCAATT 59.709 45.455 0.00 0.00 0.00 2.32
190 191 2.290367 TCGGTGTGTTCAGAAGCAATTG 59.710 45.455 0.00 0.00 0.00 2.32
191 192 2.033299 CGGTGTGTTCAGAAGCAATTGT 59.967 45.455 7.40 0.00 0.00 2.71
192 193 3.374745 GGTGTGTTCAGAAGCAATTGTG 58.625 45.455 7.40 0.00 0.00 3.33
193 194 3.066621 GGTGTGTTCAGAAGCAATTGTGA 59.933 43.478 7.40 0.00 0.00 3.58
194 195 4.261741 GGTGTGTTCAGAAGCAATTGTGAT 60.262 41.667 7.40 0.00 0.00 3.06
195 196 4.913924 GTGTGTTCAGAAGCAATTGTGATC 59.086 41.667 7.40 3.47 0.00 2.92
196 197 4.022935 TGTGTTCAGAAGCAATTGTGATCC 60.023 41.667 7.40 0.00 0.00 3.36
197 198 3.189080 TGTTCAGAAGCAATTGTGATCCG 59.811 43.478 7.40 0.00 0.00 4.18
198 199 1.739466 TCAGAAGCAATTGTGATCCGC 59.261 47.619 7.40 0.00 0.00 5.54
199 200 1.469703 CAGAAGCAATTGTGATCCGCA 59.530 47.619 7.40 0.00 0.00 5.69
200 201 1.741706 AGAAGCAATTGTGATCCGCAG 59.258 47.619 7.40 0.00 0.00 5.18
201 202 1.739466 GAAGCAATTGTGATCCGCAGA 59.261 47.619 7.40 0.00 0.00 4.26
202 203 1.825090 AGCAATTGTGATCCGCAGAA 58.175 45.000 7.40 0.00 33.94 3.02
203 204 2.161855 AGCAATTGTGATCCGCAGAAA 58.838 42.857 7.40 0.00 33.07 2.52
204 205 2.557924 AGCAATTGTGATCCGCAGAAAA 59.442 40.909 7.40 0.00 33.07 2.29
205 206 3.005684 AGCAATTGTGATCCGCAGAAAAA 59.994 39.130 7.40 0.00 33.07 1.94
206 207 3.928375 GCAATTGTGATCCGCAGAAAAAT 59.072 39.130 7.40 0.00 33.07 1.82
207 208 4.032104 GCAATTGTGATCCGCAGAAAAATC 59.968 41.667 7.40 0.00 33.07 2.17
208 209 5.404946 CAATTGTGATCCGCAGAAAAATCT 58.595 37.500 0.00 0.00 33.07 2.40
209 210 6.554419 CAATTGTGATCCGCAGAAAAATCTA 58.446 36.000 0.00 0.00 33.07 1.98
210 211 6.757897 ATTGTGATCCGCAGAAAAATCTAA 57.242 33.333 0.00 0.00 33.07 2.10
211 212 6.567687 TTGTGATCCGCAGAAAAATCTAAA 57.432 33.333 0.00 0.00 0.00 1.85
212 213 6.757897 TGTGATCCGCAGAAAAATCTAAAT 57.242 33.333 0.00 0.00 0.00 1.40
213 214 7.156876 TGTGATCCGCAGAAAAATCTAAATT 57.843 32.000 0.00 0.00 0.00 1.82
214 215 7.028962 TGTGATCCGCAGAAAAATCTAAATTG 58.971 34.615 0.00 0.00 0.00 2.32
215 216 7.029563 GTGATCCGCAGAAAAATCTAAATTGT 58.970 34.615 0.00 0.00 0.00 2.71
216 217 7.218963 GTGATCCGCAGAAAAATCTAAATTGTC 59.781 37.037 0.00 0.00 0.00 3.18
217 218 6.567687 TCCGCAGAAAAATCTAAATTGTCA 57.432 33.333 0.00 0.00 0.00 3.58
218 219 6.611381 TCCGCAGAAAAATCTAAATTGTCAG 58.389 36.000 0.00 0.00 0.00 3.51
219 220 5.801947 CCGCAGAAAAATCTAAATTGTCAGG 59.198 40.000 0.00 0.00 0.00 3.86
220 221 6.349280 CCGCAGAAAAATCTAAATTGTCAGGA 60.349 38.462 0.00 0.00 0.00 3.86
221 222 7.253422 CGCAGAAAAATCTAAATTGTCAGGAT 58.747 34.615 0.00 0.00 0.00 3.24
222 223 7.219535 CGCAGAAAAATCTAAATTGTCAGGATG 59.780 37.037 0.00 0.00 37.54 3.51
223 224 7.009907 GCAGAAAAATCTAAATTGTCAGGATGC 59.990 37.037 0.00 0.00 34.76 3.91
224 225 7.490402 CAGAAAAATCTAAATTGTCAGGATGCC 59.510 37.037 0.00 0.00 34.76 4.40
225 226 5.505173 AAATCTAAATTGTCAGGATGCCG 57.495 39.130 0.00 0.00 34.76 5.69
226 227 3.904800 TCTAAATTGTCAGGATGCCGA 57.095 42.857 0.00 0.00 34.76 5.54
227 228 3.531538 TCTAAATTGTCAGGATGCCGAC 58.468 45.455 0.00 0.00 34.76 4.79
228 229 1.086696 AAATTGTCAGGATGCCGACG 58.913 50.000 0.00 0.00 34.76 5.12
229 230 0.249120 AATTGTCAGGATGCCGACGA 59.751 50.000 0.00 0.00 34.76 4.20
230 231 0.460284 ATTGTCAGGATGCCGACGAC 60.460 55.000 0.00 0.00 34.76 4.34
231 232 1.811645 TTGTCAGGATGCCGACGACA 61.812 55.000 0.00 0.00 34.76 4.35
232 233 1.141881 GTCAGGATGCCGACGACAT 59.858 57.895 0.00 0.00 34.76 3.06
233 234 0.384309 GTCAGGATGCCGACGACATA 59.616 55.000 0.00 0.00 34.76 2.29
234 235 0.668535 TCAGGATGCCGACGACATAG 59.331 55.000 0.00 0.00 34.76 2.23
235 236 0.668535 CAGGATGCCGACGACATAGA 59.331 55.000 0.00 0.00 0.00 1.98
236 237 1.270826 CAGGATGCCGACGACATAGAT 59.729 52.381 0.00 0.00 0.00 1.98
237 238 1.542030 AGGATGCCGACGACATAGATC 59.458 52.381 0.00 0.00 0.00 2.75
238 239 1.269723 GGATGCCGACGACATAGATCA 59.730 52.381 0.00 0.00 0.00 2.92
239 240 2.288213 GGATGCCGACGACATAGATCAA 60.288 50.000 0.00 0.00 0.00 2.57
240 241 3.579709 GATGCCGACGACATAGATCAAT 58.420 45.455 0.00 0.00 0.00 2.57
241 242 2.742774 TGCCGACGACATAGATCAATG 58.257 47.619 0.00 0.00 0.00 2.82
242 243 2.061773 GCCGACGACATAGATCAATGG 58.938 52.381 0.00 0.00 0.00 3.16
243 244 2.288213 GCCGACGACATAGATCAATGGA 60.288 50.000 0.00 0.00 0.00 3.41
244 245 3.569548 CCGACGACATAGATCAATGGAG 58.430 50.000 0.00 0.00 0.00 3.86
245 246 3.004839 CCGACGACATAGATCAATGGAGT 59.995 47.826 0.00 0.00 0.00 3.85
246 247 4.215613 CCGACGACATAGATCAATGGAGTA 59.784 45.833 0.00 0.00 0.00 2.59
247 248 5.278315 CCGACGACATAGATCAATGGAGTAA 60.278 44.000 0.00 0.00 0.00 2.24
248 249 6.206498 CGACGACATAGATCAATGGAGTAAA 58.794 40.000 0.00 0.00 0.00 2.01
249 250 6.863645 CGACGACATAGATCAATGGAGTAAAT 59.136 38.462 0.00 0.00 0.00 1.40
250 251 7.382488 CGACGACATAGATCAATGGAGTAAATT 59.618 37.037 0.00 0.00 0.00 1.82
251 252 8.594881 ACGACATAGATCAATGGAGTAAATTC 57.405 34.615 0.00 0.00 0.00 2.17
252 253 8.424918 ACGACATAGATCAATGGAGTAAATTCT 58.575 33.333 0.00 0.00 0.00 2.40
253 254 8.920665 CGACATAGATCAATGGAGTAAATTCTC 58.079 37.037 0.00 0.00 0.00 2.87
254 255 9.770097 GACATAGATCAATGGAGTAAATTCTCA 57.230 33.333 0.00 0.00 36.30 3.27
255 256 9.553064 ACATAGATCAATGGAGTAAATTCTCAC 57.447 33.333 0.00 0.00 36.30 3.51
256 257 9.551734 CATAGATCAATGGAGTAAATTCTCACA 57.448 33.333 0.00 0.00 36.30 3.58
258 259 8.868522 AGATCAATGGAGTAAATTCTCACAAA 57.131 30.769 0.00 0.00 36.30 2.83
259 260 9.471702 AGATCAATGGAGTAAATTCTCACAAAT 57.528 29.630 0.00 0.00 36.30 2.32
260 261 9.512435 GATCAATGGAGTAAATTCTCACAAATG 57.488 33.333 0.00 0.00 36.30 2.32
261 262 8.634335 TCAATGGAGTAAATTCTCACAAATGA 57.366 30.769 0.00 0.00 36.30 2.57
262 263 9.076781 TCAATGGAGTAAATTCTCACAAATGAA 57.923 29.630 0.00 0.00 36.30 2.57
263 264 9.695526 CAATGGAGTAAATTCTCACAAATGAAA 57.304 29.630 0.00 0.00 36.30 2.69
265 266 9.865321 ATGGAGTAAATTCTCACAAATGAAATG 57.135 29.630 0.00 0.00 36.30 2.32
266 267 9.076781 TGGAGTAAATTCTCACAAATGAAATGA 57.923 29.630 0.00 0.00 36.30 2.57
276 277 9.177608 TCTCACAAATGAAATGATAGTTAAGGG 57.822 33.333 0.00 0.00 33.30 3.95
277 278 9.177608 CTCACAAATGAAATGATAGTTAAGGGA 57.822 33.333 0.00 0.00 33.30 4.20
278 279 9.527157 TCACAAATGAAATGATAGTTAAGGGAA 57.473 29.630 0.00 0.00 0.00 3.97
294 295 8.997734 AGTTAAGGGAATATGAATCTTGACTCT 58.002 33.333 0.00 0.00 31.60 3.24
295 296 9.050601 GTTAAGGGAATATGAATCTTGACTCTG 57.949 37.037 0.00 0.00 0.00 3.35
296 297 6.185114 AGGGAATATGAATCTTGACTCTGG 57.815 41.667 0.00 0.00 0.00 3.86
297 298 5.907662 AGGGAATATGAATCTTGACTCTGGA 59.092 40.000 0.00 0.00 0.00 3.86
298 299 6.388100 AGGGAATATGAATCTTGACTCTGGAA 59.612 38.462 0.00 0.00 0.00 3.53
490 4299 2.091665 CCTGCCAGAGATATTTTGGGGT 60.092 50.000 0.00 0.00 32.53 4.95
1282 5592 1.609208 GCCAGAGGCTGTTTCAAAGA 58.391 50.000 0.00 0.00 46.69 2.52
1405 5716 5.773680 ACAGCAACTCAAACTAGTAGTAGGA 59.226 40.000 2.50 3.64 0.00 2.94
1406 5717 6.094061 CAGCAACTCAAACTAGTAGTAGGAC 58.906 44.000 2.50 0.00 0.00 3.85
1407 5718 5.773680 AGCAACTCAAACTAGTAGTAGGACA 59.226 40.000 2.50 0.00 0.00 4.02
1426 5740 1.138661 CAACAGCAAAAAGGAAGGCCA 59.861 47.619 5.01 0.00 36.29 5.36
1448 5762 5.530915 CCAAGACTGTCCAAACTGAATTACA 59.469 40.000 3.76 0.00 0.00 2.41
1449 5763 6.207417 CCAAGACTGTCCAAACTGAATTACAT 59.793 38.462 3.76 0.00 0.00 2.29
1616 5930 3.530265 TGATCATTGGGCAGCATTTTC 57.470 42.857 0.00 0.00 0.00 2.29
1915 6229 6.828502 TCTTCATTGATAGCGTTGACATAC 57.171 37.500 0.00 0.00 0.00 2.39
1921 6235 1.191535 TAGCGTTGACATACCAGCCT 58.808 50.000 0.00 0.00 0.00 4.58
2049 6364 1.203994 GCAGCGGGTAGACTCTTAACA 59.796 52.381 0.00 0.00 0.00 2.41
2113 6428 5.782893 TTGTTTGAACCTTATGTTGGAGG 57.217 39.130 0.00 0.00 37.29 4.30
2222 6571 4.464244 AGATGAAATGAGAGTGAAGACCGA 59.536 41.667 0.00 0.00 0.00 4.69
2347 6697 3.636300 GGGTGATGTTTGGCATAGCAATA 59.364 43.478 0.00 0.00 38.06 1.90
2348 6698 4.099266 GGGTGATGTTTGGCATAGCAATAA 59.901 41.667 0.00 0.00 38.06 1.40
2349 6699 5.284079 GGTGATGTTTGGCATAGCAATAAG 58.716 41.667 0.00 0.00 38.06 1.73
3326 7679 3.637694 GGACTAGGTCTGACCCATTAGTC 59.362 52.174 29.09 29.09 40.25 2.59
3327 7680 3.637694 GACTAGGTCTGACCCATTAGTCC 59.362 52.174 27.91 17.64 39.75 3.85
3328 7681 2.950990 AGGTCTGACCCATTAGTCCT 57.049 50.000 22.81 0.00 39.75 3.85
3329 7682 4.481280 ACTAGGTCTGACCCATTAGTCCTA 59.519 45.833 22.81 5.01 39.75 2.94
3330 7683 3.917300 AGGTCTGACCCATTAGTCCTAG 58.083 50.000 22.81 0.00 39.75 3.02
3331 7684 3.532232 AGGTCTGACCCATTAGTCCTAGA 59.468 47.826 22.81 0.00 39.75 2.43
3332 7685 4.016479 AGGTCTGACCCATTAGTCCTAGAA 60.016 45.833 22.81 0.00 39.75 2.10
3333 7686 4.342665 GGTCTGACCCATTAGTCCTAGAAG 59.657 50.000 16.14 0.00 35.83 2.85
3334 7687 5.202004 GTCTGACCCATTAGTCCTAGAAGA 58.798 45.833 0.00 0.00 35.83 2.87
3335 7688 5.068067 GTCTGACCCATTAGTCCTAGAAGAC 59.932 48.000 0.00 0.00 35.83 3.01
3336 7689 4.942944 TGACCCATTAGTCCTAGAAGACA 58.057 43.478 0.00 0.00 39.34 3.41
3337 7690 5.529289 TGACCCATTAGTCCTAGAAGACAT 58.471 41.667 0.00 0.00 39.34 3.06
3338 7691 5.964477 TGACCCATTAGTCCTAGAAGACATT 59.036 40.000 0.00 0.00 39.34 2.71
3339 7692 7.130099 TGACCCATTAGTCCTAGAAGACATTA 58.870 38.462 0.00 0.00 39.34 1.90
3340 7693 7.287927 TGACCCATTAGTCCTAGAAGACATTAG 59.712 40.741 0.00 0.00 39.34 1.73
3341 7694 7.133483 ACCCATTAGTCCTAGAAGACATTAGT 58.867 38.462 0.00 0.00 39.34 2.24
3568 7924 1.988293 TGAGGACGAGGAGGATGATC 58.012 55.000 0.00 0.00 0.00 2.92
4251 9034 1.472878 ACTTGATGCTCATGCTTGCTG 59.527 47.619 0.00 0.00 40.48 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.332078 TCCCAGTGGATATGGCACACAC 62.332 54.545 11.95 6.65 37.00 3.82
3 4 2.183209 TCCCAGTGGATATGGCACACA 61.183 52.381 11.95 0.00 37.00 3.72
4 5 0.546122 TCCCAGTGGATATGGCACAC 59.454 55.000 11.95 0.00 37.00 3.82
5 6 1.294041 TTCCCAGTGGATATGGCACA 58.706 50.000 11.95 0.00 42.24 4.57
6 7 2.435372 TTTCCCAGTGGATATGGCAC 57.565 50.000 11.95 0.00 41.40 5.01
7 8 2.513317 TCATTTCCCAGTGGATATGGCA 59.487 45.455 11.95 0.00 45.21 4.92
8 9 3.228188 TCATTTCCCAGTGGATATGGC 57.772 47.619 11.95 0.00 45.21 4.40
9 10 4.581824 CAGTTCATTTCCCAGTGGATATGG 59.418 45.833 11.95 0.00 45.21 2.74
10 11 5.439721 TCAGTTCATTTCCCAGTGGATATG 58.560 41.667 11.95 10.86 46.01 1.78
11 12 5.715439 TCAGTTCATTTCCCAGTGGATAT 57.285 39.130 11.95 0.00 41.40 1.63
12 13 5.014123 ACTTCAGTTCATTTCCCAGTGGATA 59.986 40.000 11.95 0.00 41.40 2.59
13 14 4.202609 ACTTCAGTTCATTTCCCAGTGGAT 60.203 41.667 11.95 0.00 41.40 3.41
14 15 3.138283 ACTTCAGTTCATTTCCCAGTGGA 59.862 43.478 11.95 0.00 39.54 4.02
15 16 3.490348 ACTTCAGTTCATTTCCCAGTGG 58.510 45.455 0.63 0.63 0.00 4.00
16 17 5.308825 AGTACTTCAGTTCATTTCCCAGTG 58.691 41.667 0.00 0.00 0.00 3.66
17 18 5.552178 GAGTACTTCAGTTCATTTCCCAGT 58.448 41.667 0.00 0.00 0.00 4.00
18 19 4.627467 CGAGTACTTCAGTTCATTTCCCAG 59.373 45.833 0.00 0.00 0.00 4.45
19 20 4.562757 CCGAGTACTTCAGTTCATTTCCCA 60.563 45.833 0.00 0.00 0.00 4.37
20 21 3.933332 CCGAGTACTTCAGTTCATTTCCC 59.067 47.826 0.00 0.00 0.00 3.97
21 22 3.371285 GCCGAGTACTTCAGTTCATTTCC 59.629 47.826 0.00 0.00 0.00 3.13
22 23 3.371285 GGCCGAGTACTTCAGTTCATTTC 59.629 47.826 0.00 0.00 0.00 2.17
23 24 3.335579 GGCCGAGTACTTCAGTTCATTT 58.664 45.455 0.00 0.00 0.00 2.32
24 25 2.354805 GGGCCGAGTACTTCAGTTCATT 60.355 50.000 0.00 0.00 0.00 2.57
25 26 1.207329 GGGCCGAGTACTTCAGTTCAT 59.793 52.381 0.00 0.00 0.00 2.57
26 27 0.606604 GGGCCGAGTACTTCAGTTCA 59.393 55.000 0.00 0.00 0.00 3.18
27 28 0.108281 GGGGCCGAGTACTTCAGTTC 60.108 60.000 0.00 0.00 0.00 3.01
28 29 1.551019 GGGGGCCGAGTACTTCAGTT 61.551 60.000 0.00 0.00 0.00 3.16
29 30 1.988406 GGGGGCCGAGTACTTCAGT 60.988 63.158 0.00 0.00 0.00 3.41
30 31 1.550130 TTGGGGGCCGAGTACTTCAG 61.550 60.000 0.00 0.00 0.00 3.02
31 32 0.912487 ATTGGGGGCCGAGTACTTCA 60.912 55.000 0.00 0.00 0.00 3.02
32 33 1.125633 TATTGGGGGCCGAGTACTTC 58.874 55.000 0.00 0.00 0.00 3.01
33 34 1.815757 ATATTGGGGGCCGAGTACTT 58.184 50.000 0.00 0.00 0.00 2.24
34 35 1.815757 AATATTGGGGGCCGAGTACT 58.184 50.000 0.00 0.00 0.00 2.73
35 36 2.158726 TGAAATATTGGGGGCCGAGTAC 60.159 50.000 0.00 0.00 0.00 2.73
36 37 2.128535 TGAAATATTGGGGGCCGAGTA 58.871 47.619 0.00 0.00 0.00 2.59
37 38 0.923358 TGAAATATTGGGGGCCGAGT 59.077 50.000 0.00 0.00 0.00 4.18
38 39 2.292828 ATGAAATATTGGGGGCCGAG 57.707 50.000 0.00 0.00 0.00 4.63
39 40 2.714250 AGTATGAAATATTGGGGGCCGA 59.286 45.455 0.00 0.00 0.00 5.54
40 41 2.819608 CAGTATGAAATATTGGGGGCCG 59.180 50.000 0.00 0.00 39.69 6.13
41 42 4.112634 TCAGTATGAAATATTGGGGGCC 57.887 45.455 0.00 0.00 45.97 5.80
96 97 9.575868 TGTGAAATATGTTTCTACCCAAACTAA 57.424 29.630 14.97 0.00 43.30 2.24
97 98 9.747898 ATGTGAAATATGTTTCTACCCAAACTA 57.252 29.630 14.97 0.00 43.30 2.24
98 99 8.650143 ATGTGAAATATGTTTCTACCCAAACT 57.350 30.769 14.97 0.00 43.30 2.66
117 118 9.296400 GCTCCGCTTAATTAAAATTAATGTGAA 57.704 29.630 8.03 0.00 39.40 3.18
118 119 8.462811 TGCTCCGCTTAATTAAAATTAATGTGA 58.537 29.630 8.03 5.13 39.40 3.58
119 120 8.627487 TGCTCCGCTTAATTAAAATTAATGTG 57.373 30.769 8.03 8.68 39.40 3.21
120 121 8.682710 TCTGCTCCGCTTAATTAAAATTAATGT 58.317 29.630 8.03 0.00 39.40 2.71
121 122 9.173939 CTCTGCTCCGCTTAATTAAAATTAATG 57.826 33.333 8.03 5.08 39.40 1.90
122 123 8.352942 CCTCTGCTCCGCTTAATTAAAATTAAT 58.647 33.333 8.03 0.00 39.40 1.40
123 124 7.554835 TCCTCTGCTCCGCTTAATTAAAATTAA 59.445 33.333 7.47 7.47 38.24 1.40
124 125 7.051623 TCCTCTGCTCCGCTTAATTAAAATTA 58.948 34.615 0.00 0.00 0.00 1.40
125 126 5.885912 TCCTCTGCTCCGCTTAATTAAAATT 59.114 36.000 0.00 0.00 0.00 1.82
126 127 5.437060 TCCTCTGCTCCGCTTAATTAAAAT 58.563 37.500 0.00 0.00 0.00 1.82
127 128 4.839121 TCCTCTGCTCCGCTTAATTAAAA 58.161 39.130 0.00 0.00 0.00 1.52
128 129 4.481368 TCCTCTGCTCCGCTTAATTAAA 57.519 40.909 0.00 0.00 0.00 1.52
129 130 4.481368 TTCCTCTGCTCCGCTTAATTAA 57.519 40.909 0.00 0.00 0.00 1.40
130 131 4.689612 ATTCCTCTGCTCCGCTTAATTA 57.310 40.909 0.00 0.00 0.00 1.40
131 132 3.567478 ATTCCTCTGCTCCGCTTAATT 57.433 42.857 0.00 0.00 0.00 1.40
132 133 3.567478 AATTCCTCTGCTCCGCTTAAT 57.433 42.857 0.00 0.00 0.00 1.40
133 134 3.270877 GAAATTCCTCTGCTCCGCTTAA 58.729 45.455 0.00 0.00 0.00 1.85
134 135 2.420129 GGAAATTCCTCTGCTCCGCTTA 60.420 50.000 4.46 0.00 32.53 3.09
135 136 1.680249 GGAAATTCCTCTGCTCCGCTT 60.680 52.381 4.46 0.00 32.53 4.68
136 137 0.107459 GGAAATTCCTCTGCTCCGCT 60.107 55.000 4.46 0.00 32.53 5.52
137 138 0.107459 AGGAAATTCCTCTGCTCCGC 60.107 55.000 9.08 0.00 45.66 5.54
147 148 4.540715 ACCCATCTCATTGAGGAAATTCC 58.459 43.478 13.59 3.29 36.58 3.01
148 149 4.274459 CGACCCATCTCATTGAGGAAATTC 59.726 45.833 13.59 5.01 0.00 2.17
149 150 4.202441 CGACCCATCTCATTGAGGAAATT 58.798 43.478 13.59 0.00 0.00 1.82
150 151 3.434167 CCGACCCATCTCATTGAGGAAAT 60.434 47.826 13.59 0.00 0.00 2.17
151 152 2.092968 CCGACCCATCTCATTGAGGAAA 60.093 50.000 13.59 0.00 0.00 3.13
152 153 1.486310 CCGACCCATCTCATTGAGGAA 59.514 52.381 13.59 0.00 0.00 3.36
153 154 1.123077 CCGACCCATCTCATTGAGGA 58.877 55.000 13.59 1.54 0.00 3.71
154 155 0.833287 ACCGACCCATCTCATTGAGG 59.167 55.000 13.59 1.12 0.00 3.86
155 156 1.208052 ACACCGACCCATCTCATTGAG 59.792 52.381 7.38 7.38 0.00 3.02
156 157 1.066215 CACACCGACCCATCTCATTGA 60.066 52.381 0.00 0.00 0.00 2.57
157 158 1.339055 ACACACCGACCCATCTCATTG 60.339 52.381 0.00 0.00 0.00 2.82
158 159 0.984230 ACACACCGACCCATCTCATT 59.016 50.000 0.00 0.00 0.00 2.57
159 160 0.984230 AACACACCGACCCATCTCAT 59.016 50.000 0.00 0.00 0.00 2.90
160 161 0.320374 GAACACACCGACCCATCTCA 59.680 55.000 0.00 0.00 0.00 3.27
161 162 0.320374 TGAACACACCGACCCATCTC 59.680 55.000 0.00 0.00 0.00 2.75
162 163 0.321671 CTGAACACACCGACCCATCT 59.678 55.000 0.00 0.00 0.00 2.90
163 164 0.320374 TCTGAACACACCGACCCATC 59.680 55.000 0.00 0.00 0.00 3.51
164 165 0.762418 TTCTGAACACACCGACCCAT 59.238 50.000 0.00 0.00 0.00 4.00
165 166 0.105964 CTTCTGAACACACCGACCCA 59.894 55.000 0.00 0.00 0.00 4.51
166 167 1.228657 GCTTCTGAACACACCGACCC 61.229 60.000 0.00 0.00 0.00 4.46
167 168 0.531974 TGCTTCTGAACACACCGACC 60.532 55.000 0.00 0.00 0.00 4.79
168 169 1.295792 TTGCTTCTGAACACACCGAC 58.704 50.000 0.00 0.00 0.00 4.79
169 170 2.254546 ATTGCTTCTGAACACACCGA 57.745 45.000 0.00 0.00 0.00 4.69
170 171 2.033299 ACAATTGCTTCTGAACACACCG 59.967 45.455 5.05 0.00 0.00 4.94
171 172 3.066621 TCACAATTGCTTCTGAACACACC 59.933 43.478 5.05 0.00 0.00 4.16
172 173 4.291540 TCACAATTGCTTCTGAACACAC 57.708 40.909 5.05 0.00 0.00 3.82
173 174 4.022935 GGATCACAATTGCTTCTGAACACA 60.023 41.667 5.05 0.00 0.00 3.72
174 175 4.479619 GGATCACAATTGCTTCTGAACAC 58.520 43.478 5.05 0.00 0.00 3.32
175 176 3.189080 CGGATCACAATTGCTTCTGAACA 59.811 43.478 5.05 0.00 0.00 3.18
176 177 3.751621 CGGATCACAATTGCTTCTGAAC 58.248 45.455 5.05 0.59 0.00 3.18
177 178 2.162208 GCGGATCACAATTGCTTCTGAA 59.838 45.455 5.05 0.00 0.00 3.02
178 179 1.739466 GCGGATCACAATTGCTTCTGA 59.261 47.619 5.05 1.90 0.00 3.27
179 180 1.469703 TGCGGATCACAATTGCTTCTG 59.530 47.619 5.05 6.37 0.00 3.02
180 181 1.741706 CTGCGGATCACAATTGCTTCT 59.258 47.619 5.05 0.00 0.00 2.85
181 182 1.739466 TCTGCGGATCACAATTGCTTC 59.261 47.619 5.05 0.00 0.00 3.86
182 183 1.825090 TCTGCGGATCACAATTGCTT 58.175 45.000 5.05 0.00 0.00 3.91
183 184 1.825090 TTCTGCGGATCACAATTGCT 58.175 45.000 5.05 0.00 0.00 3.91
184 185 2.634982 TTTCTGCGGATCACAATTGC 57.365 45.000 5.05 0.00 0.00 3.56
185 186 5.404946 AGATTTTTCTGCGGATCACAATTG 58.595 37.500 3.24 3.24 0.00 2.32
186 187 5.649782 AGATTTTTCTGCGGATCACAATT 57.350 34.783 0.00 0.00 0.00 2.32
187 188 6.757897 TTAGATTTTTCTGCGGATCACAAT 57.242 33.333 0.00 0.00 0.00 2.71
188 189 6.567687 TTTAGATTTTTCTGCGGATCACAA 57.432 33.333 0.00 0.00 0.00 3.33
189 190 6.757897 ATTTAGATTTTTCTGCGGATCACA 57.242 33.333 0.00 0.00 0.00 3.58
190 191 7.029563 ACAATTTAGATTTTTCTGCGGATCAC 58.970 34.615 0.00 0.00 0.00 3.06
191 192 7.094420 TGACAATTTAGATTTTTCTGCGGATCA 60.094 33.333 0.00 0.00 0.00 2.92
192 193 7.250569 TGACAATTTAGATTTTTCTGCGGATC 58.749 34.615 0.00 0.00 0.00 3.36
193 194 7.156876 TGACAATTTAGATTTTTCTGCGGAT 57.843 32.000 0.00 0.00 0.00 4.18
194 195 6.349280 CCTGACAATTTAGATTTTTCTGCGGA 60.349 38.462 0.00 0.00 0.00 5.54
195 196 5.801947 CCTGACAATTTAGATTTTTCTGCGG 59.198 40.000 0.00 0.00 0.00 5.69
196 197 6.611381 TCCTGACAATTTAGATTTTTCTGCG 58.389 36.000 0.00 0.00 0.00 5.18
197 198 7.009907 GCATCCTGACAATTTAGATTTTTCTGC 59.990 37.037 0.00 0.00 0.00 4.26
198 199 7.490402 GGCATCCTGACAATTTAGATTTTTCTG 59.510 37.037 0.00 0.00 0.00 3.02
199 200 7.550712 GGCATCCTGACAATTTAGATTTTTCT 58.449 34.615 0.00 0.00 0.00 2.52
200 201 6.473455 CGGCATCCTGACAATTTAGATTTTTC 59.527 38.462 0.00 0.00 0.00 2.29
201 202 6.152661 TCGGCATCCTGACAATTTAGATTTTT 59.847 34.615 0.00 0.00 0.00 1.94
202 203 5.652014 TCGGCATCCTGACAATTTAGATTTT 59.348 36.000 0.00 0.00 0.00 1.82
203 204 5.066505 GTCGGCATCCTGACAATTTAGATTT 59.933 40.000 0.00 0.00 35.20 2.17
204 205 4.576463 GTCGGCATCCTGACAATTTAGATT 59.424 41.667 0.00 0.00 35.20 2.40
205 206 4.130118 GTCGGCATCCTGACAATTTAGAT 58.870 43.478 0.00 0.00 35.20 1.98
206 207 3.531538 GTCGGCATCCTGACAATTTAGA 58.468 45.455 0.00 0.00 35.20 2.10
207 208 2.285220 CGTCGGCATCCTGACAATTTAG 59.715 50.000 0.00 0.00 34.78 1.85
208 209 2.093921 TCGTCGGCATCCTGACAATTTA 60.094 45.455 0.00 0.00 34.78 1.40
209 210 1.086696 CGTCGGCATCCTGACAATTT 58.913 50.000 0.00 0.00 34.78 1.82
210 211 0.249120 TCGTCGGCATCCTGACAATT 59.751 50.000 0.00 0.00 34.78 2.32
211 212 0.460284 GTCGTCGGCATCCTGACAAT 60.460 55.000 0.00 0.00 34.78 2.71
212 213 1.080093 GTCGTCGGCATCCTGACAA 60.080 57.895 0.00 0.00 34.78 3.18
213 214 1.604147 ATGTCGTCGGCATCCTGACA 61.604 55.000 6.49 0.00 43.02 3.58
214 215 0.384309 TATGTCGTCGGCATCCTGAC 59.616 55.000 16.94 0.00 0.00 3.51
215 216 0.668535 CTATGTCGTCGGCATCCTGA 59.331 55.000 16.94 0.00 0.00 3.86
216 217 0.668535 TCTATGTCGTCGGCATCCTG 59.331 55.000 16.94 8.20 0.00 3.86
217 218 1.542030 GATCTATGTCGTCGGCATCCT 59.458 52.381 16.94 1.87 0.00 3.24
218 219 1.269723 TGATCTATGTCGTCGGCATCC 59.730 52.381 16.94 5.18 0.00 3.51
219 220 2.706555 TGATCTATGTCGTCGGCATC 57.293 50.000 16.94 3.18 0.00 3.91
220 221 3.320626 CATTGATCTATGTCGTCGGCAT 58.679 45.455 17.60 17.60 0.00 4.40
221 222 2.545742 CCATTGATCTATGTCGTCGGCA 60.546 50.000 14.72 0.14 0.00 5.69
222 223 2.061773 CCATTGATCTATGTCGTCGGC 58.938 52.381 14.72 0.00 0.00 5.54
223 224 3.004839 ACTCCATTGATCTATGTCGTCGG 59.995 47.826 14.72 0.45 0.00 4.79
224 225 4.230314 ACTCCATTGATCTATGTCGTCG 57.770 45.455 14.72 1.23 0.00 5.12
225 226 8.594881 AATTTACTCCATTGATCTATGTCGTC 57.405 34.615 14.72 0.00 0.00 4.20
226 227 8.424918 AGAATTTACTCCATTGATCTATGTCGT 58.575 33.333 14.72 12.75 0.00 4.34
227 228 8.824159 AGAATTTACTCCATTGATCTATGTCG 57.176 34.615 14.72 8.36 0.00 4.35
228 229 9.770097 TGAGAATTTACTCCATTGATCTATGTC 57.230 33.333 14.72 4.71 36.22 3.06
229 230 9.553064 GTGAGAATTTACTCCATTGATCTATGT 57.447 33.333 14.72 1.12 36.22 2.29
230 231 9.551734 TGTGAGAATTTACTCCATTGATCTATG 57.448 33.333 9.85 9.85 36.22 2.23
232 233 9.958180 TTTGTGAGAATTTACTCCATTGATCTA 57.042 29.630 0.00 0.00 36.22 1.98
233 234 8.868522 TTTGTGAGAATTTACTCCATTGATCT 57.131 30.769 0.00 0.00 36.22 2.75
234 235 9.512435 CATTTGTGAGAATTTACTCCATTGATC 57.488 33.333 0.00 0.00 36.22 2.92
235 236 9.246670 TCATTTGTGAGAATTTACTCCATTGAT 57.753 29.630 0.00 0.00 36.22 2.57
236 237 8.634335 TCATTTGTGAGAATTTACTCCATTGA 57.366 30.769 0.00 0.00 36.22 2.57
237 238 9.695526 TTTCATTTGTGAGAATTTACTCCATTG 57.304 29.630 0.00 0.00 36.22 2.82
239 240 9.865321 CATTTCATTTGTGAGAATTTACTCCAT 57.135 29.630 0.00 0.00 36.22 3.41
240 241 9.076781 TCATTTCATTTGTGAGAATTTACTCCA 57.923 29.630 0.00 0.00 36.22 3.86
250 251 9.177608 CCCTTAACTATCATTTCATTTGTGAGA 57.822 33.333 0.00 0.00 0.00 3.27
251 252 9.177608 TCCCTTAACTATCATTTCATTTGTGAG 57.822 33.333 0.00 0.00 0.00 3.51
252 253 9.527157 TTCCCTTAACTATCATTTCATTTGTGA 57.473 29.630 0.00 0.00 0.00 3.58
268 269 8.997734 AGAGTCAAGATTCATATTCCCTTAACT 58.002 33.333 0.00 0.00 0.00 2.24
269 270 9.050601 CAGAGTCAAGATTCATATTCCCTTAAC 57.949 37.037 0.00 0.00 0.00 2.01
270 271 8.213679 CCAGAGTCAAGATTCATATTCCCTTAA 58.786 37.037 0.00 0.00 0.00 1.85
271 272 7.568738 TCCAGAGTCAAGATTCATATTCCCTTA 59.431 37.037 0.00 0.00 0.00 2.69
272 273 6.388100 TCCAGAGTCAAGATTCATATTCCCTT 59.612 38.462 0.00 0.00 0.00 3.95
273 274 5.907662 TCCAGAGTCAAGATTCATATTCCCT 59.092 40.000 0.00 0.00 0.00 4.20
274 275 6.179906 TCCAGAGTCAAGATTCATATTCCC 57.820 41.667 0.00 0.00 0.00 3.97
275 276 7.050377 TGTTCCAGAGTCAAGATTCATATTCC 58.950 38.462 0.00 0.00 0.00 3.01
276 277 8.394121 GTTGTTCCAGAGTCAAGATTCATATTC 58.606 37.037 0.00 0.00 0.00 1.75
277 278 7.065085 CGTTGTTCCAGAGTCAAGATTCATATT 59.935 37.037 0.00 0.00 0.00 1.28
278 279 6.536582 CGTTGTTCCAGAGTCAAGATTCATAT 59.463 38.462 0.00 0.00 0.00 1.78
279 280 5.869344 CGTTGTTCCAGAGTCAAGATTCATA 59.131 40.000 0.00 0.00 0.00 2.15
280 281 4.692625 CGTTGTTCCAGAGTCAAGATTCAT 59.307 41.667 0.00 0.00 0.00 2.57
281 282 4.058124 CGTTGTTCCAGAGTCAAGATTCA 58.942 43.478 0.00 0.00 0.00 2.57
282 283 4.058817 ACGTTGTTCCAGAGTCAAGATTC 58.941 43.478 0.00 0.00 0.00 2.52
283 284 4.073293 ACGTTGTTCCAGAGTCAAGATT 57.927 40.909 0.00 0.00 0.00 2.40
284 285 3.753294 ACGTTGTTCCAGAGTCAAGAT 57.247 42.857 0.00 0.00 0.00 2.40
285 286 3.536956 AACGTTGTTCCAGAGTCAAGA 57.463 42.857 0.00 0.00 0.00 3.02
286 287 4.616181 AAAACGTTGTTCCAGAGTCAAG 57.384 40.909 0.00 0.00 0.00 3.02
287 288 4.456222 TCAAAAACGTTGTTCCAGAGTCAA 59.544 37.500 0.00 0.00 0.00 3.18
288 289 4.004314 TCAAAAACGTTGTTCCAGAGTCA 58.996 39.130 0.00 0.00 0.00 3.41
289 290 4.094442 ACTCAAAAACGTTGTTCCAGAGTC 59.906 41.667 14.00 0.00 0.00 3.36
290 291 4.007659 ACTCAAAAACGTTGTTCCAGAGT 58.992 39.130 14.00 14.00 0.00 3.24
291 292 4.588278 GACTCAAAAACGTTGTTCCAGAG 58.412 43.478 12.97 12.97 0.00 3.35
292 293 3.062909 CGACTCAAAAACGTTGTTCCAGA 59.937 43.478 0.00 0.00 0.00 3.86
293 294 3.350912 CGACTCAAAAACGTTGTTCCAG 58.649 45.455 0.00 3.30 0.00 3.86
294 295 2.476519 GCGACTCAAAAACGTTGTTCCA 60.477 45.455 0.00 0.00 0.00 3.53
295 296 2.106418 GCGACTCAAAAACGTTGTTCC 58.894 47.619 0.00 0.00 0.00 3.62
296 297 2.106418 GGCGACTCAAAAACGTTGTTC 58.894 47.619 0.00 0.00 0.00 3.18
297 298 1.530236 CGGCGACTCAAAAACGTTGTT 60.530 47.619 0.00 0.00 0.00 2.83
298 299 0.027063 CGGCGACTCAAAAACGTTGT 59.973 50.000 0.00 0.00 0.00 3.32
441 442 4.393155 TGGAGCAAGCCACGCGAT 62.393 61.111 15.93 0.00 31.66 4.58
1282 5592 3.383825 GCCTTCATGAAATCCAGCATCTT 59.616 43.478 9.88 0.00 0.00 2.40
1405 5716 1.138859 GGCCTTCCTTTTTGCTGTTGT 59.861 47.619 0.00 0.00 0.00 3.32
1406 5717 1.138661 TGGCCTTCCTTTTTGCTGTTG 59.861 47.619 3.32 0.00 0.00 3.33
1407 5718 1.494960 TGGCCTTCCTTTTTGCTGTT 58.505 45.000 3.32 0.00 0.00 3.16
1426 5740 7.936847 TGTATGTAATTCAGTTTGGACAGTCTT 59.063 33.333 0.00 0.00 0.00 3.01
1448 5762 6.463995 TTGTTCTTGAAGCCTTTTGTGTAT 57.536 33.333 0.00 0.00 0.00 2.29
1449 5763 5.906113 TTGTTCTTGAAGCCTTTTGTGTA 57.094 34.783 0.00 0.00 0.00 2.90
1623 5937 3.899052 ACATTGAAGGGAATGGCATTG 57.101 42.857 19.07 2.78 37.60 2.82
1921 6235 5.048083 CCAACAATTCTTTGCTGGCTACTAA 60.048 40.000 0.00 0.00 41.01 2.24
2049 6364 5.545723 CCACCATAATGTAGGAATCCTCTCT 59.454 44.000 4.42 0.00 34.61 3.10
2058 6373 2.021441 AGGGGTCCACCATAATGTAGGA 60.021 50.000 0.00 0.00 42.91 2.94
2113 6428 3.900388 TTGCTTGATTTTGCAAATGGC 57.100 38.095 13.65 12.73 44.75 4.40
2222 6571 1.270839 CCCTCACAAGATCACGGTTGT 60.271 52.381 0.00 0.00 37.37 3.32
2347 6697 2.561569 CGGTGAGGTTGACAACTTCTT 58.438 47.619 25.36 8.06 38.24 2.52
2348 6698 1.202651 CCGGTGAGGTTGACAACTTCT 60.203 52.381 25.36 13.03 38.24 2.85
2349 6699 1.226746 CCGGTGAGGTTGACAACTTC 58.773 55.000 20.37 20.37 37.94 3.01
3326 7679 7.996644 AGTCTTCTAGGACTAATGTCTTCTAGG 59.003 40.741 0.25 0.00 43.76 3.02
3327 7680 8.974060 AGTCTTCTAGGACTAATGTCTTCTAG 57.026 38.462 0.25 0.00 43.76 2.43
3329 7682 9.181061 GTAAGTCTTCTAGGACTAATGTCTTCT 57.819 37.037 2.52 0.00 44.67 2.85
3330 7683 8.958506 TGTAAGTCTTCTAGGACTAATGTCTTC 58.041 37.037 2.52 0.00 44.67 2.87
3331 7684 8.880991 TGTAAGTCTTCTAGGACTAATGTCTT 57.119 34.615 2.52 0.00 44.67 3.01
3332 7685 8.880991 TTGTAAGTCTTCTAGGACTAATGTCT 57.119 34.615 2.52 0.00 44.67 3.41
3333 7686 9.522804 CATTGTAAGTCTTCTAGGACTAATGTC 57.477 37.037 2.52 0.00 44.67 3.06
3334 7687 8.478877 CCATTGTAAGTCTTCTAGGACTAATGT 58.521 37.037 15.03 1.87 44.67 2.71
3335 7688 7.928706 CCCATTGTAAGTCTTCTAGGACTAATG 59.071 40.741 12.02 12.02 44.67 1.90
3336 7689 7.844779 TCCCATTGTAAGTCTTCTAGGACTAAT 59.155 37.037 2.52 0.00 44.67 1.73
3337 7690 7.123847 GTCCCATTGTAAGTCTTCTAGGACTAA 59.876 40.741 2.52 0.00 44.67 2.24
3338 7691 6.606395 GTCCCATTGTAAGTCTTCTAGGACTA 59.394 42.308 2.52 0.00 44.67 2.59
3340 7693 5.187186 TGTCCCATTGTAAGTCTTCTAGGAC 59.813 44.000 0.00 0.00 40.35 3.85
3341 7694 5.338632 TGTCCCATTGTAAGTCTTCTAGGA 58.661 41.667 0.00 0.00 0.00 2.94
3530 7883 2.373169 TCATCTTCTCCAACTTGGTGCT 59.627 45.455 7.72 0.00 39.03 4.40
3568 7924 2.490903 CAAGCTCAACCTCCTGATTTGG 59.509 50.000 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.