Multiple sequence alignment - TraesCS5A01G213000

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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 TraesCS5A01G213000 chr5A 100.000 2219 0 0 910 3128 428152994 428155212 0.000000e+00 4098.0
1 TraesCS5A01G213000 chr5A 100.000 722 0 0 1 722 428152085 428152806 0.000000e+00 1334.0
2 TraesCS5A01G213000 chr5A 90.833 840 59 10 1397 2226 428247361 428248192 0.000000e+00 1109.0
3 TraesCS5A01G213000 chr5A 94.721 341 18 0 10 350 184259276 184259616 5.940000e-147 531.0
4 TraesCS5A01G213000 chr5A 94.477 344 19 0 10 353 616635777 616635434 5.940000e-147 531.0
5 TraesCS5A01G213000 chr5A 91.031 223 16 2 1444 1666 428244809 428245027 6.560000e-77 298.0
6 TraesCS5A01G213000 chr5A 89.655 116 10 1 1663 1776 428247210 428247325 2.510000e-31 147.0
7 TraesCS5A01G213000 chr5D 91.121 1543 63 35 910 2422 328435388 328433890 0.000000e+00 2023.0
8 TraesCS5A01G213000 chr5D 91.796 646 42 5 1399 2043 328405052 328404417 0.000000e+00 889.0
9 TraesCS5A01G213000 chr5D 91.957 373 26 3 2478 2849 328433892 328433523 1.290000e-143 520.0
10 TraesCS5A01G213000 chr5D 93.913 345 17 3 10 354 104110404 104110064 4.620000e-143 518.0
11 TraesCS5A01G213000 chr5D 92.329 365 23 4 10 372 292644493 292644132 5.980000e-142 514.0
12 TraesCS5A01G213000 chr5D 87.471 431 36 7 2156 2572 328392154 328391728 6.070000e-132 481.0
13 TraesCS5A01G213000 chr5D 93.220 236 13 3 360 594 328435787 328435554 8.310000e-91 344.0
14 TraesCS5A01G213000 chr5D 90.476 189 14 4 2942 3128 328432842 328432656 2.410000e-61 246.0
15 TraesCS5A01G213000 chr5D 93.519 108 6 1 2057 2163 328402311 328402204 3.230000e-35 159.0
16 TraesCS5A01G213000 chr5D 85.714 119 5 4 616 722 328435569 328435451 7.090000e-22 115.0
17 TraesCS5A01G213000 chr5D 82.609 115 20 0 1880 1994 438360613 438360727 5.520000e-18 102.0
18 TraesCS5A01G213000 chr5D 84.848 66 9 1 3034 3098 357498703 357498768 7.240000e-07 65.8
19 TraesCS5A01G213000 chr5B 89.426 1551 87 32 1159 2674 381716091 381714583 0.000000e+00 1884.0
20 TraesCS5A01G213000 chr5B 84.722 144 9 6 923 1066 381716288 381716158 7.040000e-27 132.0
21 TraesCS5A01G213000 chr5B 78.161 87 18 1 3031 3116 21363886 21363972 2.000000e-03 54.7
22 TraesCS5A01G213000 chr4A 96.522 345 9 3 10 354 139717992 139717651 4.530000e-158 568.0
23 TraesCS5A01G213000 chr4A 93.750 112 6 1 355 465 137967029 137967140 1.930000e-37 167.0
24 TraesCS5A01G213000 chr4A 93.750 112 6 1 355 465 137972780 137972669 1.930000e-37 167.0
25 TraesCS5A01G213000 chr6D 94.901 353 16 2 1 353 5732281 5731931 4.560000e-153 551.0
26 TraesCS5A01G213000 chr6D 79.389 131 25 2 1879 2008 126871630 126871759 1.190000e-14 91.6
27 TraesCS5A01G213000 chr6D 82.500 80 13 1 3031 3109 262183528 262183607 5.600000e-08 69.4
28 TraesCS5A01G213000 chr2D 95.115 348 16 1 1 347 531751302 531751649 5.900000e-152 547.0
29 TraesCS5A01G213000 chr2D 94.428 341 19 0 10 350 640367377 640367717 2.760000e-145 525.0
30 TraesCS5A01G213000 chr3D 94.675 338 17 1 10 347 182184779 182185115 9.940000e-145 523.0
31 TraesCS5A01G213000 chr3D 92.241 116 8 1 355 469 537154752 537154867 2.500000e-36 163.0
32 TraesCS5A01G213000 chr2B 83.529 340 44 9 138 471 590166410 590166077 1.090000e-79 307.0
33 TraesCS5A01G213000 chr2B 80.357 224 42 1 1803 2026 210652590 210652369 5.370000e-38 169.0
34 TraesCS5A01G213000 chr2B 79.775 89 15 3 3036 3123 539643627 539643541 9.370000e-06 62.1
35 TraesCS5A01G213000 chr2A 80.645 217 42 0 1803 2019 148870578 148870794 5.370000e-38 169.0
36 TraesCS5A01G213000 chr4D 93.750 112 6 1 355 465 34661577 34661688 1.930000e-37 167.0
37 TraesCS5A01G213000 chr3B 92.308 117 7 2 355 469 749740790 749740674 6.940000e-37 165.0
38 TraesCS5A01G213000 chr6A 89.764 127 9 4 355 478 214179620 214179495 3.230000e-35 159.0
39 TraesCS5A01G213000 chr6A 79.851 134 25 2 1879 2011 152060967 152060835 2.570000e-16 97.1
40 TraesCS5A01G213000 chr6A 81.319 91 14 3 3034 3123 324289506 324289418 1.560000e-08 71.3
41 TraesCS5A01G213000 chr6A 76.724 116 25 2 1880 1994 61412445 61412559 2.600000e-06 63.9
42 TraesCS5A01G213000 chr6B 89.147 129 11 3 355 481 226864008 226863881 1.160000e-34 158.0
43 TraesCS5A01G213000 chr6B 80.303 132 22 4 1879 2008 225868163 225868292 2.570000e-16 97.1
44 TraesCS5A01G213000 chr1A 82.609 115 20 0 1880 1994 566564814 566564928 5.520000e-18 102.0
45 TraesCS5A01G213000 chr1D 81.739 115 21 0 1880 1994 472561557 472561671 2.570000e-16 97.1


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 TraesCS5A01G213000 chr5A 428152085 428155212 3127 False 2716.0 4098 100.000000 1 3128 2 chr5A.!!$F2 3127
1 TraesCS5A01G213000 chr5A 428244809 428248192 3383 False 518.0 1109 90.506333 1397 2226 3 chr5A.!!$F3 829
2 TraesCS5A01G213000 chr5D 328432656 328435787 3131 True 649.6 2023 90.497600 360 3128 5 chr5D.!!$R5 2768
3 TraesCS5A01G213000 chr5D 328402204 328405052 2848 True 524.0 889 92.657500 1399 2163 2 chr5D.!!$R4 764
4 TraesCS5A01G213000 chr5B 381714583 381716288 1705 True 1008.0 1884 87.074000 923 2674 2 chr5B.!!$R1 1751

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
678 680 1.135373 TGTTCAAACAAAAAGCCGCGA 60.135 42.857 8.23 0.0 35.67 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2576 5830 0.326522 TGGCTGGCTGAAGGGAGATA 60.327 55.0 2.0 0.0 0.0 1.98 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
73 74 7.872993 ACCTAGATACATAATGTACATGTGTGC 59.127 37.037 25.77 19.80 35.42 4.57
74 75 7.872483 CCTAGATACATAATGTACATGTGTGCA 59.128 37.037 25.77 14.40 44.32 4.57
75 76 9.260002 CTAGATACATAATGTACATGTGTGCAA 57.740 33.333 25.77 13.89 43.49 4.08
76 77 8.504812 AGATACATAATGTACATGTGTGCAAA 57.495 30.769 25.77 13.64 43.49 3.68
77 78 9.123902 AGATACATAATGTACATGTGTGCAAAT 57.876 29.630 25.77 16.51 43.49 2.32
80 81 8.830201 ACATAATGTACATGTGTGCAAATTTT 57.170 26.923 20.33 1.42 43.49 1.82
81 82 8.924691 ACATAATGTACATGTGTGCAAATTTTC 58.075 29.630 20.33 0.00 43.49 2.29
82 83 8.923683 CATAATGTACATGTGTGCAAATTTTCA 58.076 29.630 9.63 0.00 43.49 2.69
83 84 7.410800 AATGTACATGTGTGCAAATTTTCAG 57.589 32.000 9.63 0.00 43.49 3.02
86 87 3.181463 ACATGTGTGCAAATTTTCAGGCT 60.181 39.130 0.00 0.00 0.00 4.58
87 88 2.823984 TGTGTGCAAATTTTCAGGCTG 58.176 42.857 8.58 8.58 0.00 4.85
89 90 3.118847 TGTGTGCAAATTTTCAGGCTGAA 60.119 39.130 25.38 25.38 34.03 3.02
90 91 3.870419 GTGTGCAAATTTTCAGGCTGAAA 59.130 39.130 32.85 32.85 43.84 2.69
91 92 4.512571 GTGTGCAAATTTTCAGGCTGAAAT 59.487 37.500 35.58 23.10 44.75 2.17
92 93 5.695816 GTGTGCAAATTTTCAGGCTGAAATA 59.304 36.000 35.58 26.76 44.75 1.40
93 94 5.695816 TGTGCAAATTTTCAGGCTGAAATAC 59.304 36.000 35.58 25.90 44.75 1.89
95 96 6.369615 GTGCAAATTTTCAGGCTGAAATACAT 59.630 34.615 35.58 25.56 44.75 2.29
96 97 6.935771 TGCAAATTTTCAGGCTGAAATACATT 59.064 30.769 35.58 28.76 44.75 2.71
97 98 8.093307 TGCAAATTTTCAGGCTGAAATACATTA 58.907 29.630 35.58 23.35 44.75 1.90
98 99 8.934825 GCAAATTTTCAGGCTGAAATACATTAA 58.065 29.630 35.58 22.72 44.75 1.40
103 104 9.995003 TTTTCAGGCTGAAATACATTAAAATGT 57.005 25.926 35.58 12.61 44.75 2.71
104 105 8.984891 TTCAGGCTGAAATACATTAAAATGTG 57.015 30.769 26.78 2.27 40.45 3.21
105 106 8.801299 TTCAGGCTGAAATACATTAAAATGTGA 58.199 29.630 26.78 0.00 40.45 3.58
137 138 5.876651 AAAAGACAAATCTGGAGCCTTTT 57.123 34.783 0.00 0.00 34.48 2.27
138 139 6.976934 AAAAGACAAATCTGGAGCCTTTTA 57.023 33.333 0.00 0.00 34.48 1.52
139 140 6.581171 AAAGACAAATCTGGAGCCTTTTAG 57.419 37.500 0.00 0.00 34.48 1.85
140 141 4.013050 AGACAAATCTGGAGCCTTTTAGC 58.987 43.478 0.00 0.00 32.29 3.09
141 142 3.758554 GACAAATCTGGAGCCTTTTAGCA 59.241 43.478 0.00 0.00 34.23 3.49
143 144 5.509498 ACAAATCTGGAGCCTTTTAGCATA 58.491 37.500 0.00 0.00 34.23 3.14
145 146 6.040166 ACAAATCTGGAGCCTTTTAGCATATG 59.960 38.462 0.00 0.00 34.23 1.78
146 147 4.778213 TCTGGAGCCTTTTAGCATATGT 57.222 40.909 4.29 0.00 34.23 2.29
147 148 5.887214 TCTGGAGCCTTTTAGCATATGTA 57.113 39.130 4.29 0.00 34.23 2.29
148 149 5.611374 TCTGGAGCCTTTTAGCATATGTAC 58.389 41.667 4.29 0.00 34.23 2.90
149 150 5.366768 TCTGGAGCCTTTTAGCATATGTACT 59.633 40.000 4.29 0.00 34.23 2.73
150 151 5.368145 TGGAGCCTTTTAGCATATGTACTG 58.632 41.667 4.29 0.00 34.23 2.74
152 153 5.823045 GGAGCCTTTTAGCATATGTACTGTT 59.177 40.000 4.29 0.00 34.23 3.16
154 155 6.414732 AGCCTTTTAGCATATGTACTGTTCA 58.585 36.000 4.29 0.00 34.23 3.18
155 156 7.056635 AGCCTTTTAGCATATGTACTGTTCAT 58.943 34.615 4.29 5.26 34.23 2.57
157 158 7.227512 GCCTTTTAGCATATGTACTGTTCATCT 59.772 37.037 4.29 0.00 0.00 2.90
158 159 9.764363 CCTTTTAGCATATGTACTGTTCATCTA 57.236 33.333 4.29 0.00 0.00 1.98
169 170 9.770097 ATGTACTGTTCATCTATAAAGTCCATG 57.230 33.333 0.00 0.00 0.00 3.66
170 171 8.977412 TGTACTGTTCATCTATAAAGTCCATGA 58.023 33.333 0.00 0.00 0.00 3.07
171 172 9.988815 GTACTGTTCATCTATAAAGTCCATGAT 57.011 33.333 0.00 0.00 0.00 2.45
173 174 9.911788 ACTGTTCATCTATAAAGTCCATGATTT 57.088 29.630 0.00 0.00 0.00 2.17
214 215 6.855763 TTGCAATTCAAGGTATTTCATCCT 57.144 33.333 0.00 0.00 35.34 3.24
216 217 5.951148 TGCAATTCAAGGTATTTCATCCTGA 59.049 36.000 0.00 0.00 33.97 3.86
229 230 6.477053 TTTCATCCTGAAATTTTCCACACA 57.523 33.333 6.68 0.00 41.02 3.72
230 231 6.669125 TTCATCCTGAAATTTTCCACACAT 57.331 33.333 6.68 0.00 32.71 3.21
231 232 7.773489 TTCATCCTGAAATTTTCCACACATA 57.227 32.000 6.68 0.00 32.71 2.29
232 233 7.156876 TCATCCTGAAATTTTCCACACATAC 57.843 36.000 6.68 0.00 0.00 2.39
233 234 6.718912 TCATCCTGAAATTTTCCACACATACA 59.281 34.615 6.68 0.00 0.00 2.29
234 235 6.325919 TCCTGAAATTTTCCACACATACAC 57.674 37.500 6.68 0.00 0.00 2.90
235 236 6.068010 TCCTGAAATTTTCCACACATACACT 58.932 36.000 6.68 0.00 0.00 3.55
236 237 6.549364 TCCTGAAATTTTCCACACATACACTT 59.451 34.615 6.68 0.00 0.00 3.16
237 238 7.069331 TCCTGAAATTTTCCACACATACACTTT 59.931 33.333 6.68 0.00 0.00 2.66
238 239 8.356657 CCTGAAATTTTCCACACATACACTTTA 58.643 33.333 6.68 0.00 0.00 1.85
240 241 8.687242 TGAAATTTTCCACACATACACTTTACA 58.313 29.630 6.68 0.00 0.00 2.41
242 243 9.691362 AAATTTTCCACACATACACTTTACATC 57.309 29.630 0.00 0.00 0.00 3.06
244 245 5.755409 TCCACACATACACTTTACATCCT 57.245 39.130 0.00 0.00 0.00 3.24
245 246 6.121776 TCCACACATACACTTTACATCCTT 57.878 37.500 0.00 0.00 0.00 3.36
246 247 5.937540 TCCACACATACACTTTACATCCTTG 59.062 40.000 0.00 0.00 0.00 3.61
247 248 5.391950 CCACACATACACTTTACATCCTTGC 60.392 44.000 0.00 0.00 0.00 4.01
250 251 7.065683 CACACATACACTTTACATCCTTGCATA 59.934 37.037 0.00 0.00 0.00 3.14
251 252 7.065803 ACACATACACTTTACATCCTTGCATAC 59.934 37.037 0.00 0.00 0.00 2.39
252 253 7.065683 CACATACACTTTACATCCTTGCATACA 59.934 37.037 0.00 0.00 0.00 2.29
253 254 7.775093 ACATACACTTTACATCCTTGCATACAT 59.225 33.333 0.00 0.00 0.00 2.29
254 255 6.441093 ACACTTTACATCCTTGCATACATG 57.559 37.500 0.00 0.00 0.00 3.21
255 256 5.945784 ACACTTTACATCCTTGCATACATGT 59.054 36.000 2.69 2.69 33.95 3.21
256 257 6.127925 ACACTTTACATCCTTGCATACATGTG 60.128 38.462 9.11 0.00 31.83 3.21
257 258 5.945784 ACTTTACATCCTTGCATACATGTGT 59.054 36.000 9.11 0.00 31.83 3.72
258 259 7.065683 CACTTTACATCCTTGCATACATGTGTA 59.934 37.037 9.11 0.00 31.83 2.90
259 260 7.775093 ACTTTACATCCTTGCATACATGTGTAT 59.225 33.333 9.11 0.00 41.58 2.29
260 261 8.518430 TTTACATCCTTGCATACATGTGTATT 57.482 30.769 9.11 0.00 39.06 1.89
261 262 8.518430 TTACATCCTTGCATACATGTGTATTT 57.482 30.769 9.11 0.00 39.06 1.40
262 263 7.408756 ACATCCTTGCATACATGTGTATTTT 57.591 32.000 9.11 0.00 39.06 1.82
263 264 7.839907 ACATCCTTGCATACATGTGTATTTTT 58.160 30.769 9.11 0.00 39.06 1.94
328 329 9.874205 TTATTCAAAATAAAGGGCTTCATGAAG 57.126 29.630 27.82 27.82 41.24 3.02
339 340 3.606595 CTTCATGAAGCTCAGTCTCCA 57.393 47.619 21.96 0.00 0.00 3.86
340 341 3.935315 CTTCATGAAGCTCAGTCTCCAA 58.065 45.455 21.96 0.00 0.00 3.53
342 343 4.356405 TCATGAAGCTCAGTCTCCAAAA 57.644 40.909 0.00 0.00 0.00 2.44
343 344 4.914983 TCATGAAGCTCAGTCTCCAAAAT 58.085 39.130 0.00 0.00 0.00 1.82
344 345 4.698780 TCATGAAGCTCAGTCTCCAAAATG 59.301 41.667 0.00 0.00 0.00 2.32
345 346 2.816087 TGAAGCTCAGTCTCCAAAATGC 59.184 45.455 0.00 0.00 0.00 3.56
346 347 1.831580 AGCTCAGTCTCCAAAATGCC 58.168 50.000 0.00 0.00 0.00 4.40
348 349 1.615384 GCTCAGTCTCCAAAATGCCCT 60.615 52.381 0.00 0.00 0.00 5.19
350 351 3.873801 GCTCAGTCTCCAAAATGCCCTAA 60.874 47.826 0.00 0.00 0.00 2.69
351 352 4.530875 CTCAGTCTCCAAAATGCCCTAAT 58.469 43.478 0.00 0.00 0.00 1.73
354 355 4.891756 CAGTCTCCAAAATGCCCTAATCAT 59.108 41.667 0.00 0.00 0.00 2.45
355 356 6.064060 CAGTCTCCAAAATGCCCTAATCATA 58.936 40.000 0.00 0.00 0.00 2.15
356 357 6.016777 CAGTCTCCAAAATGCCCTAATCATAC 60.017 42.308 0.00 0.00 0.00 2.39
357 358 5.827797 GTCTCCAAAATGCCCTAATCATACA 59.172 40.000 0.00 0.00 0.00 2.29
358 359 6.491403 GTCTCCAAAATGCCCTAATCATACAT 59.509 38.462 0.00 0.00 0.00 2.29
359 360 7.665559 GTCTCCAAAATGCCCTAATCATACATA 59.334 37.037 0.00 0.00 0.00 2.29
360 361 7.665559 TCTCCAAAATGCCCTAATCATACATAC 59.334 37.037 0.00 0.00 0.00 2.39
361 362 6.429692 TCCAAAATGCCCTAATCATACATACG 59.570 38.462 0.00 0.00 0.00 3.06
362 363 6.429692 CCAAAATGCCCTAATCATACATACGA 59.570 38.462 0.00 0.00 0.00 3.43
418 419 6.040247 CACTCATTTTGCTCCGTATGTAGTA 58.960 40.000 0.00 0.00 0.00 1.82
569 571 5.047566 TGTCAAGTTTCTTCCATTCCTGA 57.952 39.130 0.00 0.00 0.00 3.86
636 638 2.225467 AGAGTTGGCTTCTTTCAGTGC 58.775 47.619 0.00 0.00 0.00 4.40
673 675 5.727592 CGTGAACAATGTTCAAACAAAAAGC 59.272 36.000 27.77 12.65 43.03 3.51
675 677 4.856115 ACAATGTTCAAACAAAAAGCCG 57.144 36.364 0.00 0.00 43.03 5.52
677 679 1.272781 TGTTCAAACAAAAAGCCGCG 58.727 45.000 0.00 0.00 35.67 6.46
678 680 1.135373 TGTTCAAACAAAAAGCCGCGA 60.135 42.857 8.23 0.00 35.67 5.87
714 728 1.468914 GAAGCCCACGAGACATTTTCC 59.531 52.381 0.00 0.00 0.00 3.13
974 988 4.115199 AGTGCCATTCCCGCTCCC 62.115 66.667 0.00 0.00 0.00 4.30
1050 1064 2.045926 GCATGTCGCCTCCAACCT 60.046 61.111 0.00 0.00 32.94 3.50
1182 1200 0.178958 ATCGAGCTTAGGATCCGGGT 60.179 55.000 5.98 6.47 0.00 5.28
1425 2582 7.065216 TGAATTTCATTTCGTCTCTGACATC 57.935 36.000 0.00 0.00 32.09 3.06
1438 2595 3.678289 TCTGACATCATTCCTGTGTTGG 58.322 45.455 0.00 0.00 0.00 3.77
1442 2599 1.135603 CATCATTCCTGTGTTGGCGTG 60.136 52.381 0.00 0.00 0.00 5.34
1445 2602 0.667993 ATTCCTGTGTTGGCGTGTTG 59.332 50.000 0.00 0.00 0.00 3.33
1446 2603 1.999071 TTCCTGTGTTGGCGTGTTGC 61.999 55.000 0.00 0.00 45.38 4.17
1704 2861 2.191375 CAGATGGCGCTCATGGGT 59.809 61.111 14.84 0.00 35.97 4.51
1974 3133 1.296715 CCCCCTCGACAACCTCTTG 59.703 63.158 0.00 0.00 0.00 3.02
2043 3202 7.707464 CGTACATACAGATACATGGTTGGTTAA 59.293 37.037 0.00 0.00 0.00 2.01
2201 5452 1.153066 TGAGCACTTTGGCGTTGGA 60.153 52.632 0.00 0.00 39.27 3.53
2213 5465 1.471676 GGCGTTGGAGTGTCATCTAGG 60.472 57.143 0.00 0.00 0.00 3.02
2214 5466 1.927895 CGTTGGAGTGTCATCTAGGC 58.072 55.000 0.00 0.00 0.00 3.93
2215 5467 1.204704 CGTTGGAGTGTCATCTAGGCA 59.795 52.381 0.00 0.00 0.00 4.75
2216 5468 2.159043 CGTTGGAGTGTCATCTAGGCAT 60.159 50.000 0.00 0.00 32.25 4.40
2217 5469 3.462021 GTTGGAGTGTCATCTAGGCATC 58.538 50.000 0.00 0.00 32.25 3.91
2218 5470 3.037851 TGGAGTGTCATCTAGGCATCT 57.962 47.619 0.00 0.00 32.25 2.90
2219 5471 4.184649 TGGAGTGTCATCTAGGCATCTA 57.815 45.455 0.00 0.00 32.25 1.98
2220 5472 4.745351 TGGAGTGTCATCTAGGCATCTAT 58.255 43.478 0.00 0.00 32.25 1.98
2253 5505 5.835113 AATGTGAATATTACAGTGCACCC 57.165 39.130 14.63 0.00 0.00 4.61
2270 5522 3.978876 CCGAAGAGGGAAATGGGTT 57.021 52.632 0.00 0.00 35.97 4.11
2274 5526 1.357761 GAAGAGGGAAATGGGTTGGGA 59.642 52.381 0.00 0.00 0.00 4.37
2303 5557 6.134055 TGCTTACCAGTACACCTCTGTATAT 58.866 40.000 0.00 0.00 35.28 0.86
2389 5643 5.063944 CAGAATCGCACAGCTGTTATACTTT 59.936 40.000 18.94 6.43 0.00 2.66
2423 5677 7.081976 CGTAATTTTCTTCTTGGTTAACCCTG 58.918 38.462 21.97 13.97 34.29 4.45
2473 5727 7.251321 AGAAAATTGAGAGTGTCAGATAGGT 57.749 36.000 0.00 0.00 36.21 3.08
2477 5731 2.497675 TGAGAGTGTCAGATAGGTTGCC 59.502 50.000 0.00 0.00 0.00 4.52
2478 5732 1.834263 AGAGTGTCAGATAGGTTGCCC 59.166 52.381 0.00 0.00 0.00 5.36
2525 5779 6.693545 CGTATGCAGTGTAAAACAAAAGGAAA 59.306 34.615 0.00 0.00 0.00 3.13
2531 5785 7.186128 CAGTGTAAAACAAAAGGAAAAATGGC 58.814 34.615 0.00 0.00 0.00 4.40
2572 5826 1.698165 CGCCGCTCGTGTATGATATT 58.302 50.000 0.00 0.00 0.00 1.28
2573 5827 1.649171 CGCCGCTCGTGTATGATATTC 59.351 52.381 0.00 0.00 0.00 1.75
2574 5828 2.672714 GCCGCTCGTGTATGATATTCA 58.327 47.619 0.00 0.00 0.00 2.57
2575 5829 2.408704 GCCGCTCGTGTATGATATTCAC 59.591 50.000 0.00 0.00 0.00 3.18
2576 5830 3.857383 GCCGCTCGTGTATGATATTCACT 60.857 47.826 0.00 0.00 0.00 3.41
2577 5831 4.615223 GCCGCTCGTGTATGATATTCACTA 60.615 45.833 0.00 0.00 0.00 2.74
2578 5832 5.641709 CCGCTCGTGTATGATATTCACTAT 58.358 41.667 0.00 0.00 0.00 2.12
2579 5833 5.739630 CCGCTCGTGTATGATATTCACTATC 59.260 44.000 0.00 0.00 37.36 2.08
2580 5834 6.403746 CCGCTCGTGTATGATATTCACTATCT 60.404 42.308 0.00 0.00 37.67 1.98
2586 5840 7.971168 CGTGTATGATATTCACTATCTCCCTTC 59.029 40.741 0.00 0.00 37.67 3.46
2636 5890 1.681538 ACCGAGCTATCATGTCGTCT 58.318 50.000 0.00 0.00 31.65 4.18
2646 5900 3.766676 TCATGTCGTCTCTTGAGCTAC 57.233 47.619 0.00 0.00 0.00 3.58
2653 5907 2.792890 CGTCTCTTGAGCTACACGATGG 60.793 54.545 0.00 0.00 0.00 3.51
2685 5939 1.446907 CGCAGGTCTTTCAGCTCAAT 58.553 50.000 0.00 0.00 0.00 2.57
2694 5948 5.330295 GTCTTTCAGCTCAATTATGTGCAG 58.670 41.667 5.77 0.00 46.03 4.41
2709 5963 2.938451 TGTGCAGATAAAATGCGAGAGG 59.062 45.455 0.00 0.00 46.87 3.69
2715 5969 5.466728 GCAGATAAAATGCGAGAGGATACAA 59.533 40.000 0.00 0.00 43.29 2.41
2720 5974 0.824109 TGCGAGAGGATACAACTGGG 59.176 55.000 0.00 0.00 41.41 4.45
2724 5978 1.414550 GAGAGGATACAACTGGGGCTC 59.585 57.143 0.00 0.00 41.41 4.70
2741 5995 4.123506 GGGCTCTTAAGAAGCATAGTGTC 58.876 47.826 20.95 5.13 0.00 3.67
2800 6054 3.903090 TCCTGGAGATTTGCAATTTTGGT 59.097 39.130 0.00 0.00 0.00 3.67
2816 6070 7.442666 GCAATTTTGGTGGTACAAGGAATTAAA 59.557 33.333 0.00 0.00 44.16 1.52
2849 6103 6.597832 AACAGTGTTAGAACATCTCTAGCT 57.402 37.500 6.75 0.00 41.59 3.32
2851 6105 5.105554 ACAGTGTTAGAACATCTCTAGCTGG 60.106 44.000 0.00 0.00 41.59 4.85
2852 6106 4.116238 GTGTTAGAACATCTCTAGCTGGC 58.884 47.826 0.00 0.00 41.59 4.85
2853 6107 3.769300 TGTTAGAACATCTCTAGCTGGCA 59.231 43.478 0.00 0.00 38.38 4.92
2854 6108 4.222810 TGTTAGAACATCTCTAGCTGGCAA 59.777 41.667 0.00 0.00 38.38 4.52
2855 6109 5.104776 TGTTAGAACATCTCTAGCTGGCAAT 60.105 40.000 0.00 0.00 38.38 3.56
2858 6112 4.639310 AGAACATCTCTAGCTGGCAATTTG 59.361 41.667 0.00 0.00 30.22 2.32
2859 6113 3.960571 ACATCTCTAGCTGGCAATTTGT 58.039 40.909 0.00 0.00 0.00 2.83
2860 6114 4.338879 ACATCTCTAGCTGGCAATTTGTT 58.661 39.130 0.00 0.00 0.00 2.83
2861 6115 4.768968 ACATCTCTAGCTGGCAATTTGTTT 59.231 37.500 0.00 0.00 0.00 2.83
2862 6116 5.244626 ACATCTCTAGCTGGCAATTTGTTTT 59.755 36.000 0.00 0.00 0.00 2.43
2863 6117 6.434028 ACATCTCTAGCTGGCAATTTGTTTTA 59.566 34.615 0.00 0.00 0.00 1.52
2864 6118 6.500684 TCTCTAGCTGGCAATTTGTTTTAG 57.499 37.500 0.00 0.00 0.00 1.85
2865 6119 5.059404 TCTAGCTGGCAATTTGTTTTAGC 57.941 39.130 0.00 3.80 0.00 3.09
2866 6120 2.676076 AGCTGGCAATTTGTTTTAGCG 58.324 42.857 0.00 0.00 35.04 4.26
2867 6121 2.035832 AGCTGGCAATTTGTTTTAGCGT 59.964 40.909 0.00 0.00 35.04 5.07
2868 6122 2.408368 GCTGGCAATTTGTTTTAGCGTC 59.592 45.455 0.00 0.00 0.00 5.19
2870 6124 2.362397 TGGCAATTTGTTTTAGCGTCCA 59.638 40.909 0.00 0.00 0.00 4.02
2871 6125 3.181475 TGGCAATTTGTTTTAGCGTCCAA 60.181 39.130 0.00 0.00 0.00 3.53
2873 6127 4.271291 GGCAATTTGTTTTAGCGTCCAAAA 59.729 37.500 0.00 0.00 31.30 2.44
2874 6128 5.194657 GCAATTTGTTTTAGCGTCCAAAAC 58.805 37.500 11.84 11.84 43.18 2.43
2882 6136 6.863230 GTTTTAGCGTCCAAAACAAATTCTC 58.137 36.000 13.12 0.00 42.67 2.87
2884 6138 4.228912 AGCGTCCAAAACAAATTCTCAG 57.771 40.909 0.00 0.00 0.00 3.35
2885 6139 2.726241 GCGTCCAAAACAAATTCTCAGC 59.274 45.455 0.00 0.00 0.00 4.26
2886 6140 3.308530 CGTCCAAAACAAATTCTCAGCC 58.691 45.455 0.00 0.00 0.00 4.85
2888 6142 4.692228 GTCCAAAACAAATTCTCAGCCAA 58.308 39.130 0.00 0.00 0.00 4.52
2889 6143 4.507756 GTCCAAAACAAATTCTCAGCCAAC 59.492 41.667 0.00 0.00 0.00 3.77
2891 6145 4.874966 CCAAAACAAATTCTCAGCCAACAA 59.125 37.500 0.00 0.00 0.00 2.83
2892 6146 5.353678 CCAAAACAAATTCTCAGCCAACAAA 59.646 36.000 0.00 0.00 0.00 2.83
2893 6147 6.128063 CCAAAACAAATTCTCAGCCAACAAAA 60.128 34.615 0.00 0.00 0.00 2.44
2894 6148 6.667007 AAACAAATTCTCAGCCAACAAAAG 57.333 33.333 0.00 0.00 0.00 2.27
2895 6149 4.696455 ACAAATTCTCAGCCAACAAAAGG 58.304 39.130 0.00 0.00 0.00 3.11
2911 6165 3.521796 GGCTTCCCTTCATGCCGC 61.522 66.667 0.00 0.00 35.79 6.53
2912 6166 2.439156 GCTTCCCTTCATGCCGCT 60.439 61.111 0.00 0.00 0.00 5.52
2913 6167 2.048603 GCTTCCCTTCATGCCGCTT 61.049 57.895 0.00 0.00 0.00 4.68
2914 6168 1.997928 GCTTCCCTTCATGCCGCTTC 61.998 60.000 0.00 0.00 0.00 3.86
2915 6169 1.378514 TTCCCTTCATGCCGCTTCC 60.379 57.895 0.00 0.00 0.00 3.46
2916 6170 2.830370 CCCTTCATGCCGCTTCCC 60.830 66.667 0.00 0.00 0.00 3.97
2917 6171 2.273449 CCTTCATGCCGCTTCCCT 59.727 61.111 0.00 0.00 0.00 4.20
2918 6172 1.379044 CCTTCATGCCGCTTCCCTT 60.379 57.895 0.00 0.00 0.00 3.95
2919 6173 1.379642 CCTTCATGCCGCTTCCCTTC 61.380 60.000 0.00 0.00 0.00 3.46
2920 6174 0.677731 CTTCATGCCGCTTCCCTTCA 60.678 55.000 0.00 0.00 0.00 3.02
2921 6175 0.034186 TTCATGCCGCTTCCCTTCAT 60.034 50.000 0.00 0.00 0.00 2.57
2922 6176 0.749091 TCATGCCGCTTCCCTTCATG 60.749 55.000 0.00 0.00 36.71 3.07
2923 6177 2.123428 ATGCCGCTTCCCTTCATGC 61.123 57.895 0.00 0.00 0.00 4.06
2924 6178 3.521796 GCCGCTTCCCTTCATGCC 61.522 66.667 0.00 0.00 0.00 4.40
2925 6179 2.045045 CCGCTTCCCTTCATGCCA 60.045 61.111 0.00 0.00 0.00 4.92
2926 6180 1.678635 CCGCTTCCCTTCATGCCAA 60.679 57.895 0.00 0.00 0.00 4.52
2927 6181 1.508088 CGCTTCCCTTCATGCCAAC 59.492 57.895 0.00 0.00 0.00 3.77
2928 6182 1.243342 CGCTTCCCTTCATGCCAACA 61.243 55.000 0.00 0.00 0.00 3.33
2929 6183 0.968405 GCTTCCCTTCATGCCAACAA 59.032 50.000 0.00 0.00 0.00 2.83
2930 6184 1.344114 GCTTCCCTTCATGCCAACAAA 59.656 47.619 0.00 0.00 0.00 2.83
2931 6185 2.224257 GCTTCCCTTCATGCCAACAAAA 60.224 45.455 0.00 0.00 0.00 2.44
2932 6186 3.656559 CTTCCCTTCATGCCAACAAAAG 58.343 45.455 0.00 0.00 0.00 2.27
2933 6187 1.969923 TCCCTTCATGCCAACAAAAGG 59.030 47.619 1.07 1.07 40.21 3.11
2934 6188 1.693606 CCCTTCATGCCAACAAAAGGT 59.306 47.619 6.40 0.00 39.47 3.50
2935 6189 2.289010 CCCTTCATGCCAACAAAAGGTC 60.289 50.000 6.40 0.00 39.47 3.85
2936 6190 2.289010 CCTTCATGCCAACAAAAGGTCC 60.289 50.000 0.00 0.00 37.72 4.46
2937 6191 2.079170 TCATGCCAACAAAAGGTCCA 57.921 45.000 0.00 0.00 0.00 4.02
2938 6192 2.392662 TCATGCCAACAAAAGGTCCAA 58.607 42.857 0.00 0.00 0.00 3.53
2939 6193 2.102252 TCATGCCAACAAAAGGTCCAAC 59.898 45.455 0.00 0.00 0.00 3.77
2940 6194 1.561643 TGCCAACAAAAGGTCCAACA 58.438 45.000 0.00 0.00 0.00 3.33
2946 6788 5.241662 CCAACAAAAGGTCCAACAAAAAGA 58.758 37.500 0.00 0.00 0.00 2.52
2949 6791 5.242434 ACAAAAGGTCCAACAAAAAGAACC 58.758 37.500 0.00 0.00 0.00 3.62
2962 6804 1.609208 AAGAACCAAGCGAGTGCAAT 58.391 45.000 0.00 0.00 46.23 3.56
2969 6811 2.179589 CAAGCGAGTGCAATATTGTGC 58.820 47.619 16.61 12.33 46.23 4.57
3051 6893 3.964031 AGGTTGCAACTTTTGGTATTGGA 59.036 39.130 27.64 0.00 0.00 3.53
3109 6952 3.435105 TTTGATGTTGGTGCACTTGTC 57.565 42.857 17.98 8.76 0.00 3.18
3111 6954 0.944386 GATGTTGGTGCACTTGTCGT 59.056 50.000 17.98 6.55 0.00 4.34
3119 6962 3.244078 TGGTGCACTTGTCGTTAGAGATT 60.244 43.478 17.98 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.872993 GCACACATGTACATTATGTATCTAGGT 59.127 37.037 17.98 4.03 36.67 3.08
48 49 7.872483 TGCACACATGTACATTATGTATCTAGG 59.128 37.037 17.98 9.14 36.67 3.02
49 50 8.816640 TGCACACATGTACATTATGTATCTAG 57.183 34.615 17.98 9.67 36.67 2.43
50 51 9.606631 TTTGCACACATGTACATTATGTATCTA 57.393 29.630 17.98 9.97 36.67 1.98
51 52 8.504812 TTTGCACACATGTACATTATGTATCT 57.495 30.769 17.98 0.00 36.67 1.98
52 53 9.734620 AATTTGCACACATGTACATTATGTATC 57.265 29.630 17.98 14.10 36.67 2.24
54 55 9.920133 AAAATTTGCACACATGTACATTATGTA 57.080 25.926 17.98 0.29 36.67 2.29
55 56 8.830201 AAAATTTGCACACATGTACATTATGT 57.170 26.923 14.24 14.24 39.23 2.29
56 57 8.923683 TGAAAATTTGCACACATGTACATTATG 58.076 29.630 5.37 10.25 0.00 1.90
57 58 9.142515 CTGAAAATTTGCACACATGTACATTAT 57.857 29.630 5.37 0.00 0.00 1.28
58 59 7.598118 CCTGAAAATTTGCACACATGTACATTA 59.402 33.333 5.37 0.00 0.00 1.90
59 60 6.424509 CCTGAAAATTTGCACACATGTACATT 59.575 34.615 5.37 0.00 0.00 2.71
60 61 5.927689 CCTGAAAATTTGCACACATGTACAT 59.072 36.000 1.41 1.41 0.00 2.29
61 62 5.288015 CCTGAAAATTTGCACACATGTACA 58.712 37.500 0.00 0.00 0.00 2.90
63 64 4.039004 AGCCTGAAAATTTGCACACATGTA 59.961 37.500 0.00 0.00 0.00 2.29
64 65 3.132925 GCCTGAAAATTTGCACACATGT 58.867 40.909 0.00 0.00 0.00 3.21
65 66 3.185594 CAGCCTGAAAATTTGCACACATG 59.814 43.478 0.00 0.00 0.00 3.21
66 67 3.069872 TCAGCCTGAAAATTTGCACACAT 59.930 39.130 0.00 0.00 0.00 3.21
67 68 2.429971 TCAGCCTGAAAATTTGCACACA 59.570 40.909 0.00 0.00 0.00 3.72
114 115 5.876651 AAAGGCTCCAGATTTGTCTTTTT 57.123 34.783 0.00 0.00 0.00 1.94
115 116 5.876651 AAAAGGCTCCAGATTTGTCTTTT 57.123 34.783 0.00 0.00 0.00 2.27
116 117 5.047731 GCTAAAAGGCTCCAGATTTGTCTTT 60.048 40.000 0.00 0.00 0.00 2.52
118 119 4.013050 GCTAAAAGGCTCCAGATTTGTCT 58.987 43.478 0.00 0.00 0.00 3.41
120 121 3.766545 TGCTAAAAGGCTCCAGATTTGT 58.233 40.909 0.00 0.00 0.00 2.83
121 122 4.996788 ATGCTAAAAGGCTCCAGATTTG 57.003 40.909 0.00 0.00 0.00 2.32
122 123 6.131961 ACATATGCTAAAAGGCTCCAGATTT 58.868 36.000 1.58 0.00 0.00 2.17
123 124 5.699143 ACATATGCTAAAAGGCTCCAGATT 58.301 37.500 1.58 0.00 0.00 2.40
124 125 5.316158 ACATATGCTAAAAGGCTCCAGAT 57.684 39.130 1.58 0.00 0.00 2.90
125 126 4.778213 ACATATGCTAAAAGGCTCCAGA 57.222 40.909 1.58 0.00 0.00 3.86
126 127 5.468072 CAGTACATATGCTAAAAGGCTCCAG 59.532 44.000 1.58 0.00 0.00 3.86
130 131 6.414732 TGAACAGTACATATGCTAAAAGGCT 58.585 36.000 1.58 0.00 0.00 4.58
131 132 6.677781 TGAACAGTACATATGCTAAAAGGC 57.322 37.500 1.58 0.00 0.00 4.35
132 133 8.668510 AGATGAACAGTACATATGCTAAAAGG 57.331 34.615 1.58 0.00 0.00 3.11
143 144 9.770097 CATGGACTTTATAGATGAACAGTACAT 57.230 33.333 0.00 0.00 36.43 2.29
145 146 9.988815 ATCATGGACTTTATAGATGAACAGTAC 57.011 33.333 0.00 0.00 0.00 2.73
147 148 9.911788 AAATCATGGACTTTATAGATGAACAGT 57.088 29.630 0.00 0.00 0.00 3.55
150 151 9.956720 CCAAAATCATGGACTTTATAGATGAAC 57.043 33.333 0.00 0.00 43.54 3.18
152 153 9.699410 AACCAAAATCATGGACTTTATAGATGA 57.301 29.630 0.00 0.00 43.54 2.92
179 180 6.586868 CTTGAATTGCAAGCTGTACAAAAA 57.413 33.333 4.94 0.00 46.67 1.94
189 190 8.579705 CAGGATGAAATACCTTGAATTGCAAGC 61.580 40.741 4.94 0.00 45.98 4.01
191 192 6.436847 TCAGGATGAAATACCTTGAATTGCAA 59.563 34.615 0.00 0.00 45.97 4.08
192 193 5.951148 TCAGGATGAAATACCTTGAATTGCA 59.049 36.000 0.00 0.00 45.97 4.08
193 194 6.455360 TCAGGATGAAATACCTTGAATTGC 57.545 37.500 0.00 0.00 45.97 3.56
210 211 6.721208 AGTGTATGTGTGGAAAATTTCAGGAT 59.279 34.615 8.09 0.00 0.00 3.24
213 214 9.180678 GTAAAGTGTATGTGTGGAAAATTTCAG 57.819 33.333 8.09 0.00 0.00 3.02
214 215 8.687242 TGTAAAGTGTATGTGTGGAAAATTTCA 58.313 29.630 8.09 0.00 0.00 2.69
216 217 9.691362 GATGTAAAGTGTATGTGTGGAAAATTT 57.309 29.630 0.00 0.00 0.00 1.82
218 219 7.669722 AGGATGTAAAGTGTATGTGTGGAAAAT 59.330 33.333 0.00 0.00 0.00 1.82
220 221 6.539173 AGGATGTAAAGTGTATGTGTGGAAA 58.461 36.000 0.00 0.00 0.00 3.13
222 223 5.755409 AGGATGTAAAGTGTATGTGTGGA 57.245 39.130 0.00 0.00 0.00 4.02
223 224 5.391950 GCAAGGATGTAAAGTGTATGTGTGG 60.392 44.000 0.00 0.00 0.00 4.17
225 226 5.312895 TGCAAGGATGTAAAGTGTATGTGT 58.687 37.500 0.00 0.00 0.00 3.72
227 228 7.109501 TGTATGCAAGGATGTAAAGTGTATGT 58.890 34.615 0.00 0.00 0.00 2.29
229 230 7.775093 ACATGTATGCAAGGATGTAAAGTGTAT 59.225 33.333 0.00 0.00 0.00 2.29
230 231 7.065683 CACATGTATGCAAGGATGTAAAGTGTA 59.934 37.037 0.00 0.00 0.00 2.90
231 232 5.945784 ACATGTATGCAAGGATGTAAAGTGT 59.054 36.000 0.00 0.00 0.00 3.55
232 233 6.127925 ACACATGTATGCAAGGATGTAAAGTG 60.128 38.462 0.00 0.00 0.00 3.16
233 234 5.945784 ACACATGTATGCAAGGATGTAAAGT 59.054 36.000 0.00 1.15 0.00 2.66
234 235 6.441093 ACACATGTATGCAAGGATGTAAAG 57.559 37.500 0.00 0.66 0.00 1.85
235 236 8.518430 AATACACATGTATGCAAGGATGTAAA 57.482 30.769 0.00 1.34 40.78 2.01
236 237 8.518430 AAATACACATGTATGCAAGGATGTAA 57.482 30.769 0.00 1.61 40.78 2.41
237 238 8.518430 AAAATACACATGTATGCAAGGATGTA 57.482 30.769 0.00 4.93 40.78 2.29
238 239 7.408756 AAAATACACATGTATGCAAGGATGT 57.591 32.000 0.00 0.00 40.78 3.06
302 303 9.874205 CTTCATGAAGCCCTTTATTTTGAATAA 57.126 29.630 21.96 0.00 0.00 1.40
319 320 3.606595 TGGAGACTGAGCTTCATGAAG 57.393 47.619 27.82 27.82 41.24 3.02
320 321 4.356405 TTTGGAGACTGAGCTTCATGAA 57.644 40.909 8.12 8.12 0.00 2.57
321 322 4.356405 TTTTGGAGACTGAGCTTCATGA 57.644 40.909 0.00 0.00 0.00 3.07
322 323 4.674623 GCATTTTGGAGACTGAGCTTCATG 60.675 45.833 0.00 0.00 0.00 3.07
325 326 2.163211 GGCATTTTGGAGACTGAGCTTC 59.837 50.000 0.00 0.00 0.00 3.86
327 328 1.615384 GGGCATTTTGGAGACTGAGCT 60.615 52.381 0.00 0.00 0.00 4.09
328 329 0.813821 GGGCATTTTGGAGACTGAGC 59.186 55.000 0.00 0.00 0.00 4.26
330 331 4.018506 TGATTAGGGCATTTTGGAGACTGA 60.019 41.667 0.00 0.00 0.00 3.41
331 332 4.272489 TGATTAGGGCATTTTGGAGACTG 58.728 43.478 0.00 0.00 0.00 3.51
333 334 5.827797 TGTATGATTAGGGCATTTTGGAGAC 59.172 40.000 0.00 0.00 0.00 3.36
334 335 6.012337 TGTATGATTAGGGCATTTTGGAGA 57.988 37.500 0.00 0.00 0.00 3.71
335 336 6.906157 ATGTATGATTAGGGCATTTTGGAG 57.094 37.500 0.00 0.00 0.00 3.86
336 337 6.429692 CGTATGTATGATTAGGGCATTTTGGA 59.570 38.462 0.00 0.00 0.00 3.53
338 339 7.433708 TCGTATGTATGATTAGGGCATTTTG 57.566 36.000 0.00 0.00 0.00 2.44
339 340 8.514594 CATTCGTATGTATGATTAGGGCATTTT 58.485 33.333 0.00 0.00 0.00 1.82
340 341 7.665559 ACATTCGTATGTATGATTAGGGCATTT 59.334 33.333 5.81 0.00 43.12 2.32
342 343 6.711277 ACATTCGTATGTATGATTAGGGCAT 58.289 36.000 5.81 0.00 43.12 4.40
343 344 6.109156 ACATTCGTATGTATGATTAGGGCA 57.891 37.500 5.81 0.00 43.12 5.36
344 345 7.094631 TGTACATTCGTATGTATGATTAGGGC 58.905 38.462 16.53 3.24 46.09 5.19
348 349 9.797556 GCCTATGTACATTCGTATGTATGATTA 57.202 33.333 14.77 7.00 46.09 1.75
350 351 7.836842 TGCCTATGTACATTCGTATGTATGAT 58.163 34.615 14.77 13.69 46.09 2.45
351 352 7.222000 TGCCTATGTACATTCGTATGTATGA 57.778 36.000 14.77 8.31 46.09 2.15
355 356 9.502091 AAAATATGCCTATGTACATTCGTATGT 57.498 29.630 14.77 12.50 46.49 2.29
359 360 9.424319 CTCTAAAATATGCCTATGTACATTCGT 57.576 33.333 14.77 7.85 0.00 3.85
360 361 9.424319 ACTCTAAAATATGCCTATGTACATTCG 57.576 33.333 14.77 5.61 0.00 3.34
387 388 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
456 457 5.376756 TGTACCAAATGTAATACTCCCCC 57.623 43.478 0.00 0.00 0.00 5.40
458 459 8.570068 TCTTTTGTACCAAATGTAATACTCCC 57.430 34.615 0.00 0.00 0.00 4.30
594 596 9.936759 ACTCTTATCCTCAAAACAAAAACAAAA 57.063 25.926 0.00 0.00 0.00 2.44
595 597 9.936759 AACTCTTATCCTCAAAACAAAAACAAA 57.063 25.926 0.00 0.00 0.00 2.83
597 599 7.978975 CCAACTCTTATCCTCAAAACAAAAACA 59.021 33.333 0.00 0.00 0.00 2.83
598 600 7.042725 GCCAACTCTTATCCTCAAAACAAAAAC 60.043 37.037 0.00 0.00 0.00 2.43
599 601 6.983890 GCCAACTCTTATCCTCAAAACAAAAA 59.016 34.615 0.00 0.00 0.00 1.94
600 602 6.323739 AGCCAACTCTTATCCTCAAAACAAAA 59.676 34.615 0.00 0.00 0.00 2.44
601 603 5.833131 AGCCAACTCTTATCCTCAAAACAAA 59.167 36.000 0.00 0.00 0.00 2.83
603 605 4.985538 AGCCAACTCTTATCCTCAAAACA 58.014 39.130 0.00 0.00 0.00 2.83
604 606 5.707764 AGAAGCCAACTCTTATCCTCAAAAC 59.292 40.000 0.00 0.00 0.00 2.43
606 608 5.505181 AGAAGCCAACTCTTATCCTCAAA 57.495 39.130 0.00 0.00 0.00 2.69
607 609 5.505181 AAGAAGCCAACTCTTATCCTCAA 57.495 39.130 0.00 0.00 0.00 3.02
608 610 5.013079 TGAAAGAAGCCAACTCTTATCCTCA 59.987 40.000 0.00 0.00 0.00 3.86
609 611 5.491982 TGAAAGAAGCCAACTCTTATCCTC 58.508 41.667 0.00 0.00 0.00 3.71
610 612 5.013599 ACTGAAAGAAGCCAACTCTTATCCT 59.986 40.000 0.00 0.00 37.43 3.24
611 613 5.123027 CACTGAAAGAAGCCAACTCTTATCC 59.877 44.000 0.00 0.00 37.43 2.59
612 614 5.391416 GCACTGAAAGAAGCCAACTCTTATC 60.391 44.000 0.00 0.00 37.43 1.75
614 616 3.815401 GCACTGAAAGAAGCCAACTCTTA 59.185 43.478 0.00 0.00 37.43 2.10
636 638 1.084370 GTTCACGGCCTTCTCGATGG 61.084 60.000 0.00 0.00 0.00 3.51
639 641 0.320374 ATTGTTCACGGCCTTCTCGA 59.680 50.000 0.00 0.00 0.00 4.04
640 642 0.443869 CATTGTTCACGGCCTTCTCG 59.556 55.000 0.00 0.00 0.00 4.04
673 675 0.179111 TCTAAGTTGGATGCTCGCGG 60.179 55.000 6.13 0.00 0.00 6.46
675 677 2.893637 TCTTCTAAGTTGGATGCTCGC 58.106 47.619 0.00 0.00 0.00 5.03
677 679 3.625313 GGCTTCTTCTAAGTTGGATGCTC 59.375 47.826 0.00 0.00 0.00 4.26
678 680 3.615155 GGCTTCTTCTAAGTTGGATGCT 58.385 45.455 0.00 0.00 0.00 3.79
949 963 4.120331 GAATGGCACTGCACCGGC 62.120 66.667 0.00 0.00 41.68 6.13
950 964 3.443045 GGAATGGCACTGCACCGG 61.443 66.667 0.00 0.00 0.00 5.28
951 965 3.443045 GGGAATGGCACTGCACCG 61.443 66.667 2.82 0.00 0.00 4.94
952 966 3.443045 CGGGAATGGCACTGCACC 61.443 66.667 2.82 0.78 0.00 5.01
1050 1064 6.811174 ACCAGAGCATGTTGGTGATTACCTA 61.811 44.000 15.06 0.00 45.66 3.08
1182 1200 2.644418 GCTTCGTGGCATGCAACA 59.356 55.556 24.66 9.32 0.00 3.33
1425 2582 0.667993 AACACGCCAACACAGGAATG 59.332 50.000 0.00 0.00 0.00 2.67
1442 2599 0.247460 GCTGAAGGGGAAATGGCAAC 59.753 55.000 0.00 0.00 0.00 4.17
1445 2602 0.615827 AAGGCTGAAGGGGAAATGGC 60.616 55.000 0.00 0.00 0.00 4.40
1446 2603 1.478631 GAAGGCTGAAGGGGAAATGG 58.521 55.000 0.00 0.00 0.00 3.16
1447 2604 1.478631 GGAAGGCTGAAGGGGAAATG 58.521 55.000 0.00 0.00 0.00 2.32
1448 2605 0.034089 CGGAAGGCTGAAGGGGAAAT 60.034 55.000 0.00 0.00 0.00 2.17
1449 2606 1.378762 CGGAAGGCTGAAGGGGAAA 59.621 57.895 0.00 0.00 0.00 3.13
2043 3202 4.755629 CAGCAGCAGAGCAAATCATACTAT 59.244 41.667 0.00 0.00 36.85 2.12
2123 5374 0.524862 CCACTCTGCCAACAATCAGC 59.475 55.000 0.00 0.00 0.00 4.26
2201 5452 4.093011 GGGATAGATGCCTAGATGACACT 58.907 47.826 0.00 0.00 35.12 3.55
2213 5465 5.360714 TCACATTTTCCAAAGGGATAGATGC 59.639 40.000 0.00 0.00 44.48 3.91
2214 5466 7.408756 TTCACATTTTCCAAAGGGATAGATG 57.591 36.000 0.00 0.00 44.48 2.90
2215 5467 9.887862 ATATTCACATTTTCCAAAGGGATAGAT 57.112 29.630 0.00 0.00 44.48 1.98
2216 5468 9.713684 AATATTCACATTTTCCAAAGGGATAGA 57.286 29.630 0.00 0.00 44.48 1.98
2219 5471 9.265862 TGTAATATTCACATTTTCCAAAGGGAT 57.734 29.630 0.00 0.00 44.48 3.85
2220 5472 8.657387 TGTAATATTCACATTTTCCAAAGGGA 57.343 30.769 0.00 0.00 43.03 4.20
2253 5505 1.463674 CCAACCCATTTCCCTCTTCG 58.536 55.000 0.00 0.00 0.00 3.79
2269 5521 3.806949 ACTGGTAAGCATCTTTCCCAA 57.193 42.857 0.79 0.00 0.00 4.12
2270 5522 3.585289 TGTACTGGTAAGCATCTTTCCCA 59.415 43.478 0.00 0.41 0.00 4.37
2274 5526 4.532521 AGAGGTGTACTGGTAAGCATCTTT 59.467 41.667 0.00 0.00 0.00 2.52
2303 5557 3.186283 TGGCCTAGTGGGAGTATTTCAA 58.814 45.455 3.32 0.00 37.23 2.69
2389 5643 7.018826 CCAAGAAGAAAATTACGCGTATCAAA 58.981 34.615 21.30 7.29 0.00 2.69
2423 5677 6.235231 TCAAGGTCATAGAAATAGGTGTCC 57.765 41.667 0.00 0.00 0.00 4.02
2455 5709 3.055819 GGCAACCTATCTGACACTCTCAA 60.056 47.826 0.00 0.00 0.00 3.02
2473 5727 2.443324 GCCTAGGGTTTGGGGCAA 59.557 61.111 11.72 0.00 43.59 4.52
2477 5731 1.609783 CTCTGGCCTAGGGTTTGGG 59.390 63.158 11.72 0.00 0.00 4.12
2478 5732 1.609783 CCTCTGGCCTAGGGTTTGG 59.390 63.158 11.72 0.00 0.00 3.28
2503 5757 7.913674 TTTTTCCTTTTGTTTTACACTGCAT 57.086 28.000 0.00 0.00 0.00 3.96
2525 5779 1.647545 CTGCATCGACCACGCCATTT 61.648 55.000 0.00 0.00 39.58 2.32
2531 5785 2.108514 ATTGCCTGCATCGACCACG 61.109 57.895 0.00 0.00 41.26 4.94
2572 5826 2.392662 CTGGCTGAAGGGAGATAGTGA 58.607 52.381 0.00 0.00 0.00 3.41
2573 5827 1.202627 GCTGGCTGAAGGGAGATAGTG 60.203 57.143 0.00 0.00 0.00 2.74
2574 5828 1.127343 GCTGGCTGAAGGGAGATAGT 58.873 55.000 0.00 0.00 0.00 2.12
2575 5829 0.396060 GGCTGGCTGAAGGGAGATAG 59.604 60.000 0.00 0.00 0.00 2.08
2576 5830 0.326522 TGGCTGGCTGAAGGGAGATA 60.327 55.000 2.00 0.00 0.00 1.98
2577 5831 0.992431 ATGGCTGGCTGAAGGGAGAT 60.992 55.000 2.00 0.00 0.00 2.75
2578 5832 1.617536 ATGGCTGGCTGAAGGGAGA 60.618 57.895 2.00 0.00 0.00 3.71
2579 5833 1.453379 CATGGCTGGCTGAAGGGAG 60.453 63.158 2.00 0.00 0.00 4.30
2580 5834 1.918467 CTCATGGCTGGCTGAAGGGA 61.918 60.000 2.00 0.00 0.00 4.20
2636 5890 1.476891 GACCCATCGTGTAGCTCAAGA 59.523 52.381 0.00 0.00 38.72 3.02
2646 5900 1.089481 CCGACCATTGACCCATCGTG 61.089 60.000 0.00 0.00 0.00 4.35
2653 5907 3.499737 CTGCGCCGACCATTGACC 61.500 66.667 4.18 0.00 0.00 4.02
2685 5939 5.237127 CCTCTCGCATTTTATCTGCACATAA 59.763 40.000 0.00 0.00 39.64 1.90
2694 5948 6.073548 CCAGTTGTATCCTCTCGCATTTTATC 60.074 42.308 0.00 0.00 0.00 1.75
2709 5963 4.755266 TCTTAAGAGCCCCAGTTGTATC 57.245 45.455 0.00 0.00 0.00 2.24
2715 5969 1.362224 TGCTTCTTAAGAGCCCCAGT 58.638 50.000 18.30 0.00 0.00 4.00
2720 5974 4.123506 GGACACTATGCTTCTTAAGAGCC 58.876 47.826 18.30 9.79 0.00 4.70
2724 5978 5.724328 TGTCAGGACACTATGCTTCTTAAG 58.276 41.667 0.00 0.00 36.21 1.85
2763 6017 2.034878 CCAGGACTACATGAGCAGCTA 58.965 52.381 0.00 0.00 0.00 3.32
2816 6070 7.222000 TGTTCTAACACTGTTTGGTTCTTTT 57.778 32.000 0.00 0.00 33.17 2.27
2849 6103 2.362397 TGGACGCTAAAACAAATTGCCA 59.638 40.909 0.00 0.00 0.00 4.92
2851 6105 5.194657 GTTTTGGACGCTAAAACAAATTGC 58.805 37.500 18.99 0.00 43.79 3.56
2858 6112 6.474102 TGAGAATTTGTTTTGGACGCTAAAAC 59.526 34.615 17.87 17.87 44.31 2.43
2859 6113 6.565234 TGAGAATTTGTTTTGGACGCTAAAA 58.435 32.000 0.00 0.00 0.00 1.52
2860 6114 6.137794 TGAGAATTTGTTTTGGACGCTAAA 57.862 33.333 0.00 0.00 0.00 1.85
2861 6115 5.757886 CTGAGAATTTGTTTTGGACGCTAA 58.242 37.500 0.00 0.00 0.00 3.09
2862 6116 4.320202 GCTGAGAATTTGTTTTGGACGCTA 60.320 41.667 0.00 0.00 0.00 4.26
2863 6117 3.550842 GCTGAGAATTTGTTTTGGACGCT 60.551 43.478 0.00 0.00 0.00 5.07
2864 6118 2.726241 GCTGAGAATTTGTTTTGGACGC 59.274 45.455 0.00 0.00 0.00 5.19
2865 6119 3.243367 TGGCTGAGAATTTGTTTTGGACG 60.243 43.478 0.00 0.00 0.00 4.79
2866 6120 4.320608 TGGCTGAGAATTTGTTTTGGAC 57.679 40.909 0.00 0.00 0.00 4.02
2867 6121 4.161189 TGTTGGCTGAGAATTTGTTTTGGA 59.839 37.500 0.00 0.00 0.00 3.53
2868 6122 4.440880 TGTTGGCTGAGAATTTGTTTTGG 58.559 39.130 0.00 0.00 0.00 3.28
2870 6124 6.093909 CCTTTTGTTGGCTGAGAATTTGTTTT 59.906 34.615 0.00 0.00 0.00 2.43
2871 6125 5.585844 CCTTTTGTTGGCTGAGAATTTGTTT 59.414 36.000 0.00 0.00 0.00 2.83
2873 6127 4.696455 CCTTTTGTTGGCTGAGAATTTGT 58.304 39.130 0.00 0.00 0.00 2.83
2874 6128 3.495753 GCCTTTTGTTGGCTGAGAATTTG 59.504 43.478 0.00 0.00 46.38 2.32
2876 6130 3.391506 GCCTTTTGTTGGCTGAGAATT 57.608 42.857 0.00 0.00 46.38 2.17
2885 6139 2.038659 TGAAGGGAAGCCTTTTGTTGG 58.961 47.619 0.00 0.00 0.00 3.77
2886 6140 3.656559 CATGAAGGGAAGCCTTTTGTTG 58.343 45.455 0.00 0.00 0.00 3.33
2888 6142 1.620323 GCATGAAGGGAAGCCTTTTGT 59.380 47.619 0.00 0.00 0.00 2.83
2889 6143 1.066645 GGCATGAAGGGAAGCCTTTTG 60.067 52.381 0.00 0.00 43.70 2.44
2891 6145 0.967380 CGGCATGAAGGGAAGCCTTT 60.967 55.000 0.00 0.00 44.85 3.11
2892 6146 1.379044 CGGCATGAAGGGAAGCCTT 60.379 57.895 0.00 0.00 44.85 4.35
2893 6147 2.273449 CGGCATGAAGGGAAGCCT 59.727 61.111 0.00 0.00 44.85 4.58
2894 6148 3.521796 GCGGCATGAAGGGAAGCC 61.522 66.667 0.00 0.00 43.61 4.35
2895 6149 1.997928 GAAGCGGCATGAAGGGAAGC 61.998 60.000 1.45 0.00 0.00 3.86
2897 6151 1.378514 GGAAGCGGCATGAAGGGAA 60.379 57.895 1.45 0.00 0.00 3.97
2898 6152 2.272146 GGAAGCGGCATGAAGGGA 59.728 61.111 1.45 0.00 0.00 4.20
2899 6153 2.830370 GGGAAGCGGCATGAAGGG 60.830 66.667 1.45 0.00 0.00 3.95
2900 6154 1.379044 AAGGGAAGCGGCATGAAGG 60.379 57.895 1.45 0.00 0.00 3.46
2901 6155 0.677731 TGAAGGGAAGCGGCATGAAG 60.678 55.000 1.45 0.00 0.00 3.02
2902 6156 0.034186 ATGAAGGGAAGCGGCATGAA 60.034 50.000 1.45 0.00 0.00 2.57
2903 6157 0.749091 CATGAAGGGAAGCGGCATGA 60.749 55.000 1.45 0.00 38.82 3.07
2904 6158 1.731700 CATGAAGGGAAGCGGCATG 59.268 57.895 1.45 0.00 0.00 4.06
2905 6159 2.123428 GCATGAAGGGAAGCGGCAT 61.123 57.895 1.45 0.00 0.00 4.40
2906 6160 2.751436 GCATGAAGGGAAGCGGCA 60.751 61.111 1.45 0.00 0.00 5.69
2907 6161 3.521796 GGCATGAAGGGAAGCGGC 61.522 66.667 0.00 0.00 0.00 6.53
2908 6162 1.678635 TTGGCATGAAGGGAAGCGG 60.679 57.895 0.00 0.00 0.00 5.52
2909 6163 1.243342 TGTTGGCATGAAGGGAAGCG 61.243 55.000 0.00 0.00 0.00 4.68
2910 6164 0.968405 TTGTTGGCATGAAGGGAAGC 59.032 50.000 0.00 0.00 0.00 3.86
2911 6165 3.555586 CCTTTTGTTGGCATGAAGGGAAG 60.556 47.826 0.00 0.00 35.96 3.46
2912 6166 2.368221 CCTTTTGTTGGCATGAAGGGAA 59.632 45.455 0.00 0.00 35.96 3.97
2913 6167 1.969923 CCTTTTGTTGGCATGAAGGGA 59.030 47.619 0.00 0.00 35.96 4.20
2914 6168 1.693606 ACCTTTTGTTGGCATGAAGGG 59.306 47.619 17.37 11.73 40.06 3.95
2915 6169 2.289010 GGACCTTTTGTTGGCATGAAGG 60.289 50.000 13.69 13.69 40.83 3.46
2916 6170 2.364970 TGGACCTTTTGTTGGCATGAAG 59.635 45.455 0.00 0.00 0.00 3.02
2917 6171 2.392662 TGGACCTTTTGTTGGCATGAA 58.607 42.857 0.00 0.00 0.00 2.57
2918 6172 2.079170 TGGACCTTTTGTTGGCATGA 57.921 45.000 0.00 0.00 0.00 3.07
2919 6173 2.158986 TGTTGGACCTTTTGTTGGCATG 60.159 45.455 0.00 0.00 0.00 4.06
2920 6174 2.114616 TGTTGGACCTTTTGTTGGCAT 58.885 42.857 0.00 0.00 0.00 4.40
2921 6175 1.561643 TGTTGGACCTTTTGTTGGCA 58.438 45.000 0.00 0.00 0.00 4.92
2922 6176 2.682155 TTGTTGGACCTTTTGTTGGC 57.318 45.000 0.00 0.00 0.00 4.52
2923 6177 5.241662 TCTTTTTGTTGGACCTTTTGTTGG 58.758 37.500 0.00 0.00 0.00 3.77
2924 6178 6.348132 GGTTCTTTTTGTTGGACCTTTTGTTG 60.348 38.462 0.00 0.00 0.00 3.33
2925 6179 5.703592 GGTTCTTTTTGTTGGACCTTTTGTT 59.296 36.000 0.00 0.00 0.00 2.83
2926 6180 5.221742 TGGTTCTTTTTGTTGGACCTTTTGT 60.222 36.000 0.00 0.00 0.00 2.83
2927 6181 5.241662 TGGTTCTTTTTGTTGGACCTTTTG 58.758 37.500 0.00 0.00 0.00 2.44
2928 6182 5.491323 TGGTTCTTTTTGTTGGACCTTTT 57.509 34.783 0.00 0.00 0.00 2.27
2929 6183 5.487433 CTTGGTTCTTTTTGTTGGACCTTT 58.513 37.500 0.00 0.00 0.00 3.11
2930 6184 4.622933 GCTTGGTTCTTTTTGTTGGACCTT 60.623 41.667 0.00 0.00 0.00 3.50
2931 6185 3.118775 GCTTGGTTCTTTTTGTTGGACCT 60.119 43.478 0.00 0.00 0.00 3.85
2932 6186 3.194861 GCTTGGTTCTTTTTGTTGGACC 58.805 45.455 0.00 0.00 0.00 4.46
2933 6187 2.857748 CGCTTGGTTCTTTTTGTTGGAC 59.142 45.455 0.00 0.00 0.00 4.02
2934 6188 2.755655 TCGCTTGGTTCTTTTTGTTGGA 59.244 40.909 0.00 0.00 0.00 3.53
2935 6189 3.115554 CTCGCTTGGTTCTTTTTGTTGG 58.884 45.455 0.00 0.00 0.00 3.77
2936 6190 3.547468 CACTCGCTTGGTTCTTTTTGTTG 59.453 43.478 0.00 0.00 0.00 3.33
2937 6191 3.769536 CACTCGCTTGGTTCTTTTTGTT 58.230 40.909 0.00 0.00 0.00 2.83
2938 6192 2.479560 GCACTCGCTTGGTTCTTTTTGT 60.480 45.455 0.00 0.00 34.30 2.83
2939 6193 2.119457 GCACTCGCTTGGTTCTTTTTG 58.881 47.619 0.00 0.00 34.30 2.44
2940 6194 1.748493 TGCACTCGCTTGGTTCTTTTT 59.252 42.857 0.00 0.00 39.64 1.94
2946 6788 2.819608 ACAATATTGCACTCGCTTGGTT 59.180 40.909 15.48 0.00 39.64 3.67
2949 6791 2.179589 GCACAATATTGCACTCGCTTG 58.820 47.619 15.48 4.88 42.49 4.01
2986 6828 1.527034 ACATTGAGCTCACATTGCGT 58.473 45.000 18.03 4.52 35.28 5.24
2987 6829 2.247637 CAACATTGAGCTCACATTGCG 58.752 47.619 18.03 6.09 35.28 4.85
3028 6870 4.407296 TCCAATACCAAAAGTTGCAACCTT 59.593 37.500 25.62 16.81 0.00 3.50
3078 6920 5.768317 CACCAACATCAAATAAACCTCGTT 58.232 37.500 0.00 0.00 0.00 3.85
3080 6922 4.165779 GCACCAACATCAAATAAACCTCG 58.834 43.478 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.