Multiple sequence alignment - TraesCS4B01G192600

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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 TraesCS4B01G192600 chr4B 100.000 3292 0 0 1 3292 415766285 415762994 0.000000e+00 6080.0
1 TraesCS4B01G192600 chr4B 96.462 1159 32 7 2138 3292 415713185 415712032 0.000000e+00 1905.0
2 TraesCS4B01G192600 chr4D 93.247 2251 88 18 739 2964 337044537 337042326 0.000000e+00 3256.0
3 TraesCS4B01G192600 chr4D 90.175 285 17 6 3018 3291 337042304 337042020 8.680000e-96 361.0
4 TraesCS4B01G192600 chr4A 90.548 2317 108 30 696 2946 136275393 136277664 0.000000e+00 2963.0
5 TraesCS4B01G192600 chr4A 88.851 296 25 6 2999 3289 136277666 136277958 1.120000e-94 357.0
6 TraesCS4B01G192600 chr4A 89.744 78 8 0 458 535 614419651 614419574 2.090000e-17 100.0
7 TraesCS4B01G192600 chr3B 96.043 278 11 0 1367 1644 26533794 26533517 1.390000e-123 453.0
8 TraesCS4B01G192600 chr3B 94.024 251 12 1 1258 1508 783881622 783881375 8.620000e-101 377.0
9 TraesCS4B01G192600 chr3B 83.051 295 31 10 394 671 814533870 814533578 1.960000e-62 250.0
10 TraesCS4B01G192600 chr3B 89.764 127 11 2 3163 3288 704570040 704570165 9.450000e-36 161.0
11 TraesCS4B01G192600 chr6B 95.683 278 12 0 1367 1644 1947104 1946827 6.480000e-122 448.0
12 TraesCS4B01G192600 chr6B 95.506 89 4 0 366 454 695074264 695074352 3.420000e-30 143.0
13 TraesCS4B01G192600 chr2D 94.902 255 10 2 1258 1512 596991386 596991135 2.380000e-106 396.0
14 TraesCS4B01G192600 chr2D 84.049 163 16 5 457 611 185214176 185214016 7.360000e-32 148.0
15 TraesCS4B01G192600 chr2D 79.695 197 20 12 278 454 185214440 185214244 1.240000e-24 124.0
16 TraesCS4B01G192600 chr2D 91.358 81 7 0 460 540 303521959 303521879 9.660000e-21 111.0
17 TraesCS4B01G192600 chr7B 94.422 251 11 1 1258 1508 411414024 411414271 1.850000e-102 383.0
18 TraesCS4B01G192600 chr7B 86.454 251 20 1 3 239 577809983 577810233 2.520000e-66 263.0
19 TraesCS4B01G192600 chr7B 92.857 112 6 1 224 333 577810035 577810146 9.450000e-36 161.0
20 TraesCS4B01G192600 chr7B 93.750 80 4 1 169 248 577810085 577810163 5.770000e-23 119.0
21 TraesCS4B01G192600 chr2A 94.422 251 11 1 1258 1508 378848036 378847789 1.850000e-102 383.0
22 TraesCS4B01G192600 chr2B 94.400 250 11 1 1263 1512 598556346 598556100 6.670000e-102 381.0
23 TraesCS4B01G192600 chr2B 88.194 144 14 3 3151 3291 704582310 704582167 5.650000e-38 169.0
24 TraesCS4B01G192600 chr1D 86.364 330 24 7 146 454 10892931 10893260 1.130000e-89 340.0
25 TraesCS4B01G192600 chr1D 87.023 131 15 2 3162 3291 439085893 439085764 2.650000e-31 147.0
26 TraesCS4B01G192600 chr7D 85.135 222 22 8 457 669 613503835 613503616 1.990000e-52 217.0
27 TraesCS4B01G192600 chr7D 93.333 90 6 0 365 454 386561465 386561376 2.060000e-27 134.0
28 TraesCS4B01G192600 chr7D 93.182 44 3 0 185 228 613504052 613504009 7.620000e-07 65.8
29 TraesCS4B01G192600 chr3D 90.698 129 10 2 3160 3288 533689340 533689466 1.570000e-38 171.0
30 TraesCS4B01G192600 chr3D 91.139 79 7 0 457 535 418208506 418208584 1.250000e-19 108.0
31 TraesCS4B01G192600 chr5D 83.854 192 12 10 282 454 382092081 382092272 7.310000e-37 165.0
32 TraesCS4B01G192600 chr5D 87.681 138 14 3 3157 3291 457669370 457669233 1.220000e-34 158.0
33 TraesCS4B01G192600 chr5A 87.671 146 12 4 6 148 671983390 671983248 7.310000e-37 165.0
34 TraesCS4B01G192600 chr3A 81.132 212 28 8 457 659 110002152 110001944 3.400000e-35 159.0
35 TraesCS4B01G192600 chr1B 88.462 130 14 1 3159 3288 581100017 581100145 4.400000e-34 156.0
36 TraesCS4B01G192600 chr1B 87.023 131 15 2 3162 3291 595351891 595351762 2.650000e-31 147.0
37 TraesCS4B01G192600 chr1A 91.346 104 9 0 452 555 306122075 306121972 3.420000e-30 143.0
38 TraesCS4B01G192600 chr1A 92.857 98 6 1 357 453 306122565 306122468 1.230000e-29 141.0
39 TraesCS4B01G192600 chr1A 82.883 111 16 2 1 111 306122866 306122759 2.700000e-16 97.1
40 TraesCS4B01G192600 chr6A 94.318 88 3 1 365 452 299720460 299720375 2.060000e-27 134.0
41 TraesCS4B01G192600 chr6A 92.222 90 7 0 365 454 7193062 7192973 9.590000e-26 128.0
42 TraesCS4B01G192600 chr6A 90.123 81 8 0 457 537 17057997 17058077 4.490000e-19 106.0
43 TraesCS4B01G192600 chr6A 90.164 61 5 1 242 302 299720541 299720482 9.790000e-11 78.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G192600 chr4B 415762994 415766285 3291 True 6080.0 6080 100.0000 1 3292 1 chr4B.!!$R2 3291
1 TraesCS4B01G192600 chr4B 415712032 415713185 1153 True 1905.0 1905 96.4620 2138 3292 1 chr4B.!!$R1 1154
2 TraesCS4B01G192600 chr4D 337042020 337044537 2517 True 1808.5 3256 91.7110 739 3291 2 chr4D.!!$R1 2552
3 TraesCS4B01G192600 chr4A 136275393 136277958 2565 False 1660.0 2963 89.6995 696 3289 2 chr4A.!!$F1 2593

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
115 116 0.032267 CTACTTCTCCGGCCGAATCC 59.968 60.0 30.73 0.0 0.00 3.01 F
577 578 0.037590 GGGGTGTACATGGCTGAACA 59.962 55.0 0.00 0.0 0.00 3.18 F
649 650 0.106419 AAAACGTTCCTGAAGGGGCA 60.106 50.0 0.00 0.0 35.41 5.36 F
688 689 0.196118 AAACCAGGAGAGGGGAGGAA 59.804 55.0 0.00 0.0 0.00 3.36 F
689 690 0.547954 AACCAGGAGAGGGGAGGAAC 60.548 60.0 0.00 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1568 0.835941 CCAGCCTATCCAGAGCAACT 59.164 55.000 0.00 0.00 0.00 3.16 R
1813 1839 0.994247 TGGACAATGAGCAGATGGGT 59.006 50.000 0.00 0.00 0.00 4.51 R
1884 1910 2.008329 GTGCTCTCAGGAATTGCAGAG 58.992 52.381 12.36 12.36 35.73 3.35 R
1983 2015 2.424956 CACTGAAGGCTAATTTGAGGCC 59.575 50.000 0.00 0.00 42.89 5.19 R
2655 2729 3.983044 AGTAAAGCAGTCTTCCGGAAT 57.017 42.857 19.21 0.00 0.00 3.01 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
44 45 4.504916 CAGCTCGGGACAGGCGAG 62.505 72.222 0.00 0.00 0.00 5.03
46 47 4.803426 GCTCGGGACAGGCGAGTG 62.803 72.222 0.00 0.00 32.89 3.51
47 48 4.803426 CTCGGGACAGGCGAGTGC 62.803 72.222 0.00 0.00 41.71 4.40
99 100 4.874977 GCCACCCGAGCTCGCTAC 62.875 72.222 30.49 13.18 38.18 3.58
100 101 3.141488 CCACCCGAGCTCGCTACT 61.141 66.667 30.49 8.84 38.18 2.57
101 102 2.711922 CCACCCGAGCTCGCTACTT 61.712 63.158 30.49 8.86 38.18 2.24
102 103 1.226717 CACCCGAGCTCGCTACTTC 60.227 63.158 30.49 0.00 38.18 3.01
103 104 1.378778 ACCCGAGCTCGCTACTTCT 60.379 57.895 30.49 3.75 38.18 2.85
104 105 1.357334 CCCGAGCTCGCTACTTCTC 59.643 63.158 30.49 0.00 38.18 2.87
105 106 1.357334 CCGAGCTCGCTACTTCTCC 59.643 63.158 30.49 0.00 38.18 3.71
106 107 1.010574 CGAGCTCGCTACTTCTCCG 60.011 63.158 25.07 0.00 0.00 4.63
107 108 1.357334 GAGCTCGCTACTTCTCCGG 59.643 63.158 0.00 0.00 0.00 5.14
108 109 2.278923 GCTCGCTACTTCTCCGGC 60.279 66.667 0.00 0.00 0.00 6.13
109 110 2.413765 CTCGCTACTTCTCCGGCC 59.586 66.667 0.00 0.00 0.00 6.13
110 111 3.471244 CTCGCTACTTCTCCGGCCG 62.471 68.421 21.04 21.04 0.00 6.13
111 112 3.515286 CGCTACTTCTCCGGCCGA 61.515 66.667 30.73 12.25 0.00 5.54
112 113 2.890371 GCTACTTCTCCGGCCGAA 59.110 61.111 30.73 4.60 0.00 4.30
113 114 1.442148 GCTACTTCTCCGGCCGAAT 59.558 57.895 30.73 7.38 0.00 3.34
114 115 0.597898 GCTACTTCTCCGGCCGAATC 60.598 60.000 30.73 0.66 0.00 2.52
115 116 0.032267 CTACTTCTCCGGCCGAATCC 59.968 60.000 30.73 0.00 0.00 3.01
116 117 1.397390 TACTTCTCCGGCCGAATCCC 61.397 60.000 30.73 0.00 0.00 3.85
117 118 2.685743 TTCTCCGGCCGAATCCCA 60.686 61.111 30.73 1.54 0.00 4.37
118 119 2.925162 CTTCTCCGGCCGAATCCCAC 62.925 65.000 30.73 0.00 0.00 4.61
119 120 4.891727 CTCCGGCCGAATCCCACG 62.892 72.222 30.73 7.15 0.00 4.94
132 133 4.803426 CCACGGGAGCTCGCTCAC 62.803 72.222 26.13 15.51 44.40 3.51
133 134 4.803426 CACGGGAGCTCGCTCACC 62.803 72.222 26.13 15.96 43.19 4.02
135 136 4.200283 CGGGAGCTCGCTCACCTC 62.200 72.222 26.13 1.57 43.19 3.85
136 137 4.200283 GGGAGCTCGCTCACCTCG 62.200 72.222 22.62 0.00 44.40 4.63
137 138 4.863925 GGAGCTCGCTCACCTCGC 62.864 72.222 19.44 0.00 44.40 5.03
138 139 3.821055 GAGCTCGCTCACCTCGCT 61.821 66.667 13.69 0.00 42.31 4.93
139 140 4.127040 AGCTCGCTCACCTCGCTG 62.127 66.667 0.00 0.00 0.00 5.18
141 142 4.127040 CTCGCTCACCTCGCTGCT 62.127 66.667 0.00 0.00 0.00 4.24
142 143 4.426112 TCGCTCACCTCGCTGCTG 62.426 66.667 0.00 0.00 0.00 4.41
144 145 4.756458 GCTCACCTCGCTGCTGCT 62.756 66.667 14.03 0.00 36.97 4.24
145 146 2.508887 CTCACCTCGCTGCTGCTC 60.509 66.667 14.03 0.00 36.97 4.26
146 147 4.426112 TCACCTCGCTGCTGCTCG 62.426 66.667 14.03 4.86 36.97 5.03
147 148 4.426112 CACCTCGCTGCTGCTCGA 62.426 66.667 14.03 14.51 36.97 4.04
148 149 4.427661 ACCTCGCTGCTGCTCGAC 62.428 66.667 14.03 0.00 36.97 4.20
180 181 4.530857 CTCCACCGGTCGCATCCC 62.531 72.222 2.59 0.00 0.00 3.85
213 214 4.849329 CGTACCGCGGCTCACCTC 62.849 72.222 28.58 6.87 36.85 3.85
214 215 3.755628 GTACCGCGGCTCACCTCA 61.756 66.667 28.58 0.00 0.00 3.86
215 216 3.755628 TACCGCGGCTCACCTCAC 61.756 66.667 28.58 0.00 0.00 3.51
219 220 4.385405 GCGGCTCACCTCACTGCT 62.385 66.667 0.00 0.00 32.83 4.24
220 221 2.433838 CGGCTCACCTCACTGCTG 60.434 66.667 0.00 0.00 0.00 4.41
221 222 2.745492 GGCTCACCTCACTGCTGC 60.745 66.667 0.00 0.00 0.00 5.25
222 223 2.346739 GCTCACCTCACTGCTGCT 59.653 61.111 0.00 0.00 0.00 4.24
223 224 1.741032 GCTCACCTCACTGCTGCTC 60.741 63.158 0.00 0.00 0.00 4.26
224 225 1.445754 CTCACCTCACTGCTGCTCG 60.446 63.158 0.00 0.00 0.00 5.03
225 226 1.871126 CTCACCTCACTGCTGCTCGA 61.871 60.000 0.00 0.00 0.00 4.04
226 227 1.445754 CACCTCACTGCTGCTCGAG 60.446 63.158 8.45 8.45 0.00 4.04
285 286 3.930012 CCTCTCCGGCCGAATCCC 61.930 72.222 30.73 0.00 0.00 3.85
286 287 4.286320 CTCTCCGGCCGAATCCCG 62.286 72.222 30.73 8.93 45.17 5.14
305 306 4.971125 GGGAGCTCGCCCGCATAC 62.971 72.222 19.61 0.00 38.58 2.39
306 307 4.971125 GGAGCTCGCCCGCATACC 62.971 72.222 7.83 0.00 0.00 2.73
314 315 4.910585 CCCGCATACCGCCTCACC 62.911 72.222 0.00 0.00 37.30 4.02
315 316 3.849951 CCGCATACCGCCTCACCT 61.850 66.667 0.00 0.00 37.30 4.00
316 317 2.279517 CGCATACCGCCTCACCTC 60.280 66.667 0.00 0.00 37.30 3.85
317 318 2.900273 GCATACCGCCTCACCTCA 59.100 61.111 0.00 0.00 32.94 3.86
318 319 1.521681 GCATACCGCCTCACCTCAC 60.522 63.158 0.00 0.00 32.94 3.51
319 320 1.961180 GCATACCGCCTCACCTCACT 61.961 60.000 0.00 0.00 32.94 3.41
320 321 0.179100 CATACCGCCTCACCTCACTG 60.179 60.000 0.00 0.00 0.00 3.66
321 322 1.961180 ATACCGCCTCACCTCACTGC 61.961 60.000 0.00 0.00 0.00 4.40
322 323 3.699894 CCGCCTCACCTCACTGCT 61.700 66.667 0.00 0.00 0.00 4.24
323 324 2.433838 CGCCTCACCTCACTGCTG 60.434 66.667 0.00 0.00 0.00 4.41
324 325 2.745492 GCCTCACCTCACTGCTGC 60.745 66.667 0.00 0.00 0.00 5.25
325 326 3.067091 CCTCACCTCACTGCTGCT 58.933 61.111 0.00 0.00 0.00 4.24
326 327 1.079266 CCTCACCTCACTGCTGCTC 60.079 63.158 0.00 0.00 0.00 4.26
327 328 1.445754 CTCACCTCACTGCTGCTCG 60.446 63.158 0.00 0.00 0.00 5.03
328 329 1.871126 CTCACCTCACTGCTGCTCGA 61.871 60.000 0.00 0.00 0.00 4.04
329 330 1.735920 CACCTCACTGCTGCTCGAC 60.736 63.158 0.00 0.00 0.00 4.20
330 331 2.505777 CCTCACTGCTGCTCGACG 60.506 66.667 0.00 0.00 0.00 5.12
331 332 2.505777 CTCACTGCTGCTCGACGG 60.506 66.667 0.00 0.00 0.00 4.79
332 333 3.978723 CTCACTGCTGCTCGACGGG 62.979 68.421 0.00 0.00 0.00 5.28
351 352 3.716006 CCGGTGTTCACGCTGCTG 61.716 66.667 0.00 0.00 0.00 4.41
352 353 2.967076 CGGTGTTCACGCTGCTGT 60.967 61.111 0.00 0.00 0.00 4.40
353 354 1.663388 CGGTGTTCACGCTGCTGTA 60.663 57.895 0.00 0.00 0.00 2.74
354 355 1.617755 CGGTGTTCACGCTGCTGTAG 61.618 60.000 0.00 0.00 0.00 2.74
355 356 1.291877 GGTGTTCACGCTGCTGTAGG 61.292 60.000 0.00 0.00 0.00 3.18
356 357 1.667830 TGTTCACGCTGCTGTAGGC 60.668 57.895 0.00 0.00 42.22 3.93
357 358 2.047274 TTCACGCTGCTGTAGGCC 60.047 61.111 0.00 0.00 40.92 5.19
358 359 2.878089 TTCACGCTGCTGTAGGCCA 61.878 57.895 5.01 0.00 40.92 5.36
359 360 3.121030 CACGCTGCTGTAGGCCAC 61.121 66.667 5.01 1.31 40.92 5.01
360 361 4.742201 ACGCTGCTGTAGGCCACG 62.742 66.667 5.01 0.00 41.75 4.94
362 363 4.767255 GCTGCTGTAGGCCACGCT 62.767 66.667 5.01 0.00 40.92 5.07
363 364 2.510238 CTGCTGTAGGCCACGCTC 60.510 66.667 5.01 0.00 40.92 5.03
364 365 4.082523 TGCTGTAGGCCACGCTCC 62.083 66.667 5.01 0.00 40.92 4.70
366 367 4.514577 CTGTAGGCCACGCTCCGG 62.515 72.222 5.01 0.00 0.00 5.14
390 391 2.747855 GCCTTTGCCTCCTCACCG 60.748 66.667 0.00 0.00 0.00 4.94
391 392 2.747855 CCTTTGCCTCCTCACCGC 60.748 66.667 0.00 0.00 0.00 5.68
392 393 2.747855 CTTTGCCTCCTCACCGCC 60.748 66.667 0.00 0.00 0.00 6.13
393 394 4.697756 TTTGCCTCCTCACCGCCG 62.698 66.667 0.00 0.00 0.00 6.46
442 443 4.154347 GCCTCTGCCTCCTCACCG 62.154 72.222 0.00 0.00 0.00 4.94
443 444 4.154347 CCTCTGCCTCCTCACCGC 62.154 72.222 0.00 0.00 0.00 5.68
444 445 4.154347 CTCTGCCTCCTCACCGCC 62.154 72.222 0.00 0.00 0.00 6.13
450 451 4.803426 CTCCTCACCGCCGCACTC 62.803 72.222 0.00 0.00 0.00 3.51
483 484 4.712425 GTGCCAAAGCCGCTGCAG 62.712 66.667 10.11 10.11 41.13 4.41
495 496 4.869440 CTGCAGGGCGAGCTCGAG 62.869 72.222 38.74 21.78 43.02 4.04
498 499 3.898509 CAGGGCGAGCTCGAGGAG 61.899 72.222 38.74 20.62 43.02 3.69
547 548 4.065281 CCACGTGTCCTCCCCGTC 62.065 72.222 15.65 0.00 31.46 4.79
548 549 4.415332 CACGTGTCCTCCCCGTCG 62.415 72.222 7.58 0.00 31.46 5.12
549 550 4.648626 ACGTGTCCTCCCCGTCGA 62.649 66.667 0.00 0.00 0.00 4.20
550 551 3.812019 CGTGTCCTCCCCGTCGAG 61.812 72.222 0.00 0.00 0.00 4.04
556 557 3.382832 CTCCCCGTCGAGGTGCTT 61.383 66.667 4.18 0.00 38.74 3.91
557 558 3.649277 CTCCCCGTCGAGGTGCTTG 62.649 68.421 4.18 0.00 38.74 4.01
558 559 4.760047 CCCCGTCGAGGTGCTTGG 62.760 72.222 4.18 0.00 38.74 3.61
559 560 4.760047 CCCGTCGAGGTGCTTGGG 62.760 72.222 4.18 0.00 38.74 4.12
560 561 4.760047 CCGTCGAGGTGCTTGGGG 62.760 72.222 4.18 0.00 34.51 4.96
561 562 4.760047 CGTCGAGGTGCTTGGGGG 62.760 72.222 0.00 0.00 0.00 5.40
562 563 3.637273 GTCGAGGTGCTTGGGGGT 61.637 66.667 0.00 0.00 0.00 4.95
563 564 3.636231 TCGAGGTGCTTGGGGGTG 61.636 66.667 0.00 0.00 0.00 4.61
564 565 3.953775 CGAGGTGCTTGGGGGTGT 61.954 66.667 0.00 0.00 0.00 4.16
565 566 2.589157 CGAGGTGCTTGGGGGTGTA 61.589 63.158 0.00 0.00 0.00 2.90
566 567 1.002502 GAGGTGCTTGGGGGTGTAC 60.003 63.158 0.00 0.00 0.00 2.90
567 568 1.772567 AGGTGCTTGGGGGTGTACA 60.773 57.895 0.00 0.00 0.00 2.90
568 569 1.140134 AGGTGCTTGGGGGTGTACAT 61.140 55.000 0.00 0.00 0.00 2.29
569 570 0.965363 GGTGCTTGGGGGTGTACATG 60.965 60.000 0.00 0.00 0.00 3.21
570 571 0.965363 GTGCTTGGGGGTGTACATGG 60.965 60.000 0.00 0.00 0.00 3.66
571 572 2.052104 GCTTGGGGGTGTACATGGC 61.052 63.158 0.00 0.00 0.00 4.40
572 573 1.691219 CTTGGGGGTGTACATGGCT 59.309 57.895 0.00 0.00 0.00 4.75
573 574 0.680921 CTTGGGGGTGTACATGGCTG 60.681 60.000 0.00 0.00 0.00 4.85
574 575 1.136961 TTGGGGGTGTACATGGCTGA 61.137 55.000 0.00 0.00 0.00 4.26
575 576 1.136961 TGGGGGTGTACATGGCTGAA 61.137 55.000 0.00 0.00 0.00 3.02
576 577 0.679960 GGGGGTGTACATGGCTGAAC 60.680 60.000 0.00 0.00 0.00 3.18
577 578 0.037590 GGGGTGTACATGGCTGAACA 59.962 55.000 0.00 0.00 0.00 3.18
578 579 1.546773 GGGGTGTACATGGCTGAACAA 60.547 52.381 0.00 0.00 0.00 2.83
579 580 2.235016 GGGTGTACATGGCTGAACAAA 58.765 47.619 0.00 0.00 0.00 2.83
580 581 2.825532 GGGTGTACATGGCTGAACAAAT 59.174 45.455 0.00 0.00 0.00 2.32
581 582 3.258123 GGGTGTACATGGCTGAACAAATT 59.742 43.478 0.00 0.00 0.00 1.82
582 583 4.262420 GGGTGTACATGGCTGAACAAATTT 60.262 41.667 0.00 0.00 0.00 1.82
583 584 4.685628 GGTGTACATGGCTGAACAAATTTG 59.314 41.667 16.67 16.67 0.00 2.32
584 585 5.288804 GTGTACATGGCTGAACAAATTTGT 58.711 37.500 18.13 18.13 44.72 2.83
585 586 5.402270 GTGTACATGGCTGAACAAATTTGTC 59.598 40.000 23.47 16.50 41.31 3.18
586 587 3.993920 ACATGGCTGAACAAATTTGTCC 58.006 40.909 23.47 19.37 41.31 4.02
587 588 3.244181 ACATGGCTGAACAAATTTGTCCC 60.244 43.478 23.47 19.46 41.31 4.46
588 589 2.676748 TGGCTGAACAAATTTGTCCCT 58.323 42.857 23.47 8.97 41.31 4.20
589 590 2.627699 TGGCTGAACAAATTTGTCCCTC 59.372 45.455 23.47 17.37 41.31 4.30
590 591 2.627699 GGCTGAACAAATTTGTCCCTCA 59.372 45.455 23.47 20.57 41.31 3.86
591 592 3.069443 GGCTGAACAAATTTGTCCCTCAA 59.931 43.478 23.47 8.34 41.31 3.02
593 594 4.507756 GCTGAACAAATTTGTCCCTCAAAC 59.492 41.667 23.47 13.95 46.77 2.93
594 595 5.017294 TGAACAAATTTGTCCCTCAAACC 57.983 39.130 23.47 6.13 46.77 3.27
595 596 4.141824 TGAACAAATTTGTCCCTCAAACCC 60.142 41.667 23.47 4.82 46.77 4.11
596 597 3.379452 ACAAATTTGTCCCTCAAACCCA 58.621 40.909 18.13 0.00 46.77 4.51
597 598 3.777522 ACAAATTTGTCCCTCAAACCCAA 59.222 39.130 18.13 0.00 46.77 4.12
598 599 4.226168 ACAAATTTGTCCCTCAAACCCAAA 59.774 37.500 18.13 0.00 46.77 3.28
599 600 5.189180 CAAATTTGTCCCTCAAACCCAAAA 58.811 37.500 10.15 0.00 46.77 2.44
600 601 3.897141 TTTGTCCCTCAAACCCAAAAC 57.103 42.857 0.00 0.00 40.56 2.43
601 602 2.838637 TGTCCCTCAAACCCAAAACT 57.161 45.000 0.00 0.00 0.00 2.66
602 603 3.108847 TGTCCCTCAAACCCAAAACTT 57.891 42.857 0.00 0.00 0.00 2.66
603 604 2.763448 TGTCCCTCAAACCCAAAACTTG 59.237 45.455 0.00 0.00 0.00 3.16
604 605 1.760029 TCCCTCAAACCCAAAACTTGC 59.240 47.619 0.00 0.00 0.00 4.01
605 606 1.484240 CCCTCAAACCCAAAACTTGCA 59.516 47.619 0.00 0.00 0.00 4.08
606 607 2.549926 CCTCAAACCCAAAACTTGCAC 58.450 47.619 0.00 0.00 0.00 4.57
607 608 2.549926 CTCAAACCCAAAACTTGCACC 58.450 47.619 0.00 0.00 0.00 5.01
608 609 1.134965 TCAAACCCAAAACTTGCACCG 60.135 47.619 0.00 0.00 0.00 4.94
609 610 0.176910 AAACCCAAAACTTGCACCGG 59.823 50.000 0.00 0.00 0.00 5.28
610 611 2.028925 CCCAAAACTTGCACCGGC 59.971 61.111 0.00 0.00 41.68 6.13
611 612 2.354539 CCAAAACTTGCACCGGCG 60.355 61.111 0.00 0.00 45.35 6.46
612 613 3.029735 CAAAACTTGCACCGGCGC 61.030 61.111 7.72 7.72 45.35 6.53
613 614 3.522731 AAAACTTGCACCGGCGCA 61.523 55.556 14.39 14.39 45.35 6.09
615 616 3.766496 AAACTTGCACCGGCGCAAC 62.766 57.895 25.38 0.00 46.61 4.17
626 627 4.043200 GCGCAACCCCAGCTGAAC 62.043 66.667 17.39 0.00 0.00 3.18
627 628 3.726517 CGCAACCCCAGCTGAACG 61.727 66.667 17.39 4.07 0.00 3.95
628 629 2.281484 GCAACCCCAGCTGAACGA 60.281 61.111 17.39 0.00 0.00 3.85
629 630 1.896660 GCAACCCCAGCTGAACGAA 60.897 57.895 17.39 0.00 0.00 3.85
630 631 1.452145 GCAACCCCAGCTGAACGAAA 61.452 55.000 17.39 0.00 0.00 3.46
631 632 1.028905 CAACCCCAGCTGAACGAAAA 58.971 50.000 17.39 0.00 0.00 2.29
632 633 1.407258 CAACCCCAGCTGAACGAAAAA 59.593 47.619 17.39 0.00 0.00 1.94
648 649 1.037493 AAAAACGTTCCTGAAGGGGC 58.963 50.000 0.00 0.00 35.41 5.80
649 650 0.106419 AAAACGTTCCTGAAGGGGCA 60.106 50.000 0.00 0.00 35.41 5.36
650 651 0.822121 AAACGTTCCTGAAGGGGCAC 60.822 55.000 0.00 0.00 35.41 5.01
651 652 1.990160 AACGTTCCTGAAGGGGCACA 61.990 55.000 0.00 0.00 35.41 4.57
652 653 1.228124 CGTTCCTGAAGGGGCACAA 60.228 57.895 0.00 0.00 35.41 3.33
653 654 1.515521 CGTTCCTGAAGGGGCACAAC 61.516 60.000 0.00 0.00 35.41 3.32
654 655 1.228124 TTCCTGAAGGGGCACAACG 60.228 57.895 0.00 0.00 35.41 4.10
655 656 2.672996 CCTGAAGGGGCACAACGG 60.673 66.667 0.00 0.00 0.00 4.44
656 657 3.365265 CTGAAGGGGCACAACGGC 61.365 66.667 0.00 0.00 40.20 5.68
657 658 3.850098 CTGAAGGGGCACAACGGCT 62.850 63.158 0.00 0.00 40.90 5.52
658 659 3.365265 GAAGGGGCACAACGGCTG 61.365 66.667 0.00 0.00 40.90 4.85
659 660 3.842925 GAAGGGGCACAACGGCTGA 62.843 63.158 0.00 0.00 40.90 4.26
660 661 3.429372 AAGGGGCACAACGGCTGAA 62.429 57.895 0.00 0.00 40.90 3.02
661 662 3.365265 GGGGCACAACGGCTGAAG 61.365 66.667 0.00 0.00 40.90 3.02
662 663 2.281484 GGGCACAACGGCTGAAGA 60.281 61.111 0.00 0.00 40.90 2.87
663 664 1.675641 GGGCACAACGGCTGAAGAT 60.676 57.895 0.00 0.00 40.90 2.40
664 665 1.503542 GGCACAACGGCTGAAGATG 59.496 57.895 0.00 0.00 37.17 2.90
665 666 1.154150 GCACAACGGCTGAAGATGC 60.154 57.895 0.00 0.00 0.00 3.91
666 667 1.580845 GCACAACGGCTGAAGATGCT 61.581 55.000 0.00 0.00 0.00 3.79
667 668 0.445436 CACAACGGCTGAAGATGCTC 59.555 55.000 0.00 0.00 0.00 4.26
668 669 0.322975 ACAACGGCTGAAGATGCTCT 59.677 50.000 0.00 0.00 0.00 4.09
669 670 1.550524 ACAACGGCTGAAGATGCTCTA 59.449 47.619 0.00 0.00 0.00 2.43
670 671 2.028112 ACAACGGCTGAAGATGCTCTAA 60.028 45.455 0.00 0.00 0.00 2.10
671 672 3.002791 CAACGGCTGAAGATGCTCTAAA 58.997 45.455 0.00 0.00 0.00 1.85
672 673 2.622436 ACGGCTGAAGATGCTCTAAAC 58.378 47.619 0.00 0.00 0.00 2.01
673 674 1.936547 CGGCTGAAGATGCTCTAAACC 59.063 52.381 0.00 0.00 0.00 3.27
674 675 2.677902 CGGCTGAAGATGCTCTAAACCA 60.678 50.000 0.00 0.00 0.00 3.67
675 676 2.941720 GGCTGAAGATGCTCTAAACCAG 59.058 50.000 0.00 0.00 0.00 4.00
676 677 2.941720 GCTGAAGATGCTCTAAACCAGG 59.058 50.000 0.00 0.00 0.00 4.45
677 678 3.369892 GCTGAAGATGCTCTAAACCAGGA 60.370 47.826 0.00 0.00 0.00 3.86
678 679 4.440880 CTGAAGATGCTCTAAACCAGGAG 58.559 47.826 0.00 0.00 0.00 3.69
679 680 4.096681 TGAAGATGCTCTAAACCAGGAGA 58.903 43.478 0.00 0.00 0.00 3.71
680 681 4.161189 TGAAGATGCTCTAAACCAGGAGAG 59.839 45.833 0.00 0.00 41.86 3.20
681 682 3.037549 AGATGCTCTAAACCAGGAGAGG 58.962 50.000 5.92 0.00 39.74 3.69
682 683 1.573108 TGCTCTAAACCAGGAGAGGG 58.427 55.000 5.92 0.00 39.74 4.30
683 684 0.833949 GCTCTAAACCAGGAGAGGGG 59.166 60.000 5.92 0.00 39.74 4.79
684 685 1.622725 GCTCTAAACCAGGAGAGGGGA 60.623 57.143 5.92 0.00 39.74 4.81
685 686 2.393646 CTCTAAACCAGGAGAGGGGAG 58.606 57.143 0.00 0.00 36.36 4.30
686 687 1.008449 TCTAAACCAGGAGAGGGGAGG 59.992 57.143 0.00 0.00 0.00 4.30
687 688 1.008449 CTAAACCAGGAGAGGGGAGGA 59.992 57.143 0.00 0.00 0.00 3.71
688 689 0.196118 AAACCAGGAGAGGGGAGGAA 59.804 55.000 0.00 0.00 0.00 3.36
689 690 0.547954 AACCAGGAGAGGGGAGGAAC 60.548 60.000 0.00 0.00 0.00 3.62
690 691 2.060980 CCAGGAGAGGGGAGGAACG 61.061 68.421 0.00 0.00 0.00 3.95
691 692 2.364448 AGGAGAGGGGAGGAACGC 60.364 66.667 0.00 0.00 0.00 4.84
704 705 1.947456 AGGAACGCCTCTTGTTTGAAC 59.053 47.619 0.00 0.00 42.19 3.18
941 957 1.870993 CGCTCGCATTGATCCATCAGA 60.871 52.381 0.00 0.00 38.19 3.27
1409 1426 0.750182 CAGGAGGACGAGGAGGAGAC 60.750 65.000 0.00 0.00 0.00 3.36
1410 1427 1.454295 GGAGGACGAGGAGGAGACC 60.454 68.421 0.00 0.00 0.00 3.85
1411 1428 1.820481 GAGGACGAGGAGGAGACCG 60.820 68.421 0.00 0.00 34.73 4.79
1412 1429 2.829458 GGACGAGGAGGAGACCGG 60.829 72.222 0.00 0.00 34.73 5.28
1515 1541 1.224592 GGAGCATCACCACGGGAAT 59.775 57.895 0.00 0.00 36.25 3.01
1797 1823 1.139095 CGGCCTAGTCGGTGAGTTC 59.861 63.158 0.00 0.00 34.25 3.01
1813 1839 3.134623 TGAGTTCTCTCTTGTTGCCTGAA 59.865 43.478 1.53 0.00 40.98 3.02
1852 1878 7.546358 TGTCCATGGTTAATGATTGTTGATTC 58.454 34.615 12.58 0.00 38.72 2.52
1884 1910 1.730547 GACGCAACATGCCTGCAAC 60.731 57.895 17.73 8.81 41.12 4.17
1981 2013 2.638480 TGCTAGAAAACAGTGTGCCT 57.362 45.000 0.00 0.00 0.00 4.75
1983 2015 1.461127 GCTAGAAAACAGTGTGCCTCG 59.539 52.381 0.00 0.00 0.00 4.63
1999 2031 1.408822 CCTCGGCCTCAAATTAGCCTT 60.409 52.381 0.00 0.00 44.84 4.35
2000 2032 1.943340 CTCGGCCTCAAATTAGCCTTC 59.057 52.381 0.00 0.00 44.84 3.46
2136 2171 3.149196 CCAGTAGAACACCAACTGCAAT 58.851 45.455 0.00 0.00 39.42 3.56
2140 2175 6.403636 CCAGTAGAACACCAACTGCAATATTC 60.404 42.308 0.00 0.00 39.42 1.75
2141 2176 6.149308 CAGTAGAACACCAACTGCAATATTCA 59.851 38.462 0.00 0.00 34.73 2.57
2619 2688 0.951558 ACCATTCGGCTGTGAAACAC 59.048 50.000 0.00 0.00 37.73 3.32
2701 2775 0.249573 ATGTGTTTGCCTGCTGTTGC 60.250 50.000 0.00 0.00 40.20 4.17
2852 2927 1.816224 GCAAGCTGGAAACGGGAATAA 59.184 47.619 0.00 0.00 37.13 1.40
2865 2940 8.984764 GGAAACGGGAATAATTATTAATTTGGC 58.015 33.333 10.68 0.00 32.38 4.52
2956 3031 4.286320 GAGCCATCCGACGCCGAT 62.286 66.667 0.00 0.00 38.22 4.18
2958 3033 3.640000 GCCATCCGACGCCGATTG 61.640 66.667 0.00 0.00 38.22 2.67
3004 3080 8.420374 TCATGGTAATCTCGTTTAGTGAAATC 57.580 34.615 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.504916 CTCGCCTGTCCCGAGCTG 62.505 72.222 0.00 0.00 44.53 4.24
82 83 4.874977 GTAGCGAGCTCGGGTGGC 62.875 72.222 35.10 19.30 40.23 5.01
83 84 2.615262 GAAGTAGCGAGCTCGGGTGG 62.615 65.000 35.10 9.75 40.23 4.61
84 85 1.226717 GAAGTAGCGAGCTCGGGTG 60.227 63.158 35.10 10.14 40.23 4.61
85 86 1.378124 GAGAAGTAGCGAGCTCGGGT 61.378 60.000 35.10 23.17 40.23 5.28
86 87 1.357334 GAGAAGTAGCGAGCTCGGG 59.643 63.158 35.10 11.31 40.23 5.14
87 88 1.357334 GGAGAAGTAGCGAGCTCGG 59.643 63.158 35.10 18.35 40.23 4.63
88 89 1.010574 CGGAGAAGTAGCGAGCTCG 60.011 63.158 31.37 31.37 43.27 5.03
89 90 1.357334 CCGGAGAAGTAGCGAGCTC 59.643 63.158 2.73 2.73 0.00 4.09
90 91 2.776913 GCCGGAGAAGTAGCGAGCT 61.777 63.158 5.05 2.25 0.00 4.09
91 92 2.278923 GCCGGAGAAGTAGCGAGC 60.279 66.667 5.05 0.00 0.00 5.03
92 93 2.413765 GGCCGGAGAAGTAGCGAG 59.586 66.667 5.05 0.00 0.00 5.03
93 94 3.515286 CGGCCGGAGAAGTAGCGA 61.515 66.667 20.10 0.00 0.00 4.93
94 95 2.351336 ATTCGGCCGGAGAAGTAGCG 62.351 60.000 27.83 0.00 0.00 4.26
95 96 0.597898 GATTCGGCCGGAGAAGTAGC 60.598 60.000 27.83 1.16 0.00 3.58
96 97 0.032267 GGATTCGGCCGGAGAAGTAG 59.968 60.000 27.83 0.00 0.00 2.57
97 98 1.397390 GGGATTCGGCCGGAGAAGTA 61.397 60.000 27.83 0.00 0.00 2.24
98 99 2.732619 GGGATTCGGCCGGAGAAGT 61.733 63.158 27.83 0.00 0.00 3.01
99 100 2.109181 GGGATTCGGCCGGAGAAG 59.891 66.667 27.83 0.00 0.00 2.85
100 101 2.685743 TGGGATTCGGCCGGAGAA 60.686 61.111 27.83 13.42 0.00 2.87
101 102 3.467226 GTGGGATTCGGCCGGAGA 61.467 66.667 27.83 12.51 0.00 3.71
102 103 4.891727 CGTGGGATTCGGCCGGAG 62.892 72.222 27.83 0.00 0.00 4.63
106 107 4.547367 CTCCCGTGGGATTCGGCC 62.547 72.222 8.37 0.00 45.71 6.13
108 109 3.447025 GAGCTCCCGTGGGATTCGG 62.447 68.421 8.37 0.00 44.24 4.30
109 110 2.107141 GAGCTCCCGTGGGATTCG 59.893 66.667 8.37 0.00 44.24 3.34
110 111 2.107141 CGAGCTCCCGTGGGATTC 59.893 66.667 8.37 8.59 44.24 2.52
111 112 4.162690 GCGAGCTCCCGTGGGATT 62.163 66.667 8.37 0.00 44.24 3.01
115 116 4.803426 GTGAGCGAGCTCCCGTGG 62.803 72.222 20.79 0.00 42.09 4.94
116 117 4.803426 GGTGAGCGAGCTCCCGTG 62.803 72.222 20.79 0.00 42.09 4.94
118 119 4.200283 GAGGTGAGCGAGCTCCCG 62.200 72.222 20.79 0.00 42.51 5.14
119 120 4.200283 CGAGGTGAGCGAGCTCCC 62.200 72.222 20.79 19.54 45.05 4.30
120 121 4.863925 GCGAGGTGAGCGAGCTCC 62.864 72.222 20.79 12.49 45.05 4.70
121 122 3.821055 AGCGAGGTGAGCGAGCTC 61.821 66.667 17.42 17.42 44.51 4.09
122 123 4.127040 CAGCGAGGTGAGCGAGCT 62.127 66.667 0.00 0.00 40.04 4.09
124 125 4.127040 AGCAGCGAGGTGAGCGAG 62.127 66.667 6.46 0.00 40.04 5.03
163 164 4.530857 GGGATGCGACCGGTGGAG 62.531 72.222 21.99 8.89 0.00 3.86
170 171 4.530857 CTCCCACGGGATGCGACC 62.531 72.222 4.97 0.00 44.24 4.79
173 174 4.899239 GAGCTCCCACGGGATGCG 62.899 72.222 4.97 0.00 44.24 4.73
174 175 4.899239 CGAGCTCCCACGGGATGC 62.899 72.222 8.47 11.32 44.24 3.91
175 176 4.899239 GCGAGCTCCCACGGGATG 62.899 72.222 8.47 1.37 44.24 3.51
197 198 3.755628 TGAGGTGAGCCGCGGTAC 61.756 66.667 28.70 21.97 40.50 3.34
198 199 3.755628 GTGAGGTGAGCCGCGGTA 61.756 66.667 28.70 11.11 40.50 4.02
202 203 4.385405 AGCAGTGAGGTGAGCCGC 62.385 66.667 0.00 0.00 40.50 6.53
209 210 2.969016 CTCGAGCAGCAGTGAGGT 59.031 61.111 0.00 0.00 0.00 3.85
268 269 3.930012 GGGATTCGGCCGGAGAGG 61.930 72.222 27.83 0.00 44.97 3.69
269 270 4.286320 CGGGATTCGGCCGGAGAG 62.286 72.222 27.83 8.59 34.75 3.20
278 279 4.951963 GAGCTCCCGCGGGATTCG 62.952 72.222 45.15 33.79 44.24 3.34
279 280 4.951963 CGAGCTCCCGCGGGATTC 62.952 72.222 45.15 37.99 44.24 2.52
288 289 4.971125 GTATGCGGGCGAGCTCCC 62.971 72.222 8.47 10.35 43.02 4.30
289 290 4.971125 GGTATGCGGGCGAGCTCC 62.971 72.222 8.47 0.47 38.13 4.70
300 301 1.521681 GTGAGGTGAGGCGGTATGC 60.522 63.158 0.00 0.00 45.38 3.14
301 302 0.179100 CAGTGAGGTGAGGCGGTATG 60.179 60.000 0.00 0.00 0.00 2.39
302 303 1.961180 GCAGTGAGGTGAGGCGGTAT 61.961 60.000 0.00 0.00 0.00 2.73
303 304 2.646175 GCAGTGAGGTGAGGCGGTA 61.646 63.158 0.00 0.00 0.00 4.02
304 305 4.008933 GCAGTGAGGTGAGGCGGT 62.009 66.667 0.00 0.00 0.00 5.68
305 306 3.699894 AGCAGTGAGGTGAGGCGG 61.700 66.667 0.00 0.00 0.00 6.13
312 313 2.653702 GTCGAGCAGCAGTGAGGT 59.346 61.111 0.00 0.00 0.00 3.85
313 314 2.505777 CGTCGAGCAGCAGTGAGG 60.506 66.667 0.00 0.00 0.00 3.86
314 315 2.505777 CCGTCGAGCAGCAGTGAG 60.506 66.667 0.00 0.00 0.00 3.51
315 316 4.056125 CCCGTCGAGCAGCAGTGA 62.056 66.667 0.00 0.00 0.00 3.41
334 335 3.716006 CAGCAGCGTGAACACCGG 61.716 66.667 0.00 0.00 0.00 5.28
335 336 1.617755 CTACAGCAGCGTGAACACCG 61.618 60.000 0.00 0.00 0.00 4.94
336 337 1.291877 CCTACAGCAGCGTGAACACC 61.292 60.000 0.00 0.00 0.00 4.16
337 338 1.901650 GCCTACAGCAGCGTGAACAC 61.902 60.000 0.79 0.00 42.97 3.32
338 339 1.667830 GCCTACAGCAGCGTGAACA 60.668 57.895 0.79 0.00 42.97 3.18
339 340 2.391389 GGCCTACAGCAGCGTGAAC 61.391 63.158 0.00 0.00 46.50 3.18
340 341 2.047274 GGCCTACAGCAGCGTGAA 60.047 61.111 0.00 0.00 46.50 3.18
341 342 3.310307 TGGCCTACAGCAGCGTGA 61.310 61.111 3.32 0.00 46.50 4.35
342 343 3.121030 GTGGCCTACAGCAGCGTG 61.121 66.667 3.32 0.00 46.50 5.34
343 344 4.742201 CGTGGCCTACAGCAGCGT 62.742 66.667 3.32 0.00 46.50 5.07
345 346 4.767255 AGCGTGGCCTACAGCAGC 62.767 66.667 3.32 0.00 46.50 5.25
346 347 2.510238 GAGCGTGGCCTACAGCAG 60.510 66.667 3.32 0.00 46.50 4.24
347 348 4.082523 GGAGCGTGGCCTACAGCA 62.083 66.667 3.32 0.00 46.50 4.41
349 350 4.514577 CCGGAGCGTGGCCTACAG 62.515 72.222 3.32 0.00 0.00 2.74
373 374 2.747855 CGGTGAGGAGGCAAAGGC 60.748 66.667 0.00 0.00 40.13 4.35
374 375 2.747855 GCGGTGAGGAGGCAAAGG 60.748 66.667 0.00 0.00 0.00 3.11
375 376 2.747855 GGCGGTGAGGAGGCAAAG 60.748 66.667 0.00 0.00 0.00 2.77
376 377 4.697756 CGGCGGTGAGGAGGCAAA 62.698 66.667 0.00 0.00 0.00 3.68
425 426 4.154347 CGGTGAGGAGGCAGAGGC 62.154 72.222 0.00 0.00 40.13 4.70
426 427 4.154347 GCGGTGAGGAGGCAGAGG 62.154 72.222 0.00 0.00 0.00 3.69
427 428 4.154347 GGCGGTGAGGAGGCAGAG 62.154 72.222 0.00 0.00 0.00 3.35
433 434 4.803426 GAGTGCGGCGGTGAGGAG 62.803 72.222 9.78 0.00 0.00 3.69
466 467 4.712425 CTGCAGCGGCTTTGGCAC 62.712 66.667 10.92 0.00 41.91 5.01
478 479 4.869440 CTCGAGCTCGCCCTGCAG 62.869 72.222 30.97 17.80 39.60 4.41
481 482 3.898509 CTCCTCGAGCTCGCCCTG 61.899 72.222 30.97 18.76 39.60 4.45
530 531 4.065281 GACGGGGAGGACACGTGG 62.065 72.222 21.57 1.23 41.40 4.94
531 532 4.415332 CGACGGGGAGGACACGTG 62.415 72.222 15.48 15.48 41.40 4.49
532 533 4.648626 TCGACGGGGAGGACACGT 62.649 66.667 0.00 0.00 44.35 4.49
533 534 3.812019 CTCGACGGGGAGGACACG 61.812 72.222 0.00 0.00 0.00 4.49
539 540 3.382832 AAGCACCTCGACGGGGAG 61.383 66.667 23.53 14.88 39.13 4.30
540 541 3.691342 CAAGCACCTCGACGGGGA 61.691 66.667 23.53 0.00 39.13 4.81
541 542 4.760047 CCAAGCACCTCGACGGGG 62.760 72.222 13.59 13.59 40.11 5.73
542 543 4.760047 CCCAAGCACCTCGACGGG 62.760 72.222 0.00 0.00 36.97 5.28
543 544 4.760047 CCCCAAGCACCTCGACGG 62.760 72.222 0.00 0.03 39.35 4.79
544 545 4.760047 CCCCCAAGCACCTCGACG 62.760 72.222 0.00 0.00 0.00 5.12
545 546 3.637273 ACCCCCAAGCACCTCGAC 61.637 66.667 0.00 0.00 0.00 4.20
546 547 3.636231 CACCCCCAAGCACCTCGA 61.636 66.667 0.00 0.00 0.00 4.04
547 548 2.589157 TACACCCCCAAGCACCTCG 61.589 63.158 0.00 0.00 0.00 4.63
548 549 1.002502 GTACACCCCCAAGCACCTC 60.003 63.158 0.00 0.00 0.00 3.85
549 550 1.140134 ATGTACACCCCCAAGCACCT 61.140 55.000 0.00 0.00 0.00 4.00
550 551 0.965363 CATGTACACCCCCAAGCACC 60.965 60.000 0.00 0.00 0.00 5.01
551 552 0.965363 CCATGTACACCCCCAAGCAC 60.965 60.000 0.00 0.00 0.00 4.40
552 553 1.382240 CCATGTACACCCCCAAGCA 59.618 57.895 0.00 0.00 0.00 3.91
553 554 2.052104 GCCATGTACACCCCCAAGC 61.052 63.158 0.00 0.00 0.00 4.01
554 555 0.680921 CAGCCATGTACACCCCCAAG 60.681 60.000 0.00 0.00 0.00 3.61
555 556 1.136961 TCAGCCATGTACACCCCCAA 61.137 55.000 0.00 0.00 0.00 4.12
556 557 1.136961 TTCAGCCATGTACACCCCCA 61.137 55.000 0.00 0.00 0.00 4.96
557 558 0.679960 GTTCAGCCATGTACACCCCC 60.680 60.000 0.00 0.00 0.00 5.40
558 559 0.037590 TGTTCAGCCATGTACACCCC 59.962 55.000 0.00 0.00 32.45 4.95
559 560 1.904287 TTGTTCAGCCATGTACACCC 58.096 50.000 0.00 0.00 36.57 4.61
560 561 4.519540 AATTTGTTCAGCCATGTACACC 57.480 40.909 0.00 0.00 36.57 4.16
561 562 5.288804 ACAAATTTGTTCAGCCATGTACAC 58.711 37.500 18.13 0.00 38.47 2.90
562 563 5.508825 GGACAAATTTGTTCAGCCATGTACA 60.509 40.000 24.02 0.00 42.43 2.90
563 564 4.923281 GGACAAATTTGTTCAGCCATGTAC 59.077 41.667 24.02 7.37 42.43 2.90
564 565 4.021544 GGGACAAATTTGTTCAGCCATGTA 60.022 41.667 27.00 0.00 42.43 2.29
565 566 3.244181 GGGACAAATTTGTTCAGCCATGT 60.244 43.478 27.00 2.00 42.43 3.21
566 567 3.007182 AGGGACAAATTTGTTCAGCCATG 59.993 43.478 27.00 0.00 42.43 3.66
567 568 3.242011 AGGGACAAATTTGTTCAGCCAT 58.758 40.909 27.00 17.41 42.43 4.40
568 569 2.627699 GAGGGACAAATTTGTTCAGCCA 59.372 45.455 27.00 0.00 42.43 4.75
569 570 2.627699 TGAGGGACAAATTTGTTCAGCC 59.372 45.455 27.00 20.87 42.43 4.85
570 571 4.320608 TTGAGGGACAAATTTGTTCAGC 57.679 40.909 27.00 18.96 42.43 4.26
580 581 3.445987 AGTTTTGGGTTTGAGGGACAAA 58.554 40.909 0.00 0.00 44.79 2.83
581 582 3.108847 AGTTTTGGGTTTGAGGGACAA 57.891 42.857 0.00 0.00 36.65 3.18
582 583 2.763448 CAAGTTTTGGGTTTGAGGGACA 59.237 45.455 0.00 0.00 0.00 4.02
583 584 2.483013 GCAAGTTTTGGGTTTGAGGGAC 60.483 50.000 0.00 0.00 0.00 4.46
584 585 1.760029 GCAAGTTTTGGGTTTGAGGGA 59.240 47.619 0.00 0.00 0.00 4.20
585 586 1.484240 TGCAAGTTTTGGGTTTGAGGG 59.516 47.619 0.00 0.00 0.00 4.30
586 587 2.549926 GTGCAAGTTTTGGGTTTGAGG 58.450 47.619 0.00 0.00 0.00 3.86
587 588 2.549926 GGTGCAAGTTTTGGGTTTGAG 58.450 47.619 0.00 0.00 0.00 3.02
588 589 1.134965 CGGTGCAAGTTTTGGGTTTGA 60.135 47.619 0.00 0.00 0.00 2.69
589 590 1.285578 CGGTGCAAGTTTTGGGTTTG 58.714 50.000 0.00 0.00 0.00 2.93
590 591 0.176910 CCGGTGCAAGTTTTGGGTTT 59.823 50.000 0.00 0.00 0.00 3.27
591 592 1.819905 CCGGTGCAAGTTTTGGGTT 59.180 52.632 0.00 0.00 0.00 4.11
592 593 2.791868 GCCGGTGCAAGTTTTGGGT 61.792 57.895 1.90 0.00 37.47 4.51
593 594 2.028925 GCCGGTGCAAGTTTTGGG 59.971 61.111 1.90 0.00 37.47 4.12
594 595 2.354539 CGCCGGTGCAAGTTTTGG 60.355 61.111 0.00 0.00 37.32 3.28
595 596 3.029735 GCGCCGGTGCAAGTTTTG 61.030 61.111 34.26 0.00 37.32 2.44
596 597 3.522731 TGCGCCGGTGCAAGTTTT 61.523 55.556 38.93 0.00 43.02 2.43
609 610 4.043200 GTTCAGCTGGGGTTGCGC 62.043 66.667 15.13 0.00 35.28 6.09
610 611 3.726517 CGTTCAGCTGGGGTTGCG 61.727 66.667 15.13 6.04 35.28 4.85
611 612 1.452145 TTTCGTTCAGCTGGGGTTGC 61.452 55.000 15.13 0.00 0.00 4.17
612 613 1.028905 TTTTCGTTCAGCTGGGGTTG 58.971 50.000 15.13 0.00 0.00 3.77
613 614 1.770294 TTTTTCGTTCAGCTGGGGTT 58.230 45.000 15.13 0.00 0.00 4.11
614 615 3.505835 TTTTTCGTTCAGCTGGGGT 57.494 47.368 15.13 0.00 0.00 4.95
629 630 1.037493 GCCCCTTCAGGAACGTTTTT 58.963 50.000 0.46 0.00 38.24 1.94
630 631 0.106419 TGCCCCTTCAGGAACGTTTT 60.106 50.000 0.46 0.00 38.24 2.43
631 632 0.822121 GTGCCCCTTCAGGAACGTTT 60.822 55.000 0.46 0.00 38.24 3.60
632 633 1.228154 GTGCCCCTTCAGGAACGTT 60.228 57.895 0.00 0.00 38.24 3.99
633 634 1.990160 TTGTGCCCCTTCAGGAACGT 61.990 55.000 0.00 0.00 38.24 3.99
634 635 1.228124 TTGTGCCCCTTCAGGAACG 60.228 57.895 0.00 0.00 38.24 3.95
635 636 1.515521 CGTTGTGCCCCTTCAGGAAC 61.516 60.000 0.00 0.00 38.24 3.62
636 637 1.228124 CGTTGTGCCCCTTCAGGAA 60.228 57.895 0.00 0.00 38.24 3.36
637 638 2.429930 CGTTGTGCCCCTTCAGGA 59.570 61.111 0.00 0.00 38.24 3.86
638 639 2.672996 CCGTTGTGCCCCTTCAGG 60.673 66.667 0.00 0.00 0.00 3.86
639 640 3.365265 GCCGTTGTGCCCCTTCAG 61.365 66.667 0.00 0.00 0.00 3.02
640 641 3.884774 AGCCGTTGTGCCCCTTCA 61.885 61.111 0.00 0.00 0.00 3.02
641 642 3.365265 CAGCCGTTGTGCCCCTTC 61.365 66.667 0.00 0.00 0.00 3.46
642 643 3.429372 TTCAGCCGTTGTGCCCCTT 62.429 57.895 0.00 0.00 0.00 3.95
643 644 3.850098 CTTCAGCCGTTGTGCCCCT 62.850 63.158 0.00 0.00 0.00 4.79
644 645 3.365265 CTTCAGCCGTTGTGCCCC 61.365 66.667 0.00 0.00 0.00 5.80
645 646 1.675641 ATCTTCAGCCGTTGTGCCC 60.676 57.895 0.00 0.00 0.00 5.36
646 647 1.503542 CATCTTCAGCCGTTGTGCC 59.496 57.895 0.00 0.00 0.00 5.01
647 648 1.154150 GCATCTTCAGCCGTTGTGC 60.154 57.895 0.00 0.00 0.00 4.57
648 649 0.445436 GAGCATCTTCAGCCGTTGTG 59.555 55.000 0.00 0.00 0.00 3.33
649 650 2.846371 GAGCATCTTCAGCCGTTGT 58.154 52.632 0.00 0.00 0.00 3.32
661 662 2.103941 CCCTCTCCTGGTTTAGAGCATC 59.896 54.545 5.57 0.00 38.33 3.91
662 663 2.122768 CCCTCTCCTGGTTTAGAGCAT 58.877 52.381 5.57 0.00 38.33 3.79
663 664 1.573108 CCCTCTCCTGGTTTAGAGCA 58.427 55.000 5.57 0.00 38.33 4.26
664 665 0.833949 CCCCTCTCCTGGTTTAGAGC 59.166 60.000 5.57 0.00 38.33 4.09
665 666 2.393646 CTCCCCTCTCCTGGTTTAGAG 58.606 57.143 4.35 4.35 39.19 2.43
666 667 1.008449 CCTCCCCTCTCCTGGTTTAGA 59.992 57.143 0.00 0.00 0.00 2.10
667 668 1.008449 TCCTCCCCTCTCCTGGTTTAG 59.992 57.143 0.00 0.00 0.00 1.85
668 669 1.098589 TCCTCCCCTCTCCTGGTTTA 58.901 55.000 0.00 0.00 0.00 2.01
669 670 0.196118 TTCCTCCCCTCTCCTGGTTT 59.804 55.000 0.00 0.00 0.00 3.27
670 671 0.547954 GTTCCTCCCCTCTCCTGGTT 60.548 60.000 0.00 0.00 0.00 3.67
671 672 1.081277 GTTCCTCCCCTCTCCTGGT 59.919 63.158 0.00 0.00 0.00 4.00
672 673 2.060980 CGTTCCTCCCCTCTCCTGG 61.061 68.421 0.00 0.00 0.00 4.45
673 674 2.726351 GCGTTCCTCCCCTCTCCTG 61.726 68.421 0.00 0.00 0.00 3.86
674 675 2.364448 GCGTTCCTCCCCTCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
675 676 3.471806 GGCGTTCCTCCCCTCTCC 61.472 72.222 0.00 0.00 0.00 3.71
676 677 2.364448 AGGCGTTCCTCCCCTCTC 60.364 66.667 0.00 0.00 38.72 3.20
685 686 1.947456 AGTTCAAACAAGAGGCGTTCC 59.053 47.619 0.00 0.00 0.00 3.62
686 687 2.612212 TGAGTTCAAACAAGAGGCGTTC 59.388 45.455 0.00 0.00 0.00 3.95
687 688 2.639065 TGAGTTCAAACAAGAGGCGTT 58.361 42.857 0.00 0.00 0.00 4.84
688 689 2.325583 TGAGTTCAAACAAGAGGCGT 57.674 45.000 0.00 0.00 0.00 5.68
689 690 2.031682 CCTTGAGTTCAAACAAGAGGCG 60.032 50.000 0.00 0.00 43.98 5.52
690 691 2.287849 GCCTTGAGTTCAAACAAGAGGC 60.288 50.000 13.76 13.76 43.98 4.70
691 692 2.031682 CGCCTTGAGTTCAAACAAGAGG 60.032 50.000 0.00 6.85 43.98 3.69
692 693 2.603173 GCGCCTTGAGTTCAAACAAGAG 60.603 50.000 0.00 0.00 43.98 2.85
693 694 1.333619 GCGCCTTGAGTTCAAACAAGA 59.666 47.619 0.00 0.00 43.98 3.02
694 695 1.065401 TGCGCCTTGAGTTCAAACAAG 59.935 47.619 4.18 0.00 41.85 3.16
704 705 2.974148 TGTGTGCTGCGCCTTGAG 60.974 61.111 11.12 0.00 0.00 3.02
725 726 1.826054 TTTGGTCCAACCGTGCCTG 60.826 57.895 2.98 0.00 42.58 4.85
941 957 4.363990 CGTGCCTGCCGTCTGAGT 62.364 66.667 0.00 0.00 0.00 3.41
971 987 2.492599 CTTTGGGAGGGAGGGAGGGA 62.493 65.000 0.00 0.00 0.00 4.20
999 1016 4.854924 TGGGCGATGGCGGACATG 62.855 66.667 0.00 0.00 40.72 3.21
1395 1412 2.829458 CCGGTCTCCTCCTCGTCC 60.829 72.222 0.00 0.00 0.00 4.79
1416 1433 2.124403 TCGCGGTAGAGGGGAGAC 60.124 66.667 6.13 0.00 0.00 3.36
1474 1500 4.742201 GGAGCTCAGCGGCGACAA 62.742 66.667 17.19 0.00 37.29 3.18
1542 1568 0.835941 CCAGCCTATCCAGAGCAACT 59.164 55.000 0.00 0.00 0.00 3.16
1544 1570 1.528824 GCCAGCCTATCCAGAGCAA 59.471 57.895 0.00 0.00 0.00 3.91
1593 1619 2.710902 CCGTGTCGCCTCCATCTGA 61.711 63.158 0.00 0.00 0.00 3.27
1797 1823 1.202806 TGGGTTCAGGCAACAAGAGAG 60.203 52.381 0.00 0.00 36.61 3.20
1813 1839 0.994247 TGGACAATGAGCAGATGGGT 59.006 50.000 0.00 0.00 0.00 4.51
1884 1910 2.008329 GTGCTCTCAGGAATTGCAGAG 58.992 52.381 12.36 12.36 35.73 3.35
1983 2015 2.424956 CACTGAAGGCTAATTTGAGGCC 59.575 50.000 0.00 0.00 42.89 5.19
2090 2125 4.991153 TGGAACAGACTACAGAGCATAG 57.009 45.455 0.00 0.00 0.00 2.23
2141 2176 9.938280 TGCTATTACTTGTTAACAGTATTCAGT 57.062 29.630 8.56 10.52 0.00 3.41
2160 2212 9.264719 CACATGATGAACAGATTACTGCTATTA 57.735 33.333 0.00 0.00 46.95 0.98
2161 2213 7.255035 GCACATGATGAACAGATTACTGCTATT 60.255 37.037 0.00 0.00 46.95 1.73
2162 2214 6.204301 GCACATGATGAACAGATTACTGCTAT 59.796 38.462 0.00 0.00 46.95 2.97
2456 2521 4.335400 AAAACCCGCAATCATTGAACTT 57.665 36.364 0.00 0.00 0.00 2.66
2619 2688 8.391075 ACCCAAAACATCATATTTACCGATAG 57.609 34.615 0.00 0.00 0.00 2.08
2655 2729 3.983044 AGTAAAGCAGTCTTCCGGAAT 57.017 42.857 19.21 0.00 0.00 3.01
2865 2940 7.820872 AGCTTCTGAAACATTCAAATTATTGGG 59.179 33.333 0.00 0.00 39.58 4.12
2956 3031 7.901029 TGATTCACCACAAATATTAAAGCCAA 58.099 30.769 0.00 0.00 0.00 4.52
2958 3033 7.439056 CCATGATTCACCACAAATATTAAAGCC 59.561 37.037 0.00 0.00 0.00 4.35
2966 3042 7.226523 CGAGATTACCATGATTCACCACAAATA 59.773 37.037 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.