Multiple sequence alignment - TraesCS3A01G355700

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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 TraesCS3A01G355700 chr3A 100.000 4398 0 0 1 4398 603789063 603793460 0.000000e+00 8122.0
1 TraesCS3A01G355700 chr3A 89.032 155 15 1 3506 3658 739801242 739801396 1.610000e-44 191.0
2 TraesCS3A01G355700 chr3D 96.146 2932 83 8 580 3499 461199045 461201958 0.000000e+00 4761.0
3 TraesCS3A01G355700 chr3D 87.963 756 27 9 3657 4398 461201959 461202664 0.000000e+00 833.0
4 TraesCS3A01G355700 chr3D 87.747 506 47 9 1 502 22936922 22936428 1.060000e-160 577.0
5 TraesCS3A01G355700 chr3D 87.500 168 17 3 3498 3662 580330744 580330578 1.610000e-44 191.0
6 TraesCS3A01G355700 chr3B 95.726 2901 94 11 580 3475 611676082 611678957 0.000000e+00 4643.0
7 TraesCS3A01G355700 chr3B 88.839 448 16 9 3965 4398 611678966 611679393 1.810000e-143 520.0
8 TraesCS3A01G355700 chr3B 88.346 266 29 2 13 278 40199289 40199026 7.100000e-83 318.0
9 TraesCS3A01G355700 chr3B 88.125 160 15 3 3503 3659 506736063 506736221 2.090000e-43 187.0
10 TraesCS3A01G355700 chr1D 91.611 2408 176 14 1120 3507 471303057 471300656 0.000000e+00 3304.0
11 TraesCS3A01G355700 chr1D 86.632 389 27 11 2943 3306 471432555 471432943 1.470000e-109 407.0
12 TraesCS3A01G355700 chr1D 89.899 198 13 5 3748 3940 471300593 471300398 9.450000e-62 248.0
13 TraesCS3A01G355700 chr1D 82.197 264 23 15 3688 3940 471297173 471296923 5.770000e-49 206.0
14 TraesCS3A01G355700 chr1D 94.030 134 7 1 3940 4073 303318837 303318969 7.460000e-48 202.0
15 TraesCS3A01G355700 chr1D 82.819 227 35 4 1 224 395052725 395052950 2.680000e-47 200.0
16 TraesCS3A01G355700 chr1B 90.959 2389 179 23 1120 3476 655104327 655101944 0.000000e+00 3181.0
17 TraesCS3A01G355700 chr1B 86.027 1052 108 25 2387 3407 655271553 655272596 0.000000e+00 1092.0
18 TraesCS3A01G355700 chr1B 86.159 289 25 7 3657 3940 655101924 655101646 9.250000e-77 298.0
19 TraesCS3A01G355700 chr1B 94.030 134 7 1 3940 4073 410798032 410798164 7.460000e-48 202.0
20 TraesCS3A01G355700 chr1B 82.468 154 27 0 15 168 107071785 107071938 7.670000e-28 135.0
21 TraesCS3A01G355700 chr1B 100.000 29 0 0 506 534 1265293 1265321 2.000000e-03 54.7
22 TraesCS3A01G355700 chr7D 96.675 1594 42 3 1914 3507 29536560 29534978 0.000000e+00 2639.0
23 TraesCS3A01G355700 chr7D 94.585 591 23 2 1327 1917 29537521 29536940 0.000000e+00 905.0
24 TraesCS3A01G355700 chr7D 94.118 306 16 2 3657 3962 29534977 29534674 8.620000e-127 464.0
25 TraesCS3A01G355700 chr7D 97.207 179 5 0 4219 4397 29534676 29534498 1.990000e-78 303.0
26 TraesCS3A01G355700 chr7D 85.366 287 25 10 3657 3939 613449745 613449472 9.310000e-72 281.0
27 TraesCS3A01G355700 chr7A 95.806 763 27 2 1327 2084 29781385 29780623 0.000000e+00 1227.0
28 TraesCS3A01G355700 chr7A 85.915 284 25 9 3657 3939 704893526 704893257 5.570000e-74 289.0
29 TraesCS3A01G355700 chr7A 81.627 332 32 11 3187 3507 704893838 704893525 9.450000e-62 248.0
30 TraesCS3A01G355700 chr7A 87.349 166 18 2 3499 3662 137770393 137770557 2.090000e-43 187.0
31 TraesCS3A01G355700 chr7A 78.339 277 48 7 226 502 624980350 624980086 7.560000e-38 169.0
32 TraesCS3A01G355700 chrUn 86.852 540 56 8 1246 1785 1368158 1368682 1.360000e-164 590.0
33 TraesCS3A01G355700 chrUn 86.547 446 40 10 1340 1785 396328458 396328033 1.430000e-129 473.0
34 TraesCS3A01G355700 chr1A 86.852 540 56 8 1246 1785 565571868 565572392 1.360000e-164 590.0
35 TraesCS3A01G355700 chr1A 88.820 161 14 3 3500 3658 516570462 516570620 1.250000e-45 195.0
36 TraesCS3A01G355700 chr1A 93.130 131 8 1 3940 4070 380951145 380951274 1.610000e-44 191.0
37 TraesCS3A01G355700 chr5A 85.265 509 62 8 1 509 524195471 524194976 3.030000e-141 512.0
38 TraesCS3A01G355700 chr2B 86.859 312 28 9 1 304 52100606 52100912 1.960000e-88 337.0
39 TraesCS3A01G355700 chr2B 88.199 161 19 0 299 459 52103745 52103905 4.490000e-45 193.0
40 TraesCS3A01G355700 chr2B 82.564 195 27 3 2 190 693907562 693907369 9.790000e-37 165.0
41 TraesCS3A01G355700 chr5D 86.232 276 38 0 227 502 510907233 510906958 2.570000e-77 300.0
42 TraesCS3A01G355700 chr5D 100.000 28 0 0 506 533 368740349 368740376 8.000000e-03 52.8
43 TraesCS3A01G355700 chr4B 89.498 219 20 3 1 217 643762134 643762351 1.560000e-69 274.0
44 TraesCS3A01G355700 chr4B 91.045 134 10 2 3940 4073 283728982 283728851 3.490000e-41 180.0
45 TraesCS3A01G355700 chr2D 89.375 160 12 4 3502 3658 29624510 29624353 3.470000e-46 196.0
46 TraesCS3A01G355700 chr2D 88.462 156 16 1 3505 3658 86085962 86086117 2.090000e-43 187.0
47 TraesCS3A01G355700 chr2D 87.975 158 17 1 3506 3661 556055812 556055655 7.510000e-43 185.0
48 TraesCS3A01G355700 chr2D 100.000 28 0 0 506 533 595556455 595556482 8.000000e-03 52.8
49 TraesCS3A01G355700 chr2A 89.103 156 14 2 3505 3658 86445857 86446011 1.610000e-44 191.0
50 TraesCS3A01G355700 chr7B 94.393 107 6 0 3097 3203 703302127 703302021 9.790000e-37 165.0
51 TraesCS3A01G355700 chr7B 92.920 113 8 0 2945 3057 703302238 703302126 9.790000e-37 165.0
52 TraesCS3A01G355700 chr6B 79.915 234 37 5 1 226 21053513 21053744 3.520000e-36 163.0


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 TraesCS3A01G355700 chr3A 603789063 603793460 4397 False 8122.000000 8122 100.000000 1 4398 1 chr3A.!!$F1 4397
1 TraesCS3A01G355700 chr3D 461199045 461202664 3619 False 2797.000000 4761 92.054500 580 4398 2 chr3D.!!$F1 3818
2 TraesCS3A01G355700 chr3B 611676082 611679393 3311 False 2581.500000 4643 92.282500 580 4398 2 chr3B.!!$F2 3818
3 TraesCS3A01G355700 chr1D 471296923 471303057 6134 True 1252.666667 3304 87.902333 1120 3940 3 chr1D.!!$R1 2820
4 TraesCS3A01G355700 chr1B 655101646 655104327 2681 True 1739.500000 3181 88.559000 1120 3940 2 chr1B.!!$R1 2820
5 TraesCS3A01G355700 chr1B 655271553 655272596 1043 False 1092.000000 1092 86.027000 2387 3407 1 chr1B.!!$F4 1020
6 TraesCS3A01G355700 chr7D 29534498 29537521 3023 True 1077.750000 2639 95.646250 1327 4397 4 chr7D.!!$R2 3070
7 TraesCS3A01G355700 chr7A 29780623 29781385 762 True 1227.000000 1227 95.806000 1327 2084 1 chr7A.!!$R1 757
8 TraesCS3A01G355700 chr7A 704893257 704893838 581 True 268.500000 289 83.771000 3187 3939 2 chr7A.!!$R3 752
9 TraesCS3A01G355700 chrUn 1368158 1368682 524 False 590.000000 590 86.852000 1246 1785 1 chrUn.!!$F1 539
10 TraesCS3A01G355700 chr1A 565571868 565572392 524 False 590.000000 590 86.852000 1246 1785 1 chr1A.!!$F3 539
11 TraesCS3A01G355700 chr2B 52100606 52103905 3299 False 265.000000 337 87.529000 1 459 2 chr2B.!!$F1 458

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
333 340 0.035739 GGCGACTACCCACAAAGGAA 59.964 55.0 0.0 0.0 41.22 3.36 F
387 394 0.039527 GGTAGGCAAACCGCAACAAG 60.040 55.0 0.0 0.0 45.17 3.16 F
554 561 0.106894 TCGTGTGGGTTGCATGTACA 59.893 50.0 0.0 0.0 0.00 2.90 F
1019 1035 0.173708 ACATCGCCGTTCTTCTCCTC 59.826 55.0 0.0 0.0 0.00 3.71 F
1020 1036 0.528684 CATCGCCGTTCTTCTCCTCC 60.529 60.0 0.0 0.0 0.00 4.30 F
1063 1079 0.602905 CAAAAACGCCTCCTCGTCCT 60.603 55.0 0.0 0.0 42.46 3.85 F
2820 5092 0.700564 AGGGAGGAATGAGCAAAGCA 59.299 50.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 2000 0.176910 GCAGCTTCAGGAGGGTAGAC 59.823 60.000 0.0 0.0 0.00 2.59 R
1911 3800 1.011968 CGAGGATTTTGGACGCACGA 61.012 55.000 0.0 0.0 0.00 4.35 R
2298 4570 3.255149 CAGTCTTCCTTGCTGCTTTCATT 59.745 43.478 0.0 0.0 0.00 2.57 R
2805 5077 1.954258 GCCTCTGCTTTGCTCATTCCT 60.954 52.381 0.0 0.0 33.53 3.36 R
2820 5092 3.241530 TTGCCACGGACAGCCTCT 61.242 61.111 0.0 0.0 0.00 3.69 R
3272 5602 9.571810 CAAACAAAAGCTGCTAATAATACATGA 57.428 29.630 0.9 0.0 0.00 3.07 R
3718 6076 0.103208 ATGGCTCGTTCTCATCCGTC 59.897 55.000 0.0 0.0 0.00 4.79 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
143 148 6.291385 CAAAAGTTGCAAAAATATCGTCAGC 58.709 36.000 0.00 0.00 0.00 4.26
145 150 5.119931 AGTTGCAAAAATATCGTCAGCAA 57.880 34.783 0.00 0.00 38.07 3.91
147 152 4.764679 TGCAAAAATATCGTCAGCAACT 57.235 36.364 0.00 0.00 0.00 3.16
165 170 0.740868 CTAGTGGCATGTCACGTGGG 60.741 60.000 23.89 11.76 42.10 4.61
187 194 2.346766 ACATGTTGTGTGAGCAAGGA 57.653 45.000 0.00 0.00 40.28 3.36
190 197 0.836606 TGTTGTGTGAGCAAGGAGGA 59.163 50.000 0.00 0.00 0.00 3.71
193 200 1.059098 TGTGTGAGCAAGGAGGACAT 58.941 50.000 0.00 0.00 0.00 3.06
202 209 2.173569 GCAAGGAGGACATATGGGTTCT 59.826 50.000 7.80 0.00 0.00 3.01
210 217 6.937465 GGAGGACATATGGGTTCTAAGAAATC 59.063 42.308 7.80 0.00 0.00 2.17
212 219 7.872138 AGGACATATGGGTTCTAAGAAATCAA 58.128 34.615 7.80 0.00 0.00 2.57
218 225 3.688185 GGGTTCTAAGAAATCAACCGGTC 59.312 47.826 8.04 0.00 39.46 4.79
219 226 4.320870 GGTTCTAAGAAATCAACCGGTCA 58.679 43.478 8.04 0.00 0.00 4.02
228 235 0.037590 TCAACCGGTCAAGGGGATTG 59.962 55.000 8.04 0.00 40.52 2.67
250 257 3.500680 GCGGAAGGACTTTTGTAACATGA 59.499 43.478 0.00 0.00 0.00 3.07
253 260 6.086222 CGGAAGGACTTTTGTAACATGAATG 58.914 40.000 0.00 0.00 0.00 2.67
280 287 6.017440 TGTTGCACAAATTAGAGGTAGAACAC 60.017 38.462 0.00 0.00 0.00 3.32
297 304 4.760204 AGAACACCATGTAAAACAGTAGCC 59.240 41.667 0.00 0.00 0.00 3.93
301 308 3.016736 CCATGTAAAACAGTAGCCTGGG 58.983 50.000 0.00 0.00 43.36 4.45
302 309 3.308117 CCATGTAAAACAGTAGCCTGGGA 60.308 47.826 0.00 0.00 43.36 4.37
304 311 4.015872 TGTAAAACAGTAGCCTGGGAAG 57.984 45.455 0.00 0.00 43.36 3.46
306 313 3.876309 AAAACAGTAGCCTGGGAAGAA 57.124 42.857 0.00 0.00 43.36 2.52
307 314 2.861147 AACAGTAGCCTGGGAAGAAC 57.139 50.000 0.00 0.00 43.36 3.01
308 315 1.729586 ACAGTAGCCTGGGAAGAACA 58.270 50.000 0.00 0.00 43.36 3.18
311 318 0.391263 GTAGCCTGGGAAGAACACGG 60.391 60.000 0.00 0.00 0.00 4.94
315 322 1.296715 CTGGGAAGAACACGGGAGG 59.703 63.158 0.00 0.00 0.00 4.30
316 323 2.046217 GGGAAGAACACGGGAGGC 60.046 66.667 0.00 0.00 0.00 4.70
317 324 2.434359 GGAAGAACACGGGAGGCG 60.434 66.667 0.00 0.00 0.00 5.52
318 325 2.654877 GAAGAACACGGGAGGCGA 59.345 61.111 0.00 0.00 0.00 5.54
319 326 1.737008 GAAGAACACGGGAGGCGAC 60.737 63.158 0.00 0.00 0.00 5.19
321 328 0.896940 AAGAACACGGGAGGCGACTA 60.897 55.000 0.00 0.00 44.43 2.59
322 329 1.153881 GAACACGGGAGGCGACTAC 60.154 63.158 0.00 0.00 44.43 2.73
328 335 3.384348 GGAGGCGACTACCCACAA 58.616 61.111 0.00 0.00 44.43 3.33
329 336 1.675219 GGAGGCGACTACCCACAAA 59.325 57.895 0.00 0.00 44.43 2.83
332 339 0.834687 AGGCGACTACCCACAAAGGA 60.835 55.000 0.00 0.00 40.61 3.36
333 340 0.035739 GGCGACTACCCACAAAGGAA 59.964 55.000 0.00 0.00 41.22 3.36
334 341 1.154197 GCGACTACCCACAAAGGAAC 58.846 55.000 0.00 0.00 41.22 3.62
335 342 1.804601 CGACTACCCACAAAGGAACC 58.195 55.000 0.00 0.00 41.22 3.62
336 343 1.071071 CGACTACCCACAAAGGAACCA 59.929 52.381 0.00 0.00 41.22 3.67
337 344 2.779506 GACTACCCACAAAGGAACCAG 58.220 52.381 0.00 0.00 41.22 4.00
340 347 2.586648 ACCCACAAAGGAACCAGATC 57.413 50.000 0.00 0.00 41.22 2.75
341 348 2.065799 ACCCACAAAGGAACCAGATCT 58.934 47.619 0.00 0.00 41.22 2.75
342 349 3.256704 ACCCACAAAGGAACCAGATCTA 58.743 45.455 0.00 0.00 41.22 1.98
343 350 3.264450 ACCCACAAAGGAACCAGATCTAG 59.736 47.826 0.00 0.00 41.22 2.43
344 351 3.519510 CCCACAAAGGAACCAGATCTAGA 59.480 47.826 0.00 0.00 41.22 2.43
345 352 4.164988 CCCACAAAGGAACCAGATCTAGAT 59.835 45.833 4.47 4.47 41.22 1.98
346 353 5.363939 CCACAAAGGAACCAGATCTAGATC 58.636 45.833 22.92 22.92 41.22 2.75
350 357 7.708752 CACAAAGGAACCAGATCTAGATCTTAC 59.291 40.741 29.03 17.62 45.31 2.34
353 360 7.354751 AGGAACCAGATCTAGATCTTACAAC 57.645 40.000 29.03 19.50 45.31 3.32
354 361 6.325286 AGGAACCAGATCTAGATCTTACAACC 59.675 42.308 29.03 24.79 45.31 3.77
355 362 6.325286 GGAACCAGATCTAGATCTTACAACCT 59.675 42.308 29.03 11.84 45.31 3.50
356 363 7.506261 GGAACCAGATCTAGATCTTACAACCTA 59.494 40.741 29.03 0.00 45.31 3.08
357 364 7.826918 ACCAGATCTAGATCTTACAACCTAC 57.173 40.000 29.03 2.31 45.31 3.18
358 365 6.487331 ACCAGATCTAGATCTTACAACCTACG 59.513 42.308 29.03 15.19 45.31 3.51
359 366 6.711194 CCAGATCTAGATCTTACAACCTACGA 59.289 42.308 29.03 0.00 45.31 3.43
361 368 7.442969 CAGATCTAGATCTTACAACCTACGAGT 59.557 40.741 29.03 3.63 45.31 4.18
362 369 7.994334 AGATCTAGATCTTACAACCTACGAGTT 59.006 37.037 26.53 1.84 45.31 3.01
363 370 8.071368 GATCTAGATCTTACAACCTACGAGTTG 58.929 40.741 23.06 13.50 42.09 3.16
369 376 0.511221 CAACCTACGAGTTGTTGCGG 59.489 55.000 8.79 0.00 41.80 5.69
370 377 0.105408 AACCTACGAGTTGTTGCGGT 59.895 50.000 0.00 0.00 0.00 5.68
371 378 0.961019 ACCTACGAGTTGTTGCGGTA 59.039 50.000 0.00 0.00 0.00 4.02
372 379 1.068055 ACCTACGAGTTGTTGCGGTAG 60.068 52.381 0.00 0.00 0.00 3.18
373 380 1.625616 CTACGAGTTGTTGCGGTAGG 58.374 55.000 0.00 0.00 0.00 3.18
374 381 0.388907 TACGAGTTGTTGCGGTAGGC 60.389 55.000 0.00 0.00 43.96 3.93
385 392 3.752704 GGTAGGCAAACCGCAACA 58.247 55.556 0.00 0.00 45.17 3.33
386 393 2.034607 GGTAGGCAAACCGCAACAA 58.965 52.632 0.00 0.00 45.17 2.83
387 394 0.039527 GGTAGGCAAACCGCAACAAG 60.040 55.000 0.00 0.00 45.17 3.16
388 395 0.663269 GTAGGCAAACCGCAACAAGC 60.663 55.000 0.00 0.00 45.17 4.01
397 404 4.216963 GCAACAAGCGCTCAGTTG 57.783 55.556 33.74 33.74 44.01 3.16
398 405 4.216963 CAACAAGCGCTCAGTTGC 57.783 55.556 30.22 0.00 36.59 4.17
399 406 1.356270 CAACAAGCGCTCAGTTGCA 59.644 52.632 30.22 0.00 36.59 4.08
400 407 0.248580 CAACAAGCGCTCAGTTGCAA 60.249 50.000 30.22 0.00 36.59 4.08
401 408 0.455410 AACAAGCGCTCAGTTGCAAA 59.545 45.000 22.56 0.00 0.00 3.68
402 409 0.455410 ACAAGCGCTCAGTTGCAAAA 59.545 45.000 12.06 0.00 0.00 2.44
403 410 0.848305 CAAGCGCTCAGTTGCAAAAC 59.152 50.000 12.06 0.00 0.00 2.43
404 411 0.740737 AAGCGCTCAGTTGCAAAACT 59.259 45.000 12.06 0.00 0.00 2.66
417 424 8.665175 CAGTTGCAAAACTGTAAGAGATAATG 57.335 34.615 9.92 0.00 43.80 1.90
418 425 8.292448 CAGTTGCAAAACTGTAAGAGATAATGT 58.708 33.333 9.92 0.00 43.80 2.71
419 426 8.850156 AGTTGCAAAACTGTAAGAGATAATGTT 58.150 29.630 0.00 0.00 37.43 2.71
422 429 8.946085 TGCAAAACTGTAAGAGATAATGTTAGG 58.054 33.333 0.00 0.00 37.43 2.69
423 430 8.947115 GCAAAACTGTAAGAGATAATGTTAGGT 58.053 33.333 0.00 0.00 37.43 3.08
426 433 9.877178 AAACTGTAAGAGATAATGTTAGGTGAG 57.123 33.333 0.00 0.00 37.43 3.51
427 434 7.493367 ACTGTAAGAGATAATGTTAGGTGAGC 58.507 38.462 0.00 0.00 37.43 4.26
428 435 6.817184 TGTAAGAGATAATGTTAGGTGAGCC 58.183 40.000 0.00 0.00 0.00 4.70
429 436 4.965200 AGAGATAATGTTAGGTGAGCCC 57.035 45.455 0.00 0.00 34.57 5.19
430 437 4.298626 AGAGATAATGTTAGGTGAGCCCA 58.701 43.478 0.00 0.00 34.66 5.36
431 438 4.101741 AGAGATAATGTTAGGTGAGCCCAC 59.898 45.833 0.00 0.00 42.46 4.61
432 439 2.684001 TAATGTTAGGTGAGCCCACG 57.316 50.000 0.00 0.00 44.09 4.94
433 440 0.676782 AATGTTAGGTGAGCCCACGC 60.677 55.000 0.00 0.00 44.09 5.34
434 441 2.813908 GTTAGGTGAGCCCACGCG 60.814 66.667 3.53 3.53 44.09 6.01
435 442 4.077184 TTAGGTGAGCCCACGCGG 62.077 66.667 12.47 0.00 44.09 6.46
452 459 4.994201 GGACACGCGTCGCACAGA 62.994 66.667 18.75 0.00 43.61 3.41
453 460 3.753539 GACACGCGTCGCACAGAC 61.754 66.667 18.75 2.79 46.16 3.51
464 471 4.794439 CACAGACGATGCGGCGGA 62.794 66.667 9.78 6.17 41.28 5.54
465 472 3.838271 ACAGACGATGCGGCGGAT 61.838 61.111 15.43 15.43 41.28 4.18
466 473 3.333189 CAGACGATGCGGCGGATG 61.333 66.667 21.21 13.56 41.28 3.51
467 474 3.838271 AGACGATGCGGCGGATGT 61.838 61.111 21.21 16.80 41.28 3.06
468 475 3.330853 GACGATGCGGCGGATGTC 61.331 66.667 21.21 20.87 35.12 3.06
469 476 4.891727 ACGATGCGGCGGATGTCC 62.892 66.667 21.21 3.21 35.12 4.02
479 486 3.330853 GGATGTCCGCGTGCGATC 61.331 66.667 16.91 10.56 42.83 3.69
480 487 3.330853 GATGTCCGCGTGCGATCC 61.331 66.667 16.91 3.43 42.83 3.36
481 488 4.141965 ATGTCCGCGTGCGATCCA 62.142 61.111 16.91 9.17 42.83 3.41
489 496 4.451150 GTGCGATCCACCGGCTGA 62.451 66.667 0.00 0.00 38.55 4.26
490 497 3.700970 TGCGATCCACCGGCTGAA 61.701 61.111 0.00 0.00 0.00 3.02
491 498 3.195698 GCGATCCACCGGCTGAAC 61.196 66.667 0.00 0.00 0.00 3.18
492 499 2.511600 CGATCCACCGGCTGAACC 60.512 66.667 0.00 0.00 0.00 3.62
493 500 2.990479 GATCCACCGGCTGAACCT 59.010 61.111 0.00 0.00 35.61 3.50
494 501 1.672854 CGATCCACCGGCTGAACCTA 61.673 60.000 0.00 0.00 35.61 3.08
495 502 0.539986 GATCCACCGGCTGAACCTAA 59.460 55.000 0.00 0.00 35.61 2.69
496 503 0.541863 ATCCACCGGCTGAACCTAAG 59.458 55.000 0.00 0.00 35.61 2.18
497 504 1.745489 CCACCGGCTGAACCTAAGC 60.745 63.158 0.00 0.00 40.06 3.09
498 505 1.003839 CACCGGCTGAACCTAAGCA 60.004 57.895 0.00 0.00 42.69 3.91
499 506 0.392998 CACCGGCTGAACCTAAGCAT 60.393 55.000 0.00 0.00 42.69 3.79
500 507 0.328258 ACCGGCTGAACCTAAGCATT 59.672 50.000 0.00 0.00 42.69 3.56
501 508 1.271926 ACCGGCTGAACCTAAGCATTT 60.272 47.619 0.00 0.00 42.69 2.32
502 509 1.818674 CCGGCTGAACCTAAGCATTTT 59.181 47.619 0.00 0.00 42.69 1.82
503 510 2.231235 CCGGCTGAACCTAAGCATTTTT 59.769 45.455 0.00 0.00 42.69 1.94
504 511 3.501950 CGGCTGAACCTAAGCATTTTTC 58.498 45.455 0.00 0.00 42.69 2.29
505 512 3.057596 CGGCTGAACCTAAGCATTTTTCA 60.058 43.478 0.00 0.00 42.69 2.69
506 513 4.558496 CGGCTGAACCTAAGCATTTTTCAA 60.558 41.667 0.00 0.00 42.69 2.69
507 514 5.482006 GGCTGAACCTAAGCATTTTTCAAT 58.518 37.500 0.00 0.00 42.69 2.57
508 515 5.934043 GGCTGAACCTAAGCATTTTTCAATT 59.066 36.000 0.00 0.00 42.69 2.32
509 516 7.096551 GGCTGAACCTAAGCATTTTTCAATTA 58.903 34.615 0.00 0.00 42.69 1.40
510 517 7.063426 GGCTGAACCTAAGCATTTTTCAATTAC 59.937 37.037 0.00 0.00 42.69 1.89
511 518 7.598493 GCTGAACCTAAGCATTTTTCAATTACA 59.402 33.333 0.00 0.00 40.52 2.41
512 519 9.474920 CTGAACCTAAGCATTTTTCAATTACAA 57.525 29.630 0.00 0.00 0.00 2.41
513 520 9.823647 TGAACCTAAGCATTTTTCAATTACAAA 57.176 25.926 0.00 0.00 0.00 2.83
544 551 8.974060 ATTAATTCTAACAATATCGTGTGGGT 57.026 30.769 0.00 0.00 0.00 4.51
545 552 8.795842 TTAATTCTAACAATATCGTGTGGGTT 57.204 30.769 0.00 0.00 0.00 4.11
546 553 6.677781 ATTCTAACAATATCGTGTGGGTTG 57.322 37.500 0.00 0.00 0.00 3.77
547 554 3.936453 TCTAACAATATCGTGTGGGTTGC 59.064 43.478 0.00 0.00 0.00 4.17
548 555 2.192664 ACAATATCGTGTGGGTTGCA 57.807 45.000 0.00 0.00 0.00 4.08
549 556 2.722094 ACAATATCGTGTGGGTTGCAT 58.278 42.857 0.00 0.00 0.00 3.96
550 557 2.423185 ACAATATCGTGTGGGTTGCATG 59.577 45.455 0.00 0.00 0.00 4.06
551 558 2.418368 ATATCGTGTGGGTTGCATGT 57.582 45.000 0.00 0.00 0.00 3.21
552 559 3.552132 ATATCGTGTGGGTTGCATGTA 57.448 42.857 0.00 0.00 0.00 2.29
553 560 1.448985 ATCGTGTGGGTTGCATGTAC 58.551 50.000 0.00 0.00 0.00 2.90
554 561 0.106894 TCGTGTGGGTTGCATGTACA 59.893 50.000 0.00 0.00 0.00 2.90
555 562 1.164411 CGTGTGGGTTGCATGTACAT 58.836 50.000 1.41 1.41 0.00 2.29
556 563 1.135717 CGTGTGGGTTGCATGTACATG 60.136 52.381 28.07 28.07 41.60 3.21
571 578 6.662616 CATGTACATGCTTGCTACTATTTCC 58.337 40.000 22.27 0.00 31.39 3.13
572 579 4.808895 TGTACATGCTTGCTACTATTTCCG 59.191 41.667 0.00 0.00 0.00 4.30
573 580 4.137116 ACATGCTTGCTACTATTTCCGA 57.863 40.909 0.00 0.00 0.00 4.55
574 581 4.708177 ACATGCTTGCTACTATTTCCGAT 58.292 39.130 0.00 0.00 0.00 4.18
575 582 5.126067 ACATGCTTGCTACTATTTCCGATT 58.874 37.500 0.00 0.00 0.00 3.34
576 583 6.288294 ACATGCTTGCTACTATTTCCGATTA 58.712 36.000 0.00 0.00 0.00 1.75
577 584 6.936900 ACATGCTTGCTACTATTTCCGATTAT 59.063 34.615 0.00 0.00 0.00 1.28
578 585 8.094548 ACATGCTTGCTACTATTTCCGATTATA 58.905 33.333 0.00 0.00 0.00 0.98
615 622 7.785033 TGAATTCATAACTGACTCAGCAGATA 58.215 34.615 3.38 0.00 39.20 1.98
616 623 8.427276 TGAATTCATAACTGACTCAGCAGATAT 58.573 33.333 3.38 0.00 39.20 1.63
617 624 9.270640 GAATTCATAACTGACTCAGCAGATATT 57.729 33.333 5.92 0.36 39.20 1.28
717 724 1.281960 CCGCGGTCGATTCGAGTAT 59.718 57.895 19.50 0.00 36.23 2.12
718 725 0.725118 CCGCGGTCGATTCGAGTATC 60.725 60.000 19.50 0.00 36.23 2.24
741 748 1.459592 GTATTCGTGTGCATATCGGCC 59.540 52.381 0.00 0.00 0.00 6.13
743 750 1.087202 TTCGTGTGCATATCGGCCAC 61.087 55.000 2.24 0.00 34.04 5.01
909 922 3.232662 GAGCTCTAACCCTAACCCTAGG 58.767 54.545 6.43 0.06 44.10 3.02
1019 1035 0.173708 ACATCGCCGTTCTTCTCCTC 59.826 55.000 0.00 0.00 0.00 3.71
1020 1036 0.528684 CATCGCCGTTCTTCTCCTCC 60.529 60.000 0.00 0.00 0.00 4.30
1021 1037 0.684805 ATCGCCGTTCTTCTCCTCCT 60.685 55.000 0.00 0.00 0.00 3.69
1063 1079 0.602905 CAAAAACGCCTCCTCGTCCT 60.603 55.000 0.00 0.00 42.46 3.85
1413 1560 1.884464 GAAGCGCGAGATGATGGCA 60.884 57.895 12.10 0.00 31.94 4.92
1416 1563 3.344215 CGCGAGATGATGGCAGCC 61.344 66.667 3.66 3.66 31.94 4.85
1911 3800 4.747529 TCTGATGCTGCACGCGCT 62.748 61.111 5.73 0.00 43.27 5.92
2136 4408 5.316987 CAGTGGAAGAAGACCCTTATTGTT 58.683 41.667 0.00 0.00 0.00 2.83
2203 4475 6.741992 TCATTCATTTGCACGATAAGAGTT 57.258 33.333 0.00 0.00 0.00 3.01
2298 4570 6.321181 AGAAGTTTGAGGTGTATGAAAAGCAA 59.679 34.615 0.00 0.00 0.00 3.91
2442 4714 2.279741 GATGATAACGTGAAGCCAGCA 58.720 47.619 0.00 0.00 0.00 4.41
2820 5092 0.700564 AGGGAGGAATGAGCAAAGCA 59.299 50.000 0.00 0.00 0.00 3.91
3180 5497 4.521146 ACAAGGATGAACTAATGGCAGAG 58.479 43.478 0.00 0.00 0.00 3.35
3272 5602 3.823304 GCTGGTTTGTTCTCCTGAAATCT 59.177 43.478 0.00 0.00 33.52 2.40
3378 5730 8.087750 CCAAGATGAGTTATTTGTTTGCCTTTA 58.912 33.333 0.00 0.00 0.00 1.85
3379 5731 9.474920 CAAGATGAGTTATTTGTTTGCCTTTAA 57.525 29.630 0.00 0.00 0.00 1.52
3431 5783 5.517054 GGTGTTTCTTTTGTACGATTTTGCA 59.483 36.000 0.00 0.00 0.00 4.08
3460 5812 2.544267 GTCGTACTAATGCATCTTGGGC 59.456 50.000 0.00 0.00 0.00 5.36
3467 5819 2.185004 ATGCATCTTGGGCGGTATAC 57.815 50.000 0.00 0.00 0.00 1.47
3468 5820 1.128200 TGCATCTTGGGCGGTATACT 58.872 50.000 2.25 0.00 0.00 2.12
3470 5822 2.143925 GCATCTTGGGCGGTATACTTC 58.856 52.381 2.25 0.00 0.00 3.01
3471 5823 2.767505 CATCTTGGGCGGTATACTTCC 58.232 52.381 2.25 4.30 0.00 3.46
3473 5825 2.404559 TCTTGGGCGGTATACTTCCAT 58.595 47.619 2.25 0.00 0.00 3.41
3480 5836 5.486063 TGGGCGGTATACTTCCATATATTGT 59.514 40.000 2.25 0.00 0.00 2.71
3508 5864 9.865321 TTTTCTCGTGTTAACTTGCTATATACT 57.135 29.630 7.22 0.00 0.00 2.12
3509 5865 9.512435 TTTCTCGTGTTAACTTGCTATATACTC 57.488 33.333 7.22 0.00 0.00 2.59
3510 5866 7.646314 TCTCGTGTTAACTTGCTATATACTCC 58.354 38.462 7.22 0.00 0.00 3.85
3511 5867 6.742109 TCGTGTTAACTTGCTATATACTCCC 58.258 40.000 7.22 0.00 0.00 4.30
3512 5868 6.548622 TCGTGTTAACTTGCTATATACTCCCT 59.451 38.462 7.22 0.00 0.00 4.20
3513 5869 6.862090 CGTGTTAACTTGCTATATACTCCCTC 59.138 42.308 7.22 0.00 0.00 4.30
3514 5870 7.153315 GTGTTAACTTGCTATATACTCCCTCC 58.847 42.308 7.22 0.00 0.00 4.30
3515 5871 6.015688 TGTTAACTTGCTATATACTCCCTCCG 60.016 42.308 7.22 0.00 0.00 4.63
3516 5872 4.115398 ACTTGCTATATACTCCCTCCGT 57.885 45.455 0.00 0.00 0.00 4.69
3517 5873 4.481072 ACTTGCTATATACTCCCTCCGTT 58.519 43.478 0.00 0.00 0.00 4.44
3518 5874 4.523558 ACTTGCTATATACTCCCTCCGTTC 59.476 45.833 0.00 0.00 0.00 3.95
3519 5875 3.428532 TGCTATATACTCCCTCCGTTCC 58.571 50.000 0.00 0.00 0.00 3.62
3520 5876 2.759535 GCTATATACTCCCTCCGTTCCC 59.240 54.545 0.00 0.00 0.00 3.97
3521 5877 3.563915 GCTATATACTCCCTCCGTTCCCT 60.564 52.174 0.00 0.00 0.00 4.20
3522 5878 3.632420 ATATACTCCCTCCGTTCCCTT 57.368 47.619 0.00 0.00 0.00 3.95
3523 5879 4.754411 ATATACTCCCTCCGTTCCCTTA 57.246 45.455 0.00 0.00 0.00 2.69
3524 5880 2.925966 TACTCCCTCCGTTCCCTTAA 57.074 50.000 0.00 0.00 0.00 1.85
3525 5881 2.034436 ACTCCCTCCGTTCCCTTAAA 57.966 50.000 0.00 0.00 0.00 1.52
3526 5882 2.341695 ACTCCCTCCGTTCCCTTAAAA 58.658 47.619 0.00 0.00 0.00 1.52
3527 5883 2.712627 ACTCCCTCCGTTCCCTTAAAAA 59.287 45.455 0.00 0.00 0.00 1.94
3553 5909 9.599866 AAGACCTTTTACCTTTTTCTTGATTTG 57.400 29.630 0.00 0.00 0.00 2.32
3554 5910 8.758829 AGACCTTTTACCTTTTTCTTGATTTGT 58.241 29.630 0.00 0.00 0.00 2.83
3562 5918 8.409358 ACCTTTTTCTTGATTTGTATGTAGCT 57.591 30.769 0.00 0.00 0.00 3.32
3563 5919 9.515226 ACCTTTTTCTTGATTTGTATGTAGCTA 57.485 29.630 0.00 0.00 0.00 3.32
3564 5920 9.994432 CCTTTTTCTTGATTTGTATGTAGCTAG 57.006 33.333 0.00 0.00 0.00 3.42
3567 5923 9.719355 TTTTCTTGATTTGTATGTAGCTAGACA 57.281 29.630 0.00 0.00 0.00 3.41
3568 5924 9.719355 TTTCTTGATTTGTATGTAGCTAGACAA 57.281 29.630 10.35 10.35 31.83 3.18
3569 5925 9.719355 TTCTTGATTTGTATGTAGCTAGACAAA 57.281 29.630 21.68 21.68 43.69 2.83
3648 6004 8.148999 AGCTAAAAGGTCTTATATTAGGGAACG 58.851 37.037 0.00 0.00 0.00 3.95
3649 6005 7.387122 GCTAAAAGGTCTTATATTAGGGAACGG 59.613 40.741 0.00 0.00 0.00 4.44
3650 6006 7.441903 AAAAGGTCTTATATTAGGGAACGGA 57.558 36.000 0.00 0.00 0.00 4.69
3651 6007 6.667558 AAGGTCTTATATTAGGGAACGGAG 57.332 41.667 0.00 0.00 0.00 4.63
3652 6008 5.085219 AGGTCTTATATTAGGGAACGGAGG 58.915 45.833 0.00 0.00 0.00 4.30
3653 6009 4.837298 GGTCTTATATTAGGGAACGGAGGT 59.163 45.833 0.00 0.00 0.00 3.85
3654 6010 6.012745 GGTCTTATATTAGGGAACGGAGGTA 58.987 44.000 0.00 0.00 0.00 3.08
3655 6011 6.152492 GGTCTTATATTAGGGAACGGAGGTAG 59.848 46.154 0.00 0.00 0.00 3.18
3718 6076 7.534085 TCTAACTATTGAAATGCTTGGTACG 57.466 36.000 0.00 0.00 0.00 3.67
3721 6079 3.740044 ATTGAAATGCTTGGTACGACG 57.260 42.857 0.00 0.00 0.00 5.12
3751 6109 2.287915 CGAGCCATTATTACAGGTGTGC 59.712 50.000 0.00 0.00 0.00 4.57
3980 6343 5.241506 CAGAGAAGTGGGTTAGCAAAATTGA 59.758 40.000 0.00 0.00 0.00 2.57
4045 6546 9.596308 TCAGTAGACCTATAATTGTTATGCCTA 57.404 33.333 0.00 0.00 0.00 3.93
4048 6549 9.991906 GTAGACCTATAATTGTTATGCCTAACA 57.008 33.333 10.15 10.15 44.21 2.41
4232 8733 8.503458 AACAAATCTGTAGATGATCTTTCCTG 57.497 34.615 0.00 0.00 33.45 3.86
4386 9781 2.290641 CCGTAGCTCTTTTGCACTTGTT 59.709 45.455 0.00 0.00 34.99 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 62 4.410492 AGCTATGTTGCAAAAAGACGAG 57.590 40.909 0.00 0.00 34.99 4.18
92 96 2.621055 TCGCCAGTGTTGCATTAGTTTT 59.379 40.909 0.00 0.00 0.00 2.43
98 102 0.961019 AACATCGCCAGTGTTGCATT 59.039 45.000 0.00 0.00 38.31 3.56
107 111 1.788308 CAACTTTTGCAACATCGCCAG 59.212 47.619 0.00 0.00 0.00 4.85
143 148 1.460743 CACGTGACATGCCACTAGTTG 59.539 52.381 10.90 0.00 35.02 3.16
145 150 0.037326 CCACGTGACATGCCACTAGT 60.037 55.000 19.30 0.00 35.02 2.57
146 151 0.740868 CCCACGTGACATGCCACTAG 60.741 60.000 19.30 2.50 35.02 2.57
147 152 1.188871 TCCCACGTGACATGCCACTA 61.189 55.000 19.30 0.00 35.02 2.74
178 185 1.770658 CCCATATGTCCTCCTTGCTCA 59.229 52.381 1.24 0.00 0.00 4.26
183 190 5.538877 TCTTAGAACCCATATGTCCTCCTT 58.461 41.667 1.24 0.00 0.00 3.36
187 194 7.451731 TGATTTCTTAGAACCCATATGTCCT 57.548 36.000 1.24 0.00 0.00 3.85
190 197 6.542370 CGGTTGATTTCTTAGAACCCATATGT 59.458 38.462 1.24 0.00 35.40 2.29
193 200 5.045432 ACCGGTTGATTTCTTAGAACCCATA 60.045 40.000 0.00 0.00 35.40 2.74
202 209 3.560453 CCCCTTGACCGGTTGATTTCTTA 60.560 47.826 9.42 0.00 0.00 2.10
210 217 1.595093 GCAATCCCCTTGACCGGTTG 61.595 60.000 9.42 0.00 36.97 3.77
212 219 2.355115 GCAATCCCCTTGACCGGT 59.645 61.111 6.92 6.92 36.97 5.28
218 225 1.032114 GTCCTTCCGCAATCCCCTTG 61.032 60.000 0.00 0.00 37.94 3.61
219 226 1.208165 AGTCCTTCCGCAATCCCCTT 61.208 55.000 0.00 0.00 0.00 3.95
228 235 3.500680 TCATGTTACAAAAGTCCTTCCGC 59.499 43.478 0.00 0.00 0.00 5.54
280 287 3.016736 CCCAGGCTACTGTTTTACATGG 58.983 50.000 0.00 0.00 43.36 3.66
282 289 4.288626 TCTTCCCAGGCTACTGTTTTACAT 59.711 41.667 0.00 0.00 43.36 2.29
287 294 2.441750 TGTTCTTCCCAGGCTACTGTTT 59.558 45.455 0.00 0.00 43.36 2.83
291 298 0.608640 CGTGTTCTTCCCAGGCTACT 59.391 55.000 0.00 0.00 0.00 2.57
293 300 1.550130 CCCGTGTTCTTCCCAGGCTA 61.550 60.000 0.00 0.00 0.00 3.93
297 304 1.296715 CCTCCCGTGTTCTTCCCAG 59.703 63.158 0.00 0.00 0.00 4.45
301 308 1.737008 GTCGCCTCCCGTGTTCTTC 60.737 63.158 0.00 0.00 38.35 2.87
302 309 0.896940 TAGTCGCCTCCCGTGTTCTT 60.897 55.000 0.00 0.00 38.35 2.52
304 311 1.153881 GTAGTCGCCTCCCGTGTTC 60.154 63.158 0.00 0.00 38.35 3.18
306 313 3.066814 GGTAGTCGCCTCCCGTGT 61.067 66.667 0.00 0.00 38.35 4.49
307 314 3.834799 GGGTAGTCGCCTCCCGTG 61.835 72.222 0.00 0.00 38.35 4.94
308 315 4.371417 TGGGTAGTCGCCTCCCGT 62.371 66.667 0.00 0.00 43.75 5.28
311 318 0.391263 CTTTGTGGGTAGTCGCCTCC 60.391 60.000 0.00 0.00 0.00 4.30
313 320 0.834687 TCCTTTGTGGGTAGTCGCCT 60.835 55.000 0.00 0.00 36.20 5.52
314 321 0.035739 TTCCTTTGTGGGTAGTCGCC 59.964 55.000 0.00 0.00 36.20 5.54
315 322 1.154197 GTTCCTTTGTGGGTAGTCGC 58.846 55.000 0.00 0.00 36.20 5.19
316 323 1.071071 TGGTTCCTTTGTGGGTAGTCG 59.929 52.381 0.00 0.00 36.20 4.18
317 324 2.370849 TCTGGTTCCTTTGTGGGTAGTC 59.629 50.000 0.00 0.00 36.20 2.59
318 325 2.414612 TCTGGTTCCTTTGTGGGTAGT 58.585 47.619 0.00 0.00 36.20 2.73
319 326 3.264450 AGATCTGGTTCCTTTGTGGGTAG 59.736 47.826 0.00 0.00 36.20 3.18
320 327 3.256704 AGATCTGGTTCCTTTGTGGGTA 58.743 45.455 0.00 0.00 36.20 3.69
321 328 2.065799 AGATCTGGTTCCTTTGTGGGT 58.934 47.619 0.00 0.00 36.20 4.51
322 329 2.887151 AGATCTGGTTCCTTTGTGGG 57.113 50.000 0.00 0.00 36.20 4.61
323 330 4.826274 TCTAGATCTGGTTCCTTTGTGG 57.174 45.455 5.18 0.00 37.10 4.17
324 331 6.232581 AGATCTAGATCTGGTTCCTTTGTG 57.767 41.667 30.29 0.00 45.77 3.33
326 333 7.786030 TGTAAGATCTAGATCTGGTTCCTTTG 58.214 38.462 31.23 0.00 46.75 2.77
327 334 7.979786 TGTAAGATCTAGATCTGGTTCCTTT 57.020 36.000 31.23 17.52 46.75 3.11
328 335 7.147637 GGTTGTAAGATCTAGATCTGGTTCCTT 60.148 40.741 31.23 18.16 46.75 3.36
329 336 6.325286 GGTTGTAAGATCTAGATCTGGTTCCT 59.675 42.308 31.23 18.80 46.75 3.36
332 339 7.013464 CGTAGGTTGTAAGATCTAGATCTGGTT 59.987 40.741 31.23 20.08 46.75 3.67
333 340 6.487331 CGTAGGTTGTAAGATCTAGATCTGGT 59.513 42.308 31.23 20.73 46.75 4.00
334 341 6.711194 TCGTAGGTTGTAAGATCTAGATCTGG 59.289 42.308 31.23 1.65 46.75 3.86
335 342 7.442969 ACTCGTAGGTTGTAAGATCTAGATCTG 59.557 40.741 31.23 17.75 46.75 2.90
337 344 7.733402 ACTCGTAGGTTGTAAGATCTAGATC 57.267 40.000 22.92 22.92 38.09 2.75
353 360 1.625616 CTACCGCAACAACTCGTAGG 58.374 55.000 0.00 0.00 0.00 3.18
354 361 1.625616 CCTACCGCAACAACTCGTAG 58.374 55.000 0.00 0.00 0.00 3.51
355 362 0.388907 GCCTACCGCAACAACTCGTA 60.389 55.000 0.00 0.00 37.47 3.43
356 363 1.666872 GCCTACCGCAACAACTCGT 60.667 57.895 0.00 0.00 37.47 4.18
357 364 3.165498 GCCTACCGCAACAACTCG 58.835 61.111 0.00 0.00 37.47 4.18
368 375 0.039527 CTTGTTGCGGTTTGCCTACC 60.040 55.000 0.00 0.00 45.60 3.18
369 376 0.663269 GCTTGTTGCGGTTTGCCTAC 60.663 55.000 0.00 0.00 45.60 3.18
370 377 1.657556 GCTTGTTGCGGTTTGCCTA 59.342 52.632 0.00 0.00 45.60 3.93
371 378 2.417097 GCTTGTTGCGGTTTGCCT 59.583 55.556 0.00 0.00 45.60 4.75
380 387 4.216963 CAACTGAGCGCTTGTTGC 57.783 55.556 30.06 13.61 35.39 4.17
381 388 0.248580 TTGCAACTGAGCGCTTGTTG 60.249 50.000 33.43 33.43 42.55 3.33
382 389 0.455410 TTTGCAACTGAGCGCTTGTT 59.545 45.000 13.26 17.29 37.31 2.83
383 390 0.455410 TTTTGCAACTGAGCGCTTGT 59.545 45.000 13.26 11.60 37.31 3.16
384 391 0.848305 GTTTTGCAACTGAGCGCTTG 59.152 50.000 13.26 10.85 37.31 4.01
385 392 0.740737 AGTTTTGCAACTGAGCGCTT 59.259 45.000 13.26 0.00 42.05 4.68
386 393 2.408333 AGTTTTGCAACTGAGCGCT 58.592 47.368 11.27 11.27 42.05 5.92
393 400 8.396272 ACATTATCTCTTACAGTTTTGCAACT 57.604 30.769 0.00 0.00 44.72 3.16
396 403 8.946085 CCTAACATTATCTCTTACAGTTTTGCA 58.054 33.333 0.00 0.00 0.00 4.08
397 404 8.947115 ACCTAACATTATCTCTTACAGTTTTGC 58.053 33.333 0.00 0.00 0.00 3.68
400 407 9.877178 CTCACCTAACATTATCTCTTACAGTTT 57.123 33.333 0.00 0.00 0.00 2.66
401 408 7.982354 GCTCACCTAACATTATCTCTTACAGTT 59.018 37.037 0.00 0.00 0.00 3.16
402 409 7.418025 GGCTCACCTAACATTATCTCTTACAGT 60.418 40.741 0.00 0.00 0.00 3.55
403 410 6.926272 GGCTCACCTAACATTATCTCTTACAG 59.074 42.308 0.00 0.00 0.00 2.74
404 411 6.183360 GGGCTCACCTAACATTATCTCTTACA 60.183 42.308 0.00 0.00 35.85 2.41
405 412 6.183360 TGGGCTCACCTAACATTATCTCTTAC 60.183 42.308 0.00 0.00 41.11 2.34
406 413 5.903010 TGGGCTCACCTAACATTATCTCTTA 59.097 40.000 0.00 0.00 41.11 2.10
407 414 4.721776 TGGGCTCACCTAACATTATCTCTT 59.278 41.667 0.00 0.00 41.11 2.85
408 415 4.101741 GTGGGCTCACCTAACATTATCTCT 59.898 45.833 5.01 0.00 41.11 3.10
409 416 4.381411 GTGGGCTCACCTAACATTATCTC 58.619 47.826 5.01 0.00 41.11 2.75
410 417 3.181465 CGTGGGCTCACCTAACATTATCT 60.181 47.826 12.09 0.00 40.65 1.98
411 418 3.131396 CGTGGGCTCACCTAACATTATC 58.869 50.000 12.09 0.00 40.65 1.75
412 419 2.745152 GCGTGGGCTCACCTAACATTAT 60.745 50.000 12.09 0.00 40.65 1.28
413 420 1.406341 GCGTGGGCTCACCTAACATTA 60.406 52.381 12.09 0.00 40.65 1.90
414 421 0.676782 GCGTGGGCTCACCTAACATT 60.677 55.000 12.09 0.00 40.65 2.71
415 422 1.078426 GCGTGGGCTCACCTAACAT 60.078 57.895 12.09 0.00 40.65 2.71
416 423 2.345991 GCGTGGGCTCACCTAACA 59.654 61.111 12.09 0.00 40.65 2.41
417 424 2.813908 CGCGTGGGCTCACCTAAC 60.814 66.667 12.09 0.00 40.65 2.34
418 425 4.077184 CCGCGTGGGCTCACCTAA 62.077 66.667 12.09 0.00 40.65 2.69
435 442 4.994201 TCTGTGCGACGCGTGTCC 62.994 66.667 20.70 15.52 42.37 4.02
436 443 3.753539 GTCTGTGCGACGCGTGTC 61.754 66.667 20.70 19.11 41.91 3.67
447 454 4.794439 TCCGCCGCATCGTCTGTG 62.794 66.667 0.00 0.00 35.02 3.66
448 455 3.838271 ATCCGCCGCATCGTCTGT 61.838 61.111 0.00 0.00 0.00 3.41
449 456 3.333189 CATCCGCCGCATCGTCTG 61.333 66.667 0.00 0.00 0.00 3.51
450 457 3.774959 GACATCCGCCGCATCGTCT 62.775 63.158 0.00 0.00 0.00 4.18
451 458 3.330853 GACATCCGCCGCATCGTC 61.331 66.667 0.00 0.00 0.00 4.20
452 459 4.891727 GGACATCCGCCGCATCGT 62.892 66.667 0.00 0.00 0.00 3.73
462 469 3.330853 GATCGCACGCGGACATCC 61.331 66.667 12.47 0.00 40.25 3.51
463 470 3.330853 GGATCGCACGCGGACATC 61.331 66.667 12.47 7.27 40.25 3.06
464 471 4.141965 TGGATCGCACGCGGACAT 62.142 61.111 12.47 0.00 40.25 3.06
472 479 3.950794 TTCAGCCGGTGGATCGCAC 62.951 63.158 1.90 5.94 0.00 5.34
473 480 3.700970 TTCAGCCGGTGGATCGCA 61.701 61.111 1.90 0.00 0.00 5.10
474 481 3.195698 GTTCAGCCGGTGGATCGC 61.196 66.667 1.90 0.00 0.00 4.58
475 482 1.672854 TAGGTTCAGCCGGTGGATCG 61.673 60.000 1.90 0.00 43.70 3.69
476 483 0.539986 TTAGGTTCAGCCGGTGGATC 59.460 55.000 1.90 0.00 43.70 3.36
477 484 0.541863 CTTAGGTTCAGCCGGTGGAT 59.458 55.000 1.90 0.00 43.70 3.41
478 485 1.980052 CTTAGGTTCAGCCGGTGGA 59.020 57.895 1.90 0.00 43.70 4.02
479 486 1.745489 GCTTAGGTTCAGCCGGTGG 60.745 63.158 1.90 0.00 43.70 4.61
480 487 0.392998 ATGCTTAGGTTCAGCCGGTG 60.393 55.000 1.90 0.00 43.70 4.94
481 488 0.328258 AATGCTTAGGTTCAGCCGGT 59.672 50.000 1.90 0.00 43.70 5.28
482 489 1.463674 AAATGCTTAGGTTCAGCCGG 58.536 50.000 0.00 0.00 43.70 6.13
483 490 3.057596 TGAAAAATGCTTAGGTTCAGCCG 60.058 43.478 0.00 0.00 43.70 5.52
484 491 4.519540 TGAAAAATGCTTAGGTTCAGCC 57.480 40.909 0.00 0.00 36.33 4.85
485 492 7.598493 TGTAATTGAAAAATGCTTAGGTTCAGC 59.402 33.333 0.00 0.00 37.82 4.26
486 493 9.474920 TTGTAATTGAAAAATGCTTAGGTTCAG 57.525 29.630 0.00 0.00 30.43 3.02
487 494 9.823647 TTTGTAATTGAAAAATGCTTAGGTTCA 57.176 25.926 0.00 0.00 0.00 3.18
518 525 9.403583 ACCCACACGATATTGTTAGAATTAATT 57.596 29.630 0.00 0.00 0.00 1.40
519 526 8.974060 ACCCACACGATATTGTTAGAATTAAT 57.026 30.769 0.00 0.00 0.00 1.40
520 527 8.670135 CAACCCACACGATATTGTTAGAATTAA 58.330 33.333 0.00 0.00 0.00 1.40
521 528 7.201661 GCAACCCACACGATATTGTTAGAATTA 60.202 37.037 0.00 0.00 0.00 1.40
522 529 6.404293 GCAACCCACACGATATTGTTAGAATT 60.404 38.462 0.00 0.00 0.00 2.17
523 530 5.065988 GCAACCCACACGATATTGTTAGAAT 59.934 40.000 0.00 0.00 0.00 2.40
524 531 4.393680 GCAACCCACACGATATTGTTAGAA 59.606 41.667 0.00 0.00 0.00 2.10
525 532 3.936453 GCAACCCACACGATATTGTTAGA 59.064 43.478 0.00 0.00 0.00 2.10
526 533 3.687212 TGCAACCCACACGATATTGTTAG 59.313 43.478 0.00 0.00 0.00 2.34
527 534 3.676093 TGCAACCCACACGATATTGTTA 58.324 40.909 0.00 0.00 0.00 2.41
528 535 2.509569 TGCAACCCACACGATATTGTT 58.490 42.857 0.00 0.00 0.00 2.83
529 536 2.192664 TGCAACCCACACGATATTGT 57.807 45.000 0.00 0.00 0.00 2.71
530 537 2.423185 ACATGCAACCCACACGATATTG 59.577 45.455 0.00 0.00 0.00 1.90
531 538 2.722094 ACATGCAACCCACACGATATT 58.278 42.857 0.00 0.00 0.00 1.28
532 539 2.418368 ACATGCAACCCACACGATAT 57.582 45.000 0.00 0.00 0.00 1.63
533 540 2.028020 TGTACATGCAACCCACACGATA 60.028 45.455 0.00 0.00 0.00 2.92
534 541 1.271108 TGTACATGCAACCCACACGAT 60.271 47.619 0.00 0.00 0.00 3.73
535 542 0.106894 TGTACATGCAACCCACACGA 59.893 50.000 0.00 0.00 0.00 4.35
536 543 1.135717 CATGTACATGCAACCCACACG 60.136 52.381 22.27 0.00 31.39 4.49
537 544 2.634982 CATGTACATGCAACCCACAC 57.365 50.000 22.27 0.00 31.39 3.82
547 554 6.564686 CGGAAATAGTAGCAAGCATGTACATG 60.565 42.308 28.07 28.07 41.60 3.21
548 555 5.466728 CGGAAATAGTAGCAAGCATGTACAT 59.533 40.000 1.41 1.41 0.00 2.29
549 556 4.808895 CGGAAATAGTAGCAAGCATGTACA 59.191 41.667 0.00 0.00 0.00 2.90
550 557 5.047847 TCGGAAATAGTAGCAAGCATGTAC 58.952 41.667 0.00 0.00 0.00 2.90
551 558 5.270893 TCGGAAATAGTAGCAAGCATGTA 57.729 39.130 0.00 0.00 0.00 2.29
552 559 4.137116 TCGGAAATAGTAGCAAGCATGT 57.863 40.909 0.00 0.00 0.00 3.21
553 560 5.679734 AATCGGAAATAGTAGCAAGCATG 57.320 39.130 0.00 0.00 0.00 4.06
554 561 8.314751 AGTATAATCGGAAATAGTAGCAAGCAT 58.685 33.333 0.00 0.00 0.00 3.79
555 562 7.667557 AGTATAATCGGAAATAGTAGCAAGCA 58.332 34.615 0.00 0.00 0.00 3.91
556 563 9.291664 CTAGTATAATCGGAAATAGTAGCAAGC 57.708 37.037 10.33 0.00 29.41 4.01
717 724 3.040099 CGATATGCACACGAATACACGA 58.960 45.455 0.00 0.00 37.03 4.35
718 725 2.153057 CCGATATGCACACGAATACACG 59.847 50.000 9.91 0.00 39.31 4.49
719 726 2.096909 GCCGATATGCACACGAATACAC 60.097 50.000 9.91 0.00 0.00 2.90
720 727 2.131972 GCCGATATGCACACGAATACA 58.868 47.619 9.91 0.00 0.00 2.29
721 728 1.459592 GGCCGATATGCACACGAATAC 59.540 52.381 9.91 0.00 0.00 1.89
722 729 1.069358 TGGCCGATATGCACACGAATA 59.931 47.619 0.00 0.00 0.00 1.75
723 730 0.179059 TGGCCGATATGCACACGAAT 60.179 50.000 0.00 0.00 0.00 3.34
724 731 1.087202 GTGGCCGATATGCACACGAA 61.087 55.000 0.00 0.00 0.00 3.85
978 994 2.710902 GGGATTTGGGTTCGGCTGC 61.711 63.158 0.00 0.00 0.00 5.25
984 1000 1.831106 GATGTTGGGGGATTTGGGTTC 59.169 52.381 0.00 0.00 0.00 3.62
1659 2000 0.176910 GCAGCTTCAGGAGGGTAGAC 59.823 60.000 0.00 0.00 0.00 2.59
1911 3800 1.011968 CGAGGATTTTGGACGCACGA 61.012 55.000 0.00 0.00 0.00 4.35
2203 4475 5.455056 AAATTACCACGGTAAACATGCAA 57.545 34.783 12.50 0.00 42.82 4.08
2298 4570 3.255149 CAGTCTTCCTTGCTGCTTTCATT 59.745 43.478 0.00 0.00 0.00 2.57
2805 5077 1.954258 GCCTCTGCTTTGCTCATTCCT 60.954 52.381 0.00 0.00 33.53 3.36
2820 5092 3.241530 TTGCCACGGACAGCCTCT 61.242 61.111 0.00 0.00 0.00 3.69
3272 5602 9.571810 CAAACAAAAGCTGCTAATAATACATGA 57.428 29.630 0.90 0.00 0.00 3.07
3379 5731 9.784531 CCAGATTTCCAGTATCTTGTAATGTAT 57.215 33.333 0.00 0.00 30.05 2.29
3431 5783 3.985008 TGCATTAGTACGACAGTGTTGT 58.015 40.909 19.92 19.92 41.18 3.32
3489 5845 7.153315 GGAGGGAGTATATAGCAAGTTAACAC 58.847 42.308 8.61 0.00 0.00 3.32
3505 5861 2.925966 TTAAGGGAACGGAGGGAGTA 57.074 50.000 0.00 0.00 0.00 2.59
3506 5862 2.034436 TTTAAGGGAACGGAGGGAGT 57.966 50.000 0.00 0.00 0.00 3.85
3507 5863 3.428413 TTTTTAAGGGAACGGAGGGAG 57.572 47.619 0.00 0.00 0.00 4.30
3527 5883 9.599866 CAAATCAAGAAAAAGGTAAAAGGTCTT 57.400 29.630 0.00 0.00 0.00 3.01
3528 5884 8.758829 ACAAATCAAGAAAAAGGTAAAAGGTCT 58.241 29.630 0.00 0.00 0.00 3.85
3529 5885 8.942338 ACAAATCAAGAAAAAGGTAAAAGGTC 57.058 30.769 0.00 0.00 0.00 3.85
3536 5892 9.515226 AGCTACATACAAATCAAGAAAAAGGTA 57.485 29.630 0.00 0.00 0.00 3.08
3537 5893 8.409358 AGCTACATACAAATCAAGAAAAAGGT 57.591 30.769 0.00 0.00 0.00 3.50
3538 5894 9.994432 CTAGCTACATACAAATCAAGAAAAAGG 57.006 33.333 0.00 0.00 0.00 3.11
3541 5897 9.719355 TGTCTAGCTACATACAAATCAAGAAAA 57.281 29.630 0.00 0.00 0.00 2.29
3542 5898 9.719355 TTGTCTAGCTACATACAAATCAAGAAA 57.281 29.630 8.42 0.00 0.00 2.52
3543 5899 9.719355 TTTGTCTAGCTACATACAAATCAAGAA 57.281 29.630 15.36 0.00 37.02 2.52
3544 5900 9.890629 ATTTGTCTAGCTACATACAAATCAAGA 57.109 29.630 20.85 1.85 44.91 3.02
3622 5978 8.148999 CGTTCCCTAATATAAGACCTTTTAGCT 58.851 37.037 0.00 0.00 0.00 3.32
3623 5979 7.387122 CCGTTCCCTAATATAAGACCTTTTAGC 59.613 40.741 0.00 0.00 0.00 3.09
3624 5980 8.645110 TCCGTTCCCTAATATAAGACCTTTTAG 58.355 37.037 0.00 0.00 0.00 1.85
3625 5981 8.551682 TCCGTTCCCTAATATAAGACCTTTTA 57.448 34.615 0.00 0.00 0.00 1.52
3626 5982 7.419865 CCTCCGTTCCCTAATATAAGACCTTTT 60.420 40.741 0.00 0.00 0.00 2.27
3627 5983 6.042897 CCTCCGTTCCCTAATATAAGACCTTT 59.957 42.308 0.00 0.00 0.00 3.11
3628 5984 5.543020 CCTCCGTTCCCTAATATAAGACCTT 59.457 44.000 0.00 0.00 0.00 3.50
3629 5985 5.085219 CCTCCGTTCCCTAATATAAGACCT 58.915 45.833 0.00 0.00 0.00 3.85
3630 5986 4.837298 ACCTCCGTTCCCTAATATAAGACC 59.163 45.833 0.00 0.00 0.00 3.85
3631 5987 6.718912 ACTACCTCCGTTCCCTAATATAAGAC 59.281 42.308 0.00 0.00 0.00 3.01
3632 5988 6.856757 ACTACCTCCGTTCCCTAATATAAGA 58.143 40.000 0.00 0.00 0.00 2.10
3633 5989 7.887495 ACTACTACCTCCGTTCCCTAATATAAG 59.113 40.741 0.00 0.00 0.00 1.73
3634 5990 7.759607 ACTACTACCTCCGTTCCCTAATATAA 58.240 38.462 0.00 0.00 0.00 0.98
3635 5991 7.335127 ACTACTACCTCCGTTCCCTAATATA 57.665 40.000 0.00 0.00 0.00 0.86
3636 5992 6.211505 ACTACTACCTCCGTTCCCTAATAT 57.788 41.667 0.00 0.00 0.00 1.28
3637 5993 5.653255 ACTACTACCTCCGTTCCCTAATA 57.347 43.478 0.00 0.00 0.00 0.98
3638 5994 4.533001 ACTACTACCTCCGTTCCCTAAT 57.467 45.455 0.00 0.00 0.00 1.73
3639 5995 4.322057 AACTACTACCTCCGTTCCCTAA 57.678 45.455 0.00 0.00 0.00 2.69
3640 5996 4.385310 GGTAACTACTACCTCCGTTCCCTA 60.385 50.000 0.00 0.00 46.05 3.53
3641 5997 2.915657 AACTACTACCTCCGTTCCCT 57.084 50.000 0.00 0.00 0.00 4.20
3642 5998 2.690497 GGTAACTACTACCTCCGTTCCC 59.310 54.545 0.00 0.00 46.05 3.97
3686 6044 6.830324 AGCATTTCAATAGTTAGAATCTGGCA 59.170 34.615 0.00 0.00 0.00 4.92
3718 6076 0.103208 ATGGCTCGTTCTCATCCGTC 59.897 55.000 0.00 0.00 0.00 4.79
3721 6079 5.297547 TGTAATAATGGCTCGTTCTCATCC 58.702 41.667 0.00 0.00 0.00 3.51
3751 6109 4.636249 ACTCTTAGACAGCTGGTTGAAAG 58.364 43.478 19.93 13.30 0.00 2.62
3843 6204 4.331108 TCAGCAGCCATAACACATAACAA 58.669 39.130 0.00 0.00 0.00 2.83
3949 6312 4.221041 GCTAACCCACTTCTCTGAGTTAGT 59.779 45.833 4.32 6.93 39.10 2.24
3980 6343 0.326264 GGCAGGCGATCCTTCCATAT 59.674 55.000 0.00 0.00 44.16 1.78
4045 6546 9.696572 TCCTTACTCATGACTACTAGTATTGTT 57.303 33.333 2.33 0.00 0.00 2.83
4048 6549 9.869667 ACATCCTTACTCATGACTACTAGTATT 57.130 33.333 2.33 0.00 0.00 1.89
4232 8733 5.235831 GCATAGGTCCAAGGTAAACGATAAC 59.764 44.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.