Multiple sequence alignment - TraesCS3D01G218300

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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 TraesCS3D01G218300 chr3D 100.000 5505 0 0 1 5505 297499796 297494292 0.000000e+00 10166.0
1 TraesCS3D01G218300 chr3D 95.455 88 4 0 2859 2946 271512582 271512669 2.070000e-29 141.0
2 TraesCS3D01G218300 chr3D 89.091 55 2 4 4396 4446 435299740 435299794 1.280000e-06 65.8
3 TraesCS3D01G218300 chr3A 96.569 3935 79 18 485 4387 391469081 391472991 0.000000e+00 6468.0
4 TraesCS3D01G218300 chr3A 95.484 1085 22 4 4429 5505 391472992 391474057 0.000000e+00 1707.0
5 TraesCS3D01G218300 chr3A 89.305 187 8 5 162 342 391468910 391469090 2.000000e-54 224.0
6 TraesCS3D01G218300 chr3B 97.189 3558 85 3 836 4384 392301457 392297906 0.000000e+00 6002.0
7 TraesCS3D01G218300 chr3B 94.620 1078 39 8 4429 5505 392297908 392296849 0.000000e+00 1652.0
8 TraesCS3D01G218300 chr3B 94.539 293 6 4 484 775 392302125 392301842 1.410000e-120 444.0
9 TraesCS3D01G218300 chr3B 87.644 348 27 6 1 345 392302459 392302125 1.860000e-104 390.0
10 TraesCS3D01G218300 chr3B 87.500 56 3 4 4397 4452 672737235 672737184 1.660000e-05 62.1
11 TraesCS3D01G218300 chr7A 91.391 151 6 2 340 483 732938460 732938610 3.360000e-47 200.0
12 TraesCS3D01G218300 chr7A 90.566 53 3 1 4381 4431 22917232 22917284 9.900000e-08 69.4
13 TraesCS3D01G218300 chr7D 91.216 148 6 2 343 483 519108336 519108189 1.560000e-45 195.0
14 TraesCS3D01G218300 chr7D 92.553 94 6 1 2852 2944 443416024 443416117 3.460000e-27 134.0
15 TraesCS3D01G218300 chr7D 93.333 45 2 1 4389 4432 637938130 637938086 1.280000e-06 65.8
16 TraesCS3D01G218300 chr6A 79.643 280 38 10 4902 5165 52719717 52719441 3.390000e-42 183.0
17 TraesCS3D01G218300 chr6A 92.632 95 5 2 2851 2944 27782692 27782785 9.620000e-28 135.0
18 TraesCS3D01G218300 chr6A 81.183 186 12 8 4830 4998 615965424 615965245 1.610000e-25 128.0
19 TraesCS3D01G218300 chr2D 89.865 148 8 2 343 483 558799701 558799554 3.390000e-42 183.0
20 TraesCS3D01G218300 chr2D 91.667 96 6 2 2852 2946 619321001 619321095 1.240000e-26 132.0
21 TraesCS3D01G218300 chr2D 92.157 51 2 1 4382 4432 588887386 588887434 2.750000e-08 71.3
22 TraesCS3D01G218300 chr1D 89.865 148 8 1 343 483 143175724 143175871 3.390000e-42 183.0
23 TraesCS3D01G218300 chr2B 88.591 149 10 2 342 483 386595100 386595248 2.040000e-39 174.0
24 TraesCS3D01G218300 chr2A 87.838 148 11 1 343 483 725349826 725349679 3.410000e-37 167.0
25 TraesCS3D01G218300 chr2A 95.238 42 2 0 4392 4433 747606224 747606265 3.560000e-07 67.6
26 TraesCS3D01G218300 chr6D 87.597 129 9 2 362 483 292962872 292962744 5.750000e-30 143.0
27 TraesCS3D01G218300 chr6D 91.753 97 8 0 2856 2952 20145814 20145718 9.620000e-28 135.0
28 TraesCS3D01G218300 chr6B 84.459 148 16 3 343 483 584581333 584581186 7.440000e-29 139.0
29 TraesCS3D01G218300 chr6B 94.444 90 3 2 2857 2945 8403637 8403549 2.670000e-28 137.0
30 TraesCS3D01G218300 chr6B 82.432 148 19 3 343 483 435851554 435851701 7.490000e-24 122.0
31 TraesCS3D01G218300 chr5A 76.817 289 38 13 4902 5165 452925625 452925341 9.620000e-28 135.0
32 TraesCS3D01G218300 chr5D 92.553 94 5 2 2860 2951 111788728 111788635 3.460000e-27 134.0
33 TraesCS3D01G218300 chr5D 82.432 148 19 1 343 483 320417851 320417704 7.490000e-24 122.0
34 TraesCS3D01G218300 chr5B 79.054 148 24 1 343 483 516949129 516949276 1.630000e-15 95.3
35 TraesCS3D01G218300 chr5B 91.379 58 3 2 4374 4430 562983212 562983156 1.640000e-10 78.7
36 TraesCS3D01G218300 chr5B 95.238 42 2 0 4396 4437 591579789 591579748 3.560000e-07 67.6
37 TraesCS3D01G218300 chr5B 91.489 47 3 1 4396 4442 33191361 33191406 4.600000e-06 63.9


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 TraesCS3D01G218300 chr3D 297494292 297499796 5504 True 10166.000000 10166 100.000 1 5505 1 chr3D.!!$R1 5504
1 TraesCS3D01G218300 chr3A 391468910 391474057 5147 False 2799.666667 6468 93.786 162 5505 3 chr3A.!!$F1 5343
2 TraesCS3D01G218300 chr3B 392296849 392302459 5610 True 2122.000000 6002 93.498 1 5505 4 chr3B.!!$R2 5504

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
435 441 0.026803 GCGAGTTCACGATGGATTGC 59.973 55.000 0.00 0.0 35.09 3.56 F
460 466 0.179145 CGTACCAAATCGGACGAGCT 60.179 55.000 0.00 0.0 39.32 4.09 F
672 680 0.250166 CTCCCCGACGTTTCAAACCT 60.250 55.000 0.00 0.0 0.00 3.50 F
803 813 1.079750 GACCACCAACGCCTCTCTC 60.080 63.158 0.00 0.0 0.00 3.20 F
804 814 1.534235 ACCACCAACGCCTCTCTCT 60.534 57.895 0.00 0.0 0.00 3.10 F
2210 2574 3.005155 GCTCAATTGCACTTCTCCACTTT 59.995 43.478 0.00 0.0 0.00 2.66 F
3078 3442 1.106351 ATGAGACCTCATCGCGCTCT 61.106 55.000 5.56 0.0 46.57 4.09 F
4403 4770 0.841289 TCCCTCTGTCCCAAAAACGT 59.159 50.000 0.00 0.0 0.00 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 2128 1.425428 GTCGAAGCAGAAATGGCGG 59.575 57.895 0.00 0.00 36.08 6.13 R
2210 2574 3.010027 TGGACTCATGTTAAATGCCAGGA 59.990 43.478 0.00 0.00 0.00 3.86 R
2483 2847 3.039011 GGGTCTACCAGGAGATAGCAAA 58.961 50.000 0.81 0.00 39.85 3.68 R
2765 3129 3.521531 TCCCTGGAATGCACAATACACTA 59.478 43.478 0.00 0.00 0.00 2.74 R
2841 3205 5.300034 GGGAGTAGTAACTAAGGAAGAGCTC 59.700 48.000 5.27 5.27 35.56 4.09 R
3638 4002 0.693049 AACTTCCTCATTCCCAGCGT 59.307 50.000 0.00 0.00 0.00 5.07 R
4427 4794 0.110823 CGGCAGCAACAGAAACGTAC 60.111 55.000 0.00 0.00 0.00 3.67 R
5406 5782 1.133253 CTCATTTCACGGCGCACAG 59.867 57.895 10.83 1.82 0.00 3.66 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
23 24 2.408704 CGAGCCTGACTAAGTGAAAACG 59.591 50.000 0.00 0.00 0.00 3.60
24 25 2.737252 GAGCCTGACTAAGTGAAAACGG 59.263 50.000 0.00 0.00 0.00 4.44
33 34 3.824414 AAGTGAAAACGGCTAATTCGG 57.176 42.857 0.00 0.00 0.00 4.30
43 44 2.483013 CGGCTAATTCGGTCATTCCTGA 60.483 50.000 0.00 0.00 0.00 3.86
53 54 3.261981 GTCATTCCTGACGGGTGTAAT 57.738 47.619 0.00 0.00 42.24 1.89
54 55 3.606687 GTCATTCCTGACGGGTGTAATT 58.393 45.455 0.00 0.00 42.24 1.40
57 58 5.236478 GTCATTCCTGACGGGTGTAATTATG 59.764 44.000 0.00 0.00 42.24 1.90
59 60 3.376636 TCCTGACGGGTGTAATTATGGA 58.623 45.455 0.00 0.00 36.25 3.41
69 70 7.286775 ACGGGTGTAATTATGGATGCTTTAAAT 59.713 33.333 0.00 0.00 0.00 1.40
71 72 9.830975 GGGTGTAATTATGGATGCTTTAAATTT 57.169 29.630 0.00 0.00 0.00 1.82
82 83 6.414987 GGATGCTTTAAATTTCGTGCTATGTC 59.585 38.462 0.00 0.00 0.00 3.06
89 90 0.739462 TTCGTGCTATGTCGGCCAAG 60.739 55.000 2.24 0.00 0.00 3.61
100 101 0.179043 TCGGCCAAGCAGTAAACACA 60.179 50.000 2.24 0.00 0.00 3.72
101 102 0.881118 CGGCCAAGCAGTAAACACAT 59.119 50.000 2.24 0.00 0.00 3.21
102 103 1.135689 CGGCCAAGCAGTAAACACATC 60.136 52.381 2.24 0.00 0.00 3.06
112 113 7.744087 AGCAGTAAACACATCATAAGAAACA 57.256 32.000 0.00 0.00 0.00 2.83
128 129 2.083167 AACAGGCCAATTTTGCATCG 57.917 45.000 5.01 0.00 0.00 3.84
130 131 1.085501 CAGGCCAATTTTGCATCGCC 61.086 55.000 5.01 0.00 33.63 5.54
134 136 1.510383 CAATTTTGCATCGCCCGGA 59.490 52.632 0.73 0.00 0.00 5.14
151 153 4.460263 CCCGGATCTGATTGAACCAAATA 58.540 43.478 0.73 0.00 37.46 1.40
158 160 4.085733 CTGATTGAACCAAATACACCCCA 58.914 43.478 0.00 0.00 0.00 4.96
159 161 3.829601 TGATTGAACCAAATACACCCCAC 59.170 43.478 0.00 0.00 0.00 4.61
160 162 2.296073 TGAACCAAATACACCCCACC 57.704 50.000 0.00 0.00 0.00 4.61
161 163 1.203075 TGAACCAAATACACCCCACCC 60.203 52.381 0.00 0.00 0.00 4.61
162 164 0.115547 AACCAAATACACCCCACCCC 59.884 55.000 0.00 0.00 0.00 4.95
163 165 1.074895 ACCAAATACACCCCACCCCA 61.075 55.000 0.00 0.00 0.00 4.96
164 166 0.613572 CCAAATACACCCCACCCCAC 60.614 60.000 0.00 0.00 0.00 4.61
165 167 0.613572 CAAATACACCCCACCCCACC 60.614 60.000 0.00 0.00 0.00 4.61
166 168 1.806690 AAATACACCCCACCCCACCC 61.807 60.000 0.00 0.00 0.00 4.61
184 186 1.301401 CCCCAGTTTTCGCTCGTGA 60.301 57.895 0.00 0.00 0.00 4.35
343 349 9.702253 AATAAACTTGTATACAGAGAGAGAGGA 57.298 33.333 16.84 0.00 0.00 3.71
344 350 7.639113 AAACTTGTATACAGAGAGAGAGGAG 57.361 40.000 16.84 7.05 0.00 3.69
345 351 5.130350 ACTTGTATACAGAGAGAGAGGAGC 58.870 45.833 16.84 0.00 0.00 4.70
346 352 3.734463 TGTATACAGAGAGAGAGGAGCG 58.266 50.000 0.08 0.00 0.00 5.03
347 353 3.134985 TGTATACAGAGAGAGAGGAGCGT 59.865 47.826 0.08 0.00 0.00 5.07
348 354 2.791347 TACAGAGAGAGAGGAGCGTT 57.209 50.000 0.00 0.00 0.00 4.84
349 355 1.173043 ACAGAGAGAGAGGAGCGTTG 58.827 55.000 0.00 0.00 0.00 4.10
350 356 0.179140 CAGAGAGAGAGGAGCGTTGC 60.179 60.000 0.00 0.00 0.00 4.17
351 357 0.323360 AGAGAGAGAGGAGCGTTGCT 60.323 55.000 0.00 0.00 43.88 3.91
352 358 1.065053 AGAGAGAGAGGAGCGTTGCTA 60.065 52.381 0.00 0.00 39.88 3.49
353 359 1.064952 GAGAGAGAGGAGCGTTGCTAC 59.935 57.143 0.00 0.00 39.88 3.58
354 360 0.811915 GAGAGAGGAGCGTTGCTACA 59.188 55.000 3.51 0.00 42.99 2.74
355 361 0.528470 AGAGAGGAGCGTTGCTACAC 59.472 55.000 3.51 0.00 42.99 2.90
356 362 0.798771 GAGAGGAGCGTTGCTACACG 60.799 60.000 3.51 0.00 42.99 4.49
357 363 1.080705 GAGGAGCGTTGCTACACGT 60.081 57.895 3.51 0.00 42.99 4.49
358 364 0.169672 GAGGAGCGTTGCTACACGTA 59.830 55.000 3.51 0.00 42.99 3.57
359 365 0.109412 AGGAGCGTTGCTACACGTAC 60.109 55.000 3.51 0.00 42.99 3.67
360 366 1.400990 GGAGCGTTGCTACACGTACG 61.401 60.000 15.01 15.01 39.71 3.67
361 367 0.453282 GAGCGTTGCTACACGTACGA 60.453 55.000 24.41 0.00 39.88 3.43
362 368 0.727122 AGCGTTGCTACACGTACGAC 60.727 55.000 24.41 6.61 42.43 4.34
363 369 0.998226 GCGTTGCTACACGTACGACA 60.998 55.000 24.41 8.79 42.43 4.35
364 370 1.397619 CGTTGCTACACGTACGACAA 58.602 50.000 24.41 14.09 36.16 3.18
365 371 1.980844 CGTTGCTACACGTACGACAAT 59.019 47.619 24.41 6.42 36.16 2.71
366 372 3.162831 CGTTGCTACACGTACGACAATA 58.837 45.455 24.41 7.26 36.16 1.90
367 373 3.787634 CGTTGCTACACGTACGACAATAT 59.212 43.478 24.41 0.00 36.16 1.28
368 374 4.263677 CGTTGCTACACGTACGACAATATT 59.736 41.667 24.41 0.00 36.16 1.28
369 375 5.220080 CGTTGCTACACGTACGACAATATTT 60.220 40.000 24.41 0.00 36.16 1.40
370 376 5.689927 TGCTACACGTACGACAATATTTG 57.310 39.130 24.41 9.52 0.00 2.32
371 377 9.432165 CGTTGCTACACGTACGACAATATTTGT 62.432 40.741 24.41 15.10 39.98 2.83
372 378 6.320944 TGCTACACGTACGACAATATTTGTA 58.679 36.000 24.41 15.42 45.52 2.41
373 379 6.974048 TGCTACACGTACGACAATATTTGTAT 59.026 34.615 24.41 0.00 45.52 2.29
374 380 7.043920 TGCTACACGTACGACAATATTTGTATG 60.044 37.037 24.41 7.20 45.52 2.39
375 381 7.166307 GCTACACGTACGACAATATTTGTATGA 59.834 37.037 24.41 0.00 45.52 2.15
376 382 7.997107 ACACGTACGACAATATTTGTATGAT 57.003 32.000 24.41 0.00 45.52 2.45
377 383 8.415192 ACACGTACGACAATATTTGTATGATT 57.585 30.769 24.41 0.00 45.52 2.57
378 384 8.875803 ACACGTACGACAATATTTGTATGATTT 58.124 29.630 24.41 0.00 45.52 2.17
379 385 9.353353 CACGTACGACAATATTTGTATGATTTC 57.647 33.333 24.41 0.00 45.52 2.17
380 386 9.309516 ACGTACGACAATATTTGTATGATTTCT 57.690 29.630 24.41 0.00 45.52 2.52
381 387 9.567917 CGTACGACAATATTTGTATGATTTCTG 57.432 33.333 10.44 0.00 45.52 3.02
393 399 9.665719 TTTGTATGATTTCTGTATGAAGTAGCA 57.334 29.630 0.00 0.00 35.89 3.49
394 400 8.877808 TGTATGATTTCTGTATGAAGTAGCAG 57.122 34.615 0.00 0.00 35.89 4.24
395 401 7.928167 TGTATGATTTCTGTATGAAGTAGCAGG 59.072 37.037 0.00 0.00 35.89 4.85
396 402 5.674525 TGATTTCTGTATGAAGTAGCAGGG 58.325 41.667 0.00 0.00 35.89 4.45
397 403 3.543680 TTCTGTATGAAGTAGCAGGGC 57.456 47.619 0.00 0.00 0.00 5.19
398 404 1.762957 TCTGTATGAAGTAGCAGGGCC 59.237 52.381 0.00 0.00 0.00 5.80
399 405 1.486310 CTGTATGAAGTAGCAGGGCCA 59.514 52.381 6.18 0.00 0.00 5.36
400 406 1.209504 TGTATGAAGTAGCAGGGCCAC 59.790 52.381 6.18 0.00 0.00 5.01
401 407 0.837272 TATGAAGTAGCAGGGCCACC 59.163 55.000 6.18 0.00 0.00 4.61
402 408 2.125106 GAAGTAGCAGGGCCACCG 60.125 66.667 6.18 0.00 43.47 4.94
403 409 2.928396 AAGTAGCAGGGCCACCGT 60.928 61.111 6.18 0.00 43.47 4.83
404 410 2.465055 GAAGTAGCAGGGCCACCGTT 62.465 60.000 6.18 0.00 43.47 4.44
405 411 2.746277 GTAGCAGGGCCACCGTTG 60.746 66.667 6.18 0.00 43.47 4.10
406 412 2.925706 TAGCAGGGCCACCGTTGA 60.926 61.111 6.18 0.00 43.47 3.18
407 413 2.297895 TAGCAGGGCCACCGTTGAT 61.298 57.895 6.18 0.00 43.47 2.57
408 414 2.252072 TAGCAGGGCCACCGTTGATC 62.252 60.000 6.18 0.00 43.47 2.92
409 415 2.350895 CAGGGCCACCGTTGATCA 59.649 61.111 6.18 0.00 43.47 2.92
410 416 1.303236 CAGGGCCACCGTTGATCAA 60.303 57.895 6.18 3.38 43.47 2.57
411 417 1.303317 AGGGCCACCGTTGATCAAC 60.303 57.895 25.68 25.68 43.47 3.18
419 425 3.561429 GTTGATCAACGCTGGCGA 58.439 55.556 22.09 0.00 42.83 5.54
420 426 1.421485 GTTGATCAACGCTGGCGAG 59.579 57.895 22.09 12.89 42.83 5.03
421 427 1.005037 TTGATCAACGCTGGCGAGT 60.005 52.632 21.77 6.08 42.83 4.18
422 428 0.602638 TTGATCAACGCTGGCGAGTT 60.603 50.000 21.77 3.51 42.83 3.01
423 429 1.014044 TGATCAACGCTGGCGAGTTC 61.014 55.000 21.77 15.85 42.83 3.01
424 430 1.005037 ATCAACGCTGGCGAGTTCA 60.005 52.632 21.77 0.00 42.83 3.18
425 431 1.291877 ATCAACGCTGGCGAGTTCAC 61.292 55.000 21.77 0.00 42.83 3.18
426 432 3.036084 AACGCTGGCGAGTTCACG 61.036 61.111 21.77 0.00 42.83 4.35
427 433 3.493830 AACGCTGGCGAGTTCACGA 62.494 57.895 21.77 0.00 42.83 4.35
428 434 2.507102 CGCTGGCGAGTTCACGAT 60.507 61.111 9.51 0.00 42.83 3.73
429 435 2.792290 CGCTGGCGAGTTCACGATG 61.792 63.158 9.51 0.00 42.83 3.84
430 436 2.456119 GCTGGCGAGTTCACGATGG 61.456 63.158 0.00 0.00 35.09 3.51
431 437 1.215382 CTGGCGAGTTCACGATGGA 59.785 57.895 0.00 0.00 35.09 3.41
432 438 0.179100 CTGGCGAGTTCACGATGGAT 60.179 55.000 0.00 0.00 35.09 3.41
433 439 0.249120 TGGCGAGTTCACGATGGATT 59.751 50.000 0.00 0.00 35.09 3.01
434 440 0.652592 GGCGAGTTCACGATGGATTG 59.347 55.000 0.00 0.00 35.09 2.67
435 441 0.026803 GCGAGTTCACGATGGATTGC 59.973 55.000 0.00 0.00 35.09 3.56
436 442 1.358877 CGAGTTCACGATGGATTGCA 58.641 50.000 0.00 0.00 35.09 4.08
437 443 1.061131 CGAGTTCACGATGGATTGCAC 59.939 52.381 0.00 0.00 35.09 4.57
438 444 2.350522 GAGTTCACGATGGATTGCACT 58.649 47.619 0.00 0.00 0.00 4.40
439 445 3.521560 GAGTTCACGATGGATTGCACTA 58.478 45.455 0.00 0.00 0.00 2.74
440 446 4.122776 GAGTTCACGATGGATTGCACTAT 58.877 43.478 0.00 0.00 0.00 2.12
441 447 4.122776 AGTTCACGATGGATTGCACTATC 58.877 43.478 0.00 0.00 0.00 2.08
446 452 2.987149 CGATGGATTGCACTATCGTACC 59.013 50.000 12.92 0.00 42.96 3.34
447 453 3.552068 CGATGGATTGCACTATCGTACCA 60.552 47.826 12.92 0.00 42.96 3.25
448 454 3.897141 TGGATTGCACTATCGTACCAA 57.103 42.857 0.00 0.00 0.00 3.67
449 455 4.209307 TGGATTGCACTATCGTACCAAA 57.791 40.909 0.00 0.00 0.00 3.28
450 456 4.776349 TGGATTGCACTATCGTACCAAAT 58.224 39.130 0.00 0.00 0.00 2.32
451 457 4.814234 TGGATTGCACTATCGTACCAAATC 59.186 41.667 0.00 0.00 0.00 2.17
452 458 4.084537 GGATTGCACTATCGTACCAAATCG 60.085 45.833 0.00 0.00 0.00 3.34
453 459 2.816689 TGCACTATCGTACCAAATCGG 58.183 47.619 0.00 0.00 42.50 4.18
454 460 2.427812 TGCACTATCGTACCAAATCGGA 59.572 45.455 0.00 0.00 38.63 4.55
455 461 2.793232 GCACTATCGTACCAAATCGGAC 59.207 50.000 0.00 0.00 38.63 4.79
456 462 3.040795 CACTATCGTACCAAATCGGACG 58.959 50.000 0.00 0.00 38.73 4.79
457 463 2.945008 ACTATCGTACCAAATCGGACGA 59.055 45.455 0.00 0.00 45.20 4.20
458 464 2.486951 ATCGTACCAAATCGGACGAG 57.513 50.000 2.23 0.00 44.72 4.18
459 465 0.179156 TCGTACCAAATCGGACGAGC 60.179 55.000 0.00 0.00 40.25 5.03
460 466 0.179145 CGTACCAAATCGGACGAGCT 60.179 55.000 0.00 0.00 39.32 4.09
461 467 1.734707 CGTACCAAATCGGACGAGCTT 60.735 52.381 0.00 0.00 39.32 3.74
462 468 2.344025 GTACCAAATCGGACGAGCTTT 58.656 47.619 0.00 0.00 38.63 3.51
463 469 1.892209 ACCAAATCGGACGAGCTTTT 58.108 45.000 0.00 0.00 38.63 2.27
464 470 3.048337 ACCAAATCGGACGAGCTTTTA 57.952 42.857 0.00 0.00 38.63 1.52
465 471 3.606687 ACCAAATCGGACGAGCTTTTAT 58.393 40.909 0.00 0.00 38.63 1.40
466 472 3.621715 ACCAAATCGGACGAGCTTTTATC 59.378 43.478 0.00 0.00 38.63 1.75
467 473 3.302480 CCAAATCGGACGAGCTTTTATCG 60.302 47.826 0.00 0.00 45.54 2.92
476 482 4.956034 CGAGCTTTTATCGTATGTGAGG 57.044 45.455 0.00 0.00 35.48 3.86
477 483 3.182572 CGAGCTTTTATCGTATGTGAGGC 59.817 47.826 0.00 0.00 35.48 4.70
478 484 4.119862 GAGCTTTTATCGTATGTGAGGCA 58.880 43.478 0.00 0.00 0.00 4.75
479 485 4.513442 AGCTTTTATCGTATGTGAGGCAA 58.487 39.130 0.00 0.00 0.00 4.52
480 486 5.126067 AGCTTTTATCGTATGTGAGGCAAT 58.874 37.500 0.00 0.00 0.00 3.56
481 487 5.590259 AGCTTTTATCGTATGTGAGGCAATT 59.410 36.000 0.00 0.00 0.00 2.32
482 488 5.909610 GCTTTTATCGTATGTGAGGCAATTC 59.090 40.000 0.00 0.00 0.00 2.17
654 662 3.039526 CCTCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
655 663 2.612251 CTCCTCCCTCCCTCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
656 664 3.036959 TCCTCCCTCCCTCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
657 665 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
672 680 0.250166 CTCCCCGACGTTTCAAACCT 60.250 55.000 0.00 0.00 0.00 3.50
679 687 2.551912 CGTTTCAAACCTGCGGCCT 61.552 57.895 0.00 0.00 0.00 5.19
784 794 4.569564 ACTGTTTCGACTTTACAAGACACC 59.430 41.667 0.00 0.00 0.00 4.16
796 806 3.343421 GACACCGACCACCAACGC 61.343 66.667 0.00 0.00 0.00 4.84
801 811 2.432628 CGACCACCAACGCCTCTC 60.433 66.667 0.00 0.00 0.00 3.20
802 812 2.932234 CGACCACCAACGCCTCTCT 61.932 63.158 0.00 0.00 0.00 3.10
803 813 1.079750 GACCACCAACGCCTCTCTC 60.080 63.158 0.00 0.00 0.00 3.20
804 814 1.534235 ACCACCAACGCCTCTCTCT 60.534 57.895 0.00 0.00 0.00 3.10
2089 2453 7.001674 AGTGGTAGTATTTGTGAAATGTTGGA 58.998 34.615 0.00 0.00 32.38 3.53
2210 2574 3.005155 GCTCAATTGCACTTCTCCACTTT 59.995 43.478 0.00 0.00 0.00 2.66
2483 2847 4.404073 GTCTACAATGAGACAGTGAGGGAT 59.596 45.833 6.22 0.00 44.49 3.85
2627 2991 7.255660 GGTGATATCAAGTTAGTAGTCCTCCTG 60.256 44.444 7.07 0.00 0.00 3.86
2841 3205 8.741101 GAGCATACTCTACAGATGAAGTAATG 57.259 38.462 0.00 0.00 40.03 1.90
2869 3233 5.254737 TCTTCCTTAGTTACTACTCCCTCCA 59.745 44.000 0.00 0.00 35.78 3.86
2887 3251 5.429762 CCCTCCATCCCATAATATAAGAGCA 59.570 44.000 0.00 0.00 0.00 4.26
2903 3267 2.160417 AGAGCATTTTTGACACTAGCGC 59.840 45.455 0.00 0.00 0.00 5.92
3078 3442 1.106351 ATGAGACCTCATCGCGCTCT 61.106 55.000 5.56 0.00 46.57 4.09
3121 3485 5.868043 TGTCAATCATGCACTTTCACTAG 57.132 39.130 0.00 0.00 0.00 2.57
3304 3668 2.202544 CGCTCACAGAGGTCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
3638 4002 6.159299 TCTTGTGATTTTTCAGCCATTGAA 57.841 33.333 0.00 0.00 43.92 2.69
3852 4216 3.657448 TACCACCACGCCATGCTCG 62.657 63.158 4.39 4.39 0.00 5.03
4162 4526 2.922503 TGAAGAGCCCGAGCCACA 60.923 61.111 0.00 0.00 41.25 4.17
4332 4696 3.702045 AGGTATAGTCCTTCAGCTCACAC 59.298 47.826 0.00 0.00 33.52 3.82
4335 4699 1.356124 AGTCCTTCAGCTCACACCAT 58.644 50.000 0.00 0.00 0.00 3.55
4351 4715 6.785076 TCACACCATTCCCAAGAGTTTATTA 58.215 36.000 0.00 0.00 0.00 0.98
4352 4716 7.410174 TCACACCATTCCCAAGAGTTTATTAT 58.590 34.615 0.00 0.00 0.00 1.28
4353 4717 8.553153 TCACACCATTCCCAAGAGTTTATTATA 58.447 33.333 0.00 0.00 0.00 0.98
4354 4718 8.840321 CACACCATTCCCAAGAGTTTATTATAG 58.160 37.037 0.00 0.00 0.00 1.31
4355 4719 8.557450 ACACCATTCCCAAGAGTTTATTATAGT 58.443 33.333 0.00 0.00 0.00 2.12
4387 4754 4.662278 TGGGCAGCATATAAATTACTCCC 58.338 43.478 0.00 0.00 0.00 4.30
4388 4755 4.353788 TGGGCAGCATATAAATTACTCCCT 59.646 41.667 0.00 0.00 0.00 4.20
4389 4756 4.944317 GGGCAGCATATAAATTACTCCCTC 59.056 45.833 0.00 0.00 0.00 4.30
4390 4757 5.280727 GGGCAGCATATAAATTACTCCCTCT 60.281 44.000 0.00 0.00 0.00 3.69
4391 4758 5.645497 GGCAGCATATAAATTACTCCCTCTG 59.355 44.000 0.00 0.00 0.00 3.35
4392 4759 6.234177 GCAGCATATAAATTACTCCCTCTGT 58.766 40.000 0.00 0.00 0.00 3.41
4393 4760 6.370166 GCAGCATATAAATTACTCCCTCTGTC 59.630 42.308 0.00 0.00 0.00 3.51
4394 4761 6.876257 CAGCATATAAATTACTCCCTCTGTCC 59.124 42.308 0.00 0.00 0.00 4.02
4395 4762 6.013293 AGCATATAAATTACTCCCTCTGTCCC 60.013 42.308 0.00 0.00 0.00 4.46
4396 4763 6.239887 GCATATAAATTACTCCCTCTGTCCCA 60.240 42.308 0.00 0.00 0.00 4.37
4397 4764 7.691791 GCATATAAATTACTCCCTCTGTCCCAA 60.692 40.741 0.00 0.00 0.00 4.12
4398 4765 6.652205 ATAAATTACTCCCTCTGTCCCAAA 57.348 37.500 0.00 0.00 0.00 3.28
4399 4766 5.333566 AAATTACTCCCTCTGTCCCAAAA 57.666 39.130 0.00 0.00 0.00 2.44
4400 4767 5.333566 AATTACTCCCTCTGTCCCAAAAA 57.666 39.130 0.00 0.00 0.00 1.94
4401 4768 2.658807 ACTCCCTCTGTCCCAAAAAC 57.341 50.000 0.00 0.00 0.00 2.43
4402 4769 1.202770 ACTCCCTCTGTCCCAAAAACG 60.203 52.381 0.00 0.00 0.00 3.60
4403 4770 0.841289 TCCCTCTGTCCCAAAAACGT 59.159 50.000 0.00 0.00 0.00 3.99
4404 4771 1.213430 TCCCTCTGTCCCAAAAACGTT 59.787 47.619 0.00 0.00 0.00 3.99
4405 4772 1.607148 CCCTCTGTCCCAAAAACGTTC 59.393 52.381 0.00 0.00 0.00 3.95
4406 4773 2.572290 CCTCTGTCCCAAAAACGTTCT 58.428 47.619 0.00 0.00 0.00 3.01
4407 4774 2.949644 CCTCTGTCCCAAAAACGTTCTT 59.050 45.455 0.00 0.00 0.00 2.52
4408 4775 4.131596 CCTCTGTCCCAAAAACGTTCTTA 58.868 43.478 0.00 0.00 0.00 2.10
4409 4776 4.760204 CCTCTGTCCCAAAAACGTTCTTAT 59.240 41.667 0.00 0.00 0.00 1.73
4410 4777 5.935789 CCTCTGTCCCAAAAACGTTCTTATA 59.064 40.000 0.00 0.00 0.00 0.98
4411 4778 6.598064 CCTCTGTCCCAAAAACGTTCTTATAT 59.402 38.462 0.00 0.00 0.00 0.86
4412 4779 7.120726 CCTCTGTCCCAAAAACGTTCTTATATT 59.879 37.037 0.00 0.00 0.00 1.28
4413 4780 9.158233 CTCTGTCCCAAAAACGTTCTTATATTA 57.842 33.333 0.00 0.00 0.00 0.98
4414 4781 9.675464 TCTGTCCCAAAAACGTTCTTATATTAT 57.325 29.630 0.00 0.00 0.00 1.28
4415 4782 9.716507 CTGTCCCAAAAACGTTCTTATATTATG 57.283 33.333 0.00 0.00 0.00 1.90
4416 4783 8.679100 TGTCCCAAAAACGTTCTTATATTATGG 58.321 33.333 0.00 2.50 0.00 2.74
4417 4784 8.132995 GTCCCAAAAACGTTCTTATATTATGGG 58.867 37.037 0.00 10.66 43.13 4.00
4418 4785 8.053963 TCCCAAAAACGTTCTTATATTATGGGA 58.946 33.333 17.64 17.64 46.92 4.37
4419 4786 8.132995 CCCAAAAACGTTCTTATATTATGGGAC 58.867 37.037 0.00 0.00 44.24 4.46
4420 4787 7.853929 CCAAAAACGTTCTTATATTATGGGACG 59.146 37.037 0.00 9.33 0.00 4.79
4421 4788 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
4422 4789 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
4423 4790 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
4424 4791 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
4425 4792 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
4426 4793 4.359105 TCTTATATTATGGGACGGAGGGG 58.641 47.826 0.00 0.00 0.00 4.79
4427 4794 1.966845 ATATTATGGGACGGAGGGGG 58.033 55.000 0.00 0.00 0.00 5.40
4604 4979 7.905604 TGCTAATTGGAGTTTATCATATCCG 57.094 36.000 0.00 0.00 34.39 4.18
4807 5182 2.559440 TGGCAAAACAAAATGACAGGC 58.441 42.857 0.00 0.00 29.35 4.85
4900 5275 4.791088 GCAAGAAGAAGAAACAGAACCAGC 60.791 45.833 0.00 0.00 0.00 4.85
5198 5574 1.273327 TGCCTGATACGATGATGCGAT 59.727 47.619 0.00 0.00 34.83 4.58
5238 5614 3.650281 TGAGCTTCCTTGGCAATATCA 57.350 42.857 0.00 0.00 0.00 2.15
5331 5707 1.072159 GCAGCTCCCACTGTCACTT 59.928 57.895 0.00 0.00 39.96 3.16
5406 5782 6.963049 TTAAAGACCGTAATGCTTTCTCTC 57.037 37.500 0.00 0.00 34.12 3.20
5447 5823 3.316029 TGACTCTTGTGCTTTCCATTGTG 59.684 43.478 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.481185 TGACCGAATTAGCCGTTTTCAC 59.519 45.455 0.00 0.00 0.00 3.18
23 24 2.872858 GTCAGGAATGACCGAATTAGCC 59.127 50.000 0.00 0.00 44.74 3.93
24 25 2.540101 CGTCAGGAATGACCGAATTAGC 59.460 50.000 2.97 0.00 44.74 3.09
33 34 2.754946 TTACACCCGTCAGGAATGAC 57.245 50.000 0.00 0.00 41.02 3.06
43 44 3.857157 AGCATCCATAATTACACCCGT 57.143 42.857 0.00 0.00 0.00 5.28
53 54 6.862209 AGCACGAAATTTAAAGCATCCATAA 58.138 32.000 9.86 0.00 0.00 1.90
54 55 6.449635 AGCACGAAATTTAAAGCATCCATA 57.550 33.333 9.86 0.00 0.00 2.74
57 58 6.265577 ACATAGCACGAAATTTAAAGCATCC 58.734 36.000 9.86 0.00 0.00 3.51
59 60 5.965334 CGACATAGCACGAAATTTAAAGCAT 59.035 36.000 9.86 1.46 0.00 3.79
69 70 0.320858 TTGGCCGACATAGCACGAAA 60.321 50.000 0.00 0.00 0.00 3.46
71 72 1.153647 CTTGGCCGACATAGCACGA 60.154 57.895 0.00 0.00 0.00 4.35
82 83 0.881118 ATGTGTTTACTGCTTGGCCG 59.119 50.000 0.00 0.00 0.00 6.13
89 90 7.023575 CCTGTTTCTTATGATGTGTTTACTGC 58.976 38.462 0.00 0.00 0.00 4.40
100 101 5.876460 GCAAAATTGGCCTGTTTCTTATGAT 59.124 36.000 3.32 0.00 0.00 2.45
101 102 5.221601 TGCAAAATTGGCCTGTTTCTTATGA 60.222 36.000 3.32 0.00 0.00 2.15
102 103 4.996122 TGCAAAATTGGCCTGTTTCTTATG 59.004 37.500 3.32 1.78 0.00 1.90
112 113 1.218854 GGCGATGCAAAATTGGCCT 59.781 52.632 3.32 0.00 37.57 5.19
128 129 0.107214 TGGTTCAATCAGATCCGGGC 60.107 55.000 0.00 0.00 38.69 6.13
130 131 4.881273 TGTATTTGGTTCAATCAGATCCGG 59.119 41.667 0.00 0.00 38.69 5.14
134 136 4.956075 GGGGTGTATTTGGTTCAATCAGAT 59.044 41.667 0.00 0.00 0.00 2.90
165 167 2.032071 ACGAGCGAAAACTGGGGG 59.968 61.111 0.00 0.00 0.00 5.40
166 168 1.301401 TCACGAGCGAAAACTGGGG 60.301 57.895 0.00 0.00 0.00 4.96
167 169 0.878523 TGTCACGAGCGAAAACTGGG 60.879 55.000 0.00 0.00 0.00 4.45
168 170 0.232303 GTGTCACGAGCGAAAACTGG 59.768 55.000 0.00 0.00 0.00 4.00
169 171 0.232303 GGTGTCACGAGCGAAAACTG 59.768 55.000 0.00 0.00 0.00 3.16
184 186 7.768240 AGAGAAAGTAAAACGAAAATTGGTGT 58.232 30.769 0.00 0.00 0.00 4.16
345 351 9.432165 ACAAATATTGTCGTACGTGTAGCAACG 62.432 40.741 16.05 0.00 44.21 4.10
346 352 5.691508 AATATTGTCGTACGTGTAGCAAC 57.308 39.130 16.05 4.58 0.00 4.17
347 353 5.634439 ACAAATATTGTCGTACGTGTAGCAA 59.366 36.000 16.05 13.21 40.56 3.91
348 354 5.162794 ACAAATATTGTCGTACGTGTAGCA 58.837 37.500 16.05 5.29 40.56 3.49
349 355 5.691508 ACAAATATTGTCGTACGTGTAGC 57.308 39.130 16.05 2.76 40.56 3.58
350 356 8.551122 TCATACAAATATTGTCGTACGTGTAG 57.449 34.615 16.05 7.93 44.12 2.74
351 357 9.518906 AATCATACAAATATTGTCGTACGTGTA 57.481 29.630 16.05 13.51 44.12 2.90
352 358 7.997107 ATCATACAAATATTGTCGTACGTGT 57.003 32.000 16.05 11.72 44.12 4.49
353 359 9.353353 GAAATCATACAAATATTGTCGTACGTG 57.647 33.333 16.05 5.93 44.12 4.49
354 360 9.309516 AGAAATCATACAAATATTGTCGTACGT 57.690 29.630 16.05 0.00 44.12 3.57
355 361 9.567917 CAGAAATCATACAAATATTGTCGTACG 57.432 33.333 9.53 9.53 44.12 3.67
367 373 9.665719 TGCTACTTCATACAGAAATCATACAAA 57.334 29.630 0.00 0.00 35.40 2.83
368 374 9.317936 CTGCTACTTCATACAGAAATCATACAA 57.682 33.333 0.00 0.00 35.40 2.41
369 375 7.928167 CCTGCTACTTCATACAGAAATCATACA 59.072 37.037 0.00 0.00 35.40 2.29
370 376 7.386299 CCCTGCTACTTCATACAGAAATCATAC 59.614 40.741 0.00 0.00 35.40 2.39
371 377 7.445121 CCCTGCTACTTCATACAGAAATCATA 58.555 38.462 0.00 0.00 35.40 2.15
372 378 6.294473 CCCTGCTACTTCATACAGAAATCAT 58.706 40.000 0.00 0.00 35.40 2.45
373 379 5.674525 CCCTGCTACTTCATACAGAAATCA 58.325 41.667 0.00 0.00 35.40 2.57
374 380 4.513318 GCCCTGCTACTTCATACAGAAATC 59.487 45.833 0.00 0.00 35.40 2.17
375 381 4.455606 GCCCTGCTACTTCATACAGAAAT 58.544 43.478 0.00 0.00 35.40 2.17
376 382 3.370527 GGCCCTGCTACTTCATACAGAAA 60.371 47.826 0.00 0.00 35.40 2.52
377 383 2.170607 GGCCCTGCTACTTCATACAGAA 59.829 50.000 0.00 0.00 31.67 3.02
378 384 1.762957 GGCCCTGCTACTTCATACAGA 59.237 52.381 0.00 0.00 31.67 3.41
379 385 1.486310 TGGCCCTGCTACTTCATACAG 59.514 52.381 0.00 0.00 0.00 2.74
380 386 1.209504 GTGGCCCTGCTACTTCATACA 59.790 52.381 0.00 0.00 37.08 2.29
381 387 1.475213 GGTGGCCCTGCTACTTCATAC 60.475 57.143 0.00 0.00 39.93 2.39
382 388 0.837272 GGTGGCCCTGCTACTTCATA 59.163 55.000 0.00 0.00 39.93 2.15
383 389 1.609783 GGTGGCCCTGCTACTTCAT 59.390 57.895 0.00 0.00 39.93 2.57
384 390 2.954684 CGGTGGCCCTGCTACTTCA 61.955 63.158 0.00 0.00 39.93 3.02
385 391 2.125106 CGGTGGCCCTGCTACTTC 60.125 66.667 0.00 0.00 39.93 3.01
386 392 2.526046 AACGGTGGCCCTGCTACTT 61.526 57.895 0.00 0.00 39.93 2.24
387 393 2.928396 AACGGTGGCCCTGCTACT 60.928 61.111 0.00 0.00 39.93 2.57
388 394 2.536997 ATCAACGGTGGCCCTGCTAC 62.537 60.000 0.00 0.00 39.31 3.58
389 395 2.252072 GATCAACGGTGGCCCTGCTA 62.252 60.000 0.00 0.00 0.00 3.49
390 396 3.628646 GATCAACGGTGGCCCTGCT 62.629 63.158 0.00 0.00 0.00 4.24
391 397 3.134127 GATCAACGGTGGCCCTGC 61.134 66.667 0.00 0.00 0.00 4.85
392 398 1.303236 TTGATCAACGGTGGCCCTG 60.303 57.895 3.38 0.00 0.00 4.45
393 399 1.303317 GTTGATCAACGGTGGCCCT 60.303 57.895 22.09 0.00 0.00 5.19
394 400 3.274067 GTTGATCAACGGTGGCCC 58.726 61.111 22.09 0.00 0.00 5.80
402 408 1.291877 ACTCGCCAGCGTTGATCAAC 61.292 55.000 25.68 25.68 40.74 3.18
403 409 0.602638 AACTCGCCAGCGTTGATCAA 60.603 50.000 12.32 3.38 40.74 2.57
404 410 1.005037 AACTCGCCAGCGTTGATCA 60.005 52.632 12.32 0.00 40.74 2.92
405 411 1.014044 TGAACTCGCCAGCGTTGATC 61.014 55.000 12.32 10.59 40.74 2.92
406 412 1.005037 TGAACTCGCCAGCGTTGAT 60.005 52.632 12.32 1.40 40.74 2.57
407 413 1.954146 GTGAACTCGCCAGCGTTGA 60.954 57.895 12.32 0.00 40.74 3.18
408 414 2.551270 GTGAACTCGCCAGCGTTG 59.449 61.111 12.32 8.84 40.74 4.10
409 415 2.765250 ATCGTGAACTCGCCAGCGTT 62.765 55.000 12.32 0.00 40.74 4.84
410 416 3.282745 ATCGTGAACTCGCCAGCGT 62.283 57.895 12.32 0.00 40.74 5.07
411 417 2.507102 ATCGTGAACTCGCCAGCG 60.507 61.111 5.50 5.50 41.35 5.18
412 418 2.456119 CCATCGTGAACTCGCCAGC 61.456 63.158 0.00 0.00 0.00 4.85
413 419 0.179100 ATCCATCGTGAACTCGCCAG 60.179 55.000 0.00 0.00 0.00 4.85
414 420 0.249120 AATCCATCGTGAACTCGCCA 59.751 50.000 0.00 0.00 0.00 5.69
415 421 0.652592 CAATCCATCGTGAACTCGCC 59.347 55.000 0.00 0.00 0.00 5.54
416 422 0.026803 GCAATCCATCGTGAACTCGC 59.973 55.000 0.00 0.00 0.00 5.03
417 423 1.061131 GTGCAATCCATCGTGAACTCG 59.939 52.381 0.00 0.00 0.00 4.18
418 424 2.350522 AGTGCAATCCATCGTGAACTC 58.649 47.619 0.00 0.00 26.05 3.01
419 425 2.479566 AGTGCAATCCATCGTGAACT 57.520 45.000 0.00 0.00 0.00 3.01
420 426 3.060272 CGATAGTGCAATCCATCGTGAAC 60.060 47.826 10.35 0.00 36.43 3.18
421 427 3.123050 CGATAGTGCAATCCATCGTGAA 58.877 45.455 10.35 0.00 36.43 3.18
422 428 2.742774 CGATAGTGCAATCCATCGTGA 58.257 47.619 10.35 0.00 36.43 4.35
435 441 3.040795 CGTCCGATTTGGTACGATAGTG 58.959 50.000 8.42 0.00 44.29 2.74
436 442 2.945008 TCGTCCGATTTGGTACGATAGT 59.055 45.455 11.33 0.00 46.00 2.12
437 443 3.552541 CTCGTCCGATTTGGTACGATAG 58.447 50.000 14.16 4.86 43.96 2.08
438 444 2.287188 GCTCGTCCGATTTGGTACGATA 60.287 50.000 14.16 0.12 43.96 2.92
439 445 1.535437 GCTCGTCCGATTTGGTACGAT 60.535 52.381 14.16 0.00 43.96 3.73
440 446 0.179156 GCTCGTCCGATTTGGTACGA 60.179 55.000 13.49 13.49 43.32 3.43
441 447 0.179145 AGCTCGTCCGATTTGGTACG 60.179 55.000 8.00 8.00 40.43 3.67
442 448 2.005971 AAGCTCGTCCGATTTGGTAC 57.994 50.000 0.00 0.00 39.52 3.34
443 449 2.754946 AAAGCTCGTCCGATTTGGTA 57.245 45.000 0.00 0.00 39.52 3.25
444 450 1.892209 AAAAGCTCGTCCGATTTGGT 58.108 45.000 0.00 0.00 39.52 3.67
445 451 3.302480 CGATAAAAGCTCGTCCGATTTGG 60.302 47.826 0.00 0.00 40.09 3.28
446 452 3.306166 ACGATAAAAGCTCGTCCGATTTG 59.694 43.478 0.00 0.00 45.63 2.32
447 453 3.518590 ACGATAAAAGCTCGTCCGATTT 58.481 40.909 0.00 0.00 45.63 2.17
448 454 3.160777 ACGATAAAAGCTCGTCCGATT 57.839 42.857 0.00 0.00 45.63 3.34
449 455 2.865343 ACGATAAAAGCTCGTCCGAT 57.135 45.000 0.00 0.00 45.63 4.18
450 456 3.065786 ACATACGATAAAAGCTCGTCCGA 59.934 43.478 0.82 0.00 45.63 4.55
451 457 3.179795 CACATACGATAAAAGCTCGTCCG 59.820 47.826 0.82 0.00 45.63 4.79
452 458 4.357142 TCACATACGATAAAAGCTCGTCC 58.643 43.478 0.82 0.00 45.63 4.79
453 459 4.441415 CCTCACATACGATAAAAGCTCGTC 59.559 45.833 0.82 0.00 45.63 4.20
455 461 3.182572 GCCTCACATACGATAAAAGCTCG 59.817 47.826 0.00 0.00 41.77 5.03
456 462 4.119862 TGCCTCACATACGATAAAAGCTC 58.880 43.478 0.00 0.00 0.00 4.09
457 463 4.137116 TGCCTCACATACGATAAAAGCT 57.863 40.909 0.00 0.00 0.00 3.74
458 464 4.875544 TTGCCTCACATACGATAAAAGC 57.124 40.909 0.00 0.00 0.00 3.51
459 465 6.019075 TCGAATTGCCTCACATACGATAAAAG 60.019 38.462 0.00 0.00 0.00 2.27
460 466 5.813157 TCGAATTGCCTCACATACGATAAAA 59.187 36.000 0.00 0.00 0.00 1.52
461 467 5.353111 TCGAATTGCCTCACATACGATAAA 58.647 37.500 0.00 0.00 0.00 1.40
462 468 4.939271 TCGAATTGCCTCACATACGATAA 58.061 39.130 0.00 0.00 0.00 1.75
463 469 4.277423 TCTCGAATTGCCTCACATACGATA 59.723 41.667 0.00 0.00 31.09 2.92
464 470 3.068165 TCTCGAATTGCCTCACATACGAT 59.932 43.478 0.00 0.00 31.09 3.73
465 471 2.425668 TCTCGAATTGCCTCACATACGA 59.574 45.455 0.00 0.00 0.00 3.43
466 472 2.791560 CTCTCGAATTGCCTCACATACG 59.208 50.000 0.00 0.00 0.00 3.06
467 473 4.046938 TCTCTCGAATTGCCTCACATAC 57.953 45.455 0.00 0.00 0.00 2.39
468 474 3.954258 TCTCTCTCGAATTGCCTCACATA 59.046 43.478 0.00 0.00 0.00 2.29
469 475 2.762887 TCTCTCTCGAATTGCCTCACAT 59.237 45.455 0.00 0.00 0.00 3.21
470 476 2.165234 CTCTCTCTCGAATTGCCTCACA 59.835 50.000 0.00 0.00 0.00 3.58
471 477 2.425312 TCTCTCTCTCGAATTGCCTCAC 59.575 50.000 0.00 0.00 0.00 3.51
472 478 2.687425 CTCTCTCTCTCGAATTGCCTCA 59.313 50.000 0.00 0.00 0.00 3.86
473 479 2.948979 TCTCTCTCTCTCGAATTGCCTC 59.051 50.000 0.00 0.00 0.00 4.70
474 480 2.951642 CTCTCTCTCTCTCGAATTGCCT 59.048 50.000 0.00 0.00 0.00 4.75
475 481 2.543653 GCTCTCTCTCTCTCGAATTGCC 60.544 54.545 0.00 0.00 0.00 4.52
476 482 2.731217 GCTCTCTCTCTCTCGAATTGC 58.269 52.381 0.00 0.00 0.00 3.56
477 483 2.286950 CCGCTCTCTCTCTCTCGAATTG 60.287 54.545 0.00 0.00 0.00 2.32
478 484 1.946768 CCGCTCTCTCTCTCTCGAATT 59.053 52.381 0.00 0.00 0.00 2.17
479 485 1.134220 ACCGCTCTCTCTCTCTCGAAT 60.134 52.381 0.00 0.00 0.00 3.34
480 486 0.250793 ACCGCTCTCTCTCTCTCGAA 59.749 55.000 0.00 0.00 0.00 3.71
481 487 0.179094 GACCGCTCTCTCTCTCTCGA 60.179 60.000 0.00 0.00 0.00 4.04
482 488 0.461163 TGACCGCTCTCTCTCTCTCG 60.461 60.000 0.00 0.00 0.00 4.04
558 564 1.829096 TGGGGTCAACAGTCGACGA 60.829 57.895 10.46 0.00 34.04 4.20
654 662 0.533308 CAGGTTTGAAACGTCGGGGA 60.533 55.000 0.00 0.00 0.00 4.81
655 663 1.946267 CAGGTTTGAAACGTCGGGG 59.054 57.895 0.00 0.00 0.00 5.73
656 664 1.281656 GCAGGTTTGAAACGTCGGG 59.718 57.895 0.00 0.00 0.00 5.14
657 665 1.083015 CGCAGGTTTGAAACGTCGG 60.083 57.895 0.00 0.00 0.00 4.79
679 687 2.016393 GAGATGGACACCGGATGCGA 62.016 60.000 9.46 0.00 0.00 5.10
691 699 3.745912 CGTCGGATCGGAGATGGA 58.254 61.111 2.75 0.00 45.12 3.41
784 794 2.432628 GAGAGGCGTTGGTGGTCG 60.433 66.667 0.00 0.00 0.00 4.79
796 806 1.421646 GGAGAGAGGGAGAGAGAGAGG 59.578 61.905 0.00 0.00 0.00 3.69
801 811 1.528309 GGCGGAGAGAGGGAGAGAG 60.528 68.421 0.00 0.00 0.00 3.20
802 812 1.990160 GAGGCGGAGAGAGGGAGAGA 61.990 65.000 0.00 0.00 0.00 3.10
803 813 1.528309 GAGGCGGAGAGAGGGAGAG 60.528 68.421 0.00 0.00 0.00 3.20
804 814 1.990160 GAGAGGCGGAGAGAGGGAGA 61.990 65.000 0.00 0.00 0.00 3.71
1128 1462 2.266055 GTGTTGGGGAGGAGCGAG 59.734 66.667 0.00 0.00 0.00 5.03
1440 1792 2.203938 TTCTCCTTGGGCTCCGGT 60.204 61.111 0.00 0.00 0.00 5.28
1692 2044 4.058124 CCTTCTTGTTGACGATCTTGACA 58.942 43.478 0.00 0.00 0.00 3.58
1776 2128 1.425428 GTCGAAGCAGAAATGGCGG 59.575 57.895 0.00 0.00 36.08 6.13
1873 2225 8.659925 AACATGTGCATTGTAAAGAAATTGAA 57.340 26.923 0.00 0.00 0.00 2.69
1927 2279 7.377928 CACAAACAACTGCATCTTCTTTCTAAG 59.622 37.037 0.00 0.00 0.00 2.18
2089 2453 4.411540 TCCTAGACCTACCATTACTCTCGT 59.588 45.833 0.00 0.00 0.00 4.18
2210 2574 3.010027 TGGACTCATGTTAAATGCCAGGA 59.990 43.478 0.00 0.00 0.00 3.86
2483 2847 3.039011 GGGTCTACCAGGAGATAGCAAA 58.961 50.000 0.81 0.00 39.85 3.68
2763 3127 4.516698 CCCTGGAATGCACAATACACTATC 59.483 45.833 0.00 0.00 0.00 2.08
2765 3129 3.521531 TCCCTGGAATGCACAATACACTA 59.478 43.478 0.00 0.00 0.00 2.74
2841 3205 5.300034 GGGAGTAGTAACTAAGGAAGAGCTC 59.700 48.000 5.27 5.27 35.56 4.09
2887 3251 1.196808 CACCGCGCTAGTGTCAAAAAT 59.803 47.619 16.71 0.00 0.00 1.82
3078 3442 5.744171 ACATTCACCTGTAGTATTGCATGA 58.256 37.500 0.00 0.00 0.00 3.07
3121 3485 2.288729 GTGGGACCGTGTTTTTCAGTAC 59.711 50.000 0.00 0.00 0.00 2.73
3304 3668 4.369182 ACCGATTTATGTTAGCTCCTTCG 58.631 43.478 0.00 0.00 0.00 3.79
3313 3677 4.261489 GCGAGGAGAGACCGATTTATGTTA 60.261 45.833 0.00 0.00 44.74 2.41
3583 3947 3.961182 TGTCACGAGTTCTGTTCAGTAC 58.039 45.455 0.00 2.18 0.00 2.73
3638 4002 0.693049 AACTTCCTCATTCCCAGCGT 59.307 50.000 0.00 0.00 0.00 5.07
3852 4216 2.287009 CCGCTTCACCTTTCTTTGTGTC 60.287 50.000 0.00 0.00 34.14 3.67
3933 4297 1.070445 CTGCAGATCCCGGACCATC 59.930 63.158 8.42 0.84 0.00 3.51
4351 4715 8.789767 ATATGCTGCCCATATAGAACTACTAT 57.210 34.615 0.00 0.00 43.61 2.12
4352 4716 9.709387 TTATATGCTGCCCATATAGAACTACTA 57.291 33.333 11.64 0.00 45.42 1.82
4353 4717 8.609617 TTATATGCTGCCCATATAGAACTACT 57.390 34.615 11.64 0.00 45.42 2.57
4354 4718 9.838339 ATTTATATGCTGCCCATATAGAACTAC 57.162 33.333 11.64 0.00 45.42 2.73
4387 4754 5.941948 ATAAGAACGTTTTTGGGACAGAG 57.058 39.130 13.87 0.00 42.39 3.35
4388 4755 7.989416 AATATAAGAACGTTTTTGGGACAGA 57.011 32.000 13.87 0.00 42.39 3.41
4389 4756 9.716507 CATAATATAAGAACGTTTTTGGGACAG 57.283 33.333 13.87 0.00 42.39 3.51
4390 4757 8.679100 CCATAATATAAGAACGTTTTTGGGACA 58.321 33.333 13.87 0.00 0.00 4.02
4391 4758 8.132995 CCCATAATATAAGAACGTTTTTGGGAC 58.867 37.037 14.35 0.00 0.00 4.46
4392 4759 8.053963 TCCCATAATATAAGAACGTTTTTGGGA 58.946 33.333 16.96 16.96 36.17 4.37
4393 4760 8.132995 GTCCCATAATATAAGAACGTTTTTGGG 58.867 37.037 13.87 13.75 0.00 4.12
4394 4761 7.853929 CGTCCCATAATATAAGAACGTTTTTGG 59.146 37.037 13.87 5.54 0.00 3.28
4395 4762 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
4396 4763 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
4397 4764 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
4398 4765 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
4399 4766 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
4400 4767 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
4401 4768 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
4402 4769 5.338137 CCCCTCCGTCCCATAATATAAGAAC 60.338 48.000 0.00 0.00 0.00 3.01
4403 4770 4.781087 CCCCTCCGTCCCATAATATAAGAA 59.219 45.833 0.00 0.00 0.00 2.52
4404 4771 4.359105 CCCCTCCGTCCCATAATATAAGA 58.641 47.826 0.00 0.00 0.00 2.10
4405 4772 3.454812 CCCCCTCCGTCCCATAATATAAG 59.545 52.174 0.00 0.00 0.00 1.73
4406 4773 3.181392 ACCCCCTCCGTCCCATAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
4407 4774 2.387861 ACCCCCTCCGTCCCATAATATA 59.612 50.000 0.00 0.00 0.00 0.86
4408 4775 1.153565 ACCCCCTCCGTCCCATAATAT 59.846 52.381 0.00 0.00 0.00 1.28
4409 4776 0.569204 ACCCCCTCCGTCCCATAATA 59.431 55.000 0.00 0.00 0.00 0.98
4410 4777 0.569204 TACCCCCTCCGTCCCATAAT 59.431 55.000 0.00 0.00 0.00 1.28
4411 4778 0.398948 GTACCCCCTCCGTCCCATAA 60.399 60.000 0.00 0.00 0.00 1.90
4412 4779 1.233949 GTACCCCCTCCGTCCCATA 59.766 63.158 0.00 0.00 0.00 2.74
4413 4780 2.041197 GTACCCCCTCCGTCCCAT 60.041 66.667 0.00 0.00 0.00 4.00
4414 4781 4.764771 CGTACCCCCTCCGTCCCA 62.765 72.222 0.00 0.00 0.00 4.37
4415 4782 4.766632 ACGTACCCCCTCCGTCCC 62.767 72.222 0.00 0.00 0.00 4.46
4416 4783 2.230994 GAAACGTACCCCCTCCGTCC 62.231 65.000 0.00 0.00 32.95 4.79
4417 4784 1.216444 GAAACGTACCCCCTCCGTC 59.784 63.158 0.00 0.00 32.95 4.79
4418 4785 1.228988 AGAAACGTACCCCCTCCGT 60.229 57.895 0.00 0.00 36.17 4.69
4419 4786 1.217244 CAGAAACGTACCCCCTCCG 59.783 63.158 0.00 0.00 0.00 4.63
4420 4787 0.689055 AACAGAAACGTACCCCCTCC 59.311 55.000 0.00 0.00 0.00 4.30
4421 4788 1.804601 CAACAGAAACGTACCCCCTC 58.195 55.000 0.00 0.00 0.00 4.30
4422 4789 0.250597 GCAACAGAAACGTACCCCCT 60.251 55.000 0.00 0.00 0.00 4.79
4423 4790 0.250597 AGCAACAGAAACGTACCCCC 60.251 55.000 0.00 0.00 0.00 5.40
4424 4791 0.872388 CAGCAACAGAAACGTACCCC 59.128 55.000 0.00 0.00 0.00 4.95
4425 4792 0.237498 GCAGCAACAGAAACGTACCC 59.763 55.000 0.00 0.00 0.00 3.69
4426 4793 0.237498 GGCAGCAACAGAAACGTACC 59.763 55.000 0.00 0.00 0.00 3.34
4427 4794 0.110823 CGGCAGCAACAGAAACGTAC 60.111 55.000 0.00 0.00 0.00 3.67
4807 5182 7.770897 AGTGAGAACTGCCCTTAACTTTATATG 59.229 37.037 0.00 0.00 0.00 1.78
4900 5275 8.933807 CAAGTTTATACTCAGATGCATATGGAG 58.066 37.037 20.58 18.03 31.99 3.86
5198 5574 5.278463 GCTCAAGACAAATTGCCAGTAGAAA 60.278 40.000 0.00 0.00 0.00 2.52
5406 5782 1.133253 CTCATTTCACGGCGCACAG 59.867 57.895 10.83 1.82 0.00 3.66
5447 5823 3.145286 GGCTCTTCCATATTGCCTCTTC 58.855 50.000 0.00 0.00 40.36 2.87


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

AutoCloner maintained by Alex Coulton.