Multiple sequence alignment - TraesCS3D01G301200

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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 TraesCS3D01G301200 chr3D 100.000 4529 0 0 1 4529 415656307 415651779 0.000000e+00 8364.0
1 TraesCS3D01G301200 chr3A 93.223 3010 139 19 783 3767 534531268 534534237 0.000000e+00 4368.0
2 TraesCS3D01G301200 chr3A 76.683 416 59 21 1 412 534529785 534530166 3.570000e-46 196.0
3 TraesCS3D01G301200 chr3A 89.726 146 12 3 526 670 534530175 534530318 2.780000e-42 183.0
4 TraesCS3D01G301200 chr3A 98.077 52 1 0 710 761 534530300 534530351 1.740000e-14 91.6
5 TraesCS3D01G301200 chr3A 80.531 113 13 6 4111 4217 714725080 714725189 1.350000e-10 78.7
6 TraesCS3D01G301200 chr3B 90.992 2420 158 26 781 3177 542165497 542163115 0.000000e+00 3206.0
7 TraesCS3D01G301200 chr3B 88.545 550 37 13 3189 3732 542163071 542162542 1.060000e-180 643.0
8 TraesCS3D01G301200 chr3B 81.220 410 53 16 3245 3651 763312027 763311639 4.400000e-80 309.0
9 TraesCS3D01G301200 chr3B 90.345 145 6 6 526 670 542166836 542166700 2.780000e-42 183.0
10 TraesCS3D01G301200 chr3B 93.103 58 2 2 710 767 542166718 542166663 2.900000e-12 84.2
11 TraesCS3D01G301200 chr7D 90.476 1407 70 28 3134 4508 6140937 6139563 0.000000e+00 1797.0
12 TraesCS3D01G301200 chr7D 94.867 487 19 4 2204 2690 6141958 6141478 0.000000e+00 756.0
13 TraesCS3D01G301200 chr7D 94.634 410 20 1 2628 3035 6141475 6141066 6.390000e-178 634.0
14 TraesCS3D01G301200 chr7D 89.535 258 16 5 921 1167 6142232 6141975 2.630000e-82 316.0
15 TraesCS3D01G301200 chr7D 92.208 77 3 2 710 786 6142358 6142285 6.200000e-19 106.0
16 TraesCS3D01G301200 chr7D 100.000 52 0 0 816 867 6142287 6142236 3.730000e-16 97.1
17 TraesCS3D01G301200 chr5A 85.090 664 56 14 1320 1975 54731636 54731008 4.940000e-179 638.0
18 TraesCS3D01G301200 chr1B 80.976 410 55 15 3245 3651 668457750 668458139 2.050000e-78 303.0
19 TraesCS3D01G301200 chr5B 80.732 410 53 17 3245 3651 106549209 106548823 3.430000e-76 296.0
20 TraesCS3D01G301200 chr7B 81.224 245 31 11 3245 3487 750368499 750368268 2.780000e-42 183.0
21 TraesCS3D01G301200 chr7B 77.778 171 23 13 33 196 137022710 137022872 1.740000e-14 91.6
22 TraesCS3D01G301200 chr6A 85.393 89 13 0 435 523 535901213 535901125 4.820000e-15 93.5
23 TraesCS3D01G301200 chr6B 78.626 131 24 4 85 213 162608986 162608858 2.900000e-12 84.2


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 TraesCS3D01G301200 chr3D 415651779 415656307 4528 True 8364.000000 8364 100.00000 1 4529 1 chr3D.!!$R1 4528
1 TraesCS3D01G301200 chr3A 534529785 534534237 4452 False 1209.650000 4368 89.42725 1 3767 4 chr3A.!!$F2 3766
2 TraesCS3D01G301200 chr3B 542162542 542166836 4294 True 1029.050000 3206 90.74625 526 3732 4 chr3B.!!$R2 3206
3 TraesCS3D01G301200 chr7D 6139563 6142358 2795 True 617.683333 1797 93.62000 710 4508 6 chr7D.!!$R1 3798
4 TraesCS3D01G301200 chr5A 54731008 54731636 628 True 638.000000 638 85.09000 1320 1975 1 chr5A.!!$R1 655

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
158 159 0.104197 GATGGGAGGGAGAGGGGAAT 60.104 60.0 0.00 0.0 0.00 3.01 F
452 454 0.166814 CGGAGCAAGTAAACTGCAGC 59.833 55.0 15.27 0.0 0.00 5.25 F
1036 2542 0.404426 AGCTGTCCCCCAAGGTAAAC 59.596 55.0 0.00 0.0 36.75 2.01 F
2171 3688 0.036732 TCAGAACACTCCATGCCACC 59.963 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 3199 0.245539 TCCGACGAAACTGATGGGTC 59.754 55.0 0.00 0.0 0.00 4.46 R
2082 3599 0.548031 AATCATCGCTGTGGGTGGAT 59.452 50.0 0.00 0.0 0.00 3.41 R
2692 4274 0.108585 TCTGAAGGCCTTTCAACGCT 59.891 50.0 21.54 0.0 44.84 5.07 R
3769 5478 0.035056 ACCTGCTCAATACACCCAGC 60.035 55.0 0.00 0.0 0.00 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.331019 AAACTGTCCACAAACGCCGC 62.331 55.000 0.00 0.00 0.00 6.53
27 28 1.657181 CACAAACGCCGCCAAGAAC 60.657 57.895 0.00 0.00 0.00 3.01
40 41 1.371389 AAGAACGGTCGTCGAGTGC 60.371 57.895 0.00 0.00 42.43 4.40
60 61 2.183811 CGTGCTGCTGGAGAGAGG 59.816 66.667 0.00 0.00 0.00 3.69
139 140 2.280389 AGTGTGTGCTGGCTGTCG 60.280 61.111 0.00 0.00 0.00 4.35
144 145 2.821366 GTGCTGGCTGTCGATGGG 60.821 66.667 0.00 0.00 0.00 4.00
150 151 2.801631 GGCTGTCGATGGGAGGGAG 61.802 68.421 0.00 0.00 0.00 4.30
151 152 1.758514 GCTGTCGATGGGAGGGAGA 60.759 63.158 0.00 0.00 0.00 3.71
154 155 1.834822 GTCGATGGGAGGGAGAGGG 60.835 68.421 0.00 0.00 0.00 4.30
155 156 2.525381 CGATGGGAGGGAGAGGGG 60.525 72.222 0.00 0.00 0.00 4.79
156 157 3.037715 GATGGGAGGGAGAGGGGA 58.962 66.667 0.00 0.00 0.00 4.81
157 158 1.318380 GATGGGAGGGAGAGGGGAA 59.682 63.158 0.00 0.00 0.00 3.97
158 159 0.104197 GATGGGAGGGAGAGGGGAAT 60.104 60.000 0.00 0.00 0.00 3.01
159 160 0.402566 ATGGGAGGGAGAGGGGAATG 60.403 60.000 0.00 0.00 0.00 2.67
160 161 1.772156 GGGAGGGAGAGGGGAATGG 60.772 68.421 0.00 0.00 0.00 3.16
161 162 1.004891 GGAGGGAGAGGGGAATGGT 59.995 63.158 0.00 0.00 0.00 3.55
200 201 2.231380 GGCCAGGGGAAGGACAAGA 61.231 63.158 0.00 0.00 33.02 3.02
201 202 1.301293 GCCAGGGGAAGGACAAGAG 59.699 63.158 0.00 0.00 0.00 2.85
202 203 1.301293 CCAGGGGAAGGACAAGAGC 59.699 63.158 0.00 0.00 0.00 4.09
203 204 1.078848 CAGGGGAAGGACAAGAGCG 60.079 63.158 0.00 0.00 0.00 5.03
204 205 1.229209 AGGGGAAGGACAAGAGCGA 60.229 57.895 0.00 0.00 0.00 4.93
205 206 1.219393 GGGGAAGGACAAGAGCGAG 59.781 63.158 0.00 0.00 0.00 5.03
206 207 1.448717 GGGAAGGACAAGAGCGAGC 60.449 63.158 0.00 0.00 0.00 5.03
208 209 1.080434 GAAGGACAAGAGCGAGCGT 60.080 57.895 0.00 0.00 0.00 5.07
231 232 4.796231 ATCGCACGTGTCCGCTCC 62.796 66.667 18.38 0.00 37.70 4.70
237 238 2.509336 CGTGTCCGCTCCATGTCC 60.509 66.667 0.00 0.00 0.00 4.02
239 240 4.451150 TGTCCGCTCCATGTCCGC 62.451 66.667 0.00 0.00 0.00 5.54
261 262 1.278637 CGTTGACGCAAACCAGACC 59.721 57.895 0.00 0.00 0.00 3.85
266 267 0.958822 GACGCAAACCAGACCCAAAT 59.041 50.000 0.00 0.00 0.00 2.32
283 284 3.941573 CAAATTTGGACCTGAAATGGGG 58.058 45.455 10.49 0.00 0.00 4.96
284 285 3.274281 AATTTGGACCTGAAATGGGGT 57.726 42.857 0.00 0.00 38.70 4.95
285 286 2.785357 TTTGGACCTGAAATGGGGTT 57.215 45.000 0.00 0.00 35.77 4.11
286 287 2.008242 TTGGACCTGAAATGGGGTTG 57.992 50.000 0.00 0.00 35.77 3.77
290 291 2.274645 CCTGAAATGGGGTTGCGCA 61.275 57.895 5.66 5.66 0.00 6.09
292 293 2.126502 GAAATGGGGTTGCGCACG 60.127 61.111 11.12 0.00 0.00 5.34
293 294 3.625082 GAAATGGGGTTGCGCACGG 62.625 63.158 11.12 0.00 0.00 4.94
320 321 5.874895 AAAAGGGACAAGCGTCTATTTAC 57.125 39.130 0.00 0.00 42.21 2.01
323 324 2.601763 GGGACAAGCGTCTATTTACGTG 59.398 50.000 0.00 0.00 44.64 4.49
325 326 1.997606 ACAAGCGTCTATTTACGTGGC 59.002 47.619 0.00 0.00 44.64 5.01
338 340 3.037249 GTGGCGCGTTGAACCGTA 61.037 61.111 8.43 0.00 0.00 4.02
345 347 2.411289 GCGCGTTGAACCGTAATTTGTA 60.411 45.455 8.43 0.00 0.00 2.41
355 357 4.493547 ACCGTAATTTGTATCCGTTTCGA 58.506 39.130 0.00 0.00 0.00 3.71
358 360 6.124759 CCGTAATTTGTATCCGTTTCGATTC 58.875 40.000 0.00 0.00 0.00 2.52
364 366 6.729391 TTGTATCCGTTTCGATTCAAATGA 57.271 33.333 0.00 0.00 29.72 2.57
366 368 6.539324 TGTATCCGTTTCGATTCAAATGAAC 58.461 36.000 0.00 0.00 36.80 3.18
369 371 2.270176 CGTTTCGATTCAAATGAACGCG 59.730 45.455 3.53 3.53 36.80 6.01
371 373 0.793250 TCGATTCAAATGAACGCGCA 59.207 45.000 5.73 0.00 36.80 6.09
372 374 1.195674 TCGATTCAAATGAACGCGCAA 59.804 42.857 5.73 0.00 36.80 4.85
373 375 1.574477 CGATTCAAATGAACGCGCAAG 59.426 47.619 5.73 0.00 36.80 4.01
393 395 0.596082 CAGTTTAGGTTGGGGCGTTG 59.404 55.000 0.00 0.00 0.00 4.10
399 401 0.475044 AGGTTGGGGCGTTGAAGTTA 59.525 50.000 0.00 0.00 0.00 2.24
405 407 2.028748 TGGGGCGTTGAAGTTACTCTAC 60.029 50.000 0.00 0.00 0.00 2.59
406 408 2.028748 GGGGCGTTGAAGTTACTCTACA 60.029 50.000 0.00 0.00 0.00 2.74
412 414 7.253422 GGCGTTGAAGTTACTCTACATACTAA 58.747 38.462 0.00 0.00 0.00 2.24
434 436 8.529476 ACTAATACTAAGATATAAAGGCCCACG 58.471 37.037 0.00 0.00 0.00 4.94
435 437 4.618920 ACTAAGATATAAAGGCCCACGG 57.381 45.455 0.00 0.00 0.00 4.94
436 438 4.228824 ACTAAGATATAAAGGCCCACGGA 58.771 43.478 0.00 0.00 0.00 4.69
437 439 3.771577 AAGATATAAAGGCCCACGGAG 57.228 47.619 0.00 0.00 0.00 4.63
438 440 1.348036 AGATATAAAGGCCCACGGAGC 59.652 52.381 0.00 0.00 0.00 4.70
439 441 1.071699 GATATAAAGGCCCACGGAGCA 59.928 52.381 0.00 0.00 0.00 4.26
440 442 0.913205 TATAAAGGCCCACGGAGCAA 59.087 50.000 0.00 0.00 0.00 3.91
441 443 0.394352 ATAAAGGCCCACGGAGCAAG 60.394 55.000 0.00 0.00 0.00 4.01
442 444 1.774894 TAAAGGCCCACGGAGCAAGT 61.775 55.000 0.00 0.00 0.00 3.16
443 445 1.774894 AAAGGCCCACGGAGCAAGTA 61.775 55.000 0.00 0.00 0.00 2.24
444 446 1.774894 AAGGCCCACGGAGCAAGTAA 61.775 55.000 0.00 0.00 0.00 2.24
445 447 1.302993 GGCCCACGGAGCAAGTAAA 60.303 57.895 0.00 0.00 0.00 2.01
446 448 1.583495 GGCCCACGGAGCAAGTAAAC 61.583 60.000 0.00 0.00 0.00 2.01
447 449 0.605589 GCCCACGGAGCAAGTAAACT 60.606 55.000 0.00 0.00 0.00 2.66
448 450 1.156736 CCCACGGAGCAAGTAAACTG 58.843 55.000 0.00 0.00 0.00 3.16
449 451 0.517316 CCACGGAGCAAGTAAACTGC 59.483 55.000 0.00 0.00 0.00 4.40
450 452 1.225855 CACGGAGCAAGTAAACTGCA 58.774 50.000 0.00 0.00 0.00 4.41
451 453 1.195448 CACGGAGCAAGTAAACTGCAG 59.805 52.381 13.48 13.48 0.00 4.41
452 454 0.166814 CGGAGCAAGTAAACTGCAGC 59.833 55.000 15.27 0.00 0.00 5.25
453 455 1.528129 GGAGCAAGTAAACTGCAGCT 58.472 50.000 15.27 2.45 33.87 4.24
454 456 1.882623 GGAGCAAGTAAACTGCAGCTT 59.117 47.619 15.27 11.11 32.19 3.74
455 457 2.095516 GGAGCAAGTAAACTGCAGCTTC 60.096 50.000 15.27 0.00 32.19 3.86
456 458 2.549754 GAGCAAGTAAACTGCAGCTTCA 59.450 45.455 15.27 0.00 32.19 3.02
457 459 3.152341 AGCAAGTAAACTGCAGCTTCAT 58.848 40.909 15.27 0.00 0.00 2.57
458 460 3.057736 AGCAAGTAAACTGCAGCTTCATG 60.058 43.478 15.27 9.08 0.00 3.07
459 461 3.058016 GCAAGTAAACTGCAGCTTCATGA 60.058 43.478 15.27 0.00 0.00 3.07
460 462 4.380233 GCAAGTAAACTGCAGCTTCATGAT 60.380 41.667 15.27 0.00 0.00 2.45
461 463 5.706916 CAAGTAAACTGCAGCTTCATGATT 58.293 37.500 15.27 0.00 0.00 2.57
462 464 5.972107 AGTAAACTGCAGCTTCATGATTT 57.028 34.783 15.27 6.77 0.00 2.17
463 465 6.336842 AGTAAACTGCAGCTTCATGATTTT 57.663 33.333 15.27 6.02 0.00 1.82
464 466 6.752168 AGTAAACTGCAGCTTCATGATTTTT 58.248 32.000 15.27 5.27 0.00 1.94
465 467 7.885297 AGTAAACTGCAGCTTCATGATTTTTA 58.115 30.769 15.27 4.25 0.00 1.52
466 468 8.359642 AGTAAACTGCAGCTTCATGATTTTTAA 58.640 29.630 15.27 0.00 0.00 1.52
467 469 9.143631 GTAAACTGCAGCTTCATGATTTTTAAT 57.856 29.630 15.27 0.00 0.00 1.40
468 470 8.611654 AAACTGCAGCTTCATGATTTTTAATT 57.388 26.923 15.27 0.00 0.00 1.40
469 471 9.709495 AAACTGCAGCTTCATGATTTTTAATTA 57.291 25.926 15.27 0.00 0.00 1.40
470 472 8.693542 ACTGCAGCTTCATGATTTTTAATTAC 57.306 30.769 15.27 0.00 0.00 1.89
471 473 8.306038 ACTGCAGCTTCATGATTTTTAATTACA 58.694 29.630 15.27 0.00 0.00 2.41
472 474 8.692110 TGCAGCTTCATGATTTTTAATTACAG 57.308 30.769 0.00 0.00 0.00 2.74
473 475 7.276218 TGCAGCTTCATGATTTTTAATTACAGC 59.724 33.333 0.00 0.00 0.00 4.40
474 476 7.490402 GCAGCTTCATGATTTTTAATTACAGCT 59.510 33.333 0.00 0.00 0.00 4.24
475 477 9.017669 CAGCTTCATGATTTTTAATTACAGCTC 57.982 33.333 7.06 0.00 0.00 4.09
476 478 8.193438 AGCTTCATGATTTTTAATTACAGCTCC 58.807 33.333 0.00 0.00 0.00 4.70
477 479 7.166473 GCTTCATGATTTTTAATTACAGCTCCG 59.834 37.037 0.00 0.00 0.00 4.63
478 480 6.494842 TCATGATTTTTAATTACAGCTCCGC 58.505 36.000 0.00 0.00 0.00 5.54
479 481 5.243426 TGATTTTTAATTACAGCTCCGCC 57.757 39.130 0.00 0.00 0.00 6.13
480 482 4.097286 TGATTTTTAATTACAGCTCCGCCC 59.903 41.667 0.00 0.00 0.00 6.13
481 483 1.658994 TTTAATTACAGCTCCGCCCG 58.341 50.000 0.00 0.00 0.00 6.13
482 484 0.812412 TTAATTACAGCTCCGCCCGC 60.812 55.000 0.00 0.00 0.00 6.13
483 485 1.682451 TAATTACAGCTCCGCCCGCT 61.682 55.000 0.00 0.00 38.49 5.52
484 486 2.925162 AATTACAGCTCCGCCCGCTC 62.925 60.000 0.00 0.00 35.07 5.03
503 505 3.827898 GGGAGCGGAGTCGTGGAG 61.828 72.222 0.00 0.00 38.89 3.86
504 506 4.500116 GGAGCGGAGTCGTGGAGC 62.500 72.222 0.00 0.00 38.89 4.70
505 507 4.838486 GAGCGGAGTCGTGGAGCG 62.838 72.222 0.00 0.00 43.01 5.03
522 524 3.564027 GGCGCGATTCCGAACAGG 61.564 66.667 12.10 0.00 42.97 4.00
523 525 2.813908 GCGCGATTCCGAACAGGT 60.814 61.111 12.10 0.00 41.99 4.00
524 526 2.799540 GCGCGATTCCGAACAGGTC 61.800 63.158 12.10 0.00 41.99 3.85
555 557 2.202703 ACCGGATACAAGCGACGC 60.203 61.111 13.03 13.03 0.00 5.19
594 596 3.003689 ACTTTGTCACCGAGCAATCAAAG 59.996 43.478 11.98 11.98 43.77 2.77
598 600 2.413453 GTCACCGAGCAATCAAAGTCTC 59.587 50.000 0.00 0.00 0.00 3.36
607 609 7.012358 CGAGCAATCAAAGTCTCTTTTTCTAC 58.988 38.462 0.00 0.00 0.00 2.59
608 610 6.892691 AGCAATCAAAGTCTCTTTTTCTACG 58.107 36.000 0.00 0.00 0.00 3.51
624 626 5.545658 TTCTACGGATGAGCAAAATCAAC 57.454 39.130 0.00 0.00 31.76 3.18
650 653 7.009815 CGTTTGATCGAAGCCTTATTTACAGTA 59.990 37.037 0.00 0.00 0.00 2.74
651 654 8.662141 GTTTGATCGAAGCCTTATTTACAGTAA 58.338 33.333 0.00 0.00 0.00 2.24
652 655 8.420374 TTGATCGAAGCCTTATTTACAGTAAG 57.580 34.615 0.00 0.00 0.00 2.34
654 657 6.290294 TCGAAGCCTTATTTACAGTAAGGT 57.710 37.500 12.13 0.00 46.43 3.50
655 658 6.103997 TCGAAGCCTTATTTACAGTAAGGTG 58.896 40.000 12.13 3.01 46.43 4.00
656 659 6.071221 TCGAAGCCTTATTTACAGTAAGGTGA 60.071 38.462 12.13 4.79 46.43 4.02
657 660 6.255887 CGAAGCCTTATTTACAGTAAGGTGAG 59.744 42.308 12.13 0.00 46.43 3.51
658 661 6.869206 AGCCTTATTTACAGTAAGGTGAGA 57.131 37.500 12.13 0.00 46.43 3.27
659 662 6.879400 AGCCTTATTTACAGTAAGGTGAGAG 58.121 40.000 12.13 0.00 46.43 3.20
660 663 5.524281 GCCTTATTTACAGTAAGGTGAGAGC 59.476 44.000 12.13 1.80 46.43 4.09
661 664 6.630638 GCCTTATTTACAGTAAGGTGAGAGCT 60.631 42.308 12.13 0.00 46.43 4.09
662 665 6.758886 CCTTATTTACAGTAAGGTGAGAGCTG 59.241 42.308 0.00 0.00 42.03 4.24
663 666 4.537135 TTTACAGTAAGGTGAGAGCTGG 57.463 45.455 0.00 0.00 0.00 4.85
664 667 2.016905 ACAGTAAGGTGAGAGCTGGT 57.983 50.000 0.00 0.00 0.00 4.00
665 668 1.620819 ACAGTAAGGTGAGAGCTGGTG 59.379 52.381 0.00 0.00 0.00 4.17
666 669 0.610687 AGTAAGGTGAGAGCTGGTGC 59.389 55.000 0.00 0.00 40.05 5.01
680 683 1.258676 TGGTGCTACCATACGACACA 58.741 50.000 4.16 0.00 44.79 3.72
681 684 1.828595 TGGTGCTACCATACGACACAT 59.171 47.619 4.16 0.00 44.79 3.21
682 685 2.201732 GGTGCTACCATACGACACATG 58.798 52.381 0.00 0.00 38.42 3.21
683 686 2.418197 GGTGCTACCATACGACACATGT 60.418 50.000 0.00 0.00 38.42 3.21
684 687 2.603110 GTGCTACCATACGACACATGTG 59.397 50.000 24.25 24.25 0.00 3.21
685 688 2.494073 TGCTACCATACGACACATGTGA 59.506 45.455 31.94 10.25 0.00 3.58
686 689 3.132111 TGCTACCATACGACACATGTGAT 59.868 43.478 31.94 18.06 0.00 3.06
687 690 4.339814 TGCTACCATACGACACATGTGATA 59.660 41.667 31.94 19.50 0.00 2.15
688 691 5.163499 TGCTACCATACGACACATGTGATAA 60.163 40.000 31.94 14.06 0.00 1.75
689 692 5.402568 GCTACCATACGACACATGTGATAAG 59.597 44.000 31.94 19.67 0.00 1.73
690 693 4.119862 ACCATACGACACATGTGATAAGC 58.880 43.478 31.94 13.57 0.00 3.09
691 694 4.119136 CCATACGACACATGTGATAAGCA 58.881 43.478 31.94 11.71 0.00 3.91
692 695 4.570369 CCATACGACACATGTGATAAGCAA 59.430 41.667 31.94 10.52 0.00 3.91
693 696 5.237127 CCATACGACACATGTGATAAGCAAT 59.763 40.000 31.94 6.96 0.00 3.56
694 697 6.423604 CCATACGACACATGTGATAAGCAATA 59.576 38.462 31.94 11.98 0.00 1.90
695 698 5.718649 ACGACACATGTGATAAGCAATAC 57.281 39.130 31.94 8.50 0.00 1.89
696 699 5.175127 ACGACACATGTGATAAGCAATACA 58.825 37.500 31.94 0.00 0.00 2.29
697 700 5.063438 ACGACACATGTGATAAGCAATACAC 59.937 40.000 31.94 0.00 0.00 2.90
698 701 5.063312 CGACACATGTGATAAGCAATACACA 59.937 40.000 31.94 0.00 45.06 3.72
699 702 6.182039 ACACATGTGATAAGCAATACACAC 57.818 37.500 31.94 0.00 44.08 3.82
700 703 5.939883 ACACATGTGATAAGCAATACACACT 59.060 36.000 31.94 0.06 44.08 3.55
701 704 7.102993 ACACATGTGATAAGCAATACACACTA 58.897 34.615 31.94 0.00 44.08 2.74
702 705 7.064609 ACACATGTGATAAGCAATACACACTAC 59.935 37.037 31.94 0.00 44.08 2.73
703 706 7.278646 CACATGTGATAAGCAATACACACTACT 59.721 37.037 21.64 0.00 44.08 2.57
704 707 7.824289 ACATGTGATAAGCAATACACACTACTT 59.176 33.333 0.00 0.00 44.08 2.24
705 708 9.313118 CATGTGATAAGCAATACACACTACTTA 57.687 33.333 0.00 0.00 44.08 2.24
706 709 9.884636 ATGTGATAAGCAATACACACTACTTAA 57.115 29.630 0.00 0.00 44.08 1.85
707 710 9.713713 TGTGATAAGCAATACACACTACTTAAA 57.286 29.630 0.00 0.00 38.14 1.52
761 764 2.165845 AGGATCCACGTCTCGGTAAAAG 59.834 50.000 15.82 0.00 0.00 2.27
770 773 6.093082 CCACGTCTCGGTAAAAGGAAAATAAT 59.907 38.462 0.00 0.00 0.00 1.28
773 776 9.218440 ACGTCTCGGTAAAAGGAAAATAATAAA 57.782 29.630 0.00 0.00 0.00 1.40
994 2494 1.743623 CAGTATTTCCACGCCGCCA 60.744 57.895 0.00 0.00 0.00 5.69
1036 2542 0.404426 AGCTGTCCCCCAAGGTAAAC 59.596 55.000 0.00 0.00 36.75 2.01
1556 3065 3.827898 CGACGAGGAGGAGGTGGC 61.828 72.222 0.00 0.00 0.00 5.01
1671 3188 2.911928 GCTCCCTTCCCTGCTACC 59.088 66.667 0.00 0.00 0.00 3.18
1682 3199 1.065854 CCCTGCTACCACTTCAGAAGG 60.066 57.143 14.90 0.94 37.34 3.46
1739 3256 1.352156 GATGTCGGTGTTCACGAGGC 61.352 60.000 0.00 0.00 41.50 4.70
1758 3275 4.785453 GTTCCTCTGCTGGGGCCG 62.785 72.222 4.23 0.00 37.74 6.13
1976 3493 5.249163 TGGATGTTCTGAAGGAAGATTCTGA 59.751 40.000 0.00 0.00 37.93 3.27
1977 3494 6.176183 GGATGTTCTGAAGGAAGATTCTGAA 58.824 40.000 0.00 0.00 41.78 3.02
2069 3586 1.219124 CGGGTGGAGATGTCACTGG 59.781 63.158 0.00 0.00 35.61 4.00
2082 3599 1.420138 GTCACTGGAGTTCCCTTTGGA 59.580 52.381 0.00 0.00 39.54 3.53
2113 3630 1.528586 GCGATGATTTGGATGAGGACG 59.471 52.381 0.00 0.00 0.00 4.79
2171 3688 0.036732 TCAGAACACTCCATGCCACC 59.963 55.000 0.00 0.00 0.00 4.61
2172 3689 0.250858 CAGAACACTCCATGCCACCA 60.251 55.000 0.00 0.00 0.00 4.17
2283 3800 0.175073 AATTCGACTCGCTGGGGTAC 59.825 55.000 0.00 0.00 0.00 3.34
2506 4023 5.180117 GTGCCAGTATTAGCTCCACATAATG 59.820 44.000 0.00 0.00 0.00 1.90
2599 4116 1.321474 CTTGGAGCTTCCTGTGCAAA 58.679 50.000 0.00 0.00 37.46 3.68
2601 4118 1.165907 TGGAGCTTCCTGTGCAAACG 61.166 55.000 0.00 0.00 37.46 3.60
2635 4152 2.306341 AGATCAATCTGTGTGCCTCG 57.694 50.000 0.00 0.00 35.42 4.63
2654 4171 2.935849 TCGATGTTCCATCAATTGGTCG 59.064 45.455 5.42 0.00 46.52 4.79
2692 4274 4.287067 AGAAAGTTCAGCAAGAGGATGGTA 59.713 41.667 0.00 0.00 32.50 3.25
2704 4292 0.733150 GGATGGTAGCGTTGAAAGGC 59.267 55.000 0.00 0.00 39.92 4.35
2840 4428 4.164294 GTCAAAGACTCAATTCAGCATGC 58.836 43.478 10.51 10.51 34.76 4.06
2845 4433 2.089980 ACTCAATTCAGCATGCTGGAC 58.910 47.619 39.72 3.33 43.75 4.02
2873 4461 3.244911 ACGGTTCAGGAATCCATGTCTTT 60.245 43.478 0.61 0.00 0.00 2.52
2918 4506 4.143263 GCAAAAGGATTCTGACAAAATGCG 60.143 41.667 0.00 0.00 30.61 4.73
2932 4520 0.609131 AATGCGAACCCCTGGTCTTG 60.609 55.000 0.00 0.00 33.12 3.02
3018 4608 2.988549 GCGAAGTGTGAGTGCGTCG 61.989 63.158 0.00 0.00 39.03 5.12
3057 4692 2.655090 TTGAGGACATCTGTTGGCAA 57.345 45.000 0.00 0.00 33.62 4.52
3058 4693 2.655090 TGAGGACATCTGTTGGCAAA 57.345 45.000 0.00 0.00 33.62 3.68
3075 4710 5.237048 TGGCAAATGCATTTTAGTTCCTTC 58.763 37.500 21.95 5.09 44.36 3.46
3079 4714 6.183360 GCAAATGCATTTTAGTTCCTTCGAAG 60.183 38.462 21.95 18.51 41.59 3.79
3080 4715 6.575162 AATGCATTTTAGTTCCTTCGAAGT 57.425 33.333 23.03 7.77 35.73 3.01
3144 4780 5.702065 TGGCCTGATAGGTGTGTTATTTA 57.298 39.130 3.32 0.00 37.80 1.40
3160 4796 8.020819 TGTGTTATTTACTGCAAATTAGACAGC 58.979 33.333 0.02 0.00 35.64 4.40
3390 5090 3.850752 TCAAGCTTTTATTCCCCCACAA 58.149 40.909 0.00 0.00 0.00 3.33
3429 5130 8.062448 GCTATTAACTCGATGTGTTGTTATTCC 58.938 37.037 0.00 0.00 0.00 3.01
3554 5255 1.285578 GCAAACACGGTGCATTTTGT 58.714 45.000 18.19 0.00 41.80 2.83
3562 5265 2.360483 ACGGTGCATTTTGTTGATGTCA 59.640 40.909 0.00 0.00 0.00 3.58
3653 5359 2.920724 TGGTGCTGTAGCTGTAACAA 57.079 45.000 5.38 0.00 42.66 2.83
3658 5364 4.389077 GGTGCTGTAGCTGTAACAAGTTAG 59.611 45.833 5.38 0.00 42.66 2.34
3690 5399 1.559831 GCTTGCAGTGTGTTTGGTTC 58.440 50.000 0.00 0.00 0.00 3.62
3692 5401 1.476085 CTTGCAGTGTGTTTGGTTCCA 59.524 47.619 0.00 0.00 0.00 3.53
3739 5448 8.869897 CATTTGACATTATTGTACTGTACTCGT 58.130 33.333 17.98 7.35 35.79 4.18
3769 5478 3.539604 CCCTAAAGGTGAAGCAGAGATG 58.460 50.000 0.00 0.00 0.00 2.90
3770 5479 2.941720 CCTAAAGGTGAAGCAGAGATGC 59.058 50.000 0.00 0.00 0.00 3.91
3772 5481 2.110901 AAGGTGAAGCAGAGATGCTG 57.889 50.000 3.09 0.00 45.54 4.41
3786 5497 1.945394 GATGCTGGGTGTATTGAGCAG 59.055 52.381 0.00 0.00 44.30 4.24
3801 5512 0.771127 AGCAGGTTTAGTCTTGCCCA 59.229 50.000 0.00 0.00 40.50 5.36
3812 5523 1.963515 GTCTTGCCCACTTTGTCCAAT 59.036 47.619 0.00 0.00 0.00 3.16
3813 5524 2.365293 GTCTTGCCCACTTTGTCCAATT 59.635 45.455 0.00 0.00 0.00 2.32
3820 5531 2.364970 CCACTTTGTCCAATTGAGCCAA 59.635 45.455 7.12 3.79 0.00 4.52
3882 5593 6.096001 GTGATTTCCCTTATGCTCTGAACATT 59.904 38.462 0.00 0.00 0.00 2.71
3902 5613 2.431260 GCAATGGCCGTTGTGCTG 60.431 61.111 32.88 13.74 34.13 4.41
4011 5722 7.011950 CCTGTGCCTAAACATTATAATCGTCAA 59.988 37.037 0.00 0.00 0.00 3.18
4012 5723 8.270080 TGTGCCTAAACATTATAATCGTCAAA 57.730 30.769 0.00 0.00 0.00 2.69
4013 5724 8.178964 TGTGCCTAAACATTATAATCGTCAAAC 58.821 33.333 0.00 0.00 0.00 2.93
4014 5725 7.372396 GTGCCTAAACATTATAATCGTCAAACG 59.628 37.037 0.00 0.00 44.19 3.60
4015 5726 6.849305 GCCTAAACATTATAATCGTCAAACGG 59.151 38.462 0.00 0.00 42.81 4.44
4016 5727 7.466320 GCCTAAACATTATAATCGTCAAACGGT 60.466 37.037 0.00 0.00 42.81 4.83
4017 5728 9.033481 CCTAAACATTATAATCGTCAAACGGTA 57.967 33.333 0.00 0.00 42.81 4.02
4019 5730 8.483307 AAACATTATAATCGTCAAACGGTAGT 57.517 30.769 0.00 0.00 42.81 2.73
4020 5731 7.689953 ACATTATAATCGTCAAACGGTAGTC 57.310 36.000 0.00 0.00 42.81 2.59
4021 5732 7.486647 ACATTATAATCGTCAAACGGTAGTCT 58.513 34.615 0.00 0.00 42.81 3.24
4022 5733 7.646922 ACATTATAATCGTCAAACGGTAGTCTC 59.353 37.037 0.00 0.00 42.81 3.36
4124 5835 9.924650 GTGACATTTAACCTATACCTATACCTG 57.075 37.037 0.00 0.00 0.00 4.00
4157 5868 3.001939 ACAAAGTAAGGTGCGTTTCTTCG 59.998 43.478 0.00 0.00 0.00 3.79
4159 5870 0.794473 GTAAGGTGCGTTTCTTCGGG 59.206 55.000 0.00 0.00 0.00 5.14
4217 5928 8.488651 ACTATTCGAGGTGGTACTAATTTTTG 57.511 34.615 0.00 0.00 0.00 2.44
4230 5941 9.961266 GGTACTAATTTTTGTTGTTGTTTTGTC 57.039 29.630 0.00 0.00 0.00 3.18
4367 6078 5.050091 CACGAAAATGTTTGCTAGTCTGACT 60.050 40.000 15.57 15.57 0.00 3.41
4508 6219 4.889995 ACCTACTACTACCGTAAATCCCAC 59.110 45.833 0.00 0.00 0.00 4.61
4509 6220 4.889409 CCTACTACTACCGTAAATCCCACA 59.111 45.833 0.00 0.00 0.00 4.17
4510 6221 4.725790 ACTACTACCGTAAATCCCACAC 57.274 45.455 0.00 0.00 0.00 3.82
4511 6222 3.448660 ACTACTACCGTAAATCCCACACC 59.551 47.826 0.00 0.00 0.00 4.16
4512 6223 1.205417 ACTACCGTAAATCCCACACCG 59.795 52.381 0.00 0.00 0.00 4.94
4513 6224 1.477700 CTACCGTAAATCCCACACCGA 59.522 52.381 0.00 0.00 0.00 4.69
4514 6225 0.037046 ACCGTAAATCCCACACCGAC 60.037 55.000 0.00 0.00 0.00 4.79
4515 6226 0.037139 CCGTAAATCCCACACCGACA 60.037 55.000 0.00 0.00 0.00 4.35
4516 6227 1.073177 CGTAAATCCCACACCGACAC 58.927 55.000 0.00 0.00 0.00 3.67
4517 6228 1.445871 GTAAATCCCACACCGACACC 58.554 55.000 0.00 0.00 0.00 4.16
4518 6229 0.037139 TAAATCCCACACCGACACCG 60.037 55.000 0.00 0.00 0.00 4.94
4519 6230 2.047213 AAATCCCACACCGACACCGT 62.047 55.000 0.00 0.00 0.00 4.83
4520 6231 2.444700 AATCCCACACCGACACCGTC 62.445 60.000 0.00 0.00 0.00 4.79
4521 6232 3.612681 CCCACACCGACACCGTCT 61.613 66.667 0.00 0.00 0.00 4.18
4522 6233 2.270257 CCCACACCGACACCGTCTA 61.270 63.158 0.00 0.00 0.00 2.59
4523 6234 1.661480 CCACACCGACACCGTCTAA 59.339 57.895 0.00 0.00 0.00 2.10
4524 6235 0.245539 CCACACCGACACCGTCTAAT 59.754 55.000 0.00 0.00 0.00 1.73
4525 6236 1.337447 CCACACCGACACCGTCTAATT 60.337 52.381 0.00 0.00 0.00 1.40
4526 6237 1.724623 CACACCGACACCGTCTAATTG 59.275 52.381 0.00 0.00 0.00 2.32
4527 6238 1.614903 ACACCGACACCGTCTAATTGA 59.385 47.619 0.00 0.00 0.00 2.57
4528 6239 2.232941 ACACCGACACCGTCTAATTGAT 59.767 45.455 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.858680 TGGCGGCGTTTGTGGACA 62.859 61.111 9.37 0.00 0.00 4.02
20 21 1.002250 CACTCGACGACCGTTCTTGG 61.002 60.000 0.00 0.00 39.75 3.61
43 44 1.315981 TACCTCTCTCCAGCAGCACG 61.316 60.000 0.00 0.00 0.00 5.34
121 122 2.601398 CGACAGCCAGCACACACTG 61.601 63.158 0.00 0.00 37.42 3.66
122 123 2.104572 ATCGACAGCCAGCACACACT 62.105 55.000 0.00 0.00 0.00 3.55
123 124 1.669115 ATCGACAGCCAGCACACAC 60.669 57.895 0.00 0.00 0.00 3.82
124 125 1.668793 CATCGACAGCCAGCACACA 60.669 57.895 0.00 0.00 0.00 3.72
125 126 2.393768 CCATCGACAGCCAGCACAC 61.394 63.158 0.00 0.00 0.00 3.82
126 127 2.046988 CCATCGACAGCCAGCACA 60.047 61.111 0.00 0.00 0.00 4.57
127 128 2.821366 CCCATCGACAGCCAGCAC 60.821 66.667 0.00 0.00 0.00 4.40
128 129 3.002583 TCCCATCGACAGCCAGCA 61.003 61.111 0.00 0.00 0.00 4.41
129 130 2.202987 CTCCCATCGACAGCCAGC 60.203 66.667 0.00 0.00 0.00 4.85
130 131 2.503061 CCTCCCATCGACAGCCAG 59.497 66.667 0.00 0.00 0.00 4.85
136 137 1.834822 CCCTCTCCCTCCCATCGAC 60.835 68.421 0.00 0.00 0.00 4.20
139 140 0.104197 ATTCCCCTCTCCCTCCCATC 60.104 60.000 0.00 0.00 0.00 3.51
144 145 0.326618 TGACCATTCCCCTCTCCCTC 60.327 60.000 0.00 0.00 0.00 4.30
150 151 2.158475 TGGCATATTGACCATTCCCCTC 60.158 50.000 0.00 0.00 0.00 4.30
151 152 1.858910 TGGCATATTGACCATTCCCCT 59.141 47.619 0.00 0.00 0.00 4.79
154 155 1.608590 CGGTGGCATATTGACCATTCC 59.391 52.381 0.00 0.00 38.46 3.01
155 156 2.290641 GTCGGTGGCATATTGACCATTC 59.709 50.000 0.00 0.00 38.46 2.67
156 157 2.092429 AGTCGGTGGCATATTGACCATT 60.092 45.455 0.00 0.00 38.46 3.16
157 158 1.490490 AGTCGGTGGCATATTGACCAT 59.510 47.619 0.00 0.00 38.46 3.55
158 159 0.908910 AGTCGGTGGCATATTGACCA 59.091 50.000 0.00 0.00 0.00 4.02
159 160 2.755650 CTAGTCGGTGGCATATTGACC 58.244 52.381 0.00 0.00 0.00 4.02
160 161 2.135933 GCTAGTCGGTGGCATATTGAC 58.864 52.381 0.00 0.00 31.47 3.18
161 162 1.760029 TGCTAGTCGGTGGCATATTGA 59.240 47.619 0.00 0.00 37.82 2.57
213 214 2.809601 GAGCGGACACGTGCGATT 60.810 61.111 17.22 4.18 44.32 3.34
219 220 2.261671 GACATGGAGCGGACACGT 59.738 61.111 0.00 0.00 43.45 4.49
222 223 4.451150 GCGGACATGGAGCGGACA 62.451 66.667 0.00 0.00 0.00 4.02
243 244 1.278637 GGTCTGGTTTGCGTCAACG 59.721 57.895 0.00 0.00 43.27 4.10
244 245 1.098712 TGGGTCTGGTTTGCGTCAAC 61.099 55.000 0.00 0.00 0.00 3.18
245 246 0.394488 TTGGGTCTGGTTTGCGTCAA 60.394 50.000 0.00 0.00 0.00 3.18
246 247 0.394488 TTTGGGTCTGGTTTGCGTCA 60.394 50.000 0.00 0.00 0.00 4.35
250 251 2.493035 CCAAATTTGGGTCTGGTTTGC 58.507 47.619 26.87 0.00 44.70 3.68
266 267 2.324541 CAACCCCATTTCAGGTCCAAA 58.675 47.619 0.00 0.00 34.45 3.28
270 271 1.883021 CGCAACCCCATTTCAGGTC 59.117 57.895 0.00 0.00 34.45 3.85
273 274 1.080569 GTGCGCAACCCCATTTCAG 60.081 57.895 14.00 0.00 0.00 3.02
276 277 3.679738 CCGTGCGCAACCCCATTT 61.680 61.111 14.00 0.00 0.00 2.32
282 283 1.226717 TTTTTGTCCGTGCGCAACC 60.227 52.632 14.00 0.00 0.00 3.77
283 284 4.386245 TTTTTGTCCGTGCGCAAC 57.614 50.000 14.00 7.93 0.00 4.17
302 303 2.601763 CACGTAAATAGACGCTTGTCCC 59.398 50.000 0.00 0.00 46.87 4.46
304 305 2.028883 GCCACGTAAATAGACGCTTGTC 59.971 50.000 0.00 0.00 46.87 3.18
306 307 1.006391 CGCCACGTAAATAGACGCTTG 60.006 52.381 0.00 0.00 46.87 4.01
307 308 1.274596 CGCCACGTAAATAGACGCTT 58.725 50.000 0.00 0.00 46.87 4.68
308 309 1.143969 GCGCCACGTAAATAGACGCT 61.144 55.000 0.00 0.00 46.87 5.07
323 324 0.110101 AAATTACGGTTCAACGCGCC 60.110 50.000 5.73 0.00 37.37 6.53
325 326 2.303707 ACAAATTACGGTTCAACGCG 57.696 45.000 3.53 3.53 37.37 6.01
332 334 4.928615 TCGAAACGGATACAAATTACGGTT 59.071 37.500 0.00 0.00 37.15 4.44
335 337 6.698107 TGAATCGAAACGGATACAAATTACG 58.302 36.000 0.00 0.00 0.00 3.18
338 340 8.240682 TCATTTGAATCGAAACGGATACAAATT 58.759 29.630 0.00 0.00 35.51 1.82
345 347 4.647964 CGTTCATTTGAATCGAAACGGAT 58.352 39.130 6.81 0.00 36.33 4.18
355 357 1.335780 TGCTTGCGCGTTCATTTGAAT 60.336 42.857 8.43 0.00 39.65 2.57
358 360 0.661187 ACTGCTTGCGCGTTCATTTG 60.661 50.000 8.43 0.00 39.65 2.32
364 366 1.164041 ACCTAAACTGCTTGCGCGTT 61.164 50.000 8.43 0.00 39.65 4.84
366 368 0.725784 CAACCTAAACTGCTTGCGCG 60.726 55.000 0.00 0.00 39.65 6.86
369 371 0.603065 CCCCAACCTAAACTGCTTGC 59.397 55.000 0.00 0.00 0.00 4.01
371 373 0.893727 CGCCCCAACCTAAACTGCTT 60.894 55.000 0.00 0.00 0.00 3.91
372 374 1.303317 CGCCCCAACCTAAACTGCT 60.303 57.895 0.00 0.00 0.00 4.24
373 375 1.176619 AACGCCCCAACCTAAACTGC 61.177 55.000 0.00 0.00 0.00 4.40
374 376 0.596082 CAACGCCCCAACCTAAACTG 59.404 55.000 0.00 0.00 0.00 3.16
375 377 0.475044 TCAACGCCCCAACCTAAACT 59.525 50.000 0.00 0.00 0.00 2.66
376 378 1.268625 CTTCAACGCCCCAACCTAAAC 59.731 52.381 0.00 0.00 0.00 2.01
377 379 1.133730 ACTTCAACGCCCCAACCTAAA 60.134 47.619 0.00 0.00 0.00 1.85
379 381 0.475044 AACTTCAACGCCCCAACCTA 59.525 50.000 0.00 0.00 0.00 3.08
380 382 0.475044 TAACTTCAACGCCCCAACCT 59.525 50.000 0.00 0.00 0.00 3.50
387 389 5.648572 AGTATGTAGAGTAACTTCAACGCC 58.351 41.667 0.00 0.00 30.30 5.68
412 414 6.021030 TCCGTGGGCCTTTATATCTTAGTAT 58.979 40.000 4.53 0.00 0.00 2.12
415 417 4.822026 CTCCGTGGGCCTTTATATCTTAG 58.178 47.826 4.53 0.00 0.00 2.18
416 418 3.007614 GCTCCGTGGGCCTTTATATCTTA 59.992 47.826 4.53 0.00 0.00 2.10
418 420 1.348036 GCTCCGTGGGCCTTTATATCT 59.652 52.381 4.53 0.00 0.00 1.98
419 421 1.071699 TGCTCCGTGGGCCTTTATATC 59.928 52.381 4.53 0.00 0.00 1.63
420 422 1.136828 TGCTCCGTGGGCCTTTATAT 58.863 50.000 4.53 0.00 0.00 0.86
421 423 0.913205 TTGCTCCGTGGGCCTTTATA 59.087 50.000 4.53 0.00 0.00 0.98
422 424 0.394352 CTTGCTCCGTGGGCCTTTAT 60.394 55.000 4.53 0.00 0.00 1.40
423 425 1.002624 CTTGCTCCGTGGGCCTTTA 60.003 57.895 4.53 0.00 0.00 1.85
424 426 1.774894 TACTTGCTCCGTGGGCCTTT 61.775 55.000 4.53 0.00 0.00 3.11
425 427 1.774894 TTACTTGCTCCGTGGGCCTT 61.775 55.000 4.53 0.00 0.00 4.35
426 428 1.774894 TTTACTTGCTCCGTGGGCCT 61.775 55.000 4.53 0.00 0.00 5.19
427 429 1.302993 TTTACTTGCTCCGTGGGCC 60.303 57.895 0.00 0.00 0.00 5.80
428 430 0.605589 AGTTTACTTGCTCCGTGGGC 60.606 55.000 0.00 0.00 0.00 5.36
429 431 1.156736 CAGTTTACTTGCTCCGTGGG 58.843 55.000 0.00 0.00 0.00 4.61
430 432 0.517316 GCAGTTTACTTGCTCCGTGG 59.483 55.000 0.00 0.00 0.00 4.94
431 433 1.195448 CTGCAGTTTACTTGCTCCGTG 59.805 52.381 5.25 0.00 0.00 4.94
432 434 1.512926 CTGCAGTTTACTTGCTCCGT 58.487 50.000 5.25 0.00 0.00 4.69
433 435 0.166814 GCTGCAGTTTACTTGCTCCG 59.833 55.000 16.64 0.00 0.00 4.63
434 436 1.528129 AGCTGCAGTTTACTTGCTCC 58.472 50.000 16.64 0.00 0.00 4.70
435 437 2.549754 TGAAGCTGCAGTTTACTTGCTC 59.450 45.455 16.35 2.52 0.00 4.26
436 438 2.575532 TGAAGCTGCAGTTTACTTGCT 58.424 42.857 16.35 0.86 0.00 3.91
437 439 3.058016 TCATGAAGCTGCAGTTTACTTGC 60.058 43.478 16.35 3.97 0.00 4.01
438 440 4.754372 TCATGAAGCTGCAGTTTACTTG 57.246 40.909 16.35 15.72 0.00 3.16
439 441 5.972107 AATCATGAAGCTGCAGTTTACTT 57.028 34.783 16.35 9.85 0.00 2.24
440 442 5.972107 AAATCATGAAGCTGCAGTTTACT 57.028 34.783 16.35 3.59 0.00 2.24
441 443 8.519492 TTAAAAATCATGAAGCTGCAGTTTAC 57.481 30.769 16.35 10.21 0.00 2.01
442 444 9.709495 AATTAAAAATCATGAAGCTGCAGTTTA 57.291 25.926 16.35 5.38 0.00 2.01
443 445 8.611654 AATTAAAAATCATGAAGCTGCAGTTT 57.388 26.923 16.33 16.33 0.00 2.66
444 446 9.143631 GTAATTAAAAATCATGAAGCTGCAGTT 57.856 29.630 16.64 6.37 0.00 3.16
445 447 8.306038 TGTAATTAAAAATCATGAAGCTGCAGT 58.694 29.630 16.64 0.00 0.00 4.40
446 448 8.692110 TGTAATTAAAAATCATGAAGCTGCAG 57.308 30.769 10.11 10.11 0.00 4.41
447 449 7.276218 GCTGTAATTAAAAATCATGAAGCTGCA 59.724 33.333 0.00 0.00 0.00 4.41
448 450 7.490402 AGCTGTAATTAAAAATCATGAAGCTGC 59.510 33.333 8.84 0.00 34.97 5.25
449 451 8.922058 AGCTGTAATTAAAAATCATGAAGCTG 57.078 30.769 8.84 0.00 34.97 4.24
450 452 8.193438 GGAGCTGTAATTAAAAATCATGAAGCT 58.807 33.333 9.29 9.29 38.72 3.74
451 453 7.166473 CGGAGCTGTAATTAAAAATCATGAAGC 59.834 37.037 0.00 0.00 0.00 3.86
452 454 8.552469 CGGAGCTGTAATTAAAAATCATGAAG 57.448 34.615 0.00 0.00 0.00 3.02
486 488 3.827898 CTCCACGACTCCGCTCCC 61.828 72.222 0.00 0.00 39.95 4.30
487 489 4.500116 GCTCCACGACTCCGCTCC 62.500 72.222 0.00 0.00 39.95 4.70
505 507 3.564027 CCTGTTCGGAATCGCGCC 61.564 66.667 0.00 0.00 36.13 6.53
506 508 2.799540 GACCTGTTCGGAATCGCGC 61.800 63.158 0.00 0.00 36.31 6.86
507 509 2.165301 GGACCTGTTCGGAATCGCG 61.165 63.158 0.00 0.00 36.31 5.87
508 510 0.672401 TTGGACCTGTTCGGAATCGC 60.672 55.000 0.00 0.00 36.31 4.58
509 511 1.732259 CTTTGGACCTGTTCGGAATCG 59.268 52.381 0.00 0.00 36.31 3.34
510 512 2.742589 GACTTTGGACCTGTTCGGAATC 59.257 50.000 0.00 0.00 36.31 2.52
511 513 2.105821 TGACTTTGGACCTGTTCGGAAT 59.894 45.455 0.00 0.00 36.31 3.01
512 514 1.487142 TGACTTTGGACCTGTTCGGAA 59.513 47.619 0.00 0.00 36.31 4.30
513 515 1.124780 TGACTTTGGACCTGTTCGGA 58.875 50.000 0.00 0.00 36.31 4.55
514 516 1.226746 GTGACTTTGGACCTGTTCGG 58.773 55.000 0.00 0.00 39.35 4.30
515 517 0.859232 CGTGACTTTGGACCTGTTCG 59.141 55.000 0.00 0.00 0.00 3.95
516 518 1.226746 CCGTGACTTTGGACCTGTTC 58.773 55.000 0.00 0.00 0.00 3.18
517 519 0.544697 ACCGTGACTTTGGACCTGTT 59.455 50.000 0.00 0.00 0.00 3.16
518 520 0.179056 CACCGTGACTTTGGACCTGT 60.179 55.000 0.00 0.00 0.00 4.00
519 521 0.105964 TCACCGTGACTTTGGACCTG 59.894 55.000 0.00 0.00 0.00 4.00
520 522 0.106149 GTCACCGTGACTTTGGACCT 59.894 55.000 22.08 0.00 43.73 3.85
521 523 0.883370 GGTCACCGTGACTTTGGACC 60.883 60.000 26.73 9.20 46.19 4.46
522 524 1.219522 CGGTCACCGTGACTTTGGAC 61.220 60.000 26.73 11.34 46.19 4.02
523 525 1.068417 CGGTCACCGTGACTTTGGA 59.932 57.895 26.73 0.00 46.19 3.53
524 526 1.959226 CCGGTCACCGTGACTTTGG 60.959 63.158 26.73 21.68 46.19 3.28
594 596 4.495422 TGCTCATCCGTAGAAAAAGAGAC 58.505 43.478 0.00 0.00 0.00 3.36
598 600 6.611381 TGATTTTGCTCATCCGTAGAAAAAG 58.389 36.000 0.00 0.00 0.00 2.27
607 609 2.900122 ACGTTGATTTTGCTCATCCG 57.100 45.000 0.00 0.00 0.00 4.18
608 610 4.545610 TCAAACGTTGATTTTGCTCATCC 58.454 39.130 0.00 0.00 34.50 3.51
624 626 6.102006 TGTAAATAAGGCTTCGATCAAACG 57.898 37.500 1.30 0.00 0.00 3.60
662 665 2.201732 CATGTGTCGTATGGTAGCACC 58.798 52.381 0.00 0.00 39.22 5.01
663 666 2.603110 CACATGTGTCGTATGGTAGCAC 59.397 50.000 18.03 0.00 0.00 4.40
664 667 2.494073 TCACATGTGTCGTATGGTAGCA 59.506 45.455 24.63 0.00 0.00 3.49
665 668 3.159353 TCACATGTGTCGTATGGTAGC 57.841 47.619 24.63 0.00 0.00 3.58
666 669 5.402568 GCTTATCACATGTGTCGTATGGTAG 59.597 44.000 24.63 11.03 0.00 3.18
667 670 5.163499 TGCTTATCACATGTGTCGTATGGTA 60.163 40.000 24.63 3.11 0.00 3.25
668 671 4.119862 GCTTATCACATGTGTCGTATGGT 58.880 43.478 24.63 0.00 0.00 3.55
669 672 4.119136 TGCTTATCACATGTGTCGTATGG 58.881 43.478 24.63 10.95 0.00 2.74
670 673 5.717038 TTGCTTATCACATGTGTCGTATG 57.283 39.130 24.63 17.09 0.00 2.39
671 674 6.983890 TGTATTGCTTATCACATGTGTCGTAT 59.016 34.615 24.63 13.52 0.00 3.06
672 675 6.254804 GTGTATTGCTTATCACATGTGTCGTA 59.745 38.462 24.63 13.52 0.00 3.43
673 676 5.063438 GTGTATTGCTTATCACATGTGTCGT 59.937 40.000 24.63 14.45 0.00 4.34
674 677 5.063312 TGTGTATTGCTTATCACATGTGTCG 59.937 40.000 24.63 12.56 36.17 4.35
675 678 6.092670 AGTGTGTATTGCTTATCACATGTGTC 59.907 38.462 24.63 10.78 41.64 3.67
676 679 5.939883 AGTGTGTATTGCTTATCACATGTGT 59.060 36.000 24.63 14.61 41.64 3.72
677 680 6.426980 AGTGTGTATTGCTTATCACATGTG 57.573 37.500 20.18 20.18 41.64 3.21
678 681 7.331026 AGTAGTGTGTATTGCTTATCACATGT 58.669 34.615 0.00 0.00 41.64 3.21
679 682 7.776933 AGTAGTGTGTATTGCTTATCACATG 57.223 36.000 0.00 0.00 41.64 3.21
680 683 9.884636 TTAAGTAGTGTGTATTGCTTATCACAT 57.115 29.630 0.00 0.00 41.64 3.21
681 684 9.713713 TTTAAGTAGTGTGTATTGCTTATCACA 57.286 29.630 0.00 0.00 38.26 3.58
686 689 9.563748 ACCTTTTTAAGTAGTGTGTATTGCTTA 57.436 29.630 0.00 0.00 0.00 3.09
687 690 8.349983 CACCTTTTTAAGTAGTGTGTATTGCTT 58.650 33.333 0.00 0.00 0.00 3.91
688 691 7.717875 TCACCTTTTTAAGTAGTGTGTATTGCT 59.282 33.333 0.00 0.00 0.00 3.91
689 692 7.867752 TCACCTTTTTAAGTAGTGTGTATTGC 58.132 34.615 0.00 0.00 0.00 3.56
690 693 9.268268 TCTCACCTTTTTAAGTAGTGTGTATTG 57.732 33.333 0.00 0.00 0.00 1.90
691 694 9.490379 CTCTCACCTTTTTAAGTAGTGTGTATT 57.510 33.333 0.00 0.00 0.00 1.89
692 695 7.603024 GCTCTCACCTTTTTAAGTAGTGTGTAT 59.397 37.037 0.00 0.00 0.00 2.29
693 696 6.927381 GCTCTCACCTTTTTAAGTAGTGTGTA 59.073 38.462 0.00 0.00 0.00 2.90
694 697 5.758784 GCTCTCACCTTTTTAAGTAGTGTGT 59.241 40.000 0.00 0.00 0.00 3.72
695 698 5.992217 AGCTCTCACCTTTTTAAGTAGTGTG 59.008 40.000 0.00 0.00 0.00 3.82
696 699 5.992217 CAGCTCTCACCTTTTTAAGTAGTGT 59.008 40.000 0.00 0.00 0.00 3.55
697 700 5.409826 CCAGCTCTCACCTTTTTAAGTAGTG 59.590 44.000 0.00 0.00 0.00 2.74
698 701 5.071923 ACCAGCTCTCACCTTTTTAAGTAGT 59.928 40.000 0.00 0.00 0.00 2.73
699 702 5.409826 CACCAGCTCTCACCTTTTTAAGTAG 59.590 44.000 0.00 0.00 0.00 2.57
700 703 5.305585 CACCAGCTCTCACCTTTTTAAGTA 58.694 41.667 0.00 0.00 0.00 2.24
701 704 4.137543 CACCAGCTCTCACCTTTTTAAGT 58.862 43.478 0.00 0.00 0.00 2.24
702 705 3.057946 GCACCAGCTCTCACCTTTTTAAG 60.058 47.826 0.00 0.00 37.91 1.85
703 706 2.884639 GCACCAGCTCTCACCTTTTTAA 59.115 45.455 0.00 0.00 37.91 1.52
704 707 2.504367 GCACCAGCTCTCACCTTTTTA 58.496 47.619 0.00 0.00 37.91 1.52
705 708 1.322442 GCACCAGCTCTCACCTTTTT 58.678 50.000 0.00 0.00 37.91 1.94
706 709 3.027419 GCACCAGCTCTCACCTTTT 57.973 52.632 0.00 0.00 37.91 2.27
707 710 4.809070 GCACCAGCTCTCACCTTT 57.191 55.556 0.00 0.00 37.91 3.11
1036 2542 2.906691 AATCAAGGAGAGGATCGCTG 57.093 50.000 0.00 0.00 42.67 5.18
1475 2981 1.536943 GGAAGACAGCACCTCCGAGT 61.537 60.000 0.00 0.00 0.00 4.18
1671 3188 2.304180 ACTGATGGGTCCTTCTGAAGTG 59.696 50.000 15.72 7.88 0.00 3.16
1682 3199 0.245539 TCCGACGAAACTGATGGGTC 59.754 55.000 0.00 0.00 0.00 4.46
1758 3275 4.125703 CTGCCTCAGGTTCATACTGAATC 58.874 47.826 0.00 0.00 43.74 2.52
1781 3298 3.222603 CCCTCCACAAATTGGCCTATAC 58.777 50.000 3.32 0.00 46.47 1.47
1976 3493 2.158957 TCCGATTTCAGCTCGCCTATTT 60.159 45.455 0.00 0.00 34.84 1.40
1977 3494 1.412710 TCCGATTTCAGCTCGCCTATT 59.587 47.619 0.00 0.00 34.84 1.73
2082 3599 0.548031 AATCATCGCTGTGGGTGGAT 59.452 50.000 0.00 0.00 0.00 3.41
2171 3688 2.330440 TTCATCCATGGTGACCGATG 57.670 50.000 12.58 10.57 34.66 3.84
2172 3689 3.582998 ATTTCATCCATGGTGACCGAT 57.417 42.857 12.58 6.46 0.00 4.18
2275 3792 0.872388 GCTGTGTTTTCGTACCCCAG 59.128 55.000 0.00 0.00 0.00 4.45
2599 4116 3.068165 TGATCTGACTCTGACAACAACGT 59.932 43.478 0.00 0.00 0.00 3.99
2601 4118 5.931146 AGATTGATCTGACTCTGACAACAAC 59.069 40.000 0.00 0.00 35.42 3.32
2654 4171 6.586344 TGAACTTTCTGATCATGATCCCTAC 58.414 40.000 28.61 14.08 37.02 3.18
2692 4274 0.108585 TCTGAAGGCCTTTCAACGCT 59.891 50.000 21.54 0.00 44.84 5.07
2704 4292 2.625737 CACAGTACTGCCATCTGAAGG 58.374 52.381 22.90 0.00 33.93 3.46
2840 4428 0.939577 CTGAACCGTGACGTGTCCAG 60.940 60.000 3.64 1.22 0.00 3.86
2845 4433 1.068474 GATTCCTGAACCGTGACGTG 58.932 55.000 3.64 0.00 0.00 4.49
2873 4461 0.249868 CTTGACCACACGCTTCCTCA 60.250 55.000 0.00 0.00 0.00 3.86
2918 4506 0.110486 TGCTTCAAGACCAGGGGTTC 59.890 55.000 0.00 0.00 35.25 3.62
2932 4520 4.568152 TTACCTTCTTTGTTGCTGCTTC 57.432 40.909 0.00 0.00 0.00 3.86
3018 4608 8.424918 TCCTCAAAAGACAGGATAATCTCATAC 58.575 37.037 0.00 0.00 33.57 2.39
3057 4692 6.575162 ACTTCGAAGGAACTAAAATGCATT 57.425 33.333 27.86 5.99 38.49 3.56
3058 4693 6.206634 TCAACTTCGAAGGAACTAAAATGCAT 59.793 34.615 27.86 0.00 38.49 3.96
3127 4762 7.987750 TTTGCAGTAAATAACACACCTATCA 57.012 32.000 0.00 0.00 0.00 2.15
3131 4766 8.512138 GTCTAATTTGCAGTAAATAACACACCT 58.488 33.333 0.00 0.00 38.01 4.00
3144 4780 4.641396 TGTGTAGCTGTCTAATTTGCAGT 58.359 39.130 0.00 4.05 33.18 4.40
3160 4796 9.165035 ACTAAGCTAGTAACTACTTCTGTGTAG 57.835 37.037 0.00 0.00 40.31 2.74
3257 4929 3.550820 TGTGCAATGTAAGGTGTTCTGT 58.449 40.909 0.00 0.00 0.00 3.41
3347 5027 3.169512 ACCAAACTTAATGTCTGGGGG 57.830 47.619 0.00 0.00 0.00 5.40
3366 5046 4.039852 TGTGGGGGAATAAAAGCTTGAAAC 59.960 41.667 0.00 0.00 0.00 2.78
3382 5062 0.901580 AGCTTGAAGCATTGTGGGGG 60.902 55.000 20.45 0.00 45.56 5.40
3390 5090 5.220739 CGAGTTAATAGCAAGCTTGAAGCAT 60.221 40.000 30.39 12.81 45.56 3.79
3429 5130 1.528586 CTTGCAGTCTCCTGTTGAACG 59.471 52.381 0.00 0.00 41.02 3.95
3554 5255 3.264947 CGAAGAATCAGCCTGACATCAA 58.735 45.455 0.00 0.00 0.00 2.57
3562 5265 0.687354 ACCACACGAAGAATCAGCCT 59.313 50.000 0.00 0.00 0.00 4.58
3653 5359 4.382147 GCAAGCCTTCTACACTAGCTAACT 60.382 45.833 0.00 0.00 32.39 2.24
3658 5364 2.275318 CTGCAAGCCTTCTACACTAGC 58.725 52.381 0.00 0.00 0.00 3.42
3692 5401 7.439056 CAAATGCAGATTTTACAGGTTTTCTGT 59.561 33.333 4.06 4.06 43.15 3.41
3706 5415 9.577110 CAGTACAATAATGTCAAATGCAGATTT 57.423 29.630 0.00 0.00 41.05 2.17
3739 5448 2.350419 TCACCTTTAGGGGCAGGTAAA 58.650 47.619 0.10 0.00 41.86 2.01
3769 5478 0.035056 ACCTGCTCAATACACCCAGC 60.035 55.000 0.00 0.00 0.00 4.85
3770 5479 2.496899 AACCTGCTCAATACACCCAG 57.503 50.000 0.00 0.00 0.00 4.45
3771 5480 2.969821 AAACCTGCTCAATACACCCA 57.030 45.000 0.00 0.00 0.00 4.51
3772 5481 3.939592 GACTAAACCTGCTCAATACACCC 59.060 47.826 0.00 0.00 0.00 4.61
3786 5497 2.956333 ACAAAGTGGGCAAGACTAAACC 59.044 45.455 0.00 0.00 0.00 3.27
3801 5512 3.299503 ACTTGGCTCAATTGGACAAAGT 58.700 40.909 13.88 13.36 0.00 2.66
3812 5523 3.795688 ATCAGGAGAAACTTGGCTCAA 57.204 42.857 0.00 0.00 32.83 3.02
3813 5524 3.795688 AATCAGGAGAAACTTGGCTCA 57.204 42.857 0.00 0.00 32.83 4.26
3848 5559 6.151144 AGCATAAGGGAAATCACAACACTAAC 59.849 38.462 0.00 0.00 0.00 2.34
3849 5560 6.245408 AGCATAAGGGAAATCACAACACTAA 58.755 36.000 0.00 0.00 0.00 2.24
3852 5563 4.702131 AGAGCATAAGGGAAATCACAACAC 59.298 41.667 0.00 0.00 0.00 3.32
3855 5566 5.178096 TCAGAGCATAAGGGAAATCACAA 57.822 39.130 0.00 0.00 0.00 3.33
3882 5593 4.340019 CACAACGGCCATTGCGCA 62.340 61.111 12.35 5.66 38.85 6.09
3895 5606 3.275617 AACAGGTACAGAACAGCACAA 57.724 42.857 0.00 0.00 0.00 3.33
3902 5613 3.586892 GAGTGGCTAACAGGTACAGAAC 58.413 50.000 0.00 0.00 0.00 3.01
4067 5778 6.544650 TGCCCCTACAAGTTTTAACTCAATA 58.455 36.000 0.00 0.00 38.57 1.90
4124 5835 9.305925 ACGCACCTTACTTTGTTATTAGTATAC 57.694 33.333 0.00 0.00 0.00 1.47
4145 5856 2.197792 AAAAACCCGAAGAAACGCAC 57.802 45.000 0.00 0.00 0.00 5.34
4197 5908 6.056884 ACAACAAAAATTAGTACCACCTCGA 58.943 36.000 0.00 0.00 0.00 4.04
4198 5909 6.308371 ACAACAAAAATTAGTACCACCTCG 57.692 37.500 0.00 0.00 0.00 4.63
4212 5923 3.186613 GCCCGACAAAACAACAACAAAAA 59.813 39.130 0.00 0.00 0.00 1.94
4217 5928 1.273688 GTGCCCGACAAAACAACAAC 58.726 50.000 0.00 0.00 0.00 3.32
4298 6009 1.296056 ATGCCCGTGCGTTGTACTTC 61.296 55.000 0.00 0.00 41.78 3.01
4299 6010 1.302192 ATGCCCGTGCGTTGTACTT 60.302 52.632 0.00 0.00 41.78 2.24
4312 6023 1.066152 GGAGAAAAGATTCGCATGCCC 59.934 52.381 13.15 0.00 40.63 5.36
4347 6058 8.129211 GTGTTTAGTCAGACTAGCAAACATTTT 58.871 33.333 23.74 0.00 36.88 1.82
4367 6078 9.787532 GTTAATACATAGGAGTACGTGTGTTTA 57.212 33.333 0.00 0.00 37.41 2.01
4435 6146 4.191033 CACAAAATGTGTATGGTGCCAT 57.809 40.909 8.89 8.89 43.08 4.40
4508 6219 2.357327 TCAATTAGACGGTGTCGGTG 57.643 50.000 0.00 0.00 41.39 4.94


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

AutoCloner maintained by Alex Coulton.