Multiple sequence alignment - TraesCS2A01G436300

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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 TraesCS2A01G436300 chr2A 100.000 3274 0 0 1 3274 688419011 688422284 0.000000e+00 6047.0
1 TraesCS2A01G436300 chr2A 94.485 544 27 3 2731 3274 29261245 29260705 0.000000e+00 835.0
2 TraesCS2A01G436300 chr2B 91.464 1851 95 23 788 2628 651732086 651730289 0.000000e+00 2484.0
3 TraesCS2A01G436300 chr2B 77.778 360 44 15 10 343 651733276 651732927 4.310000e-44 189.0
4 TraesCS2A01G436300 chr2B 81.395 86 4 7 604 688 651732249 651732175 3.530000e-05 60.2
5 TraesCS2A01G436300 chr2D 87.801 2156 129 68 605 2732 545007994 545005945 0.000000e+00 2401.0
6 TraesCS2A01G436300 chr5A 98.537 547 5 3 2728 3274 30090646 30090103 0.000000e+00 963.0
7 TraesCS2A01G436300 chr5A 98.859 526 4 2 2732 3257 553472997 553473520 0.000000e+00 937.0
8 TraesCS2A01G436300 chr5A 88.889 153 17 0 358 510 647806365 647806517 4.310000e-44 189.0
9 TraesCS2A01G436300 chr6B 94.659 543 26 3 2732 3274 167495570 167495031 0.000000e+00 839.0
10 TraesCS2A01G436300 chr6B 94.485 544 26 4 2731 3274 607003166 607002627 0.000000e+00 835.0
11 TraesCS2A01G436300 chr6B 86.154 130 18 0 381 510 702214163 702214034 1.220000e-29 141.0
12 TraesCS2A01G436300 chr3B 94.353 549 27 4 2726 3274 56444069 56444613 0.000000e+00 839.0
13 TraesCS2A01G436300 chr7B 94.475 543 27 3 2732 3274 645424865 645424326 0.000000e+00 833.0
14 TraesCS2A01G436300 chr7A 94.475 543 27 3 2732 3274 686670352 686670891 0.000000e+00 833.0
15 TraesCS2A01G436300 chr4B 94.312 545 27 4 2731 3274 570442083 570441542 0.000000e+00 832.0
16 TraesCS2A01G436300 chr6D 87.500 152 17 1 361 510 469814491 469814340 1.210000e-39 174.0


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 TraesCS2A01G436300 chr2A 688419011 688422284 3273 False 6047.000000 6047 100.000000 1 3274 1 chr2A.!!$F1 3273
1 TraesCS2A01G436300 chr2A 29260705 29261245 540 True 835.000000 835 94.485000 2731 3274 1 chr2A.!!$R1 543
2 TraesCS2A01G436300 chr2B 651730289 651733276 2987 True 911.066667 2484 83.545667 10 2628 3 chr2B.!!$R1 2618
3 TraesCS2A01G436300 chr2D 545005945 545007994 2049 True 2401.000000 2401 87.801000 605 2732 1 chr2D.!!$R1 2127
4 TraesCS2A01G436300 chr5A 30090103 30090646 543 True 963.000000 963 98.537000 2728 3274 1 chr5A.!!$R1 546
5 TraesCS2A01G436300 chr5A 553472997 553473520 523 False 937.000000 937 98.859000 2732 3257 1 chr5A.!!$F1 525
6 TraesCS2A01G436300 chr6B 167495031 167495570 539 True 839.000000 839 94.659000 2732 3274 1 chr6B.!!$R1 542
7 TraesCS2A01G436300 chr6B 607002627 607003166 539 True 835.000000 835 94.485000 2731 3274 1 chr6B.!!$R2 543
8 TraesCS2A01G436300 chr3B 56444069 56444613 544 False 839.000000 839 94.353000 2726 3274 1 chr3B.!!$F1 548
9 TraesCS2A01G436300 chr7B 645424326 645424865 539 True 833.000000 833 94.475000 2732 3274 1 chr7B.!!$R1 542
10 TraesCS2A01G436300 chr7A 686670352 686670891 539 False 833.000000 833 94.475000 2732 3274 1 chr7A.!!$F1 542
11 TraesCS2A01G436300 chr4B 570441542 570442083 541 True 832.000000 832 94.312000 2731 3274 1 chr4B.!!$R1 543

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
417 443 0.036858 TCGCACGATGGGTTGAATCA 60.037 50.0 0.0 0.0 0.0 2.57 F
1130 1596 0.037882 TGGTCGCTTCTCTTCTGCTG 60.038 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2642 1.068121 CAGTTGGAGGGAAGAAGGGT 58.932 55.000 0.0 0.0 0.0 4.34 R
3099 3601 1.757699 GAGCGTGGGAGAATAGAACCT 59.242 52.381 0.0 0.0 0.0 3.50 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
85 86 6.573664 TGAAATCACTAGGTTGAAATGTGG 57.426 37.500 0.00 0.00 0.00 4.17
92 93 5.049405 CACTAGGTTGAAATGTGGAGTTGTC 60.049 44.000 0.00 0.00 0.00 3.18
93 94 2.878406 AGGTTGAAATGTGGAGTTGTCG 59.122 45.455 0.00 0.00 0.00 4.35
101 102 3.364889 TGTGGAGTTGTCGAGTTACTG 57.635 47.619 0.00 0.00 0.00 2.74
138 139 2.839486 TTCATGAGCGGACTTCACTT 57.161 45.000 0.00 0.00 0.00 3.16
142 143 0.880278 TGAGCGGACTTCACTTGTGC 60.880 55.000 0.00 0.00 0.00 4.57
151 163 4.320057 GGACTTCACTTGTGCAGAGAAATG 60.320 45.833 7.36 0.00 32.34 2.32
309 335 8.711457 CACTTGTTTGAAATAAATGGAATCACC 58.289 33.333 0.00 0.00 39.54 4.02
312 338 9.844257 TTGTTTGAAATAAATGGAATCACCTTT 57.156 25.926 0.00 0.00 39.86 3.11
313 339 9.844257 TGTTTGAAATAAATGGAATCACCTTTT 57.156 25.926 0.00 0.00 44.52 2.27
344 370 8.880878 TTAAAGAGTTGGCTTTTGAATAAACC 57.119 30.769 0.00 0.00 38.85 3.27
345 371 5.121221 AGAGTTGGCTTTTGAATAAACCG 57.879 39.130 0.00 0.00 0.00 4.44
346 372 4.825085 AGAGTTGGCTTTTGAATAAACCGA 59.175 37.500 0.00 0.00 0.00 4.69
347 373 4.866921 AGTTGGCTTTTGAATAAACCGAC 58.133 39.130 0.00 0.00 31.26 4.79
350 376 4.804108 TGGCTTTTGAATAAACCGACATG 58.196 39.130 0.00 0.00 0.00 3.21
351 377 3.612423 GGCTTTTGAATAAACCGACATGC 59.388 43.478 0.00 0.00 0.00 4.06
352 378 4.485163 GCTTTTGAATAAACCGACATGCT 58.515 39.130 0.00 0.00 0.00 3.79
353 379 4.923281 GCTTTTGAATAAACCGACATGCTT 59.077 37.500 0.00 0.00 0.00 3.91
354 380 5.060940 GCTTTTGAATAAACCGACATGCTTC 59.939 40.000 0.00 0.00 0.00 3.86
355 381 5.697473 TTTGAATAAACCGACATGCTTCA 57.303 34.783 0.00 0.00 0.00 3.02
358 384 6.078202 TGAATAAACCGACATGCTTCAAAA 57.922 33.333 0.00 0.00 0.00 2.44
359 385 6.686630 TGAATAAACCGACATGCTTCAAAAT 58.313 32.000 0.00 0.00 0.00 1.82
360 386 6.585702 TGAATAAACCGACATGCTTCAAAATG 59.414 34.615 0.00 0.00 0.00 2.32
362 388 3.837213 ACCGACATGCTTCAAAATGAG 57.163 42.857 0.00 0.00 0.00 2.90
363 389 2.095059 ACCGACATGCTTCAAAATGAGC 60.095 45.455 0.00 0.00 0.00 4.26
365 391 2.912967 CGACATGCTTCAAAATGAGCAC 59.087 45.455 0.00 0.00 34.90 4.40
369 395 0.598065 GCTTCAAAATGAGCACCGGT 59.402 50.000 0.00 0.00 0.00 5.28
371 397 2.423538 GCTTCAAAATGAGCACCGGTAT 59.576 45.455 6.87 0.00 0.00 2.73
372 398 3.625764 GCTTCAAAATGAGCACCGGTATA 59.374 43.478 6.87 0.00 0.00 1.47
373 399 4.260784 GCTTCAAAATGAGCACCGGTATAG 60.261 45.833 6.87 0.00 0.00 1.31
374 400 3.804036 TCAAAATGAGCACCGGTATAGG 58.196 45.455 6.87 0.00 37.30 2.57
376 402 2.097110 AATGAGCACCGGTATAGGGA 57.903 50.000 6.87 0.00 35.02 4.20
377 403 1.339097 ATGAGCACCGGTATAGGGAC 58.661 55.000 6.87 0.00 35.02 4.46
378 404 1.105167 TGAGCACCGGTATAGGGACG 61.105 60.000 6.87 0.00 35.02 4.79
382 408 3.541072 CCGGTATAGGGACGGCAA 58.459 61.111 0.00 0.00 41.23 4.52
384 410 1.068585 CGGTATAGGGACGGCAACC 59.931 63.158 0.00 0.00 0.00 3.77
385 411 1.397390 CGGTATAGGGACGGCAACCT 61.397 60.000 0.00 0.00 40.89 3.50
387 413 1.202615 GGTATAGGGACGGCAACCTTC 60.203 57.143 0.00 0.00 38.30 3.46
388 414 1.761198 GTATAGGGACGGCAACCTTCT 59.239 52.381 0.00 0.00 38.30 2.85
389 415 0.541863 ATAGGGACGGCAACCTTCTG 59.458 55.000 0.00 0.00 38.30 3.02
390 416 2.180159 TAGGGACGGCAACCTTCTGC 62.180 60.000 0.00 0.00 41.85 4.26
396 422 3.502572 GCAACCTTCTGCCCGATC 58.497 61.111 0.00 0.00 36.25 3.69
397 423 1.078143 GCAACCTTCTGCCCGATCT 60.078 57.895 0.00 0.00 36.25 2.75
399 425 1.373570 CAACCTTCTGCCCGATCTTC 58.626 55.000 0.00 0.00 0.00 2.87
400 426 0.108138 AACCTTCTGCCCGATCTTCG 60.108 55.000 0.00 0.00 40.07 3.79
401 427 1.884926 CCTTCTGCCCGATCTTCGC 60.885 63.158 0.00 0.00 38.82 4.70
403 429 1.424493 CTTCTGCCCGATCTTCGCAC 61.424 60.000 0.00 0.00 38.82 5.34
404 430 3.257561 CTGCCCGATCTTCGCACG 61.258 66.667 0.00 0.00 38.82 5.34
407 433 2.589492 GCCCGATCTTCGCACGATG 61.589 63.158 0.00 0.00 38.82 3.84
408 434 1.951130 CCCGATCTTCGCACGATGG 60.951 63.158 6.16 0.00 38.82 3.51
409 435 1.951130 CCGATCTTCGCACGATGGG 60.951 63.158 6.16 0.00 38.82 4.00
411 437 0.806102 CGATCTTCGCACGATGGGTT 60.806 55.000 6.16 0.00 31.14 4.11
412 438 0.652592 GATCTTCGCACGATGGGTTG 59.347 55.000 6.16 0.00 0.00 3.77
415 441 1.086696 CTTCGCACGATGGGTTGAAT 58.913 50.000 0.00 0.00 0.00 2.57
416 442 1.062587 CTTCGCACGATGGGTTGAATC 59.937 52.381 0.00 0.00 0.00 2.52
417 443 0.036858 TCGCACGATGGGTTGAATCA 60.037 50.000 0.00 0.00 0.00 2.57
418 444 0.374758 CGCACGATGGGTTGAATCAG 59.625 55.000 0.00 0.00 0.00 2.90
419 445 0.099436 GCACGATGGGTTGAATCAGC 59.901 55.000 0.00 0.00 0.00 4.26
420 446 0.734889 CACGATGGGTTGAATCAGCC 59.265 55.000 7.66 7.66 33.90 4.85
427 453 4.524802 TGGGTTGAATCAGCCATTAGAT 57.475 40.909 17.73 0.00 39.48 1.98
428 454 4.870636 TGGGTTGAATCAGCCATTAGATT 58.129 39.130 17.73 0.00 39.48 2.40
429 455 4.646040 TGGGTTGAATCAGCCATTAGATTG 59.354 41.667 17.73 0.00 39.48 2.67
430 456 4.500375 GGGTTGAATCAGCCATTAGATTGC 60.500 45.833 17.73 0.00 36.44 3.56
433 459 5.700722 TGAATCAGCCATTAGATTGCATC 57.299 39.130 0.00 0.00 34.79 3.91
434 460 5.134661 TGAATCAGCCATTAGATTGCATCA 58.865 37.500 0.00 0.00 34.79 3.07
436 462 6.266786 TGAATCAGCCATTAGATTGCATCATT 59.733 34.615 0.00 0.00 34.79 2.57
437 463 6.665992 ATCAGCCATTAGATTGCATCATTT 57.334 33.333 0.00 0.00 0.00 2.32
438 464 6.474140 TCAGCCATTAGATTGCATCATTTT 57.526 33.333 0.00 0.00 0.00 1.82
439 465 6.277605 TCAGCCATTAGATTGCATCATTTTG 58.722 36.000 0.00 0.00 0.00 2.44
440 466 5.050363 CAGCCATTAGATTGCATCATTTTGC 60.050 40.000 0.00 0.00 43.07 3.68
441 467 4.084745 GCCATTAGATTGCATCATTTTGCG 60.085 41.667 0.00 0.00 45.77 4.85
445 471 7.358931 CCATTAGATTGCATCATTTTGCGAATC 60.359 37.037 0.00 10.72 45.77 2.52
446 472 5.001237 AGATTGCATCATTTTGCGAATCA 57.999 34.783 16.40 0.00 45.77 2.57
447 473 4.802039 AGATTGCATCATTTTGCGAATCAC 59.198 37.500 16.40 2.36 45.77 3.06
448 474 2.878580 TGCATCATTTTGCGAATCACC 58.121 42.857 0.00 0.00 45.77 4.02
449 475 1.847999 GCATCATTTTGCGAATCACCG 59.152 47.619 0.00 0.00 32.06 4.94
463 698 1.444836 TCACCGCCGTTCAAATTAGG 58.555 50.000 0.00 0.00 0.00 2.69
464 699 0.179174 CACCGCCGTTCAAATTAGGC 60.179 55.000 0.00 0.00 45.67 3.93
471 706 2.440501 CGTTCAAATTAGGCATCGTGC 58.559 47.619 1.92 1.92 44.08 5.34
485 752 1.501169 TCGTGCATGAACTGTCTGTG 58.499 50.000 6.04 0.00 0.00 3.66
491 758 2.877300 GCATGAACTGTCTGTGGACCAT 60.877 50.000 0.00 0.00 41.47 3.55
493 760 1.000843 TGAACTGTCTGTGGACCATCG 59.999 52.381 0.00 0.00 41.47 3.84
498 765 1.005037 TCTGTGGACCATCGTGTGC 60.005 57.895 0.00 0.00 0.00 4.57
500 767 3.118454 GTGGACCATCGTGTGCGG 61.118 66.667 0.00 0.00 38.89 5.69
501 768 3.307108 TGGACCATCGTGTGCGGA 61.307 61.111 0.00 0.00 38.89 5.54
502 769 2.509336 GGACCATCGTGTGCGGAG 60.509 66.667 0.00 0.00 38.89 4.63
522 789 2.589014 GCACTTCCTGCTTCAAAATCG 58.411 47.619 0.00 0.00 43.33 3.34
524 791 3.550842 GCACTTCCTGCTTCAAAATCGTT 60.551 43.478 0.00 0.00 43.33 3.85
525 792 4.222114 CACTTCCTGCTTCAAAATCGTTC 58.778 43.478 0.00 0.00 0.00 3.95
526 793 4.023707 CACTTCCTGCTTCAAAATCGTTCT 60.024 41.667 0.00 0.00 0.00 3.01
527 794 4.580580 ACTTCCTGCTTCAAAATCGTTCTT 59.419 37.500 0.00 0.00 0.00 2.52
529 796 3.502211 TCCTGCTTCAAAATCGTTCTTCC 59.498 43.478 0.00 0.00 0.00 3.46
530 797 3.503748 CCTGCTTCAAAATCGTTCTTCCT 59.496 43.478 0.00 0.00 0.00 3.36
532 799 3.253188 TGCTTCAAAATCGTTCTTCCTGG 59.747 43.478 0.00 0.00 0.00 4.45
535 802 4.351874 TCAAAATCGTTCTTCCTGGAGT 57.648 40.909 0.00 0.00 0.00 3.85
536 803 4.714632 TCAAAATCGTTCTTCCTGGAGTT 58.285 39.130 0.00 0.00 0.00 3.01
537 804 4.755123 TCAAAATCGTTCTTCCTGGAGTTC 59.245 41.667 0.00 0.00 0.00 3.01
538 805 4.351874 AAATCGTTCTTCCTGGAGTTCA 57.648 40.909 0.00 0.00 0.00 3.18
539 806 2.814280 TCGTTCTTCCTGGAGTTCAC 57.186 50.000 0.00 0.00 0.00 3.18
540 807 1.343465 TCGTTCTTCCTGGAGTTCACC 59.657 52.381 0.00 0.00 0.00 4.02
541 808 1.344763 CGTTCTTCCTGGAGTTCACCT 59.655 52.381 0.00 0.00 0.00 4.00
542 809 2.610727 CGTTCTTCCTGGAGTTCACCTC 60.611 54.545 0.00 0.00 39.67 3.85
545 812 3.318313 TCTTCCTGGAGTTCACCTCTTT 58.682 45.455 0.00 0.00 40.30 2.52
546 813 3.071602 TCTTCCTGGAGTTCACCTCTTTG 59.928 47.826 0.00 0.00 40.30 2.77
548 815 3.251484 TCCTGGAGTTCACCTCTTTGAT 58.749 45.455 0.00 0.00 40.30 2.57
549 816 3.261897 TCCTGGAGTTCACCTCTTTGATC 59.738 47.826 0.00 0.00 40.30 2.92
550 817 3.008375 CCTGGAGTTCACCTCTTTGATCA 59.992 47.826 0.00 0.00 40.30 2.92
552 819 3.244561 TGGAGTTCACCTCTTTGATCACC 60.245 47.826 0.00 0.00 40.30 4.02
554 821 2.040412 AGTTCACCTCTTTGATCACCCC 59.960 50.000 0.00 0.00 0.00 4.95
556 823 0.392998 CACCTCTTTGATCACCCCCG 60.393 60.000 0.00 0.00 0.00 5.73
557 824 0.840722 ACCTCTTTGATCACCCCCGT 60.841 55.000 0.00 0.00 0.00 5.28
559 826 0.324943 CTCTTTGATCACCCCCGTGT 59.675 55.000 0.00 0.00 41.09 4.49
579 846 4.681978 GGTGCGCTCCTCCAACGT 62.682 66.667 20.97 0.00 0.00 3.99
580 847 2.665185 GTGCGCTCCTCCAACGTT 60.665 61.111 9.73 0.00 0.00 3.99
602 869 5.643379 TGGCTTCAACATCTTCAATAACC 57.357 39.130 0.00 0.00 0.00 2.85
620 1062 4.025401 GAACTGTTGCCACGCGGG 62.025 66.667 12.47 6.05 40.85 6.13
693 1135 3.812053 CCGTGATCCTTCCAGAATCAATC 59.188 47.826 0.00 0.00 0.00 2.67
695 1137 4.877823 CGTGATCCTTCCAGAATCAATCAA 59.122 41.667 0.00 0.00 0.00 2.57
696 1138 5.530171 CGTGATCCTTCCAGAATCAATCAAT 59.470 40.000 0.00 0.00 0.00 2.57
697 1139 6.293298 CGTGATCCTTCCAGAATCAATCAATC 60.293 42.308 0.00 0.00 0.00 2.67
698 1140 5.761726 TGATCCTTCCAGAATCAATCAATCG 59.238 40.000 0.00 0.00 0.00 3.34
699 1141 5.357742 TCCTTCCAGAATCAATCAATCGA 57.642 39.130 0.00 0.00 0.00 3.59
700 1142 5.933617 TCCTTCCAGAATCAATCAATCGAT 58.066 37.500 0.00 0.00 0.00 3.59
702 1144 5.107182 CCTTCCAGAATCAATCAATCGATCG 60.107 44.000 9.36 9.36 0.00 3.69
703 1145 5.200368 TCCAGAATCAATCAATCGATCGA 57.800 39.130 21.86 21.86 0.00 3.59
704 1146 4.984785 TCCAGAATCAATCAATCGATCGAC 59.015 41.667 22.06 3.28 0.00 4.20
705 1147 4.151335 CCAGAATCAATCAATCGATCGACC 59.849 45.833 22.06 0.05 0.00 4.79
715 1157 2.105128 GATCGACCCGGAGCACAG 59.895 66.667 0.73 0.00 0.00 3.66
719 1161 4.459089 GACCCGGAGCACAGGAGC 62.459 72.222 0.73 0.00 33.26 4.70
734 1196 0.951040 GGAGCAGTCACGGGTTTGAG 60.951 60.000 0.00 0.00 0.00 3.02
744 1206 1.658114 GGGTTTGAGCCCGTGAAAC 59.342 57.895 0.00 0.00 39.17 2.78
768 1230 1.300080 CAAAACCTGCCTGCCGTTG 60.300 57.895 0.00 0.00 0.00 4.10
772 1234 3.673484 CCTGCCTGCCGTTGGTTG 61.673 66.667 0.00 0.00 0.00 3.77
773 1235 2.594303 CTGCCTGCCGTTGGTTGA 60.594 61.111 0.00 0.00 0.00 3.18
774 1236 2.124109 TGCCTGCCGTTGGTTGAA 60.124 55.556 0.00 0.00 0.00 2.69
775 1237 1.526575 CTGCCTGCCGTTGGTTGAAT 61.527 55.000 0.00 0.00 0.00 2.57
816 1278 2.100749 CCTCACACAAAAGGGTCCAAAC 59.899 50.000 0.00 0.00 0.00 2.93
869 1331 2.285144 TCCTCCCCGTCCCTTTCC 60.285 66.667 0.00 0.00 0.00 3.13
903 1365 2.466867 CGAGTTGCCCGCATAAACT 58.533 52.632 0.00 0.00 36.87 2.66
917 1379 5.512788 CCGCATAAACTACAAGCTTTGATTG 59.487 40.000 0.00 0.00 0.00 2.67
940 1402 0.322975 GGATCATCATCTCCCACCCG 59.677 60.000 0.00 0.00 0.00 5.28
1052 1518 0.874390 CTCGCAGCTAGCTCCTCTAG 59.126 60.000 16.15 3.40 46.01 2.43
1075 1541 4.067896 GACACCATGAAGAAGAAGAAGCA 58.932 43.478 0.00 0.00 0.00 3.91
1076 1542 4.070716 ACACCATGAAGAAGAAGAAGCAG 58.929 43.478 0.00 0.00 0.00 4.24
1077 1543 3.080319 ACCATGAAGAAGAAGAAGCAGC 58.920 45.455 0.00 0.00 0.00 5.25
1078 1544 3.079578 CCATGAAGAAGAAGAAGCAGCA 58.920 45.455 0.00 0.00 0.00 4.41
1079 1545 3.127203 CCATGAAGAAGAAGAAGCAGCAG 59.873 47.826 0.00 0.00 0.00 4.24
1080 1546 2.149578 TGAAGAAGAAGAAGCAGCAGC 58.850 47.619 0.00 0.00 42.56 5.25
1086 1552 0.888285 GAAGAAGCAGCAGCCAGTGT 60.888 55.000 0.00 0.00 43.56 3.55
1097 1563 0.106519 AGCCAGTGTTGTTCCTTGCT 60.107 50.000 0.00 0.00 0.00 3.91
1124 1590 0.171455 CGCTACTGGTCGCTTCTCTT 59.829 55.000 0.00 0.00 0.00 2.85
1127 1593 2.733858 GCTACTGGTCGCTTCTCTTCTG 60.734 54.545 0.00 0.00 0.00 3.02
1130 1596 0.037882 TGGTCGCTTCTCTTCTGCTG 60.038 55.000 0.00 0.00 0.00 4.41
1154 1623 4.087892 CCGTGCCAGGGGTCTCAG 62.088 72.222 0.00 0.00 0.00 3.35
1169 1638 2.190488 CTCAGGGAGCCAACCTCACC 62.190 65.000 0.00 0.00 45.57 4.02
1283 1752 5.689383 TTTCTTCCCTCGAATTTGTCTTG 57.311 39.130 0.00 0.00 0.00 3.02
1301 1770 5.006261 TGTCTTGGTATTATGCGTTTCATCG 59.994 40.000 0.00 0.00 36.63 3.84
1312 1781 2.906354 CGTTTCATCGGATTTCCTCCT 58.094 47.619 0.00 0.00 42.47 3.69
1325 1794 1.423584 TCCTCCTGTGTTCTGAAGCA 58.576 50.000 0.00 0.00 0.00 3.91
1327 1796 2.149578 CCTCCTGTGTTCTGAAGCAAG 58.850 52.381 0.00 0.00 0.00 4.01
1329 1798 1.134128 TCCTGTGTTCTGAAGCAAGCA 60.134 47.619 0.00 0.00 0.00 3.91
1331 1800 2.295349 CCTGTGTTCTGAAGCAAGCAAT 59.705 45.455 0.00 0.00 0.00 3.56
1332 1801 3.243636 CCTGTGTTCTGAAGCAAGCAATT 60.244 43.478 0.00 0.00 0.00 2.32
1333 1802 4.365723 CTGTGTTCTGAAGCAAGCAATTT 58.634 39.130 0.00 0.00 0.00 1.82
1334 1803 4.362279 TGTGTTCTGAAGCAAGCAATTTC 58.638 39.130 0.00 0.00 0.00 2.17
1339 1808 3.006110 TCTGAAGCAAGCAATTTCCCTTG 59.994 43.478 0.00 6.09 40.97 3.61
1394 1863 2.885113 CGATCAGGGTGAGCACGA 59.115 61.111 0.00 0.00 31.10 4.35
1396 1865 1.517257 GATCAGGGTGAGCACGACG 60.517 63.158 0.00 0.00 32.15 5.12
1441 1910 1.213013 CGAGAAGACCACCGACAGG 59.787 63.158 0.00 0.00 45.13 4.00
1598 2067 2.202932 CCGGCCACATCTCCTTCG 60.203 66.667 2.24 0.00 0.00 3.79
1844 2316 4.460683 CGTTCCCATTCCCGCCGA 62.461 66.667 0.00 0.00 0.00 5.54
1846 2318 1.448497 GTTCCCATTCCCGCCGATA 59.552 57.895 0.00 0.00 0.00 2.92
1966 2438 0.842030 AGTTCCCTCATCTGCCACCA 60.842 55.000 0.00 0.00 0.00 4.17
1969 2441 1.891933 TCCCTCATCTGCCACCAATA 58.108 50.000 0.00 0.00 0.00 1.90
1975 2447 4.445305 CCTCATCTGCCACCAATATTCTCA 60.445 45.833 0.00 0.00 0.00 3.27
1987 2459 4.823989 CCAATATTCTCAACACCATCTCCC 59.176 45.833 0.00 0.00 0.00 4.30
2101 2573 4.215742 TATTCGCCACCGCCTCCG 62.216 66.667 0.00 0.00 0.00 4.63
2164 2645 2.125326 GCCTTTCCCGCCATTACCC 61.125 63.158 0.00 0.00 0.00 3.69
2262 2743 2.661718 GTCCTCTTCCAAAACCCAACA 58.338 47.619 0.00 0.00 0.00 3.33
2268 2749 6.384305 TCCTCTTCCAAAACCCAACAATAAAA 59.616 34.615 0.00 0.00 0.00 1.52
2324 2805 9.667107 TCAAGGAAAGGATTACAAGTACATAAG 57.333 33.333 0.00 0.00 0.00 1.73
2358 2840 1.535833 CTCGTGCTAGGGACGGATAT 58.464 55.000 11.17 0.00 37.43 1.63
2481 2976 7.443575 TCCTCTTTTTGAGATGAAAAGACTCTG 59.556 37.037 7.68 0.64 44.06 3.35
2512 3009 2.346099 TGCAGTTTTATTGCGGCTTC 57.654 45.000 0.00 0.00 44.40 3.86
2520 3017 7.417612 CAGTTTTATTGCGGCTTCATAATACT 58.582 34.615 0.00 8.86 0.00 2.12
2521 3018 8.556194 CAGTTTTATTGCGGCTTCATAATACTA 58.444 33.333 15.50 0.00 0.00 1.82
2522 3019 8.557029 AGTTTTATTGCGGCTTCATAATACTAC 58.443 33.333 14.90 6.85 0.00 2.73
2528 3025 6.988522 TGCGGCTTCATAATACTACAGAATA 58.011 36.000 0.00 0.00 0.00 1.75
2539 3036 9.720769 ATAATACTACAGAATAACCATTTCCCG 57.279 33.333 0.00 0.00 0.00 5.14
2550 3047 3.780626 ACCATTTCCCGGGTTATTGAAA 58.219 40.909 22.86 13.04 32.12 2.69
2551 3048 4.161102 ACCATTTCCCGGGTTATTGAAAA 58.839 39.130 22.86 12.24 32.12 2.29
2552 3049 4.593634 ACCATTTCCCGGGTTATTGAAAAA 59.406 37.500 22.86 11.43 32.12 1.94
2579 3076 3.945285 TCCGGCTCCATTTGAATTTCTAC 59.055 43.478 0.00 0.00 0.00 2.59
2634 3131 6.047870 CACTAGAAAGATGACATGAGGAAGG 58.952 44.000 0.00 0.00 0.00 3.46
2635 3132 3.883669 AGAAAGATGACATGAGGAAGGC 58.116 45.455 0.00 0.00 0.00 4.35
2637 3134 2.706339 AGATGACATGAGGAAGGCAC 57.294 50.000 0.00 0.00 0.00 5.01
2644 3145 4.962362 TGACATGAGGAAGGCACTAAGATA 59.038 41.667 0.00 0.00 38.49 1.98
2645 3146 5.163405 TGACATGAGGAAGGCACTAAGATAC 60.163 44.000 0.00 0.00 38.49 2.24
2648 3149 5.282055 TGAGGAAGGCACTAAGATACATG 57.718 43.478 0.00 0.00 38.49 3.21
2654 3155 4.194640 AGGCACTAAGATACATGTTGCAG 58.805 43.478 16.01 5.29 36.02 4.41
2668 3169 4.524316 TGTTGCAGTAGTTACCGTGTAT 57.476 40.909 0.00 0.00 0.00 2.29
2704 3205 9.345517 ACGCAAATCATAATATGCATGAATAAC 57.654 29.630 10.16 0.00 38.69 1.89
2718 3219 8.334263 TGCATGAATAACTGAATACAACTGAA 57.666 30.769 0.00 0.00 0.00 3.02
3099 3601 1.234821 CCAAGCACGCTTAACTTCCA 58.765 50.000 3.53 0.00 34.50 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.300681 TGAAGACAATTATTTCAAGAACTCCAT 57.699 29.630 0.00 0.00 0.00 3.41
6 7 8.690203 TGAAGACAATTATTTCAAGAACTCCA 57.310 30.769 0.00 0.00 0.00 3.86
59 60 8.090214 CCACATTTCAACCTAGTGATTTCAATT 58.910 33.333 0.00 0.00 32.14 2.32
60 61 7.451255 TCCACATTTCAACCTAGTGATTTCAAT 59.549 33.333 0.00 0.00 32.14 2.57
67 68 4.974645 ACTCCACATTTCAACCTAGTGA 57.025 40.909 0.00 0.00 32.14 3.41
73 74 2.875933 TCGACAACTCCACATTTCAACC 59.124 45.455 0.00 0.00 0.00 3.77
74 75 3.560068 ACTCGACAACTCCACATTTCAAC 59.440 43.478 0.00 0.00 0.00 3.18
77 78 4.989168 AGTAACTCGACAACTCCACATTTC 59.011 41.667 0.00 0.00 0.00 2.17
79 80 4.038763 TCAGTAACTCGACAACTCCACATT 59.961 41.667 0.00 0.00 0.00 2.71
84 85 7.829378 ATTATTTCAGTAACTCGACAACTCC 57.171 36.000 0.00 0.00 0.00 3.85
85 86 9.784680 TCTATTATTTCAGTAACTCGACAACTC 57.215 33.333 0.00 0.00 0.00 3.01
121 122 1.462283 CACAAGTGAAGTCCGCTCATG 59.538 52.381 0.00 0.00 33.81 3.07
122 123 1.800805 CACAAGTGAAGTCCGCTCAT 58.199 50.000 0.00 0.00 33.81 2.90
127 128 1.143305 CTCTGCACAAGTGAAGTCCG 58.857 55.000 8.01 0.00 37.51 4.79
138 139 4.350368 TCAGTAACCATTTCTCTGCACA 57.650 40.909 0.00 0.00 0.00 4.57
331 357 6.148948 TGAAGCATGTCGGTTTATTCAAAAG 58.851 36.000 0.00 0.00 34.82 2.27
339 365 5.697473 TCATTTTGAAGCATGTCGGTTTA 57.303 34.783 0.00 0.00 34.82 2.01
342 368 2.095059 GCTCATTTTGAAGCATGTCGGT 60.095 45.455 0.00 0.00 0.00 4.69
343 369 2.095110 TGCTCATTTTGAAGCATGTCGG 60.095 45.455 0.00 0.00 29.93 4.79
344 370 2.912967 GTGCTCATTTTGAAGCATGTCG 59.087 45.455 0.00 0.00 34.72 4.35
345 371 3.248266 GGTGCTCATTTTGAAGCATGTC 58.752 45.455 0.00 0.00 34.72 3.06
346 372 2.352030 CGGTGCTCATTTTGAAGCATGT 60.352 45.455 0.00 0.00 34.72 3.21
347 373 2.256174 CGGTGCTCATTTTGAAGCATG 58.744 47.619 0.00 0.00 34.72 4.06
350 376 0.598065 ACCGGTGCTCATTTTGAAGC 59.402 50.000 6.12 0.00 0.00 3.86
351 377 4.273480 CCTATACCGGTGCTCATTTTGAAG 59.727 45.833 19.93 0.00 0.00 3.02
352 378 4.196193 CCTATACCGGTGCTCATTTTGAA 58.804 43.478 19.93 0.00 0.00 2.69
353 379 3.433031 CCCTATACCGGTGCTCATTTTGA 60.433 47.826 19.93 0.00 0.00 2.69
354 380 2.878406 CCCTATACCGGTGCTCATTTTG 59.122 50.000 19.93 0.00 0.00 2.44
355 381 2.775384 TCCCTATACCGGTGCTCATTTT 59.225 45.455 19.93 0.00 0.00 1.82
358 384 1.339097 GTCCCTATACCGGTGCTCAT 58.661 55.000 19.93 4.86 0.00 2.90
359 385 1.105167 CGTCCCTATACCGGTGCTCA 61.105 60.000 19.93 0.00 0.00 4.26
360 386 1.658673 CGTCCCTATACCGGTGCTC 59.341 63.158 19.93 0.00 0.00 4.26
362 388 2.732658 CCGTCCCTATACCGGTGC 59.267 66.667 19.93 0.00 37.00 5.01
363 389 1.678598 TTGCCGTCCCTATACCGGTG 61.679 60.000 19.93 0.00 43.56 4.94
365 391 1.068585 GTTGCCGTCCCTATACCGG 59.931 63.158 0.00 0.00 44.46 5.28
369 395 1.760613 CAGAAGGTTGCCGTCCCTATA 59.239 52.381 0.00 0.00 32.53 1.31
371 397 1.980052 CAGAAGGTTGCCGTCCCTA 59.020 57.895 0.00 0.00 32.53 3.53
372 398 2.750350 CAGAAGGTTGCCGTCCCT 59.250 61.111 0.00 0.00 32.53 4.20
373 399 3.056328 GCAGAAGGTTGCCGTCCC 61.056 66.667 0.00 0.00 38.13 4.46
379 405 0.678048 AAGATCGGGCAGAAGGTTGC 60.678 55.000 0.00 0.00 43.34 4.17
380 406 1.373570 GAAGATCGGGCAGAAGGTTG 58.626 55.000 0.00 0.00 0.00 3.77
381 407 0.108138 CGAAGATCGGGCAGAAGGTT 60.108 55.000 0.00 0.00 36.00 3.50
382 408 1.517832 CGAAGATCGGGCAGAAGGT 59.482 57.895 0.00 0.00 36.00 3.50
384 410 1.153568 TGCGAAGATCGGGCAGAAG 60.154 57.895 1.64 0.00 40.84 2.85
385 411 1.447838 GTGCGAAGATCGGGCAGAA 60.448 57.895 8.34 0.00 40.84 3.02
387 413 2.960957 ATCGTGCGAAGATCGGGCAG 62.961 60.000 8.34 4.51 40.84 4.85
388 414 3.076258 ATCGTGCGAAGATCGGGCA 62.076 57.895 0.00 4.58 40.84 5.36
389 415 2.279517 ATCGTGCGAAGATCGGGC 60.280 61.111 0.00 0.00 40.84 6.13
390 416 1.951130 CCATCGTGCGAAGATCGGG 60.951 63.158 0.00 0.00 40.84 5.14
391 417 1.951130 CCCATCGTGCGAAGATCGG 60.951 63.158 0.00 0.00 40.84 4.18
392 418 0.806102 AACCCATCGTGCGAAGATCG 60.806 55.000 0.00 0.00 43.89 3.69
393 419 0.652592 CAACCCATCGTGCGAAGATC 59.347 55.000 0.00 0.00 0.00 2.75
394 420 0.249120 TCAACCCATCGTGCGAAGAT 59.751 50.000 0.00 0.00 0.00 2.40
396 422 1.062587 GATTCAACCCATCGTGCGAAG 59.937 52.381 0.00 0.00 0.00 3.79
397 423 1.083489 GATTCAACCCATCGTGCGAA 58.917 50.000 0.00 0.00 0.00 4.70
399 425 0.374758 CTGATTCAACCCATCGTGCG 59.625 55.000 0.00 0.00 0.00 5.34
400 426 0.099436 GCTGATTCAACCCATCGTGC 59.901 55.000 0.00 0.00 0.00 5.34
401 427 0.734889 GGCTGATTCAACCCATCGTG 59.265 55.000 0.00 0.00 0.00 4.35
403 429 1.683943 ATGGCTGATTCAACCCATCG 58.316 50.000 11.01 0.00 32.85 3.84
404 430 4.464008 TCTAATGGCTGATTCAACCCATC 58.536 43.478 15.20 0.00 37.09 3.51
407 433 4.500375 GCAATCTAATGGCTGATTCAACCC 60.500 45.833 3.69 0.46 31.35 4.11
408 434 4.098349 TGCAATCTAATGGCTGATTCAACC 59.902 41.667 0.00 0.00 31.35 3.77
409 435 5.252969 TGCAATCTAATGGCTGATTCAAC 57.747 39.130 0.00 0.00 31.35 3.18
411 437 5.134661 TGATGCAATCTAATGGCTGATTCA 58.865 37.500 0.00 0.00 45.81 2.57
412 438 5.700722 TGATGCAATCTAATGGCTGATTC 57.299 39.130 0.00 0.00 45.81 2.52
415 441 6.277605 CAAAATGATGCAATCTAATGGCTGA 58.722 36.000 0.00 0.00 45.81 4.26
416 442 5.050363 GCAAAATGATGCAATCTAATGGCTG 60.050 40.000 0.00 0.00 45.81 4.85
417 443 5.054477 GCAAAATGATGCAATCTAATGGCT 58.946 37.500 0.00 0.00 45.81 4.75
418 444 4.084745 CGCAAAATGATGCAATCTAATGGC 60.085 41.667 0.00 0.00 46.76 4.40
419 445 5.283294 TCGCAAAATGATGCAATCTAATGG 58.717 37.500 0.00 0.00 46.76 3.16
420 446 6.815672 TTCGCAAAATGATGCAATCTAATG 57.184 33.333 0.00 0.00 46.76 1.90
421 447 7.168637 GTGATTCGCAAAATGATGCAATCTAAT 59.831 33.333 18.08 6.81 46.76 1.73
422 448 6.473131 GTGATTCGCAAAATGATGCAATCTAA 59.527 34.615 18.08 6.76 46.76 2.10
424 450 4.802039 GTGATTCGCAAAATGATGCAATCT 59.198 37.500 18.08 0.00 46.76 2.40
425 451 4.026310 GGTGATTCGCAAAATGATGCAATC 60.026 41.667 0.00 14.34 46.76 2.67
426 452 3.866910 GGTGATTCGCAAAATGATGCAAT 59.133 39.130 0.00 3.21 46.76 3.56
427 453 3.252400 GGTGATTCGCAAAATGATGCAA 58.748 40.909 0.00 0.00 46.76 4.08
428 454 2.731654 CGGTGATTCGCAAAATGATGCA 60.732 45.455 0.00 0.00 46.76 3.96
429 455 1.847999 CGGTGATTCGCAAAATGATGC 59.152 47.619 0.00 0.00 42.94 3.91
440 466 0.446222 ATTTGAACGGCGGTGATTCG 59.554 50.000 13.24 0.00 0.00 3.34
441 467 2.629639 AATTTGAACGGCGGTGATTC 57.370 45.000 13.24 6.42 0.00 2.52
445 471 0.179174 GCCTAATTTGAACGGCGGTG 60.179 55.000 13.24 0.00 32.22 4.94
446 472 0.606944 TGCCTAATTTGAACGGCGGT 60.607 50.000 13.24 3.35 45.36 5.68
447 473 0.738389 ATGCCTAATTTGAACGGCGG 59.262 50.000 13.24 0.00 45.36 6.13
448 474 1.594518 CGATGCCTAATTTGAACGGCG 60.595 52.381 4.80 4.80 45.36 6.46
449 475 1.400494 ACGATGCCTAATTTGAACGGC 59.600 47.619 0.00 0.00 42.78 5.68
450 476 2.791158 GCACGATGCCTAATTTGAACGG 60.791 50.000 0.00 0.00 37.42 4.44
451 477 2.159585 TGCACGATGCCTAATTTGAACG 60.160 45.455 7.38 0.00 44.23 3.95
452 478 3.485947 TGCACGATGCCTAATTTGAAC 57.514 42.857 7.38 0.00 44.23 3.18
463 698 1.081892 AGACAGTTCATGCACGATGC 58.918 50.000 0.00 0.00 45.29 3.91
464 699 2.071540 ACAGACAGTTCATGCACGATG 58.928 47.619 0.00 0.00 0.00 3.84
465 700 2.071540 CACAGACAGTTCATGCACGAT 58.928 47.619 0.00 0.00 0.00 3.73
466 701 1.501169 CACAGACAGTTCATGCACGA 58.499 50.000 0.00 0.00 0.00 4.35
468 703 1.532868 GTCCACAGACAGTTCATGCAC 59.467 52.381 0.00 0.00 42.99 4.57
469 704 1.543208 GGTCCACAGACAGTTCATGCA 60.543 52.381 0.00 0.00 45.48 3.96
471 706 2.549064 TGGTCCACAGACAGTTCATG 57.451 50.000 0.00 0.00 45.48 3.07
472 707 2.354103 CGATGGTCCACAGACAGTTCAT 60.354 50.000 0.00 0.00 45.48 2.57
474 709 1.000955 ACGATGGTCCACAGACAGTTC 59.999 52.381 0.00 0.00 45.48 3.01
475 710 1.048601 ACGATGGTCCACAGACAGTT 58.951 50.000 0.00 0.00 45.48 3.16
476 711 0.318441 CACGATGGTCCACAGACAGT 59.682 55.000 0.00 0.00 45.48 3.55
477 712 0.318441 ACACGATGGTCCACAGACAG 59.682 55.000 0.00 0.00 45.48 3.51
479 714 1.291877 GCACACGATGGTCCACAGAC 61.292 60.000 0.00 0.00 42.73 3.51
485 752 2.509336 CTCCGCACACGATGGTCC 60.509 66.667 0.00 0.00 43.93 4.46
503 770 3.904136 ACGATTTTGAAGCAGGAAGTG 57.096 42.857 0.00 0.00 0.00 3.16
504 771 4.137543 AGAACGATTTTGAAGCAGGAAGT 58.862 39.130 0.00 0.00 0.00 3.01
510 777 3.253188 CCAGGAAGAACGATTTTGAAGCA 59.747 43.478 0.00 0.00 0.00 3.91
511 778 3.502211 TCCAGGAAGAACGATTTTGAAGC 59.498 43.478 0.00 0.00 0.00 3.86
514 781 4.351874 ACTCCAGGAAGAACGATTTTGA 57.648 40.909 0.00 0.00 0.00 2.69
515 782 4.515191 TGAACTCCAGGAAGAACGATTTTG 59.485 41.667 0.00 0.00 0.00 2.44
516 783 4.515567 GTGAACTCCAGGAAGAACGATTTT 59.484 41.667 0.00 0.00 0.00 1.82
517 784 4.065789 GTGAACTCCAGGAAGAACGATTT 58.934 43.478 0.00 0.00 0.00 2.17
518 785 3.557264 GGTGAACTCCAGGAAGAACGATT 60.557 47.826 0.00 0.00 0.00 3.34
519 786 2.028020 GGTGAACTCCAGGAAGAACGAT 60.028 50.000 0.00 0.00 0.00 3.73
520 787 1.343465 GGTGAACTCCAGGAAGAACGA 59.657 52.381 0.00 0.00 0.00 3.85
521 788 1.344763 AGGTGAACTCCAGGAAGAACG 59.655 52.381 0.00 0.00 0.00 3.95
522 789 3.046968 GAGGTGAACTCCAGGAAGAAC 57.953 52.381 0.00 0.00 40.49 3.01
532 799 3.339141 GGGTGATCAAAGAGGTGAACTC 58.661 50.000 0.00 0.00 46.98 3.01
535 802 1.354368 GGGGGTGATCAAAGAGGTGAA 59.646 52.381 0.00 0.00 0.00 3.18
536 803 0.991920 GGGGGTGATCAAAGAGGTGA 59.008 55.000 0.00 0.00 0.00 4.02
537 804 0.392998 CGGGGGTGATCAAAGAGGTG 60.393 60.000 0.00 0.00 0.00 4.00
538 805 0.840722 ACGGGGGTGATCAAAGAGGT 60.841 55.000 0.00 0.00 0.00 3.85
539 806 0.392998 CACGGGGGTGATCAAAGAGG 60.393 60.000 0.00 0.00 0.00 3.69
540 807 0.324943 ACACGGGGGTGATCAAAGAG 59.675 55.000 0.00 0.00 0.00 2.85
541 808 0.036164 CACACGGGGGTGATCAAAGA 59.964 55.000 0.00 0.00 41.32 2.52
542 809 1.586154 GCACACGGGGGTGATCAAAG 61.586 60.000 5.01 0.00 41.32 2.77
545 812 4.386951 CGCACACGGGGGTGATCA 62.387 66.667 5.01 0.00 41.32 2.92
563 830 2.665185 AACGTTGGAGGAGCGCAC 60.665 61.111 11.47 1.97 0.00 5.34
579 846 5.335583 CGGTTATTGAAGATGTTGAAGCCAA 60.336 40.000 0.00 0.00 0.00 4.52
580 847 4.155826 CGGTTATTGAAGATGTTGAAGCCA 59.844 41.667 0.00 0.00 0.00 4.75
583 850 7.017645 CAGTTCGGTTATTGAAGATGTTGAAG 58.982 38.462 0.00 0.00 0.00 3.02
584 851 6.485313 ACAGTTCGGTTATTGAAGATGTTGAA 59.515 34.615 0.00 0.00 0.00 2.69
585 852 5.995282 ACAGTTCGGTTATTGAAGATGTTGA 59.005 36.000 0.00 0.00 0.00 3.18
588 855 5.334879 GCAACAGTTCGGTTATTGAAGATGT 60.335 40.000 0.00 0.00 31.39 3.06
589 856 5.088739 GCAACAGTTCGGTTATTGAAGATG 58.911 41.667 0.00 0.00 0.00 2.90
590 857 4.156008 GGCAACAGTTCGGTTATTGAAGAT 59.844 41.667 0.00 0.00 0.00 2.40
591 858 3.500680 GGCAACAGTTCGGTTATTGAAGA 59.499 43.478 0.00 0.00 0.00 2.87
592 859 3.252215 TGGCAACAGTTCGGTTATTGAAG 59.748 43.478 0.00 0.00 46.17 3.02
594 861 2.852449 TGGCAACAGTTCGGTTATTGA 58.148 42.857 0.00 0.00 46.17 2.57
646 1088 2.031333 GGAATGTACCGCTACTCCGTAG 60.031 54.545 0.00 0.00 38.97 3.51
649 1091 0.742505 TGGAATGTACCGCTACTCCG 59.257 55.000 0.00 0.00 0.00 4.63
650 1092 2.822764 CTTGGAATGTACCGCTACTCC 58.177 52.381 0.00 0.00 0.00 3.85
651 1093 2.202566 GCTTGGAATGTACCGCTACTC 58.797 52.381 0.00 0.00 0.00 2.59
652 1094 1.134491 GGCTTGGAATGTACCGCTACT 60.134 52.381 0.00 0.00 0.00 2.57
653 1095 1.296727 GGCTTGGAATGTACCGCTAC 58.703 55.000 0.00 0.00 0.00 3.58
654 1096 0.179094 CGGCTTGGAATGTACCGCTA 60.179 55.000 0.00 0.00 37.05 4.26
655 1097 1.449601 CGGCTTGGAATGTACCGCT 60.450 57.895 0.00 0.00 37.05 5.52
656 1098 3.098555 CGGCTTGGAATGTACCGC 58.901 61.111 0.00 0.00 37.05 5.68
658 1100 1.940613 GATCACGGCTTGGAATGTACC 59.059 52.381 0.00 0.00 0.00 3.34
693 1135 1.661821 GCTCCGGGTCGATCGATTG 60.662 63.158 22.50 13.51 0.00 2.67
695 1137 2.518587 TGCTCCGGGTCGATCGAT 60.519 61.111 22.50 0.00 0.00 3.59
696 1138 3.515286 GTGCTCCGGGTCGATCGA 61.515 66.667 15.15 15.15 0.00 3.59
697 1139 3.758088 CTGTGCTCCGGGTCGATCG 62.758 68.421 9.36 9.36 0.00 3.69
698 1140 2.105128 CTGTGCTCCGGGTCGATC 59.895 66.667 0.00 0.00 0.00 3.69
699 1141 3.461773 CCTGTGCTCCGGGTCGAT 61.462 66.667 0.00 0.00 34.56 3.59
700 1142 4.671590 TCCTGTGCTCCGGGTCGA 62.672 66.667 0.00 0.00 40.86 4.20
702 1144 4.459089 GCTCCTGTGCTCCGGGTC 62.459 72.222 0.00 0.00 40.86 4.46
704 1146 4.463879 CTGCTCCTGTGCTCCGGG 62.464 72.222 0.00 0.00 41.48 5.73
705 1147 3.655810 GACTGCTCCTGTGCTCCGG 62.656 68.421 0.00 0.00 0.00 5.14
715 1157 0.951040 CTCAAACCCGTGACTGCTCC 60.951 60.000 0.00 0.00 0.00 4.70
719 1161 1.966451 GGGCTCAAACCCGTGACTG 60.966 63.158 0.00 0.00 40.98 3.51
744 1206 0.109132 GCAGGCAGGTTTTGATTCCG 60.109 55.000 0.00 0.00 0.00 4.30
746 1208 0.109132 CGGCAGGCAGGTTTTGATTC 60.109 55.000 0.00 0.00 0.00 2.52
747 1209 0.827507 ACGGCAGGCAGGTTTTGATT 60.828 50.000 0.00 0.00 0.00 2.57
748 1210 0.827507 AACGGCAGGCAGGTTTTGAT 60.828 50.000 0.00 0.00 0.00 2.57
749 1211 1.454847 AACGGCAGGCAGGTTTTGA 60.455 52.632 0.00 0.00 0.00 2.69
750 1212 1.300080 CAACGGCAGGCAGGTTTTG 60.300 57.895 0.00 0.00 0.00 2.44
751 1213 2.498056 CCAACGGCAGGCAGGTTTT 61.498 57.895 0.00 0.00 0.00 2.43
752 1214 2.912025 CCAACGGCAGGCAGGTTT 60.912 61.111 0.00 0.00 0.00 3.27
753 1215 3.731766 AACCAACGGCAGGCAGGTT 62.732 57.895 9.04 9.04 37.73 3.50
754 1216 4.204028 AACCAACGGCAGGCAGGT 62.204 61.111 0.00 0.00 0.00 4.00
755 1217 3.673484 CAACCAACGGCAGGCAGG 61.673 66.667 0.00 0.00 0.00 4.85
756 1218 1.526575 ATTCAACCAACGGCAGGCAG 61.527 55.000 0.00 0.00 0.00 4.85
757 1219 1.530419 ATTCAACCAACGGCAGGCA 60.530 52.632 0.00 0.00 0.00 4.75
758 1220 1.080569 CATTCAACCAACGGCAGGC 60.081 57.895 0.00 0.00 0.00 4.85
768 1230 0.458370 GTGCCGCCATTCATTCAACC 60.458 55.000 0.00 0.00 0.00 3.77
772 1234 2.408835 CCGTGCCGCCATTCATTC 59.591 61.111 0.00 0.00 0.00 2.67
773 1235 3.825611 GCCGTGCCGCCATTCATT 61.826 61.111 0.00 0.00 0.00 2.57
819 1281 0.874390 GGAACAAGCGCATGTGAAGA 59.126 50.000 20.14 0.00 32.81 2.87
903 1365 5.508567 TGATCCATCCAATCAAAGCTTGTA 58.491 37.500 0.00 0.00 30.37 2.41
917 1379 2.026449 GGTGGGAGATGATGATCCATCC 60.026 54.545 7.98 0.00 42.89 3.51
940 1402 1.153958 CAAAGCCTTAGCAAGCGGC 60.154 57.895 0.00 0.00 43.56 6.53
1052 1518 3.438434 GCTTCTTCTTCTTCATGGTGTCC 59.562 47.826 0.00 0.00 0.00 4.02
1075 1541 0.106519 AAGGAACAACACTGGCTGCT 60.107 50.000 0.00 0.00 0.00 4.24
1076 1542 0.031178 CAAGGAACAACACTGGCTGC 59.969 55.000 0.00 0.00 0.00 5.25
1077 1543 0.031178 GCAAGGAACAACACTGGCTG 59.969 55.000 0.00 0.00 30.88 4.85
1078 1544 0.106519 AGCAAGGAACAACACTGGCT 60.107 50.000 0.00 0.00 39.13 4.75
1079 1545 0.746659 AAGCAAGGAACAACACTGGC 59.253 50.000 0.00 0.00 33.78 4.85
1080 1546 2.481795 CCAAAGCAAGGAACAACACTGG 60.482 50.000 0.00 0.00 0.00 4.00
1086 1552 1.039856 GCCTCCAAAGCAAGGAACAA 58.960 50.000 0.00 0.00 34.35 2.83
1097 1563 1.295423 GACCAGTAGCGCCTCCAAA 59.705 57.895 2.29 0.00 0.00 3.28
1119 1585 4.087892 GCCGGGCAGCAGAAGAGA 62.088 66.667 15.62 0.00 0.00 3.10
1138 1607 4.087892 CCTGAGACCCCTGGCACG 62.088 72.222 0.00 0.00 0.00 5.34
1154 1623 3.637273 ACGGTGAGGTTGGCTCCC 61.637 66.667 0.00 0.00 0.00 4.30
1283 1752 5.607119 AATCCGATGAAACGCATAATACC 57.393 39.130 0.00 0.00 37.34 2.73
1312 1781 4.362279 GAAATTGCTTGCTTCAGAACACA 58.638 39.130 0.00 0.00 0.00 3.72
1325 1794 4.990426 CGAACAAATCAAGGGAAATTGCTT 59.010 37.500 0.00 0.00 30.97 3.91
1327 1796 4.306600 ACGAACAAATCAAGGGAAATTGC 58.693 39.130 0.00 0.00 30.97 3.56
1329 1798 5.534654 TCTGACGAACAAATCAAGGGAAATT 59.465 36.000 0.00 0.00 0.00 1.82
1331 1800 4.456535 TCTGACGAACAAATCAAGGGAAA 58.543 39.130 0.00 0.00 0.00 3.13
1332 1801 4.079980 TCTGACGAACAAATCAAGGGAA 57.920 40.909 0.00 0.00 0.00 3.97
1333 1802 3.762407 TCTGACGAACAAATCAAGGGA 57.238 42.857 0.00 0.00 0.00 4.20
1334 1803 3.753272 ACATCTGACGAACAAATCAAGGG 59.247 43.478 0.00 0.00 0.00 3.95
1339 1808 4.452455 ACCTTCACATCTGACGAACAAATC 59.548 41.667 0.00 0.00 0.00 2.17
1394 1863 1.827969 CTTGATCTCCTCCTTGGACGT 59.172 52.381 0.00 0.00 40.56 4.34
1396 1865 3.708631 TGATCTTGATCTCCTCCTTGGAC 59.291 47.826 11.31 0.00 40.56 4.02
1612 2081 2.092882 GTTGTAGAGGCACGCGTCC 61.093 63.158 9.86 14.42 0.00 4.79
1877 2349 1.185618 AAAGGGAAAGGGAAAGCCGC 61.186 55.000 0.00 0.00 33.83 6.53
1966 2438 4.141158 GGGGGAGATGGTGTTGAGAATATT 60.141 45.833 0.00 0.00 0.00 1.28
1969 2441 1.566231 GGGGGAGATGGTGTTGAGAAT 59.434 52.381 0.00 0.00 0.00 2.40
1975 2447 3.728373 GGCGGGGGAGATGGTGTT 61.728 66.667 0.00 0.00 0.00 3.32
2134 2615 1.257743 GGAAAGGCCAAGGAAAGGAC 58.742 55.000 5.01 0.00 36.34 3.85
2161 2642 1.068121 CAGTTGGAGGGAAGAAGGGT 58.932 55.000 0.00 0.00 0.00 4.34
2164 2645 2.157738 CTTGCAGTTGGAGGGAAGAAG 58.842 52.381 0.00 0.00 34.79 2.85
2296 2777 7.979444 TGTACTTGTAATCCTTTCCTTGAAG 57.021 36.000 0.00 0.00 0.00 3.02
2313 2794 9.869844 GCAGATAAATTGCTACTTATGTACTTG 57.130 33.333 0.00 0.00 38.51 3.16
2358 2840 4.801521 TCTGCCTAGTACACCCACTATA 57.198 45.455 0.00 0.00 30.78 1.31
2481 2976 7.217070 CGCAATAAAACTGCATTTTCTCTCTAC 59.783 37.037 2.17 0.00 40.99 2.59
2520 3017 3.524380 ACCCGGGAAATGGTTATTCTGTA 59.476 43.478 32.02 0.00 0.00 2.74
2521 3018 2.310647 ACCCGGGAAATGGTTATTCTGT 59.689 45.455 32.02 0.00 0.00 3.41
2522 3019 3.012934 ACCCGGGAAATGGTTATTCTG 57.987 47.619 32.02 0.00 0.00 3.02
2528 3025 3.459710 TCAATAACCCGGGAAATGGTT 57.540 42.857 32.02 12.83 46.32 3.67
2550 3047 4.615588 TCAAATGGAGCCGGAAAATTTT 57.384 36.364 5.05 2.28 0.00 1.82
2551 3048 4.615588 TTCAAATGGAGCCGGAAAATTT 57.384 36.364 5.05 2.05 0.00 1.82
2552 3049 4.824479 ATTCAAATGGAGCCGGAAAATT 57.176 36.364 5.05 0.00 0.00 1.82
2553 3050 4.824479 AATTCAAATGGAGCCGGAAAAT 57.176 36.364 5.05 0.00 0.00 1.82
2595 3092 4.478206 TCTAGTGAAGGAGGAGCATTTG 57.522 45.455 0.00 0.00 0.00 2.32
2599 3096 3.779444 TCTTTCTAGTGAAGGAGGAGCA 58.221 45.455 8.18 0.00 34.09 4.26
2634 3131 5.812642 ACTACTGCAACATGTATCTTAGTGC 59.187 40.000 9.04 9.04 0.00 4.40
2635 3132 7.834068 AACTACTGCAACATGTATCTTAGTG 57.166 36.000 0.00 0.00 0.00 2.74
2637 3134 7.167635 CGGTAACTACTGCAACATGTATCTTAG 59.832 40.741 0.00 0.00 0.00 2.18
2638 3135 6.976349 CGGTAACTACTGCAACATGTATCTTA 59.024 38.462 0.00 0.00 0.00 2.10
2644 3145 3.064207 CACGGTAACTACTGCAACATGT 58.936 45.455 0.00 0.00 36.01 3.21
2645 3146 3.064207 ACACGGTAACTACTGCAACATG 58.936 45.455 0.00 0.00 36.01 3.21
2648 3149 8.807667 AATATATACACGGTAACTACTGCAAC 57.192 34.615 0.00 0.00 36.01 4.17
2654 3155 9.270576 CGTGATGAATATATACACGGTAACTAC 57.729 37.037 18.20 0.00 46.43 2.73
2678 3179 9.345517 GTTATTCATGCATATTATGATTTGCGT 57.654 29.630 7.87 5.35 41.40 5.24
2718 3219 5.887214 TCCACCAGTGTACATATGCTTAT 57.113 39.130 1.58 0.00 0.00 1.73
2721 3222 4.568072 TTTCCACCAGTGTACATATGCT 57.432 40.909 1.58 0.00 0.00 3.79
2727 3228 2.938838 CCCTTTTTCCACCAGTGTACA 58.061 47.619 0.00 0.00 0.00 2.90
3099 3601 1.757699 GAGCGTGGGAGAATAGAACCT 59.242 52.381 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.