Multiple sequence alignment - TraesCS6D01G365000

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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 TraesCS6D01G365000 chr6D 100.000 6715 0 0 1 6715 454485329 454492043 0.000000e+00 12401
1 TraesCS6D01G365000 chr6B 94.543 4929 215 14 1832 6709 690962942 690967867 0.000000e+00 7563
2 TraesCS6D01G365000 chr6B 83.993 1087 91 28 436 1509 690961119 690962135 0.000000e+00 966
3 TraesCS6D01G365000 chr6B 92.408 382 20 5 1 375 690960589 690960968 2.760000e-148 536
4 TraesCS6D01G365000 chr6B 94.702 151 7 1 1683 1833 690962634 690962783 4.050000e-57 233
5 TraesCS6D01G365000 chr6A 95.246 4649 160 22 1770 6385 600694473 600699093 0.000000e+00 7304
6 TraesCS6D01G365000 chr6A 89.211 760 54 11 944 1684 600693329 600694079 0.000000e+00 924
7 TraesCS6D01G365000 chr6A 85.344 655 61 20 1 639 600676254 600676889 0.000000e+00 645
8 TraesCS6D01G365000 chr6A 96.000 200 5 2 6512 6709 600701182 600701380 8.400000e-84 322
9 TraesCS6D01G365000 chr6A 94.737 133 7 0 6381 6513 600700968 600701100 2.450000e-49 207
10 TraesCS6D01G365000 chr3A 87.682 893 93 9 2494 3373 642367272 642368160 0.000000e+00 1024
11 TraesCS6D01G365000 chr3A 83.126 883 110 14 3854 4728 642368581 642369432 0.000000e+00 769
12 TraesCS6D01G365000 chr3A 87.107 636 68 7 3369 3997 642368234 642368862 0.000000e+00 708
13 TraesCS6D01G365000 chr3A 80.765 863 94 36 1683 2497 642366392 642367230 5.760000e-170 608
14 TraesCS6D01G365000 chr3A 84.696 477 63 5 5251 5721 642369766 642370238 1.020000e-127 468
15 TraesCS6D01G365000 chr3A 80.483 538 59 28 962 1469 642365138 642365659 2.960000e-98 370
16 TraesCS6D01G365000 chr3A 83.228 316 34 10 4733 5043 642369467 642369768 8.580000e-69 272
17 TraesCS6D01G365000 chr3D 87.361 902 85 9 2494 3373 504056987 504057881 0.000000e+00 1007
18 TraesCS6D01G365000 chr3D 82.766 882 106 12 3854 4728 504058308 504059150 0.000000e+00 745
19 TraesCS6D01G365000 chr3D 86.185 637 65 9 3368 3997 504057960 504058580 0.000000e+00 667
20 TraesCS6D01G365000 chr3D 80.969 867 93 34 1683 2497 504056099 504056945 7.400000e-174 621
21 TraesCS6D01G365000 chr3D 85.744 477 58 5 5251 5721 504059483 504059955 4.680000e-136 496
22 TraesCS6D01G365000 chr3D 78.727 597 82 30 962 1528 504054980 504055561 2.300000e-94 357
23 TraesCS6D01G365000 chr3D 81.098 328 44 9 4721 5043 504059171 504059485 5.200000e-61 246
24 TraesCS6D01G365000 chr3B 87.140 902 87 9 2494 3373 665466485 665467379 0.000000e+00 996
25 TraesCS6D01G365000 chr3B 82.086 882 115 11 3854 4728 665467806 665468651 0.000000e+00 713
26 TraesCS6D01G365000 chr3B 86.656 637 65 8 3368 3997 665467458 665468081 0.000000e+00 688
27 TraesCS6D01G365000 chr3B 85.325 477 60 5 5251 5721 665468984 665469456 1.010000e-132 484
28 TraesCS6D01G365000 chr3B 79.054 592 77 27 962 1528 665464502 665465071 4.950000e-96 363
29 TraesCS6D01G365000 chr3B 81.707 328 42 9 4721 5043 665468672 665468986 2.400000e-64 257
30 TraesCS6D01G365000 chr5B 85.239 691 76 8 1000 1684 590471267 590470597 0.000000e+00 688
31 TraesCS6D01G365000 chr5B 87.671 146 10 2 1681 1819 540405945 540405801 5.390000e-36 163
32 TraesCS6D01G365000 chr1B 88.194 144 9 2 1683 1819 35063881 35064023 1.500000e-36 165


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 TraesCS6D01G365000 chr6D 454485329 454492043 6714 False 12401.000000 12401 100.000000 1 6715 1 chr6D.!!$F1 6714
1 TraesCS6D01G365000 chr6B 690960589 690967867 7278 False 2324.500000 7563 91.411500 1 6709 4 chr6B.!!$F1 6708
2 TraesCS6D01G365000 chr6A 600693329 600701380 8051 False 2189.250000 7304 93.798500 944 6709 4 chr6A.!!$F2 5765
3 TraesCS6D01G365000 chr6A 600676254 600676889 635 False 645.000000 645 85.344000 1 639 1 chr6A.!!$F1 638
4 TraesCS6D01G365000 chr3A 642365138 642370238 5100 False 602.714286 1024 83.869571 962 5721 7 chr3A.!!$F1 4759
5 TraesCS6D01G365000 chr3D 504054980 504059955 4975 False 591.285714 1007 83.264286 962 5721 7 chr3D.!!$F1 4759
6 TraesCS6D01G365000 chr3B 665464502 665469456 4954 False 583.500000 996 83.661333 962 5721 6 chr3B.!!$F1 4759
7 TraesCS6D01G365000 chr5B 590470597 590471267 670 True 688.000000 688 85.239000 1000 1684 1 chr5B.!!$R2 684

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
771 880 0.041135 GGAACTCTATCGCCGAGTCG 60.041 60.000 5.29 5.29 40.65 4.18 F
2405 3653 0.188342 AGGGTGGCAAGAACAATGGT 59.812 50.000 0.00 0.00 0.00 3.55 F
2643 3972 1.409064 CGTCCATTACAGCTGAGCCTA 59.591 52.381 23.35 0.00 0.00 3.93 F
3856 5350 0.109342 AGTGTTGCTTGTCCTGAGGG 59.891 55.000 0.00 0.00 0.00 4.30 F
4480 5974 0.948623 TGGCGAAACATGAGACACCG 60.949 55.000 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2623 3952 0.176680 AGGCTCAGCTGTAATGGACG 59.823 55.000 14.67 0.00 0.0 4.79 R
3636 5127 1.774110 TGCTTTGTGCCAAGGAAAGA 58.226 45.000 0.00 0.00 42.0 2.52 R
4439 5933 3.414700 GGTGACGACTGCTTGCCG 61.415 66.667 0.00 0.00 0.0 5.69 R
4883 6428 2.167487 GAGTTGCCACTTCCTCTAGAGG 59.833 54.545 30.15 30.15 41.0 3.69 R
6469 9915 0.251916 TCCCCGGTGCTACATTGAAG 59.748 55.000 0.00 0.00 0.0 3.02 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
146 151 2.973945 AGGATTGCTCGAGTTGTTACC 58.026 47.619 15.13 10.27 0.00 2.85
149 154 2.228138 TTGCTCGAGTTGTTACCGTT 57.772 45.000 15.13 0.00 0.00 4.44
288 297 3.329225 TGGAATTGGTCTGGTGTATGTGA 59.671 43.478 0.00 0.00 0.00 3.58
308 327 6.003326 TGTGAGATTTGTTCTATTTGCTGGA 58.997 36.000 0.00 0.00 33.74 3.86
310 329 7.014134 TGTGAGATTTGTTCTATTTGCTGGAAA 59.986 33.333 0.00 0.00 33.74 3.13
313 332 8.992835 AGATTTGTTCTATTTGCTGGAAATTC 57.007 30.769 12.38 2.13 35.74 2.17
315 334 7.945033 TTTGTTCTATTTGCTGGAAATTCAC 57.055 32.000 12.38 7.72 35.74 3.18
316 335 6.024552 TGTTCTATTTGCTGGAAATTCACC 57.975 37.500 12.38 0.91 35.74 4.02
317 336 4.963276 TCTATTTGCTGGAAATTCACCG 57.037 40.909 12.38 0.00 35.74 4.94
318 337 3.694072 TCTATTTGCTGGAAATTCACCGG 59.306 43.478 12.38 0.00 35.74 5.28
323 342 1.247567 CTGGAAATTCACCGGCAGTT 58.752 50.000 0.00 0.00 0.00 3.16
324 343 2.432444 CTGGAAATTCACCGGCAGTTA 58.568 47.619 0.00 0.00 0.00 2.24
325 344 2.817258 CTGGAAATTCACCGGCAGTTAA 59.183 45.455 0.00 0.00 0.00 2.01
326 345 3.223435 TGGAAATTCACCGGCAGTTAAA 58.777 40.909 0.00 0.00 0.00 1.52
327 346 3.254657 TGGAAATTCACCGGCAGTTAAAG 59.745 43.478 0.00 0.00 0.00 1.85
328 347 3.254903 GGAAATTCACCGGCAGTTAAAGT 59.745 43.478 0.00 0.00 0.00 2.66
329 348 4.261867 GGAAATTCACCGGCAGTTAAAGTT 60.262 41.667 0.00 0.00 0.00 2.66
330 349 5.048573 GGAAATTCACCGGCAGTTAAAGTTA 60.049 40.000 0.00 0.00 0.00 2.24
331 350 6.349860 GGAAATTCACCGGCAGTTAAAGTTAT 60.350 38.462 0.00 0.00 0.00 1.89
332 351 5.560966 ATTCACCGGCAGTTAAAGTTATG 57.439 39.130 0.00 0.00 0.00 1.90
333 352 4.010667 TCACCGGCAGTTAAAGTTATGT 57.989 40.909 0.00 0.00 0.00 2.29
334 353 3.749088 TCACCGGCAGTTAAAGTTATGTG 59.251 43.478 0.00 0.00 0.00 3.21
364 383 5.603170 AATTGTAGATTTGGGCATGGAAG 57.397 39.130 0.00 0.00 0.00 3.46
365 384 3.017048 TGTAGATTTGGGCATGGAAGG 57.983 47.619 0.00 0.00 0.00 3.46
375 394 3.980022 TGGGCATGGAAGGATAGTTGATA 59.020 43.478 0.00 0.00 0.00 2.15
378 478 4.457257 GGCATGGAAGGATAGTTGATAAGC 59.543 45.833 0.00 0.00 0.00 3.09
396 496 1.618343 AGCACAAAGTTAATGTGGGGC 59.382 47.619 9.23 0.00 46.43 5.80
397 497 1.618343 GCACAAAGTTAATGTGGGGCT 59.382 47.619 9.23 0.00 46.43 5.19
399 499 3.860754 GCACAAAGTTAATGTGGGGCTTC 60.861 47.826 9.23 0.00 46.43 3.86
400 500 3.573967 CACAAAGTTAATGTGGGGCTTCT 59.426 43.478 0.46 0.00 43.45 2.85
403 503 4.929146 AAGTTAATGTGGGGCTTCTACT 57.071 40.909 0.00 0.00 0.00 2.57
404 504 4.929146 AGTTAATGTGGGGCTTCTACTT 57.071 40.909 0.00 0.00 0.00 2.24
405 505 5.256806 AGTTAATGTGGGGCTTCTACTTT 57.743 39.130 0.00 0.00 0.00 2.66
407 507 6.075315 AGTTAATGTGGGGCTTCTACTTTTT 58.925 36.000 0.00 0.00 0.00 1.94
408 508 4.871933 AATGTGGGGCTTCTACTTTTTG 57.128 40.909 0.00 0.00 0.00 2.44
409 509 3.586470 TGTGGGGCTTCTACTTTTTGA 57.414 42.857 0.00 0.00 0.00 2.69
410 510 3.904717 TGTGGGGCTTCTACTTTTTGAA 58.095 40.909 0.00 0.00 0.00 2.69
414 514 4.245660 GGGGCTTCTACTTTTTGAAATGC 58.754 43.478 0.00 0.00 0.00 3.56
415 515 4.262420 GGGGCTTCTACTTTTTGAAATGCA 60.262 41.667 0.00 0.00 0.00 3.96
416 516 5.296748 GGGCTTCTACTTTTTGAAATGCAA 58.703 37.500 0.00 0.00 33.88 4.08
417 517 5.757808 GGGCTTCTACTTTTTGAAATGCAAA 59.242 36.000 0.00 0.00 44.38 3.68
418 518 6.073602 GGGCTTCTACTTTTTGAAATGCAAAG 60.074 38.462 0.00 0.00 46.38 2.77
419 519 6.479990 GGCTTCTACTTTTTGAAATGCAAAGT 59.520 34.615 0.00 0.00 46.38 2.66
421 521 9.030301 GCTTCTACTTTTTGAAATGCAAAGTTA 57.970 29.630 3.23 0.00 46.38 2.24
427 527 8.955388 ACTTTTTGAAATGCAAAGTTAATGGTT 58.045 25.926 0.00 0.00 46.38 3.67
432 532 9.685828 TTGAAATGCAAAGTTAATGGTTAGTAC 57.314 29.630 0.00 0.00 32.46 2.73
433 533 8.851145 TGAAATGCAAAGTTAATGGTTAGTACA 58.149 29.630 0.00 0.00 0.00 2.90
484 593 8.784043 TGTATGAAAAGAAAGAGTAGAAAAGGC 58.216 33.333 0.00 0.00 0.00 4.35
485 594 7.823745 ATGAAAAGAAAGAGTAGAAAAGGCA 57.176 32.000 0.00 0.00 0.00 4.75
486 595 7.264373 TGAAAAGAAAGAGTAGAAAAGGCAG 57.736 36.000 0.00 0.00 0.00 4.85
487 596 7.054124 TGAAAAGAAAGAGTAGAAAAGGCAGA 58.946 34.615 0.00 0.00 0.00 4.26
488 597 7.556275 TGAAAAGAAAGAGTAGAAAAGGCAGAA 59.444 33.333 0.00 0.00 0.00 3.02
489 598 7.881775 AAAGAAAGAGTAGAAAAGGCAGAAA 57.118 32.000 0.00 0.00 0.00 2.52
490 599 7.881775 AAGAAAGAGTAGAAAAGGCAGAAAA 57.118 32.000 0.00 0.00 0.00 2.29
491 600 7.503521 AGAAAGAGTAGAAAAGGCAGAAAAG 57.496 36.000 0.00 0.00 0.00 2.27
492 601 7.057264 AGAAAGAGTAGAAAAGGCAGAAAAGT 58.943 34.615 0.00 0.00 0.00 2.66
493 602 6.625873 AAGAGTAGAAAAGGCAGAAAAGTG 57.374 37.500 0.00 0.00 0.00 3.16
494 603 4.517075 AGAGTAGAAAAGGCAGAAAAGTGC 59.483 41.667 0.00 0.00 43.19 4.40
495 604 4.207165 AGTAGAAAAGGCAGAAAAGTGCA 58.793 39.130 0.00 0.00 45.93 4.57
496 605 4.644685 AGTAGAAAAGGCAGAAAAGTGCAA 59.355 37.500 0.00 0.00 45.93 4.08
561 670 2.959465 AAGAAAACACCAGAGGGAGG 57.041 50.000 0.00 0.00 38.05 4.30
562 671 1.821088 AGAAAACACCAGAGGGAGGT 58.179 50.000 0.00 0.00 40.85 3.85
563 672 2.136026 AGAAAACACCAGAGGGAGGTT 58.864 47.619 0.00 0.00 36.10 3.50
564 673 2.514160 AGAAAACACCAGAGGGAGGTTT 59.486 45.455 0.00 0.00 45.75 3.27
565 674 2.364972 AAACACCAGAGGGAGGTTTG 57.635 50.000 0.00 0.00 40.79 2.93
567 676 1.518367 ACACCAGAGGGAGGTTTGAA 58.482 50.000 0.00 0.00 37.23 2.69
568 677 1.143073 ACACCAGAGGGAGGTTTGAAC 59.857 52.381 0.00 0.00 37.23 3.18
569 678 0.771755 ACCAGAGGGAGGTTTGAACC 59.228 55.000 4.72 4.72 43.01 3.62
590 699 7.661536 AACCTGCAGTTCTACATTAGATAGA 57.338 36.000 13.81 0.00 30.99 1.98
591 700 7.661536 ACCTGCAGTTCTACATTAGATAGAA 57.338 36.000 13.81 0.00 36.52 2.10
664 773 4.961438 AAAGATGGAAAAACATGGCACT 57.039 36.364 0.00 0.00 0.00 4.40
667 776 3.642848 AGATGGAAAAACATGGCACTGTT 59.357 39.130 0.00 8.77 41.01 3.16
674 783 3.719268 AACATGGCACTGTTGATAGGA 57.281 42.857 12.42 0.00 37.93 2.94
676 785 1.935873 CATGGCACTGTTGATAGGACG 59.064 52.381 0.00 0.00 0.00 4.79
697 806 4.434685 GCCTCTTGCAGATCGGAG 57.565 61.111 0.00 0.00 40.77 4.63
698 807 1.886777 GCCTCTTGCAGATCGGAGC 60.887 63.158 0.00 0.00 40.77 4.70
699 808 1.821936 CCTCTTGCAGATCGGAGCT 59.178 57.895 0.00 0.00 0.00 4.09
701 810 1.269517 CCTCTTGCAGATCGGAGCTAC 60.270 57.143 0.00 0.00 0.00 3.58
705 814 0.175760 TGCAGATCGGAGCTACAACC 59.824 55.000 0.00 0.00 0.00 3.77
713 822 0.824759 GGAGCTACAACCGTGATCCT 59.175 55.000 0.00 0.00 0.00 3.24
717 826 1.755380 GCTACAACCGTGATCCTAGGT 59.245 52.381 9.08 0.00 40.50 3.08
720 829 1.975680 ACAACCGTGATCCTAGGTGTT 59.024 47.619 9.08 1.72 38.44 3.32
724 833 1.469251 CCGTGATCCTAGGTGTTGTCG 60.469 57.143 9.08 7.61 0.00 4.35
728 837 3.056749 GTGATCCTAGGTGTTGTCGTCTT 60.057 47.826 9.08 0.00 0.00 3.01
729 838 3.576982 TGATCCTAGGTGTTGTCGTCTTT 59.423 43.478 9.08 0.00 0.00 2.52
730 839 4.768448 TGATCCTAGGTGTTGTCGTCTTTA 59.232 41.667 9.08 0.00 0.00 1.85
731 840 5.244402 TGATCCTAGGTGTTGTCGTCTTTAA 59.756 40.000 9.08 0.00 0.00 1.52
732 841 5.733620 TCCTAGGTGTTGTCGTCTTTAAT 57.266 39.130 9.08 0.00 0.00 1.40
742 851 5.524511 TGTCGTCTTTAATGAATCAACCG 57.475 39.130 0.00 0.00 0.00 4.44
746 855 6.518736 GTCGTCTTTAATGAATCAACCGTTTC 59.481 38.462 0.00 0.00 0.00 2.78
750 859 8.850452 GTCTTTAATGAATCAACCGTTTCAATC 58.150 33.333 0.00 0.00 35.14 2.67
751 860 8.026607 TCTTTAATGAATCAACCGTTTCAATCC 58.973 33.333 0.00 0.00 35.14 3.01
771 880 0.041135 GGAACTCTATCGCCGAGTCG 60.041 60.000 5.29 5.29 40.65 4.18
773 882 1.063764 GAACTCTATCGCCGAGTCGTT 59.936 52.381 12.31 0.00 40.65 3.85
774 883 1.945387 ACTCTATCGCCGAGTCGTTA 58.055 50.000 12.31 0.00 37.13 3.18
775 884 2.283298 ACTCTATCGCCGAGTCGTTAA 58.717 47.619 12.31 0.00 37.13 2.01
838 947 4.462483 GTGTCCAGCAATTATGAAGGGAAA 59.538 41.667 0.00 0.00 0.00 3.13
896 1005 6.312918 TGCAAAACGGTTAATAAAACTTGCAA 59.687 30.769 17.84 0.00 42.45 4.08
922 1031 8.738645 AAAACCATACACATAGAAATCTCTCC 57.261 34.615 0.00 0.00 32.70 3.71
923 1032 7.437713 AACCATACACATAGAAATCTCTCCA 57.562 36.000 0.00 0.00 32.70 3.86
924 1033 7.623999 ACCATACACATAGAAATCTCTCCAT 57.376 36.000 0.00 0.00 32.70 3.41
925 1034 7.448420 ACCATACACATAGAAATCTCTCCATG 58.552 38.462 0.00 0.00 32.70 3.66
926 1035 6.370994 CCATACACATAGAAATCTCTCCATGC 59.629 42.308 0.00 0.00 32.70 4.06
927 1036 4.712476 ACACATAGAAATCTCTCCATGCC 58.288 43.478 0.00 0.00 32.70 4.40
928 1037 3.744942 CACATAGAAATCTCTCCATGCCG 59.255 47.826 0.00 0.00 32.70 5.69
929 1038 2.533266 TAGAAATCTCTCCATGCCGC 57.467 50.000 0.00 0.00 32.70 6.53
930 1039 0.531532 AGAAATCTCTCCATGCCGCG 60.532 55.000 0.00 0.00 0.00 6.46
931 1040 1.502163 GAAATCTCTCCATGCCGCGG 61.502 60.000 24.05 24.05 0.00 6.46
942 1051 2.954020 ATGCCGCGGTCTGATGTACG 62.954 60.000 28.70 0.00 0.00 3.67
953 1062 4.416620 GTCTGATGTACGAGGACAAAGAG 58.583 47.826 4.93 0.00 30.80 2.85
954 1063 4.079970 TCTGATGTACGAGGACAAAGAGT 58.920 43.478 0.00 0.00 31.83 3.24
997 1106 1.203523 CTCAAACTCCTCTGGGTCTCG 59.796 57.143 0.00 0.00 0.00 4.04
1052 1169 4.742201 CTGGCACTGGGTCGTCGG 62.742 72.222 0.00 0.00 0.00 4.79
1105 1222 1.006832 CCTCATCAAAGGTAACGCCG 58.993 55.000 0.00 0.00 43.70 6.46
1107 1224 1.393539 CTCATCAAAGGTAACGCCGTG 59.606 52.381 0.00 0.00 43.70 4.94
1108 1225 1.153353 CATCAAAGGTAACGCCGTGT 58.847 50.000 0.00 0.00 43.70 4.49
1111 1229 1.665599 AAAGGTAACGCCGTGTCCG 60.666 57.895 0.00 0.00 43.70 4.79
1143 1261 2.486966 CGTACCCCGTTCGTCTCC 59.513 66.667 0.00 0.00 0.00 3.71
1149 1272 2.805353 CCGTTCGTCTCCACGCTG 60.805 66.667 0.00 0.00 46.28 5.18
1400 1561 2.284798 CTGCTCGGACAGGTATGCGT 62.285 60.000 0.00 0.00 33.85 5.24
1424 1585 2.319136 TTTGTTACCACGTGCACTCT 57.681 45.000 16.19 0.00 0.00 3.24
1631 1795 2.086610 ACCAGGGAAGTTTGCACAAT 57.913 45.000 0.00 0.00 0.00 2.71
1670 1834 6.667007 CAAATTGGATTTGTATTTCCTGGC 57.333 37.500 5.46 0.00 43.47 4.85
1680 1844 1.972872 ATTTCCTGGCGCTGATTAGG 58.027 50.000 7.64 8.04 0.00 2.69
1723 2767 5.584649 TGCTATAGTTCACCAATGTTGCTAC 59.415 40.000 0.84 0.00 0.00 3.58
1839 3070 8.876181 TGCCAATGGTATTCTAGCTAGTTATAA 58.124 33.333 20.10 7.79 0.00 0.98
1866 3097 4.344104 ACGATGTCCCCAAAGATCAAAAT 58.656 39.130 0.00 0.00 0.00 1.82
1973 3209 9.612066 TCAGATAATTATGCATGTGTTCTAACA 57.388 29.630 10.16 0.00 36.38 2.41
2168 3412 5.091261 TCAGGAAGCTTGGAGAAAGATAC 57.909 43.478 2.10 0.00 38.24 2.24
2173 3417 4.287766 AGCTTGGAGAAAGATACGGTTT 57.712 40.909 0.00 0.00 38.24 3.27
2187 3431 3.547649 ACGGTTTCGCCTTTTATCAAC 57.452 42.857 0.00 0.00 40.63 3.18
2193 3437 6.074195 CGGTTTCGCCTTTTATCAACGATATA 60.074 38.462 0.00 0.00 34.25 0.86
2222 3466 6.240145 AGTTTATATGTACCAAAACACCGGT 58.760 36.000 0.00 0.00 39.41 5.28
2280 3524 8.989653 AAAACAGTTATTCTCAAAACCGAAAA 57.010 26.923 0.00 0.00 0.00 2.29
2281 3525 9.594478 AAAACAGTTATTCTCAAAACCGAAAAT 57.406 25.926 0.00 0.00 0.00 1.82
2283 3527 9.893305 AACAGTTATTCTCAAAACCGAAAATAG 57.107 29.630 0.00 0.00 0.00 1.73
2301 3549 7.063544 CGAAAATAGAAAAGGACTCGATTCACT 59.936 37.037 5.06 0.00 0.00 3.41
2318 3566 8.197439 TCGATTCACTTATGATTAAGCTTCTCA 58.803 33.333 0.00 8.24 38.74 3.27
2405 3653 0.188342 AGGGTGGCAAGAACAATGGT 59.812 50.000 0.00 0.00 0.00 3.55
2460 3711 6.593382 GGATCATGTAAATACAGAGAGGCATC 59.407 42.308 0.00 0.00 39.92 3.91
2480 3731 2.034179 TCGGTGCCATACAGATAGTTCG 59.966 50.000 0.00 0.00 0.00 3.95
2623 3952 9.356433 GAGTCCAAGTAAAGATAGTAGAAACAC 57.644 37.037 0.00 0.00 0.00 3.32
2643 3972 1.409064 CGTCCATTACAGCTGAGCCTA 59.591 52.381 23.35 0.00 0.00 3.93
2665 3994 3.385469 AGCTAGCTGCAGTGCTGA 58.615 55.556 24.47 4.81 45.94 4.26
2681 4010 3.002791 TGCTGATTTGCTCCGAAGTAAG 58.997 45.455 0.00 0.00 0.00 2.34
2682 4011 2.352960 GCTGATTTGCTCCGAAGTAAGG 59.647 50.000 0.00 0.00 0.00 2.69
2685 4014 3.196901 TGATTTGCTCCGAAGTAAGGCTA 59.803 43.478 0.00 0.00 0.00 3.93
2735 4064 5.313712 GAGACTACCATGTCCCAAGAAAAA 58.686 41.667 0.00 0.00 37.66 1.94
3058 4390 1.453524 CGAGACAGCAGTTCAAGTTCG 59.546 52.381 0.00 0.00 0.00 3.95
3075 4407 2.822399 GGGATGAGGGTAGTGCCG 59.178 66.667 0.00 0.00 38.44 5.69
3131 4463 2.294233 TGAACTGAATCTGCAAACTGCC 59.706 45.455 0.00 0.00 44.23 4.85
3377 4868 2.221906 CTCCTTGCTGCAATGTGCCC 62.222 60.000 16.38 0.00 44.23 5.36
3605 5096 6.980397 CCGAAGCATATCAAAAGGCTAAAAAT 59.020 34.615 0.00 0.00 35.11 1.82
3666 5157 2.837498 GCACAAAGCAATTCCCAAAGT 58.163 42.857 0.00 0.00 44.79 2.66
3845 5339 6.488006 AGAGAACAAATGATACAAGTGTTGCT 59.512 34.615 0.00 0.00 32.75 3.91
3856 5350 0.109342 AGTGTTGCTTGTCCTGAGGG 59.891 55.000 0.00 0.00 0.00 4.30
4023 5517 6.483640 GGATCAGTTGAATGGGTGTAATACTC 59.516 42.308 0.00 0.00 0.00 2.59
4142 5636 1.552337 AGTGATGCTTGTCGTGAGGAT 59.448 47.619 0.00 0.00 0.00 3.24
4271 5765 2.555757 GTCTGTGGAAAATGCAGAAGCT 59.444 45.455 0.00 0.00 40.40 3.74
4287 5781 6.371885 GCAGAAGCTCATGAAGATGGTAACA 61.372 44.000 0.00 0.00 45.81 2.41
4288 5782 7.788585 GCAGAAGCTCATGAAGATGGTAACAA 61.789 42.308 0.00 0.00 45.12 2.83
4334 5828 6.047870 ACATTCATCTCAGAACAGATGTAGC 58.952 40.000 9.67 0.00 46.91 3.58
4364 5858 4.005650 TCAATCAGAATGTTGAGGCTGAC 58.994 43.478 0.00 0.00 39.88 3.51
4439 5933 5.582665 AGAAGCTACGTCTTCAAATGATTCC 59.417 40.000 16.64 0.00 43.64 3.01
4480 5974 0.948623 TGGCGAAACATGAGACACCG 60.949 55.000 0.00 0.00 0.00 4.94
4508 6002 5.979517 AGCAAAATTTCAAGAAAAGGAGACG 59.020 36.000 0.00 0.00 33.56 4.18
4518 6012 5.838531 AGAAAAGGAGACGGTAGTATCAG 57.161 43.478 0.00 0.00 40.17 2.90
4574 6068 1.475280 CACATGCCTTCACCATCAAGG 59.525 52.381 0.00 0.00 43.13 3.61
4621 6115 5.467705 CAAGCGTTAGTAAGTGTTAGGACT 58.532 41.667 0.00 0.00 0.00 3.85
4623 6117 4.082354 AGCGTTAGTAAGTGTTAGGACTGG 60.082 45.833 0.00 0.00 0.00 4.00
4638 6132 2.749621 GGACTGGGCTTCATAAACACTG 59.250 50.000 0.00 0.00 0.00 3.66
4639 6133 3.559171 GGACTGGGCTTCATAAACACTGA 60.559 47.826 0.00 0.00 0.00 3.41
4833 6369 8.079211 AGTTCTTAGTTCAGCACCATAGATAA 57.921 34.615 0.00 0.00 0.00 1.75
4883 6428 7.544566 TGATCGAAACTTTAGGAGATGTTGTAC 59.455 37.037 0.00 0.00 0.00 2.90
5013 6562 6.366332 CAGAATGAAGTTACATACGGGATAGC 59.634 42.308 0.00 0.00 39.69 2.97
5073 6622 2.159517 GCTGGCATATATTAAGGCACGC 60.160 50.000 0.00 0.00 33.99 5.34
5093 6642 7.383361 GCACGCTATTATTTTAAAGCAGTTTG 58.617 34.615 0.00 0.00 34.60 2.93
5126 6675 0.175760 TGGGCATTACTCTCGTCTGC 59.824 55.000 0.00 0.00 33.51 4.26
5159 6708 6.260714 TGCCTGCATTAACATAATCTGTACAG 59.739 38.462 17.17 17.17 36.98 2.74
5174 6723 6.392625 TCTGTACAGATAGAATGGTAGTGC 57.607 41.667 21.74 0.00 31.41 4.40
5241 6790 8.030106 AGTAGTAATGTTTCTTAGCACAGAGTC 58.970 37.037 0.00 0.00 0.00 3.36
5516 7071 6.876789 CCTTGTTACCAATGTGTATGTACTCA 59.123 38.462 0.00 0.00 34.67 3.41
5519 7074 6.315144 TGTTACCAATGTGTATGTACTCATGC 59.685 38.462 8.09 0.00 39.50 4.06
5868 7432 1.142262 TGGATATCACCTCGTCCTCGA 59.858 52.381 4.83 0.00 44.12 4.04
5925 7489 3.772853 GAGGTGTGTGGTGCAGCCA 62.773 63.158 14.36 8.70 46.95 4.75
5937 7501 1.905354 GCAGCCACCCAAGAAAGCT 60.905 57.895 0.00 0.00 0.00 3.74
5938 7502 1.962144 CAGCCACCCAAGAAAGCTG 59.038 57.895 0.00 0.00 44.31 4.24
5960 7524 2.048222 CGCGTCTGGTGGTGACAT 60.048 61.111 0.00 0.00 46.14 3.06
6022 7586 2.563798 CGCACCAAGTGGCCACAAT 61.564 57.895 36.39 22.51 39.32 2.71
6138 7705 0.924777 CGTGTACGTTGTTGCACAGA 59.075 50.000 0.00 0.00 34.11 3.41
6148 7715 0.801251 GTTGCACAGACCAGATGAGC 59.199 55.000 0.00 0.00 35.20 4.26
6156 7723 1.062275 AGACCAGATGAGCAGGAGGAT 60.062 52.381 0.00 0.00 0.00 3.24
6274 7841 0.322906 CTCCTGTTCCCTGGCTTTCC 60.323 60.000 0.00 0.00 0.00 3.13
6332 7899 6.183360 GCAAAATAAGTGTATCTGCAGGCTAA 60.183 38.462 15.13 0.00 0.00 3.09
6424 9870 3.056107 TCAAATACACCGAGGAAGTCTGG 60.056 47.826 0.00 0.00 0.00 3.86
6461 9907 8.902540 AAACTCATGTACTTGTATTCTGTTGA 57.097 30.769 8.46 0.00 0.00 3.18
6469 9915 8.492748 TGTACTTGTATTCTGTTGATTCGTTTC 58.507 33.333 0.00 0.00 0.00 2.78
6483 9929 4.742438 TTCGTTTCTTCAATGTAGCACC 57.258 40.909 0.00 0.00 0.00 5.01
6630 10159 6.070078 ACGGGGTAGTTTAGAACATTTGGATA 60.070 38.462 0.00 0.00 0.00 2.59
6709 10240 5.070001 TGCTCTAAATGTTGCTTAACCTGT 58.930 37.500 0.00 0.00 0.00 4.00
6710 10241 5.534654 TGCTCTAAATGTTGCTTAACCTGTT 59.465 36.000 0.00 0.00 0.00 3.16
6711 10242 6.086871 GCTCTAAATGTTGCTTAACCTGTTC 58.913 40.000 0.00 0.00 0.00 3.18
6712 10243 6.072452 GCTCTAAATGTTGCTTAACCTGTTCT 60.072 38.462 0.00 0.00 0.00 3.01
6713 10244 7.522236 GCTCTAAATGTTGCTTAACCTGTTCTT 60.522 37.037 0.00 0.00 0.00 2.52
6714 10245 7.871853 TCTAAATGTTGCTTAACCTGTTCTTC 58.128 34.615 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 151 0.655733 AGTTCAACCAGCGACAAACG 59.344 50.000 0.00 0.00 45.66 3.60
149 154 1.400142 CACAAGTTCAACCAGCGACAA 59.600 47.619 0.00 0.00 0.00 3.18
288 297 8.587608 TGAATTTCCAGCAAATAGAACAAATCT 58.412 29.630 0.00 0.00 42.48 2.40
308 327 4.929819 AACTTTAACTGCCGGTGAATTT 57.070 36.364 1.90 0.00 0.00 1.82
310 329 5.007682 ACATAACTTTAACTGCCGGTGAAT 58.992 37.500 1.90 0.00 0.00 2.57
313 332 3.749088 TCACATAACTTTAACTGCCGGTG 59.251 43.478 1.90 0.00 0.00 4.94
315 334 4.671766 GCTTCACATAACTTTAACTGCCGG 60.672 45.833 0.00 0.00 0.00 6.13
316 335 4.154195 AGCTTCACATAACTTTAACTGCCG 59.846 41.667 0.00 0.00 0.00 5.69
317 336 5.181245 TGAGCTTCACATAACTTTAACTGCC 59.819 40.000 0.00 0.00 0.00 4.85
318 337 6.241207 TGAGCTTCACATAACTTTAACTGC 57.759 37.500 0.00 0.00 0.00 4.40
319 338 9.683069 AATTTGAGCTTCACATAACTTTAACTG 57.317 29.630 0.00 0.00 0.00 3.16
320 339 9.683069 CAATTTGAGCTTCACATAACTTTAACT 57.317 29.630 0.00 0.00 0.00 2.24
321 340 9.463443 ACAATTTGAGCTTCACATAACTTTAAC 57.537 29.630 2.79 0.00 0.00 2.01
324 343 9.066892 TCTACAATTTGAGCTTCACATAACTTT 57.933 29.630 2.79 0.00 0.00 2.66
325 344 8.621532 TCTACAATTTGAGCTTCACATAACTT 57.378 30.769 2.79 0.00 0.00 2.66
326 345 8.798859 ATCTACAATTTGAGCTTCACATAACT 57.201 30.769 2.79 0.00 0.00 2.24
327 346 9.846248 AAATCTACAATTTGAGCTTCACATAAC 57.154 29.630 2.79 0.00 0.00 1.89
328 347 9.844790 CAAATCTACAATTTGAGCTTCACATAA 57.155 29.630 2.79 0.00 40.42 1.90
329 348 8.461222 CCAAATCTACAATTTGAGCTTCACATA 58.539 33.333 11.12 0.00 40.42 2.29
330 349 7.318141 CCAAATCTACAATTTGAGCTTCACAT 58.682 34.615 11.12 0.00 40.42 3.21
331 350 6.294675 CCCAAATCTACAATTTGAGCTTCACA 60.295 38.462 11.12 0.00 40.42 3.58
332 351 6.095377 CCCAAATCTACAATTTGAGCTTCAC 58.905 40.000 11.12 0.00 40.42 3.18
333 352 5.336690 GCCCAAATCTACAATTTGAGCTTCA 60.337 40.000 11.12 0.00 38.92 3.02
334 353 5.105063 GCCCAAATCTACAATTTGAGCTTC 58.895 41.667 11.12 0.00 38.92 3.86
364 383 9.722056 CATTAACTTTGTGCTTATCAACTATCC 57.278 33.333 0.00 0.00 0.00 2.59
375 394 2.037121 GCCCCACATTAACTTTGTGCTT 59.963 45.455 2.70 0.00 42.47 3.91
378 478 3.573967 AGAAGCCCCACATTAACTTTGTG 59.426 43.478 1.41 1.41 43.25 3.33
400 500 9.606631 ACCATTAACTTTGCATTTCAAAAAGTA 57.393 25.926 0.00 0.00 43.44 2.24
404 504 9.606631 ACTAACCATTAACTTTGCATTTCAAAA 57.393 25.926 0.00 0.00 43.44 2.44
407 507 8.851145 TGTACTAACCATTAACTTTGCATTTCA 58.149 29.630 0.00 0.00 0.00 2.69
408 508 9.685828 TTGTACTAACCATTAACTTTGCATTTC 57.314 29.630 0.00 0.00 0.00 2.17
410 510 9.691362 CTTTGTACTAACCATTAACTTTGCATT 57.309 29.630 0.00 0.00 0.00 3.56
474 583 4.568152 TGCACTTTTCTGCCTTTTCTAC 57.432 40.909 0.00 0.00 36.21 2.59
477 586 5.544136 TTTTTGCACTTTTCTGCCTTTTC 57.456 34.783 0.00 0.00 36.21 2.29
539 648 3.149981 CTCCCTCTGGTGTTTTCTTTCC 58.850 50.000 0.00 0.00 0.00 3.13
542 651 2.136026 ACCTCCCTCTGGTGTTTTCTT 58.864 47.619 0.00 0.00 36.30 2.52
551 660 3.652581 GGTTCAAACCTCCCTCTGG 57.347 57.895 4.63 0.00 45.75 3.86
567 676 7.661536 TTCTATCTAATGTAGAACTGCAGGT 57.338 36.000 19.93 12.79 38.50 4.00
602 711 9.959721 AGCCTAATGTTGTTTCTAATAGAAGAA 57.040 29.630 2.74 0.00 35.37 2.52
603 712 9.959721 AAGCCTAATGTTGTTTCTAATAGAAGA 57.040 29.630 2.74 0.00 35.37 2.87
639 748 7.226325 CAGTGCCATGTTTTTCCATCTTTTTAA 59.774 33.333 0.00 0.00 0.00 1.52
640 749 6.705381 CAGTGCCATGTTTTTCCATCTTTTTA 59.295 34.615 0.00 0.00 0.00 1.52
641 750 5.528320 CAGTGCCATGTTTTTCCATCTTTTT 59.472 36.000 0.00 0.00 0.00 1.94
642 751 5.058490 CAGTGCCATGTTTTTCCATCTTTT 58.942 37.500 0.00 0.00 0.00 2.27
643 752 4.101430 ACAGTGCCATGTTTTTCCATCTTT 59.899 37.500 0.00 0.00 0.00 2.52
644 753 3.642848 ACAGTGCCATGTTTTTCCATCTT 59.357 39.130 0.00 0.00 0.00 2.40
645 754 3.233507 ACAGTGCCATGTTTTTCCATCT 58.766 40.909 0.00 0.00 0.00 2.90
646 755 3.665745 ACAGTGCCATGTTTTTCCATC 57.334 42.857 0.00 0.00 0.00 3.51
647 756 3.387374 TCAACAGTGCCATGTTTTTCCAT 59.613 39.130 1.14 0.00 41.41 3.41
648 757 2.762887 TCAACAGTGCCATGTTTTTCCA 59.237 40.909 1.14 0.00 41.41 3.53
649 758 3.451141 TCAACAGTGCCATGTTTTTCC 57.549 42.857 1.14 0.00 41.41 3.13
650 759 5.048083 TCCTATCAACAGTGCCATGTTTTTC 60.048 40.000 1.14 0.00 41.41 2.29
651 760 4.832266 TCCTATCAACAGTGCCATGTTTTT 59.168 37.500 1.14 0.00 41.41 1.94
658 767 0.391130 GCGTCCTATCAACAGTGCCA 60.391 55.000 0.00 0.00 0.00 4.92
659 768 0.391130 TGCGTCCTATCAACAGTGCC 60.391 55.000 0.00 0.00 0.00 5.01
660 769 1.328680 CATGCGTCCTATCAACAGTGC 59.671 52.381 0.00 0.00 0.00 4.40
664 773 0.541392 AGGCATGCGTCCTATCAACA 59.459 50.000 12.44 0.00 30.79 3.33
667 776 1.123077 AAGAGGCATGCGTCCTATCA 58.877 50.000 31.05 0.00 33.24 2.15
694 803 0.824759 AGGATCACGGTTGTAGCTCC 59.175 55.000 0.00 0.00 0.00 4.70
695 804 2.034812 CCTAGGATCACGGTTGTAGCTC 59.965 54.545 1.05 0.00 0.00 4.09
696 805 2.032620 CCTAGGATCACGGTTGTAGCT 58.967 52.381 1.05 0.00 0.00 3.32
697 806 1.755380 ACCTAGGATCACGGTTGTAGC 59.245 52.381 17.98 0.00 0.00 3.58
698 807 2.758979 ACACCTAGGATCACGGTTGTAG 59.241 50.000 17.98 0.00 0.00 2.74
699 808 2.811410 ACACCTAGGATCACGGTTGTA 58.189 47.619 17.98 0.00 0.00 2.41
701 810 2.289444 ACAACACCTAGGATCACGGTTG 60.289 50.000 17.98 18.94 39.82 3.77
705 814 1.201647 ACGACAACACCTAGGATCACG 59.798 52.381 17.98 14.63 0.00 4.35
713 822 7.156000 TGATTCATTAAAGACGACAACACCTA 58.844 34.615 0.00 0.00 0.00 3.08
717 826 6.565060 CGGTTGATTCATTAAAGACGACAACA 60.565 38.462 17.28 0.00 37.43 3.33
720 829 4.992319 ACGGTTGATTCATTAAAGACGACA 59.008 37.500 0.00 0.00 0.00 4.35
724 833 8.742554 ATTGAAACGGTTGATTCATTAAAGAC 57.257 30.769 0.00 0.00 36.85 3.01
728 837 6.318628 CGGATTGAAACGGTTGATTCATTAA 58.681 36.000 0.00 0.00 36.85 1.40
729 838 5.163703 CCGGATTGAAACGGTTGATTCATTA 60.164 40.000 0.00 0.00 44.85 1.90
730 839 4.380444 CCGGATTGAAACGGTTGATTCATT 60.380 41.667 0.00 0.00 44.85 2.57
731 840 3.128589 CCGGATTGAAACGGTTGATTCAT 59.871 43.478 0.00 0.00 44.85 2.57
732 841 2.486203 CCGGATTGAAACGGTTGATTCA 59.514 45.455 0.00 0.00 44.85 2.57
742 851 3.245519 GCGATAGAGTTCCGGATTGAAAC 59.754 47.826 4.15 0.00 39.76 2.78
746 855 1.784525 GGCGATAGAGTTCCGGATTG 58.215 55.000 4.15 0.00 39.76 2.67
750 859 1.283181 CTCGGCGATAGAGTTCCGG 59.717 63.158 11.27 0.00 41.98 5.14
751 860 2.023318 ACTCGGCGATAGAGTTCCG 58.977 57.895 11.27 0.00 45.74 4.30
792 901 9.295825 ACACATGATGTCCTTTTTGTATCTTTA 57.704 29.630 0.00 0.00 36.54 1.85
793 902 8.181904 ACACATGATGTCCTTTTTGTATCTTT 57.818 30.769 0.00 0.00 36.54 2.52
819 928 5.404466 TGTTTTCCCTTCATAATTGCTGG 57.596 39.130 0.00 0.00 0.00 4.85
896 1005 9.178758 GGAGAGATTTCTATGTGTATGGTTTTT 57.821 33.333 0.00 0.00 32.53 1.94
912 1021 1.502163 CCGCGGCATGGAGAGATTTC 61.502 60.000 14.67 0.00 0.00 2.17
913 1022 1.524621 CCGCGGCATGGAGAGATTT 60.525 57.895 14.67 0.00 0.00 2.17
915 1024 3.157217 GACCGCGGCATGGAGAGAT 62.157 63.158 28.58 0.00 0.00 2.75
917 1026 3.842923 AGACCGCGGCATGGAGAG 61.843 66.667 28.58 0.00 0.00 3.20
918 1027 4.147449 CAGACCGCGGCATGGAGA 62.147 66.667 28.58 0.00 0.00 3.71
919 1028 3.451556 ATCAGACCGCGGCATGGAG 62.452 63.158 28.58 9.76 0.00 3.86
920 1029 3.469970 ATCAGACCGCGGCATGGA 61.470 61.111 28.58 18.37 0.00 3.41
921 1030 2.642996 TACATCAGACCGCGGCATGG 62.643 60.000 28.58 13.00 0.00 3.66
922 1031 1.227234 TACATCAGACCGCGGCATG 60.227 57.895 28.58 24.12 0.00 4.06
923 1032 1.227263 GTACATCAGACCGCGGCAT 60.227 57.895 28.58 11.77 0.00 4.40
924 1033 2.183300 GTACATCAGACCGCGGCA 59.817 61.111 28.58 7.17 0.00 5.69
925 1034 2.954868 CGTACATCAGACCGCGGC 60.955 66.667 28.58 18.62 0.00 6.53
926 1035 1.298413 CTCGTACATCAGACCGCGG 60.298 63.158 26.86 26.86 0.00 6.46
927 1036 1.298413 CCTCGTACATCAGACCGCG 60.298 63.158 0.00 0.00 0.00 6.46
928 1037 0.248539 GTCCTCGTACATCAGACCGC 60.249 60.000 0.00 0.00 0.00 5.68
929 1038 1.092348 TGTCCTCGTACATCAGACCG 58.908 55.000 0.00 0.00 0.00 4.79
930 1039 3.192844 TCTTTGTCCTCGTACATCAGACC 59.807 47.826 0.00 0.00 0.00 3.85
931 1040 4.082679 ACTCTTTGTCCTCGTACATCAGAC 60.083 45.833 0.00 0.00 0.00 3.51
942 1051 5.523369 CAAAATGTTCCACTCTTTGTCCTC 58.477 41.667 0.00 0.00 0.00 3.71
953 1062 3.242706 GGCAAAACTGCAAAATGTTCCAC 60.243 43.478 0.00 0.00 36.33 4.02
954 1063 2.941720 GGCAAAACTGCAAAATGTTCCA 59.058 40.909 0.00 0.00 36.33 3.53
1105 1222 1.134670 CAAGGGATCCTCTTCGGACAC 60.135 57.143 12.58 0.00 46.80 3.67
1107 1224 0.179070 GCAAGGGATCCTCTTCGGAC 60.179 60.000 12.58 0.00 46.80 4.79
1108 1225 4.928056 TACGCAAGGGATCCTCTTCGGA 62.928 54.545 12.58 12.04 45.53 4.55
1111 1229 1.202545 GGTACGCAAGGGATCCTCTTC 60.203 57.143 12.58 6.94 46.39 2.87
1143 1261 1.073216 GTGAGATGACCGACAGCGTG 61.073 60.000 0.00 0.00 40.13 5.34
1149 1272 1.033574 CCCTAGGTGAGATGACCGAC 58.966 60.000 8.29 0.00 41.35 4.79
1424 1585 3.879295 CTGAAGCTCTGAACAACCAGAAA 59.121 43.478 0.00 0.00 42.05 2.52
1481 1645 0.386476 TCAAACGCTCCACTACACGT 59.614 50.000 0.00 0.00 41.16 4.49
1482 1646 1.455786 CTTCAAACGCTCCACTACACG 59.544 52.381 0.00 0.00 0.00 4.49
1649 1813 4.680440 GCGCCAGGAAATACAAATCCAATT 60.680 41.667 0.00 0.00 38.23 2.32
1670 1834 3.455619 GTGAACAACACCTAATCAGCG 57.544 47.619 0.00 0.00 43.05 5.18
1723 2767 8.249327 AGCTCAAATAATAACATCATCTAGCG 57.751 34.615 0.00 0.00 0.00 4.26
1785 2830 3.310774 CAGGACTTGAGACATAATTGCCG 59.689 47.826 0.00 0.00 0.00 5.69
1839 3070 4.019681 TGATCTTTGGGGACATCGTAAACT 60.020 41.667 0.00 0.00 42.32 2.66
1906 3141 2.434843 CGCCACATCCCTGCTCCTA 61.435 63.158 0.00 0.00 0.00 2.94
2066 3310 6.049955 TCTAGGCATTAACTAAACTGCAGT 57.950 37.500 15.25 15.25 36.34 4.40
2081 3325 6.127535 CCTCAAAAACATCAACATCTAGGCAT 60.128 38.462 0.00 0.00 0.00 4.40
2168 3412 2.158058 TCGTTGATAAAAGGCGAAACCG 59.842 45.455 0.00 0.00 46.52 4.44
2173 3417 7.773864 TTTGTATATCGTTGATAAAAGGCGA 57.226 32.000 0.00 0.00 36.02 5.54
2193 3437 9.752961 GGTGTTTTGGTACATATAAACTTTTGT 57.247 29.630 0.00 0.00 39.30 2.83
2222 3466 8.032451 CCAACTCAAAAGAAGTTTCTGGTAAAA 58.968 33.333 0.00 0.00 37.65 1.52
2280 3524 8.696374 TCATAAGTGAATCGAGTCCTTTTCTAT 58.304 33.333 17.46 6.60 0.00 1.98
2281 3525 8.063200 TCATAAGTGAATCGAGTCCTTTTCTA 57.937 34.615 17.46 4.97 0.00 2.10
2282 3526 6.936279 TCATAAGTGAATCGAGTCCTTTTCT 58.064 36.000 17.46 4.55 0.00 2.52
2283 3527 7.778470 ATCATAAGTGAATCGAGTCCTTTTC 57.222 36.000 17.46 4.91 38.01 2.29
2318 3566 7.164122 TCACTTCTCTAAGCTGAACATCAAAT 58.836 34.615 0.00 0.00 36.05 2.32
2322 3570 5.350091 GGTTCACTTCTCTAAGCTGAACATC 59.650 44.000 21.31 10.98 44.62 3.06
2405 3653 2.813754 GCTGCAGAACAACTGGTCATTA 59.186 45.455 20.43 0.00 45.82 1.90
2416 3664 1.676635 GGGCTGATGCTGCAGAACA 60.677 57.895 20.43 12.42 38.14 3.18
2460 3711 2.394708 CGAACTATCTGTATGGCACCG 58.605 52.381 0.00 0.00 0.00 4.94
2480 3731 2.699954 TCCTTCTGTCGCTGAAAATCC 58.300 47.619 2.14 0.00 0.00 3.01
2623 3952 0.176680 AGGCTCAGCTGTAATGGACG 59.823 55.000 14.67 0.00 0.00 4.79
2665 3994 2.789409 AGCCTTACTTCGGAGCAAAT 57.211 45.000 0.00 0.00 0.00 2.32
2681 4010 4.700213 TCCTGCTTTGACATAAGTTTAGCC 59.300 41.667 0.00 0.00 0.00 3.93
2682 4011 5.880054 TCCTGCTTTGACATAAGTTTAGC 57.120 39.130 0.00 0.00 0.00 3.09
2685 4014 4.379813 CGCATCCTGCTTTGACATAAGTTT 60.380 41.667 0.00 0.00 42.25 2.66
2735 4064 3.152341 CTGAAGAATGGCAGTTGGACTT 58.848 45.455 0.00 0.00 0.00 3.01
2745 4074 1.601430 GGATTCTCGCTGAAGAATGGC 59.399 52.381 9.69 0.00 44.16 4.40
3058 4390 2.808206 CCGGCACTACCCTCATCCC 61.808 68.421 0.00 0.00 33.26 3.85
3075 4407 1.821136 CTTTTCCACTGGCTGAATCCC 59.179 52.381 0.00 0.00 0.00 3.85
3244 4576 1.883275 CCTCGAGATGAGCCTTATCGT 59.117 52.381 15.71 0.00 43.82 3.73
3377 4868 5.047377 GGCATCTTTATCCTGACTAGAGGAG 60.047 48.000 6.36 0.00 45.60 3.69
3605 5096 5.372343 TCTTCCTAGCTTCCAAATATGCA 57.628 39.130 0.00 0.00 0.00 3.96
3636 5127 1.774110 TGCTTTGTGCCAAGGAAAGA 58.226 45.000 0.00 0.00 42.00 2.52
3666 5157 8.684386 TGTTTTCCAGTAGATTGTTCATGTAA 57.316 30.769 0.00 0.00 0.00 2.41
3856 5350 6.038271 GGATGTATTACACCCATTCAACTGAC 59.962 42.308 2.01 0.00 0.00 3.51
4023 5517 5.011635 ACTTATTGTTACCTTGCCTTTTGGG 59.988 40.000 0.00 0.00 40.82 4.12
4142 5636 4.623932 AGATGCCTTTTCAGTGACTACA 57.376 40.909 0.00 0.00 0.00 2.74
4271 5765 7.757941 TGAATTGTTGTTACCATCTTCATGA 57.242 32.000 0.00 0.00 30.57 3.07
4334 5828 4.520111 TCAACATTCTGATTGACAACAGGG 59.480 41.667 14.02 9.05 35.20 4.45
4364 5858 8.344831 TGAGAATTTGTAAGACTGACATGTTTG 58.655 33.333 0.00 0.00 0.00 2.93
4439 5933 3.414700 GGTGACGACTGCTTGCCG 61.415 66.667 0.00 0.00 0.00 5.69
4480 5974 6.784176 TCCTTTTCTTGAAATTTTGCTTTGC 58.216 32.000 0.00 0.00 0.00 3.68
4518 6012 7.977904 CATCCCAATGCCTTTTTAGAATTTTC 58.022 34.615 0.00 0.00 0.00 2.29
4574 6068 4.213482 GGTGGATATGCATACTTCCGTTTC 59.787 45.833 17.61 6.53 0.00 2.78
4621 6115 5.047377 GGAAAATCAGTGTTTATGAAGCCCA 60.047 40.000 0.00 0.00 0.00 5.36
4623 6117 6.071952 TCAGGAAAATCAGTGTTTATGAAGCC 60.072 38.462 0.00 0.00 0.00 4.35
4697 6200 9.520204 CACAAGTCTAAAAAGATGTTCAATGTT 57.480 29.630 0.00 0.00 0.00 2.71
4796 6332 8.756864 GCTGAACTAAGAACTTCGAATAATAGG 58.243 37.037 0.00 0.00 0.00 2.57
4854 6390 5.980116 ACATCTCCTAAAGTTTCGATCATCG 59.020 40.000 0.00 0.00 42.10 3.84
4883 6428 2.167487 GAGTTGCCACTTCCTCTAGAGG 59.833 54.545 30.15 30.15 41.00 3.69
5013 6562 6.436261 TCAGTTAACTACAGTCTTCACTTCG 58.564 40.000 8.04 0.00 0.00 3.79
5073 6622 8.755696 TGTGCCAAACTGCTTTAAAATAATAG 57.244 30.769 0.00 0.00 0.00 1.73
5093 6642 2.730094 CCCAGTTGTGCTTGTGCC 59.270 61.111 0.00 0.00 38.71 5.01
5126 6675 2.419673 TGTTAATGCAGGCATTGTCTCG 59.580 45.455 25.35 0.00 45.15 4.04
5131 6680 6.509656 ACAGATTATGTTAATGCAGGCATTG 58.490 36.000 25.35 10.73 41.23 2.82
5198 6747 9.976511 CATTACTACTCTAAATGAAATACGGGA 57.023 33.333 0.00 0.00 33.38 5.14
5219 6768 6.166982 AGGACTCTGTGCTAAGAAACATTAC 58.833 40.000 0.00 0.00 31.10 1.89
5519 7074 4.960938 TGATGTTAGTATGCTAGCAAGGG 58.039 43.478 23.54 0.00 40.80 3.95
5756 7319 5.567025 GCTCGAGGAGGTAATAATGGGTTAG 60.567 48.000 15.58 0.00 0.00 2.34
5868 7432 1.537397 TTCACTCCTGCTGCTCCCT 60.537 57.895 0.00 0.00 0.00 4.20
5925 7489 0.537371 CGTTCCCAGCTTTCTTGGGT 60.537 55.000 9.94 0.00 43.21 4.51
5937 7501 4.308458 CCACCAGACGCGTTCCCA 62.308 66.667 15.53 0.00 0.00 4.37
5938 7502 4.309950 ACCACCAGACGCGTTCCC 62.310 66.667 15.53 0.00 0.00 3.97
6138 7705 1.129917 CATCCTCCTGCTCATCTGGT 58.870 55.000 0.00 0.00 35.49 4.00
6148 7715 1.890979 GCGCCATGACATCCTCCTG 60.891 63.158 0.00 0.00 0.00 3.86
6212 7779 2.025727 CATAGTCGTCGTCGCCCC 59.974 66.667 0.00 0.00 36.96 5.80
6274 7841 3.244561 TGCAGGGAGTTTTTCTGGTAGAG 60.245 47.826 0.00 0.00 0.00 2.43
6348 7915 2.397549 GCACTTTTAACAGGCTTGCAG 58.602 47.619 0.00 0.00 0.00 4.41
6433 9879 9.507329 AACAGAATACAAGTACATGAGTTTCAT 57.493 29.630 4.87 0.00 37.65 2.57
6461 9907 4.142902 CGGTGCTACATTGAAGAAACGAAT 60.143 41.667 0.00 0.00 0.00 3.34
6469 9915 0.251916 TCCCCGGTGCTACATTGAAG 59.748 55.000 0.00 0.00 0.00 3.02
6630 10159 8.689972 CCAGAAATGAATAGCCTTTGTAAGAAT 58.310 33.333 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.