Multiple sequence alignment - TraesCS3B01G036000

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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 TraesCS3B01G036000 chr3B 100.000 3274 0 0 1 3274 17623845 17627118 0.000000e+00 6047
1 TraesCS3B01G036000 chr3B 90.706 269 23 2 448 715 779370547 779370280 1.120000e-94 357
2 TraesCS3B01G036000 chr3B 79.762 252 44 7 196 444 17638324 17638571 3.360000e-40 176
3 TraesCS3B01G036000 chr3D 86.071 1321 110 32 1976 3274 12282761 12284029 0.000000e+00 1352
4 TraesCS3B01G036000 chr3D 79.434 1201 92 65 733 1868 12281432 12282542 0.000000e+00 706
5 TraesCS3B01G036000 chr3D 84.496 258 28 10 196 450 12281138 12281386 9.070000e-61 244
6 TraesCS3B01G036000 chr3A 84.038 1159 86 41 704 1808 24878563 24877450 0.000000e+00 1024
7 TraesCS3B01G036000 chr3A 83.418 784 83 25 2502 3274 24876079 24875332 0.000000e+00 684
8 TraesCS3B01G036000 chr3A 92.955 440 26 3 11 450 24878993 24878559 1.280000e-178 636
9 TraesCS3B01G036000 chr3A 89.906 426 21 6 1809 2230 24877420 24877013 2.240000e-146 529
10 TraesCS3B01G036000 chr3A 90.559 286 23 3 2227 2508 24876705 24876420 3.080000e-100 375
11 TraesCS3B01G036000 chr5B 95.455 264 11 1 446 708 212800083 212799820 1.400000e-113 420
12 TraesCS3B01G036000 chr1B 93.130 262 11 6 447 707 633046157 633045902 8.580000e-101 377
13 TraesCS3B01G036000 chr6D 91.603 262 21 1 447 707 24007396 24007135 8.640000e-96 361
14 TraesCS3B01G036000 chr4A 90.775 271 23 2 448 717 31579529 31579798 8.640000e-96 361
15 TraesCS3B01G036000 chr4A 90.217 276 25 2 446 719 46310456 46310181 3.110000e-95 359
16 TraesCS3B01G036000 chr6B 91.011 267 23 1 446 711 563531940 563531674 3.110000e-95 359
17 TraesCS3B01G036000 chr1D 91.288 264 21 2 446 707 258094108 258094371 3.110000e-95 359
18 TraesCS3B01G036000 chr4D 89.568 278 25 3 448 724 47750707 47750981 1.870000e-92 350


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 TraesCS3B01G036000 chr3B 17623845 17627118 3273 False 6047.000000 6047 100.000000 1 3274 1 chr3B.!!$F1 3273
1 TraesCS3B01G036000 chr3D 12281138 12284029 2891 False 767.333333 1352 83.333667 196 3274 3 chr3D.!!$F1 3078
2 TraesCS3B01G036000 chr3A 24875332 24878993 3661 True 649.600000 1024 88.175200 11 3274 5 chr3A.!!$R1 3263

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
453 455 0.032952 TGTCGTTGCACAGTACTCCC 59.967 55.0 0.0 0.0 0.00 4.30 F
1238 1317 0.174389 TGCCAAGCTTCTCTCTAGCG 59.826 55.0 0.0 0.0 43.37 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 1909 0.404040 TGACACCCACCCTCCAAATC 59.596 55.0 0.00 0.0 0.0 2.17 R
2636 3581 0.034186 TGATGCAAAAGCCCGGAGAT 60.034 50.0 0.73 0.0 0.0 2.75 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
141 142 1.472728 CCTCCGTCCGGATTTAGTTGG 60.473 57.143 7.81 1.25 44.24 3.77
146 147 1.395954 GTCCGGATTTAGTTGGCGTTC 59.604 52.381 7.81 0.00 0.00 3.95
148 149 1.807742 CCGGATTTAGTTGGCGTTCAA 59.192 47.619 0.00 0.00 0.00 2.69
189 190 3.961480 ATCATCCGTTTGAGTGTCAGA 57.039 42.857 0.00 0.00 0.00 3.27
190 191 3.961480 TCATCCGTTTGAGTGTCAGAT 57.039 42.857 0.00 0.00 0.00 2.90
193 194 3.744238 TCCGTTTGAGTGTCAGATGAA 57.256 42.857 0.00 0.00 0.00 2.57
194 195 3.653344 TCCGTTTGAGTGTCAGATGAAG 58.347 45.455 0.00 0.00 0.00 3.02
195 196 3.069586 TCCGTTTGAGTGTCAGATGAAGT 59.930 43.478 0.00 0.00 0.00 3.01
199 200 6.147821 CCGTTTGAGTGTCAGATGAAGTAAAT 59.852 38.462 0.00 0.00 0.00 1.40
285 286 5.462530 GGTGTTGTACCTGGCTTTATTTT 57.537 39.130 0.00 0.00 46.51 1.82
286 287 6.578163 GGTGTTGTACCTGGCTTTATTTTA 57.422 37.500 0.00 0.00 46.51 1.52
287 288 6.983984 GGTGTTGTACCTGGCTTTATTTTAA 58.016 36.000 0.00 0.00 46.51 1.52
437 439 6.077838 GGCCGAAATATAAATCGACATTGTC 58.922 40.000 6.73 6.73 41.43 3.18
449 451 3.169207 GACATTGTCGTTGCACAGTAC 57.831 47.619 0.13 0.00 0.00 2.73
450 452 2.800544 GACATTGTCGTTGCACAGTACT 59.199 45.455 0.13 0.00 0.00 2.73
451 453 2.800544 ACATTGTCGTTGCACAGTACTC 59.199 45.455 0.00 0.00 0.00 2.59
452 454 1.860676 TTGTCGTTGCACAGTACTCC 58.139 50.000 0.00 0.00 0.00 3.85
453 455 0.032952 TGTCGTTGCACAGTACTCCC 59.967 55.000 0.00 0.00 0.00 4.30
454 456 0.317479 GTCGTTGCACAGTACTCCCT 59.683 55.000 0.00 0.00 0.00 4.20
455 457 0.601558 TCGTTGCACAGTACTCCCTC 59.398 55.000 0.00 0.00 0.00 4.30
456 458 0.389948 CGTTGCACAGTACTCCCTCC 60.390 60.000 0.00 0.00 0.00 4.30
457 459 0.389948 GTTGCACAGTACTCCCTCCG 60.390 60.000 0.00 0.00 0.00 4.63
458 460 0.830444 TTGCACAGTACTCCCTCCGT 60.830 55.000 0.00 0.00 0.00 4.69
459 461 0.830444 TGCACAGTACTCCCTCCGTT 60.830 55.000 0.00 0.00 0.00 4.44
460 462 0.320697 GCACAGTACTCCCTCCGTTT 59.679 55.000 0.00 0.00 0.00 3.60
461 463 1.270678 GCACAGTACTCCCTCCGTTTT 60.271 52.381 0.00 0.00 0.00 2.43
462 464 2.809299 GCACAGTACTCCCTCCGTTTTT 60.809 50.000 0.00 0.00 0.00 1.94
463 465 3.555586 GCACAGTACTCCCTCCGTTTTTA 60.556 47.826 0.00 0.00 0.00 1.52
464 466 4.828829 CACAGTACTCCCTCCGTTTTTAT 58.171 43.478 0.00 0.00 0.00 1.40
465 467 5.243207 CACAGTACTCCCTCCGTTTTTATT 58.757 41.667 0.00 0.00 0.00 1.40
466 468 5.704053 CACAGTACTCCCTCCGTTTTTATTT 59.296 40.000 0.00 0.00 0.00 1.40
467 469 6.875195 CACAGTACTCCCTCCGTTTTTATTTA 59.125 38.462 0.00 0.00 0.00 1.40
468 470 6.875726 ACAGTACTCCCTCCGTTTTTATTTAC 59.124 38.462 0.00 0.00 0.00 2.01
469 471 7.101700 CAGTACTCCCTCCGTTTTTATTTACT 58.898 38.462 0.00 0.00 0.00 2.24
470 472 7.277319 CAGTACTCCCTCCGTTTTTATTTACTC 59.723 40.741 0.00 0.00 0.00 2.59
471 473 5.494724 ACTCCCTCCGTTTTTATTTACTCC 58.505 41.667 0.00 0.00 0.00 3.85
472 474 4.506758 TCCCTCCGTTTTTATTTACTCCG 58.493 43.478 0.00 0.00 0.00 4.63
473 475 3.064408 CCCTCCGTTTTTATTTACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
474 476 3.685756 CCTCCGTTTTTATTTACTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
475 477 4.334481 CCTCCGTTTTTATTTACTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
476 478 5.524646 CCTCCGTTTTTATTTACTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
477 479 6.204108 CCTCCGTTTTTATTTACTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
478 480 7.255001 CCTCCGTTTTTATTTACTCCGCATATT 60.255 37.037 0.00 0.00 0.00 1.28
479 481 8.659925 TCCGTTTTTATTTACTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
480 482 9.275398 TCCGTTTTTATTTACTCCGCATATTAT 57.725 29.630 0.00 0.00 0.00 1.28
481 483 9.537848 CCGTTTTTATTTACTCCGCATATTATC 57.462 33.333 0.00 0.00 0.00 1.75
487 489 9.787435 TTATTTACTCCGCATATTATCTTTGGT 57.213 29.630 0.00 0.00 0.00 3.67
488 490 7.724305 TTTACTCCGCATATTATCTTTGGTC 57.276 36.000 0.00 0.00 0.00 4.02
489 491 5.290493 ACTCCGCATATTATCTTTGGTCA 57.710 39.130 0.00 0.00 0.00 4.02
490 492 5.680619 ACTCCGCATATTATCTTTGGTCAA 58.319 37.500 0.00 0.00 0.00 3.18
491 493 6.119536 ACTCCGCATATTATCTTTGGTCAAA 58.880 36.000 0.00 0.00 0.00 2.69
492 494 6.260936 ACTCCGCATATTATCTTTGGTCAAAG 59.739 38.462 15.18 15.18 46.82 2.77
493 495 6.119536 TCCGCATATTATCTTTGGTCAAAGT 58.880 36.000 19.13 11.42 45.88 2.66
494 496 6.260050 TCCGCATATTATCTTTGGTCAAAGTC 59.740 38.462 19.13 3.92 45.88 3.01
495 497 6.038161 CCGCATATTATCTTTGGTCAAAGTCA 59.962 38.462 19.13 8.71 45.88 3.41
496 498 7.415095 CCGCATATTATCTTTGGTCAAAGTCAA 60.415 37.037 19.13 14.96 45.88 3.18
497 499 7.641411 CGCATATTATCTTTGGTCAAAGTCAAG 59.359 37.037 19.13 8.50 45.88 3.02
498 500 7.433425 GCATATTATCTTTGGTCAAAGTCAAGC 59.567 37.037 19.13 12.80 45.88 4.01
499 501 8.680903 CATATTATCTTTGGTCAAAGTCAAGCT 58.319 33.333 19.13 7.02 45.88 3.74
500 502 6.959639 TTATCTTTGGTCAAAGTCAAGCTT 57.040 33.333 19.13 0.00 45.88 3.74
502 504 5.248870 TCTTTGGTCAAAGTCAAGCTTTC 57.751 39.130 19.13 0.00 44.95 2.62
503 505 4.949856 TCTTTGGTCAAAGTCAAGCTTTCT 59.050 37.500 19.13 0.00 44.95 2.52
504 506 6.119536 TCTTTGGTCAAAGTCAAGCTTTCTA 58.880 36.000 19.13 0.00 44.95 2.10
505 507 6.601613 TCTTTGGTCAAAGTCAAGCTTTCTAA 59.398 34.615 19.13 0.00 44.95 2.10
506 508 6.767524 TTGGTCAAAGTCAAGCTTTCTAAA 57.232 33.333 0.00 0.00 44.95 1.85
507 509 6.131544 TGGTCAAAGTCAAGCTTTCTAAAC 57.868 37.500 0.00 0.00 44.95 2.01
508 510 5.885912 TGGTCAAAGTCAAGCTTTCTAAACT 59.114 36.000 0.00 0.00 44.95 2.66
509 511 6.377146 TGGTCAAAGTCAAGCTTTCTAAACTT 59.623 34.615 0.00 0.00 44.95 2.66
510 512 7.093945 TGGTCAAAGTCAAGCTTTCTAAACTTT 60.094 33.333 0.00 5.64 44.95 2.66
511 513 7.220875 GGTCAAAGTCAAGCTTTCTAAACTTTG 59.779 37.037 24.71 24.71 44.95 2.77
513 515 7.968405 TCAAAGTCAAGCTTTCTAAACTTTGAC 59.032 33.333 26.80 17.23 45.97 3.18
514 516 7.391148 AAGTCAAGCTTTCTAAACTTTGACA 57.609 32.000 19.25 0.00 32.57 3.58
515 517 7.391148 AGTCAAGCTTTCTAAACTTTGACAA 57.609 32.000 19.25 0.00 30.59 3.18
516 518 7.826690 AGTCAAGCTTTCTAAACTTTGACAAA 58.173 30.769 19.25 0.00 30.59 2.83
517 519 7.970614 AGTCAAGCTTTCTAAACTTTGACAAAG 59.029 33.333 23.41 23.41 44.10 2.77
562 564 8.725405 ACATATACAATAACAAATCGACACCA 57.275 30.769 0.00 0.00 0.00 4.17
563 565 9.337396 ACATATACAATAACAAATCGACACCAT 57.663 29.630 0.00 0.00 0.00 3.55
567 569 7.915293 ACAATAACAAATCGACACCATTAGA 57.085 32.000 0.00 0.00 0.00 2.10
568 570 8.506168 ACAATAACAAATCGACACCATTAGAT 57.494 30.769 0.00 0.00 0.00 1.98
569 571 8.956426 ACAATAACAAATCGACACCATTAGATT 58.044 29.630 0.00 0.00 35.12 2.40
570 572 9.438291 CAATAACAAATCGACACCATTAGATTC 57.562 33.333 0.00 0.00 32.79 2.52
571 573 8.731275 ATAACAAATCGACACCATTAGATTCA 57.269 30.769 0.00 0.00 32.79 2.57
572 574 7.630242 AACAAATCGACACCATTAGATTCAT 57.370 32.000 0.00 0.00 32.79 2.57
573 575 7.630242 ACAAATCGACACCATTAGATTCATT 57.370 32.000 0.00 0.00 32.79 2.57
574 576 8.731275 ACAAATCGACACCATTAGATTCATTA 57.269 30.769 0.00 0.00 32.79 1.90
575 577 9.342308 ACAAATCGACACCATTAGATTCATTAT 57.658 29.630 0.00 0.00 32.79 1.28
578 580 9.559732 AATCGACACCATTAGATTCATTATTGA 57.440 29.630 0.00 0.00 0.00 2.57
579 581 8.956533 TCGACACCATTAGATTCATTATTGAA 57.043 30.769 2.71 2.71 45.57 2.69
644 646 9.932207 TCGTATTCTTTTCTATAAACTTGGTCA 57.068 29.630 0.00 0.00 0.00 4.02
660 662 9.936759 AAACTTGGTCAAATTTAGAAAGTTTGA 57.063 25.926 20.74 6.31 41.98 2.69
681 683 9.047871 GTTTGACTTCAATTAACACTAATACGC 57.952 33.333 0.00 0.00 35.55 4.42
682 684 6.985013 TGACTTCAATTAACACTAATACGCG 58.015 36.000 3.53 3.53 0.00 6.01
683 685 6.035220 TGACTTCAATTAACACTAATACGCGG 59.965 38.462 12.47 0.00 0.00 6.46
684 686 6.101332 ACTTCAATTAACACTAATACGCGGA 58.899 36.000 12.47 0.00 0.00 5.54
685 687 6.255020 ACTTCAATTAACACTAATACGCGGAG 59.745 38.462 12.47 4.43 0.00 4.63
686 688 5.653507 TCAATTAACACTAATACGCGGAGT 58.346 37.500 12.47 2.60 0.00 3.85
687 689 6.794374 TCAATTAACACTAATACGCGGAGTA 58.206 36.000 12.47 4.11 40.03 2.59
688 690 7.257003 TCAATTAACACTAATACGCGGAGTAA 58.743 34.615 12.47 0.00 39.04 2.24
689 691 7.758980 TCAATTAACACTAATACGCGGAGTAAA 59.241 33.333 12.47 0.00 39.04 2.01
690 692 8.545420 CAATTAACACTAATACGCGGAGTAAAT 58.455 33.333 12.47 0.00 39.04 1.40
691 693 9.748708 AATTAACACTAATACGCGGAGTAAATA 57.251 29.630 12.47 0.00 39.04 1.40
692 694 9.748708 ATTAACACTAATACGCGGAGTAAATAA 57.251 29.630 12.47 3.08 39.04 1.40
693 695 9.579768 TTAACACTAATACGCGGAGTAAATAAA 57.420 29.630 12.47 0.00 39.04 1.40
694 696 8.477984 AACACTAATACGCGGAGTAAATAAAA 57.522 30.769 12.47 0.00 39.04 1.52
695 697 8.477984 ACACTAATACGCGGAGTAAATAAAAA 57.522 30.769 12.47 0.00 39.04 1.94
696 698 8.382875 ACACTAATACGCGGAGTAAATAAAAAC 58.617 33.333 12.47 0.00 39.04 2.43
697 699 7.576602 CACTAATACGCGGAGTAAATAAAAACG 59.423 37.037 12.47 0.00 39.04 3.60
698 700 3.727780 ACGCGGAGTAAATAAAAACGG 57.272 42.857 12.47 0.00 0.00 4.44
699 701 3.324993 ACGCGGAGTAAATAAAAACGGA 58.675 40.909 12.47 0.00 0.00 4.69
700 702 3.368843 ACGCGGAGTAAATAAAAACGGAG 59.631 43.478 12.47 0.00 0.00 4.63
701 703 3.242188 CGCGGAGTAAATAAAAACGGAGG 60.242 47.826 0.00 0.00 0.00 4.30
702 704 3.064408 GCGGAGTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
703 705 4.506758 CGGAGTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
718 720 5.017490 ACGGAGGGAGTACCAGATATTATG 58.983 45.833 0.00 0.00 43.89 1.90
728 730 8.497910 AGTACCAGATATTATGGGCATATAGG 57.502 38.462 11.44 0.00 42.48 2.57
738 761 1.348036 GGGCATATAGGTGGGTGAGTC 59.652 57.143 0.00 0.00 0.00 3.36
750 773 1.308998 GGTGAGTCATATTTGCGGGG 58.691 55.000 0.00 0.00 0.00 5.73
819 842 3.882844 GTACGTACGTGCGCGCAG 61.883 66.667 37.44 28.68 42.83 5.18
846 869 2.112928 ACACGATGCCACAAGCCA 59.887 55.556 0.00 0.00 42.71 4.75
901 954 0.376502 GCTAGGTCGTCGTCCAGTAC 59.623 60.000 11.13 0.00 0.00 2.73
911 964 0.800631 CGTCCAGTACGTACAGCTGA 59.199 55.000 26.55 13.96 46.72 4.26
950 1003 2.813754 GTCTTGCATGCTGTTACTTCCA 59.186 45.455 20.33 0.00 0.00 3.53
966 1019 3.119137 ACTTCCAGTCAACTGCCAAAAAC 60.119 43.478 4.58 0.00 42.47 2.43
969 1022 3.259374 TCCAGTCAACTGCCAAAAACAAA 59.741 39.130 4.58 0.00 42.47 2.83
970 1023 4.081198 TCCAGTCAACTGCCAAAAACAAAT 60.081 37.500 4.58 0.00 42.47 2.32
971 1024 5.127845 TCCAGTCAACTGCCAAAAACAAATA 59.872 36.000 4.58 0.00 42.47 1.40
972 1025 5.814705 CCAGTCAACTGCCAAAAACAAATAA 59.185 36.000 4.58 0.00 42.47 1.40
973 1026 6.314896 CCAGTCAACTGCCAAAAACAAATAAA 59.685 34.615 4.58 0.00 42.47 1.40
974 1027 7.148340 CCAGTCAACTGCCAAAAACAAATAAAA 60.148 33.333 4.58 0.00 42.47 1.52
975 1028 8.233190 CAGTCAACTGCCAAAAACAAATAAAAA 58.767 29.630 0.00 0.00 37.15 1.94
1014 1067 2.687425 ACGCATGCTTTATATGCCAACA 59.313 40.909 17.13 0.00 46.20 3.33
1015 1068 3.318839 ACGCATGCTTTATATGCCAACAT 59.681 39.130 17.13 0.00 46.20 2.71
1016 1069 4.518590 ACGCATGCTTTATATGCCAACATA 59.481 37.500 17.13 0.00 46.20 2.29
1047 1100 0.898320 ACACCTCATCTTCTCCACCG 59.102 55.000 0.00 0.00 0.00 4.94
1049 1102 2.100197 CACCTCATCTTCTCCACCGTA 58.900 52.381 0.00 0.00 0.00 4.02
1077 1130 4.602107 GGACCCTAGCTATCTAACCCTAG 58.398 52.174 0.00 0.00 0.00 3.02
1078 1131 4.018490 GACCCTAGCTATCTAACCCTAGC 58.982 52.174 0.00 0.00 40.52 3.42
1080 1133 4.856765 ACCCTAGCTATCTAACCCTAGCTA 59.143 45.833 10.04 10.04 46.70 3.32
1106 1159 0.456221 AGTCGACCTAACCATCGCAG 59.544 55.000 13.01 0.00 38.24 5.18
1109 1162 1.220749 GACCTAACCATCGCAGGCA 59.779 57.895 0.00 0.00 32.31 4.75
1110 1163 1.078426 ACCTAACCATCGCAGGCAC 60.078 57.895 0.00 0.00 32.31 5.01
1118 1197 3.309436 ATCGCAGGCACGCACCTAA 62.309 57.895 0.00 0.00 38.26 2.69
1129 1208 0.179073 CGCACCTAACCATGAGGGAG 60.179 60.000 0.00 0.00 41.15 4.30
1130 1209 0.464554 GCACCTAACCATGAGGGAGC 60.465 60.000 0.00 0.00 41.15 4.70
1131 1210 0.181350 CACCTAACCATGAGGGAGCC 59.819 60.000 0.00 0.00 41.15 4.70
1132 1211 0.253160 ACCTAACCATGAGGGAGCCA 60.253 55.000 0.00 0.00 41.15 4.75
1133 1212 0.181350 CCTAACCATGAGGGAGCCAC 59.819 60.000 0.00 0.00 41.15 5.01
1134 1213 0.179073 CTAACCATGAGGGAGCCACG 60.179 60.000 0.00 0.00 41.15 4.94
1182 1261 2.029964 GACGGAGAAACACGGCCA 59.970 61.111 2.24 0.00 30.28 5.36
1185 1264 3.056328 GGAGAAACACGGCCAGCC 61.056 66.667 2.24 0.00 0.00 4.85
1212 1291 3.414700 CCGGACGAACAGCAGCAC 61.415 66.667 0.00 0.00 0.00 4.40
1213 1292 3.767230 CGGACGAACAGCAGCACG 61.767 66.667 0.00 0.00 0.00 5.34
1214 1293 4.077188 GGACGAACAGCAGCACGC 62.077 66.667 0.00 0.00 42.91 5.34
1224 1303 3.120385 CAGCACGCGAGATGCCAA 61.120 61.111 15.93 0.00 44.53 4.52
1226 1305 4.527157 GCACGCGAGATGCCAAGC 62.527 66.667 15.93 0.00 42.08 4.01
1227 1306 2.816958 CACGCGAGATGCCAAGCT 60.817 61.111 15.93 0.00 42.08 3.74
1229 1308 2.103042 ACGCGAGATGCCAAGCTTC 61.103 57.895 15.93 0.00 42.08 3.86
1230 1309 1.812922 CGCGAGATGCCAAGCTTCT 60.813 57.895 0.00 4.81 43.95 2.85
1237 1316 2.102925 AGATGCCAAGCTTCTCTCTAGC 59.897 50.000 0.00 0.00 38.40 3.42
1238 1317 0.174389 TGCCAAGCTTCTCTCTAGCG 59.826 55.000 0.00 0.00 43.37 4.26
1239 1318 0.457851 GCCAAGCTTCTCTCTAGCGA 59.542 55.000 0.00 0.00 43.37 4.93
1245 1324 2.552315 AGCTTCTCTCTAGCGATAGTGC 59.448 50.000 7.70 4.45 43.37 4.40
1246 1325 2.351350 GCTTCTCTCTAGCGATAGTGCC 60.351 54.545 7.70 0.00 39.35 5.01
1248 1327 1.202663 TCTCTCTAGCGATAGTGCCGT 60.203 52.381 7.70 0.00 39.35 5.68
1251 1330 1.661821 CTAGCGATAGTGCCGTGCC 60.662 63.158 0.00 0.00 39.35 5.01
1295 1374 2.680370 GGGGGACTACTTGCTGGGG 61.680 68.421 0.00 0.00 0.00 4.96
1438 1537 0.924090 GCTGATGACGAATCACGACC 59.076 55.000 0.00 0.00 45.77 4.79
1441 1540 2.537214 CTGATGACGAATCACGACCATG 59.463 50.000 0.00 0.00 45.77 3.66
1444 1543 1.278238 GACGAATCACGACCATGTCC 58.722 55.000 0.00 0.00 45.77 4.02
1455 1554 1.826921 CCATGTCCATCCAGCTGGC 60.827 63.158 28.91 14.10 36.16 4.85
1626 1737 1.746615 GGCGAGCATCTGCAAAGGA 60.747 57.895 4.79 0.00 45.16 3.36
1628 1739 1.986575 GCGAGCATCTGCAAAGGACC 61.987 60.000 4.79 0.00 45.16 4.46
1743 1857 3.699894 CCGACAGCAGGTGCCTCT 61.700 66.667 0.00 0.00 43.38 3.69
1795 1909 1.617755 CCGTGCAGTGCGTCTACTTG 61.618 60.000 11.20 0.00 0.00 3.16
1808 1922 3.610911 GTCTACTTGATTTGGAGGGTGG 58.389 50.000 0.00 0.00 0.00 4.61
1809 1923 2.576191 TCTACTTGATTTGGAGGGTGGG 59.424 50.000 0.00 0.00 0.00 4.61
1810 1924 1.158007 ACTTGATTTGGAGGGTGGGT 58.842 50.000 0.00 0.00 0.00 4.51
1811 1925 1.203050 ACTTGATTTGGAGGGTGGGTG 60.203 52.381 0.00 0.00 0.00 4.61
1812 1926 0.856982 TTGATTTGGAGGGTGGGTGT 59.143 50.000 0.00 0.00 0.00 4.16
1813 1927 0.404040 TGATTTGGAGGGTGGGTGTC 59.596 55.000 0.00 0.00 0.00 3.67
1814 1928 0.404040 GATTTGGAGGGTGGGTGTCA 59.596 55.000 0.00 0.00 0.00 3.58
1815 1929 1.005924 GATTTGGAGGGTGGGTGTCAT 59.994 52.381 0.00 0.00 0.00 3.06
1816 1930 1.748732 TTTGGAGGGTGGGTGTCATA 58.251 50.000 0.00 0.00 0.00 2.15
1817 1931 1.979809 TTGGAGGGTGGGTGTCATAT 58.020 50.000 0.00 0.00 0.00 1.78
1818 1932 1.507140 TGGAGGGTGGGTGTCATATC 58.493 55.000 0.00 0.00 0.00 1.63
1858 1999 4.218200 TCGATGGTTTCTGTACCGTAAGAA 59.782 41.667 0.00 0.00 41.28 2.52
1867 2008 5.316167 TCTGTACCGTAAGAAACAGTCCTA 58.684 41.667 9.10 0.00 44.82 2.94
2017 2277 5.997746 TGTGTCCCTTCAAAAGTTCAGATAG 59.002 40.000 0.00 0.00 0.00 2.08
2018 2278 5.412904 GTGTCCCTTCAAAAGTTCAGATAGG 59.587 44.000 0.00 0.00 0.00 2.57
2019 2279 5.309543 TGTCCCTTCAAAAGTTCAGATAGGA 59.690 40.000 0.00 0.00 0.00 2.94
2020 2280 5.877564 GTCCCTTCAAAAGTTCAGATAGGAG 59.122 44.000 0.00 0.00 0.00 3.69
2021 2281 5.548056 TCCCTTCAAAAGTTCAGATAGGAGT 59.452 40.000 0.00 0.00 0.00 3.85
2022 2282 6.729100 TCCCTTCAAAAGTTCAGATAGGAGTA 59.271 38.462 0.00 0.00 0.00 2.59
2034 2308 8.564574 GTTCAGATAGGAGTATGAACTACTCTG 58.435 40.741 11.10 0.00 44.11 3.35
2055 2329 5.071788 TCTGGCTAATACTCCTACCCAATTG 59.928 44.000 0.00 0.00 0.00 2.32
2114 2388 6.321181 TCTTAAAATGCTTGACTTTGTGGACT 59.679 34.615 0.00 0.00 0.00 3.85
2285 2877 8.836413 GTTATGTGGCTATAAATAAAGCTCACA 58.164 33.333 15.73 15.73 45.34 3.58
2379 2973 3.327757 TGTTGCTTCCTTGGTGATCTAGT 59.672 43.478 0.00 0.00 0.00 2.57
2396 2990 8.071368 GTGATCTAGTCGAAACGAGATTTCTAT 58.929 37.037 3.27 0.00 44.77 1.98
2403 2997 7.042658 AGTCGAAACGAGATTTCTATTAATGGC 60.043 37.037 0.00 0.00 44.03 4.40
2414 3008 4.569943 TCTATTAATGGCAATCGGAGAGC 58.430 43.478 0.00 0.00 43.63 4.09
2415 3009 2.708216 TTAATGGCAATCGGAGAGCA 57.292 45.000 0.00 0.00 43.63 4.26
2416 3010 2.936919 TAATGGCAATCGGAGAGCAT 57.063 45.000 0.00 0.00 43.63 3.79
2417 3011 1.315690 AATGGCAATCGGAGAGCATG 58.684 50.000 0.00 0.00 43.63 4.06
2419 3013 3.028969 GCAATCGGAGAGCATGCC 58.971 61.111 15.66 6.03 43.63 4.40
2420 3014 1.525535 GCAATCGGAGAGCATGCCT 60.526 57.895 15.66 11.42 43.63 4.75
2422 3016 1.386533 CAATCGGAGAGCATGCCTTT 58.613 50.000 15.66 0.00 43.63 3.11
2423 3017 1.332997 CAATCGGAGAGCATGCCTTTC 59.667 52.381 15.66 9.56 43.63 2.62
2554 3497 5.954335 ACTAAACAAGCAATTGATGTAGCC 58.046 37.500 10.34 0.00 0.00 3.93
2570 3513 3.519107 TGTAGCCTTGATGATCTTGTGGA 59.481 43.478 0.00 0.00 0.00 4.02
2647 3592 3.709653 TGTAACTATCAATCTCCGGGCTT 59.290 43.478 0.00 0.00 0.00 4.35
2648 3593 3.933861 AACTATCAATCTCCGGGCTTT 57.066 42.857 0.00 0.00 0.00 3.51
2649 3594 3.933861 ACTATCAATCTCCGGGCTTTT 57.066 42.857 0.00 0.00 0.00 2.27
2650 3595 3.545703 ACTATCAATCTCCGGGCTTTTG 58.454 45.455 0.00 1.14 0.00 2.44
2651 3596 1.106285 ATCAATCTCCGGGCTTTTGC 58.894 50.000 0.00 0.00 46.64 3.68
2678 3623 4.081862 ACTTTTGCAAGATCATGGATGGTG 60.082 41.667 0.00 0.00 33.72 4.17
2682 3627 5.565455 TGCAAGATCATGGATGGTGTATA 57.435 39.130 0.00 0.00 0.00 1.47
2710 3655 6.233434 TGGACACATGGAGCAAATCTATATC 58.767 40.000 0.00 0.00 0.00 1.63
2767 3712 9.282569 GGCATTCTCTTGACTTCAATCTAATAT 57.717 33.333 0.00 0.00 35.02 1.28
2852 3798 8.514594 ACATTACGACATGATTCAAAGAACATT 58.485 29.630 0.00 0.00 0.00 2.71
2948 3895 9.810545 TCGAGTTATCATGTATTACAAATCACA 57.189 29.630 0.00 0.00 0.00 3.58
2968 3915 8.806429 ATCACAAATGGATAGTTGACAATACA 57.194 30.769 0.00 0.00 35.56 2.29
2969 3916 8.039603 TCACAAATGGATAGTTGACAATACAC 57.960 34.615 0.00 0.00 35.56 2.90
2997 3944 5.064558 TGTATCTAGCTCGCTAACTAGCTT 58.935 41.667 7.13 0.00 46.82 3.74
2999 3946 5.873179 ATCTAGCTCGCTAACTAGCTTAG 57.127 43.478 7.13 5.61 46.82 2.18
3009 3956 7.869800 TCGCTAACTAGCTTAGTACTTATTCC 58.130 38.462 0.00 0.00 46.85 3.01
3016 3963 9.198475 ACTAGCTTAGTACTTATTCCTTTAGCA 57.802 33.333 0.00 0.00 37.23 3.49
3022 3969 7.379098 AGTACTTATTCCTTTAGCAACTTGC 57.621 36.000 5.55 5.55 45.46 4.01
3023 3970 5.644977 ACTTATTCCTTTAGCAACTTGCC 57.355 39.130 10.25 0.00 46.52 4.52
3027 3974 3.780804 TCCTTTAGCAACTTGCCAGTA 57.219 42.857 10.25 0.00 46.52 2.74
3043 3990 8.174085 ACTTGCCAGTATATACTTCTCCTCTAT 58.826 37.037 12.87 0.00 33.46 1.98
3101 4048 4.263949 CCCCCAACTTCTCTCCTAAACATT 60.264 45.833 0.00 0.00 0.00 2.71
3102 4049 4.944317 CCCCAACTTCTCTCCTAAACATTC 59.056 45.833 0.00 0.00 0.00 2.67
3103 4050 5.280727 CCCCAACTTCTCTCCTAAACATTCT 60.281 44.000 0.00 0.00 0.00 2.40
3112 4059 4.082190 TCTCCTAAACATTCTGACGGACTG 60.082 45.833 0.27 0.27 0.00 3.51
3141 4088 0.597568 CGCCTGGATGCAAAAAGACA 59.402 50.000 0.00 0.00 0.00 3.41
3157 4104 2.052468 AGACAACCCTAACGAACCCTT 58.948 47.619 0.00 0.00 0.00 3.95
3167 4114 0.767060 ACGAACCCTTCCCACTTCCT 60.767 55.000 0.00 0.00 0.00 3.36
3205 4152 1.971357 GTCCGACACCCTCATATCCAT 59.029 52.381 0.00 0.00 0.00 3.41
3237 4184 3.311110 GGATATGGGGCGGCTCGA 61.311 66.667 9.56 0.00 0.00 4.04
3239 4186 1.296715 GATATGGGGCGGCTCGAAT 59.703 57.895 9.56 1.44 0.00 3.34
3259 4210 4.436998 GCCTAGGCACGTCACGCT 62.437 66.667 29.33 0.00 41.49 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.995289 TCACAAGAAAAGCAAGAAAGACAATA 58.005 30.769 0.00 0.00 0.00 1.90
42 43 5.473504 TCTGGATACCTTTCACAAGAAAAGC 59.526 40.000 0.00 0.00 42.78 3.51
141 142 6.199531 TGTATTAGATACATCCGTTTGAACGC 59.800 38.462 10.57 0.00 44.14 4.84
162 163 6.429692 TGACACTCAAACGGATGATTTTGTAT 59.570 34.615 0.00 0.00 34.81 2.29
189 190 7.767198 TCGGAACCTCGATTTAATTTACTTCAT 59.233 33.333 0.00 0.00 33.92 2.57
190 191 7.098477 TCGGAACCTCGATTTAATTTACTTCA 58.902 34.615 0.00 0.00 33.92 3.02
193 194 7.745972 GTTTCGGAACCTCGATTTAATTTACT 58.254 34.615 0.00 0.00 39.03 2.24
194 195 7.943735 GTTTCGGAACCTCGATTTAATTTAC 57.056 36.000 0.00 0.00 39.03 2.01
437 439 0.389948 GGAGGGAGTACTGTGCAACG 60.390 60.000 0.00 0.00 42.39 4.10
446 448 6.536582 GGAGTAAATAAAAACGGAGGGAGTAC 59.463 42.308 0.00 0.00 0.00 2.73
447 449 6.627953 CGGAGTAAATAAAAACGGAGGGAGTA 60.628 42.308 0.00 0.00 0.00 2.59
448 450 5.494724 GGAGTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
449 451 4.569564 CGGAGTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
450 452 4.506758 CGGAGTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
451 453 3.064408 GCGGAGTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
452 454 3.685756 TGCGGAGTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
453 455 4.932268 TGCGGAGTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
454 456 7.556733 AATATGCGGAGTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
455 457 9.537848 GATAATATGCGGAGTAAATAAAAACGG 57.462 33.333 0.00 0.00 0.00 4.44
461 463 9.787435 ACCAAAGATAATATGCGGAGTAAATAA 57.213 29.630 0.00 0.00 0.00 1.40
462 464 9.431887 GACCAAAGATAATATGCGGAGTAAATA 57.568 33.333 0.00 0.00 0.00 1.40
463 465 7.936847 TGACCAAAGATAATATGCGGAGTAAAT 59.063 33.333 0.00 0.00 0.00 1.40
464 466 7.276658 TGACCAAAGATAATATGCGGAGTAAA 58.723 34.615 0.00 0.00 0.00 2.01
465 467 6.822442 TGACCAAAGATAATATGCGGAGTAA 58.178 36.000 0.00 0.00 0.00 2.24
466 468 6.413783 TGACCAAAGATAATATGCGGAGTA 57.586 37.500 0.00 0.00 0.00 2.59
467 469 5.290493 TGACCAAAGATAATATGCGGAGT 57.710 39.130 0.00 0.00 0.00 3.85
468 470 6.618287 TTTGACCAAAGATAATATGCGGAG 57.382 37.500 0.00 0.00 0.00 4.63
475 477 9.077885 AAAGCTTGACTTTGACCAAAGATAATA 57.922 29.630 24.31 7.00 47.00 0.98
476 478 7.955918 AAAGCTTGACTTTGACCAAAGATAAT 58.044 30.769 24.31 6.33 47.00 1.28
477 479 7.346751 AAAGCTTGACTTTGACCAAAGATAA 57.653 32.000 24.31 17.24 47.00 1.75
478 480 6.959639 AAAGCTTGACTTTGACCAAAGATA 57.040 33.333 24.31 12.33 47.00 1.98
479 481 5.859205 AAAGCTTGACTTTGACCAAAGAT 57.141 34.783 24.31 11.69 47.00 2.40
490 492 7.391148 TGTCAAAGTTTAGAAAGCTTGACTT 57.609 32.000 19.71 3.36 39.29 3.01
491 493 7.391148 TTGTCAAAGTTTAGAAAGCTTGACT 57.609 32.000 19.71 5.67 39.29 3.41
492 494 8.108716 CTTTGTCAAAGTTTAGAAAGCTTGAC 57.891 34.615 15.93 15.72 39.15 3.18
536 538 9.168451 TGGTGTCGATTTGTTATTGTATATGTT 57.832 29.630 0.00 0.00 0.00 2.71
537 539 8.725405 TGGTGTCGATTTGTTATTGTATATGT 57.275 30.769 0.00 0.00 0.00 2.29
541 543 9.607988 TCTAATGGTGTCGATTTGTTATTGTAT 57.392 29.630 0.00 0.00 0.00 2.29
542 544 9.607988 ATCTAATGGTGTCGATTTGTTATTGTA 57.392 29.630 0.00 0.00 0.00 2.41
543 545 7.915293 TCTAATGGTGTCGATTTGTTATTGT 57.085 32.000 0.00 0.00 0.00 2.71
544 546 9.438291 GAATCTAATGGTGTCGATTTGTTATTG 57.562 33.333 0.00 0.00 0.00 1.90
545 547 9.173021 TGAATCTAATGGTGTCGATTTGTTATT 57.827 29.630 0.00 0.00 0.00 1.40
546 548 8.731275 TGAATCTAATGGTGTCGATTTGTTAT 57.269 30.769 0.00 0.00 0.00 1.89
547 549 8.731275 ATGAATCTAATGGTGTCGATTTGTTA 57.269 30.769 0.00 0.00 0.00 2.41
548 550 7.630242 ATGAATCTAATGGTGTCGATTTGTT 57.370 32.000 0.00 0.00 0.00 2.83
549 551 7.630242 AATGAATCTAATGGTGTCGATTTGT 57.370 32.000 0.00 0.00 0.00 2.83
552 554 9.559732 TCAATAATGAATCTAATGGTGTCGATT 57.440 29.630 0.00 0.00 30.99 3.34
553 555 9.559732 TTCAATAATGAATCTAATGGTGTCGAT 57.440 29.630 0.00 0.00 40.59 3.59
554 556 8.956533 TTCAATAATGAATCTAATGGTGTCGA 57.043 30.769 0.00 0.00 40.59 4.20
618 620 9.932207 TGACCAAGTTTATAGAAAAGAATACGA 57.068 29.630 0.00 0.00 0.00 3.43
634 636 9.936759 TCAAACTTTCTAAATTTGACCAAGTTT 57.063 25.926 17.71 17.71 41.42 2.66
655 657 9.047871 GCGTATTAGTGTTAATTGAAGTCAAAC 57.952 33.333 0.00 0.00 39.55 2.93
656 658 7.953173 CGCGTATTAGTGTTAATTGAAGTCAAA 59.047 33.333 0.00 0.00 39.55 2.69
657 659 7.412129 CCGCGTATTAGTGTTAATTGAAGTCAA 60.412 37.037 4.92 0.00 40.51 3.18
658 660 6.035220 CCGCGTATTAGTGTTAATTGAAGTCA 59.965 38.462 4.92 0.00 31.97 3.41
659 661 6.254157 TCCGCGTATTAGTGTTAATTGAAGTC 59.746 38.462 4.92 0.00 31.97 3.01
660 662 6.101332 TCCGCGTATTAGTGTTAATTGAAGT 58.899 36.000 4.92 0.00 31.97 3.01
661 663 6.255020 ACTCCGCGTATTAGTGTTAATTGAAG 59.745 38.462 4.92 0.00 31.97 3.02
662 664 6.101332 ACTCCGCGTATTAGTGTTAATTGAA 58.899 36.000 4.92 0.00 31.97 2.69
663 665 5.653507 ACTCCGCGTATTAGTGTTAATTGA 58.346 37.500 4.92 0.00 31.97 2.57
664 666 5.961395 ACTCCGCGTATTAGTGTTAATTG 57.039 39.130 4.92 0.00 31.97 2.32
665 667 8.652810 ATTTACTCCGCGTATTAGTGTTAATT 57.347 30.769 4.92 0.00 31.97 1.40
666 668 9.748708 TTATTTACTCCGCGTATTAGTGTTAAT 57.251 29.630 4.92 4.90 34.04 1.40
667 669 9.579768 TTTATTTACTCCGCGTATTAGTGTTAA 57.420 29.630 4.92 0.00 0.00 2.01
668 670 9.579768 TTTTATTTACTCCGCGTATTAGTGTTA 57.420 29.630 4.92 0.00 0.00 2.41
669 671 8.477984 TTTTATTTACTCCGCGTATTAGTGTT 57.522 30.769 4.92 0.00 0.00 3.32
670 672 8.382875 GTTTTTATTTACTCCGCGTATTAGTGT 58.617 33.333 4.92 0.00 0.00 3.55
671 673 7.576602 CGTTTTTATTTACTCCGCGTATTAGTG 59.423 37.037 4.92 0.00 0.00 2.74
672 674 7.254084 CCGTTTTTATTTACTCCGCGTATTAGT 60.254 37.037 4.92 5.63 0.00 2.24
673 675 7.043458 TCCGTTTTTATTTACTCCGCGTATTAG 60.043 37.037 4.92 0.00 0.00 1.73
674 676 6.754209 TCCGTTTTTATTTACTCCGCGTATTA 59.246 34.615 4.92 0.00 0.00 0.98
675 677 5.580297 TCCGTTTTTATTTACTCCGCGTATT 59.420 36.000 4.92 0.00 0.00 1.89
676 678 5.108517 TCCGTTTTTATTTACTCCGCGTAT 58.891 37.500 4.92 0.00 0.00 3.06
677 679 4.489810 TCCGTTTTTATTTACTCCGCGTA 58.510 39.130 4.92 0.00 0.00 4.42
678 680 3.324993 TCCGTTTTTATTTACTCCGCGT 58.675 40.909 4.92 0.00 0.00 6.01
679 681 3.242188 CCTCCGTTTTTATTTACTCCGCG 60.242 47.826 0.00 0.00 0.00 6.46
680 682 3.064408 CCCTCCGTTTTTATTTACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
681 683 4.506758 TCCCTCCGTTTTTATTTACTCCG 58.493 43.478 0.00 0.00 0.00 4.63
682 684 5.494724 ACTCCCTCCGTTTTTATTTACTCC 58.505 41.667 0.00 0.00 0.00 3.85
683 685 6.536582 GGTACTCCCTCCGTTTTTATTTACTC 59.463 42.308 0.00 0.00 0.00 2.59
684 686 6.013466 TGGTACTCCCTCCGTTTTTATTTACT 60.013 38.462 0.00 0.00 0.00 2.24
685 687 6.172630 TGGTACTCCCTCCGTTTTTATTTAC 58.827 40.000 0.00 0.00 0.00 2.01
686 688 6.213195 TCTGGTACTCCCTCCGTTTTTATTTA 59.787 38.462 0.00 0.00 0.00 1.40
687 689 5.013391 TCTGGTACTCCCTCCGTTTTTATTT 59.987 40.000 0.00 0.00 0.00 1.40
688 690 4.533311 TCTGGTACTCCCTCCGTTTTTATT 59.467 41.667 0.00 0.00 0.00 1.40
689 691 4.098894 TCTGGTACTCCCTCCGTTTTTAT 58.901 43.478 0.00 0.00 0.00 1.40
690 692 3.509442 TCTGGTACTCCCTCCGTTTTTA 58.491 45.455 0.00 0.00 0.00 1.52
691 693 2.332117 TCTGGTACTCCCTCCGTTTTT 58.668 47.619 0.00 0.00 0.00 1.94
692 694 2.019807 TCTGGTACTCCCTCCGTTTT 57.980 50.000 0.00 0.00 0.00 2.43
693 695 2.249309 ATCTGGTACTCCCTCCGTTT 57.751 50.000 0.00 0.00 0.00 3.60
694 696 3.614568 ATATCTGGTACTCCCTCCGTT 57.385 47.619 0.00 0.00 0.00 4.44
695 697 3.614568 AATATCTGGTACTCCCTCCGT 57.385 47.619 0.00 0.00 0.00 4.69
696 698 4.402793 CCATAATATCTGGTACTCCCTCCG 59.597 50.000 0.00 0.00 0.00 4.63
697 699 4.717280 CCCATAATATCTGGTACTCCCTCC 59.283 50.000 0.00 0.00 31.44 4.30
698 700 4.162509 GCCCATAATATCTGGTACTCCCTC 59.837 50.000 0.00 0.00 31.44 4.30
699 701 4.104831 GCCCATAATATCTGGTACTCCCT 58.895 47.826 0.00 0.00 31.44 4.20
700 702 3.844211 TGCCCATAATATCTGGTACTCCC 59.156 47.826 0.00 0.00 31.44 4.30
701 703 5.700402 ATGCCCATAATATCTGGTACTCC 57.300 43.478 0.00 0.00 31.44 3.85
702 704 8.589338 CCTATATGCCCATAATATCTGGTACTC 58.411 40.741 0.00 0.00 31.44 2.59
703 705 8.074363 ACCTATATGCCCATAATATCTGGTACT 58.926 37.037 0.00 0.00 31.12 2.73
718 720 1.348036 GACTCACCCACCTATATGCCC 59.652 57.143 0.00 0.00 0.00 5.36
728 730 1.670811 CCGCAAATATGACTCACCCAC 59.329 52.381 0.00 0.00 0.00 4.61
738 761 2.409975 CGTACCTACCCCGCAAATATG 58.590 52.381 0.00 0.00 0.00 1.78
819 842 4.450122 CATCGTGTGCTGCGTGCC 62.450 66.667 0.00 0.00 42.00 5.01
846 869 1.269051 GCTGCCGCTTTTGTTAGTTGT 60.269 47.619 0.00 0.00 0.00 3.32
901 954 0.179137 TGGATCGCTTCAGCTGTACG 60.179 55.000 14.67 15.53 39.32 3.67
950 1003 7.913674 TTTTATTTGTTTTTGGCAGTTGACT 57.086 28.000 0.00 0.00 0.00 3.41
972 1025 1.403249 GCGTGCATGAGCTCCATTTTT 60.403 47.619 12.15 0.00 42.74 1.94
973 1026 0.171903 GCGTGCATGAGCTCCATTTT 59.828 50.000 12.15 0.00 42.74 1.82
974 1027 0.961857 TGCGTGCATGAGCTCCATTT 60.962 50.000 12.15 0.00 42.74 2.32
975 1028 1.377594 TGCGTGCATGAGCTCCATT 60.378 52.632 12.15 0.00 42.74 3.16
976 1029 2.110967 GTGCGTGCATGAGCTCCAT 61.111 57.895 12.15 1.88 42.74 3.41
977 1030 2.743538 GTGCGTGCATGAGCTCCA 60.744 61.111 12.15 0.00 42.74 3.86
978 1031 3.857854 CGTGCGTGCATGAGCTCC 61.858 66.667 12.15 0.00 42.74 4.70
979 1032 4.511443 GCGTGCGTGCATGAGCTC 62.511 66.667 17.76 6.82 42.74 4.09
1014 1067 4.502105 TGAGGTGTGTGTGGCAATATAT 57.498 40.909 0.00 0.00 0.00 0.86
1015 1068 3.990959 TGAGGTGTGTGTGGCAATATA 57.009 42.857 0.00 0.00 0.00 0.86
1016 1069 2.877097 TGAGGTGTGTGTGGCAATAT 57.123 45.000 0.00 0.00 0.00 1.28
1017 1070 2.305635 AGATGAGGTGTGTGTGGCAATA 59.694 45.455 0.00 0.00 0.00 1.90
1077 1130 6.814506 TGGTTAGGTCGACTTAGATATAGC 57.185 41.667 16.46 7.01 0.00 2.97
1078 1131 7.676807 GCGATGGTTAGGTCGACTTAGATATAG 60.677 44.444 16.46 8.65 40.11 1.31
1079 1132 6.093219 GCGATGGTTAGGTCGACTTAGATATA 59.907 42.308 16.46 0.00 40.11 0.86
1080 1133 5.106237 GCGATGGTTAGGTCGACTTAGATAT 60.106 44.000 16.46 7.34 40.11 1.63
1106 1159 1.369091 CTCATGGTTAGGTGCGTGCC 61.369 60.000 0.00 0.00 0.00 5.01
1109 1162 0.907704 TCCCTCATGGTTAGGTGCGT 60.908 55.000 0.00 0.00 34.77 5.24
1110 1163 0.179073 CTCCCTCATGGTTAGGTGCG 60.179 60.000 0.00 0.00 34.77 5.34
1118 1197 3.402681 CCGTGGCTCCCTCATGGT 61.403 66.667 0.00 0.00 36.73 3.55
1130 1209 4.657824 ACTTCGTCGTGGCCGTGG 62.658 66.667 0.00 0.00 35.01 4.94
1131 1210 3.103911 GACTTCGTCGTGGCCGTG 61.104 66.667 0.00 0.00 35.01 4.94
1132 1211 4.353437 GGACTTCGTCGTGGCCGT 62.353 66.667 0.00 0.00 32.65 5.68
1144 1223 2.980233 GGCTGCTTGCACGGACTT 60.980 61.111 0.00 0.00 45.15 3.01
1170 1249 1.973281 CATGGCTGGCCGTGTTTCT 60.973 57.895 21.75 0.00 45.48 2.52
1198 1277 4.415501 CGCGTGCTGCTGTTCGTC 62.416 66.667 0.00 0.00 43.27 4.20
1199 1278 4.942481 TCGCGTGCTGCTGTTCGT 62.942 61.111 5.77 0.00 43.27 3.85
1200 1279 4.126390 CTCGCGTGCTGCTGTTCG 62.126 66.667 5.77 2.22 43.27 3.95
1202 1281 2.047844 ATCTCGCGTGCTGCTGTT 60.048 55.556 5.77 0.00 43.27 3.16
1203 1282 2.812609 CATCTCGCGTGCTGCTGT 60.813 61.111 5.77 0.00 43.27 4.40
1204 1283 4.219846 GCATCTCGCGTGCTGCTG 62.220 66.667 24.68 11.18 43.27 4.41
1207 1286 3.092192 CTTGGCATCTCGCGTGCTG 62.092 63.158 18.06 13.11 43.84 4.41
1208 1287 2.816958 CTTGGCATCTCGCGTGCT 60.817 61.111 18.06 0.00 43.84 4.40
1209 1288 4.527157 GCTTGGCATCTCGCGTGC 62.527 66.667 11.38 11.38 43.84 5.34
1210 1289 2.301902 GAAGCTTGGCATCTCGCGTG 62.302 60.000 2.10 3.13 43.84 5.34
1211 1290 2.046892 AAGCTTGGCATCTCGCGT 60.047 55.556 5.77 0.00 43.84 6.01
1212 1291 1.760268 GAGAAGCTTGGCATCTCGCG 61.760 60.000 2.10 0.00 42.07 5.87
1213 1292 2.013021 GAGAAGCTTGGCATCTCGC 58.987 57.895 2.10 0.00 42.07 5.03
1219 1298 0.174389 CGCTAGAGAGAAGCTTGGCA 59.826 55.000 2.10 0.00 37.85 4.92
1220 1299 0.457851 TCGCTAGAGAGAAGCTTGGC 59.542 55.000 2.10 0.00 37.85 4.52
1221 1300 3.568007 ACTATCGCTAGAGAGAAGCTTGG 59.432 47.826 2.10 0.00 37.91 3.61
1223 1302 3.004315 GCACTATCGCTAGAGAGAAGCTT 59.996 47.826 0.00 0.00 37.91 3.74
1224 1303 2.552315 GCACTATCGCTAGAGAGAAGCT 59.448 50.000 1.80 0.00 37.91 3.74
1226 1305 2.095969 CGGCACTATCGCTAGAGAGAAG 60.096 54.545 1.80 4.87 37.91 2.85
1227 1306 1.874231 CGGCACTATCGCTAGAGAGAA 59.126 52.381 1.80 0.00 37.91 2.87
1229 1308 1.069568 CACGGCACTATCGCTAGAGAG 60.070 57.143 1.80 0.00 41.25 3.20
1230 1309 0.945099 CACGGCACTATCGCTAGAGA 59.055 55.000 0.00 0.00 0.00 3.10
1231 1310 0.661780 GCACGGCACTATCGCTAGAG 60.662 60.000 0.00 0.00 0.00 2.43
1232 1311 1.359117 GCACGGCACTATCGCTAGA 59.641 57.895 0.00 0.00 0.00 2.43
1267 1346 0.831307 GTAGTCCCCCTGTAGCCTTG 59.169 60.000 0.00 0.00 0.00 3.61
1269 1348 0.717196 AAGTAGTCCCCCTGTAGCCT 59.283 55.000 0.00 0.00 0.00 4.58
1295 1374 2.437343 CGGAGAAGCTCGTCGTTGC 61.437 63.158 0.00 5.18 0.00 4.17
1297 1376 1.502640 CTCGGAGAAGCTCGTCGTT 59.497 57.895 0.00 0.00 34.09 3.85
1414 1513 2.667969 CGTGATTCGTCATCAGCAGAAA 59.332 45.455 0.95 0.00 42.98 2.52
1438 1537 3.837578 GCCAGCTGGATGGACATG 58.162 61.111 37.21 6.70 43.57 3.21
1444 1543 0.894184 GATGATGGGCCAGCTGGATG 60.894 60.000 37.21 10.80 37.39 3.51
1455 1554 4.320456 CCTCCCGGCGATGATGGG 62.320 72.222 9.30 0.00 44.75 4.00
1557 1659 3.799753 CAGTAGTGCACGATGGCC 58.200 61.111 12.01 0.00 0.00 5.36
1592 1694 1.759293 CGCCGTGCTGATCATGTGAG 61.759 60.000 0.00 0.00 0.00 3.51
1621 1732 0.684805 TTGGTTTGGCACGGTCCTTT 60.685 50.000 0.00 0.00 0.00 3.11
1626 1737 1.161563 CGTACTTGGTTTGGCACGGT 61.162 55.000 0.00 0.00 0.00 4.83
1628 1739 1.082366 GCGTACTTGGTTTGGCACG 60.082 57.895 0.00 0.00 0.00 5.34
1668 1779 2.027605 CACTGCACTGTCGTCGGT 59.972 61.111 0.00 0.00 0.00 4.69
1743 1857 1.620819 GAGCTCCAGGTTCAGTTCAGA 59.379 52.381 0.87 0.00 0.00 3.27
1795 1909 0.404040 TGACACCCACCCTCCAAATC 59.596 55.000 0.00 0.00 0.00 2.17
1808 1922 7.968956 CCGAAGTACAGTATATGATATGACACC 59.031 40.741 0.00 0.00 0.00 4.16
1809 1923 8.512956 ACCGAAGTACAGTATATGATATGACAC 58.487 37.037 0.00 0.00 0.00 3.67
1810 1924 8.631480 ACCGAAGTACAGTATATGATATGACA 57.369 34.615 0.00 0.00 0.00 3.58
1811 1925 7.903946 CGACCGAAGTACAGTATATGATATGAC 59.096 40.741 0.00 0.00 0.00 3.06
1812 1926 7.820872 TCGACCGAAGTACAGTATATGATATGA 59.179 37.037 0.00 0.00 0.00 2.15
1813 1927 7.971455 TCGACCGAAGTACAGTATATGATATG 58.029 38.462 0.00 0.00 0.00 1.78
1814 1928 8.613482 CATCGACCGAAGTACAGTATATGATAT 58.387 37.037 0.00 0.00 0.00 1.63
1815 1929 7.065443 CCATCGACCGAAGTACAGTATATGATA 59.935 40.741 0.00 0.00 0.00 2.15
1816 1930 6.127980 CCATCGACCGAAGTACAGTATATGAT 60.128 42.308 0.00 0.00 0.00 2.45
1817 1931 5.180680 CCATCGACCGAAGTACAGTATATGA 59.819 44.000 0.00 0.00 0.00 2.15
1818 1932 5.048921 ACCATCGACCGAAGTACAGTATATG 60.049 44.000 0.00 0.00 0.00 1.78
1898 2091 9.880157 TGCGTCATACATATATAGTACTAGTCA 57.120 33.333 8.85 0.00 0.00 3.41
2020 2280 7.449086 AGGAGTATTAGCCAGAGTAGTTCATAC 59.551 40.741 0.00 0.00 34.30 2.39
2021 2281 7.527796 AGGAGTATTAGCCAGAGTAGTTCATA 58.472 38.462 0.00 0.00 0.00 2.15
2022 2282 6.377912 AGGAGTATTAGCCAGAGTAGTTCAT 58.622 40.000 0.00 0.00 0.00 2.57
2034 2308 5.306114 ACAATTGGGTAGGAGTATTAGCC 57.694 43.478 10.83 0.00 38.77 3.93
2055 2329 8.247562 CCTCTACTTCTCTAATGCATGGTATAC 58.752 40.741 0.00 0.00 0.00 1.47
2230 2509 8.845227 TGTAAGTCTTTCATTTCATTGCTTACA 58.155 29.630 0.00 0.00 41.54 2.41
2317 2911 8.568794 CCTACGATCTAATAATGAGACAGTGAA 58.431 37.037 0.00 0.00 0.00 3.18
2320 2914 8.353684 CAACCTACGATCTAATAATGAGACAGT 58.646 37.037 0.00 0.00 0.00 3.55
2396 2990 2.708216 TGCTCTCCGATTGCCATTAA 57.292 45.000 0.00 0.00 0.00 1.40
2403 2997 1.332997 GAAAGGCATGCTCTCCGATTG 59.667 52.381 18.92 0.00 0.00 2.67
2414 3008 6.419980 TTTGTTTGACAAAAGAAAGGCATG 57.580 33.333 1.27 0.00 44.23 4.06
2440 3035 1.409427 CACTAACTTAGGGAGGCTCGG 59.591 57.143 8.69 0.00 0.00 4.63
2554 3497 7.868922 TGTGAAAATTTCCACAAGATCATCAAG 59.131 33.333 7.89 0.00 39.97 3.02
2570 3513 7.711772 TGACAATTCATTGAGCTGTGAAAATTT 59.288 29.630 6.53 0.00 40.14 1.82
2636 3581 0.034186 TGATGCAAAAGCCCGGAGAT 60.034 50.000 0.73 0.00 0.00 2.75
2641 3586 1.794116 CAAAAGTGATGCAAAAGCCCG 59.206 47.619 0.00 0.00 0.00 6.13
2650 3595 3.863424 CCATGATCTTGCAAAAGTGATGC 59.137 43.478 0.00 0.00 44.08 3.91
2651 3596 5.319140 TCCATGATCTTGCAAAAGTGATG 57.681 39.130 0.00 0.00 0.00 3.07
2653 3598 4.158949 CCATCCATGATCTTGCAAAAGTGA 59.841 41.667 0.00 0.00 0.00 3.41
2655 3600 4.081862 CACCATCCATGATCTTGCAAAAGT 60.082 41.667 0.00 0.00 0.00 2.66
2656 3601 4.081862 ACACCATCCATGATCTTGCAAAAG 60.082 41.667 0.00 0.00 0.00 2.27
2664 3609 6.273026 TCCAACATATACACCATCCATGATCT 59.727 38.462 0.00 0.00 0.00 2.75
2730 3675 8.358582 AGTCAAGAGAATGCCATCTTTAATTT 57.641 30.769 0.00 0.00 33.51 1.82
2731 3676 7.951347 AGTCAAGAGAATGCCATCTTTAATT 57.049 32.000 0.00 0.00 33.51 1.40
2738 3683 5.589452 AGATTGAAGTCAAGAGAATGCCATC 59.411 40.000 0.00 0.00 39.47 3.51
2820 3766 9.773328 CTTTGAATCATGTCGTAATGTAATGTT 57.227 29.630 0.00 0.00 0.00 2.71
2821 3767 9.161629 TCTTTGAATCATGTCGTAATGTAATGT 57.838 29.630 0.00 0.00 0.00 2.71
2824 3770 8.994170 TGTTCTTTGAATCATGTCGTAATGTAA 58.006 29.630 0.00 0.00 0.00 2.41
2825 3771 8.541133 TGTTCTTTGAATCATGTCGTAATGTA 57.459 30.769 0.00 0.00 0.00 2.29
2827 3773 8.900511 AATGTTCTTTGAATCATGTCGTAATG 57.099 30.769 0.00 0.00 0.00 1.90
2828 3774 8.950210 AGAATGTTCTTTGAATCATGTCGTAAT 58.050 29.630 0.00 0.00 32.55 1.89
2830 3776 7.905604 AGAATGTTCTTTGAATCATGTCGTA 57.094 32.000 0.00 0.00 32.55 3.43
2832 3778 8.229811 TGTAAGAATGTTCTTTGAATCATGTCG 58.770 33.333 12.73 0.00 44.70 4.35
2867 3813 6.093495 TGCTACAATCAACTATAACTTGTGCC 59.907 38.462 0.00 0.00 32.66 5.01
2945 3892 7.964559 CAGTGTATTGTCAACTATCCATTTGTG 59.035 37.037 0.00 0.00 0.00 3.33
2946 3893 7.665559 ACAGTGTATTGTCAACTATCCATTTGT 59.334 33.333 0.00 0.00 0.00 2.83
2947 3894 8.044060 ACAGTGTATTGTCAACTATCCATTTG 57.956 34.615 0.00 0.00 0.00 2.32
2948 3895 8.268850 GACAGTGTATTGTCAACTATCCATTT 57.731 34.615 0.00 0.00 45.32 2.32
2949 3896 7.849804 GACAGTGTATTGTCAACTATCCATT 57.150 36.000 0.00 0.00 45.32 3.16
2968 3915 2.925724 AGCGAGCTAGATACAGACAGT 58.074 47.619 0.00 0.00 0.00 3.55
2969 3916 4.513692 AGTTAGCGAGCTAGATACAGACAG 59.486 45.833 4.91 0.00 0.00 3.51
2997 3944 7.551617 GGCAAGTTGCTAAAGGAATAAGTACTA 59.448 37.037 26.16 0.00 44.28 1.82
2999 3946 6.150474 TGGCAAGTTGCTAAAGGAATAAGTAC 59.850 38.462 26.16 5.36 44.28 2.73
3009 3956 8.438676 AAGTATATACTGGCAAGTTGCTAAAG 57.561 34.615 26.16 21.50 38.44 1.85
3016 3963 6.841755 AGAGGAGAAGTATATACTGGCAAGTT 59.158 38.462 16.11 0.00 37.88 2.66
3043 3990 4.394300 GCTCTTACTTCACGTACTACTCCA 59.606 45.833 0.00 0.00 0.00 3.86
3101 4048 2.033602 TCCGAGCAGTCCGTCAGA 59.966 61.111 0.00 0.00 0.00 3.27
3102 4049 2.179517 GTCCGAGCAGTCCGTCAG 59.820 66.667 0.00 0.00 0.00 3.51
3103 4050 2.596338 TGTCCGAGCAGTCCGTCA 60.596 61.111 0.00 0.00 0.00 4.35
3130 4077 3.280295 TCGTTAGGGTTGTCTTTTTGCA 58.720 40.909 0.00 0.00 0.00 4.08
3141 4088 0.694771 GGGAAGGGTTCGTTAGGGTT 59.305 55.000 0.00 0.00 0.00 4.11
3157 4104 2.301009 GACGTTTAGGAAGGAAGTGGGA 59.699 50.000 0.00 0.00 0.00 4.37
3167 4114 1.294138 CAGCCCGGACGTTTAGGAA 59.706 57.895 0.73 0.00 0.00 3.36
3237 4184 1.470979 CGTGACGTGCCTAGGCTTATT 60.471 52.381 33.07 15.58 42.51 1.40
3239 4186 1.509463 CGTGACGTGCCTAGGCTTA 59.491 57.895 33.07 12.84 42.51 3.09


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

AutoCloner maintained by Alex Coulton.