Multiple sequence alignment - TraesCS2A01G355400

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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 TraesCS2A01G355400 chr2A 100.000 3307 0 0 1 3307 598163492 598160186 0.000000e+00 6107
1 TraesCS2A01G355400 chr2D 95.243 1892 64 15 644 2528 451287332 451289204 0.000000e+00 2972
2 TraesCS2A01G355400 chr2D 88.362 464 34 13 2853 3307 451289929 451290381 1.040000e-149 540
3 TraesCS2A01G355400 chr2D 85.268 448 26 15 1 429 451286659 451287085 3.050000e-115 425
4 TraesCS2A01G355400 chr2D 89.809 157 14 2 2606 2761 451289638 451289793 2.010000e-47 200
5 TraesCS2A01G355400 chr2D 94.737 76 4 0 2528 2603 451289379 451289454 5.800000e-23 119
6 TraesCS2A01G355400 chr2B 93.918 1447 69 10 1088 2528 531466674 531468107 0.000000e+00 2167
7 TraesCS2A01G355400 chr2B 93.069 404 12 9 659 1055 531466279 531466673 7.960000e-161 577
8 TraesCS2A01G355400 chr2B 91.576 368 12 6 1 354 531465590 531465952 1.070000e-134 490
9 TraesCS2A01G355400 chr2B 80.556 504 43 31 2595 3046 531468223 531468723 1.470000e-88 337
10 TraesCS2A01G355400 chr6B 80.463 993 188 6 1143 2132 446836288 446837277 0.000000e+00 754
11 TraesCS2A01G355400 chr5D 77.929 879 184 10 1150 2023 336223171 336224044 1.040000e-149 540
12 TraesCS2A01G355400 chr5B 77.542 895 193 8 1133 2023 394266448 394267338 1.750000e-147 532


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 TraesCS2A01G355400 chr2A 598160186 598163492 3306 True 6107.00 6107 100.00000 1 3307 1 chr2A.!!$R1 3306
1 TraesCS2A01G355400 chr2D 451286659 451290381 3722 False 851.20 2972 90.68380 1 3307 5 chr2D.!!$F1 3306
2 TraesCS2A01G355400 chr2B 531465590 531468723 3133 False 892.75 2167 89.77975 1 3046 4 chr2B.!!$F1 3045
3 TraesCS2A01G355400 chr6B 446836288 446837277 989 False 754.00 754 80.46300 1143 2132 1 chr6B.!!$F1 989
4 TraesCS2A01G355400 chr5D 336223171 336224044 873 False 540.00 540 77.92900 1150 2023 1 chr5D.!!$F1 873
5 TraesCS2A01G355400 chr5B 394266448 394267338 890 False 532.00 532 77.54200 1133 2023 1 chr5B.!!$F1 890

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
551 652 0.040425 ATGGCGCTTGTTCGTTGTTC 60.040 50.0 7.64 0.0 0.0 3.18 F
1117 1224 0.099259 CTGCTCTGCTCTCTGACTCG 59.901 60.0 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1895 0.684479 CACAGACCTCCATCTCGGGA 60.684 60.0 0.00 0.00 34.36 5.14 R
2603 2919 0.317020 CTGCGCGTACGAGATGATCA 60.317 55.0 23.53 9.42 43.93 2.92 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
66 67 1.413382 CGCCGCAGCTAGATAAGAAG 58.587 55.000 0.00 0.00 36.60 2.85
121 122 1.744114 CGAGATCTGTGTCGGGAGAGA 60.744 57.143 0.00 0.00 41.26 3.10
222 223 0.106419 AGTTTCTTCGGCCAACCCAA 60.106 50.000 2.24 0.00 0.00 4.12
246 247 7.978099 AATAATTCCCCATCCTTATTATGCC 57.022 36.000 0.00 0.00 0.00 4.40
267 268 1.066303 GCGGTAGTCTGTGGATCTCTG 59.934 57.143 0.00 0.00 0.00 3.35
269 270 1.410882 GGTAGTCTGTGGATCTCTGGC 59.589 57.143 0.00 0.00 0.00 4.85
285 286 2.012673 CTGGCTTCTAGGTCATGTTGC 58.987 52.381 0.00 0.00 0.00 4.17
340 354 6.704050 GCTAGTTTCTGTAGGAGAATTGATCC 59.296 42.308 0.00 0.00 40.53 3.36
362 386 6.582636 TCCTTGGTATAGTAGTTTGCATCTG 58.417 40.000 0.00 0.00 0.00 2.90
372 396 2.019984 GTTTGCATCTGGATCTGGGAC 58.980 52.381 0.00 0.00 0.00 4.46
375 399 0.179000 GCATCTGGATCTGGGACGTT 59.821 55.000 0.00 0.00 0.00 3.99
382 424 3.821033 CTGGATCTGGGACGTTTTCTTTT 59.179 43.478 0.00 0.00 0.00 2.27
385 427 5.221762 TGGATCTGGGACGTTTTCTTTTAGA 60.222 40.000 0.00 0.00 0.00 2.10
391 433 6.177610 TGGGACGTTTTCTTTTAGATATGCT 58.822 36.000 0.00 0.00 0.00 3.79
392 434 6.315393 TGGGACGTTTTCTTTTAGATATGCTC 59.685 38.462 0.00 0.00 0.00 4.26
393 435 6.315393 GGGACGTTTTCTTTTAGATATGCTCA 59.685 38.462 0.00 0.00 0.00 4.26
394 436 7.012421 GGGACGTTTTCTTTTAGATATGCTCAT 59.988 37.037 0.00 0.00 0.00 2.90
395 437 9.042008 GGACGTTTTCTTTTAGATATGCTCATA 57.958 33.333 0.00 0.00 0.00 2.15
398 440 9.322776 CGTTTTCTTTTAGATATGCTCATATGC 57.677 33.333 7.08 0.00 34.36 3.14
399 441 9.617975 GTTTTCTTTTAGATATGCTCATATGCC 57.382 33.333 7.08 0.00 34.36 4.40
400 442 9.578576 TTTTCTTTTAGATATGCTCATATGCCT 57.421 29.630 7.08 2.66 34.36 4.75
402 444 7.108194 TCTTTTAGATATGCTCATATGCCTGG 58.892 38.462 7.08 0.00 34.36 4.45
408 450 1.341285 TGCTCATATGCCTGGTTGCTT 60.341 47.619 0.00 0.00 0.00 3.91
416 458 2.500229 TGCCTGGTTGCTTGTAGTTAC 58.500 47.619 0.00 0.00 0.00 2.50
418 460 3.325425 TGCCTGGTTGCTTGTAGTTACTA 59.675 43.478 0.00 0.00 0.00 1.82
429 471 8.610248 TGCTTGTAGTTACTATTGTTTTGCTA 57.390 30.769 0.00 0.00 0.00 3.49
433 475 8.997621 TGTAGTTACTATTGTTTTGCTAGAGG 57.002 34.615 0.00 0.00 0.00 3.69
435 477 9.649167 GTAGTTACTATTGTTTTGCTAGAGGAA 57.351 33.333 0.00 0.00 0.00 3.36
436 478 8.779354 AGTTACTATTGTTTTGCTAGAGGAAG 57.221 34.615 0.00 0.00 0.00 3.46
438 480 8.657729 GTTACTATTGTTTTGCTAGAGGAAGTC 58.342 37.037 0.00 0.00 0.00 3.01
439 481 5.869888 ACTATTGTTTTGCTAGAGGAAGTCG 59.130 40.000 0.00 0.00 0.00 4.18
440 482 4.330944 TTGTTTTGCTAGAGGAAGTCGA 57.669 40.909 0.00 0.00 0.00 4.20
441 483 4.330944 TGTTTTGCTAGAGGAAGTCGAA 57.669 40.909 0.00 0.00 0.00 3.71
442 484 4.699637 TGTTTTGCTAGAGGAAGTCGAAA 58.300 39.130 0.00 0.00 0.00 3.46
443 485 5.305585 TGTTTTGCTAGAGGAAGTCGAAAT 58.694 37.500 0.00 0.00 0.00 2.17
445 487 3.802948 TGCTAGAGGAAGTCGAAATCC 57.197 47.619 9.24 9.24 35.88 3.01
446 488 3.096852 TGCTAGAGGAAGTCGAAATCCA 58.903 45.455 17.40 0.00 38.23 3.41
447 489 3.131223 TGCTAGAGGAAGTCGAAATCCAG 59.869 47.826 17.40 9.03 38.23 3.86
448 490 2.682155 AGAGGAAGTCGAAATCCAGC 57.318 50.000 17.40 10.21 38.23 4.85
449 491 1.134965 AGAGGAAGTCGAAATCCAGCG 60.135 52.381 17.40 0.00 38.23 5.18
450 492 0.608640 AGGAAGTCGAAATCCAGCGT 59.391 50.000 17.40 0.00 38.23 5.07
451 493 1.000145 GGAAGTCGAAATCCAGCGTC 59.000 55.000 11.81 0.00 35.71 5.19
452 494 0.640768 GAAGTCGAAATCCAGCGTCG 59.359 55.000 0.00 0.00 36.12 5.12
453 495 0.242825 AAGTCGAAATCCAGCGTCGA 59.757 50.000 0.00 0.00 41.22 4.20
454 496 0.242825 AGTCGAAATCCAGCGTCGAA 59.757 50.000 0.00 0.00 44.64 3.71
455 497 1.065358 GTCGAAATCCAGCGTCGAAA 58.935 50.000 0.00 0.00 44.64 3.46
456 498 1.458064 GTCGAAATCCAGCGTCGAAAA 59.542 47.619 0.00 0.00 44.64 2.29
457 499 1.724623 TCGAAATCCAGCGTCGAAAAG 59.275 47.619 0.00 0.00 40.59 2.27
458 500 1.786928 CGAAATCCAGCGTCGAAAAGC 60.787 52.381 0.00 0.00 36.92 3.51
459 501 1.464997 GAAATCCAGCGTCGAAAAGCT 59.535 47.619 0.00 5.60 45.74 3.74
460 502 1.523758 AATCCAGCGTCGAAAAGCTT 58.476 45.000 8.35 0.00 42.52 3.74
461 503 1.523758 ATCCAGCGTCGAAAAGCTTT 58.476 45.000 5.69 5.69 42.52 3.51
462 504 1.305201 TCCAGCGTCGAAAAGCTTTT 58.695 45.000 24.08 24.08 42.52 2.27
463 505 1.002900 TCCAGCGTCGAAAAGCTTTTG 60.003 47.619 28.42 19.09 42.52 2.44
464 506 1.002900 CCAGCGTCGAAAAGCTTTTGA 60.003 47.619 28.42 20.84 42.52 2.69
477 577 8.672405 CGAAAAGCTTTTGAAATTAAATTGTGC 58.328 29.630 28.42 7.49 0.00 4.57
511 612 9.857656 ATTTTAATCTTGAATCTGCTCCTATCA 57.142 29.630 0.00 0.00 0.00 2.15
512 613 9.857656 TTTTAATCTTGAATCTGCTCCTATCAT 57.142 29.630 0.00 0.00 0.00 2.45
513 614 9.499479 TTTAATCTTGAATCTGCTCCTATCATC 57.501 33.333 0.00 0.00 0.00 2.92
514 615 6.683312 ATCTTGAATCTGCTCCTATCATCA 57.317 37.500 0.00 0.00 0.00 3.07
515 616 6.490241 TCTTGAATCTGCTCCTATCATCAA 57.510 37.500 0.00 0.00 0.00 2.57
516 617 6.522946 TCTTGAATCTGCTCCTATCATCAAG 58.477 40.000 0.00 0.00 42.25 3.02
517 618 5.883685 TGAATCTGCTCCTATCATCAAGT 57.116 39.130 0.00 0.00 0.00 3.16
518 619 5.851720 TGAATCTGCTCCTATCATCAAGTC 58.148 41.667 0.00 0.00 0.00 3.01
520 621 4.662468 TCTGCTCCTATCATCAAGTCAC 57.338 45.455 0.00 0.00 0.00 3.67
521 622 4.285020 TCTGCTCCTATCATCAAGTCACT 58.715 43.478 0.00 0.00 0.00 3.41
523 624 5.893824 TCTGCTCCTATCATCAAGTCACTTA 59.106 40.000 0.00 0.00 0.00 2.24
524 625 6.381133 TCTGCTCCTATCATCAAGTCACTTAA 59.619 38.462 0.00 0.00 0.00 1.85
525 626 6.577103 TGCTCCTATCATCAAGTCACTTAAG 58.423 40.000 0.00 0.00 0.00 1.85
526 627 6.155221 TGCTCCTATCATCAAGTCACTTAAGT 59.845 38.462 1.12 1.12 0.00 2.24
528 629 7.223777 GCTCCTATCATCAAGTCACTTAAGTTC 59.776 40.741 5.07 2.45 0.00 3.01
531 632 5.209818 TCATCAAGTCACTTAAGTTCCGT 57.790 39.130 5.07 0.00 0.00 4.69
532 633 6.335471 TCATCAAGTCACTTAAGTTCCGTA 57.665 37.500 5.07 0.00 0.00 4.02
533 634 6.931838 TCATCAAGTCACTTAAGTTCCGTAT 58.068 36.000 5.07 0.00 0.00 3.06
534 635 6.811665 TCATCAAGTCACTTAAGTTCCGTATG 59.188 38.462 5.07 6.37 0.00 2.39
535 636 5.475719 TCAAGTCACTTAAGTTCCGTATGG 58.524 41.667 5.07 0.00 0.00 2.74
537 638 2.601763 GTCACTTAAGTTCCGTATGGCG 59.398 50.000 5.07 0.00 40.95 5.69
538 639 1.326548 CACTTAAGTTCCGTATGGCGC 59.673 52.381 5.07 0.00 39.71 6.53
539 640 1.206371 ACTTAAGTTCCGTATGGCGCT 59.794 47.619 7.64 0.00 39.71 5.92
547 648 1.632046 CCGTATGGCGCTTGTTCGTT 61.632 55.000 7.64 0.00 39.71 3.85
551 652 0.040425 ATGGCGCTTGTTCGTTGTTC 60.040 50.000 7.64 0.00 0.00 3.18
552 653 1.721133 GGCGCTTGTTCGTTGTTCG 60.721 57.895 7.64 0.00 41.41 3.95
569 670 8.661257 TCGTTGTTCGATTTTACAATATGATGT 58.339 29.630 3.88 0.00 44.01 3.06
570 671 8.933955 CGTTGTTCGATTTTACAATATGATGTC 58.066 33.333 3.88 0.00 42.86 3.06
571 672 9.221775 GTTGTTCGATTTTACAATATGATGTCC 57.778 33.333 3.88 0.00 36.72 4.02
575 676 5.049749 CGATTTTACAATATGATGTCCGGCA 60.050 40.000 0.00 0.00 34.75 5.69
585 686 4.143986 TGATGTCCGGCATGTTATGTTA 57.856 40.909 14.84 0.00 38.06 2.41
586 687 4.518249 TGATGTCCGGCATGTTATGTTAA 58.482 39.130 14.84 0.00 38.06 2.01
587 688 4.334203 TGATGTCCGGCATGTTATGTTAAC 59.666 41.667 14.84 0.00 38.06 2.01
590 691 3.630312 GTCCGGCATGTTATGTTAACCAT 59.370 43.478 2.48 0.00 37.58 3.55
592 693 3.303725 CCGGCATGTTATGTTAACCATCG 60.304 47.826 2.48 0.88 34.86 3.84
593 694 3.558006 CGGCATGTTATGTTAACCATCGA 59.442 43.478 2.48 0.00 34.86 3.59
594 695 4.034626 CGGCATGTTATGTTAACCATCGAA 59.965 41.667 2.48 0.00 34.86 3.71
595 696 5.277779 CGGCATGTTATGTTAACCATCGAAT 60.278 40.000 2.48 0.00 34.86 3.34
596 697 6.073494 CGGCATGTTATGTTAACCATCGAATA 60.073 38.462 2.48 0.00 34.86 1.75
597 698 7.519168 CGGCATGTTATGTTAACCATCGAATAA 60.519 37.037 2.48 0.00 34.86 1.40
599 700 9.677567 GCATGTTATGTTAACCATCGAATAATT 57.322 29.630 2.48 0.00 34.86 1.40
635 736 9.744468 AAGAAAATAACTGCATAGAAACGTTTT 57.256 25.926 15.89 7.85 0.00 2.43
637 738 9.176181 GAAAATAACTGCATAGAAACGTTTTCA 57.824 29.630 15.89 6.48 34.04 2.69
642 743 7.435068 ACTGCATAGAAACGTTTTCATAGTT 57.565 32.000 15.89 0.00 0.00 2.24
643 744 8.542497 ACTGCATAGAAACGTTTTCATAGTTA 57.458 30.769 15.89 0.88 0.00 2.24
644 745 9.162764 ACTGCATAGAAACGTTTTCATAGTTAT 57.837 29.630 15.89 3.01 0.00 1.89
645 746 9.638300 CTGCATAGAAACGTTTTCATAGTTATC 57.362 33.333 15.89 0.00 0.00 1.75
646 747 9.378551 TGCATAGAAACGTTTTCATAGTTATCT 57.621 29.630 15.89 6.04 0.00 1.98
650 751 8.421673 AGAAACGTTTTCATAGTTATCTAGCC 57.578 34.615 15.89 0.00 0.00 3.93
651 752 8.038944 AGAAACGTTTTCATAGTTATCTAGCCA 58.961 33.333 15.89 0.00 0.00 4.75
652 753 8.732746 AAACGTTTTCATAGTTATCTAGCCAT 57.267 30.769 7.96 0.00 0.00 4.40
653 754 7.715265 ACGTTTTCATAGTTATCTAGCCATG 57.285 36.000 0.00 0.00 0.00 3.66
654 755 7.497595 ACGTTTTCATAGTTATCTAGCCATGA 58.502 34.615 0.00 0.00 0.00 3.07
655 756 7.985184 ACGTTTTCATAGTTATCTAGCCATGAA 59.015 33.333 0.00 0.00 0.00 2.57
656 757 8.826710 CGTTTTCATAGTTATCTAGCCATGAAA 58.173 33.333 0.00 0.00 33.46 2.69
668 769 4.773323 AGCCATGAAAGTTTGCTAGAAC 57.227 40.909 0.00 0.00 0.00 3.01
672 773 4.479619 CATGAAAGTTTGCTAGAACCTGC 58.520 43.478 0.00 0.00 0.00 4.85
688 789 1.630878 CCTGCTGTCTAACCCCTCTTT 59.369 52.381 0.00 0.00 0.00 2.52
691 792 2.979678 TGCTGTCTAACCCCTCTTTTCT 59.020 45.455 0.00 0.00 0.00 2.52
692 793 3.008049 TGCTGTCTAACCCCTCTTTTCTC 59.992 47.826 0.00 0.00 0.00 2.87
693 794 3.851098 CTGTCTAACCCCTCTTTTCTCG 58.149 50.000 0.00 0.00 0.00 4.04
697 798 4.689812 GTCTAACCCCTCTTTTCTCGTTTC 59.310 45.833 0.00 0.00 0.00 2.78
773 874 1.899814 AGTTCCCTGATGTACGAAGCA 59.100 47.619 0.00 0.00 0.00 3.91
853 954 3.795826 GCTGCATACTCGAACGTAAGGAT 60.796 47.826 0.00 0.00 46.39 3.24
854 955 3.961182 TGCATACTCGAACGTAAGGATC 58.039 45.455 0.00 0.00 46.39 3.36
856 957 3.729716 GCATACTCGAACGTAAGGATCAC 59.270 47.826 0.00 0.00 46.39 3.06
857 958 2.539346 ACTCGAACGTAAGGATCACG 57.461 50.000 2.79 2.79 44.80 4.35
858 959 1.131883 ACTCGAACGTAAGGATCACGG 59.868 52.381 8.68 0.00 43.59 4.94
859 960 1.399440 CTCGAACGTAAGGATCACGGA 59.601 52.381 8.68 0.00 43.59 4.69
861 962 1.542544 GAACGTAAGGATCACGGACG 58.457 55.000 8.68 7.80 43.59 4.79
865 966 1.916000 CGTAAGGATCACGGACGAAAC 59.084 52.381 0.00 0.00 35.78 2.78
866 967 2.669113 CGTAAGGATCACGGACGAAACA 60.669 50.000 0.00 0.00 35.78 2.83
867 968 2.762535 AAGGATCACGGACGAAACAT 57.237 45.000 0.00 0.00 0.00 2.71
868 969 2.295253 AGGATCACGGACGAAACATC 57.705 50.000 0.00 0.00 0.00 3.06
869 970 1.548719 AGGATCACGGACGAAACATCA 59.451 47.619 0.00 0.00 0.00 3.07
888 989 5.069648 ACATCAGAGTCTCACTTCTGTTCAA 59.930 40.000 1.94 0.00 30.63 2.69
924 1025 5.278907 CCAGATTTGTTGCTAACCATGTGAA 60.279 40.000 0.00 0.00 0.00 3.18
925 1026 6.392354 CAGATTTGTTGCTAACCATGTGAAT 58.608 36.000 0.00 0.00 0.00 2.57
928 1029 6.841443 TTTGTTGCTAACCATGTGAATTTG 57.159 33.333 0.00 0.00 0.00 2.32
982 1089 1.203001 TCGTTTTTGGCATCCCCTTCT 60.203 47.619 0.00 0.00 0.00 2.85
1081 1188 5.986501 AATCGACCAGTTCTCTAGTCTTT 57.013 39.130 0.00 0.00 31.83 2.52
1108 1215 0.894141 TGTTCCTCTCTGCTCTGCTC 59.106 55.000 0.00 0.00 0.00 4.26
1117 1224 0.099259 CTGCTCTGCTCTCTGACTCG 59.901 60.000 0.00 0.00 0.00 4.18
1322 1430 1.343465 TCCAACAAGGACTTCGACTCC 59.657 52.381 0.58 0.58 43.07 3.85
1731 1839 6.596309 TCTTCTTCAAGACTCAAGCTGATA 57.404 37.500 0.00 0.00 33.38 2.15
1778 1886 2.364002 GACCAAGCTCTCTGGTATCTCC 59.636 54.545 8.57 0.00 35.85 3.71
1787 1895 4.474394 TCTCTGGTATCTCCGACATCATT 58.526 43.478 0.00 0.00 39.52 2.57
1999 2107 0.392327 GGCCCTTCAGAGTTCTCTGC 60.392 60.000 20.92 11.34 37.63 4.26
2133 2241 3.632604 CGTCCTCATCTACCAGAGCTTTA 59.367 47.826 0.00 0.00 0.00 1.85
2137 2245 3.362706 TCATCTACCAGAGCTTTACCGT 58.637 45.455 0.00 0.00 0.00 4.83
2210 2318 2.433318 GAGGCCGAGAGTGTGCAC 60.433 66.667 10.75 10.75 0.00 4.57
2282 2390 1.781786 CGGAGGAGGATTCTCTGGAA 58.218 55.000 0.00 0.00 39.86 3.53
2307 2415 2.661537 CGGTGCTGTGCGAGTGAA 60.662 61.111 0.00 0.00 0.00 3.18
2308 2416 2.661566 CGGTGCTGTGCGAGTGAAG 61.662 63.158 0.00 0.00 0.00 3.02
2309 2417 1.300931 GGTGCTGTGCGAGTGAAGA 60.301 57.895 0.00 0.00 0.00 2.87
2310 2418 1.560860 GGTGCTGTGCGAGTGAAGAC 61.561 60.000 0.00 0.00 0.00 3.01
2311 2419 0.875908 GTGCTGTGCGAGTGAAGACA 60.876 55.000 0.00 0.00 0.00 3.41
2312 2420 0.033920 TGCTGTGCGAGTGAAGACAT 59.966 50.000 0.00 0.00 0.00 3.06
2313 2421 0.441533 GCTGTGCGAGTGAAGACATG 59.558 55.000 0.00 0.00 0.00 3.21
2314 2422 1.936656 GCTGTGCGAGTGAAGACATGA 60.937 52.381 0.00 0.00 0.00 3.07
2327 2436 3.251479 AGACATGATTTGCTGTCGCTA 57.749 42.857 0.00 0.00 45.08 4.26
2332 2441 2.984562 TGATTTGCTGTCGCTATTCCA 58.015 42.857 0.00 0.00 36.97 3.53
2356 2465 4.816385 TCTGTGGAATTTGTTCTGACTGTC 59.184 41.667 0.00 0.00 0.00 3.51
2471 2585 0.803117 GCGTACTTCTGGGGAAAAGC 59.197 55.000 0.00 0.00 0.00 3.51
2478 2592 0.321671 TCTGGGGAAAAGCTGTCTCG 59.678 55.000 0.00 0.00 0.00 4.04
2575 2891 0.304705 GTGTGTTGACAAGCGACCAG 59.695 55.000 0.00 0.00 32.49 4.00
2592 2908 1.171308 CAGTGTGCTCATTTCCCCTG 58.829 55.000 0.00 0.00 0.00 4.45
2603 2919 2.286935 TTTCCCCTGGCCTATCTTCT 57.713 50.000 3.32 0.00 0.00 2.85
2631 3128 1.135315 TCGTACGCGCAGGAATAAACT 60.135 47.619 11.24 0.00 38.14 2.66
2640 3138 2.536365 CAGGAATAAACTACTGCGCGA 58.464 47.619 12.10 0.00 0.00 5.87
2649 3147 1.475280 ACTACTGCGCGAGGAATACAA 59.525 47.619 12.10 0.00 0.00 2.41
2652 3150 1.079474 TGCGCGAGGAATACAAGCA 60.079 52.632 12.10 0.00 0.00 3.91
2658 3156 2.351726 GCGAGGAATACAAGCACGAATT 59.648 45.455 0.00 0.00 0.00 2.17
2659 3157 3.785505 GCGAGGAATACAAGCACGAATTG 60.786 47.826 0.00 0.00 0.00 2.32
2668 3166 8.452989 AATACAAGCACGAATTGATTCTTTTC 57.547 30.769 0.00 0.00 28.74 2.29
2671 3169 6.638468 ACAAGCACGAATTGATTCTTTTCTTC 59.362 34.615 0.00 0.00 28.74 2.87
2721 3219 7.865820 TCATCCTTATCTTCCTTGTTTCTGAT 58.134 34.615 0.00 0.00 0.00 2.90
2723 3221 6.653989 TCCTTATCTTCCTTGTTTCTGATCC 58.346 40.000 0.00 0.00 0.00 3.36
2815 3367 6.749118 GTGAGTTATTGGGTGTAGTAGTAACG 59.251 42.308 0.00 0.00 0.00 3.18
2850 3403 1.263217 CTTTTGACAACGGAGGTTCGG 59.737 52.381 0.00 0.00 32.98 4.30
2857 3428 0.171903 AACGGAGGTTCGGTCGTATG 59.828 55.000 0.00 0.00 35.26 2.39
2865 3436 4.679662 AGGTTCGGTCGTATGTAATCTTG 58.320 43.478 0.00 0.00 0.00 3.02
2887 3458 3.243267 GGGCGTAAAAAGTGAAAGAGCAA 60.243 43.478 0.00 0.00 0.00 3.91
2888 3459 4.546570 GGCGTAAAAAGTGAAAGAGCAAT 58.453 39.130 0.00 0.00 0.00 3.56
2917 3493 6.653320 AGTTGTTGCGTATCTAATCTTTTGGA 59.347 34.615 0.00 0.00 0.00 3.53
2963 3540 1.222115 GACCCGTCGCCAAGATATGC 61.222 60.000 0.00 0.00 0.00 3.14
3046 3624 5.228945 ACTGTATTTAGGCTTGCCGATAT 57.771 39.130 5.95 4.66 0.00 1.63
3047 3625 4.997395 ACTGTATTTAGGCTTGCCGATATG 59.003 41.667 5.95 6.58 0.00 1.78
3078 3658 2.652496 GCGCCGACTCTCATCGTC 60.652 66.667 0.00 0.00 40.59 4.20
3087 3667 3.067106 GACTCTCATCGTCCAAAGCAAA 58.933 45.455 0.00 0.00 0.00 3.68
3092 3672 2.053627 CATCGTCCAAAGCAAAGCAAC 58.946 47.619 0.00 0.00 0.00 4.17
3110 3690 2.502213 ACTTTTTACAACCAAGCCGC 57.498 45.000 0.00 0.00 0.00 6.53
3127 3707 2.358737 CCTTGTTTCTCGCCGGCT 60.359 61.111 26.68 0.00 0.00 5.52
3134 3714 2.406002 TTTCTCGCCGGCTCCCTTTT 62.406 55.000 26.68 0.00 0.00 2.27
3135 3715 2.798148 TTCTCGCCGGCTCCCTTTTC 62.798 60.000 26.68 0.00 0.00 2.29
3174 3754 2.400269 AAAAGGCCGGCCGTCTTGTA 62.400 55.000 38.88 0.00 41.95 2.41
3175 3755 2.798148 AAAGGCCGGCCGTCTTGTAG 62.798 60.000 38.88 7.77 41.95 2.74
3177 3757 2.713967 GGCCGGCCGTCTTGTAGTA 61.714 63.158 33.60 0.00 0.00 1.82
3178 3758 1.226888 GCCGGCCGTCTTGTAGTAG 60.227 63.158 26.12 5.27 0.00 2.57
3179 3759 1.941999 GCCGGCCGTCTTGTAGTAGT 61.942 60.000 26.12 0.00 0.00 2.73
3180 3760 1.382522 CCGGCCGTCTTGTAGTAGTA 58.617 55.000 26.12 0.00 0.00 1.82
3181 3761 1.952296 CCGGCCGTCTTGTAGTAGTAT 59.048 52.381 26.12 0.00 0.00 2.12
3182 3762 2.360165 CCGGCCGTCTTGTAGTAGTATT 59.640 50.000 26.12 0.00 0.00 1.89
3183 3763 3.565482 CCGGCCGTCTTGTAGTAGTATTA 59.435 47.826 26.12 0.00 0.00 0.98
3184 3764 4.217118 CCGGCCGTCTTGTAGTAGTATTAT 59.783 45.833 26.12 0.00 0.00 1.28
3185 3765 5.278660 CCGGCCGTCTTGTAGTAGTATTATT 60.279 44.000 26.12 0.00 0.00 1.40
3186 3766 5.628193 CGGCCGTCTTGTAGTAGTATTATTG 59.372 44.000 19.50 0.00 0.00 1.90
3226 3806 1.005569 AGGCATCTCCCATGGCATATG 59.994 52.381 6.09 9.90 45.66 1.78
3229 3809 0.986527 ATCTCCCATGGCATATGCGA 59.013 50.000 21.04 18.18 43.26 5.10
3230 3810 0.035317 TCTCCCATGGCATATGCGAC 59.965 55.000 21.04 9.18 43.26 5.19
3232 3812 0.250424 TCCCATGGCATATGCGACAG 60.250 55.000 21.04 13.21 43.26 3.51
3234 3814 1.311859 CCATGGCATATGCGACAGTT 58.688 50.000 21.04 0.00 43.26 3.16
3239 3819 2.677836 TGGCATATGCGACAGTTTCTTC 59.322 45.455 21.04 3.63 43.26 2.87
3247 3827 2.221981 GCGACAGTTTCTTCTTCACCAG 59.778 50.000 0.00 0.00 0.00 4.00
3268 3848 6.155136 CCAGCCAAAGAAATTTCTCTCTTTC 58.845 40.000 20.71 8.61 39.34 2.62
3269 3849 6.239120 CCAGCCAAAGAAATTTCTCTCTTTCA 60.239 38.462 20.71 0.00 39.34 2.69
3285 3866 5.243954 TCTCTTTCATCTCCTCTCGTTTTCA 59.756 40.000 0.00 0.00 0.00 2.69
3288 3869 6.936900 TCTTTCATCTCCTCTCGTTTTCATTT 59.063 34.615 0.00 0.00 0.00 2.32
3294 3875 4.133820 TCCTCTCGTTTTCATTTGCAGAA 58.866 39.130 0.00 0.00 0.00 3.02
3296 3877 4.676924 CCTCTCGTTTTCATTTGCAGAAAC 59.323 41.667 0.00 1.69 34.94 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.363711 TTATCTAGCTGCGGCGGTGG 62.364 60.000 12.87 5.93 44.37 4.61
48 49 2.802787 TCTTCTTATCTAGCTGCGGC 57.197 50.000 10.33 10.33 39.06 6.53
72 73 2.745281 CCGACGAGTTCTTCTCTCTCTT 59.255 50.000 0.00 0.00 40.75 2.85
121 122 4.502259 CGATTCCGATCTCAAGAATTCCCT 60.502 45.833 0.65 0.00 38.22 4.20
222 223 6.607198 CGGCATAATAAGGATGGGGAATTATT 59.393 38.462 0.00 0.00 33.59 1.40
246 247 0.029567 GAGATCCACAGACTACCGCG 59.970 60.000 0.00 0.00 0.00 6.46
267 268 2.012673 CAGCAACATGACCTAGAAGCC 58.987 52.381 0.00 0.00 0.00 4.35
269 270 2.417933 GCACAGCAACATGACCTAGAAG 59.582 50.000 0.00 0.00 0.00 2.85
285 286 3.857052 TCATACGGTAAAAGGAGCACAG 58.143 45.455 0.00 0.00 0.00 3.66
340 354 6.582636 TCCAGATGCAAACTACTATACCAAG 58.417 40.000 0.00 0.00 0.00 3.61
341 355 6.553953 TCCAGATGCAAACTACTATACCAA 57.446 37.500 0.00 0.00 0.00 3.67
362 386 5.243207 TCTAAAAGAAAACGTCCCAGATCC 58.757 41.667 0.00 0.00 0.00 3.36
372 396 9.322776 GCATATGAGCATATCTAAAAGAAAACG 57.677 33.333 6.97 0.00 31.98 3.60
375 399 9.006839 CAGGCATATGAGCATATCTAAAAGAAA 57.993 33.333 6.97 0.00 31.98 2.52
382 424 5.737860 CAACCAGGCATATGAGCATATCTA 58.262 41.667 6.97 0.00 31.98 1.98
385 427 3.087031 GCAACCAGGCATATGAGCATAT 58.913 45.455 6.97 0.00 34.50 1.78
391 433 2.512692 ACAAGCAACCAGGCATATGA 57.487 45.000 6.97 0.00 35.83 2.15
392 434 3.282021 ACTACAAGCAACCAGGCATATG 58.718 45.455 0.00 0.00 35.83 1.78
393 435 3.652057 ACTACAAGCAACCAGGCATAT 57.348 42.857 0.00 0.00 35.83 1.78
394 436 3.433306 AACTACAAGCAACCAGGCATA 57.567 42.857 0.00 0.00 35.83 3.14
395 437 2.292828 AACTACAAGCAACCAGGCAT 57.707 45.000 0.00 0.00 35.83 4.40
396 438 2.105821 AGTAACTACAAGCAACCAGGCA 59.894 45.455 0.00 0.00 35.83 4.75
398 440 5.938125 ACAATAGTAACTACAAGCAACCAGG 59.062 40.000 0.00 0.00 0.00 4.45
399 441 7.435068 AACAATAGTAACTACAAGCAACCAG 57.565 36.000 0.00 0.00 0.00 4.00
400 442 7.811117 AAACAATAGTAACTACAAGCAACCA 57.189 32.000 0.00 0.00 0.00 3.67
402 444 7.860872 AGCAAAACAATAGTAACTACAAGCAAC 59.139 33.333 0.00 0.00 0.00 4.17
408 450 8.809066 TCCTCTAGCAAAACAATAGTAACTACA 58.191 33.333 0.00 0.00 0.00 2.74
416 458 6.100004 TCGACTTCCTCTAGCAAAACAATAG 58.900 40.000 0.00 0.00 0.00 1.73
418 460 4.894784 TCGACTTCCTCTAGCAAAACAAT 58.105 39.130 0.00 0.00 0.00 2.71
429 471 1.134965 CGCTGGATTTCGACTTCCTCT 60.135 52.381 12.70 0.00 32.95 3.69
432 474 1.000145 GACGCTGGATTTCGACTTCC 59.000 55.000 5.97 5.97 0.00 3.46
433 475 0.640768 CGACGCTGGATTTCGACTTC 59.359 55.000 0.00 0.00 34.62 3.01
435 477 0.242825 TTCGACGCTGGATTTCGACT 59.757 50.000 0.00 0.00 41.28 4.18
436 478 1.065358 TTTCGACGCTGGATTTCGAC 58.935 50.000 0.00 0.00 41.28 4.20
438 480 1.786928 GCTTTTCGACGCTGGATTTCG 60.787 52.381 0.00 0.00 0.00 3.46
439 481 1.464997 AGCTTTTCGACGCTGGATTTC 59.535 47.619 2.58 0.00 34.69 2.17
440 482 1.523758 AGCTTTTCGACGCTGGATTT 58.476 45.000 2.58 0.00 34.69 2.17
441 483 1.523758 AAGCTTTTCGACGCTGGATT 58.476 45.000 0.00 0.00 36.45 3.01
442 484 1.523758 AAAGCTTTTCGACGCTGGAT 58.476 45.000 5.69 0.00 36.45 3.41
443 485 1.002900 CAAAAGCTTTTCGACGCTGGA 60.003 47.619 21.45 0.00 36.45 3.86
445 487 2.383298 TCAAAAGCTTTTCGACGCTG 57.617 45.000 21.45 9.74 36.45 5.18
446 488 3.414549 TTTCAAAAGCTTTTCGACGCT 57.585 38.095 21.45 0.00 38.30 5.07
447 489 4.692371 AATTTCAAAAGCTTTTCGACGC 57.308 36.364 21.45 0.00 0.00 5.19
448 490 9.080638 CAATTTAATTTCAAAAGCTTTTCGACG 57.919 29.630 21.45 10.70 0.00 5.12
449 491 9.914923 ACAATTTAATTTCAAAAGCTTTTCGAC 57.085 25.926 21.45 0.00 0.00 4.20
450 492 9.913451 CACAATTTAATTTCAAAAGCTTTTCGA 57.087 25.926 21.45 17.93 0.00 3.71
451 493 8.672405 GCACAATTTAATTTCAAAAGCTTTTCG 58.328 29.630 21.45 16.11 0.00 3.46
452 494 9.500864 TGCACAATTTAATTTCAAAAGCTTTTC 57.499 25.926 21.45 5.46 0.00 2.29
453 495 9.852091 TTGCACAATTTAATTTCAAAAGCTTTT 57.148 22.222 18.74 18.74 0.00 2.27
454 496 9.852091 TTTGCACAATTTAATTTCAAAAGCTTT 57.148 22.222 5.69 5.69 0.00 3.51
455 497 9.852091 TTTTGCACAATTTAATTTCAAAAGCTT 57.148 22.222 13.30 0.00 31.15 3.74
492 592 6.099413 ACTTGATGATAGGAGCAGATTCAAGA 59.901 38.462 14.27 0.00 40.62 3.02
493 593 6.289834 ACTTGATGATAGGAGCAGATTCAAG 58.710 40.000 7.56 7.56 42.67 3.02
497 598 5.366186 AGTGACTTGATGATAGGAGCAGATT 59.634 40.000 0.00 0.00 0.00 2.40
507 608 6.931838 ACGGAACTTAAGTGACTTGATGATA 58.068 36.000 9.34 0.00 0.00 2.15
508 609 5.794894 ACGGAACTTAAGTGACTTGATGAT 58.205 37.500 9.34 0.00 0.00 2.45
510 611 6.036083 CCATACGGAACTTAAGTGACTTGATG 59.964 42.308 9.34 8.84 0.00 3.07
511 612 6.106673 CCATACGGAACTTAAGTGACTTGAT 58.893 40.000 9.34 0.00 0.00 2.57
512 613 5.475719 CCATACGGAACTTAAGTGACTTGA 58.524 41.667 9.34 0.00 0.00 3.02
513 614 4.092968 GCCATACGGAACTTAAGTGACTTG 59.907 45.833 9.34 3.14 0.00 3.16
514 615 4.251268 GCCATACGGAACTTAAGTGACTT 58.749 43.478 9.34 2.37 0.00 3.01
515 616 3.675228 CGCCATACGGAACTTAAGTGACT 60.675 47.826 9.34 0.00 38.44 3.41
516 617 2.601763 CGCCATACGGAACTTAAGTGAC 59.398 50.000 9.34 6.70 38.44 3.67
517 618 2.883574 CGCCATACGGAACTTAAGTGA 58.116 47.619 9.34 0.00 38.44 3.41
518 619 1.326548 GCGCCATACGGAACTTAAGTG 59.673 52.381 9.34 0.00 43.93 3.16
520 621 1.935933 AGCGCCATACGGAACTTAAG 58.064 50.000 2.29 0.00 43.93 1.85
521 622 2.004017 CAAGCGCCATACGGAACTTAA 58.996 47.619 2.29 0.00 43.93 1.85
523 624 0.321298 ACAAGCGCCATACGGAACTT 60.321 50.000 2.29 0.00 43.93 2.66
524 625 0.321298 AACAAGCGCCATACGGAACT 60.321 50.000 2.29 0.00 43.93 3.01
525 626 0.096454 GAACAAGCGCCATACGGAAC 59.904 55.000 2.29 0.00 43.93 3.62
526 627 1.355796 CGAACAAGCGCCATACGGAA 61.356 55.000 2.29 0.00 43.93 4.30
528 629 1.632046 AACGAACAAGCGCCATACGG 61.632 55.000 2.29 0.00 43.93 4.02
531 632 1.195900 GAACAACGAACAAGCGCCATA 59.804 47.619 2.29 0.00 33.86 2.74
532 633 0.040425 GAACAACGAACAAGCGCCAT 60.040 50.000 2.29 0.00 33.86 4.40
533 634 1.353804 GAACAACGAACAAGCGCCA 59.646 52.632 2.29 0.00 33.86 5.69
534 635 1.721133 CGAACAACGAACAAGCGCC 60.721 57.895 2.29 0.00 45.77 6.53
535 636 3.796709 CGAACAACGAACAAGCGC 58.203 55.556 0.00 0.00 45.77 5.92
547 648 7.254624 CCGGACATCATATTGTAAAATCGAACA 60.255 37.037 0.00 0.00 0.00 3.18
551 652 5.049749 TGCCGGACATCATATTGTAAAATCG 60.050 40.000 5.05 0.00 0.00 3.34
552 653 6.312399 TGCCGGACATCATATTGTAAAATC 57.688 37.500 5.05 0.00 0.00 2.17
568 669 3.011119 TGGTTAACATAACATGCCGGAC 58.989 45.455 5.05 0.00 0.00 4.79
569 670 3.351794 TGGTTAACATAACATGCCGGA 57.648 42.857 5.05 0.00 0.00 5.14
570 671 3.303725 CGATGGTTAACATAACATGCCGG 60.304 47.826 8.10 0.00 40.72 6.13
571 672 3.558006 TCGATGGTTAACATAACATGCCG 59.442 43.478 8.10 3.26 40.72 5.69
606 707 8.349983 ACGTTTCTATGCAGTTATTTTCTTGTT 58.650 29.630 0.00 0.00 0.00 2.83
607 708 7.871853 ACGTTTCTATGCAGTTATTTTCTTGT 58.128 30.769 0.00 0.00 0.00 3.16
608 709 8.728088 AACGTTTCTATGCAGTTATTTTCTTG 57.272 30.769 0.00 0.00 0.00 3.02
610 711 9.394477 GAAAACGTTTCTATGCAGTTATTTTCT 57.606 29.630 15.01 0.00 32.33 2.52
611 712 9.176181 TGAAAACGTTTCTATGCAGTTATTTTC 57.824 29.630 15.01 2.80 34.48 2.29
614 715 9.988350 CTATGAAAACGTTTCTATGCAGTTATT 57.012 29.630 15.01 0.00 0.00 1.40
619 720 9.638300 GATAACTATGAAAACGTTTCTATGCAG 57.362 33.333 15.01 9.40 0.00 4.41
635 736 9.330063 CAAACTTTCATGGCTAGATAACTATGA 57.670 33.333 0.00 0.00 0.00 2.15
637 738 7.995488 AGCAAACTTTCATGGCTAGATAACTAT 59.005 33.333 0.00 0.00 32.09 2.12
646 747 4.700213 GGTTCTAGCAAACTTTCATGGCTA 59.300 41.667 0.00 0.00 36.10 3.93
647 748 3.507622 GGTTCTAGCAAACTTTCATGGCT 59.492 43.478 0.00 0.00 38.55 4.75
648 749 3.507622 AGGTTCTAGCAAACTTTCATGGC 59.492 43.478 0.00 0.00 0.00 4.40
649 750 4.616835 GCAGGTTCTAGCAAACTTTCATGG 60.617 45.833 0.00 0.00 0.00 3.66
650 751 4.217118 AGCAGGTTCTAGCAAACTTTCATG 59.783 41.667 0.00 0.00 0.00 3.07
651 752 4.217118 CAGCAGGTTCTAGCAAACTTTCAT 59.783 41.667 0.00 0.00 0.00 2.57
652 753 3.565482 CAGCAGGTTCTAGCAAACTTTCA 59.435 43.478 0.00 0.00 0.00 2.69
653 754 3.565902 ACAGCAGGTTCTAGCAAACTTTC 59.434 43.478 0.00 0.00 0.00 2.62
654 755 3.555966 ACAGCAGGTTCTAGCAAACTTT 58.444 40.909 0.00 0.00 0.00 2.66
655 756 3.142174 GACAGCAGGTTCTAGCAAACTT 58.858 45.455 0.00 0.00 0.00 2.66
656 757 2.370189 AGACAGCAGGTTCTAGCAAACT 59.630 45.455 0.00 0.00 0.00 2.66
657 758 2.772287 AGACAGCAGGTTCTAGCAAAC 58.228 47.619 0.00 0.00 0.00 2.93
668 769 1.280457 AAGAGGGGTTAGACAGCAGG 58.720 55.000 0.00 0.00 0.00 4.85
672 773 3.258622 ACGAGAAAAGAGGGGTTAGACAG 59.741 47.826 0.00 0.00 0.00 3.51
688 789 3.358707 TCACTAACTGCGAAACGAGAA 57.641 42.857 0.00 0.00 0.00 2.87
691 792 3.183574 CACATTCACTAACTGCGAAACGA 59.816 43.478 0.00 0.00 0.00 3.85
692 793 3.469629 CACATTCACTAACTGCGAAACG 58.530 45.455 0.00 0.00 0.00 3.60
693 794 3.058914 AGCACATTCACTAACTGCGAAAC 60.059 43.478 0.00 0.00 32.92 2.78
697 798 4.494690 CCATTAGCACATTCACTAACTGCG 60.495 45.833 0.00 0.00 31.51 5.18
773 874 1.995626 AATGCTGTAGCCGAGGGGT 60.996 57.895 0.80 0.00 41.18 4.95
853 954 1.611977 ACTCTGATGTTTCGTCCGTGA 59.388 47.619 0.00 0.00 0.00 4.35
854 955 1.986378 GACTCTGATGTTTCGTCCGTG 59.014 52.381 0.00 0.00 0.00 4.94
856 957 2.095212 TGAGACTCTGATGTTTCGTCCG 60.095 50.000 3.68 0.00 0.00 4.79
857 958 3.057174 AGTGAGACTCTGATGTTTCGTCC 60.057 47.826 3.68 0.00 0.00 4.79
858 959 4.167554 AGTGAGACTCTGATGTTTCGTC 57.832 45.455 3.68 0.00 0.00 4.20
859 960 4.279671 AGAAGTGAGACTCTGATGTTTCGT 59.720 41.667 3.68 0.00 0.00 3.85
861 962 5.537188 ACAGAAGTGAGACTCTGATGTTTC 58.463 41.667 3.68 0.00 31.97 2.78
865 966 5.131594 TGAACAGAAGTGAGACTCTGATG 57.868 43.478 3.68 0.00 31.97 3.07
866 967 5.798125 TTGAACAGAAGTGAGACTCTGAT 57.202 39.130 3.68 0.00 31.97 2.90
867 968 5.105351 TGTTTGAACAGAAGTGAGACTCTGA 60.105 40.000 3.68 0.00 34.30 3.27
868 969 5.111989 TGTTTGAACAGAAGTGAGACTCTG 58.888 41.667 3.68 0.00 34.30 3.35
869 970 5.344743 TGTTTGAACAGAAGTGAGACTCT 57.655 39.130 3.68 0.00 34.30 3.24
888 989 7.899973 AGCAACAAATCTGGAGATAAAATGTT 58.100 30.769 0.00 0.00 33.73 2.71
924 1025 0.318955 GCGCACTGCAGGAAACAAAT 60.319 50.000 19.93 0.00 45.45 2.32
925 1026 1.065600 GCGCACTGCAGGAAACAAA 59.934 52.632 19.93 0.00 45.45 2.83
928 1029 2.770587 CTTCGCGCACTGCAGGAAAC 62.771 60.000 19.93 3.78 46.97 2.78
1081 1188 1.618345 GCAGAGAGGAACAGAGGGAGA 60.618 57.143 0.00 0.00 0.00 3.71
1108 1215 2.140065 TGTTGCAGTTCGAGTCAGAG 57.860 50.000 0.00 0.00 0.00 3.35
1117 1224 2.818350 GCAGCCATTGTTGCAGTTC 58.182 52.632 0.48 0.00 46.76 3.01
1322 1430 3.365868 GGCTCGACTCAGATAGCACATAG 60.366 52.174 0.00 0.00 36.68 2.23
1778 1886 1.341209 TCCATCTCGGGAATGATGTCG 59.659 52.381 0.00 0.00 38.59 4.35
1787 1895 0.684479 CACAGACCTCCATCTCGGGA 60.684 60.000 0.00 0.00 34.36 5.14
1999 2107 2.398554 CCAAAGATGGTGACCGCCG 61.399 63.158 0.00 0.00 42.18 6.46
2133 2241 0.878961 GCAACCTCTTCGTTCACGGT 60.879 55.000 0.00 0.00 40.29 4.83
2137 2245 1.412710 AGACAGCAACCTCTTCGTTCA 59.587 47.619 0.00 0.00 0.00 3.18
2332 2441 5.380043 ACAGTCAGAACAAATTCCACAGAT 58.620 37.500 0.00 0.00 35.18 2.90
2356 2465 4.093703 TCACAGTAACCAAACGACAAACTG 59.906 41.667 0.00 0.00 38.97 3.16
2497 2611 9.840427 CAAAATGACACTCGTTATAGGAAAAAT 57.160 29.630 0.00 0.00 0.00 1.82
2532 2848 3.206150 CAACTTGGCACAGAGTAACACT 58.794 45.455 0.00 0.00 42.39 3.55
2575 2891 1.598701 GCCAGGGGAAATGAGCACAC 61.599 60.000 0.00 0.00 0.00 3.82
2592 2908 3.509575 ACGAGATGATCAGAAGATAGGCC 59.490 47.826 0.09 0.00 33.72 5.19
2603 2919 0.317020 CTGCGCGTACGAGATGATCA 60.317 55.000 23.53 9.42 43.93 2.92
2631 3128 1.801395 GCTTGTATTCCTCGCGCAGTA 60.801 52.381 8.75 0.00 0.00 2.74
2640 3138 5.882557 AGAATCAATTCGTGCTTGTATTCCT 59.117 36.000 0.00 0.00 41.56 3.36
2649 3147 5.179368 TCGAAGAAAAGAATCAATTCGTGCT 59.821 36.000 5.22 0.00 41.56 4.40
2652 3150 7.806690 TCAATCGAAGAAAAGAATCAATTCGT 58.193 30.769 0.00 0.00 43.58 3.85
2671 3169 9.913451 GAAGAATCAAATAGTTCTCTTCAATCG 57.087 33.333 11.33 0.00 38.95 3.34
2710 3208 6.111382 TGCAGAAGATAGGATCAGAAACAAG 58.889 40.000 0.00 0.00 0.00 3.16
2711 3209 6.053632 TGCAGAAGATAGGATCAGAAACAA 57.946 37.500 0.00 0.00 0.00 2.83
2721 3219 5.987953 CGAATCAGAAATGCAGAAGATAGGA 59.012 40.000 0.00 0.00 0.00 2.94
2723 3221 6.647569 CACGAATCAGAAATGCAGAAGATAG 58.352 40.000 0.00 0.00 0.00 2.08
2815 3367 6.365305 TGTCAAAAGAACGAAACGAAAAAC 57.635 33.333 0.00 0.00 0.00 2.43
2850 3403 2.817901 ACGCCCAAGATTACATACGAC 58.182 47.619 0.00 0.00 0.00 4.34
2857 3428 5.616488 TCACTTTTTACGCCCAAGATTAC 57.384 39.130 0.00 0.00 0.00 1.89
2865 3436 2.292292 TGCTCTTTCACTTTTTACGCCC 59.708 45.455 0.00 0.00 0.00 6.13
2887 3458 6.349300 AGATTAGATACGCAACAACTTGGAT 58.651 36.000 0.00 0.00 0.00 3.41
2888 3459 5.730550 AGATTAGATACGCAACAACTTGGA 58.269 37.500 0.00 0.00 0.00 3.53
2917 3493 5.741964 GCCATCATCCATCAATCTTTGCATT 60.742 40.000 0.00 0.00 0.00 3.56
2954 3531 3.248029 GCCCTCGCGCATATCTTG 58.752 61.111 8.75 0.00 0.00 3.02
3046 3624 4.320928 CGCAAAGGAAACGGCGCA 62.321 61.111 10.83 0.00 41.60 6.09
3078 3658 5.793026 TGTAAAAAGTTGCTTTGCTTTGG 57.207 34.783 0.00 0.00 35.40 3.28
3087 3667 3.736740 CGGCTTGGTTGTAAAAAGTTGCT 60.737 43.478 0.00 0.00 0.00 3.91
3092 3672 1.339929 AGGCGGCTTGGTTGTAAAAAG 59.660 47.619 5.25 0.00 0.00 2.27
3110 3690 2.358737 AGCCGGCGAGAAACAAGG 60.359 61.111 23.20 0.00 0.00 3.61
3158 3738 3.771160 CTACAAGACGGCCGGCCT 61.771 66.667 41.01 28.46 0.00 5.19
3160 3740 1.226888 CTACTACAAGACGGCCGGC 60.227 63.158 31.76 30.01 0.00 6.13
3162 3742 3.705043 AATACTACTACAAGACGGCCG 57.295 47.619 26.86 26.86 0.00 6.13
3164 3744 6.362820 GCTCAATAATACTACTACAAGACGGC 59.637 42.308 0.00 0.00 0.00 5.68
3166 3746 7.378995 GGTGCTCAATAATACTACTACAAGACG 59.621 40.741 0.00 0.00 0.00 4.18
3167 3747 7.378995 CGGTGCTCAATAATACTACTACAAGAC 59.621 40.741 0.00 0.00 0.00 3.01
3168 3748 7.423199 CGGTGCTCAATAATACTACTACAAGA 58.577 38.462 0.00 0.00 0.00 3.02
3169 3749 6.144080 GCGGTGCTCAATAATACTACTACAAG 59.856 42.308 0.00 0.00 0.00 3.16
3174 3754 4.369182 GTGCGGTGCTCAATAATACTACT 58.631 43.478 0.00 0.00 0.00 2.57
3175 3755 3.181774 CGTGCGGTGCTCAATAATACTAC 59.818 47.826 0.00 0.00 0.00 2.73
3177 3757 2.201732 CGTGCGGTGCTCAATAATACT 58.798 47.619 0.00 0.00 0.00 2.12
3178 3758 1.260561 CCGTGCGGTGCTCAATAATAC 59.739 52.381 1.93 0.00 0.00 1.89
3179 3759 1.577468 CCGTGCGGTGCTCAATAATA 58.423 50.000 1.93 0.00 0.00 0.98
3180 3760 1.095228 CCCGTGCGGTGCTCAATAAT 61.095 55.000 9.90 0.00 0.00 1.28
3181 3761 1.743623 CCCGTGCGGTGCTCAATAA 60.744 57.895 9.90 0.00 0.00 1.40
3182 3762 2.125310 CCCGTGCGGTGCTCAATA 60.125 61.111 9.90 0.00 0.00 1.90
3217 3797 2.923121 AGAAACTGTCGCATATGCCAT 58.077 42.857 21.77 0.47 37.91 4.40
3226 3806 2.210116 TGGTGAAGAAGAAACTGTCGC 58.790 47.619 0.00 0.00 0.00 5.19
3229 3809 2.092429 TGGCTGGTGAAGAAGAAACTGT 60.092 45.455 0.00 0.00 0.00 3.55
3230 3810 2.575532 TGGCTGGTGAAGAAGAAACTG 58.424 47.619 0.00 0.00 0.00 3.16
3232 3812 3.632145 TCTTTGGCTGGTGAAGAAGAAAC 59.368 43.478 0.00 0.00 0.00 2.78
3234 3814 3.576078 TCTTTGGCTGGTGAAGAAGAA 57.424 42.857 0.00 0.00 0.00 2.52
3239 3819 5.010415 AGAGAAATTTCTTTGGCTGGTGAAG 59.990 40.000 21.33 0.00 37.73 3.02
3247 3827 7.600960 AGATGAAAGAGAGAAATTTCTTTGGC 58.399 34.615 21.33 9.08 42.13 4.52
3268 3848 4.154737 TGCAAATGAAAACGAGAGGAGATG 59.845 41.667 0.00 0.00 0.00 2.90
3269 3849 4.326826 TGCAAATGAAAACGAGAGGAGAT 58.673 39.130 0.00 0.00 0.00 2.75
3285 3866 0.165079 CCGCGTACGTTTCTGCAAAT 59.835 50.000 17.90 0.00 37.70 2.32
3288 3869 3.408020 GCCGCGTACGTTTCTGCA 61.408 61.111 17.90 0.00 37.70 4.41


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

AutoCloner maintained by Alex Coulton.