Multiple sequence alignment - TraesCS7B01G402700

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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 TraesCS7B01G402700 chr7B 100.000 2646 0 0 1 2646 670244789 670247434 0.000000e+00 4887.0
1 TraesCS7B01G402700 chr7B 97.287 516 13 1 1 515 642501838 642502353 0.000000e+00 874.0
2 TraesCS7B01G402700 chr7B 100.000 242 0 0 2918 3159 670247706 670247947 6.220000e-122 448.0
3 TraesCS7B01G402700 chr7B 84.536 97 13 2 2489 2584 670247706 670247801 9.330000e-16 95.3
4 TraesCS7B01G402700 chr7B 83.117 77 12 1 2469 2545 670247726 670247801 5.650000e-08 69.4
5 TraesCS7B01G402700 chr2D 96.553 2031 65 5 618 2646 544195964 544197991 0.000000e+00 3358.0
6 TraesCS7B01G402700 chr2D 95.359 237 10 1 2923 3159 544198389 544198624 2.970000e-100 375.0
7 TraesCS7B01G402700 chr3A 95.972 2036 76 5 613 2646 552543599 552545630 0.000000e+00 3301.0
8 TraesCS7B01G402700 chr3A 93.883 2027 90 8 618 2642 716653340 716655334 0.000000e+00 3025.0
9 TraesCS7B01G402700 chr3A 92.623 244 14 2 2919 3159 552545747 552545989 6.480000e-92 348.0
10 TraesCS7B01G402700 chr3A 84.887 311 38 6 44 349 490336348 490336654 3.960000e-79 305.0
11 TraesCS7B01G402700 chr1D 95.819 2033 64 11 616 2646 262705052 262703039 0.000000e+00 3264.0
12 TraesCS7B01G402700 chr1D 95.359 237 11 0 2923 3159 262702540 262702304 8.270000e-101 377.0
13 TraesCS7B01G402700 chr3D 94.384 2030 102 10 618 2646 454991148 454989130 0.000000e+00 3107.0
14 TraesCS7B01G402700 chr3D 95.781 237 10 0 2923 3159 316829616 316829852 1.780000e-102 383.0
15 TraesCS7B01G402700 chr3D 94.937 237 12 0 2923 3159 39880012 39879776 3.850000e-99 372.0
16 TraesCS7B01G402700 chr5A 94.729 1897 69 5 618 2513 555245008 555243142 0.000000e+00 2920.0
17 TraesCS7B01G402700 chr5A 87.747 253 25 5 95 342 37069263 37069012 1.110000e-74 291.0
18 TraesCS7B01G402700 chr5D 91.902 2050 122 30 618 2646 42030415 42028389 0.000000e+00 2826.0
19 TraesCS7B01G402700 chr5D 93.671 237 15 0 2923 3159 385974540 385974304 3.880000e-94 355.0
20 TraesCS7B01G402700 chr5D 86.475 244 28 4 103 342 46064331 46064089 2.420000e-66 263.0
21 TraesCS7B01G402700 chr2A 93.172 1816 113 7 618 2426 751036340 751034529 0.000000e+00 2656.0
22 TraesCS7B01G402700 chr7A 92.731 1816 111 9 831 2646 501145869 501144075 0.000000e+00 2603.0
23 TraesCS7B01G402700 chr7A 93.976 249 8 1 2918 3159 638856618 638856866 1.380000e-98 370.0
24 TraesCS7B01G402700 chr4A 88.819 796 71 7 617 1396 614553530 614554323 0.000000e+00 961.0
25 TraesCS7B01G402700 chr2B 96.899 516 15 1 1 515 110537555 110537040 0.000000e+00 863.0
26 TraesCS7B01G402700 chr2B 83.942 411 55 9 118 521 664126010 664125604 1.780000e-102 383.0
27 TraesCS7B01G402700 chr4B 86.015 522 65 5 1 515 192061502 192062022 1.280000e-153 553.0
28 TraesCS7B01G402700 chr3B 96.708 243 7 1 2918 3159 129257507 129257749 1.360000e-108 403.0
29 TraesCS7B01G402700 chr3B 96.111 180 7 0 2980 3159 794288640 794288819 8.570000e-76 294.0
30 TraesCS7B01G402700 chr3B 94.845 97 4 1 2918 3013 129256882 129256978 1.960000e-32 150.0
31 TraesCS7B01G402700 chr5B 83.758 314 39 7 118 420 527296539 527296851 1.430000e-73 287.0
32 TraesCS7B01G402700 chr7D 90.385 104 8 2 514 617 592201363 592201262 5.500000e-28 135.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G402700 chr7B 670244789 670247947 3158 False 1374.925 4887 91.91325 1 3159 4 chr7B.!!$F2 3158
1 TraesCS7B01G402700 chr7B 642501838 642502353 515 False 874.000 874 97.28700 1 515 1 chr7B.!!$F1 514
2 TraesCS7B01G402700 chr2D 544195964 544198624 2660 False 1866.500 3358 95.95600 618 3159 2 chr2D.!!$F1 2541
3 TraesCS7B01G402700 chr3A 716653340 716655334 1994 False 3025.000 3025 93.88300 618 2642 1 chr3A.!!$F2 2024
4 TraesCS7B01G402700 chr3A 552543599 552545989 2390 False 1824.500 3301 94.29750 613 3159 2 chr3A.!!$F3 2546
5 TraesCS7B01G402700 chr1D 262702304 262705052 2748 True 1820.500 3264 95.58900 616 3159 2 chr1D.!!$R1 2543
6 TraesCS7B01G402700 chr3D 454989130 454991148 2018 True 3107.000 3107 94.38400 618 2646 1 chr3D.!!$R2 2028
7 TraesCS7B01G402700 chr5A 555243142 555245008 1866 True 2920.000 2920 94.72900 618 2513 1 chr5A.!!$R2 1895
8 TraesCS7B01G402700 chr5D 42028389 42030415 2026 True 2826.000 2826 91.90200 618 2646 1 chr5D.!!$R1 2028
9 TraesCS7B01G402700 chr2A 751034529 751036340 1811 True 2656.000 2656 93.17200 618 2426 1 chr2A.!!$R1 1808
10 TraesCS7B01G402700 chr7A 501144075 501145869 1794 True 2603.000 2603 92.73100 831 2646 1 chr7A.!!$R1 1815
11 TraesCS7B01G402700 chr4A 614553530 614554323 793 False 961.000 961 88.81900 617 1396 1 chr4A.!!$F1 779
12 TraesCS7B01G402700 chr2B 110537040 110537555 515 True 863.000 863 96.89900 1 515 1 chr2B.!!$R1 514
13 TraesCS7B01G402700 chr4B 192061502 192062022 520 False 553.000 553 86.01500 1 515 1 chr4B.!!$F1 514
14 TraesCS7B01G402700 chr3B 129256882 129257749 867 False 276.500 403 95.77650 2918 3159 2 chr3B.!!$F2 241

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
560 568 0.035725 TTCGTCGAGGCCTCTAGTGA 60.036 55.0 29.73 16.93 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2516 2622 0.109919 GGTGAATCGGCGTTGAAACC 60.11 55.0 6.85 6.29 0.0 3.27 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
113 116 1.272147 GGTTCCAAGACCTTCATGGCT 60.272 52.381 0.00 0.00 35.36 4.75
318 326 1.449601 CCTCGCCGTGGTTTGCTAT 60.450 57.895 0.00 0.00 0.00 2.97
342 350 0.616111 AGGAGGGAGAAGCATGACGT 60.616 55.000 0.00 0.00 0.00 4.34
394 402 4.957684 AGATGAGATGCGGGCGCG 62.958 66.667 20.05 20.05 45.51 6.86
403 411 4.903010 GCGGGCGCGGGAGAAATA 62.903 66.667 25.26 0.00 0.00 1.40
404 412 2.202960 CGGGCGCGGGAGAAATAA 60.203 61.111 16.41 0.00 0.00 1.40
405 413 2.244651 CGGGCGCGGGAGAAATAAG 61.245 63.158 16.41 0.00 0.00 1.73
406 414 1.145377 GGGCGCGGGAGAAATAAGA 59.855 57.895 8.83 0.00 0.00 2.10
407 415 0.250338 GGGCGCGGGAGAAATAAGAT 60.250 55.000 8.83 0.00 0.00 2.40
408 416 1.001633 GGGCGCGGGAGAAATAAGATA 59.998 52.381 8.83 0.00 0.00 1.98
409 417 2.549349 GGGCGCGGGAGAAATAAGATAA 60.549 50.000 8.83 0.00 0.00 1.75
410 418 2.737252 GGCGCGGGAGAAATAAGATAAG 59.263 50.000 8.83 0.00 0.00 1.73
411 419 2.737252 GCGCGGGAGAAATAAGATAAGG 59.263 50.000 8.83 0.00 0.00 2.69
412 420 3.554337 GCGCGGGAGAAATAAGATAAGGA 60.554 47.826 8.83 0.00 0.00 3.36
413 421 4.628074 CGCGGGAGAAATAAGATAAGGAA 58.372 43.478 0.00 0.00 0.00 3.36
414 422 5.054477 CGCGGGAGAAATAAGATAAGGAAA 58.946 41.667 0.00 0.00 0.00 3.13
415 423 5.526111 CGCGGGAGAAATAAGATAAGGAAAA 59.474 40.000 0.00 0.00 0.00 2.29
416 424 6.292919 CGCGGGAGAAATAAGATAAGGAAAAG 60.293 42.308 0.00 0.00 0.00 2.27
417 425 6.017026 GCGGGAGAAATAAGATAAGGAAAAGG 60.017 42.308 0.00 0.00 0.00 3.11
418 426 7.280356 CGGGAGAAATAAGATAAGGAAAAGGA 58.720 38.462 0.00 0.00 0.00 3.36
419 427 7.773690 CGGGAGAAATAAGATAAGGAAAAGGAA 59.226 37.037 0.00 0.00 0.00 3.36
420 428 9.126151 GGGAGAAATAAGATAAGGAAAAGGAAG 57.874 37.037 0.00 0.00 0.00 3.46
421 429 9.688091 GGAGAAATAAGATAAGGAAAAGGAAGT 57.312 33.333 0.00 0.00 0.00 3.01
428 436 8.768501 AAGATAAGGAAAAGGAAGTTGTTTCT 57.231 30.769 0.00 0.00 36.03 2.52
429 437 8.768501 AGATAAGGAAAAGGAAGTTGTTTCTT 57.231 30.769 0.00 0.00 36.03 2.52
430 438 8.633561 AGATAAGGAAAAGGAAGTTGTTTCTTG 58.366 33.333 0.00 0.00 36.03 3.02
431 439 6.850752 AAGGAAAAGGAAGTTGTTTCTTGA 57.149 33.333 0.00 0.00 36.03 3.02
432 440 6.208988 AGGAAAAGGAAGTTGTTTCTTGAC 57.791 37.500 0.00 0.00 36.03 3.18
433 441 5.034797 GGAAAAGGAAGTTGTTTCTTGACG 58.965 41.667 0.00 0.00 36.03 4.35
434 442 3.692791 AAGGAAGTTGTTTCTTGACGC 57.307 42.857 0.00 0.00 36.03 5.19
435 443 2.639065 AGGAAGTTGTTTCTTGACGCA 58.361 42.857 0.00 0.00 36.03 5.24
436 444 3.214328 AGGAAGTTGTTTCTTGACGCAT 58.786 40.909 0.00 0.00 36.03 4.73
437 445 3.003689 AGGAAGTTGTTTCTTGACGCATG 59.996 43.478 0.00 0.00 36.03 4.06
438 446 3.300009 GAAGTTGTTTCTTGACGCATGG 58.700 45.455 0.00 0.00 32.83 3.66
439 447 1.608590 AGTTGTTTCTTGACGCATGGG 59.391 47.619 8.44 8.44 0.00 4.00
440 448 0.958091 TTGTTTCTTGACGCATGGGG 59.042 50.000 14.94 0.00 0.00 4.96
441 449 1.212751 GTTTCTTGACGCATGGGGC 59.787 57.895 14.94 12.22 39.90 5.80
442 450 1.976474 TTTCTTGACGCATGGGGCC 60.976 57.895 13.88 0.00 40.31 5.80
443 451 3.936772 TTCTTGACGCATGGGGCCC 62.937 63.158 18.17 18.17 40.31 5.80
444 452 4.431131 CTTGACGCATGGGGCCCT 62.431 66.667 25.93 6.39 40.31 5.19
445 453 4.738998 TTGACGCATGGGGCCCTG 62.739 66.667 25.93 19.72 40.31 4.45
460 468 3.807538 CTGGTGCGTGGCATGCTC 61.808 66.667 29.90 25.89 41.91 4.26
491 499 2.943653 GGAACGTTTCAGCCGGTG 59.056 61.111 0.46 0.00 0.00 4.94
492 500 2.251371 GAACGTTTCAGCCGGTGC 59.749 61.111 0.46 0.00 37.95 5.01
503 511 4.020617 CCGGTGCTCTGGCTGGAA 62.021 66.667 0.00 0.00 39.59 3.53
504 512 2.032528 CGGTGCTCTGGCTGGAAA 59.967 61.111 0.00 0.00 39.59 3.13
505 513 2.328099 CGGTGCTCTGGCTGGAAAC 61.328 63.158 0.00 0.00 39.59 2.78
506 514 2.328099 GGTGCTCTGGCTGGAAACG 61.328 63.158 0.00 0.00 39.59 3.60
507 515 1.598130 GTGCTCTGGCTGGAAACGT 60.598 57.895 0.00 0.00 39.59 3.99
508 516 1.148273 TGCTCTGGCTGGAAACGTT 59.852 52.632 0.00 0.00 39.59 3.99
509 517 0.465460 TGCTCTGGCTGGAAACGTTT 60.465 50.000 14.57 14.57 39.59 3.60
510 518 0.238553 GCTCTGGCTGGAAACGTTTC 59.761 55.000 28.83 28.83 34.53 2.78
544 552 9.644993 TTATATACAAATCAAATTGTCGCTTCG 57.355 29.630 0.00 0.00 42.33 3.79
545 553 4.223320 ACAAATCAAATTGTCGCTTCGT 57.777 36.364 0.00 0.00 39.23 3.85
546 554 4.219033 ACAAATCAAATTGTCGCTTCGTC 58.781 39.130 0.00 0.00 39.23 4.20
547 555 2.787723 ATCAAATTGTCGCTTCGTCG 57.212 45.000 0.00 0.00 0.00 5.12
548 556 1.773410 TCAAATTGTCGCTTCGTCGA 58.227 45.000 0.00 0.00 35.95 4.20
549 557 1.719246 TCAAATTGTCGCTTCGTCGAG 59.281 47.619 0.00 0.00 39.34 4.04
550 558 1.068474 AAATTGTCGCTTCGTCGAGG 58.932 50.000 0.00 0.00 39.34 4.63
551 559 1.352156 AATTGTCGCTTCGTCGAGGC 61.352 55.000 18.55 18.55 39.34 4.70
552 560 3.909258 TTGTCGCTTCGTCGAGGCC 62.909 63.158 21.89 10.64 39.34 5.19
553 561 4.117661 GTCGCTTCGTCGAGGCCT 62.118 66.667 21.89 3.86 39.34 5.19
554 562 3.812019 TCGCTTCGTCGAGGCCTC 61.812 66.667 23.79 23.79 30.69 4.70
555 563 3.816524 CGCTTCGTCGAGGCCTCT 61.817 66.667 29.73 0.00 30.69 3.69
556 564 2.470362 CGCTTCGTCGAGGCCTCTA 61.470 63.158 29.73 17.64 30.69 2.43
557 565 1.357334 GCTTCGTCGAGGCCTCTAG 59.643 63.158 29.73 19.72 0.00 2.43
558 566 1.378124 GCTTCGTCGAGGCCTCTAGT 61.378 60.000 29.73 0.00 0.00 2.57
559 567 0.378962 CTTCGTCGAGGCCTCTAGTG 59.621 60.000 29.73 14.77 0.00 2.74
560 568 0.035725 TTCGTCGAGGCCTCTAGTGA 60.036 55.000 29.73 16.93 0.00 3.41
561 569 0.035725 TCGTCGAGGCCTCTAGTGAA 60.036 55.000 29.73 8.15 0.00 3.18
562 570 0.099082 CGTCGAGGCCTCTAGTGAAC 59.901 60.000 29.73 15.82 0.00 3.18
563 571 0.456628 GTCGAGGCCTCTAGTGAACC 59.543 60.000 29.73 5.80 0.00 3.62
564 572 0.039180 TCGAGGCCTCTAGTGAACCA 59.961 55.000 29.73 0.13 0.00 3.67
565 573 0.457851 CGAGGCCTCTAGTGAACCAG 59.542 60.000 29.73 6.88 0.00 4.00
566 574 1.562783 GAGGCCTCTAGTGAACCAGT 58.437 55.000 26.25 0.00 0.00 4.00
567 575 2.736347 GAGGCCTCTAGTGAACCAGTA 58.264 52.381 26.25 0.00 0.00 2.74
568 576 3.301274 GAGGCCTCTAGTGAACCAGTAT 58.699 50.000 26.25 0.00 0.00 2.12
569 577 3.707102 GAGGCCTCTAGTGAACCAGTATT 59.293 47.826 26.25 0.00 0.00 1.89
570 578 4.880164 AGGCCTCTAGTGAACCAGTATTA 58.120 43.478 0.00 0.00 0.00 0.98
571 579 5.468658 AGGCCTCTAGTGAACCAGTATTAT 58.531 41.667 0.00 0.00 0.00 1.28
572 580 5.905913 AGGCCTCTAGTGAACCAGTATTATT 59.094 40.000 0.00 0.00 0.00 1.40
573 581 6.387220 AGGCCTCTAGTGAACCAGTATTATTT 59.613 38.462 0.00 0.00 0.00 1.40
574 582 7.054751 GGCCTCTAGTGAACCAGTATTATTTT 58.945 38.462 0.00 0.00 0.00 1.82
575 583 7.012421 GGCCTCTAGTGAACCAGTATTATTTTG 59.988 40.741 0.00 0.00 0.00 2.44
576 584 7.012421 GCCTCTAGTGAACCAGTATTATTTTGG 59.988 40.741 0.00 0.00 37.98 3.28
577 585 7.499232 CCTCTAGTGAACCAGTATTATTTTGGG 59.501 40.741 0.00 0.00 36.28 4.12
578 586 5.914898 AGTGAACCAGTATTATTTTGGGC 57.085 39.130 0.00 0.00 36.28 5.36
579 587 5.580022 AGTGAACCAGTATTATTTTGGGCT 58.420 37.500 0.00 0.00 36.28 5.19
580 588 6.016555 AGTGAACCAGTATTATTTTGGGCTT 58.983 36.000 0.00 0.00 36.28 4.35
581 589 6.152831 AGTGAACCAGTATTATTTTGGGCTTC 59.847 38.462 0.00 0.00 36.28 3.86
582 590 6.152831 GTGAACCAGTATTATTTTGGGCTTCT 59.847 38.462 0.00 0.00 36.28 2.85
583 591 7.338449 GTGAACCAGTATTATTTTGGGCTTCTA 59.662 37.037 0.00 0.00 36.28 2.10
584 592 7.338449 TGAACCAGTATTATTTTGGGCTTCTAC 59.662 37.037 0.00 0.00 36.28 2.59
585 593 6.970191 ACCAGTATTATTTTGGGCTTCTACT 58.030 36.000 0.00 0.00 36.28 2.57
586 594 7.054751 ACCAGTATTATTTTGGGCTTCTACTC 58.945 38.462 0.00 0.00 36.28 2.59
587 595 7.054124 CCAGTATTATTTTGGGCTTCTACTCA 58.946 38.462 0.00 0.00 0.00 3.41
588 596 7.012421 CCAGTATTATTTTGGGCTTCTACTCAC 59.988 40.741 0.00 0.00 0.00 3.51
589 597 7.770897 CAGTATTATTTTGGGCTTCTACTCACT 59.229 37.037 0.00 0.00 0.00 3.41
590 598 7.988028 AGTATTATTTTGGGCTTCTACTCACTC 59.012 37.037 0.00 0.00 0.00 3.51
591 599 4.640771 ATTTTGGGCTTCTACTCACTCA 57.359 40.909 0.00 0.00 0.00 3.41
592 600 4.640771 TTTTGGGCTTCTACTCACTCAT 57.359 40.909 0.00 0.00 0.00 2.90
593 601 4.640771 TTTGGGCTTCTACTCACTCATT 57.359 40.909 0.00 0.00 0.00 2.57
594 602 3.895232 TGGGCTTCTACTCACTCATTC 57.105 47.619 0.00 0.00 0.00 2.67
595 603 3.445008 TGGGCTTCTACTCACTCATTCT 58.555 45.455 0.00 0.00 0.00 2.40
596 604 3.840666 TGGGCTTCTACTCACTCATTCTT 59.159 43.478 0.00 0.00 0.00 2.52
597 605 4.287067 TGGGCTTCTACTCACTCATTCTTT 59.713 41.667 0.00 0.00 0.00 2.52
598 606 5.483937 TGGGCTTCTACTCACTCATTCTTTA 59.516 40.000 0.00 0.00 0.00 1.85
599 607 6.045955 GGGCTTCTACTCACTCATTCTTTAG 58.954 44.000 0.00 0.00 0.00 1.85
600 608 6.351456 GGGCTTCTACTCACTCATTCTTTAGT 60.351 42.308 0.00 0.00 0.00 2.24
601 609 7.147880 GGGCTTCTACTCACTCATTCTTTAGTA 60.148 40.741 0.00 0.00 0.00 1.82
602 610 8.417884 GGCTTCTACTCACTCATTCTTTAGTAT 58.582 37.037 0.00 0.00 0.00 2.12
946 964 3.898509 CTCTCTGCTCCCGCTCGG 61.899 72.222 0.48 0.48 36.97 4.63
1020 1039 3.372349 CCATGGTTTCCTGGTCTGATGAT 60.372 47.826 2.57 0.00 0.00 2.45
1025 1044 3.616956 TTCCTGGTCTGATGATGACAC 57.383 47.619 0.00 0.00 36.26 3.67
1097 1116 0.320247 AAGGTGAGTTGCTCGAGCTG 60.320 55.000 35.27 1.83 42.66 4.24
1139 1165 5.634859 GCGATTTGTGGATTTTTCTGTTGAT 59.365 36.000 0.00 0.00 0.00 2.57
1177 1214 0.185901 TGCCTTTCCTTTGCACCTCT 59.814 50.000 0.00 0.00 0.00 3.69
1203 1240 2.305928 CCTGAGACCATCGATGACTCT 58.694 52.381 31.67 26.57 34.60 3.24
1254 1291 1.926511 GCAATGAACACTCCCTGCCG 61.927 60.000 0.00 0.00 0.00 5.69
1351 1392 6.154192 TGCCAAATTTATGCTAATCTGGTCAA 59.846 34.615 11.74 0.00 29.95 3.18
1412 1453 4.382040 GCTAGTTGCTCAGTGAGGTCATTA 60.382 45.833 21.54 7.14 38.95 1.90
1510 1551 5.461516 TCTGTGATAGTAGTGGGTTAGGA 57.538 43.478 0.00 0.00 0.00 2.94
1702 1748 9.899661 TGTTACTTTATAGCATGTGGATTAGTT 57.100 29.630 0.00 0.00 0.00 2.24
1809 1857 3.372025 GGGCTAGTTGAATGGGTTGATCT 60.372 47.826 0.00 0.00 0.00 2.75
1920 1968 3.637998 AAGCTCATTTGCTGTTCACAG 57.362 42.857 2.31 2.31 43.24 3.66
2094 2144 1.467734 CATGCTCAAGAACCTGACAGC 59.532 52.381 0.00 0.00 0.00 4.40
2117 2167 2.424956 GCTCAAGCCAAAGTCATTAGGG 59.575 50.000 0.00 0.00 34.31 3.53
2228 2278 2.626743 CTGAATGGGATCAAAGCCATCC 59.373 50.000 2.15 0.00 39.45 3.51
2522 2629 0.631753 TCACTTTGGTGGGGGTTTCA 59.368 50.000 0.00 0.00 43.17 2.69
2536 2643 0.452122 GTTTCAACGCCGATTCACCG 60.452 55.000 0.00 0.00 0.00 4.94
2603 2711 3.119779 TCACTTTGGTTGGTTTTGTCGAC 60.120 43.478 9.11 9.11 0.00 4.20
2605 2713 0.099082 TTGGTTGGTTTTGTCGACGC 59.901 50.000 11.62 0.93 0.00 5.19
2625 2733 1.292061 CGAGAGACCCTAGACTCACG 58.708 60.000 13.02 13.02 40.70 4.35
2998 4104 2.183555 GGGTTTCTCGACGCCGAT 59.816 61.111 0.00 0.00 44.62 4.18
2999 4105 1.314534 TGGGTTTCTCGACGCCGATA 61.315 55.000 0.00 0.00 44.62 2.92
3047 4153 4.454678 TCATCATCCATCTAAGCCAACAC 58.545 43.478 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 116 3.084039 CCTCTTGCAAAAGCTACATCCA 58.916 45.455 0.00 0.00 0.00 3.41
243 251 2.361992 CTGCAAGCTCCATGGCCA 60.362 61.111 8.56 8.56 0.00 5.36
275 283 2.364632 CCCAAAATAGATCACCGTGCA 58.635 47.619 0.00 0.00 0.00 4.57
318 326 2.041265 GCTTCTCCCTCCTCCCCA 59.959 66.667 0.00 0.00 0.00 4.96
342 350 4.272511 TCCCCTTTTCCGCGCCAA 62.273 61.111 0.00 0.00 0.00 4.52
394 402 9.126151 CTTCCTTTTCCTTATCTTATTTCTCCC 57.874 37.037 0.00 0.00 0.00 4.30
395 403 9.688091 ACTTCCTTTTCCTTATCTTATTTCTCC 57.312 33.333 0.00 0.00 0.00 3.71
402 410 9.862149 AGAAACAACTTCCTTTTCCTTATCTTA 57.138 29.630 0.00 0.00 34.21 2.10
403 411 8.768501 AGAAACAACTTCCTTTTCCTTATCTT 57.231 30.769 0.00 0.00 34.21 2.40
404 412 8.633561 CAAGAAACAACTTCCTTTTCCTTATCT 58.366 33.333 0.00 0.00 34.21 1.98
405 413 8.630037 TCAAGAAACAACTTCCTTTTCCTTATC 58.370 33.333 0.00 0.00 34.21 1.75
406 414 8.414003 GTCAAGAAACAACTTCCTTTTCCTTAT 58.586 33.333 0.00 0.00 34.21 1.73
407 415 7.414762 CGTCAAGAAACAACTTCCTTTTCCTTA 60.415 37.037 0.00 0.00 34.21 2.69
408 416 6.625081 CGTCAAGAAACAACTTCCTTTTCCTT 60.625 38.462 0.00 0.00 34.21 3.36
409 417 5.163652 CGTCAAGAAACAACTTCCTTTTCCT 60.164 40.000 0.00 0.00 34.21 3.36
410 418 5.034797 CGTCAAGAAACAACTTCCTTTTCC 58.965 41.667 0.00 0.00 34.21 3.13
411 419 4.499399 GCGTCAAGAAACAACTTCCTTTTC 59.501 41.667 0.00 0.00 34.21 2.29
412 420 4.082463 TGCGTCAAGAAACAACTTCCTTTT 60.082 37.500 0.00 0.00 34.21 2.27
413 421 3.442273 TGCGTCAAGAAACAACTTCCTTT 59.558 39.130 0.00 0.00 34.21 3.11
414 422 3.013921 TGCGTCAAGAAACAACTTCCTT 58.986 40.909 0.00 0.00 34.21 3.36
415 423 2.639065 TGCGTCAAGAAACAACTTCCT 58.361 42.857 0.00 0.00 34.21 3.36
416 424 3.300009 CATGCGTCAAGAAACAACTTCC 58.700 45.455 0.00 0.00 34.21 3.46
417 425 3.300009 CCATGCGTCAAGAAACAACTTC 58.700 45.455 0.00 0.00 0.00 3.01
418 426 2.034558 CCCATGCGTCAAGAAACAACTT 59.965 45.455 0.00 0.00 0.00 2.66
419 427 1.608590 CCCATGCGTCAAGAAACAACT 59.391 47.619 0.00 0.00 0.00 3.16
420 428 1.335872 CCCCATGCGTCAAGAAACAAC 60.336 52.381 0.00 0.00 0.00 3.32
421 429 0.958091 CCCCATGCGTCAAGAAACAA 59.042 50.000 0.00 0.00 0.00 2.83
422 430 1.523154 GCCCCATGCGTCAAGAAACA 61.523 55.000 0.00 0.00 0.00 2.83
423 431 1.212751 GCCCCATGCGTCAAGAAAC 59.787 57.895 0.00 0.00 0.00 2.78
424 432 1.976474 GGCCCCATGCGTCAAGAAA 60.976 57.895 0.00 0.00 42.61 2.52
425 433 2.361104 GGCCCCATGCGTCAAGAA 60.361 61.111 0.00 0.00 42.61 2.52
426 434 4.424711 GGGCCCCATGCGTCAAGA 62.425 66.667 12.23 0.00 42.61 3.02
427 435 4.431131 AGGGCCCCATGCGTCAAG 62.431 66.667 21.43 0.00 42.61 3.02
428 436 4.738998 CAGGGCCCCATGCGTCAA 62.739 66.667 21.43 0.00 42.61 3.18
443 451 3.807538 GAGCATGCCACGCACCAG 61.808 66.667 15.66 0.00 43.04 4.00
466 474 3.770424 GAAACGTTCCGCCGGTCG 61.770 66.667 17.91 17.91 38.08 4.79
467 475 2.662527 TGAAACGTTCCGCCGGTC 60.663 61.111 1.63 0.00 0.00 4.79
468 476 2.663852 CTGAAACGTTCCGCCGGT 60.664 61.111 1.63 0.00 0.00 5.28
469 477 4.084888 GCTGAAACGTTCCGCCGG 62.085 66.667 0.00 0.00 34.33 6.13
472 480 4.084888 CCGGCTGAAACGTTCCGC 62.085 66.667 17.94 12.72 40.49 5.54
473 481 2.663852 ACCGGCTGAAACGTTCCG 60.664 61.111 16.77 16.77 41.41 4.30
474 482 2.943653 CACCGGCTGAAACGTTCC 59.056 61.111 0.00 0.00 0.00 3.62
475 483 2.251371 GCACCGGCTGAAACGTTC 59.749 61.111 0.00 0.00 36.96 3.95
486 494 3.551496 TTTCCAGCCAGAGCACCGG 62.551 63.158 0.00 0.00 43.56 5.28
487 495 2.032528 TTTCCAGCCAGAGCACCG 59.967 61.111 0.00 0.00 43.56 4.94
488 496 2.328099 CGTTTCCAGCCAGAGCACC 61.328 63.158 0.00 0.00 43.56 5.01
489 497 1.166531 AACGTTTCCAGCCAGAGCAC 61.167 55.000 0.00 0.00 43.56 4.40
490 498 0.465460 AAACGTTTCCAGCCAGAGCA 60.465 50.000 7.96 0.00 43.56 4.26
491 499 0.238553 GAAACGTTTCCAGCCAGAGC 59.761 55.000 27.01 1.71 40.32 4.09
518 526 9.644993 CGAAGCGACAATTTGATTTGTATATAA 57.355 29.630 2.79 0.00 39.85 0.98
519 527 8.822855 ACGAAGCGACAATTTGATTTGTATATA 58.177 29.630 2.79 0.00 39.85 0.86
520 528 7.693952 ACGAAGCGACAATTTGATTTGTATAT 58.306 30.769 2.79 0.00 39.85 0.86
521 529 7.067532 ACGAAGCGACAATTTGATTTGTATA 57.932 32.000 2.79 0.00 39.85 1.47
522 530 5.938322 ACGAAGCGACAATTTGATTTGTAT 58.062 33.333 2.79 0.00 39.85 2.29
523 531 5.351233 ACGAAGCGACAATTTGATTTGTA 57.649 34.783 2.79 0.00 39.85 2.41
524 532 4.219033 GACGAAGCGACAATTTGATTTGT 58.781 39.130 2.79 2.90 42.37 2.83
525 533 3.295397 CGACGAAGCGACAATTTGATTTG 59.705 43.478 2.79 0.00 0.00 2.32
526 534 3.185594 TCGACGAAGCGACAATTTGATTT 59.814 39.130 2.79 0.00 35.01 2.17
527 535 2.734606 TCGACGAAGCGACAATTTGATT 59.265 40.909 2.79 0.00 35.01 2.57
528 536 2.333926 TCGACGAAGCGACAATTTGAT 58.666 42.857 2.79 0.00 35.01 2.57
529 537 1.719246 CTCGACGAAGCGACAATTTGA 59.281 47.619 2.79 0.00 36.17 2.69
530 538 1.201812 CCTCGACGAAGCGACAATTTG 60.202 52.381 0.00 0.00 36.17 2.32
531 539 1.068474 CCTCGACGAAGCGACAATTT 58.932 50.000 0.00 0.00 36.17 1.82
532 540 1.352156 GCCTCGACGAAGCGACAATT 61.352 55.000 2.14 0.00 36.17 2.32
533 541 1.805945 GCCTCGACGAAGCGACAAT 60.806 57.895 2.14 0.00 36.17 2.71
534 542 2.430244 GCCTCGACGAAGCGACAA 60.430 61.111 2.14 0.00 36.17 3.18
535 543 4.415332 GGCCTCGACGAAGCGACA 62.415 66.667 12.05 0.00 36.17 4.35
536 544 4.117661 AGGCCTCGACGAAGCGAC 62.118 66.667 12.05 0.00 36.17 5.19
537 545 2.864378 TAGAGGCCTCGACGAAGCGA 62.864 60.000 26.95 2.52 38.74 4.93
538 546 2.381665 CTAGAGGCCTCGACGAAGCG 62.382 65.000 26.95 5.13 34.09 4.68
539 547 1.357334 CTAGAGGCCTCGACGAAGC 59.643 63.158 26.95 10.00 34.09 3.86
540 548 0.378962 CACTAGAGGCCTCGACGAAG 59.621 60.000 26.95 20.31 34.09 3.79
541 549 0.035725 TCACTAGAGGCCTCGACGAA 60.036 55.000 26.95 11.33 34.09 3.85
542 550 0.035725 TTCACTAGAGGCCTCGACGA 60.036 55.000 26.95 18.36 34.09 4.20
543 551 0.099082 GTTCACTAGAGGCCTCGACG 59.901 60.000 26.95 20.04 34.09 5.12
544 552 0.456628 GGTTCACTAGAGGCCTCGAC 59.543 60.000 26.95 17.64 34.09 4.20
545 553 0.039180 TGGTTCACTAGAGGCCTCGA 59.961 55.000 26.95 21.21 34.09 4.04
546 554 0.457851 CTGGTTCACTAGAGGCCTCG 59.542 60.000 26.95 16.26 34.09 4.63
547 555 1.562783 ACTGGTTCACTAGAGGCCTC 58.437 55.000 26.22 26.22 0.00 4.70
548 556 2.921834 TACTGGTTCACTAGAGGCCT 57.078 50.000 3.86 3.86 0.00 5.19
549 557 5.810080 ATAATACTGGTTCACTAGAGGCC 57.190 43.478 0.00 0.00 0.00 5.19
550 558 7.012421 CCAAAATAATACTGGTTCACTAGAGGC 59.988 40.741 0.00 0.00 0.00 4.70
551 559 7.499232 CCCAAAATAATACTGGTTCACTAGAGG 59.501 40.741 0.00 0.00 0.00 3.69
552 560 7.012421 GCCCAAAATAATACTGGTTCACTAGAG 59.988 40.741 0.00 0.00 0.00 2.43
553 561 6.826741 GCCCAAAATAATACTGGTTCACTAGA 59.173 38.462 0.00 0.00 0.00 2.43
554 562 6.828785 AGCCCAAAATAATACTGGTTCACTAG 59.171 38.462 0.00 0.00 0.00 2.57
555 563 6.727394 AGCCCAAAATAATACTGGTTCACTA 58.273 36.000 0.00 0.00 0.00 2.74
556 564 5.580022 AGCCCAAAATAATACTGGTTCACT 58.420 37.500 0.00 0.00 0.00 3.41
557 565 5.914898 AGCCCAAAATAATACTGGTTCAC 57.085 39.130 0.00 0.00 0.00 3.18
558 566 6.252995 AGAAGCCCAAAATAATACTGGTTCA 58.747 36.000 0.00 0.00 0.00 3.18
559 567 6.775594 AGAAGCCCAAAATAATACTGGTTC 57.224 37.500 0.00 0.00 0.00 3.62
560 568 7.410991 AGTAGAAGCCCAAAATAATACTGGTT 58.589 34.615 0.00 0.00 0.00 3.67
561 569 6.970191 AGTAGAAGCCCAAAATAATACTGGT 58.030 36.000 0.00 0.00 0.00 4.00
562 570 7.012421 GTGAGTAGAAGCCCAAAATAATACTGG 59.988 40.741 0.00 0.00 0.00 4.00
563 571 7.770897 AGTGAGTAGAAGCCCAAAATAATACTG 59.229 37.037 0.00 0.00 0.00 2.74
564 572 7.862675 AGTGAGTAGAAGCCCAAAATAATACT 58.137 34.615 0.00 0.00 0.00 2.12
565 573 7.769044 TGAGTGAGTAGAAGCCCAAAATAATAC 59.231 37.037 0.00 0.00 0.00 1.89
566 574 7.857456 TGAGTGAGTAGAAGCCCAAAATAATA 58.143 34.615 0.00 0.00 0.00 0.98
567 575 6.721318 TGAGTGAGTAGAAGCCCAAAATAAT 58.279 36.000 0.00 0.00 0.00 1.28
568 576 6.121776 TGAGTGAGTAGAAGCCCAAAATAA 57.878 37.500 0.00 0.00 0.00 1.40
569 577 5.755409 TGAGTGAGTAGAAGCCCAAAATA 57.245 39.130 0.00 0.00 0.00 1.40
570 578 4.640771 TGAGTGAGTAGAAGCCCAAAAT 57.359 40.909 0.00 0.00 0.00 1.82
571 579 4.640771 ATGAGTGAGTAGAAGCCCAAAA 57.359 40.909 0.00 0.00 0.00 2.44
572 580 4.287067 AGAATGAGTGAGTAGAAGCCCAAA 59.713 41.667 0.00 0.00 0.00 3.28
573 581 3.840666 AGAATGAGTGAGTAGAAGCCCAA 59.159 43.478 0.00 0.00 0.00 4.12
574 582 3.445008 AGAATGAGTGAGTAGAAGCCCA 58.555 45.455 0.00 0.00 0.00 5.36
575 583 4.479786 AAGAATGAGTGAGTAGAAGCCC 57.520 45.455 0.00 0.00 0.00 5.19
576 584 6.635755 ACTAAAGAATGAGTGAGTAGAAGCC 58.364 40.000 0.00 0.00 0.00 4.35
603 611 9.558396 TTGCAATTCACTCCTGAAATTTAATTT 57.442 25.926 2.23 2.23 39.90 1.82
604 612 9.558396 TTTGCAATTCACTCCTGAAATTTAATT 57.442 25.926 0.00 0.00 39.90 1.40
605 613 9.558396 TTTTGCAATTCACTCCTGAAATTTAAT 57.442 25.926 0.00 0.00 39.90 1.40
606 614 8.954950 TTTTGCAATTCACTCCTGAAATTTAA 57.045 26.923 0.00 0.00 39.90 1.52
607 615 8.954950 TTTTTGCAATTCACTCCTGAAATTTA 57.045 26.923 0.00 0.00 39.90 1.40
608 616 7.862512 TTTTTGCAATTCACTCCTGAAATTT 57.137 28.000 0.00 0.00 39.90 1.82
646 654 0.393944 GGTACCTGCAAACCTAGCCC 60.394 60.000 4.06 0.00 32.72 5.19
1020 1039 0.598562 GAGAGTTCTCGCTGGTGTCA 59.401 55.000 0.00 0.00 32.78 3.58
1097 1116 1.366679 GCAACCGTAACCCTAGCTTC 58.633 55.000 0.00 0.00 0.00 3.86
1110 1135 2.346099 AAATCCACAAATCGCAACCG 57.654 45.000 0.00 0.00 0.00 4.44
1139 1165 4.889409 AGGCAACAAAACTTCAGATCAAGA 59.111 37.500 0.00 0.00 41.41 3.02
1177 1214 3.074538 TCATCGATGGTCTCAGGGATCTA 59.925 47.826 24.61 0.00 0.00 1.98
1203 1240 1.610624 GGTTCAGTGCCCTCGAAATCA 60.611 52.381 0.00 0.00 0.00 2.57
1254 1291 3.426568 GCAACACGCCTCTCTGCC 61.427 66.667 0.00 0.00 32.94 4.85
1412 1453 6.017357 CACTCTGCACATGCTCACATATAAAT 60.017 38.462 5.31 0.00 42.66 1.40
1510 1551 7.779798 ACATACTGGCATATAAACAATGACCTT 59.220 33.333 0.00 0.00 30.79 3.50
1627 1673 8.848474 AGTTAAACAAACATGTATGAGCTAGT 57.152 30.769 0.00 0.00 40.83 2.57
1671 1717 8.574251 TCCACATGCTATAAAGTAACAAACAT 57.426 30.769 0.00 0.00 0.00 2.71
1702 1748 7.811117 AAGTAACAAATGGTGTAAAGTGCTA 57.189 32.000 0.00 0.00 40.60 3.49
1809 1857 3.953612 CTCCATTGTAGCTGGCCAAAATA 59.046 43.478 7.01 0.00 33.56 1.40
1853 1901 5.069648 TCCTCCTGCACTCTTCATACTTATG 59.930 44.000 0.00 0.00 35.04 1.90
1920 1968 4.084118 GCTTGATCTTCTGTTGTGTCAGAC 60.084 45.833 0.00 0.00 43.01 3.51
2015 2065 3.295093 TCTGCATCTTACCTCTCTCCAG 58.705 50.000 0.00 0.00 0.00 3.86
2063 2113 6.072286 AGGTTCTTGAGCATGTCATACTTTTG 60.072 38.462 0.00 0.00 34.17 2.44
2065 2115 5.413833 CAGGTTCTTGAGCATGTCATACTTT 59.586 40.000 0.00 0.00 34.17 2.66
2094 2144 3.128242 CCTAATGACTTTGGCTTGAGCAG 59.872 47.826 5.24 0.00 44.36 4.24
2107 2157 5.762179 TCAACTTCATGTCCCTAATGACT 57.238 39.130 0.00 0.00 33.84 3.41
2117 2167 3.251729 TCAGCAAGCTTCAACTTCATGTC 59.748 43.478 0.00 0.00 0.00 3.06
2449 2555 4.648762 ACCAACCAACAACATCAGATTCAA 59.351 37.500 0.00 0.00 0.00 2.69
2516 2622 0.109919 GGTGAATCGGCGTTGAAACC 60.110 55.000 6.85 6.29 0.00 3.27
2517 2623 0.452122 CGGTGAATCGGCGTTGAAAC 60.452 55.000 6.85 0.26 0.00 2.78
2522 2629 0.457337 GTCTACGGTGAATCGGCGTT 60.457 55.000 6.85 0.00 0.00 4.84
2532 2639 2.404215 CAACCAAGTGAGTCTACGGTG 58.596 52.381 0.00 0.00 33.89 4.94
2536 2643 4.638865 ACAAAACCAACCAAGTGAGTCTAC 59.361 41.667 0.00 0.00 0.00 2.59
2603 2711 1.153127 AGTCTAGGGTCTCTCGGCG 60.153 63.158 0.00 0.00 0.00 6.46
2605 2713 1.670791 GTGAGTCTAGGGTCTCTCGG 58.329 60.000 10.22 0.00 0.00 4.63
2625 2733 1.838568 GCGTCGAGAAACCCACCAAC 61.839 60.000 0.00 0.00 0.00 3.77
2917 3025 4.036971 CCAAAGTGAGTCTAGGGTCTATCG 59.963 50.000 0.00 0.00 0.00 2.92
2998 4104 8.170730 TGATGCTTACTATGATTCTAGGGTCTA 58.829 37.037 0.00 0.00 0.00 2.59
2999 4105 7.013220 TGATGCTTACTATGATTCTAGGGTCT 58.987 38.462 0.00 0.00 0.00 3.85
3047 4153 1.340308 TGCTGGTGATTCTGGTGATGG 60.340 52.381 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.