Multiple sequence alignment - TraesCS3A01G228300

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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 TraesCS3A01G228300 chr3A 100.000 4522 0 0 1 4522 427190528 427195049 0.000000e+00 8351.0
1 TraesCS3A01G228300 chr3A 94.752 343 18 0 286 628 427185724 427186066 6.660000e-148 534.0
2 TraesCS3A01G228300 chr3A 75.149 503 119 5 1035 1534 427092817 427092318 9.780000e-57 231.0
3 TraesCS3A01G228300 chr3D 95.524 3195 126 6 629 3814 307879622 307882808 0.000000e+00 5092.0
4 TraesCS3A01G228300 chr3D 94.872 39 0 2 2343 2379 71960141 71960103 4.890000e-05 60.2
5 TraesCS3A01G228300 chr3B 92.587 1848 81 11 629 2433 413866419 413864585 0.000000e+00 2603.0
6 TraesCS3A01G228300 chr3B 93.488 1336 60 4 2479 3814 413864206 413862898 0.000000e+00 1960.0
7 TraesCS3A01G228300 chr3B 82.961 493 76 8 3 491 685116617 685117105 5.370000e-119 438.0
8 TraesCS3A01G228300 chr3B 78.886 431 85 6 3 431 431986590 431987016 2.060000e-73 287.0
9 TraesCS3A01G228300 chr1A 98.873 710 7 1 3814 4522 49115950 49115241 0.000000e+00 1266.0
10 TraesCS3A01G228300 chr1A 84.407 590 81 8 3 587 436297642 436298225 1.830000e-158 569.0
11 TraesCS3A01G228300 chr2A 92.697 712 14 4 3815 4522 383893039 383892362 0.000000e+00 992.0
12 TraesCS3A01G228300 chr2A 81.770 938 157 12 2619 3548 174027289 174028220 0.000000e+00 773.0
13 TraesCS3A01G228300 chr2A 82.000 850 141 10 2597 3440 174245655 174246498 0.000000e+00 712.0
14 TraesCS3A01G228300 chr2A 80.734 545 100 5 990 1531 174039097 174039639 1.950000e-113 420.0
15 TraesCS3A01G228300 chr2A 80.000 545 104 5 990 1531 174244488 174245030 9.110000e-107 398.0
16 TraesCS3A01G228300 chr2A 82.927 205 29 4 2597 2800 174040262 174040461 3.590000e-41 180.0
17 TraesCS3A01G228300 chr2D 82.177 937 154 11 2619 3548 174324527 174325457 0.000000e+00 793.0
18 TraesCS3A01G228300 chr2D 81.081 777 134 10 2597 3366 174383078 174383848 3.870000e-170 608.0
19 TraesCS3A01G228300 chr2D 83.377 385 61 3 1148 1531 174382071 174382453 2.000000e-93 353.0
20 TraesCS3A01G228300 chr2B 80.662 936 169 9 2619 3548 222143177 222144106 0.000000e+00 715.0
21 TraesCS3A01G228300 chr2B 79.475 648 118 13 3 641 201233438 201234079 3.210000e-121 446.0
22 TraesCS3A01G228300 chr2B 79.401 534 83 21 106 628 766039312 766039829 7.200000e-93 351.0
23 TraesCS3A01G228300 chr6B 77.111 900 197 9 2620 3518 688470551 688471442 3.120000e-141 512.0
24 TraesCS3A01G228300 chr6B 80.471 425 75 8 1111 1531 688469653 688470073 7.300000e-83 318.0
25 TraesCS3A01G228300 chr6B 78.241 216 38 7 2166 2374 432865902 432866115 3.670000e-26 130.0
26 TraesCS3A01G228300 chr6A 76.829 902 198 11 2619 3518 599830951 599830059 8.740000e-137 497.0
27 TraesCS3A01G228300 chr6A 83.193 119 17 3 2259 2374 387971621 387971503 6.190000e-19 106.0
28 TraesCS3A01G228300 chr4A 81.848 606 97 11 3 602 372323815 372324413 8.740000e-137 497.0
29 TraesCS3A01G228300 chr4A 81.536 612 87 18 1 604 349306759 349307352 8.800000e-132 481.0
30 TraesCS3A01G228300 chr4A 87.733 375 33 5 4157 4522 642901929 642901559 4.180000e-115 425.0
31 TraesCS3A01G228300 chr4A 88.732 71 8 0 4085 4155 642902050 642901980 2.240000e-13 87.9
32 TraesCS3A01G228300 chr4A 91.379 58 5 0 4011 4068 642902097 642902040 3.750000e-11 80.5
33 TraesCS3A01G228300 chr6D 76.386 902 202 11 2619 3518 453651418 453650526 4.090000e-130 475.0
34 TraesCS3A01G228300 chr6D 77.206 816 147 29 1111 1906 453652382 453651586 1.490000e-119 440.0
35 TraesCS3A01G228300 chr5B 82.957 487 81 2 6 491 267272421 267271936 5.370000e-119 438.0
36 TraesCS3A01G228300 chr5B 84.536 97 13 2 2279 2374 688804646 688804551 1.340000e-15 95.3
37 TraesCS3A01G228300 chr5B 84.536 97 13 2 2279 2374 688840345 688840250 1.340000e-15 95.3
38 TraesCS3A01G228300 chr7D 78.384 495 97 8 3 492 3841708 3842197 3.400000e-81 313.0
39 TraesCS3A01G228300 chr7D 79.934 304 51 10 1238 1536 78214906 78214608 9.850000e-52 215.0
40 TraesCS3A01G228300 chrUn 78.241 216 38 7 2166 2374 191003550 191003763 3.670000e-26 130.0
41 TraesCS3A01G228300 chr7B 76.680 253 45 12 2132 2374 438362579 438362331 1.320000e-25 128.0


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 TraesCS3A01G228300 chr3A 427190528 427195049 4521 False 8351.0 8351 100.0000 1 4522 1 chr3A.!!$F2 4521
1 TraesCS3A01G228300 chr3D 307879622 307882808 3186 False 5092.0 5092 95.5240 629 3814 1 chr3D.!!$F1 3185
2 TraesCS3A01G228300 chr3B 413862898 413866419 3521 True 2281.5 2603 93.0375 629 3814 2 chr3B.!!$R1 3185
3 TraesCS3A01G228300 chr1A 49115241 49115950 709 True 1266.0 1266 98.8730 3814 4522 1 chr1A.!!$R1 708
4 TraesCS3A01G228300 chr1A 436297642 436298225 583 False 569.0 569 84.4070 3 587 1 chr1A.!!$F1 584
5 TraesCS3A01G228300 chr2A 383892362 383893039 677 True 992.0 992 92.6970 3815 4522 1 chr2A.!!$R1 707
6 TraesCS3A01G228300 chr2A 174027289 174028220 931 False 773.0 773 81.7700 2619 3548 1 chr2A.!!$F1 929
7 TraesCS3A01G228300 chr2A 174244488 174246498 2010 False 555.0 712 81.0000 990 3440 2 chr2A.!!$F3 2450
8 TraesCS3A01G228300 chr2A 174039097 174040461 1364 False 300.0 420 81.8305 990 2800 2 chr2A.!!$F2 1810
9 TraesCS3A01G228300 chr2D 174324527 174325457 930 False 793.0 793 82.1770 2619 3548 1 chr2D.!!$F1 929
10 TraesCS3A01G228300 chr2D 174382071 174383848 1777 False 480.5 608 82.2290 1148 3366 2 chr2D.!!$F2 2218
11 TraesCS3A01G228300 chr2B 222143177 222144106 929 False 715.0 715 80.6620 2619 3548 1 chr2B.!!$F2 929
12 TraesCS3A01G228300 chr2B 201233438 201234079 641 False 446.0 446 79.4750 3 641 1 chr2B.!!$F1 638
13 TraesCS3A01G228300 chr2B 766039312 766039829 517 False 351.0 351 79.4010 106 628 1 chr2B.!!$F3 522
14 TraesCS3A01G228300 chr6B 688469653 688471442 1789 False 415.0 512 78.7910 1111 3518 2 chr6B.!!$F2 2407
15 TraesCS3A01G228300 chr6A 599830059 599830951 892 True 497.0 497 76.8290 2619 3518 1 chr6A.!!$R2 899
16 TraesCS3A01G228300 chr4A 372323815 372324413 598 False 497.0 497 81.8480 3 602 1 chr4A.!!$F2 599
17 TraesCS3A01G228300 chr4A 349306759 349307352 593 False 481.0 481 81.5360 1 604 1 chr4A.!!$F1 603
18 TraesCS3A01G228300 chr6D 453650526 453652382 1856 True 457.5 475 76.7960 1111 3518 2 chr6D.!!$R1 2407

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
436 438 0.036858 GGACTCTGTGAGCCAACCTC 60.037 60.0 0.00 0.00 41.15 3.85 F
1425 1473 0.108585 AGAAGCTCAAGTTTCCGGCA 59.891 50.0 0.00 0.00 36.14 5.69 F
2943 3514 0.035317 AGTGGCAAGATCGTGCAAGA 59.965 50.0 30.28 14.02 46.81 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2216 1.160329 AATCAGAACCGGCTATGCGC 61.160 55.0 0.00 0.0 38.13 6.09 R
3350 3940 0.530288 GGCCAATGCAAATACGTGGT 59.470 50.0 0.00 0.0 40.13 4.16 R
4263 4857 5.068987 AGCAAACTTAAGTTGCAATGGAAGA 59.931 36.0 28.47 0.0 38.44 2.87 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
19 20 0.403271 AGGCTCAAGTGCATCCTGTT 59.597 50.000 0.00 0.00 34.04 3.16
79 80 1.137086 ACGCTGTCTCACACTGAACTT 59.863 47.619 0.00 0.00 0.00 2.66
97 98 1.139853 CTTCCTCACCCTACTGATGCC 59.860 57.143 0.00 0.00 0.00 4.40
116 117 0.182537 CCCTGTGGTTCCAGTCACAA 59.817 55.000 0.00 0.00 42.40 3.33
157 158 3.118884 GCAAGAAGAATGGTGCCATGATT 60.119 43.478 4.26 2.99 36.68 2.57
169 170 3.058293 GTGCCATGATTGAACAAGTTCGA 60.058 43.478 5.41 5.41 42.28 3.71
205 206 0.325933 CATCAGCCCTGGAAGACACA 59.674 55.000 0.00 0.00 34.07 3.72
246 247 1.150536 AAGCCCGTTTTCCTGCAGA 59.849 52.632 17.39 0.00 0.00 4.26
294 295 2.039624 AGGAGGGGATGTCAGCGT 59.960 61.111 0.00 0.00 0.00 5.07
303 304 1.394618 GATGTCAGCGTCCCTACTCT 58.605 55.000 0.00 0.00 0.00 3.24
331 332 1.226686 CTGCACCAGTCACTGACAGC 61.227 60.000 6.30 7.74 34.60 4.40
376 377 3.695606 GCTGCCTCTCGACCCACA 61.696 66.667 0.00 0.00 0.00 4.17
384 385 2.926242 TCGACCCACAAGGACCCC 60.926 66.667 0.00 0.00 39.89 4.95
399 400 2.203567 CCCGAAGCCCAACCCAAA 60.204 61.111 0.00 0.00 0.00 3.28
431 432 2.052779 CAGTGGACTCTGTGAGCCA 58.947 57.895 6.63 6.63 35.00 4.75
436 438 0.036858 GGACTCTGTGAGCCAACCTC 60.037 60.000 0.00 0.00 41.15 3.85
451 454 0.252375 ACCTCCCAACCGGCTACTTA 60.252 55.000 0.00 0.00 0.00 2.24
461 467 2.463592 GGCTACTTAAAGGCGCGTT 58.536 52.632 10.00 10.00 31.82 4.84
462 468 1.643880 GGCTACTTAAAGGCGCGTTA 58.356 50.000 16.65 6.93 31.82 3.18
494 506 1.410648 GGGCATCCAGTGGATCACAAT 60.411 52.381 22.36 0.00 40.98 2.71
516 528 0.886490 CAGCGGCACTGTTCTTCCTT 60.886 55.000 1.45 0.00 41.86 3.36
517 529 0.603975 AGCGGCACTGTTCTTCCTTC 60.604 55.000 1.45 0.00 0.00 3.46
519 531 1.433534 CGGCACTGTTCTTCCTTCTC 58.566 55.000 0.00 0.00 0.00 2.87
535 547 3.033773 TCCCCCGATCCCCTCTCA 61.034 66.667 0.00 0.00 0.00 3.27
539 551 1.689233 CCCGATCCCCTCTCACCAA 60.689 63.158 0.00 0.00 0.00 3.67
540 552 1.056700 CCCGATCCCCTCTCACCAAT 61.057 60.000 0.00 0.00 0.00 3.16
541 553 0.839946 CCGATCCCCTCTCACCAATT 59.160 55.000 0.00 0.00 0.00 2.32
542 554 1.202698 CCGATCCCCTCTCACCAATTC 60.203 57.143 0.00 0.00 0.00 2.17
543 555 1.765314 CGATCCCCTCTCACCAATTCT 59.235 52.381 0.00 0.00 0.00 2.40
544 556 2.171448 CGATCCCCTCTCACCAATTCTT 59.829 50.000 0.00 0.00 0.00 2.52
545 557 3.549794 GATCCCCTCTCACCAATTCTTG 58.450 50.000 0.00 0.00 0.00 3.02
546 558 2.348472 TCCCCTCTCACCAATTCTTGT 58.652 47.619 0.00 0.00 0.00 3.16
547 559 3.526899 TCCCCTCTCACCAATTCTTGTA 58.473 45.455 0.00 0.00 0.00 2.41
548 560 4.111577 TCCCCTCTCACCAATTCTTGTAT 58.888 43.478 0.00 0.00 0.00 2.29
549 561 4.164221 TCCCCTCTCACCAATTCTTGTATC 59.836 45.833 0.00 0.00 0.00 2.24
550 562 4.080356 CCCCTCTCACCAATTCTTGTATCA 60.080 45.833 0.00 0.00 0.00 2.15
551 563 5.121811 CCCTCTCACCAATTCTTGTATCAG 58.878 45.833 0.00 0.00 0.00 2.90
552 564 4.574013 CCTCTCACCAATTCTTGTATCAGC 59.426 45.833 0.00 0.00 0.00 4.26
553 565 5.426504 CTCTCACCAATTCTTGTATCAGCT 58.573 41.667 0.00 0.00 0.00 4.24
554 566 6.407412 CCTCTCACCAATTCTTGTATCAGCTA 60.407 42.308 0.00 0.00 0.00 3.32
555 567 6.341316 TCTCACCAATTCTTGTATCAGCTAC 58.659 40.000 0.00 0.00 0.00 3.58
556 568 6.155221 TCTCACCAATTCTTGTATCAGCTACT 59.845 38.462 0.00 0.00 0.00 2.57
557 569 7.342026 TCTCACCAATTCTTGTATCAGCTACTA 59.658 37.037 0.00 0.00 0.00 1.82
558 570 8.023021 TCACCAATTCTTGTATCAGCTACTAT 57.977 34.615 0.00 0.00 0.00 2.12
559 571 9.143155 TCACCAATTCTTGTATCAGCTACTATA 57.857 33.333 0.00 0.00 0.00 1.31
560 572 9.764363 CACCAATTCTTGTATCAGCTACTATAA 57.236 33.333 0.00 0.00 0.00 0.98
566 578 9.967346 TTCTTGTATCAGCTACTATAATCACAC 57.033 33.333 0.00 0.00 0.00 3.82
567 579 9.355916 TCTTGTATCAGCTACTATAATCACACT 57.644 33.333 0.00 0.00 0.00 3.55
568 580 9.973450 CTTGTATCAGCTACTATAATCACACTT 57.027 33.333 0.00 0.00 0.00 3.16
574 586 9.409918 TCAGCTACTATAATCACACTTAAGACT 57.590 33.333 10.09 0.00 0.00 3.24
575 587 9.672086 CAGCTACTATAATCACACTTAAGACTC 57.328 37.037 10.09 0.00 0.00 3.36
576 588 8.561212 AGCTACTATAATCACACTTAAGACTCG 58.439 37.037 10.09 0.00 0.00 4.18
577 589 8.557864 GCTACTATAATCACACTTAAGACTCGA 58.442 37.037 10.09 0.46 0.00 4.04
582 594 6.633668 AATCACACTTAAGACTCGAATTCG 57.366 37.500 21.78 21.78 41.45 3.34
583 595 5.117355 TCACACTTAAGACTCGAATTCGT 57.883 39.130 25.93 9.25 40.80 3.85
584 596 4.915667 TCACACTTAAGACTCGAATTCGTG 59.084 41.667 25.93 24.94 40.80 4.35
585 597 4.915667 CACACTTAAGACTCGAATTCGTGA 59.084 41.667 30.31 12.29 40.80 4.35
586 598 5.059832 CACACTTAAGACTCGAATTCGTGAG 59.940 44.000 30.31 21.95 40.80 3.51
588 600 5.629849 CACTTAAGACTCGAATTCGTGAGTT 59.370 40.000 30.31 23.44 45.09 3.01
589 601 6.144080 CACTTAAGACTCGAATTCGTGAGTTT 59.856 38.462 30.31 18.57 45.09 2.66
590 602 6.700520 ACTTAAGACTCGAATTCGTGAGTTTT 59.299 34.615 30.31 25.23 45.09 2.43
591 603 4.974103 AGACTCGAATTCGTGAGTTTTG 57.026 40.909 30.31 13.32 45.09 2.44
592 604 3.184581 AGACTCGAATTCGTGAGTTTTGC 59.815 43.478 30.31 14.67 45.09 3.68
593 605 2.869801 ACTCGAATTCGTGAGTTTTGCA 59.130 40.909 30.31 7.52 42.61 4.08
594 606 3.311322 ACTCGAATTCGTGAGTTTTGCAA 59.689 39.130 30.31 0.00 42.61 4.08
595 607 4.024048 ACTCGAATTCGTGAGTTTTGCAAT 60.024 37.500 30.31 6.70 42.61 3.56
596 608 5.178623 ACTCGAATTCGTGAGTTTTGCAATA 59.821 36.000 30.31 6.45 42.61 1.90
597 609 5.617609 TCGAATTCGTGAGTTTTGCAATAG 58.382 37.500 25.93 0.00 40.80 1.73
598 610 5.407084 TCGAATTCGTGAGTTTTGCAATAGA 59.593 36.000 25.93 0.00 40.80 1.98
599 611 6.092122 TCGAATTCGTGAGTTTTGCAATAGAT 59.908 34.615 25.93 0.00 40.80 1.98
600 612 6.409185 CGAATTCGTGAGTTTTGCAATAGATC 59.591 38.462 19.67 0.00 34.11 2.75
601 613 4.840401 TCGTGAGTTTTGCAATAGATCG 57.160 40.909 0.00 2.17 0.00 3.69
602 614 4.490743 TCGTGAGTTTTGCAATAGATCGA 58.509 39.130 0.00 4.61 0.00 3.59
603 615 4.562789 TCGTGAGTTTTGCAATAGATCGAG 59.437 41.667 0.00 0.00 0.00 4.04
604 616 4.562789 CGTGAGTTTTGCAATAGATCGAGA 59.437 41.667 0.00 0.00 0.00 4.04
605 617 5.276114 CGTGAGTTTTGCAATAGATCGAGAG 60.276 44.000 0.00 0.00 0.00 3.20
606 618 5.578727 GTGAGTTTTGCAATAGATCGAGAGT 59.421 40.000 0.00 0.00 0.00 3.24
607 619 6.091441 GTGAGTTTTGCAATAGATCGAGAGTT 59.909 38.462 0.00 0.00 0.00 3.01
608 620 7.275779 GTGAGTTTTGCAATAGATCGAGAGTTA 59.724 37.037 0.00 0.00 0.00 2.24
609 621 7.981789 TGAGTTTTGCAATAGATCGAGAGTTAT 59.018 33.333 0.00 0.00 0.00 1.89
610 622 9.464714 GAGTTTTGCAATAGATCGAGAGTTATA 57.535 33.333 0.00 0.00 0.00 0.98
611 623 9.988815 AGTTTTGCAATAGATCGAGAGTTATAT 57.011 29.630 0.00 0.00 0.00 0.86
616 628 8.687242 TGCAATAGATCGAGAGTTATATTAGGG 58.313 37.037 0.00 0.00 29.11 3.53
617 629 8.688151 GCAATAGATCGAGAGTTATATTAGGGT 58.312 37.037 0.00 0.00 29.11 4.34
619 631 9.976776 AATAGATCGAGAGTTATATTAGGGTGA 57.023 33.333 0.00 0.00 28.57 4.02
620 632 7.690952 AGATCGAGAGTTATATTAGGGTGAC 57.309 40.000 0.00 0.00 0.00 3.67
648 660 4.042398 CACACTACGGGAGATATGTTTCG 58.958 47.826 0.00 0.00 0.00 3.46
699 727 2.624838 CAACACACCTTTGCTCCTCAAT 59.375 45.455 0.00 0.00 34.12 2.57
701 729 2.624838 ACACACCTTTGCTCCTCAATTG 59.375 45.455 0.00 0.00 34.12 2.32
718 746 7.930325 TCCTCAATTGTAGATTTGCTAGAGATG 59.070 37.037 5.13 0.00 0.00 2.90
796 824 2.043652 GGCCATGAGTGCCCATGT 60.044 61.111 0.00 0.00 43.33 3.21
873 901 7.289317 TCAGTTTCTTCTCTACCAAGTTCCTTA 59.711 37.037 0.00 0.00 0.00 2.69
879 907 5.900437 TCTCTACCAAGTTCCTTAGGAGAA 58.100 41.667 0.00 0.00 31.21 2.87
901 929 1.221840 CATGGACCAGAGTTCCCCG 59.778 63.158 0.00 0.00 0.00 5.73
912 940 2.115291 GTTCCCCGCAGCCTTGATC 61.115 63.158 0.00 0.00 0.00 2.92
914 942 2.515523 CCCCGCAGCCTTGATCTG 60.516 66.667 0.00 0.00 34.79 2.90
1080 1128 2.629656 CCCGGGCTTTGTGCTTCTG 61.630 63.158 8.08 0.00 42.39 3.02
1294 1342 1.153647 CCGCTGCTCCACGACATTA 60.154 57.895 0.00 0.00 0.00 1.90
1425 1473 0.108585 AGAAGCTCAAGTTTCCGGCA 59.891 50.000 0.00 0.00 36.14 5.69
1479 1527 2.044946 GAGGGCGAGCAATGGGTT 60.045 61.111 0.00 0.00 0.00 4.11
1514 1562 1.396653 CTCAACCCTGCATTCCATCC 58.603 55.000 0.00 0.00 0.00 3.51
1522 1570 1.139654 CTGCATTCCATCCCGAGAAGA 59.860 52.381 0.00 0.00 0.00 2.87
1602 1690 8.351495 TCAAATGCTGGCGAAATTATAAATTC 57.649 30.769 3.54 3.54 0.00 2.17
1798 1932 1.893801 AGTAACTACGCTGAAGGTGCT 59.106 47.619 0.00 0.00 0.00 4.40
2006 2143 6.015772 TGCAAACTTTCTACCCCAAAACTATC 60.016 38.462 0.00 0.00 0.00 2.08
2053 2194 2.213499 CCTAGCAAATCGGCTTACCTG 58.787 52.381 0.00 0.00 42.71 4.00
2061 2202 5.679638 GCAAATCGGCTTACCTGAAATGAAT 60.680 40.000 0.00 0.00 0.00 2.57
2075 2216 5.221880 TGAAATGAATTTTCAGGCGACTTG 58.778 37.500 0.00 0.00 46.80 3.16
2125 2266 6.008331 CCAACATCAATCATAGGGATCATGT 58.992 40.000 0.00 0.00 34.28 3.21
2155 2297 9.167387 TCTTTAATACTTAAATAGCTAGCCCCT 57.833 33.333 12.13 0.00 34.84 4.79
2230 2372 5.600484 ACATGAAAATGACCCACCTTAACAA 59.400 36.000 0.00 0.00 0.00 2.83
2251 2393 6.347696 ACAAGCAACCATTCAAATCAAAAGA 58.652 32.000 0.00 0.00 0.00 2.52
2457 2599 1.388547 ACATTTCCACTGCAACGTGT 58.611 45.000 5.48 0.00 33.07 4.49
2624 3195 4.826274 TTGTTGGGGTGTCATTTTTCAA 57.174 36.364 0.00 0.00 0.00 2.69
2658 3229 6.272822 ACCAAAAACAATAGAAGGATGAGC 57.727 37.500 0.00 0.00 0.00 4.26
2705 3276 8.206325 TCAATTCTGCTCAATCTAATCAGAAC 57.794 34.615 5.29 0.00 43.72 3.01
2832 3403 4.080919 TCAGGAATGACGATTGATGAGGTT 60.081 41.667 0.00 0.00 0.00 3.50
2943 3514 0.035317 AGTGGCAAGATCGTGCAAGA 59.965 50.000 30.28 14.02 46.81 3.02
2990 3562 9.496873 TGGAAAGAATAAAATTGACTACGAAGA 57.503 29.630 0.00 0.00 0.00 2.87
3097 3686 9.765795 ATAAGTCATTTAGTCTACAATGTAGGC 57.234 33.333 16.56 16.56 32.96 3.93
3193 3782 5.919348 ATGGAGATTGGAGGTATCACATT 57.081 39.130 0.00 0.00 0.00 2.71
3305 3894 0.736325 GGTTCGCCGATGGGATATCG 60.736 60.000 0.00 2.53 40.86 2.92
3317 3906 2.644299 TGGGATATCGAAGGCATCCAAT 59.356 45.455 16.09 0.00 39.13 3.16
3321 3910 5.888161 GGGATATCGAAGGCATCCAATAATT 59.112 40.000 16.09 0.00 39.13 1.40
3381 3971 1.504359 CATTGGCCAACAGTTTGCAG 58.496 50.000 23.27 0.00 0.00 4.41
3390 3980 0.383231 ACAGTTTGCAGTGCTTGAGC 59.617 50.000 17.60 4.68 42.50 4.26
3414 4004 5.130292 CAAGTTTTCCTTGTGCATGATCT 57.870 39.130 0.00 0.00 44.64 2.75
3556 4146 7.039270 ACGAAAGTATGCATGTTCACTATACA 58.961 34.615 10.16 0.00 46.88 2.29
3774 4364 2.569853 TCTTCCCTTTAATGCGGTGAGA 59.430 45.455 0.00 0.00 0.00 3.27
4263 4857 8.477419 TCTGTTTCCATGGACTAGAAAATTTT 57.523 30.769 15.91 2.28 31.71 1.82
4374 4968 8.635765 AATGAAAGTTTGCTACCAAAGATAGA 57.364 30.769 0.00 0.00 41.32 1.98
4499 5093 3.401033 AGCAAGGTTATTGTTTTGGGC 57.599 42.857 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.000060 CGTAGTTGGGAGACGTGGAAA 60.000 52.381 0.00 0.00 0.00 3.13
79 80 0.691078 GGGCATCAGTAGGGTGAGGA 60.691 60.000 0.00 0.00 29.46 3.71
97 98 0.182537 TTGTGACTGGAACCACAGGG 59.817 55.000 0.00 0.00 43.20 4.45
116 117 1.091771 CGCCAACATCGCTGAAGGAT 61.092 55.000 0.00 0.00 0.00 3.24
157 158 2.198406 CAACGGACTCGAACTTGTTCA 58.802 47.619 13.05 1.25 40.11 3.18
205 206 1.074926 AGCCACTCGATCCTCCCAT 60.075 57.895 0.00 0.00 0.00 4.00
246 247 2.442413 CTTGCCCCCAAGCCTCTT 59.558 61.111 0.00 0.00 41.72 2.85
294 295 1.016415 AGGGTTAGCCAGAGTAGGGA 58.984 55.000 2.44 0.00 36.17 4.20
303 304 2.124507 GACTGGTGCAGGGTTAGCCA 62.125 60.000 2.44 0.00 35.51 4.75
376 377 2.856988 TTGGGCTTCGGGGTCCTT 60.857 61.111 1.43 0.00 0.00 3.36
384 385 0.249280 GTTGTTTGGGTTGGGCTTCG 60.249 55.000 0.00 0.00 0.00 3.79
423 424 1.150536 GTTGGGAGGTTGGCTCACA 59.849 57.895 0.00 0.00 31.64 3.58
431 432 1.131928 AAGTAGCCGGTTGGGAGGTT 61.132 55.000 1.90 0.00 38.47 3.50
436 438 1.746470 CCTTTAAGTAGCCGGTTGGG 58.254 55.000 1.90 0.00 39.58 4.12
451 454 1.445582 CTCCGAGTAACGCGCCTTT 60.446 57.895 5.73 0.00 41.07 3.11
461 467 1.202903 GGATGCCCTAGTCTCCGAGTA 60.203 57.143 0.00 0.00 0.00 2.59
462 468 0.468400 GGATGCCCTAGTCTCCGAGT 60.468 60.000 0.00 0.00 0.00 4.18
498 510 0.603975 GAAGGAAGAACAGTGCCGCT 60.604 55.000 0.00 0.00 0.00 5.52
516 528 2.704198 AGAGGGGATCGGGGGAGA 60.704 66.667 0.00 0.00 0.00 3.71
517 529 2.203714 GAGAGGGGATCGGGGGAG 60.204 72.222 0.00 0.00 0.00 4.30
519 531 2.844839 GTGAGAGGGGATCGGGGG 60.845 72.222 0.00 0.00 0.00 5.40
540 552 9.967346 GTGTGATTATAGTAGCTGATACAAGAA 57.033 33.333 5.81 0.00 36.79 2.52
541 553 9.355916 AGTGTGATTATAGTAGCTGATACAAGA 57.644 33.333 5.81 0.00 36.79 3.02
542 554 9.973450 AAGTGTGATTATAGTAGCTGATACAAG 57.027 33.333 5.81 0.00 36.79 3.16
548 560 9.409918 AGTCTTAAGTGTGATTATAGTAGCTGA 57.590 33.333 1.63 0.00 0.00 4.26
549 561 9.672086 GAGTCTTAAGTGTGATTATAGTAGCTG 57.328 37.037 1.63 0.00 0.00 4.24
550 562 8.561212 CGAGTCTTAAGTGTGATTATAGTAGCT 58.439 37.037 1.63 0.00 0.00 3.32
551 563 8.557864 TCGAGTCTTAAGTGTGATTATAGTAGC 58.442 37.037 1.63 0.00 0.00 3.58
556 568 9.447040 CGAATTCGAGTCTTAAGTGTGATTATA 57.553 33.333 23.29 0.00 43.02 0.98
557 569 7.974501 ACGAATTCGAGTCTTAAGTGTGATTAT 59.025 33.333 33.05 1.60 43.02 1.28
558 570 7.272731 CACGAATTCGAGTCTTAAGTGTGATTA 59.727 37.037 33.05 0.00 43.02 1.75
559 571 6.089551 CACGAATTCGAGTCTTAAGTGTGATT 59.910 38.462 33.05 2.30 43.02 2.57
560 572 5.573282 CACGAATTCGAGTCTTAAGTGTGAT 59.427 40.000 33.05 2.70 43.02 3.06
561 573 4.915667 CACGAATTCGAGTCTTAAGTGTGA 59.084 41.667 33.05 0.00 43.02 3.58
562 574 4.915667 TCACGAATTCGAGTCTTAAGTGTG 59.084 41.667 33.05 16.09 43.02 3.82
563 575 5.117355 TCACGAATTCGAGTCTTAAGTGT 57.883 39.130 33.05 4.07 43.02 3.55
564 576 5.154932 ACTCACGAATTCGAGTCTTAAGTG 58.845 41.667 33.05 17.27 38.03 3.16
565 577 5.373981 ACTCACGAATTCGAGTCTTAAGT 57.626 39.130 33.05 19.88 38.03 2.24
566 578 6.692232 AAACTCACGAATTCGAGTCTTAAG 57.308 37.500 33.05 19.28 41.60 1.85
567 579 6.563381 GCAAAACTCACGAATTCGAGTCTTAA 60.563 38.462 33.05 8.95 41.60 1.85
568 580 5.107607 GCAAAACTCACGAATTCGAGTCTTA 60.108 40.000 33.05 9.31 41.60 2.10
569 581 4.318831 GCAAAACTCACGAATTCGAGTCTT 60.319 41.667 33.05 17.10 41.60 3.01
570 582 3.184581 GCAAAACTCACGAATTCGAGTCT 59.815 43.478 33.05 12.01 41.60 3.24
571 583 3.059868 TGCAAAACTCACGAATTCGAGTC 60.060 43.478 33.05 14.88 41.60 3.36
572 584 2.869801 TGCAAAACTCACGAATTCGAGT 59.130 40.909 33.05 23.10 44.30 4.18
573 585 3.519908 TGCAAAACTCACGAATTCGAG 57.480 42.857 33.05 25.27 43.02 4.04
574 586 3.953874 TTGCAAAACTCACGAATTCGA 57.046 38.095 33.05 11.87 43.02 3.71
575 587 5.617609 TCTATTGCAAAACTCACGAATTCG 58.382 37.500 25.64 25.64 46.33 3.34
576 588 6.409185 CGATCTATTGCAAAACTCACGAATTC 59.591 38.462 1.71 0.00 0.00 2.17
577 589 6.092122 TCGATCTATTGCAAAACTCACGAATT 59.908 34.615 1.71 0.00 0.00 2.17
578 590 5.580691 TCGATCTATTGCAAAACTCACGAAT 59.419 36.000 1.71 0.00 0.00 3.34
579 591 4.926832 TCGATCTATTGCAAAACTCACGAA 59.073 37.500 1.71 0.00 0.00 3.85
580 592 4.490743 TCGATCTATTGCAAAACTCACGA 58.509 39.130 1.71 8.43 0.00 4.35
581 593 4.562789 TCTCGATCTATTGCAAAACTCACG 59.437 41.667 1.71 6.12 0.00 4.35
582 594 5.578727 ACTCTCGATCTATTGCAAAACTCAC 59.421 40.000 1.71 0.00 0.00 3.51
583 595 5.724328 ACTCTCGATCTATTGCAAAACTCA 58.276 37.500 1.71 0.00 0.00 3.41
584 596 6.654793 AACTCTCGATCTATTGCAAAACTC 57.345 37.500 1.71 0.00 0.00 3.01
585 597 9.988815 ATATAACTCTCGATCTATTGCAAAACT 57.011 29.630 1.71 0.00 0.00 2.66
590 602 8.687242 CCCTAATATAACTCTCGATCTATTGCA 58.313 37.037 0.00 0.00 0.00 4.08
591 603 8.688151 ACCCTAATATAACTCTCGATCTATTGC 58.312 37.037 0.00 0.00 0.00 3.56
593 605 9.976776 TCACCCTAATATAACTCTCGATCTATT 57.023 33.333 0.00 0.00 0.00 1.73
594 606 9.398538 GTCACCCTAATATAACTCTCGATCTAT 57.601 37.037 0.00 0.00 0.00 1.98
595 607 7.828223 GGTCACCCTAATATAACTCTCGATCTA 59.172 40.741 0.00 0.00 0.00 1.98
596 608 6.660094 GGTCACCCTAATATAACTCTCGATCT 59.340 42.308 0.00 0.00 0.00 2.75
597 609 6.127675 GGGTCACCCTAATATAACTCTCGATC 60.128 46.154 5.22 0.00 41.34 3.69
598 610 5.715753 GGGTCACCCTAATATAACTCTCGAT 59.284 44.000 5.22 0.00 41.34 3.59
599 611 5.075493 GGGTCACCCTAATATAACTCTCGA 58.925 45.833 5.22 0.00 41.34 4.04
600 612 5.388408 GGGTCACCCTAATATAACTCTCG 57.612 47.826 5.22 0.00 41.34 4.04
614 626 1.067354 CGTAGTGTGTTAGGGTCACCC 60.067 57.143 3.85 3.85 45.90 4.61
615 627 1.067354 CCGTAGTGTGTTAGGGTCACC 60.067 57.143 0.00 0.00 35.25 4.02
616 628 1.067354 CCCGTAGTGTGTTAGGGTCAC 60.067 57.143 0.00 0.00 37.36 3.67
617 629 1.203038 TCCCGTAGTGTGTTAGGGTCA 60.203 52.381 0.00 0.00 42.57 4.02
618 630 1.475682 CTCCCGTAGTGTGTTAGGGTC 59.524 57.143 0.00 0.00 42.57 4.46
619 631 1.076024 TCTCCCGTAGTGTGTTAGGGT 59.924 52.381 0.00 0.00 42.57 4.34
620 632 1.843368 TCTCCCGTAGTGTGTTAGGG 58.157 55.000 0.00 0.00 43.32 3.53
621 633 4.583489 ACATATCTCCCGTAGTGTGTTAGG 59.417 45.833 0.00 0.00 0.00 2.69
622 634 5.769484 ACATATCTCCCGTAGTGTGTTAG 57.231 43.478 0.00 0.00 0.00 2.34
623 635 6.534475 AAACATATCTCCCGTAGTGTGTTA 57.466 37.500 0.00 0.00 30.60 2.41
624 636 5.416271 AAACATATCTCCCGTAGTGTGTT 57.584 39.130 0.00 0.00 31.40 3.32
625 637 4.439700 CGAAACATATCTCCCGTAGTGTGT 60.440 45.833 0.00 0.00 0.00 3.72
626 638 4.042398 CGAAACATATCTCCCGTAGTGTG 58.958 47.826 0.00 0.00 0.00 3.82
627 639 3.067742 CCGAAACATATCTCCCGTAGTGT 59.932 47.826 0.00 0.00 0.00 3.55
648 660 0.319125 GCACTAGCTAGCGGATCACC 60.319 60.000 20.91 0.00 37.91 4.02
664 676 5.238583 AGGTGTGTTGATAGAGTTAAGCAC 58.761 41.667 0.00 0.00 0.00 4.40
699 727 4.410228 AGGGCATCTCTAGCAAATCTACAA 59.590 41.667 0.00 0.00 0.00 2.41
701 729 4.615588 AGGGCATCTCTAGCAAATCTAC 57.384 45.455 0.00 0.00 0.00 2.59
718 746 5.242795 ACCACTGGATGTATAATAAGGGC 57.757 43.478 0.71 0.00 0.00 5.19
873 901 0.622665 CTGGTCCATGCCTTTCTCCT 59.377 55.000 0.00 0.00 0.00 3.69
879 907 0.329596 GGAACTCTGGTCCATGCCTT 59.670 55.000 0.00 0.00 0.00 4.35
901 929 0.251354 TGGAGACAGATCAAGGCTGC 59.749 55.000 5.72 5.72 36.86 5.25
914 942 9.258826 GAGATGCATCACAATATATATGGAGAC 57.741 37.037 27.81 0.00 0.00 3.36
1425 1473 4.385405 GCGAGCAGCCTGGACAGT 62.385 66.667 0.00 0.00 40.81 3.55
1514 1562 3.376234 TGTACGTACCTTGATCTTCTCGG 59.624 47.826 22.43 0.00 0.00 4.63
1522 1570 2.165845 GGAGCAGTGTACGTACCTTGAT 59.834 50.000 22.43 18.09 0.00 2.57
1602 1690 7.008266 GCAAATTAAGTACACATGATTCCGTTG 59.992 37.037 0.00 0.00 0.00 4.10
1798 1932 3.686016 GGACTGCAACTGGAAAATCCTA 58.314 45.455 0.00 0.00 37.46 2.94
2053 2194 4.090498 GCAAGTCGCCTGAAAATTCATTTC 59.910 41.667 0.00 0.00 40.51 2.17
2075 2216 1.160329 AATCAGAACCGGCTATGCGC 61.160 55.000 0.00 0.00 38.13 6.09
2138 2279 7.299246 TGTTACTAGGGGCTAGCTATTTAAG 57.701 40.000 15.72 7.62 37.57 1.85
2202 2344 3.701040 AGGTGGGTCATTTTCATGTATGC 59.299 43.478 0.00 0.00 0.00 3.14
2206 2348 5.144100 TGTTAAGGTGGGTCATTTTCATGT 58.856 37.500 0.00 0.00 0.00 3.21
2230 2372 6.168389 GGATCTTTTGATTTGAATGGTTGCT 58.832 36.000 0.00 0.00 39.67 3.91
2251 2393 1.710244 TGTTCCCATGTTGAGGTGGAT 59.290 47.619 0.00 0.00 37.72 3.41
2423 2565 8.011106 CAGTGGAAATGTTTTGCAATGTATTTC 58.989 33.333 21.99 21.99 32.56 2.17
2429 2571 3.560481 TGCAGTGGAAATGTTTTGCAATG 59.440 39.130 14.72 14.72 38.47 2.82
2457 2599 3.186283 TCTAAACTAGACAATGCCCCCA 58.814 45.455 0.00 0.00 0.00 4.96
2490 2965 2.404693 CGCGAATTGACAAAACATGGTG 59.595 45.455 0.00 0.00 0.00 4.17
2524 2999 6.399039 CGCTACTAAATCTCATGATAACGCAC 60.399 42.308 0.00 0.00 31.70 5.34
2535 3010 5.531287 TCTGTCTATGCGCTACTAAATCTCA 59.469 40.000 9.73 0.00 0.00 3.27
2569 3079 6.461640 AGCACGGACAAACTAACTATACTTT 58.538 36.000 0.00 0.00 0.00 2.66
2587 3158 4.331717 CCCAACAAATTACTACTAGCACGG 59.668 45.833 0.00 0.00 0.00 4.94
2624 3195 2.183679 TGTTTTTGGTTGGCAAGGACT 58.816 42.857 0.00 0.00 0.00 3.85
2832 3403 2.363306 ACAACTTGCATTCCTCCACA 57.637 45.000 0.00 0.00 0.00 4.17
2990 3562 1.605232 CCGTTTTTAGTCGGCCAAAGT 59.395 47.619 2.24 0.00 40.28 2.66
3097 3686 3.551890 CACCTCGTAAAGAATCATGGTCG 59.448 47.826 0.00 0.00 0.00 4.79
3193 3782 2.189191 GATGAGCACACCAGCAGGGA 62.189 60.000 0.00 0.00 41.15 4.20
3305 3894 5.045872 GCACAAGAATTATTGGATGCCTTC 58.954 41.667 16.65 0.00 34.36 3.46
3317 3906 7.363705 CCAAATGGTAGGAATGCACAAGAATTA 60.364 37.037 0.00 0.00 0.00 1.40
3321 3910 3.763360 CCAAATGGTAGGAATGCACAAGA 59.237 43.478 0.00 0.00 0.00 3.02
3350 3940 0.530288 GGCCAATGCAAATACGTGGT 59.470 50.000 0.00 0.00 40.13 4.16
3396 3986 5.787953 TGAAAGATCATGCACAAGGAAAA 57.212 34.783 0.00 0.00 0.00 2.29
3414 4004 3.565482 AGCTCGAACTCAAAGCATTGAAA 59.435 39.130 5.79 0.00 44.64 2.69
3556 4146 8.181573 CGGTAAATAGTGAACATGCATACTTTT 58.818 33.333 0.00 5.96 0.00 2.27
3736 4326 5.543790 AGGGAAGATTGGTGCAACTAATTTT 59.456 36.000 2.04 2.98 46.51 1.82
4263 4857 5.068987 AGCAAACTTAAGTTGCAATGGAAGA 59.931 36.000 28.47 0.00 38.44 2.87
4374 4968 9.301897 GCTTTTATTGTATGGAAGAATATCCCT 57.698 33.333 0.00 0.00 38.82 4.20


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

AutoCloner maintained by Alex Coulton.