Multiple sequence alignment - TraesCS4D01G262000

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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 TraesCS4D01G262000 chr4D 100.000 2837 0 0 1 2837 432990144 432992980 0.000000e+00 5240.0
1 TraesCS4D01G262000 chr4B 91.156 2250 91 28 637 2837 531093186 531095376 0.000000e+00 2953.0
2 TraesCS4D01G262000 chr4A 91.895 1604 70 28 703 2274 34294092 34295667 0.000000e+00 2187.0
3 TraesCS4D01G262000 chr4A 88.676 521 47 9 2306 2818 34295892 34296408 2.400000e-175 625.0
4 TraesCS4D01G262000 chr4A 83.784 518 70 11 1 510 219508956 219508445 1.980000e-131 479.0
5 TraesCS4D01G262000 chr4A 81.211 479 73 12 1 469 535817763 535818234 1.240000e-98 370.0
6 TraesCS4D01G262000 chr4A 82.443 131 16 4 562 691 34291500 34291624 1.070000e-19 108.0
7 TraesCS4D01G262000 chr4A 100.000 28 0 0 2810 2837 34296558 34296585 5.000000e-03 52.8
8 TraesCS4D01G262000 chr5D 84.476 496 60 15 1 486 332788454 332787966 9.200000e-130 473.0
9 TraesCS4D01G262000 chr5D 81.545 233 34 9 2567 2794 439211027 439210799 1.740000e-42 183.0
10 TraesCS4D01G262000 chr5D 77.955 313 47 18 2493 2791 256701348 256701044 2.900000e-40 176.0
11 TraesCS4D01G262000 chr2D 83.236 513 67 15 1 504 130797646 130797144 1.200000e-123 453.0
12 TraesCS4D01G262000 chr6D 84.716 458 61 7 1 454 454577938 454578390 1.550000e-122 449.0
13 TraesCS4D01G262000 chr5B 83.660 459 67 7 2 454 388735326 388734870 2.610000e-115 425.0
14 TraesCS4D01G262000 chr1A 84.742 426 56 6 85 504 419491354 419490932 4.370000e-113 418.0
15 TraesCS4D01G262000 chr7A 80.691 492 83 9 1 486 519332491 519332976 3.450000e-99 372.0
16 TraesCS4D01G262000 chr7A 80.842 475 79 9 1 469 519576817 519577285 2.080000e-96 363.0
17 TraesCS4D01G262000 chr5A 84.356 326 31 2 1369 1685 602452642 602452328 4.590000e-78 302.0
18 TraesCS4D01G262000 chr7D 78.523 298 48 11 2507 2791 562396173 562395879 6.240000e-42 182.0
19 TraesCS4D01G262000 chr7D 78.138 247 48 6 2551 2794 182834011 182833768 4.900000e-33 152.0
20 TraesCS4D01G262000 chr7D 77.011 261 51 9 2548 2803 118823734 118823478 1.060000e-29 141.0
21 TraesCS4D01G262000 chr3B 80.000 225 40 5 2581 2801 20812840 20813063 8.130000e-36 161.0
22 TraesCS4D01G262000 chr1B 76.375 309 49 19 2507 2797 98249780 98249478 8.190000e-31 145.0


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 TraesCS4D01G262000 chr4D 432990144 432992980 2836 False 5240.0 5240 100.0000 1 2837 1 chr4D.!!$F1 2836
1 TraesCS4D01G262000 chr4B 531093186 531095376 2190 False 2953.0 2953 91.1560 637 2837 1 chr4B.!!$F1 2200
2 TraesCS4D01G262000 chr4A 34291500 34296585 5085 False 743.2 2187 90.7535 562 2837 4 chr4A.!!$F2 2275
3 TraesCS4D01G262000 chr4A 219508445 219508956 511 True 479.0 479 83.7840 1 510 1 chr4A.!!$R1 509
4 TraesCS4D01G262000 chr2D 130797144 130797646 502 True 453.0 453 83.2360 1 504 1 chr2D.!!$R1 503

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
506 512 0.105862 CCGTAGACTGGTCCCCCATA 60.106 60.0 0.0 0.0 40.9 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 4521 1.207329 GCTCCCTGTTCACGTCCTATT 59.793 52.381 0.0 0.0 0.0 1.73 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
23 24 2.438434 GTCCCATGAAGGCCACCG 60.438 66.667 5.01 0.00 35.39 4.94
24 25 4.424711 TCCCATGAAGGCCACCGC 62.425 66.667 5.01 0.00 35.39 5.68
112 113 1.442526 CGGCTGAAGCACATCCCATC 61.443 60.000 4.43 0.00 44.36 3.51
131 132 1.596934 GGTTCCACTCCGATGAGCA 59.403 57.895 0.00 0.00 42.74 4.26
137 138 2.960659 CTCCGATGAGCAGCGCTG 60.961 66.667 32.83 32.83 39.88 5.18
156 157 1.815421 CCGAACATGGGGAAGCGAG 60.815 63.158 0.00 0.00 0.00 5.03
159 160 2.819984 GAACATGGGGAAGCGAGCCA 62.820 60.000 0.00 0.00 0.00 4.75
194 195 1.002544 GCATATACCTCCAGGGCTCAC 59.997 57.143 0.00 0.00 40.27 3.51
195 196 2.329267 CATATACCTCCAGGGCTCACA 58.671 52.381 0.00 0.00 40.27 3.58
197 198 0.252696 ATACCTCCAGGGCTCACACA 60.253 55.000 0.00 0.00 40.27 3.72
198 199 0.904865 TACCTCCAGGGCTCACACAG 60.905 60.000 0.00 0.00 40.27 3.66
270 274 2.871022 GCCGATCGTAGACTAGTCAAGA 59.129 50.000 24.44 18.77 42.51 3.02
275 279 7.089538 CCGATCGTAGACTAGTCAAGAGTATA 58.910 42.308 24.44 3.78 42.51 1.47
327 331 3.588955 CGCCCGTAAACTAGTTTTACCT 58.411 45.455 25.07 4.07 44.77 3.08
429 435 4.379082 GCATGAATTTCGTCCGGTTAGTTT 60.379 41.667 0.00 0.00 0.00 2.66
430 436 4.996062 TGAATTTCGTCCGGTTAGTTTC 57.004 40.909 0.00 0.20 0.00 2.78
433 439 5.470777 TGAATTTCGTCCGGTTAGTTTCAAT 59.529 36.000 0.00 0.00 0.00 2.57
455 461 1.134175 GTGGTTGAAATGTATGCGGGG 59.866 52.381 0.00 0.00 0.00 5.73
469 475 4.115199 GGGGAGCGTTGGATGGCT 62.115 66.667 0.00 0.00 43.42 4.75
470 476 2.044946 GGGAGCGTTGGATGGCTT 60.045 61.111 0.00 0.00 40.16 4.35
471 477 2.409870 GGGAGCGTTGGATGGCTTG 61.410 63.158 0.00 0.00 40.16 4.01
472 478 2.486966 GAGCGTTGGATGGCTTGC 59.513 61.111 0.00 0.00 40.16 4.01
473 479 2.034687 AGCGTTGGATGGCTTGCT 59.965 55.556 0.00 0.00 35.61 3.91
474 480 1.986575 GAGCGTTGGATGGCTTGCTC 61.987 60.000 0.00 0.00 40.16 4.26
475 481 3.056313 GCGTTGGATGGCTTGCTCC 62.056 63.158 0.00 0.00 0.00 4.70
476 482 2.409870 CGTTGGATGGCTTGCTCCC 61.410 63.158 0.00 0.00 0.00 4.30
477 483 2.045045 TTGGATGGCTTGCTCCCG 60.045 61.111 0.00 0.00 0.00 5.14
478 484 4.802051 TGGATGGCTTGCTCCCGC 62.802 66.667 0.00 0.00 0.00 6.13
479 485 4.802051 GGATGGCTTGCTCCCGCA 62.802 66.667 0.00 0.00 46.24 5.69
494 500 4.110493 GCATCAGTGCCCGTAGAC 57.890 61.111 0.00 0.00 45.76 2.59
495 501 1.517832 GCATCAGTGCCCGTAGACT 59.482 57.895 0.00 0.00 45.76 3.24
496 502 0.807667 GCATCAGTGCCCGTAGACTG 60.808 60.000 0.00 0.00 45.76 3.51
497 503 0.179100 CATCAGTGCCCGTAGACTGG 60.179 60.000 0.00 0.00 40.11 4.00
498 504 0.614979 ATCAGTGCCCGTAGACTGGT 60.615 55.000 0.00 0.00 40.11 4.00
499 505 1.215647 CAGTGCCCGTAGACTGGTC 59.784 63.158 0.00 0.00 36.69 4.02
500 506 1.982938 AGTGCCCGTAGACTGGTCC 60.983 63.158 0.00 0.00 0.00 4.46
501 507 2.682494 TGCCCGTAGACTGGTCCC 60.682 66.667 0.00 0.00 0.00 4.46
502 508 3.468140 GCCCGTAGACTGGTCCCC 61.468 72.222 0.00 0.00 0.00 4.81
503 509 2.762875 CCCGTAGACTGGTCCCCC 60.763 72.222 0.00 0.00 0.00 5.40
504 510 2.038329 CCGTAGACTGGTCCCCCA 59.962 66.667 0.00 0.00 38.87 4.96
505 511 1.382695 CCGTAGACTGGTCCCCCAT 60.383 63.158 0.00 0.00 40.90 4.00
506 512 0.105862 CCGTAGACTGGTCCCCCATA 60.106 60.000 0.00 0.00 40.90 2.74
507 513 1.038280 CGTAGACTGGTCCCCCATAC 58.962 60.000 0.00 0.00 40.90 2.39
508 514 1.411216 CGTAGACTGGTCCCCCATACT 60.411 57.143 0.00 0.00 40.90 2.12
509 515 2.040178 GTAGACTGGTCCCCCATACTG 58.960 57.143 0.00 0.00 40.90 2.74
510 516 0.326618 AGACTGGTCCCCCATACTGG 60.327 60.000 0.00 0.00 40.90 4.00
511 517 0.326238 GACTGGTCCCCCATACTGGA 60.326 60.000 0.00 0.00 40.96 3.86
512 518 0.326618 ACTGGTCCCCCATACTGGAG 60.327 60.000 0.00 0.00 40.96 3.86
513 519 1.692749 TGGTCCCCCATACTGGAGC 60.693 63.158 0.00 0.00 46.80 4.70
514 520 1.692749 GGTCCCCCATACTGGAGCA 60.693 63.158 3.05 0.00 46.09 4.26
515 521 1.279025 GGTCCCCCATACTGGAGCAA 61.279 60.000 3.05 0.00 46.09 3.91
516 522 0.623723 GTCCCCCATACTGGAGCAAA 59.376 55.000 0.00 0.00 40.96 3.68
517 523 1.215423 GTCCCCCATACTGGAGCAAAT 59.785 52.381 0.00 0.00 40.96 2.32
518 524 1.929494 TCCCCCATACTGGAGCAAATT 59.071 47.619 0.00 0.00 40.96 1.82
519 525 2.314549 TCCCCCATACTGGAGCAAATTT 59.685 45.455 0.00 0.00 40.96 1.82
520 526 3.529734 TCCCCCATACTGGAGCAAATTTA 59.470 43.478 0.00 0.00 40.96 1.40
521 527 3.636764 CCCCCATACTGGAGCAAATTTAC 59.363 47.826 0.00 0.00 40.96 2.01
522 528 3.315191 CCCCATACTGGAGCAAATTTACG 59.685 47.826 0.00 0.00 40.96 3.18
523 529 3.315191 CCCATACTGGAGCAAATTTACGG 59.685 47.826 0.00 0.00 40.96 4.02
524 530 3.315191 CCATACTGGAGCAAATTTACGGG 59.685 47.826 0.00 0.00 40.96 5.28
525 531 2.579410 ACTGGAGCAAATTTACGGGT 57.421 45.000 0.00 0.00 0.00 5.28
526 532 2.159382 ACTGGAGCAAATTTACGGGTG 58.841 47.619 0.00 0.00 0.00 4.61
527 533 2.224670 ACTGGAGCAAATTTACGGGTGA 60.225 45.455 0.00 0.00 0.00 4.02
528 534 2.420022 CTGGAGCAAATTTACGGGTGAG 59.580 50.000 0.00 0.00 0.00 3.51
529 535 2.224670 TGGAGCAAATTTACGGGTGAGT 60.225 45.455 0.00 0.00 0.00 3.41
530 536 2.161609 GGAGCAAATTTACGGGTGAGTG 59.838 50.000 0.00 0.00 0.00 3.51
531 537 2.812011 GAGCAAATTTACGGGTGAGTGT 59.188 45.455 0.00 0.00 0.00 3.55
532 538 3.219281 AGCAAATTTACGGGTGAGTGTT 58.781 40.909 0.00 0.00 0.00 3.32
533 539 3.004315 AGCAAATTTACGGGTGAGTGTTG 59.996 43.478 0.00 0.00 0.00 3.33
534 540 3.003897 GCAAATTTACGGGTGAGTGTTGA 59.996 43.478 0.00 0.00 0.00 3.18
535 541 4.498345 GCAAATTTACGGGTGAGTGTTGAA 60.498 41.667 0.00 0.00 0.00 2.69
536 542 5.212194 CAAATTTACGGGTGAGTGTTGAAG 58.788 41.667 0.00 0.00 0.00 3.02
537 543 3.823281 TTTACGGGTGAGTGTTGAAGA 57.177 42.857 0.00 0.00 0.00 2.87
538 544 4.345859 TTTACGGGTGAGTGTTGAAGAT 57.654 40.909 0.00 0.00 0.00 2.40
539 545 2.169832 ACGGGTGAGTGTTGAAGATG 57.830 50.000 0.00 0.00 0.00 2.90
540 546 0.798776 CGGGTGAGTGTTGAAGATGC 59.201 55.000 0.00 0.00 0.00 3.91
541 547 1.168714 GGGTGAGTGTTGAAGATGCC 58.831 55.000 0.00 0.00 0.00 4.40
542 548 1.168714 GGTGAGTGTTGAAGATGCCC 58.831 55.000 0.00 0.00 0.00 5.36
543 549 1.271597 GGTGAGTGTTGAAGATGCCCT 60.272 52.381 0.00 0.00 0.00 5.19
544 550 2.027192 GGTGAGTGTTGAAGATGCCCTA 60.027 50.000 0.00 0.00 0.00 3.53
545 551 3.559171 GGTGAGTGTTGAAGATGCCCTAA 60.559 47.826 0.00 0.00 0.00 2.69
546 552 3.686726 GTGAGTGTTGAAGATGCCCTAAG 59.313 47.826 0.00 0.00 0.00 2.18
547 553 3.274288 GAGTGTTGAAGATGCCCTAAGG 58.726 50.000 0.00 0.00 0.00 2.69
548 554 2.912956 AGTGTTGAAGATGCCCTAAGGA 59.087 45.455 0.00 0.00 33.47 3.36
549 555 3.525199 AGTGTTGAAGATGCCCTAAGGAT 59.475 43.478 0.00 0.00 33.47 3.24
550 556 3.879892 GTGTTGAAGATGCCCTAAGGATC 59.120 47.826 0.00 0.00 33.47 3.36
551 557 3.782523 TGTTGAAGATGCCCTAAGGATCT 59.217 43.478 0.00 0.00 33.81 2.75
552 558 4.968719 TGTTGAAGATGCCCTAAGGATCTA 59.031 41.667 0.00 0.00 32.77 1.98
553 559 5.428457 TGTTGAAGATGCCCTAAGGATCTAA 59.572 40.000 0.00 0.00 32.77 2.10
554 560 6.101734 TGTTGAAGATGCCCTAAGGATCTAAT 59.898 38.462 0.00 0.00 32.77 1.73
555 561 6.365970 TGAAGATGCCCTAAGGATCTAATC 57.634 41.667 0.00 0.00 32.77 1.75
556 562 5.846164 TGAAGATGCCCTAAGGATCTAATCA 59.154 40.000 0.00 0.00 32.77 2.57
557 563 6.329986 TGAAGATGCCCTAAGGATCTAATCAA 59.670 38.462 0.00 0.00 32.77 2.57
558 564 6.120507 AGATGCCCTAAGGATCTAATCAAC 57.879 41.667 0.00 0.00 31.89 3.18
559 565 5.848921 AGATGCCCTAAGGATCTAATCAACT 59.151 40.000 0.00 0.00 31.89 3.16
560 566 7.019388 AGATGCCCTAAGGATCTAATCAACTA 58.981 38.462 0.00 0.00 31.89 2.24
561 567 7.514127 AGATGCCCTAAGGATCTAATCAACTAA 59.486 37.037 0.00 0.00 31.89 2.24
562 568 7.446106 TGCCCTAAGGATCTAATCAACTAAA 57.554 36.000 0.00 0.00 33.47 1.85
563 569 8.045720 TGCCCTAAGGATCTAATCAACTAAAT 57.954 34.615 0.00 0.00 33.47 1.40
564 570 8.502738 TGCCCTAAGGATCTAATCAACTAAATT 58.497 33.333 0.00 0.00 33.47 1.82
565 571 9.355916 GCCCTAAGGATCTAATCAACTAAATTT 57.644 33.333 0.00 0.00 33.47 1.82
612 618 4.703645 GAGCCCTTAAACTCCATGAAAC 57.296 45.455 0.00 0.00 0.00 2.78
613 619 3.081804 AGCCCTTAAACTCCATGAAACG 58.918 45.455 0.00 0.00 0.00 3.60
634 640 8.773404 AAACGAGTTTCAGTAATGCTATAAGT 57.227 30.769 0.00 0.00 0.00 2.24
635 641 8.773404 AACGAGTTTCAGTAATGCTATAAGTT 57.227 30.769 0.00 0.00 0.00 2.66
653 659 3.550820 AGTTTGTCTGCAATGGTGTGTA 58.449 40.909 0.00 0.00 34.18 2.90
701 3164 7.737972 TTTCTCGTGGAATAAGTCAAATTCA 57.262 32.000 0.00 0.00 35.46 2.57
705 3168 5.180492 TCGTGGAATAAGTCAAATTCACACC 59.820 40.000 0.00 0.00 35.46 4.16
729 3192 6.419710 CCATCGTAGAACAATTTCGCTACATA 59.580 38.462 0.00 0.00 43.58 2.29
769 3233 4.307032 ACAAGGCTCCACATCAGTATTT 57.693 40.909 0.00 0.00 0.00 1.40
773 3237 2.954318 GGCTCCACATCAGTATTTGCAT 59.046 45.455 0.00 0.00 0.00 3.96
777 3241 4.201657 TCCACATCAGTATTTGCATGGAG 58.798 43.478 0.00 0.00 31.88 3.86
822 3286 1.341383 ACTGATCATTTCCCACCCAGC 60.341 52.381 0.00 0.00 0.00 4.85
847 3311 2.187100 CACCAATAAAACCATGCCCCT 58.813 47.619 0.00 0.00 0.00 4.79
848 3312 2.168313 CACCAATAAAACCATGCCCCTC 59.832 50.000 0.00 0.00 0.00 4.30
849 3313 2.044353 ACCAATAAAACCATGCCCCTCT 59.956 45.455 0.00 0.00 0.00 3.69
850 3314 3.106827 CCAATAAAACCATGCCCCTCTT 58.893 45.455 0.00 0.00 0.00 2.85
851 3315 3.519107 CCAATAAAACCATGCCCCTCTTT 59.481 43.478 0.00 0.00 0.00 2.52
853 3317 1.256812 AAAACCATGCCCCTCTTTCG 58.743 50.000 0.00 0.00 0.00 3.46
936 3402 5.321516 GTCACACATTTCGCACTATAAACC 58.678 41.667 0.00 0.00 0.00 3.27
937 3403 4.092237 TCACACATTTCGCACTATAAACCG 59.908 41.667 0.00 0.00 0.00 4.44
1101 3567 4.680237 CACTCGCCGGCCTTCACA 62.680 66.667 23.46 0.00 0.00 3.58
1254 3720 2.578128 CGCTGGCTGAAGAGCTCT 59.422 61.111 11.45 11.45 45.44 4.09
1882 4357 7.338196 CCACCCTGTAAAATGTGATTATGTGTA 59.662 37.037 0.00 0.00 0.00 2.90
1915 4393 7.010183 GTGGTAGACTAGACGTACGTATGTAAA 59.990 40.741 24.74 10.36 30.94 2.01
1921 4406 9.362911 GACTAGACGTACGTATGTAAATTACTG 57.637 37.037 24.74 9.21 30.94 2.74
2021 4512 1.940883 AAATGGGCGCGACTACTCGA 61.941 55.000 13.91 0.00 43.06 4.04
2022 4513 1.735376 AATGGGCGCGACTACTCGAT 61.735 55.000 13.91 0.00 43.06 3.59
2023 4514 2.051166 GGGCGCGACTACTCGATC 60.051 66.667 13.91 0.00 43.06 3.69
2024 4515 2.713770 GGCGCGACTACTCGATCA 59.286 61.111 12.10 0.00 43.06 2.92
2030 4521 2.475487 CGCGACTACTCGATCAGATGTA 59.525 50.000 0.00 0.00 43.06 2.29
2089 4580 3.820689 CCTATTTCTCGATCTCAGCTCG 58.179 50.000 0.00 0.00 37.47 5.03
2170 4661 7.924412 TGGTGAATCGTATTTTACTACATCCTC 59.076 37.037 0.00 0.00 0.00 3.71
2442 5139 3.178046 TGTTGCACCCCTAGATTAGACA 58.822 45.455 0.00 0.00 0.00 3.41
2603 5301 9.844257 AACATTGGATTCCACAAGAAATTTTTA 57.156 25.926 4.45 0.00 38.21 1.52
2608 5306 7.757624 TGGATTCCACAAGAAATTTTTATACGC 59.242 33.333 0.00 0.00 38.21 4.42
2612 5310 7.653647 TCCACAAGAAATTTTTATACGCAACT 58.346 30.769 0.00 0.00 0.00 3.16
2613 5311 8.138712 TCCACAAGAAATTTTTATACGCAACTT 58.861 29.630 0.00 0.00 0.00 2.66
2636 5335 8.299570 ACTTTTGTACTGCATTTCATAGGAAAG 58.700 33.333 8.68 2.49 45.58 2.62
2637 5336 7.994425 TTTGTACTGCATTTCATAGGAAAGA 57.006 32.000 8.68 0.00 45.58 2.52
2655 5354 7.646884 AGGAAAGATAACCTCCATTTCAATCT 58.353 34.615 0.00 0.00 32.73 2.40
2697 5396 9.515020 TTTATTTTTCTGTGACATCAAACACTC 57.485 29.630 0.00 0.00 37.81 3.51
2710 5409 4.326826 TCAAACACTCCTTGCTAATCCTG 58.673 43.478 0.00 0.00 0.00 3.86
2746 5446 2.954318 GCATGCCACTTCAATCCTGTAT 59.046 45.455 6.36 0.00 0.00 2.29
2748 5448 4.580167 GCATGCCACTTCAATCCTGTATTA 59.420 41.667 6.36 0.00 0.00 0.98
2758 5458 7.725844 ACTTCAATCCTGTATTATTTCCATCCC 59.274 37.037 0.00 0.00 0.00 3.85
2760 5460 8.518720 TCAATCCTGTATTATTTCCATCCCTA 57.481 34.615 0.00 0.00 0.00 3.53
2762 5462 7.888514 ATCCTGTATTATTTCCATCCCTACA 57.111 36.000 0.00 0.00 0.00 2.74
2763 5463 7.699709 TCCTGTATTATTTCCATCCCTACAA 57.300 36.000 0.00 0.00 0.00 2.41
2794 5494 1.129998 CTGCGAATCAAAGAGGCACTG 59.870 52.381 0.00 0.00 41.55 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.189499 GGAATGACGATGGCCTGCC 61.189 63.158 3.32 0.00 0.00 4.85
74 75 1.492764 GTAGGGGAAGGGAATGACGA 58.507 55.000 0.00 0.00 0.00 4.20
75 76 0.104304 CGTAGGGGAAGGGAATGACG 59.896 60.000 0.00 0.00 0.00 4.35
137 138 3.508840 CGCTTCCCCATGTTCGGC 61.509 66.667 0.00 0.00 0.00 5.54
194 195 0.529337 CCGCTCATCCTACTGCTGTG 60.529 60.000 6.48 0.00 0.00 3.66
195 196 1.680522 CCCGCTCATCCTACTGCTGT 61.681 60.000 0.66 0.66 0.00 4.40
197 198 2.801631 GCCCGCTCATCCTACTGCT 61.802 63.158 0.00 0.00 0.00 4.24
198 199 2.280457 GCCCGCTCATCCTACTGC 60.280 66.667 0.00 0.00 0.00 4.40
199 200 1.068753 CAGCCCGCTCATCCTACTG 59.931 63.158 0.00 0.00 0.00 2.74
200 201 2.801631 GCAGCCCGCTCATCCTACT 61.802 63.158 0.00 0.00 37.77 2.57
201 202 2.280457 GCAGCCCGCTCATCCTAC 60.280 66.667 0.00 0.00 37.77 3.18
202 203 3.550431 GGCAGCCCGCTCATCCTA 61.550 66.667 0.00 0.00 41.91 2.94
220 221 2.681848 CTCCATTGTCTTGCTCATGTCC 59.318 50.000 0.00 0.00 0.00 4.02
227 228 1.745141 GCGGATCTCCATTGTCTTGCT 60.745 52.381 0.00 0.00 35.14 3.91
229 230 0.933097 CGCGGATCTCCATTGTCTTG 59.067 55.000 0.00 0.00 35.14 3.02
254 258 6.694844 CACGTATACTCTTGACTAGTCTACGA 59.305 42.308 29.72 19.88 45.42 3.43
270 274 3.516300 TCCATTCCCACAACACGTATACT 59.484 43.478 0.56 0.00 0.00 2.12
275 279 3.199946 AGATATCCATTCCCACAACACGT 59.800 43.478 0.00 0.00 0.00 4.49
314 318 5.305386 ACACCGGACTAAGGTAAAACTAGTT 59.695 40.000 9.46 1.12 40.59 2.24
327 331 7.283625 TGTAACTAAAACTACACCGGACTAA 57.716 36.000 9.46 0.00 0.00 2.24
379 384 3.995705 ACGACGGATTCAAAATAAACCGA 59.004 39.130 11.51 0.00 44.83 4.69
389 395 1.300481 TGCAAACACGACGGATTCAA 58.700 45.000 0.00 0.00 0.00 2.69
390 396 1.196581 CATGCAAACACGACGGATTCA 59.803 47.619 0.00 0.00 0.00 2.57
391 397 1.463056 TCATGCAAACACGACGGATTC 59.537 47.619 0.00 0.00 0.00 2.52
429 435 5.065859 CCGCATACATTTCAACCACTATTGA 59.934 40.000 0.00 0.00 36.80 2.57
430 436 5.273170 CCGCATACATTTCAACCACTATTG 58.727 41.667 0.00 0.00 0.00 1.90
433 439 3.275143 CCCGCATACATTTCAACCACTA 58.725 45.455 0.00 0.00 0.00 2.74
455 461 1.986575 GAGCAAGCCATCCAACGCTC 61.987 60.000 0.00 0.00 39.10 5.03
478 484 0.179100 CCAGTCTACGGGCACTGATG 60.179 60.000 10.51 0.00 42.37 3.07
479 485 0.614979 ACCAGTCTACGGGCACTGAT 60.615 55.000 10.51 0.00 42.37 2.90
480 486 1.228769 ACCAGTCTACGGGCACTGA 60.229 57.895 10.51 0.00 42.37 3.41
481 487 1.215647 GACCAGTCTACGGGCACTG 59.784 63.158 0.00 3.57 39.90 3.66
482 488 1.982938 GGACCAGTCTACGGGCACT 60.983 63.158 0.00 0.00 34.39 4.40
483 489 2.577593 GGACCAGTCTACGGGCAC 59.422 66.667 0.00 0.00 34.39 5.01
484 490 2.682494 GGGACCAGTCTACGGGCA 60.682 66.667 0.00 0.00 34.39 5.36
503 509 3.945285 ACCCGTAAATTTGCTCCAGTATG 59.055 43.478 0.00 0.00 0.00 2.39
504 510 3.945285 CACCCGTAAATTTGCTCCAGTAT 59.055 43.478 0.00 0.00 0.00 2.12
505 511 3.008157 TCACCCGTAAATTTGCTCCAGTA 59.992 43.478 0.00 0.00 0.00 2.74
506 512 2.159382 CACCCGTAAATTTGCTCCAGT 58.841 47.619 0.00 0.00 0.00 4.00
507 513 2.420022 CTCACCCGTAAATTTGCTCCAG 59.580 50.000 0.00 0.00 0.00 3.86
508 514 2.224670 ACTCACCCGTAAATTTGCTCCA 60.225 45.455 0.00 0.00 0.00 3.86
509 515 2.161609 CACTCACCCGTAAATTTGCTCC 59.838 50.000 0.00 0.00 0.00 4.70
510 516 2.812011 ACACTCACCCGTAAATTTGCTC 59.188 45.455 0.00 0.00 0.00 4.26
511 517 2.858745 ACACTCACCCGTAAATTTGCT 58.141 42.857 0.00 0.00 0.00 3.91
512 518 3.003897 TCAACACTCACCCGTAAATTTGC 59.996 43.478 0.00 0.00 0.00 3.68
513 519 4.822036 TCAACACTCACCCGTAAATTTG 57.178 40.909 0.00 0.00 0.00 2.32
514 520 5.127491 TCTTCAACACTCACCCGTAAATTT 58.873 37.500 0.00 0.00 0.00 1.82
515 521 4.710324 TCTTCAACACTCACCCGTAAATT 58.290 39.130 0.00 0.00 0.00 1.82
516 522 4.345859 TCTTCAACACTCACCCGTAAAT 57.654 40.909 0.00 0.00 0.00 1.40
517 523 3.823281 TCTTCAACACTCACCCGTAAA 57.177 42.857 0.00 0.00 0.00 2.01
518 524 3.659786 CATCTTCAACACTCACCCGTAA 58.340 45.455 0.00 0.00 0.00 3.18
519 525 2.611971 GCATCTTCAACACTCACCCGTA 60.612 50.000 0.00 0.00 0.00 4.02
520 526 1.878102 GCATCTTCAACACTCACCCGT 60.878 52.381 0.00 0.00 0.00 5.28
521 527 0.798776 GCATCTTCAACACTCACCCG 59.201 55.000 0.00 0.00 0.00 5.28
522 528 1.168714 GGCATCTTCAACACTCACCC 58.831 55.000 0.00 0.00 0.00 4.61
523 529 1.168714 GGGCATCTTCAACACTCACC 58.831 55.000 0.00 0.00 0.00 4.02
524 530 2.191128 AGGGCATCTTCAACACTCAC 57.809 50.000 0.00 0.00 0.00 3.51
525 531 3.307691 CCTTAGGGCATCTTCAACACTCA 60.308 47.826 0.00 0.00 0.00 3.41
526 532 3.055094 TCCTTAGGGCATCTTCAACACTC 60.055 47.826 0.00 0.00 0.00 3.51
527 533 2.912956 TCCTTAGGGCATCTTCAACACT 59.087 45.455 0.00 0.00 0.00 3.55
528 534 3.350219 TCCTTAGGGCATCTTCAACAC 57.650 47.619 0.00 0.00 0.00 3.32
529 535 3.782523 AGATCCTTAGGGCATCTTCAACA 59.217 43.478 0.00 0.00 30.72 3.33
530 536 4.429854 AGATCCTTAGGGCATCTTCAAC 57.570 45.455 0.00 0.00 30.72 3.18
531 537 6.329986 TGATTAGATCCTTAGGGCATCTTCAA 59.670 38.462 7.63 0.00 34.13 2.69
532 538 5.846164 TGATTAGATCCTTAGGGCATCTTCA 59.154 40.000 7.63 4.61 34.13 3.02
533 539 6.365970 TGATTAGATCCTTAGGGCATCTTC 57.634 41.667 7.63 2.43 34.13 2.87
534 540 6.331307 AGTTGATTAGATCCTTAGGGCATCTT 59.669 38.462 7.63 0.00 34.13 2.40
535 541 5.848921 AGTTGATTAGATCCTTAGGGCATCT 59.151 40.000 7.49 7.49 35.37 2.90
536 542 6.120507 AGTTGATTAGATCCTTAGGGCATC 57.879 41.667 0.00 0.00 0.00 3.91
537 543 7.633018 TTAGTTGATTAGATCCTTAGGGCAT 57.367 36.000 0.00 0.00 0.00 4.40
538 544 7.446106 TTTAGTTGATTAGATCCTTAGGGCA 57.554 36.000 0.00 0.00 0.00 5.36
539 545 8.926092 AATTTAGTTGATTAGATCCTTAGGGC 57.074 34.615 0.00 0.00 0.00 5.19
569 575 9.440773 GGCTCCTTTGATTTAAAAGATTTTCAT 57.559 29.630 0.00 0.00 39.12 2.57
570 576 7.877612 GGGCTCCTTTGATTTAAAAGATTTTCA 59.122 33.333 0.00 0.00 39.12 2.69
571 577 8.097038 AGGGCTCCTTTGATTTAAAAGATTTTC 58.903 33.333 0.00 0.00 39.12 2.29
578 584 8.257602 AGTTTAAGGGCTCCTTTGATTTAAAA 57.742 30.769 11.15 2.85 41.69 1.52
582 588 4.772624 GGAGTTTAAGGGCTCCTTTGATTT 59.227 41.667 11.15 0.00 41.69 2.17
612 618 8.656849 ACAAACTTATAGCATTACTGAAACTCG 58.343 33.333 0.00 0.00 0.00 4.18
613 619 9.974750 GACAAACTTATAGCATTACTGAAACTC 57.025 33.333 0.00 0.00 0.00 3.01
619 625 7.307493 TGCAGACAAACTTATAGCATTACTG 57.693 36.000 0.00 0.00 0.00 2.74
620 626 7.921786 TTGCAGACAAACTTATAGCATTACT 57.078 32.000 0.00 0.00 31.21 2.24
621 627 7.645340 CCATTGCAGACAAACTTATAGCATTAC 59.355 37.037 0.00 0.00 39.77 1.89
624 630 5.653769 ACCATTGCAGACAAACTTATAGCAT 59.346 36.000 0.00 0.00 39.77 3.79
625 631 5.009631 ACCATTGCAGACAAACTTATAGCA 58.990 37.500 0.00 0.00 39.77 3.49
626 632 5.106157 ACACCATTGCAGACAAACTTATAGC 60.106 40.000 0.00 0.00 39.77 2.97
627 633 6.072508 ACACACCATTGCAGACAAACTTATAG 60.073 38.462 0.00 0.00 39.77 1.31
628 634 5.767665 ACACACCATTGCAGACAAACTTATA 59.232 36.000 0.00 0.00 39.77 0.98
629 635 4.584325 ACACACCATTGCAGACAAACTTAT 59.416 37.500 0.00 0.00 39.77 1.73
630 636 3.951037 ACACACCATTGCAGACAAACTTA 59.049 39.130 0.00 0.00 39.77 2.24
631 637 2.760092 ACACACCATTGCAGACAAACTT 59.240 40.909 0.00 0.00 39.77 2.66
632 638 2.378038 ACACACCATTGCAGACAAACT 58.622 42.857 0.00 0.00 39.77 2.66
633 639 2.869233 ACACACCATTGCAGACAAAC 57.131 45.000 0.00 0.00 39.77 2.93
634 640 5.163468 ACAAATACACACCATTGCAGACAAA 60.163 36.000 0.00 0.00 39.77 2.83
635 641 4.340666 ACAAATACACACCATTGCAGACAA 59.659 37.500 0.00 0.00 40.87 3.18
673 680 4.832248 TGACTTATTCCACGAGAAATGCT 58.168 39.130 0.00 0.00 38.21 3.79
701 3164 3.124636 GCGAAATTGTTCTACGATGGTGT 59.875 43.478 0.00 0.00 0.00 4.16
705 3168 5.696260 TGTAGCGAAATTGTTCTACGATG 57.304 39.130 0.00 0.00 35.42 3.84
753 3217 3.243301 CCATGCAAATACTGATGTGGAGC 60.243 47.826 0.00 0.00 0.00 4.70
777 3241 0.782384 CGACTGCGTTTGTGGAGTAC 59.218 55.000 0.00 0.00 40.92 2.73
800 3264 1.005805 TGGGTGGGAAATGATCAGTGG 59.994 52.381 0.09 0.00 0.00 4.00
822 3286 3.368323 GGCATGGTTTTATTGGTGTGGAG 60.368 47.826 0.00 0.00 0.00 3.86
847 3311 2.616330 CGGCAAGGCAAGCGAAAGA 61.616 57.895 0.00 0.00 0.00 2.52
848 3312 2.126734 CGGCAAGGCAAGCGAAAG 60.127 61.111 0.00 0.00 0.00 2.62
849 3313 3.669344 CCGGCAAGGCAAGCGAAA 61.669 61.111 0.00 0.00 0.00 3.46
870 3334 1.755008 GGAGGTCAGGACTCGGGAG 60.755 68.421 0.00 0.00 35.82 4.30
871 3335 2.212794 GAGGAGGTCAGGACTCGGGA 62.213 65.000 0.00 0.00 35.82 5.14
872 3336 1.755008 GAGGAGGTCAGGACTCGGG 60.755 68.421 0.00 0.00 35.82 5.14
873 3337 1.755008 GGAGGAGGTCAGGACTCGG 60.755 68.421 0.00 0.00 35.82 4.63
874 3338 0.612174 TTGGAGGAGGTCAGGACTCG 60.612 60.000 0.00 0.00 35.82 4.18
875 3339 0.899019 GTTGGAGGAGGTCAGGACTC 59.101 60.000 0.00 0.00 0.00 3.36
876 3340 0.545548 GGTTGGAGGAGGTCAGGACT 60.546 60.000 0.00 0.00 0.00 3.85
936 3402 2.947938 AAATGAGGCTGGGATCGGCG 62.948 60.000 0.00 0.00 45.93 6.46
937 3403 0.108585 TAAATGAGGCTGGGATCGGC 59.891 55.000 0.00 0.00 44.31 5.54
987 3453 2.821366 GCCATGGGTGACGAGCAG 60.821 66.667 15.13 0.00 0.00 4.24
1254 3720 1.212751 CTCGATGACGTGCCAGTGA 59.787 57.895 0.00 0.00 40.69 3.41
1374 3840 3.062466 CCGGACGACAGGCTCTCA 61.062 66.667 0.00 0.00 0.00 3.27
1607 4082 1.995066 ACCATCTCCGCCATGGACA 60.995 57.895 18.40 0.00 43.74 4.02
1882 4357 4.841422 ACGTCTAGTCTACCACATGTACT 58.159 43.478 0.00 0.02 0.00 2.73
1915 4393 8.854614 AACAAGAAAGAACATAGAGCAGTAAT 57.145 30.769 0.00 0.00 0.00 1.89
1921 4406 5.241728 ACCCAAACAAGAAAGAACATAGAGC 59.758 40.000 0.00 0.00 0.00 4.09
2021 4512 6.461648 CCTGTTCACGTCCTATTACATCTGAT 60.462 42.308 0.00 0.00 0.00 2.90
2022 4513 5.163550 CCTGTTCACGTCCTATTACATCTGA 60.164 44.000 0.00 0.00 0.00 3.27
2023 4514 5.043903 CCTGTTCACGTCCTATTACATCTG 58.956 45.833 0.00 0.00 0.00 2.90
2024 4515 4.099573 CCCTGTTCACGTCCTATTACATCT 59.900 45.833 0.00 0.00 0.00 2.90
2030 4521 1.207329 GCTCCCTGTTCACGTCCTATT 59.793 52.381 0.00 0.00 0.00 1.73
2089 4580 4.228567 GGCTAGGCCGAGACCTGC 62.229 72.222 18.16 0.73 41.34 4.85
2133 4624 3.589988 ACGATTCACCAGAGCAACTAAG 58.410 45.455 0.00 0.00 0.00 2.18
2170 4661 4.414337 TGAAACTGGAAAACCCAATTGG 57.586 40.909 18.21 18.21 46.07 3.16
2254 4752 4.578516 CCACACAAAATGAGTTCTGTGGTA 59.421 41.667 11.97 0.00 42.76 3.25
2255 4753 3.381272 CCACACAAAATGAGTTCTGTGGT 59.619 43.478 11.97 0.00 42.76 4.16
2257 4755 3.181488 TGCCACACAAAATGAGTTCTGTG 60.181 43.478 6.46 6.46 43.81 3.66
2258 4756 3.023119 TGCCACACAAAATGAGTTCTGT 58.977 40.909 0.00 0.00 0.00 3.41
2259 4757 3.713858 TGCCACACAAAATGAGTTCTG 57.286 42.857 0.00 0.00 0.00 3.02
2442 5139 2.380064 TGGCCTCTTTGTTTGTCCAT 57.620 45.000 3.32 0.00 0.00 3.41
2597 5295 7.863375 TGCAGTACAAAAGTTGCGTATAAAAAT 59.137 29.630 0.00 0.00 39.34 1.82
2603 5301 5.371115 AATGCAGTACAAAAGTTGCGTAT 57.629 34.783 0.00 0.00 39.34 3.06
2608 5306 7.592938 TCCTATGAAATGCAGTACAAAAGTTG 58.407 34.615 0.00 0.00 0.00 3.16
2612 5310 8.402798 TCTTTCCTATGAAATGCAGTACAAAA 57.597 30.769 0.00 0.00 39.65 2.44
2613 5311 7.994425 TCTTTCCTATGAAATGCAGTACAAA 57.006 32.000 0.00 0.00 39.65 2.83
2697 5396 7.756722 CACTTGAATTTTACAGGATTAGCAAGG 59.243 37.037 0.00 0.00 34.82 3.61
2710 5409 3.261580 GGCATGCCCACTTGAATTTTAC 58.738 45.455 27.24 0.00 0.00 2.01
2748 5448 9.981460 GGATATAGAAATTGTAGGGATGGAAAT 57.019 33.333 0.00 0.00 0.00 2.17
2758 5458 8.763049 TGATTCGCAGGATATAGAAATTGTAG 57.237 34.615 0.00 0.00 0.00 2.74
2760 5460 8.450578 TTTGATTCGCAGGATATAGAAATTGT 57.549 30.769 0.00 0.00 0.00 2.71
2762 5462 8.908786 TCTTTGATTCGCAGGATATAGAAATT 57.091 30.769 0.00 0.00 0.00 1.82
2763 5463 7.605691 CCTCTTTGATTCGCAGGATATAGAAAT 59.394 37.037 0.00 0.00 0.00 2.17
2768 5468 4.040339 TGCCTCTTTGATTCGCAGGATATA 59.960 41.667 0.00 0.00 0.00 0.86
2794 5494 6.750963 GCTAGTACTCCGTATGCCAAATATAC 59.249 42.308 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.