Multiple sequence alignment - TraesCS4A01G125400

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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 TraesCS4A01G125400 chr4A 100.000 2498 0 0 1 2498 161398962 161396465 0.000000e+00 4614.0
1 TraesCS4A01G125400 chr4A 88.824 340 13 6 939 1257 596223764 596223429 6.480000e-106 394.0
2 TraesCS4A01G125400 chr1D 92.296 1311 40 8 624 1873 254634661 254635971 0.000000e+00 1805.0
3 TraesCS4A01G125400 chr1D 92.073 164 12 1 1711 1873 254634824 254634661 1.930000e-56 230.0
4 TraesCS4A01G125400 chr3D 92.284 1309 41 9 624 1872 601614756 601616064 0.000000e+00 1803.0
5 TraesCS4A01G125400 chr3D 80.507 513 54 18 1378 1873 438468645 438469128 3.950000e-93 351.0
6 TraesCS4A01G125400 chr3D 90.854 164 14 1 1711 1873 601614919 601614756 4.180000e-53 219.0
7 TraesCS4A01G125400 chr2D 91.705 1314 46 10 623 1873 480771636 480770323 0.000000e+00 1764.0
8 TraesCS4A01G125400 chr2D 94.866 818 23 2 624 1423 73845028 73844212 0.000000e+00 1260.0
9 TraesCS4A01G125400 chr2D 92.057 491 23 2 1400 1874 73835455 73834965 0.000000e+00 676.0
10 TraesCS4A01G125400 chr2D 93.252 163 11 0 1711 1873 73844866 73845028 8.930000e-60 241.0
11 TraesCS4A01G125400 chr2D 92.169 166 11 1 1711 1874 480771471 480771636 1.490000e-57 233.0
12 TraesCS4A01G125400 chr4B 91.401 628 50 4 1874 2498 392630776 392631402 0.000000e+00 857.0
13 TraesCS4A01G125400 chr4B 89.272 522 26 13 1 503 392628350 392628860 5.870000e-176 627.0
14 TraesCS4A01G125400 chr4B 89.941 338 13 3 939 1257 13285158 13284823 1.380000e-112 416.0
15 TraesCS4A01G125400 chr4D 88.657 670 35 19 1 647 314607881 314608532 0.000000e+00 778.0
16 TraesCS4A01G125400 chr4D 90.526 570 43 5 1930 2498 314608578 314609137 0.000000e+00 743.0
17 TraesCS4A01G125400 chr4D 90.541 296 7 3 980 1257 7417593 7417301 3.030000e-99 372.0
18 TraesCS4A01G125400 chr4D 86.520 319 40 3 624 941 20531004 20531320 5.110000e-92 348.0
19 TraesCS4A01G125400 chr4D 87.117 163 21 0 1711 1873 20531166 20531004 4.240000e-43 185.0
20 TraesCS4A01G125400 chr7D 81.010 495 70 17 1400 1874 139187785 139187295 3.030000e-99 372.0
21 TraesCS4A01G125400 chr7D 87.774 319 37 2 624 941 346098764 346098447 3.030000e-99 372.0
22 TraesCS4A01G125400 chr7B 87.774 319 37 2 624 941 688921493 688921176 3.030000e-99 372.0
23 TraesCS4A01G125400 chr7B 87.195 164 20 1 1711 1873 688921330 688921493 4.240000e-43 185.0
24 TraesCS4A01G125400 chr5B 87.619 315 35 4 626 937 547313238 547312925 1.830000e-96 363.0
25 TraesCS4A01G125400 chr2B 87.227 321 37 4 624 941 31069045 31068726 1.830000e-96 363.0
26 TraesCS4A01G125400 chr6D 87.931 58 6 1 1289 1346 2781563 2781619 1.600000e-07 67.6
27 TraesCS4A01G125400 chr6A 87.931 58 6 1 1289 1346 1760309 1760365 1.600000e-07 67.6


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 TraesCS4A01G125400 chr4A 161396465 161398962 2497 True 4614.0 4614 100.0000 1 2498 1 chr4A.!!$R1 2497
1 TraesCS4A01G125400 chr1D 254634661 254635971 1310 False 1805.0 1805 92.2960 624 1873 1 chr1D.!!$F1 1249
2 TraesCS4A01G125400 chr3D 601614756 601616064 1308 False 1803.0 1803 92.2840 624 1872 1 chr3D.!!$F2 1248
3 TraesCS4A01G125400 chr2D 480770323 480771636 1313 True 1764.0 1764 91.7050 623 1873 1 chr2D.!!$R3 1250
4 TraesCS4A01G125400 chr2D 73844212 73845028 816 True 1260.0 1260 94.8660 624 1423 1 chr2D.!!$R2 799
5 TraesCS4A01G125400 chr4B 392628350 392631402 3052 False 742.0 857 90.3365 1 2498 2 chr4B.!!$F1 2497
6 TraesCS4A01G125400 chr4D 314607881 314609137 1256 False 760.5 778 89.5915 1 2498 2 chr4D.!!$F2 2497

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
549 569 0.098376 CGGTCACCGTGTAGCTACTC 59.902 60.0 23.84 19.08 42.73 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 3964 0.313043 CTACCACCAGTGTCGACGTT 59.687 55.0 11.62 0.0 0.0 3.99 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
72 74 3.766691 GCGACTGGGCGAGGGTAA 61.767 66.667 0.00 0.00 0.00 2.85
227 241 1.202568 GCAATCCGCATCGATCACG 59.797 57.895 9.79 9.79 41.79 4.35
273 287 2.987547 GTCCCGGACCTGTCGTCA 60.988 66.667 0.73 0.00 43.95 4.35
275 289 4.415332 CCCGGACCTGTCGTCACG 62.415 72.222 0.73 0.00 43.95 4.35
290 304 2.476619 CGTCACGCTTGTCTGAATCTTT 59.523 45.455 0.00 0.00 0.00 2.52
296 310 5.516339 CACGCTTGTCTGAATCTTTTGTTTT 59.484 36.000 0.00 0.00 0.00 2.43
297 311 5.743872 ACGCTTGTCTGAATCTTTTGTTTTC 59.256 36.000 0.00 0.00 0.00 2.29
369 383 2.596046 ATTTCCGCGGTTGTGGCA 60.596 55.556 27.15 0.00 45.79 4.92
397 411 1.996786 ATGTCCGTACGTACAGCCGG 61.997 60.000 24.50 19.21 41.75 6.13
398 412 2.359850 TCCGTACGTACAGCCGGT 60.360 61.111 24.50 0.00 41.17 5.28
413 432 1.439228 CGGTCAGGCGATGATCTGT 59.561 57.895 0.00 0.00 40.92 3.41
470 489 4.519213 TGCTGGGTGCGTTATAGTATTTT 58.481 39.130 0.00 0.00 46.63 1.82
471 490 4.334203 TGCTGGGTGCGTTATAGTATTTTG 59.666 41.667 0.00 0.00 46.63 2.44
503 523 3.844577 ATGCTAACCGCGTACTATAGG 57.155 47.619 4.92 0.00 43.27 2.57
506 526 2.095516 GCTAACCGCGTACTATAGGGTC 60.096 54.545 4.92 0.00 0.00 4.46
508 528 2.283145 ACCGCGTACTATAGGGTCAT 57.717 50.000 4.92 0.00 0.00 3.06
509 529 3.423539 ACCGCGTACTATAGGGTCATA 57.576 47.619 4.92 0.00 0.00 2.15
510 530 3.341823 ACCGCGTACTATAGGGTCATAG 58.658 50.000 4.92 0.00 35.09 2.23
511 531 3.008375 ACCGCGTACTATAGGGTCATAGA 59.992 47.826 4.92 0.00 33.49 1.98
512 532 4.005650 CCGCGTACTATAGGGTCATAGAA 58.994 47.826 4.92 0.00 33.49 2.10
513 533 4.142730 CCGCGTACTATAGGGTCATAGAAC 60.143 50.000 4.92 0.00 33.49 3.01
514 534 4.435253 CGCGTACTATAGGGTCATAGAACG 60.435 50.000 4.43 0.00 33.49 3.95
515 535 4.671250 GCGTACTATAGGGTCATAGAACGC 60.671 50.000 4.43 0.00 33.49 4.84
516 536 4.435253 CGTACTATAGGGTCATAGAACGCG 60.435 50.000 3.53 3.53 37.20 6.01
517 537 3.748083 ACTATAGGGTCATAGAACGCGA 58.252 45.455 15.93 0.00 37.20 5.87
518 538 4.333690 ACTATAGGGTCATAGAACGCGAT 58.666 43.478 15.93 0.00 37.20 4.58
519 539 3.851976 ATAGGGTCATAGAACGCGATC 57.148 47.619 15.93 11.81 37.20 3.69
520 540 1.399714 AGGGTCATAGAACGCGATCA 58.600 50.000 15.93 1.53 37.20 2.92
521 541 1.754803 AGGGTCATAGAACGCGATCAA 59.245 47.619 15.93 0.00 37.20 2.57
522 542 2.167693 AGGGTCATAGAACGCGATCAAA 59.832 45.455 15.93 3.04 37.20 2.69
523 543 3.131396 GGGTCATAGAACGCGATCAAAT 58.869 45.455 15.93 5.70 0.00 2.32
524 544 3.560068 GGGTCATAGAACGCGATCAAATT 59.440 43.478 15.93 0.00 0.00 1.82
525 545 4.035208 GGGTCATAGAACGCGATCAAATTT 59.965 41.667 15.93 0.00 0.00 1.82
526 546 4.963953 GGTCATAGAACGCGATCAAATTTG 59.036 41.667 15.93 12.15 0.00 2.32
527 547 4.963953 GTCATAGAACGCGATCAAATTTGG 59.036 41.667 15.93 4.24 0.00 3.28
528 548 4.873259 TCATAGAACGCGATCAAATTTGGA 59.127 37.500 15.93 5.66 0.00 3.53
529 549 3.471495 AGAACGCGATCAAATTTGGAC 57.529 42.857 15.93 10.98 0.00 4.02
530 550 2.161609 AGAACGCGATCAAATTTGGACC 59.838 45.455 15.93 6.79 0.00 4.46
531 551 0.446222 ACGCGATCAAATTTGGACCG 59.554 50.000 15.93 17.50 0.00 4.79
532 552 0.248054 CGCGATCAAATTTGGACCGG 60.248 55.000 17.90 0.00 0.00 5.28
533 553 0.808755 GCGATCAAATTTGGACCGGT 59.191 50.000 17.90 6.92 0.00 5.28
534 554 1.202143 GCGATCAAATTTGGACCGGTC 60.202 52.381 27.04 27.04 0.00 4.79
535 555 2.080693 CGATCAAATTTGGACCGGTCA 58.919 47.619 34.40 18.59 0.00 4.02
536 556 2.159572 CGATCAAATTTGGACCGGTCAC 60.160 50.000 34.40 23.56 0.00 3.67
537 557 1.611519 TCAAATTTGGACCGGTCACC 58.388 50.000 34.40 20.63 0.00 4.02
539 559 0.179012 AAATTTGGACCGGTCACCGT 60.179 50.000 34.40 15.60 46.80 4.83
540 560 0.887387 AATTTGGACCGGTCACCGTG 60.887 55.000 34.40 9.41 46.80 4.94
541 561 2.047213 ATTTGGACCGGTCACCGTGT 62.047 55.000 34.40 12.95 46.80 4.49
542 562 1.398174 TTTGGACCGGTCACCGTGTA 61.398 55.000 34.40 10.39 46.80 2.90
543 563 1.808531 TTGGACCGGTCACCGTGTAG 61.809 60.000 34.40 1.43 46.80 2.74
544 564 2.126189 GACCGGTCACCGTGTAGC 60.126 66.667 29.75 0.00 46.80 3.58
545 565 2.599578 ACCGGTCACCGTGTAGCT 60.600 61.111 16.87 0.00 46.80 3.32
546 566 1.303561 ACCGGTCACCGTGTAGCTA 60.304 57.895 16.87 0.00 46.80 3.32
547 567 1.138247 CCGGTCACCGTGTAGCTAC 59.862 63.158 16.87 17.30 46.80 3.58
548 568 1.310933 CCGGTCACCGTGTAGCTACT 61.311 60.000 23.84 1.27 46.80 2.57
549 569 0.098376 CGGTCACCGTGTAGCTACTC 59.902 60.000 23.84 19.08 42.73 2.59
550 570 0.098376 GGTCACCGTGTAGCTACTCG 59.902 60.000 31.40 31.40 41.31 4.18
551 571 1.081892 GTCACCGTGTAGCTACTCGA 58.918 55.000 36.78 21.70 43.46 4.04
552 572 1.669779 GTCACCGTGTAGCTACTCGAT 59.330 52.381 36.78 25.54 43.46 3.59
553 573 2.097142 GTCACCGTGTAGCTACTCGATT 59.903 50.000 36.78 24.96 43.46 3.34
554 574 2.353889 TCACCGTGTAGCTACTCGATTC 59.646 50.000 36.78 15.77 43.46 2.52
555 575 1.674962 ACCGTGTAGCTACTCGATTCC 59.325 52.381 36.78 8.15 43.46 3.01
556 576 1.001597 CCGTGTAGCTACTCGATTCCC 60.002 57.143 36.78 7.47 43.46 3.97
557 577 1.001597 CGTGTAGCTACTCGATTCCCC 60.002 57.143 33.63 3.37 43.46 4.81
558 578 2.308690 GTGTAGCTACTCGATTCCCCT 58.691 52.381 23.84 0.00 0.00 4.79
559 579 2.034812 GTGTAGCTACTCGATTCCCCTG 59.965 54.545 23.84 0.00 0.00 4.45
560 580 2.308690 GTAGCTACTCGATTCCCCTGT 58.691 52.381 16.88 0.00 0.00 4.00
561 581 2.750141 AGCTACTCGATTCCCCTGTA 57.250 50.000 0.00 0.00 0.00 2.74
562 582 3.246416 AGCTACTCGATTCCCCTGTAT 57.754 47.619 0.00 0.00 0.00 2.29
563 583 4.383931 AGCTACTCGATTCCCCTGTATA 57.616 45.455 0.00 0.00 0.00 1.47
564 584 4.080687 AGCTACTCGATTCCCCTGTATAC 58.919 47.826 0.00 0.00 0.00 1.47
565 585 3.825014 GCTACTCGATTCCCCTGTATACA 59.175 47.826 5.25 5.25 0.00 2.29
566 586 4.082679 GCTACTCGATTCCCCTGTATACAG 60.083 50.000 23.58 23.58 43.40 2.74
567 587 2.628657 ACTCGATTCCCCTGTATACAGC 59.371 50.000 24.85 10.83 42.47 4.40
568 588 2.894126 CTCGATTCCCCTGTATACAGCT 59.106 50.000 24.85 8.25 42.47 4.24
569 589 2.628178 TCGATTCCCCTGTATACAGCTG 59.372 50.000 24.85 13.48 42.47 4.24
570 590 2.365617 CGATTCCCCTGTATACAGCTGT 59.634 50.000 25.12 25.12 42.47 4.40
571 591 3.181465 CGATTCCCCTGTATACAGCTGTT 60.181 47.826 27.06 15.06 42.47 3.16
572 592 4.038763 CGATTCCCCTGTATACAGCTGTTA 59.961 45.833 27.06 14.02 42.47 2.41
573 593 5.542779 GATTCCCCTGTATACAGCTGTTAG 58.457 45.833 27.06 17.13 42.47 2.34
574 594 4.259933 TCCCCTGTATACAGCTGTTAGA 57.740 45.455 27.06 13.95 42.47 2.10
575 595 4.816126 TCCCCTGTATACAGCTGTTAGAT 58.184 43.478 27.06 15.23 42.47 1.98
576 596 5.216622 TCCCCTGTATACAGCTGTTAGATT 58.783 41.667 27.06 7.84 42.47 2.40
577 597 5.665812 TCCCCTGTATACAGCTGTTAGATTT 59.334 40.000 27.06 0.00 42.47 2.17
578 598 5.760253 CCCCTGTATACAGCTGTTAGATTTG 59.240 44.000 27.06 9.41 42.47 2.32
579 599 5.760253 CCCTGTATACAGCTGTTAGATTTGG 59.240 44.000 27.06 17.19 42.47 3.28
580 600 5.237344 CCTGTATACAGCTGTTAGATTTGGC 59.763 44.000 27.06 6.11 42.47 4.52
581 601 5.123227 TGTATACAGCTGTTAGATTTGGCC 58.877 41.667 27.06 0.00 0.00 5.36
582 602 1.839424 ACAGCTGTTAGATTTGGCCC 58.161 50.000 15.25 0.00 0.00 5.80
583 603 1.355720 ACAGCTGTTAGATTTGGCCCT 59.644 47.619 15.25 0.00 0.00 5.19
584 604 2.225117 ACAGCTGTTAGATTTGGCCCTT 60.225 45.455 15.25 0.00 0.00 3.95
585 605 2.424956 CAGCTGTTAGATTTGGCCCTTC 59.575 50.000 5.25 0.00 0.00 3.46
586 606 1.751351 GCTGTTAGATTTGGCCCTTCC 59.249 52.381 0.00 0.00 0.00 3.46
587 607 2.379005 CTGTTAGATTTGGCCCTTCCC 58.621 52.381 0.00 0.00 0.00 3.97
588 608 2.000048 TGTTAGATTTGGCCCTTCCCT 59.000 47.619 0.00 0.00 0.00 4.20
589 609 2.025321 TGTTAGATTTGGCCCTTCCCTC 60.025 50.000 0.00 0.00 0.00 4.30
590 610 1.979809 TAGATTTGGCCCTTCCCTCA 58.020 50.000 0.00 0.00 0.00 3.86
591 611 0.332972 AGATTTGGCCCTTCCCTCAC 59.667 55.000 0.00 0.00 0.00 3.51
592 612 0.684479 GATTTGGCCCTTCCCTCACC 60.684 60.000 0.00 0.00 0.00 4.02
593 613 1.149133 ATTTGGCCCTTCCCTCACCT 61.149 55.000 0.00 0.00 0.00 4.00
594 614 1.789576 TTTGGCCCTTCCCTCACCTC 61.790 60.000 0.00 0.00 0.00 3.85
595 615 3.787001 GGCCCTTCCCTCACCTCG 61.787 72.222 0.00 0.00 0.00 4.63
596 616 3.003763 GCCCTTCCCTCACCTCGT 61.004 66.667 0.00 0.00 0.00 4.18
597 617 3.020237 GCCCTTCCCTCACCTCGTC 62.020 68.421 0.00 0.00 0.00 4.20
598 618 1.305381 CCCTTCCCTCACCTCGTCT 60.305 63.158 0.00 0.00 0.00 4.18
599 619 0.905337 CCCTTCCCTCACCTCGTCTT 60.905 60.000 0.00 0.00 0.00 3.01
600 620 0.533032 CCTTCCCTCACCTCGTCTTC 59.467 60.000 0.00 0.00 0.00 2.87
601 621 0.533032 CTTCCCTCACCTCGTCTTCC 59.467 60.000 0.00 0.00 0.00 3.46
602 622 0.114560 TTCCCTCACCTCGTCTTCCT 59.885 55.000 0.00 0.00 0.00 3.36
603 623 0.323542 TCCCTCACCTCGTCTTCCTC 60.324 60.000 0.00 0.00 0.00 3.71
604 624 1.324005 CCCTCACCTCGTCTTCCTCC 61.324 65.000 0.00 0.00 0.00 4.30
605 625 1.324005 CCTCACCTCGTCTTCCTCCC 61.324 65.000 0.00 0.00 0.00 4.30
606 626 0.323908 CTCACCTCGTCTTCCTCCCT 60.324 60.000 0.00 0.00 0.00 4.20
607 627 0.323542 TCACCTCGTCTTCCTCCCTC 60.324 60.000 0.00 0.00 0.00 4.30
608 628 1.000612 ACCTCGTCTTCCTCCCTCC 59.999 63.158 0.00 0.00 0.00 4.30
609 629 1.000486 CCTCGTCTTCCTCCCTCCA 60.000 63.158 0.00 0.00 0.00 3.86
610 630 0.397816 CCTCGTCTTCCTCCCTCCAT 60.398 60.000 0.00 0.00 0.00 3.41
611 631 1.036707 CTCGTCTTCCTCCCTCCATC 58.963 60.000 0.00 0.00 0.00 3.51
612 632 0.752009 TCGTCTTCCTCCCTCCATCG 60.752 60.000 0.00 0.00 0.00 3.84
613 633 1.443828 GTCTTCCTCCCTCCATCGC 59.556 63.158 0.00 0.00 0.00 4.58
614 634 1.045911 GTCTTCCTCCCTCCATCGCT 61.046 60.000 0.00 0.00 0.00 4.93
615 635 0.757188 TCTTCCTCCCTCCATCGCTC 60.757 60.000 0.00 0.00 0.00 5.03
616 636 1.753368 CTTCCTCCCTCCATCGCTCC 61.753 65.000 0.00 0.00 0.00 4.70
617 637 3.237741 CCTCCCTCCATCGCTCCC 61.238 72.222 0.00 0.00 0.00 4.30
618 638 3.610669 CTCCCTCCATCGCTCCCG 61.611 72.222 0.00 0.00 0.00 5.14
646 666 5.452636 GGAGTAAATTGCAAGAAACCACCAA 60.453 40.000 4.94 0.00 0.00 3.67
666 686 3.557228 ATTTGAAGGCTTGGTTTGCAA 57.443 38.095 3.46 0.00 0.00 4.08
721 742 2.420022 ACCGCATCTTGTGTAATCTTGC 59.580 45.455 0.00 0.00 0.00 4.01
773 794 6.772078 AGCGCTTTAAGTATGTTTATGACAC 58.228 36.000 2.64 0.00 42.04 3.67
869 890 9.191995 GATTTACAAACAAGTCCCTGTAATTTG 57.808 33.333 0.00 0.00 34.98 2.32
873 894 7.616313 ACAAACAAGTCCCTGTAATTTGAAAA 58.384 30.769 0.00 0.00 0.00 2.29
883 904 7.231925 TCCCTGTAATTTGAAAAGAACCCTTAC 59.768 37.037 0.00 0.00 31.15 2.34
932 953 3.605749 GAGCCTACCCAAGCACGCA 62.606 63.158 0.00 0.00 0.00 5.24
949 970 1.073722 CAAGCAGAACCCCAGAGCA 59.926 57.895 0.00 0.00 0.00 4.26
989 1010 2.046892 GCCAAAGCAGAGCTCCGA 60.047 61.111 10.93 0.00 38.25 4.55
1379 2492 3.485463 TTCTTTCGAACCTGATGTGGT 57.515 42.857 0.00 0.00 43.11 4.16
1478 2925 2.796651 GGCGTACACGGTCGATCT 59.203 61.111 3.67 0.00 40.23 2.75
1689 3423 1.122019 GGGCCCCTGTCGACTATGAT 61.122 60.000 12.23 0.00 0.00 2.45
1729 3478 1.673767 AATCTGGACCCACCTGTCAT 58.326 50.000 0.00 0.00 39.86 3.06
1748 3497 7.372451 TGTCATAAACATACTTAAAGCGCTT 57.628 32.000 18.98 18.98 31.20 4.68
1765 3514 2.869801 CGCTTTAATCCGCCAATCAGTA 59.130 45.455 0.00 0.00 0.00 2.74
1893 3645 2.303311 CCTTCCGGGAGAGAAAGAAAGT 59.697 50.000 12.85 0.00 37.23 2.66
1901 3653 6.655425 CCGGGAGAGAAAGAAAGTAAGAAATT 59.345 38.462 0.00 0.00 0.00 1.82
1928 3701 2.733301 CCCGCATGCAAAACACCA 59.267 55.556 19.57 0.00 0.00 4.17
2074 3849 0.247736 CACTCCAACCTTCTCTCCCG 59.752 60.000 0.00 0.00 0.00 5.14
2075 3850 0.905337 ACTCCAACCTTCTCTCCCGG 60.905 60.000 0.00 0.00 0.00 5.73
2095 3870 1.227292 GAATCTCGCGACCCTTCCC 60.227 63.158 3.71 0.00 0.00 3.97
2096 3871 2.955751 GAATCTCGCGACCCTTCCCG 62.956 65.000 3.71 0.00 0.00 5.14
2171 3946 1.672881 GGTTGCAGCTCTTATTCGCAT 59.327 47.619 0.00 0.00 31.67 4.73
2174 3949 1.134431 TGCAGCTCTTATTCGCATGGA 60.134 47.619 0.00 0.00 0.00 3.41
2189 3964 3.391965 GCATGGACATGAAAGCAACAAA 58.608 40.909 15.99 0.00 41.20 2.83
2204 3979 1.003851 ACAAAACGTCGACACTGGTG 58.996 50.000 17.16 8.82 0.00 4.17
2257 4032 3.961182 GACATACGGTCGCTAATCTCAA 58.039 45.455 0.00 0.00 36.65 3.02
2287 4062 8.133627 CCTCATGAAGAAATGGATGTAACAATC 58.866 37.037 0.00 0.00 0.00 2.67
2297 4072 4.142708 TGGATGTAACAATCGACAATGCAC 60.143 41.667 0.00 0.00 0.00 4.57
2330 4105 6.541111 AAAACAAAACGGTTGTAGCAAAAA 57.459 29.167 7.12 0.00 31.50 1.94
2365 4140 2.293122 CCAACAAACGAAGAGATGGCAA 59.707 45.455 0.00 0.00 0.00 4.52
2413 4188 5.705609 ACAAAGACGATGGTAGCAAATTT 57.294 34.783 0.00 0.00 0.00 1.82
2419 4194 5.880332 AGACGATGGTAGCAAATTTGTACAT 59.120 36.000 19.03 16.29 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 2.437895 GAACCTGGGGCGCTTACC 60.438 66.667 7.64 8.46 0.00 2.85
69 71 2.437895 GGAACCTGGGGCGCTTAC 60.438 66.667 7.64 0.00 0.00 2.34
70 72 2.931105 TGGAACCTGGGGCGCTTA 60.931 61.111 7.64 0.00 0.00 3.09
71 73 4.351054 CTGGAACCTGGGGCGCTT 62.351 66.667 7.64 0.00 0.00 4.68
182 195 2.124860 GGGGTGGCCATGTACGTC 60.125 66.667 9.72 0.00 0.00 4.34
227 241 1.452833 GGGCTCTGCTCCATGGAAC 60.453 63.158 17.00 12.52 0.00 3.62
261 275 2.022129 CAAGCGTGACGACAGGTCC 61.022 63.158 10.10 0.00 45.46 4.46
267 281 1.387084 GATTCAGACAAGCGTGACGAC 59.613 52.381 10.10 0.00 0.00 4.34
273 287 4.900635 AACAAAAGATTCAGACAAGCGT 57.099 36.364 0.00 0.00 0.00 5.07
275 289 7.615790 CAAGAAAACAAAAGATTCAGACAAGC 58.384 34.615 0.00 0.00 0.00 4.01
290 304 5.350504 TTCCATTGGAAGCAAGAAAACAA 57.649 34.783 14.24 0.00 36.71 2.83
296 310 4.800249 GCACAATTTCCATTGGAAGCAAGA 60.800 41.667 17.29 3.87 43.06 3.02
297 311 3.434299 GCACAATTTCCATTGGAAGCAAG 59.566 43.478 17.29 11.56 43.06 4.01
369 383 1.820519 ACGTACGGACATACACCACAT 59.179 47.619 21.06 0.00 0.00 3.21
397 411 2.200067 CTCAACAGATCATCGCCTGAC 58.800 52.381 0.00 0.00 36.48 3.51
398 412 1.137675 CCTCAACAGATCATCGCCTGA 59.862 52.381 0.00 0.00 38.53 3.86
410 429 1.800805 ATCAGACAACGCCTCAACAG 58.199 50.000 0.00 0.00 0.00 3.16
413 432 3.195610 ACTCATATCAGACAACGCCTCAA 59.804 43.478 0.00 0.00 0.00 3.02
470 489 4.250464 CGGTTAGCATACTCTTGGAAACA 58.750 43.478 0.00 0.00 39.83 2.83
471 490 4.859629 CGGTTAGCATACTCTTGGAAAC 57.140 45.455 0.00 0.00 0.00 2.78
498 518 4.329392 TGATCGCGTTCTATGACCCTATA 58.671 43.478 17.38 0.00 0.00 1.31
503 523 4.795970 AATTTGATCGCGTTCTATGACC 57.204 40.909 17.38 0.00 0.00 4.02
506 526 4.963953 GTCCAAATTTGATCGCGTTCTATG 59.036 41.667 19.86 6.30 0.00 2.23
508 528 3.372822 GGTCCAAATTTGATCGCGTTCTA 59.627 43.478 19.86 7.91 0.00 2.10
509 529 2.161609 GGTCCAAATTTGATCGCGTTCT 59.838 45.455 19.86 0.00 0.00 3.01
510 530 2.515912 GGTCCAAATTTGATCGCGTTC 58.484 47.619 19.86 8.36 0.00 3.95
511 531 1.135803 CGGTCCAAATTTGATCGCGTT 60.136 47.619 19.86 0.00 0.00 4.84
512 532 0.446222 CGGTCCAAATTTGATCGCGT 59.554 50.000 19.86 0.00 0.00 6.01
513 533 0.248054 CCGGTCCAAATTTGATCGCG 60.248 55.000 19.86 0.00 0.00 5.87
514 534 0.808755 ACCGGTCCAAATTTGATCGC 59.191 50.000 19.86 6.28 0.00 4.58
515 535 2.080693 TGACCGGTCCAAATTTGATCG 58.919 47.619 31.19 17.28 0.00 3.69
516 536 2.163613 GGTGACCGGTCCAAATTTGATC 59.836 50.000 31.19 6.98 0.00 2.92
517 537 2.167662 GGTGACCGGTCCAAATTTGAT 58.832 47.619 31.19 0.00 0.00 2.57
518 538 1.611519 GGTGACCGGTCCAAATTTGA 58.388 50.000 31.19 7.57 0.00 2.69
519 539 0.239879 CGGTGACCGGTCCAAATTTG 59.760 55.000 31.19 11.40 44.15 2.32
520 540 2.636299 CGGTGACCGGTCCAAATTT 58.364 52.632 31.19 0.00 44.15 1.82
521 541 4.390048 CGGTGACCGGTCCAAATT 57.610 55.556 31.19 0.00 44.15 1.82
531 551 0.098376 CGAGTAGCTACACGGTGACC 59.902 60.000 29.01 0.00 36.79 4.02
532 552 1.081892 TCGAGTAGCTACACGGTGAC 58.918 55.000 33.30 7.33 40.00 3.67
533 553 2.034104 ATCGAGTAGCTACACGGTGA 57.966 50.000 33.30 20.50 40.00 4.02
534 554 2.541178 GGAATCGAGTAGCTACACGGTG 60.541 54.545 33.30 16.07 40.00 4.94
535 555 1.674962 GGAATCGAGTAGCTACACGGT 59.325 52.381 33.30 28.04 40.00 4.83
536 556 1.001597 GGGAATCGAGTAGCTACACGG 60.002 57.143 33.30 19.96 40.00 4.94
537 557 1.001597 GGGGAATCGAGTAGCTACACG 60.002 57.143 30.25 30.25 40.73 4.49
538 558 2.034812 CAGGGGAATCGAGTAGCTACAC 59.965 54.545 25.28 18.10 0.00 2.90
539 559 2.307768 CAGGGGAATCGAGTAGCTACA 58.692 52.381 25.28 5.74 0.00 2.74
540 560 2.308690 ACAGGGGAATCGAGTAGCTAC 58.691 52.381 16.43 16.43 0.00 3.58
541 561 2.750141 ACAGGGGAATCGAGTAGCTA 57.250 50.000 0.00 0.00 0.00 3.32
542 562 2.750141 TACAGGGGAATCGAGTAGCT 57.250 50.000 0.00 0.00 0.00 3.32
543 563 3.825014 TGTATACAGGGGAATCGAGTAGC 59.175 47.826 0.08 0.00 0.00 3.58
544 564 4.082679 GCTGTATACAGGGGAATCGAGTAG 60.083 50.000 29.45 5.04 43.94 2.57
545 565 3.825014 GCTGTATACAGGGGAATCGAGTA 59.175 47.826 29.45 0.00 43.94 2.59
546 566 2.628657 GCTGTATACAGGGGAATCGAGT 59.371 50.000 29.45 0.00 43.94 4.18
547 567 2.894126 AGCTGTATACAGGGGAATCGAG 59.106 50.000 29.45 6.11 43.94 4.04
548 568 2.628178 CAGCTGTATACAGGGGAATCGA 59.372 50.000 29.45 0.00 43.94 3.59
549 569 2.365617 ACAGCTGTATACAGGGGAATCG 59.634 50.000 29.45 12.90 43.94 3.34
550 570 4.423625 AACAGCTGTATACAGGGGAATC 57.576 45.455 29.45 14.58 43.94 2.52
551 571 5.216622 TCTAACAGCTGTATACAGGGGAAT 58.783 41.667 29.45 1.75 43.94 3.01
552 572 4.616553 TCTAACAGCTGTATACAGGGGAA 58.383 43.478 29.45 7.34 43.94 3.97
553 573 4.259933 TCTAACAGCTGTATACAGGGGA 57.740 45.455 29.45 13.38 43.94 4.81
554 574 5.552870 AATCTAACAGCTGTATACAGGGG 57.447 43.478 29.45 10.19 43.94 4.79
555 575 5.760253 CCAAATCTAACAGCTGTATACAGGG 59.240 44.000 29.45 15.85 43.94 4.45
556 576 5.237344 GCCAAATCTAACAGCTGTATACAGG 59.763 44.000 29.45 18.35 43.94 4.00
557 577 5.237344 GGCCAAATCTAACAGCTGTATACAG 59.763 44.000 25.68 25.68 46.40 2.74
558 578 5.123227 GGCCAAATCTAACAGCTGTATACA 58.877 41.667 22.01 5.25 0.00 2.29
559 579 4.515567 GGGCCAAATCTAACAGCTGTATAC 59.484 45.833 22.01 0.00 0.00 1.47
560 580 4.412199 AGGGCCAAATCTAACAGCTGTATA 59.588 41.667 22.01 13.32 0.00 1.47
561 581 3.203040 AGGGCCAAATCTAACAGCTGTAT 59.797 43.478 22.01 12.87 0.00 2.29
562 582 2.576191 AGGGCCAAATCTAACAGCTGTA 59.424 45.455 22.01 4.74 0.00 2.74
563 583 1.355720 AGGGCCAAATCTAACAGCTGT 59.644 47.619 15.25 15.25 0.00 4.40
564 584 2.134789 AGGGCCAAATCTAACAGCTG 57.865 50.000 13.48 13.48 0.00 4.24
565 585 2.621668 GGAAGGGCCAAATCTAACAGCT 60.622 50.000 6.18 0.00 36.34 4.24
566 586 1.751351 GGAAGGGCCAAATCTAACAGC 59.249 52.381 6.18 0.00 36.34 4.40
567 587 2.024941 AGGGAAGGGCCAAATCTAACAG 60.025 50.000 6.18 0.00 38.95 3.16
568 588 2.000048 AGGGAAGGGCCAAATCTAACA 59.000 47.619 6.18 0.00 38.95 2.41
569 589 2.025321 TGAGGGAAGGGCCAAATCTAAC 60.025 50.000 6.18 0.00 38.95 2.34
570 590 2.025321 GTGAGGGAAGGGCCAAATCTAA 60.025 50.000 6.18 0.00 38.95 2.10
571 591 1.564348 GTGAGGGAAGGGCCAAATCTA 59.436 52.381 6.18 0.00 38.95 1.98
572 592 0.332972 GTGAGGGAAGGGCCAAATCT 59.667 55.000 6.18 0.00 38.95 2.40
573 593 0.684479 GGTGAGGGAAGGGCCAAATC 60.684 60.000 6.18 0.11 38.95 2.17
574 594 1.149133 AGGTGAGGGAAGGGCCAAAT 61.149 55.000 6.18 0.00 38.95 2.32
575 595 1.778383 AGGTGAGGGAAGGGCCAAA 60.778 57.895 6.18 0.00 38.95 3.28
576 596 2.121506 AGGTGAGGGAAGGGCCAA 60.122 61.111 6.18 0.00 38.95 4.52
577 597 2.610859 GAGGTGAGGGAAGGGCCA 60.611 66.667 6.18 0.00 38.95 5.36
578 598 3.787001 CGAGGTGAGGGAAGGGCC 61.787 72.222 0.00 0.00 0.00 5.80
579 599 3.003763 ACGAGGTGAGGGAAGGGC 61.004 66.667 0.00 0.00 0.00 5.19
580 600 0.905337 AAGACGAGGTGAGGGAAGGG 60.905 60.000 0.00 0.00 0.00 3.95
581 601 0.533032 GAAGACGAGGTGAGGGAAGG 59.467 60.000 0.00 0.00 0.00 3.46
582 602 0.533032 GGAAGACGAGGTGAGGGAAG 59.467 60.000 0.00 0.00 0.00 3.46
583 603 0.114560 AGGAAGACGAGGTGAGGGAA 59.885 55.000 0.00 0.00 0.00 3.97
584 604 0.323542 GAGGAAGACGAGGTGAGGGA 60.324 60.000 0.00 0.00 0.00 4.20
585 605 1.324005 GGAGGAAGACGAGGTGAGGG 61.324 65.000 0.00 0.00 0.00 4.30
586 606 1.324005 GGGAGGAAGACGAGGTGAGG 61.324 65.000 0.00 0.00 0.00 3.86
587 607 0.323908 AGGGAGGAAGACGAGGTGAG 60.324 60.000 0.00 0.00 0.00 3.51
588 608 0.323542 GAGGGAGGAAGACGAGGTGA 60.324 60.000 0.00 0.00 0.00 4.02
589 609 1.324005 GGAGGGAGGAAGACGAGGTG 61.324 65.000 0.00 0.00 0.00 4.00
590 610 1.000612 GGAGGGAGGAAGACGAGGT 59.999 63.158 0.00 0.00 0.00 3.85
591 611 0.397816 ATGGAGGGAGGAAGACGAGG 60.398 60.000 0.00 0.00 0.00 4.63
592 612 1.036707 GATGGAGGGAGGAAGACGAG 58.963 60.000 0.00 0.00 0.00 4.18
593 613 0.752009 CGATGGAGGGAGGAAGACGA 60.752 60.000 0.00 0.00 0.00 4.20
594 614 1.736586 CGATGGAGGGAGGAAGACG 59.263 63.158 0.00 0.00 0.00 4.18
595 615 1.045911 AGCGATGGAGGGAGGAAGAC 61.046 60.000 0.00 0.00 0.00 3.01
596 616 0.757188 GAGCGATGGAGGGAGGAAGA 60.757 60.000 0.00 0.00 0.00 2.87
597 617 1.745264 GAGCGATGGAGGGAGGAAG 59.255 63.158 0.00 0.00 0.00 3.46
598 618 1.762460 GGAGCGATGGAGGGAGGAA 60.762 63.158 0.00 0.00 0.00 3.36
599 619 2.123251 GGAGCGATGGAGGGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
600 620 3.237741 GGGAGCGATGGAGGGAGG 61.238 72.222 0.00 0.00 0.00 4.30
601 621 3.610669 CGGGAGCGATGGAGGGAG 61.611 72.222 0.00 0.00 0.00 4.30
602 622 4.137615 TCGGGAGCGATGGAGGGA 62.138 66.667 0.00 0.00 0.00 4.20
603 623 3.610669 CTCGGGAGCGATGGAGGG 61.611 72.222 0.00 0.00 0.00 4.30
604 624 2.519541 TCTCGGGAGCGATGGAGG 60.520 66.667 0.00 0.00 0.00 4.30
605 625 2.560119 CCTCTCGGGAGCGATGGAG 61.560 68.421 6.84 0.00 38.21 3.86
606 626 2.519541 CCTCTCGGGAGCGATGGA 60.520 66.667 6.84 0.00 38.21 3.41
607 627 2.519541 TCCTCTCGGGAGCGATGG 60.520 66.667 6.84 0.00 39.58 3.51
614 634 2.184533 TGCAATTTACTCCTCTCGGGA 58.815 47.619 0.00 0.00 42.77 5.14
615 635 2.691409 TGCAATTTACTCCTCTCGGG 57.309 50.000 0.00 0.00 0.00 5.14
616 636 3.861840 TCTTGCAATTTACTCCTCTCGG 58.138 45.455 0.00 0.00 0.00 4.63
617 637 5.390991 GGTTTCTTGCAATTTACTCCTCTCG 60.391 44.000 0.00 0.00 0.00 4.04
618 638 5.473504 TGGTTTCTTGCAATTTACTCCTCTC 59.526 40.000 0.00 0.00 0.00 3.20
619 639 5.241728 GTGGTTTCTTGCAATTTACTCCTCT 59.758 40.000 0.00 0.00 0.00 3.69
620 640 5.461526 GTGGTTTCTTGCAATTTACTCCTC 58.538 41.667 0.00 0.00 0.00 3.71
621 641 4.280929 GGTGGTTTCTTGCAATTTACTCCT 59.719 41.667 0.00 0.00 0.00 3.69
646 666 3.557228 TTGCAAACCAAGCCTTCAAAT 57.443 38.095 0.00 0.00 0.00 2.32
721 742 2.529151 GCCAATCGGTGTTATTTGCAG 58.471 47.619 0.00 0.00 33.28 4.41
773 794 1.883021 GGCAAAATCTGGACCCACG 59.117 57.895 0.00 0.00 0.00 4.94
805 826 4.421479 CGCCGTCTCAGCCGAGTT 62.421 66.667 0.00 0.00 40.44 3.01
869 890 6.811954 TGGTTTTCATGTAAGGGTTCTTTTC 58.188 36.000 0.00 0.00 34.59 2.29
873 894 6.800072 TTTTGGTTTTCATGTAAGGGTTCT 57.200 33.333 0.00 0.00 0.00 3.01
910 931 1.229496 TGCTTGGGTAGGCTCCAGA 60.229 57.895 0.00 0.00 35.48 3.86
932 953 1.377994 CTGCTCTGGGGTTCTGCTT 59.622 57.895 0.00 0.00 0.00 3.91
949 970 1.821936 CTTCTCGCTGGATCTGGCT 59.178 57.895 8.33 0.00 0.00 4.75
1478 2925 3.052793 CCTCTACTCCTCCCTGTTTCCTA 60.053 52.174 0.00 0.00 0.00 2.94
1729 3478 8.117988 CGGATTAAAGCGCTTTAAGTATGTTTA 58.882 33.333 41.44 26.23 44.95 2.01
1748 3497 9.562408 TGTAAATAATACTGATTGGCGGATTAA 57.438 29.630 0.00 0.00 0.00 1.40
1772 3521 4.083324 CCGCATCTTGTGTAATCTTGTTGT 60.083 41.667 0.00 0.00 0.00 3.32
1825 3575 4.247267 TGAAGGCTTGATTTGCAGAAAG 57.753 40.909 3.46 0.00 0.00 2.62
1836 3586 1.064017 ACCACCAGTTTGAAGGCTTGA 60.064 47.619 3.46 0.00 0.00 3.02
1859 3609 2.832672 CGGAAGGAGTAAATTGCAGC 57.167 50.000 0.00 0.00 0.00 5.25
1885 3635 7.039313 AGCGTTGGAATTTCTTACTTTCTTT 57.961 32.000 0.00 0.00 0.00 2.52
1886 3636 6.294010 GGAGCGTTGGAATTTCTTACTTTCTT 60.294 38.462 0.00 0.00 0.00 2.52
1893 3645 2.718563 GGGGAGCGTTGGAATTTCTTA 58.281 47.619 0.00 0.00 0.00 2.10
1952 3726 2.171659 AGAGACCTCATCAGAGCTCGTA 59.828 50.000 8.37 0.11 40.68 3.43
2030 3805 0.625316 TGCTGCAACCCTATCATGGT 59.375 50.000 0.00 0.00 37.85 3.55
2058 3833 2.291043 GCCGGGAGAGAAGGTTGGA 61.291 63.158 2.18 0.00 0.00 3.53
2061 3836 1.265454 ATTCGCCGGGAGAGAAGGTT 61.265 55.000 2.18 0.00 31.94 3.50
2063 3838 1.068250 GATTCGCCGGGAGAGAAGG 59.932 63.158 2.18 0.00 31.94 3.46
2095 3870 0.373716 GTTTATTCAGCCGAGGTGCG 59.626 55.000 0.00 0.00 40.47 5.34
2096 3871 1.130561 GTGTTTATTCAGCCGAGGTGC 59.869 52.381 0.00 0.00 0.00 5.01
2110 3885 1.894756 GGCGGTGCTGTGGTGTTTA 60.895 57.895 0.00 0.00 0.00 2.01
2130 3905 4.961511 AACGACGCCGAGCTGCAA 62.962 61.111 0.00 0.00 39.50 4.08
2140 3915 1.807242 GCTGCAACCAAAAACGACGC 61.807 55.000 0.00 0.00 0.00 5.19
2171 3946 3.119316 ACGTTTTGTTGCTTTCATGTCCA 60.119 39.130 0.00 0.00 0.00 4.02
2174 3949 3.105203 CGACGTTTTGTTGCTTTCATGT 58.895 40.909 0.00 0.00 0.00 3.21
2189 3964 0.313043 CTACCACCAGTGTCGACGTT 59.687 55.000 11.62 0.00 0.00 3.99
2204 3979 3.733727 CACCGTTGTCAATTTTTGCTACC 59.266 43.478 0.00 0.00 0.00 3.18
2257 4032 9.125026 GTTACATCCATTTCTTCATGAGGTTAT 57.875 33.333 4.57 0.00 0.00 1.89
2287 4062 4.661993 TTTTGCTACTAGTGCATTGTCG 57.338 40.909 17.03 0.00 40.34 4.35
2310 4085 4.568760 CCATTTTTGCTACAACCGTTTTGT 59.431 37.500 5.14 5.14 36.49 2.83
2316 4091 4.491234 TGTACCATTTTTGCTACAACCG 57.509 40.909 0.00 0.00 0.00 4.44
2382 4157 2.472488 CCATCGTCTTTGTTTTTGCTGC 59.528 45.455 0.00 0.00 0.00 5.25
2413 4188 3.222173 ACTTGCTGGAACCAATGTACA 57.778 42.857 0.00 0.00 0.00 2.90
2419 4194 4.675671 CGTTTGTTTACTTGCTGGAACCAA 60.676 41.667 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.