Multiple sequence alignment - TraesCS3B01G117700

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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 TraesCS3B01G117700 chr3B 100.000 3758 0 0 1 3758 84877988 84881745 0.000000e+00 6940.0
1 TraesCS3B01G117700 chr3B 95.142 3108 111 25 682 3758 85054647 85057745 0.000000e+00 4867.0
2 TraesCS3B01G117700 chr3B 80.989 263 20 12 2930 3186 85056664 85056902 8.290000e-42 182.0
3 TraesCS3B01G117700 chr3B 80.460 261 24 14 2930 3186 84880668 84880905 1.390000e-39 174.0
4 TraesCS3B01G117700 chr3B 80.460 261 24 14 2681 2918 84880917 84881173 1.390000e-39 174.0
5 TraesCS3B01G117700 chr3B 85.987 157 14 7 2681 2833 85056914 85057066 1.080000e-35 161.0
6 TraesCS3B01G117700 chr3D 94.359 2411 115 12 801 3209 54625365 54627756 0.000000e+00 3679.0
7 TraesCS3B01G117700 chr3D 89.494 514 46 7 1 512 110223224 110222717 0.000000e+00 643.0
8 TraesCS3B01G117700 chr3D 82.410 307 21 13 3466 3756 54808260 54808549 1.740000e-58 237.0
9 TraesCS3B01G117700 chr3D 81.538 260 20 14 2930 3186 54627234 54627468 4.960000e-44 189.0
10 TraesCS3B01G117700 chr3D 90.278 72 6 1 730 801 54625265 54625335 4.000000e-15 93.5
11 TraesCS3B01G117700 chr3A 92.267 2250 107 39 685 2924 65403512 65405704 0.000000e+00 3129.0
12 TraesCS3B01G117700 chr3A 88.942 208 13 7 3556 3756 65432651 65432855 8.060000e-62 248.0
13 TraesCS3B01G117700 chr3A 82.464 211 30 7 3118 3324 65405629 65405836 1.070000e-40 178.0
14 TraesCS3B01G117700 chr1D 87.812 960 90 11 1350 2303 396888326 396889264 0.000000e+00 1099.0
15 TraesCS3B01G117700 chr1D 90.619 533 47 3 1710 2241 396877619 396878149 0.000000e+00 704.0
16 TraesCS3B01G117700 chr1D 88.825 519 49 8 1 517 437505756 437506267 2.460000e-176 628.0
17 TraesCS3B01G117700 chr1D 88.439 519 50 9 1 517 100910639 100911149 5.330000e-173 617.0
18 TraesCS3B01G117700 chr1D 88.395 517 54 6 1 514 384778775 384778262 5.330000e-173 617.0
19 TraesCS3B01G117700 chr1D 88.511 235 26 1 1191 1425 391159466 391159233 2.210000e-72 283.0
20 TraesCS3B01G117700 chr1D 85.652 230 29 3 1472 1699 396749824 396750051 4.850000e-59 239.0
21 TraesCS3B01G117700 chr1D 87.013 154 20 0 1272 1425 391159232 391159079 1.390000e-39 174.0
22 TraesCS3B01G117700 chr1A 89.681 659 52 11 2277 2924 494320990 494321643 0.000000e+00 826.0
23 TraesCS3B01G117700 chr1A 88.780 410 36 4 1841 2250 494320590 494320989 9.380000e-136 494.0
24 TraesCS3B01G117700 chr1A 84.521 491 59 10 1077 1566 494173801 494174275 1.580000e-128 470.0
25 TraesCS3B01G117700 chr1A 86.257 342 25 8 1967 2303 494174272 494174596 5.970000e-93 351.0
26 TraesCS3B01G117700 chr1A 88.618 246 18 4 1493 1728 494320301 494320546 1.320000e-74 291.0
27 TraesCS3B01G117700 chr1A 80.000 310 35 16 2930 3231 494321395 494321685 1.770000e-48 204.0
28 TraesCS3B01G117700 chr1B 89.683 630 59 3 1675 2303 532019067 532019691 0.000000e+00 798.0
29 TraesCS3B01G117700 chr1B 86.546 721 89 2 987 1699 531858199 531858919 0.000000e+00 787.0
30 TraesCS3B01G117700 chr1B 89.961 508 42 4 1741 2241 531858932 531859437 0.000000e+00 647.0
31 TraesCS3B01G117700 chr1B 81.591 440 54 9 1231 1647 296758450 296758015 4.650000e-89 339.0
32 TraesCS3B01G117700 chr6D 89.210 519 50 6 1 517 68691790 68691276 0.000000e+00 643.0
33 TraesCS3B01G117700 chr6D 88.845 511 51 6 1 508 139385335 139385842 1.150000e-174 623.0
34 TraesCS3B01G117700 chr2D 88.846 520 54 4 1 517 108631801 108632319 1.470000e-178 636.0
35 TraesCS3B01G117700 chr2D 87.861 519 52 10 1 517 401444536 401445045 1.930000e-167 599.0
36 TraesCS3B01G117700 chr4D 88.825 519 49 8 1 517 14853398 14853909 2.460000e-176 628.0


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 TraesCS3B01G117700 chr3B 84877988 84881745 3757 False 2429.333333 6940 86.973333 1 3758 3 chr3B.!!$F1 3757
1 TraesCS3B01G117700 chr3B 85054647 85057745 3098 False 1736.666667 4867 87.372667 682 3758 3 chr3B.!!$F2 3076
2 TraesCS3B01G117700 chr3D 54625265 54627756 2491 False 1320.500000 3679 88.725000 730 3209 3 chr3D.!!$F2 2479
3 TraesCS3B01G117700 chr3D 110222717 110223224 507 True 643.000000 643 89.494000 1 512 1 chr3D.!!$R1 511
4 TraesCS3B01G117700 chr3A 65403512 65405836 2324 False 1653.500000 3129 87.365500 685 3324 2 chr3A.!!$F2 2639
5 TraesCS3B01G117700 chr1D 396888326 396889264 938 False 1099.000000 1099 87.812000 1350 2303 1 chr1D.!!$F4 953
6 TraesCS3B01G117700 chr1D 396877619 396878149 530 False 704.000000 704 90.619000 1710 2241 1 chr1D.!!$F3 531
7 TraesCS3B01G117700 chr1D 437505756 437506267 511 False 628.000000 628 88.825000 1 517 1 chr1D.!!$F5 516
8 TraesCS3B01G117700 chr1D 100910639 100911149 510 False 617.000000 617 88.439000 1 517 1 chr1D.!!$F1 516
9 TraesCS3B01G117700 chr1D 384778262 384778775 513 True 617.000000 617 88.395000 1 514 1 chr1D.!!$R1 513
10 TraesCS3B01G117700 chr1A 494320301 494321685 1384 False 453.750000 826 86.769750 1493 3231 4 chr1A.!!$F2 1738
11 TraesCS3B01G117700 chr1A 494173801 494174596 795 False 410.500000 470 85.389000 1077 2303 2 chr1A.!!$F1 1226
12 TraesCS3B01G117700 chr1B 532019067 532019691 624 False 798.000000 798 89.683000 1675 2303 1 chr1B.!!$F1 628
13 TraesCS3B01G117700 chr1B 531858199 531859437 1238 False 717.000000 787 88.253500 987 2241 2 chr1B.!!$F2 1254
14 TraesCS3B01G117700 chr6D 68691276 68691790 514 True 643.000000 643 89.210000 1 517 1 chr6D.!!$R1 516
15 TraesCS3B01G117700 chr6D 139385335 139385842 507 False 623.000000 623 88.845000 1 508 1 chr6D.!!$F1 507
16 TraesCS3B01G117700 chr2D 108631801 108632319 518 False 636.000000 636 88.846000 1 517 1 chr2D.!!$F1 516
17 TraesCS3B01G117700 chr2D 401444536 401445045 509 False 599.000000 599 87.861000 1 517 1 chr2D.!!$F2 516
18 TraesCS3B01G117700 chr4D 14853398 14853909 511 False 628.000000 628 88.825000 1 517 1 chr4D.!!$F1 516

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
885 933 0.036010 AGGAGCCCATTGTCGAACAG 60.036 55.0 0.0 0.0 0.00 3.16 F
912 960 0.261991 AACCATCTCGCTCCCCTCTA 59.738 55.0 0.0 0.0 0.00 2.43 F
1013 1066 0.824109 GATGAGATGGTGGTCGTCCA 59.176 55.0 0.0 0.0 42.05 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1871 0.333993 ACCTCCATTCCAAGCTGCAT 59.666 50.000 1.02 0.0 0.0 3.96 R
2730 2869 1.045407 AGTCCTTGCACGAACAGGTA 58.955 50.000 1.39 0.0 0.0 3.08 R
2836 2975 4.024641 TGCATCGCTGATGTATCATGAAAC 60.025 41.667 16.26 0.0 41.6 2.78 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
61 62 5.532406 ACGAGGATTATGCATATTTGTTGCT 59.468 36.000 7.36 1.57 40.77 3.91
71 72 4.673580 GCATATTTGTTGCTGAGTGGTCTG 60.674 45.833 0.00 0.00 37.14 3.51
83 84 3.103911 GGTCTGGAACACGACGCG 61.104 66.667 3.53 3.53 37.36 6.01
159 160 1.299316 CCAGCGGTTGCAACAACAG 60.299 57.895 29.55 17.10 46.23 3.16
166 167 0.913876 GTTGCAACAACAGTTCGTGC 59.086 50.000 24.52 9.85 0.00 5.34
167 168 0.179150 TTGCAACAACAGTTCGTGCC 60.179 50.000 13.03 0.13 0.00 5.01
209 210 2.296471 CAGTACCGTGACTGGAGTTTCT 59.704 50.000 6.13 0.00 42.68 2.52
237 239 1.331214 CCCATGTTGTGTCCTTTGCT 58.669 50.000 0.00 0.00 0.00 3.91
245 247 3.719268 TGTGTCCTTTGCTGGTCATAT 57.281 42.857 0.00 0.00 0.00 1.78
260 262 2.620115 GTCATATCTGGCAATGGTGGTG 59.380 50.000 0.00 0.00 0.00 4.17
267 269 0.039527 GGCAATGGTGGTGTTTCGAC 60.040 55.000 0.00 0.00 0.00 4.20
276 278 3.054878 GTGGTGTTTCGACATCGTTACT 58.945 45.455 0.54 0.00 40.80 2.24
298 300 3.965379 TGTTGAAGGCATTGCATGATT 57.035 38.095 11.39 0.00 0.00 2.57
302 304 4.274602 TGAAGGCATTGCATGATTTTGT 57.725 36.364 11.39 0.00 0.00 2.83
318 320 8.512956 CATGATTTTGTTCAGTTCTTCTCTCAT 58.487 33.333 0.00 0.00 0.00 2.90
340 342 9.092876 CTCATAGTGAAAACTCAGGATTTAGTC 57.907 37.037 0.00 0.00 0.00 2.59
357 359 2.693069 AGTCTTTGACTGAATCTGGCG 58.307 47.619 0.00 0.00 41.76 5.69
372 374 0.529773 TGGCGACAGTGACACTTGTC 60.530 55.000 19.74 19.74 39.72 3.18
386 388 4.810790 ACACTTGTCTGTCCTTATCTTCG 58.189 43.478 0.00 0.00 0.00 3.79
394 396 8.459911 TGTCTGTCCTTATCTTCGTGAATATA 57.540 34.615 0.00 0.00 0.00 0.86
415 417 9.700831 AATATATTGCTTTTGGAGAACCTACTT 57.299 29.630 0.00 0.00 37.04 2.24
423 425 0.324943 GAGAACCTACTTGCAGCCCA 59.675 55.000 0.00 0.00 0.00 5.36
457 460 1.003851 GTGCATGATGCCATTGTTGC 58.996 50.000 15.70 1.79 44.23 4.17
462 465 3.429822 GCATGATGCCATTGTTGCTTACT 60.430 43.478 6.04 0.00 37.42 2.24
479 482 2.015736 ACTGCGTGCCTTAGATCTTG 57.984 50.000 0.00 0.00 0.00 3.02
514 521 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
516 523 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
517 524 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
518 525 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
519 526 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
520 527 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
521 528 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
522 529 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
523 530 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
524 531 8.700051 TCTTCTTCTTCTTCTTCTTCTTCTTCA 58.300 33.333 0.00 0.00 0.00 3.02
525 532 9.492973 CTTCTTCTTCTTCTTCTTCTTCTTCAT 57.507 33.333 0.00 0.00 0.00 2.57
526 533 9.487790 TTCTTCTTCTTCTTCTTCTTCTTCATC 57.512 33.333 0.00 0.00 0.00 2.92
527 534 8.646004 TCTTCTTCTTCTTCTTCTTCTTCATCA 58.354 33.333 0.00 0.00 0.00 3.07
528 535 9.439500 CTTCTTCTTCTTCTTCTTCTTCATCAT 57.561 33.333 0.00 0.00 0.00 2.45
529 536 9.434420 TTCTTCTTCTTCTTCTTCTTCATCATC 57.566 33.333 0.00 0.00 0.00 2.92
530 537 8.591940 TCTTCTTCTTCTTCTTCTTCATCATCA 58.408 33.333 0.00 0.00 0.00 3.07
531 538 9.386010 CTTCTTCTTCTTCTTCTTCATCATCAT 57.614 33.333 0.00 0.00 0.00 2.45
532 539 8.945481 TCTTCTTCTTCTTCTTCATCATCATC 57.055 34.615 0.00 0.00 0.00 2.92
533 540 8.537858 TCTTCTTCTTCTTCTTCATCATCATCA 58.462 33.333 0.00 0.00 0.00 3.07
534 541 9.332502 CTTCTTCTTCTTCTTCATCATCATCAT 57.667 33.333 0.00 0.00 0.00 2.45
535 542 8.890124 TCTTCTTCTTCTTCATCATCATCATC 57.110 34.615 0.00 0.00 0.00 2.92
536 543 8.483758 TCTTCTTCTTCTTCATCATCATCATCA 58.516 33.333 0.00 0.00 0.00 3.07
537 544 9.278978 CTTCTTCTTCTTCATCATCATCATCAT 57.721 33.333 0.00 0.00 0.00 2.45
538 545 8.834749 TCTTCTTCTTCATCATCATCATCATC 57.165 34.615 0.00 0.00 0.00 2.92
539 546 8.429641 TCTTCTTCTTCATCATCATCATCATCA 58.570 33.333 0.00 0.00 0.00 3.07
540 547 9.225436 CTTCTTCTTCATCATCATCATCATCAT 57.775 33.333 0.00 0.00 0.00 2.45
541 548 8.779354 TCTTCTTCATCATCATCATCATCATC 57.221 34.615 0.00 0.00 0.00 2.92
542 549 8.375506 TCTTCTTCATCATCATCATCATCATCA 58.624 33.333 0.00 0.00 0.00 3.07
543 550 9.171877 CTTCTTCATCATCATCATCATCATCAT 57.828 33.333 0.00 0.00 0.00 2.45
544 551 8.723942 TCTTCATCATCATCATCATCATCATC 57.276 34.615 0.00 0.00 0.00 2.92
545 552 8.543774 TCTTCATCATCATCATCATCATCATCT 58.456 33.333 0.00 0.00 0.00 2.90
546 553 9.171877 CTTCATCATCATCATCATCATCATCTT 57.828 33.333 0.00 0.00 0.00 2.40
547 554 8.723942 TCATCATCATCATCATCATCATCTTC 57.276 34.615 0.00 0.00 0.00 2.87
548 555 8.543774 TCATCATCATCATCATCATCATCTTCT 58.456 33.333 0.00 0.00 0.00 2.85
549 556 9.171877 CATCATCATCATCATCATCATCTTCTT 57.828 33.333 0.00 0.00 0.00 2.52
550 557 8.779354 TCATCATCATCATCATCATCTTCTTC 57.221 34.615 0.00 0.00 0.00 2.87
551 558 8.598041 TCATCATCATCATCATCATCTTCTTCT 58.402 33.333 0.00 0.00 0.00 2.85
552 559 9.225436 CATCATCATCATCATCATCTTCTTCTT 57.775 33.333 0.00 0.00 0.00 2.52
553 560 8.834749 TCATCATCATCATCATCTTCTTCTTC 57.165 34.615 0.00 0.00 0.00 2.87
554 561 8.652290 TCATCATCATCATCATCTTCTTCTTCT 58.348 33.333 0.00 0.00 0.00 2.85
555 562 9.278978 CATCATCATCATCATCTTCTTCTTCTT 57.721 33.333 0.00 0.00 0.00 2.52
556 563 8.664211 TCATCATCATCATCTTCTTCTTCTTG 57.336 34.615 0.00 0.00 0.00 3.02
557 564 7.715686 TCATCATCATCATCTTCTTCTTCTTGG 59.284 37.037 0.00 0.00 0.00 3.61
558 565 6.955364 TCATCATCATCTTCTTCTTCTTGGT 58.045 36.000 0.00 0.00 0.00 3.67
559 566 7.400439 TCATCATCATCTTCTTCTTCTTGGTT 58.600 34.615 0.00 0.00 0.00 3.67
560 567 7.336176 TCATCATCATCTTCTTCTTCTTGGTTG 59.664 37.037 0.00 0.00 0.00 3.77
561 568 6.537355 TCATCATCTTCTTCTTCTTGGTTGT 58.463 36.000 0.00 0.00 0.00 3.32
562 569 6.429078 TCATCATCTTCTTCTTCTTGGTTGTG 59.571 38.462 0.00 0.00 0.00 3.33
563 570 5.684704 TCATCTTCTTCTTCTTGGTTGTGT 58.315 37.500 0.00 0.00 0.00 3.72
564 571 5.528690 TCATCTTCTTCTTCTTGGTTGTGTG 59.471 40.000 0.00 0.00 0.00 3.82
565 572 3.627577 TCTTCTTCTTCTTGGTTGTGTGC 59.372 43.478 0.00 0.00 0.00 4.57
566 573 2.997980 TCTTCTTCTTGGTTGTGTGCA 58.002 42.857 0.00 0.00 0.00 4.57
567 574 3.554934 TCTTCTTCTTGGTTGTGTGCAT 58.445 40.909 0.00 0.00 0.00 3.96
568 575 3.565482 TCTTCTTCTTGGTTGTGTGCATC 59.435 43.478 0.00 0.00 0.00 3.91
569 576 2.229792 TCTTCTTGGTTGTGTGCATCC 58.770 47.619 0.00 0.00 35.54 3.51
570 577 2.158623 TCTTCTTGGTTGTGTGCATCCT 60.159 45.455 0.00 0.00 35.89 3.24
571 578 2.363306 TCTTGGTTGTGTGCATCCTT 57.637 45.000 0.00 0.00 35.89 3.36
572 579 3.500448 TCTTGGTTGTGTGCATCCTTA 57.500 42.857 0.00 0.00 35.89 2.69
573 580 3.826524 TCTTGGTTGTGTGCATCCTTAA 58.173 40.909 0.00 0.00 35.89 1.85
574 581 4.406456 TCTTGGTTGTGTGCATCCTTAAT 58.594 39.130 0.00 0.00 35.89 1.40
575 582 4.218200 TCTTGGTTGTGTGCATCCTTAATG 59.782 41.667 0.00 0.00 35.89 1.90
586 593 3.893720 CATCCTTAATGCCTCGAATTGC 58.106 45.455 0.00 0.00 0.00 3.56
587 594 3.281727 TCCTTAATGCCTCGAATTGCT 57.718 42.857 3.35 0.00 0.00 3.91
588 595 3.206150 TCCTTAATGCCTCGAATTGCTC 58.794 45.455 3.35 0.00 0.00 4.26
603 610 1.154150 GCTCGTGGCATTGAGTTGC 60.154 57.895 17.48 4.68 42.01 4.17
604 611 1.580845 GCTCGTGGCATTGAGTTGCT 61.581 55.000 17.48 0.00 42.38 3.91
605 612 0.167470 CTCGTGGCATTGAGTTGCTG 59.833 55.000 10.54 0.00 42.38 4.41
606 613 1.443194 CGTGGCATTGAGTTGCTGC 60.443 57.895 0.00 0.00 42.38 5.25
607 614 1.859427 CGTGGCATTGAGTTGCTGCT 61.859 55.000 0.00 0.00 42.38 4.24
608 615 0.388134 GTGGCATTGAGTTGCTGCTG 60.388 55.000 0.00 0.00 42.38 4.41
609 616 0.537828 TGGCATTGAGTTGCTGCTGA 60.538 50.000 0.00 0.00 42.38 4.26
610 617 0.170561 GGCATTGAGTTGCTGCTGAG 59.829 55.000 0.00 0.00 42.38 3.35
611 618 0.170561 GCATTGAGTTGCTGCTGAGG 59.829 55.000 0.00 0.00 39.57 3.86
612 619 0.170561 CATTGAGTTGCTGCTGAGGC 59.829 55.000 0.00 0.00 39.26 4.70
613 620 0.964358 ATTGAGTTGCTGCTGAGGCC 60.964 55.000 0.00 0.00 37.74 5.19
614 621 3.123620 GAGTTGCTGCTGAGGCCG 61.124 66.667 0.00 0.00 37.74 6.13
615 622 4.711949 AGTTGCTGCTGAGGCCGG 62.712 66.667 0.00 0.00 37.74 6.13
620 627 3.390521 CTGCTGAGGCCGGGTGTA 61.391 66.667 2.18 0.00 37.74 2.90
621 628 3.665675 CTGCTGAGGCCGGGTGTAC 62.666 68.421 2.18 0.00 37.74 2.90
622 629 3.391382 GCTGAGGCCGGGTGTACT 61.391 66.667 2.18 0.00 0.00 2.73
623 630 2.955881 GCTGAGGCCGGGTGTACTT 61.956 63.158 2.18 0.00 0.00 2.24
624 631 1.079127 CTGAGGCCGGGTGTACTTG 60.079 63.158 2.18 0.00 0.00 3.16
625 632 1.534476 TGAGGCCGGGTGTACTTGA 60.534 57.895 2.18 0.00 0.00 3.02
626 633 0.907704 TGAGGCCGGGTGTACTTGAT 60.908 55.000 2.18 0.00 0.00 2.57
627 634 1.117150 GAGGCCGGGTGTACTTGATA 58.883 55.000 2.18 0.00 0.00 2.15
628 635 1.692519 GAGGCCGGGTGTACTTGATAT 59.307 52.381 2.18 0.00 0.00 1.63
629 636 1.692519 AGGCCGGGTGTACTTGATATC 59.307 52.381 2.18 0.00 0.00 1.63
630 637 1.414919 GGCCGGGTGTACTTGATATCA 59.585 52.381 2.18 0.00 0.00 2.15
631 638 2.038557 GGCCGGGTGTACTTGATATCAT 59.961 50.000 6.17 0.00 0.00 2.45
632 639 3.326747 GCCGGGTGTACTTGATATCATC 58.673 50.000 6.17 0.00 0.00 2.92
633 640 3.006967 GCCGGGTGTACTTGATATCATCT 59.993 47.826 6.17 0.00 0.00 2.90
634 641 4.503296 GCCGGGTGTACTTGATATCATCTT 60.503 45.833 6.17 0.00 0.00 2.40
635 642 5.230942 CCGGGTGTACTTGATATCATCTTC 58.769 45.833 6.17 0.00 0.00 2.87
636 643 5.221441 CCGGGTGTACTTGATATCATCTTCA 60.221 44.000 6.17 2.09 0.00 3.02
637 644 6.459066 CGGGTGTACTTGATATCATCTTCAT 58.541 40.000 6.17 0.00 0.00 2.57
638 645 7.309805 CCGGGTGTACTTGATATCATCTTCATA 60.310 40.741 6.17 0.00 0.00 2.15
639 646 8.088365 CGGGTGTACTTGATATCATCTTCATAA 58.912 37.037 6.17 0.00 0.00 1.90
640 647 9.950496 GGGTGTACTTGATATCATCTTCATAAT 57.050 33.333 6.17 0.00 0.00 1.28
807 853 2.125225 GGTTCACCCTCCCCCTCT 59.875 66.667 0.00 0.00 0.00 3.69
816 862 4.689549 TCCCCCTCTTCGCGGTCA 62.690 66.667 6.13 0.00 0.00 4.02
856 904 0.677098 CCTCGTCTCCGTCCTCAAGA 60.677 60.000 0.00 0.00 35.01 3.02
857 905 1.384525 CTCGTCTCCGTCCTCAAGAT 58.615 55.000 0.00 0.00 35.01 2.40
863 911 2.427245 CCGTCCTCAAGATCCGCCT 61.427 63.158 0.00 0.00 0.00 5.52
864 912 1.517832 CGTCCTCAAGATCCGCCTT 59.482 57.895 0.00 0.00 0.00 4.35
872 920 1.977293 AAGATCCGCCTTCAGGAGCC 61.977 60.000 0.00 0.00 44.67 4.70
876 924 2.273449 CGCCTTCAGGAGCCCATT 59.727 61.111 0.00 0.00 37.39 3.16
878 926 1.000396 GCCTTCAGGAGCCCATTGT 60.000 57.895 0.00 0.00 37.39 2.71
883 931 0.036388 TCAGGAGCCCATTGTCGAAC 60.036 55.000 0.00 0.00 0.00 3.95
885 933 0.036010 AGGAGCCCATTGTCGAACAG 60.036 55.000 0.00 0.00 0.00 3.16
902 950 1.081892 CAGCAGGTCAAACCATCTCG 58.918 55.000 0.00 0.00 41.95 4.04
909 957 0.909610 TCAAACCATCTCGCTCCCCT 60.910 55.000 0.00 0.00 0.00 4.79
912 960 0.261991 AACCATCTCGCTCCCCTCTA 59.738 55.000 0.00 0.00 0.00 2.43
914 962 0.894141 CCATCTCGCTCCCCTCTATG 59.106 60.000 0.00 0.00 0.00 2.23
915 963 1.626686 CATCTCGCTCCCCTCTATGT 58.373 55.000 0.00 0.00 0.00 2.29
916 964 2.555448 CCATCTCGCTCCCCTCTATGTA 60.555 54.545 0.00 0.00 0.00 2.29
917 965 2.273538 TCTCGCTCCCCTCTATGTAC 57.726 55.000 0.00 0.00 0.00 2.90
919 967 1.883275 CTCGCTCCCCTCTATGTACTG 59.117 57.143 0.00 0.00 0.00 2.74
966 1019 4.697352 GTGACTGTGAGTGAGCCATTTTAT 59.303 41.667 0.00 0.00 0.00 1.40
967 1020 5.182001 GTGACTGTGAGTGAGCCATTTTATT 59.818 40.000 0.00 0.00 0.00 1.40
968 1021 6.371548 GTGACTGTGAGTGAGCCATTTTATTA 59.628 38.462 0.00 0.00 0.00 0.98
970 1023 6.711277 ACTGTGAGTGAGCCATTTTATTAGA 58.289 36.000 0.00 0.00 0.00 2.10
971 1024 6.820656 ACTGTGAGTGAGCCATTTTATTAGAG 59.179 38.462 0.00 0.00 0.00 2.43
972 1025 6.115446 TGTGAGTGAGCCATTTTATTAGAGG 58.885 40.000 0.00 0.00 0.00 3.69
973 1026 6.070251 TGTGAGTGAGCCATTTTATTAGAGGA 60.070 38.462 0.00 0.00 0.00 3.71
980 1033 8.303876 TGAGCCATTTTATTAGAGGAAAAACAC 58.696 33.333 0.00 0.00 0.00 3.32
1013 1066 0.824109 GATGAGATGGTGGTCGTCCA 59.176 55.000 0.00 0.00 42.05 4.02
1243 1304 2.876858 ACACCCTCCCCTCCCTCT 60.877 66.667 0.00 0.00 0.00 3.69
2362 2499 4.018960 AGAAGACACCTGGATGTAGCAATT 60.019 41.667 0.00 0.00 31.24 2.32
2730 2869 5.163457 ACGTTTCCATTTGTTCAAAGATGGT 60.163 36.000 13.89 1.50 39.95 3.55
2872 3011 1.086067 CGATGCATGAGTTGAGGCGT 61.086 55.000 2.46 0.00 0.00 5.68
2891 3033 4.626172 GGCGTTAAAGTTGGTGAACAAAAA 59.374 37.500 0.00 0.00 41.58 1.94
2892 3034 5.444877 GGCGTTAAAGTTGGTGAACAAAAAC 60.445 40.000 0.00 0.00 41.58 2.43
2987 3129 8.321650 CATTTGTATAAAAATGGCACCTGTTT 57.678 30.769 17.49 0.00 41.71 2.83
3240 3392 9.636879 AATAGATATTCATGTTCGTCTCTGATG 57.363 33.333 0.00 0.00 0.00 3.07
3272 3424 7.941053 ATATTACAGGGGTATAACCTTGACA 57.059 36.000 24.72 11.02 38.64 3.58
3503 3658 2.323959 CTCAGTCAGAGTTCAAGTCGC 58.676 52.381 0.00 0.00 39.62 5.19
3514 3669 4.584394 AGTTCAAGTCGCTAAAACAAACG 58.416 39.130 0.00 0.00 0.00 3.60
3532 3687 1.137282 ACGGGCCGTTTCATTTGTTTT 59.863 42.857 28.83 0.00 36.35 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 0.387929 GTCGTGTTCCAGACCACTCA 59.612 55.000 0.00 0.0 0.00 3.41
83 84 1.355210 CACAGACAAACGCCCACAC 59.645 57.895 0.00 0.0 0.00 3.82
159 160 2.051345 CCAAACGCAGGCACGAAC 60.051 61.111 6.95 0.0 36.70 3.95
166 167 1.599518 TAGCACCACCAAACGCAGG 60.600 57.895 0.00 0.0 0.00 4.85
167 168 0.884704 AGTAGCACCACCAAACGCAG 60.885 55.000 0.00 0.0 0.00 5.18
196 197 1.801242 TCACCCAGAAACTCCAGTCA 58.199 50.000 0.00 0.0 0.00 3.41
224 226 2.363306 ATGACCAGCAAAGGACACAA 57.637 45.000 0.00 0.0 36.22 3.33
237 239 2.423231 CCACCATTGCCAGATATGACCA 60.423 50.000 0.00 0.0 0.00 4.02
245 247 1.327303 GAAACACCACCATTGCCAGA 58.673 50.000 0.00 0.0 0.00 3.86
260 262 5.730269 TCAACAAAGTAACGATGTCGAAAC 58.270 37.500 9.67 6.6 43.02 2.78
267 269 4.481930 TGCCTTCAACAAAGTAACGATG 57.518 40.909 0.00 0.0 32.69 3.84
276 278 3.747854 TCATGCAATGCCTTCAACAAA 57.252 38.095 1.53 0.0 46.21 2.83
298 300 7.726216 TCACTATGAGAGAAGAACTGAACAAA 58.274 34.615 0.00 0.0 0.00 2.83
302 304 8.424918 AGTTTTCACTATGAGAGAAGAACTGAA 58.575 33.333 10.35 0.0 31.95 3.02
318 320 9.273016 CAAAGACTAAATCCTGAGTTTTCACTA 57.727 33.333 0.00 0.0 31.22 2.74
340 342 2.414481 CTGTCGCCAGATTCAGTCAAAG 59.586 50.000 0.00 0.0 41.50 2.77
372 374 8.651588 GCAATATATTCACGAAGATAAGGACAG 58.348 37.037 0.00 0.0 29.62 3.51
386 388 8.000780 AGGTTCTCCAAAAGCAATATATTCAC 57.999 34.615 0.00 0.0 35.89 3.18
394 396 4.021981 GCAAGTAGGTTCTCCAAAAGCAAT 60.022 41.667 0.00 0.0 35.89 3.56
415 417 1.794151 CGTGACAACAATGGGCTGCA 61.794 55.000 0.50 0.0 0.00 4.41
423 425 2.248280 TGCACTACCGTGACAACAAT 57.752 45.000 0.00 0.0 43.97 2.71
442 445 3.429822 GCAGTAAGCAACAATGGCATCAT 60.430 43.478 0.00 0.0 44.79 2.45
447 450 0.240945 ACGCAGTAAGCAACAATGGC 59.759 50.000 0.00 0.0 46.13 4.40
448 451 1.967762 CACGCAGTAAGCAACAATGG 58.032 50.000 0.00 0.0 41.61 3.16
457 460 3.444703 AGATCTAAGGCACGCAGTAAG 57.555 47.619 0.00 0.0 41.61 2.34
462 465 0.613260 ACCAAGATCTAAGGCACGCA 59.387 50.000 12.76 0.0 0.00 5.24
493 500 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.0 0.00 2.85
496 503 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.0 0.00 2.85
499 506 8.885494 TGAAGAAGAAGAAGAAGAAGAAGAAG 57.115 34.615 0.00 0.0 0.00 2.85
503 510 9.434420 GATGATGAAGAAGAAGAAGAAGAAGAA 57.566 33.333 0.00 0.0 0.00 2.52
505 512 8.774890 TGATGATGAAGAAGAAGAAGAAGAAG 57.225 34.615 0.00 0.0 0.00 2.85
508 515 8.719560 TGATGATGATGAAGAAGAAGAAGAAG 57.280 34.615 0.00 0.0 0.00 2.85
514 521 8.608844 TGATGATGATGATGATGAAGAAGAAG 57.391 34.615 0.00 0.0 0.00 2.85
516 523 8.375506 TGATGATGATGATGATGATGAAGAAGA 58.624 33.333 0.00 0.0 0.00 2.87
517 524 8.553459 TGATGATGATGATGATGATGAAGAAG 57.447 34.615 0.00 0.0 0.00 2.85
518 525 9.167311 GATGATGATGATGATGATGATGAAGAA 57.833 33.333 0.00 0.0 0.00 2.52
519 526 8.543774 AGATGATGATGATGATGATGATGAAGA 58.456 33.333 0.00 0.0 0.00 2.87
520 527 8.729805 AGATGATGATGATGATGATGATGAAG 57.270 34.615 0.00 0.0 0.00 3.02
521 528 9.167311 GAAGATGATGATGATGATGATGATGAA 57.833 33.333 0.00 0.0 0.00 2.57
522 529 8.543774 AGAAGATGATGATGATGATGATGATGA 58.456 33.333 0.00 0.0 0.00 2.92
523 530 8.729805 AGAAGATGATGATGATGATGATGATG 57.270 34.615 0.00 0.0 0.00 3.07
524 531 9.389755 GAAGAAGATGATGATGATGATGATGAT 57.610 33.333 0.00 0.0 0.00 2.45
525 532 8.598041 AGAAGAAGATGATGATGATGATGATGA 58.402 33.333 0.00 0.0 0.00 2.92
526 533 8.785329 AGAAGAAGATGATGATGATGATGATG 57.215 34.615 0.00 0.0 0.00 3.07
527 534 9.443323 GAAGAAGAAGATGATGATGATGATGAT 57.557 33.333 0.00 0.0 0.00 2.45
528 535 8.652290 AGAAGAAGAAGATGATGATGATGATGA 58.348 33.333 0.00 0.0 0.00 2.92
529 536 8.840833 AGAAGAAGAAGATGATGATGATGATG 57.159 34.615 0.00 0.0 0.00 3.07
530 537 9.278978 CAAGAAGAAGAAGATGATGATGATGAT 57.721 33.333 0.00 0.0 0.00 2.45
531 538 7.715686 CCAAGAAGAAGAAGATGATGATGATGA 59.284 37.037 0.00 0.0 0.00 2.92
532 539 7.499563 ACCAAGAAGAAGAAGATGATGATGATG 59.500 37.037 0.00 0.0 0.00 3.07
533 540 7.575505 ACCAAGAAGAAGAAGATGATGATGAT 58.424 34.615 0.00 0.0 0.00 2.45
534 541 6.955364 ACCAAGAAGAAGAAGATGATGATGA 58.045 36.000 0.00 0.0 0.00 2.92
535 542 7.120873 ACAACCAAGAAGAAGAAGATGATGATG 59.879 37.037 0.00 0.0 0.00 3.07
536 543 7.120873 CACAACCAAGAAGAAGAAGATGATGAT 59.879 37.037 0.00 0.0 0.00 2.45
537 544 6.429078 CACAACCAAGAAGAAGAAGATGATGA 59.571 38.462 0.00 0.0 0.00 2.92
538 545 6.206243 ACACAACCAAGAAGAAGAAGATGATG 59.794 38.462 0.00 0.0 0.00 3.07
539 546 6.206243 CACACAACCAAGAAGAAGAAGATGAT 59.794 38.462 0.00 0.0 0.00 2.45
540 547 5.528690 CACACAACCAAGAAGAAGAAGATGA 59.471 40.000 0.00 0.0 0.00 2.92
541 548 5.755813 CACACAACCAAGAAGAAGAAGATG 58.244 41.667 0.00 0.0 0.00 2.90
542 549 4.276926 GCACACAACCAAGAAGAAGAAGAT 59.723 41.667 0.00 0.0 0.00 2.40
543 550 3.627577 GCACACAACCAAGAAGAAGAAGA 59.372 43.478 0.00 0.0 0.00 2.87
544 551 3.378112 TGCACACAACCAAGAAGAAGAAG 59.622 43.478 0.00 0.0 0.00 2.85
545 552 3.351740 TGCACACAACCAAGAAGAAGAA 58.648 40.909 0.00 0.0 0.00 2.52
546 553 2.997980 TGCACACAACCAAGAAGAAGA 58.002 42.857 0.00 0.0 0.00 2.87
547 554 3.304928 GGATGCACACAACCAAGAAGAAG 60.305 47.826 0.00 0.0 38.58 2.85
548 555 2.622942 GGATGCACACAACCAAGAAGAA 59.377 45.455 0.00 0.0 38.58 2.52
549 556 2.158623 AGGATGCACACAACCAAGAAGA 60.159 45.455 0.00 0.0 41.12 2.87
550 557 2.233271 AGGATGCACACAACCAAGAAG 58.767 47.619 0.00 0.0 41.12 2.85
551 558 2.363306 AGGATGCACACAACCAAGAA 57.637 45.000 0.00 0.0 41.12 2.52
552 559 2.363306 AAGGATGCACACAACCAAGA 57.637 45.000 0.00 0.0 41.12 3.02
553 560 4.487948 CATTAAGGATGCACACAACCAAG 58.512 43.478 0.00 0.0 41.12 3.61
554 561 4.517952 CATTAAGGATGCACACAACCAA 57.482 40.909 0.00 0.0 41.12 3.67
565 572 3.567164 AGCAATTCGAGGCATTAAGGATG 59.433 43.478 8.24 0.0 38.85 3.51
566 573 3.817647 GAGCAATTCGAGGCATTAAGGAT 59.182 43.478 8.24 0.0 0.00 3.24
567 574 3.206150 GAGCAATTCGAGGCATTAAGGA 58.794 45.455 8.24 0.0 0.00 3.36
568 575 3.615849 GAGCAATTCGAGGCATTAAGG 57.384 47.619 8.24 0.0 0.00 2.69
585 592 1.154150 GCAACTCAATGCCACGAGC 60.154 57.895 0.00 0.0 40.49 5.03
592 599 0.170561 CCTCAGCAGCAACTCAATGC 59.829 55.000 0.00 0.0 46.78 3.56
593 600 0.170561 GCCTCAGCAGCAACTCAATG 59.829 55.000 0.00 0.0 39.53 2.82
594 601 0.964358 GGCCTCAGCAGCAACTCAAT 60.964 55.000 0.00 0.0 42.56 2.57
595 602 1.601759 GGCCTCAGCAGCAACTCAA 60.602 57.895 0.00 0.0 42.56 3.02
596 603 2.033141 GGCCTCAGCAGCAACTCA 59.967 61.111 0.00 0.0 42.56 3.41
597 604 3.123620 CGGCCTCAGCAGCAACTC 61.124 66.667 0.00 0.0 42.56 3.01
598 605 4.711949 CCGGCCTCAGCAGCAACT 62.712 66.667 0.00 0.0 42.56 3.16
603 610 3.390521 TACACCCGGCCTCAGCAG 61.391 66.667 0.00 0.0 42.56 4.24
604 611 3.702048 GTACACCCGGCCTCAGCA 61.702 66.667 0.00 0.0 42.56 4.41
605 612 2.955881 AAGTACACCCGGCCTCAGC 61.956 63.158 0.00 0.0 38.76 4.26
606 613 1.079127 CAAGTACACCCGGCCTCAG 60.079 63.158 0.00 0.0 0.00 3.35
607 614 0.907704 ATCAAGTACACCCGGCCTCA 60.908 55.000 0.00 0.0 0.00 3.86
608 615 1.117150 TATCAAGTACACCCGGCCTC 58.883 55.000 0.00 0.0 0.00 4.70
609 616 1.692519 GATATCAAGTACACCCGGCCT 59.307 52.381 0.00 0.0 0.00 5.19
610 617 1.414919 TGATATCAAGTACACCCGGCC 59.585 52.381 1.98 0.0 0.00 6.13
611 618 2.902705 TGATATCAAGTACACCCGGC 57.097 50.000 1.98 0.0 0.00 6.13
612 619 4.873746 AGATGATATCAAGTACACCCGG 57.126 45.455 9.99 0.0 0.00 5.73
613 620 5.842907 TGAAGATGATATCAAGTACACCCG 58.157 41.667 9.99 0.0 0.00 5.28
614 621 9.950496 ATTATGAAGATGATATCAAGTACACCC 57.050 33.333 9.99 0.0 0.00 4.61
662 669 5.509716 AATCCCGTTTCGAAGAACTTTTT 57.490 34.783 0.00 0.0 45.90 1.94
663 670 5.509716 AAATCCCGTTTCGAAGAACTTTT 57.490 34.783 0.00 0.0 45.90 2.27
664 671 5.509716 AAAATCCCGTTTCGAAGAACTTT 57.490 34.783 0.00 0.0 45.90 2.66
665 672 5.509716 AAAAATCCCGTTTCGAAGAACTT 57.490 34.783 0.00 0.0 45.90 2.66
788 804 1.850755 GAGGGGGAGGGTGAACCAA 60.851 63.158 1.16 0.0 43.89 3.67
842 890 1.384989 GCGGATCTTGAGGACGGAGA 61.385 60.000 0.00 0.0 0.00 3.71
844 892 2.423898 GGCGGATCTTGAGGACGGA 61.424 63.158 0.00 0.0 0.00 4.69
863 911 0.690192 TTCGACAATGGGCTCCTGAA 59.310 50.000 0.00 0.0 0.00 3.02
864 912 0.036388 GTTCGACAATGGGCTCCTGA 60.036 55.000 0.00 0.0 0.00 3.86
872 920 0.798776 GACCTGCTGTTCGACAATGG 59.201 55.000 0.00 0.0 0.00 3.16
876 924 1.295792 GTTTGACCTGCTGTTCGACA 58.704 50.000 0.00 0.0 0.00 4.35
878 926 0.179234 TGGTTTGACCTGCTGTTCGA 59.821 50.000 0.00 0.0 39.58 3.71
883 931 1.081892 CGAGATGGTTTGACCTGCTG 58.918 55.000 0.00 0.0 39.58 4.41
885 933 0.674895 AGCGAGATGGTTTGACCTGC 60.675 55.000 0.00 0.0 39.58 4.85
902 950 3.491104 CGAAACAGTACATAGAGGGGAGC 60.491 52.174 0.00 0.0 0.00 4.70
966 1019 3.949113 GTGGTGGTGTGTTTTTCCTCTAA 59.051 43.478 0.00 0.0 0.00 2.10
967 1020 3.201266 AGTGGTGGTGTGTTTTTCCTCTA 59.799 43.478 0.00 0.0 0.00 2.43
968 1021 2.025321 AGTGGTGGTGTGTTTTTCCTCT 60.025 45.455 0.00 0.0 0.00 3.69
970 1023 2.525105 AGTGGTGGTGTGTTTTTCCT 57.475 45.000 0.00 0.0 0.00 3.36
971 1024 2.032426 CGTAGTGGTGGTGTGTTTTTCC 59.968 50.000 0.00 0.0 0.00 3.13
972 1025 2.679336 ACGTAGTGGTGGTGTGTTTTTC 59.321 45.455 0.00 0.0 42.51 2.29
973 1026 2.713877 ACGTAGTGGTGGTGTGTTTTT 58.286 42.857 0.00 0.0 42.51 1.94
1243 1304 2.214181 GAGAGGGCGAGCGACTTGAA 62.214 60.000 0.00 0.0 0.00 2.69
1332 1393 1.080025 GTTCACGAGGAGGAACCCG 60.080 63.158 0.00 0.0 37.92 5.28
1786 1871 0.333993 ACCTCCATTCCAAGCTGCAT 59.666 50.000 1.02 0.0 0.00 3.96
2362 2499 5.395990 GGTGGATAACTCCGTTAATCTCCAA 60.396 44.000 8.39 0.0 45.37 3.53
2730 2869 1.045407 AGTCCTTGCACGAACAGGTA 58.955 50.000 1.39 0.0 0.00 3.08
2836 2975 4.024641 TGCATCGCTGATGTATCATGAAAC 60.025 41.667 16.26 0.0 41.60 2.78
2987 3129 5.190925 AGTTACTACCAATAATCCTGGCACA 59.809 40.000 0.00 0.0 37.48 4.57
3017 3159 8.361592 ACAAGTACCGCTGTTAATACATAATC 57.638 34.615 0.00 0.0 32.86 1.75
3080 3222 6.349243 TGGGAGTATGACGAAAGAGTTTTA 57.651 37.500 0.00 0.0 0.00 1.52
3337 3489 3.535280 TTCCACAAGCCAAAAAGGTTC 57.465 42.857 0.00 0.0 40.61 3.62
3416 3568 5.753921 ACTTAGCATCGGAAATACAGCTAAC 59.246 40.000 0.00 0.0 39.01 2.34
3428 3580 3.244078 ACAGAAACACACTTAGCATCGGA 60.244 43.478 0.00 0.0 0.00 4.55
3430 3582 4.732285 AACAGAAACACACTTAGCATCG 57.268 40.909 0.00 0.0 0.00 3.84
3514 3669 2.556257 ACAAAACAAATGAAACGGCCC 58.444 42.857 0.00 0.0 0.00 5.80
3532 3687 3.483808 TGTCAGTTAGTGCCATCAACA 57.516 42.857 0.00 0.0 0.00 3.33


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

AutoCloner maintained by Alex Coulton.