Multiple sequence alignment - TraesCS4B01G115700

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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 TraesCS4B01G115700 chr4B 100.000 2642 0 0 1 2642 132330568 132333209 0.000000e+00 4879.0
1 TraesCS4B01G115700 chr4D 91.216 1958 74 44 729 2623 93840942 93842864 0.000000e+00 2573.0
2 TraesCS4B01G115700 chr4D 83.096 491 56 10 3 489 93838521 93838988 3.140000e-114 422.0
3 TraesCS4B01G115700 chr4D 96.491 57 2 0 611 667 93838987 93839043 7.790000e-16 95.3
4 TraesCS4B01G115700 chr4A 88.838 1953 93 62 691 2571 487869305 487867406 0.000000e+00 2283.0
5 TraesCS4B01G115700 chr4A 90.370 405 37 1 3 407 487870016 487869614 5.010000e-147 531.0
6 TraesCS4B01G115700 chr4A 89.647 425 19 3 1986 2401 742542810 742542402 3.900000e-143 518.0
7 TraesCS4B01G115700 chr4A 89.151 424 23 6 1987 2401 701625813 701626222 8.440000e-140 507.0
8 TraesCS4B01G115700 chr4A 95.276 127 4 2 488 612 589667294 589667168 1.600000e-47 200.0
9 TraesCS4B01G115700 chr4A 95.588 68 3 0 2558 2625 487867391 487867324 2.780000e-20 110.0
10 TraesCS4B01G115700 chr5D 84.154 650 78 15 998 1642 213129205 213129834 8.090000e-170 606.0
11 TraesCS4B01G115700 chr5D 81.288 652 93 17 998 1642 212627253 212627882 3.930000e-138 501.0
12 TraesCS4B01G115700 chr5B 84.129 649 80 13 998 1642 227120977 227121606 8.090000e-170 606.0
13 TraesCS4B01G115700 chr5B 88.651 467 25 11 1987 2444 696669731 696669284 6.430000e-151 544.0
14 TraesCS4B01G115700 chr5B 79.416 651 107 18 998 1642 226759281 226759910 4.040000e-118 435.0
15 TraesCS4B01G115700 chr5B 94.776 134 4 3 488 619 711837078 711836946 3.450000e-49 206.0
16 TraesCS4B01G115700 chr5B 93.478 138 7 2 488 623 267780957 267780820 1.240000e-48 204.0
17 TraesCS4B01G115700 chr5B 92.254 142 9 2 488 627 555175603 555175744 1.600000e-47 200.0
18 TraesCS4B01G115700 chr5B 75.298 336 66 16 1228 1555 664998552 664998226 7.620000e-31 145.0
19 TraesCS4B01G115700 chr5B 100.000 28 0 0 1667 1694 34425162 34425189 5.000000e-03 52.8
20 TraesCS4B01G115700 chr5A 83.667 649 83 13 998 1642 276980834 276980205 8.140000e-165 590.0
21 TraesCS4B01G115700 chr5A 82.226 557 76 13 998 1550 276111785 276112322 2.400000e-125 459.0
22 TraesCS4B01G115700 chr3B 89.858 424 20 5 1987 2401 805032069 805031660 8.380000e-145 523.0
23 TraesCS4B01G115700 chr2B 92.946 241 12 3 2241 2481 103687640 103687875 1.950000e-91 346.0
24 TraesCS4B01G115700 chr2B 92.632 190 12 2 1987 2175 103687442 103687630 3.350000e-69 272.0
25 TraesCS4B01G115700 chr2B 93.011 186 12 1 1987 2172 752289116 752288932 1.210000e-68 270.0
26 TraesCS4B01G115700 chr7B 86.196 326 20 4 1997 2313 655434004 655433695 1.960000e-86 329.0
27 TraesCS4B01G115700 chr7B 96.324 136 3 2 488 622 226180051 226179917 3.420000e-54 222.0
28 TraesCS4B01G115700 chr6B 90.717 237 14 3 2245 2481 36689198 36689426 2.550000e-80 309.0
29 TraesCS4B01G115700 chr6B 93.989 183 10 1 1987 2169 36689015 36689196 2.590000e-70 276.0
30 TraesCS4B01G115700 chr6B 95.489 133 5 1 488 619 502311354 502311222 7.410000e-51 211.0
31 TraesCS4B01G115700 chr6B 94.161 137 5 3 487 620 641950698 641950834 3.450000e-49 206.0
32 TraesCS4B01G115700 chr1B 94.536 183 9 1 1987 2169 276586864 276587045 5.570000e-72 281.0
33 TraesCS4B01G115700 chr1B 93.478 138 6 3 488 623 372226509 372226373 4.460000e-48 202.0
34 TraesCS4B01G115700 chr1B 90.850 153 9 5 487 634 601258970 601258818 1.600000e-47 200.0
35 TraesCS4B01G115700 chr3D 100.000 28 0 0 1667 1694 12037960 12037933 5.000000e-03 52.8
36 TraesCS4B01G115700 chr2D 100.000 28 0 0 1667 1694 101774923 101774896 5.000000e-03 52.8


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 TraesCS4B01G115700 chr4B 132330568 132333209 2641 False 4879.000000 4879 100.000000 1 2642 1 chr4B.!!$F1 2641
1 TraesCS4B01G115700 chr4D 93838521 93842864 4343 False 1030.100000 2573 90.267667 3 2623 3 chr4D.!!$F1 2620
2 TraesCS4B01G115700 chr4A 487867324 487870016 2692 True 974.666667 2283 91.598667 3 2625 3 chr4A.!!$R3 2622
3 TraesCS4B01G115700 chr5D 213129205 213129834 629 False 606.000000 606 84.154000 998 1642 1 chr5D.!!$F2 644
4 TraesCS4B01G115700 chr5D 212627253 212627882 629 False 501.000000 501 81.288000 998 1642 1 chr5D.!!$F1 644
5 TraesCS4B01G115700 chr5B 227120977 227121606 629 False 606.000000 606 84.129000 998 1642 1 chr5B.!!$F3 644
6 TraesCS4B01G115700 chr5B 226759281 226759910 629 False 435.000000 435 79.416000 998 1642 1 chr5B.!!$F2 644
7 TraesCS4B01G115700 chr5A 276980205 276980834 629 True 590.000000 590 83.667000 998 1642 1 chr5A.!!$R1 644
8 TraesCS4B01G115700 chr5A 276111785 276112322 537 False 459.000000 459 82.226000 998 1550 1 chr5A.!!$F1 552

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
934 2894 0.107752 GCCCCTCTTCTTGCTCTCTG 60.108 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 4572 0.247736 GCTCGTCATGGAGACCTTGT 59.752 55.0 3.41 0.0 44.66 3.16 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
38 39 6.624861 GCCATGAAGTTTATTGAATCCGACAA 60.625 38.462 0.00 0.00 0.00 3.18
99 100 4.571580 TGGTACATTTTTAATACGCCGGAG 59.428 41.667 5.05 3.72 0.00 4.63
173 174 8.335532 TCATGTAAGTTCACAAAATAGAAGGG 57.664 34.615 0.00 0.00 30.84 3.95
182 183 8.749354 GTTCACAAAATAGAAGGGTCCAAATAT 58.251 33.333 0.00 0.00 0.00 1.28
246 247 3.107402 TCATAGAGGCCACAAGAGAGT 57.893 47.619 5.01 0.00 0.00 3.24
273 276 0.751643 CTGGCCTTTATTGGTCGGGG 60.752 60.000 3.32 0.00 34.59 5.73
310 313 7.689812 CGATCTTGTGTCATTATCTTGTTCAAC 59.310 37.037 0.00 0.00 0.00 3.18
311 314 7.202016 TCTTGTGTCATTATCTTGTTCAACC 57.798 36.000 0.00 0.00 0.00 3.77
384 387 6.770746 ATCAAGATGAAAATCCTTGTCCAG 57.229 37.500 0.00 0.00 38.61 3.86
388 391 3.874383 TGAAAATCCTTGTCCAGACCA 57.126 42.857 0.00 0.00 0.00 4.02
399 402 2.202932 CAGACCATCTTCGGCCGG 60.203 66.667 27.83 10.69 0.00 6.13
402 405 3.000819 ACCATCTTCGGCCGGACA 61.001 61.111 27.83 3.81 0.00 4.02
424 427 1.026182 GCAACGATGGCATGAGGACA 61.026 55.000 3.81 0.00 40.35 4.02
431 434 3.496130 CGATGGCATGAGGACAGTTATTC 59.504 47.826 3.81 0.00 38.50 1.75
432 435 4.712476 GATGGCATGAGGACAGTTATTCT 58.288 43.478 3.81 0.00 38.50 2.40
435 438 4.943705 TGGCATGAGGACAGTTATTCTTTC 59.056 41.667 0.00 0.00 0.00 2.62
487 599 9.367444 CGACTTAGTATTAGGTGTTTCTTTCAT 57.633 33.333 0.00 0.00 0.00 2.57
493 605 8.265764 AGTATTAGGTGTTTCTTTCATACTCCC 58.734 37.037 0.00 0.00 0.00 4.30
494 606 6.697641 TTAGGTGTTTCTTTCATACTCCCT 57.302 37.500 0.00 0.00 0.00 4.20
495 607 5.584551 AGGTGTTTCTTTCATACTCCCTT 57.415 39.130 0.00 0.00 0.00 3.95
496 608 5.561679 AGGTGTTTCTTTCATACTCCCTTC 58.438 41.667 0.00 0.00 0.00 3.46
497 609 4.392138 GGTGTTTCTTTCATACTCCCTTCG 59.608 45.833 0.00 0.00 0.00 3.79
498 610 4.995487 GTGTTTCTTTCATACTCCCTTCGT 59.005 41.667 0.00 0.00 0.00 3.85
499 611 5.120363 GTGTTTCTTTCATACTCCCTTCGTC 59.880 44.000 0.00 0.00 0.00 4.20
500 612 4.467198 TTCTTTCATACTCCCTTCGTCC 57.533 45.455 0.00 0.00 0.00 4.79
501 613 2.426024 TCTTTCATACTCCCTTCGTCCG 59.574 50.000 0.00 0.00 0.00 4.79
502 614 2.133281 TTCATACTCCCTTCGTCCGA 57.867 50.000 0.00 0.00 0.00 4.55
503 615 2.133281 TCATACTCCCTTCGTCCGAA 57.867 50.000 1.81 1.81 0.00 4.30
504 616 2.449464 TCATACTCCCTTCGTCCGAAA 58.551 47.619 3.52 0.00 33.34 3.46
505 617 2.827322 TCATACTCCCTTCGTCCGAAAA 59.173 45.455 3.52 0.00 33.34 2.29
506 618 3.449737 TCATACTCCCTTCGTCCGAAAAT 59.550 43.478 3.52 0.00 33.34 1.82
507 619 4.646040 TCATACTCCCTTCGTCCGAAAATA 59.354 41.667 3.52 0.00 33.34 1.40
508 620 3.242549 ACTCCCTTCGTCCGAAAATAC 57.757 47.619 3.52 0.00 33.34 1.89
509 621 2.830321 ACTCCCTTCGTCCGAAAATACT 59.170 45.455 3.52 0.00 33.34 2.12
510 622 3.260128 ACTCCCTTCGTCCGAAAATACTT 59.740 43.478 3.52 0.00 33.34 2.24
511 623 3.592059 TCCCTTCGTCCGAAAATACTTG 58.408 45.455 3.52 0.00 33.34 3.16
512 624 3.007182 TCCCTTCGTCCGAAAATACTTGT 59.993 43.478 3.52 0.00 33.34 3.16
513 625 3.370061 CCCTTCGTCCGAAAATACTTGTC 59.630 47.826 3.52 0.00 33.34 3.18
514 626 3.991773 CCTTCGTCCGAAAATACTTGTCA 59.008 43.478 3.52 0.00 33.34 3.58
515 627 4.630069 CCTTCGTCCGAAAATACTTGTCAT 59.370 41.667 3.52 0.00 33.34 3.06
516 628 5.220416 CCTTCGTCCGAAAATACTTGTCATC 60.220 44.000 3.52 0.00 33.34 2.92
517 629 4.811908 TCGTCCGAAAATACTTGTCATCA 58.188 39.130 0.00 0.00 0.00 3.07
518 630 5.231702 TCGTCCGAAAATACTTGTCATCAA 58.768 37.500 0.00 0.00 0.00 2.57
519 631 5.697178 TCGTCCGAAAATACTTGTCATCAAA 59.303 36.000 0.00 0.00 32.87 2.69
520 632 6.203145 TCGTCCGAAAATACTTGTCATCAAAA 59.797 34.615 0.00 0.00 32.87 2.44
521 633 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
522 634 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
523 635 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
524 636 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
525 637 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
526 638 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
527 639 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
528 640 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
529 641 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
530 642 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
531 643 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
532 644 6.762661 ACTTGTCATCAAAATGGACAAAAAGG 59.237 34.615 7.70 0.11 34.98 3.11
533 645 6.477053 TGTCATCAAAATGGACAAAAAGGA 57.523 33.333 0.00 0.00 33.42 3.36
534 646 7.065120 TGTCATCAAAATGGACAAAAAGGAT 57.935 32.000 0.00 0.00 33.42 3.24
535 647 6.930164 TGTCATCAAAATGGACAAAAAGGATG 59.070 34.615 0.00 0.00 33.42 3.51
536 648 5.933463 TCATCAAAATGGACAAAAAGGATGC 59.067 36.000 0.00 0.00 33.42 3.91
537 649 5.287674 TCAAAATGGACAAAAAGGATGCA 57.712 34.783 0.00 0.00 0.00 3.96
538 650 5.867330 TCAAAATGGACAAAAAGGATGCAT 58.133 33.333 0.00 0.00 0.00 3.96
539 651 5.933463 TCAAAATGGACAAAAAGGATGCATC 59.067 36.000 18.81 18.81 0.00 3.91
540 652 5.750352 AAATGGACAAAAAGGATGCATCT 57.250 34.783 25.28 9.51 0.00 2.90
541 653 6.855763 AAATGGACAAAAAGGATGCATCTA 57.144 33.333 25.28 0.00 0.00 1.98
542 654 6.855763 AATGGACAAAAAGGATGCATCTAA 57.144 33.333 25.28 0.00 0.00 2.10
543 655 6.855763 ATGGACAAAAAGGATGCATCTAAA 57.144 33.333 25.28 1.73 0.00 1.85
544 656 6.662865 TGGACAAAAAGGATGCATCTAAAA 57.337 33.333 25.28 0.00 0.00 1.52
545 657 6.454795 TGGACAAAAAGGATGCATCTAAAAC 58.545 36.000 25.28 9.09 0.00 2.43
546 658 6.267471 TGGACAAAAAGGATGCATCTAAAACT 59.733 34.615 25.28 11.28 0.00 2.66
547 659 7.450014 TGGACAAAAAGGATGCATCTAAAACTA 59.550 33.333 25.28 6.22 0.00 2.24
548 660 8.303876 GGACAAAAAGGATGCATCTAAAACTAA 58.696 33.333 25.28 0.00 0.00 2.24
549 661 9.691362 GACAAAAAGGATGCATCTAAAACTAAA 57.309 29.630 25.28 0.00 0.00 1.85
598 710 8.915871 ATTCATTTTGATGACAAGTATTTCGG 57.084 30.769 0.00 0.00 37.32 4.30
599 711 6.851609 TCATTTTGATGACAAGTATTTCGGG 58.148 36.000 0.00 0.00 37.32 5.14
600 712 6.657117 TCATTTTGATGACAAGTATTTCGGGA 59.343 34.615 0.00 0.00 37.32 5.14
601 713 5.873179 TTTGATGACAAGTATTTCGGGAC 57.127 39.130 0.00 0.00 37.32 4.46
602 714 4.390603 TTTGATGACAAGTATTTCGGGACG 59.609 41.667 0.00 0.00 45.38 4.79
603 715 6.592789 TTTGATGACAAGTATTTCGGGACGG 61.593 44.000 0.00 0.00 44.62 4.79
604 716 8.687116 TTTGATGACAAGTATTTCGGGACGGA 62.687 42.308 0.00 0.00 44.62 4.69
649 762 9.442047 TTTTTATCATGGTTCACTTTGTTTTGT 57.558 25.926 0.00 0.00 0.00 2.83
686 898 8.704668 ACAATTAGGTGTTTCAATCTCCTTTTT 58.295 29.630 0.00 0.00 32.23 1.94
817 2772 0.240945 CACCAAAGAACCATGACGCC 59.759 55.000 0.00 0.00 0.00 5.68
927 2887 1.376037 GACACCGCCCCTCTTCTTG 60.376 63.158 0.00 0.00 0.00 3.02
932 2892 1.153469 CGCCCCTCTTCTTGCTCTC 60.153 63.158 0.00 0.00 0.00 3.20
933 2893 1.612395 CGCCCCTCTTCTTGCTCTCT 61.612 60.000 0.00 0.00 0.00 3.10
934 2894 0.107752 GCCCCTCTTCTTGCTCTCTG 60.108 60.000 0.00 0.00 0.00 3.35
935 2895 0.107752 CCCCTCTTCTTGCTCTCTGC 60.108 60.000 0.00 0.00 43.25 4.26
936 2896 0.903942 CCCTCTTCTTGCTCTCTGCT 59.096 55.000 0.00 0.00 43.37 4.24
937 2897 1.134729 CCCTCTTCTTGCTCTCTGCTC 60.135 57.143 0.00 0.00 43.37 4.26
938 2898 1.826720 CCTCTTCTTGCTCTCTGCTCT 59.173 52.381 0.00 0.00 43.37 4.09
944 2904 1.406539 CTTGCTCTCTGCTCTCCTCTC 59.593 57.143 0.00 0.00 43.37 3.20
954 2914 1.215423 GCTCTCCTCTCCTCTCCTCTT 59.785 57.143 0.00 0.00 0.00 2.85
1476 3452 1.123928 GGTACCTCATCCTCCAGGTG 58.876 60.000 4.06 0.00 43.30 4.00
1645 3621 2.046507 ACGTCGAGGTCTAGCCGT 60.047 61.111 4.63 0.00 43.70 5.68
1647 3623 2.821688 CGTCGAGGTCTAGCCGTCC 61.822 68.421 0.00 0.00 43.70 4.79
1648 3624 2.513204 TCGAGGTCTAGCCGTCCG 60.513 66.667 0.00 0.00 43.70 4.79
1649 3625 2.823147 CGAGGTCTAGCCGTCCGT 60.823 66.667 0.00 0.00 43.70 4.69
1668 3644 1.805945 CCGTACGTGCTCTGCTTCC 60.806 63.158 15.21 0.00 0.00 3.46
1677 3653 2.028203 GTGCTCTGCTTCCTCTTCTTCT 60.028 50.000 0.00 0.00 0.00 2.85
1678 3654 2.636893 TGCTCTGCTTCCTCTTCTTCTT 59.363 45.455 0.00 0.00 0.00 2.52
1679 3655 3.261580 GCTCTGCTTCCTCTTCTTCTTC 58.738 50.000 0.00 0.00 0.00 2.87
1680 3656 3.510719 CTCTGCTTCCTCTTCTTCTTCG 58.489 50.000 0.00 0.00 0.00 3.79
1886 3868 6.261381 TCCTACTAAATTGTGTTTTGCTCGTT 59.739 34.615 0.00 0.00 0.00 3.85
1900 3882 7.544566 TGTTTTGCTCGTTTTTAATTGTTGGTA 59.455 29.630 0.00 0.00 0.00 3.25
1927 3909 8.392612 AGGTATTTATTCCACGTTTAATTGTCG 58.607 33.333 0.00 0.00 0.00 4.35
2000 3984 5.888161 GCTGGGGTTACAAGTAGTACTAGTA 59.112 44.000 10.68 0.00 30.91 1.82
2020 4004 5.542779 AGTAGTGGTTTTGTTTTTGTTGCA 58.457 33.333 0.00 0.00 0.00 4.08
2054 4038 4.096984 AGAGAGCTTTTTGTTGTGGTTCAG 59.903 41.667 0.00 0.00 0.00 3.02
2061 4050 1.674359 TGTTGTGGTTCAGCGACAAT 58.326 45.000 0.00 0.00 45.15 2.71
2062 4051 1.333308 TGTTGTGGTTCAGCGACAATG 59.667 47.619 0.00 0.00 45.15 2.82
2064 4053 1.225855 TGTGGTTCAGCGACAATGTC 58.774 50.000 2.75 2.75 32.86 3.06
2085 4074 4.022849 GTCAGAGATTTTGTTGGAAGGGTG 60.023 45.833 0.00 0.00 0.00 4.61
2127 4125 5.086104 AGCAACAACCAGATAGTATCGTT 57.914 39.130 4.48 1.62 0.00 3.85
2128 4126 4.870426 AGCAACAACCAGATAGTATCGTTG 59.130 41.667 20.52 20.52 36.96 4.10
2129 4127 5.143916 CAACAACCAGATAGTATCGTTGC 57.856 43.478 21.40 0.00 35.42 4.17
2130 4128 3.444916 ACAACCAGATAGTATCGTTGCG 58.555 45.455 21.40 9.34 35.42 4.85
2131 4129 3.119245 ACAACCAGATAGTATCGTTGCGT 60.119 43.478 21.40 9.82 35.42 5.24
2132 4130 3.795623 ACCAGATAGTATCGTTGCGTT 57.204 42.857 4.48 0.00 0.00 4.84
2214 4225 4.858850 TGAGTAGGTACGGATTGGACTTA 58.141 43.478 0.00 0.00 0.00 2.24
2261 4284 5.272402 TCTCTCTCTCTTCTCTCTCTCTCA 58.728 45.833 0.00 0.00 0.00 3.27
2262 4285 5.901853 TCTCTCTCTCTTCTCTCTCTCTCAT 59.098 44.000 0.00 0.00 0.00 2.90
2263 4286 6.041409 TCTCTCTCTCTTCTCTCTCTCTCATC 59.959 46.154 0.00 0.00 0.00 2.92
2264 4287 5.662657 TCTCTCTCTTCTCTCTCTCTCATCA 59.337 44.000 0.00 0.00 0.00 3.07
2367 4409 6.014584 AGTGACAGAGTAATGGTGATGTGTAA 60.015 38.462 0.00 0.00 0.00 2.41
2373 4415 6.437477 AGAGTAATGGTGATGTGTAAGACTGA 59.563 38.462 0.00 0.00 0.00 3.41
2374 4416 6.398918 AGTAATGGTGATGTGTAAGACTGAC 58.601 40.000 0.00 0.00 0.00 3.51
2375 4417 5.489792 AATGGTGATGTGTAAGACTGACT 57.510 39.130 0.00 0.00 0.00 3.41
2431 4476 1.207089 TCTGTAGGCACGGAATTGAGG 59.793 52.381 0.00 0.00 37.11 3.86
2432 4477 0.981183 TGTAGGCACGGAATTGAGGT 59.019 50.000 0.00 0.00 0.00 3.85
2434 4479 0.174845 TAGGCACGGAATTGAGGTCG 59.825 55.000 0.00 0.00 0.00 4.79
2435 4480 2.750888 GGCACGGAATTGAGGTCGC 61.751 63.158 0.00 0.00 0.00 5.19
2436 4481 2.750888 GCACGGAATTGAGGTCGCC 61.751 63.158 0.00 0.00 0.00 5.54
2438 4483 0.953471 CACGGAATTGAGGTCGCCAA 60.953 55.000 0.00 0.00 0.00 4.52
2440 4485 0.878416 CGGAATTGAGGTCGCCAAAA 59.122 50.000 0.00 0.00 0.00 2.44
2441 4486 1.268352 CGGAATTGAGGTCGCCAAAAA 59.732 47.619 0.00 0.00 0.00 1.94
2617 4708 8.614994 TCGCTTTCTTTCTTTTCAAAACTAAG 57.385 30.769 0.00 0.00 0.00 2.18
2626 4717 9.952030 TTTCTTTTCAAAACTAAGGAAAATGGT 57.048 25.926 0.00 0.00 39.13 3.55
2627 4718 9.952030 TTCTTTTCAAAACTAAGGAAAATGGTT 57.048 25.926 0.00 0.00 39.13 3.67
2628 4719 9.594478 TCTTTTCAAAACTAAGGAAAATGGTTC 57.406 29.630 0.00 0.00 39.13 3.62
2629 4720 8.725405 TTTTCAAAACTAAGGAAAATGGTTCC 57.275 30.769 0.00 0.00 36.06 3.62
2630 4721 6.413783 TCAAAACTAAGGAAAATGGTTCCC 57.586 37.500 1.46 0.00 39.39 3.97
2631 4722 6.140377 TCAAAACTAAGGAAAATGGTTCCCT 58.860 36.000 1.46 0.00 39.39 4.20
2632 4723 6.266786 TCAAAACTAAGGAAAATGGTTCCCTC 59.733 38.462 1.46 0.00 39.39 4.30
2633 4724 5.333566 AACTAAGGAAAATGGTTCCCTCA 57.666 39.130 1.46 0.00 39.39 3.86
2634 4725 5.333566 ACTAAGGAAAATGGTTCCCTCAA 57.666 39.130 1.46 0.00 39.39 3.02
2635 4726 5.711698 ACTAAGGAAAATGGTTCCCTCAAA 58.288 37.500 1.46 0.00 39.39 2.69
2636 4727 6.140377 ACTAAGGAAAATGGTTCCCTCAAAA 58.860 36.000 1.46 0.00 39.39 2.44
2637 4728 5.966853 AAGGAAAATGGTTCCCTCAAAAA 57.033 34.783 1.46 0.00 39.39 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.070015 ACTTCATGGCCAACAAGAAAAGG 59.930 43.478 26.32 12.66 36.47 3.11
1 2 4.326504 ACTTCATGGCCAACAAGAAAAG 57.673 40.909 26.32 16.47 36.47 2.27
81 82 2.994849 GCCTCCGGCGTATTAAAAATG 58.005 47.619 6.01 0.00 39.62 2.32
94 95 2.721425 TACAATTTTAGGGCCTCCGG 57.279 50.000 10.74 0.00 38.33 5.14
99 100 7.064134 GCACTAACAAATTACAATTTTAGGGCC 59.936 37.037 16.01 0.00 39.70 5.80
159 160 8.292444 TGATATTTGGACCCTTCTATTTTGTG 57.708 34.615 0.00 0.00 0.00 3.33
221 222 2.237143 TCTTGTGGCCTCTATGAACCTG 59.763 50.000 3.32 0.00 0.00 4.00
246 247 2.896685 CCAATAAAGGCCAGGACAACAA 59.103 45.455 5.01 0.00 0.00 2.83
273 276 1.007336 ACAAGATCGTCGTCGCCAAC 61.007 55.000 0.00 0.00 36.96 3.77
282 285 6.893958 ACAAGATAATGACACAAGATCGTC 57.106 37.500 0.00 0.00 0.00 4.20
310 313 2.159170 ACCACAACAAATTGACAACGGG 60.159 45.455 0.00 0.00 39.30 5.28
311 314 2.857152 CACCACAACAAATTGACAACGG 59.143 45.455 0.00 0.00 39.30 4.44
384 387 2.202892 GTCCGGCCGAAGATGGTC 60.203 66.667 30.73 2.00 0.00 4.02
388 391 2.505982 CCATGTCCGGCCGAAGAT 59.494 61.111 30.73 7.80 0.00 2.40
399 402 0.248743 CATGCCATCGTTGCCATGTC 60.249 55.000 8.82 0.00 0.00 3.06
402 405 1.105167 CCTCATGCCATCGTTGCCAT 61.105 55.000 0.00 0.00 0.00 4.40
407 410 0.615331 ACTGTCCTCATGCCATCGTT 59.385 50.000 0.00 0.00 0.00 3.85
415 418 7.912056 TCAAGAAAGAATAACTGTCCTCATG 57.088 36.000 0.00 0.00 33.53 3.07
416 419 7.609532 CCTTCAAGAAAGAATAACTGTCCTCAT 59.390 37.037 0.00 0.00 37.12 2.90
424 427 5.562890 GCAACGCCTTCAAGAAAGAATAACT 60.563 40.000 0.00 0.00 37.12 2.24
431 434 3.479255 GGCAACGCCTTCAAGAAAG 57.521 52.632 0.00 0.00 46.69 2.62
451 454 7.714377 CACCTAATACTAAGTCGACTTCCTCTA 59.286 40.741 32.86 15.21 37.40 2.43
455 567 6.448207 ACACCTAATACTAAGTCGACTTCC 57.552 41.667 32.86 0.00 37.40 3.46
487 599 4.019174 AGTATTTTCGGACGAAGGGAGTA 58.981 43.478 7.25 0.00 35.38 2.59
488 600 2.830321 AGTATTTTCGGACGAAGGGAGT 59.170 45.455 7.25 0.00 35.38 3.85
489 601 3.521947 AGTATTTTCGGACGAAGGGAG 57.478 47.619 7.25 0.00 35.38 4.30
490 602 3.007182 ACAAGTATTTTCGGACGAAGGGA 59.993 43.478 7.25 0.00 35.38 4.20
491 603 3.332034 ACAAGTATTTTCGGACGAAGGG 58.668 45.455 7.25 0.00 35.38 3.95
492 604 3.991773 TGACAAGTATTTTCGGACGAAGG 59.008 43.478 7.25 0.00 35.38 3.46
493 605 5.347635 TGATGACAAGTATTTTCGGACGAAG 59.652 40.000 7.25 0.00 35.38 3.79
494 606 5.231702 TGATGACAAGTATTTTCGGACGAA 58.768 37.500 2.62 2.62 0.00 3.85
495 607 4.811908 TGATGACAAGTATTTTCGGACGA 58.188 39.130 0.00 0.00 0.00 4.20
496 608 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
497 609 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
498 610 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
499 611 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
500 612 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
501 613 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
502 614 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
503 615 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
504 616 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
505 617 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
506 618 7.925483 CCTTTTTGTCCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.13 2.24
507 619 6.762661 CCTTTTTGTCCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.13 3.16
508 620 6.985645 TCCTTTTTGTCCATTTTGATGACAAG 59.014 34.615 0.00 0.00 37.13 3.16
509 621 6.882656 TCCTTTTTGTCCATTTTGATGACAA 58.117 32.000 0.00 0.00 34.47 3.18
510 622 6.477053 TCCTTTTTGTCCATTTTGATGACA 57.523 33.333 0.00 0.00 0.00 3.58
511 623 6.128472 GCATCCTTTTTGTCCATTTTGATGAC 60.128 38.462 0.00 0.00 31.12 3.06
512 624 5.933463 GCATCCTTTTTGTCCATTTTGATGA 59.067 36.000 0.00 0.00 31.12 2.92
513 625 5.701750 TGCATCCTTTTTGTCCATTTTGATG 59.298 36.000 0.00 0.00 0.00 3.07
514 626 5.867330 TGCATCCTTTTTGTCCATTTTGAT 58.133 33.333 0.00 0.00 0.00 2.57
515 627 5.287674 TGCATCCTTTTTGTCCATTTTGA 57.712 34.783 0.00 0.00 0.00 2.69
516 628 5.935789 AGATGCATCCTTTTTGTCCATTTTG 59.064 36.000 23.06 0.00 0.00 2.44
517 629 6.117975 AGATGCATCCTTTTTGTCCATTTT 57.882 33.333 23.06 0.00 0.00 1.82
518 630 5.750352 AGATGCATCCTTTTTGTCCATTT 57.250 34.783 23.06 0.00 0.00 2.32
519 631 6.855763 TTAGATGCATCCTTTTTGTCCATT 57.144 33.333 23.06 2.35 0.00 3.16
520 632 6.855763 TTTAGATGCATCCTTTTTGTCCAT 57.144 33.333 23.06 2.56 0.00 3.41
521 633 6.267471 AGTTTTAGATGCATCCTTTTTGTCCA 59.733 34.615 23.06 0.00 0.00 4.02
522 634 6.691508 AGTTTTAGATGCATCCTTTTTGTCC 58.308 36.000 23.06 3.05 0.00 4.02
523 635 9.691362 TTTAGTTTTAGATGCATCCTTTTTGTC 57.309 29.630 23.06 6.80 0.00 3.18
573 685 7.975616 CCCGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
574 686 7.175816 TCCCGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
575 687 6.657117 TCCCGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
576 688 6.747280 GTCCCGAAATACTTGTCATCAAAATG 59.253 38.462 0.00 0.00 32.87 2.32
577 689 6.403200 CGTCCCGAAATACTTGTCATCAAAAT 60.403 38.462 0.00 0.00 32.87 1.82
578 690 5.106869 CGTCCCGAAATACTTGTCATCAAAA 60.107 40.000 0.00 0.00 32.87 2.44
579 691 4.390603 CGTCCCGAAATACTTGTCATCAAA 59.609 41.667 0.00 0.00 32.87 2.69
580 692 3.930229 CGTCCCGAAATACTTGTCATCAA 59.070 43.478 0.00 0.00 0.00 2.57
581 693 3.517602 CGTCCCGAAATACTTGTCATCA 58.482 45.455 0.00 0.00 0.00 3.07
582 694 2.864343 CCGTCCCGAAATACTTGTCATC 59.136 50.000 0.00 0.00 0.00 2.92
583 695 2.498481 TCCGTCCCGAAATACTTGTCAT 59.502 45.455 0.00 0.00 0.00 3.06
584 696 1.894466 TCCGTCCCGAAATACTTGTCA 59.106 47.619 0.00 0.00 0.00 3.58
585 697 2.537401 CTCCGTCCCGAAATACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
586 698 1.206371 CCTCCGTCCCGAAATACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
587 699 1.472728 CCCTCCGTCCCGAAATACTTG 60.473 57.143 0.00 0.00 0.00 3.16
588 700 0.828677 CCCTCCGTCCCGAAATACTT 59.171 55.000 0.00 0.00 0.00 2.24
589 701 0.032813 TCCCTCCGTCCCGAAATACT 60.033 55.000 0.00 0.00 0.00 2.12
590 702 0.388294 CTCCCTCCGTCCCGAAATAC 59.612 60.000 0.00 0.00 0.00 1.89
591 703 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
592 704 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
593 705 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.000 0.00 0.00 0.00 3.46
594 706 0.466922 GATACTCCCTCCGTCCCGAA 60.467 60.000 0.00 0.00 0.00 4.30
595 707 1.150081 GATACTCCCTCCGTCCCGA 59.850 63.158 0.00 0.00 0.00 5.14
596 708 0.467659 AAGATACTCCCTCCGTCCCG 60.468 60.000 0.00 0.00 0.00 5.14
597 709 1.041437 CAAGATACTCCCTCCGTCCC 58.959 60.000 0.00 0.00 0.00 4.46
598 710 1.777941 ACAAGATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
599 711 3.698040 TGTTACAAGATACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
600 712 3.705051 TGTTACAAGATACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
601 713 4.939052 ATGTTACAAGATACTCCCTCCG 57.061 45.455 0.00 0.00 0.00 4.63
602 714 7.939784 AAAAATGTTACAAGATACTCCCTCC 57.060 36.000 0.00 0.00 0.00 4.30
697 912 1.167851 GCAGTGCCATACAAAGCAGA 58.832 50.000 2.85 0.00 40.28 4.26
784 2739 2.685106 TTGGTGGGTCATTGCCTTTA 57.315 45.000 0.00 0.00 0.00 1.85
791 2746 2.765689 TGGTTCTTTGGTGGGTCATT 57.234 45.000 0.00 0.00 0.00 2.57
927 2887 0.106519 AGGAGAGGAGAGCAGAGAGC 60.107 60.000 0.00 0.00 46.19 4.09
932 2892 0.552848 AGGAGAGGAGAGGAGAGCAG 59.447 60.000 0.00 0.00 0.00 4.24
933 2893 0.550914 GAGGAGAGGAGAGGAGAGCA 59.449 60.000 0.00 0.00 0.00 4.26
934 2894 0.846693 AGAGGAGAGGAGAGGAGAGC 59.153 60.000 0.00 0.00 0.00 4.09
935 2895 2.780010 AGAAGAGGAGAGGAGAGGAGAG 59.220 54.545 0.00 0.00 0.00 3.20
936 2896 2.777692 GAGAAGAGGAGAGGAGAGGAGA 59.222 54.545 0.00 0.00 0.00 3.71
937 2897 2.780010 AGAGAAGAGGAGAGGAGAGGAG 59.220 54.545 0.00 0.00 0.00 3.69
938 2898 2.777692 GAGAGAAGAGGAGAGGAGAGGA 59.222 54.545 0.00 0.00 0.00 3.71
944 2904 2.158608 GGAGAGGAGAGAAGAGGAGAGG 60.159 59.091 0.00 0.00 0.00 3.69
954 2914 1.679305 GCGTGTGGGAGAGGAGAGA 60.679 63.158 0.00 0.00 0.00 3.10
1149 3125 4.742649 AGCGAGGCGTCCTGGAGA 62.743 66.667 11.06 0.00 31.76 3.71
1476 3452 4.849329 ACGCGGCCGTCGATCTTC 62.849 66.667 36.24 15.52 46.39 2.87
1595 3571 2.203788 TCTGGAACCTGAGCCCGT 60.204 61.111 0.00 0.00 0.00 5.28
1648 3624 1.071567 GAAGCAGAGCACGTACGGAC 61.072 60.000 21.06 10.97 0.00 4.79
1649 3625 1.211969 GAAGCAGAGCACGTACGGA 59.788 57.895 21.06 0.00 0.00 4.69
1668 3644 5.125417 AGAGGAAGATGACGAAGAAGAAGAG 59.875 44.000 0.00 0.00 0.00 2.85
1677 3653 1.478510 GGAGCAGAGGAAGATGACGAA 59.521 52.381 0.00 0.00 0.00 3.85
1678 3654 1.107114 GGAGCAGAGGAAGATGACGA 58.893 55.000 0.00 0.00 0.00 4.20
1679 3655 0.248825 CGGAGCAGAGGAAGATGACG 60.249 60.000 0.00 0.00 0.00 4.35
1680 3656 0.820871 ACGGAGCAGAGGAAGATGAC 59.179 55.000 0.00 0.00 0.00 3.06
1952 3934 7.759433 AGCATTAACCATTTCACTTTAATTCCG 59.241 33.333 0.00 0.00 0.00 4.30
2000 3984 4.384940 ACTGCAACAAAAACAAAACCACT 58.615 34.783 0.00 0.00 0.00 4.00
2020 4004 5.649831 ACAAAAAGCTCTCTCAACTCAAACT 59.350 36.000 0.00 0.00 0.00 2.66
2054 4038 4.410492 ACAAAATCTCTGACATTGTCGC 57.590 40.909 11.97 0.00 34.95 5.19
2061 4050 4.144297 CCCTTCCAACAAAATCTCTGACA 58.856 43.478 0.00 0.00 0.00 3.58
2062 4051 4.022849 CACCCTTCCAACAAAATCTCTGAC 60.023 45.833 0.00 0.00 0.00 3.51
2064 4053 3.305608 GCACCCTTCCAACAAAATCTCTG 60.306 47.826 0.00 0.00 0.00 3.35
2105 4099 4.737855 ACGATACTATCTGGTTGTTGCT 57.262 40.909 0.00 0.00 0.00 3.91
2127 4125 2.320745 AGCTCATCATCATCAACGCA 57.679 45.000 0.00 0.00 0.00 5.24
2128 4126 3.687572 AAAGCTCATCATCATCAACGC 57.312 42.857 0.00 0.00 0.00 4.84
2129 4127 5.237996 ACCATAAAGCTCATCATCATCAACG 59.762 40.000 0.00 0.00 0.00 4.10
2130 4128 6.630444 ACCATAAAGCTCATCATCATCAAC 57.370 37.500 0.00 0.00 0.00 3.18
2131 4129 6.938596 CCTACCATAAAGCTCATCATCATCAA 59.061 38.462 0.00 0.00 0.00 2.57
2132 4130 6.043590 ACCTACCATAAAGCTCATCATCATCA 59.956 38.462 0.00 0.00 0.00 3.07
2261 4284 0.964358 GAGCTGCCAGCAAGGTTGAT 60.964 55.000 20.53 0.00 45.56 2.57
2262 4285 1.601759 GAGCTGCCAGCAAGGTTGA 60.602 57.895 20.53 0.00 45.56 3.18
2263 4286 2.633509 GGAGCTGCCAGCAAGGTTG 61.634 63.158 20.53 0.00 45.56 3.77
2264 4287 2.282745 GGAGCTGCCAGCAAGGTT 60.283 61.111 20.53 0.00 45.56 3.50
2354 4396 4.323028 CCAGTCAGTCTTACACATCACCAT 60.323 45.833 0.00 0.00 0.00 3.55
2367 4409 1.626686 CACTCCTCACCAGTCAGTCT 58.373 55.000 0.00 0.00 0.00 3.24
2373 4415 1.136329 AATGGCCACTCCTCACCAGT 61.136 55.000 8.16 0.00 35.20 4.00
2374 4416 0.679002 CAATGGCCACTCCTCACCAG 60.679 60.000 8.16 0.00 35.20 4.00
2375 4417 1.133181 TCAATGGCCACTCCTCACCA 61.133 55.000 8.16 0.00 36.43 4.17
2404 4449 8.129496 TCAATTCCGTGCCTACAGAATATATA 57.871 34.615 0.00 0.00 33.82 0.86
2405 4450 7.004555 TCAATTCCGTGCCTACAGAATATAT 57.995 36.000 0.00 0.00 33.82 0.86
2406 4451 6.413783 TCAATTCCGTGCCTACAGAATATA 57.586 37.500 0.00 0.00 33.82 0.86
2407 4452 5.290493 TCAATTCCGTGCCTACAGAATAT 57.710 39.130 0.00 0.00 33.82 1.28
2438 4483 5.806955 TGGAAGTACCAGGGGATATTTTT 57.193 39.130 0.00 0.00 44.64 1.94
2449 4512 3.497763 TGGTTCAACCATGGAAGTACCAG 60.498 47.826 24.46 6.80 44.79 4.00
2496 4559 0.987294 ACCTTGTGCACCTGAGCTAT 59.013 50.000 15.69 0.00 34.99 2.97
2508 4571 2.001812 CTCGTCATGGAGACCTTGTG 57.998 55.000 0.00 0.00 44.66 3.33
2509 4572 0.247736 GCTCGTCATGGAGACCTTGT 59.752 55.000 3.41 0.00 44.66 3.16
2591 4682 8.614994 TTAGTTTTGAAAAGAAAGAAAGCGAG 57.385 30.769 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.