Multiple sequence alignment - TraesCS3D01G516100

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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 TraesCS3D01G516100 chr3D 100.000 4368 0 0 1 4368 599270312 599265945 0.000000e+00 8067
1 TraesCS3D01G516100 chr3D 90.067 1188 93 11 2221 3392 599177699 599178877 0.000000e+00 1517
2 TraesCS3D01G516100 chr3D 86.447 1033 69 23 941 1929 599175997 599177002 0.000000e+00 1066
3 TraesCS3D01G516100 chr3D 91.089 505 32 6 3864 4368 599195234 599195725 0.000000e+00 671
4 TraesCS3D01G516100 chr3D 84.738 688 74 19 168 844 93254357 93255024 0.000000e+00 660
5 TraesCS3D01G516100 chr3D 85.056 629 76 13 205 822 271512062 271511441 3.710000e-175 625
6 TraesCS3D01G516100 chr3D 87.442 430 33 14 3401 3821 599178747 599179164 3.950000e-130 475
7 TraesCS3D01G516100 chr3D 93.431 137 6 3 3259 3394 599266920 599266786 2.660000e-47 200
8 TraesCS3D01G516100 chr3D 93.431 137 6 3 3393 3527 599267054 599266919 2.660000e-47 200
9 TraesCS3D01G516100 chr3D 77.154 267 29 14 1983 2220 599177002 599177265 4.590000e-25 126
10 TraesCS3D01G516100 chr3A 95.212 3467 92 16 940 4368 729317208 729313778 0.000000e+00 5415
11 TraesCS3D01G516100 chr3A 89.722 1294 102 17 2122 3392 729392487 729393772 0.000000e+00 1624
12 TraesCS3D01G516100 chr3A 92.257 904 49 16 1 888 729319443 729318545 0.000000e+00 1262
13 TraesCS3D01G516100 chr3A 86.504 904 73 21 941 1819 729391492 729392371 0.000000e+00 948
14 TraesCS3D01G516100 chr3A 93.465 505 22 4 3864 4368 729405571 729406064 0.000000e+00 739
15 TraesCS3D01G516100 chr3A 85.607 667 82 9 166 821 584027972 584028635 0.000000e+00 688
16 TraesCS3D01G516100 chr3A 89.016 437 31 13 3393 3821 729393638 729394065 3.870000e-145 525
17 TraesCS3D01G516100 chr3A 95.522 134 4 1 3259 3392 729314741 729314610 3.420000e-51 213
18 TraesCS3D01G516100 chr3A 93.431 137 6 3 3393 3527 729314875 729314740 2.660000e-47 200
19 TraesCS3D01G516100 chr3A 86.239 109 9 5 740 845 690963568 690963463 3.570000e-21 113
20 TraesCS3D01G516100 chr6B 86.128 656 73 11 176 818 34815821 34815171 0.000000e+00 691
21 TraesCS3D01G516100 chr6B 84.948 671 87 9 166 825 492858077 492857410 0.000000e+00 667
22 TraesCS3D01G516100 chrUn 86.386 617 68 8 205 811 229736485 229735875 0.000000e+00 660
23 TraesCS3D01G516100 chr7B 84.195 696 91 15 165 846 28489756 28489066 0.000000e+00 658
24 TraesCS3D01G516100 chr2B 84.558 667 87 11 167 820 690213023 690213686 0.000000e+00 647
25 TraesCS3D01G516100 chr1D 84.769 650 85 9 168 807 439108967 439108322 1.320000e-179 640
26 TraesCS3D01G516100 chr1D 89.189 444 36 9 384 816 246074813 246075255 1.070000e-150 544
27 TraesCS3D01G516100 chr7D 84.522 659 84 12 164 811 91749073 91748422 1.710000e-178 636
28 TraesCS3D01G516100 chr7D 84.469 631 79 12 208 828 454676250 454676871 4.830000e-169 604
29 TraesCS3D01G516100 chr4B 85.842 558 75 3 168 724 453262960 453262406 1.350000e-164 590
30 TraesCS3D01G516100 chr5D 83.051 649 92 15 210 845 59760239 59759596 1.360000e-159 573


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 TraesCS3D01G516100 chr3D 599265945 599270312 4367 True 2822.333333 8067 95.620667 1 4368 3 chr3D.!!$R2 4367
1 TraesCS3D01G516100 chr3D 599175997 599179164 3167 False 796.000000 1517 85.277500 941 3821 4 chr3D.!!$F3 2880
2 TraesCS3D01G516100 chr3D 93254357 93255024 667 False 660.000000 660 84.738000 168 844 1 chr3D.!!$F1 676
3 TraesCS3D01G516100 chr3D 271511441 271512062 621 True 625.000000 625 85.056000 205 822 1 chr3D.!!$R1 617
4 TraesCS3D01G516100 chr3A 729313778 729319443 5665 True 1772.500000 5415 94.105500 1 4368 4 chr3A.!!$R2 4367
5 TraesCS3D01G516100 chr3A 729391492 729394065 2573 False 1032.333333 1624 88.414000 941 3821 3 chr3A.!!$F3 2880
6 TraesCS3D01G516100 chr3A 584027972 584028635 663 False 688.000000 688 85.607000 166 821 1 chr3A.!!$F1 655
7 TraesCS3D01G516100 chr6B 34815171 34815821 650 True 691.000000 691 86.128000 176 818 1 chr6B.!!$R1 642
8 TraesCS3D01G516100 chr6B 492857410 492858077 667 True 667.000000 667 84.948000 166 825 1 chr6B.!!$R2 659
9 TraesCS3D01G516100 chrUn 229735875 229736485 610 True 660.000000 660 86.386000 205 811 1 chrUn.!!$R1 606
10 TraesCS3D01G516100 chr7B 28489066 28489756 690 True 658.000000 658 84.195000 165 846 1 chr7B.!!$R1 681
11 TraesCS3D01G516100 chr2B 690213023 690213686 663 False 647.000000 647 84.558000 167 820 1 chr2B.!!$F1 653
12 TraesCS3D01G516100 chr1D 439108322 439108967 645 True 640.000000 640 84.769000 168 807 1 chr1D.!!$R1 639
13 TraesCS3D01G516100 chr7D 91748422 91749073 651 True 636.000000 636 84.522000 164 811 1 chr7D.!!$R1 647
14 TraesCS3D01G516100 chr7D 454676250 454676871 621 False 604.000000 604 84.469000 208 828 1 chr7D.!!$F1 620
15 TraesCS3D01G516100 chr4B 453262406 453262960 554 True 590.000000 590 85.842000 168 724 1 chr4B.!!$R1 556
16 TraesCS3D01G516100 chr5D 59759596 59760239 643 True 573.000000 573 83.051000 210 845 1 chr5D.!!$R1 635

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
729 747 1.275666 TGATGATCACTGGGTCGGTT 58.724 50.0 0.0 0.0 0.0 4.44 F
1558 2934 0.179067 TTTCACGGACGCCAACTTCT 60.179 50.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 4457 1.298953 ATAGGAAGGAAGCAGCCCAA 58.701 50.000 0.0 0.0 0.0 4.12 R
3456 5462 1.265635 TGTGTGCTGATTAACAACGCC 59.734 47.619 0.0 0.0 0.0 5.68 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
381 392 5.122869 TCTGCAATTAGACTTGAGCAATGAC 59.877 40.000 0.00 0.00 0.00 3.06
390 401 4.139786 ACTTGAGCAATGACATTGTCACT 58.860 39.130 25.18 13.93 45.65 3.41
391 402 4.214971 ACTTGAGCAATGACATTGTCACTC 59.785 41.667 25.18 20.91 45.65 3.51
392 403 4.011966 TGAGCAATGACATTGTCACTCT 57.988 40.909 25.18 19.60 45.65 3.24
476 490 7.586349 AGAAAGATGGGAAGCCTTTATCAATA 58.414 34.615 0.00 0.00 31.06 1.90
636 653 5.801350 TCATCAGATTCGAACAATTGGAC 57.199 39.130 10.83 2.33 0.00 4.02
656 673 3.309296 ACCTGAGAGGACAGAAAACTCA 58.691 45.455 0.00 0.00 37.67 3.41
674 691 3.053395 ACTCATTAACCTCATGGCACCAT 60.053 43.478 0.00 0.00 36.63 3.55
725 743 4.813161 CACAACTATGATGATCACTGGGTC 59.187 45.833 0.00 0.00 0.00 4.46
726 744 4.053983 CAACTATGATGATCACTGGGTCG 58.946 47.826 0.00 0.00 0.00 4.79
727 745 2.630098 ACTATGATGATCACTGGGTCGG 59.370 50.000 0.00 0.00 0.00 4.79
728 746 1.500474 ATGATGATCACTGGGTCGGT 58.500 50.000 0.00 0.00 0.00 4.69
729 747 1.275666 TGATGATCACTGGGTCGGTT 58.724 50.000 0.00 0.00 0.00 4.44
731 749 1.482593 GATGATCACTGGGTCGGTTCT 59.517 52.381 0.00 0.00 0.00 3.01
732 750 1.348064 TGATCACTGGGTCGGTTCTT 58.652 50.000 0.00 0.00 0.00 2.52
927 1041 8.265220 ACTGTTCGCTTTTCTTTTTATTTACG 57.735 30.769 0.00 0.00 0.00 3.18
928 1042 8.124199 ACTGTTCGCTTTTCTTTTTATTTACGA 58.876 29.630 0.00 0.00 0.00 3.43
929 1043 8.838452 TGTTCGCTTTTCTTTTTATTTACGAA 57.162 26.923 0.00 0.00 33.91 3.85
931 1045 9.708348 GTTCGCTTTTCTTTTTATTTACGAATG 57.292 29.630 0.00 0.00 37.99 2.67
932 1046 9.666626 TTCGCTTTTCTTTTTATTTACGAATGA 57.333 25.926 0.00 0.00 31.66 2.57
933 1047 9.325150 TCGCTTTTCTTTTTATTTACGAATGAG 57.675 29.630 0.00 0.00 0.00 2.90
934 1048 8.096109 CGCTTTTCTTTTTATTTACGAATGAGC 58.904 33.333 0.00 0.00 0.00 4.26
935 1049 9.129209 GCTTTTCTTTTTATTTACGAATGAGCT 57.871 29.630 0.00 0.00 0.00 4.09
1470 2826 0.480252 AGTTTCCTTCTTGCCTGCCT 59.520 50.000 0.00 0.00 0.00 4.75
1480 2836 2.044650 GCCTGCCTGCATCCTTGA 60.045 61.111 0.00 0.00 0.00 3.02
1487 2843 0.661552 CCTGCATCCTTGATTGCTCG 59.338 55.000 0.00 0.00 0.00 5.03
1521 2897 3.292460 TGATTGATTGATGGATGCAGCA 58.708 40.909 0.00 0.00 0.00 4.41
1558 2934 0.179067 TTTCACGGACGCCAACTTCT 60.179 50.000 0.00 0.00 0.00 2.85
1712 3088 2.484662 TCGCATGCGAAATGTGGC 59.515 55.556 38.48 0.00 46.01 5.01
1748 3124 2.000447 GGACGACTGCCAAAGTATCAC 59.000 52.381 0.00 0.00 40.07 3.06
1784 3177 4.223953 TCCCACTCTAGGACATGGATTAC 58.776 47.826 0.00 0.00 33.80 1.89
1791 3184 6.174720 TCTAGGACATGGATTACAATGGAC 57.825 41.667 0.00 0.00 0.00 4.02
1794 3187 5.579047 AGGACATGGATTACAATGGACAAA 58.421 37.500 0.00 0.00 0.00 2.83
1850 3244 6.371548 GTGCTTCACCAGACATTCATTACTTA 59.628 38.462 0.00 0.00 0.00 2.24
1920 3314 5.979517 GTCATAAGCTTTACAATTCATGCCC 59.020 40.000 3.20 0.00 0.00 5.36
1929 3323 4.354893 ACAATTCATGCCCACAAACAAT 57.645 36.364 0.00 0.00 0.00 2.71
1963 3357 5.451908 ACAAAGTTGTTGCAATACTGATCG 58.548 37.500 15.32 8.63 38.47 3.69
1964 3358 3.747099 AGTTGTTGCAATACTGATCGC 57.253 42.857 14.23 0.00 0.00 4.58
1965 3359 3.073678 AGTTGTTGCAATACTGATCGCA 58.926 40.909 14.23 0.00 0.00 5.10
1966 3360 3.501828 AGTTGTTGCAATACTGATCGCAA 59.498 39.130 14.23 3.37 41.79 4.85
1970 3364 2.971307 TGCAATACTGATCGCAACTCA 58.029 42.857 0.00 0.00 0.00 3.41
1971 3365 3.333804 TGCAATACTGATCGCAACTCAA 58.666 40.909 0.00 0.00 0.00 3.02
2046 3440 7.526608 TGCTTAATGGTTTCGAAGATAACAAG 58.473 34.615 0.00 1.57 38.90 3.16
2066 3460 7.303634 ACAAGATGCTAAATAAACCTGTACG 57.696 36.000 0.00 0.00 0.00 3.67
2167 3589 6.916387 CGCATTTGCAGATCTTCAAATTAGAT 59.084 34.615 24.87 7.62 39.92 1.98
2193 3615 6.530120 TGCTTTCCTCTGTTTGAGTATACAA 58.470 36.000 5.50 0.00 41.11 2.41
2586 4457 5.385198 ACAAATTTGTGGACTCATACAGGT 58.615 37.500 22.71 0.00 40.49 4.00
2738 4609 2.681848 TCGAGGTGTACTAACTGCTAGC 59.318 50.000 8.10 8.10 0.00 3.42
2832 4703 6.348458 CGATGGCTTTGTCAAGTTATCAAGAA 60.348 38.462 0.00 0.00 31.86 2.52
3327 5201 2.593925 TCTCTGAGAGAGACAAGCCA 57.406 50.000 8.34 0.00 45.77 4.75
3374 5380 7.503521 TTTTGAGGCCAAAATAAATTTGTCC 57.496 32.000 5.01 0.00 45.39 4.02
3380 5386 7.359262 GGCCAAAATAAATTTGTCCTTACAC 57.641 36.000 0.00 0.00 42.48 2.90
3381 5387 7.158697 GGCCAAAATAAATTTGTCCTTACACT 58.841 34.615 0.00 0.00 42.48 3.55
3382 5388 7.659799 GGCCAAAATAAATTTGTCCTTACACTT 59.340 33.333 0.00 0.00 42.48 3.16
3383 5389 8.495148 GCCAAAATAAATTTGTCCTTACACTTG 58.505 33.333 0.00 0.00 45.72 3.16
3384 5390 9.541143 CCAAAATAAATTTGTCCTTACACTTGT 57.459 29.630 0.00 0.00 45.72 3.16
3391 5397 9.541143 AAATTTGTCCTTACACTTGTAATTTGG 57.459 29.630 2.33 1.72 39.49 3.28
3392 5398 7.648039 TTTGTCCTTACACTTGTAATTTGGT 57.352 32.000 2.33 0.00 39.49 3.67
3393 5399 7.648039 TTGTCCTTACACTTGTAATTTGGTT 57.352 32.000 2.33 0.00 39.49 3.67
3394 5400 8.749026 TTGTCCTTACACTTGTAATTTGGTTA 57.251 30.769 2.33 0.00 39.49 2.85
3395 5401 8.385898 TGTCCTTACACTTGTAATTTGGTTAG 57.614 34.615 2.33 0.00 39.49 2.34
3396 5402 7.994334 TGTCCTTACACTTGTAATTTGGTTAGT 59.006 33.333 2.33 0.00 39.49 2.24
3397 5403 8.501580 GTCCTTACACTTGTAATTTGGTTAGTC 58.498 37.037 2.33 0.00 39.49 2.59
3398 5404 8.434392 TCCTTACACTTGTAATTTGGTTAGTCT 58.566 33.333 2.33 0.00 39.49 3.24
3399 5405 9.063615 CCTTACACTTGTAATTTGGTTAGTCTT 57.936 33.333 2.33 0.00 39.49 3.01
3426 5432 9.950496 TTTTAGAAGCTCACAGAGATTTTATCT 57.050 29.630 0.00 0.00 38.45 1.98
3433 5439 9.979578 AGCTCACAGAGATTTTATCTATAACTG 57.020 33.333 0.00 0.00 40.38 3.16
3434 5440 9.202273 GCTCACAGAGATTTTATCTATAACTGG 57.798 37.037 0.00 0.00 40.38 4.00
3448 5454 8.774546 ATCTATAACTGGAATGTTCTCTCTGA 57.225 34.615 0.00 0.00 0.00 3.27
3449 5455 8.231692 TCTATAACTGGAATGTTCTCTCTGAG 57.768 38.462 0.00 0.00 0.00 3.35
3450 5456 8.055790 TCTATAACTGGAATGTTCTCTCTGAGA 58.944 37.037 7.24 7.24 36.86 3.27
3451 5457 5.404466 AACTGGAATGTTCTCTCTGAGAG 57.596 43.478 25.33 25.33 43.64 3.20
3462 5468 2.276472 CTCTGAGAGAGAAGGCGTTG 57.724 55.000 2.60 0.00 45.07 4.10
3463 5469 1.543802 CTCTGAGAGAGAAGGCGTTGT 59.456 52.381 2.60 0.00 45.07 3.32
3464 5470 1.964223 TCTGAGAGAGAAGGCGTTGTT 59.036 47.619 0.00 0.00 0.00 2.83
3465 5471 3.154710 TCTGAGAGAGAAGGCGTTGTTA 58.845 45.455 0.00 0.00 0.00 2.41
3466 5472 3.572682 TCTGAGAGAGAAGGCGTTGTTAA 59.427 43.478 0.00 0.00 0.00 2.01
3467 5473 4.220821 TCTGAGAGAGAAGGCGTTGTTAAT 59.779 41.667 0.00 0.00 0.00 1.40
3468 5474 4.495422 TGAGAGAGAAGGCGTTGTTAATC 58.505 43.478 0.00 0.00 0.00 1.75
3469 5475 4.021456 TGAGAGAGAAGGCGTTGTTAATCA 60.021 41.667 0.00 0.00 0.00 2.57
3470 5476 4.499183 AGAGAGAAGGCGTTGTTAATCAG 58.501 43.478 0.00 0.00 0.00 2.90
3471 5477 3.003480 AGAGAAGGCGTTGTTAATCAGC 58.997 45.455 0.00 0.00 0.00 4.26
3472 5478 2.742053 GAGAAGGCGTTGTTAATCAGCA 59.258 45.455 0.00 0.00 0.00 4.41
3473 5479 2.484264 AGAAGGCGTTGTTAATCAGCAC 59.516 45.455 0.00 0.00 0.00 4.40
3474 5480 1.890876 AGGCGTTGTTAATCAGCACA 58.109 45.000 0.00 0.00 0.00 4.57
3475 5481 1.535462 AGGCGTTGTTAATCAGCACAC 59.465 47.619 0.00 0.00 0.00 3.82
3476 5482 1.265635 GGCGTTGTTAATCAGCACACA 59.734 47.619 0.00 0.00 0.00 3.72
3477 5483 2.095263 GGCGTTGTTAATCAGCACACAT 60.095 45.455 0.00 0.00 0.00 3.21
3478 5484 3.564511 GCGTTGTTAATCAGCACACATT 58.435 40.909 0.00 0.00 0.00 2.71
3479 5485 3.361644 GCGTTGTTAATCAGCACACATTG 59.638 43.478 0.00 0.00 0.00 2.82
3480 5486 4.536065 CGTTGTTAATCAGCACACATTGT 58.464 39.130 0.00 0.00 0.00 2.71
3481 5487 5.684850 CGTTGTTAATCAGCACACATTGTA 58.315 37.500 0.00 0.00 0.00 2.41
3482 5488 6.314018 CGTTGTTAATCAGCACACATTGTAT 58.686 36.000 0.00 0.00 0.00 2.29
3483 5489 6.801377 CGTTGTTAATCAGCACACATTGTATT 59.199 34.615 0.00 0.00 0.00 1.89
3484 5490 7.325821 CGTTGTTAATCAGCACACATTGTATTT 59.674 33.333 0.00 0.00 0.00 1.40
3485 5491 8.977505 GTTGTTAATCAGCACACATTGTATTTT 58.022 29.630 0.00 0.00 0.00 1.82
3486 5492 8.518151 TGTTAATCAGCACACATTGTATTTTG 57.482 30.769 0.00 0.00 0.00 2.44
3487 5493 8.355913 TGTTAATCAGCACACATTGTATTTTGA 58.644 29.630 0.00 0.00 0.00 2.69
3488 5494 8.853345 GTTAATCAGCACACATTGTATTTTGAG 58.147 33.333 0.00 0.00 0.00 3.02
3489 5495 5.375417 TCAGCACACATTGTATTTTGAGG 57.625 39.130 0.00 0.00 0.00 3.86
3490 5496 4.218200 TCAGCACACATTGTATTTTGAGGG 59.782 41.667 0.00 0.00 0.00 4.30
3491 5497 3.056607 AGCACACATTGTATTTTGAGGGC 60.057 43.478 0.00 0.00 33.69 5.19
3492 5498 3.305950 GCACACATTGTATTTTGAGGGCA 60.306 43.478 0.00 0.00 33.70 5.36
3493 5499 4.798924 GCACACATTGTATTTTGAGGGCAA 60.799 41.667 0.00 0.00 33.70 4.52
3494 5500 5.295950 CACACATTGTATTTTGAGGGCAAA 58.704 37.500 0.00 0.00 41.97 3.68
3546 5552 5.180117 CGGTTCAAAGTCATCAGAATCACTT 59.820 40.000 0.00 0.00 0.00 3.16
3547 5553 6.293626 CGGTTCAAAGTCATCAGAATCACTTT 60.294 38.462 0.00 0.00 39.20 2.66
3577 5583 7.531857 TTTTTGTGAAAATATGAGGCCAGTA 57.468 32.000 5.01 0.00 30.07 2.74
3616 5622 3.926058 ACCTTTACCGCCATATTCAGT 57.074 42.857 0.00 0.00 0.00 3.41
3651 5657 4.445453 CATGGCAAGCTGATGTAGTAGAA 58.555 43.478 0.00 0.00 0.00 2.10
3712 5718 8.195436 AGATTTGCGATTTTCATTGATCAAGAT 58.805 29.630 14.54 2.97 0.00 2.40
3714 5720 9.806203 ATTTGCGATTTTCATTGATCAAGATAA 57.194 25.926 14.54 12.08 0.00 1.75
3777 5783 5.804639 ACTCTTGTGGCATTACATTACTCA 58.195 37.500 0.00 0.00 0.00 3.41
3904 5910 7.500141 ACATTAAAAGCAGGAAAACATGTTCT 58.500 30.769 12.39 0.00 0.00 3.01
3957 5963 3.864583 GCTCCAGATAATGATCGATCAGC 59.135 47.826 30.11 20.87 40.64 4.26
3958 5964 4.620097 GCTCCAGATAATGATCGATCAGCA 60.620 45.833 30.11 21.01 40.64 4.41
3960 5966 4.525874 TCCAGATAATGATCGATCAGCAGT 59.474 41.667 30.11 18.25 40.64 4.40
3975 5981 5.420725 TCAGCAGTTATCACAGTACCATT 57.579 39.130 0.00 0.00 0.00 3.16
4053 6059 5.964958 TGGTAAGGCTGAATTCTTTTCAG 57.035 39.130 7.05 10.28 46.42 3.02
4081 6087 7.197017 GGACATACACAACACAACACATAAAA 58.803 34.615 0.00 0.00 0.00 1.52
4082 6088 7.166804 GGACATACACAACACAACACATAAAAC 59.833 37.037 0.00 0.00 0.00 2.43
4230 6236 6.826741 AGTACACACAAGGTAGAAAACAACAT 59.173 34.615 0.00 0.00 0.00 2.71
4274 6280 4.649088 GTGAAACTTGCAACTTTAGGGT 57.351 40.909 0.00 0.00 0.00 4.34
4280 6286 4.020543 ACTTGCAACTTTAGGGTTCAACA 58.979 39.130 0.00 0.00 0.00 3.33
4313 6319 5.202640 ACGAAATTAAACTTGCGACTTGAC 58.797 37.500 0.00 0.00 0.00 3.18
4326 6332 1.525197 GACTTGACAATTGACACGCGA 59.475 47.619 15.93 0.00 0.00 5.87
4332 6338 2.534349 GACAATTGACACGCGACGATAT 59.466 45.455 15.93 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
381 392 1.197721 GCGGGTGAAAGAGTGACAATG 59.802 52.381 0.00 0.00 0.00 2.82
390 401 0.250124 ATGTTCGTGCGGGTGAAAGA 60.250 50.000 0.00 0.00 0.00 2.52
391 402 0.591170 AATGTTCGTGCGGGTGAAAG 59.409 50.000 0.00 0.00 0.00 2.62
392 403 1.532007 GTAATGTTCGTGCGGGTGAAA 59.468 47.619 0.00 0.00 0.00 2.69
476 490 3.053245 TCATCCCGGACCCAAATACATTT 60.053 43.478 0.73 0.00 0.00 2.32
636 653 4.550076 ATGAGTTTTCTGTCCTCTCAGG 57.450 45.455 0.00 0.00 38.30 3.86
656 673 3.668141 TGATGGTGCCATGAGGTTAAT 57.332 42.857 8.64 0.00 36.70 1.40
674 691 9.511144 GAAAATAAGTTTCCTTTCGTTCTTTGA 57.489 29.630 0.00 0.00 39.91 2.69
698 716 5.876460 CCAGTGATCATCATAGTTGTGTGAA 59.124 40.000 0.00 0.00 0.00 3.18
725 743 4.372656 GGATCTTCATGACCTAAGAACCG 58.627 47.826 0.00 0.00 35.69 4.44
726 744 4.099573 TCGGATCTTCATGACCTAAGAACC 59.900 45.833 10.10 10.10 39.83 3.62
727 745 5.263968 TCGGATCTTCATGACCTAAGAAC 57.736 43.478 0.00 0.00 35.47 3.01
728 746 4.342378 CCTCGGATCTTCATGACCTAAGAA 59.658 45.833 0.00 0.00 35.47 2.52
729 747 3.891977 CCTCGGATCTTCATGACCTAAGA 59.108 47.826 0.00 0.00 36.24 2.10
731 749 3.637229 GACCTCGGATCTTCATGACCTAA 59.363 47.826 0.00 0.00 0.00 2.69
732 750 3.223435 GACCTCGGATCTTCATGACCTA 58.777 50.000 0.00 0.00 0.00 3.08
828 872 2.082231 GTTCTAGGGTTTTCCTTCGGC 58.918 52.381 0.00 0.00 45.47 5.54
830 874 4.319261 CGTTTGTTCTAGGGTTTTCCTTCG 60.319 45.833 0.00 0.00 45.47 3.79
831 875 4.556104 GCGTTTGTTCTAGGGTTTTCCTTC 60.556 45.833 0.00 0.00 45.47 3.46
832 876 3.317149 GCGTTTGTTCTAGGGTTTTCCTT 59.683 43.478 0.00 0.00 45.47 3.36
835 879 3.562557 TCAGCGTTTGTTCTAGGGTTTTC 59.437 43.478 0.00 0.00 0.00 2.29
839 883 2.301870 TGATCAGCGTTTGTTCTAGGGT 59.698 45.455 0.00 0.00 0.00 4.34
842 886 3.849911 TCCTGATCAGCGTTTGTTCTAG 58.150 45.455 17.76 0.00 0.00 2.43
843 887 3.258372 ACTCCTGATCAGCGTTTGTTCTA 59.742 43.478 17.76 0.00 0.00 2.10
845 889 2.417719 ACTCCTGATCAGCGTTTGTTC 58.582 47.619 17.76 0.00 0.00 3.18
846 890 2.550830 ACTCCTGATCAGCGTTTGTT 57.449 45.000 17.76 0.00 0.00 2.83
847 891 3.895232 ATACTCCTGATCAGCGTTTGT 57.105 42.857 17.76 12.04 0.00 2.83
851 895 6.407202 AGTTAAAAATACTCCTGATCAGCGT 58.593 36.000 17.76 17.16 0.00 5.07
887 931 7.435068 AGCGAACAGTTCAAATTAGTATGTT 57.565 32.000 13.82 0.00 32.46 2.71
888 932 7.435068 AAGCGAACAGTTCAAATTAGTATGT 57.565 32.000 13.82 0.00 0.00 2.29
889 933 8.728088 AAAAGCGAACAGTTCAAATTAGTATG 57.272 30.769 13.82 0.00 0.00 2.39
890 934 8.784043 AGAAAAGCGAACAGTTCAAATTAGTAT 58.216 29.630 13.82 0.00 0.00 2.12
926 1040 2.205074 GACCCACACATAGCTCATTCG 58.795 52.381 0.00 0.00 0.00 3.34
927 1041 2.205074 CGACCCACACATAGCTCATTC 58.795 52.381 0.00 0.00 0.00 2.67
928 1042 1.134401 CCGACCCACACATAGCTCATT 60.134 52.381 0.00 0.00 0.00 2.57
929 1043 0.465705 CCGACCCACACATAGCTCAT 59.534 55.000 0.00 0.00 0.00 2.90
931 1045 0.249398 AACCGACCCACACATAGCTC 59.751 55.000 0.00 0.00 0.00 4.09
932 1046 0.249398 GAACCGACCCACACATAGCT 59.751 55.000 0.00 0.00 0.00 3.32
933 1047 0.249398 AGAACCGACCCACACATAGC 59.751 55.000 0.00 0.00 0.00 2.97
934 1048 2.742053 CAAAGAACCGACCCACACATAG 59.258 50.000 0.00 0.00 0.00 2.23
935 1049 2.551287 CCAAAGAACCGACCCACACATA 60.551 50.000 0.00 0.00 0.00 2.29
936 1050 1.604604 CAAAGAACCGACCCACACAT 58.395 50.000 0.00 0.00 0.00 3.21
937 1051 0.464735 CCAAAGAACCGACCCACACA 60.465 55.000 0.00 0.00 0.00 3.72
938 1052 0.464916 ACCAAAGAACCGACCCACAC 60.465 55.000 0.00 0.00 0.00 3.82
1470 2826 1.089112 CACGAGCAATCAAGGATGCA 58.911 50.000 0.00 0.00 0.00 3.96
1480 2836 8.314021 TCAATCATAGGATATTACACGAGCAAT 58.686 33.333 0.00 0.00 32.09 3.56
1514 2890 1.610554 GCAGGGGATTTGTGCTGCAT 61.611 55.000 5.27 0.00 37.71 3.96
1521 2897 0.899717 AACGCATGCAGGGGATTTGT 60.900 50.000 22.86 0.41 33.80 2.83
1748 3124 3.054802 AGAGTGGGAAAATACCTGCTCAG 60.055 47.826 0.00 0.00 35.22 3.35
1784 3177 4.116961 CTGCCATTGCTATTTGTCCATTG 58.883 43.478 0.00 0.00 38.71 2.82
1791 3184 5.122554 TGAATTTTGCTGCCATTGCTATTTG 59.877 36.000 0.00 0.00 38.71 2.32
1794 3187 4.081309 AGTGAATTTTGCTGCCATTGCTAT 60.081 37.500 0.00 0.00 38.71 2.97
1850 3244 8.088981 CACTACACTAGTAAGACCAAGTTTGAT 58.911 37.037 10.57 0.00 37.23 2.57
1955 3349 5.576447 TCAGTATTGAGTTGCGATCAGTA 57.424 39.130 0.00 0.00 0.00 2.74
1956 3350 4.456280 TCAGTATTGAGTTGCGATCAGT 57.544 40.909 0.00 0.00 0.00 3.41
1957 3351 4.147826 CGATCAGTATTGAGTTGCGATCAG 59.852 45.833 0.00 0.00 36.61 2.90
1958 3352 4.044426 CGATCAGTATTGAGTTGCGATCA 58.956 43.478 0.00 0.00 36.61 2.92
1959 3353 3.121194 GCGATCAGTATTGAGTTGCGATC 60.121 47.826 0.00 0.00 36.61 3.69
1960 3354 2.797156 GCGATCAGTATTGAGTTGCGAT 59.203 45.455 0.00 0.00 36.61 4.58
1961 3355 2.193447 GCGATCAGTATTGAGTTGCGA 58.807 47.619 0.00 0.00 36.61 5.10
1962 3356 1.926510 TGCGATCAGTATTGAGTTGCG 59.073 47.619 0.00 0.00 36.61 4.85
1963 3357 3.372206 AGTTGCGATCAGTATTGAGTTGC 59.628 43.478 0.00 0.00 36.61 4.17
1964 3358 4.259570 CGAGTTGCGATCAGTATTGAGTTG 60.260 45.833 0.00 0.00 44.57 3.16
1965 3359 3.859961 CGAGTTGCGATCAGTATTGAGTT 59.140 43.478 0.00 0.00 44.57 3.01
1966 3360 3.128764 TCGAGTTGCGATCAGTATTGAGT 59.871 43.478 0.00 0.00 45.59 3.41
1967 3361 3.695816 TCGAGTTGCGATCAGTATTGAG 58.304 45.455 0.00 0.00 45.59 3.02
1968 3362 3.775661 TCGAGTTGCGATCAGTATTGA 57.224 42.857 0.00 0.00 45.59 2.57
2046 3440 7.948278 AGATCGTACAGGTTTATTTAGCATC 57.052 36.000 0.00 0.00 0.00 3.91
2066 3460 8.531146 TCATGTTAAAAATTCCCCTTCAAGATC 58.469 33.333 0.00 0.00 0.00 2.75
2586 4457 1.298953 ATAGGAAGGAAGCAGCCCAA 58.701 50.000 0.00 0.00 0.00 4.12
2738 4609 4.006319 GGATGTCTCTTTTCTTGGAGGTG 58.994 47.826 0.00 0.00 0.00 4.00
2832 4703 7.209475 CCATCCTTTTCAACACAAATAACACT 58.791 34.615 0.00 0.00 0.00 3.55
2918 4789 3.370840 TCAGCTGCAATCCAAATACCT 57.629 42.857 9.47 0.00 0.00 3.08
3171 5042 5.659440 AGTGGTATAAAACTTTGCCCATG 57.341 39.130 0.00 0.00 0.00 3.66
3327 5201 9.709495 AAAATACAATGTGTGCTGATTAACAAT 57.291 25.926 0.00 0.00 0.00 2.71
3368 5374 7.648039 ACCAAATTACAAGTGTAAGGACAAA 57.352 32.000 12.48 0.00 42.94 2.83
3369 5375 7.648039 AACCAAATTACAAGTGTAAGGACAA 57.352 32.000 12.48 0.00 42.94 3.18
3370 5376 7.994334 ACTAACCAAATTACAAGTGTAAGGACA 59.006 33.333 12.48 2.65 42.94 4.02
3371 5377 8.387190 ACTAACCAAATTACAAGTGTAAGGAC 57.613 34.615 12.48 0.00 42.94 3.85
3372 5378 8.434392 AGACTAACCAAATTACAAGTGTAAGGA 58.566 33.333 12.48 0.00 42.94 3.36
3373 5379 8.617290 AGACTAACCAAATTACAAGTGTAAGG 57.383 34.615 9.58 7.88 42.94 2.69
3400 5406 9.950496 AGATAAAATCTCTGTGAGCTTCTAAAA 57.050 29.630 0.00 0.00 33.42 1.52
3407 5413 9.979578 CAGTTATAGATAAAATCTCTGTGAGCT 57.020 33.333 0.00 0.00 40.76 4.09
3408 5414 9.202273 CCAGTTATAGATAAAATCTCTGTGAGC 57.798 37.037 0.00 0.00 40.76 4.26
3422 5428 9.868160 TCAGAGAGAACATTCCAGTTATAGATA 57.132 33.333 0.00 0.00 0.00 1.98
3423 5429 8.774546 TCAGAGAGAACATTCCAGTTATAGAT 57.225 34.615 0.00 0.00 0.00 1.98
3424 5430 8.055790 TCTCAGAGAGAACATTCCAGTTATAGA 58.944 37.037 0.00 0.00 35.59 1.98
3425 5431 8.231692 TCTCAGAGAGAACATTCCAGTTATAG 57.768 38.462 0.00 0.00 35.59 1.31
3426 5432 8.231692 CTCTCAGAGAGAACATTCCAGTTATA 57.768 38.462 21.55 0.00 45.07 0.98
3427 5433 7.111247 CTCTCAGAGAGAACATTCCAGTTAT 57.889 40.000 21.55 0.00 45.07 1.89
3428 5434 6.522625 CTCTCAGAGAGAACATTCCAGTTA 57.477 41.667 21.55 0.00 45.07 2.24
3429 5435 5.404466 CTCTCAGAGAGAACATTCCAGTT 57.596 43.478 21.55 0.00 45.07 3.16
3443 5449 1.543802 ACAACGCCTTCTCTCTCAGAG 59.456 52.381 0.00 0.00 43.64 3.35
3444 5450 1.621992 ACAACGCCTTCTCTCTCAGA 58.378 50.000 0.00 0.00 0.00 3.27
3445 5451 2.447244 AACAACGCCTTCTCTCTCAG 57.553 50.000 0.00 0.00 0.00 3.35
3446 5452 4.021456 TGATTAACAACGCCTTCTCTCTCA 60.021 41.667 0.00 0.00 0.00 3.27
3447 5453 4.495422 TGATTAACAACGCCTTCTCTCTC 58.505 43.478 0.00 0.00 0.00 3.20
3448 5454 4.499183 CTGATTAACAACGCCTTCTCTCT 58.501 43.478 0.00 0.00 0.00 3.10
3449 5455 3.062774 GCTGATTAACAACGCCTTCTCTC 59.937 47.826 0.00 0.00 0.00 3.20
3450 5456 3.003480 GCTGATTAACAACGCCTTCTCT 58.997 45.455 0.00 0.00 0.00 3.10
3451 5457 2.742053 TGCTGATTAACAACGCCTTCTC 59.258 45.455 0.00 0.00 0.00 2.87
3452 5458 2.484264 GTGCTGATTAACAACGCCTTCT 59.516 45.455 0.00 0.00 0.00 2.85
3453 5459 2.225491 TGTGCTGATTAACAACGCCTTC 59.775 45.455 0.00 0.00 0.00 3.46
3454 5460 2.031157 GTGTGCTGATTAACAACGCCTT 60.031 45.455 0.00 0.00 0.00 4.35
3455 5461 1.535462 GTGTGCTGATTAACAACGCCT 59.465 47.619 0.00 0.00 0.00 5.52
3456 5462 1.265635 TGTGTGCTGATTAACAACGCC 59.734 47.619 0.00 0.00 0.00 5.68
3457 5463 2.679355 TGTGTGCTGATTAACAACGC 57.321 45.000 0.00 0.00 0.00 4.84
3458 5464 4.536065 ACAATGTGTGCTGATTAACAACG 58.464 39.130 0.00 0.00 0.00 4.10
3459 5465 8.519492 AAATACAATGTGTGCTGATTAACAAC 57.481 30.769 0.00 0.00 0.00 3.32
3460 5466 8.976471 CAAAATACAATGTGTGCTGATTAACAA 58.024 29.630 0.00 0.00 0.00 2.83
3461 5467 8.355913 TCAAAATACAATGTGTGCTGATTAACA 58.644 29.630 0.00 0.00 0.00 2.41
3462 5468 8.741101 TCAAAATACAATGTGTGCTGATTAAC 57.259 30.769 0.00 0.00 0.00 2.01
3463 5469 8.028354 CCTCAAAATACAATGTGTGCTGATTAA 58.972 33.333 0.00 0.00 0.00 1.40
3464 5470 7.362834 CCCTCAAAATACAATGTGTGCTGATTA 60.363 37.037 0.00 0.00 0.00 1.75
3465 5471 6.392354 CCTCAAAATACAATGTGTGCTGATT 58.608 36.000 0.00 0.00 0.00 2.57
3466 5472 5.105635 CCCTCAAAATACAATGTGTGCTGAT 60.106 40.000 0.00 0.00 0.00 2.90
3467 5473 4.218200 CCCTCAAAATACAATGTGTGCTGA 59.782 41.667 0.00 0.00 0.00 4.26
3468 5474 4.487948 CCCTCAAAATACAATGTGTGCTG 58.512 43.478 0.00 0.00 0.00 4.41
3469 5475 3.056607 GCCCTCAAAATACAATGTGTGCT 60.057 43.478 0.00 0.00 0.00 4.40
3470 5476 3.253230 GCCCTCAAAATACAATGTGTGC 58.747 45.455 0.00 0.00 0.00 4.57
3471 5477 4.517952 TGCCCTCAAAATACAATGTGTG 57.482 40.909 0.00 0.00 0.00 3.82
3472 5478 5.543507 TTTGCCCTCAAAATACAATGTGT 57.456 34.783 0.00 0.00 39.08 3.72
3483 5489 6.836242 AGGACAATTTTATTTTGCCCTCAAA 58.164 32.000 0.00 0.00 32.17 2.69
3484 5490 6.432403 AGGACAATTTTATTTTGCCCTCAA 57.568 33.333 0.00 0.00 32.17 3.02
3485 5491 6.432403 AAGGACAATTTTATTTTGCCCTCA 57.568 33.333 0.00 0.00 36.11 3.86
3486 5492 8.717821 GTTTAAGGACAATTTTATTTTGCCCTC 58.282 33.333 0.00 0.00 36.11 4.30
3487 5493 8.436778 AGTTTAAGGACAATTTTATTTTGCCCT 58.563 29.630 0.00 0.00 38.43 5.19
3488 5494 8.615878 AGTTTAAGGACAATTTTATTTTGCCC 57.384 30.769 0.00 0.00 0.00 5.36
3489 5495 9.877137 CAAGTTTAAGGACAATTTTATTTTGCC 57.123 29.630 0.00 0.00 0.00 4.52
3498 5504 9.471084 CCGAAATTACAAGTTTAAGGACAATTT 57.529 29.630 0.00 0.00 0.00 1.82
3499 5505 8.635328 ACCGAAATTACAAGTTTAAGGACAATT 58.365 29.630 0.00 0.00 0.00 2.32
3522 5528 4.692625 AGTGATTCTGATGACTTTGAACCG 59.307 41.667 0.00 0.00 0.00 4.44
3577 5583 7.657023 AAAGGTACTACACGGAAAGATCTAT 57.343 36.000 0.00 0.00 38.49 1.98
3616 5622 0.250510 TGCCATGGTTAGCACGAACA 60.251 50.000 14.67 0.00 33.08 3.18
3712 5718 7.394923 CACCTTGTGGGGTTATGTCTAAAATTA 59.605 37.037 0.00 0.00 37.52 1.40
3714 5720 5.714806 CACCTTGTGGGGTTATGTCTAAAAT 59.285 40.000 0.00 0.00 37.52 1.82
3777 5783 0.806868 CAATCATGAGTGCCAAGCGT 59.193 50.000 10.61 0.00 0.00 5.07
3904 5910 3.214328 GAAGCCCTGTGAAGTTTCTTCA 58.786 45.455 7.92 7.92 0.00 3.02
3975 5981 1.605058 GGTCTGCTAGCCGAACCAGA 61.605 60.000 19.78 9.98 32.35 3.86
4000 6006 3.181450 GCACAGGCTTCCATCCTACTTAT 60.181 47.826 0.00 0.00 36.96 1.73
4016 6022 0.258484 TACCATGGGATTGGCACAGG 59.742 55.000 18.09 0.00 42.39 4.00
4053 6059 3.250040 GTGTTGTGTTGTGTATGTCCCTC 59.750 47.826 0.00 0.00 0.00 4.30
4081 6087 3.666274 TGGTTTCGATAATGTGTTCCGT 58.334 40.909 0.00 0.00 0.00 4.69
4082 6088 4.570772 AGATGGTTTCGATAATGTGTTCCG 59.429 41.667 0.00 0.00 0.00 4.30
4155 6161 7.915397 CACCTGGTTATTTCTGTATTGTATTGC 59.085 37.037 0.00 0.00 0.00 3.56
4156 6162 7.915397 GCACCTGGTTATTTCTGTATTGTATTG 59.085 37.037 0.00 0.00 0.00 1.90
4157 6163 7.613801 TGCACCTGGTTATTTCTGTATTGTATT 59.386 33.333 0.00 0.00 0.00 1.89
4158 6164 7.116075 TGCACCTGGTTATTTCTGTATTGTAT 58.884 34.615 0.00 0.00 0.00 2.29
4159 6165 6.477253 TGCACCTGGTTATTTCTGTATTGTA 58.523 36.000 0.00 0.00 0.00 2.41
4280 6286 8.219105 CGCAAGTTTAATTTCGTCTTAGTTAGT 58.781 33.333 0.00 0.00 0.00 2.24
4313 6319 2.533942 TCATATCGTCGCGTGTCAATTG 59.466 45.455 5.77 0.00 0.00 2.32
4326 6332 4.405680 TGGGTTTCAGTCTGATCATATCGT 59.594 41.667 2.68 0.00 0.00 3.73
4332 6338 1.351017 GGGTGGGTTTCAGTCTGATCA 59.649 52.381 2.68 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.