Multiple sequence alignment - TraesCS5B01G522900

Loading Multiple Alignment...

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 TraesCS5B01G522900 chr5B 100.000 5111 0 0 1 5111 684226924 684232034 0.000000e+00 9439.0
1 TraesCS5B01G522900 chr4A 93.260 2196 104 23 659 2820 626443760 626441575 0.000000e+00 3195.0
2 TraesCS5B01G522900 chr4A 92.907 1861 87 20 3052 4878 626440894 626439045 0.000000e+00 2663.0
3 TraesCS5B01G522900 chr4A 91.935 124 9 1 2936 3059 626441429 626441307 6.800000e-39 172.0
4 TraesCS5B01G522900 chr5D 93.336 2176 88 33 2860 5000 542591627 542593780 0.000000e+00 3162.0
5 TraesCS5B01G522900 chr5D 94.290 1261 41 11 659 1888 542589393 542590653 0.000000e+00 1901.0
6 TraesCS5B01G522900 chr5D 95.169 890 28 8 1916 2801 542590645 542591523 0.000000e+00 1391.0
7 TraesCS5B01G522900 chr5D 89.414 614 62 3 16 628 542588536 542589147 0.000000e+00 771.0
8 TraesCS5B01G522900 chr5D 77.709 646 118 21 1 628 336241596 336240959 6.250000e-99 372.0
9 TraesCS5B01G522900 chr5D 77.090 646 122 21 1 628 336336809 336337446 2.930000e-92 350.0
10 TraesCS5B01G522900 chr5D 78.413 542 99 16 85 620 385127888 385127359 2.280000e-88 337.0
11 TraesCS5B01G522900 chr5D 88.785 107 11 1 5006 5111 542596179 542596285 4.150000e-26 130.0
12 TraesCS5B01G522900 chr5D 87.037 54 6 1 5006 5058 337684631 337684684 5.530000e-05 60.2
13 TraesCS5B01G522900 chr2B 78.145 636 109 21 1 610 95989701 95989070 1.340000e-100 377.0
14 TraesCS5B01G522900 chr2B 78.145 636 109 21 1 610 95998007 95997376 1.340000e-100 377.0
15 TraesCS5B01G522900 chr2B 78.179 637 107 23 1 610 96006371 96005740 1.340000e-100 377.0
16 TraesCS5B01G522900 chr2B 79.096 531 101 10 86 610 96023192 96022666 1.750000e-94 357.0
17 TraesCS5B01G522900 chr2B 78.112 466 82 16 1 446 788854153 788854618 1.400000e-70 278.0
18 TraesCS5B01G522900 chr2B 77.155 232 45 6 3708 3938 598561972 598562196 1.490000e-25 128.0
19 TraesCS5B01G522900 chr2B 80.392 102 18 2 1778 1878 598561608 598561708 5.490000e-10 76.8
20 TraesCS5B01G522900 chr3D 77.554 646 125 8 3 628 48793503 48792858 6.250000e-99 372.0
21 TraesCS5B01G522900 chr3A 76.667 630 107 24 1 609 673891263 673890653 3.840000e-81 313.0
22 TraesCS5B01G522900 chr7B 81.633 294 34 9 1120 1396 708061938 708062228 5.150000e-55 226.0
23 TraesCS5B01G522900 chr3B 76.282 468 86 19 1 444 630875478 630875012 5.150000e-55 226.0
24 TraesCS5B01G522900 chr2A 82.099 162 27 2 3708 3868 653001372 653001532 2.480000e-28 137.0
25 TraesCS5B01G522900 chr2A 80.392 102 18 2 1778 1878 653001008 653001108 5.490000e-10 76.8
26 TraesCS5B01G522900 chr2D 80.864 162 29 2 3708 3868 509230534 509230694 5.370000e-25 126.0
27 TraesCS5B01G522900 chr2D 87.059 85 8 3 2 83 540304723 540304807 5.450000e-15 93.5
28 TraesCS5B01G522900 chr2D 80.392 102 18 2 1778 1878 509230170 509230270 5.490000e-10 76.8
29 TraesCS5B01G522900 chr7D 86.364 66 3 4 4996 5057 593933618 593933681 3.300000e-07 67.6
30 TraesCS5B01G522900 chr1A 76.667 120 20 7 1805 1920 339914851 339914736 5.530000e-05 60.2
31 TraesCS5B01G522900 chr1D 86.538 52 5 2 1793 1843 260589278 260589328 7.150000e-04 56.5


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 TraesCS5B01G522900 chr5B 684226924 684232034 5110 False 9439 9439 100.000000 1 5111 1 chr5B.!!$F1 5110
1 TraesCS5B01G522900 chr4A 626439045 626443760 4715 True 2010 3195 92.700667 659 4878 3 chr4A.!!$R1 4219
2 TraesCS5B01G522900 chr5D 542588536 542596285 7749 False 1471 3162 92.198800 16 5111 5 chr5D.!!$F3 5095
3 TraesCS5B01G522900 chr5D 336240959 336241596 637 True 372 372 77.709000 1 628 1 chr5D.!!$R1 627
4 TraesCS5B01G522900 chr5D 336336809 336337446 637 False 350 350 77.090000 1 628 1 chr5D.!!$F1 627
5 TraesCS5B01G522900 chr5D 385127359 385127888 529 True 337 337 78.413000 85 620 1 chr5D.!!$R2 535
6 TraesCS5B01G522900 chr2B 95989070 95989701 631 True 377 377 78.145000 1 610 1 chr2B.!!$R1 609
7 TraesCS5B01G522900 chr2B 95997376 95998007 631 True 377 377 78.145000 1 610 1 chr2B.!!$R2 609
8 TraesCS5B01G522900 chr2B 96005740 96006371 631 True 377 377 78.179000 1 610 1 chr2B.!!$R3 609
9 TraesCS5B01G522900 chr2B 96022666 96023192 526 True 357 357 79.096000 86 610 1 chr2B.!!$R4 524
10 TraesCS5B01G522900 chr3D 48792858 48793503 645 True 372 372 77.554000 3 628 1 chr3D.!!$R1 625
11 TraesCS5B01G522900 chr3A 673890653 673891263 610 True 313 313 76.667000 1 609 1 chr3A.!!$R1 608

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
763 1009 0.035317 AGCGTCTTTCATGGCAGACA 59.965 50.000 19.32 0.0 39.64 3.41 F
2257 2553 0.109735 GCGAGCATGCATCATCATGG 60.110 55.000 21.98 0.0 42.97 3.66 F
2707 3009 1.207593 GATGCACCGCACACACTTC 59.792 57.895 0.00 0.0 43.04 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2677 0.037419 ATGCATGGGACCAAAAACGC 60.037 50.0 0.00 0.0 0.0 4.84 R
3237 4026 1.484444 AAGAGACCAGACCAGGCCAC 61.484 60.0 5.01 0.0 0.0 5.01 R
4288 5088 0.104304 ACCACCGCTTATTAGGCTCG 59.896 55.0 0.00 0.0 0.0 5.03 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
161 183 3.191581 CACAGTATAGATCGAGCCGGATT 59.808 47.826 5.05 0.00 0.00 3.01
165 187 0.318699 TAGATCGAGCCGGATTTGCG 60.319 55.000 5.05 0.00 0.00 4.85
193 215 0.249911 GAGCTGTCCAACCTGTCGTT 60.250 55.000 0.00 0.00 33.90 3.85
212 240 0.693049 TTGTCCTTCTCCTCCTTGGC 59.307 55.000 0.00 0.00 35.26 4.52
243 271 3.936203 TGGCACAGACCACCCGAC 61.936 66.667 0.00 0.00 33.75 4.79
287 315 0.462581 TATTCCTCCGCTGCTGCTTG 60.463 55.000 14.03 4.92 36.97 4.01
353 381 1.522092 CTCCGCATTAGCCACCTCA 59.478 57.895 0.00 0.00 37.52 3.86
407 436 1.589414 CCACCCTCATCCTCTCCTTT 58.411 55.000 0.00 0.00 0.00 3.11
427 456 1.369692 CAAGGCGGACACACCAGTA 59.630 57.895 0.00 0.00 38.90 2.74
448 477 3.431415 ACTGGTAGCACACATACTCTGA 58.569 45.455 0.00 0.00 0.00 3.27
454 483 1.067846 GCACACATACTCTGACGGACA 60.068 52.381 0.00 0.00 0.00 4.02
463 493 3.162666 ACTCTGACGGACAACTAATGGA 58.837 45.455 0.00 0.00 0.00 3.41
483 513 3.435275 GAAAAGGGAGATTGGAAGGCTT 58.565 45.455 0.00 0.00 0.00 4.35
551 581 2.126071 CCGACGCAATGGACTCGT 60.126 61.111 0.00 0.00 39.33 4.18
597 628 1.668101 GCGATGTCCTCTCGGGAGTT 61.668 60.000 12.26 0.00 46.10 3.01
621 652 0.596082 AGTGCAATACAAACGGCCAC 59.404 50.000 2.24 0.00 0.00 5.01
635 666 2.743928 CCACTGGCTCGTTGGCTC 60.744 66.667 6.35 0.00 42.34 4.70
638 844 2.125350 CTGGCTCGTTGGCTCCTC 60.125 66.667 6.35 0.00 42.34 3.71
763 1009 0.035317 AGCGTCTTTCATGGCAGACA 59.965 50.000 19.32 0.00 39.64 3.41
792 1064 1.004927 GTCTGCGCGGTCACATTTATC 60.005 52.381 17.37 0.00 0.00 1.75
793 1065 0.304705 CTGCGCGGTCACATTTATCC 59.695 55.000 8.83 0.00 0.00 2.59
795 1067 0.944386 GCGCGGTCACATTTATCCAT 59.056 50.000 8.83 0.00 0.00 3.41
796 1068 1.333619 GCGCGGTCACATTTATCCATT 59.666 47.619 8.83 0.00 0.00 3.16
797 1069 2.223479 GCGCGGTCACATTTATCCATTT 60.223 45.455 8.83 0.00 0.00 2.32
799 1071 4.320202 GCGCGGTCACATTTATCCATTTAT 60.320 41.667 8.83 0.00 0.00 1.40
800 1072 5.106869 GCGCGGTCACATTTATCCATTTATA 60.107 40.000 8.83 0.00 0.00 0.98
801 1073 6.534059 CGCGGTCACATTTATCCATTTATAG 58.466 40.000 0.00 0.00 0.00 1.31
804 1076 7.621426 GCGGTCACATTTATCCATTTATAGACG 60.621 40.741 0.00 0.00 0.00 4.18
805 1077 7.148639 CGGTCACATTTATCCATTTATAGACGG 60.149 40.741 0.00 0.00 0.00 4.79
806 1078 7.876068 GGTCACATTTATCCATTTATAGACGGA 59.124 37.037 0.00 0.00 0.00 4.69
807 1079 8.926710 GTCACATTTATCCATTTATAGACGGAG 58.073 37.037 0.00 0.00 0.00 4.63
934 1227 4.462417 CTCTTCTCGGTCGCGCGT 62.462 66.667 30.98 0.00 0.00 6.01
976 1269 1.225376 CGACAGCAAACACCGGCTAA 61.225 55.000 0.00 0.00 38.56 3.09
1707 2000 0.393402 TCTTCCTGCTCGCCTACGTA 60.393 55.000 0.00 0.00 41.18 3.57
1917 2210 1.041437 CCGGAGTCCTTATCCAGACC 58.959 60.000 7.77 0.00 36.57 3.85
1999 2295 8.966069 AAGAATAAGATTAGGAAACACTAGCC 57.034 34.615 0.00 0.00 0.00 3.93
2000 2296 7.510407 AGAATAAGATTAGGAAACACTAGCCC 58.490 38.462 0.00 0.00 0.00 5.19
2036 2332 5.580691 GGTGTCAACTTTCCAAAAGGAAAAG 59.419 40.000 10.55 7.66 37.41 2.27
2098 2394 6.506147 TGTCATCAACTTTCCACAAAGAATG 58.494 36.000 1.50 3.30 41.60 2.67
2239 2535 3.829948 CTGGTGATGATGAGTTTGTTGC 58.170 45.455 0.00 0.00 0.00 4.17
2256 2552 0.591170 TGCGAGCATGCATCATCATG 59.409 50.000 21.98 3.04 44.93 3.07
2257 2553 0.109735 GCGAGCATGCATCATCATGG 60.110 55.000 21.98 0.00 42.97 3.66
2330 2628 3.409026 TTCTGGTGCTCTCTTTCCTTC 57.591 47.619 0.00 0.00 0.00 3.46
2364 2662 3.763360 CCTTCTGTTTTGCATGATACCCA 59.237 43.478 0.00 0.00 0.00 4.51
2379 2677 5.364778 TGATACCCAACCGATATTCACTTG 58.635 41.667 0.00 0.00 0.00 3.16
2592 2893 5.383130 GGTTCTTTAACACTTCGAAGATGC 58.617 41.667 31.08 9.72 37.34 3.91
2649 2950 3.657634 CTGCTTTGAGCTACTCTTGTCA 58.342 45.455 1.29 0.00 42.97 3.58
2707 3009 1.207593 GATGCACCGCACACACTTC 59.792 57.895 0.00 0.00 43.04 3.01
2782 3084 6.593382 GCAAAATAAATGTTGCCATACTTCCA 59.407 34.615 6.59 0.00 43.49 3.53
2802 3104 8.403606 CTTCCATTGAAGCACAAAATATCTTC 57.596 34.615 0.00 0.00 41.45 2.87
2804 3106 6.044682 CCATTGAAGCACAAAATATCTTCCC 58.955 40.000 0.86 0.00 42.03 3.97
2837 3203 5.239525 GCTGCTACCTACATATTTTCCTTGG 59.760 44.000 0.00 0.00 0.00 3.61
2849 3215 8.052748 ACATATTTTCCTTGGCTACATACTTCA 58.947 33.333 0.00 0.00 0.00 3.02
2850 3216 8.902806 CATATTTTCCTTGGCTACATACTTCAA 58.097 33.333 0.00 0.00 0.00 2.69
2851 3217 7.961326 ATTTTCCTTGGCTACATACTTCAAT 57.039 32.000 0.00 0.00 0.00 2.57
2852 3218 7.775053 TTTTCCTTGGCTACATACTTCAATT 57.225 32.000 0.00 0.00 0.00 2.32
2853 3219 7.775053 TTTCCTTGGCTACATACTTCAATTT 57.225 32.000 0.00 0.00 0.00 1.82
2854 3220 7.391148 TTCCTTGGCTACATACTTCAATTTC 57.609 36.000 0.00 0.00 0.00 2.17
2855 3221 5.584649 TCCTTGGCTACATACTTCAATTTCG 59.415 40.000 0.00 0.00 0.00 3.46
2856 3222 5.220854 CCTTGGCTACATACTTCAATTTCGG 60.221 44.000 0.00 0.00 0.00 4.30
2857 3223 4.839121 TGGCTACATACTTCAATTTCGGT 58.161 39.130 0.00 0.00 0.00 4.69
2858 3224 4.634004 TGGCTACATACTTCAATTTCGGTG 59.366 41.667 0.00 0.00 0.00 4.94
2875 3241 5.936187 TCGGTGAATTTGGGTACATACTA 57.064 39.130 0.00 0.00 0.00 1.82
2980 3346 3.313249 CGGGTAAACGGAATATTTGGACC 59.687 47.826 0.00 0.00 0.00 4.46
2988 3354 6.613755 ACGGAATATTTGGACCGAATTAAG 57.386 37.500 17.44 3.59 46.94 1.85
3046 3412 5.671493 ACGTATATTCTGAGTCCCAAAAGG 58.329 41.667 0.00 0.00 0.00 3.11
3130 3916 4.931027 TTACCCCAGGTAAAATAGTGCA 57.069 40.909 3.73 0.00 44.06 4.57
3142 3928 6.640907 GGTAAAATAGTGCAGGTGAAAAGTTG 59.359 38.462 0.00 0.00 0.00 3.16
3168 3954 4.854361 TTACTAGTTACAGCGACGAGAG 57.146 45.455 0.00 0.00 0.00 3.20
3188 3974 2.354821 AGACAGAAACGACAAGGTTTGC 59.645 45.455 0.00 0.00 40.05 3.68
3205 3994 3.451141 TTGCAGTGGTAAAAGCTTTGG 57.549 42.857 13.54 0.00 0.00 3.28
3229 4018 2.227626 GCTTTCTTCTTCTTCCACTGGC 59.772 50.000 0.00 0.00 0.00 4.85
3417 4206 1.294780 CTCCTCACTCCACTGTGGC 59.705 63.158 22.02 0.00 37.47 5.01
3439 4228 1.202177 ACTGTTTGTTTCTGCAGTGCG 60.202 47.619 14.67 5.62 40.24 5.34
3483 4272 4.837896 ATCGATCGATCTTGTTGAGCTA 57.162 40.909 24.60 0.00 0.00 3.32
3484 4273 4.837896 TCGATCGATCTTGTTGAGCTAT 57.162 40.909 22.43 0.00 0.00 2.97
3834 4628 1.859302 ACCTGCTCTCCTTCTACCTG 58.141 55.000 0.00 0.00 0.00 4.00
4181 4979 1.663643 TCGCGGTGACATGCTAAAATC 59.336 47.619 6.13 0.00 0.00 2.17
4188 4986 4.321899 GGTGACATGCTAAAATCAAGCCAA 60.322 41.667 0.00 0.00 39.30 4.52
4189 4987 5.229423 GTGACATGCTAAAATCAAGCCAAA 58.771 37.500 0.00 0.00 39.30 3.28
4190 4988 5.695816 GTGACATGCTAAAATCAAGCCAAAA 59.304 36.000 0.00 0.00 39.30 2.44
4225 5023 1.301009 GTAGGGCAGCCGTAGCATC 60.301 63.158 14.38 0.00 43.56 3.91
4282 5082 3.234349 AGCCACACAGCTCACAGT 58.766 55.556 0.00 0.00 39.48 3.55
4288 5088 0.740737 ACACAGCTCACAGTTTTGCC 59.259 50.000 0.00 0.00 0.00 4.52
4290 5090 0.463654 ACAGCTCACAGTTTTGCCGA 60.464 50.000 0.00 0.00 0.00 5.54
4291 5091 0.236711 CAGCTCACAGTTTTGCCGAG 59.763 55.000 0.00 0.00 32.82 4.63
4292 5092 1.081840 GCTCACAGTTTTGCCGAGC 60.082 57.895 0.00 0.00 42.40 5.03
4294 5094 0.886490 CTCACAGTTTTGCCGAGCCT 60.886 55.000 0.00 0.00 0.00 4.58
4295 5095 0.394938 TCACAGTTTTGCCGAGCCTA 59.605 50.000 0.00 0.00 0.00 3.93
4296 5096 1.202710 TCACAGTTTTGCCGAGCCTAA 60.203 47.619 0.00 0.00 0.00 2.69
4323 5142 2.462889 GTGGTGTGTTGCATTGAAGTG 58.537 47.619 0.00 0.00 0.00 3.16
4407 5230 4.115516 TGATCGAGCTAAGCAAGTTCATC 58.884 43.478 0.90 6.27 35.27 2.92
4437 5260 2.612212 CACGCACTTCCTTTTGTGTACT 59.388 45.455 0.00 0.00 34.71 2.73
4574 5397 5.107837 CGCATACGAGAAAGTTGGCTAATAG 60.108 44.000 0.00 0.00 43.93 1.73
4624 5454 0.818296 AACGTGAAGGATCGAGGAGG 59.182 55.000 0.00 0.00 0.00 4.30
4638 5468 0.037303 AGGAGGTTGCTGTGTGATGG 59.963 55.000 0.00 0.00 0.00 3.51
4639 5469 0.036732 GGAGGTTGCTGTGTGATGGA 59.963 55.000 0.00 0.00 0.00 3.41
4640 5470 1.340405 GGAGGTTGCTGTGTGATGGAT 60.340 52.381 0.00 0.00 0.00 3.41
4641 5471 1.741706 GAGGTTGCTGTGTGATGGATG 59.258 52.381 0.00 0.00 0.00 3.51
4642 5472 1.352017 AGGTTGCTGTGTGATGGATGA 59.648 47.619 0.00 0.00 0.00 2.92
4643 5473 2.025605 AGGTTGCTGTGTGATGGATGAT 60.026 45.455 0.00 0.00 0.00 2.45
4644 5474 2.357009 GGTTGCTGTGTGATGGATGATC 59.643 50.000 0.00 0.00 0.00 2.92
4645 5475 1.944032 TGCTGTGTGATGGATGATCG 58.056 50.000 0.00 0.00 33.17 3.69
4646 5476 1.224075 GCTGTGTGATGGATGATCGG 58.776 55.000 0.00 0.00 33.17 4.18
4727 5557 1.287739 TGGCTTTATGGGAAAGAGGGG 59.712 52.381 1.28 0.00 0.00 4.79
4747 5578 1.497991 GCGGCTTTGCTCGTCATATA 58.502 50.000 0.00 0.00 0.00 0.86
4748 5579 2.069273 GCGGCTTTGCTCGTCATATAT 58.931 47.619 0.00 0.00 0.00 0.86
4749 5580 2.480419 GCGGCTTTGCTCGTCATATATT 59.520 45.455 0.00 0.00 0.00 1.28
4783 5614 1.333881 CGGAGGACAACGTATCGCTAG 60.334 57.143 0.00 0.00 0.00 3.42
4889 5720 2.588620 TGGTTAAGGATGCGTTTGGTT 58.411 42.857 0.00 0.00 0.00 3.67
4941 5772 1.093159 GCTCATTTGAGTCTGGCTGG 58.907 55.000 9.21 0.00 43.85 4.85
4943 5774 1.004044 CTCATTTGAGTCTGGCTGGGT 59.996 52.381 0.00 0.00 37.40 4.51
4953 5784 2.238898 GTCTGGCTGGGTTAATGTAGGT 59.761 50.000 0.00 0.00 0.00 3.08
4960 5791 5.186992 GGCTGGGTTAATGTAGGTTGAAAAT 59.813 40.000 0.00 0.00 0.00 1.82
4976 5807 9.739276 AGGTTGAAAATCATGTTCTGTAGATTA 57.261 29.630 0.00 0.00 31.01 1.75
4986 5817 6.509418 TGTTCTGTAGATTATTTGGTTGCC 57.491 37.500 0.00 0.00 0.00 4.52
4989 5820 4.640201 TCTGTAGATTATTTGGTTGCCTGC 59.360 41.667 0.00 0.00 0.00 4.85
4990 5821 4.599041 TGTAGATTATTTGGTTGCCTGCT 58.401 39.130 0.00 0.00 0.00 4.24
5000 5831 3.988819 TGGTTGCCTGCTTATGTTTTTC 58.011 40.909 0.00 0.00 0.00 2.29
5001 5832 3.640967 TGGTTGCCTGCTTATGTTTTTCT 59.359 39.130 0.00 0.00 0.00 2.52
5002 5833 4.830046 TGGTTGCCTGCTTATGTTTTTCTA 59.170 37.500 0.00 0.00 0.00 2.10
5003 5834 5.480073 TGGTTGCCTGCTTATGTTTTTCTAT 59.520 36.000 0.00 0.00 0.00 1.98
5004 5835 6.036470 GGTTGCCTGCTTATGTTTTTCTATC 58.964 40.000 0.00 0.00 0.00 2.08
5006 5837 6.441093 TGCCTGCTTATGTTTTTCTATCAG 57.559 37.500 0.00 0.00 0.00 2.90
5007 5838 6.179756 TGCCTGCTTATGTTTTTCTATCAGA 58.820 36.000 0.00 0.00 0.00 3.27
5008 5839 6.317140 TGCCTGCTTATGTTTTTCTATCAGAG 59.683 38.462 0.00 0.00 0.00 3.35
5009 5840 6.238593 GCCTGCTTATGTTTTTCTATCAGAGG 60.239 42.308 0.00 0.00 0.00 3.69
5010 5841 6.261826 CCTGCTTATGTTTTTCTATCAGAGGG 59.738 42.308 0.00 0.00 0.00 4.30
5012 5843 7.175104 TGCTTATGTTTTTCTATCAGAGGGTT 58.825 34.615 0.00 0.00 0.00 4.11
5013 5844 7.669722 TGCTTATGTTTTTCTATCAGAGGGTTT 59.330 33.333 0.00 0.00 0.00 3.27
5014 5845 7.970614 GCTTATGTTTTTCTATCAGAGGGTTTG 59.029 37.037 0.00 0.00 0.00 2.93
5016 5847 4.522789 TGTTTTTCTATCAGAGGGTTTGCC 59.477 41.667 0.00 0.00 0.00 4.52
5017 5848 4.657814 TTTTCTATCAGAGGGTTTGCCT 57.342 40.909 0.00 0.00 34.45 4.75
5018 5849 3.914426 TTCTATCAGAGGGTTTGCCTC 57.086 47.619 0.00 0.00 34.45 4.70
5019 5850 3.121929 TCTATCAGAGGGTTTGCCTCT 57.878 47.619 0.00 0.00 44.41 3.69
5061 8286 0.875059 AAAAGCGAGCTACAAGCACC 59.125 50.000 0.00 0.00 45.56 5.01
5063 8288 0.250295 AAGCGAGCTACAAGCACCAA 60.250 50.000 0.00 0.00 45.56 3.67
5068 8293 3.521560 CGAGCTACAAGCACCAATCTTA 58.478 45.455 1.22 0.00 45.56 2.10
5069 8294 3.932710 CGAGCTACAAGCACCAATCTTAA 59.067 43.478 1.22 0.00 45.56 1.85
5077 8302 5.241728 ACAAGCACCAATCTTAAAAGAGGAC 59.758 40.000 5.31 0.00 38.66 3.85
5091 8316 1.000955 AGAGGACCAACAACAGCTACG 59.999 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.460261 CCGATGACATGTCTTGATGTAGTAGT 60.460 42.308 25.55 0.00 36.67 2.73
165 187 2.894387 GGACAGCTCTGGCGATGC 60.894 66.667 1.66 0.00 40.25 3.91
193 215 0.693049 GCCAAGGAGGAGAAGGACAA 59.307 55.000 0.00 0.00 41.22 3.18
237 265 2.233305 ACCTGAGAACATAGTCGGGT 57.767 50.000 0.00 0.00 45.99 5.28
243 271 1.833630 TGCCCTGACCTGAGAACATAG 59.166 52.381 0.00 0.00 0.00 2.23
287 315 2.575789 CGCGCCCGCATTGTAAAC 60.576 61.111 13.42 0.00 42.06 2.01
336 364 1.522092 CTGAGGTGGCTAATGCGGA 59.478 57.895 0.00 0.00 40.82 5.54
427 456 3.193691 GTCAGAGTATGTGTGCTACCAGT 59.806 47.826 0.00 0.00 0.00 4.00
438 467 5.394224 CCATTAGTTGTCCGTCAGAGTATGT 60.394 44.000 0.00 0.00 0.00 2.29
448 477 3.073356 TCCCTTTTCCATTAGTTGTCCGT 59.927 43.478 0.00 0.00 0.00 4.69
454 483 6.152638 TCCAATCTCCCTTTTCCATTAGTT 57.847 37.500 0.00 0.00 0.00 2.24
463 493 3.435275 GAAGCCTTCCAATCTCCCTTTT 58.565 45.455 0.00 0.00 0.00 2.27
621 652 2.125350 GAGGAGCCAACGAGCCAG 60.125 66.667 0.00 0.00 0.00 4.85
635 666 2.058595 CCACCCGACCCTACAGAGG 61.059 68.421 0.00 0.00 43.33 3.69
638 844 3.782443 GCCCACCCGACCCTACAG 61.782 72.222 0.00 0.00 0.00 2.74
657 863 4.367023 TGTGGGCAGTACGGCGTC 62.367 66.667 19.21 8.74 42.43 5.19
664 910 1.479323 GATACGAACCTGTGGGCAGTA 59.521 52.381 0.00 0.00 41.02 2.74
732 978 0.946221 AAGACGCTGCAGTTTCGAGG 60.946 55.000 16.64 0.00 0.00 4.63
792 1064 3.804036 TGGTTGCTCCGTCTATAAATGG 58.196 45.455 0.00 0.00 39.52 3.16
793 1065 5.811399 TTTGGTTGCTCCGTCTATAAATG 57.189 39.130 0.00 0.00 39.52 2.32
795 1067 4.879545 GGATTTGGTTGCTCCGTCTATAAA 59.120 41.667 0.00 0.00 39.52 1.40
796 1068 4.448210 GGATTTGGTTGCTCCGTCTATAA 58.552 43.478 0.00 0.00 39.52 0.98
797 1069 3.181458 GGGATTTGGTTGCTCCGTCTATA 60.181 47.826 0.00 0.00 39.52 1.31
799 1071 1.065709 GGGATTTGGTTGCTCCGTCTA 60.066 52.381 0.00 0.00 39.52 2.59
800 1072 0.322546 GGGATTTGGTTGCTCCGTCT 60.323 55.000 0.00 0.00 39.52 4.18
801 1073 0.608035 TGGGATTTGGTTGCTCCGTC 60.608 55.000 0.00 0.00 39.52 4.79
804 1076 1.821136 CTCTTGGGATTTGGTTGCTCC 59.179 52.381 0.00 0.00 0.00 4.70
805 1077 2.489722 GACTCTTGGGATTTGGTTGCTC 59.510 50.000 0.00 0.00 0.00 4.26
806 1078 2.158475 TGACTCTTGGGATTTGGTTGCT 60.158 45.455 0.00 0.00 0.00 3.91
807 1079 2.238521 TGACTCTTGGGATTTGGTTGC 58.761 47.619 0.00 0.00 0.00 4.17
953 1246 1.010125 CGGTGTTTGCTGTCGTTGG 60.010 57.895 0.00 0.00 0.00 3.77
976 1269 1.898574 CGCCTCTTTGTTGGCTGGT 60.899 57.895 0.00 0.00 46.42 4.00
985 1278 2.753966 CCATGTCGGCGCCTCTTTG 61.754 63.158 26.68 16.24 0.00 2.77
1233 1526 2.205074 GTGATGTTAGTGAGCCCGATG 58.795 52.381 0.00 0.00 0.00 3.84
1287 1580 2.738521 GCACAAAGCGGCTCGAGA 60.739 61.111 18.75 0.00 0.00 4.04
1537 1830 4.489771 GGTGATGCCCTGGGACCG 62.490 72.222 19.27 0.00 0.00 4.79
1818 2111 2.357517 CACCACCACTCGAGGCAC 60.358 66.667 18.41 0.00 0.00 5.01
1860 2153 2.376165 GGGGTTCTGGAGGTAGCCC 61.376 68.421 0.00 0.00 41.88 5.19
1896 2189 0.759436 TCTGGATAAGGACTCCGGCC 60.759 60.000 0.00 0.00 38.78 6.13
1899 2192 1.409427 GTGGTCTGGATAAGGACTCCG 59.591 57.143 0.00 0.00 35.41 4.63
1908 2201 0.042581 TCAGGCTGGTGGTCTGGATA 59.957 55.000 15.73 0.00 46.77 2.59
1917 2210 0.740868 CGGTGTACATCAGGCTGGTG 60.741 60.000 25.71 25.71 33.91 4.17
2000 2296 3.443045 GACACCAATGGCGGGCTG 61.443 66.667 0.00 0.00 0.00 4.85
2036 2332 8.420189 GTGTTCATTTCACGAATCAAAGATTTC 58.580 33.333 0.00 0.00 0.00 2.17
2239 2535 0.521735 CCCATGATGATGCATGCTCG 59.478 55.000 20.33 1.38 43.30 5.03
2379 2677 0.037419 ATGCATGGGACCAAAAACGC 60.037 50.000 0.00 0.00 0.00 4.84
2592 2893 1.946768 TGTCTCCCAAAAACAAGCTCG 59.053 47.619 0.00 0.00 0.00 5.03
2782 3084 6.438425 AGTGGGAAGATATTTTGTGCTTCAAT 59.562 34.615 0.00 0.00 38.72 2.57
2788 3090 8.669243 GCTATATAGTGGGAAGATATTTTGTGC 58.331 37.037 11.38 0.00 0.00 4.57
2802 3104 5.262009 TGTAGGTAGCAGCTATATAGTGGG 58.738 45.833 5.14 2.94 30.21 4.61
2837 3203 6.417191 TTCACCGAAATTGAAGTATGTAGC 57.583 37.500 0.00 0.00 0.00 3.58
2849 3215 5.993748 ATGTACCCAAATTCACCGAAATT 57.006 34.783 0.00 0.00 0.00 1.82
2850 3216 6.184789 AGTATGTACCCAAATTCACCGAAAT 58.815 36.000 0.00 0.00 0.00 2.17
2851 3217 5.562635 AGTATGTACCCAAATTCACCGAAA 58.437 37.500 0.00 0.00 0.00 3.46
2852 3218 5.168647 AGTATGTACCCAAATTCACCGAA 57.831 39.130 0.00 0.00 0.00 4.30
2853 3219 4.829872 AGTATGTACCCAAATTCACCGA 57.170 40.909 0.00 0.00 0.00 4.69
2854 3220 5.421277 TGTAGTATGTACCCAAATTCACCG 58.579 41.667 0.00 0.00 0.00 4.94
2855 3221 8.208903 AGTATGTAGTATGTACCCAAATTCACC 58.791 37.037 0.00 0.00 0.00 4.02
2856 3222 9.257651 GAGTATGTAGTATGTACCCAAATTCAC 57.742 37.037 0.00 0.00 0.00 3.18
2857 3223 9.209048 AGAGTATGTAGTATGTACCCAAATTCA 57.791 33.333 0.00 0.00 0.00 2.57
2932 3298 8.650143 ATCAGCTGGGTCTTTTTAGATAAAAA 57.350 30.769 15.13 9.49 41.36 1.94
2935 3301 6.049149 CGATCAGCTGGGTCTTTTTAGATAA 58.951 40.000 15.13 0.00 0.00 1.75
2936 3302 5.453339 CCGATCAGCTGGGTCTTTTTAGATA 60.453 44.000 15.13 0.00 0.00 1.98
2937 3303 4.446371 CGATCAGCTGGGTCTTTTTAGAT 58.554 43.478 15.13 0.00 0.00 1.98
2939 3305 2.939103 CCGATCAGCTGGGTCTTTTTAG 59.061 50.000 15.13 0.00 0.00 1.85
2940 3306 2.355716 CCCGATCAGCTGGGTCTTTTTA 60.356 50.000 15.13 0.00 40.76 1.52
2941 3307 1.614317 CCCGATCAGCTGGGTCTTTTT 60.614 52.381 15.13 0.00 40.76 1.94
2952 3318 1.949465 ATTCCGTTTACCCGATCAGC 58.051 50.000 0.00 0.00 0.00 4.26
2980 3346 6.180472 AGGGGAATATATGGCACTTAATTCG 58.820 40.000 0.00 0.00 0.00 3.34
2988 3354 7.039714 CCTTTTTCTTAGGGGAATATATGGCAC 60.040 40.741 0.00 0.00 0.00 5.01
3046 3412 0.818040 AAAGGAACGTGGGAGTGTGC 60.818 55.000 0.00 0.00 0.00 4.57
3130 3916 8.803397 AACTAGTAAAACTCAACTTTTCACCT 57.197 30.769 0.00 0.00 0.00 4.00
3142 3928 5.385617 TCGTCGCTGTAACTAGTAAAACTC 58.614 41.667 0.00 0.00 0.00 3.01
3168 3954 2.096819 TGCAAACCTTGTCGTTTCTGTC 59.903 45.455 0.00 0.00 33.69 3.51
3188 3974 3.123050 GCAACCAAAGCTTTTACCACTG 58.877 45.455 9.53 0.00 0.00 3.66
3205 3994 4.261363 CCAGTGGAAGAAGAAGAAAGCAAC 60.261 45.833 1.68 0.00 0.00 4.17
3237 4026 1.484444 AAGAGACCAGACCAGGCCAC 61.484 60.000 5.01 0.00 0.00 5.01
3439 4228 3.163630 ACACAAACACAGAAATGGTGC 57.836 42.857 0.00 0.00 39.87 5.01
4047 4841 2.040330 CCTCATCTCCTCCTGCTCG 58.960 63.158 0.00 0.00 0.00 5.03
4181 4979 3.006752 TGGAATGGCTAGTTTTTGGCTTG 59.993 43.478 0.00 0.00 0.00 4.01
4188 4986 3.418684 ACGAGTGGAATGGCTAGTTTT 57.581 42.857 0.00 0.00 0.00 2.43
4189 4987 3.118738 CCTACGAGTGGAATGGCTAGTTT 60.119 47.826 0.00 0.00 0.00 2.66
4190 4988 2.431057 CCTACGAGTGGAATGGCTAGTT 59.569 50.000 0.00 0.00 0.00 2.24
4282 5082 1.668751 CGCTTATTAGGCTCGGCAAAA 59.331 47.619 0.00 0.00 0.00 2.44
4288 5088 0.104304 ACCACCGCTTATTAGGCTCG 59.896 55.000 0.00 0.00 0.00 5.03
4290 5090 0.909623 ACACCACCGCTTATTAGGCT 59.090 50.000 0.00 0.00 0.00 4.58
4291 5091 1.014352 CACACCACCGCTTATTAGGC 58.986 55.000 0.00 0.00 0.00 3.93
4292 5092 2.396590 ACACACCACCGCTTATTAGG 57.603 50.000 0.00 0.00 0.00 2.69
4294 5094 1.807742 GCAACACACCACCGCTTATTA 59.192 47.619 0.00 0.00 0.00 0.98
4295 5095 0.596082 GCAACACACCACCGCTTATT 59.404 50.000 0.00 0.00 0.00 1.40
4296 5096 0.536233 TGCAACACACCACCGCTTAT 60.536 50.000 0.00 0.00 0.00 1.73
4323 5142 1.298859 CTCCAAGCAGCAACCGTACC 61.299 60.000 0.00 0.00 0.00 3.34
4437 5260 7.979444 AAGTGCTAATGAACTTGTTTAGCTA 57.021 32.000 13.24 0.00 45.09 3.32
4574 5397 6.876257 CAGGTTAGCATCCTATCCAAATACTC 59.124 42.308 0.00 0.00 36.34 2.59
4624 5454 2.031314 CGATCATCCATCACACAGCAAC 59.969 50.000 0.00 0.00 0.00 4.17
4638 5468 0.962489 ATCGAGACACCCCGATCATC 59.038 55.000 0.00 0.00 41.05 2.92
4639 5469 3.133437 ATCGAGACACCCCGATCAT 57.867 52.632 0.00 0.00 41.05 2.45
4640 5470 4.678423 ATCGAGACACCCCGATCA 57.322 55.556 0.00 0.00 41.05 2.92
4642 5472 0.106669 TCAGATCGAGACACCCCGAT 60.107 55.000 0.00 0.00 46.67 4.18
4643 5473 0.106669 ATCAGATCGAGACACCCCGA 60.107 55.000 0.00 0.00 39.25 5.14
4644 5474 0.312416 GATCAGATCGAGACACCCCG 59.688 60.000 0.00 0.00 0.00 5.73
4645 5475 0.676736 GGATCAGATCGAGACACCCC 59.323 60.000 4.23 0.00 0.00 4.95
4646 5476 1.339610 CAGGATCAGATCGAGACACCC 59.660 57.143 4.23 5.79 0.00 4.61
4727 5557 1.160329 ATATGACGAGCAAAGCCGCC 61.160 55.000 0.00 0.00 0.00 6.13
4747 5578 2.683475 CGCAAAGGGGAGGGGAAT 59.317 61.111 0.00 0.00 0.00 3.01
4748 5579 3.657350 CCGCAAAGGGGAGGGGAA 61.657 66.667 0.00 0.00 40.00 3.97
4749 5580 4.667935 TCCGCAAAGGGGAGGGGA 62.668 66.667 0.00 0.00 43.58 4.81
4829 5660 4.770874 GCGGGCGCAAGGTAAGGA 62.771 66.667 10.83 0.00 41.49 3.36
4889 5720 6.260050 GCAAATATGAAAGATCGGTTGAGGTA 59.740 38.462 0.00 0.00 0.00 3.08
4898 5729 6.140786 CCACTGATGCAAATATGAAAGATCG 58.859 40.000 0.00 0.00 0.00 3.69
4941 5772 9.353999 GAACATGATTTTCAACCTACATTAACC 57.646 33.333 0.00 0.00 0.00 2.85
4960 5791 7.148086 GGCAACCAAATAATCTACAGAACATGA 60.148 37.037 0.00 0.00 0.00 3.07
4976 5807 4.622260 AAACATAAGCAGGCAACCAAAT 57.378 36.364 0.00 0.00 37.17 2.32
4981 5812 6.620678 TGATAGAAAAACATAAGCAGGCAAC 58.379 36.000 0.00 0.00 0.00 4.17
4986 5817 6.825721 ACCCTCTGATAGAAAAACATAAGCAG 59.174 38.462 0.00 0.00 0.00 4.24
4989 5820 7.970614 GCAAACCCTCTGATAGAAAAACATAAG 59.029 37.037 0.00 0.00 0.00 1.73
4990 5821 7.093945 GGCAAACCCTCTGATAGAAAAACATAA 60.094 37.037 0.00 0.00 0.00 1.90
5014 5845 4.160252 TCCCTTAATGAAAATTGCAGAGGC 59.840 41.667 0.00 0.00 41.68 4.70
5016 5847 6.591448 GGTTTCCCTTAATGAAAATTGCAGAG 59.409 38.462 2.82 0.00 33.80 3.35
5017 5848 6.042552 TGGTTTCCCTTAATGAAAATTGCAGA 59.957 34.615 2.82 0.00 33.80 4.26
5018 5849 6.229733 TGGTTTCCCTTAATGAAAATTGCAG 58.770 36.000 2.82 0.00 33.80 4.41
5019 5850 6.179906 TGGTTTCCCTTAATGAAAATTGCA 57.820 33.333 2.82 0.00 33.80 4.08
5020 5851 7.503521 TTTGGTTTCCCTTAATGAAAATTGC 57.496 32.000 2.82 0.00 33.80 3.56
5021 5852 8.075574 GCTTTTGGTTTCCCTTAATGAAAATTG 58.924 33.333 2.82 0.00 33.80 2.32
5022 5853 7.041440 CGCTTTTGGTTTCCCTTAATGAAAATT 60.041 33.333 2.82 0.00 33.80 1.82
5061 8286 7.038154 TGTTGTTGGTCCTCTTTTAAGATTG 57.962 36.000 0.00 0.00 33.93 2.67
5063 8288 5.241728 GCTGTTGTTGGTCCTCTTTTAAGAT 59.758 40.000 0.00 0.00 33.93 2.40
5068 8293 3.018423 AGCTGTTGTTGGTCCTCTTTT 57.982 42.857 0.00 0.00 0.00 2.27
5069 8294 2.736670 AGCTGTTGTTGGTCCTCTTT 57.263 45.000 0.00 0.00 0.00 2.52
5077 8302 2.440539 AGTCTCGTAGCTGTTGTTGG 57.559 50.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.