Multiple sequence alignment - TraesCS5D01G535200

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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 TraesCS5D01G535200 chr5D 100.000 3773 0 0 1 3773 549263167 549259395 0.000000e+00 6968
1 TraesCS5D01G535200 chr5D 92.176 3106 147 37 665 3728 549230170 549227119 0.000000e+00 4301
2 TraesCS5D01G535200 chr5D 82.875 1635 223 35 1148 2773 549548153 549546567 0.000000e+00 1415
3 TraesCS5D01G535200 chr5D 82.127 1617 229 35 1148 2755 549430068 549428503 0.000000e+00 1330
4 TraesCS5D01G535200 chr5D 77.023 309 63 8 2127 2431 380695156 380694852 1.800000e-38 171
5 TraesCS5D01G535200 chr4A 92.416 2901 182 19 58 2938 620705699 620702817 0.000000e+00 4104
6 TraesCS5D01G535200 chr4A 90.482 788 50 12 2935 3717 620657557 620656790 0.000000e+00 1016
7 TraesCS5D01G535200 chr4A 87.059 255 28 4 3481 3733 620647381 620647130 2.220000e-72 283
8 TraesCS5D01G535200 chr5B 91.110 2261 131 22 624 2845 700857025 700854796 0.000000e+00 2998
9 TraesCS5D01G535200 chr5B 82.508 1635 231 37 1148 2773 701051702 701050114 0.000000e+00 1384
10 TraesCS5D01G535200 chr5B 88.753 898 62 12 2842 3728 700845755 700844886 0.000000e+00 1062
11 TraesCS5D01G535200 chr5B 76.774 310 64 8 2126 2431 456637949 456637644 2.330000e-37 167
12 TraesCS5D01G535200 chr7D 85.977 870 107 11 1142 1998 162823654 162822787 0.000000e+00 917
13 TraesCS5D01G535200 chr7A 85.780 872 103 15 1142 1998 163617765 163616900 0.000000e+00 904
14 TraesCS5D01G535200 chr2D 84.936 863 106 12 1148 2008 110843195 110842355 0.000000e+00 852
15 TraesCS5D01G535200 chr2B 84.820 863 107 13 1148 2008 159971028 159970188 0.000000e+00 846
16 TraesCS5D01G535200 chr2A 84.571 862 111 11 1148 2008 107182762 107181922 0.000000e+00 835
17 TraesCS5D01G535200 chr3D 78.404 639 121 15 2125 2756 426048494 426049122 2.110000e-107 399
18 TraesCS5D01G535200 chr3B 78.233 634 123 14 2129 2756 556350152 556349528 3.530000e-105 392


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 TraesCS5D01G535200 chr5D 549259395 549263167 3772 True 6968 6968 100.000 1 3773 1 chr5D.!!$R3 3772
1 TraesCS5D01G535200 chr5D 549227119 549230170 3051 True 4301 4301 92.176 665 3728 1 chr5D.!!$R2 3063
2 TraesCS5D01G535200 chr5D 549546567 549548153 1586 True 1415 1415 82.875 1148 2773 1 chr5D.!!$R5 1625
3 TraesCS5D01G535200 chr5D 549428503 549430068 1565 True 1330 1330 82.127 1148 2755 1 chr5D.!!$R4 1607
4 TraesCS5D01G535200 chr4A 620702817 620705699 2882 True 4104 4104 92.416 58 2938 1 chr4A.!!$R3 2880
5 TraesCS5D01G535200 chr4A 620656790 620657557 767 True 1016 1016 90.482 2935 3717 1 chr4A.!!$R2 782
6 TraesCS5D01G535200 chr5B 700854796 700857025 2229 True 2998 2998 91.110 624 2845 1 chr5B.!!$R3 2221
7 TraesCS5D01G535200 chr5B 701050114 701051702 1588 True 1384 1384 82.508 1148 2773 1 chr5B.!!$R4 1625
8 TraesCS5D01G535200 chr5B 700844886 700845755 869 True 1062 1062 88.753 2842 3728 1 chr5B.!!$R2 886
9 TraesCS5D01G535200 chr7D 162822787 162823654 867 True 917 917 85.977 1142 1998 1 chr7D.!!$R1 856
10 TraesCS5D01G535200 chr7A 163616900 163617765 865 True 904 904 85.780 1142 1998 1 chr7A.!!$R1 856
11 TraesCS5D01G535200 chr2D 110842355 110843195 840 True 852 852 84.936 1148 2008 1 chr2D.!!$R1 860
12 TraesCS5D01G535200 chr2B 159970188 159971028 840 True 846 846 84.820 1148 2008 1 chr2B.!!$R1 860
13 TraesCS5D01G535200 chr2A 107181922 107182762 840 True 835 835 84.571 1148 2008 1 chr2A.!!$R1 860
14 TraesCS5D01G535200 chr3D 426048494 426049122 628 False 399 399 78.404 2125 2756 1 chr3D.!!$F1 631
15 TraesCS5D01G535200 chr3B 556349528 556350152 624 True 392 392 78.233 2129 2756 1 chr3B.!!$R1 627

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
25 26 0.027586 AACTCGAGCAAAACACACGC 59.972 50.0 13.61 0.00 0.00 5.34 F
218 220 0.235404 CTTGCCCAAATTTGCGCAAC 59.765 50.0 30.04 10.16 44.32 4.17 F
1080 1135 0.242825 CCTTCACAATGCTGGTGCTG 59.757 55.0 0.00 0.00 40.48 4.41 F
1663 1727 0.464036 ATTCGGCAGGCGATACTTCA 59.536 50.0 21.13 4.05 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1064 1119 1.879380 GTAACAGCACCAGCATTGTGA 59.121 47.619 4.67 0.0 45.49 3.58 R
1695 1762 2.204136 TGCTCCACCTCCATGGGT 60.204 61.111 13.02 0.0 40.49 4.51 R
2394 2474 0.623723 GGCTTCCCTTGGGTATGTGA 59.376 55.000 5.51 0.0 0.00 3.58 R
3409 3506 0.539051 CCCTGAGAATCTTCGCCAGT 59.461 55.000 11.56 0.0 33.79 4.00 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
22 23 4.654015 GTGTAAAACTCGAGCAAAACACA 58.346 39.130 24.91 15.05 36.77 3.72
23 24 4.494410 GTGTAAAACTCGAGCAAAACACAC 59.506 41.667 24.91 20.29 36.77 3.82
24 25 2.452006 AAACTCGAGCAAAACACACG 57.548 45.000 13.61 0.00 0.00 4.49
25 26 0.027586 AACTCGAGCAAAACACACGC 59.972 50.000 13.61 0.00 0.00 5.34
26 27 1.087202 ACTCGAGCAAAACACACGCA 61.087 50.000 13.61 0.00 0.00 5.24
27 28 0.383491 CTCGAGCAAAACACACGCAG 60.383 55.000 0.00 0.00 0.00 5.18
28 29 2.005537 CGAGCAAAACACACGCAGC 61.006 57.895 0.00 0.00 0.00 5.25
29 30 1.658409 GAGCAAAACACACGCAGCC 60.658 57.895 0.00 0.00 0.00 4.85
30 31 2.658268 GCAAAACACACGCAGCCC 60.658 61.111 0.00 0.00 0.00 5.19
31 32 2.027460 CAAAACACACGCAGCCCC 59.973 61.111 0.00 0.00 0.00 5.80
32 33 2.441164 AAAACACACGCAGCCCCA 60.441 55.556 0.00 0.00 0.00 4.96
33 34 2.055042 AAAACACACGCAGCCCCAA 61.055 52.632 0.00 0.00 0.00 4.12
34 35 2.291457 AAAACACACGCAGCCCCAAC 62.291 55.000 0.00 0.00 0.00 3.77
35 36 3.714487 AACACACGCAGCCCCAACT 62.714 57.895 0.00 0.00 0.00 3.16
36 37 3.357079 CACACGCAGCCCCAACTC 61.357 66.667 0.00 0.00 0.00 3.01
37 38 4.643387 ACACGCAGCCCCAACTCC 62.643 66.667 0.00 0.00 0.00 3.85
46 47 4.323477 CCCAACTCCCACGCGGAA 62.323 66.667 12.47 0.00 41.40 4.30
47 48 3.047877 CCAACTCCCACGCGGAAC 61.048 66.667 12.47 0.00 41.40 3.62
48 49 2.280524 CAACTCCCACGCGGAACA 60.281 61.111 12.47 0.00 41.40 3.18
49 50 1.671054 CAACTCCCACGCGGAACAT 60.671 57.895 12.47 0.00 41.40 2.71
50 51 1.072505 AACTCCCACGCGGAACATT 59.927 52.632 12.47 0.00 41.40 2.71
51 52 0.953960 AACTCCCACGCGGAACATTC 60.954 55.000 12.47 0.00 41.40 2.67
52 53 1.079127 CTCCCACGCGGAACATTCT 60.079 57.895 12.47 0.00 41.40 2.40
53 54 1.079405 TCCCACGCGGAACATTCTC 60.079 57.895 12.47 0.00 37.88 2.87
54 55 2.452813 CCCACGCGGAACATTCTCG 61.453 63.158 12.47 5.66 0.00 4.04
55 56 2.395690 CACGCGGAACATTCTCGC 59.604 61.111 12.47 13.90 40.75 5.03
78 79 1.817099 CGCCTGACTTCCCATCTGC 60.817 63.158 0.00 0.00 0.00 4.26
109 110 4.227134 CCATCGACGCCTCCCCTG 62.227 72.222 0.00 0.00 0.00 4.45
111 112 2.123251 ATCGACGCCTCCCCTGAT 60.123 61.111 0.00 0.00 0.00 2.90
115 116 3.447025 GACGCCTCCCCTGATTCCG 62.447 68.421 0.00 0.00 0.00 4.30
133 134 3.484547 CGGCCGTTAACACCGCTC 61.485 66.667 19.50 6.11 40.55 5.03
147 148 4.500116 GCTCCGACGCTCCTCACC 62.500 72.222 0.00 0.00 0.00 4.02
206 207 1.756172 CCACAACCACACTTGCCCA 60.756 57.895 0.00 0.00 0.00 5.36
209 210 1.138661 CACAACCACACTTGCCCAAAT 59.861 47.619 0.00 0.00 0.00 2.32
211 212 2.238395 ACAACCACACTTGCCCAAATTT 59.762 40.909 0.00 0.00 0.00 1.82
216 218 0.879400 CACTTGCCCAAATTTGCGCA 60.879 50.000 23.18 23.18 39.93 6.09
218 220 0.235404 CTTGCCCAAATTTGCGCAAC 59.765 50.000 30.04 10.16 44.32 4.17
219 221 0.462581 TTGCCCAAATTTGCGCAACA 60.463 45.000 30.04 16.03 44.32 3.33
226 228 3.524763 AAATTTGCGCAACAGATTTGC 57.475 38.095 24.99 0.00 40.52 3.68
265 270 0.532196 GCCGCTAGAATGGTACCACC 60.532 60.000 19.09 12.42 39.22 4.61
281 286 1.915769 ACCAGCGAGGAAGAAGGCT 60.916 57.895 5.19 0.00 41.22 4.58
292 297 4.357279 GAAGGCTGCCCACCTGCT 62.357 66.667 16.57 0.00 37.67 4.24
308 313 4.047125 CTGCCACCGGGTTCCCAT 62.047 66.667 6.32 0.00 36.17 4.00
323 328 4.899239 CATGGACGCCTCCTCCGC 62.899 72.222 3.30 0.00 37.48 5.54
367 372 0.392998 GAAGAAGATGAAGGCGGCCA 60.393 55.000 23.09 0.00 0.00 5.36
368 373 0.257039 AAGAAGATGAAGGCGGCCAT 59.743 50.000 23.09 9.75 0.00 4.40
369 374 0.465097 AGAAGATGAAGGCGGCCATG 60.465 55.000 23.09 0.00 0.00 3.66
400 405 1.741770 GCTTCAACGTCATCGCCCT 60.742 57.895 0.00 0.00 41.18 5.19
402 407 1.079405 TTCAACGTCATCGCCCTCC 60.079 57.895 0.00 0.00 41.18 4.30
403 408 2.511600 CAACGTCATCGCCCTCCC 60.512 66.667 0.00 0.00 41.18 4.30
404 409 3.000819 AACGTCATCGCCCTCCCA 61.001 61.111 0.00 0.00 41.18 4.37
416 421 2.677289 CCTCCCATGCTGCTCCTGT 61.677 63.158 0.00 0.00 0.00 4.00
418 423 2.513204 CCCATGCTGCTCCTGTCG 60.513 66.667 0.00 0.00 0.00 4.35
420 425 2.435410 CATGCTGCTCCTGTCGCA 60.435 61.111 0.00 0.00 36.75 5.10
437 442 4.677151 ACCTCCTCCCCCACCACC 62.677 72.222 0.00 0.00 0.00 4.61
440 445 3.603080 TCCTCCCCCACCACCGTA 61.603 66.667 0.00 0.00 0.00 4.02
441 446 3.396570 CCTCCCCCACCACCGTAC 61.397 72.222 0.00 0.00 0.00 3.67
447 452 3.766691 CCACCACCGTACCTCCCG 61.767 72.222 0.00 0.00 0.00 5.14
450 455 3.455469 CCACCGTACCTCCCGTCC 61.455 72.222 0.00 0.00 0.00 4.79
454 459 3.512516 CGTACCTCCCGTCCCGTC 61.513 72.222 0.00 0.00 0.00 4.79
456 461 4.033776 TACCTCCCGTCCCGTCGT 62.034 66.667 0.00 0.00 0.00 4.34
466 471 1.909287 TCCCGTCGTCAACCATGGA 60.909 57.895 21.47 0.00 0.00 3.41
473 478 0.613260 CGTCAACCATGGAGGAGGAA 59.387 55.000 21.47 0.00 41.22 3.36
478 483 1.265454 ACCATGGAGGAGGAACCGTC 61.265 60.000 21.47 0.00 44.74 4.79
507 512 4.151070 CGTCGTCACCATCTTCAATTTTG 58.849 43.478 0.00 0.00 0.00 2.44
516 521 4.322877 CCATCTTCAATTTTGCATCACCCA 60.323 41.667 0.00 0.00 0.00 4.51
558 567 3.947868 ACATCATCAGTTGGAGTTGGAG 58.052 45.455 0.00 0.00 0.00 3.86
559 568 3.276857 CATCATCAGTTGGAGTTGGAGG 58.723 50.000 0.00 0.00 0.00 4.30
565 574 3.699038 TCAGTTGGAGTTGGAGGTTTTTG 59.301 43.478 0.00 0.00 0.00 2.44
580 589 6.819146 GGAGGTTTTTGATTGTGTAAAAACCA 59.181 34.615 30.24 0.00 30.65 3.67
632 641 6.710597 TTGGAGATGCTCTATAAGTACGTT 57.289 37.500 0.00 0.00 0.00 3.99
688 708 0.935831 TGTGACGTTTGAGCGTACGG 60.936 55.000 18.39 0.23 45.79 4.02
724 744 1.497716 TCTTCGATCCTAGCCACCCTA 59.502 52.381 0.00 0.00 0.00 3.53
735 761 1.375523 CCACCCTACACGCCTGTTC 60.376 63.158 0.00 0.00 0.00 3.18
739 765 2.291043 CCTACACGCCTGTTCCCCT 61.291 63.158 0.00 0.00 0.00 4.79
741 767 0.673644 CTACACGCCTGTTCCCCTTG 60.674 60.000 0.00 0.00 0.00 3.61
766 815 2.027653 GCTTAGCTGTCCCTTCTCTTGT 60.028 50.000 0.00 0.00 0.00 3.16
770 819 1.737363 GCTGTCCCTTCTCTTGTAGCG 60.737 57.143 0.00 0.00 0.00 4.26
822 871 3.072768 TCATGGGGTACGGTGTAAACTTT 59.927 43.478 0.00 0.00 0.00 2.66
895 944 3.037549 CCTTCTTCTACAGCTCTCCCAT 58.962 50.000 0.00 0.00 0.00 4.00
898 947 1.691434 CTTCTACAGCTCTCCCATCCC 59.309 57.143 0.00 0.00 0.00 3.85
903 957 0.693767 CAGCTCTCCCATCCCTCCTT 60.694 60.000 0.00 0.00 0.00 3.36
1027 1081 3.699038 AGTTGCTTTGCTCCAACTTACAA 59.301 39.130 0.56 0.00 46.86 2.41
1064 1119 3.726144 GGAGCAGCTGGGAGCCTT 61.726 66.667 17.12 0.00 43.77 4.35
1080 1135 0.242825 CCTTCACAATGCTGGTGCTG 59.757 55.000 0.00 0.00 40.48 4.41
1083 1138 2.268762 TCACAATGCTGGTGCTGTTA 57.731 45.000 0.00 0.00 40.48 2.41
1617 1681 2.102357 CACGTCGCGAGGCACTAT 59.898 61.111 27.18 5.88 41.55 2.12
1663 1727 0.464036 ATTCGGCAGGCGATACTTCA 59.536 50.000 21.13 4.05 0.00 3.02
2394 2474 1.738830 CACCAACGTCGCCGGTTAT 60.739 57.895 1.90 0.00 38.78 1.89
2509 2589 1.004292 GCCACATTAATACGACCACGC 60.004 52.381 0.00 0.00 43.96 5.34
2688 2771 4.454161 GCTATAGATCTCAGCGAGTCAGAA 59.546 45.833 12.14 0.00 0.00 3.02
2777 2861 4.082408 CCATGCCACAGCCATCTAAATATG 60.082 45.833 0.00 0.00 38.69 1.78
2849 2934 0.460987 GTGAGCCAAGATCACCTCGG 60.461 60.000 1.59 0.00 42.26 4.63
2955 3044 3.201290 CCATCCAATCGAGAACCTCTTG 58.799 50.000 0.00 0.00 0.00 3.02
2979 3068 9.567776 TTGTTTAGATCAAATGGTTCTTAGTGA 57.432 29.630 0.00 0.00 0.00 3.41
2985 3074 8.900781 AGATCAAATGGTTCTTAGTGATCATTG 58.099 33.333 12.51 0.00 42.38 2.82
3002 3091 9.884465 GTGATCATTGCAAAATAGTTATAGGTC 57.116 33.333 1.71 0.00 0.00 3.85
3180 3273 5.721000 TGGAAATGTATCTTGGCTTTCCATT 59.279 36.000 10.20 0.00 45.99 3.16
3182 3275 6.536224 GGAAATGTATCTTGGCTTTCCATTTG 59.464 38.462 7.34 0.00 42.76 2.32
3308 3403 3.355626 AAAAGGAGAGAAAACAAGCGC 57.644 42.857 0.00 0.00 0.00 5.92
3319 3414 6.806739 AGAGAAAACAAGCGCCATTTATAAAC 59.193 34.615 2.29 0.00 0.00 2.01
3366 3461 8.291191 TGTTATGGATGCATATCACTTTGAAA 57.709 30.769 12.45 0.00 34.90 2.69
3409 3506 8.905660 ACTATTAGTAGTCTTCGATGAAGCTA 57.094 34.615 2.09 3.72 39.29 3.32
3412 3509 5.493133 AGTAGTCTTCGATGAAGCTACTG 57.507 43.478 25.40 1.02 45.65 2.74
3485 3582 4.261578 TGCTAAGTACCACACCTGTAAC 57.738 45.455 0.00 0.00 0.00 2.50
3577 3676 2.076863 AGACTGTTCAAATGCTACCGC 58.923 47.619 0.00 0.00 0.00 5.68
3599 3698 4.201881 GCGCTACCAATAAAGTGTTAAGGG 60.202 45.833 0.00 0.00 0.00 3.95
3701 3808 4.697514 CCACCGAGAGATGAACAATACAT 58.302 43.478 0.00 0.00 0.00 2.29
3734 3841 4.313522 GTGAATAGCACAAAGTCACTCG 57.686 45.455 0.00 0.00 46.91 4.18
3735 3842 3.741344 GTGAATAGCACAAAGTCACTCGT 59.259 43.478 0.00 0.00 46.91 4.18
3736 3843 3.987868 TGAATAGCACAAAGTCACTCGTC 59.012 43.478 0.00 0.00 0.00 4.20
3737 3844 3.660501 ATAGCACAAAGTCACTCGTCA 57.339 42.857 0.00 0.00 0.00 4.35
3738 3845 2.533266 AGCACAAAGTCACTCGTCAT 57.467 45.000 0.00 0.00 0.00 3.06
3739 3846 2.138320 AGCACAAAGTCACTCGTCATG 58.862 47.619 0.00 0.00 0.00 3.07
3740 3847 2.135139 GCACAAAGTCACTCGTCATGA 58.865 47.619 0.00 0.00 0.00 3.07
3754 3861 6.040962 CTCGTCATGAGGTTGTATTCAATG 57.959 41.667 14.67 0.00 41.29 2.82
3755 3862 4.875536 TCGTCATGAGGTTGTATTCAATGG 59.124 41.667 14.67 0.00 35.92 3.16
3756 3863 4.635765 CGTCATGAGGTTGTATTCAATGGT 59.364 41.667 7.25 0.00 35.92 3.55
3757 3864 5.447683 CGTCATGAGGTTGTATTCAATGGTG 60.448 44.000 7.25 0.00 35.92 4.17
3758 3865 5.415701 GTCATGAGGTTGTATTCAATGGTGT 59.584 40.000 0.00 0.00 35.92 4.16
3759 3866 6.009589 TCATGAGGTTGTATTCAATGGTGTT 58.990 36.000 0.00 0.00 35.92 3.32
3760 3867 5.703978 TGAGGTTGTATTCAATGGTGTTG 57.296 39.130 0.00 0.00 35.92 3.33
3761 3868 5.136828 TGAGGTTGTATTCAATGGTGTTGT 58.863 37.500 0.00 0.00 35.92 3.32
3762 3869 6.299922 TGAGGTTGTATTCAATGGTGTTGTA 58.700 36.000 0.00 0.00 35.92 2.41
3763 3870 6.945435 TGAGGTTGTATTCAATGGTGTTGTAT 59.055 34.615 0.00 0.00 35.92 2.29
3764 3871 7.450014 TGAGGTTGTATTCAATGGTGTTGTATT 59.550 33.333 0.00 0.00 35.92 1.89
3765 3872 7.826690 AGGTTGTATTCAATGGTGTTGTATTC 58.173 34.615 0.00 0.00 35.92 1.75
3766 3873 7.450014 AGGTTGTATTCAATGGTGTTGTATTCA 59.550 33.333 0.00 0.00 35.92 2.57
3767 3874 8.250332 GGTTGTATTCAATGGTGTTGTATTCAT 58.750 33.333 0.00 0.00 35.92 2.57
3768 3875 9.075519 GTTGTATTCAATGGTGTTGTATTCATG 57.924 33.333 0.00 0.00 35.92 3.07
3769 3876 7.770201 TGTATTCAATGGTGTTGTATTCATGG 58.230 34.615 0.00 0.00 0.00 3.66
3770 3877 6.855763 ATTCAATGGTGTTGTATTCATGGT 57.144 33.333 0.00 0.00 0.00 3.55
3771 3878 7.953005 ATTCAATGGTGTTGTATTCATGGTA 57.047 32.000 0.00 0.00 0.00 3.25
3772 3879 7.767250 TTCAATGGTGTTGTATTCATGGTAA 57.233 32.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.494410 GTGTGTTTTGCTCGAGTTTTACAC 59.506 41.667 23.67 23.67 36.19 2.90
1 2 4.654015 GTGTGTTTTGCTCGAGTTTTACA 58.346 39.130 15.13 10.84 0.00 2.41
2 3 3.717404 CGTGTGTTTTGCTCGAGTTTTAC 59.283 43.478 15.13 8.40 0.00 2.01
3 4 3.786161 GCGTGTGTTTTGCTCGAGTTTTA 60.786 43.478 15.13 0.00 0.00 1.52
4 5 2.780993 CGTGTGTTTTGCTCGAGTTTT 58.219 42.857 15.13 0.00 0.00 2.43
5 6 1.531058 GCGTGTGTTTTGCTCGAGTTT 60.531 47.619 15.13 0.00 0.00 2.66
6 7 0.027586 GCGTGTGTTTTGCTCGAGTT 59.972 50.000 15.13 0.00 0.00 3.01
7 8 1.087202 TGCGTGTGTTTTGCTCGAGT 61.087 50.000 15.13 0.00 0.00 4.18
8 9 0.383491 CTGCGTGTGTTTTGCTCGAG 60.383 55.000 8.45 8.45 0.00 4.04
9 10 1.641140 CTGCGTGTGTTTTGCTCGA 59.359 52.632 0.00 0.00 0.00 4.04
10 11 2.005537 GCTGCGTGTGTTTTGCTCG 61.006 57.895 0.00 0.00 0.00 5.03
11 12 1.658409 GGCTGCGTGTGTTTTGCTC 60.658 57.895 0.00 0.00 0.00 4.26
12 13 2.412937 GGCTGCGTGTGTTTTGCT 59.587 55.556 0.00 0.00 0.00 3.91
13 14 2.658268 GGGCTGCGTGTGTTTTGC 60.658 61.111 0.00 0.00 0.00 3.68
14 15 2.027460 GGGGCTGCGTGTGTTTTG 59.973 61.111 0.00 0.00 0.00 2.44
15 16 2.055042 TTGGGGCTGCGTGTGTTTT 61.055 52.632 0.00 0.00 0.00 2.43
16 17 2.441164 TTGGGGCTGCGTGTGTTT 60.441 55.556 0.00 0.00 0.00 2.83
17 18 3.216292 GTTGGGGCTGCGTGTGTT 61.216 61.111 0.00 0.00 0.00 3.32
18 19 4.189580 AGTTGGGGCTGCGTGTGT 62.190 61.111 0.00 0.00 0.00 3.72
19 20 3.357079 GAGTTGGGGCTGCGTGTG 61.357 66.667 0.00 0.00 0.00 3.82
20 21 4.643387 GGAGTTGGGGCTGCGTGT 62.643 66.667 0.00 0.00 0.00 4.49
35 36 1.079405 GAGAATGTTCCGCGTGGGA 60.079 57.895 16.49 2.36 45.40 4.37
36 37 2.452813 CGAGAATGTTCCGCGTGGG 61.453 63.158 16.49 1.03 35.24 4.61
37 38 3.081133 CGAGAATGTTCCGCGTGG 58.919 61.111 9.28 9.28 0.00 4.94
38 39 2.395690 GCGAGAATGTTCCGCGTG 59.604 61.111 4.92 0.00 37.22 5.34
41 42 4.223964 GGCGCGAGAATGTTCCGC 62.224 66.667 12.10 14.41 43.51 5.54
42 43 2.813474 TGGCGCGAGAATGTTCCG 60.813 61.111 12.10 0.00 0.00 4.30
43 44 2.785258 GTGGCGCGAGAATGTTCC 59.215 61.111 12.10 0.00 0.00 3.62
44 45 2.395690 CGTGGCGCGAGAATGTTC 59.604 61.111 16.70 0.00 44.77 3.18
45 46 3.788766 GCGTGGCGCGAGAATGTT 61.789 61.111 26.40 0.00 44.55 2.71
56 57 3.628646 ATGGGAAGTCAGGCGTGGC 62.629 63.158 1.99 1.99 0.00 5.01
108 109 2.101835 GTTAACGGCCGCGGAATCA 61.102 57.895 33.48 5.99 0.00 2.57
109 110 2.101835 TGTTAACGGCCGCGGAATC 61.102 57.895 33.48 16.47 0.00 2.52
111 112 3.043121 GTGTTAACGGCCGCGGAA 61.043 61.111 33.48 14.38 0.00 4.30
120 121 2.430942 CGTCGGAGCGGTGTTAACG 61.431 63.158 0.00 0.00 0.00 3.18
122 123 2.431260 GCGTCGGAGCGGTGTTAA 60.431 61.111 0.00 0.00 0.00 2.01
133 134 2.202797 CATGGTGAGGAGCGTCGG 60.203 66.667 0.00 0.00 0.00 4.79
184 185 3.216292 AAGTGTGGTTGTGGCGGC 61.216 61.111 0.00 0.00 0.00 6.53
192 193 2.916640 CAAATTTGGGCAAGTGTGGTT 58.083 42.857 10.49 0.00 0.00 3.67
193 194 1.474855 GCAAATTTGGGCAAGTGTGGT 60.475 47.619 19.47 0.00 0.00 4.16
206 207 3.524763 GCAAATCTGTTGCGCAAATTT 57.475 38.095 26.87 22.83 35.58 1.82
216 218 1.526575 CGTGGGGCAGCAAATCTGTT 61.527 55.000 0.00 0.00 44.66 3.16
218 220 1.926511 GACGTGGGGCAGCAAATCTG 61.927 60.000 0.00 0.00 45.62 2.90
219 221 1.675641 GACGTGGGGCAGCAAATCT 60.676 57.895 0.00 0.00 0.00 2.40
242 244 3.159858 TACCATTCTAGCGGCGGCC 62.160 63.158 13.24 9.54 41.24 6.13
265 270 4.198625 CAGCCTTCTTCCTCGCTG 57.801 61.111 0.00 0.00 42.42 5.18
266 271 2.267324 GCAGCCTTCTTCCTCGCT 59.733 61.111 0.00 0.00 0.00 4.93
301 306 2.124695 GGAGGCGTCCATGGGAAC 60.125 66.667 20.47 2.24 43.31 3.62
303 308 2.764128 GAGGAGGCGTCCATGGGA 60.764 66.667 26.40 0.00 46.80 4.37
344 349 1.432270 CGCCTTCATCTTCTTCGCCC 61.432 60.000 0.00 0.00 0.00 6.13
345 350 1.432270 CCGCCTTCATCTTCTTCGCC 61.432 60.000 0.00 0.00 0.00 5.54
347 352 1.432270 GGCCGCCTTCATCTTCTTCG 61.432 60.000 0.71 0.00 0.00 3.79
372 377 2.900167 CGTTGAAGCAGCAGCAGCA 61.900 57.895 12.92 0.00 45.49 4.41
387 392 2.367202 ATGGGAGGGCGATGACGTT 61.367 57.895 0.00 0.00 41.98 3.99
400 405 2.993008 GACAGGAGCAGCATGGGA 59.007 61.111 0.00 0.00 35.86 4.37
402 407 3.200593 GCGACAGGAGCAGCATGG 61.201 66.667 0.00 0.00 35.86 3.66
403 408 2.435410 TGCGACAGGAGCAGCATG 60.435 61.111 0.00 0.00 40.01 4.06
404 409 2.435586 GTGCGACAGGAGCAGCAT 60.436 61.111 0.00 0.00 46.10 3.79
420 425 4.677151 GGTGGTGGGGGAGGAGGT 62.677 72.222 0.00 0.00 0.00 3.85
447 452 1.740296 CCATGGTTGACGACGGGAC 60.740 63.158 2.57 0.00 0.00 4.46
450 455 1.447838 CCTCCATGGTTGACGACGG 60.448 63.158 12.58 0.00 0.00 4.79
453 458 0.252057 TCCTCCTCCATGGTTGACGA 60.252 55.000 12.58 6.29 37.07 4.20
454 459 0.613260 TTCCTCCTCCATGGTTGACG 59.387 55.000 12.58 4.06 37.07 4.35
456 461 0.991920 GGTTCCTCCTCCATGGTTGA 59.008 55.000 12.58 8.64 37.07 3.18
466 471 3.745803 GCGTCGACGGTTCCTCCT 61.746 66.667 36.13 0.00 40.23 3.69
493 498 4.186159 GGGTGATGCAAAATTGAAGATGG 58.814 43.478 0.00 0.00 0.00 3.51
507 512 0.682209 AGTGCTCCAATGGGTGATGC 60.682 55.000 0.00 0.00 34.93 3.91
544 549 3.699038 TCAAAAACCTCCAACTCCAACTG 59.301 43.478 0.00 0.00 0.00 3.16
545 550 3.976015 TCAAAAACCTCCAACTCCAACT 58.024 40.909 0.00 0.00 0.00 3.16
688 708 2.347661 CGAAGACGCTCAAAAGTGACAC 60.348 50.000 0.00 0.00 36.80 3.67
724 744 1.412453 TACAAGGGGAACAGGCGTGT 61.412 55.000 6.15 6.15 39.19 4.49
735 761 2.565841 GACAGCTAAGCATACAAGGGG 58.434 52.381 0.00 0.00 0.00 4.79
739 765 3.519510 AGAAGGGACAGCTAAGCATACAA 59.480 43.478 0.00 0.00 0.00 2.41
741 767 3.386402 AGAGAAGGGACAGCTAAGCATAC 59.614 47.826 0.00 0.00 0.00 2.39
766 815 3.313012 ACATTAAGTGCAGTGTCGCTA 57.687 42.857 0.00 0.00 0.00 4.26
770 819 5.186198 AGGGAATACATTAAGTGCAGTGTC 58.814 41.667 0.00 0.00 0.00 3.67
822 871 6.798427 AGCTAGGTTTCTCACTATGATTGA 57.202 37.500 0.00 0.00 0.00 2.57
895 944 2.498941 CGCGCTATCCAAGGAGGGA 61.499 63.158 5.56 0.00 42.21 4.20
898 947 1.859080 GTAAACGCGCTATCCAAGGAG 59.141 52.381 5.73 0.00 0.00 3.69
903 957 1.202325 ACATCGTAAACGCGCTATCCA 60.202 47.619 5.73 0.00 39.60 3.41
1039 1094 2.415608 CCAGCTGCTCCATTGCCAG 61.416 63.158 8.66 0.00 0.00 4.85
1064 1119 1.879380 GTAACAGCACCAGCATTGTGA 59.121 47.619 4.67 0.00 45.49 3.58
1080 1135 4.398673 ACGAGGTAGATGAAGGTGAGTAAC 59.601 45.833 0.00 0.00 0.00 2.50
1083 1138 3.018149 GACGAGGTAGATGAAGGTGAGT 58.982 50.000 0.00 0.00 0.00 3.41
1617 1681 3.418913 CGGATGACGTTGCCGCAA 61.419 61.111 0.38 0.38 38.46 4.85
1695 1762 2.204136 TGCTCCACCTCCATGGGT 60.204 61.111 13.02 0.00 40.49 4.51
2394 2474 0.623723 GGCTTCCCTTGGGTATGTGA 59.376 55.000 5.51 0.00 0.00 3.58
2688 2771 1.302511 GGCCAGGAACACGTCATGT 60.303 57.895 0.00 0.00 46.42 3.21
2795 2879 6.527023 ACAATCGACCGAGCTATATTATTTCG 59.473 38.462 0.00 0.00 0.00 3.46
2929 3017 3.005897 AGGTTCTCGATTGGATGGTATCG 59.994 47.826 0.00 0.00 43.67 2.92
2979 3068 8.902540 TCGACCTATAACTATTTTGCAATGAT 57.097 30.769 0.00 0.11 0.00 2.45
2985 3074 9.651718 CAATTTCTCGACCTATAACTATTTTGC 57.348 33.333 0.00 0.00 0.00 3.68
3002 3091 7.915923 TGCTTACAGTAGATAGACAATTTCTCG 59.084 37.037 0.00 0.00 35.55 4.04
3180 3273 6.912203 TCATTAAGACAAGAACACGTTCAA 57.088 33.333 12.21 0.00 41.84 2.69
3182 3275 7.116376 TCTCATCATTAAGACAAGAACACGTTC 59.884 37.037 1.54 1.54 39.78 3.95
3229 3322 9.503399 TCTTTCTTCTTCCTTGGAATTAGTTAC 57.497 33.333 2.24 0.00 0.00 2.50
3304 3399 3.537580 TCTTCCGTTTATAAATGGCGCT 58.462 40.909 25.76 0.00 43.33 5.92
3305 3400 3.955771 TCTTCCGTTTATAAATGGCGC 57.044 42.857 25.76 0.00 43.33 6.53
3396 3491 1.202302 TCGCCAGTAGCTTCATCGAAG 60.202 52.381 0.00 0.00 42.03 3.79
3409 3506 0.539051 CCCTGAGAATCTTCGCCAGT 59.461 55.000 11.56 0.00 33.79 4.00
3412 3509 1.115467 TCTCCCTGAGAATCTTCGCC 58.885 55.000 0.00 0.00 35.59 5.54
3500 3597 2.031258 AAAAGTTTGGGTTTTGCGGG 57.969 45.000 0.00 0.00 0.00 6.13
3577 3676 5.180271 TCCCTTAACACTTTATTGGTAGCG 58.820 41.667 0.00 0.00 0.00 4.26
3615 3715 6.194796 ACATATTGTGTCAATGTTGCTACC 57.805 37.500 5.40 0.00 35.77 3.18
3725 3832 2.365617 ACAACCTCATGACGAGTGACTT 59.634 45.455 0.00 0.00 40.48 3.01
3728 3835 4.219725 TGAATACAACCTCATGACGAGTGA 59.780 41.667 0.00 0.00 40.48 3.41
3729 3836 4.494484 TGAATACAACCTCATGACGAGTG 58.506 43.478 0.00 0.00 40.48 3.51
3730 3837 4.801330 TGAATACAACCTCATGACGAGT 57.199 40.909 0.00 0.00 40.48 4.18
3731 3838 5.007039 CCATTGAATACAACCTCATGACGAG 59.993 44.000 0.00 0.00 38.90 4.18
3732 3839 4.875536 CCATTGAATACAACCTCATGACGA 59.124 41.667 0.00 0.00 38.90 4.20
3733 3840 4.635765 ACCATTGAATACAACCTCATGACG 59.364 41.667 0.00 0.00 38.90 4.35
3734 3841 5.415701 ACACCATTGAATACAACCTCATGAC 59.584 40.000 0.00 0.00 38.90 3.06
3735 3842 5.569355 ACACCATTGAATACAACCTCATGA 58.431 37.500 0.00 0.00 38.90 3.07
3736 3843 5.902613 ACACCATTGAATACAACCTCATG 57.097 39.130 0.00 0.00 38.90 3.07
3737 3844 5.774690 ACAACACCATTGAATACAACCTCAT 59.225 36.000 0.00 0.00 38.90 2.90
3738 3845 5.136828 ACAACACCATTGAATACAACCTCA 58.863 37.500 0.00 0.00 38.90 3.86
3739 3846 5.705609 ACAACACCATTGAATACAACCTC 57.294 39.130 0.00 0.00 38.90 3.85
3740 3847 7.450014 TGAATACAACACCATTGAATACAACCT 59.550 33.333 0.00 0.00 38.90 3.50
3741 3848 7.598278 TGAATACAACACCATTGAATACAACC 58.402 34.615 0.00 0.00 38.90 3.77
3742 3849 9.075519 CATGAATACAACACCATTGAATACAAC 57.924 33.333 0.00 0.00 38.90 3.32
3743 3850 8.249638 CCATGAATACAACACCATTGAATACAA 58.750 33.333 0.00 0.00 40.42 2.41
3744 3851 7.395772 ACCATGAATACAACACCATTGAATACA 59.604 33.333 0.00 0.00 0.00 2.29
3745 3852 7.771183 ACCATGAATACAACACCATTGAATAC 58.229 34.615 0.00 0.00 0.00 1.89
3746 3853 7.953005 ACCATGAATACAACACCATTGAATA 57.047 32.000 0.00 0.00 0.00 1.75
3747 3854 6.855763 ACCATGAATACAACACCATTGAAT 57.144 33.333 0.00 0.00 0.00 2.57
3748 3855 7.767250 TTACCATGAATACAACACCATTGAA 57.233 32.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.