Multiple sequence alignment - TraesCS1D01G371200

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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 TraesCS1D01G371200 chr1D 100.000 5157 0 0 1 5157 449474475 449469319 0.000000e+00 9524
1 TraesCS1D01G371200 chr1D 92.473 93 6 1 1 92 449487004 449486912 1.170000e-26 132
2 TraesCS1D01G371200 chr1B 92.296 4063 167 61 388 4373 615129628 615125635 0.000000e+00 5635
3 TraesCS1D01G371200 chr1B 87.435 772 54 18 4412 5157 615125636 615124882 0.000000e+00 848
4 TraesCS1D01G371200 chr1B 81.436 404 49 7 1 401 615130037 615129657 1.800000e-79 307
5 TraesCS1D01G371200 chr1B 94.505 91 5 0 2 92 615130127 615130037 1.940000e-29 141
6 TraesCS1D01G371200 chr1B 92.391 92 6 1 1 92 615131559 615131469 4.190000e-26 130
7 TraesCS1D01G371200 chr1A 90.088 3390 136 59 519 3807 544607007 544603717 0.000000e+00 4215
8 TraesCS1D01G371200 chr1A 90.573 838 52 13 3809 4630 544603666 544602840 0.000000e+00 1085
9 TraesCS1D01G371200 chr1A 86.148 527 45 13 4636 5157 544602789 544602286 1.260000e-150 544
10 TraesCS1D01G371200 chr1A 81.081 333 36 6 1 331 544607862 544607555 1.860000e-59 241
11 TraesCS1D01G371200 chr1A 90.244 82 7 1 12 92 544607943 544607862 7.060000e-19 106
12 TraesCS1D01G371200 chr3D 91.818 550 27 8 937 1486 201170236 201170767 0.000000e+00 750
13 TraesCS1D01G371200 chr3D 90.678 118 7 3 636 752 201169926 201170040 2.490000e-33 154


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 TraesCS1D01G371200 chr1D 449469319 449474475 5156 True 9524.0 9524 100.0000 1 5157 1 chr1D.!!$R1 5156
1 TraesCS1D01G371200 chr1B 615124882 615131559 6677 True 1412.2 5635 89.6126 1 5157 5 chr1B.!!$R1 5156
2 TraesCS1D01G371200 chr1A 544602286 544607943 5657 True 1238.2 4215 87.6268 1 5157 5 chr1A.!!$R1 5156
3 TraesCS1D01G371200 chr3D 201169926 201170767 841 False 452.0 750 91.2480 636 1486 2 chr3D.!!$F1 850

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
935 2964 0.038455 AGCCGTACTGAGGTCACTCT 59.962 55.0 0.00 0.0 44.29 3.24 F
1001 3040 0.040204 CCTCCCCTGTTTGAGGCAAT 59.960 55.0 0.00 0.0 41.59 3.56 F
1003 3042 0.251742 TCCCCTGTTTGAGGCAATGG 60.252 55.0 0.00 0.0 41.19 3.16 F
1977 4065 0.390209 GCTACCGCGTTTCTAACCCA 60.390 55.0 4.92 0.0 0.00 4.51 F
2740 4832 1.953559 TGTTGTGCCAACTCTGAGAC 58.046 50.0 12.44 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 4082 1.654220 CCACGGTTGCACTTTCCTG 59.346 57.895 0.0 0.0 0.00 3.86 R
2869 4961 4.054825 CGGCGGTGGCTGCAAAAT 62.055 61.111 0.0 0.0 39.01 1.82 R
2974 5066 5.046376 TCAGTATCAATTGCCAGAACAGAGA 60.046 40.000 0.0 0.0 0.00 3.10 R
3055 5149 0.038159 AGTTCTCCAAACTCTCGCCG 60.038 55.000 0.0 0.0 0.00 6.46 R
4299 6459 0.178975 AAAGCGGTCCATCAAACCCA 60.179 50.000 0.0 0.0 32.89 4.51 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
82 1606 3.953775 CCACCCCCTTGCGTGACT 61.954 66.667 0.00 0.00 31.36 3.41
83 1607 2.113139 CACCCCCTTGCGTGACTT 59.887 61.111 0.00 0.00 31.36 3.01
94 1618 0.739813 GCGTGACTTTATCGGCACCT 60.740 55.000 0.00 0.00 31.48 4.00
95 1619 1.470285 GCGTGACTTTATCGGCACCTA 60.470 52.381 0.00 0.00 31.48 3.08
104 1628 0.691078 ATCGGCACCTATGACCCACT 60.691 55.000 0.00 0.00 0.00 4.00
105 1629 0.907704 TCGGCACCTATGACCCACTT 60.908 55.000 0.00 0.00 0.00 3.16
113 1637 2.092753 CCTATGACCCACTTGTGATGCT 60.093 50.000 1.89 0.00 0.00 3.79
116 1640 1.421268 TGACCCACTTGTGATGCTTCT 59.579 47.619 1.89 0.00 0.00 2.85
144 1668 2.590575 CAACGCGGTCCCTGTTGT 60.591 61.111 12.47 0.00 38.47 3.32
164 1688 0.172803 GTCGCGTGATCAACCTACCT 59.827 55.000 5.77 0.00 0.00 3.08
172 1696 0.537188 ATCAACCTACCTGCACTCGG 59.463 55.000 0.00 0.00 0.00 4.63
184 1708 4.295119 ACTCGGCGTTTCTGCGGT 62.295 61.111 6.85 0.00 36.64 5.68
267 1791 4.805219 ACACCTTGTTTTCGCCATATTTC 58.195 39.130 0.00 0.00 0.00 2.17
319 1844 1.814527 GATCCGACGCCACCTAACT 59.185 57.895 0.00 0.00 0.00 2.24
321 1846 0.611714 ATCCGACGCCACCTAACTTT 59.388 50.000 0.00 0.00 0.00 2.66
352 2193 1.058695 GCCTCGTCGATTAACACGTTG 59.941 52.381 0.00 0.00 37.30 4.10
362 2203 7.125113 GTCGATTAACACGTTGAACCTTTTTA 58.875 34.615 0.00 0.00 0.00 1.52
364 2205 7.799447 TCGATTAACACGTTGAACCTTTTTATG 59.201 33.333 0.00 0.00 0.00 1.90
365 2206 7.799447 CGATTAACACGTTGAACCTTTTTATGA 59.201 33.333 0.00 0.00 0.00 2.15
390 2233 1.444836 TATCGCGTTGTTTTCCCCTG 58.555 50.000 5.77 0.00 0.00 4.45
401 2244 3.822167 TGTTTTCCCCTGTATTTCGTTCC 59.178 43.478 0.00 0.00 0.00 3.62
445 2330 4.712122 AAACGCCCGTAATTCATTCATT 57.288 36.364 0.00 0.00 0.00 2.57
446 2331 3.963383 ACGCCCGTAATTCATTCATTC 57.037 42.857 0.00 0.00 0.00 2.67
447 2332 3.275143 ACGCCCGTAATTCATTCATTCA 58.725 40.909 0.00 0.00 0.00 2.57
505 2444 8.897872 TTAGTCGTCAGATTTTCCTTTTTAGT 57.102 30.769 0.00 0.00 0.00 2.24
553 2496 3.282885 GCTAGTAGAGGGCAAAGCAAAT 58.717 45.455 0.00 0.00 0.00 2.32
601 2544 1.127951 CGAACGCGCTGGAAAACTATT 59.872 47.619 5.73 0.00 0.00 1.73
611 2554 8.889000 CGCGCTGGAAAACTATTTATAAATTAC 58.111 33.333 15.64 0.34 0.00 1.89
666 2609 2.476534 AAATTTCCAGCACGGCAGCG 62.477 55.000 0.00 0.00 40.15 5.18
752 2704 0.556380 TCTTCCTCCCTCCCCTCTCT 60.556 60.000 0.00 0.00 0.00 3.10
753 2705 1.236708 CTTCCTCCCTCCCCTCTCTA 58.763 60.000 0.00 0.00 0.00 2.43
755 2707 0.048117 TCCTCCCTCCCCTCTCTACT 59.952 60.000 0.00 0.00 0.00 2.57
756 2708 0.187361 CCTCCCTCCCCTCTCTACTG 59.813 65.000 0.00 0.00 0.00 2.74
776 2763 8.633561 TCTACTGTACTACTCGTAGCAGTATAA 58.366 37.037 17.28 10.71 39.33 0.98
801 2800 4.828925 GCCAGTGCTCCGAGCTCC 62.829 72.222 20.87 11.50 42.97 4.70
803 2802 2.729479 CCAGTGCTCCGAGCTCCAT 61.729 63.158 20.87 0.42 42.97 3.41
804 2803 1.395045 CCAGTGCTCCGAGCTCCATA 61.395 60.000 20.87 0.00 42.97 2.74
810 2809 1.626686 CTCCGAGCTCCATACCATCT 58.373 55.000 8.47 0.00 0.00 2.90
819 2818 3.425659 CTCCATACCATCTCGATCTCCA 58.574 50.000 0.00 0.00 0.00 3.86
827 2842 2.388526 TCTCGATCTCCACCCATCAT 57.611 50.000 0.00 0.00 0.00 2.45
933 2962 4.845811 AGCCGTACTGAGGTCACT 57.154 55.556 0.00 0.00 0.00 3.41
934 2963 2.569183 AGCCGTACTGAGGTCACTC 58.431 57.895 0.00 0.00 44.23 3.51
935 2964 0.038455 AGCCGTACTGAGGTCACTCT 59.962 55.000 0.00 0.00 44.29 3.24
936 2965 0.452585 GCCGTACTGAGGTCACTCTC 59.547 60.000 0.00 0.00 44.29 3.20
975 3014 1.069358 GATTTACTCCCTCCTCGGCTG 59.931 57.143 0.00 0.00 0.00 4.85
998 3037 2.356667 CCCTCCCCTGTTTGAGGC 59.643 66.667 0.00 0.00 45.64 4.70
999 3038 2.538141 CCCTCCCCTGTTTGAGGCA 61.538 63.158 0.00 0.00 45.64 4.75
1000 3039 1.460255 CCTCCCCTGTTTGAGGCAA 59.540 57.895 0.00 0.00 41.59 4.52
1001 3040 0.040204 CCTCCCCTGTTTGAGGCAAT 59.960 55.000 0.00 0.00 41.59 3.56
1002 3041 1.180029 CTCCCCTGTTTGAGGCAATG 58.820 55.000 0.00 0.00 41.19 2.82
1003 3042 0.251742 TCCCCTGTTTGAGGCAATGG 60.252 55.000 0.00 0.00 41.19 3.16
1004 3043 1.593265 CCCTGTTTGAGGCAATGGC 59.407 57.895 0.00 0.00 41.19 4.40
1185 3229 1.079819 TCTGCTTCCGCTTTCCTCG 60.080 57.895 0.00 0.00 36.97 4.63
1262 3311 5.362556 TTGCTGCTGTTAAGATTTGACTC 57.637 39.130 0.00 0.00 0.00 3.36
1301 3350 1.599240 GATCGGCTCCTTGATGGGC 60.599 63.158 0.00 0.00 36.20 5.36
1394 3443 5.955355 AGCAATTAATTTGGCTTAGTACCCA 59.045 36.000 7.10 0.00 35.75 4.51
1397 3446 8.082242 GCAATTAATTTGGCTTAGTACCCATAG 58.918 37.037 0.00 0.00 35.75 2.23
1402 3451 2.954318 TGGCTTAGTACCCATAGACGTC 59.046 50.000 7.70 7.70 0.00 4.34
1529 3601 3.095347 GCTGGAGGGCCGTTCTAGG 62.095 68.421 17.23 4.95 36.79 3.02
1557 3629 2.227388 GGAAGATGGTGCTCACAAGTTG 59.773 50.000 0.00 0.00 0.00 3.16
1558 3630 1.242076 AGATGGTGCTCACAAGTTGC 58.758 50.000 1.81 0.00 0.00 4.17
1559 3631 1.202855 AGATGGTGCTCACAAGTTGCT 60.203 47.619 1.81 0.00 0.00 3.91
1587 3660 7.396540 AGTATAGTCAAAATTTGAAGGGCAG 57.603 36.000 10.27 0.00 42.15 4.85
1604 3677 4.197107 GGCAGAATGTCAAATACGTAGC 57.803 45.455 0.08 0.00 43.01 3.58
1624 3697 4.466828 AGCAATCGTTTCTGTTTGATTCG 58.533 39.130 0.00 0.00 0.00 3.34
1633 3706 6.850823 CGTTTCTGTTTGATTCGAATTCTTCA 59.149 34.615 12.81 3.40 0.00 3.02
1645 3718 9.657121 GATTCGAATTCTTCAAAGTGGATTATC 57.343 33.333 12.81 0.00 0.00 1.75
1649 3722 9.869844 CGAATTCTTCAAAGTGGATTATCATAC 57.130 33.333 3.52 0.00 0.00 2.39
1673 3755 6.729391 TGTTATTAAAACAGAGCATGCGTA 57.271 33.333 13.01 0.00 0.00 4.42
1753 3835 3.070476 TGTTGGATCTTGCATGCTGTA 57.930 42.857 20.33 3.97 0.00 2.74
1763 3845 7.761249 GGATCTTGCATGCTGTATTTACTTTTT 59.239 33.333 20.33 0.00 0.00 1.94
1851 3939 6.494893 TCAGTTCTGCTATTTTTAACGCAT 57.505 33.333 0.00 0.00 0.00 4.73
1852 3940 6.908825 TCAGTTCTGCTATTTTTAACGCATT 58.091 32.000 0.00 0.00 0.00 3.56
1863 3951 6.698359 TTTTTAACGCATTGTGCCTTTATC 57.302 33.333 0.00 0.00 41.12 1.75
1908 3996 2.838202 ACTACAATGTACTGGGAGGTGG 59.162 50.000 0.00 0.00 0.00 4.61
1977 4065 0.390209 GCTACCGCGTTTCTAACCCA 60.390 55.000 4.92 0.00 0.00 4.51
1994 4082 4.519540 ACCCATTGTTGTTGCTAATGAC 57.480 40.909 0.00 0.00 34.55 3.06
2028 4116 2.276116 TGGGCTCTCTGTGGTCGAC 61.276 63.158 7.13 7.13 0.00 4.20
2153 4241 2.034053 TGTTGCTCCGGTGAATTTGAAC 59.966 45.455 7.92 0.00 0.00 3.18
2371 4459 6.043854 AGAACATTCTGTAGTCCCTTCTTC 57.956 41.667 0.00 0.00 35.89 2.87
2740 4832 1.953559 TGTTGTGCCAACTCTGAGAC 58.046 50.000 12.44 0.00 0.00 3.36
2945 5037 3.882888 TCTGCCGGTAAAATGATCATTCC 59.117 43.478 20.95 16.22 0.00 3.01
2973 5065 9.607988 TGTTTTCTTTTATCTTCTCTGTACACA 57.392 29.630 0.00 0.00 0.00 3.72
2982 5076 6.260870 TCTTCTCTGTACACATCTCTGTTC 57.739 41.667 0.00 0.00 31.62 3.18
3055 5149 1.142748 ATGTGCGCTGCTACTCTCC 59.857 57.895 9.73 0.00 0.00 3.71
3077 5171 2.029290 GGCGAGAGTTTGGAGAACTACA 60.029 50.000 0.00 0.00 0.00 2.74
3199 5293 6.016527 CGACCACCATTAGTCTACTTAGCATA 60.017 42.308 0.00 0.00 0.00 3.14
3311 5407 5.391203 GCCTGTTTCAAAATGAATGGCAATC 60.391 40.000 18.58 0.00 42.08 2.67
3497 5593 0.517316 GCACTACTTTGCCCTTCGTG 59.483 55.000 0.00 0.00 36.42 4.35
3629 5725 8.622948 CCTTGAGGTTTGTCTTAACTCTTAAT 57.377 34.615 0.00 0.00 0.00 1.40
3669 5765 7.727578 TGTGGACTGTAATGGATTTAGTAGA 57.272 36.000 0.00 0.00 0.00 2.59
3978 6138 4.222336 AGCTACTGGCATTCTCATACTCT 58.778 43.478 0.00 0.00 44.79 3.24
4021 6181 8.038944 TCTAACCACTGGTTTGACTATTATGTC 58.961 37.037 18.75 0.00 44.33 3.06
4024 6184 7.231467 ACCACTGGTTTGACTATTATGTCTTT 58.769 34.615 0.00 0.00 33.19 2.52
4036 6196 6.929606 ACTATTATGTCTTTCAGGCGGTATTC 59.070 38.462 0.00 0.00 0.00 1.75
4180 6340 2.026262 GGTGTCTCTTGGGCAGGAAATA 60.026 50.000 0.00 0.00 0.00 1.40
4192 6352 4.441913 GGGCAGGAAATATGTTCCATTGTG 60.442 45.833 14.95 8.33 41.00 3.33
4274 6434 1.002134 GCCTTGCTGCTCCCAGTAA 60.002 57.895 0.00 0.00 40.65 2.24
4299 6459 3.806625 AATGATGCAAGGCGCTATTTT 57.193 38.095 7.64 0.00 43.06 1.82
4346 6506 4.748892 AGACGACTGATGGTTCTGTAATG 58.251 43.478 0.00 0.00 34.54 1.90
4378 6538 3.251004 CCCTTTCGTTTGGTCTCTTCTTG 59.749 47.826 0.00 0.00 0.00 3.02
4410 6570 6.127054 TGCATTAGAGAAGTTAGCAGGTGTAT 60.127 38.462 0.00 0.00 0.00 2.29
4419 6579 0.106519 AGCAGGTGTATTCCCATGGC 60.107 55.000 6.09 0.00 0.00 4.40
4431 6591 0.529378 CCCATGGCAGTTCTTCAAGC 59.471 55.000 6.09 0.00 0.00 4.01
4492 6653 6.351711 TGAAATCAGGTGGATGTAAGATGAG 58.648 40.000 0.00 0.00 36.02 2.90
4506 6693 1.765314 AGATGAGCGCTTGGGATTACT 59.235 47.619 13.26 0.14 0.00 2.24
4507 6694 2.171448 AGATGAGCGCTTGGGATTACTT 59.829 45.455 13.26 0.00 0.00 2.24
4508 6695 3.388024 AGATGAGCGCTTGGGATTACTTA 59.612 43.478 13.26 0.00 0.00 2.24
4509 6696 2.901249 TGAGCGCTTGGGATTACTTAC 58.099 47.619 13.26 0.00 0.00 2.34
4643 6875 6.620877 TTACAGTCAGGATTATCAACACCT 57.379 37.500 0.00 0.00 0.00 4.00
4661 6893 3.068024 CACCTTTTAAAAGCCAGCAGTGA 59.932 43.478 20.45 0.00 34.69 3.41
4672 6904 5.511234 AGCCAGCAGTGATTTAAATCATC 57.489 39.130 28.66 21.82 46.17 2.92
4673 6905 5.198965 AGCCAGCAGTGATTTAAATCATCT 58.801 37.500 28.66 23.26 46.17 2.90
4724 6956 3.920412 GGTTTAAATCAGCGGCTTTTCTG 59.080 43.478 0.00 0.00 0.00 3.02
4739 6971 5.241728 GGCTTTTCTGAGAATAACAAGGTGT 59.758 40.000 0.00 0.00 0.00 4.16
4741 6973 6.205658 GCTTTTCTGAGAATAACAAGGTGTCT 59.794 38.462 0.00 0.00 0.00 3.41
4743 6975 9.273016 CTTTTCTGAGAATAACAAGGTGTCTAA 57.727 33.333 0.00 0.00 0.00 2.10
4744 6976 8.603242 TTTCTGAGAATAACAAGGTGTCTAAC 57.397 34.615 0.00 0.00 0.00 2.34
4745 6977 7.297936 TCTGAGAATAACAAGGTGTCTAACA 57.702 36.000 0.00 0.00 0.00 2.41
4746 6978 7.732025 TCTGAGAATAACAAGGTGTCTAACAA 58.268 34.615 0.00 0.00 0.00 2.83
4747 6979 7.872993 TCTGAGAATAACAAGGTGTCTAACAAG 59.127 37.037 0.00 0.00 0.00 3.16
4748 6980 6.934645 TGAGAATAACAAGGTGTCTAACAAGG 59.065 38.462 0.00 0.00 0.00 3.61
4749 6981 6.838382 AGAATAACAAGGTGTCTAACAAGGT 58.162 36.000 0.00 0.00 0.00 3.50
4750 6982 6.710744 AGAATAACAAGGTGTCTAACAAGGTG 59.289 38.462 0.00 0.00 0.00 4.00
4751 6983 4.497291 AACAAGGTGTCTAACAAGGTGA 57.503 40.909 0.00 0.00 0.00 4.02
4752 6984 3.805207 ACAAGGTGTCTAACAAGGTGAC 58.195 45.455 0.00 0.00 0.00 3.67
4753 6985 3.199071 ACAAGGTGTCTAACAAGGTGACA 59.801 43.478 0.00 0.00 38.24 3.58
4781 7013 4.137543 GGATCAGGTTCCCACATAATGAC 58.862 47.826 0.00 0.00 0.00 3.06
4784 7016 3.843619 TCAGGTTCCCACATAATGACTCA 59.156 43.478 0.00 0.00 0.00 3.41
4790 7022 4.661222 TCCCACATAATGACTCAGCAAAA 58.339 39.130 0.00 0.00 0.00 2.44
4820 7056 4.870021 AGGTTATGCCCTCATCTTCTTT 57.130 40.909 0.00 0.00 38.26 2.52
4830 7066 5.699143 CCCTCATCTTCTTTGGGTGATAAT 58.301 41.667 0.00 0.00 33.49 1.28
4860 7097 5.261744 CAGGAATCTGAGAGCTTTAGCGAC 61.262 50.000 0.00 0.00 44.01 5.19
4870 7107 3.454371 GCTTTAGCGACATAAGGAGGA 57.546 47.619 0.00 0.00 0.00 3.71
4879 7116 4.302455 CGACATAAGGAGGACAGCTTATG 58.698 47.826 2.11 2.11 42.31 1.90
4887 7124 6.603940 AGGAGGACAGCTTATGATATTCTC 57.396 41.667 0.00 0.00 0.00 2.87
4925 7162 6.095377 CCTGTTCCAGCAACAAAAGAATATC 58.905 40.000 0.00 0.00 44.71 1.63
4938 7175 6.715264 ACAAAAGAATATCGAACAAGTTCCCT 59.285 34.615 7.32 0.00 36.27 4.20
4949 7186 4.026356 ACAAGTTCCCTGATTCTCCAAG 57.974 45.455 0.00 0.00 0.00 3.61
4959 7196 4.401519 CCTGATTCTCCAAGACAAATGCAT 59.598 41.667 0.00 0.00 0.00 3.96
4962 7199 7.363181 CCTGATTCTCCAAGACAAATGCATTAA 60.363 37.037 13.39 0.00 0.00 1.40
4982 7219 4.429854 AAGATAGCACAGGGGAAGAATC 57.570 45.455 0.00 0.00 0.00 2.52
5006 7243 4.690748 CAGGGCGATTTTATGTACGATGAT 59.309 41.667 0.00 0.00 0.00 2.45
5029 7266 5.009631 TGGAACCACAAGAGAACATAATGG 58.990 41.667 0.00 0.00 0.00 3.16
5035 7272 3.445096 ACAAGAGAACATAATGGGCAAGC 59.555 43.478 0.00 0.00 0.00 4.01
5058 7295 8.169839 AGCGTGCAATATTATATACGTACTTG 57.830 34.615 0.00 0.00 34.37 3.16
5086 7323 6.949352 ATAAAGGGAGCACTTCAATACATG 57.051 37.500 0.00 0.00 0.00 3.21
5131 7370 9.860650 ACTGCTTCCACATATATGGTAATAAAA 57.139 29.630 16.96 1.44 40.95 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 1606 2.120312 TGGGTCATAGGTGCCGATAAA 58.880 47.619 0.00 0.00 0.00 1.40
83 1607 1.414919 GTGGGTCATAGGTGCCGATAA 59.585 52.381 0.00 0.00 0.00 1.75
94 1618 3.264193 AGAAGCATCACAAGTGGGTCATA 59.736 43.478 0.00 0.00 0.00 2.15
95 1619 2.040813 AGAAGCATCACAAGTGGGTCAT 59.959 45.455 0.00 0.00 0.00 3.06
104 1628 1.545428 GGACCCACAGAAGCATCACAA 60.545 52.381 0.00 0.00 0.00 3.33
105 1629 0.036732 GGACCCACAGAAGCATCACA 59.963 55.000 0.00 0.00 0.00 3.58
132 1656 3.041940 GCGACACAACAGGGACCG 61.042 66.667 0.00 0.00 0.00 4.79
139 1663 0.579630 GTTGATCACGCGACACAACA 59.420 50.000 15.93 2.00 39.49 3.33
144 1668 0.108992 GGTAGGTTGATCACGCGACA 60.109 55.000 15.93 4.40 0.00 4.35
164 1688 3.345808 GCAGAAACGCCGAGTGCA 61.346 61.111 0.00 0.00 41.33 4.57
172 1696 2.725815 GTTGCACCGCAGAAACGC 60.726 61.111 0.00 0.00 40.61 4.84
184 1708 2.023414 AACGGAGTCTGTCGGTTGCA 62.023 55.000 4.74 0.00 45.00 4.08
187 1711 0.243095 GCTAACGGAGTCTGTCGGTT 59.757 55.000 4.74 3.82 45.00 4.44
231 1755 6.687081 AACAAGGTGTCGTCAATCTAAAAA 57.313 33.333 0.00 0.00 0.00 1.94
232 1756 6.687081 AAACAAGGTGTCGTCAATCTAAAA 57.313 33.333 0.00 0.00 0.00 1.52
233 1757 6.510478 CGAAAACAAGGTGTCGTCAATCTAAA 60.510 38.462 0.00 0.00 0.00 1.85
234 1758 5.050634 CGAAAACAAGGTGTCGTCAATCTAA 60.051 40.000 0.00 0.00 0.00 2.10
235 1759 4.446385 CGAAAACAAGGTGTCGTCAATCTA 59.554 41.667 0.00 0.00 0.00 1.98
236 1760 3.247648 CGAAAACAAGGTGTCGTCAATCT 59.752 43.478 0.00 0.00 0.00 2.40
237 1761 3.541711 CGAAAACAAGGTGTCGTCAATC 58.458 45.455 0.00 0.00 0.00 2.67
238 1762 2.286772 GCGAAAACAAGGTGTCGTCAAT 60.287 45.455 0.00 0.00 35.93 2.57
239 1763 1.062880 GCGAAAACAAGGTGTCGTCAA 59.937 47.619 0.00 0.00 35.93 3.18
240 1764 0.653636 GCGAAAACAAGGTGTCGTCA 59.346 50.000 0.00 0.00 35.93 4.35
241 1765 0.041576 GGCGAAAACAAGGTGTCGTC 60.042 55.000 0.00 0.00 35.93 4.20
242 1766 0.745128 TGGCGAAAACAAGGTGTCGT 60.745 50.000 0.00 0.00 35.93 4.34
243 1767 0.591170 ATGGCGAAAACAAGGTGTCG 59.409 50.000 0.00 0.00 36.59 4.35
267 1791 6.839820 AACTAGTTTTGGTAACTGAGAACG 57.160 37.500 1.12 0.00 37.61 3.95
321 1846 2.019951 GACGAGGCGTGCTCGAAAA 61.020 57.895 16.27 0.00 46.06 2.29
335 2176 2.725723 GGTTCAACGTGTTAATCGACGA 59.274 45.455 0.00 0.00 38.94 4.20
377 2220 4.841443 ACGAAATACAGGGGAAAACAAC 57.159 40.909 0.00 0.00 0.00 3.32
418 2303 4.126208 TGAATTACGGGCGTTTAGATCA 57.874 40.909 0.00 0.00 0.00 2.92
422 2307 4.868450 TGAATGAATTACGGGCGTTTAG 57.132 40.909 0.00 0.00 0.00 1.85
445 2330 3.255395 ACATGCCGTGTTTGAATGAATGA 59.745 39.130 0.00 0.00 38.01 2.57
446 2331 3.577667 ACATGCCGTGTTTGAATGAATG 58.422 40.909 0.00 0.00 38.01 2.67
447 2332 3.940209 ACATGCCGTGTTTGAATGAAT 57.060 38.095 0.00 0.00 38.01 2.57
505 2444 1.013596 CGACCACTGACTTTGTTGCA 58.986 50.000 0.00 0.00 0.00 4.08
601 2544 6.562640 GCAGTTCGAATCCGCGTAATTTATAA 60.563 38.462 4.92 0.00 35.37 0.98
611 2554 2.878991 TCGCAGTTCGAATCCGCG 60.879 61.111 24.12 24.12 45.36 6.46
666 2609 0.664767 GCGCGATCTGGATCTGTACC 60.665 60.000 12.10 0.00 35.72 3.34
752 2704 9.599866 TTTTATACTGCTACGAGTAGTACAGTA 57.400 33.333 21.56 21.56 44.18 2.74
753 2705 8.498054 TTTTATACTGCTACGAGTAGTACAGT 57.502 34.615 19.66 19.66 44.18 3.55
776 2763 0.392998 CGGAGCACTGGCCAGTATTT 60.393 55.000 37.27 24.52 40.20 1.40
783 2770 4.828925 GAGCTCGGAGCACTGGCC 62.829 72.222 29.88 0.00 45.56 5.36
801 2800 2.232452 GGGTGGAGATCGAGATGGTATG 59.768 54.545 0.00 0.00 0.00 2.39
803 2802 1.216930 TGGGTGGAGATCGAGATGGTA 59.783 52.381 0.00 0.00 0.00 3.25
804 2803 0.032117 TGGGTGGAGATCGAGATGGT 60.032 55.000 0.00 0.00 0.00 3.55
810 2809 1.342074 GGATGATGGGTGGAGATCGA 58.658 55.000 0.00 0.00 0.00 3.59
933 2962 2.387772 CGAGAGGGAGGGAGGGAGA 61.388 68.421 0.00 0.00 0.00 3.71
934 2963 2.197324 CGAGAGGGAGGGAGGGAG 59.803 72.222 0.00 0.00 0.00 4.30
983 3022 1.180029 CATTGCCTCAAACAGGGGAG 58.820 55.000 0.00 0.00 43.70 4.30
1301 3350 0.526096 CCAAATTGATTGCGCTCCCG 60.526 55.000 9.73 0.00 37.73 5.14
1394 3443 1.076533 CGCAGCAAACCGACGTCTAT 61.077 55.000 14.70 0.00 0.00 1.98
1397 3446 4.072088 CCGCAGCAAACCGACGTC 62.072 66.667 5.18 5.18 0.00 4.34
1415 3469 3.386768 TGCTAAATACGATCCAGCCTC 57.613 47.619 0.00 0.00 0.00 4.70
1490 3561 4.039488 AGCAGATCACTTGCAATTGGAAAA 59.961 37.500 15.87 3.05 0.00 2.29
1529 3601 3.935828 GTGAGCACCATCTTCCTCTTAAC 59.064 47.826 0.00 0.00 0.00 2.01
1584 3657 4.857871 TGCTACGTATTTGACATTCTGC 57.142 40.909 0.00 0.00 0.00 4.26
1587 3660 6.032722 ACGATTGCTACGTATTTGACATTC 57.967 37.500 0.00 0.00 42.17 2.67
1604 3677 7.535258 AGAATTCGAATCAAACAGAAACGATTG 59.465 33.333 11.83 0.00 37.57 2.67
1645 3718 7.374228 CGCATGCTCTGTTTTAATAACAGTATG 59.626 37.037 17.13 20.54 45.75 2.39
1649 3722 5.631026 ACGCATGCTCTGTTTTAATAACAG 58.369 37.500 17.13 17.39 46.67 3.16
1673 3755 9.823647 CTCCACACATAGAAGTAAATAATGACT 57.176 33.333 0.00 0.00 0.00 3.41
1773 3857 6.353323 TCTGTCTGGAGTATCTTACTGAGAG 58.647 44.000 0.00 0.00 39.59 3.20
1825 3913 6.017440 TGCGTTAAAAATAGCAGAACTGAACT 60.017 34.615 5.97 0.00 34.39 3.01
1851 3939 5.533154 TCCGAAAAAGAAGATAAAGGCACAA 59.467 36.000 0.00 0.00 0.00 3.33
1852 3940 5.067273 TCCGAAAAAGAAGATAAAGGCACA 58.933 37.500 0.00 0.00 0.00 4.57
1863 3951 3.128465 GCATCTGCTCCGAAAAAGAAG 57.872 47.619 0.00 0.00 38.21 2.85
1908 3996 3.553922 CCTGTAGCTCGAATTCATCTCCC 60.554 52.174 6.22 0.00 0.00 4.30
1977 4065 6.040842 ACTTTCCTGTCATTAGCAACAACAAT 59.959 34.615 0.00 0.00 0.00 2.71
1994 4082 1.654220 CCACGGTTGCACTTTCCTG 59.346 57.895 0.00 0.00 0.00 3.86
2740 4832 5.510674 CGATGAAGCATGCTAAAGAAGTTTG 59.489 40.000 23.00 0.00 0.00 2.93
2869 4961 4.054825 CGGCGGTGGCTGCAAAAT 62.055 61.111 0.00 0.00 39.01 1.82
2973 5065 5.821470 CAGTATCAATTGCCAGAACAGAGAT 59.179 40.000 0.00 0.00 0.00 2.75
2974 5066 5.046376 TCAGTATCAATTGCCAGAACAGAGA 60.046 40.000 0.00 0.00 0.00 3.10
2982 5076 6.263344 CAGTTGAATCAGTATCAATTGCCAG 58.737 40.000 0.00 0.00 37.59 4.85
3055 5149 0.038159 AGTTCTCCAAACTCTCGCCG 60.038 55.000 0.00 0.00 0.00 6.46
3058 5152 4.230657 CACTGTAGTTCTCCAAACTCTCG 58.769 47.826 0.00 0.00 0.00 4.04
3077 5171 5.730296 ACAAGTATGTTCTCTACAGCACT 57.270 39.130 0.00 0.00 40.83 4.40
3497 5593 5.474578 TCAGTGACAGCCTCCATATTATC 57.525 43.478 0.00 0.00 0.00 1.75
3669 5765 8.360390 TGATGCGTTATACTCTGATTCATAGTT 58.640 33.333 9.66 2.39 0.00 2.24
3899 6059 4.464008 TCCAGCAAGAAGTTTTCATCAGT 58.536 39.130 0.00 0.00 0.00 3.41
3978 6138 5.186603 TGGTTAGACAATGCCATATTTTGCA 59.813 36.000 0.00 0.00 42.52 4.08
4019 6179 2.396590 TGGAATACCGCCTGAAAGAC 57.603 50.000 0.00 0.00 39.42 3.01
4021 6181 2.874701 CTCATGGAATACCGCCTGAAAG 59.125 50.000 0.00 0.00 39.42 2.62
4024 6184 1.496060 ACTCATGGAATACCGCCTGA 58.504 50.000 0.00 0.00 39.42 3.86
4036 6196 1.262950 CTCTCGCTCTCGTACTCATGG 59.737 57.143 0.00 0.00 36.96 3.66
4192 6352 5.468072 CCACTAGTCATCTATCAAACATGCC 59.532 44.000 0.00 0.00 0.00 4.40
4299 6459 0.178975 AAAGCGGTCCATCAAACCCA 60.179 50.000 0.00 0.00 32.89 4.51
4378 6538 7.974675 TGCTAACTTCTCTAATGCAACAATAC 58.025 34.615 0.00 0.00 0.00 1.89
4410 6570 2.517959 CTTGAAGAACTGCCATGGGAA 58.482 47.619 15.13 0.00 0.00 3.97
4431 6591 7.130917 GCACTGATGATTTTCATTAGCAGTAG 58.869 38.462 8.66 6.25 42.27 2.57
4492 6653 1.306148 GGGTAAGTAATCCCAAGCGC 58.694 55.000 0.00 0.00 42.95 5.92
4506 6693 1.677300 CATGTGCGCCTTGGGGTAA 60.677 57.895 4.18 0.00 34.45 2.85
4507 6694 1.920734 ATCATGTGCGCCTTGGGGTA 61.921 55.000 4.18 0.00 34.45 3.69
4508 6695 2.786512 AATCATGTGCGCCTTGGGGT 62.787 55.000 4.18 0.00 34.45 4.95
4509 6696 2.053865 AATCATGTGCGCCTTGGGG 61.054 57.895 4.18 0.00 0.00 4.96
4643 6875 8.900983 ATTTAAATCACTGCTGGCTTTTAAAA 57.099 26.923 16.04 0.00 34.27 1.52
4689 6921 8.024285 CGCTGATTTAAACCATTGGTAACTTTA 58.976 33.333 9.20 1.11 33.12 1.85
4697 6929 2.166254 AGCCGCTGATTTAAACCATTGG 59.834 45.455 0.00 0.00 0.00 3.16
4709 6941 2.479566 TTCTCAGAAAAGCCGCTGAT 57.520 45.000 0.00 0.00 40.11 2.90
4724 6956 6.935208 ACCTTGTTAGACACCTTGTTATTCTC 59.065 38.462 0.00 0.00 0.00 2.87
4739 6971 2.036733 CCTTCCGTGTCACCTTGTTAGA 59.963 50.000 0.00 0.00 0.00 2.10
4741 6973 2.040939 TCCTTCCGTGTCACCTTGTTA 58.959 47.619 0.00 0.00 0.00 2.41
4743 6975 1.002087 GATCCTTCCGTGTCACCTTGT 59.998 52.381 0.00 0.00 0.00 3.16
4744 6976 1.001974 TGATCCTTCCGTGTCACCTTG 59.998 52.381 0.00 0.00 0.00 3.61
4745 6977 1.276421 CTGATCCTTCCGTGTCACCTT 59.724 52.381 0.00 0.00 0.00 3.50
4746 6978 0.898320 CTGATCCTTCCGTGTCACCT 59.102 55.000 0.00 0.00 0.00 4.00
4747 6979 0.108138 CCTGATCCTTCCGTGTCACC 60.108 60.000 0.00 0.00 0.00 4.02
4748 6980 0.608640 ACCTGATCCTTCCGTGTCAC 59.391 55.000 0.00 0.00 0.00 3.67
4749 6981 1.275291 GAACCTGATCCTTCCGTGTCA 59.725 52.381 0.00 0.00 0.00 3.58
4750 6982 1.405661 GGAACCTGATCCTTCCGTGTC 60.406 57.143 0.00 0.00 36.50 3.67
4751 6983 0.613777 GGAACCTGATCCTTCCGTGT 59.386 55.000 0.00 0.00 36.50 4.49
4752 6984 3.460648 GGAACCTGATCCTTCCGTG 57.539 57.895 0.00 0.00 36.50 4.94
4781 7013 4.907879 ACCTTCTCTTTGTTTTGCTGAG 57.092 40.909 0.00 0.00 0.00 3.35
4784 7016 5.509670 GGCATAACCTTCTCTTTGTTTTGCT 60.510 40.000 13.74 0.00 42.61 3.91
4790 7022 3.330701 TGAGGGCATAACCTTCTCTTTGT 59.669 43.478 0.00 0.00 44.89 2.83
4820 7056 8.105197 CAGATTCCTGATATTCATTATCACCCA 58.895 37.037 0.00 0.00 41.41 4.51
4860 7097 8.538701 AGAATATCATAAGCTGTCCTCCTTATG 58.461 37.037 12.01 12.01 46.17 1.90
4866 7103 5.868801 GCTGAGAATATCATAAGCTGTCCTC 59.131 44.000 0.00 0.00 37.28 3.71
4870 7107 7.555554 ACTTTTGCTGAGAATATCATAAGCTGT 59.444 33.333 0.00 0.00 37.28 4.40
4879 7116 6.481644 CAGGGTAGACTTTTGCTGAGAATATC 59.518 42.308 0.00 0.00 0.00 1.63
4887 7124 2.814336 GGAACAGGGTAGACTTTTGCTG 59.186 50.000 0.00 0.00 0.00 4.41
4925 7162 3.003480 GGAGAATCAGGGAACTTGTTCG 58.997 50.000 7.32 0.00 40.21 3.95
4938 7175 5.988310 AATGCATTTGTCTTGGAGAATCA 57.012 34.783 5.99 0.00 36.25 2.57
4949 7186 6.204359 CCTGTGCTATCTTAATGCATTTGTC 58.796 40.000 18.75 1.45 39.00 3.18
4959 7196 5.163195 GGATTCTTCCCCTGTGCTATCTTAA 60.163 44.000 0.00 0.00 35.84 1.85
4962 7199 2.708325 GGATTCTTCCCCTGTGCTATCT 59.292 50.000 0.00 0.00 35.84 1.98
4982 7219 2.828877 TCGTACATAAAATCGCCCTGG 58.171 47.619 0.00 0.00 0.00 4.45
5006 7243 5.009631 CCATTATGTTCTCTTGTGGTTCCA 58.990 41.667 0.00 0.00 0.00 3.53
5035 7272 9.550811 TCTCAAGTACGTATATAATATTGCACG 57.449 33.333 0.00 5.04 35.62 5.34
5051 7288 5.063564 GTGCTCCCTTTATTTCTCAAGTACG 59.936 44.000 0.00 0.00 0.00 3.67
5058 7295 6.765915 ATTGAAGTGCTCCCTTTATTTCTC 57.234 37.500 0.00 0.00 0.00 2.87
5086 7323 2.084546 GTGATGTTGGTTCCCTGTAGC 58.915 52.381 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.