Multiple sequence alignment - TraesCS5B01G235500

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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 TraesCS5B01G235500 chr5B 100.000 5622 0 0 1 5622 415794801 415800422 0.000000e+00 10382.0
1 TraesCS5B01G235500 chr5D 94.156 5185 189 42 117 5251 352823371 352828491 0.000000e+00 7792.0
2 TraesCS5B01G235500 chr5D 94.346 283 16 0 5249 5531 352828620 352828902 8.650000e-118 435.0
3 TraesCS5B01G235500 chr5D 90.625 96 3 3 5533 5622 352829088 352829183 7.650000e-24 122.0
4 TraesCS5B01G235500 chr5A 90.308 4798 260 81 117 4794 453007927 453003215 0.000000e+00 6095.0
5 TraesCS5B01G235500 chr6B 85.882 255 31 4 4844 5096 100162892 100162641 3.340000e-67 267.0
6 TraesCS5B01G235500 chr6B 88.889 144 14 2 4860 5003 625368116 625367975 5.790000e-40 176.0
7 TraesCS5B01G235500 chr6B 85.714 63 8 1 5088 5150 625367534 625367473 1.310000e-06 65.8
8 TraesCS5B01G235500 chr4B 98.276 116 2 0 1 116 91735282 91735167 2.660000e-48 204.0
9 TraesCS5B01G235500 chr4B 88.679 159 18 0 4845 5003 184238147 184237989 1.600000e-45 195.0
10 TraesCS5B01G235500 chr4B 96.703 91 3 0 26 116 91735118 91735028 9.760000e-33 152.0
11 TraesCS5B01G235500 chr4A 89.744 156 14 2 4855 5010 547311376 547311223 1.240000e-46 198.0
12 TraesCS5B01G235500 chr4A 88.125 160 19 0 4844 5003 453609484 453609325 2.070000e-44 191.0
13 TraesCS5B01G235500 chr3B 97.414 116 3 0 1 116 119962592 119962707 1.240000e-46 198.0
14 TraesCS5B01G235500 chr2D 91.156 147 12 1 4857 5003 11394115 11393970 1.240000e-46 198.0
15 TraesCS5B01G235500 chr7B 95.000 120 6 0 1 120 36056214 36056095 7.440000e-44 189.0
16 TraesCS5B01G235500 chr7B 86.585 164 20 2 4840 5003 89952171 89952332 4.470000e-41 180.0
17 TraesCS5B01G235500 chr7A 86.667 165 21 1 4840 5004 128783043 128783206 1.240000e-41 182.0
18 TraesCS5B01G235500 chr1D 84.211 152 15 5 5000 5150 261744735 261744878 7.590000e-29 139.0
19 TraesCS5B01G235500 chr3D 92.727 55 4 0 5096 5150 266414300 266414246 4.670000e-11 80.5
20 TraesCS5B01G235500 chr6D 88.889 63 6 1 5088 5150 414780670 414780609 6.040000e-10 76.8
21 TraesCS5B01G235500 chr3A 90.909 55 5 0 5096 5150 301121426 301121372 2.170000e-09 75.0


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 TraesCS5B01G235500 chr5B 415794801 415800422 5621 False 10382 10382 100.000000 1 5622 1 chr5B.!!$F1 5621
1 TraesCS5B01G235500 chr5D 352823371 352829183 5812 False 2783 7792 93.042333 117 5622 3 chr5D.!!$F1 5505
2 TraesCS5B01G235500 chr5A 453003215 453007927 4712 True 6095 6095 90.308000 117 4794 1 chr5A.!!$R1 4677

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
368 375 0.106519 ACATGCTCCATGGTTAGCCC 60.107 55.000 19.80 2.04 45.16 5.19 F
728 749 0.529992 GATCGGGGGCAAACTAGTCG 60.530 60.000 0.00 0.00 0.00 4.18 F
1333 1405 0.612229 CCATGCCGATCTAGCCAGAT 59.388 55.000 0.00 0.00 44.51 2.90 F
1563 1645 0.621571 CCACCCTGGGATTCTCTCCA 60.622 60.000 22.23 0.00 46.98 3.86 F
2344 2446 1.217183 AGCATGGCATTCCCTCTCAAT 59.783 47.619 0.00 0.00 0.00 2.57 F
3241 3351 0.896226 GTAGGTCTTCTTCGCCCAGT 59.104 55.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2446 1.668826 AGGGCAATGTCCTCCTGTTA 58.331 50.000 0.00 0.00 27.34 2.41 R
2461 2563 1.152546 AGGACCGCTTTTGGCCTTT 60.153 52.632 3.32 0.00 33.47 3.11 R
2764 2866 0.299895 GCAATGACGCAGATGACTCG 59.700 55.000 0.00 0.00 0.00 4.18 R
3241 3351 0.968405 GAACAAATGAAGGCCTGGCA 59.032 50.000 22.05 8.84 0.00 4.92 R
4081 4214 0.748005 GCTGGAATTAAGAGCGCCCA 60.748 55.000 2.29 0.00 0.00 5.36 R
4672 4808 0.323629 TTCATCAACGGAGACCCCAC 59.676 55.000 0.00 0.00 34.14 4.61 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
36 37 2.542766 TTTTTCATCTCGCGAATGGC 57.457 45.000 22.32 0.00 38.69 4.40
37 38 0.732571 TTTTCATCTCGCGAATGGCC 59.267 50.000 22.32 0.00 38.94 5.36
38 39 0.392327 TTTCATCTCGCGAATGGCCA 60.392 50.000 22.32 8.56 38.94 5.36
39 40 0.392327 TTCATCTCGCGAATGGCCAA 60.392 50.000 10.96 12.34 38.94 4.52
40 41 0.392327 TCATCTCGCGAATGGCCAAA 60.392 50.000 10.96 7.87 38.94 3.28
41 42 0.664761 CATCTCGCGAATGGCCAAAT 59.335 50.000 10.96 0.29 38.94 2.32
42 43 0.664761 ATCTCGCGAATGGCCAAATG 59.335 50.000 10.96 2.77 38.94 2.32
43 44 1.064621 CTCGCGAATGGCCAAATGG 59.935 57.895 10.96 4.29 38.94 3.16
44 45 2.104729 CGCGAATGGCCAAATGGG 59.895 61.111 10.96 6.85 38.94 4.00
95 96 4.763593 CGACATTTCGGCGCAATT 57.236 50.000 10.83 0.00 41.89 2.32
96 97 3.887777 CGACATTTCGGCGCAATTA 57.112 47.368 10.83 0.00 41.89 1.40
97 98 1.730176 CGACATTTCGGCGCAATTAG 58.270 50.000 10.83 0.00 41.89 1.73
98 99 1.466855 GACATTTCGGCGCAATTAGC 58.533 50.000 10.83 0.00 40.87 3.09
111 112 2.221981 GCAATTAGCGTCACATAGGAGC 59.778 50.000 0.00 0.00 0.00 4.70
112 113 3.722147 CAATTAGCGTCACATAGGAGCT 58.278 45.455 0.00 0.00 41.45 4.09
113 114 3.651803 ATTAGCGTCACATAGGAGCTC 57.348 47.619 4.71 4.71 39.14 4.09
114 115 2.350057 TAGCGTCACATAGGAGCTCT 57.650 50.000 14.64 2.18 39.14 4.09
115 116 1.028905 AGCGTCACATAGGAGCTCTC 58.971 55.000 14.64 3.76 31.94 3.20
127 128 1.066071 GGAGCTCTCCTTTGGTACACC 60.066 57.143 14.64 0.00 46.16 4.16
128 129 1.903183 GAGCTCTCCTTTGGTACACCT 59.097 52.381 6.43 0.00 39.29 4.00
148 149 2.112297 GGAACGTTCCTGCCACCA 59.888 61.111 34.98 0.00 44.11 4.17
154 155 1.234615 CGTTCCTGCCACCAAACGAT 61.235 55.000 0.51 0.00 45.36 3.73
163 164 1.666599 CCACCAAACGATGCACACATG 60.667 52.381 0.00 0.00 36.35 3.21
167 168 2.309693 CAAACGATGCACACATGACAC 58.690 47.619 0.00 0.00 36.35 3.67
168 169 1.592064 AACGATGCACACATGACACA 58.408 45.000 0.00 0.00 36.35 3.72
169 170 1.812235 ACGATGCACACATGACACAT 58.188 45.000 0.00 0.00 36.35 3.21
170 171 1.733912 ACGATGCACACATGACACATC 59.266 47.619 0.00 6.24 36.35 3.06
171 172 2.447089 GATGCACACATGACACATCG 57.553 50.000 0.00 0.00 36.35 3.84
172 173 0.448990 ATGCACACATGACACATCGC 59.551 50.000 0.00 0.00 34.35 4.58
173 174 0.883814 TGCACACATGACACATCGCA 60.884 50.000 0.00 0.00 0.00 5.10
174 175 0.453282 GCACACATGACACATCGCAC 60.453 55.000 0.00 0.00 0.00 5.34
175 176 0.867086 CACACATGACACATCGCACA 59.133 50.000 0.00 0.00 0.00 4.57
368 375 0.106519 ACATGCTCCATGGTTAGCCC 60.107 55.000 19.80 2.04 45.16 5.19
392 399 4.093952 CTGAAACTGCGCGCCCTG 62.094 66.667 30.77 20.63 0.00 4.45
495 503 1.258676 GGACTTTCACTCCTCGACCT 58.741 55.000 0.00 0.00 0.00 3.85
588 609 1.000359 GCCATGCTGGGGTAAACCT 60.000 57.895 0.00 0.00 38.19 3.50
589 610 1.322538 GCCATGCTGGGGTAAACCTG 61.323 60.000 0.00 0.00 38.19 4.00
724 745 2.904905 CCGATCGGGGGCAAACTA 59.095 61.111 26.95 0.00 0.00 2.24
725 746 1.227556 CCGATCGGGGGCAAACTAG 60.228 63.158 26.95 0.00 0.00 2.57
726 747 1.520666 CGATCGGGGGCAAACTAGT 59.479 57.895 7.38 0.00 0.00 2.57
728 749 0.529992 GATCGGGGGCAAACTAGTCG 60.530 60.000 0.00 0.00 0.00 4.18
729 750 0.974010 ATCGGGGGCAAACTAGTCGA 60.974 55.000 0.00 0.00 0.00 4.20
730 751 0.974010 TCGGGGGCAAACTAGTCGAT 60.974 55.000 0.00 0.00 0.00 3.59
731 752 0.748450 CGGGGGCAAACTAGTCGATA 59.252 55.000 0.00 0.00 0.00 2.92
836 861 0.836830 TACACCCACGTCCCAATCCA 60.837 55.000 0.00 0.00 0.00 3.41
840 865 1.078426 CCACGTCCCAATCCACTCC 60.078 63.158 0.00 0.00 0.00 3.85
843 868 2.124695 GTCCCAATCCACTCCGCC 60.125 66.667 0.00 0.00 0.00 6.13
846 871 2.202932 CCAATCCACTCCGCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
887 912 1.949799 ATGCCAGGACTTCTCACTCT 58.050 50.000 0.00 0.00 0.00 3.24
1000 1039 7.721286 TGCTTTCTTGTTTTTGAGACAAAAA 57.279 28.000 15.30 15.30 36.64 1.94
1030 1069 2.467826 GGTGATTGCGAGCTGGAGC 61.468 63.158 0.00 0.00 42.49 4.70
1065 1107 3.787001 GAGGAGGAGGGGGTTGCG 61.787 72.222 0.00 0.00 0.00 4.85
1290 1357 4.697514 GCACATAGAATCTCTTACTGCCA 58.302 43.478 0.00 0.00 0.00 4.92
1333 1405 0.612229 CCATGCCGATCTAGCCAGAT 59.388 55.000 0.00 0.00 44.51 2.90
1412 1491 7.781324 AAAACCCAGAAATGACATGATTAGT 57.219 32.000 0.00 0.00 0.00 2.24
1442 1524 2.656560 AGCGATCTAACGACAAAGCT 57.343 45.000 0.00 0.00 35.09 3.74
1563 1645 0.621571 CCACCCTGGGATTCTCTCCA 60.622 60.000 22.23 0.00 46.98 3.86
1745 1840 5.163854 CCTTGTATTCTTACCAGCGTTCTTG 60.164 44.000 0.00 0.00 0.00 3.02
1746 1841 3.682858 TGTATTCTTACCAGCGTTCTTGC 59.317 43.478 0.00 0.00 0.00 4.01
1962 2064 3.613432 CGTACTAGGTGGTGTGAGGTTTC 60.613 52.174 0.00 0.00 0.00 2.78
2179 2281 2.159099 GGGACTTGTGTCATCGCAGATA 60.159 50.000 0.00 0.00 44.61 1.98
2200 2302 3.718210 CTCCGGCGTGTTCCCTAGC 62.718 68.421 6.01 0.00 0.00 3.42
2335 2437 2.106332 GGCAGCAGCATGGCATTC 59.894 61.111 2.65 0.00 44.71 2.67
2344 2446 1.217183 AGCATGGCATTCCCTCTCAAT 59.783 47.619 0.00 0.00 0.00 2.57
2347 2449 3.005155 GCATGGCATTCCCTCTCAATAAC 59.995 47.826 0.00 0.00 0.00 1.89
2422 2524 2.032634 GTCAAACTCCGGCGATGCA 61.033 57.895 9.30 0.00 0.00 3.96
2455 2557 2.440796 ACATTGCCCCATGCTCGG 60.441 61.111 0.00 0.00 42.00 4.63
2663 2765 1.913778 TACGAGTGGAACAGCTGGTA 58.086 50.000 19.93 4.89 41.80 3.25
2764 2866 2.032722 CCGACGACTAGATACTGCAGTC 60.033 54.545 25.56 10.38 36.23 3.51
2828 2930 6.317893 ACAAGGTATTAAGAAATTGCTACCCG 59.682 38.462 0.07 0.00 0.00 5.28
3049 3159 7.173218 CACTTCTAAGCTGAATAACACCAGAAA 59.827 37.037 0.00 0.00 32.37 2.52
3130 3240 8.031277 GCTTCTTTGTTTGGTTTCATATCAGAT 58.969 33.333 0.00 0.00 0.00 2.90
3167 3277 3.071023 CGTAGAAGATTCAGCCCCCATTA 59.929 47.826 0.00 0.00 0.00 1.90
3241 3351 0.896226 GTAGGTCTTCTTCGCCCAGT 59.104 55.000 0.00 0.00 0.00 4.00
3498 3612 7.172342 TGCACATTAAAGTAAGGGACTGTTAT 58.828 34.615 0.00 0.00 40.86 1.89
3586 3700 7.931275 ACTTGTAGCTTAACTTCTGAAAAAGG 58.069 34.615 0.00 0.00 0.00 3.11
3592 3706 7.847096 AGCTTAACTTCTGAAAAAGGGAAAAA 58.153 30.769 8.16 0.00 0.00 1.94
3593 3707 8.486210 AGCTTAACTTCTGAAAAAGGGAAAAAT 58.514 29.630 8.16 0.00 0.00 1.82
3594 3708 8.551205 GCTTAACTTCTGAAAAAGGGAAAAATG 58.449 33.333 8.16 0.00 0.00 2.32
3595 3709 6.925610 AACTTCTGAAAAAGGGAAAAATGC 57.074 33.333 0.00 0.00 0.00 3.56
3635 3749 6.638168 ATCTCGTATGATGTGCAAATATCG 57.362 37.500 0.00 0.00 0.00 2.92
3638 3752 6.868339 TCTCGTATGATGTGCAAATATCGAAT 59.132 34.615 0.00 0.00 0.00 3.34
3872 4004 9.708092 GTAAGACCCCTGCTAATATTTTACTAG 57.292 37.037 0.00 0.00 0.00 2.57
3898 4031 9.865321 GTCCATAAATATTATAGTAGCAACGGA 57.135 33.333 0.00 0.00 0.00 4.69
3942 4075 6.591750 ACTAAGCAAGTCTAGCTACAGAAA 57.408 37.500 0.00 0.00 42.53 2.52
3947 4080 6.525629 AGCAAGTCTAGCTACAGAAAAAGAA 58.474 36.000 0.00 0.00 41.32 2.52
3977 4110 4.038042 TGACTAGTCTTAGGATTGGCATCG 59.962 45.833 23.01 0.00 0.00 3.84
4019 4152 5.291971 AGCATGTGAGAACATTTTCCAAAC 58.708 37.500 0.00 0.00 31.28 2.93
4080 4213 3.817647 GGACATCAGTCATATTCTTGGGC 59.182 47.826 0.00 0.00 46.80 5.36
4081 4214 4.445448 GGACATCAGTCATATTCTTGGGCT 60.445 45.833 0.00 0.00 46.80 5.19
4082 4215 4.458397 ACATCAGTCATATTCTTGGGCTG 58.542 43.478 0.00 0.00 0.00 4.85
4083 4216 3.565764 TCAGTCATATTCTTGGGCTGG 57.434 47.619 0.00 0.00 0.00 4.85
4084 4217 2.173356 TCAGTCATATTCTTGGGCTGGG 59.827 50.000 0.00 0.00 0.00 4.45
4085 4218 1.133668 AGTCATATTCTTGGGCTGGGC 60.134 52.381 0.00 0.00 0.00 5.36
4093 4226 2.819984 CTTGGGCTGGGCGCTCTTAA 62.820 60.000 9.62 0.00 40.82 1.85
4096 4229 1.448119 GGGCTGGGCGCTCTTAATTC 61.448 60.000 9.62 0.00 38.48 2.17
4185 4318 2.477245 TCTCCAGCTGCCCAAGTATAA 58.523 47.619 8.66 0.00 0.00 0.98
4274 4409 6.873605 CCTGTAACTGTTGTCTCATGTCATTA 59.126 38.462 2.69 0.00 0.00 1.90
4383 4519 4.270834 TCTCTATTGCCGTCTAGTTGACT 58.729 43.478 3.25 0.00 43.25 3.41
4567 4703 4.616802 GCCAAAAAGACATCACATGTTACG 59.383 41.667 0.00 0.00 45.03 3.18
4672 4808 2.130395 CATACTGATGCCTGCTGTACG 58.870 52.381 0.00 0.00 0.00 3.67
4677 4813 3.329542 ATGCCTGCTGTACGTGGGG 62.330 63.158 0.00 0.00 0.00 4.96
4766 4904 2.353109 CGCTCTTTCTGTCACATCAGGA 60.353 50.000 0.00 0.00 36.25 3.86
4813 4951 7.517614 TGCCAATGTTCACTTTTCAGTATTA 57.482 32.000 0.00 0.00 0.00 0.98
4855 4996 7.113658 TGTTTAATTACAAGCTCAAAACCCA 57.886 32.000 0.00 0.00 0.00 4.51
4907 5048 6.459670 AGTGGTTCAACGTAGGAAAATTTT 57.540 33.333 2.28 2.28 0.00 1.82
4919 5060 6.586082 CGTAGGAAAATTTTGATTGGGTTGAG 59.414 38.462 8.47 0.00 0.00 3.02
4921 5062 7.135591 AGGAAAATTTTGATTGGGTTGAGAA 57.864 32.000 8.47 0.00 0.00 2.87
4979 5120 9.347240 CAAAGGTAAGGAAAGATATGATGTGAT 57.653 33.333 0.00 0.00 0.00 3.06
4989 5130 9.447040 GAAAGATATGATGTGATTGACATTGTG 57.553 33.333 0.00 0.00 45.90 3.33
4993 5134 5.529014 TGATGTGATTGACATTGTGTACG 57.471 39.130 0.00 0.00 45.90 3.67
5024 5165 3.850122 GGATTTCTTTCCCTGGAAACG 57.150 47.619 7.26 4.89 38.95 3.60
5025 5166 3.418047 GGATTTCTTTCCCTGGAAACGA 58.582 45.455 7.26 6.92 38.95 3.85
5026 5167 3.440522 GGATTTCTTTCCCTGGAAACGAG 59.559 47.826 7.26 0.00 38.95 4.18
5027 5168 2.561478 TTCTTTCCCTGGAAACGAGG 57.439 50.000 7.26 0.00 38.95 4.63
5038 5179 0.685660 GAAACGAGGAGGTGGGAGTT 59.314 55.000 0.00 0.00 0.00 3.01
5040 5181 1.481056 AACGAGGAGGTGGGAGTTGG 61.481 60.000 0.00 0.00 0.00 3.77
5102 5243 0.251608 AAAAATCGGTGGGAGGGGTG 60.252 55.000 0.00 0.00 0.00 4.61
5134 5275 3.865700 CGAAAGCAACAAACTCCCC 57.134 52.632 0.00 0.00 0.00 4.81
5155 5296 7.253421 TCCCCTTTAATAGTAGAGATATGCCA 58.747 38.462 0.00 0.00 0.00 4.92
5166 5307 6.933521 AGTAGAGATATGCCACAATGATGTTC 59.066 38.462 0.00 0.00 37.82 3.18
5175 5316 3.304592 CCACAATGATGTTCGCAGTTCAA 60.305 43.478 0.00 0.00 37.82 2.69
5183 5324 6.676950 TGATGTTCGCAGTTCAAAATTATGT 58.323 32.000 0.00 0.00 0.00 2.29
5192 5333 7.754924 CGCAGTTCAAAATTATGTCACCTAATT 59.245 33.333 0.00 0.00 31.70 1.40
5238 5379 8.050778 TGTTCACACATAAAACATAATCCCTC 57.949 34.615 0.00 0.00 0.00 4.30
5239 5380 7.667635 TGTTCACACATAAAACATAATCCCTCA 59.332 33.333 0.00 0.00 0.00 3.86
5240 5381 8.519526 GTTCACACATAAAACATAATCCCTCAA 58.480 33.333 0.00 0.00 0.00 3.02
5242 5383 9.253832 TCACACATAAAACATAATCCCTCAATT 57.746 29.630 0.00 0.00 0.00 2.32
5243 5384 9.874205 CACACATAAAACATAATCCCTCAATTT 57.126 29.630 0.00 0.00 0.00 1.82
5270 5545 2.361610 CCCCATGGCAGTGTCACC 60.362 66.667 6.09 0.00 0.00 4.02
5273 5548 3.792047 CATGGCAGTGTCACCGCG 61.792 66.667 0.00 0.00 0.00 6.46
5327 5602 2.160853 GTTGGGGAGGAGGGTGGTT 61.161 63.158 0.00 0.00 0.00 3.67
5376 5651 4.008933 GCTGGTGGTCGCAGGAGT 62.009 66.667 0.00 0.00 0.00 3.85
5427 5702 4.455533 TGACACAGCGCATAAAGAAGAAAT 59.544 37.500 11.47 0.00 0.00 2.17
5458 5733 7.027778 ACTGTGTTGATCCTTTAAGAACAAC 57.972 36.000 15.60 15.60 45.01 3.32
5490 5765 2.957402 TGATTTGAGGCAGGTTGAGT 57.043 45.000 0.00 0.00 0.00 3.41
5491 5766 3.228188 TGATTTGAGGCAGGTTGAGTT 57.772 42.857 0.00 0.00 0.00 3.01
5531 5806 5.314923 ACTTCATGCAACATGTTCCATAC 57.685 39.130 14.58 0.55 0.00 2.39
5602 6064 3.278668 GCCTCAGATGCTGGCATATAT 57.721 47.619 8.11 0.00 45.46 0.86
5603 6065 4.412796 GCCTCAGATGCTGGCATATATA 57.587 45.455 8.11 0.00 45.46 0.86
5605 6070 4.815308 GCCTCAGATGCTGGCATATATAAG 59.185 45.833 8.11 4.29 45.46 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.132262 GGCCATTCGCGAGATGAAAAA 59.868 47.619 23.73 4.36 41.60 1.94
18 19 0.732571 GGCCATTCGCGAGATGAAAA 59.267 50.000 23.73 5.04 41.60 2.29
19 20 0.392327 TGGCCATTCGCGAGATGAAA 60.392 50.000 23.73 5.72 41.60 2.69
20 21 0.392327 TTGGCCATTCGCGAGATGAA 60.392 50.000 23.73 12.89 41.60 2.57
21 22 0.392327 TTTGGCCATTCGCGAGATGA 60.392 50.000 23.73 6.75 41.60 2.92
22 23 0.664761 ATTTGGCCATTCGCGAGATG 59.335 50.000 6.09 15.41 41.60 2.90
23 24 0.664761 CATTTGGCCATTCGCGAGAT 59.335 50.000 6.09 3.28 41.60 2.75
24 25 1.375853 CCATTTGGCCATTCGCGAGA 61.376 55.000 6.09 0.55 38.94 4.04
25 26 1.064621 CCATTTGGCCATTCGCGAG 59.935 57.895 6.09 0.00 38.94 5.03
26 27 2.413963 CCCATTTGGCCATTCGCGA 61.414 57.895 6.09 3.71 38.94 5.87
27 28 2.104729 CCCATTTGGCCATTCGCG 59.895 61.111 6.09 0.00 38.94 5.87
50 51 3.726517 CTGGCGTGCCGAAACTGG 61.727 66.667 6.37 0.00 39.42 4.00
51 52 2.972505 ACTGGCGTGCCGAAACTG 60.973 61.111 6.37 0.00 39.42 3.16
52 53 2.972505 CACTGGCGTGCCGAAACT 60.973 61.111 6.37 0.00 39.42 2.66
79 80 1.466855 GCTAATTGCGCCGAAATGTC 58.533 50.000 4.18 0.00 0.00 3.06
80 81 3.622459 GCTAATTGCGCCGAAATGT 57.378 47.368 4.18 0.00 0.00 2.71
90 91 2.221981 GCTCCTATGTGACGCTAATTGC 59.778 50.000 0.00 0.00 38.57 3.56
91 92 3.722147 AGCTCCTATGTGACGCTAATTG 58.278 45.455 0.00 0.00 0.00 2.32
92 93 3.639094 AGAGCTCCTATGTGACGCTAATT 59.361 43.478 10.93 0.00 0.00 1.40
93 94 3.226777 AGAGCTCCTATGTGACGCTAAT 58.773 45.455 10.93 0.00 0.00 1.73
94 95 2.619177 GAGAGCTCCTATGTGACGCTAA 59.381 50.000 10.93 0.00 0.00 3.09
95 96 2.222886 GAGAGCTCCTATGTGACGCTA 58.777 52.381 10.93 0.00 0.00 4.26
96 97 1.028905 GAGAGCTCCTATGTGACGCT 58.971 55.000 10.93 0.00 0.00 5.07
97 98 0.031449 GGAGAGCTCCTATGTGACGC 59.969 60.000 10.93 0.00 46.16 5.19
103 104 7.420299 GGTGTACCAAAGGAGAGCTCCTATG 62.420 52.000 18.82 12.44 46.96 2.23
104 105 5.424008 GGTGTACCAAAGGAGAGCTCCTAT 61.424 50.000 18.82 7.32 46.96 2.57
105 106 4.134361 GGTGTACCAAAGGAGAGCTCCTA 61.134 52.174 18.82 0.76 46.96 2.94
107 108 1.066071 GGTGTACCAAAGGAGAGCTCC 60.066 57.143 10.93 8.50 42.15 4.70
108 109 1.903183 AGGTGTACCAAAGGAGAGCTC 59.097 52.381 5.27 5.27 38.89 4.09
109 110 2.031495 AGGTGTACCAAAGGAGAGCT 57.969 50.000 3.56 0.00 38.89 4.09
110 111 2.861147 AAGGTGTACCAAAGGAGAGC 57.139 50.000 3.56 0.00 38.89 4.09
111 112 4.094476 TCCTAAGGTGTACCAAAGGAGAG 58.906 47.826 16.19 0.00 41.45 3.20
112 113 4.136341 TCCTAAGGTGTACCAAAGGAGA 57.864 45.455 16.19 1.44 41.45 3.71
113 114 4.576879 GTTCCTAAGGTGTACCAAAGGAG 58.423 47.826 18.20 3.76 44.67 3.69
114 115 3.007182 CGTTCCTAAGGTGTACCAAAGGA 59.993 47.826 16.19 16.19 43.32 3.36
115 116 3.244318 ACGTTCCTAAGGTGTACCAAAGG 60.244 47.826 12.93 12.93 39.94 3.11
148 149 1.946081 TGTGTCATGTGTGCATCGTTT 59.054 42.857 0.00 0.00 31.99 3.60
154 155 0.883814 TGCGATGTGTCATGTGTGCA 60.884 50.000 0.00 0.00 0.00 4.57
163 164 2.746277 GGGGGTGTGCGATGTGTC 60.746 66.667 0.00 0.00 0.00 3.67
167 168 3.443045 GCTTGGGGGTGTGCGATG 61.443 66.667 0.00 0.00 0.00 3.84
168 169 3.628646 GAGCTTGGGGGTGTGCGAT 62.629 63.158 0.00 0.00 0.00 4.58
169 170 4.329545 GAGCTTGGGGGTGTGCGA 62.330 66.667 0.00 0.00 0.00 5.10
170 171 4.335647 AGAGCTTGGGGGTGTGCG 62.336 66.667 0.00 0.00 0.00 5.34
171 172 2.674380 CAGAGCTTGGGGGTGTGC 60.674 66.667 0.00 0.00 30.35 4.57
172 173 1.601759 CACAGAGCTTGGGGGTGTG 60.602 63.158 0.00 0.00 41.59 3.82
173 174 2.839098 CACAGAGCTTGGGGGTGT 59.161 61.111 0.00 0.00 0.00 4.16
174 175 2.674380 GCACAGAGCTTGGGGGTG 60.674 66.667 0.00 0.00 41.15 4.61
194 195 4.072088 GCCACGGTTCGCTGAACG 62.072 66.667 12.88 4.13 42.78 3.95
217 218 3.991051 ACGTGCCGTGCTACTGCT 61.991 61.111 0.00 0.00 39.18 4.24
301 302 3.650950 AGGTTGCATGGGTCCGCT 61.651 61.111 0.00 0.00 0.00 5.52
623 644 1.385347 TCACCAACTCCACCCACCT 60.385 57.895 0.00 0.00 0.00 4.00
722 743 5.396484 TCAACGGACAGTTTTATCGACTAG 58.604 41.667 0.00 0.00 42.02 2.57
723 744 5.375417 TCAACGGACAGTTTTATCGACTA 57.625 39.130 0.00 0.00 42.02 2.59
724 745 4.247267 TCAACGGACAGTTTTATCGACT 57.753 40.909 0.00 0.00 42.02 4.18
725 746 5.526010 AATCAACGGACAGTTTTATCGAC 57.474 39.130 0.00 0.00 42.02 4.20
726 747 5.697178 TGAAATCAACGGACAGTTTTATCGA 59.303 36.000 0.00 0.00 42.02 3.59
728 749 5.795441 GCTGAAATCAACGGACAGTTTTATC 59.205 40.000 0.00 0.00 42.02 1.75
729 750 5.616866 CGCTGAAATCAACGGACAGTTTTAT 60.617 40.000 0.00 0.00 42.02 1.40
730 751 4.319190 CGCTGAAATCAACGGACAGTTTTA 60.319 41.667 0.00 0.00 42.02 1.52
731 752 3.548014 CGCTGAAATCAACGGACAGTTTT 60.548 43.478 0.00 0.00 42.02 2.43
846 871 0.101759 TAATAGACGTGTCAGGCGGC 59.898 55.000 0.00 0.00 37.70 6.53
887 912 3.436577 TTAAAAGTGGCGGGTATGGAA 57.563 42.857 0.00 0.00 0.00 3.53
920 945 0.035630 GCTGTGCTCTCCCACTCAAT 60.036 55.000 0.00 0.00 36.68 2.57
926 951 0.250467 GAGTTTGCTGTGCTCTCCCA 60.250 55.000 0.00 0.00 0.00 4.37
1030 1069 4.250305 CCCCATTACGCCCCGGAG 62.250 72.222 0.73 0.00 0.00 4.63
1083 1125 2.892425 CGCATTGCCCTCTCCGAC 60.892 66.667 2.41 0.00 0.00 4.79
1220 1286 1.833787 GACGCCCAAGGAAGGTGGTA 61.834 60.000 0.00 0.00 39.30 3.25
1333 1405 2.584064 CGACAGGCCATGGTGCTA 59.416 61.111 14.67 0.00 0.00 3.49
1384 1463 5.389520 TCATGTCATTTCTGGGTTTTACCA 58.610 37.500 0.00 0.00 41.02 3.25
1412 1491 4.814771 TCGTTAGATCGCTAGATTCACTCA 59.185 41.667 0.00 0.00 37.19 3.41
1563 1645 2.875094 ATCTTGCAAAGCTGGAGACT 57.125 45.000 0.00 0.00 45.70 3.24
1721 1816 4.504858 AGAACGCTGGTAAGAATACAAGG 58.495 43.478 0.00 0.00 34.16 3.61
1837 1932 4.767255 CCACACTGCGCCTCCTCC 62.767 72.222 4.18 0.00 0.00 4.30
1838 1933 4.767255 CCCACACTGCGCCTCCTC 62.767 72.222 4.18 0.00 0.00 3.71
1929 2028 2.660236 CACCTAGTACGTCGCAAACTTC 59.340 50.000 0.00 0.00 0.00 3.01
1962 2064 3.674138 GCACACAAGCATACAAGATTGGG 60.674 47.826 0.00 0.00 43.56 4.12
2068 2170 3.816524 CCGAAGTCGAGCGAGGCT 61.817 66.667 1.43 0.00 43.88 4.58
2179 2281 4.699522 GGGAACACGCCGGAGCTT 62.700 66.667 5.05 0.00 36.60 3.74
2335 2437 3.107601 TGTCCTCCTGTTATTGAGAGGG 58.892 50.000 5.14 0.00 45.04 4.30
2344 2446 1.668826 AGGGCAATGTCCTCCTGTTA 58.331 50.000 0.00 0.00 27.34 2.41
2422 2524 1.816863 ATGTGGCGGTCTTCTCACGT 61.817 55.000 0.00 0.00 33.25 4.49
2461 2563 1.152546 AGGACCGCTTTTGGCCTTT 60.153 52.632 3.32 0.00 33.47 3.11
2764 2866 0.299895 GCAATGACGCAGATGACTCG 59.700 55.000 0.00 0.00 0.00 4.18
2881 2983 5.869888 CCAAACAGAGTGTTATCCTCTACAC 59.130 44.000 0.00 0.00 40.14 2.90
2973 3075 7.025485 ACCAAATGCCAAAAACTAATGTTTG 57.975 32.000 0.00 0.00 44.70 2.93
3130 3240 2.791655 TCTACGAACTCAGCCTCTTCA 58.208 47.619 0.00 0.00 0.00 3.02
3167 3277 5.132816 CCTTCCTTGAAGTTATAGGGGTGAT 59.867 44.000 3.40 0.00 37.92 3.06
3241 3351 0.968405 GAACAAATGAAGGCCTGGCA 59.032 50.000 22.05 8.84 0.00 4.92
3421 3531 7.001099 AGATTTAGAGTCCACCGTCTTTTTA 57.999 36.000 0.00 0.00 0.00 1.52
3493 3603 8.830201 AACAAAAAGCAGCATTTATCATAACA 57.170 26.923 0.00 0.00 0.00 2.41
3498 3612 5.927689 CCTGAACAAAAAGCAGCATTTATCA 59.072 36.000 0.00 1.87 0.00 2.15
3586 3700 4.567959 GCAGGTCATGTTATGCATTTTTCC 59.432 41.667 3.54 0.00 38.54 3.13
3592 3706 5.628130 AGATAAGCAGGTCATGTTATGCAT 58.372 37.500 3.79 3.79 41.14 3.96
3593 3707 5.039920 AGATAAGCAGGTCATGTTATGCA 57.960 39.130 16.88 0.00 41.14 3.96
3594 3708 4.151335 CGAGATAAGCAGGTCATGTTATGC 59.849 45.833 9.70 9.70 38.97 3.14
3595 3709 5.292765 ACGAGATAAGCAGGTCATGTTATG 58.707 41.667 0.00 0.00 0.00 1.90
3647 3761 4.307443 ACTTTGCAGAGTTTTAGCAACC 57.693 40.909 3.61 0.00 46.69 3.77
3701 3815 7.064229 TCAACCCTTTTAACAATGGTAGAGTT 58.936 34.615 0.00 0.00 0.00 3.01
3872 4004 9.865321 TCCGTTGCTACTATAATATTTATGGAC 57.135 33.333 0.00 0.00 0.00 4.02
3898 4031 5.892348 AGTTCACTATTTGGATCCTTTGGT 58.108 37.500 14.23 2.93 0.00 3.67
3947 4080 7.554476 GCCAATCCTAAGACTAGTCAGATTTTT 59.446 37.037 24.44 11.24 0.00 1.94
3977 4110 6.096001 ACATGCTTATTTTGATGGAGGAAGAC 59.904 38.462 0.00 0.00 0.00 3.01
4080 4213 1.303309 CTGGAATTAAGAGCGCCCAG 58.697 55.000 2.29 7.29 35.75 4.45
4081 4214 0.748005 GCTGGAATTAAGAGCGCCCA 60.748 55.000 2.29 0.00 0.00 5.36
4082 4215 1.448119 GGCTGGAATTAAGAGCGCCC 61.448 60.000 2.29 0.00 33.26 6.13
4083 4216 0.748005 TGGCTGGAATTAAGAGCGCC 60.748 55.000 2.29 0.00 36.64 6.53
4084 4217 1.312815 ATGGCTGGAATTAAGAGCGC 58.687 50.000 0.00 0.00 33.26 5.92
4085 4218 3.209410 AGAATGGCTGGAATTAAGAGCG 58.791 45.455 0.00 0.00 33.26 5.03
4093 4226 3.760684 GTCTGACAAAGAATGGCTGGAAT 59.239 43.478 2.24 0.00 38.19 3.01
4096 4229 2.486982 CTGTCTGACAAAGAATGGCTGG 59.513 50.000 12.16 0.00 38.19 4.85
4309 4445 8.426489 AGTAAATAATGCAAGCATCAATTCCAT 58.574 29.630 8.14 0.89 35.31 3.41
4410 4546 5.574830 CGTTTCTTCTCGAGTTTCATCTGAT 59.425 40.000 13.13 0.00 0.00 2.90
4510 4646 1.881973 TGTTCATCTTGGCTTGCTGTC 59.118 47.619 0.00 0.00 0.00 3.51
4567 4703 4.040706 AGAGATCTGATCTGGCCATTCTTC 59.959 45.833 24.04 6.51 40.38 2.87
4672 4808 0.323629 TTCATCAACGGAGACCCCAC 59.676 55.000 0.00 0.00 34.14 4.61
4677 4813 7.426410 TCACTAGAATATTCATCAACGGAGAC 58.574 38.462 17.56 0.00 0.00 3.36
4766 4904 9.744468 GGCAATTTCACGGTTTATATTATTCTT 57.256 29.630 0.00 0.00 0.00 2.52
4832 4970 7.360017 GCATGGGTTTTGAGCTTGTAATTAAAC 60.360 37.037 0.00 0.00 0.00 2.01
4833 4971 6.648725 GCATGGGTTTTGAGCTTGTAATTAAA 59.351 34.615 0.00 0.00 0.00 1.52
4834 4972 6.162777 GCATGGGTTTTGAGCTTGTAATTAA 58.837 36.000 0.00 0.00 0.00 1.40
4835 4973 5.621104 CGCATGGGTTTTGAGCTTGTAATTA 60.621 40.000 0.68 0.00 0.00 1.40
4919 5060 9.927081 ATTCCCTTCCCACAATATATATCATTC 57.073 33.333 0.00 0.00 0.00 2.67
4921 5062 8.506083 GGATTCCCTTCCCACAATATATATCAT 58.494 37.037 0.00 0.00 0.00 2.45
4979 5120 5.399006 CGTAGTTGTACGTACACAATGTCAA 59.601 40.000 27.36 8.11 45.84 3.18
4993 5134 5.791367 GGAAAGAAATCCCGTAGTTGTAC 57.209 43.478 0.00 0.00 33.05 2.90
5006 5147 3.073946 TCCTCGTTTCCAGGGAAAGAAAT 59.926 43.478 13.56 0.00 43.66 2.17
5017 5158 1.152204 TCCCACCTCCTCGTTTCCA 60.152 57.895 0.00 0.00 0.00 3.53
5018 5159 1.192803 ACTCCCACCTCCTCGTTTCC 61.193 60.000 0.00 0.00 0.00 3.13
5019 5160 0.685660 AACTCCCACCTCCTCGTTTC 59.314 55.000 0.00 0.00 0.00 2.78
5020 5161 0.396811 CAACTCCCACCTCCTCGTTT 59.603 55.000 0.00 0.00 0.00 3.60
5021 5162 1.481056 CCAACTCCCACCTCCTCGTT 61.481 60.000 0.00 0.00 0.00 3.85
5022 5163 1.913762 CCAACTCCCACCTCCTCGT 60.914 63.158 0.00 0.00 0.00 4.18
5023 5164 1.481056 AACCAACTCCCACCTCCTCG 61.481 60.000 0.00 0.00 0.00 4.63
5024 5165 0.771755 AAACCAACTCCCACCTCCTC 59.228 55.000 0.00 0.00 0.00 3.71
5025 5166 0.478507 CAAACCAACTCCCACCTCCT 59.521 55.000 0.00 0.00 0.00 3.69
5026 5167 0.539669 CCAAACCAACTCCCACCTCC 60.540 60.000 0.00 0.00 0.00 4.30
5027 5168 0.476771 TCCAAACCAACTCCCACCTC 59.523 55.000 0.00 0.00 0.00 3.85
5088 5229 4.257810 TTCCACCCCTCCCACCGA 62.258 66.667 0.00 0.00 0.00 4.69
5102 5243 1.131315 GCTTTCGCTTCCATCACTTCC 59.869 52.381 0.00 0.00 0.00 3.46
5155 5296 4.566545 TTTGAACTGCGAACATCATTGT 57.433 36.364 0.00 0.00 37.82 2.71
5166 5307 5.046910 AGGTGACATAATTTTGAACTGCG 57.953 39.130 2.69 0.00 0.00 5.18
5183 5324 6.096423 AGCTATCGACACACTAAATTAGGTGA 59.904 38.462 20.51 6.41 37.22 4.02
5192 5333 6.694877 ACATAAGAGCTATCGACACACTAA 57.305 37.500 0.00 0.00 0.00 2.24
5234 5375 1.827344 GGCTTCCTGGAAAATTGAGGG 59.173 52.381 10.86 0.00 0.00 4.30
5235 5376 1.827344 GGGCTTCCTGGAAAATTGAGG 59.173 52.381 10.86 0.00 0.00 3.86
5236 5377 1.827344 GGGGCTTCCTGGAAAATTGAG 59.173 52.381 10.86 0.00 0.00 3.02
5238 5379 1.643310 TGGGGCTTCCTGGAAAATTG 58.357 50.000 10.86 0.00 36.20 2.32
5239 5380 2.190538 CATGGGGCTTCCTGGAAAATT 58.809 47.619 10.86 0.00 36.20 1.82
5240 5381 1.623279 CCATGGGGCTTCCTGGAAAAT 60.623 52.381 10.86 0.00 36.52 1.82
5242 5383 1.387737 CCATGGGGCTTCCTGGAAA 59.612 57.895 10.86 0.00 36.52 3.13
5243 5384 3.099171 CCATGGGGCTTCCTGGAA 58.901 61.111 9.14 9.14 36.52 3.53
5298 5573 3.914713 CCCCAACCAACCCCAGCT 61.915 66.667 0.00 0.00 0.00 4.24
5358 5633 4.767255 CTCCTGCGACCACCAGCC 62.767 72.222 0.00 0.00 0.00 4.85
5363 5638 3.302347 CTCCCACTCCTGCGACCAC 62.302 68.421 0.00 0.00 0.00 4.16
5427 5702 7.719193 TCTTAAAGGATCAACACAGTCAAATCA 59.281 33.333 0.00 0.00 0.00 2.57
5458 5733 9.472361 CCTGCCTCAAATCATTTCTAAATAATG 57.528 33.333 0.00 0.00 34.94 1.90
5490 5765 5.709631 TGAAGTTCCAATGCTACAATGCTAA 59.290 36.000 0.00 0.00 0.00 3.09
5491 5766 5.252547 TGAAGTTCCAATGCTACAATGCTA 58.747 37.500 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.