Multiple sequence alignment - TraesCS5D01G425200

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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 TraesCS5D01G425200 chr5D 100.000 3539 0 0 1 3539 483805926 483809464 0.000000e+00 6536.0
1 TraesCS5D01G425200 chr5D 98.966 2805 27 2 154 2958 503284805 503282003 0.000000e+00 5018.0
2 TraesCS5D01G425200 chr5D 98.717 2805 32 3 154 2958 6183437 6186237 0.000000e+00 4977.0
3 TraesCS5D01G425200 chr5D 97.872 141 3 0 1 141 6234398 6234538 9.810000e-61 244.0
4 TraesCS5D01G425200 chr5D 81.250 80 11 4 3096 3171 370108693 370108614 1.060000e-05 62.1
5 TraesCS5D01G425200 chr6D 98.681 2806 31 5 154 2958 45514064 45516864 0.000000e+00 4972.0
6 TraesCS5D01G425200 chr1D 98.397 2807 29 9 154 2958 254403609 254400817 0.000000e+00 4920.0
7 TraesCS5D01G425200 chr1D 97.398 2806 55 12 154 2958 51880567 51883355 0.000000e+00 4761.0
8 TraesCS5D01G425200 chr1D 98.582 141 2 0 1 141 180353894 180354034 2.110000e-62 250.0
9 TraesCS5D01G425200 chr1D 96.528 144 5 0 1 144 244790515 244790372 4.570000e-59 239.0
10 TraesCS5D01G425200 chr2A 98.113 2808 42 7 154 2958 335833142 335835941 0.000000e+00 4881.0
11 TraesCS5D01G425200 chr4A 96.833 2810 68 11 154 2958 309509623 309512416 0.000000e+00 4676.0
12 TraesCS5D01G425200 chr4A 96.543 2806 75 10 154 2958 310733088 310735872 0.000000e+00 4625.0
13 TraesCS5D01G425200 chr4A 96.528 144 5 0 1 144 665560742 665560599 4.570000e-59 239.0
14 TraesCS5D01G425200 chr3D 99.170 2411 10 3 492 2902 598875971 598873571 0.000000e+00 4333.0
15 TraesCS5D01G425200 chr3D 96.528 144 5 0 1 144 222422176 222422033 4.570000e-59 239.0
16 TraesCS5D01G425200 chr3D 79.592 98 14 4 3096 3188 591660785 591660689 8.200000e-07 65.8
17 TraesCS5D01G425200 chrUn 98.012 2264 35 6 565 2828 261572019 261574272 0.000000e+00 3923.0
18 TraesCS5D01G425200 chr5B 90.725 593 26 10 2969 3539 595015142 595015727 0.000000e+00 763.0
19 TraesCS5D01G425200 chr5A 90.811 555 39 5 2963 3506 605248099 605248652 0.000000e+00 732.0
20 TraesCS5D01G425200 chr5A 83.660 153 24 1 3355 3506 453191677 453191525 3.680000e-30 143.0
21 TraesCS5D01G425200 chr2B 89.576 566 47 8 156 715 721090002 721090561 0.000000e+00 708.0
22 TraesCS5D01G425200 chr2B 91.250 80 7 0 3426 3505 1976227 1976306 3.740000e-20 110.0
23 TraesCS5D01G425200 chr7A 98.611 144 2 0 1 144 691937864 691937721 4.530000e-64 255.0
24 TraesCS5D01G425200 chr7A 95.745 141 6 0 1 141 352294960 352295100 9.880000e-56 228.0
25 TraesCS5D01G425200 chr3B 98.611 144 2 0 1 144 201494853 201494710 4.530000e-64 255.0
26 TraesCS5D01G425200 chr3B 82.653 98 11 5 3095 3186 650054926 650054829 8.140000e-12 82.4
27 TraesCS5D01G425200 chr1A 99.291 141 1 0 1 141 554444636 554444776 4.530000e-64 255.0
28 TraesCS5D01G425200 chr4B 83.838 99 9 5 3096 3188 427518859 427518762 1.750000e-13 87.9
29 TraesCS5D01G425200 chr6B 82.105 95 12 4 3096 3186 143197306 143197399 3.790000e-10 76.8
30 TraesCS5D01G425200 chr6B 78.704 108 17 6 3364 3469 127123829 127123932 2.280000e-07 67.6


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 TraesCS5D01G425200 chr5D 483805926 483809464 3538 False 6536 6536 100.000 1 3539 1 chr5D.!!$F3 3538
1 TraesCS5D01G425200 chr5D 503282003 503284805 2802 True 5018 5018 98.966 154 2958 1 chr5D.!!$R2 2804
2 TraesCS5D01G425200 chr5D 6183437 6186237 2800 False 4977 4977 98.717 154 2958 1 chr5D.!!$F1 2804
3 TraesCS5D01G425200 chr6D 45514064 45516864 2800 False 4972 4972 98.681 154 2958 1 chr6D.!!$F1 2804
4 TraesCS5D01G425200 chr1D 254400817 254403609 2792 True 4920 4920 98.397 154 2958 1 chr1D.!!$R2 2804
5 TraesCS5D01G425200 chr1D 51880567 51883355 2788 False 4761 4761 97.398 154 2958 1 chr1D.!!$F1 2804
6 TraesCS5D01G425200 chr2A 335833142 335835941 2799 False 4881 4881 98.113 154 2958 1 chr2A.!!$F1 2804
7 TraesCS5D01G425200 chr4A 309509623 309512416 2793 False 4676 4676 96.833 154 2958 1 chr4A.!!$F1 2804
8 TraesCS5D01G425200 chr4A 310733088 310735872 2784 False 4625 4625 96.543 154 2958 1 chr4A.!!$F2 2804
9 TraesCS5D01G425200 chr3D 598873571 598875971 2400 True 4333 4333 99.170 492 2902 1 chr3D.!!$R3 2410
10 TraesCS5D01G425200 chrUn 261572019 261574272 2253 False 3923 3923 98.012 565 2828 1 chrUn.!!$F1 2263
11 TraesCS5D01G425200 chr5B 595015142 595015727 585 False 763 763 90.725 2969 3539 1 chr5B.!!$F1 570
12 TraesCS5D01G425200 chr5A 605248099 605248652 553 False 732 732 90.811 2963 3506 1 chr5A.!!$F1 543
13 TraesCS5D01G425200 chr2B 721090002 721090561 559 False 708 708 89.576 156 715 1 chr2B.!!$F2 559

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
54 55 0.036388 TTCAGTCCGATTCAGGTGCC 60.036 55.0 0.0 0.0 0.00 5.01 F
135 136 0.179045 AGCCCACTAAATGCTAGGCG 60.179 55.0 0.0 0.0 45.16 5.52 F
147 148 0.249911 GCTAGGCGTAATGTGGGAGG 60.250 60.0 0.0 0.0 0.00 4.30 F
150 151 0.696501 AGGCGTAATGTGGGAGGTTT 59.303 50.0 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1053 1063 3.936372 TGAAAGAGAAGTGGGTAGACG 57.064 47.619 0.00 0.00 0.00 4.18 R
1892 1922 6.248433 AGGTAGCATTTCCATTTCTTCTTCA 58.752 36.000 0.00 0.00 0.00 3.02 R
2496 2528 9.031537 ACCAGGTCATTGATACGTATAATATCA 57.968 33.333 8.34 0.39 37.29 2.15 R
2698 2731 6.239345 CGACTTTCCCTATGTAGAAATAGCCT 60.239 42.308 0.00 0.00 31.89 4.58 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 5.195001 GAGAATAGGAGAACAGTAGCCTG 57.805 47.826 0.00 0.00 44.68 4.85
23 24 4.873010 AGAATAGGAGAACAGTAGCCTGA 58.127 43.478 0.00 0.00 41.50 3.86
24 25 4.647399 AGAATAGGAGAACAGTAGCCTGAC 59.353 45.833 0.00 0.00 41.50 3.51
25 26 2.310779 AGGAGAACAGTAGCCTGACA 57.689 50.000 0.00 0.00 41.50 3.58
26 27 2.609747 AGGAGAACAGTAGCCTGACAA 58.390 47.619 0.00 0.00 41.50 3.18
27 28 2.972713 AGGAGAACAGTAGCCTGACAAA 59.027 45.455 0.00 0.00 41.50 2.83
28 29 3.067833 GGAGAACAGTAGCCTGACAAAC 58.932 50.000 0.00 0.00 41.50 2.93
29 30 3.494398 GGAGAACAGTAGCCTGACAAACA 60.494 47.826 0.00 0.00 41.50 2.83
30 31 3.733337 AGAACAGTAGCCTGACAAACAG 58.267 45.455 0.00 0.00 41.50 3.16
31 32 3.134804 AGAACAGTAGCCTGACAAACAGT 59.865 43.478 0.00 0.00 44.40 3.55
42 43 1.865340 GACAAACAGTCGGTTCAGTCC 59.135 52.381 8.99 0.00 39.29 3.85
52 53 1.726853 GGTTCAGTCCGATTCAGGTG 58.273 55.000 0.00 0.00 0.00 4.00
53 54 1.079503 GTTCAGTCCGATTCAGGTGC 58.920 55.000 0.00 0.00 0.00 5.01
54 55 0.036388 TTCAGTCCGATTCAGGTGCC 60.036 55.000 0.00 0.00 0.00 5.01
55 56 1.191489 TCAGTCCGATTCAGGTGCCA 61.191 55.000 0.00 0.00 0.00 4.92
56 57 0.321564 CAGTCCGATTCAGGTGCCAA 60.322 55.000 0.00 0.00 0.00 4.52
57 58 0.620556 AGTCCGATTCAGGTGCCAAT 59.379 50.000 0.00 0.00 0.00 3.16
58 59 1.004745 AGTCCGATTCAGGTGCCAATT 59.995 47.619 0.00 0.00 0.00 2.32
59 60 1.401905 GTCCGATTCAGGTGCCAATTC 59.598 52.381 0.00 0.00 0.00 2.17
60 61 1.004161 TCCGATTCAGGTGCCAATTCA 59.996 47.619 0.00 0.00 0.00 2.57
61 62 1.402968 CCGATTCAGGTGCCAATTCAG 59.597 52.381 0.00 0.00 0.00 3.02
62 63 1.402968 CGATTCAGGTGCCAATTCAGG 59.597 52.381 0.00 0.00 0.00 3.86
63 64 2.450476 GATTCAGGTGCCAATTCAGGT 58.550 47.619 0.00 0.00 0.00 4.00
64 65 1.619654 TTCAGGTGCCAATTCAGGTG 58.380 50.000 0.00 0.00 0.00 4.00
65 66 0.895100 TCAGGTGCCAATTCAGGTGC 60.895 55.000 0.00 0.00 0.00 5.01
66 67 1.607467 AGGTGCCAATTCAGGTGCC 60.607 57.895 0.00 0.00 0.00 5.01
67 68 1.607467 GGTGCCAATTCAGGTGCCT 60.607 57.895 0.00 0.00 0.00 4.75
68 69 0.323360 GGTGCCAATTCAGGTGCCTA 60.323 55.000 0.00 0.00 0.00 3.93
69 70 1.544724 GTGCCAATTCAGGTGCCTAA 58.455 50.000 0.00 0.00 0.00 2.69
70 71 2.102578 GTGCCAATTCAGGTGCCTAAT 58.897 47.619 0.00 0.00 0.00 1.73
71 72 2.099756 GTGCCAATTCAGGTGCCTAATC 59.900 50.000 0.00 0.00 0.00 1.75
72 73 2.291475 TGCCAATTCAGGTGCCTAATCA 60.291 45.455 0.00 0.00 0.00 2.57
73 74 2.760092 GCCAATTCAGGTGCCTAATCAA 59.240 45.455 0.00 0.00 0.00 2.57
74 75 3.195396 GCCAATTCAGGTGCCTAATCAAA 59.805 43.478 0.00 0.00 0.00 2.69
75 76 4.141869 GCCAATTCAGGTGCCTAATCAAAT 60.142 41.667 0.00 0.00 0.00 2.32
76 77 5.068987 GCCAATTCAGGTGCCTAATCAAATA 59.931 40.000 0.00 0.00 0.00 1.40
77 78 6.736794 GCCAATTCAGGTGCCTAATCAAATAG 60.737 42.308 0.00 0.00 0.00 1.73
78 79 6.547141 CCAATTCAGGTGCCTAATCAAATAGA 59.453 38.462 0.00 0.00 0.00 1.98
79 80 7.068593 CCAATTCAGGTGCCTAATCAAATAGAA 59.931 37.037 0.00 0.00 0.00 2.10
80 81 7.573968 ATTCAGGTGCCTAATCAAATAGAAC 57.426 36.000 0.00 0.00 0.00 3.01
81 82 5.437060 TCAGGTGCCTAATCAAATAGAACC 58.563 41.667 0.00 0.00 33.24 3.62
82 83 4.580580 CAGGTGCCTAATCAAATAGAACCC 59.419 45.833 0.00 0.00 33.39 4.11
83 84 4.478686 AGGTGCCTAATCAAATAGAACCCT 59.521 41.667 0.00 0.00 33.39 4.34
84 85 5.044105 AGGTGCCTAATCAAATAGAACCCTT 60.044 40.000 0.00 0.00 33.39 3.95
85 86 6.159751 AGGTGCCTAATCAAATAGAACCCTTA 59.840 38.462 0.00 0.00 33.39 2.69
86 87 7.004691 GGTGCCTAATCAAATAGAACCCTTAT 58.995 38.462 0.00 0.00 0.00 1.73
87 88 7.040409 GGTGCCTAATCAAATAGAACCCTTATG 60.040 40.741 0.00 0.00 0.00 1.90
88 89 7.004086 TGCCTAATCAAATAGAACCCTTATGG 58.996 38.462 0.00 0.00 41.37 2.74
89 90 7.147213 TGCCTAATCAAATAGAACCCTTATGGA 60.147 37.037 0.00 0.00 38.00 3.41
90 91 7.890655 GCCTAATCAAATAGAACCCTTATGGAT 59.109 37.037 0.00 0.00 38.00 3.41
91 92 9.813826 CCTAATCAAATAGAACCCTTATGGATT 57.186 33.333 0.00 0.00 38.00 3.01
94 95 7.346751 TCAAATAGAACCCTTATGGATTTGC 57.653 36.000 11.17 0.00 34.86 3.68
95 96 7.125391 TCAAATAGAACCCTTATGGATTTGCT 58.875 34.615 11.17 0.00 34.86 3.91
96 97 8.278639 TCAAATAGAACCCTTATGGATTTGCTA 58.721 33.333 11.17 0.00 34.86 3.49
97 98 8.571336 CAAATAGAACCCTTATGGATTTGCTAG 58.429 37.037 0.00 0.00 38.00 3.42
98 99 5.717119 AGAACCCTTATGGATTTGCTAGT 57.283 39.130 0.00 0.00 38.00 2.57
99 100 6.079712 AGAACCCTTATGGATTTGCTAGTT 57.920 37.500 0.00 0.00 38.00 2.24
100 101 5.888161 AGAACCCTTATGGATTTGCTAGTTG 59.112 40.000 0.00 0.00 38.00 3.16
101 102 5.450818 ACCCTTATGGATTTGCTAGTTGA 57.549 39.130 0.00 0.00 38.00 3.18
102 103 6.018433 ACCCTTATGGATTTGCTAGTTGAT 57.982 37.500 0.00 0.00 38.00 2.57
103 104 7.149202 ACCCTTATGGATTTGCTAGTTGATA 57.851 36.000 0.00 0.00 38.00 2.15
104 105 7.582719 ACCCTTATGGATTTGCTAGTTGATAA 58.417 34.615 0.00 0.00 38.00 1.75
105 106 7.721399 ACCCTTATGGATTTGCTAGTTGATAAG 59.279 37.037 0.00 0.00 38.00 1.73
106 107 7.175641 CCCTTATGGATTTGCTAGTTGATAAGG 59.824 40.741 0.00 0.00 40.06 2.69
107 108 7.721399 CCTTATGGATTTGCTAGTTGATAAGGT 59.279 37.037 0.00 0.00 37.46 3.50
108 109 9.778741 CTTATGGATTTGCTAGTTGATAAGGTA 57.221 33.333 0.00 0.00 0.00 3.08
111 112 9.646522 ATGGATTTGCTAGTTGATAAGGTAAAT 57.353 29.630 0.00 0.00 0.00 1.40
117 118 9.778741 TTGCTAGTTGATAAGGTAAATATCCAG 57.221 33.333 0.00 0.00 0.00 3.86
118 119 7.878127 TGCTAGTTGATAAGGTAAATATCCAGC 59.122 37.037 0.00 0.00 0.00 4.85
119 120 7.334671 GCTAGTTGATAAGGTAAATATCCAGCC 59.665 40.741 0.00 0.00 0.00 4.85
120 121 6.543735 AGTTGATAAGGTAAATATCCAGCCC 58.456 40.000 0.00 0.00 0.00 5.19
121 122 6.102615 AGTTGATAAGGTAAATATCCAGCCCA 59.897 38.462 0.00 0.00 0.00 5.36
122 123 5.876357 TGATAAGGTAAATATCCAGCCCAC 58.124 41.667 0.00 0.00 0.00 4.61
123 124 5.610982 TGATAAGGTAAATATCCAGCCCACT 59.389 40.000 0.00 0.00 0.00 4.00
124 125 6.790461 TGATAAGGTAAATATCCAGCCCACTA 59.210 38.462 0.00 0.00 0.00 2.74
125 126 5.987019 AAGGTAAATATCCAGCCCACTAA 57.013 39.130 0.00 0.00 0.00 2.24
126 127 5.987019 AGGTAAATATCCAGCCCACTAAA 57.013 39.130 0.00 0.00 0.00 1.85
127 128 6.530601 AGGTAAATATCCAGCCCACTAAAT 57.469 37.500 0.00 0.00 0.00 1.40
128 129 6.306987 AGGTAAATATCCAGCCCACTAAATG 58.693 40.000 0.00 0.00 0.00 2.32
129 130 5.048013 GGTAAATATCCAGCCCACTAAATGC 60.048 44.000 0.00 0.00 0.00 3.56
130 131 4.459852 AATATCCAGCCCACTAAATGCT 57.540 40.909 0.00 0.00 35.25 3.79
131 132 5.582950 AATATCCAGCCCACTAAATGCTA 57.417 39.130 0.00 0.00 33.16 3.49
132 133 3.498774 ATCCAGCCCACTAAATGCTAG 57.501 47.619 0.00 0.00 33.16 3.42
133 134 1.490490 TCCAGCCCACTAAATGCTAGG 59.510 52.381 0.00 0.00 33.16 3.02
134 135 1.312815 CAGCCCACTAAATGCTAGGC 58.687 55.000 0.00 0.00 40.79 3.93
135 136 0.179045 AGCCCACTAAATGCTAGGCG 60.179 55.000 0.00 0.00 45.16 5.52
136 137 0.463833 GCCCACTAAATGCTAGGCGT 60.464 55.000 0.00 0.00 0.00 5.68
137 138 1.202604 GCCCACTAAATGCTAGGCGTA 60.203 52.381 0.00 0.00 0.00 4.42
138 139 2.743838 GCCCACTAAATGCTAGGCGTAA 60.744 50.000 0.00 0.00 0.00 3.18
139 140 3.740115 CCCACTAAATGCTAGGCGTAAT 58.260 45.455 0.00 0.00 0.00 1.89
140 141 3.498397 CCCACTAAATGCTAGGCGTAATG 59.502 47.826 0.00 0.00 0.00 1.90
141 142 4.127171 CCACTAAATGCTAGGCGTAATGT 58.873 43.478 0.00 0.00 0.00 2.71
142 143 4.024893 CCACTAAATGCTAGGCGTAATGTG 60.025 45.833 0.00 0.00 0.00 3.21
143 144 4.024893 CACTAAATGCTAGGCGTAATGTGG 60.025 45.833 0.00 0.00 0.00 4.17
144 145 1.967319 AATGCTAGGCGTAATGTGGG 58.033 50.000 0.00 0.00 0.00 4.61
145 146 1.128200 ATGCTAGGCGTAATGTGGGA 58.872 50.000 0.00 0.00 0.00 4.37
146 147 0.464036 TGCTAGGCGTAATGTGGGAG 59.536 55.000 0.00 0.00 0.00 4.30
147 148 0.249911 GCTAGGCGTAATGTGGGAGG 60.250 60.000 0.00 0.00 0.00 4.30
148 149 1.120530 CTAGGCGTAATGTGGGAGGT 58.879 55.000 0.00 0.00 0.00 3.85
149 150 1.485066 CTAGGCGTAATGTGGGAGGTT 59.515 52.381 0.00 0.00 0.00 3.50
150 151 0.696501 AGGCGTAATGTGGGAGGTTT 59.303 50.000 0.00 0.00 0.00 3.27
151 152 1.910671 AGGCGTAATGTGGGAGGTTTA 59.089 47.619 0.00 0.00 0.00 2.01
152 153 2.508300 AGGCGTAATGTGGGAGGTTTAT 59.492 45.455 0.00 0.00 0.00 1.40
262 265 7.165812 CCATTGATTTTTGGATTTCGATCGTAC 59.834 37.037 15.94 0.00 34.81 3.67
1074 1084 4.087182 TCGTCTACCCACTTCTCTTTCAT 58.913 43.478 0.00 0.00 0.00 2.57
1099 1109 7.089538 TGAATATATTTATGCATTTGCCCACG 58.910 34.615 3.54 0.00 41.18 4.94
2406 2437 8.009409 GGTTCGGCATTTTTAGAAGAATTTTTG 58.991 33.333 0.00 0.00 0.00 2.44
2496 2528 5.472137 ACACACTGAGCGTATTTGGTATTTT 59.528 36.000 0.00 0.00 0.00 1.82
2958 2991 2.362077 GCTGACTTGGTTGACATTGGTT 59.638 45.455 0.00 0.00 0.00 3.67
2959 2992 3.568007 GCTGACTTGGTTGACATTGGTTA 59.432 43.478 0.00 0.00 0.00 2.85
2960 2993 4.037446 GCTGACTTGGTTGACATTGGTTAA 59.963 41.667 0.00 0.00 0.00 2.01
2961 2994 5.278957 GCTGACTTGGTTGACATTGGTTAAT 60.279 40.000 0.00 0.00 0.00 1.40
2964 2997 7.881142 TGACTTGGTTGACATTGGTTAATTAG 58.119 34.615 0.00 0.00 0.00 1.73
2967 3000 4.156922 TGGTTGACATTGGTTAATTAGGCG 59.843 41.667 0.00 0.00 0.00 5.52
3015 3048 4.883585 GTGAGGCCACATAATGATTTCTCA 59.116 41.667 6.04 0.00 42.72 3.27
3017 3050 5.951148 TGAGGCCACATAATGATTTCTCAAA 59.049 36.000 5.01 0.00 34.37 2.69
3018 3051 6.436847 TGAGGCCACATAATGATTTCTCAAAA 59.563 34.615 5.01 0.00 34.37 2.44
3339 3390 1.078426 AGCGGTAGAGCGGCAAAAT 60.078 52.632 1.45 0.00 44.64 1.82
3397 3448 4.696479 AGGGAACTAGGCATACATTCAG 57.304 45.455 0.00 0.00 40.61 3.02
3402 3453 4.946478 ACTAGGCATACATTCAGTCTCC 57.054 45.455 0.00 0.00 0.00 3.71
3436 3487 6.649141 ACTTTAGACTTGCAACGATAACATCA 59.351 34.615 0.00 0.00 0.00 3.07
3476 3527 7.959658 AACTTGGGTCAATTCAATATGATCA 57.040 32.000 0.00 0.00 0.00 2.92
3506 3557 9.725019 TTCTAACATCATACTCTCAATGTTGTT 57.275 29.630 13.79 13.79 43.97 2.83
3518 3575 7.552687 ACTCTCAATGTTGTTCTTGTTTCAGTA 59.447 33.333 0.00 0.00 0.00 2.74
3519 3576 7.693952 TCTCAATGTTGTTCTTGTTTCAGTAC 58.306 34.615 0.00 0.00 0.00 2.73
3520 3577 6.482835 TCAATGTTGTTCTTGTTTCAGTACG 58.517 36.000 0.00 0.00 0.00 3.67
3521 3578 6.092944 TCAATGTTGTTCTTGTTTCAGTACGT 59.907 34.615 0.00 0.00 0.00 3.57
3522 3579 7.278203 TCAATGTTGTTCTTGTTTCAGTACGTA 59.722 33.333 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.890581 TCAGGCTACTGTTCTCCTATTCTC 59.109 45.833 0.00 0.00 45.14 2.87
1 2 4.647399 GTCAGGCTACTGTTCTCCTATTCT 59.353 45.833 0.00 0.00 45.14 2.40
4 5 3.982516 TGTCAGGCTACTGTTCTCCTAT 58.017 45.455 0.00 0.00 45.14 2.57
6 7 2.310779 TGTCAGGCTACTGTTCTCCT 57.689 50.000 0.00 0.00 45.14 3.69
7 8 3.067833 GTTTGTCAGGCTACTGTTCTCC 58.932 50.000 0.00 0.00 45.14 3.71
8 9 3.728845 TGTTTGTCAGGCTACTGTTCTC 58.271 45.455 0.00 0.00 45.14 2.87
9 10 3.733337 CTGTTTGTCAGGCTACTGTTCT 58.267 45.455 0.00 0.00 45.14 3.01
20 21 2.540101 GACTGAACCGACTGTTTGTCAG 59.460 50.000 9.95 9.01 45.60 3.51
21 22 2.546778 GACTGAACCGACTGTTTGTCA 58.453 47.619 9.95 0.00 45.60 3.58
22 23 1.865340 GGACTGAACCGACTGTTTGTC 59.135 52.381 7.69 7.69 42.06 3.18
23 24 1.949465 GGACTGAACCGACTGTTTGT 58.051 50.000 0.00 0.00 37.29 2.83
33 34 1.726853 CACCTGAATCGGACTGAACC 58.273 55.000 0.00 0.00 0.00 3.62
34 35 1.079503 GCACCTGAATCGGACTGAAC 58.920 55.000 0.00 0.00 0.00 3.18
35 36 0.036388 GGCACCTGAATCGGACTGAA 60.036 55.000 0.00 0.00 0.00 3.02
36 37 1.191489 TGGCACCTGAATCGGACTGA 61.191 55.000 0.00 0.00 0.00 3.41
37 38 0.321564 TTGGCACCTGAATCGGACTG 60.322 55.000 0.00 0.00 0.00 3.51
38 39 0.620556 ATTGGCACCTGAATCGGACT 59.379 50.000 0.00 0.00 0.00 3.85
39 40 1.401905 GAATTGGCACCTGAATCGGAC 59.598 52.381 0.00 0.00 0.00 4.79
40 41 1.004161 TGAATTGGCACCTGAATCGGA 59.996 47.619 0.00 0.00 0.00 4.55
41 42 1.402968 CTGAATTGGCACCTGAATCGG 59.597 52.381 0.00 0.00 0.00 4.18
42 43 1.402968 CCTGAATTGGCACCTGAATCG 59.597 52.381 0.00 0.00 0.00 3.34
43 44 2.165030 CACCTGAATTGGCACCTGAATC 59.835 50.000 0.00 0.00 0.00 2.52
44 45 2.173519 CACCTGAATTGGCACCTGAAT 58.826 47.619 0.00 0.00 0.00 2.57
45 46 1.619654 CACCTGAATTGGCACCTGAA 58.380 50.000 0.00 0.00 0.00 3.02
46 47 0.895100 GCACCTGAATTGGCACCTGA 60.895 55.000 0.00 0.00 0.00 3.86
47 48 1.588082 GCACCTGAATTGGCACCTG 59.412 57.895 0.00 0.00 0.00 4.00
48 49 1.607467 GGCACCTGAATTGGCACCT 60.607 57.895 0.00 0.00 39.31 4.00
49 50 0.323360 TAGGCACCTGAATTGGCACC 60.323 55.000 0.00 0.00 41.91 5.01
50 51 1.544724 TTAGGCACCTGAATTGGCAC 58.455 50.000 0.00 0.00 41.91 5.01
51 52 2.291475 TGATTAGGCACCTGAATTGGCA 60.291 45.455 0.00 0.00 41.91 4.92
52 53 2.378038 TGATTAGGCACCTGAATTGGC 58.622 47.619 0.00 0.00 39.80 4.52
53 54 5.603170 ATTTGATTAGGCACCTGAATTGG 57.397 39.130 0.00 0.00 0.00 3.16
54 55 7.572523 TCTATTTGATTAGGCACCTGAATTG 57.427 36.000 0.00 0.00 0.00 2.32
55 56 7.068716 GGTTCTATTTGATTAGGCACCTGAATT 59.931 37.037 0.00 0.00 0.00 2.17
56 57 6.547510 GGTTCTATTTGATTAGGCACCTGAAT 59.452 38.462 0.00 0.00 0.00 2.57
57 58 5.885912 GGTTCTATTTGATTAGGCACCTGAA 59.114 40.000 0.00 0.00 0.00 3.02
58 59 5.437060 GGTTCTATTTGATTAGGCACCTGA 58.563 41.667 0.00 0.00 0.00 3.86
59 60 4.580580 GGGTTCTATTTGATTAGGCACCTG 59.419 45.833 0.00 0.00 0.00 4.00
60 61 4.478686 AGGGTTCTATTTGATTAGGCACCT 59.521 41.667 0.00 0.00 0.00 4.00
61 62 4.793201 AGGGTTCTATTTGATTAGGCACC 58.207 43.478 0.00 0.00 0.00 5.01
62 63 7.040409 CCATAAGGGTTCTATTTGATTAGGCAC 60.040 40.741 0.00 0.00 0.00 5.01
63 64 7.004086 CCATAAGGGTTCTATTTGATTAGGCA 58.996 38.462 0.00 0.00 0.00 4.75
64 65 7.231467 TCCATAAGGGTTCTATTTGATTAGGC 58.769 38.462 0.00 0.00 38.11 3.93
65 66 9.813826 AATCCATAAGGGTTCTATTTGATTAGG 57.186 33.333 0.00 0.00 30.33 2.69
68 69 8.424133 GCAAATCCATAAGGGTTCTATTTGATT 58.576 33.333 10.59 0.00 37.20 2.57
69 70 7.786464 AGCAAATCCATAAGGGTTCTATTTGAT 59.214 33.333 10.59 3.65 37.20 2.57
70 71 7.125391 AGCAAATCCATAAGGGTTCTATTTGA 58.875 34.615 10.59 0.00 37.20 2.69
71 72 7.352079 AGCAAATCCATAAGGGTTCTATTTG 57.648 36.000 0.00 0.00 37.20 2.32
72 73 8.282256 ACTAGCAAATCCATAAGGGTTCTATTT 58.718 33.333 0.00 0.00 37.20 1.40
73 74 7.816411 ACTAGCAAATCCATAAGGGTTCTATT 58.184 34.615 0.00 0.00 37.20 1.73
74 75 7.394144 ACTAGCAAATCCATAAGGGTTCTAT 57.606 36.000 0.00 0.00 37.20 1.98
75 76 6.824958 ACTAGCAAATCCATAAGGGTTCTA 57.175 37.500 0.00 0.00 37.20 2.10
76 77 5.717119 ACTAGCAAATCCATAAGGGTTCT 57.283 39.130 0.00 0.00 37.20 3.01
77 78 5.885912 TCAACTAGCAAATCCATAAGGGTTC 59.114 40.000 0.00 0.00 37.20 3.62
78 79 5.826643 TCAACTAGCAAATCCATAAGGGTT 58.173 37.500 0.00 0.00 41.02 4.11
79 80 5.450818 TCAACTAGCAAATCCATAAGGGT 57.549 39.130 0.00 0.00 38.11 4.34
80 81 7.175641 CCTTATCAACTAGCAAATCCATAAGGG 59.824 40.741 11.13 0.00 38.37 3.95
81 82 7.721399 ACCTTATCAACTAGCAAATCCATAAGG 59.279 37.037 14.97 14.97 43.78 2.69
82 83 8.682936 ACCTTATCAACTAGCAAATCCATAAG 57.317 34.615 0.00 0.00 0.00 1.73
85 86 9.646522 ATTTACCTTATCAACTAGCAAATCCAT 57.353 29.630 0.00 0.00 0.00 3.41
91 92 9.778741 CTGGATATTTACCTTATCAACTAGCAA 57.221 33.333 0.00 0.00 0.00 3.91
92 93 7.878127 GCTGGATATTTACCTTATCAACTAGCA 59.122 37.037 0.00 0.00 0.00 3.49
93 94 7.334671 GGCTGGATATTTACCTTATCAACTAGC 59.665 40.741 0.00 0.00 0.00 3.42
94 95 7.824779 GGGCTGGATATTTACCTTATCAACTAG 59.175 40.741 0.00 0.00 0.00 2.57
95 96 7.293771 TGGGCTGGATATTTACCTTATCAACTA 59.706 37.037 0.00 0.00 0.00 2.24
96 97 6.102615 TGGGCTGGATATTTACCTTATCAACT 59.897 38.462 0.00 0.00 0.00 3.16
97 98 6.206829 GTGGGCTGGATATTTACCTTATCAAC 59.793 42.308 0.00 0.00 0.00 3.18
98 99 6.102615 AGTGGGCTGGATATTTACCTTATCAA 59.897 38.462 0.00 0.00 0.00 2.57
99 100 5.610982 AGTGGGCTGGATATTTACCTTATCA 59.389 40.000 0.00 0.00 0.00 2.15
100 101 6.128138 AGTGGGCTGGATATTTACCTTATC 57.872 41.667 0.00 0.00 0.00 1.75
101 102 7.642094 TTAGTGGGCTGGATATTTACCTTAT 57.358 36.000 0.00 0.00 0.00 1.73
102 103 7.454553 TTTAGTGGGCTGGATATTTACCTTA 57.545 36.000 0.00 0.00 0.00 2.69
103 104 5.987019 TTAGTGGGCTGGATATTTACCTT 57.013 39.130 0.00 0.00 0.00 3.50
104 105 5.987019 TTTAGTGGGCTGGATATTTACCT 57.013 39.130 0.00 0.00 0.00 3.08
105 106 5.048013 GCATTTAGTGGGCTGGATATTTACC 60.048 44.000 0.00 0.00 0.00 2.85
106 107 5.770162 AGCATTTAGTGGGCTGGATATTTAC 59.230 40.000 0.00 0.00 36.34 2.01
107 108 5.952387 AGCATTTAGTGGGCTGGATATTTA 58.048 37.500 0.00 0.00 36.34 1.40
108 109 4.808042 AGCATTTAGTGGGCTGGATATTT 58.192 39.130 0.00 0.00 36.34 1.40
109 110 4.459852 AGCATTTAGTGGGCTGGATATT 57.540 40.909 0.00 0.00 36.34 1.28
110 111 4.018960 CCTAGCATTTAGTGGGCTGGATAT 60.019 45.833 0.00 0.00 38.26 1.63
111 112 3.327757 CCTAGCATTTAGTGGGCTGGATA 59.672 47.826 0.00 0.00 38.26 2.59
112 113 2.107204 CCTAGCATTTAGTGGGCTGGAT 59.893 50.000 0.00 0.00 38.26 3.41
113 114 1.490490 CCTAGCATTTAGTGGGCTGGA 59.510 52.381 0.00 0.00 38.26 3.86
114 115 1.972872 CCTAGCATTTAGTGGGCTGG 58.027 55.000 0.00 0.00 38.55 4.85
115 116 1.312815 GCCTAGCATTTAGTGGGCTG 58.687 55.000 0.00 0.00 38.55 4.85
116 117 0.179045 CGCCTAGCATTTAGTGGGCT 60.179 55.000 0.00 0.00 41.51 5.19
117 118 0.463833 ACGCCTAGCATTTAGTGGGC 60.464 55.000 0.00 0.00 36.60 5.36
118 119 2.902705 TACGCCTAGCATTTAGTGGG 57.097 50.000 0.00 0.00 0.00 4.61
119 120 4.024893 CACATTACGCCTAGCATTTAGTGG 60.025 45.833 0.00 0.00 0.00 4.00
120 121 4.024893 CCACATTACGCCTAGCATTTAGTG 60.025 45.833 0.00 0.00 0.00 2.74
121 122 4.127171 CCACATTACGCCTAGCATTTAGT 58.873 43.478 0.00 0.00 0.00 2.24
122 123 3.498397 CCCACATTACGCCTAGCATTTAG 59.502 47.826 0.00 0.00 0.00 1.85
123 124 3.134985 TCCCACATTACGCCTAGCATTTA 59.865 43.478 0.00 0.00 0.00 1.40
124 125 2.092646 TCCCACATTACGCCTAGCATTT 60.093 45.455 0.00 0.00 0.00 2.32
125 126 1.488812 TCCCACATTACGCCTAGCATT 59.511 47.619 0.00 0.00 0.00 3.56
126 127 1.070758 CTCCCACATTACGCCTAGCAT 59.929 52.381 0.00 0.00 0.00 3.79
127 128 0.464036 CTCCCACATTACGCCTAGCA 59.536 55.000 0.00 0.00 0.00 3.49
128 129 0.249911 CCTCCCACATTACGCCTAGC 60.250 60.000 0.00 0.00 0.00 3.42
129 130 1.120530 ACCTCCCACATTACGCCTAG 58.879 55.000 0.00 0.00 0.00 3.02
130 131 1.575419 AACCTCCCACATTACGCCTA 58.425 50.000 0.00 0.00 0.00 3.93
131 132 0.696501 AAACCTCCCACATTACGCCT 59.303 50.000 0.00 0.00 0.00 5.52
132 133 2.406596 TAAACCTCCCACATTACGCC 57.593 50.000 0.00 0.00 0.00 5.68
133 134 6.261381 TCAAATATAAACCTCCCACATTACGC 59.739 38.462 0.00 0.00 0.00 4.42
134 135 7.497909 ACTCAAATATAAACCTCCCACATTACG 59.502 37.037 0.00 0.00 0.00 3.18
135 136 8.621286 CACTCAAATATAAACCTCCCACATTAC 58.379 37.037 0.00 0.00 0.00 1.89
136 137 8.333235 ACACTCAAATATAAACCTCCCACATTA 58.667 33.333 0.00 0.00 0.00 1.90
137 138 7.182060 ACACTCAAATATAAACCTCCCACATT 58.818 34.615 0.00 0.00 0.00 2.71
138 139 6.731467 ACACTCAAATATAAACCTCCCACAT 58.269 36.000 0.00 0.00 0.00 3.21
139 140 6.134535 ACACTCAAATATAAACCTCCCACA 57.865 37.500 0.00 0.00 0.00 4.17
140 141 7.462571 AAACACTCAAATATAAACCTCCCAC 57.537 36.000 0.00 0.00 0.00 4.61
141 142 8.485578 AAAAACACTCAAATATAAACCTCCCA 57.514 30.769 0.00 0.00 0.00 4.37
142 143 8.581578 TGAAAAACACTCAAATATAAACCTCCC 58.418 33.333 0.00 0.00 0.00 4.30
145 146 9.927668 CCATGAAAAACACTCAAATATAAACCT 57.072 29.630 0.00 0.00 0.00 3.50
146 147 9.705290 ACCATGAAAAACACTCAAATATAAACC 57.295 29.630 0.00 0.00 0.00 3.27
148 149 9.619316 CGACCATGAAAAACACTCAAATATAAA 57.381 29.630 0.00 0.00 0.00 1.40
149 150 9.004717 TCGACCATGAAAAACACTCAAATATAA 57.995 29.630 0.00 0.00 0.00 0.98
150 151 8.554835 TCGACCATGAAAAACACTCAAATATA 57.445 30.769 0.00 0.00 0.00 0.86
151 152 7.447374 TCGACCATGAAAAACACTCAAATAT 57.553 32.000 0.00 0.00 0.00 1.28
152 153 6.869315 TCGACCATGAAAAACACTCAAATA 57.131 33.333 0.00 0.00 0.00 1.40
1053 1063 3.936372 TGAAAGAGAAGTGGGTAGACG 57.064 47.619 0.00 0.00 0.00 4.18
1074 1084 7.040132 TCGTGGGCAAATGCATAAATATATTCA 60.040 33.333 0.00 0.00 44.36 2.57
1892 1922 6.248433 AGGTAGCATTTCCATTTCTTCTTCA 58.752 36.000 0.00 0.00 0.00 3.02
2496 2528 9.031537 ACCAGGTCATTGATACGTATAATATCA 57.968 33.333 8.34 0.39 37.29 2.15
2698 2731 6.239345 CGACTTTCCCTATGTAGAAATAGCCT 60.239 42.308 0.00 0.00 31.89 4.58
2958 2991 2.091499 TCCCTCTGTCTCCGCCTAATTA 60.091 50.000 0.00 0.00 0.00 1.40
2959 2992 1.123928 CCCTCTGTCTCCGCCTAATT 58.876 55.000 0.00 0.00 0.00 1.40
2960 2993 0.261991 TCCCTCTGTCTCCGCCTAAT 59.738 55.000 0.00 0.00 0.00 1.73
2961 2994 0.395862 CTCCCTCTGTCTCCGCCTAA 60.396 60.000 0.00 0.00 0.00 2.69
2964 2997 2.363147 ACTCCCTCTGTCTCCGCC 60.363 66.667 0.00 0.00 0.00 6.13
2967 3000 2.233305 TAACCACTCCCTCTGTCTCC 57.767 55.000 0.00 0.00 0.00 3.71
3194 3244 6.072175 GGGTGCATGATGAAAGTGTACTTTTA 60.072 38.462 10.98 7.79 45.37 1.52
3345 3396 4.694339 AGAGTATTGAGTCAAATACGCCC 58.306 43.478 10.14 7.98 44.34 6.13
3349 3400 8.200792 AGACCATGAGAGTATTGAGTCAAATAC 58.799 37.037 10.14 12.21 41.41 1.89
3395 3446 7.536855 AGTCTAAAGTAATAACACGGAGACTG 58.463 38.462 0.00 0.00 36.31 3.51
3397 3448 7.201418 GCAAGTCTAAAGTAATAACACGGAGAC 60.201 40.741 0.00 0.00 31.72 3.36
3402 3453 6.730619 CGTTGCAAGTCTAAAGTAATAACACG 59.269 38.462 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.