Multiple sequence alignment - TraesCS7B01G061800

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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 TraesCS7B01G061800 chr7B 100.000 2595 0 0 1 2595 64115089 64117683 0.000000e+00 4756.0
1 TraesCS7B01G061800 chr7B 100.000 145 0 0 1 145 64095210 64095354 4.260000e-68 268.0
2 TraesCS7B01G061800 chr7B 100.000 145 0 0 1 145 448546090 448545946 4.260000e-68 268.0
3 TraesCS7B01G061800 chr7B 89.552 67 5 1 1780 1846 137526402 137526338 1.650000e-12 84.2
4 TraesCS7B01G061800 chr7A 90.479 1922 111 34 589 2480 110469914 110471793 0.000000e+00 2470.0
5 TraesCS7B01G061800 chr7A 93.478 92 6 0 2504 2595 110471789 110471880 1.250000e-28 137.0
6 TraesCS7B01G061800 chr7D 91.809 1636 92 24 163 1783 105489424 105491032 0.000000e+00 2241.0
7 TraesCS7B01G061800 chr7D 84.211 741 59 18 1882 2595 105491029 105491738 0.000000e+00 667.0
8 TraesCS7B01G061800 chr7D 87.500 72 7 2 1773 1843 122836261 122836331 5.950000e-12 82.4
9 TraesCS7B01G061800 chr7D 80.556 108 13 4 1780 1883 101395203 101395306 2.770000e-10 76.8
10 TraesCS7B01G061800 chrUn 100.000 145 0 0 1 145 84757103 84757247 4.260000e-68 268.0
11 TraesCS7B01G061800 chr6B 100.000 145 0 0 1 145 524653259 524653403 4.260000e-68 268.0
12 TraesCS7B01G061800 chr4B 100.000 145 0 0 1 145 465066415 465066559 4.260000e-68 268.0
13 TraesCS7B01G061800 chr4B 83.544 79 7 4 1771 1843 460189765 460189843 4.630000e-08 69.4
14 TraesCS7B01G061800 chr3B 100.000 145 0 0 1 145 103325340 103325196 4.260000e-68 268.0
15 TraesCS7B01G061800 chr3B 75.819 397 91 3 198 592 754346670 754346277 2.040000e-46 196.0
16 TraesCS7B01G061800 chr3B 86.111 72 5 3 1776 1843 70384874 70384944 3.580000e-09 73.1
17 TraesCS7B01G061800 chr2B 100.000 145 0 0 1 145 421810362 421810218 4.260000e-68 268.0
18 TraesCS7B01G061800 chr2B 100.000 144 0 0 2 145 453769080 453768937 1.530000e-67 267.0
19 TraesCS7B01G061800 chr1D 99.310 145 1 0 1 145 327669759 327669615 1.980000e-66 263.0
20 TraesCS7B01G061800 chr1A 99.310 145 1 0 1 145 341731690 341731546 1.980000e-66 263.0
21 TraesCS7B01G061800 chr1A 82.895 152 26 0 190 341 408067855 408067704 1.250000e-28 137.0
22 TraesCS7B01G061800 chr2D 74.750 400 91 8 194 588 9864718 9865112 1.230000e-38 171.0
23 TraesCS7B01G061800 chr2D 91.837 49 4 0 1842 1890 592631037 592630989 4.630000e-08 69.4
24 TraesCS7B01G061800 chr1B 74.169 391 98 3 196 585 638442570 638442182 2.670000e-35 159.0
25 TraesCS7B01G061800 chr1B 81.633 98 11 4 1780 1870 605451144 605451241 9.960000e-10 75.0
26 TraesCS7B01G061800 chr6D 79.126 206 39 4 2388 2592 451083674 451083876 3.480000e-29 139.0
27 TraesCS7B01G061800 chr5A 89.394 66 6 1 1825 1889 151732735 151732670 5.950000e-12 82.4
28 TraesCS7B01G061800 chr5A 85.915 71 7 3 282 351 53196146 53196078 3.580000e-09 73.1
29 TraesCS7B01G061800 chr5A 90.000 50 4 1 282 331 708564713 708564761 2.160000e-06 63.9
30 TraesCS7B01G061800 chr5B 89.231 65 6 1 288 351 399217254 399217190 2.140000e-11 80.5
31 TraesCS7B01G061800 chr3A 87.879 66 4 2 1780 1841 13553858 13553923 9.960000e-10 75.0
32 TraesCS7B01G061800 chr3A 90.566 53 5 0 1838 1890 446570465 446570413 1.290000e-08 71.3
33 TraesCS7B01G061800 chr3A 93.750 48 2 1 1843 1889 479095779 479095732 1.290000e-08 71.3
34 TraesCS7B01G061800 chr5D 85.915 71 7 3 282 351 174807789 174807857 3.580000e-09 73.1
35 TraesCS7B01G061800 chr5D 95.556 45 2 0 1842 1886 538684808 538684764 3.580000e-09 73.1
36 TraesCS7B01G061800 chr4D 86.765 68 5 2 1780 1843 138259173 138259106 3.580000e-09 73.1
37 TraesCS7B01G061800 chr2A 93.617 47 3 0 1837 1883 674043493 674043539 1.290000e-08 71.3


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 TraesCS7B01G061800 chr7B 64115089 64117683 2594 False 4756.0 4756 100.0000 1 2595 1 chr7B.!!$F2 2594
1 TraesCS7B01G061800 chr7A 110469914 110471880 1966 False 1303.5 2470 91.9785 589 2595 2 chr7A.!!$F1 2006
2 TraesCS7B01G061800 chr7D 105489424 105491738 2314 False 1454.0 2241 88.0100 163 2595 2 chr7D.!!$F3 2432

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
102 103 0.038166 TCCCACTCAACTCCATTGGC 59.962 55.0 0.0 0.00 38.98 4.52 F
144 145 0.179029 ACACCTTGGTTCTTCCGGTG 60.179 55.0 0.0 5.29 46.35 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1097 1116 0.321653 GTTCGCCATGAAGACTGGGT 60.322 55.0 0.00 0.00 37.23 4.51 R
2112 2172 0.108019 AAGAGGGTTGACCGGTTGAC 59.892 55.0 9.42 10.83 46.96 3.18 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
21 22 4.637483 CTTGAGCTTGTGTTCCTTTGAA 57.363 40.909 0.00 0.00 0.00 2.69
22 23 4.604976 CTTGAGCTTGTGTTCCTTTGAAG 58.395 43.478 0.00 0.00 0.00 3.02
49 50 7.962995 AGTAGGATCATACTTCTCTTGTTGA 57.037 36.000 14.14 0.00 31.89 3.18
50 51 8.006298 AGTAGGATCATACTTCTCTTGTTGAG 57.994 38.462 14.14 0.00 43.96 3.02
51 52 6.232581 AGGATCATACTTCTCTTGTTGAGG 57.767 41.667 0.00 0.00 42.86 3.86
52 53 5.960811 AGGATCATACTTCTCTTGTTGAGGA 59.039 40.000 0.00 0.00 42.86 3.71
53 54 6.441924 AGGATCATACTTCTCTTGTTGAGGAA 59.558 38.462 0.00 0.00 42.86 3.36
54 55 6.536941 GGATCATACTTCTCTTGTTGAGGAAC 59.463 42.308 0.00 0.00 42.86 3.62
55 56 6.419484 TCATACTTCTCTTGTTGAGGAACA 57.581 37.500 0.00 0.00 42.86 3.18
64 65 4.609691 TTGTTGAGGAACAAACTTCGTC 57.390 40.909 0.00 0.00 46.75 4.20
65 66 3.869065 TGTTGAGGAACAAACTTCGTCT 58.131 40.909 4.84 0.00 39.20 4.18
66 67 4.258543 TGTTGAGGAACAAACTTCGTCTT 58.741 39.130 4.84 0.00 39.20 3.01
67 68 4.094294 TGTTGAGGAACAAACTTCGTCTTG 59.906 41.667 4.84 0.00 39.20 3.02
68 69 3.202906 TGAGGAACAAACTTCGTCTTGG 58.797 45.455 4.84 0.00 35.18 3.61
69 70 2.548480 GAGGAACAAACTTCGTCTTGGG 59.452 50.000 0.00 0.00 32.40 4.12
70 71 1.607148 GGAACAAACTTCGTCTTGGGG 59.393 52.381 0.00 0.00 0.00 4.96
71 72 2.294979 GAACAAACTTCGTCTTGGGGT 58.705 47.619 0.00 0.00 0.00 4.95
72 73 3.469739 GAACAAACTTCGTCTTGGGGTA 58.530 45.455 0.00 0.00 0.00 3.69
73 74 3.782656 ACAAACTTCGTCTTGGGGTAT 57.217 42.857 0.00 0.00 0.00 2.73
74 75 4.094830 ACAAACTTCGTCTTGGGGTATT 57.905 40.909 0.00 0.00 0.00 1.89
75 76 3.818773 ACAAACTTCGTCTTGGGGTATTG 59.181 43.478 0.00 0.00 0.00 1.90
76 77 4.069304 CAAACTTCGTCTTGGGGTATTGA 58.931 43.478 0.00 0.00 0.00 2.57
77 78 4.569719 AACTTCGTCTTGGGGTATTGAT 57.430 40.909 0.00 0.00 0.00 2.57
78 79 4.138487 ACTTCGTCTTGGGGTATTGATC 57.862 45.455 0.00 0.00 0.00 2.92
79 80 3.775316 ACTTCGTCTTGGGGTATTGATCT 59.225 43.478 0.00 0.00 0.00 2.75
80 81 4.225267 ACTTCGTCTTGGGGTATTGATCTT 59.775 41.667 0.00 0.00 0.00 2.40
81 82 4.402056 TCGTCTTGGGGTATTGATCTTC 57.598 45.455 0.00 0.00 0.00 2.87
82 83 4.030913 TCGTCTTGGGGTATTGATCTTCT 58.969 43.478 0.00 0.00 0.00 2.85
83 84 4.469945 TCGTCTTGGGGTATTGATCTTCTT 59.530 41.667 0.00 0.00 0.00 2.52
84 85 4.811557 CGTCTTGGGGTATTGATCTTCTTC 59.188 45.833 0.00 0.00 0.00 2.87
85 86 5.126779 GTCTTGGGGTATTGATCTTCTTCC 58.873 45.833 0.00 0.00 0.00 3.46
86 87 4.166144 TCTTGGGGTATTGATCTTCTTCCC 59.834 45.833 0.00 0.80 0.00 3.97
87 88 3.469859 TGGGGTATTGATCTTCTTCCCA 58.530 45.455 11.00 11.00 40.50 4.37
88 89 3.202151 TGGGGTATTGATCTTCTTCCCAC 59.798 47.826 11.00 0.00 38.18 4.61
89 90 3.459969 GGGGTATTGATCTTCTTCCCACT 59.540 47.826 12.75 0.00 35.56 4.00
90 91 4.445019 GGGGTATTGATCTTCTTCCCACTC 60.445 50.000 12.75 0.00 35.56 3.51
91 92 4.164221 GGGTATTGATCTTCTTCCCACTCA 59.836 45.833 0.00 0.00 34.20 3.41
92 93 5.339200 GGGTATTGATCTTCTTCCCACTCAA 60.339 44.000 0.00 0.00 34.20 3.02
93 94 5.586643 GGTATTGATCTTCTTCCCACTCAAC 59.413 44.000 0.00 0.00 0.00 3.18
94 95 4.982241 TTGATCTTCTTCCCACTCAACT 57.018 40.909 0.00 0.00 0.00 3.16
95 96 4.543590 TGATCTTCTTCCCACTCAACTC 57.456 45.455 0.00 0.00 0.00 3.01
96 97 3.261897 TGATCTTCTTCCCACTCAACTCC 59.738 47.826 0.00 0.00 0.00 3.85
97 98 2.689658 TCTTCTTCCCACTCAACTCCA 58.310 47.619 0.00 0.00 0.00 3.86
98 99 3.251484 TCTTCTTCCCACTCAACTCCAT 58.749 45.455 0.00 0.00 0.00 3.41
99 100 3.652869 TCTTCTTCCCACTCAACTCCATT 59.347 43.478 0.00 0.00 0.00 3.16
100 101 3.423539 TCTTCCCACTCAACTCCATTG 57.576 47.619 0.00 0.00 39.94 2.82
101 102 2.040278 TCTTCCCACTCAACTCCATTGG 59.960 50.000 0.00 0.00 38.98 3.16
102 103 0.038166 TCCCACTCAACTCCATTGGC 59.962 55.000 0.00 0.00 38.98 4.52
103 104 0.251297 CCCACTCAACTCCATTGGCA 60.251 55.000 0.00 0.00 38.98 4.92
104 105 1.617804 CCCACTCAACTCCATTGGCAT 60.618 52.381 0.00 0.00 38.98 4.40
105 106 2.173519 CCACTCAACTCCATTGGCATT 58.826 47.619 0.00 0.00 38.98 3.56
106 107 2.094390 CCACTCAACTCCATTGGCATTG 60.094 50.000 10.82 10.82 38.98 2.82
107 108 2.821378 CACTCAACTCCATTGGCATTGA 59.179 45.455 16.19 16.19 38.98 2.57
108 109 3.256383 CACTCAACTCCATTGGCATTGAA 59.744 43.478 17.19 0.00 38.98 2.69
109 110 3.256631 ACTCAACTCCATTGGCATTGAAC 59.743 43.478 17.19 0.00 38.98 3.18
110 111 3.499338 TCAACTCCATTGGCATTGAACT 58.501 40.909 15.26 0.00 38.98 3.01
111 112 3.896888 TCAACTCCATTGGCATTGAACTT 59.103 39.130 15.26 0.00 38.98 2.66
112 113 4.344679 TCAACTCCATTGGCATTGAACTTT 59.655 37.500 15.26 0.00 38.98 2.66
113 114 4.525912 ACTCCATTGGCATTGAACTTTC 57.474 40.909 10.79 0.00 0.00 2.62
114 115 3.057315 ACTCCATTGGCATTGAACTTTCG 60.057 43.478 10.79 0.00 0.00 3.46
115 116 2.890311 TCCATTGGCATTGAACTTTCGT 59.110 40.909 10.79 0.00 0.00 3.85
116 117 3.320541 TCCATTGGCATTGAACTTTCGTT 59.679 39.130 10.79 0.00 35.68 3.85
128 129 5.430220 GAACTTTCGTTCAAAACCAACAC 57.570 39.130 0.68 0.00 46.88 3.32
129 130 3.840468 ACTTTCGTTCAAAACCAACACC 58.160 40.909 0.00 0.00 0.00 4.16
130 131 3.508402 ACTTTCGTTCAAAACCAACACCT 59.492 39.130 0.00 0.00 0.00 4.00
131 132 4.021807 ACTTTCGTTCAAAACCAACACCTT 60.022 37.500 0.00 0.00 0.00 3.50
132 133 3.495670 TCGTTCAAAACCAACACCTTG 57.504 42.857 0.00 0.00 0.00 3.61
141 142 0.951558 CCAACACCTTGGTTCTTCCG 59.048 55.000 0.00 0.00 42.09 4.30
142 143 0.951558 CAACACCTTGGTTCTTCCGG 59.048 55.000 0.00 0.00 39.52 5.14
143 144 0.549469 AACACCTTGGTTCTTCCGGT 59.451 50.000 0.00 0.00 39.52 5.28
144 145 0.179029 ACACCTTGGTTCTTCCGGTG 60.179 55.000 0.00 5.29 46.35 4.94
192 193 9.297586 GAAAGTTTTAAAGTAAGGTCCAAACTG 57.702 33.333 0.00 0.00 34.15 3.16
248 249 2.334977 ACCCAGTCACACCACTTATCA 58.665 47.619 0.00 0.00 0.00 2.15
249 250 2.708861 ACCCAGTCACACCACTTATCAA 59.291 45.455 0.00 0.00 0.00 2.57
306 307 8.605746 CAAATGGCCACTTAATTTTGTCATATG 58.394 33.333 8.16 0.00 0.00 1.78
312 313 8.382875 GCCACTTAATTTTGTCATATGCTTTTC 58.617 33.333 0.00 0.00 0.00 2.29
332 333 9.663904 GCTTTTCCAAAATCCACTTTAAAAATC 57.336 29.630 0.00 0.00 0.00 2.17
373 374 4.201783 GGCACGAATAGTATTCAACGCTTT 60.202 41.667 20.24 0.00 0.00 3.51
376 377 7.095940 GGCACGAATAGTATTCAACGCTTTATA 60.096 37.037 20.24 0.00 0.00 0.98
377 378 8.433126 GCACGAATAGTATTCAACGCTTTATAT 58.567 33.333 20.24 0.00 0.00 0.86
395 396 8.568794 GCTTTATATTAAGATCACAACCCCTTC 58.431 37.037 5.66 0.00 0.00 3.46
396 397 9.853177 CTTTATATTAAGATCACAACCCCTTCT 57.147 33.333 0.00 0.00 0.00 2.85
410 411 9.273137 CACAACCCCTTCTATTATATATCTCCT 57.727 37.037 0.00 0.00 0.00 3.69
432 433 6.723977 TCCTTTTTATAAATGCTGTCTGGGTT 59.276 34.615 0.00 0.00 0.00 4.11
443 444 3.873952 GCTGTCTGGGTTGAAGATATGAC 59.126 47.826 0.00 0.00 0.00 3.06
504 505 8.514136 TTTTGGTAATGATTTTAAAGCTCACG 57.486 30.769 5.08 0.00 0.00 4.35
505 506 6.811253 TGGTAATGATTTTAAAGCTCACGT 57.189 33.333 5.08 0.00 0.00 4.49
521 522 2.752354 TCACGTTCAATAGGCAAATGGG 59.248 45.455 0.00 0.00 0.00 4.00
524 525 2.752354 CGTTCAATAGGCAAATGGGTCA 59.248 45.455 0.00 0.00 0.00 4.02
527 528 5.624281 CGTTCAATAGGCAAATGGGTCAAAT 60.624 40.000 0.00 0.00 0.00 2.32
550 551 4.511617 TTTTGTATTTGCTCGGCATCAA 57.488 36.364 0.00 2.28 38.76 2.57
559 560 2.483877 TGCTCGGCATCAACAGTTTTAG 59.516 45.455 0.00 0.00 31.71 1.85
582 583 4.105697 GGGACCAAGGTGATTATCCCATAA 59.894 45.833 0.00 0.00 41.94 1.90
637 638 7.425606 ACAACAAATACAAAAGGACATCTCAC 58.574 34.615 0.00 0.00 0.00 3.51
640 641 7.651808 ACAAATACAAAAGGACATCTCACTTG 58.348 34.615 0.00 0.00 0.00 3.16
650 651 4.093998 GGACATCTCACTTGTGTATTGCAG 59.906 45.833 0.46 0.00 0.00 4.41
870 885 7.370383 AGCATGAACGTTAGATTGACATTTTT 58.630 30.769 0.00 0.00 0.00 1.94
871 886 7.538678 AGCATGAACGTTAGATTGACATTTTTC 59.461 33.333 0.00 0.00 0.00 2.29
969 985 3.622826 CACGACAACCCTCCCCGT 61.623 66.667 0.00 0.00 0.00 5.28
1046 1062 3.985008 TGTCCGTTATAATCCACCGATG 58.015 45.455 0.00 0.00 0.00 3.84
1055 1074 0.460284 ATCCACCGATGCACGAAGAC 60.460 55.000 9.75 0.00 45.77 3.01
1079 1098 2.192861 CAACCTCGCAAGCCACCAA 61.193 57.895 0.00 0.00 37.18 3.67
1081 1100 2.032528 CCTCGCAAGCCACCAAGA 59.967 61.111 0.00 0.00 37.18 3.02
1093 1112 2.619074 GCCACCAAGACCATCTTAGCTT 60.619 50.000 0.00 0.00 33.78 3.74
1097 1116 4.761739 CACCAAGACCATCTTAGCTTCAAA 59.238 41.667 0.00 0.00 33.78 2.69
1100 1119 3.956744 AGACCATCTTAGCTTCAAACCC 58.043 45.455 0.00 0.00 0.00 4.11
1115 1136 0.400213 AACCCAGTCTTCATGGCGAA 59.600 50.000 0.00 0.00 36.43 4.70
1126 1147 3.758172 TGGCGAACCAAGCTTTCC 58.242 55.556 0.00 0.00 45.37 3.13
1128 1149 0.889186 TGGCGAACCAAGCTTTCCTC 60.889 55.000 0.00 0.00 45.37 3.71
1129 1150 1.587043 GGCGAACCAAGCTTTCCTCC 61.587 60.000 0.00 0.00 35.26 4.30
1138 1159 2.815647 CTTTCCTCCACCTCGCGC 60.816 66.667 0.00 0.00 0.00 6.86
1139 1160 3.302347 CTTTCCTCCACCTCGCGCT 62.302 63.158 5.56 0.00 0.00 5.92
1140 1161 1.945354 CTTTCCTCCACCTCGCGCTA 61.945 60.000 5.56 0.00 0.00 4.26
1206 1227 3.067106 ACACGAAGCATGTTCTTGGTAG 58.933 45.455 14.40 7.32 34.07 3.18
1208 1229 1.398390 CGAAGCATGTTCTTGGTAGGC 59.602 52.381 0.00 0.00 0.00 3.93
1214 1242 3.878778 CATGTTCTTGGTAGGCTAGCTT 58.121 45.455 22.88 10.11 0.00 3.74
1233 1261 0.326595 TGGTGTGTGGTGTGACAACT 59.673 50.000 0.97 0.00 30.65 3.16
1234 1262 0.732571 GGTGTGTGGTGTGACAACTG 59.267 55.000 0.97 0.00 0.00 3.16
1235 1263 1.677518 GGTGTGTGGTGTGACAACTGA 60.678 52.381 0.97 0.00 0.00 3.41
1236 1264 1.396996 GTGTGTGGTGTGACAACTGAC 59.603 52.381 0.97 0.00 0.00 3.51
1237 1265 1.002544 TGTGTGGTGTGACAACTGACA 59.997 47.619 0.97 1.51 0.00 3.58
1238 1266 2.080693 GTGTGGTGTGACAACTGACAA 58.919 47.619 0.97 0.00 0.00 3.18
1239 1267 2.095853 GTGTGGTGTGACAACTGACAAG 59.904 50.000 0.97 0.00 0.00 3.16
1261 1291 1.955495 TATGTGCGTGGACAGGCGAT 61.955 55.000 11.70 8.86 44.42 4.58
1366 1396 2.713967 GGGTAAGCCGGAGTACGCA 61.714 63.158 20.35 0.00 42.52 5.24
1634 1667 2.520069 CCTAGATCAGCCGATGGTACT 58.480 52.381 0.00 0.00 29.66 2.73
1635 1668 2.490115 CCTAGATCAGCCGATGGTACTC 59.510 54.545 0.00 0.00 29.66 2.59
1636 1669 2.073252 AGATCAGCCGATGGTACTCA 57.927 50.000 0.00 0.00 29.66 3.41
1637 1670 2.603021 AGATCAGCCGATGGTACTCAT 58.397 47.619 0.00 0.00 39.13 2.90
1738 1774 6.808008 TTGATATTAGCTAGGCTGATTTGC 57.192 37.500 0.00 0.00 40.10 3.68
1822 1858 8.732746 ATATAAAAGCGTTTAGATCACTTGGT 57.267 30.769 10.55 0.00 32.76 3.67
1823 1859 9.826574 ATATAAAAGCGTTTAGATCACTTGGTA 57.173 29.630 10.55 0.00 32.76 3.25
1824 1860 6.870971 AAAAGCGTTTAGATCACTTGGTAA 57.129 33.333 0.00 0.00 0.00 2.85
1825 1861 7.448748 AAAAGCGTTTAGATCACTTGGTAAT 57.551 32.000 0.00 0.00 0.00 1.89
1826 1862 6.663944 AAGCGTTTAGATCACTTGGTAATC 57.336 37.500 0.00 0.00 0.00 1.75
1827 1863 5.978814 AGCGTTTAGATCACTTGGTAATCT 58.021 37.500 0.00 0.00 34.29 2.40
1828 1864 7.108841 AGCGTTTAGATCACTTGGTAATCTA 57.891 36.000 0.00 0.00 32.25 1.98
1829 1865 7.553334 AGCGTTTAGATCACTTGGTAATCTAA 58.447 34.615 0.00 0.61 39.19 2.10
1830 1866 8.038944 AGCGTTTAGATCACTTGGTAATCTAAA 58.961 33.333 10.32 10.32 44.04 1.85
1833 1869 7.766219 TTAGATCACTTGGTAATCTAAACGC 57.234 36.000 0.00 0.00 38.44 4.84
1834 1870 5.978814 AGATCACTTGGTAATCTAAACGCT 58.021 37.500 0.00 0.00 0.00 5.07
1835 1871 6.407202 AGATCACTTGGTAATCTAAACGCTT 58.593 36.000 0.00 0.00 0.00 4.68
1836 1872 6.879458 AGATCACTTGGTAATCTAAACGCTTT 59.121 34.615 0.00 0.00 0.00 3.51
1837 1873 6.870971 TCACTTGGTAATCTAAACGCTTTT 57.129 33.333 0.00 0.00 0.00 2.27
1838 1874 7.966246 TCACTTGGTAATCTAAACGCTTTTA 57.034 32.000 0.00 0.00 0.00 1.52
1839 1875 8.556213 TCACTTGGTAATCTAAACGCTTTTAT 57.444 30.769 0.00 0.00 0.00 1.40
1840 1876 9.656040 TCACTTGGTAATCTAAACGCTTTTATA 57.344 29.630 0.00 0.00 0.00 0.98
2062 2121 2.594303 CCTTGCCTCGTTGCCACA 60.594 61.111 0.00 0.00 0.00 4.17
2089 2149 1.402896 CCTAGCCGCTCCTCCATCAA 61.403 60.000 0.00 0.00 0.00 2.57
2105 2165 1.297968 TCAAGATGCCATCTCCCCAA 58.702 50.000 7.84 0.00 39.08 4.12
2112 2172 0.035458 GCCATCTCCCCAACTATCGG 59.965 60.000 0.00 0.00 0.00 4.18
2135 2195 0.767060 ACCGGTCAACCCTCTTCCTT 60.767 55.000 0.00 0.00 0.00 3.36
2144 2204 0.393132 CCCTCTTCCTTTCCTTCGCC 60.393 60.000 0.00 0.00 0.00 5.54
2196 2256 3.570638 CATGCTTGGAGCTCGGCG 61.571 66.667 7.83 0.00 42.97 6.46
2223 2283 1.480545 TGTCTACGCATGCACCTATGT 59.519 47.619 19.57 8.69 0.00 2.29
2327 2390 8.642908 TTGTATTCGTGTCAAATCGATCTATT 57.357 30.769 0.00 0.00 36.01 1.73
2352 2415 3.511477 TCCTATCCCCTCTAGCATGAAC 58.489 50.000 0.00 0.00 0.00 3.18
2377 2440 9.233232 ACGAGATGTTGAGAACAAAATAAAAAC 57.767 29.630 0.00 0.00 45.86 2.43
2406 2471 0.259647 AGGATTGCAATAGCCAGCCA 59.740 50.000 12.97 0.00 43.88 4.75
2455 2521 3.284449 GGCACGACTGGCCGTTTT 61.284 61.111 0.00 0.00 42.39 2.43
2456 2522 2.719354 GCACGACTGGCCGTTTTT 59.281 55.556 0.00 0.00 41.29 1.94
2464 2530 1.546476 ACTGGCCGTTTTTGTGTTTGA 59.454 42.857 0.00 0.00 0.00 2.69
2471 2537 4.677584 CCGTTTTTGTGTTTGAGGAATGA 58.322 39.130 0.00 0.00 0.00 2.57
2481 2547 7.499292 TGTGTTTGAGGAATGACATTTTTGAT 58.501 30.769 1.39 0.00 0.00 2.57
2492 2559 7.852971 ATGACATTTTTGATAAAAGCATGGG 57.147 32.000 0.00 0.00 36.73 4.00
2503 2570 9.956640 TTGATAAAAGCATGGGATTTTGTTTAT 57.043 25.926 0.00 0.00 42.18 1.40
2522 2589 8.023050 TGTTTATTTTGGTGCATTTTTATCCG 57.977 30.769 0.00 0.00 0.00 4.18
2523 2590 7.118390 TGTTTATTTTGGTGCATTTTTATCCGG 59.882 33.333 0.00 0.00 0.00 5.14
2535 2602 6.628398 GCATTTTTATCCGGAAATGGTTACCA 60.628 38.462 22.14 6.53 41.35 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.569240 AAGTATGATCCTACTTCCTTCAAAGG 58.431 38.462 15.34 2.15 37.36 3.11
15 16 8.655651 GAAGTATGATCCTACTTCCTTCAAAG 57.344 38.462 27.62 0.00 46.23 2.77
24 25 8.367660 TCAACAAGAGAAGTATGATCCTACTT 57.632 34.615 19.60 19.60 43.04 2.24
25 26 7.962995 TCAACAAGAGAAGTATGATCCTACT 57.037 36.000 4.95 4.95 33.34 2.57
30 31 7.604164 TTGTTCCTCAACAAGAGAAGTATGATC 59.396 37.037 0.00 0.00 45.73 2.92
31 32 7.453393 TTGTTCCTCAACAAGAGAAGTATGAT 58.547 34.615 0.00 0.00 45.73 2.45
32 33 6.826668 TTGTTCCTCAACAAGAGAAGTATGA 58.173 36.000 0.00 0.00 45.73 2.15
58 59 4.408182 AGATCAATACCCCAAGACGAAG 57.592 45.455 0.00 0.00 0.00 3.79
59 60 4.469945 AGAAGATCAATACCCCAAGACGAA 59.530 41.667 0.00 0.00 0.00 3.85
60 61 4.030913 AGAAGATCAATACCCCAAGACGA 58.969 43.478 0.00 0.00 0.00 4.20
61 62 4.408182 AGAAGATCAATACCCCAAGACG 57.592 45.455 0.00 0.00 0.00 4.18
62 63 5.126779 GGAAGAAGATCAATACCCCAAGAC 58.873 45.833 0.00 0.00 0.00 3.01
63 64 4.166144 GGGAAGAAGATCAATACCCCAAGA 59.834 45.833 0.00 0.00 32.98 3.02
64 65 4.079787 TGGGAAGAAGATCAATACCCCAAG 60.080 45.833 11.30 0.00 39.43 3.61
65 66 3.855599 TGGGAAGAAGATCAATACCCCAA 59.144 43.478 11.30 0.00 39.43 4.12
66 67 3.202151 GTGGGAAGAAGATCAATACCCCA 59.798 47.826 10.07 10.07 40.03 4.96
67 68 3.459969 AGTGGGAAGAAGATCAATACCCC 59.540 47.826 0.00 8.42 35.48 4.95
68 69 4.164221 TGAGTGGGAAGAAGATCAATACCC 59.836 45.833 0.00 0.00 36.72 3.69
69 70 5.359194 TGAGTGGGAAGAAGATCAATACC 57.641 43.478 0.00 0.00 0.00 2.73
70 71 6.410540 AGTTGAGTGGGAAGAAGATCAATAC 58.589 40.000 0.00 0.00 0.00 1.89
71 72 6.352222 GGAGTTGAGTGGGAAGAAGATCAATA 60.352 42.308 0.00 0.00 0.00 1.90
72 73 5.495640 GAGTTGAGTGGGAAGAAGATCAAT 58.504 41.667 0.00 0.00 0.00 2.57
73 74 4.263068 GGAGTTGAGTGGGAAGAAGATCAA 60.263 45.833 0.00 0.00 0.00 2.57
74 75 3.261897 GGAGTTGAGTGGGAAGAAGATCA 59.738 47.826 0.00 0.00 0.00 2.92
75 76 3.261897 TGGAGTTGAGTGGGAAGAAGATC 59.738 47.826 0.00 0.00 0.00 2.75
76 77 3.251484 TGGAGTTGAGTGGGAAGAAGAT 58.749 45.455 0.00 0.00 0.00 2.40
77 78 2.689658 TGGAGTTGAGTGGGAAGAAGA 58.310 47.619 0.00 0.00 0.00 2.87
78 79 3.710209 ATGGAGTTGAGTGGGAAGAAG 57.290 47.619 0.00 0.00 0.00 2.85
79 80 3.498481 CCAATGGAGTTGAGTGGGAAGAA 60.498 47.826 0.00 0.00 40.37 2.52
80 81 2.040278 CCAATGGAGTTGAGTGGGAAGA 59.960 50.000 0.00 0.00 40.37 2.87
81 82 2.440409 CCAATGGAGTTGAGTGGGAAG 58.560 52.381 0.00 0.00 40.37 3.46
82 83 1.547675 GCCAATGGAGTTGAGTGGGAA 60.548 52.381 2.05 0.00 40.37 3.97
83 84 0.038166 GCCAATGGAGTTGAGTGGGA 59.962 55.000 2.05 0.00 40.37 4.37
84 85 0.251297 TGCCAATGGAGTTGAGTGGG 60.251 55.000 2.05 0.00 40.37 4.61
85 86 1.843368 ATGCCAATGGAGTTGAGTGG 58.157 50.000 2.05 0.00 40.37 4.00
86 87 2.821378 TCAATGCCAATGGAGTTGAGTG 59.179 45.455 2.05 0.00 40.37 3.51
87 88 3.159213 TCAATGCCAATGGAGTTGAGT 57.841 42.857 2.05 0.00 40.37 3.41
88 89 3.508793 AGTTCAATGCCAATGGAGTTGAG 59.491 43.478 15.71 0.00 40.37 3.02
89 90 3.499338 AGTTCAATGCCAATGGAGTTGA 58.501 40.909 2.05 9.52 40.37 3.18
90 91 3.947910 AGTTCAATGCCAATGGAGTTG 57.052 42.857 2.05 7.10 37.57 3.16
91 92 4.559300 CGAAAGTTCAATGCCAATGGAGTT 60.559 41.667 2.05 0.00 0.00 3.01
92 93 3.057315 CGAAAGTTCAATGCCAATGGAGT 60.057 43.478 2.05 0.00 0.00 3.85
93 94 3.057315 ACGAAAGTTCAATGCCAATGGAG 60.057 43.478 2.05 0.00 46.40 3.86
94 95 2.890311 ACGAAAGTTCAATGCCAATGGA 59.110 40.909 2.05 0.00 46.40 3.41
95 96 3.302365 ACGAAAGTTCAATGCCAATGG 57.698 42.857 0.00 0.00 46.40 3.16
109 110 4.104696 AGGTGTTGGTTTTGAACGAAAG 57.895 40.909 0.00 0.00 30.84 2.62
110 111 4.238514 CAAGGTGTTGGTTTTGAACGAAA 58.761 39.130 0.00 0.00 30.84 3.46
111 112 3.839293 CAAGGTGTTGGTTTTGAACGAA 58.161 40.909 0.00 0.00 0.00 3.85
112 113 3.495670 CAAGGTGTTGGTTTTGAACGA 57.504 42.857 0.00 0.00 0.00 3.85
123 124 0.951558 CCGGAAGAACCAAGGTGTTG 59.048 55.000 0.00 0.00 38.90 3.33
124 125 0.549469 ACCGGAAGAACCAAGGTGTT 59.451 50.000 9.46 0.00 38.90 3.32
125 126 0.179029 CACCGGAAGAACCAAGGTGT 60.179 55.000 9.46 0.00 41.83 4.16
126 127 2.629002 CACCGGAAGAACCAAGGTG 58.371 57.895 9.46 0.00 41.34 4.00
157 158 9.394477 CCTTACTTTAAAACTTTCGAAGGATTG 57.606 33.333 14.89 0.00 34.14 2.67
158 159 9.128404 ACCTTACTTTAAAACTTTCGAAGGATT 57.872 29.630 14.89 5.56 35.83 3.01
159 160 8.687292 ACCTTACTTTAAAACTTTCGAAGGAT 57.313 30.769 14.89 0.00 35.83 3.24
160 161 7.227314 GGACCTTACTTTAAAACTTTCGAAGGA 59.773 37.037 14.89 0.00 35.83 3.36
161 162 7.012610 TGGACCTTACTTTAAAACTTTCGAAGG 59.987 37.037 5.63 5.63 37.53 3.46
162 163 7.922837 TGGACCTTACTTTAAAACTTTCGAAG 58.077 34.615 0.00 0.00 0.00 3.79
163 164 7.862512 TGGACCTTACTTTAAAACTTTCGAA 57.137 32.000 0.00 0.00 0.00 3.71
164 165 7.862512 TTGGACCTTACTTTAAAACTTTCGA 57.137 32.000 0.00 0.00 0.00 3.71
165 166 8.186163 AGTTTGGACCTTACTTTAAAACTTTCG 58.814 33.333 0.00 0.00 33.78 3.46
192 193 4.759205 GGGGCATGTGGGGGTGAC 62.759 72.222 0.00 0.00 0.00 3.67
224 225 2.859165 AGTGGTGTGACTGGGTAATG 57.141 50.000 0.00 0.00 0.00 1.90
249 250 3.575805 TGCTGAAATTGAAAGGGTTCCT 58.424 40.909 0.00 0.00 33.87 3.36
306 307 9.663904 GATTTTTAAAGTGGATTTTGGAAAAGC 57.336 29.630 0.00 0.00 33.77 3.51
312 313 9.323985 TGTTCTGATTTTTAAAGTGGATTTTGG 57.676 29.630 0.00 0.00 32.01 3.28
365 366 7.855904 GGGTTGTGATCTTAATATAAAGCGTTG 59.144 37.037 0.00 0.00 0.00 4.10
368 369 6.710744 AGGGGTTGTGATCTTAATATAAAGCG 59.289 38.462 0.00 0.00 0.00 4.68
410 411 7.531857 TCAACCCAGACAGCATTTATAAAAA 57.468 32.000 1.21 0.00 0.00 1.94
432 433 6.358974 TGTGTTTCTCCAGTCATATCTTCA 57.641 37.500 0.00 0.00 0.00 3.02
443 444 9.877178 ATAGACTAAGTAAATGTGTTTCTCCAG 57.123 33.333 0.00 0.00 0.00 3.86
482 483 6.811253 ACGTGAGCTTTAAAATCATTACCA 57.189 33.333 6.17 0.00 0.00 3.25
504 505 4.799564 TTGACCCATTTGCCTATTGAAC 57.200 40.909 0.00 0.00 0.00 3.18
505 506 6.371595 AATTTGACCCATTTGCCTATTGAA 57.628 33.333 0.00 0.00 0.00 2.69
542 543 2.161609 GTCCCTAAAACTGTTGATGCCG 59.838 50.000 0.00 0.00 0.00 5.69
550 551 2.781174 TCACCTTGGTCCCTAAAACTGT 59.219 45.455 0.00 0.00 0.00 3.55
559 560 1.850345 TGGGATAATCACCTTGGTCCC 59.150 52.381 1.32 1.32 40.74 4.46
637 638 3.715495 TGGTTTTGCTGCAATACACAAG 58.285 40.909 28.38 0.00 29.34 3.16
640 641 4.024977 CCTTTTGGTTTTGCTGCAATACAC 60.025 41.667 28.38 20.43 34.07 2.90
969 985 2.692368 GACAGGGCCATGAGGGGA 60.692 66.667 26.87 0.00 37.04 4.81
1046 1062 1.400494 AGGTTGTTTGTGTCTTCGTGC 59.600 47.619 0.00 0.00 0.00 5.34
1055 1074 0.594796 GGCTTGCGAGGTTGTTTGTG 60.595 55.000 2.37 0.00 0.00 3.33
1079 1098 3.330701 TGGGTTTGAAGCTAAGATGGTCT 59.669 43.478 0.00 0.00 0.00 3.85
1081 1100 3.074538 ACTGGGTTTGAAGCTAAGATGGT 59.925 43.478 0.00 0.00 0.00 3.55
1093 1112 1.881925 CGCCATGAAGACTGGGTTTGA 60.882 52.381 0.00 0.00 34.16 2.69
1097 1116 0.321653 GTTCGCCATGAAGACTGGGT 60.322 55.000 0.00 0.00 37.23 4.51
1100 1119 3.231734 TGGTTCGCCATGAAGACTG 57.768 52.632 0.00 0.00 43.56 3.51
1115 1136 0.402121 GAGGTGGAGGAAAGCTTGGT 59.598 55.000 0.00 0.00 0.00 3.67
1126 1147 1.096386 AGTAGTAGCGCGAGGTGGAG 61.096 60.000 12.10 0.00 44.53 3.86
1128 1149 1.064296 CAGTAGTAGCGCGAGGTGG 59.936 63.158 12.10 0.00 44.53 4.61
1129 1150 1.586564 GCAGTAGTAGCGCGAGGTG 60.587 63.158 12.10 0.00 44.53 4.00
1138 1159 1.066908 GCAGAGGAGCAGCAGTAGTAG 59.933 57.143 0.00 0.00 0.00 2.57
1139 1160 1.107114 GCAGAGGAGCAGCAGTAGTA 58.893 55.000 0.00 0.00 0.00 1.82
1140 1161 0.902048 TGCAGAGGAGCAGCAGTAGT 60.902 55.000 0.00 0.00 40.11 2.73
1206 1227 1.073199 ACCACACACCAAGCTAGCC 59.927 57.895 12.13 0.00 0.00 3.93
1208 1229 1.202639 TCACACCACACACCAAGCTAG 60.203 52.381 0.00 0.00 0.00 3.42
1214 1242 0.326595 AGTTGTCACACCACACACCA 59.673 50.000 0.00 0.00 0.00 4.17
1233 1261 1.552792 TCCACGCACATATCCTTGTCA 59.447 47.619 0.00 0.00 0.00 3.58
1234 1262 1.933853 GTCCACGCACATATCCTTGTC 59.066 52.381 0.00 0.00 0.00 3.18
1235 1263 1.277842 TGTCCACGCACATATCCTTGT 59.722 47.619 0.00 0.00 0.00 3.16
1236 1264 1.935873 CTGTCCACGCACATATCCTTG 59.064 52.381 0.00 0.00 0.00 3.61
1237 1265 1.134401 CCTGTCCACGCACATATCCTT 60.134 52.381 0.00 0.00 0.00 3.36
1238 1266 0.465705 CCTGTCCACGCACATATCCT 59.534 55.000 0.00 0.00 0.00 3.24
1239 1267 1.160329 GCCTGTCCACGCACATATCC 61.160 60.000 0.00 0.00 0.00 2.59
1261 1291 2.588439 GCATCTGCTCCCAGCTCA 59.412 61.111 0.00 0.00 42.97 4.26
1351 1381 1.509463 CACTGCGTACTCCGGCTTA 59.491 57.895 0.00 0.00 36.94 3.09
1366 1396 3.148084 CGGTTGGTCACCTCCACT 58.852 61.111 0.00 0.00 44.69 4.00
1658 1694 2.754472 CACTACTGCACTTGTGCACTA 58.246 47.619 22.47 16.58 40.23 2.74
1700 1736 1.512926 ATCAAACGGGATAGCATCGC 58.487 50.000 0.00 0.00 38.71 4.58
1738 1774 5.062308 GTGTTACAATAGAGAGAAACCGCAG 59.938 44.000 0.00 0.00 0.00 5.18
1883 1919 9.770503 TGCGAACGTTTTTGCTATAATAATTTA 57.229 25.926 17.91 0.00 42.11 1.40
1893 1929 3.953766 TCATTTGCGAACGTTTTTGCTA 58.046 36.364 17.91 10.55 42.11 3.49
2009 2067 0.965363 CAAGCCGTTATGCCTGGGTT 60.965 55.000 0.00 0.00 43.80 4.11
2089 2149 2.196742 TAGTTGGGGAGATGGCATCT 57.803 50.000 29.19 29.19 43.70 2.90
2112 2172 0.108019 AAGAGGGTTGACCGGTTGAC 59.892 55.000 9.42 10.83 46.96 3.18
2135 2195 4.430765 GCGTCCTCGGCGAAGGAA 62.431 66.667 23.27 10.09 46.90 3.36
2196 2256 0.721718 GCATGCGTAGACAACTGGAC 59.278 55.000 0.00 0.00 0.00 4.02
2223 2283 7.654022 ACCTTTCAGTTTTAGTCAATTCCAA 57.346 32.000 0.00 0.00 0.00 3.53
2252 2315 5.886960 AATTTTTCTAATGCTCAGTCGCT 57.113 34.783 0.00 0.00 0.00 4.93
2289 2352 9.388346 TGACACGAATACAAATGTTGTTTATTC 57.612 29.630 0.00 3.37 42.22 1.75
2327 2390 1.993301 TGCTAGAGGGGATAGGATCGA 59.007 52.381 0.00 0.00 0.00 3.59
2334 2397 3.157881 CTCGTTCATGCTAGAGGGGATA 58.842 50.000 0.00 0.00 0.00 2.59
2338 2401 2.363680 ACATCTCGTTCATGCTAGAGGG 59.636 50.000 0.00 6.70 0.00 4.30
2352 2415 8.409690 CGTTTTTATTTTGTTCTCAACATCTCG 58.590 33.333 0.00 0.00 41.79 4.04
2377 2440 6.756074 TGGCTATTGCAATCCTTAATTTTTCG 59.244 34.615 16.86 0.00 41.91 3.46
2384 2449 2.958355 GGCTGGCTATTGCAATCCTTAA 59.042 45.455 16.86 0.00 41.91 1.85
2406 2471 0.389391 CATCCTGGCTATCGAACGGT 59.611 55.000 0.00 0.00 0.00 4.83
2442 2507 0.099791 AACACAAAAACGGCCAGTCG 59.900 50.000 2.24 0.00 0.00 4.18
2444 2509 1.546476 TCAAACACAAAAACGGCCAGT 59.454 42.857 2.24 0.00 0.00 4.00
2450 2515 5.098893 TGTCATTCCTCAAACACAAAAACG 58.901 37.500 0.00 0.00 0.00 3.60
2455 2521 7.326454 TCAAAAATGTCATTCCTCAAACACAA 58.674 30.769 0.00 0.00 0.00 3.33
2456 2522 6.871844 TCAAAAATGTCATTCCTCAAACACA 58.128 32.000 0.00 0.00 0.00 3.72
2464 2530 9.158233 CATGCTTTTATCAAAAATGTCATTCCT 57.842 29.630 0.00 0.00 34.18 3.36
2471 2537 8.866970 AAATCCCATGCTTTTATCAAAAATGT 57.133 26.923 0.00 0.00 34.18 2.71
2503 2570 4.873746 TCCGGATAAAAATGCACCAAAA 57.126 36.364 0.00 0.00 0.00 2.44
2522 2589 6.122277 TCAAGATCTGATGGTAACCATTTCC 58.878 40.000 0.00 0.00 45.26 3.13
2523 2590 7.500227 TGATCAAGATCTGATGGTAACCATTTC 59.500 37.037 11.04 0.00 45.23 2.17


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

AutoCloner maintained by Alex Coulton.