Multiple sequence alignment - TraesCS6D01G198200

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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 TraesCS6D01G198200 chr6D 100.000 2585 0 0 1 2585 276135419 276138003 0.000000e+00 4774.0
1 TraesCS6D01G198200 chr6D 95.161 62 3 0 2 63 304118077 304118138 5.890000e-17 99.0
2 TraesCS6D01G198200 chr7D 94.394 2426 113 7 162 2584 564521856 564524261 0.000000e+00 3705.0
3 TraesCS6D01G198200 chr7D 93.626 1914 77 14 697 2585 440576631 440574738 0.000000e+00 2817.0
4 TraesCS6D01G198200 chr7D 90.212 1604 150 5 985 2585 90647301 90645702 0.000000e+00 2085.0
5 TraesCS6D01G198200 chr7D 93.807 436 20 6 163 596 440577041 440576611 0.000000e+00 649.0
6 TraesCS6D01G198200 chr5B 91.652 2300 162 10 303 2584 693982829 693985116 0.000000e+00 3157.0
7 TraesCS6D01G198200 chr5A 90.443 2438 145 41 159 2585 556081430 556079070 0.000000e+00 3131.0
8 TraesCS6D01G198200 chr5A 89.838 1604 157 4 985 2585 678555658 678554058 0.000000e+00 2054.0
9 TraesCS6D01G198200 chr4D 92.941 1615 67 17 162 1732 40161836 40163447 0.000000e+00 2307.0
10 TraesCS6D01G198200 chr3D 90.526 1615 144 7 977 2585 485195185 485193574 0.000000e+00 2126.0
11 TraesCS6D01G198200 chr1A 90.520 1614 144 7 977 2584 171014302 171012692 0.000000e+00 2124.0
12 TraesCS6D01G198200 chr1A 90.144 1593 153 2 996 2585 118070389 118071980 0.000000e+00 2069.0
13 TraesCS6D01G198200 chr2D 89.042 1670 166 14 915 2583 272823388 272821735 0.000000e+00 2054.0
14 TraesCS6D01G198200 chr2D 83.836 365 39 15 165 519 599297799 599298153 1.920000e-86 329.0
15 TraesCS6D01G198200 chr3B 89.807 1609 150 11 977 2583 371975850 371974254 0.000000e+00 2050.0
16 TraesCS6D01G198200 chr3B 87.456 287 28 8 167 448 250972532 250972815 8.920000e-85 324.0
17 TraesCS6D01G198200 chr4B 88.871 1276 98 21 163 1434 260046143 260044908 0.000000e+00 1530.0
18 TraesCS6D01G198200 chr4B 95.312 64 3 0 3 66 286642974 286643037 4.550000e-18 102.0
19 TraesCS6D01G198200 chr7B 93.177 513 28 7 163 672 458356629 458356121 0.000000e+00 747.0
20 TraesCS6D01G198200 chr7B 92.829 516 22 6 623 1124 458356219 458355705 0.000000e+00 734.0
21 TraesCS6D01G198200 chr7B 85.050 301 30 15 167 461 290096196 290095905 2.520000e-75 292.0
22 TraesCS6D01G198200 chr7B 95.312 64 3 0 3 66 685777300 685777237 4.550000e-18 102.0
23 TraesCS6D01G198200 chr7B 91.667 72 5 1 2 73 16150443 16150373 5.890000e-17 99.0
24 TraesCS6D01G198200 chr4A 85.124 363 43 9 214 568 521274775 521275134 6.800000e-96 361.0
25 TraesCS6D01G198200 chr6B 97.143 105 0 1 62 163 438098304 438098408 9.510000e-40 174.0
26 TraesCS6D01G198200 chr6B 90.789 76 6 1 1 76 219015815 219015741 1.640000e-17 100.0
27 TraesCS6D01G198200 chr6A 95.098 102 2 1 62 160 399876130 399876029 9.580000e-35 158.0
28 TraesCS6D01G198200 chr6A 90.411 73 7 0 1 73 297650085 297650013 2.120000e-16 97.1
29 TraesCS6D01G198200 chr7A 93.939 66 4 0 1 66 545647713 545647648 1.640000e-17 100.0
30 TraesCS6D01G198200 chr5D 95.238 63 3 0 1 63 215255295 215255233 1.640000e-17 100.0
31 TraesCS6D01G198200 chr5D 95.238 63 3 0 1 63 559625871 559625933 1.640000e-17 100.0
32 TraesCS6D01G198200 chr1D 95.238 63 3 0 1 63 184474798 184474860 1.640000e-17 100.0
33 TraesCS6D01G198200 chrUn 95.082 61 3 0 6 66 105244529 105244589 2.120000e-16 97.1
34 TraesCS6D01G198200 chrUn 89.333 75 5 3 1 72 73368552 73368478 9.850000e-15 91.6


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 TraesCS6D01G198200 chr6D 276135419 276138003 2584 False 4774.0 4774 100.0000 1 2585 1 chr6D.!!$F1 2584
1 TraesCS6D01G198200 chr7D 564521856 564524261 2405 False 3705.0 3705 94.3940 162 2584 1 chr7D.!!$F1 2422
2 TraesCS6D01G198200 chr7D 90645702 90647301 1599 True 2085.0 2085 90.2120 985 2585 1 chr7D.!!$R1 1600
3 TraesCS6D01G198200 chr7D 440574738 440577041 2303 True 1733.0 2817 93.7165 163 2585 2 chr7D.!!$R2 2422
4 TraesCS6D01G198200 chr5B 693982829 693985116 2287 False 3157.0 3157 91.6520 303 2584 1 chr5B.!!$F1 2281
5 TraesCS6D01G198200 chr5A 556079070 556081430 2360 True 3131.0 3131 90.4430 159 2585 1 chr5A.!!$R1 2426
6 TraesCS6D01G198200 chr5A 678554058 678555658 1600 True 2054.0 2054 89.8380 985 2585 1 chr5A.!!$R2 1600
7 TraesCS6D01G198200 chr4D 40161836 40163447 1611 False 2307.0 2307 92.9410 162 1732 1 chr4D.!!$F1 1570
8 TraesCS6D01G198200 chr3D 485193574 485195185 1611 True 2126.0 2126 90.5260 977 2585 1 chr3D.!!$R1 1608
9 TraesCS6D01G198200 chr1A 171012692 171014302 1610 True 2124.0 2124 90.5200 977 2584 1 chr1A.!!$R1 1607
10 TraesCS6D01G198200 chr1A 118070389 118071980 1591 False 2069.0 2069 90.1440 996 2585 1 chr1A.!!$F1 1589
11 TraesCS6D01G198200 chr2D 272821735 272823388 1653 True 2054.0 2054 89.0420 915 2583 1 chr2D.!!$R1 1668
12 TraesCS6D01G198200 chr3B 371974254 371975850 1596 True 2050.0 2050 89.8070 977 2583 1 chr3B.!!$R1 1606
13 TraesCS6D01G198200 chr4B 260044908 260046143 1235 True 1530.0 1530 88.8710 163 1434 1 chr4B.!!$R1 1271
14 TraesCS6D01G198200 chr7B 458355705 458356629 924 True 740.5 747 93.0030 163 1124 2 chr7B.!!$R4 961

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
138 139 0.178975 TTTGGGACCGTCCATTTGCT 60.179 50.0 19.43 0.0 38.64 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1913 0.249155 GCAGCAGTTCAAGCAGCAAA 60.249 50.0 0.0 0.0 43.05 3.68 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 5.437383 GCTTCGTATGTAGTCACTTGTTC 57.563 43.478 0.00 0.00 0.00 3.18
23 24 4.921515 GCTTCGTATGTAGTCACTTGTTCA 59.078 41.667 0.00 0.00 0.00 3.18
24 25 5.404366 GCTTCGTATGTAGTCACTTGTTCAA 59.596 40.000 0.00 0.00 0.00 2.69
25 26 6.073980 GCTTCGTATGTAGTCACTTGTTCAAA 60.074 38.462 0.00 0.00 0.00 2.69
26 27 7.360101 GCTTCGTATGTAGTCACTTGTTCAAAT 60.360 37.037 0.00 0.00 0.00 2.32
27 28 9.135843 CTTCGTATGTAGTCACTTGTTCAAATA 57.864 33.333 0.00 0.00 0.00 1.40
28 29 9.647797 TTCGTATGTAGTCACTTGTTCAAATAT 57.352 29.630 0.00 0.00 0.00 1.28
29 30 9.297586 TCGTATGTAGTCACTTGTTCAAATATC 57.702 33.333 0.00 0.00 0.00 1.63
30 31 9.302345 CGTATGTAGTCACTTGTTCAAATATCT 57.698 33.333 0.00 0.00 0.00 1.98
57 58 8.539117 AAAAGACTTATATTTGGGAATGGAGG 57.461 34.615 0.00 0.00 0.00 4.30
58 59 6.206180 AGACTTATATTTGGGAATGGAGGG 57.794 41.667 0.00 0.00 0.00 4.30
59 60 5.917087 AGACTTATATTTGGGAATGGAGGGA 59.083 40.000 0.00 0.00 0.00 4.20
60 61 6.044871 AGACTTATATTTGGGAATGGAGGGAG 59.955 42.308 0.00 0.00 0.00 4.30
61 62 5.676811 ACTTATATTTGGGAATGGAGGGAGT 59.323 40.000 0.00 0.00 0.00 3.85
62 63 6.855061 ACTTATATTTGGGAATGGAGGGAGTA 59.145 38.462 0.00 0.00 0.00 2.59
63 64 3.953542 ATTTGGGAATGGAGGGAGTAC 57.046 47.619 0.00 0.00 0.00 2.73
64 65 2.352561 TTGGGAATGGAGGGAGTACA 57.647 50.000 0.00 0.00 0.00 2.90
65 66 2.352561 TGGGAATGGAGGGAGTACAA 57.647 50.000 0.00 0.00 0.00 2.41
66 67 1.913419 TGGGAATGGAGGGAGTACAAC 59.087 52.381 0.00 0.00 0.00 3.32
67 68 2.197465 GGGAATGGAGGGAGTACAACT 58.803 52.381 0.00 0.00 0.00 3.16
68 69 3.246203 TGGGAATGGAGGGAGTACAACTA 60.246 47.826 0.00 0.00 0.00 2.24
69 70 3.974642 GGGAATGGAGGGAGTACAACTAT 59.025 47.826 0.00 0.00 0.00 2.12
70 71 5.152934 GGGAATGGAGGGAGTACAACTATA 58.847 45.833 0.00 0.00 0.00 1.31
71 72 5.605488 GGGAATGGAGGGAGTACAACTATAA 59.395 44.000 0.00 0.00 0.00 0.98
72 73 6.272558 GGGAATGGAGGGAGTACAACTATAAT 59.727 42.308 0.00 0.00 0.00 1.28
73 74 7.202195 GGGAATGGAGGGAGTACAACTATAATT 60.202 40.741 0.00 0.00 0.00 1.40
74 75 7.661847 GGAATGGAGGGAGTACAACTATAATTG 59.338 40.741 0.00 0.00 35.59 2.32
75 76 7.691993 ATGGAGGGAGTACAACTATAATTGT 57.308 36.000 4.79 4.79 44.87 2.71
76 77 6.884832 TGGAGGGAGTACAACTATAATTGTG 58.115 40.000 9.75 0.00 42.74 3.33
77 78 6.442564 TGGAGGGAGTACAACTATAATTGTGT 59.557 38.462 9.75 0.00 42.74 3.72
78 79 7.037873 TGGAGGGAGTACAACTATAATTGTGTT 60.038 37.037 9.75 0.00 42.74 3.32
79 80 7.494952 GGAGGGAGTACAACTATAATTGTGTTC 59.505 40.741 9.75 6.89 42.74 3.18
80 81 8.147244 AGGGAGTACAACTATAATTGTGTTCT 57.853 34.615 9.75 5.60 42.74 3.01
81 82 8.041323 AGGGAGTACAACTATAATTGTGTTCTG 58.959 37.037 9.75 0.00 42.74 3.02
82 83 7.822822 GGGAGTACAACTATAATTGTGTTCTGT 59.177 37.037 9.75 0.00 42.74 3.41
83 84 8.656849 GGAGTACAACTATAATTGTGTTCTGTG 58.343 37.037 9.75 0.00 42.74 3.66
84 85 9.204570 GAGTACAACTATAATTGTGTTCTGTGT 57.795 33.333 9.75 0.00 42.74 3.72
91 92 8.883731 ACTATAATTGTGTTCTGTGTAATGAGC 58.116 33.333 0.00 0.00 0.00 4.26
92 93 7.686438 ATAATTGTGTTCTGTGTAATGAGCA 57.314 32.000 0.00 0.00 0.00 4.26
93 94 4.811555 TTGTGTTCTGTGTAATGAGCAC 57.188 40.909 0.00 0.00 42.20 4.40
94 95 3.802866 TGTGTTCTGTGTAATGAGCACA 58.197 40.909 8.20 8.20 46.57 4.57
95 96 4.388485 TGTGTTCTGTGTAATGAGCACAT 58.612 39.130 8.20 0.00 44.92 3.21
96 97 4.213906 TGTGTTCTGTGTAATGAGCACATG 59.786 41.667 8.20 0.00 44.92 3.21
97 98 4.452114 GTGTTCTGTGTAATGAGCACATGA 59.548 41.667 0.00 0.00 44.54 3.07
98 99 5.049474 GTGTTCTGTGTAATGAGCACATGAA 60.049 40.000 0.00 0.00 44.54 2.57
99 100 5.179929 TGTTCTGTGTAATGAGCACATGAAG 59.820 40.000 0.00 0.00 44.54 3.02
100 101 5.151297 TCTGTGTAATGAGCACATGAAGA 57.849 39.130 0.00 0.00 44.54 2.87
101 102 5.550290 TCTGTGTAATGAGCACATGAAGAA 58.450 37.500 0.00 0.00 44.54 2.52
102 103 5.997129 TCTGTGTAATGAGCACATGAAGAAA 59.003 36.000 0.00 0.00 44.54 2.52
103 104 6.486320 TCTGTGTAATGAGCACATGAAGAAAA 59.514 34.615 0.00 0.00 44.54 2.29
104 105 7.175467 TCTGTGTAATGAGCACATGAAGAAAAT 59.825 33.333 0.00 0.00 44.54 1.82
105 106 7.307694 TGTGTAATGAGCACATGAAGAAAATC 58.692 34.615 0.00 0.00 41.32 2.17
106 107 6.749118 GTGTAATGAGCACATGAAGAAAATCC 59.251 38.462 0.00 0.00 36.79 3.01
107 108 6.660521 TGTAATGAGCACATGAAGAAAATCCT 59.339 34.615 0.00 0.00 36.79 3.24
108 109 6.600882 AATGAGCACATGAAGAAAATCCTT 57.399 33.333 0.00 0.00 36.79 3.36
109 110 6.600882 ATGAGCACATGAAGAAAATCCTTT 57.399 33.333 0.00 0.00 35.21 3.11
110 111 6.409524 TGAGCACATGAAGAAAATCCTTTT 57.590 33.333 0.00 0.00 35.12 2.27
111 112 6.218019 TGAGCACATGAAGAAAATCCTTTTG 58.782 36.000 0.00 0.00 31.94 2.44
112 113 4.992951 AGCACATGAAGAAAATCCTTTTGC 59.007 37.500 0.00 0.00 31.94 3.68
113 114 4.751098 GCACATGAAGAAAATCCTTTTGCA 59.249 37.500 0.00 0.00 31.94 4.08
114 115 5.333568 GCACATGAAGAAAATCCTTTTGCAC 60.334 40.000 0.00 0.00 31.94 4.57
115 116 5.178067 CACATGAAGAAAATCCTTTTGCACC 59.822 40.000 0.00 0.00 31.94 5.01
116 117 5.070847 ACATGAAGAAAATCCTTTTGCACCT 59.929 36.000 0.00 0.00 31.94 4.00
117 118 5.200368 TGAAGAAAATCCTTTTGCACCTC 57.800 39.130 0.00 0.00 31.94 3.85
118 119 4.895297 TGAAGAAAATCCTTTTGCACCTCT 59.105 37.500 0.00 0.00 31.94 3.69
119 120 5.363580 TGAAGAAAATCCTTTTGCACCTCTT 59.636 36.000 0.00 0.00 31.94 2.85
120 121 5.876651 AGAAAATCCTTTTGCACCTCTTT 57.123 34.783 0.00 0.00 31.94 2.52
121 122 6.239217 AGAAAATCCTTTTGCACCTCTTTT 57.761 33.333 0.00 0.00 31.94 2.27
122 123 6.051074 AGAAAATCCTTTTGCACCTCTTTTG 58.949 36.000 0.00 0.00 31.94 2.44
123 124 4.341366 AATCCTTTTGCACCTCTTTTGG 57.659 40.909 0.00 0.00 0.00 3.28
124 125 2.038659 TCCTTTTGCACCTCTTTTGGG 58.961 47.619 0.00 0.00 0.00 4.12
125 126 2.038659 CCTTTTGCACCTCTTTTGGGA 58.961 47.619 0.00 0.00 0.00 4.37
126 127 2.224042 CCTTTTGCACCTCTTTTGGGAC 60.224 50.000 0.00 0.00 0.00 4.46
127 128 1.408969 TTTGCACCTCTTTTGGGACC 58.591 50.000 0.00 0.00 0.00 4.46
128 129 0.821711 TTGCACCTCTTTTGGGACCG 60.822 55.000 0.00 0.00 0.00 4.79
129 130 1.228154 GCACCTCTTTTGGGACCGT 60.228 57.895 0.00 0.00 0.00 4.83
130 131 1.235281 GCACCTCTTTTGGGACCGTC 61.235 60.000 0.00 0.00 0.00 4.79
131 132 0.605589 CACCTCTTTTGGGACCGTCC 60.606 60.000 9.30 9.30 35.23 4.79
132 133 1.057851 ACCTCTTTTGGGACCGTCCA 61.058 55.000 19.43 2.92 38.64 4.02
133 134 0.328258 CCTCTTTTGGGACCGTCCAT 59.672 55.000 19.43 0.00 38.64 3.41
134 135 1.271926 CCTCTTTTGGGACCGTCCATT 60.272 52.381 19.43 0.00 38.64 3.16
135 136 2.514803 CTCTTTTGGGACCGTCCATTT 58.485 47.619 19.43 0.00 38.64 2.32
136 137 2.228822 CTCTTTTGGGACCGTCCATTTG 59.771 50.000 19.43 5.38 38.64 2.32
137 138 0.676736 TTTTGGGACCGTCCATTTGC 59.323 50.000 19.43 1.98 38.64 3.68
138 139 0.178975 TTTGGGACCGTCCATTTGCT 60.179 50.000 19.43 0.00 38.64 3.91
139 140 0.893270 TTGGGACCGTCCATTTGCTG 60.893 55.000 19.43 0.00 38.64 4.41
140 141 1.002624 GGGACCGTCCATTTGCTGA 60.003 57.895 19.43 0.00 38.64 4.26
141 142 1.305930 GGGACCGTCCATTTGCTGAC 61.306 60.000 19.43 0.00 38.64 3.51
142 143 0.605319 GGACCGTCCATTTGCTGACA 60.605 55.000 13.05 0.00 36.28 3.58
143 144 0.798776 GACCGTCCATTTGCTGACAG 59.201 55.000 0.00 0.00 0.00 3.51
144 145 0.396435 ACCGTCCATTTGCTGACAGA 59.604 50.000 6.65 0.00 0.00 3.41
145 146 1.003580 ACCGTCCATTTGCTGACAGAT 59.996 47.619 6.65 0.00 0.00 2.90
146 147 1.399440 CCGTCCATTTGCTGACAGATG 59.601 52.381 6.65 1.02 37.97 2.90
152 153 3.340928 CATTTGCTGACAGATGGAGTCA 58.659 45.455 6.65 0.00 43.23 3.41
153 154 2.462456 TTGCTGACAGATGGAGTCAC 57.538 50.000 6.65 0.00 40.80 3.67
154 155 1.341080 TGCTGACAGATGGAGTCACA 58.659 50.000 6.65 0.00 40.80 3.58
155 156 1.904537 TGCTGACAGATGGAGTCACAT 59.095 47.619 6.65 0.00 40.80 3.21
156 157 2.303890 TGCTGACAGATGGAGTCACATT 59.696 45.455 6.65 0.00 40.80 2.71
157 158 3.515104 TGCTGACAGATGGAGTCACATTA 59.485 43.478 6.65 0.00 40.80 1.90
158 159 4.162888 TGCTGACAGATGGAGTCACATTAT 59.837 41.667 6.65 0.00 40.80 1.28
159 160 5.121811 GCTGACAGATGGAGTCACATTATT 58.878 41.667 6.65 0.00 40.80 1.40
160 161 5.236047 GCTGACAGATGGAGTCACATTATTC 59.764 44.000 6.65 0.00 40.80 1.75
180 181 6.824305 ATTCCTGTTAGTGATGTCTTTTGG 57.176 37.500 0.00 0.00 0.00 3.28
196 197 6.127196 TGTCTTTTGGCCTTTTGTATTCAGTT 60.127 34.615 3.32 0.00 0.00 3.16
222 226 3.265737 TGGCATTCTCCTGTAGCCTTTTA 59.734 43.478 0.00 0.00 45.42 1.52
248 252 8.427276 AGCATCCTCATGTATGTGTATATATGG 58.573 37.037 0.00 0.00 38.32 2.74
250 254 9.755804 CATCCTCATGTATGTGTATATATGGTC 57.244 37.037 0.00 0.00 38.32 4.02
408 420 1.675714 CCGTGATTCTGCTGTTGCCTA 60.676 52.381 0.00 0.00 38.71 3.93
426 438 2.034812 CCTACGTTCATCTCCAGCTACC 59.965 54.545 0.00 0.00 0.00 3.18
466 478 2.362077 GCTGTGTGGAATCCAGTGTTTT 59.638 45.455 0.27 0.00 32.34 2.43
493 507 1.077787 TGTGTTGGATCCCATCGGC 60.078 57.895 9.90 0.00 31.53 5.54
867 919 4.688770 GACTGATCGAGGTCCCCT 57.311 61.111 0.00 0.00 36.03 4.79
938 1007 1.370900 GCTGCCACTGTTTTCTGCG 60.371 57.895 0.00 0.00 0.00 5.18
974 1043 7.755591 TCGTCTACGTGGATTGATTATATACC 58.244 38.462 4.45 0.00 40.80 2.73
975 1044 6.971184 CGTCTACGTGGATTGATTATATACCC 59.029 42.308 4.45 0.00 34.11 3.69
1050 1132 0.037326 TTCCACGCTGTCTGGTGATC 60.037 55.000 0.00 0.00 36.25 2.92
1190 1286 1.972660 GCTCCTATTCCACCGCCACT 61.973 60.000 0.00 0.00 0.00 4.00
1265 1361 1.079197 TTGCTGATGATGCGGTCGT 60.079 52.632 0.00 0.00 0.00 4.34
1271 1367 0.026803 GATGATGCGGTCGTTGCTTC 59.973 55.000 0.00 5.64 37.12 3.86
1615 1713 0.457035 CTGCTGTTTGTGGCACTTGT 59.543 50.000 19.83 0.00 34.57 3.16
1703 1801 1.205893 GTGGAGAGTTTGAGCCTCGAT 59.794 52.381 0.00 0.00 34.08 3.59
1814 1913 0.398318 GCTTCAGGTTCCCTCTGTGT 59.602 55.000 0.00 0.00 34.15 3.72
1934 2036 1.132453 CTCGTCCTCGTACTCATTGCA 59.868 52.381 0.00 0.00 38.33 4.08
1957 2059 0.700564 ACTGCAACAGGGATGGTCAT 59.299 50.000 0.00 0.00 35.51 3.06
2162 2267 1.250840 TGCTTCTAGTGCTGAGCGGA 61.251 55.000 0.00 0.00 0.00 5.54
2235 2340 7.284034 AGCTTCATTTCATATGTCTTCCGATTT 59.716 33.333 1.90 0.00 0.00 2.17
2323 2428 0.970937 TTCCTGTGGCTAGTCGAGGG 60.971 60.000 11.34 3.21 0.00 4.30
2352 2457 8.977412 TCTTTCCACTTCTTCCTTTTATGTTTT 58.023 29.630 0.00 0.00 0.00 2.43
2437 2542 3.738982 TGGTTGTCGTGTCATTCTTGAT 58.261 40.909 0.00 0.00 33.56 2.57
2467 2572 1.293924 GCACAATCCAGGATCGTCAG 58.706 55.000 1.11 0.00 0.00 3.51
2550 2655 0.400213 TGGCTTCATGTTCCTTCCGT 59.600 50.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.921515 TGAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
1 2 7.402811 TTTGAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 0.00 3.79
2 3 7.956420 ATTTGAACAAGTGACTACATACGAA 57.044 32.000 0.00 0.00 0.00 3.85
3 4 9.297586 GATATTTGAACAAGTGACTACATACGA 57.702 33.333 0.00 0.00 0.00 3.43
31 32 8.981659 CCTCCATTCCCAAATATAAGTCTTTTT 58.018 33.333 0.00 0.00 0.00 1.94
32 33 7.565029 CCCTCCATTCCCAAATATAAGTCTTTT 59.435 37.037 0.00 0.00 0.00 2.27
33 34 7.069344 CCCTCCATTCCCAAATATAAGTCTTT 58.931 38.462 0.00 0.00 0.00 2.52
34 35 6.392842 TCCCTCCATTCCCAAATATAAGTCTT 59.607 38.462 0.00 0.00 0.00 3.01
35 36 5.917087 TCCCTCCATTCCCAAATATAAGTCT 59.083 40.000 0.00 0.00 0.00 3.24
36 37 6.183361 ACTCCCTCCATTCCCAAATATAAGTC 60.183 42.308 0.00 0.00 0.00 3.01
37 38 5.676811 ACTCCCTCCATTCCCAAATATAAGT 59.323 40.000 0.00 0.00 0.00 2.24
38 39 6.206180 ACTCCCTCCATTCCCAAATATAAG 57.794 41.667 0.00 0.00 0.00 1.73
39 40 6.621931 TGTACTCCCTCCATTCCCAAATATAA 59.378 38.462 0.00 0.00 0.00 0.98
40 41 6.154645 TGTACTCCCTCCATTCCCAAATATA 58.845 40.000 0.00 0.00 0.00 0.86
41 42 4.981647 TGTACTCCCTCCATTCCCAAATAT 59.018 41.667 0.00 0.00 0.00 1.28
42 43 4.376223 TGTACTCCCTCCATTCCCAAATA 58.624 43.478 0.00 0.00 0.00 1.40
43 44 3.197983 TGTACTCCCTCCATTCCCAAAT 58.802 45.455 0.00 0.00 0.00 2.32
44 45 2.638325 TGTACTCCCTCCATTCCCAAA 58.362 47.619 0.00 0.00 0.00 3.28
45 46 2.307686 GTTGTACTCCCTCCATTCCCAA 59.692 50.000 0.00 0.00 0.00 4.12
46 47 1.913419 GTTGTACTCCCTCCATTCCCA 59.087 52.381 0.00 0.00 0.00 4.37
47 48 2.197465 AGTTGTACTCCCTCCATTCCC 58.803 52.381 0.00 0.00 0.00 3.97
48 49 6.742559 TTATAGTTGTACTCCCTCCATTCC 57.257 41.667 0.00 0.00 0.00 3.01
49 50 8.211629 ACAATTATAGTTGTACTCCCTCCATTC 58.788 37.037 11.55 0.00 40.35 2.67
50 51 7.993183 CACAATTATAGTTGTACTCCCTCCATT 59.007 37.037 12.69 0.00 40.17 3.16
51 52 7.127339 ACACAATTATAGTTGTACTCCCTCCAT 59.873 37.037 12.69 0.00 40.17 3.41
52 53 6.442564 ACACAATTATAGTTGTACTCCCTCCA 59.557 38.462 12.69 0.00 40.17 3.86
53 54 6.885922 ACACAATTATAGTTGTACTCCCTCC 58.114 40.000 12.69 0.00 40.17 4.30
54 55 8.258708 AGAACACAATTATAGTTGTACTCCCTC 58.741 37.037 12.69 4.87 40.17 4.30
55 56 8.041323 CAGAACACAATTATAGTTGTACTCCCT 58.959 37.037 12.69 4.70 40.17 4.20
56 57 7.822822 ACAGAACACAATTATAGTTGTACTCCC 59.177 37.037 12.69 2.83 40.17 4.30
57 58 8.656849 CACAGAACACAATTATAGTTGTACTCC 58.343 37.037 12.69 4.28 40.17 3.85
58 59 9.204570 ACACAGAACACAATTATAGTTGTACTC 57.795 33.333 12.69 11.69 40.17 2.59
65 66 8.883731 GCTCATTACACAGAACACAATTATAGT 58.116 33.333 0.00 0.00 0.00 2.12
66 67 8.882736 TGCTCATTACACAGAACACAATTATAG 58.117 33.333 0.00 0.00 0.00 1.31
67 68 8.664798 GTGCTCATTACACAGAACACAATTATA 58.335 33.333 0.00 0.00 37.96 0.98
68 69 7.174772 TGTGCTCATTACACAGAACACAATTAT 59.825 33.333 0.00 0.00 42.88 1.28
69 70 6.484977 TGTGCTCATTACACAGAACACAATTA 59.515 34.615 0.00 0.00 42.88 1.40
70 71 5.299028 TGTGCTCATTACACAGAACACAATT 59.701 36.000 0.00 0.00 42.88 2.32
71 72 4.821260 TGTGCTCATTACACAGAACACAAT 59.179 37.500 0.00 0.00 42.88 2.71
72 73 4.195416 TGTGCTCATTACACAGAACACAA 58.805 39.130 0.00 0.00 42.88 3.33
73 74 3.802866 TGTGCTCATTACACAGAACACA 58.197 40.909 0.00 0.00 42.88 3.72
81 82 6.749118 GGATTTTCTTCATGTGCTCATTACAC 59.251 38.462 0.00 0.00 38.55 2.90
82 83 6.660521 AGGATTTTCTTCATGTGCTCATTACA 59.339 34.615 0.00 0.00 31.15 2.41
83 84 7.093322 AGGATTTTCTTCATGTGCTCATTAC 57.907 36.000 0.00 0.00 31.15 1.89
84 85 7.707624 AAGGATTTTCTTCATGTGCTCATTA 57.292 32.000 0.00 0.00 31.15 1.90
85 86 6.600882 AAGGATTTTCTTCATGTGCTCATT 57.399 33.333 0.00 0.00 31.15 2.57
86 87 6.600882 AAAGGATTTTCTTCATGTGCTCAT 57.399 33.333 0.00 0.00 31.62 2.90
101 102 4.444733 CCCAAAAGAGGTGCAAAAGGATTT 60.445 41.667 0.00 0.00 42.41 2.17
102 103 3.071457 CCCAAAAGAGGTGCAAAAGGATT 59.929 43.478 0.00 0.00 0.00 3.01
103 104 2.634453 CCCAAAAGAGGTGCAAAAGGAT 59.366 45.455 0.00 0.00 0.00 3.24
104 105 2.038659 CCCAAAAGAGGTGCAAAAGGA 58.961 47.619 0.00 0.00 0.00 3.36
105 106 2.038659 TCCCAAAAGAGGTGCAAAAGG 58.961 47.619 0.00 0.00 0.00 3.11
106 107 2.224042 GGTCCCAAAAGAGGTGCAAAAG 60.224 50.000 0.00 0.00 0.00 2.27
107 108 1.760029 GGTCCCAAAAGAGGTGCAAAA 59.240 47.619 0.00 0.00 0.00 2.44
108 109 1.408969 GGTCCCAAAAGAGGTGCAAA 58.591 50.000 0.00 0.00 0.00 3.68
109 110 0.821711 CGGTCCCAAAAGAGGTGCAA 60.822 55.000 0.00 0.00 0.00 4.08
110 111 1.228124 CGGTCCCAAAAGAGGTGCA 60.228 57.895 0.00 0.00 0.00 4.57
111 112 1.228154 ACGGTCCCAAAAGAGGTGC 60.228 57.895 0.00 0.00 0.00 5.01
112 113 0.605589 GGACGGTCCCAAAAGAGGTG 60.606 60.000 16.55 0.00 0.00 4.00
113 114 1.057851 TGGACGGTCCCAAAAGAGGT 61.058 55.000 23.81 0.00 35.03 3.85
114 115 0.328258 ATGGACGGTCCCAAAAGAGG 59.672 55.000 23.81 0.00 40.04 3.69
115 116 2.200373 AATGGACGGTCCCAAAAGAG 57.800 50.000 23.81 0.00 40.04 2.85
116 117 2.235016 CAAATGGACGGTCCCAAAAGA 58.765 47.619 23.81 4.88 40.04 2.52
117 118 1.336795 GCAAATGGACGGTCCCAAAAG 60.337 52.381 23.81 11.23 40.04 2.27
118 119 0.676736 GCAAATGGACGGTCCCAAAA 59.323 50.000 23.81 6.04 40.04 2.44
119 120 0.178975 AGCAAATGGACGGTCCCAAA 60.179 50.000 23.81 6.43 40.04 3.28
120 121 0.893270 CAGCAAATGGACGGTCCCAA 60.893 55.000 23.81 7.20 40.04 4.12
121 122 1.303236 CAGCAAATGGACGGTCCCA 60.303 57.895 23.81 12.53 41.05 4.37
122 123 1.002624 TCAGCAAATGGACGGTCCC 60.003 57.895 23.81 8.40 35.03 4.46
123 124 0.605319 TGTCAGCAAATGGACGGTCC 60.605 55.000 20.36 20.36 36.83 4.46
124 125 0.798776 CTGTCAGCAAATGGACGGTC 59.201 55.000 0.00 0.00 36.83 4.79
125 126 0.396435 TCTGTCAGCAAATGGACGGT 59.604 50.000 0.00 0.00 40.49 4.83
126 127 1.399440 CATCTGTCAGCAAATGGACGG 59.601 52.381 0.00 0.00 40.88 4.79
127 128 1.399440 CCATCTGTCAGCAAATGGACG 59.601 52.381 11.89 0.00 40.98 4.79
128 129 2.681848 CTCCATCTGTCAGCAAATGGAC 59.318 50.000 14.78 0.00 42.05 4.02
129 130 2.306805 ACTCCATCTGTCAGCAAATGGA 59.693 45.455 16.85 16.85 44.10 3.41
130 131 2.681848 GACTCCATCTGTCAGCAAATGG 59.318 50.000 11.27 11.27 40.05 3.16
131 132 3.126514 GTGACTCCATCTGTCAGCAAATG 59.873 47.826 0.00 0.00 43.90 2.32
132 133 3.244665 TGTGACTCCATCTGTCAGCAAAT 60.245 43.478 0.00 0.00 43.90 2.32
133 134 2.104622 TGTGACTCCATCTGTCAGCAAA 59.895 45.455 0.00 0.00 43.90 3.68
134 135 1.693606 TGTGACTCCATCTGTCAGCAA 59.306 47.619 0.00 0.00 43.90 3.91
135 136 1.341080 TGTGACTCCATCTGTCAGCA 58.659 50.000 0.00 0.00 43.90 4.41
136 137 2.687700 ATGTGACTCCATCTGTCAGC 57.312 50.000 0.00 0.00 43.90 4.26
137 138 5.757320 GGAATAATGTGACTCCATCTGTCAG 59.243 44.000 0.00 0.00 43.90 3.51
138 139 5.426509 AGGAATAATGTGACTCCATCTGTCA 59.573 40.000 0.00 0.00 41.48 3.58
139 140 5.757320 CAGGAATAATGTGACTCCATCTGTC 59.243 44.000 0.00 0.00 35.21 3.51
140 141 5.190528 ACAGGAATAATGTGACTCCATCTGT 59.809 40.000 0.00 0.00 0.00 3.41
141 142 5.678583 ACAGGAATAATGTGACTCCATCTG 58.321 41.667 0.00 0.00 0.00 2.90
142 143 5.965033 ACAGGAATAATGTGACTCCATCT 57.035 39.130 0.00 0.00 0.00 2.90
143 144 7.225538 CACTAACAGGAATAATGTGACTCCATC 59.774 40.741 0.00 0.00 0.00 3.51
144 145 7.050377 CACTAACAGGAATAATGTGACTCCAT 58.950 38.462 0.00 0.00 0.00 3.41
145 146 6.212589 TCACTAACAGGAATAATGTGACTCCA 59.787 38.462 0.00 0.00 0.00 3.86
146 147 6.640518 TCACTAACAGGAATAATGTGACTCC 58.359 40.000 0.00 0.00 0.00 3.85
147 148 7.766278 ACATCACTAACAGGAATAATGTGACTC 59.234 37.037 0.00 0.00 36.10 3.36
148 149 7.624549 ACATCACTAACAGGAATAATGTGACT 58.375 34.615 0.00 0.00 36.10 3.41
149 150 7.766278 AGACATCACTAACAGGAATAATGTGAC 59.234 37.037 0.00 0.00 36.10 3.67
150 151 7.851228 AGACATCACTAACAGGAATAATGTGA 58.149 34.615 0.00 0.00 37.37 3.58
151 152 8.498054 AAGACATCACTAACAGGAATAATGTG 57.502 34.615 0.00 0.00 0.00 3.21
152 153 9.520515 AAAAGACATCACTAACAGGAATAATGT 57.479 29.630 0.00 0.00 0.00 2.71
153 154 9.778993 CAAAAGACATCACTAACAGGAATAATG 57.221 33.333 0.00 0.00 0.00 1.90
154 155 8.960591 CCAAAAGACATCACTAACAGGAATAAT 58.039 33.333 0.00 0.00 0.00 1.28
155 156 7.094377 GCCAAAAGACATCACTAACAGGAATAA 60.094 37.037 0.00 0.00 0.00 1.40
156 157 6.374333 GCCAAAAGACATCACTAACAGGAATA 59.626 38.462 0.00 0.00 0.00 1.75
157 158 5.183904 GCCAAAAGACATCACTAACAGGAAT 59.816 40.000 0.00 0.00 0.00 3.01
158 159 4.518970 GCCAAAAGACATCACTAACAGGAA 59.481 41.667 0.00 0.00 0.00 3.36
159 160 4.072131 GCCAAAAGACATCACTAACAGGA 58.928 43.478 0.00 0.00 0.00 3.86
160 161 3.191371 GGCCAAAAGACATCACTAACAGG 59.809 47.826 0.00 0.00 0.00 4.00
180 181 4.686091 GCCAAGAAACTGAATACAAAAGGC 59.314 41.667 0.00 0.00 0.00 4.35
196 197 2.356125 GGCTACAGGAGAATGCCAAGAA 60.356 50.000 0.00 0.00 42.79 2.52
222 226 8.427276 CCATATATACACATACATGAGGATGCT 58.573 37.037 0.00 0.00 32.14 3.79
408 420 0.456221 CGGTAGCTGGAGATGAACGT 59.544 55.000 0.00 0.00 0.00 3.99
426 438 1.088340 CAGCTGGATGTGAAGCTCCG 61.088 60.000 5.57 0.00 46.82 4.63
470 482 0.700564 ATGGGATCCAACACACAGCT 59.299 50.000 15.23 0.00 36.95 4.24
493 507 1.367840 GGATCGATCGGGACCAAGG 59.632 63.158 18.81 0.00 0.00 3.61
608 631 4.069232 CGAAGCTGGAGGGCGTCA 62.069 66.667 9.66 0.00 39.88 4.35
861 913 4.154347 CCTCGAGCAGCAGGGGAC 62.154 72.222 6.99 0.00 0.00 4.46
862 914 4.704103 ACCTCGAGCAGCAGGGGA 62.704 66.667 13.22 0.00 33.57 4.81
863 915 3.672295 GAACCTCGAGCAGCAGGGG 62.672 68.421 6.99 5.33 33.57 4.79
864 916 2.125350 GAACCTCGAGCAGCAGGG 60.125 66.667 6.99 0.00 33.57 4.45
865 917 2.507992 CGAACCTCGAGCAGCAGG 60.508 66.667 6.99 0.00 43.74 4.85
866 918 2.568612 TCGAACCTCGAGCAGCAG 59.431 61.111 6.99 0.00 44.82 4.24
989 1071 1.410517 TCGAAGACATGATGCTCCTCC 59.589 52.381 0.00 0.00 0.00 4.30
1043 1125 2.885135 AGCACCATCAAAGATCACCA 57.115 45.000 0.00 0.00 0.00 4.17
1050 1132 4.877823 TCAGCATAGTTAGCACCATCAAAG 59.122 41.667 0.00 0.00 0.00 2.77
1190 1286 2.267642 CGCCAAGATCCGGTGGAA 59.732 61.111 12.83 0.00 37.03 3.53
1247 1343 0.673333 AACGACCGCATCATCAGCAA 60.673 50.000 0.00 0.00 0.00 3.91
1615 1713 2.179547 CACAGTCTGGCAACACGCA 61.180 57.895 4.53 0.00 46.17 5.24
1703 1801 0.657312 CGAGCAAACAACTGAGCACA 59.343 50.000 0.00 0.00 0.00 4.57
1777 1876 4.643387 AACCCAGCACCACGGAGC 62.643 66.667 0.00 0.00 0.00 4.70
1814 1913 0.249155 GCAGCAGTTCAAGCAGCAAA 60.249 50.000 0.00 0.00 43.05 3.68
1934 2036 0.254178 CCATCCCTGTTGCAGTAGCT 59.746 55.000 0.00 0.00 42.74 3.32
1957 2059 1.266178 TGAAGCAATCAGACTCGGGA 58.734 50.000 0.00 0.00 33.04 5.14
2162 2267 2.609747 ACCTGACTGTGTAGATGGTGT 58.390 47.619 0.00 0.00 0.00 4.16
2235 2340 9.349713 GAGATCTAAGAGAGGACAAGATAGAAA 57.650 37.037 0.00 0.00 0.00 2.52
2323 2428 7.445707 ACATAAAAGGAAGAAGTGGAAAGAGTC 59.554 37.037 0.00 0.00 0.00 3.36
2352 2457 4.433615 GCGAGGAACATGAGAAACATCTA 58.566 43.478 0.00 0.00 37.07 1.98
2415 2520 3.738982 TCAAGAATGACACGACAACCAT 58.261 40.909 0.00 0.00 0.00 3.55
2467 2572 0.390472 CTCCAACCAGAGCCTTCGTC 60.390 60.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.