Multiple sequence alignment - TraesCS3D01G361500

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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 TraesCS3D01G361500 chr3D 100.000 3541 0 0 1 3541 475121151 475124691 0.000000e+00 6540
1 TraesCS3D01G361500 chr3A 93.696 3220 116 26 352 3541 617531860 617535022 0.000000e+00 4741
2 TraesCS3D01G361500 chr3B 96.209 2664 65 11 624 3279 631661099 631663734 0.000000e+00 4327
3 TraesCS3D01G361500 chr3B 91.232 422 18 8 213 632 631660662 631661066 1.110000e-154 556
4 TraesCS3D01G361500 chr3B 93.190 279 16 2 3263 3541 631663760 631664035 1.180000e-109 407
5 TraesCS3D01G361500 chr1B 75.539 1345 234 65 1246 2547 499593382 499592090 1.100000e-159 573
6 TraesCS3D01G361500 chr1D 74.888 1334 246 56 1246 2547 375205557 375204281 3.130000e-145 525
7 TraesCS3D01G361500 chr1D 91.139 158 13 1 56 212 39901354 39901511 2.770000e-51 213
8 TraesCS3D01G361500 chr1A 79.052 401 62 13 1246 1639 474293209 474292824 4.540000e-64 255
9 TraesCS3D01G361500 chr4D 92.500 160 11 1 56 214 75173929 75174088 9.890000e-56 228
10 TraesCS3D01G361500 chr4D 91.139 158 13 1 56 212 36723185 36723342 2.770000e-51 213
11 TraesCS3D01G361500 chr2D 92.357 157 10 2 56 211 72825057 72825212 4.600000e-54 222
12 TraesCS3D01G361500 chr5D 91.720 157 12 1 56 211 182165622 182165778 2.140000e-52 217
13 TraesCS3D01G361500 chr5D 91.195 159 12 2 55 212 337582974 337583131 7.700000e-52 215
14 TraesCS3D01G361500 chr5B 91.667 156 12 1 58 212 363685494 363685649 7.700000e-52 215
15 TraesCS3D01G361500 chr7D 91.139 158 13 1 56 212 192762928 192763085 2.770000e-51 213
16 TraesCS3D01G361500 chr6D 91.139 158 12 2 56 212 132148143 132147987 2.770000e-51 213
17 TraesCS3D01G361500 chr6B 80.000 175 33 2 1412 1584 526337551 526337725 1.030000e-25 128


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 TraesCS3D01G361500 chr3D 475121151 475124691 3540 False 6540.000000 6540 100.000000 1 3541 1 chr3D.!!$F1 3540
1 TraesCS3D01G361500 chr3A 617531860 617535022 3162 False 4741.000000 4741 93.696000 352 3541 1 chr3A.!!$F1 3189
2 TraesCS3D01G361500 chr3B 631660662 631664035 3373 False 1763.333333 4327 93.543667 213 3541 3 chr3B.!!$F1 3328
3 TraesCS3D01G361500 chr1B 499592090 499593382 1292 True 573.000000 573 75.539000 1246 2547 1 chr1B.!!$R1 1301
4 TraesCS3D01G361500 chr1D 375204281 375205557 1276 True 525.000000 525 74.888000 1246 2547 1 chr1D.!!$R1 1301

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
143 144 0.037326 TCTCGGCTTGAGCGTTTGAT 60.037 50.000 0.00 0.0 44.86 2.57 F
144 145 0.095935 CTCGGCTTGAGCGTTTGATG 59.904 55.000 0.00 0.0 43.26 3.07 F
204 205 0.250989 TTTAGCCCGGGTTGGTCTTG 60.251 55.000 24.63 0.0 35.15 3.02 F
673 724 1.067915 CGACCCATTTCCATTTGCGTT 60.068 47.619 0.00 0.0 0.00 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1680 0.250513 GTGAAGTTGGCGAGGAGGAT 59.749 55.000 0.00 0.0 0.00 3.24 R
1902 1976 2.626780 CGCCTGTGACTCGTCCTGA 61.627 63.158 0.00 0.0 0.00 3.86 R
2100 2192 3.047718 CTGCTCCGTCCTCGCGTAA 62.048 63.158 5.77 0.0 35.54 3.18 R
2647 2751 1.536907 TTCTTGCGGGGGTGGAGTA 60.537 57.895 0.00 0.0 0.00 2.59 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
33 34 9.841295 AAAGTACAGTATAAAGAAAAGGTGTCA 57.159 29.630 0.00 0.00 0.00 3.58
34 35 8.828688 AGTACAGTATAAAGAAAAGGTGTCAC 57.171 34.615 0.00 0.00 0.00 3.67
35 36 8.648693 AGTACAGTATAAAGAAAAGGTGTCACT 58.351 33.333 2.35 0.00 0.00 3.41
36 37 7.730364 ACAGTATAAAGAAAAGGTGTCACTG 57.270 36.000 2.35 0.00 36.58 3.66
37 38 6.204882 ACAGTATAAAGAAAAGGTGTCACTGC 59.795 38.462 2.35 0.00 34.46 4.40
38 39 6.428159 CAGTATAAAGAAAAGGTGTCACTGCT 59.572 38.462 2.35 0.00 0.00 4.24
39 40 5.948992 ATAAAGAAAAGGTGTCACTGCTC 57.051 39.130 2.35 0.00 0.00 4.26
40 41 2.262423 AGAAAAGGTGTCACTGCTCC 57.738 50.000 2.35 0.00 0.00 4.70
41 42 1.202818 AGAAAAGGTGTCACTGCTCCC 60.203 52.381 2.35 0.00 0.00 4.30
42 43 0.550914 AAAAGGTGTCACTGCTCCCA 59.449 50.000 2.35 0.00 0.00 4.37
43 44 0.773644 AAAGGTGTCACTGCTCCCAT 59.226 50.000 2.35 0.00 0.00 4.00
44 45 0.326264 AAGGTGTCACTGCTCCCATC 59.674 55.000 2.35 0.00 0.00 3.51
45 46 0.546267 AGGTGTCACTGCTCCCATCT 60.546 55.000 2.35 0.00 0.00 2.90
46 47 1.195115 GGTGTCACTGCTCCCATCTA 58.805 55.000 2.35 0.00 0.00 1.98
47 48 1.555075 GGTGTCACTGCTCCCATCTAA 59.445 52.381 2.35 0.00 0.00 2.10
48 49 2.622436 GTGTCACTGCTCCCATCTAAC 58.378 52.381 0.00 0.00 0.00 2.34
49 50 2.234908 GTGTCACTGCTCCCATCTAACT 59.765 50.000 0.00 0.00 0.00 2.24
50 51 3.447586 GTGTCACTGCTCCCATCTAACTA 59.552 47.826 0.00 0.00 0.00 2.24
51 52 4.100189 GTGTCACTGCTCCCATCTAACTAT 59.900 45.833 0.00 0.00 0.00 2.12
52 53 5.302059 GTGTCACTGCTCCCATCTAACTATA 59.698 44.000 0.00 0.00 0.00 1.31
53 54 5.536538 TGTCACTGCTCCCATCTAACTATAG 59.463 44.000 0.00 0.00 0.00 1.31
54 55 5.536916 GTCACTGCTCCCATCTAACTATAGT 59.463 44.000 0.00 0.00 0.00 2.12
55 56 5.770663 TCACTGCTCCCATCTAACTATAGTC 59.229 44.000 5.70 0.00 0.00 2.59
56 57 5.772672 CACTGCTCCCATCTAACTATAGTCT 59.227 44.000 5.70 0.00 0.00 3.24
57 58 6.007703 ACTGCTCCCATCTAACTATAGTCTC 58.992 44.000 5.70 0.00 0.00 3.36
58 59 6.183361 ACTGCTCCCATCTAACTATAGTCTCT 60.183 42.308 5.70 0.00 0.00 3.10
59 60 6.615617 TGCTCCCATCTAACTATAGTCTCTT 58.384 40.000 5.70 0.00 0.00 2.85
60 61 6.491745 TGCTCCCATCTAACTATAGTCTCTTG 59.508 42.308 5.70 2.78 0.00 3.02
61 62 6.717540 GCTCCCATCTAACTATAGTCTCTTGA 59.282 42.308 5.70 0.00 0.00 3.02
62 63 7.094377 GCTCCCATCTAACTATAGTCTCTTGAG 60.094 44.444 5.70 7.86 0.00 3.02
63 64 8.046867 TCCCATCTAACTATAGTCTCTTGAGA 57.953 38.462 5.70 3.45 0.00 3.27
64 65 8.503573 TCCCATCTAACTATAGTCTCTTGAGAA 58.496 37.037 5.70 0.00 0.00 2.87
65 66 8.573035 CCCATCTAACTATAGTCTCTTGAGAAC 58.427 40.741 5.70 0.00 0.00 3.01
66 67 9.349713 CCATCTAACTATAGTCTCTTGAGAACT 57.650 37.037 5.70 5.25 0.00 3.01
69 70 9.607988 TCTAACTATAGTCTCTTGAGAACTGAG 57.392 37.037 5.70 6.99 0.00 3.35
70 71 6.693315 ACTATAGTCTCTTGAGAACTGAGC 57.307 41.667 0.00 0.00 0.00 4.26
71 72 4.630894 ATAGTCTCTTGAGAACTGAGCG 57.369 45.455 1.51 0.00 0.00 5.03
72 73 2.235016 AGTCTCTTGAGAACTGAGCGT 58.765 47.619 1.51 0.00 0.00 5.07
73 74 3.413327 AGTCTCTTGAGAACTGAGCGTA 58.587 45.455 1.51 0.00 0.00 4.42
74 75 3.438781 AGTCTCTTGAGAACTGAGCGTAG 59.561 47.826 1.51 0.00 0.00 3.51
88 89 2.460330 CGTAGCTCAGTTGGCAAGG 58.540 57.895 0.00 0.00 0.00 3.61
89 90 1.639298 CGTAGCTCAGTTGGCAAGGC 61.639 60.000 0.00 3.21 0.00 4.35
90 91 1.375908 TAGCTCAGTTGGCAAGGCG 60.376 57.895 0.00 0.00 0.00 5.52
91 92 4.410743 GCTCAGTTGGCAAGGCGC 62.411 66.667 0.00 0.00 41.28 6.53
92 93 4.093952 CTCAGTTGGCAAGGCGCG 62.094 66.667 0.00 0.00 43.84 6.86
111 112 4.704833 GAGTTCGCAGCCAGCCCA 62.705 66.667 0.00 0.00 41.38 5.36
117 118 4.666253 GCAGCCAGCCCACCAAGA 62.666 66.667 0.00 0.00 37.23 3.02
118 119 2.357836 CAGCCAGCCCACCAAGAT 59.642 61.111 0.00 0.00 0.00 2.40
119 120 1.304713 CAGCCAGCCCACCAAGATT 60.305 57.895 0.00 0.00 0.00 2.40
120 121 1.000396 AGCCAGCCCACCAAGATTC 60.000 57.895 0.00 0.00 0.00 2.52
121 122 1.304381 GCCAGCCCACCAAGATTCA 60.304 57.895 0.00 0.00 0.00 2.57
122 123 0.899717 GCCAGCCCACCAAGATTCAA 60.900 55.000 0.00 0.00 0.00 2.69
123 124 1.180029 CCAGCCCACCAAGATTCAAG 58.820 55.000 0.00 0.00 0.00 3.02
124 125 1.548582 CCAGCCCACCAAGATTCAAGT 60.549 52.381 0.00 0.00 0.00 3.16
125 126 1.815003 CAGCCCACCAAGATTCAAGTC 59.185 52.381 0.00 0.00 0.00 3.01
126 127 1.707427 AGCCCACCAAGATTCAAGTCT 59.293 47.619 0.00 0.00 0.00 3.24
127 128 2.087646 GCCCACCAAGATTCAAGTCTC 58.912 52.381 0.00 0.00 0.00 3.36
128 129 2.350522 CCCACCAAGATTCAAGTCTCG 58.649 52.381 0.00 0.00 0.00 4.04
129 130 2.350522 CCACCAAGATTCAAGTCTCGG 58.649 52.381 0.00 0.00 0.00 4.63
130 131 1.734465 CACCAAGATTCAAGTCTCGGC 59.266 52.381 0.00 0.00 0.00 5.54
131 132 1.625818 ACCAAGATTCAAGTCTCGGCT 59.374 47.619 0.00 0.00 0.00 5.52
132 133 2.039084 ACCAAGATTCAAGTCTCGGCTT 59.961 45.455 0.00 0.00 0.00 4.35
133 134 2.417933 CCAAGATTCAAGTCTCGGCTTG 59.582 50.000 4.94 4.94 45.18 4.01
136 137 4.996976 TCAAGTCTCGGCTTGAGC 57.003 55.556 9.70 0.00 46.74 4.26
137 138 1.080501 TCAAGTCTCGGCTTGAGCG 60.081 57.895 9.70 0.00 46.74 5.03
138 139 1.373497 CAAGTCTCGGCTTGAGCGT 60.373 57.895 5.36 0.00 46.34 5.07
139 140 0.946221 CAAGTCTCGGCTTGAGCGTT 60.946 55.000 5.36 0.00 46.34 4.84
140 141 0.249911 AAGTCTCGGCTTGAGCGTTT 60.250 50.000 0.00 0.00 44.86 3.60
141 142 0.946221 AGTCTCGGCTTGAGCGTTTG 60.946 55.000 0.00 0.00 44.86 2.93
142 143 0.944311 GTCTCGGCTTGAGCGTTTGA 60.944 55.000 0.00 0.00 44.86 2.69
143 144 0.037326 TCTCGGCTTGAGCGTTTGAT 60.037 50.000 0.00 0.00 44.86 2.57
144 145 0.095935 CTCGGCTTGAGCGTTTGATG 59.904 55.000 0.00 0.00 43.26 3.07
145 146 1.512734 CGGCTTGAGCGTTTGATGC 60.513 57.895 0.00 0.00 43.26 3.91
146 147 1.878775 GGCTTGAGCGTTTGATGCT 59.121 52.632 0.00 0.00 44.42 3.79
147 148 1.086696 GGCTTGAGCGTTTGATGCTA 58.913 50.000 0.00 0.00 41.24 3.49
148 149 1.672881 GGCTTGAGCGTTTGATGCTAT 59.327 47.619 0.00 0.00 41.24 2.97
149 150 2.872245 GGCTTGAGCGTTTGATGCTATA 59.128 45.455 0.00 0.00 41.24 1.31
150 151 3.059325 GGCTTGAGCGTTTGATGCTATAG 60.059 47.826 0.00 0.00 41.24 1.31
151 152 3.804325 GCTTGAGCGTTTGATGCTATAGA 59.196 43.478 3.21 0.00 41.24 1.98
152 153 4.084641 GCTTGAGCGTTTGATGCTATAGAG 60.085 45.833 3.21 0.00 41.24 2.43
153 154 4.655762 TGAGCGTTTGATGCTATAGAGT 57.344 40.909 3.21 0.00 41.24 3.24
154 155 5.011090 TGAGCGTTTGATGCTATAGAGTT 57.989 39.130 3.21 0.00 41.24 3.01
155 156 5.419542 TGAGCGTTTGATGCTATAGAGTTT 58.580 37.500 3.21 0.00 41.24 2.66
156 157 5.874810 TGAGCGTTTGATGCTATAGAGTTTT 59.125 36.000 3.21 0.00 41.24 2.43
157 158 6.036083 TGAGCGTTTGATGCTATAGAGTTTTC 59.964 38.462 3.21 0.00 41.24 2.29
158 159 6.109359 AGCGTTTGATGCTATAGAGTTTTCT 58.891 36.000 3.21 0.00 38.98 2.52
159 160 6.595716 AGCGTTTGATGCTATAGAGTTTTCTT 59.404 34.615 3.21 0.00 38.98 2.52
160 161 6.902417 GCGTTTGATGCTATAGAGTTTTCTTC 59.098 38.462 3.21 0.00 34.79 2.87
161 162 7.201565 GCGTTTGATGCTATAGAGTTTTCTTCT 60.202 37.037 3.21 0.00 34.79 2.85
162 163 9.302345 CGTTTGATGCTATAGAGTTTTCTTCTA 57.698 33.333 3.21 0.00 34.79 2.10
175 176 9.077885 AGAGTTTTCTTCTATAAAAACATGGCA 57.922 29.630 11.83 0.00 44.16 4.92
176 177 9.691362 GAGTTTTCTTCTATAAAAACATGGCAA 57.309 29.630 11.83 0.00 44.16 4.52
181 182 7.940850 TCTTCTATAAAAACATGGCAATAGGC 58.059 34.615 0.00 0.00 43.74 3.93
182 183 7.779798 TCTTCTATAAAAACATGGCAATAGGCT 59.220 33.333 0.00 0.00 44.01 4.58
183 184 8.988546 TTCTATAAAAACATGGCAATAGGCTA 57.011 30.769 0.00 0.00 44.01 3.93
184 185 8.621532 TCTATAAAAACATGGCAATAGGCTAG 57.378 34.615 0.00 0.00 44.01 3.42
185 186 8.217799 TCTATAAAAACATGGCAATAGGCTAGT 58.782 33.333 0.00 0.00 44.01 2.57
186 187 7.660030 ATAAAAACATGGCAATAGGCTAGTT 57.340 32.000 0.00 0.00 44.01 2.24
187 188 6.358974 AAAAACATGGCAATAGGCTAGTTT 57.641 33.333 0.00 0.36 43.76 2.66
188 189 7.475137 AAAAACATGGCAATAGGCTAGTTTA 57.525 32.000 0.00 0.00 42.38 2.01
189 190 6.699575 AAACATGGCAATAGGCTAGTTTAG 57.300 37.500 0.00 0.00 41.88 1.85
198 199 2.776659 GCTAGTTTAGCCCGGGTTG 58.223 57.895 24.63 3.73 45.95 3.77
199 200 0.746923 GCTAGTTTAGCCCGGGTTGG 60.747 60.000 24.63 5.23 45.95 3.77
200 201 0.616891 CTAGTTTAGCCCGGGTTGGT 59.383 55.000 24.63 7.21 35.15 3.67
201 202 0.614812 TAGTTTAGCCCGGGTTGGTC 59.385 55.000 24.63 10.66 35.15 4.02
202 203 1.131928 AGTTTAGCCCGGGTTGGTCT 61.132 55.000 24.63 12.87 35.15 3.85
203 204 0.251033 GTTTAGCCCGGGTTGGTCTT 60.251 55.000 24.63 1.83 35.15 3.01
204 205 0.250989 TTTAGCCCGGGTTGGTCTTG 60.251 55.000 24.63 0.00 35.15 3.02
205 206 1.420532 TTAGCCCGGGTTGGTCTTGT 61.421 55.000 24.63 0.00 35.15 3.16
206 207 1.420532 TAGCCCGGGTTGGTCTTGTT 61.421 55.000 24.63 0.00 35.15 2.83
207 208 1.830847 GCCCGGGTTGGTCTTGTTT 60.831 57.895 24.63 0.00 35.15 2.83
208 209 1.396607 GCCCGGGTTGGTCTTGTTTT 61.397 55.000 24.63 0.00 35.15 2.43
209 210 1.116308 CCCGGGTTGGTCTTGTTTTT 58.884 50.000 14.18 0.00 35.15 1.94
238 239 6.835914 ACTGCAGTCTCTTTATTGAAATTCG 58.164 36.000 15.25 0.00 0.00 3.34
298 301 3.641439 AGACGATTGCGAGAAATTTCG 57.359 42.857 12.42 3.85 43.23 3.46
368 371 9.979270 CGAAGCATTATATCATTAATCTTGTCC 57.021 33.333 0.00 0.00 0.00 4.02
411 415 9.850628 CATGTAATTCTGATTCTGAAAACATGT 57.149 29.630 29.21 15.94 40.14 3.21
466 470 4.509737 GAGAGGGCGGCCGTACAC 62.510 72.222 28.70 17.86 0.00 2.90
485 495 2.948979 CACAAGAGAGATAGAGACGGCT 59.051 50.000 0.00 0.00 0.00 5.52
511 521 2.507484 CAGATTCTTTGAGCACACCCA 58.493 47.619 0.00 0.00 0.00 4.51
514 524 1.444119 TTCTTTGAGCACACCCACGC 61.444 55.000 0.00 0.00 0.00 5.34
673 724 1.067915 CGACCCATTTCCATTTGCGTT 60.068 47.619 0.00 0.00 0.00 4.84
894 949 2.001838 GTTTCCCCTCCCCTCCCTC 61.002 68.421 0.00 0.00 0.00 4.30
904 959 4.179599 CCTCCCTCCCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
1227 1289 3.781770 GATCCAGGAGCTCGCCGTG 62.782 68.421 7.83 2.43 0.00 4.94
1606 1680 1.114627 CCTCATGGTCTCCGTCATGA 58.885 55.000 0.00 0.00 44.95 3.07
1647 1721 2.168521 CGTCTACTCCATGGGTGACAAT 59.831 50.000 13.02 0.00 0.00 2.71
2305 2409 4.713946 TGGTTTCTCCATGGTCGC 57.286 55.556 12.58 0.00 41.93 5.19
2306 2410 1.757949 TGGTTTCTCCATGGTCGCA 59.242 52.632 12.58 0.00 41.93 5.10
2307 2411 0.327924 TGGTTTCTCCATGGTCGCAT 59.672 50.000 12.58 0.00 41.93 4.73
2720 2824 5.815740 CCAACCACGAAGCAAATACTAGTAT 59.184 40.000 9.71 9.71 0.00 2.12
2805 2913 0.766131 TGGCTTGTTTACGGGGAGAA 59.234 50.000 0.00 0.00 0.00 2.87
2807 2915 0.794473 GCTTGTTTACGGGGAGAACG 59.206 55.000 0.00 0.00 37.36 3.95
2899 3007 3.060611 TCCTCTTCCCCTTTCTGGAAAA 58.939 45.455 0.00 0.00 41.20 2.29
3088 3199 3.858868 TTGCGGAGTCACGGTCTGC 62.859 63.158 0.00 0.00 45.17 4.26
3093 3204 1.608717 GGAGTCACGGTCTGCTGGAT 61.609 60.000 0.00 0.00 0.00 3.41
3094 3205 0.459237 GAGTCACGGTCTGCTGGATG 60.459 60.000 0.00 0.00 0.00 3.51
3099 3210 2.439156 GGTCTGCTGGATGGTGGC 60.439 66.667 0.00 0.00 0.00 5.01
3153 3266 2.699321 GGTAAAGTAGAGGGAATCCGCT 59.301 50.000 0.00 0.00 45.32 5.52
3213 3326 2.082366 GCGCGTGAACAAGCAATGG 61.082 57.895 8.43 0.00 35.53 3.16
3364 3522 5.860941 TCCTAGAGAAATGACAGGATGAC 57.139 43.478 0.00 0.00 39.69 3.06
3382 3540 4.263018 TGACAGAGATTCCACTTCAGTG 57.737 45.455 0.00 0.00 45.23 3.66
3395 3553 4.795970 ACTTCAGTGACTTGCGTTTTAG 57.204 40.909 0.00 0.00 0.00 1.85
3396 3554 4.189231 ACTTCAGTGACTTGCGTTTTAGT 58.811 39.130 0.00 0.00 0.00 2.24
3426 3589 9.871238 CCATTATCTTAATAGCTAATGTACGGT 57.129 33.333 0.00 0.00 38.16 4.83
3487 3650 4.532834 TGGCTTTTCAGGTGTCTTTAGTT 58.467 39.130 0.00 0.00 0.00 2.24
3523 3689 6.978338 TCGATGTTCCATACTCTATTGTACC 58.022 40.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.841295 TGACACCTTTTCTTTATACTGTACTTT 57.159 29.630 0.00 0.00 0.00 2.66
8 9 9.269453 GTGACACCTTTTCTTTATACTGTACTT 57.731 33.333 0.00 0.00 0.00 2.24
9 10 8.648693 AGTGACACCTTTTCTTTATACTGTACT 58.351 33.333 0.84 0.00 0.00 2.73
10 11 8.709646 CAGTGACACCTTTTCTTTATACTGTAC 58.290 37.037 0.84 0.00 0.00 2.90
11 12 7.386848 GCAGTGACACCTTTTCTTTATACTGTA 59.613 37.037 0.84 0.00 35.50 2.74
12 13 6.204882 GCAGTGACACCTTTTCTTTATACTGT 59.795 38.462 0.84 0.00 35.50 3.55
13 14 6.428159 AGCAGTGACACCTTTTCTTTATACTG 59.572 38.462 0.84 0.00 35.99 2.74
14 15 6.534634 AGCAGTGACACCTTTTCTTTATACT 58.465 36.000 0.84 0.00 0.00 2.12
15 16 6.128254 GGAGCAGTGACACCTTTTCTTTATAC 60.128 42.308 0.84 0.00 0.00 1.47
16 17 5.938125 GGAGCAGTGACACCTTTTCTTTATA 59.062 40.000 0.84 0.00 0.00 0.98
17 18 4.762251 GGAGCAGTGACACCTTTTCTTTAT 59.238 41.667 0.84 0.00 0.00 1.40
18 19 4.134563 GGAGCAGTGACACCTTTTCTTTA 58.865 43.478 0.84 0.00 0.00 1.85
19 20 2.952310 GGAGCAGTGACACCTTTTCTTT 59.048 45.455 0.84 0.00 0.00 2.52
20 21 2.576615 GGAGCAGTGACACCTTTTCTT 58.423 47.619 0.84 0.00 0.00 2.52
21 22 1.202818 GGGAGCAGTGACACCTTTTCT 60.203 52.381 0.84 0.00 0.00 2.52
22 23 1.239347 GGGAGCAGTGACACCTTTTC 58.761 55.000 0.84 0.00 0.00 2.29
23 24 0.550914 TGGGAGCAGTGACACCTTTT 59.449 50.000 0.84 0.00 0.00 2.27
24 25 0.773644 ATGGGAGCAGTGACACCTTT 59.226 50.000 0.84 0.00 0.00 3.11
25 26 0.326264 GATGGGAGCAGTGACACCTT 59.674 55.000 0.84 0.00 0.00 3.50
26 27 0.546267 AGATGGGAGCAGTGACACCT 60.546 55.000 0.84 0.00 0.00 4.00
27 28 1.195115 TAGATGGGAGCAGTGACACC 58.805 55.000 0.84 0.00 0.00 4.16
28 29 2.234908 AGTTAGATGGGAGCAGTGACAC 59.765 50.000 0.00 0.00 0.00 3.67
29 30 2.540383 AGTTAGATGGGAGCAGTGACA 58.460 47.619 0.00 0.00 0.00 3.58
30 31 4.946478 ATAGTTAGATGGGAGCAGTGAC 57.054 45.455 0.00 0.00 0.00 3.67
31 32 5.706447 ACTATAGTTAGATGGGAGCAGTGA 58.294 41.667 0.00 0.00 0.00 3.41
32 33 5.772672 AGACTATAGTTAGATGGGAGCAGTG 59.227 44.000 6.88 0.00 0.00 3.66
33 34 5.959512 AGACTATAGTTAGATGGGAGCAGT 58.040 41.667 6.88 0.00 0.00 4.40
34 35 6.245408 AGAGACTATAGTTAGATGGGAGCAG 58.755 44.000 6.88 0.00 0.00 4.24
35 36 6.207509 AGAGACTATAGTTAGATGGGAGCA 57.792 41.667 6.88 0.00 0.00 4.26
36 37 6.717540 TCAAGAGACTATAGTTAGATGGGAGC 59.282 42.308 6.88 0.00 0.00 4.70
37 38 8.160765 TCTCAAGAGACTATAGTTAGATGGGAG 58.839 40.741 6.88 8.71 31.41 4.30
38 39 8.046867 TCTCAAGAGACTATAGTTAGATGGGA 57.953 38.462 6.88 7.39 31.41 4.37
39 40 8.573035 GTTCTCAAGAGACTATAGTTAGATGGG 58.427 40.741 6.88 5.20 37.14 4.00
40 41 9.349713 AGTTCTCAAGAGACTATAGTTAGATGG 57.650 37.037 6.88 0.00 37.14 3.51
43 44 9.607988 CTCAGTTCTCAAGAGACTATAGTTAGA 57.392 37.037 6.88 1.65 37.14 2.10
44 45 8.342634 GCTCAGTTCTCAAGAGACTATAGTTAG 58.657 40.741 6.88 0.00 37.14 2.34
45 46 7.011576 CGCTCAGTTCTCAAGAGACTATAGTTA 59.988 40.741 6.88 0.00 37.14 2.24
46 47 6.183360 CGCTCAGTTCTCAAGAGACTATAGTT 60.183 42.308 6.88 0.00 37.14 2.24
47 48 5.295787 CGCTCAGTTCTCAAGAGACTATAGT 59.704 44.000 4.68 4.68 37.14 2.12
48 49 5.295787 ACGCTCAGTTCTCAAGAGACTATAG 59.704 44.000 0.00 0.00 37.14 1.31
49 50 5.186942 ACGCTCAGTTCTCAAGAGACTATA 58.813 41.667 0.00 0.00 37.14 1.31
50 51 4.013728 ACGCTCAGTTCTCAAGAGACTAT 58.986 43.478 0.00 0.00 37.14 2.12
51 52 3.413327 ACGCTCAGTTCTCAAGAGACTA 58.587 45.455 0.00 0.00 37.14 2.59
52 53 2.235016 ACGCTCAGTTCTCAAGAGACT 58.765 47.619 0.00 0.00 37.14 3.24
53 54 2.715737 ACGCTCAGTTCTCAAGAGAC 57.284 50.000 0.00 0.00 37.14 3.36
54 55 2.162608 GCTACGCTCAGTTCTCAAGAGA 59.837 50.000 0.00 0.00 35.27 3.10
55 56 2.163412 AGCTACGCTCAGTTCTCAAGAG 59.837 50.000 0.00 0.00 30.62 2.85
56 57 2.163509 AGCTACGCTCAGTTCTCAAGA 58.836 47.619 0.00 0.00 30.62 3.02
57 58 2.645730 AGCTACGCTCAGTTCTCAAG 57.354 50.000 0.00 0.00 30.62 3.02
68 69 0.671781 CTTGCCAACTGAGCTACGCT 60.672 55.000 0.00 0.00 43.88 5.07
69 70 1.639298 CCTTGCCAACTGAGCTACGC 61.639 60.000 0.00 0.00 0.00 4.42
70 71 1.639298 GCCTTGCCAACTGAGCTACG 61.639 60.000 0.00 0.00 0.00 3.51
71 72 1.639298 CGCCTTGCCAACTGAGCTAC 61.639 60.000 0.00 0.00 0.00 3.58
72 73 1.375908 CGCCTTGCCAACTGAGCTA 60.376 57.895 0.00 0.00 0.00 3.32
73 74 2.670934 CGCCTTGCCAACTGAGCT 60.671 61.111 0.00 0.00 0.00 4.09
74 75 4.410743 GCGCCTTGCCAACTGAGC 62.411 66.667 0.00 0.00 37.76 4.26
75 76 4.093952 CGCGCCTTGCCAACTGAG 62.094 66.667 0.00 0.00 42.08 3.35
94 95 4.704833 TGGGCTGGCTGCGAACTC 62.705 66.667 10.35 0.00 44.05 3.01
100 101 3.951769 ATCTTGGTGGGCTGGCTGC 62.952 63.158 7.96 7.96 41.94 5.25
101 102 1.304713 AATCTTGGTGGGCTGGCTG 60.305 57.895 0.00 0.00 0.00 4.85
102 103 1.000396 GAATCTTGGTGGGCTGGCT 60.000 57.895 0.00 0.00 0.00 4.75
103 104 0.899717 TTGAATCTTGGTGGGCTGGC 60.900 55.000 0.00 0.00 0.00 4.85
104 105 1.180029 CTTGAATCTTGGTGGGCTGG 58.820 55.000 0.00 0.00 0.00 4.85
105 106 1.815003 GACTTGAATCTTGGTGGGCTG 59.185 52.381 0.00 0.00 0.00 4.85
106 107 1.707427 AGACTTGAATCTTGGTGGGCT 59.293 47.619 0.00 0.00 0.00 5.19
107 108 2.087646 GAGACTTGAATCTTGGTGGGC 58.912 52.381 0.00 0.00 0.00 5.36
108 109 2.350522 CGAGACTTGAATCTTGGTGGG 58.649 52.381 0.00 0.00 0.00 4.61
109 110 2.350522 CCGAGACTTGAATCTTGGTGG 58.649 52.381 1.39 0.00 43.15 4.61
120 121 0.946221 AACGCTCAAGCCGAGACTTG 60.946 55.000 4.96 6.49 45.45 3.16
121 122 0.249911 AAACGCTCAAGCCGAGACTT 60.250 50.000 4.96 0.00 45.45 3.01
122 123 0.946221 CAAACGCTCAAGCCGAGACT 60.946 55.000 4.96 0.00 45.45 3.24
123 124 0.944311 TCAAACGCTCAAGCCGAGAC 60.944 55.000 4.96 0.00 45.45 3.36
124 125 0.037326 ATCAAACGCTCAAGCCGAGA 60.037 50.000 4.96 0.00 45.45 4.04
125 126 0.095935 CATCAAACGCTCAAGCCGAG 59.904 55.000 0.00 0.00 45.37 4.63
126 127 1.911293 GCATCAAACGCTCAAGCCGA 61.911 55.000 0.00 0.00 37.91 5.54
127 128 1.512734 GCATCAAACGCTCAAGCCG 60.513 57.895 0.00 0.00 37.91 5.52
128 129 1.086696 TAGCATCAAACGCTCAAGCC 58.913 50.000 0.00 0.00 40.96 4.35
129 130 3.804325 TCTATAGCATCAAACGCTCAAGC 59.196 43.478 0.00 0.00 40.96 4.01
130 131 5.046529 ACTCTATAGCATCAAACGCTCAAG 58.953 41.667 0.00 0.00 40.96 3.02
131 132 5.011090 ACTCTATAGCATCAAACGCTCAA 57.989 39.130 0.00 0.00 40.96 3.02
132 133 4.655762 ACTCTATAGCATCAAACGCTCA 57.344 40.909 0.00 0.00 40.96 4.26
133 134 5.975410 AAACTCTATAGCATCAAACGCTC 57.025 39.130 0.00 0.00 40.96 5.03
134 135 6.109359 AGAAAACTCTATAGCATCAAACGCT 58.891 36.000 0.00 0.00 43.62 5.07
135 136 6.351327 AGAAAACTCTATAGCATCAAACGC 57.649 37.500 0.00 0.00 0.00 4.84
136 137 8.190888 AGAAGAAAACTCTATAGCATCAAACG 57.809 34.615 0.00 0.00 0.00 3.60
149 150 9.077885 TGCCATGTTTTTATAGAAGAAAACTCT 57.922 29.630 11.49 0.00 42.98 3.24
150 151 9.691362 TTGCCATGTTTTTATAGAAGAAAACTC 57.309 29.630 11.49 2.23 42.98 3.01
155 156 8.413229 GCCTATTGCCATGTTTTTATAGAAGAA 58.587 33.333 0.00 0.00 0.00 2.52
156 157 7.779798 AGCCTATTGCCATGTTTTTATAGAAGA 59.220 33.333 0.00 0.00 42.71 2.87
157 158 7.945134 AGCCTATTGCCATGTTTTTATAGAAG 58.055 34.615 0.00 0.00 42.71 2.85
158 159 7.896383 AGCCTATTGCCATGTTTTTATAGAA 57.104 32.000 0.00 0.00 42.71 2.10
159 160 8.217799 ACTAGCCTATTGCCATGTTTTTATAGA 58.782 33.333 0.00 0.00 42.71 1.98
160 161 8.396272 ACTAGCCTATTGCCATGTTTTTATAG 57.604 34.615 0.00 0.00 42.71 1.31
161 162 8.760980 AACTAGCCTATTGCCATGTTTTTATA 57.239 30.769 0.00 0.00 42.71 0.98
162 163 7.660030 AACTAGCCTATTGCCATGTTTTTAT 57.340 32.000 0.00 0.00 42.71 1.40
163 164 7.475137 AAACTAGCCTATTGCCATGTTTTTA 57.525 32.000 0.00 0.00 42.71 1.52
164 165 6.358974 AAACTAGCCTATTGCCATGTTTTT 57.641 33.333 0.00 0.00 42.71 1.94
165 166 6.405842 GCTAAACTAGCCTATTGCCATGTTTT 60.406 38.462 0.00 0.00 45.95 2.43
166 167 5.067805 GCTAAACTAGCCTATTGCCATGTTT 59.932 40.000 0.00 0.00 45.95 2.83
167 168 4.580580 GCTAAACTAGCCTATTGCCATGTT 59.419 41.667 0.00 0.00 45.95 2.71
168 169 4.137543 GCTAAACTAGCCTATTGCCATGT 58.862 43.478 0.00 0.00 45.95 3.21
169 170 4.756084 GCTAAACTAGCCTATTGCCATG 57.244 45.455 0.00 0.00 45.95 3.66
181 182 0.616891 ACCAACCCGGGCTAAACTAG 59.383 55.000 24.08 3.13 40.22 2.57
182 183 0.614812 GACCAACCCGGGCTAAACTA 59.385 55.000 24.08 0.00 41.26 2.24
183 184 1.377612 GACCAACCCGGGCTAAACT 59.622 57.895 24.08 0.00 41.26 2.66
184 185 3.991999 GACCAACCCGGGCTAAAC 58.008 61.111 24.08 6.07 41.26 2.01
190 191 1.116308 AAAAACAAGACCAACCCGGG 58.884 50.000 22.25 22.25 40.22 5.73
238 239 9.921637 TCAACCTTGTAACATGAAATATTTTCC 57.078 29.630 0.00 0.00 0.00 3.13
266 268 3.501950 GCAATCGTCTTTTCCATGGTTC 58.498 45.455 12.58 0.00 0.00 3.62
298 301 8.638685 AAATGCAAAATATCTCATGTAACTGC 57.361 30.769 0.00 0.00 0.00 4.40
385 388 9.850628 ACATGTTTTCAGAATCAGAATTACATG 57.149 29.630 24.87 24.87 44.04 3.21
391 394 8.853077 TGTAGACATGTTTTCAGAATCAGAAT 57.147 30.769 0.00 0.00 0.00 2.40
392 395 8.559536 GTTGTAGACATGTTTTCAGAATCAGAA 58.440 33.333 0.00 0.00 0.00 3.02
393 396 7.173218 GGTTGTAGACATGTTTTCAGAATCAGA 59.827 37.037 0.00 0.00 0.00 3.27
394 397 7.301054 GGTTGTAGACATGTTTTCAGAATCAG 58.699 38.462 0.00 0.00 0.00 2.90
395 398 6.206634 GGGTTGTAGACATGTTTTCAGAATCA 59.793 38.462 0.00 0.00 0.00 2.57
396 399 6.206634 TGGGTTGTAGACATGTTTTCAGAATC 59.793 38.462 0.00 0.00 0.00 2.52
411 415 3.847671 TGTGTGTTCATGGGTTGTAGA 57.152 42.857 0.00 0.00 0.00 2.59
466 470 2.948979 ACAGCCGTCTCTATCTCTCTTG 59.051 50.000 0.00 0.00 0.00 3.02
485 495 2.810274 GTGCTCAAAGAATCTGCAGACA 59.190 45.455 20.97 6.14 34.15 3.41
673 724 2.083774 CCCAAAATTAGCGCTCACTCA 58.916 47.619 16.34 0.00 0.00 3.41
894 949 1.451936 CTAAATGCGAGGGAGGGGG 59.548 63.158 0.00 0.00 0.00 5.40
904 959 0.460284 ACGGTGAGAGGCTAAATGCG 60.460 55.000 0.00 0.00 44.05 4.73
1027 1086 4.247380 GCCGCCCAGAGAGGATGG 62.247 72.222 0.00 0.00 41.22 3.51
1606 1680 0.250513 GTGAAGTTGGCGAGGAGGAT 59.749 55.000 0.00 0.00 0.00 3.24
1902 1976 2.626780 CGCCTGTGACTCGTCCTGA 61.627 63.158 0.00 0.00 0.00 3.86
2100 2192 3.047718 CTGCTCCGTCCTCGCGTAA 62.048 63.158 5.77 0.00 35.54 3.18
2305 2409 3.390183 TAGTGCTCCGCCCTGCATG 62.390 63.158 0.00 0.00 41.45 4.06
2306 2410 3.083349 TAGTGCTCCGCCCTGCAT 61.083 61.111 0.00 0.00 41.45 3.96
2307 2411 4.082523 GTAGTGCTCCGCCCTGCA 62.083 66.667 0.00 0.00 36.79 4.41
2647 2751 1.536907 TTCTTGCGGGGGTGGAGTA 60.537 57.895 0.00 0.00 0.00 2.59
2648 2752 2.852075 TTCTTGCGGGGGTGGAGT 60.852 61.111 0.00 0.00 0.00 3.85
2649 2753 2.045926 CTTCTTGCGGGGGTGGAG 60.046 66.667 0.00 0.00 0.00 3.86
2650 2754 2.852075 ACTTCTTGCGGGGGTGGA 60.852 61.111 0.00 0.00 0.00 4.02
2652 2756 2.359975 GGACTTCTTGCGGGGGTG 60.360 66.667 0.00 0.00 0.00 4.61
2653 2757 2.852075 TGGACTTCTTGCGGGGGT 60.852 61.111 0.00 0.00 0.00 4.95
2655 2759 2.742372 CGTGGACTTCTTGCGGGG 60.742 66.667 0.00 0.00 0.00 5.73
2761 2866 4.691216 AGTAAAACGAGAGATTCTTGCACC 59.309 41.667 0.00 0.00 30.88 5.01
2805 2913 3.846405 TTGCACCCCTCCTCTCCGT 62.846 63.158 0.00 0.00 0.00 4.69
2807 2915 1.225704 CATTGCACCCCTCCTCTCC 59.774 63.158 0.00 0.00 0.00 3.71
2853 2961 2.053984 CGCCGAACATTCATCGCG 60.054 61.111 0.00 0.00 38.93 5.87
2854 2962 2.324477 CCGCCGAACATTCATCGC 59.676 61.111 0.00 0.00 38.93 4.58
2855 2963 1.705337 AAGCCGCCGAACATTCATCG 61.705 55.000 0.00 0.00 39.92 3.84
2856 2964 0.248215 CAAGCCGCCGAACATTCATC 60.248 55.000 0.00 0.00 0.00 2.92
2857 2965 1.802636 CAAGCCGCCGAACATTCAT 59.197 52.632 0.00 0.00 0.00 2.57
3088 3199 0.812811 CTCACATCGCCACCATCCAG 60.813 60.000 0.00 0.00 0.00 3.86
3093 3204 1.960040 CTAGCCTCACATCGCCACCA 61.960 60.000 0.00 0.00 0.00 4.17
3094 3205 1.227380 CTAGCCTCACATCGCCACC 60.227 63.158 0.00 0.00 0.00 4.61
3099 3210 1.268285 CGACAGACTAGCCTCACATCG 60.268 57.143 0.00 0.00 0.00 3.84
3153 3266 3.365472 TGCTGCTGTATACTGGAGAAGA 58.635 45.455 27.73 12.49 35.79 2.87
3154 3267 3.808466 TGCTGCTGTATACTGGAGAAG 57.192 47.619 27.73 12.48 35.79 2.85
3155 3268 4.760530 ATTGCTGCTGTATACTGGAGAA 57.239 40.909 27.73 18.78 35.79 2.87
3156 3269 4.760530 AATTGCTGCTGTATACTGGAGA 57.239 40.909 27.73 13.26 35.79 3.71
3157 3270 4.036027 CCAAATTGCTGCTGTATACTGGAG 59.964 45.833 21.84 21.84 36.58 3.86
3199 3312 5.221126 GGAGATATTCCCATTGCTTGTTCAC 60.221 44.000 0.00 0.00 40.37 3.18
3213 3326 3.326297 CAGGGGAGAACTGGAGATATTCC 59.674 52.174 0.00 0.00 46.98 3.01
3255 3369 1.069049 GGGAGAGAGAGAGATGCTTGC 59.931 57.143 0.00 0.00 0.00 4.01
3364 3522 4.533919 AGTCACTGAAGTGGAATCTCTG 57.466 45.455 10.45 0.00 45.65 3.35
3426 3589 7.687941 AATTAAGCTAAAAGTTGAGCAGCTA 57.312 32.000 11.50 0.00 41.58 3.32


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

AutoCloner maintained by Alex Coulton.