Multiple sequence alignment - TraesCS7A01G380400

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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 TraesCS7A01G380400 chr7A 100.000 2840 0 0 1 2840 555910559 555907720 0.000000e+00 5245
1 TraesCS7A01G380400 chr7A 84.305 1115 125 35 1755 2840 582572883 582573976 0.000000e+00 1044
2 TraesCS7A01G380400 chr7A 84.292 1095 127 32 1719 2783 404878632 404877553 0.000000e+00 1027
3 TraesCS7A01G380400 chr7A 86.732 814 81 17 1949 2755 385234452 385233659 0.000000e+00 880
4 TraesCS7A01G380400 chr7A 96.951 328 10 0 1 328 196367449 196367776 4.140000e-153 551
5 TraesCS7A01G380400 chr4D 90.065 2476 203 31 324 2783 226171471 226173919 0.000000e+00 3169
6 TraesCS7A01G380400 chr4D 96.646 328 11 0 1 328 106223536 106223209 1.920000e-151 545
7 TraesCS7A01G380400 chr5B 89.878 2450 210 27 324 2755 337438744 337436315 0.000000e+00 3116
8 TraesCS7A01G380400 chr2B 88.775 2539 239 39 324 2840 337500209 337502723 0.000000e+00 3068
9 TraesCS7A01G380400 chr2B 88.816 2450 230 36 324 2755 606226212 606223789 0.000000e+00 2966
10 TraesCS7A01G380400 chr2B 84.241 863 88 30 1995 2840 272993493 272992662 0.000000e+00 797
11 TraesCS7A01G380400 chr4B 89.506 2449 219 27 325 2755 349261309 349263737 0.000000e+00 3064
12 TraesCS7A01G380400 chr4B 89.188 2451 224 32 324 2755 102938178 102940606 0.000000e+00 3020
13 TraesCS7A01G380400 chr4B 86.822 2451 276 28 349 2783 162548251 162550670 0.000000e+00 2693
14 TraesCS7A01G380400 chr4B 87.429 350 30 12 2494 2834 241673956 241674300 9.540000e-105 390
15 TraesCS7A01G380400 chr6D 88.597 2473 210 37 339 2783 318408802 318406374 0.000000e+00 2939
16 TraesCS7A01G380400 chr6D 97.256 328 9 0 1 328 416002551 416002224 8.890000e-155 556
17 TraesCS7A01G380400 chr6D 97.256 328 9 0 1 328 416110445 416110118 8.890000e-155 556
18 TraesCS7A01G380400 chr6D 97.256 328 9 0 1 328 416955360 416955033 8.890000e-155 556
19 TraesCS7A01G380400 chr7B 88.044 2459 251 26 349 2783 394023378 394020939 0.000000e+00 2872
20 TraesCS7A01G380400 chr7B 82.051 1170 132 41 1710 2825 387409342 387410487 0.000000e+00 926
21 TraesCS7A01G380400 chr6A 87.217 2519 273 35 339 2840 337478191 337480677 0.000000e+00 2822
22 TraesCS7A01G380400 chr7D 85.634 1072 130 18 1719 2783 290730259 290729205 0.000000e+00 1105
23 TraesCS7A01G380400 chr7D 84.308 1077 130 28 1719 2783 281329394 281328345 0.000000e+00 1016
24 TraesCS7A01G380400 chr7D 86.013 958 98 26 1903 2840 295858827 295857886 0.000000e+00 994
25 TraesCS7A01G380400 chr3D 83.174 1153 131 40 1719 2840 197126115 197124995 0.000000e+00 996
26 TraesCS7A01G380400 chr3D 97.256 328 9 0 1 328 36064618 36064291 8.890000e-155 556
27 TraesCS7A01G380400 chr3D 96.951 328 10 0 1 328 36042160 36041833 4.140000e-153 551
28 TraesCS7A01G380400 chr4A 86.978 814 80 18 1949 2755 344963255 344962461 0.000000e+00 893
29 TraesCS7A01G380400 chr2D 97.248 327 9 0 2 328 530590605 530590931 3.200000e-154 555
30 TraesCS7A01G380400 chr3A 96.951 328 9 1 2 328 264494119 264494446 1.490000e-152 549


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 TraesCS7A01G380400 chr7A 555907720 555910559 2839 True 5245 5245 100.000 1 2840 1 chr7A.!!$R3 2839
1 TraesCS7A01G380400 chr7A 582572883 582573976 1093 False 1044 1044 84.305 1755 2840 1 chr7A.!!$F2 1085
2 TraesCS7A01G380400 chr7A 404877553 404878632 1079 True 1027 1027 84.292 1719 2783 1 chr7A.!!$R2 1064
3 TraesCS7A01G380400 chr7A 385233659 385234452 793 True 880 880 86.732 1949 2755 1 chr7A.!!$R1 806
4 TraesCS7A01G380400 chr4D 226171471 226173919 2448 False 3169 3169 90.065 324 2783 1 chr4D.!!$F1 2459
5 TraesCS7A01G380400 chr5B 337436315 337438744 2429 True 3116 3116 89.878 324 2755 1 chr5B.!!$R1 2431
6 TraesCS7A01G380400 chr2B 337500209 337502723 2514 False 3068 3068 88.775 324 2840 1 chr2B.!!$F1 2516
7 TraesCS7A01G380400 chr2B 606223789 606226212 2423 True 2966 2966 88.816 324 2755 1 chr2B.!!$R2 2431
8 TraesCS7A01G380400 chr2B 272992662 272993493 831 True 797 797 84.241 1995 2840 1 chr2B.!!$R1 845
9 TraesCS7A01G380400 chr4B 349261309 349263737 2428 False 3064 3064 89.506 325 2755 1 chr4B.!!$F4 2430
10 TraesCS7A01G380400 chr4B 102938178 102940606 2428 False 3020 3020 89.188 324 2755 1 chr4B.!!$F1 2431
11 TraesCS7A01G380400 chr4B 162548251 162550670 2419 False 2693 2693 86.822 349 2783 1 chr4B.!!$F2 2434
12 TraesCS7A01G380400 chr6D 318406374 318408802 2428 True 2939 2939 88.597 339 2783 1 chr6D.!!$R1 2444
13 TraesCS7A01G380400 chr7B 394020939 394023378 2439 True 2872 2872 88.044 349 2783 1 chr7B.!!$R1 2434
14 TraesCS7A01G380400 chr7B 387409342 387410487 1145 False 926 926 82.051 1710 2825 1 chr7B.!!$F1 1115
15 TraesCS7A01G380400 chr6A 337478191 337480677 2486 False 2822 2822 87.217 339 2840 1 chr6A.!!$F1 2501
16 TraesCS7A01G380400 chr7D 290729205 290730259 1054 True 1105 1105 85.634 1719 2783 1 chr7D.!!$R2 1064
17 TraesCS7A01G380400 chr7D 281328345 281329394 1049 True 1016 1016 84.308 1719 2783 1 chr7D.!!$R1 1064
18 TraesCS7A01G380400 chr7D 295857886 295858827 941 True 994 994 86.013 1903 2840 1 chr7D.!!$R3 937
19 TraesCS7A01G380400 chr3D 197124995 197126115 1120 True 996 996 83.174 1719 2840 1 chr3D.!!$R3 1121
20 TraesCS7A01G380400 chr4A 344962461 344963255 794 True 893 893 86.978 1949 2755 1 chr4A.!!$R1 806

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
139 140 0.040058 TGATTGCATGCCTCCCACTT 59.960 50.0 16.68 0.0 0.00 3.16 F
526 528 0.105760 TTTCACAGGGCCACATTGGT 60.106 50.0 6.18 0.0 40.46 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1499 2.191400 AGCTTGGCTCCTTGACATCTA 58.809 47.619 0.00 0.00 30.62 1.98 R
2511 2650 0.034186 TCCAGGGAACATGACATGCC 60.034 55.000 15.49 9.22 0.00 4.40 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
29 30 8.763356 TGACATGTTTGAGAATTTATTTGTTGC 58.237 29.630 0.00 0.00 0.00 4.17
30 31 8.659925 ACATGTTTGAGAATTTATTTGTTGCA 57.340 26.923 0.00 0.00 0.00 4.08
31 32 9.107177 ACATGTTTGAGAATTTATTTGTTGCAA 57.893 25.926 0.00 0.00 0.00 4.08
45 46 6.610741 TTTGTTGCAATTAATGTTTGTCCC 57.389 33.333 0.59 0.00 0.00 4.46
46 47 5.282055 TGTTGCAATTAATGTTTGTCCCA 57.718 34.783 0.59 0.00 0.00 4.37
47 48 5.674525 TGTTGCAATTAATGTTTGTCCCAA 58.325 33.333 0.59 0.00 0.00 4.12
48 49 5.757320 TGTTGCAATTAATGTTTGTCCCAAG 59.243 36.000 0.59 0.00 0.00 3.61
49 50 4.314121 TGCAATTAATGTTTGTCCCAAGC 58.686 39.130 0.00 0.00 0.00 4.01
50 51 4.040217 TGCAATTAATGTTTGTCCCAAGCT 59.960 37.500 0.00 0.00 0.00 3.74
51 52 4.996758 GCAATTAATGTTTGTCCCAAGCTT 59.003 37.500 0.00 0.00 0.00 3.74
52 53 5.106987 GCAATTAATGTTTGTCCCAAGCTTG 60.107 40.000 19.93 19.93 0.00 4.01
62 63 3.835810 CCAAGCTTGGGGATGCTAT 57.164 52.632 34.08 0.00 44.70 2.97
63 64 1.325355 CCAAGCTTGGGGATGCTATG 58.675 55.000 34.08 7.56 44.70 2.23
64 65 0.672342 CAAGCTTGGGGATGCTATGC 59.328 55.000 19.14 0.00 38.75 3.14
65 66 0.554792 AAGCTTGGGGATGCTATGCT 59.445 50.000 0.00 0.00 38.75 3.79
66 67 0.554792 AGCTTGGGGATGCTATGCTT 59.445 50.000 0.00 0.00 37.81 3.91
67 68 1.776667 AGCTTGGGGATGCTATGCTTA 59.223 47.619 0.00 0.00 37.81 3.09
68 69 2.175499 AGCTTGGGGATGCTATGCTTAA 59.825 45.455 0.00 0.00 37.81 1.85
69 70 3.160269 GCTTGGGGATGCTATGCTTAAT 58.840 45.455 0.00 0.00 0.00 1.40
70 71 3.057033 GCTTGGGGATGCTATGCTTAATG 60.057 47.826 0.00 0.00 0.00 1.90
71 72 4.401022 CTTGGGGATGCTATGCTTAATGA 58.599 43.478 0.00 0.00 0.00 2.57
72 73 4.451891 TGGGGATGCTATGCTTAATGAA 57.548 40.909 0.00 0.00 0.00 2.57
73 74 4.401022 TGGGGATGCTATGCTTAATGAAG 58.599 43.478 0.00 0.00 35.60 3.02
74 75 4.104579 TGGGGATGCTATGCTTAATGAAGA 59.895 41.667 0.00 0.00 34.25 2.87
75 76 5.222192 TGGGGATGCTATGCTTAATGAAGAT 60.222 40.000 0.00 0.00 34.25 2.40
76 77 5.125097 GGGGATGCTATGCTTAATGAAGATG 59.875 44.000 0.00 0.00 34.25 2.90
77 78 5.942236 GGGATGCTATGCTTAATGAAGATGA 59.058 40.000 0.00 0.00 34.25 2.92
78 79 6.602406 GGGATGCTATGCTTAATGAAGATGAT 59.398 38.462 0.00 0.00 34.25 2.45
79 80 7.201714 GGGATGCTATGCTTAATGAAGATGATC 60.202 40.741 0.00 0.00 34.25 2.92
80 81 7.553402 GGATGCTATGCTTAATGAAGATGATCT 59.447 37.037 0.00 0.00 34.25 2.75
81 82 8.865420 ATGCTATGCTTAATGAAGATGATCTT 57.135 30.769 7.53 7.53 39.87 2.40
82 83 8.687292 TGCTATGCTTAATGAAGATGATCTTT 57.313 30.769 9.35 0.00 36.73 2.52
83 84 9.128404 TGCTATGCTTAATGAAGATGATCTTTT 57.872 29.630 9.35 3.40 36.73 2.27
84 85 9.962783 GCTATGCTTAATGAAGATGATCTTTTT 57.037 29.630 9.35 8.92 36.73 1.94
105 106 7.610580 TTTTTGTCCCCTTACTTTGAATGAT 57.389 32.000 0.00 0.00 0.00 2.45
106 107 6.834168 TTTGTCCCCTTACTTTGAATGATC 57.166 37.500 0.00 0.00 0.00 2.92
107 108 5.512942 TGTCCCCTTACTTTGAATGATCA 57.487 39.130 0.00 0.00 0.00 2.92
108 109 5.886609 TGTCCCCTTACTTTGAATGATCAA 58.113 37.500 0.00 0.00 43.70 2.57
126 127 7.940178 TGATCAAATTTGCTATGATGATTGC 57.060 32.000 13.54 0.00 34.10 3.56
127 128 7.493367 TGATCAAATTTGCTATGATGATTGCA 58.507 30.769 13.54 0.00 38.37 4.08
128 129 8.147704 TGATCAAATTTGCTATGATGATTGCAT 58.852 29.630 13.54 0.00 39.59 3.96
129 130 7.707774 TCAAATTTGCTATGATGATTGCATG 57.292 32.000 13.54 0.00 39.59 4.06
130 131 6.201997 TCAAATTTGCTATGATGATTGCATGC 59.798 34.615 11.82 11.82 39.59 4.06
131 132 3.653539 TTGCTATGATGATTGCATGCC 57.346 42.857 16.68 0.00 39.59 4.40
132 133 2.871453 TGCTATGATGATTGCATGCCT 58.129 42.857 16.68 1.69 35.71 4.75
133 134 2.817844 TGCTATGATGATTGCATGCCTC 59.182 45.455 16.68 12.62 35.71 4.70
134 135 2.163815 GCTATGATGATTGCATGCCTCC 59.836 50.000 16.68 4.25 34.11 4.30
135 136 1.629043 ATGATGATTGCATGCCTCCC 58.371 50.000 16.68 7.43 34.11 4.30
136 137 0.259356 TGATGATTGCATGCCTCCCA 59.741 50.000 16.68 8.37 34.11 4.37
137 138 0.672342 GATGATTGCATGCCTCCCAC 59.328 55.000 16.68 1.53 34.11 4.61
138 139 0.260816 ATGATTGCATGCCTCCCACT 59.739 50.000 16.68 0.00 32.31 4.00
139 140 0.040058 TGATTGCATGCCTCCCACTT 59.960 50.000 16.68 0.00 0.00 3.16
140 141 1.284491 TGATTGCATGCCTCCCACTTA 59.716 47.619 16.68 0.00 0.00 2.24
141 142 2.091720 TGATTGCATGCCTCCCACTTAT 60.092 45.455 16.68 0.00 0.00 1.73
142 143 1.766494 TTGCATGCCTCCCACTTATG 58.234 50.000 16.68 0.00 0.00 1.90
143 144 0.918258 TGCATGCCTCCCACTTATGA 59.082 50.000 16.68 0.00 0.00 2.15
144 145 1.496001 TGCATGCCTCCCACTTATGAT 59.504 47.619 16.68 0.00 0.00 2.45
145 146 1.884579 GCATGCCTCCCACTTATGATG 59.115 52.381 6.36 0.00 0.00 3.07
146 147 2.487805 GCATGCCTCCCACTTATGATGA 60.488 50.000 6.36 0.00 0.00 2.92
147 148 3.813240 GCATGCCTCCCACTTATGATGAT 60.813 47.826 6.36 0.00 0.00 2.45
148 149 4.404640 CATGCCTCCCACTTATGATGATT 58.595 43.478 0.00 0.00 0.00 2.57
149 150 5.563592 CATGCCTCCCACTTATGATGATTA 58.436 41.667 0.00 0.00 0.00 1.75
150 151 5.848286 TGCCTCCCACTTATGATGATTAT 57.152 39.130 0.00 0.00 0.00 1.28
151 152 6.204852 TGCCTCCCACTTATGATGATTATT 57.795 37.500 0.00 0.00 0.00 1.40
152 153 7.328404 TGCCTCCCACTTATGATGATTATTA 57.672 36.000 0.00 0.00 0.00 0.98
153 154 7.932134 TGCCTCCCACTTATGATGATTATTAT 58.068 34.615 0.00 0.00 0.00 1.28
154 155 7.830697 TGCCTCCCACTTATGATGATTATTATG 59.169 37.037 0.00 0.00 0.00 1.90
155 156 8.049117 GCCTCCCACTTATGATGATTATTATGA 58.951 37.037 0.00 0.00 0.00 2.15
244 245 8.472007 ACATTACTCTTTTAATGTGGGAACAA 57.528 30.769 7.53 0.00 46.38 2.83
245 246 9.088987 ACATTACTCTTTTAATGTGGGAACAAT 57.911 29.630 7.53 0.00 46.38 2.71
246 247 9.927668 CATTACTCTTTTAATGTGGGAACAATT 57.072 29.630 0.00 0.00 46.06 2.32
258 259 9.621629 AATGTGGGAACAATTTATAGTATTCGA 57.378 29.630 0.00 0.00 46.06 3.71
259 260 8.657074 TGTGGGAACAATTTATAGTATTCGAG 57.343 34.615 0.00 0.00 46.06 4.04
260 261 8.262227 TGTGGGAACAATTTATAGTATTCGAGT 58.738 33.333 0.00 0.00 46.06 4.18
261 262 9.106070 GTGGGAACAATTTATAGTATTCGAGTT 57.894 33.333 0.00 0.00 46.06 3.01
262 263 9.675464 TGGGAACAATTTATAGTATTCGAGTTT 57.325 29.630 0.00 0.00 37.44 2.66
275 276 8.113173 AGTATTCGAGTTTCCTATGATACTCC 57.887 38.462 11.17 0.78 42.95 3.85
276 277 5.786264 TTCGAGTTTCCTATGATACTCCC 57.214 43.478 11.17 0.00 42.95 4.30
277 278 4.800023 TCGAGTTTCCTATGATACTCCCA 58.200 43.478 11.17 0.00 42.95 4.37
278 279 4.583489 TCGAGTTTCCTATGATACTCCCAC 59.417 45.833 11.17 0.00 42.95 4.61
279 280 4.585162 CGAGTTTCCTATGATACTCCCACT 59.415 45.833 11.17 0.00 42.95 4.00
280 281 5.768662 CGAGTTTCCTATGATACTCCCACTA 59.231 44.000 11.17 0.00 42.95 2.74
281 282 6.434652 CGAGTTTCCTATGATACTCCCACTAT 59.565 42.308 11.17 0.00 42.95 2.12
282 283 7.039644 CGAGTTTCCTATGATACTCCCACTATT 60.040 40.741 11.17 0.00 42.95 1.73
283 284 9.310449 GAGTTTCCTATGATACTCCCACTATTA 57.690 37.037 7.17 0.00 41.20 0.98
284 285 9.845214 AGTTTCCTATGATACTCCCACTATTAT 57.155 33.333 0.00 0.00 27.97 1.28
285 286 9.877178 GTTTCCTATGATACTCCCACTATTATG 57.123 37.037 0.00 0.00 0.00 1.90
286 287 9.837681 TTTCCTATGATACTCCCACTATTATGA 57.162 33.333 0.00 0.00 0.00 2.15
287 288 9.837681 TTCCTATGATACTCCCACTATTATGAA 57.162 33.333 0.00 0.00 0.00 2.57
292 293 8.956446 TGATACTCCCACTATTATGAATGAGA 57.044 34.615 0.00 0.00 0.00 3.27
293 294 9.379770 TGATACTCCCACTATTATGAATGAGAA 57.620 33.333 0.00 0.00 0.00 2.87
359 361 3.859411 TTTTCCTTGTTGTTGCTTCGT 57.141 38.095 0.00 0.00 0.00 3.85
457 459 8.665685 CAGGTTAATTGATAGTTACACTTGGTC 58.334 37.037 0.00 0.00 0.00 4.02
460 462 8.928733 GTTAATTGATAGTTACACTTGGTCGAA 58.071 33.333 0.00 0.00 0.00 3.71
467 469 5.801380 AGTTACACTTGGTCGAAATATGGT 58.199 37.500 0.00 0.00 0.00 3.55
521 523 0.403655 TGCTATTTCACAGGGCCACA 59.596 50.000 6.18 0.00 0.00 4.17
526 528 0.105760 TTTCACAGGGCCACATTGGT 60.106 50.000 6.18 0.00 40.46 3.67
546 548 4.528596 TGGTTGTCTTTTGAGGTGGAAAAA 59.471 37.500 0.00 0.00 0.00 1.94
552 554 6.816140 TGTCTTTTGAGGTGGAAAAATTTGAC 59.184 34.615 0.00 0.00 0.00 3.18
583 585 5.047092 CCTGGTCTTATTGCTTTGGTTCAAT 60.047 40.000 0.00 0.00 36.87 2.57
584 586 5.782047 TGGTCTTATTGCTTTGGTTCAATG 58.218 37.500 0.00 0.00 34.95 2.82
630 632 4.640771 TGAAGACCCTTATGAGCACTTT 57.359 40.909 0.00 0.00 0.00 2.66
682 684 3.983044 AGTACCATGGAGTTCCTCAAC 57.017 47.619 21.47 2.20 36.82 3.18
686 688 2.376518 ACCATGGAGTTCCTCAACATGT 59.623 45.455 21.47 0.00 37.74 3.21
707 709 7.809331 ACATGTTATCAAGTGCATGTTGTTTAG 59.191 33.333 10.56 1.55 46.49 1.85
730 732 2.942804 TCTCTCTCCGAGATGATGCTT 58.057 47.619 0.00 0.00 43.72 3.91
815 818 8.671384 TTCTTGGATAAATATTTCCCACTACG 57.329 34.615 17.14 9.53 0.00 3.51
831 834 0.457853 TACGCAAGCAGTCCACGATC 60.458 55.000 0.00 0.00 45.62 3.69
832 835 1.446792 CGCAAGCAGTCCACGATCT 60.447 57.895 0.00 0.00 0.00 2.75
911 914 5.497474 GGAGAGGTACAAAGCCTTATTCAA 58.503 41.667 0.00 0.00 36.29 2.69
936 939 1.412710 TGTCCTAATCATGGGCTCGAC 59.587 52.381 0.00 0.00 0.00 4.20
952 955 4.902443 CTCGACAGATGGTTAGAGCTAA 57.098 45.455 0.00 0.00 31.21 3.09
1023 1026 0.249911 CAGCGGGTGGAGCTATTACC 60.250 60.000 0.00 5.22 44.06 2.85
1026 1029 1.202770 GCGGGTGGAGCTATTACCAAT 60.203 52.381 13.60 0.00 37.94 3.16
1167 1170 5.127845 TCAGCCACCAATTCTTACACAAAAA 59.872 36.000 0.00 0.00 0.00 1.94
1193 1196 4.460731 TGAACCTCTATCTCAGTGTGACAG 59.539 45.833 0.00 0.00 0.00 3.51
1344 1347 2.810852 AGAGCTGCAGTTAGTTGCTTTC 59.189 45.455 16.64 0.00 44.38 2.62
1386 1389 9.276590 CCTTTAGTTGATATTGATCATGTGCTA 57.723 33.333 0.00 0.00 41.77 3.49
1489 1492 4.498682 GCTTCATGGTTGATTATGGTGAGC 60.499 45.833 0.00 0.00 0.00 4.26
1496 1499 4.646492 GGTTGATTATGGTGAGCTGGATTT 59.354 41.667 0.00 0.00 0.00 2.17
1545 1548 1.478916 TCACTTGTTGACACGAGTCCA 59.521 47.619 10.58 0.00 43.36 4.02
1546 1549 2.093921 TCACTTGTTGACACGAGTCCAA 60.094 45.455 10.58 7.39 43.36 3.53
1641 1644 5.660417 TCTCAGGTATGATCTCAGCTTTCTT 59.340 40.000 0.00 0.00 34.12 2.52
1701 1704 5.008613 ACCATGTGACTTGTTGTTGATACAC 59.991 40.000 0.00 0.00 32.98 2.90
1835 1838 4.475763 TTACACTTGTGCACCATTTACG 57.524 40.909 15.69 0.00 0.00 3.18
1947 1972 4.416533 CGAAGCTAGAGCAGGCAG 57.583 61.111 4.01 0.00 45.16 4.85
2049 2116 4.646492 GGTGAGCTATTTCATGACCCATTT 59.354 41.667 0.00 0.00 0.00 2.32
2116 2187 3.119352 GGGTTGCTTGAGCCATTTCTTAG 60.119 47.826 0.00 0.00 41.18 2.18
2123 2194 5.452078 TTGAGCCATTTCTTAGTTGTTGG 57.548 39.130 0.00 0.00 0.00 3.77
2138 2210 4.281688 AGTTGTTGGCATGCTGAAATTACT 59.718 37.500 18.92 12.92 0.00 2.24
2140 2212 5.973899 TGTTGGCATGCTGAAATTACTTA 57.026 34.783 18.92 0.00 0.00 2.24
2281 2358 9.503399 CAAATCCCTAGTACACTAGAAAACTTT 57.497 33.333 16.34 7.08 46.80 2.66
2361 2440 1.133513 TGCCAAGTGTGTTCCCATTCT 60.134 47.619 0.00 0.00 0.00 2.40
2448 2527 3.654414 ACTTGGTTGAGTGACGATTCTC 58.346 45.455 0.00 0.00 0.00 2.87
2572 2715 5.075493 TGGTAGGATCGGATAGGAGTTAAC 58.925 45.833 0.00 0.00 0.00 2.01
2575 2720 7.118060 GGTAGGATCGGATAGGAGTTAACTAT 58.882 42.308 8.42 3.02 34.00 2.12
2576 2721 8.270744 GGTAGGATCGGATAGGAGTTAACTATA 58.729 40.741 8.42 5.33 31.58 1.31
2577 2722 9.850198 GTAGGATCGGATAGGAGTTAACTATAT 57.150 37.037 8.42 10.01 31.58 0.86
2691 2856 4.201523 TGGTCGAGCCAGGTGTAA 57.798 55.556 12.85 0.00 43.61 2.41
2702 2867 2.890945 GCCAGGTGTAAACCATGTTCTT 59.109 45.455 4.48 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.763356 GCAACAAATAAATTCTCAAACATGTCA 58.237 29.630 0.00 0.00 0.00 3.58
4 5 8.763356 TGCAACAAATAAATTCTCAAACATGTC 58.237 29.630 0.00 0.00 0.00 3.06
5 6 8.659925 TGCAACAAATAAATTCTCAAACATGT 57.340 26.923 0.00 0.00 0.00 3.21
19 20 8.778358 GGGACAAACATTAATTGCAACAAATAA 58.222 29.630 0.00 0.00 0.00 1.40
20 21 7.933577 TGGGACAAACATTAATTGCAACAAATA 59.066 29.630 0.00 0.00 31.92 1.40
21 22 6.769822 TGGGACAAACATTAATTGCAACAAAT 59.230 30.769 0.00 1.32 31.92 2.32
22 23 6.115446 TGGGACAAACATTAATTGCAACAAA 58.885 32.000 0.00 0.00 31.92 2.83
23 24 5.674525 TGGGACAAACATTAATTGCAACAA 58.325 33.333 0.00 0.00 31.92 2.83
24 25 5.282055 TGGGACAAACATTAATTGCAACA 57.718 34.783 0.00 0.00 31.92 3.33
45 46 0.672342 GCATAGCATCCCCAAGCTTG 59.328 55.000 19.93 19.93 42.05 4.01
46 47 0.554792 AGCATAGCATCCCCAAGCTT 59.445 50.000 0.00 0.00 42.05 3.74
47 48 0.554792 AAGCATAGCATCCCCAAGCT 59.445 50.000 0.00 0.00 44.55 3.74
48 49 2.276732 TAAGCATAGCATCCCCAAGC 57.723 50.000 0.00 0.00 0.00 4.01
49 50 4.401022 TCATTAAGCATAGCATCCCCAAG 58.599 43.478 0.00 0.00 0.00 3.61
50 51 4.451891 TCATTAAGCATAGCATCCCCAA 57.548 40.909 0.00 0.00 0.00 4.12
51 52 4.104579 TCTTCATTAAGCATAGCATCCCCA 59.895 41.667 0.00 0.00 32.36 4.96
52 53 4.655963 TCTTCATTAAGCATAGCATCCCC 58.344 43.478 0.00 0.00 32.36 4.81
53 54 5.942236 TCATCTTCATTAAGCATAGCATCCC 59.058 40.000 0.00 0.00 32.36 3.85
54 55 7.553402 AGATCATCTTCATTAAGCATAGCATCC 59.447 37.037 0.00 0.00 32.36 3.51
55 56 8.495361 AGATCATCTTCATTAAGCATAGCATC 57.505 34.615 0.00 0.00 32.36 3.91
56 57 8.865420 AAGATCATCTTCATTAAGCATAGCAT 57.135 30.769 0.00 0.00 28.99 3.79
57 58 8.687292 AAAGATCATCTTCATTAAGCATAGCA 57.313 30.769 0.00 0.00 35.27 3.49
58 59 9.962783 AAAAAGATCATCTTCATTAAGCATAGC 57.037 29.630 0.00 0.00 35.27 2.97
81 82 7.288852 TGATCATTCAAAGTAAGGGGACAAAAA 59.711 33.333 0.00 0.00 0.00 1.94
82 83 6.780031 TGATCATTCAAAGTAAGGGGACAAAA 59.220 34.615 0.00 0.00 0.00 2.44
83 84 6.310941 TGATCATTCAAAGTAAGGGGACAAA 58.689 36.000 0.00 0.00 0.00 2.83
84 85 5.886609 TGATCATTCAAAGTAAGGGGACAA 58.113 37.500 0.00 0.00 0.00 3.18
85 86 5.512942 TGATCATTCAAAGTAAGGGGACA 57.487 39.130 0.00 0.00 0.00 4.02
86 87 6.834168 TTTGATCATTCAAAGTAAGGGGAC 57.166 37.500 0.00 0.00 44.81 4.46
100 101 8.988934 GCAATCATCATAGCAAATTTGATCATT 58.011 29.630 22.31 1.50 0.00 2.57
101 102 8.147704 TGCAATCATCATAGCAAATTTGATCAT 58.852 29.630 22.31 7.91 33.48 2.45
102 103 7.493367 TGCAATCATCATAGCAAATTTGATCA 58.507 30.769 22.31 5.86 33.48 2.92
103 104 7.940178 TGCAATCATCATAGCAAATTTGATC 57.060 32.000 22.31 5.05 33.48 2.92
104 105 7.095229 GCATGCAATCATCATAGCAAATTTGAT 60.095 33.333 22.31 18.27 40.76 2.57
105 106 6.201997 GCATGCAATCATCATAGCAAATTTGA 59.798 34.615 22.31 1.94 40.76 2.69
106 107 6.362686 GCATGCAATCATCATAGCAAATTTG 58.637 36.000 14.21 14.03 40.76 2.32
107 108 5.468746 GGCATGCAATCATCATAGCAAATTT 59.531 36.000 21.36 0.00 40.76 1.82
108 109 4.994852 GGCATGCAATCATCATAGCAAATT 59.005 37.500 21.36 0.00 40.76 1.82
109 110 4.283467 AGGCATGCAATCATCATAGCAAAT 59.717 37.500 21.36 0.00 40.76 2.32
110 111 3.639561 AGGCATGCAATCATCATAGCAAA 59.360 39.130 21.36 0.00 40.76 3.68
111 112 3.227614 AGGCATGCAATCATCATAGCAA 58.772 40.909 21.36 0.00 40.76 3.91
112 113 2.817844 GAGGCATGCAATCATCATAGCA 59.182 45.455 21.36 0.00 41.73 3.49
113 114 2.163815 GGAGGCATGCAATCATCATAGC 59.836 50.000 21.36 0.00 0.00 2.97
114 115 2.753452 GGGAGGCATGCAATCATCATAG 59.247 50.000 21.36 0.00 0.00 2.23
115 116 2.108601 TGGGAGGCATGCAATCATCATA 59.891 45.455 21.36 0.36 0.00 2.15
116 117 1.133294 TGGGAGGCATGCAATCATCAT 60.133 47.619 21.36 0.00 0.00 2.45
117 118 0.259356 TGGGAGGCATGCAATCATCA 59.741 50.000 21.36 14.76 0.00 3.07
118 119 0.672342 GTGGGAGGCATGCAATCATC 59.328 55.000 21.36 12.57 0.00 2.92
119 120 0.260816 AGTGGGAGGCATGCAATCAT 59.739 50.000 21.36 0.00 0.00 2.45
120 121 0.040058 AAGTGGGAGGCATGCAATCA 59.960 50.000 21.36 8.99 0.00 2.57
121 122 2.057137 TAAGTGGGAGGCATGCAATC 57.943 50.000 21.36 16.30 0.00 2.67
122 123 2.091720 TCATAAGTGGGAGGCATGCAAT 60.092 45.455 21.36 7.26 0.00 3.56
123 124 1.284491 TCATAAGTGGGAGGCATGCAA 59.716 47.619 21.36 0.00 0.00 4.08
124 125 0.918258 TCATAAGTGGGAGGCATGCA 59.082 50.000 21.36 0.00 0.00 3.96
125 126 1.884579 CATCATAAGTGGGAGGCATGC 59.115 52.381 9.90 9.90 0.00 4.06
126 127 3.497103 TCATCATAAGTGGGAGGCATG 57.503 47.619 0.00 0.00 0.00 4.06
127 128 4.736611 AATCATCATAAGTGGGAGGCAT 57.263 40.909 0.00 0.00 0.00 4.40
128 129 5.848286 ATAATCATCATAAGTGGGAGGCA 57.152 39.130 0.00 0.00 0.00 4.75
129 130 8.049117 TCATAATAATCATCATAAGTGGGAGGC 58.951 37.037 0.00 0.00 0.00 4.70
220 221 9.927668 AATTGTTCCCACATTAAAAGAGTAATG 57.072 29.630 3.90 3.90 43.96 1.90
232 233 9.621629 TCGAATACTATAAATTGTTCCCACATT 57.378 29.630 0.00 0.00 31.06 2.71
233 234 9.273016 CTCGAATACTATAAATTGTTCCCACAT 57.727 33.333 0.00 0.00 31.06 3.21
234 235 8.262227 ACTCGAATACTATAAATTGTTCCCACA 58.738 33.333 0.00 0.00 0.00 4.17
235 236 8.658499 ACTCGAATACTATAAATTGTTCCCAC 57.342 34.615 0.00 0.00 0.00 4.61
236 237 9.675464 AAACTCGAATACTATAAATTGTTCCCA 57.325 29.630 0.00 0.00 0.00 4.37
249 250 9.228949 GGAGTATCATAGGAAACTCGAATACTA 57.771 37.037 0.43 0.00 37.91 1.82
250 251 7.177041 GGGAGTATCATAGGAAACTCGAATACT 59.823 40.741 0.06 0.06 39.25 2.12
251 252 7.039923 TGGGAGTATCATAGGAAACTCGAATAC 60.040 40.741 0.00 0.00 39.39 1.89
252 253 7.008332 TGGGAGTATCATAGGAAACTCGAATA 58.992 38.462 0.00 0.00 39.39 1.75
253 254 5.839063 TGGGAGTATCATAGGAAACTCGAAT 59.161 40.000 0.00 0.00 39.39 3.34
254 255 5.068723 GTGGGAGTATCATAGGAAACTCGAA 59.931 44.000 0.00 0.00 39.39 3.71
255 256 4.583489 GTGGGAGTATCATAGGAAACTCGA 59.417 45.833 0.00 0.00 39.39 4.04
256 257 4.585162 AGTGGGAGTATCATAGGAAACTCG 59.415 45.833 0.00 0.00 39.39 4.18
257 258 7.784470 ATAGTGGGAGTATCATAGGAAACTC 57.216 40.000 0.00 0.00 38.57 3.01
258 259 9.845214 ATAATAGTGGGAGTATCATAGGAAACT 57.155 33.333 0.00 0.00 40.77 2.66
259 260 9.877178 CATAATAGTGGGAGTATCATAGGAAAC 57.123 37.037 0.00 0.00 36.25 2.78
260 261 9.837681 TCATAATAGTGGGAGTATCATAGGAAA 57.162 33.333 0.00 0.00 36.25 3.13
261 262 9.837681 TTCATAATAGTGGGAGTATCATAGGAA 57.162 33.333 0.00 0.00 36.25 3.36
266 267 9.552695 TCTCATTCATAATAGTGGGAGTATCAT 57.447 33.333 0.00 0.00 36.25 2.45
267 268 8.956446 TCTCATTCATAATAGTGGGAGTATCA 57.044 34.615 0.00 0.00 36.25 2.15
337 339 4.754322 ACGAAGCAACAACAAGGAAAAAT 58.246 34.783 0.00 0.00 0.00 1.82
457 459 5.678132 TCATGAAGCATCACCATATTTCG 57.322 39.130 0.00 0.00 38.69 3.46
460 462 6.971726 AACATCATGAAGCATCACCATATT 57.028 33.333 0.00 0.00 38.69 1.28
467 469 4.440940 GCATCCAAACATCATGAAGCATCA 60.441 41.667 0.00 0.00 40.57 3.07
521 523 3.909732 TCCACCTCAAAAGACAACCAAT 58.090 40.909 0.00 0.00 0.00 3.16
526 528 7.333174 GTCAAATTTTTCCACCTCAAAAGACAA 59.667 33.333 0.00 0.00 0.00 3.18
552 554 3.891049 AGCAATAAGACCAGGCTTTAGG 58.109 45.455 0.00 0.00 0.00 2.69
583 585 3.084039 GCAATCCTCCAAACTGATGTCA 58.916 45.455 0.00 0.00 0.00 3.58
584 586 2.424956 GGCAATCCTCCAAACTGATGTC 59.575 50.000 0.00 0.00 0.00 3.06
608 610 4.640771 AAGTGCTCATAAGGGTCTTCAA 57.359 40.909 0.00 0.00 0.00 2.69
615 617 2.168521 TCGGAGAAAGTGCTCATAAGGG 59.831 50.000 0.00 0.00 36.62 3.95
682 684 8.022550 TCTAAACAACATGCACTTGATAACATG 58.977 33.333 11.95 0.00 44.29 3.21
686 688 9.013229 AGAATCTAAACAACATGCACTTGATAA 57.987 29.630 11.95 0.00 0.00 1.75
730 732 0.981183 AAGGATCGGTACCAAGCACA 59.019 50.000 13.54 0.00 0.00 4.57
815 818 0.390340 TCAGATCGTGGACTGCTTGC 60.390 55.000 0.00 0.00 34.57 4.01
831 834 5.649557 ACGAAGTTGAAGATCTCATCTCAG 58.350 41.667 0.00 2.29 37.78 3.35
832 835 5.651387 ACGAAGTTGAAGATCTCATCTCA 57.349 39.130 0.00 0.00 37.78 3.27
911 914 3.582208 GAGCCCATGATTAGGACATCTCT 59.418 47.826 0.00 0.00 0.00 3.10
1023 1026 8.242053 AGAAAAGCATCATCAAGTGTCTTATTG 58.758 33.333 0.00 0.00 0.00 1.90
1026 1029 6.348786 GCAGAAAAGCATCATCAAGTGTCTTA 60.349 38.462 0.00 0.00 0.00 2.10
1167 1170 3.766591 CACACTGAGATAGAGGTTCAGGT 59.233 47.826 5.79 0.00 41.98 4.00
1193 1196 6.770746 ATATAATCCATGCAAGCTCAATCC 57.229 37.500 0.00 0.00 0.00 3.01
1386 1389 5.073437 ACTTCTCCATATCTGGCTCTAGT 57.927 43.478 0.00 0.00 42.80 2.57
1489 1492 4.133078 GGCTCCTTGACATCTAAATCCAG 58.867 47.826 0.00 0.00 0.00 3.86
1496 1499 2.191400 AGCTTGGCTCCTTGACATCTA 58.809 47.619 0.00 0.00 30.62 1.98
1545 1548 6.790319 AGGTGTGGTAGTAGAAATTTCCATT 58.210 36.000 14.61 0.61 0.00 3.16
1546 1549 6.012858 TGAGGTGTGGTAGTAGAAATTTCCAT 60.013 38.462 14.61 3.84 0.00 3.41
1701 1704 5.998454 ATCTATTGAGCAAATCAGGAACG 57.002 39.130 0.00 0.00 39.68 3.95
1753 1756 4.100373 ACAGAGAGAATGCCCTCTAAGTT 58.900 43.478 0.00 0.00 43.11 2.66
1835 1838 3.914312 TCTCGAACTTGGTCAACTCATC 58.086 45.455 0.00 0.00 0.00 2.92
1947 1972 2.509964 TCCTTTTGCTTCCCTATCCTCC 59.490 50.000 0.00 0.00 0.00 4.30
2116 2187 4.559153 AGTAATTTCAGCATGCCAACAAC 58.441 39.130 15.66 4.63 34.76 3.32
2123 2194 4.935702 TGCCATAAGTAATTTCAGCATGC 58.064 39.130 10.51 10.51 34.76 4.06
2211 2287 5.710513 TCACTAATTTCAGCAAAGCATGT 57.289 34.783 0.00 0.00 0.00 3.21
2361 2440 4.641541 CCATAGTGGTGAAATGATTGCTCA 59.358 41.667 0.00 0.00 31.80 4.26
2491 2629 7.071196 ACATGCCACTTTTAGGTAGATCAGATA 59.929 37.037 0.00 0.00 0.00 1.98
2492 2630 5.957771 TGCCACTTTTAGGTAGATCAGAT 57.042 39.130 0.00 0.00 0.00 2.90
2506 2645 1.895131 GGGAACATGACATGCCACTTT 59.105 47.619 15.49 1.66 0.00 2.66
2507 2646 1.076024 AGGGAACATGACATGCCACTT 59.924 47.619 15.49 2.04 0.00 3.16
2511 2650 0.034186 TCCAGGGAACATGACATGCC 60.034 55.000 15.49 9.22 0.00 4.40
2585 2737 9.052759 GGTATACACCTGGTTCAACAATTATAG 57.947 37.037 5.01 0.00 42.11 1.31
2691 2856 1.354368 ACCGATCCCAAGAACATGGTT 59.646 47.619 0.00 0.00 38.91 3.67
2702 2867 0.834612 GGAACATACCACCGATCCCA 59.165 55.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.