Multiple sequence alignment - TraesCS3A01G256800

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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 TraesCS3A01G256800 chr3A 100.000 3589 0 0 1 3589 478687835 478684247 0.000000e+00 6628.0
1 TraesCS3A01G256800 chr3A 82.471 348 23 11 1372 1689 504622806 504623145 1.640000e-68 270.0
2 TraesCS3A01G256800 chr2B 97.734 3398 37 10 231 3589 1246824 1243428 0.000000e+00 5812.0
3 TraesCS3A01G256800 chr2B 79.004 281 27 9 232 504 63142155 63142411 2.870000e-36 163.0
4 TraesCS3A01G256800 chr5A 95.991 3417 67 16 232 3589 35192594 35189189 0.000000e+00 5487.0
5 TraesCS3A01G256800 chr5A 96.631 2256 39 10 263 2486 322192226 322189976 0.000000e+00 3711.0
6 TraesCS3A01G256800 chr5A 98.356 1095 15 1 2495 3589 322189995 322188904 0.000000e+00 1919.0
7 TraesCS3A01G256800 chr5A 98.923 557 6 0 3033 3589 566639471 566638915 0.000000e+00 996.0
8 TraesCS3A01G256800 chr5A 92.920 452 32 0 704 1155 552504726 552504275 0.000000e+00 658.0
9 TraesCS3A01G256800 chr5A 85.055 455 56 6 701 1155 552389029 552388587 1.520000e-123 453.0
10 TraesCS3A01G256800 chr5A 88.263 213 23 2 293 504 696953913 696954124 1.650000e-63 254.0
11 TraesCS3A01G256800 chr5A 90.984 122 7 2 1181 1299 552505269 552505149 1.030000e-35 161.0
12 TraesCS3A01G256800 chr5A 87.826 115 14 0 385 499 49936501 49936615 6.250000e-28 135.0
13 TraesCS3A01G256800 chr5A 85.000 120 18 0 385 504 35551588 35551469 4.870000e-24 122.0
14 TraesCS3A01G256800 chr6A 92.969 1337 65 13 1157 2476 117193737 117195061 0.000000e+00 1921.0
15 TraesCS3A01G256800 chr6A 92.969 1337 65 13 1157 2476 117213301 117214625 0.000000e+00 1921.0
16 TraesCS3A01G256800 chr6A 94.664 1087 52 3 2505 3588 117195052 117196135 0.000000e+00 1681.0
17 TraesCS3A01G256800 chr6A 94.659 1086 54 2 2505 3588 117214616 117215699 0.000000e+00 1681.0
18 TraesCS3A01G256800 chr6A 85.890 163 13 5 228 380 597450904 597450742 7.970000e-37 165.0
19 TraesCS3A01G256800 chr5B 88.676 1201 61 16 1339 2484 369157269 369158449 0.000000e+00 1395.0
20 TraesCS3A01G256800 chr5B 94.590 610 32 1 2980 3588 369158889 369159498 0.000000e+00 942.0
21 TraesCS3A01G256800 chr5B 91.957 460 27 6 2497 2948 369158432 369158889 1.410000e-178 636.0
22 TraesCS3A01G256800 chr5B 91.429 455 39 0 701 1155 531511928 531511474 3.040000e-175 625.0
23 TraesCS3A01G256800 chr7D 90.521 960 56 10 228 1155 6962323 6961367 0.000000e+00 1236.0
24 TraesCS3A01G256800 chr7D 80.212 283 21 14 231 502 578503874 578503616 2.850000e-41 180.0
25 TraesCS3A01G256800 chr5D 90.549 455 43 0 701 1155 437289119 437288665 1.430000e-168 603.0
26 TraesCS3A01G256800 chr5D 86.047 86 8 3 701 784 437218340 437218257 4.940000e-14 89.8
27 TraesCS3A01G256800 chr3D 93.220 236 11 3 1 232 359319000 359318766 3.430000e-90 342.0
28 TraesCS3A01G256800 chr3D 83.046 348 21 12 1372 1689 381185890 381186229 7.590000e-72 281.0
29 TraesCS3A01G256800 chr3D 80.292 274 40 9 2503 2764 433964537 433964808 1.020000e-45 195.0
30 TraesCS3A01G256800 chr3B 90.795 239 15 3 1 232 465339290 465339052 2.690000e-81 313.0
31 TraesCS3A01G256800 chr7A 86.458 192 22 2 306 496 402186552 402186740 1.310000e-49 207.0
32 TraesCS3A01G256800 chr1D 80.292 274 40 11 2503 2764 96176201 96176472 1.020000e-45 195.0
33 TraesCS3A01G256800 chr2A 79.853 273 41 9 2503 2764 775772532 775772801 1.700000e-43 187.0
34 TraesCS3A01G256800 chr7B 87.342 158 7 9 231 377 11013585 11013430 6.160000e-38 169.0
35 TraesCS3A01G256800 chr4B 82.895 152 8 12 231 364 446506981 446507132 1.750000e-23 121.0


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 TraesCS3A01G256800 chr3A 478684247 478687835 3588 True 6628.0 6628 100.0000 1 3589 1 chr3A.!!$R1 3588
1 TraesCS3A01G256800 chr2B 1243428 1246824 3396 True 5812.0 5812 97.7340 231 3589 1 chr2B.!!$R1 3358
2 TraesCS3A01G256800 chr5A 35189189 35192594 3405 True 5487.0 5487 95.9910 232 3589 1 chr5A.!!$R1 3357
3 TraesCS3A01G256800 chr5A 322188904 322192226 3322 True 2815.0 3711 97.4935 263 3589 2 chr5A.!!$R5 3326
4 TraesCS3A01G256800 chr5A 566638915 566639471 556 True 996.0 996 98.9230 3033 3589 1 chr5A.!!$R4 556
5 TraesCS3A01G256800 chr5A 552504275 552505269 994 True 409.5 658 91.9520 704 1299 2 chr5A.!!$R6 595
6 TraesCS3A01G256800 chr6A 117193737 117196135 2398 False 1801.0 1921 93.8165 1157 3588 2 chr6A.!!$F1 2431
7 TraesCS3A01G256800 chr6A 117213301 117215699 2398 False 1801.0 1921 93.8140 1157 3588 2 chr6A.!!$F2 2431
8 TraesCS3A01G256800 chr5B 369157269 369159498 2229 False 991.0 1395 91.7410 1339 3588 3 chr5B.!!$F1 2249
9 TraesCS3A01G256800 chr7D 6961367 6962323 956 True 1236.0 1236 90.5210 228 1155 1 chr7D.!!$R1 927

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
117 118 0.106569 TATCCCATTGCCTGGCACTG 60.107 55.000 26.80 26.8 44.46 3.66 F
892 930 0.247736 GGTGCATGAGTCCGACTTCT 59.752 55.000 1.71 0.0 0.00 2.85 F
2410 2532 2.367241 TCACACACTTGGATCGAAGGAA 59.633 45.455 19.98 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 1930 5.049405 ACGTCTTGTTTTTCAGATGATCCAC 60.049 40.000 0.00 0.0 0.00 4.02 R
2576 2720 6.432472 TGTTATGCATCCATCAGTACACAAAA 59.568 34.615 0.19 0.0 32.85 2.44 R
3274 3427 7.437713 ACACTGAACCTTTATCATCCTATCA 57.562 36.000 0.00 0.0 0.00 2.15 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
25 26 7.836842 TGTGATGTAACACTGTACTATCATGT 58.163 34.615 0.00 0.00 40.87 3.21
26 27 8.311109 TGTGATGTAACACTGTACTATCATGTT 58.689 33.333 0.00 0.81 40.87 2.71
27 28 8.808529 GTGATGTAACACTGTACTATCATGTTC 58.191 37.037 0.00 0.00 37.73 3.18
28 29 8.749354 TGATGTAACACTGTACTATCATGTTCT 58.251 33.333 0.00 0.00 35.26 3.01
30 31 9.944376 ATGTAACACTGTACTATCATGTTCTTT 57.056 29.630 0.00 0.00 35.26 2.52
31 32 9.772973 TGTAACACTGTACTATCATGTTCTTTT 57.227 29.630 0.00 0.00 35.26 2.27
34 35 9.772973 AACACTGTACTATCATGTTCTTTTACA 57.227 29.630 0.00 0.00 0.00 2.41
35 36 9.944376 ACACTGTACTATCATGTTCTTTTACAT 57.056 29.630 0.00 0.00 39.27 2.29
42 43 4.233789 TCATGTTCTTTTACATTTGGCGC 58.766 39.130 0.00 0.00 36.64 6.53
43 44 3.019933 TGTTCTTTTACATTTGGCGCC 57.980 42.857 22.73 22.73 0.00 6.53
44 45 2.625790 TGTTCTTTTACATTTGGCGCCT 59.374 40.909 29.70 9.54 0.00 5.52
46 47 4.278669 TGTTCTTTTACATTTGGCGCCTTA 59.721 37.500 29.70 16.06 0.00 2.69
47 48 5.047660 TGTTCTTTTACATTTGGCGCCTTAT 60.048 36.000 29.70 17.73 0.00 1.73
48 49 5.652994 TCTTTTACATTTGGCGCCTTATT 57.347 34.783 29.70 10.63 0.00 1.40
51 52 4.792521 TTACATTTGGCGCCTTATTTGT 57.207 36.364 29.70 23.28 0.00 2.83
52 53 3.676291 ACATTTGGCGCCTTATTTGTT 57.324 38.095 29.70 0.92 0.00 2.83
53 54 4.792521 ACATTTGGCGCCTTATTTGTTA 57.207 36.364 29.70 0.00 0.00 2.41
54 55 4.490743 ACATTTGGCGCCTTATTTGTTAC 58.509 39.130 29.70 0.00 0.00 2.50
55 56 4.021894 ACATTTGGCGCCTTATTTGTTACA 60.022 37.500 29.70 0.00 0.00 2.41
56 57 3.840890 TTGGCGCCTTATTTGTTACAG 57.159 42.857 29.70 0.00 0.00 2.74
57 58 1.470890 TGGCGCCTTATTTGTTACAGC 59.529 47.619 29.70 0.00 0.00 4.40
58 59 1.202256 GGCGCCTTATTTGTTACAGCC 60.202 52.381 22.15 0.00 35.00 4.85
60 61 2.088423 CGCCTTATTTGTTACAGCCCA 58.912 47.619 0.00 0.00 0.00 5.36
61 62 2.097466 CGCCTTATTTGTTACAGCCCAG 59.903 50.000 0.00 0.00 0.00 4.45
62 63 3.089284 GCCTTATTTGTTACAGCCCAGT 58.911 45.455 0.00 0.00 0.00 4.00
63 64 3.509967 GCCTTATTTGTTACAGCCCAGTT 59.490 43.478 0.00 0.00 0.00 3.16
64 65 4.380550 GCCTTATTTGTTACAGCCCAGTTC 60.381 45.833 0.00 0.00 0.00 3.01
65 66 4.157840 CCTTATTTGTTACAGCCCAGTTCC 59.842 45.833 0.00 0.00 0.00 3.62
66 67 3.525800 ATTTGTTACAGCCCAGTTCCT 57.474 42.857 0.00 0.00 0.00 3.36
67 68 3.306472 TTTGTTACAGCCCAGTTCCTT 57.694 42.857 0.00 0.00 0.00 3.36
68 69 3.306472 TTGTTACAGCCCAGTTCCTTT 57.694 42.857 0.00 0.00 0.00 3.11
69 70 4.440826 TTGTTACAGCCCAGTTCCTTTA 57.559 40.909 0.00 0.00 0.00 1.85
70 71 4.650972 TGTTACAGCCCAGTTCCTTTAT 57.349 40.909 0.00 0.00 0.00 1.40
71 72 4.993028 TGTTACAGCCCAGTTCCTTTATT 58.007 39.130 0.00 0.00 0.00 1.40
72 73 5.390387 TGTTACAGCCCAGTTCCTTTATTT 58.610 37.500 0.00 0.00 0.00 1.40
73 74 5.836358 TGTTACAGCCCAGTTCCTTTATTTT 59.164 36.000 0.00 0.00 0.00 1.82
75 76 4.223144 ACAGCCCAGTTCCTTTATTTTGT 58.777 39.130 0.00 0.00 0.00 2.83
77 78 5.221441 ACAGCCCAGTTCCTTTATTTTGTTC 60.221 40.000 0.00 0.00 0.00 3.18
78 79 4.898861 AGCCCAGTTCCTTTATTTTGTTCA 59.101 37.500 0.00 0.00 0.00 3.18
80 81 5.696270 GCCCAGTTCCTTTATTTTGTTCAAG 59.304 40.000 0.00 0.00 0.00 3.02
83 84 5.977129 CAGTTCCTTTATTTTGTTCAAGCGT 59.023 36.000 0.00 0.00 0.00 5.07
84 85 6.475402 CAGTTCCTTTATTTTGTTCAAGCGTT 59.525 34.615 0.00 0.00 0.00 4.84
85 86 7.010091 CAGTTCCTTTATTTTGTTCAAGCGTTT 59.990 33.333 0.00 0.00 0.00 3.60
88 89 6.474102 TCCTTTATTTTGTTCAAGCGTTTGTC 59.526 34.615 11.93 7.32 35.73 3.18
89 90 6.475402 CCTTTATTTTGTTCAAGCGTTTGTCT 59.525 34.615 11.93 0.00 35.73 3.41
90 91 7.010091 CCTTTATTTTGTTCAAGCGTTTGTCTT 59.990 33.333 11.93 0.00 35.73 3.01
91 92 5.701029 ATTTTGTTCAAGCGTTTGTCTTG 57.299 34.783 11.93 2.74 41.57 3.02
93 94 3.840890 TGTTCAAGCGTTTGTCTTGTT 57.159 38.095 11.93 0.00 41.13 2.83
94 95 4.948608 TGTTCAAGCGTTTGTCTTGTTA 57.051 36.364 11.93 0.00 41.13 2.41
95 96 5.298197 TGTTCAAGCGTTTGTCTTGTTAA 57.702 34.783 11.93 0.00 41.13 2.01
96 97 5.700846 TGTTCAAGCGTTTGTCTTGTTAAA 58.299 33.333 11.93 0.00 41.13 1.52
97 98 6.150318 TGTTCAAGCGTTTGTCTTGTTAAAA 58.850 32.000 11.93 0.00 41.13 1.52
98 99 6.809196 TGTTCAAGCGTTTGTCTTGTTAAAAT 59.191 30.769 11.93 0.00 41.13 1.82
100 101 8.964150 GTTCAAGCGTTTGTCTTGTTAAAATAT 58.036 29.630 11.93 0.00 41.13 1.28
101 102 8.722342 TCAAGCGTTTGTCTTGTTAAAATATC 57.278 30.769 11.93 0.00 41.13 1.63
102 103 7.806014 TCAAGCGTTTGTCTTGTTAAAATATCC 59.194 33.333 11.93 0.00 41.13 2.59
106 107 7.544217 GCGTTTGTCTTGTTAAAATATCCCATT 59.456 33.333 0.00 0.00 0.00 3.16
107 108 8.859156 CGTTTGTCTTGTTAAAATATCCCATTG 58.141 33.333 0.00 0.00 0.00 2.82
108 109 8.655970 GTTTGTCTTGTTAAAATATCCCATTGC 58.344 33.333 0.00 0.00 0.00 3.56
109 110 6.872920 TGTCTTGTTAAAATATCCCATTGCC 58.127 36.000 0.00 0.00 0.00 4.52
111 112 6.980397 GTCTTGTTAAAATATCCCATTGCCTG 59.020 38.462 0.00 0.00 0.00 4.85
112 113 5.867903 TGTTAAAATATCCCATTGCCTGG 57.132 39.130 0.00 0.00 45.51 4.45
113 114 4.100808 TGTTAAAATATCCCATTGCCTGGC 59.899 41.667 12.87 12.87 44.46 4.85
115 116 1.708341 AATATCCCATTGCCTGGCAC 58.292 50.000 23.30 0.00 44.46 5.01
116 117 0.855598 ATATCCCATTGCCTGGCACT 59.144 50.000 23.30 14.24 44.46 4.40
117 118 0.106569 TATCCCATTGCCTGGCACTG 60.107 55.000 26.80 26.80 44.46 3.66
120 121 2.642254 CCATTGCCTGGCACTGTGG 61.642 63.158 29.71 26.77 38.71 4.17
122 123 1.604593 ATTGCCTGGCACTGTGGTC 60.605 57.895 23.30 0.00 38.71 4.02
123 124 2.072874 ATTGCCTGGCACTGTGGTCT 62.073 55.000 23.30 0.00 38.71 3.85
124 125 2.670934 GCCTGGCACTGTGGTCTG 60.671 66.667 15.17 0.00 0.00 3.51
126 127 2.111669 CTGGCACTGTGGTCTGCA 59.888 61.111 10.21 0.00 0.00 4.41
128 129 0.892358 CTGGCACTGTGGTCTGCATT 60.892 55.000 10.21 0.00 0.00 3.56
129 130 0.467844 TGGCACTGTGGTCTGCATTT 60.468 50.000 10.21 0.00 0.00 2.32
131 132 2.094675 GGCACTGTGGTCTGCATTTAT 58.905 47.619 10.21 0.00 0.00 1.40
132 133 3.278574 GGCACTGTGGTCTGCATTTATA 58.721 45.455 10.21 0.00 0.00 0.98
133 134 3.313526 GGCACTGTGGTCTGCATTTATAG 59.686 47.826 10.21 0.00 0.00 1.31
134 135 3.242870 GCACTGTGGTCTGCATTTATAGC 60.243 47.826 10.21 0.00 0.00 2.97
137 138 1.939934 GTGGTCTGCATTTATAGCGCA 59.060 47.619 11.47 0.00 33.85 6.09
138 139 2.549754 GTGGTCTGCATTTATAGCGCAT 59.450 45.455 11.47 3.63 34.63 4.73
139 140 2.549329 TGGTCTGCATTTATAGCGCATG 59.451 45.455 11.47 5.06 34.63 4.06
150 151 4.527157 GCGCATGCTTCCGTCTGC 62.527 66.667 17.13 5.08 38.39 4.26
151 152 2.816958 CGCATGCTTCCGTCTGCT 60.817 61.111 17.13 0.00 32.48 4.24
152 153 2.789917 GCATGCTTCCGTCTGCTG 59.210 61.111 11.37 0.00 0.00 4.41
153 154 2.758089 GCATGCTTCCGTCTGCTGG 61.758 63.158 11.37 0.00 0.00 4.85
154 155 2.437359 ATGCTTCCGTCTGCTGGC 60.437 61.111 0.00 0.00 0.00 4.85
156 157 4.742201 GCTTCCGTCTGCTGGCGA 62.742 66.667 19.76 2.43 0.00 5.54
159 160 3.158537 TTCCGTCTGCTGGCGAACA 62.159 57.895 19.76 0.00 0.00 3.18
160 161 3.414700 CCGTCTGCTGGCGAACAC 61.415 66.667 19.76 0.00 0.00 3.32
161 162 2.661537 CGTCTGCTGGCGAACACA 60.662 61.111 12.68 0.00 0.00 3.72
162 163 2.661566 CGTCTGCTGGCGAACACAG 61.662 63.158 12.68 0.00 38.95 3.66
163 164 1.300931 GTCTGCTGGCGAACACAGA 60.301 57.895 0.00 0.00 38.20 3.41
164 165 0.880278 GTCTGCTGGCGAACACAGAA 60.880 55.000 11.35 0.00 38.25 3.02
166 167 0.882042 CTGCTGGCGAACACAGAAGT 60.882 55.000 0.00 0.00 36.94 3.01
167 168 0.391228 TGCTGGCGAACACAGAAGTA 59.609 50.000 0.00 0.00 38.20 2.24
168 169 1.001974 TGCTGGCGAACACAGAAGTAT 59.998 47.619 0.00 0.00 38.20 2.12
169 170 2.076863 GCTGGCGAACACAGAAGTATT 58.923 47.619 0.00 0.00 38.20 1.89
170 171 3.259064 GCTGGCGAACACAGAAGTATTA 58.741 45.455 0.00 0.00 38.20 0.98
171 172 3.871594 GCTGGCGAACACAGAAGTATTAT 59.128 43.478 0.00 0.00 38.20 1.28
172 173 5.047847 GCTGGCGAACACAGAAGTATTATA 58.952 41.667 0.00 0.00 38.20 0.98
173 174 5.175856 GCTGGCGAACACAGAAGTATTATAG 59.824 44.000 0.00 0.00 38.20 1.31
174 175 5.047847 TGGCGAACACAGAAGTATTATAGC 58.952 41.667 0.00 0.00 0.00 2.97
175 176 5.047847 GGCGAACACAGAAGTATTATAGCA 58.952 41.667 0.00 0.00 0.00 3.49
176 177 5.696724 GGCGAACACAGAAGTATTATAGCAT 59.303 40.000 0.00 0.00 0.00 3.79
177 178 6.866770 GGCGAACACAGAAGTATTATAGCATA 59.133 38.462 0.00 0.00 0.00 3.14
178 179 7.062371 GGCGAACACAGAAGTATTATAGCATAG 59.938 40.741 0.00 0.00 0.00 2.23
179 180 7.410942 GCGAACACAGAAGTATTATAGCATAGC 60.411 40.741 0.00 0.00 0.00 2.97
181 182 9.429359 GAACACAGAAGTATTATAGCATAGCAT 57.571 33.333 0.00 0.00 0.00 3.79
182 183 8.768957 ACACAGAAGTATTATAGCATAGCATG 57.231 34.615 0.00 0.00 0.00 4.06
184 185 9.597170 CACAGAAGTATTATAGCATAGCATGAT 57.403 33.333 0.00 0.00 0.00 2.45
190 191 9.539825 AGTATTATAGCATAGCATGATTACTGC 57.460 33.333 0.00 0.38 39.97 4.40
202 203 5.289434 GCATGATTACTGCTAACCTTTTTGC 59.711 40.000 0.00 0.00 36.68 3.68
203 204 5.385509 TGATTACTGCTAACCTTTTTGCC 57.614 39.130 0.00 0.00 33.03 4.52
204 205 3.907894 TTACTGCTAACCTTTTTGCCG 57.092 42.857 0.00 0.00 33.03 5.69
205 206 1.687563 ACTGCTAACCTTTTTGCCGT 58.312 45.000 0.00 0.00 33.03 5.68
206 207 2.028876 ACTGCTAACCTTTTTGCCGTT 58.971 42.857 0.00 0.00 33.03 4.44
207 208 2.429250 ACTGCTAACCTTTTTGCCGTTT 59.571 40.909 0.00 0.00 33.03 3.60
209 210 3.449632 TGCTAACCTTTTTGCCGTTTTC 58.550 40.909 0.00 0.00 33.03 2.29
210 211 3.119101 TGCTAACCTTTTTGCCGTTTTCA 60.119 39.130 0.00 0.00 33.03 2.69
211 212 3.866327 GCTAACCTTTTTGCCGTTTTCAA 59.134 39.130 0.00 0.00 0.00 2.69
212 213 4.330347 GCTAACCTTTTTGCCGTTTTCAAA 59.670 37.500 0.00 0.00 0.00 2.69
213 214 5.007234 GCTAACCTTTTTGCCGTTTTCAAAT 59.993 36.000 0.00 0.00 33.94 2.32
217 218 6.284459 ACCTTTTTGCCGTTTTCAAATGATA 58.716 32.000 0.00 0.00 33.94 2.15
219 220 6.423604 CCTTTTTGCCGTTTTCAAATGATACT 59.576 34.615 0.00 0.00 33.94 2.12
220 221 7.359181 CCTTTTTGCCGTTTTCAAATGATACTC 60.359 37.037 0.00 0.00 33.94 2.59
221 222 5.697473 TTGCCGTTTTCAAATGATACTCA 57.303 34.783 0.00 0.00 0.00 3.41
222 223 5.295431 TGCCGTTTTCAAATGATACTCAG 57.705 39.130 0.00 0.00 0.00 3.35
223 224 4.759693 TGCCGTTTTCAAATGATACTCAGT 59.240 37.500 0.00 0.00 0.00 3.41
224 225 5.106712 TGCCGTTTTCAAATGATACTCAGTC 60.107 40.000 0.00 0.00 0.00 3.51
226 227 5.163754 CCGTTTTCAAATGATACTCAGTCCC 60.164 44.000 0.00 0.00 0.00 4.46
251 252 8.428063 CCAAAATCTCTACTCCTAATGTCTCAT 58.572 37.037 0.00 0.00 0.00 2.90
309 322 3.411517 CCCCCACCAGGCGATCTT 61.412 66.667 0.00 0.00 0.00 2.40
699 737 2.936032 GTGCCCCTCTCCCAGGTT 60.936 66.667 0.00 0.00 41.51 3.50
892 930 0.247736 GGTGCATGAGTCCGACTTCT 59.752 55.000 1.71 0.00 0.00 2.85
1772 1869 5.696724 ACTCAGGTGTTTCATAGACTTTTCG 59.303 40.000 0.00 0.00 0.00 3.46
2410 2532 2.367241 TCACACACTTGGATCGAAGGAA 59.633 45.455 19.98 0.00 0.00 3.36
2973 3125 2.685850 ACTATCGGCCAGTTACCAAC 57.314 50.000 2.24 0.00 0.00 3.77
3274 3427 4.982241 ATGGCTATGTACTGGTTATGCT 57.018 40.909 0.00 0.00 0.00 3.79
3428 3581 6.889494 TGCAATTTCTGTTGTTTTATGCATG 58.111 32.000 10.16 0.00 36.46 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.836842 ACATGATAGTACAGTGTTACATCACA 58.163 34.615 0.00 0.00 40.37 3.58
1 2 8.703604 AACATGATAGTACAGTGTTACATCAC 57.296 34.615 0.00 0.00 38.46 3.06
2 3 8.749354 AGAACATGATAGTACAGTGTTACATCA 58.251 33.333 0.00 8.32 33.55 3.07
3 4 9.587772 AAGAACATGATAGTACAGTGTTACATC 57.412 33.333 0.00 2.55 33.55 3.06
5 6 9.772973 AAAAGAACATGATAGTACAGTGTTACA 57.227 29.630 0.00 0.00 33.55 2.41
9 10 9.944376 ATGTAAAAGAACATGATAGTACAGTGT 57.056 29.630 0.00 0.00 38.65 3.55
14 15 9.503427 GCCAAATGTAAAAGAACATGATAGTAC 57.497 33.333 0.00 0.00 39.98 2.73
16 17 7.250569 CGCCAAATGTAAAAGAACATGATAGT 58.749 34.615 0.00 0.00 39.98 2.12
17 18 6.197096 GCGCCAAATGTAAAAGAACATGATAG 59.803 38.462 0.00 0.00 39.98 2.08
19 20 4.864247 GCGCCAAATGTAAAAGAACATGAT 59.136 37.500 0.00 0.00 39.98 2.45
20 21 4.233789 GCGCCAAATGTAAAAGAACATGA 58.766 39.130 0.00 0.00 39.98 3.07
21 22 3.367630 GGCGCCAAATGTAAAAGAACATG 59.632 43.478 24.80 0.00 39.98 3.21
22 23 3.258123 AGGCGCCAAATGTAAAAGAACAT 59.742 39.130 31.54 0.00 41.87 2.71
24 25 3.297830 AGGCGCCAAATGTAAAAGAAC 57.702 42.857 31.54 0.00 0.00 3.01
25 26 5.652994 ATAAGGCGCCAAATGTAAAAGAA 57.347 34.783 31.54 0.00 0.00 2.52
26 27 5.652994 AATAAGGCGCCAAATGTAAAAGA 57.347 34.783 31.54 0.00 0.00 2.52
27 28 5.637387 ACAAATAAGGCGCCAAATGTAAAAG 59.363 36.000 31.54 10.47 0.00 2.27
28 29 5.542779 ACAAATAAGGCGCCAAATGTAAAA 58.457 33.333 31.54 2.53 0.00 1.52
30 31 4.792521 ACAAATAAGGCGCCAAATGTAA 57.207 36.364 31.54 5.46 0.00 2.41
31 32 4.792521 AACAAATAAGGCGCCAAATGTA 57.207 36.364 31.54 12.54 0.00 2.29
32 33 3.676291 AACAAATAAGGCGCCAAATGT 57.324 38.095 31.54 21.62 0.00 2.71
33 34 4.489810 TGTAACAAATAAGGCGCCAAATG 58.510 39.130 31.54 20.96 0.00 2.32
34 35 4.743493 CTGTAACAAATAAGGCGCCAAAT 58.257 39.130 31.54 18.72 0.00 2.32
35 36 3.612955 GCTGTAACAAATAAGGCGCCAAA 60.613 43.478 31.54 17.02 0.00 3.28
37 38 1.470890 GCTGTAACAAATAAGGCGCCA 59.529 47.619 31.54 9.64 0.00 5.69
38 39 1.202256 GGCTGTAACAAATAAGGCGCC 60.202 52.381 21.89 21.89 0.00 6.53
39 40 1.202256 GGGCTGTAACAAATAAGGCGC 60.202 52.381 0.00 0.00 36.15 6.53
42 43 4.157840 GGAACTGGGCTGTAACAAATAAGG 59.842 45.833 0.00 0.00 0.00 2.69
43 44 5.010282 AGGAACTGGGCTGTAACAAATAAG 58.990 41.667 0.00 0.00 37.18 1.73
44 45 4.993028 AGGAACTGGGCTGTAACAAATAA 58.007 39.130 0.00 0.00 37.18 1.40
46 47 3.525800 AGGAACTGGGCTGTAACAAAT 57.474 42.857 0.00 0.00 37.18 2.32
47 48 3.306472 AAGGAACTGGGCTGTAACAAA 57.694 42.857 0.00 0.00 40.86 2.83
48 49 3.306472 AAAGGAACTGGGCTGTAACAA 57.694 42.857 0.00 0.00 40.86 2.83
51 52 5.836358 ACAAAATAAAGGAACTGGGCTGTAA 59.164 36.000 0.00 0.00 40.86 2.41
52 53 5.390387 ACAAAATAAAGGAACTGGGCTGTA 58.610 37.500 0.00 0.00 40.86 2.74
53 54 4.223144 ACAAAATAAAGGAACTGGGCTGT 58.777 39.130 0.00 0.00 40.86 4.40
54 55 4.871933 ACAAAATAAAGGAACTGGGCTG 57.128 40.909 0.00 0.00 40.86 4.85
55 56 4.898861 TGAACAAAATAAAGGAACTGGGCT 59.101 37.500 0.00 0.00 40.86 5.19
56 57 5.208463 TGAACAAAATAAAGGAACTGGGC 57.792 39.130 0.00 0.00 40.86 5.36
57 58 5.696270 GCTTGAACAAAATAAAGGAACTGGG 59.304 40.000 0.00 0.00 40.86 4.45
58 59 5.402270 CGCTTGAACAAAATAAAGGAACTGG 59.598 40.000 0.00 0.00 40.86 4.00
60 61 7.010091 CAAACGCTTGAACAAAATAAAGGAACT 59.990 33.333 0.00 0.00 35.29 3.01
61 62 6.822073 AACGCTTGAACAAAATAAAGGAAC 57.178 33.333 0.00 0.00 0.00 3.62
62 63 6.814146 ACAAACGCTTGAACAAAATAAAGGAA 59.186 30.769 5.39 0.00 36.33 3.36
63 64 6.334202 ACAAACGCTTGAACAAAATAAAGGA 58.666 32.000 5.39 0.00 36.33 3.36
64 65 6.475402 AGACAAACGCTTGAACAAAATAAAGG 59.525 34.615 5.39 0.00 36.33 3.11
65 66 7.449934 AGACAAACGCTTGAACAAAATAAAG 57.550 32.000 5.39 0.00 36.33 1.85
66 67 7.329717 ACAAGACAAACGCTTGAACAAAATAAA 59.670 29.630 5.39 0.00 44.16 1.40
67 68 6.809196 ACAAGACAAACGCTTGAACAAAATAA 59.191 30.769 5.39 0.00 44.16 1.40
68 69 6.326375 ACAAGACAAACGCTTGAACAAAATA 58.674 32.000 5.39 0.00 44.16 1.40
69 70 5.167845 ACAAGACAAACGCTTGAACAAAAT 58.832 33.333 5.39 0.00 44.16 1.82
70 71 4.551388 ACAAGACAAACGCTTGAACAAAA 58.449 34.783 5.39 0.00 44.16 2.44
71 72 4.167554 ACAAGACAAACGCTTGAACAAA 57.832 36.364 5.39 0.00 44.16 2.83
72 73 3.840890 ACAAGACAAACGCTTGAACAA 57.159 38.095 5.39 0.00 44.16 2.83
73 74 3.840890 AACAAGACAAACGCTTGAACA 57.159 38.095 5.39 0.00 44.16 3.18
75 76 9.176181 GATATTTTAACAAGACAAACGCTTGAA 57.824 29.630 5.39 0.00 44.16 2.69
77 78 7.061789 GGGATATTTTAACAAGACAAACGCTTG 59.938 37.037 0.00 0.00 46.20 4.01
78 79 7.088272 GGGATATTTTAACAAGACAAACGCTT 58.912 34.615 0.00 0.00 0.00 4.68
80 81 6.383415 TGGGATATTTTAACAAGACAAACGC 58.617 36.000 0.00 0.00 0.00 4.84
83 84 7.821846 GGCAATGGGATATTTTAACAAGACAAA 59.178 33.333 0.00 0.00 0.00 2.83
84 85 7.180051 AGGCAATGGGATATTTTAACAAGACAA 59.820 33.333 0.00 0.00 0.00 3.18
85 86 6.667414 AGGCAATGGGATATTTTAACAAGACA 59.333 34.615 0.00 0.00 0.00 3.41
88 89 6.282930 CCAGGCAATGGGATATTTTAACAAG 58.717 40.000 0.00 0.00 46.36 3.16
89 90 6.232581 CCAGGCAATGGGATATTTTAACAA 57.767 37.500 0.00 0.00 46.36 2.83
90 91 5.867903 CCAGGCAATGGGATATTTTAACA 57.132 39.130 0.00 0.00 46.36 2.41
106 107 3.170672 AGACCACAGTGCCAGGCA 61.171 61.111 11.22 11.22 35.60 4.75
107 108 2.670934 CAGACCACAGTGCCAGGC 60.671 66.667 3.66 3.66 0.00 4.85
108 109 2.670934 GCAGACCACAGTGCCAGG 60.671 66.667 0.00 0.00 33.29 4.45
109 110 0.892358 AATGCAGACCACAGTGCCAG 60.892 55.000 0.00 0.00 39.04 4.85
111 112 1.533625 TAAATGCAGACCACAGTGCC 58.466 50.000 0.00 0.00 39.04 5.01
112 113 3.242870 GCTATAAATGCAGACCACAGTGC 60.243 47.826 0.00 0.00 40.29 4.40
113 114 3.001634 CGCTATAAATGCAGACCACAGTG 59.998 47.826 0.00 0.00 0.00 3.66
115 116 2.032549 GCGCTATAAATGCAGACCACAG 60.033 50.000 0.00 0.00 0.00 3.66
116 117 1.939934 GCGCTATAAATGCAGACCACA 59.060 47.619 0.00 0.00 0.00 4.17
117 118 1.939934 TGCGCTATAAATGCAGACCAC 59.060 47.619 9.73 0.00 34.03 4.16
120 121 2.578495 GCATGCGCTATAAATGCAGAC 58.422 47.619 20.87 0.00 44.83 3.51
133 134 4.527157 GCAGACGGAAGCATGCGC 62.527 66.667 13.01 8.60 45.18 6.09
134 135 2.816958 AGCAGACGGAAGCATGCG 60.817 61.111 13.01 0.00 46.87 4.73
137 138 2.437359 GCCAGCAGACGGAAGCAT 60.437 61.111 0.00 0.00 0.00 3.79
139 140 4.742201 TCGCCAGCAGACGGAAGC 62.742 66.667 0.00 0.00 0.00 3.86
141 142 2.357034 GTTCGCCAGCAGACGGAA 60.357 61.111 0.00 0.00 0.00 4.30
142 143 3.611674 TGTTCGCCAGCAGACGGA 61.612 61.111 0.00 0.00 0.00 4.69
143 144 3.414700 GTGTTCGCCAGCAGACGG 61.415 66.667 0.00 0.00 0.00 4.79
145 146 0.880278 TTCTGTGTTCGCCAGCAGAC 60.880 55.000 0.00 0.00 37.66 3.51
146 147 0.601046 CTTCTGTGTTCGCCAGCAGA 60.601 55.000 0.00 0.00 36.35 4.26
147 148 0.882042 ACTTCTGTGTTCGCCAGCAG 60.882 55.000 0.00 0.00 30.78 4.24
148 149 0.391228 TACTTCTGTGTTCGCCAGCA 59.609 50.000 0.00 0.00 0.00 4.41
149 150 1.726853 ATACTTCTGTGTTCGCCAGC 58.273 50.000 0.00 0.00 0.00 4.85
150 151 5.175856 GCTATAATACTTCTGTGTTCGCCAG 59.824 44.000 0.00 0.00 0.00 4.85
151 152 5.047847 GCTATAATACTTCTGTGTTCGCCA 58.952 41.667 0.00 0.00 0.00 5.69
152 153 5.047847 TGCTATAATACTTCTGTGTTCGCC 58.952 41.667 0.00 0.00 0.00 5.54
153 154 6.771188 ATGCTATAATACTTCTGTGTTCGC 57.229 37.500 0.00 0.00 0.00 4.70
154 155 7.595130 TGCTATGCTATAATACTTCTGTGTTCG 59.405 37.037 0.00 0.00 0.00 3.95
155 156 8.818141 TGCTATGCTATAATACTTCTGTGTTC 57.182 34.615 0.00 0.00 0.00 3.18
156 157 9.212641 CATGCTATGCTATAATACTTCTGTGTT 57.787 33.333 0.00 0.00 0.00 3.32
164 165 9.539825 GCAGTAATCATGCTATGCTATAATACT 57.460 33.333 0.00 0.00 40.59 2.12
178 179 5.289434 GCAAAAAGGTTAGCAGTAATCATGC 59.711 40.000 0.00 0.00 44.18 4.06
179 180 5.807011 GGCAAAAAGGTTAGCAGTAATCATG 59.193 40.000 0.00 0.00 0.00 3.07
181 182 4.083003 CGGCAAAAAGGTTAGCAGTAATCA 60.083 41.667 0.00 0.00 0.00 2.57
182 183 4.082949 ACGGCAAAAAGGTTAGCAGTAATC 60.083 41.667 0.00 0.00 33.80 1.75
184 185 3.215975 ACGGCAAAAAGGTTAGCAGTAA 58.784 40.909 0.00 0.00 33.80 2.24
187 188 2.793278 AACGGCAAAAAGGTTAGCAG 57.207 45.000 0.00 0.00 0.00 4.24
189 190 3.449632 TGAAAACGGCAAAAAGGTTAGC 58.550 40.909 0.00 0.00 0.00 3.09
190 191 6.256757 TCATTTGAAAACGGCAAAAAGGTTAG 59.743 34.615 0.00 0.00 38.57 2.34
191 192 6.106673 TCATTTGAAAACGGCAAAAAGGTTA 58.893 32.000 0.00 0.00 38.57 2.85
192 193 4.938226 TCATTTGAAAACGGCAAAAAGGTT 59.062 33.333 0.00 0.00 38.57 3.50
193 194 4.508662 TCATTTGAAAACGGCAAAAAGGT 58.491 34.783 0.00 0.00 38.57 3.50
194 195 5.671742 ATCATTTGAAAACGGCAAAAAGG 57.328 34.783 0.00 0.00 38.57 3.11
195 196 7.168972 TGAGTATCATTTGAAAACGGCAAAAAG 59.831 33.333 0.00 0.00 42.56 2.27
196 197 6.980978 TGAGTATCATTTGAAAACGGCAAAAA 59.019 30.769 0.00 0.00 42.56 1.94
197 198 6.507900 TGAGTATCATTTGAAAACGGCAAAA 58.492 32.000 0.00 0.00 42.56 2.44
198 199 6.078202 TGAGTATCATTTGAAAACGGCAAA 57.922 33.333 0.00 0.00 42.56 3.68
199 200 5.697473 TGAGTATCATTTGAAAACGGCAA 57.303 34.783 0.00 0.00 42.56 4.52
217 218 4.468153 GGAGTAGAGATTTTGGGACTGAGT 59.532 45.833 0.00 0.00 0.00 3.41
219 220 4.689062 AGGAGTAGAGATTTTGGGACTGA 58.311 43.478 0.00 0.00 0.00 3.41
220 221 6.546428 TTAGGAGTAGAGATTTTGGGACTG 57.454 41.667 0.00 0.00 0.00 3.51
221 222 6.674419 ACATTAGGAGTAGAGATTTTGGGACT 59.326 38.462 0.00 0.00 0.00 3.85
222 223 6.890293 ACATTAGGAGTAGAGATTTTGGGAC 58.110 40.000 0.00 0.00 0.00 4.46
223 224 6.903534 AGACATTAGGAGTAGAGATTTTGGGA 59.096 38.462 0.00 0.00 0.00 4.37
224 225 7.130681 AGACATTAGGAGTAGAGATTTTGGG 57.869 40.000 0.00 0.00 0.00 4.12
226 227 9.829507 AATGAGACATTAGGAGTAGAGATTTTG 57.170 33.333 0.00 0.00 0.00 2.44
251 252 5.276161 GGAAACGAACGAACAACTTACGTAA 60.276 40.000 7.94 7.94 39.31 3.18
892 930 1.906995 TGCCGATGCAGAGGATCAA 59.093 52.632 13.76 0.00 44.23 2.57
1832 1930 5.049405 ACGTCTTGTTTTTCAGATGATCCAC 60.049 40.000 0.00 0.00 0.00 4.02
2410 2532 9.671279 TCTGAACAAATATACTCACATCACAAT 57.329 29.630 0.00 0.00 0.00 2.71
2576 2720 6.432472 TGTTATGCATCCATCAGTACACAAAA 59.568 34.615 0.19 0.00 32.85 2.44
3274 3427 7.437713 ACACTGAACCTTTATCATCCTATCA 57.562 36.000 0.00 0.00 0.00 2.15
3428 3581 9.616634 CTGGAACATATTGCATCATACAAATAC 57.383 33.333 0.00 0.00 38.20 1.89


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

AutoCloner maintained by Alex Coulton.