Multiple sequence alignment - TraesCS1A01G124300

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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 TraesCS1A01G124300 chr1A 100.000 3918 0 0 1 3918 146943702 146947619 0.000000e+00 7236.0
1 TraesCS1A01G124300 chr1A 96.571 175 6 0 1 175 540890088 540890262 1.380000e-74 291.0
2 TraesCS1A01G124300 chr1B 97.166 2752 63 4 404 3150 192276834 192274093 0.000000e+00 4636.0
3 TraesCS1A01G124300 chr1B 94.167 720 21 5 3207 3917 192274096 192273389 0.000000e+00 1077.0
4 TraesCS1A01G124300 chr1B 93.750 64 3 1 768 830 470588418 470588481 1.160000e-15 95.3
5 TraesCS1A01G124300 chr1D 96.575 1664 43 3 1387 3045 143258445 143256791 0.000000e+00 2745.0
6 TraesCS1A01G124300 chr1D 97.094 1170 32 1 224 1391 143264197 143263028 0.000000e+00 1971.0
7 TraesCS1A01G124300 chr1D 92.905 888 16 14 3050 3917 143256814 143255954 0.000000e+00 1247.0
8 TraesCS1A01G124300 chr7D 88.596 2087 175 28 547 2588 113448692 113446624 0.000000e+00 2477.0
9 TraesCS1A01G124300 chr7D 85.872 453 44 13 2649 3097 113446630 113446194 7.670000e-127 464.0
10 TraesCS1A01G124300 chr7D 92.623 122 8 1 396 516 113448812 113448691 1.450000e-39 174.0
11 TraesCS1A01G124300 chr7B 88.128 2089 171 32 547 2588 73137267 73135209 0.000000e+00 2412.0
12 TraesCS1A01G124300 chr7B 83.297 455 52 17 2649 3097 73135215 73134779 7.890000e-107 398.0
13 TraesCS1A01G124300 chr7B 92.265 181 11 3 1 179 290248022 290247843 1.810000e-63 254.0
14 TraesCS1A01G124300 chr7B 92.135 178 12 2 1 177 54898063 54897887 2.340000e-62 250.0
15 TraesCS1A01G124300 chr7A 89.553 1254 105 10 1355 2588 118464060 118462813 0.000000e+00 1567.0
16 TraesCS1A01G124300 chr7A 85.373 964 87 21 399 1317 118465019 118464065 0.000000e+00 950.0
17 TraesCS1A01G124300 chr7A 84.683 457 44 17 2649 3097 118462819 118462381 2.160000e-117 433.0
18 TraesCS1A01G124300 chr6A 83.789 950 88 21 476 1395 588864299 588863386 0.000000e+00 841.0
19 TraesCS1A01G124300 chr6A 93.820 178 9 1 1 176 499621968 499622145 2.320000e-67 267.0
20 TraesCS1A01G124300 chr6A 93.714 175 11 0 1 175 534981961 534981787 3.000000e-66 263.0
21 TraesCS1A01G124300 chr2A 97.143 175 5 0 1 175 346060676 346060502 2.960000e-76 296.0
22 TraesCS1A01G124300 chr2A 95.429 175 8 0 1 175 8452713 8452539 2.980000e-71 279.0
23 TraesCS1A01G124300 chr3A 94.857 175 9 0 1 175 125482865 125483039 1.390000e-69 274.0
24 TraesCS1A01G124300 chr3D 91.160 181 11 5 2 179 486686804 486686626 1.410000e-59 241.0
25 TraesCS1A01G124300 chr6B 93.750 64 3 1 768 830 22744494 22744557 1.160000e-15 95.3
26 TraesCS1A01G124300 chr6B 86.170 94 3 3 768 860 71751603 71751687 4.170000e-15 93.5


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 TraesCS1A01G124300 chr1A 146943702 146947619 3917 False 7236.000000 7236 100.000000 1 3918 1 chr1A.!!$F1 3917
1 TraesCS1A01G124300 chr1B 192273389 192276834 3445 True 2856.500000 4636 95.666500 404 3917 2 chr1B.!!$R1 3513
2 TraesCS1A01G124300 chr1D 143255954 143258445 2491 True 1996.000000 2745 94.740000 1387 3917 2 chr1D.!!$R2 2530
3 TraesCS1A01G124300 chr1D 143263028 143264197 1169 True 1971.000000 1971 97.094000 224 1391 1 chr1D.!!$R1 1167
4 TraesCS1A01G124300 chr7D 113446194 113448812 2618 True 1038.333333 2477 89.030333 396 3097 3 chr7D.!!$R1 2701
5 TraesCS1A01G124300 chr7B 73134779 73137267 2488 True 1405.000000 2412 85.712500 547 3097 2 chr7B.!!$R3 2550
6 TraesCS1A01G124300 chr7A 118462381 118465019 2638 True 983.333333 1567 86.536333 399 3097 3 chr7A.!!$R1 2698
7 TraesCS1A01G124300 chr6A 588863386 588864299 913 True 841.000000 841 83.789000 476 1395 1 chr6A.!!$R2 919

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
216 217 0.036388 ACTGACATAAGGTGGTGGCG 60.036 55.000 0.0 0.0 0.00 5.69 F
217 218 0.036388 CTGACATAAGGTGGTGGCGT 60.036 55.000 0.0 0.0 0.00 5.68 F
220 221 0.109723 ACATAAGGTGGTGGCGTGTT 59.890 50.000 0.0 0.0 0.00 3.32 F
293 294 0.608640 CCCTAGCAACGACCAGAAGT 59.391 55.000 0.0 0.0 0.00 3.01 F
1455 1519 1.001974 TGCCTGACGAAGCATGTAACT 59.998 47.619 0.0 0.0 33.08 2.24 F
2147 2233 1.141657 GCCTATCAATCAGAGCACCCA 59.858 52.381 0.0 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 1524 0.544833 ACTGGATTTGCATGGGCCAA 60.545 50.000 11.89 0.0 40.13 4.52 R
1713 1780 1.691196 CAGGAGTTCTGCCACCAAAA 58.309 50.000 0.00 0.0 36.60 2.44 R
2147 2233 2.757077 GGTGTTGGGGCTAGTGCT 59.243 61.111 0.00 0.0 39.59 4.40 R
2245 2331 3.411454 AGATTCTCAGTCCCATCCTCA 57.589 47.619 0.00 0.0 0.00 3.86 R
2419 2505 1.680651 CTTTGCATAACCCCGCCCA 60.681 57.895 0.00 0.0 0.00 5.36 R
3831 3946 0.466922 CATGAACTCCATCCTGGGGC 60.467 60.000 0.00 0.0 43.56 5.80 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
17 18 2.657237 GGTGGCTAGCGAGTGTGT 59.343 61.111 9.00 0.00 0.00 3.72
18 19 1.888018 GGTGGCTAGCGAGTGTGTA 59.112 57.895 9.00 0.00 0.00 2.90
19 20 0.460311 GGTGGCTAGCGAGTGTGTAT 59.540 55.000 9.00 0.00 0.00 2.29
20 21 1.536284 GGTGGCTAGCGAGTGTGTATC 60.536 57.143 9.00 0.00 0.00 2.24
21 22 1.134367 GTGGCTAGCGAGTGTGTATCA 59.866 52.381 9.00 0.00 0.00 2.15
22 23 1.134367 TGGCTAGCGAGTGTGTATCAC 59.866 52.381 9.00 0.00 46.46 3.06
33 34 4.373348 GTGTGTATCACTACTGGAGGTC 57.627 50.000 0.00 0.00 43.13 3.85
34 35 3.014623 TGTGTATCACTACTGGAGGTCG 58.985 50.000 0.00 0.00 35.11 4.79
35 36 3.015327 GTGTATCACTACTGGAGGTCGT 58.985 50.000 0.00 0.00 0.00 4.34
36 37 4.194640 GTGTATCACTACTGGAGGTCGTA 58.805 47.826 0.00 0.00 0.00 3.43
37 38 4.272991 GTGTATCACTACTGGAGGTCGTAG 59.727 50.000 0.00 0.00 39.14 3.51
38 39 2.414994 TCACTACTGGAGGTCGTAGG 57.585 55.000 0.00 0.00 37.90 3.18
39 40 1.632409 TCACTACTGGAGGTCGTAGGT 59.368 52.381 0.00 0.00 37.90 3.08
40 41 2.040813 TCACTACTGGAGGTCGTAGGTT 59.959 50.000 0.00 0.00 37.90 3.50
41 42 2.422832 CACTACTGGAGGTCGTAGGTTC 59.577 54.545 0.00 0.00 37.90 3.62
42 43 2.308275 ACTACTGGAGGTCGTAGGTTCT 59.692 50.000 0.00 0.00 37.90 3.01
43 44 3.521126 ACTACTGGAGGTCGTAGGTTCTA 59.479 47.826 0.00 0.00 37.90 2.10
44 45 3.666345 ACTGGAGGTCGTAGGTTCTAT 57.334 47.619 0.00 0.00 0.00 1.98
45 46 3.553904 ACTGGAGGTCGTAGGTTCTATC 58.446 50.000 0.00 0.00 0.00 2.08
46 47 2.885894 CTGGAGGTCGTAGGTTCTATCC 59.114 54.545 0.00 0.00 0.00 2.59
47 48 2.237643 GGAGGTCGTAGGTTCTATCCC 58.762 57.143 0.00 0.00 0.00 3.85
48 49 2.158490 GGAGGTCGTAGGTTCTATCCCT 60.158 54.545 0.00 0.00 36.04 4.20
49 50 3.073650 GGAGGTCGTAGGTTCTATCCCTA 59.926 52.174 0.00 0.00 33.35 3.53
50 51 4.325972 GAGGTCGTAGGTTCTATCCCTAG 58.674 52.174 0.00 0.00 35.26 3.02
51 52 2.819019 GGTCGTAGGTTCTATCCCTAGC 59.181 54.545 0.00 0.00 35.26 3.42
52 53 2.483491 GTCGTAGGTTCTATCCCTAGCG 59.517 54.545 0.00 0.00 35.26 4.26
53 54 1.199558 CGTAGGTTCTATCCCTAGCGC 59.800 57.143 0.00 0.00 35.26 5.92
54 55 1.545136 GTAGGTTCTATCCCTAGCGCC 59.455 57.143 2.29 0.00 35.26 6.53
55 56 0.105658 AGGTTCTATCCCTAGCGCCA 60.106 55.000 2.29 0.00 0.00 5.69
56 57 0.977395 GGTTCTATCCCTAGCGCCAT 59.023 55.000 2.29 0.00 0.00 4.40
57 58 1.348036 GGTTCTATCCCTAGCGCCATT 59.652 52.381 2.29 0.00 0.00 3.16
58 59 2.417719 GTTCTATCCCTAGCGCCATTG 58.582 52.381 2.29 0.00 0.00 2.82
59 60 0.976641 TCTATCCCTAGCGCCATTGG 59.023 55.000 2.29 0.00 0.00 3.16
60 61 0.687354 CTATCCCTAGCGCCATTGGT 59.313 55.000 2.29 0.00 0.00 3.67
61 62 1.072331 CTATCCCTAGCGCCATTGGTT 59.928 52.381 2.29 0.00 0.00 3.67
62 63 0.258774 ATCCCTAGCGCCATTGGTTT 59.741 50.000 2.29 0.00 0.00 3.27
63 64 0.039035 TCCCTAGCGCCATTGGTTTT 59.961 50.000 2.29 0.00 0.00 2.43
64 65 0.894835 CCCTAGCGCCATTGGTTTTT 59.105 50.000 2.29 0.00 0.00 1.94
83 84 2.956964 GCGGTTCATCTCGCGAGG 60.957 66.667 33.98 20.09 42.48 4.63
84 85 2.956964 CGGTTCATCTCGCGAGGC 60.957 66.667 33.98 18.62 0.00 4.70
95 96 4.185413 GCGAGGCGAAATCACTCA 57.815 55.556 0.00 0.00 0.00 3.41
96 97 2.456000 GCGAGGCGAAATCACTCAA 58.544 52.632 0.00 0.00 0.00 3.02
97 98 0.796312 GCGAGGCGAAATCACTCAAA 59.204 50.000 0.00 0.00 0.00 2.69
98 99 1.398390 GCGAGGCGAAATCACTCAAAT 59.602 47.619 0.00 0.00 0.00 2.32
99 100 2.159517 GCGAGGCGAAATCACTCAAATT 60.160 45.455 0.00 0.00 0.00 1.82
100 101 3.419915 CGAGGCGAAATCACTCAAATTG 58.580 45.455 0.00 0.00 0.00 2.32
101 102 3.728864 CGAGGCGAAATCACTCAAATTGG 60.729 47.826 0.00 0.00 0.00 3.16
102 103 2.094545 AGGCGAAATCACTCAAATTGGC 60.095 45.455 0.00 0.00 0.00 4.52
103 104 2.262211 GCGAAATCACTCAAATTGGCC 58.738 47.619 0.00 0.00 0.00 5.36
104 105 2.518949 CGAAATCACTCAAATTGGCCG 58.481 47.619 0.00 0.00 0.00 6.13
105 106 2.731968 CGAAATCACTCAAATTGGCCGG 60.732 50.000 0.00 0.00 0.00 6.13
106 107 0.532115 AATCACTCAAATTGGCCGGC 59.468 50.000 21.18 21.18 0.00 6.13
107 108 1.322538 ATCACTCAAATTGGCCGGCC 61.323 55.000 39.40 39.40 0.00 6.13
108 109 2.679996 ACTCAAATTGGCCGGCCC 60.680 61.111 41.75 24.44 34.56 5.80
109 110 2.679642 CTCAAATTGGCCGGCCCA 60.680 61.111 41.75 33.21 43.51 5.36
110 111 2.679642 TCAAATTGGCCGGCCCAG 60.680 61.111 41.75 25.39 46.39 4.45
111 112 3.773404 CAAATTGGCCGGCCCAGG 61.773 66.667 41.75 22.61 46.39 4.45
146 147 3.374330 CGAAGCGGCGACTACTTG 58.626 61.111 12.98 0.00 0.00 3.16
147 148 2.789203 CGAAGCGGCGACTACTTGC 61.789 63.158 12.98 0.00 0.00 4.01
153 154 2.432628 GCGACTACTTGCCGCAGT 60.433 61.111 0.00 0.00 46.67 4.40
154 155 1.153901 GCGACTACTTGCCGCAGTA 60.154 57.895 0.00 0.00 46.67 2.74
155 156 0.734942 GCGACTACTTGCCGCAGTAA 60.735 55.000 0.00 0.00 46.67 2.24
156 157 1.269166 CGACTACTTGCCGCAGTAAG 58.731 55.000 0.00 0.00 41.13 2.34
157 158 1.000145 GACTACTTGCCGCAGTAAGC 59.000 55.000 0.00 0.00 39.14 3.09
167 168 2.226269 GCAGTAAGCGGCGAATAGG 58.774 57.895 12.98 0.00 0.00 2.57
168 169 1.222115 GCAGTAAGCGGCGAATAGGG 61.222 60.000 12.98 0.00 0.00 3.53
169 170 0.387929 CAGTAAGCGGCGAATAGGGA 59.612 55.000 12.98 0.00 0.00 4.20
170 171 1.117150 AGTAAGCGGCGAATAGGGAA 58.883 50.000 12.98 0.00 0.00 3.97
171 172 1.692519 AGTAAGCGGCGAATAGGGAAT 59.307 47.619 12.98 0.00 0.00 3.01
172 173 2.104281 AGTAAGCGGCGAATAGGGAATT 59.896 45.455 12.98 0.00 0.00 2.17
173 174 1.594331 AAGCGGCGAATAGGGAATTC 58.406 50.000 12.98 0.00 40.63 2.17
174 175 0.250338 AGCGGCGAATAGGGAATTCC 60.250 55.000 16.74 16.74 40.91 3.01
176 177 1.797025 CGGCGAATAGGGAATTCCTC 58.203 55.000 23.63 13.78 44.06 3.71
177 178 1.608283 CGGCGAATAGGGAATTCCTCC 60.608 57.143 23.63 8.50 44.06 4.30
178 179 1.700186 GGCGAATAGGGAATTCCTCCT 59.300 52.381 23.63 15.35 44.06 3.69
179 180 2.551071 GGCGAATAGGGAATTCCTCCTG 60.551 54.545 23.63 10.32 44.06 3.86
180 181 2.551071 GCGAATAGGGAATTCCTCCTGG 60.551 54.545 23.63 10.32 44.06 4.45
181 182 2.551071 CGAATAGGGAATTCCTCCTGGC 60.551 54.545 23.63 6.26 44.06 4.85
182 183 2.212752 ATAGGGAATTCCTCCTGGCA 57.787 50.000 23.63 0.00 44.06 4.92
183 184 1.511613 TAGGGAATTCCTCCTGGCAG 58.488 55.000 23.63 7.75 44.06 4.85
184 185 0.253347 AGGGAATTCCTCCTGGCAGA 60.253 55.000 23.63 0.95 44.06 4.26
185 186 0.106967 GGGAATTCCTCCTGGCAGAC 60.107 60.000 23.63 0.00 44.68 3.51
186 187 0.462759 GGAATTCCTCCTGGCAGACG 60.463 60.000 17.94 6.03 41.61 4.18
187 188 1.078143 AATTCCTCCTGGCAGACGC 60.078 57.895 17.94 0.00 37.44 5.19
203 204 3.936203 GCCCCCACACGACTGACA 61.936 66.667 0.00 0.00 0.00 3.58
204 205 3.068881 CCCCCACACGACTGACAT 58.931 61.111 0.00 0.00 0.00 3.06
205 206 1.895020 GCCCCCACACGACTGACATA 61.895 60.000 0.00 0.00 0.00 2.29
206 207 0.611200 CCCCCACACGACTGACATAA 59.389 55.000 0.00 0.00 0.00 1.90
207 208 1.405526 CCCCCACACGACTGACATAAG 60.406 57.143 0.00 0.00 0.00 1.73
208 209 1.405526 CCCCACACGACTGACATAAGG 60.406 57.143 0.00 0.00 0.00 2.69
209 210 1.275291 CCCACACGACTGACATAAGGT 59.725 52.381 0.00 0.00 0.00 3.50
210 211 2.337583 CCACACGACTGACATAAGGTG 58.662 52.381 0.00 0.00 0.00 4.00
211 212 2.337583 CACACGACTGACATAAGGTGG 58.662 52.381 0.00 0.00 0.00 4.61
212 213 1.968493 ACACGACTGACATAAGGTGGT 59.032 47.619 0.00 0.00 0.00 4.16
213 214 2.288825 ACACGACTGACATAAGGTGGTG 60.289 50.000 6.27 6.27 42.45 4.17
214 215 1.275291 ACGACTGACATAAGGTGGTGG 59.725 52.381 0.00 0.00 0.00 4.61
215 216 1.739067 GACTGACATAAGGTGGTGGC 58.261 55.000 0.00 0.00 0.00 5.01
216 217 0.036388 ACTGACATAAGGTGGTGGCG 60.036 55.000 0.00 0.00 0.00 5.69
217 218 0.036388 CTGACATAAGGTGGTGGCGT 60.036 55.000 0.00 0.00 0.00 5.68
218 219 0.321210 TGACATAAGGTGGTGGCGTG 60.321 55.000 0.00 0.00 0.00 5.34
219 220 0.321298 GACATAAGGTGGTGGCGTGT 60.321 55.000 0.00 0.00 0.00 4.49
220 221 0.109723 ACATAAGGTGGTGGCGTGTT 59.890 50.000 0.00 0.00 0.00 3.32
221 222 0.802494 CATAAGGTGGTGGCGTGTTC 59.198 55.000 0.00 0.00 0.00 3.18
222 223 0.690762 ATAAGGTGGTGGCGTGTTCT 59.309 50.000 0.00 0.00 0.00 3.01
293 294 0.608640 CCCTAGCAACGACCAGAAGT 59.391 55.000 0.00 0.00 0.00 3.01
314 315 2.668550 GCCTCGCACGAAAACCCT 60.669 61.111 0.00 0.00 0.00 4.34
496 500 4.648762 TCTCCTTTCTCAGCTAAGATCCTG 59.351 45.833 0.00 0.00 0.00 3.86
600 604 8.743085 ATGATTTGTCATTAGCACTGATAAGT 57.257 30.769 0.00 0.00 0.00 2.24
687 700 1.279271 CAAGGTTAGTGGGTCTGGAGG 59.721 57.143 0.00 0.00 0.00 4.30
957 990 3.492102 AGCAACCTGAGCTAAGAACAA 57.508 42.857 0.00 0.00 41.32 2.83
1051 1090 3.074412 GCACCAACAGCACATACTAAGT 58.926 45.455 0.00 0.00 0.00 2.24
1258 1317 5.801444 CACGACGACACAAAGGTATGTATAA 59.199 40.000 0.00 0.00 30.84 0.98
1455 1519 1.001974 TGCCTGACGAAGCATGTAACT 59.998 47.619 0.00 0.00 33.08 2.24
1460 1524 4.452455 CCTGACGAAGCATGTAACTTTCTT 59.548 41.667 0.00 0.00 0.00 2.52
2147 2233 1.141657 GCCTATCAATCAGAGCACCCA 59.858 52.381 0.00 0.00 0.00 4.51
2245 2331 1.453155 GGGACGACTGCATGTCAATT 58.547 50.000 13.71 0.87 45.60 2.32
2419 2505 1.134401 CGTATCAAGACATGGCAGGGT 60.134 52.381 0.00 0.00 0.00 4.34
2443 2529 3.320826 GGCGGGGTTATGCAAAGAATATT 59.679 43.478 0.00 0.00 0.00 1.28
2708 2800 1.028868 GGCTGTGGAGGTGAGCAATC 61.029 60.000 0.00 0.00 34.20 2.67
2975 3067 4.140994 AGGCCTGCCTAGTAGTAGTTGATA 60.141 45.833 9.42 0.00 46.14 2.15
2990 3082 7.862675 AGTAGTTGATAAGCAGAAAGGGTTAT 58.137 34.615 0.00 0.00 42.39 1.89
2999 3092 3.365969 GCAGAAAGGGTTATGTGTTTCGG 60.366 47.826 0.00 0.00 34.69 4.30
3002 3095 5.646360 CAGAAAGGGTTATGTGTTTCGGTAT 59.354 40.000 0.00 0.00 34.69 2.73
3028 3124 3.055530 TCCTCTGATTCTCCAAGTGAAGC 60.056 47.826 0.00 0.00 0.00 3.86
3151 3247 1.134877 GGGCTTACGGTGAAGAGTACC 60.135 57.143 0.00 0.00 34.81 3.34
3322 3418 9.480053 CTTTTCTCTGGCTGATTATTTTCAAAA 57.520 29.630 0.00 0.00 0.00 2.44
3370 3466 0.179127 CGAAGAGAAGAGATGCGGCA 60.179 55.000 4.58 4.58 0.00 5.69
3473 3569 5.063204 ACTCAGTATGCAGTTGCTAAAACA 58.937 37.500 5.62 0.00 42.66 2.83
3596 3692 7.029563 GGTTGAACATAGCCTTCAAATTGTAG 58.970 38.462 0.00 0.00 38.92 2.74
3597 3693 7.309194 GGTTGAACATAGCCTTCAAATTGTAGT 60.309 37.037 0.00 0.00 38.92 2.73
3598 3694 8.726988 GTTGAACATAGCCTTCAAATTGTAGTA 58.273 33.333 0.00 0.00 38.92 1.82
3826 3941 2.203153 AACGGTGTGTGACAGCCC 60.203 61.111 0.00 0.00 43.18 5.19
3827 3942 3.767630 AACGGTGTGTGACAGCCCC 62.768 63.158 0.00 0.00 43.18 5.80
3828 3943 4.248842 CGGTGTGTGACAGCCCCA 62.249 66.667 0.00 0.00 43.18 4.96
3829 3944 2.594592 GGTGTGTGACAGCCCCAC 60.595 66.667 0.00 0.00 40.47 4.61
3830 3945 2.510906 GTGTGTGACAGCCCCACT 59.489 61.111 0.00 0.00 35.66 4.00
3917 4032 2.825205 CCAAGCACAAGGAAAAGTTGG 58.175 47.619 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.460311 ATACACACTCGCTAGCCACC 59.540 55.000 9.66 0.00 0.00 4.61
1 2 1.134367 TGATACACACTCGCTAGCCAC 59.866 52.381 9.66 0.00 0.00 5.01
2 3 1.134367 GTGATACACACTCGCTAGCCA 59.866 52.381 9.66 0.00 45.13 4.75
3 4 1.841450 GTGATACACACTCGCTAGCC 58.159 55.000 9.66 0.00 45.13 3.93
13 14 3.014623 CGACCTCCAGTAGTGATACACA 58.985 50.000 0.00 0.00 36.74 3.72
14 15 3.015327 ACGACCTCCAGTAGTGATACAC 58.985 50.000 0.00 0.00 32.48 2.90
15 16 3.361281 ACGACCTCCAGTAGTGATACA 57.639 47.619 0.00 0.00 32.48 2.29
16 17 3.814283 CCTACGACCTCCAGTAGTGATAC 59.186 52.174 0.00 0.00 38.82 2.24
17 18 3.457380 ACCTACGACCTCCAGTAGTGATA 59.543 47.826 0.00 0.00 38.82 2.15
18 19 2.241685 ACCTACGACCTCCAGTAGTGAT 59.758 50.000 0.00 0.00 38.82 3.06
19 20 1.632409 ACCTACGACCTCCAGTAGTGA 59.368 52.381 0.00 0.00 38.82 3.41
20 21 2.125773 ACCTACGACCTCCAGTAGTG 57.874 55.000 0.00 0.00 38.82 2.74
21 22 2.308275 AGAACCTACGACCTCCAGTAGT 59.692 50.000 0.00 0.00 38.82 2.73
22 23 3.002038 AGAACCTACGACCTCCAGTAG 57.998 52.381 0.00 0.00 39.84 2.57
23 24 4.445448 GGATAGAACCTACGACCTCCAGTA 60.445 50.000 0.00 0.00 0.00 2.74
24 25 3.553904 GATAGAACCTACGACCTCCAGT 58.446 50.000 0.00 0.00 0.00 4.00
25 26 2.885894 GGATAGAACCTACGACCTCCAG 59.114 54.545 0.00 0.00 0.00 3.86
26 27 2.423947 GGGATAGAACCTACGACCTCCA 60.424 54.545 0.00 0.00 0.00 3.86
27 28 2.158490 AGGGATAGAACCTACGACCTCC 60.158 54.545 0.00 0.00 36.32 4.30
28 29 3.226682 AGGGATAGAACCTACGACCTC 57.773 52.381 0.00 0.00 36.32 3.85
29 30 3.498301 GCTAGGGATAGAACCTACGACCT 60.498 52.174 0.00 0.00 39.54 3.85
30 31 2.819019 GCTAGGGATAGAACCTACGACC 59.181 54.545 0.00 0.00 39.54 4.79
31 32 2.483491 CGCTAGGGATAGAACCTACGAC 59.517 54.545 0.00 0.00 39.54 4.34
32 33 2.775890 CGCTAGGGATAGAACCTACGA 58.224 52.381 0.00 0.00 39.54 3.43
33 34 1.199558 GCGCTAGGGATAGAACCTACG 59.800 57.143 11.61 0.00 39.54 3.51
34 35 1.545136 GGCGCTAGGGATAGAACCTAC 59.455 57.143 11.61 0.00 39.54 3.18
35 36 1.146359 TGGCGCTAGGGATAGAACCTA 59.854 52.381 11.61 0.00 39.54 3.08
36 37 0.105658 TGGCGCTAGGGATAGAACCT 60.106 55.000 11.61 0.00 42.15 3.50
37 38 0.977395 ATGGCGCTAGGGATAGAACC 59.023 55.000 11.61 1.43 0.00 3.62
38 39 2.417719 CAATGGCGCTAGGGATAGAAC 58.582 52.381 11.61 0.00 0.00 3.01
39 40 1.347707 CCAATGGCGCTAGGGATAGAA 59.652 52.381 11.61 0.00 0.00 2.10
40 41 0.976641 CCAATGGCGCTAGGGATAGA 59.023 55.000 11.61 0.00 0.00 1.98
41 42 0.687354 ACCAATGGCGCTAGGGATAG 59.313 55.000 19.02 0.00 0.00 2.08
42 43 1.136828 AACCAATGGCGCTAGGGATA 58.863 50.000 19.02 0.00 0.00 2.59
43 44 0.258774 AAACCAATGGCGCTAGGGAT 59.741 50.000 19.02 6.26 0.00 3.85
44 45 0.039035 AAAACCAATGGCGCTAGGGA 59.961 50.000 19.02 0.00 0.00 4.20
45 46 0.894835 AAAAACCAATGGCGCTAGGG 59.105 50.000 7.64 10.26 0.00 3.53
67 68 2.956964 GCCTCGCGAGATGAACCG 60.957 66.667 36.59 18.84 40.84 4.44
78 79 0.796312 TTTGAGTGATTTCGCCTCGC 59.204 50.000 0.00 0.00 0.00 5.03
79 80 3.419915 CAATTTGAGTGATTTCGCCTCG 58.580 45.455 0.00 0.00 0.00 4.63
80 81 3.762779 CCAATTTGAGTGATTTCGCCTC 58.237 45.455 0.00 0.00 0.00 4.70
81 82 2.094545 GCCAATTTGAGTGATTTCGCCT 60.095 45.455 0.00 0.00 0.00 5.52
82 83 2.262211 GCCAATTTGAGTGATTTCGCC 58.738 47.619 0.00 0.00 0.00 5.54
83 84 2.262211 GGCCAATTTGAGTGATTTCGC 58.738 47.619 0.00 0.00 0.00 4.70
84 85 2.518949 CGGCCAATTTGAGTGATTTCG 58.481 47.619 2.24 0.00 0.00 3.46
85 86 2.879826 CCGGCCAATTTGAGTGATTTC 58.120 47.619 2.24 0.00 0.00 2.17
86 87 1.066929 GCCGGCCAATTTGAGTGATTT 60.067 47.619 18.11 0.00 0.00 2.17
87 88 0.532115 GCCGGCCAATTTGAGTGATT 59.468 50.000 18.11 0.00 0.00 2.57
88 89 1.322538 GGCCGGCCAATTTGAGTGAT 61.323 55.000 40.73 0.00 35.81 3.06
89 90 1.976474 GGCCGGCCAATTTGAGTGA 60.976 57.895 40.73 0.00 35.81 3.41
90 91 2.573340 GGCCGGCCAATTTGAGTG 59.427 61.111 40.73 0.00 35.81 3.51
91 92 2.679996 GGGCCGGCCAATTTGAGT 60.680 61.111 44.46 0.00 37.98 3.41
92 93 2.679642 TGGGCCGGCCAATTTGAG 60.680 61.111 44.46 0.00 37.98 3.02
93 94 2.679642 CTGGGCCGGCCAATTTGA 60.680 61.111 44.46 20.23 37.98 2.69
94 95 3.773404 CCTGGGCCGGCCAATTTG 61.773 66.667 44.46 27.18 37.98 2.32
124 125 3.964221 TAGTCGCCGCTTCGCACAG 62.964 63.158 0.00 0.00 0.00 3.66
125 126 4.045771 TAGTCGCCGCTTCGCACA 62.046 61.111 0.00 0.00 0.00 4.57
126 127 3.542742 GTAGTCGCCGCTTCGCAC 61.543 66.667 0.00 0.00 0.00 5.34
127 128 3.277211 AAGTAGTCGCCGCTTCGCA 62.277 57.895 0.00 0.00 0.00 5.10
128 129 2.506438 AAGTAGTCGCCGCTTCGC 60.506 61.111 0.00 0.00 0.00 4.70
129 130 2.789203 GCAAGTAGTCGCCGCTTCG 61.789 63.158 0.00 0.00 0.00 3.79
130 131 2.453638 GGCAAGTAGTCGCCGCTTC 61.454 63.158 0.00 0.00 38.82 3.86
131 132 2.434359 GGCAAGTAGTCGCCGCTT 60.434 61.111 0.00 0.00 38.82 4.68
138 139 1.000145 GCTTACTGCGGCAAGTAGTC 59.000 55.000 3.44 1.88 42.21 2.59
149 150 1.222115 CCCTATTCGCCGCTTACTGC 61.222 60.000 0.00 0.00 38.57 4.40
150 151 0.387929 TCCCTATTCGCCGCTTACTG 59.612 55.000 0.00 0.00 0.00 2.74
151 152 1.117150 TTCCCTATTCGCCGCTTACT 58.883 50.000 0.00 0.00 0.00 2.24
152 153 2.165319 ATTCCCTATTCGCCGCTTAC 57.835 50.000 0.00 0.00 0.00 2.34
153 154 2.549349 GGAATTCCCTATTCGCCGCTTA 60.549 50.000 14.03 0.00 43.01 3.09
154 155 1.594331 GAATTCCCTATTCGCCGCTT 58.406 50.000 0.00 0.00 33.79 4.68
155 156 0.250338 GGAATTCCCTATTCGCCGCT 60.250 55.000 14.03 0.00 43.01 5.52
156 157 0.250338 AGGAATTCCCTATTCGCCGC 60.250 55.000 21.22 0.00 45.48 6.53
168 169 1.092345 GCGTCTGCCAGGAGGAATTC 61.092 60.000 0.00 0.00 36.89 2.17
169 170 1.078143 GCGTCTGCCAGGAGGAATT 60.078 57.895 0.00 0.00 36.89 2.17
170 171 2.586792 GCGTCTGCCAGGAGGAAT 59.413 61.111 0.00 0.00 36.89 3.01
186 187 1.895020 TATGTCAGTCGTGTGGGGGC 61.895 60.000 0.00 0.00 0.00 5.80
187 188 0.611200 TTATGTCAGTCGTGTGGGGG 59.389 55.000 0.00 0.00 0.00 5.40
188 189 1.405526 CCTTATGTCAGTCGTGTGGGG 60.406 57.143 0.00 0.00 0.00 4.96
189 190 1.275291 ACCTTATGTCAGTCGTGTGGG 59.725 52.381 0.00 0.00 0.00 4.61
190 191 2.337583 CACCTTATGTCAGTCGTGTGG 58.662 52.381 0.00 0.00 0.00 4.17
191 192 2.288825 ACCACCTTATGTCAGTCGTGTG 60.289 50.000 0.00 0.00 0.00 3.82
192 193 1.968493 ACCACCTTATGTCAGTCGTGT 59.032 47.619 0.00 0.00 0.00 4.49
193 194 2.337583 CACCACCTTATGTCAGTCGTG 58.662 52.381 0.00 0.00 0.00 4.35
194 195 1.275291 CCACCACCTTATGTCAGTCGT 59.725 52.381 0.00 0.00 0.00 4.34
195 196 2.007049 GCCACCACCTTATGTCAGTCG 61.007 57.143 0.00 0.00 0.00 4.18
196 197 1.739067 GCCACCACCTTATGTCAGTC 58.261 55.000 0.00 0.00 0.00 3.51
197 198 0.036388 CGCCACCACCTTATGTCAGT 60.036 55.000 0.00 0.00 0.00 3.41
198 199 0.036388 ACGCCACCACCTTATGTCAG 60.036 55.000 0.00 0.00 0.00 3.51
199 200 0.321210 CACGCCACCACCTTATGTCA 60.321 55.000 0.00 0.00 0.00 3.58
200 201 0.321298 ACACGCCACCACCTTATGTC 60.321 55.000 0.00 0.00 0.00 3.06
201 202 0.109723 AACACGCCACCACCTTATGT 59.890 50.000 0.00 0.00 0.00 2.29
202 203 0.802494 GAACACGCCACCACCTTATG 59.198 55.000 0.00 0.00 0.00 1.90
203 204 0.690762 AGAACACGCCACCACCTTAT 59.309 50.000 0.00 0.00 0.00 1.73
204 205 0.250124 CAGAACACGCCACCACCTTA 60.250 55.000 0.00 0.00 0.00 2.69
205 206 1.525995 CAGAACACGCCACCACCTT 60.526 57.895 0.00 0.00 0.00 3.50
206 207 2.111043 CAGAACACGCCACCACCT 59.889 61.111 0.00 0.00 0.00 4.00
207 208 2.978010 CCAGAACACGCCACCACC 60.978 66.667 0.00 0.00 0.00 4.61
208 209 2.978010 CCCAGAACACGCCACCAC 60.978 66.667 0.00 0.00 0.00 4.16
209 210 4.947147 GCCCAGAACACGCCACCA 62.947 66.667 0.00 0.00 0.00 4.17
216 217 4.717313 GTCCCGGGCCCAGAACAC 62.717 72.222 24.92 6.59 0.00 3.32
250 251 1.966451 CAACTCCTTGGGCCACGAC 60.966 63.158 12.26 0.00 0.00 4.34
251 252 2.429930 CAACTCCTTGGGCCACGA 59.570 61.111 12.26 6.96 0.00 4.35
277 278 2.163815 GCTCTACTTCTGGTCGTTGCTA 59.836 50.000 0.00 0.00 0.00 3.49
293 294 0.389426 GGTTTTCGTGCGAGGCTCTA 60.389 55.000 13.50 0.00 0.00 2.43
474 478 4.405358 ACAGGATCTTAGCTGAGAAAGGAG 59.595 45.833 12.76 4.80 0.00 3.69
496 500 6.861065 TTCATGAACAGAGGTTTCAGTTAC 57.139 37.500 3.38 0.00 37.36 2.50
600 604 4.940654 TGGAAGTAATGAATCATCGTGCAA 59.059 37.500 0.00 0.00 0.00 4.08
957 990 4.184649 AGTTTGGTTGGAGATCTTTGGT 57.815 40.909 0.00 0.00 0.00 3.67
1051 1090 1.340088 ATGGAAGCCATTTGTGCACA 58.660 45.000 17.42 17.42 42.23 4.57
1258 1317 7.331687 GCTATGTATTTTGAGTTGGTTTTGCAT 59.668 33.333 0.00 0.00 0.00 3.96
1440 1504 5.147162 CCAAAGAAAGTTACATGCTTCGTC 58.853 41.667 0.00 0.00 0.00 4.20
1455 1519 2.290197 GGATTTGCATGGGCCAAAGAAA 60.290 45.455 11.89 10.00 40.13 2.52
1460 1524 0.544833 ACTGGATTTGCATGGGCCAA 60.545 50.000 11.89 0.00 40.13 4.52
1712 1779 2.242043 CAGGAGTTCTGCCACCAAAAT 58.758 47.619 0.00 0.00 36.60 1.82
1713 1780 1.691196 CAGGAGTTCTGCCACCAAAA 58.309 50.000 0.00 0.00 36.60 2.44
1771 1838 7.698836 AGTGTTTTTCATTAATGCACAACTC 57.301 32.000 19.03 14.45 0.00 3.01
2147 2233 2.757077 GGTGTTGGGGCTAGTGCT 59.243 61.111 0.00 0.00 39.59 4.40
2245 2331 3.411454 AGATTCTCAGTCCCATCCTCA 57.589 47.619 0.00 0.00 0.00 3.86
2387 2473 1.789464 CTTGATACGAGCTCCATTCGC 59.211 52.381 8.47 0.00 41.57 4.70
2419 2505 1.680651 CTTTGCATAACCCCGCCCA 60.681 57.895 0.00 0.00 0.00 5.36
2443 2529 7.943079 ATCCATTATCATGTTCTTGAACACA 57.057 32.000 17.02 8.49 35.22 3.72
2688 2780 1.782201 ATTGCTCACCTCCACAGCCA 61.782 55.000 0.00 0.00 31.68 4.75
2965 3057 5.763876 ACCCTTTCTGCTTATCAACTACT 57.236 39.130 0.00 0.00 0.00 2.57
2975 3067 4.023193 CGAAACACATAACCCTTTCTGCTT 60.023 41.667 0.00 0.00 0.00 3.91
2990 3082 2.301870 AGAGGAAGCATACCGAAACACA 59.698 45.455 0.00 0.00 0.00 3.72
2999 3092 4.679373 TGGAGAATCAGAGGAAGCATAC 57.321 45.455 0.00 0.00 36.25 2.39
3002 3095 2.909006 ACTTGGAGAATCAGAGGAAGCA 59.091 45.455 0.00 0.00 36.25 3.91
3103 3199 3.016736 CCCAACTATTGTGCCTACTTGG 58.983 50.000 0.00 0.00 39.35 3.61
3104 3200 3.016736 CCCCAACTATTGTGCCTACTTG 58.983 50.000 0.00 0.00 0.00 3.16
3162 3258 3.088532 CAAATTGCAAGTACCCTGCCTA 58.911 45.455 4.94 4.18 0.00 3.93
3163 3259 1.895131 CAAATTGCAAGTACCCTGCCT 59.105 47.619 4.94 0.84 0.00 4.75
3165 3261 3.874392 ATCAAATTGCAAGTACCCTGC 57.126 42.857 4.94 9.99 0.00 4.85
3166 3262 5.138125 ACAATCAAATTGCAAGTACCCTG 57.862 39.130 4.94 0.00 43.98 4.45
3167 3263 6.909550 TTACAATCAAATTGCAAGTACCCT 57.090 33.333 4.94 0.00 43.98 4.34
3283 3379 6.876257 AGCCAGAGAAAAGTACATAAGTTCTG 59.124 38.462 0.00 1.38 0.00 3.02
3322 3418 3.008266 CCCATCCAAGGTGCTTTTCAAAT 59.992 43.478 0.00 0.00 0.00 2.32
3473 3569 5.650266 TGGTTATTGTTCATAACGGAAGCAT 59.350 36.000 0.00 0.00 45.97 3.79
3510 3606 7.349598 ACCAGCTGATTTCATTAACTATTCCT 58.650 34.615 17.39 0.00 0.00 3.36
3598 3694 9.691362 GAATACAATTTTTGGATACTGTGTTGT 57.309 29.630 0.00 0.00 31.46 3.32
3757 3859 2.423538 GCCTAGGTAACGACTAAACCGA 59.576 50.000 11.31 0.00 46.39 4.69
3765 3871 1.143401 GCCAGGCCTAGGTAACGAC 59.857 63.158 3.98 0.00 46.39 4.34
3826 3941 3.016971 TCCATCCTGGGGCAGTGG 61.017 66.667 0.00 0.00 38.32 4.00
3827 3942 1.856539 AACTCCATCCTGGGGCAGTG 61.857 60.000 0.00 0.00 43.56 3.66
3828 3943 1.542375 AACTCCATCCTGGGGCAGT 60.542 57.895 0.00 0.00 43.56 4.40
3829 3944 1.225704 GAACTCCATCCTGGGGCAG 59.774 63.158 0.00 0.00 43.56 4.85
3830 3945 0.920763 ATGAACTCCATCCTGGGGCA 60.921 55.000 0.00 0.00 43.56 5.36
3831 3946 0.466922 CATGAACTCCATCCTGGGGC 60.467 60.000 0.00 0.00 43.56 5.80
3832 3947 1.133976 GTCATGAACTCCATCCTGGGG 60.134 57.143 0.00 0.00 45.84 4.96
3833 3948 1.842562 AGTCATGAACTCCATCCTGGG 59.157 52.381 0.00 0.00 38.32 4.45


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

AutoCloner maintained by Alex Coulton.