Multiple sequence alignment - TraesCS6B01G227500

Loading Multiple Alignment...

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 TraesCS6B01G227500 chr6B 100.000 3383 0 0 1 3383 352415987 352412605 0.000000e+00 6248.0
1 TraesCS6B01G227500 chr6B 82.456 171 20 6 2563 2727 126311538 126311704 1.270000e-29 141.0
2 TraesCS6B01G227500 chr6B 96.154 52 1 1 78 128 493265811 493265862 2.160000e-12 84.2
3 TraesCS6B01G227500 chr6A 96.429 1680 34 7 780 2455 330378331 330376674 0.000000e+00 2747.0
4 TraesCS6B01G227500 chr6A 88.284 606 23 13 177 782 330383199 330382642 0.000000e+00 682.0
5 TraesCS6B01G227500 chr6A 85.906 298 23 8 2447 2733 330376524 330376235 1.970000e-77 300.0
6 TraesCS6B01G227500 chr6A 86.232 138 10 6 2560 2690 112005007 112005142 1.270000e-29 141.0
7 TraesCS6B01G227500 chr6D 97.858 887 18 1 1602 2487 254839153 254840039 0.000000e+00 1531.0
8 TraesCS6B01G227500 chr6D 94.501 782 34 6 161 939 254820562 254821337 0.000000e+00 1197.0
9 TraesCS6B01G227500 chr6D 95.147 680 11 1 935 1614 254838236 254838893 0.000000e+00 1053.0
10 TraesCS6B01G227500 chr6D 83.158 380 35 16 2488 2857 254841049 254841409 1.510000e-83 320.0
11 TraesCS6B01G227500 chr6D 81.395 172 19 8 2563 2727 56124996 56125161 9.850000e-26 128.0
12 TraesCS6B01G227500 chr6D 96.154 52 1 1 78 128 423083295 423083346 2.160000e-12 84.2
13 TraesCS6B01G227500 chr6D 91.525 59 3 2 71 128 28686964 28687021 2.800000e-11 80.5
14 TraesCS6B01G227500 chr5B 93.898 508 26 3 2875 3381 87959699 87959196 0.000000e+00 761.0
15 TraesCS6B01G227500 chr5D 92.717 508 35 1 2875 3382 163993714 163993209 0.000000e+00 732.0
16 TraesCS6B01G227500 chr5D 82.965 452 65 11 2939 3383 491663362 491662916 6.800000e-107 398.0
17 TraesCS6B01G227500 chr5D 80.663 181 24 9 2207 2385 346676168 346675997 2.740000e-26 130.0
18 TraesCS6B01G227500 chr7A 86.813 455 33 14 2875 3308 565807174 565807622 1.830000e-132 483.0
19 TraesCS6B01G227500 chr1D 82.883 444 63 12 2948 3383 487202227 487202665 1.470000e-103 387.0
20 TraesCS6B01G227500 chr1D 86.466 133 13 4 2563 2690 225704785 225704917 1.270000e-29 141.0
21 TraesCS6B01G227500 chr1D 97.436 39 1 0 2689 2727 419478013 419477975 2.180000e-07 67.6
22 TraesCS6B01G227500 chr1B 82.629 426 61 12 2966 3383 389095405 389094985 6.900000e-97 364.0
23 TraesCS6B01G227500 chr4A 84.795 171 12 7 2563 2727 5222460 5222622 3.490000e-35 159.0
24 TraesCS6B01G227500 chr4A 90.625 64 4 2 2556 2619 660523834 660523895 2.160000e-12 84.2
25 TraesCS6B01G227500 chr4A 86.765 68 6 3 78 145 566775059 566774995 4.680000e-09 73.1
26 TraesCS6B01G227500 chr2D 82.857 175 22 6 2559 2727 78687886 78688058 2.100000e-32 150.0
27 TraesCS6B01G227500 chr2D 86.567 134 15 2 2560 2690 80797593 80797460 9.780000e-31 145.0
28 TraesCS6B01G227500 chr7D 82.222 180 18 8 2563 2737 397555077 397554907 3.520000e-30 143.0
29 TraesCS6B01G227500 chr7D 95.349 43 1 1 2689 2730 459937619 459937577 2.180000e-07 67.6
30 TraesCS6B01G227500 chr3A 78.488 172 24 6 2564 2730 25233042 25233205 2.150000e-17 100.0
31 TraesCS6B01G227500 chr3A 90.476 63 4 2 78 138 611959878 611959940 7.780000e-12 82.4
32 TraesCS6B01G227500 chr3A 93.023 43 3 0 2688 2730 735892997 735892955 2.820000e-06 63.9
33 TraesCS6B01G227500 chr5A 98.077 52 0 1 78 128 558336576 558336627 4.650000e-14 89.8
34 TraesCS6B01G227500 chr3D 94.737 57 2 1 73 128 54818353 54818409 1.670000e-13 87.9
35 TraesCS6B01G227500 chr3B 76.630 184 28 12 2561 2738 760608704 760608530 1.670000e-13 87.9
36 TraesCS6B01G227500 chr3B 98.000 50 0 1 78 126 811170687 811170638 6.010000e-13 86.1
37 TraesCS6B01G227500 chr3B 100.000 29 0 0 3064 3092 236352889 236352861 2.000000e-03 54.7
38 TraesCS6B01G227500 chrUn 94.444 54 2 1 75 127 348964524 348964577 7.780000e-12 82.4


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 TraesCS6B01G227500 chr6B 352412605 352415987 3382 True 6248.0 6248 100.000000 1 3383 1 chr6B.!!$R1 3382
1 TraesCS6B01G227500 chr6A 330376235 330378331 2096 True 1523.5 2747 91.167500 780 2733 2 chr6A.!!$R2 1953
2 TraesCS6B01G227500 chr6A 330382642 330383199 557 True 682.0 682 88.284000 177 782 1 chr6A.!!$R1 605
3 TraesCS6B01G227500 chr6D 254820562 254821337 775 False 1197.0 1197 94.501000 161 939 1 chr6D.!!$F3 778
4 TraesCS6B01G227500 chr6D 254838236 254841409 3173 False 968.0 1531 92.054333 935 2857 3 chr6D.!!$F5 1922
5 TraesCS6B01G227500 chr5B 87959196 87959699 503 True 761.0 761 93.898000 2875 3381 1 chr5B.!!$R1 506
6 TraesCS6B01G227500 chr5D 163993209 163993714 505 True 732.0 732 92.717000 2875 3382 1 chr5D.!!$R1 507


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
372 373 0.041684 TCCAGTCCTCCTGCTCATCA 59.958 55.0 0.0 0.0 40.06 3.07 F
961 969 0.692476 CCAGGTTGAGGGATGACACA 59.308 55.0 0.0 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 1219 0.603065 GATTGCCGCCTTCCAAGTTT 59.397 50.0 0.0 0.0 0.0 2.66 R
2872 4362 0.035056 AGGAGGAAAGATGCGTTGGG 60.035 55.0 0.0 0.0 0.0 4.12 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
18 19 2.917172 TCCGAACACGTAAAAGGCC 58.083 52.632 0.00 0.00 0.00 5.19
19 20 0.945265 TCCGAACACGTAAAAGGCCG 60.945 55.000 0.00 0.00 0.00 6.13
20 21 1.223417 CCGAACACGTAAAAGGCCGT 61.223 55.000 0.00 0.00 37.90 5.68
21 22 0.162294 CGAACACGTAAAAGGCCGTC 59.838 55.000 0.00 0.00 34.59 4.79
22 23 0.162294 GAACACGTAAAAGGCCGTCG 59.838 55.000 0.00 0.00 34.59 5.12
23 24 1.223417 AACACGTAAAAGGCCGTCGG 61.223 55.000 6.99 6.99 34.59 4.79
24 25 2.047939 ACGTAAAAGGCCGTCGGG 60.048 61.111 14.38 0.00 30.05 5.14
52 53 4.344865 GCCCGGCCTGTCCTTCAA 62.345 66.667 0.00 0.00 0.00 2.69
53 54 2.434331 CCCGGCCTGTCCTTCAAA 59.566 61.111 0.00 0.00 0.00 2.69
54 55 1.228429 CCCGGCCTGTCCTTCAAAA 60.228 57.895 0.00 0.00 0.00 2.44
55 56 0.825840 CCCGGCCTGTCCTTCAAAAA 60.826 55.000 0.00 0.00 0.00 1.94
73 74 1.708822 AAAACGCGAAAATGATGGGC 58.291 45.000 15.93 0.00 0.00 5.36
74 75 0.108851 AAACGCGAAAATGATGGGCC 60.109 50.000 15.93 0.00 0.00 5.80
75 76 1.944234 AACGCGAAAATGATGGGCCC 61.944 55.000 17.59 17.59 0.00 5.80
76 77 2.413963 CGCGAAAATGATGGGCCCA 61.414 57.895 30.92 30.92 0.00 5.36
77 78 1.438814 GCGAAAATGATGGGCCCAG 59.561 57.895 31.97 15.04 0.00 4.45
78 79 2.019897 GCGAAAATGATGGGCCCAGG 62.020 60.000 31.97 11.97 0.00 4.45
79 80 1.825341 GAAAATGATGGGCCCAGGC 59.175 57.895 31.97 24.32 41.06 4.85
101 102 2.746277 CCGGGTCAGGCTTTTCGG 60.746 66.667 0.00 0.00 0.00 4.30
102 103 2.746277 CGGGTCAGGCTTTTCGGG 60.746 66.667 0.00 0.00 0.00 5.14
103 104 3.062466 GGGTCAGGCTTTTCGGGC 61.062 66.667 0.00 0.00 0.00 6.13
127 128 2.512896 GCCCATGGCCAGGACTAG 59.487 66.667 21.32 5.63 44.06 2.57
128 129 2.512896 CCCATGGCCAGGACTAGC 59.487 66.667 21.32 0.00 0.00 3.42
129 130 2.074948 CCCATGGCCAGGACTAGCT 61.075 63.158 21.32 0.00 0.00 3.32
130 131 0.764369 CCCATGGCCAGGACTAGCTA 60.764 60.000 21.32 0.00 0.00 3.32
131 132 1.131638 CCATGGCCAGGACTAGCTAA 58.868 55.000 21.32 0.00 0.00 3.09
132 133 1.071385 CCATGGCCAGGACTAGCTAAG 59.929 57.143 21.32 0.00 0.00 2.18
133 134 2.042464 CATGGCCAGGACTAGCTAAGA 58.958 52.381 13.35 0.00 0.00 2.10
134 135 2.478872 TGGCCAGGACTAGCTAAGAT 57.521 50.000 0.00 0.00 0.00 2.40
135 136 2.042464 TGGCCAGGACTAGCTAAGATG 58.958 52.381 0.00 0.00 0.00 2.90
136 137 1.270571 GGCCAGGACTAGCTAAGATGC 60.271 57.143 0.00 0.00 0.00 3.91
137 138 1.691434 GCCAGGACTAGCTAAGATGCT 59.309 52.381 0.00 0.00 46.11 3.79
138 139 2.894126 GCCAGGACTAGCTAAGATGCTA 59.106 50.000 0.00 0.00 43.74 3.49
139 140 3.513515 GCCAGGACTAGCTAAGATGCTAT 59.486 47.826 0.00 0.00 43.54 2.97
140 141 4.381505 GCCAGGACTAGCTAAGATGCTATC 60.382 50.000 0.00 0.00 43.54 2.08
141 142 4.159506 CCAGGACTAGCTAAGATGCTATCC 59.840 50.000 0.00 12.60 43.54 2.59
142 143 5.016173 CAGGACTAGCTAAGATGCTATCCT 58.984 45.833 15.19 15.19 44.52 3.24
143 144 5.480073 CAGGACTAGCTAAGATGCTATCCTT 59.520 44.000 16.89 0.00 43.10 3.36
144 145 5.480073 AGGACTAGCTAAGATGCTATCCTTG 59.520 44.000 15.19 2.03 43.10 3.61
145 146 5.337169 GGACTAGCTAAGATGCTATCCTTGG 60.337 48.000 0.00 0.00 43.54 3.61
146 147 4.530161 ACTAGCTAAGATGCTATCCTTGGG 59.470 45.833 0.00 0.00 43.54 4.12
147 148 2.039613 AGCTAAGATGCTATCCTTGGGC 59.960 50.000 0.00 0.00 42.10 5.36
148 149 2.693069 CTAAGATGCTATCCTTGGGCG 58.307 52.381 0.00 0.00 0.00 6.13
149 150 0.109342 AAGATGCTATCCTTGGGCGG 59.891 55.000 0.00 0.00 0.00 6.13
150 151 1.056700 AGATGCTATCCTTGGGCGGT 61.057 55.000 0.00 0.00 0.00 5.68
151 152 0.886490 GATGCTATCCTTGGGCGGTG 60.886 60.000 0.00 0.00 0.00 4.94
152 153 2.203209 GCTATCCTTGGGCGGTGG 60.203 66.667 0.00 0.00 0.00 4.61
153 154 2.742116 GCTATCCTTGGGCGGTGGA 61.742 63.158 0.00 0.00 0.00 4.02
154 155 1.146263 CTATCCTTGGGCGGTGGAC 59.854 63.158 0.00 0.00 32.16 4.02
155 156 2.325393 CTATCCTTGGGCGGTGGACC 62.325 65.000 0.00 0.00 44.16 4.46
198 199 1.956170 CTGCACGCAAAGGTCGTCT 60.956 57.895 0.00 0.00 38.19 4.18
288 289 2.747686 GTTTCTCCCTCCGCCACA 59.252 61.111 0.00 0.00 0.00 4.17
289 290 1.671379 GTTTCTCCCTCCGCCACAC 60.671 63.158 0.00 0.00 0.00 3.82
310 311 1.302192 GCAACGCACCCACCTAGAA 60.302 57.895 0.00 0.00 0.00 2.10
325 326 2.162338 TAGAACTTGTCCACCGGGCG 62.162 60.000 6.32 0.00 0.00 6.13
372 373 0.041684 TCCAGTCCTCCTGCTCATCA 59.958 55.000 0.00 0.00 40.06 3.07
390 391 4.964897 TCATCATCTACTGTGTGGATCCTT 59.035 41.667 14.23 0.00 31.53 3.36
410 411 0.744874 TCTCGGTAAGCCTCGATTGG 59.255 55.000 0.00 0.00 34.77 3.16
432 433 1.498865 CCAATTCCCCGCTCGAATCG 61.499 60.000 0.00 0.00 0.00 3.34
433 434 1.887707 AATTCCCCGCTCGAATCGC 60.888 57.895 0.00 0.00 0.00 4.58
480 481 1.215244 ATTGCATCAGATGTCTCGCG 58.785 50.000 12.18 0.00 0.00 5.87
507 508 3.766691 GACAGGGCGGCTCCGTAA 61.767 66.667 9.56 0.00 42.09 3.18
549 550 3.003173 CAGGCGGGGGTCTTCTGA 61.003 66.667 0.00 0.00 0.00 3.27
550 551 2.041265 AGGCGGGGGTCTTCTGAT 59.959 61.111 0.00 0.00 0.00 2.90
551 552 1.048724 CAGGCGGGGGTCTTCTGATA 61.049 60.000 0.00 0.00 0.00 2.15
642 646 2.041081 TCTAGGGTGGAATTGGTTGTGG 59.959 50.000 0.00 0.00 0.00 4.17
659 663 2.238521 GTGGGAAAAGGTGCTTGATCA 58.761 47.619 0.00 0.00 0.00 2.92
667 671 6.928492 GGAAAAGGTGCTTGATCAAATTTGTA 59.072 34.615 17.47 5.54 0.00 2.41
670 674 5.883661 AGGTGCTTGATCAAATTTGTATCG 58.116 37.500 17.47 8.76 0.00 2.92
926 933 8.791675 TGAAGCCGATATGCATATAATTTCAAA 58.208 29.630 19.12 4.57 0.00 2.69
961 969 0.692476 CCAGGTTGAGGGATGACACA 59.308 55.000 0.00 0.00 0.00 3.72
966 974 1.537202 GTTGAGGGATGACACAACAGC 59.463 52.381 0.00 0.00 41.16 4.40
1024 1032 3.129871 GGCTCTTATCTAAGCACTGCAG 58.870 50.000 13.48 13.48 40.36 4.41
1096 1104 2.536066 ACAAAAGGGCCAAGATAACCC 58.464 47.619 6.18 0.00 44.62 4.11
1211 1219 5.222048 ACCTAAAGATGAAGTTGGTTAGCCA 60.222 40.000 0.00 0.00 44.38 4.75
1572 1580 2.557869 TGCTTGTATGTCTTAGGGGGT 58.442 47.619 0.00 0.00 0.00 4.95
1864 2159 1.135046 CGATGTGCTGAAGCCTATCG 58.865 55.000 17.81 17.81 43.68 2.92
1865 2160 0.864455 GATGTGCTGAAGCCTATCGC 59.136 55.000 0.00 0.00 41.18 4.58
1866 2161 0.533755 ATGTGCTGAAGCCTATCGCC 60.534 55.000 0.00 0.00 41.18 5.54
1867 2162 1.153369 GTGCTGAAGCCTATCGCCA 60.153 57.895 0.00 0.00 41.18 5.69
1868 2163 1.153369 TGCTGAAGCCTATCGCCAC 60.153 57.895 0.00 0.00 41.18 5.01
1869 2164 1.144936 GCTGAAGCCTATCGCCACT 59.855 57.895 0.00 0.00 38.78 4.00
1870 2165 1.156645 GCTGAAGCCTATCGCCACTG 61.157 60.000 0.00 0.00 38.78 3.66
1871 2166 0.531532 CTGAAGCCTATCGCCACTGG 60.532 60.000 0.00 0.00 38.78 4.00
1872 2167 1.227674 GAAGCCTATCGCCACTGGG 60.228 63.158 0.00 0.00 38.78 4.45
1873 2168 1.686325 GAAGCCTATCGCCACTGGGA 61.686 60.000 0.00 0.00 38.78 4.37
1874 2169 1.056700 AAGCCTATCGCCACTGGGAT 61.057 55.000 0.00 1.18 45.25 3.85
1875 2170 1.302033 GCCTATCGCCACTGGGATG 60.302 63.158 0.00 0.00 43.35 3.51
1876 2171 1.372683 CCTATCGCCACTGGGATGG 59.627 63.158 0.00 0.78 43.35 3.51
1962 2257 6.566079 ATTGGAGGTGAAATCTATGACTCA 57.434 37.500 0.00 0.00 0.00 3.41
2419 2714 2.493278 CCGGCACTGAGATTTTTCCAAT 59.507 45.455 0.00 0.00 0.00 3.16
2582 4044 6.608405 TGATGTACTCCCTCCGTTTCTAAATA 59.392 38.462 0.00 0.00 0.00 1.40
2587 4049 7.063934 ACTCCCTCCGTTTCTAAATATAAGG 57.936 40.000 0.00 0.00 0.00 2.69
2643 4123 9.188588 ACGGATGTATATAAACGTATTTGAGTG 57.811 33.333 0.00 0.00 32.30 3.51
2644 4124 9.188588 CGGATGTATATAAACGTATTTGAGTGT 57.811 33.333 0.00 0.00 0.00 3.55
2654 4134 7.956420 AACGTATTTGAGTGTTGATTCACTA 57.044 32.000 0.00 0.00 46.81 2.74
2657 4137 9.647797 ACGTATTTGAGTGTTGATTCACTATTA 57.352 29.630 0.00 0.00 46.81 0.98
2674 4154 7.966812 TCACTATTACTCCATATGCAGTTCAT 58.033 34.615 4.23 0.88 39.17 2.57
2683 4163 9.407380 ACTCCATATGCAGTTCATGTTTTAATA 57.593 29.630 0.00 0.00 36.63 0.98
2738 4218 4.158025 ACGGAAGGAGTACTAGTGAATGTG 59.842 45.833 5.39 0.00 0.00 3.21
2739 4219 4.398358 CGGAAGGAGTACTAGTGAATGTGA 59.602 45.833 5.39 0.00 0.00 3.58
2745 4225 7.120051 AGGAGTACTAGTGAATGTGATGTACT 58.880 38.462 5.39 0.00 40.85 2.73
2746 4226 7.067615 AGGAGTACTAGTGAATGTGATGTACTG 59.932 40.741 5.39 0.00 39.08 2.74
2748 4228 8.803397 AGTACTAGTGAATGTGATGTACTGTA 57.197 34.615 5.39 0.00 38.04 2.74
2749 4229 8.675504 AGTACTAGTGAATGTGATGTACTGTAC 58.324 37.037 10.98 10.98 38.04 2.90
2750 4230 7.462571 ACTAGTGAATGTGATGTACTGTACA 57.537 36.000 21.68 21.68 43.80 2.90
2751 4231 7.313646 ACTAGTGAATGTGATGTACTGTACAC 58.686 38.462 21.84 15.61 42.23 2.90
2753 4233 7.462571 AGTGAATGTGATGTACTGTACACTA 57.537 36.000 21.84 11.55 42.23 2.74
2754 4234 7.539436 AGTGAATGTGATGTACTGTACACTAG 58.461 38.462 21.84 0.00 42.23 2.57
2756 4236 7.273598 GTGAATGTGATGTACTGTACACTAGTG 59.726 40.741 21.84 21.44 42.23 2.74
2757 4237 7.175990 TGAATGTGATGTACTGTACACTAGTGA 59.824 37.037 29.30 10.19 42.23 3.41
2758 4238 6.887626 TGTGATGTACTGTACACTAGTGAA 57.112 37.500 29.30 12.81 42.23 3.18
2760 4240 7.312899 TGTGATGTACTGTACACTAGTGAATG 58.687 38.462 29.30 16.66 42.23 2.67
2779 4268 7.385205 AGTGAATGTGAATGTACTGTACACTTC 59.615 37.037 21.84 22.15 42.23 3.01
2780 4269 6.364976 TGAATGTGAATGTACTGTACACTTCG 59.635 38.462 21.84 0.00 42.23 3.79
2795 4285 3.004524 ACACTTCGTACAGTGAGGAGTTC 59.995 47.826 17.63 0.00 46.29 3.01
2809 4299 2.496470 AGGAGTTCGGTCAATGTCTACC 59.504 50.000 0.00 0.00 0.00 3.18
2835 4325 7.043656 CGTCACGCATTCTGTATCATAACTTAA 60.044 37.037 0.00 0.00 0.00 1.85
2839 4329 7.042456 ACGCATTCTGTATCATAACTTAAGCTG 60.042 37.037 1.29 0.00 0.00 4.24
2857 4347 8.534333 TTAAGCTGTACAGACTTTTGATACAG 57.466 34.615 27.08 5.53 43.62 2.74
2858 4348 5.482908 AGCTGTACAGACTTTTGATACAGG 58.517 41.667 27.08 0.00 41.91 4.00
2859 4349 4.093556 GCTGTACAGACTTTTGATACAGGC 59.906 45.833 27.08 1.84 41.91 4.85
2860 4350 4.242475 TGTACAGACTTTTGATACAGGCG 58.758 43.478 0.00 0.00 0.00 5.52
2861 4351 3.678056 ACAGACTTTTGATACAGGCGA 57.322 42.857 0.00 0.00 0.00 5.54
2862 4352 3.326747 ACAGACTTTTGATACAGGCGAC 58.673 45.455 0.00 0.00 0.00 5.19
2863 4353 3.006967 ACAGACTTTTGATACAGGCGACT 59.993 43.478 0.00 0.00 46.44 4.18
2895 4385 2.100605 ACGCATCTTTCCTCCTTCAC 57.899 50.000 0.00 0.00 0.00 3.18
2909 4399 4.122776 CTCCTTCACGTATCCTTTCCATG 58.877 47.826 0.00 0.00 0.00 3.66
2944 4434 1.448985 GAAACATGGCTGCCGTTCTA 58.551 50.000 11.51 0.00 0.00 2.10
3073 4563 1.669184 TTTCGTCGCAGCAAATTTCG 58.331 45.000 0.00 0.00 0.00 3.46
3114 4605 4.165779 GCCGATGATGGTTGTAACAAAAG 58.834 43.478 0.00 0.00 0.00 2.27
3154 4645 1.086067 CAGCTCGTCGCACCATGAAT 61.086 55.000 0.00 0.00 42.61 2.57
3206 4697 3.457263 TAGGCGACGGCATGCTCA 61.457 61.111 24.23 0.00 42.47 4.26
3209 4700 3.422303 GCGACGGCATGCTCACAA 61.422 61.111 18.92 0.00 39.62 3.33
3254 4746 1.901464 GGAGCGGGTTCCAGCAAAA 60.901 57.895 15.37 0.00 37.20 2.44
3270 4762 2.676076 CAAAAGCCAAATCCGGTGAAG 58.324 47.619 0.00 0.00 0.00 3.02
3317 4809 3.782889 AATCAAAAAGGCGATGGTAGC 57.217 42.857 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.945265 CGGCCTTTTACGTGTTCGGA 60.945 55.000 0.00 0.00 41.85 4.55
1 2 1.223417 ACGGCCTTTTACGTGTTCGG 61.223 55.000 0.00 0.00 42.39 4.30
2 3 0.162294 GACGGCCTTTTACGTGTTCG 59.838 55.000 0.00 0.00 44.24 3.95
3 4 0.162294 CGACGGCCTTTTACGTGTTC 59.838 55.000 0.00 0.00 44.24 3.18
4 5 1.223417 CCGACGGCCTTTTACGTGTT 61.223 55.000 0.00 0.00 44.24 3.32
5 6 1.665599 CCGACGGCCTTTTACGTGT 60.666 57.895 0.00 0.00 44.24 4.49
6 7 2.385091 CCCGACGGCCTTTTACGTG 61.385 63.158 8.86 0.00 44.24 4.49
35 36 3.860930 TTTGAAGGACAGGCCGGGC 62.861 63.158 22.67 22.67 43.43 6.13
36 37 0.825840 TTTTTGAAGGACAGGCCGGG 60.826 55.000 8.08 1.20 43.43 5.73
37 38 2.727103 TTTTTGAAGGACAGGCCGG 58.273 52.632 0.00 0.00 43.43 6.13
53 54 2.065512 GCCCATCATTTTCGCGTTTTT 58.934 42.857 5.77 0.00 0.00 1.94
54 55 1.671556 GGCCCATCATTTTCGCGTTTT 60.672 47.619 5.77 0.00 0.00 2.43
55 56 0.108851 GGCCCATCATTTTCGCGTTT 60.109 50.000 5.77 0.00 0.00 3.60
56 57 1.510844 GGCCCATCATTTTCGCGTT 59.489 52.632 5.77 0.00 0.00 4.84
57 58 2.414785 GGGCCCATCATTTTCGCGT 61.415 57.895 19.95 0.00 0.00 6.01
58 59 2.340453 CTGGGCCCATCATTTTCGCG 62.340 60.000 28.82 5.25 0.00 5.87
59 60 1.438814 CTGGGCCCATCATTTTCGC 59.561 57.895 28.82 0.00 0.00 4.70
60 61 2.019897 GCCTGGGCCCATCATTTTCG 62.020 60.000 28.82 11.09 34.56 3.46
61 62 1.825341 GCCTGGGCCCATCATTTTC 59.175 57.895 28.82 5.60 34.56 2.29
62 63 4.055178 GCCTGGGCCCATCATTTT 57.945 55.556 28.82 0.00 34.56 1.82
84 85 2.746277 CCGAAAAGCCTGACCCGG 60.746 66.667 0.00 0.00 0.00 5.73
85 86 2.746277 CCCGAAAAGCCTGACCCG 60.746 66.667 0.00 0.00 0.00 5.28
86 87 3.062466 GCCCGAAAAGCCTGACCC 61.062 66.667 0.00 0.00 0.00 4.46
111 112 0.764369 TAGCTAGTCCTGGCCATGGG 60.764 60.000 15.13 4.96 37.85 4.00
112 113 1.071385 CTTAGCTAGTCCTGGCCATGG 59.929 57.143 5.51 7.63 37.85 3.66
113 114 2.042464 TCTTAGCTAGTCCTGGCCATG 58.958 52.381 5.51 2.84 37.85 3.66
114 115 2.478872 TCTTAGCTAGTCCTGGCCAT 57.521 50.000 5.51 0.00 37.85 4.40
115 116 2.042464 CATCTTAGCTAGTCCTGGCCA 58.958 52.381 4.71 4.71 37.85 5.36
116 117 1.270571 GCATCTTAGCTAGTCCTGGCC 60.271 57.143 0.00 0.00 37.85 5.36
117 118 1.691434 AGCATCTTAGCTAGTCCTGGC 59.309 52.381 0.00 0.00 44.50 4.85
127 128 2.431454 GCCCAAGGATAGCATCTTAGC 58.569 52.381 0.00 0.00 0.00 3.09
128 129 2.613977 CCGCCCAAGGATAGCATCTTAG 60.614 54.545 0.00 0.00 0.00 2.18
129 130 1.347707 CCGCCCAAGGATAGCATCTTA 59.652 52.381 0.00 0.00 0.00 2.10
130 131 0.109342 CCGCCCAAGGATAGCATCTT 59.891 55.000 0.00 0.00 0.00 2.40
131 132 1.056700 ACCGCCCAAGGATAGCATCT 61.057 55.000 0.00 0.00 34.73 2.90
132 133 0.886490 CACCGCCCAAGGATAGCATC 60.886 60.000 0.00 0.00 34.73 3.91
133 134 1.149174 CACCGCCCAAGGATAGCAT 59.851 57.895 0.00 0.00 34.73 3.79
134 135 2.589540 CACCGCCCAAGGATAGCA 59.410 61.111 0.00 0.00 34.73 3.49
135 136 2.203209 CCACCGCCCAAGGATAGC 60.203 66.667 0.00 0.00 34.73 2.97
136 137 1.146263 GTCCACCGCCCAAGGATAG 59.854 63.158 0.00 0.00 33.33 2.08
137 138 2.372074 GGTCCACCGCCCAAGGATA 61.372 63.158 0.00 0.00 33.33 2.59
138 139 3.728373 GGTCCACCGCCCAAGGAT 61.728 66.667 0.00 0.00 33.33 3.24
148 149 2.438434 CCAAGCATCGGGTCCACC 60.438 66.667 0.00 0.00 0.00 4.61
149 150 3.134127 GCCAAGCATCGGGTCCAC 61.134 66.667 0.00 0.00 0.00 4.02
150 151 3.329889 AGCCAAGCATCGGGTCCA 61.330 61.111 0.00 0.00 0.00 4.02
151 152 2.825836 CAGCCAAGCATCGGGTCC 60.826 66.667 0.00 0.00 29.87 4.46
152 153 3.512516 GCAGCCAAGCATCGGGTC 61.513 66.667 0.00 0.00 29.87 4.46
153 154 3.866379 TTGCAGCCAAGCATCGGGT 62.866 57.895 0.00 0.00 45.19 5.28
154 155 3.063704 TTGCAGCCAAGCATCGGG 61.064 61.111 0.00 0.00 45.19 5.14
155 156 2.180017 GTTGCAGCCAAGCATCGG 59.820 61.111 0.00 0.00 45.19 4.18
156 157 1.443194 GTGTTGCAGCCAAGCATCG 60.443 57.895 0.00 0.00 45.19 3.84
157 158 1.443194 CGTGTTGCAGCCAAGCATC 60.443 57.895 0.00 0.00 45.19 3.91
158 159 1.898094 TCGTGTTGCAGCCAAGCAT 60.898 52.632 0.00 0.00 45.19 3.79
159 160 2.515757 TCGTGTTGCAGCCAAGCA 60.516 55.556 0.00 0.00 43.99 3.91
214 215 2.534396 TTCGCAGGGAATGGGTGGT 61.534 57.895 0.00 0.00 42.34 4.16
294 295 0.763035 AAGTTCTAGGTGGGTGCGTT 59.237 50.000 0.00 0.00 0.00 4.84
325 326 1.663074 CTGCTAAGGATCTCGCCGC 60.663 63.158 0.00 0.00 0.00 6.53
372 373 4.098654 CGAGAAAGGATCCACACAGTAGAT 59.901 45.833 15.82 0.00 0.00 1.98
390 391 1.136305 CCAATCGAGGCTTACCGAGAA 59.864 52.381 3.19 0.00 42.76 2.87
410 411 2.513897 CGAGCGGGGAATTGGGAC 60.514 66.667 0.00 0.00 0.00 4.46
432 433 2.480419 ACAGTAACTTGCACAGAATCGC 59.520 45.455 0.00 0.00 0.00 4.58
433 434 4.732285 AACAGTAACTTGCACAGAATCG 57.268 40.909 0.00 0.00 0.00 3.34
507 508 1.183676 AACAACCTAGTCGGACGCCT 61.184 55.000 1.89 0.00 36.31 5.52
549 550 6.006449 GCCCACCAGTTCATCAATCTATTAT 58.994 40.000 0.00 0.00 0.00 1.28
550 551 5.376625 GCCCACCAGTTCATCAATCTATTA 58.623 41.667 0.00 0.00 0.00 0.98
551 552 4.210331 GCCCACCAGTTCATCAATCTATT 58.790 43.478 0.00 0.00 0.00 1.73
642 646 5.759763 ACAAATTTGATCAAGCACCTTTTCC 59.240 36.000 24.64 0.00 0.00 3.13
659 663 9.599322 GATCGATAATCAAAGCGATACAAATTT 57.401 29.630 0.00 0.00 42.78 1.82
775 779 7.476667 CCAACATTGTTTCAACTACAGTAACA 58.523 34.615 0.00 0.00 0.00 2.41
776 780 6.416750 GCCAACATTGTTTCAACTACAGTAAC 59.583 38.462 0.00 0.00 0.00 2.50
793 797 2.561478 AACAGTACGAGGCCAACATT 57.439 45.000 5.01 0.00 0.00 2.71
830 834 9.418045 ACAAACATACCAGTTGCATTTATTAAC 57.582 29.630 0.00 0.00 0.00 2.01
832 836 8.247562 GGACAAACATACCAGTTGCATTTATTA 58.752 33.333 0.00 0.00 0.00 0.98
834 838 6.437162 AGGACAAACATACCAGTTGCATTTAT 59.563 34.615 0.00 0.00 0.00 1.40
835 839 5.772672 AGGACAAACATACCAGTTGCATTTA 59.227 36.000 0.00 0.00 0.00 1.40
961 969 4.883083 TCAAAGTCAGATAACTCGCTGTT 58.117 39.130 0.00 0.00 42.31 3.16
966 974 8.314635 CGTTTATCTTCAAAGTCAGATAACTCG 58.685 37.037 1.87 6.33 40.26 4.18
1024 1032 2.546795 CCATGGATCGAGCCTTACTGAC 60.547 54.545 22.18 0.00 0.00 3.51
1211 1219 0.603065 GATTGCCGCCTTCCAAGTTT 59.397 50.000 0.00 0.00 0.00 2.66
1572 1580 3.055530 TCAAGGCAACAGCTTTGGAAAAA 60.056 39.130 11.53 0.00 43.24 1.94
1872 2167 3.437049 GCTTTCCGTTATAGGATGCCATC 59.563 47.826 0.00 0.00 40.48 3.51
1873 2168 3.073062 AGCTTTCCGTTATAGGATGCCAT 59.927 43.478 7.53 0.00 40.48 4.40
1874 2169 2.438021 AGCTTTCCGTTATAGGATGCCA 59.562 45.455 7.53 0.00 40.48 4.92
1875 2170 3.067833 GAGCTTTCCGTTATAGGATGCC 58.932 50.000 0.00 0.00 40.48 4.40
1876 2171 3.996480 AGAGCTTTCCGTTATAGGATGC 58.004 45.455 0.00 4.24 40.48 3.91
1877 2172 6.692486 ACATAGAGCTTTCCGTTATAGGATG 58.308 40.000 0.00 0.00 40.48 3.51
1935 2230 8.267620 AGTCATAGATTTCACCTCCAATATCA 57.732 34.615 0.00 0.00 0.00 2.15
1962 2257 7.121315 GGCATAGTTGACCAAGAGTTTAATTCT 59.879 37.037 0.00 0.00 0.00 2.40
2295 2590 5.223449 TCCATAAGACGTTTTCTTCAGGT 57.777 39.130 0.00 0.00 44.02 4.00
2554 4016 3.543680 AACGGAGGGAGTACATCAATG 57.456 47.619 0.00 0.00 0.00 2.82
2587 4049 8.457238 AGTCCATATTGAAATCTCTAAAAGGC 57.543 34.615 0.00 0.00 0.00 4.35
2632 4112 9.901724 GTAATAGTGAATCAACACTCAAATACG 57.098 33.333 4.63 0.00 46.36 3.06
2635 4115 9.167311 GGAGTAATAGTGAATCAACACTCAAAT 57.833 33.333 4.63 0.00 46.36 2.32
2636 4116 8.154203 TGGAGTAATAGTGAATCAACACTCAAA 58.846 33.333 4.63 0.00 46.36 2.69
2637 4117 7.676004 TGGAGTAATAGTGAATCAACACTCAA 58.324 34.615 4.63 1.06 46.36 3.02
2639 4119 9.988815 ATATGGAGTAATAGTGAATCAACACTC 57.011 33.333 4.63 0.00 46.36 3.51
2641 4121 8.499162 GCATATGGAGTAATAGTGAATCAACAC 58.501 37.037 4.56 0.00 40.60 3.32
2642 4122 8.210265 TGCATATGGAGTAATAGTGAATCAACA 58.790 33.333 4.56 0.00 0.00 3.33
2643 4123 8.607441 TGCATATGGAGTAATAGTGAATCAAC 57.393 34.615 4.56 0.00 0.00 3.18
2644 4124 8.432013 ACTGCATATGGAGTAATAGTGAATCAA 58.568 33.333 26.44 0.00 45.07 2.57
2645 4125 7.966812 ACTGCATATGGAGTAATAGTGAATCA 58.033 34.615 26.44 0.00 45.07 2.57
2646 4126 8.839310 AACTGCATATGGAGTAATAGTGAATC 57.161 34.615 27.58 0.00 46.21 2.52
2647 4127 8.432013 TGAACTGCATATGGAGTAATAGTGAAT 58.568 33.333 27.58 10.75 46.21 2.57
2648 4128 7.791029 TGAACTGCATATGGAGTAATAGTGAA 58.209 34.615 27.58 7.09 46.21 3.18
2649 4129 7.360113 TGAACTGCATATGGAGTAATAGTGA 57.640 36.000 27.58 5.74 46.21 3.41
2650 4130 7.658982 ACATGAACTGCATATGGAGTAATAGTG 59.341 37.037 27.58 21.71 46.21 2.74
2651 4131 7.739825 ACATGAACTGCATATGGAGTAATAGT 58.260 34.615 27.58 20.29 46.21 2.12
2652 4132 8.613060 AACATGAACTGCATATGGAGTAATAG 57.387 34.615 27.58 19.74 46.21 1.73
2653 4133 8.978874 AAACATGAACTGCATATGGAGTAATA 57.021 30.769 27.58 17.52 46.21 0.98
2654 4134 7.886629 AAACATGAACTGCATATGGAGTAAT 57.113 32.000 27.58 20.80 46.21 1.89
2712 4192 4.298103 TCACTAGTACTCCTTCCGTTCT 57.702 45.455 0.00 0.00 0.00 3.01
2720 4200 7.067615 CAGTACATCACATTCACTAGTACTCCT 59.932 40.741 0.00 0.00 38.76 3.69
2721 4201 7.148052 ACAGTACATCACATTCACTAGTACTCC 60.148 40.741 0.00 0.00 38.76 3.85
2738 4218 7.535997 TCACATTCACTAGTGTACAGTACATC 58.464 38.462 21.99 10.23 41.34 3.06
2739 4219 7.462571 TCACATTCACTAGTGTACAGTACAT 57.537 36.000 21.99 8.42 41.34 2.29
2745 4225 7.812669 CAGTACATTCACATTCACTAGTGTACA 59.187 37.037 21.99 8.49 41.69 2.90
2746 4226 7.813148 ACAGTACATTCACATTCACTAGTGTAC 59.187 37.037 21.99 12.54 40.34 2.90
2748 4228 6.759272 ACAGTACATTCACATTCACTAGTGT 58.241 36.000 21.99 1.10 37.07 3.55
2749 4229 7.812669 TGTACAGTACATTCACATTCACTAGTG 59.187 37.037 17.17 17.17 33.83 2.74
2750 4230 7.813148 GTGTACAGTACATTCACATTCACTAGT 59.187 37.037 16.57 0.00 41.34 2.57
2751 4231 8.029522 AGTGTACAGTACATTCACATTCACTAG 58.970 37.037 16.57 0.00 41.34 2.57
2753 4233 6.759272 AGTGTACAGTACATTCACATTCACT 58.241 36.000 16.57 2.41 41.34 3.41
2754 4234 7.421530 AAGTGTACAGTACATTCACATTCAC 57.578 36.000 16.57 0.10 41.34 3.18
2756 4236 6.365247 ACGAAGTGTACAGTACATTCACATTC 59.635 38.462 16.57 12.03 42.51 2.67
2757 4237 6.220930 ACGAAGTGTACAGTACATTCACATT 58.779 36.000 16.57 5.56 42.51 2.71
2758 4238 5.779922 ACGAAGTGTACAGTACATTCACAT 58.220 37.500 16.57 0.00 42.51 3.21
2779 4268 0.879765 ACCGAACTCCTCACTGTACG 59.120 55.000 0.00 0.00 0.00 3.67
2780 4269 1.884579 TGACCGAACTCCTCACTGTAC 59.115 52.381 0.00 0.00 0.00 2.90
2809 4299 4.740205 AGTTATGATACAGAATGCGTGACG 59.260 41.667 0.00 0.00 42.53 4.35
2835 4325 5.482908 CCTGTATCAAAAGTCTGTACAGCT 58.517 41.667 18.45 14.93 40.37 4.24
2839 4329 4.326548 GTCGCCTGTATCAAAAGTCTGTAC 59.673 45.833 0.00 0.00 0.00 2.90
2871 4361 1.657751 GGAGGAAAGATGCGTTGGGC 61.658 60.000 0.00 0.00 43.96 5.36
2872 4362 0.035056 AGGAGGAAAGATGCGTTGGG 60.035 55.000 0.00 0.00 0.00 4.12
2873 4363 1.740025 GAAGGAGGAAAGATGCGTTGG 59.260 52.381 0.00 0.00 0.00 3.77
2895 4385 2.509052 TCTCGCATGGAAAGGATACG 57.491 50.000 0.00 0.00 46.39 3.06
2909 4399 5.572896 CCATGTTTCCTTTGTTATTTCTCGC 59.427 40.000 0.00 0.00 0.00 5.03
3073 4563 1.918543 GCGTTTGCTACAACCGACAAC 60.919 52.381 1.29 0.00 38.39 3.32
3114 4605 2.482839 GCAACTGAGGGTCTGCTCTATC 60.483 54.545 0.00 0.00 32.93 2.08
3154 4645 4.460683 GGTATGGTGCGGCCGACA 62.461 66.667 33.48 24.22 41.21 4.35
3206 4697 0.973496 ACCACCGGCTTTTTGGTTGT 60.973 50.000 7.84 0.00 40.98 3.32
3209 4700 1.176619 GCTACCACCGGCTTTTTGGT 61.177 55.000 16.99 16.99 45.78 3.67
3254 4746 1.678970 GCCTTCACCGGATTTGGCT 60.679 57.895 9.46 0.00 37.58 4.75
3270 4762 4.147449 GGAGCCGCCCAAAATGCC 62.147 66.667 0.00 0.00 0.00 4.40
3317 4809 0.732538 GGAACGAGCGCCCAAATTTG 60.733 55.000 11.40 11.40 0.00 2.32



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

AutoCloner maintained by Alex Coulton.