Multiple sequence alignment - TraesCS7B01G130000

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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 TraesCS7B01G130000 chr7B 100.000 7134 0 0 851 7984 156625396 156632529 0.000000e+00 13175.0
1 TraesCS7B01G130000 chr7B 100.000 394 0 0 1 394 156624546 156624939 0.000000e+00 728.0
2 TraesCS7B01G130000 chr7B 78.862 123 25 1 4013 4135 64475656 64475535 1.850000e-11 82.4
3 TraesCS7B01G130000 chr7B 100.000 29 0 0 5920 5948 540167824 540167796 4.000000e-03 54.7
4 TraesCS7B01G130000 chr7D 95.051 7194 240 51 851 7984 193197135 193204272 0.000000e+00 11206.0
5 TraesCS7B01G130000 chr7D 93.247 385 13 4 1 385 193196726 193197097 9.050000e-154 555.0
6 TraesCS7B01G130000 chr7D 90.741 54 2 3 5941 5992 26500397 26500449 1.440000e-07 69.4
7 TraesCS7B01G130000 chr7D 88.462 52 3 3 5941 5992 26457931 26457883 8.650000e-05 60.2
8 TraesCS7B01G130000 chr7A 95.400 5109 159 35 851 5926 202718029 202723094 0.000000e+00 8063.0
9 TraesCS7B01G130000 chr7A 94.298 1403 49 19 6158 7555 202723561 202724937 0.000000e+00 2119.0
10 TraesCS7B01G130000 chr7A 92.839 391 25 3 7596 7984 202724934 202725323 1.500000e-156 564.0
11 TraesCS7B01G130000 chr7A 92.051 390 11 6 1 385 202717614 202717988 1.530000e-146 531.0
12 TraesCS7B01G130000 chr7A 94.578 166 9 0 5953 6118 202723085 202723250 2.860000e-64 257.0
13 TraesCS7B01G130000 chr7A 100.000 30 0 0 7753 7782 183649639 183649610 1.000000e-03 56.5
14 TraesCS7B01G130000 chr6B 80.995 563 84 12 5368 5924 526734880 526734335 7.410000e-115 425.0
15 TraesCS7B01G130000 chr6B 85.714 91 11 2 3781 3870 658537965 658538054 2.370000e-15 95.3
16 TraesCS7B01G130000 chr6B 79.646 113 22 1 4025 4136 36824184 36824296 6.640000e-11 80.5
17 TraesCS7B01G130000 chr6B 97.619 42 1 0 5946 5987 552501445 552501404 1.110000e-08 73.1
18 TraesCS7B01G130000 chr6B 100.000 29 0 0 5920 5948 462436650 462436678 4.000000e-03 54.7
19 TraesCS7B01G130000 chr6D 79.964 554 73 16 5376 5924 352259306 352259826 2.720000e-99 374.0
20 TraesCS7B01G130000 chr5A 84.795 171 25 1 5730 5899 604725513 604725683 3.830000e-38 171.0
21 TraesCS7B01G130000 chr5B 86.813 91 10 2 3781 3870 649883026 649883115 5.100000e-17 100.0
22 TraesCS7B01G130000 chr5B 100.000 29 0 0 5920 5948 385602212 385602240 4.000000e-03 54.7
23 TraesCS7B01G130000 chr4A 86.813 91 10 2 3781 3870 111289964 111289875 5.100000e-17 100.0
24 TraesCS7B01G130000 chr4A 100.000 30 0 0 5918 5947 631500794 631500765 1.000000e-03 56.5
25 TraesCS7B01G130000 chr3B 86.813 91 10 2 3781 3870 773361434 773361523 5.100000e-17 100.0
26 TraesCS7B01G130000 chr3B 85.714 91 11 2 3781 3870 43288291 43288202 2.370000e-15 95.3
27 TraesCS7B01G130000 chr3B 92.063 63 3 1 5925 5985 650065022 650064960 3.970000e-13 87.9
28 TraesCS7B01G130000 chr3A 86.813 91 10 2 3781 3870 25275316 25275227 5.100000e-17 100.0
29 TraesCS7B01G130000 chr2B 86.813 91 10 2 3781 3870 76067134 76067045 5.100000e-17 100.0
30 TraesCS7B01G130000 chr2B 100.000 29 0 0 5959 5987 23054815 23054843 4.000000e-03 54.7
31 TraesCS7B01G130000 chr3D 79.839 124 24 1 4013 4136 550511883 550512005 1.100000e-13 89.8
32 TraesCS7B01G130000 chr3D 97.436 39 1 0 5946 5984 341659418 341659456 5.170000e-07 67.6
33 TraesCS7B01G130000 chr3D 100.000 30 0 0 5959 5988 580330968 580330939 1.000000e-03 56.5
34 TraesCS7B01G130000 chr3D 94.444 36 0 2 5957 5992 547002762 547002729 4.000000e-03 54.7
35 TraesCS7B01G130000 chr5D 86.301 73 10 0 4025 4097 239234036 239233964 6.640000e-11 80.5
36 TraesCS7B01G130000 chr4B 86.301 73 10 0 4025 4097 665221697 665221769 6.640000e-11 80.5
37 TraesCS7B01G130000 chr4B 90.164 61 4 1 5922 5982 97076851 97076909 2.390000e-10 78.7
38 TraesCS7B01G130000 chr4B 100.000 29 0 0 5919 5947 106547363 106547391 4.000000e-03 54.7
39 TraesCS7B01G130000 chr2D 100.000 36 0 0 5949 5984 555158733 555158698 5.170000e-07 67.6
40 TraesCS7B01G130000 chr1B 97.143 35 1 0 4025 4059 194770296 194770262 8.650000e-05 60.2
41 TraesCS7B01G130000 chr1B 94.595 37 1 1 5911 5947 388007661 388007696 1.000000e-03 56.5


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 TraesCS7B01G130000 chr7B 156624546 156632529 7983 False 6951.5 13175 100.0000 1 7984 2 chr7B.!!$F1 7983
1 TraesCS7B01G130000 chr7D 193196726 193204272 7546 False 5880.5 11206 94.1490 1 7984 2 chr7D.!!$F2 7983
2 TraesCS7B01G130000 chr7A 202717614 202725323 7709 False 2306.8 8063 93.8332 1 7984 5 chr7A.!!$F1 7983
3 TraesCS7B01G130000 chr6B 526734335 526734880 545 True 425.0 425 80.9950 5368 5924 1 chr6B.!!$R1 556
4 TraesCS7B01G130000 chr6D 352259306 352259826 520 False 374.0 374 79.9640 5376 5924 1 chr6D.!!$F1 548

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
60 61 0.748450 ACGGACGGACAGAAACAAGA 59.252 50.000 0.00 0.00 0.00 3.02 F
362 368 0.882927 CGAGGCGTTTCTTGGGTTCA 60.883 55.000 0.00 0.00 0.00 3.18 F
1287 1296 0.626382 TCGTCTCAGGGATCCTCACT 59.374 55.000 12.58 0.00 0.00 3.41 F
1368 1377 0.443869 CGGCGACCATGTTGAAAGAG 59.556 55.000 0.00 0.00 0.00 2.85 F
1567 1582 1.337167 GCTTAACAAGGACGTACGGGT 60.337 52.381 21.06 6.59 0.00 5.28 F
3528 3563 0.684479 TCCGTCTGCTAGCCATCTGT 60.684 55.000 13.29 0.00 0.00 3.41 F
4871 4917 0.098376 GCTCTTCAGGCATCAAAGCG 59.902 55.000 0.00 0.00 34.64 4.68 F
5312 5359 0.112995 TTGAAGGGATGCAGGTTGCT 59.887 50.000 2.48 0.00 45.31 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1075 1084 0.036388 TTGGAGTGATCTTCGGTGGC 60.036 55.000 0.00 0.00 0.0 5.01 R
1368 1377 0.919289 TCCTCCAATCCTCAACCCCC 60.919 60.000 0.00 0.00 0.0 5.40 R
2949 2984 5.163754 CCGTTTTAGCTCACCATTCCTTAAG 60.164 44.000 0.00 0.00 0.0 1.85 R
3528 3563 6.976934 TCTACTTCAGGTATGCATGTATGA 57.023 37.500 10.16 7.43 0.0 2.15 R
3585 3620 2.799017 ACAAATGCAGCTTCATCAGGA 58.201 42.857 0.00 0.00 0.0 3.86 R
5444 5491 1.028905 CCAAAAGCAACCGTTCCAGA 58.971 50.000 0.00 0.00 0.0 3.86 R
6121 6201 1.064003 TTGGGCAAGAGGACTGCTTA 58.936 50.000 0.00 0.00 0.0 3.09 R
7239 7593 0.454196 GGGGAAACACACACACACAC 59.546 55.000 0.00 0.00 0.0 3.82 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
50 51 3.808656 GAGGACGGACGGACGGAC 61.809 72.222 6.00 0.00 38.39 4.79
56 57 1.731969 CGGACGGACGGACAGAAAC 60.732 63.158 0.00 0.00 0.00 2.78
60 61 0.748450 ACGGACGGACAGAAACAAGA 59.252 50.000 0.00 0.00 0.00 3.02
61 62 1.137479 ACGGACGGACAGAAACAAGAA 59.863 47.619 0.00 0.00 0.00 2.52
62 63 2.206750 CGGACGGACAGAAACAAGAAA 58.793 47.619 0.00 0.00 0.00 2.52
66 67 1.333791 CGGACAGAAACAAGAAACGCC 60.334 52.381 0.00 0.00 0.00 5.68
143 144 4.452733 GACGCGGGAGTTCAGGGG 62.453 72.222 12.47 0.00 0.00 4.79
148 149 3.787001 GGGAGTTCAGGGGCGGAG 61.787 72.222 0.00 0.00 0.00 4.63
149 150 3.787001 GGAGTTCAGGGGCGGAGG 61.787 72.222 0.00 0.00 0.00 4.30
150 151 3.787001 GAGTTCAGGGGCGGAGGG 61.787 72.222 0.00 0.00 0.00 4.30
221 222 2.035442 GCTCTGTTGAGGCGTTCCC 61.035 63.158 0.00 0.00 40.53 3.97
362 368 0.882927 CGAGGCGTTTCTTGGGTTCA 60.883 55.000 0.00 0.00 0.00 3.18
385 394 5.407995 CACACCTGAAATCTGACTTCTTCTC 59.592 44.000 0.30 0.00 0.00 2.87
388 397 4.493547 CTGAAATCTGACTTCTTCTCGCT 58.506 43.478 0.30 0.00 0.00 4.93
1145 1154 4.674362 CGTCTACGTCAATGATCCAGACAA 60.674 45.833 16.01 0.00 32.39 3.18
1167 1176 3.483352 TGAAGAGGAGGGCTTCAGT 57.517 52.632 0.00 0.00 44.81 3.41
1275 1284 3.506455 CCAACTTCTACTTCCTCGTCTCA 59.494 47.826 0.00 0.00 0.00 3.27
1287 1296 0.626382 TCGTCTCAGGGATCCTCACT 59.374 55.000 12.58 0.00 0.00 3.41
1288 1297 1.006043 TCGTCTCAGGGATCCTCACTT 59.994 52.381 12.58 0.00 0.00 3.16
1296 1305 0.991920 GGATCCTCACTTTGACCCCA 59.008 55.000 3.84 0.00 0.00 4.96
1311 1320 4.554363 CCACTCGCGCCCTACTCG 62.554 72.222 0.00 0.00 0.00 4.18
1339 1348 2.100631 GCGCTACTGCCATTGTCGT 61.101 57.895 0.00 0.00 35.36 4.34
1360 1369 0.804544 CGTGATTACGGCGACCATGT 60.805 55.000 16.62 0.00 46.23 3.21
1368 1377 0.443869 CGGCGACCATGTTGAAAGAG 59.556 55.000 0.00 0.00 0.00 2.85
1438 1447 6.361433 TCTTCTGTTCAAATCCTACCACAAA 58.639 36.000 0.00 0.00 0.00 2.83
1454 1463 9.663904 CCTACCACAAATGAATCATATTTAACG 57.336 33.333 0.00 0.00 0.00 3.18
1521 1533 5.195940 ACTTAACATGCCTGCACATAATCT 58.804 37.500 0.00 0.00 0.00 2.40
1532 1544 4.009675 TGCACATAATCTGACCTTTCCAC 58.990 43.478 0.00 0.00 0.00 4.02
1567 1582 1.337167 GCTTAACAAGGACGTACGGGT 60.337 52.381 21.06 6.59 0.00 5.28
1680 1700 7.092979 ACAAAGTAGGGAGGAACCTAAATCTAC 60.093 40.741 0.00 4.38 44.34 2.59
1685 1705 4.345547 GGGAGGAACCTAAATCTACTGGAG 59.654 50.000 0.00 0.00 38.98 3.86
1864 1884 9.755064 GATACGTTGGATGTTAACATAATATGC 57.245 33.333 20.83 7.53 36.57 3.14
1873 1893 9.398170 GATGTTAACATAATATGCGATGCTTTT 57.602 29.630 20.83 0.00 36.57 2.27
2053 2073 5.964958 ATGTCATTGTGAGTTTTACTGGG 57.035 39.130 0.00 0.00 0.00 4.45
2115 2135 9.760077 GGAAGAATTTATAATCTCGGTTGTAGA 57.240 33.333 0.00 0.00 0.00 2.59
2225 2247 3.673746 TGAATTTCCATTCATCGACGC 57.326 42.857 0.00 0.00 43.32 5.19
2294 2316 9.855021 TTTAAATTTTGCTGCTTTATCTCTACC 57.145 29.630 0.00 0.00 0.00 3.18
2326 2348 8.620416 GTTGGTTTGTATGTCTATGCATATTCA 58.380 33.333 6.92 9.79 34.35 2.57
2751 2786 2.342179 CTTCTTCGGGACTCAAAGCTC 58.658 52.381 0.00 0.00 0.00 4.09
2796 2831 2.072298 GCTGTCATCTTCACAGGTCAC 58.928 52.381 2.21 0.00 41.49 3.67
2891 2926 3.221771 TCATTTACCTGCTGCTGTGTTT 58.778 40.909 0.00 0.00 0.00 2.83
2949 2984 7.859325 TTTTGGTATATGGACTAAAGCTGAC 57.141 36.000 0.00 0.00 32.27 3.51
3091 3126 9.444600 TGTACAACTACTTTATCCCAATTTCTC 57.555 33.333 0.00 0.00 0.00 2.87
3528 3563 0.684479 TCCGTCTGCTAGCCATCTGT 60.684 55.000 13.29 0.00 0.00 3.41
3585 3620 4.792521 AGTTTCATACGAAGCTGAGTCT 57.207 40.909 0.00 0.00 40.75 3.24
3778 3815 6.293735 CGTAAATTTGACTTTTAGCACCCTCA 60.294 38.462 0.00 0.00 0.00 3.86
3922 3965 7.596749 AGTACTCCACATGTTCTAAATTTCG 57.403 36.000 0.00 0.00 0.00 3.46
3925 3968 5.181245 ACTCCACATGTTCTAAATTTCGGTG 59.819 40.000 0.00 0.00 0.00 4.94
3927 3970 5.180492 TCCACATGTTCTAAATTTCGGTGTC 59.820 40.000 0.00 0.00 0.00 3.67
3946 3989 1.194997 TCGTTTCACAATTAACGGGCG 59.805 47.619 10.43 0.00 45.19 6.13
3954 3997 2.031508 ACAATTAACGGGCGAACTTGTG 60.032 45.455 0.00 0.00 0.00 3.33
3992 4037 6.634805 TCTTATCTGTCTTCTCCATGTGAAC 58.365 40.000 0.00 0.00 0.00 3.18
4128 4173 4.618460 GCGTCTTGGATGAGAAAGAGTACA 60.618 45.833 0.00 0.00 33.21 2.90
4175 4220 5.240713 CTGCCAAAATATCTGGAAGTGTC 57.759 43.478 7.79 0.00 35.13 3.67
4464 4509 8.368668 AGACAGCTATCAATATTGGGTACTTAC 58.631 37.037 15.36 3.24 0.00 2.34
4497 4542 7.716799 TGCATGGAAATGGTCTTTTTAGTAT 57.283 32.000 0.00 0.00 0.00 2.12
4542 4587 9.688592 CAAGCTGACTATTTCTTTTTCTGATTT 57.311 29.630 0.00 0.00 0.00 2.17
4692 4737 5.125900 CCAAGGTGAATAAATGACTGATGCA 59.874 40.000 0.00 0.00 0.00 3.96
4871 4917 0.098376 GCTCTTCAGGCATCAAAGCG 59.902 55.000 0.00 0.00 34.64 4.68
5208 5255 6.419710 GGTTACAAGGCTTGTTAAACATTCAC 59.580 38.462 35.13 17.36 42.22 3.18
5282 5329 0.625849 AAGCTGACATAGGGGTTGGG 59.374 55.000 0.00 0.00 0.00 4.12
5312 5359 0.112995 TTGAAGGGATGCAGGTTGCT 59.887 50.000 2.48 0.00 45.31 3.91
5332 5379 8.720562 GGTTGCTTATTTTGATGCTTTGTAAAT 58.279 29.630 0.00 0.00 0.00 1.40
5444 5491 2.040544 CATCGCCCAGTTCCGCTTT 61.041 57.895 0.00 0.00 0.00 3.51
5522 5573 7.171678 GTGATGGTATACTCTATGTTCCTTTGC 59.828 40.741 2.25 0.00 0.00 3.68
5756 5807 6.183360 GCGTATTTGATCAGGATGTTTCTTCA 60.183 38.462 0.00 0.00 37.40 3.02
5820 5874 2.860735 AGACGCAATCTTTCGTGATAGC 59.139 45.455 0.00 0.00 39.22 2.97
5875 5930 7.587037 TCCAAATTCTCTTGAAACATGTTCT 57.413 32.000 12.39 2.19 35.63 3.01
5933 5988 5.852807 TCACTCTACTCCATATACTCCCTCT 59.147 44.000 0.00 0.00 0.00 3.69
5934 5989 5.943416 CACTCTACTCCATATACTCCCTCTG 59.057 48.000 0.00 0.00 0.00 3.35
5987 6067 1.135333 GAACGGAGGGAGTAGAAGCTG 59.865 57.143 0.00 0.00 0.00 4.24
6080 6160 7.669427 AGGTAAAAGTTTGATGATTTCATGCA 58.331 30.769 0.00 0.00 36.57 3.96
6135 6215 8.041323 TCCTACTTAATTTAAGCAGTCCTCTTG 58.959 37.037 14.67 0.00 39.39 3.02
6153 6233 4.798433 CCCAAAAGGGCAAAAGGC 57.202 55.556 0.00 0.00 43.74 4.35
6168 6519 1.476007 AAGGCGTCTCAAGGCTCAGT 61.476 55.000 0.00 0.00 44.05 3.41
6169 6520 1.004440 GGCGTCTCAAGGCTCAGTT 60.004 57.895 0.00 0.00 36.52 3.16
6179 6530 5.899547 TCTCAAGGCTCAGTTATCCTATTCA 59.100 40.000 0.00 0.00 0.00 2.57
6196 6547 3.926821 TTCATGCCGTTTTAAGTTCCC 57.073 42.857 0.00 0.00 0.00 3.97
6252 6603 8.604640 ATCATTCTATCTTTCATACTGCACAG 57.395 34.615 0.00 0.00 0.00 3.66
6779 7131 1.540607 CGTACTTCTGCTATGCCGCG 61.541 60.000 0.00 0.00 0.00 6.46
6854 7206 4.468689 GGGAAGGCCGAAGACCCG 62.469 72.222 0.00 0.00 33.83 5.28
6893 7245 3.307108 TCACGGCACCGGACATCA 61.307 61.111 9.46 0.00 44.69 3.07
6965 7317 6.458210 CATGCAAGTTAAAAAGGGAACTGAT 58.542 36.000 0.00 0.00 42.68 2.90
7137 7489 4.518970 CCAGTTCAGAGGATAGAGCTAGAC 59.481 50.000 0.00 0.00 0.00 2.59
7166 7518 4.386867 TTTCGTAGATAGGCCACAAGAG 57.613 45.455 5.01 0.00 35.04 2.85
7233 7587 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7235 7589 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7236 7590 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7237 7591 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7238 7592 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7239 7593 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7240 7594 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7241 7595 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7242 7596 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7243 7597 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7244 7598 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7245 7599 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7246 7600 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7247 7601 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7248 7602 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7249 7603 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7250 7604 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7251 7605 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7252 7606 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7253 7607 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
7254 7608 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
7255 7609 2.031595 TGTGTGTGTGTGTGTGTGTTTC 60.032 45.455 0.00 0.00 0.00 2.78
7356 7710 3.503891 GTTTTGCCACGTAACTGTTGTT 58.496 40.909 2.69 0.00 39.98 2.83
7458 7815 2.987413 TCAGTGCTTAAATGCAACCG 57.013 45.000 0.00 0.00 45.12 4.44
7497 7856 8.299570 GTGTTTGAAGACAACCTCATGATATTT 58.700 33.333 0.00 0.00 35.63 1.40
7498 7857 8.859090 TGTTTGAAGACAACCTCATGATATTTT 58.141 29.630 0.00 0.00 35.63 1.82
7539 7899 6.420903 TGACACTATATATTCTTTGCTGCGAC 59.579 38.462 0.00 0.00 0.00 5.19
7787 8154 6.382859 TCTCCTATCATACTAACCTGCAAACA 59.617 38.462 0.00 0.00 0.00 2.83
7810 8178 0.247736 GCAAAGAGAAGAGCGGGAGA 59.752 55.000 0.00 0.00 0.00 3.71
7818 8186 4.200283 GAGCGGGAGACTGAGGCG 62.200 72.222 0.00 0.00 39.98 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.281970 AAACGTCCCCGGGAAAGC 60.282 61.111 26.32 7.82 38.78 3.51
49 50 0.661020 CGGGCGTTTCTTGTTTCTGT 59.339 50.000 0.00 0.00 0.00 3.41
50 51 0.660300 GCGGGCGTTTCTTGTTTCTG 60.660 55.000 0.00 0.00 0.00 3.02
56 57 4.404654 GGCAGCGGGCGTTTCTTG 62.405 66.667 0.00 0.00 46.16 3.02
221 222 2.233922 ACTGGACTAAATCACCTGACCG 59.766 50.000 0.00 0.00 0.00 4.79
362 368 5.546526 GAGAAGAAGTCAGATTTCAGGTGT 58.453 41.667 8.28 0.00 0.00 4.16
852 861 1.152030 AGCCCTCAAGGACCAGTGA 60.152 57.895 0.00 0.00 38.24 3.41
860 869 3.863142 CTGAAAATTCAGCCCTCAAGG 57.137 47.619 10.00 0.00 46.97 3.61
1075 1084 0.036388 TTGGAGTGATCTTCGGTGGC 60.036 55.000 0.00 0.00 0.00 5.01
1145 1154 0.545646 GAAGCCCTCCTCTTCATGCT 59.454 55.000 0.00 0.00 39.64 3.79
1167 1176 3.396276 TGGACACCTCATTTCTTGGGTAA 59.604 43.478 0.00 0.00 30.47 2.85
1275 1284 1.290134 GGGTCAAAGTGAGGATCCCT 58.710 55.000 8.55 0.00 36.03 4.20
1353 1362 1.075536 ACCCCCTCTTTCAACATGGTC 59.924 52.381 0.00 0.00 0.00 4.02
1360 1369 1.827792 TCCTCAACCCCCTCTTTCAA 58.172 50.000 0.00 0.00 0.00 2.69
1368 1377 0.919289 TCCTCCAATCCTCAACCCCC 60.919 60.000 0.00 0.00 0.00 5.40
1452 1461 2.795175 TGAGTCGAAAGAAAGCTCGT 57.205 45.000 0.00 0.00 45.01 4.18
1454 1463 5.793026 ATTCATGAGTCGAAAGAAAGCTC 57.207 39.130 0.00 0.00 45.01 4.09
1456 1465 6.654793 ACTATTCATGAGTCGAAAGAAAGC 57.345 37.500 0.00 0.00 45.01 3.51
1521 1533 3.117701 TCATGAAACCAGTGGAAAGGTCA 60.118 43.478 18.40 11.29 37.07 4.02
1532 1544 5.437289 TGTTAAGCAGTTCATGAAACCAG 57.563 39.130 10.35 1.69 38.76 4.00
1567 1582 7.069826 ACACCTCATCATCAAGAAAAAGGAAAA 59.930 33.333 0.00 0.00 31.35 2.29
1680 1700 3.947868 TGATCCAGAAAGAAAGCTCCAG 58.052 45.455 0.00 0.00 0.00 3.86
1916 1936 5.430089 AGATAGGAAGCTCATAGGTTGGTTT 59.570 40.000 0.00 0.00 35.86 3.27
2053 2073 2.962421 AGCTGCCTAGGATAGAACAGAC 59.038 50.000 14.75 5.69 42.77 3.51
2115 2135 6.385649 AAGTTGATACAACGAAACCATGTT 57.614 33.333 8.60 0.00 0.00 2.71
2180 2202 8.784043 CATAACAAATTTAGCTATGGTCTACCC 58.216 37.037 0.00 0.00 34.29 3.69
2293 2315 7.915397 GCATAGACATACAAACCAACTAAATGG 59.085 37.037 0.00 0.00 46.38 3.16
2294 2316 8.458052 TGCATAGACATACAAACCAACTAAATG 58.542 33.333 0.00 0.00 0.00 2.32
2520 2555 7.728083 AGGTTCATAGTCTCTACATAGCAGATT 59.272 37.037 0.00 0.00 0.00 2.40
2751 2786 5.874810 CCCATATATGTAATCAGTGTTCCGG 59.125 44.000 11.73 0.00 0.00 5.14
2796 2831 5.778134 GCATTTTGCATCACTTTTGTATCG 58.222 37.500 0.00 0.00 44.26 2.92
2891 2926 7.787028 ACCAAGTAAAGCAATTCCAAGTAAAA 58.213 30.769 0.00 0.00 0.00 1.52
2949 2984 5.163754 CCGTTTTAGCTCACCATTCCTTAAG 60.164 44.000 0.00 0.00 0.00 1.85
3528 3563 6.976934 TCTACTTCAGGTATGCATGTATGA 57.023 37.500 10.16 7.43 0.00 2.15
3585 3620 2.799017 ACAAATGCAGCTTCATCAGGA 58.201 42.857 0.00 0.00 0.00 3.86
3765 3802 8.902806 CATATTTTCTGTATGAGGGTGCTAAAA 58.097 33.333 0.00 0.00 32.52 1.52
3927 3970 1.194997 TCGCCCGTTAATTGTGAAACG 59.805 47.619 4.58 4.58 46.05 3.60
4007 4052 0.322816 TTCCATCTGGTGCAAGCCTC 60.323 55.000 0.00 0.00 36.34 4.70
4029 4074 6.431234 TGCCTTTTAGTCTCTTCCTCAAATTC 59.569 38.462 0.00 0.00 0.00 2.17
4174 4219 4.002982 CCCAATTTGTTCATCTCTGTCGA 58.997 43.478 0.00 0.00 0.00 4.20
4175 4220 3.127548 CCCCAATTTGTTCATCTCTGTCG 59.872 47.826 0.00 0.00 0.00 4.35
4464 4509 6.400568 AGACCATTTCCATGCAAAAATACAG 58.599 36.000 0.00 0.00 0.00 2.74
4497 4542 5.247110 AGCTTGAACTTCTAGAATCCAGTCA 59.753 40.000 5.44 3.07 0.00 3.41
4692 4737 7.603180 TTACATAGGCAGTGATTCAGTAGAT 57.397 36.000 0.00 0.00 0.00 1.98
4742 4787 7.012515 TGGTAAACATTTACGAGTGATTGTTGT 59.987 33.333 8.11 3.96 42.97 3.32
4814 4860 9.893305 AAGTAACTATTGCAGTTTTGAATGTAC 57.107 29.630 0.00 0.00 45.54 2.90
4871 4917 5.598830 TCCTCTATCTGACCCATAACACTTC 59.401 44.000 0.00 0.00 0.00 3.01
5154 5201 9.035607 CAATAGTTGCGACAGATTAATAACTCT 57.964 33.333 6.90 0.00 0.00 3.24
5282 5329 3.378427 GCATCCCTTCAACACCACTAATC 59.622 47.826 0.00 0.00 0.00 1.75
5332 5379 5.519566 GTGATCACAAGCACATTCACAAAAA 59.480 36.000 21.07 0.00 41.49 1.94
5372 5419 8.050778 ACATTGTGAAGAGAAACAACTAACAA 57.949 30.769 0.00 0.00 39.00 2.83
5373 5420 7.552687 AGACATTGTGAAGAGAAACAACTAACA 59.447 33.333 0.00 0.00 39.00 2.41
5444 5491 1.028905 CCAAAAGCAACCGTTCCAGA 58.971 50.000 0.00 0.00 0.00 3.86
5756 5807 1.603678 CGTACCTGTAAACACAGCCGT 60.604 52.381 0.00 0.00 36.46 5.68
5813 5867 5.392767 TCCCTAATTCGATCTGCTATCAC 57.607 43.478 0.00 0.00 0.00 3.06
5820 5874 5.023533 TGGACTTTCCCTAATTCGATCTG 57.976 43.478 0.00 0.00 35.03 2.90
5887 5942 7.177568 AGTGACATAGACACTGTACTTTCTCAT 59.822 37.037 0.00 0.00 45.19 2.90
5900 5955 7.753309 ATATGGAGTAGAGTGACATAGACAC 57.247 40.000 0.00 0.00 38.38 3.67
5987 6067 7.938563 TGTCTTAAACAAAACATAACCATGC 57.061 32.000 0.00 0.00 33.16 4.06
6121 6201 1.064003 TTGGGCAAGAGGACTGCTTA 58.936 50.000 0.00 0.00 0.00 3.09
6153 6233 2.428890 AGGATAACTGAGCCTTGAGACG 59.571 50.000 0.00 0.00 43.33 4.18
6168 6519 8.514330 AACTTAAAACGGCATGAATAGGATAA 57.486 30.769 0.00 0.00 0.00 1.75
6169 6520 7.227910 GGAACTTAAAACGGCATGAATAGGATA 59.772 37.037 0.00 0.00 0.00 2.59
6196 6547 7.832503 ATTTGTCCAAGAAAACAGTGAAAAG 57.167 32.000 0.00 0.00 0.00 2.27
6590 6942 4.588899 TGCTACCCCATATGAATATGTGC 58.411 43.478 3.65 0.76 38.73 4.57
6779 7131 5.880054 TTGGAAAGAAACGGATCTGAATC 57.120 39.130 9.00 5.91 0.00 2.52
6854 7206 2.276309 ATAGCTGCCTTGCCACCTCC 62.276 60.000 0.00 0.00 0.00 4.30
6893 7245 1.691219 AACCATCCTTGGGTGCGAT 59.309 52.632 0.00 0.00 43.13 4.58
6962 7314 4.777366 TGTCATCCTTCAACCTCTACATCA 59.223 41.667 0.00 0.00 0.00 3.07
6965 7317 5.485353 AGAATGTCATCCTTCAACCTCTACA 59.515 40.000 0.00 0.00 0.00 2.74
7137 7489 4.058817 GGCCTATCTACGAAATTCTGTGG 58.941 47.826 0.00 0.00 0.00 4.17
7166 7518 2.224402 ACAGCAGGTCTTCTCTTGTTCC 60.224 50.000 0.00 0.00 0.00 3.62
7233 7587 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
7235 7589 2.580589 GAAACACACACACACACACAC 58.419 47.619 0.00 0.00 0.00 3.82
7236 7590 1.537638 GGAAACACACACACACACACA 59.462 47.619 0.00 0.00 0.00 3.72
7237 7591 1.135517 GGGAAACACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
7238 7592 1.169577 GGGAAACACACACACACACA 58.830 50.000 0.00 0.00 0.00 3.72
7239 7593 0.454196 GGGGAAACACACACACACAC 59.546 55.000 0.00 0.00 0.00 3.82
7240 7594 0.681564 GGGGGAAACACACACACACA 60.682 55.000 0.00 0.00 32.66 3.72
7241 7595 2.112029 GGGGGAAACACACACACAC 58.888 57.895 0.00 0.00 32.66 3.82
7242 7596 4.668151 GGGGGAAACACACACACA 57.332 55.556 0.00 0.00 32.66 3.72
7316 7670 2.472816 ACGCAAAAGCCATGAAACAAG 58.527 42.857 0.00 0.00 0.00 3.16
7393 7747 9.628500 ATGCAGTGCAATCATCTCATTATATAT 57.372 29.630 23.90 0.00 43.62 0.86
7458 7815 6.650807 TGTCTTCAAACACTTCCATATCAGAC 59.349 38.462 0.00 0.00 0.00 3.51
7497 7856 6.605471 AGTGTCATGGTAGATCAGTTGTAA 57.395 37.500 0.00 0.00 0.00 2.41
7498 7857 7.898014 ATAGTGTCATGGTAGATCAGTTGTA 57.102 36.000 0.00 0.00 0.00 2.41
7499 7858 6.798427 ATAGTGTCATGGTAGATCAGTTGT 57.202 37.500 0.00 0.00 0.00 3.32
7539 7899 8.397906 TGTCACACTTAATGTTCTCTTTTCTTG 58.602 33.333 0.00 0.00 40.64 3.02
7575 7935 1.834896 TGCCTGAAATCCTACCGCTTA 59.165 47.619 0.00 0.00 0.00 3.09
7578 7938 1.095807 GGTGCCTGAAATCCTACCGC 61.096 60.000 0.00 0.00 0.00 5.68
7579 7939 0.541863 AGGTGCCTGAAATCCTACCG 59.458 55.000 0.00 0.00 33.55 4.02
7787 8154 0.673022 CCGCTCTTCTCTTTGCTGCT 60.673 55.000 0.00 0.00 0.00 4.24
7810 8178 1.330655 AATGATCGGTCCGCCTCAGT 61.331 55.000 17.66 13.93 0.00 3.41
7940 8308 1.443872 CGAGTGGTACGACTGCACC 60.444 63.158 15.86 0.00 35.24 5.01
7942 8310 1.167781 TGACGAGTGGTACGACTGCA 61.168 55.000 15.86 7.83 34.70 4.41


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

AutoCloner maintained by Alex Coulton.