Multiple sequence alignment - TraesCS5B01G353800

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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 TraesCS5B01G353800 chr5B 100.000 2885 0 0 1 2885 533377026 533374142 0.000000e+00 5328
1 TraesCS5B01G353800 chr5B 77.850 1544 277 53 362 1886 533509305 533507808 0.000000e+00 896
2 TraesCS5B01G353800 chr5B 77.532 1540 292 46 371 1891 533494252 533492748 0.000000e+00 878
3 TraesCS5B01G353800 chrUn 88.808 1930 183 15 111 2025 345139765 345137854 0.000000e+00 2337
4 TraesCS5B01G353800 chr1B 94.840 814 17 5 2027 2815 252370972 252370159 0.000000e+00 1247
5 TraesCS5B01G353800 chr1B 94.717 814 18 8 2027 2815 252364174 252363361 0.000000e+00 1242
6 TraesCS5B01G353800 chr1B 91.677 817 40 9 2027 2818 340401222 340402035 0.000000e+00 1107
7 TraesCS5B01G353800 chr1B 93.478 92 2 2 2798 2885 668496222 668496313 1.800000e-27 134
8 TraesCS5B01G353800 chr7B 94.595 814 18 6 2027 2815 85549153 85549965 0.000000e+00 1236
9 TraesCS5B01G353800 chr7B 94.595 814 19 3 2027 2815 85556016 85556829 0.000000e+00 1236
10 TraesCS5B01G353800 chr7B 94.103 814 23 3 2027 2815 616847024 616846211 0.000000e+00 1214
11 TraesCS5B01G353800 chr7B 76.600 953 178 34 491 1426 59066423 59067347 1.550000e-132 483
12 TraesCS5B01G353800 chr6B 94.370 817 21 7 2024 2815 651468950 651469766 0.000000e+00 1230
13 TraesCS5B01G353800 chr6B 91.626 824 35 11 2027 2818 102454869 102455690 0.000000e+00 1109
14 TraesCS5B01G353800 chr2A 80.703 1622 277 28 317 1919 52763142 52761538 0.000000e+00 1229
15 TraesCS5B01G353800 chr4B 94.479 797 35 5 2027 2815 51906392 51907187 0.000000e+00 1219
16 TraesCS5B01G353800 chr4B 94.228 797 37 5 2027 2815 51899525 51900320 0.000000e+00 1208
17 TraesCS5B01G353800 chr2B 90.201 796 56 18 2027 2815 173219574 173220354 0.000000e+00 1018
18 TraesCS5B01G353800 chr7D 86.343 886 66 35 2027 2884 29008870 29008012 0.000000e+00 915
19 TraesCS5B01G353800 chr7D 77.311 952 181 28 491 1426 101732744 101733676 1.970000e-146 529
20 TraesCS5B01G353800 chr5A 77.929 1545 285 46 371 1891 554201335 554199823 0.000000e+00 913
21 TraesCS5B01G353800 chr5A 77.352 1541 282 47 375 1898 554228847 554227357 0.000000e+00 850
22 TraesCS5B01G353800 chr5A 77.446 1441 277 27 375 1803 554060480 554059076 0.000000e+00 817
23 TraesCS5B01G353800 chr5A 100.000 77 0 0 2809 2885 547101311 547101387 3.000000e-30 143
24 TraesCS5B01G353800 chr3D 86.234 879 69 30 2027 2880 234726467 234725616 0.000000e+00 905
25 TraesCS5B01G353800 chr3D 76.893 1030 203 23 465 1482 7498343 7497337 4.200000e-153 551
26 TraesCS5B01G353800 chr3D 86.957 115 12 2 2767 2881 54746960 54747071 3.020000e-25 126
27 TraesCS5B01G353800 chr5D 77.720 1544 280 53 362 1886 438605225 438603727 0.000000e+00 887
28 TraesCS5B01G353800 chr5D 77.626 1542 288 48 371 1891 438589662 438588157 0.000000e+00 883
29 TraesCS5B01G353800 chr5D 77.988 1481 271 45 341 1806 438559120 438557680 0.000000e+00 878
30 TraesCS5B01G353800 chr1D 85.504 883 80 31 2027 2885 3944951 3944093 0.000000e+00 878
31 TraesCS5B01G353800 chr3B 77.382 1123 214 28 376 1482 9569970 9568872 5.250000e-177 630
32 TraesCS5B01G353800 chr2D 93.210 162 7 4 2662 2821 351585160 351585001 4.810000e-58 235
33 TraesCS5B01G353800 chr4D 89.474 114 8 1 2767 2880 504122054 504122163 1.080000e-29 141
34 TraesCS5B01G353800 chr6A 92.000 100 1 6 2787 2885 550849745 550849652 1.800000e-27 134
35 TraesCS5B01G353800 chr6D 93.182 88 3 3 2799 2885 473129477 473129392 3.020000e-25 126


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 TraesCS5B01G353800 chr5B 533374142 533377026 2884 True 5328 5328 100.000 1 2885 1 chr5B.!!$R1 2884
1 TraesCS5B01G353800 chr5B 533507808 533509305 1497 True 896 896 77.850 362 1886 1 chr5B.!!$R3 1524
2 TraesCS5B01G353800 chr5B 533492748 533494252 1504 True 878 878 77.532 371 1891 1 chr5B.!!$R2 1520
3 TraesCS5B01G353800 chrUn 345137854 345139765 1911 True 2337 2337 88.808 111 2025 1 chrUn.!!$R1 1914
4 TraesCS5B01G353800 chr1B 252370159 252370972 813 True 1247 1247 94.840 2027 2815 1 chr1B.!!$R2 788
5 TraesCS5B01G353800 chr1B 252363361 252364174 813 True 1242 1242 94.717 2027 2815 1 chr1B.!!$R1 788
6 TraesCS5B01G353800 chr1B 340401222 340402035 813 False 1107 1107 91.677 2027 2818 1 chr1B.!!$F1 791
7 TraesCS5B01G353800 chr7B 85549153 85549965 812 False 1236 1236 94.595 2027 2815 1 chr7B.!!$F2 788
8 TraesCS5B01G353800 chr7B 85556016 85556829 813 False 1236 1236 94.595 2027 2815 1 chr7B.!!$F3 788
9 TraesCS5B01G353800 chr7B 616846211 616847024 813 True 1214 1214 94.103 2027 2815 1 chr7B.!!$R1 788
10 TraesCS5B01G353800 chr7B 59066423 59067347 924 False 483 483 76.600 491 1426 1 chr7B.!!$F1 935
11 TraesCS5B01G353800 chr6B 651468950 651469766 816 False 1230 1230 94.370 2024 2815 1 chr6B.!!$F2 791
12 TraesCS5B01G353800 chr6B 102454869 102455690 821 False 1109 1109 91.626 2027 2818 1 chr6B.!!$F1 791
13 TraesCS5B01G353800 chr2A 52761538 52763142 1604 True 1229 1229 80.703 317 1919 1 chr2A.!!$R1 1602
14 TraesCS5B01G353800 chr4B 51906392 51907187 795 False 1219 1219 94.479 2027 2815 1 chr4B.!!$F2 788
15 TraesCS5B01G353800 chr4B 51899525 51900320 795 False 1208 1208 94.228 2027 2815 1 chr4B.!!$F1 788
16 TraesCS5B01G353800 chr2B 173219574 173220354 780 False 1018 1018 90.201 2027 2815 1 chr2B.!!$F1 788
17 TraesCS5B01G353800 chr7D 29008012 29008870 858 True 915 915 86.343 2027 2884 1 chr7D.!!$R1 857
18 TraesCS5B01G353800 chr7D 101732744 101733676 932 False 529 529 77.311 491 1426 1 chr7D.!!$F1 935
19 TraesCS5B01G353800 chr5A 554199823 554201335 1512 True 913 913 77.929 371 1891 1 chr5A.!!$R2 1520
20 TraesCS5B01G353800 chr5A 554227357 554228847 1490 True 850 850 77.352 375 1898 1 chr5A.!!$R3 1523
21 TraesCS5B01G353800 chr5A 554059076 554060480 1404 True 817 817 77.446 375 1803 1 chr5A.!!$R1 1428
22 TraesCS5B01G353800 chr3D 234725616 234726467 851 True 905 905 86.234 2027 2880 1 chr3D.!!$R2 853
23 TraesCS5B01G353800 chr3D 7497337 7498343 1006 True 551 551 76.893 465 1482 1 chr3D.!!$R1 1017
24 TraesCS5B01G353800 chr5D 438603727 438605225 1498 True 887 887 77.720 362 1886 1 chr5D.!!$R3 1524
25 TraesCS5B01G353800 chr5D 438588157 438589662 1505 True 883 883 77.626 371 1891 1 chr5D.!!$R2 1520
26 TraesCS5B01G353800 chr5D 438557680 438559120 1440 True 878 878 77.988 341 1806 1 chr5D.!!$R1 1465
27 TraesCS5B01G353800 chr1D 3944093 3944951 858 True 878 878 85.504 2027 2885 1 chr1D.!!$R1 858
28 TraesCS5B01G353800 chr3B 9568872 9569970 1098 True 630 630 77.382 376 1482 1 chr3B.!!$R1 1106

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
24 25 0.782384 GCGGGAGTTTATATGCGTCG 59.218 55.0 0.0 0.0 0.0 5.12 F
55 56 0.995024 AGGTTGCTACTTCCCATGCT 59.005 50.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1800 0.036388 TGTTGTGCTTCCGATCTCCC 60.036 55.0 0.0 0.0 0.00 4.3 R
1963 2021 1.126948 AATGGCCCCAAACCAACTGG 61.127 55.0 0.0 0.0 41.49 4.0 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
20 21 3.542712 CACATGCGGGAGTTTATATGC 57.457 47.619 0.00 0.00 0.00 3.14
21 22 2.096268 CACATGCGGGAGTTTATATGCG 60.096 50.000 0.00 0.00 0.00 4.73
22 23 2.143122 CATGCGGGAGTTTATATGCGT 58.857 47.619 0.00 0.00 0.00 5.24
23 24 1.860676 TGCGGGAGTTTATATGCGTC 58.139 50.000 0.00 0.00 0.00 5.19
24 25 0.782384 GCGGGAGTTTATATGCGTCG 59.218 55.000 0.00 0.00 0.00 5.12
25 26 1.601162 GCGGGAGTTTATATGCGTCGA 60.601 52.381 0.00 0.00 0.00 4.20
26 27 2.925306 GCGGGAGTTTATATGCGTCGAT 60.925 50.000 0.00 0.00 0.00 3.59
27 28 2.915463 CGGGAGTTTATATGCGTCGATC 59.085 50.000 0.00 0.00 0.00 3.69
28 29 2.915463 GGGAGTTTATATGCGTCGATCG 59.085 50.000 9.36 9.36 43.12 3.69
29 30 3.365666 GGGAGTTTATATGCGTCGATCGA 60.366 47.826 15.15 15.15 42.86 3.59
30 31 4.224433 GGAGTTTATATGCGTCGATCGAA 58.776 43.478 21.31 4.66 42.86 3.71
31 32 4.857588 GGAGTTTATATGCGTCGATCGAAT 59.142 41.667 21.31 12.63 42.86 3.34
32 33 5.345202 GGAGTTTATATGCGTCGATCGAATT 59.655 40.000 21.31 7.44 42.86 2.17
33 34 6.128902 GGAGTTTATATGCGTCGATCGAATTT 60.129 38.462 21.31 7.84 42.86 1.82
34 35 7.173863 AGTTTATATGCGTCGATCGAATTTT 57.826 32.000 21.31 8.17 42.86 1.82
35 36 7.063456 AGTTTATATGCGTCGATCGAATTTTG 58.937 34.615 21.31 8.64 42.86 2.44
36 37 6.757026 TTATATGCGTCGATCGAATTTTGA 57.243 33.333 21.31 4.35 42.86 2.69
37 38 3.575858 ATGCGTCGATCGAATTTTGAG 57.424 42.857 21.31 6.59 42.86 3.02
38 39 1.658596 TGCGTCGATCGAATTTTGAGG 59.341 47.619 21.31 2.61 42.86 3.86
39 40 1.659098 GCGTCGATCGAATTTTGAGGT 59.341 47.619 21.31 0.00 42.86 3.85
40 41 2.093783 GCGTCGATCGAATTTTGAGGTT 59.906 45.455 21.31 0.00 42.86 3.50
41 42 3.659735 CGTCGATCGAATTTTGAGGTTG 58.340 45.455 21.31 0.00 42.86 3.77
42 43 3.417185 GTCGATCGAATTTTGAGGTTGC 58.583 45.455 21.31 0.00 0.00 4.17
43 44 3.125316 GTCGATCGAATTTTGAGGTTGCT 59.875 43.478 21.31 0.00 0.00 3.91
44 45 4.328983 GTCGATCGAATTTTGAGGTTGCTA 59.671 41.667 21.31 0.00 0.00 3.49
45 46 4.328983 TCGATCGAATTTTGAGGTTGCTAC 59.671 41.667 16.99 0.00 0.00 3.58
46 47 4.330074 CGATCGAATTTTGAGGTTGCTACT 59.670 41.667 10.26 0.00 0.00 2.57
47 48 5.163854 CGATCGAATTTTGAGGTTGCTACTT 60.164 40.000 10.26 0.00 0.00 2.24
48 49 5.607119 TCGAATTTTGAGGTTGCTACTTC 57.393 39.130 3.49 3.49 0.00 3.01
49 50 4.454504 TCGAATTTTGAGGTTGCTACTTCC 59.545 41.667 7.87 0.00 29.74 3.46
50 51 4.379499 CGAATTTTGAGGTTGCTACTTCCC 60.379 45.833 7.87 0.00 29.74 3.97
51 52 3.586470 TTTTGAGGTTGCTACTTCCCA 57.414 42.857 7.87 0.00 29.74 4.37
52 53 3.806949 TTTGAGGTTGCTACTTCCCAT 57.193 42.857 7.87 0.00 29.74 4.00
53 54 2.787473 TGAGGTTGCTACTTCCCATG 57.213 50.000 7.87 0.00 29.74 3.66
54 55 1.340017 TGAGGTTGCTACTTCCCATGC 60.340 52.381 7.87 0.00 29.74 4.06
55 56 0.995024 AGGTTGCTACTTCCCATGCT 59.005 50.000 0.00 0.00 0.00 3.79
56 57 1.065126 AGGTTGCTACTTCCCATGCTC 60.065 52.381 0.00 0.00 0.00 4.26
57 58 1.340017 GGTTGCTACTTCCCATGCTCA 60.340 52.381 0.00 0.00 0.00 4.26
58 59 2.436417 GTTGCTACTTCCCATGCTCAA 58.564 47.619 0.00 0.00 0.00 3.02
59 60 2.408271 TGCTACTTCCCATGCTCAAG 57.592 50.000 0.00 0.00 0.00 3.02
60 61 1.630369 TGCTACTTCCCATGCTCAAGT 59.370 47.619 7.18 7.18 34.68 3.16
61 62 2.837591 TGCTACTTCCCATGCTCAAGTA 59.162 45.455 8.34 8.34 32.56 2.24
62 63 3.263170 TGCTACTTCCCATGCTCAAGTAA 59.737 43.478 9.41 0.00 33.30 2.24
63 64 4.080356 TGCTACTTCCCATGCTCAAGTAAT 60.080 41.667 9.41 0.00 33.30 1.89
64 65 4.513318 GCTACTTCCCATGCTCAAGTAATC 59.487 45.833 9.41 3.63 33.30 1.75
65 66 4.574674 ACTTCCCATGCTCAAGTAATCA 57.425 40.909 1.46 0.00 0.00 2.57
66 67 4.265073 ACTTCCCATGCTCAAGTAATCAC 58.735 43.478 1.46 0.00 0.00 3.06
67 68 3.998913 TCCCATGCTCAAGTAATCACA 57.001 42.857 0.00 0.00 0.00 3.58
68 69 4.299586 TCCCATGCTCAAGTAATCACAA 57.700 40.909 0.00 0.00 0.00 3.33
69 70 4.858850 TCCCATGCTCAAGTAATCACAAT 58.141 39.130 0.00 0.00 0.00 2.71
70 71 5.263599 TCCCATGCTCAAGTAATCACAATT 58.736 37.500 0.00 0.00 0.00 2.32
71 72 5.716228 TCCCATGCTCAAGTAATCACAATTT 59.284 36.000 0.00 0.00 0.00 1.82
72 73 6.211184 TCCCATGCTCAAGTAATCACAATTTT 59.789 34.615 0.00 0.00 0.00 1.82
73 74 7.395772 TCCCATGCTCAAGTAATCACAATTTTA 59.604 33.333 0.00 0.00 0.00 1.52
74 75 7.703621 CCCATGCTCAAGTAATCACAATTTTAG 59.296 37.037 0.00 0.00 0.00 1.85
75 76 8.461222 CCATGCTCAAGTAATCACAATTTTAGA 58.539 33.333 0.00 0.00 0.00 2.10
76 77 9.844790 CATGCTCAAGTAATCACAATTTTAGAA 57.155 29.630 0.00 0.00 0.00 2.10
96 97 9.760077 TTTAGAAATACTCGATATTGAAGGGAC 57.240 33.333 0.00 0.00 33.53 4.46
97 98 7.604657 AGAAATACTCGATATTGAAGGGACT 57.395 36.000 0.00 0.00 34.67 3.85
98 99 8.707796 AGAAATACTCGATATTGAAGGGACTA 57.292 34.615 0.00 0.00 32.69 2.59
99 100 8.578151 AGAAATACTCGATATTGAAGGGACTAC 58.422 37.037 0.00 0.00 32.69 2.73
100 101 4.832590 ACTCGATATTGAAGGGACTACG 57.167 45.455 0.00 0.00 38.49 3.51
101 102 4.458397 ACTCGATATTGAAGGGACTACGA 58.542 43.478 0.00 0.00 38.49 3.43
102 103 4.515944 ACTCGATATTGAAGGGACTACGAG 59.484 45.833 0.00 0.00 46.13 4.18
103 104 4.711399 TCGATATTGAAGGGACTACGAGA 58.289 43.478 0.00 0.00 38.49 4.04
104 105 4.514441 TCGATATTGAAGGGACTACGAGAC 59.486 45.833 0.00 0.00 38.49 3.36
105 106 4.275196 CGATATTGAAGGGACTACGAGACA 59.725 45.833 0.00 0.00 38.49 3.41
106 107 5.220989 CGATATTGAAGGGACTACGAGACAA 60.221 44.000 0.00 0.00 38.49 3.18
107 108 3.936372 TTGAAGGGACTACGAGACAAG 57.064 47.619 0.00 0.00 38.49 3.16
108 109 3.150458 TGAAGGGACTACGAGACAAGA 57.850 47.619 0.00 0.00 38.49 3.02
109 110 3.493334 TGAAGGGACTACGAGACAAGAA 58.507 45.455 0.00 0.00 38.49 2.52
116 117 5.120363 GGGACTACGAGACAAGAAAAATGTC 59.880 44.000 0.00 0.00 45.94 3.06
124 125 5.499139 GACAAGAAAAATGTCTGGACACA 57.501 39.130 5.52 0.00 45.05 3.72
125 126 5.505173 ACAAGAAAAATGTCTGGACACAG 57.495 39.130 5.52 0.00 45.05 3.66
173 181 5.880164 TGTATGATTTTCGTGGGATAGGA 57.120 39.130 0.00 0.00 0.00 2.94
180 188 4.737855 TTTCGTGGGATAGGAGAAGAAG 57.262 45.455 0.00 0.00 0.00 2.85
189 197 4.412528 GGATAGGAGAAGAAGGGGCTTAAA 59.587 45.833 0.00 0.00 0.00 1.52
191 199 4.741928 AGGAGAAGAAGGGGCTTAAAAA 57.258 40.909 0.00 0.00 0.00 1.94
218 228 4.002982 TCCATCAAGTTGTCTTTGATCGG 58.997 43.478 2.11 4.54 0.00 4.18
232 242 8.210946 TGTCTTTGATCGGTATCCATTTTATCT 58.789 33.333 0.00 0.00 0.00 1.98
235 245 6.680148 TGATCGGTATCCATTTTATCTGGA 57.320 37.500 0.00 0.00 46.45 3.86
242 252 4.524802 TCCATTTTATCTGGACAGCCAT 57.475 40.909 0.00 0.00 44.91 4.40
244 254 5.271598 TCCATTTTATCTGGACAGCCATTT 58.728 37.500 0.00 0.00 44.91 2.32
246 256 6.044682 CCATTTTATCTGGACAGCCATTTTC 58.955 40.000 0.00 0.00 44.91 2.29
247 257 5.659440 TTTTATCTGGACAGCCATTTTCC 57.341 39.130 0.00 0.00 44.91 3.13
259 269 2.689983 GCCATTTTCCATGGTGGTAGAG 59.310 50.000 17.88 3.19 41.17 2.43
260 270 3.290710 CCATTTTCCATGGTGGTAGAGG 58.709 50.000 12.58 2.99 39.03 3.69
267 277 1.837439 CATGGTGGTAGAGGTGCCTTA 59.163 52.381 0.00 0.00 0.00 2.69
295 305 3.535280 TTTTGTCTTGTTTTGGGAGGC 57.465 42.857 0.00 0.00 0.00 4.70
297 307 1.981256 TGTCTTGTTTTGGGAGGCTC 58.019 50.000 5.78 5.78 0.00 4.70
302 312 2.151502 TGTTTTGGGAGGCTCACAAA 57.848 45.000 34.74 34.74 46.92 2.83
310 320 1.611936 GGAGGCTCACAAAGGGAAGAC 60.612 57.143 17.69 0.00 0.00 3.01
321 331 7.685481 TCACAAAGGGAAGACTAATGAACATA 58.315 34.615 0.00 0.00 0.00 2.29
388 406 6.828785 GCTCTTGGAAGGGAAATGACTATTAA 59.171 38.462 0.00 0.00 0.00 1.40
410 428 4.861102 ATTGTGGAAGCAGGAAAGAAAG 57.139 40.909 0.00 0.00 0.00 2.62
414 432 4.578928 TGTGGAAGCAGGAAAGAAAGTAAC 59.421 41.667 0.00 0.00 0.00 2.50
504 522 4.897076 CCATCCCCATGATCAAGAATTTCA 59.103 41.667 0.00 0.00 30.57 2.69
531 549 5.601662 TGTAAGATTAGAAGAGATTGCCCG 58.398 41.667 0.00 0.00 0.00 6.13
594 612 3.344515 GAGGCTTCGGGAAAGTTTACAT 58.655 45.455 0.00 0.00 37.31 2.29
605 623 6.567132 CGGGAAAGTTTACATGGTAACTTGAC 60.567 42.308 21.04 17.91 42.17 3.18
606 624 6.263617 GGGAAAGTTTACATGGTAACTTGACA 59.736 38.462 21.04 0.00 42.17 3.58
745 776 2.751806 GCTGTCAAGAGGCTAAGCAAAT 59.248 45.455 0.00 0.00 0.00 2.32
920 953 6.628185 CCACCCTCTTTGGTATATATACGAC 58.372 44.000 15.15 4.85 36.67 4.34
923 956 8.457261 CACCCTCTTTGGTATATATACGACTAC 58.543 40.741 15.15 3.60 36.67 2.73
924 957 8.389366 ACCCTCTTTGGTATATATACGACTACT 58.611 37.037 15.15 0.00 36.67 2.57
1165 1204 7.118723 ACCTAAGATTGCAGATTTTGGTATGA 58.881 34.615 9.34 0.00 29.13 2.15
1300 1340 8.908903 TCTTCCATTTGCTAACTCTTTTGTTTA 58.091 29.630 0.00 0.00 0.00 2.01
1432 1475 6.267014 CCGGTATAAGGAGAAACTCTAATGGA 59.733 42.308 0.00 0.00 0.00 3.41
1451 1494 3.631686 TGGACACACAATGAGTTTTCCTG 59.368 43.478 8.84 0.00 0.00 3.86
1459 1502 2.526304 TGAGTTTTCCTGGTCTCACG 57.474 50.000 0.00 0.00 32.95 4.35
1645 1700 3.886505 AGACTCGTCTCTCATGGATAACC 59.113 47.826 0.00 0.00 34.17 2.85
1709 1764 1.067060 GTGTGTCCAAGAAAACCCAGC 59.933 52.381 0.00 0.00 0.00 4.85
1745 1800 4.271590 TGTCAAATGTTGTGTTCGTCTG 57.728 40.909 0.00 0.00 0.00 3.51
1751 1806 1.691976 TGTTGTGTTCGTCTGGGAGAT 59.308 47.619 0.00 0.00 0.00 2.75
1752 1807 2.288825 TGTTGTGTTCGTCTGGGAGATC 60.289 50.000 0.00 0.00 0.00 2.75
1808 1863 1.279527 TACTTTGCACGACGAAGCGG 61.280 55.000 0.00 2.90 42.81 5.52
1810 1865 3.793775 TTTGCACGACGAAGCGGGA 62.794 57.895 0.00 0.00 36.64 5.14
1819 1874 2.202566 GACGAAGCGGGAAAATAGAGG 58.797 52.381 0.00 0.00 0.00 3.69
1823 1878 3.687698 CGAAGCGGGAAAATAGAGGAAAA 59.312 43.478 0.00 0.00 0.00 2.29
1956 2014 3.250762 GCCAGGAAAAGAAACAAAATGGC 59.749 43.478 0.00 0.00 43.33 4.40
1963 2021 2.769893 AGAAACAAAATGGCCATGCAC 58.230 42.857 21.63 7.07 0.00 4.57
1966 2024 0.322322 ACAAAATGGCCATGCACCAG 59.678 50.000 21.63 9.03 41.46 4.00
1980 2038 2.123077 CCAGTTGGTTTGGGGCCA 60.123 61.111 4.39 0.00 31.87 5.36
1985 2043 2.168313 CAGTTGGTTTGGGGCCATTATC 59.832 50.000 4.39 0.00 35.71 1.75
1987 2045 2.157640 TGGTTTGGGGCCATTATCTG 57.842 50.000 4.39 0.00 0.00 2.90
1993 2051 5.076873 GTTTGGGGCCATTATCTGCTAATA 58.923 41.667 4.39 0.00 0.00 0.98
1994 2052 4.574674 TGGGGCCATTATCTGCTAATAG 57.425 45.455 4.39 0.00 0.00 1.73
2108 2167 2.168728 GACTAGCAACGAGGGGAAGAAT 59.831 50.000 0.00 0.00 0.00 2.40
2174 2233 1.071857 GAGAACGGGGTTGAAGGAGTT 59.928 52.381 0.00 0.00 0.00 3.01
2217 2276 0.962489 CGGAGATCCTAGTGCCGAAT 59.038 55.000 0.00 0.00 44.43 3.34
2230 2289 2.579201 CGAATGGACGGCACCTCT 59.421 61.111 0.00 0.00 0.00 3.69
2542 2608 7.122650 GTGGGAGGAAAGAAATCACATCATTTA 59.877 37.037 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.096268 CGCATATAAACTCCCGCATGTG 60.096 50.000 0.00 0.00 0.00 3.21
1 2 2.143122 CGCATATAAACTCCCGCATGT 58.857 47.619 0.00 0.00 0.00 3.21
2 3 2.143122 ACGCATATAAACTCCCGCATG 58.857 47.619 0.00 0.00 0.00 4.06
3 4 2.413837 GACGCATATAAACTCCCGCAT 58.586 47.619 0.00 0.00 0.00 4.73
4 5 1.860676 GACGCATATAAACTCCCGCA 58.139 50.000 0.00 0.00 0.00 5.69
5 6 0.782384 CGACGCATATAAACTCCCGC 59.218 55.000 0.00 0.00 0.00 6.13
6 7 2.410785 TCGACGCATATAAACTCCCG 57.589 50.000 0.00 0.00 0.00 5.14
7 8 2.915463 CGATCGACGCATATAAACTCCC 59.085 50.000 10.26 0.00 34.51 4.30
8 9 3.818387 TCGATCGACGCATATAAACTCC 58.182 45.455 15.15 0.00 42.26 3.85
9 10 5.994235 ATTCGATCGACGCATATAAACTC 57.006 39.130 19.26 0.00 42.26 3.01
10 11 6.764877 AAATTCGATCGACGCATATAAACT 57.235 33.333 19.26 0.00 42.26 2.66
11 12 7.061027 TCAAAATTCGATCGACGCATATAAAC 58.939 34.615 19.26 0.00 42.26 2.01
12 13 7.167831 TCAAAATTCGATCGACGCATATAAA 57.832 32.000 19.26 0.00 42.26 1.40
13 14 6.128929 CCTCAAAATTCGATCGACGCATATAA 60.129 38.462 19.26 0.00 42.26 0.98
14 15 5.344933 CCTCAAAATTCGATCGACGCATATA 59.655 40.000 19.26 0.81 42.26 0.86
15 16 4.150627 CCTCAAAATTCGATCGACGCATAT 59.849 41.667 19.26 5.25 42.26 1.78
16 17 3.489416 CCTCAAAATTCGATCGACGCATA 59.511 43.478 19.26 2.54 42.26 3.14
17 18 2.285220 CCTCAAAATTCGATCGACGCAT 59.715 45.455 19.26 6.09 42.26 4.73
18 19 1.658596 CCTCAAAATTCGATCGACGCA 59.341 47.619 19.26 3.42 42.26 5.24
19 20 1.659098 ACCTCAAAATTCGATCGACGC 59.341 47.619 19.26 0.00 42.26 5.19
20 21 3.659735 CAACCTCAAAATTCGATCGACG 58.340 45.455 19.26 4.38 44.09 5.12
21 22 3.125316 AGCAACCTCAAAATTCGATCGAC 59.875 43.478 19.26 1.06 0.00 4.20
22 23 3.334691 AGCAACCTCAAAATTCGATCGA 58.665 40.909 15.15 15.15 0.00 3.59
23 24 3.747099 AGCAACCTCAAAATTCGATCG 57.253 42.857 9.36 9.36 0.00 3.69
24 25 5.803020 AGTAGCAACCTCAAAATTCGATC 57.197 39.130 0.00 0.00 0.00 3.69
25 26 5.123979 GGAAGTAGCAACCTCAAAATTCGAT 59.876 40.000 0.00 0.00 0.00 3.59
26 27 4.454504 GGAAGTAGCAACCTCAAAATTCGA 59.545 41.667 0.00 0.00 0.00 3.71
27 28 4.379499 GGGAAGTAGCAACCTCAAAATTCG 60.379 45.833 0.00 0.00 0.00 3.34
28 29 4.522789 TGGGAAGTAGCAACCTCAAAATTC 59.477 41.667 0.00 0.00 0.00 2.17
29 30 4.479158 TGGGAAGTAGCAACCTCAAAATT 58.521 39.130 0.00 0.00 0.00 1.82
30 31 4.112634 TGGGAAGTAGCAACCTCAAAAT 57.887 40.909 0.00 0.00 0.00 1.82
31 32 3.586470 TGGGAAGTAGCAACCTCAAAA 57.414 42.857 0.00 0.00 0.00 2.44
32 33 3.420893 CATGGGAAGTAGCAACCTCAAA 58.579 45.455 0.00 0.00 0.00 2.69
33 34 2.879756 GCATGGGAAGTAGCAACCTCAA 60.880 50.000 0.00 0.00 0.00 3.02
34 35 1.340017 GCATGGGAAGTAGCAACCTCA 60.340 52.381 0.00 0.00 0.00 3.86
35 36 1.065126 AGCATGGGAAGTAGCAACCTC 60.065 52.381 0.00 0.00 0.00 3.85
36 37 0.995024 AGCATGGGAAGTAGCAACCT 59.005 50.000 0.00 0.00 0.00 3.50
37 38 1.340017 TGAGCATGGGAAGTAGCAACC 60.340 52.381 0.00 0.00 0.00 3.77
38 39 2.113860 TGAGCATGGGAAGTAGCAAC 57.886 50.000 0.00 0.00 0.00 4.17
39 40 2.040278 ACTTGAGCATGGGAAGTAGCAA 59.960 45.455 0.00 0.00 0.00 3.91
40 41 1.630369 ACTTGAGCATGGGAAGTAGCA 59.370 47.619 0.00 0.00 0.00 3.49
41 42 2.409948 ACTTGAGCATGGGAAGTAGC 57.590 50.000 0.00 0.00 0.00 3.58
42 43 5.525378 GTGATTACTTGAGCATGGGAAGTAG 59.475 44.000 0.00 0.00 34.51 2.57
43 44 5.045942 TGTGATTACTTGAGCATGGGAAGTA 60.046 40.000 0.00 0.00 32.27 2.24
44 45 4.263462 TGTGATTACTTGAGCATGGGAAGT 60.263 41.667 0.00 0.00 34.36 3.01
45 46 4.264253 TGTGATTACTTGAGCATGGGAAG 58.736 43.478 0.00 0.00 0.00 3.46
46 47 4.299586 TGTGATTACTTGAGCATGGGAA 57.700 40.909 0.00 0.00 0.00 3.97
47 48 3.998913 TGTGATTACTTGAGCATGGGA 57.001 42.857 0.00 0.00 0.00 4.37
48 49 5.587388 AATTGTGATTACTTGAGCATGGG 57.413 39.130 0.00 0.00 0.00 4.00
49 50 8.461222 TCTAAAATTGTGATTACTTGAGCATGG 58.539 33.333 0.00 0.00 0.00 3.66
50 51 9.844790 TTCTAAAATTGTGATTACTTGAGCATG 57.155 29.630 0.00 0.00 0.00 4.06
70 71 9.760077 GTCCCTTCAATATCGAGTATTTCTAAA 57.240 33.333 0.00 0.00 30.53 1.85
71 72 9.144298 AGTCCCTTCAATATCGAGTATTTCTAA 57.856 33.333 0.00 0.00 30.53 2.10
72 73 8.707796 AGTCCCTTCAATATCGAGTATTTCTA 57.292 34.615 0.00 0.00 30.53 2.10
73 74 7.604657 AGTCCCTTCAATATCGAGTATTTCT 57.395 36.000 0.00 0.00 30.53 2.52
74 75 7.537991 CGTAGTCCCTTCAATATCGAGTATTTC 59.462 40.741 0.00 0.00 30.53 2.17
75 76 7.230108 TCGTAGTCCCTTCAATATCGAGTATTT 59.770 37.037 0.00 0.00 30.53 1.40
76 77 6.713903 TCGTAGTCCCTTCAATATCGAGTATT 59.286 38.462 0.00 0.00 33.23 1.89
77 78 6.236409 TCGTAGTCCCTTCAATATCGAGTAT 58.764 40.000 0.00 0.00 0.00 2.12
78 79 5.614308 TCGTAGTCCCTTCAATATCGAGTA 58.386 41.667 0.00 0.00 0.00 2.59
79 80 4.458397 TCGTAGTCCCTTCAATATCGAGT 58.542 43.478 0.00 0.00 0.00 4.18
80 81 4.755629 TCTCGTAGTCCCTTCAATATCGAG 59.244 45.833 0.00 0.00 41.94 4.04
81 82 4.514441 GTCTCGTAGTCCCTTCAATATCGA 59.486 45.833 0.00 0.00 0.00 3.59
82 83 4.275196 TGTCTCGTAGTCCCTTCAATATCG 59.725 45.833 0.00 0.00 0.00 2.92
83 84 5.769484 TGTCTCGTAGTCCCTTCAATATC 57.231 43.478 0.00 0.00 0.00 1.63
84 85 5.892119 TCTTGTCTCGTAGTCCCTTCAATAT 59.108 40.000 0.00 0.00 0.00 1.28
85 86 5.258841 TCTTGTCTCGTAGTCCCTTCAATA 58.741 41.667 0.00 0.00 0.00 1.90
86 87 4.087182 TCTTGTCTCGTAGTCCCTTCAAT 58.913 43.478 0.00 0.00 0.00 2.57
87 88 3.493334 TCTTGTCTCGTAGTCCCTTCAA 58.507 45.455 0.00 0.00 0.00 2.69
88 89 3.150458 TCTTGTCTCGTAGTCCCTTCA 57.850 47.619 0.00 0.00 0.00 3.02
89 90 4.516365 TTTCTTGTCTCGTAGTCCCTTC 57.484 45.455 0.00 0.00 0.00 3.46
90 91 4.950205 TTTTCTTGTCTCGTAGTCCCTT 57.050 40.909 0.00 0.00 0.00 3.95
91 92 4.950205 TTTTTCTTGTCTCGTAGTCCCT 57.050 40.909 0.00 0.00 0.00 4.20
92 93 4.995487 ACATTTTTCTTGTCTCGTAGTCCC 59.005 41.667 0.00 0.00 0.00 4.46
93 94 6.154451 GACATTTTTCTTGTCTCGTAGTCC 57.846 41.667 0.00 0.00 40.26 3.85
102 103 5.066505 ACTGTGTCCAGACATTTTTCTTGTC 59.933 40.000 3.41 0.00 43.97 3.18
103 104 4.949856 ACTGTGTCCAGACATTTTTCTTGT 59.050 37.500 3.41 0.00 43.97 3.16
104 105 5.276270 CACTGTGTCCAGACATTTTTCTTG 58.724 41.667 3.41 0.00 43.97 3.02
105 106 4.202050 GCACTGTGTCCAGACATTTTTCTT 60.202 41.667 9.86 0.00 43.97 2.52
106 107 3.316308 GCACTGTGTCCAGACATTTTTCT 59.684 43.478 9.86 0.00 43.97 2.52
107 108 3.066621 TGCACTGTGTCCAGACATTTTTC 59.933 43.478 9.86 0.00 43.97 2.29
108 109 3.023119 TGCACTGTGTCCAGACATTTTT 58.977 40.909 9.86 0.00 43.97 1.94
109 110 2.653726 TGCACTGTGTCCAGACATTTT 58.346 42.857 9.86 0.00 43.97 1.82
116 117 1.955778 TCCATTTTGCACTGTGTCCAG 59.044 47.619 9.86 0.00 44.68 3.86
124 125 2.242043 CCCTCAAGTCCATTTTGCACT 58.758 47.619 0.00 0.00 0.00 4.40
125 126 1.963515 ACCCTCAAGTCCATTTTGCAC 59.036 47.619 0.00 0.00 0.00 4.57
139 140 6.039941 ACGAAAATCATACAAACAAACCCTCA 59.960 34.615 0.00 0.00 0.00 3.86
191 199 7.596248 CGATCAAAGACAACTTGATGGAATTTT 59.404 33.333 2.92 0.00 36.39 1.82
192 200 7.086376 CGATCAAAGACAACTTGATGGAATTT 58.914 34.615 2.92 0.00 36.39 1.82
193 201 6.349611 CCGATCAAAGACAACTTGATGGAATT 60.350 38.462 8.55 0.00 36.39 2.17
194 202 5.124457 CCGATCAAAGACAACTTGATGGAAT 59.876 40.000 8.55 0.00 36.39 3.01
196 204 4.002982 CCGATCAAAGACAACTTGATGGA 58.997 43.478 8.55 0.00 36.39 3.41
197 205 3.753272 ACCGATCAAAGACAACTTGATGG 59.247 43.478 2.92 7.36 36.39 3.51
198 206 6.238211 GGATACCGATCAAAGACAACTTGATG 60.238 42.308 2.92 0.00 36.39 3.07
199 207 5.817816 GGATACCGATCAAAGACAACTTGAT 59.182 40.000 0.00 0.00 36.39 2.57
200 208 5.175859 GGATACCGATCAAAGACAACTTGA 58.824 41.667 0.00 0.00 36.39 3.02
201 209 4.935205 TGGATACCGATCAAAGACAACTTG 59.065 41.667 0.00 0.00 36.39 3.16
205 215 8.746052 ATAAAATGGATACCGATCAAAGACAA 57.254 30.769 0.00 0.00 33.27 3.18
206 216 8.210946 AGATAAAATGGATACCGATCAAAGACA 58.789 33.333 0.00 0.00 33.27 3.41
208 218 7.661437 CCAGATAAAATGGATACCGATCAAAGA 59.339 37.037 0.00 0.00 40.51 2.52
235 245 1.269012 CCACCATGGAAAATGGCTGT 58.731 50.000 21.47 0.00 40.96 4.40
242 252 2.554344 GCACCTCTACCACCATGGAAAA 60.554 50.000 21.47 0.00 40.96 2.29
244 254 0.618458 GCACCTCTACCACCATGGAA 59.382 55.000 21.47 0.00 40.96 3.53
246 256 1.224592 GGCACCTCTACCACCATGG 59.775 63.158 11.19 11.19 45.02 3.66
247 257 0.620556 AAGGCACCTCTACCACCATG 59.379 55.000 0.00 0.00 0.00 3.66
259 269 6.280855 AGACAAAATAAACCATAAGGCACC 57.719 37.500 0.00 0.00 39.06 5.01
260 270 7.151976 ACAAGACAAAATAAACCATAAGGCAC 58.848 34.615 0.00 0.00 39.06 5.01
267 277 7.569240 TCCCAAAACAAGACAAAATAAACCAT 58.431 30.769 0.00 0.00 0.00 3.55
290 300 0.693049 TCTTCCCTTTGTGAGCCTCC 59.307 55.000 0.00 0.00 0.00 4.30
295 305 5.997746 TGTTCATTAGTCTTCCCTTTGTGAG 59.002 40.000 0.00 0.00 0.00 3.51
297 307 6.824305 ATGTTCATTAGTCTTCCCTTTGTG 57.176 37.500 0.00 0.00 0.00 3.33
302 312 6.215636 ACCACTTATGTTCATTAGTCTTCCCT 59.784 38.462 2.14 0.00 0.00 4.20
360 371 3.379688 GTCATTTCCCTTCCAAGAGCATC 59.620 47.826 0.00 0.00 0.00 3.91
388 406 4.651045 ACTTTCTTTCCTGCTTCCACAATT 59.349 37.500 0.00 0.00 0.00 2.32
410 428 5.545658 TTCTTGCGATTTCTCCATGTTAC 57.454 39.130 0.00 0.00 0.00 2.50
414 432 8.315391 TCTTATATTCTTGCGATTTCTCCATG 57.685 34.615 0.00 0.00 0.00 3.66
504 522 8.907885 GGGCAATCTCTTCTAATCTTACAAAAT 58.092 33.333 0.00 0.00 0.00 1.82
531 549 6.531240 TGTTTCAGAGAAATTTTGAGTTGCAC 59.469 34.615 0.00 0.00 0.00 4.57
541 559 9.865321 CCAATGATACATGTTTCAGAGAAATTT 57.135 29.630 21.10 8.61 0.00 1.82
562 580 1.098050 CGAAGCCTCCCTTTCCAATG 58.902 55.000 0.00 0.00 32.78 2.82
695 726 5.307196 TCTTGACCACCTAATATTCCCTAGC 59.693 44.000 0.00 0.00 0.00 3.42
745 776 4.361783 TCCTGTGTTCCCTGATGAGAATA 58.638 43.478 0.00 0.00 0.00 1.75
881 914 1.383523 GGTGGCATCTAAGCTTCCAC 58.616 55.000 20.68 20.68 44.71 4.02
1000 1039 2.693074 GTGTTCCCCAGTTCAACAACAT 59.307 45.455 0.00 0.00 34.60 2.71
1165 1204 3.146847 GGTTTTCACCAAAGATCCTCGT 58.853 45.455 0.00 0.00 43.61 4.18
1300 1340 2.052782 AGCCACTTCTTGACCGTTTT 57.947 45.000 0.00 0.00 0.00 2.43
1432 1475 3.631250 ACCAGGAAAACTCATTGTGTGT 58.369 40.909 0.00 0.00 0.00 3.72
1459 1502 7.907214 AATCTTGTCTGTACTCACATAAACC 57.093 36.000 0.00 0.00 33.14 3.27
1654 1709 3.575256 TGGATGCAGAGCAAAACTTCATT 59.425 39.130 0.00 0.00 43.62 2.57
1709 1764 0.322648 TGACATGAGTGGCCTGTCAG 59.677 55.000 18.12 10.31 43.10 3.51
1745 1800 0.036388 TGTTGTGCTTCCGATCTCCC 60.036 55.000 0.00 0.00 0.00 4.30
1808 1863 5.773176 TCAACCCTGTTTTCCTCTATTTTCC 59.227 40.000 0.00 0.00 0.00 3.13
1810 1865 9.547279 AATATCAACCCTGTTTTCCTCTATTTT 57.453 29.630 0.00 0.00 0.00 1.82
1819 1874 6.909909 AGTTTCGAATATCAACCCTGTTTTC 58.090 36.000 0.00 0.00 0.00 2.29
1823 1878 4.514401 GGAGTTTCGAATATCAACCCTGT 58.486 43.478 0.00 0.00 0.00 4.00
1940 1998 4.036616 GTGCATGGCCATTTTGTTTCTTTT 59.963 37.500 17.92 0.00 0.00 2.27
1941 1999 3.565063 GTGCATGGCCATTTTGTTTCTTT 59.435 39.130 17.92 0.00 0.00 2.52
1963 2021 1.126948 AATGGCCCCAAACCAACTGG 61.127 55.000 0.00 0.00 41.49 4.00
1966 2024 2.168313 CAGATAATGGCCCCAAACCAAC 59.832 50.000 0.00 0.00 41.49 3.77
2005 2063 8.001292 CCCCAAGAATAATACTGAAAGAGGAAT 58.999 37.037 0.00 0.00 37.43 3.01
2006 2064 7.183839 TCCCCAAGAATAATACTGAAAGAGGAA 59.816 37.037 0.00 0.00 37.43 3.36
2008 2066 6.900194 TCCCCAAGAATAATACTGAAAGAGG 58.100 40.000 0.00 0.00 37.43 3.69
2019 2077 6.266131 TCTGCTATGTTCCCCAAGAATAAT 57.734 37.500 0.00 0.00 36.69 1.28
2025 2083 4.706476 TGAATTTCTGCTATGTTCCCCAAG 59.294 41.667 0.00 0.00 0.00 3.61
2174 2233 3.191791 TGATTTGGATCACGACGAGTACA 59.808 43.478 0.00 0.00 37.37 2.90
2467 2532 1.675641 CAAGAAACCAGCCCCCTCG 60.676 63.158 0.00 0.00 0.00 4.63
2542 2608 2.092592 GGATAACAATCGGTGGGGAAGT 60.093 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.