Multiple sequence alignment - TraesCS5A01G146100

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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 TraesCS5A01G146100 chr5A 100.000 3573 0 0 1 3573 322192473 322188901 0.000000e+00 6599.0
1 TraesCS5A01G146100 chr5A 96.633 2287 52 14 228 2498 35192590 35190313 0.000000e+00 3773.0
2 TraesCS5A01G146100 chr5A 97.634 1099 22 2 2479 3573 35190284 35189186 0.000000e+00 1882.0
3 TraesCS5A01G146100 chr5A 97.707 567 9 2 3010 3573 566639477 566638912 0.000000e+00 972.0
4 TraesCS5A01G146100 chr5A 91.048 458 39 1 700 1155 552504732 552504275 5.070000e-173 617.0
5 TraesCS5A01G146100 chr5A 83.624 458 61 10 700 1155 552389032 552388587 5.520000e-113 418.0
6 TraesCS5A01G146100 chr5A 88.115 244 25 4 278 520 696953912 696954152 1.620000e-73 287.0
7 TraesCS5A01G146100 chr5A 78.621 290 32 15 237 520 49936383 49936648 7.940000e-37 165.0
8 TraesCS5A01G146100 chr5A 87.500 144 12 4 1181 1320 552505269 552505128 1.030000e-35 161.0
9 TraesCS5A01G146100 chr5A 89.764 127 6 6 241 364 338888617 338888739 4.780000e-34 156.0
10 TraesCS5A01G146100 chr5A 84.713 157 21 3 372 527 35551588 35551434 1.720000e-33 154.0
11 TraesCS5A01G146100 chr2B 96.948 2261 45 9 246 2498 1246786 1244542 0.000000e+00 3771.0
12 TraesCS5A01G146100 chr2B 98.543 1098 12 2 2479 3573 1244521 1243425 0.000000e+00 1936.0
13 TraesCS5A01G146100 chr2B 80.488 246 19 9 278 520 63142220 63142439 1.030000e-35 161.0
14 TraesCS5A01G146100 chr3A 96.631 2256 39 10 248 2498 478687573 478685350 0.000000e+00 3711.0
15 TraesCS5A01G146100 chr3A 98.361 1098 15 1 2479 3573 478685341 478684244 0.000000e+00 1925.0
16 TraesCS5A01G146100 chr3A 94.372 231 11 1 1 229 564328762 564328532 1.580000e-93 353.0
17 TraesCS5A01G146100 chr3A 82.184 348 24 11 1386 1703 504622806 504623145 7.610000e-67 265.0
18 TraesCS5A01G146100 chr6A 93.652 2426 122 14 1157 3573 117193737 117196139 0.000000e+00 3598.0
19 TraesCS5A01G146100 chr6A 93.649 2425 124 13 1157 3573 117213301 117215703 0.000000e+00 3598.0
20 TraesCS5A01G146100 chr6A 94.372 231 11 1 1 229 230805165 230804935 1.580000e-93 353.0
21 TraesCS5A01G146100 chr5B 89.605 1645 82 25 1353 2932 369157269 369158889 0.000000e+00 2008.0
22 TraesCS5A01G146100 chr5B 94.625 614 29 2 2964 3573 369158889 369159502 0.000000e+00 948.0
23 TraesCS5A01G146100 chr5B 89.738 458 45 1 700 1155 531511931 531511474 5.140000e-163 584.0
24 TraesCS5A01G146100 chr7D 91.234 924 63 8 248 1155 6962288 6961367 0.000000e+00 1242.0
25 TraesCS5A01G146100 chr5D 89.083 458 48 1 700 1155 437289122 437288665 5.180000e-158 568.0
26 TraesCS5A01G146100 chr5D 85.393 89 9 3 700 786 437218343 437218257 4.910000e-14 89.8
27 TraesCS5A01G146100 chr4A 94.805 231 10 1 1 229 47172189 47172419 3.390000e-95 359.0
28 TraesCS5A01G146100 chr4A 94.372 231 11 1 1 229 451974795 451974565 1.580000e-93 353.0
29 TraesCS5A01G146100 chr7A 94.372 231 11 1 1 229 105988668 105988438 1.580000e-93 353.0
30 TraesCS5A01G146100 chr7A 94.372 231 11 1 1 229 716907579 716907349 1.580000e-93 353.0
31 TraesCS5A01G146100 chr7A 86.857 175 20 1 292 466 402186552 402186723 3.640000e-45 193.0
32 TraesCS5A01G146100 chr7A 90.909 121 7 4 246 364 104639871 104639989 3.690000e-35 159.0
33 TraesCS5A01G146100 chr2A 94.372 231 11 1 1 229 458206026 458205796 1.580000e-93 353.0
34 TraesCS5A01G146100 chr2A 94.372 231 11 1 1 229 473468774 473469004 1.580000e-93 353.0
35 TraesCS5A01G146100 chr2A 76.860 363 54 18 2405 2748 775772450 775772801 1.020000e-40 178.0
36 TraesCS5A01G146100 chr1A 94.372 231 11 1 1 229 85524504 85524274 1.580000e-93 353.0
37 TraesCS5A01G146100 chr3D 86.022 279 30 4 245 523 602475949 602475680 1.250000e-74 291.0
38 TraesCS5A01G146100 chr3D 82.759 348 22 12 1386 1703 381185890 381186229 3.510000e-70 276.0
39 TraesCS5A01G146100 chr3D 77.067 375 52 21 2395 2748 433964447 433964808 6.090000e-43 185.0
40 TraesCS5A01G146100 chr1D 77.067 375 52 23 2395 2748 96176111 96176472 6.090000e-43 185.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G146100 chr5A 322188901 322192473 3572 True 6599.0 6599 100.0000 1 3573 1 chr5A.!!$R2 3572
1 TraesCS5A01G146100 chr5A 35189186 35192590 3404 True 2827.5 3773 97.1335 228 3573 2 chr5A.!!$R5 3345
2 TraesCS5A01G146100 chr5A 566638912 566639477 565 True 972.0 972 97.7070 3010 3573 1 chr5A.!!$R4 563
3 TraesCS5A01G146100 chr5A 552504275 552505269 994 True 389.0 617 89.2740 700 1320 2 chr5A.!!$R6 620
4 TraesCS5A01G146100 chr2B 1243425 1246786 3361 True 2853.5 3771 97.7455 246 3573 2 chr2B.!!$R1 3327
5 TraesCS5A01G146100 chr3A 478684244 478687573 3329 True 2818.0 3711 97.4960 248 3573 2 chr3A.!!$R2 3325
6 TraesCS5A01G146100 chr6A 117193737 117196139 2402 False 3598.0 3598 93.6520 1157 3573 1 chr6A.!!$F1 2416
7 TraesCS5A01G146100 chr6A 117213301 117215703 2402 False 3598.0 3598 93.6490 1157 3573 1 chr6A.!!$F2 2416
8 TraesCS5A01G146100 chr5B 369157269 369159502 2233 False 1478.0 2008 92.1150 1353 3573 2 chr5B.!!$F1 2220
9 TraesCS5A01G146100 chr7D 6961367 6962288 921 True 1242.0 1242 91.2340 248 1155 1 chr7D.!!$R1 907

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
82 83 0.111253 GGCCTGCATGGGTAGCTAAT 59.889 55.000 0.00 0.00 36.00 1.73 F
176 177 0.823460 TGCACCTAGATCGTGATGCA 59.177 50.000 11.99 11.99 40.57 3.96 F
179 180 1.410517 CACCTAGATCGTGATGCACCT 59.589 52.381 0.00 0.00 32.77 4.00 F
1278 1301 1.093159 GAATGGCAGTGAGCTCCAAG 58.907 55.000 12.15 1.39 44.79 3.61 F
1285 1308 2.843701 CAGTGAGCTCCAAGTTCAACT 58.156 47.619 12.15 1.97 37.20 3.16 F
1879 1941 5.644636 TGAAAAACAAGACGTTACAGTTCCT 59.355 36.000 0.00 0.00 36.59 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 1152 1.619654 CAATGAGGGTTCTGGCACAA 58.380 50.000 0.00 0.00 38.7 3.33 R
1267 1290 2.838736 TCAGTTGAACTTGGAGCTCAC 58.161 47.619 17.19 5.63 0.0 3.51 R
1325 1348 4.110036 TCATTGATATGGTAGCGGATCG 57.890 45.455 2.55 0.00 32.4 3.69 R
2476 2569 1.136565 GTGTGTGTGTGTGTGTGGC 59.863 57.895 0.00 0.00 0.0 5.01 R
2507 2650 6.970484 ACGTGAAGAAAAGAACATGCTAAAT 58.030 32.000 0.00 0.00 0.0 1.40 R
3041 3193 7.854534 TGAAGGTTTAAAGTTTTAGCGAGTAC 58.145 34.615 0.00 0.00 0.0 2.73 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
19 20 0.236187 GCAACACGTTCATGCGGTTA 59.764 50.000 1.71 0.00 35.98 2.85
20 21 1.135803 GCAACACGTTCATGCGGTTAT 60.136 47.619 1.71 0.00 35.98 1.89
22 23 3.425094 GCAACACGTTCATGCGGTTATTA 60.425 43.478 1.71 0.00 35.98 0.98
23 24 4.331137 CAACACGTTCATGCGGTTATTAG 58.669 43.478 0.00 0.00 35.98 1.73
24 25 2.933906 ACACGTTCATGCGGTTATTAGG 59.066 45.455 0.00 0.00 35.98 2.69
25 26 1.937899 ACGTTCATGCGGTTATTAGGC 59.062 47.619 0.00 0.00 35.98 3.93
26 27 1.937223 CGTTCATGCGGTTATTAGGCA 59.063 47.619 0.00 0.00 41.48 4.75
27 28 2.353269 CGTTCATGCGGTTATTAGGCAA 59.647 45.455 0.00 0.00 40.49 4.52
28 29 3.546020 CGTTCATGCGGTTATTAGGCAAG 60.546 47.826 0.00 0.00 40.49 4.01
29 30 3.552132 TCATGCGGTTATTAGGCAAGA 57.448 42.857 0.00 0.00 40.49 3.02
30 31 3.879998 TCATGCGGTTATTAGGCAAGAA 58.120 40.909 0.00 0.00 40.49 2.52
31 32 4.265893 TCATGCGGTTATTAGGCAAGAAA 58.734 39.130 0.00 0.00 40.49 2.52
34 35 6.544197 TCATGCGGTTATTAGGCAAGAAATAA 59.456 34.615 0.00 0.00 40.49 1.40
36 37 7.159322 TGCGGTTATTAGGCAAGAAATAAAA 57.841 32.000 0.00 0.00 33.01 1.52
37 38 7.254852 TGCGGTTATTAGGCAAGAAATAAAAG 58.745 34.615 0.00 0.00 33.01 2.27
38 39 7.094118 TGCGGTTATTAGGCAAGAAATAAAAGT 60.094 33.333 0.00 0.00 33.01 2.66
39 40 7.220108 GCGGTTATTAGGCAAGAAATAAAAGTG 59.780 37.037 0.00 0.00 31.30 3.16
41 42 8.251026 GGTTATTAGGCAAGAAATAAAAGTGCT 58.749 33.333 0.00 0.00 35.53 4.40
42 43 9.639601 GTTATTAGGCAAGAAATAAAAGTGCTT 57.360 29.630 0.00 0.00 35.53 3.91
44 45 7.945033 TTAGGCAAGAAATAAAAGTGCTTTG 57.055 32.000 0.00 0.00 35.53 2.77
45 46 4.751600 AGGCAAGAAATAAAAGTGCTTTGC 59.248 37.500 0.00 0.00 35.53 3.68
46 47 4.511082 GGCAAGAAATAAAAGTGCTTTGCA 59.489 37.500 7.96 0.00 35.53 4.08
47 48 5.179929 GGCAAGAAATAAAAGTGCTTTGCAT 59.820 36.000 7.96 0.00 41.91 3.96
48 49 6.075280 GCAAGAAATAAAAGTGCTTTGCATG 58.925 36.000 0.00 0.00 41.91 4.06
49 50 5.851047 AGAAATAAAAGTGCTTTGCATGC 57.149 34.783 11.82 11.82 41.91 4.06
50 51 5.544650 AGAAATAAAAGTGCTTTGCATGCT 58.455 33.333 20.33 0.00 41.91 3.79
52 53 7.325694 AGAAATAAAAGTGCTTTGCATGCTAT 58.674 30.769 20.33 1.01 41.91 2.97
54 55 4.524316 AAAAGTGCTTTGCATGCTATGA 57.476 36.364 20.33 0.00 41.91 2.15
55 56 4.524316 AAAGTGCTTTGCATGCTATGAA 57.476 36.364 20.33 5.35 41.91 2.57
56 57 4.730949 AAGTGCTTTGCATGCTATGAAT 57.269 36.364 20.33 0.80 41.91 2.57
57 58 4.730949 AGTGCTTTGCATGCTATGAATT 57.269 36.364 20.33 2.09 41.91 2.17
60 61 4.438797 GTGCTTTGCATGCTATGAATTACG 59.561 41.667 20.33 0.00 41.91 3.18
62 63 5.008911 TGCTTTGCATGCTATGAATTACGAT 59.991 36.000 20.33 0.00 31.71 3.73
63 64 5.341462 GCTTTGCATGCTATGAATTACGATG 59.659 40.000 20.33 0.00 0.00 3.84
64 65 5.361135 TTGCATGCTATGAATTACGATGG 57.639 39.130 20.33 0.00 0.00 3.51
65 66 3.189080 TGCATGCTATGAATTACGATGGC 59.811 43.478 20.33 0.00 0.00 4.40
66 67 3.426695 GCATGCTATGAATTACGATGGCC 60.427 47.826 11.37 0.00 0.00 5.36
67 68 3.769739 TGCTATGAATTACGATGGCCT 57.230 42.857 3.32 0.00 0.00 5.19
68 69 3.402110 TGCTATGAATTACGATGGCCTG 58.598 45.455 3.32 0.00 0.00 4.85
69 70 2.160417 GCTATGAATTACGATGGCCTGC 59.840 50.000 3.32 0.00 0.00 4.85
70 71 2.346766 ATGAATTACGATGGCCTGCA 57.653 45.000 3.32 0.00 0.00 4.41
71 72 2.346766 TGAATTACGATGGCCTGCAT 57.653 45.000 3.32 0.00 0.00 3.96
72 73 1.948834 TGAATTACGATGGCCTGCATG 59.051 47.619 3.32 0.00 0.00 4.06
73 74 1.267806 GAATTACGATGGCCTGCATGG 59.732 52.381 3.32 0.00 39.35 3.66
75 76 1.920734 TTACGATGGCCTGCATGGGT 61.921 55.000 3.32 0.00 36.00 4.51
76 77 1.051556 TACGATGGCCTGCATGGGTA 61.052 55.000 3.32 0.00 36.00 3.69
77 78 1.598962 CGATGGCCTGCATGGGTAG 60.599 63.158 3.32 0.00 36.00 3.18
78 79 1.900498 GATGGCCTGCATGGGTAGC 60.900 63.158 3.32 0.00 36.00 3.58
79 80 2.349100 GATGGCCTGCATGGGTAGCT 62.349 60.000 3.32 0.00 36.00 3.32
81 82 1.278302 TGGCCTGCATGGGTAGCTAA 61.278 55.000 3.32 0.00 36.00 3.09
82 83 0.111253 GGCCTGCATGGGTAGCTAAT 59.889 55.000 0.00 0.00 36.00 1.73
83 84 1.351017 GGCCTGCATGGGTAGCTAATA 59.649 52.381 0.00 0.00 36.00 0.98
84 85 2.224769 GGCCTGCATGGGTAGCTAATAA 60.225 50.000 0.00 0.00 36.00 1.40
85 86 3.077359 GCCTGCATGGGTAGCTAATAAG 58.923 50.000 0.00 0.00 36.00 1.73
87 88 3.327757 CCTGCATGGGTAGCTAATAAGGA 59.672 47.826 0.00 0.00 0.00 3.36
88 89 4.202461 CCTGCATGGGTAGCTAATAAGGAA 60.202 45.833 0.00 0.00 0.00 3.36
89 90 5.515534 CCTGCATGGGTAGCTAATAAGGAAT 60.516 44.000 0.00 0.00 0.00 3.01
91 92 5.310594 TGCATGGGTAGCTAATAAGGAATCT 59.689 40.000 0.00 0.00 0.00 2.40
94 95 7.684529 CATGGGTAGCTAATAAGGAATCTTCT 58.315 38.462 0.00 0.00 34.59 2.85
96 97 8.792830 TGGGTAGCTAATAAGGAATCTTCTTA 57.207 34.615 0.00 0.00 34.59 2.10
97 98 9.220906 TGGGTAGCTAATAAGGAATCTTCTTAA 57.779 33.333 0.00 0.00 34.59 1.85
98 99 9.491675 GGGTAGCTAATAAGGAATCTTCTTAAC 57.508 37.037 0.00 0.00 34.59 2.01
101 102 8.669946 AGCTAATAAGGAATCTTCTTAACTGC 57.330 34.615 0.00 0.00 34.59 4.40
103 104 8.555361 GCTAATAAGGAATCTTCTTAACTGCTG 58.445 37.037 0.00 0.00 34.59 4.41
104 105 9.606631 CTAATAAGGAATCTTCTTAACTGCTGT 57.393 33.333 0.00 0.00 34.59 4.40
105 106 7.856145 ATAAGGAATCTTCTTAACTGCTGTG 57.144 36.000 0.00 0.00 34.59 3.66
106 107 5.489792 AGGAATCTTCTTAACTGCTGTGA 57.510 39.130 0.00 0.00 0.00 3.58
107 108 6.059787 AGGAATCTTCTTAACTGCTGTGAT 57.940 37.500 0.00 0.00 0.00 3.06
108 109 6.479884 AGGAATCTTCTTAACTGCTGTGATT 58.520 36.000 0.00 0.89 0.00 2.57
110 111 8.103305 AGGAATCTTCTTAACTGCTGTGATTAA 58.897 33.333 0.00 0.00 0.00 1.40
111 112 8.730680 GGAATCTTCTTAACTGCTGTGATTAAA 58.269 33.333 0.00 0.00 0.00 1.52
114 115 8.621532 TCTTCTTAACTGCTGTGATTAAATGT 57.378 30.769 0.00 0.00 0.00 2.71
115 116 9.066892 TCTTCTTAACTGCTGTGATTAAATGTT 57.933 29.630 0.00 0.00 0.00 2.71
116 117 9.121517 CTTCTTAACTGCTGTGATTAAATGTTG 57.878 33.333 0.00 0.00 0.00 3.33
117 118 8.165239 TCTTAACTGCTGTGATTAAATGTTGT 57.835 30.769 0.00 0.00 0.00 3.32
118 119 8.075574 TCTTAACTGCTGTGATTAAATGTTGTG 58.924 33.333 0.00 0.00 0.00 3.33
119 120 5.772825 ACTGCTGTGATTAAATGTTGTGT 57.227 34.783 0.00 0.00 0.00 3.72
120 121 6.147864 ACTGCTGTGATTAAATGTTGTGTT 57.852 33.333 0.00 0.00 0.00 3.32
122 123 7.711846 ACTGCTGTGATTAAATGTTGTGTTTA 58.288 30.769 0.00 0.00 0.00 2.01
123 124 7.862372 ACTGCTGTGATTAAATGTTGTGTTTAG 59.138 33.333 0.00 0.00 0.00 1.85
125 126 8.409371 TGCTGTGATTAAATGTTGTGTTTAGAA 58.591 29.630 0.00 0.00 0.00 2.10
155 156 8.848182 AGAAATATTCTTCTTCCATCAATCTGC 58.152 33.333 0.00 0.00 36.36 4.26
157 158 8.763984 AATATTCTTCTTCCATCAATCTGCTT 57.236 30.769 0.00 0.00 0.00 3.91
158 159 5.892160 TTCTTCTTCCATCAATCTGCTTG 57.108 39.130 0.00 0.00 36.09 4.01
161 162 2.751259 TCTTCCATCAATCTGCTTGCAC 59.249 45.455 0.00 0.00 34.66 4.57
163 164 1.005097 TCCATCAATCTGCTTGCACCT 59.995 47.619 0.00 0.00 34.66 4.00
164 165 2.239402 TCCATCAATCTGCTTGCACCTA 59.761 45.455 0.00 0.00 34.66 3.08
166 167 3.538591 CATCAATCTGCTTGCACCTAGA 58.461 45.455 0.00 0.00 34.66 2.43
167 168 3.920231 TCAATCTGCTTGCACCTAGAT 57.080 42.857 0.00 0.00 34.66 1.98
169 170 2.522836 ATCTGCTTGCACCTAGATCG 57.477 50.000 0.00 0.00 0.00 3.69
170 171 1.186200 TCTGCTTGCACCTAGATCGT 58.814 50.000 0.00 0.00 0.00 3.73
171 172 1.134995 TCTGCTTGCACCTAGATCGTG 60.135 52.381 0.00 0.00 0.00 4.35
172 173 0.894835 TGCTTGCACCTAGATCGTGA 59.105 50.000 3.69 0.00 32.77 4.35
173 174 1.482182 TGCTTGCACCTAGATCGTGAT 59.518 47.619 3.69 0.00 32.77 3.06
176 177 0.823460 TGCACCTAGATCGTGATGCA 59.177 50.000 11.99 11.99 40.57 3.96
178 179 1.858091 CACCTAGATCGTGATGCACC 58.142 55.000 0.00 0.00 32.77 5.01
179 180 1.410517 CACCTAGATCGTGATGCACCT 59.589 52.381 0.00 0.00 32.77 4.00
180 181 2.111384 ACCTAGATCGTGATGCACCTT 58.889 47.619 0.00 0.00 0.00 3.50
181 182 2.101582 ACCTAGATCGTGATGCACCTTC 59.898 50.000 0.00 0.00 0.00 3.46
182 183 2.363680 CCTAGATCGTGATGCACCTTCT 59.636 50.000 0.00 0.00 0.00 2.85
184 185 4.038042 CCTAGATCGTGATGCACCTTCTAA 59.962 45.833 0.00 0.00 29.93 2.10
187 188 5.533482 AGATCGTGATGCACCTTCTAATAC 58.467 41.667 0.00 0.00 0.00 1.89
188 189 3.702330 TCGTGATGCACCTTCTAATACG 58.298 45.455 0.00 0.00 0.00 3.06
190 191 3.486108 CGTGATGCACCTTCTAATACGAC 59.514 47.826 0.00 0.00 0.00 4.34
191 192 4.683832 GTGATGCACCTTCTAATACGACT 58.316 43.478 0.00 0.00 0.00 4.18
193 194 6.270815 GTGATGCACCTTCTAATACGACTTA 58.729 40.000 0.00 0.00 0.00 2.24
194 195 6.924060 GTGATGCACCTTCTAATACGACTTAT 59.076 38.462 0.00 0.00 0.00 1.73
195 196 7.438459 GTGATGCACCTTCTAATACGACTTATT 59.562 37.037 0.00 0.00 34.55 1.40
198 199 6.755141 TGCACCTTCTAATACGACTTATTCAC 59.245 38.462 0.00 0.00 32.31 3.18
201 202 8.627403 CACCTTCTAATACGACTTATTCACCTA 58.373 37.037 0.00 0.00 32.31 3.08
209 210 9.570468 AATACGACTTATTCACCTATACAGAGA 57.430 33.333 0.00 0.00 0.00 3.10
210 211 7.876936 ACGACTTATTCACCTATACAGAGAA 57.123 36.000 0.00 0.00 0.00 2.87
211 212 8.289939 ACGACTTATTCACCTATACAGAGAAA 57.710 34.615 0.00 0.00 0.00 2.52
212 213 8.407064 ACGACTTATTCACCTATACAGAGAAAG 58.593 37.037 0.00 0.00 0.00 2.62
213 214 8.407064 CGACTTATTCACCTATACAGAGAAAGT 58.593 37.037 0.00 0.00 0.00 2.66
254 258 4.625742 CCTAATGTCTCATGTCGTTCGTTT 59.374 41.667 0.00 0.00 0.00 3.60
356 362 2.847717 CGGTTTTCATTCATGCATCACG 59.152 45.455 0.00 0.00 0.00 4.35
470 476 4.903149 TCCTTCCCTTCCATATACCAGAA 58.097 43.478 0.00 0.00 0.00 3.02
542 548 2.782341 CAATCTTTCCATCCTCCCCTCT 59.218 50.000 0.00 0.00 0.00 3.69
840 854 3.958860 GCCTCACTGTGGGCCACT 61.959 66.667 34.69 15.52 42.30 4.00
842 856 2.033141 CTCACTGTGGGCCACTGG 59.967 66.667 36.64 29.25 37.57 4.00
924 938 3.899981 ATCGGCAGTTTCAGCGGCA 62.900 57.895 1.45 0.00 33.00 5.69
1048 1071 1.558167 TAAGGGGAAGCGCATCACCA 61.558 55.000 33.34 13.29 45.94 4.17
1051 1074 1.451927 GGGAAGCGCATCACCATCA 60.452 57.895 15.31 0.00 0.00 3.07
1067 1090 1.863155 ATCATGGGGTCCGGCAAGTT 61.863 55.000 0.00 0.00 0.00 2.66
1278 1301 1.093159 GAATGGCAGTGAGCTCCAAG 58.907 55.000 12.15 1.39 44.79 3.61
1285 1308 2.843701 CAGTGAGCTCCAAGTTCAACT 58.156 47.619 12.15 1.97 37.20 3.16
1557 1612 9.498039 TGATGATCAGGTCAGGTATAATATCAT 57.502 33.333 0.09 0.00 40.92 2.45
1879 1941 5.644636 TGAAAAACAAGACGTTACAGTTCCT 59.355 36.000 0.00 0.00 36.59 3.36
1880 1942 6.149807 TGAAAAACAAGACGTTACAGTTCCTT 59.850 34.615 0.00 0.00 36.59 3.36
1881 1943 7.333921 TGAAAAACAAGACGTTACAGTTCCTTA 59.666 33.333 0.00 0.00 36.59 2.69
1882 1944 7.614124 AAAACAAGACGTTACAGTTCCTTAA 57.386 32.000 0.00 0.00 36.59 1.85
1883 1945 7.614124 AAACAAGACGTTACAGTTCCTTAAA 57.386 32.000 0.00 0.00 36.59 1.52
1884 1946 7.614124 AACAAGACGTTACAGTTCCTTAAAA 57.386 32.000 0.00 0.00 35.52 1.52
2507 2650 3.882288 ACACACACACACATGCATAGAAA 59.118 39.130 0.00 0.00 0.00 2.52
2535 2678 6.603095 AGCATGTTCTTTTCTTCACGTAATC 58.397 36.000 0.00 0.00 0.00 1.75
3259 3412 2.774809 TGGCTATGTACTGGTTATGCCA 59.225 45.455 0.00 0.00 46.95 4.92
3393 3549 4.734398 TGTCTTTGGTGTCTGCAATTTT 57.266 36.364 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.236187 TAACCGCATGAACGTGTTGC 59.764 50.000 0.00 7.38 31.82 4.17
4 5 2.286184 GCCTAATAACCGCATGAACGTG 60.286 50.000 0.00 0.00 0.00 4.49
6 7 1.937223 TGCCTAATAACCGCATGAACG 59.063 47.619 0.00 0.00 0.00 3.95
7 8 3.625764 TCTTGCCTAATAACCGCATGAAC 59.374 43.478 0.00 0.00 34.78 3.18
8 9 3.879998 TCTTGCCTAATAACCGCATGAA 58.120 40.909 0.00 0.00 34.78 2.57
10 11 4.630894 TTTCTTGCCTAATAACCGCATG 57.369 40.909 0.00 0.00 31.44 4.06
11 12 6.952773 TTATTTCTTGCCTAATAACCGCAT 57.047 33.333 0.00 0.00 31.44 4.73
13 14 7.220108 CACTTTTATTTCTTGCCTAATAACCGC 59.780 37.037 0.00 0.00 0.00 5.68
14 15 7.220108 GCACTTTTATTTCTTGCCTAATAACCG 59.780 37.037 0.00 0.00 0.00 4.44
15 16 8.251026 AGCACTTTTATTTCTTGCCTAATAACC 58.749 33.333 0.00 0.00 33.48 2.85
16 17 9.639601 AAGCACTTTTATTTCTTGCCTAATAAC 57.360 29.630 0.00 0.00 33.48 1.89
19 20 7.118245 GCAAAGCACTTTTATTTCTTGCCTAAT 59.882 33.333 0.00 0.00 33.48 1.73
20 21 6.423604 GCAAAGCACTTTTATTTCTTGCCTAA 59.576 34.615 0.00 0.00 33.48 2.69
22 23 4.751600 GCAAAGCACTTTTATTTCTTGCCT 59.248 37.500 0.00 0.00 33.48 4.75
23 24 4.511082 TGCAAAGCACTTTTATTTCTTGCC 59.489 37.500 0.00 0.00 31.71 4.52
24 25 5.655893 TGCAAAGCACTTTTATTTCTTGC 57.344 34.783 0.00 0.00 31.71 4.01
25 26 6.073440 AGCATGCAAAGCACTTTTATTTCTTG 60.073 34.615 21.98 0.00 43.04 3.02
26 27 5.993441 AGCATGCAAAGCACTTTTATTTCTT 59.007 32.000 21.98 0.00 43.04 2.52
27 28 5.544650 AGCATGCAAAGCACTTTTATTTCT 58.455 33.333 21.98 0.00 43.04 2.52
28 29 5.851047 AGCATGCAAAGCACTTTTATTTC 57.149 34.783 21.98 0.00 43.04 2.17
29 30 7.098477 TCATAGCATGCAAAGCACTTTTATTT 58.902 30.769 21.98 0.00 43.04 1.40
30 31 6.632909 TCATAGCATGCAAAGCACTTTTATT 58.367 32.000 21.98 0.00 43.04 1.40
31 32 6.211587 TCATAGCATGCAAAGCACTTTTAT 57.788 33.333 21.98 1.58 43.04 1.40
34 35 4.524316 TTCATAGCATGCAAAGCACTTT 57.476 36.364 21.98 0.00 43.04 2.66
36 37 4.730949 AATTCATAGCATGCAAAGCACT 57.269 36.364 21.98 0.00 43.04 4.40
37 38 4.438797 CGTAATTCATAGCATGCAAAGCAC 59.561 41.667 21.98 6.07 43.04 4.40
38 39 4.335037 TCGTAATTCATAGCATGCAAAGCA 59.665 37.500 21.98 0.36 44.86 3.91
39 40 4.847633 TCGTAATTCATAGCATGCAAAGC 58.152 39.130 21.98 6.40 0.00 3.51
41 42 5.761003 CCATCGTAATTCATAGCATGCAAA 58.239 37.500 21.98 7.96 0.00 3.68
42 43 4.320421 GCCATCGTAATTCATAGCATGCAA 60.320 41.667 21.98 5.44 0.00 4.08
43 44 3.189080 GCCATCGTAATTCATAGCATGCA 59.811 43.478 21.98 6.36 0.00 3.96
44 45 3.426695 GGCCATCGTAATTCATAGCATGC 60.427 47.826 10.51 10.51 0.00 4.06
45 46 4.005650 AGGCCATCGTAATTCATAGCATG 58.994 43.478 5.01 0.00 0.00 4.06
46 47 4.005650 CAGGCCATCGTAATTCATAGCAT 58.994 43.478 5.01 0.00 0.00 3.79
47 48 3.402110 CAGGCCATCGTAATTCATAGCA 58.598 45.455 5.01 0.00 0.00 3.49
48 49 2.160417 GCAGGCCATCGTAATTCATAGC 59.840 50.000 5.01 0.00 0.00 2.97
49 50 3.402110 TGCAGGCCATCGTAATTCATAG 58.598 45.455 5.01 0.00 0.00 2.23
50 51 3.483808 TGCAGGCCATCGTAATTCATA 57.516 42.857 5.01 0.00 0.00 2.15
52 53 1.948834 CATGCAGGCCATCGTAATTCA 59.051 47.619 5.01 0.00 29.71 2.57
54 55 1.321474 CCATGCAGGCCATCGTAATT 58.679 50.000 5.01 0.00 29.71 1.40
55 56 0.538057 CCCATGCAGGCCATCGTAAT 60.538 55.000 5.01 0.00 35.39 1.89
56 57 1.152984 CCCATGCAGGCCATCGTAA 60.153 57.895 5.01 0.00 35.39 3.18
57 58 1.051556 TACCCATGCAGGCCATCGTA 61.052 55.000 5.01 0.00 35.39 3.43
60 61 1.900498 GCTACCCATGCAGGCCATC 60.900 63.158 5.01 0.00 35.39 3.51
62 63 1.278302 TTAGCTACCCATGCAGGCCA 61.278 55.000 5.01 0.00 35.39 5.36
63 64 0.111253 ATTAGCTACCCATGCAGGCC 59.889 55.000 0.00 0.00 35.39 5.19
64 65 2.859165 TATTAGCTACCCATGCAGGC 57.141 50.000 0.00 0.00 35.39 4.85
65 66 3.327757 TCCTTATTAGCTACCCATGCAGG 59.672 47.826 0.00 0.00 37.03 4.85
66 67 4.623932 TCCTTATTAGCTACCCATGCAG 57.376 45.455 0.00 0.00 0.00 4.41
67 68 5.310594 AGATTCCTTATTAGCTACCCATGCA 59.689 40.000 0.00 0.00 0.00 3.96
68 69 5.810095 AGATTCCTTATTAGCTACCCATGC 58.190 41.667 0.00 0.00 0.00 4.06
69 70 7.684529 AGAAGATTCCTTATTAGCTACCCATG 58.315 38.462 0.00 0.00 31.62 3.66
70 71 7.880265 AGAAGATTCCTTATTAGCTACCCAT 57.120 36.000 0.00 0.00 31.62 4.00
71 72 7.691993 AAGAAGATTCCTTATTAGCTACCCA 57.308 36.000 0.00 0.00 32.57 4.51
72 73 9.491675 GTTAAGAAGATTCCTTATTAGCTACCC 57.508 37.037 0.00 0.00 37.38 3.69
75 76 9.765795 GCAGTTAAGAAGATTCCTTATTAGCTA 57.234 33.333 8.02 0.00 42.02 3.32
76 77 8.490311 AGCAGTTAAGAAGATTCCTTATTAGCT 58.510 33.333 0.00 0.00 43.53 3.32
77 78 8.555361 CAGCAGTTAAGAAGATTCCTTATTAGC 58.445 37.037 0.00 0.00 37.38 3.09
78 79 9.606631 ACAGCAGTTAAGAAGATTCCTTATTAG 57.393 33.333 0.00 0.00 37.38 1.73
79 80 9.383519 CACAGCAGTTAAGAAGATTCCTTATTA 57.616 33.333 0.00 0.00 35.63 0.98
81 82 7.624549 TCACAGCAGTTAAGAAGATTCCTTAT 58.375 34.615 0.00 0.00 31.62 1.73
82 83 7.004555 TCACAGCAGTTAAGAAGATTCCTTA 57.995 36.000 0.00 0.00 31.62 2.69
83 84 5.869579 TCACAGCAGTTAAGAAGATTCCTT 58.130 37.500 0.00 0.00 34.81 3.36
84 85 5.489792 TCACAGCAGTTAAGAAGATTCCT 57.510 39.130 0.00 0.00 0.00 3.36
85 86 6.749923 AATCACAGCAGTTAAGAAGATTCC 57.250 37.500 0.00 0.00 0.00 3.01
88 89 9.236006 ACATTTAATCACAGCAGTTAAGAAGAT 57.764 29.630 0.00 0.00 0.00 2.40
89 90 8.621532 ACATTTAATCACAGCAGTTAAGAAGA 57.378 30.769 0.00 0.00 0.00 2.87
91 92 8.629158 ACAACATTTAATCACAGCAGTTAAGAA 58.371 29.630 0.00 0.00 0.00 2.52
94 95 7.711846 ACACAACATTTAATCACAGCAGTTAA 58.288 30.769 0.00 0.00 0.00 2.01
96 97 6.147864 ACACAACATTTAATCACAGCAGTT 57.852 33.333 0.00 0.00 0.00 3.16
97 98 5.772825 ACACAACATTTAATCACAGCAGT 57.227 34.783 0.00 0.00 0.00 4.40
98 99 8.075574 TCTAAACACAACATTTAATCACAGCAG 58.924 33.333 0.00 0.00 0.00 4.24
99 100 7.935520 TCTAAACACAACATTTAATCACAGCA 58.064 30.769 0.00 0.00 0.00 4.41
100 101 8.795786 TTCTAAACACAACATTTAATCACAGC 57.204 30.769 0.00 0.00 0.00 4.40
123 124 9.829507 TGATGGAAGAAGAATATTTCTCTCTTC 57.170 33.333 19.95 19.95 43.55 2.87
130 131 8.848182 AGCAGATTGATGGAAGAAGAATATTTC 58.152 33.333 0.00 0.00 0.00 2.17
131 132 8.763984 AGCAGATTGATGGAAGAAGAATATTT 57.236 30.769 0.00 0.00 0.00 1.40
132 133 8.630917 CAAGCAGATTGATGGAAGAAGAATATT 58.369 33.333 0.00 0.00 41.83 1.28
134 135 6.039047 GCAAGCAGATTGATGGAAGAAGAATA 59.961 38.462 1.54 0.00 41.83 1.75
135 136 5.163540 GCAAGCAGATTGATGGAAGAAGAAT 60.164 40.000 1.54 0.00 41.83 2.40
136 137 4.157289 GCAAGCAGATTGATGGAAGAAGAA 59.843 41.667 1.54 0.00 41.83 2.52
137 138 3.693085 GCAAGCAGATTGATGGAAGAAGA 59.307 43.478 1.54 0.00 41.83 2.87
138 139 3.442625 TGCAAGCAGATTGATGGAAGAAG 59.557 43.478 1.54 0.00 41.83 2.85
139 140 3.192001 GTGCAAGCAGATTGATGGAAGAA 59.808 43.478 1.54 0.00 41.83 2.52
140 141 2.751259 GTGCAAGCAGATTGATGGAAGA 59.249 45.455 1.54 0.00 41.83 2.87
142 143 1.820519 GGTGCAAGCAGATTGATGGAA 59.179 47.619 1.54 0.00 41.83 3.53
143 144 1.005097 AGGTGCAAGCAGATTGATGGA 59.995 47.619 1.54 0.00 41.83 3.41
145 146 3.538591 TCTAGGTGCAAGCAGATTGATG 58.461 45.455 1.54 0.00 41.83 3.07
146 147 3.920231 TCTAGGTGCAAGCAGATTGAT 57.080 42.857 1.54 0.00 41.83 2.57
147 148 3.739209 CGATCTAGGTGCAAGCAGATTGA 60.739 47.826 1.54 0.00 41.83 2.57
148 149 2.543012 CGATCTAGGTGCAAGCAGATTG 59.457 50.000 0.00 0.00 42.20 2.67
150 151 1.759445 ACGATCTAGGTGCAAGCAGAT 59.241 47.619 0.00 5.19 35.80 2.90
151 152 1.134995 CACGATCTAGGTGCAAGCAGA 60.135 52.381 0.00 0.00 36.26 4.26
152 153 1.134995 TCACGATCTAGGTGCAAGCAG 60.135 52.381 0.00 0.00 36.26 4.24
154 155 1.863454 CATCACGATCTAGGTGCAAGC 59.137 52.381 0.00 0.00 35.39 4.01
155 156 1.863454 GCATCACGATCTAGGTGCAAG 59.137 52.381 12.86 0.00 35.39 4.01
157 158 0.823460 TGCATCACGATCTAGGTGCA 59.177 50.000 15.57 15.57 39.94 4.57
158 159 1.212616 GTGCATCACGATCTAGGTGC 58.787 55.000 11.33 11.33 35.39 5.01
161 162 2.363680 AGAAGGTGCATCACGATCTAGG 59.636 50.000 0.00 0.00 34.83 3.02
163 164 5.791336 ATTAGAAGGTGCATCACGATCTA 57.209 39.130 0.00 0.00 33.94 1.98
164 165 4.679373 ATTAGAAGGTGCATCACGATCT 57.321 40.909 0.00 0.00 35.36 2.75
166 167 4.037565 TCGTATTAGAAGGTGCATCACGAT 59.962 41.667 0.00 0.00 34.83 3.73
167 168 3.379057 TCGTATTAGAAGGTGCATCACGA 59.621 43.478 0.00 0.35 34.83 4.35
169 170 4.683832 AGTCGTATTAGAAGGTGCATCAC 58.316 43.478 0.00 0.00 0.00 3.06
170 171 5.339008 AAGTCGTATTAGAAGGTGCATCA 57.661 39.130 0.00 0.00 0.00 3.07
171 172 7.652105 TGAATAAGTCGTATTAGAAGGTGCATC 59.348 37.037 0.00 0.00 32.26 3.91
172 173 7.438459 GTGAATAAGTCGTATTAGAAGGTGCAT 59.562 37.037 0.00 0.00 32.26 3.96
173 174 6.755141 GTGAATAAGTCGTATTAGAAGGTGCA 59.245 38.462 0.00 0.00 32.26 4.57
176 177 7.657023 AGGTGAATAAGTCGTATTAGAAGGT 57.343 36.000 0.00 0.00 32.26 3.50
184 185 9.570468 TTCTCTGTATAGGTGAATAAGTCGTAT 57.430 33.333 0.00 0.00 0.00 3.06
187 188 8.407064 ACTTTCTCTGTATAGGTGAATAAGTCG 58.593 37.037 0.00 0.00 0.00 4.18
223 224 9.516546 AACGACATGAGACATTAGGAGTATATA 57.483 33.333 0.00 0.00 0.00 0.86
225 226 7.307811 CGAACGACATGAGACATTAGGAGTATA 60.308 40.741 0.00 0.00 0.00 1.47
244 245 1.596220 GGCTGGAAACAAACGAACGAC 60.596 52.381 0.14 0.00 42.06 4.34
245 246 0.658897 GGCTGGAAACAAACGAACGA 59.341 50.000 0.14 0.00 42.06 3.85
254 258 0.181587 TCGTTGGAAGGCTGGAAACA 59.818 50.000 0.00 0.00 39.59 2.83
356 362 2.040544 CATGGGGCGTGTGGTTCTC 61.041 63.158 0.00 0.00 0.00 2.87
507 513 6.310941 TGGAAAGATTGGTGTTTATGGAAGA 58.689 36.000 0.00 0.00 0.00 2.87
542 548 4.811024 GCATCTGTATGGAAAGAATCGTGA 59.189 41.667 0.00 0.00 33.38 4.35
760 774 3.602030 ACCTCTCCCACCGGTCCT 61.602 66.667 2.59 0.00 0.00 3.85
815 829 3.860605 ACAGTGAGGCGCCACACA 61.861 61.111 43.94 30.58 39.42 3.72
863 877 1.000993 ATGCACCTCCTCCGTCTCT 59.999 57.895 0.00 0.00 0.00 3.10
924 938 2.440796 CGCTGGGATGTTGGGCAT 60.441 61.111 0.00 0.00 41.24 4.40
1048 1071 1.863155 AACTTGCCGGACCCCATGAT 61.863 55.000 5.05 0.00 0.00 2.45
1051 1074 2.035626 CAACTTGCCGGACCCCAT 59.964 61.111 5.05 0.00 0.00 4.00
1067 1090 4.207281 CGGCGATCTCGAAGGCCA 62.207 66.667 5.01 0.00 45.85 5.36
1129 1152 1.619654 CAATGAGGGTTCTGGCACAA 58.380 50.000 0.00 0.00 38.70 3.33
1253 1276 3.432749 GGAGCTCACTGCCATTCAATCTA 60.433 47.826 17.19 0.00 44.23 1.98
1267 1290 2.838736 TCAGTTGAACTTGGAGCTCAC 58.161 47.619 17.19 5.63 0.00 3.51
1278 1301 7.531871 CGTGCAGCATTATATAATCAGTTGAAC 59.468 37.037 4.93 7.58 0.00 3.18
1285 1308 7.063780 CAGATCACGTGCAGCATTATATAATCA 59.936 37.037 11.67 0.00 0.00 2.57
1325 1348 4.110036 TCATTGATATGGTAGCGGATCG 57.890 45.455 2.55 0.00 32.40 3.69
1879 1941 9.943163 GGCAAGCAATTTCACTTTTAATTTTAA 57.057 25.926 0.00 0.00 0.00 1.52
1880 1942 9.113838 TGGCAAGCAATTTCACTTTTAATTTTA 57.886 25.926 0.00 0.00 0.00 1.52
1881 1943 7.994194 TGGCAAGCAATTTCACTTTTAATTTT 58.006 26.923 0.00 0.00 0.00 1.82
1882 1944 7.565323 TGGCAAGCAATTTCACTTTTAATTT 57.435 28.000 0.00 0.00 0.00 1.82
1883 1945 7.565323 TTGGCAAGCAATTTCACTTTTAATT 57.435 28.000 0.00 0.00 0.00 1.40
1884 1946 7.565323 TTTGGCAAGCAATTTCACTTTTAAT 57.435 28.000 0.00 0.00 0.00 1.40
2476 2569 1.136565 GTGTGTGTGTGTGTGTGGC 59.863 57.895 0.00 0.00 0.00 5.01
2507 2650 6.970484 ACGTGAAGAAAAGAACATGCTAAAT 58.030 32.000 0.00 0.00 0.00 1.40
3041 3193 7.854534 TGAAGGTTTAAAGTTTTAGCGAGTAC 58.145 34.615 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.