Multiple sequence alignment - TraesCS6A01G353200

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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 TraesCS6A01G353200 chr6A 100.000 3317 0 0 1 3317 585107581 585110897 0.000000e+00 6126.0
1 TraesCS6A01G353200 chr6D 91.850 2724 95 64 659 3317 436832065 436834726 0.000000e+00 3683.0
2 TraesCS6A01G353200 chr6D 86.066 488 24 17 167 630 436831285 436831752 4.980000e-133 484.0
3 TraesCS6A01G353200 chr6B 89.489 2721 104 64 665 3317 660564723 660562117 0.000000e+00 3273.0
4 TraesCS6A01G353200 chr6B 87.212 391 19 11 265 640 660565376 660565002 1.840000e-112 416.0
5 TraesCS6A01G353200 chr7D 87.054 1290 164 3 1012 2301 101783170 101781884 0.000000e+00 1454.0
6 TraesCS6A01G353200 chr7A 86.832 1291 165 5 1012 2301 105641655 105640369 0.000000e+00 1437.0
7 TraesCS6A01G353200 chr7A 91.379 58 5 0 1 58 535918712 535918769 2.740000e-11 80.5
8 TraesCS6A01G353200 chr7A 91.837 49 4 0 9 57 63873465 63873513 5.940000e-08 69.4
9 TraesCS6A01G353200 chr7B 86.367 1291 173 3 1012 2302 59100888 59099601 0.000000e+00 1406.0
10 TraesCS6A01G353200 chr7B 78.184 1013 199 19 1289 2287 204686952 204685948 7.810000e-176 627.0
11 TraesCS6A01G353200 chr5B 80.957 982 147 30 1289 2253 466333657 466332699 0.000000e+00 741.0
12 TraesCS6A01G353200 chr5D 80.734 981 151 28 1289 2253 387728912 387727954 0.000000e+00 730.0
13 TraesCS6A01G353200 chr5A 80.410 975 153 29 1295 2253 490816292 490815340 0.000000e+00 708.0
14 TraesCS6A01G353200 chr4A 91.228 57 5 0 1 57 312709595 312709651 9.870000e-11 78.7
15 TraesCS6A01G353200 chr2D 92.453 53 4 0 1 53 261736735 261736787 3.550000e-10 76.8
16 TraesCS6A01G353200 chr1A 93.182 44 3 0 10 53 540502236 540502193 7.680000e-07 65.8
17 TraesCS6A01G353200 chr3B 83.636 55 9 0 3 57 553603670 553603724 6.000000e-03 52.8


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 TraesCS6A01G353200 chr6A 585107581 585110897 3316 False 6126.0 6126 100.0000 1 3317 1 chr6A.!!$F1 3316
1 TraesCS6A01G353200 chr6D 436831285 436834726 3441 False 2083.5 3683 88.9580 167 3317 2 chr6D.!!$F1 3150
2 TraesCS6A01G353200 chr6B 660562117 660565376 3259 True 1844.5 3273 88.3505 265 3317 2 chr6B.!!$R1 3052
3 TraesCS6A01G353200 chr7D 101781884 101783170 1286 True 1454.0 1454 87.0540 1012 2301 1 chr7D.!!$R1 1289
4 TraesCS6A01G353200 chr7A 105640369 105641655 1286 True 1437.0 1437 86.8320 1012 2301 1 chr7A.!!$R1 1289
5 TraesCS6A01G353200 chr7B 59099601 59100888 1287 True 1406.0 1406 86.3670 1012 2302 1 chr7B.!!$R1 1290
6 TraesCS6A01G353200 chr7B 204685948 204686952 1004 True 627.0 627 78.1840 1289 2287 1 chr7B.!!$R2 998
7 TraesCS6A01G353200 chr5B 466332699 466333657 958 True 741.0 741 80.9570 1289 2253 1 chr5B.!!$R1 964
8 TraesCS6A01G353200 chr5D 387727954 387728912 958 True 730.0 730 80.7340 1289 2253 1 chr5D.!!$R1 964
9 TraesCS6A01G353200 chr5A 490815340 490816292 952 True 708.0 708 80.4100 1295 2253 1 chr5A.!!$R1 958

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
215 220 0.179225 CGAAGAAACGCACCAATCCG 60.179 55.0 0.0 0.0 0.0 4.18 F
899 1239 0.251634 GGACAAGGAGGAGGAGCAAG 59.748 60.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1110 1450 1.904771 CGCCCAGAGGAACATGGTA 59.095 57.895 0.00 0.0 34.58 3.25 R
2762 3140 0.245539 TTAGAAGAACCGGGTCAGCG 59.754 55.000 24.28 0.0 0.00 5.18 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
24 25 7.579761 GAGATTAATTGGATCTGCCTCTTTT 57.420 36.000 9.96 0.00 34.13 2.27
25 26 7.344095 AGATTAATTGGATCTGCCTCTTTTG 57.656 36.000 5.62 0.00 37.63 2.44
26 27 7.121382 AGATTAATTGGATCTGCCTCTTTTGA 58.879 34.615 5.62 0.00 37.63 2.69
27 28 7.783596 AGATTAATTGGATCTGCCTCTTTTGAT 59.216 33.333 5.62 0.00 37.63 2.57
28 29 5.848833 AATTGGATCTGCCTCTTTTGATC 57.151 39.130 0.00 0.00 37.63 2.92
29 30 4.581309 TTGGATCTGCCTCTTTTGATCT 57.419 40.909 0.00 0.00 36.51 2.75
30 31 4.581309 TGGATCTGCCTCTTTTGATCTT 57.419 40.909 0.00 0.00 36.51 2.40
31 32 4.927049 TGGATCTGCCTCTTTTGATCTTT 58.073 39.130 0.00 0.00 36.51 2.52
32 33 5.327732 TGGATCTGCCTCTTTTGATCTTTT 58.672 37.500 0.00 0.00 36.51 2.27
33 34 5.776716 TGGATCTGCCTCTTTTGATCTTTTT 59.223 36.000 0.00 0.00 36.51 1.94
34 35 6.947733 TGGATCTGCCTCTTTTGATCTTTTTA 59.052 34.615 0.00 0.00 36.51 1.52
35 36 7.616935 TGGATCTGCCTCTTTTGATCTTTTTAT 59.383 33.333 0.00 0.00 36.51 1.40
36 37 9.125026 GGATCTGCCTCTTTTGATCTTTTTATA 57.875 33.333 0.00 0.00 36.51 0.98
40 41 9.525409 CTGCCTCTTTTGATCTTTTTATATTGG 57.475 33.333 0.00 0.00 0.00 3.16
41 42 9.034800 TGCCTCTTTTGATCTTTTTATATTGGT 57.965 29.630 0.00 0.00 0.00 3.67
90 91 7.694886 AGAGCGTTTAGAATTTATAAAGCACC 58.305 34.615 3.94 9.22 0.00 5.01
91 92 7.553044 AGAGCGTTTAGAATTTATAAAGCACCT 59.447 33.333 3.94 1.41 0.00 4.00
92 93 8.051901 AGCGTTTAGAATTTATAAAGCACCTT 57.948 30.769 3.94 0.00 0.00 3.50
93 94 7.968405 AGCGTTTAGAATTTATAAAGCACCTTG 59.032 33.333 3.94 0.00 0.00 3.61
94 95 7.253651 GCGTTTAGAATTTATAAAGCACCTTGC 60.254 37.037 3.94 0.00 45.46 4.01
105 106 2.338577 GCACCTTGCATGGTCTATCT 57.661 50.000 20.81 0.00 44.26 1.98
106 107 2.648059 GCACCTTGCATGGTCTATCTT 58.352 47.619 20.81 0.00 44.26 2.40
107 108 3.019564 GCACCTTGCATGGTCTATCTTT 58.980 45.455 20.81 0.00 44.26 2.52
108 109 3.181493 GCACCTTGCATGGTCTATCTTTG 60.181 47.826 20.81 8.93 44.26 2.77
109 110 4.264253 CACCTTGCATGGTCTATCTTTGA 58.736 43.478 20.81 0.00 38.45 2.69
110 111 4.885907 CACCTTGCATGGTCTATCTTTGAT 59.114 41.667 20.81 0.00 38.45 2.57
111 112 6.057533 CACCTTGCATGGTCTATCTTTGATA 58.942 40.000 20.81 0.00 38.45 2.15
112 113 6.017605 CACCTTGCATGGTCTATCTTTGATAC 60.018 42.308 20.81 0.00 38.45 2.24
113 114 6.126652 ACCTTGCATGGTCTATCTTTGATACT 60.127 38.462 18.18 0.00 34.86 2.12
114 115 7.071196 ACCTTGCATGGTCTATCTTTGATACTA 59.929 37.037 18.18 0.00 34.86 1.82
115 116 8.099537 CCTTGCATGGTCTATCTTTGATACTAT 58.900 37.037 10.48 0.00 0.00 2.12
116 117 9.149225 CTTGCATGGTCTATCTTTGATACTATC 57.851 37.037 0.00 0.00 0.00 2.08
117 118 8.427902 TGCATGGTCTATCTTTGATACTATCT 57.572 34.615 0.00 0.00 0.00 1.98
118 119 8.526978 TGCATGGTCTATCTTTGATACTATCTC 58.473 37.037 0.00 0.00 0.00 2.75
119 120 8.526978 GCATGGTCTATCTTTGATACTATCTCA 58.473 37.037 0.00 0.00 0.00 3.27
141 142 9.905171 TCTCATATCTCAGATTACGAATTTGAG 57.095 33.333 15.64 15.64 46.16 3.02
142 143 8.526218 TCATATCTCAGATTACGAATTTGAGC 57.474 34.615 16.38 0.00 45.07 4.26
143 144 7.600375 TCATATCTCAGATTACGAATTTGAGCC 59.400 37.037 16.38 0.00 45.07 4.70
144 145 4.442706 TCTCAGATTACGAATTTGAGCCC 58.557 43.478 16.38 0.00 45.07 5.19
145 146 4.162320 TCTCAGATTACGAATTTGAGCCCT 59.838 41.667 16.38 0.00 45.07 5.19
146 147 4.442706 TCAGATTACGAATTTGAGCCCTC 58.557 43.478 0.00 0.00 29.67 4.30
147 148 3.246226 CAGATTACGAATTTGAGCCCTCG 59.754 47.826 0.00 0.00 37.33 4.63
148 149 2.754946 TTACGAATTTGAGCCCTCGT 57.245 45.000 0.00 1.36 45.71 4.18
149 150 3.872511 TTACGAATTTGAGCCCTCGTA 57.127 42.857 0.00 0.00 42.36 3.43
150 151 2.981859 ACGAATTTGAGCCCTCGTAT 57.018 45.000 0.00 0.00 42.36 3.06
151 152 5.518848 TTACGAATTTGAGCCCTCGTATA 57.481 39.130 0.00 0.00 43.86 1.47
152 153 3.714391 ACGAATTTGAGCCCTCGTATAC 58.286 45.455 0.00 0.00 42.36 1.47
153 154 3.383825 ACGAATTTGAGCCCTCGTATACT 59.616 43.478 0.00 0.00 42.36 2.12
154 155 3.982058 CGAATTTGAGCCCTCGTATACTC 59.018 47.826 0.56 0.00 0.00 2.59
155 156 4.499188 CGAATTTGAGCCCTCGTATACTCA 60.499 45.833 0.56 0.00 37.38 3.41
156 157 5.542779 GAATTTGAGCCCTCGTATACTCAT 58.457 41.667 0.56 0.00 38.84 2.90
157 158 4.585955 TTTGAGCCCTCGTATACTCATC 57.414 45.455 0.56 0.00 38.84 2.92
158 159 3.223674 TGAGCCCTCGTATACTCATCA 57.776 47.619 0.56 0.00 34.35 3.07
159 160 3.767711 TGAGCCCTCGTATACTCATCAT 58.232 45.455 0.56 0.00 34.35 2.45
160 161 3.507622 TGAGCCCTCGTATACTCATCATG 59.492 47.826 0.56 0.00 34.35 3.07
161 162 2.828520 AGCCCTCGTATACTCATCATGG 59.171 50.000 0.56 0.00 0.00 3.66
162 163 2.563179 GCCCTCGTATACTCATCATGGT 59.437 50.000 0.56 0.00 0.00 3.55
163 164 3.762288 GCCCTCGTATACTCATCATGGTA 59.238 47.826 0.56 0.00 0.00 3.25
164 165 4.219944 GCCCTCGTATACTCATCATGGTAA 59.780 45.833 0.56 0.00 0.00 2.85
165 166 5.279306 GCCCTCGTATACTCATCATGGTAAA 60.279 44.000 0.56 0.00 0.00 2.01
166 167 6.740401 GCCCTCGTATACTCATCATGGTAAAA 60.740 42.308 0.56 0.00 0.00 1.52
167 168 7.214381 CCCTCGTATACTCATCATGGTAAAAA 58.786 38.462 0.56 0.00 0.00 1.94
185 186 4.336532 AAAAAGTTCGATACGGCATCAC 57.663 40.909 0.00 0.00 32.71 3.06
207 208 2.358247 GAGGCCCGAAGAAACGCA 60.358 61.111 0.00 0.00 0.00 5.24
215 220 0.179225 CGAAGAAACGCACCAATCCG 60.179 55.000 0.00 0.00 0.00 4.18
233 238 2.107953 GCCCGAGGATCAGTCAGC 59.892 66.667 0.00 0.00 33.17 4.26
234 239 2.725312 GCCCGAGGATCAGTCAGCA 61.725 63.158 0.00 0.00 33.17 4.41
236 241 1.227205 CCGAGGATCAGTCAGCAGC 60.227 63.158 0.00 0.00 33.17 5.25
237 242 1.514553 CGAGGATCAGTCAGCAGCA 59.485 57.895 0.00 0.00 33.17 4.41
238 243 0.528033 CGAGGATCAGTCAGCAGCAG 60.528 60.000 0.00 0.00 33.17 4.24
239 244 0.536260 GAGGATCAGTCAGCAGCAGT 59.464 55.000 0.00 0.00 33.17 4.40
242 247 1.338484 GGATCAGTCAGCAGCAGTCAA 60.338 52.381 0.00 0.00 0.00 3.18
243 248 2.420642 GATCAGTCAGCAGCAGTCAAA 58.579 47.619 0.00 0.00 0.00 2.69
244 249 1.586422 TCAGTCAGCAGCAGTCAAAC 58.414 50.000 0.00 0.00 0.00 2.93
261 266 2.217429 AACCAAACACCAATTCACGC 57.783 45.000 0.00 0.00 0.00 5.34
283 288 1.302112 TCACGCGGCAGAAAATCCA 60.302 52.632 12.47 0.00 0.00 3.41
284 289 1.154225 CACGCGGCAGAAAATCCAC 60.154 57.895 12.47 0.00 0.00 4.02
286 291 2.885113 GCGGCAGAAAATCCACCC 59.115 61.111 0.00 0.00 0.00 4.61
287 292 3.051392 GCGGCAGAAAATCCACCCG 62.051 63.158 0.00 0.00 38.76 5.28
334 339 2.021793 CGGCATCGCATTCACACG 59.978 61.111 0.00 0.00 0.00 4.49
358 366 3.413142 CGACGCGTAAAAAGTGAAAACAG 59.587 43.478 13.97 0.00 0.00 3.16
360 368 2.466205 CGCGTAAAAAGTGAAAACAGCC 59.534 45.455 0.00 0.00 0.00 4.85
361 369 2.792674 GCGTAAAAAGTGAAAACAGCCC 59.207 45.455 0.00 0.00 0.00 5.19
362 370 3.490249 GCGTAAAAAGTGAAAACAGCCCT 60.490 43.478 0.00 0.00 0.00 5.19
363 371 4.041723 CGTAAAAAGTGAAAACAGCCCTG 58.958 43.478 0.00 0.00 0.00 4.45
364 372 3.541996 AAAAAGTGAAAACAGCCCTGG 57.458 42.857 0.00 0.00 34.19 4.45
365 373 0.752658 AAAGTGAAAACAGCCCTGGC 59.247 50.000 0.00 0.00 42.33 4.85
366 374 1.115326 AAGTGAAAACAGCCCTGGCC 61.115 55.000 4.13 0.00 43.17 5.36
367 375 2.597217 TGAAAACAGCCCTGGCCG 60.597 61.111 4.13 0.00 43.17 6.13
368 376 4.056125 GAAAACAGCCCTGGCCGC 62.056 66.667 4.13 0.00 43.17 6.53
394 402 2.671963 GGAAACCCAGCCCGTGAC 60.672 66.667 0.00 0.00 0.00 3.67
457 466 2.028420 ATACCGCCGGAAACTAAACC 57.972 50.000 11.71 0.00 0.00 3.27
580 601 2.327958 AATCCTCCCCTCCCCTACCG 62.328 65.000 0.00 0.00 0.00 4.02
640 674 3.682696 CTTTCCCCTATTTATACCCGCC 58.317 50.000 0.00 0.00 0.00 6.13
641 675 1.660242 TCCCCTATTTATACCCGCCC 58.340 55.000 0.00 0.00 0.00 6.13
642 676 0.622136 CCCCTATTTATACCCGCCCC 59.378 60.000 0.00 0.00 0.00 5.80
643 677 1.665137 CCCTATTTATACCCGCCCCT 58.335 55.000 0.00 0.00 0.00 4.79
644 678 1.558294 CCCTATTTATACCCGCCCCTC 59.442 57.143 0.00 0.00 0.00 4.30
645 679 1.558294 CCTATTTATACCCGCCCCTCC 59.442 57.143 0.00 0.00 0.00 4.30
646 680 1.558294 CTATTTATACCCGCCCCTCCC 59.442 57.143 0.00 0.00 0.00 4.30
647 681 1.138228 ATTTATACCCGCCCCTCCCC 61.138 60.000 0.00 0.00 0.00 4.81
648 682 4.626402 TATACCCGCCCCTCCCCG 62.626 72.222 0.00 0.00 0.00 5.73
893 1233 2.038975 TCCGGGACAAGGAGGAGG 59.961 66.667 0.00 0.00 33.19 4.30
895 1235 2.060980 CCGGGACAAGGAGGAGGAG 61.061 68.421 0.00 0.00 0.00 3.69
896 1236 2.726351 CGGGACAAGGAGGAGGAGC 61.726 68.421 0.00 0.00 0.00 4.70
897 1237 1.613630 GGGACAAGGAGGAGGAGCA 60.614 63.158 0.00 0.00 0.00 4.26
898 1238 1.201429 GGGACAAGGAGGAGGAGCAA 61.201 60.000 0.00 0.00 0.00 3.91
899 1239 0.251634 GGACAAGGAGGAGGAGCAAG 59.748 60.000 0.00 0.00 0.00 4.01
916 1256 1.214992 AAGGGGGTGTGAGGGATTCC 61.215 60.000 0.00 0.00 0.00 3.01
1110 1450 0.456995 GCTGCTTCGCTTCGACTAGT 60.457 55.000 0.00 0.00 34.89 2.57
2082 2431 4.366684 CTGGGCAACACCTCCCCC 62.367 72.222 0.00 0.00 41.92 5.40
2321 2670 0.534203 TCCAAGAACTTGTGACCGCC 60.534 55.000 12.54 0.00 38.85 6.13
2322 2671 1.569493 CAAGAACTTGTGACCGCCG 59.431 57.895 6.41 0.00 35.92 6.46
2323 2672 1.597027 AAGAACTTGTGACCGCCGG 60.597 57.895 0.00 0.00 0.00 6.13
2324 2673 3.723348 GAACTTGTGACCGCCGGC 61.723 66.667 19.07 19.07 0.00 6.13
2361 2710 0.833949 GCCCGAATTCTTCTCCTCCT 59.166 55.000 3.52 0.00 0.00 3.69
2395 2746 5.413499 CAACCCCTGCTGATTCTTTATTTG 58.587 41.667 0.00 0.00 0.00 2.32
2396 2747 4.026052 ACCCCTGCTGATTCTTTATTTGG 58.974 43.478 0.00 0.00 0.00 3.28
2397 2748 4.264352 ACCCCTGCTGATTCTTTATTTGGA 60.264 41.667 0.00 0.00 0.00 3.53
2398 2749 4.897670 CCCCTGCTGATTCTTTATTTGGAT 59.102 41.667 0.00 0.00 0.00 3.41
2399 2750 5.010415 CCCCTGCTGATTCTTTATTTGGATC 59.990 44.000 0.00 0.00 0.00 3.36
2400 2751 5.832060 CCCTGCTGATTCTTTATTTGGATCT 59.168 40.000 0.00 0.00 0.00 2.75
2401 2752 6.016443 CCCTGCTGATTCTTTATTTGGATCTC 60.016 42.308 0.00 0.00 0.00 2.75
2402 2753 6.016443 CCTGCTGATTCTTTATTTGGATCTCC 60.016 42.308 0.00 0.00 0.00 3.71
2403 2754 6.666678 TGCTGATTCTTTATTTGGATCTCCT 58.333 36.000 0.00 0.00 36.82 3.69
2404 2755 7.121382 TGCTGATTCTTTATTTGGATCTCCTT 58.879 34.615 0.00 0.00 36.82 3.36
2405 2756 7.284034 TGCTGATTCTTTATTTGGATCTCCTTC 59.716 37.037 0.00 0.00 36.82 3.46
2406 2757 7.501892 GCTGATTCTTTATTTGGATCTCCTTCT 59.498 37.037 0.00 0.00 36.82 2.85
2509 2864 5.076873 TGTCTCGATTCTTTTTGGGGAAAT 58.923 37.500 0.00 0.00 0.00 2.17
2510 2865 5.048083 TGTCTCGATTCTTTTTGGGGAAATG 60.048 40.000 0.00 0.00 0.00 2.32
2511 2866 4.082245 TCTCGATTCTTTTTGGGGAAATGC 60.082 41.667 0.00 0.00 0.00 3.56
2543 2901 4.456535 TGGTGTTCTCCGATCAAGAAAAA 58.543 39.130 8.66 0.16 34.68 1.94
2572 2934 3.838244 ATCCCGGATCGAATTCTTTCA 57.162 42.857 0.73 0.00 0.00 2.69
2588 2951 2.436646 CATTCCCTTGCGCCGAGT 60.437 61.111 4.18 0.00 0.00 4.18
2635 2998 7.926018 AGCGAAACCTTTTCTCATTGTTTATTT 59.074 29.630 0.00 0.00 29.89 1.40
2677 3054 5.534654 CCCCTTGTTCAATCTGTAAAGACAA 59.465 40.000 0.00 0.00 34.35 3.18
2678 3055 6.040391 CCCCTTGTTCAATCTGTAAAGACAAA 59.960 38.462 0.00 0.00 34.35 2.83
2714 3091 1.841334 TTCTTCTTTTCCCCTCCCCA 58.159 50.000 0.00 0.00 0.00 4.96
2715 3092 2.074922 TCTTCTTTTCCCCTCCCCAT 57.925 50.000 0.00 0.00 0.00 4.00
2716 3093 1.923148 TCTTCTTTTCCCCTCCCCATC 59.077 52.381 0.00 0.00 0.00 3.51
2718 3095 2.982842 TCTTTTCCCCTCCCCATCTA 57.017 50.000 0.00 0.00 0.00 1.98
2719 3096 2.488836 TCTTTTCCCCTCCCCATCTAC 58.511 52.381 0.00 0.00 0.00 2.59
2721 3098 3.276578 TCTTTTCCCCTCCCCATCTACTA 59.723 47.826 0.00 0.00 0.00 1.82
2722 3099 2.789323 TTCCCCTCCCCATCTACTAC 57.211 55.000 0.00 0.00 0.00 2.73
2723 3100 0.865362 TCCCCTCCCCATCTACTACC 59.135 60.000 0.00 0.00 0.00 3.18
2775 3153 0.458669 TAATCTCGCTGACCCGGTTC 59.541 55.000 0.00 0.00 0.00 3.62
2782 3160 1.134788 CGCTGACCCGGTTCTTCTAAT 60.135 52.381 0.00 0.00 0.00 1.73
2783 3161 2.552031 GCTGACCCGGTTCTTCTAATC 58.448 52.381 0.00 0.00 0.00 1.75
2785 3163 3.383825 GCTGACCCGGTTCTTCTAATCTA 59.616 47.826 0.00 0.00 0.00 1.98
2786 3164 4.500035 GCTGACCCGGTTCTTCTAATCTAG 60.500 50.000 0.00 0.00 0.00 2.43
2788 3166 4.643784 TGACCCGGTTCTTCTAATCTAGTC 59.356 45.833 0.00 0.00 0.00 2.59
2789 3167 4.869451 ACCCGGTTCTTCTAATCTAGTCT 58.131 43.478 0.00 0.00 0.00 3.24
2790 3168 6.011122 ACCCGGTTCTTCTAATCTAGTCTA 57.989 41.667 0.00 0.00 0.00 2.59
2791 3169 6.430007 ACCCGGTTCTTCTAATCTAGTCTAA 58.570 40.000 0.00 0.00 0.00 2.10
2792 3170 6.320926 ACCCGGTTCTTCTAATCTAGTCTAAC 59.679 42.308 0.00 0.00 0.00 2.34
2793 3171 6.546772 CCCGGTTCTTCTAATCTAGTCTAACT 59.453 42.308 0.00 0.00 0.00 2.24
2796 3174 9.328845 CGGTTCTTCTAATCTAGTCTAACTAGT 57.671 37.037 12.53 0.00 46.31 2.57
2827 3205 1.068741 ACGAACTGGCTTATCCGATCC 59.931 52.381 0.00 0.00 37.80 3.36
2868 3247 1.006337 GGGCGATTTGTTGCTTGCA 60.006 52.632 0.00 0.00 0.00 4.08
3124 3528 3.646715 CTGGGAGTGGGGCCGAAA 61.647 66.667 0.00 0.00 0.00 3.46
3136 3540 1.427819 GCCGAAATGTCGCCGATTT 59.572 52.632 0.00 0.00 46.28 2.17
3194 3599 4.444838 CCCGTCAACGCCGATGGA 62.445 66.667 13.22 0.00 43.72 3.41
3238 3664 7.374491 GCTGTATTCGAACTGCATTTCTTTATC 59.626 37.037 14.08 4.01 42.13 1.75
3249 3682 4.209911 GCATTTCTTTATCCGTACGTACCC 59.790 45.833 19.67 0.00 0.00 3.69
3259 3692 2.632377 CGTACGTACCCAGTTCTAGGA 58.368 52.381 19.67 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.284034 TCAAAAGAGGCAGATCCAATTAATCTC 59.716 37.037 0.62 0.00 37.29 2.75
2 3 7.338800 TCAAAAGAGGCAGATCCAATTAATC 57.661 36.000 0.00 0.00 37.29 1.75
3 4 7.783596 AGATCAAAAGAGGCAGATCCAATTAAT 59.216 33.333 0.00 0.00 38.06 1.40
5 6 6.666678 AGATCAAAAGAGGCAGATCCAATTA 58.333 36.000 0.00 0.00 38.06 1.40
6 7 5.516984 AGATCAAAAGAGGCAGATCCAATT 58.483 37.500 0.00 0.00 38.06 2.32
7 8 5.126699 AGATCAAAAGAGGCAGATCCAAT 57.873 39.130 0.00 0.00 38.06 3.16
8 9 4.581309 AGATCAAAAGAGGCAGATCCAA 57.419 40.909 0.00 0.00 38.06 3.53
9 10 4.581309 AAGATCAAAAGAGGCAGATCCA 57.419 40.909 0.00 0.00 38.06 3.41
10 11 5.911378 AAAAGATCAAAAGAGGCAGATCC 57.089 39.130 0.00 0.00 38.06 3.36
14 15 9.525409 CCAATATAAAAAGATCAAAAGAGGCAG 57.475 33.333 0.00 0.00 0.00 4.85
15 16 9.034800 ACCAATATAAAAAGATCAAAAGAGGCA 57.965 29.630 0.00 0.00 0.00 4.75
64 65 8.182227 GGTGCTTTATAAATTCTAAACGCTCTT 58.818 33.333 0.00 0.00 0.00 2.85
65 66 7.553044 AGGTGCTTTATAAATTCTAAACGCTCT 59.447 33.333 0.00 0.00 0.00 4.09
66 67 7.694886 AGGTGCTTTATAAATTCTAAACGCTC 58.305 34.615 0.00 0.00 0.00 5.03
67 68 7.625828 AGGTGCTTTATAAATTCTAAACGCT 57.374 32.000 0.00 0.00 0.00 5.07
68 69 7.253651 GCAAGGTGCTTTATAAATTCTAAACGC 60.254 37.037 0.00 0.00 40.96 4.84
69 70 7.753132 TGCAAGGTGCTTTATAAATTCTAAACG 59.247 33.333 0.00 0.00 45.31 3.60
70 71 8.980143 TGCAAGGTGCTTTATAAATTCTAAAC 57.020 30.769 0.00 0.00 45.31 2.01
71 72 9.585099 CATGCAAGGTGCTTTATAAATTCTAAA 57.415 29.630 0.00 0.00 45.31 1.85
72 73 8.196771 CCATGCAAGGTGCTTTATAAATTCTAA 58.803 33.333 0.00 0.00 45.31 2.10
73 74 7.341769 ACCATGCAAGGTGCTTTATAAATTCTA 59.658 33.333 13.91 0.00 45.31 2.10
74 75 6.155049 ACCATGCAAGGTGCTTTATAAATTCT 59.845 34.615 13.91 0.00 45.31 2.40
75 76 6.340522 ACCATGCAAGGTGCTTTATAAATTC 58.659 36.000 13.91 0.00 45.31 2.17
76 77 6.155049 AGACCATGCAAGGTGCTTTATAAATT 59.845 34.615 20.20 0.00 45.31 1.82
77 78 5.658190 AGACCATGCAAGGTGCTTTATAAAT 59.342 36.000 20.20 0.00 45.31 1.40
78 79 5.016173 AGACCATGCAAGGTGCTTTATAAA 58.984 37.500 20.20 0.00 45.31 1.40
79 80 4.599041 AGACCATGCAAGGTGCTTTATAA 58.401 39.130 20.20 0.00 45.31 0.98
80 81 4.235079 AGACCATGCAAGGTGCTTTATA 57.765 40.909 20.20 0.00 45.31 0.98
81 82 3.091633 AGACCATGCAAGGTGCTTTAT 57.908 42.857 20.20 0.00 45.31 1.40
82 83 2.584835 AGACCATGCAAGGTGCTTTA 57.415 45.000 20.20 0.00 45.31 1.85
83 84 2.584835 TAGACCATGCAAGGTGCTTT 57.415 45.000 20.20 3.92 45.31 3.51
84 85 2.240667 AGATAGACCATGCAAGGTGCTT 59.759 45.455 20.20 6.48 45.31 3.91
85 86 1.842562 AGATAGACCATGCAAGGTGCT 59.157 47.619 20.20 16.63 45.31 4.40
86 87 2.338577 AGATAGACCATGCAAGGTGC 57.661 50.000 20.20 10.17 43.38 5.01
87 88 4.264253 TCAAAGATAGACCATGCAAGGTG 58.736 43.478 20.20 1.18 43.38 4.00
88 89 4.574674 TCAAAGATAGACCATGCAAGGT 57.425 40.909 14.67 14.67 46.82 3.50
89 90 6.294473 AGTATCAAAGATAGACCATGCAAGG 58.706 40.000 6.39 6.39 0.00 3.61
90 91 9.149225 GATAGTATCAAAGATAGACCATGCAAG 57.851 37.037 5.21 0.00 0.00 4.01
91 92 8.874156 AGATAGTATCAAAGATAGACCATGCAA 58.126 33.333 12.66 0.00 0.00 4.08
92 93 8.427902 AGATAGTATCAAAGATAGACCATGCA 57.572 34.615 12.66 0.00 0.00 3.96
93 94 8.526978 TGAGATAGTATCAAAGATAGACCATGC 58.473 37.037 12.66 0.00 0.00 4.06
115 116 9.905171 CTCAAATTCGTAATCTGAGATATGAGA 57.095 33.333 0.00 0.00 36.44 3.27
116 117 8.646356 GCTCAAATTCGTAATCTGAGATATGAG 58.354 37.037 12.30 2.15 36.44 2.90
117 118 7.600375 GGCTCAAATTCGTAATCTGAGATATGA 59.400 37.037 12.30 0.00 36.44 2.15
118 119 7.148507 GGGCTCAAATTCGTAATCTGAGATATG 60.149 40.741 12.30 0.00 36.44 1.78
119 120 6.876257 GGGCTCAAATTCGTAATCTGAGATAT 59.124 38.462 12.30 0.00 36.44 1.63
120 121 6.042093 AGGGCTCAAATTCGTAATCTGAGATA 59.958 38.462 12.30 0.00 36.44 1.98
121 122 5.059833 GGGCTCAAATTCGTAATCTGAGAT 58.940 41.667 12.30 0.00 36.44 2.75
122 123 4.162320 AGGGCTCAAATTCGTAATCTGAGA 59.838 41.667 12.30 0.00 36.44 3.27
123 124 4.446371 AGGGCTCAAATTCGTAATCTGAG 58.554 43.478 6.57 6.57 37.23 3.35
124 125 4.442706 GAGGGCTCAAATTCGTAATCTGA 58.557 43.478 0.00 0.00 0.00 3.27
125 126 3.246226 CGAGGGCTCAAATTCGTAATCTG 59.754 47.826 0.00 0.00 0.00 2.90
126 127 3.118738 ACGAGGGCTCAAATTCGTAATCT 60.119 43.478 0.00 0.00 43.64 2.40
127 128 3.195661 ACGAGGGCTCAAATTCGTAATC 58.804 45.455 0.00 0.00 43.64 1.75
128 129 3.261981 ACGAGGGCTCAAATTCGTAAT 57.738 42.857 0.00 0.00 43.64 1.89
129 130 2.754946 ACGAGGGCTCAAATTCGTAA 57.245 45.000 0.00 0.00 43.64 3.18
131 132 2.981859 ATACGAGGGCTCAAATTCGT 57.018 45.000 3.94 3.94 46.63 3.85
132 133 3.978687 AGTATACGAGGGCTCAAATTCG 58.021 45.455 0.00 0.00 38.88 3.34
133 134 4.945246 TGAGTATACGAGGGCTCAAATTC 58.055 43.478 0.00 0.00 35.36 2.17
134 135 5.070446 TGATGAGTATACGAGGGCTCAAATT 59.930 40.000 0.00 0.00 40.71 1.82
135 136 4.588951 TGATGAGTATACGAGGGCTCAAAT 59.411 41.667 0.00 0.00 40.71 2.32
136 137 3.958147 TGATGAGTATACGAGGGCTCAAA 59.042 43.478 0.00 0.00 40.71 2.69
137 138 3.562182 TGATGAGTATACGAGGGCTCAA 58.438 45.455 0.00 0.00 40.71 3.02
138 139 3.223674 TGATGAGTATACGAGGGCTCA 57.776 47.619 0.00 0.00 41.43 4.26
139 140 3.119316 CCATGATGAGTATACGAGGGCTC 60.119 52.174 0.00 0.00 0.00 4.70
140 141 2.828520 CCATGATGAGTATACGAGGGCT 59.171 50.000 0.00 0.00 0.00 5.19
141 142 2.563179 ACCATGATGAGTATACGAGGGC 59.437 50.000 0.00 0.00 0.00 5.19
142 143 5.977489 TTACCATGATGAGTATACGAGGG 57.023 43.478 0.00 0.00 0.00 4.30
164 165 3.181524 CGTGATGCCGTATCGAACTTTTT 60.182 43.478 0.00 0.00 38.71 1.94
165 166 2.347452 CGTGATGCCGTATCGAACTTTT 59.653 45.455 0.00 0.00 38.71 2.27
166 167 1.924524 CGTGATGCCGTATCGAACTTT 59.075 47.619 0.00 0.00 38.71 2.66
167 168 1.556564 CGTGATGCCGTATCGAACTT 58.443 50.000 0.00 0.00 38.71 2.66
168 169 0.870307 GCGTGATGCCGTATCGAACT 60.870 55.000 0.00 0.00 38.71 3.01
169 170 1.558383 GCGTGATGCCGTATCGAAC 59.442 57.895 0.00 0.00 38.71 3.95
170 171 4.006532 GCGTGATGCCGTATCGAA 57.993 55.556 0.00 0.00 38.71 3.71
196 197 0.179225 CGGATTGGTGCGTTTCTTCG 60.179 55.000 0.00 0.00 34.19 3.79
215 220 2.818132 CTGACTGATCCTCGGGCC 59.182 66.667 0.00 0.00 26.42 5.80
222 227 0.248565 TGACTGCTGCTGACTGATCC 59.751 55.000 13.69 0.00 0.00 3.36
233 238 1.476085 TGGTGTTTGGTTTGACTGCTG 59.524 47.619 0.00 0.00 0.00 4.41
234 239 1.846007 TGGTGTTTGGTTTGACTGCT 58.154 45.000 0.00 0.00 0.00 4.24
236 241 4.566360 GTGAATTGGTGTTTGGTTTGACTG 59.434 41.667 0.00 0.00 0.00 3.51
237 242 4.676723 CGTGAATTGGTGTTTGGTTTGACT 60.677 41.667 0.00 0.00 0.00 3.41
238 243 3.549873 CGTGAATTGGTGTTTGGTTTGAC 59.450 43.478 0.00 0.00 0.00 3.18
239 244 3.775202 CGTGAATTGGTGTTTGGTTTGA 58.225 40.909 0.00 0.00 0.00 2.69
242 247 1.478510 TGCGTGAATTGGTGTTTGGTT 59.521 42.857 0.00 0.00 0.00 3.67
243 248 1.107114 TGCGTGAATTGGTGTTTGGT 58.893 45.000 0.00 0.00 0.00 3.67
244 249 2.126467 CTTGCGTGAATTGGTGTTTGG 58.874 47.619 0.00 0.00 0.00 3.28
261 266 0.238289 ATTTTCTGCCGCGTGACTTG 59.762 50.000 4.92 0.00 0.00 3.16
283 288 2.046314 CATTGGCGAGGAACGGGT 60.046 61.111 0.00 0.00 42.83 5.28
284 289 0.748005 ATTCATTGGCGAGGAACGGG 60.748 55.000 3.58 0.00 42.83 5.28
286 291 0.248215 GCATTCATTGGCGAGGAACG 60.248 55.000 3.58 0.00 45.66 3.95
287 292 3.629858 GCATTCATTGGCGAGGAAC 57.370 52.632 3.58 0.00 29.76 3.62
334 339 0.232816 TTCACTTTTTACGCGTCGGC 59.767 50.000 18.63 0.00 0.00 5.54
394 402 4.380974 GGGTTTATTATTACTCGTCGCTCG 59.619 45.833 0.00 0.00 41.41 5.03
645 679 4.944069 CTAGGGGAGGAGGGCGGG 62.944 77.778 0.00 0.00 0.00 6.13
893 1233 2.352805 CCTCACACCCCCTTGCTC 59.647 66.667 0.00 0.00 0.00 4.26
895 1235 2.155197 AATCCCTCACACCCCCTTGC 62.155 60.000 0.00 0.00 0.00 4.01
896 1236 0.034089 GAATCCCTCACACCCCCTTG 60.034 60.000 0.00 0.00 0.00 3.61
897 1237 1.214992 GGAATCCCTCACACCCCCTT 61.215 60.000 0.00 0.00 0.00 3.95
898 1238 1.619669 GGAATCCCTCACACCCCCT 60.620 63.158 0.00 0.00 0.00 4.79
899 1239 1.619669 AGGAATCCCTCACACCCCC 60.620 63.158 0.00 0.00 38.86 5.40
916 1256 4.096984 GCCAACCAATCAAGAAGATACCAG 59.903 45.833 0.00 0.00 35.39 4.00
1110 1450 1.904771 CGCCCAGAGGAACATGGTA 59.095 57.895 0.00 0.00 34.58 3.25
2361 2710 4.364686 GGGGTTGGGGGAGGAGGA 62.365 72.222 0.00 0.00 0.00 3.71
2395 2746 0.747852 GTGGTCGGAGAAGGAGATCC 59.252 60.000 0.00 0.00 39.69 3.36
2396 2747 1.679153 GAGTGGTCGGAGAAGGAGATC 59.321 57.143 0.00 0.00 39.69 2.75
2397 2748 1.686741 GGAGTGGTCGGAGAAGGAGAT 60.687 57.143 0.00 0.00 39.69 2.75
2398 2749 0.323542 GGAGTGGTCGGAGAAGGAGA 60.324 60.000 0.00 0.00 39.69 3.71
2399 2750 1.324005 GGGAGTGGTCGGAGAAGGAG 61.324 65.000 0.00 0.00 39.69 3.69
2400 2751 1.305046 GGGAGTGGTCGGAGAAGGA 60.305 63.158 0.00 0.00 39.69 3.36
2401 2752 2.711922 CGGGAGTGGTCGGAGAAGG 61.712 68.421 0.00 0.00 39.69 3.46
2402 2753 2.885861 CGGGAGTGGTCGGAGAAG 59.114 66.667 0.00 0.00 39.69 2.85
2509 2864 3.998341 GGAGAACACCATAAAACGTAGCA 59.002 43.478 0.00 0.00 0.00 3.49
2510 2865 3.061697 CGGAGAACACCATAAAACGTAGC 59.938 47.826 0.00 0.00 0.00 3.58
2511 2866 4.487948 TCGGAGAACACCATAAAACGTAG 58.512 43.478 0.00 0.00 0.00 3.51
2543 2901 3.838244 TCGATCCGGGATTGATTTTCT 57.162 42.857 20.85 0.00 28.51 2.52
2572 2934 2.436646 CACTCGGCGCAAGGGAAT 60.437 61.111 10.83 0.00 38.28 3.01
2588 2951 0.516877 CATTGCTTTCTTCGTCGGCA 59.483 50.000 0.00 0.00 0.00 5.69
2648 3011 4.453480 ACAGATTGAACAAGGGGAGAAA 57.547 40.909 0.00 0.00 0.00 2.52
2650 3013 5.309543 TCTTTACAGATTGAACAAGGGGAGA 59.690 40.000 0.00 0.00 0.00 3.71
2651 3014 5.412904 GTCTTTACAGATTGAACAAGGGGAG 59.587 44.000 0.00 0.00 0.00 4.30
2652 3015 5.163141 TGTCTTTACAGATTGAACAAGGGGA 60.163 40.000 0.00 0.00 0.00 4.81
2653 3016 5.070001 TGTCTTTACAGATTGAACAAGGGG 58.930 41.667 0.00 0.00 0.00 4.79
2677 3054 6.538263 AGAAGAAACTAATCAAGAGCCACTT 58.462 36.000 0.00 0.00 39.70 3.16
2678 3055 6.120507 AGAAGAAACTAATCAAGAGCCACT 57.879 37.500 0.00 0.00 0.00 4.00
2743 3120 7.592533 GGTCAGCGAGATTACATACGTTAATTA 59.407 37.037 0.00 0.00 0.00 1.40
2750 3128 2.662700 GGGTCAGCGAGATTACATACG 58.337 52.381 0.00 0.00 0.00 3.06
2762 3140 0.245539 TTAGAAGAACCGGGTCAGCG 59.754 55.000 24.28 0.00 0.00 5.18
2785 3163 5.293079 CGTAGCTTCCGTTACTAGTTAGACT 59.707 44.000 0.00 0.00 0.00 3.24
2786 3164 5.292101 TCGTAGCTTCCGTTACTAGTTAGAC 59.708 44.000 0.00 0.00 0.00 2.59
2788 3166 5.725110 TCGTAGCTTCCGTTACTAGTTAG 57.275 43.478 0.00 0.00 0.00 2.34
2789 3167 5.643777 AGTTCGTAGCTTCCGTTACTAGTTA 59.356 40.000 0.00 0.00 0.00 2.24
2790 3168 4.457257 AGTTCGTAGCTTCCGTTACTAGTT 59.543 41.667 0.00 0.00 0.00 2.24
2791 3169 4.006319 AGTTCGTAGCTTCCGTTACTAGT 58.994 43.478 0.00 0.00 0.00 2.57
2792 3170 4.341099 CAGTTCGTAGCTTCCGTTACTAG 58.659 47.826 0.00 0.00 0.00 2.57
2793 3171 3.127548 CCAGTTCGTAGCTTCCGTTACTA 59.872 47.826 0.00 0.00 0.00 1.82
2795 3173 2.257034 CCAGTTCGTAGCTTCCGTTAC 58.743 52.381 0.00 0.00 0.00 2.50
2796 3174 1.403249 GCCAGTTCGTAGCTTCCGTTA 60.403 52.381 0.00 0.00 0.00 3.18
2797 3175 0.669625 GCCAGTTCGTAGCTTCCGTT 60.670 55.000 0.00 0.00 0.00 4.44
2798 3176 1.080025 GCCAGTTCGTAGCTTCCGT 60.080 57.895 0.00 0.00 0.00 4.69
2799 3177 0.389948 AAGCCAGTTCGTAGCTTCCG 60.390 55.000 0.00 0.00 43.12 4.30
2800 3178 2.667473 TAAGCCAGTTCGTAGCTTCC 57.333 50.000 0.00 0.00 43.12 3.46
2855 3233 1.680735 TCGGAACTGCAAGCAACAAAT 59.319 42.857 0.00 0.00 37.60 2.32
2862 3240 0.373716 CGGTAATCGGAACTGCAAGC 59.626 55.000 0.00 0.00 33.64 4.01
2868 3247 1.683418 GGGGAGCGGTAATCGGAACT 61.683 60.000 0.00 0.00 39.69 3.01
2929 3319 4.187810 GAATTTTCCGGGCCGCCG 62.188 66.667 23.20 8.37 0.00 6.46
2933 3323 4.187810 CCGCGAATTTTCCGGGCC 62.188 66.667 8.23 0.00 37.37 5.80
2992 3382 1.133668 AGCTTATCCCCATTGCTCCAC 60.134 52.381 0.00 0.00 0.00 4.02
2999 3389 2.091111 CCCTCCAAAGCTTATCCCCATT 60.091 50.000 0.00 0.00 0.00 3.16
3028 3418 3.135382 CTCGTGCGCTTCGATGCAG 62.135 63.158 22.91 15.04 42.68 4.41
3121 3525 1.797964 CGACAAATCGGCGACATTTC 58.202 50.000 13.76 5.77 44.99 2.17
3122 3526 3.967734 CGACAAATCGGCGACATTT 57.032 47.368 13.76 7.28 44.99 2.32
3194 3599 0.901124 GCTCATCCTGGAGTGTCACT 59.099 55.000 4.81 4.81 37.24 3.41
3204 3630 3.801050 CAGTTCGAATACAGCTCATCCTG 59.199 47.826 0.00 0.00 38.78 3.86
3238 3664 1.672881 CCTAGAACTGGGTACGTACGG 59.327 57.143 21.06 13.54 0.00 4.02


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

AutoCloner maintained by Alex Coulton.